title: Branched-Chain Amino Acids Contribute to Diabetic Kidney Disease Progression via PKM2-Mediated Podocyte Metabolic Reprogramming and Apoptosis

city: Xi’an, China

first: zhao

last: huishou

state: Please select...

address: 127 West Changle Rd, Xi’an, China, 710032

institute: Xijing Hospital

summary: Approximately 30-40% of people living with diabetes develop diabetic kidney disease (DKD). It is of great importance to identify the “decisive factors” for DKD initiation. Recently, high levels of plasma and urinary branched-chain animo acid (BCAA) metabolites were shown to predict the future risk of DKD. Here, we observed that glomerular podocytes in male and female patients with DKD and db/db mice specifically displayed BCAA catabolic defects. Podocyte-specific knockout of PP2Cm, a key enzyme involved in BCAA catabolism, or exogenous supplementation of BCAAs induced DKD phenotypes in high-fat (HF) diet-fed male mice as manifested by podocyte dysfunction and apoptosis, glomerular pathological changes, and proteinuria. Mechanistically, BCAAs promoted PKM2 depolymerization and inactivation in podocytes. Depolymerized PKM2 suppressed glucose oxidative phosphorylation (OXPHOS) and promoted a shift in glucose metabolism to serine and folate biosynthesis. Depolymerized PKM2 is also cotransported to the nucleus with DDIT3, acting as a novel cotranscriptional factor to increase DDIT3 transcriptional activity, which promotes Chac1 and Trib3 expression and directly induces podocyte apoptosis. We concluded that BCAA catabolic defects may be one of the missing factors that determine DKD initiation. Targeting BCAA catabolism or PKM2 activation is a promising strategy for preventing DKD progression.

overall_design: Gene expression profiling analysis of RNA-seq data from MPC-5 podocytes exposed to high glucose (HG, 25 mM glucose), HG plus 3 mM branched chain amino acids (BCAAs), or HG/BCAA with 20 nM TEPP46. Samples were collected after indicated treatment of 24 hrs in duplicate

first: Huishou

last: Zhao

first: Dan

last: Sun

first: Shan

first: Yi

last: Liu

first: Wenjun

last: Yan

first: Ling

last: Tao


title: Opposing lineage specifiers induce a pro-tumor hybrid-identity state in lung adenocarcinoma [RNA-seq]

status: Public on Jun 13 2025

city: Salt Lake City

first: Gabriela

last: Fort

state: UT

address: 2000 Circle of Hope Drive

country: USA

institute: Huntsman Cancer Institute, University of Utah

type: Expression profiling by high throughput sequencing

summary: Lineage plasticity is critical for tumor progression and therapy resistance, but the molecular mechanisms underlying cell identity shifts in cancer remain poorly understood. In lung adenocarcinoma (LUAD), the loss of pulmonary lineage fidelity and acquisition of alternate identity programs converge on hybrid-identity (hybrid-ID) states which are postulated to be key intermediates in LUAD evolution and are characterized by the co-activation of developmentally incompatible identity programs within individual cells. Here, we uncover a previously unrecognized role for the gastrointestinal transcriptional regulator HNF4α in driving tumor growth and hybrid-ID states in LUAD. In LUAD cells expressing the lung lineage specifier NKX2-1, HNF4α induces a GI/liver-like state by directly binding and activating its canonical targets. HNF4α also disrupts NKX2-1 genomic localization and dampens pulmonary identity within hybrid-ID LUAD. We show that this hybrid-ID state is maintained by sustained by RAS/MEK signaling. Inhibition of the RAS/MEK signaling cascade augments NKX2-1 chromatin binding at pulmonary-specific genes and induces drug resistance-associated pulmonary signatures. Finally, we demonstrate that HNF4α depletion sensitizes LUAD cells to KRASG12D inhibition. Collectively, our data show that co-expression of opposing lineage specifiers is a novel mechanism of identity dysregulation in LUAD that influences both tumor progression and response to targeted therapy.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: RNA-seq was performed on murine 3154 organoids treated with EtOH or 4OHT to delete Hnf4a, human H1651 cells treated with dox (or vehicle) to overexpress HNF4α, murine 3311 cells treated with Trametinib (MEKi) (or vehicle), murine 1027B organoids treated with Trametinib (MEKi), MRTX1133 (KRASG12Di) (or vehicle), human H358 cells treated with Trametinib (MEKi) (or vehicle), human H1651 cells treated with Trametinib (MEKi) (or vehicle), and murine 3154 organoids treated with MRTX1133 and/or 4OHT to delete Hnf4a.

first: Eric

middle: L

last: Snyder


title: PUS10-induced tRNA fragmentation impacts retrotransposon-driven inflammation

status: Public on Jun 14 2025

city: Lund

first: Phuong

last: Cao Thi Ngoc

address: BMC, B1222b, Klinikgatan 26

country: Sweden

institute: Lund University

type: Non-coding RNA profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series

first: Magdalena

last: Madej

first: Sowndarya

last: Muthukumar

first: Anna

last: Konturek-Cieśla

first: Silvia

last: Tucciarone

first: Alexandre

last: Germanos

first: Christian

last: Ashworth

first: Knut

last: Kotarsky

first: Sudip

last: Ghosh

first: Zhimeng

last: Fan

first: Helena

last: Fritz

first: Izei

last: Pascual-Gonzalez

first: Alain

last: Huerta

first: Nicola

last: Guzzi

first: Anita

last: Colazzo

first: Giulia

last: Beneventi

first: Hang-Mao

last: Lee

first: Maciej

last: Cieśla

first: Christopher

last: Douse

first: Hiroki

last: Kato

first: Vinay

last: Swaminathan

first: William

middle: W

last: Agace

first: Ainara

last: Castellanos-Rubio

first: Paolo

last: Salomoni

first: David

last: Bryder

first: Cristian

last: Bellodi


title: ATAC-seq of human plasmacytoid dendritic cells in adult and elderly donors

city: Palo Alto

first: Rebeca

last: Arroyo Hornero

state: California

address: Campus Drive

institute: Stanford

summary: Aging is associated with profound changes in immune cell function. To investigate how aging impacts plasmacytoid dendritic cells (pDCs), we profiled purified pDCs from healthy adult (20–40 years) and elderly (>65 years) human donors. Using bulk RNA-seq (GSE269411) and bulk ATAC-seq (GSE279911), we identified transcriptional and epigenetic changes that occur with age. These datasets provide a resource to explore age-associated alterations in pDC identity, gene regulation, and chromatin accessibility.

overall_design: pDCs were FACS-sorted from 6 adult (20-40 years old) and 6 elderly (>65 years old). DNA extraction and library preparation was performed by the Stanford Functional Genomics Core. DNA was stored at -20C post transposase reaction until all samples had been collected. Samples were sequenced on a NovaSeq 6000.

first: Juliana

last: Idoyaga


title: Rapid generation of functional vascular organoids via simultaneous transcription factor activation of endothelial and mural lineages

city: Boston

first: Yonglin

last: Zhu

state: MA

address: 300 Longwood Ave

department: Cardiac Surgery

institute: Boston Children's Hospital

summary: Vascular organoids (VOs) are valuable tools for studying vascular development, disease, and regenerative medicine. However, controlling endothelial and mural compartments independently remains challenging. Here, we present a streamlined method to generate VOs from induced pluripotent stem cells (iPSCs) via orthogonal activation of the transcription factors ETV2 and NKX3.1 using Dox-inducible or modRNA systems. This approach enables efficient co-differentiation of endothelial (iECs) and mural cells (iMCs), producing functional 3D VOs in five days without ECM embedding. VOs matured further upon ECM exposure, forming larger, structured vessels. Single-cell RNA sequencing revealed vascular heterogeneity, and temporal regulation of transcription factor expression allowed modulation of arterial and angiogenic iEC phenotypes. In vivo, VOs engrafted into immunodeficient mice, formed perfused vasculature, and promoted revascularization in models of hind limb ischemia and pancreatic islet transplantation. These findings establish a rapid and versatile VO platform with broad potential for vascular modeling, disease studies, and regenerative cell therapy.

overall_design: Using bulk RNA sequencing, we compared gene expression profiles of induced endothelial cells between 2D (2D-iEC) and VO (VO-iEC), and also the gene expression profiles of induced mural cells between 2D (2D-iMC) and VO (VO-iMC). By comparing these samples, we can assess the maturation potential of VO-derived iECs and iMCs compared to monolayer differentiation protocols. Employing single cell RNA sequencing (scRNA-seq), we investigated Dox1-VOs (dox1_S6) and Dox3-VOs (dox3_S7), as well as Dox3-VOs (S3-7_S8) cultured for an additional seven days without Dox exposure, to further investigate the vascular cell heterogeneity within VOs.

first: Juan

last: Melero-Martin

first: Liyan

last: Gong

first: Yadong

last: Zhang


title: Opposing lineage specifiers induce a pro-tumor hybrid-identity state in lung adenocarcinoma [ChIP-seq]

first: Gabriela

last: Fort

overall_design: ChIP-seq was performed on murine 3154 organoids treated with EtOH or 4OHT to delete Hnf4a, human H1651 cells treated with dox (or vehicle) to overexpress HNF4α, murine 3311 cells treated with Trametinib (MEKi) (or vehicle), murine 1027B organoids treated with Trametinib (MEKi) (or vehicle), human H358 cells treated with Trametinib (MEKi) (or vehicle). Sequential ChIP-seq (ChIP-re-ChIP) was performed on murine 3311 cells for HNF4α and NKX2-1.

first: Eric

last: Snyder


title: RNAseq of human plasmacytoid dendritic cells in adult and elderly donors

overall_design: pDCs were FACS-sorted from 6 adult (20-40 years old) and 6 elderly (>65 years old) donors directly into Qiazol lysis buffer (Quiagen) and frozen at -80C for RNA sequencing. RNA extraction and library preparation were performed by the Stanford Functional Genomics Core. Amplification and qPCR were performed simultaneously after all samples were collected. Quality control was conducted using the Bioanalyzer analysis through the Stanford Functional Genomics Core. Samples were barcoded and pooled for sequencing. Samples were sequenced on a NovaSeq 6000 through the Stanford Functional Genomics Core.


title: Gene expression profile at single cell level of tumor-infiltrating neutrophils (TINs) of cholangiocarcinoma (CCA) tumors

city: Bunkyo-ku

first: Osamu

last: Sugahara

state: Tokyo

address: Yushima 1-5-45

department: Advanced Research Initiative

country: Japan

institute: Institute of Science Tokyo

summary: To investigate the mechanism of tumor inhibitory effect of rhG-CSF administration, TINs were obtained from control and rhG-CSF–treated CCA-bearing mice and analyzed by scRNA-seq.

overall_design: TINs (CD45+CD11b+Ly6G+) were obtained from control (n = 2) and rhG-CSF–treated (n = 2) CCA-bearing mice by fluorescence-activated cell sorting and analyzed by CEL-Seq2 (control_1: 14 plates, control_2: 12 plates, G-CSF_1: 13 plates, G-CSF_2: 13 plates). Sequencing was performed on Illumina NovaSeq 6000.

first: Tsunaki

last: Higa

first: Keiichi

middle: I

last: Nakayama


title: Endogenous FGF gradients are required for cell fate patterning in 2D human gastruloids

city: Ann Arbor

first: Michigan

middle: CDB

last: Bioinformatics

state: MI

address: 109 Zina Pitcher Pl

department: Cell & Developmental Biology

institute: University of Michigan

summary: The role of FGF is the least understood of the morphogens driving mammalian gastrulation. Here we investigated the function of FGF in a stem cell model for human gastrulation known as a 2D gastruloid. We found a ring of FGF-dependent ERK activity closely follows the emergence of primitive streak (PS)-like cells but expands further inward. We showed that this ERK activity pattern is required for PS-like differentiation and depends on localized activation of basally polarized FGF receptors (FGFR) by endogenous FGF gradients. By single cell RNA-sequencing, we identified the main receptor to be FGFR1 and the key ligands FGF2/4/17 and showed that this is similar to the human and monkey embryo but different from the mouse.

overall_design:
Micropatterned human pluripotent stem cells (hPSCs) were collected at 42 hours after treatment with BMP4 for single cell RNA sequencing with 10X Genomics Chromium Controller.

GSE271604_42h_rep1_filtered_Counts.csv.gz is reanalyzed data for GEO sample GSM5517031 (Series GSE182057).

first: Zhiyuan

last: Yu

first: Idse

last: Heemskerk

first: Craig

last: Johnson


title: CRAMP1 CUT&RUN in K562 cells

city: Cambridge

first: Iva

last: Tchasovnikarova

address: Tennis Court Road

department: Gurdon Institute

country: United Kingdom

institute: University of Cambridge

summary: The essential role of the core histones (H2A, H2B, H3 and H4) in DNA packaging has been well understood for decades, but the function of the linker histone (H1) remains enigmatic. H1 compacts nucleosome arrays in vitro, but the multiple H1 subtypes and variants encoded in mammalian genomes (11 in both mice and humans) hamper genetic studies to determine H1 function in vivo. Challenging the prevailing view that linker histones are a general feature of heterochromatin, here we show a critical requirement for linker histones in the function of Polycomb Repressive complex 2 (PRC2). Through a CRISPR/Cas9 genetic screen in a fluorescent reporter cell line responsive to PRC2 perturbation, we identified an essential requirement for the poorly characterised gene CRAMP1 in PRC2-mediated repression. CRAMP1 localises to the promoters of all expressed H1 genes where it acts as a positive transcriptional regulator. Ablation of CRAMP1 provides a unique tool to simultaneously deplete all linker histones, which results in selective decompaction of H3K27me3-marked loci and derepression of PRC2 target genes without concomitant loss of PRC2 occupancy or enzymatic activity. Strikingly, in contrast to the broad genomic distribution previously ascribed to H1, we find that linker histones selectively localise to genomic loci marked by H3K27me3 across diverse cell types and organisms. Altogether, our data demonstrate a prominent role for linker histones in epigenetic repression by PRC2.

overall_design: V5 CUT&RUN was performed in K562 cells expressing V5-tagged full-length CRAMP1 or three domain truncation mutants. V5 CUT&RUN in wild-type cells served as a negative control.

first: Rachael

middle: E

last: Matthews

middle: A


title: Single-nuclei multiome (ATAC + Gene Expression) sequencing of purified human dendritic cells

first: Rebeca

last: Arroyo Hornero

summary: Plasmacytoid and conventional dendritic cells (pDCs and cDCs, respectively) are closely related immune lineages with distinct functions. Whether pDCs can switch fate into the cDC lineage has remained controversial. Here, we sequenced purified pDCs and DCs to create a reference map of the transcriptome and chromatin landscape of all major human blood DC populations (GSE267174 and GSE267100). We compared this reference map to the transcriptomic and epigenetic profile of activated pDCs (GSE267099 and GSE266889). We show that activation of purified, bona fide human pDCs induces transcriptional and epigenetic heterogeneity at the single-cell level. A fraction of activated pDCs retains classical pDC features, while others acquire a cDC2-like identity through an intermediate state resembling transitional dendritic cells (tDCs). These datasets—generated using single-cell multiomic profiling (scRNA-seq and scATAC-seq) and SMART-seq—provide a resource to investigate the molecular basis of pDC-to-cDC2 fate transition.

overall_design: Single nuclei were extracted from isolated human dendritic cells and subjected to 10X Genomics single nuclei multiome (ATAC + GEX) sequencing to evaluate the transcriptomic and epigenomic profile of dendritic cell subsets.


title: Opposing lineage specifiers induce a pro-tumor hybrid-identity state in lung adenocarcinoma [scRNA-seq]

overall_design: scRNA-seq was performed on tumor cells derived from KPH mice treated with vehicle or tamoxifen to delete Hnf4a.


title: Inactivation of histone chaperone HIRA unmasks a link between normal embryonic development of melanoblasts and maintenance of adult melanocyte stem cells

city: La Jolla

first: Xue

last: Lei

state: CA

address: 10901 N Torrey Pines Rd

institute: SBP medical discovery institute


title: Bulk RNA-Seq of Inha KO mouse placenta exposed to DEHP

status: Public on Jun 12 2025

city: Clayton

first: Kate

last: Loveland

state: Victoria

address: 27-31 Wright St

country: Australia

institute: Hudson Institute of Medical Research

summary: Introduction: In the placenta, activin A affects decidualisation and trophoblast growth and invasion. Levels increase during pregnancy to peak at parturition, while premature elevation is a hallmark of several pregnancy disorders. Here we examine the impact of elevated activin A bioactivity in the inhibin α knockout (Inha KO) mouse placenta. We also investigate whether simultaneous exposure to the endocrine disruptor, diethyl-hexyl phthalate (DEHP), which impairs normal placental function, exacerbates effects on placental morphology and gene expression in this model. Methods: Litters of Inha WT, Het and KO fetuses were collected at E15.5 from time-mated Inha heterozygous pregnant mice randomly assigned to three groups: untreated, corn oil (Vehicle) or DEHP 500 mg/kg/day, from E12.5-14.5 (n=2-17). Gross and histological placental morphology was analysed, and bulk RNA-sequencing conducted. Results: Placentae of Inha WT, Het and KO fetuses exhibited no gross differences, and no differentially expressed genes. However, sex differences included a significant increase in labyrinth area and placental size from WT males compared to WT females. DEHP exposure significantly increased fetal resorption at E15.5 but yielded little differences in placental morphology. Transcript analysis identified sex- and genotype-specific transcript alterations resulting from DEHP treatment. Eight transcripts were altered by DEHP exposure across all genotypes (Cts3, Ceacam13, Gm5155, Ssr4, Sec11c, Psg18, Psg-ps1, Taf7l). Discussion: Despite minimal morphological changes, transcriptomic differences suggest that spongiotrophoblast cells and syncytiotrophoblast giant cells are key targets of DEHP exposure, with CEA family transcripts susceptible to its effects. Additionally, DEHP exposure also modulates gene transcript responses to elevated activin A.

overall_design:
RNA extracted from placentae of E15.5 Inha WT, Het and KO mouse fetuses was analysed by bulk RNA-seq
Fetuses received either no treatment, treatment with corn oil (vehicle control) or treatment with 500 mg/kg/day DEHP delivererd orally to the pregnant dam daily from E12.5-14.5

first: Lacey

last: Klompmaker

first: Sarah

middle: C

last: Moody

first: Junlan

last: Ma

last: Marshall

first: Emily

middle: J

last: Camm

first: Constance

last: Malliaras


title: A20’s Linear Ubiquitin Binding Motif Restrains Pathogenic Activation of TH17/22 cells and IL-22 Driven Enteritis [scRNA-seq]

city: San Francisco

first: Averil

address: 513 Parnassus Avenue

institute: University of California, San Francisco

summary: A20, encoded by the TNFAIP3 gene, is a protein linked to Crohn and celiac disease in humans. We show that mice expressing point mutations in A20’s M1-ubiquitin binding zinc-finger 7 (ZF7) domain spontaneously develop proximal enteritis that requires both luminal microbes and T cells. Cellular and transcriptomic profiling reveal expansion of TH17/22 cells and exuberant expression of IL-17A and IL-22 in intestinal lamina propria of A20ZF7 mice. While deletion of IL-17A from A20ZF7 mice exacerbates enteritis, deletion of IL-22 abrogates intestinal epithelial cell hyperproliferation, barrier dysfunction, and alarmin expression. Colonization of adult germ-free mice with normal luminal flora drives duodenal IL-22 expression and duodenitis. A20ZF7 TH17/22 cells autonomously express more RORgammat and IL-22 after differentiation in vitro. ATAC sequencing identified an enhancer region upstream of the Il22 gene, and this enhancer demonstrated increased activating histone acetylation coupled with exaggerated Il22 transcription in A20ZF7 T cells. Acute inhibition of RORgammat normalized histone acetylation at this enhancer. Finally, CRISPR/Cas9-mediated ablation of A20ZF7 in human T cells increases RORgammat expression and IL22 transcription. These studies link A20’s M1-ubiquitin binding function with RORgammat expression, expansion of TH17/22 cells, and epigenetic activation of IL-22 driven enteritis.

overall_design: Intact proximal small intestines from 12-week-old mice were lysed in TRIzol and used to isolate total RNA. One microgram of total RNA was subsequently used to generate libraries for bulk RNAseq.

first: Christopher

last: Bowman


title: Effect of depletion of Endothelial Cell STING in response to pressure overload induced heart failure

first: Erin

last: Sanders

address: 150 Harrison Ave

department: Immunology

institute: Tufts University

summary: Capillary rarefaction and cardiomyocyte (CM) hypertrophy are hallmarks of the complex syndrome of heart failure (HF), a leading cause of hospitalization and death. Molecular signals within and between cellular components of the heart have emerged as central hubs that modulate cardiac pathophysiology. Here, we discovered that the Stimulator of Interferon Genes (STING) is highly expressed in human and mouse cardiac endothelial cells (EC) and is activated in the onset of HF. Using global and inducible EC-specific STING-/- mice, we report that EC STING is required for contractile dysfunction in an experimental model of HF induced by transverse aortic constriction (TAC), through the regulation of CM hypertrophy and capillary rarefaction. We report that ECs sorted from TAC EC-STING-/- mice are enriched in gene sets related to integrin and cell adhesion pathways to extracellular matrix (ECM) compared to controls and have decreased expression of the pro-hypertrophic gene IL-6. CellChat analysis of human cardiac cells from patients with non-ischemic cardiomyopathy revealed EC-CM communication, and mechanistically, we found that STING activation induces IL-6 secretion, and that EC derived IL-6 is necessary to induce pro-hypertrophic gene expression in CMs in a STING dependent manner. Our study demonstrates a novel role for STING in ECs contributing to hypertrophy and contractile dysfunction in experimental HF.

overall_design: RNA-seq profiling of CD45- CD31+ Endothelial Cells flow cytommetry sorted out from murine hearts of Cad5CreERT2+/+STINGfl/fl and Cad5CreERT2-/-STINGfl/fl mice subjected to 4 weeks of transverse aortic constriction (TAC) or sham surgery.

first: Pilar

last: Alcaide


title: NSUN5 Mediates Resistance to Doxorubicin via Upregulation of DNA Damage Repair Proteins BRCA2 and BRIP1 in Colorectal Cancer

city: Guangzhou

first: Chao

last: Qin

address: Guangdong Province

country: China

institute: sun yat-sen university

summary: Despite advancements in diagnosis and therapy, chemotherapy resistance and metastasis remain significant challenges for colorectal cancer (CRC) patients. Addressing resistance to cell death is crucial for improving cancer treatment outcomes. NOP2/Sun RNA methyltransferase 5 (NSUN5) has been implicated in cancers, but its role in chemotherapy resistance of CRC remains unclear. Herein we reveal that NSUN5 is highly expressed in CRC through bioinformatics analysis and validation using human and mice CRC tissues. High expression of NSUN5 predicted poorer disease-free survival in CRC patients. Nsun5-deficient mice exhibited reduced tumor incidence and malignancy in an AOM/DSS-induced CRC model. NSUN5 knockdown or knockout showed diminished proliferation and migration in CRC cell lines, which was reversed by NSUN5 overexpression or reintroduction. Intriguingly, overexpression of NSUN5 conferred resistance to doxorubicin, an effective chemotherapeutic agent leads to DNA damage, whereas NSUN5 deficiency increased CRC cells' sensitivity to the drug, both in vitro and in vivo. Mechanistically, NSUN5 upregulated BRCA2 and BRCA1-interacting helicase 1 (BRIP1) expression and interacted with these proteins to prevent cell death in response to DNA damage. Analysis of our local cohort and public data sets showed a positive correlation between NSUN5, BRCA2, and BRIP1 in CRC patients. Collectively, we uncover the role of NSUN5 in CRC progression from the perspective of chemotherapy resistance, potentially offering innovative insight on the clinical therapy and prognosis of CRC.

overall_design: Stable NSUN5-overexpressing HCT15 cell lines were generated via lentiviral transduction, and empty vector-transfected cells served as controls, RNA-seq was employed.

first: Wen

last: Ni

first: Yuanyuan

last: Xu


title: shRNA-mediated knockdown of PRMT5 gene in LNCaP cells

city: West Lafayette

first: Chang-Deng

last: Hu

state: IN

address: 201 S. University St, Hansen Life Sciences Building, Room 401A

department: Department of Medicinal Chemistry and Molecular Pharmacology

institute: Purdue University

summary: We performed shRNA-mediated knockdown of PRMT5 in LNCaP cells via dox-inducible expression system. We sought to compare transcriptome with- and without PRMT5 knockdown across three biological replicates

overall_design: Identify differentially expressed genes in LNCaP cells following PRMT5 knockdown across three biological replicates

first: Xuehong

last: Deng

first: Andrew

last: Asberry

first: Jun

last: Wan

first: Sheng

last: Liu


title: Single-nuclei multiome (ATAC + Gene Expression) sequencing of CD40L-activated human plasmacytoid dendritic cells

first: Rebeca

last: Arroyo Hornero

overall_design: Single nuclei were extracted from CD40L-stimulated human plasmacytoid dendritic cells and subjected to 10X Genomics single nuclei multiome (ATAC + GEX) sequencing to evaluate cellular heterogeneity.

first: Juliana

last: Idoyaga


title: Non-canonical AMPA receptor blockade reduces lymph node egress and neuroinflammation [Bulk RNA-seq]

city: Mainz

first: Frauke

last: Zipp

address: Langenbeckstraße 1

department: Department of Neurology

country: Germany

institute: University Medical Center Mainz

summary: Disturbances in the glutamatergic system have been linked to neuronal pathology. Investigating therapeutic translation, we discovered immune-related effects for the selective non-competitive AMPA receptor blocker perampanel in mouse models of multiple sclerosis.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for EAE perampanel treated mice and controls

first: Beatrice

last: Wasser

first: Manuela

last: Ecker

first: Nicholas

last: Hanuscheck

first: Erik

last: Ellward

first: Muthuraman

last: Muthuraman

first: Mohammadsaleh

last: Oshaghi

first: Stefan

last: Bittner


title: The PARP1-EXD2 Axis Orchestrates R-Loop Resolution to Safeguard Genome Stability

city: Hangzhou

first: Dong

last: Fang

state: Zhejiang

address: 866 Yuhangtang Road

department: Life Sciences Institute

institute: Zhejiang University

summary: R-loops represent three-stranded nucleic acid structures comprising an RNA-DNA hybrid and a displaced single-stranded DNA. Deregulation of R-loop dynamics can obstruct DNA transcription and replication processes, compromising genome integrity and contributing to human diseases. Here, we identify EXD2(exonuclease 3′–5′ domain-containing 2) as a crucial R-Loop resolvase. We demonstrate that EXD2, through direct interaction with PARP1 via poly(ADP-ribose) (PAR) polymers, is recruited proximally to R-loops, where it undergoes acetylation by the acetyl-transferase CBP at Lys416. This modification increases EXD2’s binding affinity towards R-loop structures, enabling its transition to and retention on R-loops, despite the rapid turnover of PAR polymers. Once localized, EXD2 acts as an exonuclease, preferentially degrading RNA strands within R-loops to promote their resolution. Consequently, loss of EXD2 results in the intracellular accumulation of R-loops, exacerbating transcription-replication conflicts, and ultimately leading to genomic instability. These findings support a model in which R-loop-triggered PARP1 activation orchestrates EXD2-mediated resolution of R-loops, thereby preserving genome stability.

overall_design: CUT&Tag of Rloop in HeLa (ctrl, ctrl_RNaseH, ctrl_MMS, EXD2_KO1_MMS, EXD2_KO2_MMS)


title: Systems-level analysis provides insights on methanol-based production of l-glutamate and its decarboxylation product γ-aminobutyric acid by Bacillus methanolicus

city: Trondheim

first: Luciana

last: Fernandes de Brito

address: Kjemi 3, 3.237, Gløshaugen, Sem Sælandsvei 6/8

department: Department of Biotechnology and food science

country: Norway

institute: Norwegian University of Science and Technology

summary: Bacillus methanolicus is the next workhorse in biotechnology using methanol, an alternative and economical one-carbon feedstock that can be obtained directly from carbon dioxide, as both carbon and energy source for the production of various value-added chemicals. The wild-type strain MGA3 of B. methanolicus naturally overproduces l-glutamate in methanol-based fed-batch fermentations. Here we generated, by directed evolution, a B. methanolicus mutant strain exhibiting enhanced l-glutamate production capability (> 150%). To showcase the potential of the evolved strain, further metabolic engineering enabled the production of γ-aminobutyric acid (GABA) directly from l-glutamate, with a yield of >13 g/L from methanol during fed-batch fermentations. By using a system level analysis, encompassing whole-genome sequencing, RNA sequencing, fluxome analysis and metabolic modelling, we were able to elucidate the metabolic and regulatory adaptations that sustain the biosynthesis of these products. The metabolism of the mutant strain evolved to prioritize energy conservation and efficient carbon utilization. Key metabolic shifts include the downregulation of energy-intensive processes such as flagellation and motility and the rerouting of carbon fluxes towards α-ketoglutarate and its derivative, l-glutamate. Moreover, we observed that transformation of the evolved strain with a GABA biosynthesis plasmid had a positive effect on l-glutamate production and explained it by an upregulation of various transaminases involved in the l-glutamate biosynthesis from α-ketoglutarate. These insights provide a foundation for further rational metabolic engineering and bioprocess optimization, enhancing the industrial viability of B. methanolicus for sustainable production of l-glutamate and its derivatives.

overall_design:
Transcriptomic data was conducted for the following Bacillus methanolicus strains and conditions: MGA3gad (wild-type with vector pBV2xp-gadST), ABBM4307 (mutant), ABBM4307gad (mutant with vector pBV2xp-gadST)) and ABBM4307gad NI (mutant with uninduced vector pBV2xp-gadST)
The processed data comprise the same transcriptome reads mapped onto the reference's chromosome (Chr_*) and native plasmids (pBM19_* and pBM69_*).

first: Marta

last: Irla

first: Nærdal

last: Ingemar

first: Virant

last: David

first: Brautaset

last: Trygve

first: Busche

last: Tobias

first: Goranovič

last: Dušan

first: Haupka

last: Carsten

first: Heux

last: Stephanie

first: Kosec

last: Gregor

first: Rückert

last: Christian

first: Wendisch

last: Volker F

first: Brito

last: Luciana F

first: Vicente

last: Cláudia M


title: Non-canonical AMPA receptor blockade reduces lymph node egress and neuroinflammation [scRNA-seq]

first: Frauke

last: Zipp

first: Beatrice

last: Wasser

first: Manuela

last: Ecker

first: Nicholas

last: Hanuscheck

first: Erik

last: Ellward

first: Muthuraman

last: Muthuraman

first: Mohammadsaleh

last: Oshaghi


title: Single-nuclei multiome (ATAC + Gene Expression) sequencing of human plasmacytoid dendritic cells

first: Rebeca

last: Arroyo Hornero

overall_design: Single nuclei were extracted from isolated human plasmacytoid dendritic cells and subjected to 10X Genomics single nuclei multiome (ATAC + GEX) sequencing to evaluate the purity of isolated cells.

first: Juliana

last: Idoyaga


title: Single-cell RNA sequencing of mouse articular cells

city: Shanghai

first: Dandan

last: Cao

address: 1239 Siping Road, Yangpu District

institute: Tongji University

summary:
This SuperSeries is composed of the SubSeries listed below.
GSE278533
GSE295257

overall_design: Refer to individual Series


title: Mapping complex multimodal phenotypes in tissue with mosaic genetic screens

first: Reuben

last: Saunders

address: 455 Main St

institute: Whitehead Institute

summary: The function of organs in an animal requires the coordinated activity of thousands of genes in multiple, spatially organized cell types. Understanding the basis of this emergent tissue function will require new approaches to dissect how gene activity controls diverse cellular and tissue phenotypes in vivo. Here, we develop paired imaging and sequencing methods to construct large-scale spatial and transcriptional genotype-phenotypes maps in tissue infected in a mosaic with pooled genetic perturbations. Using imaging, we identify perturbed cells in fixed tissue sections while simultaneously measuring gene expression and subcellular morphology. Using single-cell sequencing, we then measure transcriptome-wide cellular states caused by the same genetic perturbations in dissociated fixed cells. We apply this multimodal approach to study hundreds of knockouts in a genetic mosaic mouse liver. We discover novel regulators of hepatocyte zonation, characterize a liver-specific component of the unfolded protein response, and identify distinct pathways that cause convergent hepatocyte steatosis. Our approach will enable new ways of interrogating the genetic basis of complex cellular and organismal physiology and will provide crucial training data for emerging machine learning models of cellular function.

overall_design: Hepatocytes were dissociated from PFA-fixed liver tissue and enriched by FACS either by forward scatter and side scatter (WT samples) or by forward scatter, side scatter, mTurquioise expression (reflecting expression of an sgRNA) and GFP expression (reflecting expression of Cas9); or, fixed K562s were sorted for sgRNA expression.

first: Saunders

last: Reuben

first: Allen

last: Will

first: Zhuang

last: Xiaowei

first: Weissman

last: Jonathan


title: Human airway submucosal gland organoids to study respiratory inflammation and infection [RNA-seq]

city: Utrecht

first: Carla

last: Pou Casellas

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

summary: The human airway lining consists of two physiologically distinct compartments: the surface airway epithelium (SAE) and the submucosal glands (SMGs). Despite their critical role, SMGs have remained largely overlooked in airway in vitro modeling of respiratory inflammation and infection. In this study, we leverage long-term cultured organoids derived separately from SAE and SMG to investigate their unique physiological characteristics. Single-cell RNA sequencing (scRNA-seq) analysis confirms that these organoid models accurately replicate the cellular heterogeneity inherent to each tissue type. Specifically, SMG organoids are enriched in MUC5B-producing mucous cells and generate alpha-Smooth Muscle Actin (αSMA)-expressing myoepithelial cells. We identify ANPEP/CD13 as a specific cell surface marker for SMG secretory cells. Exposure to cytokines elicits distinct transcriptomic responses in SMG secretory cells, providing insights into the cellular mechanisms underpinning inflammatory pathogenesis. Infection assays with human alpha-coronavirus 229E (HCoV-229E) reveal a selective vulnerability of CD13-positive secretory cells within SMG organoids, triggering a specific unfolded protein response associated with endoplasmic reticulum (ER) stress. These findings broaden the utility of airway organoids for precision modeling of respiratory (patho-)physiology

overall_design: Bulk RNA sequencing of CD13- and CD13+ cells from human primary tissue-derived SMG organoids (3 different donors) unexposed or exposed to hCoV-229E-EGFP

first: Lin

last: Lin

first: Hans

last: Clevers


title: A20’s Linear Ubiquitin Binding Motif Restrains Pathogenic Activation of TH17/22 cells and IL-22 Driven Enteritis [ATAC-seq]

first: Averil

last: Ma

overall_design: Naive CD4 T cells were isolated from murine spleens of WT and A20ZF& mice and differentiated in TH17 medium with/without 100 nM FICZ for four days. Nuclei were isolated to generate Tn5-tagmented DNA for ATACseq.

first: Christopher

last: Bowman


title: SMART-seq2 of activated human plasmacytoid dendritic cells

address: Campus Drive

institute: Stanford

overall_design: Human plasmacytoid dendritic cells were activated with CD40L for two days, single-cell FACS sorted and scRNA sequenced by SMARTseq2. SMARTseq2 was also performed on purified plasmacytoid and transitional dendritic cells (without activation). Sequencing was performed in two independent blood donors.


title: Human airway submucosal gland organoids to study respiratory inflammation and infection [bulk RNA-seq]

overall_design: Bulk RNA sequencing of CD13- and CD13+ cells from human primary tissue-derived SMG organoids untreated or treated with IL-1B, IL-13, or TNFa (2 replicates per condition)


title: Human airway submucosal gland organoids to study respiratory inflammation and infection

overall_design:
Single-cell RNA sequencing of human primary tissue-derived SAE and SMG organoids (culturing passage 4)

LX199: SAE organoids
LX200: SMG organoids


title: Pan-viral ORFs discovery using massively parallel ribosome profiling

first: Shira

last: Weingarten-Gabbay

address: 75 Ames St

institute: The Broad Institute

summary: Defining viral proteomes is crucial to understanding viral life cycles and immune recognition but the landscape of translated regions remains unknown for most viruses. We have developed massively parallel ribosome profiling (MPRP) to determine open reading frames (ORFs) across tens of thousands of designed oligonucleotides. MPRP identified 4208 unannotated ORFs in 679 human-associated viral genomes. We found viral peptides originating from detected noncanonical ORFs presented on class-I human leukocyte antigen (HLA-I) in infected cells and hundreds of upstream ORFs that likely modulate translation initiation of viral proteins. The discovery of viral ORFs across a wide range of viral families—including highly pathogenic viruses—expands the repertoire of vaccine targets and reveals potential cis-regulatory sequences.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: Ribo-seq of human lung A549 cells and human kidney HEK293T trasnfected with a synthetic pan-viral library

first: Pardis

last: Sabeti


title: Non-canonical AMPA receptor blockade reduces lymph node egress and neuroinflammation

first: Frauke

last: Zipp

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


title: Unraveling the Cellular Landscape of Abdominal Aortic Aneurysm Using High-Resolution Spatial Transcriptomics:

first: Jun Hee

last: Lee

summary:
We used Sequence-Scope (Seq-Scope), which can generate ultra-high definition images of sequence-based molecular signatures resolved at a submicrometer scale, for profiling spatial transcriptome associated with abdominal aortic aneurysm
Experimental Methods: Seq-Scope experiment is divided into two consecutive sequencing steps: 1st-Seq and 2nd-Seq. 1st-Seq of Seq-Scope starts with the solid-phase amplification of a single-stranded synthetic oligonucleotide library using an Illumina sequencing-by-synthesis (SBS) platform. 2nd-Seq of Seq-scope begins with overlaying the tissue section slice onto the HDMI-array.    Computational Methods: Tissue boundaries are detected by using a custom python code to draw a smoothed density plot to visualize the density of HiSeq reads in a given XY space of each tile. Digital gene expression (DGE) matrices are  generate using STAR/STARsolo 2.7.5c with Gene,GeneFull, Velocyto, and polyAtrimming options.  Data binning is performed by dividing the imaging space into 100 μm2 square grid with 10 μm simple side or 25 μm2 square grid with 5 μm side and collapsing all HDMI-UMI information into one barcode. Binned DGE matrix was analyzed in the Seurat v4 package for clustering analysis.

sample_organism:
Mus musculus
synthetic construct

platform_organism:
Mus musculus
synthetic construct

overall_design: Sixteen-week-old Apoe -/- male mice fed a normal diet were subcutaneously implanted minipumps to delivery AngII (1,000ng/ml, 5 mice) or saline (5 mice) for 4 weeks. No significant difference was found in body weight, TC, and TG between the two groups at 4 weeks after minipump implantation. The extraluminal diameters were significantly increased in AngII group, in which 3 mice developed AAA (60% incidence). The fresh frozen suprarenal abdominal aortas from 3 AAAs and 3 normal controls were pair-embedded in OCT and cut into 10 μm sections. A total of 20 aortic sections (10 normal aortic sections and 10 aneurysmal sections) were attached onto HDMI-array slide for histological staining, library preparation and sequencing.

first: Guizhen

last: Zhao

first: Chun-Seok

last: Cho

first: Hongyu

last: Liu

first: Hyun

middle: M

last: Kang

first: Jifeng

last: Zhang

first: Jun

middle: H

first: Y

last: Chen


title: Human Cytomegalovirus long non-coding RNA counteracts nuclear cGAS to facilitate immune evasion

city: Seoul

first: Hyejun

last: Kim

address: 1 Gwanak-ro, Gwanak-gu

department: School of Biological Sciences

country: South Korea

institute: Seoul National University

summary: Viruses have evolved diverse immune evasion strategies including targeting host pattern recognition receptors. The role of viral non-coding RNAs in modulating PRR activity is unclear. Here, we show that human cytomegalovirus (HCMV) produces long non-coding RNA4.9 that counteracts nuclear cyclic GMP-AMP synthase (cGAS)-mediated immune response to facilitate viral infection in primary human foreskin fibroblasts (HFFs). RNA4.9 interacts with host cGAS via its 75-nucleotide (nt) RNA region with predicted hairpin loops. Binding of RNA4.9 to cGAS inhibits cGAS enzymatic activity and downstream interferon response, and facilitates productive viral replication. Sterically blocking the folding of 75-nt region with antisense oligonucleotides during HCMV infection restores cGAS activity and impairs viral replication. We also found that the specific localization of RNA4.9, which concentrates near HCMV DNA, is correlated with its efficient binding to cGAS and subsequent immune suppression. Our findings demonstrate viral non-coding RNAs as critical cGAS regulators and potential therapeutic targets.

overall_design: To identify cGAS-bound domain within RNA4.9, HFFs were infected with WT HCMV and cross-linked by UV irradiation. cGAS-RNA complexes were selectively purified by two individual antibodies (D1D3G and E9G9G). The enriched RNAs were fragmented and subjected to construction of cross-linking and immunoprecipitation (CLIP)-libraries. RNAs extracted from non-crosslinked-HCMV infected HFFs were subjected to rRNA depletion, RNA fragmentation, then construction of size-matched input (SMI)-libraries.

first: Sungwon

first: Sungchul

first: Dohoon

first: Dongjoon

last: Jeong

first: Hyewon

first: Junhyun

last: Park

first: Kiwon

first: Jin

last: Hur

first: Sun

first: V. Narry

first: Kwangseog

last: Ahn


title: Transcriptomic profiling of lesional and healthy skin in pemphigus patients reveals IL-17–driven immune response

status: Public on Jun 11 2025

city: Berlin

first: Alberto

last: Mesas-Fernández

state: Berlin

address: Luisenstraße 2

department: Dermatology

institute: Charité - Universitätsmedizin Berlin

summary: Pemphigus is a rare autoimmune blistering skin disease characterized by autoantibodies against desmoglein 1 and/or 3. To better understand the immunopathology of pemphigus, we performed RNA sequencing of lesional skin biopsies from pemphigus patients (n=6) and compared them to skin biopsies from healthy controls (n=6). Our data reveal an IL-17/IL-21–dominated transcriptional signature, with upregulation of inflammatory cytokines, chemokines, and tissue remodeling genes. These findings support the hypothesis that pemphigus pathogenesis is driven by a TH17/TFH17-type immune response and offer insights into potential therapeutic targets.

overall_design: Skin punch biopsies were obtained from six patients with clinically active pemphigus (lesional skin) and six age- and sex-matched healthy individuals (control skin). Total RNA was isolated and quality-controlled using Nanodrop, Qubit, and Bioanalyzer. RNA-seq libraries were prepared and sequenced using the Illumina NextSeq 500 platform (single-end, 75 bp). Raw reads were aligned to the GRCh37 reference genome using STAR, and gene-level expression quantification was performed with Subread.

first: Julia

last: Holstein

first: Farzan

last: Solimani

first: Kamran

last: Ghoreschi


title: Single nucleus multiome (GEX and ATAC) and bulk RNA-sq analysis of control and Mycn conditional knockout in the neonatal mouse heart

city: Minneapolis

first: Daniel

last: Garry

state: MN

address: 2231 6th Street SE, 4th Floor

department: Lillehei Heart Institute

institute: University of Minnesota

summary:
To investigate the role of MYCN in neonatal heart development, we performed Single nucleus multiome (GEX and ATAC) on isolated nuclei from control and Mycn conditional knockout (CKO) P4 mouse ventricles. Clustering analysis assigned cardiomyocytes (CMs) into five previously defined neonatal states (CM1–CM5). CKO hearts showed a marked depletion of proliferative CM2 and CM4 populations and an increase in differentiated CM1 cells. G2/M phase CMs were significantly reduced in the CKO, particularly within CM4. RNA velocity analysis revealed disrupted transitions from immature CM states to mature ones in the CKO. Latent time and metabolic profiling further confirmed a shift toward a mature, non-regenerative phenotype, with upregulation of hypertrophic and fatty acid oxidation pathways and downregulation of glycolysis and cell cycle genes. These results highlight MYCN’s role in maintaining proliferative, regenerative CM states during neonatal heart development.
Bulk RNA-seq was performed on P30 mouse ventriclar tissue 28 days after ischemic injury to compare Mycn conditional knockout (CKO) and control groups. The analysis revealed that cell cycle and muscle development pathways were downregulated, while inflammatory pathways were upregulated in the Mycn CKO hearts. These findings suggest that MYCN is essential for maintaining proliferative and regenerative gene programs following cardiac injury, and its deletion impairs regenerative potential at the transcriptomic level.

overall_design:
Single nucleus multiome (GEX and ATAC) was performed on P4 mouse ventricular tissue from Mycn conditional knockout (CKO) and control littermates
Bulk RNA-seq was performed on mouse ventricles from Mycn conditional knockout (CKO) and control neonatal mice 28 days after LAD-induced ischemic injury. Mycn CKO was achieved by 4-OHT-induced Cre recombination from P0–P2. LAD ligation surgery was performed at P2.

first: Xiao

last: Ma

first: Satyabrata

last: Das

first: Kidus

last: Hailemariam

first: Thijs

last: Larson


title: A20’s Linear Ubiquitin Binding Motif Restrains Pathogenic Activation of TH17/22 cells and IL-22 Driven Enteritis [RNA-Seq]

first: Averil

overall_design: Intact proximal small intestines from 12-week-old mice were lysed in TRIzol and used to isolate total RNA. One microgram of total RNA was subsequently used to generate libraries for bulk RNAseq.

first: Christopher

last: Bowman


title: Chronic hyperactivation of midbrain dopamine neurons causes preferential dopamine neuron degeneration

first: Ken

last: Nakamura

address: 1650 Owens St

institute: Gladstone Institutes

summary: Parkinson’s disease (PD) is characterized by the death of substantia nigra (SNc) dopamine (DA) neurons, but the pathophysiological mechanisms that precede and drive their death remain unknown. The activity of DA neurons is likely altered in PD, but we understand little about if or how chronic changes in activity may contribute to degeneration. To address this question, we developed a chemogenetic (DREADD) mouse model to chronically increase DA neuron activity, and confirmed this increase using ex vivo electrophysiology. Chronic hyperactivation of DA neurons resulted in prolonged increases in locomotor activity during the light cycle and decreases during the dark cycle, consistent with chronic changes in DA release and circadian disturbances. We also observed early, preferential degeneration of SNc projections, recapitulating the PD hallmarks of selective vulnerability of SNc axons and the comparative resilience of ventral tegmental area axons. This was followed by eventual loss of midbrain DA neurons. Continuous DREADD activation resulted in a sustained increase in baseline calcium levels, supporting a role for increased calcium in the neurodegeneration process. Finally, spatial transcriptomics from DREADD mice examining midbrain DA neurons and striatal targets, and cross-validation with human patient samples, provided insights into potential mechanisms of hyperactivity-induced toxicity and PD. Our results thus reveal the preferential vulnerability of SNc DA neurons to increased neural activity, and support a potential role for increased neural activity in driving degeneration in PD.

overall_design: Homozygous 3-4mo male DATiCre mice (Jax 006660) were split into 3 groups. The experimental group (GqCNO, N=3) was bilaterally injected in the midbrain with a conditional AAV to express excitatory hM3Dq(Gq)-DREADDs specifically in dopamine neurons. These mice were administered the DREADD ligand clozapine-N-oxide (CNO) via their drinking water for one week (300mg/L, with 2% sucrose) to chronically activate dopamine neurons. Two control groups were included: one where mice were bilaterally injected with the DREADD and given vehicle (sucrose) water (GqVeh, N=3), and another where mice were not injected but were given CNO water (CNOAlone, N=2). Midbrain and striatal slices from each mouse (16 slices total) were analyzed using spatial transcriptomics.

first: Rademacher

last: Katerina

first: Doric

last: Zak

first: Sei

last: Yoshitaka

first: Nakamura

last: Ken


title: Jpx RNA controls Xist induction through spatial reorganization of the mouse X-inactivation center [CHART-seq]

city: Boston

first: Hyun Jung

last: Oh

address: 185 Cambridge St.

institute: MGH

summary: Known to regulate chromosome looping on a genome-wide scale, the noncoding Jpx RNA was originally shown to control X-chromosome counting and induce Xist expression during X-chromosome inactivation (XCI). Not fully understood is how Jpx upregulates Xist in coordination with Tsix downregulation in cis. Here, by integrating epigenomic data and polymer modeling in a mouse embryonic stem cell model, we demonstrate that Jpx controls architectural and transcriptional dynamics within anti- and pro-XCI zones of the X-inactivation center. Distinct topological changes occur on the future active (Xa) and inactive (Xi) chromosomes. Jpx binds the enhancer of Tsix on the future Xi and alters loop formation to favor Xist induction, coordinately releasing CTCF from Tsix and Xist in cis on the future Xi.  Thus, by controlling a dynamic rewiring of functional loops, Jpx flips a transcriptional switch to control mutually exclusive Tsix and Xist expression in cis.

overall_design: We performed d7 Jpx CHART-seq in CTCF-WT ES cells and CTCF-degron ES cells treated with DMSO or dTAG-13.

first: Roy

last: Blum

first: Jeannie

middle: T

last: Lee


title: DNA and histone modifications identify a putative controlling element (CE) on the X chromosome of Sciara coprophila

city: Novosibirsk

first: Daniil

last: Maksimov

address: Lavrentjeva ave., 8/2

country: Russia

institute: MCB NSC RAS

type: Methylation profiling by high throughput sequencing

summary: In Sciara coprophila, paternally inherited X chromosomes are imprinted and selectively eliminated during early embryonic development. A controlling element (CE) located on the X chromosome is known to play a decisive role in this process, although the exact mechanism remains unknown. In this study, we test a proposed model in which the maternal cytoplasm regulates CE activity and thereby controls Xp elimination during embryogenesis. Using our de novo Sciara genome assembly, along with ChIP-Seq and MeDIP analyses, we identified a 1.2 Mb region within the CE locus that exhibits a repressive epigenetic signature on X chromosomes that are retained. These findings provide molecular support for the model. Remarkably, this signature also includes a unique enrichment of CpG methylation, suggesting a strong evolutionary conservation of imprinting mechanisms and identifying a promising candidate for the long-sought CE locus responsible for somatic Xp-chromosome elimination.

overall_design: ChIP-seq with H3K9me3-specific antibodies in 72h Sciara coprophila embryos


title: Biologically-inspired melt electrowriting for the generation of highly biomimetic functional myocardium

city: Pamplona

first: Asier

last: Ullate-Agote

state: Navarra

address: Av. de Pío XII, 55

department: Hemato-Oncology

country: Spain

institute: CIMA

summary: In the heart, the specific 3D structure of myocardial layers produces an efficient ejection of blood. When myocardial infarction strikes, this architecture is disrupted, adding a disarranged contraction to the decreased availability of pumping units (cardiomyocytes, CMs). In this work, we characterize the alignment of cardiac fibers in a large animal model (pig) and employ melt electrowriting (MEW) to fabricate a bio-inspired scaffold with diamond-shaped pores. Using human induced pluripotent stem cell-derived CMs and cardiac fibroblasts, we generate human cardiac tissues with a biomimetic in-plane contraction. Our tissues beat macroscopically for over one month, with significantly faster kinetics, increased force and higher conduction velocity than those based on square or rectangular pores. Our diamond design induces a specific hiPSC-CM alignment resulting in the observed in-plane contraction. Transcriptomic analysis using bulk RNA-seq reveals diamond-MEW tissues present features of maturation as compared to traditional 2D cultures. Finally, we employ the bio-inspired cardiac tissues to treat an infarction model in athymic rats, showing a significant benefit on systolic function and remodeling, tied to the presence of large grafts of human cells remuscularizing the ventricular wall. All in all, we demonstrate that the new design generates superior human cardiac tissues with therapeutic capacity.

overall_design: Bulk RNA-seq for a mix at a 9:1 proportion of hiPSC derived cardiomyocytes (CMs) and hiPSC derived fibroblasts (CFs) at day 0 and at day 30 of maturation in conventional 2D culture and 3D tissues in a scaffold with diamond-shaped pores

first: Olalla

last: Iglesias-Garcia

first: Manuel

last: M. Mazo


title: Jpx RNA controls Xist induction through spatial reorganization of the mouse X-inactivation center [RNA-Seq]

overall_design: We conducted RNA-seq in d0, d4 and d7 mouse ES cells.


title: ETS1 Downregulation Regulated by a Novel miRNA: Insights into the Anti-Angiogenic Shift in Non-Proliferative Diabetic Retinopathy

city: Changchun

first: Peng

last: Chen

address: Xinmin Street 126

department: Department of genetics

institute: Jilin University

summary: Non-proliferative Diabetic retinopathy (NPDR) is the early stage of diabetic retinopathy, which features the imbalance between anti-angiogenic and pro-angiogenic factors. The exact regulatory mechanism is still unclear. In this study, we aimed to unravel novel insights into the regulatory mechanisms underlying the endothelial dysfunction in NPDR by investigating the newly discovered miRNAs that enriched in the plasma of DR.

overall_design: Circulating cell-free miRNA was sequenced using next-generation sequencing (miRNA-seq).

first: Zimeng

last: Li

first: Qing

last: Wang

first: Aowen

last: Tian

first: Zewen

last: Sun

first: Jianyu

last: Zhao


title: RNA sequencing to compare gene expression in control and CMTM6 knockdown colon cancer cells

city: Austin

first: Ningling

last: Kang

address: 801 16th Ave NE

institute: Hormel Institute

summary:
Human colorectal cancer cell line  HCT116 was purchased from ATCC (Manassas, VA, USA). They were transduced with lentiviruses encoding control shRNA or CMTM6 shRNA.
Cells were collected for RNA isolation and RNA sequencing. The goal of this study is to identify genes transcriptionally regulated by CMTM6 knockdown.

overall_design: Comparative gene expression profiling analysis of colorectal cancer cells

first: Aurpita

last: Shaha


title: Transcriptomic profiling of MC38 tumor cells on murine MC38 liver metastasis sections by NanoString GeoMX DSP

summary: To study how targeting CMTM6 inCRCs influences the transcritome. Control MC38 and CMTM6-deficient MC38 were subjected to spatial transcriptomic profiling with the NanoString GeoMx DSP

overall_design: Two months old C57BL6 mice received implantation of MC38 murine colorectal cancer cells by portal vein injection. Cryo-sections of MC38 liver metastases were fixed with formalin, hybridized with NanoString mouse whole transcriptome atlas, followed by immunofluorescence staining with anti-desmin to label CAFs, anti-pan cytokeratin for MC38 cells, and SYTO13 for cell nuclei. Regions of Interest (ROIs) were selected for data requisition and analysis. CAFs (Desmin+) within a ROI were collected for transcriptomic profiling and MC38 cancer cells (Desmin-) within a same ROI were collected for transcriptomic profiling as well. Segments 1-15 (12 is not included) were ROIs from control MC38 liver metastases and 16-28 were from CMTM6 knockdown MC38 liver metastases. 54 sequencing data were generated for MC38 cancer cells due to dual-indexing primers-based sequencing.


title: Establishment of chromatin architecture interplays with embryo hypertranscription

city: Beijing

first: Wei

last: Xie

state: Beijing

address: Qinghuayuan

department: School of Life Science

institute: Tsinghua University

summary: After fertilization, early embryos undergo dissolution of conventional chromatin organization including topologically associating domains (TADs). Zygotic genome activation then commences amid unusually slow de novo establishment of three-dimensional chromatin architecture. How chromatin organization is established and how it interplays with transcription in early mammalian embryos remain elusive. Here we show that CTCF occupies chromatin throughout mouse early development. By contrast, cohesin poorly binds chromatin in one-cell embryos, coinciding with TAD dissolution. Cohesin binding then progressively increases from two- to eight-cell embryos, accompanying TAD establishment. Unexpectedly, strong ‘genic cohesin islands’ (GCIs) emerge across gene bodies of active genes in this period. GCI genes enrich for cell identity and regulatory genes, exhibit broad H3K4me3 at promoters, and display strong binding of transcription factors and the cohesin loader NIPBL at nearby enhancers. We show that transcription is hyperactive in two- to eight-cell embryos and is required for GCI formation. Conversely, induced transcription can also create GCIs. Finally, GCIs can function as insulation boundaries and form contact domains with nearby CTCF sites, promoting both the transcription levels and stability of GCI genes. These data reveal a hypertranscription state in early embryos that both shapes and is fostered by the three-dimensional genome organization, revealing an intimate interplay between chromatin structure and transcription.

overall_design: Examination of CTCF/Cohesin binding dynamics and 3D genome structures in mouse early embryos following transcription inhibition/cohesin KD/ADNP KO

first: Guang

last: Yu

first: Kai

last: Xu

first: Weikun

last: Xia

first: Ke

last: Zhang


title: C38 tumor cells

overall_design: Refer to individual Series


title: Jpx RNA controls Xist induction through spatial reorganization of the mouse X-inactivation center [Capture Hi-C]

first: Hyun Jung

last: Oh

overall_design: We performed in situ Hi-C^2 experiments in d0, d4 and d7 (control and Jpx-depleted) mouse ES cells.

first: Andrea

last: Kriz

first: Jeannie

last: Lee


title: A dataset of spatially resolved transcriptomics of post-natal cardiac development in mice

status: Public on Jun 10 2025

city: Luzhou city

first: Yuqing

last: Zheng

state: Sichuan province

address: Longmatan district No.1 Xianglin Road Section 1

institute: Southwest medical university

summary: The post-natal development and maturation of the mammalian heart involve highly intricate processes that remain incompletely understood, particularly concerning the molecular signature and roles of the diverse cell types involved. In this study, we present a comprehensive dataset generated from murine hearts at three key post-natal developmental stages using Spatio-temporal Enhanced Resolution Omics-Sequencing (Stereo-seq), an advanced spatially resolved transcriptomic technology. This dataset encompasses spatial transcriptomes of approximately 0.186 million individual cells within intact sections of murine hearts at post-natal developmental stages. Our dataset serves as a valuable resource for investigating the mechanisms underlying mammalian heart development and maturation. Through initial analyses, we identified distinct cell types and their spatial distributions, including 93,826 cardiomyocytes within a single heart section. This extensive dataset provides researchers with opportunities for data mining and facilitates diverse analyses, including studies on transcriptional regulation, cell-to-cell communication, and the functional activities of genes and signalling molecules during critical phases of heart development.

overall_design: Hearts of wild-type C57Bl/6J mice at postnatal day 0 (P0), postnatal day 7 (P7), and postnatal day 56 (P56) were used for Stereo seq.

first: Tianyi

first: Zhaoli

last: Pu

first: Li

first: Xingyue

last: Wu

first: Yan

last: Yang

first: Ming

last: Lei

first: Xiaoqiu

last: Tan

first: Tao

first: Tangting

first: Xianhong

last: Ou


title: Assessing the Impact of Metabolic Competence on Estrogenic Chemical Bioactivity in High-Throughput Profiling Assays

city: RTP

first: Monique

last: Hazemi

state: NC

address: 109 T.W. Alexander Dr

institute: US EPA

summary: High-throughput profiling assays such as high-throughput phenotypic profiling (HTPP) with Cell Painting and high-throughput transcriptomics (HTTr) with TempO-SeqTM are new approach methods that have been used to characterize the bioactivity and potential hazards of chemicals. To better account for potential in vivo hazards in screening, we previously coupled both assays to an in vitro metabolism platform, Alginate Immobilization of Metabolic Enzymes (AIME). In this study, we expanded upon our previous results in estrogenic reference chemicals by screening an additional 40 chemicals in VM7Luc4E2 breast cells anticipated to have varied activity and/or shifts in activity with metabolism in an estrogen receptor transactivation assay (ERTA) using the AIME platform. Our results demonstrate how HTTr could detect ER activity and the influence of metabolism on estrogenicity through the activation of ER high-confidence (ERHC) gene signatures and metabolism-induced shifts in ERHC signature enrichment. Additionally, HTPP could detect cases where metabolism impacted chemical cytotoxicity and detect generation of metabolites that were bioactive in a different way than their respective parent compounds when comparing the profiles of active features between AIME conditions. Notably, our findings highlighted examples of chemicals that had very different phenotypic and gene expression profiles between metabolic conditions that would not be observed in traditional chemical screening in most cell models. This study exhibited how high-throughput profiling assays could distinguish changes in bioactivity with metabolic competence using the AIME platform, which will ultimately better inform next generation risk assessment by providing more comprehensive hazard characterizations.

overall_design: The AIME platform was used in a "nomet" and "met" condition in VM7Luc4E2 breast cells. Cells were treated with 40 test chemicals and three estrogenic reference chemicals at eight concentrations, one estrogen receptor active control (17B-estradiol) at one concentration, one cell viability control (staurosporine) at one concentration, and a vehicle control (DMSO). Each TC plate was randomized and analyzed using the human whole transcriptome TempO-Seq assay. Three independent assay plates were sequenced per AIME condition.

first: Amanda

last: Jurgelewicz

first: Kristen

last: Breaux

first: Clinton

last: Willis

first: Felix

middle: R

last: Harris

first: Gabrielle

last: Byrd

first: Joshua

last: Witten

first: Derik

last: Haggard

first: Chad

last: Deisenroth

last: Harrill


title: Jpx RNA controls Xist induction through spatial reorganization of the mouse X-inactivation center

first: Hyun Jung

last: Oh


title: WNT Mimetic-Induced Lacrimal Gland Regeneration

city: South San Francisco

first: Russell

last: Fletcher

address: 171 Oyster Point Blvd, Suite 400

department: Discovery Biology

institute: Surrozen, Inc.

summary: Although tear replacement and anti-inflammatory treatments have been thoroughly investigated, a method to induce epithelial restoration is lacking. Here, we asked whether WNT signaling activation via an antibody-based WNT mimetic platform might activate lacrimal gland acinar cells and restore tear secretion. Transcriptional and cellular changes were investigated using single cell sequencing. In a mouse model of dry eye disease, and intra-lacrimal gland treatment with a WNT mimetic targeting FZD1, 2, and 7 reversed aqueous tear deficiency. After excretory duct ligation damage, WNT mimetic treatment promoted acinar cell restoration and increased detectable tear volume production. We demonstrate a role for WNT signaling in acinar cell proliferation, and scRNA-seq revealed that the WNT mimetic promotes pathway activation and proliferation in injury-induced states. Our findings extend the potential for WNT pathway activation via a ligand mimetic platform to lacrimal gland regeneration.

overall_design: Lacrimal gland duct ligation was used to cause damage to the lacrimal gland. After three days, the ligation was removed and animals were treated with either a control treatment or a WNT mimetic. At the indicated endpoint, the lacrimal gland was removed and dissociated. Viable cells were selected by DAPI exclusion and FACS purified. 10x Genomics 3' v3.1 chemistry was used for scRNA-seq, and tissue was collected from uninjured animals, day 1, day 5, and day 7. Our attempt to collect day 3 failed due to a clog in the cell capture device.

middle: B

first: Yorick

last: Post

first: Huy

last: Nguyen

first: Mengrui

last: Zhang

first: Elizabeth

last: Whistler

first: Tom

last: Lopez

first: Yang

last: Li


title: Decoding cellular stress states for toxicology using single-cell transcriptomics

city: Research Triangle Park

first: Imran

last: Shah

address: Mail Code: D143-02

department: Office of Research and Development

institute: US Environmental Protection Agency

summary: Single-cell transcriptomics (SCTr) offers a powerful platform for decoding the complexities of cellular stress responses to chemical exposures, capturing rare and transient subpopulations that can be obscured in bulk measurements. This study employs SCTr to profile the responses of HepaRG liver cells to various stress-inducing chemicals, providing detailed insights into adaptive stress response pathways (SRPs), encompassing the response to unfolded proteins, oxidative stress, heat shock, and DNA damage. By leveraging SCTr, we identify distinct cellular subpopulations and elucidate their transcriptomic profiles, linking specific gene expression patterns to biological mechanisms underlying stress responses. Our findings demonstrate the utility of SCTr in discerning the dose-dependent effects of chemicals at a granular level, highlighted by key differences between pseudo-bulk and single-cell analysis. Chemicals such as troglitazone, brefeldin A, rotenone, and tunicamycin induced unique transcriptional signatures associated with specific stress response pathways. Single-cell connectivity mapping with signatures of SRPs and cell fates, including autophagy and apoptosis, revealed clusters of cells with adaptive and potentially adverse phenotypes. These SCTr data have implications for identifying toxicological and disease mechanisms involving adaptive stress pathways. The data can also provide unique insights into toxicological processes by beginning to resolve adaptive chemical exposures, where cells recover, from those that are adverse from which cells do not recover, offering potentially new approaches for chemical safety assessments.

overall_design: We profiled reference perturbagens known to induce stress responses, including the unfolded protein response (UPR), oxidative stress response (OSR), heat-shock response (HSR), response to hypoxia (HPX), and DNA damage response (DDR), in the differentiated HepaRG human liver cell model at three different concentrations. HepaRG cells were dissociated and fixed for single-cell transcriptomic (SCTr) assessments. Here, cells were profiled with Biospyder TempO-LINC v1.0.

first: David

last: Gallegos

first: Brian

last: Robinette

first: Bryant

last: Chambers

first: Dennis

last: Eastburn

first: Douglas

last: Bell

first: Salvatore

last: Camiolo

first: Kevin

last: White

first: Nicole

last: Martin

first: Gioele

last: Montis

first: Joel

last: McComb

first: Bruce

last: Seligmann

last: Chorley


title: Transcriptomic profiling of Adjacents CAFs of MC38 tumor cells on murine MC38 liver metastasis sections by NanoString GeoMX DSP

first: Ningling

last: Kang

summary: To study how targeting CMTM6 in CRCs influences the transcritome. Adjacents CAFs of Control MC38 and CMTM6-deficient MC38 were subjected to spatial transcriptomic profiling with the NanoString GeoMx DSP

overall_design: Two months old C57BL6 mice were received implantation of MC38 murine colorectal cancer cells by portal vein injection. Cryo-sections of MC38 liver metastases were fixed with formalin, hybridized with NanoString mouse whole transcriptome atlas, followed by immunofluorescence staining with anti-desmin to label CAFs, anti-pan-cytokeratin for MC38 cells, and SYTO13 for cell nuclei. Regions of Interest (ROIs) were selected for data requisition and analysis. CAFs (Desmin+) within a ROI were collected for transcriptomic profiling and MC38 cancer cells (Desmin-) within a same ROI were collected for transcriptomic profiling as well. Segments 1-15 (12 is not included) were ROIs from control MC38 liver metastases and 16-28 were from CMTM6 knockdown MC38 liver metastases. 54 sequencing data were generated for MC38 cancer cells due to dual-indexing primers-based sequencing.

first: Aurpita

last: Shaha


title: Rewired type I IFN signaling is linked to age-dependent differences in COVID-19

first: Lev

last: Petrov

address: Charitépl. 1

department: BIH Translational Immunology

institute: Charite, BIH

summary: Advanced age is the most important risk factor for severe or even lethal COVID-19, but a thorough understanding of the underlying differences in infection-induced inflammation and cellular pathogenesis is missing. In samples from SARS-CoV-2 infected patients aged 1 to 84 years, we observed a continuous rewiring of type I interferon signaling and signal transducer and activator of transcription (STAT) usage across monocytes, CD4+ T cells and B cells during aging. In vitro investigations using cells from controls confirmed this as a general age-induced phenomenon. Conversion in interferon signaling from STAT1 to STAT3 was associated with increased inflammatory profiles, cytokine release and delayed contraction of infection-induced CD4+ T cells. A shift from solely interferon-responsive germinal center B (GCB) cells towards CD69high GCB and atypical B cells was linked to formation of IgA in children vs complement fixing IgG in adults. Our data provide molecular explanations for inflammation-prone responses to infections during aging.

overall_design:
Blood was collected from children and adults acutely infected with COVID-19 as well as age- and sex-matched uninfected donors. PBMCs were isolated and a part of the PBMCs from each donor was enriched for B cells. Total PBMCs and enriched B cells were subjected to 5' GEX scRNAseq and 5' VDJ library preparation. Samples were pooled with Antibody-based Hashtags and demultiplexed based on both Hashtags and SNPs. Sample groups included are : uninfected children (median age = 7), uninfected adults (median age = 66), infected children (median age = 9; asymptomatic n = 5, symptomatic n = 8) and infected adults (median age = 67; mild n = 5, severe n = 7, severe with IFN autoantibodies n = 7).

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Submitter states that missing raw files are due to patient privacy concerns.
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first: Sophia

last: Brumhard

first: Sebastian

last: Wisniewski

first: Philipp

last: Georg

last: Hillus

first: Anna

last: Hiller

first: Rosario

last: Astaburuaga-García

first: Nils

last: Blüthgen

first: Emanuel

last: Wyler

first: Katrin

last: Vogt

first: Hannah-Philine

last: Dey

first: Saskia

last: von Stillfried

first: Christina

last: Iwert

first: Roman

middle: D

last: Bülow

first: Bruno

last: Märkl

first: Lukas

last: Maas

first: Christine

last: Langner

first: Tim

last: Meyer

first: Jennifer

last: Loske

first: Roland

last: Eils

first: Irina

last: Lehmann

first: Benjamin

last: Ondruschka

first: Markus

last: Ralser

first: Jakob

last: Trimpert

first: Peter

last: Boor

first: Sammy

last: Bedoui

first: Christian

last: Meisel

first: Marcus

last: Mall

first: Victor

last: Corman

first: Leif

last: Sander

first: Jobst

last: Röhmel

first: Birgit

last: Sawitzki


title: A STUB1-CHIC2 complex decreases IL-27Rα expression on CD8+ T cells to restrain tumor immunity [RNAseq_STUB1KO]

first: Martin

middle: Wallace

last: LaFleur

address: 4 Blackfan Circle Room 140

institute: Harvard Medical School

summary: In vivo CRISPR screens in CD8+ T cells have previously uncovered targets for cancer immunotherapy, yet they have not been used to compare the key regulators important at different stages of CD8+ T cell activation. Here we present two 899-gene in vivo CRISPR screens using naive or activated CD8+ T cells to address this gap. These screens identified the E3 ubiquitin ligase STUB1 as a novel negative regulator of anti-tumor CD8+ T cells. Stub1 knockout (KO) CD8+ T cells control tumor growth across multiple murine models. Mechanistically, STUB1 interacts with the adapter protein CHIC2 to regulate cytokine receptor expression in mouse and human CD8+ T cells. Among the cytokine receptors regulated by this complex, IL-27Ra is essential for Stub1/Chic2 KO-mediated tumor growth control. Together, these findings establish that the STUB1-CHIC2 complex as a novel regulator of cytokine receptor expression in CD8+ T cells and provide rationale for inhibiting this pathway to enhance CD8+ T cell-mediated anti-tumor immunity.

overall_design: To investigate the differential genes between control and Stub1 KO CD8+ T cells in tumors we performed RNAseq

first: Thao

last: Nguyen


title: Benralizumab treatment in patients with severe asthma: A comparative analysis of T-cell gene expression profiles and identification of response-associated genes

city: Matsumoto

first: Keita

last: Hirai

state: Nagano

address: 3-1-1 Asahi

department: Graduate School of Medicine

institute: Shinshu University

summary: Benralizumab, an antibody that targets the interleukin-5 (IL-5) receptor, suppresses IL-5 activity, which plays a critical role in eosinophil development. Clinical studies have shown its efficacy in reducing eosinophil counts in both the blood and sputum, which has been shown to be beneficial for patients with severe asthma. In this study, we analyzed the gene expression patterns of T cells in 17 patients with severe asthma treated with benralizumab. Comparisons were made between baseline (week 0) and post-treatment (week 24) samples. In addition, this study aimed to identify specific genes associated with the treatment response.

overall_design: A comparative study examined T-cell gene expression patterns in patients with severe asthma, evaluating changes from baseline (week 0) to 24 weeks after the initiation of benralizumab therapy.

first: Toshihiro

last: Shirai


title: Single-cell RNA sequencing analysis of E13.5 mouse skin data

city: New Haven

first: Ruiqi

last: Li

address: 300 George St

institute: Yale University

summary: Mouse embryo skin samples were collected around embryonic day 13.5 (E13.5). Cells from the wildtype and the SmoM2YFP mutant were pooled for analyses.

overall_design: Axin2CreER (Amerongen et al., 2012) mice were bred to Rosa-lox-STOP-lox-SmoM2YFP (Jeong et al., 2004) mice. Chromium Single cell 3’ GEM Library and Gel Bead Kit v3.1 (PN-1000121) was used for single-cell RNA sequencing.

first: Peggy

last: Myung


title: The canonical Wnt/β-catenin signaling pathway upregulates carbonic anhydrase 2 via transcription factor 7-like 2 to promote cardiomyopathy in type 2 diabetic mice

city: Guangzhou

first: Ning

last: Hou

address: No.1 Xinzao Road

institute: Guangzhou Medical University

summary: Diabetic cardiomyopathy (DCM) is a major complication of diabetes mellitus. Excessive activation of the canonical Wnt/β-catenin pathway contributes to the development of cardiomyopathy in type 1 diabetes mellitus (T1DM). Transcription factor 7-like 2 (TCF7L2) is the main β-catenin partner of the TCF family in adult human hearts. In this study, we investigated the role of Wnt/β-catenin in the development of cardiomyopathy in type 2 diabetes mellitus (T2DM) by using streptozotocin (STZ)/high-fat diet (HFD)-induced diabetic mice and high glucose-stimulated neonatal rat cardiomyocytes (NRCMs) as in-vivo and in-vitro models of T2DM, respectively. Compared with the control mice, the T2DM mice exhibited increased myocardial β-catenin and TCF7L2 expression that was concentrated in the nucleus. Treatment of diabetic mice with the β-catenin/TCF7L2 bipartite inhibitor iCRT14 prevented myocardial remodeling and improved cardiac dysfunction. iCRT14 also prevented high glucose-induced hypertrophy in NRCMs, while the β-catenin stabilizer SKL2001 worsened hypertrophy. Immunoprecipitation experiments confirmed the formation of the β-catenin/TCF7L2 bipartite in the control and T2DM mouse cardiomyocytes. Moreover, carbonic anhydrase 2 (CA2) was upregulated in T2DM cardiomyocytes in vitro and in vivo. TCF7L2 overexpression upregulated CA2, while iCRT14 treatment or TCF7L2 knockdown downregulated CA2. Chromatin immunoprecipitation (ChIP) experiments revealed an increased interaction between β-catenin/TCF7L2 and the transcription initiation region of CA2 in the heart tissue of T2DM mice. CA2 knockdown ameliorated NRCM hypertrophy induced by high glucose and SKL2001. A luciferase reporter assay confirmed that CA2 is directly regulated by the β-catenin/TCF7L2 bipartite. Collectively, these results indicate that the canonical Wnt/β-catenin pathway upregulates CA2 via TCF7L2 to promote cardiomyopathy in T2DM. This research sheds new light on the pathogenesis of DCM and presents new potential therapeutic targets for this disease.

overall_design: Primary neonatal rat cardiomyocytes (NRCMs) were isolated from 1–2-day-old neonatal SD rats. In brief, hearts collected from anesthetized neonatal rats were digested with pancreatic enzymes and type II collagenase. For TCF7L2 overexpression or knockdown, the NRCMs were infected with Lenti-TCF7L2, Lenti-shTCF7L2 , or Lenti-NC (Lentiviral vector control) for 16 h, followed by incubation in culture medium containing 10% fetal bovine serum and 1% penicillin-streptomycin for 48 h. Total RNA was extracted from lenti-TCF7L2-, lenti-shTCF7L2 -or lenti-NC-infected NRCMs using a Trizol reagent kit. We then performed gene expression profiling analysis using data obtained fromRNA-seq of lentiviral infected cardiomyocytes. Comparative gene expression profilling analysis of RNA-Seq data for infected cells.

first: Conglin

first: Xun

last: Yuan


title: The RRM domain-containing protein Rbp3 interacts with ribosomes and the 3’ ends of mRNAs encoding photosynthesis proteins

city: Freiburg

first: Wolfgang

middle: R.

last: Hess

state: Baden-Würtemberg

address: Schänzlestrasse 1

department: Institute of Biology III

institute: University of Freiburg

summary: Gene expression changes were monitored in cultures of the cyanobacterium Synechocystis sp. PCC 6803 at 30 min after a shift from cultivation under standard light conditions (50 µmol photons m-2 s-1) to high light (HL; 250 µmol photons m-2 s-1) and 1 h after a shift from the standard growth temperature of 30°C to 20°C (cold). Acclimation to shifts in light and temperature is critical for photoautotrophic organisms such as cyanobacteria. The RRM domain proteins Rbp2 and Rpb3 are RNA-binding proteins that bind specific mRNAs and are involved in the localization of these mRNAs to the thylakoid membrane. Here, we investigated the effects of Rpb2 and Rbp3 on gene expression changes during the acclimation responses to an increase in light intensity and a decrease in temperature. We analyzed cultures of the wild-type (WT) and of the Δrbp2Δrbp3 double mutant, which lacks Rbp2 and Rbp3. We found that the transcript levels of psaA and psaB genes were significantly decreased in cells of the Δrbp2Δrbp3 double mutant upon cold stress and 30 min of high light compared to wild type. In addition, the transcript levels of Rbp1, another RRM domain-containing protein, were greatly increased.

overall_design: Total RNA was prepared from cells of Synechocystis sp. PCC 6803 wild type, and the Δrbp2Δrbp3 double mutant, which lacks Rbp2 and Rbp3. Samples were taken in biological duplicates. Total RNA was DNase-treated using TURBO DNase (Thermo Fisher Scientific). 2 µg DNase-treated RNA were labeled with Cy3 using the ULS Fluorescent Labeling Kit for Agilent arrays (Kreatech). A high-resolution microarray manufactured by Agilent (Design ID 075764, format 8 × 60 K, slide Layout = IS-62976-8-V2) was used. 600 ng labeled RNA were used for hybridization for 17 h at 65 °C, per array.

first: Luisa

last: Hemm

first: Elisabeth

last: Lichtenberg

first: Stefan

last: Tholen

first: Viktoria

last: Reimann

first: Kenta

last: Kakazu

first: Sotaro

last: Machida

first: Moontaha

last: Mahbub

first: Oliver

last: Schilling

first: Conrad

last: Mullineaux

first: Annegret

last: Wilde

first: Satoru

last: Watanabe


title: Transcriptome analysis of dark grown wild-type and lon1-1 mutant seedlings

city: Athens

first: Stamatis

last: Rigas

state: Attiki

address: Iera Odos 75

department: Biotechnology

country: Greece

institute: Agricultural University of Athens

summary: Intracellular selective proteolysis is an important protein quality control process for maintenance of protein homeostasis by removing either defective polypeptides or deleterious protein aggregates. The ATP-dependent Lon protease is a key component of protein quality control and highly conserved across the kingdoms of living organisms. In Arabidopsis thaliana Lon1 protease (AT5G26860) is dual targeted to mitochondria and chloroplasts. Lon1 mutant plants (lon1-1) exhibit a post-embryonic growth retardation phenotype accompanied with aberrant mitochondria morphology and reduced respiratory capacity. Here, we present the results of a deep RNA-sequencing (RNA-seq) analysis to characterize the dynamic gene expression profile of Arabidopsis upon loss of Lon1 function.

overall_design: Col-0 (control) and lon1-1 mutant seedlings were grown for 6 days on Petri dishes in the dark. Samples were snap frozen in liquid nitrogen and total RNA was extracted from 3 independent biological replicates of Col-0 (control) and lon1-1 mutant plants. The stranded RNA-seq libraries were generated by BGI using the in-house rRNA Removal Library Construction Protocol and Sequencing was performed by a DNBSEQ G400 platform

first: Fengoula

last: Avgeri

first: Dikran

last: Tsitsekian

first: Gerasimos

last: Daras


title: Epigenetic and 3D genome reprogramming during the aging of human hippocampus

city: La Jolla

first: Seoyeon

last: Lee

state: California

address: 9500 Gilman Dr.

institute: University of California, San Diego

summary: Age-related cognitive decline is associated with altered physiology of the hippocampus. While changes in gene expression have been observed in aging brain, the regulatory mechanisms underlying these changes remain underexplored. We generated single-nucleus gene expression, chromatin accessibility, DNA methylation, and 3D genome data from 40 human hippocampal tissues spanning adult lifespan. We observed a striking loss of astrocytes, OPC, and endothelial cells during aging, including astrocytes that play a role in regulating synapses. Microglia undergo a dramatic switch from a homeostatic state to a primed inflammatory state through DNA methylome and 3D genome reprogramming. Aged cells experience erosion of their 3D genome architecture. Our study identifies age-associated changes in cell types/states and gene regulatory features that provide insight into cognitive decline during human aging.

overall_design: Analysis of  single-nucleus methyl-3C (snm3C) of hippocampal tissues from 40 postmortem neurotypical human donors

first: Nathan

last: Zemke

first: Bing

last: Ren


title: EGR2 O-GlcNAcylation Orchestrates the Development of Protumoral Macrophages to Limit CD8+ T Cell Antitumor Responses.

first: Hang

middle: Hubert

last: Yin

address: Shuangqing Road

summary: Tumor associated macrophages (TAMs) exihibit a high capacity to take up glucose, however, how metabolic cues derived from glucose uptake rewire TAMs remains unclear. Here, we report that glucose metabolism-driven protein O-GlcNAcylation shapes the differentiation of protumoral TAMs, thereby accelerating tumor progression. We constructed O-GlcNAc transferase (OGT) conditional-deletion mice to examine MC38 tumor growth.

overall_design:
ATAC-seq on tumor-associated macrophages(TAMs) from mouse MC38 tumor, tumor-associated macrophages expressing or not the O-GlcNAc transferase(OGT), and CUT-tag-seq with early growth response gene(EGR2) on TAMs in MC38 tumor from Ogt-flox(WT) or Ogt-flox Lyz2-cre(KO) mice.

ChIP-seq of EGR2 on TAMs in MC38 tumor from WT mice. RNA-seq of TAMs and scRNA-seq of CD45+ immune cells in MC38 tumor from Ogt-flox(WT) or Ogt-flox Lyz2-cre(KO) mice.


title: Core splicing architecture and early spliceosomal recognition determine microexon sensitivity to SRRM3/4

city: Barcelona

first: Manuel

last: Irimia

state: Barcelona

address: 88 Dr. Aiguader

department: MELIS

institute: Universitat Pompeu Fabra - Centre for Genomic Regulation

summary: Microexons are essential for proper functioning of neurons and pancreatic endocrine cells, where their inclusion depends on the splicing factors SRRM3/4. However, in pancreatic cells, their lower expression limits inclusion to only the most sensitive neuronal microexons. Although various cis-acting elements are known to contribute to microexon regulation, how they determine this differential dose response and sensitivity to SRRM3/4 remains unknown. Here, through Massively Parallel Splicing Assays probing 28,535 variants, we found that sensitivity to SRRM4 is conserved across vertebrates and overall consistent with a regulatory model whereby the main determinants of microexon sensitivity are related to differences in the interplay between core splicing architecture and length constraints. This conclusion is further supported by distinct spliceosome activity in the absence of SRRM3/4 and by a mathematical model that assumes that the two types of microexons differ only in their efficiency of recruitment of early spliceosomal components.

overall_design: RNA seq from HEK 293 Flp-In T-Rex cells expressing SRRM4 in an inducible manner. Amplicon seq from 5 MaPSy in different experimental conditions (GFP vs different levels of expression of SRRM4 in HEK 293 Flp-In T-Rex cells)

first: Sophie

last: Bonnal

first: Simon

last: Bajew

first: Rosa

last: Corral


title: A STUB1-CHIC2 complex decreases IL-27Rα expression on CD8+ T cells to restrain tumor immunity

city: Boston

first: Martin

last: LaFleur

state: MA

summary: In vivo CRISPR screens using activated CD8+ T cells have uncovered novel immunotherapy targets for cancer, yet similar high-throughput screens have not been performed using naive CD8+ T cells. Here we present an 899-gene in vivo CRISPR screen using naive CD8+ T cells, which identified the E3 ubiquitin ligase STUB1 as a novel negative regulator of anti-tumor CD8+ T cell responses. Stub1 knockout (KO) CD8+ T cells control tumor growth across multiple murine models. Mechanistically, STUB1 interacts with the adapter protein CHIC2 to regulate IL-27Rα expression in mouse and human CD8+ T cells. IL-27Rα expression is essential for the accumulation of Stub1 KO or Chic2 KO CD8+ T cells in tumors and tumor growth control. Together, these findings demonstrate that the STUB1-CHIC2 complex is a novel regulator of cytokine receptor expression in CD8+ T cells and provide the rationale for inhibiting this pathway to improve CD8+ T cell-mediated anti-tumor immunity.

overall_design: To investigate the genes expressed in naïve CD8+ T cells and CD8+ T cells responding to the tdLN and tumor in isotype treated or PD-1 blockade-treated mice we performed RNAseq.

first: Thao

last: Nguyen


title: Single cell RNA sequencing (scRNA-seq) data on the human CD45+ cells and tumor cells collected from four different treatment groups of hCD34+ humanized mice with human TNBC xenografic tumor model (mixed sample, non-demultiplexed)

city: Pittsburgh

first: Min

last: Zhang

state: PA

address: Salk Hall, 3501 Terrace St

institute: University of Pittsburgh

summary: Using a hCD34+ humanized mouse tumor model, the single-cell sequencing analysis revealed that in vivo knockdown of EPIC1 enhanced the T cells and macrophage infiltration by activating type I IFNs signaling.

overall_design:
To study how in vivo knockdown of EPIC1 regulates the tumor microenvironment and  pembrolizumab response, we first established a hCD34+ humanized mouse model (HuCD34-NCG mice, Charles River) with human TNBC (MDA-MB-468) xenografic tumor model. Then we performed single cell RNA sequencing (scRNA-seq) analysis on the CD45+ cells and tumor cells collected from four treatment mice groups: LNA-control + isotype control (IgG) antibody (n=1), LNA-EPIC1 + isotype control (IgG) antibody (n=1),  LNA control + human anti-PD-1 antibody pembrolizumab (Pem) (n=1), and LNA-EPIC1 + human anti-PD-1 antibody pembrolizumab (Pem) (n=2).

Processed data file contents:
HumanHTO3_exp_scale.csv: CD45+ cells, LNA-control + isotype control (IgG) antibody
HumanHTO6_exp_scale.csv: CD45+ cells, LNA-EPIC1 + isotype control (IgG) antibody
HumanHTO9_exp_scale.csv: CD45+ cells, LNA control + human anti-PD-1 antibody pembrolizumab
HumanHTO12_exp_scale.csv: CD45+ cells, LNA-EPIC1 + human anti-PD-1 antibody pembrolizumab
HumanHTO14_exp_scale.csv: CD45+ cells, LNA-EPIC1 + human anti-PD-1 antibody pembrolizumab

first: Dhamotharan

last: Pattarayan

first: Xiaofei

last: Wang

first: Zehua

first: Da

last: Yang


title: Role of EPIC1 in cancer cells

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

overall_design: Refer to individual Series


title: Mesenchymal-epithelial transition reduces proliferation but increases immune evasion in tumor spheroids

city: Dresden

first: Gina

last: Dimari

address: Arnoldstrasse 18

department: Physics of Life

institute: Dresden University of Technology

summary: The mesenchymal-epithelial transition (MET) has been implicated in secondary tumor growth during metastasis, yet the underlying mechanisms remain unclear. Here, we explore whether MET enhances tumor outgrowth by boosting proliferation, using MET-inducible mesenchymal breast cancer cells. Surprisingly, we found that crowding inhibition of proliferation persists both before and after MET, with mesenchymal cells exhibiting a proliferative edge through more effective escape from crowded cell islands. In three-dimensional culture, MET caused a reduction in proliferation, accompanied by distinct changes in proliferative signalling of focal adhesions and actomyosin. However, Src inhibition led to enhanced proliferation upon MET. Furthermore, co-culture experiments with peripheral blood mononuclear cells reveal that MET-induced spheroids demonstrate an increased ability to evade immune cell attacks. This effect is likely mediated by the confined epithelial morphology and alterations in the expression of key immunomodulatory molecules. Together, these findings suggest that MET may contribute to secondary tumor outgrowth, not by boosting proliferation, but by enhancing survival in immune-challenging environments.

overall_design: RNAseq profiling of MDA-MB-231 and ES-2 cells bearing an inducible construct for miR-200c and miR-141 overexpression, under control or induced conditions (4-day treatment with doxycycline)

first: Yueyuan

last: Hu

first: Annika

last: Frenzel

first: Anke

last: Fuchs

first: Alexander

last: Wurm

first: Elisabeth

last: Fischer-Friedrich


title: Effect of overexpression of EPIC1 on gene expression in MCF7 cells [RNA-seq I]

summary: To investigate and determine the role of EPIC1 overexpression in cancer cells, we established EPIC1 overexpressing MCF7 stable cells.

overall_design: Full-length EPIC1 was amplified from total RNAs of MCF7 cells, retroviral EPIC1 expression plasmids constructed and stable EPIC1 overexpressing MCF7 cell line was established.

first: Yue


title: Transcriptomic changes induced by knocking down EPIC1 in cancer cell lines [RNA-seq II]

summary: To investigate and determine the function of EPIC1 in cancer cells, we knockdown EPIC1 in Hs578T, A2780, and A2780cis cells using siRNA.

overall_design: After EPIC1 siRNA and control siRNA treatment, RNA were extracted to prepare for RNA-seq.


title: NanoString PanCancer Immune Profiling of Th17 cell treated melanoma mice

status: Public on Jun 09 2025

city: Atlanta

first: Chrystal

last: Paulos

state: GA

address: 1365 Clifton Rd NE

department: Surgery

institute: Emory University

summary: nCounter platform from Nanostring Technologies (Mouse PanCancer Immune Profiling Panel) was used to assess differential gene expression between NT and Th17 cell treated B16F10 melanoma bearing mice in the tumor and tumor-draining lymph nodes.

overall_design: Mice bearing established B16F10 were given 5 Gy total body irradiation and then one day later got adoptive cell transfer (ACT) of Th17 cell ACT or no T cells (NT) (n=4 mice/group). 12 days after ACT, tumors and tumor-draining lymph nodes were harvested, processed, and RNA was extracted.  770 genes (730 immune genes and 40 housekeeping genes) were assayed via nCounter platform from Nanostring Technologies (Mouse PanCancer Immune Profiling Panel).

first: Anna

last: Cole

first: Hannah

last: Knochelmann


title: Endoplasmic reticulum stress sensor protein PERK in hepatic stellate cells promotes the progression of hepatocellular carcinoma via p38δ MAPK/IL-1β axis

status: Public on Jun 07 2025

city: Toon

first: Makoto

last: Morita

address: 454 Shitsukawa

institute: Ehime University Graduate School of Medicine

summary: Palmitic acid (PA) absorption from the intestine is increased in metabolic dysfunction-associated steatohepatitis (MASH). It induces endoplasmic reticulum (ER) stress and interleukin-1 beta (IL-1β) production in hepatic stellate cells (HSCs). Protein kinase R-like endoplasmic reticulum kinase (PERK) is an ER stress sensor protein involved in HSC activation and liver fibrosis. However, its role in HSCs during hepatocellular carcinoma (HCC) progression remains unclear. This study clarified the process of IL-1β production via PERK in HSCs and explored the mechanism underlying MASH-related HCC progression. HSCs were treated with PA or transfected with PERK small-interfering RNA (siRNA) or PERK plasmid. Proliferation, scratch, and Transwell assays were performed on HCC cells cultured in the conditioned medium (CM) from HSCs. PA treatment increased PERK and IL-1β expressions in HSCs. PERK knockdown decreased IL-1β expression, while its overexpression increased it in HSCs. The CM from PA-treated HSCs showed elevated IL-1β levels and enhanced HCC cells’ proliferation, migration, and invasion; however, these effects were suppressed by PERK knockdown in HSCs. RNA-sequencing analysis revealed that p38δ mitogen-activated protein kinase (MAPK) is the intermediate molecule between PERK and IL-1β in HSCs. In the tumor microenvironment of MASH-related HCC, PERK in HSCs promotes HCC progression via the p38δ MAPK/IL-1β axis.

overall_design: RNA-seq profiling of LX-2 cells transfected with control or PERK siRNA and then treated with palmitic acid

first: Yoshio

last: Tokumoto


title: scRNA-seq of wild type and Sarm1-/- GBM mouse models

city: London

first: Simona

last: Parrinello

address: 72 Huntley Street

institute: UCL Cancer Institute

summary: Gene expression profiles of tdTomato labeled tumours generated in wild type and Sarm1-/- mice and analysed at terminal disease stage

overall_design: Tumour bulk was isolated from mouse brain using immunofluorescent guidance. The tissue was then dissociated into single cells and analysed using scRNA-seq.

first: Zan

last: Florjanic Baronik

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last: Tang

first: Sam

last: Marguerat

first: Ciaran

middle: S

last: Hill