title: Defining the unique and shared gene regulatory network components of IRE1αandXBP1in β-cells ofNOD mice

city: Madison

first: Hugo

last: Lee

state: WI

address: 440 Henry Mall

institute: University of Wisconsin-Madison

summary: Clinical and preclinical evidence suggest that β-cell endoplasmic reticulum stress and dysregulated unfolded protein response (UPR) contribute to type 1 diabetes (T1D) pathogenesis. During stress adaptation, IRE1α, a key UPR sensor, can exhibit pleiotropic roles. Its deletion in β-cells of non-obese diabetic (NOD) mice prior to insulitis (Ire1αβ-/-) confers protection against T1D. However, specific downstream effectors mediating this protective effect remain unknown. Here we show that β-cell-specific deletion of Xbp1, IRE1α’s downstream effector, protects mice against T1D. Histological and single-cell transcriptomic analyses indicate that Xbp1β-/- mice largely phenocopy Ire1αβ-/- mice. Comparative single-cell transcriptome and gene regulatory network analyses in islets of Ire1αβ-/- and Xbp1β-/- mice reveal unique transcriptional networks, biological processes and network regulators not only in β-cells a but other non-islet β-cell as well. Our findings define the role of β-cell IRE1α/XBP1 pathway and identify previously unrecognized networks and regulatory nodes of this pathway in NOD mice.

overall_design: Single cell RNA-seq of 5-week-old Xbp1fl/fl (WT) and Xbp1β-/- (KO) mice were done with n = 2 per group

first: Khagani

last: Eynullazada

first: Qiaodan

last: Ou

first: Junha

last: Shin

first: Sushmita

last: Roy

first: Feyza

last: Engin


title: Usp21 knockout causes abnormal lipid metabolism in mouse and its polymorphism correlates with hypercholesterolemia in outpatients

status: Public on Oct 06 2025

city: Nagasaki

first: Takashi

last: Ito

address: 1-12-4, Sakamoto, Nagasaki

department: Biomedical Sciences

country: Japan

institute: Nagasaki University

type: Expression profiling by high throughput sequencing

summary: USP21, a member of the ubiquitin protease family, plays a vital role in various biological functions. However, the effects of USP21 dysfunction remain incompletely understood. In this study, we generated Usp21 knockout (KO) mice. Blood tests showed no impairment of liver function but did reveal elevated levels of total cholesterol and free fatty acids in Usp21 KO mice compared to wild-type (WT) mice. Next, we performed RNA-sequencing (RNA-seq) to identify genes that Usp21 regulates. The results highlighted several candidate genes based on their biological relevance, and their expression levels were validated by RT-qPCR. The Usp21 KO mice exhibited significant elevations in the expression of the genes Fabp7, Nlrc5, and Ppargc1a which play an important role in lipid metabolism, compared to WT. These data suggest that Usp21 may play roles in lipid metabolism in association with Fabp7, Nlrc5 and Ppargc1a. To clarify the involvement of USP21 in human hypercholesterolemia, we examined single nucleotide polymorphisms (SNPs) around USP21 in non-hypercholesterolemic and hypercholesterolemic outpatients. We found that the rs11421 SNP downstream of USP21 was significantly associated with hypercholesterolemia. These data suggest that USP21 plays a role in mice and human lipid metabolism and that its polymorphism may be a diagnostic marker for human hypercholesterolemia.

overall_design: The changes in gene expresion was observed in Usp21 KO mice compared to WT.

first: Sailakshmi

last: Iyer

first: Naoko

last: Hattori

first: Hiroshi

last: Okuda

first: Takeya

last: Nakagawa

first: Satoshi

last: Fuji

first: Takahiro

last: Maeda

first: Haruhiko

last: Koseki


title: Exceptional diversity of allorecognition receptors in a nonvertebrate chordate reveals principles of innate allelic discrimination

city: San Francisco

first: Henry

last: Rodriguez

address: 1322 3rd avenue

country: USA

institute: University of California San Francisco

summary: Highly polymorphic allorecognition systems have been characterized in numerous invertebrate species, and exhibit discriminatory capabilities reminiscent of vertebrate adaptive immunity. As these systems utilize germline encoded receptors, the mechanisms underlying allelic discrimination are unknown. The invertebrate chordate, Botryllus schlosseri, undergoes a natural transplantation reaction controlled by a highly polymorphic, polygenic locus (called the fuhc) with over 1,000 allelic haplotypes found worldwide. Two individuals are compatible if they share one or both fuhc alleles, and we had found that polymorphic discrimination is due to the integration of signals from two allorecognition receptors encoded within the fuhc locus, called fester and uncle fester. Here we show that these two receptors are members of an extended family consisting of >35 genes, now called the Fester family (FF), and co-expressed with members of another diverse gene family, the fester co-receptors (FcoR). Both FF and FcoR are Immunoglobulin superfamily members and each FcoR encodes conserved tyrosine signal transduction motifs, including ITIMs or hemITAMs. FF and FcoR are expressed and encoded as cognate pairs in two polymorphic haplotypes: one within the fuhc locus, and another on a separate chromosome, and remarkably, copy number variation between haplotypes is of gene pairs. Furthermore, two FcoR genes can swap ITIMs and hemITAMs by alternative splicing, suggesting that dynamic tuning of activating and inhibitory signaling is required for allelic discrimination. These results indicate that conserved signal processing mechanisms are the foundation of both allelic discrimination in Botryllus, and recurring convergent evolution of allorecognition receptors observed from invertebrates to mammals.

overall_design: We used the fester (DQ517888.1) and uncle fester (JF806283.1) genes of Botryllus schlosseri as queries in tBLASTx searches against multiple B. schlosseri transcriptomes, both publicly available and previously sequenced in our laboratory. The Botryllus transcriptomes include samples from whole colonies, blood cells, vasculature systems, blastogenetic stages, and Integrin alpha-6-positive cells, ALDH cells, or BSA-positive cells. To identify FcoR genes, the fester genes from B. schlosseri were initially used as queries in tBLASTx searches against the transcriptomes and genomes of this species. Finally, the identified FcoR genes were used as queries in additional tBLASTx searches to identify further FcoR genes in the databases of this species.

last: Rodriguez-Valbuena

first: Jorge

last: Salcedo

first: Olivier

last: De Thier

first: Jean-Francois

last: Flot

first: Stefano

last: Tiozzo

first: Anthony

middle: W

last: De Tomaso


title: S100A6 drives lymphatic metastasis of liver cancer via activation of the RAGE/NF-kb/VEGF-D pathway

status: Public on Oct 07 2025

city: Hangzhou

first: Yunkun

last: Lu

state: Zhejiang

address: No. 3, Qingchun East Rd

department: Sir Run Run Shaw Hospital

country: China

institute: Zhejiang University

summary: Patients diagnosed with lymph node (LN) metastatic liver cancer face an exceedingly grim prognosis. In-depth analysis of LN metastatic patients’ characteristics and tumor cells’ interactions with human lymphatic endothelial cells (HLECs), can provide important biological and therapeutic insights. Here we identify at the single-cell level that S100A6 expression differs between primary tumor and their LN metastasis. Of particular significance, we uncovered the disparity in S100A6 expression between tumors and normal tissues is greater in intrahepatic cholangiocarcinoma (ICC) patients, frequently accompanied by LN metastases, than that in hepatocellular carcinoma (HCC), with rare occurrence of LN metastasis. Furthermore, in the infrequent instances of LN metastasis in HCC, heightened S100A6 expression was observed, suggesting a critical role of S100A6 in the process of LN metastasis. Subsequent experiments further uncovered that S100A6 secreted from tumor cells promotes lymphangiogenesis by upregulating the expression and secretion of vascular endothelial growth factor-D (VEGF-D) in HLECs through the RAGE/NF-kb/VEGF-D pathway while overexpression of S100A6 in tumor cells also augmented their migration and invasion. Taken together, these data reveal the dual effects of S100A6 in promoting LN metastasis in liver cancer, thus highlighting its potential as a promising therapeutic target.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HLEC cells treated with or without recombinant S100A6. Single-cell RNA sequencing analysis of patients' tissues.

first: Tianyi

last: Chen


title: Dupilumab inhibits proliferation of malignant lymphocytes in Sezary syndrome and boosts anti-tumor immunity

city: Pittsburgh

first: Patrizia

last: Fuschiotti

state: PA

address: 200 Lothrop St

institute: University of Pittsburgh

summary: Patients with Sezary syndrome (SS), the aggressive leukemic variant of cutaneous T-cell lymphoma, have few therapeutic options and a poor prognosis. We previously showed that the IL4/IL13 signaling pathway is critical in SS tumorigenesis. Here we investigated the potential therapeutic effect of inhibiting IL4/IL13 signaling with REGN668 (Dupilumab), a monoclonal antibody that blocks the IL4/IL13 pathway by targeting IL4Rα, the common subunit of the IL4 and IL13 receptors. Using recent advances in single-cell RNA sequencing we defined transcriptional changes and molecular mechanisms associated with REGN668 treatment in malignant and reactive T lymphocytes as well as in monocytes and dendritic cells from the peripheral blood of SS patients. We observed variable responses across patient samples and downregulation of patient-specific pathways in malignant and reactive immune cells. Significantly, we found that REGN668 downregulates expression of common pro-tumorigenic processes in malignant lymphocytes, including cell division, DNA damage/repair, autophagy, and various pathways associated with T-cell signaling. A key finding from functional ex vivo studies was that REGN668 inhibits proliferation of malignant lymphocytes more efficiently than blocking either IL4 or IL13 signaling alone. Furthermore, we found that Dupilumab also reverts the immunosuppressive phenotype of non-clonal T lymphocytes and myeloid cells in the SS tumor microenvironment, including the function of MDSCs as well as Th2 and exhaustion pathways. Although some case reports have cast doubt on the efficacy of Dupilumab in treating SS patients, our results suggest that the effects of Dupilumab are pathway-specific and that it may be a critical component of a multi-pathway treatment.

overall_design:
SS samples and healthy PBMC samples were cultured for 2 days and analyzed by scRNAseq.  Raw data are unvailable due to patient privacy concerns

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

middle: M

last: Gaydosik

first: Brigit

last: Lapolla

first: Larisa

middle: J

last: Geskin


title: WEE1 inhibitors trigger GCN2-mediated activation of the integrated stress response.

city: Toronto

first: Daniel

last: Durocher

state: ON

address: 600 University

country: Canada

institute: Lunenfeld Tanenbaum Research Institute

summary: The WEE1 kinase negatively regulates CDK1/2 to control DNA replication and mitotic entry. Genetic factors that determine sensitivity to WEE1 inhibition (WEE1i) are largely unknown. A genome-wide insertional mutagenesis screen revealed that mutation of the alternative translation initiation factor EIF2A sensitized to WEE1i. Mechanistically, WEE1i triggers a translational shut-down, which is lethal in combination with the reduced translation of EIF2AKO cells. A genome-wide CRISPR-Cas9 screen revealed that inactivation of integrated stress response (ISR) kinases GCN1/2 rescued WEE1i-mediated cytotoxicity. Accordingly, WEE1i induced GCN2 activation, ATF4 upregulation, and altered ribosome dynamics. Accordingly, loss of the collided ribosome sensor ZNF598 increased sensitivity to WEE1i. Notably, the ISR was not required for WEE1i to induce DNA damage, premature mitotic entry nor sensitization to DNA-damaging chemotherapeutics. Conversely, ISR activation was independent of CDK1/2 activation. WEE1i-mediated ISR activation was independent of WEE1 presence, pointing at off-target effects, which are shared by multiple chemically distinct WEE1 inhibitors. This response was also observed in peripheral blood monocytic cells. Importantly, WEE1 inhibition at doses that do not induce ISR activation still synergized with PKMYT1 inhibition. Taken together, WEE1i triggers cytotoxic ISR activation and translational shutdown, which can be prevented by low-dose treatments, while retaining the cell cycle checkpoint-perturbing effects.

overall_design: mRNA-seq  was performed on RPE1 TP53.KO PAC.KO cells after 48 h of treatment with DMSO or 250nM AZD1775 for differential expression analysis.

first: Timothy

middle: F

last: Ng


title: Macrophages expressing chimeric cytokine receptors have an inflammatory phenotype and anti-tumoral activity upon IL-10 or TGFβ stimulation

city: Zurich

first: Sabrina

last: Traxel

address: Raemistrasse 100

department: Department of Infectious Diseases and Hospital Epidemiology

country: Switzerland

institute: University Hospital Zurich

summary: Background Triple-negative breast cancer (TNBC) is a highly aggressive subtype of breast cancer that lacks hormone receptors and HER2 amplification, making it unresponsive to standard hormone or HER2-targeted therapies. Although immune checkpoint inhibitors (ICIs) have shown promise in tumors with high lymphocyte infiltration, their efficacy remains limited in tumors with minimal lymphocyte infiltration. To overcome this challenge, we developed a novel approach to reprogram tumor-associated macrophages (TAMs) from an immunosuppressive to an inflammatory phenotype within the tumor microenvironment (TME), aiming to enhance therapeutic outcomes in TNBC. Methods We designed a chimeric cytokine receptor (ChCR) that triggers STAT1 signaling upon stimulation with IL-10 or TGFβ, cytokines prevalent in the TME that typically drive immunosuppression. Human primary macrophages were transduced with a lentiviral vector expressing the ChCR, and changes in their phenotype, secretome, and transcriptome were analyzed following stimulation. The anti-tumoral activity of these reprogrammed macrophages was assessed using co-culture assays with 3D TNBC spheroids. Results ChCR-expressing macrophages showed robust STAT1 activation in response to IL-10 or TGFβ stimulation, resulting in an inflammatory phenotype similar to IFNγ activation, as confirmed by phenotypic markers, and transcriptomic profiling. These ChCR-stimulated macrophages demonstrated significant anti-tumoral effects in 3D TNBC spheroids. Moreover, ChCR stimulation led to the upregulation of CXCL9 and CXCL10, chemokines essential for lymphocyte recruitment, and genes associated with good response to ICIs. Conclusion We successfully engineered a ChCR that reprograms TAMs within an IL-10- and TGFβ-rich environment, inducing an inflammatory phenotype and anti-tumoral activity. The expression of CXCL9 and CXCL10 further supports lymphocyte recruitment, potentially facilitating greater lymphocyte infiltration and disrupting the immunosuppressive TME. This approach offers a promising strategy to improve immunotherapy outcomes in TNBC patients, particularly those with low immune cell infiltration, thereby addressing a critical unmet clinical need.

overall_design: To characterize macrophages expressing ChCRs, we transduced primary human monocytes with lentivirus and differentiated them to macrophages. Macrophages were stimulated for 2 days (unstimulated, IL-10, TGFb or IFNγ). Thereafter, gene expression was analyzed by bulk RNA sequencing.

first: Simon

last: Bredl

first: Roberto

last: Speck


title: Twist family BHLH transcription factor 1 is required for the maintenance of leukemia stem cell in MLL-AF9+ acute myeloid leukemia

city: TianJin

first: Xiao Tong

last: Ma

state: TianJin

address: Blood hospital, 288 Nanjing Road

department: Institute of Hematology & Blood Diseases Hospital

institute: Chinese Academy of Medical Sciences

summary: To identify the downstream targets of TWIST1 or Hoxa9, we carried out RNA sequencing to characterize transcriptional changes upon Twist1 deletion or Hoxa9 knockdown in LSCs from MLL-AF9+ AML mice.

overall_design: a) RNA-seq in Twist1-deleted and control leukemia stem cells from MLL-AF9+ AML mice; b) RNA-seq in  Hoxa9 knockdown and control leukemia stem cells from MLL-AF9+ AML mice.

first: Xiaotong

last: Wang

first: Jing

last: Yin

last: You


title: Productive mRNA Chromatin Escape is Promoted by PRMT5 Methylation of SNRPB -PROSeq after PRMT inhibition and Dexamethasone treatment

city: Bronx

first: David

last: Shechter

state: New York

address: 1300 Morris Park Ave

department: Biochemistry

institute: Albert Einstein College of Medicine

summary: Protein Arginine Methyltransferase 5 (PRMT5) regulates RNA splicing and transcription by symmetric dimethylation of arginine residues (Rme2s/SDMA) in many RNA binding proteins. However, the mechanism by which PRMT5 couples splicing to transcriptional output is unknown. Here, we demonstrate that a major function of PRMT5 activity is to promote chromatin escape of a novel, large class of mRNAs that we term Genomically Retained Incompletely Processed Polyadenylated Transcripts (GRIPPs). Using nascent and total transcriptomics, spike-in controlled fractionated cell transcriptomics, and total and fractionated cell proteomics, we show that PRMT5 inhibition and knockdown of the PRMT5 SNRP (Sm protein) adapter protein pICln (CLNS1A) —but not type I PRMT inhibition—leads to gross detention of mRNA, SNRPB, and SNRPD3 proteins on chromatin. Compared to most transcripts, these chromatin-trapped polyadenylated RNA transcripts have more introns, are spliced slower, and are enriched in detained introns. Using a combination of PRMT5 inhibition and inducible isogenic wildtype and arginine-mutant SNRPB, we show that arginine methylation of these snRNPs is critical for mediating their homeostatic chromatin and RNA interactions. Overall, we conclude that a major role for PRMT5 is in controlling transcript processing and splicing completion to promote chromatin escape and subsequent nuclear export.

overall_design:
To measure nascent transcription of A549 cells in response to Type I and Type II PRMT inhibition and also in response to independent or co-treatment with Dexamethasone (glucocorticoid), PRO-Seq (Precision Run-on Sequencing) was performed
This series with matched untreated control includes Dexamethasone (Dex) for 15 min and 3hrs, co-treatment with Dex and GSK591 (PRMT5i) or MS023 (Type I PRMTi), 2 days, 4 days, and 1 week (7 days) GSK591 or MS023 treatment, and 1 week GSK591 or MS023 treatment followed by 15 min or 3hrs of Dex

first: Maxim

middle: I

last: Maron

first: Joseph

middle: D

last: DeAngelo


title: The cAMP receptor protein, SyCRP1 acts as a transcriptional repressor of CO2-concentrating mechanism genes at high inorganic carbon levels in cyanobacteria

status: Public on Oct 05 2025

city: Hyderabad

first: Suraj

last: Chauhan

state: Telangana

address: Prof. C.R. Rao Road, Central University P.O., Gachibowli

department: Biotechnology and Bioinformatics

country: India

institute: University of Hyderabad

type: Genome binding/occupancy profiling by high throughput sequencing

summary: CO2-concentrating mechanism (CCM) is a unique adaptation that evolved in cyanobacteria for inorganic carbon (Ci) sequestration under limiting Ci levels. The CCM is based on several Ci uptake systems and the carboxysome in which RubisCO is confined in a high CO2 environment. Many CCM components are transcriptionally upregulated under low Ci levels through the combined action of the transcriptional factors NdhR, CmpR and the cAMP-binding SyCRP1. Here we show that, SyCRP1 senses the high Ci levels through high cAMP thereby repressing CCM genes. SyCRP1 possess low- and high-affinity cAMP binding sites. Further, the specific interaction of SyCRP1 with membrane lipids was shown. Flag-tagged SyCRP1, when ectopically expressed, was localized to the membrane and released to the cytosol upon cAMP binding under high Ci levels. Finally, ChIP-seq experiments revealed that SyCRP1 binds cis-acting elements at the promoters of multiple transcription units, mainly those involved in CCM. EMSA confirmed SyCRP1’s binding to target DNA-elements. Collectively, our results establish SyCRP1 as a transcriptional repressor of the cyanobacterial CCM under high Ci conditions.

overall_design: ChIP-seq of 3XFlag tagged SyCRP1 from Synechocystis PCC 6803 grown in BG11 with high CO2 condition. SyCRP1 was expresesed in BG11 that contains 0.17 µM cobalt. Cells grown till 1 OD (730 nm) and for high CO2  condition, 5% (v/v) was supplemented in sterile air for bublling the cultures.

first: Prakash

middle: S

last: Jogadhenu


title: Effect of the Bryostatin 1 in B cells

city: Bunkyo-ku

first: Naoki

last: MORITA

state: Tokyo

address: 1-1-1 Yayoi

institute: The University of Tokyo

summary: Effect of the Bryostatin 1 in B cells is remain unclear. We here reported the effect of Bryostain 1 in the class-swithing.

overall_design: L-4 stimulated B cells were cultured wit or without B cells. Two days later, B cells were harvested.

first: Reiko

last: SHINKURA


title: Crosstalk between EZH2 and m6A RNA methylation promotes prostate cancer progression through modulating an m6A autoregulation pathway

city: Chicago

first: Yang

last: Yi

state: IL

address: 303 E Superior St

department: Department of Urology

institute: Northwestern University

summary: N6-methyladenosine (m6A), the most predominant RNA modification in humans, participates in various fundamental and pathological bioprocesses. Dynamic manipulation of m6A deposition in the transcriptome is critical for cancer progression, while how this regulation is achieved remains understudied. Here, we report that in prostate cancer (PCa), Polycomb group (PcG) protein Enhancer of Zeste Homolog 2 (EZH2) exerts an additional function in m6A regulation via its enzymatic activity. Mechanistically, EZH2 methylates and stabilizes FOXA1 proteins from degradation, which in turn facilitates the transcription of m6A reader YTHDF1. Through activating a m6A autoregulation pathway, YTHDF1 enhances the translation of METTL14 and WTAP, two critical components of the m6A methyltransferase complex (MTC), and thereby upregulates the global m6A level in PCa cells. We further demonstrate that inhibiting the catalytic activity of EZH2 suppresses the translation process globally through targeting the YTHDF1-m6A axis. By disrupting both the expression and interaction of key m6A MTC subunits, combinational treatment of EZH2 degrader MS8815 and m6A inhibitor STM2457 mitigates PCa tumor growth synergistically. Together, our study decodes a previously hidden interrelationship between EZH2 and RNA modification, which may be leveraged to advance the EZH2-targeting curative strategies in cancer.

overall_design: Nanopore Direct RNA sequencing of C4-2 cells after silencing EZH2 and METTL3, with two replicates each. RNA-sequencing of C4-2 cells after silencing YTHDF1 and treatment with EZH2 enzymatic inhibitor EPZ6438. In parallel, we performed ribosome profiling of both conditions using RiboLace library construction.

first: Joshua

last: Fry

first: Rendong

last: Yang

first: Qi

last: Cao


title: Cancer-derived exosomal DPP3 promotes lung metastasis by activating the RAP1 signaling pathway

city: wuhan

first: Wei

last: Yan

state: Hubei

address: Bayi Street 229 in Wuchang district

department: College of life science

institute: Wuhan University

summary: Metastasis is the leading cause of breast cancer-related death, with lung metastasis occurring in more than 60% of breast cancer (BRCA) patients. Small extracellular vesicles (sEVs) play crucial roles in breast cancer metastasis. Dipeptidyl peptidase 3 (DPP3) is an enzyme that hydrolyzes various peptides, and its dysregulation contributes to multiple pathology processes. However, the role of DPP3 in breast cancer lung metastasis is poorly understood. In this study, we discovered a novel mechanism whereby DPP3, packaged in small extracellular vesicles (sEVs) from breast cancer, is delivered to lung tissue to remodel the vascular niche to promote lung metastasis.

overall_design: To investigate the mechanism of breast cancer-secreted exosomal DPP3 on lung metastasis, we subcutaneously injected MDA-MB-231 and MDA-MB-231/DPP3 KO cells into the fourth mammary fat pat of NSG mice to construct orthotopic xenograft.After 5 weeks, mice were sacrificed, and lung tissue was collected for gene expression profiling analysis.

first: Xu

last: Li


title: Intra-leukemic interferon signaling suppresses expansion and mediates chemoresistance in human AML

first: Amy

last: Fan

state: CA

address: 769 25th Ave

department: Pathology

institute: UCSF

summary: Intra-tumoral heterogeneity can impact the competitive fitness and chemoresistance of individual cancer cells. In acute myeloid leukemia (AML), both genetic and functional heterogeneity contribute to chemoresistance, resulting in relapse after chemotherapy. While the role of cell-extrinsic factors such as interactions with non-leukemic cells has been described for AML relapse, whether interactions between cancer cells affects chemoresistance is not fully known. Here, we demonstrate that a dominant leukemic fraction can suppress the proliferation and expansion of other leukemic cells and that this suppression is reversible. We show that this suppression is mediated in part by both type I and type II intra-leukemic interferon (IFN) signaling and dependent on BST2. Importantly, blocking antibodies to type II IFN receptor activated the cycling of this suppressed cell fraction and sensitized the cells to subsequent chemotherapy treatment. Our findings suggest that interactions between functionally heterogeneous leukemic fractions can affect competitive fitness and treatment response, highlighting IFN signaling as a potential therapeutic target to counter chemoresistance.

overall_design: Human cells were engrafted in 4 to 12 week old male or female mice either without irradiation or 2 to 24h after sublethal irradiation (100-200 rad) by intra-venous or intra-femoral injection of 1,000-50,000 iAML cells or 1-5 million AML cells. BFP and mCherry iAML subclones were co-injected (competitive engraftment) or injected alone, or 3 separate pairs of 2 patient sample were co-injected (competitive engraftment) or injected alone. 5 weeks after iAML engraftment or 12-18 weeks after AML cell engraftment, human cells were isolated from crushed whole bone marrow by FACS. For chemotherapy experiments, engrafted iAML or AML samples were sorted from bone marrow aspirates or whole bone marrow 4 weeks after engraftment, 4 weeks after chemotherapy treatment (100 mg/kg cytarabine i.p. 5 days + 1.5 mg/kg doxorubicin i.p. 3 days),  8 weeks after chemotherapy treatment, or at experimental endpoint. For all experiments, total RNA was extracted using QIAGEN miRNeasy micro kit for RNA sequencing by SMART-Seq v4.

first: Fan

last: Amy C.

first: Karigane

last: Daiki

first: Majeti

last: Ravindra


title: WEE1 inhibition triggers GCN2-mediated activation of the integrated stress response

city: Utrecht

first: Michael

last: VanInsberghe

state: Utrecht

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

summary: The WEE1 kinase negatively regulates the CDK1/2 kinases to control DNA replication and prevent premature entry into mitosis. Pharmacological inhibition of WEE1 (WEE1i) causes hyperactivation of CDK1 and CDK2, leading to premature mitosis in the presence of DNA lesions. WEE1i treatment is particularly cytotoxic in cells with oncogene-induced or treatment-induced replication stress. To uncover genetic factors that sensitize cancer cells to WEE1i, a genome-wide insertional mutagenesis screen was performed and identified that mutation of the alternative translation initiation factor EIF2A sensitized cells to WEE1i. WEE1i sensitivity of EIF2AKO cells was not explained by altered replication kinetics. Rather, WEE1i leads to a translational shut-down which is lethal in combination with the reduced translation in EIF2AKO cells. A genome-wide CRISPR-Cas9 screen in WEE1i-treated cells revealed that inactivation of the integrated stress response (ISR) kinase GCN2 rescued WEE1i-mediated cytotoxicity. In line with these findings, WEE1i resulted in GCN2 activation, ATF4 upregulation and a translational shutdown. Moreover, WEE1 inhibition leads to altered ribosome dynamics and increased ribosome collisions. Accordingly, cells lacking the collided ribosome sensor ZNF598 show increased sensitivity to WEE1i. This response was not restricted to cancer cells, but was also observed in peripheral blood monocytic cells. The GCN2-mediated ISR was not required for WEE1i to induce DNA damage in S-phase, premature mitotic entry nor the sensitizing effects to DNA damaging chemotherapeutics. Conversely, ISR activation and translational shut-down are independent on WEE1i-mediated activation of CDK1/2. WEE1i-mediated ISR activation was independent of the presence of WEE1, pointing at an off-target effect, which is shared by multiple chemically distinct WEE1 inhibitors. Importantly, WEE1 inhibition at doses that do not induce the ISR can still synergize with PKMYT1 inhibition. Taken together, pharmacological WEE1 inhibition triggers cytotoxic ISR activation and translational shutdown, which can be prevented by low-dose treatments, while retaining the cell cycle checkpoint-perturbing effects.

overall_design: Ribosome profiling and RNA-seq in RPE-1 hTERT TP53-KO cells that were untreated or treated with AZD1775 WEEi inhibitor

first: Rinskje

middle: B

last: Tjeerdsma

first: Timothy

last: Ng

first: Maurits

last: Roorda

first: Danielle

last: Bianchi

first: Sora

first: Clara

last: Bonnet

first: Marieke

last: Everts

first: Femke

last: Bakker

first: Rolf

last: de Boer

first: Nathalie

last: Moatti

first: Nicole

last: Hustedt

first: Matthew

last: Leibovitch

first: Krzysztof

last: Szkop

first: Shannon

last: Mclaughlan

first: Lisa

last: Hoeg

first: Ivan

last: Topisirovic

first: Ola

last: Larsson

first: Alexander

last: van Oudenaarden

first: Steven

last: de Jong

first: Jeroen

last: van den Berg

first: Marvin

middle: E

last: Tanenbaum

first: Thijn

middle: R

last: Brummelkamp

first: Daniel

last: Durocher

first: Marcel

middle: A

last: van Vugt


title: Transcriptomic profiling of lung alveolar macrophages reveals distinct contribution of sterol metabolism in macrophage response to Cryptococcus gattii infection

city: klong luang

first: Siranart

last: Jeerawattanawart

state: Not US or Canada

address: 99 Moo 18, Paholyothin Road

department: Department of Medical Technology,Faculty of Allied Health Sciences

country: Thailand

institute: Thammasat University

summary: Alveolar macrophages are key first responders to pulmonary cryptococcosis, but there is still limited knowledge on the dynamic molecular changes during Cryptococcus gattii infection. We therefore analyzed the transcriptional profiles of alveolar macrophages isolated from mice infected intranasally with C. gattii and compared those infected with C. neoformans or treated with PBS at 7 days postinfection, using RNA sequencing. In C. gattii-infected mice, alveolar macrophages displayed the alteration of gene expression linked to sterol biosynthesis, while macrophages from C. neoformans-infected mice were primarily associated with interferon and cytokine signaling pathways. Thus, our research revealed the distinct patterns in the alveolar macrophage response to C. gattii infection.

overall_design:
To investigate the transcriptional characteristics of alveolar macrophages isolated from mice intranasally infected with C. gattii R265 using RNA sequencing analysis. A pairwise comparison of DEGs was carried out, which included (1) AMs of the PBS-treated mice (submitted to GEO previously as GSM6597668) compared with those of the C. gattii R265-infected mice at 7 days after infection and (2) AMs of the C. neoformans H99-infected mice (submitted to GEO previously as GSM6597669) compared with those of the C. gattii R265-infected mice at 7 days after infection.

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

last: Hansakon

first: Rudi

last: Alberts

first: Yongliang

last: Zhang

first: Pornpimon

last: Angkasekwinai


title: Integration of Imaging-based and Sequencing-based Spatial Omics Mapping on the Same Tissue Section via DBiTplus

status: Public on Oct 04 2025

city: New Haven

first: Rong

last: Fan

state: CT

address: 55 Prospect Street

department: Biomedical Engineering

institute: Yale University

summary: DBiTplus utilizes in situ reverse transcription, in-tissue delivery of DNA oligos for spatial barcoding, and RNaseH-mediated selective cDNA retrieval, preserving tissue architecture to enable highly multiplexed protein imaging and spatial transcriptomics on the same slide. Computational pipelines seamlessly integrates these modalities, allowing imaging-guided deconvolution to generate genome-scale, single-cell-resolved spatial transcriptome atlases. DBiTplus was demonstrated across diverse samples including mouse embryos, normal human lymph nodes, and formalin-fixed paraffin-embedded (FFPE) human lymphoma tissues, highlighting its compatibility with challenging clinical specimens. Applying DBiTplus to human lymphoma samples reveals key mechanisms driving lymphomagenesis, progression, and notably, the progression of indolent marginal zone lymphoma (MZL) or the transformation from chronic lymphocytic leukemia (CLL) to diffuse large B-cell lymphoma (DLBCL), including uniquely, the spatially resolved involvement of microRNAs in modulating the transformation dynamics. Thus, DBiTplus is a unified workflow including integrative experimental procedure and computational innovation for spatially resolved single-cell atlasing and exploration of biological pathways cell-by-cell at genome-scale.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: DBiT-seq spatial transcriptomics is performed on a tissue section followed by RNaseH-mediated selective cDNA retrieval. Multiplexed immunofluorescence imaging (using the PhenoCycler Fusion or CellScape) on the same tissue.

first: Archibald

last: Enninful

first: Oliver

last: Braubach

first: Zongming

last: Ma

first: Zhaojun

first: Mina

last: Xu


title: Targeting PTPN2 enhances human CAR T cell efficacy and the development of long-term memory [scRNA-Seq]

city: Melbourne

first: Tony

last: Tiganis

state: Victoria

address: 23 Innovation Walk, Monash University, Clayton

country: Australia

institute: Monash University

summary: CAR T cells have been ineffective against solid tumors, where the hostile tumor microenvironment limits CAR T cell function and persistence. Here we have used CRISPR/Cas9 gene-editing, or a small molecule inhibitor to target protein tyrosine phosphatase N2 (PTPN2) in human CAR T cells specific for the Lewis Y (LeY) neo-antigen. Targeting PTPN2 increased CAR and cytokine signaling and enhanced the activation and cytotoxicity of anti-LeY CAR T cells. The deletion or the systemic inhibition of PTPN2 in human CAR T cells repressed the growth of human tumor xenografts or patient-derived xenografts in mice and prolonged survival. PTPN2 deletion or inhibition promoted the generation and intratumoral accumulation of stem cell memory CD8+ CAR T cells that are associated with persistent CAR T cell-mediated tumor repression and improved clinical outcomes in patients. These findings support the use of gene-editing or small molecule inhibitors for targeting PTPN2 in human CAR T cells to combat solid tumors.

overall_design:
CAR T cells specific to Lewis Y antigen, derived from donor PBMCs, with or without CRISPR/Cas9-mediated deletion of PTPN2, extracted from spleen of OVCAR-3 tumour-bearing NSG mice 14 days after adoptive transfer.

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there are privacy concerns regarding public access to the raw data.
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first: Eamon

last: Coughlan


title: WEE1 inhibition triggers GCN2-mediated activation of the integrated stress response.

first: Jeroen

last: van den Berg

overall_design: RPE-1 hTERT TP53KO and EIF2AKO cells treated with 125nM WEE1i (6hr) cells subjected to a single pulse of EdU (10uM for 15 min). Next, cells were sorted in 384 well plates and subjected to scEdU-seq (van den Berg et al., 2024) .

first: Rinskje

last: Tjeerdsma


title: Loss of aquaporin-1 triggers epithelial-mesenchymal transition in human cholangiocarcinoma

city: Austin

first: Sergio

last: Gradilone

address: 801 16th Avenue NE

department: The Hormel Institute

institute: University of Minnesota

summary: Background and Aims: Epithelial-mesenchymal transition (EMT) is involved in metastatic dissemination and associated with the progression of cholangiocarcinoma (CCA). Aquaporin-1 (AQP1) is a water channel expressed by cholangiocytes described to modulate cell proliferation and invasion in several cancers. However, the role of AQP1 in CCA remains unknown. Our aim was to study the function of AQP1 in CCA. Material and methods: AQP1 expression was evaluated in 39 human intrahepatic CCA (iCCA) by transcriptomic analysis. AQP1-KO in CCA cells, HucCCT1 was achieved by CRISPR/Cas9. Incucyte live-cell imaging system was used for functional studies. Next-generation sequencing (RNAseq) was used to further study the consequences of AQP1 KO. EMT and signaling pathways were evaluated by RT-qPCR, western blot, and immunostaining. In vivo experiments were performed using a xenograft CCA model.  Results: AQP1 expression correlated positively with overall survival in patients with iCCA and negatively with EMT, stemness, and proliferative signatures. In vitro, RNA-seq analysis of CCA cells depleted for AQP1 showed a downregulation of epithelial markers (CDH1 and KRT19; p< 0.001) and an upregulation of mesenchymal markers (VIM and FN1; p < 0.001). In these cells, we observed a phenotypic change with induction of cell scattering, a loss of cell-cell junction protein E-cadherin, and a higher expression of vimentin and ZEB1, an EMT-inducing transcription factor. Functionally, loss of AQP1 is associated with increased cell migration and proliferation. Moreover, we found an activation of the IGF2/IGF1R/IR pathway in AQP1-depleted CCA cells. In vivo, AQP1-depleted CCA cells displayed a higher tumorigenic potential and tumor burden than control cells.  Conclusion: Our data suggest that AQP1 acts as a tumor suppressor in CCA by acting both on cell proliferation and migration through an EMT process. Therefore, AQP1 might have an important role in the regulation of CCA progression.

overall_design: AQP1-KO in CCA cells, HucCCT1 was achieved by CRISPR/Cas9. Next-generation sequencing (RNAseq) was used to further study the consequences of AQP1 KO.

first: Cesar

last: Gaspari

first: Carine

last: Beaupere

first: Seth

last: Richard

first: Estanislao

last: Peixoto

first: Javier

last: Vaquero

first: Marie

last: Vallette

first: Ander

last: Arbelaiz

first: Corentin

last: Louis

first: Cedric

last: Coulouam

first: Raul

last: Marinelli

first: Laura

last: Fouassier

first: Juan

last: Abrahante


title: Tumor derived exosomal DDAH1 promotes lung aging and metastasis

city: Wuhan

first: Wei

last: Yan

address: College of Life Science, Wuhan University, Luojiashan Road, Wuchang District, Wuhan City, Hubei Province, China

institute: Wuhan university

summary: Extracellular vesicles can remodel the premetastatic microenvironment of target organs by packaging various bioactive substances (including proteins and small RNA molecules) to promote tumor development and metastasis. DDAH1 is an asymmetric dimethylarginine hydrolase, which catalyzes the hydrolysis of ADMA to nitric oxide and citrulline to promote tumor development and angiogenesis. However, the role of DDAH1 carried by tumor-derived small extracellular vesicles in lung metastasis has not been reported. In this study, we revealed that tumor-derived small extracellular vesicles carry DDAH1 and promote its accumulation in the lung, facilitating the formation of the senescent matrix microenvironment in the lung and thereby affecting tumor metastasis.

overall_design: To study the effect of breast cancer small extracellular vesicles (EVs) derived DDAH1 on the lung of mice, we constructed an orthotopic breast cancer bearing mouse model. 4T1 and 4T1/DDAH1 KO cells were subcutaneously injected into the fourth pair of mammary glands of mice, respectively. After 5 weeks, the mice were sacrificed and the lungs were removed for preparation of single cell suspension for scRNA Seq.

first: Liu

last: Liu


title: Tumour derived exosomal DDAH1 promotes lung aging and metastasis

overall_design: To explore the effects of DDAH1 derived from breast cancer small extracellular vesicles (EVs) on mouse lung, two mouse models were constructed. The first mouse model was EVs tail vein injection mouse model. EVs derived from cultured cells were extracted and then injected into mice by tail vein injection twice a week for 5 weeks. After 5 weeks, mice were sacrificed and lung tissues were collected for gene expression profiling. The second mouse model was MDA-MB-231/DDAH1 knockout cell tumor-bearing model. MDA-MB-231/DDAH1 knockout cells were subcutaneously injected into the fourth pair of mammary glands of NSG mice to construct an orthotopic xenograft mouse model. After 5 weeks, mice were sacrificed and lung tissues were collected for gene expression profiling. The lung tissues of tumor-free mice served as a control for the lung tissues of tumor-bearing mice, which were not implanted under the fourth pair of mammary glands.


title: Investigating the Molecular Impact of GGMSC on Redox and Metabolic Pathways in Pancreatic Cancer Cells

status: Public on Oct 03 2025

city: Stockholm

first: Mehran

last: Ghaderi

state: Huddinge

address: Forskningsgatan 46

department: Clintech

country: Sweden

institute: Karolinska Institutet

summary: Pancreatic ductal adenocarcinoma (PDAC) remains a highly aggressive malignancy with limited treatment options. Targeting metabolic vulnerabilities and disrupting redox stress pathways has gained increasing attention as a potential therapeutic strategy. γ-Glutamyl-selenomethylselenocysteine (GGMSC) is a selenium-containing compound structurally related to seleno-L-methylselenocysteine (MSC), which has shown anticancer potential in preclinical models, although its molecular effects in PDAC are not well defined. In this study, we investigated the transcriptomic response to high-dose GGMSC in two PDAC cell lines, CAPAN-2 and HPAF-II. RNA sequencing and cytotoxicity assays revealed marked sensitivity to GGMSC in CAPAN-2 cells, associated with activation of oxidative stress and ferroptosis-related pathways, alongside downregulation of metabolic and cell cycle genes. Conversely, HPAF-II cells displayed limited transcriptional alterations and maintained proliferative and metabolic programs. These findings offer insights into the molecular mechanisms underlying GGMSC-induced transcriptional responses in PDAC and suggest potential avenues for future investigations of selenium-based therapies in pancreatic cancer.

overall_design: RNA-seq of pancreatic ductal adenocarcinoma (PDAC) cell line, CAPAN-2 was performed to assess differential gene expression induced by 500 µM GGMSC at 8 h and 20 h.

first: Ghaderi

last: Mehran

first: Selvam

last: Arun kumar


title: Dysregulation of AGO2-miRNA dynamics underlies the AGO2-associated Lessel-Kreienkamp syndrome [RNA-Seq, 2]

city: Hamburg

first: Jan Broder

last: Engler

address: Falkenried 94

department: Institut für Neuroimmunologie und Multiple Sklerose

country: Germany

institute: Universitätsklinikum Hamburg-Eppendorf

summary: Mutations in human Argonaute genes, AGO1 and AGO2, are associated with neurodevelopmental disorders. Although multiple patients have been identified, the underlying molecular basis for pathogenesis remains unclear. Here, we biochemically examined five AGO2 mutations (p.L192P, p.A367P, p.T357M, p.F182del, and p.G733R) linked to different clinical severities. Except for G733R, all AGO2 mutant proteins maintained a stable fold, capable of binding and using microRNA (miRNA) guides. Kinetic studies showed that the L192P, A367P, and T357M mutants have prolonged dwell times on target RNAs, indicating impaired target release. The L192P and A367P variants also display slow target RNA association kinetics. RNA Bind-n-Seq experiments showed that in vitro, the L192P, A367P, T357M, and F182D mutants are prone to mis-targeting. In cultured murine cortical neurons, the L192P mutant altered the miRNA complement associated with AGO2, altered guide strand selectivity, and increased the accumulation of 3' isomiRs, suggesting altered miRNA loading and increased miRNA 3' end exposure. In vivo, mice carrying the p.L192P variant, but not p.G733R, demonstrated strongly reduced breeding ability, altered cortical transcriptomes, and over-repression of miRNA targets. The combined results suggest patient mutations impact AGO2 targeting dynamics in a gain-of-function manner, leading to deregulation of the neuronal transcriptome and the observed neurodevelopmental anomalies.

overall_design: RNA was extracted from cerebral cortex tissue of heterozygous Ago2 G733R mutant mice and wildtype controls. Isolated RNA was subjected to RNA-sequencing.

first: Debora

last: Tibbe

first: Hans-Jürgen

last: Kreienkamp

first: Davor

last: Lessel


title: Targeting PTPN2 enhances human CAR T cell efficacy and the development of long-term memory [RNA-seq]

first: Tony

last: Tiganis

overall_design:
CAR T cells specific to Lewis Y antigen, derived from donor PBMCs, with or without CRISPR/Cas9-mediated deletion of PTPN2. stimulated with plate-coated anti-idiotype antibody (1 ?g/ml) to crosslink the LeY CAR for 6h. RNA-seq libraries were prepared from RNA using the Quant-seq 3 mRNA-seq Library Prep Kit for Illumina (Lexogen) as per the manufacturer’s instructions. NextSeq (Illumina, Inc., San Diego, CA) sequencing was performed to generate single-end, 75-bp RNA-seq short reads and subsequently CASAVA 1.8.2 was used for base calling.

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there are privacy concerns regarding public access to the raw data
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first: Eamon

last: Coughlan


title: Dysregulation of AGO2-miRNA dynamics underlies the AGO2-associated Lessel-Kreienkamp syndrome

type: Non-coding RNA profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Circulating microRNA Profiles in Acute Spinal Cord Injury: Evidence for Distinct Plasma Signatures Compared with Polytrauma Patients

city: Frankfurt

first: Jason-Alexander

last: Hörauf

state: Hesse

address: Theodor-Stern-Kai 7

department: Trauma Surgery and Orthopedics

institute: University Hospital Frankfurt

summary: Background: Traumatic spinal cord injury (SCI) is a devastating complication of trauma, causing long-term disability and significant socioeconomic burden. Beyond the primary mechanical insult, secondary injury cascades involving apoptosis, oxidative stress, and inflammation amplify tissue damage. MicroRNAs (miRNAs) regulate these processes at the post-transcriptional level, yet data on circulating miRNAs in human SCI remain scarce. Objective: This study aimed to characterize acute plasma miRNA expression patterns in isolated SCI that may indicate SCI-specific signatures. Methods: Plasma was collected from five SCI patients at admission and 48 h post-injury and five healthy controls (HC) and Next-generation sequencing (NGS) was performed on plasma RNAs. Differentially expressed miRNAs were identified and selected candidate miRNAs were validated by droplet digital PCR (ddPCR) in an expanded cohort of SCI patients, polytrauma patients without neurotrauma (PT), and HC (each n=8). Pathway enrichment and validated target analysis were performed to assess biological relevance of candidate miRNAs. Results: At emergency room admission, 46 miRNAs were differentially expressed in SCI plasma (18 upregulated, 28 downregulated). By 48 h, a global downregulation was observed, with 47 miRNAs significantly decreased compared with HC. ddPCR validation revealed markedly stronger suppression of miR-182-5p, miR-190a-5p, miR-144-5p, and miR-30c-5p expression levels in SCI compared with PT, suggesting a neurogenic rather than trauma-related regulation. Pathway analysis indicated enrichment of mitochondrial oxidative phosphorylation pathways, and target prediction suggested that the identified miRNAs may be linked to neuroprotective and regenerative functions. Conclusion: Our findings demonstrate early and profound alterations in circulating miRNAs after acute SCI. The downregulation of the identified miRNAs may reflect maladaptive changes that promote neuroinflammation and hinder axonal regeneration, although the exact functional consequences remain to be clarified. These data suggest that circulating miRNAs could hold promise as diagnostic and prognostic biomarkers and, potentially, as therapeutic targets to influence secondary injury processes.

overall_design: RNA-seq profiling of plasma from trauma patients with isolated spinal cord injury, collected at emergency room admission and 48 hours after trauma, compared with healthy controls.

first: Miriam

last: Saenger

first: André

last: El Saman

first: Ingo

last: Marzi

first: Dirk

last: Henrich

first: Liudmila

last: Leppik

first: Cora Rebecca

last: Schindler


title: Systematic benchmarking of imaging spatial transcriptomics platforms in FFPE tissues - MERSCOPE Data

city: Cambridge

first: Samouil

middle: L

last: Farhi

state: MA

address: 75 Ames St

department: Spatial Technology Platform

institute: Broad Institute of MIT and Harvard

summary: Emerging imaging spatial transcriptomics (iST) platforms and coupled analytical methods can recover cell-to-cell interactions, groups of spatially covarying genes, and gene signatures associated with pathological features, and are thus particularly well-suited for applications in formalin fixed paraffin embedded (FFPE) tissues. Here, we benchmark the performance of three commercial iST platforms—10X Xenium, Vizgen MERSCOPE, and Nanostring CosMx—on serial sections from tissue microarrays (TMAs) containing 17 tumor and 16 normal tissue types for both relative technical and biological performance. On matched genes, we find that Xenium consistently generates higher transcript counts per gene without sacrificing specificity. Xenium and CosMx measure RNA transcripts in concordance with orthogonal single-cell transcriptomics.  All three platforms can perform spatially resolved cell typing with varying degrees of sub-clustering capabilities, with Xenium and CosMx finding slightly more clusters than MERSCOPE, albeit with different false discovery rates and cell segmentation error frequencies. Taken together, our analyses provide a comprehensive benchmark to guide the choice of iST method as researchers design studies with precious samples in this rapidly evolving field.

overall_design: In this study, we compared currently available FFPE-compatible iST platforms on matched tissue samples. We prepared a set of samples representative of typical archival FFPE tissues, comprised of 33 different tumor and normal tissue types, and acquired matched data from sequential sections according to the manufacturer’s best practices at the time of writing, generating a dataset of > 5.0 M cells. We analyzed the relative sensitivity and specificity of each method on shared transcripts and further quantified the concordance of the iST data across each platform with paired scRNA-seq data collected by 10x Chromium Single Cell Gene Expression FLEX. Then we focused on cell-level comparisons, evaluating the out-of-the-box segmentation for each platform based on detected genes and transcripts and coexpression patterns of known disjoint markers. Finally, we cross-compared the ability of each platform to identify cell type clusters with breast and breast cancer tissues as an example use case. Taken together, our work provides the first head-to-head comparison of these platforms across multiple archival healthy and cancerous FFPE tissue types.

first: Huan

last: Wang

first: Ruixu

last: Huang

first: Jack

last: Nelson

first: Ce

last: Gao

first: Miles

last: Tran

first: Anna

last: Yeaton

first: Sachi

last: Krishna

first: Kristen

last: Felt

first: Kathleen

last: Pfaff

first: Teri

last: Bowman

first: Scott

last: Rodig

first: Kevin

last: Wei

first: Brittany

last: Goods


title: Microbiome Modulation Uncouples Efficacy and Toxicity Induced by Programmed Death-1/Programmed Death-Ligand1 Blockade in multiple myeloma

city: Milano MI

first: Aurora

last: Maurizio

state: Italy

address: Via Olgettina, 60

department: Center for Omics Sciences (COSR)

country: Italy

institute: IRCCS Ospedale San Raffaele

summary: Intestinal microbiota and gut-born T helper-17 (Th17) lymphocytes may act as drivers of smoldering multiple myeloma (SMM) to MM evolution. We demonstrate here that administering the human commensal Prevotella melaninogenica to transgenic Vk*MYC mice affected by Early-MM, mimicking human SMM, significantly delayed evolution to full-blown MM. Mechanistically, P. melaninogenica increased the production of short-chain fatty acids (SCFAs), preventing skew of dendritic cells towards a pro-Th17 phenotype and accumulation of Th17 cells in the bone marrow of treated mice. P. melaninogenica or butyrate synergized with anti-PD-L1 antibodies by restraining Th17 cell expansion while unleashing immune checkpoint blockade (ICB)-induced effector CD8+ T cells. P. melaninogenica also attenuated IL-17-mediated skin lesions that mimicked ICB-induced immune-related adverse events. Thus, modulation of the gut microbiota or SCFAs administration with or without ICB might represent treatment options for patients affected by plasma cell dyscrasias and other hematologic or solid tumors where IL-17 acts as driving force.

overall_design: Bulk RNA-Seq of  Bone Marrow Dendritic Cells (BMDCs) cultured either with P. melaninogenica (PM) or P. heparinolytica (PH).

first: Laura Lucia

last: Cogrossi

first: Matteo

last: Bellone


title: Integration of scRNA-seq and scATAC-seq reveals malignant characteristics of clear cell renal cell carcinoma with sarcomatoid differentiation

city: Nanning

first: Zhenyuan

last: Yu

state: Guangxi

address: Shuangyong road 22

department: Center for Genomic and Personalized Medicine

institute: Guangxi Medical University

summary: Clear cell renal cell carcinoma (ccRCC) is the most common histological type of kidney cancer. The appearance of spindle cell proliferation is generally considered as sarcomatoid differentiation. To further understand the malignant characteristics of this special histological type of ccRCC, it is a promising direction to study it at the level of genetics, cellular and molecular levels. In this study, we integrated scRNA-seq, scATAC-seq and WES analysis on a sample of sarcomatoid ccRCC, and discovered the characteristics of malignant progression. These findings provided a new reference for the diagnosis and treatment of ccRCC with sarcomatoid differentiation in the future.

overall_design: clear cell renal cell carcinoma with sarcomatoid differentiation was used for scRNA-seq and scATAC-seq by 10X Genomics.

first: Wenhao

last: Lu

first: Yixuan

last: Liu

first: Jizhen

last: Cen

first: Shengzhu

first: Zheng

last: Wen

first: Jiaping

last: Li

first: Zengnan

last: Mo

first: Xuefang

last: Liang

first: Cheng

last: Su


title: Systematic benchmarking of imaging spatial transcriptomics platforms in FFPE tissues - Xenium Data

first: Samouil

last: Farhi

first: Huan

last: Wang

first: Ruixu

last: Huang

first: Jack

last: Nelson

first: Ce

last: Gao

first: Miles

last: Tran

first: Anna

last: Yeaton

first: Sachi

last: Krishna

first: Kristen

last: Felt

first: Kathleen

last: Pfaff

first: Teri


title: Leptin as a Key Driver for Organ Fibrogenesis

city: Dallas

first: Xuenan

last: Sun

state: TX

address: Internal Medicine/Touchstone diabetes Center,55235 Harry Hines BLVD L5.100

department: Internal Medicine Touch Stone Diabetes Center

institute: UT Southwestern Medical Center

summary: Leptin, a hormone primarily secreted by adipocytes, plays a central role in the regulation of energy balance and systemic metabolism through its interaction with the leptin receptor (LEPR). Beyond these functions, leptin signaling has been implicated in the pathogenesis of tissue fibrosis. Here, we report the X-ray crystal structures of a leptin-neutralizing antibody (hLep3) in the unbound and leptin-bound states. The interaction of this antibody with leptin mimics the interaction of the LEPR with leptin, providing direct insights into the mechanism by which the antibody disrupts leptin signaling. We furthermore evaluate the therapeutic potential of neutralizing leptin with this antibody across distinct mouse models of fibrosis affecting the kidney, liver, lung, heart, and blood vessels, respectively. Leptin neutralization significantly inhibited fibrosis progression in all models. Mechanistically, suppression of leptin activity reduces local pro-inflammatory and pro-fibrotic processes, underscoring its therapeutic potential. These findings suggest that leptin signaling plays a crucial role in tissue fibrosis and that treatment with a leptin-neutralizing antibody may be a promising therapeutic approach.

overall_design: RNA-seq for the kidneys of mice subjected to folic acid or vehicle treatment, followed by administration of either IgG or leptin antibody after folic acid–induced kidney injury. RNA-seq for the lungs from mice treated with bleomycin or vehicle, followed by IgG (IgGL) or leptin antibody (LepL) administration.

first: Shuihwei

last: Chen

first: Shangang

last: Zhao

first: Jan-Bernd

last: Funcke

first: Megan

last: Virostek

first: Line

last: Pedersen

first: Chao

first: Chanmin

last: Joung

first: Qian

last: Lin

first: Yan

first: Ayanna

last: Cobb

first: May-Yun

first: Kyounghee

last: Min

first: Lisandro

last: Maya-Ramos

first: Giovanna

last: Degasperi

first: Junquan

last: Liu

first: Ningyan

last: Zhang

first: Zhiqiang

last: An

first: Diana

last: Tomchick

first: R

last: Wynn

first: Da Young

last: Oh

first: Philipp

last: Scherer


title: Adipose Cullin 3 knockout transcriptomics

city: Oklahoma City

first: Tiangang

last: Li

state: OK

address: 975 NE 10TH ST

institute: University of Oklahoma Health Sciences Center

summary: To analyze the transcriptomic profiles of adipose tissue from wild-type (WT) and adipose-specific Cullin 3 knockout (KO) mice after 8 weeks on a Western diet (WD).

overall_design: WT (Cul3-flox/flox) and adipose Cullin 3 knockout (KO, AdipoQ-Cre;Cul3-flox/flox) mice were fed Western diet for 8 weeks. Mice were fasting for 6 hours and epididymal white adipose tissue were collected for analysis.

first: Lijie

last: Gu


title: Systematic benchmarking of imaging spatial transcriptomics platforms in FFPE tissues - scRNA-seq Data

first: Samouil

last: Farhi

overall_design: Tumor TMA 1 (tTMA1) consisted of one hundred and seventy 0.6 mm diameter cores (i.e. sampled regions) from seven different cancer types, with 3-6 patients per cancer type, and 3-6 cores per patient. Tumor TMA 2 (tTMA2) consisted of forty-eight 1.2 mm diameter cores from nineteen different cancer types, with each tissue type coming from one or two patients and represented in 2-3 cores.

first: Huan

last: Wang

first: Ruixu

last: Huang

first: Jack

last: Nelson

first: Ce

last: Gao

first: Miles

last: Tran

first: Anna

last: Yeaton

first: Sachi

last: Krishna

first: Kristen

last: Felt

first: Kathleen

last: Pfaff

first: Teri

last: Bowman

first: Scott

last: Rodig

first: Kevin

last: Wei

first: Brittany

last: Goods


title: Systematic benchmarking of imaging spatial transcriptomics platforms in FFPE tissues - CosMx Data


title: Single-cell dynamics of genome-nucleolus interactions captured by nucleolar laser microdissection (NoLMseq)

city: Zurich

first: Raffaella

last: Santoro

address: Winterthurerstrasse 190

department: Dep. of Molecular Mechanisms  of Disease

institute: University of Zurich

summary:
This SuperSeries is composed of the SubSeries listed below.
Gene positioning in nuclear space is central to regulation, with repressive chromatin domains often contacting the nuclear lamina or nucleoli. The nucleolus undergoes structural changes in different cellular states, potentially altering genome organization. Yet, how nucleolar states influence 3D-genome architecture remains underexplored, largely due to the lack of methods able to map nucleolar-associated domains (NADs) in single cells and stressed nucleoli. We developed NoLMseq, a technique combining laser-capture microdissection and DNA sequencing to map NADs in single cells. NoLMseq uncovered unexplored features of chromosome organization around nucleoli, including NAD heterogeneity in mouse embryonic stem cells, yielding two major populations with distinct chromatin and developmental states. NADs predominantly contact nucleoli monoallelically, with contact frequency correlating with gene expression and chromatin states. Under nucleolar stress, NoLMseq revealed extensive chromosome reorganization, highlighting the importance of nucleolus integrity in genome organization. Thus, NoLMseq provides a critical tool to study 3D-genome responses to nucleolar states in health and disease.

first: Kaivalya

last: Walavalkar

first: Shivani

last: Gupta

first: Jelena

last: Kresoja-Rakic

first: Mathieu

last: Raingeval

first: Chiara

last: Mungo

first: Philip

last: Rubin


title: Dysregulation of AGO2-miRNA dynamics underlies the AGO2-associated Lessel-Kreienkamp syndrome [RNA-Seq]

first: Jan Broder

last: Engler

summary: Mutations in human Argonaute genes, AGO1 and AGO2, are associated with neurodevelopmental disorders. Although multiple patients have been identified, the underlying molecular basis for pathogenesis remains unclear. Here, we performed an extensive investigation of five AGO2 mutations (p.L192P, p.A367P, p.T357M, p.F182del, and p.G733R) linked to different clinical severities.

overall_design: RNA was extracted from cerebral cortex tissue of heterozygous AGO2 L192P mutant mice and wildtype controls. Isolated RNA was subjected to RNA-sequencing.

first: Debora

last: Tibbe

first: Hans-Jürgen

last: Kreienkamp


title: Pericytes orchestrate a tumor-restraining microenvironment in glioblastoma [scRNA-seq]

city: Lund

first: Kristian

last: Pietras

address: Sheelevägen 2

department: Division of Translational Cancer Research

institute: Lund University

summary: To functionally assess the role of pericytes in glioma development and progression, we study the effects of pericyte depletion in orthotopic and transgenic mouse models of high-grade glioma using single-cell and spatial transcriptomics. We present evidence that pericytes mitigate glioma development by orchestrating a tumor-suppressive microenvironment, challenging the concept of pericytes as merely pro-oncogenic cells, and underscoring the importance of pericyte preservation in future GBM therapies.

overall_design: High-grade gliomas were initiated by stereotactically delivering the glioma oncogenic drivers PDGFB and shp53 into the subventricular zone of transgenic adult Ntv-a mice that were either pericyte-poor (Pdgfbret/ret) or control (Pdgfbret/+). 7 Pdgfbret/+ and 4 Pdgfbret/ret mice were sacrificed when displaying severe symptoms. Single-cell RNA-seq libraries were prepared using 10x Chromium system.

first: Sebastian

last: Braun

first: Paulina

last: Bolivar

first: Clara

last: Oudenaarden

first: Jonas

last: Sjölund

first: Matteo

last: Bocci

first: Katja

last: Harbst

first: Mehrnaz

last: Talkhoncheh

first: Bengt

last: Phung

first: Eugenia

last: Cordero

first: Rebecca

last: Rosberg

first: Elinn

last: Johansson

first: Göran

last: Jönsson

first: Alexander


title: Pericytes orchestrate a tumor-restraining microenvironment in glioblastoma [Spatial Transcriptomics]

overall_design: High-grade gliomas were initiated by stereotactically delivering the glioma oncogenic drivers PDGFB and shp53 into the subventricular zone of transgenic adult Ntv-a mice that were either pericyte-poor (Pdgfbret/ret) or control (Pdgfbret/+). 4 Pdgfbret/+ and 4 Pdgfbret/ret mice were sacrificed when displaying severe symptoms. Spatial transcriptomics sequencing was performed using the 10X Genomics Visium system.


title: Multi-level expression profiling of cardiac and musculoskeletal Schwann cells, in young and old mice.

city: Freiburg im Breisgau

first: Luis

last: Hortells

address: Albertstraße 25

institute: University of Freiburg

summary: Schwann cells (SC) are crucial for normal conduction in peripheral nerves. They produce myelin, provide axonal metabolic support, and activate a reparatory phenotype after nerve injury. During aging, peripheral nerves present abnormal myelin, reduced SC density, and increased senescence. All these changes induce abnormal electrical conduction and consequently impaired function of target tissues, like for example, skeletal muscle weakness and cardiac arrhythmia. In order to understand differences between cardiac and sciatic nerve (SN) SC, as well as to explore age-related changes of function, we characterize two inducible CRE mouse models, Sox10CreERT2 and Plp1CreERT, to genetically trace SC by combining them with TdT reporter mice. To do this, we use FACS to sort tdt (+) cells from the heart and SN, and further perform RNAseq to characterize their gene expression. Complementarily, we confirm protein expression using immunofluorescence. Our data indicates that cardiac SC detected using the Plp1CreERT model are enriched for MPZ (+) myelinating SC. In addition, we describe a novel pro-angiogenic function for cardiac SC in young mice. Furthermore, we found that during aging, SC from SN activate collagen remodeling and secrete pro-inflammatory signals like TNFα. Finally, we detect increased neural-death associated genes in cardiac SC, which also have less expression of the fatty acid co-transporter FABP4, suggesting abnormal myelin formation. Thus, cardiac and musculoskeletal SC have different expression profiles, and undergo different but remarkable changes during aging, which can contribute to abnormal nerve function.

overall_design: To study sciatic and cardiac Schwann cells, we used two different inducible CRE models crossed with a TDT reporter mouse line. We harvested the heart and the sicatic nerve from young (2-3 months old) and old (20-24 months old) Sox10CRERT2;R26TDT and Plp1CREER;R26TDT. We FACSed viable TDT+ cells and performed RNAseq from them. Then compared conditions (tissue/model/age)

last: Preissl

first: Clauida

last: Domisch

first: Severin

last: Haider


title: Dysregulation of AGO2-miRNA dynamics underlies the AGO2-associated Lessel-Kreienkamp syndrome [miRNA-Seq]

first: Jan Broder

last: Engler

overall_design: Primary mouse cortical neurons were transduced with AAVs to express EGFP-AGO2-WT or EGFP-AGO2-L192P and immunoprecipitation against EGFP was performed to enrich AGO2-bound miRNA for subsequent miRNA sequencing.

first: Debora

last: Tibbe

first: Hans-Jürgen

last: Kreienkamp


title: Transcriptional profiling by 3' digital gene expression of human HSPCs isolated from the bone marrow of fetal, adult or elderly donors

city: Rennes

first: Frédéric

last: Chalmel

state: France

address: 9 avenue du Pr. Léon Bernard

department: Physiology and physiopathology of the urogenital tract

country: France

institute: Inserm U1085-Irset

summary: This study aims to define ontogeny-related in the gene signatures of the indicated HSPC subsets

overall_design:
The indicated CD34+ HSPC subsets were directly sorted from the bone marrow of primary donors

**RAW data not provided, the raw files will be uploaded to EGA**

first: Bruno

last: Canque

first: Kutaiba

last: Alhaj Hussen

first: Aurélie

last: Lardenois


title: The syntenic lncRNA DANCR is a human melanoma oncogene and an essential regulator of zebrafish development

city: Bath

first: Keith

middle: William

last: Vance

state: Somerset

address: University of Bath

department: Department of Biology and Biochemistry

country: United Kingdom

institute: University of Bath

summary: Long non-coding RNAs (lncRNAs) play crucial roles in regulating gene expression. Some are essential for organismal development and physiology, and they can contribute to diseases such as cancer. Whilst most lncRNAs exhibit little sequence similarity, conservation of lncRNA transcription relative to neighbouring protein-coding genes suggests potential functional significance. Nevertheless, most positionally equivalent lncRNAs are uncharacterized and it remains unclear whether they exert similar roles in distant species. Here, we identified syntenic melanoma-associated lncRNAs predicted to be components of the MITF gene regulatory network in human melanoma, with positionally equivalent transcripts in zebrafish. Among these, we prioritized Differentiation Antagonizing Non-Protein Coding RNA (DANCR), a cancer-associated lncRNA critical for maintaining somatic progenitor cells in human models, for functional investigation. Dancr is a multi-exonic, cytoplasmically enriched lncRNA transcribed from syntenic regions in the human and zebrafish genomes. MITF and c-MYC, key melanoma transcription factors, regulate human DANCR expression and melanoma patients with high DANCR display significantly decreased survival. DANCR is a melanoma oncogene that controls cancer-associated gene expression networks and promotes human melanoma cell proliferation and migration. Zebrafish dancr is dynamically expressed across multiple different cell types in the developing embryo, regulates genes involved in cell death, and is essential for embryonic development. Our work suggests that cancer-critical lncRNAs such as Dancr, expressed from similar regions in vertebrate genomes, may regulate related genes and processes involved in both embryonic development and tumorigenesis across species.

overall_design: RNA-sequencing of DANCR loss-of-function human melanoma cells and whole zebrafish embryos and controls

first: Stephanie

last: Jones

first: Elizabeth

last: Coe

first: Michael

last: Shapiro

first: Igor

last: Ulitsky

first: Robert

middle: N

last: Kelsh


title: Bespoke strategies of Paxillus involutus to extract potassium from diverse phyllosilicates

city: Monterotondo (RM), Italy

first: Flavia

last: Pinzari

state: Rome

address: Area della Ricerca di Roma 1

department: Institute for Biological Systems (IBS)

institute: Council of National Research of Italy (CNR)

summary:
Purpose: Fungi actively weather silicate minerals to extract nutrients, using different mechanisms. However, it is not clear whether the same mechanism(s) is used for all minerals. The question addressed here is whether distinct minerals can stimulate different weathering mechanisms and lead to a shift in fungal genes expression.
Methods: Microcosm experiments were set up with one fungus and three minerals containing the same targeted metal nutrient (K), but with a variable degree of resistance to dissolution. The experiment used transcriptomics to compare the active gene expression of the ectomycorrhizal basidiomycetes Paxillus involutus fungus in response to developing on each of the three minerals as sole K sources. The selected minerals, with a decreasing resistance to K extraction, were: muscovite, phlogopite, and K-exchanged vermiculite.
Results: Gene expression analysis after the experiments indicated that the level of K-deprivation stress was muscovite > phlogopite >> K-vermiculite. Genes and functions overexpressed in the experiments indicated meaningful metabolic activities including K extraction and transport.
Conclusions: The fungus Paxillus involutus activated different metabolic pathways and, accordingly, switched on or off different genes depending on the minerals from which it was forced to obtain potassium, a fundamental nutrient for its growth. The differential expression of the fungal genes generated alternative chemical attacks on the minerals, resulting in a tailored kind of dissolution and selective uptake of chemical elements. When exposed to K-vermiculite, the fungus overexpressed gene sets related to the organisation of the cytoskeleton and also to vesicle-mediated transport. If phlogopite was supplied, the fungus overexpressed gene sets involved with organic acid and oxoacid metabolic processes. When the only source of potassium was muscovite, the fungus overexpressed monooxygenase activity and oxidoreductase activity. These changing strategies, which resulted in a different impact on the fungal uptake of the elements, always granted some potassium to the fungus.

overall_design:
Five conditions, five biological replicates each (25 samples): 1) Paxillus involutus ectomycorrhizal fungus grown on MMN potassium-depleted medium (negative control), 2) on MMN complete medium (positive control, with available potassium), 3) with MMN potassium-depleted medium and phlogopite minerals, 4) with MMN potassium-depleted medium and k-vermiculite minerals, 5) with MMN potassium-depleted medium and muscovite minerals.
Project funding: Newton International Fellowship NF170295, Royal Society, UK

first: Anne

last: Jungblut

first: Javier

last: Cuadros


title: Hydroxyurea induces an oxidative stress response that triggers ER expansion and cytoplasmic protein aggregation

city: Sevilla

first: Antonio

last: Perez-Pulido

state: Sevilla

address: Ctra/ Utrera, km.1

department: Genetics

country: Spain

institute: University Pablo de Olavide

summary: The endoplasmic reticulum (ER) lumen provides the proper redox environment for disulfide bond formation, which is essential for the correct folding of proteins entering the secretory pathway and forming membranes. However, the precise mechanisms by which disruptions in protein folding within the ER activate proteostatic mechanisms remain to be fully elucidated. In this study, we demonstrate that in Schizosaccaromyces pombe the antineoplastic agent hydroxyurea (HU) induces a transient perinuclear ER expansion, Bip1 accumulation and the clustering of nuclear pore complexes in a specific region of the nuclear envelope. This striking phenotype is mimicked by diamide (DIA), a specific inducer of thiol stress, and can be prevented or rapidly reversed by dithiothreitol, a reducing agent, suggesting that ER expansion results from disulfide stress. Furthermore, HU or DIA treatments resulted in the accumulation of misfolded proteins in cytoplasmic foci containing Hsp104 disaggregase and Hsp70/Ssa1 chaperones. Our data show that HU impacts redox-dependent protein folding, impairs the secretory pathway and activates specific proteostatic mechanisms in both the ER and the cytoplasm.

overall_design: RNA-Seq profiling of wildtype S. pombe cells in control conditions, after incubation with 75 mM hydroxyurea for 60 minutes [HU60] and for 150 minutes [HU150]; and cultures treated with 3 mM diamide for 30 minutes [DIA30] and for 60 minutes [DIA60] or after incubation.

first: Ana

last: Sanchez-Molina

first: Manuel

last: Bernal

first: Joel

last: Posligua-García

first: Antonio J.

last: Pérez-Pulido

first: Laura

last: de Cubas

first: Elena

last: Hidalgo

last: Valdivieso

first: Silvia

last: Salas-Pino

first: Rafael

last: R. Daga


title: Antigen reactivity defines tissue-resident memory and exhausted T cells in tumours.

status: Public on Oct 02 2025

city: Melbourne

first: Lachlan

last: Dryburgh

address: 792 Elizabeth Street

department: The Department of Microbiology and Immunology,  The University of Melbourne

institute: The Peter Doherty Institute for Infection and Immunity

summary: CD8+ T cells are a key weapon in the therapeutic armamentarium against cancer. While CD8+CD103+ T cells with a tissue-resident memory T (TRM) cell phenotype associate with favourable prognoses, the tumour microenvironment also contains dysfunctional exhausted T (TEX) cells that exhibit a myriad of TRM-like features. Here, we deconvolute TRM and TEX cells across human cancers, ascribing markers and gene signatures that distinguish these populations and enable their functional distinction. While TRM cells exhibit superior functionality and are associated with long-term survival post-tumour resection, they are not associated with responsiveness to immune checkpoint blockade. Tumour-associated TEX and TRM cells are clonally distinct, with the latter comprising tumour-independent bystanders and tumour-specific cells segregated from cognate antigen. Intratumoural TRM cells can be forced towards an exhausted fate when chronic antigen stimulation occurs, arguing that the presence or absence of continuous antigen exposure within the microenvironment is the key distinction between tumour-associated TEX and TRM populations. These results suggest unique roles for TRM and TEX cells in tumour control, underscoring the need for distinct strategies to harness these populations in novel cancer therapies.

overall_design: scRNA-seq with CITE-seq and V(D)J profiling of CD3⁺ T cells isolated from colorectal cancer liver metastases, distal non-cancerous liver, and liver from cancer-free donors. Samples were collected from four patients with liver metastases and two cancer-free donors. Cells were loaded across 3 lanes of 10x Genomics 5' v2 kit, with unrelated CD3+CD8+ cells from PBMCs spiked across all 3 lanes to permit any batch corrections if necessary.

middle: K

last: Mackay

first: Thomas

last: Burn

first: Jan

last: Schroeder


title: Loss of TRPV4 reduces pancreatic cancer growth and metastasis

city: Durham

first: Sandip

middle: Madhusudan

last: Swain

state: NC

address: 905 South Lasalle St, Room 1043

department: Medicine

institute: Duke University

summary: Pancreatic ductal adenocarcinoma (PDAC) is a rapidly metastasizing cancer characterized by a dense desmoplastic stroma made up of extracellular matrix (ECM) proteins, which complicates treatment. Upon stimulation, pancreatic stellate cells (PSCs) differentiate into cancer-associated fibroblasts (CAFs) that are the source of ECM and cytokines in PDAC. We previously reported that mechanical stress activates PSCs and induces fibrosis through mechanical ion channel Piezo1-mediated TRPV4 channel activation, but its role in PDAC remains unclear. Here we report that pathological activation of Piezo1 differentiates human PSCs into an inflammatory CAF phenotype that expresses chemoresistance and cancer stemness markers CD10 and GPR77. In an orthotopic PDAC model, TRPV4 knockout mice exhibit a significant reduction in tumor size, circulating inflammatory cytokines, tissue inhibitor of metalloproteinases-1 (TIMP1), and pre-metastatic niche markers, serum amyloid A (SAA) proteins. A similar trend is observed in mice lacking functional Piezo1 in PSCs.  The livers of TRPV4 knockout mice exhibit fewer cancer cell microlesions, lack macro tumors, produce lower levels of inflammatory protein S100A8, and develop fewer inflammatory cell clusters. In orthotopic and genetically engineered models of PDAC, these mice also have improved survival, suggesting that blocking TRPV4 channels may be a promising therapeutic target for PDAC.

overall_design: RNA seq profiling of livers from WT and TRPV4 KO or WT treated with the GSK2193874 TRPV4 antogonist in a murine orthotopic model of PDAC.  RNA seq profiling of mouse pancreatic stellate cells activatated by the PIEZO1 agonist Yoda1.

first: Joelle

last: Romac

first: Nidulla

last: Mullappillay

first: Bandana

last: Bindhani

first: Rodger

last: Liddle


title: Characterization of excitotoxicity induced transcriptional dysregulation

city: Jena

first: Philipp

last: Koch

address: Beutenbergstraße 11

department: Core Facility Life Science Computing

institute: Leibniz Institute on Aging - Fritz Lipmann Institute

summary: We describe the dysregulation of neuronal-activity dependent genes during the condition of toxic glutamate concentrations in primary hippocampal neurons. Genes differed in their response towards the loss of neuronal activity and the active shut-off of transcription. The most shut-off genes also show more direct synaptic function than the passively downregulated genes hinting to functional relevance of the shut-off mechanism. Findings were confirmed in an in vivo excitotoxicty model of Huntington´s disease.

overall_design: Five independent primary hippocampal preparations were treated with the GABAA receptor inhibitor bicuculline to induce transcription of synaptic-activity dependent genes. Following different durations of bicuculline treatment the active transcription shut-off was introduced by NMDA application and the passive shut-off by TTX application.

first: Kristin

last: Oberländer

first: Karol

last: Szafranski

first: David

last: Ibberson


title: Bulk RNA-seq of in vitro-expanded human spinal cord central canal-derived cell cultures

city: Ottawa

first: Sasi Kumar

last: Jagadeesan

state: ON

address: 1053 Carling Avenue,

department: Neuroscience

institute: Ottawa Hospital Research Institute

summary: Adult human spinal cord tissue was obtained from organ donors under institutional research ethics approval. Primary spinal cord central canal-derived cell cultures were established and expanded in vitro. Bulk RNA sequencing was performed on six donor-derived cultures. Total RNA was extracted and libraries were prepared using the Illumina TruSeq Stranded mRNA kit. Sequencing was performed on an Illumina NovaSeq 6000 (paired-end, 150 bp). Transcript abundances were quantified using Salmon against the GENCODE v35 transcriptome. Raw FASTQ files and processed quantifications are provided.

overall_design: Bulk RNA sequencing was performed on six independent donor-derived human spinal cord cell cultures. Each sample represents a single donor-derived culture and constitutes a biological replicate. No dye-swaps were performed.  The dataset does not include experimental treatment groups or perturbations. All samples were processed using the same library preparation and sequencing platform.

first: Eve C

last: Tsai

first: Ryan Vimukthie

last: Sandarage

first: Ahmad

last: Galuta


title: Context-dependent regulation of T follicular helper cell formation, expansion and differentiation into T-regulatory type 1 cells by multiple transcription factors

city: Barcelona

first: Josep

last: Garnica

address: Rosselló, 149

institute: IDIBAPS

summary: Differentiation of naïve T cell precursors into distinct T helper cell subsets, including T follicular helper (TFH) cells, is driven by the expression/repression of subset-specific transcription factors (TFs) that have well defined effects on the acquisition of alternative gene expression programs. Repetitive antigen encounters by TFH cells can trigger their differentiation into IL-10-producing Foxp3– and Foxp3+ T-regulatory type 1 (TR1) cells. Since TFH cells are epigenetically poised to differentiate into TR1 cells, we hypothesized that the cell conversion events underpinning this process are regulated at the transcriptional level. Here, we interrogate the role of 20 TFs that bind to motifs enriched in open chromatin regions along the TFH-TR1 cell axis, on the size and function of the pre-treatment TFH cell pool and the size and transcriptional make-up of the various antigen-specific TFH/TR1 cell subsets arising in vivo post repetitive antigen challenge. We find that certain TFH TFs, such as TCF-1 and TOX-2, contribute to TFH cell genesis and TFH cell function but are dispensable for antigen-specific TFH cell expansion and TR1 transdifferentiation. Eleven other TFs, including ATF-6, BATF, BCL-6, BHLHE40, BLIMP-1, ELK-4, IRF4, c-MAF, STAT-3, STAT-4 and T-BET, play distinct roles at different stages of this pathway in a context-dependent manner. Most of these TFs simultaneously promote and suppress different cell conversion events along the axis and promote the expression of subset-specific signature genes at specific cell stages while simultaneously suppressing the expression of such genes at other cell stages in the pathway. This indicates that differentiation of TFH cells into TR1 progeny is driven by a carefully orchestrated sequence of TF gene expression and silencing events that yields dynamic combinations of TFs that enable cell-to-cell transitions. The transcriptional context in which specific TFs are expressed determines their ability to either drive or suppress such transitions and promote or inhibit the expression of alternative gene expression programs at different cell states.

overall_design: Single-cell RNA sequencing (scRNA-seq) was performed on T cells deficient for 11 transcription factors to investigate their roles in the TFH-to-TR1 differentiation pathway. Samples from control and TF-deficient mice were included in each sequencing run to enable accurate cell annotation across the four Tet+ subpopulations (TFH, TR1.1, Foxp3– TR1.2, and Foxp3+ TR1.2).

first: Enric

last: Canut

first: Mireia

last: Palou

first: Pere

last: Santamaria


title: Mechanisms of maternal antibody interference to rotavirus vaccination

city: Ithaca

first: Tawny

last: Chandler

address: 235 Hungerford Hill Rd

institute: Cornell University

summary: We have employed a single-cell sequencing approach using the 10x Genomics scRNAseq pipeline to study the effect of maternal antibodies on the response to vaccination in the mesenteric lymph node. Given the ability of maternal antibodies to intefere with sero-conversion to rotatvirus vaccination we hypothesized that maternal antibodies would alter the activation and differentiation of lymphocytes. This study presents data on transcriptome dynamics of the mesenteric lymph node following rotavirus vaccination in the absence or presence of maternal antibodies.

overall_design: Following oral rotavirus vaccination at 7 days of age, the mesenteric lymph node chain was isolated at 10 days post-infection from C57Bl/6 mouse pups and a single-cell suspension was analyzed using scRNA-seq. Samples were analyzed from two pups that were vaccinated without maternal antibodies (naive) and samples were analyzed from two pups that were vaccinated with maternal antibodies (MatAb).

first: Sarah

last: Woodyear

first: Faraz

last: Ahmed

last: Caddy


title: CHCHD2 Mutant Mice Link Mitochondrial Deficits to PD Pathophysiology

city: San Francisco

first: Szu-Chi

last: Liao

state: CA

address: 1600 fourth St

department: Biochemistry and Biophysics

institute: UCSF

summary: Mitochondrial dysfunction is a hallmark of Parkinson’s disease (PD), but the mechanisms by which it drives autosomal dominant and idiopathic forms of PD remain unclear. To investigate this, we generated and performed a comprehensive phenotypic analysis of a knock-in mouse model carrying the T61I mutation in the mitochondrial protein CHCHD2, which causes late-onset symptoms indistinguishable from idiopathic PD. We observed pronounced mitochondrial disruption in substantia nigra (SN) dopaminergic neurons, including distorted ultrastructure and CHCHD2 aggregation, as well as disrupted mitochondrial protein-protein interactions in brain lysates. These abnormalities were associated with a whole-body metabolic shift towards glycolysis, elevated mitochondrial ROS, and progressive accumulation of aggregated α-synuclein. In idiopathic PD, CHCHD2 gene expression also correlated with α-synuclein levels in vulnerable dopaminergic neurons, and CHCHD2 protein accumulated in early Lewy aggregates. These findings delineate a pathogenic cascade in which CHCHD2 accumulation impairs mitochondrial respiration and increases ROS production, driving α-synuclein aggregation and neurodegeneration.

overall_design: Midbrain sections from 16-month-old CHCHD2 T61I mutant mice (n = 8) and 13-month-old CHCHD2 knockout mice (n = 4), along with their respective littermate controls, were analyzed in this study.

first: Yoshitaka

last: Sei

first: Ken

last: Nakamura


title: ZAK activation at the collided ribosome

city: Baltimore

first: James

last: Saba

state: MD

address: 725 N Wolfe St, 714 PCTB

department: Molecular Biology and Genetics

institute: Johns Hopkins

summary: Ribosome collisions activate the ribotoxic stress response mediated by the MAP3K ZAK, which in turn regulates cell-fate consequences through downstream phosphorylation of the MAPKs p38 and JNK1. Despite the critical role of ZAK during cellular stress, a mechanistic and structural understanding of ZAK-ribosome interactions and how these lead to activation remain elusive. Here we combine biochemistry and cryo-electron microscopy to discover distinct ZAK-ribosome interactions required for constitutive recruitment and for activation. We find that upon induction of ribosome collisions, interactions between ZAK and the ribosomal protein RACK1 enable its activation by dimerization of its SAM domains at the collision interface. Furthermore, we discover how this process is negatively regulated by the ribosome-binding protein SERBP1 to prevent constitutive ZAK activation. Characterization of novel SAM variants as well as a known pathogenic variant of the SAM domain of ZAK supports a key role of the SAM domain in regulating kinase activity on and off the ribosome, with some mutants bypassing the ribosome requirement for ZAK activation. Collectively, our data provide a mechanistic blueprint of the kinase activity of ZAK at the collided ribosome interface.

overall_design: CLIP-seq of ZAK-KO HEK293T cells transfected with different ZAK constructs (Full-length (WT), Activation Loop mutant (ActLoopD), 1-649 truncation (RBRdel), overexpressed Activation Loop Mutant (OX-ActLoopD), or mock (ZAK-KO), treated with or without Anisomycin. Two replicates for each group.

first: Vienna

last: Huso

first: Shuangshuang

last: Niu

first: Roland

last: Beckmann

first: Rachel

last: Green


title: VDAC2 primes Myeloma cells for BAK-dependent apoptosis by stabilizing BAK and not BAX and represents a novel therapeutic target

city: Nantes

first: David

last: Chiron

address: 8 quai Moncousu

institute: CRCI2NA, INSERM_U1307, CNRS_6075, Nantes_Université

summary: We demonstrated that VDAC2 plays a critical role in the apoptotic response by regulating the expression and function of BAK, but not BAX

overall_design: RNA human myeloma cell lines control (CTR) and VDAC2 -/- (STOP)  were extracted with RNeasy Mini Kit (Qiagen) and gene expression profile was performed using RNA-Seq (3'SRP)

first: Ophélie

last: Champion

first: Sophie

last: Maïga

first: Chloé

last: Antier

first: Christelle

last: Dousset

first: Agnès

last: Moreau-Aubry

first: Céline

last: Bellanger

first: Géraldine

last: Descamps

first: François

last: Guillonneau

first: Jose Antonio

last: Moreno

first: Ohyun

last: Kwon

first: Nicoletta

last: Libera Lilli

first: Philippe

last: Moreau

first: Cyrille

last: Touzeau

first: Catherine

last: Pellat-Deceunynck

first: Patricia

last: Gomez-Bougie


title: Transcriptome profile of hepatocellular carcinoma in patients with atezolizumab plus bevacizumab therapy.

city: Chiba-shi

first: Hiroaki

last: Kanzaki

state: Chiba

address: 1-8-1 Inohana, Chuo-ku

department: Department of Gastroenterology

institute: Graduate School of Medicine, Chiba University

summary: Hepatocellular carcinoma (HCC) is a rapidly increasing and highly lethal cancer worldwide, with many patients diagnosed at advanced stages and early-stage patients often experiencing high recurrence rates. The combination of atezolizumab plus bevacizumab emerged as a groundbreaking immunotherapy, establishing a new standard of care for advanced HCC. There's an urgent need for reliable biomarkers to predict patient responses and personalize treatment. We collected tumor samples from advanced HCC patients wirth atezolizumab plus bevacizumab therapy and performed comprehensive analyses of the tumor microenvironment using bulk RNA sequencing to identify key features influencing the effectiveness of atezolizumab plus bevacizumab.

overall_design: HCC tumor tissues were obtained from a total of 73 patients who underwent diagnostic liver biopsy and used for RNA isolation and genome-wide transcriptome profiling by bulk RNA sequencing.

first: Takamasa

last: Ishino

first: Sadahisa

last: Ogasawara

first: Yosuke

last: Togashi


title: Esophageal progenitor cell plasticity; a 3D organotypic model of epithelial regeneration [scATAC-seq]

city: Cambridge

first: Maria

middle: Pilar

last: Alcolea

state: Cambridgeshire

address: Jeffrey Cheah Biomedical Centre Cambridge Biomedical Campus, Puddicombe Way

department: Cambridge Stem Cell Institute

institute: University of Cambridge

summary: Epithelial stem cells are capable of remarkable plasticity, facilitating efficient regenerative responses following damage. Here, we present a versatile model of ectopic niche regeneration that provides evidence of a switch in epithelial stem cell identity as a response to foreign microenvironmental signals. A combination of 3D organotypic cultures, 3D confocal imaging and Next-Generation Sequencing reveal events of epithelial plasticity during the reepithelialization of denuded stroma. In this study we provide new insights on the mechanisms driving cell fate flexibility in adult epithelial stem cells.

overall_design: Single-cell ATAC sequencing of murine esophageal epithelial cells, cultured in a 3D organotypic system that recapitulates wound healing. Cells growing over their native stroma (eEE) were compared to those growing over the foreign stroma of the dermis (eSKIN).

middle: T

last: Bejar

first: Harikrishnan

last: Ajith

middle: P


title: Transcriptional profiling by 3' digital gene expression of human CD34+ HSPCs isolated from the umbilical cord blood

first: Frédéric

last: Chalmel

summary: This study aims at comparing the gene signatures of fetal and postnatal multi-lymphoid progenitors (MLPs)

overall_design:
The indicated CD34+ HSPC subsets were directly sorted from the neonatal umbilical cord blood

**RAW data not provided, will be submitted to EGA**

first: Bruno

last: Canque

first: Kutaiba

last: Alhaj Hussen

first: Aurélie

last: Lardenois


title: Human iPSCs-based modeling unveils a dominant role of SETBP1 mutation in shaping stable chromatin accessibility landscape in GATA2 deficiency

city: Hospitalet de Llobregat

first: Loris

last: Mularoni

state: Barcelona

address: Gran Via de l'Hospitalet, 199

department: P-CMR[C]

institute: IDIBELL

summary: Patients with GATA2 deficiency are predisposed to developing myelodysplastic syndrome (MDS), which can progress to acute myeloid leukemia (AML). This progression is often associated with the acquisition of additional cytogenetic and somatic alterations. Mutations in SETBP1 and ASXL1 genes are recurrently observed in GATA2 patients, but their precise roles in disease progression remain poorly understood. Here we developed a hiPSC-based system to investigate the functional impact of SETBP1 and ASXL1 mutations in the context of germline GATA2 haploinsufficiency. Using precise genome editing, we recreated patient-relevant combinations of these mutations to model distinct premalignant stages of GATA2 deficiency. We demonstrate that heterozygous GATA2 mutation alone has a limited impact on early hematopoietic progenitors, without disrupting myeloid differentiation. In contrast, acquisition of SETBP1 or ASXL1 mutations impairs hematopoietic differentiation in a GATA2 deficient background, leading to a premalignant state marked by reduced myeloid progenitor output. Strikingly, the combination of all three mutations results in a severe depletion of myeloid progenitors, closely recapitulating hematopoietic defects observed in GATA2-related MDS and highlighting a synergistic interplay among the mutations. We provide new insights into the molecular mechanism underlying GATA2 deficiency progression, revealing that SETBP1 mutation plays a dominant role in establishing a stable chromatin accessibility landscape, even when co-occurring with ASXL1. Our study establishes a novel humanized model system for studying GATA2 deficiency. This model provides new insights into the cellular and molecular events underlying the progression of myeloid impairment in GATA2 deficiency and represents a platform for testing future therapeutic strategies.

overall_design: On day 15 of hematopoietic differentiation, 200 hiPSC-derived myeloid progenitors (CD34⁺CD43⁺CD33⁺CD45⁺) derived from parental and mutant hiPSCs were sorted .

first: Alessandra

last: Giorgetti


title: Preclinical Pediatric Molecular Analysis for Therapy Choice (MATCH)

city: Memphis

first: Gang

last: Wu

address: 262 Danny Thomas Place

institute: St Jude Children's Research Hospital

type: Methylation profiling by genome tiling array

summary: Pediatric solid tumors arise from diverse tissues during development and exhibit a wide range of molecular, cellular and genetic features. This diversity, combined with the low incidence of pediatric cancer makes it increasingly difficult to personalize therapy for individual patients based on the unique features of their tumors. Therefore, well-credentialed preclinical models that capture the diversity and heterogeneity of pediatric solid tumors are essential for identifying molecular targeted therapeutics for precision medicine.

overall_design: Here, we report 286 orthotopic patient derived xenografts (O-PDXs) from 227 patients representing 24 different types of pediatric solid tumors. We have performed DNA methylation characterization of the O-PDXs and compared them to their corresponding patient tumors.

first: Michael

last: Dyer

first: Elizabeth

last: Stewart

first: Cynthia

last: Cline