title: ATF3-dependent formation of inclusion bodies in polyQ-expressing human iPSC-derived neurons confers cellular protection [RNAseq]

city: Jerusalem

first: Walaa

middle: Ziad

last: Oweis

state: Israel

country: Israel

institute: Hebrew University of Jerusalem

summary: Huntington’s disease (HD) is an incurable, neurodegenerative disorder. While the causative mutation – CAG expansions within the coding region of the Huntingtin (HTT) gene – has been identified over 30 years ago, the pathological mechanisms underlying HD are still not clear. The abnormal CAG track encodes a polyglutamine (polyQ) expanded protein, which leads to HTT protein misfolding. These polyQ aggregates can form insoluble inclusion bodies (IBs); however, whether IBs are protective or detrimental remains debatable. To ask whether IBs are protective or harmful in human neuronal cells, and to elucidate the pathological pathways involved in polyQ IB formation, we developed an iPSC-based human neuronal models for polyQ-related disorders. We ectopically expressed the first 21 exons of the HTT gene, containing either 18Q or 105Q fused with GFP in HD patient-derived iPSCs containing 180Q or their isogenic corrected cells, respectively, differentiated them into neuronal progenitor cells (NPCs), and enriched for a pure population of polyQ IBs-containing cells (IB+). Comparing gene expression profiles between IB+ and IB- NPCs, growing side-by-side, in both systems, we identified ATF3 as responsible for inducing neuroinflammatory genes specifically in IB+ cells. ChIP-seq for ATF3 confirmed direct binding at their promoters, exclusively in IB+ NPCs. Remarkably, knocking out (KO) ATF3 completely prevented polyQ-IB formation in NPCs and rendered the cells more vulnerable to induced stress. Finally, using time-lapse imaging comparing cell death in IB+ and IB- NPCs, we demonstrate that polyQ IBs have a significant protective effect. Taken together, our results highlight ATF3’s role in polyQ IB formation in human NPCs, acting as an activator of inflammatory genes, and demonstrate that polyQ IBs protect cells from stress-induced death.

overall_design: RNA-seq profiling of differentially expressed genes between cells with and without IBs. RNA-seq analysis was performed on ATF3 wild-type and ATF3 knock-out 105Q-NPCs


title: T, NK, NKT cells in the brain from WT or 15q dup mice [multiple tissues]

status: Public on Apr 01 2026

city: Fukuoka

first: Minako

last: Ito

address: 3-1-1 Maidashi, Higashi-ku

country: Japan

institute: Kyushu University

type: Expression profiling by high throughput sequencing

summary: Autism Spectrum Disorder (ASD) is a neurodevelopmental disorder with no effective treatment, caused by genetic factors such as copy number variations (CNVs) and immunological factors such as maternal infection. The role of immunity in genetic ASD remains unclear. Here, we investigated the immun cells in the several tissues (brain, blood dura, lung, colon, spleen, thymus) of a mouse model of ASD (15q11-13 duplication), a common CNV associated with ASD.

overall_design: TCR-Vγ6+ γδ T cells from the brain, dura, thymus, blood, spleen, lung, and colon at 3 weeks of age (brain; n = 21 (WT); n = 22 (15q), dura; n = 7 (WT); n = 10 (15q), blood; n = 7 (WT); n = 10 (15q), thymus; n = 7 (WT); n = 7 (15q), spleen; n = 7 (WT); n = 7 (15q), lung; n = 7 (WT); n = 5 (15q), colon; n = 7 (WT); n = 5 (15q)) and performed scRNA-seq.

first: Natsumi

last: Takayama


title: ATF3-dependent formation of inclusion bodies in polyQ-expressing human iPSC-derived neurons confers cellular protection [ChIPseq]

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: ChIP-seq of ATF3 in 105Q-NPCs with and without IBs, and with and without ATF3.


title: Widespread gene-environment interactions shape the immune response to SARS-CoV-2 infection in hospitalized COVID-19 patients

city: Chicago

first: Luis

middle: B

last: Barreiro

state: Illinois

address: 5841 S Maryland Ave

department: Department of Medicine

country: USA

institute: University of Chicago

summary: Genome-wide association studies performed in COVID-19 patients have uncovered various loci significantly associated with susceptibility to SARS-CoV-2 infection and disease severity. However, the underlying cis-regulatory genetic factors contributing to heterogeneity in the response to SARS-CoV-2 infection and their impact on clinical phenotypes remain enigmatic. Here, we use single-cell RNA-sequencing to quantify genetic contributions to cis-regulatory variation in 361,119 peripheral blood mononuclear cells of 63 acute COVID-19 patients, 39 convalescent samples, and 106 healthy controls. Expression quantitative trait loci mapping across cell types within each disease state group reveals thousands of cis-associated variants, of which hundreds are detected exclusively in immune cells derived from acute patients. Patient-specific genetic effects dissipate as infection resolves, suggesting that distinct gene regulatory networks are at play in the active infection state. Further, 20.3% of tested loci demonstrate significant cell state interactions with genotype, with pathways related to interferon responses and oxidative phosphorylation showing pronounced cell state-dependent variation, predominantly in CD14+ monocytes. Overall, we estimate that 16.8% of tested genes exhibit gene-environment interaction effects, highlighting the importance of environmental modifiers in the transcriptional regulation of the immune response to SARS-CoV-2. Our findings argue for the existence of extensive gene-environment effects among patients responding to an infection.

overall_design: Multiplexed single-cell RNA expression profiles of peripheral blood mononuclear cells (PBMCs) collected from COVID-19 patients, COVID-19 follow-ups, and healthy controls

first: Haley

middle: E

last: Randolph

first: Raúl

last: Aguirre-Gamboa

first: Elsa

last: Brunet-Ratnasingham

first: Tomoko

last: Nakanishi

first: Veronica

last: Locher

first: Ellen

last: Ketter

first: Cary

last: Brandolino

first: Catherine

last: Larochelle

first: Alexandre

last: Prat

first: Nathalie

last: Arbour

first: Anne

last: Dumaine

first: Andrés

last: Finzi

first: Madeleine

last: Durand

first: J Brent

last: Richards

first: Daniel

last: Kaufmann


title: Compressive Force Induces Differential Gene Expression in Uterine Fibroids

city: Cincinnati

first: Stacey

middle: C

last: Schutte

state: OH

address: 2901 Woodside Dr.

department: Biomedical Engineering

institute: University of Cincinnati

summary: We investigated how compressive force influences fibroid and myometrial cells. Patient-matched cells were isolated from women undergoing hysterectomy or myomectomy for the treatment of uterine fibroids. Samples from five women with no hormonal modulation within three months of surgery were used for this study. Spheroids fabricated from fibroid or myometrial cells were embedded in agarose hydrogels and exposed to compressive force for seven days. RNA sequencing was performed to identify genes and signaling pathways altered in fibroids in response to compression.

overall_design: Gene expression profiling analysis of RNA-seq data from uterine fibroid and myometrial cell spheroids with and without compression.

first: Carolyn

middle: A

last: Nietupski

first: Megan

last: Sax

first: Rose

last: Dean

first: Andreja

last: Moset Zupan

first: Emily

middle: G

last: Hurley


title: Sequencing experiments on poly(U) mutants in C. elegans adults and embryos

city: Bloomington

first: Leanne

last: Kelley

state: IN

address: 1001 E Third St

institute: Indiana University

summary: To investigate mRNAs that are influenced by poly(U) polymerases in C. elegans adults and embryos/

overall_design: We performed Illumina-based mRNA-seq on various poly(U) polymerase deletion mutants at the adult and early embryonic stages.

first: Kelley

last: Leanne

first: Maine

last: Eleanor


title: Gene expression of human macrophages differentially activated in vitro

city: Lyon

first: Benedicte

last: Chazaud

address: 8 Avenue Rockefeller

department: Institut NeuroMyoGène

country: France

institute: Université Claude Bernard Lyon 1

overall_design: Human macrophages were isolated from blood monocytes from healthy donors. After differentiation in macrophages (one week in serum containing medium), they were either i) untreated,ii) treated with IL-4, iii) treated with LPS, iv) treated with IL-10+dexamethasone as described in Saclier et al 2013 (PMID: 23169615). n=3 for each condition.

first: Bénédicte


title: GW4064-induced genes in mouse livers

status: Public on Mar 31 2026

city: Phoenix

first: Yanqiao

last: Zhang

state: AZ

address: 475 N 5th Street

institute: University of Arizona COM - Phoenix

summary:
Fxr+/+ or Fxr-/- mice were gavaged with vehicle or GW4064 (30 mg/kg, twice a day) for 7 days. Livers were collected.
Hepatic mRNA levels were determined using Sentrix MouseRef-8 v2 Expression BeadChip.

overall_design: To determine FXR-reguated genes in the liver, we treated Fxr+/+ and Fxr-/- mice with either vehicle or GW4064 for 7 days. Each sample was pooled from 3-4 individual samples.


title: Expression data from budding yeast sec12-4 and sec12-4 ino2Δino4Δ mutant cells

city: Kagamiyama, Higashi-Hiroshima

first: MUNEYOSHI

last: KANAI

institute: National Research Institute of Brewing

summary:
Sec12 is a guanine nucleotide exchange factor (GEF) required for the initiation of COPII vesicle formation in ER to Golgi transport.  The sec12-4 mutant cells show temperature sensitivity in growth and a defect in ER-to-Golgi protein transport. Ino2/Ino4 are components of the heteromeric basic helix-loop-helix transcription activator that binds inositol/choline-responsive elements (ICREs) and are required for derepression of phospholipid biosynthetic genes in response to inositol depletion.
We used microarrays to compare the global gene expression profiles between sec12-4 and sec12-4 ino2Δino4Δmutant cells.

platform_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

overall_design: sec12-4 (FKY4415 MATa sec12-4, his3, leu2, ade2, lys2, trp1, ura3, bar1-1) and sec12-4 ino2Δ ino4Δ (FKY4418 MAT a sec12-4, his3, leu2, lys2, trp1, ura3, bar1-1, ino2Δ::HIS3, ino4Δ::LEU2) cells were grown to log phase at 25°C in YPD medium for RNA extraction and hybridization on Affymetrix microarrays. In order to obtain new insights into the role of Ino2/Ino4, transcription activator in COPII-mediated protein transport, we perfomed the genome-wide expression analysis of sec12-4 and sec12-4 ino2Δino4Δ mutant cells.

first: Mei

last: Kato

first: Atsuko

last: Ikeda

first: Yukari

last: Yabuki

first: Muneyoshi

last: Kanai

first: Kouichi

last: Funato


title: Distinct pathophysiological mechanisms of CEP152 variants in microcephaly and brain abnormalities

first: Reut

last: Suliman

address: Givat ram campus

department: Genetics

institute: The Hebrew University of Jerusalem

summary: Centrosomal protein 152 (CEP152) is essential for centriole function, cell polarity, and neurodevelopment. Pathogenic variants in CEP152 cause autosomal recessive primary microcephaly 9 (MCPH9), though the underlying mechanisms remain poorly understood. Here, we identified novel compound heterozygous variants, c.314G>A,p.(W105*) and c.2689A>T,p.(K897*) in a patient with microcephaly, and analyzed them alongside a homozygous variant, c.95A>C,p.(Q32P), which is associated with atypically severe brain malformations in addition to microcephaly. Functional assays revealed distinct variant-specific effects: p.K897* disrupted centrosomal localization, p.W105* led to protein degradation, and p.Q32P retained centrosomal localization but impaired interaction with Polo-like kinase 4, a CEP152 partner and a microcephaly-causative protein. To assess pathogenicity in vivo, we generated Cep152W105*/K897* and Cep152 18 Q32P/Q32P mouse models. Both exhibited microcephaly with reduced body weight, but Cep152 19 Q32P/Q32P mice additionally displayed severe brain malformations, including ventricular dilation and neuronal mispositioning. Cellular analyses revealed centrosome dysfunction, mitotic abnormalities, and increased apoptosis, which were more pronounced in Cep152Q32P/Q32P mice. Electrophysiological and gene expression studies further confirmed variant-specific neuronal impairments, potentially explaining the clinical diversity and severity observed in patients. These findings provide mechanistic insights into how CEP152 variants differently disrupt centrosome function and highlight distinct molecular mechanisms underlying CEP152-related microcephaly and cortical malformations.

overall_design: RNA-seq profiling of primary and secondary somatosensory areas from adult mice carrying two kinds of mutations in the Cep152 gene.

first: Nanako

last: Hamada

first: Lama

last: AlAbdi

first: Tomoko

last: Uehara

first: Looprasertkul

last: Sasikarn

first: Takuma

last: Nishijo

last: Suliman-Lavie

first: Mais O

last: Hashem

first: Majid

last: Alfadhel

first: Shatha

last: Alhefdhi

first: Brahim

last: Tabarki

first: Malak

last: Alghamdi

first: Ikuko

last: Iwamoto

first: Toshiki

last: Takenouchi

first: Kenjiro

last: Kosaki

first: Sagiv

last: Shifman

first: Seiji

last: Mizuno

first: Nobuhiko

last: Ohno

first: Fowzan S

last: Alkuraya

first: Koh-ichi

last: Nagata


title: Expression profiling of mouse hippocampus from Apex1 conditional knockout and caloric restriction models across aging

city: Pittsburgh

first: Yejie

last: Shi

state: PA

address: S-510 Biomedical Science Tower, 3500 Terrace Street

department: Neurology

institute: University of Pittsburgh

summary:
Accumulation of oxidative DNA damage is a key contributor to brain aging and cognitive decline. The DNA repair enzyme apurinic/apyrimidinic endonuclease-1 (Apex1) plays a central role in base-excision repair, but its contribution to transcriptional programs associated with brain aging remains incompletely understood. In this study, we performed genome-wide expression profiling of mouse hippocampus to examine the effects of forebrain-specific Apex1 deletion and caloric restriction on age-associated transcriptional changes.
Hippocampal tissues were collected from male mice at young (8-12 weeks) and aged (48 weeks) time points across six experimental groups: young wild-type ad libitum (WT AL), young Apex1 conditional knockout ad libitum (cKO AL), aged WT AL, aged cKO AL, aged WT caloric restriction (WT CR), and aged cKO CR. Apex1 conditional knockout mice carried the genotype Camk2a-Cre+/−;Apex1^flox/flox, while hemizygous CaMKIIα-Cre+/− littermates served as age-matched controls. Microarray analyses were performed to identify transcriptional changes associated with Apex1 deficiency, aging, and dietary intervention. The dataset provides a resource for investigating molecular pathways related to genomic maintenance, metabolism, and neuronal function during brain aging.

overall_design:
Genome-wide transcriptional profiling of mouse hippocampal tissue was performed using Affymetrix Clariom S mouse arrays. Six experimental groups were included: young WT AL, young Apex1 cKO AL, aged WT AL, aged Apex1 cKO AL, aged WT CR, and aged Apex1 cKO CR. Hippocampal tissue from one hemisphere (left or right) of each mouse was collected for RNA extraction. Four biological replicates were generated for each group, yielding a total of 24 samples.
All samples were processed in a single experimental batch. In the associated manuscript, transcriptomic analyses focused on the four aged groups (aged WT AL, aged cKO AL, aged WT CR, aged cKO CR). During downstream statistical analysis, one sample from the aged Apex1 cKO AL group (JC-51) was identified as an outlier and excluded from differential expression analyses; however, the raw microarray data for this sample are included in the deposited dataset.

first: Jun

last: Chen


title: Microglial dynamics and ferroptosis induction in human iPSC-derived neuron-astrocyte-microglia tri-cultures

city: Fujisawa

first: Hiroko

last: Ohmiya

address: 2-26-1, Muraoka-Higashi

department: Computational Science

institute: Takeda Pharmaceutical Company

summary: The dynamics of microglial activity within neuron-astrocyte-microglia tri-cultures derived from human induced pluripotent stem cells (iPSCs) present a complex interplay and offer an opportunity to obtain new insights into neuron-glia interactions. Iron-laden microglia, correlating with functional changes, represent a key pathological feature of Alzheimer's disease (AD). This study characterized the cellular crosstalk and transcriptional states of microglia in tri-cultures. Complement C3 can be detected in culture media when microglia are cocultured with neurons, and the addition of astrocytes in the coculture led to an increased amount of C3, indicating that the impact of glial interactions can be evaluated in this model system. We compared microglial gene expression profiles comprehensively in monoculture, coculture, and tri-culture settings. Single-cell RNA sequencing (scRNA-seq) revealed various microglial states with gene expression changes associated with endocytosis and neuron-related functions in tri-culture settings, suggesting that microglial behavior is profoundly impacted by the presence of neurons and astrocytes. We assessed microglial responses to iron overload combined with the ferroptosis inducer RSL3 (a GPX4 inhibitor) in tri-cultures. Microglial cell death was accompanied by ferritin heavy-chain expression, indicating microglia ferroptosis. scRNA-seq analyses highlighted alterations in pathways related to ferroptosis, stress response, and autophagy, indicating substantial shifts in microglial profiles upon iron perturbation. These findings underscore the necessity of using tri-cultures as a model to capture certain degrees of complex cellular interactions occurring in vivo. These results offer critical insights for establishing in vitro models for therapeutic development of neurodegenerative diseases, including AD.

overall_design:
RNA-seq profiling of human iPSC-derived microglia cultured under three conditions: (i) microglia monoculture, (ii) microglia–neuron co-culture, and (iii) microglia–neuron–astrocyte tri-culture. Tri-cultures were treated with iron plus RSL3 or vehicle control.

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human privacy
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first: Masato

last: Yugami

first: Yan

last: Ling


title: Aortic carboxypeptidase-like protein potentiates β1 integrin signaling in mesenchymal progenitors (Primary stromal cells)

city: Boston

first: Cheyanne

middle: Lynne

last: Frosti

state: MA

address: 72 E. Concord Street

department: Biochemistry & Cell Biology

institute: Boston University

summary: Fibrosis is a pathological process characterized by persistent fibroblast activation and excessive extracellular matrix (ECM) accumulation. Aortic carboxypeptidase-like protein (ACLP), an ECM-associated protein that binds fibrillar collagen, is upregulated in fibrotic tissues and promotes fibroblast differentiation through canonical TGFβ receptor I signaling. We hypothesized that when presented within the collagen matrix, ACLP engages mechanically driven signaling pathway that contribute to fibroblast activation. Here, we identified a previously unrecognized mechanism through which collagen-bound ACLP activates primary stromal cells towards a myofibroblast phenotype via β1 integrin-mediated signaling. Collagen-bound ACLP induced rapid fibroblast spreading, increased β1 integrin activation, and promoted focal adhesion maturation. These early adhesion events were followed by elevated activation of the GTPases RhoA and Rac1, with enhanced F-actin assembly and nuclear accumulation of myocardin-related transcription factor A (MRTFA), a key regulator of activated fibroblast gene expression. Transcriptomic profiling revealed enrichment of focal adhesion, ECM–receptor interaction, and actin cytoskeletal gene pathways in response to collagen-bound ACLP. These findings establish collagen-bound ACLP as an ECM-derived cue that links matrix composition to fibroblast activation pathways.

overall_design: RNA-seq profiling of mouse primary stromal cells cells cultured for 48 hours on col1 or col1-ACLP hydrogels.

middle: L

first: Diana

last: Yeritsyan

first: Matthew

middle: D

last: Layne


title: Acute High-Intensity Exercise Alters Gut Microbiota Composition and Energy Metabolism in Different Strains of Mice

city: Tianjin

first: ruolin

last: gao

address: No. 16 Donghai Road, Xiqing District

country: China

institute: Tianjin University of Sport

summary: The gut microbiota plays a critical role in host energy metabolism and immune regulation, yet the temporal dynamics of microbial community responses to acute physiological stressors remain poorly characterized. While exercise is recognized as a modulator of gut microbial composition, the immediate post-exercise shifts in microbial community structure across different genetic backgrounds have not been systematically examined. Here, we present a longitudinal 16S rRNA gene sequencing dataset profiling the temporal dynamics of gut microbiota following acute high-intensity exercise in two widely used laboratory mouse strains. Age-matched male BALB/c  and C57BL/6J  mice were subjected to a single bout of acute exercise. The colonic content samples were collected to capture early temporal responsesat. Total genomic DNA was extracted from colonic contents and the 16S rRNA V4 region was amplified and sequenced on the NovaSeq6000 platform.  This dataset enables identification of strain-specific and conserved exercise-responsive microbial taxa,  and supports functional predictions related to energy metabolism and intestinal homeostasis.

overall_design: BALB/c and C57BL/6J mice were subjected to a single high-intensity treadmill run, with colonic contents collected at 0, 30, and 60 minutes post-exercise for 16S rRNA gene sequencing.


title: Therapeutic targeting of eIF4E cap-binding domain reveals control of lineage fate in prostate cancer [CUT&Run]

city: Seattle

first: Sonali

last: Arora

state: WA

address: 1100 Fairview Ave N,

institute: FHCRC

summary: We demonstrate mRNA translation controls basal to luminal lineage plasticity of prostate epithelium through eIF4E cap-binding domain. Mechanistically, this plasticity is driven by translational repression of basal keratins via cis-regulatory elements in the 5' untranslated regions (UTRs) of their transcripts, alongside promoting androgen receptor (AR) protein stability through the translational upregulation of deubiquitinases BAP1 and OTUD3. This lineage switch is essential for cell survival and represents a druggable vulnerability. In castration-resistant prostate cancer (CRPC), high eIF4E expression is associated with basal phenotype, reduced luminal differentiation and accelerated resistance to AR pathway inhibitors (ARPIs). Notably, tumors resistant to enzalutamide regain sensitivity upon inhibition of the eIF4E cap-binding domain, which reprograms them toward a luminal state. These discoveries uncover a novel oncogenic role of the eIF4E cap-binding domain in lineage plasticity and therapy resistance and suggest that inhibition of this domain offers a promising strategy to overcome treatment resistance in prostate cancer.

overall_design: Cut & Run data  of DMSO, PF, and R1881 samples using AR antibody

first: Rashmi

last: Mishra

first: Andrew

last: Hsieh


title: Addressing transcriptomic assay heterogeneity for predictive modeling in cancer (RNA-seq)

city: Aurora

first: Benjamin

last: Bitler

state: Colorado

address: CU Anschutz Research Complex II  12700 East 19th Avenue  3400D

department: Cancer Biology

institute: University of Colorado-Anschutz

summary: The goal of this study was to evaluate how best to preprocess RNA-seq and NanoString data to, if possible, combine these data for larger cohort sizes in predictive modeling of clinical features. High-grade serous Ovarian Cancer is a highly heterogeneous disease with most data split into Microarray, NanoString, and RNA-seq. NanoString and RNA-seq showed the greatest similarities in dynamic range across these datasets. Therefore, we performed bulk RNA-seq and NanoString (PanCancer IO360 panel) on sequential samples of 26 patients to evaluate how comparable gene expression patterns were captured and if preprocessing steps could improve this. In the preprocessing steps for RNA-seq, we considered counting over genes or exons to which NanoString probes mapped.

overall_design: 26 sequential FFPE samples from patients with HGSOC had RNA extraction and quantification with either bulk RNA-sequencing (here, Tempus xR) or NanoString (separate GEO) for downstream comparison. Tumor samples from interval debulking surgery following neoadjuvant chemotherapy (NACT). NanoString data can be found at GSE322784 with the paired samples listed in the metadata below. Library name numbers do not match sample names so ensure metadata is used carefully.

first: Hope

last: Townsend

first: Aaron

last: Clauset

first: Robin

last: Dowell


title: Increased Yolk Lipid Mobilization Promotes Zebrafish Post-Segmentation Growth via an Hnf4-Lipoprotein Axis

city: Shanghai

first: Wei

last: Dai

address: Room E7005, Interdisciplinary Building No.2, No. 2005, Songhu Road

department: IMIB

institute: Fudan University

summary: Embryogenesis is a period of rapid growth that places ever-increasing demands on nutrients, yet how maternal stores are temporally supplied to meet successive developmental stages remains poorly understood. In egg-laying animals, all maternal nutrients are sealed within the yolk, creating a closed system ideal for addressing this question. Using zebrafish, we tracked the mobilization of the two principal yolk reserves, proteins and lipids, throughout development. Protein catabolism proceeds continuously from cleavage to hatching, whereas large-scale lipid mobilization is postponed until after segmentation. This lipid switch is initiated by zygotic activation of the transcription factors Hnf4a/b, which induce the acidic lipase Pla2g15 to hydrolyze lipids stored in yolk granules. The released lipids are subsequently transferred to the yolk-syncytial-layer endoplasmic reticulum, packaged into lipoproteins, and transported through the circulation to distant tissues. Inhibiting protein mobilization disrupts development at all stages, whereas blocking the lipid pathway spares early embryos but compromises post-segmentation growth. These findings uncover a two-phase, transcriptionally gated program that reallocates maternal nutrients to satisfy the embryo’s escalating energetic and biosynthetic demands.

overall_design: RNA-seq profiling of whole-embryo samples from zebrafish lipf and pla2g15 mutant embryos (with clear genotypic segregation into siblings [sib] and mutants [mut]) at 24 hpf and 48 hpf.

first: Yizhu

last: Tao

first: Yingjie

last: Zeng


title: Cd7 drives T cell exhaustion during chronic viral infection

city: Iowa City

first: Ryan

last: Zander

state: IA

address: 51 Newton Road

institute: University of Iowa

summary: We have employed use of scRNA-seq (10X Genomics) to assess the transcriptional landscape of control and CD7-deleted TCR transgenic P14 cells during chronic LCMV Cl13 infection.

overall_design: Co-transferred sgCtrl (CD90.1/CD90.1) and sgCd7 (CD90.1/CD90.2) P14 CD8 T cells were FACS-sorted from LCMV Cl13-infected donor mice (n=5 samples pooled) on day 20 post infection and were subsequently loaded onto the Chromium X Controller (10X Genomics). Single-cell RNA-seq libraries were prepared using Chromium GEM-X Single Cell 3’ Expression v4 - dual index (10x Genomics) according to the manufacture’s protocol.


title: ZipV is required for oxidative stress resistance and pathogenicity in Aspergillus fumigatus

city: Debrecen

first: Tamas

last: Emri

address: Egyetem ter 1

country: Hungary

institute: University of Debrecen

summary: The function of ZipV (Afu3g032301) putative bZIP transcription factor was studied using wild-type, gene-deficient, and complemented strains of Aspergillus fumigatus. Deletion of zipV increased oxidative stress sensitivity and reduced in vivo virulence in a Galleria mellonella model, while complementation of the gene deletion restored the wild-type phenotype. Transcriptomic data from growing cultures and reverse transcription quantitative real-time PCR performed on samples taken from conidia-producing cultures suggested that ZipV regulates the development of certain conidial traits. In the delta-zipV mutant, the transcription of catA encoding conidial catalase, was impaired. This explains the oxidative stress sensitivity of this strain and may contribute to its reduced virulence. The increased transcriptional activity of the alternative oxidase gene aoxA observed in the absence of ZipV suggests that cells attempt to alleviate oxidative stress sensitivity by upregulating this antioxidative gene.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for mycelia of Aspergillus fumigatus reference strain, and delta-zipV mutant under untreated and H2O2 treated conditions with three biological replicates.

first: Kinga

last: Varga

first: Tamás

first: Károly

last: Antal

first: István

last: Pócsi


overall_design: RNA-seq profiling of whole-embryo samples from zebrafish mttp mutant embryos (with clear genotypic segregation into siblings [sib] and mutants [mut]) at 24 hpf and 48 hpf.

first: Tong

last: Sun


overall_design:
RNA-seq profiling of whole-embryo and yolk tissue samples from zebrafish wild type embryos at 6 hpf, 10hpf, 26hpf and 48 hpf.
RNA-seq profiling of body tissue samples from zebrafish wild type embryos at 6 hpf, 10hpf, 26hpf and 48 hpf.


overall_design: E64D is a cell-permeable inhibitor of cysteine proteases that can be effectively absorbed by zebrafish embryos when added directly to the embryo medium. To assess its impact on gene expression, wild-type AB zebrafish embryos were treated with either 3 μM E64D or 0.5% DMSO (vehicle control) from 1 to 24 hours post-fertilization (hpf). Total RNA was extracted for RNA sequencing. For each treatment group, four biological replicates were collected, with each replicate comprising seven pooled embryos.

first: Ran

last: Ai


title: Therapeutic targeting of eIF4E cap-binding domain reveals control of lineage fate in prostate cancer

first: Sonali

last: Arora

overall_design: RNASeq of treated (4EI) and untreated ( DMSO) prostate samples at 6hr and 72 hr

first: Rashmi


overall_design: RNA-seq profiling of whole-embryo samples from zebrafish hnf4a and hnf4b mutant embryos (with clear genotypic segregation into siblings [sib] and mutants [mut]) at 34 hpf and 48 hpf.


title: Physiological and transcriptional response of VPZ trangenic soybean lines under elevated CO2

city: Urbana

first: Steven

middle: James

last: Burgess

state: IL

address: 1201 W Gregory Dr

department: Plant Biology

institute: University of Illinois, Urbana-Champaign

summary: VPZ transgenic soybean plants have been showen to have faster non-chemical quenching (NPQ) relaxation To explore the effects of elevated CO2 on these transgenic plants we tested the physioloigcal and transcxriptional response to the VPZ plants under elevated CO2. We found that faster NPQ and higher photsynthetic efficiency of VPZ soybean is not affetced by elevated CO2.

overall_design: To investigate effect of elevated CO2 on VPZ soybean and WT soybean, VPZ and WT soybean plants were grown in Free Air-Carbon enrichment Field (FACE) facility in eight different plots/blocks/rings (R1-R8). RNA seq samples were collected at two different growth stages vegetative stage (V4-V5) and reproductive stage (R6). Four replicates were collected for each treatment, genotype, stage combination

first: Amanda

middle: P

last: De Souza

first: Dilkaran

last: Singh

first: Lynn

last: Doran

first: Jeffrey

last: Hansen

last: Long

first: Amy

last: Marshall-Colon

middle: J


title: Transcriptional changes in GNAQ R183Q mouse back skin

status: Public on Mar 30 2026

city: Madison

first: Hao

last: Chang

state: WI

address: 1111 Highland Ave

department: Dermatology

institute: University of Wisconsin-Madison

summary: We used RNA-Seq to search for potential downstream effectors of GNAQ R183Q during the developent of vascular phenotypes in the mouse back skin.

overall_design: We profiled the transcriptomes of E14.5 back skin from wild type and GNAQ R183Q embryos. Four biologically independent samples were collected for each genotype.

first: Beth

last: Drolet


title: multiplexed RNA imaging of human forebrain organoids from typical and autism subjects [MERFISH]

city: Singapore

first: Jinyue

last: Liu

address: 60 Biopolis Street

country: Singapore

institute: Genome Institute of Singapore

summary: the goal of this experiment is to define cellular phenotypes in human brain organoid models of autism.

overall_design:
human forebrain organoids were cultured with minor modifications using a published protocol (Qian et al. 2016), harvested at 8-weeks, cryosectioned and imaged using multiplexed error-robust fluorescence in situ hybridization.

***Submitters declare that the raw image data will be made available through a generalist archive -or- upon request.

first: Li

last: Lin

first: Wan

middle: K

last: Chock


title: Loss of CARM1 alters the developmental programming of Glioma stem-like cells and creates a druggable NGFR/NTRK dependency

status: Public on Mar 29 2026

city: Bronx

first: Ronald

last: Cutler

state: NY

address: 1300 Morris Park Ave

department: Genetics & Biochemistry

institute: Albert Einstein College of Medicine

summary: A key driver of Glioblastoma (GBM) heterogeneity and therapy resistance is the capacity of glioma stem-like cells (GSCs) to hijack developmental signaling programs. However, it remains unclear how GSCs regulate these adapted developmental signaling pathways and how these pathways might be therapeutically exploited. The arginine methyltransferase, CARM1, has been shown to play critical roles in maintaining stem cell pluripotency, preventing differentiation, and recently was discovered to be upregulated in Glioblastoma. To date, there is little to no understanding of the role that CARM1 plays in regulating developmental processes in Glioblastoma. To address this gap in knowledge, we applied a multi-omics approach to characterize developmental processes that are specifically regulated by CARM1 in GSCs. We found that loss of CARM1 results in dysregulation of several developmental markers: ARX, GFAP, NGFR, PDGFRA and results in both a proteomic and transcriptomic shift towards the radial glia cell lineage. Moreover, CARM1 depleted cells reprogram their signaling to develop an increased survival dependency on NGFR/NTRK signaling and are hypersensitive to the FDA approved brain penetrant NTRK inhibitor—Entrectinib. Mechanistically, we find that NFIA is a CARM1 substrate and can repress NGFR signaling just as CARM1 does, and thus the CARM1/NFIA relationship is likely a key regulator of NGFR/NTRK signaling in GSCs. Altogether, we demonstrate that CARM1 regulates the cell lineage of GSCs at the transcriptomic and proteomic level, and naturally represses NGFR/NTRK signaling—likely through CARM1 dependent methylation of NFIA. Further, CARM1 depletion leads GSCs to develop a survival dependency on NGFR/NTRK signaling and creates a therapeutic vulnerability to NTRK inhibition.

overall_design: RNA-Sequencing of glioblastoma cell line with and without CARM1 knockdown

first: Dejauwne

last: Young

first: Simone

last: Sidoli


title: Machine-learning prediction of affinity and epistasis in the bovine pancreatic trypsin inhibitor–chymotrypsin complex

status: Public on Mar 28 2026

city: Be'er Sheva

first: Noam

last: Tzuri

address: David Ben Gurion Blvd 1

institute: Ben Gurion University

summary: Protein–protein interactions (PPIs) are shaped by evolutionary pressures that fine-tune binding affinities and drive the epistatic relationships that support functional outcomes. Here, we used the complex of bovine pancreatic trypsin inhibitor (BPTI) and chymotrypsin as a model system to study how mutations at one or two positions affect binding affinity and epistasis. To predict the binding affinity landscape of the BPTI–chymotrypsin complex, we combined deep sequencing data, obtained from a saturation scanning mutagenesis BPTI library, with a machine-learning (ML) model. Using this ML model, which was trained on a subset of experimental binding data, we predicted the binding affinities and epistatic interactions across thousands of single and double BPTI mutants, including those not observed in the library. Our predictive approach completed missing data points and enabled us to reveal global trends in affinity changes and mutation couplings within specific binding interface positions. Our analysis revealed that different mutations in the same position may have different effects on affinity, with most double mutations leading to increased epistasis, particularly at hotspot positions, thereby indicating a cooperative binding effect. In most cases, affinity and epistasis were inversely correlated, with affinity enhancement of double-mutant variants being associated with negative epistasis. Our approach can be readily generalized to predict mutation effects in larger combinatorial libraries and in proteins for which structural information is lacking.

overall_design: This study investigates the binding affinity of BPTI variants toward chymotrypsin. A yeast surface display (YSD) library containing single- and double-mutant BPTI variants at selected positions was generated. The variants were sorted by fluorescence-activated cell sorting (FACS) into four affinity gates (HI, WT, SL, and LO) using labeled chymotrypsin. The sorted populations were analyzed by next-generation sequencing (NGS) on the Illumina platform to determine variant frequencies in each gate

first: Itamar

last: Kass

first: Yaron

last: Orenstein

first: Niv

last: Papo


title: Base editing restores CDKL5 expression and rescues neuronal deficits in a patient-derived model of CDKL5 deficiency disorder

status: Public on Mar 27 2026

city: Shatin

first: Yao

last: Zhu

address: CUHK

country: Hong Kong

institute: The Chinese University of Hong Kong

summary: CDKL5 (Cyclin-dependent kinase like 5) deficiency disorder (CDD) is a rare monogenic neurodevelopmental disorder caused by pathogenic mutations in the CDKL5 gene, with approximately 50% of reported variants being point mutations. Base editing presents a promising therapeutic strategy to correct such mutations, restore endogenous CDKL5 expression, and pave the way for novel treatments for CDD. To assess the therapeutic potential of base editing for CDD, we applied adenine base editing (ABE) to correct a CDKL5-R550* (c.1648C>T) mutation in induced pluripotent stem cells (iPSCs) derived from a CDD patient. Isogenic control, CDKL5-R550* mutant, and ABE-corrected iPSCs were differentiated into neurons and the restoration of CDKL5-related and functional recovery were assessed. In this study, we demonstrated that ABE successfully restored CDKL5 protein levels and CDKL5-dependent signalling pathways in edited iPSC-differentiated neurons to levels comparable to the isogenic control. Morphological deficits, and genes expression were normalized in the ABE-corrected neurons. This study provides evidence that ABE can precisely correct pathogenic mutation and functionally rescue some CDD-associated neuronal phenotypes in patient-derived cells, supporting its potential as a valuable gene therapy for CDD. Moreover, these findings underscore the broader applicability of base editing for treating other monogenic neurodevelopmental disorders caused by point mutations.

overall_design: isogenic Control, CDKL5-R550*, ABE-corrected iPSC-induced Day28 cortical neurons

first: Yue

last: Chai

first: Jiayi

first: Mingfeng

last: Guan

first: Zhongyu

last: Zheng

first: Yu

last: Chen

first: Wing Sum

last: Tsang

first: Tao

last: Ye

first: Pak Kan

last: Ip


title: Spatial predictors of response to chemo-immunotherapy in microsatellite stable metastatic colorectal cancer

first: Solomonraj

last: Wilson

address: 8A Biomedical Grove

institute: SIgN

summary: Microsatellite-stable (MSS) colorectal cancers (CRC) are largely unresponsive to immune checkpoint inhibition (ICI). The MAYA trial used temozolomide (TMZ) in MGMT-silenced MSS mCRC, hypothesizing that TMZ-induced hypermutation could sensitize tumors to ICI; the primary endpoint was met, showing durable responses with TMZ plus ipilimumab and nivolumab. We perform integrated spatial, transcriptomic, and immune profiling of longitudinal tumor and blood samples from patients treated on the MAYA trial. Post-TMZ increases in tumor mutational burden associate with improved progression-free survival. Spatial profiling demonstrates that clinical benefit is greatest in permissive tumor microenvironments. Responders exhibit enrichment of cytotoxic T cells across tumor and stromal compartments, whereas non-responders display heterogeneous cellular neighborhoods, with fibroblasts in close spatial proximity to T cells, consistent with barriers to immune mediated clearance. Longitudinal peripheral immune profiling shows that early upregulation of TIGIT and PD-1 following TMZ exposure predicts resistance. Together, these findings indicate that both mutational evolution and spatial immune architecture contribute to immune sensitization in MGMT-silenced MSS CRC.

overall_design: We profiled formalin-fixed and paraffin embedded (FFPE) tumor samples from patients with MSS colorectal cancer who received Nivolumab + Ipilimumab + Temozolomide on the MAYA study to generate histologic and  spatial transcriptomics profiling using Visium  (10x Genomics, Inc.).

first: Joan

last: Choo

first: Joseph J

last: Zhao

first: Mai Chan

last: Lau

first: Raghav

last: Sundar

first: Filippo

last: Pietrantonio


title: Depletion of IRX3 promotes early cardiac commitment and maturation of human Ipsc-derived cardiomyocytes

city: Sao Paulo

first: Jose

last: Krieger

state: SP

address: Av Dr Eneas C Aguiar 44 10ofl

department: Cardiology

country: Brazil

institute: Heart Institute (InCor)/Univ Sao Paulo Med Sch

summary: The limited regenerative capacity of the adult human heart makes human induced pluripotent stem cell (hiPSC)-based therapies a promising approach for treating myocardial infarction. However, hiPSC-derived cardiomyocytes (hiPSC-CM) display immature features. In this study, we demonstrate that depletion of the transcription factor IRX3 promotes early cardiac commitment and enhances the maturation of hiPSC-CMs. We first established the temporal expression of IRX3 during hiPSC-CM differentiation and subsequently investigated its role by generating two IRX3 mutant hiPSC lines. IRX3-depleted cardiac progenitors exhibited increased expression of GATA4, NKX2-5, TBX5 and Wnt signaling-related genes, along with increased proliferation. Differentiation of IRX3-depleted cells yielded more cardiomyocytes with enhanced expression of TNNI1 and CX43. Notably, IRX3-depleted cardiomyocytes showed improved sarcomere alignment, enhanced cell-to-cell communication, and electrophysiological maturation. Furthermore, in silico analysis suggests that IRX3 regulates cardiomyocyte differentiation by modulating TBX5, GATA4 and NKX2-5 transcription along with their targets. Collectively, our findings underscore the potential of IRX3 depletion in facilitating the molecular and functional development of human cardiomyocytes.

overall_design:
4 samples were analyzed, 2 control samples (Wt_D4) and 2 IRX3-depleted samples (KO_D4)
Total RNA extracted from hPSC commited to cardiomyocytes differentiation protocol in differentiation day 4 of development

first: Agatha

middle: R

last: Silva

first: Nikolas

last: Ferreira

first: Caio

middle: M

first: Iuri

last: Valadão

first: Iguaracy

last: de Sousa

first: Ester

last: Bertoldi

first: Vanessa

last: Lima

first: Lauro

middle: T

last: Turaca

first: Ana

last: Barbosa

first: Elida

last: Neri

first: José


title: Impaired redox adaptation through SLC38A5-dependent glutamine metabolism contributes to melatonin-mediated anoikis sensitivity and metastasis suppression in bone cancer

status: Public on Mar 26 2026

city: Taichung

first: Chih-Hsin

last: Tang

address: 91 Xueshi

country: Taiwan

institute: China Medical University

summary: Malignant bone cancer, including osteosarcoma and chondrosarcoma as popular subtypes, are aggressive neoplasms which arise from bone tissue and have lung metastasis. Tumor cells evade anoikis through reactive oxygen species (ROS)-mediated redox homeostasis, which modulates signaling cascades that promote proliferation, survival, and metastatic invasion into distant sites. Melatonin, synthesized primarily by the pineal gland, has been implicated in cancer prevention and therapy due to its inhibitory effects on bone cancer growth and progression. Little is known about the mechanisms underlying anoikis resistance in bone cancer cells or whether melatonin can therapeutically modulate this process. We demonstrated that glutamine metabolism is essential for bone cancer cells to maintain anoikis resistance. Melatonin treatment disrupted glutamine metabolism and altered redox homeostasis, as evidenced by increased ROS accumulation and reduced NADPH/NADP⁺ ratios under anchorage-independent conditions. Notably, solute carrier family 38 member 5 (SLC38A5), a glutamine transporter, was identified as a critical regulator of bone cancer progression, with higher SLC38A5 expression correlating with poorer clinical outcomes. Melatonin suppressed SLC38A5 expression and attenuated anoikis resistance through inhibition of the PI3K-Akt signaling pathway. Consistently, reduced SLC38A5 expression was associated with decreased lung metastasis in melatonin-treated groups in an orthotopic mouse model. Collectively, our findings reveal a previously unrecognized role of melatonin in modulating glutamine-dependent redox balance and anoikis resistance in bone cancer. This study highlights SLC38A5-mediated glutamine metabolism as a critical determinant of metastatic potential and supports melatonin and SLC38A5 as promising therapeutic targets for osteosarcoma and chondrosarcoma.

overall_design: JJ012 and 143B cells were cultured under suspension conditions and treated with melatonin (1 mM, 72 h) or left untreated as controls for RNA-seq analysis.

first: Bao-Tran

last: Nguyen


title: Syncytin-a deficiency compromises murine sperm function by suppressing PRL/PGE2 and PI3K/AKT/mTOR pathway

first: Honglian

last: Yu

address: No. 279, Zhouzhu Highway

institute: Shanghai University of Medicine and Health Sciences

summary: The human endogenous retrovirus W envelope protein syncytin-1 (syncytin-a in mus) can be involved in fetal development and tumorigenesis. The role of syncytin-1 in male infertility has not been identified. To explore the mechanisms of syncytin-1 in male infertility, the prostatic epithelial-specific syncytin-a knockout (syna CKO) mouse model was constructed. Firstly, male infertility, abnormal testicular seminiferous tubule, and prostate gland were discovered in syna CKO mice. Then, irregular sperm motility, morphology, and MMAF-associated gene expression (AKAP3, SPAG6) were detected in syna CKO mice. Increased PGE2 and PRL modulate the lipid metabolism of the testis in syna CKO mice. Syna CKO with inhibitor or activator treatment identified that syna knockout could inhibit the PI3K/AKT/mTOR pathway, Ca²⁺ levels, and elevate caspase 3 expression. Therefore, we propose a hypothesis that syna deficiency exacerbates testicular lipid accumulation and apoptosis by suppressing the PI3K/AKT/mTOR and Ca2+ pathway, ultimately leading to spermatogenic dysfunction and male infertility. The study initially included 3 WT and 3 KO samples. After quality control and exploratory analysis, one control sample (WT1) was identified as a biological outlier and excluded from the final differential expression analysis.

overall_design: We performed RNA-seq on mouse testes from WT and KO groups (n=3 per group).

first: Qianqian

last: Wang

first: Zhenwei

first: Zhenpeng

last: Li

first: Dongle

last: Liu

first: Xiaotong

last: Yan

first: Yan

last: Zhang

first: Ning

last: Chi

first: Qiang

last: Bian

first: Zhankui


title: Human Macrophages Encode Stimulus-Specific Information of Prior Exposures Through Trained Immunity

city: Philadelphia

first: Aoife

last: O'Farrell

address: 415 Curie Blvd

institute: University of Pennsylvania

summary: Trained immunity (a form of innate immune memory), defined in part by heightened responses to pathogen restimulation, can be generated by many different stimuli. However, both the quantitative differences in trained states generated by different stimuli and the downstream consequences of those differences remain unclear. Here, we used primary human monocyte-derived macrophages to demonstrate phenotypic and molecular stimulus specificity of trained immunity six days after initial exposure. Quantification of cytokine production with single-molecule RNA imaging demonstrated stimulus-specific patterns of response to restimulation, with trained cells showed stronger responses to secondary stimuli more similar to their initial stimulation. Differential licensing of inflammatory transcription factors was associated with encoding of specificities in chromatin six days after training, while memory of some, but not all, training stimuli is lost by eleven days post-training in vitro. Overall, our findings demonstrate that different training stimuli can impart specific memories which generate distinct training phenotypes.

overall_design: To assess whether different training stimuli generated distinct epigenetic changes, we assessed chromatin accessibility by ATACseq six days and eleven days after training with various stimuli in primary human monocyte-derived macrophages.

first: Jingxin

first: Arjun

last: Raj


title: PWWP-mutants of the transcriptional cofactor JASPer divert promoter and enhancer activities and suppress position effect variegation in Drosophila

city: Freiburg im Breisgau

first: Derek

last: Atkinson

address: Stübeweg 51

country: Germany

institute: Max Planck Institute for immunobiology and epigenetics

summary: Su(var) genes control heterochromatin establishment and maintenance in Drosophila melanogaster. Through a new Su(var) screen, we identified Su140 and Su113 as very strong Su(var) mutants that are epistatic over Su(var)3-9 in the In(1)wm4h PEV rearrangement. Both Su140 and Su113 encode point mutations in the PWWP domain of the transcriptional cofactor JASPer that has described functions in protecting gene activity in euchromatin. In JasperSu140/Su140 and JasperSu113/Su113 nuclear cycle (NC14) mutant embryos, heterochromatic marks (H3K9me2 and H3K9me3) are reduced, while activating histone modifications (H3K4me1 and H3K27ac) become enriched at heterochromatin. Whereas wild-type JASPer is enriched over H3K36me3-positive regions in gene bodies, JASPerSu140 is redistributed to regulatory elements in promoters and enhancers. JASPerSu140 directly binds and activates the white gene enhancer in NC14 embryos and JasperSu140/Su140 mutants induce a partial decompaction of the heterochromatin compartment containing the In(1)wm4h rearrangement. In addition, JasperSu140/Su140 and JasperSu113/su113 mutants also display elevated levels for 359bp (satellite) repeat transcripts at later stages of development. Together, these data define Jasper mutants as novel Su(var) genes and highlight the importance of maintaining the balance between euchromatic and heterochromatic domains for controlling position effect variegation.

overall_design: Expression profiling by high throughput sequencing at NC14 (st5) and St7-8 embryos

first: Thomas

last: Jenuwein


title: PWWP-mutants of the transcriptional cofactor JASPer divert promoter and enhancer activities and suppress position effect variegation in Drosophila [ChIP-Seq]

summary: Su(var) genes control heterochromatin establishment and maintenance in Drosophila melanogaster. Through a new Su(var) screen, we identified Su140 and Su113 as very strong Su(var) mutants that are epistatic over Su(var)3-9 in the In(1)wm4h PEV rearrangement. Both Su140 and Su113 encode point mutations in the PWWP domain of the transcriptional cofactor JASPer that has described functions in protecting gene activity in euchromatin. In JasperSu140/Su140 and JasperSu113/Su113 nuclear cycle (NC14) mutant embryos, heterochromatic marks (H3K9me2 and H3K9me3) are reduced, while activating histone modifications (H3K4me1 and H3K27ac) become enriched at heterochromatin. Whereas epitope-tagged wild-type JASPer accumulates over H3K36me3-positive regions in gene bodies, mutant JASPerSu140 is redistributed to cis-regulatory motifs (CRM) in promoters and enhancers. At genes, JASPerSu140 relocates to transcriptional start sites (TSS). Also, one third of developmentally regulated enhancers, including the white enhancer, show enrichment for JASPerSu140 and display elevated levels of eRNA in JasperSu140/Su140 NC14 embryos. In addition, JasperSu140/Su140 mutants induce a partial decompaction of the heterochromatin compartment containing the In(1)wm4h rearrangement and activate satellite repeat expression. Together, these data define Jasper mutants as novel Su(var) genes and highlight the importance of maintaining the balance between euchromatic and heterochromatic domains for controlling position effect variegation.

overall_design: Genome binding/occupancy profiling of JASPER protein by high throughput sequencing comparing Jasper::V5-3xFlag with JasperSu140::V5-3xFlag NC14 (st5) embryos

first: Karolina

last: Barucka


title: PWWP-mutants of the transcriptional cofactor JASPer divert promoter and enhancer activities and suppress position effect variegation in Drosophila [Cut & Tag]

overall_design: Genome binding/occupancy profiling of selected chromatin marks by high throughput sequencing comparing wildtype and JasperSu140 NC14 (st5) embryos


title: Comparative transcriptomic profiling of human 3D endometrial stromal organoids under distinct decidualization stimuli

status: Public on Mar 25 2026

city: Pitscataway

first: Shuo

last: Xiao

state: NJ

address: 170 Frelinghuysen Rd, Room 404

department: Pharmacology & Toxicology

institute: Rutgers University

summary: Endometrial stromal decidualization is a hormone-regulated process essential for establishing uterine receptivity and supporting embryo implantation. Three-dimensional (3D) endometrial organoid systems provide a physiologically relevant platform to study this process; however, how different stimulatory conditions influence decidualization responses in 3D culture remains incompletely characterized. In this study, we generated 3D human endometrial stromal organoids and subjected them to four experimental conditions: vehicle control, cyclic adenosine monophosphate (cAMP) stimulation, combined estrogen–progesterone–cAMP (EPC) treatment, and co-culture with in vitro–grown follicles derived from mouse ovary. Organoids were cultured for 6 days under each condition, followed by bulk RNA sequencing. Principal component analysis (PCA) revealed clear separation between control and stimulated groups, with cAMP, EPC, and follicle co-culture conditions showing distinct but partially overlapping transcriptional profiles. Differential gene expression analysis identified both shared and condition-specific transcriptional changes across the four treatments. Pathway-level analysis using gene set variation analysis (GSVA) further demonstrated common decidualization-associated biological processes alongside stimulus-specific functional responses. This dataset provides a comprehensive resource for investigating how distinct biochemical and paracrine stimuli regulate decidualization in 3D endometrial organoid systems. It enables comparative analysis of canonical cAMP-driven responses, hormone-mediated signaling, and follicle-derived paracrine effects on endometrial stromal decidualization.

overall_design: Human primary endometrial stromal cells were seeded into agarose-based 3D Petri Dish molds to generate Endo-organoids and cultured for 6 days under four conditions: vehicle control, cAMP alone (0.5 mM), EPC treatment consisting of estradiol (E2, 10 nM), progesterone (P4, 1 μM), and cAMP (0.5 mM), or co-culture with four in vitro–grown ovarian follicles in the presence of cAMP (0.5 mM). Endo-organoids collected after 6 days of treatment were subjected to bulk RNA sequencing analysis to compare shared and stimulus-specific transcriptomic responses under distinct decidualization-related conditions.

first: Shichao

first: Yubing

first: Jiyang

first: Tingjie

last: Zhan

first: Nataki

last: Douglas

first: Xiaoqin

last: Ye


title: Accelerated cerebromicrovascular senescence contributes to cognitive decline in a mouse model of paclitaxel (Taxol)-induced chemobrain [Spatial Transcriptomics]

city: Oklahoma City

first: Roland

last: Patai

state: Oklahoma

address: 975 NE 10th street

department: Department of Neurosurgery

institute: University of Oklahoma Health Campus

summary: Chemotherapy-induced cognitive impairment ("chemobrain") is a frequent side-effect in cancer survivors treated with paclitaxel (PTX). The mechanisms responsible for PTX-induced cognitive impairment remain obscure, and there are no effective treatments or prevention strategies. Here, we test the hypothesis that PTX induces endothelial senescence, which impairs microvascular function and contributes to the genesis of cognitive decline. We treated transgenic p16-3MR mice, which allows the detection and selective elimination of senescent cells, with PTX (5 mg/kg/day, 2 cycles; 5 days/cycle). PTX-treated and control mice were tested for spatial memory performance, neurovascular coupling (NVC) responses (whisker-stimulation-induced increases in cerebral blood flow), microvascular density, blood-brain barrier (BBB) permeability and the presence of senescent endothelial cells (by flow cytometry and single-cell transcriptomics) at 6 months post-treatment. PTX induced senescence in endothelial cells, which associated with microvascular rarefaction, NVC dysfunction, BBB disruption, neuroinflammation, and impaired performance on cognitive tasks. To establish a causal relationship between PTX-induced senescence and impaired microvascular functions, senescent cells were depleted from PTX-treated animals (at 3 months post-treatment) by genetic (ganciclovir) or pharmacological (treatment with the senolytic drug ABT263/Navitoclax) means. In PTX treated mice, both treatments effectively eliminated senescent endothelial cells, rescued endothelium-mediated NVC responses and BBB integrity, increased capillarization and improved cognitive performance. Our findings suggest that senolytic treatments can be a promising strategy for preventing chemotherapy-induced cognitive impairment.

overall_design: The authors performed spatial transcriptomics to assess the anatomical distribution of senescent cells in the brains of paclitaxel (PTX)-treated p16-3MR mice. Mice were treated with PTX or vehicle and, following a 6-month post-treatment period with or without senolytic interventions (GCV or ABT263), brains were collected and sectioned for spatially resolved transcriptomic analysis. Tissue sections were processed to capture whole-transcriptome mRNA expression while preserving histological context, enabling the mapping of senescence-associated gene expression (e.g., Cdkn2a) to specific brain regions. This approach allowed comparison of the spatial distribution and abundance of senescent cells across experimental groups, including cortex, white matter, and hippocampus.

first: Anna

last: Csiszar

first: Zoltan

last: Ungvari

first: Tripti

last: Gautam

first: Tamas

last: Kiss


title: Single-cell transcriptome profiling of hematopoietic stem and progenitor cells in mice

city: Chengdu

first: chen

last: li

address: Renmin South Road

institute: Sichuan Univercity

summary:
The regulatory dynamics of transcription start sites (TSS) within mouse bone marrow hematopoietic stem cells are not yet fully understood. To address this, our research employed 5' scRNA-seq to ensure thorough capture of TSS data, an outcome not readily achievable with conventional 3' scRNA-seq. This technique enables the precise characterization of the transcriptome for each respective stage of cellular differentiation [CITE-seq].
To complement our 5' CITE-seq data, we also generated a 3' single-cell RNA sequencing dataset. While 5' sequencing is optimal for TSS analysis, 3'-based scRNA-seq is a robust and widely-used method for defining cell states and quantifying gene expression. This dataset serves as a foundational reference, allowing for direct comparison with the vast majority of public scRNA-seq data and providing a benchmark for validating the cellular heterogeneity within our HSPC population [3scRNAseq].
To achieve a comprehensive understanding of the transcriptomic landscape, we employed single-cell Oxford Nanopore (scONT) sequencing. This long-read, full-length transcript sequencing approach overcomes the limitations of short-read methods, enabling the identification and quantification of distinct transcript isoforms. This dataset provides critical auxiliary validation for our findings from the 5' and 3' platforms and offers deeper insights into the role of alternative splicing and isoform usage during hematopoiesis [scONT].

overall_design: Lineage-negative (Lin⁻) hematopoietic stem and progenitor cells (HSPCs) from the bone marrow of C57BL/6J mice were isolated by magnetic-activated cell sorting (MACS) and analyzed using CITE-seq、3‘ scRNA-seq and scONT.

first: Zijie

last: Xu


title: Integrated Perturb-seq and Computational Modeling Identifies KAT6A-Menin-DOT1L Synergy and Associated Gene Program as Therapeutic Targets in Acute Myeloid Leukemia [Perturb-seq]

city: Birmingham

first: Changde

last: Cheng

state: Alabama

address: 1824 6th Ave S, WTI 510G

department: Department of Medicine - Hematology & Oncology

institute: The University of Alabama at Birmingham

summary:
Background:
Acute myeloid leukemia (AML) is a heterogeneous malignancy characterized by genetic and epigenetic dysregulation. Despite advances in targeted therapies against individual epigenetic regulators, clinical responses are often transient due to complex compensatory mechanisms. Identifying functional interactions between chromatin regulators and their associated transcriptional programs represents a promising strategy to overcome resistance and enhance therapeutic efficacy.

Results:
Using Perturb-seq combined with computational modeling and machine learning approaches, we systematically investigated 16 key epigenetic regulators across the Menin-MLL, Polycomb, and histone acetyltransferase complexes in MOLM-13 cells. Single-cell transcriptomic analysis of 31,015 cells revealed 17 distinct gene programs with differential impacts on AML pathogenesis. We identified strong synergy between KAT6A and the Menin-DOT1L axis in regulating oncogenic pathways, particularly gene program P-15 (Pro-Differentiation Program), which significantly correlates with favorable clinical outcomes in both TCGA and Beat-AML cohorts. Notably, P-15 showed high expression in NPM1-mutated AML and remission-stage patients but was suppressed in TP53-mutated cases with poor prognosis. Validating our computational predictions, dual inhibition of Menin (VTP-50469) and KAT6A (WM119, a preclinical compound) demonstrated significant therapeutic synergy in MOLM-13 cells, reducing the IC50 from 35nM to 12nM. Conversely, PCGF1 disruption conferred resistance to DOT1L inhibition, revealing a novel mechanism of therapeutic resistance. Bulk RNA-seq analysis of combination treatments confirmed that dual KAT6A-Menin inhibition uniquely modulates specific gene modules associated with myeloid differentiation.

Conclusions:
Our integrated experimental-computational approach, distinct from prior studies examining individual epigenetic regulators in isolation, identifies the KAT6A-Menin-DOT1L axis as a critical regulator of AML transcriptional programs in MLL-rearranged leukemia and reveals gene program P-15 as both a favorable prognostic biomarker and potential therapeutic target. These findings provide mechanistic insights into epigenetic regulation in AML and establish a framework for developing rational combination therapies targeting cooperative epigenetic dependencies while preventing compensatory resistance mechanisms.

overall_design: Perturb seq against 16 AML target genes.

first: Sajesan

last: Aryal

first: Rui

last: Lu


title: Impact of ATEVs on transcriptional profile of pancreatic tumor tissues derived from a poorly immunogenic pancreatic cancer cell clone

status: Public on Mar 24 2026

city: Columbus

first: Mengying

last: Hu

state: Ohio

address: 496 W 12th Ave

department: Pharmaceutics and Pharmacology

institute: The Ohio State University

summary: Antigen processing and presentation (APP) is essential for adaptive immunosurveillance. We uncover a mechanism whereby activated T cell-derived extracellular vesicles (ATEVs) drive a positive feedback loop that enhances antigen presentation and immune responses in normal physiology and cancer. ATEV-induced immunogenicity relies on extracellular vesicular double-stranded DNA (EVDNA), which is notably abundant and primarily composed of genomic DNA enriched in immune-related genes, including those encoding APP machinery. Mechanistically, granzyme B (Gzmb) packaged by ATEVs disrupts the nuclear envelope of recipient cells, facilitating intranuclear transfer and subsequent transient expression of EVDNA encoding APP genes. DNase treatment removes most AT-EVDNA, abrogating APP upregulation and thus T cell activation and recruitment to tumors. Notably, ATEVs hold promise as an acellular immunotherapy, restoring APP and synergizing with checkpoint blockade in immunotherapy-refractory tumors. Collectively, our findings uncover a mechanism of transient, non-viral gene delivery by ATEVs which boosts APP and anti-tumor immunity while limiting autoimmunity.

overall_design: Bulk RNAseq profiling of pancreatic tumor tissues derived from an immunogenic pancreatic cancer cell clone (KrasLSL-G12D/+; Trp53LSL-R172H/+; Pdx1-Cre; Rosa26YFP/YFP), after intratumoral injections with PBS or ATEVs in vivo


title: Robust generation of distal respiratory airway organoids by an engineered cuboid chip to therapy chronic obstructive pulmonary disease

city: Guangzhou

first: Yin

middle: Jia

last: Xiang

address: Building B, Guangzhou Laboratory, No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou 510005, Guangdong Province, China

institute: Guangzhou Laboratory

summary: Background Human distal respiratory airway (DRA) cells are located in the smallest conducting airways of the human lung, specifically in the terminal and respiratory bronchioles, and represent a newly discovered cell type. Due to their absence in mice and the limited existing research on these cells, there is an urgent need to establish an in vitro model of human distal respiratory airways to study the role of such cells in respiratory diseases. Results Here, we developed a robust differentiation protocol to derive DRA organoids (DRAOs) from human pluripotent stem cells (hPSCs) and investigated their role in the treatment of chronic obstructive pulmonary disease (COPD). We engineered a cuboid chip-based culture platform, where seeding single-cell suspensions mixed with Matrigel onto the chip increased lung progenitor cell (LPC) spheroid yield by 7.5-fold and upregulated NKX2.1 expression nearly 300-fold. Single-cell transcriptomic analysis further demonstrated that the platform enhanced distal lung-related gene expression. Prolonged culture of LPC spheroids yielded expandable hollow lung organoids. The resulting cells exhibited protein and molecular profiles closely resembling native human DRA cells, with over 70% co-expressing SFTPB and SCGB3A2. Using this method, we demonstrate accelerated production of DRAOs with significantly enhanced structural and functional maturity in 30 days. Furthermore, these DRAOs retain the potential to undergo alveolar differentiation. By exposing these organoids to cigarette smoke extract (CSE), we established a COPD-like model. In addition, DRAOs can survive in COPD mice, repair alveolar structural damage, and alleviate COPD symptoms. Conclusions Our method will facilitate increasingly widespread culture and differentiation of organoids, paving the way for constructing more accurate models of complex organs that mimic in vivo structures and functions. Furthermore, the favorable applicability of DRAOs in cell therapy studies using a mouse model of COPD-related alveolar injury provides critical insights for cell therapy in respiratory diseases.

overall_design: scRNA-seq revealed that the cuboid chip facilitates the generation of distal-LPCs. scRNA-seq revealed that the major cell population within the organoids was lung epithelial cells scRNA-seq revealed that these cells can be classified into 8 distinct populations.

first: Jiaxiang

last: Yin

first: Zirong

last: Bi

first: Tiankai

last: Dai

first: Hao

last: Meng

first: Jiaqi

last: Sun

first: Tao

first: Huisheng

last: Liu


title: Rejuvenation of the Aged Cerebrovascular System via Protein Corona–Guided Fusogenic Liposome Delivery

first: Roland

last: Patai

summary: Brain vascular aging is increasingly recognized as a critical therapeutic target for age-related cognitive decline. Oxidative stress, bioenergetic dysfunction, and molecular damage play central roles in the progression of vascular aging, contributing to cerebrovascular dysfunction and impaired cognitive function. While naturally occurring polyphenols such as resveratrol (RSV) have demonstrated potential in mitigating aging-related pathologies, their poor bioavailability and limited brain targeting efficiency significantly constrain their therapeutic impact. As a result, high doses or advanced drug delivery strategies are necessary to achieve meaningful physiological effects. We introduce a novel nanocarrier system designed to enhance RSV delivery to the cerebral endothelium by leveraging the natural formation of an apolipoprotein E (ApoE)-enriched protein corona around fusogenic liposomes (FL) in vivo. These nanoparticles directly fuse with cytoplasmic cell membranes and thus evade endocytosis. We found that once in the circulation FL spontaneously acquire a protein corona, which is highly enriched in ApoE, a key ligand for brain endothelial low-density lipoprotein receptors (LDLR). Based on this observation, we engineered an ApoE-functionalized protein corona around FL (ApoE-FL) to systematically evaluate whether this mechanism could be exploited for targeted brain delivery. Following optimization and physicochemical characterization, the RSV-loaded liposomes were evaluated in vitro using human cerebral microvascular endothelial cells and in vivo C57BL/6 aged mice to assess their therapeutic potential. Both FL and engineered ApoE-FL liposomal delivery systems exhibited a strong affinity for endothelial cell membranes in vitro. The knockdown of the ApoE receptor, low-density lipoprotein receptor-related protein 1 (LRP1), significantly reduced liposomal docking. Microscopy analysis revealed that both ApoE-FL and non-functionalized FL directly fused with endothelial plasma membranes, thus bypassing intracellular organelles and minimizing lysosomal degradation. This suggests that the naturally formed ApoE corona in vivo may contribute to efficient cerebrovascular targeting, a property successfully replicated by the engineered ApoE corona strategy. In vivo biodistribution and kinetic studies demonstrated that especially ApoE-FL achieved enhanced brain-targeting efficiency, prolonged cerebrovascular retention, and extended targeting distance along the arteriovenous axis. This emphasizes that fusogenic liposomes effectively engage almost the entire microvascular network, including capillaries and post-capillary venules. Functionally, fusogenic liposome-delivered RSV improved blood-brain barrier (BBB) integrity, enhanced neurovascular coupling (NVC) responses, and promoted brain vascularization in aged mice. Single-cell RNA sequencing (scRNA-seq) revealed enhanced endothelial angiogenesis and barrier protective transcriptional profiles in cerebrovascular cells treated with ApoE-FL/RSV, suggesting a molecular basis for the observed vascular benefits. Liposomal RSV delivery achieved near-complete cerebrovascular and cognitive rejuvenation in aged mice applying a 2000-fold lower RSV dose than oral administration used as control sample. Thus, ApoE-FL liposomes exhibited exceptionally high delivery efficiency in deeper brain regions, further expanding their therapeutic potential. These findings underscore the importance of targeted drug delivery in optimizing therapeutic outcomes and establish ApoE-functionalized fusogenic liposomes as a promising strategy for mitigating brain vascular aging and cognitive decline.

overall_design: The authors used single-cell RNA sequencing to characterize cerebrovascular cell populations and transcriptional changes associated with aging and treatment. Brains were collected after PBS perfusion from young and aged mice (n =4-5 per group), dissociated into single-cell suspensions, cleared of debris, and enriched for viable cells using low-pressure FACS following SYTOX Green live/dead staining. The resulting cells were processed using the 10x Genomics Chromium Single Cell 3′ platform, with libraries prepared using the Next GEM 3′ Gene Expression v3 kit and sequenced on an Illumina NovaSeq 6000. Downstream analysis included clustering to identify major cell types such as endothelial cells, pericytes, and glial populations, followed by comparative analyses across experimental groups (young, aged, and liposome-treated conditions). The design incorporated differential cell abundance, gene ontology enrichment, and cell–cell interaction/network analyses to evaluate pathways related to angiogenesis, blood–brain barrier integrity, inflammation, and cellular senescence, thereby linking transcriptional changes, particularly in endothelial cells, to functional vascular outcomes.

first: Anna

last: Csiszar

first: Agnes

first: Tae-Gyu

last: Oh

first: Jenny

last: Gipson

first: Makayla

last: Foster


title: Facultative predation expands the ecological repertoire of Streptomyces

city: Turku

first: Mikko

last: Metsä-Ketelä

address: Tykistökatu 6A

department: Department of Life Technologies

country: Finland

institute: University of Turku

summary: Soil is a rich environment for microbes, where they compete for space and resources. Streptomyces bacteria are well-known for their ability to synthesize natural products, particularly antibiotics, that are used in chemical defense against competing microbes. Here we show that Streptomyces are, in fact, predatory bacteria. Upon encountering yeast cells, Streptomyces initiate the production of numerous enzymes that digest the cell wall and cell membrane. In addition, the interaction triggers the production of natural products that destabilize the yeast cell membrane. Collectively these actions lead to the death of yeast cells and release of cellular building blocks that Streptomyces can use as nutrients. The work fundamentally shifts the paradigm of how Streptomyces are perceived within the soil microbiome ecosystem.

sample_organism:
Streptomyces lavendulae
Saccharomyces cerevisiae

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Streptomyces lavendulae cells and Saccharomyces cerevisiae cells between axenic and co-cultures.

first: Keith

last: Yamada

first: Arina

last: Koroleva

first: Heli

last: Tirkkonen

first: Vilja

last: Siitonen

first: Mitchell

last: Laughlin

first: Amanda

last: Moglia

first: Soheila

last: Matroodi

first: Amir

last: Akhgari

first: Guillaume

last: Mazurier

first: Jarmo

last: Niemi


title: DGAT1 Drives Racially Divergent Fibroblast Activation via ERK1/2-Dependent Tumorigenic Signaling in Prostate Cancer

city: Shreveport

first: Omar

last: E. Franco

state: LA

address: 1501 Kings Hwy

department: Biochemistry and Molecular Biology

institute: LSU Health Shreveport

summary: Lethal prostate cancer (PCa) disproportionately affects African American (AA) men, who experience a higher incidence and earlier onset compared to Caucasian (Cau) men, reflecting a persistent biological and clinical disparity. Recent studies have implicated raceassociated differences in lipid metabolic reprogramming as key contributors to this disparity. We recently identified carcinoma-associated fibroblasts (CAFs) as a major stromal component that mediates racial disparities in tumor progression. Here, we demonstrate that lipid-laden CAF from AA patients (AACAF) display enhanced protumorigenic properties compared with CAFs from Cau patients (CauCAF). Lipid droplet (LD) biogenesis and storage analysis revealed a robust diacylglycerol O-acyltransferase 1 (DGAT1) enzyme-dependent LD accumulation in AACAF . Ectopic DGAT1 expression in benign fibroblasts induced canonical CAF markers (FAP1 and ⍺SMA) expression linked to fibroblast activation, altered the secretome, and significantly enhanced PCa cells’ growth in vivo. Integrative transcriptomic and secretome analyses identified novel DGAT1- regulated genes involved in CAF linked to metabolism, cell–cell communication, motility, and angiogenesis, mediated mainly through ERK1/2 signaling activation. Pharmacological DGAT1 inhibition suppressed these pathways and elicited racially distinct regulation of tumor-promoting mediators, including BDNF, VEGF, and TSP1. Mechanistic experiments show that functionally, lipid-laden CAF from AA patients exhibit increased fibroblast activation and a secretory phenotype with greater pro-tumor activity compared to CAF from Cau patients. Collectively, these findings reveal that DGAT1 is a pivotal enzymatic regulator of fibroblast activation and lipid-driven remodeling in the PCa tumor microenvironment (TME) of AA men. Targeting DGAT1 represents a promising strategy for disrupting metabolic-stromal crosstalk to mitigate race-associated disparities in PCa progression.

overall_design: RNA-Seq profiling of BHPrS1-WT and DGAT1 overexpressing BHPrS1 cells after three days of culture.

first: Sathyavathi

last: ChallaSivaKanaka

first: Mamatha

last: Kakarla

first: Renee

last: E. Vickman

first: Yana

last: Filipovich

first: Philip

last: Fitchev

first: Md Maksudul

last: Alam

first: Md Niaz

last: Morshed

first: Pooja

last: Talaty

first: Brian

last: T. Helfan

first: David

last: Price

first: Simon

last: W. Hayward

first: Susan

last: E Crawford

last: E Franco


title: Hypoxic regulation of chromatin and gene transcription [ChIP-Seq]

city: Oxford

middle: Robert

last: Mole

address: Roosevelt Drive, Headington

department: Nuffield Department of Medicine

country: United Kingdom

institute: University of Oxford

summary: Pan-genomic analysis of normoxic and hypoxic histone trimethylation by ChIP-seq in cancer cell lines using a Drosophila spike-in normalisation control.

overall_design: Genome-wide assays of histone trimethylation in PC3 and HCT-116 in normoxia and 0.5% hypoxia for 16 hours using a Drosophila spike-in normalisation control

first: Jessica

last: Kindrick


title: Aortic carboxypeptidase-like protein potentiates β1 integrin signaling in mesenchymal progenitors (10T1/2 fibroblasts)

city: Boston

first: Cheyanne

last: Frosti

address: 72 E. Concord Street

institute: Boston University

summary: Fibrosis is a pathological process characterized by persistent fibroblast activation and excessive extracellular matrix (ECM) accumulation. Aortic carboxypeptidase-like protein (ACLP), an ECM-associated protein that binds fibrillar collagen, is upregulated in fibrotic tissues and promotes fibroblast differentiation through canonical TGFβ receptor I signaling. We hypothesized that when presented within the collagen matrix, ACLP engages mechanically driven signaling pathway that contribute to fibroblast activation. Here, we identified a previously unrecognized mechanism through which collagen-bound ACLP activates fibroblasts via β1 integrin-mediated signaling. Collagen-bound ACLP induced rapid fibroblast spreading, increased β1 integrin activation, and promoted focal adhesion maturation. These early adhesion events were followed by elevated activation of the GTPases RhoA and Rac1, with enhanced F-actin assembly and nuclear accumulation of myocardin-related transcription factor A (MRTFA), a key regulator of activated fibroblast gene expression. Transcriptomic profiling revealed enrichment of focal adhesion, ECM–receptor interaction, and actin cytoskeletal gene pathways in response to collagen-bound ACLP. These findings establish collagen-bound ACLP as an ECM-derived cue that links matrix composition to fibroblast activation pathways.

overall_design: RNA-seq profiling of C3H10T1/2 cells cultured for 18 hours on col1, col1-ACLP, or col1-ACLP + SB hydrogels.

first: Diana

last: Yeritsyan

first: Matthew

last: Layne


title: Hypoxic regulation of chromatin and gene transcription

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

overall_design: Refer to individual Series


title: Addressing transcriptomic assay heterogeneity for predictive modeling in cancer (NanoString)

city: Aurora

first: Benjamin

last: Bitler

address: CU Anschutz Research Complex II  12700 East 19th Avenue  3400D

institute: University of Colorado-Anschutz

summary: The goal of this study was to evaluate how best to preprocess RNA-seq and NanoString data to, if possible, combine these data for larger cohort sizes in predictive modeling of clinical features. High-grade serous Ovarian Cancer is a highly heterogeneous disease with most data split into Microarray, NanoString, and RNA-seq. NanoString and RNA-seq showed the greatest similarities in dynamic range across these datasets. Therefore, we performed bulk RNA-seq and NanoString (PanCancer IO360 panel) on sequential samples of 26 patients to evaluate how comparable gene expression patterns were captured and if preprocessing steps could improve this. In the preprocessing steps for RNA-seq, we considered counting over genes or exons to which NanoString probes mapped.

overall_design:
26 sequential FFPE samples from patients with HGSOC had RNA extraction and quantification with either bulk RNA-sequencing (Tempus xR, separate GEO) or NanoString (here) for downstream comparison. Tumor samples from interval debulking surgery following neoadjuvant chemotherapy (NACT). Sample number in title refers to the sample number and is shared between the RNA-seq and NanoString data.
The sample number (in the sample titles) is based on the patient (which is shared between RNA-seq and NanoString) and the X (in 'Nano_X' indicated in the sample description field) is based on the NanoString sequencing number

first: Hope

last: Townsend

first: Robin

last: Dowell

first: Aaron

last: Clauset


title: Tape strips capture immune and epidermal hyperplasia markers in the major orphan ichthyoses

city: New York

first: Madeline

last: Kim

address: 1 Gustave Levy Place

institute: Icahn School of Medicine at Mount Sinai

summary: This pilot study examined gene expression in tape strip samples obtained from 9 patients with Netherton Syndrome (NS), 6 patients with congenital ichthyosiform erythroderma (CIE), 7 patients with lamellar ichthyosis (LI), and 5 patients with epidermolytic ichthyosis (EI), as well as from 18 demographically matched healthy controls. Differential expression was defined with |fold-change/FCH|>2 and false discovery rate/FDR<0.05. All subtypes shared significant Th17/Th22 upregulation, and Th2 products were particularly increased in NS. Tape strips additionally captured common increases in Th1 and IL4R upregulation in NS, LI, and EI. Epidermal differentiation complex/cornified envelope (EDC-CE) genes were increased in all or most subtypes. Changes in immune and EDC-CE tape-strip markers correlated significantly and positively with those measured in biopsies.

first: Meredith

last: Manson

first: Ying

last: Liu

first: Stephanie

last: Rangel

first: Nihal

last: Kaplan

first: Lydia

last: Rabbaa Kabbaz

first: Keith

last: Choate

first: Swaroop

last: Bose

first: Ragasruti

last: Metukuru

first: Xinyi

last: Lin

first: Joseph

last: Largen

first: Manali

last: Shah

first: Yeriel

last: Estrada

first: Amy

middle: S

last: Paller

first: Emma

last: Guttman-Yassky


title: Hypoxic regulation of chromatin and gene transcription [RNA-seq]

first: David

last: Mole

summary: Pan-genomic analysis of poly-adenylated transcript levels in normoxic and hypoxic cancer cell lines

overall_design: PolyA RNA-seq analysis of gene expression in PC3 and HCT-116 incubated in 21% oxygen and 0.5% oxygen for 16 hours

first: Jessica

last: Kindrick


title: Structural and functional characterization of  Mycobacterium tuberculosis VapBC52 (Rv2514c-Rv2515c) toxin-antitoxin system reveals role in bacterial physiology and phage defence.

city: Bangalore

first: Munmun

last: Bhasin

state: Karnataka

address: CV Raman Rd

department: Molecular Biophysics Unit

country: India

institute: Indian Institute of Science

summary: Using Total RNA sequencing, We report the effects of VapC52 overexpression on the transcriptome of M. tuberculosis. For RNA-seq experiments, early-log phase cultures (OD600nm ~ 0.2-0.3) of M. tuberculosis strains lacking vapBC52 locus that harbors either pTetRint or pTetRint-vapC52  were induced with the addition of 50 ng/ml Atc for 24 h. For total RNA isolation, induced cultures were harvested by centrifugation, washed twice with 1x PBS and lysed by bead beating in Trizol. Total RNA was extracted by phenol-chloroform, precipitated with isopropanol and eluted using Qiagen RNA isolation kit as per manufacturer’s instructions. We report that VapC52 resulted in increased transcripts levels of proteins involved in cell wall and cell processes, several transfer RNA (tRNA)  were also observed to be markedly decreased in the overexpression strain of M. tuberculosis.

overall_design: VapBC52 deletion mutant of M. tuberculosis harbouring pTetRint (Vector only) or pTetRint VapC52 were used for RNA-Seq analysis. Experiments were performed thrice for each strain.

first: Manisha

last: Singh

first: Charandeep

first: Akshay

middle: V

last: Nair

first: Imran

last: Ahmad

first: Arun

last: Sharma

first: Vikas

last: Jain

first: Raghavan

last: Vardarajan

first: Ramandeep

first: Krishan Gopal

last: Thakur


title: Hypoxic regulation of chromatin and gene transcription [ChIP-seq]


title: Comparative single cell genomics of facial signaling centers of avian and murine embryos [ME11_scRNA]

city: Plön

first: Stella

last: Kyomen

address: August-Thienemann-Strasse 2

institute: Max Planck Institute for Evolutionary Biology

summary: Morphogens are crucial in craniofacial development, directing cellular processes that shape facial features in vertebrates. In this study, we used single-cell RNA and ATAC sequencing to investigate the genomic regulation underlying species-specific morphogen expression in mouse and chicken embryos. We identified unique expression patterns of morphogens and receptors across facial prominences in both species and predicted cellular communication between cell populations involved in facial development. Our analysis revealed highly specific morphogen expression, predominantly originating from spatially segregated regions known as signaling centers. By examining the chromatin landscape, we uncovered species-specific regulatory elements and accessibility patterns that control gene expression and facial morphogenesis. We validated candidate enhancers in vivo, demonstrating that their activity correlates with the expression of morphogen ligands in the embryonic face. This study underscores the complex and species-specific regulation of facial morphogenesis, offering insights for comparative genomics across vertebrates with distinct facial morphologies.

overall_design: Single-cell RNA-seq of facial prominences from wild type mouse embryos (embryonic stage E11.5).

first: Louk

last: Seton


title: Comparative single cell genomics of facial signaling centers of avian and murine embryos [ME11_scATAC-seq]

overall_design: Single-cell ATAC-seq of facial prominences from wild type mouse embryos (embryonic stage E11.5).


title: Single-cell RNA sequencing of human forebrain organoids from typical and autism subjects

city: Singapore

first: Jinyue

last: Liu

address: 60 Biopolis Street

institute: Genome Institute of Singapore

summary: The goal of this experiment is to define cellular phenotypes in human brain organoid models of autism.

overall_design: Human forebrain organoids were cultured with minor modifications using a published protocol (Qian et al. 2016), harvested at 8-weeks, dissociated and processed for single-cell RNA sequencing as per manufacturer's recommendations (10x genomics).

first: Li

last: Lin

first: Wan

last: Chock


title: Comparative single cell genomics of facial signaling centers of avian and murine embryos [HH22_scRNA-seq]

overall_design: Single-cell RNA-seq of facial prominences from wild type chicken embryos (embryonic stage HH22).


title: Cell size-dependent mRNA transcription drives proteome remodeling [SLAM-seq]

city: Stanford

first: Dong Shin

last: You

address: 327 Campus Drive

institute: Stanford University

summary: Increasing cell size drives proteomic changes that impact cell physiology. However, the molecular basis of size-dependent proteome remodeling has remained unclear. Here, we develop an inducible Cyclin D1 expression system in human cells to generate proliferating cells spanning over a two-fold size range. We use this system to make comprehensive genome-wide measurements of mRNA and protein concentrations and stability. We find that protein and mRNA turnover rates are weakly related to cell size, but that mRNA concentrations are strongly size-dependent. This establishes that transcriptional regulation is the basis of proteome remodeling. Live-cell imaging of nascent mRNAs using the MS2 system is used to measure how transcriptional dynamics change with cell size. Larger cells prolong transcriptional bursts and shorten inactive periods between bursts but maintain similar burst amplitudes to achieve transcriptional scaling. Together, our results show how transcription is modulated by cell size to remodel the proteome and alter cell physiology.

overall_design: SLAM-seq profiling of CCND1 overexpression or knockdown hTERT-RPE-1 lines with  induction by doxycycline at day 4. Cells are pulsed with 10uM thiouridine at day 4 for 24 hours, with the media refreshed every 3 hours. Chase is started by washing twice with PBS and applying growth media with 1mM uridine. Negative control of unlabelled samples are also provided. Note that time points are not uniform across replicates and samples as only high quality datasets were selected for downstream analysis and upload

first: Christopher

middle: H

last: Bohrer

first: Purva

last: Rumde

first: Ioannis

last: Sanidas

first: Matthew

last: Swaffer

first: Daniel

last: Larson

first: Josh

middle: E

last: Elias

first: Michael

middle: C

last: Lanz

first: Jan

last: Skotheim


title: Single-cell and spatial transcriptomic analyses of gene therapy-associated retinal inflammation in non-human primates

first: Kanmin

last: Xue

address: Nuffield Department of Clinical Neurosciences, Level 6, West Wing, John Radcliffe Hospital

summary: Adeno-associated viral (AAV) vectors are rapidly advancing as gene therapies for inherited and common retinal disorders, but gene therapy-associated uveitis (GTAU) limits their broader application. To investigate the primate ocular immune response, we administered subretinal AAV gene therapy to two non-human primates (NHPs): NHP1 received AAV2-CAG-hRPE65 (voretigene neparvovec) bilaterally at clinical dose; NHP2 received AAV8-GRK1-hRPGRco alongside an analogous mScarlet reporter vector in separate blebs. Longitudinal assessments over three months included multimodal imaging, electroretinography and cytokine profiling, followed by immunohistological, single-cell and spatial transcriptomic analyses of retinal punches. Both therapies were well-tolerated, with preserved retinal structure and function. Single-cell RNA-sequencing revealed that the AAV8 vector transduced 80% of cones/rods in treated areas, while AAV2 targeted 30% of retinal pigment epithelium (RPE)/rods. Transgene expression did not correlate with apoptotic markers. Persistent immune infiltration (dominated by myeloid and T cells) suggested a type 1 cell-mediated response. Adjunctive intravitreal anti-TNFα (adalimumab) did not appear to mitigate this anti-viral response. Spatial analysis highlighted microglia migration to the subretinal space, consistent with upregulated cytokines (MCP-1/CCL2, IP-10/CXCL10, IL-8/CXCL8, IL-6), which implicate monocytic phagocytes in driving local inflammation. These findings elucidate the mechanism of GTAU and identify potential therapeutic targets to prevent immune-mediated complications in retinal gene therapy.

overall_design: NHPs received subretinal injections of AAV vectors as follows: NHP1 AAV2-CAG-hRPE65 in both eyes; NHP2 AAV8-GRK1-mScarlet AND AAV8-GRK1-hRPGR in two separate blebs per eye. Retinal biopsies were taken from injected blebs, as well as an uninjected control area.

first: Célia

last: Sourd

first: Joel

last: Quinn

first: Molly

last: John

first: Cristina

last: Martinez-Fernandez de la Camara

first: Lakshanie

last: Wickramasinghe

first: Moustafa

last: Attar

first: Hoda

last: Shamsnajafabadi

first: Ahmed

last: Salman

first: Sally

middle: A

last: Cowley

first: Calliope

last: Dendrou

first: Robert

last: MacLaren

first: Jasmina

last: Cehajic-Kapetanovic


title: Single-cell and spatial transcriptomic analyses of gene therapy-associated retinal inflammation in non-human primates [scRNA-seq]


title: Comparative single cell genomics of facial signaling centers of avian and murine embryos [HH22_scATAC-seq]

first: Stella

last: Kyomen

overall_design: Single-cell ATAC-seq of facial prominences from wild type chicken embryos (embryonic stage HH22).

first: Louk

last: Seton


title: Evidence for coordinate epigenomic roles for CTCF and histone H3.3 in K27M diffuse midline gliomas

city: Sacramento

first: Paul

last: Knoepfler

state: CA

address: 2425 Stockton Blvd, Room 633

department: Cell Biology and Human Anatomy

institute: University of California Davis

summary: In this study we identified and characterized key chromatin domains in diffuse midline glioma cells, looking at well known types of domains including super enhancers, bivalent domains, and H3K4me3 broad domains as well as the chromatin states identified by chromHMM. In this context, we identified a key role for CTCF in maintaining H3K27me3 levels at bivalent domains, and demonstrated that the H3.3K27M mutation affects both CTCF localization and H3K27me3 at these regions. We further characterized a functional interaction between H3.3 and CTCF in diffuse midline glioma cells, finding that the H3.3K27M mutation affects CTCF localization, leading to an expansion of CTCF-bound domains including a large number of ectopic CTCF binding sites found in H3.3K27M but not WT cells. We also found that CTCF knockdown increases cell viability in H3.3K27M cells, and affected the expression of a set of genes highly enriched in active chromatin states and likely important for some of the oncogenic properties of these cells. Together, our results identified complex chromatin domains defined by combinations of epigenetic modifications, which may have implications for designing therapy regimens that include multiple epigenetic drugs to more effectively target the numerous changes in chromatin observed in glioma cells with H3.3K27M. We also defined an important role for the structural protein and transcription factor CTCF in influencing the epigenetic landscape and transcriptome in the context of the H3.3K27M mutation in diffuse midline glioma cells.

overall_design: RNA-seq was performed in duplicate in DIPG XIII cells with CTCF knockdown or scramble control transfection

first: Rachel

last: Klein


title: Evidence for coordinate epigenomic roles for CTCF and histone H3.3 in K27M diffuse midline gliomas [CUT&RUN]

overall_design: To determine CTCF localization and the effect of the H3.3K27M muation on CTCF localizaion in DIPG cells, CTCF Cut&Run was performed in duplicate in DIPG XIII cells that were either WT for histone H3.3 or contained the H3.3K27M mutation. To determine the effect of loss of CTCF on histone H3.3 and histone modification H3K27me3, Cut&Run was performed in duplicate for both total H3.3 and H3K27me3 after CTCF knockdown and compared to Cut&Run for total H3.3 or H3K27me3 in cells treated with a scramble control siRNA.


title: bulk RNA sequencing of human forebrain organoids from typical and autism subjects

first: Jinyue

last: Liu

overall_design: Human forebrain organoids were cultured with minor modifications using a published protocol (Qian et al. 2016), harvested at 33 days, and processed for bulk RNAseq.

first: Li

last: Lin

first: Wan

last: Chock