title: The binding RNAs of Prrc2b in brain tissues of Prrc2b-HA knock-in mice [RIP-Seq]

summary: We performed HA RIP-seq in cerebral cortexes of WT and Prrc2b-HA knockin mice at P4 to further analyze genes that Prrc2b selectively binds.

overall_design: In view of poor antibodies of Prrc2b for immunoprecipitation, we generated C-terminal HA-tag Prrc2b knock-in mice.mRNAs were isolated from cerebral cortex of WT and Prrc2b-HA knock-in mice by HA-RIP and subjected to sequencing.


title: Chemotherapy Modulation by a Cancer-Associated Microbiota Metabolite

status: Public on Sep 15 2025

city: London

first: Daniel

middle: Martinez

last: Martinez

state: London

address: Hammersmith Hospital, Du Cane Road

country: United Kingdom

institute: Medical Research Council

type: Expression profiling by high throughput sequencing

summary: The microbiota plays a major role in cancer. How the microbiota interacts with nutrients to produce regulatory metabolites is of significance for cancer therapy. Using a host-microbe-drug-nutrient 4-way screening approach, we evaluated the role of nutrition at the molecular level in the context of 5-fluorouracil toxicity. Notably, we identified the metabolite 2-methylisocitrate to be produced and enriched in human tumor-associated microbiomes. 2-methylisocitrate exhibits anti-proliferative properties across genetically- and tissue-diverse cancer cell lines, 3D spheroids, and an in vivo Drosophila gut tumor model, where it reduced tumor dissemination and increased survival. Drug-metabolite screening traced the chemotherapeutic signatures indicating synergy between 5-fluorouracil and 2-methylisocitrate, and multi-omic analyses revealed that 2-methylisocitrate acts via multiple cellular pathways linking metabolism and DNA damage to regulate chemotherapy. Finally, building on nature’s template, we altered the chemical structure of 2-methylisocitrate, enhancing its potency. This work highlights the great impact of microbiome-derived metabolites on tumor proliferation, and their potential as promising co-adjuvants for cancer treatment.

overall_design:
Transcriptome from the cancer cell human line HCT116 (ATCC Cat#CCL-247), LoVo (ATCC Cat#CCL-229), DLD-1 (ATCC Cat#CCL-221) and SW948 (ATCC Cat#CCL-237) treated with 10 mM of 2-methylisocitrate and in control conditions
Transcriptome from human lines HT29, SKCO1, and SW1417, treated with 10 mM of 2-methylisocitrate and in control conditions

last: Martinez-Martinez

first: Tanara

middle: V

last: Peres

first: Kristin

last: Gehling

first: Leonor

last: Quintaneiro

first: Cecilia

last: Cabrera

first: Stephen

middle: J

last: Cutty

first: Lena

last: Best

first: Georgios

last: Marinos

first: Johannes

last: Zimmermann

first: Ayesha

last: Safoor

first: Despoina

last: Chrysostomou

first: Masuma

last: Begum

first: Joao

middle: B

last: Mokochinsky

first: Alex

last: Montoya

first: Michalina

last: Zatorska

first: Timothy

last: Scott

first: Ivan

last: Andrew

first: Bian

last: Zhan

first: Holger

last: Kramer

first: Bernard

last: Golding

first: Julian

middle: R

last: Marchesi

first: Susumu

last: Hirabayashi

first: Christoph

last: Kaleta

first: Alexis

last: Barr

first: Christian

last: Frezza

first: Helena

middle: M

last: Cocheme

first: Filipe

last: Cabreiro


title: Transcriptional changes associated with Myrf deletion in mouse ES cells.

city: Toronto

first: Jennifer

last: Mitchell

state: Ontario

address: 25 Harbord Street

department: Cell and Systems Biology

country: Canada

institute: University of Toronto

summary: We investigated gene expression in wild type (WT), Myrf +/- (HET), and null (-/-) ES cells isolated from embryos.

overall_design: Total RNA was collected from ES cells using Trizol (Invitrogen) lysis buffer and subsequent chloroform and isopropanol isolation following manufactures instructions. RNA isolation was followed by DNaseI digestion. RNA was submitted for ribo-depleted total RNA-seq in three replicates each.

first: Lida

last: Langroudi

first: Luis

middle: E

last: Abatti

middle: A


title: Belantamab Mafodotin Triggers Immune Invigoration in Multiple Myeloma Via Inflammatory and Immunogenic Cell Death [scRNA-seq]

status: Public on Sep 14 2025

city: Oxford

first: Edmund

middle: C R

last: Watson

address: Windmill Road

department: NDORMS

institute: University of Oxford

summary: Belantamab mafodotin, an antibody-drug conjugate targeting B-cell maturation antigen, has demonstrated significant clinical efficacy in combination therapies for relapsed or refractory multiple myeloma. Belantamab mafodotin exerts therapeutic effects through the cytotoxic action of its payload, monomethyl auristatin F, along with its ability to mediate antibody-induced cell death. Significant long-term clinical responses were previously observed in monotherapy treatment – even in patients undergoing dose holds – suggesting involvement of the adaptive immune system. Here, we show that belantamab mafodotin induces markers of immunogenic and inflammatory cell death in vitro and ex vivo. Belantamab mafodotin monotherapy treatment results in an acute inflammatory response that is detectable in patient serum within 24 hours, with increases in granzyme B, CXCL9, CCL3, and CCL4 linked to response depth. High expression of receptors LRP1 and TLR2 that mediate immunogenic cell death on patients’ monocytoid (monocyte/macrophage) cells suggests an important function of the monocytoid lineage to mediate the observed inflammation and immunogenic cell death cascades. Inflammation is followed by remodeling of the innate and adaptive immune system, with a reduction in immune inhibitory signaling alongside the emergence of a CD4 granzyme B-expressing cell population in patients who are in remission vs those that relapse. The ability of belantamab mafodotin to promote adaptive immune responses in addition to its cytotoxic activity may help explain the durable responses observed in treated patients with relapsed/refractory multiple myeloma, despite dose and schedule modifications.

overall_design: Viably frozen bone marrow mononuclear cells, taken from patients treated with belantamab mafodotin, were defrosted and underwent long read single cell RNA sequencing via a 10X encapsulation protocol and cDNA library amplification, followed by conversion to an ONT long read library that was then sequenced on a Promethion flow cell. Additionally, freshly isolated bone marrow mononuclear cells from non-malignant control patients underwent the same sequencing approach.

first: Edmund CR

first: Halima

last: Ali Shuwa

first: Morgan

last: Heycock

first: Jenny

last: Wade

first: Chen-Yi

last: Wang

first: Mint

last: Htun

first: Lingzi

last: Li

first: Vivianne

last: Niehaus

first: Warren

last: Baker

first: Benjamin

last: Miller

first: Ruben M

last: Drews

first: Paul R

last: Barber

first: Yinjiao

last: Ma

first: Diana

last: Munera

first: Qingqing

last: Hong

first: Daniel E

last: Lowther

first: Ali Cenk

last: Aksu

first: Lydia

last: Lee

first: H. Christian

last: Eberl

first: Eleanor

last: Calcutt

first: Sarah

last: Gooding

first: Yuqi

last: Shen

first: Abdullah

last: Khan

first: Joanna

last: Hester

first: Fadi

last: Issa

first: Giorgio

last: Napolitani

first: Hanny

last: Musa

first: Karthik

last: Ramasamy

first: Udo

last: Oppermann

first: Sue

last: Griffin


title: The role of PDE7A in Triple negative breast cancer (TNBC) growth and progression

city: Birmimgham

first: Romi

last: Gupta

state: Alabama

address: 720, 20th street south

country: USA

institute: University of Alabama at Birmingham

summary: Triple-negative breast cancer (TNBC) is an aggressive subtype of breast cancer, associated with poor response to therapies and high mortality. We identify that phosphodiesterase 7A (PDE7A) is overexpressed in the majority of TNBC, and a higher level of PDE7A associates with poor prognosis. The PI3K/AKT pathway, via the transcription factor IRF1, stimulates the expression of PDE7A in TNBC cells. PDE7A inhibition attenuates TNBC growth in both cell culture and mouse models of TNBC. Inhibition of PDE7A suppresses de novo pyrimidine biosynthesis, in part through the downregulation of the enzyme dihydroorotate dehydrogenase (DHODH). DHODH suppression attenuates TNBC tumor growth, mirroring the effects of PDE7A inhibition, and ectopic DHODH expression rescues PDE7A-inhibition-induced tumor suppression. Pharmacological co-targeting of PDE7A and DHODH potently inhibits TNBC tumor growth and metastasis. These findings identify the PDE7A→ DHODH→ de novo pyrimidine biosynthesis pathway as a key driver of TNBC, offering additional therapeutic opportunities for TNBC patients.

overall_design: MDA-MB-231 were treated with  PDE7A inhibitor (50 micomolar) BRL-50481 for 72 hours, samples were harvested and were used to prepare the total RNA, followed by RiboRNA depletion with random priming and RNASeq Illumina Hi-Seq 2500 platform, with three biological replicates for each sample.

first: Narendra

last: Wajapeyee

first: Parmanand

last: Malvi

first: Suresh

last: Bugide

first: Roshan

last: Dutta

first: Kiran

middle: K

last: Reddi

first: Yvonne

last: Edwards

first: Kamaljeet

last: Singh


title: Coordinated control of genome-nuclear lamina interactions by Topoisomerase 2B and Lamin B receptor (pA-DamID)

city: Milano

first: Stefano

middle: Giustino

last: Manzo

state: MI

address: Via Celoria 26, Dipartimento Bioscienze, Torre A, Piano 4

department: Biosciences

country: Italy

institute: University of Milan

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Lamina-associated domains (LADs) are megabase-sized genomic regions anchored to the nuclear lamina (NL). Factors controlling the interactions of the genome with the NL have largely remained elusive. Here, we identified DNA topoisomerase 2 beta (TOP2B) as a regulator of these interactions. TOP2B binds predominantly to inter-LAD (iLAD) chromatin and its depletion results in a partial loss of genomic partitioning between LADs and iLADs, suggesting that this enzyme might protect specific iLADs from interacting with the NL. TOP2B depletion affects LAD interactions with lamin B receptor (LBR) more than with lamins. LBR depletion phenocopies the effects of TOP2B depletion, despite the different positioning of the two proteins in the genome. This suggests a complementary mechanism for organising the genome at the NL. Indeed, co-depletion of TOP2B and LBR causes partial LAD/iLAD inversion, reflecting changes typical of oncogene-induced senescence. We propose that a coordinated axis controlled by TOP2B in iLADs and LBR in LADs maintains the partitioning of the genome between the NL and the nuclear interior.

overall_design: pA-DamID experiment were performed on RPE1(SunTag and iCUT), K

middle: G

first: Tom

last: van Schaik

first: Marcel

last: de Haas

first: Jeremie

last: Breda

first: Mikhail

last: Magnitov

first: Elzo

last: de Wit

first: Anna

last: Manjon

first: Rene

middle: H

last: Medema

first: Adam

last: Buckle

first: Catherine

last: Naughton

first: Nick

last: Gilbert

first: Bas

last: van Steensel


title: Belantamab Mafodotin Triggers Immune Invigoration in Multiple Myeloma Via Inflammatory and Immunogenic Cell Death [Xenium]

first: Edmund

last: Watson

overall_design: For this Xenium analysis, a pair of bone marrow trephine slides from one patient (pre-treatment, and remission on-treatment) were analysed alongside a sample from a separate patient (relapse on-treatment). Comparisons were made across all three samples.

middle: C

first: Chen-Yi

last: Wang

first: Warren

last: Baker

first: Joanna

last: Hester

first: Fadi

last: Issa

first: Udo

last: Oppermann


title: Multi-omics profiling elucidates defense-related pathways and metabolites against clubroot in Chinese cabbage

city: Beijing

first: xinyue

last: wang

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

country: China

institute: China Agricultural University

summary: Clubroot disease, caused by Plasmodiophora brassicae Woronin, leads to substantial yield losses in Brassica crops worldwide, including Chinese cabbage. Nevertheless, the molecular mechanisms underlying host defense responses remain poorly understood. In this study, we assessed clubroot resistance by comparing the resistant line ‘CR Jingqiu Xinsanhao’ (JQX3) with the susceptible cultivar ‘Zhongbai 76’ (ZB76) through histological analysis of root tissues and monitoring of disease progression in pot trials. Integrated transcriptomic and metabolomic approaches were employed to characterize the defense mechanisms of JQX3 against P. brassicae infection. Marked metabolic reprogramming was detected during both the primary (3 days after inoculation, DAI) and secondary (10 DAI) infection stages. Four pathways—tyrosine metabolism, phenylpropanoid biosynthesis, valine, leucine and isoleucine biosynthesis, and glucosinolate biosynthesis—were significantly enriched at both time points. Notably, differential expression of key enzymatic genes and accumulation of intermediates in the lignin biosynthesis pathway underscored the importance of lignification in the JQX3–P. brassicae interaction. Furthermore, the intermediates p-coumaric acid and coniferaldehyde markedly inhibited P. brassicae spore germination, demonstrating their direct antifungal activity and potential as natural agents for disease control. These findings elucidate key defense-related pathways in Chinese cabbage and offer valuable insights for the development of sustainable clubroot management strategies.

overall_design: RNA-seq profiling of JQX samples at 0 DAI (CK), 3 DAI and 10 DAI.

first: Xinyue

first: Zengxi

last: Wu

first: Jinqi

last: Zhang

first: Zixian

last: Jia

first: Yu

last: Yang

first: Lingyun

first: Ping


title: Single-cell and spatial transcriptomic atlas of pathological scars uncovers neuro-fibroblast crosstalk mechanisms across scar types

city: 杭州市

first: Yao

last: Jie

state: 浙江

address: 浙江大学紫金港校区农学院A

institute: ZheJiang University

summary: Pathological scars, including hypertrophic scars and keloids, arise from excessive production and deposition of connective tissue such as collagen during wound healing, posing significant clinical challenges. Understanding the cellular and molecular dynamics underlying these scars is critical for developing effective therapies. Here, we integrate single-cell and spatial transcriptomics to characterize the cellular heterogeneity and molecular signatures of key scar-associated cell types, including pericytes, fibroblasts, and endothelial cells. Notably, we identify ECM-activated fibroblasts as a prominent subtype associated with pathological scarring. Cell-cell communication analysis reveals significantly enhanced interactions between fibroblasts and neural cells in pathological scars, especially in hypertrophic scars—a finding that aligns with clinical features such as fibrosis and pruritus. Moreover, we identify subtype-specific ligand-receptor pairs, including LAMB2–ITGA6 in hypertrophic scar and NLGN2–NRXN1 in keloid, mediating these fibroblast–neural communications. To support future research, we developed CellCellMarker 3.0, an updated and curated database integrating experimentally validated and transcriptomics-derived scar marker genes, along with ScarGPT, an intelligent Q&A system optimized using the DeepSeek R1 large language model, integrated with CellCellMarker data and a large corpus of scar-related publications.

overall_design:
To comprehensively characterize the cellular heterogeneity of pathologic scars, we analyzed single-cell RNA-sequencing (scRNA-seq) data comprising two biological replicates for each scar type—keloid, hypertrophic scar. After quality control, we obtained a total of 42,607 single cells, including 17,915 cells from hypertrophic scars, 11,594 cells from keloids, and 13,098 cells from normal scars. This integrated dataset forms the basis for exploring the cellular architecture and molecular pathways underlying distinct pathologic scar phenotypes. Unsupervised clustering identified 23 discrete cell populations. In addition, one spatial transcriptomics sample from hypertrophic scar and one from keloid were included.

***************************************************************
Due to privacy and ethical considerations, raw sequencing data from human scar tissue samples are not publicly available
***************************************************************

first: Jie

last: Yao

first: Ruizhe

last: He

first: Longjiang

last: Fan

first: Yinbo

last: Peng

first: Yan

last: Zheng


title: Widespread DNA off-targeting confounds studies of RNA chromatin occupancy

city: Gent

first: Louis

last: Delhaye

address: Corneel Heymanslaan 10

country: Belgium

institute: Ghent University

summary: The importance of long noncoding RNA (lncRNA) functions is recognized across biological systems, but their modes of action remain poorly understood. One mechanism proposed to be particularly common is gene expression regulation via recruitment to specific genomic regions. Several high-throughput sequencing methods were developed for studying the genome-wide chromatin occupancy of lncRNAs, including ChIRP-seq, CHART-seq, and RAP-seq. These methods utilize biotin-labeled probes targeting the RNA of interest to isolate and recover the chromatin associated with it. Surprisingly, many of the datasets obtained with these methods contain many thousands of binding sites, in apparent contradiction with the low abundance of the interrogated lncRNAs. We studied the chromatin interactome of NESPR lncRNA in cells with varying levels of endogenous expression, and then performed a meta-analysis using dozens of RNA-chromatin interaction datasets in human and mouse cells. We show that thousands of regions reported to bind lncRNAs in the published studies most likely arise from spurious recovery of DNA elements with partial complementarity of the ends of the recovered DNA fragments with the probes used for the pulldown. In addition, studies profiling RNA-chromatin interactions often lack crucial controls and replicates.  Therefore, the vast majority of chromatin regions reported as bound by trans-acting RNAs in recent studies in mammalian cells appear to be technical artifacts. We provide suggestions for bioinformatic workflows for assessing RNA-chromatin dataset quality.

overall_design: ChIRP-seq of the long non-coding RNA NESPR in IMR32, RNase-treated IMR32, and SHEP neuroblastoma cells with a NESPR-targeting probe set, a LacZ-targeting probe set.

first: Pieter

last: Mestdagh


title: Loss of cell-autonomously secreted laminin-α2 drives muscle stem cell dysfunction in LAMA2-related muscular dystrophy

city: Krakow

first: Krzysztof

last: Szade

address: Gronostajowa 7

country: Poland

institute: Jagiellonian University

summary: The extracellular matrix protein laminin-α2 is essential for preserving the integrity of skeletal muscle fibers during contraction. Its importance is reflected by the severe, congenital LAMA2-related muscular dystrophy (LAMA2 MD) caused by loss-of-function mutations in the LAMA2 gene. While laminin-α2 has an established role in structurally supporting muscle fibers, it remains unclear whether it exerts additional functions that contribute to the maintenance of skeletal muscle integrity. Submitted transcriptomic data represents  gene expression profile of control and LAMA2-deficient human myogenic precursor cells derived from induced pluripotent stem cells which was analyzed to better understand the role of laminin-α2 in human cells.

overall_design: Human induced pluripotent stem cells (hiPSCs) from a healthy donor in which exon 3 of the LAMA2 gene was deleted using CRISPR/Cas9 method, together with the isogenic control counterparts, were subjected to myogenic differention using Skeletal Muscle Differentiation Kit (Amsbio). RNA was isolated from four independent differentiations at the stage of myogenic precursors and subjected to next generation RNA-sequencing..

first: Józef

last: Dulak

first: Jacek

last: Stępniewski

first: Timothy

last: McGowan

first: Markus

last: Rüegg


title: OVEREXPRESSION OF TEMPRANILLO-LIKE PROTEINS PROMOTES DORMANCY RELEASE IN POPLAR

city: Madrid

first: Daniela

last: Gomez Soto

address: Parque Científico y Tecnológico, UPM Campus de Montegancedo, Ctra, M-40, km 38

country: Spain

institute: CBGP

summary: We investigated the effect of Populus TEML1 and TEML2 on the dormancy transcriptome through RNAseq experiments. We suggest these two genes play a role during poplar annual cycle, most specifically during dormancy based on their expression analysis. For this reason, we collected apical buds and generated bulk RNAseq libraries of overexpressing plants and their controls. We evaluated pathways which were altered in the transgenic lines and their role during the annual cycle.

overall_design: In vitro-cultivated hybrid poplars of TEML1ox, TEML2ox and WT were transfered to pots containing peat, and grown under LD and 22ºC conditions for 6 weeks. After this time, plants were moved to a short-day chamber for 8 weeks, where they ceased growth and set buds. After the 8 weeks of treatment, we collected the apical buds, grouping 3 buds per replicate, and 2 biological replicates. The remaining plants were subjected to a two-weeks of cold treatment and after this time, apical buds were collected following the short-day experimental design. RNA extraction was performed by adding to grinded frozen buds tissue CTAB extraction buffer with 2% β-mercaptoethanol, following by 3 washes with chloroform. After that, 7.5 M LiCl2:50mM EDTA was added, and samples were precipitated overnight at 4ºC. Next day, RNA was then purified according to the manufacturer’s instructions of NZY RNA purification kit (NZYTech, Lisboa, Portugal). A total of 100 ng of extracted RNA was used to generate the RNA-seq libraries. Libraries were generated from cDNA samples using the TruSeq Stranded mRNA Library Prep Kit (Nat Rev Genet. 2011 Sep 7;12(10):671-82) and they were sequenced on the Illumina platform (MACROGEN, Seúl, South Korea).

last: Gómez-Soto

first: Paolo Maria

last: Triozzi

first: Daniel

last: Conde

first: Cristina

last: del Barrio

first: Isabel

last: Allona

first: Mariano

last: Perales


title: Comprehensive investigation identifies CPSF3 as a novel prognostic and oncogenic biomarker in bladder cancer

city: Shanghai

first: Zhiyang

last: Ma

address: 197 Ruijin Second Road

institute: Ruijin Hospital, Shanghai Jiao Tong University School of Medcine

summary: Background Bladder cancer (BC) remains a prevalent malignancy worldwide, with rising incidence rates each year. Despite progress in therapeutic strategies, many patients suffer recurrence or progression, emphasizing the urgent need for novel prognostic biomarkers and therapeutic targets. This research evaluated the prognostic relevance and functional role of Cleavage and Polyadenylation Specificity Factor 3 (CPSF3) in BC. Methods We analyzed CPSF3 expression using The Cancer Genome Atlas data and immunohistochemistry on a cohort of 203 BC patients. A nomogram incorporating CPSF3 expression was developed based on CPSF3 expression for prediction of overall survival and disease-free survival. Immune infiltration analyses and transcriptome sequencing were performed to explore underlying biological mechanisms. In vitro and in vivo experiments were utilized to examine the results of CPSF3 silencing on bladder cancer cell growth, colony-forming ability and cell cycle transitions. Results Elevated CPSF3 expression was significantly linked to unfavorable overall survival and disease-free survival both in TCGA datasets and our cohort. The CPSF3-based nomogram outperformed conventional prognostic models. CPSF3 expression was associated with tumor-infiltrating immune cells and immune checkpoint markers. Enrichment analysis revealed CPSF3 enrichment in cell cycle-related pathways. Suppression of CPSF3 expression led to marked reductions in cell proliferation, colony formation, tumor growth in animal models and inhibited G1 to S phase progression. Conclusion CPSF3 is a promising prognostic biomarker for BC and may play a crucial role in BC progression.  Incorporating CPSF3 into clinical prognostic models may enhance prediction of patient outcomes. CPSF3 may represent a promising therapeutic target for BC management.

overall_design: human bladder cancer cell line UMUC3, CPSF3-downregulation and negative control, 3 replicates per group


title: An MGRN1-Based Biomarker Combination Accurately Predicts Melanoma Patient Survival

city: Murcia

first: José

last: Sánchez Beltrán

state: Murcia

address: Av. Buenavista, 32, 30120 El Palmar, Murcia

department: Biochemistry and Molecular Biology and Immunology

institute: University of Murcia

summary: With ever-increasing incidence and high metastatic potential, cutaneous melanoma is the deadliest skin cancer. Risk prediction based on the Tumor-Node-Metastasis (TNM) staging system has medium accuracy with intermediate IIB-IIIB stages, as roughly 25% of patients with low-medium-grade TNM, and hence a favorable prognostic, undergo an aggressive disease with short survival and around 15% of deaths arise from metastases of thin, low-risk lesions. Therefore, reliable prognostic biomarkers are required. We used genomic and clinical information of melanoma patients from the TCGA-SKCM cohort and two GEO studies for discovery and validation of potential biomarkers, respectively. Neither mutation nor overexpression of major melanoma driver genes provided significant prognostic information. Conversely, expression of MGRN1 and the melanocyte-specific genes MLANA, PMEL, and TYRP1 provided a simple 4-gene signature identifying with high-sensitivity (>80%), low-medium TNM patients with adverse outcomes. Transcriptomic analysis of tumors with this signature, or from low-medium-grade TNM patients with poor outcomes, revealed comparable dysregulation of an inflammatory response, cell cycle progression, and DNA damage/repair programs. A functional analysis of MGRN1- knockout cells confirmed these molecular features. Therefore, the simple MGRN1-MLANAPMEL- TYRP1 combination of biomarkers complemented TNM staging prognostic accuracy and pointed to the dysregulation of immunological responses and genomic stability as determinants of a melanoma outcome.

overall_design: RNAseq profiling of MGRN1-KO (CRISPR-Cas9) and CTR HBL human melanoma cells cultured in DMEM-GlutaMAX enriched with 10% fetal bovine serum (FBS), 100 U/mL penicillin, and 100 μg/mL streptomycin sulfate

last: Sánchez-Beltrán

first: Javier

last: Soler-Díaz

first: Cecilia

last: Herraiz

first: Conchi

last: Olivares

first: Sonia

last: Cerdido

first: Pablo

last: Cerezuela-Fuentes

first: Jose Carlos

last: García-Borrón

first: Celia

last: Jiménez-Cervantes


title: Stress Promotes Lung Metastasis in Breast Cancer by Altering Neutrophil Differentiation

first: Pengfei

last: Liu

address: 150 Jimo Road

institute: Shanghai East Hospital, Tongji University School of Medicine

summary: Mental stress is widely recognized as a significant risk factor for breast cancer, exerting detrimental effects on both progression and prognosis. Herein, we investigated the role of stress in regulating breast cancer metastasis. In genetically engineered and transplantation breast cancer mouse models, chronic stress stimulation increased tumor growth and lung metastasis. Single-cell RNA-sequencing analysis of the pre-metastatic lung microenvironment revealed induction of a previously unrecognized subtype of cancer stress-primed (CSP) neutrophils, characterized by the overexpression of Ccl3, Ccl4, Cxcl2, Il1r2, and Cebpb. Pseudotime trajectory analysis demonstrated that chronic stress caused a shift of neutrophils from the cancer-primed (CP) neutrophil subtype to the CSP subtype in the lung. Activation of the glucocorticoid receptor NR3C1 by the stress hormone corticosterone induced expression of Cebpb in neutrophils, which then promoted transcription of Ccl3 and Ccl4. The differentiation of neutrophils into the CSP subtype promoted lung metastasis of CCR1+ breast cancer cells via CCL3/CCL4-mediated recruitment. Targeting this axis using an anti-Ly6G antibody to deplete neutrophils, a CRISPR/Cas9-mediated approach to conditionally knockout Ccl3/Ccl4 in neutrophils, and BX471 treatment to inhibit CCR1 in cancer cells all significantly reduced breast cancer lung metastasis. Together, this study not only demonstrates a stress-neutrophil-cancer axis that promotes lung metastasis in breast cancer but also provides potential strategies for reducing lung metastasis by targeting CSP neutrophils or CCR1+ breast cancer cells.

overall_design: This study includes 4 single-cell RNA sequencing samples, all derived from lung tissues of 10-week-old female MMTV-PyMT mice. The samples were divided into two groups: Experimental group (CS, n=2): Lung tissues from MMTV-PyMT mice subjected to four weeks of Chronic Mild Unpredictable Stress (CMUS)treatment； Control group (NC, n=2): Lung tissues from untreated MMTV-PyMT mice.

first: Jie

last: Zheng

first: Wenjing

first: Jinhui

last: Lü

first: Qian

last: Zhao

first: Danni

last: Li

first: Xiaoyan

last: Jiang

first: Haikun

last: Wang

first: Haiyun

first: Zuoren

last: Yu


title: SUPER to Probe the Site-Specific DNA-Binding Protein Complex [bulkRNA-seq]

city: New York

first: Shuibing

last: Chen

state: NY

address: A 827B, 1300 York Ave

department: Surgery

institute: Weill Cornell Medical College

summary: Site-specific DNA binding by proteins is critical for regulating genetic activity and cell fate decision. However, identifying proteins bound to specific genomic regions (e.g., promoter or enhancer) remains challenging. To address this, we developed the Site-specific non-canonical amino acid resolved Protein EnRichment (SUPER) system, incorporating a photo-crosslinking amino acid into nuclease-deficient dCas9 mutant. Human pluripotent stem cells (hPSCs) carrying SUPER enables the capture of proteins bound to, in theory, any genomic location, facilitating the study of the cell context-dependent DNA-protein interactions. Using SUPER, we identified OCT4/SOX2/CARHSP1 complex binding to the NANOG promoter to maintain pluripotency in hPSCs. During ectoderm differentiation, ZIC2 acts as a competitive inhibitor, binding the same promoter to downregulate NANOG expression and promote differentiation. Additionally, SUPER identified ZNF8 binding to the distal regulatory region of OCT4 and maintain naïve pluripotency. In summary, SUPER provides a robust system for uncovering the cell context-dependent, site-specific genome regulators, offering valuable insights into gene regulation networks driving cell fate transitions.

overall_design: RNA-seq profiling of CARHSP1 knock down hPSCs and nontargeting control hPSCs, ZNF8 knock down naïve hPSCs and nontargeting control naïve hPSCs, ZIC2 knock down differentiating ectoderm cells at day2 and nontargeting control.

first: Jiajun

last: Zhu


title: Comparison of Different Approaches to Single Cell RNA Sequencing of Cancer Associated Fibroblasts

city: Baltimore

first: Heng Chung

last: Kung

state: Maryland

address: 1650 Orleans Street

department: Department of Oncology

institute: Johns Hopkins University School of Medicine

summary: Cancer associated fibroblasts (CAFs) represent a major stromal component of PDAC with both tumor-promoting and restraining properties. Studies have demonstrated functional heterogeneity among different subpopulations of CAFs, highlighting the need to identify specific subpopulations when targeting CAFs. We hereby used two types of processing method, whole tumor or negatively-isolated CAFs, to determine how best to uncover CAF heterogeneity with single-cell RNA sequencing (scRNA-seq).

overall_design: Murine orthotopic pancreatic tumors were dissected and collected on day 13 after tumor implantation for scRNA-seq processing. Tumors were mechanically and enzymatically processed with the mouse Miltenyi Tumor Dissociation Kit (Miltenyi Biotec) and gentleMACS Octo Dissociator (Miltenyi Biotec). Samples were then filtered through 100 µm strainer, which was then washed with 10 mL T cell media. Cell suspensions were centrifuged at 1500 RPM for 5 minutes. Cell pellets were resuspended in 10 mL T cell media, filtered through 100 µm strainer, and centrifuged again at 1500 RPM for 5 minutes.  For fibroblast enrichment, cells were resuspended with PBS and blocked with anti-mouse Fc antibody (BD Biosciences) in FACS buffer for 10 minutes on ice. Cells were then stained with CD45-AF657 (BioLegend clone 30-F11, 1:20), CD31-AF647 (BioLegend clone 390, 1:20), EPCAM-AF647 (BioLegend, clone G8.8, 1:20), and TER119-AF647 (BioLegend clone TER-119 1:20) for 30 minutes on ice. Single cell suspension was mixed every 10 minutes. Cells were washed with PBS twice, resuspended at 5-10 million cells/mL in T cell media, and filtered through 35 µm flow cytometry tubes (Falcon 352235). Sorting for CD45-, CD31-, EPCAM-, and TER119-negative cells was performed to obtain the fibroblast enriched fraction. Both the unenriched and enriched samples were washed and resuspended to cell concentration of 700-1200 cells/µL in PBS + 0.1% BSA for loading onto 10X Chromium microfluidic chips

first: Zheng

last: Lei

first: Loycano

last: Michael

first: Chen

last: Sophia

first: Kung

last: Heng-Chung


title: RXRα Modulates Hepatic Stellate Cell Activation and Liver Fibrosis by Targeting CaMKKβ-AMPKα Axis

city: Xiamen

first: Lijun

last: Cai

address: No. 668, Jinhu Road

department: Central Laboratory,

institute: Zhongshan Hospital (Xiamen), Fudan University

summary: Hepatic stellate cells (HSCs) represent a dominant fibrogenic cell population in the liver, whose activation is a key event in the development and progression of hepatic fibrosis. We report here that retinoid X receptor-alpha (RXRα), a unique member of the nuclear receptor superfamily, is a critical modulator of HSC activation and liver fibrosis through its regulation of calcium/calmodulin-dependent protein kinase kinase β (CaMKKβ)-mediated activation of AMP-activated protein kinase-alpha (AMPKα). K-80003, which binds RXRα by a unique mechanism, effectively inhibits the activation, proliferation and migration of HSCs and inhibits liver fibrosis in the CCl4 and AMLN animal models by AMPKα activation, which promotes mitophagy in HSCs. Mechanistically, K-80003 activation of AMPKα requires its induction of RXRα formation of condensates with CaMKKβ and AMPKα via a two-phase mechanism. The formation of RXRα condensates is mediated by the N-terminal intrinsically disorder region of RXRα and is dependent on its phosphorylation by CaMKKβ. Our results therefore unravel an important RXRα-CaMKKβ-AMPKα axis in the modulation of HSC activation through phase separation and identify K-80003 as a potent inhibitor of HSC activation and liver fibrosis by targeting the axis.

overall_design: Primary mouse hepatic stellate cells (mHSCs) isolated from mice were treated with TGF-β and K-80003 and divided into three groups: Control, TGF-beta, and TGF-beta-K-80003, with 2 replicates in each group.


title: CAR-SPLASH identifies nascent pre-mRNA structures implicated in kinetic coupling and alternative splicing [RNA-Seq]

city: Aurora

first: David

last: Bentley

state: Colorado

department: BMG

institute: UCD AMC

summary: Transcription and co-transcriptional pre-mRNA splicing are kinetically coupled as shown by the widespread effects of transcription speed on alternative splicing. The molecular basis for kinetic coupling is incompletely understood, but one potential mechanism is through elongation rate dependent alternative folding pathways of the nascent pre-mRNA. To search for RNA structures in nascent pre-mRNA, we modified SPLASH (1) (Sequencing of Psoralen Crosslinked, Ligated And Selected Hybrids) for use with Chromatin Associated RNA. We applied this new method called CAR-SPLASH to cells expressing WT and slow mutant pol II and identified >3000 intragenic RNA structures of which  >400 are proximal to splice sites. ASO disruption of several structures identified by CAR-SPLASH that sequester splice sites changed alternative splicing outcomes in vivo. We identified three examples of novel regulatory elements we designate “RNA kinetic switches”. ASO disruption of these structures modified alternative splicing of NISCH Exon 18 GAK Exon 7 and MEGF8 Exon 24 in a way that depended on the rate of transcription elongation. These results demonstrate that individual RNA structures can mediate kinetic coupling between transcription and pre-mRNA splicing and that nascent RNA structures can serve as targets for splice modifying ASO’s.

overall_design: pre-mRNA alternative splicing was analyzed by  in isogenic human HEK293 cell lines that inducibly express a-amanitin resistant  WT RNA polymerase II large subunit Rpb1 or the slow elongation mutant  (R749H).

first: Hossein

last: Shenasa

first: Benjamin

last: Erickson


title: Gene expression profile at single cell level of cells from cholangiocarcinoma(CCA) and adjacent tissues.

city: JiNan

first: Anda

last: Shi

address: Culture West Road num 107

institute: Qilu Hospital

summary: Multiple tumor-associated cells in the complex CCA microenvironment.We used single cell RNA sequencing (scRNA-seq) to analyze the gene expression diversity of cells in the CCA and adjacent tissues.

overall_design: After dissociating tumor and adjacent tissues, lysing red blood cells and removing dead cells, candidate cells were scaptured to analyze used scRNA-seq.

first: Zongli

last: Zhang

first: Yunfei

last: Xu


title: 84-B10 alleviates cisplatin-induced acute kidney injury in mice

city: Nanjing

first: Fan

middle: Jiao

last: Jiao

address: 72 Guangzhou Road

institute: Children’s Hospital of Nanjing Medical University

summary: Mice were pre-treated with different doses of 84-B10 for 48h before cisplatin (25mg/kg, intraperitoneal) challenge in both cisplatin and cisplatin +84-B10 group, then treatment groups were received 84-B10 daily. After 72h cisplatin challenge, mice of all groups were sacrificed and RNA-Seq were performed.

overall_design: Cisplatin was induced as described in the previous section (n = 4 in each group). The mice were pretreated with 84-B10 for   48 h in cisplatin + 84-B10 group at a dose of 15 mg/kg before cisplatin treatment.Cisplatin was challenged to the mice by aintraperitoneal (i.p.) injection (25 mg/kg) in both cisplatin and cisplatin + 84-B10 group. The vehicel mice received an i.p. injection of saline. Kidney tissues were harvested and perform RNA-Seq.

first: Jiaojiao

last: Fan

first: Xinyue

first: Mengqiu

last: Wu


title: Pre-Treatment peripheral Immune composition can accurately predict CAR-T outcomes in patients with Large B-Cell Lymphoma

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

summary: Chimeric Antigen Receptor (CAR)-T cell therapy has revolutionized the treatment landscape for relapsed/refractory B-cell malignancies. Despite its success, approximately 60% of patients experience treatment failure, underscoring the need to better understand the determinants of response and resistance. We performed single-cell RNA-sequencing of pre-treatment peripheral blood samples and anti-CD19 CAR-T products from 57 diffuse large B-cell lymphomas (DLBCL), correlating molecular and cellular features with clinical outcomes. At the time of leukapheresis, responders presented elevated levels of CD16+ monocytes and CD4+ effector memory T cells. In contrast, non-responders showed an inflammation-driven gene expression signature across T-cell and myeloid compartments, marked by upregulation of TNF-α response signaling pathways. Notably, the presence of malignant or healthy B cells (13 of 57 patients) was strongly associated with a favorable response. These findings shed light on the immune landscape conducive to successful CAR-T therapy and offer a molecular framework for developing personalized tools to improve patient selection, stratification, and the design of next-generation CAR-T treatments.

overall_design:
We performed single-cell RNA sequencing of pre-treatment peripheral blood samples from 43 Diffuse Large B-Cell patients, receiving anti CD-19 CAR-T products: axicabtagene ciloleucel (axi-cel) or tisagenlecleucel (tisa-cel) and correlated their molecular and cellular features with treatment outcome at three months post-infusion.
Please note that the Bulk_* samples were only used as a reference genome to demultiplex the cells from the 10x sequencing.

first: Gurevich-Shapiro

last: Anna

first: Zwicky

last: Pascale

first: Winter

last: Eithan

first: Zada

last: Mor

first: Shapira

last: Noam

first: Barboy

last: Oren

first: Chalan

last: Paulina

first: Sharet-Eshed

last: Reut

first: Kedmi

last: Merav

first: Florian

last: Ingelfinger

first: Truong-San

last: Phan

last: Eyal

first: R

last: Shouval

first: D

last: Luan

last: Sandeep

first: M

last: Shapiro

first: O

last: Itzhaki

first: Accav N

last: Golan

first: A

last: Avigdor

first: Avivi

last: Irit

first: Weiner

last: Assaf

first: Ram

last: Ron

first: Amit

last: Ido


title: Multi-omics reveals cholesterol-driven macrophage metabolic reprogramming and inflammation in chronic obstructive pulmonary disease

status: Public on Sep 13 2025

city: Guangzhou

first: Zhandong

last: Yang

address: No. 9, Xingdao Ring North Road, International Biomedical Island

institute: Guangzhou National Laboratory

summary: Cholesterol accumulation contributes to COPD pathogenesis by inducing metabolic reprogramming and proinflammatory signaling pathway in macrophages, which provides novel insights into the prevention and treatment of this disease clinically.

overall_design: Multi-omics including metabolomics, RNA_Suq and scRNA_Suq were integrated for disclosing the underlying mechanisms of COPD.

first: Xinru

last: Ran

first: Li

last: Cheng

first: Weidong

last: Li

first: Feng

last: Guo

first: Pixin


title: Eukaryotic translation elongation factor EEF1G orchestrates the translational program to ensure meiotic progression in transcriptionally silent spermatocytes [Ribo-Seq]

city: Jinan

first: Jianze

last: Xu

state: Shandong

address: Jinan

institute: Shangdong university

summary: During meiotic prophase I, mammalian spermatocytes face a critical challenge that they need to synthesize recombination and synapsis proteins while global transcriptional suppression occurs at leptotene/zygotene stages. Here, we identify a spermatogenic cell highly expressed protein, eukaryotic translation elongation factor 1 gamma (EEF1G), as a master regulator of translational adaptation in mouse spermatocytes. Germ cell-specific Eef1g knockout causes complete male infertility due to the meiotic arrest at the zygotene stage, which is characterized by unresolved DNA double-strand breaks, failed homologous chromosome synapsis, and abolished crossover formation. Mechanistically, EEF1G can interact with ribosome proteins and RNA-binding factors. Ribosome profiling reveals that EEF1G deficiency reduces ribosome processivity, leading to ribosomal stalling and decreased protein production. Consequently, proteomic analyses show a specific decrease of synapsis (e.g., SYCP1/SYCE1) and recombination (e.g., MSH4/TEX11) proteins. This study establishes EEF1G as a critical coordinator of spatial translation in transcriptionally silent spermatocytes, bridging limited mRNA engagement to explosive protein synthesis for meiotic progression. Our work challenges traditional views of meiotic control by highlighting translation elongation, not just as a housekeeping process, but as a stage-specific regulator of germ cell development.

overall_design: Ribosome profiling (Ribo-seq) was carried out to investigate the translational regulation associated with EEF1G in early meiotic spermatocytes. Testes were collected from postnatal day 12 (PD12) mice, a developmental stage enriched for leptotene and zygotene spermatocytes. To obtain highly purified populations, spermatocytes at the leptotene (L) and zygotene (Z) stages were isolated by fluorescence-activated cell sorting (FACS). Both wild-type (WT) and Eef1g conditional knockout (cKO) groups were included in the design, and each group contained two independent biological replicates to ensure reproducibility and statistical robustness. Ribosome-protected fragments (RPFs) were prepared using the QEZ-seq kit (Hangzhou NeoRibo Biotechnology Co., Ltd., Cat. R1024L) following the manufacturer's instructions, and the resulting libraries were sequenced on an Illumina platform. This design allowed a direct comparison of translational profiles between WT and Eef1g cKO spermatocytes at the L and Z stages, thereby providing insights into the functional role of EEF1G during meiotic progression in male germ cells.


title: Cancer therapy induced effects on lung organoids as suitable in vitro model [scRNA]

city: Essen

first: Bettina

last: Budeus

address: Virchowstrasse 173

department: Institute for Cell Biology

country: Germany

institute: University Hospital Essen

summary: Generation of lung organoids as model for genotoxic stress

overall_design: iPSC-derived lung organoids were either treated with radiation or not prior RNAseq analysis

first: Chiara

last: Kroepel

first: Lisa-Marie

last: Stasch

first: Diana

last: Klein


title: SUPER to Probe the Site-Specific DNA-Binding Protein Complex [scRNA-seq]

first: Shuibing

last: Chen

overall_design: We first incorporated a random 22 nucleotide barcodes (GBC) into the backbone plasmid pPS. The pooled sgRNA mixture was PCR amplified and ligated into this plasmid. The sgRNA-GBC correlation reference table was generated by sequencing. Next, we cloned an EGFP coding sequence along with the EF1α promoter and inserted it between the sgRNA and GBC elements. The final construct was packaged into lentivirus in 293T cells. A separated plasmid containing the CRIPSR/Cas9 coding gene and co-expressed mCherry was packaged into lentivirus. The hPSC cells were infected with lentivirus and sorted based on fluorescence protein expression. The sorted cells were recovered for one week, followed by induced differentiation towards ectoderm lineage. Ectoderm cells were collected and prepared for single cell RNA-seq .

first: Jiajun

last: Zhu


title: Role of the transcription factors Tac1a and Tac1b in azole resistance in Candida auris

city: Montreal

first: Adnane

last: Sellam

address: 5000, rue Bélanger

institute: Universite de Montreal

summary: Candida auris (Candidozyma auris) is a yeast pathogen that poses a public health threat because of its ability to develop antifungal resistance. Notably, most C. auris isolates are resistant to fluconazole. The efflux pump Cdr1 is a key contributor of azole resistance in C. auris. In C. albicans, Cdr1 is regulated by the transcription factor Tac1, which has two orthologs in C. auris (Tac1a and Tac1b). While the role of Tac1b has been described, little is known about Tac1a. In this study, we characterized the respective roles of Tac1a and Tac1b in azole resistance. To investigate their transcriptional regulation and binding targets, we performed RNA sequencing and ChEC-seq (Chromatin endogenous cleavage sequencing) for both transcription factors. RNA sequencing was carried out by comparing hyperactivated mutants (TAC1a-HA or TAC1b-HA) with the wild-type strain IV.1. ChEC-seq was performed in strains carrying endogenous C-terminal MNase fusions (TAC1a-MNase and TAC1b-MNase) and in a control strain expressing ectopically MNase  (Free MNase). Both Tac1a and Tac1b mediate azole resistance in C. auris via regulation of Cdr1, with overlapping downstream targets and evidence of autoregulation.

overall_design: We used ChEC-seq (Chromatin endogenous cleavage sequencing) analysis to map the genomic occupancy of two zinc-finger transcription factor transcriptions, Tac1a and Tac1b, in the opportunistic yeast Candida auris. DNA- binding was determined by comparing DNA sequence counts in strains where Tac1a and Tac1b were MNase-tagged (Tac1a-Mnase and Tac1b-MNase) at their C-terminal regions to that of a control strain ectopically expressing MNase.

first: Jizhou

last: LI

first: Camille

last: MARCHETTI

first: Danielle

last: BRANDALISE

first: Antony

last: VINCENT

first: Charles

last: GIBERT

first: Faiza

last: TEBBJI

first: Alix

last: COSTE

first: Dominique

last: SANGLARD

last: SELLAM

first: Frederic

last: LAMOTH


title: miRNAs profile of Fusobacterium nucleatum infected SW480 cells [cells]

first: Xin

last: Zhang

address: 107 Wenhua Xi Road

institute: Qilu Hospital, Shandong University

type: Non-coding RNA profiling by high throughput sequencing

summary: MicroRNAs play important roles in the tumorigenesis and metastasis of colorectal cancer (CRC). Recently, some studies have reported Fusobacterium nucleatum could influence microRNAs expression. This study aims to use a microRNA sequencing to analyze the microRNA expression profiles in Fusobacterium nucleatum-infected CRC cells.

overall_design: Detection of microRNA expression profile in SW480 cells treated with or without Fusobacterium nucleatum.

first: Mengjiao


title: Exosomal miRNAs profile in serum of colorectal cancer patients with Fusobacterium nucleatum infection [serum]

summary: MicroRNAs play important roles in the tumorigenesis and metastasis of colorectal cancer (CRC). Recently, some studies have reported Fusobacterium nucleatum (Fn) could influence microRNAs expression. This study aims to use a microRNA sequencing to analyze the microRNA expression profiles in serum exosomes of CRC patients with Fn infection.

overall_design: Serum samples were collected from 12 CRC patients, including 6 cases with high Fn abundance and 6 cases with low Fn abundance. Exosomes were isolated from serum using ultracentrifugation, and then analyzed the microRNAs profile using miRNA-sequencing.


title: miRNAs profile of exosomes derived from Fusobacterium nucleatum infected SW480 cells [exosomes]

summary: MicroRNAs play important roles in the tumorigenesis and metastasis of colorectal cancer (CRC). Recently, some studies have reported Fusobacterium nucleatum could influence microRNAs expression. This study aims to use a microRNA sequencing to analyze the microRNA expression profiles in Fn-infected CRC cells-derived exosomes.

overall_design: Detection of microRNA expression profile in exosomes isolated from SW480 cells treated with or without Fusobacterium nucleatum.


title: miRNAs profiles of Fusobacterium nucleatum infected SW480 cells, exosomes derived from Fusobacterium nucleatum infected SW480 cells, and exosomes from serum of colorectal cancer patients with Fusobacterium nucleatum infection

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

overall_design: Refer to individual Series


title: Assessing developmental neurotoxicity of emerging environmental chemicals using multiple in vitro models: A comparative analysis.

city: 北京市

first: Renjun

last: Yang

state: 北京

address: 双清路18号林业大学北门

institute: RCEES

summary: Newly synthesized chemicals are being introduced into the environment without undergoing proper toxicological evaluation, particularly in terms of their effects on the vulnerable neurodevelopment. Thus, it is important to carefully assess the developmental neurotoxicity of these novel environmental contaminants using methods that are closely relevant to human physiology. This study comparatively evaluated the potential developmental neurotoxicity of 19 prevalent environmental chemicals including neonicotinoids (NEOs), organophosphate esters (OPEs), and synthetic phenolic antioxidants (SPAs) at environment-relevant doses (100 nM and 1 μM), using three commonly employed in vitro neurotoxicity models: human neural stem cells (NSCs), as well as the SK-N-SH and PC12 cell lines. Our results showed that NSCs were more sensitive than SK-N-SH and PC12 cell lines. Among all the chemicals tested, the two NEOs imidaclothiz (IMZ) and cycloxaprid (CYC), as well as the OPE tris(1,3dichloro-2-propyl) phosphate (TDCIPP), generated the most noticeable perturbation by impairing NSC maintenance and neuronal differentiation, as well as promoting the epithelial-mesenchymal transition process, likely via activating NF-κB signaling. Our data indicate that novel NEOs and OPEs, particularly IMZ, CYC, and TDCIPP, may not be safe alternatives as they can affect NSC maintenance and differentiation, potentially leading to neural tube defects and neuronal differentiation dysplasia in fetuses.

sample_organism:
Homo sapiens
Rattus norvegicus

platform_organism:
Homo sapiens
Rattus norvegicus

overall_design: Samples includes rat pheochromocytoma cell line PC12, human neuroblastoma cell line SK-N-SH, and neural stem cells induced from human embryonic stem cells (H9) treated with neonicotinoids, organophophate esters, and antioxidants. All samples were in two replicates and 0.1% DMSO was used as vehicle control.

first: Shichang

last: Li

first: Nuoya

last: Yin

first: Francesco

last: Faiola

first: Miaomiao

last: Zhao

first: Shuxian


title: Monolayer cells transcriptome of human embryonic stem cell differentiation

address: 双清路18号林业大学北门

summary: We examined the toxic effects of environmental pollutants on embryonic stem cell induced monolayer differentiation by RNA sequencing. RNA extraction was performed on monolayer cells exposed to multiple compounds during monolayer differentiation. The toxic effect of the compound on early embryonic development was obtained by analyzing the difference in RNA expression. Our study provides data closer to the toxic effects of human exposure to neonicotinoids, organophosphate esters and synthetic phenolic antioxidants.

overall_design: The differences of RNA expression in monolayer cells after exposure to different compounds were examined.


title: Autologous multiantigen-targeted T cell therapy for pancreatic ductal adenocarcinoma: results of a Phase I, three-arm, nonrandomized clinical trial (TACTOPS)

status: Public on Sep 12 2025

city: Houston

first: Shamika

last: Ketkar

state: Texas

address: One Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of edicine

summary: T-cell therapy has thus far proven ineffective for treating pancreatic ductal adenocarcinoma (PDAC), in part due to heterogeneous expression of tumor-associated antigens (TAAs). In a Phase I/II trial, autologous ex vivo expanded T-cells targeting five TAAs - PRAME, SSX2, MAGEA4, Survivin, and NY-ESO-1 - were prepared and administered (1x107 cells/m2/infusion) monthly to subjects with advanced PDAC responding (Arm A, n=13) or refractory to (Arm B, n=12) first-line chemotherapy, or to those with potentially resectable disease (Arm C, n=12). Primary endpoints were safety and feasibility of delivering 6 infusions; additional endpoints were clinical and immunologic response. Of 56 subjects procured, 37 were infused (median 3 doses), with only one treatment-related serious adverse event reported. Disease control rates in Arms A and B were 84.6% (95% CI: 54.6%-98.1%) and 25% (95% CI: 5.5%-57.2%), respectively; in Arm C, 2/9 resected subjects remain disease-free at 55 and 66 months. The infused cells persisted for up to 12 months post-infusion, and elevated levels of effector, tumor-directed T cells were detected both during dosing (p=0.027) and follow-up in “responders” (objective response in Arms A/B, no relapse in Arm C) compared to “non-responders” (progression in Arms A/B, relapse in Arm C).

overall_design:
Transcriptomic characteristics were explored in a subset of antigen-stimulated (vs unstimulated) mTAA T cell products (n=7) by single cell RNA sequencing (scRNAseq).
Please note that processed data files generated from both V(D)J and 5′ expression libraries are linked to the corresponding GEX sample records

first: Ann

last: Leen


title: Strain variation identifies a neural substrate for behavioral evolution in Drosophila

first: Anna

last: Ryba

state: New York

address: 1230 York Avenue

institute: Rockefeller University

summary: Sexual selection acts on heritable differences within species, driving the parallel diversification of signal production in one sex and behavioral responses in the other. This coevolution implies that sensory preferences are themselves variable traits, yet the neural basis of such variation remains unclear. Here, we identify striking strain-specific differences in Drosophila melanogaster male mate preferences that arise from differential sensitivity to heterospecific female pheromones. We map this variation to an ascending inhibitory pathway targeting a central circuit node known to dynamically pattern courtship. Inhibitory circuits thus emerge as a key locus for shaping mate discrimination via transient suppression of a male’s pursuit. Our findings highlight how variation within sensory circuitry serves as a substrate for selection, fueling the evolution of reproductive barriers between species.

overall_design: RNA-seq profiling of male foreleg tissue from selective (CO13N, CS-CO13N hybrid) and promiscuous (CS, RG11N) strains of D. melanogaster.

first: Philipp

last: Brand

first: Rory

middle: T

last: Coleman

first: Yarden

last: Greenfeld

first: Yael

middle: N

last: Tsitohay

first: Florian

last: Hollunder

first: Katharine

last: Keller

first: Murtaza

last: Hathiyari

first: Tianyi

last: Wei

first: Paolo Emilio

last: Barbano

first: Vanessa

last: Ruta


title: Plasma-derived exosomal miRNA profiling in dengue patients with and without warning signs

city: Kubang Kerian, Kota Bharu

first: Gokulakannan

last: Venkatesan

state: Kelantan

address: Kampus Kesihatan Universiti Sains Malaysia, Jalan Raja Perempuan Zainab 2, Kubang Kerian, 16150 Kota Bharu, Kelantan

department: School of Dental Sciences

country: Malaysia

institute: Universiti Sains Malaysia

summary: Dengue virus infection is recognized as one of the most important mosquitos borne human diseases of the 21st century. It can manifest clinically as a moderate febrile illness, or a severe life-threatening disease called dengue haemorrhagic fever. Notably, there are currently no predictive diagnostic values for individuals prone to bleeding manifestations associated with this infection. This study explores the potential solution by focusing on exosomes, lipid vesicles enriched in specific microRNA. These exosomal microRNAs have the potential to form a disease-specific diagnostic signature, paving the way for an analysis of exosomal plasma microRNA expression to predict bleeding tendency in dengue infection. In total, 6 blood plasma exosome samples, dengue without warning sign (n = 3) and dengue with warning sign (n = 3) were used to isolate total RNA. Small RNA analysis and microarray-based expression profiling was used to detect the miRNA profile of plasma exosomes to identify predictive biomarker for bleeding manifestations in patients with warning sign as compared to patients without warning signs. Microarray profiling revealed that 24 miRNAs were upregulated in the plasma derived exosome miRNA in the dengue patients with warning signs. Functional analysis of target genes of these miRNAs in silico indicated their involvement in bleeding manifestation in dengue infection.

overall_design: miRNA expression profiling of plasma exosomes from dengue patients with warning signs (n=3) and without warning signs (n=3) using Agilent Human miRNA microarray one-color platform.

first: Wan

last: Rahman

last: Shahidan

first: Gnanasoundari

last: Gokulakannan

first: Nik

last: Kamal


title: Single cell RNA sequencing of lateral and medial olivocochlear efferent neurons using PatchSeq

city: Bethesda

first: Robert

last: Morell

state: MD

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

institute: National Institute on Deafness and Other Communication Disorders

summary: Olivocochlear (OC) efferent neurons are the final component of the descending auditory system. The lateral olivocochlear (LOC) neurons innervate type I spiral ganglion neurons (SGN). Their role in hearing is unknown, but they may have roles in protection from noise trauma or changing the threshold of SGN activation. The medial olivocochlear (MOC) efferent neurons innervate outer hair cells (OHC), inhibiting OHC function and thus dampening cochlear vibrations. LOC and MOC function is poorly understood at the single cell level, but recent use of transgenic mice (ChAT-IRES-Cre; tdTomato) expressing fluorescent reporters in cholinergic neurons, including LOC and MOC neurons, has allowed patch-clamp recordings from the neurons in mouse brainstem slices to begin to characterize their intrinsic electrical properties and synaptic activity. Recent single nucleus sequencing experiments from LOC and MOC neurons has given insight into the genetic programs that generate their function, including changes to expression profiles following noise trauma. Here we utilize the PatchSeq technique to combine patch-clamp electrophysiological recordings with deep single-cell transcriptome analysis from identified LOC and MOC neurons in transgenic ChAT-IRES-Cre; tdTomato mice. In this preliminary dataset, we generated patch-clamp electrophysiology data and single cell transcriptome data from 18 identified LOC and 13 identified MOC neurons.

overall_design: Patch-clamp recordings were performed from red fluorescent neurons in the lateral superior olive for lateral olivocochlear (LOC) neurons or ventral nucleus of the trapezoid body for medial olivocochlear (MOC) neurons in brainstem slices from ChAT-IRES-Cre; tdTomato transgenic mice. Following recordings, cellular contents were aspirated, cDNA libraries were generated according to the SmartSEQ2 protocol, and individual cell libraries were prepared using Nextera DNA Library Preparation kits (Illumina) and sequenced on an Illumina MiSeq in 75 bp paired end configuration.

first: Michelle

last: Frank

first: Sian

last: Kitcher

first: Matthew

last: Fischl

first: Lester

last: Torres Cadenas

first: Lisa

last: Goodrich

first: Catherine

last: Weisz


title: RNA-seq analysis of SMARCA4-deficient NCI-H838 xenograft tumors treated with PRT3789, docetaxel, nab-paclitaxel, or combination regimens

city: Wilmington

first: Michael

last: Hulse

state: DE

address: 175 Innovation Blvd

institute: Prelude Therapeutics

summary: The goal of this study was to examine transcriptional responses to the SMARCA2-selective degrader PRT3789, standard chemotherapies, and their combinations in SMARCA4-deficient NCI-H838 xenograft tumors. Six treatment groups were evaluated: (1) vehicle control, (2) PRT3789, (3) docetaxel, (4) nab-paclitaxel, (5) PRT3789 plus docetaxel, and (6) PRT3789 plus nab-paclitaxel. RNA-seq was performed on tumors collected 120 hours post–first dose to investigate treatment-specific gene expression signatures.

overall_design:
Female NOD/SCID mice bearing NCI-H838 xenografts were randomized into six groups (n=3 per group) and treated as follows:
Group 1: Vehicle for PRT3789 (s.c., Day 0 and Day 3) plus saline (i.v., Day 0)
Group 2: PRT3789, 100 mg/kg (10 mg/mL, 10 mL/kg, s.c., Day 0 and Day 3)
Group 3: Docetaxel, 25 mg/kg (2.5 mg/mL, 10 mL/kg, i.v., Day 0)
Group 4: Nab-paclitaxel, 30 mg/kg (3 mg/mL, 10 mL/kg, i.v., Day 0)
Group 5: PRT3789, 100 mg/kg (s.c., Day 0 and Day 3) plus docetaxel, 25 mg/kg (i.v., Day 0)
Group 6: PRT3789, 100 mg/kg (s.c., Day 0 and Day 3) plus nab-paclitaxel, 30 mg/kg (i.v., Day 0)
The in vivo study and RNA-seq were conducted by Crown Bioscience. Tumors were harvested from all groups 120 hours after the first dose. RNA was extracted, libraries were prepared, and sequencing was performed by Crown Bioscience. Downstream analysis was performed using Pluto Bio (https://pluto.bio).


title: TDRD3, a Tudor Domain-Containing Protein, Regulates Klf2-Dependent Treg differentiation and function to Modulate Immune Tolerance

city: Duarte

first: Yate-Ching

last: Yuan

state: CA

address: 1500 East Duarte

institute: City of Hope

summary: Tudor domain-containing protein 3 (TDRD3) functions as a methylarginine reader that relays post-translational arginine methylation signals to the transcriptional machinery, thereby regulating cellular functions through modulation of gene expression. Regulatory T cells (Tregs) are pivotal for establishing and maintaining immune tolerance. In this study, we demonstrate that while TDRD3 is dispensable for thymic Tregs, it is essential for the differentiation of induced Tregs (iTregs) from naïve CD4⁺ T cells and for their immunosuppressive function. Mice with Treg-specific deletion of TDRD3 (Tdrd3fl/fl/Foxp3YFP-Cre) exhibit severely impaired iTreg, but not thymic Treg, differentiation and develop exacerbated experimental autoimmune encephalomyelitis (EAE), correlating with reduced Treg populations. Moreover, iTregs, but not thymic Tregs, derived from these mice fail to suppress colitis in adoptive transfer models, indicating compromised inhibitory capacity. Aged TDRD3-deficient mice also show spontaneous autoinflammation, characterized by splenomegaly and inflammatory infiltration in the lungs and liver, accompanied by increased IFN-γ–producing CD4⁺ T cells. Mechanistically, TDRD3 is recruited by the transcription factor FOXO1, presumably in a methylation-dependent manner, to activate Klf2 expression, which is essential for Treg differentiation. Notably, the enforced expression of Klf2 in TDRD3-deficient CD4⁺ T cells rescue both iTreg development and suppressive function. Collectively, our findings identify TDRD3 as a central transcriptional regulator of iTreg differentiation and immune homeostasis, highlighting it as a potential therapeutic target for modulating immune tolerance.

overall_design: Overall design RNA-seq analysis was performed to detect the transcriptome of Foxp3YFP-Cre and TDRD3fl/fl/Foxp3YFP-Cre CD4+ cells 36 hours post Treg polarization.

first: Yun

last: Shi

first: Xiaoqun

last: Tao

first: Lei

last: Shen

first: Guangpeng

last: Wang

first: Yanzhong

last: Yang

first: Zuoming

last: Sun


title: RNA-seq analysis of NCI-H1693 cells treated with the selective SMARCA2 degrader PRT3789

summary: The goal of this study was to examine the transcriptional consequences of selective SMARCA2 degradation in a SMARCA4-deficient non-small cell lung cancer (NSCLC) model. NCI-H1693 cells were treated with the SMARCA2 degrader PRT3789 (50 nM) or vehicle control for 6 h, 48 h, and 72 h. RNA-seq was performed to identify changes in gene expression that could reveal pathways associated with synthetic lethality and clarify the mechanism of action of SMARCA2 degraders in the absence of SMARCA4.

overall_design: For each of three time points (6 h, 48 h, 72 h), NCI-H1693 cells were treated with PRT3789 (50 nM) or DMSO control in triplicate. Cell pellets were collected, flash-frozen, and shipped to GENEWIZ (now Azenta Life Sciences) for RNA extraction, library preparation, and sequencing. Poly(A)-enriched stranded mRNA libraries were prepared and sequenced on an Illumina platform to generate paired-end 150 bp reads. Downstream analysis, including quality control, read alignment to the human reference genome (GRCh38), and quantification of gene-level counts, was performed using Pluto Bio (https://pluto.bio). Briefly, paired-end FASTQ files were processed using the nf-core/rnaseq pipeline (v3.17.0) (auto strandedness). Adapter sequences were removed with Trim Galore. Reads were aligned with STAR to GRCh38 (NCBI, p.14, release 110) and quantified to gene counts using RSEM.


title: ATAC-seq analysis of NCI-H1693 cells treated with the selective SMARCA2 degrader PRT3789

summary: The goal of this study was to characterize genome-wide chromatin accessibility changes induced by SMARCA2 degradation in a SMARCA4-deficient non-small cell lung cancer model. NCI-H1693 cells were treated with the selective SMARCA2 degrader PRT3789 (50 nM) or vehicle control (DMSO) for 48 h. ATAC-seq was performed to identify regions of differential accessibility that may help explain the mechanism of synthetic lethality in SMARCA4-deficient contexts.

overall_design: NCI-H1693 cells were treated with PRT3789 (50 nM) or DMSO control for 48 h in triplicate.Viable cells were cryopreserved, frozen, and shipped to GENEWIZ (now Azenta Life Sciences) for ATAC-seq library preparation and sequencing . Libraries were sequenced on an Illumina platform to generate paired-end 150 bp reads. Downstream analysis, including quality control, read alignment to the human reference genome (GRCh38), peak calling, and quantification of accessibility, was performed using Pluto Bio (https://pluto.bio). Briefly, paired-end FASTQ files were processed using the nf-core/atacseq pipeline (v2.0). Adapter sequences were removed with Trim Galore. Reads were aligned with Bowtie2 to GRCh38 (NCBI, p.14, release 110) and duplicates were marked and removed from all samples with picard. Peaks were called with macs2 (peak mode: narrow) using a p-value threshold of 0.00001 and an effective genome size of 2,940,000,000. Consensus peaks were merged across all samples using BEDTools and annotated to the nearest gene transcriptional start site using HOMER. Peak counts were generated using featureCounts.


title: Cell-cycle dynamics of nascent transcription and mature RNA accumulation are concordant in normal fibroblasts

city: Cincinnati

first: Kohta

last: Ikegami

state: OH

address: 240 Albert Sabin Way, Cincinnati, OH 45229

department: Division of Molecular Cardiovascular Biology

institute: Cincinnati Children's Hospital Medical Center


title: Cell-cycle dynamics of nascent transcription and mature RNA accumulation are concordant in normal fibroblasts [RNA-seq]

summary: Dynamic changes of gene expression is fundamental to cell cycle control. A prevailing hypothesis states that cell-cycle gene expression dynamics is driven by a widespread transcription-to-maturation lag, in which nascent transcription occurs in a cell-cycle phase preceding the phase with mature RNA accumulation, based on a study in cancer cells. Here, we test this paradigm in non-transformed human fibroblasts. We define mature RNAs and nascent transcription during the cell cycle using FUCCI reporters. The two dynamics are strongly concordant without a lag. Our data suggest a widespread transcription-to-maturation lag may be a feature of some cancer cells, but not of normal cells.

overall_design: To investigate cell-cycle dynamics of gene expression in cycling non-transformed cells, we introduced the Fucci4 cell-cycle fluorescent reporters to the hTERT-immortalized human fibroblast cell line BJ-5ta (BJ-Fucci). We sorted BJ-Fucci cells into early G1 (mKO2–Clover–mTurquoise2–), G1 (mKO2+Clover–), early-S (mKO2+Clover+mTurquois+), and late-S/G2/M (mKO2–Clover+) phases using FACS. We sequenced poly A-selected RNAs using RNA-seq in these sorted populations. To define the nascent transcriptional dynamics, we sorted early G1, G1, and late-S/G2/M BJ-Fucci cells and performed GRO-seq, which quantifies nascent transcripts produced during a short incubation of permeabilized cells with bromouridine (BrU) by sequencing of BrU-incorporated RNAs.


title: Targeting EZH2 and HDACs in hematological cancers induces transcriptional and metabolic deregulation causing ferroptosis

city: Leuven

first: Sofie

last: Demeyer

address: Herestraat 49, Campus Gasthuisberg, O&N 4, 9e verd, bus 912

institute: VIB-KU Leuven Center for Cancer Biology

summary: The methyltransferase EZH2 functions as the enzymatic component of the PRC2 complex, which deposits methyl groups on H3K27, leading to chromatin condensation and gene repression. Recent studies have shown that EZH2 can also act as a transcriptional modulator, independently of the PRC2 complex and its methyltransferase activity. In this study, we demonstrate that EZH2 degradation is more effective in blocking cellular proliferation compared to EZH2 enzymatic inhibition. Strikingly, the combination of EZH2 degradation and HDAC inhibition exhibited potent synergy in a broad spectrum of hematological malignancies. The dual inhibition led to increased H3K27 acetylation and transcriptional deregulation, revealing that the observed synergy is driven by metabolic reprogramming. A metabolism-centered analysis showed upregulation of cholesterol biosynthesis in several hematological malignancies upon combined inhibition of EZH2 and HDACs. Interestingly, EZH2 degradation and HDAC inhibition also independently modulate distinct metabolic pathways: EZH2 degradation enhances fatty acid biosynthesis, while HDAC inhibition activates the tricarboxylic acid (TCA) cycle. The overactivation of cholesterol and fatty acid synthesis, of the TCA cycle, and histone hyperacetylation, strongly suggests induction of metabolic stress. Indeed, as a result of EZH2 degradation and HDAC inhibition, we observed an increase of reactive oxygen species (ROS), promoting lipid peroxidation and ultimately triggering ferroptotic cell death. Together, our findings highlight that co-targeting EZH2 and HDAC leads to an increase of histone acetylation and the overactivation of several metabolic pathways, leading to strong metabolic stress and induction of ferroptotic cell death.

overall_design: RNA-sequencing of EOL1 and HH cells upon treatment with DMSO, Romidepsin, MS1943 or a combination of these compounds

first: Alexandra

last: Veloso

first: Marlies

last: Vanden Bempt

first: Jan

last: Cools


title: Exploring mechanisms of scar-free skin wound healing in adult zebrafish

city: Zürich

first: Ismail

last: Kücükaylak

address: Otto-Stern-Weg 7

country: Switzerland

institute: ETH Zurich

summary: We performed single-cell RNA sequencing to better characterize the dynamics and heterogeneity of involved cell types during different stages of zebrafish cutaneous wound healing.

overall_design: Full-thickness wounds of adult zebrafish with a diameter of 2 mm were introduced with a clinical dermatology laser. For single cell RNA sequencing, single cell suspensions were prepared. For this task, unwounded skin tissue from three adult zebrafish was collected. In addition, the wound tissues for 2 dpw, 4 dpw and 6 dpw were collected using a biopsy punch with a diameter of 4 mm from three adult zebrafish each.

first: Matthias

last: Hammerschmidt


title: Cell-cycle dynamics of nascent transcription and mature RNA accumulation are concordant in normal fibroblasts [GRO-seq]


title: Wdr4-mediated m7G modification on let-7 miRNA to Maintain Steady-State Ribosome Biogenesis for Intestinal Homeostasis

city: Nangang

first: Kreeti

last: Kajal

state: Taipei City

address: R337, Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan

country: Taiwan

summary: Ribosome biogenesis is recently known to control stem cell fate, while its role and regulation in intestinal stem cells (ISCs) remain unexplored. Here, we report that WD repeat protein 4 (Wdr4) complexes with Mettl1, an RNA methyltransferase, mediates m7G modification to preserve steady-state ribosome biogenesis in ISCs of the Drosophila midgut, functional equivalent to mammalian small intestines. Diminishing Wdr4 or Mettl1 elevates ribosome biogenesis, driving ISC overprolifaeration and misdifferentiation, leading to short lifespan. Mechanistically, Wdr4 or Mettl1 depletion in ISCs reduces m 7 G levels and let-7 expression, resulting in increased TOR signaling and ROS levels, which activate the JNK-dMyc signaling cascade. Concurrently, TOR signaling and dMyc enhance ribosome biogenesis. Furthermore, overexpression of human WDR4 and METTL1 in fly ISCs respectively restores the phenotypes caused by Wdr4 and Mettl1 loss, indicating a conserved role of m7G modification to maintain ISC homeostasis across species. Together, our findings unravel miRNA modulation in growth signaling and ribosome biogenesis for ISC homeostasis, offering new avenues for therapeutic interventions.

overall_design: RNA-seq profiling of wildtype and wdr4 mutant intestine of 7-day old drosophila

first: Elham

last: Rastegari

first: Wen-Der

first: Jian-Chiuan

last: Li

first: Chun-Hong

last: Chen

first: Wan-Hsuan

last: Chou

first: Wei-Chiao

last: Chang

first: Tzu-Yang

last: Lin

first: Kevin

last: Tsai

first: Tsai-Ming

last: Lu

first: Kartik

last: Venkatachalam

first: Hwei-Jan

last: Hsu


title: In vitro Derivation of Midbrain Dopaminergic Neurons from Porcine Embryonic Stem Cells in Multi-dimensional Conditions [bulkRNA-seq]

city: Cheongju

first: Sang-Hwan

last: Hyun

state: Please select your state

address: 1 Chungdae-ro, Seowon-gu

department: Veterinary Medical Center and College of Veterinary Medicine

country: South Korea

institute: Chungbuk national university

summary: The generation of human-relevant dopaminergic (DA) neurons in large-animal models holds significant promises for translational neuroscience and regenerative medicine. Here, we establish a robust protocol to induce caudal ventral midbrain (VM) fate and generate functional midbrain DA (mDA) neurons and porcine midbrain-like organoids (pMLOs) from porcine embryonic stem cells (pESCs). Optimization of GSK3 inhibition and SHH signaling revealed species-specific requirements for inducing porcine VM progenitors, including a higher sensitivity threshold compared to human cells. Single-cell and bulk transcriptomic analyses demonstrated progressive lineage specification and functional maturation of mDA neurons, with IVF-derived pESCs showing superior differentiation potential over PA-derived cells. Moreover, 3D differentiation led to the formation of uniform neuroepithelial structures and enhanced electrophysiological activity and dopamine release. Notably, dopaminergic markers emerged across multiple neuronal clusters, reflecting a continuum of identity acquisition captured by high-resolution single-cell RNA sequencing. Compared to in vivo transgenic pig models, this platform enables rapid, scalable, and ethically favorable investigation of midbrain development and DA neuron biology. These findings position pig-derived organoids as a powerful tool for modeling human neurodevelopment and disease in a large-animal context.

overall_design: To investigate temporal gene expression dynamics during the differentiation of midbrain dopaminergic (mDA) neurons, bulk RNA sequencing was conducted using two porcine embryonic stem cell (pESC) lines derived from different embryonic origins: in vitro fertilization (IVF) and parthenogenetic activation (PA). Cells from both lines were collected at four representative time points during differentiation: day 0 (undifferentiated), day 16 (early neuronal specification), day 28 (synaptic maturation), and day 45 (late-stage differentiation). Each time point included biological duplicates, resulting in a total of 16 samples.  The experimental design aimed to capture transcriptomic changes over time and to compare differentiation patterns between IVF- and PA-derived mDA neurons. Correlation and gene ontology analyses were performed to assess temporal progression and functional enrichment. The dataset enables evaluation of key gene expression programs involved in neurogenesis, synaptogenesis, cellular responses, and lineage-specific differentiation during in vitro mDA neuron development.

first: Hyerin

last: Choi

first: Dongjin

last: Oh

first: Ali

last: Jawad

first: Jaehyung

last: Ham


title: Characterising transcriptional changes throughout c-MYC-driven tumorigenesis in the mammary gland (MMTV-cMYC mouse model)

city: London

first: Mariia

last: Yuneva

address: 1 Midland Road

institute: The Francis Crick Institute

summary: c-MYC oncogene is one of the driver lesions in many types of cancer. Among breast cancers, triple negative subtype (TNBC) is characterised by high aggressivness and is associated with high transcriptional activity of MYC. MMTV-cMYC mouse model, in which ectopic expression of c-MYC is driven by mouse mammary tumour virus promoter, is a widely used model of MYC-driven breast cancer. MMTV-cMYC mice develop tumours in the mammary gland(s) at ages ranging from 6 to 10 months.  MYC regulates activity of multiple processes including cell cyle, proliferation, metabolism, protein translation, inflammation and apoptosis among others. Previous studies demonstrated that MMTV-cMYC tumours are very heterogeneous. However, how different procecesses regulated by MYC contribute to different steps of the transformation process and tumour development is not known. To evaluate how the expression of genes changes from the initiation of transformation process by ectopic expression of c-MYC in mammary gland epithelial cells to the development of tumours, we perfomed RNAseq analysis of tissues collected from mammary glands and tumours of MMTV-cMYC mice of different ages. Wild type age-matched littermates were used as controls.

overall_design: Hyperplastic 6 week and 12 week old mammary glands as well as small (less than 3X3 mm in diameter) and large (10X10 mm in diameter) tumours were colelcted from MMTV-cMYC female mice on FVBN/J background.  Normal mammary glands were collected from 6 week old MMTV-cMYC negative littermate controls. This study also aimed to evalute how glucose metabolism changes throughout MYC-induced mammary gland tumorigenesis. Hence all mice received a bolus injection of [U-13C]-glucose i.v. at  570 mg/kg (calculated as 20 mg of [U-13C]-glucose for an average body weight of 35g dissolved in 100 μl of saline). Tissues were snap frozen in liquid nitrogen and ground.

first: Chandan

last: Seth Nanda

first: Michael

last: Kossifos

first: Ersa

last: Gjelaj

first: Maria

last: Rodriguez

first: Hubert

last: Slawinski

first: Deborah

last: Schneider-Luftman


title: In vitro Derivation of Midbrain Dopaminergic Neurons from Porcine Embryonic Stem Cells in Multi-dimensional Conditions [scRNA-seq]

overall_design: Single-cell RNA sequencing was performed on pigMLOs at days 11, 28, and 45 of differentiation to characterize temporal changes in cellular composition and transcriptional dynamics. After alignment to the Sus scrofa Sscrofa11.1 genome and downstream processing, 103,310 high-quality cells were obtained and visualized via UMAP.


title: Prevention of Mechanics-Induced Hyperproliferative Fibroblast States Alleviates Dilated Cardiomyopathy

city: Seattle

first: Jennifer

last: Davis

state: WA

address: 850 Republican St, Brotman #343

department: Lab Medicine and Pathology

institute: University of Washington

summary: Cardiomyocyte hypocontractility underlies inherited dilated cardiomyopathy (DCM), but the fibroblasts’ impact on DCM phenotypes is poorly understood despite its regulation of fibrosis, which is a strong predictor of disease severity. DCM mice with an I61Q variant of cardiac troponin c (cTnC)  had elevated diastolic tension sensation at fibroblast focal adhesions and matrix-integrin receptor interactions that initiated de novo  formation of hyperproliferative-mechanosensitized states and doubled the population . These fibroblast adaptations drove fibrosis-independent myocardial stiffening and subsequent cardiomyocyte dilation. Genetically disabling mechanotransduction arrested the fibroblast response, which in turn prevented dilated myocyte remodeling and drastically improved myocyte hypocontractility and myocardial function. In conclusion, noncanonical  fibroblast-dependent stiffening of the myocardium proved essential to the DCM phenotype, marking a potential  cellular target for therapeutic intervention.

overall_design: Single nucleus RNA sequencing of cardiac ventricles from mice of WT, I61Q mutant, or I61Q mutant and fibroblast-specific p38 knockout mice (I61Q-p38).

first: Ross

last: Bretherton

first: Logan

last: Bailey


title: Cell type- and chromosome-specific chromatin landscapes and DNA replication programs of Drosophila testis stem cells [scRNA-seq]

city: Baltimore

first: Daniel

last: Ringwalt

address: 3400N Charles St

department: Biology

institute: Johns Hopkins University

summary: Stem cells have the unique ability to self-renew and differentiate into specialized cell types. Among the many factors influencing cell fate, epigenetic mechanisms, like histones, play a crucial role in regulating genomic programs like gene transcription and DNA replication, which are integral to a cell’s identity. However, the transcriptional, chromatin, and DNA replication timing profiles of stem cells within in vivo tissues remain poorly understood. The Drosophila testis serves as an excellent in vivo model for studying stem cells, as it contains two stem cell populations: the germline stem cells (GSC) and somatic cyst stem cells (CySC). Despite this, a comprehensive understanding of genome regulation in these cell types has been limited by the small number of stem cells and heterogeneity of the testis. In this study, we developed cell-specific genomic techniques to analyze the transcriptome, histone modification patterns, and replication timing profiles of GSCs and CySCs. Our single cell RNA-sequencing validated previous cell-biological and genetic studies on the role of intercellular communication between GSCs and CySCs while revealing high expression of chromatin regulators in GSCs. To characterize chromatin landscapes, we developed a cell-specific chromatin profiling assay to map H3K4me3, H3K27me3, and H3K9me3. These posttranslational modifications define euchromatic, facultative heterochromatic, and constitutive heterochromatic domains, respectively. Finally, we determined the cell-specific replication timing profiles of GSCs and CySCs, integrating our in vivo datasets with published in vitro data. Our results reveal that the replication program of GSCs is distinct from somatic lineages and that these differences align with variations in chromatin patterns. Collectively, our integrated genomic datasets build a framework for understanding genome-wide regulatory differences in two in vivo stem cell populations, demonstrating the power of combining transcriptomic, chromatin, and replication datasets to uncover cell-specific features of genome regulation.

overall_design: Drosophila melanogaster testis tumors were produced by overexpressing the Unpaired (Upd) ligand via two genetic strategies. Upd was either overexpressed using the germline-specific nanos promoter or cyst cell-specific traffic jam promoter. From each genetic strategy, approximately 18-20 testis pairs were dissected and dissociated to create a single cell suspension. Two replicates of each genetic type (four samples total) were proccessed for single cell RNA-sequencing using the 10X Genomics platform.

last: Urban

first: John

first: Wingel

last: Xue

first: Ryan

last: Gleason

first: Keji

last: Zhao

first: Xin

last: Chen


title: Exercise-induced cellular changes promote improved function in ischemic hearts

city: Zurich

first: Genome

last: Informatics

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich (FGCZ)

institute: ETH ZURICH / University of Zurich

summary: Ischemic heart disease (IHD) remains a leading cause of mortality worldwide, often culminating in myocardial infarction (MI) and subsequent heart failure due to adverse fibrotic remodeling of the myocardium. Despite the lack of effective treatments, exercise has emerged as a promising strategy to reduce mortality risk and improve cardiac function post-MI. This study investigates the molecular mechanisms underlying exercise-induced cardioprotection by analyzing changes in several key cardiac cell populations after MI in a murine model. We assessed the effect of exercise preconditioning in mouse MI model through echocardiography, followed by single nuclei RNA-seq of cardiac cells, and validation by microscopy and flow cytometry. Our findings demonstrate that exercise significantly enhances cardiac function post-MI, as evidenced by improved ejection fraction and stroke volume in exercised mice. These improvements are linked to adaptive changes across multiple cardiac cell types. Notably, in infarcted mice, exercise caused a downregulation of cardiomyopathy-associated pathways, accompanied by changes in ECs, macrophages, fibroblasts and cardiomyocytes. Exercise stimulated formation of new capillaries which post-MI resulted in a more vascularized infarct border zone. Additionally, exercised hearts displayed a shift in macrophage populations towards a pro-regenerative phenotype, marked by an increase in resident CCR2- macrophages and a reduction in pro-inflammatory M1-gene expression. In cardiomyocytes, exercise enhanced pathways related to endothelial support and ATP biosynthesis, mitigating the upregulation of cardiomyopathy-associated pathways observed post-MI. Importantly, exercise also restored calcium signaling and reversed pathological potassium signaling, thereby preserving contractile function. Fibroblast analysis revealed that exercise stimulated activation of these cells to participate in scar formation. In conclusion, this study provides new insights into the cellular and molecular mechanisms through which exercise enhances cardiac function and provides cardio-protection post-MI, offering potential avenues for targeted therapies in patients with IHD.

overall_design: The effect of running on changes in cardiac cell types was studied by single nuclei RNA-sequencing. To this end, male and female 8-week-old mice were first subjected to 16 weeks of voluntary wheel running (n=6). Sedentary mice were used as controls (n=6). After 16 weeks, 2 mice from both sedentary and runnning group were sacrificed for heart collection (Sedentary and Running samples). The other 4 mice from each group were subjected to myocardial infarction surgery and sacrificed 2 weeks later for heart collection (Sedentary-infarct and Running-infarct samples).

first: Tea

last: Kocijan

first: Moheb

last: Ghobrial

first: Guillermo

last: Turiel

first: Jing

last: Zhang

first: Katrien

last: DeBock


title: Total RNA Sequencing in HCC Patients

summary: Total RNA Sequencing in HCC Patients

overall_design: Liver resection was performed on HCC patients. Samples were carefully disected to separate tumor tissues from the adjacent CLD tissues. Normal liver tissue was obtained from healthy donors or liver resections resulted from other medical conditions. All samples were examined and verified by experienced pathologists. Total RNAseq was performed to compare the changes in their transcriptomic signatures.

first: Marc

last: Healy

first: Peter

last: Leary

first: Lap Kwan

last: Chan

first: Achim

last: Weber


title: Identification of epigenetic regulators of fibrotic transformation in cardiac fibroblasts through bulk and single-cell CRISPR screens (RNA-seq)

city: Pamplona

first: Laura

last: Pilar Aguado Alvaro

address: Av. de Pío XII, 55

institute: Center for Applied Medical Research (CIMA)- University of Navarra

summary: Cardiac fibrosis is mediated by the persistent activity of myofibroblasts, which differentiate from resident cardiac fibroblasts in response to tissue damage and stress signals. The signaling pathways and transcription factors regulating fibrotic transformation have been thoroughly studied. By contrast, the roles of chromatin factors in fibroblast differentiation and their contribution to pathogenic cardiac fibrosis remain poorly understood. Here, we have combined bulk and single-cell CRISPR screens to characterize the roles of chromatin factors in ex vivo fibroblast differentiation. We uncover strong regulators of fibrotic states including Srcap and Tip60 chromatin remodelers, the NSL complex and the co-factors Hcfc1 and Wdr82. We confirm these factors are required for cellular processes underlying fibrosis including collagen synthesis and cell contractility. We use epigenetic profiling to demonstrate these chromatin factors facilitate the activity of pro-fibrotic transcription factors. Finally, using chemical perturbation in primary human cardiac fibroblasts we suggest Tip60 inhibition as a potential therapeutic approach for cardiac fibrosis.

overall_design: Here we have used RNA-seq to analyse differential gene expression of primary cardiac fibroblasts grown on two different culture media under basal or fibrotic ex vivo conditions

middle: P

last: Aguado-Alvaro

first: Nerea

last: Garitano

first: Wolfgang

last: Esser-Skala

first: Judy

last: Sayers

first: Cynthia

last: del Valle

last: Alameda

first: Julen

last: Mendieta-Esteban

first: Maria

last: Calleja-Cervantes

first: Ainhoa

last: Goñi-Salaverri

first: Jon

last: Zazpe

first: Anna

last: de Vito

first: Francesco

last: Marchese

first: Diego

last: Alignani

first: Juliana

last: Cudini

first: Torsten

last: Gross

first: Gregorio

last: Rábago

first: Nisha

last: Narayan

last: Martinez

first: Sonia

first: Arantxa

last: Gonzalez-Miqueo

first: Brian

last: Huntly

first: Paul

last: Riley

first: Nikolaus

last: Fortelny

first: Jake

last: Taylor-King

first: Beatriz

last: Pelacho

first: David

last: Lara-Astiaso


title: Identification of epigenetic regulators of fibrotic transformation in cardiac fibroblasts through bulk and single-cell CRISPR screens (ATAC-Seq_2)

first: Laura

last: Pilar Aguado Alvaro

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Here we have used ATAC-seq to analyse the chromatin accessibility patterns of primary cardiac fibroblasts knocked-out for specific Chromatin Factors ex vivo differentiated under TGFb stimulation.

last: Aguado-Alvaro

first: Nerea

last: Garitano

first: Wolfgang

last: Esser-Skala

first: Judy

last: Sayers

first: Cynthia

last: del Valle

first: Daniel

last: Alameda

first: Julen

last: Mendieta-Esteban

first: Maria

last: Calleja-Cervantes

first: Ainhoa

last: Goñi-Salaverri


title: Cell type- and chromosome-specific chromatin landscapes and DNA replication programs of Drosophila testis stem cells [Repli-seq]

last: Ringwalt

overall_design: Drosophila melanogaster testis tumors were produced by overexpressing the Unpaired (Upd) ligand via two genetic strategies. Upd was either co-expressed with GFP-tagged H3 histone using the germline-specific nanos promoter or cyst cell-specific traffic jam promoter. From each genetic strategy, 100-200 testis pairs were dissected and nuclei extracted. GFP-positive nucei were collected on a MoFlo XDP cell sorter. The nuclei were further sorted by DNA content, separating into one of four S-phase fractions (early, early-mid, late-mid, and late replicating). For each (stem cell-type) biological replicate, the replicating DNA from each of the four S-phase fractions was enriched and prepared for next generation sequencing (Repli-seq).

first: Jennifer

last: Urban

first: John

first: Wingel

last: Xue

first: Ryan

last: Gleason

first: Keji

last: Zhao

first: Xin

last: Chen


title: Exploring the bioactive properties of fucoidan from Sugar kelp to modulate the immune response and gut microbiota of Atlantic salmon

city: Ås

first: Byron

last: Morales Lange

address: Arboretveien 6

country: Norway

institute: Norwegian University of Life Sciences

summary: Long chain sulfated polysaccharides such as fucoidans are promising feed additives to improve animal health and welfare.  Thus, our study evaluated the bioactive properties of a fucoidan-enriched fraction from sugar kelp (Saccharina lattissima) on the intestinal transcriptome of  pre-smolts Atlantic salmon (Salmo salar) fed with novel functional aquafeeds for 5 weeks in freshwater.

overall_design: Following a 5-week feeding experiment with Atlantic salmon (Salmo salar) pre-smolts fed supplemented diets containing fucoidan from Saccharina lattissima, intestinal samples were collected for transcriptomic analysis by RNA sequencing to explore the potential immunomodulatory properties of these compounds in fish.

first: B

last: Morales-Lange

first: M

last: Øverland


title: Cell type- and chromosome-specific chromatin landscapes and DNA replication programs of Drosophila testis stem cells

overall_design: Refer to individual Series


title: Gene expression profiling by RNA-seq of control and TRIM21-knockdownHCT8 cells

city: Shanghai

first: Xintian

last: Zhang

address: 639 Zhi Zao Ju Road

institute: Shanghai Jiao Tong University

summary: In order to define the cohort of genes whose expression is regulated by TRIM21 in CRC,  we constructed HCT8 cells stably infected with lentivirus carrying control shRNA (shNC) or TRIM21 shRNA (sh1). Subsequently, total RNA was isolated and then performed transcriptome RNA sequence.

overall_design: We had two groups: (1) shNC and (2) sh1. Each group had 3 biological replicates.

first: Xiangjun

last: Meng


title: Mitochondrial iron transport via MFRN1 is required for erythroid cell cycle progression

city: Pittsburgh

first: Yvette

last: Yien

state: PA

address: 200 Lothrop St

institute: University of Pittsburgh

summary: The goal of the scRNAseq study was to identify developmental defects and differential gene expression in MFRN1 mutant d3 zebrafish embryos

overall_design: 10 Tg(lcr:GFP) and Tg(lcr:GFP); MFRN1 mutant 3 dpf zebrafish embryos of the AB strain were homogenized and subjected to scRNAseq anlysis.  GFP is under the control of the globin promoter and its expression is restricted to the erythroid lineage. The goal was to identify lineage defects (erythroid and other) that resulted from MFRN1 deficiency, as well as identify differnetially expressed genes.