title: SUV39H1 Maintains Cancer Stem Cells in Glioblastoma [RNA-seq]

overall_design: To investigate the function SUV39H1 in the regulation cancer stem cells in glioblastoma , we established GSC3565 and GSC1914 cell lines in which each SUV39H1 has been knocked down by shRNA. We then performed gene expression profiling analysis using data obtained from RNA-seq of 2 different cells. Comparative gene expression profiling analysis of RNA-seq data for GSC3565 and GSC1914 cells and its KD derivatives.


title: Immune Modules to guide Diagnosis and Personalized Treatment of Inflammatory Skin Diseases

status: Public on Nov 08 2024

city: Lausanne

first: JEREMY

last: DI DOMIZIO

state: Vaud

address: Av Boveresses 155, 1066 Epalinges

country: Switzerland

institute: CHUV

summary: we profiled the inflammatory transcriptome of skin lesions from patients with inflammatory skin diseases

overall_design: Inflammation-oriented transcriptomics was performed on RNA extracted from skin biopsies using NanoString technologies

first: Jeremy

last: Di Domizio


title: DNA Methylation profiles of subjects in the Healthy Brain Initiative study.

city: Miami

first: Lily

last: Wang

address: 1120 NW 14th St

country: USA

institute: University of Miami

type: Methylation profiling by genome tiling array

summary: The Healthy Brain Initiative (HBI) is a longitudinal study focused on older adults in South Florida, with the goal of advancing dementia prevention and promoting brain health. We generated DNA methylation profiles for 88 HBI participants aged over 65. The Illumina MethylationEPIC v2.0 Beadchip was used to obtain DNA methylation profiles across approximately 935k CpGs from human blood samples.

overall_design: Bisulfite-converted DNA for 88 human blood samples were hybridized to the Illumina MethylationEPIC v2.0 Beadchip

first: David

last: Lukacsovich

first: Deirdre

middle: M

last: O'Shea

first: James

middle: E

last: Galvin


title: Rapgef3 modulates macrophage reprogramming and exacerbates synovitis and osteoarthritis under excessive mechanical loading

status: Public on Nov 04 2024

city: guangzhou

first: wen

middle: feng

last: shao

state: guangdong

address: tonghe

country: China

institute: Southern Medical University

type: Expression profiling by high throughput sequencing

summary: Evidences indicate that mechanical loading plays an important role in osteoarthritis (OA) progression, while the specific pathological changes of the synovium under excessive mechanical loading are unclear. Results showed excessive mechanical loading caused pro-inflammatory of synovial macrophages, which has been confirmed to exists in OA. High Rapgef3 expression level was found in RNA sequencing of RAW246.7 subjected to 0.5Hz-20%-cyclic tensile strain. We verified this in the synovium of OA patients and DMM-OA mice. Interestingly, the Rapgef3 content of chondrocytes was very low. Primary chondrocytes treated with Rapgef3 alone did not show metabolic phenotype, but an OA phenotype appeared when treated with Rapgef3-stimulated macrophage culture supernatant. Mechanically, excessive mechanical loading activated p65-NF-κB pathway through Rapgef3, which promoted  the inflammatory of macrophage, resulting in severe articular cartilage injury. Intra-articular Rapgef3 knockout reversed synovitis and cartilage degeneration, which might provide a therapeutic target for osteoarthritis.

overall_design: differentially expressed in RAW246.7 cells treated with normal and 20% elongation strain loading for 24 hours

first: Wen

last: Tang

first: Jianbin

last: Yin

first: Rengui

last: Lin

first: Haiyan

last: Zhang


title: Thrombospondin-1 modulation by Bifidobacterium spp. mitigates lung damage in an acute lung injury mouse model

city: Gwangju

first: YouMin

last: KIM

address: 123, Cheomdangwagi-ro, Buk-gu

department: DEPARTMENT OF BIOMEDICAL SCIENCE AND ENGINEERING

country: South Korea

institute: Gwangju Institute of Science and Technology

summary: Acute lung injury/acute respiratory distress syndrome (ALI/ARDS) is a life-threatening condition characterized by lung inflammation and damage. Mechanical ventilation can exacerbate this condition. The gut microbiome, known to impact health, might have implications for ALI/ARDS outcomes. This study aimed to investigate the effects of probiotics in a murine ALI model. Using a two-hit approach combining lipopolysaccharide-induced inflammation and mechanical ventilation-induced injury, a severe lung injury model was established in mice. Probiotics containing Bifidobacterium spp. were administered due to their known interactions with immune cells and immune pathway modulation. The effects of probiotic administration on lung inflammation severity were evalu ated through biochemical, and histological analyses of lung tissue, and single-cell RNA sequencing analysis. Probiotic administration increased Bifidobacterium spp. composition in the gut microbiota and mitigated lung damage and inflammation. Single-cell RNA sequencing revealed the stimulation of Anxa1high macrophages, possibly promoting anti-inflammatory responses.

overall_design: Probiotics containing diets were prepared as follows: Bifidus-diets were prepared by spraying 3 times of mixed fluid including 1g of Bifidus and 25mL of phosphate buffer saline (PBS, pH 7.2) with a dedicated sprayer, and kept in the refrigerator at 4℃ for 1 day. Then fresh diets were given to mice. The diets were changed every 2 days.

first: YuMin

last: Kim

first: MinSe

last: Ki

first: Chang-Myung

last: Oh

first: Sang Hoon

last: Lee


title: Comprehensive characterization of transcript isoform in mouse retina with ONT long read single-cell RNA sequencing

city: Houston

first: Rui

last: Chen

state: Texas

address: One Baylor Plaza

department: Department of Molecular and Human Genetics

institute: Baylor College of Medicine

summary: The retina, a complex neural tissue, encompasses a vast diversity of over 100 distinct cell types, each characterized by unique features such as morphology, function, location, and transcriptomic profiles. However, the extent of mRNA alternative splicing within individual cell types in the retina remains largely uncharted territory. To bridge this knowledge gap, we employed single-cell RNA sequencing, utilizing both short-read and long-read high-throughput technologies. Our comprehensive analysis profiled the transcriptomes of 29,191 mouse retina cells, resulting in a dataset comprising 1.54 billion Illumina short reads and 1.40 billion Oxford Nanopore long reads. Remarkably, this exploration unveiled a staggering 44,325 transcript isoforms, with 38% of them representing entirely novel discoveries and 17% exhibiting cell-class-specific expression patterns. Intriguingly, while many isoforms were expressed across various cell types, their distribution often displayed variability among them. This research substantially enriches the catalog of transcript isoforms, laying the groundwork for further investigations into the role of alternative splicing in retinal biology and its implications for related diseases. It represents a crucial step toward unraveling the intricacies of retinal function and offers promising insights into the molecular mechanisms underlying retinal disorders.

overall_design: 2 samples were dissociated retinal cells with no enrichment method and 2 samples were enriched for neuronal cells using CD73 and CD90.2 markers using FACS.

first: Meng

first: Yumei

last: Li


title: HIF-alpha signaling mediates the macrophage inflammatory response during Leishmania majorinfection

status: Public on Nov 01 2024

city: Little Rock

first: Stephanie

last: Byrum

state: AR

address: 4301 W Markham St, slot 510

department: Dept of Biochemistry and Molecular Biology

institute: University of Arkansas for Medical Sciences

summary: Cutaneous leishmaniasis (CL) is responsible for a significant burden of the global incidence of neglected tropical diseases, with 12 million people currently infected with Leishmania parasites. CL contains a spectrum of disease manifestations, ranging from self-healing skin lesions to permanent disfigurations. Currently there is no vaccine available, and many patients are refractory to treatment, emphasizing the need for new therapeutic targets. Previous work has demonstrated the necessity of macrophage HIF-alpha-mediated lymphangiogenesis to achieve efficient wound resolution during murine L. major infection. Here we investigate the role of macrophage HIF-alpha signaling separate from lymphangiogenesis, employing RNA-Seq transcriptome analysis on macrophages with intact or compromised HIF-alpha signaling, LysMCreARNTf/+ or LysMCreARNTf/f respectively, during L. major infection and under pro-inflammatory stimulus. We report that L. major infection alone is enough to induce HIF-alpha dependent transcriptomic changes while infection with L. major and pro-inflammatory stimuli administration instigates transcriptomic changes both dependent and independent of HIF-alpha signaling. Additionally, by coupling transcriptomic analysis with several pathway analyses, we found during L. major infection and in a pro-inflammatory environment, HIF-alpha suppresses pathways involved in protein translation such as the ribosome pathway and EIF2 signaling. Together this work supports infection with L. major induces a HIF-alpha transcriptomic program, but only in a pro-inflammatory environment does HIF-alpha suppress protein translation.

overall_design: Bulk RNA-Seq of bone marrow derived macrophages that are either from mice with intact myeloid HIF-alpha signaling (LysMCre ARNT f/+) or deleted myeloid HIF-alpha signaling (LysMCre ARNT f/f). Macrophages from both strains of mice were 1) cultured in media alone, 2) infection with Leishmania major metacyclic promastigote parasites, or 3) infected with L. major parasites and LPS plus IFNg for 8 hours

first: Lucy

last: Fry

first: Charity

middle: L

last: Washam

first: Hayden

last: Roys

first: Anne

last: Bowlin

first: Gopinath

last: Venugopal

first: Jordan

middle: T

last: Bird

middle: D

first: Tiffany

last: Weinkopff


title: Genome-wide mapping of human SMYD3 and H3K4me3 in the HN-6 (control) and 5-3 (SMYD3 KO) HPV-negative head and neck squamous cell carcinoma cell line.

city: ROCKVILLE

first: Vassiliki

last: Saloura

state: MARYLAND

address: 11705 STONEWOOD LN

department: TGMB

institute: NCI

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We used CUT&RUN to evaluate the genome-wide mapping of human SMYD3 and H3K4me3 in HN-6 and 5-3 (SMYD3 KO) cells.

overall_design: HN-6 and 5-3 cell lines were cultured in-vitro in three separate 10cm dishes per condition and were collected at ~80% confluence. 500,000 cells from each of the plates were obtained and processed per EpiCypher's CUT&RUN assay protocol.

first: Madhavi

last: Murali

first: Sohyoung


title: RNA-seq of HN-6 (control) and 5-3 (SMYD3 KO) cell lines.

summary: We used RNA-seq to evaluate the transcriptomic changes induced by permanent SMYD3 KO in the HPV-negative head and neck squamous cell carcinoma cell lines HN-6.

overall_design: HN-6 and 5-3 cell lines were cultured in-vitro in three separate 10cm dishes per condition and were collected at ~80% confluence. Pellets were frozen at -80oC and when ready, RNA extraction was conducted.


title: Transcriptomic study on the effect of Igf1r deficiency in control and bleomycin-challenged mouse lungs.

city: Logroño

first: Jose

middle: Garcia

last: pichel

state: La Rioja

address: Piqueras 98

department: Oncology

country: Spain

institute: FUNDACIÓN RIOJA SALUD - CIBIR

summary: Acute lung injury (ALI), ARDS and COVID-19 usually involve a “cytokine storm”. IGF1R (Insulin-like growth factor receptor 1) maintains lung homeostasis and is implicated in these pulmonary inflammatory diseases. In mice, widespread IGF1R  deficiency was reported to counteract respiratory inflammation and alveolar damage after bleomycin (BLM)-induced ALI. To explore the molecular mechanisms mediated by Igf1r signaling after BLM challenge, we performed RNA-sequencing in lungs of IGF1R-deficient mice after BLM or saline (SAL) instillation. Transcriptomic analysis identified differentially expressed genes between BLM-challenged and SAL-treated control lungs, detecting biological processes and signaling pathways involved in ALI pathobiology. Igf1r depletion in BLM-challenged mice reversed large part of the transcriptional changes triggered by BLM, counteracting the transcriptomic profile of the inflammatory "cytokine storm". Data mining also identified changes in the expression of gene clusters with key roles in DNA damage, metabolic reprogramming, mitochondrial homeostasis, and epigenetics. Exploration of these functional groups, together with validation studies, provide new insights into the molecular mechanisms underlying the attenuating effect of Igf1r deficiency on ALI. These findings allow a more comprehensive view of IGF1R signaling at the transcriptional level, reinforcing its important role in promoting ALI and postulating it as a global epigenetic regulator in ARDS.

overall_design: In order to evaluate the effect of generalized Igf1r deficiency in the context of BLM-mediated ALI on the transcriptome, lung RNA samples from the following four groups of mice were sequenced, (3 samples per group, 12 samples in total): 1) SAL-treated Igf1rfl/fl 2) SAL-treated UBC-CreERT2; Igf1rΔ/Δ (Igf1r-deficient; CreERT2) 3) BLM-challenged Igf1rfl/fl (Igf1rfl/fl-BLM)4) BLM-challenged CreERT2 (CreERT2-BLM)  Three differential gene expression comparisons were established between experimental groups: i) CreERT2 vs Igf1rfl/fl ("mutation") ii) Igf1rfl/fl-BLM vs Igf1rfl/fl ("injury") iii) CreERT2-BLM vs Igf1rfl/fl-BLM lungs ("attenuation")  Analysis of differenial gene expression, gene set enrichment analysis (GSEA) and intensive data mining were performed to thoroughly explore transcriptomic data. Additional experimental techniques were used to further investigate transcriptomic results.

first: Alfredo

last: Urtubia

first: María

last: De Toro

first: Sergio

last: Piñeiro-Hermida

first: Elvira

last: Alfaro-Arnedo

first: Marta

last: Canalejo

first: José

middle: G

last: Pichel

first: Icíar

middle: P

last: López


title: Identification of a miRNA panel as a promising biomarker for diagnosis of glioblastoma patients using next-generation RNA sequencing

status: Public on Oct 31 2024

city: Debrecen

first: Zsuzsanna

last: Birkó

address: Egyetem tér 1.

department: Humangenetics

country: Hungary

institute: University of Debrecen

type: Non-coding RNA profiling by high throughput sequencing

summary: Applying Next Generation Sequencing technique we compared the miRNA expression pattern of tumor tissue sample of 6 GPs and peritumoral region of 6 lower grade (I-II) Glioma patients, serving as control group. To determine the difference on miRNA expresion level between GBM and control cases, we performed cluster analysis on the NGS dataset of 6 replicates for each of the two goups of samples with iDEP 96 software. In order to characterize the extent of up- or downregulation, log2FC values were calculated using the iDEP.96 web tool applying the DESeq2 algorithm. On the base of that 117 known miRNAs were identified to be differentially expressed using a threshold of false discovery rate (FDR) <0.05 and fold-change> 2 during the analysis. Among them, 35 miRNAs were upregulated (log2FC > 2) and 82 miRNAs were downregulated (log2FC < -2) with biological revelance in tissue samples comparing with the control samples. To validate our results obtained by NGS, five upregulated miRNAs: hsa-miR-196a-5p, hsa-miR-21-3p, hsa-miR-92b-5p, hsa-miR-10b-3p, hsa-miR-503-5p and three downregulated miRNAs: hsa-mir-383-5p, hsa-mir-490-3p, hsa-mir-1224-3p were chosen for RT-qPCR analysis. As the result of that hsa-miR-196a-5p, hsa-miR-21-3p, and hsa-miR-10b-3p was significantly upregulated while hsa-mir-383-5p  and hsa-mir-490-3p was significantly downregulated, compared with those in the control samples. The other three miRNAs: hsa-miR-1224-3p, hsa-miR-92b-5p, hsa-miR-503-5p  did not show significant difference between the control group and GPs.

overall_design: Tissue samples were gathered from peritumoral region of six individuals diagnosed with lower grade (Grade I-II.) glioma, serving as control group, and from six patients with GBM. All samples in both group were confirmed histopathologically. These intraoperative quick-frozen tissue samples were stored at -80⁰C until further processing. Total RNA was isolated from  the tissue samples of GBM and control group as well. Global transcriptomic profile was studied by RNA-sequencing applying the Illumina NextSeq500 platform including microRNA sequencing. In the case of all samples 3 replicates were included. In order to identify up-, or down-regulated microRNAs the GBM samples were compared to the  control samples.

first: Dóra

last: Géczi

first: Álmos

last: Klekner

first: István

last: Balogh

first: András

last: Penyige

first: Melinda

last: Szilágyi

first: József

last: Virga

first: Andrea

last: Bakó

first: Bálint

last: Nagy

first: Bernadett

last: Torner


title: Group 2 innate lymphoid cells promote inhibitory synapse development and social behavior [snRNA-Seq]

city: San Francisco

first: Ari

last: Molofsky

state: CA

address: 513 Parnassus Ave

department: Laboratory Medicine

institute: UCSF

summary: The innate immune system shapes brain development and is implicated in neurodevelopmental diseases. It is critical to define the relevant immune cells and signals and their impact on brain circuits. Here we show that group 2 innate lymphoid cells (ILC2s) and their cytokine Interleukin-13 (IL-13) signal directly to inhibitory interneurons to increase inhibitory synapse density in the developing brain. ILC2s expanded and produced IL-13 in the developing brain meninges. Loss of ILC2s or IL-13 signaling to interneurons decreased inhibitory, but not excitatory, cortical synapses. Conversely, ILC2s and IL-13 were sufficient to increase inhibitory 30 synapses. Loss of this signaling pathway led to selective impairments in social interaction. These data define a type 2 neuroimmune circuit in early life that shapes inhibitory synapse development and behavior.

overall_design: Single nucleus gene expression profiling of cortical interneurons comparing the transcriptional effect of IL-13 versus saline exposure at postnatal day 15.

first: Jerika

last: Barron

first: Anna


title: Targeting CD206+ macrophages disrupts the establishment of a key anti-tumor immune axis

first: Bushra

last: Samad

address: 505 Parnassus Ave

institute: USCF Immunoprofiler

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: RNA-seq analysis of DLBCL cell lines in response to chemotherapy

status: Public on Oct 29 2024

city: Berlin

first: Paulina

last: Richter-Pechanska

address: Augustenburgerplatz 1

country: Germany

institute: Charite

summary:
Despite the long-standing role of standard chemotherapy in human diffuse large B cell lymphoma (DLBCL), the basis for individual tumor responses and how they associate with different transcriptional programs are incompletely understood.
Hence we aimed to classify DLBCL cell lines by their ability to undergo therapy-induced senescence (TIS) in response to adriamycin (aka doxorubicin) and acquire gene expression profiles before and after chemotherapy by RNA-seq.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for DLBCL cell lines categroized by their ability to senescence in response to adriamycin treatment.

first: Dimitri

last: Belenki

first: Clemens

middle: A

last: Schmitt


title: Gene expression profile of FACS sorted cranial neural crest cells from E12.5-E13.5 mouse embryonic head

city: Vestec

first: Lukas

last: Valihrach

address: Prumyslova 595

country: Czech Republic

institute: Institute of Biotechnology, Czech Academy of Science

summary: Craniofacial morphogenesis depends on complex cell fate decisions during the differentiation of post-migratory cranial neural crest cells. Molecular mechanisms of cell differentiation of mesenchymal cells to developing bones, cartilage, teeth, tongue, and other craniofacial tissues are still poorly understood. We performed single-cell transcriptomic analysis of craniofacial mesenchymal cells derived from cranial NCCs in mouse embryo. Using FACS sorting of Wnt1-Cre2 progeny, we carefully map the cell heterogeneity in the craniofacial region during the initial stages of bone and cartilage formation.

overall_design: Using FACS sorting of Wnt1-Cre2 progeny, we isolated cranial neural crest cells from control Wnt1-Cre2; Meis2fl/+; R26R-EYFPfl/+  and Meis2 cKO Wnt1-Cre2; Meis2fl/fl; R26R-EYFPfl/+  mouse embryo heads at E12.5 and E13.5. On FACS sorted cells we performed scRNA-seq using 10x Genomics Chromium platform.

first: Michaela

last: Krausova

first: Pavel

last: Abaffy

first: Ondrej

last: Machon


title: Group 2 innate lymphoid cells promote inhibitory synapse development and social behavior

summary: The innate immune system plays essential roles in brain development, including the remodeling of neuronal synapses. Innate lymphocytes are the most recently discovered member of the innate immune arsenal, whose developmental expansion and activation make them potential mediators of brain-immune communication during synapse formation. Here we show that group 2 innate lymphoid cells (ILC2s) and their cytokine Interleukin-13 (IL-13) signal directly to inhibitory interneurons to increase inhibitory synapse density in the developing brain. ILC2s expanded and produced IL-13 in the developing brain meninges. Loss of ILC2s or IL-13 signaling to interneurons decreased inhibitory, but not excitatory, cortical synapses. Conversely, ILC2s and IL-13 were sufficient to increase inhibitory synapses. Loss of this signaling pathway led to selective impairments in social interaction. These data define a type 2 neuroimmune circuit in early life that shapes inhibitory synapse development and behavior.

overall_design: Comparison between IL-33-/- mice and IL-33+/- mice to address the role of IL-33 signaling in dural meninges at postnatal day 14.

middle: J

first: Madelene

middle: W

last: Dahlgren

middle: B

middle: V


title: Combination of menin and kinase inhibitors as a novel treatment for NUP98-rearranged leukemia

status: Public on Oct 30 2024

city: Indianapolis

first: James

last: Ropa

state: IN

address: 950 W Walnut St

institute: Indiana University

summary: Chromosomal translocations involving the nucleoporin 98 (NUP98) gene at chromosome 11p15 are found in pediatric and adult Acute Myeloid Leukemia (AML) patients, representing one of the most common genetic alterations in pediatric AMLs found in ~10% of these patients. Previous studies demonstrated that NUP98 fusion proteins interact with MLL1 (Mixed Lineage Leukemia 1 also known as KMT2A) protein complex, and colocalize with MLL1 on Hoxa/b cluster genes, supporting MLL1 as a molecular dependency in the NUP98-r leukemia. Importantly, recent work has validated an important role of the scaffold protein menin, which directly interacts with the N-terminus of MLL1, in the NUP98-r leukemia. Here, we explored the effect of combining our menin inhibitor MI-3454 with CDK6 or FLT3 kinase inhibitors in the NUP98-r leukemia models as a possible way to enhance the anti-leukemic effect.

overall_design: This project explored the effects of combining MENIN inhibition with kinase inhibitors on the growth and gene expression of acute myeloid leukemia cells. Primary AML patient samples with NUP98 translocations were obtained from 1) adult bone marrow harboring a NUP98-HOXA9 mutation or 2) pediatric bone marrow harboring NUP98-NSD1 mutation. The adult AML primary sample was treated with MI3454 (MENIN inhibitor), Gilteritinib (FLT3 kinase inhibitor), Palbociclib (CDK4/6 kinase inhibitor), or combinations of MI3454 with each of the kinase inhibitors (in triplicate for each treatment group). The pediatric primary AML sample was amplified in vivo by transplantation to mice, then cells were harvested and treated with MI3454, Palbociclib, or a combination of the two (in triplicate for each treatment group). Differential gene expression for each single agent treatment or combination compared to vehicle controls were then calculated and compared across treatments and patient samples.

first: Jolanta

last: Grembecka

first: Tomasz

last: Cierpicki

first: Hongzhi

last: Miao


title: Gene expression profile at single cell level of conditional senescence in mouse Emu-myc B-cell lymphoma model

status: Public on Oct 28 2024

first: Zhiting

last: Shao

state: Berlin

address: Augustenburger Platz 1, Forum 4, 13353 Berlin

department: Hematology, Oncology, and Tumor Immunology Charité - Universitätsmedizin Berlin (CVK)

institute: Charité – Universitätsmedizin Berlin

summary: Based on the senescence switch Suv39h1, the same lymphoma population enters senescence (TIS) or non-senescence (non-TIS) status.

overall_design: Lymohoma cells are exposed to ADR ± 4-OHT to enter non-TIS or TIS status for scRNAseq analysis.

first: Dorothy

middle: N

last: Fan

first: Maja

last: Milanovic


title: Differential roles of copper-binding transcription factors and the subfamilies of the SWI/SNF complex in the transcriptional regulation of the skeletal muscle lineage [CUT&RUN]

status: Public on Oct 26 2024

city: Pittsburgh

first: David

last: Klein

state: PA

address: 4249 Fifth Ave

department: Biological Sciences

institute: University of Pittsburgh

summary: Copper (Cu)-binding transcription factors are emerging as important regulators of gene expression during skeletal muscle differentiation. Our group has shown that the classic Metal Transcription Factor 1, MTF1, works cooperatively with the myogenic factor MyoD to promote skeletal muscle differentiation and ensure viability of murine primary myoblasts. Preliminary evidence showed that MTF1 interacts with members of the mammalian SWItch/Sucrose Non-Fermentable (mSWI/SNF) family of ATP-dependent chromatin remodeling enzymes to promote differential gene expression in proliferating and differentiating myoblasts. mSWI/SNF complexes are assembled into three major subfamilies that are distinguished by the presence of mutually exclusive subunits: cBAF (canonical BRG1 or BRM-Associated Factor), PBAF (Polybromo containing BAF), or ncBAF (non-canonical BAF). The mechanisms by which each subfamily contributes to the establishment or function of specific cell lineages are poorly understood. We determined the contributions of the BAF, ncBAF, and PBAF complexes to myoblast proliferation, differentiation, and metal homeostasis via knock-down (KD) of a distinguishing subunit of each complex (Baf250A, Brd9, and Baf180, respectively). Biochemical, molecular and RNA-seq analyses showed that Baf250A KD reduced myoblast proliferation rate and differentiation. Brd9 KD resulted in a minor proliferation defect and a delay in myogenesis. KD of Baf180 and other PBAF-specific subunits did not impact proliferation or differentiation but affected the maintenance of metal homeostasis in myoblasts. The data support a model for differential roles and interactions between MTF1 and a novel category of Cu-binding transcription factors and the SWI/SNF enzymes in the development and homeostasis of the skeletal muscle lineage.

overall_design: Three replicates of CUT&RUN targeting MTF1 or untargeted IgG control were performed on proliferating myoblast cells treated with either copper or no treatment.

first: Monserrat

last: Olea-Flores

middle: C

first: Nick

last: Carulli

first: Yaje

last: Nshanji

first: Cat

last: McCann

first: Sabriya

last: Syed

first: Anthony

last: Imbalzano

first: Sarah

last: Hainer

first: Teresita

last: Padilla-Benavides


title: Differential roles of copper-binding transcription factors and the subfamilies of the SWI/SNF complex in the transcriptional regulation of the skeletal muscle lineage


title: Rapid discovery of cyclic peptide protein aggregation inhibitors through continuous selection HTS data

status: Public on Oct 25 2024

city: Madiso

first: Linwei

last: Yang

state: WI

address: 1101 University Ave

department: Chemistry

institute: UW-Madison

summary: We report a new platform for the rapid phenotypic selection of protein aggregation inhibitors from genetically encoded cyclic peptide libraries in E. coli based on phage-assisted continuous evolution (PACE). Here, we developed a new PACE-compatible selection for protein aggregation inhibition and employed it to identify cyclic peptides that suppress amyloid-β42 (Aβ42) and human islet amyloid polypeptide (hIAPP) aggregation. Additionally, we integrated a negative selection that removes false positives and off-target hits, significantly improving cyclic peptide selectivity. We show that selected inhibitors are active when chemically re-synthesized in in vitro assays. Our platform provides a powerful new approach for the rapid discovery of cyclic peptide inhibitors of protein aggregation and may serve as the basis for the future evolution of cyclic peptides with a broad spectrum of inhibitory activities. Data deposited here are HTS data critical to the conclusions of this study.

overall_design: Samples analyzed here are post-selection M13 phage pools. Gene of interest encoding cyclic peptide sequence in those samples were amplified via standard PCRs using primers included in this study. The resulted PCR products were pooled together based on library ID. Pooled libraries were subjected to NGS using Illumina NovaSeq platform. Raw sequencing data were processed using a customized script included in this study to calculate the read frequency of cyclic peptide sequence to discover enriched peptide sequence after selection.

first: Tina

last: Wang


title: SCN1A pathogenic variants do not have a distinctive blood-derived DNA methylation signature

city: Memphis

first: Heather

last: Mefford

state: FL

address: 262 Danny Thomas Pl

department: Center for Pediatric Neurological Disease Research

institute: St. Jude Children's Research Hospital

summary: SCN1A, encoding the sodium channel protein type 1 alpha subunit, is the most implicated gene in epilepsy. Pathogenic loss-of-function variants that result in SCN1A haploinsufficiency cause the most common DEE, known as Dravet syndrome (DS). Pathogenic gain-of-function variants have been found to cause a more severe, early-onset epilepsy syndrome that is distinct from DS. Here, we investigated DNA methylation patterns in these individuals with SCN1A variants.

overall_design: We generated genome-wide DNA methylation data (Illumina EPIC 850K v1 and 935K v2) for individuals with Dravet syndrome due to pathogenic loss-of-function (LOF) variants in SCN1A and individuals with early infantile SCN1A developmental and epileptic encephalopathies.

first: Christy

last: LaFlamme


title: Genome-wide DNA methylation pattern changes in ESC, and EPSC after treated with T09

status: Public on Oct 23 2024

city: Singapore

first: Yingying

last: Zeng

state: --- Select a state ---

address: 61 Biopolis Drive

country: Singapore

institute: Institute of Molecular and Cell Biology

type: Methylation profiling by high throughput sequencing

summary: Embryonic stem cells upon extrinsic induction could self-assemble into blastocyst-like structures. However, the intrinsic regulation of such blastoid forming potential remain to be addressed. We discover that the activity of nuclear receptor subfamily 1, group H, member 2 (Nr1h2) in expanded potential stem cell (EPSC) positively correlates with blastoid efficiency and quality. In addition, Nr1h2 agonist, T0901317, improves natural blastocyst development. Surprisingly, Nr1h2-activated ESC (NrESC) is rewired towards a distinct pluripotency state that is capable of self-organizing into blastoids and contribute to embryonic and extraembryonic lineage. We hypothesize that Nr1h2 activation broadly affects the DNA methylation to rewire ESC state. Indeed, from WGBS data, we observe that genome-wide DNA methylation differences in NrESC or EPSC after treated with T09 . In summary, our study demonstrates a novel Nr1h2-centric regulation of expanded pluripotency.

overall_design: Examination of genome-wide DNA methylation in mouse embryonic stem cells and expanded pluripotent stem cells after adding T09 Drug

first: K

last: Wong

first: Y

middle: Y

first: H

last: Li

last: Loh


title: Single-cell RNA-seq for mouse NrESC-blastoids

summary: Embryonic stem cells upon extrinsic induction could self-assemble into blastocyst-like structures. However, the intrinsic regulation of such blastoid forming potential remain to be addressed. We discover that the activity of nuclear receptor subfamily 1, group H, member 2 (Nr1h2) in expanded potential stem cell (EPSC) positively correlates with blastoid efficiency and quality. In addition, Nr1h2 agonist, T0901317, improves natural blastocyst development. Surprisingly, Nr1h2-activated ESC (NrESC) is rewired towards a distinct pluripotency state that is capable of self-organizing into blastoids and contribute to embryonic and extraembryonic lineage. We aim at characterizing the NrESC-derived blastoids by single-cell RNA-seq and show that blastoid comprise of epiblast-like, trophectoderm-like and primitive endoderm-like populations, which is the same as blastocyst composition and shows respective gene marker expression for each cluster. Thus, NrESC has attained a unique expanded pluripotency state driven by Nr1h2 activation.

overall_design: Single-cell RNA-seq was applied on mouse NrESC-derived blastoids to examine the single cell transcriptome of different lineages in the organoid


title: Single-cell RNA-seq for mouse type I to III EPS-blastoids

summary: Single-cell RNA-seq was performed for mouse type I to III EPS-blastoids differentiated from E14 EPSC

overall_design: Transcritional profiles of mouse type I to III EPS-blastoids were shown by RNA-seq


title: Analysis of Nr1h2 and H3K27ac genomic binding targets in ESC and EPSC under Nr1h2 activation

summary:
ChIP-seq for Nr1h2 in NrESC, ESC. H3K27ac ChIP-seq in NrESC, ESC, EPSC, EPSCT09
Embryonic stem cells upon extrinsic induction could self-assemble into blastocyst-like structures. However, the intrinsic regulation of such blastoid forming potential remain to be addressed. We discover that the activity of nuclear receptor subfamily 1, group H, member 2 (Nr1h2) in expanded potential stem cell (EPSC) positively correlates with blastoid efficiency and quality. In addition, Nr1h2 agonist, T0901317, improves natural blastocyst development. Surprisingly, Nr1h2-activated ESC (NrESC) is rewired towards a distinct pluripotency state that is capable of self-organizing into blastoids and contribute to embryonic and extraembryonic lineage. We hypothesize that Nr1h2 activation broadly affects the transcriptome landscape by regulating chromatin accessibility and epigenome to rewire ESC state. Indeed, from Nr1h2 and H3K27Ac ChIP-seq, we observe that annotated genes with upregulated Nr1h2 binding as well as H3K27Ac marks in NrESC or EPSC treated with T09 are enriched in processes such as lipid metabolism, pluripotency maintenance and trophectoderm maturation, which are known to be essential to blastocyst development. In summary, our study demonstrates a novel Nr1h2-centric regulation of expanded pluripotency.

overall_design: Nr1h2 and H3K27Ac ChIP-seq were applied on mouse ESC, EPSC, NrESC and EPSC with T09 treatment to examine the changes in Nr1h2 binding as well as epigenetic state

first: Yao

last: Yi


title: ATAC-seq in NrESC

summary:
ATAC-seq in NrESC_1, NrESC_16, ESC, EPSC
Embryonic stem cells upon extrinsic induction could self-assemble into blastocyst-like structures. However, the intrinsic regulation of such blastoid forming potential remain to be addressed. We discover that the activity of nuclear receptor subfamily 1, group H, member 2 (Nr1h2) in expanded potential stem cell (EPSC) positively correlates with blastoid efficiency and quality. In addition, Nr1h2 agonist, T0901317, improves natural blastocyst development. Surprisingly, Nr1h2-activated ESC (NrESC) is rewired towards a distinct pluripotency state that is capable of self-organizing into blastoids and contribute to embryonic and extraembryonic lineage. We hypothesize that Nr1h2 activation broadly affects the transcriptome landscape by regulating chromatin accessibility and epigenome to rewire ESC state. Indeed, from ATAC-seq analysis, we observe some genomic regions progressively gained accessibility in NrESC over passages, which lead to a unique chromatin accessibility profile in NrESC compared to conventional ESC and EPSC. Binding motifs of Pou5f1, Sox2 and Tead4, which are known master regulator of blastocyst lineage specification, showed gained accessibility in NrESC. In summary, our study demonstrates a novel Nr1h2-centric regulation of expanded pluripotency in terms of chromatin reorganization.

overall_design: ATAC-seq was applied on mouse ESC, EPSC, NrESC (1st and 16th passage) to examine the changes in chromatin state


title: RNA-sequencing data of bovine blastocysts produced from oocytes matured in the presence of preovulatory follicular fluid

status: Public on Oct 22 2024

city: Knoxville

last: Moorey

state: Tennessee

address: 2506 River Drive

department: Animal Science

institute: University of Tennessee

summary: Oocyte competence for early embryo development relies on intercellular communication between the maturing oocyte and preovulatory follicle. Preovulatory follicle maturity, as indicated by serum estradiol concentration or follicle diameter, has previously been linked to pregnancy, follicular fluid metabolites, cumulus-oocyte metabolism, and oocyte competency for embryo development. Such relationships indicate metabolic and developmental programming of the oocyte based on the preovulatory follicle’s physiological status, but downstream impacts on the molecular signature of blastocysts have not been examined. We hypothesized that supplementing maturing oocytes with follicular fluid originating from preovulatory follicles of greater or lesser maturity would impact the transcriptome of resulting blastocysts and indicate metabolic programming of the embryo that originated from the oocyte’s maturation environment. The objective was to investigate the effect of follicle maturity on metabolic preparation of the oocyte by examining the functional genome of blastocysts originating from oocytes matured in the presence of follicular fluid from preovulatory follicles of greater or lesser maturity.  In vitro maturing oocytes were supplemented with follicular fluid collected from preovulatory follicles of greater or lesser maturity. Following identical embryo culture procedures, RNA-sequencing was performed on pools of 2 blastocysts (Greater, n = 12; Lesser, n = 15; all with stage code = 7 and quality code = 1). A total of 12,310 gene transcripts were identified in blastocysts after filtering to remove lowly abundant transcripts. There were 113 transcripts that differed in abundance between blastocysts originating from oocytes matured in greater versus lesser maturity follicular fluid (eFDR < 0.01). Although no pathways were significantly enriched with differentially abundant transcripts, transcriptome profiles suggested improved Wnt/β-catenin signaling, metabolism, and protection from oxidative stress in blastocysts derived from oocytes matured in greater maturity follicular fluid, while unregulated cell growth presented in blastocysts resulting from the lesser follicle maturity treatment.

overall_design: Bovine oocytes were in vitro matured in the presence of preovulatory follicular fluid collected from follicles of greater or lesser maturity. Total RNA was extracted from pools of 2 blastocysts from each oocyte maturation group, and 3' RNA sequencing libraries were generated and sequenced. Differences in transcript abundance between blastocyst pools originating from each oocyte maturation category were assessed.

first: Allyson

last: Stokes

first: Hannah

middle: M

last: Clark

first: Lannett

last: Edwards

first: Rebecca

middle: R

last: Payton

first: Jon

last: Beever

first: Trevor

middle: F

last: Freeman

first: Emma

last: Hessock

first: Neal

last: Schrick


title: RNA-seq for siNr1h2 in mouse blastoid samples and T0901317-treatment in mouse ESC and EPSC

summary: Bulk RNA-seq were performed on E14 EPSCs knockdown during blastoid formation with siRNA, as well as E14 ESC and EPSC treated with T0901317

overall_design: Transcritional profiles of mouse embryonic stem cells upon factor knockdowns, or activation by agonist were shown by RNA-seq


title: Differential roles of copper-binding transcription factors and the subfamilies of the SWI/SNF complex in the transcriptional regulation of the skeletal muscle lineage [RNA-seq]

first: David

last: Klein

overall_design: Two replicates of RNAseq were performed for knockdowns targeting the Baf180, Baf250, Brd9 genes (and a SCR control). Within each of these knockdowns, cells were treated with addition of Cu, Zn, or no treatment.

first: Monserrat

last: Olea-Flores

first: Nick

last: Carulli

first: Yaje

last: Nshanji

first: Cat

last: McCann

first: Sabriya

last: Syed

first: Anthony

last: Imbalzano

first: Sarah

last: Hainer

first: Teresita

last: Padilla-Benavides


title: GENERATION OF MOUSE NEOCORTICAL ORGANOIDS TO MODEL THE IMPACT OF CIS-REGULATORY VARIATION ON CORTICAL NEUROGENESIS ACROSS EVOLUTIONARY TIMESCALES  (scATAC-Seq)

status: Public on Oct 20 2024

city: New York

first: Daniel

last: Medina Cano

email: medinacd@mskcc.org, dmcdmc156@gmail.com

state: New York

address: 411E 67th St

department: Developmental Biology

institute: MSKCC

summary: Natural selection has shaped the gene regulatory networks that orchestrate the development of the neocortex, leading to diverse neocortical structure and function across mammals, but the molecular and cellular mechanisms driving phenotypic changes have proven difficult to characterize. Here, we develop a reproducible protocol to generate cortical organoids from mouse epiblast stem cells that enable in depth mechanistic studies of cortical developmental in vitro. Cortical organoids develop with similar kinetics to the mouse cortex in vivo, recapitulate the cellular diversity present in the embryonic neocortex, and undergo relatively rapid maturation compared to human organoids. We generated cortical organoids from F1 hybrid epiblast stem cell lines from crosses between standard laboratory mice (C57Bl/6J) and four wild-derived inbred mouse strains from distinct sub-species that span ~1 million years of evolutionary divergence. Using scRNA-seq and allele-specific expression analysis we identified hundreds of genes that exhibit differential cis-regulation during cortical neurogenesis. These experimental methods and cellular resources represent a powerful new platform for investigating gene regulatory mechanisms across evolutionary timescales.

overall_design:
To investigate how natural selection has shaped development across mouse subspecies, we generated F1 hybrid epiblast stem cell lines from crosses between standard laboratory mice (C57Bl/6J) and four wild-derived inbred mouse strains from distinct sub-species that span ~1 million years of evolutionary divergence.
We also generated cortical organoids from the F1 hybrid epiblast stem cells, as described in the article, and performed scATAC-seq on day18 organoids

last: Medina-Cano

first: Mohammed

last: Islam

first: Thomas

last: Vierbuchen


title: GENERATION OF MOUSE NEOCORTICAL ORGANOIDS TO MODEL THE IMPACT OF CIS-REGULATORY VARIATION ON CORTICAL NEUROGENESIS ACROSS EVOLUTIONARY TIMESCALES  (scRNA-Seq)

overall_design:
To investigate how natural selection has shaped development across mouse subspecies, we generated F1 hybrid epiblast stem cell lines from crosses between standard laboratory mice (C57Bl/6J) and four wild-derived inbred mouse strains from distinct sub-species that span ~1 million years of evolutionary divergence.
We also generated cortical organoids from the F1 hybrid epiblast stem cells, as described in the article, and performed scRNA-seq on the epiblast stem cells, scRNA-seq on the day12 cortical organoids, and snRNA-seq on the day18 organoids


title: Reciprocal Regulation of ASPM and FoxM1

city: Xi'an

first: Xunliang

last: Jiang

address: No. 169, Changle West Road, Xincheng District, Xi'an, Shaanxi

institute: Air Force Military Medical University

summary: Fork-head box protein M1 (FoxM1) is a transcription factor which plays critical roles in development and progression of multiple cancers, including human hepatocellular carcinoma (HCC). However, the regulatory mechanism of FoxM1 itself remains largely unclear. Here, we discovered a novel role of abnormal spindle-like microcephaly associated (ASPM) in HCC, which binds to FoxM1 protein and enhances its stability by preventing proteasome-mediated degradation. ChIP-sequencing data showed that ASPM and FoxM1 co-occupies on the promoter region of multiple genes to promote their transcriptions, leading to the enhancement of a FoxM1-driven oncogenic progression. Intriguingly, FoxM1 binds to the promoter region of ASPM and transcriptionally activates the ASPM expression. Furthermore, data from clinical samples showed that a higher co-expression of ASPM and FoxM1 significantly correlates with poor prognosis in HCC, indicating that a positive feedforward loop between ASPM and FoxM1 coordinately promotes the aggressive progression in HCC. Collectively, our study reveals that reciprocal regulation of ASPM and FoxM1 amplifies the oncogenic progression and emphasizes an ASPM-FoxM1 feedforward loop could be a potential biomarker and therapeutic target in HCC.

overall_design: ASPM and FoxM1 ChIP-seq data for human hepatocellular carcinoma cell line HepG2. ChIP-seq data of the control group (HCC-Input) and the experience group (ASPM or FoxM1 antibody) were generated by deep sequencing.

first: Rui

last: Zhang

first: Xiang


title: Systems analysis of long-term heat stress responses in the C4 grass Setaria viridis

city: Acton

first: Peng

state: ACT

address: 134 Linnaeus Way

country: Australia

institute: The Australian National University

summary: Abiotic stress is a major limitation on agricultural crop productivity and the steady rising of ambient air temperatures due to global climate change are predicted to have a negative impact on plant growth and crop yield.  Plants using equipped with the C4 pathway of photosynthesis are thought to have evolved under warm and dry conditions and it is hypothesized that this biochemical and anatomical specialization serves to alleviate the cost of photorespiration at higher temperatures by saturating Rubisco with CO2. In this study Setaria viridis, an emerging C4 model grass, was grown under high temperature for two weeks (42°C as compared to 28°C). High temperature resulted in stunted growth, but surprisingly had little impact on leaf area based photosynthetic rates. Rates of dark respiration significantly increased and there were major alterations in carbon and nitrogen metabolism in the heat-stressed plants, including reduced starch levels, accumulation of soluble sugars and an increase in leaf nitrogen content. The levelsMeasurements of major phytohormones showed revealed a dramatic increase in abscisic acid in the heat-stressed plants. Leaf transcriptomics, proteomics and metabolomics analyses were carried out and mapped onto metabolic pathways of photosynthesis, respiration, carbon/nitrogen metabolism and hormone synthesis and signaling.  Overall, an upregulation of a number of stress signaling pathways was observed, consistent with multiple potent signals leading to reduced plant growth.  A systems model of plant response is presented based on oxidative stress, hormone and sugar signaling pathways.

overall_design: Setaria viridis plants are grown at high temperature of 42ºC for two weeks. Leaf samples are analysed by RNASeq. This is compared with leaf samples of control plants grown at 28ºC for the entire duration. There are 5 samples from the control group, 6 samples from the heat treatment group. Pair-end reads are performed.


title: Effects of engineered IL-18BP on attenuation of hepatic stellate cell activation

status: Public on Oct 18 2024

city: Chuncheon-si

first: Yong-Hyun

last: Han

state: Kangwondo

address: 307-ho, College of Pharmacy, 1, Kangwondaehak-gil

department: College of Pharmacy

institute: Kangwon National University

summary: Metabolic dysfunction-associated steatohepatitis (MASH) is a chronic liver disease associated with hepatic inflammation and fibrosis. Inflammasome-mediated IL-18 signaling is enhanced under MASH condition. IL-18 binding protein (IL-18BP) is a soluble protein that can block IL-18 actions and therapeutic potential of IL-18BP for MASH-induced fibrosis is largely unknown. We newly developed a human IL-18BP biologics (APB-R3) and injected it to mice to evaluate its pharmacologic efficacy. APB-R3 strikingly abolished hepatic fibrosis and reduced collagen markers. We further investigated whether APB-R3 could inhibit fibrotic activation of hepatic stellate cells (HSCs). This study proposes that abrogation of IL-18 signaling by boosting IL-18BP can strongly inhibit the development of MASH-induced fibrosis and our engineered IL-18BP biologics can become promising therapeutic candidate for curing MASH.

overall_design: Isolated hepatic stellate cells (HSCs) were incubated with 150 ug/ml of APB-R3 or vehicle for 24 hour.

first: Hanna

last: Lee


title: Effects of engineered IL-18BP on attenuation of MASH liver

overall_design: C57BL/6J wild-type were fed FPC diet for 19 weeks. Drugs were administered from 11 to 19 weeks. 8 mg/kg of APB-R3 (SAFA-hIL18BP) were administered three times a week. Liver was havested after sacrifice of mice.

first: Dong-Hyun

last: Kim


title: SFSWAP is a negative regulator of OGT intron detention and global pre-mRNA splicing [CRISPR]

status: Public on Oct 16 2024

city: Dallas

first: Nicholas

middle: K

last: Conrad

address: 6000 Harry Hines Blvd

department: Microbiology

institute: UT Southwestern Medical Center

summary: In this study, we identified SFSWAP as a negative regulator of O-GlcNAc transferase (OGT) intron 4 detention and global pre-mRNA splicing. To do this, we performed CRISPR knockout screens using the Brunello knockout library on Thiamet G (TG)-treated HCT116 cells containing an O-GlcNAc responsive GFP reporter (GFP-β-OGT) integrated at the AAVS1  locus. Knockout of negative regulatory factors which regulate OGT intron 4 detention lead to increased GFP expression. Using replicate screens and further biochemical validation, we identified SFSWAP as one of the top hits affecting OGT intron 4 detention.

overall_design: CRISPR knockout screens were performed in biological triplicates. Reporter lines were infected with lentiviral particles encoding the Brunello knockout library at 0.3 MOI and selected on puromycin for 8 days starting at day 2 post infection (total 10 days). Unselected cells were used to estimate library representation (sample 'library'). Cells were treated with 1 μM TG for 24 hours (replenished every 12 hours) on day 9 and sorted for high GFP expression at the end of day 10 ('sorted' samples). Unsorted cells were used as control ('input' samples). The pilot screen (biological replicate 1) was performed at 100X library coverage and replicate screens (biological replicates 2 and 3) were performed at 300X library coverage.

first: Ashwin

last: Govindan


title: Interleukin-2 receptor signaling acts as a checkpoint that shapes the distribution of regulatory T cell subsets

city: Miami

last: Malek

address: 1600 NW 10th Avenue

department: Microbiology/Immunology

institute: University of Miami

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

overall_design: Refer to individual Series


title: SFSWAP is a negative regulator of OGT intron detention and global pre-mRNA splicing [RNA-seq II]

summary: In this study, we identified SFSWAP as a negative regulator of O-GlcNAc transferase (OGT) intron 4 detention and global pre-mRNA splicing using a CRISPR knockout screen in an O-GlcNAc responsive GFP reporter cell line. In order to characterize the functions of the protein, we performed siRNA mediated knockdown of SFSWAP followed by RNA-seq analysis under TG-treated conditions. In addition, we performed the same analysis under UPF1 knockdown conditions to stabilize NMD targeted transcripts. Alternate splicing analysis using rMATS (and other tools) revealed enhanced splicing of retained introns and increased inclusion of cassette exons upon knockdown of SFSWAP, supporting an inhibitory role for SFSWAP in splicing.

overall_design: RNA-seq was performed in biological triplicates in either siNT (non-target), siSFSWAP (SFSWAP knockdown), siNT/siUPF1 or siSFSWAP/siUPF1 cells. Knockdowns were done for 5 days and cells were treated with TG for 6 hours.


title: Metabolic modeling reveals the aging-associated decline of host-microbiome metabolic interactions in mice

status: Public on Oct 15 2024

city: Kiel

first: Lena

last: Best

address: Michaelis-Straße 5

department: Institute of Experimental Medicine

institute: Christian-Albrechts-University Kiel

summary: Aging is the predominant cause of morbidity and mortality in industrialized countries, yet the molecular mechanisms driving aging and especially the contribution by the microbiome remain unclear. We combined multi-omics with metabolic modeling to comprehensively characterize host–microbiome interactions during aging in mice. Our findings reveal a complex dependency of host metabolism on known and novel microbial interactions. We observed a pronounced reduction in metabolic activity within the aging microbiome accompanied by reduced beneficial interactions between bacterial species. These microbial changes coincided with increased inflammaging as well as a corresponding downregulation of key host pathways, predicted by our model to be microbiome-dependent, that are crucial for maintaining intestinal barrier function, cellular replication, and homeostasis. Our results elucidate microbiome–host interactions that potentially influence host aging processes, focusing on microbial nucleotide metabolism as a pivotal factor in aging dynamics. These pathways could serve as future targets for the development of microbiome-based anti-aging therapies.

overall_design: RNA sequencing with Illumina’s TruSeq stranded kit, with polyA enrichment, 100bp paired end sequencing of 24 total-RNA samples each from female mice’s (C57BL/6J) colons, livers, brains, quadriceps and gonadal white adipose tissue (gWAT) at 12 weeks of age raised with conventional gut microbiome (CONVR), germ-free and then conventional microbiome introduced (CONVD) or raised germ free (GF).

last: Dost

first: Daniela

last: Esser

first: Stefano

last: Flor

first: Andy

last: Gamarra

first: Madlen

last: Haase

first: Samer

last: Kadibalban

first: Georgios

last: Marinos

first: Alesia

last: Walker

first: Johannes

last: Zimmermann

first: Rowena

last: Simon

first: Silvio

last: Schmidt

first: Jan

last: Taubenheim

first: Sven

last: Künzel

first: Robert

last: Häsler

first: Sören

last: Franzenburg

first: Marco

last: Groth

last: Waschina

first: Philip

last: Rosenstiel

first: Felix

last: Sommer

first: Otto

last: Witte

first: Philippe

last: Schmitt-Kopplin

first: John

last: Baines

first: Christiane

last: Frahm

first: Christoph

last: Kaleta


title: Immature neutrophil subsets and emergency granulopoiesis drive sepsis immune suppression and a specific extreme response to infection [HSPC_ECG]

city: Oxford

first: Julian

last: Knight

address: Roosevelt Drive, Headington

department: Wellcome Centre for Human Genetics

country: United Kingdom

institute: University of Oxford

summary: Sepsis, the dysregulated host response to infection leading to organ dysfunction, arises from diverse mechanisms that are poorly resolved by sepsis as a syndromic classification, confounding immunotherapy trials. Here we delineate neutrophil and granulopoietic disturbances underlying sepsis pathophysiology. We present a whole blood single-cell multiomic sepsis response atlas (272,993 cells, n=39 individuals), revealing multiple immature neutrophil populations that were collectively immunosuppressive, inhibiting CD4+ T cell proliferation and activation in co-culture. We traced this to altered granulopoiesis using single-cell multiomic mapping of circulating hematopoietic stem cells (HSCs) (29,366 cells, n=27). We show how these features are enriched in a subset of patients, resolving a specific poor outcome endotype (sepsis response signature SRS1). SRS1 patients have increased IL1R2+ immature neutrophils, epigenetic signatures of emergency granulopoiesis transcription factors in HSCs, and STAT3 features across infectious disease settings.  Our findings delineate an immunohematopoietic axis, therapeutic targets and stratified medicine approach to sepsis.

overall_design: Cryopreserved PBMCs from sepsis patients and healthy volunteers were thawed, MACS enriched for CD34+ HSPCs, FACS sorted for CD34+CD45+ HSPCs then subjected to 10X multiome single-nucleus ATAC-seq and RNA-seq

first: J

first: A

last: Kwok

first: E

last: Cano-Gamez

first: Alice

last: Allcock

first: Ricardo

last: Ferreira


title: Immature neutrophil subsets and emergency granulopoiesis drive sepsis immune suppression and a specific extreme response to infection


title: Emerging cooperativity between Oct4 and Sox2 governs the pluripotency network in mouse early embryos [ATAC-seq]

status: Public on Oct 14 2024

city: Muenster

first: Yanlin

last: Hou

address: Röntgenstrasse 20

institute: Max Planck Institute for Molecular Biomedicine

summary: During the first lineage segregation, mammalian embryos generate the inner cell mass (ICM) and trophectoderm (TE). ICM gives rise to the epiblast (EPI) that forms all cell types of the body, an ability referred to as pluripotency. The molecular mechanisms that induce pluripotency in embryos remain incompletely elucidated. Using knockout (KO) mouse models in conjunction with low-input ATAC-seq and RNA-seq, we found that  Oct4 and Sox2 gradually come into play in the early ICM, coinciding with the initiation of Sox2 expression. Oct4 and Sox2 directly activate the pluripotency-related genes through the corresponding OCT-SOX enhancers in the early ICM. Furthermore, we observed a substantial reorganization of chromatin landscape and transcriptome from the morula to the early ICM stages, which was partially driven by Oct4 and Sox2, highlighting their pivotal role in promoting the developmental trajectory towards the ICM. Our study provides new insights into the establishment of the pluripotency network in mouse preimplantation embryos.

overall_design: To investigate the role of Oct4 and Sox2 in the development of preimplantation embryos, we produced four transgenic mouse lines: Oct4 KO labeled with mKO2 (monomeric kusabira-orange 2, Oct4mKO2), Sox2 KO labeled with EGFP (Sox2EGFP), floxed Oct4 (Oct4flox) and floxed Sox2 (Sox2flox). Oct4 +/mKO2 and Sox2 +/EGFP heterozygous male mice were mated with Oct4 flox/flox; ZP3-Cre and Sox2 flox/flox; ZP3-Cre maternal KO female mice, respectively, to generate fluorescently labeled maternal-zygotic KO and unlabeled maternal KO (herein called control, Ctrl) embryos. To assess the genome-wide molecular impact of the loss of Oct4 and Sox2, we performed low-input ATAC-seq and RNA-seq using early (E2.75) and late (E3.25) compacted morulae, as well as early (E3.75) and late (E4.5) ICMs. For ATAC-seq, we pooled embryos based on our reporter systems because single-embryo samples yielded sparse signals and too few peaks. We opted to collect single morulae or ICMs for RNA-seq, as this approach enabled us to account for embryo-to-embryo variability and detect transcripts with greater sensitivity compared to scRNA-seq. Given that the ICM consists of the progenitors of EPI and PE cells, we treated the embryos with the MEKi (PD0325901) from E2.5 to suppress PE development and specify the entire ICM to the EPI.

first: Kenjiro

last: Adachi

first: Guangming

last: Wu


title: Anti-Tumour Immunity Relies on Targeting Tissue Homeostasis Through Monocyte-Driven Responses Rather Than Direct Tumour Cytotoxicity

status: Public on Oct 10 2024

city: Richmond

first: Nicholas

last: Koelsch

state: Virginia

address: 1810 East Cary Street Apt MG02

department: Microbiology & Immunology

institute: Virginia Commonwealth University

summary:
Metabolic dysfunction–associated fatty liver disease (MAFLD) can progress to hepatocellular carcinoma (HCC), yet the immune mechanisms driving this transition remain unclear.

In a chronic Western diet (WD) mouse model, we performed single-nuclei RNA sequencing to track MAFLD progression into HCC and subsequent tumor inhibition upon dietary correction.

Carcinogenesis begins during MAFLD, with tumor cells entering dormancy when HCC is mitigated. Rather than purely tolerogenic, the liver actively engages immune responses targeting myofibroblasts, fibroblasts and hepatocytes to maintain tissue homeostasis. Cytotoxic cells contribute to turnover of liver cells but do not primarily target the tumor. NKT cells predominate under chronic WD, while monocytes join them in HCC progression on a WD. Upon dietary correction, monocyte-driven immunity confers protection against HCC through targeting tissue homeostatic pathways and antioxidant mechanisms. Crucially, liver tissue response—not merely immune activation—dictates whether tumors grow or regress, emphasizing the importance of restoring liver tissue integrity. Also, protection against HCC is linked to a distinct immunological pattern, differing from healthy controls, underscoring the need for immune reprogramming.

These findings reveal the dual roles of similar pathways, where immune patterns targeting different cells shape distinct outcomes. Restoring tissue homeostasis and regeneration creates a tumor-hostile microenvironment, whereas tumor-directed approaches fail to remodel the TME. This underscores the need for tissue remodeling strategies in cancer prevention and treatment.

Our study challenges the traditional view that the liver is purely tolerant to immune responses, revealing that it actively regulates immunity to maintain tissue health. We found that liver cancer (HCC) begins during fatty liver disease (MAFLD) but can be halted if immune cells—especially monocytes—restore tissue integrity. Instead of focusing solely on killing tumors, effective immunotherapy should harness the body’s natural ability to repair the liver, creating an environment where cancer cannot thrive. This discovery paves the way for innovative treatments that promote immune-driven tissue regeneration as a strategy for cancer prevention and therapy.

overall_design: Eight DIAMOND mice (129A1/SvIm and C57BL/6J cross mice) were stratified into experimental groups receiving different diets at two months of age. Three mice (n=3) were on a high-fat high-sugar Western Diet (WD) for 48 weeks that developed hepatocellular carcinoma (HCC). Five mice underwent diet reversal to a standard chow diet (CD) following 36 weeks on WD, in which two mice developed HCC (n=2; RD1 and RD5), whereas 3 mice were rescued from HCC development and did not have any detectable HCC (n=3; R2, R3, and R4)

first: Faridoddin

last: Mirshahi

first: Hussein

last: Aqbi

first: Mulugeta

last: Seneshaw

first: Michael

middle: O

last: Idowu

first: Amy

middle: L

last: Olex

first: Arun

last: Sanyal

first: Masoud

middle: H

last: Manjili


title: LncRNA ENST00000581911 regulates extraocular muscle remodeling by interacting with KHSRP in Graves’ ophthalmopathy

status: Public on Oct 12 2024

city: Shanghai

first: Mingsu

last: Shi

state: Shanghai

address: Dongan Road

institute: Eye & ENT Hospital of Fudan University

summary:
To reveal the potential role of lncRNAs in the extraocular muscles (EOMs) of Graves' ophthalmopathy (GO), we performed lncRNA expression profiling and compared their expression differences between EOM tissues sampled from GO and concomitant esotropia (CET) patients using microarray analysis.
To reveal the potential role of lncRNAs in the extraocular muscles (EOMs) of Graves' ophthalmopathy (GO), we performed lncRNA expression profiling and compared their expression differences between EOM tissues sampled from GO and concomitant esotropia (CET) patients using microarray analysis.

overall_design: EOMs were collected from the surgical wastes of 5 GO patients and 5 CET patients who underwent strabismus surgery. All EOMs were lateral rectus muscles.

first: Lianqun


status: Public on Oct 02 2024

city: Hangzhou

first: Shudi

last: Zhao

address: Yuhangtang Road No.866

institute: Zhejiang University

summary: To investigate the Binding density of BmGATA on silkworm genome

overall_design: To investigate the transcriptional regulatory role of the transcription factor BmGATA.


title: Ampk activation by glycogen expenditure primes the exit of naïve pluripotency

city: Seoul

first: Eun-Ji

last: Kwon

address: 1, Gwanak-ro

institute: Seoul National University

summary: Embryonic and epiblast stem cells in pre-and post-implantation embryos are characterized by their naïve and primed states, respectively, which represent distinct phases of pluripotency. Thus, the cellular transition from naïve to primed pluripotency recapitulates a drastic metabolic and cellular remodeling after implantation to adapt to changes in extracellular conditions. Here, we found that inhibition of Ampk occurred during naïve transition with two conventional inhibitors (2i) of the Mek1 and Gsk3 pathways. The accumulation of glycogen due to the inhibition of Gsk3 was responsible for Ampk inhibition, which accounted for high de novo fatty acid synthesis in naïve embryonic stem cells (ESCs). The knockout of glycogen synthase 1 (Gys1) in naïve ESCs (GKO), resulting in a drastic glycogen loss, led to a robust Ampk activation and lowered the level of fatty acids. GKO lost the cellular characteristics of naïve ESCs and rapidly transitioned to a primed state. The characteristics of GKO were restored by the simultaneous knockout of Ampk. These findings suggest that glycogen in naïve ESCs within the blastocyst may act as a signaling molecule for the timely activation of Ampk, thus ultimately contributing to the transition to the epiblast stage.

overall_design: To investigate the effects of knocking out Gys1 and AMPK individually and simultaneously in J1 cells

first: Hyuk-Jin

last: Cha


title: SFSWAP is a negative regulator of OGT intron detention and global pre-mRNA splicing

last: Conrad

state: Texas


title: Transcriptional regulatory role of BmGATA

status: Public on Oct 01 2024

summary: To investigate the transcriptional regulatory role of the transcription factor BmGATA, and the impact of BmNPV infection on its activation capacity


title: Spatial transcriptomic analysis of liver-innervating cholinergic neurons

city: Bronx

first: Jeffrey

middle: E

last: Pessin

state: NY

address: 1301 Morris Park Avenue

department: Medicine and Molecular Pharmacology

institute: Albert Einstein College of Medicine

summary: We report the effect of ablating liver-innervating cholinergic neurons in the dorsal motor nucleus of the vagus in diet-induced obese male mice

overall_design: Examination of diet-induced obese male mice in either ChATCre+GRP or ChATCre+dTA

first: Jiyeon

last: Hwang

first: Junichi

last: Okada

first: Li

last: Liu

first: Young-Hwan

last: Jo


title: Functional analysis of BmNPV cis-interacting sites

summary: RNA-seq of BmNPV cells infected by indicated mutant BmNPV to determine the impact on viral gene expression of the cis-interacting sites on BmNPV by knocking out them via RED system

overall_design: To investigate the function of BmNPV cis-interacting sites


title: Generation of Alveolar Assembloids (AlvAssemb) with Functional Alveolar-like Macrophages

status: Public on Sep 30 2024

city: Cheongju-si

first: Dayeon

last: Gil

state: Chungcheongbuk-do

address: 202 Osongsaengmyung 2-ro, Heungdeok-gu

department: Division of intractable disease research

institute: Korea national institute of health

summary: Within the human lung, interplay between alveolar epithelial cells and resident macrophages shape lung development and function in both health and disease. To study these processes, we devised a strategy for co-culturing hPSC-derived alveolar epithelial organoids and induced macrophages to form functional environment, which we name alveolar assembloids (AlvAssemb). By scRNAseq and functional analysis of AlvAssemb, we identified alveolar type 2-like cells that produced GM-CSF, a response associated with tissue adaptation of macrophages, and that resident alveolar macrophage-like cells secreted interleukin-1β and interleukin-6, a core immune response function, and expressed genes required for surfactant metabolism. Remarkably, in response to alveolar epithelial injury, we found that macrophage-like cells within AlvAssemb efficiently eliminated damaged cells and absorbed oxidized lipids. Moreover, in response to lipopolysaccharide exposure and Mycobacterium tuberculosis infection, we found that core features of the human respiratory defense response were replicated in AlvAssemb. These findings support that AlvAssemb could serve as a valuable platform to investigate human lung development and pathology.

overall_design:
We cultured iMφ with and without GM-CSF (10 ng/ml) for 7 days. The cells were then infected with M.tb (H37Rv) at MOIs of 5 and 10 for 48 hours. Following infection, RNA sequencing libraries were prepared and the results were analyzed using RNA-seq.
Please note that GSM4106642 (Ni, huPrimary_0_r1) and GSM4106641 (Moi-20,  huPrimary_20) data (in GSE138398) was re-analyzed in the current study.

first: Youngsun

last: Lee

first: Mi-Ok

first: Jung-Hyun

last: Kim


title: Sex-specific attenuation of photoreceptor degeneration by reserpine in a rhodopsin P23H rat model of autosomal dominant retinitis pigmentosa

status: Public on Sep 27 2024

city: Bethesda

first: Zachary

last: Batz

state: MD

address: 6 Center Dr Bldg 6, Rm 303

department: NEI

institute: NIH

summary: Inherited retinal degenerations (IRDs) constitute a group of clinically and genetically diverse vision-impairing disorders. Retinitis pigmentosa (RP), the most common form of IRD, is characterized by gradual dysfunction and degeneration of rod photoreceptors, followed by the loss of cone photoreceptors. Recently, we identified reserpine as a lead molecule for maintaining rod survival in mouse and human retinal organoids as well as in the rd16 mouse, which phenocopy Leber congenital amaurosis caused by mutations in the cilia-centrosomal gene CEP290 (Chen et al. eLife 2023;12:e83205. DOI: https://doi.org/10.7554/eLife.83205). Here, we show the therapeutic potential of reserpine in a rhodopsin P23H rat model of autosomal dominant RP. At postnatal day (P) 68, when males and females are analyzed together, the reserpine-treated rats exhibit higher rod-derived scotopic b-wave amplitudes compared to the controls with little or no change in scotopic a-wave or cone-derived photopic b-wave. Interestingly, the reserpine-treated female rats display enhanced scotopic a- and b-waves and photopic b-wave responses at P68, along with a better contrast threshold and increased outer nuclear layer thickness. The female rats demonstrate better preservation of both rod and cone photoreceptors following reserpine treatment. Retinal transcriptome analysis reveals sex-specific responses to reserpine, with significant upregulation of phototransduction genes and proteostasis-related pathways, and notably, genes associated with stress response. This study builds upon our previously reported results reaffirming the potential of reserpine for gene-agnostic treatment of IRDs and emphasizes the importance of biological sex in retinal disease research and therapy development.

overall_design: Total RNA was purified from homogenized rat retinas (WT, DMSO controls, and reserpine-treated samples) using TriPure isolation reagent (Roche, Indianapolis, IN) according to the manufacturer’s protocol. The quality and quantity of RNA were both assessed using the RNA ScreenTape assay on the Agilent TapeStation system. Samples (with RNA integrity number >8) were used for library generation using the TrueSeq RNA sample Prep Kit v2 (Illumina).

first: Hyun Beom

last: Song

first: Laura

last: Campello

first: Anupam

last: Mondal

first: Holly

last: Chen

first: Milton

last: English

first: Michael

last: Glen

first: Philip

last: Vanlandingham

first: Rafal

last: Farjo

first: Anand

last: Swaroop


title: Epigenomic landscape of homologous recombination deficient (HRD) triple-negative breast cancer (TNBC)

status: Public on Sep 26 2024

city: Lebanon

first: Youdinghuan

state: NH

address: Hinman Box 7650

department: Epidemiology

institute: Dartmouth College

summary: Profiling of genome-wide DNA methylation and copy number in TNBCs classified as HRD by the multiplex ligation-dependent probe amplification assay

overall_design: Two indepentent cohorts of TNBCs (n=32 and n=58) where measured on MethylationEPIC array and subjected to HRD classification by MLPA


title: Mitochondrial fusion limits breast cancer metastasis

status: Public on Sep 25 2024

city: Ottawa

first: Julie

last: St-Pierre

address: 451 Smyth Rd

country: Canada

institute: University of Ottawa

summary: Mitochondrial metabolism plays a central role in promoting cancer growth and metastatic progression. The transition between a hyperfused and fragmented mitochondrial network is termed mitochondrial dynamics and is important for many mitochondria-associated functions; however, little is known regarding how this process influences metastasis. Here, we show that breast cancer cells with low metastatic potential exhibit a more fused mitochondrial network compared to highly metastatic breast cancer cells. To examine whether a fused mitochondrial network could impair metastasis, we inhibited mitochondrial fission in metastatic breast cancer cells by individual genetic deletion of three key regulators of mitochondrial fission (Drp1, Fis1 and Mff) or pharmacological intervention using leflunomide, an anti-rheumatic drug. These cells displayed a fused mitochondrial network and limited survival under anoikis conditions, consistent with mitochondrial fusion limiting metastasis. Transcriptomics and metabolomics analyses revealed that mitochondrial fusion causes significant alterations in metabolic pathways and processes related to cell adhesion. Functional bioenergetics assays demonstrated that mitochondrial fusion limited the mitochondrial capacity of cancer cells. Mitochondrial fusion in breast cancer cells had no significant effect on primary tumor growth but almost completely ablated lung metastasis in vivo. Furthermore, the transcriptomics signature associated with enhanced mitochondrial fusion correlated with improved survival in patients with breast cancer. Overall, our findings highlight mitochondrial fusion as a therapeutic opportunity for breast cancer.

overall_design: We generated two independent CRISPR-Cas9 KO clones using the highly metastatic 4T1 cell line for Dynamin-related protein 1 (Drp1), mitochondrial fission 1 protein (Fis1) and mitochondrial fission factor (Mff). In addition, we treated 4T1 cells with leflunomide or vehicle control (DMSO) for 3 days. We then performed gene expression profiling analysis from RNA-Seq. We compared KO clones to parental 4T1 and leflunomide-treated cells to vehicle control.

first: Lucía

last: Minarrieta


title: SFSWAP is a negative regulator of OGT intron detention and global pre-mRNA splicing [RNA-seq I]

first: Nicholas

last: Conrad

summary: In this study, we identified SFSWAP as a negative regulator of O-GlcNAc transferase (OGT) intron 4 detention and global pre-mRNA splicing using a CRISPR knockout screen in an O-GlcNAc responsive GFP reporter cell line. In order to characterize the functions of the protein, we performed siRNA mediated knockdown of SFSWAP followed by RNA-seq analysis under untreated conditions. Alternate splicing analysis using rMATS (and other tools) revealed enhanced splicing of retained introns and increased inclusion of cassette exons upon knockdown of SFSWAP, supporting an inhibitory role for SFSWAP in splicing.

overall_design: RNA-seq was performed in biological triplicates in either siNT (non-target) or siSFSWAP (SFSWAP knockdown) cells. Knockdowns were done for 5 days and cells were left untreated.

first: Ashwin

last: Govindan


title: Palmitic acid induced lncRNA PARAIL regulates inflammation via interaction with RNA-binding protein HuR in monocytes and macrophages

city: Duarte

first: Rama

last: Natarajan

state: California

address: 1500 E Duarte Rd

department: Department of Diabetes Complications and Metabolism

institute: Beckman Research Institute, City of Hope

summary: BACKGROUND: Obesity and diabetes are associated with elevated free fatty acids like palmitic acid (PA), which promote chronic inflammation and impaired inflammation resolution associated with cardiometabolic disorders. Long non-coding RNAs (lncRNAs) are implicated in inflammatory processes, however, their roles in PA-regulated inflammation and resolution are unclear.  METHODS: We performed RNA-seq analysis to identify PA-regulated coding genes and novel lncRNAs in CD14+ monocytes from healthy volunteers. We investigated the regulation and function of an uncharacterized PA-induced lncRNA PARAIL (PA-regulated anti-inflammatory lncRNA). We examined its role in inflammation resolution employing knockdown and overexpression strategies in human and mouse macrophages. We also used RNA-pulldown coupled to mass spectrometry to identify PARAIL interacting nuclear proteins and their mechanistic involvement in PARAIL functions in human macrophages.  RESULTS: Treatment of human CD14+ monocytes with PA     induced several lncRNAs and genes associated with inflammatory phenotype. PA strongly induced lncRNA PARAIL expressed near RIPK2. PARAIL was also induced by cytokines and infectious agents in human monocytes/macrophages and was regulated by NF-kB. Time course studies showed PARAIL was induced during inflammation resolution phase in PA treated macrophages. Knockdown of PARAIL with antisense oligonucleotides upregulated key inflammatory genes and vice versa with PARAIL overexpression. We found that PARAIL interacts with Human Antigen R (HuR) protein via AU-rich elements (AREs). HuR knockdown inhibited the anti-inflammatory functions of PARAIL. Moreover, PARAIL knockdown increased cytosolic localization of HuR and increased the stability of ARE-containing inflammatory mRNAs. Mouse orthologous Parail was downregulated in macrophages from mice with diabetes and atherosclerosis. Parail overexpression attenuated pro-inflammatory genes in mouse macrophages.  CONCLUSIONS: Upregulation of PARAIL under acute inflammatory conditions contributes to pro-resolution mechanisms via PARAIL-HuR interactions. Conversely, PARAIL downregulation in cardiometabolic diseases enhances HuR function and impairs inflammation resolution to further augment inflammation. Thus, inflammation-resolving lncRNAs like PARAIL represent novel tools to combat inflammatory cardiometabolic diseases.

first: Vinay

middle: S

last: Tanwar

first: Marpadga

last: Reddy


title: The response to desiccation in Acinetobacter baumannii

status: Public on Sep 23 2024

city: Rome

first: Massimiliano

last: Lucidi

state: Rome

address: Viale Guglielmo Marconi 446

department: Sciences

country: Italy

institute: University of Roma Tre

summary: The long-term resistance to desiccation on abiotic surfaces is a key determinant of the adaptive success of Acinetobacter baumannii as a healthcare-associated bacterial pathogen. Here, the cellular and molecular mechanisms enabling A. baumannii to resist desiccation and persist on abiotic surfaces were investigated. Experiments were set up to mimic the A. baumannii response to air-drying that would occur when bacterial cells contaminate fomites in hospitals. Resistance to desiccation and transition to the “viable but nonculturable” (VBNC) state were determined in the laboratory-adapted strain ATCC 19606T and the epidemic strain ACICU. Culturability, membrane integrity, metabolic activity, virulence, and gene expression profile were compared between the two strains at different stages of desiccation. Upon desiccation, ATCC 19606T and ACICU cells lose culturability and membrane integrity, lower their metabolism, and enter the VBNC state. However, desiccated A. baumannii cells fully recover culturability and virulence in an insect infection model following rehydration in physiological buffers or human biological fluids. Transcriptome and chemical analyses of A. baumannii cells during desiccation unveiled the production of protective metabolites (L-cysteine and L-glutamate) and decreased energetic metabolism consequent to activation of the glyoxylate shunt (GS) pathway, as confirmed by reduced resuscitation efficiency of aceA mutants, lacking the key enzyme of the GS pathway. VBNC cell formation and extensive metabolic reprogramming provide a biological basis for the response of A. baumannii to desiccation, with implications on environmental control measures aimed at preventing the transmission of A. baumannii infection in hospitals.

sample_organism: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841

overall_design: The two strains of A. baumannii, namely ATCC 19606T and ACICU, underwent desiccation for 1 week. Before and after the desiccation process, samples were collected for RNA isolation and purification, involving three independent procedures for each sample. The RNA-seq analysis, RNA quality assessment, library preparation, sequencing, and subsequent statistical analysis were conducted at the GENEWIZ Biotechnology Facility, as previously described [doi: 10.1128/spectrum.00961-22]. Comparative expression analysis, utilizing pairwise comparisons between samples before and after desiccation, was carried out to determine the genes that play a pivotal role in desiccation resistance within these two strains.

first: Giulia

last: Capecchi

first: Cinzia

last: Spagnoli

first: Arianna

last: Basile

first: Irene

last: Artuso

first: Luca

last: Persichetti

first: Elisa

last: Fardelli

first: Giovanni

last: Capellini

first: Daniela

last: Visaggio

first: Francesco

last: Imperi

first: Giordano

last: Rampioni

first: Livia

last: Leoni

first: Paolo

last: Visca


title: A two-step de-differentiation and maturation of primary human hepatocytes in vitro with efficient metabolic and regenerative capacities

city: luzhou

last: Jiang

address: Zhong Shan Road

institute: SWMU

summary: Hepatocytes hold significant promise for applications in drug screening, disease modeling, and clinical cell transplantation. Generating large amouts of hepatocyte in vitro for those application is still challenging. We have previously established a 5C medium for long-term culture and functional maintanace human primary hepatocytes (PHHs) in vitro. However, 5C condtion could not support hepatocyte expansion, which limited its application. In this study, we established a new hepatocyte expansion medium (NHEM) for efficient hepatocyte expansion, which turned the PHHs into hepatic progenitor-like cells (HPLCs). We also generated an optimized 6C condtion for HPLCs maturation. Overall, this study provide a new strategy to generate large amounts of hepatocytes in vitro.

overall_design: One single-cell RNA sequencing data of primary human hepatocytes(PHHs) was analyzed as the input for SiPer.

first: Bingqing

last: Xie


title: Emerging cooperativity between Oct4 and Sox2 governs the pluripotency network in mouse early embryos [RNA-seq]

first: Yanlin

last: Hou

first: Kenjiro

last: Adachi

first: Guangming

last: Wu


title: effect of depletion of PRCAT71 and KHSRP on gene expression in prostate cancer cells

city: Chicago

first: Yongyong

last: Yang

state: IL

address: 303 E Superior ST

department: Department of Urology

institute: Northwestern University

summary: Mounting evidence indicates that long non-coding RNAs (lncRNAs) play vital roles in tumorigenesis and progression of cancers. However, the functions and regulatory mechanisms of lncRNAs in prostate cancer (PCa) are still largely unknown. In this study, we discovered a PCa-specific lncRNA, PRCAT71, significantly highly expressed in metastatic and primary PCa compared to benign prostate tissues. Silencing PRCAT71 inhibited cancerous properties of PCa cells, as well as androgen receptor (AR) signaling. Mechanismly, PRCAT71 acts as a scaffold to recruit KH-type splicing regulatory protein (KHSRP) to AR mRNA and stabilize AR mRNA. Furthermore, PRCAT71 is transcriptionally regulated by AR, thus forming a positive regulatory loop between AR and PRCAT71 in PCa. Our findings demonstrate that the PRCAT71-KHSRP-AR axis is a promising therapeutic target to treat PCa.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for LNCaP cells stably expressing shRNA targeting PRCAT71/shRNA control, or for C4-2 cells stably expressing shRNA targeting KHSRP/shRNA control.

first: Ting-You

last: Wang

first: Rendong

first: Qi

last: Cao


title: miRNA profile of mice skeletal muscle at 7 days after contusion

status: Public on Oct 03 2024

first: laimeng

last: song

address: 五角镇街道佳木斯路2号复旦大学科技园2号楼216

institute: University of Shanghai for Science and Technology

summary: Traumatic skeletal muscle fibrosis is disastrous to muscle performance. In this dataset, mice gastrocnemius was subjrct to contusion injury and then measured by miRNA microarray to identify potential therapeutic targets.

overall_design: According to the miR expression profile of skeletal muscle tissue after contusion, miRs that potentially play a role in skeletal muscle fibrosis are identified

first: Luze

last: Shi

first: Laimeng

last: Song


title: Possible involvement of Toll-like receptor 8-positive monocytes/macrophages in the pathogenesis of Sjögren's disease

status: Public on Oct 19 2024

city: Fukuoka

first: Lijing

last: Yan

address: Maidashi 3-1-1, Higashi-ku

country: Japan

institute: Kyushu University

summary: Sjögren's disease (SjD) is an autoimmune disease marked by lymphocytic infiltration of salivary and lacrimal glands, leading to glandular dysfunction, where CD4-positive helper T (Th) cells and their cytokines are crucial in the pathogenesis. Recent studies have demonstrated that Toll-like receptors (TLRs), particularly those recognizing immune complexes containing DNA and RNA, contribute to Th cell activation in various autoimmune diseases.  This study explores the expression and function of these TLRs in SjD. In scRNA-seq analysis, the TLR8-expressing cluster comprised macrophages and monocytes, which also produced T cell activation genes like CD86, suggesting that infiltrating monocytes and macrophages may produce cytokines and chemokines through TLR8 stimulation, potentially enhancing B7 molecule expression, promoting the adaptive immune response, and contributing to SjD pathogenesis.

overall_design: CD45+ cells were isolated from a fresh SjD biopsy tissue sample obtained from surgery, and were loaded into a 10x Genomics Chromium device according to the protocol of Chromium Single Cell 5' Reagent Kits (v2).

first: Yuka

last: Miyahara

first: Mizuki

last: Sakamoto

first: Naoki

last: Kaneko

first: Hu

last: Chen

first: Junsei

last: Sameshima

first: Hajime

last: Kido

first: Shiho

last: Yokomizo

first: Tomoki

last: Sueyoshi

first: Haruki

last: Nagano

first: Yukiko

last: Ohyama

first: Seiji

last: Nakamura

first: Shintaro

last: Kawano

first: Masafumi

last: Moriyama


title: The INO80E at 16p11.2 locus increases risk of schizophrenia in humans and induces schizophrenia-like phenotypes in mice

city: Kunming

first: Ming

last: Li

state: Yunnan

address: NO 32 Jiao-Chang Donglu

institute: Kunming Institute of Zoology, Chinese Academy of Sciences

summary: Background Chromosome 16p11.2 is one of the most significant loci in the genome-wide association study (GWAS) of schizophrenia.  Despite several integrative analyses and functional genomics studies have been carried out to identify possible risk genes, their impacts in the pathogenesis of schizophrenia remain to be fully characterized. Methods We performed expression quantitative trait loci (eQTL) and summary-data-based Mendelian randomization (SMR) analyses to identify schizophrenia risk genes in the 16p11.2 GWAS locus.  We constructed the murine model with dysregulated expression of risk gene in the medial prefrontal cortex (mPFC) using stereotaxic injection of Adeno-associated Virus (AAV), followed by behavioral assessments, dendritic spine analyses and RNA sequencing. Findings We identified significant associations between elevated INO80E mRNA expression in frontal cortex and risk of schizophrenia.  The mice overexpressing Ino80e in mPFC (Ino80e-OE) exhibited schizophrenia-like behaviors, including increased anxiety behavior, anhedonia, and impaired prepulse inhibition (PPI) when compared with control group.  The neuronal sparse labeling assay showed that the density of mushroom spines in the pyramidal neurons of mPFC was significantly decreased in Ino80e-OE mice compared with control mice, accompanied by a notable increase in the density of stubby spines.  Transcriptomic analysis in the mPFC revealed significant alterations in the mRNA levels of schizophrenia-related genes and processes related to synapses upon overexpressing Ino80e . Interpretation Our results suggest that upregulation of the Ino80e gene in mPFC may induce schizophrenia-like behaviors in mice, further supporting the hypothesis that INO80E is an authentic risk gene.

overall_design: We first identified schizophrenia risk genes at the 16p11.2 GWAS locus by expression quantitative trait loci (eQTL) and Mendelian randomization (SMR) analysis based on aggregated data. Then we constructed the Adeno-associated Virus(AAV). We constructed the murine model with dysregulated expression of risk gene in the medial prefrontal cortex (mPFC) using  stereotaxic injection of Adeno-associated Virus (AAV). We then performed behavioral assessment, dendritic spine analysis, and RNA sequencing to assess the difference between the murine model with dysregulated expression of risk gene and that of the control murine.

first: Bo

last: Hu

first: Mei-Yu

last: Yin

first: Chu-Yi

last: Zhang

first: Zhe

first: Lu

last: Wang

first: Xiaoming

last: Lei

first: Shi-Wu

first: Qin-Hui

last: Tuo


title: X chromosome encoded histone demethylase UTX regulates mammalian axon regeneration via microRNA-124

city: Beijing

first: Tao

last: Huang

state: Beijing

address: Dong Da Jie No.8

institute: The Fifth Medical Center of Chinese PLA General Hospital

summary: Neurons in the mammalian central nervous system (CNS) gradually lose their intrinsic regeneration capacity during maturation mainly because of altered transcription profile. Recent studies have made great progress by identifying genes that can be manipulated to enhance CNS regeneration. However, as a complex process involving many genes and signaling networks, it is of great importance to deciphering the underlying neuronal chromatin and transcriptomic landscape coordinating CNSregeneration. Here we identify UTX, an X-chromosome associated gene encoding a histone demethylase, as a novel regulator of mammalian neural regeneration. We demonstrate that UTX acts as a repressor of spontaneous axon regeneration in the peripheral nerve system (PNS). In the CNS, either knocking out or pharmacological inhibiting UTX in retinal ganglion cells (RGCs) leads to significantly enhanced neuronal survival and optic nerve regeneration. RNA-seq profiling revealed that deleting UTX switches the RGC transcriptomics into a developmental-like state. Moreover, microRNA-124, one of the most abundant microRNAs in mature neurons, is identified as a downstream target of UTX and blocking endogenous microRNA124-5p results in robust optic nerve regeneration. These findings revealed a novel histone modification-microRNA epigenetic signaling network orchestrating transcriptomic landscape supporting CNS.

overall_design: To gain mechanistic insights into promoting effect of UTX on axon regeneration, we performed RNA sequencing (RNA-seq) of the enriched RGCs across different developmental stages (postnatal day 1, 14 and 21) and at 3 days after injury of adult (P42) wild type (AAV2-GFP) or UTX knockout mice (AAV2-Cre). Dissociated RGCs were labeled with Thy1.2 antibody, subjected to  fluorescence-activated cell sorting (FACS) for RGC enrichment, and identified by labelling for Tuj1. Totally, 13 bulk RNA-seq libraries were generated from FACS-purified RGCs.

first: Shu-Guang

last: Yang

first: Xue-Wei

first: Chang-Ping


title: Single-cell analysis of bidirectional reprogramming between early embryonic states reveals mechanisms of differential lineage plasticities [scATAC-seq]

status: Public on Sep 09 2024

city: New York

first: Yang

address: 417 E 68th St

institute: Memorial Sloan Kettering Cancer Center

summary: Two distinct lineages, pluripotent epiblast (EPI) and primitive (extra-embryonic) endoderm (PrE), arise from common inner cell mass (ICM) progenitor cells in mammalian embryos. To study how these sister identities are forged, we leveraged embryonic (ES) and eXtraembryonic ENdoderm (XEN) stem cells – in vitro counterparts of the EPI and PrE. Bidirectional reprogramming between ES and XEN coupled with single-cell RNA and ATAC-seq analyses uncovered distinct rates, efficiencies and trajectories of state conversions, identifying drivers and roadblocks of reciprocal conversions. While GATA4-mediated ES-to-iXEN conversion was rapid and nearly deterministic, OCT4, KLF4 and SOX2-induced XEN-to-iPS reprogramming progressed with diminished efficiency and kinetics. A dominant PrE transcriptional program, safeguarded by Gata4, and globally elevated chromatin accessibility of EPI underscored the differential plasticities of the two states. Mapping in vitro to embryo trajectories revealed reprogramming in either direction tracked along, and toggled between, EPI and PrE in vivo states without transitioning through the ICM.

overall_design: Reprogramming XEN-to-iPS and ES-to-iXEN cells were assayed for chromatin accessibility using single-cell ATAC-seq. Given the low proportions of cells undergoing lineage conversion (based on marker expression) from XEN to iPS cells at all timepoints assessed, and ES cells at the 9h timepoint, subpopulations were isolated using fluorescence-activated cell sorting (FACS) and reconstituted at roughly equal proportions. This serves to: (1) retain all the heterogeneity within the reprogramming population, and (2) enrich for cells undergoing key lineage marker expression changes. In addition to reprogramming stages, cells at starting and final states were also sampled.


title: Empagliflozin in acute myocardial infarction reduces no-reflow and preserves cardiac function by preventing endothelial damage

status: Public on Sep 13 2024

city: Lamia

first: Artemis

middle: Georgia

last: Hatzigeorgiou

state: Galaneika

address: Papasiopoulou 2-4

department: Computer Science and Biomedical Informatics

country: Greece

institute: University of Thessaly

summary: Myocardial infarct size (IS) and now reflow are major determinants of prognosis and currently there are no effective treatments. We investigated the effects of empagliflozin on cardiac cell populations affected by myocardial ischemia reperfusion injury (IRI), and its cardioprotective potential in terms of IS and no-reflow.

overall_design: 38 total RNA samples were used for library construction. RNA concentration was determined using a Qubit-4 Fluorometer (Invitrogen) and the Qubit RNA HS Assay Kit (Invitrogen).RNA quality was determined on an Agilent 2100 Bioanalyzer(Agilent) using the Agilent RNA 6000 Nano Kit (Agilent) and protocol. For library preparation, the QuantSeq 3‘ mRNA-Seq Library Prep Kit for Illumina (FWD) (Lexogen) was used according to manufacturer’s instructions. Briefly, up to 500 ng of RNA from each sample were used for first strand synthesis, followed by RNA template removal. Second strand synthesis was initiated by random primers containing compatible linker sequences at its 5’ end. In-line barcodes were introduced during second strand synthesis followed by magnetic bead-based purification; the resulting libraries were amplified for up to 15 cycles and re-purified. Quality and quantity of libraries were assessed on an Agilent 2100 Bioanalyzer using the High Sensitivity DNA Kit reagents and protocol (Agilent). The quantified libraries were pooled at a final concentration of 2 nM and sequenced on a  NextSeq 550 System (Illumina), according to manufacturer’s instructions.

first: Panagiota-Efstathia

last: Nikolaou

first: Lara

last: Konijnenberg

first: Ioannis

last: Kostopoulos

first: Gaëtan

last: Pallot

first: Pierre

last: Boucher

first: Marios

last: Miliotis

first: Nikolaos

last: Mylonas

first: Anastasios

last: Georgoulis

first: George

last: Pavlidis

first: Carolien

middle: T

last: Kuster

first: Vince

last: van Reijmersdal

first: Anna

last: Agapaki

last: Orologas

last: Kostomitsopoulos

first: Michael

middle: P

last: Pieper

first: Coert

last: Zuurbier

first: Ignatios

last: Ikonomidis

middle: G

first: Ourania

last: Tsitsilonis

first: Stéphane

last: Germain

first: Robin

last: Nijveldt

first: Niels

last: van Royen

first: Ioanna

last: Andreadou