title: Distinct NK Cell Function and Gene Expression in Children with Acute Lymphoblastic Leukemia in Remission Before and After Acute Exercise

city: Irvine

first: ABEL

last: PLAZA FLORIDO

state: California

address: 101 Academy, Suite 150 Irvine

department: Department of Pediatrics, UC Irvine School of Medicine

institute: Pediatric Exercise and Genomics Research Center (PERC)

summary: Children and adolescents who have acute lymphoblastic leukemia (ALL), often display an impaired natural killer cell (NK) function. Brief bouts of exercise mobilize NK cells and influence their gene expression, but little is known about the effect of exercise on NK cell function and gene expression in pediatric ALL survivors, which remains unclear. This study examined the effect of exercise on NK gene expression and cytotoxic activity (NKCA) in pediatric ALL patients in remission. Nine B-cell ALL children in remission and 9 sex and age-matched healthy controls with no history of cancer (14.8±1 and 15±1 y/o, respectively; 2 girls per group) performed eight 2-min bouts of cycle ergometry at 60% of peak work rate (71±2% of V̇O 2 peak) interspersed with 1-min rest intervals. Circulating NK cells gene expression profile (RNA-seq) and NKCA (in vitro) were performed before and after exercise. NK cell function (NK cell cytotoxicity assay) and gene expression (RNAseq) analyses were performed. Exercise altered the expression of thousands of NK cell genes in both ALL and controls, with a distinct pattern in ALL both at baseline (294 Genes) and in response to exercise (179 genes). At baseline, nine gene pathways involved in NK cell function were affected, and following exercise, 28 pathways related to inflammatory response and cancer were impacted. NKCA was lower at baseline in survivors compared to controls. The reduced activity was partially mitigated following exercise but remained lower in ALL compared to controls. Exercise may improve NK cell function, specifically in immune surveillance in ALL children in remission, and has the potential to be used as adjunctive therapy in ALL. The differential gene expression response to exercise suggest that NK cells in ALL may adopt a different molecular strategy to fight infections or tumors.

overall_design: Nine B-cell ALL children in remission and 9 sex and age-matched healthy controls with no history of cancer (14.8±1 and 15±1 y/o, respectively; 2 girls per group) performed eight 2-min bouts of cycle ergometry at 60% of peak work rate (71±2% of V̇O 2 peak) interspersed with 1-min rest intervals. Circulating NK cells gene expression profile (RNA-seq) was performed before and after exercise.

first: Abel

last: Plaza-Florido

first: Martin

last: Perlsteyn

first: Leonard

last: Sender

first: Fadia

last: Haddad

first: Dan

last: Cooper

first: Ronen

last: Bar-Yoseph

first: Alejandro

last: Lucia

first: Shlomit

last: Radom-Aizik


title: Imaging-based drug screening combined with moleuclar profiling identifies signatures and drivers of therapy resistance in pediatric AML [RNA-seq]

status: Public on Jul 14 2025

city: Vienna

first: Kaan

last: Boztug

state: Vienna

address: Zimmermannplatz 10

country: Austria

institute: St. Anna Children's Cancer Research Institute

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Despite recent advances in the understanding of genomic landscape of pediatric acute myeloid leukemia (pedAML), targeted treatments are only available for selected genomic alterations and the functional link between genotype and outcome remains partially elusive. Functional precision medicine approaches to investigate treatment resistance and patient risk have not been applied systematically for pedAML. We established an advanced functional screening platform combining high-content imaging and deep-learning-based phenotyping. In 45 pedAML patients, we identify BCL2 and FLT3 inhibitors and standard chemotherapy as major drivers of the chemosensitivity landscape, reveal substantial differential sensitivities between risk groups, and may effectively predict individual measurable residual disease and patient risk. Integration with genomic and epigenomic data uncovers a chemotherapy-resistant primitive state vulnerable to combined BCL2 and MDM2 inhibition and HDAC inhibition. Overall, we identify early present signatures of therapy resistance across genetic subgroups and prioritize targeted treatments for these functionally and epigenetically defined patient subsets.

overall_design: 28 RNA-seq samples from isolated blasts from pedAML patients sampled at diagnosis.

first: Ben

last: Haladik

first: Margarita

last: Maurer-Granofszky

first: Peter

last: Zoescher

first: Raul

last: Jimenez-Heredia

first: Alexandra

last: Frohne

first: Anna

last: Segarra-Roca

first: Chloe

last: Casey

first: Felix

last: Kartnig

first: Sarah

last: Giuliani

first: Christina

last: Rashkova

last: Repiscak

first: Michael

middle: N

last: Dworzak

first: Giulio

last: Superti-Furga


title: Dual mitotic bookmarking by GAF condensates and H3K27ac orchestrates differential propagation of cell fate memory in neural development [RNA-seq]

city: Beijing

first: Yan

last: Song

state: 北京

address: No.5 Yiheyuan Road

country: China

institute: Peking University

summary: In brain development, neural stem cells (NSCs) undergo asymmetric cell divisions to replicate themselves and meanwhile produce differentiating siblings. It remains obscure how NSCs preserve their self-renewing fate across mitosis. Even less is known how cell fate memory is differentially propagated to sibling daughter cells adopting distinct cell fates. Here we found that key differentiation genes are dually bookmarked by pioneer factor GAF (GAGA factor) and H3K27ac in asymmetrically-dividing Drosophila central brain NSCs. In daughter cells adopting NSC fate, GAF promotes self-renewal through timely inhibiting differentiation genes via HDAC1-mediated H3K27 deacetylation, whereas in sibling daughter cells adopting a differentiating fate, GAF occupancy is replaced by competitor SWI/SNF complex, allowing H3K27ac deposition retained and fast activation of differentiation genes. Thus, our study unveils a new paradigm by which cell fate memory can be differentially transmitted to sibling daughter cells via dual antagonistic mitotic bookmarking and selective molecular competition mechanism.

overall_design: To investigate the function of GAF, HDAC1 and Osa in neural development, we compared the transcriptomes between control and GAF-knockdown, HDAC1-knockdown or Osa-knockdown NSCs.

first: Rulan

last: Zhang

first: Jie

last: Liu

first: Zimo

first: Tanpeng

last: Wang

first: Yuying

last: Shen

first: Zejun

last: Lan

first: Jingyi

last: Chu

first: Haoxuan

last: Tang


title: Idelalisib Modulates CD4+ T Cell Responses to Mitigate Rejection of Allografts in Mice

status: Public on Jul 13 2025

city: tianjin

first: hu

last: lu

state: State

address: fu kang lu

institute: TMU

summary: Immune rejection remains a major cause of graft loss following organ transplantation, with CD4+ T cells playing a central role in this process. The PI3K/AKT/mTOR signaling pathway is critical for CD4+ T cells activation, proliferation, and metabolic reprogramming, making it a promising therapeutic target. The role of Idelalisib (ID), a selective PI3Kδ inhibitor, in transplant immunity remains underexplored. Here, we demonstrated ID significantly suppressed CD4+ T cells activation, proliferation, and Th1 differentiation while enhancing cell survival. In the skin and heart transplantation model, ID attenuated acute rejection, prolonged graft survival, and reduced CD4+ T cells and B cells proliferation. Transcriptomics revealed downregulation of T cells activation and differentiation genes and glycolysis marker. Functional assays confirmed impaired glucose uptake and lactate production in ID-treated cells. Conclusions. ID uniquely modulates T cells responses via PI3Kδ inhibition, offering a distinct immunosuppressive mechanism compared to mTOR inhibitors. Taken together, our data highlight ID’s potential as a therapeutic agent for mitigating transplant rejection and elucidates the interplay between PI3K signaling and CD4+ T cells metabolism.

overall_design: Purified CD4+ T cells from C57BL/6 mouse spleens were cultured with Idelalisib (ID). Activation, proliferation, differentiation and survival were assessed. The regulatory mechanism of ID was analyzed using  RNA-seq.

first: weiqi

last: zhang

first: xiaohan

first: lu

last: hu

first: shuai

last: jin


title: An ancient and essential miRNA family controls cellular interaction pathways in C. elegans [miRNA-Seq]

status: Public on Jul 10 2025

city: Baltimore

first: Luisa

last: Cochella

state: Maryland

address: 725 N. Wolfe Street, PCTB 803

country: USA

institute: Johns Hopkins School of Medicine

type: Non-coding RNA profiling by high throughput sequencing

summary: The transition from unicellular to multicellular life required the acquisition of coordinated and regulated cellular behaviors, including adhesion and migration. In metazoans, this relies on cell adhesion proteins, signaling systems, and an elaborate extracellular matrix (ECM) that contributes to cell adhesion and to the milieu in which signaling interactions occur. Innovations in these pathways that enabled complex multicellularity occurred at the level of new genes, new functions for existing genes, but also at the regulatory level. Gene regulation by microRNAs expanded with the evolution of multicellularity, but the functions of individual microRNAs in this context are largely unexplored. A single microRNA, miR-100, arose in the last common eumetazoan ancestor and is widely conserved across animals. Here, we reveal the molecular function of the homolog of miR-100 in C. elegans, the miR-51 family. The miR-51 family acts in a dose dependent manner to control morphogenesis by regulating several genes involved in cell signaling, adhesion and migration, including modifiers of the ECM, specifically heparan sulfate sulfotransferases (HSTs). Specific HSTs and signaling pathway components are also predicted conserved targets of miR-100 across vertebrates. Our work suggests that this miRNA provided an innovation in the regulation of cellular interactions early in metazoan evolution, as animals evolved to form more complex bodies.

overall_design: Small RNA sequencing of C. elegans embryos at the comma stage. Embryos of eight different genotypes were sequenced, wildtype (N2) and animals with deletions or mutations in various members of the miR-51 miRNA family. Libraries for all genotypes were prepared in biological duplicates. Spike in oligos were added based on (Lutzmayer et al., 2017, Sci Rep). Protocol details can be found in Dexheimer PJ, Wang J, Cochella L. Two MicroRNAs Are Sufficient for Embryonic Patterning in C. elegans. Curr Biol 2020 Dec 21;30(24):5058-5065.e5. PMID: 33125867

first: Emilio

last: Santillan

first: Jingkui


title: An ancient and essential miRNA family controls cellular interaction pathways in C. elegans

overall_design: Quant-seq mRNA sequencing from embryos of defined developmental stages, of either wildtype genotype or with deletions of the complete miR-51/miR-100 family


title: INSM1 governs a neuronal progenitor state that drives glioblastoma in a human stem cell model

status: Public on Jul 15 2025

city: Saint Louis

first: Patrick

last: DeSouza

state: MO

address: 4515 McKinley Ave.

department: Neurosurgery

institute: Washington University School of Medicine

summary: Glioblastoma (GBM) is an aggressivea lethal brain tumorcancer marked by functional plasticity driven by the interplay between tumor cell-intrinsic mutations and -extrinsic heterogeneity, enabling rapid evolutiontheir interplay with developmental programs. To investigate how canonical GBM glioblastoma mutations promote functional plasticity, we have developeded an isogenic human neural stem cell (NSC) model of glioblastoma GBM by sequential addition of TERT promoter, TP53, and PDGFRA point mutations. TP53 loss-of-function increasesd TERT TERT expression during serial mutagenesis, but only triple mutant NSCs reliably formed lethal brain tumors in vivo that recapitulate glioblastomaGBM. Tumor cell evolution triggersed stress-related metabolic changes and transitionsed toward a neuronal progenitor network driven by transcription factor INSM1. INSM1 is highly expressed in human glioblastoma GBM tumors and, during cortical development, in intermediate progenitor cells (IPC), which give rise to neurons. Remarkably, INSM1 knockdown in triple mutant NSCs and primary glioblastoma GBM cells disrupted disrupts oncogenic gene expression and function and inhibited inhibits the in vivo tumorigenicity of triple mutant NSCs, highlighting the functional importance of an intermediate progenitor cellIPC-like cell state in glioblastoma GBM pathogenesis.

overall_design: Proneural in vitro serial mutagenesis scRNA-seq: H1 human embryonic stem cells (hESCs) were CRISPR edited to create single mutant TERTp C228T and double mutant TERTp+TP53 G743A hESCs. Cells exposed to CRISPR reagents but non-mutagenized were wildtype (WT) controls. WT, single, and double mutant hESCs were differentiated to neural stem cells and transduced with empty vector or mutPDGFRA D842V expression construct to create 4 Proneural genotypes: WT, single mutant TERTp, double mutant TERTp+TP53, and triple mutant TERTp+TP53+mutPDGFRA (PRO) engineered neural stem cells (eNSCs). Proneural genotypes were uniquely labeled with hashtag oligos (HTOs) and pooled for multiplexed scRNA-seq. Proneural in vitro multiomic scRNA+scATAC-seq: 2 biological replicates (independent differentiation, same genetic clone) of WT and PRO eNSCs were profiled for joint gene expression and chromatin accessibility at single cell resolution. Each condition was submitted independently for sequencing. Proneural in vivo scRNA-seq: PRO eNSCs were intracranially xenografting in the striatum of athymic nude mice, which formed tumors and caused animal death within 109 days. Tumors harvested from 3 mice (mouse-35, mouse-38, mouse-42) 100 days post-injection were dissociated into single cells and tumor cells were isolated by FACS for double human nuclear antigen+/CD45- populations. Tumors cells from each mouse were submitted independently for scRNA-seq. PRO eNSC in vitro RNAi scRNA-seq: PRO eNSCs were transduced with two independent RNA inhibition (RNAi) lentivirus constructs targeting transcription factors INSM1, TCF4, or SOX4, versus non-target control plasmid. For each gene, RNAi conditions (shCtrl vs. 2x RNAi) were uniquely labeled with HTOs and pooled for multiplexed scRNA-seq, resulting in 3 datasets with 3 samples each.

middle: A

first: Jeffrey

middle: R

last: Millman

first: Albert

middle: H

last: Kim


title: Single-cell DNA methylome and 3D genome atlas of human subcutaneous adipose tissue [snm3C-seq3]

city: Los Angeles

first: Asha

last: Kar

state: CA

address: 695 Charles E. Young Drive South

department: Human Genetics

institute: University of California Los Angeles

type: Methylation profiling by high throughput sequencing

summary: We performed single-nucleus RNA-seq and single-nucleus methyl-3C seq on subcutaneous adipose tissue (SAT) biopsies from Finnish women who underwent abdominal SAT liposuction at Tilkka Hospital, Helsinki, Finland. The purpose of this study was to understand the epigenomic, 3D topology, and transcriptomic dynamics across the SAT cell-types.

overall_design:
We performed snRNA-seq on subcutaneous adipose tissue (SAT) biopsies from eight participants, and snm3C-seq3 on five of the eight SAT biopsies.
snm3C-seq3: An Arima Genomics Arima-HiC Kit was used for the in situ chromatin conformation capture (3C), the fluorescence-activated nuclei sorting (FANS) and library preparation were performed using the snm3C-seq3 workflow, and libraries were sequenced using the Illumina NovaSeq 6000 instrument with S4 flow cells generating 150 bp paired-end reads.
snRNA-seq: The single-nucleus sequencing libraries were either constructed using the Chromium Single Cell 3’ v3.1 chemistry and sequenced on an Illumina NovaSeq S4 with a target sequencing depth of 600 million read pairs (n=6), or constructed using the Single Cell Multiome ATAC + Gene Expression Reagent Kit and sequenced on an Illumina NovaSeq SP with a target sequencing depth of 400 million reads (n=5).

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

first: Zeyuan Johnson

last: Chen

first: Seung Hyuk

middle: T

last: Lee

first: Kevin

middle: D

last: Abuhanna

first: Marcus

last: Alvarez

first: Yi

first: Sini

last: Heinonen

first: Hilkka

last: Peltoniemi

first: Kirsi

last: Pietiläinen

first: Chongyuan

last: Luo

first: Paivi

last: Pajukanta


title: ALS/FTD-linked TBK1 deficiency in microglia induces an aged-like microglial signature and drives social recognition deficits [FACS_SpinalCord_Microglia & LPS_Brain_SpinalCord]

status: Public on Jul 09 2025

city: Paris

first: Isadora

last: Lenoel

address: 47 Boulevard de l'hopital

country: France

institute: Paris Brain Institute

summary: TANK-Binding Kinase 1 (TBK1) is involved in autophagy and immune signaling. Dominant loss-of-function mutations in TBK1 are linked to Amyotrophic Lateral Sclerosis (ALS), Fronto-temporal dementia (FTD) and ALS/FTD. However, pathogenic mechanisms remain unclear, particularly the cell-type specific disease contributions of TBK1 mutations. Here, we focus on cell-specific Tbk1 deletion in motor neurons or microglia. We find that deleting Tbk1 from mouse motor neurons does not induce transcriptional stress, despite lifelong signs of autophagy deregulations. Conversely, Tbk1 deletion in microglia alters their homeostasis and reactive responses. In both spinal cord and brain, Tbk1 deletion leads to a pro-inflammatory, primed microglial signature with features of ageing and neurodegeneration. While it does not induce or modify ALS-like motor neuron damage, microglial Tbk1 deletion causes early FTD-like social recognition deficits. This phenotype is linked to focal microglial activation and T cell infiltration in the substantia nigra pars reticulata and pallidum. Our results reveal that part of TBK1-linked FTD disease originates from microglial dysfunction.

overall_design: FAC-sorted microglial cells from the spinal cord of young (4 months) and aged (22months) mice from 2 different genotypes : deletion of Tbk1 specifically in microglial cells of respectively 0 Tbk1 allele (WT), 2 Tbk1 alleles (KO). Tbk1fl/fl, Cx3CR1-Cre- mice = WT; Tbk1fl/+, Cx3CR1-Cre+ = HET; Tbk1fl/fl, Cx3CR1-Cre+ = KO. Biological replicates (mice) are between 4 and 5 per genotype. In addition, FAC-sorted microglial cells from the spinal cord and the brain of LPS-stimulated young (4 months) mice from the 2 genotypes.

first: Christian

middle: S

last: Lobsiger


title: Endothelial c-Maf protects against liver fibrosis by regulating chromatin accessibility to suppress pathogenic microvascular cell subsets

status: Public on Jul 17 2025

city: Mannheim

first: Gergana

last: Dobreva

state: Baden Württemberg

address: Ludolf-Krehl-Str. 7-11

department: Cardiovascular Genomics and Epigenomics

country: Germany

institute: Medical Faculty Mannheim/University of Heidelberg

summary: Liver sinusoidal endothelial cells (LSEC) are highly specialized within the hepatic vascular niche, controlling liver function and disease pathogenesis by angiocrine signaling. Recently, we identified GATA4 as a major transcription factor controlling LSEC development and protecting against liver fibrosis. As the transcription factor c-Maf was strongly downregulated in Gata4-deficient LSEC, we hypothesized that c-Maf might be an important downstream effector of GATA4 in LSEC differentiation and liver fibrogenesis. Clec4g-iCre/Maffl/fl mice (MafLSEC-KO) mice with LSEC-specific Maf deficiency were generated and liver tissue was analyzed by histology, immunofluorescence, and in situ-hybridization at the age of three months. LSECs were isolated for RNA-, ATAC-seq, and single-cell RNA-seq (scRNA-seq) analysis. The expression of MAF and its targets were analyzed in published human scRNA-seq data. Endothelial Maf deficiency resulted in perisinusoidal liver fibrosis without affecting metabolic liver zonation, accompanied by a switch from sinusoidal to continuous endothelial differentiation. Furthermore, endothelial Maf deficiency caused hepatic endothelial proliferation and expression of profibrotic angiocrine factors such as Pdgfb, Igfbp5, Sparcl-1, and Flrt2. scRNA-seq revealed replacement of zonated LSEC subpopulations by capillarized, proliferative, sprouting and secretory endothelial cell subsets promoting liver fibrogenesis and angiogenesis. This fundamental dysregulation of LSEC gene expression and differentiation was caused by changes in chromatin accessibility and transcription factor network alterations at promoter and enhancer regions following loss of Maf. Notably, endothelial MAF expression was also significantly reduced in human liver cirrhosis patients. Hepatic endothelial c-Maf protects against metabolic dysfunction-associated steatohepatitis-like liver fibrosis and regulates endothelial differentiation and zonation by controlling chromatin opening. Notably, our findings may open up new avenues to develop angiotargeted strategies for hepatic disease prevention and liver repair.

overall_design: LSEC were isolated from three 12 weeks old control and MafLSEC-KO mice were isolated and processed to perform ATAC-seq

first: Julio

last: Cordero

last: Schmid


title: Hypoxia-Driven Ribosome Biogenesis: Unveiling a Novel Regulatory Role of HIF1α in Breast Cancer Progression and Metastasis [SUM1315_Hypoxia_RNA-seq]

city: Birmingham

first: Dongquan

state: AL

address: 1717 11th Ave South

department: Medicine

institute: Univ of Alabama at Birmingham

summary: Solid tumors such as breast cancer have intratumoral regions of low oxygen tension, which promotes cancer cell invasion and metastasis. Hypoxia-Inducible Factor 1-alpha (HIF1α) represents the principal transcription factor orchestrating cellular responses to hypoxic conditions, mediating the regulation of genes implicated in oxygen homeostasis. Here we describe our findings that demonstrate upregulation of RNA Polymerase I activity in cells exposed to hypoxic conditions.  RNA Polymerase I is responsible for transcription of rDNA. Using confocal microscopy, we discovered that in hypoxia, HIF1ɑ localizes to the nucleolus, dependent on a previously unknown nucleolar localization signal in HIF1ɑ. Further detailed analysis by chromatin immunoprecipitation revealed that HIF1ɑ binds rDNA promoter at -230 and -350 bp. Ribosome biogenesis is important in supporting cellular metabolic processes and invasion and metastasis. Our analysis of publicly available data sets reveals that HIF1ɑ and rRNA biogenesis are upregulated in breast cancer patients and are associated with poor prognosis. Our studies show that inhibition of RNA Pol I diminished hypoxia-triggered invasion of breast cancer cells. Cumulatively our work unravels a novel role of HIF1ɑ in regulating rRNA biogenesis in breast cancer.

overall_design:
We investigated the impact of hypoxia on ribosome and rRNA biogenesis in human breast cancer SUM1315 cells. The cells were cultured for 24 hours under hypoxic (1% O2) and normoxic (21% O2) conditions to study the molecular mechanisms involved.
We performed RNA-sequencing on total RNA from hypoxic and normoxic SUM1315 cells. This high-throughput sequencing approach provided a global view of the transcriptomic changes due to hypoxia, offering insights into cancer cell adaptation to low oxygen levels.

first: Lalita

last: Samant

first: Rajeev

first: Amr

last: Elhamamsy


title: Hypoxia-Driven Ribosome Biogenesis: Unveiling a Novel Regulatory Role of HIF1α in Breast Cancer Progression and Metastasis [Polysome_RNA-seq]

overall_design:
To investigate the impact of hypoxia on the translation of transcripts and associated protein networks, we conducted polysome profiling on T47D, SUM1315, and SKBR3 breast cancer cells. Polysomes were enriched from these cells using a sucrose gradient fractionation system.
RNA-seq was then performed on the polysome fractions to identify the transcripts actively being translated by ribosomes under hypoxic conditions. This method enabled us to analyze how hypoxia influences translation.


title: ALS/FTD-linked TBK1 deficiency in microglia induces an aged-like microglial signature and drives social recognition deficits [Microdissected_Motor Neurons]

overall_design: Laser-microdissected motor neurons from the spinal cord of aged mice (20 months) from  different genotypes : deletion of Tbk1 specifically in motor neurons of respectively 0 Tbk1 allele (WT), or  2 Tbk1 alleles (KO). Tbk1fl/fl, Cx3CR1-Cre- mice = WT;  Tbk1fl/fl, Cx3CR1-Cre+ = KO. Biological replicates (mice) are 6 per genotype


title: ALS/FTD-linked TBK1 deficiency in microglia induces an aged-like microglial signature and drives social recognition deficits. [FACS_Brain_Microglia]

overall_design: FAC-sorted microglial cells from the brain of young (4 months) and aged (22months) mice from 3 different genotypes : deletion of Tbk1 specifically in microglial cells of respectively 0 Tbk1 allele (WT), 1 Tbk1 allele (HET), 2 Tbk1 alleles (KO). Tbk1fl/fl, Cx3CR1-Cre- mice = WT; Tbk1fl/+, Cx3CR1-Cre+ = HET; Tbk1fl/fl, Cx3CR1-Cre+ = KO. Biological replicates (mice) are between 5 and 7 per genotype


title: Thymic epithelia amplify noise in chromatin accessibility via p53 repression to impose immune tolerance [P53-WT-cKO_BulkRNA]

status: Public on Jul 08 2025

city: Chicago

first: Noah

last: Gamble

state: IL

department: Pathology

institute: University of Chicago

summary: Phenotypic plasticity of somatic cells is a principal feature of vertebrate adaptation as well as a hallmark of tumorigenesis. However, the determinants and mechanisms that regulate the stability of somatic cell identities remain unclear. Here, using the somatic plasticity of thymic epithelial cells – which facilitates the selection of a self-discriminating T cell repertoire – as a physiological model system, we show that stochastic fluctuations in background chromatin accessibility at nucleosome-dense regions are amplified by thymic epithelial cells to ectopically express thousands of genes highly restricted to other specialized cell types. We found broad regions of inaccessible chromatin flanking tissue-specific genes become ‘destabilized’ during thymic epithelial maturation independently of AIRE-induced transcription of these genes, but concurrently with the repression of the tumor suppressor p53. Augmenting p53 activity in thymic epithelial cells reduced noise in chromatin accessibility at nucleosome-dense regions, inhibited ectopic expression of tissue-specific genes and caused multi-organ autoimmunity. Furthermore, we found p53-regulated fluctuations in background chromatin accessibility in lung adenocarcinoma to be associated with high plasticity states that promote tumor progression. Taken together, our findings establish p53-dependent stabilization of nucleosomal barriers to cellular reprogramming as a fulcrum of cell fate integrity that underlies critical components of immune tolerance induction and oncogenic potential.

overall_design: Thymic epithelial cells were isolated using a previously published protocol (Kim & Serwold, Methods in Molecular Biology, 2019) with minor modifications. Briefly, thymi from 4-5 week-old mice were harvested and connective tissue was removed. Stromal tissue was perforated using scissors and incubated with rotation in DMEM-F12 (Sigma D6421) at room temperature for for 10min to liberate thymocytes. Remaining stromal tissue was enzymatically digested (0.5mg/mL Collagenase D (Sigma 11088858001), 0.2mg/mL DNaseI (Sigma 10104159001), 0.5mg/mL Papain (Worthington Biochemical LS003126)). Cells were stained with anti-EpCAM antibodies conjugated to APC-Cy7 and EpCAM+ cells were enriched via positive selection using magnetic anti-Cy7 beads (Miltenyi 130-091-652). Enriched fraction was stained with fluorescently conjugated antibodies for FACS or analysis.  75,000 primary mTECs were FACS-sorted directly into RULT lysis buffer (Qiagen RNEasy Kit) and total RNA was extracted using manufacturer’s instructions. mRNA was enriched and RNA-seq libraries were constructed using the Illumina TruSeq Stranded mRNA Kit. Paired-end, dual-index sequencing was performed on the Illumina NovaSeq 6000 platform.

first: Jason

last: Caldwell

first: Caroline

last: Kaiser

first: Joshua

last: McKeever

first: Alexandra

last: Bradu

first: Sandy

last: Klemm

first: William

middle: J

last: Greenleaf

first: Narutoshi

last: Hibino

first: Aaron

last: Dinner

first: Andrew

last: Koh


title: ALS/FTD-linked TBK1 deficiency in microglia induces an aged-like microglial signature and drives social recognition deficits. [in vitro_Microglia]

first: Isadora

last: Lenoel

overall_design: Microglial cells primary cultures from P0/P1 mouse pups. Mice had a deletion of Tbk1 in microglial cells specifically of respectively 0 Tbk1 allele (WT), 1 Tbk1 allele (HET), 2 Tbk1 alleles (KO). Tbk1fl/fl, Cx3CR1-Cre- mice = WT; Tbk1fl/+, Cx3CR1-Cre+ = HET; Tbk1fl/fl, Cx3CR1-Cre+ = KO. Microglial cultures were unstimulated (untreated, UT), treated with lipopolysaccharide (LPS) or interleukin-4 (IL4) or poly(I:C) for 24h. Biological replicates were 5 independant cultures.

first: Christian


title: ALS/FTD-linked TBK1 deficiency in microglia induces an aged-like microglial signature and drives social recognition deficits in mice

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

overall_design: Refer to individual Series


title: FOXP1 and FOXP4 function in mouse regulatory T cells [RNA-seq]

city: Palo Alto

first: Jonathan

last: Maltzman

address: 3801 Miranda Ave

institute: Stanford University

summary: FOXP3+ Treg cells are critical for immune tolerance. Genetic deletion of the Forkhead domain containing proteins of the FOXP-subfamily member FOXP1 from Tregs results in impaired function associated with reduced CD25 expression and IL-2 signaling, but to date the only other FOXP family member expressed in Tregs, FOXP4, has been minimally studied. To investigate the potential functional interactions among FOXP family members in Treg cells, we specifically deleted Foxp1, Foxp4 or both in FOXP3+ committed Treg cells in mice. Our findings show that mice with combined, but not individual, deficiency in FOXP1 and FOXP4 exhibit lymphoproliferation, inflammation, autoimmunity, and early lethality. The combined absence of FOXP1 and FOXP4 in Tregs results in an activated/effector-like phenotype with compromised suppressive function in peripheral lymphoid organs, an enhanced germinal center response and proinflammatory cytokine production. We further show that FOXP1 and FOXP4 bind to Il2ra promoter regions to regulate CD25 expression in Tregs. Through pairwise comparison among mouse strains with Treg-specific deletion of Foxp1, Foxp4 or both, our findings indicate a non-redundant but insufficient role of FOXP4 in Treg cell function.

overall_design: Transcriptomic profiling of FOXP1/FOXP4-deficient regulatory T cells and their wild-type counterparts using bulk RNA sequencing.

first: Dachuan

last: Dong

first: Vishal

last: Sindhava


title: Comprehensive multi-omics analysis uncovers potential risks of aged sperm on offspring development after short-term storage [RNA-Seq]

city: Vodnany

first: Yu

last: Cheng

state: South Bohemia

address: Zátiší 728/II

department: Faculty of Fisheries and Protection of Waters

country: Czech Republic

institute: University of South Bohemia in Ceske Budejovice

summary: In vitro short-term sperm storage is a common method used for artificial reproduction of fishes in aquaculture. Recent studies have demonstrated that prolonged sperm storage adversely affects offspring through epigenetics, yet its broader effects on other molecular levels such as transcription in progeny have been rarely explored. We employed comprehensive multi-omics approaches to uncover storage-induced epigenetic changes in sperm, and their effects on embryonic development and offspring health. Sperm from common carp (Cyprinus carpio) was stored in vitro in artificial seminal plasma for 14 days, and the impacts of storage on functional properties of sperm and progeny development were investigated. We combined DNA methylome and transcriptomic data to elucidate the potential mechanisms by which sperm storage influences progeny development.

overall_design: We have performed whole genome bisulfite sequencing of genomic DNA and RNA-seq from fresh and aged sperm after storage for 14 days post-stripping and their embryos from mid-blastula stage.

first: Sayyed

last: Mohammad Hadi Alavi

first: Songpei

last: Zhang

first: Rigolin

last: Nayak

first: Swapnil

last: Gorakh Waghmare

first: Deepali

last: Rahi Roy

first: Nururshopa Eskander

last: Shazada

first: Zhijun

last: Ma

first: Otomar

last: Linhart

first: Zuzana

last: Linhartová


title: Comprehensive multi-omics analysis uncovers potential risks of aged sperm on offspring development after short-term storage [WGBS]


title: Chronic social defeat stress induces meningeal neutrophilia via type I interferon signaling in males

status: Public on Jul 07 2025

city: Cambridge

first: Stacey

middle: L

last: Kigar

address: Herchel Smith Building, Robinson Way

department: Departments of Medicine and Psychiatry

country: United Kingdom

institute: University of Cambridge

summary: Animal models of stress and stress-related disorders are also associated with blood neutrophilia. The mechanistic relevance of this to symptoms or behavior is unclear. We used cytometry, immunohistochemistry, whole tissue clearing, and single-cell sequencing to characterize the meningeal immune response to chronic social defeat (CSD) stress in mice. We find that chronic, but not acute, stress causes meningeal neutrophil accumulation, and CSD increases neutrophil trafficking in vascular channels emanating from skull bone marrow (BM). Transcriptional analysis suggested CSD increases type I interferon (IFN-I) signaling in meningeal neutrophils. Blocking this pathway via the IFN-I receptor (IFNAR) protected against the anhedonic and anxiogenic effects of CSD stress, potentially through reduced infiltration of IFNAR+ neutrophils into the meninges from skull BM. Our identification of IFN-I signaling as a putative mediator of meningeal neutrophil recruitment may facilitate development of new therapies for stress-related disorders.

overall_design:
Following chronic social defeat, live cells from the meninges of stress-susceptible and unstressed homecage control (HC) C57 BL/6J mice were isolated by fluorescence-activated cell sorting and analyzed via scRNAseq.

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Submitter states that missing raw files are due to file loss.
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first: Mary-Ellen

last: Lynall

first: Allison

middle: E

last: DePuyt

first: Robert

last: Atkinson

first: Virginia

last: Sun

first: Joshua

last: Samuels

first: Nicole

last: Eassa

first: Chelsie

last: Poffenberger

first: Michael

last: Lehmann

first: Samuel

last: Listwak

first: Ferenc

last: Livak

first: Abdel

middle: G

last: Elkahloun

first: Menna

last: Clatworthy

first: Edward

last: Bullmore

first: Miles

last: Herkenham


title: STAMP: Single-Cell Transcriptomics Analysis and Multimodal Profiling through Imaging [Merscope]

status: Public on Jul 06 2025

city: Memphis

first: Jasmine

last: Plummer

state: TN

address: 262 Danny Thomas Pl

department: Developmental Neurobiology

institute: St. Jude Children's Research Hospital

summary: Single-cell RNA sequencing (scRNA-seq) has revolutionized our understanding of cellular diversity, but remains constrained by scalability, high costs, and the destruction of cells during analysis. To overcome these challenges, we developed STAMP (Single-Cell Transcriptomics Analysis and Multimodal Profiling), a highly scalable approach for the profiling of single cells. By leveraging transcriptomics and proteomics imaging platforms, STAMP eliminates sequencing costs, enabling single-cell genomics of hundreds to millions of cells at an unprecedented affordability. Immobilizing (‘stamping’) cells in suspension onto imaging slides, STAMP supports single-modal (RNA or protein) and multimodal (RNA, protein and H&E) profiling, while retaining cellular structure and morphology. Its flexible, ultra-high-throughput formats facilitate the analysis of single or multiple samples in the same experiment, enhancing experimental scalability and adaptability. We demonstrate STAMP's versatility across diverse experimental contexts, including the profiling of peripheral blood mononuclear cells (PBMCs), cell lines and stem cells. We also stamped cells and nuclei from dissociated tissues from mouse organs to simulate the generation of cell atlases. Accessibility was further enlarged by analyzing nuclei from archival formalin fixed and paraffin embedded (FFPE) tissue samples. Combining RNA and protein profiling, we applied STAMP for high-throughput immuno-phenotyping of millions of blood cells, providing multimodal insights into cellular heterogeneity. We highlight the capability of STAMP to identify ultra-rare cell populations, simulating clinical applications for detecting circulating tumor cells (CTCs). By capturing lineage dynamics during stem cell differentiation and subtle changes in in vitro activated PBMCs, we further showed its utility for large-scale perturbation studies. These results validate STAMP as a first-of-its-kind single-cell imaging analysis strategy. We present data for 10,962,092 high quality cells/nuclei and 6,030,429,954 high quality transcripts. By replacing sequencing with imaging, STAMP enables high-resolution cellular profiling that is more accessible, scalable, and cost-effective. STAMP has the potential to transform our ability to map biological diversity and dynamics, significantly advancing research and clinical applications.

overall_design: In this study, we transformed four advanced imaging platforms—Xenium Analyzer (10X Genomics), CosMx Spatial Molecular Imager (NanoString Technologies/Bruker), MERSCOPE (Vizgen), and PhenoCyler Fusion (Akoya Biosciences)—into scalable, flexible single-cell profiling tools. We termed this approach Single-Cell Transcriptomics Analysis and Multimodal Profiling (STAMP) through imaging.    STAMP leverages single-molecule imaging to analyze hundreds to millions of individual cells with unprecedented flexibility and scalability. The platform supports both single-modal (RNA or protein) and multimodal (RNA, protein, and H&E) profiling in single- or multi-sample configurations. We validated its performance across diverse sample types and experimental conditions, comparing its quality control metrics to classical single-cell analysis methods.    To assess scalability, STAMP was applied to cell populations ranging from hundreds to millions, demonstrating adaptability to varying sample sizes. It successfully profiled both whole cells and nuclei (from fresh-frozen and FFPE samples), enabling the analysis of archival tissues. Functional applications included:    -Immunophenotyping millions of peripheral blood mononuclear cells (PBMCs), capturing subtle compositional and transcriptional shifts induced by in vitro perturbations.  -Detection of ultra-rare cell populations, such as circulating tumor cells (CTCs), which are often undetectable using conventional scRNA-seq methods.  -Cellular differentiation and lineage tracing, where STAMP was used to study human embryonic stem cell (hESC) differentiation induced by bone morphogenetic protein 4 (BMP4), effectively modeling early embryonic gastrulation.  -Application to induced pluripotent stem cells (iPSCs), highlighting STAMP’s potential for large-scale perturbation and drug screening studies.

first: Emanuele

middle: P

last: Pitino

first: Anna

last: Reguant

first: Felipe

last: Dezem

first: Kellie

last: Wise

first: Irepan

last: Martinez

first: Helena

last: Crowell

first: Maycon

last: Marção

first: Sara

last: Ruiz

first: Elise

last: Courtois

first: William

middle: F

last: Flynn

first: Santhosh

last: Sivajothi

first: Emily

last: Soja

first: Ginevra

last: Caratù

first: German

last: Roldan

first: B

middle: K

last: Dredge

first: Yutian

last: Liu

first: Hannah

last: Chasteen

first: Monika

last: Mohenska

first: Juan

middle: C

last: Nieto

first: Raymond

last: Yip

first: Ruvimbo

last: Mishi

first: José

middle: M

last: Polo

first: Adrienne

last: Sullivan

first: Holger

last: Heyn

first: Luciano

last: Martelotto


title: Study of the impact of the lncRNA HSCHARME knock-out on human cardiomyocites [RNA-seq]

city: Rome

first: Alessandro

last: Palma

address: Piazzale Aldo Moro 5

department: Biology and Biotechnologies "Charles Darwin"

country: Italy

institute: Sapienza University of Rome

summary: We identified the human HSCHARME lncRNA and performed its functional inactivation in cardiomyocytes (CM) to study its impact on CM maturation and pathology-associated pathways.

overall_design: We performed RNA-seq and DE analysis on total RNA collected from isogenic HSCHARME WT and HSCHARME KO iPSC-derived cardiomyocytes (days 10 and 20 of differentiation).

first: Monica

last: Ballarino

first: Giulia

last: Buonaiuto


title: A parabrachial hub for the prioritization of survival behavior during pain

city: Philadelphia

first: John

middle: Nicholas

last: Betley

state: Pennsylvania

address: 433 S University Avenue, Lynch Bldg, Rm 321

department: Biology

institute: University of Pennsylvania

summary: Long-term sustained pain following acute physical injury is a prominent feature of chronic pain conditions. Populations of neurons that rapidly respond to noxious stimuli or tissue damage have been identified in the spinal cord and several nuclei in the brain. Understanding the central mechanisms that signal ongoing sustained pain, including after tissue healing, remains a challenge. In this study, spatial transcriptomics, neural manipulations, activity recordings and computational modeling demonstrate that activity in an ensemble of anatomically and molecularly diverse parabrachial neurons that express the NPY Y1 receptor is elevated following injury and predicts functional coping behavior. Regardless of the injury type, hunger, thirst, or predator cues suppressed sustained pain by inhibiting PBN Y1R neurons via the release of NPY. Together, our results demonstrate an endogenous analgesic hub at pain-responsive parabrachial Y1R neurons

overall_design: To identify brain regions and cell types involved in persistent pain, we performed spatial transcriptomic profiling of the parabrachial nucleus (PBN) in mice following formalin-induced inflammatory injury. Mice were injected with 2% formalin into the dorsal hind paw, and brain tissue was collected one hour post-injection to capture ongoing pain-related gene expression. Coronal sections of the hindbrain encompassing the PBN were subjected to high-plex spatial transcriptomics using the NanoString CosMx platform. The goal was to identify molecularly and spatially defined populations of neurons activated during sustained pain, with a particular focus on NPY Y1 receptor-expressing (Y1R) neurons. Spatial and computational analyses were used to define transcriptomic clusters, assess activity-induced gene expression, and map neuronal subpopulations implicated in chronic pain processing.

first: Nitsan

last: Goldstein

first: Amadeus

last: Maes

first: Heather

last: Allen

first: Tyler

last: Nelson

first: Kayla

last: Kruger

first: Nicholas

last: Smith

first: Albert

last: Yeung

first: Morgan

last: Kindel

first: Jamie

last: Carty

first: Lavinia

last: Boccia

first: Niklas

last: Blank

first: Emily

last: Lo

first: Rachael

last: Villari

first: Ella

last: Cho

first: Erin

last: Marble

first: Michelle

last: Awh

first: Yasmina

last: Dumiaty

first: Melissa

last: Chee

first: Rajesh

last: Khanna

first: Christoph

last: Thaiss

first: Bradley

last: Taylor

first: Ann

last: Kennedy


title: A PHOT2-NPH3-CAMTA2 light-temperature coincidence detection system in Arabidopsis I

status: Public on Jul 04 2025

city: La Jolla

first: Adam

last: Seluzicki

address: 10010 N. Torrey Pines Rd.

department: Plant Biology Laboratory

institute: HHMI, Salk Institute for Biological Studies

summary: Light and temperature variations are inescapable in nature, providing many types of information and influencing development and physiology. PHOTOTROPIN (PHOT) blue light receptor-kinases play well-characterized roles in multiple processes in short time scales, but functions over days, weeks, or seasons have rarely been explored. Here we show that PHOT2 integrates blue light and low temperature signals to control leaf number at flowering. Plants lacking PHOT2 show delayed flowering, specifically when grown in low temperature. This effect is blocked by loss of NON-PHOTOTROPIC HYPOCOTYL 3 (NPH3), and can be phenocopied by reduced blue light intensity, and by removal of CAMTA2. PHOT2 and CAMTA2 show non-additive genetic interactions, and a deep RNA-sequencing time course reveals highly overlapping phot2- and camta2-dependent effects on gene expression patterns across the day. Network-based co-expression analysis indicates system-level up-regulation of key growth modules in phot2 and camta2 mutants. Temperature- and genotype-dependent modulation of florigen-anti-florigen balance in phot2 and camta2 mutants is consistent with the phenotype. Together these data establish PHOT2 and NPH3 as a light-temperature coincidence detection module, operating with CAMTA2 as a downstream or parallel regulator of PHOT2-dependent gene expression.

overall_design: We aimed to understand temperature-dependent molecular  links between PHOTOTROPIN2 and CAMTA2,and functions of these genes over daily cycles.  Arabidopsis thaliana plants (gl1 (background control), phot1-5 gl1, and phot2-1 gl1)  were germinated on 1/2x Linsmaier & Skoog medium, transplanted to soil two days after germinating, and moved to growth chambers under 16h light:8h dark cycles, light intensity ~100μmol m-2 s-1 at 20°C and 15°C. Shoot tissue (above ground) from three plants per sample was harvested at ZT16 (just prior to lights-off) and ZT24 (just prior to the following lights-on) of day 14. Each genotype, temperature, and timepoint was collected in biological duplicate.

first: Joanne

last: Chory


title: Genetic architecture of a light-temperature coincidence detector


title: A PHOT2-NPH3-CAMTA2 light-temperature coincidence detection system in Arabidopsis II

overall_design: We aimed to understand temperature-dependent molecular  links between PHOTOTROPIN2 and CAMTA2,and functions of these genes over daily cycles.  Arabidopsis thaliana plants (Col0, phot2, camta2, and phot2 camta2)  were germinated on 1/2x Linsmaier & Skoog medium, transplanted to soil two days after germinating, and moved  to growth chambers under 16h light:8h dark cycles, light intensity ~100μmol m-2 s-1 at 20°C and 15°C. Shoot tissue (above ground) from six plants per sample was harvested at four hour intervals, starting at ZT0 (lights-on) of day 10, continuing until lights-on of day 11. Each genotype, temperature, and timepoint was collected in biological triplicate.


title: STAMP: Single-Cell Transcriptomics Analysis and Multimodal Profiling through Imaging [scRNA-seq]

status: Public on Jul 03 2025

first: Jasmine

last: Plummer

overall_design: In this study, we transformed four advanced imaging platforms—Xenium Analyzer (10X Genomics), CosMx Spatial Molecular Imager (NanoString Technologies/Bruker), MERSCOPE (Vizgen), and PhenoCyler Fusion (Akoya Biosciences)—into scalable, flexible single-cell profiling tools. We termed this approach Single-Cell Transcriptomics Analysis and Multimodal Profiling (STAMP) through imaging.  STAMP leverages single-molecule imaging to analyze hundreds to millions of individual cells with unprecedented flexibility and scalability. The platform supports both single-modal (RNA or protein) and multimodal (RNA, protein, and H&E) profiling in single- or multi-sample configurations. We validated its performance across diverse sample types and experimental conditions, comparing its quality control metrics to classical single-cell analysis methods.  To assess scalability, STAMP was applied to cell populations ranging from hundreds to millions, demonstrating adaptability to varying sample sizes. It successfully profiled both whole cells and nuclei (from fresh-frozen and FFPE samples), enabling the analysis of archival tissues. Functional applications included:  -Immunophenotyping millions of peripheral blood mononuclear cells (PBMCs), capturing subtle compositional and transcriptional shifts induced by in vitro perturbations. -Detection of ultra-rare cell populations, such as circulating tumor cells (CTCs), which are often undetectable using conventional scRNA-seq methods. -Cellular differentiation and lineage tracing, where STAMP was used to study human embryonic stem cell (hESC) differentiation induced by bone morphogenetic protein 4 (BMP4), effectively modeling early embryonic gastrulation. -Application to induced pluripotent stem cells (iPSCs), highlighting STAMP’s potential for large-scale perturbation and drug screening studies.

first: Emanuele

last: Pitino

first: Anna

last: Pascual-Reguant

first: Felipe

last: Dezem

first: Kellie

last: Wise

first: Irepan

last: Martinez

first: Helena

last: Crowell

first: Maycon

last: Marção

first: Sara

last: Ruiz

first: Elise

last: Courtois

first: William

last: Flynn

first: Santhosh

last: Sivajothi

last: Soja

first: Ginevra

last: Caratù

first: German

last: Mora Roldan

first: Dredge

middle: B

last: Kate

first: Yutian

last: Liu

first: Hannah

last: Chasteen

first: Monika

last: Mohenska

first: Juan

last: Nieto

first: Raymond

last: H. Yip

first: Ruvimbo

last: Mishi

first: José

last: Polo

first: Adrienne

last: Sullivan

first: Holger

last: Heyn

first: Luciano

last: Martelotto


title: MYST-mediated epigenetic regulation determines the adaptive artemisinin-resistant in Plasmodium falciparum [WGS]

city: Shanghai

first: Jincan

last: He

address: siping road 1239

institute: Tongji university

summary: To investigate the artemisinin resistance mechanism, we conducted a systematical evaluation of histone acetyltransferase expression in 45 cloned P. falciparum parasites and 30 wild-type field isolates. Remarkably, PfMYST, a member of the histone acetyltransferase MYST family, emerged as the sole candidate significantly associated with prolonged ring-survive of parasites. WGS analysis confirmed the genomic consistency among different parasite subclones. CHIP-seq analysis revealed PfMYST’s pivotal role in mediating histone modifications, particularly in H4K5ac and H4K8ac, within the P. falciparum genome. Through single-cell RNA sequence and conditional knockdown approaches, we identified and functionally validated PfMYST-targeted genes contributing to Plasmodium’s adaptive artemisinin resistance.

overall_design: Parasites were harvested to perform next-generation whole genome sequencing assay using  genomic DNA.

first: Cizhong

last: Jiang

first: Qingfeng

last: Zhang


title: MYST-mediated epigenetic regulation determines the adaptive artemisinin-resistant in Plasmodium falciparum [ChIP-Seq]

summary: To investigate the artemisinin resistance mechanism, we conducted a systematical evaluation of histone acetyltransferase expression in 45 cloned P. falciparum parasites and 30 wild-type field isolates. Remarkably, PfMYST, a member of the histone acetyltransferase MYST family, emerged as the sole candidate significantly associated with prolonged ring-survive of parasites. CHIP-seq analysis revealed PfMYST’s pivotal role in mediating histone modifications, particularly in H4K5ac and H4K8ac, within the P. falciparum genome. Through single-cell RNA sequence and conditional knockdown approaches, we identified and functionally validated PfMYST-targeted genes contributing to Plasmodium’s adaptive artemisinin resistance.

overall_design: We generated transgenic parasite lines tagged with HA and GFP (PfMYST-HA_GFP) in 3D7 stain using the CRISPR-Cas9 technique. To explore changes in histone acetylation upon PfMYST knockdown, we conducted a series of chromatin immunoprecipitation and high-throughput sequencing (ChIP-seq) assays targeting PfMYST, H4K5ac, H4K8ac, H4K12ac, and H4K16ac in both ring-stage and schizont-stage of PfMYST-HA_GFP and PfMYST-Ribo (PfMYST-off and wild type clones) respectively.


title: Defining Cellular Diversity at the Swine Maternal-Fetal Interface Using Spatial Transcriptomics and Organoids

status: Public on Jul 02 2025

city: Durham

first: Cole

last: McCutcheon

state: North Carolina

address: 3 Genome Court

department: Department of Integrative Immunobiology

institute: Duke University

summary:
n this study we had two primary aims: 1.) spatially define the transcriptional signatures of porcine maternal-fetal interface and 2.) develop and validate an organoid model which better recapitulated the porcine placenta. Using mid-gestation maternal-fetal interfaces of commercial landrace/large white composite gilts we performed spatial transcriptomics (n=4 interfaces) using Visium v1 spatial transcriptomics. We then went on to isolate trophoblast organoids from fresh-term placentas from crossbred sows consisting

655 of Yorkshire, Large White, and Landrace breeds. We then characterized the transcriptional profile of these organoids using bulk RNA-seq from 3 seperate lines using a standard Illumina library preparation. To characterize these organoids we performed single cell RNA-sequencing on 3 separate lines of swine trophoblast organoids using a standard 10x Genomics Single Cell 3' Gene Expression platform. All reads/samples were mapped to Sus scrofa v11.1.

overall_design: Bulk RNA-seq was performed on term porcine placentas from two independent animals using standard protocols.

first: Carolyn

last: Coyne


title: A genome-wide screen reveals Ints7 deficiency activates endogenous retrovirus MERVL, accompanied by anastasis of embryonic stem cells [CUT&Tag]

status: Public on Jul 01 2025

city: changsha

first: shen

last: yunfan

state: hunan

address: xiangya road

institute: central south university

summary: The murine endogenous retrovirus MERVL is closely associated with the developmental potential of totipotency, manifesting dynamic and reversible activation within a small population of in vitro-cultured mouse embryonic stem cells (mESCs). While numerous regulators have been identified to influence the on and off switches of MERVL, how its activation is linked to the cellular decision-making of mESCs remains poorly understood. In this study, our genome-wide knockout screen uncovered an intimate relationship between MERVL activation and DNA damage response pathways. Specifically, we found that deficiency of Ints7, a backbone subunit of the Integrator complex, resulted in increased DNA damage, stabilization of p53, and hence transcriptional activation of MERVL. Moreover, we revealed that MERVL activation upon Ints7 knockdown was frequently accompanied by the activation of caspase 3. Intriguingly, a proportion of the caspase-activated mESCs were able to switch on MERVL meanwhile circumvent apoptosis and evade cell death, resembling a process known as anastasis. Altogether, our study highlights an association between MERVL activation and the p53-dependent cell fate plasticity in response to DNA damage, suggesting that limited caspase activation can alter developmental potential of stem cells.

overall_design: CUT&Tag are performed in shInts7 and shNT group E14TG2a cells. CUT&Tag targets Kap1, H3K9me2, and H3K9me3.

first: Shen

last: Yunfan

first: Ni

last: Huiling

first: Li

last: Li

first: Yuan

last: Kai


title: Inhibition of proprotein convertase SKI-1 prevents blood vessel alteration following stroke

city: Toronto

first: Philippe

middle: P.

last: Monnier

state: ON

address: 60 Leonard Ave., 7KD-407

country: Canada

institute: University Health Network

summary: Neutralizing factors involved in blood vessel dysfunction offer a promising strategy for stroke recovery. Many extracellular proteins need enzymatic activation to function, and blocking this activation is an untapped approach to restoring vessel integrity. Here, we demonstrate that inhibition of the extracellular protease SKI-1 with PF-429242 restores blood-vessel integrity and promotes functional recovery in both large- and small-animal models for stroke. Single-cell mRNA sequencing identified molecular signatures suggesting that PF-429242 restores the expression of genes involved in vessel integrity in endothelial cells. Moreover, we identify a mechanism whereby RGMa cleavage by SKI-1 is required for RGMa to interact with Neogenin and alter vessel integrity. Either preventing RGMa cleavage or deleting Neogenin on endothelial cells reduced blood vessel dysfunction, increased tissue preservation, and restored brain function following stroke. This work identifies a much-needed therapeutic strategy which restores blood vessel integrity and functionality, showing efficacy in small- and large-animals.

overall_design: After middle cerebral artery occlusion (or surgical sham) mice were treated with PF-429242 or vehicle.  Hemispheres were separated and brain endothelial cell were isolated using tissue digestion, centrifuation, and FACS sorting.  FACS-sorted cells were analyzed using scRNA-seq.

first: Alireza

last: Shabanzadeh

first: Dene

last: Ringuette

first: Michal

last: Syonov

first: Qisi

last: Wu

first: Nardos

last: Tassew

first: Eric

last: Mun

first: Autumn

last: Meek

first: Starlee

last: Lively

first: Samuel

last: Suntharalingham

first: Mia

last: Mojica

first: Leonardo

last: Olijnyk

first: Beiping

last: Qiang

first: Warren

last: Foltz

first: Mark

last: Reed

first: Ignace

last: Moya

first: Carla

last: Brown

first: Jinzhou

last: Feng

first: Xinyue

last: Qin

first: Pavan

last: Akula

first: Thomas

last: Wälchli

first: Peter

last: Carlen

first: Paula

last: Alcaide Leon


title: Epigenetically conferred ring-stage survival in Plasmodium falciparum against artemisinin treatment

first: Jincan

last: He


title: Anti-Neoplastic Activity of Estrogen Receptor Beta in Chemoresistant Triple-Negative Breast Cancer

city: Rochester

first: Xiyin

last: Wang

state: Minnesota

address: 200 First St SW

department: Biochemistry and Molecular Biology

institute: Mayo Clinic

summary: The standard of care for triple-negative breast cancer is chemotherapy followed by surgical resection, and in most cases, additional rounds of chemotherapy treatment. While highly effective, approximately half of patients will experience disease recurrence that does not respond to additional rounds of treatment. Previous findings demonstrate that estrogen receptor beta (ERb) is expressed in upwards of 20% of triple-negative tumors, and that ERb functions as a tumor suppressor in triple-negative breast cancer models, it was of interest to determine if the tumor-suppressive effects of ERb persisted in chemo-therapy-resistant forms of the disease. Here, we demonstrate that the activation of ERb in chemotherapy-resistant triple-negative breast cancer cell lines elicits equivalent or superior inhibitory effects compared to chemotherapy-sensitive counterparts. These findings support the potential use of ERb-targeting agents in advanced forms of the disease.

overall_design: Cells were plated in triplicate in charcoal-stripped FBS containing medium plus 100 ng/mL doxycycline to induce ERb expression. After 24 h, a medium change was performed containing either ethanol vehicle or 1nM E2. Triplicate for each treatment. Twenty-four hours post-treatment, total RNA was isolated and RNA seq was performed using an Illumina HiSeq 4000 platform.

first: Michael

last: Emch

first: John

middle: R

last: Hawse


title: MYST-mediated epigenetic regulation determines the adaptive artemisinin-resistant in Plasmodium falciparum [scRNA-Seq]

overall_design: We conducted single-cell RNA sequencing experiments comparing wild-type and PfMYST-kd clones in response to artemisinin treatment. Single-cell transcriptomes were generated at 0, 6, and 9 h post-invasion (hpi) under 200nM artemisinin treatment for these parasites.

first: Cizhong

last: Jiang

first: Qingfeng

last: Zhang


title: Cardiomyocyte-specific Deletion of Med13 and Med13L Results in Dysregulated Gene Expression and Lethal Heart Failure

city: Iowa City

first: Chad

last: Grueter

state: IA

address: 169 Newton Rd, 4332 PBDB

department: Internal Medicine

institute: University of Iowa

summary: Background: Previous studies have linked mutations in the Mediator complex, specifically Mediator 13 (Med13) and Mediator 13-like (Med13L), with both congenital heart defects and cardiovascular diseases. Med13 and Med13L are mutually exclusive paralogs within the kinase submodule of the Mediator complex that have been shown to have partially redundant functions in embryonic development and transcription, but their combined roles have not been investigated in the adult heart. We investigated the critical yet redundant roles of Med13 and Med13L in adult murine cardiomyocytes for basal cardiac function. Methods: We generated an inducible Med13 and Med13L cardiomyocyte-specific knockout mouse model to investigate Med13 and Med13L regulation of cardiac function and transcription. We performed RNAseq on mice four weeks after the start of tamoxifen to identify changes in gene expression. Differentially expressed genes were compared across cardiac knockouts of Med13/13L, Med13, Med12, Med1, and Med30 elucidating similar mechanisms of cardiac dysfunction. Results: Med13/13L knockout resulted in decreased cardiac function leading to lethal heart failure in a median timeframe of 6 weeks from the start of tamoxifen. There is significant gene dysregulation after Med13/13L knockout with similar gene dysregulation of fibrotic pathways and calcium handling across Mediator cardiac knockouts. Conclusions: Med13 and Med13L function partially redundantly within the heart to maintain basal cardiac function and transcription, as well as redundancies within cardiac phenotypes related to mediator complex disruptions.

overall_design: RNA-seq profiling of Med13/13L knockout cardiac ventricles compared to Med13/13L fl/fl cardiac ventricles 4 weeks after tamoxifen at 12 weeks of age.

first: Kayla

last: Henry


title: Maintenance of neuronal TDP-43 expression requires axonal lysosome transport

city: Rockville

first: Veronica

last: Ryan

state: MD

address: 9000 Rockville Pike

department: Center for Alzheimer's and Related Dementias, Alzheimer's and Related Dementias Independent Scholar

institute: National Institute on Aging

summary: TDP-43 mislocalization and pathology occurs across a range of neurodegenerative diseases, but the pathways that modulate TDP-43 in neurons are not well understood. We generated a Halo-TDP-43 knock-in iPSC line and performed a genome-wide CRISPR interference FACS-based screen to identify modifiers of TDP-43 levels in neurons. A meta-analysis of our screen and publicly available screens identified both specific hits and pathways present across multiple screens, the latter likely responsible for generic protein level maintenance. We identified BORC, a complex required for anterograde lysosome transport, as a specific modifier of TDP-43 protein, but not mRNA, levels in neurons. BORC loss led to longer half-life of TDP-43 and other proteins, suggesting lysosome location is required for proper protein turnover. As such, lysosome location and function are crucial for maintaining TDP-43 protein levels in neurons.

overall_design: RNA-seq of i11w-hT iPSC-derived neurons at d7 post dox induction of NGN2 expression containing either a non-targeting (NT) or BORCS6 KD sgRNA.

middle: H

first: Sydney

last: Lawton

first: Joel

last: Reyes

first: James

last: Hawrot

first: Ashley

last: Frankenfield

first: Sahba

last: Seddighi

first: Daniel

last: Ramos

first: Jacob

last: Esptein

first: Faraz

last: Faghri

first: Weller

last: Cory

first: Jizhong

last: Zou

first: Martin

last: Kampmann

last: Replogle

first: Yue

middle: A

last: Qi

first: Hebao

last: Yuan

first: Kory

last: Johnson

first: Dragan

last: Maric

first: Ling

last: Hao

first: Mike

last: Nalls

last: Ward


title: SMARCA3 is a histone H3K23 ubiquitin ligase that regulates H3K9me3 in cancer [ChIP-seq]

city: New York

first: Yael

last: David

state: NY

department: Chemical Biology

institute: Memorial Sloan Kettering Cancer Center

summary: Histone ubiquitination is a crucial post-translational modification (PTM) regulating chromatin function, yet many histone ubiquitination sites and their regulatory enzymes remain poorly understood. Here, we identify SMARCA3, a SWI/SNF-related protein frequently downregulated in colorectal cancer (CRC), as an E3 ubiquitin ligase that targets histone H3 at lysine 23 (H3K23). We demonstrate that SMARCA3 histone ubiquitination activity is stimulated by the repressive H3K9me3 mark. Loss of SMARCA3 reduces both H3K23Ub and H3K9me3, increasing chromatin accessibility at promoters and enhancers enriched for pioneer transcription factor motifs. This chromatin ‘rewiring’ alters the transcriptional landscape, driving upregulation of cancer-promoting genes. We validate this mechanism in CRC cell lines and patient-derived organoids, where SMARCA3 loss reduces H3K23Ub and H3K9me3. In xenograft mouse models, overexpression of wild type SMARCA3, but not a RING domain mutant, suppresses tumor growth. Together, our findings define SMARCA3 as a key chromatin regulator contributing to CRC pathogenesis through epigenetic mechanisms.

overall_design: H3K27ac ChIP-seq on three replicates of wildtpye and SMARCA3 KO HEK293T cells

first: Ifé

last: Akano

first: Jakob

last: Hebert

first: Rochelle

last: Tiedemann

first: Richard

last: Koche

first: Yang

last: Xiao

first: Scott

last: Rothbart


title: Gene expression changes in three Pisolithus microcarpus monokaryon strains and one dikaryon strain during colonisation of Poplar roots compared to free-living mycelium.

city: Champenoux

first: Annegret

last: Kohler

address: Centre Grand Est Nancy

institute: INRAE

summary: Illumina  technology was used to generate mRNA profiles of three Pisolithus microcarpus monokaryon (M057, M091, and M120) and one dikaryon (D002) strains. Total RNAs was extracted from ectomycorrhizal (ECM) tissues and free-living mycelium (FLM) using a CTAB and lithium chloride (LiCl)-based method.TruSeq mRNA Stranded libraries were constructed and 2 x 125 bp sequenced using Illumina HiSeq 2500 at the Genotoul sequencing facilities (Toulouse, France).Raw reads were trimmed for low quality (quality score 0.05), Illumina adapters and sequences shorter than 15 nucleotides and aligned to the P. microcarpus 441 v. 2 primary scaffolds reference transcripts available at the JGI database  (https://mycocosm.jgi.doe.gov) using CLC Genomics Workbench 21.0.3.

overall_design: mRNA profiles of of three Pisolithus microcarpus monokaryon (M057, M091, and M120) and one dikaryon (D002) strains were generated by Illumina HiSeq 2500 (2x125bp). Three biological replicates were sequenced.

first: Maira

last: de Freitas Pereira

first: Francis

last: Martin


title: SMARCA3 is a histone H3K23 ubiquitin ligase that regulates H3K9me3 in cancer [RNA-Seq]

overall_design: RNA-seq on three replicates of wildtpye and SMARCA3 KO HEK293T cells


title: SMARCA3 is a histone H3K23 ubiquitin ligase that regulates H3K9me3 in cancer [ATAC-seq]

overall_design: ATAC-seq on three replicates of wildtpye and SMARCA3 KO HEK293T cells


title: Survey of maize differential expression upon environmental exposure to the tar spot pathogen Phyllahcora maydis

city: Auburn

first: Emily

last: Roggenkamp

address: 209 Rouse Life Science Bldg

institute: Auburn University

summary: Tar spot of maize, caused by Phyllachora maydis, is an emerging threat to crop production across the United States and Canada. Current effective management of the disease includes application of fungicides and use of partially resistant maize varieties. Several studies have focused on mapping of tar spot resistant loci from maize diversity panels. However, no additional analyses have been reported to further our understanding of the maize defense response to P. maydis. Therefore, prior to the availability of inoculation procedures, we performed transcriptome sequencing from maize leaf tissue exposed to P. maydis from a tar spot infested field and assessed differential gene transcript expression. Over the course of disease development, leaves were sampled at two timepoints: 10 days and 24 days post-exposure. Differentially expressed genes (DEGs) were determined by comparing gene transcript expression of the exposed samples to non-exposed controls at the respective timepoints.

sample_organism:
Zea mays
Phyllachora maydis

platform_organism:
Zea mays
Phyllachora maydis

overall_design: RNAseq of maize cv. B73 after environmental exposure to a high inoculum load of Phyllachora maydis in an infested field. Plants were exposed for a 10 days in the field. then brought back to the greenhouse. A subset of plants were not placed in the field (non-exposed). Samples were collected at two times during the experiment 10 days and 24 days after the start of the exposure.

first: Namrata

last: Jaiswal

first: Matthew

last: Helm

first: Martin

last: Chilvers


title: Investigating the cell of origin and novel molecular targets in Merkel cell carcinoma: a historic misnomer

city: Montreal

first: Richie

last: Jeremian

state: Quebec

address: 1001 Decarie Blvd, Research Institute of the McGill University Health Centre (RI-MUHC)

institute: McGill University Division of Dermatology

summary: Merkel cell carcinoma (MCC) is a highly aggressive skin cancer with the poorest prognosis, posited to be derived from Merkel cells. Emerging evidence, however, suggests other potential origins for MCC including hematological lineages. Given the high fatality of MCCs and that many arise in the immune suppressed population, often precluding the use of immunotherapy, it is important to determine the cell of origin for these cancers to elucidate targetable pathways to enable novel treatment approaches. We utilized targeted and multi-omics approaches to explore expression patterns at both the protein and RNA level of MCCs. Western blotting, immunofluorescence, and immunohistochemistry were performed for two patient-derived MCC samples, one MCC cell line, and 92 FFPE samples, respectively, for numerous B-cell markers. Further, RNA sequencing was performed on 17 FFPE patient-derived MCC samples and evaluated by principal component analysis for differentially expressed genes between samples based on sex and MCPyV status. Finally, weighted gene correlation network analysis (WGCNA) and cell type enrichment analyses were employed to determine pathway and cell type enrichment, respectively. MCC patient-derived and cell line samples heterogeneously expressed B-cell and neuroendocrine markers including PAX5, TdT, IgA, CD19, CK20, and chromogranin A. Further, transcriptome analysis demonstrated differentially expressed genes based on sex and MCPyV status. MCPyV+ tumors notably demonstrated significant upregulation of genes involved in immune cell function and downregulation of processes related to neuronal activity. Finally, WGCNA highlighted enrichment for pathways involved in immune function including B-cell differentiation. Cell type enrichment analysis highlighted enrichment for multipotent stem cells, several immune cell types, and keratinocytes. Our findings together with previous results indicate that MCCs are not derived from Merkel cells and instead from multiple or divergent cell types, including those of B-cell lineage. Further, MCC cell of origin may depend on patient and tumour specific characteristics including sex and cell type/differentiation state of a cell infected by the MCPyV. Our work highlights the need for a more personalized approach to diagnosis/characterization and treatment of MCCs given the variability of potentially targetable pathways.

overall_design: Total RNA was quantified for 17 FFPE-preserved MCC samples, and its integrity was assessed on a PerkinElmer LabChip GXII (Massachusetts, USA). rRNA was depleted from 125 ng of total RNA using the QIAseq FastSelect platform (QIAGEN, Hilden, Germany). cDNA synthesis was achieved with the NEBNext RNA First Strand Synthesis and NEBNext Ultra Directional RNA Second Strand Synthesis Modules. The remaining steps of library preparation were carried out using and the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England BioLabs, Massachusetts, USA). Adapters and PCR primers were purchased from New England BioLabs. Libraries were quantified using the KAPA Library Quanitification Complete Kit (Kapa Biosystems, Massachusetts, USA). Average size fragment was determined using a LabChip GXII (PerkinElmer) instrument (Massachusetts, USA). The libraries were normalized and pooled and then denatured in 0.05N NaOH and neutralized using HT1 buffer. The pool was loaded at 175pM on the Illumina NovaSeq S4 lane using the Xp protocol per the manufacturer’s recommendations. The run was performed for 2x100 cycles (paired-end mode). A phiX library was used as a control and mixed with libraries at 1% level. Base calling was performed using Real Time Analysis v3.4.4. Program bcl2fastq2 v2.20 was then used to demultiplex samples and generate FASTQ reads, which were subsequently aligned to the hg19 reference genome (Illumina, California, USA).

first: Ivan

middle: V

last: Litvinov


title: Ex vivo Model of Functioning Human Lymph Node Reveals Role for Innate Lymphocytes and Stroma in Response to Vaccine Adjuvant

city: Oxford

first: Jacqueline

middle: HY

last: Siu

address: Roosevelt Drive

department: Kennedy Institute of Rheumatology

institute: University of Oxford

summary: Immunological processes that underpin human immune responses to therapeutics and vaccine components, such as vaccine adjuvants, remain poorly defined due to a paucity of models that can faithfully recapitulate immune activation in lymphoid tissues. We describe precision-cut human lymph node (LN) slices as a functioning, architecturally-preserved, full-organ cross-sectional model system. Using single cell transcriptomics and multiplexed imaging we explored early inflammatory response to a potent, clinically-relevant liposomal vaccine adjuvant containing a TLR4-agonist and QS-21 saponin. Both TLR4 and NLRP3 inflammasome activation were involved in the direct initiation of the inflammatory response to adjuvant by monocytes and macrophages (Mon./Mac.) with secretion of IL-1b, but not IL-18, found to be TLR4-dependent. Innate lymphoid cells, including NK cells, were indirectly activated by Mon./Mac.-produced cytokines, signalling downstream to B cells via IFNg secretion. Resident LN stromal populations were primed both directly and indirectly by vaccine adjuvant and were instrumental in mediating inflammatory cell recruitment, particularly neutrophils.

overall_design: Healthy human cystic lymph nodes, obtained from routine cholecystectomy, enzymatically digested and sorted to remove dead (fixable live/dead-, 7AAD-) and red blood cells (CD235a+) and to deplete the majority of T (CD20-CD3+) and B (CD20+CD3-) cells which were spiked back at a 1:20 ratio. Lymph nodes were processed either as whole organs or precision cut slices cultured for 20 hours with or without adjuvant LMQ, a liposome-based adjuvant containing a synthetic toll-like receptor 4 (TLR4) agonist 3D-6-acyl-PHAD and QS-21 saponin.

first: Joannah

last: Fergusson

first: Moustafa

last: Attar

first: Alex

last: Gordon-Weeks

first: Mark

last: Coles

first: Calliope

last: Dendrou

first: Anita

last: Milicic


title: Oncogenic YAP sensitizes cells to CHK1 inhibition via CDK4/6 driven G1 acceleration

city: Wuerzburg

first: Stefan

last: Gaubatz

address: Am Hubland

department: Biochemistry and Cell Biology

institute: University of Wuerzburg

summary: Replication stress is a driver of genomic instability, contributing to carcinogenesis by causing DNA damage and mutations. While YAP, the downstream co-activator of the Hippo signaling pathway, plays a crucial role in regulating cell growth and differentiation, it is unclear whether it generates replication stress exploitable for therapy. Here, we report that oncogenic YAP shortens the G1 phase through increased CDK4/6 activity, leading to early S-phase entry. This causes origin under-licensing, an overall reduced rate of DNA replication, and, untypically, an accelerated speed of individual replication forks. CHK1 inhibition in cells expressing oncogenic YAP results in DNA damage during S-phase, which is not due to premature CDK1 activation or mitotic entry. Sensitivity to CHK1 inhibition depends on the YAP-TEAD interaction and involves a global increase in transcription and an increase in transcription-replication conflicts (TRCs). Replication stress from oncogenic YAP can be mitigated by restoring G1 length through partial CDK4/6 inhibition or by reducing YAP-induced hypertranscription. Our findings suggest a potential therapeutic strategy for targeting YAP-dependent cancers by exploiting their vulnerability to replication stress.

overall_design: MapR of MCF10A cells with doxycycline inducible YAP5SA to detect R-loops. Control MCF10A cells and YAP5SA expressing cells were treated with the CHK1 inhibitor prexasertib. As a positive control for MapR, MCF10A cells were treated with the BRD4 inhibitor JQ1.

first: Ann Lena

last: Mattes

first: Dörthe

last: Gertzmann

first: Carsten

last: Ade


title: TAX1BP3 is a SUMOylated Nucleocytoplasmic Shuttling Protein and Protects Against Vascular Neointimal Hyperplasia

city: Guangzhou

first: Hanyan

last: Yang

address: Zhujiang Hospital, Southern Medical University, Haizhu District, Guangzhou City, Guangdong Province

institute: Southern Medical University

summary: BACKGROUND: Neointimal hyperplasia is the major cause of significant vascular complications following arterial interventions. Despite the advancements in strategies such as drug-eluting stents (DES) to minimize neointimal hyperplasia, achieving consistently effective long-term outcomes remains a challenge. Protein-protein interactions (PPIs) mediated by PDZ domains are essential for numerous biological processes. However, little is known about the role of PDZ proteins in neointima formation. This study aims to explore the role of TAX1BP3, a singular PDZ protein, in phenotypic switching of VSMCs and its implication in neointimal hyperplasia. METHODS: Subcellular localization of TAX1BP3 was assessed in isolated VSMCs or arteries obtained from mice with neointima formation. TAX1BP3 mutants were constructed to study the role of SUMOylation on TAX1BP3 nucleocytoplasmic shuttling. VSMC-specific Tax1bp3 knockout mice were generated to determine the relevant phenotypes in a carotid artery wire injury model. RNA sequencing, ATAC-sequencing, computational prediction of complex structures, and Co-immunoprecipitation (Co-IP) were performed to elucidate the underlying molecular mechanisms. AAV-mediated Tax1bp3 gene delivery and engineered AIENPs-TAX1BP3 were employed to investigate the potential translational relevance. RESULTS: TAX1BP3 exhibited dynamic nucleocytoplasmic shuttling during phenotypic switching of VSMCs. TAX1BP3 is SUMOylated at K116 and its SUMOylation is essential for maintaining the nuclear localization of TAX1BP3. Deficiency of TAX1BP3 facilitated the transition from a contractile to synthetic phenotype and aggravated neointima formation following vascular injury in mice. The integration of RNA sequencing and ATAC sequencing unveiled that TAX1BP3 primarily regulated the cell cycle progression and cell proliferation of VSMCs through YAP-TEAD transcription activity. The computational prediction of TAX1BP3/YAP1 complex structures and protein interaction related experiments revealed TAX1BP3 and TEAD1 compete for binding to YAP through its TEAD binding domain via a non-canonical PDZ manner. AAV-mediated Tax1bp3 gene delivery significantly attenuated post-injury neointima formation and the progression of atherosclerosis. AIENPs-TAX1BP3 administration effectively reduced VSMCs phenotypic switching and neointimal hyperplasia. CONCLUSIONS: These results demonstrated SUMOylation of TAX1BP3 at K116 enables its nucleocytoplasmic shuttling during phenotypic switching of VSMCs. TAX1BP3 competitively interacts with YAP-TEAD complex in a non-canonical PDZ manner and exerted its protective role in vascular neointimal hyperplasia primarily through the regulation of cell proliferation.

overall_design: RNA-seq profiling of human aortic smooth muscle cells (HASMCs) treated with 0.1% BSA solution (Ctrl) or PDGF-BB dissolved in 0.1% BSA solution (PDGF-BB group) for 48 h.

first: Canzhao

last: Liu

first: Shanshan

last: Ai

first: Zhi

last: Zeng

first: Yulong

last: Zhong

first: Wenjie

last: Guo

first: Wenjing


title: Impacts of Glut1 Deficiency and High Glucose Exposure on Transcriptomic Profiling in Human Brain Microvascular Endothelial Cells

city: Mineola

first: Qing

middle: Robert

last: Miao

address: 101 Mineola Blvd

department: Foundations of Medicine

institute: NYU Long Island School of Medicine

summary: We used RNA-seq analysis to determine the alteration of transcriptomic profiling in human brain microvascular endothelial cells

overall_design: We utilized validated siRNA to suppress Glut1 expression and applied high glucose treatment in human brain microvascular endothelial cells. Following treatment, we isolated RNA to analyze changes in transcriptomic profiles via RNA sequencing

last: Fang

first: Wenquan

last: Hu

first: Xiang

last: Wang


title: Lipid nanoparticles as a tool to dissect dendritic cell maturation pathways

city: Zwijnaarde

first: Sophie

last: Janssens

address: Technologiepark 71

department: Inflammation Research Center

country: Belgium

institute: VIB/UGhent

summary: Dendritic cells (DCs) are short-lived immune cells that continuously roam our body in search for foreign or self-antigens. Upon acquisition of antigen, they mature and start migrating to the lymph node to present the antigen to naïve T cells. Depending on the context wherein the antigen is acquired, DCs will mature in a homeostatic or immunogenic manner. So far, the field is lacking proper tools to distinguish between the two maturation states. Most maturation markers are shared between the two states and therefore inappropriate to use. Still, defining the proper maturation type is crucial as it determines how the DCs will instruct the T cells towards antigen expressing cells. In this study, we used a lipid nanoparticle (LNP)-based approach to steer DC maturation pathways in vivo. CITE-seq analysis allowed us to design a panel of flow cytometry markers that reliably annotates the two DC maturation states, as validated in an infection and in a tumor model. Furthermore, the data corroborated that uptake of empty LNPs in DCs induces their homeostatic maturation, in contrast to uptake of mRNA-LNPs or TLR ligand-adjuvanted LNPs, leading to distinct effector T cell outputs. This reveals that LNPs themselves are not being decoded as “danger” by cDC1s, and that the cargo is essential to provide adjuvants activity, which is highly relevant for targeted design of LNP-based therapies.

overall_design: We performed CITE-seq to compare cDC1 maturation across various conditions within the spleen. Combining the measurement of the transcriptome and the surface epitopes of cDC1s facilitated a detailed analysis of the various stages cDC1s go through during this maturation process.

first: Sofie

last: Rennen

first: Victor

last: Bosteels

first: Clint

last: De Nolf

first: Karo

last: Van Lil

first: Sandra

last: Maréchal

first: Jessica

last: Vetters

first: Evelien

last: Van De Velde

first: Farzaneh

last: Fayazpour

first: Ria

last: Roelandt

first: Niels

last: Van Damme

first: Kevin

last: Verstaen

first: Rein

last: Verbeke

first: Sabrina

last: Marion

first: Bruno

last: De Geest

first: Ine

last: Lentacker


title: Ripk1 is critical for preserving effector regulatory T cells and the suppressive transcriptional program in regulatory T cells (scRNA-Seq)

city: Bochum

first: Carlos

last: Plaza Sirvent

address: Universitätstr. 150

institute: Ruhr University Bochum

summary: Ripk1 plays an important role as a regulator of programmed cell death processes such as apoptosis and necroptosis, and is involved in the initiation of pro-inflammatory NF-kB signaling. Immune tolerance depends on the proper function and homeostasis of regulatory T cells. Here, we show that Treg-specific ablation of Ripk1 in mice leads to a reduction of Treg cells and spontaneous systemic autoimmunity. Using chimeric mice that allowed us to study Treg cells in the absence of inflammatory conditions, we observed a disadvantage of Ripk1-deficient compared to Ripk1-proficient Treg cells. Importantly, we did not observe impaired viability of the Ripk1-deficient Treg cells. Furthermore, single-cell RNA sequencing revealed that Ripk1 is required for the maintenance of the Treg cell transcriptional signature, which is essential for the suppressive function of Treg cells. Together, these findings highlight the fundamental role of Ripk1 in maintaining immune homeostasis by preserving the suppressive phenotype of Treg cells

overall_design: Comparative gene expression profilling analysis at single cell level of Ripk1-proficient and Ripk1-deficient Treg cells. CD4+ CD25+ Treg cells were FACS sorted from pooled spleen+lymph nodes of chimeric mice carrying Ripk1-proficient and Ripk1-deficient Treg cells, which were generated using the loxp-Cre system. Ripk1 floxed mice were crossed to Foxp3Cre-YFP mice to obtain Ripk1fl/fl Foxp3Cre-YFP/wt chimeric female mice.  Ripk1 -deficient Treg cells were sorted based on YFP expression.

first: R

last: Geffers


title: Ripk1 is critical for preserving effector regulatory T cells and the suppressive transcriptional program in regulatory T cells (RNA-Seq)

overall_design: Comparative gene expression profilling analysis of Ripk1-proficient and Ripk1-deficient Treg cells. CD4+ CD25+ Treg cells were FACS sorted from pooled spleen+lymph nodes of chimeric mice carrying Ripk1-proficient and Ripk1-deficient Treg cells, which were generated using the loxp-Cre system. Ripk1 floxed mice were crossed to Foxp3Cre-YFP mice to obtain Ripk1fl/fl Foxp3Cre-YFP/wt chimeric female mice.  Ripk1 -deficient Treg cells were sorted based on YFP expression.


title: Vitamin D3 and its active compound calcitriol inhibits leukemia through the CHAC1-mediated NOTCH1 downregulation

city: Guiyang

first: Jiankun

last: Hong

state: Guizhou

address: Province science city, high tech, zone, Baiyun district

department: State Key Laboratory for Functions and Applications of Medicinal Plants

institute: Guizhou Medical University

summary:
Background: Vitamin D3 (VD3), a crucial fat-soluble vitamin, primarily exists in the form of calcitriol, a steroid hormone. Both exhibit anti-neoplastic activity towards several types of cancer, although the underlying mechanism is still not fully understood. Herein, we investigated the mechanism of inhibition of erytho-leukemogenesis by VD3 and calcitriol.
Methods: RNAseq analysis was used to explore the effect of VD3 and calcitriol on gene expression in leukemic cells. An animal model of erythro-leukemia was used to test the effect of both compounds in vivo. CHAC1 and VDR expression was knocked-downed in leukemia cells (genotype of the samples: chac1/vdr knockdown) via lentivirus-shRNA. CHAC1 expression was overexpressed in leukemia cells (genotype of the samples: chac1 overexpression) via lentivirus-RNA. Western blotting, RT-qPCR, cell cycle analysis and apoptosis assays were used to determine the effect of VD3 and calcitriol-induced growth suppression in leukemic cells in vitro.
Results: VD3 and calcitriol treatment strongly inhibited cancer progression in a mouse model of erythroleukemia induced by the Friend virus. In tissue culture, VD3 and calcitriol inhibited cell proliferation of leukemia cell lines. This leukemic inhibition was associated with the induction of G1 phase cell cycle arrest and apoptosis. Interestingly, RNAseq analysis supported by RT-qPCR revealed that both VD3 and calcitriol induced most known genes associated with the metabolic pathway in leukemic cells. The transcription of the VD3 receptor VDR is strongly induced by both VD3 and calcitriol treated cells. However, leukemia growth suppression by VD3/CA is shown to be independent of the activation of VDR. However, these compounds appeared to suppress the oncogene NOTCH1 by upregulating the cytosolic glutathione degradase CHAC1. Accordingly, lentivirus-mediated knockdown of CHAC1 antagonized leukemia cell suppression induced by VD3 and calcitriol, associated with higher NOTCH1 activation compared to control. Lentivirus-mediated overexpression of CHAC1 suppressed leukemia cell growth and inhibited the expression of NOTCH1. Additionally, glutathione antagonized leukemia cell suppression induced by VD3 and calcitriol, suggesting further that VD3 and calcitriol may inhibit the proliferation of leukemic cells by regulating the CHAC1 pathway.
Conclusions: These results demonstrated strong anti-leukemia activity of VD3 and Calcitriol. Moreover, the above results implicated CHAC1-mediated NOTCH1 suppression as the mechanism of leukemia cell growth inhibition by VD3 and calcitriol.

overall_design: Red leukaemia cells HEL were used as experimental subjects and HEL cells were treated with 25 µmol of calcitriol for 24 hours. CA sample: HEL treated with 25 µmol of calcitriol for 24 hours。

first: Yaacov

last: ben-david


title: Basal cell of origin resolves neuroendocrine-tuft lineage plasticity in cancer [Single cell RNA-seq]

city: Durham

first: Trudy

last: Oliver

email: tgo@duke.edu, trudy.oliver@duke.edu

state: NC

address: Duke University, Box 3813, LSRC Room C138B, 308 Research Drive

department: Pharmacology & Cancer Biology

institute: Duke University

summary: Neuroendocrine and tuft cells are rare, chemosensory epithelial lineages defined by expression of ASCL1 and POU2F3 transcription factors, respectively. Neuroendocrine cancers, including small cell lung cancer (SCLC), frequently display tuft-like subsets, a feature linked to poor patient outcomes. The mechanisms driving neuroendocrine–tuft tumour heterogeneity, and the origins of tuft-like cancers are unknown. Using multiple genetically-engineered animal models of SCLC, we demonstrate that a basal cell of origin (but not the accepted neuroendocrine origin) generates neuroendocrine–tuft-like tumours that highly recapitulate human SCLC. Single-cell clonal analyses of basal-derived SCLC further uncovers unexpected transcriptional states and lineage trajectories underlying neuroendocrine–tuft plasticity. Uniquely in basal cells, introduction of genetic alterations enriched in human tuft-like SCLC, including high MYC, PTEN loss, and ASCL1 suppression, cooperate to promote tuft-like tumours. Transcriptomics of 944 human SCLCs reveal a basal-like subset and a tuft-ionocyte-like state that altogether demonstrate remarkable conservation between cancer states and normal basal cell injury response mechanisms. Together, these data suggest that the basal cell is a plausible origin for SCLC and other neuroendocrine-tuft cancers that can explain neuroendocrine–tuft heterogeneity—offering new insights for targeting lineage plasticity.

overall_design:
For basal organoids, mouse tracheas from Rb1 fl/fl; Trp53 fl/fl; Rbl1/p130 fl/fl (RPR2), Rb1 fl/fl; Trp53 fl/fl;H11b-LSL-MycT58A-Ires-Luc (RPM), and Rb1 fl/fl; Trp53 fl/fl;H11b-LSL-MycT58A-Ires-Luc; Ascl1 fl/fl (RPMA) mouse models (not exposed to Cre recombinase) were isolated and ITGA6+ basal cells were live-sorted and propogated as organoids. Organoids from each genotype were lineage tagged with the CellTag V1 lentiviral library (Kong et al., Nature Protocols, 2020) pre-transformation ("CellTagged Pre-Cre"; to trace lineage from a single normal basal cell of origin) and one set of RPM organoids were rather "CellTagged Post-Cre" (to trace lineage from a single transformed basal cell of origin). Wildtype organoids (no CellTag information used) were subject to 10X single cell RNA-sequencing (scRNA-seq) and then recombined via Adenoviral-CMV-Cre. "Celltagged Pre-Cre" recombined organoids were subject to scRNA-seq and were submitted as one sample, but multiplexed using 10X Genomics CellPlex Kit (CellPlex oligos included as metadata information). RPM "CellTagged Post-Cre" recombined organoids were also subject to 10X scRNA-seq. On the same day of scRNA-seq sample preparation of transformed organoids, RPM ("CellTagged Pre-Cre" and "CellTagged Post-Cre"), RPR2, and RPMA organoids were allografted into flanks of scid/beige mouse hosts. Resulting allograft tumors (n=2 RPM "CellTagged Post-Cre", n=1 RPM "CellTagged Pre-Cre", n=1 RPMA, and n=1 RPR2) were subject to mechanical and enzymatic digestion into a single-cell suspension, then underwent 10X scRNA-seq library prep. For primary tumors, Rb1 fl/fl; Trp53 fl/fl;H11b-LSL-MycT58A-Ires-Luc (RPM) mice were treated with naphthalene to stimulate basal cell proliferation, then 72 hours later received KRT5-Cre to initiate tumors from basal cells in the mouse lung. Upon tumor formation, n=2 tumors from n=2 K5-Cre initiated mice were isolated, digested, pooled (one pool multiplexed), then subject to scRNA-seq. In addition, n=1 primary RPM tumor and n=1 primary RPM-Cas9-GFP tumor, initiated by CGRP-Cre were isolated (one tumor per animal), digested, pooled and multiplexed using 10X CellPlex oligos, and subject to scRNA-seq. See associated GEO metadata and manuscript methods for additional detail.

Source code and additional metadata used to reproduce these analyses are also publicly available on Github (https://github.com/TGOliver-lab/Ireland_Basal_SCLC_2025).

CellTag Experiment "A"= RPM matching organoids and resulting allograft, CellTagged pre-Cre; CellTag Experiment "B"= RPM matching organoids and resulting allografts (n=2), CellTagged post-Cre; CellTag Experiment "C"= RPMA matching organoids and resulting allograft, CellTagged pre-Cre.

first: A

middle: S

last: Ireland

first: T


title: Ripk1 is critical for preserving effector regulatory T cells and the suppressive transcriptional program in regulatory T cells

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

overall_design: Refer to individual Series


title: Mitochondrial Complex I inhibition enhances astrocyte responsiveness to pro-inflammatory stimuli

city: Bonn

first: Daniele

last: Bano

state: NRW

address: Venusberg Campus 1, Gebaeude 99

institute: DZNE, German Center for Neurodegenerative Diseases

summary: Inhibition of the mitochondrial oxidative phosphorylation (OXPHOS) system can lead to metabolic disorders and neurodegenerative diseases. In primary mitochondrial disorders, reactive astrocytes often accompany neuronal degeneration and may contribute to neurotoxic inflammatory cascades that elicit brain lesions. The influence of mitochondria to astrocyte reactivity as well as the underlying molecular mechanisms remain elusive. Here we report that mitochondrial Complex I dysfunction promotes neural progenitor cell differentiation into astrocytes that are more responsive to neuroinflammatory stimuli. We show that the SWI/SNF/BAF chromatin remodeling complex takes part in the epigenetic regulation of astrocyte responsiveness, since its pharmacological inhibition abrogates the expression of inflammatory genes. Furthermore, we demonstrate that Complex I deficient human iPSC-derived astrocytes negatively influence neuronal physiology upon cytokine stimulation. Together, our data describe the SWI/SNF/BAF complex as a sensor of altered mitochondrial OXPHOS and a downstream epigenetic regulator of astrocyte-mediated neuroinflammation.

overall_design: To investigate molecular mechanisms underlying impaired neuronal differentiation of mitochondrial deficient neural progenitor cells, we performed RNA-seq in Hq versus wt proliferating as well as 48h-differentiated cells.

first: Lena

last: Wischhof

first: Lorenzo

last: Bonaguro


title: Somatic mutations in TBX3 promote hepatic clonal expansion by accelerating VLDL secretion

status: Public on Jun 30 2025

city: Dallas

first: Gabriella

last: Quinn

state: TX

address: 5323 Harry Hines Blvd

institute: UT Southwestern Medical Center

summary: We’ve previously demonstrated that hepatocytes with Tbx3 deletions have increased cellular fitness and clonally expand during metabolic-dysfunction associated steatotic liver disease (MASLD) development. TBX3 is a transcription factor that is critical for embryonic development, but has never been studied within the context of MASLD. Here, we show that somatic mutations in TBX3 are found in human patients with MASLD. Liver specific deletion of Tbx3 in mice protects against diet induced MASLD through upregulating VLDL-TG particle secretion. TBX3 transcriptionally suppresses the conventional secretory pathway and cholesterol biosynthesis. Hdlbp is a direct target of TBX3 that is responsible for altered VLDL secretion. In contrast to WT TBX3, TBX3 harboring somatic mutations found in humans failed to suppress VLDL secretion in vivo. In conclusion, mutations in TBX3 promote clonal expansion during MASLD development through increased lipid disposal, demonstrating clonal fitness can benefit the liver even at the cost of hyperlipidemia.

overall_design: High throughput sequencing of DNA from the CUT&RUN protocol of stable H2.35 mouse hepatocyte cell line overexpressing a V5 tagged mouse Tbx3 compared to an IgG isotype control (n=3) and ChIP-sequencing of human TBX3 from mouse livers overexpressing Ty1 tagged TBX3 via AAV compared to an IgG isotype control (n=4).

first: Gregory

last: Mannino

first: Min

last: Zhu

first: Zixi

last: Wang

first: Xun

first: Boyuan

last: Li

first: Meng-Hsiung

last: Hsieh

first: Thomas

last: Mathews

first: Lauren

last: Zacharias

first: Wen

last: Gu

first: Purva

last: Gopal

first: Natalia

last: Brzozowska

first: Peter

last: Campbell

first: Matt

last: Hoare

first: Glen

last: Liszczak

first: Hao