title: Metabolic adaptations direct cell fate during tissue regeneration [crypts RNA-seq]

status: Public on Apr 10 2025

city: New York

first: Yu-Jui

last: Ho

state: New York

address: 417 E 68th St

department: Cancer Biology & Genetics Program

institute: Memorial Sloan Kettering Cancer Center

summary: Although cell fate specification is generally attributed to transcriptional regulation, emerging data also indicate a role for molecules linked with intermediary metabolism. For example, α-ketoglutarate (αKG), which fuels energy production and biosynthetic pathways in the tricarboxylic acid (TCA) cycle, is also a co-factor for chromatin-modifying enzymes1-3. Nevertheless, whether TCA cycle metabolites regulate cell fate during tissue homeostasis and regeneration remains unexplored. In the intestine, we discovered unexpectedly heterogeneous expression of TCA cycle enzymes, with αKG dehydrogenase complex components4-6 upregulated in the absorptive lineage and downregulated in the secretory lineage. Using genetically modified mouse models and organoids, we demonstrated a dual, lineage-specific role for 2-oxoglutarate dehydrogenase (OGDH), the enzymatic subunit of αKG dehydrogenase complex. In the absorptive lineage, OGDH is upregulated by Hnf4 transcription factors to maintain the bioenergetic and biosynthetic needs of enterocytes. In the secretory lineage, OGDH is downregulated through a process that, when modeled, increases αKG levels and stimulates secretory cell differentiation. Consistent with this, in murine colitis models with impaired secretory cell number and maturation, OGDH inhibition or αKG supplementation reversed these impairments and promoted tissue healing. Hence, OGDH dependency is lineage-specific, and its regulation helps direct cell fate, offering insights for targeted therapies in regenerative medicine.

overall_design: RNA sequencing of murine isolated crypts from C57Bl/6 mice, treated or not with 500 mg/Kg of 2DG

first: Almudena

last: Chaves-Perez

first: Scott

last: Millman

first: Sudha

last: Janaki-Raman

first: Clemens

last: Hinterleitner

first: Valentin

last: A. Barthet

first: John

last: Morris IV

first: Francisco

last: Barriga

first: Jose

last: Reyes

first: Aye

last: Kyaw

first: H. Amalia

last: Pasolli

first: Dana

last: Pe’er

first: Craig

last: Thompson

first: Lydia

last: S. Finley

first: Justin

middle: R

last: Cross

last: Lowe


title: Single-cell Transcriptional Analysis Reveals Allergen-specific Signatures in Human γδT Cells

city: La Jolla

first: Kendall

last: Kearns

state: CA

address: 9420 Athena Cir

country: USA

institute: La Jolla Institute for Immunology

type: Expression profiling by high throughput sequencing

summary: The role of gamma-delta T (γδT) cells in immune responses to common allergens is poorly understood. Here, we utilized single-cell (sc) transcriptomic analysis of allergen-reactive γδT cells in humans to characterize the transcriptional landscapes and TCR repertoires in response to cockroach (CR) and mouse (MO) allergens. Using a novel Activation-Induced Marker (AIM) assay that allows detection of γδT cells combined with scRNA sequencing and TCR repertoire analysis, we identified both shared and allergen-specific γδT cell activation patterns and gene expression profiles. While CR extract activated both Vδ1 and Vδ2 subsets, MO extract primarily stimulated Vδ2 cells. Our analysis revealed allergen-specific clusters with distinct functional signatures, including enhanced inflammatory responses and cytotoxic effector functions in MO-specific γδT cells and natural killer cell-mediated immunity and IFNγ signaling in CR-specific populations. Comparison of allergic and non-allergic individuals highlighted differences in gene expression and TCR repertoires, including a higher IFNG expression in the CR-allergic compared to non-allergic cohorts, suggesting that phenotypic and functional differences are associated with γδT allergen responses. This study provides insights into the cellular and molecular heterogeneity and functionality of allergen-reactive γδT cells, offering a foundation for understanding their role in allergic diseases and potential therapeutic interventions.

overall_design: PBMCs were isolated from 53 donors, of which 37 were sensitized to either mouse (MO, n=17) or cockroach (CR, n=20), 1 donor was sensitized to both MO and CR, and 15 were non-allergic healthy control subjects with undetectable IgE titers for both MO and CR allergens. Briefly, after overnight resting PBMCs were stimulated with extracts (10 µg/ml) or HDMAPP (10 µg/ml), or medium alone as negative control, and incubated for 24h at 37ºC. AIM+ (CD69+CD137+) Vδ1 and Vδ2 cells were captured by fluorescence-activated cell sorting and underwent 10x single-cell RNA sequencing.

first: Sloan

middle: A

last: Davis

first: Esther Dawen

last: Yu

first: Adam

last: Abawi

first: Eric

last: Wang

first: Synaida

last: Maiche

first: Monalisa

last: Mondal

first: Pandurangan

last: Vijayanand

first: Grégory

last: Seumois

first: Bjoern

last: Peters

first: Alessando

last: Sette

first: Ricardo

last: da Silva Antunes


title: MeDIP-seq profile of Sam-S overexpressed female Drosophila germline.

city: Fukuoka

first: Yoshiki

last: Hayashi

state: Fukuoka

address: 744, Moto-oka, Nishi-ku

department: Department of Biology

country: Japan

institute: Kyushu University

type: Methylation profiling by high throughput sequencing

summary: S-adenosylmethionine (SAM) is the principal cellular donor of methyl-moiety in methylation reaction and regulates gene expression by regulating methylation related cellular events, such as epigenetic regulation. Although SAM biosynthesis affects variety of biological phenomena including disease and aging, whether cell-specific SAM biosynthesis status present and how it contributes cellular function are largely unknow. Here, we firstly showed that Drosophila germline in gametogenesis has repressive SAM biosynthesis status through observation of SAM synthetase (Sam-S), a key enzyme for SAM biosynthesis. In addition, our study showed that germline-unique repressive SAM biosynthesis status contributes to inhibition of retrotransposon expression; enhancement of SAM biosynthesis in germline caused excessive expression of retrotransposons including HeT-A, a telomere-specific retroelement, as the most affected target. We found that promoter activity of HeT-A is enhanced in SAM increased condition with increased accumulation of 6mA DNA methylation, the major DNA methylation modification in Drosophila genome. Interestingly, the enhanced 6mA enrichment and gene expression in enriched loci was not correlated in neither other retrotransposons nor structural genes. Taken together, our results suggest SAM-deficient status in germline uniquely regulates HeT-A transcription via 6mA methylation modification. Thus, our study provides new understanding how germline unique metabolic status contributes to regulation of retrotransposon expression.

overall_design: MeDIP-seq  profile of ovaries from wildtype and Sam-S overexperssing germline.

first: Shinjiro

last: Hino

first: Tetsuya

last: Sato

first: Ban

first: Natsuko

last: Kawano

first: Mitsuyoshi

last: Nakao

first: Mikita

last: Suyama


title: Transcriptomic analysis reveals jejunal mechanisms underlying postbiotic mediated immune systems in calves

city: Nakhon Ratchasima

first: Chao

last: Ban

address: 111 University Avenue Muang,

country: Thailand

institute: Suranaree University of Technology

summary: This study aimed to investigate the effect of dietary supplementation with postbiotic from dead cell Lactobacillus ingluviei CR37 (DCLI) on blood biochemical parameters, and jejunal epithelium transcriptomic profiles in calves. Transcriptomic analysis identified 76 DEGs, with significant upregulation of genes involved in fatty acid metabolism (FABP1), intestinal barrier function (B4GALNT2), and detoxification (GSTA1), alongside downregulation of immune response regulation (FCRLA, FCRL4). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses highlighted enrichment in pathways related to Glutathione metabolism, Drug metabolism, and Vitamin digestion, indicating postbiotic supplementation improved detoxification, oxidative stress defense, and nutrient absorption in calves. This study provides novel insights into the molecular mechanisms underlying the benefits of postbiotics and supports their potential as a sustainable alternative to probiotics in calf nutrition

overall_design: Fourteen Holstein bull calves were assigned to 2 treatment groups: CON (n = 7) or DCLI (n = 7, fed 1 g/d of dead cell Lactobacillus ingluviei CR37 strain, containing 108 CFU/g). Calves received milk replacer (MR) at 1.75% of BW (based on air-dry weight) and the amount was adjusted weekly according to body weight, while fresh and clean water was provided ad libitum. All calves had free access to starter starting on day 33. On day 82, the MR solution was reduced to 50% of the previous week's allocation, and calves were completely weaned by day 89. On the last day of the experimental period (d 90), prior to morning feeding. Four calves were randomly selected from each group and euthanized using captive bolt stunning and exsanguinated. The abdominal cavity was quickly opened. The jejunum was defined as starting at 100 cm caudal to the pylorus. Jejunal samples were collected approximately 30 cm proximal to the collateral branch of the cranial mesenteric artery, rinsed three times with sterile phosphate-buffered saline (PBS, pH = 7.0), and immediately placed into sterile RNase-free tubes. The samples were then flash-frozen in liquid nitrogen and stored at -80°C until RNA extraction.

first: Supreena

last: Srisaikham

first: Guilan

last: Wen

first: Xingzhou

last: Tian

first: Pipat

last: Lounglawan


title: RNA-seq profile of Sam-S overexpressed female Drosophila germline.

overall_design: RNA-seq  profile of ovaries from wildtype and Sam-S overexperssing germline.


title: Comparing DNA binding specificities between orthologous Pho4 transcription factors

city: Iowa City

first: Bin

last: He

email: emptyhb@gmail.com, bin-he@uiowa.edu

state: IA

address: 129 East Jefferson St., Biology Building 450

department: Biology

institute: the University of Iowa

summary: Combinatorial control by multiple transcription factors (TFs) is a hallmark of eukaryotic gene regulation. Despite its prevalence and crucial roles in enhancing specificity and integrating information, the mechanisms behind why eukaryotic TFs depend on one another, and whether such interdependence evolves, are not well understood. We exploit natural variation in co-TF dependence in the yeast phosphate starvation (PHO) response to address this question. In the model yeast Saccharomyces cerevisiae, the main TF, Pho4, relies on the co-TF Pho2 to regulate ~28 genes. In a related yeast pathogen, Candida glabrata, its Pho4 exhibits significantly reduced Pho2 dependence and has an expanded target set of ~70 genes. Chomatin IP based motifs for the two orthologous Pho4s are highly similar, with no detectable difference in their core E-box motif. However, past studies found that preference for sequences flanking the core motif can provide additional specificities to TFs in the same family. To determine if ScPho4 and CgPho4 differ in their flanking nucleotide preference, we conducted the universal Protein Binding Microarray (uPBM) to interrogate all possible 9-mers, from which a robust 7-mer enrichmement score can be calculated.

sample_organism:
Saccharomyces cerevisiae
Nakaseomyces glabratus

overall_design: Universal protein-binding microarray (PBM) experiments were performed for recombinant, full-length and orthologous transcription factors Pho4 from two yeast species, S. cerevisiae and C. glabrata. Briefly, universal PBMs involved binding of GST-tagged transcription factors to double-stranded 8x15K Agilent microarrays containing a DNA library designed to cover all possible 9-bp sequences, with every 8-mer occurring in at least 16 different spots on the array. This design allows comprehensive and unbiased characterization of the binding specificity of transcription factors for all possible 7-bp sequences.

first: Zhang

last: Yuning

first: Snyder

last: Lindsey

first: Gordan

last: Raluca

first: He

last: Bin


title: Kaposi's sarcoma-associated herpesvirus induces mitochondrial fission to evade host immune responses and promote viral production

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

summary: Mitochondrial dynamics are pivotal for host immune responses upon infection, yet how viruses manipulate these processes to impair host defense and enhance viral fitness remain unclear. Here we show that Kaposi's sarcoma-associated herpesvirus (KSHV), an oncogenic virus also known as human herpesvirus 8, encodes Bcl-2 (vBcl-2), which reprograms mitochondrial architecture. It binds with NM23-H2, a host nucleoside diphosphate (NDP) kinase, to stimulate GTP-loading of the dynamin-related protein (DRP1) GTPase, which triggers mitochondrial fission, inhibits mitochondrial antiviral signaling protein (MAVS) aggregation and impairs interferon responses. An NM23-H2-binding-defective vBcl-2 mutant fails to evoke fission, leading to defective virion assembly due to activated MAVS-IFN signaling. Notably, we identify two key interferon-stimulated genes restricting vBcl-2-dependent virion morphogenesis. Using a high-throughput drug screening, we discover an inhibitor targeting vBcl-2-NM23-H2 interaction that blocks virion production in vitro. Our study identifies a mechanism in which KSHV manipulates mitochondrial dynamics to allow for virus assembly, and shows that targeting the virus-mitochondria interface represents a potential therapeutic strategy

overall_design: RNAseq for empty vector, mutant E14A and WT vBcl-2 gene knock-in

first: Qing

last: Zhu

first: Chengyu

last: Liang


title: Effect of CD154:CD11b blockade on antigen-specific CD8 T cell response to murine Epstein-Barr virus infection

status: Public on Apr 11 2025

city: Atlanta

first: Mandy

middle: L

last: Ford

state: GA

address: 101 Woodruff Cir

department: Surgery

institute: Emory University School of Medicine

summary: CD154 is a promising target for immunosuppression in transplantation, autoimmunity, and inflammatory diseases. We previously identified CD11b as a novel alternate receptor for CD154 during alloimmunity. However, the impact of specific CD154:CD11b blockade on immune responses to infection has not been well characterized. Here, we have shown that in contrast to its immunosuppressive effect on graft-specific CD8+ T cells, CD154:CD11b blockade unexpectedly improved both the quantity and quality of murine herpesvirus-68 (MHV)-specific CD8+ T cells as measured by an increase in tetramer-positive KLRG1loCD127hi memory precursor effector cells (MPECs). RNAseq of antigen-specific CD8+ T cells identified using an MHV68-specific MHC tetramer reveals specific pathways altered following cM7 treatment during MHV68 infection, including transcripts associated with T cell activation and survival. The differential effect of CD154:CD11b blockade on graft-vs. virus-specific CD8+ T cells was underpinned by differences in phospho-S6 downstream of mTORC1, however differential expression of key transcription factors Eomes and TCF-1 was dictated by the type of antigen stimulus. These data demonstrate that priming conditions play an important role in determining the outcome of immunotherapy and suggest that specific inhibition of CD154:CD11b interactions could be effective for suppressing alloimmune responses while maintaining protective immunity to minimize infectious complications following transplantation.

overall_design: RNAseq profiling of p79/Kb tetramer postive antigen-specific CD8 T cells from wildtype C57Bl/6 mice on Day 10 post-MHV68 infection with or withour treatment with CD154:CD11b blockade (cM7)

first: Katie

last: Alexander


title: Targeting WEE1 in tumor-associated dendritic cells potentiates antitumor immunity

city: Beijing

first: Haidong

last: Tang

address: Shuangqing Road

country: China

institute: Tsinghua University

summary: DNA damage is a prevalent event within the tumor microenvironment, significantly influencing cancer initiation, progression, metastasis, and immune cell functionality. Here, we observed that oxidative stress induces DNA damage in tumor-associated dendritic cells (TADCs), leading to the activation of the serine/threonine kinase WEE1, which facilitates DNA repair. Notably, this DNA damage also acts as a stimulus for DC activation. Pharmacological inhibition of WEE1 activates TADCs via the cGAS/STING pathway, resulting in an enhanced antitumor immune response and improved tumor control. Furthermore, WEE1 inhibition augments the efficacy of DC vaccines and work synergistically with immune checkpoint blockade therapy. These findings underscore the critical role of WEE1-mediated signaling in DNA damage repair in immune cells in the tumor microenvironment, which in turn dampens the antitumor immune response. Thus, targeting WEE1 in DCs presents a promising strategy to enhance DC-mediated T cell activation and improve the effectiveness of cancer immunotherapy strategies.

overall_design: Gene expression profiling analysis of RNA-seq data for bone marrow-derived dendrtic cells (BMDCs) treated with vehicle control or AZD1775.


title: YAP/TAZ activity in PDGFRa-expressing alveolar fibroblasts modulates lung fibroblast-epithelial cell crosstalk through Wnt4 [scATAC-seq]

city: South San Francisco

first: David

last: Garfield

address: 1 DNA Way

department: OMNI Bx

institute: Genentech

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The Hippo signaling pathway, mediated by its transcriptional effectors YAP and TAZ, play vital roles in maintaining lung homeostasis and facilitating injury repair. While the roles of the Hippo pathway in epithelial cells are well-established, its regulatory effects on lung fibroblasts remain less understood. Here, we engineered a novel mouse allele to allow inducible knockdown of YAP and TAZ, and show that fibroblast-specific knockdown enhances the ability of PDGFRa+ alveolar fibroblasts to support organoids derived from alveolar epithelial stem cells in vitro. Single-cell multiomic profiling revealed changes in fibroblast subpopulations, including the emergence of an Mmp9+ cluster containing Wnt4+ cells. Analyses demonstrated shifts in the epigenomic landscape leading to varied enrichment of transcription factor motifs across both fibroblasts and epithelial cells in response to targeted suppression of YAP/TAZ in fibroblasts. Further computational analyses identified an increase in epithelial Wnt signaling which was confirmed by in vivo studies. We found that Wnt4 expression was increased in PDGFRa-lineage+ fibroblasts and enhanced proliferation of SPC+ AT2 cells following fibroblast-specific YAP/TAZ knockdown. These results shed new light on the mechanistic role of YAP/TAZ in PDGFRa+ alveolar fibroblasts in supporting AT2 cell maintenance and proliferation via Wnt4 secretion.

overall_design: We submitted samples of alveolospheres from co-cultures of lysotracker+ AT2s and PDGFRα+ fibroblasts, with fibroblast-specific YAP/TAZ knockdown induced by doxycycline on day 7. There are biological replicates of n=2 for both control and knockdown (KD) conditions for a total of 4 samples.

first: Jane

last: Song

first: Fabien

last: Wehbe

first: Arron

last: Wong

first: Ben

last: Hall

first: Jason

last: Vander Heiden

first: Hans

last: Brightbill

first: Joseph

last: Arron

first: Anwesha

last: Dey

last: Rock


title: Molecular consequences of a PHF21A variant, c.1285G>A, associated with autism spectrum disorder

city: Ann Arbor

first: Shigeki

last: Iwase

state: Michigan

address: 1241 E. Catherine St.

department: Human Genetics

institute: University of Michigan

summary: PHF21A is a histone reader protein that recognizes unmethylated H3 lysine 4 and binds to DNA through its AT-hook motif. PHF21A heterozygosity is associated with intellectual disability, behavioral issues, and craniofacial dysmorphism, with or without seizures (IDDBCS), also known as PHF21A-related neurodevelopmental disorders. To date, the only missense variant associated with PHF21A-related disorders is c.1285G>A, which substitutes one of the core amino acids consisting of the AT-hook motif. This variant, located at the last nucleotide of exon 13, potentially disrupt both alternative splicing and the DNA binding function, providing a unique opportunity to investigate the molecular mechanisms underlying PHF21A-related disorders. Here, we systematically investigated the consequences of this variant on mRNA splicing and DNA binding. Our results indicate that the variant significantly reduced the splicing efficiency of PHF21A isoforms while maintaining DNA binding capability. Thus, reduced dosage rather than impaired DNA binding likely contributes to the cognitive impairments seen in the individual with this variant.

overall_design: MiSeq was performed using PCR-amplified cDNA from wild-type (WT) and mutant mini PHF21A genes carrying the c.1285G>A variant, which were introduced into 293T cells and mouse cortical neuron cultures.

first: Cecilia

middle: M

last: Gavilan

first: Yumie

last: Murata-Nakamura

first: Robert

last: Porter

first: Bradley

last: Cutler

first: Sehj

last: Rai

first: Hyung-Goo

last: Kim


title: Probing condensate microenvironments and functions with a micropeptide “killswitch”

city: Berlin

first: Alexandre

middle: P

last: Magalhaes

address: Ihnestrasse 63-73

country: Germany

institute: Max Planck Institute for Molecular Genetics

summary: Biomolecular condensates are implicated in many cellular processes, and are thought to create subcellular microenvironments that regulate specific biochemical activities 1-7. For example, in vitro experiments suggest that condensates enable non-stochiometric enrichment of small molecules within condensates 8-12. However, probing the microenvironments of condensates in cells is a major challenge, because tools to selectively manipulate specific condensates in living cells are limited. Here we developed a non-natural micropeptide (i.e., the “killswitch”) and a Nanobody-based recruitment system as a universal approach to probe endogenous condensates, and demonstrate direct links between condensate microenvironments and function in cells. The killswitch is a hydrophobic, aromatic-rich sequence with an ability to self-associate, and no homology to human proteins. When recruited to endogenous and disease-specific condensates in human cells, the killswitch arrested the dynamics of the condensate-forming proteins, which led to predicted and unexpected effects. Targeting the killswitch to the nucleolar protein NPM1 altered nucleolar composition, and inhibited the dynamics of a ribosomal protein within nucleoli. Targeting the killswitch to fusion oncoprotein condensates inhibited the dynamics of effector proteins in the condensates, altered condensate composition, and inhibited proliferation of condensate-driven leukemia cells. In adenoviral nuclear condensates, the killswitch inhibited partitioning of capsid protein into condensates, and suppressed viral particle assembly. The results suggest that the microenvironment within cellular condensates has an essential contribution to non-stochiometric enrichment and the dynamics of effector proteins. The killswitch is a widely applicable tool to alter the material properties of endogenous condensates, and as a consequence, to probe functions of condensates linked to diverse physiological and pathological processes in living systems.

overall_design: Full transcriptome RNA-seq of HEK293T cells ectopically expressing EGFP-BRD4::NUT or BRD4::NUT-killswitch(KS) sequence variants. Samples include three replicates of each and untransfected HEK293T and EGFP expressing HEK293T cells as controls

first: Alexandre P

last: Magalhes

first: Henri

last: Niskanen

first: Yaotian

last: Zhang

first: Denes

last: Hnisz


title: Mitochondrial Ca2+ controls pancreatic cancer growth and metastasis by regulating epithelial cell plasticity

first: J. Kevin

last: Foskett

address: CRB Room 720, 415 Curie Blvd

department: Physiology

institute: University of Pennsylvania

summary: Endoplasmic reticulum to mitochondria Ca2+ transfer is important for cancer cell survival, but the role of mitochondrial Ca2+ uptake through the mitochondrial Ca2+ uniporter (MCU) in pancreatic adenocarcinoma (PDAC) is poorly understood. Here, we show that increased MCU expression is associated with malignancy and poorer outcomes in PDAC patients. In isogenic murine PDAC models, Mcu deletion (McuKO) ablated mitochondrial Ca2+ uptake, which reduced proliferation and inhibited self-renewal. Orthotopic implantation of MCU-null tumor cells reduced primary tumor growth and metastasis. Mcu deletion reduced the cellular plasticity of tumor cells by inhibiting epithelial-to- mesenchymal transition (EMT), which contributes to metastatic competency in PDAC. Mechanistically, the loss of mitochondrial Ca2+ uptake reduced expression of the key EMT transcription factor Snail and secretion of the EMT-inducing ligand TGFβ. Snail re-expression and TGFβ treatment rescued deficits in McuKO cells and restored their metastatic ability. Thus, MCU may present a therapeutic target in PDAC to limit cancer-cell-induced EMT and metastasis.

overall_design: Cell Lines developed from (KrasLSL-G12D/+; Trp53 LSL-R172H/+; Pdx1-Cre; R26LSL-Yfp/LSL-Yfp, ‘KPCY’ mice) with or without MCU floxed were used to develop stable, isogenic cell lines which express or do not express the gene for the mitochondrial calcium uniporter, Mcu. RNA was isolated with a RNeasy Mini kit (Qiagen 74104) from 10-15-cm dishes and sequenced by Novogene with a NovoSeq PE150 at ~20 M paired-end reads. Raw reads were processed with Salmon and DESeq2 before analysis.

first: Jillian

middle: S

last: Weissenrieder


title: YAP/TAZ activity in PDGFRa-expressing alveolar fibroblasts modulates lung fibroblast-epithelial cell crosstalk through Wnt4 [scRNA-seq]

first: David

last: Garfield

first: Jane

last: Song

first: Fabien

last: Wehbe

first: Arron

last: Wong

first: Ben

last: Hall

first: Jason

last: Vander Heiden

first: Hans

last: Brightbill

last: Arron


title: Isocitrate Dehydrogenase 1 Primes Group-3 Medulloblastomas For Cuproptosis

first: Sriram

last: Venneti

address: 1500 E Medical Center Dr

department: Pathology

summary: MYC-driven Group-3 medulloblastomas (MB) are malignant pediatric brain cancers without cures. To define actionable metabolic dependencies, we identified upregulationof dihydrolipoyl transacetylase (DLAT), the E2-subunit of pyruvate dehydrogenasecomplex (PDC) in a subset of Group-3 MB with poor prognosis. DLAT was induced by c-MYC and targeting DLAT lowered TCA-cycle metabolism and glutathione synthesis in Group-3 MB cells. We also noted upregulation of isocitrate dehydrogenase 1 (IDH1) in Group-3 MB. Remarkably, genetic and pharmacologic suppression of IDH1 epigenetically reduced c-MYC and downstream DLAT levels. DLAT is a central regulator of cuproptosis, a copper-dependent cell death mechanism induced by the copper ionophore elesclomol. DLAT expression in Group-3 MB cells correlated with increased sensitivity to cuproptosis. Elesclomol was CNS-penetrant and suppressed tumor growth in vivo in Group-3 MB animal models. Our data uncover an IDH1/c-MYC dependent vulnerability that regulates DLAT levels and can be targeted to kill Group-3MB by cuproptosis.

overall_design:
To understand the changes in gene expression upon induction of cuproptosis in Gr3 medulloblastoma, D283 medulloblastoma cells were treated with copper ionophore Elesclomol. RNAseq was performed in D283 cells with or without elesclomol (12.5 nM) treatment for 48 hrs.
To understand the role of overexpression of c-MYC protein in Gr3 medulloblastoma, c-MYC was overexpressed in   human cerebellar neuronal stem cells [Hanaford et al, 2017]. RNASeq was performed in cell with or without c-MYC overexpression.
To understand the role of IDH1 protein expression in Gr3 medulloblastoma, D283 medulloblastoma cells were transfected with siRNA targeting IDH1.
To understand the role of IDH1 protein expression in Gr3 medulloblastoma, D283 medulloblastoma cells were treated with IDH1 inhibitor and Cut and Run was performed.


title: Single-embryo RNA-seq analysis in LAD disrupted 2-cell embryos.

city: Munich

first: Maria-Elena

last: Torres-Padilla

address: Feodor-Lynen-Strasse 21

department: Institute of Epigenetics and Stem Cells

institute: Helmholtz Zentrum München

summary: We investigated whether LAD disruption phenotypes are associated with transcriptional changes during zygotic genome activation (ZGA). To address this, we performed single-embryo RNA sequencing at the late 2-cell stage and analyzed the transcriptome.

overall_design: Mouse embryos (zygotes) were microinjected with mRNA(s) encoding either mGFP alone (Control) or candidate proteins from the respective pools. The embryos were cultured until the late 2-cell stage and collected for Smart-Seq+5' analysis. Embryos were processed in two batches: batch 1 (collections 1 and 2) included mGFP, Pool J, and Pool M samples, while batch 2 (collections 3 and 4) consisted of Pool I, Pool N, and an additional set of mGFP embryos as controls.

first: Mrinmoy

last: Pal

first: Tamas

last: Schauer


title: Role of rs3129882 SNP in Monocyte Chromatin Accessibility Programs

first: Chris

last: Scharer

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

summary: The rs312889 SNP is located in the MHCII locus and conferrs susceptibility to Parkinson's Disease.  As the disease associated allele is non-coding, we sought to test if it was linked to epigenetic changes within the MHCII locus or more broadly in antigen presenting cells.  In this study, monocytes were purified from individuals with the AA protective or GG risk alleles that were diagnosed with Parkinsons's disease or healthy.  Monocytes were stimulated with IFNg for 18 hours or allowed to rest and then subjected to ATAC-seq analysis.

overall_design: ATAC-seq of four-five replicates of each indicated sample.

first: Christopher

middle: D


title: Mapping H3K9me3 enrichment upon heterochromatin induction in early embryos.

summary: We mapped genome-wide H3K9me3 enrichment upon heterochromatin induction to investigate the association of H3K9me3 domains with nuclear lamina in 2-cell embryos. We particularly focused on the expression of Suv39h1 alone and the coexpression of Suv39h1 along with heterochromatin reader proteins Hp1a and Hp1g (Pool J). To examine the changes in H3K9me3 enrichment, we performed CUT&RUN at the late 2-cell stage.

overall_design: Low-input CUT&RUN targeting H3K9me3 in late 2-cell stage embryos.

first: Adam

last: Burton


title: RNA m6A methylome in human oocytes and preimplantation embryos

first: Kin Fai

last: Au

state: MI

address: 100 Washtenaw Avenue

department: Department of Computational Medicine and Bioinformatics

summary: RNA N6-methyladenosine (m6A) modification is a critical regulator for a range of physiological and pathological processes. Despite its significance, the dynamic m6A profiles within human preimplantation embryos remain uncharacterized, primarily due to technical challenges and the scarcity of material. Here we present the first transcriptome-wide m6A landscape of single human oocytes and early embryos, utilizing the ultrasensitive m6A mapping approach picoMeRIP-seq that we have recently developed. Comparative analyses with mouse data reveal a conserved m6A methylome between humans and mice, with intriguing divergences during the window of zygotic genome activation. m6A-modified genes, including maternally-inherited RNAs and zygotically-activated transcripts, are involved in regulation of gene transcription, while unmodified genes are mainly associated with basic metabolic processes. Maternal RNAs destined for degradation after fertilization exhibit a propensity for m6A modifications, and m6A-modified genes are more likely to be targeted by miRNAs. Genes that are constantly-expressed across all developmental stages demonstrate higher translation efficiency for m6A-modified genes, intensified when m6A resides within coding regions. Moreover, we observe frequent m6A enrichment on stage-specifically expressed retrotransposons, particularly within young subfamilies such as HERVH, L1HS, and SVA_D. We also show a diminution of m6A levels both transcriptome-wide and on retrotransposons following inhibition of m6A writer activity in human embryonic stem cells. Our study provides a valuable resource for future investigations into the regulatory mechanisms of m6A in the human oocyte-to-embryo transition, and delivers epitranscriptomomic insights into human reproductive health.

overall_design:
Using picoMeRIP-seq we have developed, the transcriptome-wide m6A maps are generated in human oocytes at germinal vesicle (GV) and metaphase II (MII) stages, and human embryos at zygote (1C), 2-cell (2C), 8-cell (8C) and blastocyst (BLT) stages, with 2-4 biological replicates for each stage; and in human embryonic stem cells (ESC) starting with 1000 cells, 100 cells and 10 cells; and human embryonic stem cells treated by STM2457 inhibotor and DMSO control.
***Please note that raw sequencing data of human oocytes and early embryos, which were generated in Norway, are not provided as per Norway data policy.

first: Yanjiao

last: Li

first: Yunhao

last: Wang

first: Aylin

last: Cengiz

first: John

last: Dahl

first: Gareth

last: Greggains

first: Arne

last: Klungland


title: Assembly and annotation of Solanum dulcamara and Solanum nigrum plant genomes, two nightshades with contrasting susceptibilities to Ralstonia solanacearum  [RNAseq_expression_tissues]

status: Public on Apr 09 2025

city: Heslington, York

first: Sara

last: Franco Ortega

address: Wentworth Way

country: United Kingdom

institute: Centre for Novel Agricultural Products, University of York

summary: Ralstonia solanacearum causes disease in more than 200 plant species including bacterial wilt of tomatoes and brown rot of potatoes. This bacterium is a soilborne and waterborne pathogen, with a worldwide distribution and is on the EPPO A2 list of quarantine pathogens. ln the UK, the bacterium is present in the rivers, but its prevalence depends on the season; it is highly abundant in the summer and undetectable during winter. To survive the cold winter temperatures, R. solanacearum overwinters inside plants growing alongside the rivers such as Solanum dulcamara. Interestingly, this plant species doesn’t show bacterial wilt symptoms. To understand genomic differences with susceptible hosts, we assembled the genome using Oxford Nanopore Technologies and Illumina sequencing. We have used the mRNA-Seq used for de-novo annotation to assess the expression of selected PRRs in roots, stem, leaves, flowers and berries.

overall_design: We collected roots, stems, leaves, flowers and berries of Solanum dulcamara in liquid nitrogen. All tissues were sampled at the same time and stored at -80°C for further RNA extractions (Royal Botanic Gardens; Kew ID=39087). We extracted mRNA-Seq from these 5 tissues by grounding using liquid nitrogen and extracting total RNA using the E.Z.N.A. ® Plant RNA Kit, which included DNase treatment to remove residual DNA according to the manufacturer’s instructions. The quality of the RNA was assessed with Nanodrop and Qubit 4.0. using the Qubit™ RNA Broad Range kit and the Agilent Technology 2100 Bioanalyzer. We generated PromethION 9.4.1 cDNA libraries using total RNA from the 5 independently collected tissue samples which were kept separate.

first: Andrea

last: Harper


title: Mapping H3K4me3 enrichment upon LAD perturbation in early embryos.

summary: We investigated whether LAD disruption phenotypes are associated with genome-wide changes in H3K4me3 enrichment. To do this, we focused on two pathways that produce distinct LAD phenotypes. The first is the constitutive heterochromatin pathway involving Suv39h1, Hp1a, and Hp1g (Pool J), which leads to the collapse of control LADs and causes LAD 'flattening' in 2-cell embryos. The second is the H3K9me2/K27me2 demethylase pathway involving Kdm7a, Kdm7c, and Lsd1 (Pool I), which causes the collapse of control 2-cell LADs through the formation of broad ectopic LADs. To examine changes in H3K4me3 under these perturbations, we performed CUT&Tag at the late 2-cell stage.

overall_design: Low-input CUT&Tag targeting H3K4me3 in late 2-cell stage embryos.

first: Tsunetoshi

last: Nakatani


title: Germline ELP1 deficiency sensitizes cerebellar granule neuron progenitors to SHH medulloblastoma [bulkRNA]

city: Memphis

first: Paul

middle: A.

last: Northcott

address: 262 Danny Thomas Place

department: Developmental Neurobiology

institute: St. Jude Children's Research Hospital

summary: Germline loss-of-function (LOF) variants in Elongator complex protein 1 (ELP1) are the most prevalent predisposing genetic events in childhood medulloblastoma (MB), accounting for ~30% of the Sonic Hedgehog (SHH) 3 subtype. The underlying mechanism(s) by which germline ELP1 deficiency provokes SHH-MB pathogenesis remain unknown. Genetically engineered mice mimicking heterozygous Elp1 LOF (Elp1HET) seen in affected germline carriers exhibit hallmark features of cancer predisposition in cerebellar granule neuron progenitors (GNPs), including increased DNA replication stress, genomic instability, accelerated cell cycle, and stalled differentiation. Orthotopic transplantation of Elp1HET GNPs harboring somatic Ptch1 inactivation yielded SHH-MB-like tumors with compromised p53 signaling, providing an explanation for the exclusivity of ELP1-associated tumors in SHH-3. Preclinical treatment of ELP1-mutant patient-derived xenografts with an FDA-approved MDM2 inhibitor reactivated p53-dependent apoptosis and extended survival. Our findings functionally substantiate the role of ELP1 deficiency in SHH-MB predisposition and nominate therapeutics that overcome p53 inhibition as a rational treatment option.

overall_design: Transcriptome and polysome profiling for GNP and mouse tumors by bulk RNA-seq


title: Establishment of nuclear organization in mouse embryos is regulated by multiple and redundant epigenetic pathways.

first: Maria-Elena

summary: How the pillars of nuclear organization are first established during development is not fully understood at the molecular level. Here, we investigated one of the foundations of nuclear organization, the lamina-associated domains (LADs) and undertook a screening to identify the molecular pathways regulating LAD establishment in vivo, in early mouse embryos.

overall_design: LaminB1 DamID in control or manipulated late zygote and late 2-cell stage embryos.


title: In vivo programming of adult pericytes aids axon regeneration by providing cellular bridges for SCI repair

city: Columbus

first: Heithem

last: El-Hodiri

state: OH

address: 333 W 10th Ave

institute: Ohio State University College of Medicine

summary: Pericytes are contractile cells of the microcirculation that participate in wound healing after spinal cord injury (SCI). Thus far, the extent to which pericytes cause or contribute to axon growth and regeneration failure after SCI remains controversial. Here, we found that SCI leads to profound changes in vasculature architecture and pericyte coverage. We demonstrated that pericytes constrain sensory axons on their surface, causing detrimental structural and functional changes in adult DRG neurons that contribute to axon regeneration failure after SCI. Perhaps more excitingly, we discovered that in vivo programming of adult pericytes via local administration of platelet-derived growth factor BB (PDGF-BB) effectively promotes axon regeneration and recovery of hindlimb function by contributing to the formation of cellular bridges that span the lesion. Ultrastructural analysis showed that PDGF-BB induced fibronectin fibril alignment and extension, effectively converting adult pericytes into a permissive substrate for axon growth. In addition, PDGF-BB localized delivery positively affects the physical and chemical nature of the lesion environment, thereby creating more favorable conditions for SCI repair. Thus, therapeutic manipulation rather than wholesale ablation of pericytes can be exploited to prime axon regeneration and SCI repair.

overall_design: Spinal cords were obtained from adult (12-14 weeks old) NG2-eGFP mice at 3, 7 and 14 days (e.g., 10, 14 and 21 days after SCI) after vehicle and PDGF-BB administration. Three (for naïve, 3 and 7 days) and two (for 14 days) cords (~2 mm centered at the lesion site) were pulled to obtain ~20-25 mg of tissue mass for each time point/experimental condition and analyzed using scRNA-Seq

first: Wenjing

last: Sun

first: Elliot

last: Dion

first: Fabio

last: Laredo

first: Allyson

last: Okonak

first: Jesse

last: Sepeda

first: Esraa

last: Haykal

first: Min

last: Zhou

first: Andy

last: Fischer

first: Jerry

last: Silver

first: Juan

last: Peng

first: Andrew

last: Sas

last: Tedeschi


title: Aromatic acid metabolism in Methylobacterium extorquens reveals interplay between methylotrophic and heterotrophic pathways

city: Berkeley

first: N. Cecilia

last: Martinez-Gomez

address: 421 Koshland Hall

department: Plant and Microbial Biology

institute: UC Berkeley

summary: Efforts towards microbial conversion of lignin to value-added products face many challenges because lignin’s methoxylated aromatic monomers release toxic C1 byproducts such as formaldehyde. The ability to grow on methoxylated aromatic acids (e.g., vanillic acid) has recently been identified in certain clades of methylotrophs, bacteria characterized by their unique ability to tolerate and metabolize high concentrations of formaldehyde. Here, we use a phyllosphere methylotroph isolate, Methylobacterium extorquens SLI 505, as a model to identify the fate of formaldehyde during methylotrophic growth on vanillic acids. M. extorquens SLI 505 displays concentration-dependent growth phenotypes on vanillic acid without concomitant formaldehyde accumulation. We conclude that M. extorquens SLI 505 overcomes potential metabolic bottlenecks from simultaneous assimilation of multicarbon and C1 intermediates by allocating formaldehyde towards dissimilation and assimilating the ring carbons of vanillic acid heterotrophically. We correlate this strategy with maximization of bioenergetic yields and demonstrate that formaldehyde dissimilation for energy generation rather than formaldehyde detoxification is advantageous for growth on aromatic acids. M. extorquens SLI 505 also exhibits catabolite repression during growth on methanol and low concentrations of vanillic acid, but no diauxie during growth on methanol and high concentrations of vanillic acid. Results from this study outline metabolic strategies employed by M. extorquens SLI 505 for growth on a complex single substrate that generates both C1 and multicarbon intermediates and emphasizes the robustness of M. extorquens for biotechnological applications for lignin valorization.

overall_design: To understand how Methylobacterium extorquens SLI 505's transcriptome responds to different substrates, RNA-seq was performed on M. extorquens cultures growth in 5 or 10 mM vanillic acid, 50 mM methanol, or 10 mM acetate. Three biological replicates were analyzed for each of the four conditions

first: Alekhya

last: Govindaraju

first: N

middle: C


title: Assembly and annotation of Solanum dulcamara and Solanum nigrum plant genomes, two nightshades with contrasting susceptibilities to Ralstonia solanacearum

first: Sara

last: Franco Ortega

summary: Ralstonia solanacearum causes disease in more than 200 plant species including bacterial wilt of tomatoes and brown rot of potatoes. This bacterium is a soilborne and waterborne pathogen, with a worldwide distribution and is on the EPPO A2 list of quarantine pathogens. ln the UK, the bacterium is present in the rivers, but its prevalence depends on the season; it is highly abundant in the summer and undetectable during winter. To survive the cold winter temperatures, R. solanacearum overwinters inside plants growing alongside the rivers such as Solanum dulcamara. Interestingly, this plant species doesn’t show bacterial wilt symptoms. To understand genomic differences with susceptible hosts, we assembled the genome using Oxford Nanopore Technologies and Illumina sequencing.

overall_design: Solanum dulcamara (Royal Botanic Gardens, Kew ID=39087) leaves were collected from 3-month old adult plant. DNA was extacted following the High molecular weight gDNA extraction from plant leaves protocol, Oxford Nanopore Technologies [ONT]), which utilised Carlson buffer and further purification using QIAGEN genomic-tip, see preprint Vaillancourt and Buell (2019) for details.The libraries were prepared using the SQK-LSK109 ligation sequencing kit and run with PromethION R9.4.1 (FLO-PRO002) flow cells. Base calling was obtained onboard with Guppy. f5c v1.2 was used to identify the methylated regions as well as the frequency of methylation in the whole genome.

first: Andrea

last: Harper


title: Programmed cell death-1 receptor deficiency enhances CD30+ T regulatory cell function in Melanoma [Murine scRNAseq]

city: Newcastle Upon Tyne

first: Jing Xuan

last: Lim

address: Framlington Place

department: Bioscience Institute

institute: Newcastle University

summary: Regulatory T cells (Tregs) are vital for immune suppression rendering their function through multiple pathways including the expression of co-inhibitory receptors. The role of co-receptors namely PD1 in Treg function remains controversial. We demonstrate that PD1 is a master checkpoint in Tregs controlling several aspects of Treg biology in tumor immunity. Our data demonstrates that PD1 controls the expression and function of a unique co-inhibitory receptor network that dictates Treg function. We found that CD30 plays a central role within this network in driving Treg suppressive function within the tumor microenvironment (TME). Mechanistically, PD1 deficiency unleashed enhanced STAT5 signaling in Tregs, which drove CD30 expression. Our work highlights a new role for PD1 as a checkpoint that negatively controls CD30 expression in Tregs thereby dampening their function. Understanding the landscape changes that PD1 renders to Treg function can enable the use of combination therapies for better treatment outcomes in cancer.

overall_design: Tumors were harvested from C57BL/6 WT and B6.PD1KO mice. Tumour infiltrating lymphocytes were isolated from B16 tumor using ficol density gradient centrifugation. Cells were then debulked with Thy1 microbeads and then stained with sample tags and Abseq antibodies along with Lineage cocktail antibodies and Thy1. Lin+Thy1+ cells were enriched through flow sorting and then loaded onto cartridge and subjected to Rhapsody analysis.

first: Shoba

last: Amarnath

first: Tegan

last: McTaggart


title: Genetic modeling of ELP1-associated Sonic hedgehog medulloblastoma identifies MDM2 as a selective therapeutic target

first: Paul

last: Northcott

type: Methylation profiling by genome tiling array

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

overall_design: Refer to individual Series


title: Genetic modeling of ELP1-associated Sonic hedgehog medulloblastoma identifies MDM2 as a selective therapeutic target [DNA_methylation_array]

summary: Mouse tumor methylation profiling by MouseMethylation Beadchips (MM285) platform

overall_design: The study utilizes the MouseMethylation Beadchips (MM285) platform, focusing on the epigenetic profiling of mouse tumors. We compare genotypes Elp1HET;Ptch1gRNA to Elp1WT;Ptch1gRNA, and Elp1HET;Ptch1gRNA;p53null to Elp1WT;Ptch1gRNA;p53null, exploring tumor epigenetics and comparion with CNS patient methylation

first: Yiran

last: Li


summary: Germline loss-of-function (LOF) variants in Elongator Acetyltransferase Complex Subunit 1 (ELP1) are the most prevalent predisposing genetic events in childhood medulloblastoma (MB), accounting for ~30% of the Sonic Hedgehog (SHH) 3 subtype. The mechanism(s) by which germline ELP1 deficiency provokes SHH-MB pathogenesis remain unknown. Genetically engineered mice mimicking heterozygous Elp1 LOF (Elp1HET) seen in affected germline carriers exhibit hallmark features of premalignancy in cerebellar granule neuron progenitors (GNPs), including increased DNA replication stress, genomic instability, accelerated cell cycle, and stalled differentiation. Orthotopic transplantation of Elp1HET GNPs harboring somatic Ptch1 inactivation yielded SHH-MB-like tumors with compromised p53 signaling, providing a plausible explanation for the exclusivity of ELP1-associated MBs in the SHH-3 subtype. Preclinical treatment of ELP1-mutant patient-derived xenografts with an FDA-approved MDM2 inhibitor reactivated p53-dependent apoptosis and extended survival. Our findings functionally substantiate the role of ELP1 deficiency in SHH-MB predisposition and nominate therapeutics targeting MDM2 as a rational treatment option.

overall_design: Transcriptome profiling by scRNA-seq in the developing cerebellum from wild-type and Elp1+/- mice at P7. The study included six replicates in each group (five single mouse samples and one pooled sample per group). snRNA-seq data were generated for mouse tumors from orthotopic transplantation models.


title: A multilayered regulation of stem cell gene expression by EMB1579 defines root meristem function.

city: Seoul

first: Zeeshan

last: Nasim

address: Anam-ro 145, Seongbuk-Gu

department: School of Life Sciences and Biotechnology

country: South Korea

institute: Korea University

summary: In the Arabidopsis root meristem, stem cell maintenance relies on the combined activity of transcription factor networks. The transcriptional regulator EMBRYO DEFECTIVE 1579 (EMB1579) controls many aspects of plant growth. The molecular mechanisms underlying its function in root development, and tissue patterning remain elusive. Here, we show that EMB1579 is required for stem cell maintenance and cell division orientation in the root meristem. EMB1579 modulates the function of two root stem cells' regulatory modules, PLETHORAS and SCARECROW-SHORT-ROOT, in a process that involves transcriptional regulation and post-transcriptional modification. We demonstrate that EMB1579 acts as a catalyst for stem cell gene expression, and its activity is fine-tuned through physical association with the RNA splicing factors; importantly, we unveil that the formation of nuclear condensates is essential for regulating the expression of root stem cell genes. Our data unveil a mechanism by which EMB1579 regulates stem cell determinants in the root meristem.

overall_design: To investigate the role of EMB1579 in regulating the expression of genes involved in root growth and development, we performed RNA sequencing of wild-type (Col-0) and two emb1579 mutant lines (emb1579-1 and emb1579-3), using three biological replicates for each.

first: Fatimah

last: Aljedaani

first: Yinghui

last: Luo

first: Yanming

last: Deng

first: Wouter

last: Smet

first: Ikram

last: Blilou


title: Extensive N4 Cytosine Methylation is Essential for Marchantia Transcriptional Programming and Sperm Function [2]

city: Norwich

first: Xiaoqi

last: Feng

state: Norfolk

address: Norwich Research Park

department: Cell and Developmental Biology

institute: John Innes Centre

summary: Global N4 cytosine methylation catalyzed by a novel DNA methyltransferase is important for transcriptional programming, sperm mobility, and post-fertilization in Marchantia

overall_design: Profiling and understanding the methylome during sperm development in Marchantia

first: James

last: Walker

first: Jingyi

last: Zhang

first: Yalin

last: Liu

first: Shujuan

last: Xu

first: Martin

last: Vickers


title: Extensive N4 Cytosine Methylation is Essential for Marchantia Transcriptional Programming and Sperm Function


title: Expression data from NRF3 overexpression cells treated with forskolin

city: Kyotanabe

first: Tsuyoshi

last: Waku

address: 1-3 Tatara Miyakodani

institute: Doshisha University

summary:
A CNC-family transcription factor, Nrf3, is highly expressed in the basal cell layer of the epidermis where melanocytes resident, although the melanogenic function of Nrf3 remains unclear.
We used microarrays to identify NRF3-regulated gene expression network related to melanogenesis.

overall_design: For RNA extraction and hybridization on Affymetrix microarrays, we generated B16F10 cells stably expressing Nrf3 or GFP and treated with forslokin

first: Akira

last: Kobayashi


title: Multidimensional single-cell sequencing profiles the bone marrow immune microenvironment in chronic myeloid leukemia

city: Wuhan

first: Chunjiang

last: He

state: Hubei

address: Donghu Road 185

institute: Wuhan University

summary: The immune system plays an important role in the response to therapy in chronic myeloid leukemia (CML). However, there is no comprehensive high-throughput analysis of the bone marrow immune microenvironment in patients diagnosed with CML. Here, we combined single-cell transcriptome, single-T cell, and single-cell TCR sequencing to comprehensively analyze the bone marrow immune changes in CML patients.

overall_design: Bone marrow from 5 CML patients and 2 normal subjects was extracted for single cell sequencing and CD3+ cells were isolated for further detection of T cell expression and TCR repertoire at single cell resolution

first: Yu

last: Hou


title: Loss of VHL-mediated pRb regulation promotes clear cell renal cell carcinoma

status: Public on Apr 08 2025

city: Ottawa

first: Mercy

last: Akuma

state: Ontario

address: 451, Smyth road

department: Cellular and Molecular Medicine

country: Canada

institute: University of Ottawa

summary: The von Hippel-Lindau (VHL) tumor suppressor is a substrate-defining component of E3 ubiquitin ligase complexes that target cellular substrates for proteasome-mediated degradation. VHL inactivation by mutation or transcriptional silencing is observed in most sporadic cases of clear cell renal cell carcinoma (ccRCC). VHL loss in ccRCC leads to constitutive stabilization of E3 ligase substrates, including hypoxia inducible factor α (HIFα). HIFα stabilization upon VHL loss is known to contribute to ccRCC development through transactivation of hypoxia-responsive genes. HIF-independent VHL targets have been implicated in oncogenesis, although those mechanisms are less well-defined than for HIFα. Using proximity labeling to identify proteasomal-sensitive VHL interactors, we identified retinoblastoma protein (pRb) as a novel substrate of VHL. Mechanistically, VHL interacts with pRb in a proteasomal-sensitive manner, promoting its ubiquitin-mediated degradation. Concordantly, VHL-inactivation results in pRb hyperstabilization. Functionally, loss of pRb in ccRCC led to increased cell death, transcriptional changes, and loss of oncogenic properties in vitro and in vivo. We also show that downstream transcriptional changes induced by pRb hyperstabilization may contribute to ccRCC tumor development. Together, our findings reveal a novel VHL-related pathway which can be therapeutically targeted to inhibit ccRCC tumor development.

overall_design: RNA-seq profiling of 786-O wildtype and VHL-reconstituted cells, and their RB1 knockout derivatives.

first: Ryan

last: Russell

first: Minjun

last: Kim

first: Yasser

last: Riazalhosseini


title: Low-input genomics screening reveals epigenetic pathways that orchestrate nuclear organization in early mouse embryos.

first: Maria-Elena

last: Torres-Padilla

summary:
The three-dimensional folding of the genome within the nuclear space is fundamental for regulating various DNA-related processes. How nuclear organization is first established during development is not understood at the molecular level. The formation of lamina-associated domains (LADs) at the nuclear periphery represents the earliest feature of nuclear organization. In this study, we conducted a screening to investigate the molecular mechanisms regulating LAD establishment in vivo, using mouse embryos. Our findings identify histone methylation pathways that cause severe disruption of nuclear architecture in early embryos. This research provides an unprecedented resource for understanding the molecular basis of nuclear organization establishment highlighting the hierarchical relationships between chromatin pathways during epigenome formation and allows for interrogation of its impact at the onset of mammalian development.

This SuperSeries is composed of the SubSeries listed below.

first: Mrinmoy

last: Pal

first: Tamas

last: Schauer


title: Single-Cell Analysis of Host Responses in Bovine Milk Somatic Cells (bMSCs) Following HPAIV bovine-H5N1 Influenza Infection.

city: Manhattan

first: Gagandeep

last: Singh

state: KS

address: 1800 Denison Ave

institute: Kansas State Univeristy

summary: The 2024 outbreak of highly pathogenic avian influenza virus (HPAIV) H5N1 in U.S. dairy cattle presented an unprecedented scenario where the virus infected bovine mammary glands and was detected in milk, raising serious concerns for public health and the dairy industry. Unlike previously described subclinical influenza A virus (IAV) infections in cattle, H5N1 infection induced severe clinical symptoms, including respiratory distress, mastitis, and abnormal milk production. To understand the host immune responses and changes particularly in the mammary gland, we performed scRNA-seq analysis on bovine milk somatic cells (bMSC) in-vitro infected with H5N1 isolate from dairy farm. We identified ten distinct cell clusters and observed a shift toward type-2 immune responses, characterized by T-cells expressing IL13 and GATA3, and three different subtypes of epithelial cells based on expression of genes associated with milk production. Our study revealed temporal dynamics in cytokine expression, with a rapid decline in luminal epithelial cells and an increase in macrophages and dendritic cells, suggesting a role in increased antigen presentation. These findings indicate that bovine H5N1 infection triggers complex immune responses involving both pro-inflammatory and regulatory pathways. This research fills a critical gap in understanding the immune responses of bovine mammary glands to H5N1 infection and highlights the need for further investigation into therapeutic strategies for managing such outbreaks.

overall_design: Bovine Milk Somatic Cells (bMSCs) were isolated from the raw milk of three multiparous Holstein-Friesian cows, followed by in-vitro infection (24 hrs) with bovine-H5N1 HPAIV (A/dairy cattle/Kansas/5/2024), and analyzed using scRNASeq.


title: Transcriptomics on MDA-MB-231 cells adapted to methionine-free medium

city: Solna

first: Roland

last: Nilsson

address: Akademiska Stråket 1

department: Dept. of Medicine, Solna

country: Sweden

institute: Karolinska Institutet

summary: Human cells can synthesize methionine from homocysteine and folate-coupled methyl groups via the B12-dependent enzyme methionine synthase (MTR). Yet, it has been known for decades that cancer cells fail to grow when methionine is replaced by homocysteine, a phenomenon known as methionine dependence. Here, we report single-cell RNA-sequencing data from MDA-MB-231 breast cancer cells adapted to grow without methionine in the presence of high levels of vitamin B12 for 21 days. Compared to parental cells (D0), the adapted “revertant” cells (D21) display gene expression signatures consistent with reduced invasion and metastasis.

overall_design: One sample of parental MDA-MB-231 cells was taken at day 0 (D0), and one after 21 days of adaptation in B12-containing homocysteine medium (D21).

first: Mohamed

last: El Husseiny


title: Rat mammary cancer induced by radiation exposure at 3 or 7 weeks of age

city: Chiba

first: Tatsuhiko

last: Imaoka

address: 4-9-1 Anagawa, Inage-ku

department: National Institute of Radiological Sciences

institute: National Institutes for Quantum and Radiological Science and Technology

summary: The risk of developing secondary cancer after radiotherapy, especially after treatment of childhood cancers, remains a matter of concern. The present study is aimed to investigate the effect of gamma-ray irradiation in childhood on breast carcinogenesis using a rat model of mammary carcinogenesis.

overall_design: A set of 15 mammary tumors diagnosed as adenocarcinoma and 3 normal mammary gland tissue [PMID: 21374731, 23084769] were used for a gene expression analysis. Includes 13 microarrays previously deposited in GSE22770.

first: Yukiko

last: Nishimura

first: Daisuke

last: Iizuka

first: Masaru

last: Takabatake

first: Kazuhiro

last: Daino

first: Mayumi

first: Takamitsu

last: Morioka

first: Yoshiya

last: Shimada

first: Shizuko

last: Kakinuma


title: SEMA3B switches axon-axon to axon-glia interactions required for unmyelinated axon envelopment and integrity

city: Hangzhou

first: Xiaolong

last: Xin

state: Zhejiang

address: Research Building 866 Yu Hang Tang Road, Zhejiang University Zijingang Campus

department: School of Basic Medical Sciences

institute: Zhejiang University

summary: During peripheral nerve (PN) development, unmyelinated axons (nmAs) initially form tight fascicles before being separated and enveloped by non-myelinating Schwann cells (nmSCs), which are essential for maintaining nmA integrity. The mechanism underlying this transition from axon-axon to axon-glia interactions remains unclear. Here, we found that inactivating nmSC-derived SEMA3B or its axonal receptor components in mice led to incomplete nmA separation and envelopment by nmSCs, leading to nmA dysfunction and inducing hyperalgesia and allodynia. Conversely, increasing SEMA3B levels in nmSCs accelerated nmA separation and envelopment. SEMA3B transiently promoted nmA defasciculation accompanied by cell adhesion molecule (CAM) endocytosis, thus facilitating subsequent CAM-mediated nmA-mSC association. Restoring SEMA3B expression post-PN injury promoted nmA-nmSC re-association and alleviated hyperalgesia and allodynia. We propose that SEMA3B-induced CAM turnover facilitates the switch from axon-axon to axon-glia interactions, promoting nmA envelopment by nmSCs, which may be exploited to alleviate PN injury-induced pain by accelerating the restoration of nmA integrity.

overall_design: We performed single-cell RNA sequencing (scRNA-seq) of sciatic nerves at five critical developmental times, i.e., P0, P7, P14, P28, and P60, encompassing the time window of RB (Remak bundle) assembly,to elucidate the mechaisms driving the transition from axon-axon to axon-glia interaction during RB assembly and markers fro nmscs during this transition.To investigate the presence of potential SEMA3B receptor components on nmAs during RB assembly, we conducted snRNA-seq of dorsal root ganglia (DRGs), comprising primary somatosensory neurons (SNs) projecting mAs and nmAs through the sciatic nerves, from P14 mice

first: Li

last: Liu

first: Zhigang

last: Gao

first: Xueyuan

last: Niu

first: Yanlan

last: Gu

first: Genghai

last: Ma

first: Yan


title: Rat mammary cancer (290 MeV/u carbon ions, 6 cm spread-out Bragg peak) (high corn oil diet)

summary: Purpose: The high relative biologic effectiveness (RBE) of high-linear energy transfer (LET) heavy-ion radiation has enabled powerful radiotherapy. The potential risk of later onset of secondary cancers, however, has not been adequately studied. We undertook the present study to clarify the RBE of therapeutic carbon ion radiation and molecular changes that occur in the rat mammary cancer model. Methods and materials: We observed 7-8-week-old rats (ACI, F344, Wistar, and Sprague-Dawley) until 1 year of age after irradiation (0.05-2 Gy) with either 290 MeV/u carbon ions with a spread out Bragg peak (LET 40-90 keV/mum) generated from the Heavy-Ion Medical Accelerator in Chiba or (137)Cs gamma-rays. Results: Carbon ions significantly induced mammary carcinomas in Sprague-Dawley rats but less so in other strains. The dose-effect relationship for carcinoma incidence in the Sprague-Dawley rats was concave downward, providing an RBE of 2 at a typical therapeutic dose per fraction. In contrast, approximately 10 should be considered for radiation protection at low doses. Immunohistochemically, 14 of 18 carcinomas were positive for estrogen receptor alpha. All carcinomas examined were free of common H-ras and Tp53 mutations. Importantly, lung metastasis (7%) was characteristic of carbon ion-irradiated rats. Conclusions: We found clear genetic variability in the susceptibility to carbon ion-induced mammary carcinomas. The high RBE for carbon ion radiation further supports the importance of precise dose localization in radiotherapy. Common point mutations in H-ras and Tp53 were not involved in carbon ion induction of rat mammary carcinomas.

overall_design: Mammary cancers were from rats treated with carbon-ion irradiation radiation (0.5 Gy; n = 4). Experiments were matched with GSE44786.

first: Daizuke


title: Genomic instability of Jurkat clone E6-1 T-cell lines affect gene expression and function: implications for T-cell researchers

city: Wellington

first: Andrew

middle: David

last: Wilson

address: Gate 7 Kelburn Parade, Victoria University of Wellington

country: New Zealand

institute: Malaghan Institute of Medical Research

type: Genome variation profiling by genome tiling array

summary: Jurkat clone E6-1 is a human T-cell line derived from a paediatric case of acute leukaemia, and is frequently employed as a model T-cell for immunology research. In this study, we characterised genomic, transcriptomic, and functional features of Jurkat clone E6-1 cells stored in three different laboratories, and compared these to Jurkat E6-1 cells from the ATCC. Jurkat clone E6-1 populations were first karyotyped, which results showing marked cytogenomic heterogeneity between cell line. These results were confirmed through chromosomal microarray analysis. Whole exome sequencing was then conducted on each cell line, and revealed distinct mutational profiles between populations. Mutational differences between Jurkat clone E6-1 populations detected by cytogenomic approaches and whole exome sequencing led to divergent transcriptomic profiles identified by bulk RNA sequencing, which, in turn, impacted cellular phenotype and function shown by flow cytometry and multiplex cytokine bead array data.     Overall, we found substantial genomic heterogeneity between and within Jurkat clone E6-1 cells, resulting in significant differences in gene expression and function. This research highlights the extreme genomic instability of Jurkat clone E6-1 cells, the importance of monitoring cell passage number and procuring fresh cell line stocks, and the value of multi-omic approaches to characterise cell lines to improve the accuracy, reproducibility, and translatability of research.

overall_design: DNA extracts from each Jurkat clone E6-1 population were analysed by CMA to confirm karyotype findings. Each DNA extract was run in singlicate.

first: Rachel

last: Beddow

first: Tina

last: Lillis

first: Tom

last: Chin

first: Robert

last: Weinkove

first: Michelle

last: McCulley


title: Extensive N4 cytosine methylation of Marchantia genes is essential for sperm function [1]

first: Xiaoqi

last: Feng

summary: Sperm mobility in Marchantia requires global N4 cytosine methylation catalysed by two novel DNA methyltransferases.

overall_design: Profiling of methylome during sperm development in Marchantia

first: James

last: Walker

first: Jingyi

last: Zhang

first: Martin

last: Vickers


title: Rat mammary cancer induced by radiation exposure at 1, 3, or 7 weeks of age

first: Tatsuhiko

last: Imaoka

overall_design: A set of 24 mammary tumors diagnosed as adenocarcinoma [PMID: 23084769] were used for a gene expression analysis

first: Yukiko

last: Nishimura

last: Iizuka

first: Masaru

last: Takabatake

first: Kazuhiro

last: Daino

first: Mayumi

first: Takamitsu

last: Morioka

first: Yoshiya

last: Shimada

first: Shizuko

last: Kakinuma


title: Expression profile of microglia from Egln3–/–, App-Psen1 and App-Psen1

status: Public on Apr 15 2025

city: Seville

first: Clara

last: Ortega-de San Luis

address: Av. Manuel Siurot S/N

country: Spain

institute: Instituto de Biomedicina de Sevilla (IBiS); Hospital Universitario Virgen del Rocio/CSIC/Universidad de Sevilla

summary: Microglia was isolated from Egln3–/–; App-Psen1 and App-Psen1 mice using flow cytometry to identify changes in their expression profile and phenotype associated with the absence of  Prolyl Hydroxylase 3 (PHD3).

overall_design: 6 Total samples were analyzed (3 samples per group). We compared microglial expression profiles from Egln3–/–; App-Psen1 and App-Psen1.

first: Manuel

last: Sanchez-Garcia

first: Rosana

last: March-Diaz

first: Antonio

last: Heras-Garvin

first: Nieves

last: Lara-Ureña

first: Alberto

last: Pascual


title: comparative analysis of the effects of various chamomile extracts and characteristic pure compounds on human T cells

city: Heidelberg

first: Yvonne

last: Samstag

address: INF 305

department: Institute of Immunology

institute: Heidelberg University Hospital

summary: In this study, we have characterized and compared the effects of differently prepared chamomile extracts and characteristic pure compounds on the T cell redox milieu as well as on the migration, activation, proliferation, and cytokine production of primary human T cells. Futhermore, nCounter based gene expression profiling was performed on the most promising extracts (Chamomile aqueous total fermented-CT, aqueous toot fermented-CR, and ethanolic flower-CF) and pure compounds (Apigenin-Ap and Chamazulene-Cz) to identify the genes related to different T cell functions, that were targeted by the different treatment conditions.

overall_design: in this study, total RNA samples were extracted from costimulated T cells of healthy volunteers left unstimulated, or stimulated, each stimulation subjected to a particular treatment condition or not. 4 to 5 healthy donors were taken for each condition, treated or untreated

first: Divya

last: Lairikyengbam


title: Firre promotes myocardial proliferation and repair via binding to PTBP1 and activating the Akt pathway

status: Public on Apr 07 2025

city: Guangzhou

first: Jianning

last: Chen

address: No. 12 Minyou Road

institute: The Second Affiliated Hospital of Guangdong Medical University

summary: The neonatal mammalian heart retains transient regenerative capacity that diminishes shortly after birth. Reactivation of cardiomyocyte proliferation represents a promising strategy for cardiac repair. This study identifies the nuclear-enriched long non-coding RNA FIRRE (Firre) as a critical regulator of cardiac development and regeneration. In vitro overexpression of Firre significantly enhanced cardiomyocyte proliferation, evidenced by increased S-phase entry. In vivo, AAV9-mediated cardiac-specific delivery of Firre extended the regenerative window in neonatal mice by promoting cardiomyocyte proliferation and reducing fibrotic scar area following myocardial injury. Remarkably, Firre administration improved cardiac function, attenuated infarct size, and stimulated cardiomyocyte proliferation in adult mice post-myocardial infarction. Mechanistically, RNA immunoprecipitation revealed direct interaction between Firre and Polypyrimidine Tract Binding Protein 1 (PTBP1). Transcriptome profiling demonstrated Firre-mediated activation of the PI3K/AKT signaling pathway. Furthermore, we identified Phlda3 (Pleckstrin Homology-like Domain Family A Member 3) as a downstream effector, through which Firre facilitates cardiac regeneration by modulating SFPQ-NONO heteromer stability and enhancing DNA repair capacity. These findings establish Firre as a potential therapeutic target for augmenting myocardial repair and regeneration.

overall_design: RNA-seq profiling of mouse cardiomyocyte in control negative and experiment LncFirre overexpresssion group


title: Single cell atlas of amnion development of the first trimester of human pregnancy

city: Pasadena

first: Magdalena

last: Zernicka Goetz

state: CALIFORNIA

address: CALIFORNIA INSTITUTE OF TECHNOLOGY

institute: California Institute of Technolog

summary: The amnion is an essential extraembryonic tissue that maintains the intrauterine environment during pregnancy, yet its development remains enigmatic given the scarcity of samples from early-stage pregnancies. Here, we performed single-cell transcriptomic analysis of the amnion across three stages in the first trimester of pregnancy. We identified 13 distinct cell types, including amnion epithelial stem cells (AESCs), amnion mesenchymal stem cells (AMSCs), and several known and novel cell types. Epithelial lineages predominate in the early amnion, with mesenchymal and ectodermal, ectodermal cells arising later. We identify a population of bipotent progenitors that generates both AESCs and AMSCs. Trajectory and RNA velocity analyses of amniotic cells revealed epithelial, mesenchymal, and ectodermal trajectories. Moreover, the expression of secreted ligands uncovered four signaling patterns that change as development progresses. Finally, we detected mixed fetal and maternal blood and immune cells within the amnion. This cellular map highlights the landscape and complexity of the human amnion and serves as a resource for further studies of amnion development, physiology, and therapeutic applications.

overall_design: All tissues for sequencing and spatial work were collected in HypoThermosol FRS preservation solution (H4416-100ML Merck) and stored at 4 °C until processing. Tissue dissociation was conducted within 24 h of tissue retrieval. Tissues were cut into <1 mm3 segments before being digested with Trypsin/EDTA 0.25% phenol red for 10-15 min at 37 °C with intermittent shaking. Digested tissue was passed through a 100 µm filter and cells collected by centrifugation (500g for 5 min at 4 °C). Cells were washed with PBS and then resuspended in PBS 0.04% BSA before cell counting. cells were loaded according to the manufacturer’s protocol for the Chromium Next GEM Single Cell 5 v2 (Dual index) kit for CS17 amnion and Chromium Next GEM Single Cell 3 v3.1 (Dual index) kit for CS19 and CS22 amnion from 10X Genomics to attain 7,000 cells per reaction. Library preparation was carried out according to the manufacturer’s protocol. Libraries were sequenced, aiming at a minimum coverage of 20,000 raw reads per cell, on the Illumina HiSeq4000 or Novaseq 6000 systems using the sequencing format: read 1, 26 cycles; i7 index, 8 cycles, i5 index, 0 cycles; read 2, 98 cycles

first: Wenqi

last: Hu

first: Carmen

last: Sancho-Serra

first: Carlos

middle: W

last: Gantner

last: Zernicka-Goetz


title: ALS associated TDP-43 aggregates drive innate and adaptive immune cell activation

city: Chapel Hill

first: Todd

last: Cohen

state: NC

address: 115 Mason Farm Rd

institute: University of North Carolina at Chapel Hill

summary: Amyotrophic lateral sclerosis is the most common and fatal motor neuron disease. Approximately 90% of ALS patients exhibit pathology of the master RNA regulator, Transactive Response DNA Binding protein (TDP-43). Despite the prevalence TDP-43 pathology in ALS motor neurons, recent findings suggest immune dysfunction is a determinant of disease progression in patients. Whether TDP-43 aggregates elicit immune responses remains underexplored. In this study, we demonstrate that TDP-43 aggregates are internalized by antigen presenting cell populations, cause vesicle rupture, and drive innate and adaptive immune cell activation by way of antigen presentation. Using a multiplex imaging platform, we observed enrichment of activated microglia/macrophages in ALS white matter that correlated with phosphorylated TDP-43 accumulation, CD8 T-cell infiltration, and major histocompatibility complex expression. Taken together, this study sheds light on a novel cellular response to TDP43 aggregates through an immunological lens.

overall_design: Primary monocyte derived macrophages were stimulated with TDP-43 aggregates, amyloid beta oligomers, lipopolysaccharide, or vehicle control (PBS) for either 12 hours or 6 days

first: Baggio

last: Evangelista

first: Joey

last: Ragusa

first: Kyle

last: Pellegrino

first: Yijia

last: Wu

first: Ivana Yoseli

last: Quiroga-Barber

first: Shannon

last: Cahalan

first: Omeed

last: Arooji

first: Jillann

last: Madren

first: Sally

last: Schroeter

first: Joe

last: Cozzarin

first: Ling

last: Xie

first: Xian

first: Kristen

last: White

first: J. Ashley

last: Ezzell

first: Marie

last: Iannone

first: Sarah

first: Douglas

last: Phanstiel

first: Rick

last: Meeker


title: RNAseq analysis of streptomycin on SW620 colon cancer cell line

city: Montpellier cedex 5

first: Francoise

last: Macari

address: 208 avenue des Apothicaires

country: France

institute: INSERM

summary: To understand the mechanism of action of streptomycin, we performed RNA-seq in the SW620 colon cancer cell line after treatment with streptomycin or dihydrostreptomycin as a control.

overall_design: SW620 cells were cultured in suspension with or without streptomycine (SM), dihydrostreptomycin (DSM) at 120µM (EC50) for 2 days in 3 biological replicates.

first: Hélène

last: Guillorit

first: Alexandre

last: David

first: Maria

last: Duca


title: 5-aza-2-deoxycytidine improves skeletal muscle function in a mouse model for recessive RYR1-related congenital myopathy

city: Basel

first: Faiza

last: Noreen

address: Mattenstrasse 28

department: Department of Biomedicine

country: Switzerland

institute: University of Basel

summary: RYR1 congenital myopathies are rare disorders severely impacting muscle function and impairing the quality of life of patients and their families, yet to date, no pharmacological therapies are available to treat the severe muscle weakness of affected patients. The recessive forms of RYR1-related congenital myopathies caused by nonsense/ frameshift mutations in one allele and a missense mutation in the other allele, resulting in the homozygous and reduced expression of the missense mutation are the most severe forms. They are often accompanied by a reduction of RyR1 protein and significant changes in the biochemical composition of muscles. Using a mouse model carrying the RyR1 p.Q1970fsX16+p.A4329D compound heterozygous mutations (dHT mice),we performed a pre-clinical study and injected mice for 15 weeks with 0.05 mg/kg of the FDA approved drug 5-aza-2-deoxycytidine which targets the epigenetic enzymes DNA methyltransferases. We evaluated muscle strength, calcium homeostasis and proteome and report that drug treatment improves all investigated muscle function in drug treated dHT mice. Importantly, the beneficial effects were particularly significant in fast twitch muscles which are the first muscles to be impaired in patients. In conclusion, this study provides proof of concept for the pharmacological treatment of patients with congenital myopathies linked to recessive RYR1 mutations, leading the path to a phase 1 clinical study by repurposing an FDA approved drug.

overall_design: We aimed to investigate the effects of 5-aza-2'-deoxycytidine on the methylation status of skeletal muscles in a congenital myopathy model. A mouse model was developed, including both wild-type (WT) and heterozygous RYR1 mutation (dHT) carriers. Genomic DNA from 45 samples was analyzed using the Infinium Mouse Methylation Array (Illumina). These samples consisted of 15 from WT mice and 30 from dHT mice, divided into vehicle-treated and TMP269-5Aza-treated groups. Methylation patterns were profiled across three distinct muscle types: extensor digitorum longus (EDL), flexor digitorum brevis (FDB), and soleus (SOL).

first: Susan

last: Treves

first: Alexis

last: Ruiz

first: Francesco

last: Zorzato


title: Poverty shapes the transcriptome of immune cells

city: Detroit

first: Roger

last: Pique-Regi

address: 540 E Canfield (Scott Hall 3309)

institute: Wayne State University

summary: Social determinants of health influence health outcomes and life expectancy. Specifically, individuals living in poverty often have adverse health outcomes related to chronic inflammation that affect the cardiovascular, renal, and pulmonary systems. However, the underlying mechanisms by which poverty increases the risk of disease and health disparities are still not fully understood. To bridge the gap in our understanding of the link between living in poverty and adverse health outcomes, we performed RNA sequencing of blood immune cells from 204 participants of the Healthy Aging in Neighborhoods of Diversity across the Life Span (HANDLS) study in Baltimore City, Maryland. This study cohort included men and women self-identified as African American and White. We identified genes differentially expressed in association with poverty. Our results suggest that living in poverty influences inflammation and the risk for chronic disease through gene expression changes in immune cells, and that some of the effects of living in poverty are different in women and men.

overall_design: Gene expression profiling through RNAsequencing of PBMCs from individuals living in poverty or above poverty.

first: Nicole

last: Arnold

first: Justyna

last: Resztak

first: Adnan

last: Alazizi

middle: N

last: Hooten

first: Michele

middle: K

last: Evans

first: Valerie

last: Odera-Marah

middle: F

last: Dluzen

first: Francesca

last: Luca


title: Overexpression of barley heat stress transcription factor HvHsfA6a provide thermotolerance by thermopriming

city: Uttarakhand

first: Harsh

last: Chauhan

state: Haridwar

address: Roorkee-Haridwar Highway, Roorkee

department: Department of Biosciences and Bioengineering

country: India

institute: Indian Institute of Technology Roorkee

summary: In plants, heat shock factors (HSFs) are terminal components of heat stressresponse. Here, we functionally characterized a highly heat stress responsive HvHSFA6a in barley by developing constitutively overexpressing transgenic lines. These transgenic lines showed heat tolerant phenotype via improved photosynthesis, antioxidants and upregulation of HSPs and metabolites involved in stress amelioration and keeping thermomemory as compared to wild type plants.

overall_design: In this study, a highly heat-inducible HSF, HvHSFA6a was constitutively expressed in barley (Hordeum vulgare L.) to investigate its role in heat stress response.

first: Reeku

last: Chaudhary

first: Suchi

last: Baliyan

first: Lisha

last: Khungar

first: Parul

last: Sirohi

first: Sweta

last: Singh

first: Sumit

last: Mishra

first: Mohan

last: Rajkumar

first: Shashank

last: Saini

first: Hugo

last: Germain

first: Debabrata

last: Sircar


title: Brain-wide mapping of immune receptors uncovers a neuro-modulatory role of interleukin-17E and the receptor IL-17RB.

city: Cambridge

first: Myriam

last: Heiman

state: Massachusetts

address: 43 Vassar St

institute: Massachusetts Institute of Technology

summary: Cytokines engage with their receptor complexes to orchestrate diverse processes -- from immune responses to modulating behaviors. Interleukin-17A (IL-17A) mediates protective immune responses by binding to IL-17 receptor A (IL-17A) and IL-17RC subunits. IL-17A also modulates social interaction, but the role of cytokine receptors in this process and their expression in the brain is not well characterized. Here, we mapped the brain-region-specific expression of all major IL-17R subunits and discovered that IL-17RB, not IL-17RC, expression in the cortex plays a role in social behaviors. Through genetic experiments, we further showed that IL-17E, a ligand for the IL-17RB-containing receptor complex, enhances social interaction by directly impacting IL-17RB-expressing neurons in the cortex. These findings highlight a novel IL-17 circuit operating within the cortex to modulate social behaviors. Thus, characterizing spatially restricted cytokine receptor expression can be leveraged to  elucidate how cytokines function as critical messengers mediating neuro-immune interactions to shape animal behaviors.

overall_design: Cell type-specific profiling of IL-17RA+, IL-17RB+, and IL-17RC+ cells in the primary somatosensory cortex of Il-17ra-, Il-17rb-, and Il-17Rc-Cre mice, respectively, using Translating Ribosome Affinity Purification (TRAP).

first: Hyeseung

last: Lee

first: Tomoe

last: Ishikawa

first: Gloria

last: Choi


title: Impaired parvalbumin interneurons in the retrosplenial cortex as the cause of sex-dependent vulnerability in Alzheimer’s disease [Xenium]

status: Public on Apr 13 2025

city: Calgary

first: Jonathan

last: Epp

state: Alberta

address: 2500 University Drive NW

institute: University of Calgary

summary: Alzheimer’s disease is a debilitating neurodegenerative disorder with no cure and few treatment options. In early stages of Alzheimer’s disease, impaired metabolism and functional connectivity of the retrosplenial cortex strongly predict future cognitive impairments. Therefore, understanding Alzheimer’s disease-related deficits in the retrosplenial cortex is critical for understanding the origins of cognitive impairment and identifying early treatment targets. Using the 5xFAD mouse model, we discovered early, sex-dependent alterations in parvalbumin-interneuron transcriptomic profiles. This corresponded with impaired parvalbumin-interneuron activity, which was sufficient to induce cognitive impairments and dysregulate retrosplenial functional connectivity. In fMRI scans from patients with mild cognitive impairment and Alzheimer’s disease, we observed a similar sex-dependent dysregulation of retrosplenial cortex functional connectivity and, in post-mortem tissue from subjects with Alzheimer’s disease, a loss of parvalbumin interneurons. Reversal of cognitive deficits by stimulation of parvalbumin interneurons in the retrosplenial cortex suggests that this may serve as a promising novel therapeutic strategy.

overall_design:
The retrosplenial cortices of four female wildtype mice, four male wildtype mice, four female 5xFAD mice, and four male 5xFAD mice were analyzed using 10xGenomics Xenium Spatial Transcriptomics. Samples were analyzed using the 247 gene Xenium Mouse Brain Panel
Alzheimer's Disease Neuroimaging Initiative (contributor)

first: Dylan

last: Terstege

first: Yi

last: Ren

first: Bo Young

last: Ahn

first: Heewon

last: Seo

first: Kabirat

last: Adigun

first: Liisa

last: Galea

first: Derya

last: Sargin


title: STAT3 signalling drives tissue expansion during postimplantation mouse development [RNA-seq]

city: Edinburgh

first: Takuya

last: Azami

address: Crewe Road

department: Institute of Genetics and Cancer

institute: The University of Edinburgh

summary: STAT3 has been studied extensively in the context of self-renewal of naïve pluripotent mouse embryonic stem cells (mESCs). Although STAT3 is required to maintain ICM lineages when maternally eliminated, the role of STAT3 during gastrulation is unclear as the conventional knockout of Stat3 develops until E6.5. In this study, we observed that zygotic loss of Stat3 on CD1 genetic background leads to consistent developmental retardation from implantation to mid-gestation, beginning with a significant reduction in the number of epiblast cells by the time of implantation. Remarkably, mutants appear to scale normally and resemble non-affected embryos from the previous day at all postimplantation stages examined. Bulk RNA-seq analysis using isolated epiblast cells revealeed that E6.5 null epiblasts were intermediate between WT E5.5 and E6.5; E7.5 null epiblasts grouped more closely with WT E6.5 than E7.5 epiblasts. Gene ontology analysis revealed lipid metabolism was compromised in Stat3 null embryos as early as E6.5. Interestingly, Socs3, downstream target of STAT3, was not induced in WT rpiblast cells until E7.5. We found Y705 phospholylated STAT3 was not exist postimplantation epiblast, but S727 phoshorylated STAT3 was abundant over the time, suggesting postimplantation specific roles of S727 phosphorylated STAT3 in growth and differentiation. Our study revealed that while Stat3 null epiblast cells progress along a near normal differentiation trajectory, Stat3 deletion compromises lipid metabolism as early as E6.5.

overall_design: Bulk RNA-seq for post-implantation epiblast cells from WT and Stat3 null embryos; WT and Stat null embryos were collected from E5.5 to E7.5 and isolated epiblast manually. Genotype was detemined using extraembryonic tissue by genomic PCR.

first: Jennifer

last: Nichols

first: Bart

last: Theeuwes

first: Berthold

last: Gottgens


title: Histone marks enable formation of immiscible phase-separated chromatin compartments

city: Beijing

first: Jiacheng

last: Wang

address: No. 30 Shuangqing Road

institute: Tsinghua University

summary: Eukaryotic chromatin is organized into compartments for gene expression regulation, but the underlying mechanisms remain unclear. Here, we demonstrate that multivalent H3K27me3 and its reader, CBX7-PRC1, regulate facultative heterochromatin via a phase separation mechanism, similar to constitutive heterochromatin. Facultative and constitutive heterochromatin represent distinct, coexisting repressive condensates in nuclei. H3K27me3- and H3K9me3-marked nucleosomal arrays and their reader complexes phase separate into immiscible condensates, analogous to the relationship between facultative and constitutive heterochromatin in vivo. Overexpression of CBX7-PRC1 causes aberrant chromatin compartmentalization in vivo and up-regulation of cancer-related genes. CBX7 inhibitor effectively inhibits cancer cell proliferation possibly through phase separation-mediated compartment reorganization. Our data suggest that histone marks mediate chromatin compartmentalization via phase separation, and offer potential epigenetic mechanistic insights into tumor development and cancer therapy.

overall_design: By employing RNA-seq, ChIP-seq, CUT&Tag, and Hi-C, we systematically examined the change in chromatin features and transcriptome upon overexpression of CBX7 in NIH3T3 cells.

first: Wenjing

last: Sun

first: Wei

last: Xie

first: Pilong

last: Li


title: Tracking the genome-wide occupancy of LEAFY COTYLEDON1 provides insights into its role in endosperm development

status: Public on Apr 06 2025

city: Saskatoon

first: Jingpu

last: Song

address: 110 Gymnasium Pl

institute: NRC

summary: LEAFY COTYLEDON1 (LEC1), expressed in both endosperm and embryo, acts as a central regulator that controls diverse aspects of seed development including embryogenesis and seed maturation. LEC1 expression in the endosperm can be detected within one day after fertilization. The gene networks and developmental processes controlled by LEC1 in endosperm remain unclear. Here, we applied a modified INTACT system to purify endosperm nuclei and used for ChIP-seq to identify the genome-wide occupancy of LEC1 in the developing endosperms at three stages, namely nuclei proliferation, cellularization, and degeneration. The ChIP-seq in combination with transcriptome analyses indicated a regulatory role of LEC1 in controlling diverse biological processes in the developing endosperm. In particular, lack of LEC1 led to an altered endosperm metabolic phenotype in storage lipid content and fatty acid composition. Together, our findings provide important insights into the requirement of LEC1 for endosperm development.

overall_design: ChIP-seq profiling of  LEC1-bindings in the developing endosperms at nuclear proliferation  (1-3 day after pollination), cellularization (5 day after pollination) and degenerateion (7 day after pollination) stages.

first: Yuhai

last: Cui

first: Jitao

last: Zou


title: Diurnal variation of cellullar populations in mouse tongue epithelium

city: Hirakata

first: Toru

last: Matsu-ura

state: Osaka

address: 2-5-1 Shin-mach

department: Pathology

institute: Kansai Medical University

summary: We employed single-cell sequencing using 10x Genomics scRNA-seq to investigate circadian variations in cellular populations within the mouse tongue epithelium. This study demonstrates that circadian clock-regulated cell divisions lead to diurnal fluctuations in the population of type II taste cells in the tongues of nocturnal animals like mice.

overall_design: Tongue epithelial cells were isolated from male B57BL/6 mice at two distinct circadian time points (ZT0 and ZT12) and analyzed via scRNA-seq.

first: Atsunori

last: Nasu

first: Suengwon

last: Lee

first: Naoko

last: Yoshida

first: Kaoru

last: Matsuura

first: Masaharu

last: Yasuda

first: Kae

last: Nakamura

first: Chiristian

middle: I

last: Hong

first: Koji

last: Tsuta


title: Mechanical stimulation on superificial cervical lymphatics enhances cerebropsinal fluid draiange

city: Gyeonggi-do

first: Hokyung

last: Jin

address: 2066, Seobu-ro, Jangan-gu, Suwon-si

department: Otolaryngology

institute: Sungkyunkwan University

summary: To gain further insight into ageing-related changes in the superficial cervical lymphatics, we performed scRNA-seq on cells isolated from the superficial cervical lymphatic system.

overall_design: Afferent lymphatics (scLV-1 and scLV-2) of submandibular lymph nodes of six adult mice and six aged mice were harvested and single-cell libraries were made.

first: Jin-Hui

last: Yoon

first: Myung

last: Yang

first: Gou

middle: Y

last: Koh


title: Secretory IgA binding to FCRL3 triggers shared inflammatory cytokine secretion by human regulatory T cells and effector T cells

city: Silver Spring

first: Frederick

middle: Curtis

last: Mills

state: Maryland

address: 10903 New Hampshire Avenue

department: CDER/OPQR/OPQRIV

institute: FDA

summary: Several human lymphocyte subsets express the novel secretory IgA receptor FCRL3.  Secretory IgA binding to FCRL3 mAb diminishes the inhibitory capacity of regulatory T cells and promotes a Th17-like phenotype.  Here we report that in CD4+ regulatory T cells and CD8+ terminal effector T cells secretory IgA induced a shared inflammatory gene signature that included PTGS2 encoding COX2, and the prototypic inflammatory cytokine genes IL1A, IL1B, and IL8. Secretory IgA in regulatory T cells also elevated gene transcripts required for lineage identity and function.  Secretory IgA promoted IL-1β, IL-6, IL-8, IL-10, IFN-γ, and TNF-α protein secretion by both T cell types.  .    We propose that secretory IgA provokes in regulatory and effector T cells a coordinated inflammatory response to facilitate mucosal pathogen clearance.

overall_design: We assessed the impact of secretory IgA (SIgA) and anti-FCRL3 mAb antibody stimulation on human CD4+ regulatory T cells and CD8+ effector T cells at two time points using bulk RNA-seq.   CD4+CD25hiCD127dim CD14- regulatory T cells and CD8+CD45RO-CCR7- terminal effector T cells were sorted from peripheral blood and stimulated with (1) biotinylated secretory lgA followed by streptavidin; (2) biotinylated FCRL3 mAb mAb followed by streptavidin; (3) streptavidin as control.                             Transcript abundances of secretory lgA and FCRL3 mAb mAb stimulated samples were compared with that of the control.

first: Mate

last: Tolnay

first: Svetlana

last: Petrovskaya


title: Enhancement of Chikungunya virus genome replication in mammalian cells at sub-physiological temperatures

city: Princeton

first: Aaron

middle: E

last: Lin

state: NJ

address: Washington Road

department: Molecular Biology

institute: Princeton University

summary: Chikungunya virus (CHIKV) is an Alphavirus transmitted by Aedes mosquitoes, causing fever, rash and arthralgia in mammals. The function of the CHIKV non-structural protein 3 (nsP3) remains enigmatic. Building on previous studies, we generated a panel of mutants in a conserved and surface-exposed cluster in the nsP3 alphavirus unique domain (AUD) and tested their replication using a sub-genomic replicon (SGR). Three of these SGR mutants replicated well in mosquito cells but poorly in mammalian cells. We observed that this difference was due to cell culture temperature (mosquito cells: 28 °C; mammalian cells: 37 °C) as the mutants exhibited no replication defect in mammalian cells grown at a sub-physiological temperature (28 °C). Similar effects were observed for infectious CHIKV and the closely related O'nyong-nyong virus. Intriguingly, the wildtype SGR replicated more efficiently in mammalian cells at 28 °C compared to 37 °C. To explore the mechanism behind this difference, we focused on two known antiviral pathways: interferon-stimulated genes (ISGs) and stress granules (SG). SGR replication correlated strongly with increased expression of ISGs at 37°C, but only weakly correlated at 28 °C. We also observed enhanced recruitment of SG proteins (G3BP, eIF4G, and TIA-1) into cytoplasmic sites of genome replication at 28 °C. These findings may have real-world implications as when a mosquito bites a mammal, the virus first infects cells in peripheral tissues which are often at sub-physiological temperatures. We propose that alphaviruses such as CHIKV have evolved mechanisms to both promote viral genome replication and concomitantly limit antiviral responses in these cells.

overall_design: Comparative gene expression profiling (RNA-seq) of C2C12 cells transfected with CHIKV-D-SGR WT, GAA, or mock, incubated at 37C or 28 °C, for 12 h or 24 h.

first: Jinchao

last: Guo

first: Chetan

last: Aditya

first: Alexander

last: Ploss

first: Mark

last: Harris


title: Investigating ovarian disrupting effects of per- and polyfluoroalkyl substances

city: Piscataway

first: Shuo

last: Xiao

address: 170 Frelinghuysen Rd

department: Pharmacology and Toxicology

institute: Rutgers University

summary: To investigate the effects of Perfluorononanoic Acid (PFNA) exposure to 3D cultured ovarian follicles during gonadotrophin-dependent maturation and ovulation

overall_design: We performed gene expression analysis using data obtained from RNA-seq of ovarian follicles exposed to PFNA during the gonadotropin-dependent follicle maturation and during hCG induced ovulation

first: Pawat

last: Pattarawat

first: Tingjie

last: Zhan

first: Jiyang

last: Zhang

first: Eunchong

last: Kim