title: Single-cell Profiling Reveals Diverse γδ T Cell Subsets in Ulcerative Colitis

city: Freiburg

first: Jakob

last: Arnold

address: Breisacher Str. 66

institute: Uniklinik Freiburg

summary: γδ T cells maintain intestinal immune homeostasis, but their contributions to human ulcerative colitis (UC) are poorly understood. We characterized γδ T cells in intestinal biopsies obtained from patients  with UC and healthy donors using single-cell RNA sequencing, T cell receptor profiling, and mass cytometry. UC reduced CD103+Vγ4Vδ1+  intraepithelial γδ lymphocytes (γδ IELs) and increased γδ T cell subsets with stem-like phenotypes expressing T cell factor-1 (TCF-1) and programmed cell death receptor 1 (PD-1), or effector-like phenotypes expressing granzyme B, perforin, and T-box expressed in T cells (T-bet). γδ T cell composition changes in UC correlated with decreased expression of epithelial BTNL3 and BTNL8   and increased BTN3A1 and BTN3A3  , suggesting altered recruitment and activation  . Clinical improvement recovered γδ IELs and reduced inflammation-associated subsets. Inflammation-associated changes were observed in peripheral blood γδ T cells. Thus, distinct γδ T cell subsets in different niches exert protective or pathogenic functions in UC.

overall_design:
scRNA-seq, CITE-seq, TCR-seq

GSM9444084: Colonic gdT cells (batch #1); samples of HD and UC donors are multiplexed (table matching each barcode to a specific donor is provided with FLASHseq_R1_meta.tsv)
GSM9444085: Colonic gdT cells (batch #2); samples of HD and UC donors are multiplexed (table matching each barcode to a specific donor is provided with FLASHseq_R2_meta.tsv)
GSM9444086: PBMC derived TCRgd Vd1 cells (batch #1, GEX); samples of HD and UC donors are multiplexed by cell hashing (HTO); HD donors: Hu.Hashtag_1, Hu.Hashtag_2, Hu.Hashtag_3; UC donors: Hu.Hashtag_4, Hu.Hashtag_5, Hu.Hashtag_6
GSM9444087: PBMC derived TCRgd Vd1 cells (batch #1, HTO); samples of HD and UC donors are multiplexed by cell hashing (HTO); HD donors: Hu.Hashtag_1, Hu.Hashtag_2, Hu.Hashtag_3; UC donors: Hu.Hashtag_4, Hu.Hashtag_5, Hu.Hashtag_6
GSM9444088: PBMC derived TCRgd Vd1 cells (batch #1, TCR); samples of HD and UC donors are multiplexed by cell hashing (HTO); HD donors: Hu.Hashtag_1, Hu.Hashtag_2, Hu.Hashtag_3; UC donors: Hu.Hashtag_4, Hu.Hashtag_5, Hu.Hashtag_6
GSM9444089: PBMC derived TCRgd Vd1 cells (batch #2, GEX); samples of HD and UC donors are multiplexed by cell hashing (HTO); HD donors: Hu.Hashtag_1, Hu.Hashtag_2; UC donors: Hu.Hashtag_3, Hu.Hashtag_4, Hu.Hashtag_5, Hu.Hashtag_6
GSM9444090: PBMC derived TCRgd Vd1 cells (batch #2, HTO); samples of HD and UC donors are multiplexed by cell hashing (HTO); HD donors: Hu.Hashtag_1, Hu.Hashtag_2; UC donors: Hu.Hashtag_3, Hu.Hashtag_4, Hu.Hashtag_5, Hu.Hashtag_6
GSM9444091: PBMC derived TCRgd Vd1 cells (batch #2, TCR); samples of HD and UC donors are multiplexed by cell hashing (HTO); HD donors: Hu.Hashtag_1, Hu.Hashtag_2; UC donors: Hu.Hashtag_3, Hu.Hashtag_4, Hu.Hashtag_5, Hu.Hashtag_6
GSM9444092: PBMC derived TCRgd Vd2 cells (batch #1, GEX); samples of HD and UC donors are multiplexed by cell hashing (HTO); HD donors: Hu.Hashtag_1, Hu.Hashtag_2, Hu.Hashtag_3; UC donors: Hu.Hashtag_4, Hu.Hashtag_5, Hu.Hashtag_6
GSM9444093: PBMC derived TCRgd Vd2 cells (batch #1, HTO); samples of HD and UC donors are multiplexed by cell hashing (HTO); HD donors: Hu.Hashtag_1, Hu.Hashtag_2, Hu.Hashtag_3; UC donors: Hu.Hashtag_4, Hu.Hashtag_5, Hu.Hashtag_6
GSM9444094: PBMC derived TCRgd Vd2 cells (batch #1, TCR); samples of HD and UC donors are multiplexed by cell hashing (HTO); HD donors: Hu.Hashtag_1, Hu.Hashtag_2, Hu.Hashtag_3; UC donors: Hu.Hashtag_4, Hu.Hashtag_5, Hu.Hashtag_6
GSM9444095: PBMC derived TCRgd Vd2 cells (batch #2, GEX); samples of HD and UC donors are multiplexed by cell hashing (HTO); HD donors: Hu.Hashtag_1, Hu.Hashtag_2; UC donors: Hu.Hashtag_3, Hu.Hashtag_4, Hu.Hashtag_5, Hu.Hashtag_6
GSM9444096: PBMC derived TCRgd Vd2 cells (batch #2, HTO); samples of HD and UC donors are multiplexed by cell hashing (HTO); HD donors: Hu.Hashtag_1, Hu.Hashtag_2; UC donors: Hu.Hashtag_3, Hu.Hashtag_4, Hu.Hashtag_5, Hu.Hashtag_6
GSM9444097: PBMC derived TCRgd Vd2 cells (batch #2, TCR); samples of HD and UC donors are multiplexed by cell hashing (HTO); HD donors: Hu.Hashtag_1, Hu.Hashtag_2; UC donors: Hu.Hashtag_3, Hu.Hashtag_4, Hu.Hashtag_5, Hu.Hashtag_6

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


title: A combinatorial transcription factor screening platform for immune cell reprogramming [scRNA-seq]

status: Public on Jan 14 2026

city: Lund

first: Ilia

last: Kurochkin

state: Skane

address: BMC A12, Sölvegatan 17

country: Sweden

institute: Lund University

type: Expression profiling by high throughput sequencing

summary: Direct reprogramming of immune cells holds promise for immunotherapy but is constrained by limited knowledge of transcription factor (TF) networks. Here, we developed REPROcode, a combinatorial single-cell screening platform to identify TF combinations for immune cell reprogramming. We first validated REPROcode by inducing Type-1 Conventional Dendritic Cells (cDC1) with multiplexed sets of 9, 22, and 42 factors. With cDC1-enriched TFs, REPROcode enabled identification of optimal TF stoichiometry, fidelity enhancers, and regulators of cDC1 states. We then constructed an arrayed lentiviral library of 408 barcoded immune TFs to explore broader reprogramming capacity. Screening 48 TFs enriched in dendritic cell subsets yielded myeloid and lymphoid phenotypes and enabled the construction of a TF hierarchy map to guide immune reprogramming. Finally, we validated REPROcode’s discovery power by inducing Natural Killer (NK)-like cells. This study deepens our understanding of immune transcriptional control and provides a versatile toolbox for engineering immune cells to advance immunotherapy.

overall_design: 9 TF, 22 TF, 42 TF and 48TF-transduced fibroblasts were FACS sorted for CD45+HLA-DRA+ or CD45+, and CD45-HLA-DRA-day9 (d9) and profiled by single cell RNA sequencing.  Cells were sorted live at day 2 (d2) to capture TF representation.

first: Abigail

last: Altman

first: Olga

last: Zimmermannova

first: Carlos-Filipe

last: Pereira


title: M-cadherin regulates the formation of adherens junctions and secondary myofibers during fetal myogenesis to determine adult myofiber number and muscle mass

status: Public on Jan 13 2026

city: Tarrytown

first: Michael

last: Stec

state: NY

address: 777 Old Saw Mill River Rd

country: USA

institute: Regeneron Pharmaceuticals

summary: Cadherin-mediated adhesion of skeletal muscle stem cells within their niche is necessary for normal adult muscle maintenance and regeneration; however, the role of cadherins in regulating muscle development and growth has not yet been elucidated. Here, we show that M-cadherin protein is localized to adherens junctions in developing muscle, and that deletion of CDH15, the gene encoding M-cadherin, results in the loss of adherens junctions in fetal mouse muscle. This loss of adherens junctions is associated with reduced secondary myofiber formation, ultimately resulting in reduced adult myofiber number and muscle mass. Concordantly, via large-scale exome sequencing, we found that humans with predicted loss-of-function variants in the CDH15 gene had significantly reduced lean mass, indicating that M-cadherin functions to regulate muscle mass in both mice and humans. Overall, these data highlight a previously unrecognized role of M-cadherin in controlling fetal myofiber formation and establishment of adult muscle mass.

overall_design: Bulk RNASeq sequencing of WT and Cdh15 KO mice from multiple tissues

first: David

last: R. Golann

first: Patrick

last: J. Ferrara

first: Naveen

last: P. Khan

first: Margaret

last: Hung

first: Virgiinia

last: Hughes

first: Samer

last: Nuwayhid

first: Jonas

last: Bovijn

first: Peter

last: Dornbos

first: Luca

last: Lotta

first: Peisheng

last: Shi

first: Qi

last: Su

first: Yajun

last: Tang

first: Mark

last: W. Sleenman

last: J. Stec


title: A combinatorial transcription factor screening platform for immune cell reprogramming [bulkRNA-seq]

first: Ilia

last: Kurochkin

overall_design: TENE-transduced fibroblasts were FACS sorted for CD56 positive at day 12. Untransduced HEF and peripheral blood- derived CD56Bright CD16- and CD56dim CD16+ NK cells were included as controls

first: Inês

last: Maria Nascimento Caiado


title: YWHAZ is Downregulated in the Proliferative Eutopic Endometrium in Endometriosis and Is Required Downstream of Progesterone Receptor and STAT3 Signaling.

city: Columbia

first: Jae-Wook

last: Jeong

state: MO

address: Rutland Drive

department: Obstetrics, Gynecology and Women’s Health

institute: University of Missouri

summary: We performed RNA sequencing on proliferative-phase eutopic endometrium from women with endometriosis (n = 4) and without endometriosis (n = 4). Histological dating of endometrial samples was performed by a certified pathologist. Transcriptomic analysis identified 44 differentially expressed genes, including 13 upregulated and 31 downregulated transcripts in women with endometriosis compared with controls, indicating a distinct transcriptional profile associated with endometriosis. This dataset provides a resource for understanding molecular pertubations associated with the disease.

overall_design: Human eutopic endometrial biopsies were collected from women with and without endometriosis during the proliferative phase, stored in RNA-later until  total RNA was isolated for RNA-seq analysis. Control (n = 4); Endometriosis (n = 4).

first: Tae Hoon

last: Kim

first: Jae Wook


title: Rainbow trout adipose tissue depots (VAT, SAT, IMAT) - miRNAs

city: Barcelona

first: Enrique

last: Rosell-Moll

address: Av Diagonal, 643 4º floor

country: Spain

institute: University of Barcelona

type: Non-coding RNA profiling by high throughput sequencing

summary: The aim of this study was to characterize different adipose tissue depots in rainbow trout (Oncorhynchus mykiss) through the analysis of mRNA and miRNA expression profiles. Mature adipocytes were isolated from visceral (VAT), subcutaneous (SAT), and intramuscular (IMAT) adipose tissues, and RNA sequencing (RNA-seq) was performed. Data were curated, quality-checked, and filtered prior to downstream analyses. This dataset contains the FASTQ files generated in the study. The results will contribute to a better understanding of the molecular differences and similarities among adipose depots in fish reared under standard aquaculture conditions, providing a foundation for improving adiposity control, animal health, fillet yield, and overall product quality.

overall_design: Cell type comparison design. Three adipose tissue depots (VAT, SAT and IMAT) in rainbow trout under standard aquaculture conditions.

first: E

last: Capilla

first: I

last: Navarro

first: D

last: Garcia de la serrana


title: Rainbow trout adipose tissue depots (VAT, SAT, IMAT) - mRNAs


title: Chromatin-mediated anticipatory control of type I interferon production in plasmacytoid dendritic cells (Combined snRNA-seq and snATAC-seq of ΔTB pDC activation)

city: New York City

first: Eduardo

last: Esteva

state: New York

address: 550 1st Ave

institute: NYU Grossman School of Medicine

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Type I interferons (IFN-I) including IFN-β and multiple IFN-α subtypes are key antiviral proteins encoded within a single locus. The antiviral response of most cell types involves primarily IFN-β, whereas professional IFN-I-producing plasmacytoid dendritic cells (pDCs) secrete all IFN-I subtypes. We report that the IFN-I locus in quiescent pDCs showed multiple distinct features, including i) localization in the active intranuclear chromosomal compartment; ii) distinct three-dimensional chromatin organization, and iii) poised promoters at multiple Ifna genes. Accordingly, IFN-I production specifically by pDCs was dependent on the chromatin-organizing cohesin complex. The intranuclear translocation and promoter poising were mediated by the pDC-enriched transcription factor IRF8. Finally, we identified several IRF8- and/or cohesin-binding regulatory regions across the IFN-I locus. One of these enhanced IFN-β induction in all cells, whereas two others enhanced pDC-specific induction of adjacent Ifna genes. Thus, the unique IFN-I-producing capacity of pDCs is facilitated by the anticipatory chromatin organization imparted by IRF8 and cohesin.

overall_design: Combined snRNA-seq and snATAC-seq was performed on pDCs from unstimulated or CpG-stimulated FL-BMDC cultures derived from mice expressing green fluorescent protein (GFP) transgene driven by the CAGGS promoter (control) and IfnΔTB2/TB3/TB4 (ΔTB) mice.

first: N

last: Adams

first: B

last: Reizis


title: Cohesin-mediated chromatin remodeling controls the differentiation and function of conventional dendritic cells (CITE-Seq of SMC3 KO splenic cDCs +/- activation)

summary: The cohesin protein complex extrudes chromatin loops between CTCF-bound sites to organize chromosomes into topologically associated domains, yet biological implications of this process remain obscure. We show that cohesin is required for the post-mitotic differentiation and function of antigen-presenting dendritic cells (DCs), particularly for antigen cross-presentation and IL-12 secretion by type 1 conventional DCs (cDC1s) in vivo. The chromatin organization of DCs was shaped by cohesin and the DC-specifying transcription factor IRF8, which controlled chromatin looping and chromosome compartmentalization, respectively. Notably, optimal expression of IRF8 itself required CTCF/cohesin-binding sites demarcating the Irf8 gene. During DC activation, cohesin was required for the induction of a subset of genes with distal enhancers. Accordingly, the deletion of CTCF sites flanking the Il12b gene reduced IL-12 production by cDC1s. Our data reveal an essential role of cohesin-mediated chromatin regulation in cell differentiation and function in vivo, and its bi-directional crosstalk with lineage-specifying transcription factors.

overall_design: scRNA-seq with "hashtagging" according to the CITE-seq protocol was performed on cDCs from the spleen of CD11c-Cre/+ (Control) or CD11c-Cre/+ Smc3fl/fl (Smc3ΔDC) mice, either in the presence or absence of in vivo treatment with LPS and profilin

first: A

last: Ra


title: Cohesin-mediated chromatin remodeling controls the differentiation and function of conventional dendritic cells (H3K27me3 CUT&RUN of SMC3KO FL-BMDCs +/- activation)

overall_design: CUT&RUN for H3K27me3 was performed on cDCs purified from 4-OHT-treated FL-BMDC cultures from Rosa26CreER/+ or Rosa26CreER/+ Smc3fl/fl mice, after cultures were either unstimulated or stimulated with CpG-B for 6 hours (2 replicates per genotype/stimulation condition).

last: Martinez-Krams

last: Galitsyna


title: Allelic chromatin structure is a pervasive feature of imprinted domains and functions cooperatively with cis-acting long non-coding RNAs at the Mest-Copg2 locus [CUT&Tag]

city: Cambridge

first: Bongmin

last: Bae

state: MA

address: 16 Divinity Ave

institute: Harvard University

summary: Genomic imprinting is an epigenetic phenomenon in which genes exhibit restricted or biased expression from one allele according to parental origin. Imprinted gene expression plays a crucial role in the development, including the brain. Higher-order chromatin structure has long been associated with gene regulation, particularly in the context of spatial enhancer-promoter interactions. Given the characteristic parental allele-biased expression pattern of imprinted genes, a compelling question is whether the three-dimensional organization of parental genomes plays a role in imprinted gene regulation. Using a capture Hi-C approach, we identifiedparental allele-specific higher-order chromatin structures across multiple imprinted domains in the mouse brain. These allele-specific structural features largely stem from annotated imprinting control regions (ICRs), concomitant with allele-specific binding of CTCF. Detailed analysis suggests that transcriptional start sites (TSS) of active and inactive alleles of imprinted genes form distinct chromatin interactions, differing in degree and/or type. CRISPRi screeningrevealed a distal cis-regulatory element that modulates imprinted expression of the Mest-Copg2locus in neurons, and its regulatory mechanism is tightly associated with allele-specific chromatin interactions. Further investigation revealed that both a cis-acting long non-coding RNA and allele-specific enhancer-promoter architecture modulates Mest-Copg2 imprinted expression. Together, this study highlights the interplay between chromatin structure and regulatory landscapes that modulate allele-specific expression of imprinted genes.

overall_design:
CTCF CUT&Tag from primary cortical neurons isolated from F1 E16 embryos, including forward (BxC) and reverse (CxB) crosses. / H3K27ac CUT&Tag from hybrid KRABxCast NPC-derived neurons, treated with scramble (LV-Scrb) or enhancer-targeting (LV-E105) gRNAs. / CTCF CUT&Tag from hybrid mESC, treated with DMSO or DNMTi (GSK-3484862).

H3K36me3 CUT&Tag from primary cortical neurons obtained from F1 E16 embryos. Forward BxC and reverse CxB crosses. / H3K9me3 CUT&Tag from hybrid KRABxCast NPC differentiated neurons. Cells treated with LV-Scrb, LV-E104, LV-E105, LV-E111 gRNAs. / CTCF CUT&Tag from hybrid BxC NPC and NPC differentiated neurons

first: Amanda

middle: J

last: Whipple


title: Loss of Mtarc1 Protects Against Steatotic Liver Disease in Mice

last: Chaffin

address: 75 Ames Street

department: Cardiovascular Disease Initiative

institute: Broad Institute of MIT and Harvard

summary: Background & Aims: Metabolic dysfunction-associated steatotic liver disease (MASLD) spans from simple steatosis to metabolic dysfunction-associated steatohepatitis (MASH) and can progress to cirrhosis or hepatocellular carcinoma. Despite its prevalence, effective therapies are lacking. Recent genome-wide association studies identified a common missense variant (rs2642438) in the Mitochondrial Amidoxime Reducing Component 1 (MTARC1) gene that protects against liver cirrhosis without increasing cardiovascular disease risk. Biochemical and disease risk signatures associated with carriers of this missense variant also aligned with those of a known loss-of-function MTARC1 variant, suggesting mARC1 inhibition as a potential MASLD treatment.  Methods: To validate mARC1 loss-of-function as protective against MASLD, we generated Mtarc1 knockout (KO) mice and placed them on a choline-deficient, L-amino acid-defined, high-fat diet (CDAHFD). Effects of Mtarc1 KO on obesity and type 2 diabetes were explored using a high-fat diet. Hepatocytes from Mtarc1 KO mice were isolated to explore the molecular mechanisms by which Mtarc1 KO impacts lipid metabolism.  Results:  Mtarc1 KO mice exhibited no vital growth or development defects. With a high-fat diet-induced obesity model, obese Mtarc1 KO mice exhibited reduced liver mass and lower cholesterol levels, with no effect on glucose homeostasis. In a CDAHFD-induced MASLD model, mARC1 deficiency significantly reduced liver steatosis, profibrosis, and inflammation. Untargeted metabolomics profiling further showed hepatic enrichment of phospholipids in Mtarc1 KO mice. Primary hepatocytes isolated from Mtarc1 KO mice exhibited reduced lipid droplet accumulation, decreased fatty acid uptake, and increased lipid secretion.  Conclusions: These findings support mARC1 inhibition as a promising therapeutic strategy for MASLD/MASH.

overall_design: RNA-seq profiling of  liver tissue from wildtype, Mtarc1 heterozygous knockout, and Mtarc1 homozygous knockout  mice on a choline-deficient, L-amino acid-defined, high-fat diet. Wildtype mice on normal chow diet were also included.

first: Xiaofei

last: Yin

first: Patrick

last: Ellinor


title: DAXX Directs H3.4-to-H3.3 Histone Replacement During Spermatogenesis

city: Davis

first: Satoshi

last: Namekawa

state: CA

address: One Shields Avenue

institute: University of California, Davis

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

overall_design: Refer to individual Series


title: Myelin antigen capture in the CNS by B cells expressing EBV latent membrane protein 1 leads to demyelinating lesion formation

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel


title: Optimizing intestinal glucotonic effect via atypical protein kinase C

city: Seoul

first: Hyeonuk

last: Jeon

address: 50-1, Yonsei-ro, Seodaemun-gu

department: College of Medicine

country: South Korea

institute: Yonsei University

summary: Intestinal glucotonic transformation, defined as increased intestinal serum glucose uptake and secretion into the lumen, influences bariatric surgery-associated glycermic control. This study aims to identify downstream molecules that mediate the function of the identified target as an effective intestinjal glucotonic activator. Altered transcriptomes were evaluated in variable intestinal glucotonic models and big data-based drug discovery systems. Protein kinase C (PKC) activation mimicked transcriptome alterations observed during intestinal glucotonic transformation. Among the PKC subfamilies, atypical PKC (aPKC) promoted glucose transporter 1 (GLUT1)-mediated intestinal glucotonic transformation without inducing oncogenic proliferation. Intestinal aPKC activation via a transposon expression vector induced serum glucose uptake into intestinal tissues and excretion into the lumen. Prostratin, a non-tumorigenic phorbol ester, activated aPKC and induced a similar glucotonic effect. Collectively, we identified the prostratin and aPKC/GLUT1 signaling pathways as effective targets for treating diabetes, providing insights into the future development of antidiabetic and weight loss drugs.

overall_design: Following RYGB surgery, intestinal tissues from rats were isolated and analyzed using scRNA-seq to investigate the molecular mechanism of aPKC/GLUT1-mediated glucotonic transformation.

first: Chan Woo

last: Kang

first: Zhen-Yu

last: Hong

first: Sungsoon

last: Fang

first: Insuk

last: Sohn

first: Cheol Ryong

last: Ku


title: Ramalin ameliorates Alzheimer's disease pathology by targeting BACE1, HDAC6, and MAPK pathways

city: Suwon

first: Dong-Gyu

last: Jo

address: 2066, Seobu-ro, Jangan-gu

institute: Sungkyunkwan University

summary: The accumulation of β-amyloid (Aβ) and hyperphosphorylated tau, along with neuroinflammation, are key drivers of Alzheimer’s disease (AD) pathology. Here, we identify ramalin, a natural antioxidant, as a promising therapeutic agent that targets multiple pathological mechanisms in AD models. Ramalin reduces BACE1 protein levels, without affecting its transcription, translation, or proteolytic activity. This reduction is mediated through selective inhibition of histone deacetylase 6 (HDAC6), as confirmed by genome-wide drug target screening and HDAC activity assays. Knockdown of HDAC6 resulted in decreases in BACE1 levels, positioning HDAC6 as a mediator of BACE1 regulation. Ramalin exhibits anti-inflammatory effects by downregulating iNOS and the NLRP3 inflammasome. In AD mouse models, ramalin treatment significantly reduced neuroinflammation, Aβ plaque burden, tau hyperphosphorylation and improved cognitive performance. Notably, ramalin reversed Aβ oligomer-induced synaptic transmission impairment and restored synaptic vesicle recycling in hippocampal neurons. Transcriptomic analysis revealed ramalin modulates MAPK signaling pathway, reducing phosphorylation of JNK and ERK, which are implicated in tau pathology. These findings position ramalin as a multi-target therapeutic agent, offering neuroprotection through coordinated modulation of BACE1, tau phosphorylation, and inflammatory pathways. Given these promising results, ramalin represents a potential breakthrough for the treatment of AD by targeting key pathogenic processes at multiple levels.

overall_design: RNA-seq analysis of cortical tissues from 3xTg-AD mice treated with vehicle or ramalin

first: Yongeun

last: Cho

first: Jeongmi

last: Lee

first: Bo Youn

last: Choi

first: Jin-Ho

last: Yun

first: Sukmin

last: Han

first: Seung Hyun

last: Baek

first: Jinsu

last: Park

first: Yoonsuk

first: Hark Kyun

last: Kim

first: Eunae

first: Leon

middle: F

last: Palomera

first: Jeein

last: Lim

first: Yeji

first: Jeonghyeong

last: Im

first: Ju-Mi

first: Tai Kyoung

first: Sung Hyun

first: Joung Han

last: Yim


title: DAXX Directs H3.4-to-H3.3 Histone Replacement During Spermatogenesis [RNA-Seq]

first: Satoshi

last: Namekawa

summary: During spermatogenesis, extensive chromatin remodeling and histone replacement reshape the male germline epigenome. While HIRA is known to mediate transcription-coupled incorporation of histone variant H3.3, we identify DAXX as a key histone chaperone directing genome-wide, transcription-dependent replacement of H3.4 (H3T) with H3.3 on autosomes during male meiosis. Simultaneously, DAXX also directs transcription-independent H3.4-to-H3.3 replacement on the sex chromosomes during meiotic sex chromosome inactivation (MSCI). These distinct, chromosome-specific modes of DAXX-mediated H3.3 deposition are essential for epigenomic integrity in the male germline. Loss of DAXX disrupts this process, leading to widespread transcriptional dysregulation in haploid round spermatids and male infertility.

overall_design: RNA-seq analysis using DAXX-ctrl and DAXX-cKO 4wk FACS sorted pachytene spermatocytes (PS) and round spermatids (RS);CUT&Run analysis on H3.1/H3.2, H3.3, H3t, H3K27ac, and H3K9me3 using DAXX-ctrl and DAXX-cKO 4wk sorted pachytene spermatocytes (PS) and round spermatids (RS).

middle: H

first: Yu-Han

last: Yeh


title: Intestinal Epithelial Tet2 Deficiency Reprograms the Gut Microbiota through Bile Acid Metabolic Alterations

city: Shanghai

first: Hailiang

last: Liu

address: NO 1239, siping road

country: China

institute: Tongji university

summary: Epigenetic mechanisms are increasingly recognized as critical regulators of host-microbiota interactions. Here, we report that intestinal epithelial-specific deletion of Tet2, a key DNA demethylase, leads to structural abnormalities, impaired barrier function, and remarkable reprogramming of the gut microbial community. Mechanistically, Tet2 deficiency significantly downregulated the expression of the apical sodium-dependent bile acid transporter (ASBT/Slc10a2), resulting in altered bile acid homeostasis with specific accumulation of hyocholic acid (HCA) in the intestinal lumen. This metabolic shift created a favorable niche for selective expansion of bile salt hydrolase (BSH)-expressing Lactobacillus species. Furthermore, we identified an age-dependent regulatory role of HCA in shaping microbial composition, promoting Lactobacillus in young mice while enriching Akkermansia in aged animals. Our findings unveil an epigenetic-metabolic-microbial axis centered on Tet2-mediated regulation of bile acid metabolism, providing new insights into how host epigenetic factors shape the gut microbial ecosystem.

overall_design: The gut microbiota is shaped by host-derived factors through mechanisms that remain incompletely understood. This study demonstrates that intestinal epithelial Tet2, an epigenetic modulator, plays a pivotal role in determining gut microbial composition through regulation of bile acid metabolism. Tet2 deficiency downregulates ASBT expression, leading to altered bile acid profiles with accumulation of hyocholic acid (HCA), which in turn selectively enriches BSH-expressing Lactobacillus species. Notably, the effects of HCA on microbial communities are age-dependent. Our work establishes Tet2 as a key epigenetic regulator at the host-microbiota interface and reveals a previously unrecognized connection between DNA demethylation, bile acid transport, and microbial ecology. These findings provide a foundation for developing novel therapeutic strategies targeting the epigenetic-metabolic axis to modulate gut microbiota in diseases associated with microbial dysbiosis.


title: Structure of the MIWI endoribonuclease bound to pachytene piRNAs from mouse testes

city: Gneveva

first: Ramesh

last: Pillai

address: 30, Quai Ernest-Ansermet

department: Department of Molecular Biology

institute: University of Geneva

summary: Animal germlines express small RNAs called PIWI-interacting RNAs (piRNAs) that guide their associated PIWI endoribonucleases to destroy transposon transcripts, ensuring animal fertility. Mouse MIWI binds millions of sequences called pachytene piRNAs that use partial complementarity to target transposons and cellular mRNAs. Here we report the first cryo-EM structure of the MIWI-pachytene piRNA complex isolated from mouse testes. It shows a positively charged channel where the piRNA is held, with specific recognition of the signature first nucleotide uridine being mediated by amino acids within the MID and PIWI domains. The first six nucleotides of the guide RNA are visible and take up the A-form conformation to facilitate pairing with the target. Importantly, part of the channel accommodating the seed sequence is wider than that for insect PIWI, likely explaining the reported tolerance of MIWI to seed sequence mismatches. The catalytic site in the PIWI endonuclease domain presents an inactive state, with the loop containing one of the catalytic residues (E671) requiring structural re-orientation to adopt the catalytically competent state. Finally, we identify a conserved pre-formed pocket on the PIWI domain that may serve to accommodate a conserved tryptophan from the interacting factor GTSF1. Modelling shows how this interaction with GTSF1 can allosterically enforce reorganization of the catalytic pocket to promote small RNA-guided endoribonuclease activity. Our structure informs how MIWI functions using relaxed target engagement rules and associates with its interacting partner.

overall_design: Long RNA sequencing was used to check the gene and repeat expression in the sorted germ cells from two Strep-Miwi knock-in lines and small RNA sequencing was used to verify the proper piRNA loading of Strep-MIWI. Purified mouse Strep-MIWI was then used to slice the artificial piRNA target RNAs. Two RNA pools were generated: "Perfect" with 15,000 RNA targets perfectly complementary to mouse MIWI-bound piRNAs and "Bulge" with 15,000 RNA molecules with 2-nucleotide mismatch to the piRNA nucleotides 10 and 11, and small RNA sequencing was used to identify the potential MIWI slice products in both RNA pools.

first: Nicole

last: Raad

first: Carmen

last: Rodriguez

first: Radha

middle: R

last: Pandey

first: Inayathulla

last: Mohammed

first: Emiko

last: Uchikawa

first: Fabienne

last: Burger

first: David

last: Homolka

middle: S


title: Novel syngeneic cell lines for studying high-risk BRAFV600E-driven colorectal cancer in vivo [RNA-seq_organoids]

first: Ariane

last: Lehmann

address: Breisacher Strasse 153

department: IBSM

country: Germany

institute: Medical Center Freiburg

summary: Combining anti-EGFR antibodies with BRAF/MEK/ERK-pathway blockade opened new treatment options for BRAFV600E driven colorectal cancer (CRC). Nevertheless, responses of these poor-prognostic cancers are short-lived and heterogeneous, thereby highlighting the unmet need for novel concepts integrating targeted therapy and immuno-oncology. To this end, an immunocompetent mouse model with reliable disease onset and responding to clinically relevant drugs is essential but unavailable. Here, we generated three cell lines from peritoneal metastases originating from orthotopically transplanted organoids carrying BRAFV600E, Trp53R172H and Apc mutations and characterized their ground state and responses to targeted therapy compounds in detail by RNAseq, WES and various functional assays. Interestingly, these NaJa lines displayed distinct differentiation states and responses to the clinically relevant RAF inhibitors (RAFi) encorafenib and exarafenib, thereby resembling the clinical heterogeneity of BRAFV600E driven CRC. RAFi resistance was overcome by the EGFR-family inhibitor afatinib. RAFi also influenced the expression of the antigen presentation machinery, cytokines and other immunomodulatory factors. Upon re-transplantation into syngeneic mice, all NaJa lines established aggressive tumors with distinct tumor microenvironments correlated with their differentiation states. Thus, the NaJa lines provide a unique tool to study tumor heterogeneity, drug resistance and the interplay between tumor, stroma and immune cells in BRAFV600E driven CRC.

overall_design: Colonic (COL) organoids of 1-2 donor mice per genotype were cultured. Cre recombination was induced with 4-Hydroxytamoxifen (3.5 µM) in duplicates in-vitro for 24 hours. Control organoids were treated with ethanol (EtOH). Isolated mRNA was sequenced on an Illumina HiSeq4000.

first: Jasmin

last: Traichel

last: Metzger

first: Maria

last: Walz

first: Reinhild

last: Feuerstein

first: Nadine

last: Wohlfeil

first: Patrick

first: Lisa

last: Marx

first: Célia

last: Asdih

first: Agnes

last: Lindenthal

first: Alina

last: Seger

first: Jule

last: Schrimpf

first: Luigi

middle: L

last: Nardella

first: Silke

last: Kowar

first: Ian

last: Frew

first: Sebastian

last: Halbach

first: Rebecca

last: Kesselring

first: Melanie

last: Boerries

first: Ricarda

last: Griffin

first: Tilman

last: Brummer


title: Determinants of “placental” versus “maternal” preeclampsia

city: La Jolla

first: Mariko

last: Horii

address: 2880 Torrey Pines Scenic Dr

department: Pathology

institute: UCSD

summary: Background: The placenta is known to be critical in the etiology of preeclampsia (PE). However, there is a subset of PE cases without identifiable placental pathology. We evaluated which clinical PE classification system best distinguishes PE with placental pathology from PE without placental pathology. Methods: We evaluated five placental pathologic features in 197 placentas from PE patients grouped by three clinical PE subclasses. 1. PE with calculated infant birthweight <10th percentile (small) for gestational age (SGA PE) versus PE with birthweight ≥10th percentile for gestational age (NSGA PE). 2. PE with delivery before 34 weeks of gestation (EDPE) versus PE with delivery at or after 34 weeks of gestation (LDPE) and 3. PE with severe features versus PE without severe features. Clinical, histologic and molecular findings in patients with PE were compared to normotensive patients, with and without SGA infants (N = 1,078 total). Results: The SGA versus NSGA PE classification system performed best (likelihood ratios (95% CI) for ≥ 3 of 5 placenta pathologic findings: 15.7 (6.5, 38.1) in SGA PE vs. NSGA PE; 6.8 (4.3, 10.8) in EDPE vs. LDPE and 5.2 (1.95, 14.1) in PE with SF vs. PE without SF; all p <.0001). SGA PE and SGA normotensive placentas were abnormal and shared alterations in hypoxia, TNF alpha, glycolysis, unfolded protein response, estrogen response, UV response, p53, TGF beta and mTORC1 signaling pathways. Conclusions: Classifying PE based on birthweight percentile for gestational age is the most useful system for consistently identifying PE associated with placenta pathology.


title: ADAR1 regulates dsRNA formation in nuclear and mitochondrial transcripts  through editing-dependent and -independent mechanisms

city: New York

first: Hachung

last: Chung

address: 701 W 168th St, HHSC Rm 1506

department: Microbiology & Immunology

institute: Columbia University

summary: Endogenous (self) double-stranded RNAs (dsRNAs) in human cells can activate innate immune responses. ADAR1, an A-to-I editing enzyme of dsRNAs, suppresses aberrant immune activation by self-dsRNAs. However, how ADAR1 influences the cellular dsRNA landscape remains unclear. We show that human ADAR1 downregulates self-dsRNA abundance through editing-dependent and editing-independent mechanisms. We further conducted quantitative dsRNA-sequencing on wild-type and ADAR1-deficient cells. dsRNAs are enriched in protein-coding mRNAs − especially those with repetitive elements and elongated 3’UTRs − and mitochondrial RNAs. ADAR1 loss markedly increased dsRNA quantity but minimally impacted dsRNA identity. ADAR1-regulated dsRNA transcripts consist of nuclear-encoded mRNAs and, unexpectedly, mitochondria-encoded RNAs rarely edited by ADAR1. Accordingly, dsRNAs accumulate to high levels within the mitochondria of ADAR1-deficient cells. Notably, ADAR1 loss sensitizes cells to inflammation under mitochondrial stress (e.g., mitochondrial herniation, X-ray radiation). Hence, we show that dsRNAs regulated by ADAR1 go beyond A-to-I edited transcripts, and that ADAR1 can control mitochondrial-dsRNAs.

overall_design: Double-stranded RNA (dsRNA)-prone transcripts were enriched by immunoprecipitation with the J2 monoclonal antibody (SCICONS), which recognizes dsRNA structures. The enriched RNAs were then converted into a sequencing library, resulting in a dsRNA-seq library. For input control, total RNA was extracted from the cell lysate and converted into a total RNA-seq library. Experiments were performed using WT, ADAR1-E912A KI, and ADAR1 KO Hap1 cells.

first: Heegwon

last: Shin

first: Tyler

last: Dorrity


title: Piezo1-dependent activation of stromal cells ignites muscle inflammation in exercise and injury and is associated with inflammaging

city: Boston

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

summary: As the actuator of movement and a key regulator of organismal metabolism, skeletal muscle is a site at which inflammatory responses must be carefully calibrated to counteract imposed stressors while preventing protracted functional impairments. Exercise, injury, and aging are common forms of stress associated with inflammation, particularly in skeletal muscle, yet the specific inducers and sensors driving such inflammation are not fully understood. Multi-pronged assessment of acute and chronic endurance-exercise models allowed us to evidence a role for MmSCs in transducing exercise-induced mechanical stress into local inflammatory responses. We identified the mechanosensitive ion channel Piezo1 as the molecular sensor of such mechanical stress. We also demonstrated that mechanosensing by stromal cells is necessary for appropriately timed inflammatory and myogenic responses to acute muscle injury and is associated with age-related muscle inflammation. Taken together, these findings highlight recognition of altered tissue stiffness by the Piezo1:MmSC pair as a fundamental mechanism of stress-induced immunomodulation in skeletal muscle.

overall_design: To investigate the potential of acute exercise (AEX/exe) and exercise training (EXT) to modulate muscle mesenchymal stromal cells (MmSCs), 1000 MmSCs were cytofluorometrically sorted (PDGFRa+Sca1+CD31-CD45-DAPI-) from hindlimb muscles of 8 to 10-week old AEX and EXT mice, as well as from sedentary (SED) controls. MmSCs were sorted directly into TCL buffer for subsequent RNA isolation, library construction, and population-level RNA-seq. To determine whether mechanical stress was sufficient to induce an inflammatory reaction, MmSCs were cytofluorometrically sorted and briefly cultured in the presence of the Piezo1-specific agonist, Yoda1 (25uM), or vehicle prior to lysis in TCL buffer, library construction and population-level RNA-seq. For loss-of-function experiments, Pdgfra-Cre.Piezo1f/f (mutant) and Pdgfra-Cre.Piezo1+/+ (WT) mice were injured by intramuscular injection of cardiotoxin (CTX), and tibialis anterior (TA) muscles were dissected and homogenized in TRIzol for RNA isolation, library construction and whole-tissue RNA-seq on days 1, 3 and 7 of recovery. Hearts from a separate cohort of Piezo1 mutant and WT littermates were also dissected 3 days after CTX injury to skeletal muscles (perfused), and RNA was extracted and used for library construction as before. Whole-tissue RNA-seq was also performed on Qd muscles, hearts (perfused), and liver specimens (perfused) from separate cohorts of uninjured, SED mutant and WT littermates. MmSCs were sorted from hindlimb muscles of mutant and WT mice on day 1 after AEX (versus SED controls) or on day 1 after cardiotoxin (CTX)-induced injury. Sorting and sequencing was the same as for AEX and EXT experiments described above.

first: Paul

middle: K

last: Langston

first: Diane

last: Mathis


title: Analysis of gene expression in pancreatic cancer cells induced by  treatment of conditioned medium (CM) from cancer-associated fibroblast cells (CAFs)

city: Tokyo

first: Junjiro

last: Yoshida

address: 3-14-23 Kamiosaki, Shinagawa-ku

country: Japan

institute: Institute of Microbial Chemistry

summary: We hypothesized that CAF-induced malignant phenotypes of pancreatic cancer cells may reveal novel therapeutic targets. To explore this possibility, we first analyzed the phenotypic changes in pancreatic cancer cells treated with CAF-CM.

overall_design: Panc-1, pancreatic cancer cell line, cells were cultured in control medium (DMEM with 1% D-FBS), CM of CAFs, or DMEM with 10% FBS for three consecutive cycles of 3 days culture.


title: Phase II Trial of Ixazomib combined with Gemcitabine and Doxorubicin in Patients with SMARCB1-Deficient Renal Medullary Carcinoma

city: Houston

first: Pavlos

last: Msaouel

state: Texas

address: 1155 Pressler Street, Unit 1374

department: Genitourinary Medical Oncology

institute: The University of Texas MD Anderson Cancer Center

summary: SMARCB1-deficient renal medullary carcinoma (RMC) is an aggressive kidney cancer lacking mechanism-directed therapies. We conducted a single-center, single-arm, phase II study (NCT03587662) testing the oral proteasome inhibitor ixazomib combined with gemcitabine and doxorubicin. Thirty consecutive patients (median age 34.5 years old, 90% Black, 83.3% metastatic at diagnosis) were treated between September 2018 and June 2022. Ixazomib 5.5 mg, gemcitabine 756 mg/m² and doxorubicin 42 mg/m² were given every 2 weeks for up to 13 cycles, followed by ixazomib plus gemcitabine maintenance. Co-primary endpoints were objective response rate (ORR) and 28-week disease-control rate (DCR) versus historical gemcitabine plus doxorubicin controls. Secondary endpoints included progression-free survival (PFS), overall survival (OS) and safety. The posterior ORR was 36% (95% credible interval [CrI], 21–54 %) with a 91.4% probability of exceeding historical doublet therapy. However, the 28-week DCR was 17 % (95% CrI 6–31%), crossing the predefined futility boundary. Median PFS and OS were 3.5 months (95% confidence intervals [CI] 1.9–4.9) and 7.4 months (95% CI 2.1-4.9), respectively. Grade ≥ 3 toxicities were predominantly hematologic (thrombocytopenia 20 %, leukopenia 17%) and manageable. No treatment-related deaths occurred. Single-cell and bulk multi-omics from 11 patients revealed that immune-inflamed tumors enriched for T/NK cells, plasmacytoid and conventional dendritic cells, and S100A8/IL-1ß-skewed monocytes correlated with response, whereas stromal-myeloid niches and proliferative or neuroendocrine-squamous plastic epithelial states were associated with resistance. Resistant lesions upregulated unfolded-protein-response and Hippo pathways. These results pave the way for future biomarker-guided patient selection and rational combination or microenvironment-targeted therapies.

overall_design:
We performed single cell RNA sequencing (scRNAseq) on 15 tissue samples collected from 11 patients with RMC who were enrolled and treated in the trial. Baseline samples were collected from 10 patients (samples from 7 patients coded as “Pre_NR” who did not demonstrate an objective response to trial therapy, and from 3 patients coded as “Pre_R” who showed an objective response to trial therapy), while 3 patients also had samples collected at week 12 of trial therapy (“Post” timepoint), and 2 patients also had samples at the end of treatment (“EOT” timepoint) due to disease progression. Longitudinally collected samples were biopsied from the same organ site in all cases except patient RMC73 who underwent baseline biopsy of a liver metastasis and then in a lung metastasis during trial therapy due to disease response leading to near-resolution of the liver lesions.contributor: Moon Shots Cancer Genomics Laboratory (CGL) contributor: MD Anderson institutional Advanced Genomics Technology Core (AGTC).
***Raw sequencing data (FASTQ files) are not provided due to patient privacy and consent restrictions***

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

first: Yu

last: Kai

first: Msaouel

last: Pavlos

first: Wang

last: Linghua

first: Gao

last: Jianjun


title: H4K16 acylations fine-tune transcriptional response to short-chain acyl-CoA dehydrogenase deficiency (ChIP-seq)

city: Munich

first: Tamas

last: Schauer

address: Feodor-Lynen-Straße 21

department: Institute of Epigenetics and Stem Cells

institute: Helmholtz Zentrum München

summary: We investigated the combined effects of H4K16 acylations in vivo using a mouse model of short-chain acyl-CoA dehydrogenase deficiency (SCADD), which causes metabolic challenges and systemic shifts in acyl-CoA ratios. Our findings indicate that H4K16 acylations modulate transcriptional responses in a concerted manner, providing insights into an adaptive chromatin regulation in response to metabolic stress.

overall_design: H4K16ac, H4K16pr, H4K16bu, H3K9ac ChIP-seq on WT and SCADD male mouse livers in 2 biological replicates.

first: Sandra

last: Nitsch

first: Pablo

last: Ranea-Robles

first: Sander

last: Houten

first: Robert

last: Schneider


title: DAXX Directs H3.4-to-H3.3 Histone Replacement During Spermatogenesis [Cut & Run]

first: Satoshi

last: Namekawa

first: Yu-Han

last: Yeh


title: Regulation of the type I interferon response by chromatin organization (ATAC-seq of KO HoxB8-FL cells)

first: Eduardo

last: Esteva

summary: Antiviral type I interferons (IFN-I) including IFN-β and multiple subtypes of IFN-α are encoded within a single locus. Whereas most cell types produce primarily IFN-β, plasmacytoid dendritic cells (pDCs) respond to viruses by rapidly producing all IFN-I subtypes. We show that during pDC differentiation, the IFN-I locus translocates from the nuclear periphery and undergoes reorganization of topologically associated domains (TADs). Accordingly, IFN-I production by pDCs was strictly dependent on the TAD-organizing cohesin complex. Promoters of Ifna genes in pDCs were poised, which was imparted by the pDC-enriched transcription factor IRF8. Finally, we identified two distal regulatory regions that facilitated the expression of adjacent IFN-I genes. Thus, the IFN-I response is controlled by multilevel chromatin organization of the IFN-I locus, including its unique poised state in pDCs.

overall_design: ATAC-seq was performed on purified pDCs (or bulk DCs for Irf8Δ) differentiated from HoxB8-FL progenitors transfected with sgRNAs targeting either Ifnar1, Irf7, Spib, Irf8 or a non-targeting sgRNA as a control (2 replicates per genotype).

first: Nicholas

last: Adams

first: Ai

last: Ra

first: Boris

last: Reizis


title: Myelin antigen capture in the CNS by B cells expressing EBV latent membrane protein 1 leads to demyelinating lesion formation [scRNA-Seq]

first: DBM Bioinformatics

last: Core Facility

summary: The efficacy of B cell depletion therapies, and association with the B lymphotropic Epstein- Barr virus (EBV) implicate B cells in the demyelinating autoimmune disease multiple sclerosis. After observing myelin-reactive B cells in the naïve human repertoire, we studied how such cells behave in the central nervous system. In mice, viral infections induce infiltration of B cells independent of phenotype and specificity into the otherwise lymphocyte-poor brain, and myelin-reactive B cells then capture antigen directly from parenchyma. Trafficking of these antigen-loaded B cells to draining lymph nodes was not observed, and without T cell help, antigen-capturing B cells die rapidly. CD40L signaling or EBV latent membrane protein 1 (LMP1) can override this checkpoint, leading to in situ plasma cell differentiation and antibody-mediated, demyelinating lesion formation. These observations explain the dependency of disease incidence on prior EBV infection, and the increased risk associated with brain infections, and suggest possible treatment strategies.

overall_design: B cells were sorted from mouse brain and lymph node samples and analyzed by single cell RNA sequencing using the 10X Genomics platform.

first: Julien

last: Roux

last: Sanderson

first: Mika

first: Hyein

last: Kim

first: Tobias

last: Derfuss


title: Regulation of the type I interferon response by chromatin organization (RNA-seq of L929 fibroblasts +/- SEV)

overall_design: RNA-seq was performed on L929 fibroblasts infected with Sendai virus for 4 hours, 8 hours, and 16 hours as well as fibroblasts left uninfected as a control (3 replicates per timepoint).


title: Regulation of the type I interferon response by chromatin organization (RNA-seq of IFN-I TB2/TB4 DKO FL-BMDC activation)

overall_design: RNA-seq was performed on FL-BMDCs from control and IfnΔΤΒ2/ΤΒ4 mice stimulated with CpG-A for 6 hours (2 replicates per genotype).


title: Novel syngeneic cell lines for studying high-risk BRAFV600E-driven colorectal cancer in vivo [RNA-seq_NaJa]

city: Freiburg

first: Ariane

last: Lehmann

overall_design: RNA-seq profiling of the three NaJa cell lines NaJa-D, -F and -G at Day1 or Day5 under encorafenib treatment compared to the correspondent DMSO control.

first: Jasmin

last: Traichel

last: Metzger

first: Maria

last: Walz

first: Reinhild

last: Feuerstein

first: Nadine

last: Wohlfeil

first: Patrick

first: Lisa

last: Marx

first: Célia

last: Asdih

first: Agnes

last: Lindenthal

first: Alina

last: Seger

first: Jule

last: Schrimpf

first: Luigi

last: Nardella

first: Silke

last: Kowar

first: Ian

last: Frew

first: Sebastian

last: Halbach

first: Rebecca

last: Kesselring

first: Melanie

last: Boerries

first: Ricarda

last: Griffin

first: Tilman

last: Brummer


title: Regulation of the type I interferon response by chromatin organization (ATAC-seq of IRF8 KO splenic pDCs)

first: Eduardo

last: Esteva

overall_design: ATAC-seq was performed on pDCs purified from the spleen of Irf8-/- mice (2 replicates).

first: Nicholas

last: Adams

first: Ai

last: Ra

first: Boris

last: Reizis


title: Transcriptome-wide profiling of human stromal cells in mouse xenografts during preclinical treatment involving chemotherapy and/or the novel senomorphic agent dihydromyricetin

first: Yu

last: Sun

address: 320 Yueyang Rd, Life Sciences Building A #1508

department: Shanghai Institute of Nutrition and Health

institute: Chinese Academy of Sciences

summary: Aging is a major risk factor for the vast majority of geriatric conditions, including various malignancies. Although cancer development can be generally attributed to the accumulation of genetic mutations, biological processes associated with aging also hold the potential to regulate cancer progression. Cellular senescence is a cell state characterized by a permanent cell cycle arrest. Senescent cells tend to accumulate with aging, exhibit pro-inflammatory activities (SASP) and promote cancer development. However, as the effect of cellular senescence on cancer progression is heterogeneous and complicated, detailed mechanisms remain to be unraveled. Fortunately, senescent cells can be eliminated by several strategies, a situation that allows to prevent incidence of chronic disorders and prolong healthspan of mammalians. Strategies involving senolytics, which can selectively remove senescent cells by targeting the SCAP, have recently emerged as a prominent and competent solution to ameliorate diverse age-related pathologies. Achieving the goal using synthetic or natural agents (the latter more preferred in clinical settings) would generate a tremendous impact on the quality of life. Here, we test the potential of dihydromyricetin (DMY), a bioactive compound extracted from Salvia miltiorrhiza, in targeting senescent cells through inhibiting the SASP in a preclinical regimen. This study demonstrates the efficacy of DMY in downregulating the SASP expression and reducing the influence of senescent stromal cells in treatment-damaged tumor microenvironment and provides a strong rationale for its future development in anti-aging pipelines.

overall_design:
Examination of the in vivo efficacy of DMY in targeting human senescent stromal cells. Experimental mice xenografted with human stromal cells (PCS27) and prostate cancer epithelial cells (PC3) were administered with vehicle, mitoxantrone (MIT) or MIT/DMY as three independent arms in a 8-week preclinical regimen. Upon completion of treatment, mice were sacrificed and tumors were collected for histological analyses. Stromal cells were isolated from tumor tissues by laser capture microdissection (LCM) and subject to RNA preparation, library construction and high throughput sequencing. This trial was performed beyond previous studies reporting DMY effects in treatment of disorders implicating its anti-inflammatory, antioxidant, anticancer and neuroprotective capacities.

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


title: H4K16 acylations fine-tune transcriptional response to short-chain acyl-CoA dehydrogenase deficiency (RNA-seq)

first: Tamas

last: Schauer

overall_design: RNA-seq on WT and SCADD male mouse livers in 3 biological replicates.

first: Sandra

last: Nitsch

first: Pablo

last: Ranea-Robles

first: Sander

last: Houten

first: Robert

last: Schneider


title: Cohesin-mediated chromatin remodeling controls the differentiation and function of conventional dendritic cells (RAD21 and CTCF ChIP-seq of Hoxb8-FL differentiation)

address: 550 1st Ave

institute: NYU Grossman School of Medicine

summary: The cohesin protein complex extrudes chromatin between CTCF binding sites and organizes it into topologically associated domains (TADs), yet the biological implications of this regulatory mechanism are poorly understood. We show that the cohesin subunit Smc3 is required for the postmitotic differentiation and function of antigen-presenting dendritic cells (DCs). In particular, Smc3 deletion impaired antigen cross-presentation and IL-12 secretion by type 1 conventional DCs (cDC1s), thereby crippling antimicrobial and antitumor immune responses. The chromatin profile of DCs was shaped by the interplay of cohesin and the cDC1-specifying transcription factor IRF8. Conversely, optimal expression of IRF8 itself required CTCF/cohesin-binding elements demarcating the Irf8 gene. Cohesin-mediated chromatin remodeling facilitated chromatin priming at activation-inducible genes; accordingly, deletion of CTCF/cohesin-binding sites flanking the Il12b gene reduced basal and activation-induced IL-12 production by cDC1s. Our data reveal an essential role for cohesin-mediated chromatin regulation in the differentiation and function of a key immune cell type.

overall_design: ChIP-seq for RAD21 and CTCF were performed on undifferentiated HoxB8-FL progenitors, differentiated cDCs and pDCs (1 replicates per cell type).

first: Aleksandra

last: Galitsyna


title: Regulation of the type I interferon response by chromatin organization (ATAC-seq of L929 fibroblasts +/- SEV)

overall_design: ATAC-seq was performed on L929 fibroblasts infected with Sendai virus for 8 hours or left unstimulated as a control (2 replicates per condition).


title: Regulation of the type I interferon response by chromatin organization (Hi-C of L929 fibroblasts +/- SEV)

overall_design: Hi-C was performed on L929 fibroblasts infected with Sendai virus for 8 hours or left unstimulated as a control (1 replicate per condition).


title: Cohesin-mediated chromatin remodeling controls the differentiation and function of conventional dendritic cells (Hi-C of HoxB8-FL differentiation)

overall_design: Hi-C was performed on undifferentiated HoxB8-FL progenitors, differentiated cDCs and pDCs, as well as differentiated pDCs stimulated with CpG-A for 6 hours (2 replicates per cell type).


title: Cohesin-mediated chromatin remodeling controls the differentiation and function of conventional dendritic cells (Hi-C of SMC3 KO FL-BMDCs)

overall_design: Hi-C was performed on cDCs and pDCs purified from 4-OHT-treated FL-BMDC cultures from Rosa26CreER/+ or Rosa26CreER/+ Smc3fl/fl mice (2 replicates per cell type and genotype).


title: Co-translational determination of quaternary structures in chaperone factories

city: Montpellier cedex 05

first: Séverine

last: Boulon

address: 141 rue de la Cardonille

country: France

institute: CNRS

summary: The HSP90/R2TP quaternary chaperone assembles key cellular machines, including the three nuclear RNA polymerases and many non-coding RNPs. Here, we characterized the RNA associated to R2TP and found that it binds many partners co-translationally. Its co-translational interactome further reveals many novel potential clients and identifies clients bound only co-translationally, only post-translationally, or both. For pairs of subunits assembling together and bound co-translationally by R2TP, only a marginal proportion of their mRNAs is co-localized and co-translated. Instead, the HSP90 and R2TP chaperones induce the formation of condensates accumulating client mRNAs and thus favoring co-translational interactions between chaperones and clients. The R2TP then cycles between co- and post-translational steps and this is regulated by ATP: it binds co-translationally in absence of ATP and becomes released from post-translational assembly intermediates by ATP hydrolysis. Assembly of protein complexes is thus initiated early by chaperones and this mechanism, dubbed co-translational chaperone channeling (cha-cha), substitutes for the rarity of co-localized/co-translated mRNAs.

overall_design: RIP-seq analysis of RNA samples following affinity purification of proteins of interest from HCT116 cells, under different drug treatments (puromycin, CB-6644). HCT116 cells lines expressing GFP-tagged protein where constructed via CRISPR/Cas9 edition.

first: Manon

last: Philippe

first: Soha

last: Salloum

first: Jacques

last: Imbert

first: Simon

last: Georges


title: RNA-seq analysis of EpCAM-GFP and GFP overexpression in FLO-1 esophageal adenocarcinoma

city: Kuala Lumpur

first: M. Aiman

last: Mohtar

state: (select)

address: UKM Medical Molecular Biology Institute (UMBI)

country: Malaysia

institute: Universiti Kebangsaan Malaysia

summary: EpCAM is one of the highly expressed marker in esophageal adenocarcinoma as identidied in several multi-OMICS platform. We utilize FLO-1 cells which are lacking in EpCAM expresssion and use overexpression strategy to elucidate the function of EpCAM in this cells. Recombinant EpCAM-GFP or GFP only was trasnfected in FLO-1 cells, and the stable cells after antibiotic selection were isolated and expanded. The cells were then subjected to mRNA sequencing.

overall_design: The stable FLO-1 cells overexpressing EpCAM-GFP or GFP were subjected to RNA-seq analysis

first: M

last: Aiman Mohtar


title: Regulation of the type I interferon response by chromatin organization (RNA-seq of SMC3 KO pDC activation)

city: New York City

first: Eduardo

last: Esteva

overall_design: RNA-seq was performed on pDCs purified from 4-OHT-treated FL-BMDC cultures from R26CreER/+ or R26CreER/+ Smc3fl/fl mice and stimulated with CpG-A for 6 or 24 hours or left unstimulated as a control for 6 hours (3 replicates per genotype and stimulation condition).

first: Nicholas

last: Adams


title: Transcriptomic characterization of human microglial cells upon therapy-induced senescence and treatment by a natural flavonoid dihydromyricetin

summary: The central mechanisms underlying development of central nervous system (CNS) diseases remain unclear, limiting the development of effective therapeutic strategies. Cellular senescence, a biological phenomenon observed in cultured fibroblasts in vitro, has been reported to be a crucial intrinsic mechanism that influences homeostasis of the brain microenvironment and contributes to the onset and progression of CNS pathologies. Cellular senescence has been observed in disease models established in vitro and in vivo, and in bodily fluids or tissues from patients with CNS diseases. These findings raise senescent cells as a potential target for preventing, delaying and treating CNS diseases. Emerging therapies that target senescent cells have shown promising therapeutic effects in preclinical and clinical studies on aging and age-related diseases. Such innovative therapies can potentially avoid brain cell loss and functional changes, thus improving the prognosis of CNS disorders and providing alternative treatments for CNS patients. Microglia, a group of unique myeloid cells residing in mammalian brain parenchyma, represent the first line of immune defense within the central nervous system (CNS). In addition to their immune functions, microglial cells are actively implicated in other cerebral processes including regulation of synaptic architecture and neurogenesis. However, chronic microglial activation is usually detrimental, and is considered a pathogenic mechanism shared by several neurological disorders. To date, the expression pattern of senescent human microglial cells and their susceptibility to senolytic agents remain underexplored. The human microglial clone 3 cell line, HMC3, was established in 1995, through SV40-dependent immortalization of human embryonic microglial cells. In this study, we treated these cells with a chemotherapeutic agent bleomycin (BLEO), which induces therapy-induced senescence (TIS). We established the expression landscape of senescent microglial cells to characterize their senescence-associated expression pattern. Further, we treated senescent microglial cells with dihydromyricetin (DMY), a natural flavonoid that exhibits senolytic activity against certain types of stromal cells, and investigated their overall transcriptomic expression changes. The senotherapeutic effect of DMY can be partially reflected by the genome-wide expression of senescent microglial cells, which are abundant in the brain and can serve as a novel target for treatment of chronic neurodegenerative diseases.

overall_design: High-throughput RNA-seq examination of genome-wide transcriptional alterations of human microglial cells (HMC3) that underwent senescence-inducing treatment by the chemotherapeutic agent bleomycin.


title: Cohesin-mediated chromatin remodeling controls the differentiation and function of conventional dendritic cells (RNA-seq of SMC3 KO splenic cDCs)

overall_design: RNA-seq was performed on cDC1s and cDC2s purified from the spleen of CD11cCre/+ (3 replicates for each cDC subset), CD11cCre/+ Smc3fl/fl (3 replicates for each cDC subset), and CD11cCre/+ Smc3fl/- (2 replicates for each cDC subset)

first: N

first: E

first: B

last: Reizis


title: Cohesin-mediated chromatin organization controls the differentiation and function of dendritic cells (RNA-seq of SMC3 KO FL-BMDC differentiation and activation)

overall_design: RNA-seq was performed on cDC1s, cDC2s and pDCs purified from 4-OHT-treated FL-BMDC cultures from Rosa26CreER/+ or Rosa26CreER/+ Smc3fl/fl mice as well as cDC1s and cDC2s from FL-BMDC cultures stimulated with CpG-A and CpG-B for 6 hours (3 replicates per genotype and cell type without stimulation, 2 replicates with stimulation).

first: A

last: Khodadadi-Jamayran


title: Cohesin-mediated chromatin remodeling controls the differentiation and function of conventional dendritic cells (CUT&RUN of FL-BMDCs and HoxB8-FL progenitors)

overall_design: CUT&RUN for H3K4me1, H3K4me3, H3K9me3, H3K27Ac, H3K27me3 were performed on undifferentiated HoxB8-FL progenitors as well as cDC1s, cDC2s and pDCs purified from FL-BMDC cultures (1 replicate per histone mark and cell type)


title: Cohesin-mediated chromatin organization controls the differentiation and function of dendritic cells

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

overall_design: Refer to individual Series


title: Uncovering a Key Metabolic Role of the GATA1 N-Terminus in Red Blood Cell Development [CUT&RUN]

status: Public on Jan 12 2026

city: Memphis

first: Te

last: Ling

state: TN

address: 262 Danny Thomas Pl

institute: St. Jude Children's Research Hospital

summary: Mutations in GATA1 that result in skipping of exon 2, which encodes the N-terminus, are associated with the myeloid leukemia of Down syndrome and Diamond-Blackfan anemia (DBA). To elucidate the molecular functions of the N-terminus, we employed single-cell RNA sequencing (scRNA-seq) of fetal liver cells derived from Gata1 mutant embryos that express the GATA1 short (GATA1s) isoform in place of full-length GATA1 (GATA1FL). scRNA-seq highlighted defects in erythropoiesis and revealed that the absence of the N-terminus resulted in elevated expression of genes involved in glycolysis, such as the rate-limiting pyruvate kinase PKM. To elucidate the regulation of the PKM gene, we performed precision nuclear run-on sequencing and cleavage under targets and release using nuclease on erythroid cells following acute deletion of GATA1 and determined that PKM is a direct target of GATA1. Mechanistically, we found that substitution of GATA1FL with GATA1s led to increased glycolysis in erythroid progenitor cells but did not affect oxidative phosphorylation. We further discovered that the expression of PKM is significantly elevated in DBA patients with RPS19 mutations, consistent with a role for GATA1 regulation of glycolysis in erythropoiesis. Together, these findings reveal that GATA1 controls not just heme metabolism, but also glycolysis.

overall_design: CD71hiTer119hi erythroblasts were isolated from E13.5 embryos. Occupancy profiling was performed using the CUT&RUN method.

first: Rashid

last: Mehmood

first: John

middle: D

last: Crispino


title: Spatial Transcriptomic Landscape of Invasion Patterns in Human Papillomavirus-Associated Endocervical Adenocarcinoma

city: St Louis

first: Margaret

last: Axelrod

address: 660 South Euclid Avenue, Campus Box 8118

department: Pathology and Immunology

institute: Washington University in St. Louis

summary: Human papillomavirus (HPV)-associated endocervical adenocarcinoma is the second-most common cancer of the uterine cervix. HPV-associated endocervical adenocarcinoma can be classified into histologic Silva patterns of invasion, which are associated with clinical outcome. However, the mechanisms underlying these patterns of invasion are incompletely understood. We used whole transcriptome spatial transcriptomics to examine gene expression differences separately in the tumor epithelium and the surrounding stromal immune microenvironment (SIME). Seven cases were evaluated, focusing on cases with two distinct patterns of invasion within the same tumor, to control for inter-patient heterogeneity. The most strongly upregulated pathways in both higher-risk tumor epithelium and SIME were associated with extracellular matrix (ECM) remodeling. Transcriptomic-based inference of immune cell populations showed an increase in macrophage populations in higher-risk tumor areas, confirmed by immunohistochemistry. Finally, we derived a four-gene signature from genes upregulated in higher-risk tumor epithelium (KRT6A, TNC, LAMC2 and FN1), which was associated with worse clinical outcome in an independent dataset (The Cancer Genome Atlas). Overall, this work demonstrates that ECM remodeling and macrophage presence are important in the progression to high-risk patterns of invasion in HPV-associated endocervical adenocarcinoma. In addition, we established a prognostic four-gene signature that is predictive of poor outcome.

overall_design: NanoString GeoMX was performed on human HPV associated endocervical adenocarcinoma with tumor (cytokeratin positive) profiled separately from the stromal immune microenvironment (cytokeratin negative)

first: Lulu

last: Sun


title: Uncovering a Key Metabolic Role of the GATA1 N-Terminus in Red Blood Cell Development [Bulk RNA-seq]

overall_design: Transcriptional profiling utilizing Illumina® Stranded mRNA sequencing was conducted on HUDEP1 clones expressing either the full-length GATA1 (GATA1FL) or the short isoform (GATA1s_1D5 and GATA1s_1KI9) under expansion or differentiation (day 4) conditions, respectively.


title: Characterization of Subchronic Lung and Brain Consequences Caused by Mouse-Adapted SARS-CoV-2 and Influenza A Infection of C57BL6 mice

city: New Orleans

first: Xuebin

last: Qin

state: LA

address: 1430 Tulane Avenue

institute: Tulane University

summary: SARS-CoV-2 and, to a lesser extent, influenza A can lead to long-term complications in the respiratory and nervous systems. However, the mechanisms driving post-viral sequelae remain poorly understood. To address this gap, we longitudinally characterized C57BL/6 mice infected with sublethal doses of mouse-adapted SARS-CoV-2 (MA30) or influenza A (PR8). Lung and brain tissues were analyzed at 14-, 21-, and 28-days post-infection (DPI) using histological analysis and bulk-RNA sequencing. In the lungs, both infections caused prolonged inflammation and fibrosis. MA30-infected lungs showed persistent upregulation of inflammatory, coagulation, complement, as well as fibrotic, and extracellular matrix (ECM) remodeling pathways at 21 DPI, alongside downregulation of epithelial junction and metabolic program pathways. In contrast, PR8-infected lungs exhibited a strong acute interferon response and chronic upregulation of basal epithelial markers (e.g., Krt5, Krt14), consistent with epithelial regeneration. Notably, only PR8-infected mice displayed KRT5+ progenitor cell migration into damaged lung regions, indicating divergence in repair mechanisms. Neither MA30-infected, nor PR8-infected mice had detectable brain infection. However, MA30 mice, but not PR8-infected mice exhibited an elevated frequency of microhemorrhages at early timepoints and marked neuroinflammation at all timepoints. Transcriptomic profiling of MA30-infected brains showed enrichment for up-regulation of ECM remodeling, vascular dysfunction, IL6-signaling pathways along with a virus-specific disruption of the hypothalamic–pituitary axis with MA30 infection not seen in PR8-infected brains. These included genes linked to neuroinflammation, sensory processing disruption, and microvascular injury, mirroring clinical features of Long COVID. Together, these findings establish distinct tissue-specific trajectories of long-term pathology following SARS-CoV-2 and influenza infection and provide a foundation for dissecting the mechanisms of post-viral lung and brain disease.

overall_design: Comparative gene expression profiling analysis of RNA-seq data of lung and brain tissues from noninfected, MA30-infected, and PR8-infected B6 mice at acute (7, and 8-9 DPI for MA30 and PR8 infection, respectively) and subchronic phase (21 DPI for both MA30 and PR8 infection).

first: Joshua

last: Currey

first: Chenxiao

last: Wang

first: Meredith

middle: G

last: Mayer

first: Yilin

last: Chen

first: Ana Karina

last: Nisperuza Vidal

first: Michaela

last: Allen

first: Mst Shamima

last: Khatun

first: Calder

last: Ellsworth

first: Mohammad

last: Islamuddin

first: Jefferson

last: Evangelista

first: Skye

middle: M

last: Minor

first: Nadia

middle: A

last: Golden

first: Kevin

last: Zwezdaryk

last: Maness

first: Robert

last: Blair

first: Jay

last: Kolls

first: Derek

last: Pociask

first: Tracy

last: Fischer


title: Cohesin-mediated chromatin remodeling controls the differentiation and function of conventional dendritic cells (RNA-seq of IRF8 KO HoxB8-FL DCs)

first: Eduardo

last: Esteva

overall_design: RNA-seq was performed on bulk DCs differentiated from either control or Irf8-mutant HoxB8-FL progenitors (3 replicates per genotype).

first: N

last: Adams

first: E

first: B

last: Reizis


title: Uncovering a Key Metabolic Role of the GATA1 N-Terminus in Red Blood Cell Development [CUT&RUN Human]

first: Te

last: Ling

overall_design: HUDEP2 cells expressing FKBP12F36V-GATA1 were cultured under differentiation conditions for 24 hours. GATA1 occupancy profiling was conducted at 0.5, 3, and 6 hours in the presence of the acute degradation inducer dTAG-13 (100 nM) using the CUT&RUN method.

first: Rashid

last: Mehmood

first: John

last: Crispino


title: Evaluation of targeted and immune combination therapies in a rat model of hormone receptor-positive breast cancer  [RNA]

first: Kornelia

last: Polyak

address: 450 Brookline Ave. S1070

institute: Dana-Farber Cancer Institute

summary: Breast cancer hormone receptor (HR) estrogen and progesterone (ER/PR) positive tumors were generated in an outbred rat model (Sprague-Dawley) through the injection of the carcinogen N-nitrosomethylurea (NMU). These tumors were treated with immune checkpoint blockade (anti PD-L1) in combination with targeted therapies, including an TNK1/IKBKE inhibitor, a KMT5B/C inhibitor, a TGF-b inhibitor, and a selective estrogen receptor degrader (SERD). This dataset includes single-cell RNA sequencing (scRNA-seq) data from tumors subjected to various treatment setups. Whole-tumor digestion was performed to preserve a comprehensive representation of the tumor microenvironment. The study aims to identify mechanisms that sensitize HR postive tumor subtypes to immune checkpoint blockade therapy.

overall_design: Tumors were induced by intraperitoneal injection of 50 mg/kg NMU on days 46 and 53 of age. Treatment with NIS793 (a TGFBR inhibitor), IKBKEi (a TNK1/IKBKE inhibitor), A196 (a SUV420H1/SUV420H1 inhibitor), Fulvestrant (an estrogen receptor antagonist), ⍺PD-L1, or a combination of targeted therapy with immune checkpoint blockade (ICB) was initiated when tumors reached 8 mm in size, more than one tumor was detected, or a tumor remained unchanged in size for more than three days. Rats were randomly assigned to treatment groups, and tumor size was measured every other day using calipers.

first: Ernesto

last: Rojas Jimenez

first: Triet

last: Bui

first: Pengze

last: Yan

first: Marco

last: Seehawer

first: Jun

last: Nishida


title: An α-specific PI3K inhibitor improves chemotherapy efficacy by inhibiting hepatic stellate cell activation in liver cancer

city: Woolloongabba

first: Qi

last: Ruan

state: QLD

address: 37 Kent Street

department: Frazer Institute

country: Australia

institute: The University of Queensland

summary: The poor response to current systemic treatments in liver cancer has been associated with the activation of cancer-associated fibroblasts (CAFs). Herein, we aimed to investigate the effects of chemotherapy on hepatic stellate cells (HSCs), the main origin of CAFs in liver cancer. In vitro experiments demonstrated that cisplatin activated HSCs through a paracrine effect from HCC tumour cells while the mechanism remains unknown. RNA sequencing of human primary HSCs incubated in untreated or cisplatin-pretreated Huh7 conditioned medium revealed a PI3K signaling pathwayof HSC activation. Further analyses showed that PI3K pathway, especially PI3K p110a is crucial for HSC activation and by targeting PI3K p110a, HSC activation induced by cisplatin can be completely inhibited and improves cisplatin therapeutic efficacy.

overall_design: RNA-seq profiling of human primary hepatic stellate cells incubated in untreated or cisplatin-pretreated Huh7 cell conditioned medium for 24 hours.

first: Xiaowen

last: Liang


title: Protocol for massively parallel RNA assay coupled with immunoprecipitation (MPRNA-IP)

city: Baltimore

first: Taeyoung

last: Hwang

state: MD

address: 855 N. Wolfe St, 3rd floor, Suite 300

institute: Lieber Institute for Brain Development

summary: RNA mediates many cellular functions through interactions with RNA-binding proteins (RBPs), and defining the molecular principles underlying these interactions is essential for understanding RNA biology. Here, we describe a detailed protocol for MPRNA-IP, a Massively Parallel RNA assay coupled with ImmunoPrecipitation that enables high-throughput dissection of RNA–protein interactions in cells. This protocol provides a complete experimental and computational workflow, including the design of RNA tiles, large-scale oligonucleotide cloning, mammalian cell transfection, immunoprecipitation of RNA–protein complexes, sequencing library preparation, and downstream data analysis. As an example application, we synthesized a pool of oligonucleotides tiling six lncRNAs and studied PUM2-binding motifs. Together, these procedures allow high-throughput interrogation of RNA sequences to detect sequence and structural elements that contribute to protein binding. For further information on the development and applications of MPRNA-IP, see Lee et al., Nucleic Acids Research, 2024 (https://doi.org/10.1093/nar/gkae334).

overall_design:
Overexpress a pool of oligonucleotides and perform immunoprecipitation in three biological replicates

UPDATE: [Apr-20-2026] GSE315146_GEO_count.csv was replaced with GSE315146_TestPool_count_updated.csv.

first: Yu Hsuan

last: Lee


title: A High-Resolution Map Predicts Lineage and Birth Order Underlying Neuronal Identity

city: Oxford

first: Aaron

middle: Munro

last: Allen

address: Tinsley Building, Mansfield Road

department: DPAG

country: United Kingdom

institute: University of Oxford

summary: We have used single-cell RNA-sequencing to profile dissected central brains from female and male adult Drosophila melanogaster.

overall_design: Virgin female and male flies were collected and stored individually until the age of 5 days post-eclosion at 25°C prior to dissection. Two female replicates and two male replicates were processed with 20 brains each. The flies were transgenically expressing GFP under the control of the gene doublesex.

first: Stephen

last: Goodwin


title: Discovery of a global translation activator in Pseudomonas aeruginosa [CLIP-Seq]

first: Simon

last: Dove

state: Massachusetts

address: Boston Childrens Hospital, 300 Longwood Avenue EN761.1

department: Infectious Diseases

institute: Boston Children's Hospital

summary: We identified PhaF as an RNA binding protein in Pseudomonas aeruginosa. In order to identify the different target transcripts of PhaF, we carried out the CLIP (Crosslinking and immunoprecipitation) and CLAP-Seq (Covalent linkage affinity purification) approaches, which utilizes UV irradiation to crosslink PhaF with the transcripts that are in close vicinity to it. For CLIP-Seq experiments, we used the Pseudomonas aeruginosa PAO1 strain along with a derivative of PAO1 that harbors a C-terminal VSVG tag on PhaF. In order to determine the importance of the C-terminal domain (CTD) of PhaF on RNA binding, we used PAO1ΔphaF strains carrying plasmids that express a C-terminal VSVG tagged version of PhaF-CTD (pPhaF-CTD-V), along with a control strain that carries the same plasmid (pPhaF-CTD) but without the VSVG tag. For CLAP-Seq experiments, we used the Pseudomonas aeruginosa PAO1 strain along with a derivative of PAO1 that harbors a C-terminal Halo tag on PhaF. All the strains were subjected to UV irradiation, lysed, immunoprecipitated using either anti-VSVG-antibody coated beads or Magne Halo tagged beads. Following immunoprecipitation, the RNAs were purified. We also purified Total (Tot) RNA (samples collected before immunoprecipitation) from the PAO1 strains harboring the C-terminal VSVG tag on PhaF. The purified RNA samples were converted to cDNA libraries, which were subsequently sequenced using the Illumina NextSeq. The sequences were mapped to the genome to identify the target transcripts. In a separate series of experiments we also carried out RNA-Seq to identify the genes that are differentially regulated using Pseudomonas aeruginosa PAO1 and PAO1ΔphaF strains. The isolated RNA was sent to SeqCenter (Pittsburgh, PA) and the sequences obtained were mapped to the genome and DESeq analysis was performed.

overall_design: Strains used for CLIP-Seq were PAO1 and a derivative of PAO1 that harbors a C-terminal VSVG tag on PhaF along with PAO1 ΔphaF strains carrying plasmids that express a C-terminal VSVG tagged version of PhaF-CTD (pPhaF-CTD-V), and a control strain that carries the same plasmid (pPhaF-CTD) but without the VSVG tag. For CLAP-Seq we used PAO1 strain along with a derivative of PAO1 that harbors a C-terminal Halo tag on PhaF. In both CLIP-Seq and CLAP-Seq experiments, LB grown overnight cultures were back-diluted to an OD600 of 0.01. The strains were grown with aeration at 37°C to an OD600 of 2.0. For expressing the CTD of PhaF (either pPhaF-CTD or pPhaF-CTD-V, cloned in the pPSV38 plasmid background), 2mM IPTG was added to the culture to induce expression along with 30 μg/ml of Gentamicin.

first: Pallabi

last: Basu


title: Transcriptome analysis of mural granulosa cells and cumulus cells during ovulation in mouse ovary

city: Ube

first: Amon

last: Shiroshita

state: Yamaguchi

address: Minamikogushi 1-1-1

institute: Yamaguchi university

summary: This study investigates the transcriptomic changes in mural granulosa cells and cumulus cells collected at different time points during the ovulation process in mice following hCG stimulation. RNA-seq was performed to identify dynamic gene expression patterns associated with ovulation, and the data serve as a resource for understanding temporal regulation of ovarian function.

overall_design: Total RNA was extracted from mural granulosa cells and cumulus cells isolated from mouse ovaries at multiple time points (0h, 4h, 12h) after hCG injection. PolyA-enriched libraries were prepared and sequenced on an Illumina NovaSeq 6000 platform. Read alignment and gene expression quantification were performed using CLC Genomics Workbench with default parameters.


title: Scalable single-cell total RNA sequencing unifies coding and non-coding transcriptomics

city: Stanford

first: Alina

last: Isakova

address: 290 Jane Stanford Way

institute: Stanford University

summary: Current single-cell RNA atlases largely capture polyadenylated transcripts while missing critical regulatory layers from non-coding RNA. To address this, we developed TotalX - a generalizable framework that adapts Smart-seq total RNA profiling for use in droplet-based platforms, and captures a broad complement of coding and non-coding RNAsusing a unified pipeline. Applying this approach to developing human brain, we generate a dataset mapping diverse RNA biotypes across all neuronal and non-neuronal lineages, revealingbiotype-specific expression programs with cell-type and temporal specificity. Tracking miRNA dynamics in Cajal–Retzius neurons, transient and early-born neurons in the cortex, we show the enrichment and target anti-correlation of MIR137, associated with schizophrenia and intellectual disability, suggesting tight regulatory control. We apply TotalX to human peripheral blood mononuclear cells and identify transcriptional modules combining coding and non-coding RNAs and tRNA dynamics. Additionally, we analyze dengue-infected hepatocytes and capture non-adenylated viral transcripts that distinguish infection states. This expanded coverage helps with understanding cellular identity and gene regulation at atlas scale

overall_design: HEK293T cells and DENV2 infected Huh7 cells were processed using TotalX method. We also compared TotalX implementations without as well as with two rounds of DASH in miRNA(+) configurations on HEK293T cells


title: TWIST1 drives endothelial-to-mesenchymal-transition to stabilize atherosclerotic plaques [AEBP1 RNA-Seq]

city: London

first: Paul

last: Evans

address: Charterhouse square

institute: QMUL

summary: The effect of AEBP1 and PELP1 deletion was studied in human aortic endothelial cells exposed to atheroprone WSS, using the orbital system.

overall_design: Human aortic endothelial cells (HAoECs) were seeded onto gelatin-coated six-well plates and transfected with AEBP1 siRNA (siAEBP1), PELP1 siRNA (siPELP1), or scrambled control siRNA (sictrl) using the Lipofectamine RNAiMAX transfection system. After a six-hour incubation, the media was replaced, and cells were exposed to flow on an orbital shaker for 72 hours. Cells subjected to disturbed flow in the center of the well were scratched, and total RNA was extracted and analyzed via bulk RNA sequencing.

first: Mannekomba

last: Diagbouga

first: Mark

last: Dunning

first: Blanca

last: Tardajos Ayllon


title: Discovery of a global translation activator in Pseudomonas aeruginosa [RNA-seq]

city: Boston

overall_design: Strains used for RNA-Seq were Pseudomonas aeruginosa PAO1 and PAO1 ΔphaF strains carrying the empty vector pPSV38 (pEV). LB grown overnight cultures were back-diluted to an OD600 of 0.01. The strains were grown with aeration at 37°C to an OD600 of 2.0. 2mM IPTG was added along with 30 μg/ml of Gentamicin.


title: TWIST1 drives endothelial-to-mesenchymal-transition to stabilize atherosclerotic plaques [Twist1 RNA-Seq]

summary: The effect of TWIST1 deletion was studied in human aortic endothelial cells exposed to atheroprone or atheroprotective wall shear stress.

overall_design: Human aortic endothelial cells (HAoECs) were seeded Ibidi slides I 0.4 coated with gelatin and transfected with a TWIST1 siRNA (siT1) or a scrambled siRNA (control, siNT) using the Lipofectamine RNAiMAX transfection system. After a 6 hour incubation, media was replaced and cells were exposed to different flow patterns using the Ibidi flow system for 72 hours. The different flow conditions were: High laminar shear stress (HSS; 13 dynes/cm²), low laminar shear stress (LSS; 4 dynes/cm²) and low oscillatory shear stress (LOSS; ±4 dynes/cm², 0.5 Hz). Total RNA from HAoECs was extracted and analysed using bulk RNA sequencing.


title: Uncovering a Key Metabolic Role of the GATA1 N-Terminus in Red Blood Cell Development

first: Te

last: Ling

overall_design: HUDEP2 cells expressing FKBP12F36V-GATA1 (two clones 6F8 and 7C4) were cultured under differentiation conditions for 24 hours. PRO-seq was conducted at 0.5, 3, and 6 hours in the presence of the acute degradation inducer dTAG-13 (100 nM) to monitor the nascent transcripts.

first: Rashid

last: Mehmood

first: John

last: Crispino


title: Regulation of the type I interferon response by chromatin organization (ATAC-seq of HoxB8-FL pDC activation)

first: Eduardo

last: Esteva

summary: Antiviral type I interferons (IFN-I) including IFN-β and multiple subtypes of IFN-α are encoded within a single locus. Whereas most cell types produce primarily IFN-β, plasmacytoid dendritic cells (pDCs) respond to viruses by rapidly producing all IFN-I subtypes. We show that during pDC differentiation, the IFN-I locus translocates from the nuclear periphery and undergoes reorganization of topologically associated domains (TADs). Accordingly, IFN-I production by pDCs was strictly dependent on the TAD-organizing cohesin complex. Promoters of Ifna genes in pDCs were poised, which was imparted by the pDC-enriched transcription factor IRF8. Finally, we identified two distal regulatory regions that facilitated the expression of adjacent IFN-I genes. Thus, the IFN-I response is controlled by multilevel chromatin organization of the IFN-I locus, including its unique poised state in pDCs.

overall_design: ATAC-seq was performed on purified HoxB8-FL pDCs stimulated with CpG-A for 6 hours and 24 hours, as well as unstimulated pDCs at the same timepoints as a control (2 replicates per stimulation condition and timepoint).

first: N

last: Adams

first: I

last: Tiniakou

first: E

first: A

last: Khodadadi-Jamayran

first: B

last: Reizis


title: ATRX loss couples genome instability at a G-rich repeat to dysregulation of human alpha-globin expression [scRNA-seq]

first: Yuqi

last: Shen

state: Oxfordshiore

address: MRC WIMM, University of Oxford

department: Radcliffe Department of Medicine

summary: Germline mutations in the chromatin remodelling protein ATRX cause a severe developmental disorder associated with α-thalassemia. In addition, ATRX is amongst the twenty genes most frequently mutated in cancer. How ATRX mutations alter gene expression remains unclear. Using the α-globin locus as a model, here we show that ATRX deficiency downregulates α-globin in a subset of cells exhibiting DNA damage. A G-rich repeat at the α-globin locus serves as a potential site of G-quadruplex formation and DNA damage. ATRX binds this repeat co-transcriptionally, and its loss increases R-loop accumulation at this site, leading to local DNA damage and transcriptional disruption in cis. Deletion of this repeat abolishes this effect, while targeted DNA damage reinstates it. These findings reveal a mechanism linking ATRX’s role in genome stability to transcriptional regulation, and uncover a molecular basis of human genetic disease mediated by a long-range G-rich repeat.

overall_design: ATRX was knocked out using CRISPR-Cas9 in CD34+ haematopoietic stem cells (HSCs) derived from healthy donors. These cells were then differentiated into erythroid cells and analysed for gene expression using single-cell RNA sequencing (Smart-seq2).

first: Sean

last: Wen


title: Fecal microbiota transplantation mitigates cardiac remodeling and functional impairment in mice with chronic colitis

city: Galveston

first: Kevin

middle: M.

last: Lopez

address: 301 University Blvd

department: Internal Medicine

institute: University of Texas Medical Branch at Galveston

summary: Inflammatory bowel disease (IBD) is a chronic inflammatory disorder with significant extraintestinal manifestations, including cardiovascular derangements. However, whether and how chronic colitis impairs heart function remain unclear. We investigated the impact of chronic colitis on heart function and transcriptome using two mouse models: DSS-treated and Il10-/- mice. Echocardiography was employed to assess heart function and molecular characterization was performed using RNA-sequencing, RT-qPCR, and western blot. Both models exhibited significant cardiac impairment, including reduced ejection fraction and fractional shortening, along with increased collagen deposition, inflammation, and myofibril reorganization. Molecular analyses revealed upregulation of fibrosis markers and β-catenin reactivation, indicating a pro-fibrotic cardiac environment. RNA-sequencing unveiled a shared upregulation of eicosanoid-associated and inflammatory genes (Cyp2e1, Map3k6, Pck1, Cfd) across both models, along with model-specific alterations in pathways governing cAMP and cGMP signaling, arachidonic and linoleic acid metabolism, and immune cell responses. DSS colitis caused differential regulation of 232 cardiac genes, while Il10-/- colitis yielded 105 dysregulated genes. Importantly, therapeutic fecal microbiota transplantation (FMT) restored heart function in both models, characterized by reduced fibrosis markers and downregulated pro-inflammatory genes, while also mitigating intestinal inflammation. Notably, Il10-/- mice showed relatively less cardiac recovery following FMT, highlighting IL-10’s cardioprotective and anti-inflammatory contribution. Our findings provide direct evidence that chronic colitis impairs heart function, elucidate novel insights into colitis-induced cardiac remodeling, and suggest that FMT mitigates cardiac dysfunction by attenuating systemic inflammation and correcting gut dysbiosis. Further evaluation of gut-heart interactions and microbiome-based therapies is needed to improve cardiovascular health in IBD patients.

overall_design: To investigate the genetic and transcriptomic changes to the heart in chronic colitis and how therapeutic fecal microbiota transplantation affects such changes. Differential gene expression profile analysis was performed using RNA sequencing of total RNAs isolated from the colons of two independent mouse models using C57BL/6J mice and 129(B6)-Il10tm1Cgn/J mice strains. The comparative groups for C57BL/6J mice include (1) vehicle control, (2) DSS, (3) DSS+FMT. The comparative groups for 129(B6)-Il10tm1Cgn/J mice include (1) wild type, (2) IL-10 KO, and (3) IL-10 KO+FMT. Gene ontology and KEGG pathway encrichment was performed on the gene lists for each model, independently.

first: Xiaoying

last: Zhong

first: Max

last: Liu

first: Ying

last: Xiao

first: Rongliwen

last: Ou

first: Thierry

last: Kochkarian

first: Don

middle: W

last: Powell

first: Ken

last: Fujise

first: Qingjie

last: Li


title: Evaluation of targeted and immune combination therapies in a rat model of hormone receptor-positive breast cancer

first: Kornelia

last: Polyak

overall_design: Refer to individual Series


title: Cellular and transcriptional trajectories of adult neural fate specification in a sea anemone

city: Chicago

first: Heather

last: Marlow

state: IL

address: 920 E 58th Street

department: Organismal Biology and Anatomy

institute: University of Chicago

summary: We investigated the cellular and transcriptional trajectories of adult neurogenesis in the sea anemone Nematostella vectensis through single-cell transcriptome analysis of Elav>KikGR+, FoxL2>KikGR+, SoxC>KikGR+ body wall with mesenteries (no oral region) adult samples.

overall_design: Adult sea anemones (Nematostella vectensis) with a transgenic photoconvertible reporter (either Elav>KikGR, SoxC>KikGR, or FoxL2>KikGR) were photoconverted. At 2, 4 or 7 days post-photoconversion, animals were amputated below the pharynx and the body wall with mesenteries region was dissociated into single cells, KikGR+ cells were sorted using Fluorescence-Activated Flow Cytometry (FACS) into individual wells of 384-well plates. Single cell RNA-Seq libraries were generated with the MARS-Seq protocol (one scRNA-Seq library for each half-plate). Each sample here is one of 84 half-plate scRNA-Seq library.

first: Flora

last: Plessier


title: TWIST1 drives endothelial-to-mesenchymal-transition to stabilize atherosclerotic plaques

first: Paul

last: Evans

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Pooled single-cell screening in colorectal cancer identifies transcriptional modules of clinical relevance unlocked by oncogenes

city: Berlin

first: Nils

last: Blüthgen

address: Chariteplatz 1

department: Institute of Pathology

institute: Charite Universitätsmedizin Berlin

summary:
While oncogenic mutations shape colorectal cancer biology and therapy response, their prognostic value remains low. Cluster-based classification of patient cancer transcriptomes has shown greater promise for prognosis, yet these systems do not account for the roles of oncogenes in establishing cancer phenotypes. Here, we create and validate a prognostic classifier for colorectal cancer based on transcriptional programs induced by oncogenes.
To systematically investigate oncogenic drivers, we employed a barcoded library of colorectal cancer-associated oncogene variants across a panel of genetically diverse colorectal cancer cell lines. We profiled the transcriptomes of over 100,000 transgenic cells and used machine learning to define transcriptional modules capturing key functional traits.
Our analysis revealed heterogeneity on the cell-to-cell level and context-dependent gene expression patterns induced by oncogenes. We identified overarching gene expression modules reflecting core oncogenic processes, including cancer cell plasticity, inflammatory response, replicative stress, and epithelial-to-mesenchymal transition. These modules enabled a functional classification that linked oncogenic signalling states to distinct transcriptional profiles. We demonstrated their prognostic value by stratifying clinical colorectal cancer cohorts into high- and low-risk groups. Although partially correlated with established clinical parameters, the modules provided additional prognostic information, improving survival prediction and therapy stratification beyond existing classification systems.
In summary, our study establishes a framework that connects oncogenic mutations to core transcriptional modules. By integrating experimental models with clinical data, we provide a resource for investigating colorectal cancer progression and oncogene-specific vulnerabilities, facilitating future research and precision oncology.

overall_design: We cultured Caco-2-et, HT-29-et, RKO-et, SW480-et and HCT 116 cells transfected with pooled viral oncogenes. Four day post infection, we harvested cells, FACS sorted them and subjected cells to scRNA-seq.

first: Viola

last: Hollek

first: Francisca

last: Böhning

first: Markus

last: Morkel


title: ATRX loss couples genome instability at a G-rich repeat to dysregulation of human alpha-globin expression [ChIP-seq]

first: Yuqi

last: Shen

overall_design: To determine ATRX binding pattern during erythroid differentiation, the immortalised erythroid progenitor cell line HUDEP-2 were differentiated and samples from different differentiation stages were collected for ATRX ChIP-seq.