title: High affinity chimeric antigen receptor signaling induces an inflammatory program in human regulatory T cells

status: Public on Nov 30 2024

city: Charleston

first: Stefano

last: Berto

state: SC

address: 68 President Street

department: Neuroscience

institute: Medical University of South Carolina

summary: Regulatory T cells (Tregs) are promising cellular therapies to induce immune tolerance in organ transplantation and autoimmune disease. The success of chimeric antigen receptor (CAR) T-cell therapy for cancer has sparked interest in using CARs to generate antigen-specific Tregs. Here, we compared CAR with endogenous T cell receptor (TCR)/CD28 activation in human Tregs. Strikingly, CAR Tregs displayed increased cytotoxicity and diminished suppression of antigen-presenting cells and effector T (Teff) cells compared with TCR/CD28 activated Tregs. RNA sequencing revealed that CAR Tregs activate Teff cell gene programs. Indeed, CAR Tregs secreted high levels of inflammatory cytokines, with a subset of FOXP3+ CAR Tregs uniquely acquiring CD40L surface expression and producing IFNγ. Interestingly, decreasing CAR antigen affinity reduced Teff cell gene expression and inflammatory cytokine production by CAR Tregs. Our findings showcase the impact of engineered receptor activation on Treg biology and support tailoring CAR constructs to Tregs for maximal therapeutic efficacy.

overall_design: CAR Tregs and CAR Teff cells were co-cultured with irradiated K562 (No Activation), CD19-K562 (CAR Activation) or CD64-CD80-K562 loaded with anti-CD3 antibody (TCR/CD28 Activation) at a 1:1 ratio in RPMI10 medium. CAR Treg co-cultures were supplemented with 1,000 IU/ml IL-2. After 24h, CD4+ cells were isolated using the EasySep Human CD4 Positive Selection Kit (STEMCELL Technologies), following the manufacturer’s instructions. At least two independent blood donors per condition were analyzed. With this experimental design, we kept CAR lentivirus transduction and sorting for CAR+ cells constant across all samples and kept the number of irradiated K562 target cells constant across the three modes of activation to rigorously compare the impact of activation via endogenous CD3 and CD28 with activation via CAR intracellular domain CD3 and CD28.

first: Bryan

last: Granger

first: Russell W.

last: Cochrane

first: Leonardo M.R.

last: Ferreira


title: Osmotic disruption of chromatin induces Topoisomerase 2 activity at sites of transcriptional stress [Mnase-Seq]

status: Public on Dec 01 2024

city: Brighton

first: William

last: Gittens

state: I am not in the U.S. or Canada

address: Science Park Road

department: Genome Damage and Stability Centre

country: United Kingdom

institute: University of Sussex

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Transcription generates superhelical stress in DNA that poses problems for genome stability, but determining when and where such stress arises within chromosomes is challenging. Here, using G1-arrested S. cerevisiae cells, and employing rapid fixation and ultra-sensitive enrichment, we utilise the physiological activity of endogenous topoisomerase 2 (Top2) as a probe of transcription-induced superhelicity. We demonstrate that Top2 activity is surprisingly uncorrelated with transcriptional activity, suggesting that superhelical stress is obscured from Top2 within chromatin in vivo. We test this idea using osmotic perturbation—a treatment that transiently destabilises chromatin in vivo—revealing that Top2 activity redistributes within sub-minute timescales into broad zones patterned by long genes, convergent gene arrays, and transposon elements—and also by acute transcriptional induction. We propose that latent superhelical stress is normally absorbed by the intrinsic topological buffering capacity of chromatin, helping to avoid spurious topoisomerase activity arising within the essential coding regions of the genome.

overall_design: Maps of nucleosome occupancy in the S. cerevisisae genome generated by MNase-seq under untreated conditions, or at time points following an acute osmotic shock with 0.6M sorbitol.

middle: H

first: Matthew

middle: J

last: Neale


title: Small RNA Analysis within Human Trophoblast-Derived Extracellular Vesicles and Effect of These Structures on the Transcriptome Profile of Human Neural Progenitor Cells [small RNAseq]

city: Columbia

first: Pallav

last: Singh

state: Missouri

address: CE720 Clinical Support and Education

department: Institute for Data Science and Informatics

country: USA

institute: University of Missouri

type: Non-coding RNA profiling by high throughput sequencing

summary: The fetal brain is thought to be dependent upon the placenta for factors that play a specific role in its early development. The tight linkage between the two organs has given rise to the term, the placenta-brain axis. The mouse placenta produces a unique signature pattern of miRNAs target transcripts associated with early fetal brain development, including ones regulating neurogenesis. We hypothesize that placenta-derived extracellular vesicles (EV) transport their molecular cargo, including small RNA, from the placenta to the brain, whereupon their contents can induce pleiotropic effects. We isolated EV from human trophoblast (TB) differentiated in vitro and the parental induced pluripotent stem cells (iPSC) from which the TB was derived, and small RNAseq was done to characterize small RNA profiles within these EV. Human neural progenitor cells (NPC) generated from the same iPSC were exposed to EV derived from TB or iPSC or only treated with control media. Results indicate EV derived from human TB cells contain unique profiles of miRNA and long non-coding RNA (lncRNA) relative to EV isolated from parental iPS cells. Human TB-derived EV readily internalized by human NPC. EV from TB cells induce transcripts in NPC associated with forebrain formation and neurogenesis, suggesting that such EV might program early fetal brain development. Results shed light on the inner workings of the placenta-brain axis. Understanding how contents of TB-derived EV, namely small RNA, affect NPC might yield new insights and potential treatment strategies for neurobehavioral disorders that originate in utero, such as autism spectrum disorders (ASD).  The fetal brain is thought to be dependent upon the placenta for factors that play a specific role in its early development. The tight linkage between the two organs has given rise to the term, the placenta-brain axis. The mouse placenta produces a unique signature pattern of miRNAs target transcripts associated with early fetal brain development, including ones regulating neurogenesis. We hypothesize that placenta-derived extracellular vesicles (EV) transport their molecular cargo, including small RNA, from the placenta to the brain, whereupon their contents can induce pleiotropic effects. We isolated EV from human trophoblast (TB) differentiated in vitro and the parental induced pluripotent stem cells (iPSC) from which the TB was derived, and small RNAseq was done to characterize small RNA profiles within these EV. Human neural progenitor cells (NPC) generated from the same iPSC were exposed to EV derived from TB or iPSC or only treated with control media. Results indicate EV derived from human TB cells contain unique profiles of miRNA and long non-coding RNA (lncRNA) relative to EV isolated from parental iPS cells. Human TB-derived EV readily internalized by human NPC. EV from TB cells induce transcripts in NPC associated with forebrain formation and neurogenesis, suggesting that such EV might program early fetal brain development. Results shed light on the inner workings of the placenta-brain axis. Understanding how contents of TB-derived EV, namely small RNA, affect NPC might yield new insights and potential treatment strategies for neurobehavioral disorders that originate in utero, such as autism spectrum disorders (ASD).

overall_design: 3 Treatment groups of neural progenitor cells--one group which received EVs from day 6 iPS cells for 24 hours; one group which received EVs from day 6 TB cells for 24 hours; and one control group which did not receive any EVs for 24 hours; each group has four replicates

first: Jessica

middle: A

last: Kinkade

first: Mohit

last: Verma

first: Teka

last: Khan

first: Toshihiko

last: Ezashi

first: Nathan

last: Bivens

first: R

middle: M

last: Roberts

first: Trupti

last: Joshi

first: Cheryl

middle: S

last: Rosenfeld


title: Osmotic disruption of chromatin induces Topoisomerase 2 activity at sites of transcriptional stress [CC-seq-v2]

overall_design: Genome-wide maps of Top2ccs in G1-arrested S. cerevisisae under various conditions, generated by CC-seq-v2.


title: E93 controls adult differentiation by repressing broad in Drosophila

city: Barcelona

first: Manuel

last: Irimia

state: Barcelona

address: 88 Dr. Aiguader

department: MELIS

country: Spain

institute: Universitat Pompeu Fabra - Centre for Genomic Regulation

type: Expression profiling by high throughput sequencing

summary: In Drosophila melanogaster, successful development relies on the precise coordination of both spatial and temporal regulatory axes. The temporal axis governs stage-specific identity and developmental transitions through a number of genes, collectively forming the Metamorphic Gene Network. Among these, Ecdysone inducible protein 93F (E93) serves as the critical determinant for adult specification, but its mechanism of action remains unclear. Here, we found that, rather than acting mainly as an instructive signal, E93 promotes adult differentiation through the repression of the pupal specifier broad (br). In the absence of E93, sustained high levels of Br during the pupal stage strongly represses pupal-specific enhancers that are essential for the terminal differentiation of the wing. Notably, RNA-seq analysis confirmed that the majority of E93-dependent transcriptomic changes in pupal wings are primarily driven by br repression. In addition, we also show that Br represses the pupal-enhancers during the larval and prepupal stages preventing the premature implementation of the adult genetic program, and that it also dampens the activity of larval enhancers during the latter stages of larval development. This mechanism of action seems to be a derived feature acquired in Diptera, as in the coleopteran Tribolium castaneum, repression of br by E93 is not sufficient to allow adult differentiation. In summary, our study elucidates the crucial role of the intricate interplay between E93 and Br as the governing mechanism in the process of terminal differentiation in Drosophila. This discovery holds significant implications for advancing our understanding of the evolution of insect metamorphosis.

overall_design: To explore whether the majority of transcriptional changes regulated by E93 during the pupal stage are primarily mediated through the repression of br, we performed a transcriptomic analysis using bulk RNA sequencing (RNA-seq). This analysis was conducted on E93RNAi and E93RNAi+brRNAi wings at 24 and 44 hours after puparium formation, utilizing the rn-Gal4 driver.

first: Josefa

last: Cruz

first: Enric

last: Ureña

first: Luis

middle: P

last: Iñiguez

first: Xavier

last: Franch-Marro

first: David

last: Martín


title: A negatively-charged region within C-terminal domain maintains proper CTCF DNA binding (ATAC-Seq)

city: Shanghai

first: lian

last: liu

address: No.800 Dongchuan Road,Minhang district

country: China

institute: Shanghai Jiao Tong University

summary: As an essential regulator of higher-order chromatin structures, CTCF is a highly conserved DNA binding protein with a central DNA-binding domain of 11 tandem zinc fingers, which are flanked by N- and C-terminal domains of intrinsically disordered regions. The N-terminal domain interacts with cohesin complex and the central ZF domains recognize a large range of diverse genomic sites. However, the function of C-terminal unstructured domain remains less understood. Here, we found that deletion of C-terminal fragment of 116 amino acid increases CTCF-DNA binding. By genetic dissection of this fragment, we uncovered a negatively-charged region responsible for repressing CTCF binding to DNA. Thus, the unstructured C-terminal domain play an important role in maintaining proper CTCF-DNA interactions.

overall_design: To investgate to foucntion of C-termnail of CTCF protein, we estabished several cell line of diifferent mutaion of CTCF and found a part of CTCF could repreess ite binding

first: Lian

last: Liu

first: Qiang

last: Wu


title: A negatively-charged region within C-terminal domain maintains proper CTCF DNA binding (ChIP-Seq)


title: A negatively-charged region within C-terminal domain maintains proper CTCF DNA binding (4C-Seq)


title: A negatively-charged region within C-terminal domain maintains proper CTCF DNA binding (RNA-Seq)


title: Genome-wide expression profiling and phenotypic analysis of downstream targets identify the Fox transcription factor Jumeau as a master regulator of cardiac progenitor cell division

city: Terre Haute

first: Shaad

middle: M.

last: Ahmad

state: IN

address: Science Building, Room 277, 600 Chestnut St.

department: Department of Biology

institute: Indiana State University

summary: Forkhead box (Fox) transcription factors (TFs) mediate multiple conserved cardiogenic processes in both mammals and Drosophila. Our prior work identified the roles of two Drosophila Fox genes, jumeau (jumu) and Checkpoint suppressor 1-like (CHES-1-like), in cardiac progenitor cell specification and division, and in the proper positioning of cardiac cell subtypes. Fox TF binding sites are also significantly enriched in the enhancers of genes expressed in the heart, suggesting that these genes may play a core regulatory role in one or more of these cardiogenic processes. We identified downstream targets of Jumu by comparing transcriptional expression profiles of flow cytometry-sorted mesodermal cells from wild-type embryos and embryos completely lacking the jumu gene and found that genes with functional annotation and ontological features suggesting roles in cell division were overrepresented among Jumu targets. Phenotypic analysis of a subset of these targets identified 21 jumu-regulated genes that mediate cardiac progenitor cell division, one of which, Retinal Homeobox (Rx), was characterized in more detail. Finally, the observation that many of these 21 genes and/or their orthologs exhibit genetic or physical interactions among themselves indicates that Jumu is a master regulator acting as a hub of a cardiac progenitor cell division-mediating network.

overall_design: In order to identify the genes regulated by the Fox TFs Jumu and CHES-1-like, FACS was used to isolate mesodermal cells (GFP-positive cells) from Stage 11-early Stage 12 Drosophila embryos of the following six genotypes:   1: twi-GAL4 UAS-2EGFP/+                                  2: twi-GAL4 Df(3R)Exel6157/UAS-2EGFP Df(3R)Exel6157  3: Df(1)CHES-1-like1; twi-GAL4 UAS-2EGFP/+ 4: Df(1)CHES-1-like1; twi-GAL4 Df(3R)Exel6157/UAS-2EGFP Df(3R)Exel6157 5: twi-GAL4 UAS-2EGFP/UAS-jumu 6: twi-GAL4 UAS-2EGFP/UAS-CHES-1-like  These corresponded respectively to mesodermal cells that (1) were wild type, (2) were homozygous for a jumu null deficiency, (3) were homozygous for a CHES-1-like null deficiency, (4) were doubly homozygous for  both the jumu and CHES-1-like null deficiencies, (5) overexpressed jumu, and (6) overexpressed CHES-1-like. Four biological replicates were obtained for each genotype.    Gene expression profiling was performed using data obtained from RNA-seq for each replicate of these six genotypes. Comparative gene expression profiling analysis was then used to identify genes regulated by Jumu and/or CHES-1-like.

first: Ye

last: Chen


title: Enhancement of adult liver regeneration in mice through the hepsin-mediated epidermal growth factor receptor signaling pathway

city: TAIPEI

first: YU FEI

last: TSAI

address: No. 7, Chung-San S. Rd

country: Taiwan

institute: CLSMB, NTU

summary:
Transcriptome analysis of mouse whole liver. Array raw data was processed by Transcriptome Analysis Console (TAC) Software. Subsequent analyses, including Gene Ontology analysis and Functional Enrichment Analysis (FEA), were performed using the TAC software and the DAVID platform, leveraging WikiPathways. Gene Set Enrichment Analysis (GSEA) was conducted using GSAE software version 4.3.2. All the results, including the list of Differential Expression Genes (DEGs) and outcomes from the aforementioned analyses, have been documented in Supplementary Data 1 and 2 as Excel files.

Given the widespread use of partial hepatectomy for treating various liver pathologies, understanding the mechanisms of liver regeneration is vital for enhancing liver resection and transplantation therapies. Here, we demonstrate the critical role of the serine protease Hepsin in promoting hepatocyte hypertrophy and proliferation. Under steady-state conditions, liver-specific overexpression of Hepsin in adult wild-type mice triggers hepatocyte hypertrophy and subsequent proliferation, significantly increasing liver size. This effect is predominantly driven by the catalytic activity of Hepsin, engaging the EGFR-Raf-MEK-ERK signaling pathway. Significantly, administering Hepsin substantially enhances hepatocyte proliferation and facilitates liver regeneration following a 70% partial hepatectomy. Crucially, the proliferation induced by Hepsin is a transient event, without leading to long-term adverse effects such as liver fibrosis or hepatocellular carcinoma, as evidenced by extensive observation. These results offer substantial potential for future clinical applications and translational research endeavors in the field of liver regeneration post-hepatectomy.

overall_design: We analyzed liver from 18  male mice with AAV transduction for liver-specific hepsin overexpression using the Affymetrix GeneChip MTA 1.0 platform. Array data was processed by Transcriptome Analysis Console (TAC) Software.

first: Yu-Fei

last: Tsai

first: Yu-Chen

last: Hsu

first: Shu-Wha

last: Lin


title: ‘QuickDASH’ to find Unique Genes and Biological Processes Associated with Shoulder Osteoarthritis: a prospective case-control study

status: Public on Dec 03 2024

city: Melbourne

first: Mark

middle: D

last: Ziemann

state: VIC

address: 85 Commercial Rd

department: Bioinformatics Working Group

country: Australia

institute: Burnet Institute

summary: Osteoarthritis (OA) is a disease impacting the synovial joint complex, yet transcriptional changes specific to shoulder OA remain underexplored. This study aims to profile transcriptomic changes in periarticular tissues from patients undergoing shoulder replacement for OA. By correlating these profiles with QuickDASH scores—a validated measure of worsening shoulder function—this research seeks to understand the gene expression changes associated with clinical decline. Capsular tissue biopsies from shoulder OA patients were compared with those from a control group undergoing shoulder stabilization for recurrent instability. This investigation forms part of a larger transcriptomic analysis of painful shoulder conditions which will address the current gap in knowledge regarding the molecular and genetic underpinnings of shoulder OA, rotator cuff tears and cuff-tear arthropathy.

overall_design: Tissue samples were collected from OA patients with a range of QuickDASH scores and underwent transcriptome profiling to understand the gene associations with shoulder joint symptoms and disability. Bone, muscle, capsule, fat and synovium are included from n=6 patients.

first: Samuel

last: Lynskey

first: Stephen

last: Gill

first: Sean

middle: L

last: McGee

first: Richard

last: Page


title: Small RNA Analysis within Human Trophoblast-Derived Extracellular Vesicles and Effect of These Structures on the Transcriptome Profile of Human Neural Progenitor Cells [bulk RNAseq]

first: Pallav

last: Singh

summary:
The fetal brain is thought to be dependent upon the placenta for factors that play a specific role in its early development. The tight linkage between the two organs has given rise to the term, the placenta-brain axis. The mouse placenta produces a unique signature pattern of miRNAs target transcripts associated with early fetal brain development, including ones regulating neurogenesis. We hypothesize that placenta-derived extracellular vesicles (EV) transport their molecular cargo, including small RNA, from the placenta to the brain, whereupon their contents can induce pleiotropic effects. We isolated EV from human trophoblast (TB) differentiated in vitro and the parental induced pluripotent stem cells (iPSC) from which the TB was derived, and small RNAseq was done to characterize small RNA profiles within these EV. Human neural progenitor cells (NPC) generated from the same iPSC were exposed to EV derived from TB or iPSC or only treated with control media. Results indicate EV derived from human TB cells contain unique profiles of miRNA and long non-coding RNA (lncRNA) relative to EV isolated from parental iPS cells. Human TB-derived EV readily internalized by human NPC. EV from TB cells induce transcripts in NPC associated with forebrain formation and neurogenesis, suggesting that such EV might program early fetal brain development. Results shed light on the inner workings of the placenta-brain axis. Understanding how contents of TB-derived EV, namely small RNA, affect NPC might yield new insights and potential treatment strategies for neurobehavioral disorders that originate in utero, such as autism spectrum disorders (ASD).
The fetal brain is thought to be dependent upon the placenta for factors that play a specific role in its early development. The tight linkage between the two organs has given rise to the term, the placenta-brain axis. The mouse placenta produces a unique signature pattern of miRNAs target transcripts associated with early fetal brain development, including ones regulating neurogenesis. We hypothesize that placenta-derived extracellular vesicles (EV) transport their molecular cargo, including small RNA, from the placenta to the brain, whereupon their contents can induce pleiotropic effects. We isolated EV from human trophoblast (TB) differentiated in vitro and the parental induced pluripotent stem cells (iPSC) from which the TB was derived, and small RNAseq was done to characterize small RNA profiles within these EV. Human neural progenitor cells (NPC) generated from the same iPSC were exposed to EV derived from TB or iPSC or only treated with control media. Results indicate EV derived from human TB cells contain unique profiles of miRNA and long non-coding RNA (lncRNA) relative to EV isolated from parental iPS cells. Human TB-derived EV readily internalized by human NPC. EV from TB cells induce transcripts in NPC associated with forebrain formation and neurogenesis, suggesting that such EV might program early fetal brain development. Results shed light on the inner workings of the placenta-brain axis. Understanding how contents of TB-derived EV, namely small RNA, affect NPC might yield new insights and potential treatment strategies for neurobehavioral disorders that originate in utero, such as autism spectrum disorders (ASD).

first: Jessica

last: Kinkade

first: Mohit

last: Verma

first: Teka

last: Khan

first: Toshihiko

last: Ezashi

first: Nathan

last: Bivens

first: R

last: Roberts

first: Trupti

last: Joshi

first: Cheryl

last: Rosenfeld


title: Gonadal sex reversal at single-cell resolution in Znrf3-deficient mice

status: Public on Nov 29 2024

city: Oxford

first: Michelle

last: Simon

state: Oxfordshire

address: Harwell

department: Bioinformatics

institute: MRC

summary: Early gonadal-mesonephros tissues give rise to the developing gonad, with potential to diverge towards either a testis or ovarian gonadal fate. ZNRF3 mutant homozygotic mice develop a variable sex reversal previously uncharacterised at the single cell level. We used scRNA-Seq to compare XX and XY WT C57BL/6J mouse gonads to ZNRF3-deficient mice across multiple timepoints, during and after initial sex determination.

overall_design: C57BL/6J mouse gonads were dissected away from the mesonephros at 11.5, 12.5 and 14.5 dpc for XX WT, XY WT and XY ZNRF3-deficient mice, and isolated for analysis via scRNA-Seq. Gonadal tissue at 14.5 dpc could further be phenotyed as ovarian, testis, or ovotestis.

first: Raissa

last: Kay

last: Reeves

first: Andy

last: Greenfield


title: Side- and disease-dependent changes in human aortic valve cell population and transcriptomic heterogeneity determined by single-cell RNA sequencing

city: Atlanta

first: Hanjoong

last: Jo

state: GA

address: 1760 Haygood Drive NE

department: Biomedical Engineering

institute: Georgia Tech & Emory University

summary: Calcific aortic valve disease develops preferentially on the fibrosa side while the ventricularis side remains relatively spared with unknown mechanisms. We hypothesized that the fibrosa is prone to the disease due to side-dependent differences in transcriptomic patterns and cell phenotypes. To test this hypothesis, we performed single-cell RNA-sequencing using a new method to collect endothelial-enriched samples from either the fibrosa or ventricularis of freshly-obtained human AV leaflets from 5 donors ranging from non-diseased to fibrocalcific stages.

overall_design: Human aortic valve cells, including valvular endothelial cells (VEC), valvular interstitial cells (VIC), immune cells (macrophages, t-cells), transitional cells, and stromal cells from 5 donors ranging from non-diseased to fibrocalcific

first: Nicolas

last: Villa-Roel


title: DNA Methylation dependent and independent binding of CDX2 imparts distinct developmental and homeostatic functions. [CrossLinkedChIPseq]

city: Los Angeles

first: Unmesh

last: Jadhav

state: California

address: 1425 San Pablo Street

department: Stem Cell and Regenerative Medicine

institute: University of Southern California

summary: Precise spatiotemporal and cell type-specific gene expression is essential for proper tissue development and function. Transcription factors (TFs) guide this process by binding to developmental stage-specific targets and establishing an appropriate enhancer landscape. DNA and chromatin modifications form barriers to the genomic binding of TFs, however, the details of how TFs navigate various chromatin features and selectively bind a small portion of the millions of possible genomic target loci remain unknown. Here we show that Cdx2, a pioneer TF that binds distinct targets in developing and adult intestinal epithelial cells, has a preferential affinity to a non-canonical CpG-containing motif in vivo. A higher frequency of this motif at the embryonic and fetal target loci of Cdx2 and the methylated state of the CpG particularly during development allows its selective binding and activation of developmental enhancers and linked genes. Conversely, demethylation at these enhancers prohibits ectopic Cdx2 binding in adult cells, where Cdx2 binds the canonical motif without a CpG. This distinct Cdx2 binding allows corecruitment of Ctcf and Hnf4 facilitating the establishment of intestinal superenhancers during development and enhancers activating adult tissue functions, respectively. Induced gain of DNA methylation in the adult epithelium in vivo or in cultured cells causes recruitment of Cdx2 to the developmental target loci and cobinding of the partner TFs. Our results demonstrate that the distinct propensities of Cdx2 to bind motifs with and without CpGs and the divergent distribution of these motifs at developmental and adult target sites allow Cdx2 to navigate distinct DNA methylation profiles and activate cell type-specific enhancers and genes.

overall_design: Villi cells were extracted in wild type and Eed KO mice and profiled for H3K9me3

first: Alireza

last: Lorzadeh

first: George

last: Ye

first: Sweta

last: Sharma


title: DNA Methylation dependent and independent binding of CDX2 imparts distinct developmental and homeostatic functions. [cutAndRun]

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Epithelial cells were extracted in E12.5, E16.5, adult and adult Eed KO mice and profiled for Cdx2, Ctcf, and Hnf4. HCT116 was treated with DMSO or GSK-3484862 and profiled for CDX2


title: DNA Methylation dependent and independent binding of CDX2 imparts distinct developmental and homeostatic functions. [ATAC-Seq]

overall_design: Villi cells were extracted in Eed KO mice and profiled for ATAC


title: N-terminus of Drosophila MSL1 is critical for dosage compensation

city: Moscow

first: Anastasia

last: Revel-Muroz

address: 34/5 Vavilov St.

country: Russia

institute: Institute of Gene Biology, Russian Academy of Sciences

summary: The male-specific dosage compensation complex (DCC), which consists of five proteins and two non-coding roX RNAs, is necessary for the transcriptional enhancement of X-linked genes to compensate for the sex chromosome monosomy in Drosophila XY males, compared with XX females. The MSL1 and MSL2 proteins form the heterotetrameric core of DCC and are critical for the specific recruitment of the DCC to the high-affinity “entry” sites (HAS) on the X chromosome. Here we demonstrated that the N-terminal region of MSL1 is critical for its stability and functions.  Amino acid deletions and substitutions in the N-terminal region of MSL1 strongly affect both interaction with roX2 RNA and DCC binding to HAS on the X chromosome. In particular, substitution of the conserved N-terminal amino-acids 3-7 in MSL1GS has an affect on dosage compensation similar to inactivation of genes encoding roX RNAs. MSL1GS binds to promoters like MSL1WT but does not co-bind with MSL2 and MSL3 to X chromosomal HAS. However, over-expression of MSL2 partially restores the functional activity of MSL1GS in dosage compensation. Thus, the interaction of MSL1 with roX RNA is critical for the efficient assembly of DCCs on HAS of the male X chromosome.

overall_design: ChIP-seq signal of the MSL1, MSL2 and MSL3 proteins occupancy in adult males and females represented as wt, M1[wt], M1[wt]_M2, M1[Δ41-85]_M2, M1[Δ1-15]_M2 and M1[2*G;3*S]_M2 lines.

first: O

last: Maksimenko

first: A


title: Engraftment of self-renewing endometrial epithelial organoids promotes endometrial regeneration by differentiating into functional glands in rats

city: Hangzhou

first: Xiaona

last: Lin

address: No.3 Qingchun East Road

institute: Sir Run Run Shaw Hospital Affiliated to Zhejiang University School of Medicine

summary: Extensive trauma disrupts endometrial regeneration by diminishing endometrial stem or progenitor cells. Endometrial epithelial organoids (EEOs) are used for endometrial regeneration. However, how EEOs repair injured endometrial tissues and their advantages over bone marrow mesenchymal stem cells (BMSCs) are unclear. This study explored whether EEOs surpass BMSCs to repair injured endometrium and examined whether endometrial restoration involves integrating EEOs into the endometrial tissue of the recipient. Rat EEOs (rEEOs) mimicking the features of the rat endometrium were developed. An endometrial injury rat model was used to compare the effects of rEEOs and rat BMSCs (rBMSCs) on endometrial regeneration and reproductive recovery. Bulk RNA-sequencing analysis was conducted to investigate the capacity of rEEOs for endometrial regeneration and identify discrepancies between rEEOs and rBMSCs. Green fluorescent protein (GFP)-labeled rEEOs or red fluorescent protein-labeled rBMSCs were transplanted to track the transplanted cells in vivo. Fertility recovery in rats transplanted with rEEOs was more comparable to that of normal rats than in rBMSC-treated rats. rEEOs had a high concentration of endometrial epithelial stem or progenitor cells and secreted vascular endothelial growth factor-A to promote endometrial neovascularization. Cells from GFP-labeled rEEOs integrated and differentiated into functional glands within the injured endometrium. Transplanting EEOs restored the morphology and function of severe endometrial injury better than BMSC transplantation. EEO cells repair the endometrium by differentiating into functional glandular epithelial cells. These findings offer preclinical evidence supporting in vitro expansion and transplanting of EEOs as promising approaches to restore fertility in women with insufficient endometrial regeneration.

overall_design: This study aims to explore whether EEOs surpass BMSCs in their ability to repair injured endometrium and to examine whether the restoration process involves the integration of EEOs into the endometrial tissue of the recipient.

first: Yana

last: Ma

first: Jingjing

last: Qian

first: Mengying

last: Liu


title: An Epigenetic Trigger for Induction of Genomic Plasticity  Following Exposure to Space Environment: Mission SpaceX CRS-19 RRR-1 [RNA-seq]

status: Public on Nov 28 2024

city: Pittsburgh

first: CHANDAN K

last: SEN

state: PA

address: 221 Republic Street

institute: University of Pittsburgh

summary: Genomic plasticity helps adapt to extreme environmental conditions. We tested the hypothesis that exposure to space environment (ESE) impacts the epigenome as marked by DNA hypomethylation to induce genomic plasticity in responders. Murine skin samples from the Rodent Research Reference Mission-1 were procured from the International Space Station (ISS) National Lab.  Targeted RNA sequencing to test differential gene expression between the skin of ESE versus ground controls revealed upregulation of VEGF mediated angiogenesis pathways secondary to promoter hypomethylation in responder ESE cohort. Methylome sequencing identified ESE-sensitive candidate hypomethylated genes including developmental angiogenic genes Araf, VegfbandVegfr1.  Based on differentially expressed genes, the angiogenesis biofunction was enriched in responders compared to non-responders. The induction of genomic plasticity in response to ESE, as reported herein, may be viewed as a mark of biological resilience that is evident in a minority of organisms, responders but not in non-responders, exposed to the same stressor. Inducible genomic plasticity may be implicated in natural resilience to ESE.

overall_design: Femoral skin samples from 35 young (~10-16 weeks) female BALB/cAnNTac mice (Taconic Biosciences) were obtained through the International Space Station (ISS) National Laboratory’s Biospecimen Sharing Program, and no live animals were involved in this study. These mice belonged to the SpaceX CRS-19 Rodent Research-8 mission [also known as Rodent Research Reference Mission-1 (RRR1)] were procured from ISS National Laboratory in collaboration with Dr. Liz Warren. The detailed information regarding the RRR-1 mission is available through ISS laboratory’s Center for the Advancement of Science in Space (CASIS) research archive (www.iss-casis.org/research-on-the-iss/solicitations/2018-rodent-research/). Briefly, this study investigated skin samples from 17 mice that were flown to space (10 euthanized in space; 8 euthanized post-landing) for a total of ~40 days and 18 mice age-matched ground control animals.For targeted RNA sequencing, total RNA was extracted using ABI Picopure RNA isolation kit and quality assessment was performed using Agilent 2100 Bioanalyzer.

first: Kanhaiya

last: Singh

first: Priyanka

last: Verma

first: Chandan

middle: K

last: Sen


title: Influence of the MUC16 on gene expression of cancer cells from PDAC

city: omaha

first: Prakash

last: Radhakrishnan

state: NE

address: 986805 Nebraska Medical Center

department: Eppley Institute for Research in Cancer

institute: University of Nebraska Medical Center

summary:
To investigate the differentially expressed genes and the pathways they might alter upon loss of MUC16 and subsequent perturbation of its downstream signaling
We  performed gene expression profiling analysis using data obtained from RNA-seq of the two different conditions (WT versus MUC16-knockout) (three replicates each).

overall_design: Comparative gene expression profiling analysis of RNA-seq data from WT versus MUC16-knockout T3M4 cells.


title: An Epigenetic Trigger for Induction of Genomic Plasticity Following Exposure to Space Environment: Mission SpaceX CRS-19 RRR-1 [RRBS]

type: Methylation profiling by high throughput sequencing

overall_design: Femoral skin samples from 35 young (~10-16 weeks) female BALB/cAnNTac mice (Taconic Biosciences) were obtained through the International Space Station (ISS) National Laboratory’s Biospecimen Sharing Program, and no live animals were involved in this study. These mice belonged to the SpaceX CRS-19 Rodent Research-8 mission [also known as Rodent Research Reference Mission-1 (RRR1)] and were procured from ISS National Laboratory in collaboration with Dr. Liz Warren. The detailed information regarding the RRR-1 mission is available through ISS laboratory’s Center for the Advancement of Science in Space (CASIS) research archive (www.iss-casis.org/research-on-the-iss/solicitations/2018-rodent-research/). Briefly, this study investigated skin samples from 17 mice that were flown to space (10 euthanized in space; 8 euthanized post-landing) for a total of ~40 days and 18 mice age-matched ground control animals.For targeted RNA sequencing, total RNA was extracted using ABI Picopure RNA isolation kit and quality assessment was performed using Agilent 2100 Bioanalyzer.


title: DNA methylation biomarkers predict Wilms tumor disease progression

city: Cairo

first: Deena

last: Jalal

address: 1 Seket Al-Emam Street, El-Madbah El-Kadeem Yard,El-Saida Zenab

country: Egypt

institute: Children Cancer Hospital Egypt 57357

type: Methylation profiling by genome tiling array

summary: Wilms tumor (WT), also known as nephroblastoma, is the most commonly observed renal tumor within the genitourinary tract of children and constitutes 5% of all childhood malignancies. In this study, we used microarray technology to explore methylation patterns in both WT and adjacent healthy tissues from excised kidneys prior to any chemotherapy treatment in stage I and II WTs. We report several differentially methylated regions that show potential as prognostic biomarkers for disease relapse, and overall patient survival. To explain the mechanistic role of DNA methylation changes in WT relapse, we explore the genes controlled by the differentially methylated IGF2 region, and show elevated expression of INS-IGF2 transcript in tumour tissue of patients that have relapsed after treatment. Altogether, this study provides insights into causes of chemotherapy resistance in patients with low risk WT.

overall_design: In the aim to identify methylation biomarkers for disease prognosis, tumor and normal FFPE tissue samples that were surgically removed before treatment were collected from the Pathology department from nine patients who had complete response to treatment and nine patients who had recurrent disease. DNA samples were analyzed Illumina Infinium Human Methylation EPIC bead chips.

first: Mohamed

middle: Y

last: Ali

first: Abdelaziz

last: Abdelaziz

first: Naglaa

last: Elkinaai

first: Wael

last: Zekri

first: Ahmed

last: Sayed


title: Widespread termination of mammalian RNA polymerase II at T-rich DNA sequences (nuclear RNA-Seq)

city: Exeter

first: Steven

last: West

state: Devon

address: Stocker Rd

department: Living Systems Institute

institute: University of Exeter

summary: The best-studied mechanism of eukaryotic RNA polymerase II (RNAPII) transcriptional termination is at protein-coding genes and involves endonucleolytic cleavage of the nascent RNA at the polyadenylation site. The RNAPII-associated cleavage product is then degraded 5'→3’ by XRN2 to elicit termination. In contrast, prokaryotic RNAP and eukaryotic RNAPIII often terminate directly over T-tracts in the non-template DNA strand. Here, we demonstrate a similar capability for mammalian RNAPII. This mechanism terminates snRNA transcription, which we unexpectedly show to be Integrator-independent. It is more generally employed where RNAPII elongation competence is low, especially in promoter-proximal regions and downstream of some protein-coding genes. In contrast, RNAPII within gene bodies does not terminate at T-tracts. Finally, XRN2-dependent, and T-tract termination are usually independent: the former acts following polyadenylation site cleavage, whereas the latter is employed where XRN2 cannot be engaged. Overall, we propose that RNAP’s retain the potential to terminate over T-rich sequences throughout evolution.

overall_design: Comparative meta and gene expression analysis of nuclear RNA sequencing (RNA-Seq) for EXOSC3-dTAG and unmodified HCT116 degron cell lines (with or without KD)

first: Lee

last: Davidson

first: Jérôme

middle: O

last: Rouvière

first: Rui

last: Sousa-Luís

first: Takayuki

last: Nojima

first: Nicholas

last: Proudfoot

first: Torben

last: Heick Jensen

first: Steve


title: Widespread termination of mammalian RNA polymerase II at T-rich DNA sequences (POINT-Seq)

summary: The best-studied mechanism of eukaryotic RNA polymerase II (RNAPII) transcriptional termination is at protein-coding genes and involves endonucleolytic cleavage of the nascent RNA at the polyadenylation site. The RNAPII-associated cleavage product is then degraded 5'→3’ by XRN2 to elicit termination. In contrast, prokaryotic RNAP and eukaryotic RNAPIII often terminate directly over T-tracts in the non-template DNA strand. Here, we demonstrate a similar capability for mammalian RNAPII. This mechanism terminates snRNA transcription, which we unexpectedly show to be Integrator-independent. It is more generally employed where RNAPII elongation competence is low, especially in promoter-proximal regions and downstream of some protein-coding genes. In contrast, RNAPII within gene bodies does not terminate at T-tracts. Finally, XRN2-dependent, and T-tract termination are usually independent: the former acts following polyadenylation site cleavage, whereas the latter is employed where XRN2 cannot be engaged. Overall, we propose that RNAP’s retain the potential to terminate over T-rich sequences throughout evolution

overall_design: Comparative meta and gene expression analysis of POINT-seq technology for HCT116 INTS1-AID degron cell lines (with or without KD)


title: Widespread termination of mammalian RNA polymerase II at T-rich DNA sequences (POINT5-Seq)

overall_design: Comparative meta and gene expression analysis of POINT5-seq technology for HCT116 INTS1-AID degron cell lines (with or without KD)


title: Gene ontology defines pre-post- hatch energy dynamics in the complexus muscle of broiler chickens

status: Public on Nov 27 2024

city: Rehovot

first: Jonathan

last: Dayan

address: Herzel 229

country: Israel

institute: Faculty of Agriculture Hebrew University of Jerusalem

summary:
Abstract
Background
Chicken embryos emerge from their shell by the piercing movement of the hatching muscle. Although considered a key player during hatching, with activity that imposes a substantial metabolic demand, data are still limited. The study provides a bioenergetic and transcriptomic analyses during the pre-post-hatching period.
Methods
Weight and morphology alongside content determination of creatine and glycogen were analysed. Transcriptome identified differentially expressed genes and enriched biological processes associated with hatching muscle development, catabolism, and energy provision. Using gene set enrichment, we followed the dynamics of gene-sets involved in energy pathways of oxidative phosphorylation, protein catabolism, glycolysis/gluconeogenesis, and glycogen metabolism.
Results
Results show several significant findings: (A) Creatine plays a crucial role in the energy metabolism of the hatching muscle, with its concentration remaining stable while glycogen concentration is depleted at hatch and placement. (B) The hatching muscle has the capacity for de-novo creatine synthesis, as indicated by the expression of related genes (AGAT, GAMT). (C) Transcriptome provided insights into genes related to energy pathways under conditions of pre-hatch oxygen and post-hatch glucose limitations (oxidative phosphorylation: NDUF, MT-ND, SDH, UQCR, COX, MT-CO, ATP5, MT-ATP; glycolysis/gluconeogenesis: FBP,G6PC, PFKM; glycogen metabolism: PPP1, PYGL, GYG1). (D) The post-hatch upregulation of protein catabolic processes genes (PSMA, RNF, UBE, FBX), which align with the muscle's weight dynamics, indicates a functional shift from movement during hatching to lifting the head during feeding.
Conclusions
There is a dynamic metabolic switch in the hatching muscle during embryo-to-hatchling transition. When glycogen concentration depletes, energy supply is maintained by creatine and its de-novo synthesis. Understanding the hatching muscle's energy dynamics is crucial, for reducing hatching failures in endangered avian species, and in domesticated chickens.

overall_design: MARS-Seq transcriptome analysis (E15, E17, E19, hatch and chick placement, n=6,6,5,5,4 per day, respectively).

first: Zehava

last: Uni


title: NK2R control of energy expenditure and feeding to treat metabolic diseases

city: Köln

first: Jens

middle: C

last: Brüning

address: Gleueler Str. 50

department: Neuronal Control of Metabolism

country: Germany

institute: Max Planck Institute for Metabolism Research

summary: The combination of decreasing food intake and increasing energy expenditure represents a powerful strategy for counteracting cardiometabolic diseases, such as obesity and type 2 diabetes1. Yet current approaches require conjugating multiple receptor agonists to achieve both effects2–4 and, thus far, no safe energy-expending option has reached the clinic. Here we show that activation of Neurokinin 2 Receptor (NK2R) is sufficient to suppress appetite centrally and increase energy expenditure peripherally. We focused on NK2R after discovering its genetic links to obesity and glucose control. However, therapeutically exploiting NK2R signalling has previously been unattainable because its endogenous ligand, Neurokinin A (NKA), is short-lived and lacks receptor specificity5,6. Therefore, we developed selective, long-acting NK2R agonists, with potential for once-weekly administration in humans. In mice, these agonists elicit weight loss by inducing energy expenditure and non-aversive appetite suppression that circumvents canonical leptin signalling. Additionally, a hyperinsulinemic-euglycemic clamp reveals that NK2R agonism acutely enhances insulin sensitization. In diabetic, obese nonhuman primates, NK2R activation significantly decreases body weight, blood glucose, triglycerides, and cholesterol, and ameliorates insulin resistance. These findings identify a single receptor target that leverages both energy-expending and appetite-suppressing programs to improve energy homeostasis and reverse cardiometabolic dysfunction across species.

overall_design: Hindbrains (DVC) of mice treated either with NK2R agonist or vehicle were subjected to single-nucleus RNA-seq to investigate activated cell populations. Samples from the same experimental condition were pooled together (n = 5 mice/group) for a total of 3 samples per condition.

first: Zachary

last: Gerhart-Hines

first: Corinna

last: Bauder

first: Lukas

last: Steuernagel

first: Jenny

last: Brown

first: Frederike

last: Sass


title: Motif distribution and DNA methylation underlie distinct Cdx2 binding during development and homeostasis

first: Unmesh

last: Jadhav

summary: Transcription factors guide tissue development by binding to developmental stage-specific targets and establishing an appropriate enhancer landscape. In turn, DNA and chromatin modifications direct the genomic binding of transcription factors. However, how transcription factors navigate chromatin features to selectively bind a small subset of all the possible genomic target loci remains poorly understood. Here we show that Cdx2 - a lineage defining transcription factor that binds distinct targets in developing versus adult intestinal epithelial cells - has a preferential affinity for a non-canonical CpG-containing motif in vivo. A higher frequency of this motif at embryonic Cdx2 targets and methylated state of the CpG during development enables selective Cdx2 binding and activation of developmental enhancers and genes. In adult cells, demethylation at these enhancers prevents ectopic Cdx2 binding, instead directing Cdx2 to its canonical motif without a CpG. This shift in Cdx2 binding facilitates Ctcf and Hnf4 recruitment, establishing super-enhancers during development and homeostatic enhancers in adult cells, respectively. Induced DNA methylation in adult mouse epithelium or cultured cells recruits Cdx2 to developmental targets, promoting corecruitment of partner transcription factors. Thus, Cdx2’s differential CpG motif preferences enable it to navigate distinct DNA methylation profiles, activating genes specific to appropriate developmental stages.

overall_design: Refer to individual Series

first: Alireza

last: Lorzadeh

first: George

last: Ye

first: Sweta

last: Sharma


title: Herpes simplex virus 1 infection of human brain organoids and pancreatic stem cell-islets drives transcripts associated with Alzheimer’s disease and autoimmune diseases

city: Worcester

first: Elaine

last: Lim

state: MA

address: 366 Plantation Street, Paul J DiMare 5-1025

institute: UMass Chan Medical School

summary: Viral infections leading to inflammation have been implicated in several common diseases such as Alzheimer’s disease (AD) and type 1 diabetes (T1D). Of note, herpes simplex virus 1 (HSV-1) has been reported to be associated with AD. We sought to identify the transcriptomic changes due to HSV-1 infection and anti-viral drug (acyclovir, ACV) treatment of HSV-1 infection in dissoci-ated cells from human cerebral organoids (dcOrgs) versus stem cell-derived pancreatic islets (sc-islets) to gain potential biological insights into the relevance of HSV-1-induced inflammation in AD and T1D. We observed that differentially expressed genes (DEGs) in HSV-1-infected sc-islets were enriched for genes associated with several autoimmune diseases, most significantly T1D but also rheumatoid arthritis, psoriasis, Crohn’s disease, and multiple sclerosis, whereas DEGs in HSV-1-infected dcOrgs were exclusively enriched for genes associated with AD. ACV treatment of sc-islets did not rescue transcript expression of autoimmune disease-associated genes. Finally, we identified gene ontology categories that were enriched for DEGs that were in common across, or unique to, viral treatment of dcOrgs and sc-islets, such as categories involved in the transferase complex, mitochondrial and autophagy function. Collectively, this studies pro-vide insight to the molecular effects of inflammation in AD and T1D.

overall_design: We performed RNA sequencing on uninfected, HSV-1-infected, as well as HSV-1-infected and ACV-treated sc-islets in triplicates.


title: A Novel Human Protein-Coding Locus Identified Using a Targeted RNA Enrichment Technique

city: Xiamen

first: Lu

last: Tang

address: Jimei road

institute: HuaQiao university

summary: Accurate and comprehensive genomic annotation, including the full list of protein-coding genes, is vital for understanding the molecular mechanisms of human biology. We have previously shown that the genome contains a multitude of yet hidden functional exons and transcripts, some of which might represent novel mRNAs. These results resonate with those from other groups and strongly argue that two decades after the completion of the first draft of the human genome sequence, the current annotation of human genes and transcripts remains far from being complete. Using a targeted RNA enrichment technique, we showed that one of the novel functional exons previously discovered by us and currently annotated as part of a long non-coding RNA, is actually a part of a novel protein-coding gene, InSETG-4, which encodes a novel human protein with no known homologs or motifs. We found that InSETG-4 is induced by various DNA-damaging agents across multiple cell types and therefore might represent a novel component of DNA damage response. Despite its low abundance in bulk cell populations, InSETG-4 exhibited expression restricted to a small fraction of cells, as demonstrated by the amplification-based single-molecule fluorescence in situ hybridization (asmFISH) analysis. This study argues that yet undiscovered human protein-coding genes exist and provides an example of how targeted RNA enrichment techniques can help to fill this major gap in our knowledge of the information encoded in the human genome.

overall_design: This experiment employed rapid amplification of cDNA ends (RACE) to enrich for full-length transcripts, specifically targeting 2 anchor exons of the InSETG-4 gene. The goal is to enhance genome annotations by identifying and characterizing novel transcripts.

first: Dongyang

last: Xu

first: Philipp

last: Kapranov


overall_design: Villi cells were extracted in wild type and Eed KO mice and profiled for H3K27ac, H3K27me1, H3K27me2, H3K27me3, H3K36me2, H3K36me3, H2AK119Ub


title: DNA methylation epigenome analysis of articular cartilage from human foetal femur samples using Illumina methylation EPIC 850k (v1.0) arrays.

city: Newcastle upon Tyne

first: Sarah

last: Rice

address: Central Parkway

department: Biosciences Institute

institute: Newcastle University

summary: DNA methylation profiling of the entire genome of articular cartilage extracted from human foetal samples across a range of gestational periods. Profiling of 72 samples was performed with Illumina HumanMethylation850 EPIC v1.0 microarrays, measuring methylation at approximately 850K sites.

overall_design: DNA was bisulfite-converted for 72 samples and hybridised to the Illumina HumanMethylation850 EPIC version 1.0 array.

first: Euan

last: McDonnell

middle: E

last: Orr

first: Matthew

last: Barter

first: Danielle

last: Rux

first: Abby

last: Brumwell

first: Nicola

last: Wrobel

first: Lee

last: Murphy

first: Lynne

last: Overmann

first: Antony

last: Sorial

first: David

last: Young

first: Jamie

last: Soul


title: Ldb1 establishes multi-enhancer networks to regulate gene expression

city: Cambridge

first: Viraat

middle: Yogi

last: Goel

state: Massachusetts

department: Biological Engineering

institute: Massachusetts Institute of Technology (MIT)

summary: How enhancers specifically connect to gene promoters is still unclear. Besides the CTCF/cohesin machinery, only a small set of nuclear factors have been studied for a direct role in physically connecting regulatory elements. Here, we show via acute degradation experiments that LDB1 directly and broadly promotes enhancer-promoter loops. Utilizing multiple degron systems, we demonstrate that most endogenous LDB1-mediated contacts can form in the absence of CTCF, cohesin and YY1. Furthermore, an engineered/forced, LDB1-driven chromatin loop can form in the absence of cohesin. Yet, in a fraction of cases cohesin driven extrusion may promote LDB1 anchored loops. Leveraging the dynamic reorganization of nuclear architecture during the transition from mitosis to G1 phase, we establish a relationship between LDB1-dependent interactions in the context of TAD organization and gene activation. Tri-C and Region Capture Micro-C reveal that LDB1 organizes multi-enhancer networks to activate transcription. This establishes LDB1 as direct driver of connectivity between regulatory elements.

overall_design: Region Capture Micro-C was performed in LDB1-AID cells (untreated and 4 hour auxin-treated conditions).

first: Nicholas

middle: G

last: Aboreden

first: Gerd

last: Blobel

first: Anders

last: Hansen


title: ASCL1 phospho-regulation during lineage restrictions of embryonic stem cells (ATAC-Seq)

city: London

first: Roberta

last: Azzarelli

address: 29-39 Brunswick square

department: School of Pharmacy

institute: University College London

summary: Here we investigate how ASCL1 levels and phosphorylation modulate its activity during lineage restrictions of embryonic stem cells.

overall_design: ATAC-seq in mESCs in neuroectoderm media with the induction of either WT of SA (phosphomutant) ASCL1 expression. Four biological replicates per condition.

last: Gillen

first: Anna

last: Philpott


title: ASCL1 phospho-regulation during lineage restrictions of embryonic stem cells (RNA-Seq)

overall_design: RNA-seq in mESCs in neuroectoderm media with the induction of either WT of SA (phosphomutant) ASCL1 expression. Three biological replicates per condition.

first: Sarah


title: Ldb1 establishes multi-enhancer networks to regulate gene expression [RNA-seq]

city: Philadelphia

address: 3615 Civic Center Blvd

institute: University of Pennsylvania

overall_design: RNA-seq in parental G1E-ER4 cells and two LDB1-AID-mCherry clones under untreated conditions. To measure concordance amongst transcriptomes between clonal lines expressing the LDB1-AID-mCherry fusion protein compared to parental G1E-ER4 cells.


title: CHD6 eviction of promoter nucleosomes maintains housekeeping transcriptional program in prostate cancer

city: beijing

first: Lina

last: Bu

state: Beijing

address: xueyuanlu 38

institute: peking university

summary: Genome-wide binding profile of CHD6 (Bethyl, catalog: A301-221A) in HEK293 were profiled using cleavage under targets and tagmentation sequencing (CUT&Tag-seq).

overall_design: CUT&Tag-seq library of CHD6 associated chromatin were immunoprecipitated in HEK293

first: Shaodong

last: Huang

first: Dongyu

last: Zhao


title: Chromosome-level genome assembly of the ratmouth barbel, Ptychidio jordani

status: Public on Nov 26 2024

city: Guangzhou

first: Xidong

last: Mu

address: No.1 Xingyu Road

institute: Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences

summary: The ratmouth barbel (Ptychidio jordani) is a critically endangered freshwater fish from the Cyprinidae family, primarily due to overfishing and habitat disruption. To address the challenges of its shrinking wild populations and the difficulties in artificial reproduction, we sequenced, assembled, and annotated a high-quality chromosome-level genome of P. jordani using next-generation short-read sequencing, third-generation long-read sequencing, and Hi-C sequencing. The final genome assembly was 1.14 Gb, consisting of 25 chromosomes with a contig N50 of 25.14 Mb and a scaffold N50 of 42.91 Mb. We identified 25,183 protein-coding genes, 751.75 Mb of repeats, and 19,373 ncRNAs. Methylation loci on most chromosomes ranged from 1,000 to 3,000 per 100 kb window. Gene expression levels across various tissues were analyzed, revealing 12,135 (caudal fin), 11,465 (liver), 14,438 (gill), 12,413 (heart), 8,301 (spleen), and 3,578 (kidney) differentially expressed genes compared to muscle. The comprehensive genomic and transcriptomic resources generated here will aid in understanding the ecology, adaptation, and environmental responses of P. jordani, supporting future research and conservation efforts.

overall_design: Methylation profiling of muscle

first: Yuanyuan

last: Wang


title: Chromosome-level genome assembly of the ratmouth barbel, Ptychidio jordani [RNA-seq]

overall_design: RNA-seq profiling of muscle, caudal fin, liver, gill, heart, spleen and kidney.


title: Remodeling of the chromatin landscape in peripheral blood cells in patients with severe Delta COVID-19

first: Vasiliy

last: Akimov

email: VAkimov@cspfmba.ru, vasoakim@gmail.com

address: Pogodinskaya Street, 10, bld. 1

institute: Centre for Strategic Planning of FMBA of Russia

summary: COVID-19 is characterized by systemic proinflammatory shifts with development of serious alterations in the functioning of the immune system. Investigations of the gene expression changes accompanying infection state provide insight towards understanding of the molecular and cellular processes depending on the sickness severity and virus variant. Severe Delta COVID-19 have been characterized by the appearance of the monocyte subset enriched for the proinflammatory gene expression signatures and shift of the ligand-receptor interactions. We profiled the chromatin accessibility landscape of 140,000 nuclei of the PBMC samples from healthy people or individuals with COVID-19. We investigated cis-regulatory elements and identified core transcription factors governing the gene expression state in immune cells during COVID-19. For the severe cases we discovered that regulome and chromatin co-accessibility modules significantly altered across many cell types. Moreover, cases with the Delta variant are accompanied by specific monocyte subtype discovered with the scATAC-seq data. From our analysis follows that immune cells of individuals with severe Delta COVID-19 undergo significant remodeling of the chromatin accessibility landscape and development of the proinflammatory expression pattern. With a gene regulatory network modeling approach we investigated core transcription factors governing cell state and identified the most pronounced chromatin changes in CD14+ monocytes from individuals with severe Delta COVID-19. Together, our results provide novel insight into the cis-regulatory module organization and their impact on gene activity in immune cells during SARS-CoV-2 infection.

overall_design: PBMCs were collected from patients with varying degrees of COVID-19 severity and analyzed using 10x Chromium scATACseq


title: Ldb1 establishes multi-enhancer networks to regulate gene expression [micro-C-Seq]

overall_design: Micro-C was performed in LDB1-AID cells (untreated and 4 hour auxin-treated conditions).


title: Chondroprotective functions of neutrophil-derived extracellular vesicles via promoting the production of secreted frizzled related protein 5 in cartilage

city: Sapporo

first: Mohamad Alaa

last: Terkawi

state: Hokkaido

address: Kita-15, Nish-7, Kita-ku

department: Department of Orthopedic Surgery

country: Japan

institute: Hokkaido University

summary: Neutrophil extracellular vesicles (EVs) are known to play a protective role in arthritic joints by suppressing inflammation and cartilage degeneration. In the current study, we investigated the functional characteristics of EVs derived from stimulated neutrophils and their protective effects in cartilage repair in vitro. We first optimized the stimulation conditions of neutrophils that led to production of EVs with chondroprotective function. To understand this protective mechanism, EVs from TGF-β-stimulated neutrophils were added to stimulated chondrocytes with IL-1β, and their responses were examined by bulk-RNA  analysis.

overall_design: RNA-seq for human chondrocyte cell line stimulated by IL-1 β and Evs derived from neutrophils

first: Keita

last: Kitahara

first: Mohamad

last: Aterkawi

first: Taku

last: Ebata

first: Norimasa

last: Iwasaki


title: Patient-derived lymphomoids preserve the tumor architecture and allow testing response to therapies in lymphoma [scRNA-seq]

city: Lausanne

first: Divyanshu

last: Srivastava

address: SV, Station 19

country: Switzerland

institute: EPFL

summary: We designed an ex vivo system to culture tissue explants from lymphoma tissue. To determine if the explants derived from vavP-Bcl2 mouse spleens  retained the cellular composition and transcriptional profile of the cells in the original tissue, we analyzed six lymphomoids derived from the spleens of two mice, after one or two weeks in culture, and the original spleen tissues by single-cell RNA-sequencing.

overall_design: Two lymph node biopsies were used for this analysis. One biopsy was taken from a patient with DLBCL  (patient 08 in this study) and a second biopsy contained reactive lymphoid tissue ( (patient 03 in this study). In addition, for patient 08, we analysed tissue explants grown for 3 days untreated or treated with 2 mM ibrutinib or 10 mM idelalisib.

first: Albert

last: Santamaria-Martínez

first: Justine

last: Epiney

first: Daniele

last: Tavernari

first: Marco

last: Varrone

first: Dina

last: Milowich

first: Igor

last: Letovanec

first: Thorsten

last: Krueger

first: Rafael

last: Duran

first: Giovanni

last: Ciriello

first: Anne

last: Cairoli

first: Elisa

last: Oricchio


title: Gene expression analysis in liver of rats fed with atherogenic diet (1% cholesterol) and supplemented with 5% Geneva or 5% Hayward kiwifruit lyophylisate

city: Warsaw

first: Tomasz

last: Sadkowski

address: Nowoursynowska 159

department: Department of Physiological Sciences

country: Poland

institute: Warsaw University of Life Sciences - SGGW

summary: Transcriptional profiling of liver tissue from rats fed with standard diet with 1% cholesterol (control diet) and the same diet supplemented with 5% Geneva (test sample1) or 5% Hayward (test sample2) kiwifruit lyophylisate. The goal was to determine the anti-atherogenic effect of kiwi fruit supplementation and their impact on gene expression preventing hepatic steatosis

overall_design: Three-condition experiment. (1) Liver samples from rats fed with standard diet with 1% cholesterol (control diet) vs. the same diet supplemented with (2) 5% Geneva (test sample1) or (3) 5% Hayward (test sample2) kiwifruit lyophylisate. Biological replicates: 8 control replicates (1), 8 reps of examined condition1 (2) , 8 reps of examined condition2 (3)

first: Anna

last: Ciecierska


title: C9orf72 expansion creates the unstable folate-sensitive fragile site FRA9A

city: Las Vegas

first: Łukasz

middle: J.

last: Sznajder

state: Nevada

address: 4505 S. Maryland Pkwy.

department: Chemistry and Biochemistry

institute: University of Nevada-Las Vegas (UNLV)

summary: The hyper-unstable Chr9p21 locus, harbouring the interferon gene cluster, oncogenes and C9orf72, is linked to multiple diseases. C9orf72 (GGGGCC)n expansions (C9orf72Exp) are associated with incompletely penetrant amyotrophic lateral sclerosis, frontotemporal dementia and autoimmune disorders. C9orf72Exp patients display hyperactive cGAS-STING-linked interferon immune and DNA damage responses, but the source of immuno-stimulatory or damaged DNA is unknown. Here, we show C9orf72Exp in pre-symptomatic and ALS-FTD patient cells and brains cause the folate-sensitive chromosomal fragile site, FRA9A. FRA9A centers on > 33kb of C9orf72 as highly-compacted chromatin embedded in an 8.2Mb fragility zone spanning 9p21, encompassing 46 genes, making FRA9A one of the largest fragile sites. C9orf72Exp cells show chromosomal instability, heightened global- and Chr9p-enriched sister-chromatid exchanges, truncated-Chr9s, acentric-Chr9s and Chr9-containing micronuclei, providing endogenous sources of damaged and immunostimulatory DNA. Cells from one C9orf72Exp patient contained highly-rearranged FRA9A-expressing Chr9 with Chr9-wide dysregulated gene expression. Somatic C9orf72Exp repeat instability and chromosomal fragility are sensitive to folate-deficiency. Age-dependent repeat instability, chromosomal fragility, and chromosomal instability can be transferred to CNS and peripheral tissues of transgenic C9orf72Exp mice, implicating C9orf72Exp as the source. Our results highlight unappreciated effects of C9orf72 expansions that trigger vitamin-sensitive chromosome fragility, adding structural variations to the disease-enriched 9p21 locus, and likely elsewhere.

overall_design: Chromosome 9 gene expression analysis in the P8 lymphoblastoid cell line (LCL) compared to other LCLs with C9orf72 (GGGGCC)n expansions (unmethylated and methylated).

first: Lukasz

first: Mila

last: Mirceta

first: Peixiang

last: Wang

first: Maurice

last: Swanson

first: Christopher

last: Pearson


title: Kir6.1, a component of an ATP-sensitive potassium channel, regulates natural killer cell development

status: Public on Nov 24 2024

city: New York

first: William

last: Coetzee

state: United States

address: 550 First Ave

department: Pathology

institute: NYU School of Medicine

summary: Involved in immunity and reproduction, natural killer (NK) cells offer opportunities to develop new immunotherapies to treat infections and cancer or to alleviate pregnancy complications. Most current strategies use cytokines or antibodies to enhance NK-cell function, but none use ion channel modulators, which are widely used in clinical practice to treat hypertension, diabetes, epilepsy, and other conditions. Little is known about ion channels in NK cells. We show that Kcnj8, which codes for the Kir6.1 subunit of a certain type of ATP-sensitive potassium (KATP) channel, is highly expressed in murine splenic and uterine NK cells compared to other K+ channels previously identified in NK cells.  Kcnj8 expression is highest in the most mature subset of splenic NK cells (CD27-/CD11b+) and in NKG2A+ or Ly49C/I+ educated uterine NK cells. Using patch clamping, we show that a subset of NK cells expresses a current sensitive to the Kir6.1 blocker PNU-37883A. Kcnj8 does not participate in NK cell degranulation in response to tumor cells in vitro or rejection of tumor cells in vivo, or IFN-γ release. Transcriptomics show that genes previously implicated in NK cell development are amongst those differentially expressed in CD27-/CD11b+ NK cells deficient of Kcnj8. Indeed, we found that mice with NK-cell specific Kcnj8 gene ablation have fewer CD11b+CD27- and KLRG-1+ NK cells in the bone barrow and spleen. These results show that the KATP subunit Kir6.1 has a key role in NK-cell development.

overall_design: Splenocytes were isolated from wild-type mice, and Kir6.1flx/flx x NKp46-CreERT2 mice immediately following 4 days of tamoxifen induction (respectively WT and LKO; n=2 each). Cells were first gated for NK cell markers NK1.1 and NKp46, then sorted into four pools: CD27-/CD27b- (population 3), CD27+/CD27b- (population 2), CD27+/CD27b+ (population 1), and CD27-/CD27b+ (population 0).


title: Ldb1 establishes multi-enhancer networks to regulate gene expression [Tri-C-Seq]

first: Nicholas

last: Aboreden

overall_design: Tri-c was performed in LDB1-AID cells (untreated and 4 hour auxin-treated conditions). Capture probe for Myc promoter used.

first: Gerd

last: Blobel


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

overall_design: Refer to individual Series


title: Ldb1 establishes multi-enhancer networks to regulate gene expression [ChIP-Seq]

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for Pol2, LDB1, CTCF, RAD21 and YY1 in LDB1-AID cells (untreated and 4 hour auxin-treated conditions). ChIP-seq for LDB1 and RAD21 in SMC3-AID cells (untreated and 4 hour auxin-treated conditions). ChIP-seq for LDB1 in G1E-ER4 md-mCherry subline (nocodazole 8.5 hours). ChIP-seq for CTCF and LDB1 in CTCF-AID cells (untreated and 4 hour auxin-treated conditions).


title: Differential gene expression in HCC cell lines Huh7 and PLC under high and low glucose culturement

city: Shanghai

first: Xianghuo

last: He

address: No 270, Dong An Road

institute: Fudan University

summary: To gain a deeper understanding of the mechanism by lncRNAs involved in glucose metabolism during the progression of HCC, we conducted transcriptome sequencing on HCC cells treated with low (5 mM) and high (25 mM)  glucose and carried out analyses for the lncRNAs with a significant change of expression combined with TCGA-LIHC data. Huh7 and PLC cells were treated with low glucose (5mM) or high glucose (25mM) for 48 h, whole-transcriptome sequencing (RNA-Seq) was performed to identify the significant changed lncRNAs with glucose.

overall_design: To investigate the role of glucose-related lncRNAs in HCC，we performed an RNA-sequencing analysis with Huh7 and PLC cells cultured in low glucose (5 mM) and high glucose (25 mM) for 48 h.Comparative gene expression profiling analysis of RNA-seq data for high glucose and low glucose treatment for 48 h in Huh7 and PLC cells.

first: Yanfang

last: Liu


title: Patient-derived lymphomoids preserve the tumor architecture and allow testing response to therapies in lymphoma [Spatial Transcriptomics]

first: Divyanshu

last: Srivastava

summary: We designed an ex vivo system to culture tissue explants from lymphoma tissue. To characterize the spatial and molecular structure of human lymphomoids and their tissue of origin, we performed spatial transcriptomics analyses on original tissues and lymphomoids obtained from 2 patients using the 10x Genomics Visium technology.

first: Albert

last: Santamaria-Martínez

first: Justine

last: Epiney

first: Daniele

last: Tavernari

first: Marco

last: Varrone

first: Dina

last: Milowich

first: Igor

last: Letovanec

first: Thorsten

last: Krueger

first: Rafael


title: Roadmap and Considerations for Genome Editing in a Non-model Organism: Genetic Variations and Off-target Profiling

status: Public on Nov 22 2024

city: BEER SHEVA

first: Hanin

last: Wattad

state: SOUTH DISTRICT

address: DAVUD BEN GURION BLVD 1

department: Department of Life Sciences

institute: Ben-gurion University of The Negev

summary: The CRISPR/Cas genome editing approach in non-model organisms poses challenges that remain to be resolved.Here, we demonstrated a generalized roadmap for a de-novo genome-annotation approach applied to the non-model organism Macrobrachium rosenbergii. We also addressed typical genome editing challenges arising from genetic variations, such as a high frequency of single nucleotide polymorphisms, differences in sex chromosomes, and repetitive sequences that can lead to off-target events. For genome editing of M. rosenbergii, our laboratory recently adapted the CRISPR/Cas genome-editing approach to embryos and embryonic primary cell culture. In this continuation study, an annotation pipeline was trained to predict gene models by leveraging available genomic, transcriptomic, and proteomic data, enabling accurate gene prediction and guide design for knock-outs. Next-generation sequencing analysis demonstrated a high frequency of genetic variations in genes on both autosomal and sex chromosomes, which have been shown to affect the accuracy of editing analyses. To enable future applications based on the CRISPR/Cas tool in non-model organisms, we also verified the reliability of editing efficiency and tracked off-target frequencies. Despite the lack of comprehensive information on non-model organisms, this study provides an example of the feasibility of selecting and editing specific genes with a high degree of certainty.

overall_design: To illustrate the immediate effects of CRISPR/cas9 activity on the Macrobrachium rosenbergii  genome, we conducted 16 nucleofection experiments on embryonic primary cell culture and targeted Mr- cofilin gene for the negative and positive controls.

first: Jonathan

last: Molcho

first: Rivka

last: Manor

first: Simy

last: Weil

first: Eliahu

last: Aflalo

first: Vered

last: Chalifa-Caspi

first: Amir

last: Sagi


title: RNA-Seq of shallow-water mussel Mytilus galloprovincialis under in situ hydrostatic pressure exposure

city: Qingdao

first: Luyang

last: Sun

state: Shandong

address: Songling Road 189#

department: Single-Cell Center

institute: Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences

summary: Recent studies have unveiled the deep sea as a rich biosphere, populated by species descended from shallow-water ancestors post-mass extinctions. Research on genomic evolution and microbial symbiosis has shed light on how these species thrive in extreme deep-sea conditions. However, early adaptation stages, particularly the roles of conserved genes and symbiotic microbes, remain inadequately understood. This study examined transcriptomic and microbiome changes in shallow-water mussels Mytilus galloprovincialis exposed to deep-sea conditions at the Site-F cold seep in the South China Sea. Results reveal complex gene expression adjustments in stress response, immune defense, homeostasis, and energy metabolism pathways during adaptation. After 10 days of deep-sea exposure, shallow-water mussels and their microbial communities closely resembled those of native deep-sea mussels, demonstrating host and microbiome convergence in response to adaptive shifts. Notably, methanotrophic bacteria, key symbionts in native deep-sea mussels, emerged as a dominant group in the exposed mussels. Host genes involved in immune recognition and endocytosis correlated significantly with the abundance of these bacteria. Overall, our analyses provide insights into adaptive transcriptional regulation and microbiome dynamics of mussels in deep-sea environments, highlighting the roles of conserved genes and microbial community shifts in adapting to extreme environments.

overall_design: In the present study, we conducted an experiment on shallow-water mussels (Mytilus galloprovincialis) at a depth of 1,119 meters in the South China Sea, as the short and mid-term simulation of the adaption process of shallow sea mussels into deep sea environments, aiming to deeply explore the deep-sea adaptation mechanism of the mussels. Both in situ deep-sea experiments and in situ sample fixation were performed to maximize the most primitive transcriptional and metagenomic changes of the organism due to deep-sea adaptation.

first: Xiaolu

first: Li

last: Zhou

first: Hao

last: Wang

first: Chao

last: Lian

first: Zhaoshan

last: Zhong

first: Minxiao

last: Chen

first: Chaolun

last: Li


title: Mutations disrupting the kinase domain of IKKα lead to immunodeficiency and immune dysregulation in humans

city: Paris

first: Quentin

last: Riller

address: 24 Boulevard du Montparnasse

country: France

institute: INSERM UMRS 1163, Imagine Institute

summary: IKKα, encoded by CHUK, is crucial in the non-canonical NF-κB pathway and part of the IKK complex activating the canonical pathway alongside IKKβ. The absence of IKKα causes fetal encasement syndrome in humans, fatal in utero, while an impaired IKKα-NIK interaction was reported in a single patient and causes combined immunodeficiency. Here, we describe compound heterozygous variants in the kinase domain of IKKα in a female patient with hypogammaglobulinemia, recurrent lung infections, and Hay-Wells syndrome-like features. We showed that both variants were loss-of-function. Non-canonical NF-κB activation was profoundly diminished in stromal and immune cells while the canonical pathway was unexpectedly partially impaired. Reintroducing wt CHUK restored non-canonical NF-κB activation. The patient had neutralizing autoantibodies against type I IFN, akin to non-canonical NF-κB pathway deficiencies. Thus, this is the first case of biallelic CHUK mutations disrupting IKKα kinase function, broadening non-canonical NF-κB defect understanding, and suggesting IKKα's role in canonical NF-κB target gene expression in humans.

overall_design: SV40-fibroblasts were stimulated with human TNFalpha 10 ng/mL or Poly I:C 10 ug/mL for 6h or left unstimulated and RNA were harvested with a DNAse digestion step. RNA sequencing was performed on total RNA extracts.

first: Frédéric

last: Rieux-Laucat


title: Cellular signatures in human blood track bone mineral density in postmenopausal women

city: NEW YORK CITY

first: Kyung-Hyun

last: Park-min

state: NY

address: 535 E 70th st

institute: Hospital for Special Surgery

summary: Osteoclasts are sole bone-resorbing cells and are formed by the fusion of osteoclast precursor cells (OCPs) derived from myeloid lineage cells. Animal studies reveal that circulating osteoclast precursor cells (cOCPs) in blood travel to bone and fuse with bone-resident osteoclasts. However, the characteristics of human cOCPs and their association with bone diseases remain elusive. We have identified and characterized human cOCPs and found a positive association between cOCPs and osteoporosis. Sorted cOCPs have a higher osteoclastogenic potential than other myeloid cells and effectively differentiate into osteoclasts. cOCPs exhibit distinct morphology and transcriptomic signatures. The frequency of cOCPs in the blood varies among treatment-naïve postmenopausal women and has an inverse correlation with lumbar spine bone density and a positive correlation with serum CTX, a bone resorption marker. The increased cOCPs in treatment-naïve osteoporosis patients were significantly diminished by denosumab, a widely used antiresorptive therapy. Our study reveals the distinctive identity of human cOCPs and the potential link between the dynamic regulation of cOCPs and osteoporosis and its treatment. Taken together, our study enhances our understanding of human cOCPs and highlights a potential opportunity to measure cOCPs through a simple blood test, which could potentially identify high-risk individuals.

overall_design: cOCPs and MOs are sorted from PBMCs of 11 donors by flow cytometry. Sorted cells are pooled as two biological replicates (rep1 from 5 donors,  rep2 from 6 donors)

last: Park-Min

first: Evgenia

last: Giannopoulou


title: Chondroprotective functions of neutrophil-derived extracellular vesicles via promoting the production of secreted frizzled related protein 5 in cartilage [SFRP5]

first: Mohamad Alaa

last: Terkawi

overall_design: RNA-seq for mice chondrocytes stimulated by IL-1β and SFRP5 recombinant

first: Keita

last: Kitahara

first: Mohamad

last: Aterkawi

first: Taku

last: Ebata

first: Norimasa

last: Iwasaki


title: Reprogramming of epidermal keratinocytes by PITX1 transforms the cutaneous cellular landscape and promotes wound healing [Xenium]

city: Bethesda

first: Stephen

middle: R

last: Brooks

state: MD

address: 50 SOUTH DR, RM 1140

department: Biodata Mining and Discovery Section

institute: NIAMS/NIH

summary: Skin injuries heal slowly, compared to oral epithelial tissues, and often do not regenerate lost adnexa. Using a murine mouse model expressing the oral epithelial transcription factor PITX1 in the skin, we performed Xenium in situ analysis in healthy and wounded skin and healthy oral mucosa to delineate the cellular and molecular changes underpinning the superior oral wounding response.

overall_design: Formalin-fixed, paraffin-embedded murine skin (healthy or POD4-wounds, Control and PITX1+) or buccal mucosa (healthy Control) was processed for Xenium in situ analysis to determine spatial localization and expression of selected mRNA transcripts.

first: Andrew

last: Overmiller

first: Maria

middle: I

last: Morasso


title: Effect of fyn kinase driven inflammatory cytokine associated dopaminergic neurodegeneration and microglia activation in zebrafish.

status: Public on Nov 25 2024

city: Ames

first: Sahiba

last: Siddiqui

state: IA

address: 2213 Pammel Dr

department: Genetics, Development, and Cell Biology

institute: Iowa State University

summary: The Alzheimer's Disease and Parkinson's Disease risk locus Fyn kinase is implicated in protein pathophysiology and NF-κB microglia inflammatory signaling. To investigate in vivo mechanisms of Fyn driven neurodegeneration, we built a zebrafish neural specific Gal4:UAS model of constitutively active FynY531F signaling. Using in vivo live imaging we demonstrate neural FynY531F expression leads to dopaminergic neuron loss and mitochondrial aggregation in 5 day larval brain. Gene expression analyses reveal reduction in neuroprotective genes, and elevated inflammatory cytokines Il-1β, IL-12 and TNF-α and genes associated with oxidative stress. These phenotypes correlate with microglia activation in the larval brain. Chemical inhibition demonstrates dopaminergic neuron loss is dependent on Fyn and NF-κB/Caspase 1 signaling. We identify Stat3 activation as a novel downstream effector of Fyn signaling that acts synergistically with NF-κB in dopaminergic neuron degeneration. These results show Fyn drives neurodegeneration through NF-κB inflammatory signaling and Stat3 pathways. Activation of Stat3 provides a potential link from Fyn to mitochondrial dysfunction associated with dopaminergic neuron loss.

overall_design:
To investigate the role of fyn kinase in mediating neurodegeneration, we established the overexpression of constitutively active mutant FynY531F in zebrafish neurons..
We then performed gene expression analysis using data obtained from RNA -seq of three different lines, at 2 time points, 3dpf and 5dpf.
Comparisons were made between 2 controls (+/+ and elav3:gal4) and fyn model (elav3:gal4;UAS:fynY531F) at both time points and model compared between both time points.
Please note that the "_deg_all.txt" includes all deg's while "_deg.txt" includes statistically significant deg's.

first: Fang

last: Liu

first: Anumantha

last: Kanthasamy

first: Maura

last: McGrail


title: Magnesium supplementation modifies synovial and splenic transcriptomic signatures and biologic pathways in arthritis mice

status: Public on Nov 21 2024

first: Teresina

last: Laragione

address: 1468 Madison Ave

department: Medicine

institute: Icahn School of Medicine at Mount Sinai

summary: Rheumatoid arthritis (RA) is a common chronic autoimmune and inflammatory disease that can cause joint pain and disability. We have recently reported that oral magnesium supplementation significantly reduces disease severity and joint damage in two models of RA. In the synovial tissues. There was an enrichment for differentially expressed genes (DEGs) belonging to pathways implicated in transcription regulation, nuclear receptor signaling, and pathways implicated in RA pathogenesis such as RHO GTPases, RUNX1 pathway, oxidative stress induced senescence, senescence-associated secretory phenotype (SASP) and cell migration in synovial tissues . In the synovial tissues Actc1 and Nr4a3 were among the genes with the highest expression, while Krt79 and Ffar2 were among the genes with the most significantly decreased expression in Mg2800 group compared with Mg500. Spleens had an enrichment for Metabolism of folate and pterines, HSP90 chaperone cycle for steroid hormone receptor. Syt5 and Hspa1a were among the genes with the highest expression, while Ano2 and Ascl4 were among the genes with the lowest expression levels in spleens from Mg2800 compared with Mg500. We describe the tissue transcriptomic consequences of the arthritis-protecting increased Mg dietary intake in KSIA mice. These results show that oral Mg supplementation may interfere with pathways implicated response to oxidative stress and senescence, and other processes known to participate in RA pathogenesis. Our findings provide new evidence supporting the disease-suppressing effect of increased Mg intake in arthritis. Oral Mg supplementation has the potential to become a new addition to the therapeutic options for RA and other autoimmune and inflammatory diseases.

overall_design: In the present study we analyze the transcriptome of spleens and synovial tissues obtained from mice with KRN serum induced arthritis (KSIA) in either the Mg supplemented diet (Mg2800; n=5) or the normal diet (Mg500; n=5). Tissues were collected at the end of a 15-day KSIA experiment. RNA was purified and used for RNA sequencing, and groups compared using DESq2 R package, followed by pathway analyses using Reactome and Gene Ontology (GO).

first: Carolyn

last: Harris

first: Percio

last: Gulko


title: Transcriptome profiling of cartilage progenitor cells over-expressing miR-138 or miR-181a/b-1 during chondrogenic induction

city: Durham

first: Austin

last: Bell-Hensley

state: NC

address: 111 TW Alexander Dr

institute: NIEHS

summary: The goal of this study was to investigate the effects of miR-138 or miR-181a/b-1 on regulating chondrogenesis. Gene expression profiles were analyzed in human cartilage progenitor cells (CPCs) over-expressing either miR-138 or miR-181a/b-1 following 7 days of chondrogenic induction in high cell density pellet cultures under hypoxic conditions (5% O2). CPCs were isolated from human osteoarthritic articular cartilage and over-expression of miR-138 or miR-181a/b-1 was achieved via lentiviral transduction of the precursor form of miR-138 or miR-181a/b-1. Control CPCs were transduced with lentivirus expressing a non-silencing (NS) control RNA sequence. Total RNA was harvested at day 7 of chondrogenic induction and subjected to RNA-Seq analysis.

overall_design: Quadruplet samples of cartilage progenitor cells at P6-7 were transduced with lentivirus expressing either precuror miR-138, precursor miR-181/b-1, or a non-silencing (NS) control precursor RNA. High cell density pellet cultures were formed using transduced cells and the pellets were then induced to undergo chondrogenic differentiation under hypoxia (5% O2). At day 7 following chondrogenic induction, total RNA was isolated and processed for high throughput RNA sequencing.

first: Hongjun

last: Zheng

first: Victor

last: Balera Brito

first: Kathryn

last: Feeney

first: Jin

first: Lei

last: Cai

first: Audrey

last: McAlinden


title: Identify the interplay between N6-methyladenine and gene regulation under hypoxia by randomized empirical model (RNA-seq)

city: Taoyuang

first: Kou-Juey

last: Wu

state: Taiwan

address: No.15, Wenhua 1st Road, Gueishan Dist

department: Cancer Genome Research Center

institute: Chang Gung Memorial Hospital at Linkou

summary: In this study, we employed RNA-seq to investigate the role of N6-methyladenine (6mA) in chromatin accessibility under hypoxic conditions.

overall_design: FaDu, a head and neck cancer cell line, was purchased from Bioresource Collection and Research Center (BCRC, Hsinchu, Taiwan). The cell line was cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% FBS, 1 mM sodium pyruvate, and 1× Antibiotic-Antimycotic (Gibco), under the conditions of 5% CO2 at 37°C. The mycoplasma absence was tested by Mycoplasma PCR Detection Kit (abm) before the experiments. Knockdown of METTL4 was achieved using a previously established method with lenti-virus infection. For hypoxic conditions, cells were incubated in an environment of 1% O2, 5% CO2, and 94% N2 at 37°C for 18 hours.

first: Kai-Wen

last: Hsu

first: Joseph

last: Lai


title: Effect of PPARβ/δ agonist GW501516 on human and murine mesenchymal stromal cells

city: Montpellier

first: Claudia

last: Terraza Aguirre

address: 80, Avenue Augustin Fliche

institute: Inserm U1183

summary: This study employed 3’ RNA-Seq profiling (3RSP) to investigate the transcriptomic effects of the PPARβ/δ agonist GW501516 (1 μM, 24 hours) on mesenchymal stromal cells (MSCs). Treated samples were compared with untreated controls to identify differentially expressed genes. The analysis revealed ANGPTL4 as the most significantly overexpressed gene in the treated condition across multiple experimental models, including murine and human MSCs. Importantly, this upregulation was observed in human MSCs derived from diverse tissues, such as adipose tissue, bone marrow, and umbilical cord, highlighting the consistent response of MSCs to PPARβ/δ activation across species and sources. Further functional experiments demonstrated that ANGPTL4 plays a pivotal role in enhancing the anti-apoptotic properties of MSCs. This effect was evident in both autocrine (self-regulating) and paracrine (targeting other cells) mechanisms, suggesting that ANGPTL4 may act as a key mediator of MSC-based therapeutic effect.

overall_design: Bone marrow murine MSC and human MSC (from bone marrow, adipose tissue and umbilical cord) were treated with GW501516 (1 uM) for 24 hours. Then, 3RSP profiling of control and PPAR agonist-treated cells was performed.

last: Terraza-Aguirre

first: Rafael

last: Contreras

first: Cecil

last: Boyer

first: Claire

last: Vinatier

first: Jerome

last: Guicheux

first: Farida

last: Djouad


title: Reprogramming of epidermal keratinocytes by PITX1 transforms the cutaneous cellular landscape and promotes wound healing [scRNA-seq]

first: Stephen

last: Brooks

summary: Skin injuries heal slowly, compared to oral epithelial tissues, and often do not regenerate lost adnexa. Using a murine mouse model expressing the oral epithelial transcription factor PITX1 in the skin, we performed scRNA-seq in healthy and wounded skin and healthy oral mucosa to delineate the cellular and molecular changes underpinning the superior oral wounding response.

overall_design: Whole murine skin (healthy and POD4-wounded, Control and PITX1+) or buccal mucosa (healthy Control) was dissociated into single cells and analyzed via scRNA-seq.

first: Andrew Michael

last: Overmiller

first: Stephen R

first: Maria Irene

last: Morasso


title: Vascular dysfunction is the primary cause of symptom onset in a mouse  model of oxaliplatin-induced peripheral neuropathy: comparison of gene expression in mice injected with Oxaliplatine or control solution [BHN-OXA_A2020]

city: PARIS

first: Stephane

last: Le Crom

address: 46 rue Ulm

department: Genomic Core Facility

institute: IBENS

summary: Oxaliplatin-induced peripheral neuropathy (OIPN) is an adverse side effect of this chemotherapy used for gastrointestinal cancers. The continuous pain experienced by OIPN patients often result in the reduction or discontinuation of chemotherapy, thereby affecting patient survival. Several pathogenic mechanisms involving sensory neurons were shown to participate in the occurrence of OIPN symptoms. However, the dysfunction of the blood-nerve barrier as a source of nerve alteration had not been thoroughly explored. To characterise the vascular contribution to OIPN symptoms, we undertook two comparative transcriptomic analyses from mouse purified brain and sciatic nerve blood vessels (BVs), and nerve BVs after oxaliplatin or control administration. The dataset provided here show raw data obtained when gene expression regulation was assessed by transcriptomic analyses where we compared purified blood vessels (endothelial cells and mural cells incl. smooth muscle cells and pericytes) from sciatic nerves of mice intraveinously injected with control (sham) or oxaliplatin (oxa) solution.

overall_design:
Comparison of gene expression in mice injected with Oxaliplatine or control solution
The mouse strain for both experiments (GSE255096 and GSE255097) was C57BL/6.

first: Sonia

last: Taïb

first: Juliette

last: Durand

first: Anne-Cécile

last: Boulais

first: Vianney

last: Dehais

first: Sabrina

last: Martin

first: Martine

last: Cohen-Salmon

first: Corinne

last: Blugeon

first: Laurent

last: Jourdren

first: Jamilé

last: Hazan

first: Isabelle

last: Brunet


title: Sp140L Is a Herpesvirus Restriction Factor [scRNA-seq]

status: Public on Nov 20 2024

first: Jana

last: Cable

address: 213 Research Dr.

department: Molecular Genetics and Microbiology

institute: Duke University

summary: Herpesviruses, including the oncogenic Epstein-Barr Virus (EBV), must bypass host DNA sensing mechanisms to drive infection and pathogenesis. The first viral latency protein expressed, EBNA-LP, is essential for the transformation of naïve B cells, yet its role in evading host defenses remains unclear. Using single-cell RNA sequencing of EBNA-LP-Knockout (LPKO)-infected B cells, we reveal an antiviral response landscape implicating the ‘speckled proteins’ as key restriction factors countered by EBNA-LP. Specifically, loss of SP100 or the primate-specific SP140L reverses the restriction of LPKO, suppresses a subset of canonically interferon-stimulated genes, and restores viral gene transcription and cellular proliferation. Notably, we also identify Sp140L as a restriction target of the herpesvirus saimiri ORF3 protein, implying a role in immunity to other DNA viruses. This study reveals Sp140L as a restriction factor that we propose links sensing and transcriptional suppression of viral DNA to an IFN-independent innate immune response, likely relevant to all nuclear DNA viruses.

overall_design: Single cell RNAseq data from B cells in a timecourse of LPKO or WT EBV infection. Samples including uninfected (Day 0), and 2, 5, and 8 days post-infection.

last: M Cable

first: Wiyada

last: Wongwiwat

first: Jenna

last: C Grabowski

first: Robert

last: E White

first: Micah

last: A Luftig


title: NtCP29A depletion leads to a 50% loss of the rbcL transcript under cold conditions

city: Berlin

first: Florian

last: Rösch

address: Unter den Linden 6

institute: Humboldt Universität zu Berlin

summary: The nuclear-encoded chloroplastic RNA-binding protein CP29A is important for the cold response in Arabidopsis thaliana. Knockout mutations in this plant species lead to a bleaching phenotype in the newly developing tissue. Important for the function of AtCP29A is a long prion like domain, which is located between the two RNA Recognition Motifs (RRM). In contrast, the CP29A variant of N. tabacum contains only a short linker between the two RRMs. Knockout mutants of this gene show a phenotype when analysed by pulse amplitude modulation (PAM) fluorometry. In this study, we analysed the differentially expressed chloroplast genes of the NtCP29A mutant compared to the wild-type of N. tabacum (Petit havana) under normal (24°C) and under cold (12°C) growth conditions. While no gene was significantly deregulated under normal conditions, RbcL proved to be the only gene that was significantly downregulated under cold conditions in the mutant.

overall_design:
NtCP29A was knocked out with CRISPR-Cas9. Homozygous mutants were grown together with wt plants first at 24°C and then at 12°C. Samples were taken in replicates for both genotypes under both conditions.

Please note that the raw data files for GSM7917392, and the processed data 'raw_counts.csv' file have been replaced on Jan 3, 2025.


title: Bulk RNAseq of mononucleated cells isolated from resting and regenerating adult and aged skeletal mouse muscle

city: Lyon

first: Benedicte

last: Chazaud

address: 8 Avenue Rockefeller

department: Institut NeuroMyoGène

institute: Université Claude Bernard Lyon 1

summary: Muscle regeneration is impaired in the aged organism, due to both intrinsic defects of muscle stem cells (MuSCs) and alterations of their environmental niche. However, the latter has still been poorly explored. Here, we compared and analyzed the time course of the various cell types constituting the MuSC niche during muscle generation in young and old mice. Aging altered the amplification of all niche cells with particularly prominent phenotypes in macrophages that impaired the resolution of inflammation in the old regenerating muscle. RNAsequencing of FACs-isolated MuSCs and non-myogenic niche cells during  regeneration uncovered specific profiles and kinetics of genes and molecular pathways differentially regulated in old versus young regenerating muscle, indicating that each cell type responded to aging in a specific manner. These data provide a unique resource to study the aging of the MuSC niche.

overall_design: Adult (3 months) and aged (22-24 months) WT C57/B6 mice were subjected to a skeletal muscle injury and the mononucleated cells (muscle stem cells, fibroadipogenic precursor cells, endothelial cells, neutrophils, macrophages) were FACS-isolated at 0, 2, 4, and 7 days post injury and were proceed for bulk RNASeq

first: Bénédicte

first: Jérôme

last: N Feige

first: Rémi

last: Mounier