title: High-resolution immune atlas of murine healthy prostate and prostate cancer from neoplasia to adenocarcinoma stage in the inducible PTEN(i)pe-/- mice

city: Marseille

first: Lionel

last: Spinelli

address: Avenue de Luminy

institute: CIML

summary: Prostate cancer (PCa) is the most commonly diagnosed cancer and the second leading cause of cancer-related mortility among men in western societies. PCa exhibits a protracted progression, initiating as Prostatic Intraepithelial Neoplasia (PIN), advancing to adenocarcinoma, and eventually culminating in metastatic dissemination. The advent of Immune Checkpoint Inhibitors (ICI) has been revolutionized the field of cancer immunology. However, the efficacy of immunotherapy in PCa has been limited, and the role of immune cells in prostate tumorigenesis has only recently been explored. In this study, we performed an in-depth characterization of immune cells in healthy murine prostate and during PCa progression in PTEN(i)pe-/- mice. In this model, the PTEN gene is selectively ablated in prostatic luminal epithelial cells at adulthood (PSA-CreERT2), closely mimicking human PCa development. Notably, tumor progression in this model is gradual, with the PIN stage manifesting at 3 months post-gene invalidation and the adenocarcinoma stage at 9 months. The strict temporal control of PTEN depletion coupled with the slow tumor progression, makes the PTEN(i)pe-/- mouse model an invaluable tool for delineating immune infiltration during tumor development and evaluating therapeutic interventions.  Here we performed scRNAseq on CD45+ immune cells residing in the dorsolateral lobes of prostate at respectively 3 and 9 months post tamoxifen treatment of PTEN(i)pe-/- and control mice, allowing to establish a high-resolution immune atlas of murine PCa from neoplasia to adenocarcinoma. Our findings reveal significant heterogeneity among mononuclear phagocytes (dendritic cells and macrophages), neutrophils and lymphoid immune cells in the prostate. Various neutrophil clusters exhibit an immunosuppressive signature from the PIN stage onward. We observed the recruitment of Trem2+ tumor-associated macrophage subset during PCa, potentially contributing to tumorigenesis. Additionally, there was an increase in CD8+ T lymphocytes in PCa, which exhibited an activated/exhausted phenotype. Our study elucidates the intricate dynamics of immune cell behavior in PCa from early to late stages. These insights pave the way for novel immunotherapeutic strategies to treat prostate cancer, thereby advancing the field of tumor immunology.

overall_design: To establish a high-resolution immune atlas of healthy prostate and prostate cancer we performed scRNA-seq on sorted tissue resident CD45+ immune cells from the inducible adult PTEN(i)pe-/- mice at the Prostatic Intraepithelila Neoplasia stage (PIN) and Adenocarcinoma stages, and age-matched healthy PTENL2/L2 control individuals at 3months and 9months post tamoxifen administration respectively. Few minutes prior sacrifice, mice were injected intravenously with fluorescent anti-CD45.2 antibodies to perform blood/tissue partitioning, allowing to exclude cells present in the vasculature and ensure to study solely the immune cells present in prostate parenchyma. Cells were extracted from DLV prostate lobes by enzymatic digestion. Prostate samples from three PTEN(i)pe-/- mice at 3months post tamoxifen were pooled prior to sorting. Similarly, prostate samples from five  sex-matched PTENL2/L2 control littermates at 3months post-tamoxifen were also pooled prior to sorting. The same approach was applied for the 9months samples of PTEN(i)pe-/- and control mice respectively. Tissue resident CD45+ immune cells were sorted by fluorescence-activated cell sorting (FACS). As we found previously that neutrophils were prevalent within the leukocyte infiltrate from PIN to adenocarcinoma stages of Pten(i)pe-/-prostate, neutrophils were sorted separately from the other CD45+ immune cells and cells were mixed again at a 25% ratio of neutrophils with 75% of CD45+ non neutrophil immune cells prior 10X Genomics Chromium System encapsulation and scRNAsequencing. We included 8 independent samples encompassing 2 replicates of PtenL2/L2 control 3 months, PtenL2/L2 control 9 months, Pten(i)pe-/- 3 months PIN and Pten(i)pe-/- 9 months adenocarcinoma.

first: Despoina

last: Pervizou

first: Joanna

last: De Chiara

last: Chasson

first: Frédéric

last: Fiore

first: Marc

last: Bajénoff

first: Bernard

last: Malissen

first: Daniel

last: Metzger

first: Gilles

last: Laverny

first: Sandrine

last: Henri


title: Multi-organ transcriptome changes in response to acute cold exposure

status: Public on Sep 30 2025

city: Barcelona

first: Francesc

last: Villarroya

state: Barcelona

address: Diagonal 643

department: Biochemistry and Molecular Biomedicine

country: Spain

institute: University of Barcelona

type: Expression profiling by high throughput sequencing

summary: Cold adaptation is a canonical model to study the induction of thermogenic and mitochondrial activity in adipose tissues. Yet, the effects of thermal adaptation in other metabolic-relevant tissues, such as the liver, are poorly explored. Here, we present a dataset that allows us to contrast the effects of acute cold exposure (24h, 4C) in a multi-tissue RNA sequencing approach.

overall_design: C57BL/6 adult mice were put under thermoneutral (30C) or cold (4C) conditions for 24 hours. Mice were sacrificed for tissues and blood samples to be collected. Interescapular brown adipose tissue, inguinal white adipose tissue, and liver were snap-frozen. From these tissues, RNA was purified and processed for sequencing.

first: Tania

last: Quesada-López

first: Albert

last: Mestres-Arenas

first: Joan

first: Marta

last: Giralt


title: VH gene accessibility in pro-B cells

city: Chicago

first: Amy

last: Kenter

state: IL

address: 835 S Wolcott

country: USA

institute: UIC

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The generation of a diverse immunoglobulin repertoire is essential for humoral immunity and requires the participation of all V genes in V(D)J recombination.  Efficient repertoire formation depends on the access of approximately 100 functional VH genes spread over 2.4 Mb of the Igh locus to the DH and JH segment clusters located in the recombination center (RC) with the intronic Em enhancer.  A process termed locus contraction is thought to generate proximity of the distal VH genes to the RC.  Here, we explore the function of newly discovered novel enhancers and a highly transcribed VH promoter and their impact on VH gene accessibility in chromatin.  We demonstrate that these transcriptional elements determines regional Igh gene transcription but have little impact on chromatin accessibility.

overall_design: ATAC-seq was performed on BM derived Rag2-/-, Rag2-/-SiteI.3Pr-/- and Rag1-/-NE1-/-  murine pro-B cells following 5 days of ex vivo IL7 expansion.

first: Ellen

last: Drake

first: Sarah

last: Naiyer

middle: L


title: Methamphetamine Induces Metallothionein 1 Expression and an Inflammatory Phenotype in Primary Human HIV-infected Macrophages [JW98_JW100]

status: Public on Sep 29 2025

city: Bronx

first: Jessica

last: Weiselberg

state: NY

address: 1300 Morris Park Avenue, Forchheimer 727

department: Pathology

institute: Albert Einstein College of Medicine

summary: HIV associated neurocognitive impairment (HIV-NCI), a comorbidity of HIV infection, affects up to 50% of people with HIV (PWH). HIV-infected monocytes that transmigrate across the blood brain barrier and differentiate into macrophages establish a CNS viral reservoir that activates and infects parenchymal cells, contributing to neuronal damage that characterizes HIV-NCI. Methamphetamine (meth) use is prevalent in PWH and further impairs cognitive functioning. To examine whether meth-mediated dysregulation of macrophage functions may contribute to increased HIV-NCI, we characterized differential gene expression in primary human HIV-infected macrophages treated daily with meth for five days by RNA-sequencing. We identified increases in multiple gene isoforms of metallothionein 1 (MT1), a heavy metal binding protein involved in protective mechanisms against metal toxicity and oxidative stress. Nuclear localization of MT1 protein was previously shown to either positively or negatively affect NF-κB activity in a cell type specific manner, with nuclear MT1 contributing to LPS-induced TNF-α and IL-6 in macrophages. We found that daily meth treatment for one to five days increased nuclear localization of MT1 in macrophages acutely infected with HIV which was associated with increased LPS-induced CXCL8 and CCL8, and a trend towards increased basal and/or LPS-induced expression of other cytokines/chemokines, including TNF-α and IL-6, that was donor specific. ROS levels were not changed with meth treatment although there was a donor specific trend towards increased ROS with multiple days of meth treatment. These data indicate that repeated exposure of macrophages to meth in the context of HIV increases nuclear MT1 localization, which is associated with increased inflammatory mediator production, and therefore may be a mechanism that contributes to meth-mediated exacerbation of HIV-NCI.

overall_design:
Primary human macrophages were obtained from culturing monocytes from healthy individuals and were infected with HIV or left uninfected. After three days of infection, HIV-infected macrophages were treated daily with meth for five days. Uninfected samples were treated daily with emth begining at the same timepoint.

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

first: Meng

last: Niu

first: Cristian

middle: A

last: Hernandez

first: Howard

middle: S

last: Fox

first: Tina

middle: M

last: Calderon

middle: W

last: Berman


title: IG-DMR escapes from global hypomethylation during adult neural stem cells reprogramming [MeDIP-seq]

city: Valencia

first: Jordi

last: Planells

state: Valencia

address: Doctor Moliner, 50 street

department: Biologia celular, biologia funcional y antropologia fisica

institute: Universitat de València

type: Methylation profiling by high throughput sequencing

summary: Genomic imprinting is an epigenetic mechanism that causes monoallelic expression of genes depending on their parental origin. Loss of imprinting (LOI) is associated with cancer progression and human imprinting disorders (IDs), impacting foetal development, metabolism and cognition. Imprinted genes, organized in clusters, rely on methylation at imprint control regions (ICRs), which are differentially methylated regions (DMRs) on both parental chromosomes. Somatic cell reprogramming into induced pluripotent stem cells (iPSCs) is a valuable tool to understand the mechanisms associated with pluripotency and holds promise for generating patient-specific stem cells for therapeutical applications to treat different pathologies such as IDs. Here, we conduct genome-wide RNA-seq and MeDIP-seq analysis on mouse iPSCs derived from adult neural stem cells (NSCs). Our findings reveal a comprehensive alteration in iPSCs transcriptome profile, aligning with DNA hypomethylation. This correlation is pivotal in discerning which modifications in genomic imprinting during the reprogramming process represent undesirable epigenetic abnormalities that could compromise the quality of iPSCs. Simultaneously, it helps identify genuine epigenetic modifications that are inherently linked to pluripotency, thus ensuring a clearer understanding of the factors influencing iPSC quality and pluripotent potential

overall_design:
Gene imprinting is a molecular mechanism by which the expression of a gene is limited in a parent-of-origin manner. It has been shown that methylation in imprinting control regions (ICRs) is crucial for monoallelic expression. We isolated neural stem cells (NSCs) from the sub-ventricular zone of adult mouse brains. We then reprogrammed adult NSCs to iPSCs by co-transfection of Oct4 and Klf4 plasmids in retroviral vectors.
We have profiled the methylome genome-wide with  Methylated DNA immunoprecipitation sequencing (MeDIP-seq) in NSCs (n = 3) and reprogrammed adults NSCs (iPSCs) (n = 3) to compare the methylation profiles, with particular attention to imprinted genes.

first: Laura

last: Lázaro-Carot

first: Esteban

last: Jiménez-Villalba

first: Anna

last: Lozano-Ureña

first: Raquel

last: Montalbán-Loro

first: Jennifer

last: Díaz-Moncho

first: Adela

last: Lleches-Pradilla

first: Martina

last: Kirstein

first: Mitsuteru

last: Ito

first: Elisabeth J.

last: Radford

first: Sacri R.

last: Ferrón


title: Spatial Transcriptomics of Controlled vs Uncontrolled Tuberculosis in a Mouse Model

city: Mountain View

first: Lester

last: Kobzik

state: California

address: 320 Logue Avenue

institute: Cellecta, Inc

summary: To further characterize gene expression in controlled vs uncontrolled tuberculosis lung lesions, we performed spatial transcriptomics analysis using the NanostringGeoMX Digital Spatial Profiler (DSP) system.

overall_design: Based on routine hematoxyline and eosin histopathology, we selected lungs from 2 mice with paucibacillary controlled lesions and 2 mice with advanced uncontrolled multibacillary lesions with necrotic areas. Additional FFPE sections were stained with fluorescent CD45-, pan-keratin-specific antibodies and DAPI. Diseased regions of interest (ROI) were selected to focus on myeloid-rich areas avoiding necrosis and tertiary lymphoid tissue . Eight ROI each of contolled and uncontrolled lesions (respectively) were studied. The profiling used the Mouse Whole Transcriptome Atlas (WTA) panel which targets ~21,000+ transcripts for mouse protein coding genes

first: Igor

last: Kramnik


title: Methamphetamine Induces Metallothionein 1 Expression and an Inflammatory Phenotype in Primary Human HIV-infected Macrophages

first: Jessica

last: Weiselberg

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

overall_design: Refer to individual Series


title: Effect of pressure-overload on cardiac endothelial cells in Balb/c mice

city: Rouen

first: Ebba

last: Brakenhielm

address: Inserm U1096

country: France

institute: Inserm

summary: We performed single-cell RNA-seq analysis of FACS-sorted cardiac blood vascular and lymphatic endothelial cells in the heart of Balb/c female mice in a model of pressure-overload.

overall_design: Cardiac CD31+ CD45neg endothelial cells, and Lyve1/Podoplanin-expressing lymphatic endothelial cells (LEC) were extracted from hearts of mice 8 weeks after pressure-overload or sham surgery in a murine model of transaortic constriction, and analyzed by single-cell RNA-sequencing. Briefly, cardiac single cell suspensions were sorted by FACS (ARIA II, BD Biosciences). BECs were defined as live CD45-/CD31+/Lyve1- cells, whereas LECs were identified as CD45-/CD31+/Lyve1+/Pdpn+ cells. A 1:3 mix of cardiac LECs and BECs were included in each sample prepared using the 10X Genomics Chromium Next Gem Single Cell 3' kit. For each group 1-2 reactions were performed using each time pooled cells from 10 mouse hearts. Samples were sequenced using Illumina NextSeq550 at an estimated sequencing depth of 20 000 reads per cell. Reads were aligned to the mouse reference genome (GRCm39.111) using STARsolo RNA-seq aligner (v2.7) to produce raw UMI count matrix. Data filtering, normalization, integration, principal component-based unsupervised clustering, and differential analysis were performed using the Seurat package (version 5.0.2) in R (version 4.1.2). For low-quality data filtering, genes expressed by <10 cells, and cells expressing <500 genes, were excluded, as were cells with UMI numbers <500 or cells with >10% mitochondria-derived UMI counts.  Among 3908 total sequenced cells, 3436 cardiac cells remained post-filtering, including 1932 cells from sham-operated BALB/c controls and 1504 from post-TAC mice.

first: Coraline

last: Heron

first: Theo

last: Lemarcis

first: Oceane

last: Laguerre

first: Benjamin

last: Bourgeois

first: Corentin

last: Thuilliez

first: Chloe

last: Valentin

first: Anais

last: Dumesnil

first: Manon

last: Valet

first: Gaetan

last: Riou

first: Sophie

last: Candon

first: Celine

last: Derambure

first: Caroline

last: Berard

first: Helene

last: Dauchel

first: Virginie

last: Tardif

first: Brakenhielm

last: Ebba


title: Molecular Consequences of CCN6 Variants Encoding WISP3 in Progressive Pseudorheumatoid Dysplasia

city: Istanbul

first: Eda

last: Tahir Turanli

address: Kayisdagi St.

country: Turkey

institute: Acibadem University

summary: Progressive pseudorheumatoid dysplasia (PPD) is a rare autosomal recessive cartilage disorder caused by biallelic variants in CCN6, encoding the matricellular protein WISP3. To investigate how disease-associated CCN6 variants impact chondrocytes, we overexpressed two clinically relevant variants—p.Cys52* and p.Cys114Trp—both located in the IGFBP domain, and assessed their effects on redox balance, ER stress, ECM remodeling, gene expression, and protein–protein interactions. The p.Cys52* variant led to rapid degradation of WISP3, consistent with complete loss-of-function. In contrast, p.Cys114Trp induced severe protein destabilization, mitochondrial ROS accumulation, and elevated ER stress. Proteomic analysis revealed that p.Cys114Trp established novel interactions, suggesting a gain-of-function effect. These variant-specific differences highlight how structural context influences cellular outcomes beyond variant type alone. Altogether, our findings emphasize the necessity of functional characterization to better model PPD pathogenesis and provide mechanistic insights that may guide future therapeutic strategies.

overall_design: RNA-seq profiling of human chondrocyte cell line 402-05A following plasmid-mediated overexpression of wild-type CCN6 or its variants (p.Cys52, p.Cys114Trp). Cells were harvested 48 hours post-transfection for total RNA extraction and library preparation.

first: Gulipek

last: Guven Tasbicen

first: Alper

last: Bulbul

first: Dilay Hazal

last: Ayhan

first: Yasemin

last: Alanay


title: IG-DMR escapes from global hypomethylation during adult neural stem cells reprogramming [RNA-seq]

first: Jordi

last: Planells

overall_design:
Gene imprinting is a molecular mechanism by which the expression of a gene is limited in a parent-of-origin manner. It has been shown that methylation in imprinting control regions (ICRs) is crucial for monoallelic expression. We isolated neural stem cells (NSCs) from the sub-ventricular zone of adult mouse brains. We then reprogrammed adult NSCs to iPSCs by co-transfection of Oct4 and Klf4 plasmids in retroviral vectors.
We have profiled the methylome genome-wide with  Methylated DNA immunoprecipitation sequencing (MeDIP-seq) in NSCs (n = 3) and reprogrammed adults NSCs (iPSCs) (n = 2) to compare the methylation profiles, with particular attention to imprinted genes.

first: Laura

last: Lázaro-Carot

first: Esteban

last: Jiménez-Villalba

first: Anna

last: Lozano-Ureña

first: Raquel

last: Montalbán-Loro

first: Jennifer

last: Díaz-Moncho

first: Adela

last: Lleches-Pradilla

first: Martina

last: Kirstein

first: Mitsuteru

last: Ito

first: Elisabeth J.

last: Radford

first: Sacri R.

last: Ferrón


title: A Murine Model of Glioblastoma Initiating Cells and Human Brain Organoid Xenograft for Photodynamic Therapy Testing

city: Badalona

first: Mar

last: Mallo

address: Ctra de Can Ruti, s/n, camí de les escoles. Edifici IMPPC

institute: Josep Carreras Leukaemia Research Institute

summary: Despite decades of research, brain tumours remain among the deadliest of all forms of cancer. As recurrence in glioblastoma is locally generated around the resection cavity, the ability of these tumours to resist almost all conventional and novel treatments relates, in part, to the unique cell-intrinsic and microenvironmental properties of neural tissues. Photodynamic therapy (PDT) relies on photo-toxic effects induced by specific molecules (photosensitisers) upon absorption of photons from a light source. Such toxic effects are not specific to a particular molecular fingerprint of GBM, but rather depend on selective accumulation of the photosensitiser inside tumour cells and their sensitivity to the effects, triggered by light. Here we report four new GICs obtained in Hospital Clinic Barcelona, HCB-GICs, to optimize preclinical studies of PDT, and to explore neoadjuvant protocols for a more effective PDT and photodiagnostic visualization. HCB-GIC cells express the known “stemness” markers Nestin and SOX2, Vimentin and CD44, contributing to invasiveness and to infiltrative ability within brain organoids, properties associated also to mesenchymal phenotype.  HCB-GICs are susceptible to be treated with PDT, since the burden of cells into organoids decreased while increased cell death after irradiation. Moreover, we optimize an experimental in vivo model, able to assess the antitumoral effect of 5-ALA mediated PDT in engraftments of HCB-GICs co-cultures on the kidneys of high immunosupressed mice. In conclusion, we suggest that PDT might be an effective therapy to kill GICs with heterogeneous molecular fingerprint that achieve high levels of PPIX accumulation in tumor niche.

overall_design: Comparison of HCB-GICs (glioblastoma initiating cells) obtained by primary culture of GB biopsies and their original tumor (4 samples)

first: Angeles

last: Sierra


title: Effect of estradiol on thermoregulatory responses in ovariectomized rats administered ostruthin, a TWIK-related potassium channel agonist

status: Public on Sep 27 2025

city: Tokyo

first: Yuki

last: Uchida

state: Shinagawa

address: 1-5-8 Hatanodai

department: Department of Physiology

country: Japan

institute: Showa University School of Medicine

summary: This study investigated the effects of estradiol (E2) on ostruthin-induced thermoregulatory responses in ovariectomized rats, a menopausal model. Ostruthin, a component extracted from Paramignya trimera, is an agonist of cold receptors, specifically the TWIK-related potassium channels 1 (TREK1) and 2 (TREK2). Wistar rats were ovariectomized and implanted with a silastic tube with or without E2 (E2(+) and E2(−) groups). Ostruthin or vehicle was injected intraperitoneally. Body temperature (Tb), locomotor activity, tail skin temperature (Ttail), oxygen consumption, and tail-hiding behavior were measured continuously. Plasma concentrations of catecholamines, triiodothyronine, and thyroxine were measured. mRNA expression levels of TWIK-related potassium channels, transient receptor potential cation channels, E2 receptors, and selected four genes in dorsal root ganglia were assessed. For the electrophysiological study, ventral root reflex responses induced by dorsal root stimulation were measured in in vitro preparations of neonatal rat spinal cord applied 500 μM ostruthin. Ostruthin increased Tb in the E2(+) group. In ostruthin-treated groups, Tb in the E2(+) group was greater than that in the E2(−) group. Ostruthin decreased Ttail. There was a tendency for E2 to decrease Ttail. E2 increased plasma triiodothyronine. E2 increased TREK1, nerve growth factor-inducible, and nitric oxide synthase 1 mRNA level. No significant differences in other measurements were observed among the groups. The excitation of sensory nerves by ostruthin and the increase of TREK1 by E2 may facilitate cold sensitivity. Ostruthin and E2 suppressed heat dissipation by tail skin vasomotor control. E2 may increase Tb in a menopausal model, potentially through modulation of TREK1.

overall_design: To investigate the effects of estradiol (E2) on ostruthin-induced thermoregulatory responses in ovariectomized rats, the dorsal root ganglia in rats were analyzed by RNA-seq.

first: Shotaro

last: Kamijo

last: Samejima

first: Hiroshi

last: Onimaru

first: Masahiro

last: Hosonuma

first: Hikaru

last: Isobe

first: Keiko

last: Ikeda

first: Motoyasu

last: Honma

first: Yuri

last: Masaoka

first: Masahiko

last: Izumizaki


title: Impact of radiation dose and time since radiation exposure on host-microbe relationship

city: Silver Spring

first: Aarti

last: Gautam

state: MD

address: 503 Robert Grant Avenue

department: Medical Readiness Systems Biology

institute: WRAIR

summary: The microorganisms that colonized in or on hosts play significant roles in regulating host’s immunological fitness and bioenergy production, thus controls the host’s response to stress or foreign stimuli. Since radiation typically causes a pro-inflammatory and bioenergy expensive condition, we speculate that the radiation could influence gut microbial compositions, thereof the host-microbe bidirectional relationship. Pertinent model included exposing the young adult mice to total body irradiation (TBI) at doses of 9.5Gy and 11Gy, respectively. Descending colon contents (DCC) were collected from non-irradiated mice (baseline control), and irradiated mice euthanized on days 1, 3 and 9 post-TBI. DCC’s 16s ribosomal DNAs were screened for bacterial taxonomic classification and bacterial abundance profile informed metagenome-specific biofunctions. A second aliquot of same DCC was screened for untargeted metabolomics assay to find most perturbed metabolite-enriched networks. Dose-independent temporal delay since TBI emerged as the primary factor explaining the increased richness of bacterial community and the diversity of metabolite landscape. Among the mice exposed to 11Gy TBI, an increased abundance of Firmicutes, an anti-inflammatory and efficient energy harvesting bacteria accompanied an increment of pro-inflammatory Deferribacteres. Systems evaluation of the functional networks linked to DCC’s metagenome and metabolite, respectively, suggested a diverging trend between host and DCC microbes in regulating the network clusters, such as lipid metabolism, bioenergy synthesis, particularly at the later time points post-11Gy TBI. This analysis potentially suggested a disrupted symbiotic relationship between the host and microbes when the host became moribund.

overall_design: 38 samples with different amounts of radiation and time points

first: Nabarun

last: Chakraborty

first: Allison

last: Hoke

first: Ross

last: Campbell

first: Gregory

last: Holmes-Hampton

first: Vidya

middle: P

last: Kumar

first: Candace

last: Moyler

first: Rasha

last: Hammamieh

first: Sanchita

last: Ghosh


title: Methamphetamine Induces Metallothionein 1 Expression and an Inflammatory Phenotype in Primary Human HIV-infected Macrophages [JW81_JW82_JW84]

first: Jessica

last: Weiselberg

first: Meng

last: Niu

first: Cristian

last: Hernandez

first: Howard

last: Fox

first: Tina

last: Calderon

first: Joan

last: Berman


title: Iron-sensitive RNA regulation by poly C binding proteins [DKD_RNASeq]

status: Public on Sep 26 2025

city: Chapel Hill

first: Maria

last: Aleman

state: NC

address: 120 Mason Farm Rd.

institute: University of North Carolina at Chapel Hill

summary: Iron is important for normal cellular function and posttranscriptional mechanisms regulate the cellular response to iron deficiency. In this study we explore how RNA binding proteins, PCBP1 and PCBP2, exhibit iron-sensitive RNA regulation.

overall_design: K562 cells were treated with DMSO or 10 µM iron chelator 21H7 after being transduced to express short hairpin RNAs targeting luciferase (shCtrl) or PCBP1 (shPCBP1) and PCBP2 (shPCBP2).

first: Daniel

last: Dominguez


title: ChIP-seq to measure binding of NIPBL/MAU2, RAD21, and CTCF in mouse embryonic stem cells and neural progenitor cells

city: San Francisco

first: Elphege

last: Nora

state: CA

address: 555 Mission Bay Blvd S

department: CVRI

institute: UCSF

summary: Mammalian chromosomes are folded by the cohesin complex, which creates chromatin loops that are extruded as cohesin translocates along the chromatin fiber. This dynamic process regulates gene expression by controlling the frequency of contacts between enhancers and promoters. We analyzed where in the genome loop extrusion occurs to discover where extrusion initiates and whether particular regions are extruded more than others. We measured NIPBL/MAU2 binding in mouse embryonic stem cells and neural progenitor cells, and found that NIPBL/MAU2 is enriched at enhancers compared to promoters. We used the amount of cohesin binding at CTCF sites as a readout of cohesin traffic, and found that the NIPBL/MAU2 binding sites only modestly boost nearby cohesin levels.

overall_design: We measured NIPBL and MAU2 binding by performing spike-in calibrated HA ChIP-seq in cell lines in which NIPBL or MAU2 was tagged with an HA epitope and FKBP degron. Cells treated with dTAG for 24 hours to deplete NIPBL or MAU2 and untagged cell lines are used as negative controls. We also measured RAD21 and CTCF binding with endogenous antibodies. We used mouse embryonic stem cells and neural progenitor cells.

first: Erika

middle: C

last: Anderson

first: Rini

last: Shah

first: Karissa

last: Hansen


title: DNA methylation patterns facilitate tracing the origin of neuroendocrine neoplasms

city: Heidelberg

first: Stephanie

last: Roessler

address: Im Neuenheimer Feld 224

country: Germany

institute: Heidelberg University Hospital

summary: Neuroendocrine neoplasms (NEN) are thought to originate from diffuse endocrine networks and therefore most frequently occur in the gastrointestinal tract and lungs. The liver is a frequent site of metastasis of NEN but also the presence of primary hepatic NEN has been proposed. Due to the impact on disease management, it is urgently required to discriminate the origin of hepatic NEN metastases and to identify clinically relevant subgroups.

overall_design: Using a comprehensive set of NEN (N=198), we showed that the DNA methylation profile of NEN of distinct anatomical localizations differed significantly and primary tumor-metastasis pairs clustered together, enabling us to identify the tumor origin.

first: Reka

last: Toth


title: Iron-sensitive RNA regulation by poly C binding proteins [RIP-Seq]

overall_design: K562 cells were induced (with doxycycline) to expressed either a Flag-tagged PCBP1, wildtype (WT), a non-iron binding mutant (∆Fe), a non-RNA binding mutant (∆RNA), or Flag-tagged-GFP. Cells  were then treated overnight with DMSO (control) or 10 µM iron chelator (21H7). With two biological replicates, cells were subjected to formaldehyde crosslinking and immunoprecipitation using anti-Flag antibodies. Bound RNA was isolated and sequenced along side inputs.

first: Aleman

last: Maria

first: Dominguez

last: Daniel


title: E2F1 induces a G0-G1 re-entry transcriptional program without changing chromatin accessibility [ATAC-seq]

city: Santa Cruz

first: Ali

last: Shariati

address: 1156 High St

department: Biomolecular Engineering

institute: University of California Santa Cruz

summary: Many cells in our body reside in a reversible nondividing state termed G0 or quiescence. Precise regulation of entry and exit from G0 is critical for maintaining tissue homeostasis. G0 entry can occur when cells do not receive the required signals for cell cycle progression, leading to active repression of cell cycle genes through several mechanisms, including formation of repressor complexes to restrict chromatin accessibility for transcriptional activators. G0 cells can re-enter the G1 phase of the cell cycle upon receiving growth factor signals, resulting in activation of the Mitogen-Activated Protein Kinase pathway, converging on E2F transcription factors. Ectopic expression of E2F1 alone, a transcriptional activator, is sufficient to promote G0 exit without requiring the upstream signals, but it is unclear how E2F1 can overcome the chromatin lockdown in G0 cells to activate cell cycle genes. To better understand this mechanism, we compared dynamics, gene regulation and chromatin accessibility state between E2F1-mediated and growth factor (serum)-induced cell cycle reentry. Using live cell single cell tracking, we observe that E2F1 induction leads to accelerated cell cycle progression compared to regular serum-induced cell cycle re-entry. This accelerated cell cycle re-entry by E2F1 is accompanied by faster upregulation of cell cycle genes. Interestingly, we find that E2F1 preferentially binds to gene promoters that remain in a poised chromatin state after G0 induction, suggesting that G0 cells are prepared for cell cycle re-entry via regulating chromatin states in essential cell cycle genes.

overall_design: Constucts for doxycycline inducible expression of E2F1 or empty-vector (EV) control were stably integrated into 3T3 cells. The E2F1 and EV 3T3 cells were serum starved for 48 hours to induce a G0-like state, followed by E2F1 induction, EV induction or 10% serum addition, to induce G1/S phase reentry. Samples were collected at 0, 2, 6 and 12 hours after induction or serum addition. RNA was extracted for RNA-sequencing and nuclei were extracted for ATAC-Seq. In addition, cells were prepared for E2F1 ChIP-Seq at the 12 hour time point only. Together the RNA-Seq, ATAC-Seq and ChIP-Seq were used to identify E2F1 gene regulatory network involved in cell cycle reentry from G0.

first: Gerrald

last: Lodewijk

first: Benjamin

middle: R

last: Topacio

first: Silvart

last: Arabian

first: Seungho

last: Lee

first: Abolfazl

last: Zargari

first: Znala

last: Williams

first: Edward

last: Wu

first: Sayaka

last: Kozuki

first: Rana

last: Rahimi

first: Neda

last: Bidoki

first: Vanessa

last: Jonsson

first: Eric

last: Malekos

first: Susan

last: Carpenter

first: Gerd

last: Muller

first: Seth

last: Rubin


title: Bulk RNA-seq of MDA-MB-231 cells under dasatinib treatment

city: Taipa

first: feng

last: yu

address: Avenida de Universidade

country: Macau

institute: University of Macau

summary: Triple-negative breast cancer (TNBC) is characterized by high metastatic potential and poor prognosis, underscoring the urgent need for effective therapeutic strategies.  Dasatinib emerged as a promising anti-metastatic agent in TNBC.To elucidate the molecular mechanisms by which dasatinib inhibits breast cancer progression, we conducted bulk RNA sequencing (RNA-seq) on MDA-MB-231 cells treated for 6, 12, 24, and 48 hours.

overall_design: Transcriptomic analysis of MDA-MB-231 cells following dasatinib 0,6,12,24,48 hours-treatment.

first: Xinyu

last: Guo

first: Heng

last: Sun

first: Feng

last: Yu

first: Rong

last: Zhou

first: Chu-xia

last: Deng


title: Identification of SLC7A1 as a potential therapeutic target for high-grade meningioma

city: Beijing

first: lairong

last: song

state: 北京

address: South Fourth Ring West Road 119, Fengtai District

country: China

institute: Beijing Tiantan hospital

summary: High-grade meningioma remains a therapeutic challenge to medical oncologists. It is urgent to uncover novel molecular targets. Solute carrier family 7 member 1 (SLC7A1) was highly expressed in high-grade meningioma and associated with poor prognosis of patients. SLC7A1 knockdown significantly inhibited the proliferation and invasion of malignant meningioma cells. In addition, the small-molecule drug AZ628 showed an excellent antiproliferative effect on malignant meningioma cells, indicating that it is a potential antitumor drug for high-grade meningioma. Our study revealed the essential roles of SLC7A1 in the malignant progression of meningioma, suggesting SLC7A1 as a potential antitumor target for high-grade meningioma.

overall_design: In order to verify the molecular function of SLC7A1 in meningioma cells, we knocked down the expression of SLC7A1 in two meningioma cell lines and performed RNA sequencing. Additionally, to explore the anti-tumor mechanism of AZ628, we treated two meningioma cell lines with AZ628 and conducted RNA sequencing.

first: Lairong

last: Song


title: The first embryonic replication critically affects the outcome of pronuclear transfer

city: Gainesville

first: Zongliang

last: Jiang

state: FL

address: 2033 Mowry Rd

department: Animal Sciences

institute: University of Florida

summary: Pronuclear (PN) transfer has been successfully used in human assisted reproduction to suppress the negative effects of a defective egg cytoplasm or to bypass an idiopathic developmental arrest. However, the effects of a pronucleus formation and initial parental genome remodelling in a defective cytoplasm on subsequent development have not been systematically studied. Using the PN transfer in the pre-replication and post-replication mouse embryos, we show that the first embryonic S-phase plays a critical role. Although the developmental rates of pre-and post-replication PN transfer embryos were comparable and apparently normal looking blastocysts were formed in both groups, the post-replication PN transfer led to changes in the embryonic gene expression. Furthermore, differences in the blastocyst quality in the post-replication PN transfer embryos were detected. Therefore, although the PN transfer is the method of choice to mitigate the impact of a faulty egg cytoplasm on early development, our results show that the timing of this intervention should be restricted to the pre-replication phase.

overall_design:
Three embryos from each experimental condition collected at 34h post fertilization were pooled and used for library preparation, followed by RNA-sequencing analysis.
SPN: sham pronuclear transfer
EPN: early pronuclear transfer
LPN: later pronuclear transfer
SPN is regarded as control, EPN and LPN refer two different timing of the PN procedures.

first: Zongliagn

first: Helena

last: Fulka

first: Hao

last: Ming


title: RNA Expression of TH10785 treated human T cells

city: Magdebrug

first: Dimitrios

last: Mougiakakos

address: Leipziger Str. 44

department: Universitätsklinik für Hämatologie, Onkologie und Zelltherapie

institute: Universitätsklinikum  Magdeburg A.ö.R.

summary: To investigate the transcriptomic effects of the OGG1 agonist TH10785, we treated T cells with the compound and analyzed gene expression profiles. Our aim was to evaluate the potential of OGG1 activation as a strategy to restore and preserve T cell function under conditions of oxidative stress.

overall_design: Isolated human T cells untreated  (Sample6,7,29,30) or treated (Sample6_10785,Sample7_10785,Sample29_10785,Sample30_10785) with TH10785 at a concentration of  7.5 μM. T cells were co-cultured with Nalm6 and CD19xCD3. RNA was isolated on day 10.

first: Domenica

last: Saul

first: Christopher

last: Lischer

first: Heiko

last: Bruns

first: Nicole

last: Ziegler

first: Aimo

last: Kannt

first: Maruice

last: Michel


title: Iron-sensitive RNA regulation by poly C binding proteins

first: Maria

last: Aleman

overall_design: Stable K562 cells were treated with or without doxycycline to induce overexpression of flag-tagged PCBP1

first: Daniel

last: Dominguez


title: Therapeutic JAK1 inhibition reverses lupus nephritis in a mouse model and demonstrates transcriptional changes consistent with human disease

city: Wocester

first: Rachel

middle: E

last: Twomey

state: MA

address: 100 Research Drive

department: Immunology

institute: AbbVie

summary: Janus kinase family members are essential for signaling by multiple cytokines, including many implicated in SLE pathogenesis. To test whether inhibition of JAK1 signaling can be efficacious in SLE, we used a JAK1-selective inhibitor (ABT-317) and evaluated its ability to ameliorate disease in murine SLE.

overall_design: 48 NZB/W-F1 mice were treated with anti-CD40 or anti-JAK1 and kidney and salivary gland tissue were used for NA extraction. Young mice and baseline (disease onset) mice were used as controls.


title: E2F1 induces a G0-G1 re-entry transcriptional program without changing chromatin accessibility [RNA-seq]

first: Ali

last: Shariati

first: Gerrald

last: Lodewijk

first: Benjamin

last: Topacio

first: Silvart

last: Arabian

first: Seungho

last: Lee

first: Abolfazl

last: Zargari

first: Znala

last: Williams

first: Edward

last: Wu

first: Sayaka

last: Kozuki

first: Rana

last: Rahimi

first: Neda

last: Bidoki

first: Vanessa

last: Jonsson

first: Eric

last: Malekos

first: Susan

last: Carpenter

first: Gerd

last: Muller

first: Seth

last: Rubin


title: DNA methylation patterns of neuroendocrine neoplasms

first: Stephanie

last: Roessler

type: Methylation profiling by genome tiling array

summary: Neuroendocrine neoplasms (NEN) are thought to originate from diffuse endocrine networks and therefore most frequently occur in the gastrointestinal tract and lungs. The liver is a frequent site of metastasis of NEN but also the presence of primary hepatic NEN (PHNEN) has been proposed. Due to the impact on disease management, it is urgently required to discriminate the origin of hepatic NEN metastases and to identify clinically relevant subgroups.

overall_design: A set of 15 PHNEN was analyzed by Illumina DNA methylation.

first: Reka

last: Toth


title: Iron-sensitive RNA regulation by poly C binding proteins [P1KD]

first: Maria

last: Aleman

overall_design: K562 cells were transduced to express short hairpin RNAs targeting luciferase (shCtrl) or PCBP1 (shPCBP1).

first: Daniel

last: Dominguez


title: E2F1 induces a G0-G1 re-entry transcriptional program without changing chromatin accessibility [ChIP-seq]

first: Ali

last: Shariati

first: Gerrald

last: Lodewijk

first: Benjamin

last: Topacio

first: Silvart

last: Arabian


title: Iron-sensitive RNA regulation by poly C binding proteins [chelator]

overall_design: K562 cells were treated overnight with DMSO (control) or iron chelator (21H7) with three biological replicates per condition.


title: Lack of dystrophin disrupts fetal muscle stem cell polarity and commitment during secondary myogenesis

city: Ottawa

first: Theodore

last: Perkins

state: ON

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

country: Canada

institute: Ottawa Hospital Research Institute

summary: No cure exists for Duchenne Muscular Dystrophy (DMD), a devastating and fatal muscle degenerative disease caused by a loss-of-function mutations to the DMD gene which encode the large cytoskeleton protein dystrophin. Conventionally, the disease is thought to manifest around 3-5 years of age when fragile myofibers become damaged from patient ambulation. However, we find that perturbation in fetal muscle stem cell (fMuSC) commitment and polarity occur during secondary myogenesis in the mdx mouse, a model of DMD. To study the cell state and the transcriptomic profileof mdx fMuSCs, we conducted single cell RNA-sequencing of myogenic cells derived from the limbs of E17.5 Pax7-nGFP embryos on the C57BL/10ScSnJ and mdx backgrounds.

overall_design: Fetal muscle stem cells were FACS-isolated from the limbs of the limbs of E17.5 Pax7-nGFP embryos on the C57BL/10ScSnJ and mdx backgrounds.The experiment was performed on biological duplicates.

first: Marie

last: Esper

first: Alexander

middle: Y

last: Lin

first: Dallas

last: Bennett

first: Michael

last: Rudnicki


title: Pharmacological Targeting of RIG-I Selectively Activates the Integrated Stress Response

city: La Jolla

first: Jeffery

last: Kelly

address: 10550 North Torrey Pines Road

department: Chemistry

institute: The Scripps Research Institute

summary: The integrated stress response (ISR) is a eukaryotic pathway that attenuates global protein synthesis while allowing selective translation of specific mRNAs, which together can reestablish homeostasis following an acute stress. Diverse pathologic insults activate one or more of the four ISR kinases, which selectively phosphorylate eIF2a to induce translational and transcriptional adaptation of multiple biological functions. Recent results suggest that enhancing ISR kinase activity could ameliorate pathologies linked to numerous diseases, including many neurodegenerative disorders. However, few pharmacological strategies exist to selectively activate ISR kinases and downstream adaptive signaling. Here, we describe compound A8 and its cyclized metabolite CC81 as highly-selective ISR activators that activate the heme-regulated inhibitor (HRI) ISR kinase through a mechanism involving binding of the cytosolic pattern recognition receptor RIG-I. Our results establish a pharmacological strategy to selectively activate HRI-dependent ISR signaling by targeting RIG-I, revealing new mechanistic options for ameliorating etiologically diverse diseases through ISR activation.

overall_design: Total RNASequencing of A8 treated HEK293T cells to determine mechanism of action. RNA was submitted to BGI Genomics Co., Ltd. for strand-specific mRNA sequencing on their DNBSEQ platform with three biological replicates per condition.

first: Caroline

last: Cuoco

first: Leonard

last: Yoon

first: Jessica

last: Rosarda

first: Evan

middle: T

last: Powers

first: R

last: Wiseman


title: Gene expression profile of Kelly and SH-SY5Y cells after treatment with retinoic acid

city: Kiel

first: Meike

last: Kaehler

state: Schleswig-Holstein

address: Hospitalstraße 4

department: Institute of Experimental and Clinical Pharmacology

institute: University Hospital Schleswig-Holstein, Campus Kiel

summary: Kelly and SH-SY5Y neuroblastoma cells were treated with retinoic acid for 3 days. Gene expression profiles from untreated and treated cells were obtained using microarrays (Clariom D) to analyze the retinoic acid-induced changes.

overall_design: RNA from Kelly and SH-SY5Y cells was isolated and microarrays were run including four technical replicates. Treatment with retinoic acid was performed for 3 d.

first: M

first: V

last: Waetzig


title: The transaminase-ω-amidase pathway is a redox switch in glutamine metabolism that generates α-ketoglutarate [RNA-seq_NIT2_aKGM_4h_24h]

status: Public on Sep 25 2025

city: Frankfurt am Main

first: Timothy

last: Warwick

state: Hesse

address: Theodor-Stern-Kai 7

department: Institute for Cardiovascular Physiology

institute: Goethe Universität Frankfurt am Main

summary: Oxidative stress is caused by short-lived molecules and metabolic changes are fast cellular responses. Here we studied how the endothelial cell metabolome reacts to oxidative challenges to identify redox-sensitive metabolic enzymes. H2O2 selectively increased α-ketoglutaramate (αKGM), a largely uncharacterized metabolite produced by glutamine transamination and an unrecognized intermediate of endothelial glutamine catabolism. The enzyme nitrilase-like 2 ω-amidase (NIT2) converts αKGM to α-ketoglutarate (αKG). Reversible oxidation of specific cysteine in NIT2 inhibited its catalytic activity. Furthermore, a variant in the NIT2 gene that decreases its expression is associated with increased plasma αKGM in humans. Endothelial-specific knockout mice of NIT2 exhibited increased levels of αKGM and impaired angiogenesis. Knockout of NIT2 impaired endothelial cell proliferation, sprouting and induced senescence. In conclusion, we show that the glutamine transaminase-ω-amidase pathway is a metabolic switch where NIT2 is the redox-sensitive enzyme. The pathway is modulated in humans and functionally important for endothelial glutamine metabolism.

overall_design: RNA-seq of human umbilical vein endothelial cells treated with alpha-ketoglutaramate for either 4 or 24 hours.

first: Niklas

last: Heerle

first: Pedro Felipe

last: Malacarne

first: Flávia

last: Rezende


title: The transaminase-ω-amidase pathway is a redox switch in glutamine metabolism that generates α-ketoglutarate.

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

overall_design: Refer to individual Series


title: The transaminase-ω-amidase pathway is a redox switch in glutamine metabolism that generates α-ketoglutarate [RNA-seq_NIT2-GLS1-KO]

overall_design: RNA-seq of human umbilical vein endothelial cells after knockout of NIT2 or GLS1, compared to non-targeting control.


title: Temporal RNA-seq atlas of breast muscle development in purebred and crossbred broilers

first: Qiang

last: Huang

address: No. 2 Yuanmingyuan West Road, Haidian District, Beijing

institute: China Agricultural University

summary: A total of 460.76 Gb of high-quality bulk RNA-Seq data were generated from six biological replicates per group at each time point. This dataset can be used to study molecular networks during muscle development, and serves as a reference model for comparative analyses of growth heterosis in animals.

overall_design: We sequenced 72 breast muscle samples collected at embryonic day 17 and post-hatching days 1, 21, and 42 across Cornish purebred, White Plymouth Rock purebred, and their crossbred progeny.

first: Huang

last: Qiang

first: Shuang

last: Gu

first: Yuchen

last: Jie

first: Ning

last: Yang

first: Chaoliang

last: Wen


title: BrainSTEM: A multi-resolution fetal brain atlas to assess the fidelity of human midbrain cultures

city: Singapore

first: John

middle: F

last: Ouyang

address: 8 College Road

country: Singapore

institute: Duke-NUS Medical School

summary: Midbrain dopaminergic neuron (mDA) differentiation protocols for Parkinson's disease (PD) modeling and cell replacement therapy lack comprehensive transcriptomic evaluations against in vivo references. To address this, we constructed an integrated human fetal whole brain atlas and a midbrain subatlas to use as standards of comparison. From the whole brain atlas, we observed distinct brain-region-specific gene expression in most neural cell types, emphasizing the need to first evaluate protocols at the whole brain level to identify midbrain cells. These cells are then mapped to the midbrain subatlas for more refined neuronal subtype annotation. Using this biologically-driven multi-resolution mapping strategy which we termed BrainSTEM (Brain Single-cell Two tiEr Mapping), we extensively surveyed publicly available single-cell datasets of human midbrain culture models. We confirmed the presence of multiple midbrain cell types (‘on-target’), but also a substantial proportion of cells associated with non-midbrain regions (‘off-target’). This leads to an overall 'inflation' of mDA presence across all published protocols. BrainSTEM offers a systematic and unbiased framework for understanding the current state of midbrain models, providing a foundation for guiding future improvement of midbrain differentiation protocols for PD studies.

overall_design: Single-cell time course RNA seq of midbrain organoids, from day 20 to day 60 in culture.

first: Hilary

last: Toh

first: Lisheng

last: Xu

first: Alfred

middle: X

last: Sun


title: CRISPRi Screening of Enhancers in Human Primary Astrocytes Identifies Regulatory Circuitry Disrupted in Alzheimer’s Disease

city: Kensington

first: Irina

last: Voineagu

state: NSW

address: High St

department: Biotechnology and Biomolecular Sciences

country: Australia

institute: The University of New South Wales

summary: We used CROP-seq to perform a high-throughput, parallel screen of 979 candidate enhancer perturbations in normal human astrocytes (NHAs), a primary cell-line. We identified the target gene(s) for 145 of these candidates, which were enriched for transcription with eRNA, transcription factor footprinting, and superenhancer annotation. Most regulatory interactions were <50kb, targeting the nearest gene in ~50% of cases, but were not typically captured by eQTL or in silico predictions. These data elucidate the regulatory network of an understudied-but-crucial brain cell-type.

overall_design: To identify regions of open chromatin, ATAC-seq was performed on Normal Human Astrocytes (NHA; Lonza) stably expressing dCas9-KRAB-Blast

first: Nicole

middle: O

last: Green

first: Gavin

middle: J

last: Sutton

first: Samuel

last: Bagot

first: Hannah

last: Danon

first: Juli

last: Wang

first: Akira

last: Gokool

first: Samantha

last: Miles

first: Charles

last: Herring

first: Hamid

last: Alinejad-Rokny

first: Ryan

last: Lister

first: Joseph

last: Rosenbluh

first: Johann

last: Gagnon Bartsch


title: CRISPRi Screening of Enhancers in Human Primary Astrocytes Identifies Regulatory Circuitry Disrupted in Alzheimer’s Disease [RNA-seq]

overall_design:
To investigate basal gene and eRNA expression, RNA sequencing was performed on Normal Human Astrocytes (NHA; Lonza) stably expressing dCas9-KRAB-Blast
Three distinct libraries were prepared; mRNA-seq (to compare to scRNA-seq), ribo-depleted RNA-seq (to compare to TT-seq), and ribo-depleted RNA-seq of transient transcriptome sequencing (TT-seq) samples.
Please note that the 'TTseq_RiboDep.csv' contains processed data for both 'ribo-depleted RNA-seq' and 'TT-seq' samples, and is linked to the 'ribo-depleted RNA-seq' sample records.


title: Spatial transcriptomic analysis of 53 pre-treatment biopsies from LARC patients using GeoMx technology

city: Geneva

first: MELIVOIA

last: RAPTI

address: Rue du Général-Dufour

department: Medicine

country: Switzerland

institute: University of Geneva

summary:
Locally Advanced Rectal cancer (LARC) is treated using neoadjuvant chemoradiotherapy (nCRT) followed by surgery. On average 15% of tumors at surgery will present a pathological complete response (pCR). Increasing pCR can be done at the cost of treatment intensification usually combining nCRT and chemotherapy which comes with higher toxicity. However, many LARC patients do not respond to the current neoadjuvant treatments while experiencing important treatment related side effects. Predicting pCR following nCRT opens the door to non-surgical management - the watch and wait strategy and avoid escalation as well as sparring non-responders from nCRT in patients not eligible for intensification. Using RNA expression data, several groups have defined predictive signatures, however, none have made it into clinical practice.
A comprehensive differential expression analysis was conducted across six Gene Expression Omnibus (GEO) datasets, followed by integration with four microarray datasets for refinement. A machine learning approach was employed to identify a 186-gene signature predictive of response to nCRT, validated using cross-validation. Gene set enrichment analysis (GSEA) was performed to explore biological pathways associated with treatment response. Spatial transcriptomic profiling of pre-treatment biopsies further examined gene expression in tumor and stroma compartments and identified eight compartment-specific genes significantly associated with response, with tumor-associated genes showing greater predictive value than stroma-associated genes.
This study identifies a novel 186-gene signature associated with nCRT response in LARC, with potential clinical utility in guiding personalized treatment. Further validation in larger cohorts and exploration of spatial biomarkers are needed to confirm its clinical relevance.

first: Petros

last: Tsantoulis

first: Thibaud

last: Koessler


title: Endothelial RNF20 Suppresses Endothelial-to-Mesenchymal Transition and Safeguards Physiological Angiocrine Signaling to Prevent Congenital Heart Disease [Bulk_polyA RNA-seq]

status: Public on Sep 24 2025

city: Mannheim

first: Gergana

last: Dobreva

state: Baden Württemberg

address: Ludolf-Krehl-Str. 7-11

department: Cardiovascular Genomics and Epigenomics

institute: Medical Faculty Mannheim/University of Heidelberg

summary: Heart development and function rely on intricate communication among distinct cardiac cell types. How their co-development and crosstalk are coordinated is largely unexplored. Our study unveils novel functions of the histone H2B ubiquitin (H2Bub1) ligase RNF20 in second heart field development and cardiac endothelial cells, essential for proper cardiac morphogenesis and function. We demonstrate that RNF20-H2Bub1-dependent reduction in Nrg1 expression, coupled with heightened TGF-β signaling due to RNF20's role in inducing RNA polymerase II pausing at TGF-β targets, drives increased endothelial-to-mesenchymal transition (EndMT), abnormal cardiomyocyte proliferation, and irregular contractility upon endothelial RNF20 loss. Importantly, RNF20 expression is significantly reduced in cardiac endothelial cells from congenital heart disease patients showing a positive correlation with oxygen saturation and a negative correlation with key components and downstream effectors of TGF-β signaling. In summary, our work identifies a novel role of RNF20 in controlling signaling inputs that safeguard physiological angiocrine signaling ensuring proper cardiac morphogenesis and function.

overall_design: RNA-seq profiling of Right ventricle of heart tissue from tetralogy of Fallot patients

first: Yonggang

last: Ren

first: Yu-wen

last: Chen

first: Julio

middle: D

last: Cordero Henriquez


title: Nucleosome context regulates chromatin reader preference

city: Durham

first: Michael-Christopher

last: Keogh

address: 6 Davis Dr

institute: EpiCypher, Inc

summary: Chromatin is more than a simple genome packaging system, and locally distinguished by histone post-translational modifications (PTMs) that can change nucleosome structure and / or be “read” by chromatin-associated proteins to mediate downstream events. An accurate understanding of histone PTM binding preference is vital to understanding chromatin function and disease development, and has led to the identification of multiple therapeutic targets. Such studies most often use histone peptides, even though this cannot explore the full regulatory potential of nucleosome context. Here we apply a range of complementary and easily adoptable biochemical and genomic approaches to interrogate fully defined peptide and nucleosome targets containing acyl, methyl, methyl analog and phospho PTMs with a diversity of mono- or multi- valent chromatin readers. Nucleosome context consistently refined reader binding, and was particularly informative when analyzing multivalent engagement. This included abrogating the binding of L3LBTL1 MBT to histone tails with lower methyl states (me1 or me2 at H3K4, H3K9, H3K27, H3K36 or H4K20); and demonstrating that specificity of the CBX7 chromodomain for H3K27me3 is enabled by an adjacent DNA-binding AT-hook like (ATL[MK1] ) motif. Further, the in vitro binding preferences of readers to nucleosomes was confirmed by in vivo reader-CUT&RUN genomic mapping. Such data confirms that interrogating with more representative substrates provides greater insight to chromatin reader capability and biological mechanism.

overall_design: CUT&RUN reactions performed in K562 cells.

first: Matthew

last: Marunde

first: Irina

middle: K

last: Popova

first: Nathan

last: Hall

first: Anup

last: Vaidya

first: James

last: Bone

first: Brandon

last: Boone

first: Peter

last: Brown

last: Ezell

first: Tessa

last: Firestone

first: Harrison

last: Fuchs

first: Elisa

last: Gibson

first: Zachary

middle: B

last: Gillespie

first: Susan

last: Gloor

first: Allison

last: Hickman

first: Sarah

last: Howard

first: Natalia

last: Husby

first: Victoria

last: Hsiung

first: Andrea

last: Johnstone

first: Laiba

last: Khan

first: Krzysztof

last: Krajewski

first: Alexander

last: Lee

first: Eileen

last: McAnarney

first: Keith

last: Maier

first: Danielle

middle: N

last: Maryanski

first: Jamie

last: McCuiston

first: Kelsey

last: Noll

first: Katherine

last: Novitzky

first: Emily

last: Patteson

first: Keli

last: Rodriguez

last: Sanchez

first: Luis

last: Schachner

first: Catherine

last: Smith


title: Discovery of Long-Acting APOC3 siRNA for Treating Patients with Hypertriglyceridemia

city: Carlsbad

first: Sagar

last: Damle

address: 2855 Gazelle Ct

institute: Ionis Pharmaceuticals

summary: Apolipoprotein C-III (APOC3) plays a crucial role in triglyceride metabolism, and its high expression leads to hypertriglyceridemia, a condition associated with an increased risk of cardiovascular disease and acute pancreatitis. However, loss-of-function variants in APOC3 are linked to lower triglyceride levels and reduced incidence of coronary artery diseases. APOC3 mRNA, primarily synthesized by hepatocytes, is an ideal target for GalNAc-conjugated small interference RNA (siRNA) mediated gene silencing. Our research takes a unique approach, conducting systematic structure-activity relationship (SAR) studies to identify a long-acting APOC3 siRNA with a minimal number of 2’-F nucleotides. We evaluated the use of 5’-vinylphosphonate (5’-VP), 5’-methylene phosphonate (5’-MP), FHNA, and methane sulphonyl phosphoramidite backbone chemistry in APOC3 siRNA design and employed deoxynucleotides or 2’-O-methyl  (OMe) to replace 2’-F residues. Additionally, we utilized 2’-O-methoxyethyl (MOE) nucleotides in conjunction with phosphorothioate modification to enhance metabolic stability. To ensure the preferential loading of the antisense strand, we strategically placed MOE nucleotides at specific sites in the antisense strand.  These efforts led to the identification of APOC3 siRNA containing a novel chemical scaffold with a long duration of action (DOA) and tolerability in rodents and nonhuman primates. A comparative analysis of preclinical and clinical data of plozasiran surrogate suggests that our APOC3 siRNA may provide clinical benefits with less frequent exposure (>6 months apart), which could significantly improve the treatment of patients with hypertriglyceridemia.

first: Thazha

last: Prakash

first: Adam

last: Mullick

middle: S

first: Eric

last: Swayze


title: Secreted β-helix protein YjbI controls bimodal antibiotic susceptibilities from an asymmetric surface disposition

city: Geneva 4

first: Patrick

middle: H.

last: Viollier

address: Rue Michel Servet 1

department: Dept.  Microbiology and Molecular Medicine

institute: University of Geneva, Faculty of Medicine / CMU

summary: While cytoplasmic pentapeptide repeat proteins (PRPs) protect DNA gyrase from cytotoxic quinolones, the function of secreted (s)PRPs remains unknown. We show that a YjbI-type sPRP regulates antibiotic sensitivity, bimodally for small or large molecules, from the Caulobacter crescentus outer membrane (OM). YjbI silences two converging envelope stress pathways that globally reprogram the OM proteome via TonB-dependent receptors (TBDRs), periplasmic proteases and AcrAB-NodT, a multidrug efflux pump whose induction by small molecules and antibiotics is lethal to yjbI mutant cells. Loss of YjbI also confers sensitivity to vancomycin and bacitracin, two large peptidoglycan-targeting and zinc-binding antibiotics that permeate the OM via the uncharacterized TBDR BugA and orthologs. Zinc stress triggers YjbI’s rapid proteolytic removal and transcriptionally activates BugA, other TBDRs, and (ultimately replenishes) YjbI. Molecular dynamics simulations and reactive thiol-probing imply an asymmetric surface disposition of YjbI, explaining the differential accessibility of its conserved cysteine pairs that flank the quadrilateral β-helix.

overall_design: Examination of HA-ChvI and HA-UzcR whole genome binding/occupancy (ChIP-Seq) in Caulobacter crescentus NA1000 (WT and yjbI::Tn mutant)

first: Jordan

last: Costafrolaz

first: Laurence

last: Degeorges

first: Gaël

last: Panis

first: Simon-Ulysse

last: Vallet

first: Manuel

last: Velasco Gomariz

first: Fernando

last: Teixeira Pinto Meireles

first: Matteo

last: Dal Peraro

first: Kathrin

last: Fröhlich

middle: H


title: Sexually dimorphic changes in liver and muscle transcriptome of 4-month-old dairy calves derived from artificial insemination or the transfer of a frozen-thawed in vitro produced embryo

city: Dublin

first: Laura

last: Thompson

address: Belfield

country: Ireland

institute: University College Dublin

summary: More than 1.2 million in vitro produced (IVP) bovine embryos are transferred annually worldwide, significantly outnumbering those from traditional superovulation, but there are limited reports on the birth and postnatal development of such calves. The conditions imposed during in vitro embryo culture may cause modifications of the embryo genome, including the transcriptome, potentially affecting postnatal organ function. This study compared the liver and muscle transcriptome in 4-month-old male and female dairy calves conceived by artificial insemination (AI) or IVP (n = 4 per sex per treatment). Biopsy tissue samples were collected and processed for RNA sequencing. Analysis of the RNAseq data revealed a distinct separation between the liver transcriptomes of female and male calves, regardless of method of production. Moreover, within the cohort of female calves, a strong separation between female calves derived from IVP vs AI was observed. Analysis of differentially expressed genes (DEGs) indicated downregulation of oxidative phosphorylation pathways and upregulation of pathways strongly enriching immune system processes, specifically Th17 cell differentiation and antigen processing and presentation. For the muscle transcriptome, the separation between male and female calves was less apparent compared with liver transcriptome, but there was still a clear separation between female calves derived from IVP vs AI, with downregulated genes enriching the p53 signalling pathway and upregulated genes enriching muscle structure development pathways. These results suggest that female embryos derived from IVP vs AI have developmental differences that manifest as differential transcriptomic profiles postnatally. In conclusion, these findings demonstrate that the IVP process induces significant alterations in the liver and muscle transcriptome of female postnatal calves. Further exploration is necessary to understand the potential implications for lifetime growth, health and production characteristics.

overall_design: Heifers were randomly assigned to one of the two groups; those receiving timed AI with frozen thawed semen (AI, n=8) and those transferred a single frozen-thawed Grade 1 Day 7 or Day 8 in vitro produced embryo (IVP, n=8). Resulting calves were divided into two groups based on their origin, AI (n=8; 4 male, 4 female) or IVP (n=8; 4 male, 4 female). Calves in both groups were raised in similar conditions up to 4 months of age, at which point biopsies were taken from the liver and muscle using a percutaneous punch technique. RNA extraction, quality control, library preparation, and sequencing was performed on the liver and muscle tissue samples. The subsequent read count files were employed to determine the differentially expressed genes (DEG) with the edgeR package for the R software and the gene expression counts were normalized by library size with edgeR methods. The DEG between groups were defined as those with false discovery rate (FDR) <0.05. The EntrezID corresponding to the DEG, was interrogated for enriched Gene Ontology and KEGG pathways using ShinyGO V0.77.

first: Alan

last: Crowe

first: Maria

last: Rabaglino

first: Stephen

last: Butler

first: Pat

last: Lonergan


title: Temporal dynamics of collateral RNA cleavage by LbuCas13a in human cells

city: Leiden

first: Niels

last: Geijsen

address: Einthovenweg 20

department: Anatomy and Embryology

country: Netherlands

institute: LUMC

summary: We have found that LbuCas13a exhibits collateral RNA cleavage activity in human cells after activation by the target RNA. Here we use total RNA sequencing to explore which RNAs are depleted by the collateral activity of LbuCas13a. ERCC spike-in RNAs were used for normalization between samples. This revealed near global depletion of mRNAs at 50 and 200 minutes after Cas13 protein and guide delivery. Mitochondrial and nuclear transcripts were not affected.

overall_design: Total RNA sequencing of HAP1-dEGFP cells with ERCC spike-in control RNAs. Cells were either left untreated, transfected with an empty iTOP transfection, transfected with LbuCas13a and a non-targeting gRNA by iTOP, or transfected with LbuCas13a and a dEGFP targeting gRNA by iTOP. Cells were harvested at 50, 200 and 1440 minutes after transfection.

first: Jorik

last: Bot

first: Zhihan

last: Zhao

first: Mengyuan

last: Li

first: Darnell

last: Kammeron

first: Peng

last: Shang


title: A multimodal cross-species comparison of pancreas development [scRNA-seq]

city: Neuherberg

first: Heiko

last: Lickert

address: Ingolstaedter Landstraße 1

department: Institute of Diabetes and Regeneration Research

institute: Helmholtz Zentrum München German Research Center for Environmental Health

summary: Human pancreas development remains incompletely characterized due to restricted sample access. We investigate whether pigs resemble humans in pancreas development, offering a complementary large-animal model. As pig pancreas organogenesis is unexplored, we first annotate developmental hallmarks throughout its 114-day gestation. Building on this, we construct a pig single-cell multiome pancreas atlas across all trimesters. Cross-species comparisons reveal pig closely resembles human in developmental tempo, epigenetic and transcriptional regulation, and gene regulatory networks. This further extends to progenitor dynamics and endocrine fate acquisition. Transcription factors regulated by NEUROG3, the endocrine master regulator, are over 50% conserved between pig and human, many being validated in human stem cell models. Notably, we uncover that during embryonic development, emerging beta-cell heterogeneity coincides with a species-conserved primed endocrine cell (PEC) population alongside NEUROG3-expressing cells. Overall, our work lays the foundation for comparative investigations and offers unprecedented insights into evolutionary-conserved pancreas organogenesis mechanisms across animal models.

overall_design: Pig pancreases from E22, 32, 40, 54, 63 and 85 were analyzed by scRNA-seq

first: Kaiyuan

last: Yang

first: Hannah

last: Spitzer

first: Michael

last: Sterr

first: Karin

last: Hrovatin

first: Sean

last: de la O

first: Xinghao

last: Zhang

first: Eunike

last: Setyono

first: Minhaz

last: Ud-Dean

first: Thomas

last: Walzthoeni

first: Krzysztof

last: Flisikowski

first: Tatiana

last: Flisikowska

first: Angelika

last: Schnieke

first: Katharina

last: Scheibner

first: James

middle: M

last: Wells

first: Julie

last: Sneddon

first: Barbara

last: Kessler

first: Eckhard

last: Wolf

first: Elisabeth

last: Kemter

first: Fabian

last: Theis


title: MnSOD non-acetylation mimic knock-in mice exhibit dilated cardiomyopathy

city: San Antonio

first: Joseph

last: Schell

state: TX

address: 4939 Charles Katz

institute: UT Health San Antonio

summary: Manganese superoxide dismutase (MnSOD/SOD2) is an essential mitochondrial enzyme that detoxifies superoxide radicals generated during oxidative respiration. MnSOD/SOD2 lysine 68 acetylation (K68-Ac) is an important post-translational modification (PTM) that regulates enzymatic activity, responding to nutrient status or oxidative stress, and elevated levels have been associated with human illness. To determine the in vivo role of MnSOD-K68 in the heart, we used a whole-body non-acetylation mimic mutant (MnSODK68R) knock-in mouse. These mice exhibited several cardiovascular phenotypes, including lower blood pressure, decreased ejection fraction, and importantly, dilated cardiomyopathy, as evidenced by echocardiography at four months of age. In addition, both mouse embryo fibroblasts (MEFs) and myocytes from MnSODK68R/K68R mice exhibited an increase in cellular senescence. Finally, MnSODK68R/K68R mouse hearts also showed an increase in lipid peroxidation. We conclude that constitutively active MnSOD detoxification activity, lacking the normal switch between non-acetylated and acetylated forms, dysregulates mitochondrial physiology during development, leading to dilated cardiomyopathy.

overall_design: Mouse embryonic fibroblasts were isolated from WT and mutant SOD2K68R mice with a C57BL/6 background. The SOD2K68R mutation was generated via CRISPR. The MEFs were cultured briefly and then RNA was extracted for sequencing using standard protocols.

first: Sung-Jen

last: Wei

first: Zhao

last: Lai

first: David

last: Gius


title: A multimodal cross-species comparison of pancreas development [multiome]

first: Heiko

last: Lickert

first: Kaiyuan

last: Yang

first: Hannah

last: Spitzer

first: Michael

last: Sterr

first: Karin

last: Hrovatin

first: Sean

last: de la O

first: Xinghao

last: Zhang

first: Eunike

last: Setyono


title: Investigations into the basal neural-like properties of dental pulp stem cells reveals they possess a functional type 2 muscarinic receptor which regulates quiescence

city: Sakaka

first: Saeed

last: Alqahtani

country: Saudi Arabia

institute: Jouf University-College of Dentistry

summary: Dental pulp stem cells (DPSCs) are a population of mesenchyme-derived cells residing within the dental pulp known for their multipotent differentiation potential and neural-like properties. While a functional cholinergic system has been described in various mesenchymal stem cell (MSC) populations, its presence and role in DPSCs remain unexplored. This study investigated the neurotransmitter-associated gene expression profile of human DPSCs using a targeted array panel and immunocytochemistry. The functionality of acetylcholine receptors (AChRs) was assessed through pharmacological activation and inhibition using receptor-specific agonists and antagonists. Cellular responses to cholinergic modulation, including effects on viability and proliferation, were evaluated via LDH release, CCK-8, and annexin V/PI staining assays. Among the 92 neurotransmitter-associated genes profiled, 43 were expressed, including multiple muscarinic receptors and nicotinic receptor subunits. Protein level expression of the m2, m3, and m5 muscarinic receptors was confirmed. Furthermore, activation of the m2AChR, using arecaidine propargyl ester hydrobromide (APE), led to a reversible reduction in DPSC proliferation without compromising cell viability. The findings demonstrate that DPSCs exhibit cholinoceptive properties and identify the m2AChR as a key modulator of cell cycle arrest. This receptor may serve as a therapeutic target for regulating DPSC behaviour and maintaining stem cell quiescence in regenerative applications.

overall_design: RNA-Seq profiling of untreated DPSCs and DPSCs stiumulatied with 100 μM arecaidine propargyl ester hydrobromide (APE) for 4 and 24 hours.

first: Christopher

last: Nile


title: Induction of CDX2 as a differentiation therapy in colorectal cancers

city: La Jolla, CA 92093

first: Pradipta

last: Ghosh

address: 9500 Gilman Drive (MC 0651)

department: Departments of Medicine and Cellular and Molecular Medicine

institute: University of California San Diego


title: Th1 effector CD4 T cells rely on IFN-g production to induce Alopecia areata

status: Public on Sep 23 2025

city: Iowa City

first: Ali

last: Jabbari

state: IA

address: 25 South Grand Ave

department: Dermatology

institute: University of Iowa

summary: Alopecia areata (AA) is an autoimmune disease that is characterized by hair loss clinically and peribulbar infiltration of CD8 and CD4 T cells histologically. Prior studies have focused on the role of CD8 T cells in the development of AA; however, the role of CD4 T cells is unclear. Here, we demonstrate that CD4 T cells from the skin draining lymph nodes (SDLN) of AA mice could transfer disease into recipient mice. Further, these cells exhibited a T-helper type 1 (Th1) effector transcriptional and phenotypic profile. Pathogenic activity of these CD4 T cells was dependent upon the presence of endogenous CD8 T cells and host IFN-g signaling. Targeted removal of CD4 T cell-mediated production of IFN-g abrogated the ability of this cell population to transfer disease. Together, our study provides mechanistic insights into pathways that lead to AA development, heightening our understanding of the disease and inviting studies into exploring novel therapeutic strategies for human patients.

overall_design: RNA-seq profiling of live TCRβ+CD4+ T cells that were sorted (Becton Dickinson FACS Aria Fusion) from skin draining lymph nodes (SDLNs) of unaffected (UA) and alopeica areata (AA) affected C3H/HeJ mice.

first: Sam

last: Connell

first: Ryan

last: Reis


title: A C1qTNF3 collagen domain fusion chaperones diverse secreted proteins and anti-Ab scFvs: Applications for gene therapies

city: Atlanta

first: Karen

last: McFarland

state: GA

address: 100 Woodruff Circle

department: Pharmacology

institute: Emory University

summary: Enhancing production of protein cargoes delivered by gene therapies can improve efficacy by reducing the amount of vector or simply increasing transgene expression levels. We explored the utility of a 126-amino acid collagen domain (CD) derived from the C1qTNF3 protein as a fusion partner to chaperone secreted proteins, extracellular "decoy receptor" domains, and single-chain variable fragments (scFvs). Fusions to the CD domain result in multimerization and enhanced levels of secretion of numerous fusion proteins while maintaining functionality. Efficient creation of bifunctional proteins using the CD domain is also demonstrated. Recombinant adeno-associated viral vector delivery of the CD with a signal peptide resulted in high-level expression with minimal biological impact as assessed by whole-brain transcriptomics. As a proof-of-concept in vivo study, we evaluated three different anti-amyloid Aβ scFvs (anti-Aβ scFvs), alone or expressed as CD fusions, following viral delivery to neonatal CRND8 mice. The CD fusion increased half-life, expression levels, and improved efficacy for amyloid lowering of a weaker binding anti-Aβ scFv. These studies validate the potential utility of this small CD as a fusion partner for secretory cargoes delivered by gene therapy and demonstrate that it is feasible to use this CD fusion to create biotherapeutic molecules with enhanced avidity or bifunctionality.

overall_design: Gene expression profiling of RNA from somatic transgenic mouse brains expressing a collagen domain transgene or controls.

first: Brenda

last: Moore

first: Todd

last: Golde


title: Injury-Induced Connexin 43 Expression Regulates Endothelial Wound Healing

city: Roanoke

first: Mark

middle: Colin

last: Renton

state: VA

address: 4 Riverside Circle, Room 2208

department: Fralin Biomedical Research Institute

institute: Virginia Tech

summary: Endothelial cell (EC) injury is a major contributing factor to vascular surgical failure. As such, understanding the mechanisms of endothelial healing is essential to the development of vascular therapeutics and procedures. Gap junctions formed by connexin 43 (Cx43) are implicated in regulating skin wound healing, but their role in endothelial healing is unknown. Secondary analysis of RNAseq data from in vivo injured mouse aortas (GEO: GSE115618), identified significant Cx43 upregulation in EC post-injury. We developed a novel in vivo model of EC injury using mouse carotid artery ligation to test the role of Cx43. We identified that EC immediately adjacent to the wound edge upregulate Cx43 protein expression, predominantly at cell-cell junctions. We show significantly delayed EC healing in a mouse model of inducible EC-specific Cx43 deletion (EC-Cx43 KO) at 24 hr post ligation. Single cell RNAseq analysis of 10,829 cells from 18 hr injured EC-WT and EC-Cx43 KO carotids revealed a Cx43-associated reduction in enrichment of EC pathways associated with migration, proliferation, and ERK/MAPK signaling pathways. Finally, the importance of Cx43 phosphorylation on EC healing was tested in mice with single-point alanine mutations (phospho-null) in known phosphorylation sites that alter Cx43 channel assembly and opening. Mice containing alanine mutations at ERK phosphorylated Cx43 serines (Cx43S255/262/279/282A) reduces healing rates similar to EC-Cx43 KO. These data suggest that EC injury-induced Cx43 upregulation, and subsequent Cx43 gap junction-mediated cell-to-cell communication are required for normal EC migration during wound healing after vascular injury.

overall_design: scRNAseq analysis of mouse carotid arteries harvested 18hrs after temporary ligation-induced endothelial injury. One sample is from mice with an inducible endothelial-specific coonexin knockout mouse and the second sample is from a control mouse. Carotids were enzymatically digested to generate a single cell suspension, frozen in 10% DMSO, then submitted for sequencing.

first: Meghan

middle: W

last: Sedovy

middle: C

first: Kailynn

last: Roberts

first: Xinyan

last: Leng

first: Clare

middle: L

last: Dennison

first: Caroline

last: Toler

first: Melissa

last: Leaf

first: Paul

last: Lampe

first: Angela

last: Best

first: Brant

last: Isakson

first: Scott

last: Johnstone


title: Kinetic measurement of gene-specific RNAPII transcription elongation rates

city: Copenhagen

first: Haiyue

last: Liu

address: Blegdamsvej 3B

department: Department of Cellular and Molecular Medicine

country: Denmark

institute: University of Copenhagen

summary: Transcription is regulated at multiple levels, including initiation, elongation, and termination.  Whereas much research has focused on initiation of transcription, regulation of elongation plays an important role not only for transcription dynamics, but also for co-transcriptional RNA processing as the RNAPII elongation rate can influence maturation of the nascent RNA transcript. Despite advances in high-throughput approaches for global identification of RNAPII speed, RNAPII elongation rate studies have been largely limited to a small number of genes. Here, we present DRB/TTchem-seq2, a modified version of DRB/TTchem-seq method, to measure gene-specific elongation rates of more than 3,000 genes. By approximating the distance traveled by RNAPII in certain time intervals using the wave fronts post RNAPII release. Our direct RNAPII elongation rate quantification reveals that elongation rates vary not only among genes but also within genes. Additionally, specific histone modifications and elongation factors are tightly correlated with the elongation rates. Together, we present a robust and powerful method for RNAPII transcription elongation rate measurement.

overall_design: Nascent transcripts following RNA Pol II (RNAPII) stalling and released from promoter-proximal pausing were captured and subsequently sequenced in four different time points (i.e., 5, 10, 15 and 20 minutes) in both U2OS and DLD-1 cells. RNAPII elongation rates were estimated based on the distances traveled by RNAPII in certain time periods for both U2OS and DLD-1 cells.

first: Lea

last: Gregersen


title: Transcriptome analysis of Pseudomonas syringae pv. tomato DAPP-PG 215 in response to silver nanoparticles exposure

city: Perugia

first: Benedetta

last: Orfei

address: Borgo XX Giugno 74

country: Italy

institute: University of Perugia

summary: Silver nanoparticles (AgNPs) are one of the most promising options for the control of bacterial pathogens. The effectiveness of AgNPs has been proven by several recent research studies in which toxicity against a broad range of human and plant pathogenic bacteria was observed, even when used at low doses compared to other conventional bactericides. Nevertheless, the antibacterial mechanism of AgNPs is yet to be completely understood. This study investiagted the first response of Pseudomonas syringae pv. tomato strain DAPP-PG 215, the causative agent of bacterial speck disease of tomato, to AgNPs. Gene expression of P. syringae pv. tomato in response to AgNPs was observed after 10 and 30 minutes of exposure. A total of 78 and 66 genes were identified as differentially expressed, respectively. Gene ontology and KEGG pathway enrichment analysis revealed a high representation of genes related to stress resistance, energy metabolism, and metal ion binding proteins, with different transporters involved. Validation of four selected genes by quantitative RT-PCR analysis, confirmed these observations. These results not only supported initial findings on the antimicrobial action of AgNPs, but also suggested a significant impact of different heavy metal – toxin transporters in the silver detoxification mechanism of bacteria.

overall_design: Transcriptomic response of Pseudomonas syringae pv. tomato strain DAPP-PG 215 to sub-lethal silver nanoparticles (AgNPs) exposure (0.125 ppm) at 10 and 30 minutes

first: Joël

last: Pothier

first: Luca

last: Scotti

first: Antonio

last: Aceto

first: Chiaraluce

last: Moretti

first: Roberto

last: Buonaurio

first: Theo

last: Smits


title: Induction of CDX2 as a differentiation therapy in colorectal cancers [cell lines]

first: Pradipta

last: Ghosh

summary:
Background: Lack of expression of the transcription factor CDX2 identifies a subset of poorly differentiated colorectal cancers (CRCs) that are associated with lower overall (OS) and disease-free (DFS) survival, independent of ethnicity, MSI status, or stage. CDX2 expression lowers risk of death and disease recurrence by ~50%. Induction of CDX2 as a therapeutic strategy is yet to be implemented in clinical practice.
Methods: We used a novel network-based computational model to identify and prioritize therapeutic targets that can robustly augment CDX2 expression and, consequently, differentiation. The top candidate with available clinical-grade pharmacophore was tested for efficacy in 3 models: CRC lines in vitro, xenografts in mice, and in prospective cohorts of CRC patient-derived organoids (PDOs; n = 23).
Results:  Our network-derived gene clusters reliably classified healthy and CRC tissues in diverse publicly available gene expression datasets (>10,000 human and >250 mouse samples). The target showed potent anti-cancer activity, induced crypt differentiation signatures in all models tested, and shifted the network in predictable ways. Effective pairing of therapy (IC50 of the target) and CDX2 expression (companion biomarker) was confirmed in an independent cohort of CRC PDOs. A multivariate analysis revealed KRAS mutation and high-CDX2 as key determinants of resistance to the target.
Conclusions: Induction of CDX2 expression by the target augments differentiation and shows potent anti-cancer effect on CRCs that lack CDX2 expression. This benefit of drug-biomarker pairing should be considered for confirmatory studies in randomized clinical trials.

overall_design: Two colorectal cancer cell lines  representing the colorectal cancer were used in  this study. Standard cell biological, functional and phenotypic assays were used to assess the prodifferantiation and anticancer actions of the PF compound : 1) prodifferantiation induction, 2) cytotoxicity assay  3)apoptosis, 4) invivo anticancer effect, 4) RNA sequencing

first: Saptarshi

last: Sinha


title: A multimodal cross-species comparison of pancreas development

first: Heiko

last: Lickert

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

overall_design: Refer to individual Series


title: Extracellular Vesicle miRNAs as Biomarkers of Asthma Severity

city: Kansas City

first: Isaac Kirubakaran

last: Sundar

state: KS

address: University of Kansas Medical Center, Dept. of Internal Medicine/Pulmonary Critical Care and Sleep Medicine

department: Internal Medicine

institute: University of Kansas Medical Center

type: Non-coding RNA profiling by high throughput sequencing

summary: Asthma is a chronic lung disease with various clinical phenotypes, complicating its diagnosis and treatment. The micro-RNA (miRNA) profile of plasma-derived extracellular vesicles (EVs) may serve as potential circulating biomarkers for differentiating asthma phenotypes/endotypes. This study aims to characterize and compare the miRNA profiles in plasma-derived EVs across healthy controls (HC), non-severe asthmatics (NS), and severe asthmatics (SA). EVs were isolated from plasma samples of HC, NS, and SA, followed by physiochemical characterization and RNA isolation. Small RNA sequencing was performed, and differentially expressed (DE) miRNAs were identified through DESeq2 analysis. DE miRNAs and their predicted mRNA targets were identified using Ingenuity Pathway Analysis (IPA), and pathway enrichment was conducted using STRING DB and Enrichr. EVs from all groups were predominantly ~150-200 nm in size, with significantly higher EV counts in SA compared to HC and NS. miRNA expression analysis revealed unique and shared DE miRNAs across the three comparisons (HC vs. NS; HC vs. SA; NS vs. SA). A total of 16 unique DE miRNAs among these comparisons, between which in the NS vs. SA comparison, miR-515-3p positively correlates with lung function, and exacerbation and miR-133a-3p and miR-9-5p with ACT score. Target and pathway analyses from the NS vs. SA comparison indicated the enrichment of key pathways, including IL-4/IL-13, Th1, Th2, and Th17 cell differentiation, MAPK, PI3K-Akt, and receptor tyrosine kinase signaling. This study identified distinct miRNAs in plasma-derived EVs from NS vs. SA which could serve as potential circulating biomarkers for differentiating asthma severity.

first: Sundar

last: Isaac Kirubakaran

first: Pei

last: Dong

first: Griffard

last: Rachel

first: Prasad

last: Chandrashekar


title: E. coli are poised to grow using 5’-deoxynucleosides via MtnR and CRP regulation of DHAP shunt gene expression

city: Columbus

first: Justin

last: North

address: 484 W 12th Ave

department: Department of Microbiology

institute: Ohio State University

summary: The dihydroxyacetone phosphate (DHAP) shunt is a multifunctional pathway for the metabolism of 5’-deoxynucleosides and 5-deoxypentose sugars, such as 5’-methylthioadenosine (MTA) and 5’-deoxyadenosine (5dAdo), into DHAP and an aldehyde species depending on the substrate. Previous work revealed that E. coli strains with the DHAP shunt can utilize exogenous MTA, 5dAdo, and derivatives thereof as sole carbon and energy sources for growth. However, if and how the DHAP shunt was regulated for 5-deoxynucleoside and 5-deoxypentose sugar metabolism remained unknown. In the present work, the DHAP shunt genes (mtnK, mtnA, ald2) and a putative transporter gene of E. coli ATCC 25922 are observed to form an operon, which can be expressed from two separate transcription start sites (TSSs). The distal, low-activity TSS appears to be constitutive, while the proximal primary TSS is regulated based on the identity of available growth substrates by at least two transcriptional regulators. First YjhU, a DeoR family regulator previously of unknown function that we designate as MtnR, functions as a repressor of the DHAP shunt operon when DHAP shunt substrates are absent. Further, the cyclic AMP receptor protein (CRP) imposes carbon catabolite repression while glucose is available. Based on comparative sequence analysis, the E. coli DHAP shunt promoter region is highly conserved, including strains of the globally disseminated ST131 lineage of Extraintestinal Pathogenic E. coli, indicating a similar regulatory paradigm. Thus the E. coli DHAP shunt is a previously unrecognized pathway for use of 5-deoxynucleosides and 5-deoxypentose sugars as alternative carbon sources when glucose is scarce.

overall_design: RNA-Seq analysis of wild-type E. coli versus DmtnR strains

first: Katherine

middle: A

last: Huening

first: Caitlin

last: Wingerd

first: Joshua

middle: T

last: Groves

first: Katelyn

last: Kapusta

first: Laiba

last: Khan

first: Robert

last: Tabita


title: Induction of CDX2 as a differentiation therapy in colorectal cancers [CRC organoids]

overall_design: Eleven patient derived organoids representing the colorectal cancer were used in  this study. Standard cell biological, functional and phenotypic assays were used to assess the prodifferantiation and anticancer actions of the PF compound : 1) prodifferantiation induction, 2) cytotoxicity assay, 3)qPCRt , 4) RNA sequencing


title: Induction of CDX2 as a differentiation therapy in colorectal cancers [xenograft]

overall_design: CRC xenograft nude mice model representing the colorectal cancer was used in  this study. Standard cell biological, functional and phenotypic assays were used to assess the prodifferantiation and anticancer actions of the PF compound : 1) prodifferantiation induction, 2) cytotoxicity through calculating the tumor volume


title: Spatial transcriptomics reveals the cellular neighborhood of erythropoietin-producing cells in the mouse kidney

status: Public on Sep 22 2025

city: Zürich

first: Olga

middle: Maria

last: Lempke

address: Winterthurerstrasse 190

institute: Univeristy of Zurich

summary: The main source of circulating erythropoietin (Epo) in the adult are kidney Norn cells. To shed new lights on the mechanisms governing Epo production, we combined spatial transcriptomics, mRNA-FISH and sequential immunofluorescence, enabling the identification of the direct neighborhood of active REP cells. While in the hypoxic mouse kidney REP cells are closest to proximal tubule (PT) segments (S) S1 to S2/3 and endothelial cells, Epo is re-induced by HIF-stabilizers in damaged kidneys in REP cells in the vicinity of injured PT (but normal endothelial) cells.

overall_design: All tissues analyzed in this work were derived from re-used frozen kidneys originally reported by Dahl et al. Acta Physiol. (Oxf.) 234, e13768. Hypoxic stimulation by exposure to 0.1% CO for 4 hours, unilateral ureteral obstruction (UUO) for 7 days, and the treatment with FG-4592/roxadustat for 90 minutes were described therein.

first: Olga M.

first: Thomas

last: Knöpfel

first: Stellor Nlandu

last: Khodo

first: Roland H.

last: Wenger


title: Comparative gene expression profiling of RNA-seq data from islets of β-cell-specific ZZEF1 knockout mice (βZKO-Mip) and their littermate controls, treated with either azoramide or DMSO.

city: shanghai

first: jingminjie

state: CN

address: shanghai

institute: Ruijin Hospital

summary: To investigate the global molecular mechanisms underlying the phenotype induced by ZZEF1 loss in pancreatic β-cells and subsequent treatment with azoramide, we isolated pancreatic islets from β-cell-specific ZZEF1 knockout mice (βZKO-Mip) and their littermate controls. Both groups were fed a HFD for four weeks and treated with either azoramide (10 µM) or DMSO (10 µM) for 24 hours.

overall_design: We then conducted gene expression profiling using RNA-seq data from pancreatic islets isolated from β-cell-specific ZZEF1 knockout mice (βZKO-Mip) and their littermate controls. Both groups were fed a HFD for four weeks and , treated with either azoramide (10 µM) or DMSO (10 µM) for 24 hours. For each islet sample, no fewer than three mice with the same genotype were used.

first: Yanan

last: Cao

first: Jingminjie


title: Single-cell gene expression profiles of pancreatic islets from two β-cell specific knockout mouse models (βZKO-Mip and βZKO-Rip), along with RIP-Cre and MIP-Cre mice, were analyzed after being fed a high-fat diet (HFD).

summary: The islet is composed of diverse cell types that work together to regulate its endocrine function. To investigate this, we performed comparative single-cell RNA sequencing (scRNA-seq) on islets from 16-week-old βZKO-Mip, βZKO-Rip, RIP-Cre, and MIP-Cre mice, all of which were fed a high-fat diet (HFD) from 12 to 16 weeks. Sequencing was carried out using the Chromium Next GEM Single Cell 3' Reagent Kits. Each islet sample was derived from at least three mice with the same genotype.

overall_design: Briefly, two β-cell-specific knockout mouse models (βZKO-Mip and βZKO-Rip) were generated by crossing C57BL/6N mice carrying floxed exon 15 (Zzef1f/f) with MIP-Cre or RIP-Cre mice. Each islet sample was derived from at least three mice with the same genotype. The purified islets were then treated with 2 mL of 0.05% TryLE at 37°C for 4 minutes, followed by gentle pipetting (~20 times). The resulting cell suspension was stained with 0.4% trypan blue to assess cell viability under a microscope. Cells with viability greater than 85% were sorted and used for 3’ digital gene expression profiling, with approximately 10,000 individual cells per sample, using the 10x Chromium Single-Cell 3’ Reagent Kit (10x Genomics, USA) according to the manufacturer’s instructions.


title: RNAseq analysis of cytokine-treated human neutrophils

city: Liverpool

first: Helen

middle: Louise

last: Wright

address: 6 West Derby Street

department: Institute of Life Course and Medical Sciences

country: United Kingdom

institute: University of Liverpool

summary: We report gene expression profiles of blood neutrophils from healthy individuals treated with cytokines G-CSF, GM-CSF, IFNalpha, IFNgamma, IL-1beta, IL-8, TNFalpha or untreated for 1h in vitro.

overall_design: Neutrophils (purity >97%) were isolated from peripheral blood by centrifugation through density-gradient reagent (Polymorphprep). RNA was isolated using Trizol:chloroform, cleaned up by Qiagen RNeasy kit including on-column DNase digest and sequenced on the Illumina HiSeq 2000 platform.

first: Huw

last: Thomas

first: Steven

last: Edwards


title: Perturb-seq (CRISPR-based screens with single-cell RNA-sequencing readouts) screens Endoc-betaH1 cell line targeting 61 T2D coding variants genes and 40 RQC function genes.

summary: Two set of genes were selected for Perturb-seq experiments. sgRNAs targeting each gene were selected according to previously published algorithm and cloned into the lentivirus construct containing sgRNA cassette available for 3’ direct capture Perturb-seq: hU6-gRNA with CR1CS1-EF1α-BFP.

overall_design: 1) Lentiviral production.HEK293T cells were transfected with lentiviral backbone encoding CRISPRi effector or sgRNA library and two other helper plasmids (psPAX2 and pMD2.G). Forty-eight hours later, viral supernatant was harvested and filtered through a 0.45 μm cellulose acetate filter and frozen at -80°C prior to transduction.2) 3’ direct-capture Perturb-seq.EndoC-βH1 cells were infected with lentivirus expressing Zim3 KRAB-dCas9-NLS-P2A-EGFP supplemented with 5 μg/mL polybrene. GFP+ cells were sorted for generating CRISPRi cell line. Then, CRISPRi EndoC-βH1 cells were transduced with a low multiplicity of infection (MOI) of lentivirus containing sgRNA library cassette in order that less than 20% of the cells were BFP+ to ensure the majority cells received only one lentivirus per cell. At 14 days post transduction, the treated cells were sorted using fluorescence activated cell sorting (FACS) and processed according to 10x Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 User Guide with Feature Barcode technology for CRISPR Screening.