title: Engineered mesenchymal stromal cells with bispecific polyvalent peptides suppress excessive neutrophil infiltration and boost therapy

city: guangzhou

first: Tenghui

last: Ye

address: 777 Xingye Avenue

department: School of Biomedical Science and Engineering

institute: South China University of Technology

summary: Excessive neutrophil infiltration can exacerbate inflammation and tissue damage, contributing to conditions like autoimmune disorders and liver diseases. Mesenchymal stromal cells (MSCs) share homing mechanisms with neutrophils, showing promise for treating such diseases. However, ex vivo expanded MSCs often suffer from reduced homing efficiency due to the loss of essential ligands. Here, we engineer MSCs with P-selectin and E-selectin targeting peptides, assembling them into bispecific polyvalent structures using DNA self-assembly technology. This modification allows engineered MSCs to compete with chemotactic neutrophils for selectin binding sites on endothelial cells. In a mouse model of acute liver failure, engineered MSCs effectively home to the damaged liver and significantly inhibit excessive neutrophil infiltration. The combination of inhibiting neutrophil infiltration and the MSCs’ inherent therapeutic properties lead to superior therapeutic outcomes. Single cell RNA sequencing reveals that engineered MSCs elevate the levels of Marco_macrophage which possess neutrophil-inhibitory effects. Our study offers a perspective for advancing MSC-based therapies in tissue repair.

overall_design: 6 hours after injection of 500 mg/kg APAP, mice were then injected with PBS, native MSCs, or engineered MSCs (n=1 for each group). After 4 days, the liver samples were collected, digested, and subjected to scRNA-seq.

first: Zixin

last: Wu

first: Xi

last: Liu

first: Jiamin

first: Qin

last: Fu

first: Jie

last: Cao

first: Di

last: Zhang

first: Peng


title: Variable DPP4 expression in multiciliated cells of the human nasal epithelium as a determinant for MERS-CoV tropism

status: Public on Feb 24 2025

city: Rotterdam

first: Bart

last: Haagmans

address: Wytemaweg 80

country: Netherlands

institute: Erasmus MC

type: Expression profiling by high throughput sequencing

summary: Transmissibility of respiratory viruses is a complex viral trait that is intricately linked to tropism. Several highly transmissible viruses, including SARS-CoV-2 and Influenza viruses, specifically target multiciliated cells in the upper respiratory tract to facilitate efficient human-to-human transmission. In contrast, the zoonotic MERS-CoV generally transmits poorly between humans, which is largely attributed to the absence of its receptor DPP4 in the upper respiratory tract. At the same time, MERS-CoV epidemiology is characterized by occasional superspreading events, suggesting that some individuals can disseminate this virus effectively. Here, we utilized well-differentiated human pulmonary and nasal airway organoid-derived cultures to further delineate the respiratory tropism of MERS-CoV. We find that MERS-CoV replicated to high titers in both pulmonary and nasal airway cultures. Using single-cell mRNA sequencing, immunofluorescence and immunohistochemistry, we show that MERS-CoV preferentially targeted multiciliated cells, leading to loss of ciliary coverage. MERS-CoV cellular tropism was dependent on the differentiation of the organoid-derived cultures, and replication efficiency varied considerably between donors. Similarly, variable and focal expression of DPP4 was revealed in human nose tissues. This study indicates that the upper respiratory tract tropism of MERS-CoV may vary between individuals due to differences in DPP4 expression, providing an explanation for the unpredictable transmission pattern of MERS-CoV.

overall_design: Human pulmonary airway organoids were derived from adult stem cells isolated from dissected lung parenchyma of a single donor and differentiated at the air–liquid interface into small pulmonary airway organoid-derived epithelial cultures (SAECs). After six weeks of differentiation, the SAECs were infected with MERS-CoV at a multiplicity of infection (moi) of 1. Cells were harvested for scRNA-seq 24 hours post-infection (hpi).

first: Tim

middle: I

last: Breugem

first: Samra

last: Riesebosch

first: Jingshu

first: Anna

middle: Z

last: Mykytyn

first: Lisette

last: Krabbendam

first: Nathalie

last: Groen

first: Sivana

last: Baptista Varela

first: Debby

last: Schipper

first: Petra

middle: B

last: van den Doel

first: Romy

last: van Acker

first: Ralph

last: Stadhouders

first: Mart

middle: M

last: Lamers

middle: L


title: Progressive CD4 T cell dysfunction is associated with bacterial recrudescence during chronic tuberculosis.

city: Worcester

first: Samuel

last: Behar

address: 55 Lake Ave N

department: Microbiology and Physiological Systems (MaPS)

country: USA

institute: UMass Chan Medical School

summary: While most people contain Mycobacterium tuberculosis infection, some individuals develop active disease, usually within two years of infection. Why immunity fails after initially controlling infection is unknown. C57BL/6 mice control Mycobacterium tuberculosis for up to a year but ultimately succumb to disease. We hypothesize that the development of CD4 T cell dysfunction permits bacterial recrudescence. Transcriptomic analysis reveals that only a small proportion of CD4 T cells in the lungs of chronically infected mice are polyfunctional; most are hypofunctional. We developed a reductionist model to assess antigen-specific T cells during chronic infection and found evidence of senescence and exhaustion. In C57BL/6 mice, CD4 T cells upregulate inhibitory receptors and lose effector cytokine production. While the origin and causal relationship between T-cell dysfunction and recrudescence remains uncertain, we propose these factors promote a feed-forward loop that causes loss of T cell function, increased bacillary numbers, and the development of progressive tuberculosis.

overall_design: Naïve ESAT-6 specific CD4 TCR transgenic (C7) T cells were isolated from spleens and lymph nodes of TCR transgenic mice and transferred intravascularly into TCRα KO mice. Mice were then infected with Mtb Erdman through the aerosol route 16-24 hours later. Parenchymal (CD45 IV Neg) C7 T-cells were then sorted from the lungs of infected mice at 4 and 25 weeks post-infection (wpi). RNAseq was performed on RNA isolated from sorted C7 T cells.

first: Evelyn

last: Chang


title: Single cell gene expression of ESAT-6 specific CD4 TCR Transgenic T-cells

summary: Single cell gene expression profile of intravascularly transferred C7 and C24 TCR Transgenic T-cells from the lungs of Mycobacterium tuberculosis infected TCR⍺ KO mice at 26 weeks post-infection

overall_design: Co-transferred CD3+ TCR[b]+ TCR transgenic T-cells were sorted from the lungs of Mtb infected TCR⍺ KO mice. Gene expression and V(D)J profiles were analyzed using single-cell RNA sequencing (scRNAseq)


title: OBSCN undergoes extensive alternative splicing throughout human cardiac and skeletal muscle development

city: Helsinki

first: Marco

last: Savarese

address: Topeliuksenkatu 20

department: Samfundet Folkhälsan i svenska Finland r.f.

country: Finland

institute: Folkhälsan Research Center

summary: Highly expressed in skeletal muscles, the gene Obscurin (i.e. OBSCN) has 121 non-overlapping exons and codes for some of the largest known mRNAs in human genome. Furthermore, it is known to play an essential role in muscle development and function. Mutations within OBSCN are known to cause several hypertrophic cardiomyopathies and muscular disorders. Even though OBSCN undergoes extensive alternative splicing, its splicing regulation associated with skeletal and cardiac muscle development has not previously been thoroughly studied. We study splicing of OBSCN in skeletal and cardiac muscles extracted from 41 postnatal individuals and 6 fetuses. We detect several splicing regulations located in 5’end, 3’ end, as well as in the middle of OBSCN. Many of these alternative splicing events have not previously been reported. These findings are essential for an accurate pre- and postnatal diagnosis and prognosis of OBSCN exonic variants. The muscle development OBSCN exon inclusion map is available at https://gacatag.shinyapps.io/OBSCN_PSIVIS/ .

overall_design:
Fetal skeletal muscles (n=20) and fetal heart muscles (n=2), without muscle pathology, was obtained from voluntary termination of pregnancy (TOP). Furthermore, sample biopsies from an internal cohort of 41 individuals was collected. From the 2 fetuses (denoted with F1 and F2) various different muscle samples have been extracted.
-------------------------------------
Authors state 'Raw data  is not availalbe due to GDPR. For any further enquiries regarding the studied samples please contact marco.savarese@helsinki.fi".

first: Ali

last: Oghabian

first: Per

middle: H

last: Jonson

first: Mridul

last: Johari

first: David

middle: G

last: Andres

first: Francina

last: Munell

first: Jessica

middle: C

last: Soriano

first: Maria

middle: S

last: Duran

first: Juha

last: Sinisalo

first: Heli

last: Tolppanen

first: Johanna

last: Tolva

first: Peter

last: Hackman

first: Bjarne

last: Udd


title: Regulatory B cells suppress GVHD and prolong survival of GVHD via membrane-bound IL-35 and secretion of exosomes with membrane-bound IL-35

city: Bethesda

first: Vijay

last: Nagarajan

state: Maryland

address: 10 Center Drive, 10/10N248

department: National Eye Institute

institute: National Institutes Of Health

summary: Interleukin 35-producing B-cells (i35-Bregs) suppress autoimmune diseases and IL-35 is immunosuppressive member of IL-12 cytokine family. It is comprised of p35 and Ebi3 subunits which are assumed to be independently secreted proteins that associate in-vivo to form non-covalently linked heterodimeric IL-35. In view of recent reports that p35 and Ebi3 are not secreted as a heterodimer but act as independent anti-inflammatory cytokines, we investigated whether i35-Bregs can suppress GVHD by secreting p35, Ebi3 or heterodimeric IL-35. Surprisingly, i35-Bregs ameliorate and prolong survival of Graft-Versus-Host-Disease (GVHD) via membrane-bound IL-35 and secrete exosomes with membrane-bound IL-35 (i35-exosomes) that upregulate checkpoint inhibitors (PD-1/LAG-3) and induce T-cell exhaustion, thereby rendering allogeneic T-cells less active, with diminished proinflammatory effects. i35-exosomes also propagate infectious tolerance mechanism by binding bystander B-lymphocytes and converting them to IL-35 producers. Adoptive transfer of i35-Bregs or i35-exosomes suppress GVHD through these mechanisms, indicating that i35-Bregs/i35-exosomes combination-immunotherapy maybe effective therapy for GVHD.

overall_design: To understand the mechanism of GVHD suppression by IL-35, we performed a transcriptome analysis on the IL-35-producing B cells and compared it with the control B cells.

first: Jin

middle: K

last: Choi

first: Evaristus

last: Mbanefo

first: Manoj

last: Yadav

first: Sahar

middle: A

last: Alhakeem

first: Vijayaraj

first: Natalia

last: Nunes

first: Christopher

last: Kanakry

first: Charles

middle: E

last: Egwuagu


title: KAT6B overexpression rescues embryonic lethality in homozygous null KAT6A mice restoring vitality and normal lifespan [RNA-seq]

city: Parkville

first: Alexandra

last: Garnham

state: Victoria

address: 1G Royal Parade

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

summary: Closely related genes typically display common essential functions but also functional diversification, ensuring retention of both genes throughout evolution. The histone lysine acetyltransferases KAT6A (MOZ) and KAT6B (QKF/MORF), sharing identical protein domain structure, are mutually exclusive catalytic subunits of a multiprotein complex. Mutations in either KAT6A or KAT6B result in congenital intellectual disability disorders in human patients. In mice, loss of function of either gene results in distinct, severe phenotypic consequences. In this dataset, we investigate the effects of overexpression of KAT6B on the gene expression changes caused by loss of KAT6A in mouse E9.5 embryos. We show that Kat6b overexpression reverses critical gene expression anomalies in Kat6a mutant embryos.

overall_design: RNA-sequencing of N= 4 Kat6a–/–Kat6b+/+, 4 Kat6a+/+Kat6b+/+, 4 Kat6a–/–Tg(Kat6b) and 4 Kat6a+/+Tg(Kat6b) E9.5 mouse embryos.

first: Anne

last: Voss

first: Tim

last: Thomas


title: Evaluation of altered cell-cell communication between glia and neurons in the hippocampus of 3xTg-AD mice at two time points

city: Birmingham

first: Brittany

last: Lasseigne

state: AL

address: 1900 University Boulevard

department: Cell, Developmental and Integrative Biology

institute: University of Alabama at Birmingham

summary: Alzheimer’s disease (AD) is the most prevalent neurodegenerative disease and the most common form of dementia. AD is characterized by progressive memory loss and cognitive decline, affecting behavior, speech, and motor abilities. The neuropathology of AD includes the formation of extracellular amyloid-β plaques and intracellular neurofibrillary tangles of phosphorylated tau, as well as neuronal loss. Although neuronal loss is a primary hallmark of AD, non-neuronal cell populations are known to maintain brain homeostasis and neuronal health through neuron-glia and glial cell crosstalk via chemical messengers. To investigate altered glia-neuron communication in the presence of amyloid-β and tau pathology, we generated snRNA-seq data from the hippocampus of 3xTg-AD mice at 6 and 12 months and age-matched wild-type littermates. We predicted altered glia-neuron interactions between senders (astrocytes, microglia, oligodendrocytes, and OPCs) and receivers (excitatory and inhibitory neurons) across time points. We further investigated these interactions through pseudo-bulk differential expression, functional enrichment, and gene regulatory analyses.

overall_design: We anesthetized and perfused 3xTg-AD mice (B6;129-Tg(APPSwe,tauP301L)1Lfa Psen1tm1Mpm/Mmjax: JAX MMRRC Stock# 034830) and wild-type littermates before dissecting brain regions to obtain hippocampal samples. We isolated nuclei from the left hippocampus of 12 female mice (6 3xTg-AD, 6 wild-type) from two time points (6 and 12 months; n = 6 per time point). The 3xTg-AD mouse model exhibits amyloid-β and tau pathology occurring as early as 6 and 12 months, respectively.

first: Tabea

last: Soelter

first: Timothy

last: Howton

first: Jordan

last: Whitlock

middle: N


title: Single cell gene expression of Mycobacterium tuberculosis (Mtb) specific T-cells

first: Samuel

last: Behar

summary: Single cell gene expression profile of total CD3+ TCR[b]+ T-cells from lungs of infected C57Bl/6 (B6) mice at 6 and 41 weeks post-infection (wpi) with Mtb

overall_design: CD3+ TCR[b]+ T-cells were sorted from the lungs of Mtb infected B6 mice. Gene expression and V(D)J profiles were analyzed using single-cell RNA sequencing (scRNAseq)

first: Evelyn

last: Chang

first: Tomoyo

last: Shinkawa


title: The nuclear exosome co-factor MTR4 shapes the transcriptome for meiotic initiation (RNA-Seq)

status: Public on Feb 23 2025

city: Shanghai

first: Hong

last: Cheng

address: 320 Yue Yang Road

country: China

institute: Shanghai Institute of Biochemistry and Cell Biology, CAS

summary: Nuclear RNA decay has emerged as a mechanism for post-transcriptional gene regulation in cultured cells.  However, whether this actually occurs in animals and is biologically relevant remains largely unexplored.  Here, we demonstrate that MTR4, a central cofactor of the nuclear RNA exosome complex, is required for embryogenesis and spermatogenesis.  Embryonic development of MTR4 knockout mice arrests at 6.5 days.  Specific knock out of MTR4 in mouse advanced germ cells results in male infertility with a severe defect in meiotic initiation, with pre-meiotic germ cells accumulating a dysregulated transcriptome with mixed features of mitosis and meiosis.  Interestingly, MTR4 pervasively binds to various types of RNAs but selectively degrades those exhibiting specific binding patterns.  Moreover, polyadenylated retrotransposon RNAs are removed by the nuclear exosome, preventing their negative impacts on gene expression and potential mutagenic threat.  Our work underscores the importance of nuclear RNA decay in regulating germline transcripts to ensure a gene expression program for the mitotic-to-meiotic transition.

overall_design: To investigate which and how many RNAs are regulated by MTR4 in spermatogenesis, we sorted differented spermatogonia and conducted RNA-seq.

first: Li

last: Zhang

first: Jianshu

last: Wang

first: Zhidong

last: Tang

first: Zhen

last: Lin

first: Ruibao

last: Su

first: Naijing

last: Hu

first: Yao

first: Gaoxiang

last: Ge

first: Jin

last: Fan

first: Yuanchao

last: Xue

first: Ming-Han

last: Tong

first: Yu

last: Zhou


title: Single-nuclei RNA Sequencing Reveals Distinct Transcriptomic Signatures of Rat Dorsal Root Ganglia in a Disc-associated Chronic Low Back Pain Model

status: Public on Feb 22 2025

city: Dallas

first: Theodore

last: Price

state: TX

address: 800 W Campbell Rd

institute: The University of Texas at Dallas

summary: This study presents the first application of comprehensive single-nuclei RNA sequencing (snRNA-seq) of dorsal root ganglion (DRG) neurons in a rat model using Parse technology. Our dataset includes two experimental models: (1) control rats representing both sexes and (2) rats with disc-associated chronic lower back pain, alongside sham-treated animals. By leveraging high-resolution transcriptomic profiling, this study provides novel insights into the molecular landscape of DRG neurons, offering a valuable resource for understanding the cellular mechanisms underlying chronic pain.

overall_design: Nuclei were isolated from  T13-L1 DRGs rat dorsal root ganglion followed by fixation and  barcoding using the parse split seq technology.

first: Ishwarya

last: Sankaranarayanan


title: RNA-seq analysis of differentially expressed genes between WT and KD ZC3H18 KYSE150/ECA109 cells.

status: Public on Feb 21 2025

city: Suzhou

first: Xiaoqin

last: Yang

state: Jiangsu

address: NO. 199 Renai Road

institute: Soochow University

summary: Small interfering RNAs (siRNAs) targeting ZC3H18 were purchased from Suzhou Hongxun Biotechnology Co., Ltd. (Suzhou, China), with an empty vector serving as the control (si-nc). ZC3H18 siRNA sequences were GGGGTGAGGGCTTCTGATCT and TCGTCGGAGTGATTATCTTCCT. These siRNAs were introduced into KYSE150 and ECA109 cells using DharmaFect1 (Suzhou Hongxun Biotechnology Co., Ltd., Suzhou, China).

overall_design: Comparative gene expression profiling analysis of RNA-seq data for KYSE150/ECA109 cells and their KD derivatives (siRNAs targeting ZC3H18).

first: Dong

last: Jiang


title: The essential clathrin adaptor protein complex-2 is tumor suppressive specifically in vivo [CRISPR Screen]

city: Durham

first: Seth

last: Zimmerman

state: NC

address: 308 Research Dr.

institute: Duke University

summary: The microenvironment is a rich source of new cancer targets.  While whole-genome CRISPR/Cas9 screens have identified vulnerabilities in cultured cells, it is a challenge to use this approach in tumors to interrogate the microenvironment.  To this end, we screened a panel of pancreatic cancer lines grown in culture versus as tumors with a phosphatidylinositol metabolism CRISPR/Cas9 library.  This revealed the Adaptor Protein complex-2 (AP2) of clathrin-mediated endocytosis behaves as common essential in culture but tumor suppressive in vivo.  These polar-opposite phenotypes were attributed to different microenvironments.  In culture, AP2 loss reduces endocytosis of transferrin and iron import.  In tumors, alternative iron transport pathways allow pro-tumor signaling to manifest.  In the most sensitive case, AP2 loss reprograms the plasma membrane proteome, retaining integrins on the surface leading to downregulation of the tumor-suppressor PTEN.  Analysis of human tumors suggests a similar tumor suppressive activity.  AP2 may foreshadow other proteins unique to the tumor-microenvironment.

overall_design: In Vivo and in vitro CRISPR screen across 5 cell lines in culture and in xenograft samples. sgRNA library targeted PtdINS library

middle: P

first: Christopher

last: Counter


title: The nuclear exosome co-factor MTR4 shapes the transcriptome for meiotic initiation (LACE-Seq)

first: Hong

last: Cheng

overall_design: To investigate which RNAs are bound by MTR4 in spermatogenesis, we sorted differented spermatogonia and conducted LACE-seq to detect the substrate of MTR4

first: Li

last: Zhang

first: Jianshu


title: Identification of two transitional stem-like memory CD8+ T cell states during viral infection and vaccination

first: Joanna

last: Groom

state: VIC

institute: WEHI

summary: Stem-like CD8+ T cells are a key feature of chronic conditions and long-lived memory. Currently stem-like CD8+ T cells are named according to their environment, where precursors of exhausted (TPEX) cells arise in chronic viral infections, autoimmunity and cancer, while stem cell-like memory (TSCM) cells are associated with acute infection and vaccination. Here, we established and validated a method to monitor the transition between transcriptionally distinct TPEX and TSCM cell states. We reveal a linear and reversible developmental trajectory that is concomitant with viral clearance. Further, we demonstrate that TPEX to TSCM cell conversion is observed during acute viral infection and vaccination, aligning the processes that establish stem-like CD8+ T cells in acute and chronic settings. This work supports the potential to monitor stem-like CD8+ T cell conversion as biomarkers of disease in patients with chronic infection, cancer, and autoimmunity and broadens the importance of this transition during the establishment of vaccine-induced long-lived immune protection.

overall_design: Paired single cell RNA sequencing (scRNAseq) and surface protein sequencing (CITEseq) analysis compared P14 cells from day 8 acute LCMV Armstrong infection (4499 cells) and chronic LCMV Docile infection (4967 cells) with days 0-1 IFNAR blocked LCMV Armstrong at both day 8 (5061 cells) and day 14 (3102 cells).

first: Benjamin

last: Broomfield

first: Chin Wee

last: Tan


title: Corneal keratocytes, fibroblasts, and myofibroblasts exhibit distinct transcriptional profiles in vitro

first: Kara

last: Poole

address: 5323 Harry Hines Blvd

department: Ophthalmology

institute: UT Southwestern Medical Center

summary: After stromal injury to the cornea, the release of growth factors and pro-inflammatory cytokines promotes the activation of quiescent keratocytes into a migratory fibroblast and/or fibrotic myofibroblast phenotype. Persistence of the myofibroblast phenotype can lead to corneal fibrosis and scarring, which are leading causes of blindness worldwide. This study aims to establish comprehensive transcriptional profiles for cultured corneal keratocytes, fibroblasts, and myofibroblasts to gain insights into the mechanisms through which these phenotypic changes occur. Primary rabbit corneal keratocytes were cultured in either defined serum-free media (SF), fetal bovine serum (FBS) containing media, or in the presence of TGF-β1 to induce keratocyte, fibroblast, or myofibroblast phenotypes, respectively. Bulk RNA sequencing followed by bioinformatic analyses was performed to identify significant differentially expressed genes (DEGs) and enriched biological pathways for each phenotype. Genes commonly associated with keratocytes, fibroblasts, or myofibroblasts showed high relative expression in SF, FBS, or TGF-β1 culture conditions, respectively. Differential expression and functional analyses revealed novel DEGs for each cell type, as well as enriched pathways indicative of differences in proliferation, apoptosis, extracellular matrix (ECM) synthesis, cell-ECM interactions, cytokine signaling, and cell mechanics. Overall, these data demonstrate distinct transcriptional differences among cultured corneal keratocytes, fibroblasts, and myofibroblasts. We have identified genes and signaling pathways that may play important roles in keratocyte differentiation, including many related to mechanotransduction and ECM biology. Our findings have revealed novel molecular markers for each cell type, as well as possible targets for modulating cell behavior and promoting physiological corneal wound healing.

overall_design: Comparative gene expression profiling analysis of bulk RNA-seq data from primary rabbit corneal keratocytes cultured in serum-free media, serum-containing media, or in the presence of TGF-β1.

first: Krithika

last: Iyer

first: David

middle: W

last: Schmidtke

first: Matthew

last: Petroll

first: Victor

middle: D

last: Varner


title: Adenosine 5’-tetraphosphate and adenosine triphosphate signaling in THP-1 macrophages.

city: Bonn

first: Günther

last: Weindl

address: Gerhard-Domagk-Str. 3

department: Pharmaceutical Institute

country: Germany

institute: University of Bonn

summary: The endogenous nucleotide adenosine 5’-tetraphosphate (Ap4) has emerged as a potent vasoconstrictor. Despite its structural similarity to the danger signal adenosine triphosphate (ATP), the immunomodulatory effects of Ap4 remain unclear. To gain a deeper insight into the biological processes underlying Ap4- and ATP-mediated responses, RNA-sequence analysis of transcriptional changes in THP-1 macropahges was performed. After 3 hours of stimulation with Ap4 or ATP, THP-1 macrophages showed significant changes in RNA expression compared to the unstimulated control.

overall_design: THP-1 macrophages were timulated with Ap4 or ATP for 3 hours. Unstimulated cells served as control.

first: Judith

last: Bockstiegel


title: Gain-of-function ENL YEATS domain mutations impede nephrogenesis through gene expression control [Spatial Transcriptomics]

status: Public on Feb 20 2025

city: Grand Rapids

first: Xiaobing

last: Shi

address: 333 Bostwick Ave. NE

institute: Van Andel Institute

summary: Hotspot gain-of-function mutations in the YEATS domain of the histone reader protein ENL have been identified in Wilms’ tumor. To investigate the pathogenic role of these cancer-associated ENL mutations in kidney development and tumorigenesis in vivo, we generated conditional knock-in mouse models mimicking patient-derived ENL YEATS mutations. Mice with heterozygous expression of ENLT mutants in either Six2+ nephrogenic or Foxd1+ stromal lineage exhibit severe yet distinct defects in kidney development, both resulting in neonatal lethality. The Six2-ENLT mutant kidney rudiments display compromised cap mesenchyme, scant proximal tubules and cystic glomeruli, indicative of premature commitment and differentiation blockade during nephrogenesis. Bulk and spatial transcriptomic analyses uncover aberrant activation of Hox genes and genes involved in cell fate commitment, especially the Wnt signaling pathway, in ENLT mutant-expressing nephrogenic cells. In contrast, the Foxd1-ENLT mutant kidneys exhibit expansion in renal capsule and cap mesenchyme, accompanied with dysregulation of stromal genes involved in nephrogenesis and stroma-nephron crosstalk. Collectively, our study sheds lights on how ENL YEATS domain mutations impede nephrogenesis through different pathways in nephrogenic and stromal lineages, paving the way for further investigations into their roles in tumorigenesis.

overall_design: Floxed Enl T mutant alleles were crossed with Cre strains (Foxd1-GC/+ or Six2-TGC tg/+) with or without LSL-tdT Cre reporter allele to get embryonic kidney at E14.5 and E18.5 stage. RNA was extracted from whole kidney or sorted tdT+ cells for sequencing.

first: Zhaoyu

last: Xue

first: Hongwen

last: Xuan

first: Kin

last: Lau

last: Wen


title: Glucose controls protein-protein interactions and tissue differentiation

city: Stanford

first: Vanessa

last: Lopez-Pajares

state: CA

address: 269 Campus Dr., CCSR 2150

department: Dermatology

institute: Stanford University

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


title: Gain-of-function ENL YEATS domain mutations impede nephrogenesis through gene expression control


title: IL-1 protects from fatal systemic candidiasis by inhibition of oxidative phosphorylation and hypoxia [snRNA-Seq]

city: Zürich

first: Manfred

last: Kopf

address: Otto-Stern-Weg 7

department: Biologie

country: Switzerland

institute: ETH Zürich

summary: Invasive C. albicans infections result in high mortality rates. While IL-1 is important to combat these infections, the precise mode of action remains unclear. Using global and conditional Il1r1 knockouts in mice, we found that IL-1R-signaling in non-hematopoietic cells in the kidney and brain is crucial for a protective response. In the kidney, endothelial IL-1R contributes to fungal clearance independent of neutrophil recruitment, while IL-1R in hematopoietic cells is dispensable. In the brain, IL-1R-signaling indirectly recruits neutrophils and monocytes by regulating chemokines and adhesion molecules. Single-nucleus-RNA-sequencing revealed Il1r1-mediated NF-B-activation in distinct kidney cell types. Our data reveal excessive metabolic activity and oxidative phosphorylation across all cell types in the kidney of Il1r1-deficient mice within a few hours upon infection, associated with localized hypoxia at infection foci. By showing that hypoxia promotes fungal growth and pathogenicity, our data suggest that IL-1R-signaling in non-hematopoietic cells is required to prevent fatal candidiasis by inhibiting a metabolic shift, including excessive oxidative phosphorylation and hypoxia.

overall_design: Single nucleus RNA sequencing from whole kidneys, isolated from Il1r1+/- and Il1r1-/- mice, 8 hours after i.v. infection with C. albicans

first: Sofia

last: Horn

first: Mareike

last: Schmid

first: Ivan

last: Berest

first: Federica

last: Piattini

first: Jing

last: Zhang

first: Katrien

last: de Bock

first: Olivier

last: Devuyst

first: Stellor

last: Nlandu Khodo

first: Jan

last: Kisielow


title: Study of the effect of the trancription factor SARO_RS14285 in aromatics degradation in Novosphingobium aromaticivorans

city: Madison

first: Kevin

last: Myers

state: WI

address: 5127 WEI, 1552 University Ave

department: Great Lakes Bioenergy Research Center

institute: University of Wisconsin - Madison

summary: Novosphingobium aromaticivorans DSM12444 is a bacterium capable of catabolizing several lignin aromatics. A main degradation pathway for these compounds is the protocatechuate (PCA) meta-cleavage. Nevertheless, the transcriptional regulation of this pathway is still unknown. Immediately upstream of the genes encoding the enzymes for this pathway, the LysR-type transcription factor (LTTF) SARO_RS14285 was identified. To evaluate the functionality of this LTTF, a deletion mutant was constructed. A transcriptomic analysis of the mutant strain cultured in several aromatic compounds is included in this report.

sample_organism: Novosphingobium aromaticivorans DSM 12444

overall_design: RNA-seq profiling of the WT and the deletion mutant cultured in minimal medium with glucose and one of the following aromatics: protocatechuic acid (PCA), 4-coumaric acid (4-CA), vanillic acid (VA) or syringic acid (SA).

first: Laura

last: Rodríguez-Castro

first: Daniel

middle: R

last: Noguera

first: Timothy

middle: J

last: Donohue


title: IL-1 protects from fatal systemic candidiasis by inhibition of oxidative phosphorylation and hypoxia


title: Functional Investigation of a Novel PIWIL4 Mutation in Nonobstructive Azoospermia During the First Wave of Spermatogenesis

city: Nanjing

first: Feng

last: Li

address: Longmian Avenue 101

institute: Nanjing Medical University

summary: PIWI-interacting RNAs (piRNAs) are small noncoding RNAs that are almost exclusively expressed in germ cells where they work to silence harmful transposons to maintain genomic stability. It is proposed that the associated piRNAs guide the nuclear PIWIL4 to transposable elements where it recruits the DNA methylation apparatus and instructs de novo DNA methylation. Herein we identify a missense variant of PIWIL4 (c.805 C>T p.R269W) in two infertile males. Though male homozygous knock-in mice harboring the orthologous variant exhibit normal sperm counts and morphology, they display increased expression of transposable elements and abnormal gene expression during the first wave of spermatogenesis. Mechanistically, the mutated site impairs the piRNA-binding ability of PIWIL4 and leads to the derepression of some LINE-1 elements. In summary, we have identified a piRNA binding mutation in PIWIL4 that may be involved in human non-obstructive azoospermia.

overall_design: RNA-sequencing on 3-week-old wild-type, piwil4WT/R264W and piwil4R264W/R264W testes.

first: Xiayu

last: Wang

first: Qian

last: Du


title: Gain-of-function ENL YEATS domain mutations impede nephrogenesis through gene expression control [RNA-seq]

first: Xiaobing

last: Shi

first: Zhaoyu

last: Xue

first: Hongwen

last: Xuan

first: Kin

last: Lau

first: Hong

last: Wen


title: IL-1 protects from fatal systemic candidiasis by inhibition of oxidative phosphorylation and hypoxia [bulk RNA-Seq]

first: Manfred

last: Kopf

overall_design: Bulk RNA Sequencing of brains, isolated from Il1r1+/- and Il1r1-/- mice, 8 hourse after i.v. infection with C. albicans

first: Sofia

last: Horn

first: Mareike

last: Schmid

first: Ivan

last: Berest

first: Federica

last: Piattini

first: Jing

last: Zhang


title: Diabetes induces exacerbated SARS-CoV-2 replication partly associated with ineffective pulmonary interferon responses, delayed cell-mediated immunity, and disruption of leptin receptor signaling

status: Public on Feb 19 2025

city: Baton Rouge

first: Jaroslaw

last: Staszkiewicz

state: LA

address: 6400 Perkins Rd

department: Genomics Core Facility

institute: Pennington Biomedical Research Center

summary: We evaluated the susceptibility and lung responses of type 2 diabetic and lean mice following intranasal SARS-CoV-2 infection using the mouse-adapted MA10 strain

overall_design: Diabetic Leprdb mice and lean heterozygote mice were intranasally inoculated with 20,000 PFU of mouse-adapted SARS-CoV-2 MA10 strain and lungs were collected and processed for analysis at 2 and 4 days post-infection. Total RNA was isolated from homogenized lung and subjected to RNAseq

first: Come

last: Thieulent

first: Udeni

last: Balasuriya

first: Mariano

last: Carossino


title: Examining patient-specific responses to PARP inhibitors in a novel, human induced pluripotent stem cell-based model of breast cancer

city: Chicago

first: Paul

middle: W.

last: Burridge

state: IL

address: 320 East Superior Street

institute: Northwestern University

summary: Preclinical models of breast cancer that better predict patient-specific drug responses are critical for expanding the clinical utility of targeted therapies, including for inhibitors of poly(ADP-ribose) polymerase (PARP). Reprogramming primary cancer cells into human induced pluripotent stem cells (hiPSCs) recently emerged as a powerful tool to model drug response phenotypes, but its use to date has been limited to hematopoietic malignancies. We designed an optimized reprogramming methodology to generate breast cancer-derived hiPSCs (BC-hiPSCs) from nine patients representing all major subtypes of breast cancer. BC-hiPSCs retain patient-specific oncogenic variants, including variants unique to individual tumor subclones. Additionally, we developed a protocol to differentiate BC-hiPSCs into mammary epithelial cells and mammary-like organoids for in vitro disease modeling, including drug response phenotyping. Using these tools, we demonstrated that BC-hiPSCs can be used to screen for differential sensitivity to PARP inhibitors and mechanistically investigated the causal genetic variant driving drug sensitivity in one patient.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for primary breast cancer derived mammary epithelial cells (MEC), undifferentiated hiPSCs, and hiPSCs differentiated into mammary epithelial cells (hiPSC-MEC), endothelial cells (hiPSC-EC), or cardiomyocytes (hiPSC-CM). Three to five biological replicates (independent cell lines) provided for each cell type.

first: Carly

last: Weddle


title: Design, Development, and Evaluation of Gene Therapeutics Specific to KSHV-Associated Diseases

city: Sacramento

first: Yoshihiro

last: Izumiya

institute: UC Davis

summary: Kaposi's sarcoma-associated herpesvirus (KSHV) is the causative agent of Kaposi's sarcoma (KS) and two human lymphoproliferative diseases: primary effusion lymphoma and AIDS-related multicentric Castleman's disease. KSHV latency-associated nuclear antigen (LANA) is expressed in KSHV-infected cancer cells and is responsible for maintaining viral genomes in infected cells. Thus, LANA is an attractive target for therapeutic intervention for KSHV-associated diseases.  Here, we devised a gene therapy vector using the adeno-associated virus (AAV), which capitalizes the LANA's function to tether terminal repeat (TR) containing circular genome in latently infected cells and the TR's enhancer function for KSHV inducible gene promoters. By including two TR copies with a lytic inducible gene promoter (TR2-Orip), we generated an AAV vector, which expresses an engineered thymidine kinase (TK) selectively in KSHV-infected cells. Ganciclovir (GCV), an anti-herpesvirus drug, effectively eradicated multiple KSHV-infected cells that include iPSC derived epithelial colony forming cells, but not non-KSHV-infected counterparts in the presence of AAV8-TR2-Orip-TK. In addition, AAV8-TR2-Orip-TK prevents KSHV virion production from reactivated cells, hence spreading KSHV infections from reactivated cells. Anti-cancer drugs, known to reactivate KSHV, stimulated TK expression from the vector and, therefore, synergized with AAV8 TR2-Orip-TK to induce KSHV-infected cancer cell death. Finally, the AAV8-TR2-Orip-TK with GCV completely diminished KSHV-infected cancer cells in the xenograft tumor model. Our new cancer gene therapy should augment the current clinical protocol for KS.

overall_design: RNA-seq profiling of KSHV-infected  iSLK cells or 293 cells under GCV treatment after AAV8-TR2-Orip-TK treatment.

first: Tomoki

last: Inagaki

first: Jonna

last: Espera

first: Kang-Hsin

last: Wang

first: Sonali

last: Nair

first: Somayeh

last: Komaki

first: Ryan

last: Davis

first: Ashish

last: Kumar

first: Ken-ichi

last: Nakajima


title: Targeting Insulin-Like Growth Factor 1 Receptor Restricts Development and Severity of Secondary Lymphedema in Mice

city: Fitzroy

first: Yinan

last: Yuan

address: 9 Princes St

institute: St. Vincent's Institute of Medical Research

summary: Secondary lymphedema is a debilitating chronic tissue swelling in a limb caused by inadequate interstitial fluid drainage due to dysfunctional lymphatic vessels. Pathological enlargement of small lymphatics contributes to lymphatic dysfunction in secondary lymphedema, but the molecular mechanisms driving this remodelling are unclear. Here, using a surgical mouse model of secondary lymphedema and whole-genome microarray, we identified the transcript for insulin-like growth factor binding protein 5 (IGFBP5), a negative regulator of IGF signaling, as the most profoundly down-regulated mRNA in lymphedematous tissue. Notably, IGF signalling via IGF1 receptor (IGF1R) was previously shown to promote lymphatic remodelling. We therefore targeted IGF1R in the mouse model using the small molecule IGF1R inhibitor linsitinib. Linsitinib was effective in restricting enlargement of small lymphatics and tissue swelling during lymphedema development. Importantly, linsitinib profoundly reduced tissue swelling in mice with chronic lymphedema suggesting that IGF signalling could be a therapeutic target in clinical secondary lymphedema.

overall_design: Gene candidates involved in pathological lymphatic remodelling in lymphedema were identified by whole-genome microarray analysis for mouse lymphedema model and non-operated control groups. The effects of inhibiting IGF1R signalling during lymphedema development in the model were then assessed by treating the mice with linsitinib. In addition, whether linsitinib could restrict tissue swelling in established lymphedema was assessed.

first: Sidney

last: Levy

first: Yong

middle: Q

last: Yeo

first: Ramin

last: Shayan

first: Tara

last: Karnezis

first: Steven

last: Stacker

first: Marc

last: Achen


title: Cold and hot fibrosis define clinically distinct cardiac pathologies

status: Public on Feb 18 2025

city: Vienna

first: Jingkui

address: Campus-Vienna-Biocenter 1

country: Austria

institute: Research Institute of Molecular Pathology (IMP)

summary: Fibrosis is a broad pathology of excessive scarring with substantial medical implications. The fibrotic scar is produced by myofibroblasts that interact with macrophages. Fibrosis is a complex process involving thousands of factors, therefore, to better understand fibrosis and develop new therapeutic approaches, it is necessary to simplify and clarify the underlying concepts. Recently, we described a mathematical model for a macrophage-myofibroblast cell circuit, predicting two types of fibrosis - hot fibrosis with abundant macrophages and myofibroblasts, and cold fibrosis dominated by myofibroblasts alone. To test these concepts and intervention strategies in a medically relevant system, we use a widely studied in-vivo injury model for fibrosis, myocardial infarction (MI). We show that cold fibrosis is the final outcome of MI in both mice and pigs and demonstrate that fibrosis can shift toward healing in regenerative settings. MI begind with an increase of myofibroblasts and macrophages, followed by macrophage decline leading to persistent cold fibrosis (only myofibroblasts). During this process, fibroblasts, unlike macrophages, acquire distinct fate changes. Using mathematical modeling we predict that targeting of the autocrine signal for myofibroblast division could block cold fibrosis. We identify TIMP1 as an autocrine cardiac myofibroblast growth factor in-vitro. Treatment of adult mice after MI with anti-TIMP1 antibodies reduces fibrosis in-vivo. This study shows the utility of the concepts of hot and cold fibrosis and the feasibility of our circuit-to-target approach to reduce fibrosis after acute cardiac injury by inhibiting the myofibroblast autocrine loop.

overall_design: Hearts from 12 week old mice were subjected to left anterior descending artery ligation and were harvested at 1,4,7 and 14 day after injury. The hearts were harvested and flesh frozen for spatial transcriptomics. Hearts were  sectioned until injured area was apparant and then prepared for downstream pipeline.

first: Shoval

last: Miyara

first: Miri

last: Adler

first: Elad

last: Bassat

first: Yalin

last: Divinsky

first: Kfir

middle: B

last: Umansky

first: Jacob

last: Elkahal

first: Alexander

last: Genzelinakh

first: David

last: Kain

first: Daria

last: Lendengolts

first: Tali

last: Shalit

first: Michael

last: Gershovits

first: Avraham

last: Shakked

first: Lingling

last: Zhang

first: Danielle

middle: M

last: Kimchi

first: Andrea

last: Baehr

first: Rachel

last: Sarig

first: Christian

last: Kupatt

first: Elly

last: Tanaka

first: Ruslan

last: Medzhitov

first: Avi

last: Mayo

first: Uri

last: Alon

first: Eldad

last: Tzahor


title: Transcriptome Sequencing Data of Peripheral Blood Neutrophils in Multiple Sclerosis Patients and Healthy Volunteers

status: Public on Feb 17 2025

city: Shijiazhuang

first: Huining

address: Academician Building, The Second Hospital of Hebei Medical University, No. 215 West Heping Road, Xinhua District, Shijiazhuang City, Hebei Province, China

summary: Multiple sclerosis (MS) is a chronic, inflammatory, and demyelinating disease of the central nervous system. To explore the transcriptomic characteristics of peripheral blood neutrophils during the acute phase of MS, we conducted transcriptome sequencing analysis. Peripheral blood neutrophils were isolated from 8 MS patients in the acute phase and 29 age- and sex-matched healthy volunteers using density gradient centrifugation. RNA was extracted and sequenced on the Illumina platform to identify differentially expressed genes (DEGs) and their associated pathways. Bioinformatic analyses revealed significant alterations in genes related to immune response, neutrophil degranulation, and intracellular signaling. These findings provide insights into the molecular mechanisms underlying MS pathology and offer potential biomarkers for diagnosis and therapeutic targets.

overall_design: RNA sequencing was performed on peripheral blood neutrophils collected from 8 MS patients during the acute phase and 29 healthy volunteers using density gradient centrifugation. The MS patients were recruited based on clinical diagnosis and had not received immunosuppressive or disease-modifying therapies within one month prior to sampling. All healthy volunteers were matched for age and sex. Total RNA was extracted from neutrophils and subjected to library preparation and sequencing using the Illumina platform. Quality control and downstream bioinformatics analyses were conducted to identify differentially expressed genes and enriched biological pathways. Data were generated in compliance with standard experimental protocols to ensure reproducibility and accuracy.

first: Ruoyi

last: Guo

first: Moyuan

last: Quan


title: Piezo1 promotes the progression of necrotizing enterocolitis via activating Ca2(+)/CaMKII-dependent pathway

city: Changchun

first: Zhenyu

last: Li

address: No.1 Xinmin Street

institute: The First Hospital of Jilin University

summary: Necrotizing enterocolitis (NEC) is a devastating inflammatory bowel necrosis of very preterm infants with limited therapeutic approaches. Mounting evidence supports the role of Piezo1, a widely distributed mechanosensor on intestinal epithelial cells (IECs), in intestinal inflammation, but its underlying mechanism in the development of NEC has not been explored. Here we demonstrated that Piezo1 protein expression was higher in very preterm infants compared to full-term infants, and positively associated with serum inflammation levels in NEC patients. C57BL/6J mice in which Piezo1 was selectively deleted IECs (villin specific knockout; CKO) and floxed control mice were subjected to induce NEC, and Piezo1 regulated intestinal barrier function, restricted cytokines secretion, and diminished the inflammatory response in NEC mouse models.

overall_design: RNA-seq profiling of small intestine fromC57BL/6J mice with IEC-specific Piezo1 knockout (CKO) and their floxed control mice, including NEC-induced and control groups.

first: Qinlei

last: Jiang

first: Jiaqi

last: Wei

first: Dan

last: Dang

first: Hui

last: Wu


title: Molecular characterization of human ACTH-producing tumors

city: Moscow

first: Rustam

last: Heydarov

address: 8-2 Trubetskaya str.

country: Russia

institute: I.M. Sechenov First Moscow State Medical University

summary: This study investigates the molecular features of ACTH-secreting tumors to uncover gene expression patterns specific to this condition. By analyzing RNA-seq data from a diverse set of 36 samples, including pituitary adenomas with ACTH secretion, pituitary tissues, and other neuroendocrine tumors with ectopic ACTH secretion, we aim to identify distinct molecular signatures associated with ACTH production.

overall_design: The study involved RNA sequencing of 36 samples, including 22 pituitary adenomas with confirmed ACTH secretion, 7 healthy pituitary tissue samples serving as controls, 6 lung carcinoids with ectopic ACTH secretion, and 1 pancreatic neuroendocrine tumor with ectopic ACTH secretion. All samples were derived from formalin-fixed, paraffin-embedded (FFPE) tissues.

first: Anton

last: Buzdin

first: Maria

last: Suntsova

first: Maxim

last: Sorokin


title: Transcriptomic effects of purine metabolism inhibition and nucleolus rRNA synthesis disruption on murine acute myeloid leukemia stem cell

city: Houston

first: Xiangguo

last: Shi

state: Texas

address: 1 Baylor Plz

department: Molecular and Human Genetics

institute: Baylor College of Medicine

summary: Through targeted metabolomics analysis of bulk leukemia cells and leukemia stem cells (LSCs) derived from the MLL-AF9-driven acute myeloid leukemia (AML) model, in comparison with normal granulocyte-monocyte progenitor (GMP) cells and whole bone marrow (WBM) cells from normal mice, we identified enhanced purine metabolism in AML LSCs. Pharmacological targeting of the purine metabolism using mycophenolate mofetil (MMF) resulted in decreased levels of purine metabolites crucial for nucleolus rRNA synthesis. Importantly, inhibition of purine metabolism or disruption of the nucleolus rRNA synthesis, achieved by inhibiting pol I activity with CX-5461, triggered myeloid differentiation in the MLL-AF9-driven AML LSCs. These findings unveil a regulatory axis involving purine metabolism and nucleolar rRNA synthesis in maintaining AML LSC activity.

overall_design: To investigate the function of purine metabolism and nucleolus rRNA synthesis in sustaining AML LSC activity, we isolated LSCs (defined by L-GMP immunophenotype) from MLL-AF9-driven AML mice and then treated them with MMF, CX-5461, Guanosine, or a combination of MMF and Guanosine. We performed gene expression profiling analysis using data obtained from these five distinct experimental groups. Our comparative analysis focused on the gene expression profiles of AML LSCs and treated LSCs.

first: Shi

last: Xiangguo

first: Nakada

last: Daisuke

first: Liu

last: Zian

first: Samee

last: Md Abul Hassan


title: Intracellular HIV-1 Tat regulator induces epigenetic changes in the DNA methylation landscape.[EPIC]

city: Majadahonda

first: Ruben

last: Ayala-Suárez

state: Madrid

address: Crta Pozuelo Km 2

department: AIDS Immunopathology Unit

country: Spain

institute: Instituto de Salud Carlos III

type: Methylation profiling by genome tiling array

summary: The HIV regulatory protein Tat enhances viral transcription but also modifies host gene expression, affecting cell functions like cell cycle and apoptosis. Cohort studies indicate that, despite virological suppression, people with HIV (PWH) are at increased risk of comorbidities linked to chronic inflammation, accelerated immune-aging and cellular senescence, sometimes associated with abnormal genomic methylation patterns. In this study, we analyzed whether Tat influences DNA methylation and subsequently impact the transcriptional signature, contributing to inflammation and accelerated aging. To this aim, Jurkat cells were transfected with full-length Tat (Tat101), Tat’s first exon (Tat72), or an empty vector (TetOFF) and DNA methylation changes were assessed. Differentially expressed genes (DEG) were identified via RNA-seq. Results showed that Tat101 expression resulted in major hyper- and hypomethylations changes at individual CpG sites resulting in a slightly global DNA hypermethylation. Methylation changes at gene promoters and bodies resulted in altered gene expression, specifically regulating gene transcription in 5.1% of DEG in Tat101 expressing cells. In contrast Tat72 had a minimal impact on this epigenetic process. The observed differentially methylated and expressed genes were involved in inflammatory responses, lipid antigen presentation, and apoptosis, and may constitute a key epigenetic mechanism contributing to HIV pathogenesis and chronic inflammation.

overall_design: We aimed to profile the epigenetic changes at DNA methylation level induced by HIV protein Tat with an InfiniumEPIC Methylation array to study the effects of Tat in gene regulation. Jurkat TetOFF cell line from Clontech was stably transfected with a pTRE2hyg plasmid encoding full-length HIV-Tat cDNA (101aa; Tat101), a pTRE2hyg plasmid encoding only the first exon of HIV-Tat (72aa; Tat72), or an empty pTRE2hyg vector as a control (TetOFF). In this model, the administration of 1 μg/ml doxycycline  to the culture medium for 48h repress Tat expression. A total of 400.000 Jurkat cells per well with the different HIV-Tat constructs or the empty vector control (3 biological replicates) were grown in the presence or absence of 1 μg/ml doxycycline for 2 days. Cell pellets were then obtained and frozen. Genomic DNA was isolated and used for bisulfite conversion. Subsequently, all the samples were assayed with the Infinium MethylationEPIC BeadChip microarray v1.0 (Illumina) in a HISCanSQ Analysis System (Illumina).Beta values were obtained with minfi and differentially methylated regions were calculated between groups using MissMethyl R package.

first: Andrea

last: Rodriguez-Agustin

first: Izar

last: de Villasante

first: Angelika

last: Merkel

first: Núria

last: Climent


title: Accessible chromatin profiles (ATAC) at single-cell level of human post-mortem brain tissue from the orbitofrontal cortex

city: Munich

first: Elisabeth

last: Binder

address: Kraepelinstr. 2-10

institute: Max Planck Institute of Psychiatry

summary: The human cortex consists of a variety of different cell types. We used single-nuclei ATAC sequencing to characterize cell-type specific open chromatin profiles in a cohort of psychiatrically healthy controls and individuals diagnosed with psychiatric disease.

overall_design: Fresh-frozen post mortem orbitofrontal cortex tissues of Brodmann area 11 (BA 11) was obtained from the NSW Brain Tissue Resource Centre in Sydney, Australia. Single-nucleus ATAC sequencing from tissue samples from 35 psychiatrically healthy donors and 57 donors diagnosed with a psychiatric disease was performed.

first: Nathalie

last: Gerstner

first: Anna

last: Fröhlich

first: Miriam

last: Gagliardi

first: Maik

last: Ködel

first: Natalie

last: Matosin

first: Simone

last: Roeh

first: Vanessa

last: Murek

first: Janine

last: Knauer-Arloth

first: Michael

last: Ziller


title: Differential accessibility landscapes in MLL-AF9-driven leukemia stem cells upon inhibiiton of purine metabolism

first: Xiangguo

last: Shi

summary: Targeted metabolomics analysis of bulk leukemia cells and leukemia stem cells (LSCs) derived from the MLL-AF9-driven acute myeloid leukemia (AML) model, and normal granulocyte-monocyte progenitor (GMP) cells and whole bone marrow (WBM) cells from healthy mice, revealed an enhanced purine metabolism in AML LSCs. Inhibiting the purine biosynthetic pathway using mycophenolate mofetil (MMF) promoted myeloid differentiation and induced alterations in the chromatin accessibility landscape. These findings underscore the pivotal role of purine metabolism in regulating LSC activity.

overall_design: To investigate the alterations of chromatin accessibility landscape in MLL-AF9-driven leukemia stem cells (LSCs), control or MMF-treated LSCs were subjected to tagmentation using Tn5. The assay for transposase-accessible chromatin with sequencing (ATAC-Seq) was performed and the obtained sequencing data were analyzed to identify and characterize changes in the chromatin accessibility landscape. Comparative analysis was conducted between MMF-treated and untreated MLL-AF9-driven LSCs to identify differential chromatin accessibility patterns.

first: Daisuke

last: Nakada

first: Zian

last: Liu

first: M

last: Samee


title: RNA-seq of wild-type and ZNF217-knockout KOPN-8 cells

status: Public on Feb 16 2025

city: Monrovia

first: Jianjun

last: Chen

department: Systems Biology

institute: Beckman Research Institute of City of Hope

summary: Here, we demonstrate that ZNF217 plays an oncogenic role in B-ALL.  To investigate the underlying mechanisms and pinpoint potential downstream targets that contribute to ZNF217's oncogenic role, we conducted high-throughput RNA-seq on both wild-type and ZNF217-knockout KOPN-8 cells. Our analysis revealed that FOS is An important target of ZNF217 in B-ALL.

overall_design: Single-cloned KOPN-8 cells stably expressing Cas9 were transduced with either ZNF217 sgRNA (sgZNF217 #1 or sgZNF217 #2) or a scrambled sgRNA control. Following validation of ZNF217 knockout efficiency, cells were harvested to isolate total RNA. After that, poly(A)+ mRNAs were enriched for sequencing. For each group, the samples were prepared and sequenced in biological duplicates.

first: Xi

last: Qin

first: Keren

last: Zhou

first: Lei

last: Dong


title: CUT&RUN sequencing of wild-type and ZNF217-knockdown KOPN-8 cells

summary: Here, we elucidate the oncogenic role of ZNF217 in B-ALL and reveal that ZNF217 interacts with the CoREST complex to mediate histone modifications such as H3K4me1, H3K4me2, and H3K27ac. This interaction partially contributes to ZNF217’s oncogenic function in B-ALL. To identify genes directly bound by ZNF217, we conducted high-throughput CUT&RUN sequencing using an anti-ZNF217 antibody in both wild-type and ZNF217-knockdown KOPN-8 cells. Additionally, to distinguish between CoREST-dependent and CoREST-independent targets, we performed CUT&RUN sequencing in the same cell models using an antibody against LSD1, a core component of the CoREST complex that interacts with ZNF217, as well as antibodies against  H3K4me1, H3K4me2, and H3K27ac.

overall_design: KOPN-8 cells transduced with either a ZNF217-targeting shRNA or a scrambled shRNA control were used in CUT&RUN assays. In the ZNF217 and LSD1 groups, live cells were used, while in the H3K4me1, H3K4me2, and H3K27ac groups, cells were lightly cross-linked with 0.1% formaldehyde for 1 minute. The antibodies employed included anti-ZNF217 (A303-265A, Thermo Fisher Scientific), anti-LSD1 (2139S, Cell Signaling Technology), anti-H3K4me1 (5326T, Active Motif), anti-H3K4me2 (9725T, Active Motif), and anti-H3K27ac (39034, Active Motif). For each sample, 10 ng of CUT&RUN-enriched DNA was used for library construction.


city: Rehovot

first: Shoval

last: Miyara

address: Herzl St 234

country: Israel

institute: Weizmann Institute of Science

summary: Fibrosis is a pathology of excessive scarring and a major unmet medical need. Identifying key simplifying principles is needed to better understand fibrosis and may yield new therapeutic approaches. Fibrosis is driven by myofibroblasts that interact with macrophages. We developed a cell-circuit model that predicted two types of fibrosis - ‘hot fibrosis’ that includes both macrophages and myofibroblasts, and ‘cold fibrosis’ dominated by myofibroblasts alone. Here, we tested these concepts using an in-vivo pathological model for cardiac fibrosis resulting from myocardial infarction (MI). We show that MI progresses into cold fibrosis in both mice and pigs. We used the cell-circuit model to find a fragility of cold fibrosis - the autocrine loop which supports myofibroblast growth. We identified the growth factors in the autocrine loop and demonstrate that one of these factors- TIMP1- can stimulate cardiac myofibroblast proliferation in vitro. Inhibiting TIMP1 in-vivo reduced fibrosis in adult mice after MI. This study demonstrates the concept of cold fibrosis following acute MI and the feasibility of our circuit-to-target approach to better understand and treat fibrosis.

overall_design: Landrace pigs, 3 months old (male and female) ~22-35 kg, were purchased from a local farm. Animal care and all experimental procedures were performed in strict accordance with the German and National Institutes of Health animal legislation guidelines and were approved by the local animal care and use committees. Experimental approach: Briefly, a balloon was placed in the LAD distal to the bifurcation of the first diagonal branch and inflated with 6 atm. Correct localization of the coronary occlusion and patency of the first diagonal branch was ensured by injection of contrast agent. The percutaneous transluminal coronary angioplasty balloon was deflated after 60 minutes of ischemia; the onset of reperfusion was documented angiographically. At the onset of reperfusion, animals were treated with 33 µg/Kg (in 5mL of saline) of rhAgrin (#6624-AG, R&D Biosystems) or saline alone as control. Pig heart samples were collected at day 3 and 28 following the MI. Hearts were harvested and stained by Tetrazolium chloride (TTC) to visualize scar/infarct. Left ventricles were dissected transversely to 5, 1cm thick slices, and each slice was further sectioned into 4/8 sections. Sections were annotated as infarct zones (positive for TTC) and remote zones (TTC negative). Sections were frozen on dry ice for further analysis and were later subjected to RNA purification/ histological staining. Total RNA was extracted from 28 frozen pig samples in a paired manner (Remote and Infarct zones from the same animal were used to obtain optimal internal control [rhAgrin day 3 (n = 4), Saline day 3 (n = 3), rhAgrin day 28 (n = 4), Saline day 28 (n = 3)]. Following acquisition, frozen samples were crushed into fine powder using a mortar and pestle and further processed using miRNeasy Mini Kit (Qiagen, Cat# 217004) according to RNA-seq libraries were prepared at the Crown Genomics institute of the Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science. Libraries were prepared using the INCPM-mRNA-seq protocol. Briefly, the polyA fraction (mRNA) was purified from 500ng of total input RNA followed by fragmentation and the generation of double-stranded cDNA. After Agencourt Ampure XP beads cleanup (Beckman Coulter), end repair, A base addition, adapter ligation, and PCR amplification steps were performed. Libraries were quantified by Qubit (Thermo fisher scientific) and TapeStation (Agilent). Sequencing libraries were constructed with barcodes to allow multiplexing. Sequencing was done on a NovaSeq600 instrument (Illumina) using an S1 100 cycles kit, allocating approximately ±35.7million single-end 100-base-pair reads per sample (single read sequencing). Fastq files for each sample were generated by the usage bcl2fastq v2.20.0.422.  manufacturer's guidelines. Replicates of high RNA integrity (RIN), determined by TapeStation (Agilent) (RIN=8.2±0.1) were processed for RNA-seq library preparation.

first: Kfir

last: Baruch Umansky

first: Tali

last: Shalit

first: Uri

last: Alon

first: Eldad

last: Tzahor


title: Human Genome Encodes Multiple Novel miRNAs

city: Xiamen

first: Fan

last: Gao

state: Fujian

address: 668 Jimei Road

institute: Huaqiao University

type: Non-coding RNA profiling by high throughput sequencing

summary: Human cells generate a vast complexity of non-coding RNAs, the so called “RNA dark matter”, which includes small RNA transcriptome represented by hundreds of thousands of entities which outnumber members of known classes of small RNAs by orders of magnitude. Biogenesis, biological relevance, and mechanisms of action of most of these transcripts remain unknown and many of them are assumed to represent degradation products of known genes.  In this study, we aimed to functionally characterize human sRNA transcriptome by attempting to answer the following question — can a significant number of novel sRNAs correspond to novel members of known classes of sRNA, specifically, miRNAs? We show that at the very least, 2726 novel miRNAs exist in just one human cell line. Furthermore, potentially thousands other novel members of this class may exist. Strikingly, many novel miRNAs are derived from exons of protein-coding genes. These results suggest that mammalian novel sRNA transcriptome harbors multitude of novel functional transcripts, at least some of which belong to known classes of sRNAs.

overall_design: We developed a miRNA discovery pipeline that detects novel miRNAs that combine the features of being generated in vivo using the Drosha/DGCR8 biogenesis pathway with correct RNA secondary structure. We further validated the pipeline by detecting in vivo signatures of Dicer cleavage. Using this approach, we discovered thousands of novel miRNAs in just one human cell line and suggest that many others exist.

first: Philipp

last: Kaparnov

first: Fang

last: Wang


title: Foxa2-dependent uterine glandular cell differentiation is essential for successful implantation

status: Public on Feb 15 2025

city: Jinan

first: Zhaoyu

last: Jia

state: Shandong

address: 44 Wenhua Xi Road

department: Advanced Medical Research Institute

institute: Shandong University

summary: Uterine receptivity (the window of implantation) is essential for successful implantation. The concept of uterine receptivity was first discovered 50 years ago by Psychoyos. In mice, uterine receptivity begins with the secretion of LIF from uterine glands stimulated by estrogen on the morning of day 4 pregnancies. However, some implantation failure is due to the lack of responses to the estrogen secretion. The current study reveals that uterine glands undergo a differentiation process with increases in more branches during the preimplantation period. The single cell RNA profiling of glandular cells identifies that LIF is expressed exclusively in a Prss29+ subgroup of glands in response to estrogen secretion on day 4 of pregnancy. Previous studies have shown that Foxa2 deficiency in uterine glands results in implantation failure due to lack of LIF production. Interestingly, Foxa2-deficient glands fail to develop branches and the functional Prss29+ subgroup of gland cells, indicating FOXA2 is obligatory for normal glandular differentiation prior to implantation. We found that this group develops by the evening of day 3 of pregnancy prior to estrogen secretion on day 4 mornings. We noticed that Lif mRNA signals are detected in the uterus comprising the Prss29+ subgroup. Our findings indicate that uterine glands undergo a FOXA2-dependent maturation process to acquire the competence, which we have termed the “transitional phase,” necessary to respond to estrogen. This newly identified glandular "transitional phase" represents a landmark concept in the study of uterine receptivity and implantation biology.

overall_design: Rosa26tdTomato LtfCre/+ female mice were uterus were collected at pregnancy day 4. After separating the epithelial layer and muscle layer, red fluorescent positive cells, namely glandular epithelial cells, were obtained through flow cytometry sorting. Single-cell sequencing of mouse uteri and uteri glandular epithelial cells at day 4 of pregnancy were implemented.

first: Bo

last: Li

first: Mitsunori

last: Matsuo

first: Amanda

last: Dewar

first: Anxhela

last: Mustafaraj

first: Sudhansu

last: Dey

first: Jia

last: Yuan

first: Xiaofei

last: Sun


title: Genome-wide investigation of the functions of MADS-Box genes in Lumnitzera littorea (Jack) Voigt

status: Public on Feb 14 2025

city: Guangzhou

first: Yuchen

last: Yang

state: Guangdong

address: Xingangxi Road 135

institute: Sun Yat-sen University

summary: In this study, salt stress was posed to Lumnitzera littorea seedlings to investigate the transcriptional responses in leaves

overall_design: We posed salt treatments on Lumnitzera littorea seedlings and investigated the transcriptional responses in leaves

first: Zhang

last: Linbi

last: Ying

first: Yang

last: Yuchen


title: Checkpoint kinases regulate the circadian clock after DNA damage by influencing chromatin dynamics [ChIP-Seq]

city: beijing

first: Yulin

state: Beijing

address: Institute of Microbiology

institute: University of Chinese Academy of Sciences

summary: Circadian rhythms allow organisms to adjust to daily environmental fluctuations. The interplay between the circadian clock, the cell cycle, and DNA repair has been extensively documented, yet the epigenetic control of the circadian clock by the DNA damage response pathway remains relatively unexplored. Here, we showed that checkpoint kinases CHK1 and CHK2 regulate chromatin structure under DNA damage stress in Neurospora crassa to maintain robust circadian rhythms. Under DNA damage stress, deletion of chk1 and chk2 disrupted the rhythmic transcription of the clock gene frq by suppressing the rhythmic binding of the transcription activator WCC at the frq promoter, as the chromatin structure remained condensed. Mechanistically, CHK1 and CHK2 interacted and bound at the frq promoter to phosphorylate H3T11, promoting H3 acetylation, especially H3K56 acetylation, to counteract the histone variant H2A.Z deposition, establishing a suitable chromatin state to maintain the robust circadian rhythm despite DNA damage. Additionally, a genome-wide correlation was discovered between H3T11 phosphorylation and H3K56 acetylation, showing a specific function at the frq promoter that is dependent on CHK1 and CHK2. Furthermore, transcriptome analysis revealed that CHK1 and CHK2 are responsible for robust rhythmic transcription of metabolic and DNA repair genes under DNA damage stress. These findings highlight the essential role of checkpoint kinases in maintaining robust circadian rhythms under DNA damage stress.

overall_design: ChIP assays were performed as previously described. Cultures were grown in 300 ml 2 % glucose media containing HU at 25℃. The samples were crosslinked with 1% formaldehyde and the crosslinking was quenched by glycine. Cultures were washed with PBS, ground with liquid nitrogen and lysed in lysis buffer (50 mM HEPES-NaOH, pH7.5, 1 mM EDTA, 0.1% SDS, 1% Triton X-100, 0.1% Na deoxycholate, 137 mM NaCl, 1 mM PMSF, 1 μg/mL leupeptin, 1 μg/mL pepstatin A). Chromatin was sonicated to an average size of ~500 bp and 1 mg protein was subjected to immunoprecipitation with 2 μL WC-2, 1 μL H3, 1 μL Pol II S2P (Abcam, ab5095), 4 μL H3T11ph, 1 μL H3K56ac (HUABIO, ET1608), 1 μL H3ac (Millipore, 06-599), 2 μL H2A.Z (30), c-Myc, and CHK-2 antibodies at 4 °C overnight. The beads were then washed successively with lysis buffer, lysis buffer + 0.5 M NaCl, buffer II (10 mM Tris, pH 8.0, 1 mM EDTA, 0.25 M LiCl, 1% NP-40, 1% Na deoxycholate) and buffer III (50 mM Tris, pH 8.0, 1 mM EDTA). The eluted DNA/protein complexes were treated at 65 °C overnight and then treated with 2 µL Proteinase K (10 µg/µL) to remove proteins at 45 °C for 1 hour. The DNA purified with ethanol precipitation. For ChIP-qPCR analysis, occupancies were normalized by the ratio of ChIP to Input DNA. The ChIP signals for H3ac, H3T11ph and H3K56ac were normalized to H3.

first: Zeyu

last: Duan

first: Xiao

last: Liu


title: Deletion of Xist repeat B disrupts cell cycle and asymmetric cell division through Usp9x hyperactivation in mice [II]

city: ChangChun

first: Mingming

last: Liang

address: xi an Road 5333

institute: Jilin university

summary: During X-inactivation (XCI), Xist RNA establishes silencing by coating the chromosome in cis and binding diverse proteins to promote formation of a heterochromatic domain. However, Xist repeat B role beyond initiation of XCI remains unclear. Here, we ﬁnd that loss of Xist repeat B in female mice allows survival and leads to a small body size persisting throughout life. Epigenetic and transcriptomic analyses reveal low levels of H3K27me3 and H2AK119ub occupancy on the X chromosome, except in certain CpG island regions, and partial reactivation of X-linked genes on the inactive X across multiple tissues. Notably, overdosage of Usp9x promotes centrosome ampliﬁcation and chromosome instability, increasing the propensity of tumorigenesis. We further demonstrate that Usp9x overdosage leads to abnormalities in asymmetric cell division, thereby affecting the process of cell differentiation. Thus, Xist repeat B is necessary for gene-speciﬁc silencing during XCI maintenance and impacts cell proliferation and differentiation during development. This provides insights into repeat B importance in maintaining XCI.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChiP-seq) for histone modifications H3K27me3, H2AK119ub and  in mouse WT and repeat B knockout primary MEF cells. ATAC-seq for mouse WT and repeat B knockout primary MEF cells.

first: Wanhua

last: Xie

first: Lichao

last: Zhang

first: Zhanjun


title: Deletion of Xist repeat B disrupts cell cycle and asymmetric cell division through Usp9x hyperactivation in mice

overall_design: mRNA profiles of mouse liver, brain and primary MEF cells following Xist repeat B knockout. The mRNA-seqencing was performed  in three replications.


title: Transcriptomic differences between radioresistant MDA-MB-468 and parental MDA-MB-468

status: Public on Feb 13 2025

city: Worcester

first: Rui

state: Massachusetts

address: 364 Plantation Street, LRB

department: MCCB

institute: University of Massachusetts Medical School

summary: A radioresistant MDA-MB-468 cell line, a human TNBC cell lines, was developed by giving a total dose of 50Gy (2gyx5, 4Gyx3, 6Gyx3, and 10Gyx1) to the parental cell line. The trancriptomic changes that occur include enhanced antioxidant response, increase in DNA repair pathways, and invasion/metastasis features.

overall_design: RNA-seq of MDA-MB-468 radioresistant vs parental cell lines

first: Ayush

last: Kumar

first: Arthur

last: Mercurio


title: Primed bovine embryonic stem cell lines can be derived at diverse stages of blastocyst development with similar efficiency and molecular characteristics

city: Davis

first: Anna

middle: Carolina

last: Denicol

address: 450 BIOLETTI WAY, MEYER HALL

department: Animal Science

institute: University of California Davis

summary: In this study, we established bovine embryonic stem cell (bESC) lines from early (eBL) and full (BL) blastocysts to determine the efficiency of bESC derivation from an earlier embryonic stage and compare the characteristics of the resulting lines. Using established medium and protocols for derivation of primed bESCs from expanded blastocysts, we derived bESC lines from eBLs and BLs with the same efficiency (4/12 each, 33%). Regardless of original blastocyst stage, bESC lines had a similar phenotype, including differentiation capacity, stable karyotype, and pluripotency marker expression over feeder-free transition and long-term culture. Transcriptome and functional analyses indicated that eBL- and BL-derived lines were in primed pluripotency. We additionally compared RNA-sequencing data from our lines to bovine embryos and stem cells from other recent reports, finding that base medium was the predominant source of variation among cell lines. In conclusion, our results show that indistinguishable bESC lines can be readily derived from eBL and BL, widening the pool of embryos available for bESC establishment. Finally, our investigation points to sources of variation in cell phenotype among recently reported bESC conditions, opening the door to future studies investigating the impact of factors aside from signaling molecules on ESC derivation, maintenance, and performance.

sample_organism:
Bos taurus
Mus musculus

platform_organism:
Bos taurus
Mus musculus

overall_design: Bovine embryonic stem cells were derived from early and full blastocysts using the same methods and medium. RNA sequencing was performed on two cell lines/embryo stage at passage 9 (cells maintained on MEF feeders) and 23-36 (after transtion to feeder-free conditons and long-term culture). Pure MEF were also sequenced and any aligned counts to the bovine genome were subtracted from MEF-cultured bESC sample data.

first: Carly

last: Guiltinan

first: Ramon

last: Botigelli

first: Juliana

last: Candelaria

first: Justin

last: Smith

first: Rachel

last: Arcanjo


title: Mast cell - tumor cell interaction related gene and microRNA expression profiles in oral squamous cell carcinoma

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

summary: In the tumor microenvironment (TME) of oral squamous cell carcinoma (OSCC), mast cells have a prognostic impact on overall patient survival. In addition, these cells interact with OSCC tumor cells and alter their cellular properties such as proliferation and invasion. To gain further insight into the gene and miRNA expression profiles of both cell types, a transcriptome and miRNA sequencing analysis of both cell populations in monoculture and co-culture was performed.

overall_design: Three biological replicates were performed in each case. The samples were three OSCC tumor cell lysates (PCI-13) from monoculture and three OSCC tumor cell lysates (PCI-13) after 48h co-culture with mast cells (LUVA).  In addition, three mast cell lysates (LUVA) from monoculture and three mast cell lysates (LUVA) after 48h co-culture with OSCC tumor cells (PCI-13) were examined.

first: Tatjana

last: Khromov

first: Maren

last: Sitte

first: Boris

last: Schminke

first: Andreas

last: Fischer

first: Henning

last: Schliephake

first: Phillipp

last: Brockmeyer


title: CRISPR screening identifies regulators of enhancer mediated androgen receptor transcription in advanced prostate cancer [ChIP-Seq]

city: Bethesda

first: David

last: Takeda

state: MD

address: 37 Convent Drive

department: National Cancer Institute

institute: National Institutes of Health

summary: Amplification of the androgen receptor (AR) locus is the most frequent alteration in metastatic treatment resistant prostate cancer. Recently it was discovered that an enhancer of the AR is co-amplified with the AR gene body and contributes to increased AR transcription and resistance to androgen deprivation therapy. However, the mechanism of enhancer activation in advanced disease is unknown. Here, we used functional genetic screening to identify transcription factors that bind to the AR enhancer and are required for enhancer mediated AR transcription. We validated binding of the transcription factors, HOXB13, GATA2, and TFAP2C in patient derived xenografts and demonstrated differential effects on features associated with active chromatin state including H3K27ac, DNA accessibility, and enhancer-promoter interaction frequency. Interestingly, the AR enhancer belongs to a set of regulatory elements that requires HOXB13 to maintain FOXA1 binding, uncovering a novel role for HOXB13 in castration-resistant prostate cancer. This work provides a framework to functionally identify trans-acting factors required for activation of disease related noncoding regulatory elements.

overall_design: ChIP-sequencing following suppression of candidate transcription factors by siRNA

last: Yang

first: Shin-Ai

last: Lee

first: Caroline

middle: F

last: Tyndall

first: JuanJuan

last: Yin

first: Casey

last: Singler

first: Benjamin

last: Hauk

first: Matthew

last: Kipp

middle: Y


title: CRISPR screening identifies regulators of enhancer mediated androgen receptor transcription in advanced prostate cancer (RNA-Seq)

overall_design: Differential gene expression following suppression of candidate transcription factors by siRNA


title: SR-A3 suppresses AKT activation to protect against MAFLD by inhibiting XIAP-mediated PTEN degradation

city: 海淀区

first: YiRan

last: Liu

state: 北京市

department: Department of Biomedical Informatics, State Key Laboratory of Vascular Homeostasis and Remodeling, School of Basic Medical Sciences, Peking University, Beijing, China

institute: PKU

summary: Scavenger receptor class A member 3 (SR-A3) is implicated in metabolic diseases; however, the relationship between SR-A3 and metabolic dysfunction-associated fatty liver disease (MAFLD) has not been documented. Here, we show that hepatic SR-A3 expression is significantly reduced in human and animal models in the context of MAFLD. Genetic inhibition of SR-A3 in hamsters elicits hyperlipidemia, hyperglycemia, insulin resistance, and hepatic steatosis under chow-diet condition, yet escalates in diet-induced MAFLD. Mechanistically, SR-A3 ablation enhances E3 ligase XIAP-mediated proteasomal ubiquitination of PTEN, leading to AKT hyperactivation. By contrast, hepatic overexpression of human SR-A3 is sufficient to attenuate metabolic disorders in WT hamsters fed a high-fat-high-cholesterol diet and ob/ob mice via suppressing the XIAP/PTEN/AKT axis. In parallel, pharmacological intervention by PTEN agonist oroxin B or lipid lowering agent ezetimibe differentially corrects MAFLD in hamsters.

overall_design: RNA-seq profiling of wildtype(W) golden hamsters fed with chow diet(CD), chow diet with 12h fasted treatment(fCD) and high fat diet(HFD) and their knockdown derivatives(SCARA3 knockdown, S).

first: Pingping

last: Lai

first: Yiran


title: CRISPR screening identifies regulators of enhancer mediated androgen receptor transcription in advanced prostate cancer (ATAC-Seq)

overall_design: ATAC-sequencing following suppression of candidate transcription factors by siRNA

first: Rachel


title: The circular RNA circbabo(5,6,7,8S) regulates lipid metabolism and neuronal integrity in Drosophila

city: St Petersburg

first: Rui

last: Zhou

state: FL

address: REB 4130, 501 6th Ave S

institute: Johns Hopkins University

summary: Circular RNAs (circRNAs) are widely expressed in eukaryotes. However, only a subset has been functionally characterized. Here we report that the circRNA circbabo(5,6,7,8S) regulates lipid metabolism and neuronal integrity in Drosophila. We show that circbabo(5,6,7,8S) is derived from the babo pre-mRNA by back-splicing, and is widely distributed in Drosophila tissues. Depletion of circbabo(5,6,7,8S) in the fat body and neurons, respectively, causes elevated lipid droplet (LD) accumulation, and progressive photoreceptor cell loss and shortened lifespan, phenotypes that are rescued by restoring circbabo(5,6,7,8S) expression. In addition, RNA-seq and epistasis analyses reveal that these abnormalities are caused by aberrant activation of the SREBP signaling pathway. Furthermore, circbabo(5,6,7,8S)-depleted tissues display enhanced activation of the TGF-β signaling pathway and compromised mitochondrial function, resulting in a reduction in ATP levels and upregulation of ROS. Moreover, we provide evidence that circbabo(5,6,7,8S) encodes the protein circbabo(5,6,7,8S)-p, which inhibits the TGF-β signaling pathway by interfering with the assembly of babo/put heterodimer complex. Lastly, we show that the ROS/JNK/SREBP signaling cascade is implicated in the LD accumulation, neurodegeneration, and shortened lifespan phenotypes elicited by circbabo(5,6,7,8S) depletion. Thus, our study demonstrates the physiological role of the protein-coding circRNA circbabo(5,6,7,8S) in regulating lipid metabolism and neuronal integrity.

overall_design: This study aims to identify RNAs that are differentially expressed upon depletion of the circular RNA circbabo(5,6,7,8S) in vivo. Flies carrying a shRNA transgene against circbabo(5,6,7,8S) or a control shRNA transgene against GFP were crossed to flies carrying the fat body expressed cg-Gal4 driver. Total RNAs were extracted from fat bodies of 3rd instar wandering larvae of cg>shGFP and cg>sh-circbabo(5,6,7,8S) flies and subjected to RNA-seq to identify genes that are impacted by circbabo(5,6,7,8S) depletion.

first: Jie

last: Sheng

first: Xuemei

last: Zhang

first: Weihong

last: Liang

first: Junfang

last: Lyu

first: Bei

last: Min

first: Jennifer

last: Li

first: Jian

middle: L

first: Wei


title: CRISPR screening identifies regulators of enhancer mediated androgen receptor transcription in advanced prostate cancer (4C-Seq)

first: David

last: Takeda

overall_design: 4C-sequencing following suppression of candidate transcription factors by siRNA

first: Shin-Ai

first: Caroline

first: JuanJuan


title: Grr1-mediated Ubp3 degradation is crucial for HAC1 mRNA translation and unfolded stress response in yeast [RNAseq]

city: Tokyo

first: Nichika

last: Sato

address: 4-6-1, Shirokanedai, Minato-ku

department: The Institute of Medical Science

country: Japan

institute: The University of Tokyo

summary: Ribosome ubiquitination induced by ribosome stalling is crucial for quality control pathways targeting mRNA, nascent polypeptides, and non-functional ribosomes. Besides quality control, Not4-mediated monoubiquitination of eS7A is crucial for the efficient translation of HAC1i mRNA in the unfolded protein response (UPR). In this study, we identified a novel E3 ligase, Grr1, an F-box protein component of the SCF ubiquitin ligase complex that is involved in Ubp3 degradation thereby HAC1i mRNA translation. Grr1 degrades Ubp3, a deubiquitinating enzyme of eS7A, under ER stress, thereby increasing eS7A ubiquitination, which facilitates HAC1i translation. Translation of HAC1i mRNA requires Grr1 and eS7 ubiquitination regardless of ER stress. ER stress-specific expression of Hac1 protein is ensured by the multi-step regulation of HAC1u mRNA, including localization on the ER membrane and stress-mediated splicing. Translation of HAC1i mRNA in UPR requires Grr1-mediated eS7 ubiquitination. More importantly, exon 1 of the HAC1i mRNA is crucial for translation activation by eS7 ubiquitination. Collectively, we propose that Grr1 upregulates eS7A monoubiquitination, thereby HAC1i translation and plays a crucial role in UPR.

overall_design: To investigate the transcriptome profile under ER stress conditions, we performed RNA-seq of tunicamycin-treated W303 strains. The dataset includes 4 types of RNA-seq samples in biological replicates (indicated as rep1 and rep2; 8 samples in total). Samples differ by the genotype (wild-type or grr1 deficient), and tunicamycin treatment time (0, 4 hr). We then calculated Translation efficiency (TE) using the read counts from Ribo-seq data shown in another file and the read counts from RNA-seq data. For each genotype (wild-type or grr1 deficient), 0 hr data was compared against data of 4 hr data.


title: Hierarchical Lineage Tracing Reveals Diverse Pathways of AML Treatment Resistance [DNA-seq]

status: Public on Feb 12 2025

city: Lebanon

middle: Danielle

last: Saxe

state: New Hampshire

address: 1 Medical Center Dr

institute: Dartmouth Cancer Center

summary: Cancer cells adapt to treatment, leading to the emergence of clones that are more aggressive and resistant to anti-cancer therapies. We have a limited understanding of the evolution of treatment resistance as we have lacked technologies to map the evolution of cancer under the selective pressures. To address this, we developed a hierarchical, dynamic lineage tracing method called FLARE (Following Lineage Adaptation and Resistance Evolution). We use this technique to track the progression of acute myeloid leukemia (AML) cell lines through exposure to Cytarabine (AraC), a front-line treatment in AML, in vitro and in vivo. We map distinct cellular lineages in murine and human AML cell lines that are predisposed to AraC persistence and/or resistance via upregulation of cell adhesion and motility pathways. Additionally, we highlight heritable increased expression of immunoproteasome 11S regulatory cap subunits as a potential mechanism aiding AML cell survival, proliferation, and immune escape in vivo. Finally, we validate the clinical relevance of these signatures in the TARGET-AML cohort, with a bisected response in blood and bone marrow. Our findings reveal a broad spectrum of resistance signatures attributed to significant cell transcriptional changes, and we expect this high-resolution profiling of treatment response to be a useful tool to dissect the evolution of treatment response in a wide range of tumor types.

overall_design: Sequencing of cultured AML cell transcriptomes and FLARE lineage tags and recorders to follow the emergence of AraC resistance in vitro and in vivo.


title: Disruption of the moonlighting function of CTF18 in a patient with T-lymphopenia

city: Philadelphia

last: Wiest

address: 333 Cottman Ave

institute: Fox Chase Cancer Center

summary: Newborn screening for immunodeficiency has led to the identification of numerous cases for which the causal etiology is unknown. Here we report the diagnosis of T lymphopenia of unknown etiology in a male proband. Whole exome sequencing (WES) nominated as the top candidate variants, missense mutations in CHTF18 that were inherited in an autosomal recessive manner. CTF18, encoded by the CHTF18 gene, is a component of a secondary clamp loader, which is primarily thought to function by promoting DNA replication. We determined that the patient’s variants in CHTF18 (CTF18 R751W and E851Q) were damaging to function and severely attenuated the capacity of CTF18 to support hematopoiesis and lymphoid development, strongly suggesting that they were responsible for his T lymphopenia; however, the attenuation of CTF18 function appeared to be unrelated to its role as a clamp loader. DNA-damage, expected when replication is impaired, was not evident by expression profiling in murine Chtf18 mutant hematopoietic stem and progenitor cells (HSPC), nor was development of Ctf18-deficient progenitors rescued by p53 loss. Instead, we observed an expression signature suggesting disruption of HSPC positioning and migration. Indeed, the positioning of HSPC in ctf18 morphant zebrafish embryos was perturbed, suggesting that HSPC function was impaired through disrupted positioning in hematopoietic organs. Accordingly, we propose that T lymphopenia in our patient resulted from disturbed cell-cell contacts and migration of HSPC, caused by a non-canonical function of CHTF18 in regulating gene expression.

overall_design: 10X Chromium Single Cell 3’ libraries were prepared with 30,000 Lineage-depleted HSPCs from Wildtype and Chtf18 mutant mice

first: Robert

last: Sertori

first: Billy

last: Truong

first: Susan

last: Shinton

first: Rachael

last: Price

first: Manoj

last: Singh


title: Mediator kinase inhibition drives myometrial stem cell differentiation and the uterine fibroid phenotype through super-enhancer reprogramming [RNA-seq]

city: San Antonio

first: Subash

last: Khadka

state: TX

address: 7703 Floyd Curl Dr

institute: UT Health San Antonio

summary: Although it is known that the uterine fibroid linked MED12 mutations disrupt the CDK8/19 kinase activity, how CDK8/19 disruption contributes to making the myometrial stem cell tumorigenic and form uterine fibroids. This study seeks to determine the molecular consequences of pharmacologically disrupting mediator kinase activity in myometrial stem cells, the presumptive cell of origin for uterine fibroids, through parallel transcriptomic and epigenomic profiling by bulk RNA-seq and H3K27ac CUT&RUN.

overall_design: We treated myometrial stem cells with CDK8/19 inhibitor CCT251545 (treatment) or DMSO (control) at two timepoints and processed the treated cells for bulk mRNA sequencing and enhancer profiling by H3K27ac CUT&RUN in parallel at each timepoints.

first: Azad

last: Khosh


title: Checkpoint kinases regulate the circadian clock after DNA damage by influencing chromatin dynamics [RNA-Seq]

first: Yulin

last: Yang

overall_design: The WT and chk1KOchk2KO strains’ mats were cut into discs and transferred into medium-containing flasks and were harvested at DD18. Total RNAs were extracted using Trizol reagents. Libraries were prepared according to the manufacturer’s instructions and analyzed using 150 bp paired-end Illumina sequencing (Annoroad Gene Technology, Beijing). After sequencing, the raw data were treated and mapped to the genome of Neurospora crassa (GCF_000182925.2) and transformed into expression value. The gene-expression level was measured in TPM using StringTie v1.3.3. The differentially expressed genes were assessed using the DEseq2 v1.16.1 Bioconductor package and defined based on the fold change criterion (|log2fold change|) > 0.5,Padj< 0.1). The functional category enrichments, including Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) terms, were analyzed by TBtools, and visualized by R package ggplot2 v3.3.6.

first: Zeyu

last: Duan

first: Xiao

last: Liu


title: Grr1-mediated Ubp3 degradation is crucial for HAC1 mRNA translation and unfolded stress response in yeast [Riboseq]

overall_design: To investigate how ER stress affects translation, we performed ribosome profiling (Ribo-seq) of tunicamycin-treated W303 strains. The dataset includes 4 types of Ribo-seq samples in biological replicates (indicated as rep1 and rep2; 8 samples in total). Samples differ by the genotype (wild-type or grr1 deficient), and tunicamycin treatment time (0, 4 hr). We then calculated Translation efficiency (TE) using the read counts from Ribo-seq data and the read counts from RNA-seq data shown in another file. Besides, we analyzed ribosome footprints throughout HAC1i mRNA. For each genotype (wild-type or grr1 deficient), 0 hr data was compared against data of 4 hr data.


title: Attractor landscape analysis reveals a reversion switch in the transition of colorectal tumorigenesis

city: Yuseong-gu

first: Jeong-Ryeol

last: Gong

state: Daejeon

address: 291, Daehak-ro

country: South Korea

institute: KAIST

summary: A cell fate change such as tumorigenesis incurs critical transition. It remains a longstanding challenge whether we can unravel the underlying mechanism and find a molecular switch that can reverse such transition. Here we present a systems framework, REVERT with which we can reconstruct the core molecular regulatory network model and identify a reversion switch based on single-cell transcriptome data over the transition process. We demonstrate the usefulness of REVERT by applying it to single-cell transcriptome of patient-derived matched organoids of colon cancer and normal colon. REVERT is a generic framework that can be applied to investigate various cell fate transition phenomena.

overall_design: Establishing and preprocessing single-cell RNA sequencing libraries from dissociated organoids using 10x genomics: Organoids were dissociated into single cells for RNA sequencing analysis. Following rinsing with phosphate-buffered saline (PBS), organoids were enzymatically dissociated using TrypLE Express (Gibco) and incubated at 37°C for 15 minutes. During incubation, the mixture was pipetted every 5 minutes to promote complete dissociation. The enzymatic reaction was halted by adding Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS). The resultant cell suspension was filtered through a 40 μm cell strainer to achieve a uniform single-cell suspension. Cell viability and density were assessed using Trypan Blue exclusion with a hemocytometer to ensure optimal cell concentration for sequencing. For library preparation, the single-cell RNA sequencing library was constructed using the Chromium Single Cell Instrument (10x Genomics), following the manufacturer’s protocol. The process involved loading cells into a Chromium Chip B where cells, master mix, and partitioning oil were combined to generate single-cell gel beads in emulsion (GEMs). Post GEM-RT reaction, GEMs were broken, and the barcoded cDNA was isolated, cleaned using DynaBeads MyOne Silane Beads (Invitrogen), and amplified by PCR. The quality and quantity of the amplified cDNA libraries were evaluated using an Agilent 4200 Tapestation system (Agilent Technologies). The libraries were sequenced on an Illumina Nova-seq 6000 system, employing paired-end sequencing as recommended by the manufacturer. This method ensures the generation of high-quality data for transcriptomic analysis. In addition, we excluded apoptotic cells that express more than 15% mitochondrial transcripts, as these are considered low-quality cells. Following this filtering step, 18049 cells were retained for further analysis. Each cell underwent log normalization by scaling to a constant total read count per cell (100,000), followed by log transformation. For visualization, principal component analysis (PCA) was initially conducted using 2,000 highly variable genes for dimensionality reduction. Subsequently, PCA dimensions were utilized to project into 2D space. All these analyses were conducted using the Seurat v4.0.2 package in R (v4.2.0).

first: Dongkwan

last: Shin

first: Seoyoon D.

last: Jeong

first: Youngwon

last: Cho

first: Hwang-Phill

last: Kim

first: Tae-You

first: Kwang-Hyun


title: Hierarchical Lineage Tracing Reveals Diverse Pathways of AML Treatment Resistance [scRNA-seq]

first: Rachel

last: Saxe

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Mediator kinase inhibition drives myometrial stem cell differentiation and the uterine fibroid phenotype through super-enhancer reprogramming [CUT&RUN]


title: RNA-sequencing of testes from control and Hormad1&2SFB/SFB mice

city: Hangzhou

first: Lin-Yu

last: Lu

state: Zhejiang

address: 268 Kaixuan Road, North Central Building, Room 536

institute: Zhejiang University

summary: To examine whether Hormad1&2SFB/SFB (dsfb) male mice has defect in the meiotic sex chromosome inactivation (MSCI) process or not, three pairs of P19 testes were collected from each strain and mRNA-sequencing was performed. The data revealed that the transcription of X and Y chromosomes, but not autosomes, were specifically elevated. Therefore, MSCI was defective in dsfb spermatocytes.

overall_design: Three pairs of PD19 testes from different mice were isolated and mRNA-sequencing was performed on the samples.

first: Zhongyang

last: Liang

first: Yidan


title: Single Cell Analysis of the Developing Diaphragm at GD 13.5

city: Edmonton

first: Robin

last: Clugston

state: Alberta

address: 7-49 Medical Sciences Building

department: Physiology

country: Canada

institute: University of Alberta

summary: We sequenced more than 13000 cells of the pleuroperitoneal folds of a mouse embryo to better understand the mosaic nature of the developing diaphragm. We identified 18 different clusters, and 10 unique cell types. Through our analysis, we were able to determine that most of the developing diaphragm is comprised of mesenchymal cells, and that genes necessary for proper diaphragm development are expressed in these types of cells. These observations provide a strong basis for furhter studies about the development and physiology of the diaphragm.

overall_design: We performed single cell RNA-seq on the developing diaphragm of a mouse embryo at GD 13.5, when the pleuroperitoneal folds are present. After meticulous dissection of the pleuroperitoneal folds from a mouse embryo, the tissue was dissociated into a single cell suspension. 13,482 cells were subsequently captured and used for cDNA library synthesis, sequencing, and cluster analysis. Expression information was recovered from each cell.

first: Juan

last: Garcia-Rivas