summary: To probe drug mechanism of action (MOA) and interrogate the genetic architecture of human cells, we carried out isogenic genome-wide CRISPR/Cas9 knockout screens against 310 diverse drugs, bioactive compounds, and stress conditions. Stringent statistical correction for gene knockout fitness defects yielded a large-scale matrix of >12,000 high confidence chemical-genetic interactions (CGIs). This dataset revealed many previously unappreciated off-target effects for well-characterized compounds and novel MOAs for uncharacterized compounds. The CGI matrix uncovered dense genetic modules that yielded new biological insights into phospholipidosis, mitotic regulation, metabolism, the DNA damage response, and mTOR signaling. The dataset allowed identification of multi-drug sensitization and resistance mechanisms, inference of gene function, elaboration of cross-process connectivity, evaluation of the cell type-specificity of CGIs, prediction of chemical synergism, and extensive annotation of understudied genes. This resource provides a map of the genetic landscape in human cells and a framework to help guide drug discovery.

overall_design: sgRNA profiling of a genome-wide knock-out library in Nalm-6 cells after 8 days of compound treatment, along with untreated control samples profiled every two days from day 0 to day 8


title: Regenerative base editing enables deep lineage recording

status: Public on Mar 13 2026

city: Pasadena

first: Michael

last: Elowitz

state: CA

address: 1200 E California Blvd

country: USA

institute: Caltech

summary: Reconstructing the lineage histories of individual cells can reveal the dynamics of developmental and disease processes. In engineered recording systems, cells stochastically edit synthetic barcode sequences as they proliferate, creating distinct, heritable edit patterns that can be used to reconstruct the lineage trees relating individual cells in a manner analogous to phylogenetic reconstruction. However, recording depth is often limited by the kinetics of the editing process: the rate of editing declines exponentially over time for an array of independently editable targets, leading to most edits occurring in early generations. Here, we introduce the hypercascade, a regenerative molecular recording system that takes advantage of the predictability of A-to-G base editing to progressively create new target sites over time. The hypercascade packs  4 editable target sites in every 20 bp of sequence, enabling high density information storage. More importantly, the hypercascade’s regenerative logic leads to an approximately constant rate of mutation accumulation over time. This in turn facilitates reconstruction of deep lineage relationships. We demonstrate this by reconstructing trees spanning 23 days of editing and approximately 17 generations after a single polyclonal engineering step. Finally, simulations show that the hypercascade has the potential to record chromatin state transition dynamics across multiple genomic loci in parallel. The hypercascade thus provides a flexible and broadly useful tool for molecular recording.

sample_organism:
Homo sapiens
Mus musculus
Mus spretus

platform_organism:
Homo sapiens
Mus musculus
Mus spretus

overall_design: Base editing analysis at synthetic and endogenous target sites by amplicon sequencing of engineered Patski and human induced plurpotent stem cells.

first: Duncan

middle: M

last: Chadly

first: Ron

last: Hadas

first: Leslie

last: Klock

first: Jiahe

last: Yue

first: Felix

last: Horns

first: Amjad

last: Askary

first: Alejandro

last: Granados

first: Remco

last: Bouckaert

first: Carlos

last: Lois

first: Long

last: Cai

middle: B


title: Cell-free RNA reveals host and microbial correlates of broadly neutralizing antibody development against HIV

city: Gothenburg

first: Joan

last: Camunas-Soler

address: Medicinaregatan 9C

country: Sweden

institute: University of Gothenburg

type: Expression profiling by high throughput sequencing

summary: An effective broadly reactive antibody response is crucial to prevent viral infections. A small number of people living with HIV (PLWH) develop broadly neutralizing antibodies (bNAbs) targeting multiple HIV strains. We performed combined cell-free DNA (cfDNA) and cell-free RNA (cfRNA) sequencing in 42 plasma samples from a longitudinal cohort of 14 PLWH, of whom 7 developed bNAbs and 7 matched controls. cfRNA profiling revealed early immune activation signatures and distinct microbial associations linked to bNAb development.

overall_design: Longitudinal human plasma cfRNA and cfDNA sequencing from CAPRISA participants (paired-end; cfRNA on NovaSeq 6000, cfDNA on NextSeq 500). Libraries prepared with SMARTer Stranded Total RNA Pico Input Mammalian (cfRNA) and Ovation SP Ultralow (cfDNA). Host transcriptome, virome, and microbiome profiled; raw reads deposited under dbGaP controlled access; processed matrices public in GEO.

first: Mark

last: Kowarsky

first: Mercedes

last: Dalman

first: Mira

middle: N

last: Moufarrej

first: Jennifer

last: Okamoto

first: Yike

last: Xie

first: Norma

middle: F

last: Neff

first: Salim

middle: S

last: Abdool Karim

first: Nigel

middle: J

last: Garrett

first: Penny

middle: L

last: Moore

first: Stephen

middle: R

last: Quake


title: GFI1 regulates NK cell maturation and function [scMultiome-seq].

city: Brisbane

first: M. Zeeshan

last: Chaudhry

state: Queensland

address: 37 Kent Street

country: Australia

institute: The University of Queensland

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Natural killer cells defend against malignancies and viral infections through a tightly controlled program of differentiation and maturation. However, the transcriptional mechanisms guiding this process remains incompletely defined. Using paired single cell multiomic profiling, we show that the transcriptional repressor GFI1 epigenetically regulates key molecular programs, including EOMES and T-BET balance, to promote NK cell proliferation and transition from immature to terminally differentiated NK stages. GFI1 was shown to repress FOXO1 chromatin accessibility in mature NK cells, which normally represses NK cell proliferation and maturation. Co-deletion of both GFI1 and FOXO1 largely rescued NK cell differentiation identifying a critical GFI1-FOXO1 axis essential for protection against tumour metastasis. These findings position GFI1 as an important transcriptional node integrating NK cell differentiation, activation, and effector programming.

overall_design: NK cells isolated from spleen of naïve NcriCreT/+, NcriCreT/+Gfi1fl/fl, NcriCreT/+Foxo1fl/fl and NcriCreT/+Gfi1fl/flFoxo1fl/fl mice were sequenced using BD Rhapsody WTA+ATAC sequencing kit.

first: Zeeshan

first: Gabrielle

last: Belz


title: Gene expression profiling of vomeronasal organ in Cnpy1 knockout and wildtype mice.

city: Hyderabad

first: Adish

last: Dani

state: Telangana

address: 36/P, Gopanpally

country: India

institute: Tata Institute of Fundamental Research, Hyderabad

summary: Distinct families of V1R or V2R type GPCRs G-protein coupled receptors (GPCRs) are expressed in the mouse vomeronasal organ within spatially segregated vomeronasal sensory neurons (VSNs) that are also identified by the expression of cognate G-protein subunits, Gαi2 or Gαo. How vomeronasal GPCRs detect chemo-signals important for innate social and reproductive behaviors, requires understanding the molecular and cellular diversification accompanying VSN differentiation from a stem cell population. Here, we identify mouse Cnpy1 as a novel VNO specific ER chaperone, with expression restricted to Gαo VSNs. Absence of Cnpy1 leads to reduced neuronal activation, behavioral defects and a substantial loss of neurons by apoptosis during postnatal development. Co-immunoprecipitation followed by mass spectrometry, identified specific interactions of Cnpy1 with V2R GPCRs along with other ER chaperones.  Together with our earlier findings of hypertrophic and gyroid ER in Gαo neurons, these results highlight a critical role for ER chaperones and ER architecture, necessary for the proper function of Gαo sensory neurons.

overall_design: Poly-A mRNA sequencing was performed on vomeronasal organs from wildtype (Cnpy1+/+) and Cnpy1 knockout (Cnpy1-/-) littermate mice at 60 days postnatal age.

first: GVS

last: Devakinandan


title: DNMT3L crosstalk with piRNA biogenesis in postnatal spermatogonial progenitor cells

city: Taipei City

first: Shau-Ping

last: Lin

state: select a state

address: 4F, No. 81, Chang-Xing St.,

department: Institute of Biotechnology

country: Taiwan

institute: National Taiwan University

type: Non-coding RNA profiling by high throughput sequencing

summary: We analyzed small RNAs expression profiles of defferent developmental stage (0 dpp and 8 dpp) to investigate the potential role of DNMT3L in spermatogonial stem cell. We observed that relative proportion of microRNA and piRNA were similar betwee wild type and Dnmt3l knouckout mice. However, piRNA origin and composition significantly differed in 8 ddp Dnmt3l-deficiency samples, and genomic location of predicted precursors remarkably shitfted as well.

overall_design: This study provides small RNA-seq profiling derived from the same RNA samples previously used for long RNA-seq analysis in GSE54411. One pair of samples were enriched neonatal germ cells (P0) and 2 pair of samples were from THY1+ spermatogonia stem/progenitor cells (SSCa/SPCs) derived from testes of Dnmt3l knockout (KO) and wild type (WT) mice at postnatal Day0 and Day8, respectively.

first: Hung-Fu

last: Liao

first: Johnson Sheng-Jia

last: Zhou

first: Hsien-Hen

first: Kai-Wei

last: Chang

last: Chungunco

first: Pauline

last: Yen


title: Performance differences in spatial transcriptomics platforms identify Treg biology in human inflammatory bowel disease [Xenium]

city: Chicago

first: Parambir

last: Dulai

state: IL

address: 259 E Erie St Ste 1600

institute: Northwestern University

summary: Spatial transcriptomics is a rapidly growing field with the potential to enhance our ability to uncover novel biology, support drug development, and guide biomarker discovery. However, a biologically validated comparison of leading single-cell-level spatial transcriptomics platforms to guide scientists is lacking in the field. Using intestinal biopsies (n = 40) from patients with inflammatory bowel disease (IBD) of varying disease states and disease locations and non-diseased controls, we systematically compared two imaging based spatial transcriptomics platforms (CosMx and Xenium) to guide translational work for two NIDDK supported IBD consortiums and the Crohn’s and Colitis Foundation Plexus Biorepository.  In vitro experiments were conducted to validate key biologic findings. We present a comprehensive data resource of over 1.5 million spatially profiled intestinal cells from healthy and IBD samples. We observed CosMx to have overall better data quality than Xenium in both ulcerative colitis and Crohn’s disease across the full spectrum of commercially available panels. The performance of Xenium, but not CosMx, was significantly influenced by block quality and panel size, with a decline in data quality as the panel size increased. We demonstrate operational feasibility for CosMx in multi-center studies, and CosMx uniquely identified Treg-associated biology in both ulcerative colitis and Crohn’s disease which was validated by in vitro experiments. This study highlights the performance differences between CosMx and Xenium, demonstrating the strengths of CosMx for biology discovery in IBD research. Further studies are needed to explore the broader applicability of CosMx in other gastrointestinal conditions.

overall_design: 16 Xenium multi-tissue 337 panel (Ileum_CD_Inflamed: 2, Ileum_CD_NonInflamed: 2, Ileum_UC_NonInflamed: 2, Rectum_CD_Noninflamed: 2, Rectum_CD_inflamed: 2, Rectum_UC_inflamed: 4, Rectum_UC_Noninflamed: 2); 4 Xenium multi-tissue 377 panel with segmentation (Rectum_HC:1, Rectum_UC_nonInflamed: 1, Rectum_UC_inflamed: 2); 4 Xenium multi-tissue 377 panel without segmentation (Rectum_HC:1, Rectum_UC_nonInflamed: 1, Rectum_UC_inflamed: 2); 4 Xenium colon-specific panel (Rectum_HC:1, Rectum_UC_nonInflamed: 1, Rectum_UC_inflamed: 2); 4 Xenium 5K panel (Rectum_HC:1, Rectum_UC_nonInflamed: 1, Rectum_UC_inflamed: 2)

first: Yiming

last: Li

first: Wenjing

last: Yang

first: Hai

last: Wang

first: Alan

last: Robinson

first: Tianming

last: Yu

first: Jenny

middle: Y

last: Ding

first: Cenfu

last: Wei

last: Hanauer

first: Emanuelle

last: Bellaguarda

first: Laura

last: Yun

first: Ronen

last: Sumagin

first: Guang-Yu

first: James

middle: D

last: Lewis

first: Deyu

last: Fang

first: Yingzi

last: Cong

first: Yuan

last: Luo


title: Mismatch tolerance of a gRNA for CRISPR-based gene activation confers broad activity critical for cell reprogramming

city: Durham

first: Samuel

last: Reisman

state: NC

address: 1328 Campus Drive

institute: Duke University

summary: CRISPR activation and interference systems (CRISPRa/i) are widely used for programmable transcriptional control without introducing DNA edits. Although these technologies are capable of highly specific single-gene activity, some applications of transcriptional network reprogramming require broad, genome-wide effects. In this study, we identify a CRISPRa gRNA that is highly effective at reprogramming astrocyte transcriptional state. However, closer analysis revealed that this gRNA achieves this with widespread off-target activity capable of inducing expression changes in thousands of genes, in contrast to gRNAs targeting neighboring sites and regulating the same target gene. We use this promiscuous gRNA to further study the determinants of gRNA-driven off-target dCas9 binding in the context of transcriptional reprogramming. Employing a combination of ChIP-seq, high-throughput in vitro protein-binding microarrays, and high-throughput screening of gRNA-variant libraries in cells, we demonstrate that critical PAM-proximal bases within the gRNA seed sequence determine genomic binding, that mismatch tolerance varies by gRNA and base residue, and that mutating the PAM-proximal sequence of promiscuous gRNAs can modulate specificity. Finally, we find that CRISPRa-driven phenotypes can result from simultaneous contributions of active off-target effects and dose-dependent on-target activity. These findings highlight the potentially widespread impacts of CRISPRa off-target activity by gRNAs, underscore the need to account for cryptic effects when selecting and evaluating gRNAs for programming cell phenotypes, and demonstrate that multi-site binding in CRISPRa systems, typically viewed as a limitation, can also be exploited as a feature for network-level perturbations in cell reprogramming.

overall_design: ChIP-seq with anti-FLAG antibody to profile genomic binding of 3xFLAG-VP64-dSpCas9-VP64 in primary human astrocytes 8 days after transduction when complexed with gRNA-hit or a non-targeting gRNA

first: Wei

last: Zhu

first: Samantha

middle: E

last: Miller

first: Dahlia

last: Halabi

first: Nicholas

last: Sangvai

first: Gregory

last: Crawford

first: Raluca

last: Gordan

first: Charles

middle: A

last: Gersbach


title: Mismatch tolerance of a gRNA for CRISPR-based gene activation confers broad activity critical for cell reprogramming [FOXO4_gRNAs_RNAseq]

overall_design: RNA-seq profiling of primary human astrocytes from three donors 10 days after transduction with VP64-dSpCas9-VP64 and gRNA-hit, other FOXO4-targeting gRNAs, or a non-targeting gRNA


title: Performance differences in spatial transcriptomics platforms identify Treg biology in human inflammatory bowel disease [CosMx]

first: Parambir

last: Dulai

overall_design: 24 CosMx multi-tissue 1K panel (Ileum_CD_Inflamed: 5, Ileum_CD_NonInflamed: 5, Ileum_UC_NonInflamed: 2, Rectum_CD_Noninflamed: 2, Rectum_CD_inflamed: 2, Rectum_UC_inflamed: 6, Rectum_UC_Noninflamed: 2); 16 Xenium multi-tissue 337 panel (Ileum_CD_Inflamed: 2, Ileum_CD_NonInflamed: 2, Ileum_UC_NonInflamed: 2, Rectum_CD_Noninflamed: 2, Rectum_CD_inflamed: 2, Rectum_UC_inflamed: 4, Rectum_UC_Noninflamed: 2); 4 CosMx multi-tissue 6K panel (Rectum_HC:1, Rectum_UC_nonInflamed: 1, Rectum_UC_inflamed: 2); 4 Xenium multi-tissue 337 panel with segmentation (Rectum_HC:1, Rectum_UC_nonInflamed: 1, Rectum_UC_inflamed: 2); 4 Xenium multi-tissue 377 panel without segmentation (Rectum_HC:1, Rectum_UC_nonInflamed: 1, Rectum_UC_inflamed: 2); 4 Xenium colon-specific panel (Rectum_HC:1, Rectum_UC_nonInflamed: 1, Rectum_UC_inflamed: 2); 4 Xenium 5K panel (Rectum_HC:1, Rectum_UC_nonInflamed: 1, Rectum_UC_inflamed: 2); 38 CosMx multi-tissue 1k panel for different slide processing conditions (thickness_um: 4,5,6,7; fixation_time_hr: 6,24,48,72; delayed_cut_week:0,2,4,6; storage_vacuum: NA, FALSE, TRUE); 2 CosMx 2.0 multi-tissue 1k panel for comparison between different AtoMx platform version

first: Yiming

last: Li

first: Wenjing

last: Yang

first: Hai

last: Wang

first: Alan

last: Robinson

first: Tianming

last: Yu

first: Jenny

last: Ding

first: Cenfu

last: Wei

first: Stephen


title: Glutamine Deprivation Triggers TRIB3-Dependent G4-DNA Resolution to Maintain DNA Repair and Tumor Survival [Glutamin deprivation]

city: Zhengzhou

first: QIang

last: Ji

state: Henan

address: Jinshui Rd

department: Translational Research Institute

country: China

institute: Henan People's Hospital

summary: Glutamine, the most abundant circulating amino acid, is a central metabolite critical for the survival and growth of many tumor cells. Efforts to exploit this vulnerability have met with limited success, due to the inherent adaptability of tumor cells to withstand nutrient scarcity in the tumor microenvironment. This resilience has rendered glutamine-targeting therapies ineffective in clinical trials, demanding new mechanistic insights. Here, we identify the pseudokinase TRIB3 as a key mediator of the metabolic adaptation of hepatocellular carcinoma (HCC) cells to limiting glutamine availability. TRIB3 is upregulated under glutamine deprivation in a c-Jun-dependent manner, functioning in the nucleus to safeguard DNA repair fidelity, allowing the timely resolution of DNA damage and preventing replication catastrophe. TRIB3 binds to G-quadruplex DNA (G4-DNA) structures throughout the genome, recruiting the helicase DDX5 to resolve them as a cooperative functional complex. Depleting TRIB3 or DDX5 in HCC cells leads to exaggerated G4-DNA accumulation and heightened DNA damage associated with the downregulation of DNA damage response (DDR) pathways. We illustrate this effect on homologous recombination (HR) pathway genes, finding that TRIB3-DDX5 preventing G4-DNA accumulation at the BRCA1 and RAD51AP1 promoter regions that would otherwise suppress transcription. In vivo, TRIB3 silencing suppresses HCC xenograft growth, patently increasing DNA damage and apoptosis when mice were maintained on glutamine-deficient diets. Clinically, TRIB3 is overexpressed in HCC where its elevated levels correlate with poorer patient prognosis. Together findings nominate TRIB3-DDX5-G4 axis as a therapeutically exploitable metabolic dependency in HCC and possibly other malignancies with elevated TRIB3 expression.

overall_design: This study investigates the RNA expression profiles in Hep G2 cells (HB-8065, ATCC) cultured in high-glucose DMEM following either glutamine deprivation or knockdown of the TRIB3 gene. For the glutamine deprivation experiment, Hep G2 cells were seeded in 60 mm culture dishes. At 24 hours post-seeding, the culture medium was replaced with glutamine-free DMEM (supplemented with GlutaMAX™ as a glutamine substitute), and cells were cultured for an additional 12 or 24 hours. RNA was then extracted using TRIZOL® Reagent.

first: Qiang

first: Xuedan

last: Sun

first: Zhangran

first: Mengfan

first: Xinyu

last: Cheng

first: Shuai

last: Tian

first: Rick

last: Thorne

first: Jinming

first: Guangzhi

last: Liu

first: Mian

last: Wu

first: Xiaoying


title: p38 delta systemic genetic deletion mitigates anthracycline cardiotoxicity in female mice

first: Katy

last: Trampel

state: Illinois

address: 303 East Superior Street

summary: Doxorubicin (DOX) is an effective anthracycline chemotherapy, but its clinical use is limited by dose-dependent cardiotoxicity. We previously found that systemic genetic deletion of the p38δ kinase protects female mice from DOX-induced cardiotoxicity (DIC), suggesting that selective inhibition of this kinase may be a therapeutic strategy. To explore the mechanisms underlying this protection, we performed bulk RNA sequencing to profile transcriptomic changes associated with p38δ deletion during DIC.

overall_design: Female wildtype and p38δ germline knockout mice (C57BL/6J background) were administered a single intraperitoneal injection of doxorubicin (30 mg/kg). Hearts were collected 72 hours post-treatment, and bulk RNA sequencing was performed to assess transcriptomic changes caused by p38δ deletion.

first: Igor

last: Efimov

first: Tatiana

last: Efimova


title: Transcriptional consequences of herpes simplex virus 1 ICP4 inducible expression in uninfected cells

city: New York

first: Angus

middle: C

last: Wilson

state: NY

department: Department of Microbiology

institute: NYU Langone Health

summary: Successful viral infections reflect the balanced outcome of a tightly regulated program of viral gene expression and manipulation of the host cell to favor production of new infectious particles. The productive replication cycle of herpes simplex virus 1 (HSV-1) is dependent on the immediate-early essential transcription factor ICP4, which positively or negatively regulates transcription of immediate-early, early, and late HSV-1 genes at different steps in the temporal cascade, largely through sequence-specific binding to cis-acting regulatory elements. In contrast, direct regulation of host transcription programming by ICP4 is less well understood. In this study we exogenously expressed doxycycline-inducible wild-type and mutant ICP4 proteins in uninfected primary human fibroblasts and performed RNA-Seq to identify ICP4-driven changes to the host transcriptome. Cross-referencing our findings to a published dataset of ICP4-dependent changes to the host transcriptome in cells infected with HSV-1 provided validation for a subset of ICP4-regulated differentially-expressed genes. Furthermore, mutations in ICP4 that disrupt interactions with the host transcriptional machinery or interfere with site-specific DNA binding further modified this ICP4-driven remodeling of host transcription programming. Taken together, these data provide a comprehensive transcriptomic analysis of ICP4-driven dysregulation of host gene expression in uninfected cells.

overall_design: RNA-Seq of normal human dermal fibroblasts (NHDFs) mock-transduced or transduced with wild type, n6, n208, or mDBD isoforms of ICP4 from HSV-1 (KOS strain). Sequences for the indicated isoforms were codon-optimized to drive better expression. Cells were induced with doxycycline for 9 h to drive expression of the constructs.

first: Nora

last: Herzog

first: Sarah

last: Keegan

first: Daniel

last: Drafta

first: Rebecca

last: Plessel

first: Liam

last: Holt

first: Ian

last: Mohr


title: Age- and sex-specific modulation of human cardiac electrophysiology by doxorubicin.

city: Pittsburgh

first: Sharon Ann

last: George

state: PA

address: 200 Lothrop Street W1355

institute: University of Pittsburgh

summary: Background: Acute doxorubicin (DOX)-induced cardiotoxicity leads to electrophysiological changes, including QT prolongation, reduced QRS voltages, and T wave abnormalities. We previously demonstrated in mice that the effects of DOX on cardiac electrophysiology are sex-dependent. Objectives: Determine sex- and age-specific cardiotoxic effects of DOX on human cardiac electrophysiology and whether targeting p38 MAPKs could be cardioprotective in human hearts. Methods: Human cardiac slices were cultured for 24 hours with DOX (0-50 M). Slices were optically mapped to measure action potential duration (APD80) and transverse conduction velocity (CVT). Tissues were preserved for RNA sequencing. In separate slices, p38 MAPK inhibitors SB203580 or Compound 62, were applied alongside DOX. Results: DOX induced dose-dependent APD80 prolongation in young female and old hearts of both sexes. Phase 3 APD80 prolongation was associated with increased Cacna1c expression in young females. DOX also slowed CVT in young males and females, as well as in old males, despite increased Scn5a gene expression in young hearts of both sexes and increased Gja1 in young females. Furthermore, inhibiting p38 MAPKs with SB203580 did not prevent DOX-induced APD80 prolongation and CVT slowing, while pan-p38 MAPK inhibitor Compound 62 attenuated these effects in male and female hearts, suggesting a role for p38 and/or p38 MAPKs in mediating DOX cardiotoxicity in human hearts. Conclusions: Acute DOX-induced electrophysiological cardiotoxicity is sex- and age-dependent. This study introduces novel patient-specific diagnostic markers for detecting acute DOX-induced cardiotoxicity. Additionally, targeting p38γ and p38δ MAPKs in human hearts could offer a new cardioprotective therapy during DOX chemotherapy.

overall_design: RNA sequencing was performed on human cardiac slices that were cultured for 24 hours in the absence (Control) or presence of Doxorubicin. Slices from male and female, young (50 or less) and old (>50) are included for age and sex specific analyses.

first: Sharon


title: Discovery of a druggable site regulating DNA Binding of the AP1 transcription factor, deltaFOSb

first: Molly

last: Estill

address: 1 Gustave L. Levy Place

department: Neuroscience

institute: Mount Sinai School of Medicine

summary: ΔFOSB, a member of the AP1 family of transcription factors, mediates long-term neuroadaptations underlying drug addiction, seizure-related cognitive decline, dyskinesias, and several other chronic conditions. AP1 transcription factors are notoriously difficult to modulate pharmacologically due to the absence of well-defined binding pockets. Here, we identify a novel allosteric site on ΔFOSB, located outside the DNA-binding cleft, that accommodates small molecules and regulates DNA binding and release. We show that sulfonic acid-containing compounds bind to this site via an induced-fit mechanism, reorienting side chains critical for DNA binding, thereby likely hindering the ΔFOSB bZIP α-helix from binding in the major groove of DNA. In vivo, direct administration of lead compound JPC0661 into the brain reduces ΔFOSB occupancy at genomic AP1 consensus sites by approximately 60% as determined by CUT&RUN-sequencing. These findings demonstrate that DNA binding and release by AP1 transcription factors can be controlled via small molecules docking into a novel allosteric binding site.

overall_design: In vivo studies were performed in 2–3-month-old heterozygous transgenic male and female mice expressing human amyloid precursor protein (APP) carrying Swedish (K670N, M671L) and Indiana (V717F) mutations linked to familial Alzheimer’s disease. After three days of intra-hippocampal infusion of JPC0661 or vehicle, brains were removed for analysis of ΔFOSB binding. Nuclei were assessed with CUT&RUN for ΔFOSB binding.

first: Sean

last: McNeme

first: Yun

last: Young Yim

first: Ashwani

last: Kumar

first: Yi

last: Li

first: Brandon

last: Hughes

first: Corey

middle: P

last: St. Romain

first: Galina

last: Aglyamova

first: Jianping

last: Chen

first: Nghi

last: Nguyen

first: Shanghua

last: Fan

first: Gabriel

last: Stephens

first: Wen-Ning

last: Zhao

first: Samantha

last: Kruzshak

first: Corrine

last: Brener

first: Solange

last: Tofani

first: Anil

first: Earnest

first: Alfred

last: Robinson

first: Haiying

first: Reid

middle: T

last: Powell

first: Stephen

last: Haggarty

first: Clifford

last: Stephan

first: Eric

last: Nestler

first: Jeannie

last: Chin

first: Mischa

last: Machius

first: Jia

last: Zhou

first: Gabrielle

last: Rudenko


title: Glutamine Deprivation Triggers TRIB3-Dependent G4-DNA Resolution to Maintain DNA Repair and Tumor Survival [CUT&Tag]

first: QIang

last: Ji

overall_design: This study investigates the G4-DNA profiles or TRIB3/DDX5 interact with genome in Hep G2 cells (HB-8065, ATCC) cultured in high-glucose DMEM following either glutamine deprivation or knockdown of the TRIB3 gene. For the glutamine deprivation experiment, Hep G2 cells were seeded in 60 mm culture dishes. At 24 hours post-seeding, the culture medium was replaced with glutamine-free DMEM (supplemented with GlutaMAX™ as a glutamine substitute), and cells were cultured for an additional 12 hours. For the TRIB3 knockdown experiment, Hep G2 cells were infected with lentivirus carrying either Control shRNA, TRIB3 sh1 or TRIB3 sh2. After 48 hours of infection, cells were selected with puromycin for another 48 hours. The P2 generation of cells was collected. These cells are analyzed through CUT&Tag (profiling BG4, TRIB3 or DDX5 antibody).

first: Qiang

first: Xuedan

last: Sun

first: Zhangran

first: Mengfan

last: Li

first: Xinyu

last: Cheng

first: Shuai

last: Tian

first: Rick

last: Thorne

first: Jinming

first: Guangzhi

last: Liu

first: Mian

last: Wu

first: Xiaoying


title: Mismatch tolerance of a gRNA for CRISPR-based gene activation confers broad activity critical for cell reprogramming [perturb-seq]

first: Samuel

last: Reisman

overall_design: RNA-seq profiling of primary human astrocytes from three donors 10 days after transduction with VP64-dSpCas9-VP64 and gRNA-hit or with VP64-dSpCas9-VP64 and a non-targeting gRNA

first: Wei

last: Zhu

first: Samantha

last: Miller

first: Dahlia

last: Halabi

first: Nicholas

last: Sangvai

first: Gregory

last: Crawford

first: Raluca

last: Gordan

first: Charles

last: Gersbach


title: Mismatch tolerance of a gRNA for CRISPR-based gene activation confers broad activity critical for cell reprogramming [RNA-Seq]


title: Identification and validation of liquid biopsy-based methylation biomarkers: a  germ cell tumor subtype-specific study [2]

city: Utrecht

first: Leendert

last: Looijenga

address: Heidelberglaan 25

department: Research

country: Netherlands

institute: Princess Maxima Center

summary: Human germ cell tumors (GCTs) occur in infants, children, and adults, and present as germinomatous and/or non-germinomatous (embryonal carcinoma, teratoma, yolk sac tumor (YST), and choriocarcinoma) histologies at gonadal or extragonadal locations. Accurate subtyping is crucial for prognosis and treatment, but current clinical biomarkers lack sensitivity and specificity (serum proteins) or require a tissue biopsy (immunohistochemistry). Hence, less-invasive and improved subtype-specific biomarkers have potential for clinical utility. We conducted a meta-analysis of DNA methylation data (450K/EPIC array) from 15 (three original and 12 published) datasets including 713 GCTs, 109 healthy testis, and 221 healthy peripheral blood samples, revealing that GCT histology is the primary driver of methylation profiles, regardless of tumor location and patient’s age or sex. Per subtype, we identified differentially methylated regions as potential biomarkers. As proof of concept, we identified and validated two YST-specific biomarkers, i.e., APC and DPP7 promotor methylation, using methylation-sensitive restriction enzyme-based qPCR, of which DPP7 was also detectable in GCT serum-derived cell-free DNA. In conclusion, we present a novel method for in silico identification and in vitro and in vivo validation of YST subtype-specific liquid biopsy-based biomarkers. Our bioinformatic pipeline is also easily transferrable encouraging additional applications in pan(pediatric)-cancer studies beyond GCTs.

overall_design: Bisulfite converted DNA from 16 GCT tumor samples was hybridized to the Illumina EPIC BeadChip array

first: L


title: TET3-mediated DNA demethylation contributes to the formation of stable epialleles in tomato [RNA-seq]

city: Coventry

first: Javier

last: Antunez Sanchez

address: Gibbet Hill Campus

department: Life Sciences

country: United Kingdom

institute: University of Warwick

summary: DNA methylation is a critical epigenetic modification in plants that regulates gene expression, silences transposable elements (TEs), and supports proper development. Traditionally, heritable epimutations in plants have been generated using genetic mutants or chemical inhibitors, but these approaches often lack precision or stability. In this study, we investigated the effects of globally altering DNA methylation in tomato, a species with a large, TE-rich genome, through the ectopic expression of the catalytic domain of the human DNA demethylase TEN-ELEVEN TRANSLOCATION3 (hTET3cd). We found that TET3-mediated demethylation induced stable hypomethylation at CG and CHG sites and that these changes were inherited across multiple generations, including in non-transgenic siblings. Interestingly, demethylation in heterochromatic pericentromeric regions was often accompanied by gains in CHH methylation, suggesting the compensatory activation of the RNA-directed DNA methylation (RdDM) pathway. Differentially methylated region (DMR) analysis revealed that CG and CHG methylation loss was widespread, while CHH DMRs showed complex patterns of gain and loss, particularly near gene-rich regions and transposable elements enriched for 24-nt small RNAs. Transcriptomic analyses showed distinct gene expression profiles in both TET3 and non-transgenic progeny, with altered expression of TEs and associated genes. These findings demonstrate that enzymatic manipulation of the methylome via hTET3cd can generate stable, heritable epigenetic variation, and highlight the dynamic interplay between targeted DNA demethylation and endogenous mechanisms that act to restore epigenetic homeostasis.

overall_design: To determine the effect of TET3 mediated demethylation, we performed a transcriptome RNA-seq analysis using expanded leaves from wild-type, hTET3cd transgenic plants, and a Non-Transgenic Sibling (WT, TET3, NTS).

last: Antunez-Sanchez


title: CHI3L1 contributes to an immune suppressed tumour microenvironment in highly invasive brain metastases

city: Montreal

first: Peter

last: Siegel

state: Quebec

address: 1160 Pine Ave. West

department: Rosalind and Morris Goodman Cancer Research Centre

country: Canada

institute: McGill University

summary: Brain metastases (BrM) occur in up to 40% of cancer patients, causing nearly one-fifth of cancer deaths. While immune checkpoint inhibitors (ICIs) benefit some BrM patients, responses remain highly variable. This variability partly reflects distinct histopathological growth patterns that include minimally invasive (MI) and highly invasive (HI) brain BrM. Here we show that MI BrM exhibit robust immune infiltration, whereas HI lesions are immunosuppressed. However, histological differentiation between MI and HI can be challenging due to subjective margin assessment. Here, using highly multiplexed spatial proteomics on 119 tumour sections from 46 patients with BrM, we identify CHI3L1 as a key mediator of the immunosuppressive microenvironment in HI BrM. In preclinical models, genetic deletion of CHI3L1 converts immune-cold metastases into lymphocyte-rich, ICI-responsive lesions infiltrated by granzyme-B+ CD8+ T cells. In BrM patients treated with ICI, immunohistochemical quantification of CHI3L1 expression was a stronger predictor of ICI response than traditional MI/HI classification. Thus, CHI3L1 represents a promising biomarker and therapeutic target for BrM.

overall_design: Nanostring Digital Spatial profiling using the Cancer Transcriptome Atlas to characterize transcriptional differences between cancer cells of highly invasive and minimally invasive Brain metastases.

first: Sarah

last: Maritan

first: Elham

last: Karimi

first: Matthew

last: Dankner

first: Aldo

last: Hernandez-Corchado

first: Miranda

middle: W

last: Yu

middle: G

last: Annis

first: Yashar

last: Aghazadeh-Habashi

first: Morteza

last: Rezanejad

first: Bridget

first: Nebras

last: Koudieh

first: Emilie

last: Pichette

first: Benoit

last: Fiset

first: Yuhong

last: Wei

first: Ali

last: Nehme

first: Chun

last: Lee

first: Jack

last: Elias

first: Morag

last: Park

first: Yasser

last: Riazalhosseini

first: Hamed

last: Najafabadi

first: Kevin

last: Petrecca

first: Marie-Christine

last: Guiot

first: Daniela

last: Quail

first: Logan

last: Walsh

first: Parvaneh

last: Fallah


title: Identification and validation of liquid biopsy-based methylation biomarkers: a  germ cell tumor subtype-specific study [7]

first: Leendert

last: Looijenga

overall_design: Bisulfite converted DNA from 17 GCT tumor samples was hybridized to the Illumina EPIC BeadChip array

first: L


title: Signatures of Innovation and Selection in the Extremotolerant Yeast Kluyveromyces marxianus

city: Berkeley

first: Kaylee

middle: Elizabeth

last: Christensen

address: Koshland Hall rm 321

department: Plant and Microbial Biology

institute: UC Berkeley

summary: Organisms specialized to extreme environments can be the product of millions of years of evolutionary engineering and refinement. The underlying genetics can be quite distinct from those operating at earlier stages of trait innovation. In this work, we have developed the multistress-resistant yeast Kluyveromyces marxianus, which diverged from its closest relative >20 million years ago, as a model for interspecies comparative biology and genomics. In growth assays of the Kluyveromyces genus, we found that K. marxianus exhibited unique tolerance of high heat and a subset of chemical stress conditions. We then generated and analyzed omic profiles from across the genus to find molecular features associated with—and potentially causal for—K. marxianus traits. Expression profiling revealed divergent lipid processing and membrane transport programs in K. marxianus, borne out in changes in lipid utilization in experimental assays. Sequence analyses found robust evidence for expansions in gene families in the K. marxianus genome, most notably among transmembrane transporters and in metabolic enzymes. In molecular-evolution tests, we identified adaptive protein variants throughout the K. marxianus genome, among which plasma membrane transporters were over-represented. These data enable a model of the molecular mechanisms and evolutionary pressures underlying K. marxianus traits, including adaptive changes to transporters, lipid processing, and membrane functions mediating stress resistance.

sample_organism:
Kluyveromyces marxianus
Kluyveromyces lactis

overall_design: RNA-seq of K. marxianus and K. lactis cultures in control and stress (heat, MMS, ethanol, caffeine) conditions. Each condition has three biological replicates.

first: Aniliese

last: Deal

first: Jun-Ting Johnson

last: Wang

first: Abel

last: Duarte

first: Judith

last: Edwards

first: Zhenzhen

last: Ma

first: Jasmine

last: Goodman

first: Sasha

middle: I

last: Padilla

first: Edyta

last: Szewczyk

first: Catherine

last: Rha

first: Rachel

last: Brem


title: TET3-mediated DNA demethylation contributes to the formation of stable epialleles in tomato [low coverage WGBS]

first: Javier

last: Antunez Sanchez

type: Methylation profiling by high throughput sequencing

overall_design: To determine the efect of TET3 mediated demethylation, we performed a low coverage Whole Genome Bisulfite Sequencing (WGBS) on yong leavels of an array of plants from different transgenic lines. After selecting 2 plants for further analysis, we performed deep coverage WGBS using expanded leaves from wild-type, hTET3cd transgenic plants, and a Non-Transgenic Sibling (WT, TET3, NTS).

last: Antunez-Sanchez


title: Gene expression profiles of malignant peripheral nerve sheath tumors (MPNSTs).

city: Oslo

first: Anita

last: Sveen

address: P.O.Box 4953, Nydalen

department: Department of Molecular Oncology

country: Norway

institute: Institute for Cancer Research, Oslo University Hospital

summary: We have performed gene expression profiling of tumor samples from patients included in a clinical trial of immune checkpoint inhibition for advanced MPNSTs.

overall_design: This series consists of tissue samples of advanced MPNSTs (n=13) from patients treated with pembrolizumab. All samples were analyzed on Affymetrix Human Transcriptome 2.0 Arrays.

first: Ragnhild

last: Lothe


title: Drosophila 3rd instar larvae, full body at single-nucleus transcriptome resolution

city: Boston

first: Yanhui

last: Hu

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

summary: Drosophila 3rd instar larvae contain numerous developing and differentiated tissue-types and organs. We generated this single-nucleus transcriptome to help compare the results of a companion tissue secretome proteomic dataset.

overall_design: Whole Drosophila 3rd instar larvae were pooled, dissasociated into nuclei, and sequenced separately, then bioinformatically pooled to make an atlas.

first: Justin

last: Bosch

first: Norbert

last: Perrimon


title: Tpsb2-CreERT2 system did not alter mast cell viability or development

city: Beijing

first: Qingqing

last: Li

address: Shuangqing Road, No. 30

department: Institute for Immunology and School of Basic Medical Sciences

institute: Tsinghua University

summary: The selection of an appropriate Cre line is critical for ensuring the accuracy of cell type–specific investigations. We generated a Tpsb2-CreERT2 mouse line that enables precise and efficient labeling of target mast cells, with no detectable off-target recombination or cytotoxic effects, making it a reliable tool for lineage tracing and functional studies. To assess potential Cre-mediated toxicity, we performed transcriptomic analysis of peritoneal mast cells, which revealed no significant alterations in gene expression profiles, further supporting the importance of this model.

overall_design: Mast cell specific tdTomato knockin mice (Tpsb2-CreERT2;Ai14fl/+) were bred. Mast cells (sort purified as CD45+CD117+FceRIa+) of the peritoneal cavity from mast cell specific tdTomato knockin mice were prepared for sequencing. We analysed gene expression with 3 biological replication from different mice each replication.

first: Wenwen

last: Zeng


title: IL-33 priming promotes chromatin accessibility in peritoneal cells derived mast cells

summary: Dynamic changes in chromatin accessibility are fundamental to transcriptional regulation. Here we reported that the overall chromatin accessibility underwent significant changes following IL-33 priming.

overall_design: Peritoneal cells-derived mast cells (PCMC) were primed with 200 ng/ml IL-33 for 24 h, followed by ATAC sequencing analysis. We analysed chromatin accessibility from ATAC seq of 2 treatment with 2 biological replication.


title: Plant hormone and peptide signaling converge in the genetic network regulating cambium activation in Arabidopsis roots [ipt1,3,5,7_RNA-Seq]

city: Helsinki

first: Tiina

last: Blomster

address: Viikinkaari 1 (P.O. Box 65)

country: Finland

institute: University of Helsinki

summary: Plant secondary growth is driven by two concentric meristems, the inner vascular cambium and outer cork cambium. The periclinal cell divisions of both meristems, providing thickness and protection to plant organs, are activated with a delay after the primary development. Cytokinins and a set of downstream transcription factors are key players in promoting transition from primary to secondary development, however it is unknown whether other factors play a role in this transition. Here, using time-course transcriptome analysis of cytokinin-treated, cytokinin deficient isopentenyltransferase1,3,5,7 (ipt1,3,5,7) mutant we show that during cambium activation cytokinins positively regulate auxin and TRACHEARY ELEMENT DIFFERENTIATION INHIBITORY FACTOR (TDIF) peptide signaling in Arabidopsis (Arabidopsis thaliana) root. Correspondingly, mutants defective in TDIF peptide signaling displayed reduced cytokinin-induced secondary growth and auxin signaling was found to be required for proper cytokinin response. Additionally, auxin and cytokinin signaling transiently overlapped in activating procambial cells and acted additively in promoting secondary development. Network analysis revealed that transcription factors belonging to the DNA-BINDING WITH ONE FINGER (DOF) and ETHYLENE RESPONSE FACTOR (ERF) gene families are regulated by cytokinin during cambium activation and mutant analysis demonstrated delayed cambium activation and xylem formation phenotypes. Overall, we find that cytokinin, auxin and TDIF form a tightly intertwined network of positive regulators for activation of secondary growth in the Arabidopsis root indicating extensive redundancy in this process.

overall_design: To study cytokinin-dependent gene expression during secondary growth activation, isopentenyltransferase1,3,5,7 (ipt1,3,5,7) mutants were treated with cytokinin (1µM BAP) for 4h and compared to mock-treated (1h DMSO) ipt1,3,5,7 mutant.

first: Riccardo

last: Siligato

first: Riikka

last: Mäkilä

first: Wiktoria

last: Fatz

first: Munan

last: Lyu

first: Maria Angels

last: de Luis Balaguer

first: Lingling

last: Ye

first: Iris

last: Gildea

first: Omid

last: Safronov

first: Panu

last: Somervuo

first: Kamil

last: Růžička

first: Jarkko

last: Salojärvi

first: Rossangela

last: Sozzani

first: Melis

last: Kucukoglu Topcu

first: Ari Pekka

last: Mähönen


title: Glutamine Deprivation Triggers TRIB3-Dependent G4-DNA Resolution to Maintain DNA Repair and Tumor Survival  [TRIB3]

first: QIang

last: Ji

overall_design: This study investigates the RNA expression profiles in Hep G2 cells (HB-8065, ATCC) cultured in high-glucose DMEM following either glutamine deprivation or knockdown of the TRIB3 gene. For the TRIB3 knockdown experiment, Hep G2 cells were infected with lentivirus carrying either Control shRNA, TRIB3 sh1, or TRIB3 sh2. After 48 hours of infection, cells were selected with puromycin for another 48 hours. The P2 generation of cells was collected, and RNA was extracted using TRIZOL® Reagent.

first: Qiang

first: Xuedan

last: Sun

first: Zhangran

first: Mengfan

last: Li

first: Xinyu

last: Cheng

first: Shuai

last: Tian

first: Rick

last: Thorne

first: Jinming

first: Guangzhi

last: Liu

first: Mian

last: Wu

first: Xiaoying


title: Plant hormone and peptide signaling converge in the genetic network regulating cambium activation in Arabidopsis roots.

first: Tiina

last: Blomster

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

first: Riccardo

last: Siligato

first: Riikka

last: Mäkilä

first: Wiktoria

last: Fatz

first: Munan

last: Lyu

first: Maria Angels

last: de Luis Balaguer

first: Lingling

last: Ye

first: Iris

first: Omid

first: Panu

first: Kamil


title: ST2 signaling orchestrates mast cell transcriptional activation during viral infection

first: Qingqing

summary: The role of meningeal mast cells ST2 signaling in meningeal antiviral immunity has been poorly studied. Here we investigated the important role of meningeal mast cells ST2 signaling in combating LCMV viral infection.

overall_design: Mast cell specific ST2 knockout mice (Tpsb2-CreERT2;Il1rl1fl/fl) were bred. The model for inducing meningitis was established by intravenously injecting each mouse with 2 x 10^5 PFU LCMV Armstrong. 0，4，5，6 days post LCMV infection, the dural meninges  were carefully collected and digested. Mast cells (sort purified as CD45+CD11b-CD8a-CD19-CD117+FceRIa+) of the dural meninges from mast cell specific ST2 knockout mice were prepared for sequencing. We analysed gene expression with 3 biological replication from different mice each replication.

first: Wenwen

last: Zeng


title: Linking trajectories of cerebrovascular remodeling and dysfunction to cross-species brain vessel transcriptome in Alzheimer’s disease

first: Iliya

last: Lefterov

address: 130 De Soto St

department: Environmental and Occupational Health

summary: Growing evidence implicates dysfunctional brain vasculature occurring early in Alzheimer’s disease (AD) progression. Few studies have attempted to bridge transcriptomic signatures with early neuroimaging observations of vascular abnormalities. We leveraged longitudinal in vivo imaging of the cerebrovascular tree in APP/PS1 mice to identify when vascular abnormalities emerge, followed by bulk RNA-seq of isolated brain vessels at this time point. At 9–11 months of age, AD mice exhibited microvascular remodeling and dysfunction, including increased tortuosity, decreased capillary blood flow and reduced vascular density. Enriched gene pathways highlighted increased neuroinflammation, dysfunctional angiogenesis, and deficits in actin-mediated muscle contractility. Mapping transcriptional changes to a mouse vascular atlas implicated endothelial cells and microglia in impaired angiogenesis, while mural cells showed actin-filament and ion channel deficits. Mapping to a human vascular atlas identified translational targets to alleviate actin-mediated contractility deficits. Our integrated framework advances cerebrovascular biomarker understanding and informs early-stage AD therapeutic targets.

overall_design: We leveraged longitudinal in vivo imaging of the cerebrovascular tree in APP/PS1 mice (9-11 months of age, 6 mice per sex and phenotype, total of 24 mice)  to identify when vascular abnormalities emerge, followed by bulk RNA-seq of isolated brain vessels at this time point. Brain vessels with isolated with CD31+ magnetic beads followed by mRNA isolation, library generation and bulk mRNAseq.


title: Alcohol consumption in metabolic associated liver disease (MASLD)

city: Madrid

first: Yulia

last: Nevzorova

state: Madrid

address: C/Doctor Severo Ochoa, 9, pl. 2, Lab IV

department: Department of Immunology, Ophthalmology & ENT

country: Spain

institute: Complutense University (UCM) School of Medicine

summary: Recently, alcohol consumption in metabolic associated steatotic liver disease (MASLD) patients is increasing its incidence. However the pathophysiological mechanisms triggering liver damage in this condition remain unclear. In the present study we aimed to elucidate liver phenotype and gut-liver crosstalk in the context of SLD induced by simultaneous and deleterious association of alcohol and metabolic risk factors.

overall_design: 10-week-C57bl6 mice were fed with a WD and 10% alcohol in the sweetened drinking water for a period of 23 weeks (N=5). Mice fed with chow diet and standard tap water were used as controls. (N=4).

first: Raquel

last: Benedé-Ubieto

last: A. Nevzorova


title: Depolymerizing F-actin accelerates the exit from pluripotency to enhance stem cell-derived islet differentiation [scRNA-Seq]

city: St. Louis

first: Jeffrey

middle: Robert

last: Millman

state: MO

address: 660 South Euclid

institute: Washington University in St. Louis

summary: In this study, we performed single-cell RNA sequencing and single-nuclei multiomic sequencing (RNA+ATAC) at various stages during the differentiation of human pluripotent stem cells to stem cell-derived islets after treatment with the actin depolymerizing compound latrunculin A (latA) during the first 24 hours of differentiation. We show that depolymerizing F-actin with latA during the first 24 hours of definitive endoderm formation (stage 1) facilitates rapid exit from pluripotency and alters Activin/Nodal, BMP, JNK-JUN, and WNT pathway signaling dynamics. These signaling changes influence downstream patterning of the gut tube, leading to improved pancreatic progenitor identity and decreased expression of markers associated with other endodermal lineages. Continued differentiation generates islets containing a higher percentage of β cells that exhibit improved maturation, insulin secretion, and ability to reverse hyperglycemia. Furthermore, this latA treatment reduces enterochromaffin cells in the final cell population and corrects differentiations from hPSC lines that otherwise fail to consistently produce pancreatic islets, highlighting the importance of cytoskeletal signaling at the onset of directed differentiation.

overall_design: Human pluripotent stem cells were differentiated to stem cell-derived islets (SC-islets). During the first 24 hours of differentiation in stage 1, latA was added to the indicated samples, and these were compared to untreated samples (control). When looking at the effects of latA treatment during stage 1, a range of concentrations were tested (either 0.1uM, 0.175uM, or 1.5uM). For later experiments (stages 3-6), only 0.175uM latA was used. Single-cell RNA sequencing was performed everyday of stage 1, at the start of stages 3, 4, and 5, as well as one week into stage 6.

first: Nathaniel

last: Hogrebe

first: Mason

last: Schmidt

first: Punn

last: Augsornworawat


title: Multi-omics analysis of brain metastasis elucidates obesity induced prostaglandin crosstalk in tumor microenvironment restrain CD8T cell expansion (RNA-seq)

first: Yu

last: Wang

address: No.1 Shuaifuyuan Wangfujing Dongcheng District

department: Department of Neurosurgery

institute: Peking Union Medical College Hospital

summary: Brain metastasis (BrM) is one of the most crucial complications in tumor patients. Obesity contributes to the metabolic remodeling of tumor cells, yet the how obesity impact tumor microenvironment still remains unclear. We utilized RNA-seq on 115 tumor or peritumor samples in 81 patients to investigate obesity's effect on BrM.

overall_design:
Transcriptomic profilling performed on 68 tumor tissue and 47 peritumor tissues resected from 81 patients. Patients were grouped into obese and normal weighted group by BMI.

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

first: Zhanao

last: Xu

first: Yuekun


title: Single Cell Transcriptional Characterization of the Developing Organ of Corti Identifies Etv4/5/1 as Regulators of Lateral Cell Identity

city: Bethesda

first: Robert

last: Morell

state: MD

address: 35A Convent Drive, Room 1F-103

institute: National Institute on Deafness and Other Communication Disorders

summary: The mammalian auditory sensory epithelium, the organ of Corti, is comprised of a complex and highly ordered cellular mosaic that includes multiple unique cell types.  The small number of each of these cell types and their close association with one another has limited efforts to transcriptionally characterize the development of these cells.  To provide a better understanding of the development events that regulate cell type specification, we dissociated developing cochlear ducts at time points between embryonic day 11 and 16 and collected duct epithelial cells for single cell RNA-sequencing.  From the resulting data we were able to build a developmental trajectory from undifferentiated precursor cells to each of the major cell types in the organ of Corti.  Bioinformatic analyses including SCENIC, TradeSeq and CellOracle were then used to identify transcription factors  and other genes that may regulate different phases of cell type development.  To validate the analysis, the role of one set of candidate transcription factors, Etv4/5/1 was examined by generating triple knock out mice.  As predicted from the bioinformatic analysis, results demonstrated key roles for Etvs in the development of inner and outer pillar cells. and accurately identified down-stream Etv targets.  This data set will provide significant insights regarding the specification of unique cochlear cell types which will have implications for understanding congenital deficits and potential applications in the development of regenerative strategies.

overall_design: For the analysis of wild-type cochlear sensory epithelium, cochlear epithelium from wild-type mice at embryonic days (E) 11 and 16 was used. For the analysis of Fgfr3 knockout (KO) mice, cochlear epithelium from Fgfr3 KO mice and their wild-type littermates at E 16 was used.

first: Susumu

last: Sakamoto

first: Matthew

last: Kelley


title: CUT-TAG for Kasumi-1 cell line

city: Suzhou

first: Fang

last: Fang

state: Jiangsu

address: 92 Zhongnan street

institute: Children’s Hospital of Soochow University

summary: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to explore CUT-TAG results in Kasumi-1 cell line.

overall_design: CUT-TAG for Kasumi-1 cell line

first: Jian

last: Pan

first: Shaoyan

last: Hu

first: Zhiheng

last: Li

first: Fenli

last: Zhang


title: Synergistic effect of IL-33 priming and ATP stimulation in peritoneal cells derived mast cells

first: Qingqing

summary: Synergy of signals often causes cells to exhibit stronger physiological responses, especially immune cells. Here we reported that priming of interleukin-33 (IL-33) played a crucial role in the subsequent response of mast cells to ATP. Judging from the levels of cytokines and chemokines, the synergy of IL-33 priming and ATP stimulation was as high as 65%. At the entire transcriptional level, high synergy was also observed. This provided evidence supporting the sequential release of IL-33 and ATP derived from stromal cells on mast cells in vivo. Likewise, the upregulation of numerous cytokines and chemokines provided enormous support for mast cells to regulate antiviral immunity.

overall_design: Mast cell specific ST2 knockout mice (Tpsb2-CreERT2;Il1rl1fl/fl) were bred. Peritoneal cells-derived mast cells (PCMC) were primed with 200 ng/ml IL-33 for 24 h, followed by 1 mM ATP stimulation for 4 h, before undergoing transcriptome sequencing analysis.  We analysed gene expression from RNA seq of 6 treatment with 3 biological replication.

first: Wenwen

last: Zeng


title: Human scFv based, ALPPL2-specific CAR expressing T cells induce potent antitumor activity in an IL15-dependent manner

city: Seattle

first: Andras

last: Heczey

state: WA

address: 4800 Sand Point Way NE

institute: Seattle Children's Hospital

summary: Chimeric antigen receptor (CAR) T cells have robust antitumor activity against hematologic malignancies and have the potential to benefit patients with solid tumors. Immune recognition of murine proteins expressed in adoptively transferred T cells and lack of homeostatic in the tumor microenvironment can limit expansion and persistence of CAR T cells. CARs generated only from human sequences reduce the risk of immune mediated rejection and Interleukin-15, which promotes T cell survival and fitness can improve the expansion and persistence of T cells. In this study, we report a CAR T construct (ABBz) assembled from only human sequences including an scFv specific to ALPPL2 selected through an unbiased, high-throughput screen of human antibody-based, phage-displayed scFv library based on binding specificity, stringency, and low dissociation constant. We demonstrate specificity to the antigen, effective cytolytic function, and cytokine production induction in ABBz T cells. We detail key transcriptomic, phenotypic and functional changes specific to IL15 coexpression in ABBz T cells. Lastly, we demonstrate that ABBz CAR T cells have robust anti-tumor activity which is further enhanced through IL15 co-expression resulting in increased cytolytic capacity and superior expansion secondary to reduced apoptosis of CAR T cells.

overall_design: RNA-Seq profiles paired and in triplicate of ABBz and 15.ABBz CAR at baseline and 2 rounds of co-culture with Capan-1 target cells

first: David

last: Cunningham

first: Junquan

last: Liu

last: de la Cerda

first: Nisha

last: Gatwai

first: Amy

last: Courtney

first: Linji

last: Guo

first: Purva

last: Rathi

first: Yao

last: Qizhi Cathy

first: Ningyan

first: Zhiqiang

last: An


title: Plant hormone and peptide signaling converge in the genetic network regulating cambium activation in Arabidopsis roots [axr3-1_RNA-Seq]

first: Tiina

last: Blomster

overall_design: Auxin signaling is inhibited by the expression of auxin resistant 3-1 (axr3-1). We used the estradiol-inducible pANT:XVE>>axr3-1-YFP line to profile the transcriptomic interaction of auxin and cytokinin signaling in vascular cambium. Samples from roots with already active cambium treated with estradiol (5µM EST), cytokinin (1µM BAP) or both (5µM EST+1µM BAP) were harvested with the DMSO-treated controls at 4h and 24h time points for RNA-Seq. Experiments for both time points were performed in triplicate.

first: Riccardo

last: Siligato

first: Riikka

last: Mäkilä

first: Wiktoria

last: Fatz

first: Munan

last: Lyu

first: Maria Angels

last: de Luis Balaguer

first: Lingling

last: Ye

first: Iris

last: Gildea

first: Omid

last: Safronov

first: Panu

last: Somervuo

first: Kamil

last: Růžička

first: Jarkko

last: Salojärvi

first: Rossangela

last: Sozzani

first: Melis

last: Kucukoglu Topcu

first: Ari Pekka

last: Mähönen


title: The long noncoding RNA C1QTNF1-AS1 interacts with RSRC2 to ensure mitotic fidelity

city: London

first: Eleni

last: Maniati

address: John Vane Science Centre, Charterhouse Square

department: Barts Cancer Institute

institute: Queen Mary University of London

summary: Chromosome congression, a process of chromosome alignment at the spindle equator, is a key step in cell division. While much work has addressed the role of protein networks in controlling cell division, we have very little understanding how long noncoding RNAs (lncRNAs) and RNA binding proteins (RBPs) contribute to the fidelity of cell division. To investigate the role of  lncRNA C1QTNF1-AS1 and its interacting protein partner RSRC2 in cell division, we depleted C1QTNF1-AS1 and RSRC2 with LNA gapmers and siRNAs, respectively, in HCT116 cells and analysed their impact on gene expression and splicing alterations.

overall_design: Three LNA gapmers were used to deplete C1QTNF1-AS1 alongside negative control LNA A (LNA A), with four independent experimental replicates performed per each LNA. RSRC2 depletion was examined using targeting or control siRNA in four independent experimental replicates in HCT116 cells. C1QTNF1-AS1 LNA 4 was renamed to LNA 2, and  C1QTNF1-AS1 LNA 5 was renamed to LNA 3.

first: Kaliya

last: Georgieva

first: Alice. O

last: Coomer

first: Giulia

last: Guiducci

first: Anisha

last: Thind

first: Jun

last: Wang

first: Lovorka

last: Stojic


title: Plant hormone and peptide signaling converge in the genetic network regulating cambium activation in Arabidopsis roots [Agilent microarray]

first: Tiina

last: Blomster

overall_design:
Three-dye gene expression study with three biological replicates. Time course study with four time points, mutant vs. wild type comparison, young vs. old root comparison.
Please note that each raw data file contains raw data for three samples as indicated in the corresponding sample description field.

first: Riccardo

last: Siligato

first: Riikka

last: Mäkilä

first: Wiktoria

last: Fatz

first: Munan

last: Lyu

first: Maria Angels

last: de Luis Balaguer


title: GFI1-FOXO1 axis regulate NK cell maturation and function [RNA-seq]

city: Brisbane

first: M. Zeeshan

last: Chaudhry

address: 37 Kent Street

institute: The University of Queensland

summary: Natural killer cells protect against malignant and virally-infected cells through a tightly regulated differentiation, maturation, and homeostatic program. The signals guiding differentiation of NK cells has not yet been fully elucidated. GFI1 is a transcriptional repressor broadly expressed in bone marrow progenitors and adaptive immune cells and acts to shape differentiation but has not been defined in NK cells. We show that GFI1 is differentially expressed across NK cell subsets but is not required for the development of immature (Imm) NK cell. Instead, GFI1 regulates the checkpoints that control the transition from Imm to mature NK stages (M1 and M2). Using multiomics approaches, we show that GFI1 regulates FOXO1 and EOMES signalling in mature NK cells and is critical for NK cell division and maturation. Furthermore, we show that the GFI1-FOXO1 axis is essential for protection against tumor metastasis through NK cell activation and effector functions, highlighting the important role of GFI1 in innate immune regulation.

overall_design: For NK cell RNA-seq, NK cell subsets including CD11a-KLRG1- Immature NK, CD11a+KLRG1- M1 NK and CD11a+KLRG1+ M2 NK cells were isoalted from spleen of Ncr-cre, Ncr-cre.Gfi1fl/fl, Ncr-cre.Foxo1fl/fl and Ncr-cre.Gfi1fl/fl.Foxo1fl/fl. Total RNA was isolated from the NK cells and RNA-seq was performed.

first: Zeeshan

first: Qiutong

last: Huang

first: Gabrielle

last: Belz


title: Identification and validation of liquid biopsy-based methylation biomarkers: a  germ cell tumor subtype-specific study [3]

first: Leendert

last: Looijenga

address: Heidelberglaan 25

summary: Human germ cell tumors (GCTs) occur in infants, children, and adults, and present as germinomatous and/or non-germinomatous (embryonal carcinoma, teratoma, yolk sac tumor (YST), and choriocarcinoma) histologies at gonadal or extragonadal locations. Accurate subtyping is crucial for prognosis and treatment, but current clinical biomarkers lack sensitivity and specificity (serum proteins) or require a tissue biopsy (immunohistochemistry). Hence, less-invasive and improved subtype-specific biomarkers have potential for clinical utility. We conducted a meta-analysis of DNA methylation data (450K/EPIC array) from 15 (three original and 12 published) datasets including 713 GCTs, 109 healthy testis, and 221 healthy peripheral blood samples, revealing that GCT histology is the primary driver of methylation profiles, regardless of tumor location and patient’s age or sex. Per subtype, we identified differentially methylated regions as potential biomarkers. As proof of concept, we identified and validated two YST-specific biomarkers, i.e., APC and DPP7 promotor methylation, using methylation-sensitive restriction enzyme-based qPCR, of which DPP7 was also detectable in GCT serum-derived cell-free DNA. In conclusion, we present a novel method for in silico identification and in vitro and in vivo validation of YST subtype-specific liquid biopsy-based biomarkers. Our bioinformatic pipeline is also easily transferrable encouraging additional applications in pan(pediatric)-cancer studies beyond GCTs.

overall_design: Bisulfite converted DNA from 54 GCT tumor samples was hybridized to the Illumina 450K BeadChip array

first: L


title: Response of meningeal mast cells against virus infection

first: Qingqing

last: Li

summary: The role of meningeal mast cells in meningeal antiviral immunity has been poorly studied. Here we investigated the important role of meningeal mast cells in combating LCMV viral infection.

overall_design: Mast cell specific reporter mice (Tpsb2-CreERT2;Ai14fl/-) were bred. The model for inducing meningitis was established by intravenously injecting each mouse with 4 x 10^5 PFU LCMV Armstrong. 6 days post LCMV infection, the dural meninges  were carefully collected and digested. Mast cells (sort purified as tdTomato+) of the dural meninges from mast cell specific reporter mice were prepared for sequencing. We analyzed gene expression with 3 or 4 biological replication from different mice each replication.

first: Wenwen

last: Zeng


title: Synergistic effect of IL-33 priming and Gq signaling activation in peritoneal cells derived mast cells

summary: Synergy of signals often causes cells to exhibit stronger physiological responses, especially immune cells. Here we reported that priming of interleukin-33 (IL-33) played a crucial role in the subsequent response of mast cells with Gq signaling. Judging from the levels of cytokines and chemokines, the synergy of IL-33 priming and Gq signaling activation was as high as 53%. At the entire transcriptional level, high synergy was also observed. This provided evidence supporting the sequential release of IL-33 and Gq signaling activator derived from stromal cells on mast cells in vivo. Likewise, the upregulation of numerous cytokines and chemokines provided enormous support for mast cells to regulate antiviral immunity.

overall_design: Mast cell specific DREADD-Gq knockin mice (Tpsb2-CreERT2;hM3Dqfl/-) were bred. Peritoneal cells-derived mast cells (PCMC) were primed with 200 ng/ml IL-33 for 24 h, followed by 10 nM clozapine stimulation for 4 h, before undergoing transcriptome sequencing analysis. We analyzed gene expression from RNA seq of 4 treatment with 3 biological replication.


title: Spatial transcriptomics identifies regional disruptions in brain rhythmic gene expression in a mouse model of Alzheimer’s disease

city: La Jolla

first: Paula

last: Desplats

state: CA

address: 9500 Gilman Dr. MTF346 MC0624

department: Department of Neuroscience and  Department of Pathology

institute: University California San Diego

summary: Alzheimer's disease (AD) is a progressive neurodegenerative disorder that impairs memory, cognitive function, and the ability to perform everyday activities. In addition to cognitive decline, behavioral disturbances in the sleep-wake cycle such as progressive fragmentation of sleep, decreased total sleep time, and increased confusion or restlessness in the evening (sundowning) are a hallmark of AD. Emerging evidence suggests that these disruptions in sleep and behavior may be underpinned by molecular dysregulation of the circadian clock. Here, we utilize Visium spatial transcriptomics to characterize diurnal transcriptional rhythms across various brain regions in APP23 transgenic mice, a model of AD, and their non-transgenic littermates in 7- and 14-month old mice. We reveal significant alterations in rhythmic gene expression in APP23-TG mice, particularly in the hippocampus and cortex. These changes were evident in 7-month-old animals, coinciding with early amyloid deposition and persisted with advancing pathology.  This study offers novel insights into the large-scale dysregulation of rhythmic gene expression in AD, highlighting molecular pathways connected to circadian disruption at various stages of the disease. It underscores the potential role of these disruptions in AD progression and opens new avenues for diagnosis, treatment, and management.

overall_design: Spatial transcriptomics on sagittal brain sections from APP23 transgenic and non-transgenic control mice, collected at four Zeitgeber time points (ZT0, ZT6, ZT12, ZT18) at either 7 or 14 months of age.

first: Alon

last: Gelber

first: Haylie

last: Romero

first: Dominic

last: Burrows

first: Daniel

last: Carlin

first: Eran

last: Mukamel


title: Response of meningeal stromal cells against virus infection

summary: The role of meningeal stromal cells in meningeal antiviral immunity has been poorly studied. Here we investigated the response of meningeal stromal cells in combating LCMV viral infection.

overall_design: The meningeal stromal cells were cultured and infected with LCMV Armstrong. Meningeal stromal cells was collected after 1 day infection for sequencing. We analyzed gene expression with 3 biological replication from different mice each replication.


title: Characterization of the dural meninges against viral infection

summary: The meninges serve as a protective barrier for the brain and are essential in combating pathogen attacks, such as viral infections, that could otherwise result in fatal outcomes. To delineate the immune response during viral infection, we performed sc-RNA sequencing after 6 days LCMV Armstrong infection when the immune response was highly active.

overall_design: The model for inducing meningitis was established by intravenously injecting each mouse with 4 x 10^5 PFU. The cells were isolated from the dural meninges 6 days post infection for scRNA seq.


title: Stromal-mast cell communication orchestrates anti-viral immunity in meninges

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

overall_design: Refer to individual Series


title: Depolymerizing F-actin accelerates the exit from pluripotency to enhance stem cell-derived islet differentiation [Multiomics]

first: Jeffrey

last: Millman

summary: In this study, we performed single-cell RNA sequencing and single-nuclei multiomic sequencing (RNA + ATAC) at various stages during the differentiation of human pluripotent stem cells to stem cell-derived islets after treatment with the actin depolymerizing compound latrunculin A (latA) during the first 24 hours of differentiation. We show that depolymerizing F-actin with latA during the first 24 hours of definitive endoderm formation (stage 1) facilitates rapid exit from pluripotency and alters Activin/Nodal, BMP, JNK-JUN, and WNT pathway signaling dynamics. These signaling changes influence downstream patterning of the gut tube, leading to improved pancreatic progenitor identity and decreased expression of markers associated with other endodermal lineages. Continued differentiation generates islets containing a higher percentage of β cells that exhibit improved maturation, insulin secretion, and ability to reverse hyperglycemia. Furthermore, this latA treatment reduces enterochromaffin cells in the final cell population and corrects differentiations from hPSC lines that otherwise fail to consistently produce pancreatic islets, highlighting the importance of cytoskeletal signaling at the onset of directed differentiation.

overall_design: Human pluripotent stem cells were differentiated to stem cell-derived islets (SC-islets). During the first 24 hours of differentiation in stage 1, 0.175uM latA was added to half the samples. Multiomic (RNA + ATAC) sequencing was performed at the definitive endoderm stage (stage 2, day 1) and on the final differentiated SC-islets (stage 6, day 15), comparing latA-treated cells with untreated cells (control).

first: Nathaniel

last: Hogrebe

first: Mason

last: Schmidt

first: Punn

last: Augsornworawat


title: Single-cell RNA-sequencing and paired TCR-sequencing of CD4⁺ and CD8⁺ T-cell differentiation in a mouse DNA vaccination model with or without CD4⁺ T-cell help

city: Leiden

first: Jannie

last: Borst

address: Albinusdreef 2

institute: Leiden University Medical Center

summary:
The data deposited in the GSE series support two independent studies that use a shared in vivo mouse vaccination model to trace activation and effector differentiation of endogenous polyclonal CD8⁺ and CD4⁺ T cells. Briefly, we employed a DNA vaccination model in C57BL/6 mice based on epidermal “tattoo” delivery of plasmid DNA encoding the HPV E7 (E7₄₈–₅₇) MHC-I epitope either alone or linked to three MHC-II helper epitopes (P30, PADRE, NEF). Vaccination on days 0, 3, and 6 induces antigen expression in keratinocytes and delivery to the draining lymph node (dLN) via migratory conventional dendritic cells and passive drainage. This model allows parallel tracking of antigen-specific CD8⁺ T cells (H-2Dᵇ/E7 tetramer) and CD4⁺ T cells (PADRE MHC-II tetramer), enabling controlled comparison of CD8⁺ T-cell responses in the presence or absence of CD4⁺ T-cell help, as well as mapping the differentiation trajectories of polyclonal CD4⁺ T cells.
We provide single-cell RNA sequencing and paired TCR sequencing of CD3+CD44+CD62L- activated T cells isolated from pooled draining lymph nodes (dLN) and non-draining lymph nodes (ndLN) at days 5 and 10 post-vaccination.

overall_design: Mice were vaccinated under two conditions: “Help”, consisting of the MHC-I epitope linked to three MHC-II helper epitopes, and “No Help”, consisting of the MHC-I epitope alone. Each sample contains pooled activated T cells from 8 experimental conditions: Day-5-Help-dLN, Day-5-Help-ndLN, Day-5-No-Help-dLN, Day 5-No-Help-ndLN, Day-10-Help-dLN, Day-10-Help-ndLN, Day-10-No-Help-dLN, Day-10-No-Help-ndLN. Cells from each experimental condition were labeled with a separate HTO. scRNAseq (Project_202102035) and scTCRseq (Project_202102035a) were performed on the same sample.

first: Julia

last: Busselaar

first: Douwe

middle: M

last: Bosma

first: Mo

last: Staal

first: Xin

last: Lei

first: Yanling

last: Xiao

first: Mylene

last: de Koning

first: Mirna

last: Reljic

first: Tom

last: de Wit

first: Fiamma

last: Salerno


title: Effect of Ethoxysanguinarine treatment on gene expression after Angiotensin-II infused C57BL/6 mice

city: Fuzhou

first: Jun

last: Peng

state: Fujian

address: 1 Qiuyang Road, Minhou Shangjie

department: Academy of Integrative Medicine

institute: Fujian University of Traditional Chinese Medicine

summary: The goals of this study is to identify the differential expressed genes in cardiac tissue of C57BL/6 mice with or without Angiotensin II (AngII) treatment, and compare the differential expressed genes in the cardiac tissue of Ang II infused C57BL/6 mice after Ethoxysanguinarine (ETH) treatment. Briefly, the mice (n=18) were randomly divided into 3 groups: control, AngII, AngII + ETH (n=6 for each group). Mice in Control and AngII groups were infused with saline and 500 ng/kg/min of AngII respectively, and orally administrated with saline; the mice in AngII + ETH group were infused with AngII (500 ng/kg/min) and orally administrated with 10 mg/kg /day of ETH daily for total 4 weeks. Then the cardiac tissue were used to identify differentially expressed genes among different groups.

overall_design: RNA sequencing was performed with cardiac tissue of  mice in 6 groups: control, AngII, AngII + ETH (n=6 for each group) to identify the differently expressed genes and related pathway.

first: Aling

last: Shen

first: Ying

last: Cheng

first: Yi

last: Xie

first: Bihan

last: Xuan


title: Wnt/hippo/TGF beta signaling pathways involved in the treatment for Papillon Lefevre syndrome with acitretin

city: Chengdu

first: Lei

last: Chu

state: SICHUAN

address: 37 Guoxue Road

department: Dermatology

institute: West China Hospital

summary:
As far as our best known, there is no record on molecular dynamic changes during the treatment for it. In our case, we report our obeservations both in clinic and also in a comprehensive molecular dynamic level,
We believe it will help us known more on this disease treatment and also will help improve the understanding on this disease.

overall_design: Comparisons between families invidually, and comparison between before treatment and after treatment will help us understand the details on molecular expressions behind Papillon Lefevre syndrome, which is of significance for investigation on Papillion Lefevre syndrome and therefore might be a practical approach for Hereditary disorders.

first: Yuping

last: Ran


title: Synergistic effect of IL-33 priming and ATP stimulation in bone marrow derived mast cells

first: Qingqing

last: Li

summary: Synergy of signals often causes cells to exhibit stronger physiological responses, especially immune cells. Here we reported that priming of interleukin-33 (IL-33) played a crucial role in the subsequent response of mast cells to ATP. Judging from the levels of cytokines and chemokines, the synergy of IL-33 priming and ATP stimulation was as high as 64%. At the entire transcriptional level, high synergy was also observed. This provided evidence supporting the sequential release of IL-33 and ATP derived from stromal cells on mast cells in vivo. Likewise, the upregulation of numerous cytokines and chemokines provided enormous support for mast cells to regulate antiviral immunity.

overall_design: Bone marrow-derived mast cells (BMMC) were primed with 200 ng/ml IL-33 for 24 h, followed by 1 mM ATP stimulation for 4 h, before undergoing transcriptome sequencing analysis.  We analyzed gene expression from RNA seq of 4 treatment with 3 biological replication.

first: Wenwen

last: Zeng


title: AtDEK2, a dual histone mark reader regulates plant immunity [ChIP-seq]

city: Gif Sur Yvette

first: Xiaoning

last: HE

address: 630,Rue Noetzlin

country: France

institute: universite-paris-saclay

summary: Arabidopsis DEK2, a nuclear protein involved in multiple chromatin-related processes, was found to be phosphorylated in response to flg22 treatment suggesting a role in plant immunity to bacterial pathogens. dek2 loss of function mutants were susceptible to bacterial as well as fungal pathogens. Transcriptome data of the dek2-1 mutant shows that AtDEK2 is a transcriptional repressor of defense related genes, hormone synthesis & signaling genes. ChIP-Seq analysis indicates that DEK2 binds to motifs of several families of transcription factors (TFs) and to class I TCP binding motif regions with the highest affinity. We determined that DEK2 is recruited to specific regions on the chromatin by transcription factors. Our data suggests that DEK2 is a reader of the dual histone mark, H3K4me3K27me3. Finally, based on our data we postulate a hypothetical working model for the function of DEK2 as a transcriptional repressor and targets regions with H3K4me3K27me3 marks.

overall_design: WT (col-0) and dek2-1 mutant plans were either mock treated or with the bacteria Pst DC3000 hrcC- strain. For each sample 3 biological replicates were used.

first: Hanna

last: Alhoraibi

first: Santiago

last: Alejandro-Martinez

first: David

last: Latrasse

first: Papita

last: Mandal

first: Léa

last: Faivre

first: Deborah

last: Manza

first: Aala

last: Abulfaraj

first: Siba

last: Alharbi

first: Kiruthiga

last: Mariappan

first: Olga

last: Artyukh

first: Fatimah

last: Abdulhakim

last: Aljedaani

first: Stefan

last: David

first: Marilia

last: Almeida-Trapp

first: Jean

last: Bigeard

first: Delphine

last: Pflieger

first: Wolfgang

last: Fischle

last: Arold

last: Colcombet

first: Daniel

last: Schubert

first: Moussa

last: Benhamed

first: Ikram

last: Blilou

first: Heribert

last: Hirt

first: Naganand

last: Rayapuram


title: Clusia genomes shed light on the evolution and diversity of CAM physiotypes (GEO series)

city: Vienna

first: Hannes

middle: M.

last: Kramml

address: Djerassiplatz 1

department: Functional and Evolutionary Ecology

country: Austria

institute: University of Vienna

summary: More than 200 years ago, Alexander von Humboldt documented his first observations of a peculiar phenomenon in Clusia rosea (Clusiaceae), the first tree known to perform crassulacean acid metabolism (CAM). Since then, the photosynthetic and ecophysiological plasticity of Clusia species have captivated the minds of plant scientists worldwide. CAM is a physiological adaptation to low water availability. While stomata are closed during the day, RuBisCO is supplied with CO2 via decarboxylation of organic acids that have been stored and synthesized during the night by phosphoenolpyruvate carboxylases (PEPC). How the physiological reprogramming necessary for CAM evolved remains enigmatic. Photosynthetic physiotypes of CAM, including weak CAM, inducible CAM, and CAM-cycling have additionally fueled a debate on the evolutionary constraints of CAM and the prospects of engineering CAM into C3 crops. Here, we de novo sequenced the genomes of three Clusia species to capture genetic snapshots along an evo-ecophysiological continuum from weak over inducible to strong CAM. Through a combination of chromosome level assembly and annotation, comparative multiomics, and physiological phenotyping, we identify a strong association between diploidization of polyploids and the physiotype diversity of CAM. We illustrate that Clusia major, a plant that seems to exhibits a C3-type mode of photosynthesis, retained almost all hallmarks of CAM. Transposon-mediated genic diploidization, however, acted upon homoeologs in CAM-related gene families, particularly those involved in phosphoenolpyruvate (PEP) recycling via phosphorolytic leaf starch metabolization. In effect, this rendered a plant capable of C3+CAM with open stomata during the day by shifting carbohydrate supply (PEP) to viable soluble sugars. Our findings indicate that polyploidization during genus evolution and subsequent diploidization shaped the emergence of extant physiotypes in Clusia.

sample_organism:
Clusia rosea
Clusia major

platform_organism:
Clusia rosea
Clusia major

overall_design: Plant material for experimentation was generated by producing cuttings from mother plants. Clusia spp. were propagated in a clonal fashion from those shrubs, which we used for DNA extractions and genome sequencing. Cuttings were cultivated in the greenhouse for eight months until all plants reached at least a four-leaf stage. We selected six uniform cuttings from each plant species, namely C. major and C. rosea, and randomly divided them into two groups. The experiment was conducted during a sunny summer week in July. For one week, the stress group was exposed to direct sunlight. There was no precipitation, and the plants were not irrigated. The control group was placed beneath a shaded stand and each pot received 50 mL of water at 7 am each day. After one week, we sampled leaf tissue on four time points across a 24-hour period, at 4 am, 8 am, 1 pm, and 7 pm, respectively. We used sterile punch pliers with a 5 mm diameter to punch four holes into one leaf of each plant. At each time-point a new leaf section (with respect to the main nerve) was used to reduce the amount of injury related signals. The leaf tissue was transferred into 2 mL centrifuge tubes and was immediately snap-frozen in liquid nitrogen and stored at -80 °C for subsequent RNA-Seq.

first: Johannes

middle: B

last: Herpell

first: Clara

last: Priemer

first: Zoe

last: Wessely

first: Florian

last: Schindler

last: Plott

first: Tamara

last: Schmidt

first: Peter

last: Kerpan

first: Leila

last: Afjehi-Sadat

first: Palak

last: Chaturvedi

first: Arindam

last: Ghatak

first: Iro

last: Pierides

first: Lena

last: Fragner

first: Eva

last: Temsch

first: Fabio

last: Trevisan

first: Menriti

last: Ibrahim

first: Felix

last: Fromwald

first: Anke

last: Bellaire

first: Oleg

last: Simakov

first: Werner

last: Huber

first: Ovidiu

last: Paun

first: Susann

last: Wicke

first: Hanna

last: Weiss-Schneeweiss

first: Gert

last: Bachmann

first: Wolfram

last: Weckwerth

first: Andreas

last: Berger

first: Maximilian

last: Kellner

first: Martin

last: Brenner

first: Ulrich

last: Lüttge

first: Agnes

last: Dohovits


title: Total RNA Sequencing analysis of total RNA and RNA isolated from mitochondrial pellets in CSDE1-knockdown sensory neurons

status: Public on Mar 12 2026

city: Daegu

first: Hoyong

last: Jin

address: E4-222, 333, Techno jungang-daero, Hyeonpung-eup, Dalseong-gun

country: South Korea

institute: DGIST

summary: CSDE1 is an RNA-binding protein that associates with a subset of mitochondria-related transcripts. We previously observed that RNAs encoding mitochondrial proteins localized to the mitochondrial inner membrane (MIM), intermembrane space (IMS), matrix, and outer membrane (MOM) are enriched within the CSDE1-bound RNA pool. To determine whether CSDE1 regulates the abundance and mitochondrial localization of mitochondria-associated RNAs in sensory neurons, we performed RNA sequencing of both total RNA and RNA extracted from isolated mitochondria isolated from CSDE1-knockdown sensory neurons. CSDE1 knockdown was achieved using lentiviral transduction, and sequencing results were compared with control neurons infected with empty vector (pLKO).

overall_design: Dorsal root ganglia (DRG) were dissected from embryonic day 13.5 (E13.5) mouse embryos. To enrich for neuronal populations, dissociated DRG cells were cultured in medium containing 5-fluoro-2′-deoxyuridine (FDU) to eliminate non-neuronal cells. Sensory neurons were transduced with lentivirus expressing shRNA targeting CSDE1 or control empty vector (pLKO). Total RNA and RNA extracted from isolated mitochondria were isolated from cultured neurons. RNA sequencing was performed to compare transcriptomic changes in total RNA and RNA extracted from isolated mitochondria between control and CSDE1-knockdown conditions.

first: Ho-Yong

first: Yong-Cheol

last: Cho


title: Transcriptomic profiling of plants in response to CLE9 treatment

city: shijiazhuang

first: jiaojiao

last: bai

address: huaizhong road No.286

institute: UCAS

summary: we performed RNA sequencing (RNA-seq) to analyze genes that were differentially expressed upon CLE9 treatment.A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. We using an optimized data analysis workflow.

overall_design: RNA-seq pfofiling of 7-day-old Arabidopsis seedlings treated with 200 nM CLE9

first: Yuanyuan

last: Zhou

first: Jiaojiao

last: Bai

first: Dongping

last: Lu


title: A sequence motif for DNA double-strand break and telomere healing during programmed DNA elimination [CRISPR]

city: Knoxville

first: Jianbin

last: Wang

state: TN

address: 1311 Cumberland Avenue 309 Ken and Blaire Mossman Bldg

department: Biochemistry & Cellular and Molecular Biology

institute: The University of Tennessee Knoxville

summary: Programmed DNA Elimination (PDE) is an exception to the paradigm of genome integrity, removing selected DNA sequences during development. PDE is observed in hundreds of metazoan species from diverse phyla, but its molecular mechanisms and biological significance in most metazoa remain largely unknown. During PDE in the nematode Oscheius tipulae, DNA double-strand breaks (DSBs) are generated at subtelomeric regions, followed by the loss of DNA at chromosome ends and the healing of the DSBs with de novo telomere synthesis. By mutating a 29-bp degenerated palindromic Sequence For Elimination (SFE) motif at the break sites, we determined the sequence requirement for DSB generation and demonstrated that the conserved GGC/GCC sites are used for neotelomere formation. Introducing the SFE to the retained region adjacent to a native SFE induces DNA cleavage, telomere healing, and loss of additional DNA. Moreover, insertion of the SFE in the middle of the sex chromosome splits it into two functional chromosomes, demonstrating that the SFE function is not constrained by its genomic location. Overall, our data show that the SFE motif is both necessary and sufficient for the generation of DSBs and the healing of DSB ends via telomere addition, playing key roles in Oscheius PDE.

overall_design: Illumina sequencing was performed using mixed embryo samples to validate the generated CRISPR mutants in O. tipulae

first: Jansirani

last: Srinivasan


title: Caste specialisation of cellular identities in the termite Zootermopsis nevadensis

city: Sydney

first: Catherine

middle: Rose

last: Gatt

state: NSW

address: UNSW Sydney High St Kensington

department: School of Clinical Medicine

institute: University of New South Wales

summary: Here, we generated whole-body cell atlases of the king, queen, soldier, and working castes of the termite Zootermopsis nevadensis to investigate caste specialisation of cellular types and transcriptomes. Out of 24 cell clusters, 18 could be annotated based on sister cell types in Drosophila melanogaster and six appeared novel.

overall_design: Nuclei dissociation, fluorescence-activated (FACS) nuclei sorting, droplet-based libraries (10X genomics), and short-read sequencing, was used to obtain single-nuclei transcriptomic data from whole individual termites. We processed one library per caste and obtained 2,288 nuclei from one king, 6,529 nuclei from one queen, 4,805 nuclei from one soldier, and 10,630 nuclei from a pool of six individuals of the worker caste, for a total of 24,252 nuclei and 13,413 genes.

first: Kensei

last: Kikuchi

first: Esra

last: Kaymak

first: Simon

last: Hellemans

first: Fuka

last: Koja

first: Thomas

last: Bourguignon

first: Fabio

last: Zanini


title: Cross-Species Transcriptomic Integration Reveals a Conserved, MIRO1-Mediated Macrophage-to-T Cell Signaling Axis Driving Immunosuppression in Glioma [snRNA-Seq]

city: Palo Alto

first: Xinnan

address: 1201 Welch Road, MSLS Building, Rm P151

department: Neurosurgery

institute: Stanford University

summary: We generated single-nucleus RNA sequencing (snRNA-seq) data from murine gliomas treated in vivo with a MIRO1-binding compound or vehicle control. Tumors were dissociated and processed for nucleus isolation followed by high-throughput transcriptomic profiling to characterize cell-type-specific gene expression programs within the tumor microenvironment (TME). The dataset captures malignant cells and diverse stromal and immune populations, including macrophages, microglia, and T cells, enabling analysis of treatment-associated transcriptional changes at single-cell resolution. These data provide a resource for investigating mitochondrial-associated transcriptional regulation and immune microenvironment remodeling in murine glioma.

overall_design: Single-nucleus RNA-seq profiling of nuclei isolated from orthotopic GL261-Luc mouse glioma tissues following intracranial treatment with 10 μM MIRO1-binding compound (MR3) or vehicle control (DMSO) on days 11 and 18 post-implantation, with tissues collected on day 22 for transcriptomic analysis.

first: Menghan

last: Li

first: Brandon

last: Bergsneider

first: Zehui

last: Du


title: A sequence motif for DNA double-strand break and telomere healing during programmed DNA elimination [Hi-C]

overall_design: Hi-C was performed using samples from larval stages of O.tipulae and the O.tipulae mutant.


title: A sequence motif for DNA double-strand break and telomere healing during programmed DNA elimination [CUT&Run]

overall_design: Cut & Run was performed using sample from different stages for H3K9me3 and H3K4me3.


title: A sequence motif for DNA double-strand break and telomere healing during programmed DNA elimination [END-seq]

overall_design: END-seq was performed on early embryos of the generated O. tipulae CRISPR mutants to evaluate telomere addition sites.


title: Comparative RNA seq analysis of Salmonella Typhimurium and pimt gene deletion strain

city: Bareilly

first: Mahindhan

last: R

state: Uttar Pradesh

address: Division of Biochemistry, IVRI, Izatnagar

department: Division of Biochemistry

institute: ICAR-Indian Veterinary Research Institute

summary: Inside the host, Salmonella Typhimurium suffers but survives various stresses. Proteins are the prime targets of host inflammatory responses. S. Typhimurium encodes two key protein repair enzymes, methionine sulfoxide reductase (Msr) and protein iso-aspartate methyltransferase (PIMT), that reactivates damaged proteins without their translational synthesis. Under stress, the accumulation of L-isoaspartate (Iso-asp) residues causes defects in protein shape and function, which lead to impaired bacterial survival. To examine the global transcriptional consequences of deleting pimt gene, RNA sequencing was performed on S. Typhimurium and Δpimt mutant strains. This dataset provides a comprehensive transcriptomic resource for investigating the impact of pimt deletion on virulence and pathogenicity in S. Typhimurium.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium

overall_design: S. Typhimurium and Δpimt mutant strains were grown to mid-logarithmic phase (OD₆₀₀ ≈ 1.0). Total RNA was extracted, ribodepleted, and strand-specific RNA-seq libraries were prepared and sequenced on an Illumina platform. Sequencing reads were quality filtered, rRNA reads were removed, and the remaining reads were aligned to the Salmonella Typhimurium LT2 GenBank complete genome sequence (GCA_000006945.2). Gene-level read counts were generated and normalized for comparative analysis of gene expression between the two strains.

first: Tapan Kumar

last: Singh Chauhan

first: Lalhmangaihzuali

last: Lalhmangaihzuali

first: Darshini

last: Chandra

first: Manish

last: Mahawar