title: small RNA seq of patient-derived glioma cells (GBM1,GBM2, GG3)

city: Genova

first: Kiril

last: Tuntevski

address: Via Morego 30

institute: Istituto Italiano di Tecnologia

summary: Glioblastoma (GBM) has a poor prognosis due to infiltrative and therapy-resistant glioma stem-like cells. MicroRNAs (miRNAs) synergistically modulate biological pathways by repressing tumor-related genes, a mechanism lost in cancer.

overall_design: GBM1-2 (glioblastoma) and GG3 (glioma grade III) patient-derived cells were cultured in glioma stem cell medium (Griffero et al., 10.1074/jbc.M807111200) and total RNA extracted for small RNA sequencing.

first: Silvia

last: Rancati

first: Rui

middle: C

last: Pereira

first: Michele

last: Schlich

first: Stefania

last: Sgroi

last: Beatini

first: Letizia

last: La Rosa

first: Lidia

last: Giantomasi

first: Roberta

last: Pelizzoli

first: Clarissa

last: Braccia

first: Carlotta

last: Spattini

first: Amanda

last: Lo Van

first: Meritxell

last: Pons-Espinal

first: Anna Lisa

last: Palange

first: Adriana

last: Bajetto

first: Antonio

last: Daga

first: Andrea

last: Armirotti

first: Tullio

last: Florio

first: Paolo

last: Decuzzi

first: Davide

last: De Pietri Tonelli


title: Prevotella copri facilitates wound healing in mice through the sphingosine-CerS1-ceramide metabolic pathway

status: Public on Oct 28 2025

city: Shanghai

first: Hailiang

last: Liu

address: NO 1239, siping road

country: China

institute: Tongji university

type: Expression profiling by high throughput sequencing

summary: Skin wound repair constitutes a sophisticated biological process involving spatiotemporally coordinated molecular cascades, with emerging evidence highlighting the dynamic regulatory role of skin microbiota. Utilizing a broad-spectrum antibiotic-treated (ABX) murine model, we identified Prevotella copri as a core functional commensal in the wound microecosystem that orchestrates tissue regeneration through metabolite-host crosstalk. ABX-induced microbial remodeling significantly enriched P. copri relative abundance, accelerated wound closure, and upregulated pro-regenerative factors VEGF and FGF-2. Metabolomic profiling revealed that P. copri-secreted sphingosine undergoes bioconversion to C18-ceramide via the non-canonical CerS1 pathway, driving keratinocyte hyperproliferation and neoangiogenesis. Pharmacological inhibition of CerS1 with P053 suppressed ceramide synthesis and delayed healing, mechanistically validating the sphingosine-CerS1-ceramide axis. Crucially, P. copri exhibits dual regulatory modalities: ecologically, β-lactamase-mediated antibiotic resistance establishes microbial dominance, while metabolically, sphingolipid-driven spatiotemporal signaling remodels the regenerative microenvironment. This paradigm shifts the pathocentric view of wound microbiota, proposing a synergistic strategy combining "functional microbiota enrichment" and "metabolic axis targeting". Our findings elucidate a microecology-metabolism circuit that transitions wound management from passive anti-infection to precision intervention, providing a molecular blueprint for developing microbiome-reprogramming therapies in regenerative medicine.

overall_design: Traditional wound repair research often focuses on microbial diversity, neglecting the critical role of specific taxa in tissue regeneration. Our study challenges this by highlighting Prevotella copri as a key species in wound healing, operating through the Prevotella copri-sphingosine-CerS1-ceramide signaling pathway. This discovery reshapes the understanding of microbiome-host interactions and paves the way for precision microbial therapies. By showing that a single bacterium can replace complex community dynamics, we connect ecological theory with regenerative applications, offering a strategy to use microbial metabolism for precise wound healing.


title: RNA-seq of gubernaculum and testis from wild-type, cetacean INSL3 knock-in, and INSL3 knockout mice across developmental stages

city: Nanjing

first: Yu

last: Zheng

state: Jiangsu Sheng

address: No.1 Wenyuan Road, Xianlin University Town, Qixia District, Nanjing, Jiangsu Province

institute: NANJING NORMAL UNIVERSITY

summary: This dataset contains high-throughput RNA sequencing (RNA-seq) data generated from gubernaculum and testis samples of wild-type (WT), cetacean INSL3 knock-in (KI), and INSL3 knockout (KO) mice at selected postnatal developmental stages. The purpose of the study was to investigate the molecular consequences of replacing the endogenous mouse Insl3 coding sequence with the cetacean INSL3 ortholog, and to compare transcriptomic profiles among WT, KI, and KO mice to elucidate the functional role of INSL3 in testicular descent and cryptorchidism. RNA-seq was performed on gubernaculum tissue at postnatal day 8 (P8) and testis tissue at P8, P23, and P40 (with some groups excluded due to degeneration or non-specific damage). The dataset supports integrative analyses of developmental stage–specific and genotype–specific gene expression changes in reproductive tissues.

overall_design: Male C57BL/6J background mice of three genotypes were used: wild-type (WT), cetacean INSL3 knock-in (KI), and INSL3 knockout (KO). In the KI model, the endogenous mouse Insl3 coding sequence was precisely replaced with the cetacean ortholog at the native genomic locus, preserving all mouse promoter and regulatory elements. For WT and KI mice, RNA-seq was performed on gubernaculum at postnatal day 8 (P8) and on testes at P8, P23, and P40. For KO mice, RNA-seq was performed on gubernaculum at P8 and testes at P8 and P23.

first: Simin

last: Chai

first: Cuijuan

last: Zhong

first: Yixuan

last: Sun

first: Guang

last: Yang


title: Impacts of DNA methylation on H2A.Z deposition and nucleosome stability

city: New York

first: Rochelle

middle: Makanani

last: Shih

state: NY

address: 1230 York Ave

country: USA

institute: Rockefeller University

type: Genome binding/occupancy profiling by high throughput sequencing

type: Methylation profiling by high throughput sequencing

summary: DNA methylation and the histone variant H2A.Z are maintained in mutually exclusive sections of the genome. How this antagonism is established, however, remains an open question. Here, we examined the impacts of DNA methylation on both the intrinsic stability of H2A.Z nucleosomes and chaperone-mediated H2A.Z deposition. Cryo-EM and endonuclease-based assays show that H2A.Z nucleosomes on methylated DNA substrates are more open and accessible compared to their unmethylated counterparts. In Xenopus, H2A.Z preferentially associates with unmethylated DNA of both sperm pronuclei in the transcriptionally silent egg extract as well as in somatic cells, though a substantial proportion of H2A.Z colocalizes with DNA methylation in sperm pronuclei. By monitoring nucleosome assembly on synthetic DNA constructs in egg extract, we find that the H2A.Z bias for unmethylated substrates is dependent on the SRCAP complex. Accordingly, DNA-binding of SRCAP is suppressed by DNA methylation. Altogether, we propose that the SRCAP complex is the major determinant for preferential H2A.Z enrichment on unmethylated DNA, and that DNA methylation destabilizes DNA wrapping in H2A.Z-containing nucleosomes.

overall_design: CUT&Tag-bisulfite sequencing (Li et al. 2021; https://doi.org/10.1016/j.crmeth.2021.100118) on H3 and H2A.Z in Xenopus laevis sperm pronuclei incubated in interphase-cycled Xenopus egg extract as well as XTC-2 cells (a Xenopus laevis fibroblast cell line).

middle: M

first: Yasuhiro

last: Arimura

first: Hide

middle: A

last: Konishi

first: Hironori

last: Funabiki


title: In Vivo Imaging Reveals Exosome-Mediated Intercellular Communication in Lens Development

status: Public on Oct 30 2025

city: Guangzhou

first: jingyu

last: Ma

state: Guangdong

address: No. 7 Jinsui Rd

institute: SUN YAT-SEN UNIVERSITY

summary: The transparency of lens relies on proper intercellular communication. Exosomes are crucial mediators of intercellular communication and play a key role in organ homeostasis and development. However, their presence and dynamics in the lens remain unclear. This study aimed to investigate the existence of endogenous exosomes in the lens and explore their potential functions. Using the cryaa promoter to drive Cd63-AcGFP expression, we achieved lens-specific exosome labeling in zebrafish.  Live imaging revealed the presence of exosomes in lens cells during development and their movement trajectory under physiological conditions. Additionally, lens-derived exosomes (lens-Exos) facilitate communication not only between lens cells but also with surrounding tissues. We also identified that the biogenesis of Cd63+ exosomes in the lens is regulated by the Syntenin-a pathway. As knockdown of Syntenin-a in zebrafish resulted in delayed lens development, indicating a potential role for exosomes in normal lens development. Furthermore, in vitro hESC-lentoid induction showed that extracellular vesicles from ROR1+ lens progenitor cells (ROR1+ LPCs-EVs) promote lentoid differentiation. Proteomic analysis provided insights into the functions of ROR1+ LPCs-EVs. Overall, our study is the first to observe endogenous exosomes in the lens, providing new insights into lens pathophysiology and a potential strategy for modulating the lens microenvironment.

overall_design: ROR1+ cells were magnetically isolated at D30 from hESC-derived lentoid bodies induction system, and RNA-seq was performed on three biological replicates (Passage 0) for transcriptome profiling.

first: Jingyu

first: Qihang

first: Yijia

last: Chen

first: Jinyan

last: Li

first: Shuai

last: Ouyang

first: Shurui

last: Ke

first: Jiani

first: Huilin

last: Liang

first: Shuyi

first: Lixia

last: Luo


title: Fibroblast-Derived Thrombospondin 2 Shapes the Immune-Exclusionary Environment at Invasive Fronts in Colorectal Cancer [Visium

city: Kyoto-City

first: Kosuke

last: Iwane

address: 54 Shogoin-Kawahara-Cho, Sakyo-Ku

department: Department of Gastroenterology and Hepatology

country: Japan

institute: Kyoto University Graduated School of Medicine

summary: Fibrotic colorectal cancers (CRC) are characterized by immune exclusion driven by activated stroma, particularly by cancer-associated fibroblasts (CAFs). This study aims to describe characteristics of spatial immune landscape of CRCs, which are subtyped by transcriptomic signatures and microsatellite instability.

overall_design: Four slides from FFPE blocks of surgically resected CRC specimens, which were determined as CMS1/MSI, CMS2, or CMS4 using bulk-RNA-seq data, were analyzed using spatial transcriptomics (ST).

first: Yuki

last: Nakanishi

first: Yu

last: Muta

last: Fukui

first: Hiroaki

last: Kasashima


title: Fibroblast-Derived Thrombospondin 2 Shapes the Immune-Exclusionary Environment at Invasive Fronts in Colorectal Cancer [scRNA-seq]

summary: Fibrotic colorectal cancers (CRC) are characterized by immune exclusion driven by activated stroma, particularly by cancer-associated fibroblasts (CAFs). We identified that the matricellular protein thrombospondin-2 (THBS2) is highly expressed in the stroma of fibrotic CRCs. We performed orthotopic implantation of CMS4-like mouse tumor organoid (MTO) into WT and Thbs2 KO mice. Tumors developed in Thbs2 KO mice were considerably smaller and exhibited increased CD8 T cell infiltration and higher numbers of apoptotic tumor cells compared with WT mice. Our aim is to elucidate how Thbs2 in tumor microenvironment influences tumor growth.

overall_design: Tumors derived from orthotopic implanted mouse tumor organoids (MTOs) harboring mutations in Apc, Trp53, Kras, and Tgfbr2 in the rectum of wild-type, Thbs1KO and Thbs2KO mice were processed into single-cell suspension and analyzed using scRNA-seq

first: Mayuki

last: Omatsu

first: Nobuyuki

last: Kakiuchi

first: Masahiro

last: Nakagawa


title: Fibroblast-Derived Thrombospondin 2 Shapes the Immune-Exclusionary Environment at Invasive Fronts in Colorectal Cancer [RNA-seq_Human_CRC]

summary: Fibrotic colorectal cancers (CRC) are characterized by immune exclusion driven by activated stroma, particularly by cancer-associated fibroblasts (CAFs). We identified that the matricellular protein thrombospondin-2 (THBS2) is highly expressed in the stroma of fibrotic CRCs. We performed orthotopic implantation of CMS4-like mouse tumor organoid (MTO) into WT and Thbs2 KO mice. Tumors developed in Thbs2 KO mice were considerably smaller and exhibited increased CD8 T cell infiltration and higher numbers of apoptotic tumor cells compared with WT mice. This study aims to elucidate the interaction between fibrotic CRCs and CAFs by comparing the phenotypic characteristics of bulk tumor tissues and their corresponding CAFs.

overall_design: RNA-seq profiling of fresh samples of surgically resected human colorectal carcinoma

first: Yasuhiro


title: PolyA RNA seq of human glioblastoma cells treated with a pool of 11 miRNAs in vitro and in vivo (orthotopic tumors in mice)

status: Public on Oct 29 2025

first: Kiril

last: Tuntevski

country: Italy

summary: Glioblastoma (GBM) has a poor prognosis due to infiltrative and therapy-resistant glioma stem-like cells. MicroRNAs (miRNAs) synergistically modulate biological pathways by repressing tumor-related genes, a mechanism lost in cancer. This study aimed to test a combination of different miRNAs exploiting their synergism as a multimodal therapy for GBM.

overall_design: In vitro: patient-derived GBM cells (GBM1 and GBM2) were transfected with a pool of 11 miRNAs or with scrambled control, in 2D adherent condition (glioma stem cell medium, matrigel-coated plastic). Cells were then cultured in speroid-permissive condition (glioma stem cell medium, uncoated plastic) for 3 days. In vivo: orthotopic tumors (GBM2 Luc+) were established in NOD/SCID mice striatum; after 42-49 days, animals received intratumoral injection of ApoE-coated LNP loaded with either the 11 miRNA pool or scrambled control. Animals were sacrificed 14 days after treatment and brain dissected to harvest tumoral tissue.

first: Silvia

last: Rancati

first: Rui

last: Pereira

first: Michele

last: Schlich

first: Stefania

last: Sgroi

last: Beatini

first: Letizia

last: La Rosa

first: Lidia

last: Giantomasi

first: Roberta

last: Pelizzoli

first: Clarissa

last: Braccia

first: Carlotta

last: Spattini

first: Amanda

last: Lo Van

first: Meritxell

last: Pons-Espinal

first: Anna Lisa

last: Palange

first: Adriana

last: Bajetto

first: Antonio

last: Daga

first: Andrea

last: Armirotti

first: Tullio

last: Florio

first: Paolo

last: Decuzzi

first: Davide

last: De Pietri Tonelli


title: A small cationic probe highly selective for RNA tertiary structure

city: Chapel Hill

first: David

last: Qiu

state: NC

address: 104 Airport Dr

department: Chemistry

institute: UNC Chapel Hill

summary: RNA is unique among the large biomolecules due to the intersection of its distinctive electrostatic properties, created by the permanent charge at each phosphate group, coupled with its ability to form diverse three-dimensional tertiary structures. We demonstrate that at rare, but distinctive, sites tertiary folding creates electronegative pockets that preferentially react with a small positively-charged chemical probe, trimethyloxonium (TMO), which alkylates RNA. TMO performs the same chemistry with RNA as the classical uncharged probe, dimethyl sulfate (DMS). Sites preferentially reactive with the TMO cation, relative to the uncharged DMS, are detected efficiently by massively parallel sequencing, at low read depths. These motifs, which we call T-sites, reflect preferential interaction of TMO at an electronegative pocket created by juxtaposition of a reactive nucleobase with non-bridging oxygen atoms, and specifically map to the centers of higher-order structural interactions and functional cores in model RNAs. T-site probing is a facile robust strategy, poised to create broad opportunities to detect and analyze RNA tertiary structures transcriptome-wide.

sample_organism:
Escherichia coli
Geobacillus stearothermophilus
Oceanobacillus iheyensis
Orthoflavivirus denguei

overall_design: In-vitro transcribed TPP riboswitch aptamer domain, Group II intron catalytic domain, and RNase P catalytic domain constructs with structure cassettes, either native sequence or various mutants, were refolded and structure was probed with TMO, DMS, or a non-reactive control. Naked RNA extracted from dengue virions was also chemically probed. Modified RNA was reverse transcribed under MaP conditions using SuperScript II. cDNA sequencing libraries were prepared and sequenced on an Illumina MiSeq instrument.

first: Jeffrey

middle: E

last: Ehrhardt

middle: Y

first: Shouhong

last: Jin

first: Caroline

middle: J

last: Aufgebauer

first: Mark

last: Boerneke

first: Stacy

last: Horner

first: Kevin

last: Weeks


title: EZH2 directs breast cancer progression through the modulation of epithelial cellular plasticity

city: Montreal

first: William

last: Muller

state: Quebec

address: 1160 Av des Pins O

department: Biochemistry

country: Canada

institute: McGill University

summary: Breast cancer remains a leading cause of death among women, encompassing diverse molecular subtypes with distinct clinical outcomes. The HER2+ subtype is particularly aggressive, with many patients eventually developing resistance to HER2-targeted therapies, underscoring the urgent need for alternative treatment strategies. Enhancer of Zeste Homolog 2 (EZH2), the catalytic subunit of Polycomb Repressive Complex 2, represses the expression of genetic programs crucial for differentiation, control of proliferation, and apoptosis through histone H3 lysine 27 trimethylation (H3K27me3). To investigate the role of EZH2 in HER2+ tumor progression, we crossed a genetically engineered mouse model (GEMM) of HER2-driven breast cancer with a conditional Ezh2 knockout strain. The results showed that Ezh2 is essential for accelerating tumor initiation and metastatic dissemination in HER2-driven breast cancer. Combined bulk and single cell RNA sequencing analyses revealed a significant downregulation of basal cell populations in the absence of Ezh2, characterized by the loss of Tp63 expression, and an upregulation of luminal progenitor cell populations, driven by crucial transcription factors such as Esr1, thereby driving luminal lineage commitment. Further, inhibition of EZH2 in vitro resulted in increased expression of ER in HER2+ human breast cancer cell lines and rendered them susceptible to tamoxifen. Altogether, these findings demonstrate that EZH2 dictates breast cancer plasticity through control of cellular identity and provides rationale for combining EZH2 inhibitors with endocrine therapies to improve outcomes in HER2+ breast cancer.

overall_design: Single-nucleus RNA sequencing (snRNA-seq) of wild-type EIC/EZH2 tumor cells and EIC/EZH2 knockout tumor cells collected from mice at endpoint; two biological replicates per group.

first: Linshan

last: Liu

first: Ellie

last: Massey

first: Dongmei

last: Zuo

first: Alain

last: Pacis

first: Mert

last: Demirdizen

first: Jessica

last: Cinkornpumin

first: Yu

last: Gu

first: Elizabeth

last: Podleszanski

first: Hailey

last: Proud

first: Virginie

last: Sanguin-Gendreau

first: Vasilios

last: Papavasiliou

first: Zhengze

last: Jiang

first: Harvey W.

last: Smith

last: Pastor

last: Ceppi

first: William J.


title: Regulated TRESLIN-MTBP loading governs initiation zones and replication timing in human DNA replication [RNA-Seq]

status: Public on Oct 27 2025

city: Mishima

first: Masato

last: Kanemaki

state: Shizuoka

address: Yata 1111

department: Department of Chromosome Science

institute: National Institute of Genetics

summary: Replication origins in human cells form clusters ranging from tens to hundreds of kilobases called initiation zones (IZs), typically located in intergenic regions between active genes. On a larger megabase scale, chromosomes replicate in a temporally defined replication timing (RT) pattern, where euchromatic regions replicate early, and heterochromatic regions replicate late. Although the stochastic model of IZ firing with a temporally regulated limiting factor can explain RT formation, this limiting factor in human cells remains unclear. To investigate the relationship between IZ and RT, we mapped the temporal firing pattern of IZs and examined the genome-wide distributions of replication licensing and firing factors in human cells. We identified TRESLIN-MTBP as the key limiting firing factor for replication initiation. Its loading onto phosphorylated MCM2–7 double hexamer (MCM-DH) is controlled by the opposing phosphorylation events on MCM-DH by Dbf4-dependent kinase and RIF1-Protein Phosphatase 1, which ultimately determine IZs and establish RT.

overall_design: RNA-seq were conducted using control HCT116 (LIG1/3-mAID2) and RIF1-KO HCT116 cells.


title: dHyperCas12a enables multiplexed CRISPRi screens

city: Durham

first: Schuyler

last: Melore

state: North Carolina

address: 101 Science Dr

institute: Duke University

summary: Interactions between multiple genes or cis-regulatory elements (CREs) underlie a wide range of biological processes in both health and disease. Here, we combine a hyper-efficient version of Lachnospiraceae bacterium dCas12a (dHyperLbCas12a) with RNA Polymerase II expression of long CRISPR RNA (crRNA) arrays to enable efficient highly-multiplexed epigenome editing. We demonstrate that the dCas12a system is highly effective for high-throughput screens. We use four different dCas12a repressors and a ~900-member library of crRNA arrays containing four crRNAs each to target the promoters of essential genes or cell surface negative controls. This fitness screen allows us to compare the activity of different dCas12a repressors across many genomic loci.

overall_design:
To perform a combinatorial screen at the PER1 locus, we created two crRNA array plasmid libraries, with each construct containing six crRNAs and a unique barcode. The PER1-targeting library contains ~9,000 crRNA arrays and the Non-targteing library contains ~10,000 crRNA arrays. Each plasmid library was sequenced twice. These libraries were then transduced into cells at low MOI and selected with puromycin for ten days. On day ten they were rreated with different concentrations of dexamethasone, and sorted on PER1 expression. Top and bottom 12% PER1-expressing cells were sorted and sequenced, as well as bulk unsorted cells (Input).
To perform a fitness screen in A549 cells, we created two crRNA array plasmid libraries, containing the same spacers but either the As or Lb Cas12a direct repeat sequence, with each array construct containing four crRNAs. Each library contained ~900 crRNA arrays. These libraries were then transduced into A549 cells that stably express either dHyperLbCas12a-KRAB, dHyperLbCas12a-4xSID, dEnAsCas12a-KRAB, or dEnAsCas12a-4xSID repressors at low MOI (~0.2) and selected with puromycin. Three independent transductions were performed for each repressor cell line. Cells were passaged for three weeks post-transduction and cell pellets were collected at days 5, 7, 14, and 21 (post-transduction). crRNA array sequences were amplified from these cell pellets as well as the plasmid libraries and sequenced on the NextSeq2000.

first: Timothy

last: Reddy

first: Marisa

last: Hamilton

first: Christian

middle: D

last: McRoberts Amador

first: Charles

last: Gersbach


title: Fibroblast-Derived Thrombospondin 2 Shapes the Immune-Exclusionary Environment at Invasive Fronts in Colorectal Cancer [RNA-seq_Mouse_Tumor]

first: Kosuke

last: Iwane

overall_design: RNA-seq profiling of bulk-tumors derived from orthotopic implanted mouse tumor organoids (MTOs) harboring mutations in Apc, Trp53, Kras, and Tgfbr2 in the rectum of wild-type (WT) and Thbs2KO mice

first: Yuki

last: Nakanishi

last: Muta


title: Fibroblast Derived Thrombospondin-2 Shapes the Immune-Exclusionary Environment at Invasive Fronts in Colorectal Cancer [RNA-seq_Mouse_CAF]

overall_design: RNA-seq profiling of CAFs isolated from tumors derived from orthotopic implanted mouse tumor organoids (MTOs) in the rectum of wild-type (WT) and Thbs2KO mice


title: Single cell transcriptomes of genetic landscape from actinic keratosis to cutaneous squamous cell carcinoma

first: Tao

last: Xu

state: Shanghai

address: Fengyang road

department: dermatology

institute: Changzheng hospital

summary: Here, we performed scRNA-seq to compare the transcriptomes of individual cells from three groups: (1) healthy sun-exposed skin; (2) AK samples; (3) cSCC samples. A total of 81792 cells from 8 AK samples, 3 cSCC samples and 3 control skin tissue were characterized, which comprising representatives from each of the major dermal cell types. Our results demonstrate the heterogeneity within tissues/patients and corroborated the effect of the tumor environment during carcinogenesis, especially immune cell populations. Additionally, we identified a list of gene expression changes that affected several known cancerous pathways, with potential evolution trajectory from a subset of AK premalignant cells to cSCC cells. Our findings will improve current understanding about the mechanism of AK-cSCC progression, and are potentially valuable in providing novel precautionary/ therapeutic markers.

overall_design: Single-cell sequencing has been performed on three kinds of human skin samples: normal sun-exposed skin, actinic keratosis and cutaneous squamous cell carcinoma samples.

first: Chen

last: Jianghan

first: Wang

last: Zhongzhi

first: Xu

last: Tao

first: Li

last: Shengli


title: Regulated TRESLIN-MTBP loading governs initiation zones and replication timing in human DNA replication [IP-seq]

overall_design: TRESLIN-IP was performed using a cell line expressing 3xFLAG-TRESLIN and GINS4-mAID2. Cells were synchronized with nocodazole and released into early S-phase. 5-Ph-IAA or DDKi was added to the culture medium 2 hours after nocodazole release. A control experiment was conducted using a cell line without any FLAG-tagging.


title: Regulated TRESLIN-MTBP loading governs initiation zones and replication timing in human DNA replication [LD-OK-seq]

overall_design: Ligase-depleted Okazaki-sequencing (LD-OK-seq) was performed using HCT116 cells. LD-OK-seq experiments were conducted under both asynchronous and synchronous conditions. Synchronous LD-OK-seq was carried out at six time points across the S phase. The same LD-OK-seq experiments were also performed using HCT116 cells with RIF1 knockout (RIF1-KO). Additionally, RIF1-KO cells with reintroduction of either wild-type RIF1 (WT-RIF1) or a RIF1-ppC mutant were used. Furthermore, cells overexpressing TRESLIN-MTBP were also subjected to LD-OK-seq.


title: Effect of nucleolin-binding aptamer AS1411 on gene expression in 3T3 cells

city: Tallinn

first: Indrek

last: Koppel

address: Akadeemia tee 15-241

department: Department of Chemistry and Biotechnology

country: Estonia

institute: Tallinn University of Technology

summary: AS1411 is a G-rich DNA aptamer that targets the multifunctional RNA-binding protein nucleolin. AS1411 has both antiproliferative and cell size-regulating activities and has been evaluated for clinical utility, reaching phase II trials as an anticancer agent. The mechanisms underlying the different activities of AS1411 are not completely understood and broad characterization of its molecular effects is lacking. Here, we used a multi-omics approach to profile transcriptome, proteome and lipidome changes in AS1411-treated NIH-3T3 cells, which increase in size in response to the aptamer. We found that AS1411 caused downregulation of cholesterol biosynthesis pathway enzymes at both mRNA and protein levels, without an accompanying drop in cellular cholesterol levels. In addition, AS1411 induced changes in several lipid classes, including increases in phospatidylethanolamine levels. Thus, nucleolin regulates lipid biosynthesis and homeostasis, potentially underlying its roles in cell proliferation and size control.

overall_design: NIH-3T3 cells were treated with 10 µM nucleolin-binding aptamer AS1411 (AS) or 10 µM control aptamer (CTR) for 24-48h and profiled gene expression changes using bulk RNA-seq


title: Effects of Normoxia, Hypoxia, Oscillatory Hypoxia, and Lactate on Wild-Type, NOTCH1-Knockdown, and TP53-Knockdown MDA-MB-231 Cells

city: Farmington

first: Xihua

last: Qiu

state: CT

address: 263 Farmington Ave

department: Biomedical Engineering

institute: University of Connecticut

summary: Wild-type, NOTCH1-knockdown, and TP53-knockdown MDA-MB-231 cells were cultured under normoxia, hypoxia, oscillatory hypoxia, and lactate treatment, and subjected to RNA sequencing to assess transcriptional changes.

overall_design: Three replicates were collected for each condition (normoxia, hypoxia, oscillatory hypoxia, and lactate treatment) in wild-type, NOTCH1-knockdown, and TP53-knockdown MDA-MB-231 cells.

last: Kshitiz

first: Liu

last: Yamin

first: Suhail

last: Yasir

first: Qiu

last: Xihua


title: CRISPR-free RNA Base Editing Mediated PTC-readthrough Restores Hearing in Humanized Mice with Otof Nonsense Mutation [RNA-seq]

city: Beijing

first: Wenqing

last: Liu

email: puyulwq@163.com, liuwq21@gamils.com

address: No. 5 Summer Palace Road, Haidian District, Beijing

institute: Peking University

summary: Today, the gene editing for hereditary deafness is becoming a promising field with global interest. Among them, AAV-mediated otoferlin overexpression is undoubtedly the most successful representative of deaf-related gene therapy. However, it remains challenging to realize physiological, endogenous pattern of otoferlin expression. Here, we firstly generated a humanized homology Otof c.1315C>T (p.R439X), equivalent to OTOF c.1273C>T (p.R425X) identified in human with profound hearing loss, nonsense mutation-caused deaf mice model. We then delivered the ‘RESTART v3’ system, which is a CRISPR-free RNA base editor for nonsense mutation suppression, into the cochlea of the mice model. We accomplished a physiological manner of otoferlin expression; moreover, the edited premature termination codon is precisely reversed back to the original amino acid. Using multiple assays to estimate hearing restoration, we identified a significant reduced thresholds of auditory brain response (ABR) and statistical enhanced amplitudes of behavioral auditory startle reflex (ASR) in the treated mice with the RNA editing system. Thus, our study presented a successful CRISPR-free RNA editing approach to significantly restore hereditary deafness carrying humanized Otof c.1315C>T (p.R439X) non-sense mutation, providing a great promise for future clinical translation.

overall_design: we examined the global modification level of cochlear tissues with or without RESTART treatment to evaluate the off-target events.


title: CRISPR-free RNA Base Editing Mediated PTC-readthrough Restores Hearing in Humanized Mice with Otof Nonsense Mutation [PRAISE]


title: Loss of METTL3 potentiates transposable element expression and drives inflammation-induced cell plasticity in the mammary epithelium

city: Boston

first: Xintao

state: MA

address: 440 brookline ave

institute: Dana Faber Cancer Institute

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

overall_design: Refer to individual Series


title: Off-Target RNA editing induced by RECODE in Mouse Quadratus Femoris Muscle

status: Public on Oct 26 2025

city: Fukuoka City

first: Soichi

last: Ozaki

state: Fukuoka

address: West Zone 5 #430, Kyushu University, 744 Motooka, Nishi-ku,

institute: EditForce, Inc.

summary: Programmable guide-RNA-dependent cytidine deaminase tools to convert cytidine-to-uridine (C-to-U) have limitations such as low editing efficiency, limited targetable sequence flexibility, and off-target RNA editing. Here, we report the editing activity of a novel guide-free C-to-U editing tool, named RECODE, based on RNA-binding pentatricopeptide repeat proteins. We show that RECODE, delivered via AAV, is functional in mice, demonstrating high editing efficiency and low off-target effects in quadratus femoris, a skeletal muscle. These results suggest its therapeutic potential for various diseases.

overall_design: RNA-seq to identify global C-to-U substitution events induced by RECODE-WW[F75F] and RECODE-PG[I83I] in the transcriptome of mouse quadratus femoris two months after infection.


title: C-to-U RNA editing with RECODE in human cells

summary: Guide-RNA-dependent cytidine deaminase tools to convert cytidine-to-uridine (C-to-U) have limitations such as low editing efficiency, limited targetable sequence flexibility, and off-target RNA editing. Here, we report the editing efficiency in HEK293T human cells of a novel guide-free C-to-U editing tool, named RECODE, based on RNA-binding pentatricopeptide repeat proteins naturally fused to a C-terminal DYW cytidine deaminase domain. The RECODE specificity domain was engineered to enable retargeting, while its length and sequence were optimized to reduce off-target effects. Further optimization of the C-terminal catalytic region increased both the editing activity and the translation of the edited RNA. The programmability, high editing efficiency, reduced neighboring nucleotide preference and gRNA-free design establish the RECODE technology as a versatile platform with potential applications beyond cellular systems, such as therapeutic approaches for repairing disease-causing mutations and modifying protein functions to enable novel treatments.

overall_design: RNA-seq to identify global C-to-U substitution events induced by RECODE or RESCUE-S, 48 hours after transfection.


title: Regulated TRESLIN-MTBP loading governs initiation zones and replication timing in human DNA replication [ChIP-Seq]

first: Masato

last: Kanemaki

overall_design: Proteins of interest were CRISPR-edited and tagged with 3xFLAG. All ChIP-seq experiments were conducted using anti-FLAG M2 antibody. Control experiments were performed using cell line without any FLAG-tagged proteins. Cells with different genetic backgrounds were used to explore target enrichments at different conditions.


title: CRISPR-free RNA Base Editing Mediated PTC-readthrough Restores Hearing in Humanized Mice with Otof Nonsense Mutation [TargetSeq]

sample_organism:
Homo sapiens
Mus

platform_organism:
Homo sapiens
Mus

overall_design: we examined the modification level of the PTC sites in HEK293T cells or cochlear tissues with or without RESTART treatment to evaluate the eidting efficiency.


title: MIF Nuclease Inhibition Protects CNS Neurons following Inflammation

status: Public on Oct 24 2025

city: Baltimore

first: Matthew

last: Smith

state: MD

address: 600 N Wolfe Street

department: Neurology

institute: Johns Hopkins University

summary: In its early phases, multiple sclerosis (MS) is characterized by relapses mediated by immune cell infiltration into the central nervous system, which can mostly be managed with existing therapies. However, there is concomitant axonal injury and neuronal loss associated with these exacerbations which gradually accumulate and cause worsening of disability. This neurodegenerative pathology is not directly targeted by existing therapies. The precise mechanism(s) of cell death that neurons undergo in MS remains unclear. Here we show that parthanatos, a recently described caspase-independent, DNA damage-induced cell death program contributes to neuron death in a mouse model of autoimmune neuroinflammation, experimental autoimmune encephalomyelitis (EAE). We show that DNA damage increases in neurons during EAE, and that they are progressively lost over the disease duration. Furthermore, at early timepoints the inflamed neurons express markers of parthanatos, including accumulation of cytoplasmic poly-ADP-ribose (PAR) and nuclear macrophage migration inhibitory factor (MIF). Genetic or pharmacologic blockade of the final step in parthanatos, MIF nuclease, reduces neuron loss and disease severity. Transcriptomic characterization of these neurons reveals parthanatos-dependent differences in response to EAE. Together, this work establishes parthanatos as a key mechanism of neuron cell death during neuroinflammation.

overall_design: Mice with a homozygous point mutation neutralizing MIF nuclease activity (MIF-E22Q) as well as wild type controls were immunized with MOG35-55 to induce experimental autoimmune encephalomyelitis (EAE). At day 14 lumbar spines were collected from WT EAE (n=3), MIF-E22Q EAE (n=3), WT CFA controls (no mog peptide) (n=2), and MIF-E22Q CFA controls (n=2). Nuclei were isolated and subjected to probe based single nucleus transcriptomics.

first: Sachin

middle: P

last: Gadani

first: Jackson

middle: W

last: Mace

first: Peter

last: Calabresi


title: Single nuclei transcriptomics from lumbar spinal cord of EAE mice treated with MIF nuclease inhibitor PAANIB1

summary: Central nervous system inflammation is implicated in neurodegeneration across several disorders, including multiple sclerosis (MS). While marked therapeutic progress has been made through the suppression of immune cell trafficking and function, primary neuroprotection in MS remains elusive. This, in part, is due to an incomplete understanding of the molecular signaling pathways involved in immune-mediated neuronal death. Here, we show that parthanatos, a recently described caspase-independent and DNA damage-induced cell death program, contributes to neuron death in the experimental autoimmune encephalomyelitis (EAE) mouse model of autoimmune neuroinflammation. We revealed that DNA damage increases in neurons during EAE, and that neurons are progressively lost over the disease course. Neurons in affected areas display intercellular hallmarks of the parthanatos cascade. Genetic or pharmacologic blockade of the final step in parthanatos, genomic fragmentation by MIF nuclease, reduces neuron loss and disease severity. Transcriptomic characterization of these neurons reveals parthanatos-dependent differences in response to EAE. Together, this work establishes parthanatos as a key mechanism of neuron cell death during neuroinflammation.

overall_design: 16 wild type C57BL6J mice were treated with either MIF-nuclease inhibitor PAANIB1 (n=8) or vehicle control (n=8) daily starting 2 days prior to immunization with emulsion. Mice were immunized with emulsion containing either MOG35-55 peptide (to induce Experimental Autoimmune Encephalomyelitis, EAE, n = 12) or no peptide (CFA only, n = 4). Mice were then euthanized 16 days post-immunization at which point paralysis had developed and lumbar spinal cords were dissected out, dissociated to single nuclei, then fixed and subjected to single-nucleus transcriptomics with 10X Genomics Flex (probe-based Fixed RNA profiling) technology. Final groups include EAE-PAANIB1 (n=6), EAE-Vehicle (n=6), CFA-PAANIB1 (n=2), and CFA-Vehicle (n=2).


title: MIF Nuclease Inhibition Protects CNS Neurons following Inflammation.


title: Perturbational single-cell RNA-seq time course of CD34+ HSPC megakaryocyte differentiation with CMO multiplexing (Days 0–7, 1 uM compounds)

status: Public on Oct 23 2025

city: Somerville

first: Mauricio

last: Cortes

address: 101 South Street

institute: Cellarity

summary: We profiled transcriptomic responses of a panel of small molecules during in vitro megakaryocyte (Mk) differentiation of CD34+ hematopoietic progenitors from a single donor. Cells were cultured in SFEM with TPO and CC100; an untreated Day 0 sample (unhashed) was collected, and additional samples on Days 1, 2, 5, and 7 were multiplexed with Cell Multiplexing Oligos (CMOs) and pooled 12 samples per library (~100k cells per well contributed), with duplicates for each compound distributed across libraries and plate-level positive/negative controls. Libraries were prepared with 10x Genomics Single Cell 3’ v3.1 and sequenced on Illumina NovaSeq 6000. FASTQs were generated with bcl2fastq and processed with Cell Ranger (STAR/GRCh38). Hashed data were QC-filtered, demultiplexed by Gaussian mixture modeling of CLR-normalized CMO counts, and further filtered to singlets; counts were then normalized to 10,000 per cell and log-transformed. For consistent annotation, the dataset was mapped to a hematopoiesis reference using harmony-corrected PCs and SymphonyPy KNN label transfer, with robustness assessed by distance/similarity metrics and marker expression. This submission provides Day 0 raw counts, Days 1–7 raw counts (pre-demultiplexing), demultiplexed singlet counts with well/treatment assignments, and normalized counts with transferred cell-type labels.

overall_design: Dual-mobilized peripheral blood CD34+ HSPCs were thawed and cultured; on Day 0 cells were plated for Mk differentiation (60,000 cells per well, round-bottom plates). Compounds were applied at a final concentration of 1 uM (DMSO controls included); treatments occurred on Days 0, 2, and 5. Sampling for scRNA-seq occurred at Day 0 (unhashed) and at Days 1, 2, 5, and 7 (hashed). For hashed time points, 12 CMO-tagged samples were pooled per library; each compound was sequenced in biological duplicate with duplicates distributed across libraries, and each library contained positive and negative controls alongside hit and non-hit compounds. Sequencing used 10x Genomics Single Cell 3’ v3.1 and Illumina NovaSeq 6000. Processing included bcl2fastq, Cell Ranger on GRCh38 (STAR), pre-demultiplexing QC (counts 5,000–80,000; mitochondrial fraction <20%), demultiplexing by Gaussian mixtures on CLR-normalized CMO counts (singlets retained), post-demultiplexing QC (<2,500 or >60,000 counts and <1,600 or >9,000 genes removed), per-cell normalization to 10,000 counts with log transform, and reference mapping plus label transfer with harmony and SymphonyPy.

first: Inna

last: Lipchina

first: Daniel

last: Burkhardt

first: Charlotte

last: Nesbitt

first: Samuel

last: Miller

first: Benjamin

last: DeMeo

first: Thomas

last: Pfefer

first: Doris

last: Fu


title: A novel subtype of astrocytes critical for HIV-associated pain pathogenesis

city: Stony Brook

first: Shao-Jun

last: Tang

state: New York

address: 101 Nicolls Road

institute: Renaissance School of Medicine at Stony Brook University

summary: Pathological pain is a frequent complication in HIV patients, yet the underlying mechanism remains elusive, and effective therapeutic targets have not been identified. Reactive astrocytes are specifically activated in the spinal dorsal horn (SDH) of HIV patients with pathological pain and required for HIV-associated pain development in mouse models. These findings suggest that reactive astrocytes play a crucial role in the pathogenesis of HIV-associated pain. However, due to the heterogeneity of reactive astrocytes, the pathogenic subtype remains unknown. In this study, we used single-nucleus RNA-seq (snRNA-seq) transcriptomic analysis to identify a novel subtype of HIV-pain-associated astrocytes (HIPAs) in the lumbar spinal cord of HIV-1 gp120 transgenic models and in the spinal cord of HIV patients. HIPAs express galectin 3 (Gal3) and exhibit transcriptomic signatures of phagocytosis and inflammation. We demonstrated that HIPAs phagocytose neuronal components and are associated with neuronal degeneration. We also found that knockout (KO) of Gal3 in gp120 transgenic mice reduced the number of HIPAs. Furthermore, Gal3 KO inhibited the expression of mechanical allodynia and HIV pain-related pathogenic processes, including neuronal degeneration and neuroinflammation, in gp120 transgenic mice. Our data collectively suggest that HIPAs are a novel Gal3-expressing astrocytic subtype that plays a critical role in gp120-induced pathogenesis in the spinal pain neural circuit. Targeting HIPAs may provide a potential therapeutic strategy for treating HIV-associated pain.

overall_design: All cell types from the lumbar spine of wild-type, gp120Tg, gal3KO, and gp120Tg/gal3KO mice were isolated and analyzed using snRNAseq

first: Junying

last: Zheng

first: Michael

last: Spurgat

first: Subo

last: Yuan

first: Xin

last: Gelman


title: Monitoring rapid degradation of NANOG reveals UTP15 maintains pluripotency by regulating nascent transcripts

city: Guanzhou

first: dongmei

last: he

address: Yunpu Street

institute: University of Chinese Academy of Sciences

summary: Master transcription factors (MTFs) are key regulators in cell fate determination. However, an approach to profile MTF’s direct transcriptional targets together with their associated RNA-binding proteins (RBPs), is still lacking. Here, we applied 5-ethynyluridine RNA metabolic labelling and click chemistry to map the dynamics of the transcriptional targets and the RBPs interacting with the newly transcribed RNAs upon acute NANOG degradation in mouse embryonic stem cells (mESCs). We identified UTP15, a classic rRNA-biogenesis regulator, acts as a key activator of pluripotency-associated gene transcription independently of rRNA biogenesis. Importantly, NANOG-regulated transcription enhances UTP15 binding to transcription start sites (TSSs), associated with increased Pol II binding and more active transcription. Moreover, UTP15 promotes the assembly of Pol II biomolecular condensates, thereby potentially driving pluripotency gene transcription. Collectively, our study uncovers a NANOG-nascent transcript-UTP15 regulatory axis to activate pluripotency gene transcription, providing a distinct approach for studying MTF’s function during cell fate determination.

overall_design: To investigate the cooperative function NANOG/UTP15 in the regulation of pluripotency, we established NANOG-AID and UTP15-AID cell lines in which each target protein was allowed to be acute degradation.We then performed gene transcription profiling analysis using data obtained from nascent RNA-seq at different time points after target protein degradation.Comparative gene transcription profiling analysis of nascent RNA-seq data from NANOG-AID/UTP15-AID cells at different time points after target protein degradation

first: Mingqiang

last: Deng

first: Dongmei

last: He

first: Xiwei

last: Wang

first: Xichen

last: Bao


title: EZH2 directs breast cancer progression through the modulation of epithelial cellular plasticity [ChIP-Seq]

first: William

last: Muller

overall_design:
1) ChIP-seq was performed on wild-type EIC/EZH2 and EIC/EZH2 knockout tumor cells, collected at endpoint from mice; two biological replicates were included per group.
2) ChIP-seq was performed on SKBR3 cell lines treated with either DMSO or EPZ6438 for 7 days; two technical replicates were included per condition.

first: Linshan

last: Liu

first: Ellie

last: Massey

last: Zuo

first: Alain

last: Pacis

first: Mert

last: Demirdizen

first: Jessica

last: Cinkornpumin

first: Yu

last: Gu

first: Elizabeth

last: Podleszanski

first: Hailey

last: Proud

first: Virginie

last: Sanguin-Gendreau

first: Vasilios

last: Papavasiliou

first: Zhengze

last: Jiang

first: Harvey W.

last: Smith

last: Pastor

first: Paolo

last: Ceppi

first: William J.


first: dongmei

last: he

first: Mingqiang

last: Deng

first: Dongmei

last: He

first: Xiwei

last: Wang

last: Bao


title: The RNA-binding protein PRRC2B preserves 5' TOP mRNA during starvation to maintain ribosome biogenesis   during recovery

city: Rehovot

first: Tsviya

last: Olender

address: 234 Herzl St.

department: Molecular Genetics

country: Israel

institute: The Weizmann Institute

summary: PRRC2B is an intrinsically disordered RNA-binding protein that is part of the cell’s translation machinery. Here we show that PRRC2B has two alternatively spliced mRNA transcripts producing major long and minor short isoforms. Mass spectrometry-based interaction studies indicated that both isoforms associate with the 40S ribosomal subunit and translation initiation factors. Importantly, the long isoform also interacted with additional RNA-binding proteins through its unique Arg/Gly-rich region. Among these is LARP1, a regulator of 5' TOP mRNAs under conditions of mTOR inhibition. We discovered that like LARP1, PRRC2B is an important regulator of 5' TOP mRNA levels during starvation, particularly those encoding ribosomal proteins. Overall, our study elucidates a newly discovered function for PRRC2B as an RNA-binding protein that regulates ribosomal biogenesis, establishing it as a global regulator of translation in addition to its function in initiating specific target translation.

overall_design:
To invesigate the role of PRRC2B in TOP mRNA stabilty during starvation we first used CRISPR to reduce the levels of PRRC2B in HEK293T cells. We infected the cells with lentiviral particles carrying 2 guides targeting PRRC2B. As control we used non targeting guide rna.
We then replaced the medium of the cells to EBSS for 48hrs followed by total RNA extraction using a commercial kit. We then preformed gene profiling expression data based on 4 different biological repetitions

first: Nadav

last: Goldberg

first: Doron

last: Bril

first: Miriam

last: Eisenstein

first: Alon

last: Savidor

first: Shani

last: Bialik

first: Shmuel

last: Pietrokovsky

first: Adi

last: Kimchi


title: Monitoring rapid degradation of NANOG reveals UTP15 maintains pluripotency by regulating nascent transcripts [RNA-seq]

first: Xichen


title: Dominant intragraft plasma cells targeting bilirubin implicate local heme catabolism in human cardiac allograft vasculopathy

city: New York

first: Sarah

middle: B

last: See

address: 1300 York Ave

institute: WCM

summary: Cardiac allograft vasculopathy (CAV) is invariably associated with immune infiltrates around affected coronary arteries, including antibody-producing plasma cells (PC). We used single-cell-RNA-sequencing and IGHV profiling to characterize these infiltrating PC. We then generated 37 recombinant monoclonal antibodies (mAb) using rearranged immunoglobulin gene sequences from dominant intragraft PC clones as well as 24 control mab from peripheral blood PC. Unexpectedly, a majority (21/37) of mAb derived from intragraft PC, but none of the control mAb derived from blood PC, reacted to bilirubin, a by-product of heme degradation. Furthermore, we observed the deposition of bilirubin within lymphocytic aggregates of cardiac grafts with CAV but not in healthy heart tissue. Bilirubin also accumulated in the cytoplasm and the nuclei of smooth muscle cells in the tunica media of coronary arteries with CAV lesions. Lastly, expression of heme-oxygenase-1 and biliverdin reductases in graft-infiltrating macrophages as well as presence of Fe2+ ion in the media of arteries with hyperplasia further supported the implication of heme catabolism in CAV. Collectively, our findings suggest a key role for bilirubin in CAV. The enrichment of PC clones reactive to this metabolite within graft infiltrates indicates that it acts as a prominent target of local antibody responses.

overall_design: Cardiac tissue from explanted hearts with CAV were collected, dissociated and sorted for scRNA-seq profiling

first: Talita

last: Aguiar

first: Max

last: Dietzel

first: Mattea

last: Ausmeier

first: Hang

middle: T

last: Nguyen

first: Shunya

last: Mashiko

first: Laura

last: Donadeu-Casassas

first: Hector

last: Cordero

first: Poulomi

last: Roy

first: Lorea

last: Roson

first: Charles

last: Marboe

first: Matthias

last: Szabolcs

first: Maryjane

last: Farr

first: Jose

last: González-Costello

first: Aleix

last: Olivella

first: Yoshi

last: Naka

first: Koji

last: Takeda

first: Rodica

last: Vasilescu

first: Kevin

last: Clerkin

first: Gilles

last: Benichou

first: Joren

last: Madsen

first: Rodney

middle: G

last: King

first: Oriol

last: Bestard

first: Evan

last: Kransdorf

first: Emmanuel

last: Zorn


title: CHAMP1 is an essential regulator for human myoblast fusion and muscle development

city: Athens

first: Pengpeng

last: Bi

state: GA

address: 315 Riverbend Rd

institute: University of Georgia

summary: Human skeletal muscle is composed of myofibers, each formed by the fusion of thousands of individual myoblasts. This process requires tightly regulated expression of muscle-specific fusogens, which confer both efficiency and muscle specificity to cell-cell fusion. Currently, the genetic regulation of this process remains poorly understood. Here, we identify CHAMP1, a chromosome alignment factor, as a surprising upstream activator of human myoblast fusion. Genetic deletion of CHAMP1 in human myoblasts led to profound fusion defects in vitro and in vivo following transplantation. Leveraging genomics approach and protein interaction assays, we uncovered a noncanonical role for CHAMP1 as a transcriptional cofactor for MyoD, directly activating the expression of the key muscle fusogen Myomaker. CHAMP1 mutations in human patients cause developmental delay, hypotonia, and muscle weakness, hallmarks of fusion myopathy that are also observed with Myomaker mutations. Importantly, CHAMP1 patient-derived cells exhibit severe fusion defects that can be fully rescued by restoring Myomaker expression. Structure and function analysis identified C2H2-type zinc finger motifs on CHAMP1 protein that are both necessary and sufficient for interaction with MyoD, activation of Myomaker transcription and human myoblast fusion. These findings highlight the muscle-autonomous role of CHAMP1 in muscle development and disease, and point to therapeutic avenues for treating muscle development defect caused by CHAMP1 mutations.

overall_design: RNA-Seq profile of CHAMP1 knock-out (KO) or isogenic rescue (RES) human myoblast at different stages, including myoblast in growth medium (GM), differentiate for 2 days (DM2d), differentiate for 6 days (DM6d).

first: Haifeng

last: Zhang

first: Min

last: Zhou

first: Zheng

first: Zhaoning

last: Wang


title: Structural mechanism of the Retron-Eco7 anti-phage defense system

city: Shinjuku-ku

first: Aa

middle: Haeruman

last: Azam

state: Tokyo

address: Toyama 1-23-1

department: Research Center for Therapeutic Drugs and Vaccines Development

institute: The National Institute of Infectious Diseases

type: Non-coding RNA profiling by high throughput sequencing

summary: Retrons are prokaryotic genetic elements involved in anti-phage defense and consist of a non-coding RNA, a reverse transcriptase (RT), and various effector proteins. Retron-Eco7 (previously known as Retron-Ec78) from Escherichia coli encodes two effector proteins (a PtuA ATPase and a PtuB nuclease) and degrades host tRNATyr upon phage infection, thereby protecting host cells against invading phages. However, its defense mechanism remains elusive. Here, we report the cryo-electron microscopy structures of the Retron-Eco7 complex, comprising the RT, multicopy single-stranded DNA (msDNA), PtuA, and PtuB. The Retron-Eco7 structure reveals that the RT–msDNA complex associates with two PtuA–PtuB complexes, potentially inhibiting their nuclease activity and suppressing bacterial growth arrest prior to phage infection. Furthermore, we found that a phage-encoded D15 nuclease acts as a trigger for the Retron-Eco7 system, cleaving the msDNA bound to the complex and facilitating the dissociation of PtuA–PtuB from RT–msDNA. Our data indicate that msDNA cleavage by D15 is the initial step required for the specific cleavage of host tRNATyr by the PtuA–PtuB nuclease, which leads to abortive infection. Overall, this study provides mechanistic insights into the Retron-Eco7 system and highlights the diversity of prokaryotic anti-phage defense mechanisms.

sample_organism: Escherichia coli str. K-12 substr. DH10B

overall_design: Overnight cultures of E. coli (DH10B) cells containing either the plasmid pBAD-PtuA–PtuB or the full set of retron-Eco7 (pLG008) were grown in 10 mL of LB medium until reaching an OD₆₀₀ of 0.3. The bacteria carrying pBAD-PtuA–PtuB were induced with 0.2% arabinose to promote PtuAB expression, whereas those containing pLG008 were infected with phage SP15 and cultured at 37°C with shaking at 200 rpm for either 1 hour or 20 minutes, respectively. Following incubation, the cultures were centrifuged at 6,000 × g for 5 minutes, and the pellets were washed twice with PBS buffer. Total RNA was extracted using a miRNA isolation kit (Qiagen) following the manufacturer’s instructions. Additionally, E. coli (DH10B) cells containing the Retron-Eco7 plasmid or an empty vector were infected with SP15 (MOI = 10) for 20 minutes, with uninfected cells serving as negative controls. The cells were then centrifuged at 10,000 × g for 10 minutes and washed twice with SM buffer. Total RNA was extracted using the miRNA isolation kit (Qiagen). The extracted RNAs were then submitted for tRNA-fragment sequencing.

first: Ishikawa

last: Junichiro

first: Yoneyama

last: Kanta

first: Azam

last: Aa Haeruman

first: Nagao

last: Asuteka

first: Mitsuda

last: Yoshihisa

first: Nakazaki

last: Ren

first: Kotaro

last: Chihara

first: Hiraizumi

last: Masahiro

first: Yamashita

last: Keitaro

first: Suzuki

last: Tsutomu

first: Kiga

last: Kotaro

first: Nishimasu

last: Hiroshi


title: Guanine- and cytosine-rich genes are actively transcribed at the nuclear Lmnb1 compartment

city: Cold Spring Harbor

first: Gayan

middle: Indhu

last: Balasooriya

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

summary: Chromatin organization in the mammalian cell nucleus plays a vital role in the regulation of gene expression. The lamina-associated domain at the inner nuclear membrane has been proposed to harbor heterochromatin, while the nuclear interior has been shown to contain most of the euchromatin. Here, we show that a sub-set of actively transcribing genes, marked by RNA Pol II pSer2, are associated with Lmnb1 at the inner nuclear envelop in mESCs and the number of genes proportionally increases upon in vitro differentiation of mESC to olfactory precursor cells. These nuclear periphery-associated actively transcribing genes primarily represent housekeeping genes, and their gene bodies are significantly enriched with guanine and cytosine compared to genes actively transcribed at the nuclear interior. We found the promoters of these gene’s to also be significantly enriched with guanine and to be predominantly regulated by zinc finger protein transcription factors. We provide evidence supporting the emerging notion that the Lmnb1 region is not solely transcriptionally silent.

overall_design: Lmnb1-associated actively transcribing gene in male mESCs and mESC derived OPCs immunoprecipitation by sequential ChIP assay (Lmnb1 and RNA Pol II pSer2) and DNA-sequencing.

middle: I

first: David

middle: L

last: Spector


title: Differential Gene Expression During CAR T Cells Activation

status: Public on Oct 22 2025

city: Shen Zhen

first: Rui

last: Li

address: SZ

institute: BME

summary: Mechanical force generation at the immunological synapse is a hallmark of CAR T cell cytotoxicity and a key determinant of functional potency. However, the underlying mechanobiological mechanisms remain poorly understood. Here, we real-time measured the mechanical allostasis of single CAR T cells involving spatiotemporal dynamics of synaptic force and cellular metabolic activity upon CD19 antigen activation, and revealed that the CAR T cell activation is governed by sophisticated mechano-energetic mechanisms. We identify a Piezo1–Ca²⁺–Wnt axis that integrates force transduction with actin remodeling and metabolic reprogramming. Notably, functional heterogeneity across CAR T cell products from different patients as well as with different designs and manufacturing protocols correlates with variation in this mechano-metabolic program. Our findings revealed the reciprocal relationship between mechanosensation and metabolic switch, thus providing a new framework for (pre-)clinical screening of CAR T cell functional state and engineering CAR T cells with enhanced mechanical fitness, energetic resilience, and therapeutic efficacy.

overall_design: cells were treated with either CD19, ICAM-1, CD3e , or CD28 before testing.

first: Li

last: Rui

first: Luu

last: Bao Ngoc


title: Chemotherapy-driven intestinal dysbiosis and microbial indole-3-propionic acid rewire bone marrow myelopoiesis to promote anti-metastatic immunity [16S rRNA-Seq]

city: Lausanne

first: Tania

last: Wyss

address: Rue du Bugnon 25A

country: Switzerland

institute: SIB Swiss Institute of Bioinformatics

summary: Chemotherapy induced intestinal mucositis drives microbial dysbiosis and IPA production.

overall_design: 16S rRNA gene sequencing of fecal samples from mice treated with vehicule or FO (5-FU + oxaliplatin) chemotherapy. Samples were collected 5 days post treatment.

first: Ludivine

last: Bersier

first: Tatiana

middle: V

last: Petrova


title: Fibroblast mechanoperception instructs pulmonary developmental and pattern specification gene expression programs [RNA-seq]

city: Charlottesville

first: Andrew

last: Miller

state: Virginia

address: 415 Lane Rd.

institute: University of Virginia

summary: Dysregulation of the cellular mechanisms that coordinate the interpretation and transduction of microenvironmental biophysical signals are a unifying feature of tissue remodeling pathologies such as fibrosis and cancer. While genomic regulation downstream of normal mechanotransduction (i.e. cases where cells sense soft and stiff appropriately) is well studied, significantly less is known about the consequences of abnormal mechanoperception and subsequent misinterpretation of the mechanical environment. Leveraging Thy-1 (a.k.a. CD90) loss as a model of impaired mechanoperception, we employed ATAC- and RNA-sequencing in parallel to characterize the changes in lung fibroblast genomic activity in response to a combination of substrate stiffness and culture time. Notably, we find perturbed mechanoperception elicits a near-complete shutdown of HOXA5, a transcription factor responsible for pattern specification and development in the nascent lung. In vitro investigation of HOXA5 expression reveals a potential mechanism connecting increased αv integrin signaling, cytoskeletal tension, and SRC kinase activity to HOXA5 silencing. These results establish novel links between integrin signaling and the expression dynamics of genes necessary for tissue formation and regeneration in the injured and/or developing lung, particularly HOXA5.

overall_design: RNA-sequencing of WT and CD90/Thy-1 CRISPR KO immortalized human lung fibroblasts cultured on 4kPa, 25kPa, and tissue culture plastic (TCP) substrates for periods of 24hr or 72hr. A 0-hr sample was collected from cell suspension as samples were seeded.

first: Ping

last: Hu

first: Rishi

last: Bhogaraju

first: Riley

last: Hannan

first: Daniel

last: Abebayehu

first: Mete

last: Civelek

first: Thomas

middle: H

last: Barker


title: Fibroblast mechanoperception instructs pulmonary developmental and pattern specification gene expression programs

overall_design: Refer to individual Series


title: Contribution of macrophage subsets to scarless skin regeneration in Xenopus laevis frogs

city: Washington DC

first: Leon

last: Grayfer

address: 800 22nd ST NW

department: Biological Sciences

institute: George Washington University

summary: Xenopus laevis juvenile frogs are uniquely capable of scarless skin regeneration, but the cellular and molecular mechanisms guiding this process remain incompletely understood. Macrophages are known as key regulators of wound healing, yet how their phenotypes shift over time and influence downstream regeneration in X. laevis has not been previously defined. It is well established that macrophage functions are imperative to mammalian wound healing. In vertebrate biology, macrophage polarization is dictated by two colony-stimulating factor-1 (CSF1) receptor ligands: CSF1 and interleukin-34 (IL34). While IL34 in mammals is critical to the development of epidermal macrophages known as Langerhans cells, the contribution of CSF1- and IL34-derived macrophages to skin wound repair remains unexplored. Pertinently, using the X. laevis model, previous work from our lab showed that CSF1- and IL34- macrophages are functionally distinct, formulating our hypothesis that these subsets play distinct roles during different phases of cutaneous wound repair. We therefore characterized full-thickness (epidermis and dermis) skin wounds in juvenile X. laevis during regeneration, analyzing transcript levels reflecting: M( infiltration (csf1r) and phenotype abundance (csf1 and il34), fibroblast activation (αSMA/acta2), and wound bed collagen composition (Picrosirius red staining). To assess the functional roles of macrophage phenotypes, we enriched wounds with recombinant X. laevis CSF1, IL34, or a vector control 3 days post-wounding (dpw) and analyzed wound responses at 7 and 14 dpw. Normal scarless regeneration in these juveniles demonstrated that macrophages transiently accumulated in the wound bed, peaking at 7–14 dpw. This coincided with elevated csf1 expression, which later declined as il34 levels rose. Fibroblast activation into myofibroblasts as well as collagen deposition followed this cytokine shift and restored collagen to pre-wound levels by 60 dpw. Subcutaneous IL34 enrichment at 3 dpw led to significantly increased αSMA expression at 7 and 14 dpw, a higher type I:III collagen ratio at 7 dpw, and suppression of inflammatory mediators coupled with enhancement of other, anti-inflammatory mediators at 7dpw. CSF1 enrichment had no significant effect on αSMA expression or subsequent collagen deposition, but did show a bias towards inflammatory mediators and the suppression of resolving and pro-reparative transcripts at 7 dpw. These findings suggest that early IL34 supplementation promotes a pro-regenerative macrophage phenotype that enhances myofibroblast activation and matrix remodeling while early CSF1 supplementation may contribute to prolonged inflammation and impaired tissue regeneration. Temporal modulation of macrophage-derived signals, particularly IL34, plays a critical role in directing scarless skin regeneration in X. laevis. These findings identify a conserved immunoregulatory axis with potential relevance to improving wound healing in non-regenerative species. Xenopus laevis juvenile frogs are uniquely capable of scarless skin regeneration, but the cellular and molecular mechanisms guiding this process remain incompletely understood. Macrophages are known as key regulators of wound healing, yet how their phenotypes shift over time and influence downstream regeneration in X. laevis has not been previously defined. It is well established that M( functions are imperative to mammalian wound healing. In vertebrate biology, M( polarization is dictated by two colony-stimulating factor-1 (CSF1) receptor ligands: CSF1 and interleukin-34 (IL34). While IL34 in mammals is critical to the development of epidermal M(s known as Langerhans cells, the contribution of CSF1- and IL34-derived macrophages to skin wound repair remains unexplored. Pertinently, using the X. laevis model, previous work from our lab showed that CSF1- and IL34- M(s are functionally distinct, formulating our hypothesis that these subsets play distinct roles during different phases of cutaneous wound repair. We therefore characterized full-thickness (epidermis and dermis) skin wounds in juvenile X. laevis during regeneration, analyzing transcript levels reflecting: macrophage infiltration (csf1r) and phenotype abundance (csf1 and il34), fibroblast activation (αSMA/acta2), and wound bed collagen composition (Picrosirius red staining). To assess the functional roles of macrophage phenotypes, we enriched wounds with recombinant X. laevis CSF1, IL34, or a vector control 3 days post-wounding (dpw) and analyzed wound responses at 7 and 14 dpw. Normal scarless regeneration in these juveniles demonstrated that macrophages transiently accumulated in the wound bed, peaking at 7–14 dpw. This coincided with elevated csf1 expression, which later declined as il34 levels rose. Fibroblast activation into myofibroblasts as well as collagen deposition followed this cytokine shift and restored collagen to pre-wound levels by 60 dpw. Subcutaneous IL34 enrichment at 3 dpw led to significantly increased αSMA expression at 7 and 14 dpw, a higher type I:III collagen ratio at 7 dpw, and suppression of inflammatory mediators coupled with enhancement of other, anti-inflammatory mediators at 7dpw. CSF1 enrichment had no significant effect on αSMA expression or subsequent collagen deposition, but did show a bias towards inflammatory mediators and the suppression of resolving and pro-reparative transcripts at 7 dpw. These findings suggest that early IL34 supplementation promotes a pro-regenerative M( phenotype that enhances myofibroblast activation and matrix remodeling while early CSF1 supplementation may contribute to prolonged inflammation and impaired tissue regeneration. Temporal modulation of macrophage-derived signals, particularly IL34, plays a critical role in directing scarless skin regeneration in X. laevis. These findings identify a conserved immunoregulatory axis with potential relevance to improving wound healing in non-regenerative species.

overall_design: RNA-seq profiling of recombinant control, csf1, or il34 enriched healing outbred X. laevis skin wounds 7 and 14 days post wounding.

first: Christina

last: Garvey Griffith

first: Kelsey

last: Hauser

first: Bradley

last: Abramson

first: Katharine

last: Jennings

first: Elissa

middle: R

last: Chapkin

first: Elizabeth

last: Jones

first: Anju

last: Duttargi


title: RNA sequencing profiling of circular RNA during during megakaryocyte maturation.

city: Chongqing

first: Huang

last: Wu

state: Chongqing

address: 10 Changjiang Access Road

department: Department of Blood Transfusion

institute: Daping Hospital, Army Medical University

summary: To profile the landscape of circRNAs during megakaryocyte differentiation, we conducted circRNA expression profiling analysis on day 6 and day 13.

overall_design: By day 6 and 13, CD34+ cells differentiated into mature MKs to extract total RNA. RiboMinus/RNaseR-treated RNA sequencing (RNA-seq) was performed. Totaol RNA from MK cultures at days 6 and 13, RiboMinus/RNaseR-treated RNA -seq were performed.


title: SELEX-seq of AP1 homodimer

city: Berlin

first: Jose

middle: M.

last: Muino

address: Max-Dohrn-Str. 8-10

country: Germany

institute: German Federal Institute for Risk Assessment

summary: These datasets represent the results of a SELEX-seq experiment to identify the DNA binding specificity of Arabidopsis thaliana AP1-AP1 dimers

overall_design: Starting from a set of DNA oligos with random sequence, 4 rounds of enrichment were done using the AP1 proteins

first: Peilin

last: Chen

middle: M

first: Cezary

last: Smaczniak

first: Kerstin

last: Kaufmann


title: Fibroblast mechanoperception instructs pulmonary developmental and pattern specification gene expression programs [ATAC-seq]

first: Andrew

last: Miller

overall_design: ATAC-sequencing of WT and CD90/Thy-1 CRISPR KO immortalized human lung fibroblasts cultured on 4kPa, 25kPa, and tissue culture plastic (TCP) substrates for periods of 24hr or 72hr. A 0-hr sample was collected from cell suspension as samples were seeded.

middle: E

first: Ping

last: Hu

first: Rishi

last: Bhogaraju

first: Riley

last: Hannan


title: the transcriptomic profiling of HCECs (PAI-2 knockout and control) exposed to PM2.5 for 3 hours

city: Hangzhou

first: Shengjie

last: Hao

address: 1 Xihu Avenue

institute: Zhejiang University

summary: We previously found that PAI-2 mediates long-term PM2.5 exposure-induced corneal damage in vivo and in vitro, while its role during subclinical stage remains unclear. In this study,we constructed PAI-2 knockout-human corneal epithelial cells (KO) and the negative control (NC).  Transcriptome analysis was performed in three groups: NC, PM2.5-exposed NC, KO and PM2.5-exposed KO. These analysis suggested cell-ECM interactions might play an important role in PAI-2-induced corneal injury upon PM2.5 exposure.

overall_design: PAI-2 KO and NC were exposed to PM2.5 for 3 hours and mRNA was isolated for RNA sequencing.

first: Ke

last: Yao

first: Qiuli

last: Fu


title: BRMS1L promotes chemotherapy sensitivity by inhibiting autophagy in breast cancer

status: Public on Oct 21 2025

city: Guangzhou

first: Shaohua

last: Qu

address: No. 613, Huangpu West Avenue, Tianhe District, Guangzhou, Guangdong, P.R. China

institute: Department of Breast Surgery, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou, China

summary: BRMS1L (Breast cancer metastasis suppressor 1 like), a component of Sin3A-histone deacetylase (HDAC) co-repressor complex, has been shown to provide an epigenetic regulation ofWnt signal pathway and act as a metastasis suppressor in breast cancer. However, the role of BRMS1L in the progression and chemosensitivity has not been explored. In the present study, we for the first time showed that reduced BRMS1L expression correlates with poor response to neoadjuvant chemotherapy and poor prognosis in patients with breast cancer. Additionally, chemoresistant breast cancer cells exhibited decreased BRMS1L expression and increased autophagy levels. Furthermore, ectopic expression of BRMS1L significantly enhanced chemotherapy sensitivity via inhibiting protective autophagy in breast cancer cells. In vivo, the experiments in nude mice showed that BRMS1L strengthened the chemotherapy effects on xenografts. Collectively, these results revealed that BRMS1L enhances chemotherapy sensitivity via inhibiting autophagy. Our findings uncover a novel role of BRMS1L in drug sensitivity and highlight the potential clinical application of BRMS1L in the treatment of breast cancer.

overall_design: RNA sequencing (RNA-seq) on MCF-7 and MCF-7/ADR cells

first: Yuan

last: Li

first: Dian

last: Zhang

first: Junhao

last: Zhao

first: Mei

last: Yang

first: Yiping

last: Wang

first: Peiyao

last: Lee


title: PROTON GRADIENT REGULATION 5 enables efficient C4 photosynthesis under fluctuating light

city: Melbourne

first: Russell

last: Woodford

state: Victoria

address: 25 Rainforest Walk, Monash University, Clayton

department: School of Biological Sciences

country: Australia

institute: Monash University

summary: PROTON GRADIENT REGULATION 5 (PGR5) plays a critical role in generating proton motive force across thylakoid membranes and supporting photoprotection under fluctuating light in C3 plants. It is proposed that this function is achieved by regulating cyclic electron flow around Photosystem I. During the evolutionary transition from C3 to C4 photosynthesis, PGR5 abundance in leaves has increased, coinciding with an enhancement in cyclic electron flow rate. To investigate the role of PGR5 in C4 photosynthesis and photoprotection, we generated Setaria viridis (a model C4 monocot) lines with null PGR5 alleles. We demonstrate that loss of PGR5 severely impairs the establishment of proton motive force, photosynthetic control, and energy-dependent non-photochemical quenching at high irradiances, leading to a loss of Photosystem I activity under light stress. Furthermore, plants lacking PGR5 exhibit drastically reduced growth and photosynthesis when grown under fluctuating daylight; however, they are less severely affected than C3  pgr5 mutants. This relative tolerance arises from the ability of S. viridis lacking PGR5 to maintain significant levels of photosynthetic control, in contrast to C3 mutants. Additionally, in the absence of PGR5 and qE, a slower-relaxing, zeaxanthin-dependent form of non-photochemical quenching supports survival under fluctuating light, albeit at the cost of reduced photochemical efficiency and assimilation. Our findings highlight the essential role of PGR5 in enabling efficient C4 photosynthesis under fluctuating light by regulating photosynthetic control and energy-dependent non-photochemical quenching. This study also uncovers the interplay between multiple photoprotective mechanisms safeguarding C4 photosynthesis under light stress.

overall_design: PolyA-enriched RNA-seq was performed on S. viridis leaf discs harvested from WT, null NdhO and null PGR5 plants. Plants were germinated in 0.5 L pots with seed raising mix (Debco, Tyabb, Australia) containing 5 g L-1 of Osmocote fertiliser (Scotts, Bella Vista, Australia). Seeds were covered with inverted plastic cups to maintain humidity, with the cups removed one week after germination. Plants were grown in a controlled-environment chamber with a 16 h light/8 h dark photoperiod, an irradiance of 380 µmol m−2 s−1, ambient CO2, 28°C day, 22°C night and 60% humidity. The position of WT and edited plants within the chamber was blocked and randomised to minimise positional effects. Plants were analysed 3-4 weeks after sowing, with the youngest fully expanded leaves used for analysis. WT S. viridis plants were used as a control for all experiments.

first: Jacinta

last: Watkins

first: Marten

last: Moore

first: Samuel

middle: J

last: Nix

first: Suyan

last: Yee

first: Kai

middle: X

last: Chan

first: Barry

last: Pogson

first: Susanne

last: von Caemmerer

first: Robert

last: Furbank

first: Maria

last: Ermakova


title: Multiomic analyses on the contribution of transposable elements to the cis-regulatory landscape of different types of immune cells[ChIP-seq]

city: Yangzhou

first: Cui

last: Du

state: Jiangsu

address: NO.88 University South Road

institute: Yangzhou University

summary: Transposable elements (TEs) are key contributors to genetic novelty. Despite increasing evidence of their importance, their roles in shaping the regulatory landscape of different immune cell populations remain largely unclear. Using single-cell multiome from human peripheral blood mononuclear cells, we annotated the cell-specific cis-regulatory elements for diverse immune cells and identified a highly cell-specific signature regarding overrepresented TE families. Focusing on monocytes that bear fast-evolving transcriptomes, we found that high proportions of their enhancers are TE-derived and bound by multiple pioneer transcription factors. Among them, we confirmed that the core myeloid regulator SPI1 can bind and regulate hundreds of TE-derived enhancers, which affect the expression of adjacent immune genes. Interspecies comparison reveals that non-conserved monocyte enhancers are frequently generated by lineage-specific TE insertions, and correlate with the evolved gene expression between human and mouse. Our study highlights the importance of TEs in shaping the regulatory landscape of diverse immune cells.

overall_design: Two biological replicates were used per sample of siSPI1(SPI1 knockdown) ChIP-seq for H3K27ac in THP-1 cells.

first: Hairui

last: Fan

first: Wenbin

last: Bao

first: Ming-an

last: Sun


title: Chemotherapy-driven intestinal dysbiosis and microbial indole-3-propionic acid rewire bone marrow myelopoiesis to promote anti-metastatic immunity

first: Tania

last: Wyss

summary: We investigated how microbial derived product influence myeloid cell differentiation in vitro.

overall_design: To assess the effect of indole-3-propionic acid (IPA) on MDSC generation, we exposed bone marrow cells to MDSC-inducing media in the presence of vehicle, 10uM IPA or 50uM IPA.

first: Ludivine

last: Bersier

first: Tatiana

last: Petrova


title: Multiomic analyses on the contribution of transposable elements to the cis-regulatory landscape of different types of immune cells[RNA-seq]

overall_design: Three biological replicates were used per sample of siSPI1(SPI1 knockdown) RNA-seq in THP-1 cells.


title: Regulatory T cells in skin utilize the Cxcr4-Cxcl12 axis to promote hair follicle regeneration

city: San Francisco

first: Jarish

last: Cohen

state: CA

address: 513 Parnassus Ave, HSW12 Room 1201B

department: Dermatology

institute: University of California, San Francisco

summary: We have employed a fixed single nuclear RNA sequencing using the 10X Genomics FLEX assay to characterize the cellular constituents in healthy human scalp skin. Hair follicles are microanatomic niches that attract immune cells. Therefore, we generated this dataset to gain further insight into the chemokines kerotinocytes in skin express, and expression their cognate receptors on skin lymphocytes.

overall_design: Two formalin-fixed paraffin-embedded healthy human scalp skin specimens were retrieved, and underwent tissue microtomy to generate three 50 micron thick tissue scrolls. The thick tissue scrolls underwent deparaffinization, rehydration, and mechanical and enzymatic dissocation using a Miltenyi GentleMacs Octodissociator with heaters. The resulting suspension was passed through a 30 micron strainer. Nuclei were counted using a Cellaca cell counter and submitted for standard 10X Genomics Flex assay.

first: Michael

last: Rosenblum


title: Immunoresponsive gene 1 like/itaconate axis promotes neuromast size via metabolic reprogramming to induce Yap signaling

city: Nantong City

first: Xin

last: Wang

state: Jiangsu Province

address: No.9, Seyuan Road

institute: Nantong University

summary: The organ size control and tissue homeostasis maintenance are vital in the formation of vertebrate sensory organs, which are tightly regulated. Here, we identify a metabolic regulatory axis, Irg1l, a zebrafish homologue of the mammalian mitochondrial enzyme immunoresponsive gene 1, and its product itaconate in neuromast development. It was demonstrated that irg1l was found to be highly and specifically expressed in supporting cells of developing neuromast, and decreased along the hair cell trajectory. Loss-of-function of irg1l caused neuromast size reduction and auditory dysfunction. Conversely, gain-of-function of irg1l increased the neuromast size. We found that excessive proliferation of supporting cells results in the larger neuromast. Notably, 4-octyl itaconate (4-OI), an itaconate derivative, recapitulates the phenotype of irg1l overexpression and increases the neuromast size. Mechanistically, Irg1l and itaconate induce succinate accumulation, which could lead to disruptions of the TCA cycle. It was confirmed by transcriptome sequencing and metabolic pathway inhibitor treatment. Inhibiting and activating YAP, respectively, can rescue the up- or down-regulation of Irg1l/itaconate-induced phenotypes, suggesting that YAP signaling acts downstream of metabolic reprograming induced by irg1l/ITA axis. Collectively, these results provide a novel insight into the role of metabolic signaling and its transduction during sensory organ development. Targeting this metabolic regulatory pathway within supporting cells may prove useful in further regulating sensory hair cell development and regeneration.

overall_design: This experimental study aimed to investigate a role of Irg1l/itaconate axis in zebrafish neuromast development using RNA-seq analysis. At 5dpf, Larvae treated with 4-octyl itaconate was preformed to subsequent transcriptomic analysis.

first: Rui-jun

last: Shi

first: Yu-Qing

last: Xiang

first: Dong

last: Liu


title: Gene expression of TPO-stimulated HSC-derived murine Evi1+AML

city: Basel

first: Jonathan

last: Seguin

address: Spitalstrasse 33

institute: UKBB-DBM

summary: To characterize the cellular origin of ecotropic virus integration site 1 (EVI1)-expressing aggressive KMT2A-rearranged acute myeloid leukaemia (AML), we integrated an Evi1-GFP reporter allele in the inducible iKMT2A-MLLT3 mouse model. Single injection of thrombopoietin (TPO) was done to observe the effects on Evi1+ haematopoietic stem cells (HSC) and its consequences on AML. To better characterized the effects of Evi1 and TPO, gene expression was determined by RNA sequencing from HSC-derived iKMT2A-MLLT3-driven AML expressing different levels of Evi1 (GFP+ , GFP- and bulk fractions) treated or not with TPO.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HSC-derived murine AML with or without Evi1+ (GFP+) expression treated or not with TPO

first: Hugues-Etienne

last: Chatel-Soulet

first: Athimed

last: El Taher

first: Juerg

last: Schwaller


title: Next Generation Sequencing Analysis of control and siHNRNPM treated RKO cells Transcriptomes

status: Public on Oct 20 2025

city: Nanjing

first: Weizhen

address: No.138,Xianlin Avenue,Qixia District

institute: Nanjing University Of Chinese Medicine

summary: We treated the RKO cells with siHNRNPM or control siRNA for 48 hours.Then, we extracted RNAs and performed next generation sequencing. By comparing sequencing data from control and siHNRNPM samples, we profiled the alternative splicing events and gene expression regulated by HNRNPM in CRC.

overall_design: RKO cells mRNA profiles of control and siHNRNPM were generated by deep sequencing, using HiSeq X(Illumina, San Diego, CA).

first: Linlin

last: Chen


title: Heritable changes in chromatin contacts linked to transgenerational obesity [ChIP-seq]

status: Public on Oct 17 2025

city: Charlestown

first: Toshihiro

last: Shioda

address: Building 149 - 7th Floor, 13th Street

department: Center for Cancer Research

institute: MGH Cancer Center

summary: Burgeoning evidence demonstrates that responses to environmental exposures can be transmitted to subsequent generations through the germline without DNA mutations. This is controversial because underlying mechanisms remain to be identified. Therefore, understanding how effects of environmental exposures are transmitted to unexposed generations without DNA mutations is a fundamental unanswered question in biology. Here, we used an established murine model of transgenerational obesity to show that direct or ancestral exposure to the obesogen tributyltin (TBT) elicited persistent changes in topologically associating domains (TADs) in primordial germ cells (PGCs) isolated from embryos of exposed and subsequent unexposed generations. New TAD boundaries were formed within the Ide gene encoding insulin degrading enzyme in the exposed PGCs, then stably maintained in PGCs of the subsequent (unexposed) two generations. Concomitantly, Ide mRNA expression was decreased in livers of male descendants from the exposed dams. These animals were hyperinsulinemic and hyperglycemic, phenocopying Ide-deficient mice that are predisposed to adult-onset obesity. Creation of new TAD boundaries in PGCs, suppression of hepatic Ide mRNA, increased fat mass, hyperinsulinemia and hyperglycemia were male-specific. Our results provide a plausible molecular mechanism underlying transmission of the transgenerational predisposition to obesity caused by gestational exposure to an environmental obesogen. They also provide an entry point for future studies aimed at understanding how environmental exposures alter chromatin structure to influence physiology across multiple generations in mammals.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for CTCF in adult male mouse liver.

first: Shioda

last: Toshihiro

first: Chang

middle: C

last: Richard

first: Blumberg

last: Bruce


title: Integrative analysis reveals synergistic regulation of Sp7 by BRD9 and Wnt/β-catenin signaling during osteogenic differentiation

status: Public on Oct 16 2025

city: 苏州市

first: lyp

last: l

address: 斜塘街道

institute: 苏州大学

summary: Osteoporosis is a skeletal disorder involving low bone mineral density (BMD) and elevated fracture risk. While epigenetic mechanisms like DNA methylation are well-studied, the role of chromatin remodeling remains less clear. Using integrative genetics and functional studies, we identified BRD9—a non-canonical BAF subunit—as critical for osteoblast differentiation. BRD9 activates Wnt/β-catenin signaling and directly upregulates the key osteogenic factor Sp7. Our findings reveal a novel osteogenic role for BRD9 and suggest its potential as a biomarker and therapeutic target for bone-related diseases.

overall_design: HEK293T and MC3T3-E1 cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM, Gibco) and MEM Alpha Modification (Cytiva) respectively, with addition of 10% fetal bovine serum (FBS, Biological Industries) and 1% penicillin/streptomycin. For in vitro osteogenic differentiation, MC3T3-E1 cell line was maintained in basic medium supplemented with 10 mM M‐glycerol phosphate, 0.25 mM ascorbic acid and 0.1 μM dexamethasone (all from Sigma‐Aldrich, USA). For the BRD9 inhibition assays, cells were treated with either DMSO or I-BRD9 at the final concentrations of 10 μM.


title: Heritable changes in chromatin contacts linked to transgenerational obesity

summary: Burgeoning evidence demonstrates that responses to environmental exposures can be transmitted to subsequent generations through the germline without DNA mutations1,2. This is controversial because underlying mechanisms remain to be identified. Therefore, understanding how effects of environmental exposures are transmitted to unexposed generations without DNA mutations is a fundamental unanswered question in biology. Here, we used an established murine model of transgenerational obesity to show that direct or ancestral exposure to the obesogen tributyltin (TBT) elicited persistent changes in topologically associating domains (TADs) in primordial germ cells (PGCs) isolated from embryos of exposed and subsequent unexposed generations. New TAD boundaries were formed within the Ide gene encoding insulin degrading enzyme in the exposed PGCs, then stably maintained in PGCs of the subsequent (unexposed) two generations. Concomitantly, Ide mRNA expression was decreased in livers of male descendants from the exposed dams. These animals were hyperinsulinemic and hyperglycemic, phenocopying Ide-deficient mice that are predisposed to adult-onset obesity. Creation of new TAD boundaries in PGCs, suppression of hepatic Ide mRNA, increased fat mass, hyperinsulinemia and hyperglycemia were male-specific. Our results provide a plausible molecular mechanism underlying transmission of the transgenerational predisposition to obesity caused by gestational exposure to an environmental obesogen. They also provide an entry point for future studies aimed at understanding how environmental exposures alter chromatin structure to influence physiology across multiple generations in mammals.

overall_design: C57BL/6 F0 mother mice were exposed to tributyltin (TBT) or control (DMSO) via drinking water. Primordial germ cells were isolated from F1-F3 offspring embryos and subjected to Hi-C sequencing.

first: Richard

last: Chang

first: Riann

last: Egusquiza

first: Zhuorui

last: Li

first: Angélica

middle: A

last: Amato

first: Erika

last: Joloya

first: Hailey

last: Wheeler

first: Angela

last: Nguyen

first: Keiko

first: Junko

last: Odajima

first: Toshi

first: Bruce

last: Blumberg

middle: S

last: Lawrence


title: Xevinapant plus chemoradiotherapy negatively sculpts the tumour immune microenvironment in head and neck cancer

city: London

first: Anton

last: Patrikeev

state: London

address: Chester Beatty Laboratories, 237 Fulham Rd.

department: Targeted Therapy

country: United Kingdom

institute: The Institute of Cancer Research

summary: Xevinapant is an orally bioavailable antagonist of select members of the inhibitor of apoptosis protein (IAP) family. Despite promising initial data, combining xevinapant with chemoradiation (CRT) failed to improve outcomes in the TrilynX phase III trial for locally-advanced head and neck squamous cell cancer (SCCHN). We investigated the addition of xevinapant to CRT in immunocompetent mouse models of SCCHN and found maintained or improved locoregional control in vivo in a CD8+ T-cell-independent manner. In mEER, numbers of tumour-infiltrating cytotoxic CD8+ T-cells and NK cells were reduced, with remaining CD8+ T-cells characterised by PD-1hi CD38hi expression and Nr4a3 dynamics consistent with non-responsiveness to antigenic re-stimulation. Furthermore, xevinapant plus CRT significantly downregulated gene expression associated with immune-related pathways, increased levels of immunodysregulatory acute phase proteins and decreased levels of necroptosis mediator RIPK3. Overall, xevinapant plus CRT has an immunosuppressive effect on the tumour-immune microenvironment which may explain its lack of clinical benefit.

overall_design: RNA-seq profiling of 8- to 14-week-old females C57BL/6 WT mice, inoculated with head and neck cancer cells from two cell lines and treated with vehicle, radiotherapy and chemoradiotherapy with or without combination with Xevinapant (5 mice per treatment group). Two models of murine immunocompetent HPV-negative and HPV-positive head and neck cancer were used, MOC1 and mEER, respectively.


title: tert-Butylhydroquinone (TBHQ) suppresses LPS- and Poly (I: C)- induced RAW 264.7 macrophage activation through reduced NF-κB/type 1 interferon and enhanced antioxidant-related pathways

city: Clemson

first: Alyssa

middle: Marie

last: Whisel

state: SC

address: 132 Long Hall

institute: Clemson University

summary: The global demand for processed foods has increased reliance on synthetic phenolic antioxidants (SPAs), including tert-butylhydroquinone (TBHQ), a widely additive used to prevent lipid oxidation and extend shelf life. TBHQ is considered safe at present regulated levels; though studies suggest potential adverse effects, including oxidative stress, genotoxicity, and impacts on immune function, raising concerns about human health and ecological risks. Herein, we investigated the immunomodulatory effects of TBHQ on RAW 264.7 murine macrophages pre-exposed to TBHQ and then stimulated with lipopolysaccharide (LPS) or polyinosinic-polycytidylic acid (poly I:C, PIC) to model bacterial and viral immune challenges. We then used functional assays and transcriptomic profiling to assess inflammatory responses and oxidative stress signaling. TBHQ reduced nitric oxide production and IL-10 secretion at the highest non-cytotoxic dose, and enhanced phagocytosis and IL-6 secretion at the lowest concentrations. Overall, transcriptomics revealed significant downregulation of proinflammatory pathways and induction of glutathione and xenobiotic metabolism. Pre-treatment with TBHQ increased gene transcript counts of key metabolic genes/transporters such as Cbr3, Adh7, Gstp1/3, Gsta3, Hmox1, and Gclm prior to LPS or PIC treatments. Following treatment with LPS or PIC several genes for classical proinflammatory chemokines and cytokines such as Cxcl2, Ccl2, Ccl12, Acod1, Ptgs2, Nos2, and Il6 were downregulated.  Genes involved in N-κB signaling, such as Nfkbia, Nfkb1, and Ikbke were also downregulated.  Our study suggests that the induction of Nrf2-related antioxidant pathways by TBHQ is the main driver for reduced inflammatory signaling in macrophages.

overall_design: RNA-seq profiling of RAW 264.7 macrophages pre-treated with tert-butylhydroquinone (TBHQ) for 4 hours and/or stimulated with lipopolysaccharide (LPS) or polyinosinic:polycytidylic acid (poly I:C, PIC) for 12 hours.

first: Charles

middle: D

last: Rice


title: Human oligodendrocyte progenitor cells mediate synapse elimination through TAM receptor activation

city: Stockholm

first: Carl

last: Sellgren

address: Solnavagen 1

country: Sweden

institute: Karolinska Institute

summary: Recent work in animal models suggests that oligodendrocyte progenitor cells (OPCs) contribute to elimination of synapses in the developing brain. However, a mechanistic understanding of this process is still missing, and it remains uncertain whether human OPCs also display this feature. In this study, we develop a human multi-lineage forebrain organoid model in which OPCs, alongside microglia, exhibit close interactions with synapses and spontaneously internalize synaptic material. Unbiased cell-cell communication analysis based on single-nucleus transcriptomic profiling predicted GAS6-TAM receptor interaction as a major signaling pathway, with neurons and microglia expressing GAS6 ligand and certain OPCs expressing the TAM receptor AXL. Dose-dependent pharmacological inhibition of TAM receptors then demonstrated the importance of AXL receptor activation, and specific knockdown of AXL in OPCs resulted in impaired uptake of synaptic material. In summary, these data define a role of GAS6-AXL signaling in promoting OPC-mediated internalization of synaptic structures during early brain development.

overall_design: Four forebrain organoids per subject (n=2 subjects) were pooled and dissociated to isolate nuclei. High qulaity nuclei were processed for single-nuclei RNA sequencing using 10X Genomics 3' Chromium platform (dual index). The barcoded library was sequenced on Illumina Novaseq. S1-100.

first: Susmita

last: Malwade

first: S

last: Samudyata