title: Sex Differences in BAT Thermogenesis in PGC1α Knockout Mice [ATAC-Seq]

city: Tokyo

first: Kazutaka

last: Tsujimoto

address: 1-5-45 Yushima, Bunkyo-ku

institute: Institute of Science Tokyo

summary: To elucidate the sex-specific role of PGC1α in brown adipose tissue (BAT), we performed ATAC-seq analysis on BAT from male and female PGC1α knockout mice.

overall_design: experiment 1: PGC-1α knockout experiment Tamoxifen-inducible adipocyte-specific PGC-1α knockout (KO) mice were generated by crossing Ppargc1a flox/flox mice with Adipoq-CreERT2 mice. Eight-week-old male and female KO and Ppargc1a flox/flox control mice were intraperitoneally injected with tamoxifen for 5 consecutive days. BAT samples were collected and analyzed at least 8 weeks after the final injection. The study included four groups based on sex and genotype: Male Control, Male KO (PGC-1α KO), Female Control, Female KO (PGC-1α KO)

first: Akira

last: Takeuchi


title: Sex Differences in BAT Thermogenesis in PGC1α Knockout Mice

status: Public on Apr 06 2025

country: Japan

type: Expression profiling by high throughput sequencing

summary: To elucidate the sex-specific role of PGC1α in brown adipose tissue (BAT), we performed RNA-seq analysis on BAT from male and female PGC1α knockout mice. Furthermore, to investigate the effects of estrogen on BAT, we conducted RNA-seq analysis on BAT from male and female wild-type mice treated with tamoxifen.

overall_design: experiment 1: PGC-1α knockout experiment Tamoxifen-inducible adipocyte-specific PGC-1α knockout (KO) mice were generated by crossing Ppargc1a flox/flox mice with Adipoq-CreERT2 mice. Eight-week-old male and female KO and Ppargc1a flox/flox control mice were intraperitoneally injected with tamoxifen for 5 consecutive days. BAT samples were collected and analyzed at least 8 weeks after the final injection. The study included four groups based on sex and genotype: Male Control, Male KO (PGC-1α KO), Female Control, Female KO (PGC-1α KO)  experiment 2: Tamoxifen treatment experiment In this experiment, eight-week-old male and female wild-type mice were intraperitoneally injected with tamoxifen for 5 consecutive days to evaluate the direct effects of tamoxifen on BAT gene expression. BAT samples were collected and analyzed 2 weeks after the final injection. The study included four groups based on sex and treatment: Male Vehicle (Veh), Male Tamoxifen (TMX), Female Vehicle (Veh), Female Tamoxifen (TMX)


title: Enhanced differentiation of Alzheimer's disease neural progenitor cells into vulnerable immature neurons

city: Seoul

first: Jinsoo

last: Seo

address: 50 Yonsei-ro

department: Department of Systems Biology

country: South Korea

institute: Yonsei University

summary: Alterations in neural cells preceding the onset of Alzheimer’s disease (AD) have remained elusive. Using isogenic human induced pluripotent stem cells (hiPSCs) with an APPswe mutation, we find that APPswe neural progenitor cells (NPCs) exhibit early neuronal differentiation and remain immature, and increased ROS levels were necessary for this premature differentiation. APPswe neural cells showed heightened susceptibility to toxicity, highlighting their vulnerability in early AD stages.

overall_design: To investigate transcriptomic alterations in NPC by APPswe or high levels of reactive oxygen species

first: Joonho

last: Cho

first: Fan

last: Gao


title: O-GlcNAcylation of FOXK1 co-opts BAP1 to orchestrate the E2F pathway and promote oncogenesis

city: Montreal

first: Louis

last: Masclef

state: QC

address: 5415 Boulevard de l'Assomption

department: Biochemistry

country: Canada

institute: University of Montreal

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The E2F transcription factors constitute a core transcriptional network that governs cell division and oncogenesis in multi-cellular organisms, although their molecular mechanisms remain incompletely understood. Here, we show that elevated expression of the transcription factor FOXK1 promotes transcription of E2F target genes and cellular transformation. High expression of FOXK1 in patient tumors is also strongly correlated with E2F gene expression. Mechanistically, we demonstrate that FOXK1 is O-GlcNAcylated, and loss of this modification impairs FOXK1 ability to promote cell proliferation and tumor growth. We also show that expression of FOXK1 O-GlcNAcylation-defective mutants results in reduced recruitment of the H2AK119 deubiquitinase and tumor suppressor BAP1 to E2F target genes. This event is associated with a transcriptional repressive chromatin environment and reduced cell proliferation. Our results define an essential role of FOXK1 O-GlcNAcylation in co-opting the tumor suppressor BAP1 to promote cancer cell progression through orchestration of the E2F pathway.

overall_design:
Chromatine immunoprecipitation and DNA-sequencing (ChIPseq) for endogenous FOXK1, FOXK2 in IMR90 cells as well as ChIPseq of exogenous 3Flag tagged FOXK1, FOXK2 and FOXK1 O-GlcNAc mutants FOXK1-7A, and FOXK1-11A. ChIPseq for endogenous FOXK1 and Flag tag FOXK1, FOXK1-7A in U2OS cells. ChIPseq for flag tag FOXK1 and FOXK2 in K562 cells. Cut&Run for BAP1, H3K4me1 and H2Aub performed in IMR90 cells expressing either FOXK1, FOXK1-7A or FOXK1-11A O-GlcNAc mutants. Cut&Run for FOXK1 and FOXK2 during cell cycle progression in synchronized IMR90 and U2OS cells. Cut&Run for BAP1 in U2OS knock-out for endogenous FOXK1 expression and expressing either FOXK1 or FOXK1-11A O-GlcNAc mutant.

Chromatine immunoprecipitation and DNA-sequencing (ChIPseq) for endogenous FOXK1, FOXK2 in IMR90 cells as well as ChIPseq of exogenous 3Flag tagged FOXK1, FOXK2 and FOXK1 O-GlcNAc mutants FOXK1-7A, and FOXK1-11A. ChIPseq for endogenous FOXK1 and Flag tag FOXK1, FOXK1-7A in U2OS cells. ChIPseq for flag tag FOXK1 and FOXK2 in K562 cells. Cut&Run for BAP1, H3K4me1 and H2Aub performed in IMR90 cells expressing either FOXK1, FOXK1-7A or FOXK1-11A O-GlcNAc mutants. Cut&Run for FOXK1 and FOXK2 during cell cycle progression in synchronized IMR90 and U2OS cells. Cut&Run for BAP1 in U2OS knock-out for endogenous FOXK1 expression and expressing either FOXK1 or FOXK1-11A O-GlcNAc mutant. Chromatin accessibility (ATACseq) performed on U2OS cells expressing FOXK1 or FOXK1-7A and treated with siRNA targeting endogenous FOXK1 for knock-down. Transcriptomic analysis (RNA-seq) conducted on IMR90 cells expressing either a control vector, FOXK1, or FOXK2.

first: Oumaima

last: Ahmed

first: Nicholas

last: Iannantuono

first: Jessica

last: Gagnon

first: Mila

last: Gushul-Leclaire

first: Karine

last: Boulay

first: Benjamin

last: Estavoyer

first: Mohamed

last: Echbicheb

first: Kalidou

last: Ali Boubacar

first: Marty

last: Poy

first: Amina

last: Boubekeur

first: Saad

last: Menggad

first: Alejandro

last: Schcolnik-Cabrera

first: Aurelio

last: Balsalobre

first: Eric

last: Bonneil

first: Pierre

last: Thibault

first: Laura

last: Hulea

first: Frédérick

last: Antoine-Mallette

first: Jacques

last: Drouin

first: Yoshiaki

last: Tanaka

first: El Bachir

last: Affar


title: Multitissue Single-Cell Analysis Reveals Differential Tissue, Cellular, and Molecular Sensitivity between Fructose and High fat high sucrose Diets

city: Los Angeles

first: Yen-Wei

last: Chen

address: 650 Charles E. Young Dr. South  16-035 Center for Health Sciences

department: IDP Molecular Toxicology

country: USA

institute: University of California, Los Angeles

summary: Metabolic syndrome (MetS) is a complex disorder with multidimensional etiology that encompasses diverse symptoms such as hyperlipidemia, abdominal obesity, and insulin resistance. Western diets such as the high fat high sucrose diet (HFHS) and those high in fructose ave been associated with increased prevalence of MetS. Despite the fact that various metabolic tissues have been implicated in MetS pathogenesis, the role of individual cell types embedded in these tissues has yet to be elucidated. To address this, we performed single cell RNA sequencing to examine thousands of individual cells from the hypothalamus, liver, adipose, and small intestine from both HFHS- and fructose-induced MetS mouse models. We found differential sensitivity of responsive cell types, genes, and pathways between HFHS and fructose diets, with hypothalamic neurons particularly sensitive to the high fructose diet and adipose progenitor cells particularly sensitive to HFHS diet.  Network analysis identified both known (Avp, Apoe, C3) and novel ligands (Gal and Fga) that mediate ligand-receptor crosstalk between tissues in MetS. The identification of major cell types, molecular pathways, and regulators of MetS induced by different risk diets facilitates precision treatment of MetS subtypes.

overall_design: Chow (control), Fructose and HFHSeight-week-old C57BL/6J (B6) male mice were fed a chow diet with water, chow diet with water containing 15% fructose mimicking the prevalent uptake route of fructose through liquid drinks, and a high fat high sucrose diet containing 16.8% kcal protein, 51.4% kcal carbohydrate, and 31.8% kcal fat with water mimicking the Western diet for 11 weeks. Chow and water were changed once a week, and HFHS diet and fructose solutions were changed twice a week. Food and liquid were accessed ad libitum and the intake amount for each was measured. After 11 weeks, mice were sacrificed, and tissues including hypothalamus, gonadal adipose tissue, whole liver, and the small intestine (including duodenum, jejunum, and ileum) were collected for scRNA-seq using Drop-seq. For each tissue, n=2-5 independent biological replicates were processed from each diet group.

first: Xia

last: Yang

first: In

middle: S

last: Ahn


title: Tumor-Derived Exosomal CCT6A Serves as a Matchmaker Introducing Chemokines to Tumor-Associated Macrophages in Pancreatic Ductal Adenocarcinoma [human RNA-seq]

city: Wuhan

first: Minghe

last: Zhang

state: Hubei

address: Donghu Road

country: China

institute: WuHan University

summary: M2-polarized tumor-associated macrophages (TAMs) are a key factor contributing to the poor prognosis of pancreatic ductal adenocarcinoma (PDAC). While various factors within the tumor microenvironment drive their formation, the role of PDAC-derived exosomes in this process remains unclear. We aim to clarify the regulatory impacts of tumor-derived exosomes to TAMs. Through multi-Omics analysis, we identified CCT6A as a novel tumor-derived exosomal protein, bridging TAMs M2 polarization and PDAC prognosis. Co-culture with exosomes derived from CCT6Ahigh PDAC leads to greater M2 phenotype of TAMs via PI3K-AKT signaling. According to proteomics data, chemokines’ abundance reduces over tenfold once exosomal CCT6A absence, including CXCL1, CXCL3, CXCL20 and CCL5, whose interaction with CCT6A in PDAC cells was confirmed by interactomics data. Morever, we found CCT6A clearance abrogated the antagonism effects of CD47 antibody immunotherapy. The subunit of the T-complex protein Ring Complex (TRiC) CCT6A serves as a matchmaker, during exosomes-mediated chemokines transfer from PDAC to TAMs.

overall_design: Human macrophage cell line THP-1 was treated with exosomes derived from either sh-CCT6A or sh-NC BxPC-3 PDAC cell lines. Subsequently, THP-1 cells were harvested for RNA sequencing and transcriptome analysis.

first: Tianyin

last: Ma

first: Yufeng

last: Yuan


title: Molecular dissection of cobra venom highlights heparinoids as an effective snakebite antidote

city: Camperdown

first: Graham

middle: Gregory

last: Neely

state: NSW

address: John Hopkins Dr

country: Australia

institute: Charles Perkins Centre, The University of Sydney

summary: Snakebite affects ~1.8 million people annually. The current standard of care are antibody-based antivenoms, which are difficult to access and are not effective against local tissue injury, the primary cause of morbidity. Here we use a functional genomics approach to define human genes that genetically interact with spitting cobra venoms. Most genes that confer resistance to venom cytotoxicity control proteoglycan biosynthesis, suggesting heparinoids as possible inhibitors. Here we show that heparinoids prevent venom cytotoxicity by inhibiting three-finger cytotoxins. Critically, the FDA-approved heparinoid tinzaparin was found to reduce tissue damage in vivo when given via a medically relevant route and dose. Overall, our systematic molecular dissection of cobra venom mechanisms provides new insight into how we can treat cobra bites, information that can help improve the lives of millions of people worldwide.

overall_design: Whole genome pooled KO CRISPR screen using Toronto KnockOut Library v3 (TKOv3) on HAPI cells treated with venom from Naja pallida and Naja nigricollis cobra venoms. Cells from treated and control were taken for Next Generation Sequencing (NGS).

first: Tian

middle: Y

last: Du

first: Felicity

last: Chung

first: Sergey

last: Kurdyukov

middle: G


title: mRNA-seq analysis of Caenorhabditis elegans wild type N2, daf-16(mu86), daf-18(ok480) and daf-16(mu86); daf-18(ok480) starved L1 larvae

status: Public on Apr 05 2025

city: Durham

first: L. Ryan

last: Baugh

state: North Carolina

address: 124 Science Dr, FFSC 4336

department: Biology

institute: Duke University

summary: Embryos of wild type N2, daf-16(mu86), daf-18(ok480) and daf-16(mu86); daf-18(ok480) were collected by hypochlorite-treat gravid adult worms and were put in virgin S-basal with 0.1% EtOH at 20 °C. After hatching, those embryos entered L1 arrest. Arrested L1s were collected 16 hr post hypochlorite treatment (about 4 hr of starvation).

overall_design: Three biological replicates were performed for each of wild type N2, daf-16(mu86), daf-18(ok480) and daf-16(mu86); daf-18(ok480). Arrested L1s were collected after ~4 hr of starvation in virgin S-basal with 0.1% EtOH at 20 °C.

first: Chen

last: Jingxian

first: Rojin

last: Chitrakar

first: Larry Ryan


title: PP1 PNUTS binds the “restrictor” and dephosphorylates pol II CTD Ser5 to stimulate RNA pol II transcription termination [eNET-seq]

city: Aurora

first: David

last: Bentley

state: Colorado

department: BMG

institute: UCD AMC

type: Non-coding RNA profiling by high throughput sequencing

summary: The restrictor complex, WDR82/ZC3H4, is the major termination factor for antisense transcription from bidirectional promoters, but its mechanism of action is poorly understood. We report that the PP1 phosphatase nuclear targeting subunit PNUTS binds to restrictor via its WDR82 subunit. AlphaFold predicts a quaternary complex, PPWZ, in which PP1-associated PNUTS and ZC3H4 both contact WDR82.  A chimera comprising inactive PP1H66K fused to the C-terminal PNUTS sequences including its WDR82 binding domain binds to restrictor and acts as a dominant negative inhibitor of antisense termination and CTD Ser5 dephosphorylation. The PP1H66K-PNUTS is a substrate trap that also interacts with pol II large subunit and nuclear exosome components. Ser5 hyperphosphorylated pol II has increased processivity and pauses less frequently than total pol II. We speculate that the elevated  elongation efficiency of Ser5-P pol II antagonizes early termination and that Ser5 dephosphorylation by PP1/PNUTS/WDR82/ZC3H4  is coupled to termination of antisense transcription.

overall_design: eNETseq in HEK293 cells and those expressing  doxycycline (dox)  inducible PP1-PNUTS fusion proteins

first: Benjamin

last: Erickson


title: PP1 PNUTS binds the “restrictor” and dephosphorylates pol II CTD Ser5 to stimulate RNA pol II transcription termination [ChIP-seq]

overall_design: ChIP-seq in HEK293 cells expressing Avitag doxycycline (dox)  inducible PP1-PNUTS fusion proteins


title: Landscape of the Epstein-Barr virus-host chromatin interactome and gene regulation

city: Shenzhen

last: (Simon) Zhongyuan

state: Guangdong

address: 1088 Xueyuan Avenue

department: School of Life Sciences

institute: Southern University of Science and Technology (SUSTech)

summary: The three-dimensional (3D) chromatin structure of Epstein–Barr virus (EBV) within host cells and the underlying mechanisms of chromatin interaction and gene regulation, particularly those involving EBV’s noncoding RNAs (ncRNAs), have remained incompletely characterized. In this study, we employed state-of-the-art techniques of 3D genome mapping, including protein-associated chromatin interaction analysis with paired-end tag sequencing (ChIA-PET), RNA-associated chromatin interaction technique (RDD), and super-resolution microscopy, to delineate the spatial architecture of EBV in human lymphoblastoid cells. We systematically analyzed EBV-to-EBV (E–E), EBV-to-host (E–H), and host-to-host (H–H) interactions linked to host proteins and EBV RNAs. Our findings reveal that EBV utilizes host CCCTC-binding factor (CTCF) and RNA polymerase II (RNAPII) to form distinct chromatin contact domains (CCDs) and RNAPII-associated interaction domains (RAIDs). The anchors of these chromatin domains serve as platforms for extensive interactions with host chromatin, thus modulating host gene expression. Notably, EBV ncRNAs, especially Epstein–Barr-encoded RNAs (EBERs), target and interact with less accessible regions of host chromatin to repress a subset of genes via the inhibition of RNAPII-associated chromatin loops. This process involves the cofactor nucleolin (NCL) and its RNA recognition motifs, and depletion of either NCL or EBERs alters expression of genes crucial for host infection control, immune response, and cell cycle regulation. These findings unveil a sophisticated interplay between EBV and host chromatin.

overall_design: We generated RDD data for ncRNA, including EBERs, v-snoRNA, miR-BART, and MALAT1, in GM12878 cells. For EBERs, there are three biological replicates: replicate 1 consists of three experiments (EBERs_RDD_rep1_exp1-3), replicate 2 consists of six experiments (EBERs_RDD_rep2_exp1-6), and replicate 3 consists of ten experiments (EBERs_RDD_rep3_exp1-10). Both v-snoRNA and miR-BART have two biological replicates, and MALAT1 has three biological replicates. For ChIA-PET data, there are two biological replicates for each condition. These include GM12878 cells with EBERs knockdown (EBERs-KD) and scrambled oligos serving as a negative control (EBERs-NC), as well as siRNA knockdown for NCL (NCL-KD) and its scrambled control (NCL-NC). ChIA-PET experiments were also conducted on HEK293T cells (NCL-KD, NCL-NC). ChIP-seq data for HSPA9 and NCL has two biological replicates in GM12878 cells (EBERs-KD, EBERs-NC). The ATAC-seq experiments on GM12878 cells included three biological replicates for EBERs-NC and two for EBERs-KD. RNA-seq experiments were conducted with two biological replicates in GM12878 cells for both EBERs-KD and EBERs-NC, and CLIP-seq experiments also had two biological replicates in GM12878 cells.

first: Meizhen

last: Zheng

first: Simon Zhongyuan

last: Tian

first: Yang

first: Duo

last: Ning


title: KIL1 and KIL2 promote endosperm elimination in maize

status: Public on Apr 04 2025

city: Lyon

first: Nicolas

last: Doll

address: 46 allée d'Italie

department: RDP

country: France

institute: ENS de Lyon

summary: The endosperm is a nutritive tissue that supports the growing embryo. Endosperm life span is restricted to seed development and germination. During maize kernel development in maize, two distinct endosperm cell death processes occur. The endosperm adjacent to the embryo scutellum (EAS) undergoes a lytic cell death supposedly to allow embryo expansion, whereas the starchy endosperm (SE) dies after kernel filling producing cell corpses that store nutrients required during germination. Here, we present a detailed analysis of these divergent cell death processes. During SE cell death, mitochondria, nuclei, and the endoplasmic reticulum disintegrate, while nuclear chromatin, cell walls, starch granules, and protein bodies are preserved. In contrast, EAS cells remobilize their stored nutrients, secrete extracellular vesicles, before the cells collapse and a complex post-mortem corpse clearance process ensues. Using single-nucleus RNA-sequencing transcriptome analysis of the developing endosperm, we identified the NAC transcription factors KIL1 and KIL2 as specifically expressed in the EAS. Dominant and recessive loss-of-function approaches demonstrate that KIL1 and KIL2 redundantly promote cell death execution and corpse clearance of the EAS, but are not required for SE cell death. The reduction of EAS cell death in loss-of-function lines strongly impeded embryo growth. Interestingly, KIL1 and KIL2 expression are promoted by DED1, an imprinted paternally expressed transcription factor, suggesting a paternal control over EAS cell death and embryo growth in maize.

overall_design: To investigate the consequence of KIL1 and KIL2 loss of function we carried out an RNA-seq on EAS enriched endosperm, 19 days after pollination


title: Tumor associated myeloid cells support CNS invasive murine T-cell acute lymphoblastic leukemia

city: Austin

first: Ryan

last: Humphrey

state: Texas

address: 1900 Burton Dr. Apt 157

institute: University of Texas at Austin

summary: Single cell RNA sequencing analysis of leukemia cells (T-ALL) and myeloid cells from the leukemic and healthy murine CNS

overall_design: Myeloid and lymphoid cells were FACS sorted from the CNS of leukemic and healthy mice based on CD11b and CD11c expression

first: Ehrlich

last: Lauren

first: Humphrey

last: Ryan

first: Nam

last: Seohee

first: Wylie

last: Dennis


title: Combinatorial transcriptional regulation establishes subtype-appropriate synaptic properties in auditory neurons

city: Boston

first: Isle

last: Bastille

state: MA

address: 220 Longwood Avenue

department: Neurobiology

institute: Harvard University

summary: Primary auditory neurons, or spiral ganglion neurons (SGNs) contain diverse synaptic properties. We used single cell RNA sequencing (scRNA-seq) to analyze the contributions of two transcription factors, c-Maf and Mafb, to the development and diversification of these synapses.

overall_design: Cells from the entire cochlea were dissociated and analyzed using scRNAseq. Neurons were identified during computational analysis.

first: Bastille

last: Isle

first: Goodrich

last: Lisa


title: scRNA sequence study of mouse model lung cancer evolution

status: Public on Apr 03 2025

city: Houston

first: Jianjuan

last: Zhang

address: 1515 Holcombe Blvd.

institute: MD Anderson Cancer Center

summary: In this study, we established one urethane induced mouse precancer mouse, and scRNA sequence profiling validated the new target for the lung precancer interception.

overall_design: Collect the samples of normal lung and tumor tissues from different timepoint of mouse model after Urethane induction, and scRNA sequence profiling of collected samples for lung precancer interception new strategy.

first: Bo

last: Zhu

first: Jianjun

first: Xin

last: Hu


title: Dominant foliar endophytes in soybean

city: Urbana

first: Katy

middle: D

last: Heath

state: IL

address: 1201 W. Gregory Dr

department: Plant Biology

institute: University of Illinois

summary: We seek to determine the effects of foliar endophytes on soybean physiological traits, and their effect on plant responses to elevated carbon dioxide. We are using three dominant endophytes extracted from the SoyFACE facility at UIUC.

overall_design: This experiment took place in February of 2020.  Soybeans were grown in chambers in sterile soil.  Methods include inoculting plants with endopytes individually and in combination to determine infection rate and plant response. Endophytes were grown on MEA plates and cultures mixed with autoclaved milli-q water in equal combinations and sprayed onto soybeans. Soybeans were covered with opaque bags for one day to encourage colonization of endophytes. After bags were removed and leaves allowed to dry, soybeans were randomized in chambers and let sit for 8 days. Gas exchange data was taken after 7 days. After this time, leaf punches were taken from the top, middle, and bottoms leaves and used for RNA sequence data. The plant was then harvested for biomass the next day.

first: Karla

last: Griesbaum

first: Lindsay

middle: V

last: Clark

first: Ivan

last: Sosa

first: Natalie

last: Christian


title: Identification of a Selective Pharmacologic IRE1/XBP1s Activator with Enhanced Tissue Exposure

city: La Jolla

first: R

middle: Luke

last: Wiseman

state: California

address: 10550 N Torrey Pines Rd, Mb110 Receiving Department

institute: The Scripps Research Institute

summary: Activation of the IRE1/XBP1s signaling arm of the unfolded protein response (UPR) has emerged as a promising strategy to mitigate etiologically-diverse diseases. Despite this promise, few compounds are available to selectively activate IRE1/XBP1s signaling to probe the biologic and therapeutic implications of this pathway in human disease. Recently, we identified the compound IXA4 as a highly-selective activator of protective IRE1/XBP1s signaling. While IXA4 has proven useful for increasing IRE1/XBP1s signaling in cultured cells and mouse liver, the utility of this compound is restricted by its limited activity in other tissues. To broaden our ability to pharmacologically interrogate the impact of IRE1/XBP1s signaling in vivo, we sought to identify IRE1/XBP1s activators with greater tissue activity than IXA4. We re-analyzed ‘hits’ from the high throughput screen used to identify IXA4, selecting compounds from structural classes not previously pursued. We then performed global RNAseq to confirm that these compounds showed transcriptome-wide selectivity for IRE1/XBP1s activation. Functional profiling revealed compound IXA62 as a selective IRE1/XBP1s activator that reduced A secretion from CHO7PA2 cells and enhanced glucose-stimulated insulin secretion from rat insulinoma cells, mimicking the effects of IXA4 in these assays. IXA62 robustly and selectively activated IRE1/XBP1s signaling in the liver of mice dosed compound intraperitoneally or orally. In treated mice, IXA62 showed broader tissue activity, relative to IXA4, inducing expression of IRE1/XBP1s target genes in additional tissues such as kidney and lung. Collectively, our results designate IXA62 as a selective IRE1/XBP1s signaling activating compound with enhanced tissue activity, which increases our ability to pharmacologically probe the biologic significance and potential therapeutic utility of enhancing adaptive IRE1/XBP1s signaling in vivo.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: RNA-seq profilling from liver or kidney of mice IP administered vehicle or IXA62 (50 mpk) daily for 7 days. RNA-seq profilling from HEK293 treated for 6 h with the indicated IRE1/XBP1s activating compound (10 µM) or thapsigargin (Tg; 0.5 µM).

first: Jie

last: Sun

first: Kyunga

last: Lee

first: Sergei

last: Kutseikin

first: Adrian

last: Guerrero

first: Bibiana

last: Rius

first: Aparajita

last: Madhavan

first: Dorian

middle: A

last: Rosen

first: Leonard

last: Yoon

first: Maziar

last: Ardejani

first: Jessica

last: Rosarda

first: Alejandra

last: Mendoza

first: Enrique

last: Saez

first: Jeffer

middle: W

last: Kelly

middle: L


title: Btg2 Inhibits the UFMylation of Fmo1 thus Restricting Taurine Synthesis and Exacerbating Ferroptosis in Hepatic Ischemia-Reperfusion Injury in Mice

city: chongqing

first: Dadi

last: Peng

address: 1 Mittraphap Road Street, yuanjiagang

department: Department of Hepatobiliary Surgery

institute: the First Affiliated Hospital of Chongqing Medical University

summary: Hepatic ischemia‒reperfusion (I/R) injury (HIRI) represents a frequently occurring pathological phenomenon during liver surgery, yet the mechanisms governing HIRI remain inadequately comprehended. This study intends to explore the role of B-cell translocation gene 2 (Btg2) in HIRI.

overall_design: We find that Btg2 expression is up-regulated following HIRI. We subsequently develop an HIRl model utilizing hepatocyte-specific Btg2 transgenic over-expression and systemic Btg2 knockout male mice, discovering that Btg2 deletion mitigates inflammation and apoptosis. Furthermore, cellular experiments confirm that Btg2 knockdown alleviates inflammation and mitochondrial stress generated by hypoxia/reoxygenation (H/R). Metabolomics reveals enrichment of taurine metabolism pathway in the Btg2-/- mice. Mechanistically, we demonstrate that Btg2 restricts the UFMylation of flavin-containing monooxygenase 1 (Fmo1), the essential enzyme for taurine synthesis, by the E3 ligase UFM1-specific ligase 1 (Ufl1), consequently facilitating the K48 ubiquitination-mediated degradation of Fmo1. Adeno-associated virus-mediated Fmo1 over-expression inhibits ferroptosis and HIRI significantly in vivo, while adenovirus-mediated Btg2 over-expression mitigates ferroptosis and hypoxia/reoxygenation damage in vitro. Moreover, virtual screening of natural compounds reveals that Daturataturin A inhibits Btg2 and attenuates ferroptosis and HIRI sufficiently. These results propose that Btg2 may constitute a promising therapeutics target for HIRI.

first: Zhongjun

last: Wu


title: Atf3 controls transitioning in female mitochondrial cardiomyopathy as identified by single-cell transcriptomics [Spatial Transcriptomics]

city: Osaka

first: Yasunori

last: Shintani

address: 6-1, Kishibe-shinmachi, Suita

department: Molecular Pharmacology

institute: National Cerebral and Cardiovascular Center

summary: Oxidative phosphorylation defects results in mitochondrial diseases, with cardiac involvement markedly impacting prognosis. However, the mechanisms underlying the transition from compensation to dysfunction in response to metabolic deficiency remain unclear, impeding the development of effective treatments. Here, we employed single-nucleus RNA sequencing (snRNA-seq) on hearts from mitochondrial cardiomyopathy (MCM) mice with cardiac-specific Ndufs6 knockdown of (FS6KD). Pseudotime trajectory analysis of cardiomyocytes from early stage of female FS6KD hearts revealed dynamic cellular state transitioning from compensation to severe compromise, coincided with transient upregulation of a critical transcription factor, activating transcription factor 3 (Atf3). Genetic ablation or adeno-associated virus-mediated Atf3 knockdown in FS6KD mice effectively delayed cardiomyopathy progression in a female-specific manner. Notably, human MCM snRNA-seq revealed a similar transition, including the dynamic expression of ATF3. In conclusion, our findings highlight a fate-determining role of Atf3 in female MCM progression, providing a promising therapeutic candidate for the currently intractable disease.

overall_design: Human: heart tissue from human mitochondrial cardiomyopathy (young), sample size = 1.


title: Rorγt-positive dendritic cells are required for the induction of peripheral regulatory T cells in response to oral antigens

city: St. Louis

first: Marco

last: Colonna

state: MO

address: 660 S. Euclid Ave.

department: Pathology and Immunology

institute: Washington University School of Medicine in St. Louis

summary: The intestinal immune system maintains tolerance to harmless food proteins and gut microbiota through peripherally-derived RORγt+Tregs (pTregs), which prevent food intolerance and inflammatory bowel disease. Recent studies suggested that RORγt+ antigen-presenting cells (APCs), which encompass rare dendritic cell (DC) subsets and type 3 innate lymphoid cells (ILC3s), are key to pTregs induction. Here, we developed a mouse with reduced RORγt+APCs by deleting a specific cis-regulatory element of Rorc encoding RORγt. Single-cell RNA-sequencing and flow cytometry analyses confirmed the depletion of a RORγt+DC subset and ILC3s. These mice showed a secondary reduction in pTregs, impaired tolerance to oral antigens and increase in Th2 cells. Conversely, newly and previously generated ILC3-deficient mice showed no pTregs or Th2 cells abnormalities. Lineage tracing revealed that RORγt+DCs share a lymphoid origin with ILC3s, consistent with their similar phenotypic traits. These findings highlight a unique role of lymphoid RORγt+DCs in maintaining intestinal immune balance and preventing conditions like food allergies.

overall_design: We performed single-cell RNA sequencing on sort purified CD3-B220-CD11c+MHC-II+ DCs as well as CD3-B220-CD11c-MHC-II+ CCR6+ ILC3 extracted from mLNs of 15days old Rorc+7kbE WT/WT and Rorc+7kbE KO/KO mice. Each line included four biological replicates, uniquely identified by the labeling of four distinct Hashtag antibodies.

first: Patrick

last: Fernandes Rodrigues


title: Reactive cholangiocyte-derived ORM2 drives a pathogenic modulation of the injured biliary niche through macrophage reprogramming

city: Berlin

first: Hanyang

last: Liu

address: Augustenburger Platz 1

department: Department of Hepatology and Gastroenterology (CCM/CVK),

country: Germany

institute: Charité Universitätsmedizin Berlin

summary: Upon liver injury, altered cholangiocyte functions can lead to a process referred to as ductular reaction (DR), which is an umbrella term harboring not excessive cell proliferation, but also intricate inflammation and fibrogenesis modulation. DR has been considered as an essential hallmark and promising therapeutic target in a variety of liver diseases. However, the potentially broad implications of DR are rarely known due to the lack of effective investigational models. In this study, transcriptomic exploration methods were utilized to determine key factors resulting from injured cholangiocytes and in macrophage alterations, while multiplex immunofluorescent detection together with an in-house optimized image processing approaches were utilized to explore spatial counterparts in situ. Furthermore, co-culture systems (microchambers and liver-on-a-chip) equipped with multiple mouse strain-derived primary liver and circulating immune cells were employed to capitulate multi-cellular interactions upon biliary injury and to study mechanistic influencers. Results illustrated that Orosomucoid 2 (ORM2) was screened out as one of the most strongly induced secretory factors expressed by mouse-derived intrahepatic cholangiocytes under bile duct injury. Furthermore, ORM2-induced monocyte recruitment and potent transcriptome alterations in liver macrophages are associated with an increase of pro-inflammatory cytokine secretion and expression of cell stress-related genes. Furthermore, ORM2-activated macrophages not only exacerbated cell stress and Orm2 expression in both cholangiocytes and hepatocytes, but also promoted fibrogenesis in hepatic stellate cells. In addition, ORM2 regulated liver macrophage functions via an ITPR2-dependent calcium pathway. In conclusion, cholangiocyte-derived ORM2 induces liver macrophage reprogramming via an ITPR2-dependent calcium pathway in response to acute and chronic biliary injury, serving as a promoter of liver disease progression. This study reveals a novel mechanism for cholangiocyte-macrophage crosstalk upon liver injury, which may draw more attention to this cellular duet as a potential therapeutic target.

overall_design: Primary liver macrophages (F4/80+) were isolated from C57BL/6J wild-type mice (18 – 24-week-old). Macrophages were harvested for bulk transcriptomic analyses upon 24-hour ORM2 treatment (1 µg/mL) or no treatment. Sample size: 1) untreated: 5; 2) ORM2-treated: 4.

first: Hayang

first: Hilmar

last: Berger

first: Adrien

last: Guillot

first: Frank

last: Tacke


title: Gene expression profiling of neutrophils isolated from bone marrow, spleen and tumor of H16sc-IS1-tumor-bearing mice treated with anti-IL1RAP or untreated.

city: Lausanne

first: Nadine

last: Fournier

state: Vaud

address: Agora Cancer Research Center, Bugon 25A

country: Switzerland

institute: Agora Cancer Research Center & Swiss Institute of Bioinformatics

summary: It is well established that symptomatic cancers evade immune destruction by coalescing lesional and tumor microenvironments to suppress adaptive immunity. Additionally, mouse models of cervical and other cancers have revealed a capability of tumors to systemically induce the expansion of myeloid cells that cripple T cell development in spleen and lymph nodes, further impairing immune responses.  We show that HPV16-driven cervical cancers release into the circulatory system four immunoregulatory ligands – IL1α, IL1ß, IL33, and IL36ß – that bias the bone marrow toward granulocytic myelopoiesis, producing immunosuppressive neutrophils and myeloid progenitors differentially populating spleens and tumors to facilitate immune evasion. A pan-IL1 receptor antagonist, anti-IL1RAP, attenuates this myeloid expansion and complements an HPV-E7 peptide vaccine plus anti-CTLA4 to elicit anti-tumor immunity. Evidence for similar systemic activity of these four IL1 ligands in human cervical and other cancers encourages multi-targeting this signaling axis to broaden the scope of cancer immunotherapy.

overall_design: Comparative gene expression profiling of neutrophils isolated from bone marrow, spleen and tumor of H16sc-IS1-tumor-bearing mice treated with anti-IL1RAP versus untreated controls.

first: Morgane

last: Lecointre

first: Jeremy

first: Douglas

last: Hanahan

first: Rachel

last: Marcone


title: Gene expression profiling of H16sc-IS1, Control H16sc-ImP and ILs-OE H16sc-ImP cancer cells.

overall_design: Comparative gene expression profiling of H16sc-IS1, Imp cells with ILs-OE and Imp controls.


title: HPV16-expressing tumors release multiple IL-1 ligands to orchestrate systemic immunosuppression whose disruption enables efficacy of a therapeutic vaccine.

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

overall_design: Refer to individual Series


title: A scalable gut epithelial organoid model reveals the genome-wide colonization landscape of a human-adapted pathogen

city: Würzburg

first: Laura

last: Jenniches

address: Josef-Schneider-Straße 2/D15

institute: Helmholtz Institute for RNA-based Infection Research

summary: Studying the pathogenesis of human-restricted microbes is challenging, since small animal models often fail to recapitulate human physiology and suffer from infection bottlenecks that confound genetic screens. Hence, the comprehensive genetic and regulatory circuits driving the infection process of major human pathogens like Shigella flexneri remain to be defined. We combined large-scale Shigella infections of enteroids and colonoids with Transposon Directed Insertion Sequencing (TraDIS) and Bayesian statistical modelling, thereby establishing the first genome-wide map of Shigella genes required to colonize human intestinal epithelium. Our study revealed the Shigella virulence effectors essential for epithelial cell invasion across geometries and intestinal segments, identified over 100 chromosomal genes involved in the process, and uncovered a post-transcriptional mechanism whereby tRNA modification enzymes exert global control of a bacterial virulence program. Our findings provide a broadly applicable framework for combining advanced organotypic tissue culture with computational tools to map human – microbe interactions at scale.

overall_design: RNA-sequencing in a wt or virF mutant Shigella strain grown at 30° or 37°C

first: Maria

last: Di Martino

first: Anjeela

last: Bhetwal

first: Jens

last: Eriksson

first: Ana

middle: C

last: Lopes

first: Angelika

last: Ntokaki

first: Martina

last: Pasqua

first: Magnus

last: Sundbom

first: Martin

last: Skogar

first: Wilhelm

last: Graf

first: Dominic-Luc

last: Webb

first: Per

middle: M

last: Hellström

first: André

last: Mateus

first: Lars

last: Barquist

first: Mikael

middle: E

last: Sellin


overall_design: TraDIS with Shigella flexneri under different growth conditions.


title: The transcriptome expression differences between GDNF-treated and anti-NCAM1-treated EO771-tdT-LM2 cells under glucose-deprived media treatment

first: Dorothy

middle: Anna

last: Sipkins

address: 905 S. LaSalle St.

summary: The molecular mechanisms that regulate breast cancer cell (BCC) metastasis and proliferation within the leptomeninges (LM) are poorly understood, limiting development of effective therapies. Here we show that BCCs in mice can invade the LM by abluminal migration along blood vessels that connect vertebral/calvarial bone marrow and meninges, bypassing the blood-brain barrier. This process is dependent on BCC engagement with vascular basement membrane laminin through expression of the neuronal pathfinding molecule integrin α6. Once in the LM, BCCs co-localize with perivascular meningeal macrophages and induce their expression of the pro-survival neurotrophin, GDNF. Intrathecal GDNF blockade, macrophage-specific GDNF ablation, or deletion of the GDNF receptor, NCAM, from BCCs, inhibit BC growth within LM. Here, we performed RNA-seq analysis of GDNF-treated and/or anti-NCAM1-treated EO771-tdT-LM2 cells under glucose-deprived media treatment.

overall_design: Examination and comparision of the transcriptome expression in GDNF-treated and/or anti-NCAM1-treated EO771-tdT-LM2 cells


overall_design: Infection of human organoids with a Shigella flexneri M90T Tn5 mutant library containing 10,000 or 30,000 mutants.


title: Physical Phase Transition of Mineralocorticoid Receptors Determines Preservation Quality of Donor Hearts for Transplantation

city: Rochester

first: IENG LAM

last: LEI

state: MN

address: 321 3rd Street SW

institute: Mayo Clinic

summary: We examine the single nuclear RNA profile in the human donor heart at baseline and 10 hours of storage in HTK with/without canrenone. We also analyze the genomic occupancy of MR in these conditions.

overall_design: For snRNA-seq, single nuclei was isolated from human heart tissues and subject to sequencing using 10x platform. For Cut&run seq, single nuclei was isolated from human donor heart and fixed with 0.1% formaldehyde for 1 minutes. The cut&run assay were then performed using Epicypher Cun&run kit.

first: Ienglam

last: Lei

first: Paul

last: Tang


title: PP1 PNUTS binds the “restrictor” and dephosphorylates pol II CTD Ser5 to stimulate RNA pol II transcription termination [nascent RNA-seq]

first: David

last: Bentley

summary: The restrictor complex, WDR82/ZC3H4, is the major termination factor for antisense transcription from bidirectional promoters, but its mechanism of action is poorly understood. We report that the PP1 phosphatase nuclear targeting subunit PNUTS binds to restrictor via its WDR82 subunit. AlphaFold predicts a quaternary complex, PPWZ, in which PP1-associated PNUTS and ZC3H4 both contact WDR82. A chimera comprising inactive PP1H66K fused to C-terminal PNUTS sequences is a dominant-negative inhibitor of antisense termination and CTD Ser5 dephosphorylation and both activities require the PNUTS WDR82 binding domain. PP1H66K-PNUTS is a substrate trap that also interacts with pol II large subunit and nuclear exosome components. Ser5 hyperphosphorylated pol II has increased processivity and pauses less frequently than total pol II. We propose that the elevated elongation efficiency of Ser5-P pol II antagonizes early termination and that Ser5 dephosphorylation by PP1/PNUTS/WDR82/ZC3H4 is coupled to termination of antisense transcription.

overall_design: nascent RNA seq in Bromouridine pulse labelled HEK293 cells expressing doxycycline (dox)  inducible PP1-PNUTS fusion proteins

first: Benjamin

last: Erickson


title: Single cell RNA (scRNAseq) and T cell receptor sequencing (scTCRseq) of cerebrospinal fluid (CSF) samples from three patients with spinal cord injury (SCI) [scRNA-seq]

city: Nanjing

first: xuhui

last: Ge

address: Hanzhong Road

institute: Nanjing medical university

summary: The CSF encompasses a highly controlled immune system. However, little is known about the alterations in CSF immune microenvironment after SCI. Here, we performed scRNA and TCRseq on CSF collected from three SCI patients caused by car accidents to analyze the transcriptomic changes of CSF immune cells.

overall_design: The CSF of three SCI patients  were isolated  via lumbar puncture within 48 hours after injury. Following red blood cell lysis and magnet-activated cell sorting (MACS) for live singlets, CSF samples were then analyzed by scRNAseq and scTCRseq.


first: Laura

last: Jenniches

overall_design: Infection of human organoids with a Shigella flexneri Tn5 mutant library

first: Maria

last: Di Martino

first: Anjeela

last: Bhetwal

first: Jens

last: Eriksson

first: Ana

last: Lopes

first: Angelika

last: Ntokaki


title: Single cell RNA (scRNAseq) and T cell receptor sequencing (scTCRseq) of cerebrospinal fluid (CSF) samples from three patients with spinal cord injury (SCI) [TCR-seq]


title: Convergent evolution of monocyte differentiation in adult skin instructs Langerhans cell identity

city: Southampton

first: Andres

middle: Felipe

last: Vallejo Pulido

address: University of Southampton

department: Medicine

country: United Kingdom

institute: University of Southampton

summary: Langerhans cells (LCs) maintain tissue and immunological homeostasis at the epidermal barrier site. They are unique among phagocytes in functioning both as embryo-derived, tissue-resident macrophages that influence skin innervation and repair, and as migrating professional antigen presenting cells, a capability classically assigned to dendritic cells (DC). Here we report the mechanisms that determine this dual identity. Using ablation of embryo-derived LCs in murine adult skin and tracked differentiation of incoming monocyte-derived replacements, we reveal intrinsic intra-epidermal heterogeneity. Macrophage-dendritic cell precursors are selected for survival in the skin environment, by-passing gene programs that specify a macrophage fate. We demonstrate that the hair follicle niche provides Notch signals that impose LC identity. In human skin, we show that embryo-derived (e)LCs in newborns retain transcriptional evidence of their macrophage origin, but this is superseded by distinct DC-like immune modules after expansion of the eLC network. Thus, cellular adaptation to the adult skin niche replicates conditioning of eLC, instructing DC-like programmes within macrophages

overall_design: Skin samples were collected from healthy donors aged 0-15 yo and epidermal cell suspensions were obtained. CD207+CD1a+ cells were FACS purified directly into Trizol. d, days; mo, months; yo, years old.

first: Marta

last: Polak

first: Sofia

last: Sirvent-Bernal

middle: F

last: Vallejo


title: PROTein Evolution Using Selection (PROTEUS) [Nanopore]

city: Camperdown

first: Graham

last: Neely

address: John Hopkins Drive

institute: Charles Perkins Centre, The University of Sydney

summary: Directed evolution (DE) is a process of mutation and iterative artificial selection to breed biomolecules with new or improved activity. DE platforms are primarily prokaryotic or yeast-based, and stable highly mutagenic mammalian systems have been challenging to establish and apply. To this end, we developed PROTein Evolution Using Selection (PROTEUS), a new platform that uses chimeric virus-like vesicles (VLVs) to enable extended mammalian DE campaigns without loss of system integrity. This platform, consisting of a minimal modified Semliki Forest virus genome controlling expression of the Indiana vesiculovirus G coat protein, is stable and can generate sufficient diversity for DE in mammalian systems. Using PROTEUS, we altered the doxycycline responsiveness of tetracycline-controlled transactivators, generating a more sensitive TetON-4G tool for gene regulation. PROTEUS is also compatible with intracellular nanobody evolution, and we use it to design a novel DNA damage-responsive anti-p53 nanobody. Overall, PROTEUS is a robust, efficient, and stable platform to direct evolution of biomolecules within mammalian cells.

overall_design: Long-read nanopore sequencing and short-read Illumina sequencing of VLP transgenes to determine transgene sequence proportions and mutations. Long-read sequencing samples arise from pooled (N=6) VLP samples at each sampling timepoint. Short-read sequencing samples arise from single VLP samples at each sampling timepoint.

first: Alexander

middle: J

last: Cole

first: Christopher

last: Denes

first: Daniel

last: Hesselson


title: Atf3 controls transitioning in female mitochondrial cardiomyopathy as identified by single-cell transcriptomics [snRNA-seq]

first: Yasunori

last: Shintani

overall_design: Mouse: heart tissue from CI-deficiency mitochondrial cardiomyopathy model (FS6KD) of young (8 weeks) versus old (17 weeks) compared to control ( WT 8 weeks), sample size = 1 per group.  Human: heart tissue from human mitochondrial cardiomyopathy (young), sample size = 1. Nuclei were isolated and snRNA sequencing was performed by 10X Genomics.


title: Atf3 controls transitioning in female mitochondrial cardiomyopathy as identified by single-cell transcriptomics [RNA-seq]

overall_design: CRISPR-Cas9 knockout of Atf3 (n = 4 per group) and muscle-specific knockdown of Atf3 in FS6KD in neonatal mice (n = 3 per group) to evaluate the effect of Atf3 loss on cardiac function and metabolic profile. RNA was isolated from heart tissue collected after 12 weeks of Atf3 knockout or Atf3 WT FS6KD or post injection with MyoAAV2-shAtf3 or MyoAAV2-shCtrl. RNA-sequencing was performed.


title: Atf3 controls transitioning in female mitochondrial cardiomyopathy as identified by single-cell transcriptomics [PIC_RNA-seq]

overall_design: Isolate gene expression profiles from high Atf3 expression cardiomyocytes versus low Atf3 expression cardiomyocytes out of fresh frozen FS6KD heart tissues. Sample size = 3 per group


title: Comparing the transcriptome expression differences between breast cancer cells EO771-tdT-Parental and EO771-tdT-LM2 using high-throughput sequencing.

city: Durham

first: Dorothy

last: Sipkins

institute: Duke University

summary: The molecular mechanisms that regulate breast cancer cell (BCC) metastasis and proliferation within the leptomeninges (LM) are poorly understood, limiting development of effective therapies. Here we show that BCCs in mice can invade the LM by abluminal migration along blood vessels that connect vertebral/calvarial bone marrow and meninges, bypassing the blood-brain barrier. To screen for signaling pathways in EO-LM2 cells that could support their survival or proliferation in the meningeal niche, we performed RNA-seq analysis of EO771-tdT-Parental and EO771-tdT-LM2 to compare their transcriptome expression differences.

overall_design: Examination and comparision of the transcriptome expression in 2 cell types (EO771-tdT-Parental and EO771-tdT-LM2).


title: Atf3 controls transitioning in female mitochondrial cardiomyopathy as identified by single-cell transcriptomics


title: A Living Organoid Biobank of Crohn’s Disease Patients Reveals Distinct Clinical Correlates of Molecular Subtypes of Disease

status: Public on Apr 02 2025

city: La Jolla, CA 92093

first: Pradipta

last: Ghosh

state: CA

address: 9500 Gilman Drive (MC 0651)

department: Departments of Medicine and Cellular and Molecular Medicine

institute: University of California San Diego

summary: In this work, Penrose et al. demonstrate the potential of PDOs as predictive tools in Crohn’s disease, that that capture the past, present, and future of disease behavior, thereby advancing PDO-informed precision medicine beyond oncology into complex inflammatory diseases.

overall_design: PDOs were isolated from colonic tissue specimens collected from CD subjects using established crypt isolation protocols as previously summarized [PMID:  39332415]. These intestinal crypts, which contain crypt-base columnar (CBC) cells, were enzymatically dissociated and processed for 3D organoid culture. Organoids and monolayers were lysed using 200 μl of RNA lysis buffer followed by RNA extraction per Zymo Research Quick-RNA MicroPrep Kit instructions (see key resources table). Tissue samples were lysed in TRI-Reagent and RNA was extracted using Zymo Research Direct-zol RNA Miniprep.

first: Saptarshi

last: Sinha

first: Harrison

last: Penrose

first: Brigid

middle: S

last: Boland

first: Courtney

last: Tindle


title: Type I interferons dominate cutaneous lichen planus inflammatory landscape driving the interface dermatitis reaction [NTERT]

city: Paris

first: Chloé

last: Grolleau

address: 1 avenue Claude Vellefaux

department: Hopital saint Louis

institute: INSERM U1342, eq 16

summary: Cutaneous lichen planus (LP) is a chronic inflammatory skin disease histologically characterized by an interface dermatitis with lymphocyte infiltration and keratinocyte cell-death. Previous studies suggest that LP inflammation is dominated by a type I immune response involving IFN-g but its pathogenesis remains not fully elucidated yet. To investigate the inflammatory mechanisms underlying LP, we performed single-cell RNA sequencing on LP compared with healthy control skins. We demonstrate that lesional skin from patient with LP is imprinted by a type I interferon (IFN-I)-rich environment, involving all the main skin cell components. While all immune cells are imbued with this interferon signature, we highlight unique subsets of inflammatory keratinocytes and fibroblasts highly influenced by IFN-I near the epidermis-dermis junction. We also show a unique CD8+CXCL13+ T cell population exhibiting cytotoxic and epidermis-homing markers together with an enrichment in inflammatory CD16+ myeloid cells in LP skin. Herein, we illustrate that IFN-I education on all major skin cell types and particularly in keratinocytes drives the interface dermatitis reaction, thus orchestrating the cross-talk between immune and stromal cells in LP skin. Last, we suggest the effectiveness of targeting the common IFN-I receptor, IFNAR1, to switch off the activation of inflammatory pathways in an ex-vivo model of LP skin and in on patient with lupus lichen skin lesions. Together, our data provide a comprehensive characterization of LP immunopathogenesis and demonstrate the strong involvement of IFN-I in its inflammatory landscape, providing arguments for the therapeutic use of drugs targeting IFN-I pathway in patients with LP.

overall_design: Immortalized primary human keratinocytes (N/TERT) in culture were treated for 24 hours with 3 differents subtypes of interferons and their gene expression prolifing were studied using microarray.

first: Hélène

last: Le Buanec

first: Jean-David

last: Bouaziz


title: Morphology-guided organoid classification reveals prognosis of oral cancer [dataset 2]

city: Goyang-si

first: Mi Rim

last: Lee

address: 323, Ilsan-ro

institute: National Cancer Center Research Institute

summary: Oral cancer is an aggressive malignancy with a survival rate below 50% in advanced stages due to low mutation rates, lack of molecular subtypes, and limited treatment targets. This study presents a pioneering approach to classifying oral cancer subtypes based on the morphology of patient-derived organoids (PDOs) and proposes a novel therapeutic strategy. We successfully established 76 cancer and 81 normal PDOs. For cancer PDOs, both manual classification and AI-based scoring were utilized to categorize them into three distinct subtypes: normal-like, dense, and grape-like. These subtypes correlated with unique transcriptomic profiles, genetic mutations, and clinical outcomes, with patients harboring dense and grape-like organoids exhibiting poorer prognoses. Furthermore, drug response assessments of 14 single agents and Cisplatin combination therapies identified a synergistic treatment approach for resistant subtypes. This study highlights the potential of integrating morphology-based classification with genomic and transcriptomic analyses to refine oral cancer subtyping and develop effective treatment strategies.

overall_design:
RNA-seq profiling was performed on 40 patient-derived oral squamous cell carcinoma (OSCC) organoid. Total RNA was extracted, and libraries were prepared using the TruSeq Stranded mRNA protocol. Sequencing was conducted on the Illumina NovaSeq 6000 platform (GSE293370).
In addition, Exome-seq was performed  as part of this study. Although the original raw Exome-seq files are no longer available, mutation annotation files (MAF format) are provided as supplementary files. The MAF files contain high-confidence somatic mutations annotated from tumor-normal paired Exome-seq.

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Submitter states that missing raw files are due to file loss.
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first: Sumin

last: Kang

first: Jonghyn

first: Dongkwan

last: Shin

first: Ik-Jae

last: Kwon

first: Sung-Woen

last: Choi

first: Yun-Hee

last: Kim


title: Morphology-guided organoid classification reveals prognosis of oral cancer [dataset 1]

overall_design:
RNA-seq profiling was performed on 40 patient-derived oral squamous cell carcinoma (OSCC) organoid. Total RNA was extracted, and libraries were prepared using the TruSeq Stranded mRNA protocol. Sequencing was conducted on the Illumina NovaSeq 6000 platform.
In addition, Exome-seq was performed  as part of this study. Although the original raw Exome-seq files are no longer available, mutation annotation files (MAF format) are provided as supplementary files. The MAF files contain high-confidence somatic mutations annotated from tumor-normal paired Exome-seq (GSE293371).


title: Metabolic adaptations direct cell fate during tissue regeneration [shOGDH_Mice_RNA-seq]

city: New York

first: Yu-Jui

last: Ho

state: New York

address: 417 E 68th St

department: Cancer Biology & Genetics Program

institute: Memorial Sloan Kettering Cancer Center

summary: Although cell fate specification is generally attributed to transcriptional regulation, emerging data also indicate a role for molecules linked with intermediary metabolism. For example, α-ketoglutarate (αKG), which fuels energy production and biosynthetic pathways in the tricarboxylic acid (TCA) cycle, is also a co-factor for chromatin-modifying enzymes1-3. Nevertheless, whether TCA cycle metabolites regulate cell fate during tissue homeostasis and regeneration remains unexplored. In the intestine, we discovered unexpectedly heterogeneous expression of TCA cycle enzymes, with αKG dehydrogenase complex components4-6 upregulated in the absorptive lineage and downregulated in the secretory lineage. Using genetically modified mouse models and organoids, we demonstrated a dual, lineage-specific role for 2-oxoglutarate dehydrogenase (OGDH), the enzymatic subunit of αKG dehydrogenase complex. In the absorptive lineage, OGDH is upregulated by Hnf4 transcription factors to maintain the bioenergetic and biosynthetic needs of enterocytes. In the secretory lineage, OGDH is downregulated through a process that, when modeled, increases αKG levels and stimulates secretory cell differentiation. Consistent with this, in murine colitis models with impaired secretory cell number and maturation, OGDH inhibition or αKG supplementation reversed these impairments and promoted tissue healing. Hence, OGDH dependency is lineage-specific, and its regulation helps direct cell fate, offering insights for targeted therapies in regenerative medicine.

overall_design: RNA sequencing of murine isolated crypts at day 3 after induction of the indicated GFP-linked shRNAs with doxycycline. Two independent shRNAs targeting Ogdh (shOgdh346 and shOgdh2081) and a control shRNA (shRen713) were used.

first: Almudena

last: Chaves-Perez

first: Scott

last: Millman

first: Sudha

last: Janaki-Raman

first: Clemens

last: Hinterleitner

first: Valentin

last: A. Barthet

first: John

middle: P

last: Morris IV

first: Francisco

last: Barriga

first: Jose

last: Reyes

first: Aye

last: Kyaw

first: H. Amalia

last: Pasolli

first: Dana

last: Pe’er

first: Craig

middle: B

last: Thompson

first: Lydia

last: S. Finley

first: Justin

middle: R

last: Cross

last: Lowe


title: Single cell transcriptomics of several organs in K14HPV16/H2b and FVBN/H2b mice.

first: Nadine

last: Fournier

overall_design: scRNAseq profiling of cervix, spleen, bone marrow, ear skin and blood of K14HPV16/H2b and FVBN/H2b mice.

first: Morgane

last: Lecointre

first: Jeremy

last: Guillot

first: Douglas

last: Hanahan

first: Rachel

last: Marcone


title: Metabolic adaptations direct cell fate during tissue regeneration

first: Yu-Jui

last: Ho

overall_design: Refer to individual Series


title: Metabolic adaptations direct cell fate during tissue regeneration [Organoids_RNA-seq]

overall_design: RNA sequencing of organoids enriched for ISCs treated with 600 mg/ Kg of DM-aKG or doxycycline

first: Almudena

last: Chaves-Perez

first: Scott

last: Millman

first: Sudha

last: Janaki-Raman

first: Clemens

last: Hinterleitner

last: A. Barthet


title: Metabolic adaptations direct cell fate during tissue regeneration [DMaKG_Mice_RNA-seq]

overall_design: RNA sequencing of murine isolated crypts from C57Bl/6 mice, treated or not with 600 mg/ Kg of DM-aKG.

first: Valentin

first: John

last: Morris IV

first: Francisco

last: Barriga

first: Jose

last: Reyes

last: Kyaw

last: Pasolli


title: Vitrification preserves oocyte transcriptome in a 3D in vitro follicle development and oocyte maturation system

city: Pitscataway

first: Shuo

last: Xiao

state: NJ

address: 170 Frelinghuysen Rd, Room 404

department: Pharmacology & Toxicology

institute: Rutgers University

summary: Vitrification is increasingly used to cryopreserve gametes and embryos in assisted reproductive technology (ART). Our prior research demonstrates that vitrification preserves the viability and functionality of ovarian follicles. However, its impact on follicle-enclosed oocyte remains unknown. The current study investigates whether vitrification, combined with a 3D encapsulated in vitro follicle growth (eIVFG) system, maintains oocyte transcriptome during in vitro follicle development and oocyte maturation. Immature mouse preantral follicles were vitrified and cultured in eIVFG for 8 days to grow to the preovulatory stage, followed with the induction of ovulation and oocyte maturation on day 9, with fresh follicles as the control. Oocytes at germinal vesicle (GV) stage from grown preovulatory follicles on day 8 and oocytes at metaphase II (MII) upon ovulation on day 9 were collected for single-oocyte Smart-Seq2 RNA sequencing analysis. The principal component analysis (PCA) separated GV and MII oocytes into two distinct clusters, but oocytes from fresh and vitrified follicles were largely overlapped. Differential gene expression (DEG) analysis revealed that GV or MII oocytes from fresh and vitrified follicles had comparable expression of maternal effect genes and other genes related to oocyte meiotic and developmental competence. There was a significant transcriptomic change during the GV-to-MII transition. Gene ontology (GO) and KEGG analysis identified DEGs between GV and MII oocytes related to cell cycle, RNA processing, mitochondria, and ribosome. In summary, our study demonstrates that vitrification preserves oocyte transcriptome during in vitro follicle development and oocyte maturation, supporting its potential in fertility preservation. Moreover, our single-oocyte RNA sequencing analysis identifies key DEGs upon GV-to-MII transition, indicating their potential functions in underpinning oocyte meiotic and developmental competence.

first: Jiyang

last: Zhang

first: Wenlong

last: Zhao

first: Samantha

last: Cheron

first: Mary

last: Zelinski

first: Qiang


title: RNA-seq analysis of  the brain of mice following recombinant HSV-1 carrying the S302A mutation in vUNG and the repaired HSV-1 strain

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

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

summary: To investigate the relationship between the host factor APOBEC1 and the viral factor vUNG in the pathogenesis of herpes encephalitis, wild-type and Apobec1-deficient mice were infected with vUNG mutants and their repaired strains. Brain tissues were collected, and host mRNA expression was analyzed using RNA sequencing.

overall_design: Five-week-old C57BL/6 wild-type (WT) and Apobec1 knockout (Apobec1-KO) mice were intracranially infected with 1,000 PFU of a recombinant HSV-1 harboring the S302A mutation in vUNG or a repaired version of HSV-1. The mice were sacrificed 5 days post-infection. To investigate the impact of APOBEC1 and vUNG on host gene expression, total RNA was extracted from the brain and subjected to RNA sequencing (RNA-seq) analysis.

first: Akihisa

last: Kato

first: Hayato

last: Harima

first: Yasushi

last: Kawaguchi


title: A mannitol-based buffer improves single-cell RNA sequencing of high-salt marine cells

city: Boston

first: Tal

middle: Deborah

last: Scully

address: 200 Longwood Ave

department: Systems Biology

institute: Harvard Medical School

summary: Single-cell RNA sequencing (scRNA-seq) enables discovery of novel cell states by transcriptomic profiling with minimal prior knowledge, making it useful for studying non-model organisms. For most marine organisms, however, cells are viable at a higher salinity than is compatible with scRNA-seq, impacting data quality and cell representation. We show that a low-salinity phosphate buffer supplemented with D-mannitol (PBS-M) enables higher-quality scRNA-seq of blood cells from the tunicate Ciona robusta. Using PBS-M reduces cell death and ambient mRNA, revealing cell states not otherwise detected. This simple protocol modification could enable or improve scRNA-seq for the majority of marine organisms.

overall_design: Circulating cells were collected from adult Ciona robusta animals, then run directly analyzed with scRNA-seq. One sample was prepared in high-salt buffer (Ca- and Mg-free buffered artificial seawater), then diluted shortly before scRNA-seq encapsulation with water (libarary name Cr_blood_asw). The other sample was prepared in a low-salt, high osmolarity buffer (0.7 M D-mannitol in PBS) (library name Cr_blood_mannitol).

middle: D

first: Allon

last: Klein


title: PHLPP2 is a pseudophosphatase that lost activity in the metazoan ancestor

city: Wien

first: Luis

middle: Miguel

last: Cerron Alvan

address: Dr. Bohr Gasse 9

country: Austria

institute: Max Perutz Labs

summary: The phosphoinositide 3-kinase (PI3K) pathway is a major regulator of cell and organismal growth. Consequently, hyperactivation of PI3K and its downstream effector kinase, Akt, is observed in many human cancers. PH domain leucine-rich repeat-containing protein phosphatases (PHLPP), two paralogous members of the metal-dependent protein phosphatase family, have been reported as negative regulators of Akt signaling and, therefore, tumor suppressors. However, the stoichiometry and identity of the bound metal ion(s), mechanism of action, and enzymatic specificity of these proteins are not known. Seeking to fill these gaps in our understanding of PHLPP biology, we unexpectedly discovered that PHLPP2 has no catalytic activity in vitro. Instead, we found that PHLPP2 is a pseudophosphatase with a single zinc ion bound in its catalytic center. Furthermore, we found that cancer genomics data do not support the proposed role of PHLPP1 or PHLPP2 as tumor suppressors. Phylogenetic analyses revealed an ancestral phosphatase that arose more than 1000 Mya, but that lost activity at the base of the metazoan lineage. Surface conservation indicates that PHLPP2 may have lost catalytic activity, but retained substrate binding. Finally, using phylogenomics, we identify co-evolving genes consistent with a scaffolding role for PHLPP2 on membranes. In summary, our results provide a molecular explanation for the inconclusive results that have hampered research on PHLPP and argue for a new focus on non-catalytic roles of PHLPP1 and PHLPP2.

overall_design: HEK293 cell lines (WT and PHLPP2 KO9 were cultured in DMEM high glucose (Sigma Aldrich) supplemented with 10 % FBS (Sigma Aldrich) and 1 % Penicillin/Streptomycin (Sigma Aldrich) at 37 °C and 5 % CO2.

first: Tarik

last: Husremović

first: Vanessa

last: Meier

first: Lucas

last: Piëch

first: Katharina M.

last: Siess

first: Sumire

last: Antonioli

first: Irina

last: Grishkovskaya

first: Nikoleta

last: Kircheva

first: Silvia E.

last: Angelova

first: Karoline

last: Wenzl

first: Andreas

last: Brandstätter

first: Jiri

last: Veis

first: Fran

last: Miočić-Stošić

first: Dorothea

last: Anrather

first: Markus

last: Hartl

first: Luis M.

last: Cerron-Alvan

first: Martin

last: Leeb

first: Bojan

last: Žagrović

first: Stephan

last: Hann

first: Christoph

last: Bock

first: Egon

last: Ogris

first: Todor

last: Dudev

first: Nicholas A.T.

last: Irwin

first: David

last: Haselbach

first: Thomas A.

last: Leonard


title: TFE3 fusion oncoprotein condensates drive epigenetic reprogramming and cancer progression [CUT&RUN]

city: Baltimore

first: Wanlu

last: Chen

state: MD

address: 615 N. Wolfe Street

institute: Johns Hopkins University

summary: Translocation renal cell carcinoma (tRCC) presents a significant clinical challenge due to its aggressiveness and limited treatment options. This cancer is primarily driven by fusion oncoproteins (FOs) arising from chromosomal rearrangements, yet their role in oncogenesis remains incompletely understood. Here we investigate TFE3 fusion in tRCC, focusing on NONO::TFE3 and SFPQ::TFE3, constituting 30-40% of all TFE3 FOs. We find that TFE3 FOs form liquid-like condensates with heightened transcriptional activity, selectively recruiting active transcription markers to TFE3 target genes and promoting cell proliferation, migration, and drug resistance. The coiled-coil domains (CCD) of NONO and SFPQ are essential for condensate formation, prolonging TFE3 FOs' chromatin binding time and enhancing transcription. We comprehensively investigated the genome-wide recruitment of TFE3 FOs and their CCD-altered variants, uncovering widespread changes in chromatin accessibility and genomic binding specifically at TFE3 and AP-1 regulated loci. We also observe altered H3K27ac deposition at enhancers and super-enhancers notably at pro-growth and stemness markers such as BCL2 and CD44, and identify novel oncogenic target genes of TFE3 FOs. Disruption of condensate formation, resulting from CCD domain alterations in FOs, robustly dysregulates their role in chromatin accessibility, chromatin binding, H3K27ac occupancy, and gene expression. Altogether our integrated analyses underscore the critical functions of TFE3 FO condensates in driving RCC progression, offering pivotal insights for future targeted therapeutic strategies.

overall_design:
To investigate the function of fusion TFE3 and mutants (NONO::TFE3, NONOdeltaCCD::TFE3, NONOmut::TFE3, SFPQ::TFE3, SFPQdeltaCCD::TFE3, TFE3), we rescued these proteins in UOK109 KO cells (knocking out NONO::TFE3).
We then assess the genome-wide chromatin binding of TFE3 FOs using data obtained from CUT&RUN-seq of these seven cell lines (KO and six rescues). We also assess the H3K27ac marks in the seven cell lines using data obtained from CUT&RUN-seq with H3K27ac antibody.

first: Choon Leng

last: So

first: Ye Jin

last: Lee

first: Bujamin

middle: H

last: Vokshi

first: Binglin

last: Huang

first: Yangzhenyu

last: Gao

first: Marie Elena

last: Portuallo

first: Sumaiya

last: Begum

first: Kasturee

last: Jagirdar

first: W. Marston

last: Linehan

first: Vito

last: Rebecca

first: Hongkai

last: Ji

first: Eneda

last: Toska

first: Danfeng

last: Cai


title: m6A-seq analysis of T-ALL cells following FTO silencing

city: wuhan

first: dan

middle: hu

last: liu

state: hubei

address: Donghu Road, No. 115, Wuchang District, Wuhan, Hubei Province, P.R. China

institute: wuhan university

type: Methylation profiling by high throughput sequencing

summary: To identify transcripts directly regulated by FTO through m6A modification in T-ALL, we conducted m6A-seq after silencing FTO in KOPTK1 cells

overall_design: After silencing FTO in KOPTK1 cells, total RNA extraction was performed using Trizol. Genomic DNA was eliminated through in-solution DNase I treatment (Thermo Scientific). Subsequently, poly(A) mRNA was purified from the total RNA using the Dynabeads mRNA purification kit (Invitrogen) and randomly fragmented with RNA fragmentation reagents (Ambion). m6A antibody (Abcam) was used to immunoprecipitate m6A RNA.RNA libraries were then constructed using the NEB Next Ultra Directional RNA Library Prep Kit (NEB) and subjected to sequencing as 150 bp paired-end reads on the NovaSeq 6000 platform.

first: Hudan

last: Liu

first: Guoliang

last: Qing

first: Hao


title: DDX5 super-enhancer promote vasculogenic mimicry formation and metastasis in nasopharyngeal carcinoma by enhancing ADAM10 transcription

city: Nantong

first: Tian

last: Xia

address: Xisi Road 20, Nantong, Jiangsu Province

department: Institute of Otolaryngology-Head and Neck Surgery

institute: Affiliated Hospital of Nantong University

summary: Antiangiogenetic therapies (AATs) have limited effects owing to most patients with cancer inevitably developing resistance to them. In this study, data generated using a nasopharyngeal carcinoma orthotopic mouse model in combination with clinical data suggested compensatory vasculogenic mimicry (VM) formation during AATs and the association of VM with poor prognosis of nasopharyngeal carcinoma. Additionally, data-independent acquisition mass spectrometry-based proteomics demonstrated that ADAM10 upregulation contributes to VM. Mechanistically, epigenetic and high-resolution chromatin interaction landscape analyses revealed that while ADAM10 does not interact with either the proximal or distal enhancers, DDX5, a transcription factor of ADAM10, is regulated by long-range looping enhancer-promoter interactions. Further analysis identified transcription factors bound to critical constituents of the DDX5 super-enhancer. Ingenol Mebutate, which docked excellently with DDX5, reversed ADAM10-mediated changes in gene expression, thereby effectively suppressing compensatory VM formation and metastasis and improving prognosis. Collectively, these findings provide insights into the clinical application of AATs.

overall_design: CUT&Tag is applied to CNE2 cell line and NP69 cell line.

first: Xia

last: Tian

first: You

last: Yiwen

last: bo


title: RNA-seq analysis of T-ALL cells following FTO or ELK3 silencing

summary: FTO serves as one of the demethylases for RNA N (6)-methyladenosine (m6A). ELK3 is responsible for encoding a member within the ETS-domain transcription factor family and the ternary complex factor (TCF) subfamily. To elucidate the roles and mechanisms of FTO and ELK3 in human T-cell acute lymphoblastic leukemia (T-ALL), we conducted RNA-seq analyses in KOPTK1 or CUTLL1 T-ALL cells following the silencing of FTO or ELK3

overall_design: After silencing FTO or ELK3 in T-ALL cells, total RNA extraction was performed using Trizol. Genomic DNA was eliminated through in-solution DNase I treatment (Thermo Scientific). Subsequently, poly (A) mRNA was purified from the total RNA using the Dynabeads mRNA purification kit (Invitrogen). RNA libraries were then constructed using the NEB Next Ultra Directional RNA Library Prep Kit (NEB) and subjected to sequencing as 150 bp paired-end reads on the NovaSeq 6000 platform.

last: Huang


title: ChIP-seq analysis of ELK3 in T-ALL cells

summary: ELK3 is responsible for encoding a member within the ETS-domain transcription factor family and the ternary complex factor  (TCF) subfamily.To identify downstream target genes directly regulated by ELK3 and reveal its critical role in T-ALL, we performed immunoprecipitation analysis using ELK3 antibodies in KOPTK1 cells

overall_design: Fragmentation of the genome of KOPTK1 was achieved using ultrasonication, followed by immunoprecipitation with ELK3 antibodies  (Novus)


title: A scalable gut epithelial organoid model reveals the genome-wide colonization landscape of a human-adapted pathogen

city: Würzburg

first: Laura

last: Jenniches

address: Josef-Schneider-Straße 2/D15

institute: Helmholtz Institute for RNA-based Infection Research

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

first: Maria

middle: L

last: Di Martino

first: Anjeela

last: Bhetwal

first: Jens

last: Eriksson

first: Ana

last: Lopes

first: Angelika

last: Ntokaki

first: Martina

last: Pasqua

first: Magnus

last: Sundbom

first: Martin

last: Skogar

first: Wilhelm

last: Graf

first: Dominic-Luc

last: Webb

first: Per

last: Hellström

first: André

last: Mateus

first: Lars

last: Barquist

first: Mikael

last: Sellin


title: A visual–omics foundation model to bridge histopathology image with transcriptomics

status: Public on Apr 01 2025

city: Houston

first: Tu N

last: Tran

address: 6670 Bertner Ave,

department: Cardiovascular

institute: Houston Methodist Research Institute

summary: Artificial intelligence has significantly advanced computational biology. Recent developments in omics technologies, such as single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics (ST), provide detailed genomic data alongside tissue histology. However, current computational models often focus on either omics- or image-based analysis, lacking integration of both. To address this, we developed OmiCLIP, a visual-omics foundation model linking hematoxylin and eosin (H&E) images and transcriptomics using tissue patches from Visium data. For transcriptomics, we created 'sentences' by concatenating top-expressed gene symbols from tissue patches. We curated a dataset of 2.2 million paired tissue images and transcriptomic data across 32 organs to train OmiCLIP integrating histology and transcriptomics. Building on OmiCLIP, we created the Loki platform, which offers five key functions: tissue alignment, tissue annotation based on bulk RNA-seq or marker genes, cell type decomposition, image–transcriptomics retrieval, and ST gene expression prediction from H&E images. Compared with 22 state-of-the-art models on 5 simulations, 19 public, and 4 in-house experimental datasets, Loki demonstrated consistent accuracy and robustness in all tasks.

overall_design: The triple-negative breast cancer patient-derived xenograft sample was snap freeze using 10x Genomics protocol # CG000663. Frozen OCT tumors were sectioned using cryostat as per 10x Genomics protocol # CG000579 (Rev E) and mounted directly on the Xenium slide. Next, sections on Xenium slides were processed as per 10x Genomics protocol # CG000613 (Rev B). For the probes, we used a 10x pre-designed human breast panel that has 280 genes on the panel. Slides were profiled using Xenium Analyzer (10x Genomics).

first: Weiqing

last: Chen

first: Guangyu

last: Wang

first: Vrutant

middle: V

last: Shah

first: Kristopher W

last: Brannan


title: Targeting LTBP2 Derived from Cancer-Associated Fibroblasts Sensitizes Esophageal Squamous Cell Carcinoma to Chemotherapy

city: Guangzhou

first: Yinghui

last: Zhu

state: Guangzhou

address: 651 Dongfeng Road East, Yuexiu District

institute: Sun Yat-sen University Cancer Center

summary: Cancer-associated fibroblasts (CAFs) are pivotal constituents of the tumor microenvironment that significantly influence cancer aggressiveness through the secretion of various factors. A more detailed characterization of the specific secretions exclusive to CAFs that drive tumor progression could identify potential targets to perturb this intracellular crosstalk. Here, we identified latent transforming growth factor β binding protein 2 (LTBP2) as a unique protein secreted exclusively by esophageal squamous cell carcinoma (ESCC) CAFs that promotes metastasis and chemoresistance. LTBP2 exerted its oncogenic effects by interacting with integrin α6β4, which serves as a functional receptor, and thereby activating Src signaling in ESCC cells. Notably, targeting LTBP2 with specific antagonistic antibodies markedly increased the susceptibility of ESCC cells to chemotherapeutic agents. These findings highlight the pivotal role of LTBP2 as a crucial mediator of CAF-induced cancer cell aggression and introduce it as a promising target to enhance chemotherapeutic efficacy in ESCC.

overall_design: Cancer-associated fibroblasts (CAFs) and normal fibroblasts (NFs) were isolated from surgically resected ESCC and adjacent normal tissues of 3 ESCC patients. Gene expression profiles were generated using RNA-seq on the Illumina NovaSeq 6000 platform

first: Jiarong

last: Zhan

first: Xin-Yuan

last: Guan

first: Ying-Hui


title: Transcription factor cooperativity at a GATA3 tandem DNA sequence determines oncogenic enhancer-mediated activation.

city: London

first: Stephen

last: Henderson

address: Paul O'Gorman Building

department: Cancer Institute

institute: University College London

summary: The TAL1 oncogene driving T-cell lymphoblastic leukemia (T-ALL) is frequently activated through a mutated cis-regulatory element, whereby small indels create a binding site for the transcription factor MYB. Unravelling how noncoding mutations create oncogenic enhancers is key to understanding cancer biology and can provide important insights into fundamental mechanisms of gene regulation. Utilising a CRISPR-Cas9 screening approach, we identified GATA3 as the key transcriptional regulator of enhancer-mediated TAL1 overexpression. CRISPR-Cas9 engineering of the mutant enhancer revealed a tandem GATA3 site that is required for binding of GATA3, acquisition of an open chromatin state and recruitment of MYB. Reciprocally, MYB binding to its motif is required for GATA3 recruitment, consistent with a transcription factor cooperativity model. Importantly, we show that GATA3 stabilises a TAL1-MYB interaction and that complex formation requires GATA3 binding to DNA. Our work sheds light on the mechanisms of enhancer-mediated oncogene activation, where key TFs cooperate to achieve maximal transcriptional output and thereby support leukemogenesis.

overall_design: ATAC-Seq on JURKAT cell line expressing endogenous GFP-tagged TAL1 with different modification of TAL1 enhancer by CRISPR (wildtype (WT), mutation of the TAL1 enhancer-repaired (MuTER), GATA3 binding sites 2 and 3 disrupted (2m3m)), and KOPT-K1 cell line as a control with low TAL1 expression.

first: Joana

last: Costa

first: Yang

last: Li

first: Nurkaiyisah

middle: Z

last: Anuar

first: David

last: O’Connor

first: Sunniyat

last: Rahman

first: Tanya

last: Rapoz-D’Silva

first: Kent

middle: T

last: Fung

first: Rachael

last: Pockock

first: Zhaodong

first: Lingyi

first: Mateja

last: Krulik

first: Sara

last: Hyseni

first: Nivedita

last: Singh

first: George

last: Morrow

first: Yanping

last: Guo

first: Daisy

middle: O

last: Gresham

first: Javier

last: Herrero

first: Richard

middle: G

last: Jenner

first: A. Thomas

last: Look

first: Dennis

last: Kappei

first: Marc

last: Mansour


title: Single cell profiling of lichen planus identifies type I interferon response and potential therapeutic targeting

first: Chloé

last: Grolleau

summary: Cutaneous lichen planus (LP) is an inflammatory skin disease characterized by an interface dermatitis with lymphocyte infiltration and keratinocyte cell-death. Previous studies suggest that LP inflammation is dominated by a type I immune response involving IFN-g but its pathogenesis remains not fully elucidated yet. To investigate the inflammatory mechanisms underlying LP, we performed single-cell RNA sequencing on LP compared with healthy control skins. We demonstrate that LP skin is imprinted by a type I interferon (IFN-I)-rich environment. While all immune cells are imbued with this interferon signature, we highlight unique subsets of inflammatory keratinocytes and fibroblasts highly influenced by IFN-I.

overall_design:
Single-cell RNA-sequencing on cutaneous lichen planus and healthy control skins
Please note that GSM8513934 sample from GSE277089 was re-analyzed and the re-analyzed data is linked as Series supplementary file.

***************************************************************
The table below lists GEO/SRA accessions reused/reanalyzed for this study.
***************************************************************

first: Thomas

last: Poisot

first: Camille

last: Roux

first: Laura

last: Perray

first: Kevin

last: Serror

first: Antonio

last: Alberdi

first: Alexandre

last: How-Kit

first: David

last: Bergerat

first: Karim

last: Dorgham

first: Rachel

last: Onifarasoaniaina

first: François

last: Chasset

first: Estelle

last: Charvet

first: Thibault

last: Mahevas

first: Alizée

last: Bozonnat

first: Gilles

last: Battesti

first: Maëlle

last: Dumont

first: Marie

last: Jachiet

first: Adèle

last: De Masson

first: Stanislas

last: Lipin

first: Damien

last: Ulveling

first: Maxime

last: Battistella

first: Hélène

last: Le Buanec

first: Jean-David

last: Bouaziz


first: Tian

last: Xia

overall_design: HiC is applied to CNE2 cell line.

first: Xia

last: Tian

first: You

last: Yiwen

last: bo


title: Neurodevelopmental hijacking of oligodendrocyte lineage programs drives glioblastoma infiltration [Spatial transcriptomics]

city: Toronto

first: Federico

last: Gaiti

state: Ontario

address: 101 college street

institute: Princess Margaret Cancer Centre

summary: Glioblastoma cells infiltrate and incorporate into the normal brain parenchyma. We conduct unbiased multimodal single-cell and spatial sequencing to capture GBM cells and the surrounding tumor microenvironment using a regional sampling strategy. For each patient, we profile the peritumoral region, tumor edge, and tumor core, providing a comprehensive characterization of the transcriptional and epigenetic landscape of GBM spatial heterogeneity, with a specific focus on infiltrative cells.

overall_design:
Regionally sampled GBM patient tissue were processed with 10x Genomics VisiumHD platform

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

first: Yiyan

last: Wu


title: Role of VAV2 in EGFR-mediated Rac1 responses in human prostate cancer

city: Manchester

first: Martin

middle: James

last: Baker

state: England

address: 555 Wilmslow Rd

department: Division of Cancer Sciences

institute: University of Manchester

summary: The small G-protein Rac1, a member of the Rho family of GTPases, is a central player in cancer progression and metastatic dissemination. Rac1 has been established as a bona fide effector of receptor tyrosine kinases, acting as a signaling node for growth factor-mediated responses such as motility, invasiveness, mitogenesis and gene expression. Previous studies demonstrated that Rac1 is aberrantly hyperactivated in aggressive cellular models of prostate cancer. Here we show that CRISPR-mediated knockout of Rac1 in prostate cancer cells leads to impaired proliferation and migration. Rac1-null cells display major alterations in gene expression, most notably affecting transcriptional programs associated with cell adhesion and extracellular matrix (ECM) regulation, but not those related to epithelial-to-mesenchymal (EMT) transition. Expression analysis of GEFs, the guanine nucleotide exchange factors responsible for Rac1 activation, followed by an unbiased RNAi screening, identified VAV2 as the foremost mediator of epidermal growth factor (EGF)-induced GTP loading onto Rac1 in prostate cancer cells. VAV2-deficient prostate cancer cells display significant proliferative and migratory defects, without noticeable changes in the expression of Rac1-regulated genes such as CDH1 and CDH3, indicating that VAV2 controls a discrete subset of Rac1-dependent responses. Finally, immunohistochemical assessment of VAV2 expression in human prostate specimens revealed significant VAV2 up-regulation in tumoral vs. non-tumoral areas. Our studies revealed important contributions of VAV2 to Rac1 activation in prostate cancer cells and highlight its potential prognostic value as a marker of prostate cancer progression.

overall_design: DU145 prostate cancer cell cloness with knockout of RAC1 compared to RAC1 positive clones (parental and non-target control sgRNA)

first: Suli

last: Zhang

first: Daniel

last: Y Zhang

first: Joshua

last: Searle

first: Priti

last: Lal

first: Cornelis

last: Vlaar

first: Suranganie

last: Dharmawardhane

first: Martín

middle: C

last: Abba

first: Marcelo

last: Kazanietz

first: Mariana

last: Cooke


title: The effect of PROTAC-mediated depletion of TAF1 on gene expression

city: Tampa

first: Jiandong

last: Chen

state: FL

address: 12902 Magnolia Drive

department: Molecular Oncology Department

institute: Moffitt Cancer Center

summary: The goal of this experiment was to determine the change in gene expression after transient depletion of the TAF1 transcription factor (aka TFII-250) using a PROTAC molecule (ZS3-046) containing GNE371 as TAF1 ligand and pomalidomide as CRBN ligand.

overall_design: Molm13 cells were treated with 100 nM ZS3-046 for 8 hr in triplicate. Total RNA samples were prepared using RNeasy min kit (Qiagen). RNA-seq analysis including rRNA depletion, library preparation, multiplexing and cluster generation, sequencing on Illumina HiSeq2500, and differential gene expression initial analysis, were performed by Azenta Life Sciences.

first: Lihong

first: Zachary

last: Shultz

first: Marianna

last: Sansone

first: Ernst

last: Schönbrunn

first: Justin

last: Lopchuk


title: Retrospective and multifactorial single-cell profiling reveals sequential chromatin reorganization during X inactivation

city: Utrecht

first: Jop

last: Kind

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

summary: The regulation of gene expression is governed at multiple levels of chromatin organization. However, how gene regulation is coordinated remains relatively unexplored. Here we develop Dam&ChIC, a method that enables retrospective and multifactorial chromatin profiling in single cells. Dam&ChIC employs in vivo chromatin labeling with m6A to acquire a past chromatin state, coupled with an antibody-mediated readout to capture the present chromatin state. Analyses of diverse chromatin combinations highlight its versatility and superior resolution. By tracking LAD inheritance over the cell cycle, we showcase that Dam&ChIC provides retrospective single-cell chromatin data. Importantly, by applying Dam&ChIC in random X chromosome inactivation, we disentangle the temporal order of chromatin remodeling events. Our data reveals that upon mitotic exit, the inactive X chromosome undergoes extensive genome-lamina detachment, preceding H3K27me3 spreading.  We anticipate that Dam&ChIC will be instrumental in unraveling the interconnectivity and order of gene-regulatory events underlying cell-state changes during development.

overall_design: Single cell Dam&ChIC was performed for combination of a Dam fusion protein for DamID (Dam-LMNB1) and antibody for ChIC (H2AK119Ub) in haploid Kbm7 cells as well hybrid mESCs undergoing Vitamin C induced differentiation. Also, scDam&T-seq was performed on the same differentiation system with a Dam fusion protein for DamID (Dam-LMNB1).


title: Neurodevelopmental hijacking of oligodendrocyte lineage programs drives glioblastoma infiltration [methylation]

first: Federico

last: Gaiti

overall_design:
Regionally sampled GBM patient tissue were dissociated and nuclei were processed for single cell DNA methylation processing

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

first: Yiyan

last: Wu


title: Reduced  EIF6 dosage attenuates TP53 activation in models  of Shwachman-Diamond syndrome

city: Cleveland

first: Usua

last: Oyarbide

state: Ohio

address: Cleveland Clinic, Lerner Research Institute NE6-205

institute: Cleveland Clinic

summary: Shwachman-Diamond syndrome (SDS) is characterized by neutropenia, exocrine pancreatic insufficiency, and bony abnormalities with an increased risk of myeloid neoplasia.  Almost all cases of SDS result from biallelic mutations in SBDS. SBDS interacts with EFL1 to displace EIF6 from the 60S ribosomal subunit. Released EIF6 permits the assembly of ribosomal large and small subunits in the cytoplasm. Decreased EIF6 levels due to haploinsufficiency or missense mutations which lead to decreased protein expression may provide a somatic genetic rescue and anti-leukemic effects.  We observed accumulation of EIF6 protein in sbds knockout (KO) zebrafish models, confirmed in patient-derived tissues, and correlated with changes in ribosome proteins and TP53 pathways. The mechanism of action for this adaptive response is unknown. To address this, we generated an eif6 zebrafish KO line which do not survive past 10 days post fertilization. We also created two mutants with low Eif6 expression, 5-25% of the wildtype levels, that can survive until adulthood. We bred them with sbds-null strains and analyzed their phenotype and biochemical properties. Low Eif6 levels reduced Tp53 pathway activation but did not rescue neutropenia in Sbds-deficient zebrafish. Further studies elucidating the interplay between SBDS, EIF6, TP53, and cellular stress responses offer promising insights into SDS pathogenesis, somatic genetic rescue, and therapeutic strategies.

overall_design: RNA was extracted from pools of 8–9 individually genotyped larvae at 10 dpf using TRIzol. Three pools of eif6-/- or wildtype from the same clutch were compared. RNA quality was determined by Bioanalyzer (Agilent), and eif6 mRNA expression was measured by RT-qPCR. RNA-Seq library preparation and sequencing and mapping of 3 pools of eif6-/- and 3 pools of eif6+/+ were performed by the Beijing Genome Institute (4). Based on the FPKM values (39), we used EBSeq R package for differentially expressed gene detection between eif6-/- and eif6+/+ (fold change > 2, and P < 0.05).

first: Seth J

last: Corey


title: Single-cell multi-omics reveals the TNF-α activation threshold for Classical Monocytes by studying healthy donors and rheumatoid arthritis patients

city: Novosibirsk

first: Roman

middle: Yurievich

last: Perik-Zavodskii

state: Novosibirsk region

address: Yadrincevskaya 14

country: Russia

institute: "Research Institute of Fundamental and Clinical Immunology" (RIFCI)

summary: Tumor Necrosis Factor Alpha is a known pro-inflammatory cytokine that plays a key role in the pathogenesis of rheumatoid arthritis. Anti-cytokine therapies targeting Tumor Necrosis Factor Alpha have greatly succeeded in treating rheumatoid arthritis in many patients. Despite these developments, many of the mechanisms of Tumor Necrosis Factor Alpha action have yet to be uncovered.  In this study, we incubated PBMCs from healthy donors and rheumatoid arthritis patients with Tumor Necrosis Factor Alpha and then performed their single-cell multi-omics analysis via BD Rhapsody. We have observed that Classical Monocytes have responded to the Tumor Necrosis Factor Alpha stimulation the most and that there was an activational threshold for such response that was dependent on the TNFR2 protein expression level. The profiling of TNFR2 protein expression level on immune cell populations can be a good predictive factor for the assessment of their activation by Tumor Necrosis Factor Alpha.

overall_design: PBMCs were incubated with TNF-a at the concentration of 5 ng/µl for 6h and then loaded onto BD Rhapsody single-cell analysis system

first: Saleh

last: Alrhmoun

first: Olga

last: Perik-Zavodskaia


title: SAM-synthase specific effects on metabolism and mitochondria underlie resistance to heat stress in C. elegans

city: Worcester

first: Amy

last: Walker

state: MA

address: 373 Plantation Street

institute: UMass Medical School

summary: S-adenosylmethionine (SAM), produced by SAM synthases, is critical for various cellular regulatory pathways and the synthesis of diverse metabolites. Studies have often equated the effects of knocking down one synthase with broader SAM-dependent outcomes such as histone methylation or phosphatidylcholine (PC) production. However, many organisms express multiple synthase genes including humans and Caenorhabditis elegans. Evidence in C. elegans, which possesses an expanded family of SAM synthases, suggest that the enzymatic source of SAM impacts its function. For instance, loss of sams-1 leads to enhanced heat shock survival and increased lifespan, whereas reducing sams-4 adversely affects heat stress survival. Here, we reveal that loss of sams-1 exerts age-dependent effects on nuclear-encoded mitochondrial gene expression, mitochondrial metabolites, and mitophagy. Notably, we find that that SAMS-1 exerts synthase-specific effects on PC production. We propose a mechanistic framework wherein the reduced SAM from SAMS-1 acts through PC to impact mitochondrial fission and mitophagy, thereby enhancing survival during heat stress. This study highlights multifaceted roles of SAM across metabolic pathways and synthase-specific SAM functions.

overall_design: Lysis of young adult C. elegans was performed in 0.5% SDS, 5% β-ME, 10 mM EDTA, 10 mM Tris-HCl ph7.4, 0.5 mg/ml Proteinase K, before purification of RNA by TRI-Reagent (Sigma). cDNA was produced with Transcriptor First-strand cDNA kits (Roche), and RT-PCR was performed using Kappa SYBR Green 2X Mastermix. RNA for sequencing was purified using RNAeasy columns (Qiagen). RNA sequencing (including library construction was performed by BGI (Hong Kong). Reads were analyzed through the NextFlow analysis platform (https://github.com/DanHUMassMed/RNA-Seq-Nextflow), using DeSeq2 to identify differentially expressed genes. Gene set enrichment was performed using WormCat (http://www.wormcat.com).

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title: Hypoxia-inducible factor 2α promotes protective Th2 cell responses during intestinal helminth infection.

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

institute: Benaroya Research Institute

overall_design: Refer to individual Series