title: Perk is dispensable for smooth muscle cell phenotype switching in atherosclerosis

first: Chenyi

last: Xue

state: NY

institute: Columbia University

summary: Smooth muscle cell (SMC) derived cells (SDCs) form the bulk of cells in atherosclerotic lesions and modulate lesion stability and cardiovascular disease outcomes. Unfolded protein response (UPR) markers, thin fibrous caps, and inflammation correlate with human lesion instability and rupture. In mice, UPR drives macrophage and endothelial apoptosis and inflammation, but its impact on lesion stability through SMC modulation is debated. The UPR protein Perk was recently shown to drive SMC modulation in vivo, suggesting that depletion of SMC Perk may regulate lesion stability. We sought to determine if inducible SMC-specific Perk deletion in adult mice improves characterizations of lesion stability during development and progression of disease.

overall_design: Perk was depleted from the SMCs of adult Ldlr-/- hypercholesterolemic mice via tamoxifen-induced Cre under a Myh11 promotor, which also activated the expression of ZsGreen lineage tracing marker in these cells. Mice were assayed at 0, 4, 8, 12, and 16 weeks of western diet feeding. Aortic tissue from the ascending aorta (root to the distal arch) were isolated from three age-matched male mice of each genotype at each timepoint, hashed with 10X Cell Multiplexing Oligos, sorted for viable ZsGreen1+ and ZsGreen1- populations, pooled by Perk genotype, and subject to scRNA-seq.

first: Lucie

last: Zhu


title: A Translocation within an Ogataea Clade Species Alters Local Subtelomeric Chromatin while Maintaining Global Genome Organization [Hi-C]

status: Public on Mar 05 2026

city: Colorado Springs

first: Andrew

middle: David

last: Klocko

state: Colorado

address: 278 Centennial Hall, 1420 Austin Bluffs Pkwy

department: Chemistry and Biochemistry

country: USA

institute: University of Colorado Colorado Springs

summary: Eukaryotic genomic DNA is packaged in the nucleus as chromatin – a DNA-protein aggregate regulating genome function, including transcription. Chromatin is classified as either active euchromatin or silent heterochromatin, with each marked by distinct histone post-translational modifications (PTMs). Chromatin composition also mediates genome organization, including how heterochromatin aggregates at the nuclear periphery while euchromatin localizes to the nucleus center. In fungi, heterochromatic loci cluster, including independent centromere and telomere clusters that form the Rabl chromosome conformation. However, it is unknown if chromatin composition and genome organization are conserved in closely related fungi, including some yeast species. Here, we examined differences in histone PTM deposition, gene expression, and genome organization in two yeast species from the order Pichiales, which diverged from a common ancestor with Saccharomyces cerevisiae more than 200 million years ago. We focused on Ogataea polymorpha, which is used for industrial protein production, and Ogataea haglerorum, an isolate of which harbors a translocation between chromosomes 1 and 6. We show that the enrichment of three activating PTMs – the trimethylation of lysine 4 of histone H3 (H3K4me3) and the acetylation of lysine 9 of histone H3 (H3K9ac) or lysine 16 of histone H4 (H4K16ac) – are similar genome-wide yet individual gene orthologs have distinct chromatin and expression patterns. While both Ogataea genomes organize into a Rabl conformation, the O. haglerorum translocation alters subtelomeric chromatin composition and expression of genes affected by the translocation. Our work highlights the genome function differences that occur on a microevolutionary scale.

sample_organism:
Ogataea polymorpha
Ogataea haglerorum

platform_organism:
Ogataea polymorpha
Ogataea haglerorum

overall_design: Chromosome conformation capture coupled with high-throughput sequencing of two closely related species within the Ogataea clade, Ogataea polymorpha and Ogataea haglerorum, to assess whether changes in three dimensional genome organization occur following speciation

first: Tiffany

middle: J

last: Lundberg

first: Nickolas

middle: M

last: Lande

first: Daniel

last: Turevski

first: Riley

last: Figueroa

first: Mai

last: Nguyen

first: Collin

last: Ralston

first: Sara

last: Hanson

middle: D


title: RNA-seq of human NK cells that were co-cultured with DU-145 cells, which were pre-treated with hIgG1 isotype, 7C6-hIgG1, or 7C6-GAALIE

city: New York

first: Lucas

last: Ferrari de Andrade

address: 1425 Madison Avenue

institute: Ichan School of Medicine at Mount Sinai

type: Expression profiling by high throughput sequencing

summary: 7C6 is a monoclonal antibody that inhibits the shedding of MICA and MICB, which are stress-induced ligands often expressed by tumor cells. We developed a new version of 7C6, 7C6-GAALIE, which better binds Fc gamma-activating receptors, and analyzed how it reprograms human NK cell gene expression in vitro after co-culture with a target cell line, DU-145.

overall_design: Human NK cells were isolated from volunteer donors and co-cultured for four hours with DU-145 cells, which represent human prostate cancer. Such target cells were pre-treated overnight with hIgG1 isotype, 7C6-hIgG1, or 7C6-GAALIE. After the co-culture, NK cells were collected, and NK cell mRNA was isolated with genomic DNA removal and analyzed by RNA-seq.

first: Ferrari de Andrade

last: Lucas

first: Pimenta

last: Ruan


title: A Translocation within an Ogataea Clade Species Alters Local Subtelomeric Chromatin while Maintaining Global Genome Organization [ChIP-Seq]

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: Chromatin Immunoprecipitation-sequencing (ChIP-seq) of either the trimethylation of lysine 4 on histone H3, or the acetylation of either lysine 9 on histone H3 (H3K9ac) or lysine 16 on histone H4 (H4K16ac) in two closely related species of the Ogataea clade, Ogataea polymorpha or Ogataea haglerorum, to assess the changes in chromatin composition that could occur following speciation.


title: Transient high fat diet causes persistent susceptibility to ferroptosis in CD8 T cells [Ex_vivo_RNAseq]

status: Public on Mar 06 2026

city: Kyoto

first: Masaki

last: Tajima

address: Yoshidakonoe cho

country: Japan

institute: Kyoto University

summary: Chronic metabolic stress impacts the immune cell function, increasing the incidence of autoimmune diseases and cancers. Whether past history of a high fat diet (HFD) leads to immune dysfunction is less understood. Moreover, whether factors other than persistent epigenetic changes would impact on the immune function remain unknown. We find that even a transient exposure to HFD causes persistent metabolome changes and long-term vulnerability of CD8 T cells to oxidative stress. The past HFD signature of CD8 T cells includes enrichment of lipid species highly susceptible to ferroptosis, and depletion of metabolites with anti-oxidant function. We find that xanthine, through the salvage purine pathway fuels the GTP, which is subsequently converted to tetrahydrobiopterin (BH4) and dihydrobiopterin (BH2). Xanthine-derived biopterins serve as ROS scavengers, rescuing CD8 T cells from activation-induced ferroptosis. Administration of xanthine or BH2 markedly reduces tumor growth in mice transiently fed HFD. Our data uncover that metabolic stress remains tattooed on membrane lipids, generating vulnerability to oxidative stress and ferroptosis, that can be mitigated by purine salvage pathway through the replenishment of guanines and biopterins pools.

overall_design: To explore the global transcriptome landscape of CD8 T cells, CD4 T cells, and  B cells from mice treated with normal diet (12 weeks), high fat diet (12 weeks), and switched diet (high fat diet for 6 weeks and then normal diet for 6 weeks) , RNA were isolated from FACS-sorted cells and processed for RNA sequencing.

first: Baihao

last: Zhang

first: Yuhsien

last: Lin

first: Ryoma

last: Kato

first: Sidonia

last: Fagarasan


title: A Translocation within an Ogataea Clade Species Alters Local Subtelomeric Chromatin while Maintaining Global Genome Organization [RNA-Seq]

overall_design: polyadenylated messenger RNA-sequencing (RNA-seq) of log phase growth cultures of the strain Ogataea haglerorum to assess the gene expression within this species (and for comparison with another closely related species in the Ogataea clade, Ogataea polymorpha)


title: BRD9 Reads Lactate-Induced H3K18 Lactylation to Drive Oncogenic Chromatin Remodeling in Hepatocellular Carcinoma

city: Changchun

first: enwei

last: Wei

address: Xinjiang Street

country: China

institute: the first hospital of Jilin University

summary: Histone lactylation bridges glycolytic metabolism to oncogenic transcription, but its mechanistic readers remain poorly defined. Here, we identify bromodomain-containing protein 9 (BRD9) as a lactyl-lysine reader that links lactate-driven H3K18 lactylation (H3K18la) to chromatin remodeling in hepatocellular carcinoma (HCC). Clinically, elevated H3K18la levels correlate with poor HCC prognosis. Structural (NMR) and biophysical analyses demonstrate BRD9’s bromodomain engages H3K18la through its acetyl-lysine pocket with weak, transient affinity, distinct from stable H3K18ac binding, enabling lactate-dependent chromatin interactions. Multi-omics profiling reveals H3K18la recruits BRD9 and the non-canonical BRG1-associated factor (ncBAF) complex to active enhancers and promoters, promoting chromatin accessibility and oncogenic transcription (SPARC, TMEM64, ANGEL1, SCARB1). Glycolytic inhibition or BRD9 targeting displaces BRD9 from chromatin, suppresses oncogenes, and impairs HCC proliferation. p300 or HDAC inhibition attenuates H3K18la-driven oncogenic transcription and tumor viability. Our findings establish BRD9 as a metabolic-epigenetic mediator that translates glycolytic flux into chromatin remodeling, offering actionable therapeutic targets for HCC.

overall_design: This study aims to investigate the transcriptional and epigenetic alterations in HepG2 cells induced by metabolite stress. The overall design encompasses three distinct sequencing assays. RNA-seq: HepG2 cells were treated under three conditions: negative control (NC), Nala (40 mM, 24h), and 2-DG (40 mM, 48h). Each treatment group had three biological replicates (n=3). ChIP-seq: HepG2 cells treated with NC or 2-DG (40 mM, 48h) were subjected to chromatin immunoprecipitation using antibodies against H3K18la and BRD9 (n=1). ATAC-seq: HepG2 cells were treated with NC or 2-DG (40 mM, 48h) to assess changes in chromatin accessibility (n=1).

first: Enwei

first: Donglei

last: Ji

first: Yanjie

last: Jia

first: Ze

last: Sun

first: Chunfeng

last: Gao

first: Caroline

last: Zeng

first: Chunyu

last: Wang

first: Miaomiao

last: Yu

first: Guanglei

last: Shang

first: Linying

last: Xie

first: Wenju

first: Yameng

last: Li

first: Yingying

last: Liang

first: Bai

first: Yanzhu

last: Yue

first: Yahui

last: Liu

first: Ming-Ming

last: Zhou

first: Lei


title: Deep profiling of multiple mouse tumor microenvironments using scRNAseq

city: San Francisco

first: Tristan

last: Courau

state: CA

address: 513 Parnassu Ave

department: Pathology

institute: UCSF

summary: The HuMu dataset (https://www.biorxiv.org/content/10.1101/2025.07.01.661217v1) contains single-cell sequencing data from 9 mouse tumor models that we use to dissect gene expression profiles across populations and tumor models. The data can be readily queried here https://quipi.org/app/quipi_humu

overall_design: Tumors were grown in mice before harvesting at day 14 or ~500mm3, enzymatic dissociation, hashing using TotalSeq A, FACS-based denrichment of lymphoid and myeloid populations, and scRNAseq processing using 10X V3 3' chemistry


title: Transcriptomic and proteomic insights into progressive myoclonus epilepsy, EPM1

city: Helsinki

first: Tarja

middle: Hannele

last: Joensuu

address: P.O. Box 63 (Haartmaninkatu 8)

country: Finland

institute: Folkhälsan Research Center/Medicum

summary: Progressive myoclonus epilepsy EPM1 is a rare neurodegenerative disease caused by partial loss of function of cystatin B (CSTB), a cysteine protease inhibitor with known neuroprotective roles. The disease mechanisms remain largely unsolved, and no treatments are available to control the debilitating myoclonus in EPM1. We investigated the impact of CSTB loss on transcriptome in three regions of CSTB-deficient (Cstb-/-) mouse brain — the cerebellum, cerebral cortex, and hippocampus — during disease progression, providing comprehensive insights into the molecular changes and disease mechanisms.

overall_design: RNA-seq analysis of the cerebellum, cortex, and hippocampus in Cstb⁻/⁻ and wild-type mice across four time points: P14 (14 days, pre-symptomatic, early microglial activation), 1 month (disease onset with myoclonic seizures and glial activation in cerebellum and cortex), 3 months (progressive neuronal loss and brain atrophy), and 6 months (widespread brain atrophy).

first: Alina

last: Malyutina

first: Carina

last: Lund

first: Saara

last: Tegelberg

first: Paula

last: Hakala

first: Tuula

middle: A

last: Nyman

first: Anna-Elina

last: Lehesjoki


title: Change in miRNA levels in SH-SY5Y cells after electroporation of peptide nucleic acid (PNA) targeting precursor micro RNA

city: Kobe

first: Tamai

last: Endoh

address: 7-1-20, Minatojima-minamimachi, Chuo-ku

department: FIRST/FIBER

institute: Konan University

type: Non-coding RNA profiling by high throughput sequencing

summary: Peptide nucleic acid (PNA) is a neutral DNA analog uniquely suited for triple helical recognition of nucleic acids. However, the practical applications of triplex-forming PNAs have been limited by sequence restrictions, as stable base triples are formed only with purines. Hoogsteen recognition of pyrimidines has been a long-standing challenge. Here, a new approach to improve pyrimidine recognition by enhancing nucleobase stacking in the PNA strand is demonstrated by targeting procursor micro RNA (pre-miRNA).  Placing 5-triazolyl uridine adjacent to the modified nucleobases designed for Hoogsteen recognition of pyrimidines in double helical RNA increased the binding affinity while maintaining sequence specificity.  The increased binding affinity improved the biological activity of triplex-forming PNAs. RNA-seq analysis targeting mature microRNAs showed that a PNA recognizing a mixed sequence of three nucleobases (G, A, and U) had higher specificity than a similar PNA featuring a uniform purine recognition tract. These results demonstrate a novel strategy to address the issue of pyrimidine recognition, which has been the critical bottleneck for triple helical targeting of nucleic acids.

overall_design:
Triplicate of miRNA profiling using MCF7 cell lines with or without electroporation of PNA, which targets miRNA-155 or miR-197, after 66-incubation by using QIAseq miRNA Library Kit for Thermo Fisher Scientific NGS Systems and Ion GeneStudio S5 system.
PNA21: targets miR-155
PNA22: does not have exact target miRNA (scrambled control of PNA21)
PNA23: targets miR-197
PNA24: targets miR-197
PNA25: does not have exact target miRNA (scrambled control of PNA24)

first: Sara Farshineh

last: Saei

first: Tamaki

first: Vladislavs

last: Baskevics

first: Ilze

last: Kumpina

first: Martins

last: Katkevics

first: Naoki

last: Sugimoto

first: Eriks

last: Rozners


title: H3K27me3 spreading organizes canonical PRC1 chromatin architecture to regulate developmental programs [scRNA-seq]

status: Public on Mar 09 2026

city: Montreal

first: Jacek

last: Majewski

state: Quebec

address: 740 Dr. Penfield

department: Human Genetics

country: Canada

institute: McGill University

summary: Polycomb Repressive Complex 2 (PRC2) deposits H3K27me3 to recruit canonical PRC1 (cPRC1) that establishes repressive heterochromatin. Higher order cPRC1-mediated chromatin interactions characterize early development and resolve during cell differentiation. Here, we use two opposing models of H3K27me3 dysregulation to elucidate how these long-range loops affect gene expression and cellular phenotypes. Aggressive gliomas driven by histone H3 Lys-27-Met (H3K27M) mutations or EZH-Interacting Protein (EZHIP) expression confine H3K27me3 deposition to PRC2 nucleation sites, while loss of the H3K36 methyltransferase NSD1 in pluripotent stem cells leads to its unrestrained spread from these sites.  In H3K27M mutant tumours, focal H3K27me3 deposition concentrates chromatin occupancy of cPRC1 complexes, which results in long-range chromatin interactions anchored in polycomb bodies, mirroring patterns found in stem cells. Conversely, spread of H3K27me3 due to NSD1 loss dilutes cPRC1 deposition and disrupts polycomb body architecture. In H3K27M cells, H3K27me3 confinement sustains repression of genes tethered to the polycomb bodies, promoting self-renewing progenitor states required for tumour development. Maintenance of progenitor states depends on cPRC1 interaction with H3K27me3, as chemical allosteric modulation of chromodomains alleviates repression of transcription and promotes differentiation. These results suggest that H3K27me3 spread from CGIs modulates cPRC1 gene expression programs to orchestrate developmental transitions through the maintenance or dissolution of repressive 3D loop architecture at polycomb bodies. Imbalances in the spread of H3K27me3 altering chromatin architecture in disease including H3K27M-expressing neoplasms or following NSD1 loss contribute to explain pathogenic states.

overall_design: Hi-C, ChIP-seq, bulk and single-cell RNA-seq on model systems with altered H3K27me3 spread

first: Nada

last: Jabado

first: Chao

last: Lu


title: Transcriptional Response of pe/ppe Knockout Mutants in Mycobacterium tuberculosis

city: Seattle

first: Christoph

last: Grundner

state: WA

address: 1900 9th Ave

department: Center for Global Infectious Disease Research

institute: Seattle Children's Research Institute

summary: To investigate the impact of ppe51, pe25/ppe41 and ppe42 deletion on global transcriptional changes in Mycobacterium tuberculosis, we compared gene expression profiles of the knockout strains with wild-type H37Rv.

overall_design: Wild-type (WT) H37Rv and the ppe51, pe25/ppe41 and ppe42 deletion strains were cultured in 7H9 medium supplemented with 10% OADC, 0.5% glycerol, 0.05% Tyloxapol, and 100 μM sodium propionate until an OD600 of 0.8 was reached. Cells were then pelleted, resuspended in buffered water, and incubated for an additional 5 hours. Bacterial pellets were collected, RNA was isolated and gene expression quantified by sequencing.

first: Vishant

last: Boradia

first: Andrew

last: Frando


title: Unconventional Control of Fetal Hematopoiesis by Ribosomal Subunits RPS19 and RPL5

city: Memphis

first: Te

last: Ling

state: TN

address: 262 Danny Thomas Pl

institute: St. Jude Children's Research Hospital

summary: Ribosomopathies are associated with anemia; yet, the precise control of ribosomal protein (RP) stoichiometry and activity during erythroid development remains elusive. Using Diamond-Blackfan anemia (DBA) as a model, we generated novel in vivo models of RP haploinsufficiency to define the roles of small and large RP subunits in fetal hematopoiesis. Rpl5 haploinsufficiency caused prenatal lethality due to a reduction in erythroid translation. Conversely, Rps19 haploinsufficiency led to neonatal stem cell exhaustion and impaired erythroid progenitor expansion, resulting from combined translational and transcriptional defects. The stem cell factor RUNX1 is upregulated in RPS19-haploinsufficient DBA patients and its deletion partially rescued hematopoiesis in Rps19 mutant mice. Our findings reveal distinct, subunit-specific roles for RPs in fetal hematopoiesis and demonstrate that imbalanced RP stoichiometry disrupts developmental programs, providing key insights into DBA pathogenesis and patient heterogeneity while underscoring the importance of balanced RP expression in stem cell and erythroid progenitor development.

overall_design: Fetal liver cells from E13.5 embryos were used for scRNA-seq or scMultiome-seq and 2 individual fetal livers from the same genotype group were utilized.

first: Yuefeng

last: Tang

first: Rashid

last: Mehmood

first: John

last: Crispino

first: Lionel

last: Blanc


title: scRNA-seq of wildtype and MZwnt11/slb zebrafish embryos

city: Heidelberg

first: Nicoletta

last: Petridou

state: BW

address: Meyerhofstrasse 1

department: DB

country: Germany

institute: EMBL

summary: Transcriptomics dataset for the study of developmental differences between wildtype and MZwnt11/slb mutants at shield stage

overall_design: scRNA-seq using ACME dissociation fixation of zebrafish wildtype and MZwnt11/slb embryos at shield stage

first: Camilla

last: Autorino

first: Cristina

last: Pallares Cartes

first: Louise

last: Harari

first: Michael

last: Dorrity


title: Gene expression profiles of CBPWTp53-floxed, CBPAAp53-floxed,CBPWTp53ΔIEC and  CBPAAp53ΔIEC  intestinal cyrpts

city: Taipei

first: Yi-Ting

last: Lin

address: No. 1, Jen-Ai Road, 1st Section

department: Department of Pharmacology

country: Taiwan

institute: College of Medicine, National Taiwan University

summary: CREB-binding protein (CBP) is a coactivator modulating DNA accessibility for transcription factors.CBP phosphorylation at Ser1382/1386 enhanced NF-𝜅B- while suppressed p53-mediated gene expression to promote cell growth, suggesting that post-translational modification of CBP regulates cell fate. Here we report that CBP knock-in mice (CBPAA), in which Ser1383/1387 are replaced with alanines, develop a phenotype resembling ulcerative colitis (UC) driven by non-hematopoietic cells. These mice exhibit reduced organoid formation, intestinal epithelial cell (IEC) proliferation, accompanied by increased CBP/p53 binding. All findings are reversed in CBPAA mice with IEC-specific p53 deletion (CBPAAp53ΔIEC) mice. To investigate how impaired CBP phosphorylation results in dampened IEC stemness, RNA-seq was performed to profile the transcriptome of colonic crypt.

overall_design: Crypts were disaggregated from intestinal epithelium of CBPWTp53-floxed, CBPAAp53-floxed,CBPWTp53ΔIEC and CBPAAp53ΔIEC mice. Total RNAs were extracted from colonic crypts, and sequenced by Illumina NovaSeq 6000.


title: Comparative analysis of nuclei isolation protocols for transcriptomic profiling of brain tissue

city: Indianapolis

first: Holly

last: Kersey

state: Indiana

address: 320 West 15th Street | NB 103

department: Medical & Molecular Genetics

institute: Indiana University

summary: Single-nucleus RNA sequencing (snRNA-seq) enables gene expression analysis at the single-cell level in complex tissues like the brain. The technique's effectiveness depends on obtaining high-quality nuclei suspensions, characterized by high yield, minimal cell-type biases, low contamination, and accurate gene expression profiles. This study compares three nuclei isolation methods using mouse brain tissue: sucrose gradient centrifugation, a spin column-based method, and a machine-assisted platform. Sucrose gradient centrifugation yielded the highest nuclei recovery with minimal doublets. The machine-assisted platform produced the highest viability with the lowest mitochondrial and RNA contamination. The column-based method had the lowest nuclei yield and highest ambient RNA contamination. These findings highlight the impact of isolation techniques on snRNA-seq data quality, with implications for optimizing neuroscience research and improving the study of brain cell-type diversity and disease mechanisms at the single-nucleus level.

overall_design: Mouse cortex was used to prepare nuclei isolation methods using three differing methods, (1) sucrose gradient centrifugation-based, (2) spin column-based, and (3) and a machine assisted platform, for snRNA-seq (N=2/condition)

middle: N

first: Dominic

last: Acri

first: Luke

middle: C

last: Dabin

first: Kelly

last: Hartigan

first: Jung Hyun

last: Park

first: Jungsu

last: Kim


title: Transcriptional changes in the guts of Drosophila malanogaster upon tyramine treatment

city: London

first: Nazif

last: Alic

address: Gower St

country: United Kingdom

institute: UCL

summary: Adrenergic signalling is heavily implicated in human age-related disease and yet the potential for this neuroendocrine signalling pathway to modulate ageing has received little attention. Here, we use Drosophila melanogaster to test if adrenergic-like signalling can promote longevity by manipulating tyramine (TA) or octopamine (OA), the invertebrate equivalents of adrenergic hormones. Increased neuronal synthesis of TA boosts health and longevity in both sexes, whereas OA is marginally beneficial in males. Orally administered TA or OA extend female or male lifespan, respectively. Increased activation of the ß-adrenergic-like signalling in the gut, by manipulating a ß-adrenergic-like receptor, PKA or CrebB, is sufficient to delay female ageing. Transcriptional profiling reveals that CrebB links the ß-adrenergic pathway to longevity-promoting processes in the gut where its function is required for the beneficial effects of TA feeding in females. Here we show that localised activation of ß-adrenergic signalling has the potential to counter animal ageing.

overall_design: For RNA extraction, eight mid-guts from Tyramine (TA: 100 µg/ml) or control food-fed flies were dissected at indicated times in ice-cold PBS and placed into ice-cold TRIzol (Thermo Fisher Scientific, 15596026). Five experimental replicates were performed and RNA samples were preserved in -80oC freezer prior to extraction by TRIzol/choloroform method as per manufacturer’s instructions and quantified by NanoDrop 2000c spectrophotometer. For RNA sequencing, library preparation (Illumina, strand-specific RNA-seq with PolyA selection) and sequencing (Illumina NovaSeq 2 x 150 bp sequencing) were performed by Azenta Life Sciences (GENEWIZ UK Ltd., Essex, UK). Read quality was assessed with FastQC and transcript abundance was estimated with Salmon against the fasta file containing all Drosophila transcripts (Flybase, r6.55). Data was imported into R with RStudio, using tximport package and differential expression assessed with DESeq2 and ihw packages.

first: Ahmed

last: Sumit

first: Shajahan

last: Anver


title: Transcriptional changes in the guts of Drosophila melanogaster upon gut specific CrebB induction

overall_design: For RNA extraction, eight mid-guts were dissected from gut-induced CrebB (TIGS>CrebB- plusRU486) flies, non-induced CrebB (TIGS>CrebB- minusRU486) flies, driver alone (TIGS only- plusRU486) and driver alone (TIGS only- minus RU486) flies at indicated times in ice-cold PBS and placed into ice-cold TRIzol (Thermo Fisher Scientific, 15596026). Five experimental replicates were performed and RNA samples were preserved in -80oC freezer prior to extraction by TRIzol/choloroform method as per manufacturer’s instructions and quantified by NanoDrop 2000c spectrophotometer. For RNA sequencing, library preparation (Illumina, strand-specific RNA-seq with PolyA selection) and sequencing (Illumina NovaSeq 2 x 150 bp sequencing) were performed by Azenta Life Sciences (GENEWIZ UK Ltd., Essex, UK). Read quality was assessed with FastQC and transcript abundance was estimated with Salmon against the fasta file containing all Drosophila transcripts (Flybase, r6.55). Data was imported into R with RStudio, using tximport package and differential expression assessed with DESeq2 and ihw packages.


title: Functional characterization of immune-related cells in a cnidarian

city: Barcelona

first: Arnau

last: Sebe-Pedros

address: Dr. Aiguader 88

department: Systems Biology

country: Spain

institute: Centre for Genomic Regulation

summary: We performed single-cell transcriptome analysis of a Nematostella vectensis transgenic line expressing RLRb::mCherry. We sampled gastrula stage embryo, including a control group of non-injected embryos, a control group injected with NaCl, and a group injected with poly(I:C)

overall_design: Adult specimens were fixed, dissociated and pooled before sorting single-cells for scRNAseq. Some samples were mixed (cross-species or cross-treatments) and processed together. Instructions for demultiplexing cells are provided.

first: Shani

last: Levy

first: Yehu

last: Moran

first: Itamar

last: Kozlovski


title: Plasmodesmal closure triggers stress responses

city: Hangzhou

first: Hannah

middle: Rae

last: Thomas

state: Zhejiang

address: 866 Yuhangtang Road

department: Horticulture

institute: Zhejiang University

summary: Plant cells function cell autonomously, but are connected to their cellular neighbors via plasmodesmata. Changes in cellular connectivity is required for cell signaling, with elicitor-induced plasmodesmal closure and consequent cellular isolation required for a full immune response. To understand what occurs when plasmodesmal closure is initiated, we generated two inducible transgenic lines (LexA::PD-Plug and LexA::icals3m). Inducing these genetic tools results in callose deposition at plasmodesmata, leading to plasmodesmal closure and cellular isolation, independent of a stimulus. We found that prolonged cellular isolation led to the upregulation of stress responsive genes and accumulation of salicylic acid, in addition to increased resistance to Pseudomonas syringae DC3000. We observed a more homogenous cellular isolation in LexA::icals3m lines in comparison to a heterogenous cellular isolation in LexA::PD-Plug, the latter which reflects more biological relevant observations in response stress elicitors. Interestingly, the LexA::icals3m displayed detrimental phenotypes with prolonged plasmodesmal closure in the form of hypersensitivity to Botrytis cinerea, perturbations of photoassimilate distribution with the accumulation of starch and sugars, and decrease in size of leaves and increased leaf senescence. These findings of what happens when a cell is isolated from its neighbors indicates we need to consider these factors in any context which plasmodesmata close, and also defines why cell-to-cell connectivity is regulated during key biological processes.

overall_design:
To investigate the downstream effects of plasmodesmal closure, we utilized two estradiol-inducible lines, LexA::PD-Plug (PD-plug) and LexA::icals3m (icals3m), which close plasmodesma in response to estadiol. These lines along with Col-0 wildtype were grown on plates and treated with esradiol or DMSO (mock).
2 leaves from four plants were collected for each samples, with 3 biological replicates. Samples were collected 12, 24, 48, and 72 hours after estradiol treatment. RNA was extracted and sequenced
Differential gene expression analysis was conducted on total RNA.

first: Estee

middle: E

last: Tee

first: Andrew

last: Breakspear

first: Diana

last: Papp

middle: R

first: Catherine

last: Walker

first: Annalisa

last: Bellandi

first: Christine

last: Faulkner


title: Aging-induced Suppression of Cirbp Compromises DHODH-Mediated Ferroptosis Defense and Attenuates Hypothermic Cardioprotection during Heart Transplantation

city: Shanghai

first: Yifan

last: Zhu

state: Shanghai

address: No.1678, Road Dongfang, Pudong district

institute: shanghai children’s medical center

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

overall_design: Refer to individual Series


title: Aging-induced Suppression of Cirbp Compromises DHODH-Mediated Ferroptosis Defense and Attenuates Hypothermic Cardioprotection during Heart Transplantation [RNA-seq]

summary: The purpose of this study was to explore the potential mechanism of attenuated hypothermic cardioprotection in the aging donor heart during transplantation and investigate its translational values.

overall_design: By using aging donors in the rat model of heart transplantation, we attempted to identify the most relevant protein in the process by using RNA sequencing.

first: Chenyu

last: Jiang

first: Yiwei

last: Liu

first: Hao

last: Zhang


title: Co-regulated Transcription Termination by SMN, FUS, TDP-43, and arginine dimethylation of the RNA Polymerase II CTD

city: Toronto

first: Ulrich

last: Braunschweig

state: Ontario

address: 160 College Street

department: Donnelly Centre

institute: University of Toronto

summary: The carboxy-terminal domain (CTD) of the RNA polymerase II (RNAPII) subunit POLR2A is a platform for modifications specifying the recruitment of factors that regulate transcription, mRNA processing, and chromatin remodelling. We previously found that symmetrical demethylation (me2s) of a CTD Arginine residue (R1810 in human) causes recruitment of the Tudor domain of SMN, which interacts with Senataxin.  SMN is mutated in spinal muscular atrophy (SMA), and Senataxin is sometimes mutated in Amyotrophic Lateral Sclerosis (ALS).  R1810me2s and SMN, like Senataxin, are important for resolving R-loops (DNA:RNA hybrids) at transcription terminators.  FUS and TDP-43 (TARDBP) are DNA/RNA binding proteins that are sometimes mutated in ALS and FTD (Frontotemporal dementia).  Here we show that TDP-43 and, to some extent, FUS are recruited by the R1810me2s-SMN pathway.  Defects in FUS and TDP-43 recruitment influence RNAPII termination and R-loop accumulation, leading to elevated DNA damage at terminators that may contribute to neurodegenerative disorders like ALS and FTD.

overall_design:
ChIP-Seq of RNA polymerase II in control, FUS and TDP-43 knockout HEK293 cells
Authors state that the 'processed data' consist of a plot only since the analyses (including the plots as supplementary files) were done directly from BAM files.

first: Dorothy

middle: Y

last: Zhao

first: Zuyao

last: Ni

first: Shuye

last: Pu

first: Guoqing

last: Zhong

first: Frank

last: Schmitges

first: Benjamin

last: Blencowe

first: Jack

middle: F

last: Greenblatt


title: Aging-induced Suppression of Cirbp Compromises DHODH-Mediated Ferroptosis Defense and Attenuates Hypothermic Cardioprotection during Heart Transplantation [ChIP-seq]

summary: The purpose of this study was to explore the potential mechanism of attenuated hypothermic cardioprotection in the aging donor heart during transplantation and investigate its translational values. We performed chromatin occupancy of Sp1 profiling analysis using data obtained from chromatin immunoprecipitation-sequencing (ChIP-seq) of LV myocardium from the wild-type rat

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for SP1 in left ventricular myocardium in WT Sprague-Dawley (SD) rat


title: Diagnostic performance comparison of SE-SPTM-PCR and miRNA deep sequencing using 2-fold gradient dilutions of simulated HCMV viral infection samples

status: Public on Mar 04 2026

city: Xiamen

first: Weida

last: Huang

state: Fujian

address: Xiangshan Street

department: School of Public Health

institute: Xiamen University

summary: MicroRNAs are promising liquid biopsy biomarkers, but their clinical translation is hindered by detection challenges, including low abundance, high sequence similarity, and background interference. We developed SE-SPTM-PCR, a detection platform integrating selective miRNA enrichment using locked nucleic acid probes with specific probe terminal-mediated RT-qPCR. To evaluate the ability of the SE-SPTM-PCR platform to discriminate samples with only slight differences in load, we tested simulated specimens with two-fold serial dilutions using both SE-SPTM-PCR and miRNA sequencing. These simulated specimens were prepared by spiking HCMV viral culture supernatant (propagated in MRC5 cells) into plasma samples obtained from three groups of age- and sex-matched healthy donors (n=10 per group). The results demonstrated that the diagnostic performance of the SE-SPTM-PCR platform significantly outperformed that of miRNA sequencing.

overall_design: Simulated specimens were prepared in three groups (n=10 per group) at volume ratios of plasma to HCMV supernatant to PBS of 90:10:0, 90:5:5, and 90:2.5:7.5, respectively.Nucleic acid extraction was performed from 600 μL of each simulated specimen using the miRNeasy Serum/Plasma Kit (Qiagen). Small RNA libraries were constructed using the VAHTS Small RNA Library Prep Kit for Illumina V2 (Vazyme).

first: Zecheng

first: Shiyin


title: Metastasis-associated wound repair promotes reciprocal lung epithelium activation and breast cancer metastatic outgrowth

city: Aurora

first: Jessica

last: Christenson

state: CO

institute: University of Colorado Anschutz Medical Campus

summary: When tumor cells colonize distant organs during metastasis, they interact extensively with surrounding cells. These interactions often change the behavior of surrounding cell populations which collectively induce a pro-tumor microenvironment that permits tumor cell outgrowth into overt, clinically detectable metastatic disease. The lung is one of the most common sites of breast cancer (BC) metastasis. A chronic wound repair-related phenotype developed within the lung microenvironment during metastatic outgrowth in immunocompetent preclinical mouse models of BC. This phenotype was characterized by an increased number and activation of lung type II alveolar epithelial (AT2) cells surrounding growing metastases. Metastatic outgrowth significantly changed AT2 gene expression, resulting in a modified secretome. AT2-derived secreted factors also promote triple-negative breast cancer (TNBC) growth. AT2 secreted factors are regulated by the cyclic adenosine monophosphate (cAMP) response element-binding protein (CREB). Targeting CREB signaling with the phosphodiesterase 4 (PDE4) inhibitor roflumilast reduced AT2-BC reciprocal interactions in vitro and metastatic outgrowth in vivo. Finally, AT2 cells adjacent to metastases in lungs from patients with metastatic BC express higher PDE4B compared to AT2 cells in normal lungs.  Alveolar epithelial cells are the most common cell type in the lung. Our studies demonstrate the potential for targeting metastasis-associated wound repair and lung epithelial cell activation during metastatic outgrowth with FDA-approved PDE4 inhibitors. This strategy may be an effective way to treat and manage progression of established metastatic BC within the lung.

overall_design: To study the latter stages of lung metastasis, such as metastatic outgrowth, 5x105 Met-1 mouse mammary carcinoma cells in 100µL 1X PBS were intravenously (IV) injected into the tail veins of 10-week-old female FVB/NJ mice (The Jackson Laboratory, No. 001800, RRID:IMSR_JAX:001800). Alternatively, 3x105 66Cl4 mouse mammary carcinoma cells in 100uL 1X PBS were IV injected into the tail veins of 10-week-old female BALB/cJ mice (The Jackson Laboratory, No. 000651, RRID:IMSR_JAX:001026). To examine how the metastatic microenvironment is altered during outgrowth, lungs with a low versus high metastatic burden were compared. Lungs were collected 1 week following IV injection as a model for low metastatic burden and 3 weeks post-injection as a model for high metastatic burden.

middle: L

first: Nicole

middle: S

last: Spoelstra

first: Michelle

last: Williams

first: Linda

last: Logan

first: Kathleen

middle: I

last: O'Neill

first: David

last: Orlicky

first: Nolan

middle: T

last: Baker

first: Jennifer

last: Wagner

first: Alyse

middle: W

last: Staley

first: Adrie

last: van Bokhoven

first: Andrew

last: Goodspeed

first: Li Wei

last: Kuo

first: Lyndsey

last: Crump

last: Diamond

middle: K

last: Richer


title: Vasculogenic tissue nanotransfection accelerates functional recovery after peripheral nerve injury

city: Columbus

first: Ana

middle: Isabel

last: Salazar Puerta

state: OH

address: 140 W 19th Ave Building 151

institute: The Ohio State University

summary: Peripheral nerve injuries (PNI) often result in persistent sensory, motor, and functional deficits, even after surgical reconstruction. While gene and cell therapies offer promise for enhancing regenerative outcomes, effective and targeted delivery remains a significant challenge. Here, we explored vasculogenic Tissue Nano-Transfection (TNT) as a novel, non-viral, reprogramming-based cell therapy to improve outcomes following graft reconstruction surgery. TNT aims to improve nerve regeneration by inducing vasculogenic reprogramming and promoting neovascularization to support axonal growth. Through a combination of in vitro screening and in vivo testing in a nerve crush model, we identified an optimal formulation of the vasculogenic genes, Etv2, Fli1, and Foxc2 (EFF), for enhancing reprogramming and axonal repair. TNT-based deployment EFF in a long segmental nerve defect reconstructed with isografts resulted in significant improvements in functional recovery, including grip strength and muscle contractility. Histological analyses demonstrated increased vascular density and myelinated axon counts. These findings support the therapeutic potential of TNT-mediated vasculogenic reprogramming as an adjunct to surgical repair of complex PNI offering a promising strategy to improve nerve regeneration and functional outcomes.

overall_design: RNAseq profiling of Sciatic nerve tissue. Mice were subjected to crush injury followed by electrotransfected with TFs Etv2, Fli1, Foxc2 (111 and 112 ratios) using TNT. Sciatic nerve tissue was collected 7 days post-transfection, compared to sham-transfected tissue and healthy tissue.

last: Salazar-Puerta

first: Sara

last: Kheirkhah

first: Jonathan

middle: P

last: Stranan

first: Hallie

last: Harris

first: Nada

last: Khattab

first: Megumi

last: Fukuda

first: Grant

last: Barringer

first: Carlos

last: Vasquez-Martinez

first: Samuel

last: Cortes

first: Neil

last: Ott

first: William

last: Lawrence

first: Devleena

last: Das

first: Jordan

last: Moore

first: Tiam

middle: M

last: Saffari

first: Juan

last: Salazar-Gil

first: Diego

last: Alzate-Correa

first: Junyan

last: Yu

first: Kavya

last: Dathathreya

first: Natalia

last: Higuita-Castro

first: Tatiana

middle: Z

last: Cuellar-Gaviria

last: Arnold

first: Amy

first: Daniel

last: Gallego Perez


title: Single cell and spatial sequencing analysis of cancer associated fibroblasts in the brain metastasis tumor microenvironment

city: Los Angeles

first: Bodour

last: Salhia

address: 1450 Biggy Street

department: Department of Cancer Biology

institute: University of Southern California

summary: Brain metastasis (BM) remains largely incurable. Cancer-associated fibroblasts (CAFs) can either support or inhibit tumor growth in the tumor microenvironment (TME), yet their roles in BM remain under-described. Here we report a single-cell and spatial sequencing analysis of human BM tissues and define four transcriptionally distinct CAF subpopulations. BM CAF subpopulations are characterized by either extracellular matrix (ECM), immune, contractile, or neural features, and show distinct spatial distributions within the BM TME. Further analyses reveal that BM CAFs engage extensively in cell-cell communication and adopt distinct cell states, including an ECM CAF cell state marked by high levels of immunoglobulin superfamily containing leucine rich repeat expression (ISLR-CAFs). Functionally, ISLR-CAFs reduce BM tumor cell viability in vitro, consistent with a tumor-inhibitory role. These findings highlight the heterogeneity and plasticity of CAFs in BM, emphasizing the importance of precision in defining stromal contributions to disease progression and therapeutic response.

overall_design: The spatial organization of BM TME cell types was investigated through spatial transcriptomic profiling of four BM tissue samples (BBM-USC-5-1, LBM-RIH-2, LBM-RIH-3, and LBM-USC-2-1). Three samples were from lung-to-brain metastases (LBM) and one from a breast-to-brain metastasis (BBM).

first: Thomas

last: Simon

first: David

middle: N

last: Buckley

first: Zeyi

last: Yang

first: Chikako

last: Matsuba

first: Ben

last: Tew

first: Gerald

last: Gooden

first: Kyle

last: Hurth

first: Steven

middle: A

last: Toms

middle: D

last: Tran

first: Gabriel

last: Zada

first: Matthew

last: Salomon


first: Ana

last: Salazar Puerta

overall_design: RNAseq profiling of sciatic nerve tissue electrotransfected with TFs Etv2, Fli1, Foxc2 using TNT. A segmental nerve isograft was transected into the nerve gap of mice following TNT. Sciatic nerve tissue was collected 13 weeks post-transfection and grafting, compared to sham-transfected nerve, healthy nerve and cut and no repair nerves as a negative control.

last: Salazar-Puerta

first: Sara

last: Kheirkhah

first: Jonathan

last: Stranan

first: Hallie

last: Harris

first: Nada

last: Khattab

first: Megumi

last: Fukuda

first: Grant

last: Barringer

first: Carlos

last: Vasquez-Martinez

first: Samuel

last: Cortes

first: Neil

last: Ott

first: William

last: Lawrence

first: Devleena

last: Das

first: Jordan

last: Moore

first: Tiam

last: Saffari

first: Juan

last: Salazar-Gil

first: Diego

last: Alzate-Correa

first: Junyan

last: Yu

last: Dathathreya


first: Ana

last: Salazar Puerta

overall_design: RNAseq profiling of fibroblasts cultures electrotransfected with TFs Etv2, Fli1, Foxc2 24 hours post-transfection, compared to sham-transfected cells and naïve cells.

last: Salazar-Puerta

last: Kheirkhah

first: Kavya

first: Natalia

last: Higuita-Castro

first: Tatiana

last: Cuellar-Gaviria

last: Arnold

first: Amy

first: Daniel

last: Gallego Perez


title: A Translocation within an Ogataea Clade Species Alters Local Subtelomeric Chromatin while Maintaining Global Genome Organization

city: Colorado Springs

first: Andrew

middle: David

last: Klocko

address: 278 Centennial Hall, 1420 Austin Bluffs Pkwy

institute: University of Colorado Colorado Springs


title: Regulation of Downstream Processing by Different Expression Levels of FLP-17

city: Bethesda

first: Ashley

last: Frakes

state: MD

address: 9000 Rockville Pike, 10N219

department: NIDDK, Genetics & Biochemistry Branch

institute: National Institutes of Health

summary: Our work seeks to understand the role of neuropeptide signaling in the regulation of metabolism and cellular stress. The primary goal of this sequencing experiment was to determine how whole animal expression of FLP-17 changes in the context of different extrachromasomal arrays and how this corresponds to hsp-4p::gfp reporter expression. As a secondary goal, we sought to determine how increasing FLP-17 expression modulates downstream transcriptional pathways.

overall_design: 200-500 animals were isolated per sample and 5-6 sample replicates were taken per genotype. Five strains were included for comparison: AEF276 (flp-17(n4894)IV; zcls4[hsp-4p::GFP]V), AEF231 (zcls4[hsp-4p::GFP]V), AEF378 (ashEx67[gcy-31p::flp-17::GFP; coel::RFP]; zcls4[hsp-4p::GFP]V), AEF373 (zcls4[hsp-4p::GFP]V; Ex[flp17p::FLP-17::flp-17 3’UTR + unc-122p::mCherry]), and AEF149 (ssrEx1193[flp-17p::flp-17::GFP, myo-3p:mCherry]; zcls4[hsp-4p::GFP]V). AEF231 is a 6x outcross of SJ4005 into an N2 background. AEF276, AEF373, and AEF378 are within the AEF231 background. AEF149 is in the SJ4005 background.

first: Carrie

last: Sheeler


title: The Role of EGL-6 Expression in FLP-17 Mediated Signaling

summary: Our work seeks to understand the role of neuropeptide signaling in the regulation of metabolism and cellular stress. The goal of this sequencing experiment was to determine how loss of function of the GPCR EGL-6 changes transcriptional profiles in adult C. elegans in the context of overexpression of the neuropeptide FLP-17.

overall_design: 500-600 animals were isolated per sample and 5 sample replicates were taken per genotype. Five strains were included for comparison: AEF243 (flp-17 (n4894)IV), AEF236 (egl-6 (n4537)X), AEF148 (flp-17oe; SSR1463 6x), AEF237 (egl-6 (n4537)X;SSR1463 6x), and N2 (background control). All experimental strains were outcrossed 6x into N2 before the start of the experiment.


title: Transient SUMOylation Inhibition In Human Pre-adipocytes Stably Imprints a Transcriptional Beiging Fate

city: Oslo

first: Pierre

last: Chymkowitch

address: Blindernveien 31

department: Biosciences

country: Norway

institute: University of Oslo

summary: Assess chromatin opening in response to TAK981 treatment in human pre-adipocytes.

overall_design: Chromatin accessiblity sequencing of differentiated immortalized human white adipocytes that have been treated transiently with TAK-981 or DMSO as vehicle control and collected at different timepoints during differentiation

first: Patrizia

last: Nothnagel

first: Paul-Arthur

last: Meslin

first: Jonas

last: Wik

first: Yunna

middle: E

last: Strøm

first: Magnar

last: Bjørås

first: Jorrit

last: Enserink

first: Bjørn

last: Skålhegg

first: Nolwenn

last: Briand

first: Anthony

last: Mathelier


title: Doxorubicin induces immediate transcriptional change and apoptosis in spermatogonia from prepubertal rats.

city: Laval

first: Geraldine

last: Delbes

state: QC

address: 531 boulevard des Prairies

institute: Institut national de la recherche scientifique

summary: Chemotherapy can compromise the fertility of boys with cancer, yet no standard protocols exist to preserve their reproductive potential. Before puberty, germ cells are almost exclusively spermatogonia that can be the target of anticancer drugs. Doxorubicin (DXO), a widely used anthracycline in pediatric oncology, has been associated with infertility in adulthood, but its immediate effects on prepubertal germ cells remain poorly understood. In the present study, a preclinical rat model of prepubertal DXO exposure was developed to characterize the mechanisms underlying immediate DXO-induced germ cell damage. Six-day-old pups, received a single intraperitoneal injection of DXO (5 mg/kg) and effects were measure after 24 or 48 h. DXO exposure significantly reduced relative testis weight from 24 h and significantly increased apoptosis and germ cell loss at 48 h, while circulating testosterone remained unchanged, suggesting a selective germline effect. RNA-seq was done on GFP-positive germ cells purified at 24 h. Transcriptomic analysis confirmed the enrichment in spermatogonial stem cells (SSCs) in the GFP-sorted population. Moreover, DXO induced 51 differentially expressed genes (49 upregulated, 2 down regulated) that were mostly related the p53-dependant apoptosis pathway. Pro-apoptotic genes (Cdkn1a, Bbc3/Puma, Tp53inp1, Fas) and oxidative stress regulators (Sesn2, Eda2r, Abhd4) were induced, whereas DNA repair genes (Mgmt, Xrcc1, Polh, Gadd45α, ...) were not activated. Our data revealed the DXO-induced immediate transcriptomic response after 24h, leading to germ cell death observed by histology at 48h. These findings suggest that SSCs respond to DXO by favoring apoptosis and stress regulation, a strategy that may preserve germline integrity and reduce the risk of transmitting genetic damage to the next generation.

overall_design: RNA-seq profiling of GFP-positive germ cells isolated from prepubertal rats 24 h after in vivo exposure to doxorubicin (5 mg/kg) or vehicle control at PND6.

first: Hermance

last: Beaud

first: Elisa

last: Hug

first: Marie-Pier

last: Scott-Boyer

first: Arlette

last: Rwigemera

first: Amélie

last: Tremblay

first: Arnaud

last: Droit

first: Géraldine

last: Delbès


first: Pierre

last: Chymkowitch

summary: Adaptive thermogenesis, or beiging, involves the conversion of energy-storing white adipocytes into energy-dissipating beige adipocytes, enabling physiological adaptation to environmental stressors such as hypothermia. While white and beige adipocytes share a largely similar transcriptome, this identity shift requires significant transcriptional and epigenetic reprogramming. However, the molecular mechanisms governing this transition remain incompletely understood.  Here, we identify SUMOylation as a critical repressor of adipocyte beiging. Using the small-molecule SUMOylation inhibitor TAK-981, we demonstrate that transient SUMOylation inhibition primes human adipocytes to express beiging genes including UCP1 and induce mitochondrial uncoupling in a rosiglitazone-dependent manner. Furthermore, SUMOylation suppresses both the de novo differentiation of human adipose stem cells into beige adipocytes and the transdifferentiation of mature white adipocytes into beige cells. Mechanistically, TAK-981 modulates the cAMP-PKA-p38 signaling axis, ultimately affecting downstream transcriptional programs under the control of PPARG and PPARA enhancers.  Our findings establish SUMOylation as a fundamental barrier to white-to-beige adipocyte reprogramming and suggest that the pharmacological combination of PPARG partial agonists with TAK-981 could promote metabolically beneficial adipose tissue remodeling in clinical settings.

overall_design: RNA sequencing of differentiated immortalized human white adipocytes that have been treated transiently with TAK-981 and/or Rosiglitazone.


title: The long noncoding RNA lnc13 restrains inflammatory responses to maintain oral tolerance to gluten

city: New York

first: Ruxiao

last: Yang-Fischer

institute: Columbia University

summary: Celiac disease (CeD) is an autoimmune disorder triggered by dietary gluten. While HLA-DQ2/8-mediated presentation of gliadin peptides is required for disease, the mechanisms that underlie the loss of oral tolerance to gluten remain incompletely understood. Long noncoding RNAs (lncRNAs) have been increasingly recognized as regulators of immune function, yet their role in oral tolerance has not been previously explored. Using a screen designed to identify lncRNAs responsive to T  cell activation and enriched for CeD-associated GWAS variants, we identified lnc13 as a top candidate. In HLA-DQ8 transgenic mice lacking lnc13, unmanipulated gluten ingestion led to hallmark features of loss of oral tolerance to gluten:  reduced regulatory T cells, and increased IFN-γ⁺ lymphocytes, IL-12⁺ myeloid cells, cytotoxic intraepithelial immune cells and crypt hyperplasia in the small intestine. Mechanistically, lnc13 binds specific DNA regulatory regions and limits inflammatory responses to pro-inflammatory signals. In particular, lnc13 restrains IL-15-driven differentiation of CD8⁺ NK-like lymphokine-activated killer cells—an IL-15–dependent pathway strongly implicated in CeD. These findings establish lnc13 as a critical noncoding modulator of oral gluten tolerance.

overall_design: data include: gluten challenged lnc13-KO-DQ8 and lnc13-WT-DQ8 mice whole tissue, LPLs or IELs subjected for RNA-seq;IEL CD8ab+ T cells post gluten challenge are also subjected to RNA-seq; lnc13 RAP-DNA-seq; and lnc13 WT and KO CD8a+ IELs after 48h cultured in IL-15.

first: Sankar

last: Ghosh


title: RNA-seq of the central amygdala of rats with painful diabetic neuropathy

status: Public on Mar 03 2026

city: Hefei

first: xiaomin

last: nie

address: 17 Lujiang Road

institute: The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China

summary: Painful diabetic neuropathy (PDN) is a debilitating complication of diabetes, yet its central nervous system pathogenesis remains poorly understood. We investigated transcriptomic alterations in the central amygdala (CeA) in a diabetic rat model exhibiting neuropathic pain behavior. Male Sprague-Dawley rats were intraperitoneally injected a single dose of streptozotocin to induce diabetes. Six weeks following administration, the development of neuropathic pain was confirmed by the von Frey filament test. Subsequently, RNA sequencing of the CeA tissues identified 157 differentially expressed genes. This RNA sequencing dataset of the CeA in a neuropathic pain-exhibiting diabetic rat model provides insights into central nervous system adaptations in PDN and highlights potential molecular targets for therapeutic intervention.

overall_design: Male Sprague-Dawley rats were administered a single intraperitoneal dose of 60 mg/kg STZ to induce diabetes. Six weeks post-injection, neuralgia was confirmed in diabetic rats through a significant reduction in the withdrawal threshold in the von Frey test. Transcriptomic analysis of the central amygdala was performed on the rats with painful diabetic neuropathy compared with the non-diabetic controls.

first: Xiaomin

last: Nie


title: Monocytes provoke breast cancer cells to express PD-L1 via a cell-to-cell interaction involving CD44 and Moesin

city: Kyoto

first: Kenta

last: Yamamoto

address: Kajicho 465

department: Immunology

institute: Kyoto Prefectural University of Medicine

summary: In recent years, immunotherapy using immune checkpoint inhibitors has been conducted for TNBC patients. While a limited proportion of patients show excellent response, about a half of the patients do not significantly respond to the immunotherapy. Monocytes are the progenitors of macrophages that are most abundantly seen in the tumor microenvironment (TME), but the influence of monocytes on BCCs has not been fully clarified. Thus, we examined whether monocytes prompted BCCs to express PD-L1. As a result, PD-L1 expression in BCCs was upregulated by co-culturing them with monocytes. RNA sequencing analysis revealed overexpression of Moesin mRNA in the BCCs co-cultured with monocytes. These findings may suggest a novel machinery of tumor escape from anti-tumor immunity, potentially providing a way to improve immunotherapy against TNBCs that are resistant to current immune-checkpoint blockade therapy.

overall_design: Two biological replicates were analyzed for each of 2 conditions (control MDAMB-231, MDAMB-231 co-cultured with human monocytes)

first: Saya

last: Matsumoto


title: E1A transactivation through superinfection turns iPSC-derived macrophages from a quiescent to a productive adenovirus cell state

city: Zurich

first: Maarit

last: Suomalainen

address: Winterthurerstrasse 190

department: DMLS

country: Switzerland

institute: University of Zurich

summary: Macrophages are a first line defense against pathogens. Human adenovirus C5 (AdV-C5) infection is inefficient in human iPSC-derived macrophages, partially due to poor activity of the enhancer/promoter (e/p) of the virus immediate early gene E1A. The E1A proteins are needed to activate other viral transcription units and to rewire the host cell for efficient virus replication. The E1A restriction can be overcome by coinfection of the wt virus together with a non-replicating AdV in which the E1A e/p has been replaced by the cytomegalovirus immediate early e/p (AdV-C5-CMV-E1A virus). We report here bulk RNA-seq results from noninfected iPSC-derived macrophages (NI samples), single wild type AdV-C5 (wt samples) and wt and AdV-C5-CMV-E1A coinfections (wtCMV samples) at 12 h and 27 h (marked as 24 h in the files) post infection. All samples had three technical replicates.

overall_design: Bulk RNA-Seq of noninfected, AdV-C5 wild type (wt)-infected and AdV-C5 wt and AdV-C5-CMV-E1A (wtCMV) coinfected human iPSC-derived macrophages. Samples collected at 12h and 27h (file names 24h) post infection. All samples had three technical replicates

first: Walther

last: Haenseler

first: Urs

last: Greber


title: Targeting BMP and TAZ/TEAD mechanotransduction pathways impairs AML chemoresistance

city: Lyon

first: Kevin

last: Geistlich

address: 28 rue Laennec

country: France

institute: CRCL

summary: Despite extensive research and intensive use of chemotherapies in clinics, the 5-year overall survival of Acute Myeloid Leukemia (AML) patients does not exceed 20%. The clonal expansion of leukemic blasts leads to modifications of the bone marrow physical properties, including increased extracellular matrix stiffening, upregulation of intramedullary pressure and reduction of the space available for cells. These biomechanical modifications are speculated to alter therapeutic response and cause treatment resistance. This project aims to decipher the role of mechanotransduction pathways in specially the Hippo pathway in resistant AML.

overall_design: The AML cell line used, ML2 (RRID:CVCL_1418) was cultured in RPMI 1640 with 10% fetal bovine serum (FBS). Resistant cells were permanently cultured with Cytarabine (ara-C) or venetoclax at 1 µM. Stable ML2-R were transduced with lentivirus shCtl or dual shYAP/TAZ names shTAZ#1 and shTAZ#2 (constructs generously given by Rob Bremner lab) including a EGFP marker and sorted by cytometry.

first: Sylvain

last: Lefort

first: Nicolas

last: Lespinasse

first: Lea

last: Barral

first: Véronique

last: Maguer-Satta


title: PAF1C-driven restoration of RNAPII elongation after DNA damage occurs independently of transcription-associated histone mark deposition

city: Leiden

first: Martijn

middle: S.

last: Luijsterburg

state: zuid-holland

address: Einthovenweg 20

country: Netherlands

institute: LUMC

summary: DNA lesions block the progression of RNA polymerase II (RNAPII) during transcription, impeding gene expression and threatening genome integrity. When RNAPII stalls on transcription-blocking lesions, the transcription-coupled DNA repair pathway is activated to remove the DNA damage. Following DNA repair, efficient transcription restart depends on the PAF1 elongation complex (PAF1C). PAF1C contributes to deposition of transcription-associated histone marks, including H2B-K120Ub, H3K4me3 and H3K79me. These marks are enriched at actively transcribed genes and have been associated with regulation of post-repair transcription restart. Here, we show that the H2B-K120 E3 ubiquitin ligase RNF20/RNF40, the H3K4-methyltransferase SET1/COMPASS complex, and the H3K79-methyltransferase DOT1L are dispensable for transcription restart. Moreover, levels of H2B-K120Ub and H3K4me3 do not correlate with transcription restoration following DNA damage. Additionally, we observe that, unlike PAF1, the dissociable PAF1C subunit RTF1, while stimulating H2B-K120Ub and H3K4me3, does not play a role in transcription restart. Together, these data suggest that transcription restoration after DNA damage is stimulated by the PAF1C elongation complex, independently of transcription-associated histone mark deposition.

overall_design: To study how the recovery of transcription after DNA damage correlates with transcription-associated histon mark deposition, we performed ChIP-seq for ubH2B before and after UV-C irradiation in WT RPE1 cells

first: Janne

last: van Schie

first: Bram

last: de Groot


title: Sequence-specific RNA recognition drives Restrictor-mediated termination of extragenic transcription

city: Milano

first: Gaurav

last: Mandana

address: Via Adamello 16

country: Italy

institute: European Institute of Oncology

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

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: Refer to individual Series


title: Neural Crest Cell Signatures Drive TSC and LAM Tumorigenesis [human]

first: Uchenna

last: Unachukwu

state: New York

address: 630 West 168th Street, P&S 7-430

department: Anesthesiology

institute: Columbia University Medical Center

summary: This study was performed to test the hypothesis that neural crest cells (NCCs) are causative cells for multi-systemic neoplasms occurring in Tuberous Sclerosis Complex (TSC) and Lymphangioleiomyomatosis (LAM) disorders. The hypothesis stemmed from the mesenchymal phenotypes of TSC and LAM neoplasms and their occurrence in patients at known ontogenetic destinations for maturing neural crest cells. We determined differential gene expression between single cell populations in wildtype mice renal cortical tissues versus renal cystadenomas of the tuberous sclerosis mice model by RNA sequencing, and validated our findings by immunohistochemistry, RT-qPCR, western blots, and tumorigenicity assays. Based on our results, we pioneer the characterization of cranial NCC-induced tumorigenesis in TSC and LAM and identify the crucial role of novel neurocristopathic markers: secreted phosphoprotein (SPP1) and cytokeratin 18 (Krt18) in disease pathogenesis. Genetic inhibition of Spp1 yields an anti-tumorigenic phenotypes in NCCs.

overall_design: Neoplastic lesions were excised from fresh lung tissues biopsied from de-identified Lymphangioleiomyomatosis (LAM) patients (N=4) and supplied by the National Disease Research Interchange (NDRI) in DMEM containing  1% penicillin-streptomycin, 48 hrs after surgery. Tissues were minced under sterile conditions, enzymatically digested, and single cells sequenced on a NovaSeq6000 System (Illumina, San Diego, CA) using the 10x Genomics 3’ Single Cell Gene Expression (GEX) workflow. Cell type classifiers in the CLC Genomics knowledgebase (Qiagen, CA) were trained to annotate neural crest cells in pulmonary neoplastic cell populations based on identifying markers in the study by Soldatov et al. (2019) (PMID: 31171666). Differential gene expression based on the generalized linear model (GLM) fit was performed for cell clusters within pulmonary LAM tumors, cell types within resolved clusters, and cranial neural crest cells (CNCCs) versus other cell types in clusters and whole tumors to identify novel neurocristopathic tumor markers in LAM.

first: Jeanine

last: D'Armiento


title: AF9/KLF2 gene regulatory circuit links histone lactylation to breast cancer metastasis [RNA-seq]

city: Beijing

first: Huida

last: Ma

address: No. 30 Shuangqing Road, Haidian District

institute: Tsinghua University

summary: Histone lysine L-lactylation (hereafter referred to as histone Kla) is a novel epigenetic mark induced by glycolytic metabolism, serving as a link between metabolic reprogramming and epigenetic regulation. In this study, we uncover an epigenetic-genetic transcriptional regulatory circuit involving AF9 and KLF2 that drives luminal breast cancer progression. AF9, identified as a reader of histone H3 lysine 9 lactylation (H3K9la), promotes KLF2 expression, while KLF2, functioning as a transcription factor for AF9, forms a positive feedback loop that amplifies lactylation-dependent effects. This circuit activates tumor-associated pathways, including TGFβ1, glucose and lactate transporters, and metabolic enzymes essential for glycolysis and serine biosynthesis, driving tumorigenesis and metastasis. Spatial and single-cell transcriptomics show AF9-positive tumor cells enriched in regions of active lactylation, correlated with immune evasion through interactions with M2 macrophages. Together, AF9, H3K9la, and KLF2 integrate metabolism, epigenetics, and signaling to promote tumor growth and metastasis, highlighting AF9's central role as a histone lactylation reader and a potential therapeutic target in breast cancer.

overall_design: RNA-seq samples in MCF7 breast cancer cell line, as well as knockdown and overexpression derivates (shAF9 and AF9OE).

first: Ming

last: Yuan

first: Chenxuan

last: Yang

first: Yuchen

first: Xin

last: Wang

first: Zhonghui

last: Tang

first: Haitao

last: Li


title: AF9/KLF2 gene regulatory circuit links histone lactylation to breast cancer metastasis [CUT&Tag]

overall_design: CUT&Tag samples in MCF7 breast cancer cell line.


title: Neural Crest Cell Signatures Drive TSC and LAM Tumorigenesis

overall_design: Single-cell isolates from renal cortical tissues of the B6129SF2/J wildtype mice and spontaneously occurring renal cystadenomas in the Tuberous Sclerosis Tsc2+/- mice model were sequenced on a NovaSeq6000 System (Illumina, San Diego, CA) using the 10x Genomics 3’ Single Cell Gene Expression (GEX) workflow. Cell type classifiers in the CLC Genomics knowledgebase (Qiagen, CA) were trained to annotate neural crest cells in renal tissue/tumor cell populations based on identifying markers in the study by Soldatov et al. (2019) (PMID: 31171666). Differential gene expression and signaling pathway analyses were used to resolve NCC-induced tumorigenic pathways and novel neurocristopathic markers in TSC and LAM. CRISPR/Cas9-mediated gene recombination was used to perform loss-of-function tests assessing the role of identified NCC markers and pathogenic pathways.


title: Genomic characterization of sub-populations in human pluripotent stem cell-derived retinal progenitor cells that drive retinal layer structure

city: Kobe

first: YASUAKI

last: IWAMA

address: 2-1-8, Minatojimaminamimachi, Chuo-ku

department: Research Center

institute: Kobe City Eye Hospital

summary: The mechanisms of layer formation of retinal spheroids were investigated using Rax::GFP-positive retinal progenitor cells (RPCs) obtained from human embryonic stem cell-derived retinal organoids. Single-cell RNA sequencing revealed that well-layered spheroids exhibited a transient activation of canonical WNT2B–FZD7 signaling followed by a temporary expression of non-canonical WNT5A, processes associated with the formation of organized retinal layers. Despite structural differences in vitro, both non-layered and well-layered retinal spheroids of differentiation day 60 successfully developed into each cone and rod subtypes of photoreceptors and established synaptic connections with host bipolar cells after transplantation in retinal degeneration model rats, resulting in light-evoked functional recovery.　Additionally, part of the presumable RPCs differentiated into non-retinal lineages, including ciliary marginal zone-like, retinal pigment epithelium-, and spinal cord-like tissues in vitro, reflecting the developmental plasticity of RAX-positive cells. These findings suggest that canonical and non-canonical WNT signaling pathways sequentially orchestrate early retinal morphogenesis, while environmental factors within the host retina strongly drive the alignment and functional integration of graft photoreceptors.

overall_design: Human retinal spheroids were dissociated into a single cell suspension and run on the 10x Genomics Chromium Single Cell System platform using ver3.1 chemistry. Libraries were sequenced on Illumina HiSeq X and processed through the Cell Ranger pipeline using the GRCh38 reference genome.

first: Yasusaki

last: Iwama

first: Tomohiro

last: Masuda

first: Mika

last: Yoshimura

first: Masayo

last: Takahashi

first: Itoshi

last: Nikaido

first: Michiko

last: Mandai


title: Hepatocyte-specific CEBPA-ORM1 axis restricts alcohol-associated liver disease

city: Bethesda, MD

first: Frank

last: Gonzalez

address: Bldg. 37 National Institutes of Health

department: Center for Cancer Research

institute: National Institutes of Health, National Cancer Institute

summary: Alcohol-associated liver disease (ALD) affects millions of people worldwide, while pharmacological therapies are limited. CCAAT/enhancer binding protein α (CEBPA) in hepatocytes is known to regulate the progression of liver fibrosis; however, the role of hepatocyte-specific CEBPA in modulating the ALD progression is still unknown. Here, hepatic CEBPA expression was found to be decreased during ALD progression in humans. CebpaΔHep mice had enhanced ALD induced both in short-term and long-term alcohol feeding. Temporal and spatial hepatocyte-specific CEBPA loss at the later stage of ALD in CebpaΔHep,ERT2 mice functionally promoted ALD. Mechanistically, hepatocyte CEBPA loss directly deactivated Orm1 expression in hepatocytes that resulted in reduced secretion of ORM1 and enhancement of ALD progression. Both hepatocyte ORM1 expression and serum ORM1 levels were found to be negatively correlated with the ALD progression in humans, while loss of hepatocyte ORM1 in mice sharply enhanced ALD. Both forced hepatocyte-specific CEBPA overexpression and hepatocyte-specific ORM1 overexpression by adeno-associated viruses rescued the progression of ALD in CebpaΔHep mice. Notably, treatment of recombinant ORM1 protein improved the progression of ALD in CebpaΔHep mice. These results reveal a key role for hepatocyte-specific CEBPA-ORM1 axis in ALD progression, which supports hepatocyte CEBPA to be a novel therapeutic target for the treatment of ALD.

overall_design: Ten-week-old, body weight-matched Cebpafl/fl and CebpaΔHep mice were acclimated to a liquid control diet (F1259SP, BioServ) for 5 days first, followed by a 5% (vol/vol) ethanol liquid diet (F1258SP, BioServ) feeding for 4 weeks. Samples were collected for further analysis.

first: Yan

last: Nana

first: Tingting

last: Yan

middle: J

first: Vorthon

last: Sawaswong


title: Transforming growth factor-β1 induces super-enhancers at the loci of the epithelial-mesenchymal transition-related genes in human keratinocyte HaCaT cells

city: Fukuoka

first: Mitsutoki

last: Hatta

state: Fukuoka

address: 2-15-1 Tamura Sawara-ku

institute: Fukuoka Dental College

summary: An enhancer is a genomic DNA sequence that substantially enhances the transcriptional activity of a target gene by recruiting transcription factors. The large clusters of enhancers identified through the ChIP-seq analysis of histone H3 lysine 27 acetylation (H3K27ac) are called super-enhancers (SEs). This study examined the dynamics of SEs during transforming growth factor (TGF)-β1-mediated epithelial-mesenchymal transition (EMT) in the human keratinocyte cell line HaCaT. Initially, we identified the constitutive and the TGF-β1 signal-dependent SE regions across the HaCaT genome. The TGF-β1-induced SEs were detected at the loci of genes associated with the cell cycle, cell death, and extracellular matrix organization. Notably, the EMT-related mesenchymal genes such as FN1 and SERPINE1 gained the SEs on their loci in response to TGF-β1. Next, we investigated the functional role of BRD4, a transcriptional mediator that binds to the SEs, in the expression of TGF-β1-induced SE-associated genes. JQ-1, a potent inhibitor of BRD4, effectively reduced the TGF-β1-induced mRNA expression of FN1 and SERPINE1. In conclusion, this study demonstrated that the rearrangement of SEs is crucial for the transcriptional regulation of the TGF-β1-induced EMT in HaCaT cells.

overall_design: ChIP-seq of the histone modification H3K27ac in HaCaT cells under the control and TGF-β1-treated conditions.

first: Kana

last: Takeda

first: Yoshiyuki

last: Nagaoka

first: Sachio

last: Tamaoki


title: Commun Biol . 2026 Apr 2;9(1):726. doi: 10.1038/s42003-026-09975-3. TWEAK-induced alternative NF-κB signaling regulates Cxcl10 and Mymx to promote myoblast-to-myotube fusion and muscle regeneration

city: Ottawa

first: Neena

last: Lala-Tabbert

address: 401 Smyth Rd

institute: CHEO Research Insitute

summary: Repair of adult skeletal muscle relies on molecular and cellular mechanisms that sustain tissue homeostasis during regeneration of injured myofibers. The NF-κB pathway has emerged as an important signaling network in skeletal muscle. Depending on the type of stimulus, activation of NF-κB signaling can occur through the classical or alternative pathway. TWEAK is a membrane bound and soluble cytokine that signals through Fn14, a highly inducible cell-surface receptor that is upstream of numerous signaling pathways including NF-κB. Upregulation of Fn14 signaling is associated with the progression of several chronic atrophic muscle disorders. In contrast, TWEAK/Fn14 signaling has also been suggested to play a beneficial role during muscle regeneration by promoting myoblast proliferation and fusion. In this study, we demonstrate that TWEAK promotes secondary fusion through direct transcriptional activation of Myomixer and CXCL10 by alternative NF-κB. Overall, our study demonstrates that TWEAK is beneficial for myoblast fusion and may be a potential approach to improve muscle regeneration in degenerative disorders.

overall_design: To examine the molecular mechanism by which TWEAK stimulates myoblast-to-myotube fusion we treated nascent C2C12 myotubes (differentiated for 3 days) with 10ng/ml TWEAK for 12 hours. Untreated cells were used as controls. We performed RNA-Sequencing to examine differential gene expression between untreated and treated myotubes.

first: Robert

middle: G

last: Korneluk


title: Transcriptome analysis of wild type and MafB knockout macrophages stimulated for 24 h with IL-4

city: Seoul

first: June

last: Yang

address: 145, Anam-ro, Seongbuk-gu, Seoul, Republic of Korea

department: Biotechnology

country: South Korea

institute: Korea University

summary: The functional polarity of macrophages driven by specific cues within local milieu can play a pivotal role in the pathogenesis of various human diseases. Identifying a key regulator to control macrophage polarization is of great importance in the therapeutic strategies for modulating macrophage function to improve clinical outcome. Here, we identify MafB as an essential transcription factor to induce M2 macrophage polarization. The myeloid-specific genetic ablation of Mafb in mice causes a severe defect in M2 macrophage polarization, ultimately leading to a deterioration of inflammatory diseases such as experimental sepsis or colitis.

overall_design: Wild type and MafB-deficient macrophages stimulated for 24 h with IL-4 were profiled for mRNA expression by RNA-sequencing analysis.

first: Jun


title: Trabectedin and low-dose irinotecan to target EWS::FLI1 in Ewing sarcoma: a phase 1/2 trial

status: Public on Mar 02 2026

city: Ann Arbor

first: Patrick

last: Grohar

state: MI

address: 1600 Huron Parkway

institute: University of Michigan Medical School

summary: Ewing sarcoma (ES) is a bone and soft tissue sarcoma that is absolutely dependent on the EWS::FLI1 transcription factor for cell survival. No compound has been shown to reverse EWS::FLI1 activity in patients, and outcomes for relapsed patients remain poor. Trabectedin above a threshold concentration reverses the activity of EWS::FLI1 and is potentiated by low-dose irinotecan in vivo. This open-label phase 1/2 trial of trabectedin with irinotecan (SARC037) enrolled 37 relapsed/refractory patients with ES. The primary objectives were to determine the safety, tolerability, recommended phase 2 dose (RP2D; phase 1) and objective response rate (ORR; phase 2) of trabectedin administered as a 1-hour infusion in combination with low-dose irinotecan in patients with ES. The secondary objectives were to determine the progression-free survival (PFS), 6-month PFS, duration of response and 18F-fluorothymidine positron emission tomography (18F-FLT PET) avidity of ES tumors. The RP2D was trabectedin 1.0 mg m−2 over 1 hour (day 1) and irinotecan 25 mg m−2 (days 2 and 4) of a 21-day cycle. Toxicities were manageable with grade 3 or higher toxicities (>15%) of myelosuppression and alanine aminotransferase elevations at RP2D. The phase 2 ORR was 33% (39%, including RP2D phase 1 patients), and 6-month PFS was 48%. Transcriptional profiling demonstrated reversal of the EWS::FLI1 transcriptome in tumors from a subset of patients. Additional correlative objectives captured molecular profiling, circulating tumor DNA levels, pharmacokinetics and 18F-FLT PET avidity. Here we provide the basis for further development of trabectedin/irinotecan for patients with ES by the international cooperative groups. ClinicalTrials.gov: NCT04067115.

overall_design: Tumor needle biopsies from five patients with relapsed, treatment-refractory, Ewing sarcoma and documented EWS::FLI1 fusion/breakpoint, before and after treatment with 1h trabectedin infusion and prior to irinotecan administration.

first: Gretchen

middle: Y

last: Lam


first: Rebecca

last: Kaufman


title: Differential Expression and Target Gene Analysis of PBMC-Derived microRNAs as Prognostic Biomarkers in Acute Lymphoblastic Leukemia

city: Riyadh

first: Ghaida

last: Almuneef

address: KSA-Riyadh

country: Saudi Arabia

institute: King Abdullah International Medical Research Center

summary:
Clinical specimens were collected from patients with Acute Lymphoblastic Leukemia (ALL) and from non-leukemic controls. Total RNA (including small RNA) was profiled using the Affymetrix GeneChip miRNA 4.0 array to identify differentially expressed miRNAs between ALL and controls
Raw CEL files were generated using standard Affymetrix GeneChip scanning and feature extraction (AGCC or equivalent). Expression values were obtained in R using RMA normalization, followed by probe filtering was applied. Differential expression was assessed with limma using an ALL vs CTRL contrast with Benjamini–Hochberg FDR correction.

overall_design: Case–control study comparing ALL vs non-leukemic controls, one microarray per sample (Affymetrix GeneChip miRNA 4.0). miRNA differential expression was tested between groups

first: Fatemah

middle: S

last: Basingab

first: Hadil

last: Alahdal

first: Deemah

last: Alwadaani

first: Ahmed

last: Barefah

first: Ali

middle: H

last: Algiraigri

first: Rawan

last: Hammad

first: Mohamed

last: Elnakeeb

first: Jehan

last: Alrahimi

first: Kawther

last: Zaher

first: Alia

last: Aldahlawi


title: microRNA-21 promotes dysregulated lipid metabolism and hepatocellular carcinoma [bulk RNA-Seq]

city: Salt Lake City

first: Kimberley

middle: Jane

last: Evason

state: UT

address: 2000 Circle of Hope

department: Pathology

institute: University of Utah

summary: The prevalence of hepatocellular carcinoma (HCC) is rising in parallel with increasing obesity and metabolic dysfunction-associated steatohepatitis (MASH). MicroRNAs are key post-transcriptional regulators of gene expression and are attractive targets for HCC therapy. Here we sought to identify and characterize dysregulated microRNAs in MASH-driven HCC (MASH-HCC). We profiled microRNA expression in liver tissue from patients with MASH or MASH-HCC and in zebrafish HCC driven by activated β-catenin (ABC), one of the most commonly mutated oncogenes in MASH-HCC. We found overlap between dysregulated human and zebrafish miRNAs, including miR-21, which was increasingly upregulated from normal liver to MASH to MASH-HCC. We generated transgenic zebrafish that overexpress or sponge miR-21 in hepatocytes. We found that miR-21 overexpression caused larval liver overgrowth and increased HCC, while miR-21 sponge suppressed β-catenin-driven larval liver overgrowth. By performing histologic and lipidomic analysis, we found that overexpression of miR-21, like ABC, suppressed lipid accumulation in response to a high cholesterol diet and increased accumulation of acylcarnitines. Thus miR-21, which is similarly upregulated in human and zebrafish HCC, promotes lipid metabolic changes that may help drive hepatocarcinogenesis.

overall_design: The goal of this study was to profile mRNAs in liver tissues from 13 dpf zebrafish, with and without hepatocyte-specific overexpression of microRNA-21, fed either high cholesterol diet or normal control diet from 6 dpf to 13 dpf.

first: Chad

last: VanSant-Webb

first: Jessye

middle: C

last: Castro

first: Audrey

last: Su

first: Kiandra

last: Hawkins

first: Aavrati

last: Saxena

first: Jillian

last: Wright

first: Richard

last: Smith

first: Marco

last: Fragoso- García

first: Yian

last: Chen

first: Carrie

last: Barton

first: Chris

last: Stubben

first: Ryan

last: O'Connell

first: Gregory

last: Ducker


title: microRNA-21 promotes dysregulated lipid metabolism and hepatocellular carcinoma [miRNA-Seq]

overall_design: The goal of this study was to profile microRNAs in liver tissues from transgenic adult male zebrafish expressing hepatocyte-specific activated beta-catenin compared to non-transgenic sibling controls.


title: Gene syntax defines supercoiling-mediated transcriptional feedback [CUT&Tag II]

city: Cambridge

first: Christopher

middle: Patrick

last: Johnstone

state: Massachusetts

department: Chemical Engineering

institute: Massachusetts Institute of Technology

summary: Gene syntax---the order and arrangement of genes and their regulatory elements---shapes the dynamic coordination of both natural and synthetic gene circuits. Transcription at one locus profoundly impacts the transcription of nearby adjacent genes, but the molecular basis of this effect remains poorly understood. Here, using integrated reporter circuits in human cells, we show that the reciprocal effects of transcription and DNA supercoiling, which we term supercoiling-mediated feedback, regulates expression of adjacent genes in a syntax-specific manner. Using a suite of chromatin state assays, we measure syntax- and induction-dependent formation of chromatin structures in human induced pluripotent stem cells. Applying syntax as a design parameter and without altering sequence or copy number, we built compact gene circuits, tuning the expression mean, noise, and stoichiometry across diverse delivery methods and cell types. Integrating supercoiling-mediated feedback into models of gene regulation will expand our understanding of native systems and enhance the design of synthetic gene circuits.

overall_design: CUT&Tag profiling of hiPSC lines containing integrated synthetic gene pairs. Gene pairs with one of the four possible syntaxes (divergent, convergent, upstream tandem, downstream tandem) were integrated homozygously at the CYLBL locus in hiPSCs. The two genes were mTagBFP2-T2A-rtTA expressed constitutively from the CAG promoter, and mScarlet expressed from the inducible TRE promoter. These four lines were split into plus and minus induction conditions. The induced condition was treated with treated with 1000 ng/mL doxycycline for three days. Around 500k cells were collected per condition and per antibody (for H3K27me3, H3K4me3, H3K27ac, Pol II (ser2)) and bound to ConA beads before processing with a CUT&Tag protocol.

first: Kasey

last: Love

first: Sneha

middle: R

last: Kabaria

first: Albert

last: Blanch-Asensio

first: Deon

last: Ploessl

first: Emma

middle: L

last: Peterman

first: Rachel

last: Lee

first: Jiyoung

last: Yun

first: Conrad

last: Oakes

first: Christine

last: Mummery

last: Davis

first: Brandon

last: DeKosky

first: Peter

middle: W

last: Zandstra

first: Kate

last: Galloway


title: Gene syntax defines supercoiling-mediated transcriptional feedback [CUT&RUN]

overall_design: GapRUN profiling of hiPSC lines containing integrated synthetic gene pairs. Gene pairs with one of the four possible syntaxes (divergent, convergent, upstream tandem, downstream tandem) were integrated homozygously at the CYLBL locus in hiPSCs. The two genes were mTagBFP2-T2A-rtTA expressed constitutively from the CAG promoter, and mScarlet expressed from the inducible TRE promoter. These four lines were split into plus and minus induction conditions. The induced condition was treated with treated with 1000 ng/mL doxycycline for three days. Two days prior to collection, the cells were transduced with a lentivirus expressing EGFP-GapR from an EF1a promoter. Around 500k cells were collected and bound to ConA beads. A fusion protein of MNase and a nanobody targeting EGFP was purified separately and added to the cells. After nanobody binding and wash steps, the MNase was activated to fragment the DNA, as in CUT&RUN. The resulting library was prepared as in CUT&RUN. The GapRUN protocol was derived from dx.doi.org/10.1016/j.molcel.2024.10.007; see the attached work here for protocol details.

middle: P

first: Richard


title: Gene syntax defines supercoiling-mediated transcriptional feedback [Micro-C]

overall_design: Region Capture Micro-C profiling of hiPSC lines containing integrated synthetic gene pairs. Gene pairs with one of the four possible syntaxes (divergent, convergent, upstream tandem, downstream tandem) were integrated homozygously at the CYLBL locus in hiPSCs. The two genes were mTagBFP2-T2A-rtTA expressed constitutively from the CAG promoter, and mScarlet expressed from the inducible TRE promoter. These four lines were split into plus and minus induction conditions. The induced condition was treated with treated with 1000 ng/mL doxycycline for three days. Around 15M cells per condition were collected, crosslinked, and treated according to a Micro-C protocol. After library construction, a biotinylated oligo library was used to capture 3 loci: ~600 kb around the CLYBL locus, the region around the Rogi2 locus, and the region around the AAVS1 locus. The resulting capture libraries were amplified and sequenced.


title: Gene syntax defines supercoiling-mediated transcriptional feedback [RNA-seq]

overall_design: RNA-seq profiling of hiPSC lines containing integrated synthetic gene pairs. Gene pairs with one of the four possible syntaxes (divergent, convergent, upstream tandem, downstream tandem) were integrated homozygously at the CYLBL locus in hiPSCs. The two genes were mTagBFP2-T2A-rtTA expressed constitutively from the CAG promoter, and mScarlet expressed from the inducible TRE promoter. These four lines were split into plus and minus induction conditions. The induced condition was treated with treated with 1000 ng/mL doxycycline for three days. Around 300k cells per condition were collected, then RNA was extracted and sequenced using poly(A) selection.


title: Elucidation of a Potent Pro-Resolving Mediator of Inflammation-Resolution via Human Neutrophil-Vascular Endothelial Cell Interactions

city: Boston

last: Chiang

state: MA

address: 60 Fenwood Rd. 3016Q

institute: Brigham and Women's Hospital

summary: We examined the impact of the new compound VL-Rv on TNF-stimulated HUVEC using RNAseq

overall_design: HUVEC (~1 million cells) were incubated with vehicle, TNF (10 ng/mL) and TNF plus VL-Rv (10 nM) for 48h. Cells were collected and total RNA prepared for RNAseq.

first: Charles

middle: N

last: Serhan

first: Robert

last: Nshimiyimana


title: ACSS2 plays a role in mediating lasting transcriptomic dysregulation in the dorsal hippocampus and cerebellar vermis of mice chronically prenatally exposed to alcohol

city: St. Louis

first: Gabor

last: Egervari

email: gabor@wustl.edu, egervarilab@gmail.com

state: MO

address: 4515 McKinley Ave, Couch Building

department: Genetics, Biochemistry and Molecular Biophysics

institute: Washington University School of Medicine

summary: BACKGROUND: Recent findings showed that alcohol-derived acetate contributes to ACSS2-dependent histone acetylation in the brain, and this metabolic-epigenetic mechanism regulates alcohol-associated learning. Further, alcohol-derived acetate is incorporated into histone acetylation in gestating fetal brains following acute maternal alcohol exposure in late pregnancy (E18.5). GOAL: Determine any role of ACSS2 in mediating chronic prenatal alcohol exposure (cPAE)-driven lasting transcriptomic effects in the brain. APPROACH: We used RNA sequencing to investigate the lasting cPAE-related transcriptomic effects in the dorsal hippocampus (dHPC) and cerebellar vermis of adolescent WT and ACSS2 KO mice. These two brain regions were selected because of their implications in hallmark FASD phenotypes (long-term memory impairments and motor deficits, respectively). The chronic prenatal exposure model was a daily i.p. injection (3 g/kg ethanol or equivalent volume saline) to pregnant dams from E0.5 until pups were born. FINDINGS: cPAE resulted in lasting gene and transcript expression changes in both of these brain regions of both genotypes compared to respective saline (cPSE)-treated controls. There were few enriched biological processes, indicating cPAE has widespread lasting transcriptomic effects across a variety of pathways. cPAE-related differentially expressed features (DEFs: DEGs and DETs) were nearly entirely specific to genotype, evidenced by very few DEFs overlapping between genotypes. All but one of these overlapping DEFs were oppositely affected between genotypes. Further, there were hundreds of DEFs exhibiting significant interaction between genotype and prenatal exposure. Taken together, these findings suggest that lasting cPAE-related transcriptomic dysregulation is in part modulated by ACSS2.

overall_design: RNA sequencing of the dorsal hippocampus [dHPC] and cerebellar vermis [Vms] collected from WT and ACSS2 KO mice that were subjected to chronic prenatal alcohol exposure [cPAE] or chronic prenatal saline exposure [cPSE] (control). For each genotype, samples were extracted from 4 biological replicates (mice; 2 females [F] and 2 males [M]) per prenatal exposure condition.

first: Kala

middle: M

last: Dodson

first: Erica

last: Periandri

first: Anjali

last: Yadav

first: Mariana

last: Lopes

first: Amelia

last: Barfield

first: Anjola

last: Ola

first: Francisca

last: de Luna Vitorino

first: Cory

last: Cearlock

first: Benjamin

middle: A

last: Garcia

first: Cheryl

last: Hill

first: Susan

last: Maloney


title: Molecular basis of target RNA cleavage by Cas13 III

city: Hong Kong

first: Joe

last: Lam

address: 21 Sassoon road

department: School of Biomedical Sciences

country: Hong Kong

institute: The University of Hong Kong

summary: RNA-targeting CRISPR-Cas13 enzymes are robust RNA knockdown tools with both on-target and collateral cleavage activities. However, to this date, the in vivo RNA cleavage mechanisms remain poorly understood. Here, we combine in vitro and in vivo methods to elucidate the exact cleavage sites of Cas13. We reveal that some subtypes of Cas13, including Cas13b and Cas13bt, cleave the target RNA in predominant positions, and rational engineering of Cas13 further improves the precision. Building on this fact, we developed RNA segment editing (RSE), a targeted RNA cleavage and repair method, to restore dysfunctional RNA in cells. We anticipate that RSE will enable precision RNA engineering for therapeutics and basic research.

overall_design: Cleavage site and preference analysis of different PspCas13b mutants using in vivo adaptor ligation

first: SC

last: Kwon


title: Molecular basis of target RNA cleavage by Cas13 II

overall_design: Cleavage site analysis of Cas13 proteins and other RNA cleavage samples using different methods (5' RACE and in vivo adaptor ligation)


title: Exposed phosphatidylserine is a non-classical inhibitory molecule during CD8 T cell exhaustion

city: Tampa

first: Christopher

middle: Bernardo

last: Medina

state: FL

address: 3011 W Holly Dirve

country: USA

institute: Moffitt Cancer Center

summary: In cancer and chronic infection CD8 T cell exhaustion is hallmarked by expression of inhibitory surface receptors such as PD-1, TIM-3, CTLA-4, LAG-3, and TIGIT. Thus, inhibitory receptor focus has been limited to surface expressed proteins and an expansion into different classes of inhibitory molecules is needed. In this study we identify the lipid metabolite phosphatidylserine (PS) as a regulator of T cell exhaustion. PS localizes to the inner plasma membrane of live cells but is externalized to the outer membrane of apoptotic cells where it can function as a potent inhibitory ligand. However, the role of PS on live immune cells is less clear4. We show that live, exhausted, antigen specific CD8 T cells externalize PS during chronic lymphocytic choriomeningitis virus (LCMV) infection. PS exposure is initiated upon T cell activation and chronic antigen stimulation led to continued externalization. PD-1+ Tcf1+ stem-like, Tim-3+ transitory, and Tim3+ terminally differentiated/exhausted cells all expose PS. Furthermore, transcriptomic and lipidomic analyses identified increased PS metabolism during exhaustion. To evaluate the inhibitory function of exposed PS in exhaustion we treated chronically infected mice with the PS-targeting antibody (mch1N11)5 and found that monotherapy alone expanded the PD-1+ LCMV-specific CD8 T cell immune response. Most significantly, PD-1+ Tcf1+ stem-like CD8 T cells downregulated quiescence-associated gene modules and increased proliferation and self-renewal after treatment. Mechanistically, we found that exposed PS from exhausted T cells could suppress co-stimulatory molecule expression on neighboring dendritic cells to limit PD-1+ CD8 T cell proliferation. Combination of PS-targeting with aPD-L1 synergized to further increase the CD8 T cell effector response and improve viral control. Lastly, we identify that CD8 tumor infiltrating lymphocytes from human clear cell renal cell carcinoma (ccRCC) and human non-small cell lung cancer (NSCLC) patient tumors similarly expose PS indicating its translational potential. In fact, clinical trials combining PS-targeting antibodies and PD-L1 antibodies have recently been used in combination therapies. Therefore, our work details live PS CD8 T cell biology and provides a potential mechanism of action by which exposed PS facilitates suppressive T cell – DC interactions to function as a ‘non-classical’ inhibitory molecule during exhaustion.

overall_design: LCMV Cl. 13 chronically infected mice were treated with control IgG or mch1N11 PS-targeting antibodies every 3 days at 200ug per injection IP for two weeks. Spleen were isolated post-treatment and PD-1+ Tim3- CD73+ Stem-like, PD-1+ Tim3+ CD101- Transitory, and PD-1+ Tim3+ CD101+ TD cells were isolated from respective groups and RNAsequencing was perfromed.

middle: B

first: Rafi

last: Ahmed


title: MORC3 represses a tandem repeat enhancer to regulate interferon

city: Vienna

first: Moritz

last: Gaidt

address: Campus-Vienna-Biocenter 1

country: Austria

institute: Research Institute of Molecular Pathology

summary: The antiviral protein MORC3 is frequently inhibited by viruses. To counteract viral antagonism, MORC3 represses a noncanonical pathway of type-I-interferon (IFN) such that viral inhibition of MORC3 triggers (>10,000-fold) IFN induction. How MORC3 represses this pathway, and why IFN induction upon MORC3 loss is so potent without canonical IRF3/7 transcription factors, is unknown. Here, we show that MORC3 restricts chromatin accessibility at tandem repeat elements harboring up to 61 homotypic transcription factor motifs. One such element becomes a potent enhancer of IFNB1 upon MORC3 loss. Its motif cluster contains 45 PU.1 binding sites and is necessary and sufficient for MORC3-mediated repression and enhancer activity upon MORC3 loss. PU.1 recruits MORC3 to repress this enhancer by recruiting DAXX and enabling H3.3 incorporation. Upon MORC3 loss, PU.1 drives IRF3/7-independent IFN induction. Other restricted tandem repeats contain homotypic motif clusters of SPI, AP-1, and SP/KLF transcription factors. Our findings uncover a TF motif cluster–driven repression mechanism by MORC3 at tandem repeats, enabling specific repression of an IFNB1 enhancer such that viral antagonism of MORC3 induces interferon.

overall_design: The goal of this study was to identify the regulatory mechanism behind the repression and activation of the MORC3-repressed tandem repeat element

first: Luisa

last: Krumwiede

first: David

last: Hollaus

first: Erika

last: Valeri

first: Karina

last: Schindler-Schumitsch

first: Monika

last: Bazyl

first: Johanna

last: Schiedlbauer

first: Nanette

last: Becht

first: Markus

last: Jaritz

first: Bernardo

last: de Almeida

first: Siegfried

last: Schloissnig

first: Dara

last: Burdette

first: Jacob

last: Schreiber

first: Alex

last: Stark