title: Transcription factor REST regulates activation and growth of human Hepatic Stellate Cells

city: Solna

first: Vladimir

middle: S.

last: Shavva

address: Solnavägen 30

department: Department of Medicine, Solna

institute: Karolinska Institutet

summary: Activation of hepatic stellate cells (HSC) is a key component in the progression of metabolic dysfunction-associated steatotic liver disease (MASLD) to metabolic-associated steatohepatitis (MASH) and hepatocellular carcinoma (HCC). Targeting HSC activation to prevent MASH and HCC pathogenesis showed promise in mouse models, suggesting that development of therapeutic strategies to abrogate HSC activation could be a promising approach to combat liver disease. Metabolic alterations were suggested to play a pivotal role in HSC activation, yet the mechanisms linking these processes have not been fully elucidated. Here we observe a key role of the RE1-silencing transcription factor (REST) in linking HSC activation, lipid utilization, and mitochondrial metabolism, suggesting that REST is a mechanistic link between HSC metabolism and activation.

overall_design: Primary human Hepatic Stellate Cells isolated from four donors were activated by plating and transfected with scrambled siRNA or siRNA targeting REST. RNA was isolated 12 days following transfection and plating.


title: Csep1P protein from Campylobacter concisus induces a chemokine-dominant inflammatory state in macrophages and enhances proinflammatory response to gut bacteria

status: Public on Feb 01 2026

city: Sydney

first: Li

last: Zhang

state: NSW

address: Botany Street

department: School of Biotechnology and Biomolecular Sciences

country: Australia

institute: University of New South Wales

type: Expression profiling by high throughput sequencing

summary: The THP-1 macrophage gene responses to csep1 protein and the pathogenic mechanisms were investigated by comparative differential expression analysis

overall_design: Comparative gene expression profiling analysis of RNA-seq data for THP-1 macrophage cells with and without csep1 protein treatment


title: Ustilago maydis disrupts carbohydrate signaling networks to induce hypertrophy in host cells

status: Public on Jan 29 2026

city: Köln

first: Gunther

last: Doehlemann

address: Zülpicher Straße 47a

country: Germany

institute: University of Cologne/ Universität zu Köln

summary: Ustilago maydis infection in maize causes hypertrophic leaf tumors; however, the underlying mechanisms driving this excessive cell growth are unknown. In this study, we identify Hap1 (hypertrophy-associated protein 1) as an effector and virulence factor that regulates mesophyll cell hypertrophy. Using CRISPR-Cas9 mutagenesis, we demonstrate that Hap1 contributes to endoreduplication and starch accumulation in infected tissues. Transcriptomics revealed Hap1-dependent upregulation of starch biosynthesis and cell cycle genes, as well as suppression of plant defense. This links Hap1 to metabolic and cell cycle reprogramming, and immune suppression. To identify the target of Hap1 that drives metabolic reprogramming, we investigated its interaction with ZmSnRK1α in maize. We found that Hap1 interferes with the phosphorylation of SnRK1 substrates and that two Hap1-interacting effectors, Hip1 and Hip2, enhance its protein stability. We conclude that Hap1 contributes to the reprogramming of maize metabolism and cell cycle, as well as mesophyll cell hypertrophy, by modulating the SnRK1 signaling pathway to regulate starch biosynthesis and host defense responses.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for maize leaves treated with water (control), SG200, SG200_CR-Hap1. Three biological replicates were generated.

first: Yoon Joo

last: Lee

first: Dong

first: Sara

middle: C

last: Stolze

first: Georgios

last: Saridis

first: Malaika

middle: K

last: Ebert

first: Hirofumi

last: Nakagami


title: Molecular responses of amaranth species to abiotic stresses

city: Irapuato

first: Alfredo

middle: Heriberto

last: Herrera

state: Guanajuato

address: Libr.  Norte Carr. Leon Km 9.6

department: LANGEBIO

country: Mexico

institute: LANGEBIO

summary: Abiotic stress triggered by Drought or soil salinity impacts  negatively on crop production. To better understand amaranth responses to those environmental stresses, transcriptomics approaches were applied to investigate changes at molecular level in leaves of two Amaranthus species: A. hybridus, a wild species that grows in saline soils and A. hypochondriacus, the most cultivated species for grain production. Under control conditions, A. hybridus showed up-regulation of organic hydroxyl and sulfur compound processes, while A. hypochondriacus showed up-regulation of genes related to photosynthetic process, amino acids, fatty acids, and secondary metabolism. Under salt stress, significantly fewer DEGs were observed in A. hybridus, interestingly those were related to phosphonate and phosphinate metabolism, phosphorous mobilization, and steroid biosynthesis. In contrast, A. hypochondriacus response to salt stress was characterized by starch, sucrose, and trehalose metabolism, porphyrin, monoterpenoid and organonitrogen compounds biosynthetic process.Under water deficit, both species showed similar transcriptional response by up-regulation of LEAs, dehydrins, and genes related to the biosynthesis of Raffinose Family Oligosaccharides. A. hypochondriacus better adaptation to grow under drought and salt stress could be due to its fast response observed by the up-regulation of MAPK signaling pathways, ABC transporters, and production of defense compounds such as glucosinolates. The common response in both amaranth species to both type of stresses was observed by modulation of secondary metabolism, which was directed towards cell wall modification, cuticle and wax metabolism, and the production of antimicrobial and antifungal metabolites

sample_organism:
Amaranthus hybridus
Amaranthus hypochondriacus

overall_design: RNAseq of A. hybridus or A. hypochondriacus plants well watered (Control) or subjected to saline (salinity stress) or water stress (drought) were sequenced by triplicate. Differentially expressed genes were obtained from stress vs control treatments in each amaranth species.

first: Ana

middle: P

last: Barba

first: José

last: Cetz

first: Esaú

last: Bojorquez

first: Jose

last: Martinez

first: Antonio

middle: D

last: Leon

first: Eduardo

last: Espitia


title: Trans-regulation of heterochromatin underlies genetic variation in 3D genome contacts I

status: Public on Jan 30 2026

city: Bar Harbor

first: Christopher

middle: Lee

last: Baker

state: ME

address: 600 Main Street

department: Research

country: USA

institute: The Jackson Laboratory

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Background Genetic variation drives phenotypic diversity and disease susceptibility. Trans-acting genetic variation coordinates genome-wide chromatin changes, yet the molecular mechanisms underlying this regulation remain largely unknown. Here, we use the power of mouse genetics to investigate how genetic variation at trans-acting loci regulates 3D chromatin interactions. Results Genetically variable 3D interactions were identified using HiChIP to map H3K27ac-associated regulatory elements in C57BL/6J (B6) and DBA/2J (D2) embryonic stem cells (ESCs). We identified 4,962 strain-differential interactions (~5% of total interactions), 71% of which overlapped chromatin accessibility quantitative trait loci (caQTL), establishing that chromatin interaction variation is predominantly heritable. These differential interactions showed coordinated changes in chromatin state and gene expression, with stronger interactions associated with increased accessibility and transcription. Notably, loci regulated in trans exhibited a unique chromatin signature where weaker interactions were enriched for H3K9me3-marked heterochromatin. This pattern was 20-fold more enriched at trans-regulated targets compared to cis, implicating heterochromatin in trans-regulation of 3D genome structure. Analysis of F1 hybrids revealed dominant repressive effects, consistent with heterochromatin-mediated trans-regulation. To causally test this mechanism, we generated reciprocal congenic mouse strains carrying a Chr13 trans-QTL region on otherwise inbred genetic backgrounds. Integrated multiomic profiling of congenic ESC lines demonstrated that this single locus coordinates changes in H3K9me3, H3K27ac, chromatin accessibility, and 3D contact frequency at hundreds of distal genomic regions. Remarkably, 73-83% of differential interactions at Chr13 trans-QTL targets changed in the predicted direction, demonstrating that heterochromatin-mediated trans-regulation coordinately regulates hundreds of regulatory loci. Conclusions This work establishes heterochromatin formation as a mechanism by which genetic variation at trans-acting loci coordinates changes across chromatin accessibility, histone modifications, and 3D genome organization, providing a framework for understanding how early developmental chromatin states could generate phenotypic variation while preserving essential developmental programs.

overall_design:
ATAC-seq in C57BL/6J, DBA/2J, B6.D2-(rs30079041-rs51756099)/Bakr (QJ), and D2.B6-(rs29224292-rs51756099)/Bakr (XE) mouse embryonic stem cells (2 or 3 technical replicates each).

** QJ and XE are congenic strain designations used internally within the lab. For clarity and consistency with standardized nomenclature, QJ samples are referred to as B6-13D2 and XE samples as D2-13B6 throughout the manuscript.


title: Cell confinement memory initiates heritable loss of chromosomes and a persistently dysregulated division program

status: Public on Jan 28 2026

city: Philadelphia

first: Dennis

last: Discher

state: Pennsylvania

address: 129 Towne Bldg

institute: University of Pennsylvania

summary: Heritable genetic changes continually arise in cancer, especially in solid tumors where cells sometimes appear compressed. Rare heritable losses of chromosomes in live cells are quantified here with chromosome reporters (ChReporters) that show similar losses after mild or strong compression. Mild compression (to <40% of interphase height) perturbs mitotic spindles and prolongs pro/metaphase but ruptures few nuclei compared to strong compression. Unexpectedly, chromosome mis-segregation into micronuclei emerges only after release from mild confinement, but arrest and death predominate. All such effects are phenocopied by Nocodazole washout that induces a ‘memory’ of prolonged mitosis. The results differ from transient inhibition of the spindle assembly checkpoint and cell cycle entry with a CDK4/6-inhibitor – both of which quickly generate micronuclei. Single-cell-RNA-sequencing confirms chromosome loss days after confinement and reveals persistent upregulation of chromosome segregation. The results suggest a mitotic memory of confinement, addressing a significant gap in mechanobiology and cancer evolution.

overall_design: Our focus on the very rare cells that are ChReporter-negative (~1-per-500 cells). Therefore we sorted live cells for ChReporter loss after the 48h recovery from confinement or 2D controls, and then we used single-cell RNA-seq (scRNAseq) to quantify transcript changes.  RNA libraries were constructed using the Chromium Single Cell Gene Expression kit (v3.1, single index, Catalog no. PN-1000128; PN-1000127; PN-1000213) from 10X Genomics per the manufacturer's instructions. The libraries were submitted to the University of Pennsylvania's Next Generation Sequencing Core for sequencing using NovaSeq 6000 (100 cycles) from Illumina. Raw base call (BCL) files were analyzed using CellRanger (version 5.0.1) to generate FASTQ files and the ‘count’ command was used to generate raw count matrices aligned to GRCh38 provided by 10X genomics.

first: Mai

last: Wang


title: Charting the DNA methylation landscape of the Killifish across age and tissues

city: Berlin

first: Helene

last: Kretzmer

address: Ihnestraße 63

department: Genome Regulation

institute: Max Planck Institute for Molecular Genetics

type: Methylation profiling by high throughput sequencing

summary: Killifish are among the shortest-lived vertebrates and are considered a promising model organism for aging. However, so far virtually nothing is known about its DNA methylome, which is frequently used for age and health status predictions in mammals. Here, we provide a comprehensive whole-genome killifish methylation map covering different tissues, age groups, and species. We show that the methylome of all individuals follows the typical, bimodal distribution of either high or low methylation rates. Furthermore, we find the major methylation variance within a species is driven by cell type-specific methylation and small but detectable aging related dynamics separating the age groups.

sample_organism:
Nothobranchius furzeri
Nothobranchius orthonotus

overall_design: Analysis of the DNA methylome of different tissues and age goups from the turquoise (Nothobranchius furzeri) and spotted killifish (Nothobranchius orthonotus).

first: Dario

middle: R

last: Valenzano

first: Alexander

last: Meissner

first: Mara

last: Steiger


title: Single-cell transcriptomics identifies altered neutrophil dynamics and accentuated T-cell cytotoxicity in tobacco -flavored e-cigarette -exposed mouse lungs

city: Rochester

first: Gagandeep

last: Kaur

address: 601 Elmwood Ave

department: Environmental Medicine

institute: University of Rochester Medical Center

summary: E-cigarettes (e-cigs) are a public health concern for young adults due to evidence for increased oxidative stress, lipid dysfunction, and inflammation. Yet an extensive study defining the cell-specific alterations on exposure to flavored e-cigs remains elusive. To understand the immunological lung landscape upon exposure to flavored e-cig (mango-, menthol- or tobacco-flavor) aerosols we performed single cell RNA sequencing (scRNA seq).

overall_design: C57BL/6J mice were exposed to 5-day nose-only exposure to air, propylene glycol: vegetable glycerin (PG:VG), mango-, menthol- and tobacco-flavored e-cig aerosols. Following exposure the mouse lungs were perfused, harvested and digested to obtain single cell suspension. scRNA seq was performed on the thus obtained single cell suspension.

first: Thomas

last: Lamb

first: Ariel

last: Tjitropranoto

first: Irfan

last: Rahman


title: Trans-regulation of heterochromatin underlies genetic variation in 3D genome contacts

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

overall_design: Refer to individual Series


title: Regulation of transcriptomic profile by ZL0580 and JQ1

status: Public on Jan 27 2026

city: Galveston

first: Haiping

last: Hao

state: Texas

address: 301 University Blvd

institute: UTMB NGS Core

summary: Epigenetic suppression and durable silencing of HIV represent a promising strategy to achieve ART-free remission, consistent with the “block and lock” HIV cure paradigm. BRD4 is a host epigenetic reader and plays a critical role in HIV transcriptional regulation. We previously identified ZL0580, a first-in-class BRD4-selective small molecule that epigenetically suppresses HIV, whereas the pan-BET/BRD4 inhibitor JQ1 activates HIV transcription. The present study utilizes RNA-Sequencing (RNA-Seq) to examine the impact of ZL0580 and JQ1 on transcriptomic profile in the latently HIV-infected J-Lat cells (Clone 10.6). In summary, ZL0580 induces a transcriptomic profile opposing to that induced by JQ1, which is highly consistent the opposing effects of the two compounds on HIV transcription and latency.

overall_design: J-Lat cells (10.6) were treated with DMSO (as negative control), ZL0580 (5 uM), or JQ1 (5 uM). 24 hours after treatment, cells were subjected to bulk RNA-Seq analysis.

first: Haitao

last: Hu

first: Naveen

last: Kumar


title: Non-disruptive in vitro monitoring of cellular states with cell-free DNA methylation

first: Anja

last: Hess

email: ahess@molgen.mpg.de, anja.hess@mail.de

address: Ihnestrasse 63-67

institute: Max-Planck-Institut für molekulare Genetik

summary: Regenerative cell therapies and stem-based in vitro models all aspire the approximation of a given start cell to an alternate (often more mature) cell state. However, ‘monitoring’, hence controlling, such a dynamic process requires disruption of the precious sample, destroying architecture and introducing variation. Here, we establish real time-compatible, fully non-invasive monitoring of cell fates through simple cell-free DNA medium sampling. We demonstrate that cell-free DNA methylation non-disruptively reveals genome-wide DNA methylation transitions during epigenetic drug treatment in stem cells, and reports the gradual maturation of 3D hepatocytes grown in bioreactors. Our cell-free DNA methylation platform enables monitoring a broad variety of in vitro systems, has implications for the real-time evaluation human therapeutic cells, and the potential to be readily integrated into large-scale bioreactor workflows.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
Whole genome bisulfite profiling of cell-free and genomic DNA from KH2 mESCs treated with DNMT1-Inhibitor GSK-3484862 for four days, followed by a two day recovery period. DMSO-treated cells served as a negative control.

Whole genome Nanopore-Sequencing of differentiating 3D bioreactor hepatocytes over 20 days.

last: Kovacsovics

first: Fabian

last: Bachinger

first: Ludovic

last: Vallier


title: Effects of ACTH and Dexamethasone on the Transcriptomic Profile of the Rat Adrenal Gland: An In Vivo Study

city: Poznan

first: Marcin

last: Rucinski

address: Swiecicki 6

department: Histology and Embriology

country: Poland

institute: Poznan University of Medical Science

summary:
The hypothalamic-pituitary-adrenal (HPA) axis plays a pivotal role in regulating stress responses through ACTH-stimulated glucocorticoid production. Adult male Wistar rats were subjected to acute ACTH stimulation (single injection, 1 h), prolonged ACTH exposure (three injections over 36 h), or Dexamethasone treatment (three injections over 36 h). Plasma corticosterone levels were measured using ELISA. Adrenal transcriptome profiling was performed using Affymetrix Rat Gene 1.1 ST Arrays. Differentially expressed genes (DEGs; |fold change| >= 1.8, adjusted p < 0.05) were analyzed using limma, followed by pathway and network analyses.
Acute ACTH exposure resulted in induction of 569 DEGs (357 upregulated), including immediate-early genes (Nr4a family, AP-1 factors), cAMP-PKA-CREB signalling components, and heat shock proteins. Prolonged ACTH resulted in 98 DEGs (predominantly downregulated), including suppression of mitochondrial genes and upregulation of Polycomb repressive complex 2 components. Dexamethasone treatment yielded 75 DEGs with selective suppression of SREBP-mediated cholesterol biosynthesis and uptake pathways.

overall_design: Adult male Wistar rats (160-200 g) were randomly assigned to four experimental groups (n=3 per group, 12 animals total). Control group (C) received saline injections at 0, 12, and 24 h and were decapitated 12 h after the last injection. Acute ACTH group (ACTH_A) received a single ACTH injection (Synacthen, 5 μg/rat) and were decapitated 1 h post-injection. Prolonged ACTH group (ACTH_P) received ACTH injections at 0, 12, and 24 h and were decapitated 12 h after the last injection. Dexamethasone group (DEX) received Dexamethasone injections (5 μg/rat) at 0, 12, and 24 h and were decapitated 12 h after the last injection. Total RNA was extracted from adrenal glands and analyzed using Affymetrix Rat Gene 1.1 ST Arrays.

first: Emilia

last: Cicha

first: Małgorzata

last: Blatkiewicz

first: Karol

last: Jopek

first: Marta

last: Szyszka

first: Piotr

middle: W

last: Malendowicz

first: Anna

last: Olechnowicz

first: Ludwik


title: Characterization of gRNA-Dependent and gRNA-Independent Off-Target Binding Sites of PspCas13b and RfxCas13d in Mammalian Cells [CLIP-seq]

city: Shanghai

first: Li

last: Zhixue

address: 320 Yueyang Road, Xuhui District

country: China

institute: CAS Center for Excellence in Molecular Cell Science

summary: CRISPR-Cas13 systems, harnessed for RNA-guided transcriptome editing, hold significant promise for clinical and in vivo therapeutic applications. However, understanding their in vivo target specificity and recognition rules remains a challenge. In this study, we employed the uSpyCLIP method, which enhances sensitivity and specificity for identifying RNA-binding protein (RBP) binding sites, to map the transcriptome-wide binding sites of catalytically inactive PspCas13b (dPspCas13b) and RfxCas13d (dRfxCas13d) in HEK293T cells, using a variety of single guide RNAs (gRNAs). Surprisingly, we identified both gRNA-dependent and gRNA-independent off-target binding sites for both dCas13 complexes. These off-target sites exhibited distinct RNA structural and sequence signatures: dPspCas13b's gRNA-independent binding was associated with specific RNA structural features, while dRfxCas13d's was linked to unique sequence motifs. Analysis of gRNA-dependent off-target sites revealed the crucial role of the DR-distal and middle regions of the gRNA in determining binding specificity. mRNA sequencing and biochemical assays further indicated that while off-target binding does not directly affect mRNA levels, it can perturb the expression of certain endogenous proteins. Therefore, our findings provide important insights into the characteristics of gRNA-dependent and gRNA-independent off-target binding for PspCas13b and RfxCas13d, offering valuable guidance for optimizing Cas13 and gRNA design in future applications.

overall_design: uSpyCLIP-seq of PTBP1 with 10,000,000 cells, 100,000 cells, 10,000 cells, or 1000 cellls; uSpyCLIP-seq of RBFOX2 with 10,000,000 cells;  uSpyCLIP-seq of dPspCas13b and dPspCas13b-gRNA;  uSpyCLIP-seq of dRfxCas13d and dRfxCas13d-gRNA; uSpyCLIP-seq for comparing the efficiency of Spycatcher V1.0 and  Spycatcher V2.0.

first: Huanhuan

last: Feng

first: Zhixue

last: Li

first: Ligang

last: Wu

first: Lin

last: Zou


title: Sex-Based Differences in Cell Types and Gene Expression within the Anterior Cruciate Ligament

city: San Francisco

first: Brian

middle: T

last: Feeley

state: CA

address: 1700 Owens St

department: Orthopedic Surgery

institute: University of California, San Francisco

summary: ACL tear rates in females is significantly higher compared to their male counterpart. We utilized 9 patient samples to explore the biological and transcriptomic differences that exist in male and female ACL.

overall_design:
Human anterior cruciate ligament was mechanically and enzymatically digested. Live cells were sorted by FACS and then sequenced. All cells were analyzed by 10x Genomics 3' single cell RNA sequencing.

Please note that the processed data files for GSM8656015 sample have been replaced with individual files for each patient on Feb 25, 2026.

first: Justin

last: Lau

first: Steven

middle: M

last: Garcia

first: Xuhui

last: Liu

first: Stephanie

last: Wong


title: High Frequency Loss of 17q11.2 and Downregulation   of the Cancer Metastasis Suppression microRNA miR-193a-3p in Prostate Cancer Bone Metastasis

city: London

first: Yong-Jie

last: Lu

address: Barbican

country: United Kingdom

institute: Queen Mary University of London

type:
Genome variation profiling by SNP array
SNP genotyping by SNP array

summary: Metastasis is the main cause of death from prostate cancer (PCa), a common malignant disease. 90% of PCa metastasis occurs in the bone, thus understanding the genetic chang-es underlying bone preference is critical. However, due to the difficulty in getting samples from the bone and other reasons, limited bone metastasis specific genomic alteration pro-files, particularly at individual sample level, have been published. Here we generated in-dividually genomic change profiles for six PCa bone metastasis samples and identified bone metastasis specific genomic changes. One of them, loss of 17q11.2 genomic region, was further confirmed by another genetic method in further 14/21 PCa bone metastasis samples but only in 9/151 localized PCa. The function of a well-established tumor sup-pressor, miR-193a-3p, located in this lost genomic region, was reduced in bone metastasis,  leading to overaction of two well-established genes to promote cancer metastasis. It pro-vides new insight into bone metastasis development.

overall_design: DNA was extracted from six fresh frozen bone metastases. Samples preparation for hybridization onto Affymetrix SNP 6.0 array chips (Affymetrix, Santa Clara, CA, USA) was performed according to the manufacturer’s protocols.

first: Elzbieta

last: Stankiewicz

first: Sarah

last: McCarley

first: Xueying

last: Mao

first: Sakunthala

last: Kudahetti

first: Tim

last: Oliver

first: Jonathan

last: Shamash

first: Trevor

last: Graham

first: Daniel

last: Berney


title: Systematic Identification of Germ Granule Proteins Reveals Specialized Roles in RNAi and Small RNA Inheritance

city: Los Angeles

first: Carolyn

middle: Marie

last: Phillips

address: 1050 Childs Way, RRI 201

department: Biological Sciences

institute: University of Southern California

summary: Biomolecular condensates, such as germ granules, organize RNA pathways critical for fertility and genome regulation. Yet, the protein composition and functional specialization of these condensates remain poorly defined. Here, we applied TurboID proximity labeling to the Caenorhabditis elegans germ granule protein SIMR-1, integrating mass spectrometry with genetic screening, CRISPR-based tagging, and small RNA sequencing. This systematic approach identified several previously uncharacterized germ granule proteins that are required for fertility, germline immortality, exogenous RNAi, and transgenerational inheritance. Small RNA sequencing of 21 mutants revealed broad and class-specific defects in siRNA and miRNA biogenesis, with distinct factors required for amplification of WAGO-class 22G-RNAs, CSR-class 22G-RNAs, or histone-directed small RNAs. Among these, we identified PINT-1, a highly disordered protein that directly interacts with and is recruited to germ granules by the PIWI Argonaute PRG-1. PINT-1 is required for piRNA-dependent and -independent secondary siRNA biogenesis and germline development. Comparative genomics revealed that PINT-1 has co-evolved with PRG-1 across nematodes, with a conserved structured N-terminus and a rapidly diverging repeat-rich intrinsically disordered region. Together, our findings expand the germ granule proteome and reveal how distinct condensate components contribute to specialized functions within the small RNA pathways, while highlighting an evolutionarily co-adapted PIWI interactor critical for siRNA biogenesis.

overall_design: Total small RNA sequencing of wild-type and RNAi pathway mutants in day-1-adult animals.

first: Shihui

last: Chen

first: Lucas

middle: H

last: Prescott

first: Craig

last: Mello


title: Synergistic Targeting of eIF4A - Mediated Translation Initiation and Apoptosis in Acute Myeloid Leukemia

city: Boston

first: Peter

last: van Galen

state: Massachusetts

address: 4 Blackfan Circle

department: Hematology

institute: Brigham and Women's Hospital / Broad Institute of MIT and Harvard

summary: Targeted therapies, such as the BCL-2 inhibitor venetoclax, have expanded the treatment options for patients with acute myeloid leukemia (AML), but survival remains poor because of drug resistance and disease relapse. We found that the translation initiation factor EIF4A1, which unwinds complex messenger RNA structures in the 5' untranslated region (UTR) of oncogenic transcripts, is highly expressed in AML stem- and progenitor-like cells relative to healthy hematopoietic stem and progenitor cells. Inhibition of eukaryotic initiation factor 4A (eIF4A) with the first-in-class small molecule zotatifin reduces the translation efficiency of transcripts related to the cell cycle and oncogenic signaling via the PI3K/AKT/mTOR pathway, as shown by ribosome profiling and gene set enrichment analysis. Western blot analysis corroborated these findings and demonstrated the downregulation of AKT, STAT-5, and MCL-1, factors implicated in resistance to venetoclax-based regimens. The combination of zotatifin and venetoclax synergistically kills AML cells in vitro and induces apoptosis across AML genotypes with selectivity toward progenitor-like cells in primary AML bone marrow (BM); however, its effect in primary healthy BM is limited. Using 3 in vivo xenograft models derived from patients with relapsed/refractory AML, the combination significantly suppressed the tumor burden and prolonged survival. These results support eIF4A-mediated protein translation as a therapeutic target in AML and highlight the potential of zotatifin and venetoclax in relapsed/refractory disease.

overall_design: MOLM-13 cells were treated with DMSO (control) or the eIF4A inhibitor Zotatifin for four hours. Then cells were harvested for RNA-seq and Ribo-sequencing.

first: Yoke Seng

last: Lee

first: Noha

last: Awais

first: Jingting

last: Lin


title: The Rpd3 histone deacetylase is critical for temperature-mediated morphogenesis and virulence in the human fungal pathogen Histoplasma

status: Public on Jan 26 2026

first: Mark

last: Voorhies

address: 513 Parnassus, S472

department: Microbiology and Immunology

institute: University of California


title: Two thymidylate synthase inhibitory drugs induce markedly different genomic uracil patterns, mutagenic processes and cellular response in HCT116 colon cancer cells [re-analysis of GSE126822]

status: Public on Jan 31 2026

city: Budapest

first: Angela

last: Bekesi

address: Műegyetem rakpart 3.

department: Department of Applied Biotechnology and Food Science

country: Hungary

institute: Budapest University of Technology and Economics, Faculty of Chemical Technology and Biotechnology

summary: The presence of genomic uracil and its respective repair play key roles in colorectal, gastric, and other solid tumor therapies targeting thymidylate biosynthesis. Previously, we established that the treatment of HCT116 colon cancer cell lines with either raltitrexed (RTX) or 5-fluoro-2’-deoxyuridine (5FdUR), two potent inhibitors of thymidylate synthase, results in characteristic uracil patterns (PMID: 32956035). Here, we focus on drug-specific differences in the genomic uracil profiles that associate with altered cytotoxicity and drug-induced mutagenesis. Both genome segmentation and U-score as a quantitative measure of gene-level uracil-content revealed biased uracilation upon the two drug-treatments. The corresponding genes are functionally related and characteristic for the applied drug, supporting the impact of genomic uracil patterns in the cellular responses. Mutational analysis revealed a significant increase in the frequency of C-to-T somatic transitions selectively upon high-dose 5FdUR treatment in DNA-repair deficient cells. The mutational spectra and the clustered nature of these transitions pointed to the action of DNA cytidine deaminases. Indeed, an induction of some APOBEC3 enzymes was experimentally confirmed upon the high-dose 5FdUR treatment, in parallel with decreased cytotoxicity, as compared to the low-dose, or any efficient doses of RTX. The observed drug-induced mutagenicity and decreased cytotoxicity might be relevant for personalized cancer therapy.

relation:
Reanalysis of: GSM4644430
Reanalysis of: GSM4644429
Reanalysis of: GSM4644428
Reanalysis of: GSM4644427
Reanalysis of: GSM4644426
Reanalysis of: GSM4644425
Reanalysis of: GSM4644424
Reanalysis of: GSM4644423
Reanalysis of: GSM4644422
Reanalysis of: GSM4644421
Reanalysis of: GSM4644420
Reanalysis of: GSM4644419
Reanalysis of: GSM4144355
Reanalysis of: GSM4144354
Reanalysis of: GSM4144353
Reanalysis of: GSM4144352
Reanalysis of: GSM4144351
Reanalysis of: GSM4144350
Reanalysis of: GSM4144349
Reanalysis of: GSM4144348
Reanalysis of: GSM4144347
Reanalysis of: GSM4144346
Reanalysis of: GSM4144345
Reanalysis of: GSM4144344
Reanalysis of: GSM4144343
Reanalysis of: GSM4144342
Reanalysis of: GSM4144341
Reanalysis of: GSM4144340

overall_design:
Genomic uracil patterns were determined in drug-treated (5FdUR or RTX) HCT116 cells that are either deficient (HCT116) or proficient in mismatch repair (HCT116MMR) and stably express the UNG inhibitor protein, UGI (samples are as follows: 5FdUR_UGI_HCT116, RTX_UGI_HCT116, 5FdUR_UGI_HCT116MMR, RTX_UGI_HCT116MMR). These were compared to the non-treated UGI-expressing (NT_UGI_HCT116 and NT_UGI_HCT116MMR), as well as to the wild-type HCT116 (WT_HCT116) cells. For each samples, two independent biological replicates were measured (rep1 and rep2).  Genomic DNA was isolated from each sample and fragmented to approximately 300 bp fragments by sonication (“input” samples (son)). A part of the input sample was incubated with FLAG-tagged uracil-DNA sensor, which was finally precipitated by anti-FLAG beads, resulting in the “enriched U-DNA” sample (IP). Input, U-DNA enriched, and control samples were sequenced by Illumina paired-end reads (PE) 100 bp in a HiSeq 4000 or by PE 150 bp in a Novaseq 6000 platform. Reads were filtered and aligned to the reference human genome (GRCh38.d1.vd1, (https://gdc.cancer.gov/about-data/data-harmonization-and-generation/gdc-reference-files)). The genomic uracilation profiles previously were reported as log2(fold change) curves (bw files) and intervals (bed files) under GEO Series GSE126822. Here we provide the following processed files: 1) two interval files from genome segmentation based on all genomic uracilation tracks (segway_merged12_GEO_headed.bed and segway_reps12_GEO_headed.bed); 2) and the applied blacklist (blacklist_HCT116_merged_d500.sorted.bed); 3) U-probability tracks for individual replicates as well as for merged data (p-trackM.bw); 4) One xlsx file including U-scores for genes (defined in Gencode v34 annotation) calculated based on p-trackM.bw files for all samples; 5.) Genomic variants called using mutect2 (GATK4) from treated vs. non-treated input samples in several arrangements defined in the names of each file. These csv files contain filtered lists of single-base substitutions and the corresponding allele frequencies. For details, see the Supplementary Method of the related publication.

This study represents a re-analysis of the raw data generated for GSE126822. The reanalysis was done from a different point of view, as detailed in the 'readme_data_processing.txt'.

***************************************************************
The table below lists GEO accessions reused/reanalyzed for this study.
***************************************************************

first: Eszter

last: Holub

first: Gábor

last: Papp

first: Hajnalka

middle: L

last: Pálinkás

first: Milda

middle: B

last: Szajkó

first: Richard

last: Izrael

first: Beáta

middle: G

last: Vértessy

first: Angéla

last: Békési


title: CUL5 E3 ubiquitin ligase regulates the evasion of bladder cancer cells to CD8+ T cell-mediated killing by inhibiting autophagy

city: Wuhan

first: Xincheng

last: Gao

state: Hubei

address: 1277 Jiefang Avenue

department: Urology

institute: Union Hospital, Tongji Medical College, Huazhong University of Science and Technology

summary: CD8+ T cells are capable of specifically targeting and eliminating malignant tumor cells, but tumor cells can develop resistance mechanisms to escape CD8+ T cell-mediated killing. Here, we performed a whole genome CRISPR-Cas9 knockout screen under CD8+ T cells pressure and identified the E3 ubiquitin ligase CUL5 as an essential factor required for escaping CD8+ T cells killing in bladder cancer cells. We found that CUL5 knockout promoted the sensitivity of bladder cancer cells to CD8+ T cell-mediated killing both in vivo and in vitro. Mechanistically, CUL5 loss reduced the ubiquitination of PTBP1, which regulated alternative splicing of RUBCN pre-mRNA and led to an increase in the levels of the RUBCN-S isoform, thereby preventing immune evasion of bladder cancer cells by inhibiting autophagy. Importantly, CUL5 knockout significantly enhanced the efficacy of anti-PD-1 immunotherapy in a xenograft model. Collectively, these findings reveal a novel mechanism of bladder cancer immune evasion, providing potential targets for cancer immunotherapy.

overall_design: Considering that PTBP1 acts as a classical splicing factor, we conducted high-throughput sequencing of RNA (RNA-Seq) on the CUL5-WT and CUL5-KO T24 cells to analyze the changes of alternative splicing (AS).

first: Hui

last: Zhang

first: Guosong

last: Jiang


title: Targeting Fused in Sarcoma (FUS): A Novel Antisense Strategy for Treating Idiopathic Pulmonary Fibrosis [RNA-Seq IPF]

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

summary: Fused in Sarcoma (FUS) is a highly conserved RNA-binding protein with essential roles in RNA processing and genomic stability. While extensively studied in the context of neurodegeneration, its involvement in fibrotic diseases—particularly idiopathic pulmonary fibrosis (IPF)—remains largely unexplored. This study investigates the pathological role of FUS in IPF and assesses its viability as a therapeutic target. Specifically, we examine how FUS dysregulation contributes to fibrotic signaling and evaluate whether therapeutic silencing of FUS offers a rational strategy to modulate disease progression. Functional assays were performed on primary lung fibroblasts derived from healthy donors and IPF patients to assess the effects of FUS overexpression and knockdown. Precision-cut lung slices (PCLS) and 3D-alveolosphere cultures from IPF patients were treated with a FUS-targeted antisense oligonucleotide (ASO;ION363). FUS-RNA interactions were mapped using CLIP-Seq, and global transcriptional changes following FUS inhibition were analyzed via RNA sequencing. FUS overexpression in healthy fibroblasts promoted proliferation, while its knockdown attenuated the hyperproliferative phenotype in IPF fibroblasts. IPF cells demonstrated aberrant cytoplasmic mislocalization of FUS. Standard-of-care treatments (pirfenidone, nintedanib) reduced FUS expression in PCLS. CLIP-Seq revealed FUS binding to a distinct set of pro-fibrotic RNAs in IPF. ION363 treatment downregulated fibrotic gene programs, including those linked to ECM remodeling, TGF-β signaling, and epithelial dysfunction. On the contrary, ION363 promoted functional markers and improved morphology in patient derived 3D-alveolospheres. We conclude that FUS is a pivotal regulator of fibrotic signaling in IPF and targeting FUS via ASO represents a promising therapeutic avenue for IPF.

overall_design: RNA-Seq profiling of IPF fibroblasts treated or transfected as follows: Scr-ASO, ION363 (FUS-ASO), non-targeting siRNA (Scr), siRNA for FUS.

first: Poornima

last: Mahavadi

last: Guenther


title: African Pygmy Mouse iPSCs as a Model for In Vitro Embryogenesis, Interspecies Chimerism, and Blastocyst Complementation

city: Schwerzenbach

first: Adhideb

last: Ghosh

address: Schorenstrasse 16

department: Health Sciences and Technology

country: Switzerland

institute: ETH Zurich

summary: Somatic cell reprogramming into induced pluripotent stem cells (iPSCs) was achieved in various mammals, however assessing iPSC contribution to full-term chimeras beyond laboratory rodents remains challenging. Here, we demonstrate induction of pluripotency in male and female fibroblasts from the African Pygmy Mouse (APM), one of the smallest mammals. Using transcription factors and small molecules, we derived expandable APM-iPSCs that express pluripotency markers, differentiate into various cell types in vitro, and form gastruloids. Injection of APM-iPSCs into house mouse blastocysts generated full-term interspecies chimeras demonstrating extensive contribution to various tissues, including testicular germ cells. Notably, high APM contribution in organs such as heart and testes correlated with reduced organ size compared with mouse organs. Lastly, injection of APM-iPSCs into mouse blastocysts carrying a Pax7 ablation system enabled substantial production of APM muscle stem cells in chimeras. Collectively, this study establishes APM-iPSCs as a developmental model for pluripotency, differentiation and interspecies chimerism.

overall_design: Mouse-APM interspecies chimeras were produced through blastocyst injection into the Pax7-Cre/ERT2; Rosa26-loxP-STOP-loxP-Diphtheria toxin A (DTA) (B6.Cg-Pax7tm1(cre/ERT2)Gaka/J; B6.129P2-Gt(ROSA)26Sortm1(DTA)Lky/J) host, followed by tamoxifen-induced ablation of Pax7 expressing host cells.

first: Pjeter

last: Gjonlleshaj

first: Ajda

last: Lenardič

first: Monika

last: Tarnowska-Sengül

first: David

last: Taborsky

first: Christine L

last: Trautmann

first: João A

last: de Sousa

first: Nicola

last: Bundschuh

first: Frédéric

last: Veyrunes

first: Ataman

last: Sendoel

first: Ori

last: Bar-Nur


title: Meningeal Lymphatic Vessel Dysfunction Exacerbates Brain Injury in CVST Mice via Endoplasmic Reticulum and Oxidative Stress Pathways.

city: fuzhou

first: jianbin

last: ying

address: No. 156, North Section of West Second Ring Road, Gulou District

institute: Fuzong Clinical Medical College of Fujian Medical University

summary: Meningeal lymphatic vessels (mLVs) play a crucial role in maintaining neurological homeostasis and disease development. However, their function in brain injury following cerebral venous sinus thrombosis (CVST) remains unclear. This study investigates how dysfunction of meningeal lymphatic vessels influences the pathological progression of CVST by regulating the endoplasmic reticulum (ER) and oxidative stress (OS) pathways.

overall_design: Through RNA sequencing (RNA-seq) analysis, we induced cerebral venous sinus thrombosis (CVST) models and divided them into three groups: one CVST group, one CVST group with bilateral cervical lymph node ligation, and one CVST+ group receiving 4-PBA intervention after lymph node ligation. On day 2 post-modeling, differentially expressed genes (DEGs) were identified among cortical tissues across the three groups.

first: jin

last: li

first: junjie

last: jing

first: shousen

last: wang


title: BCL-xL as a therapeutic target in cetuximab-refractory colorectal cancer

city: Stuttgart

first: Steven

middle: A

last: Johnsen

address: Auerbachstrasse 112

institute: Robert Bosch Center for Tumor Diseases

summary: Despite recent medical advances, colorectal cancer (CRC) remains the second-leading cause of cancer-related death worldwide. For patients with KRAS wild-type metastatic CRC, the monoclonal antibody cetuximab, which targets the epidermal growth factor receptor (EGFR), is an approved treatment option. However, therapeutic success is often limited by the emergence of drug-resistant cancer cell populations within a few months. Therefore, alternative strategies to effectively target cetuximab-refractory CRC are urgently needed. Here, we sought to identify second-line therapeutic strategies using a CRC cell line with acquired cetuximab resistance as a model. Transcriptomic profiling of the resistant cells identified the apoptosis pathway as a potential therapeutic target, which was supported by their increased susceptibility to BH3-mimetics targeting the anti-apoptotic proteins MCL-1 and BCL-xL under both 2D and 3D culture conditions. These findings were validated in organotypic CRC slice cultures generated from cetuximab- resistant patient-derived xenografts (PDXs). Multiplex immunofluorescence staining demonstrated that BCL-xL inhibition effectively triggered apoptosis in heterogeneous PDX tumor slice models, including models harboring oncogenic BRAF mutations. Our findings suggest that cetuximab-resistant CRC retains apoptotic competence, and that BCL-xL inhibition serves as a robust alternative therapeutic strategy that is largely independent of the tumor mutational profile.

overall_design: To investigate resistance to cetuximab in colorectal cancer, we performed RNAseq in parental and resistant LIM1215 cells.

first: Stella

last: Asmanidou

first: Thomas

last: Ekstrom

first: Monilola

last: Olayioye


title: Colorectal cancer-derived osteopontin rewires macrophages into a pro-metastatic M2 state via the PI3K/AKT/CSF1-CSF1R axis

city: GuangZhou

first: xiaoxia

last: Liang

address: 26 Yuancun Er Heng Road

institute: Sixth Affiliated Hospital of Sun Yat-sen University

summary: Metastasis remains the primary cause of mortality in colorectal cancer (CRC), with a 5-year survival rate of approximately 14%, despite advancements in treatment. SPP1+ tumor-associated macrophages (TAMs) are implicated in promoting tumor growth, angiogenesis, and immune evasion. Osteopontin (OPN), encoded by the SPP1 gene, is a critical regulator of TAMs M2 polarization and CRC metastasis. However, the mechanisms by which CRC-derived OPN interacts with M2-TAMs to promote metastasis remain unclear. Here, We found that OPN is highly expressed in metastatic CRC and is associated with poor prognosis. However, knockdown or overexpression of OPN in CRC cells did not directly affect tumor cell invasion and metastasis, which is inconsistent with previously reported trends. Additionally, OPN expression levels were positively correlated with M2-like TAMs infiltration. Using an in vitro co-culture system, we found that CRC-derived OPN induces M2-like polarization of TAMs, and the two mutually promote chemotactic migration. Mechanistically, high OPN expression activates the PI3K/AKT signaling pathway in macrophages, promoting the secretion of CSF1, which induces M2-like polarization of macrophages to facilitate tumor metastasis. Finally, in a mouse metastasis model, blocking the CSF1/CSF1R axis with a CSF1R inhibitor reduced the recruitment of M2-TAMs and CRC tumor metastasis.Our study demonstrates that the OPN/CSF1/CSF1R/PI3K/AKT axis plays a crucial role in CRC metastasis. Blocking CSF1/CSF1R reduces M2-TAM infiltration and tumor metastasis, thereby enhancing the therapeutic efficacy for metastatic CRC.

overall_design: RNA-seq profiling of THP-1 cells treated with PMA and co-cultured with conditioned medium (CM) from SW480 cells with OPN knockdown derivatives (shNC and sh) for 48 hours.


title: Context-dependent translation inhibition as a novel oncology therapeutic modality [RNA-seq]

city: SOUTH SAN FRANCISCO

first: Paige

last: Diamond

state: California

address: 201 HASKINS WAY

institute: Interdict Bio

summary: Inhibitors of protein synthesis, including anisomycin, homoharringtonine, and other natural products bind in the peptidyl-transferase center (PTC) of the eukaryotic ribosome to inhibit translation. Recent work has demonstrated that some PTC-binding antibiotics act in a sequence-selective manner, inhibiting translation elongation at specific amino acids while the polypeptide is engaged in the PTC. However, this phenomenon has yet to be documented for compounds that inhibit translation by the human ribosome. Here we use structure-based design to guide synthesis of molecules called interdictors that bind to the human ribosome PTC and act in a context-selective manner to inhibit translation elongation. Using ribosome profiling, in combination with in vitro biochemistry and cryo-electron microscopy, we characterize the context selectivity of unique analogues and observe their preferred interactions with nascent chain residues with complementary properties. Furthermore, we present a structure for an interdictor bound to a portion of the MYC protein at ~ 1.9 Å resolution and identify resulting structural rearrangements in both the nascent chain and ribosomal RNA. Finally, we document how these compounds differentially impact the ribotoxic stress response pathway which monitors ribosome collisions and can lead to apoptosis. Together, our data establish sequence-selective inhibition of translation as a novel small-molecule therapeutic modality for historically difficult to address cancers by targeting translation of oncogenic dependency factors in the human ribosome PTC.

overall_design: To determine the impact and context selectivity of Interdictors on translation, we treated HCC1143 TNBC cells with compound for 1 hour and performed ribosome profiling. DMSO treated samples were used as a control.

first: Paul

middle: V

last: Sauer

first: Mikael

last: Holm

first: Canessa

middle: J

last: Swanson-Swett

first: Lucas

last: Ferguson

first: Natalie

last: Bratset

first: Grant

last: Wienker

first: Justin

middle: S

last: Sim

first: Hailey

last: Adams

first: Lillian

last: Kenner

first: Margot

last: Meyers

last: Gygi

first: Zef

last: Könst

first: Sogole

last: Bahmanyar

first: Lawrence

last: Hamann

first: Anthony

last: Schuller


title: Characterization of gRNA-Dependent and gRNA-Independent Off-Target Binding Sites of PspCas13b and RfxCas13d in Mammalian Cells [RNA-Seq]

first: Li

last: Zhixue

overall_design: Lenti-X 293T cells transfected with empty vector, Lenti-X 293T cells transfected with dPspCas13b expression plasmid,  Lenti-X 293T cells co-transfected with dPspCas13b expression plasmid and  a non-targeting gRNA (gNT) constructs,  Lenti-X 293T cells co-transfected with dPspCas13b expression plasmid and a targeting gRNA (EZH2-g1, EZH2-g2 or TP53-g1) constructs, Lenti-X 293T cells transfected with dRfxCas13d expression plasmid,  Lenti-X 293T cells co-transfected with dRfxCas13d expression plasmid and  a non-targeting gRNA (gNT) constructs,  Lenti-X 293T cells co-transfected with dRfxCas13d expression plasmid and a targeting gRNA  (EZH2-g1, EZH2-g2 or TP53-g1) constructs were prapared for RNA-seq.

first: Huanhuan

last: Feng

first: Zhixue

last: Li

first: Ligang

last: Wu

first: Lin

last: Zou


title: Targeting ADAR1-mediated RNA editing inhibits hepatic stellate cell activation and liver fibrosis by enhancing HSC-intrinsic IFN signaling

status: Public on Jan 23 2026

first: Yue

last: Xi

address: 81 St

department: College of life sciences

institute: Wuhan University

summary: This study aims to characterize the RNA editome during fibrogenesis and to elucidate the role of ADAR1 in hepatic stellate cell (HSC) activation and liver fibrosis. We showed that ADAR1 ablation in primary mouse HSCs ameliorated HSC activation. Mechanistically, ADAR1 ablation led to dsRNA accumulation and activated HSC-intrinsic IFN signaling in an MDA5-dependent manner. RNA editome analysis revealed that the 3’ UTR of the pro-fibrogenic gene Col3a1 was highly edited by ADAR1, leading to mRNA stabilization and increased protein expression. Targeting ADAR1-mediated RNA editing in HSCs holds promise to prevent and treat liver fibrosis.

overall_design: Primary HSCs isolated from Adar1f/f/Cre-ER mice were treated with vehicle or 100 nM of 4-OHT to induce Adar1 ablation and culture-activated for 4 days.

first: Min

last: Zhang

first: Pengfei

last: Xu

first: Wen

last: Xie


title: Context-dependent translation inhibition as a novel oncology therapeutic modality

first: Paige

last: Diamond

first: Paul

last: Sauer

first: Mikael

last: Holm

first: Canessa

last: Swanson-Swett

first: Lucas

last: Ferguson

first: Natalie

last: Bratset

first: Grant

last: Wienker

first: Justin

last: Sim

middle: K

last: Adams

first: David


title: A Nanopore-Based HIV-1 Reference Epitranscriptome

status: Public on Jan 22 2026

city: Winston-Salem

first: Keith

last: Gagnon

state: NC

address: 575 Patterson Ave

department: Biochemistry

institute: Wake Forest Baptist Medical Center

summary: Post-transcriptional modifications to RNA, which comprise the epitranscriptome, play important roles in RNA metabolism, gene regulation, and disease pathogenesis. However, mapping modifications and characterizing their function is often challenged by a lack of consensus on their presence and significance. The availability of reference epitranscriptomes to benchmark data would significantly advance epitranscriptomic studies. Toward this goal, we established a reference epitranscriptome for human immunodeficiency virus 1 (HIV-1), an important human pathogen. We sequenced a model HIV-1 genome from infected T cells using the latest nanopore technology. A sense and novel preliminary antisense HIV-1 epitranscriptome were generated where N6-methyladenosine, 5-methylcytosine, pseudouridine, inosine, and 2'-O-methyl modifications were mapped by multiplexed base calling at nucleotide resolution. Modification miscalling due to sequence and modification context was corrected with synthetic RNA fragments and m6A was validated with an inhibitor. Modifications were stable under combination antiretroviral therapy (cART) treatment, in primary CD4+ T cells, and in HIV-1 virions. In contrast, spliced transcript-dependent modification levels were observed. Sequencing samples from people living with HIV (PLWH) revealed substantial conservation of m6A in circulating strains. Our approach offers a benchmark reference to advance HIV-1 epitranscriptomics and provides a roadmap for the creation of reference epitranscriptomes for other viruses or pathogens.

overall_design:
Nanopore direct RNA-seq of Jurkat and CD4+ T cells, infected with HIV-1 and treated with or without cART, in order to detect changes in HIV-1 RNA modification patterns. Synthesized fragments with known RNA modifications were used as modification-calling controls.
POD5 files for these samples are available at https://zenodo.org/records/18223642 .

first: Michael

last: Bosmeny

first: Adrian

last: Pater

first: Li

first: Lydia

last: Larkai

first: Beverly

middle: E

last: Sha

first: Zidi

last: Lyu

first: Masad

last: Damha

first: João

middle: I

last: Mamede


title: HIV impairs and exploits pulmonary Th17 and Th22 cell-mediated immune responses to Mycobacterium tuberculosis

first: Haiping

last: Hao

address: 301 University Blvd

institute: UTMB NGS Core

summary: Tuberculosis (TB), caused by the bacteria Mycobacterium tuberculosis (Mtb), is the world’s leading cause of death by infectious disease, as well as the leading cause of death in people with HIV.  The cytokines interleukin (IL)-17 and IL-22 are chemical messengers that are essential for a protective immune response to Mtb infections and tissue repair following bacterial clearance, respectively. The CD4+ T cell subsets that are primary sources of these cytokines, Th17 and Th22 cells, are also primary targets for HIV infection at mucosal surfaces like the gut and lung. Our work reveals Th17 as important HIV viral reservoirs in organs of Mtb/HIV co-infection, with defective immune signals compared to Mtb single infection in the humanized mouse model. Th22 responses were also decreased by HIV in both mono- and Mtb/HIV co-infection as early as nine days after infection. These results have potential applications for future TB therapeutic vaccine design and may implicate possible targets to augment TB therapy.

overall_design: RNA-seq profiling lung tissues of mouse with human immune stem cells either mock infected, infected with TB, infected with HIV, or co-infected with TB and HIV.

first: Yazmin

last: Martinez-Martinez

first: Matthew

last: Huante

first: Kubra

middle: F

last: Naqvi

first: Mithil

middle: N

last: Shah

first: Joshua

last: Lisinicchia

first: Megan

last: Files

first: Jaid

last: Perez

first: Benjamin

last: Gelman

first: Mark

last: Endsley

first: Janice


title: Targeting Fused in Sarcoma (FUS): A Novel Antisense Strategy for Treating Idiopathic Pulmonary Fibrosis [CLIP-Seq]

first: Stefan

last: Günther

overall_design: CLIP-Seq of FUS from healthy donor (HD) and IPF fibroblasts and respective inputs (RNA from total cells)

first: Poornima

last: Mahavadi

last: Guenther


title: RNA-seq analysis of periostin-stimulated human nasal epithelial cells

city: Sakado

first: Yusuke

last: Ando

state: Saitama

address: 1-1, Keyaki-dai

country: Japan

institute: Josai University

summary: This study investigates transcriptomic changes induced by recombinant human periostin in cultured normal human nasal epithelial cells using bulk RNA sequencing.

overall_design: Primary human nasal epithelial cells were cultured in vitro and treated with recombinant human periostin or vehicle control. Total RNA was extracted and subjected to paired-end bulk RNA sequencing to compare gene expression profiles between conditions.

first: Yoshihiko

last: Chiba


title: Notch signaling in the embryonic ectoderm promotes periderm cell fate and represses mineralization of vibrissa hair follicles

city: Aurora

first: Hong

last: Li

state: CO

department: Craniofacial Biology

institute: University of Colorado Denver Anschutz Medical Campus

summary: The Notch signaling pathway is a critical means to regulate cell face choice in animals.  Appropriate regulation of this pathway is also required for human face formation as both loss and gain of function mutations of Notch signaling can cause craniofacial syndromes.  Here we examine the consequences of manipulation of Notch signaling in the early mouse embryonic ectoderm by either removing the transcriptional effector Rbpj or expressing a constitutively active form of the Notch1 intracellular domain.  Loss of Rbpj resulted in cleft secondary palate but strikingly was also associated with the ectopic mineralization of vibrissal follicles.  In contrast, activation of Notch signaling resulted in multiple embryonic defects including a fully penetrant bilateral cleft lip and palate.  Further, single cell RNA-seq data indicated a switch from a basal epithelial cell identity towards periderm when Notch signal transduction was elevated.  These cell fate changes were accompanied by misregulation of genes and pathways known to impact human and mouse orofacial clefting including Grhl3, Irf6, and the Wnt pathway.  Together, these findings provide insight into human craniofacial conditions caused by misregulated Notch activity.

overall_design: Single-cell RNA sequencing was performed on microdissected regions of the upper face where the nasal and maxillary prominences are juxtaposed, including the lambdoid junction, nasolacrimal groove, and nasal fin, from E11.5 control and NotchGOF mutant embryos. For each condition, tissue from two embryos with 43 somites was pooled prior to library preparation. Control and mutant samples were processed separately and sequenced as independent datasets. A total of 11,618 cells were obtained for the control dataset (NotchGOF_Control) and 12,220 cells for the mutant dataset (NotchGOF_mutant). Cells were sequenced to an average depth of 38,111 reads per control cell and 36,122 reads per mutant cell.


title: Targeting Fused in Sarcoma (FUS): A Novel Antisense Strategy for Treating Idiopathic Pulmonary Fibrosis [RNA-Seq PCLS]

overall_design: RNA-Seq profiling of precision cut lung slices (PCLS) from explanted lungs of IPF patients


title: Induced uterine infection alters bovine endometrial function and embryonic competence

city: Gainesville

first: John

middle: James

last: Bromfield

state: FL

address: 2250 Shealy Drive, Dept of Animal Sciences, Rm 108

department: Animal Sciences

institute: University of Florida

summary: Uterine diseases in dairy cattle are associated with reduced fertility, but the specific mechanisms of disease mediated subfertility are not fully elucidated. We hypothesized that an intrauterine infusion of Escherichia coli and Trueperella pyogenes would alter the endometrial transcriptome at a time coincident with conceptus elongation, and compromise oocyte developmental competence. Sixty-one non-lactating Holstein cows received an intrauterine infusion of either saline (n = 29) or pathogenic E. coli and T. pyogenes (n = 32) to induce acute endometrial inflammation. Endometrial samples were collected via cytobrush 41 d after infusion and analyzed by RNA sequencing. Bacteria infusion altered the expression of 203 genes in the endometrium 41 d after infusion. Top upregulated genes were GSTA3, PVALB, JAKMIP2, FOLH1B, TCF23, and top downregulated genes were MYMK, LOC104974498, CDRT1, KIAA0408, SLC45A2. The differentially expressed genes were functionally annotated to 54 canonical pathways with glutathione-mediated detoxification being the top predicted pathway altered following bacteria infusion. Collectively, this work demonstrates that bacterial infections can have lasting effects on the uterus which may provide a link to the long-term subfertility of cows after uterine disease.

overall_design: RNA-seq profiling of endometrial cytobrush samples collected on day 16 of the esrous cycle, 41 days after intrauterne infusion of E. coli MS499 and T. pyogenes MS249 or PBS control.

first: Zackary

last: Seekford


title: Brain lipid profiles and oligodendrocyte gene expression show discordant responses to high-fat diet in Alzheimer’s disease mice.

status: Public on Jan 25 2026

city: Nagoya

first: Noe

last: Kawade

address: Furo-cho, Chikusa-ku

institute: Nagoya university

summary: The brain is a lipid-rich organ, with myelin sheaths containing exceptionally high levels of lipids. Oligodendrocyte dysfunction and myelin lipid deregulation have been implicated in Alzheimer’s disease (AD), yet their precise roles remain unclear. In this study, we examined lipid metabolic alterations, with focus on primary myelin lipids, in AppNL-G-F/NL-G-F (App) AD model mice fed either a normal control diet (NCD) or a high-fat diet (HFD). Brain lipid profiles were altered in App mice, with differential effects depending on diet. Notably, oligodendrocyte gene expression patterns, including those involved in myelin lipid metabolic pathways, were similar between NCD- and HFD-fed App mice and did not correspond with the observed changes in brain lipid composition. This discrepancy indicates that myelin lipid homeostasis in the AD brain is regulated by mechanisms beyond transcriptional control, likely involving post-translational regulation, inter-glial metabolic interactions, and brain-periphery lipid exchange. Importantly, HFD intake did not exacerbate cognitive impairment or neuroinflammation in App mice; rather, HFD-fed App mice showed improved learning during behavioral testing and reduced astrocytic activation. These findings suggest that dietary fat intake does not worsen—and may partially ameliorate—certain aspect of AD pathology, highlighting the complex and context-dependent relationship between metabolic interventions and neurodegenerative disease.

overall_design: RNA-seq profiling of oligodendrocytes isolated from the brains of wildtype C57BL/6J Jcl mice and App NL-G-F/NL-G-F mice fed normal control diet of high-fat diet for 6 months.

first: Okiru

last: Komine

first: Akira

last: Sobue

first: Chihiro

last: Kakimi

first: Miyako

last: Tanaka

first: Takayoshi

last: Suganami

first: Mayuko

last: Shimada

first: Tomoo

last: Ogi

first: Kazutaka

last: Ikeda

first: Mai

last: Horiuchi

first: Seiji

last: Watanabe

first: Takashi

last: Saito

first: Koji

last: Yamanaka


title: The miRNA expression profiles in exosomes derived from M0 macrophages (M0-Exo) and M2 macrophages (M2-Exo).

city: Lanzhou

first: Zhenchang

last: Zhang

state: Gansu

address: No. 222, Tianshui South Road

department: The Second Hospital & Clinical Medical School

institute: Lanzhou University

type: Non-coding RNA profiling by high throughput sequencing

summary: Macrophage-derived exosomes hold significant promise for clinical disease therapy. Macrophages can be categorized into several subtypes. The resting state is known as the M0 subtype, and the exosomes they secrete are termed M0-Exo. Macrophages can be polarized to the M2 subtype by combined induction with IL-4 and IL-13, and the exosomes derived from M2 macrophages are referred to as M2-Exo. miRNAs are important cargo within exosomes. Since both M0-Exo and M2-Exo exhibit therapeutic effects in inflammatory responses, we performed miRNA sequencing on the contents of M0-Exo and M2-Exo to investigate the underlying mechanisms of their therapeutic actions.

overall_design: To ensure sufficient exosome yield, Raw264.7 cells were utilized for exosome isolation. The cells were divided into two groups. M0-Exo group: Raw264.7 cells were cultured under normal conditions for 24 hours, followed by a switch to serum-free medium. The supernatant was then collected for M0-Exo extraction.M2-Exo group: Raw264.7 cells were co-induced with 20 ng/ml IL-4 and 20 ng/ml IL-13 for 24 hours. Subsequently, the medium was replaced with serum-free medium, and the supernatant was collected for M2-Exo extraction.High-throughput sequencing was performed to analyze the miRNA expression profiles in both M0-Exo and M2-Exo.

first: Jinyang

last: Song

first: Gang

last: Su

first: Wei

last: Cheng

first: Xiaodong

last: Xie


title: A novel pyrrolidine-chalcone derivative exhibits synergistic anti-cervical cancer activity by dual-targeting MDM2-p53 axis and ferroptosis pathway

city: Urumqi

first: xinyi

last: deng

address: No. 393 Xinyi Road

department: College of Pharmacy

institute: Xinjiang Medical University

summary: Cervical cancer remains a serious threat to women’s health, driving the need for effective and low-toxicity therapeutics.

overall_design: In this study, we designed and synthesized a novel series of pyrrolidine-chalcone derivatives targeting the MDM2-p53 interaction. The lead compound, B1, exhibited potent, nanomolar- level cytotoxicity against cervical cancer cells (HeLa/SiHa; IC50 = 0.22/0.24 µM) with minimal toxicity to normal cervical epithelial cells (H8). Mechanistic studies revealed that B1 acts through a novel dual mechanism: it activates the p53 pathway by downregulating MDM2, inducing cell cycle arrest and apoptosis, while simultaneously triggering ferroptosis via reactive oxygen species accumulation, glutathione depletion, and suppression of SLC7A11/ GPX4. These findings identify B1 as a promising dual-mechanism lead compound worthy of further investigation in cervical cancer.

first: Xinyi

last: Deng


title: Transcriptional Heterogeneity of Progression in MYOD1-mutant spindle cell rhabdomyosarcoma

city: New York

first: Cristina

last: Antonescu

state: NY

address: 1275 York Avenue

institute: Memorial Sloan Kettering Cancer Center

summary: We perform single nuclei transcriptomics (snRNA-seq) analysis of patient-derived tumor samples to define the dynamic myogenic cell states and intratumoral transcriptional heterogeneity of MYOD1-mutant spindle cell/sclerosing rhabdomyosarcoma.

overall_design: Primary and recurrent/metastatic, snap-frozen patient-derived samples (n = 6) of MYOD1-mutant spRMS were profiled by snRNA-seq using the 10X Genomics platform.

first: Josephine Kam Tai

last: Dermawan

first: Fabio

last: Vanoli

first: Henry

last: De Traux

first: Leonard

last: Wexler

first: Jovana

last: Pavisic

first: Alice

last: Soragni

first: Filemon

last: Dela Cruz


title: Single-cell RNA sequencing of thioglycollate-elicited peritoneal cells from myeloid-specific S1pr1 gain- and loss-of-function mice

status: Public on Jan 21 2026

city: Boston

first: Yueh-Chien

last: Lin

address: 1 Blackfan Circle, Karp Research Building, 12F

department: Vascular Biology Program

institute: Boston Children's Hospital

summary: Sphingosine-1-phosphate receptor 1 (S1pr1) plays an important role in myeloid cell trafficking and inflammatory responses. Here, single-cell RNA sequencing was performed on thioglycollate-elicited peritoneal cells isolated from mice with myeloid-specific S1pr1 gain-of-function or knockout, as well as their corresponding Cre-negative controls. This dataset enables interrogation of S1pr1-dependent transcriptional programs across inflammatory myeloid populations, with downstream analyses focusing on neutrophils.

overall_design: Thioglycollate was administered to elicit inflammatory peritoneal cells in mice. Single-cell suspensions were prepared from the peritoneal cavity and subjected to single-cell RNA sequencing. Mice included myeloid-specific S1pr1 gain-of-function and knockout models generated using LysM-Cre, along with Cre-negative littermate controls. Although multiple myeloid populations were captured, downstream analyses focused on neutrophil subsets identified based on canonical marker expression.

first: Michel

last: Levesque

first: Reed

last: Crocker

first: Timothy

last: Hla


title: Early-stage Col8a2Q455K mutant mouse corneal endothelium Late-stage Col8a2Q455K mutant mouse corneal endothelium Early-stage wild-type mouse corneal endothelium Late-stage wild-type mouse corneal endothelium

city: Qingdao

first: Xintian

last: Zhao

address: shangma road,Qingdao,Shangdong,China

institute: Qingdao Eye Research Institute

summary: Col8a2 mutation is one of the genetic causes of Fuchs endothelial corneal dystrophy (FECD). The Col8a2Q455K homozygous mutant mouse serves as a disease model for FECD. Corneal endothelial cells were isolated from early-stage (≤ 2 months old) and late-stage (≥ 8 months old) Col8a2Q455K homozygous mutant mice and their age-matched wild-type controls. This study investigates transcriptomic alterations associated with FECD progression caused by the Col8a2 mutation.

overall_design: This study includes corneal endothelium samples from Col8a2Q455K homozygous mutant and wild-type mice at early (≤ 2 months) and late (≥ 8 months) disease stages. Each group contains three biological replicates. RNA was extracted from the corneal endothelium and subjected to paired-end RNA sequencing on the Illumina Nova6000 platform. The goal is to elucidate transcriptomic changes underlying the early and late phases of FECD caused by the Col8a2 mutation.

first: Haoyun

last: Duan

first: ZongYi

last: Li


title: Targeting Fused in Sarcoma (FUS): A Novel Antisense Strategy for Treating Idiopathic Pulmonary Fibrosis

status: Public on Jan 20 2026

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

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

overall_design: Refer to individual Series


title: Omics-aided design genome editing strategy for challenging immortalized cell models

city: Mölndal

first: Benjamin

last: Keith

address: Pepparedsleden 1

country: Sweden

institute: AstraZeneca

summary: CRISPR-Cas9 has become a popular genome editing tool for biomedical research and drug development due to its capability to enable precise correction or integration of genetic mutations in the genome. However, precise genome editing competency varies dramatically between cell types depending on their capabilities for DNA damage.  In this proof-of-concept study, we took the example of HepG2 and MCF7 to show that omics profiling identifies bottlenecks that are associated with poor precise knock-in (KI) efficiency in hard-to-engineer cells. These bottlenecks include previously described factors such as the predominance of non-homologous end joining (NHEJ) repair and impaired homologous recombination (HR) capability, but also reveals apoptotic priming status of the cells as a limiting factor. Upon further comparative analysis between HepG2 and MCF7 cells, we pinpointed and validated the proliferating cell nuclear antigen (PCNA) as a target to overexpress to enhance precise KI efficiency in MCF7. Overall, we describe how employing a multi-omics approach to characterize cell models of interest can facilitate an in-depth understanding of their editability molecular signature, empowering us to manipulate the activity of key pathways for precise editing, and therefore increase efficiency of desired editing outcomes.

overall_design: In this study we applied an omics profiling approach to investigate CRISPR-induced DDR in HepG2 (HRD score = 9) and MCF7 (HRD score = 61). Both cell types were electroporated with the same CRISPR ribonucleoprotein (RNP) complex (see “Transfections” section in the methods section of the manuscript) and cultured in separate plates to avoid cross-contamination. RNA  samples were collected 24 and 48 hours after electroporation. As a result, there are two hard-to-change factors in this study. To be able to compare between different cell lines and time points, we applied the split plot design, in which each plate is considered as a whole plot.

first: Patricia

last: Mendoza-Garcia

first: Xiang

last: Zhang


title: Genetic recording of pancreatic beta cell proliferation

city: Shanghai

first: Zhixin

last: Kang

address: 320 Yue Yang Road, Shanghai

institute: Shanghai Institute of Biochemistry and Cell Biology

summary: Pancreatic beta cell generation and proliferation primarily rely on the self renewal of preexisting beta cells, making precise quantification of beta cell proliferation essential for understanding pancreatic homeostasis and pathogenesis. However, previous methods had limitations and were unable to trace beta cell proliferation in vivo over extended periods. Here, we developed beta cell ProTracer, a genetic system that uses dual recombinase technology to enable continuous and cell type–specific recording of beta cell proliferation in mice. The beta cell ProTracer system allows for the quantification of the proliferation rate of adult pancreatic beta cells during homeostasis and in response to injury or drug treatment. Clonal analysis of the proliferated beta cell population reveals a uniform proliferative capacity among these cells. Our findings enhance the understanding of beta cell proliferation dynamics in homeostasis, repair, and regeneration.

overall_design: Pancreatic live cell of beta cell-ProTracer system were isolated and performed scRNA-seq.

first: Huan

first: Hui

last: Chen


title: Dysregulation of microtubule dynamics caused by LOXL3 knockout triggers mitosis catastrophe and senescence in U87MG and U251 cells

city: São Paulo

first: Talita

middle: Sousa

last: Laurentino

state: São Paulo

address: Av Dr Arnaldo, 455. Room 4110

department: Neurologia

country: Brazil

institute: Faculdade de Medicina da Universidade de S&#x00E3

summary: The amine oxidase LOXL3 has been implicated in tumor development and progression, with elevated expression in glioblastoma (GBM). This enzyme influences GBM cell adhesion, migration, and proliferation, and is demonstrated correlation with tubulin expression. Microtubules, as the major component of the cytoskeleton, are crucial for cell cycle and mitotic progression. In this study, LOXL3 knockout was performed using CRISPR-Cas9 in two GBM cell lines, U87MG and U251, to achieve high silencing efficiency. The knockdown resulted in decreased cell viability in both cell lines. Transcriptome enrichment analysis of U87MG cells revealed downregulation of genes associated to tubulin acetylation, which was subsequently confirmed by Western blot analysis. Both U87MG and U251 cells exhibited downregulation of cell cycle and proliferation-related genes. Functional assays confirmed that LOXL3-knockout cells exhibited delayed cell cycle progression and significant alterations in mitotic spindles during metaphase-anaphase transition. Nuclear analysis revealed morphological changes indicative of mitotic catastrophe in U87MG cells and senescence in U251 cells. Additionally, LOXL3-knockout clones displayed reduced cell adhesion and migration. Interestingly, LOXL3 knockdown in GBM cell lines reduces tubulin acetylation, leading to mitotic catastrophe and subsequent cell death in a TP53 mutation-dependent manner. These findings highlight the potential of targeting LOXL3 as a combinatory strategy for advancing research and developing novel therapeutic approaches in TP53-mutated GBM.

overall_design: RNAseq profiling of wilditype U87MG and U251 glioblastoma cells and their permanent LOXL3 knockdown (LOXL3-KD), through CRISPR-Cas9 system.

first: Roseli

last: Soares

first: Antônio

last: Lerario

first: Ricardo

middle: C

last: Cintra

first: Suely

last: Marie

first: Sueli

last: Oba-Shinjo


title: Embryonic stem cell factors DPPA2/4 amplify active H3K4me3-H2AK119ub chromatin domains in non-small cell lung cancer (RNA-seq)

city: Melbourne

first: Janith

last: Seneviratne

state: VIC

address: Peter MacCallum Cancer Centre, 305 Grattan Street

institute: Peter MacCallum Cancer Centre

summary: Embryonic regulators are often re-expressed in cancers, however the functional and molecular significance of this is not always understood. The epigenetic priming factors Developmental Pluripotency Associated 2 and 4 (DPPA2/4) have crucial roles in early development and are implicated in cancer pathogenesis. We reveal in non-small cell lung cancer (NSCLC), DPPA2/4 co-expression is associated with poorly differentiated tumours and impaired patient outcomes. Biochemically, human DPPA2/4 multimerise for their protein stability and enhanced nucleosome binding activity. In NSCLC cells, DPPA2/4 bind CG-rich sequences including promoters of developmental, Wnt signaling and catabolic genes. Chromatin state modelling revealed DPPA2/4 preferentially bind active H3K4me3 and H3K27ac domains that were intriguingly also enriched for PRC1 and its product H2AK119ub, validated by H3K4me3-H2AK119ub sequential ChIP. Knockdown experiments revealed DPPA2/4 were required to maintain RING1B and H2AK119ub at these domains. Surprisingly, despite the presence of PRC2.1, these regions lacked any detectable H3K27me3, suggesting an uncoupling between the recruitment of PRC2 to chromatin and its catalytic product. When exogenously over-expressed in NSCLC cells where they are not normally present, DPPA2/4 bind to and promote active chromatin states, resulting in an increase in vivo xenograft tumour growth. Our results demonstrate how in NSCLC cells, DPPA2/4 act as molecular amplifiers of active and poised chromatin. Together, this highlights how aberrant re-activation of embryonic factors in cancers may take on new functions, promoting tumourigenesis.

overall_design: The NCI-H661 cell line is derived from lung large cell carcinoma (subtype of non-small cell lung cancer) metastases and expresses both DPPA2 and DPPA4 highly at the mRNA and protein level. In order to investigate the functional consequence of peturbing DPPA2/4 we performed CRISPR-Cas9 mediated knockout, shRNA-mediated knockdown or siRNA-mediated knockdown of DPPA2 or/and DPPA4 in NCI-H661 cells followed by RNA-seq analyses. For CRISPR-Cas9, analyses of the parental (PAR) cell line as well as wild type (WT) and knockout clones (KO) were conducted. We included two clones per genotype for analyses to determine functional phenotypes while accounting for those attributed to clonal heterogeneity. Analyses were conducted for shRNA models as well following 7 days of induction with either H20 vehicle control or 2ug/mL doxycyline, for control shRNA (shREN), shDPPA2, shDPPA4 or both shDPPA2+4. Analyses were conducted for siRNA models following 96h of knockdown with either control siRNA, siDPPA2, siDPPA4 or both siDPPA2+4. All conditions were done in biological triplicates. For siRNA models we additionally assessed DPPA2 or DPPA4 knockdown in  A427, COV318, DMS114 and HUTU80 cancer cell lines. We also performed analyses on NCI-H661 cells treated with either a vehicle control (DMSO) or the p300/CBP inhibitor A-485 (10uM).

first: Melanie

last: Eckersley-Maslin


title: Transcriptional profiles of macrophages during wound healing in zebrafish

city: Montpellier

first: Mai-Eva

last: Nguyen-chi

address: Pl. Eugène Bataillon

country: France

institute: CNRS

summary:
To investigate the polarization status of macrophages during wound healing in zebrafish we performed fin fold amputation at 3 days-post-fertilization and isolated macrophages at different time after wounding.
The objective is to characterize the transcriptional profile of macrophages at different time points after wounding.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for macrophages CUT larvae at 2 hours post-amputation (4 replicates), 5 hours post-amputation (4 replicates) and 29 hours post-amputation (4 replicates). Controls are macrophages from non-amputated larvae at 2 hours post-infection (4 replicates), 5 hours post-amputation (4 replicates) and 29 hours post-amputation (4 replicates).

first: Christina

last: Begon-Pescia

first: Mai

last: Nguyen-Chi

first: Laurent

last: Manchon


title: Distinct SOX9 single-molecule dynamics characterize adult differentiation and fetal-like reprogrammed states in intestinal organoids

city: Berkeley

first: Robert

last: Tjian

address: University of California, Berkeley 450 Li Ka Shing #3370

department: MCB

institute: UC Berkeley

summary:
Transcription factors (TFs) mediate gene expression changes during differentiation and development. However, how TF biophysical properties and abundance dynamically regulate specific cell state transitions remains poorly understood.

Using automated live-cell single-molecule tracking (SMT) in intestinal organoid models, we revealed an expression level-independent decrease in the fraction of immobile SOX9 molecules during differentiation from ~48% to ~38%, largely dependent on DNA binding. Strikingly, long-term SOX9 overexpression caused organoids to transition from budding to spheroid morphology accompanied by increased proliferation and a loss in gene expression signatures for intestinal identity and function. In this fetal-like reprogrammed state, a larger fraction of partially self-interacting SOX9 molecules (~61%) binds to DNA.

Our results suggest context-dependent SOX9 single-molecule dynamics during adult intestinal differentiation and fetal-like reversion in consequence to long-term SOX9 overexpression. Our work underpins the power of our automated live-cell SMT framework to generate testable hypotheses towards unraveling molecular mechanisms underlying tissue-level phenotypes.

Contact: nikewalther.science@gmail.com

overall_design: Please check the following: Poly-A RNA-seq profiling of mouse small intestinal organoids stably expressing Halo-NLS (control organoids, 3 biological replicates) or Halo- or mEGFP-tagged Sox9 (organoids and "spheroids", 3 biological replicates each)

first: Nike

last: Walther

first: Claudia

last: Cattoglio


title: RNA-seq analysis of MDA-MB-231 triple-negative breast cancer cells treated with CIr2 for 24 h

city: Guilin

first: Houmin

last: Lin

state: Guangxi

address: 15 Lequn Road, Guilin, 541001, Guangxi, China

institute: The First Affiliated Hospital of Guilin Medical University

summary: This study investigates the transcriptomic alterations induced by a novel cyclometalated iridium(III) compound, CIr2, in triple-negative breast cancer (TNBC) cells. MDA-MB-231 cells were treated with CIr2 for 24 h, followed by RNA sequencing to profile global gene expression changes. The RNA-seq data were integrated with functional assays and morphological analyses to explore cellular responses associated with mitochondrial dysfunction, reactive oxygen species production, endoplasmic reticulum stress, and MAPK signaling. This dataset provides a resource for examining CIr2-induced transcriptional programs related to non-apoptotic cell death pathways in TNBC cells.

overall_design: RNA-seq was performed to compare global gene expression profiles of MDA-MB-231 triple-negative breast cancer cells treated with vehicle control or 500 nM CIr2 for 24 h.

first: Jianhua

last: Wei

first: Wenmin

last: Yao

first: Qinqin

last: Zhang

first: Junfei

last: Jin


title: Diploid Hepatocytes Resist Acetaminophen-Induced Liver Injury Through Suppressed JNK Signaling

city: Pittsburgh

first: Shuchang

last: Liu

state: PA

address: 203 Lothrop Street

institute: University of Pittsburgh

summary: Background & Aims: The liver contains both diploid and polyploid hepatocytes, but their functional differences remain poorly understood. Emerging evidence suggests that each ploidy state contributes to regeneration in an injury-specific manner. We hypothesized that diploid hepatocytes promote healing after acetaminophen (APAP)-induced liver injury. Approach & Results: To study ploidy populations in vivo, we utilized mice with a lifelong liver-specific knockout of E2f7/E2f8 (LKO), which are enriched in diploid hepatocytes (>70%) but otherwise normal. Control and LKO mice were treated with APAP (300 or 600 mg/kg), and injury was assessed over 0-96 hours. Although both groups sustained injury, LKO mice showed improved survival, lower serum liver enzyme levels, and reduced necrosis and DNA fragmentation, indicating resistance to APAP-induced injury. To determine if resistance was due to E2f7/E2f8 loss or increased diploidy, we deleted E2f7/E2f8 in adult hepatocytes (HKO), a model that does not alter ploidy. Injury was similar between controls and HKO, ruling out gene deletion as the protective factor. Transcriptomic and protein analyses revealed minimal baseline differences; however, following APAP treatment, LKO livers exhibited reduced JNK activation and less mitochondrial injury. Finally, APAP-treated wild-type hepatocytes exhibited a shift toward lower ploidy, supporting the idea that diploid cells are more resistant to injury. Conclusions: Diploid hepatocytes resist APAP-induced liver injury through reduced JNK activation and mitochondrial damage. These findings highlight hepatocyte ploidy as a key determinant of injury response and suggest a protective role for diploid hepatocytes in promoting liver resilience and regeneration.

overall_design: Wild-type (WT) and Alb-Cre–driven liver-specific E2f7/E2f8 knockout mice (LKO; indicated as “KO” in the sample list) were used. Hepatocyte-specific knockouts (HKO; indicated as “CRE” in the sample list) were generated by intravenous injection of AAV8-TBG-Cre viral particles into 2-month-old floxed mice; control mice (indicated as “NULL” in the sample list) received AAV8-TBG-Null. Male, 2.5-month old mice were fasted overnight (~16 hours) and administered 300 mg/kg acetaminophen (APAP) via intraperitoneal injection. Livers were harvested at 0, 12, 24, 48, 72, and 96 hours post-injection and snap-frozen. Total RNA was extracted from frozen liver tissue using TRIzol reagent. For baseline (0 hour) samples, RNA was isolated from individual mice (n = 4 per genotype). For time points from 12 to 96 hours, RNA from three biological replicates per genotype per time point was pooled prior to sequencing (n = 3 mice pooled per group).

first: Sierra

middle: R

last: Wilson

first: Evan

last: Delgado

first: Frances

last: Alencastro

first: Rosa

last: Loewenstein

first: Madeleine

middle: P

last: Leek

first: Leah

last: Peters

first: Kerollos

last: Kamel

first: Patrick

middle: D

last: Wilkinson

first: Siddhi

last: Jain

first: Joseph

last: Locker

first: Silvia

first: Bharat

last: Bhushan

first: Andrew

middle: W

last: Duncan


title: NF-κB activation in astrocytes critically affects wound regeneration after traumatic brain injury II

city: Ulm

first: Bernd

last: Baumann

address: Albert-Einstein-Allee 11

institute: Ulm University

summary: Traumatic brain injury (TBI) is a complex condition in which multiple pathophysiological mechanisms influence the course of the disease. After the primary mechanical impact, neuroinflammatory reactions of glial cells along with infiltrating peripheral immune cells mainly determine the overall clinical outcome. However, these secondary processes and their molecular determinants promoting either beneficial or detrimental consequences are not well-defined. Here, we show that TBI-mediated NF-κB activation in astrocytes impairs their homeostatic functions and acts as a key regulator of multiple post-traumatic responses in mice. We determined striking deficits in CNS scar formation after TBI using a combination of NF-κB-reporter mice, conditional mouse models allowing astrocytic NF-κB modulation, and analysis of transcriptomic signatures. Importantly, the development of wound healing deficits depends on paracrine signaling of NF-κB-activated astrocytes and cross-responsive microglial cells.Our findings identify astrocytic NF-κB activation as a critical pathological amplification factor interfering with the restoration of CNS integrity at wound lesion sites.

overall_design: Wildtype mice were subjected to TBI/closed head injury (CHI). Tissue was taken from the insult area at day 3 post TBI or sham treatment and used for RNA sequencing. The was the identification of pathways prominently activated in response to TBI, as well as the analysis of NF-kappaB-associated activation patterns.

first: Heinrich

last: Wendt

first: Tabea

middle: M

last: Hein

first: Thomas

last: Wirth


title: Embryonic stem cell factors DPPA2/4 amplify active H3K4me3-H2AK119ub chromatin domains in non-small cell lung cancer

first: Janith

last: Seneviratne


title: Metabolic reprogramming regulates histone lactylation during zebrafish caudal fin regeneration

status: Public on Jan 19 2026

city: Lisobon

first: António

last: Jacinto

address: Campus de Campolide

country: Portugal

institute: NIMSB - NOVA Institute for Medical Systens Biology

summary: Tissue regeneration relies on precise molecular mechanisms controlling cell fate transitions, with cell metabolism emerging as a key regulator. Lactate-derived histone lactylation has recently been identified as an important epigenetic modification involved in the regulation of gene expression across various biological processes. In this study, we report an increase in global histone lactylation and H3K18Lac levels in the mesenchyme and osteoblasts of the zebrafish caudal fin, during the early stages of regeneration. Our findings demonstrate that this epigenetic modification is functionally regulated by increased lactate levels, while inhibition of glycolysis and lactate production significantly reduces histone lactylation. These results suggest that metabolic reprogramming, in response to caudal fin injury, regulates histone lactylation, potentially modulating gene expression essential for cell plasticity and proliferation. This study expands our understanding of how metabolic-epigenetic interactions influence regenerative processes, providing valuable insights for the development of novel therapeutic strategies to enhance tissue repair.

overall_design: RNA-seq profiling of zebrafish caudal fin regenerating tissue treated with Galloflavin or Vehicle (DMSO) and collected 24h after amputation.

first: Jorge

last: Borbinha

first: Raquel

last: Lourenço

first: Ana

last: Brandão

first: Daniel

last: Ribeiro

last: Carvalho

first: Rune

last: Matthiesen


title: NF-κB activation in astrocytes critically affects wound regeneration after traumatic brain injury

summary:
Traumatic brain injury (TBI) is a complex condition in which multiple pathophysiological mechanisms influence the course of the disease. After the primary mechanical impact, neuroinflammatory reactions of glial cells along with infiltrating peripheral immune cells mainly determine the overall clinical outcome. However, these secondary processes and their molecular determinants promoting either beneficial or detrimental consequences are not well-defined. Here, we show that TBI-mediated NF-κB activation in astrocytes impairs their homeostatic functions and acts as a key regulator of multiple post-traumatic responses in mice. We determined striking deficits in CNS scar formation after TBI using a combination of NF-κB-reporter mice, conditional mouse models allowing astrocytic NF-κB modulation, and analysis of transcriptomic signatures. Importantly, the development of wound healing deficits depends on paracrine signaling of NF-κB-activated astrocytes and cross-responsive microglial cells.
Our findings identify astrocytic NF-κB activation as a critical pathological amplification factor interfering with the restoration of CNS integrity at wound lesion sites.

overall_design: To further analyzed the impact of astrocytic IKK/NF-kappaB modulation on the post-traumatic transcriptome using an IKK2 gain-of-function (GoF) and IKK2 loss-of-function (LoF) mouse model


title: Embryonic stem cell factors DPPA2/4 amplify active H3K4me3-H2AK119ub chromatin domains in non-small cell lung cancer (BS-seq)

overall_design: The NCI-H661 cell line is derived from lung large cell carcinoma (subtype of non-small cell lung cancer) metastases and expresses both DPPA2 and DPPA4 highly at the mRNA and protein level. In order to investigate the functional consequence of peturbing DPPA2/4 we performed siRNA-mediated knockdown of DPPA2 or/and DPPA4 in NCI-H661 cells followed by whole genome bisulfite sequencing (WGBS) analyses. Analyses were conducted for siRNA models following 96h of knockdown with either control siRNA, siDPPA2, siDPPA4 or both siDPPA2+4. All conditions were done in biological triplicates. We additionally assessed DPPA4 knockdown in the COV318 ovarian cancer cell line.

middle: A

first: Melanie

last: Eckersley-Maslin


title: Embryonic stem cell factors DPPA2/4 amplify active H3K4me3-H2AK119ub chromatin domains in non-small cell lung cancer (CUT&Run)

overall_design: The NCI-H661 cell line is derived from lung large cell carcinoma (subtype of non-small cell lung cancer) metastases and expresses both DPPA2 and DPPA4 highly at the mRNA and protein level. In order to investigate DPPA2 and DPPA4 co-occupancy as well as other associated transcription factors/histone modifications (RING1B, MTF2, EP300, PCGF1, SOX2, H3K4me3) in NCI-H661 cells we performed cleaveage under targets and release using nuclease (CUT&RUN) analyses of these proteins/modifications. Analyses were conducted in parental H661 cells and also following shRNA mediated knockdown of DPPA2/4. We additionally profiling exogenously expressed DPPA2 (with Flag-tag) and DPPA4 (with V5-tag) in the NCI-H1299 non-small cell lung cancer cell line. All assays were controlled with isotype controls (Rabbit or Mouse IgG's) having either a singular or duplicate replicates.


title: Single-cell RNA sequencing revealed cell heterogeneity in sagittal suture mesenchyme

city: Wuhan

first: Kai

last: Sun

address: No. 237, Luoyu Road, Hongshan District, Wuhan City, Hubei Province

institute: Wuhan university

summary: The formation and homeostatic maintenance of cranial sutures rely on cellular activities within the suture mesenchyme. Mesenchymal stem cells in this niche are characterized by self-renewal capacity and low proliferative activity. However, how they rapidly and extensively contribute to suture formation during early development remains insufficiently explored. In this study, we combined 10x Genomics and Smart-seq3 single-cell transcriptomic sequencing to analyze cellular subpopulations within the sagittal suture mesenchyme.

overall_design: RNA-seq profiling of  sagittal suture  dissected from PN7 wildtype C57BL/6J mice or Gli1-CreERT2; tdTomato mice with tamoxifen induction.

first: Chengyan

last: Ren

first: Ran

last: Wu

first: Chenxin

last: Geng

first: Hu

last: Zhao

first: Weihui

last: Chen


title: A beneficial environment promotes immune resilience through epigenetic regulation

city: München

last: Conlon

address: Ingolstädter Landstraße 1

institute: Helmholtz Zentrum München

summary: Environmental factors are often detrimental; however, certain environments enhance immune resilience. Notably, children raised on traditional farms show reduced allergies and asthma prevalence. Here, we investigated how a beneficial environment, using farm dust (FD) extract, influenced lung immune function in OVA-induced allergic inflammation. FD-exposure reduced allergic lung inflammation and increased monocyte-derived macrophage (MDM) recruitment. scRNA-seq revealed that FD-exposed MDMs had altered gene expression, including dampened Ccl8 and MHCII expression, impairing eosinophil recruitment and antigen presentation. RNA-seq and ATAC-seq confirmed FD-induced epigenetic reprogramming ex-vivo, on bone marrow-derived macrophages. This modulation, seen in both human and murine cells, relied on HDAC activity sustained by PPARγ signaling. These findings suggest that beneficial environmental exposures can reprogram immune cells and may offer a novel strategy for asthma prevention.

overall_design: ATAC-seq profiling of mouse BMDM and BMDC treated with 100 µg/ml FD or PBS twice over a 24-hour period then incubated with 10 ng/ml LPS for 6 hours

first: Markus

last: Klotz

first: Guilherme

last: Dragunas

first: Sirui

first: Deepesh

last: Dhakad

first: Ali

last: Önder Yildirim


title: A comprehensive atlas of testicular interstitium reveals Cd34+/Sox4+ mesenchymal cells as potential Leydig cell progenitors [CUT&Tag]

city: Guangzhou

first: Jia

middle: Xiao

last: Huang

state: Guangdong

address: Zhongshan 2rd

institute: GDPH

summary: Decreasing fertility rates has emerged as a significant social and medical concern, with male infertility accounting for at least half of the cases. Conventional semen analysis offers restricted prognostic utility for male fertility, largely because a considerable number of male infertility incidents are attributed to dysfunctions in the testicular interstitium. Here we have not only characterized transcriptome data and reveals Cd34+/Sox4+ mesenchymal cells as potential Leydig cell progenitor, but also examined super enhancers information in both young, adult and aged mice Leydig cell progenitors. Our findings reveal A comprehensive atlas of testicular interstitium during aging in both H3K27ac modifications and gene expression alterations. Specifically, the transcriptional activities of key genes involved in progenitor stemness appear to be regulated by super-enhancers. These discoveries offer pivotal insights for developing novel cell-based therapies to ameliorate testicular dysfunction in older individuals.

overall_design: To investigate the gene expression and histone modifications changes , we utilized scRNA-seq to delve into the molecular diversity patterns of Leydig cells within the testicular interstitium across postnatal development and aging.


title: A comprehensive atlas of testicular interstitium reveals Cd34+/Sox4+ mesenchymal cells as potential Leydig cell progenitors [scRNA-Seq]