title: Coordination of protein synthesis and decay in mammalian cells

city: Lausanne

first: Benjamin

last: Martin

state: Vaud

address: Rte Cantonale

country: Switzerland

institute: EPFL

summary: Protein synthesis and decay rates must be tightly coordinated to ensure proteome homeostasis. How this coordination is established is unknown. Here we use quantitative live cell imaging combined with computational inference and proteomics to determine how changes in global protein synthesis rates alter protein decay rates. A passive adaptation of protein degradation and dilution rates operates in cells tightly coupling proliferation rate to protein synthesis rates, allowing to partially buffer changes in proteome concentrations with increased loss of short-lived proteins. In contrast, the proliferation rate of Mus musculus embryonic stem cells (mESCs) is hyposensitive to moderate changes in protein synthesis. mESCs uncouple protein degradation and dilution rates and robustly maintain their protein levels. Finally, we also show that terminally differentiated human glial cells strongly adapt protein degradation rates to altered protein synthesis. Our work illuminates the complex interplay between protein synthesis, degradation, and cell division to regulate proteome homeostasis.

overall_design: We performed RNAseq to investigate the early transcriptomic response of NIH/3T3 and mESC to protein synthesis inhibition mediated by CHX treatment. The experiment was performed in triplicate for each cell line. A timecourse was performed and samples were collected after 0 h, 1 h, 2 h, 5 h, or 48 h of CHX treatment. Differential expression analysis with respect to the initial timepoint (0 hours) was then performed for each timepoint of each cell line.

first: Michael Shoujie

last: Sun

first: Joanna

last: Dembska

first: Ekaterina

last: Lyublinskaya

first: Cédric

last: Deluz

first: David M.

last: Suter


title: Aging synaptosomes

status: Public on Oct 07 2025

city: Jena

first: Marco

last: Groth

address: Beutenbergstraße 11

department: Core Facility - Next Generation Sequencing

country: Germany

institute: Leibniz Institute on Aging - FLI

type: Expression profiling by high throughput sequencing

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

overall_design: Refer to individual Series


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

city: Chicago

first: weijie

last: guo

state: IL

address: 929 East 57th Street, GCIS W423N

country: USA

institute: university of Chicago

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

overall_design: To test whether Sox2 is responsible for endowing tSCs with the capacity in modulating neutrophils and suppressing their ability to respond to interferons, we grafted either parental Sox2low control or Sox2Hi SCC cells on the ‘CatchupIVM-red’ mice. When the SCC tumors are established, we treated the mice bearing these two groups of tumors with anti-PDL1/CD40 agonist. We then isolated Tomato+ neutrophils from both untreated naïve or treated Sox2low control or Sox2Hi SCC tumors and subjected them to bulk-RNA-seq.

first: Weijie

last: Guo

first: Yuxuan

last: Miao


title: Tumor-Initiating Stem Cells Fine-tune the Cell States of Neutrophils to Drive Cancer Relapse from Immunotherapy [tumor cell bulk RNAseq]

overall_design: To explore the underlying mechanisms activated by Sox2 in tSCs that is responsible for modulating neutrophils, we isolated Sox2low and Sox2Hi SCC cells from grafted tumors and then subjected these cells for bulk RNA-seq.


title: Tumor-Initiating Stem Cells Fine-tune the Cell States of Neutrophils to Drive Cancer Relapse from Immunotherapy [Cut and Run]

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: We performed a Cut & Run assay in the PDV cell lines to profile the direct binding of Sox2 to the target genes.


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

first: Enrico

last: Garbe

address: Albert-Einstein-Straße 10

department: (Epi-)Genetics of Fungal Infections

institute: HKI Jena

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

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

first: Sascha

last: Schäuble

first: Bettina

last: Böttcher

first: Dominik

last: Driesch

first: Slavena

last: Vylkova


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

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

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


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

city: Bron

first: Hector

last: Hernandez-Vargas

state: Rhone

address: 36 bis Rue de la Batterie

country: France

institute: Genomics Consulting

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

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

first: Kevin

last: Berthenet

first: Gabriel

last: Ichim


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

city: San Antonio

first: Pei

last: Wang

state: TX

address: 7703 Floyd Curl Dr

institute: UT Health San Antonio

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

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

first: Yi

last: Xu

first: Michael

last: Nipper

first: Angel

last: Dominguez

first: Chenhui

last: He

first: Francis

last: Sharkey

first: Sajid

last: Khan

first: Daohong

last: Zhou

first: Lei

last: Zheng

first: Yu

last: Luan

first: Jun

last: Liu


title: The role of DPF2 in mouse radiation-induced intestinal injury [scRNA-seq]

city: Suzhou

first: Mintao

last: Ji

address: Renai road

country: China

institute: Soochow University

summary: We have employed a single-cell sequencing approach using 10x Genomics ScRNA-seq to study the role of DPF2 in immune cells of Radiation-induced intestinal injury (RIII). The intestinal immune system has been increasingly recognized for their roles in regulating intestinal inflammation. This study represents the SWI/SNF chromatin-remodeling subunit DPF2 mediates the inflammatory network in intestinal injury and provides new insights in RIII.

overall_design: Following 10 Gy X-ray irradiation, immune cells from the intestines of WT and Dpf2 KO mice were isolated by Fluorescence-activated cell sorting (FACS) and analyzed using scRNA-seg.

last: Chang


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

city: Seattle

first: David

middle: J

last: Ottenheimer

state: WA

address: 1959 NE Pacific St

institute: University of Washington

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

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus

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

first: Rhiana

middle: C

last: Simon

first: Cassidy

middle: T

last: Burke

first: Garret

middle: D

last: Stuber


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

city: Hangzhou

first: Yunkun

last: Lu

state: Zhejiang

address: No. 3, Qingchun East Rd

department: Sir Run Run Shaw Hospital

institute: Zhejiang University

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

overall_design: To investigate the potential biomarker of TNBC

first: Shuai

last: Yuan

first: Sijie

last: Feng

first: Jiangxia

last: Li


title: Vaping versus Smoking: A Quest for Long-term impact in a mouse model

city: lille

first: frédéric

last: leprêtre

address: Boulevard du Pr Leclercq

department: CHU of Lille, CBP

institute: Lille University

summary: Most smokers consider that electronic cigarettes are safer than tobacco and are marketed as safe products. Nevertheless, recent reports show the exposure to high levels of electronic cigarette vapors (ECV) activates lung cells and triggers lung inflammation and structural alterations after chronic exposure. In order to assess the potential harmful effect of moderate exposure to ECV, we investigated in mice, its effect on lung and systemic inflammation and on lung structure and function.

overall_design: To reproduce closely the situation frequently encountered in human, we exposed mice during 1h/day during 3 or 6 months with two levels of electronic cigarette power in comparison with mice exposed to cigarette smoke (CS). Lung and systemic inflammation was evaluated by measuring cell recruitment and activation as well as cytokine concentrations. Lung transcriptome, respiratory function and body weight were also measured.

first: Sébastien

last: Antherieu


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


title: Hippo deficient cardiac fibroblasts differentiate into osteochondroprogenitors (snRNA-Seq)

city: Houston

first: Yi

last: Zhao

state: Texas

address: 6770 Bertner Avenue

institute: The Texas Heart Institute at Baylor College of Medicine

summary: We investigated how Hippo deficient CFs alter their cell state and interact with immune cells during cardiac fibrosis. To study the role of the Hippo pathway in CFs, we conditionally knocked out Lats1/2 specifically in the CFs of mouse hearts (Lats1/2-CF) and performed single-nucleus RNA sequencing (snRNA-seq) to profile the cellular landscape of the left and right atria.

overall_design: Single nuclei RNA sequencing  were performed to examine left and right atrial cells, with or without Lats1 and Lats2 conditional knockout in the fibroblasts. All mice were adult with age of 10-12 weeks

first: Chang-Ru

last: Tsai

first: Xiao

first: James

middle: F

last: Martin


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

first: weijie

last: guo

overall_design: To profile the neutrophils at different regions in the TME and their responses to immunotherapies, we employed spatial transcriptomics analysis to determine the distribution patterns of neutrophil responses in the spontaneous mouse SCCs.

first: Weijie

last: Guo

first: Yuxuan

last: Miao


title: Hippo deficient cardiac fibroblasts differentiate into osteochondroprogenitors (ST)

summary: We investigated how Hippo-deficient cardiac fibroblasts (CFs) alter their cell state and interact with immune cells during cardiac fibrosis. To study the role of the Hippo pathway in CFs, we conditionally knocked out Lats1/2 specifically in the CFs of mouse hearts (Lats1/2CKO). To test the role of Hippo-deficient CF-induced macrophages, we treated the control and Lats1/2CKO mice with or without CSF1R inhibitor to block macrophage expansion and performed ST.

overall_design: Spatial Transcriptomics sequencing (ST) were performed using control and Lats1/2 conditional knockout mouse hearts. Control and Lats1/2 knockout mice were treated with or without vehicle and CSF1R inhibitor. All mice were adult with age of around 10-12 weeks when collected.


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

city: Debrecen

first: Laszlo

last: Nagy

address: Egyetem ter 1.

country: Hungary

institute: University of Debrecen

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

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

first: Dora

last: Bojcsuk

first: Benjamin-Rego

last: Barath


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

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


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

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: Tumor-Initiating Stem Cells Fine-tune the Cell States of Neutrophils to Drive Cancer Relapse from Immunotherapy [Parse scRNAseq]

overall_design: To define how immunotherapy treatments impact TANs, we sought to employ a highly immunogenetic mouse cancer model that is induced by exposing the mouse skin epithelium to chemical mutagen 7,12-dimethylbenz[a]anthracene (DMBA) followed by repeated applications of phorbol ester 12-O-tetradecanoylphorbol 13-acetate (TPA). With this ideal model, we next treated the mice bearing spontaneous skin SCCs with PDL1 blocking and CD40 agonist antibodies which were recently demonstrated to induce anti-tumor activities in neutrophil. Immediately after the treatment (e.g. day two after the last dose), we collected these tumors, isolated total CD45+ immune cells, and subjected them, together with immune cells isolated from untreated naïve tumors, to single cell RNA-sequencing.


title: Hippo deficient cardiac fibroblasts differentiate into osteochondroprogenitors (snMultiomics)

summary: We investigated how Hippo deficient CFs alter their cell state and interact with immune cells during cardiac fibrosis. To study the role of the Hippo pathway in CFs, we conditionally knocked out Lats1/2 specifically in the CFs of mouse hearts (Lats1/2-CF) and performed single-nucleus RNA sequencing (snRNA-seq) and single-nucleus multiomics to profile the cellular landscape of the right atria, with and without Csf1r inhibitor

overall_design: Single nuclei RNA+ATAC multiomics sequencing  were performed to examine right atrial cells, with or without Lats1 and Lats2 conditional knockout in the fibroblasts and with or without Csf1 inhibitor injection. All mice were adult with age of around 9 weeks. Tissue from both male and female mice were pooled for all samples.


title: BCAT1 drives cardiac fibrosis by promoting proline synthesis machinery

city: Fukuoka

first: Miciho

last: Nakaya

state: Fukuoka

address: Maidashi 3-1-1, Higashiku

department: Graduate School of Pharmaceutical Sciences

country: Japan

institute: Kyushu University

summary: Fibrosis is a disease condition with excessive deposition of extracellular matrix (ECM) components such as collagens in tissues and has been reported to be associated with approximately 45% of deaths in developed countries. The cells that produce excessive ECM in fibrotic tissue are called myofibroblasts which do not exist in normal tissue but appear only in fibrotic tissue. In this time, we knocked down BCAT1 in cardiac myofibroblasts using siRNA.

overall_design: Gene expression profiling (RNA-seq) of cardiac myofibroblasts treated with siControl or siBcat1

first: Michio

first: Noburo

last: Takizawa

first: Takanori

last: Hironaka

first: Haruna

last: Suetsugu

first: Keisuke

last: Yoshioka

first: Hayato

last: Watanabe

first: Yuma

last: Horii


title: KDM4A/KDM4C lysine demethylases sustain an oncogenic transcriptional program in diffuse large B-cell lymphoma

city: Rochester

first: Hu

last: Li

state: MN

address: 200 First Street, Gonda Building G19-408

department: Molecular Pharmacology & Experimental Therapeutics

institute: Mayo Clinic

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

overall_design: Refer to individual Series


title: Hippo deficient cardiac fibroblasts promote atrial remodeling

first: Yi

last: Zhao


title: Human kinome CRISPR knockout screen in H358 parental and sotorasib resistant H358 cells

city: Tampa

first: jiqiang

last: yao

address: 12902 USF Magnolia Drive

institute: moffitt cancer center

summary: A human kinome CRISPR knockout screen in H358 parental and sotorasib-R H358 cells using Addgene pooled libraries (#75314).

overall_design: Parental cells were cultured with DMSO, while resistant cells were cultured with sotorasib for 2 weeks. Integrated sgRNAs were amplified from genomic DNA and sequenced. We analyzed depleted sgRNAs in sotorasib-R H358 cells compared to reference or parental cells.

first: Eric

middle: B

last: Haura

first: Aobuli

last: Xieraili

first: Hitendra

middle: S

last: Solanki


title: KDM4A/KDM4C lysine demethylases sustain an oncogenic transcriptional program in diffuse large B-cell lymphoma [RNA-Seq]

summary: OCI_Ly1 cells treated with either DMSO or two different concentrations (150nM and 500nM) of the KDM4 inhibitor, JIB-04 were used for RNA-seq

overall_design: 9 samples

first: Deepak

last: Kumar Jha

first: Cheng

last: Zhang

first: George

last: Daley


title: RNAseq analysis of LU65 parental and cells that have acquired resistance to RMC-4998

summary:
To investigate the transcriptinal alterations in RMC-4998 sensitive LU65 cells and cells that have acquired resistance to RMC-4998. The resistant cell lines of LU65 was generated following chronic treatment with RMC-4998.
We then performed gene expression profiling analysis using data obtained from RNA-seq of parental and resistant lines.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for  LU65 cells and their RMC-4998 resistant isogenic line. The experiment was perfomed in biological triplicates.

first: Jiqiang

last: Yao

first: Paul

middle: A

last: Stewart


title: RNAseq analysis of Sotorasib sensitive and cells acquired resistance to Sotorasib

summary:
To investigate the transcriptinal alterations in Sotorasib sensitive and cells acquired resistance to Sotorasib. The Sotorasib resistant cell lines of H358 and LU65 were generated following chronic treatment with Sotorasib.
We then performed gene expression profiling analysis using data obtained from RNA-seq of parental and resistant lines.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for NSCLC cells (H358 and LU65) cells and their Sotorasib resistant isogenic lines (H358-AMGR and LU65-AMGR). The experiment was perfomed in biologicall triplicates.

last: stewart


title: Acetate Triggers Epigenetic Activation of Cell Cycle Arrest via ACSS2-H2A.Zac Axis in Esophageal Squamous Cell Carcinoma [ChIP-seq]

status: Public on Oct 06 2025

city: Wenzhou

first: Chenghao

address: Wenzhou Medical University, Xueyuan Xi Road

institute: Wenzhou Medical University

summary: Short-chain fatty acids (SCFAs) are closely associated with cancer, yet their involvement in the progression of esophageal squamous cell carcinoma (ESCC) remains unexplored. Here, we show a significantly decreased transcriptional activity of the SCFA metabolic pathway along with a reduced acetate accumulation in ESCC tissues compared to adjacent normal tissues. Exogenous acetate supplementation significantly suppresses ESCC proliferation both in vitro and in vivo. Mechanistically, acetate promotes the incorporation of the transcriptional active histone modification H2A.Zac into chromatin through ACSS2, an enzyme that converts acetate to acetyl-CoA and is aberrantly downregulated in ESCC. H2A.Zac subsequently activates the transcription of cell cycle arrest regulators like ATM and ACSS2 itself to form a positive feedback loop that facilitates acetate utilization, thereby slowing tumor growth. Either mutating the three H2A.Z acetylation sites from lysine to arginine or ACSS2 knockdown abrogated the anti-tumor effects of acetate. Taken together, our findings reveal a previously unrecognized metabolic-epigenetic regulatory loop orchestrated by acetate-ACSS2-H2A.Zac-ATM axis in ESCC, which offers novel insights for its diagnosis and therapy.

overall_design: ChIP-seq of H2AZac and paired RNA-seq were performed in the esophageal squamous cell carcinoma cell line KSE450 before and after acetate treatment.

first: Zhenhui

last: Chen

first: Yunxi

first: Xuanxuan

last: Gou

first: Jiangcong

last: Ma

first: Wenyan

last: Sun

first: Jianzhong

last: Su


title: High-throughput characterization of transcription factors that modulate UV damage formation and repair at single-nucleotide resolution

city: Durham

first: Hana

middle: Isadora

last: Wasserman

state: NC

address: 3308 Old Chapel Hill Road

institute: Duke University

summary: Genomic studies have revealed elevated damage and mutation rates in active transcription factor (TF) binding sites of UV-linked cancers. Previous research investigating the relationship between TF activity and UV DNA damage have primarily focused on select TFs or been done in aggregate across large cohorts of TFs at kilobase resolution. While collectively, there is evidence that TFs contribute to UV-induced mutagenesis by both enhancing initial damage formation and attenuating repair, no method exists to comprehensively characterize these mechanisms driving downstream mutation enrichment on a per-TF basis. Using genome-wide maps of UV damage from human skin fibroblasts, we developed a scalable statistical framework to identify and deconvolve TF-mediated mutagenic mechanisms across hundreds of TFs. We show that numerous previously unidentified TFs significantly modulate damage formation in their binding sites. Our systematic survey of TF-DNA complexes reveals that TF-induced structural distortions predispose DNA to specific photodimer types and coincide with UV damage enrichment, highlighting the role of structure in UV damage formation. Additionally, we analyzed repair efficiency in TF binding sites with unprecedented resolution, identifying specific TFs and binding site positions likely driving competition with repair factors. By comparing these results with skin cancer sample mutations, we can distinguish mutation peaks driven by increased damage susceptibility versus attenuated repair, illustrating that the mechanisms of TF-mediated mutagenesis are both TF- and position-specific. Our approach provides a robust statistical framework to elucidate the mechanisms of mutagenic TF-binding and offers novel insights into the complex interplay between protein interactions with DNA damage and repair.

overall_design: ATAC-seq performed using four biological replicates to define open chromatin regions for the human skin fibroblast cell line, CS1AN/CSBWT

middle: I

first: Alexias

last: Safi

first: Gregory

middle: E

last: Crawford

first: Raluca

last: Gordân

first: Peng

last: Mao


title: Acetate Triggers Epigenetic Activation of Cell Cycle Arrest via ACSS2-H2A.Zac Axis in Esophageal Squamous Cell Carcinoma [RNA-seq]

last: Li


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

city: Laramie

first: Yun

state: WY

address: 1000 E University Ave

department: Zoology and Physiology

institute: University of Wyoming

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

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

first: Rashmi

last: Thapa

first: Navin

last: Adhikari

first: Sishir

last: Gautam

first: Mingming

first: Sierra

last: McOmie

first: Viyaleta

last: Davydzenka

first: Derek

last: Smith

first: Jack

last: Syring

first: Harlie

last: Kaligis

first: Jade Marie

last: Kosmicki

first: Rong


title: Analysis of SARS-CoV-2 replication using human nasal organoids comprising olfactory and respiratory epithelium

city: Kyoto

first: Eiraku

last: Mototsugu

state: Kyoto

address: 53, Kawahara-cho

department: Institute for Life and Medical Sciences

institute: Kyoto University

summary: SARS-CoV-2 infects the nasal epithelium (NE) and can cause olfactory dysfunction. Because the virus cannot infect olfactory sensory neurons (OSNs) which detect odorants, the underlying mechanisms remain unknown. Here, using human embryonic stem cells, we were the first to develop human NE organoids comprising both olfactory neuroepithelia (OE) and nasal respiratory epithelia (NRE). SARS-CoV-2 initially replicated in the NRE and then spread to the OE where angiotensin converting enzyme 2 was expressed after virus replication in NRE. Importantly, a significant proportion of neural precursor cells (NPCs) and basal stem cells in the OE, both of which constantly differentiate into OSNs, were infected. Viral infection upregulated cell death-associated genes in the NPCs and basal stem cells, suggesting that SARS-CoV-2 infection disrupts the repair and renewal of OSNs. Taken together, our human nasal organoid model would be useful for the investigation of a potential mechanism underlying olfactory dysfunction in COVID-19 patients.

overall_design:
We performed scRNA-seq of mock-infected and virus-infected NE organoids collected 1, 2, 7 and 11 days after SARS-CoV-2 infection.

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

first: Mototsugu

last: Eiraku

first: Takeshi

last: Noda


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

first: Laszlo

last: Nagy

first: Dora

last: Bojcsuk

first: Benjamin-Rego

last: Barath


title: Increased Reproducibility of Brain Organoids through Controlled Fluid Dynamics

city: Lausanne

first: Giuseppe

last: Aiello

address: Rue du Bugnon,9

institute: University of Lausanne

summary: Brain organoids are a promising model for studying human neurodevelopment and disease. Despite the potential, their 3D structure exhibits high variability during differentiation across batches and cell lines, presenting a significant challenge for biomedical applications. During development, organoids are exposed to fluid flow shear stress (fFSS) generated by the flow of culture media over the developing tissue. This stress is thought to disrupt cellular integrity and morphogenesis, leading to variation in organoids architecture, ultimately affecting reproducibility. Understanding the interplay between tissue morphology, cell identity and organoid development is therefore essential for advancing the use of brain organoids. Here, we demonstrate that reducing fFSS, by employing a vertically rotating chamber during neuronal induction, a critical phase for organoid morphogenesis, along with an extended cell aggregation phase to minimize fusions, significantly improves the reproducibility of brain organoids. Remarkably, reducing fFSS minimized morphological structure variation and preserved transcriptional signature fidelity across differentiation batches and cell lines. This approach could enhance the reliability of brain organoid models, with important implications for neurodevelopmental research and preclinical studies.

overall_design: In order to assess the cellular diversity of RC brain organoids, we performed single cell RNA sequencing at day 90. A pool of three organoids per hiPSC line (RC-Line1 and RC-Line2) was used. Libraries were sequenced using the Element Biosciences AVITI.


title: Expression profiling of THP-1 cells with and without infection by Francisella tularensis and with or without treatment with Dillapiole

city: Huntington

first: James

last: Denvir

state: WV

address: One John Marshall Drive

department: Biochemistry and Microbiology

institute: Marshall University School of Medicine

summary: In order to assess the effect of treatment by Dillapiole on human monocyte THP-1 cells infected by Francisella tulerensis, we performed expression profiling by RNA sequencing on THP-1 cells with and without infection and with or without treatment. Differential expression analysis revealed 1174 genes whose expression was affected by the Dillapiole treatment differently in the infected cells when compared to the treatment effect in the uninfected cells. These genes identified 45 biological pathways, including an inhibitory effect on the TNF-receptor pathway.

overall_design: THP-1 cells were either infected by Francisella tularensis or grown without infection. Infected and uninfected cells were treated by either Dillapiole or a control vehicle. Five biological replicates for each of the resulting four experimental groups were utilized for expression profiling by RNA-Seq.

first: Elliot

middle: M

last: Collins

first: Anthony

last: Sako

first: Kristen

last: Sikorsky

first: Jun

last: Fan

first: Donald

last: Primerano

first: Deanna

last: Schmitt

first: Stuart

last: Cantlay

first: Roger

last: Seeber

first: Francisco

last: León

first: Joseph

last: Horzempa


title: Bulk RNA sequencing of kidneys from control and KC-Tie2 model of psoriasis

city: Nashville

first: Matthew

last: Alexander

state: TN

address: 1211 Medical Center Drive

institute: Vanderbilt University Medical Center

summary: Using a mouse model of psoriasis with Tie2 overexpression in keratinocytes (KC-Tie2) we compared transcriptomes of kidneys from these mice and littermate controls. We then performed bulk RNA sequencing of KC-Tie2 and littermate control kidneys at 10 weeks of age. Results revealed over-representation of gene ontology terms related to lupus and NETosis in KC-Tie2 kidneys. Together, these findings suggest that KC-Tie2 mice exhibit increased renal damage at least in part through enhanced neutrophil recruitment and NET formation.

overall_design: After saline perfusion, kidneys from KC-Tie2 and control mice were homogenized and RNA was extracted with Trizol reagent.

first: Alexander

last: Matthew


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

city: Nagasaki

first: Takashi

last: Ito

address: 1-12-4, Sakamoto, Nagasaki

department: Biomedical Sciences

institute: Nagasaki University

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: TCRs enable traceability of CAR-T cells but impair function in dual target cell contexts [car_post_infusion]

city: Erlangen

first: Kilian

last: Schober

state: Bavaria

address: Maximiliansplatz 2

department: Mikrobiologisches Institut – Klinische Mikrobiologie, Immunologie und Hygiene

institute: Universitätsklinikum Erlangen

summary: Chimeric antigen receptor (CAR) T cells are powerful tools against cancer and autoimmunity. CARs are typically introduced into T cells with endogenous T cell receptors (TCRs), enabling clonotype tracking. Also, CAR expression in T cells with virus-specific TCRs may enhance CAR-T efficacy. However, the functional impact of endogenous TCR activity on CAR-T behavior remains unclear. We here traced anti-CD19 CAR-T clonotypes in patients with B-cell malignancies using single-cell RNA-, TCR-, and CITE-seq. An IFNG-positive phenotype, but not short-term reactivity, predicted clinical CAR-T persistence. To test intrinsic TCR effects, we combined CAR transduction with orthotopic TCR replacement in human T cells. Inactive TCRs did not alter CAR-T function and may serve as molecular barcodes. In contrast, active TCRs modulated CAR signaling as agonists and CAR cytotoxicity as antagonists in an avidity-dependent manner, while CAR activity had no effect on TCR cytotoxicity. Therefore, spatial antigen separation alters TCR/CAR interplay with implications for therapeutic CAR-T design.

overall_design: Patient-derived CAR T cells isolated post-infusion were identified by DNA-barcoded CD19-multimers (dCODE Dextramers) and Dextramer+ cells were sort-enrichted by FACS. Sorted cells were subjected to 5' scRNAseq on a 10x Genomics platform including CITEseq for Dextramers, indicated surface proteins and TotalSeq-C anti-human hashtag antibodies. Hashtag antibodies were included to identify cells from different donors.

first: Carolin

last: Moosmann

first: Felix

last: Drost


title: Oligo-CALL: A Next-Generation Barcoding Platform for Studying Resistance to Targeted Therapy [bulk RNA-seq]

city: New York

first: Dingcheng

last: Gao

state: NY

address: 1300 York Ave

department: CT Surgery

institute: Weill Cornell Medical College

summary: Deconvolving heterogeneous cell populations and tracing individual clonal trajectories are essential for unraveling complex biological processes, such as therapy resistance. Although CRISPR-assisted cellular barcoding holds promises for lineage tracing, current platforms exhibit limitations underscored by suboptimal efficiencies and incompatibilities with single-cell transcriptomics. We introduce Oligo-CALL (Oligonucleotide-induced CRISPRa-Assisted Lineage Labeling), a new cellular barcoding system enabling precise tumor clone tracking, convenient live-clone isolation without additional genomic modification, and compatibility with single-cell RNA sequencing. Applying Oligo-CALL to human lung cancer cells revealed key insights into the resistance to KRAS G12C inhibitors (G12Ci). Clonal fate assays demonstrated that certain clones were repeatedly enriched under G12Ci pressure, indicating a “predestined” rather than “stochastic” mode of resistance. Paired functional assays of treatment-naïve versus resistant clones revealed clone-specific, acquired resistance phenotypes, manifesting as transient or permanent. Single-cell transcriptomics confirmed the activation of diverse yet clone-specific adaptive pathways underlying G12Ci resistance. Together, Oligo-CALL offers a powerful way to investigate the evolution of resistance to targeted therapies.

overall_design: Matched pairs of Oligo-CALL barcoded H358 clones were isolated from treatment-naïve and AMG510-resistant cell pools. Each clone pair was derived from cells carrying the same barcode and expanded separately. Clones were treated with AMG510 (2 μM) or vehicle for 3 days. Bulk RNA sequencing was performed to assess transcriptional responses to treatment. The analysis included three matched clone pairs— Clone #1(Cont_102_130 vs. AMG_102_130), Clone #2 (Cont_103_117 vs. AMG_103_107), Clone#3 (Cont_106_125 vs. AMG_106_125), as well as the parental naive and resistant pools (Cont_pool vs AMG_pool).

first: Yingzhuo

last: Liu

first: Yi

last: Ban


title: Oligo-CALL: A Next-Generation Barcoding Platform for Studying Resistance to Targeted Therapy [scRNA-seq]

overall_design: Two pools of Oligo-CALL labeled H358 cells (each comprising ~1,000 clones) were seeded in 10cm plates (2×10^6 cells per plate). Cells were treated with AMG510 (2μM) or vehicle (DMSO) for 2 weeks. During the treatment, medium was replenished every 3 days, and cells were sub-cultured at 80% confluence to maintain exponential growth. scRNA-sequencing was performed with live cells at the end of treatment. Four samples were included: X1 (H358 cells labeled by Lib3, treated with AMG510), X2 (H358 cells labeled by Lib3 treated with Vehicle), X3 (H358 cells labeled by Lib3b treatedwith Vehicle), and X4 (H358 cells labeled by Lib3b treated with AMG510). Transcriptome library and gRNA barcode library were prepared from each sample and sequenced in two runs of illunima sequencing.


title: KDM4A/KDM4C lysine demethylases sustain an oncogenic transcriptional program in diffuse large B-cell lymphoma [ChIP-Seq]

first: Hu

last: Li

summary: OCI_Ly1 cells treated with either DMSO or two different concentrations (150nM and 500nM) of the KDM4 inhibitor, JIB-04 were used for chip-seq

first: Deepak

last: Kumar Jha

first: Cheng

last: Zhang

first: Benoit

last: Laurent

first: Yang

last: Shi

first: George

middle: Q

last: Daley


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.
***************************************************************

first: Alyxzandria

last: Gaydosik

first: Brigit

last: Lapolla

first: Larisa

last: Geskin


title: Exceptional diversity of allorecognition receptors in a non-vertebrate chordate reveal principles of innate allelic discrimination

city: San Francisco

first: Henry

last: Rodriguez

address: 1322 3rd avenue

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: Chemotherapy-induced CAR cell senescence disrupts bone homeostasis to induce bone loss

city: St. Louis

first: Ganesh

middle: Kumar

last: Raut

address: Euclid Ave

institute: Washington University School of Medicine

summary: To identify which bone resident cells senesced in response to chemotherapy, we performed scRNA-Seq on bone marrow depleted of CD45+, CD71+, Ter119+, CD31+ cells. Our scRNA-Seq analysis identified seven clusters in both Veh- and Doxo-treated mice: CAR cells, three fibroblast populations, chondrocytes, endothelial cells, and osteoblasts that were identified based on cell specific markers. Next, we assessed the expression of the senescence markers (p16 and p21), cell proliferation marker (Mki67) and SASP factors (IL6, Spp1, Cstb, Serpine1, Mmp3). As expected, we found a down regulation of Mki67 and upregulation of senescence markers and SASP factors in the Doxo-treated group compared to Veh. we also checked senescence markers across the clusters and found CAR cells undergo senescence and impact bone homeostasis.

overall_design: 12-week-old mice were treated with Veh- and Doxo (10 mg/kg) for 96 hours. Bones (femurs and tibias) were harvested from euthanized mice and placed in cold DMEM/F12 (Gibco). Muscle and connective tissues were removed. Bones were gently ground and then cut into small fragments. Fragments were transferred and digested with fresh 2 mg/ml collagenase (Sigma, C0130) in DMEM/F12 on a rotating water bath at 37°C for 30 min. Following the first digestion, the released cell suspension was filtered through a 70-μm nylon mesh into a collection tube and placed on ice. A second digestion of the remaining fragments was performed and the cell suspension was filtered into the same collection tube. Reactions were quenched with FACS buffer (PBS plus 0.5% BSA) with 2mM EDTA. Following FACS buffer wash and RBC lysis, dissociated cells were labeled with anti-CD45 magnet microbeads and enriched into a CD45+ fraction and CD45- fraction by MACS (magnetic-activated cell sorting, Miltenyi Biotech). Cells were stained with fluorochrome antibodies for 20 min on ice for cell sorting. We used CD45, CD71, Ter119 and CD31 to deplete CD45+ CD71+, Ter119+, CD31+ populations using a BD FACS Aria III Cell Sorter. After sorting, cells were delivered for library construction using 10X Genomics Chromium 3′ GEM Single-Cell Library v3 kit (10X Genomics).

last: Kumar Raut

first: Zhangting

last: Yao

first: Sheila

last: A Stewart


title: BACH2 dosage establishes the hierarchy of stemness and fine-tunes antitumor immunity in CAR T cells

city: Dallas

first: Chen

address: 5901 FOREST PARK RD, NS6 218

institute: UT Southwestern Medical Center

summary: Self-renewing stem-like T cells promote the efficacy of cancer immunotherapy and are a heterogeneous population with sub-lineages demonstrating different degrees of stemness. At the apex of this hierarchy is long-term (LT) stem-like T cells with the highest capacity of persistence, repopulation and response to immune checkpoint inhibitors (ICI). However, the pathway that establishes the hierarchy of stemness in chimeric antigen receptor (CAR) T cells and its role in antitumor efficacy of CAR T cells are unclear. Here, we demonstrate that LT stem-like differentiation and antitumor immunity of CAR T cells are dose-dependently regulated by BACH2. Pre-infusion LT stem-like CAR T cells showed epigenetic activation of BACH2 and superior antitumor response in mice and humans. After clearing tumor in vivo, LT stem-like T cells emerged as a CAR subset that transcriptionally and epigenetically upregulated BACH2 and downregulated TOX. Loss-of-function experiments revealed an essential role of BACH2 in the antitumor response of CAR T cells and the transcriptional program of LT stem-like CAR T cells. In exhaustion-prone GD2 CAR T cells with high tonic signaling, we showed that quantitative control of BACH2 protein level by a small molecule drug fine-tuned the degree of stemness and exhaustion in CAR T cells. Chemically inducing temporal BACH2 activation during manufacture of GD2 CAR T cells imprinted greater antitumor immunity against solid tumor after infusion. Together, we show that BACH2 dosage establishes the hierarchy of stem-like CAR T cells and can be temporally and tunably controlled in CAR T cells to optimize differentiation and antitumor immunity.

overall_design: We performed single-cell ATAC+RNA sequencing on in vitro clutured CAR T cells and CAR T cells isolated from tumor bearing mice on day 20 after infusion. We performed scRNAseq on WT and BACH2 inducible knock out CAR T cells isolated from tumor bearing mice on day 7 after infusion. We performed ChIP-seq

first: Tuoqi

last: Wu

first: Ziang

last: Zhu

first: Taidou

last: Hu

first: Ying

last: Luo


title: Single-cell clonal lineage tracing identifies the transcriptional program controlling the cell fate decisions by neoantigen-specific CD8+ T cells

summary: Neoantigen-specific T cells specifically recognize tumor cells and are critical for cancer immunotherapies. However, the transcriptional program controlling the cell fate decisions by neoantigen-specific T cells is incompletely understood. Here, using joint single-cell transcriptome and TCR profiling, we mapped the clonal expansion and differentiation of neoantigen-specific CD8+ T cells in the tumor and draining lymph node in mouse prostate cancer. Compared to other antitumor CD8+ T cells and bystanders, neoantigen-specific CD8+ tumor-infiltrating T cells (TILs) upregulated gene signatures of T cell activation and exhaustion. In the tumor draining lymph node, we identified TCF1+TOX- TSCM, TCF1+TOX+ TPEX, and TCF1-TOX+ effector-like TEX subsets among neoantigen-specific CD8+ T cells. Clonal tracing analysis of neoantigen-specific CD8+ T cells revealed greater clonal expansion in divergent clones and less expansion in clones biased towards TEX, TPEX, or TSCM. The TPEX subset had greater clonal diversity and likely represented the root of neoantigen-specific CD8+ T cell differentiation, whereas highly clonally expanded effector-like TEX cells were positioned at the branch point where neoantigen-specific clones exited the lymph node and differentiated into TEX TILs. Notably, TSCM differentiation of neoantigen-specific CD8+ clones in the lymph node negatively correlated with exhaustion and clonal expansion of the same clones in the tumor. In addition, the gene signature of neoantigen-specific clones biased toward tumor infiltration relative to lymph node residence predicted a poorer response to immune checkpoint inhibitor. Together, we identified the transcriptional program that controls the cell fate choices by neoantigen-specific CD8+ T cells and correlates with clinical outcomes in cancer patients.

overall_design: We performed single-cell RNA and TCR sequencing on SPAS1 tetramer-positive CD8 T cells,  SPAS1 tetramer-negative, PD1-positive, IFNg-posigive CD8 T cells and SPAS1 tetramer-negative, PD1-negative, IFNg-negative CD8 T cells from the tumor and SPAS1 tetramer-positive CD8 T cells from the lymph node from IFNg-YFP reporter (GREAT) mice inoculated with TRAMP-C2.


title: TCRs enable traceability of CAR-T cells but impair function in dual target cell contexts [car_pre_infusion]

first: Kilian

last: Schober

overall_design: For three donors, 10^6 leftover clinical anti-CD19 CAR T cells (Kymriah, Novartis) were either cultured in the presence (=stimulated) or absence (=unstimulated) of 5x10^5 CD19-expressing Nalm6 at 37°C, 5% CO2 for 24h, respectively. Single, live CD19- CD3+ lymphocytes were sorted. Sorted cells were subjected to 5' scRNAseq on a 10x Genomics platform.

first: Martin

last: Böttcher

first: Felix

last: Drost


title: Challenging the Traditional  Dormancy Assumption: Antibiotic  Persisters are Metabolically Active, Non-Growing Cells

city: Brookings

first: Xuan

last: Butzin

state: SD

address: 1451 Stadium Rd

department: Biology and Microbiology

institute: South Dakota State University

summary: Bacterial persisters are a subpopulation of multidrug-tolerant cells capable of surviving and resuming activity after exposure to lethal antibiotic treatments, contributing to relapsing infections and the development of antibiotic resistance. We challenge the conventional view that persisters are metabolically dormant by providing compelling evidence that an isogenic population of Escherichia coli remains metabolically active in persistence. Our transcriptomic analysis, conducted at various time points following exposure to lethal concentrations of ampicillin (Amp), revealed a number of genes with differential expression over time. Some genes were consistently upregulated in Amp treated persisters compared to the untreated controls, a change that can only occur in metabolically active cells capable of increasing RNA levels. Some of these genes have been previously linked to persister cells, while others have not been associated with them before. If persister cells were metabolically dormant, we would expect minimal changes in the gene network across different time points of Amp treatment. However, network analysis revealed major shifts in gene network activity at various time points of antibiotic exposure. To explore gene activation in persisters, we developed a new promoter system in which an Amp resistance gene is activated specifically in persister cells. Following treatment with lethal Amp, the Amp resistance gene conferred resistance after ~8 h. This gene’s activation requires the production of both mRNA and protein, processes that can only occur in metabolically active cells. These findings reveal that persisters are metabolically active, non-dividing cells, thereby challenging the notion that they are dormant.

overall_design: E.coli cells were grown to mid-log phase (OD ~0.5) and then treated with ampicillin (0.1 mg/ml) for 24 hours. RNA samples were collected at four time points: before antibiotic treatment (0 h) and after antibiotic treatment at 3 h, 6 h, and 24 h, in biological triplicates, for RNA sequencing analysis.

first: K M Taufiqur

last: Rahman

first: Ruqayyah

last: Amaratunga

middle: Y

first: Abhyudai

last: Singh

first: Tahmina

last: Hossain

first: Nicholas


title: Loss of SPHK1 fuels inflammation to drive KRAS-mutated lung adenocarcinoma

city: Vienna

first: Herwig

middle: P

last: Moll

address: Waehringer Strasse 13a

country: Austria

institute: Medical University of Vienna

summary: Inflammation is a widely recognized key contributor to KRAS-driven lung adenocarcinoma. Tumor associated macrophages are integral part of the tumor microenvironment, creating a supportive niche to sustain tumorigenesis. In the present study, we unravel a dichotomic role of sphingosine kinase 1 (SPHK1). We delineate SPHK1 as an oncogene, where its deletion markedly reduced proliferation of KRAS-mutated lung adenocarcinoma cells. However, in pre-clinical models, SPHK1 is a tumor suppressor, where its tumor intrinsic loss leads to disrupted lipid homeostasis, increased inflammation and hence augmented tumorigenesis.

overall_design: Lung tumors were induced in KP and KPdSPHK1 mice 14 weeks prior of organ harvesting. Tissue was then frozen and RNA was from bulk lung tissue.

first: Andreea

last: Luca

first: Emilio

last: Casanova


title: On the origin of the mammalian piRNA pathway

city: Haining

first: Xinyu

last: Xiang

address: 718 East Haizhou Road

institute: Zhejiang University

type: Non-coding RNA profiling by high throughput sequencing

type: Methylation profiling by high throughput sequencing

summary: The piRNA pathway protects animal germlines form active transposons. Mammals employ a cytoplasmic pathway to post-transcriptionally destroy transposon transcripts and a nuclear pathway that mediates DNA methylation to epigenetically silence transposon expression. When the modern version of these pathways evolved remains unknown. We found that the mammalian version of the cytoplasmic pathway evolved in lobe-finned fish, as defined by the use of the 3ʹ exonuclease Pnldc1 for precursor piRNA trimming. The nuclear pathway evolved during early in tetrapod evolution and is already found in its current configuration in the salamander, Ambystoma mexicanum. Interestingly, the nuclear pathway was lost during bird evolution. We found evidence that both the cytoplasmic and nuclear piRNA pathways are active in both the male and female axolotl germlines. Analysis of axolotl testes and oocytes revealed diverse repertoires of piRNAs and persuasive post-transcriptional targeting of young transposons. We found high levels of genome methylation in axolotl spermatozoa with full-length transposons being highly methylated. Furthermore, CpG island methylation in axolotl is associated with transposon silencing. In summary, we find that the mammalian version of the piRNA pathway has ancient vertebrate origins, and it has been safeguarding the germline across most of tetrapod evolution.

overall_design: Small RNA-seq was performed on axolotl testis and oocyte samples, each with two biological replicates. EM-seq was performed on axolotl spermatozoa with three biological replicates. Samples were collected from the d/d white axolotl strain with hCG (human chorionic gonadotropin) injection to induce gamete maturation in adult axolotl.

first: Donal

last: O'Carroll

first: Diego

last: Rodriguez Terrones

first: Francisco

last: Falcon


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

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: 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

last: Maron

first: Joseph

last: DeAngelo


title: Gene expression of Francisella tularensis LVS treated with and without Dillapiole

first: James

last: Denvir

summary: RNA-seq analysis was conducted on F. tularensis incubated in the presence of dillapiole. We observed a significant decrease in virulence factor expression, specifically genes under the control of the master virulence regulators MglA and SspA, compared to bacteria treated with vehicle-alone.

overall_design: Expression profiling by RNA-Seq of F. tularensis treated with Dillapiole or vehicle control.

first: Elliot

last: Collins

first: Anthony

last: Sako

first: Kristen

last: Sikorsky

first: Jun

last: Fan

first: Donald

last: Primerano

first: Deanna

last: Schmitt

first: Stuart

last: Cantlay

first: Roger

last: Seeber

last: León

last: Horzempa


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: Palmitate suppresses CD8+ T cell antitumoral response by disrupting mitochondrial metabolism [RNA-seq]

city: Milano

first: Teresa

last: Manzo

state: Milano

address: Via Adamello 16

department: Department of Experimental Oncology

country: Italy

institute: IEO

summary: Accumulation of lipids in the tumor microenvironment (TME) is a feature of several solid tumors and increased palmitate (PA) availability fosters tumor progression and metastases. The intrinsic effects of PA on cancer cells are well understood, but its role in modulating CD8+ T cells (CTL) functional performances remains elusive. Here, we found that PA alters the mitochondrial metabolism of CTL and prevents their effector functions in an irreversible manner, resulting in impaired antitumoral immunity. Mechanistically, PA-induced mitochondrial blocking demotes histone acetylation and chromatin accessibility and decreases the transcription of genes promoting DNA replication and production of effector molecule production. We identified the metabolic enzyme Sphingosine Kinase 2 (SPHK2) as a molecular target of PA in establishing CTL dysfunction. Consistently, pharmacological inhibition of SPHK2 restored CTL mitochondrial fitness, effector functions and anti-tumor potential. Thus, we reveal that PA fosters tumor progression by impairing CTL antitumor immunity and highlight the therapeutic potential of inhibiting SPHK2 activity to optimize T cellfunctionality.

overall_design: To investigate the effects of Palmitate on CD8+ T cell function, RNA Sequencing of Palmitate-treated vs control cells was carried out after 48 hours of treatment

first: Silvia

last: Tiberti

first: Marine

last: Romeo

first: Carina

last: Nava

first: Ilir

last: Sheraj

first: Carlotta

last: Catozzi

first: Roberta

last: Noberini

first: Davide

last: Olivari

first: Tiziano

last: Dallavilla

first: Serena

last: Galie’

first: Mattia

last: Ballerini

first: Alessia

last: Loffreda

first: Martin

middle: H

last: Schaefer

first: Eric

last: Camerer

first: Tiziana

last: Bonaldi

first: Luigi

last: Nezi

first: Sara

last: Sdelci


title: Palmitate suppresses CD8+ T cell antitumoral response by disrupting mitochondrial metabolism [ATAC-seq]

first: Teresa

last: Manzo

overall_design: To investigate the effects of Palmitate on CD8+ T cell function, ATAC-seq of Palmitate-treated vs control cells was carried out after 48 hours of treatment


title: Experimental challenge of African green monkeys with contemporary Hendra virus isolates produces divergent clinical disease

city: Galveston

first: Jacquelyn

last: Turcinovic

state: TX

address: Galveston National Laboratory, 301 University Blvd.

department: Microbiology and Immunology

institute: University of Texas Medical Branch

summary: Hendra virus (HeV) is a medically important, zoonotic paramyxovirus that emerged over thirty years ago which causes severe, often fatal disease in humans and animals. There are presently no medical countermeasures approved to prevent or treat human HeV disease, although many are in various stages of development. Critical to the stringent evaluation of these experimental countermeasures are nonhuman primate models of HeV disease which accurately recapitulate the pathogenesis of human infection. The continued emergence of HeV since its initial discovery in 1994 has recently expanded to include the identification of a new variant with enough genetic divergence to require the creation of a second genotype. Although this variant HeV has produced fatal equine disease, its pathogenesis and lethality are unknown in humans. In the present study, we investigated the pathogenicity of clinically relevant and contemporary HeV isolates from genotype 1 (HeV/Australia/Horse/2008/Redlands) and genotype 2 (HeV-var/Australia/Horse/2015/Gympie) in the African green monkey (AGM) model of henipavirus disease. Experimental challenge of AGMs with 5.0E5 PFU of HeV genotype 1 (HeV-g1) or genotype 2 (HeV-g2) isolates via the combined intranasal/intratracheal route of exposure produced divergent survival outcomes, with four of five AGMs infected with the HeV-g2 isolate surviving until the predetermined scientific endpoint of the study. All five HeV-g1 infected subjects developed acute HeV disease which accurately recapitulated HeV pathogenesis reported in humans. Our findings revealed that HeV-g2 is less pathogenic than HeV-g1 in the AGM animal model and suggests that HeV-g2 may be less pathogenic in humans.

overall_design: Serially sampled circulating blood from african green monkeys

first: Declan

last: Pigeaud

first: Robert

last: Cross

first: Thomas

last: Geisbert


title: LGALS1  plays an anti-oncogenic role in cervical cancer by synthetically regulating transcriptome profile in HeLa cells

city: changchun

first: Zanhui

last: Jia

address: The Second Hospital of Jilin University, 2nd Building, 218 Pingzhi Street, Changchun

institute: Second Hospital of Jilin University

summary: Long non-coding RNAs (lncRNAs) have been extensively studied as key regulators of cancer development in various cancers. *** is a newly identified lncRNA in recent years, and several studies have shown that *** may play oncogenic or anti-oncogenic roles in different cancers. Pan-cancer analysis showed that high *** expression was significantly associated with better prognosis. Nevertheless, the role of *** in the development of cervical cancer is unclear. In our study, we constructed a *** overexpression model in HeLa cell line. We found that *** overexpression significantly inhibited cell proliferation and induced apoptosis, and *** may be a novel anti-oncogenic factor in cervical cancer. Mechanistically, overexpression of *** could activate type I interferon signaling pathways and inhibits the expression of genes involved in DNA damage responses. Meanwhile, *** could regulate the expression of a large number of RNA binding protein genes thereby potentially affecting the alternative splicing of genes involved in cell proliferation or apoptosis regulation. We also established a ceRNA network to predict the regulatory effect of *** on gene expression through miRNA. Our study highlights the essential role of lncRNA *** in the development of cervical cancer and suggests the potential regulatory mechanisms.

overall_design: We constructed a LGALS1 overexpression model in HeLa cell line, coupled with RNA-seq sequences, to comprehensively reveal the biological function of LGALS1 in HeLa cell and analyze the alterations of transcriptional profiles upon LGALS1 overexpression.

first: Xuejian

last: Li

first: Huifei

last: Wang

first: Aran

first: Yuanyuan

last: Cao

first: Liuqing

last: Yang


title: Multi-scaled transcriptomics of chronically inflamed nasal epithelium reveals immune-epithelial dynamics and tissue remodeling in nasal polyp formation

city: Boston

first: Guanrui

last: Liao

state: Massachusetts

address: 3 Blackfan Circle

institute: BIDMC

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

overall_design: Refer to individual Series


title: Obesity promotes inflammatory, metabolic, and proliferative transcriptional programs in orthotopically transplanted murine colon tumors

city: Chapel Hill

first: Stephen

last: Hursting

state: North Carolina

address: 215B MHRC

institute: University of North Carolina - Chapel Hill

summary: The mechanisms driving obesity-associated colon cancer progression are not completely understood. This study leveraged RNA sequencing data from control and obese C57BL/6 mice to identify obesity-associated transcriptomic signatures. Bulk EpCAM+ epithelial tumor transcriptomic analyses revealed obesity-driven enrichment of inflammation, proliferation, and metabolic pathways.

overall_design: RNAseq profiling of EpCAM+ epithelial tumor cells from orthotopically transplanted colon organoids in control and obese mice.

first: Elaine

last: Glenny


title: In vivo differentiation of embryonic cells devoid of key reprogramming factors

status: Public on Oct 05 2025

city: New Haven

first: Scott

middle: Elliot

last: Youlten

state: CONNECTICUT

address: 333 Cedar Street, SHM-I

institute: Yale University

summary: Embryonic cell differentiation depends on the reprogramming of the oocyte and sperm nucleus into a transient totipotent state. In zebrafish, this coincides with genome activation, which is regulated by the pioneer factors Nanog, Pou5f3, and Sox19b (NPS). Here, we investigate the role of NPS in developmental reprogramming and differentiation by analyzing the fate of NPS mutant cells in a wild-type embryo using single-cell RNA-seq. We find that many cells fail to activate transcription or undergo cell death, while others acquire gene expression profiles that resemble germ cells, neural progenitors, and motoneuron states. These cells achieve intermediate transcriptional states revealing the essential role of NPS in coordinating nuclear and cytoplasmic reprogramming and preventing the premature activation of lineage-specific differentiation programs. These results demonstrate that most developmental programs require developmental reprogramming by NPS, yet some cell can bypass transient totipotency to achieve intermediate developmental states resembling wild type states in vivo.

overall_design: Donor embryos (WT or MZnps mutants) were injected with fluorescent reporters and transplanted into host wild-type embryos at the 1-cell stage. Embryos were dissociated at 11–12 hpf and enriched for donor-derived cells using hCD4 magnetic selection. Single-cell suspensions were loaded onto 10x Genomics Chromium chips (v3 chemistry), and three libraries were sequenced (two MZnps donor replicates, one WT donor).

first: Liyun

last: Miao

first: Caroline

last: Hoppe

first: Curtis

last: Boswell

first: Damir

last: Musaev

first: Mario

last: Abdelmessih

first: Damilola

last: Olowookere

first: Linnea

last: Weiss

first: Smita

last: Krishnaswamy

first: Antonio

middle: J

last: Giraldez

first: Valerie

last: Tornini


title: Clinical value and mechanism of CDKN2A in clear cell renal cell carcinoma

city: Xiamen

first: Songsong

last: Wang

address: Xiangan South Road

institute: Xiamen university

summary: Background: Clear cell renal cell carcinoma (ccRCC) is the most common type of kidney cancer, with its incidence increasing annually. This study aims to investigate the role of the Cyclin-Dependent Kinase Inhibitor 2A (CDKN2A) in ccRCC. Methods: We analyzed ccRCC-related data from the TCGA and GEO databases. First, we systematically assessed the expression levels of CDKN2A and its correlation with clinical features, such as tumor staging and prognosis. Additionally, regarding biological function, we explored the relationship between CDKN2A expression and immune cell infiltration, along with the mechanisms underlying this relationship. We also examined the association between CDKN2A and drug sensitivity through drug sensitivity analysis. Furthermore, we experimentally validated the differential expression of CDKN2A in ccRCC and its impact on the cellular behaviors of ccRCC cells. Results: The results revealed that CDKN2A expression was significantly higher in ccRCC tissues compared to normal kidney tissues, affecting patient prognosis by modulating the tumor microenvironment. Moreover, based on data from the GDSC, and CTRP databases, we found that high CDKN2A expression was closely associated with sensitivity to certain small-molecule drugs. These drugs particularly target the MAPK pathway. Experimental findings indicated that CDKN2A promotes the proliferation, migration, and invasion of ccRCC cells via the MAPK pathway. Conclusions: Our study suggests that CDKN2A has an oncogenic role in ccRCC and may serve as a potential therapeutic target.

overall_design: RORC-targeting siRNAs (hCDKN2A-412,hCDKN2A-770) were transfected into the cells using DharmaFECTTM 1 Transfection Kit according to the manufacturer's instructions. The siRNAs were sourced from Wuhan Biotech (Sangon Biotech). Total RNA was extracted from confluent 786-O and OS-RC-2 cells in both the CDKN2A knockout group and the blank control group, cultured in 60 mm dishes, using TRIzol® reagent (AgRNA ex Pro Regent, China). The extracted RNA samples were subsequently sent to Novogene (Beijing) for whole transcriptome resequencing using the Illumina HiSeq platform.

first: Yan

last: Li

first: Ziming

last: Liu


title: Epigenomic and transcriptomic profiling of cnidocyte subtypes in the sea anemone Nematostella vectensis [Cut & Tag]

city: Jerusalem

first: Itamar

last: Kozlovski

address: Alexander Silberman Institute of Life Sciences

department: Ecology, Evolution and Behavior

country: Israel

institute: The Hebrew University of Jerusalem

summary: Cnidarians, including corals, sea anemones, and jellyfish, possess specialized stinging cells called cnidocytes that function in prey capture and defense. These cells represent a striking evolutionary innovation and include distinct types such as venom injecting nematocytes and mechanically acting spirocytes. While their biomechanics and transcriptional regulation have been studied extensively, little is known about their epigenetic regulation. Here, we combined epigenetic profiling with RNA sequencing in the sea anemone Nematostella vectensis to explore regulatory programs underlying cnidocyte diversity. We identified cell type specific regulatory elements in promoter and enhancer regions and linked them to distinct gene expression programs. This analysis revealed fundamental differences between nematocytes and spirocytes and uncovered a previously unrecognized nematocyte population that expresses the nep3 toxin but lacks most other toxins. These findings highlight the complexity of cnidocyte regulation and suggest greater cellular diversity within this defining cnidarian cell type than previously appreciated.

overall_design: This study investigates the chromatin and transcriptional programs underlying cnidocyte specialization in the sea anemone Nematostella vectensis. Cnidocyte types (Ncol3⁺ and Nep3⁺) and their negative counterparts were isolated from adult polyps by fluorescence activated cell sorting (FACS). CUT&Tag (H3K27ac) and RNA-seq were performed in four biological replicates per condition to identify cell type-specific regulatory regions and gene expression programs. The design allows direct comparisons between positive and negative populations for each reporter line.

first: Adrian

last: Jaimes-Becerra

first: Daria

last: Aleshkina

first: Matan

last: Levy

first: Yehu

last: Moran


title: Epigenomic and transcriptomic profiling of cnidocyte subtypes in the sea anemone Nematostella vectensis [RNA-Seq]


title: Productive mRNA Chromatin Escape is Promoted by PRMT5 Methylation of SNRPB - PROSeq Nascent Transcriptome after PRMT inhibition 15m 3hr

first: David

last: Shechter

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 GSK591 (PRMT5i) or MS023 (Type I PRMTi) for 15 min alone or co-treated with Dexamethasone (Dex) for 15 min or GSK591 or MS023 for 3 hours

first: Maxim

last: Maron

first: Joseph

middle: D

last: DeAngelo


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

city: San Francisco

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: CDK7-targeted therapy effectively disrupts cell cycle progression and oncogenic signaling in head and neck squamous cell carcinoma. [PDX]

city: Oviedo

first: Francisco

last: Hermida-Prado

address: Av del Hospital Universitario s/n

department: Head and Neck Lab

country: Spain

institute: Instituto de Investigación Sanitaria del Principado de Asturias

summary: Head and neck squamous cell carcinoma (HNSCC) remains a prevalent and aggressive malignancy, characterized by a lack of targeted therapies and limited clinical benefits. Here, we conducted an optimized whole-genome CRISPR screen across five HNSCC cell lines aimed at identifying actionable genetic vulnerabilities for rapid preclinical evaluation as novel targeted therapies. Given their critical role in cancer, cyclin-dependent kinases (CDKs) were prioritized for further investigation. Among these, CDK7 was identified as an essential and targetable gene across all five cell lines, prompting its selection for in-depth functional and molecular characterization. Genetic and pharmacological inhibition of CDK7 significantly and consistently reduced tumor cell proliferation due to generalized cell cycle arrest and apoptosis induction. Additionally, CDK7 knockout (KO) and selective inhibitors (YKL-5-124 and samuraciclib) demonstrated potent antitumor activity, effectively suppressing tumor growth in HNSCC patient-derived organoids (PDOs), as well as in both cell line- and patient-derived xenograft (PDX) mouse models with minimal toxicity. Mechanistically, CDK7 inhibition led to a broad downregulation of gene sets related to cell cycle progression and DNA repair, and significantly reduced the transcription of essential genes and untargetable vulnerabilities identified by our CRISPR screen. These findings highlight CDK7 as a promising therapeutic target for HNSCC. Our study provides strong evidence of the robust antitumor activity of CDK7-selective inhibition in disease-relevant preclinical models, strongly supporting its progression to clinical testing.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from a patient-derived xenograft (PDX) model subcutaneously implanted into the flank of Athymic Nude-Fox1nu mice and treated with vehicle, Samuraciclib (70 mg/kg, 5 doses/week, orally) and YKL-5-124 (10 mg/kg, 5 doses/week, intraperitoneal) for 5 days.

first: Maria

last: Otero-Rosales

first: Irene

last: Pazos

last: Ferrer

first: Monica

last: Alvarez-Fernandez

first: Juana

last: Garcia-Pedrero


title: CDK7-targeted therapy effectively disrupts cell cycle progression and oncogenic signaling in head and neck cancer

overall_design: Comparative gene expression profiling analysis of RNA-seq data from FaDu cells treated with vehicle, Samuraciclib (250nM) and YKL-5-124 (250nM) for 72h