title: MNase-seq data in 4 modified strains of Saccharomyces cerevisiae, treated or not with 10-Phenanthroline

city: Barcelona

first: Isabelle

middle: Brun

last: Heath

state: Barcelona

address: Carrer Baldiri Reixac, 10-12

department: Molecular Modelling and Bioinformatics

country: Spain

institute: IRB Barcelona

summary: We showed that the introduction of a 81bp DNA segment in phase genes leads to the generation of fuzzier nucleosome arrays, but neither to a significant change in the placement of the +1 and –last nucleosomes, nor to a coordinate sliding of nucleosomes. This suggests that irrespectively of other nucleosomes, the +1 and –last nucleosomes are placed in well-defined regions marked by sequence-dependent intrinsic and extrinsic factors, while the rest of the nucleosomes are placed based on periodicity considerations.

overall_design: In order to test the effect of gene-length modification on Nucleosome periodicity in G1 synchronized cells, we performed MNase-seq in 4 modified strains of Saccharomyces cerevisiae containing 81bp (5'-GCGTGTTGTGTTTTCTCCGAGGAGAAACATTCAAATCTTGTGCTATGGCTTTGCCTACCGTCTGCGCCATCCATCTTTCGC-3') inserted in the middle of 2 selected genes in each strain. The 4 strains were then  treated or not with 10-Phenanthroline to test the effect of transcription on nucleosome periodicity. The exact position of the 81bp insertion can be found in the publication : An integrated machine-learning model to predict nucleosome architecture, Sala et al, Submited to NAR

last: Brun Heath

first: Mireia

last: Labrador

first: Alba

last: Sala

first: Modesto

last: Orozco

first: Pau

last: De George

first: Diana

last: Buitrago


title: Genome-wide analysis reveals the repression of MORC3 on PD-L1 expression in head and neck cancer

status: Public on Oct 02 2024

city: Nanchang

first: Wenxuan

last: Fu

address: china

country: China

institute: Nanchang university

type: Expression profiling by high throughput sequencing

summary: The expression and roles of MORC3 in cancers remain largely unknown. To understand the expression and roles of MORC3 in head and neck cancer, MORC3 was knocked down in CAL 27 cells with siRNA. Total RNAs were collected for mRNA sequencing assay.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for CAL 27 cells treated with siRNA against MORC3 or non-specific siRNA.

first: Xiaomeng

last: Chang

first: Kun

last: Ye

first: Zige

last: Zheng

first: Qianyi

last: Lai

first: Minyang

last: Ge

first: Yan

last: Shi


title: SHISA3 reprograms tumor-associated macrophages toward an M1 phenotype and enhances cancer immunotherapy

city: Guangzhou

first: shimeng

last: zhang

address: 651 Dongfeng Road East, Yuexiu District

institute: Sun Yat-sen University Cancer Center

summary:
The main challenge for immune checkpoint blockade (ICB) therapy lies in immunosuppressive tumor microenvironment (TME). Repolarizing M2-like tumor-associated macrophages (TAMs) into inflammatory M1 phenotype is a promising strategy for cancer immunotherapy. Here, we found that the transmembrane protein SHISA3 is induced by DAMPs/PAMPs in macrophages via nuclear factor-κB (NF-κB) transcription factors, and SHISA3 forms complex with HSPA8 to reciprocally activates NF-κB signaling thus maintains M1 polarization of macrophages. Enforced expression of Shisa3 in TAMs increases their phagocytosis and antigen presentation abilities and promotes CD8+ T cell-mediated antitumor immunity. Local delivery of mRNA encoding Shisa3 enables therapy of cancer by dual effects on tumor cells and TAMs, and enhance the efficacy of PD-1 antibody. Taken together, our findings describe the role of SHISA3 in reprogramming TAMs that ameliorates cancer immunotherapy
To find new molecules that regulate macrophage polarization, we performed transcriptomic analysis on early macrophages polarization induced by LPS for 0, 2, 4 hours.

overall_design:
Comparative gene expression profiling analysis of RNA-seq data for BMDM induced by LPS for 0, 2, 4 hours.  AAV-mediated Shisa3 overexpression in BMDMs were used for RNA-seq (AAV-Shisa3 BMDMs and AAV-GFP BMDMs) .

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Submitter states that missing raw files are due to file loss.
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first: Shimeng

last: Zhang

first: Shuai

last: Chen


title: Zinc-finger protein ZFP488 regulates the timing of oligodendrocyte myelination and remyelination (CUT&Tag)

city: Cincinnati

first: Richard

last: Lu

state: Ohio

country: USA

institute: CINCINNATI CHILDREN'S HOSPITAL MEDICAL CENTER

type: Genome binding/occupancy profiling by high throughput sequencing

summary: To identified  ZFP488 binding sites in Ols, we performed Zfp488-HA CUT&Tag-seq to identify site of ZFP488 binding within the genome.

overall_design: Zfp488-HA CUT&Tag-seq in lentivirus transfected Zfp488-HA mouse OPC.

first: Siying

last: Cui

first: Tong

first: Dazhuan

last: Xin


title: Zinc-finger protein ZFP488 regulates the timing of oligodendrocyte myelination and remyelination (RNA-Seq)

summary: To investigate how ZFP488 regulates myelination, we performed transcriptome profiling on OLs (O4+GalC+) isolated from the cortices of control and Zfp488KI/KI mice at P5 using fluorescence activated cell sorting.

overall_design: Transcriptome profiling on OLs (O4+GalC+) isolated from the cortices of control and Zfp488KI/KI mice at P5 using fluorescence activated cell sorting.


title: Zinc-finger protein ZFP488 regulates the timing of oligodendrocyte myelination and remyelination

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

overall_design: Refer to individual Series


title: Biphasic response of human iPSC-derived neural network activity following exposure to a sarin-surrogate nerve agent

city: Livermore

first: Aimy

last: Sebastian

state: CA

address: 7000 East Ave

department: BBTD

institute: LLNL

summary: In a concentration-response study, we have employed a human-relevant brain microphysiological system (bMPS), containing human-iPSC derived glutamatergic and GABAergic neurons co-cultured with primary human astrocytes, to monitor and detect the changes in the electrical activity of engineered human iPSC-derived neural networks to increasing concentrations of the sarin surrogate, 4-nitrophenylisopropyl methylphosphonate (NIMP). Transcriptomic analysis was conducted at 6-days post exposure to evaluate gene expression changes that could have contributed to how neurons communicated following NIMP exposure.

overall_design: human iPSC-derived glutamatergic and GABAergic neurons co-cultured with primary human astrocytes were co-cultured on a 6-well multi-electrode array. Co-cultures were allowed to mature for up to 25 DIV before exposed to one of 3 concentrations  of NIMP (0,  4, and 100 micromolar) for 24 hours. After 24 hours NIMP was removed, and co-cultures were maintained for up to 6-days post-exposure. At 6-days post-exposure, RNA was isolated and sequnced to determine NIMP exposure induced transcriptional changes.

first: Doris

last: Lam


title: Identification of natriuretic peptide receptor A (NPR-A) expression signatures in podocytes in vivo reveals baseline control of protective pathways including Protein S

city: Regensburg

first: Uwe

last: Schwartz

address: Universitätstraße 32

department: NGS Analysis Center

country: Germany

institute: University of Regensburg

summary: Natriuretic peptide receptor-A (NPR-A) is the principal receptor for the natriuretic peptides ANP and BNP. Targeted deletion of NPR-A in mouse glomerular podocytes significantly enhances renal injury in vivo in the DOCA-salt experimental model. It was therefore hypothesized that natriuretic peptides exert a direct protective effect on glomerular barrier integrity through activation of NPR-A and modulation of gene expression patterns in podocytes. RNA-seq analysis revealed a total of 158 DEGs with 81 downregulated DEGs and 77 upregulated DEGs in Npr1 deficient podocytes. Among the downregulated genes were protein S and semaphorin 3G, which are known to have a protective effect in podocytes. Protein S was also expressed in and secreted from isolated human glomeruli. GO enrichment analysis revealed that the upregulated DEGs in NPR-A deficient podocytes were associated with cell migration and motility. In line, BNP significantly decreased podocyte outgrowth from cultured glomeruli.

overall_design: Green fluorescence-positive podocytes from mice with a conditional deletion of Npr1 encoding NPR-A were isolated by fluorescence-activated cell sorting (FACS). Differentially expressed genes (DEGs) in podocytes were identified by RNA sequencing of podocytes from wild-type and NPR-A deleted mice

first: Mia

last: Jensen

first: Anna

last: Federlein

first: Frank

last: Schweda


title: Global epigenetic stability of liver-resident invariant natural killer T cells in response to cues capable of inducing transcriptional re-programming

first: Josep

last: Garnica

address: Rosselló, 149

institute: IDIBAPS

type: Methylation profiling by high throughput sequencing

summary: Unlike conventional CD4+ T cells, which are phenotypically and functionally plastic, invariant NKT (iNKT) cells generally exist in a terminally differentiated state. Although peripheral CD4+ T cells can acquire alternative epigenetic states in response to different cues, it remains unclear whether peripheral iNKT cells are epigenetically stable or maleable. Repetitive encounters of liver-resident iNKT cells (LiNKTs) with galactosylceramide (aGalCer)/CD1d-coated nanoparticles (NPs) can trigger their differentiation into a LiNKT cell subset (LiNKTR1) expressing a T regulatory type 1 (TR1)-like transcriptional signature. Here we use a broad range of omics tools to dissect the epigenetic underpinnings of the LiNKT-LiNKTR1 transdifferentiation process as compared to those underlying the T-conv-to-T-follicular helper (TFH) and TFH-to-TR1 differentiation pathways. We show that LiNKTR1 cell generation is partially associated with treatment induced hypo-methylation of gene bodies and regulatory elements of upregulated genes, in the absence of significant changes in chromatin exposure, deposition of expression-promoting histone marks, or removal of their repressive counterparts from bivalent regulatory elements. In contrast, the Tconv-TFH differentiation process involves extensive remodeling of the chromatin and the acquisition of a broad repertoire of epigenetic modifications that are then inherited by TFH cell-derived TR1 cell progeny. These results suggest that peripheral tissue-resident iNKT cells, unlike conventional T cells but like TFH cells, are epigenetically stable and that such stability contributes to their phenotypic and functional stability.

overall_design: Liver-resident aGalCer/CD1d tetramer+ cells isolated from both aGalCer/CD1d-NP-treated and untreated NOD mice were processed for bulk ATAC-seq, ChIP-seq for H3K27Ac, H3K4me3, and H327me3, whole genome methylome, as well as single-cell scRNA-seq + scATAC-seq multiome, in order to underpin the epigenetic changes during their  transdifferenation into LiNKTR1 induced by aGalcer/CD1d-NP .

first: Joel

last: Moro

first: Pere

last: Santamaria


title: The chromatin landscape of high-grade serous ovarian cancer metastasis identifies potential regulatory drivers of chemoresistant tumour cells

city: Birmingham

first: Paul

last: Moss

state: West Midlands

address: Vincent Drive

department: Immunology and Immunotherapy

country: United Kingdom

institute: University of Birmingham

summary: Disease recurrence following chemotherapy is a major clinical challenge in ovarian cancer (OC) but little is known regarding how the tumour epigenome regulates transcriptional programs underpinning chemoresistance. We determined the single cell chromatin accessibility landscape of omental OC metastasis from treatment naïve and neoadjuvant chemotherapy-treated patients and defined the chromatin accessibility profiles of epithelial, fibroblast, myeloid and lymphoid cells. Epithelial tumour cells displayed open chromatin regions enriched with motifs for the oncogenic transcription factors MEIS and PBX. Chemotherapy drove profound tumour heterogeneity and selection for cells with accessible chromatin enriched for TP53, TP63 and resistance-pathway-activating TF motifs. Nuclear receptors RORa, NR2F6 and HNF4NG were identified as candidate transcriptional drivers of stress-associated chemotherapy resistance whilst closure of binding sites for E2F2 and E2F4 indicated low proliferative capacity of resistant tumour subsets. Delineation of the epigenetic landscape of chemoresistant ovarian cancer therefore reveals core transcriptional regulators of chemoresistance and identifies potential novel therapeutic approaches for improving clinical outcome.

overall_design:
To investigate the single cell chromatin accessibility landscape of HGSOC omental metastasis tumour microenvironments in pre vs post NACT-treated patients
Tumour omentum tissue biopsies from pre and post NACT-treated patients  were obtained following the surgical resection of omental tissue and were immediately snap frozen in liquid nitrogen

first: W

last: Croft

first: R

last: Pounds

first: K

last: Singh

first: J

last: Balega

first: S

last: Sundar

first: D

last: Jeevan

last: Ganesan

last: Kehoe

last: Zuo

first: Jason

last: Yap


title: CD70 identifies donor derived alloreactive T cells in severe acute Graft vs Host Disease post allogeneic SCT

summary: Graft-versus-host disease (GvHD) remains a major challenge post allogeneic hematopoietic stem cell transplantation (allo-HSCT) and understanding its immunopathology is crucial for effective therapeutic intervention. Here we investigated the significance of CD70, a co-stimulatory molecule, in the context of aGvHD. CD70 was found to be transiently expressed on activated T cells during early immune reconstitution post-transplantation but persisted longer in aGvHD. Our findings illustrate that CD70+ T cells are characterized by upregulated activation receptors and enhanced cytokine production, while displaying signs of exhaustion. Remarkably, CD70+ T cells expressed chemokine receptors CCR4 and CCR6 and were actively recruited to inflamed tissues, implicating them in aGvHD pathogenesis. The chromatin at transcription factor MGA and NFAT5 loci was found to be selectively altered upon allo-antigenic stimulation in CD70+ T cells ex-vivo. Gene transcriptions of Toll-like receptors and MAPK signalling pathway were also found to differ in CD70+ and CD70- T cells of aGvHD patients. Insights into the clonality and antigen specificity of CD70+ T cell populations revealed potential novel antigenic targets. Further blocking CD70 in allogeneic T cells from aGvHD patients primed with autologous antigen presenting cells prior to HSCT demonstrated that anti-CD70 antibody reduced T cell proliferation and cytokine production. These findings implicate CD70 as a potential therapeutic target to modulate T cell responses and mitigate aGvHD. Targeting the CD70-CD27 co-stimulation pathway holds promise for prophylactic treatment.

overall_design:
To investigate the gene expression, T cell receptor clonality and chromatin accessibility profile in CD70+/- T cells within 1 week of the onset of acute graft vs host disease post allogeneic stem cell transplant
CD70+ and CD70- T cells were isolated by flow cytometry from aGvHD patients post stem cell transplant at 2-7 days prior to the onset of aGvHD and libraries were prepared for RNA, TCR and ATAC sequencing

first: Kriti

last: Verma

first: Wayne


title: A Nucleolar Mechanism Suppresses Organismal Proteostasis by Modulating Signaling of the TGF-β/ERK Axis

city: Jerusalem

first: Inbar

last: Plaschkes

address: The Hebrew University of Jerusalem - Ein Kerem

department: The Faculty of Medicine - Ein Kerem

country: Israel

institute: HUJI

summary: The protein homeostasis (proteostasis) network encompasses a myriad of mechanisms that maintain the integrity of the proteome by controlling various biological functions, including protein folding and degradation. Alas, aging-associated decline in the efficiency of this network enables protein aggregation and consequently the development of late onset neurodegenerative disorders, such as Alzheimer’s disease (AD). Accordingly, the maintenance of proteostasis through late stages of life bears the promise to delay the emergence of these devastating diseases. Yet, the identification of proteostasis-regulators is needed to assess the feasibility of this approach. Here we report that knocking down the activity of the nucleolar FIB-1-NOL-56 complex, protects model nematodes from proteotoxicity of the AD-causing, Aβ peptide. This mechanism promotes proteostasis across tissues by modulating the activity of TGF-β signaling and by enhancing proteasome activity. Our findings point at new research avenues toward the development of proteostasis-promoting therapies for neurodegenerative maladies.

overall_design: Three synchronized groups of CL2006 worms (expressing Aβ) were included in the experiment: Animals after hatching were grown on EV bacteria until L4 larva stage then separate into different goups: (i) animals that were grown on EV bacteria  or (ii) treated with nol-56 RNAi. These worms express Aβ uninterruptedly and thus, were challenged by high levels of proteotoxicity.

first: Ehud

last: Cohen

first: Huadong

last: Zhu

first: Irit

first: Reut

last: Bruck-Haimson

first: Adam

last: Zaretsky

first: Roni

last: Falk

first: Hanna

last: Achache

first: Yonatan

last: Tzur


title: Circular RNA expression profiling in UVA-treated HaCaT cells

city: luzhou

first: yi

last: peng

address: xianglinlu

institute: 西南医科大学

summary: This RNA sequencing dataset analyzes circRNA expression changes in HaCaT keratinocytes after UVA irradiation. Cells were exposed to 5 J/cm2 UVA and profiled using ribosomal RNA-depleted RNA sequencing on an Illumina platform. Differentially expressed circRNAs were identified by computational pipelines. The data provide insights into circRNA regulation during photo-oxidative stress.

overall_design: HaCaT cells were cultured in DMEM with 10% FBS and antibiotics. For UVA treatment, cells at 70% confluence were exposed to 5 J/cm2 UVA irradiation using a UV lamp. Control cells were sham irradiated. After 6 hours, total RNA was isolated using TRIzol reagent. Ribosomal RNA was removed and sequencing libraries constructed for Illumina sequencing. Raw reads were aligned to the hg38 human reference genome. Back-spliced junction reads were used to identify and quantify circRNA expression.

first: JianGuo

last: Feng

first: Peng

last: Yi

first: Yan

last: Huang

first: Menghong

last: Long


title: Interaction between stem cells and CNT@graphene oxide nanoribbon bilayer membrane with similar structure and different electrical conductivity.

city: Cheonan

first: Yu

middle: Meng

last: Li

address: Pharmacy Bldg, Cheonan 31116, Republic of Korea

department: Department of Nanobiomedical Science

country: South Korea

institute: Institute of Tissue Regeneration Engineering (ITREN)

summary: We report the potential modulation effects of electroconductivity itself for neural stem/progenitor cells.

overall_design: Examination of neural stem/progenitor cells cultured on a virous electroconductive carbon films.

first: Yu-Meng

first: Jung-Hwan

last: Lee

first: Hae-Won

last: Kim


title: Effect of ferrostatin-1 on living myocardial slices derived from heart failure patients

city: Hannover

first: Maximilian

last: Fuchs

address: Carl-Neuberg-Str. 1

department: IMTTS

institute: Hanover Medical School

summary: Cardiac injury remains a leading cause of death globally with limited availability of therapeutic approaches. In this study, we employed living myocardial slices (LMS) as an ex vivo model of cardiac injury to investigate underlying mechanisms and potential therapeutic targets. Cryoinjury was induced in adult rat LMS, resulting in 30% tissue damage. Cryoinjured LMS demonstrated impaired contractile function, cardiomyocyte hypertrophy, inflammation, and cardiac fibrosis, closely resembling in vivo cardiac injury characteristics. Proteomic analysis revealed an enrichment of factors associated with ferroptosis in the injured LMS, suggesting a potential causative role. To test this hypothesis, we pharmacologically inhibited ferroptosis using ferrostatin (Fer-1) in the cryoinjured rat LMS, resulting in attenuation of structural changes and repression of pro-fibrotic processes. Furthermore, LMS generated from failing human hearts were used as a model of chronic heart failure. In this model, Fer-1 treatment was observed to reduce the expression of ferroptotic genes and enhance contractile function. Blocking ferroptosis in human cardiac fibroblasts (HCFs) resulted in a downregulation of fibroblast activation genes, a decrease in fibroblast migration capacity, and a reduction in reactive oxygen species production. Analysis of RNA sequencing data from Fer-1-treated human LMS revealed that metallothioneins, a group of cysteine-rich proteins recognized for their antioxidative attributes and capacity to neutralize free radicals and reactive oxygen species, might serve as a potential mechanism underlying the suppression of ferroptosis. This effect is likely to be mediated by replenishing the existing glutathione reserves within the cells, which are then harnessed to combat lipid peroxidation and ferroptosis. These findings highlight the potential of targeting ferroptosis and metallothioneins as a promising strategy for the treatment of heart disease.

overall_design: Living myocardial slices were generated from human hearts obtained from heart failure patients at the time of transplanation. To investigate the role of ferroptosis in heart failure, LMS were treated with either ferrostatin-1 [10µM] or vehicle control for 72 hours and then subjected to RNA seq.

first: Naisam

last: Abbas

first: Florian

middle: J

last: Waleczek

first: Fuchs

last: Maximilian

first: Annette

last: Just

first: Angelika

last: Pfanne

first: Andreas

last: Pich

first: Filippo

last: Perbellini

first: Christopher

last: Werlein

first: Wilhelm

last: Korte

first: Fabio

last: Ius

first: Arjang

last: Ruhparwar

first: Natalie

last: Weber

first: Jan

last: Fiedler

first: Thomas

last: Thum


title: COL6A6 peptide vaccine ameliorates atherosclerosis through inducing immune response and regulating lipid metabolism in ApoE-/- mice

first: Dongmei

last: Tang

state: GuangDonng Province

address: Jingxi Street

department: pathophysiology

institute: Southern Medical University

summary: Atherosclerosis is an autoimmune disease characterized by lipid imbalances and chronic inflammation within blood vessels with limited preventive and treatment options currently available. Previous experiments have demonstrated the atheroprotective potential of collagen 6 subtype alpha6 (COL6A6) in apolipoprotein E-deficient (ApoE-/-) mice with hyperlipidemia. However, the mechanism underlying the anti-atherosclerotic effects of COL6A6 remains elusive. This knowledge gap was addressed in the present study by immunizing ApoE-/- mice with the Pep_A6 vaccine, comprising a COL6A6 peptide-KLH (keyhole limpet hemocyanin) conjugate and aluminum (Alum) hydroxide adjuvant, and conducting a series of experiments. Our objective was to investigate the efficacy of the Pep_A6 vaccine, focusing on immune responses and lipid metabolism. Our finding showed that the Pep_A6 vaccine represents a novel approach to combat atherosclerosis by inducing a large increase in Treg cells, the generation of antigen-specific antibodies and regulating lipid metabolism.

overall_design: To investigate the effect of vaccine on lipid metabolism, livers were collected from ApoE-/- mice subjected to a normal diet or a high-fat diet immunized with the Pep_A6 vaccine or PBS. Each group contained 3-5 replicates, and subsequently the samples were analyzed by transcriptome sequencing. The high-fat diet was fed for 20 weeks, and the Chow mice, as the normal control group, was continuously fed a normal diet throughout the study period.

first: Yan

last: Liu

first: Rui

last: Duan

first: Run

last: Lin

first: Sujun

last: Xiao

first: Zhonghao

last: Li

first: Xianyan

first: Jingrong

last: Huang

first: Ming

last: Zhao


title: Characterization of human CD56+ MAIT cells in peripheral blood

city: Huddinge

first: Johan

middle: K.

last: Sandberg

state: Stockholms

address: Alfred Nobels Allé 8b

department: Department of Medicine Huddinge

country: Sweden

institute: Karolinska Institutet

summary: A CD56+ MAIT cell population shows features of enhanced innate-like functionality and reduced TCR repertoire diversity.

overall_design:
MAIT cells, T cells and NK cells were isolated from healthy human peripheral blood donations and subjected to single cell sequencing of gene expression (GEX), surface epitome (ADT) and TCR information. Data that passed quality control and were used for conclusions are summarized in the supplementary files.

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Submitter states that due to the EU privacy protection act they are not permitted to share raw data of human individual-specific sequencing results.
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first: Tobias

last: Kammann

first: Curtis

last: Cai


title: Downregulation of UBA1 Expression in Myelodysplastic Syndrome

city: Houston

first: Ziyi

state: TX

address: 1400 Pressler Street

institute: MD Anderson Cancer Center

summary: Somatic loss-of-function mutations of the ubiquitin-activating enzyme E1 gene (UBA1) that occur in VEXAS syndrome (vacuoles, E1 enzyme, X-linked, auto-inflammatory, somatic) also occur in myelodysplastic syndrome (MDS). This suggests that impairment of UBA1 activity contributes to the pathogenesis of these diseases, which are both characterized by systemic inflammation. We sought to determine whether abnormal expression of UBA1 in MDS contributes to disease development. We analyzed RNA sequencing results obtained from CD34+ bone marrow hematopoietic stem and progenitor cells of patients with treatment-naive MDS or chronic myelomonocytic leukemia and from heathy donors, and we detected significant downregulation of UBA1 RNA expression in MDS. In patients with MDS without excess blasts, UBA1 downregulation was associated with altered innate immune and autophagy signaling and co-occurred with SF3B1 mutations. Moreover, in cultured human bone marrow hematopoietic stem and progenitor cells and in mice, pharmacologic inhibition of UBA1 led to impaired hematopoietic repopulating activity, particularly in the erythroid compartment. These results indicate that, in addition to somatic mutations, downregulation of UBA1 may play a role in MDS pathogenesis.

overall_design: RNA-seq of 8 mouse bone marrow LSK samples, 4 treated by TAC-243 and the other 4 are treated by vehicle control

first: Yue

last: Wei


title: Wnt signaling dosage controlled by a Ctnnb1 enhancer balances homeostasis and tumorigenesis of intestinal epithelia [RNA-Seq]

city: wuhan

first: zhao

last: chen

state: Hubei

address: shuiguohu

department: BIOLOGY

institute: wuhan university

summary: β-catenin-dependent canonical Wnt signaling plays a plethora of roles in organ development, tissue homeostasis and cancer. Here we identified an upstream enhancer of Ctnnb1 - ieCtnnb1 - that controls intestinal homeostasis. ieCtnnb1 is specifically active in crypts of small and large intestines. Single-cell sequencing revealed that ieCtnnb1 knockout (ieCtnnb1KO) biased epithelial composition and functions of small intestinal crypts – leaning toward absorptive functions at the expense of secretive roles. Deletion of ieCtnnb1 hampered epithelial turnovers in physiologic and regenerative conditions. In contrast, deletion of ieCtnnb1 prevents occurrence and progression of Wnt/β-catenin driving colorectal cancers. The human ieCTNNB1 specifically drives reporter in intestinal crypts and contains a SNP that is associated with CTNNB1 expression levels in human gastrointestinal epithelia. The enhancer activity of ieCTNNB1 in colorectal cancer tissues is higher than that in adjacent normal tissues and positively correlates with CTNNB1 expression levels. Key trans-factors that bind to ieCTNNB1 and regulate CTNNB1 transcription were identified. Together, these findings revealed an enhancer-dependent mechanism that controls the dosage of Wnt signaling, hence homeostasis of intestinal epithelia.

overall_design: Comparative gene expression profiling analysis of RNA seq data in the small intestine crypt of adult wild-type and ieCtnnb1 knockout mice

first: Xiaojiao

last: Hua

first: Chen

first: Jianbo

last: Tian

first: Junbao

last: Wang

first: Xiaoping

last: Miao

first: Gen

last: Zhen

first: Min

last: Wu

first: Mei

last: Ye

first: Ying

last: Zhou


title: PICKLE-mediated nucleosome condensing drives H3K27me3 spreading for the inheritance of Polycomb memory during differentiation [ATAC-Seq]

first: Liang

last: Zhenwei

state: Guangdong

address: Xingang West Road

department: School of Life Science

institute: Sun Yat-sen University

summary: The Polycomb repressive complex 2 (PRC2) is an essential epigenetic regulator that deposits repressive H3K27me3 for transcriptional gene silencing in eukaryotes. The PRC2-mediated gene silencing process occurs in two steps: the initial H3K27me3 deposition at the nucleation region, and the subsequent spreading of H3K27me3 over the entire gene. Lack of H3K27me3 spreading gives rise to a metastable state that could lead to loss of silencing. H3K27me3 spreading is thus a key step critical for the establishment of stable long-term Polycomb silencing in both animals and plants.Here, we uncover that Arabidopsis thaliana PICKLE (PKL), a member of the conserved Chromodomain Helicase DNA-binding (CHD) family of chromatin remodeling ATPase13, is dispensable for the nucleation but especially  required for the efficient spreading of H3K27me3 at thousands of Polycomb target genes. PKL localizes to the spreading regions in a non-DNA-sequence-specific manner through its SANT-SILDE domain. PKL then upregulates the chromatin density  by its CHROMODOMAIN and ATPase domain , enabling the H3K27me3 methyltransferase CURLY LEAF (CLF) to deposit H3K27me3 on nucleosomes in the spreading regions to facilitate the H3K27me3 spreading.

overall_design: Examination of chromatin accessibility in 14-day-old WT and differet mutants

first: Zhenwei

last: Liang

first: Chenlong


title: Wnt signaling dosage controlled by a Ctnnb1 enhancer balances homeostasis and tumorigenesis of intestinal epithelia


title: Single cell RNA-Seq analysis of irradiated and non-irradiated skin cells in a nuclear accident patient.

city: suzhou

first: zhang

middle: shu

last: yu

address: No. 199, Ren'ai Road

department: soochow university

institute: Soochow University

summary: This study aims to compare mRNA expression between irradiated and non-irradiated people’s skin by single cell RNA-Seq.The patient was a nuclear accident patient exposed to an X-ray spectrometer. In this study, the skin tissues was isolated from patient's different parts. The Control group of skin was collected from the patient belly without radiation for RNA-seq. The skin of IR group was collected from the irradiated skin tissue on the right hand of patients during skin grafting.

overall_design: Single cell RNA-Seq analysis of skin tissue from irradiated and non-irradiated parts of nuclear accident patient. ScRNA sequencing libraries were further generated by the 10x Chromium Single Cell 3′ Library & Single Cell 3’ v3 Gel Beads (10x Genomics). Briefly, gel beads with cell barcodes and skin cell suspension were wrapped in liquid droplets by a microfluidic platform (10x Genomics). A droplet containing single cells was collected and then lysed to generate Gel Bead-In Emulsions (GEMs).

first: Shuyu

last: Zhang

first: Tao

last: Yan

first: Daojiang

last: Yu


title: PICKLE-mediated nucleosome condensing drives H3K27me3 spreading for the inheritance of Polycomb memory during differentiation


title: Interleukin 27 Protects From Gastric Atrophy and Metaplasia During Chronic Autoimmune Gastritis

status: Public on Oct 01 2024

city: St. Louis

first: Richard

last: DiPaolo

state: MO

address: 1100 S Grand Ave

institute: Saint Louis Univeristy

summary: Background & Aims: The association between chronic inflammation and gastric carcinogenesis is well established, but it is not clear how immune cells and cytokines regulate this process. We investigated the role of interleukin 27 (IL27) in the development of gastric atrophy, hyperplasia, and metaplasia (preneoplastic lesions associated with inflammation-induced gastric cancer) in mice with autoimmune gastritis. Methods: We performed studies with TxA23 mice (control mice), which express a T-cell receptor against the H+/K+ adenosine triphosphatase α chain and develop autoimmune gastritis, and TxA23xEbi3-/- mice, which develop gastritis but do not express IL27. In some experiments, mice were given high-dose tamoxifen to induce parietal cell atrophy and spasmolytic polypeptide-expressing metaplasia (SPEM). Recombinant IL27 was administered to mice with mini osmotic pumps. Stomachs were collected and analyzed by histopathology and immunofluorescence; we used flow cytometry to measure IL27 and identify immune cells that secrete IL27 in the gastric mucosa. Single-cell RNA sequencing was performed on immune cells that infiltrated stomach tissues. Results: We identified IL27-secreting macrophages and dendritic cell in the corpus of mice with chronic gastritis (TxA23 mice). Mice deficient in IL27 developed more severe gastritis, atrophy, and SPEM than control mice. Administration of recombinant IL27 significantly reduced the severity of inflammation, atrophy, and SPEM in mice with gastritis. Single-cell RNA sequencing showed that IL27 acted almost exclusively on stomach-infiltrating CD4+ T cells to suppress expression of inflammatory genes.  Conclusions: In studies of mice with autoimmune gastritis, we found that IL27 is an inhibitor of gastritis and SPEM, suppressing CD4+ T-cell–mediated inflammation in the gastric mucosa.

overall_design: 800 ng of carrier-free rIL27 (2799-ML-010/CF; R&D Systems, Minneapolis, MN) in 200 uL of sterile PBS was loaded into mini osmotic pumps (model 2004; Alzet, Cupertino, CA) based on published effective doses in mice. Pumps were implanted subcutaneously into control TxA23 mice at 3 months of age. Mice were euthanized 4 weeks after implantation. Pumps containing only sterile PBS were used as sham controls. For scRNA sequencing analysis, CD45+ propidium iodide cells- were sorted from the gastric mucosa to separate live immune cells from dead and epithelial cells. These cell suspensions then were washed once and loaded onto the 10X Genomics Chromium Controller using the 5' v1.1 protocol following manufacturer's recommendations.

first: Kevin

middle: A

last: Bockerstett


title: Acidic microenvironment and transcriptomic genes in pancreatic cancer cells

city: hang zhou

first: de yang

last: mu

address: 杭州医学院临安校区

institute: hang zhou medical college

summary: Investigating the effect of acidic microenvironment on mRNA transcriptome gene expression in pancreatic cancer cells

overall_design: The acidic microenvironment was simulated in vitro by dividing into 2 groups of ASPC-1 cells cultured in pH 7.4 and pH 6.4 medium, with three replicates in each group

first: Deyang

last: Mu

first: Jungang


title: PICKLE-mediated nucleosome condensing drives H3K27me3 spreading for the inheritance of Polycomb memory during differentiation [ChIP-Seq]

overall_design: Examination of H3K27me3 enrichment and PKL occupancy and  in 14-day-old WT and differet mutants

last: Li


title: Single-cell sequencing identifies characteristics of disease and bone marrow in concurrent multiple myeloma and myelodysplastic syndrome

city: Jinan

first: jingjing

last: wang

address: No. 440 Jiyan Road, Huaiyin District, Jinan City, Shandong Province

institute: Shandong First Medical University and Shandong Academy of Medical Sciences

summary: In the current study, we applied single-cell sequencing to the bone marrow cells of four patients with concurrent MM and MDS (MM-MDS) to identify distinct cell type distributions and transcriptome signatures compared to that from MM patients and healthy donors. Despite of heterogeneity, the degree of plasma cell expansion and malignancy in the concurrent patients were inferior than that in MM patients. Additionally, the differentiation of hematopoietic stem cells is incomplete, involving abnormalities in red blood cell differentiation, higher frequency of B cell enrichment accompanying positive regulation of immune response, as well as differences in the pathways and endpoints of myeloid differentiation, leading to the appearance of neutrophil-like monocytes. In MM patients, B cells and stromal cells interact with plasma cells mainly via IL-16/CD4 signaling, however in MM-MDS patients, B cells interact with plasma cells mainly via BTLA-TNFRSF14 signaling and stromal cells via CXCL12-CXCR4 signaling, respectively.

overall_design: Bone marrow aspirates were isolated from four patients diagnosied with concurrent MM and MDS. The scRNA-seq data from 4 healthy donors (HDs) and MM patients were downloaded from the Gene Expression Omnibus database (GSE120221), and healthy donor (n = 4) without MM or MDS disease obtained from GSE189460 served as the control group.

first: Jingjing

last: Wang

first: Xu

last: Zhu

first: Xiuli

last: Sun

first: Yesong

last: Fu


title: The Aggregates of Mesenchymal stem cell with Cadherin/IGF1 Functionalized PLGA composite Microparticles Improve Systemic Lupus Erythematosus Treatment in MRL/lpr mice

city: No. 94, Weijin Road, Nankai District, Tianjin

first: guoqiang

last: chen

state: Tianjin

institute: nankai university

summary: Mesenchymal stem cell (MSC) therapy is a promising candidate for systemic lupus erythematosus (SLE), while more researches are needed to further improve therapeutic efficacy. In this study, engineered MSC aggregates are composited with MSC and cadherin/IGF1 functionalized PLGA composite microparticles, and are able to stimulate the microenvironment in vivo and enhance MSC functions of immunoregulation and cytokine secretion. Comprehensive characterization of these PLGA composite microparticles coated with E-cadherin/N-cadherin, enhancing MSC viability and cytokine secretion, followed by transcriptomic analysis to evaluate their potential advantages. We detected engineered MSC aggregates further ameliorated skin and lupus nephritis, compared with MSCs in MRL/lpr mice. In addition, engineered MSC aggregates enhanced Treg differentiation in vitro and in the spleen and lumph node of MRL/lpr mice. These findings suggested that engineered MSC aggregates represented a promising bioengineered approach for treating SLE, broadening the clinical applications of MSC-based therapies.

overall_design: To further understand the functional advantage of the engineered MSC aggregates  over the normal MSC, we conducted RNA-seq analysis to uncover potential enhancements in therapeutic functions

first: Shanshan

last: Liu

first: Guoqiang

last: Chen


title: Regulation of hsa_circ_0070512-gene overexpression on human prostate cancer epithelial cells PC3

city: kunming

first: Gao

last: hang

address: kunming

institute: Kunming Medical University

summary: To investigate the regulatory effect of hsa_circ_0070512 gene on prostate cancer cell line PC3, we established the PC3 hsa_circ_0070512 overexpressing cell line (OE) and its negative control group (vector). Then we used RNA-seq to obtain gene expression profile analysis

overall_design: Comparison of gene expression profiles of PC3 overexpression hsa_circ_0070512 gene human prostate cancer cells (OE)and their negative control group (vector) RNA-seq data

first: Delin

last: Yang

first: Pingxin

first: Hang

last: Gao

first: Chengxing

last: Xia


title: Transcriptomic response of the xylose-selective strain derived from E. coli BL21(DE3) growing on xylose or glucose

city: Cuernavaca

first: Alfredo

last: Martínez

state: Morelos

address: Av. Universidad 2001, Col. Chamilpa

department: Departamento de Ingeniería Celular y Biocatálisis

country: Mexico

institute: Instituto de Biotecnología, Universidad Nacional Autónoma de México

summary: Different genetic engineering strategies have been proposed to obtain E. coli strains that selectively consume xylose. In this study, a previously reported strategy for obtaining a xylose-selective strain in E. coli K12 was applied to E. coli BL21 (DE3). While this approach resulted in the expected xylose-selective phenotype, a low xylose consumption rate was recorded when the strain was grown on a mixture of xylose and glucose. To enhance xylose consumption, a variant of the transcriptional activator XylR was expressed. The resulting strain not only exhibited an improved capacity to consume xylose but also slightly recovered the ability to consume glucose. The aim of the microarray analysis was to identify the transcriptional changes associated with glucose assimilation in the BL21(DE3) derived xylose-selective strain.

overall_design: The analysis compared the transcriptomic response of a xylose-selective strain (derived from BL21(DE3)) when growing in xylose or glucose against the wild-type strain  BL21(DE3) growing in the respective sugar.

first: Eliseo

middle: R

last: Molina-Vazquez


title: The six unique histone deacetylase (HDAC) 1 complexes vary greatly in abundance and utilize distinct molecular assemblies

city: Leicester

first: Shaun

last: Cowley

address: Henry Wellcome Building, Lancaster Road

department: Molecular and Cell Biology

institute: University of Leicester

summary: Histone deacetylase 1 and 2 (HDAC1/2) are highly related enzymes that that regulate histone acetylation levels in all cells, as catalytic and structural components of six unique multi-protein complexes: SIN3, NuRD, CoREST, MIDAC, MIER1 and RERE. Co-immunoprecipitation of HDAC1-Flag followed by mass-spectrometry revealed that 92% of the HDAC1 in mouse embryonic stem cells resides in 3 complexes, NuRD (49%), CoREST (28%) and SIN3 (15%).  To delineate the function of these different biochemical entities we compared binary structures of the MTA1:HDAC1 and MIDAC:HDAC1 to identify conserved residues on the surface of HDAC1 that would potentially perturb one or more complexes. A single mutation, Y48E, disrupts binding to all complexes with the exception of SIN3. Remarkably, rescue experiments performed with HDAC1-Y48E in HDAC1/2 double-knockout cells, showed that retention of SIN3 binding alone is sufficient for cell viability. Gene expression and histone acetylation patterns were perturbed in both Y48E and a second mutant cell line, HDAC1-E63R, indicating that cells require a full repertoire of the HDAC1/2 complexes to regulate their transcriptome appropriately. Comparative analysis of SIN3/HDAC1 and MTA1/HDAC1 structures confirmed the differential modes of HDAC1 recruitment, with the surface including Y48 bound only by ELM2/SANT domain containing complexes. We provide novel molecular insights into the abundance, co-factors and assemblies of this crucial family of chromatin modifying machines.

overall_design: To investigate the functions of the distinct HDAC1 corepressor containing complexes we stably expressed a variety of HDAC1-Flag constructs (WT, Y48E, E63R) in Hdac1/2 conditional double knockout ESCs. With the aim of disrupting complex specific interactions between HDAC1 and its binding partners. Following deletion of endogenous Hdac1/2 we performed bulk RNA-seq to determine the consequences of the Y48E and E63R mutations on gene expression in ESCs relative to the WT HDAC1 construct.

first: Ahmad

last: Alshehri

first: India

middle: M

last: Baker

first: David

last: English

first: Trong

last: Khoa Pham

first: Louise

last: Fairall

first: Mark

middle: O

last: Collins

first: John

last: Schwabe


title: Rio-seq Analysis on SETD2-Deficient and Control Intestinal Epithelial Cells

city: Shanghai

first: Rao

last: hanyu

address: Huashan Road NO.1954

institute: Shanghai Jiao Tong University

summary: Protein abundance does not necessarily correlate with mRNA levels, highlighting the highly variable efficiency of translation. Ribosome biogenesis, the process of ribosome production, affects translation efficiency and plays a crucial role in various biological processes. However, its role in maintaining epithelial barrier integrity has not been definitively established. SETD2 is a methyltransferase critical for the integrity of epithelial barrier. Here, we examined intact intestinal barrier with SETD2 present and compromised intestinal barrier with SETD2 loss.

overall_design: Since mRNA translation in ribosomes determines protein abundance and discordant translational efficiency (TE) causes protein-mRNA discrepancies, we utilized ribosome profiling sequencing (Ribo-seq) to investigate genome-wide TE changes during the loss of epithelial integrity. In this process, mRNA undergoing translation, represented as ribosome footprints (RFs), was sequenced and compared to total mRNA sequencing data to illustrate changes in the TE of genes.

first: Hanyu

last: Rao

first: Aiting

last: Wang

first: Li

last: Li

first: Xianting

last: Ding


title: Gene expression profile at single cell level of CD4+ and CD8+ tumor infiltrating lymphocytes (TIL) originiating from the EMT6 tumor model from mSTAR1302 treatment

city: Cambridge

first: Jonathan

last: Hsu

state: MA

address: 840 Memorial Dr 4th Floor

institute: Marengo Therapeutics

summary: mSTAR1302 treatment induces a shift in gene expression in TILs that promotes a highly active TEM and TEFF cell phenotypes immune to exhaustion and desensitized TCR signalling

overall_design: CD4+ and CD8+ TILs from EMT6 tumor bearing mice from mSTAR1302 treatment were isolated and purified by magnetic separation.


title: The impact of brain insulin receptor isoform A on brain sparing effect in fetal growth restricted rat

city: Kyoto

first: Yutaro

last: Tomobe

address: 54 Kawaharacho Shogoin Sakyoku

department: Pediatrics

country: Japan

institute: Graduate School of Medicine, Kyoto University

summary: This study aims to investigate the influence of brain IR-A in fetal growth restricted (FGR) neonates.

overall_design:
An FGR model rat was generated by maternal caloric restriction (CR). Pups were born by Caesarean section and whole brain samples were dissected immidiately.
Then we analyzed differentially expressed genes using data obtained from RNA-sequiencing of 3 samples each from CR and control group.


title: ACSS2-coupled KAT2A regulates histone H3 lactylation in gene promoter regions and gene expression

city: Hangzhou

first: Rongxuan

last: Zhu

address: No. 268 Kaixuan Road

institute: Zhejiang University

summary: We report EGFR activation induces ERK-mediated S267 phosphorylation of acetyl-CoA synthetase 2 (ACSS2) and its subsequent nuclear translocation and complex formation with lysine acetyltransferase 2A (KAT2A).Consequently, KAT2A acts as a lactyltransferase to lactylate histone H3, leading to expression of Wnt/β-catenin, NFκB, and PD-L1, and brain tumor growth and immune evasion.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for ACSS2,KAT2A and H3K18la with EGF treatment in GBM cells.


title: Bulk RNA seq data for sorted human CD34+CD38low cells after DMSO or 78c treatment

city: Bethesda

first: Jianyi

state: MD

address: 9000 Rockville Pike

department: CMTB

institute: NHLBI, NIH

summary: Hematopoietic stem cells (HSCs) balance self-renewal and differentiation within the bone marrow, a process that is disrupted under in vitro conditions, posing challenges for ex vivo studies and clinical applications such as gene therapy. This study examines the role of CD38, a glycoprotein involved in NAD+ metabolism, in regulating HSC function. Inhibition of CD38 activity with the small molecule 78c significantly increased the percentage of phenotypic HSCs and maintained their engraftment potential in mice, akin to uncultured cells.Here we performed bulk RNA seq on DMSO and 78c treated human CD34+CD38low cells to look for the transcriptomic differences between the two groups.

overall_design: Human CD34+CD38low hematopoietic stem and progenitor cells isolated from mobilized peripheral blood CD34+ cells and cultured for 24 hours in the presence of cytokines (SCF, FLT3, and TPO) with either 5 μM of the CD38 inhibitor 78c or a DMSO vehicle control. Following culture, cells were harvested, and RNA was extracted using the RNeasy Plus Mini Kit (Qiagen) as per the manufacturer’s protocol. The sequencing libraries were constructed from 800 ng of total RNA using the Illumina Stranded mRNA library prep kit (#20040534, Illumina) following the manufacturer instruction. The fragment size of RNA seq libraries was verified using the Agilent 2100 Bioanalyzer (Agilent) and the concentrations were determined using Qubit instrument (LifeTech). The libraries were loaded onto the Illumina Novaseq 6000 SP flow cell for 2x100 bp paired end read sequencing, generating approximately 50 million reads per sample. The fastq files were generated using the bcl2fastq software for further analysis. Subsequent analysis involved aligning the reads to a reference genome, followed by differential gene expression analysis to identify key pathways and molecular mechanisms modulated by CD38 inhibition.

first: Andre

last: Larochelle


title: PI3K regulates TAZ/YAP and mTORC1 and can synergistically be targeted in sarcomas

city: Iowa City

first: Michael

middle: S

last: Chimenti

state: IA

address: 431 Newton Road

department: Iowa Institute of Human Genetics

institute: University of Iowa

summary: Sarcomas encompass heterogenous, difficult to treat cancers, lacking common therapeutic targets. Phosphatidylinositol-3 kinase (PI3K) signaling is activated in sarcomas to a greater degree than previously appreciated due to phosphatase and tensin homolog (PTEN) loss, and could represent such a target. Targeting PI3K signaling has largely focused on targeting mTORC1, considered the main effector of PI3K signaling, but this has not translated to success in the clinic, suggesting that there may be other effectors downstream of PI3K. One gap in our understanding of the PI3K signaling pathway has been the absence of a known oncogenic transcription factor. Herein we implicate TAZ and YAP as additional transcriptional effectors downstream of PI3K signaling regulated by a LATS1/2 dependent mechanism. Using in vitro and in vivo approaches, we show that TAZ and YAP are central oncoproteins in PI3K driven oncogenesis along with mTORC1, providing a rationale for combination therapy. Leveraging these findings, we describe a therapeutic approach that builds upon pre-existing therapeutic strategies utilizing mTORC1 inhibitors and combines them with new TEAD inhibitors that target YAP and TAZ. Combination therapy using everolimus and IK-930, an inhibitor targeting autopalmitoylation of the TEADs, synergistically diminished proliferation and anchorage dependent growth of PI3K activated sarcoma cell lines at low, physiologically achievable doses. In vivo, this combination therapy showed a synergistic effect, contrasting with the lack of effect of the individual single agent therapies, suggesting that an integrated view of PI3K and Hippo signaling can be leveraged therapeutically in PI3K activated sarcomas.

overall_design:
RNA was isolated from the tumors of genetically engineered mouse. Where, "Skel" is the control group and "PTEN", "YAP", "TAZ", "Quad" represent the experimental group. Each sample group had 5 replicates. RNA-seq was done to evaluate and study the differentially expressed genes in each group.

PTEN: Trp53fl/fl Ptenfl/fl
YAP: Trp53fl/fl Ptenfl/flYapfl/fl
TAZ: Trp53fl/flPtenfl/flTazfl/fl
QUAD: Trp53fl/flPtenfl/flYapfl/flTazfl/fl
SKEL: skeletal muscle control

first: Keith

last: Garcia

first: Ali

last: Khan

first: Krishnendu

last: Ghosh

first: Souradip

last: Sinha

first: Nicholas

last: Scalora

first: Gillianm

last: DeWane

first: Colleen

last: Fullenkamp

first: Nicole

last: Merritt

first: Yuliia

last: Drebo

first: Samuel

last: Yu

first: Mariah

last: Leidinger

last: D. Henry

first: Patrick

last: Breheny

first: Munir

last: Tanas


title: Uncovering the Dynamics of Immune Cell Populations in the First Week of Life: The Interplay of Neutrophils and Breastfeeding

city: Boston

first: Ofer

last: Levy

address: 300 Longwood Avenue

department: Infectious Disease

institute: Boston Children's Hospital

summary: The first few days of life are characterized by rapid external and internal changes that require rapid host adaptations. Despite growing evidence of the impact of this period on an individual’s lifelong health trajectory, this period remains largely uncharted. To decipher key factors associated with changes in peripheral blood cell composition we conducted a stringently standardized, high-throughput immune phenotyping investigation on 796 newborns across diverse settings (The Gambia, West Africa and Papua New Guinea, Australasia) in the framework of a Human Immunology Project Consortium study. Samples were collected twice from each newborn during the first week of life and analyzed via high throughput flow cytometry with an unbiased automated gating algorithm to capture cell compositional changes at an unprecedented level of detail. We found that immune cell composition in peripheral blood changes along patterns highly conserved across populations and environments. Changes with age/day of life were most pronounced in the innate myeloid compartment. While there was minimal impact of sex, season of birth, mother’s age or origin (i.e., environmental and genetic background), breastfeeding and vaccination were strongly associated with increase in cell counts of peripheral blood neutrophils and monocytes. Our results may suggest a possible association of initiation of breastfeeding with changes in immune ontogeny, and thus possibly host immune-mediated protection from infection. These data begin to outline a specific window of opportunity for interventions that can deliberately direct immune ontogeny.

overall_design: longitudinal neonatal cohort study

first: Tobias

last: Kollmann

first: Sebastiano

last: Montante

first: Joann

last: Arce

first: Rym

last: Ben-Othman

first: EPIC

last: Consortium


title: PBAF associates with repressed chromatin to enable REST occupancy (RNA-Seq)

city: New York

first: Elena

last: Grossi

state: NY

address: 1470 Madison Ave

department: Oncological Sciences

institute: Icahn School of Medicine at Mount Sinai

summary: Multimeric SWI/SNF chromatin remodelers assemble in distinct conformations, with individual functions difficult to dissect. Importantly, mutations in specific SWI/SNF genes are enriched in distinct cancers, as the PBAF-specific component ARID2 in melanoma. Through comprehensive epigenomic profiling of SWI/SNF complexes and their associated chromatin states in melanoma and melanocytes, we found that a subset of PBAF-exclusive regions unexpectedly coexists with PRC2 and repressed chromatin. Time-resolved approaches revealed that PBAF regions are generally less sensitive to ATPase-mediated remodeling compared to BAF sites. Notably, PBAF/PRC2-bound loci are enriched for REST, a transcription factor that represses neuronal genes. In turn, absence of ARID2 and consequent PBAF loss hinders REST ability to bind and inactivate its targets, leading to upregulation of neuronal and synaptic transcripts, a gene signature also associated with ARID2 mutations in melanoma patients. In sum, we demonstrate a unique role for PBAF in generating accessibility for a silencing transcription factor at repressed chromatin.

overall_design: RNA sequencing (RNA-seq) in control and ARID2 KO melanoma 113/6-4L cells (4L) and normal human epithelial melanocytes (NHEM)

first: Emily

last: Bernstein


title: The effect of co-culture on MMTV-HER2 early lesion or primary tumor cell and alveolar macrophages

city: The Bronx

first: Michael

last: Papanicolaou

state: New York

address: 1300 Morris Park Avenue

department: Cell Biology

institute: Albert Einstein College of Medicine

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

overall_design: Refer to individual Series


title: Wnt signaling dosage controlled by a Ctnnb1 enhancer balances homeostasis and tumorigenesis of intestinal epithelia [scRNA-Seq]

city: wuhan

first: zhao

last: chen

address: shuiguohu

institute: wuhan university

summary: β-catenin-dependent canonical Wnt signaling plays a plethora of roles in organ development, tissue homeostasis and cancer. Here we identified an upstream enhancer of Ctnnb1 - ieCtnnb1 - that controls intestinal homeostasis. ieCtnnb1 is specifically active in crypts of small and large intestines. Single-cell sequencing revealed that ieCtnnb1 knockout (ieCtnnb1KO) biased epithelial composition and functions of small intestinal crypts – leaning toward absorptive functions at the expense of secretive roles. Deletion of ieCtnnb1 hampered epithelial turnovers in physiologic and regenerative conditions. In contrast, deletion of ieCtnnb1 prevents occurrence and progression of Wnt/β-catenin driving colorectal cancers. The human ieCTNNB1 specifically drives reporter in intestinal crypts and contains a SNP that is associated with CTNNB1 expression levels in human gastrointestinal epithelia. The enhancer activity of ieCTNNB1 in colorectal cancer tissues is higher than that in adjacent normal tissues and positively correlates with CTNNB1 expression levels. Key trans-factors that bind to ieCTNNB1 and regulate CTNNB1 transcription were identified. Together, these findings revealed an enhancer-dependent mechanism that controls the dosage of Wnt signaling, hence homeostasis of intestinal epithelia.

overall_design: Single cell sequencing of small intestinal crypts in adult wild-type and ieCtnnb1 knockout mice

first: Xiaojiao

last: Hua

first: Chen

last: Zhao

first: Jianbo

last: Tian

first: Junbao

last: Wang

first: Xiaoping

last: Miao

first: Gen

last: Zhen

first: Min

last: Wu

first: Mei

last: Ye

first: Ying

last: Liu

first: Yan

last: Zhou


title: Inflammatory Signatures of Microglia in the Mouse Model of Corticosterone-Induced Depression

city: Beijing

first: Yingying

last: Huang

address: Yanyuan Street

institute: Peking University

summary: Microglia-mediated inflammation has been recognized as a key feature of major depressive disorder. Although hypercortisolemia is commonly observed in depressed patients and can be predictive of treatment response, how such chronic exposure to this stress hormone may influence microglia is incompletely characterized. Here, we exploited a standard mouse model of depressive-like behaviors induced by repeated peripheral administration of corticosterone. Microglia in the prefrontal cortex of mice were profiled by bulk RNA sequencing, which exhibited increased expression of inflammatory markers. In addition, single-cell RNA sequencing further identified distinct molecular patterns of microglial responses. Moreover, we revealed the up-regulation of Pu.1 and Irf8, the two central transcription factors governing microglia-mediated inflammation, in the prefrontal cortex and hippocampus of corticosterone-treated mice, which similarly occurred in depressed patients' microglia. These results have established the inflammatory signatures of microglia in the mouse model recapitulating hypercortisolemia-related depression, providing new insights into developing diagnostic and therapeutic strategies.

overall_design: The C57BL/6 mice were treated with corticosterone by oral gavage for the model of hypercotisolemia-related depression. Then the microglia were sorted as CD45low CD11b+ by the common standard from the prefrontal cortex of vehicle- or corticosterone-treated mice and analyzed using scRNA-seq.


title: Downregulation of Glucose-Energy Metabolism via AMPK Signaling Pathway in Granulosa Cells of Diminished Ovarian Reserve Patients

first: Qinyign

last: Zhu

address: 9 Dongdan Santiao, Dongcheng District

institute: Peking Union Medical College

summary: Glucose metabolism plays a crucial role in the function of granulosa cells (GCs) and the development of follicles. In cases of diminished ovarian reserve (DOR), alterations in these processes can impact female fertility. This study aims to investigate changes in glucose-energy metabolism in GCs of young DOR patients aged 20 to 35 years and their correlation with the onset and progression of DOR. 72 DOR cases and 75 women with normal ovarian reserve (NOR) as controls were included based on the POSEIDON and Bologna criteria. Samples of GCs and follicular fluid (FF) were collected for a comprehensive analysis involving transcriptomics, metabolomics, RT-qPCR, JC-1 staining, and flow cytometry. The study identified differentially expressed genes and metabolites in GCs of DOR and NOR groups, revealing 7 common pathways related to glucose-energy metabolism, along with 11 downregulated genes and 14 metabolites. Key substances in the glucose-energy metabolism pathway, such as succinate, lactate, NADP, ATP, and ADP, showed decreased levels, with the DOR group exhibiting a reduced ADP/ATP ratio. Downregulation of genes involved in glycolysis (HK, PGK, LDH1), the TCA cycle (CS), and gluconeogenesis (PCK) was observed, along with reduced glucose content and expression of glucose transporter genes (GLUT1 and GLUT3) in DOR GCs. Additionally, decreased AMPK pathway activity and impaired mitochondrial function in DOR suggest a connection between mitochondrial dysfunction and disrupted energy metabolism. Above all, the decline in glucose-energy metabolism in DOR is closely associated with its onset and progression. Reduced glucose uptake and impaired mitochondrial function in DOR GCs lead to internal energy imbalances, hindering the AMPK signaling pathway, limiting energy production and supply, and ultimately impacting follicle development and maturation.

overall_design: This study aimed to investigate the alterations in glucose-energy metabolism in granulosa cells (GCs) of patients with diminished ovarian reserve (DOR).Initially, transcriptome analysis was conducted on three GCs from each group to assess gene expression differences. Following this, non-targeted metabolomic and targeted metabolite analyses were performed on three GCs from each group. ATP levels were measured using six GCs from each group, while mitochondrial membrane potential was assessed using the JC-1 assay on ten GCs from each group. AMPK and GLUT1 protein levels were analyzed in four GCs from each group, and glucose content was measured in nine GCs from each group. Additionally, follicular fluid analysis was conducted on five samples from each group to evaluate sugars and sugar alcohols. All experiments were approved by the ethics committee of the First Hospital of Lanzhou University (LDYYLL2019-44).

first: Zhu

last: Qinying

first: Liang

last: xiaole

first: Du

last: junhong

first: He

last: ruifen


title: A LOX-simulated enzyme peptide is used to promote bone healing in diabetes

city: Nanjing

first: Liu

last: Xu

address: No.138,Xianlin Avenue,Qixia District,Nanjing City

institute: Nanjing University of Chinese medicine

summary: To investigate the potential osteogenic mechanism of PMLGH, we performed an mRNA expression profiling microarray.Male Sprague Dawley rats (10 weeks old, 320-350 g weight) were used to test the engineered hydrogels in vivo. For gene expression profiling microarray analysis, tibias were harvested at week 3.

overall_design: Comparative gene expression profiling of RNA-seq data of PMLGH-treated, GelMA-treated and model groups

first: Shan

first: Jian

last: zhang


title: Effects of HMGA1 internalization in melanoma cells [ATACseq_reHMGA1]

first: Ting-Hsiang

institute: Memorial Sloan Ketteting Cancer Center

summary: To study chromatin accessibility  of melanoma cells upon reHMGA1 uptake, we stimulated A375 cells using recombinant HMGA1 for 2 and 18-hrs followed by ATAC-seq analysis with 2 biological replicates.

overall_design: Differential gene expression profiling to identify upregulated targets and gene signatures through GSEA analysis.

first: Richard

last: Koche


title: Activation of Toll-like receptor 2 promotes mesenchymal stem/stromal cell-mediated immunoregulation and angiostasis through AKR1C1.

city: Seoul

first: Joo Youn

last: Oh

state: Korea, Republic of

address: 103 Daehakro, Jongrogu, Yeongondong

department: Ophthalmology

institute: Seoul National University College of Medicine

summary: Background: Mesenchymal stem/stromal cells (MSCs) maintain tissue homeostasis in response to microenvironmental perturbations. Toll-like receptors (TLRs) are key sensors for exogenous and endogenous signals produced during injury. In this study, we aimed to investigate whether TLRs affect the homeostatic functions of MSCs after injury. Methods: We examined the expression of TLR2, TLR3 and TLR4 in MSCs, and analyzed the functional significance of TLR2 activation using single-cell RNA sequencing. Additionally, we investigated the effects and mechanisms of TLR2 and its downstream activation in MSCs on monocytes/macrophages and a mouse model of sterile injury-induced inflammatory corneal angiogenesis.  Results: MSCs expressed TLR2, which was upregulated by monocytes/macrophages. Activation of TLR2 in MSCs promoted their immunoregulatory and angiostatic functions in monocytes/macrophages and in mice with inflammatory corneal angiogenesis, whereas TLR2 inhibition attenuated these functions. Single-cell RNA sequencing revealed AKR1C1, a gene encoding aldo-keto reductase family 1 member C1, as the most significantly inducible gene in MSCs upon TLR2 stimulation, though its stimulation did not affect cell compositions. AKR1C1 protected MSCs against ferroptosis, increased secretion of anti-inflammatory cytokines, and enhanced their ability to drive monocytes/macrophages towards immunoregulatory phenotypes, leading to amelioration of inflammatory corneal neovascularization in mice.  Conclusion: Our findings suggest that activation of TLR2-AKR1C1 signaling in MSCs serves as an important pathway for MSCs’ survival and homeostatic activities during injury.

overall_design: MSCs were treated with 100 ng/mL Pam2CSK4 (InvivoGen, San Diego, CA) for 24 hours. Pam2CSK4-treated MSCs and untreated MSCs were subjected to scRNA-seq using the 10x Genomics Chromium platform.

first: Jung

last: Ko

first: Joo


title: Single cell gene expression profile for normal adult canine neuroretina

city: Philadelphia

first: Raghavi

last: Sudharsan

address: 3900 Delancey Street

institute: University of Pennsylvania

summary: Retinal single cell gene expression profile from two male dogs at 40 weeks of age.

overall_design: Retinal punches were collected from canine neuroretina and dissociated into single cells for scRNAseq analysis.

first: William

last: Beltran


title: Single Cell Gene Expression Profiling of CD45+ Cells in Mouse Liver with or without Empagliflozin (EMPA) Treatment

city: Guangzhou

first: Huijie

last: Zhang

address: No. 1838, North Guangzhou Avenue, Baiyun District, Guangzhou

institute: Nanfang Hospital, Southern Medical University

summary: Single-Cell Sequencing Reveals Immune Cell Subtype Differences in Mouse Liver Between MCD and MCD+Empagliflozin (EMPA) Treatment.

overall_design: CD45+ cells from NASH mouse models were isolated using Fluorescence-Activated Cell Sorting (FACS) based on the presence of APC signal and subsequently analyzed through scRNA-seq.


title: Function of Ets1 in regulating macrophage polarization and adipose inflammation

first: Kai

last: Li

address: #818, East Tianyuan Road

institute: Nanjing Medical University

summary:
To investigate the cooperative function Ets1 in macrophage, we generats Ets1 knockout mice.We then performed gene expression profiling analysis in macrophages seperated from either control or ko mice.
We also performed Ets1 ChIP-seq, using M1 and M2 macrophages seperated from wild type C57 bone marrow, for mechanism study.

overall_design:
Transcription sequencing (RNA-seq)  in macrophages seperated from either Ets1 null or control mice, were perfomed.
Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for Ets1  in M1 and M2 macrophages, were perfomed.

first: Jiahao

last: Ni


title: Single cell RNA sequencing of human primary glioblastoma

city: Harbin

first: Jinquan

last: Cai

address: Xuefu Road

institute: Harbin Medical University

summary: Glioblastoma (GBM) is the most lethal form of central nervous system cancer with a median survival of less than 2 years. Here, we examined the single-cell transcriptomes of primary GBM excised tumors from five different patients to explore the underlying mechanisms of GBM development.

overall_design: We performed the single-cell RNA sequencing of primary GBM excised tumors from five different patients. Tumour specimens were washed by PBS and mechanically cut into small pieces using sterile surgical scissors, and then digested into single cell suspensions. Single-cell RNA libraries were constructed and suquenced using Chromium Next GEM Single Cell 5’ V2 GEM, Library & Gel Bead Kit (10×Genomics) and Illumina NovaSeq 6000.

first: Xiangqi

last: Meng

first: Jie

last: Qin


title: Hepatic Lcmr1 activates the transcription of G6pc and is needed for gluconeogenesis

summary: To investigate the cooperative function Lcmr1 in the regulation of hepatic gluco-lipid homeostasis, we generats hepatic Lcmr1 knockout mice.We then performed gene expression profiling analysis, as well as RNA pol II ChIP-seq, using primary hepatocyte obtained from liver sample of the control or null mice.

overall_design: Transcription sequencing (RNA-seq) and Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for Lcmr1  in mature hepatocytes seperated from either hepatic Lcmr1 null or control mice, were perfomed.

first: Lu

last: Liu

first: Liangan

last: Chen


title: The Senescence-associated Secretome of Hedgehog-deficient Hepatocytes Drives MASLD Progression

city: Durham

first: KUO

last: DU

state: NC

address: 905 SOUTH LASALLE STREET, Room 1063

department: Medicine

institute: Duke Universty

summary: The burden of senescent hepatocytes correlates with MASLD severity but mechanisms driving senescence, and how it exacerbates MASLD are poorly understood. Hepatocytes become senescent when Smoothened (Smo) is deleted to disrupt Hedgehog signaling. We aimed to determine if the secretomes of Smo-deficient hepatocytes perpetuate senescence to drive MASLD progression. RNA seq analysis confirmed that hepatocyte populations of MASLD livers are depleted of Smo(+) cells and enriched with senescent cells. When fed CDA-HFD, Smo(-) mice had lower antioxidant markers and developed worse DNA damage, senescence, MASH and liver fibrosis than Smo(+) mice. Sera and hepatocyte-conditioned medium from Smo(-) mice were depleted of thymidine phosphorylase (TP), a protein that maintains mitochondrial fitness. Treating Smo(-) hepatocytes with TP reduced senescence and lipotoxicity; inhibiting TP in Smo(+) hepatocytes had the opposite effects and exacerbated hepatocyte senescence, MASH, and fibrosis in CDA-HFD-fed mice.Therefore, we found that inhibiting Hedgehog signaling in hepatocytes promotes MASLD by suppressing hepatocyte production of proteins that prevent lipotoxicity and senescence.

overall_design: Adult male Smo tm2Amc /J (Smoflox/flox) mice on a C57Bl6/J background (JAX stock# 004526; The Jackson Laboratory, Bar Harbor, ME) were used. To examine the impact of Smo on MASLD susceptibility,  Smo flox/flox mice were fed with a CDA-HFD diet (A06071302, choline-deficient, L-amino acid defined diet with 60 kcal% fat; Research Diets, Inc, New Brunswick, NJ) for 6 weeks. 1 week before sacrifice, mice were injected by tail vein with 5 × 10e11 genome equivalents of AAV8-TBG-Luciferase (control) or AAV8-TBG-Cre Recombinase (Smo KO) to selectively delete Smo in hepatocytes. RNA was isolated from liver tissue and sent for RNA-seq analyses.

first: Ji

last: Jun

first: Kuo

last: Du

first: Rajesh

last: Dutta

first: Anna

last: Diehl


title: Gene expression profile of sorted microglia and CD206 border-associated macrophages obtained from mice

city: Singapore

first: James

middle: Alastair

last: Miller

address: 11 Mandalay Road

department: Lee Kong Chian School of Medicine

country: Singapore

institute: Nanyang Technological University

summary: Brain macrophages have long been considered a homogenous population as determined by flow cytometry. We use scRNAseq to investigate the significant pheotypic heterogeneity of brain macrophages, especially under neurodegenerative disorders, based on their transcriptional profile.

overall_design: Microglia and CD206+ border-associated macrophages were isolated from 6-month-old  healthy and APP(NL-G-F) mice, with FIT2-WT or FIT2-Mut, respectively, to study their transcriptome alteration during Alzheimer's disease progression.

first: Christiane

last: Ruedl

first: Xiaoting

last: Wu


title: MEOX2 Regulates Adipogenic Differentiation of Adipose-Derived Stromal Vascular Fractions through PI3K/AKT Signaling Pathway

city: Taigu

first: 弼时

last: 赵

state: --- Select One ---

address: Mingxian South Road

institute: Shanxi Agricultural University

summary: The fat tail of sheep is an important organ that has evolved to adapt to extreme environmental conditions. Mesenchyme homeobox 2 (MEOX2) can inhibit adipogenic differentiation of stromal vascular fractions (SVFs) isolated from ovine tail adipose tissue. However, the underlying mechanism through which MEOX2 regulates ovine adipogenesis remains unclear. Therefore, this study aims to employ RNA sequencing (RNA-seq) to explore the downstream genes regulated by MEOX2 during the adipogenic differentiation of ovine SVFs. Based on RNA sequencing, several differentially expressed genes (DEGs) were identified in response to MEOX2 overexpression. The PI3K/AKT signaling pathway was significantly enriched in DEGs, indicating its importance in mediating fat accumulation regulated by MEOX2. Additionally, the PI3K/AKT signaling pathway activation was found to be crucial for ovine SVF adipogenic differentiation. Mechanistically, MEOX2 inhibited the PI3K/AKT pathway. These findings highlight the significance of the PI3K/AKT signaling pathway during ovine SVF adipogenic differentiation. Furthermore, they shed light on the involvement of MEOX2 in this differentiation via the PI3K/AKT pathway. Our findings provide novel insights into the critical role of MEOX2 as an adipogenetic differentiation regulator, potentially enhancing our understanding of ovine fat development and its regulatory processes.

overall_design: After overexpression of MEOX2 in sheep SVFs, transcriptome sequencing was performed to screen the differential genes compared with the control group.


title: MicroRNA dysregulation in Ataxia Telangiectasia

city: Napoli

first: Aannamaria

last: Carissimo

address: via Pietro Castellino

department: IAC

country: Italy

institute: CNR Italy

type: Non-coding RNA profiling by high throughput sequencing

summary: Ataxia Telangiectasia (AT) is a rare disorder characterized by neurodegeneration, combined immunodeficiency, predisposition to malignancies and high clinical variability. MicroRNAs (miRNAs) profiling may provide information on the pathophysiology of complex rare human diseases as they are involved in numerous biological functions including proliferation, differentiation, and DNA repair. To investigate the differential expression of miRNAs in AT patient samples with the aim of identifying miRNA signatures and correlate these patterns with disease pathogenesis. Twenty AT patients (mean age 17.7 + 9.6 years) were enrolled in the study. Clinical and genetic data were collected. We performed a small RNA-seq analysis in PBMCs and fibroblasts to compare miRNA expression profiles in AT patients and controls, and to identify specific expression signatures for AT. We found 42 differentially expressed (DE)-miRNAs in blood samples and 26 in fibroblasts samples. Three DE-miRNAs, miR-342-3p, miR-30a-5p, and miR-195-5p were validated in further AT samples and their dysregulation was confirmed.We identified for the first time, an AT-associated miRNA signature in blood cells and fibroblast samples obtained from a cohort of AT patients. Several pathways were predicted commonly deregulated, mainly involved in cancer. miRNAs may provide information on AT pathophysiology and tumorigenesis.

overall_design: To investigate the differential expression of miRNAs in blood cellsfromAT patients and healthy control participants, with the aim to identify miRNA signatures for AT and correlate these patterns with disease pathophysiology.

first: Emilia

last: Cirillo

first: Antonietta

last: Tarallo

first: Annamaria

first: Claudio

last: Pignata


title: The Long Non-coding RNA NEAT1 is regulated by QKI and forms nuclear paraspeckles in glioma

city: Atlanta

first: Bing

last: Yao

address: 615 Michael Street

department: Department of Human Genetics

institute: Emory University

summary: The long noncoding RNA (lncRNA) Nuclear Enriched Abundant Transcript 1 (NEAT1) is a lncRNA involved in a variety of human cancers and diseases. The human NEAT1 gene produces two distinct isoforms, NEAT1 Long and NEAT1 Short, through alternative 3’ end formation. NEAT1 Long is an essential factor for nuclear paraspeckle formation, while the role of NEAT1 Short is poorly understood. Previous studies have often failed to distinctly detect the two NEAT1 isoforms and reported controversial NEAT1 dysregulation. Moreover, the molecular mechanisms which underlie the dysregulation of NEAT1 isoforms and their functional importance in tumorigenesis remain poorly characterized. We investigated whether usage of the proximal polyadenylation site (PAS) within the NEAT1 transcript is regulated to govern the biogenesis of NEAT1 isoforms in human glioma cells. We found differential dysregulation of NEAT1 isoforms in patient-derived human glioblastoma multiforme (GBM) stem cells. We further show deletion of the NEAT1 PAS reduced NEAT1 Short and increased NEAT1 Long. We identified the RNA binding protein QKI, a risk factor for glioma, facilitates the utilization of the NEAT1 PAS. We present evidence indicating the imbalance of NEAT1 isoforms correlates with transcriptomic pathway changes. We propose QKI-5 regulates NEAT1 isoform biogenesis through modulating the NEAT1 PAS in human glioma cells.

overall_design: CRISPR-Cas9 deletion of the NEAT1 PAS to identify how isoform imbalance affects glioma tumorigenesis.

first: Paul

last: Zakutansky

first: Yilin

last: Wang

first: Yangping

last: Li

first: Yue

last: Feng


title: Translation elongation inhibitors stabilize select transcripts

city: Baltimore

first: Nicolle

last: Rosa Mercado

address: 725 N. Wolfe Street  714 PCTB

department: Molecular Biology and Genetics

institute: Johns Hopkins University School of Medicine

summary: The ribosome is central to cellular stress responses because it serves as a sensor to activate signaling pathways that determine cell fate. While the activation of these signaling pathways by translation elongation inhibitors has been well characterized, the impact of these inhibitors on mRNA dynamics remains unclear. Here we use TimeLapse sequencing to investigate how translational stress impacts mRNA dynamics in human cells. Our results reveal that a distinct group of transcripts is stabilized in response to the translation elongation inhibitor emetine. These stabilized mRNAs are short-lived at steady state and many of them encode C2H2 zinc finger proteins. The codon compositions of these stabilized transcripts are suboptimal compared to short-lived mRNAs that are not stabilized. Finally, we show that stabilization of these transcripts is independent of the signaling pathways activated by ribosome collisions, as well as of canonical ribosome quality control factors. Our data describe a group of transcripts whose degradation is particularly sensitive to the inhibition of translation elongation.

overall_design: HEK-293T cells were treated with 500 µM 4-thiouridine (s4U) and with 1.8 µM emetine for 1 hour or left untreated. For 2 hour treatments, cells were incubated with 250µM s4U and treated with 1.8µM or 240µM emetine.TimeLapse sequencing was then performed and samples were sequenced on a Nova-seq platform.

last: Rosa-Mercado

first: Allen

last: Buskirk

first: Rachel

last: Green


title: Analysis of microRNA levels in fibroblast of Ataxia Telangiectasia

city: Orbassano

first: Giulio

last: Ferrero

state: TO

address: Regione Gonzole, 10

department: Dept. Clinical and Biological Sciences

institute: University of Turin

summary: Ataxia Telangiectasia (AT) is a rare disorder characterized by neurodegeneration, combined immunodeficiency, a predisposition to malignancies and high clinical variability. Profiling of microRNAs (miRNAs) may offer insights into the underlying mechanisms of complex rare human diseases, as miRNA play a role in various biological functions including proliferation, differentiation, and DNA repair. To investigate the differential expression of miRNAs in samples from AT patients with the aim of identifying miRNA patterns and to investigate how these patterns are related to the disease. We performed short a small RNA-seq analysis on fibroblasts to compare the miRNA expression profile between AT patients and controls. We identified, an AT-related miRNA signature in blood cells and fibroblast samples collected from a group of AT patients. We also predicted several dysregulated pathways, primarily related to cancer, immune system control or inflammatory processes. The findings suggest that miRNAs may provide insights into the pathophysiology and tumorigenesis of AT and have the potential to serve as useful biomarkers in cancer research.

overall_design: Fibroblasts were obtained from three additional AT participants (ATF1-3; 3 males) and three healthy controls (1 male).

first: Ferrero

last: Giulio


title: Effect of overexpssion Kallistatin(SERPINA4) in HGC-27 cell line

first: Caiqi

last: Ma

address: No.1 Xinzao Road, Panyu District

institute: Guangzhou Medical Univercity

summary: Kallistatin has been demonstrated to possess inhibitory effects across several malignancies, including hepatocellular carcinoma, gastric cancer and breast cancer. Subsequent evidence has increasingly suggested that KS has pleiotropic roles in modulating a broad spectrum of diseases, including in diabetic nephropathy, idiopathic pulmonary fibrosis and autoimmune uveitis. However, the precise function and molecular mechanisms underlying tumor-induced immune escape attributed to KS remain unclear, necessitating further investigation to determine its role in this context.For this propose, we establish SERPINA4 stably expressed cell line(and control) in HGC-27 cells, and RNA-seq was performed to reveal the trancriptome changes between there two cell lines.

overall_design:
To investigate the function of SERPINA4 gene in HGC-27 cell line, we established a HGC cell line which stably overexpressed SERPINA4 or control vector using lentivirus.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 6 samples

first: Ma

last: Caiqi

first: Zhang

last: Zhi-Yu


title: Role of LARP7 in meiotic sex chromosome silencing

city: Sendai

first: Yukiko

last: Tando

state: Miyagi

address: Seiryo-machi 4-1, Sendai, Miyagi 980-8575

institute: Institute of Development, Aging and Cancer, Tohoku University

summary: Meiotic sex chromosome inactivation (MSCI) is an essential event in meiotic progression in mammalian spermatogenesis. We found that La Ribonucleoprotein 7 (LARP7) is involved in MSCI. LARP7 plays a role in fetal germ cells to promote their proliferation, but is once abolished in postnatal gonocytes and re-expresses in spermatocytes at the onset of meiosis. In spermatocytes, LARP7 localizes to the XY body, a compartmentalized chromatin domain on sex chromosomes. This study aimed to elucidate a possible function of LARP7 in the XY body by using germline-specific Larp7-deficient mice.

overall_design: To investigate the function of LRP7 in the spermatogenesis, we generated germline-specific Larp7 knocknout mice and evaluated gene expression in the spermatocyte.

first: Atsuto

last: Nonomura

first: Yumi

last: Ito-Matsuoka

first: Asuka

last: Takehara

first: Daiji

last: Okamura

first: Yasuhisa

last: Matsui


title: Regulation of heterochromatin formation and tumor suppression in leukemia by IKAROS, HDAC1 and EZH2 [RNA-seq]

city: Hershey

first: Bing

last: He

state: PA

address: 500 University Dr

institute: Penn State University

summary: The IKZF1 gene encodes IKAROS – a DNA binding protein that acts as a tumor suppressor in  T-cell acute lymphoblastic leukemia (T-ALL). IKAROS can act as a transcriptional repressor via chromatin remodeling, however the mechanisms through which Ikaros exerts its tumor suppressor function via heterochromatin in T-ALL are largely unknown. We studied human and mouse T-ALL using loss-of-function and Ikzf1 re-expression approach, along with Ikzf1-wildtype primary human and mouse T-ALL and thymocytes to establish the role of  Ikaros and Ikaros-associated protein histone deacetylase 1 (HDAC1)  in global regulation of facultative heterochromatin and transcriptional repression in T-ALL.   Results identified novel Ikaros and HDAC1 functions in T-ALL: Ikaros and HDAC1 are essential for EZH2 histone methyltransferase activity, and formation of facultative heterochromatin; Recruitment of HDAC1 by Ikaros is critical for establishment of H3K27me3 and repression of active enhancers; and Ikaros-HDAC1 complexes promote formation and expansion of H3K27me3 large organized chromatin lysine domains (LOCKs) and broad genic repression domains (BGRDs) in T-ALL.  Our results establish that Ikaros’ tumor suppressor function in T-ALL occurs via activation of EZH2 and HDAC1 function, global regulation of the facultative heterochromatin landscape and silencing of active enhancers that regulate oncogene expression.

overall_design: DN3 cells were transduced with retrovirus that contains HA-tagged wild-type murine Ikaros for 1 day, 2 days and 3 days. RNA-seq was performed for cells from these four time points.

first: Sinisa

last: Dovat

first: Yali

last: Ding


title: Paternal high-fat diet affects weight and DNA methylation of their offspring

city: Rishon LeZiyyon

first: Noam

last: Meiri

address: 68 HaMakkabbim Road

institute: Aro, The Volcani Center

summary: paternal transmission of CpG methylation

overall_design: First-generation male Wistar rats were fed either a high-fat diet (HF) or chow and were mated with females fed chow. The resulting offspring were raised on a chow diet until day 35, after which they underwent a dietary challenge. Methylation at the  hypothalamic Arc nucluse was analysed using RRBS


title: Single Cell Transcriptomics Reveals a Tumor Promoting Mammary Cell Niche in Brca1 Heterozygous Breast Cancer Mouse Model

city: Boston

first: Joshua

last: Rivera

address: 110 William T Morrisey Blvd

institute: University of Massachusetts, Boston

summary: Women carrying BRCA1 (B1) mutations face an elevated risk of developing breast cancer, yet effective preventive strategies remain limited. To design innovative strategies, it is critical to understand the early events driving tumorigenesis. Here we present a unique mouse model which is conditionally heterozygous for B1 and deleted for Trp53, specifically in the mammary epithelial cells, and forms triple-negative mammary tumors under replication stress. Our single-cell RNA sequencing analysis, spanning various stages of mammary tumorigenesis in this model, reveals early tumor-promoting transcriptomic alterations. We identify a distinct, proliferative bi-potent cell population expressing both luminal progenitor and basal epithelial markers, uniquely enriched in Brca1 heterozygous mammary tissue upon replication stress. Notably, the transcriptomic changes in this population correlate with poor outcomes in human breast cancer. Transcriptomic analysis, combined with transcription factor analysis, along the trajectory from normal to precancerous and tumor stages, implicates the AP-1 complex, specifically the FRA-1 transcription factor, as an early driver in BRCA1 mutant breast cancer. Furthermore, pseudo-time analysis along this trajectory identifies alveolar luminal progenitor cells as the likely cell-of-origin. Luminal cells also show reduced efficiency of DNA damage repair when compared to basal cells. In conclusion, we have established the first Brca1 heterozygous mouse model for studying the effects of DNA replication stress on breast cancer and have identified early precancerous transcriptomic changes stemming from BRCA1 haploinsufficiency and replication stress. This study provides critical insights into the molecular mechanisms that drive breast cancer in BRCA1 mutation carriers.

overall_design: Mouse mammary glands from replication stress driven Brca1 heterozygous model. Samples for submission include 12x vehicle or 600mg/mL or tumor sample.

first: Rivera

last: Joshua

first: Zarringhalam

last: Kourosh

first: Pathania

last: Shailja


title: Neural zinc finger protein Myt1 drives oligodendrocyte differentiation via repressing HDAC1-mediated histone deacetylation [ATAC-seq]

first: 敏溪

last: 方

address: 杭师大仓前

institute: 浙江大学

summary: Members of the Myt (myelin transcription factor) family have been implicated in neuronal development. However, their in vivo roles in OL lineage development have not been systematically investigated. Here, we identified Myt1 transcription factor as a crucial regulator of oligodendrocyte differentiation in the developing central nervous system. Conventional knockout of Myt1 causes a remarkable delay in the initiation of OL differentiation, without affecting the generation and proliferation of OPCs. Conversely, hyperactivation of Myt1 induces precocious OL differentiation both in vitro and in vivo. Using a combination of RNA-seq and ChIP-seq analyses, we identified Nkx2.2 as a key target of Myt1 to switch on the OL differentiation program. Mechanistically, specific binding of Myt1 in the Nkx2.2 gene loci inhibits the nucleosomal histone deacetylation via hindering the HDAC1 repressor complex integrity and reducing the deacetylation activity of HDAC1. Additionally, we demonstrated that Myt1 functions downstream of Notch signaling pathway in controlling the timing of OL differentiation. Collectively, our data demonstrate that Myt1 is a major regulator of OL differentiation and provide insight into the epigenetic regulatory mechanisms under OL development. Myt1 is, therefore, a promising therapeutic target for enhancing the OL differentiation and myelination/remyelination during development or after demyelination insults.

overall_design: In light of our findings that loss of Myt1 expression delayed OL differentiation, we sought to identify Myt1-regulated downstream target genes by RNA-sequencing (RNA-seq) in mouse P0 Myt1-/- and wild type spinal cords

first: Xiaofeng

last: Xu

first: Minxi

last: Fang

first: Lixia

last: Chen

first: Hao

last: Huang

first: Junlin

last: Yang

first: Mengsheng

last: Qiu


title: Neural zinc finger protein Myt1 drives oligodendrocyte differentiation via repressing HDAC1-mediated histone deacetylation [RNA-seq]


title: Neural zinc finger protein Myt1 drives oligodendrocyte differentiation via repressing HDAC1-mediated histone deacetylation [H3K9 ChIP-seq]


title: Neural zinc finger protein Myt1 drives oligodendrocyte differentiation via repressing HDAC1-mediated histone deacetylation [MYT ChIP-seq]


title: Magnesum Isoglycyrrhizinate augments lipid catabolism via immune-neuro modulation of catecholamine pathways

city: Shanghai

first: Wenjiao

last: Jiang

address: No. 1, Zhongke Road

institute: Chinese Academy of Sciences

summary: Glycyrrhetinic acid (GA) and its derivative, magnesium isoglycyrrhizinate, exhibit promising anti-obesity effects through mechanisms that are not fully understood. Here, we showed that GA mitigated white adipose tissue remodeling and diet-induced obesity by enhancing lipid catabolism. GA indirectly promoted adipocyte lipolysis and thermogenesis by modulating catecholamine pathways, facilitated by increased intra-fat sympathetic innervation and reduced protein expression of monoamine oxidase A (MAOA), which degrades norepinephrine. In suit visualization of MAOA identified adipose tissue macrophages (ATMs) as key mediators of intra-fat catecholamine degradation. RNA sequencing of sorted ATMs revealed that GA reduced pro-inflammatory shifts and altered macrophage polarity, preventing activation of the Toll-like receptor 4 (TLR4) signaling pathway, as supported by molecular docking analysis and binding assays. Moreover, the anti-obesity effects of GA were absent in TLR4-deletive mice, which exhibited decreased MAOA protein levels and sensitivity to FUNDC1-mediated mitophagy in ATMs. These findings suggest that GA targets macrophage-sympathetic neuron crosstalk, offering a promising therapeutic approach for obesity by preserving NE availability and promoting lipid catabolism.

overall_design: To gain further insight in MGIG’s anti-obesity, we performed bulk RNA sequencing on F4/80+CD11b+ ATMs sorted from high-fat diet mice with and without MGIG treatment.

first: Sasa

last: Zhang

last: Xie

first: Kun

last: Hao


title: Particle uptake by macrophages triggers bifurcated transcriptional pathways that differentially regulate inflammation and lysosomal gene expression.

city: La Jolla

first: Christopher

last: Glass

state: CA

address: 9500 Gilman Dr.

department: CMM

institute: University of California, San Diego

summary: Exposure to physical particles is a driver of several inflammatory diseases. Here, we systematically investigated responses of macrophages to pathogenic forms of monosodium urate crystals, calcium pyrophosphate crystals, aluminium salts, and silica nanoparticles. While each particle induced a distinct pattern of gene expression, we also identified a common signature that was preferentially linked to inflammation and acute activation of genes required for lysosomal acidification. Using monosodium urate crystals as a model system, we obtained evidence that the program of lysosomal gene expression was regulated by a network of transcription factors that included TFEB and TFE3 and the epigenetic regulators DNMT3A and DOT1L. This lysosomal acidification network operated in parallel with, but largely independently of, a JNK and AP-1 dependent transcription factor network that drove crystal induced chemokine and cytokine gene expression. Mechanistically, the uptake of particles led to early activation of AMPK signalling that was required for activation of TFEB and TFE3 in a process independent of reduced mTOR signalling. These results thereby revealed a mechanism by which the functions of TFEB and TFE3 can be preferentially targeted to specific aspects of lysosomal gene expression, which may provide insights into therapeutic approaches to treat individuals with particle-associated diseases.

overall_design: We performed histone acetylation analysis by ChIP-Seq of the enhancer landscape of macrophages exposed to particles. We used RNA-Seq to undestand the underlying transcriptional response. We used ChIP-Seq for certain transcription factors to understand the underlying molecular mechanisms. Flushed bone marrow from both femurs and tibias of C57BL/6, Tfeb-Tg, Bhlhe40-/- and Bhlhe41-/- mice were cultured in DMEM medium supplemented with 10% de-complemented FBS, Penicillin-Streptomycin 100 U/mL and 16 ng/mL of recombinant murine M-CSF (Peprotech, #315-02). Fresh M-CSF was added 72h after seeding. Ampkα1-/-  BMDM were generated as explained elsewhere (Wang et al. 2016). Briefly, bone marrows from 7-week-old to 8-week-old Ampkα1-/- and congenic WT mice were cultured in complete Roswell Park Memorial Institute (RPMI) media containing 10% fetal bovine serum (FBS), penicillin (100 U/mL) and streptomycin (100 μg/mL) in the presence of 5 ng/mL of MCSF (R&D Systems). On day six after seeding, BMDM were scrapped out and plated one day prior treatment with Metformin (MP Biomedicals, #151691), 125 mM A769662 (Sigma, # SML2578), or since day 0 with 1 μM SGC0946 (Selleckchem, #S7079). BMDM were then treated with control PBS or 250 μg/mL of MSUc, calcium pyrophosphate dihydrate crystals, silica nanoparticles (Invivogen, #tlrl-sio-2), or aluminum hydroxide salt (Invivogen, #tlrl-aloh) at various timepoints as explained in the text and Figure legends.

first: Isidoro

last: Cobo

first: Jessica

last: Murillo

first: Mohnish

last: Alishala

first: Stephen

last: Calderon

first: Roxana

last: Coras

first: Nathan

last: Spann

first: Thomas

last: Prohaska

first: Paulo

middle: V

last: Alabarse

first: Se-Jin

last: Yeong

first: Christian

middle: K

last: Nickl

last: Le

first: Anyan

last: Cheng

first: Benjamin

last: Li

first: Andrea

last: Vogel

last: Weichhart

first: José

last: Fuster

first: Tara

last: Bradstreet

first: Ashlee

last: Webber

first: Brian

middle: T

last: Edelson

first: Babak

last: Razani

middle: L

last: Ebert

first: Reshma

last: Taneja

first: Robert

last: Terkeltaub

first: Ru

last: Bryan

first: Monica

last: Guma


title: Neural zinc finger protein Myt1 drives oligodendrocyte differentiation via repressing HDAC1-mediated histone deacetylation

first: 敏溪

last: 方

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

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: Refer to individual Series