title: In vivo CRISPR screening identifies geranylgeranyl diphosphate as a pancreatic cancer tumor growth dependency.

city: Baltimore

first: Peter

middle: J

last: Espenshade

address: 725 N Wolfe St

institute: Johns Hopkins University

summary: Cancer cells must maintain lipid supplies for their proliferation and do so by upregulating lipid metabolic gene expression. The sterol regulatory element-binding proteins (SREBPs) act as modulators of lipid homeostasis by acting as transcriptional activators of fatty acid and cholesterol synthesis genes. SREBPs have been recognized as chemotherapeutic targets in multiple cancers, however, it is not understood which lipid metabolic genes are essential for tumorigenesis.Using an in vivo CRISPR knockout screening method, we identified the mevalonate pathway genes as essential for pancreatic ductal adenocarcinoma (PDAC) tumor development. Specifically, we identify geranylgeranyldiphosphate (GGPP) as an essential lipid for tumor growth. Additionally, we propose a combination drug treatment to improve cancer cell killing in statin treated PDAC cells that prevents restoration of lipid homeostasis through SREBPs. Our findings suggest that PDAC tumors selectively require GGPP over other lipids such as cholesterol and fatty acids and that this is a targetable vulnerability of cancer cells.

overall_design: To determine the gene expression changes in PDAC cells treated with a statin and SREBP inhibitor, we grew Pa03c cells in lipoprotein deficient medium and treated them for 16 hours and conducted RNA-seq. We included vehicle controls and two biological replicates for each condition and analyzed gene expression changes in each drug treated condition relative to the respective vehicle control.

first: Casie

last: Kubota


title: Multi-omics Reveals Different Signatures of Obesity-Prone and Obesity-Resistant Mice

status: Public on Dec 31 2024

city: Hangzhou

first: Fei

last: Yang

address: 866 Yu-hang-tang Road

country: China

institute: Zhejiang University

type: Expression profiling by high throughput sequencing

summary: The expression profiles of mRNAs in colon were investigated by high-throughput RNA sequencing using HFD-induced C57BL/6J mice. Genes that play roles in obesity and related pathways were identified.

overall_design: The expression profiles of mRNAs in colons by high-throughput RNA sequencing using HFD-induced C57BL/6J mice.

first: Congcong

last: Wang

first: Jinhua

last: Lin

first: Shankuan

last: Zhu


title: Genomic regions occupied by both RARα and VDR are involved in the convergence and cooperation of retinoid and vitamin D signaling pathways.

city: DEBRECEN

first: LAJOS

last: SZELES

address: NAGYERDEI KRT 98

country: Hungary

institute: UNIVERSITY OF DEBRECEN

summary: In this study, the retinoid and vitamin D pathways were investigated in PMA-differentiated THP-1 cells treated with or without the RARa agonist, AM580, and/or the VDR agonist, 1,25-dihydroxyvitamin D3 (1,25-vitD or calcitriol), using global approaches. Binding regions of RARa and VDR were determined in PMA-differentiated THP-1 cells using chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-seq). The gene sets regulated by AM580 and/or 1,25-vitD were identified by RNA-sequencing (RNA-seq). The activity of the regulatory regions was determined by MED1 (a subunit of the Mediator complex) ChIP-seq and chromatin openness was measured using assay for transposase-accessible chromatin with sequencing (ATAC-seq).

overall_design: THP1 cells were stimulated with 20 nM PMA for 16 hours. PMA-differentiated THP-1 cells were treated with vehicle (DMSO:EtOH), RARa agonist (100 nM AM580) and/or VDR agonist (100 nM calcitriol or 1,25-vitD) for 6 hours. Three replicates of each condition were analyzed by RNA-seq.

first: Hamidreza

last: Mianesaz

first: Lina

last: Fadel

first: György

last: Vámosi

first: Lajos

last: Széles

first: Loránd

last: Göczi


type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: THP1 cells were stimulated with 20 nM PMA for 16 hours. In the case of RARa and VDR ChIP-seq samples: PMA-differentiated THP-1 cells were treated with vehicle (DMSO:EtOH), RARa agonist (100 nM AM580) or VDR agonist (100 nM calcitriol or 1,25-vitD) for 1 hour. Two replicates of each condition were analyzed by ChIP-seq. In the case of MED1 ChIP-seq samples: PMA-differentiated THP-1 cells were treated with vehicle (DMSO:EtOH), RARa agonist (100 nM AM580) and/or VDR agonist (100 nM calcitriol or 1,25-vitD) for 2 hour. Three replicates of each condition were analyzed by ChIP-seq.


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

overall_design: Refer to individual Series


overall_design: THP-1 cells were stimulated with 20 nM PMA for 16 hours. PMA-differentiated THP-1 cells were treated with vehicle (DMSO:EtOH) or 100 nM AM580 for 1 hour. Two replicates for each treatment condition were analyzed for ATAC-seq.


title: Signaling pathways associated with Lgr6 to regulate osteogenesis

city: Farmington

first: Justin

middle: S

last: King

state: Connecticut

address: 263 Farmington Ave

country: USA

institute: UConn Health

summary: Fracture management largely relies on the bone's inherent healing capabilities and, when necessary, surgical intervention. Currently, there are limited osteoinductive therapies to promote healing, making targeting skeletal stem/progenitor cells (SSPCs) a promising avenue for therapeutic development. A limiting factor for this approach is our incomplete understanding of the molecular mechanisms governing SSPCs' behavior. We have recently identified that the Leucine-rich repeat-containing G-protein coupled receptor 6 (Lgr6) is expressed in sub-populations of SSPCs, and is required for maintaining bone volume during adulthood and for proper fracture healing. Lgr family members (Lgr4-6) are markers of stem cell niches and play a role in tissue regeneration primarily by binding R-Spondin (Rspo1-4). This interaction promotes canonical Wnt (cWnt) signaling by stabilizing Frizzled receptors. Interestingly, our findings here indicate that Lgr6 may also influence cWnt-independent pathways. Remarkably, Lgr6 expression was enhanced during Bmp-mediated osteogenesis of both human and murine cells. Using biochemical approaches, RNA sequencing, and bioinformatic analysis of published single-cell data, we found that elements of BMP signaling, including its target gene, pSMAD, and gene ontology pathways, are downregulated in the absence of Lgr6. Our findings uncover a molecular interdependency between the Bmp pathway and Lgr6, offering new insights into osteogenesis and potential targets for enhancing fracture healing.

overall_design: Gene expression of adult murine bone marrow stromal cells from Lgr6-null and control mice following osteogenic differentation.

first: Sanjay

last: Archana


title: Dysfunctional effector memory CD8 T cells in the bronchoalveolar compartment of people living with HIV

city: Cape Town

first: Valentin

last: Voillet

state: Western Cape

address: First Floor Wembley Square, 3 McKenzie St, Gardens

country: South Africa

institute: cape town hvtn immunology laboratory

summary: Mechanisms by which HIV causes susceptibility to respiratory pathogens remain incompletely understood. We obtained whole blood and bronchoalveolar lavage (BAL) from people with latent TB infection in the presence or absence of ARV-naïve HIV co-infection. Transcriptomic and flow cytometric analyses demonstrated HIV-associated cell proliferation and type I interferon activity in blood and effector memory CD8 T-cells in BAL. Both compartments displayed reduced induction of CD8 T cell-related IL-17A in people with HIV, associated with elevated T cell regulatory molecule expression. We propose dysfunctional CD8 T cell responses in uncontrolled HIV contribute to susceptibility to secondary bacterial infections, including tuberculosis.

overall_design: Transcriptional profilling of 10 pairs of blood and BAL samples from people living with HIV and those without HIV

first: M

last: Mthembu

first: V

first: G

last: Pollara

first: E

middle: B

last: Wong


title: Identification of differentially expressed mRNAs in LX-2 cells treated with cholic acid (CA)

city: chongqin

first: wu

last: kang

address: chongqin

institute: CQMU

summary: In this study, high-throughput RNA sequencing technology combined with bioinformatics analysis was used to compare the differentially expressed mRNA of cholic acid-treated LX-2 cells with that of the control group in hopes of gaining a deeper understanding of the biological function and signaling pathway changes in the activation process of LX-2 cells, as well as to identify potential key genes regulating HSC activation.

overall_design: LX-2 cells were divided into two groups. The experimental group received 50μM cholic acid stimulation (n=3), while the control group received vehicle treatment (n=3). After 48 hours, total RNA was sequenced by transcriptome to screening for differentially expressed genes (DEGs), and DEGs were bioinformatically analyzed.


title: Distinct blood CD3+ CD14+ T Cell-Monocyte complexes harbor HIV and are dynamic, glucose-dependent and increased in individuals with glucose intolerance

city: Nashville

first: Lindsey

middle: "Joey"

last: Stolze

state: TN

address: 1211 Medical Center Dr

institute: Vanderbilt University Medical Center

summary: Persistent systemic inflammation in persons with HIV (PWH) is accompanied by an increased risk of metabolic and cardiovascular diseases. Yet, changes in the innate and the adaptive immune in PWH who develop cardiometabolic disease remain insufficiently defined. Using mass cytometry we showed that PWH with prediabetes/diabetes had a significantly higher proportion of circulating CD14+ monocytes complexed with T cells. The CD3+ T cells and CD14+ monocytes consisted of dynamic heterogeneous complexes. Furthermore, we detected more HIV DNA in T cell-monocyte complexes compared to CD14+ monocytes or CD4+ T cells alone. Our results demonstrate that CD3+ CD14+ T cell-monocyte pairs are functional and physically interacting immune cell complexes that are higher among PWH with diabetes, suggesting that they may contribute to metabolic disease pathogenesis, and provide a strong incentive for future studies to investigate T cell-monocyte immune complexes as mechanistic in HIV cure reservoir and other diseases of aging.

overall_design: PBMCs were isolated from the blood\ patients and single cell RNA was sequenced through 10X Genomics.

first: Celestine

last: Wanjalla

first: Tarek

last: Absi


title: Spliceosomal complex components are critical for the adjusting the C:N balance during high-light acclimation

city: Rostock

first: Andreas

middle: Sven

last: Richter

address: Albert-Einstein-Strasse 3

department: Institute for Biosciences

country: Germany

institute: University of Rostock

summary: Plant acclimation to an ever-changing environment is decisive for growth, reproduction, and survival. Light availability limits biomass production on both ends of the intensity spectrum. Therefore, the adjustment of plant metabolism is central to high-light (HL) acclimation, and the accumulation of photoprotective anthocyanins is commonly observed. However, mechanisms and factors regulating the HL acclimation response are less clear. Two Arabidopsis mutants of spliceosome components exhibiting a pronounced anthocyanin overaccumulation in HL were isolated from a forward genetic screen for new factors crucial for plant acclimation. Time-resolved physiological, transcriptome, and metabolome analysis revealed a vital function of the spliceosome components for rapidly adjusting gene expression and metabolism. Deficiency of INCREASED LEVEL OF POLYPLOIDY1 (ILP1), NTC-RELATED PROTEIN1 (NTR1), and PLEIOTROPIC REGULATORY LOCUS1 (PRL1) resulted in a marked overaccumulation of carbohydrates and strongly diminished amino acid biosynthesis in HL. While not generally limited in N-assimilation, ilp1, ntr1, and prl1 showed higher glutamate levels and reduced amino acid biosynthesis in HL. The comprehensive analysis reveals a function of the spliceosome components in the conditional regulation of the carbon:nitrogen balance and the accumulation of anthocyanins during HL acclimation. The importance of gene expression, metabolic regulation, and re-direction of carbon towards anthocyanin biosynthesis for HL acclimation are discussed.

overall_design: High light shift (HL) experiment. WT and ilp1-1 mutant were shifted to HL (500µmol photons m-2 s-1) two hours after the onset of light (2h 100µmol m-2 s-1). Plants were exposed to continuous HL for 24h and were subjected to normal light conditions for 6 h afterwards.


title: PGPR induced IST in cucumber shoot under salt stress

first: Gengwei

last: Wu

state: Zhejiang

address: No.298, Desheng Middle Road

institute: Zhejiang Academy of Agricultural Sciences

summary: RNA Seq was extracted from cucumber leaves after 7 days of bacteria inoculated in shoot and salt stress treatment. There were four treatment in this study, : ‘CK’ stands for seedlings under 0 mM NaCl without BC56 inoculation; ‘BC56’ refers to seedlings under 0 mM NaCl with BC56 inoculation; ‘Salt’ means seedlings under 100 mM NaCl without BC56 inoculation; ‘BC56+Salt’ indicates seedlings under 100 mM NaCl with BC56 inoculation.GO was used to assign putative functions to all identified DEGs into three principal categories, namely cellular component, molecular function, and biological process. An analysis of the GO terms suggested that ‘nucleus’, ‘plasma membrane’, and ‘integral component of membrane’ were the most dominant terms in the cellular component. While ‘biological process’, ‘regulation of transcription, DNA -templated’ and ‘transcription, DNA-templated’ were the most abundant terms in the biological process. In addition ‘molecular function’, ‘protein binding’ and ‘DNA-binding transcription factor activity’ were the major terms in the molecular function category. KEGG pathway analysis of DEGs in different comparison group suggested that in the BC56 vs CK comparison group DEGs were mainly enriched in four pathways which are ‘photosynthesis - antenna proteins’, ‘phenylpropanoid biosynthesis’, ‘metabolic pathways’ and ‘MAPK signaling pathway – plant’. In the BC56 vs CK comparison group DEGs were mainly enriched in seven pathways which are ‘phenylpropanoid biosynthesis’, ‘plant hormone signal transduction’, ‘biosynthesis of secondary metabolites’, ‘flavonoid biosynthesis’, ‘metabolic pathways’, ‘carotenoid biosynthesis’ and ‘stilbenoid, diarylheptanoid and gingerol biosynthesis’. In addition, compared with BC56+Salt vs CK, ‘ABC transporters’, ‘nitrogen metabolism’ and ‘phenylalanine metabolism’ is only significantly enriched in Salt vs CK.

overall_design: 4 sample, 3 replicated

first: Hanru

last: Song

first: Hua

last: Wang

first: Ruizhi

last: Huang


title: Xist RNA regulates remodeling of the Xi during B cell stimulation [Hi-C]

city: PHILADELPHIA

first: MONTSERRAT

last: ANGUERA

state: PA

address: 380 S. University Ave, Room 390EB

department: Biomedical Sciences

institute: University of Pennsylvania

summary: The inactive X (Xi) is formed by a process called X-Chromosome Inactivation (XCI), with Xist upregulation, retention of Xist RNA transcripts at the Xi, chromatin re-organization, and transcriptional silencing. Female lymphocytes have ‘dynamic’ XCI maintenance where Xist RNA is transcribed but absent from the Xi in naïve lymphocytes and re-localizes after in-vitro activation. How ‘dynamic’ XCI impacts Xi dosage and nuclear organization, or where Xist RNA interacts with the Xi is unknown. Here we find maintenance of Xi dosage and global structure despite the absence of Xist RNA in naïve B-cells. However, we identified 104 escape genes and observe a gain of de-novo TADs on the Xi. Stimulation-dependent Xi remodeling co-occurs with Xist RNA re-accumulation at the Xi, and loss of Xist increases TAD remodeling and decompacts the Xi in both naïve and stimulated B-cells. Altogether, these results reveal B-cell specific Xi plasticity which could underlie female-specific mechanisms in lymphocytes.

overall_design: Allele-specific Hi-C in female mouse primary splenic CD23+ B cells across three timepoints, 0hr (naïve) and 12hr, 24hr stimulated

first: Montserrat

last: Anguera

first: Isabel

last: Sierra

first: Sarah

last: Pyfrom

first: Natalie

last: Toothacre


title: Hypoxia-induced CTCF mediates alternative splicing via coupling chromatin looping and RNA Pol II pause to promote EMT in breast cancer

city: Bhopal

first: Sanjeev

last: Shukla

state: Madhya Prades

address: Bhopal Bypass Road, Bhauri Bhopal 462 066 Madhya Pradesh, INDIA

department: Biological Sciences

country: India

institute: Indian Institute of Science Education and Research Bhopal

summary: Cancer cells experiencing hypoxic stress employ epithelial-mesenchymal transition (EMT) to undergo metastasis through rewiring of the chromatin landscape, epigenetics and importantly alternative splicing. However, how hypoxia influences expression and genome-wide redistribution  of CTCF is still not known. Here, we performed CTCF-ChIP-seq and CUT&RUN assay to analyze differential occupancy of CTCF in normoxic and hypoxic breast cancer cell line. We discovered that hypoxia-induced gain of CTCF occupancy across the genome regulates EMT in hypoxic cells. Specifically, we did 4C-seq experiments on COL5A1 (EMT associated gene) gene loci and showed that CTCF-mediated promoter-exon upstream looping regulates epigenetic mark mainly DNA demethylation at distal alternatively spliced exon 64 and regulates CTCF-mediated RNA Pol II pausing at COL5A1exon64A that decides the outcome of splicing to favor EMT under hypoxia. Overall, we uncover that hypoxia-induced differential CTCF occupancy across the genome is associated with gene expression and alternative splicing events related to cancer progression, similarly to the proposed model.

overall_design: Breast cancer cell line MCF7 was cultured in either 21% O2 (normoxic) or 1% O2 (hypoxic) for 24 hours. Post 24 hours CTCF-ChIP-seq, CTCF-CUT&RUN and COL5A1-promoter-4C-seq assay was performed


title: Eomes expression identifies the early bone marrow precursor to classical NK cells

city: Chicago

first: Benjamin

last: McDonald

state: IL

address: 924 E. 57th Street BSLC

institute: University of Chicago

summary: Classical NK cells are the prototypical type 1 innate lymphocytes mounting cytolytic and IFNγ responses to intracellular pathogens and tumors. A similar but distinct population termed ILC1 was recently described, differing from NK cells in multiple though relatively subtle ways, including tissue residency vs recirculation, and levels of NK receptors. Whether the differences reflect distinct lineages or mere variations in program expression is not fully understood. Here, using transcription factor reporter mice and cell transfers of bone marrow precursors, we found that, upon transfer in vivo, Eomes-expressing, lineage-negative, NK receptor-negative cells acquired properties typically associated with classical NK cells including the capacity to prevent metatstatic disease. In contrast, as previously reported, PLZF-expressing cells mostly gave rise to ILC1 cells. These findings identify the Eomes-expressing NK precursor as the long-elusive bone marrow precursor to classical NK cells, and demonstrate that the NK and ILC1 lineages diverge early during development.

overall_design: we used muli-transcription factor reporter mice to study NK cell development in the bone marrow

first: Zhitao

last: Liang

first: Hope

last: Anderson

first: Crystal

last: O'Leary

first: Bana

last: Jabri

first: Albert

last: Bendelac


title: Histone methyltransferase Setd2 mitigates T cell-mediated autoimmunity by targeting Lpcat4-mediated phospholipid remodeling

city: shanghai

first: Yali

last: Chen

address: 800 Xiangyin Road

institute: Second Military Medical University

summary: This SuperSeries is composed of the SubSeries listed below. Includs GSE235822, GSE235823, GSE235825, GSE235826, and GSE247616.


title: Spatial Transcriptomic Profiling of Male Germ Cells from Control and Cbfb cKO mice

city: Pullman

first: Nathan

middle: C

last: Law

state: WA

address: 100 Dairy Road

department: School of Molecular Biology

institute: Washington State University

summary: Much of the framework for spermatogenesis is established postnatally before sexual maturation. To evaluate the role of core-binding factor subunit β (CBFβ) in prepubertal male germline development, we generated male mice with conditional knockout of Cbfb using Blimp1-Cre (denoted Blimp1-Cbfb cKO). Outcomes from phenotype analysis revealed that Blimp1-Cbfb cKO males were completely infertile and experienced rapid germline degeneration prior to puberty. To evaluate the pathways downstream of Cbfb that coincide with this degeneration, we conducted spatial transcriptomics of heterozygous control and Blimp1-Cbfb cKO testes at postnatal days 6 (P6) and 21 (P21) and used fluorescence immunostaining to identify and capture cell-type specific transcriptomic signatures. Collectively, our analysis revealed central roles of CBFβ in maintenance, differentiation, and cell cycle checkpoint regulation within the prepubertal male germline.

overall_design: Spatial transcriptomic signatures were obtained from both heterozygous control and Blimp1-Cbfb cKO male mice at P6 and P21 using NanoString whole-transcriptome analysis (WTA). Briefly, tissue cross-sections were generated from paraformaldehyde fixed, paraffin embedded testes. For P6, triplicate tissue cross-sections were generated from three males of each genotype to yield triplicate technical and n=3 biological replication per genotype for a total of 18 sections evaluated. For P21, triplicate cross-sections were generated from duplicate males of each genotype to yield triplicate technical and n=2 biological replication per genotype for a total of 12 sections evaluated. Tissue sections were placed on glass slides and processed for immunofluorescence staining using antibodies recognizing the undifferentiated spermatogonia marker LIN28A and the pan-germ cell marker DDX4 alongside the nuclear stain SYTO13. One circular region of interest (ROI) was randomly placed on each tissue section and segmented using florescent signal to capture cell populations corresponding to undifferentiated spermatogonia (LIN28A+, DDX4+, SYTO13+) and other germ cells (LIN28A-, DDX4+, SYTO13+). Resulting transcriptomic signatures were captured using photo-cleavable probes and analyzed following the manufacturers protocol.


title: Xist RNA regulates remodeling of the Xi during B cell stimulation [RNA-seq]

sample_organism:
Mus
Mus musculus

platform_organism:
Mus
Mus musculus

overall_design: RNAseq data generated from female mouse primary fibroblasts and  splenic CD23+ B cells, both naïve and in vitro CpG stimulated for 12hr and 24hr


title: Adaptive responses of Trichlorobacter lovleyi to nitrite detoxification reveal overlooked contributions of Geobacterales to nitrate ammonification

city: EAST LANSING

first: MARCELA

last: TABARES

state: MI

address: 567 WILSON RD

department: MMG

institute: MICHIGAN STATE UNIVERSITY

summary: Poorly understood microorganisms "short-circuit" the nitrogen cycle via the dissimilatory nitrate reduction to ammonium to retain the element in agricultural lands and stimulate crop productivity. The prevalence of Geobacterales closely related to Trichlorobacter lovleyi in nitrate ammonification hotspots motivated us to investigate adaptive responses contributing to ammonification rates in the laboratory type strain T. lovleyi SZ. Here we describe the identification of tightly regulated pathways for efficient nitrate foraging and respiration with acetate, an important intermediate of organic matter degradation that Geobacterales efficiently assimilate and oxidize. Challenging the established dogma that high carbon/nitrate ratios stimulate the reduction of nitrate to ammonium, T. lovleyi doubled rapidly across a wide range of ratios provided nitrate concentrations were low enough to prevent the accumulation of the toxic nitrite intermediate. Yet, excess electrons during hydrogenotrophic growth alleviated nitrite toxicity and stimulated the reduction of nitrate to ammonium even under conditions of severe acetate limitation. These findings underscore the importance of nitrite toxicity in the ammonification of nitrate by Geobacterales and provide much needed mechanistic understanding of microbial adaptations contributing to soil nitrogen conservation. This information is critical to enhance the predictive value of genomic-based traits in environmental surveys and to guide strategies for sustainable management of nitrogen fertilization as well as mitigation of green-house emissions and agrochemical leaching from agricultural lands.

overall_design: We extracted total RNA from exponential phase of growth in Geobacter lovleyi SZ when growth with or without 5 mM sodium nitrate.

first: Marcela

last: Tabares

first: Gemma

last: Reguera


title: Effect of tobacco smoke exposure cessation on lung response to crystalline silica exposure in rats

city: Morgantown

first: Pius

last: Joseph

state: WV

address: 1095 Willowdale Road

department: Health Effects Laboratory Division/Toxicology and Molecular Biology Branch

institute: National Institute for Occupational Safety and Health (NIOSh)

summary: Our previous studies have shown that tobacco smoke exposure exacerbated the lung response to crystalline silica exposure in rats. The objective of the present study, a follow-up to our previous study, was to determine the effect of tobacco smoke exposure cessation on the lung response to crystalline silica exposure in the rats. Rats were exposed to air, crystalline silica (1 week followed by a 1 year progression/recovery period with no exposure), tobacco smoke (6 months of exposure followed by 6 months of recovery with no exposure), or crystalline silica (1 week) plus tobacco smoke (6 months of exposure followed by 6 months of recovery with no exposure). Lung toxicity was determined at the end of the 1-year progression/recovery period in all 4 groups of the rats. Silica exposure resulted in significant lung toxicity which was further exacerbated by tobacco smoke exposure in the rats. Cessation of cigarette smoke exposure did not result in reversal of the silica-induced lung toxicity despite exacerbation of the toxicity by tobacco smoke.

overall_design: Approximately 3 months old, healthy male Fischer rats (Charles River Laboratories, Wilmington, MA) were used in this study. The study was conducted in an Association for Assessment and Accreditation of Laboratory Animal Care International approved animal facility (NIOSH, Morgantown, WV) following a protocol approved by the Animal Care and Use Committee. The rats were housed in groups of 3 rats/cage and maintained on a 12-hour light-dark cycle in a temperature (68-72oF) and humidity (30-70%) controlled room with free access to filtered tap water and Teklad rodent diet (Envigo, Indianapolis, IN). The rats were divided into 4 groups (n=6) and exposed to air (control) tobacco smoke (80 mg/m3, twice weekly, 6 months), crystalline silica (15 mg/m3, 6 hours/day, 5 days) or crystalline silica (15 mg/m3, 6 hours/day, 5 days) followed by tobacco smoke (80 mg/m3, twice weekly, 6 months) by whole-body inhalation (exposure period). Following the 6 months exposure period, all four groups of rats were maintained approximately for an additional 6 months without any further exposure (recovery period). At the end of the recovery period, the rats from all four groups were euthanized and lung gene expression profiles determined by RNA sequencing. Next generation sequencing libraries prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina, Inc, San Diego, CA) were used in the sequencing.

first: Tina

last: Sager

first: Elijah

last: Lowe

first: Naveena

last: Yanamala


title: Xist RNA regulates remodeling of the Xi during B cell stimulation

first: MONTSERRAT

last: ANGUERA

first: Natalie

last: Toothacre


title: The neuroinflammatory interleukin-12 signaling pathway drives Alzheimer's disease-like pathology by perturbing oligodendrocyte survival and neuronal homeostasis

city: Berlin

first: Nikolaus

last: Rajewsky

address: Hannoversche Str. 28

department: BIMSB

institute: Max Delbrück Center for Molecular Medicine

summary: Central in AD-related neuroinflammation is the proinflammatory interleukin-12 (IL-12)/IL-23 signaling pathway whose inhibition has been shown to attenuate pathology and cognitive defects in AD-like mice. In order to explore which cell types are involved in this neuroinflammatory cascade, we used single-nuclei RNA sequencing in AD-like APPPS1 mice lacking or harboring IL-12/IL-23 signaling.

overall_design: Single-nuclei RNAseq of FACs sorted nuclei extracted from snap frozen mouse hippocampus of 250 day old animals

first: Seungjoon

last: Kim

first: Shirin

last: Schneeberger

first: Christine

last: Kocks

first: Ana

last: Boltengagen

first: Caroline

last: Braeuning

first: Frank

last: Heppner


title: Generation of hESC-derived expandable hepatoblast organoids and their derivatives of functional polarized hepatocyte organoids under 3D suspended culture conditions

status: Public on Dec 30 2024

city: Guangdong

first: Wu

last: Haibin

state: 广州

address: No. 382 Waihuan East Rd., Guangzhou University City, Panyu District, Guangzhou, Guangdong, P.R.China

institute: South China University of technology

summary:
Background & Aims: The increasing requirements for hepatocytes in therapeutics and pharmacy call for an efficient system that enables large-scale production of functional hepatocytes in vitro. Hepatoblast (HB) hold the ability to regenerate liver when damaged, combined with organoid (org) technology, the culture of human pluripotent stem cell (hPSCs) derived HB-orgs was established under 2D culture system, enabling long-term expansion of HB in vitro. However, the expensive cost and the limitation of existing methods impede the further scale up of the production.
Methods: Under 3D suspension culture conditions with the support of Matrigel at low concentration in conjunction with employing the developed (defined) medium, we developed a novel system to efficiently and reproducibly generate expandable HB-orgs and functional polarized hepatocyte organoids (P-hep-orgs) derived from hESCs. HB-orgs were further scaled up by dynamic culture in spinner flasks, and the maturity and function of P-hep-orgs was validated by transcriptome analysis and in vitro and in vivo hepatic functional assays. scRNA-seq was used to further profile HB-orgs and P-hep-orgs.
Results: Our HB-orgs exhibited biopotency that could differentiate into functional hepatocytes and cholangiocytes. They proliferated actively at least for 15 passages with defined medium through avoiding the excessive autophagy under 3D suspension culture condition. HB-orgs showed higher proliferation rate in dynamic culture conditions and could reach 10^12 cell number at the initiate number of 3 million cells in only 4 weeks. With further differentiation, P-hep-orgs displayed characteristics of hepatocytes in liver, including the polarization state which mediated by integrin-AMPK signalling pathway, molecular features and improved liver functions. Moreover, P-hep-orgs were used for predicting the toxicity of various compounds, and modeling the development of hepatic lipid accumulation, as well as rescuing acute liver failure of mice.
Conclusion: Our work provided a cost-efficient method for large-scale generation of 3D HB-orgs and 3D P-hep-orgs that hold considerable potential to be a robust platform for disease research, drug screening/development and toxic study, as well as clinical applications.

overall_design: H9 was cultured on MEFs. MG- HB-orgs were hepatoblasts differentiated from H9 and cultured in our hepatoblast expansion medium without Matrigel supplement. MG+ HB-orgs were hepatoblasts differentiated from H9 and cultured in our hepatoblast expansion medium with Matrigel supplement. NP-hep-spheres were hepatocytes differentiated from our HB-orgs, cultured in HCM without Matrigel supplement. P-hep-orgs were hepatocytes differentiated from our HB-orgs, cultured in HCM with Matrigel supplement. PHH was primary human hepatocytes separated from patient.

first: Yuyou

last: Duan

first: Haibin

last: Wu

first: Jinghe

last: Xie


title: ZFP982 confers mouse embryonic stem cell characteristics by regulating expression of Nanog, Zfp42, and Dppa3

city: Freiburg

first: Patrick

middle: Piero

last: Bovio

address: Albertstr. 19

department: Department of Molecular Embryology

institute: Albert-Ludwigs University Freiburg, Institute of Anatomy and Cell Biology

summary:
Abstract
Background: Understanding the genetic underpinnings of protein networks conferring stemness is of broad interest for basic and translational research.

Methods: We used multi-omics analyses to identify and characterize stemness genes, and focused on the zinc finger protein 982 (Zfp982) that regulates stemness through the expression of Nanog, Zfp42, and Dppa3 in mouse embryonic stem cells (mESC).

Results: Zfp982 was expressed in stem cells, and bound to chromatin through a GCAGAGKC motif, for example near the stemness genes Nanog, Zfp42, and Dppa3. Nanog and Zfp42 were direct targets of ZFP982 that decreased in expression upon knockdown and increased upon overexpression of Zfp982. We show that ZFP982 expression strongly correlated with stem cell characteristics, both on the transcriptional and morphological levels. Zfp982 expression decreased with progressive differentiation into ecto-, endo- and mesodermal cell lineages, and knockdown of Zfp982 correlated with morphological and transcriptional features of differentiated cells. Zfp982 showed transcriptional overlap with members of the Hippo signaling pathway, one of which was Yap1, the major co-activator of Hippo signaling. Despite the observation that ZFP982 and YAP1 interacted and localized predominantly to the cytoplasm upon differentiation, the localization of YAP1 was not influenced by ZFP982 localization.

Conclusions: Together, our study identified ZFP982 as a transcriptional regulator of early stemness genes, and since ZFP982 is under the control of the Hippo pathway, underscored the importance of the context-dependent Hippo signals for stem cell characteristics.

Keywords: Hippo pathway; Nanog; Pluripotency; Stemness; Yap1; ZFP982.

overall_design:
Assesment of ZFP982 direct targets via ChIP of mESCs which transfected with ZFP982-MYC tagged expression vector.

2. Materials and methods

2.3. ChIP and ChIP-seq
Chromatin-immunoprecipitation (ZFP982-ChIP-seq) was performed from chromatin of mESC transfected with pEXP-Empty and pEXP-ZFP982, using the MYC-Tag according to NEXSON protocol [26]. For MYC-Tag ChIP, cells were fixed for 5 min at room temperature with 1 % methanol-free formaldehyde (Thermo Scientific, #28906). Cells were lysed using ice-cold Farnham lab buffer supplemented with a complete protease inhibitor cocktail (#4693159001, Roche, Switzerland). Chromatin was sheared with Bioruptor (Diagenode, Belgium) at low power for three cycles 15 s on, 30 s off. ChIP-sequencing was performed on an Illumina HiSeq 2500 (single-end, read length of 50 bp, 50 Mio/reads per sample). Quality control of sequencing reads was performed using FastQC [27]. CG bias and ChIP to input efficiency were controlled by computeCGBias and bamFingerprint [28]. Reads were mapped to the UCSC-main RefSeq GRCm38/mm10 reference genome using Bowtie2 [29,30]. Samples were deduplicated using MarkDuplicates (http://broadinstitute.github.io/picard/). Signal extraction scaling (SES) was used for data normalization [31] and log2 (ratio of the number of reads) of ChIP to input was calculated by bamCompare using a pseudocount of 1 and a bin size of 25 bp. ComputeMatrix, plotHeatmap, and deepTools2 were used for plotting. Motif analysis was performed using MEME-ChIP version 4.11.2 [32]. The Galaxy Platform (https://usegalaxy.eu) was used for ChIP-seq analyses [33].
For the published ChIP-seq datasets of histone marks (Fig. 4E, S5) in mESC (GSE135318 [34]) fastq files were downloaded and reanalyzed as described. Individual replicates were averaged after normalization. Further information about the workflow and Bioinformatic analysis can be found at https://github.com/Vogel-lab/ZFP982-confers-mESC-characteristics.

first: Fariba

last: Dehghanian

middle: P

first: Fabian

last: Gather

first: Simone

last: Probst

first: Amirhosein

last: Naghsh-Nilchi

first: Tanja

last: Vogel


title: Identification of a TNIK-CDK9 Axis as a Targetable Strategy for Platinum-Resistant Ovarian Cancer

status: Public on Dec 27 2024

city: Ann Arbor

first: Karan

last: Bedi

address: 1600 Huron Pkwy

department: Biostatistics

institute: University of Michigan

summary: Up to 90% of high grade serous ovarian cancer (HGSC) patients will become resistant to frontline platinum chemotherapy, necessitating innovative treatments for recurrent disease. Here we leveraged the Benevolent artificial intelligence (AI) PlatformTM in combination with in-silico modeling and patient-derived chemotherapy-resistant 3D models to identify dual targeting of TNIK and CDK9 as a promising therapeutic approach. Combined TNIK and CDK9 knockdown markedly diminished chemotherapy-resistant cell viability and inhibition of TNIK and CDK9 by NCB-0846 could sensitize platinum-resistant cells to cisplatin and showed efficacy against a panel of clinically validated HGSC organoids. Additionally, CDK9 was found to be a mediator of canonical Wnt activity which can drive progression and resistance across multiple cancers including HGSC. In sum, an innovative AI approach resulted in the identification of a druggable TNIK-CDK9 axis that can target chemotherapy-resistant HGSC, presenting a model for further drug development or patient stratification of CDK9 inhibitors in clinical trials.

overall_design: To investigate the gene expression differences between a HGSC cell line and its cisplatin resistant counterpart. This was done in three replicates. We then performed pathway analysis using the data derived from this RNAseq dataset.

first: Noah

last: Puleo

first: Michele

middle: L

last: Dziubinski

first: Dylan

last: Carvette

first: Harini

last: Ram

first: Jessica

last: Teitel

first: Sreeja

last: Sekhar

first: Arron

last: Robida

first: Sadaf

last: Farsinejad

first: Marcin

last: Iwanicki

first: Wojciech

last: Senkowski

first: James

last: Dunbar

first: Andrea

last: Taddei

first: Chantelle

last: Hudson

first: Analisa

last: DiFeo


title: RNA-seq analysis of neuronal differentiation of KAT6A/B knockout mouse embryonic stem cells

city: Cambridge

first: Simon

middle: Richard

last: Andrews

state: Cambs

address: Babraham Research Campus

department: Science Services

country: United Kingdom

institute: The Babraham Institute

summary: Promoters of developmental genes in embryonic stem cells (ESCs) are marked by histone H3 lysine 4 trimethylation (H3K4me3) and H3K27me3 in an asymmetric nucleosomal conformation, with each sister histone H3 carrying one of the two marks. These so-called bivalent domains are thought to poise genes for timely activation upon differentiation. Here we show that asymmetric bivalent nucleosomes recruit repressive H3K27me3 binders but fail to enrich activating H3K4me3 binders, despite presence of H3K4me3, thereby promoting a poised state. Strikingly, the bivalent mark combination further promotes binding of chromatin proteins that are not recruited by each mark individually, including the histone acetyltransferase complex KAT6B (MORF). Knockout of KAT6B blocks neuronal differentiation, demonstrating that bivalency-specific readers are critical for proper ESC differentiation. These findings reveal how histone mark bivalency directly promotes establishment of a poised state at developmental genes, while highlighting how nucleosomal asymmetry is critical for histone mark readout and function.

overall_design: RNA-seq analysis was performed for undifferentiated embryonic stem cell lines (E14 control, KAT6A knockout, KAT6B knockout, and KAT6A/B double knockout) and on day 2, day 6, and day 15 of the neuronal differentiation protocol. Three replicates were analyzed derived from three independent differentiation experiments.

first: Marie

last: Warburton

first: Kimberly

middle: M

last: Webb

first: Elana

last: Bryan

first: Philipp

last: Voigt


title: single cell RNA-seq analysis of H9-derived expandable hepatoblast organoids and their derivatitives of functional polarized hepatocyte organoids under 3D suspended culture conditions

first: Wu

last: Haibin

summary: The increasing requirements for hepatocytes in therapeutics and pharmacy call for an efficient system that enables large-scale production of functional hepatocytes in vitro. We developed a method to obtain HB-orgs and mature P-hep-orgs from hPSCs under 3D suspension culture system.  HB-orgs showed bipotency and proliferate capacity, and P-hep-orgs exhibited hepatic polarization and mature hepatic functions.  Single cell RNAseq was used to further profile HB-orgs and P-hep-orgs.

overall_design: HB-orgs and P-hep-orgs differentiated from H9 were used for single cell RNA sequencing by BD Rhapsody system.

first: Yuyou

last: Duan

first: Haibin

last: Wu

first: Xueyan

last: Zhang

first: Jinghe

last: Xie


title: Serine mistranslation induces the integrated stress response through the P1 stalk

status: Public on Dec 23 2024

city: College Park

first: Jiqiang

last: Ling

state: MD

address: 2202 Microbiology Bldg., 4062 Campus Dr.

department: Cell Biology and Molecular Genetics

institute: The University of Maryland, College Park

summary: Aminoacyl-tRNA synthetases (aaRSs) are essential enzymes that support robust and accurate protein synthesis. A rapidly expanding number of studies show that mutations in aaRSs lead to multiple human diseases, including neurological disorders and cancer. Much remains unknown about how aaRS mutations impact human health. In particular, how aminoacylation errors affect stress responses and fitness in eukaryotic cells remains poorly understood. The integrated stress response (ISR) is an adaptive mechanism in response to multiple stresses. However, chronic activation of the ISR contributes to the development of multiple diseases (e.g., neuropathies). Here we show that Ser misincorporation into Ala and Thr codons, resulting from aaRS editing defects or mutations in tRNAs, constitutively active the ISR. Such activation does not appear to depend on the accumulation of uncharged tRNAs, implicating that Ser mistranslation may lead to ribosome stalling and collision.

overall_design: RNA sequencing of Saccharomyces cerevisiae wild type and threonyl-tRNA synthetase mutants grown at 30 degrees and challenged at 37 degrees. Overall design: yeast strains were pregrown at 30 degrees, and shifted to 37 degrees for 2 hours. Cells were collected and total RNA was prepared for Illumina sequencing.

first: Zhang

last: Hong

first: Ling

last: Jiqiang


title: Drosophila AHR limits tumor growth and stem cell proliferation in the intestine

city: London

first: Nicola

middle: Laura

last: Diny

address: 1 Midland Rd

institute: The Francis Crick Institute

summary:
Background
The aryl hydrocarbon receptor (AHR) plays important roles in intestinal homeostasis, limiting tumour growth and promoting differentiation in the intestinal epithelium. Spineless, the Drosophila homolog of AHR, has only been studied in the context of development but not in the adult intestine.

Methods
The role of Spineless in the Drosophila midgut was studied by overexpression or inactivation of Spineless in infection and tumour models and RNA sequencing of sorted midgut progenitor cells.

Results
We show that spineless is upregulated in the adult intestinal epithelium after infection with Pseudomonas entomophila (P.e.). Spineless inactivation increased stem cell proliferation following infection-induced injury. Spineless overexpression limited intestinal stem cell proliferation and reduced survival after infection. In two tumour models, using either Notch RNAi or constitutively active Yorkie, Spineless suppressed tumour growth and doubled the lifespan of tumour-bearing flies. At the transcriptional level it reversed the gene expression changes induced in Yorkie tumours, counteracting cell proliferation and altered metabolism.

Conclusions
These findings demonstrate a new role for Spineless in the adult Drosophila midgut and highlight the evolutionarily conserved functions of AHR/Spineless in the control of proliferation and differentiation of the intestinal epithelium.

overall_design: RNA sequencing of FACS isolated midgut intestinal stem cells and enteroblasts from adult female flies with or without ykiact tumour and with or without spineless overexpression

first: Michael

last: Shapiro

first: Brigitta

last: Stockinger


title: YAP1 regulates thrombopoiesis by binding to MYH9 in immune thrombocytopenia

status: Public on Dec 22 2024

city: Suzhou

first: Shuhong

last: Hu

address: No.188 Shizi Street

institute: The First Affiliated Hospital of Soochow University

summary: Immune thrombocytopenia (ITP) is a complicated bleeding disease characterized by sharp platelet reduction. As a dominating element involved in ITP, megakaryocytes (MKs) are responsible for thrombopoiesis. However, the mechanism behind the dysregulation of thrombopoiesis in ITP remains undetermined. In this study, we examined the role of YAP1, Yes-associated protein 1, in thrombopoiesis during ITP. We observed a reduced YAP1 expression with cytoskeletal actin misalignment in MKs of ITP patients. Using experimental ITP mice, we showed that YAP1 reduction induced aberrant MK distribution, reduced the percentage of late MKs in total MKs, and caused submaximal platelet recovery. Mechanistically, YAP1 upregulation by GATA1 binding to its promoter promoted MK maturation. Phosphorylated YAP1 facilitated cytoskeletal activation by binding of its WW2 domain to MYH9, facilitating thrombopoiesis. Targeting YAP1 by its activator XMU-MP-1 was sufficient to rescue cytoskeleton defects and thrombopoiesis in YAP1+/- ITP mice and ITP patients. Taken together, these results demonstrate a crucial role for YAP1 in thrombopoiesis, providing a potential for the development of diagnostic markers and therapeutic options for ITP.

overall_design: Compare gene expression profiling analysis using data obtained from RNA-seq of 4 healthy controls and 7 ITP patients.

first: Yifei

last: Liu

first: Depei

first: Yang

last: Xu


title: Transcriptional levels of sialic-binding proteins in 293T cells.

status: Public on Dec 21 2024

city: fuzhou

first: Zhihua

last: Feng

state: Fujian

address: Fujian Normal University, Qishan Campus, No.8 Xuefu South Road, Shangjie, Minhou, Fuzhou, Fujian,China

institute: Fujian Normal University

summary: Sialic acid-binding proteins are implicated in the infection process of pathogenic microorganisms. Measuring the expression levels of these genes in cells can provide valuable insights into the susceptibility of cells to specific pathogens.

overall_design: RNA was extracted from 1 × 10^⁷ 293T cells per sample, with three biological replicates, for RNA sequencing.

first: Yajuan

last: Fu

first: Sheng

last: Yang

first: Heng

last: Zhao


title: Genome-wide mapping of chromatin structure remodeling RSC1 during growth mycelia in the Magnaporthe oryzae [ChIP-seq + Mnase-seq]

city: Hangzhou

first: mengting

last: xu

state: ZheJiang

address: Zhejiang University

institute: mengtingxu

summary: A bromodomain and BAH containing Remodels the Structure of Chromatin 1 (RSC1), which play key roles  in the filamentous fungus Magnaporthe oryzae.

overall_design: Examination of 3 different mutants in Magnaporthe oryzae strain

first: Zeng

last: Tao


title: High-resolution spatial multi-omics reveals cell-type specific nuclear compartments

city: Pasadena

first: Yodai

last: Takei

state: CA

address: 1200 E California Blvd

institute: Caltech

summary: The mammalian nucleus is compartmentalized by diverse subnuclear structures. These subnuclear structures, marked by nuclear bodies and histone modifications, are often cell-type specific and affect gene regulation and 3D genome organization. Understanding nuclear organization and its role in gene expression requires identifying the molecular constituents of subnuclear structures and mapping their associations with specific genomic loci and their transcriptional levels in individual cells, within complex tissues. Here, we introduce two-layer DNA seqFISH+, which allows simultaneous mapping of 100,049 genomic loci, together with nascent transcriptome for 17,856 genes and a diverse set of immunofluorescently labeled subnuclear structures all in single cells in both cell lines and complex tissues. These data enable imaging-based chromatin profiling of diverse subnuclear markers and capture changes in chromatin organization at genomic scales from 100–200 kb to approximately 1 Mb, depending on the subnuclear marker and DNA locus. Using multi-omics datasets in the adult mouse cerebellum, we showed that repressive chromatin regions are more variable by cell type than active regions across the genome. We also discovered RNA polymerase II (RNAPII)-enriched foci were locally associated with long, cell-type specific genes (> 200kb), in a manner distinct from nuclear speckles. Further, our analysis revealed that cell-type specific facultative and constitutive heterochromatin regions marked by H3K27me3 and H4K20me3 are enriched at specific genes and gene clusters, respectively, and shape radial chromosomal positioning and inter-chromosomal interactions in neurons and glial cells. Together, our results provide a single-cell high-resolution multi-omics view of subnuclear structures and chromatin marks, associated genomic loci, and their impacts on gene regulation, directly within complex tissues.

overall_design: CUT&Tag for RNA Polymerase II phospho Ser5 (RNAPIISer5-P) and histone modfication H3K27me3 and CUT&RUN for Lamin B1 and histone modfications H3K4me3, H3K9me9 in mouse embryonic stem cells and mammary gland cells.

first: Isabel

middle: N

last: Goronzy

first: Yujing

first: Mitchell

last: Guttman

first: Long

last: Cai


title: Differential responses to selective CDK2 inhibitor BLU-222 is conditioned by tumor suppressors

city: Buffalo

first: Jianxin

last: Wang

state: NY

address: 665 Elm Street

department: Molecular and Cellular Biology

institute: Roswell Park Comprehensive Cancer Center

summary: The selective CDK2 inhibitor BLU-222 was evaluated for mechanisms of response in the context of ovarian and breast cancer models. Using sensors of cellular CDK activity, it was found that sensitivity to either CDK4/6 or CDK2 inhibition is related to the differential dependence on a single CDK for G1/S transition. Unlike CDK4/6 inhibitors, BLU-222 was able to robustly inhibit proliferation through cell cycle inhibition in both G1 and G2 phases. However, it remained possible for cells to re-enter the cell cycle upon drug withdrawal. The anti-proliferative strength and impact on G1/S versus G2/M accumulation was found to be mediated by the RB tumor suppressor, as determined by functional perturbation strategies. To broaden the sensitivity to CDK2 inhibition, combinatorial drug screens were performed that identified both synergistic (e.g., CDK4/6 inhibitors) and antagonistic (e.g., WEE1 inhibitors) relationships. Models that were exceptionally sensitive to CDK2 inhibition displayed coordinate expression of Cyclin E1 and P16INK4A, an endogenous CDK4/6 inhibitor. Functional studies demonstrated that P16INK4A and CDK4/6 activity were key mediators of sensitivity to BLU-222. Clinical gene and protein expression analysis revealed a positive correlation between Cyclin E1 and P16INK4A and that ~25% of ovarian cancers exhibited coordinate expression of Cyclin E, P16INK4A, and RB, indicative of strong sensitivity to CDK2 inhibition. Together, this work advances a precision strategy for the use of CDK2 inhibitors in the context of ovarian and breast cancers.

overall_design: The ovarian (kuramochi and OVCAR-8) and triple negative breast (MDA-MB-157) cancer cell lines (Homo sapien) were evaluated for differential transcriptional response to the investigational CDK2 inhibitor BLU-222. Three biological replicates were performed for each condition. Cells were treated with either 0.1% DMSO (n=3 per cell line) or 125 nM BLU-222 (kuramochi, n=3), 100 nM BLU-222 (MDA-MB-157, n=3), or 250 nM BLU-222 (OVCAR-8, n=3) for 48 hrs.

first: Adam

last: Dommer

first: Vishnu

last: Kumarasamy

first: Thomas

last: O'Connor

first: Michelle

last: Roti

first: Sidney

last: Mahan

first: Karen

last: McLean

first: Erik

last: Knudsen

first: Agnieszka

middle: K

last: Witkiewicz


title: Genome-wide distribution of KAT6B and H3K23ac in mouse embryonic stem cells

first: Simon

last: Andrews

sample_organism:
Drosophila melanogaster
Mus musculus

platform_organism:
Drosophila melanogaster
Mus musculus

overall_design: E14 mouse embryonic stem cells were engineered to express HA-tagged KAT6B from its endogenous locus. In addition, mutations were introduced to render MLL2 catalytically inactive (Y2688A mutation) or to abrogate PRC2 function (EZH2-/-; EZH1-/-). KAT6B distribution was profiled via the added HA tag, while antibodies against H3K23ac, H3K4me3, and H3K27me3 were used to profile the corresponding histone modifications. Further, mutations were introduced in subunits of the KAT6B complex (ING2 Y188A, KAT6B D290A, BRPF1 D270/272A, BRPF2 D212/214A) and KAT6B (via HA tag) and H3K23ac were profiled. Furthermore, E14 mouse embryonic stem cells both wild-type and deficient for KAT6A and KAT6B (KAT6A-/-; KAT6B-/-) were profiled for distribution of H3K23ac, H3K4me3, and H3K27me3. Drosophila spike-in calibration was applied to enable quantitative comparisons within the following sets of samples: HA-KAT6B line with and without catalytically inactive MLL2 and EZH1/2 double knockout; HA-KAT6B line with and without point mutations in histone mark binding domains; E14 cells with and without KAT6A/B knockouts.

first: Nwamaka

last: Idigo

first: Kimberly

last: Webb

first: Elana

last: Bryan

first: Valsakumar

last: Devisree

first: Simone

last: Lenci

first: Viktoria

last: Major

first: Marie

last: Warburton

first: Philipp

last: Voigt


title: Single-cell RNA-sequencing identifies unique cell-specific gene expression profiles in high-grade cardiac allograft vasculopathy

city: Nashville

first: Kaushik

last: Amancherla

address: 1211 Medical Center Dr

institute: Vanderbilt University Medical Center

summary: Background: Cardiac allograft vasculopathy (CAV), a diffuse thickening of the intima of the coronary arteries and microvasculature, is the leading cause of late graft failure and mortality after heart transplantation (HT). Diagnosis involves invasive coronary angiography, which carries substantial risk, and minimally-invasive approaches to CAV diagnosis are urgently needed. Using single-cell RNA-sequencing in peripheral blood mononuclear cells (PBMCs), we sought to identify cell-specific gene expression profiles in CAV. Methods: Whole blood was collected from 22 HT recipients with angiographically-confirmed CAV and 18 HT recipients without CAV. PBMCs were isolated and subjected to single-cell RNA-sequencing using a 10X Genomics microfluidic platform. Downstream analyses focused on differential expression of genes, cell compositional changes, and T cell receptor repertoire analyses. Results: Across 40 PBMC samples, we isolated 134,984 cells spanning 8 major clusters and 31 subclusters of cell types. Compositional analyses showed subtle, but significant increases in CD4+ T central memory cells, and CD14+ and CD16+ monocytes in high-grade CAV (CAV-2 and CAV-3) as compared to low-grade or absent CAV. After adjusting for age, gender, and prednisone use, 745 genes were differentially expressed in a cell-specific manner in high-grade CAV. Weighted gene co-expression network analyses showed enrichment for putative pathways involved in inflammation and angiogenesis. There were no significant differences in T cell clonality or diversity with increasing CAV severity. Conclusions: Unbiased whole transcriptomic analyses at single-cell resolution identify unique, cell-specific gene expression patterns in CAV, suggesting the potential utility of peripheral gene expression biomarkers in diagnosing CAV.

overall_design:
40 samples underwent 5' v2 (10X Genomics) single-cell RNA-sequencing
22 patients with CAV and 18 patients without


title: Ensembles of genome-coverage single-cell histone modifications reveal epigenetic lineages during mouse preimplantation development II

city: Beijing

first: Min

last: Liu

state: Beijing

address: Yan  yuan street

institute: 北京大学

summary: Profound epigenetic resetting during early embryo development from fertilization to blastocyst ensures zygotic genome activation and also begets progressive cellular heterogeneities1-6. Mapping single-cell epigenomic profiles of core histone modifications covering each individual cell onto the lineage tree (epigenetic lineages) is a fundamental goal in developmental biology. Here, we develop a method, TACIT, achieving genome-coverage single-cell profiling of seven histone modifications in mouse early embryos from zygotes to blastocysts. TACIT yields up to half million fragments per cell with peaks equivalent of bulk assays. Integrating these single-cell histone modifications with scRNA-seq data7, we chart a cell-kinship informed epigenetic lineage landscape. Multimodal chromatin state annotations show that the ZGA onset at early 2-cell stage already primes heterogeneities in totipotency. Epigenetic lineages also allow for nominating totipotency gene regulatory networks including stage-specific transposable elements and putative transcription factors (TFs). In addition, machine learning models together with single-cell co-profiles of multiple histone modifications facilitate prediction of the earliest cell branching toward inner cell mass (ICM) and trophectoderm (TE) in latent multimodal space as well as feature regulatory elements and previously unknown lineage-specifying TFs. Together, our work reconstructs single-cell holistic epigenetic lineages, elucidating multimodal regulation of cellular heterogeneities and cell fate priming during mouse pre-implantation development.

overall_design: For validation, we first conducted experiments in mouse embryonic stem cells (mESCs) with antibodies specific to H3K4me3, H3K27ac, H3K36me3, and H3K27me3. Next, we applied TACIT to generate genome-wide maps of histone modification for embryonic cells collected from zygote, 2-cell, 4-cell, 8-cell, morula, and blastocyst stages.

first: Aibin

last: He

first: Yanzhu

last: Yue

first: Xubin

last: Chen

first: Kexin

last: Xian

first: Chao

last: Dong

first: Shu

last: Gao

first: Haiqing

last: Xiong


title: Evaluation  of pharmacological effects of ginsenoside Rk2 on hepatic ischemia/reperfusion-injury in vivo and in vitro [HuH7]

status: Public on Dec 20 2024

city: MACAU

first: HONG

last: SHEN

state: MACAU

address: Room 6034, Building N22, Avenida da Universidade, Taipa

department: Institute of Chinese Medical Sciences

institute: UNIVERSITY OF MACAU

summary: Hepatic ischemia-reperfusion injury (IRI) poses a significant concern in conditions such as hemorrhagic shock, hepatic resection, and liver transplantation. Recent studies have highlighted the potential of phytomedicines and natural products in effectively protecting against various forms of IRIs. In this particular investigation, we conducted high-throughput screening and identified ginsenoside Rk2 (RK), a rare dehydroprotopanaxadiol saponin, as a promising agent for hepatic IRI. Our subsequent in vivo and in vitro studies demonstrated that Rk2 effectively mitigated inflammation and apoptosis induced by hepatic IRI in a dose-dependent manner. In this study, we comprehensively investigate the pharmacological effects of ginsenoside Rk2 in the treatment of hepatic IRI and elucidate potential molecular mechanisms in vitro.

overall_design: RNA-seq profiling of wildtype HuH7 cells treated with or without ginsenoside Rk2 under oxygen-glucose deprivation and reperfusion (OGD/R) conditions.

first: Hong

last: Shen

first: Jiajun

last: Fu

first: Kun

last: Wang

first: Xiao-Jing

last: Zhang

first: Jian-Bo

last: Wan


title: Parathyroid tissue transcriptome of control, untreated uremic and Cinacalcet-treated uremic rats at two timepoints

status: Public on Dec 19 2024

city: Copenhagen

first: Søren

last: Egstrand

address: Blegdamsvej 9

department: Depart. of Nephrology

country: Denmark

institute: Rigshospitalet

summary: We investigate whether Cinacalcet treatment timed to the expression of its drug target; the Calcium-Sensing Receptor, could improve efficacy of treatment in secondary hyperparathyroidism. We found that proliferation rate of parathyroid glands of uremic rats was markedly reduced when Cinacalcet was administered in the early inactive phase compared to conventional timing early in the active phase. We use RNAseq of parathyroid tissue to investigate the possible mechanism behind this enhanced anti-proliferative effect.

overall_design: CKD was induced by one-step 5/6 nephrectomy in 40 rats. After four weeks of uremia, 20 CKD rats were assigned to two treatment groups: Cina1 and Cina2 receiving Cinacalcet either morning (ZT2, N=10) or evening (ZT14, N=10), respectively. The remaining 20 untreated CKD rats were assigned to morning (PNX1, N=10) or evening (PNX2, N=10) investigation. Likewise, the 20 normal control rats were assigned to morning (ctrl1, N=10) or evening (ctrl2, N=10) investigation. After three weeks of treatment, parathyroid glands were investigated using Ki-67 immunostaining and RNAseq at the assigned time point, that is, morning (ZT2) for groups: Cina1, PNX1, and ctrl1, and evening (ZT14) for groups: Cina2, PNX2, and ctrl2.

first: Maria

last: Mace

first: Marya

last: Morevati

first: Lars

middle: H

last: Engelholm

first: Jesper

last: Thomsen

first: Annemarie

last: Brüel

first: Klaus

last: Olgaard

first: Ewa

last: Lewin


title: STING Mediates Increased Self-Renewal and Lineage Skewing in DNMT3A-Mutated Hematopoietic Stem/Progenitor Cells

city: Shang Hai

first: Yin

state: Shanghai

address: Dong An street

institute: Fudan university

summary: Somatic mutations in DNA methyltransferase 3A (DNMT3A) are frequently observed in patients with hematological malignancies. Hematopoietic stem/progenitor cells (HSPCs) with mutated DNMT3A demonstrate increased self-renewal activity and skewed lineage differentiation. However, the molecular mechanisms underlying these changes remain largely unexplored. In this study, we show that Dnmt3a loss leads to the upregulation of endogenous retroviruses (ERVs) in HSPCs, subsequently activating the cGAS-STING pathway and triggering inflammatory responses in these cells. Both genetic and pharmacological inhibition of STING effectively corrects the increased self-renewal activity and differentiation skewing induced by Dnmt3a deficiency in mice. Notably, targeting STING showed inhibited acute myeloid leukemia (AML) development in a Dnmt3a-KO; Flt3-ITD AML model, comparable to AC220, an FDA-approved FLT3-ITD inhibitor. A patient-derived xenograft (PDX) model further demonstrated that targeting STING effectively alleviates the leukemic burden of DNMT3A-mutant AML. Collectively, our findings highlight a critical role for STING in hematopoietic disorders induced by DNMT3A mutations and propose STING as a potential therapeutic target for preventing the progression of DNMT3A mutation-associated leukemia.

overall_design: To address the intrinsic factors in DNMT3A mutated cells required for the development of hematopoietic diseases, we initiated our study by performing a transcriptome analysis to examine the differences in gene expression between Dnmt3af/f, Mx1-Cre and wild type HSPCs.

first: Jingru

last: Huang

first: Jiaying

last: Xie

first: Yuheng

last: Shi


title: Ensembles of genome-coverage single-cell histone modifications reveal epigenetic lineages during mouse preimplantation development

first: Min

last: Liu

summary:
We applied TACIT to profile seven histone modifications at single-cell resolution in mouse early embryos from zygotes to blastocysts.
Profound epigenetic resetting during early embryo development from fertilization to blastocyst ensures zygotic genome activation and also begets progressive cellular heterogeneities1-6. Mapping single-cell epigenomic profiles of core histone modifications covering each individual cell onto the lineage tree (epigenetic lineages) is a fundamental goal in developmental biology. Here, we develop a method, TACIT, achieving genome-coverage single-cell profiling of seven histone modifications in mouse early embryos from zygotes to blastocysts. TACIT yields up to half million fragments per cell with peaks equivalent of bulk assays. Integrating these single-cell histone modifications with scRNA-seq data7, we chart a cell-kinship informed epigenetic lineage landscape. Multimodal chromatin state annotations show that the ZGA onset at early 2-cell stage already primes heterogeneities in totipotency. Epigenetic lineages also allow for nominating totipotency gene regulatory networks including stage-specific transposable elements and putative transcription factors (TFs). In addition, machine learning models together with single-cell co-profiles of multiple histone modifications facilitate prediction of the earliest cell branching toward inner cell mass (ICM) and trophectoderm (TE) in latent multimodal space as well as feature regulatory elements and previously unknown lineage-specifying TFs. Together, our work reconstructs single-cell holistic epigenetic lineages, elucidating multimodal regulation of cellular heterogeneities and cell fate priming during mouse pre-implantation development.

first: Aibin

last: He

first: Shu

last: Gao

first: Haiqing

last: Xiong


title: LncRNAs expressed in triple negative breast cancer of Mexican patients

city: Mexico City

first: Patricia

middle: Piña

last: Sánchez

state: CDMX

address: Cuauhtémoc Avenue

department: Medical Research Unit in Oncological Diseases

country: Mexico

institute: IMSS

summary: We provide a detailed analysis of the expression of lncRNAs in TNBC versus Luminal tumors of breast cancer patients

overall_design: We employed HTA 2.0 microarrays to analyze the transcriptome of TNBC and Luminal tumors.

last: Piña-Sánchez

first: Rosario

last: Castro-Oropeza

first: Karla

last: Vazquez-Santillan


title: Deep profiling deconstructs features associated with memory CD8+ T cell tissue residence [CITE-Seq]

city: Minneapolis

first: David

last: Masopust

state: MN

address: 2101 6th St SE

department: Microbiology and Immunology

institute: University of Minnesota

summary: Tissue resident memory CD8+ T cells (Trm) control infections and cancer and are defined by their lack of recirculation. Because migration is difficult to assess, residence is usually inferred by putative residence-defining phenotypic and gene signature proxies. We assessed the validity and universality of residence proxies by integrating mouse parabiosis, multi-organ sampling, intravascular staining, acute and chronic infection models, dirty mice, and single-cell multi-omics. We report that memory T cells integrate a constellation of inputs— location, stimulation history, antigen persistence, and environment— resulting in myriad differentiation states. Thus, current Trm-defining methodologies have implicit limitations, and a universal residence-specific signature may not exist. However, we define genes and phenotypes that more robustly correlate with tissue residence across the broad range of conditions that we tested. This study reveals broad adaptability of T cells to diverse stimulatory and environmental inputs and provides practical recommendations for evaluating Trm cells.

overall_design:
To define features unique to tissue resident memory CD8+ T cells, we leveraged Cellular Indexing of Transcriptomes and Epitopes sequencing (CITE-seq). We first established parabionts containing either LCMV Armstrong- or influenza PR8-induced memory P14 cells. We then performed in vivo intravascular staining with biotin anti-CD8a, isolated lymphocytes from tissues, stained cells with CITE-seq and flow cytometry compatible antibodies, FACS sorted for P14 cells, and performed single-cell RNA-sequencing. Since our main objective was to evaluate the influence of tissue location, migration property, and vascular localization on gene expression profiles in the context of two different infections, we stained cells with CITE-seq compatible antibodies targeting congenic markers (Thy1.1 and CD45.1) and i.v. antibody-labeled cells, along with a select few cell surface markers: CD69, CD103, Ly6C, CD127, CD62L, CX3CR1, and KLRG1. For multiplexing purposes, cells from each tissue were stained with a unique TotalSeq-A anti-mouse oligonucleotide hashtag. After sorting, cells from all tissues for each parabiont (CD45.1 host or Thy1.1 host) were pooled to constitute one technical replicate. Pooled cells from the CD45.1 parabiont host were designated as replicate "A". Pooled cells from the Thy1.1 parabiont host were designated as replicate "B". We followed the 10X Genomics Chromium Single Cell 3’ v3 protocol to prepare RNA, antibody-derived-tag (ADT), and hashtag oligos (HTO) libraries. To maintain the identify of each parabiont, cells from each parabiont (CD45.1 parabiont = "A" and Thy.1 parabiont = "B") were captured separately and sequenced on separate 10X lanes.  Each cell suspension was loaded onto a 10X Genomics Chromium Controller at a concentration of 1,200 cells per microliter to target about 40,000 cells per the two technical replicates, "A" and "B". RNA, ADT, and HTO libraires were sequenced with an Illumina NovaSeq S4. Reads were processed with 10X Genomics Cell Ranger v.7.0.0 with feature barcoding, where RNA reads were mapped to the mouse mm10–2.1.0 mouse reference and antibody reads mapped to known barcodes. LCMV Armstrong is shortened to "arm" in the data files for the LCMV Arm CITE-seq experiment. PR8-gp33 is shortened to "flu" in the data files for the PR8-gp33 CITE-seq experiment.

[April 30, 2025] Some of the fastq files uploaded for GSE277081 were the shallow/QC sequencing files instead of the full depth sequencing files. The proper files have been linked to Samples GSM8513844-GSM8513849.

first: Milcah

last: Scott

first: Zoë

last: Steier

first: Mark

last: Pierson

first: Michael

last: Stolley

first: Stephen

middle: D

last: O’Flanagan

first: Andrew

middle: G

last: Soerens

first: Sathi

last: Wijeyesinghe

first: Lalit

last: Beura

first: Gayathri

last: Dileepan

first: Brandon

last: Burbach

first: Marco

last: Künzli

first: Clare

middle: F

last: Quarnstrom

first: Olivia

last: Ghirardelli Smith

first: Eyob

last: Weyu

first: Sara

middle: E

last: Hamilton

first: Vaiva

last: Vezys

first: Alex

last: Shalek


title: Effects of StcE treatment on in vitro brain endothelial cell line bEnd.3

status: Public on Dec 17 2024

city: Stanford

first: Sophia

middle: Michelle

last: Shi

state: California

address: 63 Abrams Court

institute: Stanford University

summary: Mucin-domain glycoproteins populate the brain endothelial cell surface, but their roles as a class of glycoconjugates are largely unknown. Here, we perform bulk RNA-sequencing of bEnd.3 cells treated with StcE, which enzymatically degrades cell surface mucins, in order to understand the effects of mucin removal on brain endothelial cell function.

overall_design: Bulk RNA-sequencing of bEnd.3 cells treated with StcE or saline in growth media

first: Tony

last: Wyss-Coray


title: Evaluation  of pharmacological effects of ginsenoside Rk2 on hepatic ischemia/reperfusion-injury in vivo and in vitro [mouse]

first: HONG

last: SHEN

summary: Hepatic ischemia-reperfusion injury (IRI) poses a significant concern in conditions such as hemorrhagic shock, hepatic resection, and liver transplantation. Recent studies have highlighted the potential of phytomedicines and natural products in effectively protecting against various forms of IRIs. In this particular investigation, we conducted high-throughput screening and identified ginsenoside Rk2 (Rk2), a rare dehydroprotopanaxadiol saponin, as a promising agent for hepatic IRI. Our subsequent in vivo and in vitro studies demonstrated that Rk2 effectively mitigated inflammation and apoptosis induced by hepatic IRI in a dose-dependent manner. In this study, we comprehensively investigate the pharmacological effects of ginsenoside Rk2 in the treatment of hepatic IRI and elucidate potential molecular mechanisms in vivo.

overall_design: RNA-sequencing was performed on wild-type C57BL/6 mice administered with and without ginsenoside Rk2 under conditions of ischemia-reperfusion injury.

first: Hong

last: Shen

first: Jiajun

last: Fu

first: Kun

last: Wang

first: Xiao-Jing

last: Zhang

first: Jian-Bo

last: Wan


title: Epitranscriptomic program promotes skeletal stem cell quiescence and pluripotency by regulating proteostasis via METTL3-FEM1B-GLI1 axis

status: Public on Dec 18 2024

city: Wuhan

first: weidong

last: liu

address: donghu street

institute: Wuhan University

summary: Skeletal stem cells (SSCs) maintain the hierarchy of skeletal system via pluripotency and differentiation capacity. However, it remains largely unknown how these cells adapt its highly nutrient-deficient niche and precisely regulate their function to keep this skeletal hierarchical organization. Here, we delineate a comprehensive m6A landscape across skeletal hierarchy, and identify a new epitranscriptomic program to promote SSCs quiescence and potency by regulating proteostasis via METTL3-FEM1B-GLI1 axis. We find m6A modifications arise mostly from skeletal stem cells (SSCs) in stem-progenitor population and play critical roles in cell fate maintenance and transformation in skeletal hierarchy. Genetic deletion of Mettl3 in skeletal stem and progenitors impairs bone development with shortened limbs, disturbs growth plate, and decreases bone mass. Moreover, Mettl3 loss induces quiescence loss, and damages the self-renewal ability, and differentiation ability of SSCs. Mechanistically, Mettl3-mediated m6A modification reduces mRNA stability of a Cul2-RING E3 ligase complex substrate-recognition subunit Fem1b, which subsequently influences proteostasis of SSCs and stabilizes Gli1 protein, a key transcription factor of Hedgehog pathway for maintaining SSC identity and function. Thus, our findings present a fascinating portrait of m6A modification of skeletal hierarchy and reveal the essential role of an epitranscriptome-proteostasis axis in maintaining SSC function.

overall_design: SLIM-seq profiling of  skeletal hierarchy cells and their kncokout Mettl3 at day 3.

first: Jing

first: Weidong

last: Liu

first: Jihua

last: Chai

first: Haojian


title: Overexpression of brain endothelial mucin-type O-glycan biosynthesis promotes brain homeostasis in aged mice

summary: In our study, we find that AAV-mediated brain endothelial B3GNT3 overexpression reduces neuroinflammatory markers and cognitive deficits in aged mice. Here, we perform snRNA-seq to characterize the cellular and molecular changes induced by brain endothelial B3GNT3 overexpression.

overall_design: snRNA-sequencing of pooled cortical and hippocampal tissues from aged mice treated with AAV-EGFP, aged mice treated with AAV-B3GNT3, and young mice treated with AAV-EGFP

first: Micaiah

last: Atkins


title: Comprehensive sequencing of the lung neuroimmune landscape in response to asthmatic induction

status: Public on Dec 16 2024

city: Torrance

first: Hayden

last: McSwiggin

address: 1124 W. Carson St.

department: Endocrinology

institute: The Lundquist Institute

summary: Here, we examined transcriptional changes in lung and vagal ganglia after asthma induction using bulk RNA-seq, single-cell RNA-seq and spatial transcriptomics.

overall_design: Examination of lung and vagal ganglia transcriptomes after asthma induction.

first: N

last: Jendzjowsky

first: W

last: Yan


title: An ageing bone marrow exacerbates lung fibrosis via a dysregulated regulatory T cell driven axis, fuelling profibrotic macrophage persistence

city: Wien

first: Jörg

last: Menche

state: Wien

address: Augasse 2-6,

country: Austria

institute: Ludwig Boltzmann Institute for Network Medicine

summary: Pulmonary fibrosis is an incurable disease, which increasingly manifests with advanced age. Yet, how the ageing hematopoietic niche influences immune cell function and fibrosis progression in the lungs remains elusive. Using heterochronic transplant mouse models, we discovered that an aged bone marrow exacerbates lung fibrosis irrespective of lung tissue age. Upon lung injury, there was an increased pulmonary infiltration of monocyte-derived alveolar macrophages (Mo-AMs) from an aged bone marrow. These Mo-AMs displayed an enhanced profibrotic profile and a delayed transition in acquiring a homeostatic tissue-resident phenotype. This impaired Mo-AM differentiation was attributed to diminished numbers of regulatory T cells (Tregs) and the reduced availability of the anti-inflammatory cytokine IL-10 in the lung microenvironment of mice engrafted with aged bone marrow. Mechanistically, we show that Tregs are crucial providers of IL-10 that promote timely Mo-AM maturation and attenuate fibrosis progression. Our findings demonstrate the critical influence of an aged bone marrow on the development of lung fibrosis and identify a Treg-mediated resolutory axis as a potential therapeutic target for accelerated tissue repair.

overall_design: To investigate the expression of IL10ra/IL10rb on different lung macrophage populations at D7 post bleomycin treatment, we performed single-cell RNA seq on cells derived from the broncheoalveolar lavage (BALF) of 8-week old (young) mice at D7 post bleomycin treatment.

first: Asma

last: Farhat

first: Anna

last: Hakobyan

first: Sylvia

last: Knapp


title: Host response to Merkel cell polyomavirus oncogenes in neonatal human dermal fibroblast

city: Tucson

first: Jiawen

last: Yang

state: Arizona

address: 1515 N Campbell Ave

department: University of Arizona Cancer Center

institute: The University of Arizona

summary: Merkel cell polyomavirus (MCPyV) early region (ER) and vector control inducible vectors were introduced into neonatal human dermal fibroblasts (nHDFs). Total RNA was then extracted and sequenced in triplicate at 0, 48 and 96 hours post-induction with doxycycline treatment. The purpose of this experiment was to identify the host response to MCPyV ER at the transcriptomic level, using both differential expression analysis and transcriptional network reconstruction. Together with our previous IMR90 model, we aim to systematically understand the initial steps toward Merkel cell carcinoma in different potential precursor cell types.

overall_design: Expression of MCPyV early region (extracted from MCCL21) or an empty control was induced in nHDFs, and triplicate RNA samples were exectaed and sequenced at 0, 48 and 96  hours.

first: Megha

last: Padi


title: RNA-seq analysis of WT and Tmem11 KO Th1 cells

status: Public on Dec 14 2024

city: Los Angeles

first: Yousang

last: Gwack

address: 10833 Le Conte Ave, 53-159 CHS

department: Physiology

institute: Uuniversity of California Los Angeles

summary: Loss of TMEM11 did not influence T cell differentiation but selectively impaired effector functions of Th1 cells, resulting in reduced severity of symptoms in an animal model of autoimmunity. To find out genes influenced by Tmem11 knockout, we conducted RNA-seq analysis using Th1 cells after re-stimulation.

overall_design: Naive CD4+ T-cells were isolated and purified from either wild-type or TMEM11 KO mice. Naïve CD4+ T cells were enriched by magnetic sorting from single-cell suspensions generated by mechanical disruption of spleens and lymph nodes of adult mice using MagniSort naïve CD4+ T cell enrichment kit (catalog # 8804-6824-74,ThermoFisher Scientific). For effector T cell differentiation, cells were stimulated with anti-CD3 antibody (1452C11, Bio X Cell) and anti-CD28 antibody (Clone 37.51, Bio X Cell) for 48 hours on a plate coated with rabbit anti-hamster antibody (MP Biomedicals). CD4 + CD25 - T cells were cultured with anti-IL-4 antibody (Peprotech) and IL-12 for Th1 differentiation. After detaching from the plate, cells were further cultured for 48 hours and re-stimulated with anti-CD3 and anti-CD28 antibodies. Bulk RNA sequencing analysis was performed to identify transcriptomic changes associated with loss of TMEM11 in Th1 cells.

first: Beibei

last: Wu

first: Spyridon

last: Hasiakos

first: Jinseok

last: Woo

first: Shawn

last: Cokus

first: Matteo

last: Pellegrini

first: Sonal

last: Srikanth


title: T cell populations correlate with response and resistance to anti-PD-1 plus lenvatinib combination therapy in hepatocellular carcinoma

first: Chen

last: Dong

state: Zhejiang

address: Shilongshan Street No.18, Xihu District

institute: Westlake University

summary: The combination of immune checkpoint blockade and tyrosine kinase inhibitors has shown promising clinical benefits, but the underlying mechanisms driving response and resistance are poorly understood. Here, we performed single-cell RNA- and TCR-sequencing, together with a HBV-peptide-barcoded single-cell RNA-sequencing approach, on paired tumor and blood samples to track the dynamic changes of T cells in HBV+ hepatocellular carcinoma (HCC) patients before or after anti-PD-1 plus lenvatinib combination therapy.

overall_design:
We generated scRNA-seq data, scTCR-seq, and dCODE-Dextramer-seq from patients with HBV+ HCC to investigate the dynamics of immune cell subsets durint ICB treatment. Raw sequence data were provided at: China Genomic Sequence Archive (GSA), and we will provide the accession number once the paper is accepted.
--------------------
Authors state:

The raw data have been deposited in China Genomic Sequence Archive (GSA), and the accession number is PRJCA032479:
https://ngdc.cncb.ac.cn/gsa-human/browse/HRA009324
The raw data will be released once GEO data is released for public access.

first: Xinyi

last: Guo

first: Hu

last: Nie

first: Wenwen

last: Zhang

first: Jiesheng

last: Li

first: Jing

last: Ge

first: Bowen

last: Xie

first: Wenbo

last: Hu

first: Yicheng

last: Zhu

last: Zhong

first: Xinmei

first: Xiaohong

last: Zhao

first: Xiaoshuang

last: Wang

first: Qinli

last: Sun

first: Kun

last: Wei

first: Xiaoyuan

last: Chen

first: Ling

last: Ni

first: Ting

first: Shichun

last: Lu

first: Lei


title: Differential unfolded protein response regulation in KRAS silencing sensitive versus innately resistant colorectal cancer cells [SW480 and SW837]

status: Public on Dec 12 2024

city: Porto

first: Flávia

middle: Oliveira

last: Martins

address: Rua Alfredo Allen, 208

country: Portugal

summary: Colorectal cancer (CRC) responses to mutant-selective KRAS inhibitors remain modest, with stable disease and rapid recurrence as the most common outcomes. The molecular mechanisms enabling CRC cells to tolerate KRAS inhibition and ultimately develop resistance remain poorly understood. Here, we investigated early transcriptional and proteomic responses to KRAS silencing in 3D CRC cell line spheroid models, aiming to identify pathways associated with sensitivity or resistance to KRAS blockade. Cell lines were stratified into KRAS silencing-sensitive (HCT116 and SW480) and -resistant (LS174T and SW837) groups based on spheroid growth, cell cycle progression, and apoptosis induction. Transcriptional profiling revealed the unfolded protein response (UPR) and WNT/β-catenin signaling as pathways specifically upregulated in KRAS silencing-sensitive cells and downregulated in resistant cells. Proteomic analysis of membrane-enriched fractions further supported UPR deregulation, showing a pronounced downregulation of translation-related proteins in sensitive cells. Functional assays validated that the sensitive cell line HCT116 exhibits reduced protein aggregation and lower translational capacity upon KRAS knockdown, consistent with UPR activation. Pharmacological inhibition of IRE1α-mediated UPR signaling did not revert KRAS silencing-induced cell cycle arrest or apoptosis in this cell line. Collectively, our results highlight the UPR activation as an early adaptive response of KRAS-dependent CRC cells tolerant to KRAS silencing.

overall_design: To investigate the effect of KRAS inhibition in colorectal cancer cell lines, we used 4 different KRAS mutant colorectal cancer cell lines (HCT116, LS174T, SW480 and SW837). We then silenced cells using siRNA and performed gene expression profilling analysis using data obtained from RNA-seq of the different cell lines from silenced cells (siKRAS) or its control (siControl).

first: Ana

last: Machado

first: Catarina

last: Almeida

first: Joana

last: Carvalho

first: Hans

last: Beck

middle: S

first: Vadim

last: Backman

first: Rune

last: Matthiesen

first: Sérgia

last: Velho


title: Manipulating the lysine-arginine balance for successful therapy of malignant glioma by targeting lysosomal membrane integrity [III]

status: Public on Dec 11 2024

city: Kanazawa

first: Masahiko

last: Kobayashi

address: Kakuma machi

department: Cancer Research Institute

country: Japan

institute: Kanazawa University

summary: To investigate the role of TFE3  induced the transcriptional alterations of glioblastoma cells

overall_design: Total RNA was extracted from glioblastoma cells

first: Yongwei

last: Jing

first: Ha

last: Thi Vu

first: Hiroshi

last: Arakawa

first: Hemragul

last: Sabit

first: Sadahiro

last: Iwabuchi

first: Atsuko

last: Kasahara

first: Masaya

last: Ueno

first: Yuko

last: Tadokoro

first: Kenta

last: Kurayoshi

first: Xi

first: Yuhang

last: Yan

first: Mahmoud

middle: I

last: Shoulkamy

first: Shinichi

last: Hashimoto

first: Tomoyoshi

last: Soga

first: Tomoki

last: Todo

first: Mitsutoshi

last: Nakada

first: Atsushi

last: Hirao


title: Sensory input, sex, and function shape hypothalamic cell type development

city: Cambridge

first: Harris

last: Kaplan

state: MA

address: 16 Divinity Ave., Room 4019

department: MCB

institute: Harvard University

summary: Mammalian behavior and physiology undergo dramatic changes in early life. Young animals rely on conspecifics to meet their needs and start displaying nutritional independence and sex-specific social interactions at weaning and puberty, respectively. How neuronal populations regulating homeostatic functions and social behaviors develop during these transitions remains unclear. We used paired transcriptomic and chromatin accessibility profiling to examine the developmental trajectories of neuronal populations in the hypothalamic preoptic region, where cell types with key roles in physiological and behavioral control have been identified1–6. These data reveal a remarkable diversity of developmental trajectories shaped by the sex of the animal, and the location and behavioral or physiological function of the corresponding cell types. We identify key stages of preoptic development, including early diversification, perinatal emergence of sex differences, postnatal maturation and refinement of signaling networks, and nonlinear transcriptional changes accelerating at the time of weaning and puberty. We assessed preoptic development in various sensory mutants and find a major role for vomeronasal sensing in the timing of preoptic cell type maturation. These results provide novel insights into the development of neurons controlling homeostatic functions and social behaviors and lay ground for examining the dynamics of these functions in early life.

overall_design: To build a transcriptional atlas of POA development, we performed droplet-based paired snRNA-seq and snATAC-seq at nine ages from E14 to P65, using the 10x Multiome kit, separately in males and females. We performed POA multiome sequencing on mutant and littermate control strains as well, focusing on mutants that affect specific sensory modalities, as well as dark-reared animals. In our initial submission to GEO, we are uploading only GEX (i.e. snRNA-seq) data; ATAC-seq data will follow.

first: Catherine

last: Dulac


title: Manipulating the lysine-arginine balance for successful therapy of malignant glioma by targeting lysosomal membrane integrity [II]

first: Masahiko

last: Kobayashi

first: Yongwei

last: Jing

first: Ha

last: Thi Vu

first: Hiroshi

last: Chen


title: Genetic and epigenetic regulation of Treg cell fitness by autism-related chromatin remodeler CHD8

city: Cincinnati

first: Fukun

last: Guo

state: OH

address: 3333 Burnet Avenue

institute: Children's Hospital Medical Center

summary: Chromatin remodeler CHD8 defines a subtype of autism. Its role in regulatory T cells (Tregs) that maintain immune tolerance through suppressing CD4+ and CD8+ effector T cells remain unknown.  In this study, we found that Treg-specific CHD8 deletion led to early, fatal inflammatory disorders, due to increased CD4+ and CD8+ effector T cells. CHD8 deletion increased Treg plasticity as evidenced by elevated effector T cell cytokine expression in Tregs.  CHIP-seq uncovered that CHD8 binding genes were enriched in PI3K-Akt-mTOR signaling and several other pathways. RNA-seq and ATAC-seq revealed that CHD8 deletion upregulated a number of pathways, notably mTORC1 signaling and its mediated glycolysis that have been reported to promote Treg plasticity. Integrating RNA-seq data with ATAC-seq and/or CHIP-seq data indicates that CHD8 regulates gene expression in either chromatin remodeling- and/or CHD8 binding-dependent or -independent manner. Collectively, our findings suggest that CHD8 plays an important role in maintaining Treg fitness via genetic and epigenetic mechanisms.

overall_design: Yang et al. demonstrate that autism-related CHD8 is important for maintaining Treg cell fitness by controlling gene expression and chromatin remodeling in CHD8 binding-dependent or -independent manner.In this study, in order to investigate the effects of CHD8 on Tregs, we conditionally deleted CHD8 in Tregs using the Foxp3-YFP/Cre driver. We found that loss of CHD8 dampened Treg fitness, which was associated with genetic and epigenetic alterations, leading to early, fatal, effector T cell-mediated inflammation. We used RNA-seq, ChIP seq and ATAC seq to investigate the molecular changes upon the Treg disregulation


title: Lysine-arginine imbalance overcomes therapeutic tolerance governed by the transcription factor E3-lysosome axis in glioblastoma

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

overall_design: Refer to individual Series


title: Transcriptomic comparison of long- vs. short-lived C. elegans

status: Public on Dec 09 2024

city: St. Louis

first: Matthew

last: Mosley

state: MO

address: 660 S. Euclid Ave.

department: Developmental Biology

institute: Washington University in St. Louis School of Medicine

summary: Variability in lifespan among individuals of the same species is a poorly understood phenomenon. Even among isogenic C. elegans reared in identical environments, we observe considerable variance in lifepsan. To better understand the differences in gene expression that underly this variability, we characterized the transcriptomes associated with long vs. short lifespan. We isolated the longest- and shortest-lived members from their respective populations using biomarkers of aging--predictive markers whose expression levels correlate with an individual's future lifespan. Specifically, we sorted animals by the expression of lin-4p::GFP, mir-243p::GFP, mir-240/786p::GFP, and autofluorescence. All populations were chronologically five days old at time of sorting. We subsequently compared the transcriptomes of future lifespan within and between different biomarkers to identify a gene expression signature of future lifespan.

overall_design: Transgenic C. elegans strains were grown containing lifespan-predictive biomarkers lin-4p::GFP, mir-243p::GFP, and mir-240/786p::GFP. To sterilize animals, all strains also contained a temperature sensitive mutation in the spermatogenesis gene spe-9. Populations were synchronized by hypochlorite treatment and cultured at the restrictive temperature of 25 degrees C on NGM plates seeded with E. coli OP50. After five days, worms were sorted by the fluorescence intensity of each transgenic biomarker, as well as by autofluorescence in the “red” channel. Between 3-6 sorts were carried out for each biomarker, with “high” and “low” fluorescence defined as the top or bottom tenth percentile relative to the rest of the populations. Animals in these high and low categories were recovered, lysed, and total RNA was collected.

first: Mosley

last: Matthew

first: Kinser

last: Holly

first: Pincus

last: Zachary


title: Manipulating the lysine-arginine balance for successful therapy of malignant glioma by targeting lysosomal membrane integrity [I]

summary: To investigate the role of lysosomal activity induced the transcriptional alterations of glioblastoma cells

last: Arakawa

first: Hemragul

last: Sabit

first: Sadahiro

last: Iwabuchi

first: Atsuko

last: Kasahara

first: Masaya

last: Ueno

first: Yuko

last: Tadokoro

first: Kenta

last: Kurayoshi

first: Xi

first: Yuhang

last: Yan

first: Mahmoud

last: Shoulkamy


title: Maresin-1 promotes neuroprotection in relapsing remitting mouse model of multiple sclerosis

status: Public on Dec 08 2024

city: detroit

first: Shailendra

last: Giri

state: MI

address: 2799 W grand boul

department: Neurology Research

institute: henry ford hospital

summary: Multiple sclerosis (MS) is a prevalent inflammatory neurodegenerative disease in young people, causing neurological abnormalities and impairment. We investigated the effect of maresin 1 (MaR1) on the progression of disease in relapsing remitting form of experimental autoimmune encephalomyelitis (RR-EAE). Treatment with MaR1 in RR-EAE accelerated inflammation resolution, protected against neurological impairments, and delayed disease development by reducing immune cell infiltration (CD4+IL17+ and CD4+IFNg+) into the CNS. Furthermore, injection of MaR1 enhanced IL-10 production, primarily in macrophages and CD4+ cells. However, neutralizing IL-10 with an anti-IL-10 antibody eliminated MaR1's protective impact on RR-EAE, implying that IL-10 plays a role in MaR1's EAE protection. Metabolism is increasingly being recognized as a critical element controlling the effector activity of many immune cells. Our investigation found that, when compared to vehicle treatment, MaR1 administration significantly repaired the metabolic dysregulation seen in CD4+ cells, macrophages, and microglia in the treated group. Furthermore, MaR1 treatment restored defective efferocytosis in EAE mice, which was potentially facilitated by the induction of metabolic alterations in macrophages and microglia. MaR1 also preserved myelin in the EAE group and regulated O4+ oligodendrocyte metabolism by reversing metabolic dysregulation via increased mitochondrial activity and decreased glycolysis. Overall, in a preclinical MS animal model, MaR1 therapy has anti-inflammatory and neuroprotective properties. It also induced metabolic reprogramming in disease-associated cell types, increased efferocytosis, and maintained myelination. These findings suggest MaR1's potential as a novel therapeutic agent for MS and other autoimmune diseases

overall_design: To investigate the role of MaR1 in preclinical animal model of multiple sclerosis (EAE), the SJL model was used. We then performed RNA-seq gene expression profiling analysis using data obtained from RNA-seq of CFA, EAE, and MaR1.


title: DNA methylation dynamics play crucial roles in shaping the distinct transcriptomic profiles for different root-type initiation in rice

status: Public on Dec 04 2024

first: shaoli

last: zhou

state: Hubei

address: shizishan street

department: National Key Laboratory of Crop Genetic Improvement

institute: Huazhong Agricultural University

type: Methylation profiling by high throughput sequencing

summary: Monocots possess a fibrous root system comprising an embryonic root (ER), crown roots (CR), and lateral roots (LR), which share striking similarities in adult anatomical structures and functions across the three root types. Nonetheless, their distinct cellular origins highlight the diversity of the initiation mechanism. Through our study, we conducted a comprehensive transcriptome and DNA methylome assay of these root types during their initiation. Our findings indicated significant divergence in transcriptome regulation trajectories with apparent transcriptional activation in post-embryonic root initials (CR and LR) contrasted by suppression in embryonic root (ER) generation. Additionally, CHH methylation was found dynamically and differentially regulated across the initiation stages of the various root types, and significantly associated with the short transposon element within the promoter regions of functional genes, which played crucial roles in determining the genes’ spatiotemporal transcription. Moreover, our work revealed that the activation of DNG702 and repression of DRM2 played important roles in the erasure of CHH methylation and activation of functional genes during the processes, such as a novel identified key regulatory bZip65, thus directly impacting the initiation of post-embryonic roots in rice. In conclusion, our extensive analysis delineates the landscapes of spatiotemporal transcriptomes and DNA methylomes during the initiation of the three root types in rice, shedding light on the pivotal role of CHH methylation in the spatiotemporal regulation of various key genes, ensuring the successful initiation of distinct root types in rice.

overall_design: RNA-seq and BS-seq data of four stages of rice crown, lateral, embryonic root initials derived from laser microdissection, two biological replicates were represented for each sample.

first: Zhou

last: Zhou

first: Shaoli