title: Targeted protein evolution in the gut microbiome by diversity-generating retroelements

city: Los Angeles

first: Benjamin

last: Macadangdang

state: CA

address: 10833 Le Conte Ave, MDCC B2-375

institute: University of California, Los Angeles

summary: Diversity-generating retroelements (DGRs) accelerate evolution by rapidly diversifying variable proteins. The human gastrointestinal microbiota harbors the greatest density of DGRs known in nature, suggesting they play adaptive roles in this environment. We identified >1,100 unique DGRs among human-associated Bacteroides species and discovered a subset that diversify adhesive components of Type V pili and related proteins. We show that Bacteroides DGRs are horizontally transferred across species, that some are highly active while others are tightly controlled, and that they preferentially alter the functional characteristics of ligand-binding residues on adhesive organelles. Specific variable protein sequences are enriched when Bacteroides strains compete with other commensal bacteria in gnotobiotic mice. Analysis of >2,700 DGRs from diverse phyla in mother-infant pairs shows that Bacteroides DGRs are preferentially transferred to vaginally delivered infants where they actively diversify. Our observations provide a foundation for understanding the roles of stochastic, targeted genome plasticity in shaping host-associated microbial communities.

sample_organism:
Bacteroides thetaiotaomicron VPI-5482
Bacteroides ovatus ATCC 8483
Bacteroides uniformis ATCC 8492
Bacteroides fragilis 638R
Bacteroides finegoldii CL09T03C10

overall_design: To investigate if Bacteroides DGR activity is controlled at the transcriptional level, we grew five strains of Bacteroides in culture that each had varying levels of DGR activity for 24 hours for gene expression profiling.

first: Umesh

last: Ahuja

first: Bennett

last: Shaw

first: Jeff

last: Miller


title: Targeting De Novo Cholesterol Synthesis as a Therapeutic Strategy in Rhabdomyosarcoma

status: Public on Oct 10 2025

city: Helsinki

first: Nebeyu

middle: Yosef

last: Gizaw

state: Helsinki

address: Haartmaninkatu

department: Biomedicine

country: Finland

institute: University of Helsinki

type: Expression profiling by high throughput sequencing

summary: Rhabdomyosarcoma (RMS) is the most common soft tissue sarcoma in children, but outcomes for high-risk patients remain dismal, underscoring the critical need for novel therapeutic strategies. Our study demonstrates that RMS exhibits elevated de novo cholesterol biosynthesis. Silencing key cholesterol biosynthesis genes, such as DHCR7, disrupts cell cycle progression by inducing G2/M phase arrest. Additionally, inhibiting this pathway triggers endoplasmic reticulum (ER) stress, activates the unfolded protein response (UPR), and leads to apoptosis. These findings emphasize the essential role of de novo cholesterol synthesis in RMS and highlight a novel therapeutic strategy that targets this metabolic pathway to suppress tumor growth and promote apoptosis.

overall_design: To investigate the role of cholesterol biosynthesis in RMS tumorigenesis, we established an RD cell line with DHCR7 knockdown using shRNA. We then perform RNA sequencing (RNA-seq) analysis of four biological replicates of DHCR7 silenced (75% deletion) and control RD cells.

middle: Y

first: Riikka

last: Kivelä


title: Next Generation Sequencing analysis of the global expression profiling in bone marrow-derived macrophages (BMDMs) from wild-type and RBP4-deficient mice.

city: Taian

first: Yingli

last: Shang

state: Shandong

address: No. 61, Daizong Street

country: China

institute: Shandong Agricultural University

summary: To investigate the influence of retinol-binding protein 4 (RBP4) deficiency on the expression of genes related to cholesterol metabolism, we examined the expression profiling of global genes in BMDMs from wild-type(WT) and RBP4-deficient mice (RBP4-KO) by RNA-seq. The results revealed that expression of 71 genes were greater than twofold in RBP4-KO BMDMs relative to their expression levels in WT cells.In addition, the expression of 158 genes were lower than in RBP4-KO BMDMs compared to that of WT cells. Clustering analysis suggested that deficiency of RBP4 suppressed the expression of a subset of cholesterol uptake-associated genes without affecting the expression of genes related to cholesterol synthesis or efflux, indicating that RBP4 is likely involved in regulating cholesterol homeostasis.

overall_design: mRNA profiles of BMDMs from WT and RBP4-deficient mice.

first: Hejiao

last: Zhao


title: Patterns of hypermutation shape gliomagenesis and immunotherapy response in mismatch repair deficient glioma

status: Public on Oct 09 2025

city: Toronto

first: Uri

last: Tabori

state: Ontario

address: 170 Elizabeth St

department: Haematology/Oncology

country: Canada

institute: Sick Kids

type: Methylation profiling by genome tiling array

summary: Primary mismatch-repair deficient (priMMRD) gliomas are lethal tumours characterized by hypermutation, resistance to chemoradiation, and variable response to immunotherapy.To investigate the mechanisms governing the emergence of driver mutations and their impact on gliomagenesis and outcome, we analyzed genomic and clinical data of 162 priMMRD gliomas. We identified three subgroups defined by secondary driver mutations in replicative DNA polymerases or IDH1. These subgroups converge on glioma drivers through distinct combinations of genomic instability-generating mechanisms, displaying an inverse correlation between point mutation and copy number alteration. MMRD signaturesdrive the emergence of specific mutations in TP53 and IDH1, notably excluding common pediatric glioma drivers. Global hypomethylation stratifies priMMRD gliomas into a unique methylation cluster. DNA-polymerasemut priMMRD gliomas exhibit ultrahypermutation, an immune-hot microenvironment, and immunotherapy responsiveness, whereas IDH1mut priMMRD gliomas are immune-cold and immunotherapy resistant. MMRD-driven gliomagenesis defines the role of non-random mutagenesis-patterns in cancer development, providing frameworks for targeted and immune-therapeutics.

overall_design: This study evaluated methylation profiling through the Illumina 450K or EPIC array platforms for n = 77 primary MMRD glioma. Comparisons were made between global methylation profiles on the basis of three priMMRD glioma subgroups (priMMRD-1/2/3) and in comparison to previously published mismatch repair proficient glioma cohorts.

first: Tabori

last: Uri

first: Hawkins

last: Cynthia


city: Shanghai

first: Ke

last: Tang

address: Tongji University, No. 1239, Siping Road, Shanghai

institute: Tongji University

summary: To quantitively evaluate MetroSCREEN’s performance in predicting MRs, we performed CRISPR knockout (CRISPR KO) screens on the PC cell line, targeting four well-known MRs: CTNNB159, ATF460, MYC61, and JUN62.

overall_design: CRISPR knockout (CRISPR KO) screens on the PC cell line, targeting four well-known MRs: CTNNB, ATF, MYC, and JUN. After lentiviral library infection and puromycin selection, the sequences encoding the sgRNAs were PCR-amplified from the transduced cells and quantified by high-throughput sequencing. We conducted the screen with 10x Genomics droplet-based 3’ scRNA-seq and direct sgRNA capture.

first: Ya

last: Han

first: Qiu

last: Wu

first: Chenfei

last: Wang


title: Transcriptome Regulation by PARP13 in Basal and Antiviral States in Human Cells (RNA-Seq)

city: La Jolla

first: Gene

last: Yeo

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

country: USA

institute: UCSD

summary: The RNA-binding protein PARP13 is a primary factor in the innate antiviral response. PARP13 can suppress translation and drive decay of bound viral and host RNA. PARP13 interacts with many proteins encoded by interferon-stimulated genes (ISG) to perform its antiviral activities, such as activation of the pathway mediated by post-translational addition ISG15 or ISGylation. The RNA-binding domains of both PARP13 and its primary cofactor, TRIM25, are required for antiviral activity. Here we perform enhanced crosslinking immunoprecipitation (eCLIP) and RNA-seq to investigate the role of PARP13 expression and RNA binding in transcriptome regulation within human cells. We find that PARP13 regulates the transcriptome in basal and antiviral states and that the antiviral response shifts PARP13 target localization, but not its binding preferences. We demonstrate that PARP13 expression supports the expression of ISGylation-related genes, including TRIM25. Using the common targets PARP13 and TRIM25 share, we assess their spatial relationship along transcripts and show that PARP13 and TRIM25 associate in part via RNA-protein interactions. Evidence from genomic data and molecular biology experiments provide insight into the geometry of PARP13's interface with its cofactor TRIM25 and implicates PARP13 in creating and maintaining a cellular environment poised for an antiviral response.

overall_design: RNA-seq was performed on WT and PARP13 KO HEK293T cells 24 h after transfection with either an ssRNA control or a 3p-RNA viral mimic in duplicate.

first: Veronica

middle: F

last: Busa

first: Yoshinari

last: Ando

first: Stefan

last: Aigner

first: Brian

middle: A

last: Yee

middle: W

first: Anthony

middle: L

last: Leung


title: ERBB2 signaling drives immune cell evasion and resistance against immunotherapy in small cell lung cancer II

city: Erlangen

first: Lydia

last: Meder

state: Bavaria

address: Glückstr. 6

department: Experimentelle Medizin 1

country: Germany

summary: Small cell lung cancer (SCLC) represents ~15% of all lung cancers and is characterized by its highly aggressive phenotype and its dismal outcome. Though the addition of immune checkpoint blockade to carboplatin and etoposide treatment has improved outcome in SCLC patients, SCLC cells finally acquire the ability to evade immunosurveillance and resistance against immune checkpoint blockade. To elaborate molecular mechanisms that mediate SCLC immune evasion, we performed high dimensional profiling of human and murine SCLC specimens. We herein comprehensively analyzed matched human samples of primary and metastatic SCLC and found a loss of MHC-I in SCLC metastases indicating that MHC-I loss mediates SCLC immune evasion. Silencing MHC-I in SCLC cells drastically diminished immune cell infiltration and facilitated the formation of metastasis in mice by circumventing immune surveillance. Using mass spectrometry and phospho-tyrosine kinase analysis, we discovered that ERBB2 signaling suppresses MHC-I expression in SCLC cells and stimulates immune modulating transcripts. Mechanistically, genetic and/or pharmacologic blockade of the ERBB2 signaling axis was sufficient to induce MHC-I expression and to prevent immune evasion in autochthonous murine SCLC in a STING-dependent manner. Finally, we demonstrate that the ERBB2 signaling axis regulates MHC-I expression on SCLC cells and is critical in maintaining immune evasion in SCLC. Most strikingly, we here uncover synergistic treatment efficacy by combining ERBB2 inhibition with PD-1 blockade eliciting profound responses in preclinical SCLC models and circumventing MHC-I loss under immunotherapy, suggesting this combination for future clinical trials in patients with SCLC.

overall_design: We used an autochthonous Rb1/Trp53-deleted mouse model to generate tumor-derived cell lines. Three cell lines were established from primary lung tumors of individual mice, and one from a liver metastasis of a separate mouse. All were cultured under identical conditions and subjected to bulk RNA sequencing to compare transcriptional profiles between primary and metastatic tumor-derived cells.

first: Charlotte

middle: I

last: Orschel

first: Cyrielle

last: Bouchez

first: Rahil

last: Gholamipoorfard

first: Claudia

middle: V

first: David

last: Stahl

first: Christoph

last: Kreer

first: Mirjam

last: Koker

first: Xinlei

first: Marieke

last: Nill

first: Ilayda

middle: G

last: Kocak

first: Ka-Won

last: Noh

first: Leon

last: Ullrich

first: Björn

last: Häupl

first: Josefine

last: Jakob

first: Marie-Lisa

last: Eich

first: Alexandra

last: Florin

first: Holger

last: Grüll

first: Jürgen

last: Wolf

first: Reinhard

last: Büttner

first: Thomas

last: Oellerich

first: Florian

last: Klein

first: Johannes

last: Brägelmann

first: Christian

last: Reinhardt

first: Nima

last: Abedpour

first: Roland

middle: T


title: pS6-IP RNA-seq of mouse olfactory epithelium upon binary odor mixture stimulation under different delivery methods

city: Dalseong-gun

first: Minseok

last: Kim

state: Daegu

address: 333, Techno jungang-daero, Hyeonpung-eup

department: Department of Brain Sciences

country: South Korea

institute: Daegu Gyeongbuk Institute of Science & Technology

summary: Phosphorylation of ribosomal protein S6 (pS6) serves as a molecular marker of neuronal activation by external stimuli. In this study, olfactory epithelium tissues were obtained from mice exposed to binary odor mixtures consisting of acetophenone–decanal or octanal–cis-3-hexenol. To examine how different delivery methods of odor presentation influence neural responses, two paradigms for binary mixtures were employed. In the “+” condition, the two odorants were directly combined on a single piece of filter paper, allowing interaction prior to volatilization. In contrast, in the “&” condition, the odorants were applied separately to two filter papers placed in close proximity (~1 mm apart), such that the components mixed only in the air upon evaporation. Using these approaches, four experimental odor groups were generated (A+D, A&D, O+C, and O&C), along with a no-odor control, resulting in a total of five groups. Following stimulation, pS6-associated ribosome complexes were isolated from olfactory epithelium lysates through immunoprecipitation, selectively enriching mRNAs undergoing active translation in odor-activated cells. RNA sequencing of these samples enabled transcriptomic profiling within activated neuronal populations, providing insights into gene expression programs associated with distinct delivery methods of binary odor stimulation.

overall_design: C57BL/6J wild-type male mice (8 weeks old) were individually housed in sealed, odor-proof containers and habituated in an odorless environment for 4 hours prior to stimulation. Mice were then exposed for 90 minutes to binary odor mixtures delivered by two different methods. In the “+” condition, both odorants were applied to a single piece of filter paper, allowing direct mixing prior to volatilization. In the “&” condition, the odorants were applied separately to two filter papers placed in close proximity (~1 mm apart), enabling mixing in the air without physical contact on the filter. These procedures generated four binary mixture groups (A+D, A&D, O+C, and O&C), along with a no-odor control. Immediately following stimulation, olfactory epithelium tissues were collected, perfused, and homogenized. pS6-associated ribosome complexes were isolated from the homogenates through immunoprecipitation, selectively enriching ribosome-bound mRNAs from odor-activated cells. Three biological replicates were obtained for each condition, and the immunoprecipitated mRNAs were subsequently purified and processed for RNA sequencing.

first: Han Kyoung

last: Choe


title: Metabolic Dependency on De Novo Pyrimidine Synthesis in Platinum Resistant Ovarian Cancer

city: Chicago

first: Daniela

middle: Elena

last: Matei

state: IL

address: 303 E Superior St

department: Obstetrics and Gynecology

institute: Northwestern University

summary: Recurrent high grade serous ovarian cancer (OC) is mostly lethal due to development of resistance to platinum-based chemotherapy. We used cisplatin resistant (Cis-R) cells generated by repeat cisplatin treatment of sensitive (Cis-S) OC cell lines, and metabolomics to identify critical factors associated with platinum resistance. Pathway analysis of differentially abundant metabolites in Cis-R vs. Cis-S OVCAR5 and COV362 cells identified enrichment of pyrimidine metabolism (FDR<0.05) produced by increased de novo pyrimidine synthesis which was subsequently confirmed by flux analysis. Inhibition of this pathway using the DHODH inhibitor brequinar (BRQ) decreased viability, and produced expression changes in genes of the mitochondrial electron transport in Cis-R compared with Cis-S cells. Oxygen consumption rate (OCR) measured with a Seahorse assay indicated lower (P<0.05) OCR (baseline, ATP-related, and maximal) and spare respiratory capacity (SRC) in Cis-R vs. Cis-S OVCAR5 cells. In addition, BRQ had dose-related inhibitory effects on OCR across assay conditions in both Cis-R and Cis-S cells, SRC however, was inhibited by BRQ only in Cis-R cells. In vivo, BRQ attenuated growth of intraperitoneal (ip) Cis-R tumor xenografts but did not alter Cis-S tumors. Similarly, tumor growth was inhibited (p<0.01) by BRQ in a Cis-R PDX model. BRQ plus carboplatin enhanced (p<0.05) the inhibitory effects of carboplatin alone on total tumor weight and numbers of Cis-R ip tumor xenografts. Results indicate that Cis-R cells develop mechanisms that enhance de novo pyrimidine synthesis and maintain relatively low levels of mitochondrial oxidation, however these changes make Cis-R cells vulnerable to inhibitors of these processes.

overall_design: To determine the relevance of de novo pyrimidine synthesis in resistance to cisplatin in ovarian cancer cells, we performed RNA-seq analysis of cisplatin resistant vs. cisplatin sensitive OVCAR5 cells treated with vehicle (control) or the DHODH inhibitor, brequinar (n=3 samples per group).

first: Horacio

last: Cardenas

first: Guangyuan

last: Zhao

first: Ana Maria

last: Isac

first: Wenan

last: Qiang


title: Origin of Ewing sarcoma by embryonic reprogramming of neural crest to mesoderm

first: Claire

last: Arata

email: carata@usc.edu, clairearata@gmail.com

address: 1425 San Pablo St

department: Stem Cell

institute: University of Southern California

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Ewing sarcoma is a malignant small round blue cell tumor of bones and soft tissues, predominantly affecting children, adolescents and young adults. Ewing sarcoma is caused by chromosomal translocations that generate aberrant chimeric transcription factors, most frequently EWSR1::FLI1. Ewing sarcomas exhibit features of both neural and mesenchymal cells. The cell of origin of Ewing sarcoma and the mechanisms of EWSR1::FLI1-driven cell transformation are the subjects of long-standing debates, largely due to the absence of a representative animal model. By developing a robust Ewing sarcoma model in zebrafish, we provide evidence for a neural crest origin of this cancer. We show that neural crest-derived cells (NCCs) uniquely tolerate expression of the human EWSR1::FLI1 oncofusion protein in vivo and that targeted expression of the oncofusion in NCCs is sufficient to generate Ewing sarcoma tumors. In the trunk, EWSR1::FLI1 reprogrammed NCCs to a mesoderm-like state, including upregulation of the early mesoderm specifier tbxta (Brachyury/T) and mesenchymal genes pdgfra, twist1a, and prrx1a. Mesodermal reprogramming of trunk neural crest was evident by the ability of EWSR1::FLI1-expressing cells to induce ectopic fins throughout the body. Single-nucleus analysis of RNA expression and chromatin accessibility, combined with genome-wide profiling of EWSR1::FLI1 binding, revealed that EWSR1::FLI1 targets single GGAA-containing ETS sites in mesodermal developmental enhancers for neural crest to mesoderm reprogramming during cancer initiation, also binding  to GGAA repeats in established tumors. These findings show that EWSR1::FLI1 hijacks normal ETS-dependent developmental pathways in embryonic NCCs to drive initiation of Ewing sarcoma.

overall_design: Tissue from GFP+ embryos expressing EWSR1-FLI1 at 24hpf and tumors were dissociated and processed for CUT&RUN using Cell Signaling Technology's CUT&RUN Assay Kit #86652.

first: Elena

last: Vasileva

middle: E

first: Gage

last: Crump

first: James

last: Amatruda


title: mRNA Initiation and Termination are Spatially Coordinated

city: Worcester

first: Athma

last: Pai

state: MA

address: 368 Plantation Street, AS5-2057

department: RNA Therapeutics Institute

institute: UMASS Medical School

summary: ABSTRACT: The expression of a precise mRNA transcriptome is crucial for establishing cell identity andfunction, with dozens of alternative isoforms produced for a single gene sequence. The regulationof mRNA isoform usage occurs by the coordination of co-transcriptional mRNA processingmechanisms across a gene. Decisions involved in mRNA initiation and termination underlie thelargest extent of mRNA isoform diversity, but little is known about any relationships betweendecisions at both ends of mRNA molecules. Here, we systematically profile the joint usage ofmRNA transcription start sites (TSSs) and polyadenylation sites (PASs) across tissues andspecies. Using both short and long read RNA-seq data, we observe that mRNAs preferentiallyusing upstream TSSs also tend to use upstream PASs, and congruently, the usage ofdownstream sites is similarly paired. This observation suggests that mRNA 5’ end choice maydirectly influence mRNA 3’ ends. Our results suggest a novel “Positional Initiation-TerminationAxis” (PITA), in which the usage of alternative terminal sites are coupled based on the order inwhich they appear in the genome.To examine the direct influence of promoter (AFE) choice on ALE decisions, we performed a series of CRISPR modulations on HEK293 cells to either activate or repress AFEs and measure the change in ALE usage.

overall_design: K562 cells passage 10-12 were grown in RMPI medium supplemented with  cells were treated with DRB 100uM for 3 hours. During the last 5 minnutes of DRB, 4su was added to a final concentration of 1mM. After PBS wash, cells were resuspended in 4su 1mM for a 10m labeling. Treated cells were transferred to low-bind tubes, spin down 2 minutes at 1000rcf, followed by Trizol/Chloroform extraction. Then, the aqueous phase was cleanup using the zymo-clean up kit. We enriched labeled RNA using MTSEA biotin-XX pulldown, followed by RNAseH-based ribosomal RNA depletion. Then, we did a polyI tailing and direct RNA nanopore library prep. For cDNA libraries, polyI tailing was followed by strand-switching RT and PCR, followed by cdna library prep following manufacture's instructions.

first: Ezequiel

last: Calvo-Roitberg

first: Christine

last: Carroll

first: GyeungYun

first: Valeria

last: Sanabria

first: Maritere

last: Uriostegui-Arcos

first: Joseph

last: Paquette

first: Steven

last: Mick

first: Sergey

last: Venev

first: Job

last: Dekker

first: Ana

last: Fiszbein


title: pS6 immunoprecipitation RNA-seq of mouse olfactory epithelium in response to single odorants, binary mixtures, and complex fragrances

first: Minseok

last: Kim

summary: Phosphorylation of ribosomal protein S6 (pS6) serves as a molecular marker of neuronal activation by external stimuli. In this study, olfactory epithelium tissues were collected from mice exposed to single odorants (acetophenone, decanal, octanal, and cis-3-hexenol), binary mixtures (acetophenone–decanal and octanal–cis-3-hexenol), or complex fragrances (floral, mint, and floral–mint combination). To selectively capture transcripts undergoing active translation in odor-activated cells, pS6-associated ribosome complexes were isolated from tissue lysates through immunoprecipitation. The enriched mRNAs were subsequently purified and subjected to RNA sequencing, enabling transcriptomic profiling specifically within odor-activated neuronal populations, particularly olfactory sensory neurons. This approach provides a targeted view of gene expression programs induced by diverse odor stimulation paradigms in the heterogeneous olfactory epithelium.

overall_design: C57BL/6J wild-type male mice (8 weeks old) were individually housed in sealed, odor-proof containers and habituated in an odorless environment for 4 hours prior to stimulation. Mice were then exposed for 90 minutes to one of the following conditions: single odorants (acetophenone, decanal, octanal, cis-3-hexenol), binary mixtures (acetophenone–decanal, octanal–cis-3-hexenol), or complex fragrances (floral, mint, floral–mint). Immediately following exposure, olfactory epithelium tissues were collected, perfused, and homogenized. pS6-associated ribosome complexes were isolated from the homogenates through immunoprecipitation, selectively enriching ribosome-bound mRNAs from odor-activated cells. Three biological replicates were obtained for each condition, and the immunoprecipitated mRNAs were subsequently purified and processed for RNA sequencing.

first: Jeongyoon

last: Lee

first: Han Kyoung

last: Choe


title: Potentiation of Noncanonical NF-𝛋B Signaling and Marginal Zone B Cell Expansion by CARD11-mediated Regulation of p100 Processing

city: Baltimore

first: Joel

last: Pomerantz

address: 733 N. Broadway

department: Biological Chemistry

institute: Johns Hopkins University School of Medicine

summary: Caspase recruitment domain-containing protein 11 (CARD11) is a multi-domain scaffolding protein critical for the adaptive immune response that is required for antigen receptor signaling to canonical NF-kB, mTOR, JNK, and AKT. Oncogenic gain-of-function (GOF) CARD11 mutants, implicated in a variety of lymphomas, bypass normal regulation and signal constitutively. In a mouse model expressing the lymphoma-associated GOF mutation CARD11 C49Y, we observed splenomegaly concomitant with B cell expansion that was most pronounced for Marginal Zone (MZ) B cells. CARD11C49Y/C49Y MZ B cells exhibited enhanced cell-autonomous survivability and elevated basal levels of the precursor NF-kB subunit p100, which was inducibly processed, leading to elevated nuclear p52 levels in response to BAFF. We show in a heterologous assay that active CARD11 variants can inhibit basal NIK-induced p100 processing to p52 independently of their ability to activate canonical NF-kB. Our results reveal an unexpected ability of CARD11 GOF mutants to potentiate the noncanonical NF-kB pathway through p100 accumulation, which likely contributes to the dysregulated B cell expansion observed in lymphomas that harbor CARD11 GOF variants.

overall_design: To analyze differentially expressed genes between CARD11+/+, CARD11+/C49Y and CARD11C49Y/C49Y Follicular (FO) and Marginal Zone (MZ) B cells both unstimulated and in response to stimulation. FO and MZ B cells were harvested from spleens of CARD11+/+, CARD11+/C49Y and CARD11C49Y/C49Y mice and stimulated under the following conditions: unstim; 4µg/mL anti-IgM (24hrs). Three replicates per stimulation condition per B cell type per genotype were included.

first: Anushka

last: Ghosh

first: Tyler

last: Jones

first: Sophie

last: Mackinnon

first: Shelby

middle: M

last: Hutcherson

first: Julia

last: Tritapoe

first: Piyusha

last: Mongia

first: Neha

last: Shah

first: Emma

last: Mehlhop

first: Nicole

last: Carter


title: ERBB2 signaling drives immune cell evasion and resistance against immunotherapy in small cell lung cancer [scRNA-Seq]

first: Lydia

last: Meder

summary: Small cell lung cancer (SCLC) represents ~15% of all lung cancers and is characterized by its highly aggressive phenotype and its dismal outcome. Though the addition of immune checkpoint blockade to carboplatin and etoposide treatment has improved outcome in SCLC patients, SCLC cells finally acquire the ability to evade immunosurveillance and resistance against immune check point blockade. To elaborate molecular mechanisms that mediate SCLC immune cell evasion we performed high dimensional profiling of human and murine SCLC specimens. We herein comprehensively analyzed matched human samples of primary and metastatic SCLC and found a loss of MHC-I in SCLC metastases indicating that MHC-I loss mediates SCLC immune cell evasion. Silencing MHC-I in SCLC cells drastically diminished immune cell infiltration and facilitated the formation of metastasis in mice by circumventing immune surveillance. Using mass spectrometry and phospho tyrosine kinase analysis we discovered that ERBB2 signaling suppresses MHC-I expression in SCLC cells and stimulates immune modulating transcripts. Mechanistically, genetic and/or pharmacologic blockade of the ERBB2 signaling axis was sufficient to induce MHC-I expression and to prevent immune evasion in autochthonous murine SCLC in a STING dependent manner. Finally, we demonstrate that ERBB2 signaling axis regulates MHC-I expression on SCLC cells and is critical in maintaining immune evasion in SCLC. Most strikingly, we here uncover synergistic treatment efficacy by combining ERBB2 with anti-PD-1 targeted treatment that elicits profound responses in preclinical SCLC models suggesting this combination for future clinical trials in patients with SCLC.

overall_design: Rb1/Trp53-deleted SCLC mice were randomized and systemically treated with vehicle, an anti-PD-1 inhibitor, an ERBB2 inhibitor, and with the combination of an ERBB2 inhibitor and an anti–PD-1 inhibitor. SCLC lung tumor was analyzed regarding antigen presentation, T-cell recruitment and restistance mechanisms..

first: Charlotte

last: Orschel

first: Cyrielle

last: Bouchez

first: Rahil

last: Gholamipoorfard

first: Claudia

first: David

last: Stahl

first: Christoph

last: Kreer

first: Mirjam

last: Koker

first: Xinlei

last: Zhao

first: Marieke

last: Nill

first: Leon

last: Ullrich

first: Marie-Lisa

last: Eich

first: Alexandra

last: Florin

first: Holger

last: Grüll

first: Jürgen

last: Wolf

first: Reinhard

last: Büttner

first: Florian

last: Klein

first: Johannes

last: Brägelmann

first: Christian

last: Reinhardt

first: Nima

last: Abedpour

first: Roland


title: Total RNA-seq of mouse olfactory epithelium in response to single odorants and binary mixtures

first: Minseok

last: Kim

summary: Total RNA was extracted from olfactory epithelium tissues of mice exposed to single odorants (acetophenone, decanal, octanal, and cis-3-hexenol) or binary mixtures (acetophenone–decanal and octanal–cis-3-hexenol). The extracted RNA was subjected to high-throughput sequencing to profile genome-wide transcriptional changes across all cell types of the olfactory epithelium following odor stimulation. This dataset provides a baseline reference for comparing odor-induced gene expression programs in the olfactory epithelium with transcriptomic profiles obtained from odor-activated neuronal populations enriched by pS6 immunoprecipitation.

overall_design: C57BL/6J wild-type male mice (8 weeks old) were individually housed in sealed, odor-proof containers and habituated in an odorless environment for 4 hours prior to stimulation. Mice were then exposed for 90 minutes to one of the following conditions: single odorants (acetophenone, decanal, octanal, cis-3-hexenol) or binary mixtures (acetophenone–decanal and octanal–cis-3-hexenol). Immediately following exposure, olfactory epithelium tissues were collected, perfused, and homogenized. Total RNA was extracted from the homogenates, purified, and processed for RNA sequencing. Three biological replicates were obtained for each condition.

first: Jeongyoon

last: Lee

first: Han Kyoung

last: Choe


title: Comparative analysis of mouse and human ovaries across age [mouse data]

city: San Francisco

first: Diana

middle: Matthew

last: Laird

address: 35 Medical Center Way RM913D

institute: University of California

summary: A combination of droplet based and plate based single cell sequencing was used to profile and compare all cell types in the mouse and human ovaries throughout the reproductive span.

overall_design: For each sample, the ovary was dissociated and cells were size filtered to separate large oocytes from small oocytes and somatic cells. Large oocytes were sequenced using SmartSeq2 while the suspension of small cells was sequenced using 10X Genomics.

first: Ryan

last: Samuel

first: Eliza

last: Gaylord

first: Mariko

last: Foecke


title: ERBB2 signaling drives immune cell evasion and resistance against immunotherapy in small cell lung cancer

first: Lydia

last: Meder

overall_design: To investigate the role of  ERBB2 in SCLC we created an ERBB2KO cell line and compared it to the wild type regarding antigen presentation pathways.

first: Charlotte

last: Orschel

first: Cyrielle

last: Bouchez

first: Rahil

last: Gholamipoorfard

first: Claudia

first: David

last: Stahl

first: Christoph

last: Kreer

first: Mirjam

last: Koker

first: Xinlei

last: Zhao

first: Marieke

last: Nill

first: Leon

last: Ullrich

first: Marie-Lisa


overall_design: We compared vehicle treated to anti-PD-1 and ERBB2 inhibition combination therapy treated mice.

last: Eich

first: Alexandra

last: Florin

first: Holger

last: Grüll

first: Jürgen

last: Wolf

first: Reinhard

last: Büttner

first: Florian

last: Klein

first: Johannes

last: Brägelmann

first: Christian

last: Reinhardt

first: Nima

last: Abedpour

first: Roland


title: High resolution spatially resolved transcriptomic analysis of mouse pancreatic sections during embryonic development

city: London

first: Francesca

middle: M.

last: Spagnoli

address: Great Maze Pond

department: CGTRM

country: United Kingdom

institute: King's College London

summary: The pancreas is an endodermal organ with exocrine and endocrine cell compartments. The embryonic development of the pancreas relies on the the coordinated action of pancreatic progenitors and its surrounding microenvironments. The most abundant cell type of the pancreatic microenviroment are mesenchymal cells. These cells are known to contribute to the pancreas organ growth, morphogenesis and differentiation. In this study, we used hybridization-based in situ sequencing (HybISS) to spatially characterize  pancreatic progenitor populations and microenviroment cell types in the pancreas of the mouse embryos.

overall_design: Pancreatic spatial transcriptomics data were generated by RNA hybridization-based in situ sequencing (HybISS, Cartana part of 10xGenomics)

first: Alejo

last: Torres-Cano

first: Jean-Francois

last: Darrigrand

first: Gabriel

last: Herrera-Oropeza

first: Georgina

last: Goss

first: Anna

last: Salowka

first: Debashish

last: Chitnis

first: Morgane

last: Rouault

first: Alessandra

last: Vigilante


title: Comparative analysis of mouse and human ovaries across age [human data]

first: Diana

last: Laird

first: Ryan

last: Samuel

first: Eliza

last: Gaylord

first: Mariko

last: Foecke


first: Claire

last: Arata

overall_design: Dissected trunks of -28.5Sox10:BFP>dsRed -28.5Sox10:dsRed>eGFP-2A-EF1 zebrafish at 7dpf were dissociated and cells were identified by Fluorescence-activated cell sorting (FACS). Dissected tissue from a wild type fish at 3mpf, a -28.5Sox10:dsRed>eGFP-2A-EF1 trunk tumor at 3mpf, and a EWSFLI mosaic model head tumor at 9mpf  were dissociated and processed with no sorting. All samples were subjected to nuclei isolation and processed for snATACseq and/or snRNAseq with 10x Genomics.

first: Elena

last: Vasileva

first: Gage

last: Crump

first: James

last: Amatruda


title: βIV-spectrin/STAT3 complex regulates the orientation of hypertrophic growth

status: Public on Oct 08 2025

city: Columbus

first: Thomas

last: Hund

state: OH

address: 473 W 12th Ave

institute: Ohio State University

summary: Background: Cardiac hypertrophy, defined as a stress-induced increase in heart mass/size, is a major risk factor for adverse cardiovascular events including heart failure and arrhythmia. Within this general definition, the orientation of cell and organ growth varies considerably depending on stress type and duration with important implications for cardiac function, yet, little is known regarding the mechanisms that regulate hypertrophic orientation. Here, we evaluated the role of the cytoskeletal protein βIV-spectrin and associated pro-hypertrophic signal transducer and activator of transcription (STAT3) to direct the orientation of hypertrophic growth.  Methods: Transgenic mouse models with altered STAT3 signaling through modified interaction with its scaffolding partner βIV-spectrin, or phospho-regulation of STAT3 directly, were evaluated at baseline, and following transaortic constriction (TAC), or aortocaval fistula (ACF). Unbiased screening of gene expression from these structurally divergent states were evaluated for pathways responsible for directing myocyte length/width. These pathways were tested in vitro using primary mouse myocytes and in vivo to tune growth patterns for therapeutic intervention. Results: Loss of βIV-spectrin or direct STAT3 activation promoted a preferential increase in myocyte length over width, resulting in dilation of the left ventricular (LV) chamber (eccentric hypertrophy) and decreased systolic function. Conversely, preservation of βIV-spectrin favored an increase in myocyte width without LV dilation (concentric hypertrophy) and preserved systolic function in response to TAC or ACF. Differential expression of genes associated with microtubules, including the trafficking kinesin motor, KIF20A, were identified in concentric vs. eccentric hypertrophic states. In vitro assays revealed a relationship between βIV-spectrin/STAT3 signaling, KIF20A expression, microtubule density, and spatial distribution of mRNA for the sarcomeric gene actc1. Finally, intervention with pharmacologic STAT3 inhibition following chronic 6-week TAC successfully recovered concentric growth with improved systolic function. Conclusions: These data identify a novel and pivotal role for βIV-spectrin/STAT3 to direct myocyte geometry in response to chronic stress. These studies further illustrate the unique separation of hypertrophic growth and orientation as distinct pathways in cardiac remodeling.

overall_design: RNA-seq profiling of wildtype mice and STAT3 S727A phosphoablated mutant mice from whole heart samples following 4 weeks of transortic constriction to promote hypertrophic growth.

first: Drew

last: Nassal

first: Shivangi

last: Mohta

first: Rebecca

last: Shaheen

first: Benjamin

last: Buck

first: Simon

last: Lococo

first: Haiyan

last: Liu

first: Omer

last: Cavus

first: Alexander

middle: J

last: Winkle

first: Jolie

last: Pyles

first: Nicholas

last: Leahy

first: Xianyao

last: Xu


title: DROSHA and DICER RNA products control BMI1-dependent transcriptional repression at DNA damage sites

city: Pavia

first: Sofia

last: Francia

address: Via Abbiategrasso, 207

country: Italy

institute: Istituto di Genetica Molecolare - Consiglio Nazionale delle Ricerche (IGM-CNR)

summary: The activation of the DNA-damage response (DDR) enforces the transcriptional silencing of genes near DNA double-strand breaks (DSBs), a process called DSB-induced silencing in cis (DISC). DISC involves the kinase ATM and the polycomb repressive complex 1 (PRC1) component BMI1. Conversely, DSBs also trigger transcription of damage-induced long non-coding RNAs (dilncRNAs) in an MRE11-RAD50-NBS1 (MRN)-complex-dependent manner. MRN recruits the ribonuclease DROSHA, which, along with DICER, enhances DDR signaling and repair. We show that dilncRNAs, DROSHA, and DICER regulate DISC. MRN or ATM inhibition disrupts DISC, while enoxacin, a DICER activator, restores it even without ATM activity. Mechanistically, DROSHA and DICER enable BMI1 recruitment and H2A-K119 ubiquitination at DSBs. BMI1 interacts with DROSHA and dilncRNAs in a DICER-dependent manner. Blocking dilncRNAs by antisense oligonucleotide and Cas13 reduces BMI1 recruitment and DISC. We propose that DROSHA, DICER, and dilncRNAs mediate DISC by promoting PRC1 recruitment and chromatin modification at DSBs.

overall_design: RNA-seq,  1 cell line, 6 conditions (siCTL Induced, siCTL Uninduced, siATM Induced,  siATM Uninduced, siDIC-DRO Induced, siDIC-DRO Uninduced), 3 replicates per condition

first: Francesca

last: Esposito

first: Ilaria

last: Capozzo

first: Stefania

last: Modafferi

first: Letizia

last: Manfredi

first: Fabio

last: Iannelli

first: Ubaldo

last: Gioia

first: Alessia

last: di Lillo

first: Sara

last: Tavella

first: Matteo

last: Cabrini

first: Fabrizio

last: d?Adda di Fagagna


title: Independent mechanisms of myeloid bias and inflammation driven by UBA1 mutation

city: New York

first: Caleb

last: Lareau

state: New York

address: 417 E 68th St, Zuckerman - ZRC 1132

institute: Memorial Sloan Kettering

summary: Somatically acquired mutations in the E1 ubiquitin-activating enzyme UBA1 within hematopoietic stem and progenitor cells (HSPCs) were recently identified as the cause of the adult-onset autoinflammatory syndrome VEXAS (vacuoles, E1 enzyme, X linked, autoinflammatory, somatic)1. Most VEXAS-associated mutations occur at Met41 in UBA1 and lead to clonal expansion within the HSPC and myeloid, but not lymphoid, compartments. Despite its severity and prevalence, the mechanisms whereby UBA1 mutations cause multiorgan autoinflammation and hematologic disease are unknown. Here, we employ mRNA-based electroporation of adenine base editing enzymes to mutate endogenous Uba1, generating canonical VEXAS-associated Met41 mutations in murine or human HSPCs and macrophages. Expression of Met41-mutant UBA1 in macrophages aberrantly triggered apoptotic and necroptotic inflammatory cell death programs upon exposure to TNF or LPS, which could be fully reversed by combined deletion of Mlkl or Ripk3 plus Casp8, or partially by genetic or pharmacologic targeting of RIPK1 kinase activity. In mice challenged with TNF or LPS, the UBA1 inhibitor TAK-243 exacerbated inflammation, which was mediated by RIPK1 kinase activity and RIPK3-Caspase-8, respectively. In contrast, Uba1-mutant HSPCs displayed an unfolded protein response signature and spontaneous myeloid skewing that were independent of RIPK3-Caspase-8, thereby propagating an inflammatory cycle driven by their mature myeloid progeny. Mechanistically, we traced the dysregulated cell death response of Uba1-mutant macrophages to a cascading, kinetic defect in Lys63/Met1 (i.e., linear) polyubiquitylation of inflammatory signaling complexes. Collectively, our results link the pathogenesis of VEXAS with that of rarer germline monogenic causes of autoinflammation; highlight specific ubiquitin-associated defects stemming from an apical mutation in the ubiquitylation cascade; and nominate the RIPK1-RIPK3-caspase-8 death axis as a therapeutic target in VEXAS.

overall_design: Mouse HSPCs were electroporated with either the Abe8e-SpRY adenine base editor along with either control sgRNA targeting Rosa26 (Uba1-WT) or an sgRNA designed to introduce the M41T mutation in Uba1 (Uba1M41T/y). Cells were subsequently harvested 5- or 8-days after culture, hashtagged and submitted for single cell RNA-seq.

first: Narendra

last: Varun

first: Lareau

last: Caleb


title: An antagonistic epigenetic mechanism regulating gene expression in pollen revealed through single-nucleus multiomics

first: Colette

last: Picard

state: California

address: 610 Charles E Young Dr East, Room 4045

department: Molecular, Cell and Developmental Biology

institute: University of California - Los Angeles

type: Methylation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Targeting p300/CBP abolishes HOXB13 loss-induced lipogenesis and tumor metastasis [RNA-seq]

city: Atlanta

first: Jindan

last: Yu

state: GA

address: E330, 1760 Haygood Dr NE

department: Urology

institute: Emory University

summary: HOXB13 is a prostate-specific homeodomain transcription factor that is mainly known as an androgen receptor (AR) cofactor. Recent studies have revealed AR-independent roles of HOXB13 in recruiting HDAC3 to suppress lipogenic programs in prostate cancer (PCa). As such, HOXB13 down-regulation leads to lipid accumulation and tumor metastasis, the molecular mechanisms of which, however, are incompletely understood. Here, we demonstrate that p300/CBP co-occupies HOXB13/HDAC3-repressed lipogenic enhancers and is required for their activation and target gene expression upon HOXB13 loss. We found that HOXB13 is down-regulated in metastatic hormone-sensitive PCa compared to their matched primary prostate tumors. HOXB13 loss induces matrix metalloproteinases (MMPs), which mediate HOXB13-depleted cell motility. Critically, CCS1477, a pharmacological inhibitor of p300/CBP, abolished HOXB13-loss-induced lipid accumulation, MMP gene expression, cell motility in vitro, and tumor metastasis in vivo. Taken together, our results suggest HOXB13 as a significant metastasis suppressor and identify p300/CBP as critical therapeutic targets in HOXB13-low metastatic PCa.

overall_design: To evaluate whether HOXB13 loss induces lipogenic programs through p300/CBP, we performed RNA-seq in control and HOXB13-KD LNCaP cells with concomitant p300 and/or CBP KD, or treated with DMSO or 250nM CCS1477 for 48 hours

first: Xiaodong

last: Lu

first: Qi

last: Chu

first: Jonathan

middle: C

last: Zhao


title: The effect of Neurensin-2 overexpression on gene expression in N2a cells

city: Jerusalem

first: Gali

last: Umschweif

address: Ein Karem Campus | Jerusalem

department: pharmacology section. school of pharmacy

country: Israel

institute: The Hebrew University of Jeursalem

summary: Neurensin-2 is a stress-responsive vesicular protein. Nonetheless, the cellular mechanisms by which Neurensin-2 regulates depression and anxiety remain unexplored. To identify the cellular pathways regulated by Neurensin-2, we overexpressed Neurensin-2 in a N2a neuroblastoma cell line, followed by RNA sequencing

overall_design: To investigate the stress-induced gene expression changes, we extract RNA from control and  overexpressed Neurensin-2 in a N2a neuroblastoma cell line .On the RNA, which was extracted from cells , we preformed sequencing, gene expression profiling and pathway analysis.


title: Emergence of Endothelial Cell Subtypes and Role of Cell Cycle Control in Arterial-Venous Specification During Embryonic Vascular Development [bulk RNA-seq]

city: Charlottesville

first: Jordon

last: Aragon

state: VA

department: Cell Biology

institute: University of Virginia

summary: During embryonic vascular development, endothelial cells that line all blood vessels undergo specification into arterial, capillary, and venous subtypes to form a circulatory network. Regulation of endothelial cell cycle state has been shown to play a critical role in enabling arterial-venous specification and remodeling in a postnatal, blood flow-mediated, and tissue specific manner; however, if a similar cell cycle-mediated mechanism is a common mechanism that regulates embryonic vascular development, even prior to blood flow, is unknown. To investigate this, we first defined the emergence of distinct subtypes by isolating endothelial cells from wild type embryos at embryonic day (E)8.0, prior to blood flow; E8.5, just after flow begins; and E9.5. We performed single cell RNA sequencing and analyses, and found increased specification of arterial, venous and hemogenic subtypes over time, concomitant with decreased primordial and capillary endothelial cells. Gene Ontology analysis revealed that cell cycle control was significantly enriched over time, and we found arterial identity highly correlated with growth arrest. To gain more insight into the potential role of cell cycle control in specification, we isolated similar endothelial cells from Fucci-expressing embryos, sorted them into distinct cell cycle states (early G1, late G1 and S/G2/M), performed bulk RNA sequencing, and bioinformatically correlated endothelial cell cycle states with subtype identities. We found venous endothelial cells are highly enriched in early G1 and arterial endothelial cells highly enriched in late G1, which was corroborated with fluorescent imaging of Fucci embryos. Furthermore, we showed that endothelial cell hyperproliferation, induced by deletion of cell cycle inhibitor Cdkn1b (p27), impaired arterial-venous specification and vascular development. These results support that at the earliest stage of vascular development, endothelial cells in arterial and venous vessels reside in different cell cycle states and endothelial cell cycle control is required for their specification.

overall_design: CD31+ CD45- murine embryonic endothelial cells sorted from Fucci E8.0 (pre-blood flow, E8.5, and E9.5 embyos in early G1, late G1, and S/G2/M.

first: Aragon

last: Jordon

first: Nelson

last: Elizabeth

first: Chavkin

last: Nicholas

first: Jackson

last: Madeline

first: Heo

last: Won

first: Cain

middle: R

last: Shelby

first: Markowska

last: Zaneta

first: Bradecamp

last: Grace

first: Genet

last: Gael

first: Cwiek

last: Aleksandra

first: Hirschi

middle: K

last: Karen


title: Single-cell RNA-seq analysis of pancreatic progenitor cells and mesenchyme from mouse embryos

first: Francesca

last: Spagnoli

summary: The pancreas is an endodermal organ with exocrine and endocrine cell compartments. The embryonic development of the pancreas relies on the the coordinated action of pancreatic progenitors and its surrounding microenvironments. The most abundant cell type of the pancreatic microenviroment are mesenchymal cells. These cells are known to contribute to the pancreas organ growth, morphogenesis and differentiation. In this study, we used single-cell RNA sequencing to molecularly characterize mesenchymal and pancreatic progenitor populations in the dorsal pancreas of the mouse embryos.

overall_design: Single cells were isolated by FACS from the dorsal pancreatic tissue of Tg(Prox1-EGFP), Tg(Nkx2.5-Cre;mTmG) and Tg(Nkx3.2-Cre;mTmG) transgenic mouse embryos at embryonic day (E) 12.5 and processed for single-cell RNA sequencing using SmartSeq2 method.

first: Alejo

last: Torres-Cano

first: Jean-Francois

last: Darrigrand

first: Gabriel

last: Herrera-Oropeza

first: Georgina

last: Goss

first: Alessandra

last: Vigilante

first: Francesca M.


title: Oral 4`fluorouridine rescues nonhuman primates from advanced Lassa fever

city: Galveston

first: Jacquelyn

last: Turcinovic

state: TX

address: Galveston National Laboratory, 301 University Blvd.

department: Microbiology and Immunology

institute: University of Texas Medical Branch

summary: There are no approved treatments for Lassa fever, which is estimated to cause 100,000 to 300,000 infections and 5,000 deaths annually in West Africa. Recently, it was shown that 4'-fluorouridine (also known as EIDD-2749), an orally available ribonucleoside analogue, protected guinea pigs from lethal challenge with the lineage IV prototype Josiah strain of Lassa virus when treatment was delayed beyond the onset of clinical signs of disease. Here we assessed the therapeutic efficacy of 4'-fluorouridine in an African green monkey model of Lassa fever using the contemporary and apparently more pathogenic lineage VII Togo strain of Lassa virus. Daily treatment with 4'-fluorouridine beginning 6 days after Lassa virus infection, when the monkeys were viraemic and clinically ill, resulted in rapid and complete clearance of infectious virus in 4 out of 5 monkeys, and all treated monkeys survived to the pre-determined study end-point. Targeted transcriptomics showed that cellular responses and control of cytokinaemia contributed to the development of immunity. Our findings support the further development of 4'-fluorouridine both as a post-exposure prophylaxis to control outbreaks and as a therapeutic agent to treat symptomatic patients.

overall_design: Time series NanoString data from African green monkeys challenged Lassa virus

first: Robert

last: Cross

first: Thomas

last: Geisbert


title: Single-cell Multiomics Analysis Reveals CTCF as a Key Regulator of Lung Morphogenesis and Progenitor Maintenance

city: shenzhen

first: Jiang

last: Yamei

address: longfei

institute: The Chinese University of Hong Kong-Shenzhen

summary: Lung development generates a complex tree-like architecture through proximal-distal patterning and branching morphogenesis. However, the gene regulatory programs governing embryonic lung development remain poorly understood. Here, we present a comprehensive single-cell multi-omics atlas of mouse embryonic lungs, integrating gene expression and chromatin accessibility profiles. Through systematic analysis, we identify 13 distinct cell types and map cis-regulatory elements, peak-to-gene linkages, and transcription factors underlying lung development. Leveraging this multi-modal dataset, we uncover lineage-determining transcription factors  driving cell differentiation, including the Activated Protein-1 complex. We further delineate gene regulatory networks involving diverse transcription regulators, including CCCTC-binding factor. Using the Ctcf conditional knockout mouse, coupled with histological and multi-omics analyses, we demonstrate that CCCTC-binding factor  orchestrates lung progenitor maintenance and branching morphogenesis by modulating both gene expression and chromatin accessibility. Thus, our study provides a multi-omics resource and mechanistic insights for transcriptional regulation of lung morphogenesis.

overall_design: To comprehensively study the heterogeneity and regulatory mechanisms of lung morphogenesis, we performed ATAC-seq profiling of nuclei extracted from embryonic day 12.5 (E12.5) lungs.

first: Shenfei

last: Sun

first: Yamei

last: Jiang

first: Fujing

last: Huang

first: Wei

last: Wei

first: Mathias

last: Hochgerner

first: Tianmin

last: Xu

first: Xiaoting

last: Wang

first: Kaijun

last: Lin

first: Xinna

last: Zhang

first: Yanli

first: Hua

last: He

first: Miao

last: Yu

first: Xiaofang

last: Tang

first: Xinhua


title: Emergence of Endothelial Cell Subtypes and Role of Cell Cycle Control in Arterial-Venous Specification During Embryonic Vascular Development [scRNA-seq]

first: Jordon

last: Aragon

overall_design: CD31+ CD45- murine embryonic endothelial cells sorted from C57Bl6J E8.0 (pre-blood flow, E8.5, and E9.5 embyos.

first: Elizabeth

last: Nelson

first: Nicholas

last: Chavkin

first: Madeline

last: Jackson

first: Won

last: Heo

first: Shelby

last: Cain

first: Zaneta

last: Markowska

first: Grace

last: Bradecamp

first: Gael

last: Genet

first: Cwiek

last: Aleksandra

first: Hirschi

last: Karen


first: Jiang

last: Yamei

overall_design: To comprehensively study the heterogeneity and regulatory mechanisms of lung morphogenesis, we performed CUTnTag profiling of nuclei extracted from embryonic day 12.5 (E12.5) lungs.

first: Shenfei

last: Sun

first: Yamei

last: Jiang

first: Fujing

last: Huang

first: Wei

last: Wei

first: Mathias

last: Hochgerner

first: Tianmin

last: Xu

first: Xiaoting

last: Wang

first: Kaijun

first: Xinna


title: Tel1 is recruited at chromosomal loop/axis contact sites to modulate meiotic DNA double-strand breaks interference

city: MARSEILLE CEDEX 09

first: Christelle

last: Cayrou

address: 27 Boulevard Lei Roure

country: France

institute: CRCM

summary: During meiosis, the programmed formation of DNA double-strand breaks (DSBs) by Spo11, a conserved topoisomerase-like protein, initiates homologous recombination that leads to crossovers between homologous chromosomes, essential for accurate segregation and genome evolution. Because DSBs are a threat to genome integrity, their number, distribution and timing of formation are regulated during the meiotic program. In S. cerevisiae, DSB interference prevents the coincident formation of DSBs in neighboring hotspots through a Tel1/ATM dependent mechanism that remains unexplored. Here, we demonstrate that Tel1 is recruited to meiotic DSB hotspots in response to Spo11-DSB formation. We further show that Tel1 localizes to chromosomal axis sites in a DSB-dependent manner, thus supporting the tethered loop-axis complex (TLAC) model that postulates meiotic DSBs are formed within the chromosome axis environment. Tel1 recruitment to meiotic DSBs, DSB interference and the meiotic DNA damage checkpoint are dependent on both the Tel1-FATC domain and the C-terminal moiety of Xrs2, known to mediate Tel1-Xrs2 interaction in somatic cells. However, in a xrs2-K846/F847 mutant, DSBs interference remains functional despite Tel1 binding to DSB sites being significantly reduced and the Tel1-dependent DNA damage checkpoint abolished. Altogether, this work highlights the complex regulation of Tel1 multiple various functions in meiotic cells, and fine-tuning through interaction with Xrs2.

overall_design: Chromatin immunoprecipitation (ChIP) For each meiotic time point, 2 x 108 cells were fixed in paraformaldehyde (1% final). FLAG-Tel1 cells were fixed for 30min, while FLAG-Spo11 strain were fixed for 15min, quenched by glycine for 5min (125mM final) and washed in TBS 1X two times. Cells were lysed using mechanical lysis (Fastprep, 4 cycles at 6.5M/sec 30sec) together with a Lysis buffer (50mM HEPES-KOH, 140mM NaCl, 1mM EDTA pH8, 1% Triton X100, 0.1% Sodium Deoxycholate) complemented with protease inhibitor cocktail tablet (Roche, Ref 05 892 791 001), PMSF (1mM final), pepstatin (0.1mM final) and leupeptin (1mM final). After cell lysis, chromatin was sheared by sonication into 500 – 1000pb fragment (30sec ON/30sec OFF, 6 cycles, 4°C, Diagenode Bioruptor Pico). 10µl was kept aside as the input, and samples were divided in two halves, for minus and plus antibody treatment. FLAG-Tel1 immunoprecipitation was performed with 2µl of anti-FLAG antibody (M2 monoclonal, Sigma, Ref F1804) and incubation at 4°C for 2 hours. Pan-IgG mouse magnetic beads were incorporated for 2 more hours at 4°C. IP samples were washed by a 500mM NaCl containing lysis buffer and LiCl buffer (10mM Tris-HCl pH8, 0.25LiCl, 1mM EDTA pH8, 0.5% Triton X-100, 0.5% Sodium Deoxycholate). Chromatin was eluted from magnetic beads in elution buffer (TE 1X, 0.5% SDS) at 65°C for 10min. DNA-protein interaction was disrupted by incubation at 65°C overnight for IP and input samples. RNA was digested by RNAse A treatment (20µg total, 15min at 37°C) and proteins by proteinase K treatment (100µg total, 1hour at 42°C). DNA was purified on column (Qiagen DNA purification kit).  ChIP-seq Tel1 and Spo11 ChIP-seq were performed following the ChIP-qPCR protocol with some modifications. For both FLAG-Tel1 and FLAG-Spo11 strain, cells were fixed in paraformaldehyde for 30min. Protein G magnetic beads were washed (0.1M NaHPO4 pH7.5, 0.01%Tween20, pH8.2) and saturated with BSA (0.1M NaP, 0.01% Tween20, 5mg/ml BSA) for 3hours at 4°C. Anti-FLAG antibody (M2 Monoclonal, Sigma) was pre-incubated with saturated-magnetic beads for 4hours at 4°C. Cell lysis was performed as for the ChIP-qPCR protocol. Chromatin shearing was performed in Diagenode tube 15ml with beads (900 – 1000mg) by 7 cycles of sonication (30sec ON/30sec OFF, 4°C). Chromatin was immunoprecipitated with antibody-protein G mix by overnight incubation at 4°C. Samples were washed as for the ChIP-seq protocol, and DNA was eluted with IPure v2 Diagenode kit. DNA quantity was measured by QuBit and fragmentation quality was controlled by Agilent chip (Bio-analyser). DNA was sequenced with a NovaSeq sequencer (Illumina) using a 100nt paired-end protocol (TruSeq) at the Institut Curie sequencing facility (Paris, France).

first: Valérie

last: Garcia

first: Pierre

last: Luciano

first: Marie

last: Dorme

last: Borde

first: Julien

last: Vernerey


title: Adenosine to Inosine RNA editing level in mouse lungs from Adar1 K999N mutants or hypoxia-exposed mice

city: Pittsburgh

first: Shu-Ting

last: Cho

state: PA

address: 450 Technology Drive

department: Computational and Systems Biology

institute: University of Pittsburgh

summary: Hypoxia is a PH trigger which significantly downregulates ADAR1 and reduces A-to-(I)G editing in mouse lungs. Mice have Adar1 misssense mutation K999N were used to determine specific ADAR1-specific RNA editing sites in lungs. We performed RNA sequencing on the lung tissues isolated from mice carrying Adar1 K999N mutations and exposed to 3 week hypoxia.

overall_design: To investigate the effect of hypoxia on ADAR1-mediated RNA editing in mouse lungs, we treated wildtype or Adar1 K999N mice with hypoxia (10% oxygen) exposure for 3 weeks. RNA sequencing was performed and the overall A-to-I(G) RNA editing level was analyzed.

first: Chen-Shan

last: Woodcock

first: Stephen

last: Chan


title: Adenosine to Inosine RNA editing level in ADAR1-deficient or hypoxia-exposed human pulmonary artery endothelial cells

summary: Hypoxia is a PH trigger which significantly downregulates ADAR1 and reduces A-to-(I)G editing in human PAECs. By RNA sequencing of PAECs after ADAR1 knockdown, we have identified the circadian gene Nocturnin (NOCT) as a direct ADAR1 target. NOCT carries two active A-to-I RNA editing sites in the 3’UTR. In addition, hypoxia significantly reduced A-to-G editing in human PAECs

overall_design:
To identify the genes regulated by ADAR1-induced RNA editing, RNA sequencing (RNA-seq) analysis was conducted in PAECs after ADAR1 knockdown.
To investigate the effect of hypoxia on ADAR1-mediated RNA editing in hPAECs, we treated human PAEC with 48 hr hypoxia (1% oxygen) explosure. RNA sequence was perfermed and the overall A-to-I(G) RNA editing level was analyzed.


title: Targeting p300/CBP abolishes HOXB13 loss-induced lipogenesis and tumor metastasis

first: Jindan

last: Yu


title: A Large-Scale Human Toxicogenomics Resource for Drug-Induced Liver Injury Prediction

status: Public on Oct 07 2025

city: Somerville

first: Volker

last: Bergen

address: 101 South St

institute: Cellarity

summary: Drug-Induced Liver Injury (DILI) remains one of the most critical challenges in drug development, causing patient safety concerns, clinical trial failures and drug withdrawals. We introduce ToxPredictor, a toxicogenomics framework combining RNA-seq data from primary human hepatocytes with pharmacokinetic data to predict dose-resolved DILI risks and safety margins. At its core is DILImap, an RNA-seq library tailored for DILI research, comprising 300 compounds at multiple concentrations. ToxPredictor achieves 88% sensitivity at 100% specificity in blind validation, outperforming state-of-the-art methods. It flagged recent phase III clinical failures, including Evobrutinib, TAK-875, and BMS-986142, overlooked by animal studies. Beyond prediction, ToxPredictor provides mechanistic insights into hepatotoxic pathways, enabling early de-risking and actionable safety decisions. Unlike single-endpoint readouts—even from 3D models—transcriptomics offers a multi-dimensional system-level view of hepatocyte responses, capable of detecting diverse DILI mechanisms not captured by conventional assays. Scalable, actionable, and integrated into a broader AI/ML drug discovery platform, this work establishes toxicogenomics as a transformative tool for developing safer therapeutics and addressing one of the most pressing challenges in toxicology.

overall_design:
RNA-seq profiling of 300 DILI positive and negative drug perturbations profiles at multiple concentrations in primary human hepatocytes. The cell metadata (.obs in the h5ad) include all experimental and treatment details.

The raw data contain proprietary information and are therefore not publicly available, as agreed with the Nature Communications editors.  Academic researchers may request access for internal, non-commercial use.

first: Konstantia

last: Kodella

first: Sreenath

last: Srikrishnan

first: Ornella

last: Barrandon

first: Sara

last: Anderson

first: Max

last: Rogers-Grazado

first: Casey

last: Fowler

first: Hirit

last: Beyene

first: Nicole

last: Robichaud

first: Timothy

last: Fulton

first: Nina

last: Lapchyk

first: Mauricio

last: Cortes

first: Nick

last: Plugis

first: Matthew

last: Goddeeris

first: Mahdi

last: Zamanighomi


title: HIF-2-dependent Regulation of PTHrP and Paraneoplastic Hypercalcemia in Aggressive Clear Cell Renal Cell Carcinoma [RNA-seq]

city: Dallas

first: Bingqing

last: Xie

state: Texas

address: 6001 Forest Park Rd

department: Internal medicine

institute: University of Texas Southwestern medical center

summary: Hypercalcemia (HC) in renal cell carcinoma (RCC) patients is associated with reduced survival. HC often involves PTHrP. PTHrP is induced by hypoxia, but whether HIF-2 plays a role in HC is unknown. Here we show that HC is reproduced by transplanting patient tumors (tumorgrafts, TG) in mice resulting in functional deterioration, weight loss, calcium deposition and organ damage. Treatment with PT2399, a specific HIF-2 inhibitor, rapidly normalized calcium levels, downregulated PTHrP and reduced HIF-2 binding to the PTHLH promoter. Interestingly, while the PTHLH locus was generally more accessible in TG(HC), PT2399 did not grossly affect chromatin accessibility, which was consistent with genome-wide studies where promoter accessibility was only reduced in a minority of PT2399-downregulated genes. As in TGs, paraneoplastic HC in humans was associated with clear cell histology and sarcomatoid/rhabdoid differentiation. Interestingly, HC (and PTHrP) was swiftly corrected by the related PT2977/belzutifan drug in a prospective patient with sarcomatoid ccRCC. Our data supports the evaluation of HIF-2 antagonists for ccRCC patients with humoral hypercalcemia of malignancy, which may serve as a predictive biomarker of response (along with PTHrP reduction).

overall_design: RNAseq profile of hypercalcemic ccRCC PDXs (XP771b, XP945, XP1169d, XP1139, XP899, XP1087, XP1152, XP1059 and XP1631) and normocalcemic ccRCC PDX (XP374, XP1487) on vehicle and PT2399 treatment. Additionally, matched RNAseq profile of PDX lines without treatment for which ATAC seq have been performed. The additional normocalcemic PDX lines are XP143, XP165d7, XP1676 and hypercalecmic ones are XP1139, XP945, XP165, XP289.

first: Arijit

last: Mal

first: Charlotte

last: Small

first: Alana

last: Christie

first: Vanina

last: Tcheuyap

first: Brooklyn

last: Jackson

first: James

last: Brugarolas


title: Targeting p300/CBP abolishes HOXB13 loss-induced lipogenesis and tumor metastasis [ChIP-seq]

first: Jindan

last: Yu

overall_design: To evaluate whether HOXB13 loss induces lipogenic enhancer activation through p300/CBP, we performed H3K27ac ChIP-seq in control and HOXB13-KD LNCaP cells with concomitant p300 and/or CBP KD, or treated with DMSO or 250nM CCS1477 for 24 hours

first: Xiaodong

last: Lu

first: Qi

last: Chu

first: Jonathan

last: Zhao


title: Loss of NF2 drives malignant transformation of human pancreatic acinar cells and enhances cell fitness under nutrient deprivation and therapeutical stress [bulk_RNAseq]

city: San Antonio

first: Pei

last: Wang

address: 7703 Floyd Curl Dr

institute: UT Health San Antonio

summary: Pancreatic ductal adenocarcinoma (PDAC) occurs as a complex, multifaceted event driven by the interplay of tumor permissive genetic mutations, nature of cellular origin and microenvironmental stress. In this study, we present a novel model to screen previously underappreciated tumor suppressor genes in human pancreatic acinar-derived PDAC and probe their implications under nutrient deprived environmental context. Primary human pancreatic acinar 3D organoids were engineered to harbor triple PDAC driver mutations—KRAS G12V, TP53 inactivation, and CDKN2A deletion (designated as KPT organoids). Using a pooled CRISPR knockout library targeting 199 potential tumor suppressors curated from recurrent mutations in clinical PDAC samples, we performed in vivo and in vitro screening with KPT cells and revealed significant enrichment of a list of candidate tumor suppressors, with NF2 emerging as the top target. Functional validation confirmed that loss of NF2 promotes the transition of PDAC from a non-invasive to an invasive state, potentially through extracellular matrix (ECM) modulation. Additionally, we found that the fibroblast heterogeneity in these organoids-derived tumors correlates with the cancer progression, suggesting the important roles of cancer-stroma communications in tumor evolution. Strikingly, NF2 inactivation was found to enhance PDAC cell fitness under nutrient starvation, a condition reflective of the harsh tumor microenvironment. This adaptation not only reinforces the oncogenic state but also confers therapeutical resistance. These findings establish NF2 as a critical tumor suppressor in PDAC and uncover its role in mediating nutrient adaptation and drug resistance. Importantly, this study provides new insights into drug resistance mechanisms and potential therapeutic targets in PDAC.

overall_design: In order to investigate the gene expression changes induced by NF2 knockout, bulk RNA seq was performed using 6 independent KPT organoid samples, 6  KPTN organoid samples, 3  KPT-derived xenograft tumor samples and 3  KPTN-derived xenograft tumor samples,

first: Yi

last: Xu

first: Michael

last: Nipper

first: Angel

last: Dominguez

first: Chenhui

last: He

first: Francis

last: Sharkey

first: Sajid

last: Khan

first: Daohong

last: Zhou

first: Lei

last: Zheng

first: Yu

last: Luan

first: Jun

last: Liu


title: Tumor-Initiating Stem Cells Fine-tune the Cell States of Neutrophils to Drive Cancer Relapse from Immunotherapy [SCC bulk RNA-Seq]

city: Chicago

first: weijie

last: guo

address: 929 East 57th Street, GCIS W423N

institute: university of Chicago

summary: The highly heterogeneous and plastic nature of tumor-associated neutrophils (TANs) has been recognized, but how different cell states of TANs emerge, evolve, distribute, and impact cancer immunotherapy efficacy remains elusive. Using single-cell RNA sequencing, spatial transcriptomic analysis, and genetic manipulations, we show that, while anti-PDL1/CD40 agonist immunotherapy can reprogram TANs to gain strong anti-tumor activities in squamous cell carcinomas (SCCs), a subset of neutrophils residing at the tumor-stroma interface can preserve their immune-suppressive state. Importantly, we identified a group of Sox2Hi tumor-initiating stem cells (tSCs) at the tumor-stroma interface that can activate Fatty Acid Desaturase 1 (Fads1) and produce arachidonic acid (AA) to induce autocrine prostaglandin E2 signaling which can disrupt the interferon responses in neutrophils. Thus, through this interaction, tSCs fine-tunes the cell states of neutrophils, shapes neutrophil heterogeneity, and sculpts a protective micro-niche to drive cancer relapse following immunotherapy.

overall_design: To investigate the mechanisms by which tSCs modulate neutrophils, we isolated Itga6hi CD80+ tumor stem-like cells and Itga6low CD80⁻ differentiated cancer cells from DMBA/TPA-induced skin squamous cell carcinoma (SCC), and performed bulk RNA sequencing on these populations.

first: Weijie

last: Guo

first: Yuxuan

last: Miao


title: Leveraging Medulloblastoma Clonal Dynamics to Overcome Treatment Resistance

city: Hamilton

first: Sheila

last: Singh

state: ON

address: 1280 Main Street West

department: Biochemistry and Biomedical Sciences

institute: McMaster University

summary: Medulloblastoma (MB) is a common pediatric brain tumor with distinct molecular subgroups, of which, Group 3 MB is associated with increased recurrence, metastatic potential and poor patient outcomes. Small molecule inhibitors targeting BMI1 have been shown to be efficacious against several types of malignant tumors, including pediatric MB. While our previously published in vivo study provides a promising proof-of-concept for the therapeutic targeting of BMI1 in Group 3 MB with small molecule inhibitor, it is not sufficient to eradicate the tumour.

overall_design:
In this study, following preclinical validation of BMI1 inhibitor PTC596, DNA barcoding technology was leveraged to profile in vivo clonal dynamics of Group 3 MB in response to the established chemoradiotherapy regimen alone and in combination with PTC596. Following demonstration of a small number of treatment-refractory clones we sought to identify potential druggable molecular vulnerabilities by utilizing phosphoproteomic profiling and genome-wide CRISPR screening.

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The table below lists GEO accessions reused/reanalyzed for this study.
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first: David

last: Bakhshinyan

first: Laura

last: Escudero

first: Kevin

last: Brown

first: Jason

last: Moffat


title: Fibroblast STAT3 activation drives organ-specific premetastatic niche formation

city: Ann Arbor

first: Emily

last: Lasse-Opsahl

state: Michigan

address: 1500 E Medical Center Dr Rm 6110

department: Cancer Biology

institute: University of Michigan

summary: Pancreatic cancer is associated with a high rate of metastasis and poor prognosis. The formation of a premetastatic niche (PMN) facilitates cancer cell spread and contributes to cancer mortality. Using murine pancreatic cancer models based on expression of oncogenic KRAS in the pancreas epithelium, we discovered that remodeling of the lung microenvironment occurred in mice bearing pancreatic precursor lesions prior to cancer formation. This early lesion premetastatic niche (EL-PMN) resembled the PMN in cancer-bearing mice, and both feature characteristics of overt metastasis, such as transcriptional reprogramming, activation of fibroblast STAT3 signaling, and infiltration of immunosuppressive ARG1+ macrophages. Both pancreatic cancer patients and mouse models demonstrated elevated serum IL6. Inactivating oncogenic KRAS reduced serum IL6 and reverted fibroblast STAT3 phosphorylation in mouse lungs; loss of lung fibroblast STAT3 phosphorylation was similarly observed when mice were treated with the pan-RAS inhibitor RMC7977. While ARG1+ macrophage infiltration was dispensable for fibroblast STAT3 activation, IL6 blockade inhibited lung fibroblast STAT3 activation. Functionally, fibroblast STAT3 activation was necessary for lung metastasis establishment and growth. Interestingly, activation of STAT3 in the PMN was present in the lungs but not in the liver, where fibroblast reprogramming occurred only in overt metastasis, pointing to organ-specific PMN formation. In human metastasis samples, phosphorylated STAT3 in fibroblasts was similarly more abundant in the lungs than liver. Together, these data point to organ-specific mechanisms driving formation of the PMN and indicate that reprogramming of the microenvironment prior to metastasis might support early dissemination of pancreatic cancer.

overall_design: We harvest the right lung and pancreas from iKRAS mice on doxycycline for 16 weeks at which point they have precursor lesions in the pancreas, but no tumor. We also harvested the right lung and bone marrow from iKRAS;p53 mice on doxycycline for 20 weeks a which point all mice had primary pancreatic cancer. Mice were split into groups based on the prescence or absence of lung metastases. Additionally, we harvested the right lung from KC or KPC mice with pancreatic tumors. All samples were taken for single cell RNA sequencing - Samples were run using 50-cycle paired-end reads on the Illumina NovaSeq 6000 to a depth of 100,000 reads with an intital expected cell count of 10,000 cells per sample.

last: Lasse Opsahl

first: Marina

last: Pasca di Magliano


title: Loss of NF2 drives malignant transformation of human pancreatic acinar cells and enhances cell fitness under nutrient deprivation and therapeutical stress [single_cell_RNAseq]

first: Pei

last: Wang

overall_design: In order to investigate the gene expression changes induced by NF2 knockout, single cell RNA seq was performed using wild type, KPT and KPTN organoid samples, as well as KPT-derived and KPTN-derived xenograft tumor samples.

first: Yi

last: Xu

first: Michael

last: Nipper

first: Angel

last: Dominguez

first: Chenhui

last: He

last: Sharkey


title: Loss of NF2 drives malignant transformation of human pancreatic acinar cells and enhances cell fitness under nutrient deprivation and therapeutical stress [CRISPR_screen]

overall_design: In order to identify potential driver mutations in PDAC, we curated a list of 199 potential tumor suppressors associated with recurrent loss of function mutations in clinical PDAC samples. We then isolated primary acinar cells from healthy human pancreatic tissues which were maintained as 3D organoid culture. The organoids were engineered to carry three key PDAC driver mutations: oncogenic KRAS G12V, CRISPR-mediated knockout of TP53 and CDKN2A (designated as KPT organoids). A pooled CRISPR knockout library targeting the curated 199 genes was introduced into KPT organoids by lentivirus infection. The transduced cells were expanded for one passage, a fraction of cells was collected to serve as a reference control. For the in vivo screen, the expanded cells were subcutaneously transplanted into the hind flank of NSG (NOD/SCID/gamma) mice. The xenograft tumor tissues were collected after 8 weeks followed by DNA extraction. For the in vitro screen, the expanded cells were continuously passaged for 8 weeks (7-9 passages), followed by extraction of cellular DNA. The screen was performed using 4 independently established cultures, for each, one control sample, one organoid sample and two tumor samples were collected.

first: Francis

first: Sajid

last: Khan

first: Daohong

last: Zhou

first: Lei

last: Zheng

first: Yu

last: Luan

last: Liu


title: Brain immune responses to systemic inflammation in postnatal mice

city: Mitaka

first: Atsuyoshi

last: Shimada

state: Tokyo

address: 5-4-1 Shimorenjaku

department: Health Sciences

country: Japan

institute: Kyorin University

summary: In newborn mouse, systemic bacterial infection damages the brain even in the absence of direct bacterial invasion.  However, the early immune reactions by intracranial tissues remain an enigma.  We injected lipopolysaccharide (LPS) intraperitoneally into 7-day-old mice to induce systemic inflammation.  Brains were removed and dissociated 24 h after LPS injection, and CD11b(+) cells were isolated using the magnetic-activated cell sorting.  Total RNA samples were extracted from the brain CD11b(+) cells and were analyzed with Gene Expression Microarray.  The results indicated that the transcript expressions of the following nine genes were strikingly increased: Saa3, Saa1, Saa2, Cxcl13, Ccl5, Irg1, Cxcl9, Lcn2, and Slfn4.  In situ hybridization indicated that Saa 3, 2, and 1, Cxcl13, Irg1, and Ccl5 were expressed by macrophages in the meningeal and perivascular space and choroid plexus, whereas Cxcl9 and Lcn2 were expressed by arachnoid, pial, and perivascular fibroblasts.  In conclusion, immune reactions of the brain to systemic inflammation were initiated by leptomeningeal and choroid plexus macrophages and leptomeningeal and perivascular fibroblasts in postnatal mice.

overall_design: We prepared 8 tubes (4 tubes for saline-injected mice and 4 for LPS-treated). Two brains from two mice that were treated with the same way were dissociated in a single tube. CD11b(+) cells were isolated using the magnetic-activated cell sorting. Total RNA samples were extrtacted from the CD11b(+) cells. Four RNA samples prepared from the LPS-treated mice were compared with for samples from the saline-injected mice.


title: Distinct components of nucleoside-modified messenger RNA vaccines cooperate to instruct efficient germinal center responses

city: Los Angeles

first: Roberto

last: Spreafico

state: CA

address: UCLA

department: Institute for Quantitative and Computational Biosciences

institute: University of Califonia Los Angeles

summary: Nucleoside-modified mRNA vaccines elicit protective antibodies through their ability to promote T follicular helper (Tfh) cells. The lipid nanoparticle (LNP) component of mRNA vaccines possesses inherent adjuvant activity. However, to what extent the nucleoside-modified mRNA can be sensed and contribute to Tfh cell responses remains largely undefined. Herein, we deconvoluted the signals induced by LNP and mRNA that instruct dendritic cells (DCs) to promote Tfh cell differentiation. We demonstrated that the nucleoside-modified mRNA drives the production of type I interferons that act on DCs to induce their maturation and the induction of Th1-biased Tfh responses. Conversely, LNP favors the acquisition of a Tfh cell-inducing program in DCs, a stronger Th2 polarization in Tfh cells, and allows for rapid mRNA translation by DCs within the draining lymph node. Our work unravels distinct adjuvant features of mRNA and LNP necessary for the induction of Tfh cells, with implications for vaccine design.

overall_design: We sought to evaluate the impact of the nucleoside-modified mRNA and LNP vaccine components on the transcriptional program of DCs and utilized the LIPSTIC system to probe this in relation to their antigen-presenting status. We created a construct consisting of the RBD of SARS-CoV-2 spike protein fused via a GS linker to the chicken ovalbumin peptide sequence recognized by OT-II CD4 T cells (RBD-OVA). Mice were immunized with either mRNA-LNP encoding RBD-OVA (mRNA_LNP), recombinant RBD-OVA mixed with empty LNP (protein_LNP), or recombinant RBD-OVA mixed with AddaVax (protein_Addavax) and DCs in the draining lymph nodes were analyzed 24-hours later.

last: Bettini

first: Aleksey

last: Chudnovskiy

first: Giulia

last: Protti

first: Sandra

last: Nakadakari-Higa

first: Simona

last: Ceglia

first: Diana

last: Castaño

first: Joy

last: Chui

first: Hiromi

last: Muramatsu

first: Thandiswa

last: Mdluli

first: Edit

last: Abraham

first: Zoltan

last: Lipinszki

first: Ivan

last: Maillard

first: Ying

last: Tam

first: Andrea

last: Reboldi

first: Norbert

last: Pardi

first: Gabriel

middle: D

last: Victora

first: Michela

last: Locci


title: Transcriptional response of Candida albicans to the utilization of aromatic compounds as the sole carbon source

city: Jena

first: Enrico

last: Garbe

address: Albert-Einstein-Straße 10

department: (Epi-)Genetics of Fungal Infections

institute: HKI Jena

summary: Main goal of this analysis was to idnetify metabolic adaptation processes in C. albicans when aromatic compounds, like catechol or hydroquinone are used as the sole carbon source (C-source) and how this is mediated on the transcriptional level. Further, a suspected regulatory activity of the transcription factors Stp2, a central regulator of amino acid metabolism, and Zcf25, a putative regulator of the oxoadipate pathway, on these processes was investigated. Therefore, the SC5314 wild type and single and dual knockout strains of the aforementioned regulators (stp2Δ, zcf25Δ, stp2Δ/zcf25Δ) were incubated in medium containing either glucose (SD), a mixture of proteinogenioc amino acids (SC), catechol (CAT) or hydroquinone (HQN) as the sole C-source and the cellular transcriptome investigated via RNA-Sequencing to define trasncriptional changes in response to the indicated different C-sources.

overall_design: Indicated C. albicans strains were pre-incubated in SD minimal medium and transferred to experimental medium containing only the indicated C-source (SD, SC, CAT, HQN) and incubated for 4 h. Cellular transcriptomes were assessed via RNA-Sequencing in biological triplicates.

first: Sascha

last: Schäuble

first: Bettina

last: Böttcher

first: Dominik

last: Driesch

first: Slavena

last: Vylkova


title: Transcriptional response of Candida albicans to the utilization of amino acids as the sole carbon source

summary: Purpose of this study was to define the transcriptional response of Candida albicans to the utilization of amino acids as the sole carbon source (C-source) in order to study regulation of metabolic adaptation of the fungus to amino acid-rich media. Furthermore, potential regulatory activities of the transcription factor Stp2 exceeding the described role in amino acid-uptake have been investigated. Therefore, the SC5314 wild type and a deletion strain of Stp2 (stp2Δ) were incubated in medium containing either glucose (SD) or a mixture of proteinogenioc amino acids (SC) as the sole C-source and the cellular transcriptome defined using RNA-sequencing.

overall_design: Indicated C. albicans strains were pre-incubated in SD minimal medium and transferred to experimental medium containing only the indicated C-source (SD, SC) and incubated for 1 h. Cellular transcriptomes were assessed via RNA-Sequencing in biological triplicates.


title: Atypical contribution of caspase-3 to melanoma cancer cell motility by regulating coronin-1B activity

city: Bron

first: Hector

last: Hernandez-Vargas

state: Rhone

address: 36 bis Rue de la Batterie

institute: Genomics Consulting

summary: Recent studies have unveiled unexpected connections between cell death and cell motility involving caspases, key regulators of apoptosis. While traditionally recognized for their pro-apoptotic roles, caspases have emerged as regulators of physiological processes beyond cell death, including cellular differentiation and motility. In some particularly aggressive cancers like melanoma, caspase-3, a prominent executioner caspase, is unexpectedly and inexplicably highly expressed. Here, we describe a novel non-apoptotic role for caspase-3 in melanoma cell motility. Through comprehensive molecular and cellular analyses, we demonstrate that caspase-3 is constitutively associated with the cytoskeleton and crucially regulates melanoma cell migration and invasion in vitro and in vivo. Mechanistically, caspase-3 interacts with and modulates the activity of coronin1-B, a key regulator of actin polymerization, thereby promoting melanoma cell motility, independently of its apoptotic protease function. Furthermore, we identify specificity protein 1 (SP1) as a transcriptional regulator of CASP3 expression, and show that its inhibition reduces caspase-3 expression and impairs melanoma cell migration. Overall, this study provides insights into the multifaceted roles of caspase-3 in cancer progression, highlighting its relevance as a novel target for anti-metastatic therapies.

overall_design: To get a glimpse into the molecular and cellular pathways that might be regulated by caspase-3, CASP3 expression was reduced using RNA interference, in the melanoma cell line WM793

first: Kevin

last: Berthenet

last: Ichim


title: Single-cell Multiomics Analysis Reveals CTCF as a Key Regulator of Lung Morphogenesis and Progenitor Maintenance

first: Jiang

last: Yamei

overall_design: To comprehensively study the heterogeneity and regulatory mechanisms of lung morphogenesis, we performed RNA-seq profiling of nuclei extracted from embryonic day 12.5 (E12.5) lungs.

first: Shenfei

last: Sun

first: Yamei

last: Jiang

first: Fujing

last: Huang

first: Wei

last: Wei

first: Mathias

last: Hochgerner

first: Tianmin

last: Xu

first: Xiaoting

last: Wang

first: Kaijun

last: Lin

first: Xinna

last: Zhang

first: Yanli

first: Hua

last: He

first: Miao

last: Yu

first: Xiaofang

last: Tang

first: Xinhua


title: Identification of CLIC3 as a novel prognostic biomarker in triple-negative breast cancer via characteristic analysis (WES)

city: Hangzhou

first: Yunkun

last: Lu

state: Zhejiang

address: No. 3, Qingchun East Rd

department: Sir Run Run Shaw Hospital

institute: Zhejiang University

summary: The lack of prognostic biomarkers and therapeutic targets in triple-negative breast cancer (TNBC) underscores an urgent need for the identification of novel biomarkers and effective treatment targets. In this study,  we collected tumor and adjacent normal samples of four TNBC and four non-TNBC patients for  whole-exome sequencing (WES).Comparative WES analysis uncovered the distinct landscape of somatic mutations and driver genes in TNBC.

overall_design: To investigate the potential biomarker of TNBC

first: Shuai

last: Yuan

first: Sijie

last: Feng

first: Jiangxia

last: Li


title: Identification of CLIC3 as a novel prognostic biomarker in triple-negative breast cancer via characteristic analysis (RNA-Seq)

summary: The lack of prognostic biomarkers and therapeutic targets in triple-negative breast cancer (TNBC) underscores an urgent need for the identification of novel biomarkers and effective treatment targets. In this study,  we collected tumor and adjacent normal samples of four TNBC and four non-TNBC patients for  RNA sequencing.TNBC exhibited distinguished gene expression and splicing patterns in contrast to non-TNBC. Notably, we identified four genes that were exclusively responsive and significantly correlated with prognosis in TNBC, but not non-TNBC. Immunohistochemical analysis confirmed the preferential expression of Chloride Intracellular Channel 3 (CLIC3) in TNBC, proposing CLIC3 as a potential prognostic biomarker for TNBC.


title: Identification of CLIC3 as a novel prognostic biomarker in triple-negative breast cancer via characteristic analysis

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

overall_design: Refer to individual Series


title: HIF-2-dependent Regulation of PTHrP and Paraneoplastic Hypercalcemia in Aggressive Clear Cell Renal Cell Carcinoma [ATAC-seq]

first: Bingqing

last: Xie

overall_design: ATAC-seq performed on RCC PDX lines and one HCC PDX line without treatment, vehicle treated, and PT2399 treated. The normocalcemic PDX lines are XP1487, XP374, XP1657d, XP1676, XP296, XP490, XP143 and hypercalecmic ones are XP1631, XP771b, XP1139, XP165, XP289, XP1059, XP899, HCC4068, XP1087, XP1152, XP945.

first: Arijit

last: Mal

first: Charlotte

last: Small

first: Alana

last: Christie

first: Vanina

last: Tcheuyap

first: Brooklyn

last: Jackson

first: James

last: Brugarolas


title: Hofbauer cells are transcriptionally and epigenomically unique programmable tissue macrophages in human placentas [ATAC-seq]

city: Debrecen

first: Laszlo

last: Nagy

address: Egyetem ter 1.

country: Hungary

institute: University of Debrecen

summary: Tissue-resident macrophage Hofbauer cells (HB cells) play a central role in maintaining placental tissue integrity and homeostasis. HB cells are responsible for fetal immune functions and contribute to angiogenesis, regeneration, and metabolism of chorionic villi. All of these roles have a major impact on the course and outcome of pregnancy through the performance of placental functions. In this study, we sought answers to the following questions: what are the regulatory mechanisms that ensure the specific gene expression of these cells? Are there subgroups within the population of HB cells that were previously thought to be homogeneous? Are HB cells programmable? To answer these questions, Hofbauer cells were isolated from placental villous tissue using enzymatic digestion, gradient-based centrifugation, and both negative and positive immunopurification. ATAC-seq, bulk RNA-seq, in vitro stimulation studies, re-analysis of bulk and single-cell RNA sequencing, and CyTOF were used to assess chromatin accessibility, gene expression regulation, programmability, and heterogeneity of human HB cells. Using these approaches, we found that compared to other adult and fetal macrophages, HB cells have a unique transcriptional regulatory profile that is regulated by the transcription factor-coding NR4A2, NR4A3, GR, and RFX genes. In addition, HB cells showed unique gene expression changes upon stimulation with IL-4 and the PPAR𝛾 agonist Rosiglitazone. Based on the re-analysis of single-cell RNA-seq data from the first-trimester fetal-maternal interface and CyTOF analysis of our isolates, heterogeneous HB cell subpopulations were identified based on either gene or marker protein expression.

overall_design: Transcriptomic and epigenetic profiling of human Hofbauer cells from healthy term placentas using high throughput sequencing (ATAC-seq and RNA-seq).

first: Dora

last: Bojcsuk

first: Benjamin-Rego

last: Barath


title: Hofbauer cells are transcriptionally and epigenomically unique programmable tissue macrophages in human placentas [RNA-seq]


title: mRNA Initiation and Termination are Spatially Coordinated

city: Worcester

first: Athma

last: Pai

address: 368 Plantation Street, AS5-2057

institute: UMASS Medical School

summary: ABSTRACT: The expression of a precise mRNA transcriptome is crucial for establishing cell identity andfunction, with dozens of alternative isoforms produced for a single gene sequence. The regulationof mRNA isoform usage occurs by the coordination of co-transcriptional mRNA processingmechanisms across a gene. Decisions involved in mRNA initiation and termination underlie thelargest extent of mRNA isoform diversity, but little is known about any relationships betweendecisions at both ends of mRNA molecules. Here, we systematically profile the joint usage ofmRNA transcription start sites (TSSs) and polyadenylation sites (PASs) across tissues andspecies. Using both short and long read RNA-seq data, we observe that mRNAs preferentiallyusing upstream TSSs also tend to use upstream PASs, and congruently, the usage ofdownstream sites is similarly paired. This observation suggests that mRNA 5’ end choice maydirectly influence mRNA 3’ ends. Our results suggest a novel “Positional Initiation-TerminationAxis” (PITA), in which the usage of alternative terminal sites are coupled based on the order inwhich they appear in the genome.To examine the direct influence of promoter (AFE) choice on ALE decisions, we performed a series of CRISPR modulations on HEK293 cells to either activate or repress AFEs and measure the change in ALE usage.

overall_design: HEK293 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) containing D-Glucose (4.5 g/L), L-Glutamine and 10% fetal bovine serum (FBS). Cells were seeded into 6-well plates and transiently transfected ~16 hours later, at ~80% confluency, using lipofectamine3000 (Invitrogen L3000001) CRISPR activaton experiments were transfected with either UniSAM empty vector (Addgene #99866) or UniSAM vector containing sgRNA targeting the promoter region of the targeted first exon. CRISPR inteference experiments were transfected with either dCas9-P2A-EGFP empty vector (Addgene #159086) or dCas9-P2A-EGFP vector containing sgRNA targeting downstream of the transcription start site of the targeted first exon. 48 hours post transfection, total RNA was extracted using RNeasy Mini Kit according to the manufacturer’s instructions. Reverse transcription was performed in a reaction mix containing 1 μg of total RNA, using Maxima H Minus First Strand cDNA Synthesis Kit (Thermo Scientific, K1652) according to the manufacturer’s instructions. Two seperate batches with different experimental targets were sequenced. The first was sequenced xxxx. The second batch of Total RNA was sent to Novogene on dry ice. Novogene performed poly-A selection paired-end RNA-sequencing.Paired-end Illumina libraries were sequenced on Illumina Novaseq 6000.

first: Ezequiel

last: Calvo-Roitberg

first: Christine

last: Carroll

first: GyeungYun

last: Kim

first: Valeria

last: Sanabria

first: Maritere

last: Uriostegui-Arcos

first: Joseph

last: Paquette

first: Steven

last: Mick

first: Sergey

last: Venev

first: Job

last: Dekker

first: Ana

last: Fiszbein

middle: A


title: Single-nucleus RNA Sequencing Reveals GABAergic Vulnerability and Reactive Gliosis Driven by Loss of TDP-43

status: Public on Oct 06 2025

city: Laramie

first: Yun

last: Li

state: WY

address: 1000 E University Ave

department: Zoology and Physiology

institute: University of Wyoming

summary: TDP-43 is an RNA-binding protein important for RNA processing, whose loss-of-function is involved in multiple neurodegenerative disorders, including frontotemporal dementia (FTD), amyotrophic lateral sclerosis (ALS), and Alzheimer’s disease (AD). We performed single-nucleus RNA-sequencing to study the convergent and divergent molecular signatures of short-term and long-term TDP-43 depletion in the medial prefrontal cortex (mPFC) using Tdp-43F/F mice, compared with that of 5xFAD mice, a well-established AD mouse model with β-amyloid plaque pathology. Our results demonstrated a significant loss of GABAergic neurons in the mPFC after short-term TDP-43 depletion. This was accompanied by a remarkable reactive gliosis in the mPFC. Our results revealed a strong GABAergic and glial involvement during early stages of TDP-43 loss-of-function, suggesting that the GABAergic system is vulnerable to TDP-43 pathology and could be considered a potential target for developing therapeutic strategies and biomarkers for early detection in TDP-43 linked AD-related dementia.

overall_design: TDP-43 loss-of-function in the medial prefrontal cortex (mPFC) was investigeted using a conditional knockout mouse model Tdp-43 F/F with focally injected AAV viruses expressing either Cre recombinase or GCaMP6f control, alongside 5xFAD mice as AD controls. Short-term (2 months) and long-term (6 months) knockout cohorts, with corresponding age-matched controls, were analyzed. Freshly dissected mPFC tissues were pooled and subjected to single-nucleus RNA sequencing (10x Genomics 3' platform).

first: Rashmi

last: Thapa

first: Navin

last: Adhikari

first: Sishir

last: Gautam

first: Mingming

last: Sun

first: Sierra

last: McOmie

first: Viyaleta

last: Davydzenka

first: Derek

last: Smith

first: Jack

last: Syring

first: Harlie

last: Kaligis

first: Jade Marie

last: Kosmicki

first: Rong

last: Chen


title: Transcriptional characterization of mouse and rat ventral pallidum using single nucleus RNA-sequencing

city: Seattle

first: David

last: Ottenheimer

state: WA

address: 1959 NE Pacific St

institute: University of Washington

summary: The ventral pallidum (VP) was defined as a basal ganglia nucleus and a major output of the nucleus accumbens. It is known to be involved in motivated behaviors, including feeding. We sought to further characterize VP by sequencing the RNA from individual nuclei in mouse and rat VP and analyzing neuronal expression patterns. We also investigated the impact of a high-fat diet on VP transcription. These data will be useful for understanding cell type diversity in VP, homology between mouse and rat VP, and the impact of diet on VP gene expression.

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: We microdissected VP tissue from adult male and female mice and rats. We also dissected tissue from the nucleus accumbens in rats. We pooled tissue from all subjects in each experimental group, isolated nuclei, prepared cDNA libraries with 10x Chromium Next Gem Single Cell 3' v3.1 (Dual Index) kits, and sequenced on Illumina platforms. Our mouse experimental groups were high-fat diet (2 weeks), control (standard facility chow, 2 weeks), high-fat diet (5 weeks), and matched diet (5 weeks). All 4 rat libraries contain tissue from the same 4 rats; nuclei from each dissection region were split into two separate batches.

first: Rhiana

last: Simon

first: Cassidy

last: Burke

first: Garret

last: Stuber