title: The mitophagy receptor BNIP3 is critical for the regulation of metabolic homeostasis and mitochondrial function in the nucleus pulposus cells of the intervertebral disc

city: Philadelphia

first: Makarand

last: Risbud

state: Pennsylvania

address: Walnut 1025, College Building, Suite 511

department: Orthopaedic Surgery

institute: Thomas Jefferson University

summary:
Transcriptional analysis of BNIP3-knockdown rat NP cells and ShRNA control cells
The transcriptomic analysis of the BNIP3-deficient cells showed dysregulation of cellular functions including membrane and cytoskeletal integrity, ECM-growth factor signaling, protein quality control with an overall increase in themes related to angiogenesis and innate immune response.

overall_design: The nucleus pulposus (NP) was harvested from the intervertebral discs of 3-4 month old rat. The cells were transduced with BNIP3, lentiviral particle or control ShRNA pLKO.1  after 4 days cells were collected for RNA extraction and hybridization using Affymetrix microarray.

first: Vedavathi

last: Madhu


title: CRISPR GENome and Epigenome Engineering (CRISPRgenee) improves loss-of-function genetic screening approaches

status: Public on May 05 2025

city: Stuttgart

first: Philipp

last: Rathert

state: Germany

address: Allmandring 31

department: Biochemistry

country: Germany

institute: University Stuttgart

summary: The CRISPR/Cas9 technology has revolutionized genotype-to-phenotype assignments through large-scale loss-of-function (LOF) screens. However, limitations like editing inefficiencies and unperturbed genes cause significant noise in data collection. To address this, we introduce CRISPR Gene and Epigenome Engineering (CRISPRgenee), which uses two specific sgRNAs to simultaneously repress and cleave the target gene within the same cell, increasing LOF efficiencies and reproducibility. CRISPRgenee outperforms conventional CRISPRko, CRISPRi, or CRISPRoff systems in suppressing challenging targets and regulators of cell proliferation. Additionally, it efficiently suppresses modulators of epithelial-to-mesenchymal transition (EMT) and impairs neuronal differentiation in a human induced pluripotent stem cell (iPSC) model. CRISPRgenee exhibits improved depletion efficiency, reduced sgRNA performance variance, and accelerated gene depletion compared to individual CRISPRi or CRISPRko screens, ensuring consistency in phenotypic effects and identifying more significant gene hits. By combining CRISPRko and CRISPRi, CRISPRgenee increases LOF rates without increasing genotoxic stress, facilitating library size reduction for advanced LOF screens.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: To investigate the benefitial effect when screening using CRISPRgenee we performed a dropout loss-of-function screen in TF-1 cells. Cells were transduced with a dual sgRNA library targeting 1137 genes involved in epigenetic regulation and cultivated for 14 days (~4 splits). To investigate if truncating a sgRNA to the length of 15 nt does not induce DNA cleavage we transduced ZIM3-Cas9 expressing cells with full length and truncated sgRNAs targeting either CD13 or CD33, measured depletion of CD13 and CD33 and harvested the cells after 14 days. The genomic DNA was isolated and the region where the sgRNA should cut was amplified via PCR while simultaneously adding illumina adapter sequences.The amplicon was sequenced and the amount of InDels calculated for the truncated and normal lengths sgRNA as well as for a non-targeting sgRNA control. To investigate the off-target effects when truncating an sgRNA to 15 nt we designed two sgRNAs targeting CD33 and performed RNA sequencing on cells co-expressing CRISPRgate and one of the sgRNAs either full length or  truncated.

first: Jannis

last: Stadager

first: Chiara

last: Bernardini

first: Laura

last: Hartmann

first: Henrik

last: May

first: Jessica

last: Wiepcke

first: Monika

last: Kuban

first: Zeynab

last: Najafova

first: Steven

middle: A

last: Johnsen

first: Stefan

last: Legewie

first: Franziska

middle: R

last: Traube

first: Julian

last: Jude


title: Induced loss of TREX1 in host cells inflames the tumor micromilieu and invigorates CTL-mediated cancer control

status: Public on May 04 2025

city: Heidelberg

first: Axel

last: Roers

address: Im Neuenheimer Feld 305

department: Immunologie

institute: Universitätklinikum Heidelberg

type: Expression profiling by high throughput sequencing

summary: Activation of local innate immunity in tumor tissue, aiming at induction of adaptive responses, is a major concept in cancer immunotherapy. The cGAS/STING pathway triggers type I IFN and pro-inflammatory cytokine responses upon detection of cytosolic DNA and can robustly enhance anti-tumor immunity. The DNase 3’ repair exonuclease 1 (TREX1) is a central component of cellular DNA disposal preventing accumulation of endogenous DNA in the cytosol, activation of cGAS and cell-intrinsic innate immune responses. While constitutive TREX1-deficiency causes severe mendelian autoimmunity, temporary pharmacological inhibition of the enzyme may represent an efficient means to activate anti-tumor immunity. Induced inactivation of the Trex1 gene in mice (TREX1 iKO) resulted in improved immune control of established syngeneic tumors that was type I IFN- and CD8+ T cell-dependent. This was associated with a dramatic increase of immune cell infiltration of tumor tissue while other (non-tumor) tissues were not or marginally affected. TREX1 iKO triggered an inflammatory switch of intra-tumoral monocyte, macrophage and dendritic cell populations, associated with enhanced antigen presentation capacity. Invigoration of CD8 T cell responses was reflected in robust increase in cells differentiating along the exhaustion trajectory but expressing significant signatures of effector function. Combination of TREX1 iKO with immune checkpoint inhibition synergistically promoted tumor control. In addition to improved anti-tumor immunity upon loss of TREX1 in host cells, we also show that cancer cell-specific TREX1 deficiency synergizes with irradiation and checkpoint inhibition to enable tumor rejection and formation of long-term memory. We conclude that pharmacological TREX1 inhibition is a promising therapeutic approach to boost anti-tumor immunity.

overall_design: To illustrate how the Trex1 knockout-induced immune response regulates tumor growth, an inducible Trex1 knockout mouse model bearing syngeneic melanoma B16 tumors was used to generate the single cell RNAseq data of tumor-infiltrating-Immune cells.

first: Emilija

last: Marinkovic

first: Minyi

last: Chen

first: Nadja

last: Schubert

first: Elif

last: Dogan Dar

first: Tanja

last: Poth

first: Janet

middle: Y

last: Leung

first: Jack

last: Lohre

first: Jennifer

middle: M

last: Sahni

first: Christine

last: Tun

first: Pavithra

last: Rajeswaran

last: Mehlo-Jensen

first: Olivia

last: Perng

first: Mark

middle: C

last: Hill

first: Pallavur

last: Sivakumar

first: Michael

last: Barnes

first: Rohit

last: Malik

first: Rayk

last: Behrendt


title: Control of citrate utilization by Candida albicans Adr1

city: Athens

first: Amelia

last: White

state: GA

address: 120 E Green Street

department: Microbiology

country: USA

institute: University of Georgia

summary: Opportunistic fungal pathogen Candida albicans often encounters host niches where it must survive on alternative carbon sources alone. In Saccharomyces cerevisiae, transcription factor Adr1 activates genes required for acetate and glycerol utilization. However, previous researchers found that CaADR1 deletion mutants have robust growth on acetate and glycerol. We have found that Adr1 is required for growth on citrate. This phenotype is manifested among multiple strains isolated from all known host niches. RNA sequencing analyses of adr1Δ/Δ and wild-type strains show that Adr1 is required for expression of genes within the TCA cycle and gluconeogenesis. Major targets include enzymes Mdh1 and Pck1. Unexpectedly, one of the most downregulated genes is not within the central metabolic pathway. HGT17 is a putative glucose transporter. Phenotypic analyses support the hypothesis that Hgt17 is able to transport citrate.

overall_design: RNA-seq profiling of WT C. albicans cells and their knockdown derivatives (adr1ΔΔ and hgt17ΔΔ). Cells were grown for 4h at 37 degrees in either YNB+1% citrate or YNB + 1% acetate

first: Amelia M

first: Aaron P

last: Mitchell


title: Transcriptomic profiles of Penicillium citrinum growing on tobacco leaves

city: Hangzhou

first: Shenghua

last: Ying

state: Zhejiang

address: Yu-hang-tang Road 688

country: China

institute: Zhejiang University

summary: The saprotrophic fungus P. citrinum is a dorminant leaf-degrading fungus in tobacco industry.  The genome-wide exprssion analysis involved in fungal growth was analyzed by using high throughput sequencing (RNA-Seq) on two substrates and time points. Our transcriptional profiles revealed that numerous differentially expressed genes (DEGs), of which involved in metabolism, cell transport and cell rescue, were significantly involved in tobacco-degradation process of  P. citrinum.

overall_design: Comparison was conducted among total RNA obtained from P. citrinum grown on different substrates and time points.

first: Sheng-Hua

first: Bo-Ka

last: Xiang


title: A coordinated cellular network regulates tolerance to food

city: Rehovot

first: Anna

last: Rudnitsky

department: Systems Immunology

country: Israel

institute: Weizmann Institute

summary: To absorb nutrients and support commensal microbes, the host induces tolerogenic immune responses via peripheral regulatory T cells (pTregs) . Prior studies identified type 1 dendritic cells (cDC1) as initiators of dietary pTregs. However, we now report that food-specific pTreg cells are exclusively induced by the recently identified RORγt APCs and not by cDCs. Instead, our data suggest that pTreg–cDC1 interactions in steady-state limit the expansion of food-specific CD8αβ T cells. This regulation breaks during infection or food poisoning, enabling dietary CD8αβ T cells to expand and acquire effector functions in response to mimicked food antigens. Unlike in typical infections, after the pathogen is cleared, dietary CD8αβ T cells do not expand in response to their corresponding dietary antigens. Thus, we propose that in response to dietary antigens, tolerance is mediated by a circuit of dedicated antigen-presenting cells (APCs) and T cells. When the host is challenged by infection, this circuit permits the transient expansion of protective effector responses without compromising the overall strategy of tolerance that ensures safe food consumption.

overall_design: C57BL66 week old female mice were either fed OVA or just PBS by gavage and later infected with Listeria expressing OVA (LmOVA). Small intestine lamina propria was extracted and used for analysis.

first: Hanna

last: Oh

first: Inbar

last: Shteinberg

first: Maya

last: Margolin

first: Ranit

last: Kedmi


title: Induction of the ISR by AB5 subtilase cytotoxin drives type-I IFN expression in pDCs via STING activation

city: Paris

first: Mickael

middle: Mathieu

last: Menager

address: 24 Boulevard du Montparnasse

country: France

institute: Institut Imagine

summary: We demonstrate that exposure to the Shiga AB5 subtilase cytotoxin (SubAB) induces the unfolded protein response (UPR) in human peripheral blood mononuclear cells, concomitant with a pro-inflammatory response across distinct cell subsets. Notably, SubAB selectively induces type-I interferon (IFN) expression in plasmacytoid dendritic cells, acting synergistically with Toll-like receptor 7 stimulation. The induction of type-I IFN in response to SubAB relies on stimulator of interferon genes (STING) activation, coupled with protein synthesis inhibition mediated by protein kinase R-like endoplasmic reticulum kinase and phosphorylation of the eukaryotic translation initiation factor 2 subunit-alpha. By impeding mRNA translation through the integrated stress response, SubAB precipitates the downregulation of the negative innate signaling feedback regulator Tax1-binding protein 1. This downregulation is necessary to unleash TANK-binding kinase 1 signaling associated with STING activation. These findings shed new light on how UPR-inducing conditions may regulate the immune system during infection or pathogenesis.

overall_design: To comprehensively study the impact of SubAB on human cells, we performed single-cell transcriptomics analysis of human Peripheral blood mononuclear cells ( PBMCs) submitted to different stimulatory conditions, including 6 h of SubAB (1 mg/ml) exposure and/or TLR7 stimulation with the adenine analog CL307 (1mM). Samples are mock treated (NT), SubAB-treated (Toxin), CL307-treated (CL307) or both (CL307-Toxin)

first: Daniela

last: Barros

first: Philippe

last: Pierre

first: Beatriz

last: H Ferreira

first: Mickaël

last: Ménager

first: Francesco

last: Carbone


title: Mapping the genetic landscape establishing a tumor immune microenvironment favorable for anti-PD-1 response in mice and humans.

city: Bar Harbor

first: Daniel

last: Skelly

state: ME

address: 600 Main St

institute: Jackson Laboratory

summary: Identifying host genetic factors modulating immune checkpoint inhibitor (ICI) efficacy has been experimentally challenging because of variations in both host and tumor genomes, differences in the microbiome, and patient life exposures. Utilizing the Collaborative Cross (CC) multi-parent mouse genetic resource population, we developed an approach that fixes the tumor genomic configuration while varying host genetics. With this approach, we discovered that response to anti-PD-1 (aPD1) immunotherapy was significantly heritable in four distinct murine tumor models (H2 between 0.18-0.40). For the MC38 colorectal carcinoma system (H2 = 0.40), we mapped four significant ICI response quantitative trait loci (QTL) localized to mouse chromosomes (mChr) 5, 9, 15 and 17, and identified significant epistatic interactions between specific QTL pairs. Differentially expressed genes within these QTL were highly enriched for immune genes and pathways mediating allograft rejection and graft vs host disease. Using a cross species analytical approach, we found a core network of 48 genes within the four QTLs that showed significant prognostic value for overall survival in aPD1 treated human cohorts that outperformed all other existing validated immunotherapy biomarkers, especially in human tumors of the previously defined immune subtype 4. Functional blockade of two top candidate immune targets within the 48 gene network, GM-CSF and high affinity IL-2/IL-15 signaling, completely abrogated the MC38 tumor transcriptional response to aPD1 therapy in vivo. Thus, we have established a powerful cross species in vivo platform capable of uncovering host genetic factors that establish the tumor immune microenvironment configuration propitious for ICI response.

overall_design: In this study we investigated variation in responsiveness to anti-PD-1 using a model where we implanted the MC38 colorectal cancer cell line in genetically diverse host mice. To quantify differences in gene expression between tumors from responder and non-responder lines,we profiled four tumors from each of three responder lines and three non-responder lines. Of the four tumors from each line, two were treated with anti-PD-1 and two were treated with isotype control antibody.

first: John

middle: P

last: Graham

first: Edison

middle: T

last: Liu


title: KIF2A stabilises intercellular bridge microtubules to maintain mouse embryonic stem cell cytokinesis

status: Public on May 06 2025

city: Rotterdam

first: Niels

last: Galjart

department: Cell Biology

country: Netherlands

institute: Erasmus University Medical Centre

summary: Cytokinesis, the final stage of cell division, serves to physically separate daughter cells. In cultured naïve mouse embryonic stem cells cytokinesis lasts unusually long. Here, we describe a novel function for the kinesin-13 member KIF2A in this process. In genome-engineered mouse embryonic stem cells we find that KIF2A localises to spindle poles during metaphase and regulates spindle length in a manner consistent with its known role as microtubule minus-end depolymerase. By contrast, during cytokinesis we observe tight binding of KIF2A to intercellular bridge microtubules. At this stage KIF2A maintains microtubule length and number, and controls microtubule acetylation. We propose that the conversion of KIF2A from a depolymerase to a stabiliser is driven both by the inhibition of its ATPase activity, which increases lattice affinity, and a preference for compacted lattices. In turn, KIF2A might maintain the compacted microtubule state at the intercellular bridge, thereby dampening acetylation. As KIF2A depletion causes pluripotency problems and affects mRNA homeostasis our results furthermore indicate that KIF2A-mediated microtubule stabilisation prolongs cytokinesis to maintain pluripotency.

overall_design: RNA-Seq of mRNA derived from mouse ES cells (mESCs). We compared RNA isolated from wild-type (WT) mESCs with RNA isolated from two independently edited Kif2a knockout lines, in which the Kif2a gene was removed (KO1 and KO2). RNA-Seq libraries were prepared from triplicate samples of the lines.


title: Mapping the genetic landscape establishing a tumor immune microenvironment favorable for anti-PD-1 response in mice and humans (RNA-Seq II).


title: Mapping the genetic landscape establishing a tumor immune microenvironment favorable for anti-PD-1 response in mice and humans (RNA-Seq I).


title: Epigenomic profiling of active regulatory elements by enrichment of unmodified CpG dinucleotides

city: Birmingham

first: Robert

last: Neely

address: 97 Vincent Drive

country: United Kingdom

institute: Tagomics LTD

type: Methylation profiling by high throughput sequencing

summary: In this study we present an enrichment-based and bisulfite-free approach for epigenomic profiling named ‘Active-Seq’ (Azide Click Tagging for In Vitro Epigenomic sequencing) that achieves genome-wide profiling of DNA, by enriching for non-modified CpG sites using a mutated methyltransferase enzyme. Active-Seq is a fast epigenetic profiling platform with a simple and streamlined workflow, performed in tandem with sequencing library preparation. The enzymatic chemistry is non-damaging toward the DNA which is critical for working with low concentration DNA input and will facilitate the future development of multiomics assays.

overall_design:
In order to compare Active-seq to orthogonal technologies, we performed Active-seq and MeDIP-seq on DNA derived from GM12878 cell line and compared the processed signal.

In order to measure the reproducibility of the Active-Seq assay, we performed Active-Seq in three replicates in the following cell lines: MCF7, HEPG2, SW48, HT29, HCC1937.

first: Luca

last: Tosti

first: Calum

last: Mould

first: Imogen

last: Gatehouse

first: Anyela

last: Camargo

first: Anthony

last: Smith

first: Krystian

last: Ubych

first: Jack

last: Kennefick

first: Peter

middle: W

last: Laird

middle: K


title: CD4+ T cells license Kupffer cells to reverse the CD8+ T cell dysfunction induced by hepatocellular priming

status: Public on May 03 2025

city: Milano

first: Pietro

last: Delfino

address: Via Olgettina 58

country: Italy

institute: San Raffaele Scientific Institute

summary: CD4⁺ T cells are believed to be essential for effective CD8⁺ T cell responses against hepatotropic viruses like hepatitis B virus (HBV). However, the specific locations and the cellular and molecular mechanisms through which CD4⁺ T cells help CD8⁺ T cells remain unclear. In this study, we generated HBV-specific CD4⁺ TCR transgenic mice to demonstrate that effector CD4⁺ T cells can prevent or reverse the dysfunction of CD8⁺ T cells caused by hepatocellular priming. This, in turn, enhances CD8⁺ T cell effector function and suppresses viral replication. Notably, CD4⁺ T cell help to CD8+ T cells occurs directly in the liver, independent of secondary lymphoid organs, and requires local antigen recognition but not epitope linkage. While dendritic cells were found to be dispensable, Kupffer cells (KCs) emerged as the critical cellular platform for this effect. Mechanistically, CD4⁺ T cells engage KCs via CD40-CD40L interactions, leading to the production of IL-12 and IL-27. IL-12 promotes further CD4⁺ T cell expansion, whereas IL-27 serves as the key cytokine that restores CD8⁺ T cell functionality. Furthermore, we show that exogenous IL-27 administration can reverse HBV-specific CD8⁺ T cell dysfunction in mice and in chronically infected patients. These findings reveal a novel mechanism of CD4⁺ T cell help to CD8⁺ T cells that occurs outside secondary lymphoid organs, specifically in the liver, and involves antigen-presenting cells other than conventional dendritic cells, offering new insights for immunotherapeutic strategies against chronic HBV infection.

overall_design: We generated an HBV-specific CD4+ TCR transgenic (Tg) mouse model. Wild-type (WT) mice were immunized with the I-Ab-restricted immunodominant Env126-138 peptide from the preS2 region of the HBV genome. After immunization, we isolated splenocytes and restimulated them ex vivo with the Env126-138 peptide. Single-cell sorting and TCR sequencing of IFN- producing CD4+ T cells identified two distinct variable TCR region genes for the alpha and beta chains. These genes were cloned into TCR expression vectors known for efficient TCR gene expression. The vectors were co-injected into fertilized C57BL/6 eggs, generating two transgenic mouse lines expressing the alpha and beta chains of the Env126-138 TCR. These lines were crossbred to produce HBV-specific CD4+ TCR transgenic mice (referred to as Env126 mice).

first: Valentina

last: Venzin

first: Cristian G.

last: Beccaria

first: Chiara

last: Perucchini

first: Elisa

last: Bono

first: Leonardo

last: Giustini

first: Federica

last: Moalli

first: Marta

last: Grillo

first: Valeria

last: Fumagalli

last: Laura

last: Di Lucia

first: Katharina

last: Reinhard

first: Jutta

last: Petschenka

first: Tana Annmarie

last: Omokoko

first: Sabrina

last: Ottolini

first: Anna

last: Celant

first: Keigo

last: Kawashima

first: Micol

last: Ravà

first: Marco

last: De Giovanni

first: Donato

last: Inverso

first: Mirela

last: Kuka

first: Patrick T. F.

last: Kennedy

first: Martin

last: Guilliams

first: Giulia

last: Casorati

last: Pedica

first: Maurilio

last: Ponzoni

first: Uğur

last: Şahin

first: Nina

last: Le Bert

first: Antonio

last: Bertoletti

first: Fulvia

last: Vascotto

first: Luca G.

last: Guidotti

first: Matteo

last: Iannacone


title: Transcriptomic profile in in vitro produced mouse morula stage embryos treated with siRNA targeting Pwp1

city: Kyoto

first: Shinnosuke

last: Honda

address: Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto-shi

country: Japan

institute: Kyoto University

summary: We obtained transcriptomic profiles in mouse morula stage embryos (72 h post-insemination (hpi)) which had been in vitro treated with siRNA targeting Pwp1 from one-cell stage (3 hpi).

overall_design: In vitro produced mouse morula stage embryos were processed to RNA-Seq. The experiments were duplicated using ten embryos per group.

first: Takuto

last: Yamamoto

first: Atsushi

last: Takasu

first: Yasuhiro

last: Isumi

first: Satoshi

last: Mashiko

first: Daiki

last: Shikata

first: Naojiro

last: Minami

first: Shuntaro

last: Ikeda


title: A Dominant mutation in Dnmt1 leads epigenetic changes (rrbs)

city: los angeles

first: Guoping

last: Fan

state: ca

address: 695 Charles E Young Drive South

department: Human Genetics

institute: university of california, los angeles

summary: We report the application of Enzymatic Methyl-seq in the prefrontal cortex from the Dnmt1 A560V mice

overall_design: Examination the epigeneitc changes and gene expression changes due to Dnmt1 mutation

first: Jing

last: Wang


title: Glomerular Haematopoietic Prostaglandin D Synthase‐Prostaglandin D2 Axis Contributes to the Periodontitis‐Related Exacerbation of Diabetic Nephropathy in KK‐Ay Mice

city: Fukuoka

first: Takanori

last: Shinjo

state: fukuoka

address: Maidashi 3-1-1

department: Section of Periodontology

institute: Kyushu University

summary: Diabetic nephropathy (DN) is the leading cause of dialysis and is associated with cardiovascular diseases. To prevent the progression of DN, not only glycemic control but also intervention to exacerbating factors such as chronic inflammation and infection. Recent clinical studies have shown the possible association between chronic kidney disease including DN, and periodontitis. However, the causal relationship that periodontitis could contribute to the progression of DN and its molecular mechanisms has not been understood. In the present study, we investigated ligature-induced experimental periodontitis that might exacerbate glomerular pathology in a DN model KK-Ay mice and the underlying molecular mechanisms. KK-Ay mice with experimental periodontitis showed significantly increased urinary albumin to creatinine ratio, and glomerular pathologies such as glomerular size, mesangial expansion area, fibrotic area, and number of CD68-positive leukocytes compared to those without ligatures. RNA-sequencing in the glomeruli revealed that hematopoietic prostaglandin d2 synthase (Hpgds) was the possible factor bridging periodontitis with the progression of DN. We also found that Hpgds expression was significantly upregulated by hyperglycemia and inflammatory stimuli in mesangial cells. Prostaglandin D2 enhanced hyperglycemia-induced collagen expression in mesangial cells and downregulated the tight junction in renal endothelial cells. Lastly, oral administration with an HPGDS inhibitor HQL-79 successfully prevented the progression of DN in KK-Ay mice by experimental periodontitis. Taken together, experimental periodontitis might contribute to the progression of DN via acceleration of glomerular pathology by upregulation of HPGDS in mesangial cells.

overall_design:
Male KK-Ay and C57 BL/6 mice at 13 weeks old were placed 6-0 silk ligatures around the maxillary second molars for 3 weeks. 16 weeks old mice were sacrificed to isolate glomeruli fractions from their kidneys and RNA were extracted from them using RNA extraction kit (PureLink).
We then performed RNA-seq using glomerular RNA from C57BL/6, C57BL/6 with experimental periodontitis, KK-Ay, and KK-Ay with experimental periodontitis. Comparative gene expression analysis among 4 groups were performed.

first: Kohei

last: Sato

first: Tatsuro

last: Zeze

first: Al-kafee

last: Ahmed

first: Honoka

last: Otsuka

first: Hisashi

last: Yokomizo

first: Naoichi

first: Mio

last: Imagawa

first: Yuki

last: Nishimura

first: Naoaki

last: Ryo

first: Akiko

last: Yamashita

first: Takao

last: Fukuda

first: Terukazu

last: Sanui

first: Misaki

last: Iwashita

first: Fusanori


title: Mitotic chromosome condensation resets chromatin to maintain post-anaphase transcriptional homeostasis (RNA-Seq III)

city: Oslo

first: Pierre

last: Chymkowitch

address: Blindernveien 31

department: Biosciences

country: Norway

institute: University of Oslo

summary: Mitotic entry correlates with remodeling of histone modifications, chromatin condensation, exclusion of transcription factors from the DNA and broad downregulation of transcription. However, whether mitotic condensation also influences interphase transcription is a question that has not been addressed yet. In this study, we reveal that loss of mitotic chromatin condensation results in a dramatic and spontaneous recruitment of the transcription machinery and unscheduled initiation of gene expression. This includes activation of inducible transcriptional programs, which occurs even in absence of relevant stimuli, such as the GAL system. Strikingly, such an erratic gene expression goes on after exit from mitosis. Thus, we reveal a novel function of mitotic chromosome condensation, i.e. resetting the transcriptome to prevent gene expression from drifting and maintain transcriptional homeostasis during interphase.

overall_design: ChIPseq time-course experiment in CEN4 and CEN4* cells at 0, 30, 60, 120 and 180 minutes after the addition of beta-estradiol. Two independent experiments, 6 antibodies, total of 130 samples including INPUTs. In the CEN4 control strain, the centromere of Chromosome IV is not flaked with lox site. When the centromere of chromosome IV is flanked by lox recombination sites, it is referred to as CEN4* before excision and cen4- after excision by the Cre recombinase.

first: Lucía

last: Ramos-Alonso

first: Petter

last: Holland

first: Xu

last: Zhao

first: Stephanie

last: Le Gras

first: Bernard

last: Jost

first: Magnar

last: Bjørås

first: Yves

last: Barral

first: Jorrit

last: Enserink


title: Autoreactive effector Treg cells with a compromised regulatory program in patients with coronary artery disease

city: Augusta

first: Klaus

last: Ley

state: Georgia

address: 1410 Laney Walker Blvd

department: Immunology Center of Georgia

institute: Augusta University

summary: Atherosclerosis, a pathological condition underlying cardiovascular diseases, involves chronic inflammation with a strong autoimmune component. Detailed molecular definition of autoreactive CD4+T cells in atherosclerotic patients is critical for understanding their role in disease pathogenesis. Apolipoprotein B (APOB) is a clinically relevant atherosclerosis-related autoantigen. Here, we used an activation-induced marker assay to conduct deep transcriptomic analyses of circulating APOB-reactive CD4+T cells from 40 patients with coronary artery disease. We identified autoreactive T cells expressing tissue-homing chemokine receptors and effector Treg signatures, suggesting recirculation of APOB-specific CD4+T cells between blood and atherosclerotic plaques. Treg gene signature and oligoclonality peaked in patients with mild disease, but declined in those with severe atherosclerosis. By contrast, clonal expansion and expression of effector molecules in inflammatory APOB-specific CD4+T cells increased with progressing disease severity. Thus, the autoimmune response in atherosclerosis starts with an atheroprotective regulatory program but switches to an inflammatory phenotype, likely accelerating disease progression.

overall_design: Low input Smartseq-2-based bulk RNA-seq of sorted APOB-reactive and control human CD4+T cells from patients with coronary artery disease

first: Payel

last: Roy

first: Sujit

middle: S

last: Suthahar

first: Mohammad

last: Oliaeimotlagh

first: Jeffrey

last: Makings

first: Runpei

last: Wu

first: Qingkang

last: Lyu

first: Smriti

last: Parashar

first: Anusha

last: Bellapu

first: Sunil

last: Kumar

first: Megh

last: Mehta

first: Austin

last: Chiang

first: Alessandro

last: Sette

first: Coleen

last: McNamara


title: Microarray analysis in the thalamus of mouse exposed to pain-stimulated ultrasound vocalizations

city: Noda

first: Satoka

last: Kasai

state: Chiba

address: 2641, Yamazaki

institute: Tokyo University of Science

summary: In this study, sounds in the ultrasonic domain that were recorded during pain stimulation in mice were used as sound stress to examine the effects of psychological stress caused by exposure to ultrasound on tactile thresholds. DNA microarray analysis of the mouse thalamus exposed to sound stress revealed increased expression of inflammation-related genes, Ptgs2 and Cxcl1. Their respective inhibitors, loxoprofen and SB225002, significantly improved hyperalgesia induced by sound stress.

overall_design: Two-condition experiment, The thalamus of the control mouse vs. the thalamus of the mouse exposed to pain-stimulated ultrasound vocalizations. Biological replicates: 1 control replicates, 1 exposed to sound replicates.

first: Kazumi

last: Yoshizawa


title: A Dominant mutation in Dnmt1 leads epigenetic changes (Emseq)

first: Guoping

last: Fan

first: Jing

last: Wang


title: Comparative analysis of mouse strains for in vivo induction of reprogramming factors

city: Lausanne

first: Alejandro

last: Ocampo

address: Rue du Bugnon 27

country: Switzerland

institute: University of Lausanne

summary: In vivo reprogramming through the forced expression of Oct4, Sox2, Klf4, and c-Myc (OSKM) has demonstrated great potential for reversing age-associated phenotypes, as the combination of these transcription factors actively promote cell regeneration and rejuvenation in various tissues and organs. However, continuous in vivo OSKM expression raised safety concerns due to loss of cell identity, decrease in body weight, and premature death. Although cyclic short-term or targeted expression of the reprogramming factors can mitigate some of these detrimental effects in mice, systemic rejuvenation of wild type mice has remained elusive potentially due to these current technical limitations. To improve the fundamental understanding of in vivo reprogramming, we conducted a comparative analysis across multiple reprogrammable mouse strains, tissues, and expression methods, presenting a comprehensive atlas of formerly established strains. In addition, we developed novel reprogrammable mouse strains by avoiding OSKM expression in specific organs, in dividing cells, or implementing chimeric expression approaches within specific cells, thereby offering safer strategies to induce in vivo reprogramming and fully harness its potential. We hope that these new tools will become valuable resources for future research in this very exciting field of research with potential implications to human health.

overall_design: Comparative gene expression profiling analysis across multiple reprogrammable mouse strains and tissues. 5 mouse genotypes: control: WT and reprogrammable strains: 4Fj, 4FsB, 4Fk, 4FsA. Tissues analyzed: Liver, Small intestine, Kidney, Heart, Brain, Skeletal muscle, Spleen (only WT, 4Fj and 4FsA). 2 month-old mice.


title: Mitotic chromosome condensation resets chromatin to maintain post-anaphase transcriptional homeostasis (RNA-Seq II)

first: Pierre

last: Chymkowitch

overall_design: RNAseq of mCh* strain with loxed mCherry. Addition of beta-estradiol triggers the excision of mCh* (mCh-). cells at 0  and 180 minutes after the addition of beta-estradiol. Three independent experiments, total of 6 samples.

first: Lucía

last: Ramos-Alonso

first: Petter

last: Holland

first: Xu

last: Zhao

first: Stephanie

last: Le Gras

first: Bernard

last: Jost

first: Magnar

last: Bjørås

first: Yves

last: Barral

first: Jorrit

last: Enserink


title: Mitotic chromosome condensation resets chromatin to maintain post-anaphase transcriptional homeostasis (RNA-Seq I)

overall_design: RNAseq time-course experiment in CEN4 and CEN4* cells at 0, 30, 60, 120 and 180 minutes after the addition of beta-estradiol. Three independent experiments, total of 30 samples. In the CEN4 control strain, the centromere of Chromosome IV is not flaked with lox site. When the centromere of chromosome IV is flanked by lox recombination sites, it is referred to as CEN4* before excision and cen4- after excision by the Cre recombinase.


title: Mapping the genetic landscape establishing a tumor immune microenvironment favorable for anti-PD-1 response in mice and humans (Visium).

first: Daniel

last: Skelly

first: John

last: Graham

first: Edison

last: Liu


title: Mitotic chromosome condensation resets chromatin to maintain post-anaphase transcriptional homeostasis

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Mitotic chromosome condensation resets chromatin to maintain post-anaphase transcriptional homeostasis (ATAC-Seq)

overall_design: ATACseq experiment in CEN4 and CEN4*cells at 0 and 180 minutes after the addition of beta-estradiol. Two independent experiments, total of 8 samples. In the CEN4 control strain, the centromere of Chromosome IV is not flaked with lox site. When the centromere of chromosome IV is flanked by lox recombination sites, it is referred to as CEN4* before excision and cen4- after excision by the Cre recombinase.


title: A proinflammatory response and polarized differentiation of stromal elements characterizes the murine myeloma bone marrow niche

status: Public on May 02 2025

city: New York

first: Gareth

last: Morgan

address: 550 1st Avenue

institute: NYU Langone Health

summary: To address the role of the non-hematopoietic bone marrow (BM) niche in multiple myeloma (MM) pathogenesis, we utilized the 5TGM1 murine model. During the asymptomatic precursor stage of the model, we isolated the rare non-hematopoietic cells and performed single-cell RNA sequencing. Using in-silico methods, we characterized the individual cellular components of the niche, their relative abundance, and differentation state both before and after exposure to MM cells, as well as their intercellular interactions. MM cells impact the BM niche by generating a pro-inflammatory microenvironment with MSC differentiation being changed away from osteocyte formation and towards adiopcytes, which helps to generate cell subsets that favor MM growth and survival.

overall_design: KalwRij mice were injected with 5TGM1 murine MM cells and BM stromal cells were enriched by FACS sorting. 10x single-cell libraries were generated, pooled libraries were sequenced on a Novaseq 6000, and gene expression count matrices were generated using cellranger v5. Single-cell RNA analysis was performed in R using Seurat.

first: Ghamlouch

last: Hussein

first: Gagler

last: C. Dylan

first: Blaney

last: Patrick

first: Boyle

last: M. Eileen

first: Wang

last: Yubao

first: Avigan

last: Jason

first: Choi

last: Jinyoung

first: Landgren

last: Ola

first: Tsirigos

last: Aristotelis

first: Maura

last: Francesco

first: Morgan

last: J. Gareth

first: Davies

last: E. Faith


title: Tracing the evolution of single-cell 3D genomes in Kras-driven cancers

city: New Haven

first: Siyuan

last: Wang

state: CT

address: 333 Cedar Street

department: Department of Genetics and Department of Cell Biology

institute: Yale University

summary: Although three-dimensional (3D) genome structures are altered in cancer cells, little is known about how these changes evolve and diversify during cancer progression. Leveraging genome-wide chromatin tracing to visualize 3D genome folding directly in tissues, we generated 3D genome cancer atlases of oncogenic Kras-driven murine lung and pancreatic adenocarcinoma. Our data reveal stereotypical, non-monotonic, and stage-specific alterations in 3D genome folding compaction, heterogeneity, and compartmentalization as cancers progress from normal to preinvasive and ultimately to invasive tumors, discovering a potential structural bottleneck in early tumor progression. Remarkably, 3D genome architectures distinguish morphologic cancer states in single cells, despite considerable cell-to-cell heterogeneity. Gene-level analyses of evolutionary changes in 3D genome compartmentalization not only showed that compartment-associated genes are more homogeneously regulated but also elucidated prognostic and dependency genes in lung adenocarcinoma and a previously unappreciated role for polycomb-group protein Rnf2 in 3D genome regulation. Our results demonstrate the utility of mapping the single-cell cancer 3D genome in tissues and illuminate its potential to identify new diagnostic, prognostic, and therapeutic biomarkers in cancer.

overall_design: CUT&RUN of RNF2, H3K4me3, H3K27me3, H2AK119ub, BMI-1, RNA Pol II p-ser5 and IgG in the mouse KP LUAD cell line (31671) stably transfected with shRNAs targeting Rnf2 (shRnf2-3) and a non-targeting control (shNTC). The cell line was derived from an autochthonous KrasLSL-G12D/WT; Trp53flox/flox mouse administered with Adeno-Cre.

first: Miao

first: Mandar

last: Muzumdar


title: Mitotic chromosome condensation resets chromatin to maintain post-anaphase transcriptional homeostasis (ChIP-Seq)

first: Pierre

last: Chymkowitch

first: Lucía

last: Ramos-Alonso

first: Petter

last: Holland

first: Xu

last: Zhao

first: Stephanie

last: Le Gras

first: Bernard

last: Jost

first: Magnar

last: Bjørås

first: Yves

last: Barral

first: Jorrit

last: Enserink


title: UPF1 knockdown in IPSC-derived cortical neurons

status: Public on May 01 2025

city: Leuven

first: Sam

last: Bryce-Smith

address: Herestraat 49

department: VIB-KU Leuven Center for Brain and Disease Research

country: Belgium

institute: KU Leuven

summary: UPF1 is a key regulator of the nonsense-mediated decay (NMD) RNA degradation/quality control pathway. In this study, UPF1 knockdown was performed in IPSC-derived cortical-like neurons (NGN2) to characterise the transcriptome changes upon loss of UPF1 and NMD activity

overall_design: short-read bulk RNA-sequencing of IPSC-derived cortical neurons with and without UPF1 knockdown

first: Matteo

last: Zanovello

first: Matthew

last: Keuss

first: Anna-Leigh

last: Brown

first: Alla

last: Mikheenko


title: Unveiling the Molecular Mechanisms of HPL in Enhancing Endometrial Receptivity

city: Toronto

first: Stewart

last: Russell

state: ON

address: 790 Bay St

country: Canada

institute: create fertility centre

summary:
Summary Answer: HPL treatment stimulates endometrial growth and trophoblast attachment by activating cell proliferation, and modulating cell-cell signaling and extracellular matrix organization.
What is known already: Despite advancements in RIF management, there is currently no standard therapy, and existing treatments have variable effectiveness and do not consistently improve clinical pregnancy rates. There is a general consensus that intrauterine infusion of aPRP, before embryo transfer, promotes endometrial growth and may be the most effective immunomodulatory intervention to significantly improving pregnancy outcomes in RIF patients.
Study design, size, duration: Cross-sectional (control versus treatment) study including five non-RIF (control) patients and eighteen RIF patients from the CReATe Fertility Centre, Toronto. The eighteen RIF patients were categorized into two sub-groups: RIF and RIF+TE.
Participants/materials, setting, methods: Endometrial tissue was collected from pre-menopausal women (32-47 years of age) during routine biopsy procedures at the CReATe Fertility Centre, Toronto. Primary endometrial epithelial (EECs) and stromal cells (ESCs) were enzymatically isolated, cultured separately, and treated for 48 hours with either SFM (SFM) as the untreated control, or SFM supplemented with 1% HPL (EECs), or 10% HPL (ESCs). Cell proliferation was assessed using the PrestoBlueTM reagent (metabolic assay) and immunocytochemistry for Ki-67 expression. Following 48-hour treatment, total RNA was isolated from untreated and treated cells to prepare pooled RNA libraries, which were then subjected to RNA sequencing (150 cycles paired-end). Differential gene expression was performed using the DESeq2 package and RStudio/R. Significant differentially expressed genes were determined with the following cut off values: log2FoldChange >|2| and padj <0.05. Pathway enrichment analysis was then performed with Enrichr (Reactome 2022 database) to identify enriched pathways. After 48-hour treatment with SFM or HPL, a trophoblast attachment assay was also performed with fluorescently labeled HTR-8/SVneo trophoblast spheroids, where spheroids were seeded on top of pre-treated EEC monolayers for a 1-hour incubation to allow for attachment. Fluorescent microscopy and ImageJ™ software were used to image and quantify the total number of seeded and attached spheroids.
Main results and the role of chance: Treatment with non-autologous HPL for 48 hours significantly increased EEC proliferation by 1.24- to 1.49-fold (P<.05) in all groups. ESCs showed a significant proliferation increase of 1.29-fold in the proliferative phase RIF group and 1.92-fold in the secretory phase RIF+TE group (P<.05). HPL treatment upregulated 45 genes in EECs, including MMP1, MMP9, and ADAMTS18, while 378 genes were upregulated in ESCs, such as BUB1, CDK1, MKI67, and PLK1. Twenty-two common genes were significantly upregulated in both cell types. EECs had 30 downregulated genes, including KL and ADRA2A, while ESCs had 429 downregulated genes, such as PTGIS, PTGDS, and PTGES, with seven common genes downregulated in both cell types. Pathway enrichment analysis revealed that upregulated pathways in EECs included extracellular matrix organization and degradation, while ESCs showed enrichment in cell cycle (mitotic), cell cycle checkpoints, and extracellular matrix degradation. Downregulated pathways included receptor signaling of the fibroblast growth factor receptor 1 in EECs, prostaglandin synthesis in ESCs, and G-protein coupled receptor signaling in both cell types. HPL treatment also increased primary EEC attachment to trophoblast spheroids compared to the untreated control. This increased attachment was consistent in EECs from RIF patients, regardless of endometrial thickness, with a 26% increase (from 42.58% to 68.90%, P<.01) in RIF cultures and a significant 29% increase (from 57.52% to 86.5%, P<.01) in RIF+TE cultures.
Limitations, reasons for caution: One limitation is the small sample size of primary human endometrial samples (N=23), divided into four patient groups (N=5-6 per group). Additionally, all participants were pre-menopausal women aged 32-47, most of whom fall into the advanced reproductive age category (>35 years), a group often recommended for infertility assessment after six months of unsuccessful conception attempts. Although our study utilized primary endometrial cells and indicates that HPL may be an effective treatment for RIF and TE, these in vitro findings need to be validated in vivo. Clinical studies, such as randomized controlled trials, are necessary to evaluate and compare the efficacy of commercial HPL as a treatment alternative to aPRP. These trials would also allow for testing the safety of using a commercial non-autologous HPL product in human patients and help optimize treatment protocols, including the ideal dosage, concentration, timing, and treatment duration to maximize therapeutic benefits and develop more effective treatments for patients with endometrial causes of RIF.
Wider implications of the findings: Platelet-rich plasma (PRP) treatment for RIF and TE is increasingly being adopted by fertility clinics worldwide. Our research represents the first detailed investigation into the molecular effects of HPL, a derivative of PRP, on primary endometrial cells from patients with RIF, establishing a foundation for understanding how PRP/HPL impacts endometrial growth and receptivity. Our study demonstrated that commercial non-autologous HPL stimulates endometrial cell proliferation, modulates the expression of factors related to cell mitosis, extracellular matrix remodeling, and cell-cell signaling, and enhances endometrial-embryo attachment. By elucidating the mechanistic actions of HPL, our research provides valuable insights into this therapeutic approach and informs future treatments aimed at improving embryo transfer success. While these findings suggest that HPL could be as effective as aPRP, further investigation is necessary to evaluate its safety and efficacy in humans, necessitating comprehensive studies before HPL can be routinely used in clinical practice.
Study funding/competing interest(s): This study was funded by the CReATe Fertility Centre.

overall_design: Human primary endometrial cells, stromal or epithelial. Cells originated from patients with RIF with or without thin endometria, from the secretory or proliferative phases. Control samples from patients with successful pregnancies were also included. Cells were either at P0 immediately post collection, or at P1 with or without treatment of HPL.

first: Tina Tu-Thu Ngoc

last: Nguyen

first: Yat Sze Sheila

last: Kwok

first: Carol

last: Zhang

middle: J

first: Clifford

middle: L

last: Librach


title: Induced loss of TREX1 in host cells inflames the tumor micromilieu and invigorates CTL-mediated cancer control

city: Heidelberg

first: Axel

last: Roers

address: Im Neuenheimer Feld 305

institute: Universitätklinikum Heidelberg

summary: Activation of local innate immunity in tumor tissue, aiming at induction of adaptive responses, is a major concept in cancer immunotherapy. The cGAS/STING pathway triggers type I IFN and pro-inflammatory cytokine responses upon detection of cytosolic DNA and can robustly enhance anti-tumor immunity. The DNase 3’ repair exonuclease 1 (TREX1) is a central component of cellular DNA disposal preventing accumulation of endogenous DNA in the cytosol, activation of cGAS and cell-intrinsic innate immune responses. While constitutive TREX1-deficiency causes severe mendelian autoimmunity, temporary pharmacological inhibition of the enzyme may represent an efficient means to activate anti-tumor immunity. Induced inactivation of the Trex1 gene in mice (TREX1 iKO) resulted in improved immune control of established syngeneic tumors that was type I IFN- and CD8+ T cell-dependent. This was associated with a dramatic increase of immune cell infiltration of tumor tissue while other (non-tumor) tissues were not or marginally affected. TREX1 iKO triggered an inflammatory switch of intra-tumoral monocyte, macrophage and dendritic cell populations, associated with enhanced antigen presentation capacity. Invigoration of CD8 T cell responses was reflected in robust increase in cells differentiating along the exhaustion trajectory but expressing significant signatures of effector function. Combination of TREX1 iKO with immune checkpoint inhibition synergistically promoted tumor control. In addition to improved anti-tumor immunity upon loss of TREX1 in host cells, we also show that cancer cell-specific TREX1 deficiency synergizes with irradiation and checkpoint inhibition to enable tumor rejection and formation of long-term memory. We conclude that pharmacological TREX1 inhibition is a promising therapeutic approach to boost anti-tumor immunity.

overall_design:
To illustrate how the Trex1 knockout-induced immune response regulates tumor growth, an inducible Trex1 knockout mouse model bearing syngeneic melanoma B16 tumors was used to generate the single cell RNAseq data of tumor-infiltrating-Immune cells.
Please note that the additional sequences information for demultiplexing the different hashtaged samples is provided in the 'GEO Sequences Supplimentary.xlsx' file.

first: Emilija

last: Marinkovic

first: Minyi

last: Chen

first: Nadja

last: Schubert

first: Elif Dogan

last: Dar

first: Tanja

last: Poth

first: Janet

last: Leung

first: Jack

last: Lohre

first: Jennifer

last: Sahni

first: Christine

last: Tun

first: Pavithra

last: Rajeswaran

last: Mehlo-Jensen

first: Olivia

last: Perng

first: Mark

last: Hill

first: Pallavur

last: Sivakumar

first: Michael

last: Barnes

first: Rohit

last: Malik

first: Rayk

last: Behrendt


title: RNA-seq study of curcumin transforming phenotype of PRV-infected BV2 cells

city: chongqin

first: luqiu

last: feng

address: 160 Xueyuan Road, Rongchang District, Chongqing

department: College of Veterinary Medicine

institute: Southwest university

summary: Purpose: Next Generation sequencing (NGS) has revolutionized system-based cellular pathway analysis. The aim of this study was to infect differentially expressed genes for the BV2 phenotype with cur-transformed PRV and to predict possible molecular mechanisms involved in phenotypic transformation.Methods: The BV2 cells in the three treatment groups were sequenced by Illumina sequencing platform, and three repeated mRNA maps of BV2 cells were obtained. The cells were divided into control group: normal BV2 cells were cultured for 48 hours; PRV infection group: BV2 cells were infected with 1.66×106TCID50 PRV for 48h; CUR treatment group: BV2 cells were infected with 1.66×106TCID50 PRV for 24h and then treated with 20μM CUR for 24h.Results:The number of differentially expressed genes in PRV group and CON group was 306, including 242 biologically significant up-regulated genes and 64 biologically significant down-regulated genes. The number of differentially expressed genes in PRV+CUR group and PRV group was 5073, among which 2661 were biologically significant up-regulated genes and 2412 were biologically significant down-regulated genes. Compared with CON group, 1785 differentially expressed genes were found in PRV+CUR group, including 788 biologically significant up-regulated genes and 997 biologically significant down-regulated genes.Conclusions: Bioinformatics analysis of transcriptome characteristics and differentially expressed genes of BV2 in different phenotypes after PRV infection and CUR treatment showed that glycolysis, oxidative phosphorylation, Alzheimer's disease and fatty acid synthesis pathway may be involved in the process of BV2 activation into M1 type. Glycolysis, gluconeogenesis, insulin signaling pathway, NF-κB pathway, AMPK pathway, oxidative phosphorylation and fatty acid synthesis may be involved in the phenotypic transformation of PRV-infected BV2 with CUR. Among them, AMPK may influence phenotypic transformation by controlling the transformation of energy metabolism.

overall_design: The samples were BV2 cell lines with three biological replicates in each group. They were divided into Control group, PRV group and PRV+CUR group.Retinal mRNA profiles of BV2

first: Ling

last: Gan

first: Luqiu

last: Feng

first: Chen

last: Zhang


title: Alteration in the Morphological and Transcriptomic Profiles of Acinetobacter baumannii after Exposure to Colistin

city: Cheongju-si

first: Eun-Jeong

last: YOON

address: Osongsaengmyeong-ro

country: South Korea

institute: KNIH

summary: Acinetobacter baumannii is often highly resistant to multiple antimicrobials, posing a risk of treatment failure, and colistin is a "last resort" for treatment of the bacterial infection. However, colistin resistance is easily developed when the bacteria are exposed to the drug, and a comprehensive analysis of colistin-mediated changes in colistin-susceptible and -resistant A. baumannii is needed. In this study, using an isogenic pair of colistin-susceptible and -resistant A. baumannii isolates, alterations in morphologic and transcriptomic characteristics associated with colistin resistance were revealed. Whole-genome sequencing showed that the resistant isolate harbored a PmrBL208F mutation conferring colistin resistance, and all other single-nucleotide alterations were located in intergenic regions. Using scanning electron microscopy, it was determined that the colistin-resistant mutant had a shorter cell length than the parental isolate, and filamented cells were found when both isolates were exposed to the inhibitory concentration of colistin. When the isolates were treated with inhibitory concentrations of colistin, more than 80% of the genes were upregulated, including genes associated with antioxidative stress response pathways. The results elucidate the morphological difference between the colistin-susceptible and -resistant isolates and different colistin-mediated responses in A. baumannii isolates depending on their susceptibility to this drug.

overall_design: For two isolgenic colistin-susceptible or -resistant isolates, transcriptional level of a total of 3,731 geneswas analyzed after the treatment with colistin of subinhibitory and inhibitory concentrations.

last: Yoon

first: Jun

last: Mo


title: Molecular and Mechanical Signatures Contributing to Epidermal Differentiation and Barrier Formation

city: Durham

first: Alexandra

last: Prado Mantilla

state: NC

address: 307 Research Dr, Durham, NC 27710

institute: Duke University

summary: Formation of the skin barrier requires rapid proliferation coupled with differentiation and stratification of the embryonic epidermis. Basal progenitors give rise to progeny throughout development – first to intermediate cells, a transient proliferative suprabasal cell population, and later to spinous cells. Neither the function nor the differentiation trajectory of intermediate cells has been documented. We generated transcriptomes of intermediate and spinous cells and identified specific markers that distinguish these two populations. Further, we found that intermediate cells express a subset of genes in common with granular cells of the epidermis – the terminal living cell type that helps establish the barrier. Lineage tracing revealed that most intermediate cells directly transition to granular cells without expressing markers specific to spinous cells, thus revealing a distinct lineage pathway leading to granular fate. In addition to their transcriptional similarities, intermediate and granular cells both had hallmarks of increased actomyosin contractility. We found that rather than simply lying downstream of cell fate pathways, contractility was sufficient to suppress spinous fate and promote granular gene expression. Together, these data establish the molecular and mechanical characteristics of the developing epidermis that allow this tissue to rapidly develop barrier activity.

overall_design: RNA-seq profiling was performed on epidermal basal cells and their corresponding first layers of suprabasal cells, intermediate cells at E14.5 and spinous cells at E16.5, from mouse embryos. K10-rtTA;TRE-H2B-GFP;K14-RFP pregnant dams were fed doxycycline chow since E12.5. Back skin samples were collected at E14.5 and E16.5, epidermis was dissociated by dispase treatment, and single-cell suspensions were prepared with trypsin+versene. Granular cells were exclude from E16.5 samples using UEA1 lectin labeling. Intermediate cells (K10-GFP⁺;K14-RFP⁻;APC-UEA1⁻), spinous cells (K10-GFP⁺;K14-RFP⁻;APC-UEA1⁻), and basal cells (K10-GFP⁻;K14-RFP⁺) were FACS sorted. RNA was extracted from sorted populations, and three biological replicates per group were collected for sequencing.

last: Prado-Mantilla

first: Wenxiu

last: Ning

first: Terry

last: Lechler


title: DYRK1A Inhibition via Conditional Knockout

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

institute: Benaroya Research Institute

summary: Chemical inhibition of DYRK1A (e.g. using harmine) inhibits Th17 and promotes Treg differentiation. To better understand the mechanisms by which DYRK1A regulates Th17 differentiation, we are comparing expression profiles of naïve CD4+ T cells during the course of Th17 differentiation in the presence or absence of harmine.

overall_design: We MACS-isolated naïve CD4+ T cells from 4 mice on C57/Bl6 background. These were plated in pro-Th17 conditions in the presence or absence of 10 uM harmine. Cells were harvested at 0 and 5 hours and RNA isolated by RNeasy Micro & Mini kits. pro-Th17 conditions: 2ug/mL Anti-Il-4 2ug/mL Anti-Il-12 2ug/mL Anti-IFNγ 20ng/mL Il-6 20ng/mL Il1β 0.1ng/mL TGFB

first: Bernard

last: Khor

first: Matt

last: Malueg


title: Analysis of mRNA expression profiles in reactivated neurons from latent PRV infection

city: Chongqing

first: Zhang

last: Chen

address: No. 160 Xueyuan Road, Changyuan Street

institute: Southwest University

summary:
Little is known about the latent infection period and lytic infection mechanism of pseudorabies virus. The advent of high-throughput sequencing technologies has allowed us to examine many different biological components simultaneously.
To examine the effects of glucocorticoids on latently infected PRV neurons, we constructed gene expression profiles of RNA-seq data from PC-12 cell with a PRV latent infection model group (PRV group), a reactivation model group (DEX group) and a blank control group (CON group).

overall_design: Comparative gene expression profiling of RNA-seq data from PC-12 cells in different states of PRV infection.


title: Transcriptomic analysis of peripheral blood mononuclear cells reveals age specific differences at baseline and response to acute exercise

city: Salt Lake City

first: Joel

middle: Douglas

last: Trinity

state: Utah

address: 500 Foothill Drive

institute: University of Utah

summary: Aging is associated with alterations in immune cell function, contributing to age-related diseases and frailty. As key drivers of the immune response, we investigated the transcriptome of peripheral blood mononuclear cells (PBMCs) using RNA-sequencing before and after high-intensity single-leg knee-extension exercise in young (Young; n=7, 23±4 years) and older individuals (Old; n=8, 65±7 years). Bioinformatic analyses revealed biological processes and pathways that were altered with aging and response to exercise. At baseline, 665 out of 19,762 genes differed in PBMCs with notable differences relating to pathways involved in DNA Damage/Telomere Stress Induced Senescence, NAD Signaling Pathway, and Oxidative Stress Induced Senescence. After exercise, 53 out of 13,695 genes were differentially expressed in the Young, while 1,026 out of 19,101 genes changed in the Old. In Young, the enriched processes and predicted pathways were linked to natural killer cells, while in Old, they focused on cell signaling immune responses. Lastly, 26 genes exhibited similar responses to exercise between groups, enriching the biological process of natural killer cell-mediated immunity regulation. Our findings indicate that PBMC gene expression is altered with aging and in response to acute exercise in older adults, with exercise having a more substantial modulating effect on the immune system response with aging. The underlying causes and functional consequences of the observed transcriptional differences require additional investigation.

overall_design: Experimental Design At visit 1, an informed consent and health history questionnaire were completed, and participants were given an accelerometer to wear for a minimum of seven days. At visit 2, participants performed a graded single-leg knee extension exercise test to determine maximal work rate. Lastly, during visit 3, participants reported to the lab following an overnight fast, height and weight were recorded, and venous blood was obtained via venipuncture prior to and immediately following a single bout of a 60-minute high-intensity aerobic exercise. Max Test During visit 2, participants completed testing to determine their single leg maximal work rate on a custom knee extension ergometer, as previously described (18, 19). After a brief bout of familiarization, participants performed an incremental repeated knee extensor test composed of consecutive 1-min stages at 60 rpm starting at zero watts. Resistance was added by the application of friction to the flywheel to increase the work rate, which increased by five watts every stage until the participant reached volitional exhaustion. Before the completion of each stage, blood pressure, heart rate, and ratings of perceived exertion were recorded. Maximal work rate was determined by the highest work rate maintained for greater than 30 seconds. After completing the test, participants rested for 10 min before completing 3 minutes of single-leg knee extensions at 80% of their maximal work rate as a verification to ensure that participants could achieve this work rate on visit 3. Testing Protocol Participants performed single-leg knee extension exercise. This small muscle mass exercise paradigm isolates the quadriceps and minimizes central limitations to exercise that may be present when comparing young and older adults. Single-leg knee extension exercise started at 20% of maximal work rate and increased by 20% every three minutes. Following this initial progression, 3-minute intervals were performed at 80% of maximal work rate. Three minutes of passive recovery separated each high intensity interval. A total of nine intervals were performed and the total duration of the exercise bout was ~1 hour. Collection of Peripheral Blood Mononuclear Cells Prior to and immediately following the testing protocol venous blood was obtained in two, 10ml BD K2EDTA vacutainers (Cat No: BD-366643; VWR Avantor, Radnor PA) for fresh PBMC isolation. PBMCs were separated by density-gradient centrifugation using SepMateTM -50 (Cat No: 85450; STEMCELL technologies, Vancouver, Canada) tubes with 15ml of a density gradient medium, Histopaque (Cat No: 10771; Sigma-Aldrich, St. Louis, MO). Next, EDTA anti-coagulated blood was diluted 1:1 with phosphate-buffered saline (PBS) by mixing 14-16ml of whole blood with 14-16ml of PBS and centrifuged at 1200g for 10 minutes at room temperature (with the brake on). The PBMC layer was carefully transferred into a 50ml conical tube with 25ml PBS and centrifuged at 700g for 10 minutes. PBMCs were then washed by discarding the supernatant, resuspending the pellet in 1ml PBS before bringing the total volume to 45ml and centrifuging again at 700g for 10 minutes. The final PBMC pellet was resuspended in 5ml of freezing media (fetal bovine serum, supplemented with 10% dimethyl sulfoxide, Sigma-Aldrich, St. Louis, MO and EBM-2, Lonza, Basel Switzerland) to be stored at -80°C for 24 hours before the vials were transferred and stored at -150°C until RNA isolation described below. Cell count and viability were determined from a hemocytometer from a 20-fold dilution using 90µl of freezing media, 10µl of PBMCs and 10µl of trypan blue (Cat No: T10282; Thermo Fisher).

first: Bradley

last: Ruple

first: Nicholas

last: Carlini

first: Jason

last: Koefed

first: Helya

last: Rostamkhani

first: Brady

middle: E

last: Hanson

first: Isaac

last: Wilcox

first: Jesse

last: Craig

first: Shelby

last: Osburn

first: Micah

last: Drummond

first: Ryan

last: Broxtermann

middle: D


title: Next Generation Sequencing Facilitates Quantitative Analysis of 77-39 in ovarian cancer Transcriptomes

city: shenzhen

first: jingxin

last: ma

address: Xueyuan Avenue, Nanshan District, Shenzhen

institute: shenzhen university

summary: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compareExamining the role of sirt3 inhibitor 77-39 in ovarian granulosa cancer cells,kgn cell line,cov434 cell line by RNA-seq

overall_design: 2 cell types(kgn cell line,cov434 cell line) treat with sirt3 inhibitor for 3-day old  were generated by deep sequencing

first: xueqing

last: wu


title: Defining molecular circuits of CD8+ T cell responses in tissues during latent viral infection

first: Endi

last: Santosa

state: New York

address: 417 E 68th St

department: Immunology

institute: Memorial Sloan Kettering Cancer Center

summary: Latent viral infections rely on a precise coordination of the immune response to control sporadic viral reactivation. CD8+ T cells play a crucial role in controlling viral latency by generating diverse memory responses in an epitope-specific manner. Among these distinct responses, conventional and inflationary memory responses have been described during herpesvirus infections. Using a newly generated T cell receptor transgenic mouse strain, we investigated the transcriptomic and epigenetic remodeling of distinct epitope-specific CD8+ T cells during cytomegalovirus (CMV) infection across tissues at both population and single-cell levels. Our findings reveal that whereas the transcriptomic and epigenetic landscape of conventional and inflationary memory responses diverge in the spleen and liver, these molecular programs converge in the salivary gland, a site of CMV persistence. Thus, we provide evidence that the dynamics of memory CD8+ T cell responses are nuanced and exquisitely distinct between tissues.

overall_design: For preparation of transgenic cells for single-cell multiome sequencing, congenically marked naïve TCRTg cells (M45Tg and M38Tg) were transferred into congenically distinct naïve recipient mice prior to infection with MCMV. On the day of cell isolation, each mouse was injected with 50µg of anti-ARTC2 nanobody (i.p.) 30 minutes before sacrifice (BioLegend, Catalog No. 149803, Clone S+16a). Intravenous (I.V.) labeling was not performed prior to sorting due to its limited ability to distinguish circulating from bona fide tissue-resident cells in the liver. Notably, I.V. labeling showed minimal signal in the salivary gland, comparable to the lymph nodes, which remain unlabeled (data not shown). Upon cell sorting into 1× PBS + 0.04% BSA, TCRTg cells were stained with mouse TotalSeq-A Hash Tag Oligonucleotides antibodies (BioLegend, tag number A0301-A0310), oligo-tagged anti-rat/mouse CD90.1 (BioLegend, Catalog No. 202547, Clone OX-7), and anti-mouse CD90.2 (BioLegend, Catalog No. 105345, Clone 30-H12). Hash tagged cells were then pooled at approximately equal ratios for multiome sequencing.

first: Joseph

last: Sun


title: Multi-omics analysis identifies erythroid cells as the major population in mouse placentas expressing the MHC class II antigen presentation, chemokine, and antibacterial immune response genes [Spatial Transcriptomics]

city: Novosibirsk

first: Roman

middle: Yurievich

last: Perik-Zavodskii

state: Novosibirsk region

address: Yadrincevskaya 14

country: Russia

institute: "Research Institute of Fundamental and Clinical Immunology" (RIFCI)

summary: Pregnancy is one of the most important processes for mammals, which is deeply controlled by the immune system. We performed spatial transcriptomics to profile mouse placentas from semi-allogeneic and syngeneic pregnancies at E12.5 to elucidate differences between these types of pregnancies. Our analysis showed that erythroid cells were the major immunoregulatory population in both types of pregnancies.

overall_design: We collected murine placentas at E12.5 from both syngeneic and semi-allogenic pregnancies, froze them in OCT, cut 10mm sections, placed them on a cryoslide, and performed 10X Genomics Visium CytAssist spacial transcriptomic analysis.

first: Olga

last: Perik-Zavodskaia

first: Saleh

last: Alrhmoun


title: Multi-omics analysis identifies erythroid cells as the major population in mouse placentas expressing the MHC class II antigen presentation, chemokine, and antibacterial immune response genes [Nanostring]

summary: Pregnancy is one of the most important processes for mammals, which is deeply controlled by the immune system. We performed NanoString Immune Transcriptome to profile erythroid cells from mouse placentas from semi-allogeneic and syngeneic pregnancies at E12.5 and E19.5 to elucidate the differences between these types of pregnancies.

overall_design: We collected murine placentas at E12.5 and E19.5 from both syngeneic and semi-allogenic pregnancies, extracted Ter-119 Erythroid cells and performed NanoString Immune transcriptome analysis

first: Perik-Zavodskaia

last: Olga

first: Perik-Zavodskii

last: Roman


title: Super-Enhancer-driven LncRNA UNC5B-AS1 Inhibits Inflammatory Phenotypic Transition in Pulmonary Artery Smooth Muscle Cells via Lactylation

city: daqing

first: Xiangrui

last: Zhu

state: heilongjiang

address: 39 Xinyang Road

institute: Harbin Medical University

summary: Background: The phenotypic transition of pulmonary artery smooth muscle cells (PASMCs) is a central pathological alteration in pulmonary artery remodeling, contributing to pulmonary hypertension (PH). Super-enhancers (SEs) are characterized by histone modifications and the binding of coactivators, which drive the expression of prominent genes which define cellular identity. The specific role of SEs, especially SE-driven long non-coding RNAs (lncRNAs), in hypoxia-induced phenotypic plasticity of PASMCs remains unclear. Methods: In this study, the lncRNA UNC5B-AS1 regulated by SEs was screened in hypoxic PASMCs using RNA sequencing and H3K27ac chromatin immunoprecipitation (ChIP) sequencing. Overexpression or knockdown of UNC5B-AS1 in vitro was performed to elucidate its role in PH pathogenesis. A serotype 5 adenovirus-associated virus carrying a conserved functional fragment of UNC5B-AS1 was used to treat PH in vivo. Results: We identified UNC5B-AS1 as an SE-driven lncRNA transcriptionally activated by the transcription factor FOXP3, which regulates phenotypic transition in PASMCs. Notably, we demonstrated that UNC5B-AS1 interacts with key glycolytic enzymes in the cytoplasm, and likely serves as a molecular scaffold for Leucine-Rich PPR Motif-Containing Protein (LRPPRC) and oxidative respiratory chain complex IV in the mitochondria. Consequently, the deficiency of UNC5B-AS1 in PASMCs promotes the lactylation of promoter regions within inflammatory genes, including those of IL-1β, IL-6, and TNF-α, under hypoxic conditions, ultimately leading to phenotypic transition of PASMCs. Conclusions: Our findings identify SE-driven UNC5B-AS1 as a novel regulatory factor in the hypoxia-induced phenotypic transition of PASMCs and suggest that overexpression of UNC5B-AS1 may represent a promising therapeutic strategy for PH.

overall_design:
RNA-seq profiling of human pulmonary artery smooth muscle cells under normoxia or hypoxia for 24 hours.
ChIP-seq of the histone modification H3K27Ac in human pulmonary artery smooth muscle cells under normoxia or hypoxia for 24 hours.

first: Xiangming

last: Pang

first: Xiaoying

last: Wang

first: Xiaoyu

last: Guan

first: Yujing

last: Tang

first: Zhaosi

first: Lixin

last: Zhang

first: Xiaodong

last: Zheng

first: Fei

last: Li

first: Jian

last: Mei

first: Langlin

last: Ou

first: Yuxiang

last: Liu

first: Zitong

last: Meng

first: Yingli

last: Chen

first: Cui

last: Ma


title: Integrated network pharmacology and transcriptomics to explore the mechanism of Gui-qi-yi-shen granules in the treatment of IgA nephropathy

city: Hangzhou

first: Cao

last: Jiawei

address: No. 1630 Huan Ding Road, Shangcheng District

institute: Hangzhou TCM Hospital Affiliated to Zhejiang Chinese Medical University

summary: To elucidate the underlying therapeutic mechanisms of Gui-qi-yi-shen granules (GQYS) in the treatment of IgAN, we have employed transcriptome sequencing of 9 mice kidney samples. 155 differentially genes were identified between IgAN and control groups, with 125 upregulated and 30 downregulated. Meanwhile, 403 genes differed between GQYS and IgAN groups, including 171 upregulated and 332 downregulated genes.

overall_design: RNA-seq profiling of kidney samples from wild-type C57/BL6 mice, Itgam-IRES-hCD89 mice and Itgam-IRES-hCD89 mice which were daily gavage with GQYS for 5 months.

first: Feng

last: Wan

first: Jiawei

last: Cao


title: Sustained macrophage reprogramming is required for CD8 T cell-dependent long-term tumor resolution

city: Lisboa

first: Nuno

middle: Luís

last: Barbosa-Morais

address: Av. Prof. Egas Moniz

country: Portugal

institute: Instituto de Medicina Molecular João Lobo Antunes

summary: Tumor-associated macrophages (TAMs) exhibit a dual role in tumor progression and antitumor immunity. However, understanding the functional states and molecular mechanisms of antitumor TAMs remains a challenge. Here, we show that combined TLR3 and CD40 agonists (myeloid cell treatment, MCT) reprogram TAMs to adopt a protective antitumor phenotype in an orthotopic mouse breast cancer model, leading to tumor regression. Single-cell RNA sequencing of TAMs from different tumor stages and post-MCT treatment revealed a transient antitumor TAM phenotype, present at 12h post-MCT, characterized by markers such as iNOS and CD38, which was replaced by TAMs co-expressing tumor-limiting and promoting features by 72h post-MCT. Maintenance of antitumor TAMs required repeated MCT administrations, and reactive oxygen species and TNF-α were pivotal molecular mechanisms in TAM-mediated tumor control. Importantly, repeated MCT promoted the activation of CD8 T cells and long-term tumor eradication. Our findings uncover the vulnerability of transient TAM reprogramming which can be overcome by repeated MCT administrations to sustain efficient immune responses.

overall_design: We analyzed TAMs at 12h and 72h post-MCT to capture early dynamics and later stages of tumor regression. For the 72h time point, we selected responders with a tumor size ratio (T3/T0) close or inferior to 1. To differentiate between protumor and antitumor inflammation originating from TAMs, we collected tumor-infiltrating myeloid cells from mice with progressing tumors (PT), defined as those exceeding 500 mm³ in volume. Each group (NT, MCT-72h, PT) included a minimum of three samples from distinct biological replicates, except for MCT-12h, which had two biological replicates. To integrate the four groups and mitigate potential batch effects, we included an NT sample in each FACS-sorting session. A permissive gating approach, including all live CD45+CD19-CD3-NK1.1- cells was used to sort all myeloid cell subsets. Isolated immune cells were processed using 10X Genomics chromium technology to prepare libraries for single-cell RNA-sequencing.

first: Carolina

last: Jardim

first: Marta

last: Bica

first: Mariana

last: Reis-Sobreiro

first: Afonso

last: Teixeira da Mota

first: Raquel

last: Lopes

first: Miguel

last: Pinto

first: Neuza

last: Sousa

first: Sofia

last: Mensurado

first: Henning

last: Boekhoff

first: Tommaso

last: Scolaro

first: Maud

last: Reugebrink

first: Natacha

last: Gonçalvez-Sousa

first: Hiroshi

last: Kubo

first: Catarina

last: Gomes

last: Brito

first: Rafael

last: Arguello

first: Elvira

last: Leites

first: Vanessa

middle: A

last: Morais

first: Bruno

last: Silva-Santos

first: Karine

last: Serre


title: Sensitization of non-M3 acute myeloid leukemia blasts to all-trans retinoic acid by the LSD1 inhibitor tranylcypromine: TRANSATRA phase I study

city: Freiburg im Breisgau

first: Michael

last: Kruszewski

state: Baden-Württemberg

address: Hugstetter Str. 55

institute: Universitätsklinikum Freiburg

summary: Elderly, non-fit AML/MDS patients relapsed/refractory (R/R) after HMA-based treatment represent a highly unmet clinical need, necessitating the development of age-appropriate therapies with an acceptable safety profile, e.g. with all-trans retinoic acid (ATRA). As histone demethylase LSD1 (KDM1A) is a rational therapeutic target in AML, we conducted a phase I trial with the LSD1 inhibitor tranylcypromine (TCP, dose levels [DL] 20, 40, 60, 80mg p.o. d1-28) combined with fixed-dose ATRA (45mg/m2 p.o. d10-28) and low-dose cytarabine (LDAC, 40mg s.c. d1-10). The primary endpoint was dose limiting toxicity (DLT) in the first 28 days of treatment. The aim was the determination of the maximum tolerated dose (MTD). Enrollment into DLs was performed using the rolling six design. Twenty-three patients with R/R AML and 2 with relapsed MDS were accrued, with a median age 75 years (range 62-84), after a median of two prior treatment lines (range, 1-5). Three, 6, 6 and 10 patients were allocated to DL 20, 40, 60, and 80 mg TCP, respectively, with 3, 12, 6 , 4 patients achieving the respective dose of 20, 40, 60, and 80 mg, and 3 patients on each DL being fully evaluable for MTD. TCP was administered for a median of 39.5 days (range 11-228), for >60 days in 30% of patients. No dose-limiting toxicities (DLTs) were observed at any DL, MTD could not be established. Most common adverse events > grade 3 occurring in >10% of patients were:  pneumonia (16%) and febrile neutropenia (12%). No differentiation syndrome occurred. Two patients attained a partial remission; stable disease was achieved in 10 of 22 evaluable patients. Median overall survival was 62 days (range 14-325). Accompanying studies included pharmacokinetics, serial determinations of fetal hemoglobin and genes known to be regulated by LSD1 or ATRA, such as CD86, CD38 and GFI1B. Patients’ quality of life, anxiety and depression were determined before and after treatment. In conclusion, the combination of TCP with ATRA and LDAC was well feasible, even at the highest DL. Almost half of the patients attained stable disease, indicating limited cross-resistance with prior HMA treatment. Hence, studies with more potent LSD1 inhibitors appear warranted.

overall_design: Sampling of peripheral blood was perforemd during the trial to investigate changes in gene expression in peripheral blood blasts. Smapling was performed at screening, d10, d20, d28 (end of cycle one), and at the end of every following cycle as well as at EOT.

last: Kuszewski

first: Usama-Ur

last: Rehman

last: Lübbert


title: Transcriptomic and epigenomic consequences of heterozygous loss-of-function mutations in AKAP11, a shared risk gene for bipolar disorder and schizophrenia [ChIP-seq]

city: Montreal

first: Alain

last: Pacis

state: QC

address: 1010 Sherbrooke #1800

institute: Canadian Centre for Computational Genomics (C3G)

summary: The gene A-kinase anchoring protein 11 (AKAP11) recently emerged as a shared risk factor between bipolar disorder and schizophrenia, driven by large-effect loss-of-function (LoF) variants. Recent research has uncovered the neurophysiological characteristics and synapse proteomics profile of Akap11-mutant mouse models. Considering the role of AKAP11 in binding cAMP-dependent protein kinase A (PKA) and mediating phosphorylation of numerous substrates, such as transcription factors and epigenetic regulators, and given that chromatin alterations have been implicated in the brains of patients with bipolar disorder and schizophrenia, it is crucial to uncover the transcriptomic and chromatin dysregulations following the heterozygous knockout of AKAP11, particularly in human neurons. In this study, we use genome-wide approaches to investigate such aberrations in human induced pluripotent stem cell (iPSC)-derived neurons. We show the impact of heterozygous AKAP11 LoF mutations on the gene expression landscape and profile the methylomic and acetylomic modifications. Altogether we highlight the involvement of aberrant activity of intergenic and intronic enhancers, which are enriched in PBX homeobox 2 (PBX2) and Nuclear Factor-1 (NF1) known binding motifs, respectively, in transcription dysregulations of genes functioning as DNA-binding transcription factors, actin and cytoskeleton regulators, and cytokine receptors, as well as genes involved in G-protein-coupled receptors (GPCRs) binding and signaling. We also show significant downregulation of pathways related to ribosome structure and function, a pathway also altered in BD and SCZ post-mortem brain tissues and heterozygous Akap11-KO mice synapse proteomics. A better understanding of the dysregulations resulting from haploinsufficiency in AKAP11 improves our knowledge of the biological roots and pathophysiology of BD and SCZ, paving the way for better therapeutic approaches.

overall_design: Chromatin Immunoprecipitation followed by sequencing (ChIP-seq) for Histone H3 Lysine 27 Acetylation (H3K27ac), marker of active enhancers, in Het-AKAP11-KO clones and WT counterpart reps human iPSC-derived neurons.

first: Nargess

last: Farhangdoost

first: Calwing

last: Liao

first: Yumin

last: Liu

first: Daniel

last: Rochefort

first: Farah

last: Aboasali

first: Alessia

last: Pietrantonio

first: Martin

last: Alda

first: Patrick

last: Dion

first: Anouar

last: Khayachi

first: Boris

last: Chaumette

first: Guy

last: Rouleau


title: Transcriptomic and epigenomic consequences of heterozygous loss-of-function mutations in AKAP11, a shared risk gene for bipolar disorder and schizophrenia [RNA-seq]

overall_design: Using a human iPSC, from the lymphoblasts of an unaffected individual, we generated 3 heterozygous AKAP11-knockout (Het-AKAP11-KO) isogenic neuronal clones, each carrying a different heterozygous frameshift mutation. We then performed gene expression profiling of the 3 Het-AKAP11-KO clones and the 3 WT counterpart replicates to determine the differentially expressed genes in Het-AKAP11-KO vs. WT.


title: Methylation profile of H3K27M-mutant diffuse gliomas with a non-midline location 1

city: Bron

first: Marc

last: Barritault

address: 59 boulevard Pinel

institute: Hospices Civils de Lyon

summary: Genome wide DNA methylation profiling of an H3K27M-mutant diffuse gliomas with a non-midline location. The Illumina Infinium Human EPIC DNA methylation Beadchip was used to obtain DNA methylation profiles from more than 850,000 CpGs from a FFPE sample.

overall_design:
Bisulphite converted DNA from 1 FFPE sample was hybridised to the Illumina Infinium MethylationEPIC v2.0 BeadChip
Processed data not provided for this submission.


title: Methylation profile of H3K27M-mutant diffuse gliomas with a non-midline location 2

summary: Genome wide DNA methylation profiling of an H3K27M-mutant diffuse gliomas with a non-midline location. The Illumina Infinium Human EPICV2 DNA methylation Beadchip was used to obtain DNA methylation profiles across more than 935,000 CpGs from a FFPE sample.


title: Characterization of the genes that were regulated by feeding Lactiplantibacillus sp. MH-1 during the largval stages

city: Kyoto

first: Eriko

last: Kage-Nakadai

state: Kyoto

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

institute: Koyto Univ.

summary: In the present study, we investigated the effects of feeding Lactiplantibacillus sp. MH-1 using Caenorhabditis elegans as a model animal. The survival of the adult C. elegans fed MH-1 was significantly better than that of unfed animals (control) upon infection with pathogens.

overall_design: Transcriptional profiling of one-day-old worms that were fed Lactiplantibacillus sp. MH-1  or E. coli OP50 (control) for two day, by deep sequencing, using Illumina NEXTSeq2000.


title: Transcriptomic and epigenomic consequences of heterozygous loss-of-function mutations in AKAP11, a shared risk gene for bipolar disorder and schizophrenia [WGBS]

summary: The gene A-kinase anchoring protein 11 (AKAP11) recently emerged as a shared risk factor between bipolar disorder and schizophrenia, driven by large-effect loss-of-function (LoF) variants. Recent research has uncovered the neurophysiological characteristics and synapse proteomics profile of Akap11-mutant mouse models. Considering the role of AKAP11 in binding cAMP-dependent protein kinase A (PKA) and mediating phosphorylation of numerous substrates, such as transcription factors and epigenetic regulators, and given that chromatin alterations have been implicated in the brains of patients with bipolar disorder and schizophrenia, it is crucial to uncover the transcriptomic and chromatin dysregulations following the heterozygous knockout of AKAP11, particularly in human neurons. In this study, we use genome-wide approaches to investigate such aberrations in human induced pluripotent stem cell (iPSC)-derived neurons. We show the impact of heterozygous AKAP11 LoF mutations on the gene expression landscape and profile the methylomic and acetylomic modifications. Altogether we highlight the involvement of aberrant activity of intergenic and intronic enhancers, which are enriched in PBX homeobox 2 (PBX2) and Nuclear Factor-1 (NF1) known binding motifs, respectively, in transcription dysregulations of genes functioning as DNA-binding transcription factors, actin and cytoskeleton regulators, and cytokine receptors, as well as genes involved in G-protein-coupled receptors (GPCRs) binding and signaling. We also show significant downregulation of pathways related to ribosome structure and function, a pathway also altered in BD and SCZ post-mortem brain tissues and heterozygous Akap11-KO mice synapse proteomics.  A better understanding of the dysregulations resulting from haploinsufficiency in AKAP11 improves our knowledge of the biological roots and pathophysiology of BD and SCZ, paving the way for better therapeutic approaches.

overall_design: We performed whole-genome bisulfite sequencing (WGBS) to profile genome-wide differentially methylated regions (DMRs) in 3 heterozygous AKAP11-KO clones vs. 3 WT counterpart reps.


title: Resolution of acinar dedifferentiation regulates tissue remodeling in pancreatic injury and cancer initiation.

city: Copenhagen

first: Luis

last: Arnes

address: Ole Maaløes Vej 5

country: Denmark

institute: Biotech Research & Innovation Centre

summary: Background and Aims: Acinar to ductal metaplasia (ADM) is crucial in the development of pancreatic ductal adenocarcinoma (PDAC). However, our understanding of the induction and resolution of ADM remains limited. We conducted comparative transcriptome analyses to identify conserved mechanisms of ADM in mouse and human.   Methods: We identified Sox4 among the top upregulated genes. We validated the analysis by RNA in situ hybridization (ISH). We performed experiments in mice with acinar-specific deletion of Sox4 (Ptf1a: CreER; Rosa26-LSL-YFPLSL-YFP; Sox4fl/fl ) with and without an activating mutation in Kras (KrasLSL-G12D/+). Mice were given caerulein to induce pancreatitis. We performed phenotypic analysis by immunohistochemistry, tissue decellularization and single cell RNA sequencing.   Results: We demonstrated that Sox4 is reactivated in ADM and PanINs. Contrary to findings in other tissues, Sox4 actually counteracts cellular dedifferentiation and helps maintain tissue homeostasis. Moreover, our investigations unveiled the indispensable role of Sox4 in the specification of mucin-producing cells and tuft-like cells from acinar cells. We identified Sox4-dependent non-cell-autonomous mechanisms regulating the stromal reaction during disease progression. Notably, Sox4-inferred targets are activated upon KRAS inactivation and tumor regression.  Conclusions: Our results indicate that our transcriptome analysis can be used to investigate conserved mechanisms of tissue injury. We demonstrate that Sox4 acts as a switch to promote healing in pancreatic injury and cancer initiation and is activated upon Kras ablation and tumor regression in mice. By uncovering novel potential strategies to promote tissue homeostasis, our findings offer new avenues for preventing the development of PDAC.

overall_design:
To investigate the effect of Sox4 on acinar metaplasia and neoplastic development we knocked out Sox4 in the mouse acinar lineage by using the following alleles: LSL-KrasG12D, Ptf1aCreER, R26RYFP, and Sox4flox. Tissue injury was induced by repetitive caerulein injections over 2 days. The RNA was extracted from bulk pancreas at day 2 for study of acinar regeneration and at day 21 for the study of prenoeoplastic development.
LSL-KrasG12D (MGI:2429948), Ptf1aCreER (MGI:3771322), R26RYFP (MGI:2449038), and Sox4flox (MGI:3773012) mouse strains were used for breeding. Mice were maintained on a genetically mixed background. Tamoxifen (T5648; Sigma-Aldrich) was administered through intraperitoneal injections every other day for 5 days (e.g., Monday, Wednesday, Friday) at a dose of 3mg per injection. Tamoxifen was dissolved in corn oil (C8267; Sigma-Aldrich) at a stock concentration of 30mg/ml (100l/injection). A standard wash-out of 2 weeks was performed. To induce tissue injury in the pancreas, the cholecystokinin analogue caerulein (C9026; Sigma-Aldrich) was administered through intraperitoneal injections every hour for 7 hours (8 injections/day) on 2 consecutive days at a concentration of 125g/kg body weight. Control mice were injected with equivalent volume of PBS following the same protocol. Pancreas tissue was finely chopped with scissors in digestion buffer (1mg/ml Collagenase (C9407-1G, Sigma-Aldrich), 1mg/ml DNase I (Sigma-Aldrich, 11284932001), 0,1mg/ml soybean trypsin inhibitor (STI, Fisher Scientific, 17-075-029) dissolved in Hank´s balanced salt solution (HBSS)). Digestion was performed in gentleMACS C Tubes using mTDK1 program on a gentleMACS™ Dissociator (Miltenyi Biotec). Reaction was stopped with STOP buffer (1mg/ml DNase I (Sigma-Aldrich, 11284932001), 0,1mg/ml STI and 5% Fetal bovine serum (FBS) dissolved in HBSS). Digested tissue was centrifuged 5 minutes at 2000 rpm and resuspended in 3 ml RBC lysis buffer (Thermo Scientific, 00-4333-57). After 2 minutes incubation cells were washed with STOP buffer twice and filtered through a 40 µm cell strainer. Cells were further processed for single cell sequencing. Nomenclature: CSox4WT: Ptf1CreER; -lslYFP. CSox4KO: Ptf1CreER; Sox4fl/fl; -lslYFP. KCSox4WT: Ptf1CreER; lsl-KrasG12D; -lslYFP. KCSox4KO: Ptf1CreER; Sox4fl/fl; lsl-KrasG12D; -lslYFP.

first: Jonathan

last: Baldan


title: DNA methylome and transcriptome landscapes of cancer-associated fibroblasts reveal a smoking-associated malignancy index

city: Taipei

first: Chao-Chi

last: Ho

address: 1 Jen Ai Road, Section 1

department: Department of Internal Medicine

country: Taiwan

institute: National Taiwan University Hospital and National Taiwan University College of Medicine

summary: Unlike the better-studied aberrant epigenome in the tumor, the clinicopathologic impact of DNA methylation in the tumor microenvironment (TME), especially the contribution from cancer-associated fibroblasts (CAFs), remains elusive. CAFs exhibit profound patient-to-patient tumorigenic heterogeneity. We asked whether such heterogeneity may be exploited to quantify the level of TME malignancy. We developed a robust and efficient methylome/transcriptome co-analytical system for CAFs and paired normal fibroblasts (NFs) from non-small-cell lung cancer patients. We found 14,781 CpG sites of CAF/NF differential methylation, of which 3,707 sites showed higher methylation changes in ever-smokers than in nonsmokers. Concomitant CAF/NF differential gene expression analysis pointed to a subset of 54 smoking-associated CpG sites with strong methylation-regulated gene expression. A methylation index that summarizes the β values of these CpGs was built for NF/CAF discrimination (MIND) with high sensitivity and specificity. The potential of MIND in detecting premalignancy across individual patients was shown. MIND succeeded in predicting tumor recurrence in multiple lung cancer cohorts without reliance on patient survival data, suggesting that the malignancy level of TME may be effectively graded by this index. Precision TME grading may provide additional pathological information to guide cancer prognosis and open up more options in personalized medicine.

overall_design: Purified RNAs from paired NF/CAF samples as DNAs from 25 NSCLC patients were processed onto Affymetrix GeneChip Human Genome U133 Plus 2.0 Array.

first: Sheng-Fang

last: Su

first: Hao

first: Hsu-Chieh

last: Wang

first: Jia-Hua

last: Li

first: Hsiang-Yuan

last: Yeh

first: Shuenn-Wen

last: Kuo

first: Ker-Chau


type:
Methylation profiling by array
Expression profiling by array

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

overall_design: Refer to individual Series


title: Spatial distribution and chromatin accessibility determine the therapeutic capacity of microglial subsets during neurodegeneration [scRNAseq2_Csf1]

status: Public on Apr 30 2025

first: Marco

last: Prinz

address: Breisacher Str. 64, C/O Institut für Neuropathologie

department: Institut für Neuropathologie

country: Germany

summary: Microglial spatial heterogeneity remains a crucial yet poorly studied question in light of potential cell-directed therapies for Alzheimer`s disease (AD). Little is known about the dynamics of spatially distinct microglia states, which are either adjacent or non-associated with the plaque site, and their selective contributions to neurodegeneration in vivo. So far, research has essentially focused on pathology-associated microglia. Here, we combined novel multicolour fluorescence fate mapping, single-cell transcriptional analysis, epigenetic profiling, advanced immunohistochemistry and computational modelling to comprehensively characterize the relation of plaque-associated and non-plaque-associated microglia during neurodegeneration in female mice. This approach enabled us to identify and characterize non-plaque-associated microglia as a unique and highly dynamic microglial state in a mouse model of AD. Non-plaque-associated microglia modulate network expansion, quickly adapt to environmental cues and their transition to plaque-associated microglia can be specifically modulated during disease, contrary to their reputation as a passive bystander subpopulation. This description of the dynamics of spatially segregated microglial states and their distinct molecular features may therefore open promising new avenues for state-specific therapeutic interventions during neurodegeneration.

overall_design: Following either colony stimulating factor 1 (Csf1) or PBS (control) treatment, microglia from early stage (ES) 5xFAD positive and negative mice were sorted by fluorescence-activated cell sorting (FACS) and analyzed by single cell RNA seq.

first: Alberto

last: Arudura-Fabregat

first: Roman

last: Sankowski


title: Spatial distribution and chromatin accessibility determine the therapeutic capacity of microglial subsets during neurodegeneration [ATAC-seq]

overall_design: Following either colony stimulating factor 1 (Csf1) or PBS (control) treatment, CD11c positive and negative microglia from early stage (ES) 5xFAD positive and negative mice were sorted by fluorescence-activated cell sorting (FACS) and analyzed by ATACseq.

first: Emile

last: Wogram

first: Omar

last: Mossad

first: Fang

first: Nicola

last: Iovino

first: Samuel

last: Wald

first: Sebastian

last: Preissl