title: Genome-wide profiling the epigenetic landscape of histone variant TH2B in murine oocytes and pre-implantation embryos [ChIP-seq]

city: Mumbai

first: Priyanka

last: Parte

state: Maharashtra

address: J.M.Street, Parel

department: Gamete Immunobiology

country: India

institute: ICMR-National Institute for Research in Reproductive and Child Health

summary: The testis-specific histone variant of H2B, TH2B, is enriched in the oocytes, sperm and early embryos, with levels decreasing as the embryos differentiate into pre-gastrula stages. However, the involvement of TH2B in epigenetic reprogramming in the preimplantation embryos is largely unknown. The current study mapped the genome-wide epigenetics of TH2B in MII oocytes and early embryos using ultra-low-input ChIP-seq (ULI-ChIP). We demonstrate that TH2B deposition varies greatly between gametes; however, following fertilization, TH2B from gametes is swiftly redistributed in 2-cell embryos. A considerable enrichment of TH2B at the transcription start site (TSS) was identified in sperm chromatin compared to that in oocytes. We also found some overlap between the dynamics of the sperm and the 2 cell, which contain genes related to transcription regulation. Additionally, TH2B was enriched at zygotic genome activation (ZGA) genes. H2A.Z and TH2B were associated, as was discovered in the presence of H2AK119ub1. The correct execution of ZGA and other developmental programs, such as timing the expression or repression of particular genes, may involve TH2B along with H2A.Z, and H2AK119ub1, the latter two regulating the aforementioned processes. Also, early embryos had H3K9me3 deposited at TH2B-bound loci, which is a sign of heterochromatin and functions in regulating retrotransposons. In our study, we found that TH2B was enriched in LTRs. Thus, TH2B chromatin in gametes and preimplantation embryos has distinctive properties, as highlighted by our study, and they also present fresh opportunities to investigate the epigenetic dynamics in murine preimplantation embryos.

overall_design: Owing to the limited cell numbers in oocyte and early embryos (2-cell and 8-cell), TH2B ultra-low-input native chromatin immunoprecipitation and sequencing (ULI-NChIP-seq) was employed. For allele specific alignment of parental TH2B dynamics SNPsplit was used.

first: Isha

last: Singh


title: TRANSCRIPTIONAL AND HORMONAL DEFENCE-GROWTH TRADEOFFS DETERMINE PLANT SURVIVAL AND FITNESS UPON SPIDER MITE INFESTATION

status: Public on Aug 31 2024

city: Madrid

first: Alejandro

last: García

address: Parque Científico y Tecnológico, UPM Campus de Montegancedo, Ctra, M-40, km 38

country: Spain

institute: Universidad Politécnica de Madrid

type: Expression profiling by high throughput sequencing

summary: Tetranychus urticae is an important pest that causes severe damage on a wide variety of plants and crops, leading to a substantial loss of productivity. Previous research has focused on the study of Arabidopsis short-term response to T. urticae, but a comprehensive evaluation of the interaction through whole plant life cycle has not been previously studied. Here, through a physiological trait, transcriptomic and hormonomic evaluation we uncovered the molecular pathways directing the interaction of T. urticae during the complete plant life cycle. Upon mite infestation, plant suffers a process of adaptation to cope the stress and survive, led by the establishment of defence-growth trade-offs in the plant. Transcriptional and hormonal evaluation reveal how plant defence response upon mite perception determines the later growth responses and plant survival. In addition, a delay in plant development with a negative effect on plant fitness was observed, being fitness negatively affected with seed ageing.  Taken together, our findings uncover the dynamics regulating plant-mite interactions and determining plant survival and reproductive success, providing new potential targets for improving plant response. Additionally, trade-offs suppose a cost on final plant fitness, demonstrating the underlying impact of the mite on the establishment of the offspring.

overall_design: Three-week-old Arabidopsis thaliana Col-0 plants were infested with twenty T. urticae female adults per plant. Control plants without mites were carried out in parallel. Each plant was covered by a cylinder that enabled the correct growth and development of the plant while avoiding the mites to escape from infested to control plants. Plant material from control and mite-infested plants was analysed at specific ontological stages of the plant development, coinciding with 30 min, 24 h, 4 d, 7 d, 12 d and 15 d post-mite infestation (dpi).Plant aerial parts were sampled and frozen. Four biological replicates composed by pools of four plants were used for each time point and condition. Frozen material was thoroughly grinded on liquid nitrogen and total RNA was extracted by means of the RNeasy plant mini kit (Qiagen), and a DNase treatment (Qiagen) following manufacturer´s instructions.

last: Garcia

first: Lucia

last: Talavera-Mateo

first: Estrella

middle: M

last: Santamaria


title: Epigenome analysis of nodal marginal zone lymphoma and diffuse large b cell lymphoma

city: Ulm

first: Thomas

last: Barth

state: Baden-Württemberg

address: Albert Einstein Allee 23

department: Pathology

country: Germany

institute: Ulm University

type: Methylation profiling by genome tiling array

summary: Primary nodal marginal B cell lymphoma (nMZoL) is rare and is histologically very variable. Its distinction from nodal diffuse large B cell lymphoma (nDLBCL) is often difficult due to the absence of specific markers for marginal zone lymphomas in general. Using a comprehensive cohort of nMZoL and a control cohort of nDLBCL we conducted a methylome analysis on subgroups of both.

overall_design: Bisulphite converted DNA from 35 nMZoL and 17 nDLBCL samples were amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC BeadChip.

first: Francesca

last: Spada

middle: F

first: Peter

last: Möller


title: RNAseq analysis of human CD14+ monocytes exposed or not to IL4 and ligands of Aryl Hydrocarbon Receptor

city: Paris

first: Elodie

last: Segura

address: 156 rue de Vaugirard

department: INSERM U1151

country: France

institute: INSERM

summary: Human CD14+ monocytes were cultured with or without IL-4, in presence of AhR inhibitor or agonist, for 3h.

first: Alba

last: De Juan


title: Spatiotemporal dynamics of the developing zebrafish enteric nervous system at the whole organ level

status: Public on Aug 30 2024

city: PASADENA

first: Can

last: Li

state: California

address: 1200 E.California Blvd MC156-29, Caltech

department: Biology and Biological Engineering

country: USA

institute: Caltech

summary: Neural crest cells give rise to the neurons of the enteric nervous system (ENS) that innervate the gastrointestinal tract to regulate gut motility. The immense size and distinct subregions of the gut present a challenge to understanding the spatial organization and sequential differentiation of different neuronal subtypes. Here, we profile enteric neurons and progenitors at single cell resolution during zebrafish embryonic and larval development to provide a near complete picture of transcriptional changes that accompany emergence of ENS neurons throughout the gastrointestinal tract. Multiplex spatial RNA transcript analysis reveals the temporal order and distinct localization patterns of neuronal subtypes along the length of the gut. Finally, we show that functional perturbation of select transcription factors Ebf1a, Gata3 and Satb2 alters the cell fate choice, respectively, of inhibitory, excitatory and serotonergic neuronal subtypes in the developing ENS.

overall_design: Cells in the developing ENS of the Tg(Phox2bb:mNeonGreen) zebrafish were isolated by Fluorescence-activated cell sorting (FACS) according to the presence of mNeonGreen signal and used for scRNA-seq experiment.

first: Jase

last: Gehring

first: Marianne

middle: E

last: Bronner


title: Effect of PRMT5 inhibitor on gene expression in MTAP null pancreatic cell lines

city: Thousand Oaks

first: Paul

last: Hughes

state: CA

address: 1 Amgen Center Dr

institute: Amgen Inc

summary: One of the most robust synthetic lethal interactions observed in multiple functional genomic screens has been the dependency on PRMT5 in cancer cells with MTAP deletion. Here we report the discovery of the clinical stage MTA-cooperative PRMT5 inhibitor, AMG 193. AMG 193 preferentially binds PRMT5 in the presence of MTA and has potent biochemical and cellular activity in MTAP-deleted cells across multiple cancer lineages. In vitro, PRMT5 inhibition induces DNA damage, cell cycle arrest, and aberrant alternative mRNA splicing in MTAP-deleted cells. In human cell line and patient-derived xenograft models, AMG 193 induces robust anti-tumor activity and is well tolerated with no impact on normal hematopoietic cell lineages. AMG 193 synergizes with chemotherapies or the KRASG12C inhibitor sotorasib in vitro, and combination treatment in vivo significantly inhibits tumor growth. Finally, AMG 193 is demonstrating promising evidence of clinical activity, including confirmed partial responses in patients with MTAP-deleted solid tumors from an ongoing phase 1 / 2 clinical study.

overall_design: To investigate the mechanism of action of the MTA-cooperative PRMT5 inhibitors, we performed bulk RNA-seq on three MTAP-deleted pancreatic cancer cell lines (BxPC3, MIAPACA2 and PSN1) treated with tool compound AM-9747 and DMSO control for 6 days and assessed the global gene expression alterations induced by PRMT5 inhibition.

first: Katherine

middle: K

last: Slemmons

first: Chun

last: Su


title: Polyclonal interactions overcome fitness barriers in Apc-driven intestinal tumorigenesis

city: Cambridge

first: Elisa

last: Moutin

address: Robinson Way

department: CRUK Cambridge Institute

country: United Kingdom

institute: University of Cambridge

summary: Loss-of-function mutations in the tumour suppressor APC are an initial step in intestinal tumorigenesis. APC-mutant intestinal stem cells (ISCs) outcompete their wild type neighbours through the secretion of Wnt antagonists, accelerating the fixation and subsequent rapid clonal expansion of mutants. Reports of polyclonal intestinal tumours in patients and mouse models appear at odds with this process. Here we combine multicolour lineage tracing with chemical mutagenesis in mice to show that a large proportion of intestinal tumours have a multiancestral origin. Polyclonal tumours retain a structure comprising subclones with distinct Apc mutations and transcriptional states, driven predominantly by differences in KRAS and MYC signalling. These pathway level changes are accompanied by profound cancer stem cell phenotypic differences. Importantly, these findings are confirmed by introducing an oncogenic Kras mutation that results in predominantly monoclonal tumour formation. Further, polyclonal tumours have accelerated growth dynamics suggesting a link between polyclonality and tumour progression. Together, these findings demonstrate the role of interclonal interactions in promoting tumorigenesis through non-cell autonomous pathways dependent on the differential activation of oncogenic pathways between clones.

overall_design: Paired end bulk RNA sequencing was performed on a set of 20 monoclonal tumours, 20 major clones and 20 minor clones that were micro-dissected from tumours in the Apchet + ENU mouse model.

first: Iannish

last: Sadien

first: Shenay

last: Mehmed

first: Sam

last: Adler

first: Sasha

last: Bailey

first: Ashley

last: Sawle

first: Dominique-Laurent

last: Couturier

first: Matthew

last: Eldridge

first: David

last: Adams

first: Richard

last: Kemp

first: Filipe

last: Lourenco

first: Doug

last: Winton


title: Transcriptomic studies in NR4A1 overexpressing MIN6 cells and the effect of EGCG by RNA seq analysis

city: Hyderabad

first: Divya Tej

last: Sowpati

state: Telangana

address: Habsiguda

institute: CSIR Centre for Cellular and Molecular biology

summary: MIN6 cells were transfected with pLenti-NR4A1 plasmid and the expression profile of genes was studied using NGS

overall_design: One set of MIN6 cells in triplicates was used for NR4A1 overexpression and other set in triplicates was used for treatment with EGCG upon NR4A1 overexpression

first: Sheethal

last: Galande

first: Sasikala

last: Mitnala

first: Divya

last: Tej Sowpati

first: Archana

last: Verma


title: RNA analysis of overexpression of a splicing isoform of PD-1

city: Nanjing

first: Shan

last: Gao

address: No. 2 Sipailou, Xuanwu District

country: China

institute: Southeast University

summary: We overexpressed PD-1^28 in Jurkat cells and performed RNA-sequencing (RNA-seq).

overall_design: Targeting the programmed cell death 1 (PD-1) receptor and PD-1 ligand 1 (PD-L1) have achieved some benefits in various cancer types. However, the majorities of cancer patients are less responsive. It is urgent to identify new immune checkpoint (IC) genes and dissect their potential mechanisms. PD-1 receptor maintains peripheral immune tolerance and mediates immune escape of tumor cells as an immune checkpoint.  Whether PD-1 splicing variants mediate resistance to PD-1/ PD-L1 blockade remains largely unknown.We identified an alternative splicing isoform of human PDCD1 with a 28-base pair retention from the start of intron 2, encoding PD-1^28.To explore the potential underlying function of PD-1^28 in T cells and to further gain insights into the downstream signaling pathway, we performed RNA-sequencing (RNA-seq) in PDCD1^28 OE cells.

first: Xuetong

last: Wang

first: Tongfeng

last: Liu

first: Chang

last: Zhang

first: Yinmin

last: Gu

first: Shuwen

last: Cheng

first: Liqiang

last: Duan

first: Jihang

first: Rong

last: Yin

first: Xujie

last: Zhao


title: scRNAseq analysis of mouse draining lymph nodes during Ross River virus or LCMV infection

status: Public on Aug 29 2024

first: Scott

last: Handley

state: MO

address: 660 S Euclid Ave

institute: Washington University in St.Louis

summary: The aim of this study was to compare murine immune responses, particularly CD8+ T cell activation, in acute infection of either Ross River virus (RRV) or lymphocytic choriomeningitis virus (LCMV). LCMV induces a strong CD8+ T cell response that is required for viral clearance. RRV induces CD8+ T cells that only affect viral clearance in certain tissue and do not contribute to prevention of viral RNA persistence in lymphoid and joint-associated tissue. We sequenced cells from the draining lymph node at 5 days post infection to assess activation states of CD8+ T cells at this timepoint.

overall_design: To study immune responses in the draining lymph node after viral infection, with a focus on CD8+ T cell activation, three samples were generated: naive, RRV, and LCMV. Wild type mice each received adoptive transfer of 1 x 10^6 CD8+ T cells from a P14 transgenic mouse (specific for the gp33 epitope naturally found in LCMV and genetically expressed by RRV-gp33) and were then inoculated in the footpad with 10^3 infectious units of RRV-gp33 or LCMV. Five days post infection, draining lymph nodes (popliteal) were harvested from the infected mice and also uninfected wild type and P14 transgenic mice as a naive control. Cells from 7 mice were pooled for each group: naive, RRV, and LCMV. A portion of each sample was enriched for transgenic CD8+ T cells by magnetic bead negative selection and fluorescence-activated cell sorting and added back to the bulk sample at a 1:4 ratio. Libraries were prepared from 20,000 cells from each sample using a 10x Genomics Chromium Single Cell 5' Reagent Kit v2 with TCR enrichment and sequenced.

first: Bullock

middle: B

last: Christopher

first: Wang

last: Leran

first: Ware

middle: C

last: Brian

first: Wagoner

last: Ngan

first: Ohara

middle: A

last: Ray

first: Liu

middle: T

last: Tian-tian

first: Peters

last: Bjoern

first: Murphy

last: Kenneth

first: Handley

last: Scott

first: Morrison

last: Thomas

first: Diamond

middle: S

last: Michael


title: Identification of formononetin as the active compound of CR-SR in hepatocellular carcinoma treatment: An integrated approach combining network pharmacology and weighted gene co-expression networks

city: luzhou

first: chun

last: li

state: sichuan

address: No. 182 Chunhui Road, Longmatan District

institute: the Affiliated Traditional Chinese Medicine  Hospital of Southwest Medical University

summary: Curcumae Rhizoma and Sparganii Rhizoma (CR-SR) is a classic herbal combination for treating HCC in China. Formononetin is the main active ingredient in CR-SR. To understand the pharmacological properties of formononetin, human hepatoma HepG2 cells were stimulated with or without 625μM formononetin for 72 h. Then, total RNA was extracted for gene expression profile analysis.

overall_design: We performed gene expression profiling analysis using data obtained from RNA-seq of HepG2 cells treated with or without  formononetin.

first: Chun

last: Li

first: Yuxin

last: Xie

first: Shaoyu

last: Hu

first: Long

last: Gu

first: Hong

last: Yu

first: Yunke

last: Xu

first: Hongping

last: Shen

first: Yuan

last: Yuan

first: Bangming

last: Pu


title: Gene expression profiling of human neuroblastoma cell line BE(2)-C infected with lentiviruses expressing shRNA to GFP (GFPsh) or human PUS7 (PUS7sh#33) for 6 days

city: Birmingham

first: Han-Fei

last: Ding

state: Alabama

address: WTI 602D, 1824 6th Avenue South

institute: University of Alabama at Birmingham

summary: Microarray gene expression profiling reveals PUS7 knockdown reponsive genes involved in DNA replication stress and repair, cholesterol biosynthesis, amino acid and one-carbon metabolism, and adaptive stress responses.

overall_design: Affymetrix microarray assays were performed according to the manufacturer's directions on total RNA isolated from three independent samples of BE(2)-C cells infected with lentiviruses expressing GFPsh or PUS7sh#33 for 6 days

first: Jane


title: Wild type and EGR2 knock-out mouse alveolar macrophages

city: Debrecen

first: Laszlo

last: Nagy

address: Egyetem ter 1.

country: Hungary

institute: University of Debrecen

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


city: Rehovot

first: Daniella

last: Apelblat

address: Hertzl

department: Neuroscience

country: Israel

institute: Weizmann Institute of Science

summary: Gene expression profiling analysis  of RNA-seq data derived from mice' visual cortex total RNA. Tissues were harvested at specific time points over the day either over a normal 12/12 light/dark cycle, or in a control condition where the mice were also housed in 12/12 conditions but the light did not turn on for the last day, the day of tissue collection.

first: Dahlia

last: Kushinsky

first: Emmanouil

last: Tsivourakis

first: Ori

last: Roethler

first: Mor

last: Breger-Mikulincer

first: Katayun

last: Cohen-Kashi Malina

first: Ivo

last: Spiegel


title: Genetic of multiple primary cancers

city: Liège

first: Maria

middle: Valeria

last: Freire

address: Av. Hippocrate 1/11

department: Human Genetics

country: Belgium

institute: Uliege

summary: Within the frame of inherited cancer predisposition, single gene carriers of pathogenic variants (PVs) have been extensively represented in the literature, whereas the oligogenic coinheritance of heterozygous PVs in cancer-related genes is a poorly studied event. Currently, due to the increment of cancer survivors, the probability of presenting multiple primary cancers (MPC) is higher. This study included MPC patients ≤45 years without known PVs in common cancer predisposition genes. We used whole exome sequencing (WES) of germline and tumoral DNA, chromosomal microarray analysis (CMA) on germline DNA (patient 1-7, and patient 9-10), and karyotype of patient 8to detect variants associated with the disease. The ten patients included in the study presented a mean of 3 cancers per patient. CMA showed two microduplications and one microdeletion, while WES of the germline DNA identified 1-3 single nucleotide variants of potential interest to the disease in each patient and two additional copy number variants. Most of the identified variants were classified as variants of uncertain significance. The mapping of the germline variants into their pathways showed a possible additive effect of these as the cause of the cancer. Twelve somatic samples from 5 patients were available for sequencing. All the germline variants were also present in the somatic samples, while no second hits were identified in the same genes. The sequencing of patients with early cancers, family history and multiple tumors is already a standard of care. However, the growing evidence suggests that patient´s assessment should not stop at the identification of one PV in a cancer predisposition gene.

overall_design: A CMA identifies losses (deletion) or gains (duplication or amplification) between a tested DNA and a reference DNA which can be either the DNA of another individual or a mixture of DNA from several people. The tested DNA is labeled with a nucleotide coupled to a fluorophore (Cyanine-5-dCTP) and the reference DNA with a nucleotide coupled to another fluorophore (Cyanine-3 dCTP). These DNAs are mixed and hybridized on a microchip on which DNA fragments (oligonucleotides in the case of Agilent) corresponding to specific regions of the genome studied are deposited in specific locations. After washing the microchip, the fluorescence is measured in the emission wavelengths corresponding to the 2 fluorophores used. A fluorescence ratio is calculated at the level of each fixed DNA fragment (comparison of the patient DNA/control DNA ratio). Statistical processing of the data is then carried out using dedicated software and the result (existence of a gain or loss of a genomic segment of the patient) will be detected by a variation in the fluorescence intensity ratio beyond of a determined threshold.

middle: V

first: Vincent

last: Bours


title: IL-12/IL-23 blockade reveals patterns of asynchronous inflammation in pyoderma gangrenosum

status: Public on Aug 28 2024

city: Portland

first: Joshua

last: Moreau

state: OR

address: 2720 S Moody Ave.

department: Department of Dermatology

institute: Oregon Health & Science University

summary: Pyoderma Gangrenosum (PG) is a rare and extremely painful neutrophilic dermatosis associated with non-healing cutaneous ulcers affecting 3-10 individuals per million people. The etiology and molecular pathogenetic events of this disease are yet unknown. To investigate how this therapeutic regime shaped the underlying inflammatory response, we performed spatial transcriptomics on lesional biopsies from patients before and after ustekinumab treatment. Our study provides high resolution temporal insights into the inflammatory environment of PG lesional skin following treatment with IL-12/IL-23 blockade in two patients with classic and peristomal PG. This work highlights that while inhibition of representative cytokines of the Th1 and Th17 pathways shows promise as a treatment for PG patients, it does not dampen all active inflammatory pathways.

overall_design: Two PG patients with a samples/skin biopsy before and after ustekinumab administration. All samples were used for the spatial transcriptomic analysis.

first: Alex

middle: G

last: Ortega-Loayza

first: Rashi

last: Yadav


title: Transcriptomic dataset of Phaseolus vulgaris leaves in response to the inoculation of pathogenic Xanthomonas citri pv. fuscans and its type 3 secretion system-defective mutant hrcV.

city: Angers

first: Jerome

last: Verdier

address: Rue Georges Morel

institute: INRAE / IRHS

summary: Common Bacterial Blight (CBB) is a major threat to bean crops caused by Xanthomonas citri pv. fuscans (Xcf). The pathogenicity of Xcf is known to be dependent upon a functional Type 3 Secretion System (T3SS), that allows the injection of numerous Type III Effectors (T3Es) into plant cells. We generated a transcriptomic dataset to compare the response of susceptible and resistant cultivars of Phaseolus vulgaris to the inoculation of the virulent strain Xcf CFBP4885 or its avirulent T3SS-defective hrcV mutant (CFBP13802). This dataset is a valuable resource to investigate the role of T3Es in subverting the cellular functions of bean.

overall_design: Common bean (Phaseolus vulgaris) plants from two cultivars, Flavert (FL) and Vezer (VZ) were grown in growth chamber for 16 days. Then, plant leaves were inoculated with a virulent Xcf strain (CFBP4885), its T3SS defective hrcV mutant (CFBP13802) or water (Mock). Gene expression profiling by RNAseq were performed on the inoculated leaf samples collected 24h or 48h after inoculation from 6 independant plants for each modality. A total of 36 samples were obtained from three biological replicates.

first: Christopher

last: Gihaut

first: Chrystelle

last: Brin

first: Tristan

last: Boureau


title: Gene expression of peripheral blood cells reveals pathways downstream of glucocortoroid receptor antagonism and nab-paclitaxel treatment

city: Chicago

first: Anna

last: Di Rienzo

state: IL

institute: University of Chicago

summary: Provide insights into the mechanisms of paclitaxel and glucocortoroid receptor inhibition in peripheral blood cells.

overall_design:
Microarray profiling of gene expression in peripheral blood cells from each of four patients at baseline, after placebo/nanoparticle albumin-bound paclitaxel (nab-paclitaxel) treatment, and after mifepristone/nab-paclitaxel treatment.
***submitters state that IDAT files are unavailable***

first: Joseph

last: Maranville

first: Rita

last: Nanda

first: Gini

last: Fleming

first: Maxwell

middle: N

last: Skor

first: Suzanne

middle: D

last: Conzen


title: Interferon-responsive neutrophils and macrophages extricate SARS-CoV-2 Omicron critical patients from the nasty fate of sepsis

status: Public on Aug 26 2024

city: Yangpu District, Shanghai

first: Mu

last: Wang

state: Shanghai

address: 800 Xiangyin Road, Shanghai 200433, China

department: Institute of Immunology

institute: National Key Laboratory of Immunity and Inflammation, Institute of Immunology, Second Milltary Medical University

summary: Immune characteristics associated with the SARS-CoV-2 Omicron variant of critical-ill patients are currently unclear. Severe disease has been associated with reconfiguration in the immune activity of the lung. Here we investigated the immune cell characteristics including myeloid cells, lymphocytes and alveolar epithelial cells in the bronchoalveolar lavage fluid (BALF) of 26 critical mechanical ventilation-required patients. The whole alveolar microenvironment of critical Omicron manifested apparent heterogeneous proinflammatory and interferon-stimulated gene (ISG) signature. CXCL5+ macrophages, VCAN+ macrophages, PI3+ neutrophils and CST7+ neutrophils contributed to the most proinflammatory phenotypes and were positively correlated with disease severity whereas ISG15+ neutrophils and CXCL10+ macrophages contributed to the most ISG phenotype and were negatively correlated with disease severity. Lymphocyte subsets were rare manifesting the lymphopenia in the alveoli and these lymphocyte subsets did not express substantial proinflammatory cytokines. Four different epithelial cell subsets were observed in BALF. The percentages of ISG15+ neutrophils were accompanied by more protective alveolar epithelial cells and may serve as the reshaping of exhaustive phenotype for CD4+ T cells. The CXCL10+ macrophages may promote plasmablast/plasma cell survival and activation. This atlas reveals a potential immune landscape in the bronchoalveolar microenvironment for severe and critical Omicron disease.

overall_design: Sort whole living cells in the bronchoalveolar lavage fluid (BALF) from 26 severe and critical Omicron COVID-19 petients.Using Singleron Matrix® Single Cell Processing System and  the GEXSCOPE® Single Cell RNA Library Kits (Singleron) to measure single-cell RNA sequence (3' scRNA-seq) to comprehensively characterize the lung immune mincroenvironment.

first: Wang

last: Mu

first: Li

last: Zhixuan

first: Hou

last: Jin


title: Nonpathogenic E. coli displaying decoy-resistant IL18 mutein enhance the efficacy of cancer immunotherapies

status: Public on Aug 22 2024

city: Boston

first: Michal

last: Sheffer

state: MA

address: 450 Brookline Avenue

department: Medical Oncology

institute: Dana-Farber

summary: The tumor microenvironment can inhibit the efficacy of cancer therapies through mechanisms such as poor trafficking and exhaustion of immune cells. To address this challenge, we exploited the safety, tumor tropism, and ease of genetic manipulation of non-pathogenic Escherichia coli (E. coli) to deliver key immune-activating cytokines to tumors via surface display on the outer membrane of E. coli K-12 DH5a. Non-pathogenic E.coli  expressing murine decoy-resistant IL18 mutein (DR18) induced robust CD8+ T and NK cell-dependent immune responses and suppressed tumor progression in immune-competent colorectal carcinoma and melanoma mouse models. E. coli K-12 DH5a engineered to display human DR18 potently activated mesothelin-targeting CAR NK cells and enhance their trafficking into tumors, which extended survival in an NK cell treatment-resistant mesothelioma xenograft model by enhancing TNFa signaling and upregulating NK activation markers. Our live bacteria-based immunotherapeutic system safely and effectively induces potent anti-tumor responses in treatment-resistant solid tumors, motivating further evaluation of this approach in the clinic.

overall_design: To investigate the effect of human DR18 displaying E.coli on MSLN-CAR NK cells, NK cells isolated from 4 donors were treated for 3 hours with YiaT232-hDR18, E. coli (MOI = 1000), YiaT232, E. coli (MOI = 1000), hDR18 (no bacteria, 100ng/ml) and PBS. We then performed gene expression analysis using RNAseq (2 replicates per RNAseq run).

first: Shaobo

last: Yang

first: Isabel

last: Kaplan

first: Zongqi

first: Mubin

last: Tarannum

first: Khanhlinh

last: Dinh

first: Yasmin

last: Abdulhamid

first: Eden

last: Bobilev

first: Roman

last: Shapiro

first: Rebecca

last: Porter

first: Robert

last: Soiffer

last: Ritz

first: John

last: Koreth

first: Yun

last: Wei

first: Peiru

last: Chen

first: Ke

last: Zhang

first: Valeria

last: Márquez-Pellegrin

first: Shanna

last: Bonanno

first: Neel

last: Joshi

first: Ming

last: Guan

first: Mengdi

first: Deng

last: Li

first: Chiara

last: Bellini

first: Fuguo

last: Liu

first: Jianzhu

first: Catherine

middle: J

last: Wu

first: David

last: Barbie

first: Jiahe

first: Rizwan

last: Romee


title: ZNF143 is a transcriptional regulator of nuclear-encoded mitochondrial genes that acts independently of looping and CTCF

status: Public on Aug 23 2024

city: Amsterdam

first: Mikhail

last: Magnitov

address: Plesmanlaan 121

country: Netherlands

institute: The Netherlands Cancer Institute

summary: Gene expression is orchestrated by transcription factors, which function within the context of a three-dimensional genome. Zinc finger protein 143 (ZNF143/ZFP143) is a transcription factor that has been implicated in both gene activation and chromatin looping. To study the direct consequences of ZNF143/ZFP143 loss, we generated a ZNF143/ZFP143 degron line. Our results show that ZNF143/ZFP143 depletion has no effect on chromatin looping. Systematic analysis of ZNF143/ZFP143 occupancy data revealed that a commonly used antibody cross-reacts with CTCF, leading to its incorrect association with chromatin loops. Nevertheless, ZNF143/ZFP143 specifically activates nuclear-encoded mitochondrial genes and its loss leads to severe mitochondrial dysfunction. Using an in vitro embryo model, we find that ZNF143/ZFP143 is an essential regulator of organismal development. Our results establish ZNF143/ZFP143 as a conserved transcriptional regulator of cell proliferation and differentiation by safeguarding mitochondrial activity.

overall_design: Analysis of ZNF143 and CTCF chromatin occupancy with and without depletion of the ZNF143 transcription factor using the dTAG depletion system in HEK293T cells.

first: Jinhong

last: Dong

first: Kizhakke

last: Sathyan

first: Michael

last: Guertin

first: Elzo

last: de Wit


title: Transcriptional changes after controlled cortical impact in mice

city: Aurora

first: Joseph

middle: Alan

last: Hippensteel

state: Colorado

department: Medicine

institute: University of Colorado Anschutz Medical Campus

summary:
Many extracellular matrix (ECM) changes occur in the brain after traumatic brain injury. This work sought to understand the dynamics of ECM modifications after TBI by comparing RNA transcription between ipsilateral and contralateral brain regions.
Mice underwent controlled cortical impact (with a 2mm depth) using a pneumatic impactor. Seven days later, brain tissue was harvested from the site of injury and from the corresponding contralateral cortex. Microarrays were used to measure gene expression to compare these tissues.

overall_design: Brain tissue ipsilateral (experimental) and contralateral (control) to controlled cortical impact were dissected 7 days after injury. RNA was extracted and gene expression levels were measured using Affymetrix microarrays. There were 5 biological replicates for ipsilateral and contralateral tissue.

first: James

last: Orfila


title: LHP1 and INO80 cooperate with ethylene signaling for warm ambient temperature response by activating specific bivalent genes

city: Austin

first: Zhengyao

last: Shao

state: TX

address: 2506 Speedway, NMS 5.324

department: MBS

institute: University of Texas at Austin

summary: Next-generation sequencing (NGS) has been used to study the differential gene expression in Arabidopsis green seedlings under warm temperature. The goal of this study is to investigate how ethylene signaling and epigenetic modification  are  involved in transcriptional regulation in response to warm temperature.

overall_design: Five-day-old green Arabidopsis seedling mRNA profiles of wild-type and mutants were generated by sequencing, in 2 replications, using Illumina HiSeq 2000

first: Hong

last: Qiao


title: Mice livers: high fat diet versus high fat diet (HF) supplemented with pirfenidone (HFP)

city: Guadalajara

first: Ana

middle: Soledad

last: Sandoval-Rodriguez

state: Jalisco

address: Sierra Mojada 950

department: Molecular Biology and Genomics

country: Mexico

institute: University of Guadalajara

summary: Background & Aims: NASH is characterized by hepatic lipid accumulation and inflammation; and JMJD2B – a histone demethylase - upregulation has been linked to its progression. Pirfenidone is an antifibrotic agent with anti-inflammatory and antioxidant effects recognized to decrease NASH symptoms. Herein, our aim was to investigate PFD-induced epigenetics mechanisms involving JMJD2B and histone modifications in experimental NASH. Methods: Male C57BL/6J mice were fed with normo-diet, or high fat/carbohydrate diet (HF) for 16 weeks.  A HF-subgroup was treated with PFD 300 mg/kg/d from week 8th to the end of protocol. Insulin tolerance test and liver and fat histological and biochemical analyses were carried out. Hepatic transcriptome was examined.  Liver proteins were studied by western blot (WB) and Chromatin immunoprecipitation. In vitro, lipotoxicity was induced in HepG2 cells and proteins were evaluated using WB. Molecular docking was used to explore binding of PFD to JMJD2B. Results: Mice treated with PFD reduced weight gain, epididymal fat and inflammatory nodules, and steatosis in liver tissue, as well as, improved biochemical test. PFD modified the expression of Jmjd2b, Pparg, Fasn and Srebp1, and restored JMJD2B protein and H3K9me3 repressive mark, both in animal and cell models. PFD increased hepatic enrichment of H3K9me2 and H3K9me3 at the promoter region of Fasn and Srebp1, and Pparg. In HepG2 cells, PFD reduced lipid vacuole accumulation. In silico, PFD interacted with JMJD2B catalytic site. Conclusion: PFD is an epigenetic regulator modifying JMJD2B activity, resulting in reduced NASH traits.

overall_design: Two-condition experiment, HF vs HFP sifrom the liver of a mouse. Biological mRNA polled from array.

first: A


title: Aristolochic acid-related renal cell carcinoma exhibits a distinct tumor immune microenvironment and may be more responsive to immune checkpoint blockade

status: Public on Aug 21 2024

city: Singapore

first: Abner

last: Lim

address: 30 Hospital Boulevard

department: Division of Medical Oncology

country: Singapore

institute: National Cancer Center Singapore

summary: We aimed to investigate the immune profile of AA-related RCC and explore its potential role as a predictive biomarker for ICB. Three distinct clusters were found through functional pathway analysis using the NanoString gene expression panel. AA-positive ccRCC comprised the majority of cluster 1 and 3, and the two patients with good response to ICB were grouped to Cluster 3. Cluster 3 exhibited higher tumor inflammation signature (TIS) and immune cell type scores.

overall_design: Tissue samples from two patients with metastatic RCC (mRCC) who responded well to ICB and twenty-two additional tumor-normal tissue paired clear cell renal cell carcinoma (ccRCC)  were profiled for gene expressions using NanoString PanCancer IO360.

first: Po-Hung

last: Lin


title: BCG vaccination alters the epigenetic landscape of progenitor cells in human bone marrow to influence innate immune responses

first: Sarah

last: Sun

state: Illinois

address: 900 E 57th Street


title: Prostate adenocarcinoma transition to neuroendocrine small cell tumors requires ASCL1

city: Dallas

first: Lei

last: Guo

address: 5323 Harry Hines Blvd

department: Department of Population and Data Sciences

institute: University of Texas Southwestern Medical Center

summary: Most patients with prostate adenocarcinoma develop resistance to therapies targeting the androgen receptor (AR). Consequently, a portion of these patients develop AR-indifferent neuroendocrine prostate cancer (NEPC), a rapidly progressing cancer with limited therapies and poor survival outcomes. Current research to understand the transition to NEPC suggests a model of lineage plasticity, where AR-dependent luminal tumors progress towards an AR-independent neuroendocrine (NE) lineage. Genetic analysis of human NEPC showed a frequent loss of RB1 and TP53, and in experimental models, loss of both genes facilitates the transition to a NE lineage. Transcriptomics has shown the lineage transcription factors ASCL1 and NEUROD1 are present in NEPC. In this study, we used genetically engineered mouse models harboring Cre induced loss of Rb1 and Trp53 with MycT58A overexpression (RPM), to model prostate adenocarcinoma with NEPC by establishing prostate organoids that are subsequently used to generate subcutaneous allograft tumors. These tumors are heterogeneous and display adenocarcinoma, squamous, and NE features. ASCL1 and NEUROD1 are expressed within the NE defined regions, with ASCL1 being more predominant than NEUROD1. Genetic loss of ASCL1 in this model does not decrease tumor growth or tumor formation, however, there is a notable decrease in NE identity and an increase in cells with basal-like cell identity. This study provides a new in vivo model to study the progression of prostate cancer to NEPC and establishes the requirement for ASCL1 in driving neuroendocrine differentiation.

overall_design:
Organoids from prostates of Genetically Engineered Mouse Models (GEMMs) harboring Rb1flox/flox, Trp53flox/flox, and CAG-LSLMycT58A (RPM: JAX #029971) or Rb1flox/flox, Trp53flox/flox, and CAG-LSLMycT58A with Ascl1flox/flox (RPMA), infected with lentivirus expressing Cre recombinase, were maintained in culture. RNA was isolated from multiple RPM or RPMA organoids for bulk-RNA sequencing.
Nuclei were isolated from subcutaneous allograft tumors derived from RPM and RPMA prostate organoids and submitted for single-nuclei RNA sequencing.

first: Kathia

last: Rodarte

first: Lin

last: Xu

first: Jane

last: Johnson


title: BCG vaccination impacts the epigenetic landscape of progenitor cells in human bone marrow (scATAC-Seq)

summary: While the Bacille-Calmette-Guérin (BCG) vaccine is used to prevent tuberculosis, it also offers protection against a diverse range of non-mycobacterial infections. However, the underlying protective mechanisms in humans are not yet fully understood. Here, we surveyed at single-cell resolution the gene expression and chromatin landscape of human bone marrow, aspirated before and 90 days after BCG vaccination or placebo administration. We show that BCG vaccination significantly alters both the gene expression and epigenetic profiles of human hematopoietic stem and progenitor cells (HSPCs). Changes in gene expression occur primarily on the most uncommitted stem cells and are reflective of a persistent myeloid bias. In contrast, BCG-induced changes in chromatin accessibility are most prevalent within differentiated progenitor cells at sites influenced by Kruppel-like factor (KLF)/SP and EGR transcription factors (TFs). These TFs are also activated in the most uncommitted stem cells, indicating that activated TFs, which drive persistent changes in HSC gene expression, likely also drive chromatin dynamics appearing within downstream progenitor cells. This perspective contests the prevailing notion that epigenetic modifications linked to innate immune memory transfer directly from stem cells to their differentiated derivatives. Finally, we show that alterations in gene expression and chromatin accessibility in HSPCs due to BCG vaccination were highly correlated (r>0.8) with the IL-1β secretion capacity of paired PBMCs upon secondary immune challenge. Overall, our findings shed light on BCG vaccination's profound and lasting effects on HSPCs and its influence on innate immune responses.

overall_design: Multi-plexed chromatin accessibility profiles of HSPCs isolated from the bone marrow of individuals before and 90 days after either BCG vaccination or placebo

first: Raul

last: Aguirre-Gamboa

first: Charlotte

last: de Bree

first: Joaquin

last: Sanz

first: Anne

last: Dumaine

first: Leo

last: Joosten

first: Maziar

last: Divangahi

first: Mihai

last: Netea

first: Luis

last: Barreiro


title: Transcriptome analysis of neuronal-like cells conversed from U251 cells incubated with SLCDS

status: Public on Aug 17 2024

city: Guangzhou

first: Wenqiang

last: Che

state: Guangdong Province

address: No. 613, West Huangpu Avenue, Tianhe District, Guangzhou

department: Neurosurgery

institute: Jinan university

summary: Glioma, the most common primary tumor in the central nervous system, presents significant challenges in treatment. Researchers are now investigating novel approaches to convert glioma cells into functional neurons. This study explores the conversion process using a combination of small molecule compounds (SLCDS) and examines the underlying mechanisms. Results demonstrate that SLCDS effectively transforms human glioma cells into mature neurons while suppressing markers associated with glioma malignancy. Upregulation of neuronal transcription factors and inhibition of glioma proliferation, angiogenesis, invasion, and metastasis are observed with SLCDS treatment. These findings suggest a promising therapeutic strategy for glioma treatment.

overall_design: Comparative gene expression analysis of RNA-seq data for U251 cells incubated with the small-molecule combination SLCDS for 18 days in three experimental samples and three control samples.

first: Yongjun

last: Yi

first: Ping

first: Xiangyu

last: Wang


title: Mechanical confinement prevents ectopic platelet release

status: Public on Aug 20 2024

city: Strasbourg

first: Catherine

last: Leon

address: 10 rue Spielmann

institute: Inserm

summary: The aim of the project is to identify the genes in megakaryocytes whose expression is modified upon 3D methylcellulose hydrogel culture compared to liquid culture. Megakaryocytes are the precursor cells of platelets. We previously showed that growing megakaryocytes in 3D hydrogel strongly modifies their differentiation and their morphology, being closer to the one in situ. We were thus interested into identifying these mechanobiological pathways induced by the confinement. We found that 3D culture notably upregulated genes related to the Rho GTPase pathway.

overall_design: 4 independent biological replicates: 4 cultures of MK grown either in liquid or in 3D hydrogel

first: Josiane

last: Weber

first: Laurie

last: Ruch

first: Ines

last: Guinard


title: Iron-related gene expression in MSA

city: Toronto

first: Gabor

last: Kovacs

state: Ontario

address: 60 Leonard Ave, Room 6KD414

country: Canada

institute: University of Toronto

summary: Human post-portem Multiple System Atrophy (MSA) and control aged brains were examined for mRNA expression of iron-related genes

overall_design: Globus pallidus, putamen, substantia nigra, and frontal cortex of 7 Multiple System Atrophy (MSA) and 6 age-matched control human brains were examined for mRNA expression of select iron-related genes, using a Nanostring custom nCounter panel.

first: Seojin

last: Lee


title: A PD-1-targeted, receptor-masked IL-2 immunocytokine that engages IL-2Rα strengthens T cell-mediated anti-tumor therapies

city: Tarrytown

first: Qingqing

state: NY

address: 777 Old Saw Mill River Road

institute: Regeneron Pharmaceuticals

summary: IL-2 is a cytokine approved for the treatment of melanoma and renal cell carcinoma and induced complete, durable tumor regression in some patients. However, its broader use in cancer immunotherapy has been limited by severe toxicity. A new generation of IL-2 therapies with decreased binding to IL-2 receptor alpha chain (IL-2Rα), intended to mitigate toxicity and Treg expansion, are being developed. However to date these have had limited clinical success. Here, we demonstrate that the ability to engage IL-2Rα is critical for the anti-tumor activity of a systemic IL-2 therapy. Despite inducing systemic expansion of CD8+ T cells and NK cells over Tregs, an IL-2 mutein with abolished IL-2Rα binding demonstrated limited anti-tumor efficacy compared to wild-type IL-2. Based on these findings, we developed a PD-1-targeted, receptor-masked IL-2 immunocytokine, PD1-IL2Ra-IL2, with attenuated systemic IL-2 activity but maintained the capacity to engage IL-2Rα on PD-1+ T cells. PD1-IL2Ra-IL2 (REGN10597) shows PD-1-targeting-dependent IL-2 activity in vitro and drives selective expansion of tumor-infiltrating PD-1+ CD8+ T cells with vigorous effector profiles in vivo. PD1-IL2Ra-IL2 treated mice displayed no signs of systemic toxicities observed with unmasked IL-2 treatment, yet achieved robust tumor growth control. Finally, we demonstrate that PD1-IL2Ra-IL2 can be effectively combined with several other T cell-mediated immunotherapies (anti-PD-1, CD3 bispecific antibodies, and CAR-T cells) to potentiate antitumor responses. Collectively, these results provide unique insights into the functional mechanism of IL-2 based therapeutics and highlight the therapeutic potential of PD1-IL2Ra-IL2 as a novel targeted, receptor masked, and “α-maintained” IL-2 therapy for cancer treatment.

overall_design: To prepare TIL samples for single cell RNA-seq and TCRseq, human PD-1 knock-in mice were subcutaneously implanted with MC38 tumor cells on both left and right flanks. When tumors were established, mice were randomized and treated on days 10 and 13 post tumor engraftment with the indicated molecules through intraperitoneal injection. On day 16 post tumor engraftment, mice were euthanized, and tumors were dissected and dissociated into single cell suspensions using a tumor isolation kit (Miltenyi 130-096-730). Right and left flank tumors from the same mouse were pooled. Single-cell suspensions were enriched for CD45+ tumor-infiltrating lymphocytes using positive selection using magnetic beads (Miltenyi 130-110-618) to achieve >95% CD45+ purity in live cells as assessed by flow cytometry (Miltenyi 130-110-797).

first: Jiaxi

last: Wu


title: Differential effects of inosine monophosphate dehydrogenase (IMPDH/GuaB) inhibition in Acinetobacter baumannii and Escherichia coli

status: Public on Aug 25 2024

city: South San Francisco

first: Yutian

last: Peng

address: 340 Point San Bruno

institute: Genentech Inc.

summary: Inosine 5’-monophosphate dehydrogenase (IMPDH) catalyzes the rate-limiting step in the de novo guanine biosynthesis and is conserved from humans to bacteria, where it is called GuaB. We developed a series of potent inhibitors that selectively target GuaB over its human homolog. Here we show that these GuaB inhibitors are bactericidal, generate phenotypic signatures that are distinct from other antibiotics, and elicit different time-kill kinetics and regulatory responses in two important gram-negative pathogens: Acinetobacter baumannii and Escherichia coli. Specifically, the GuaB inhibitor G6 rapidly kills A. baumannii but only kills E. coli after 24 hours. After exposure to G6, the expression of genes involved in purine biosynthesis and stress responses change in opposite directions while siderophore biosynthesis is downregulated in both species. Our results suggest that different species respond to GuaB inhibition using distinct regulatory programs, and possibly explain the different bactericidal kinetics upon GuaB inhibition. The comparison highlights opportunities for developing GuaB inhibitors as novel antibiotics.

sample_organism:
Acinetobacter baumannii
Escherichia coli

overall_design: In this study, we examined the transcriptional responses to GuaB-specific inhibitors in A. baumannii and E. coli.

first: Elizabeth

last: Skippington


title: METTL3 governs thymocyte development and thymic involution by regulating ferroptosis

status: Public on Aug 18 2024

city: wuhan

first: huiru

last: jing

address: Donghu Road, No. 115, Wuchang District, Wuhan, Hubei Province

institute: wuhan university

summary: Given its central role in immune aging, identifying regulators of thymic involution is important. While conventional programmed cell death plays a fundamental role in thymocyte development, how cell death pathways contribute to thymic involution remains unclear. In this study, we found that CD4+CD8+ double positive (DP) thymocytes acquired characteristics of senescence in aged mice undergoing thymic involution, while expression of the m6A methyltransferase METTL3 (enriched in DP cells from young mice) decreased with aging. By conditionally deleting METTL3 in T cells, we revealed a critical role for METTL3 in DP cell survival, and in restraining features of aging in DP thymocytes by preventing ferroptosis signaling, through glutathione peroxidase 4 (GPX4). Mechanistically, GPX4 was maintained by METTL3 at the translational level, independent of its methyltransferase activity. Furthermore, we found that pharmacological inhibition of ferroptosis promoted DP cell survival, and attenuate  d features of aging in DP thymocytes. These findings uncover a role for METTL3-regulated ferroptosis in thymic involution, and identify strategies to restore thymic function.

overall_design:
Thymocytes were obtained through flow sorting from 10-week-old young mice, 60-week-old aged mice, 10-week-old WT (Mettl3flox/wt; Cd4Cre) mice, and 10-week-old KO (Mettl3flox/flox; Cd4Cre) mice.

'DN' refers to CD4-CD8- double negative cells, and 'DP' refers to CD4+CD8+ double positive cells. In the thymus development process, T cells go through several developmental stages, including the double negative (DN) and double positive (DP) stages.
The double negative (DN) stage is an early stage in T cell development. At this stage, T cells do not express the CD4 and CD8 surface markers, hence they are called double negative. During this stage, T cells undergo TCR (T cell receptor) gene rearrangement, which is essential for generating a diverse and functional TCR repertoire.
The double positive (DP) stage is an intermediate stage in T cell development. At this stage, T cells express both CD4 and CD8 surface markers, hence they are called double positive. T cells at this stage undergo both positive and negative selection:
Positive Selection: Ensures that T cells can recognize antigen peptides bound to MHC molecules, allowing for effective immune responses against pathogens.
Negative Selection: Eliminates T cells that strongly react to self-antigens, helping to prevent autoimmune diseases and ensuring that the immune system does not attack the body's own tissues.

first: Huiru

last: Jing

first: Jiayu

last: Song

first: Jie

last: Sun

first: Shaojun

last: Su

first: Jin

last: Hu

first: Haojian

last: Zhang

first: Yanmin

last: Bi

first: Bing


title: BCG vaccination impacts the epigenetic landscape of progenitor cells in human bone marrow (scRNA-Seq)

first: Sarah

overall_design: Multi-plexed RNA expression profiles of HSPCs isolated from the bone marrow of individuals before and 90 days after either BCG vaccination or placebo

first: Raul

last: Aguirre-Gamboa

first: Charlotte

last: de Bree

first: Joaquin

last: Sanz

first: Anne

last: Dumaine

first: Leo

last: Joosten

first: Maziar

last: Divangahi

first: Mihai

last: Netea

first: Luis

last: Barreiro


title: Development of an orally bioavailable CDK12/13 degrader and induction of synthetic lethality with AKT pathway inhibition [bulk]

status: Public on Aug 14 2024

city: Ann Arbor

first: Arul

middle: M.

last: Chinnaiyan

state: MICHIGAN

address: 1500 E. Medical Center Dr

institute: University of Michigan

summary: Cyclin-dependent kinases 12 and 13 (CDK12 and CDK13) play pivotal roles in orchestrating transcription elongation, DNA damage response, and maintenance of genomic stability. Aberrant CDK12 expression, homozygous loss, and mutations have been documented in various malignancies. Previous studies have demonstrated CDK12 and 13 are promising therapeutic targets in cancer. In this study, we developed a selective CDK12/13 PROTAC degrader YJ9069, which in a panel of cancer cell lines, affirm its effectiveness in inhibiting cell proliferation in subsets of cancer. CDK12/13 degradation rapidly triggers gene-length dependent transcriptional elongation defects, leading to DNA damage and cell cycle arrest. In vivo, YJ9069 significantly suppresses tumor growth in prostate cancer cell line-derived xenograft (CDX) and patient-derived xenograft (PDX) models. Modifications of YJ9069 yielded a first-in-class orally bioavailable CDK12/13 degrader, YJ1206, which exhibits a comparable efficacy with significantly less toxicity. To identify pathways that may be synthetically lethal upon CDK12/13 degradation, we screened phosphorylation pathway arrays employing cell lines treated with YJ1206.  Interestingly, degradation or genetic knock-down of CDK12/13, led to activation of the Akt pathway. Degradation of CDK12/13 with YJ1206, combined with AKT pathway inhibition with uprosertib, led to a striking synthetic lethal effect in pre-clinical models of prostate cancer.  Taken together, these studies demonstrate that combination CDK12/13 and AKT pathway antagonism induces drug-drug synthetic lethality.

overall_design: The experimental design involved the treatment of VCaP cells with YJ9069 at a concentration of 500 nM for 12 hours, followed by RNA sequencing analysis.

first: Yu

last: Chang

first: Xiaoju

last: Wang

first: Jianzhang

last: Yang

first: Jean

last: Tien

first: Rahul

last: Mannan

first: Gabriel

last: Cruz

first: Yuping

first: Brian

last: Magnuson

first: Somnath

last: Mahapatra

first: Cynthia

first: Zhen

first: Licheng

last: Zhou

first: Kaijie

first: Yang

first: Pujuan

first: Weixue

last: Huang

first: Lanbo

last: Xiao

first: Weihuang

middle: R

last: Liu

first: Fengyun

first: Rui

first: Stephanie

last: Miner

first: Xuhong

last: Cao

first: Yunhui

last: Cheng

first: Rohit

last: Mehra

first: Ke

last: Ding

middle: M


title: Human biallelic deletion involving MAB21L2 regulatory sequences reveals key to structural eye anomalies across species

status: Public on Aug 13 2024

city: Oxford

first: Samuel

last: Clokie

state: Oxfordshire

address: Harcourt Hill Campus

department: Dept of Biological & Medical Science

institute: Oxford Brookes University

summary: Anophthalmia, microphthalmia and coloboma (AMC) comprise a spectrum of developmental eye disorders, accounting for approximately 20% of childhood visual impairment. While non-coding regulatory sequences are increasingly recognised as contributing to disease burden, characterising their impact on gene function and phenotype remains challenging. Furthermore, little is known of the nature and extent of their contribution to AMC phenotypes. We identified two families with variants in or near MAB21L2. The first proband, with microphthalmia and coloboma, had a likely pathogenic missense variant (c.338G>C; p.[Trp113Ser]), segregating within the family. The second individual, presenting with microphthalmia, had an ~113.5kb homozygous deletion 19.38kb upstream of MAB21L2. Modelling the deletion led to transient small lens and coloboma in zebrafish, and microphthalmia and coloboma in Xenopus tropicalis. Conservation analysis identified 15 non-genic conserved elements (CE) within the deleted region, while ChIP-seq data from mouse embryonic stem cells demonstrated one of these (CE14) binds OTX2, a protein with an established role in eye development. Targeted disruption of CE14 in Xenopus tropicalis recapitulated an ocular coloboma phenotype, supporting its role in eye development. Together, our data provides insights into regulatory mechanisms underlying eye development, and highlights the importance of non-coding sequences as a source of genetic diagnoses in AMC.

overall_design: Chip-Seq was performed using antibodies raised against the transcription factors OTX2 and SOX2 in Murine stem cells.

first: Fabiola

last: Ceroni

first: Munevver

last: Cicekdal

first: Richard

last: Holt

first: Elena

last: Sorokina

first: Nicolas

last: Chassaing

first: Sam

first: Thomas

last: Naert

first: Lidiya

last: Talbot

first: Sanaa

last: Muheisen

first: Dorine

last: Bax

first: Yesim

last: Kesim

first: Emma

last: Kivuva

first: Catherine

last: Vincent-Delorme

first: Soeren

last: Lienkamp

first: Julie

last: Plaisancie

first: Elfride

last: De Baere

first: Patrick

last: Calvas

first: Kris

last: Vleminckx

last: Semina

first: Nicola

middle: K

last: Ragge


title: A single-cell analysis of nasal epithelial cells development in domestic pig

status: Public on Aug 12 2024

city: Nanjing

first: Wenqian

last: Wang

address: No.1 Weigang, Xuanwu District

institute: Nanjing Agricultural University

summary: We used single cell RNA sequencing to investigate the heterogeneity of nasal mucosal cells in healthy piglets

overall_design: Two control nasal samples from the healthy piglets

first: Qiu

last: Zhong

first: Jiaxin

last: Qi

first: Qian

last: Yang

first: Ruiling

last: Liu

first: Yunlei

last: Cao

first: Yuchen

last: Li


title: Nervonic acid improves the fat transplantation by promoting adipogenesis and angiogenesis

city: Seoul

first: Jae Hoon

last: Song

address: 201 Songpa-daero, Songpa-gu

country: South Korea

institute: ENCell Co., Ltd.

summary: Adipose tissue engraftment has become a promising strategy for reconstruction in the field of regenerative surgery. However, there are significant challenges such as reabsorption of 50–90% of the transplanted fat or cyst formation due to fat necrosis after fat transplantation. Thus, identifying novel materials or methods to improve the engraftment efficiency is crucial. Here, we investigated the effects of nervonic acid (NA) on adipogenesis and fat transplantation and its underlying mechanisms. We found that NA treatment accelerated adipogenesis through activation of the AKT/mTOR pathway and inhibition of Wnt signaling. Additionally, NA treatment enriched the expression of AKT-mTOR signaling-related genes and increased the expression of genes involved in angiogenesis and fat differentiation. Furthermore, NA effectively improved the outcome of adipose tissue engraftment. Treatment of NA reduced the resorption of transplanted fat and increased the proportion of perilipin-1+ adipocytes with a lower portion of vacuoles. Moreover, the NA-treated group showed decreased pro-inflammatory response and had more CD31+ vessel structures, which were relatively evenly distributed among viable adipocytes, facilitating the successful engraftment. In summary, we demonstrated that NA not only stimulates adipogenesis by regulating in human MSCs but improve the outcome of fat transplantation by reducing inflammation and stimulating angiogenesis. We suggest that NA could be an adjuvant strategy to support the fat transfer in regenerative surgery.

overall_design: To investigate the function of nervonic acid in adipogenic differentiation of human MSCs, MSCs differentiated in adipogenic condition with nervonic acid or without nervonic acid and relative gene expression profiles were analyzed.

first: Jae

middle: H

first: Sun

last: Kim

first: Soojin

last: Kwon

first: Su

middle: Y

last: Jeon

first: Sang

middle: E

last: Park

first: Suk-joo

last: Choi

first: Soo-young

last: Oh

first: Hong

middle: B

first: Jong

middle: W

last: Chang


title: Development of an orally bioavailable CDK12/13 degrader and induction of synthetic lethality with AKT pathway inhibition [nascent]

first: Arul

last: Chinnaiyan

overall_design: To investigate the cooperative function CDK12/13 in the regulation of gene expression, we performed Nascent RNA-seq in Vcap cells with the treatment of CDK12/13 degrader YJ9069 (500 nM) at various time points.

first: Yu

first: Xiaoju

first: Jianzhang

first: Jean

middle: C

last: Tien

first: Rahul

last: Mannan

first: Gabriel

last: Cruz

first: Yuping

last: Zhang

first: Brian

last: Magnuson

first: Somnath

last: Mahapatra

first: Cynthia

first: Zhen

first: Licheng

last: Zhou

first: Kaijie

first: Yang

first: Pujuan

first: Weixue

last: Huang

first: Lanbo

last: Xiao

first: Weihuang

first: Fengyun

last: Su

first: Rui

first: Stephanie

last: Miner

first: Xuhong

first: Yunhui

last: Cheng

first: Rohit

last: Mehra

first: Ke

last: Ding


title: Amino Acids as a Major Carbon Source for Hepatic Lipogenesis

city: Zhongshan

first: Yilie

last: Liao

state: China

address: Tsuihang New District

institute: Zhongshan Institute for Drug Discovery

summary: Through a series of epidemiological analyses, flux analyses, and genetic interventions, we identified amino acid as a primary carbon source in hepatic de novo lipogenesis (DNL), and revealed the vital role of dietary protein in non-alcoholic fatty liver disease (NAFLD). To evaluate whether this finding can be applied to treat hepatic steatosis, we implemented protein restriction in obese mice. A short-term low-protein diet (5% kcal protein intake) not only reduced food intake and body weight gain of mice but also ameliorated hepatic lipid accumulation and liver damage. Here, we conducted RNA sequencing for liver samples from these mice and demonstrated a global downregulation of lipogenic genes. Together, this study uncovers a significant role of amino acids in hepatic DNL, and suggests a previously unappreciated target for NAFLD.

overall_design: To investigate the effect of protein restriction on liver metabolism and hepatic steatosis, we fed 8-week-old genetic obese (ob/ob) male mice with either standard protein diet (SPD, 25% kcal protein) or low protein diet (LPD, 5% kcal protein) for 3 weeks. The liver samples were then harvested and snap-frozen in liquid nitrogen for subsequent transcriptomic analysis.

first: Qishan

last: Chen

first: Weiping

last: Han

first: Suneng

last: Fu


title: Regulation of the hematopoietic stem cell pool by c-Kit-associated trogocytosis

status: Public on Aug 09 2024

city: Madison

first: Xin

last: GAO

state: WI

address: 1111 Highland Ave

department: Pathology and Laboratory Medicine

institute: University of Wisconsin-Madison

summary: Hematopoietic stem cells (HSCs) are routinely mobilized from the bone marrow (BM) to the blood circulation for clinical transplantation. However, the mechanisms by which HSCs exit the marrow are not well understood. We found that most BM HSCs present the macrophage marker F4/80 on their cell surface. Upon enforced mobilization induced by granulocyte-colony-stimulating factor or CXCR4 antagonist, F4/80+ HSCs were selectively retained in the BM while F4/80— HSCs were mobilized to the blood. Remarkably, F4/80 was acquired through direct transfer via c-Kit-mediated trogocytosis from BM resident macrophages in mouse and human settings. Our study uncovers a function for BM-resident macrophages in controlling the HSC mobilizable pool, and identifies mechanisms that may be used to improve HSC yield for transplantation.

overall_design: mRNA profiles of sorted F4/80 negative and F4/80 positive hematopoietic stem cells from bone marrow in triplicates

last: Gao

first: Britta

last: Will

first: Ulrich

last: Steidl

first: Paul

last: Frenette


title: Gene regulatory divergence in spermatogenesis between mouse and opossum

status: Public on Aug 16 2024

city: New Haven

first: Bluma

last: Lesch

state: CT

address: 333 Cedar Street

department: Genetics

institute: Yale University

summary: Mammalian spermatogenesis is a highly stereotyped and conserved developmental process that is essential for fitness. At the same time, gene expression in spermatogenic cells is rapidly evolving. This combination of features has been suggested to drive rapid fixation of new gene expression patterns. Using a high-resolution dataset comprising bulk and single-cell data from juvenile and adult testes of the opossum Monodelphis domestica, a model marsupial, we define the developmental timing of the spermatogenic first wave in opossum and delineate conserved and divergent gene expression programs across the placental-marsupial split by comparison to equivalent data from mouse, a model placental mammal. Epigenomic data confirmed divergent regulation at the level of transcription, and comparison to data from four additional amniote species identified hundreds of genes with evidence of rapid fixation of expression. This gene set encompasses known and previously undescribed regulators of spermatogenic development.

sample_organism:
Mus musculus
Monodelphis domestica

platform_organism:
Mus musculus
Monodelphis domestica

overall_design: scRNA-seq (10x genomics) and bulk RNA-seq from testes of mouse (Mus musculus) and opossum (Monodelphis domestica)

first: Kira

middle: L

last: Marshall


title: Function and Mechanism of NAT10-mediated N4-acetylcytidine modification in osteosarcoma [mRNA-seq]

first: Yutong

last: Zou

address: No.58, Zhongshan Rd.2

institute: The First Affiliated Hospital of Sun Yat-sen University

summary: Despite the advance in diagnosis and treatment, the prognosis of osteosarcoma patients remains unsatisfied. Therefore, it is imperative to identify novel therapeutic targets for osteosarcoma. Through RNA sequencing (RNA-seq) combined with functional screening, N4-acetylcytidine (ac4C) acetyltransferase 10 (NAT10) was identified as a candidate therapeutic target in osteosarcoma. Upregulated NAT10 correlated with poor prognosis in osteosarcoma patients and NAT10 knockout drastically inhibited cell proliferation and metastasis in vitro and in vivo. NAT10 enhanced mRNA stability and translation efficiency of activating transcription factor 4 (ATF4) through ac4C modification. ATF4 induced transcription of asparagine synthetase (ASNS), which catalyzes asparagine (Asn) biosynthesis. Asn promote protein and nucleotide synthesis, facilitating osteosarcoma progression. Overexpression of ATF4, ASNS or supplementation of asparagine rescue the tumor inhibitory effect of NAT10 knockout.

overall_design: RNA-Seq was used to study the differentially expressed genes in the NAT10 knockout and control cells.

first: Xianbiao

last: Xie


title: Integrative analysis of long isoform sequencing and functional data identifies distinct cortical layer neuronal subtypes derived from human iPSC

status: Public on Aug 08 2024

city: Dubai

first: Muhammad

last: Kumail

state: Dubai

address: Al Razi road

department: CATG

country: United Arab Emirates

institute: Mohammad Bin Rashid University

summary: Generation of human induced pluripotent stem cells (iPSCs) through reprogramming was a transformational change in the field of regenerative medicine that led to new possibilities for drug discovery and cell replacement therapy. Several protocols have been established to differentiate hiPSCs into neuronal lineages. However, low differentiation efficiency is one of the major drawbacks of these approaches. Here, we compared the efficiency of two methods of neuronal differentiation from iPSCs cultured in two different culture media, StemFlex Medium (SFM) and Essential 8 Medium (E8M). The results indicated that iPSCs cultured in E8M efficiently generated different types of neurons in a shorter time and without the growth of undifferentiated nonneuronal cells in the culture as compared with those generated from iPSCs in SFM. Furthermore, these neurons were validated as functional units immunocytochemically by confirming the expression of mature neuronal markers (i.e., NeuN, b tubulin, and Synapsin I) and whole cell patch-clamp recordings. Long-read single-cell RNA sequencing confirms the presence of upper and deep layer cortical layer excitatory and inhibitory neuronal subtypes in addition to small populations of GABAergic neurons in day 30 neuronal cultures. Pathway analysis in

overall_design: Time-efficient and robust approach of neuronal differentiation leading to the generation of functional brain units, cortical layer neurons. iPSCs cultured in Essential 8 media (E8M) analyzed using scRNA-seq

first: Zehra

last: Binte

first: Mohammed

last: Nesrin

first: Farhat

last: Ahmad

first: Uddin

last: Mohammed


title: Adipocyte associated glucocorticoid signaling regulates normal fibroblast function which is lost in inflammatory arthritis [synovium_scRNA-seq]

city: Boston

first: Heather

last: Faust

address: 60 Fenwood Road

institute: Brigham and Women's Hopsital

summary: Fibroblasts play critical roles in tissue homeostasis, but in pathologic states can drive fibrosis, inflammation, and tissue destruction. In the joint synovium, fibroblasts provide homeostatic maintenance and lubrication. Little is known about what regulates the homeostatic functions of fibroblasts in healthy conditions. We performed RNA sequencing of healthy human synovial tissue and identified a fibroblast gene expression program characterized by enhanced fatty acid metabolism and lipid transport. We found that fat-conditioned media reproduces key aspects of the lipid-related gene signature in cultured fibroblasts. Fractionation and mass spectrometry identified cortisol in driving the healthy fibroblast phenotype, confirmed using glucocorticoid receptor gene (NR3C1) deleted cells. Depletion of synovial adipocytes in mice resulted in loss of the healthy fibroblast phenotype and revealed adipocytes as a major contributor to active cortisol generation via Hsd11β1 expression. Cortisol signaling in fibroblasts mitigated matrix remodeling induced by TNFα- and TGFβ, while stimulation with these cytokines repressed cortisol signaling and adipogenesis. Together, these findings demonstrate the importance of adipocytes and cortisol signaling in driving the healthy synovial fibroblast state that is lost in disease.

overall_design:
Comparative gene expression profiling analysis of single cell RNA-seq data for healthy human synovial tissue live cells.
*** Submitter declares that human raw data are being deposited to dbGaP***

first: Michael

last: Brenner


title: Adipocyte associated glucocorticoid signaling regulates normal fibroblast function which is lost in inflammatory arthritis

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

overall_design: Refer to individual Series


title: Function and Mechanism of NAT10-mediated N4-acetylcytidine modification in osteosarcoma [RIP-seq]

overall_design: Acetylated RNA immunoprecipitation sequencing(acRIP-Seq) was used to analysis the N4-acetylcytidine modification of mRNA in the NAT10 knockout and control osteosarcoma cells.


title: Genetic and pharmacological targeting of hepatic oxalate overproduction ameliorates metabolic dysfunction-associated steatohepatitis

status: Public on Aug 07 2024

city: Shreveport

first: Sandeep

last: Das

state: LA

address: 1501 Kings Highway

department: Pathology

institute: LSU Health Shreveport

type: Methylation profiling by high throughput sequencing

summary: Metabolic dysfunction-associated steatohepatitis (MASH) is on the rise, and with limited pharmacological therapy available, identification of new metabolic targets is urgently needed. Oxalate is a terminal metabolite produced from glyoxylate by lactate dehydrogenase (LDHA). The liver-specific alanine-glyoxylate aminotransferase (AGXT) detoxifies glyoxylate, preventing oxalate accumulation. We report that AGXT is suppressed and LDHA is activated in livers from patients and mice with MASH, leading to oxalate overproduction. In turn, oxalate promotes steatosis in hepatocytes by inhibiting peroxisome proliferator activated receptor-alpha (PPARα) transcription and fatty acid β-oxidation (FAO), and induces monocyte chemotaxis via C-C motif chemokine ligand 2. In male mice with diet-induced MASH, blocking oxalate overproduction through hepatocyte-specific AGXT overexpression or pharmacological inhibition of LDHA potently lower steatosis, inflammation, and fibrosis by inducing PPARα-driven FAO, and suppressing monocyte chemotaxis, nuclear factor-kappaB and transforming growth factor-beta targets. These findings highlight hepatic oxalate overproduction as a new target for the treatment of MASH.

overall_design: The genome-wide analysis of DNA methylation in CpG islands through unbiased reduced representation bisulfite sequencing (RRBS) between control and MASH condition in either chow diet or MASH diet fed mice for 24 weeks.

first: Sumit

last: Anand

first: Oren

last: Rom


title: An sRNA overexpression library reveals AbnZ as a negative regulator of an essential translocation module in Caulobacter crescentus

status: Public on Aug 02 2024

city: Würzburg

first: Manuel

last: Velasco Gomariz

address: Josef-Schneider-Straße 2/D15

institute: Helmholtz Institute for RNA-based Infection Research (HIRI)

summary: Small RNAs (sRNAs) play a crucial role in modulating target gene expression through short base-pairing interactions and serve as integral components of many stress response pathways and regulatory circuits in bacteria. Transcriptome analyses have facilitated the annotation of dozens of sRNA candidates in the ubiquitous environmental model bacterium Caulobacter crescentus, but their physiological functions have not been systematically investigated so far. To address this gap, we have established CauloSOEP, a multi-copy plasmid library of C. crescentus sRNAs, which can be studied in a chosen genetic background and under select conditions. Demonstrating the power of CauloSOEP, we identified sRNA AbnZ to impair cell viability and morphology. AbnZ is processed from the 3' end of the polycistronic abn mRNA encoding the tripartite envelope-spanning efflux pump AcrAB-NodT. A combinatorial approach revealed the essential membrane translocation module TamAB as a target of AbnZ, implying that growth inhibition by AbnZ is linked to repression of this system.

overall_design: Transcriptomic of Caulobacter NA100 ΔvanAB pBVMCS6-EV (KFS-96) & Caulobacter NA100 ΔvanAB pBVMCS6-AbnZ (KFS-1421) after 15´ of addition on 500 µM Vanillate to induce the sRNA. Cells were growing in PYE medium at 30°C until they reached OD660=0.4. 500 µM Vanillate was added to the cells and after 15´ samples were collected for RNAprep.

first: Kathrin

middle: S

last: Fröhlich


title: Human norovirus replicates in macrophages migrating to intestinal tissues and changes their transcriptional profile

city: Leuven

first: Joana

last: Rocha-Pereira

address: Herestraat 49 box 1043

department: Department of Microbiology, Immunology, and Transplantation

institute: KU Leuven, Rega Institute

summary:
Human noroviruses (HuNoVs) are a major cause of diarrheal disease, yet critical aspects of their biology, including cellular tropism, remain unclear. While research traditionally focused on the intestinal epithelium, the hypothesis that HuNoV infects macrophages has been recurrently discussed and is investigated here by a zebrafish larval model.
Our study reveals that HuNoV capsid proteins and double-stranded RNA colocalize within intestinal macrophages of infected zebrafish larvae, while the negative-strand RNA intermediate was detected within FACS-sorted macrophages. Flow cytometry confirms viral replication within these macrophages, constituting ~9% of HuNoV?s host cells. Single-cell RNA-sequencing reaffirms their role in viral replication, as all three open reading frames were mapped to individual macrophages. Yet, macrophages were not required for productive infection given the limited changes in viral loads upon their absence. Identifying macrophages as host cells prompts a reevaluation of their role in HuNoV pathogenesis, offering new directions for understanding and controlling this infection.

overall_design: Intestines of uninfected and HuNoV-infected zebrafish larvae were dissected and subjected to the preparation of a single-cell suspension that was analyzed using scRNAseq. Subsequently, an additional sample was analyzed on FACS-sorted macrophages of HuNoV-infected zebrafish larvae.

first: Emma

last: Roux

first: Reegan

last: Willms

first: Jana

last: Van Dycke

first: Lore

last: Van Espen

first: Geert

last: Schoofs

first: Jelle

last: Matthijnssens

first: Johan

last: Neyts

first: Peter

last: de Witte

first: Edan

last: Foley

last: Rocha-Perereira


title: An sRNA overexpression library reveals AbnZ as a negative regulator of an essential translocation module in Caulobacter crescentus  [RNA-Seq 2]

overall_design: Transcriptomic of Caulobacter NA100 ΔvanAB Hfq-3xFLAG pBVMCS6-AbnZ (KFS-1907) after 15´ of addition on 500 µM Vanillate to induce the sRNA followed by pull-down with AbnZ DNA-antisense oligos (plus) or scrambled oligos (minus). Cells were growing in PYE medium at 30°C until they reached OD660=0.4. 500 µM Vanillate was added to the cells and after 15´ samples were collected for RNAprep & pull-down


title: Generating iAstrocytes from hiPSCs by combining low-density passaging of NPCs and NFIA transdifferentiation

status: Public on Aug 01 2024

city: New York

first: Andrew

middle: A

last: Sproul

address: 650 West 168th Street

institute: Columbia Univeristy

summary: Astrocytes are key regulators of CNS homeostasis and their dysfunction is implicated in neurological and neurodegenerative disorders. Here, we describe a two-step protocol to generate astrocytes from iPSCs using a bankable neural progenitor cell (NPC) intermediate, followed by low-density passaging and overexpression of the gliogenic transcription factor NFIA. A bankable NPC intermediates allows for facile differentiation into both purified neuronal and astrocyte cell types in parallel from the same genetic background, depending on the experimental needs. This article presents a protocol to generate NPCs from iPSCs (Basic Protocol 1), which are then differentiated into iPSC-derived astrocytes, termed iAstrocytes (Basic Protocol 2). The resulting iAstrocytes express key markers of astrocyte identity at transcript and protein levels by bulk RNA-seq and immunocytochemistry respectively. Additionally, they respond to the inflammatory stimuli poly(I:C) and generate waves of calcium activity in response to either physical activity or addition of ATP. Our approach offers a simple and robust method to generate and characterize human astrocytes which can be used to model human disease affecting this cell type.

overall_design: Describing new differentiation protocol for Astrocytes from IPSC. FA10 NPC No NFIA (1-3) is previous described differentiation protocol. FA10 NPC NFIA (1-3) is new protocol (Basic Protocol 1) and IMR90-iPSC-NFIA-SOX9 (1-3) is another protocol we generated for generating iAstrocytes from IPS cell lines.

first: Patrick

last: Bosco

first: Ugur

last: Akcan

first: Damian

last: Williams

first: Heather

last: Buchanan

first: Dritan

last: Agalliu

first: Adnrew


title: HDAC1 restricts fungal-induced Th17 polarization to restrain tissue damage [Kidney RNA-seq]

city: Vienna

first: Philipp

last: Penninger

address: Dr. Bohr-Gasse 9

country: Austria

institute: Medical University of Vienna

summary: Epigenetic mechanisms contribute to shaping many aspects of adaptive immunity, including T cell lineage functions in anti-infective surveillance. Histone deacetylases (HDAC) control T cell polarization but a role in fungal-specific T cell responses remains poorly understood. Here we show that CD4+ T cells are an integral part of the adaptive immune defense against invasive fungal infections. Temporally-resolved in vivo transcriptional profiles of splenic Th cells from infected mice harboring a CD4+-specific ablation of HDAC1 reveals its critical role in limiting T cell polarization towards Th17 at the expense of Th1-lineage commitment. Mechanistically, HDAC1 restricts expression of the cytokine receptors gp130 and TGFbRII on the T cell surface thus limiting Stat3 and Smad2/3 signaling in a fungal-specific manner. Controlled release of Th17-associated cytokines IL-17A and GM-CSF is vital to minimize epithelial apoptotic processes in renal tubular epithelial cells (RTECs) in vitro as well as during systemic infections in vivo. Consequently, protecting the host from excessive organ pathology, loss of kidney functionality and limiting fungal burdens, thus reducing sepsis-induced death during fungal infections. Collectively, this work shows that HDAC1 controls T cell lineage polarization, thus playing a critical role in the antifungal immune defense and infection outcome.

overall_design: Mouse line harbouring CD4+ T cells with conditional deleted HDAC1 (KO mice) or WT CD4+ T cells were systemically infected (i.v.) with 1*10^4 C. albicans yeast cells per 21,5g body weight. Kidneys from uninfected and 7-day infected animals were isolated for whole-organ RNAseq to compare genotype-specific infection responses.

first: Karl

last: Kuchler


title: Cohesin chromatin loop formation by an extrinsic motor

status: Public on Aug 04 2024

city: London

first: Thomas

last: Guerin

address: nw1 1at, 1 Midland Road

institute: The Francis Crick Institute

summary:
This SuperSeries is composed of the SubSeries listed below

GSE248280 contains ChIP-Seq input (IN) and IP (IP) data.
GSE248281 contains micro-C in the mcool format.
N1 and N2 represent repeats 1 and 2. For ChIP, Merged represent the Merged IP

Merged mcool files are in supplementary files of the serie GSE248280

sample_organism:
Saccharomyces cerevisiae
Nakaseomyces glabratus


title: Selective Utilisation of Glucose Metabolism Guides Mammalian Gastrulation

first: Jenna

middle: Michal

last: Bergmann

state: Connecticut

address: 333 Cedar Street, I-168

summary: The prevailing dogma for morphological patterning in developing organisms argues that the combined inputs of transcription factor networks and signalling morphogens generate spatially and temporally distinct expression patterns1. However, recent work spanning multiple disciplines has highlighted the role of metabolic pathways as developmental regulators2-7, independent of energy production and growth. Yet, the mechanistic role of nutrient utilisation in instructing cellular programs to shape the in vivo developing mammalian embryo is unknown. Here, we discover two spatially-resolved waves of glucose metabolism in a cell type- and stage-specific manner in mammalian gastrulation by using quantitative live-imaging of developing mouse embryos at single-cell resolution, stem cell models, and embryo-derived tissue explants.  By selectively inhibiting key enzymes involved in different branches of glucose metabolism, we identify that the first finely-tuned spatiotemporal wave of glucose metabolism occurs through the hexosamine biosynthetic pathway to drive fate acquisition in the epiblast, while the second wave uses glycolysis to support mesoderm migration and lateral expansion. Furthermore, we demonstrate that glucose exerts its influence on these developmental processes through cell signalling pathways, with distinct mechanisms connecting glucose with the ERK activity in each wave. Our findings underscore the integral role of cellular metabolism in guiding cell fate and specialized functions during development, interfacing with genetic mechanisms and morphogenic gradients. This study provides valuable insights into various developmental contexts including embryonic lethality, congenital disease, and cancer, challenging previous notions about the generic and housekeeping nature of cellular metabolism.

overall_design: We isolated bone fide mesoderm explants from E7.25/5 LS/no bud stage mouse embryos of TCF/Lef:H2B-GFP reporter mice, and cultured them for 24h ex situ. Explants We then performed RNA-sequencing on mesoderm explants treated with PD or YZ9 ex situ.

first: Dominica

last: Cao

first: Berna

last: Sozen


title: IL-22 resolves MASLD via enterocyte STAT3 restoration of diet perturbed intestinal homeostasis

city: San Diego

first: Peng

last: Zhang

state: CA

address: 9500 Gilman Dr.

institute: UCSD

sample_organism:
Mus musculus
feces metagenome

platform_organism:
Mus musculus
feces metagenome


title: IL-22 resolves MASLD via enterocyte STAT3 restoration of diet perturbed intestinal homeostasis [16s rDNA-seq]

summary: IL22 induces antimicrobial peptides which influnce microbiota. We used 16s rRNA gene sequencing (16s DNA-seq) to analyze the microbiota with Fc or IL-22Fc treatment.

overall_design: Male Il22ra1f/f, Il22ra1ΔHep, Il22ra1ΔIEC and C57BL/6 mice with Abx (10 weeks old) were fed with HFD+30% fructose water for 16 weeks, and were intraperitoneally (i.p.) injected with 10μg mFc or rmIL-22-Fc /mouse every 3 days for last 4 weeks. We collected the colon feces from above mice were subjected to 16s DNA sequencing.

first: Suling

last: Zeng


title: PTK6 regulates secretory cell production and innate immunity in a sex-dependent manner in the intestine

city: Chicago

first: Angela

last: Tyner

address: 900 S Ashland Ave

institute: University of Illinois at Chicago

summary: PTK6 regulates regeneration and repair of the intestinal epithelium.  Analysis of publicly available datasets showed Ptk6 is upregulated in tuft cells upon activation of type 2 immunity. We found that disruption of Ptk6 influences gene expression involved in intestinal immune responses. Administration of succinate, which mimics infection and activates tuft cells, revealed PTK6-dependent activation of innate immune responses in male but not female mice. In contrast to wild type and Ptk6-/- female mice, Ptk6-/- male mice do not upregulate innate immunity or differentiation of secretory cell lineages following succinate treatment. Mechanistically, we found PTK6 regulates IL-25 expression and its effector functions, which are required for activation of type 2 innate immunity only in male mice. In patients with Crohn’s disease, PTK6 is upregulated in tuft cells in noninflamed regions of intestine. These data highlight roles for PTK6 in regulating sex differences in intestinal innate immunity and provide insight into the regulation of IL-25.

overall_design: Male and female wild type and Ptk6-/- mice were given 100 mM succinate in drinking water for 7 days. Total RNA was isolated from terminal jejunums using TRIzol. Poly(A) RNA was prepared from total RNA and analyzed using RNA-seq.

first: Katarina

last: Vlajic


title: Dopamine-regulated biomarkers in peripheral blood of HIV+ Methamphetamine users

status: Public on Jul 31 2024

first: Maria

middle: Cecilia

last: Marcondes

address: 3525 John Hopkins Ct. #200

institute: San Diego Biomedical Research Institute

summary:
HIV and Methamphetamine study - Translational Methamphetamine AIDS Research Center - Dopamine-regulated inflammatory biomarkers
A digital transcript panel was custom-made based on Hs_NeuroPath_v1 (Nanostring) to accommodate dopamine-regulated inflammatory genes that were previously identified in vitro, and hypothesized to cluster HIV+ Methamphetamine users.

overall_design: Specimens were peripheral blood leukocytes isolated from participants that included adults enrolled by NIH-funded studies at the University of California San Diego’s HIV Neurobehavioral Research Program (HNRP) and Translational Methamphetamine Research Center (TMARC) under informed consent and approved protocols. The subset of PWH and PWoH selected for this study were by design males, between 35 – 44 years old, due to cohort characteristics and to increase statistical power. The participants were divided based on HIV serostatus (HIV+/-) and Meth use (METH+/-). METH+ was defined as meeting lifetime DSM-IV criteria for methamphetamine use or dependence, and METH dependence or abuse within 18 months (LT Methamphetamine Dx), with 8.2% urine toxicology positive/current METH users. A cross-sectional design assembled the following groups: HIV-METH- , HIV+METH- , HIV-METH+ , and HIV+METH+. Exclusion criteria were a history of non-HIV-related neurological, medical, or psychiatric disorders that affect brain function (e.g., schizophrenia, traumatic brain injury, epilepsy), learning disabilities, or dementia.

first: Liana

last: Basova


title: Neuronal SLC39A8 deficiency impairs cerebellar development and function by dysregulating brain Mn homeostasis

city: Ann Arbor

first: Shigeki

last: Iwase

address: 1241 E. Catherine St.

institute: University of Michigan

summary: RNAseq was performed using cerebellum tissue of WT and neuron-specific slc39a8-KO mice

overall_design: Three mice per genotype

first: Young

last: Seo


title: Expression profiles of lncRNAs, miRNAs, and mRNAs and interaction analysis indicate their potential involvement during testicular fusion in Spodoptera litura

city: Guangzhou

first: Chen

last: Yaqing

state: Guangdong

address: South China Normal University

department: School of Life Sciences

institute: South China Normal University

type: Non-coding RNA profiling by high throughput sequencing

summary: Spodoptera litura (Lepidoptera: Noctuidae), which has a strong and rapid reproductive capacity, is a polyphagous pest with great destruction to many crops, causing economic loss to agricultural production worldwide. Its two testes fuse into a single one during the larva-to-pupa metamorphosis, which was favorable to the sperm development. However the mechanism of testicular fusion is still not fully understood. In this study, we analyzed long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) in the testes by high-throughout RNA-seq to explore the mechanism of testicular fusion in S. litura. In total, 2,150 lncRNAs, 2,742 target mRNAs and 347 miRNAs were identified in the testes from 4-day-old sixth instar larvae (L6D4) (before fusion), 6-day-old sixth instar larvae (L6D6, prepupae) (on fusing) and 0-day-old pupae (P0D) (after fusion). It was found that a large number of DElncRNAs, DEmRNAs and a little number of DEmiRNAs were up-regulated from L6D4 to L6D6 when the testes began to fuse, a little number of DElncRNAs, DEmRNAs and a large number of DEmiRNAs were down-regulated from L6D6 to P0D after the testicular fusion. The GO terms and KEGG pathway enrichment analysis of DElncRNAs target DEmRNAs showed that ECM remodeling enzymes including stromelysin, A disintegrin and metalloproteinase with thrombospondin motifs (ADAMTs) and inducible metalloproteinase inhibitor protein (IMIPs), ECM-intergrin interaction pathway and cell adhesion molecules (integrin, cadherin) may be involved in the testicular fusion. The DElncRNA-DEmiRNA-DEmRNA regulatory network related to ECM remodeling enzymes and its signal pathway may play important roles in cell adhesion when the testicular fusion occured. Our study will provide comprehensive information to study the mechanism of testicular fusion, and especially, will promote the functional study of non-coding RNAs (lncRNAs and miRNAs) during the testicular fusion in S. litura.

overall_design: To study the mechanism of testicular fusion in Spodoptera litura, the testes from 4-day-old sixth instar larvae (L6D4) (before fusion), 6-day-old sixth instar larvae (L6D6, prepupae) (on fusing) and 0-day-old pupae (P0D) (after fusion) were collected for RNA-sequencing. Long non-coding RNA and mRNA were studied and analyzed during the testicular fusion in S. litura.

first: Yaqing

last: Chen

first: Yu

first: Xiao-qiang

last: Yu

first: Qili

last: Feng

first: Xiaoyun

last: Wang

first: Lin

last: Liu


title: IL-22 resolves MASLD via enterocyte STAT3 restoration of diet perturbed intestinal homeostasis [scRNA-seq]

summary: We found IL22 could reduce intestinal fatty acid transporters expression. We used single cell RNA sequencing (scRNA-seq) to analyze the cell population and gene expression with Fc or IL-22Fc treatment.

overall_design: Male C57BL/6 mice (10 weeks old) were fed with HFD+30% fructose water for 16 weeks, and were intraperitoneally (i.p.) injected with 10μg mFc or rmIL-22-Fc /mouse every 3 days for last 4 weeks. Single intestinal epithelial cells and lamina propria lymphocytes were subjected to RNA sequencing.


title: Pharmacological Repositioning of the transcription factor PU.1 [RNA-seq]

city: Bronx

first: Samuel

middle: John

last: Taylor

address: 1300 Morris Park Ave, Chanin building 601

institute: Albert Einstein College of Medicine

summary: To investigate the effects of DB2115 (PU.1 binding-site inhibitor/redistributor) upon the transcriptome of the AML cell line MOLM-13.

overall_design: MOLM-13 cells grown in 10% FBS, 1% Pen Strep, RPMI media were treated with 5uM of DB2115 for 20hr before cells were harvested and RNA was extracted for RNA-seq.

first: Ulrich

last: Steidl

first: Emily

last: Schwenger


title: Cohesin chromatin loop formation by an extrinsic motor (Micro-C)

first: Thomas

last: Guerin

summary: The ring-shaped cohesin complex topologically entraps two DNAs to establish sister chromatid cohesion. Cohesin also shapes the interphase chromatin landscape, with wide-ranging implications for gene regulation, which cohesin is thought to achieve by actively extruding DNA loops without topologically entrapping DNA. The ‘loop extrusion’ model find motivation from in vitro observations - whether this process indeed underlies chromatin loop formation in vivo remains untested. Here, using the budding yeast S. cerevisiae, we generate cohesin variants that have lost their ability to extrude DNA loops but retain their ability to topologically entrap DNA. Analysis of these variants suggests that in vivo chromatin loops form independently of loop extrusion. Instead, we find that transcription promotes loop formation, likely by generating DNA substrates for topological loop capture. Transcription furthermore acts as an extrinsic motor that, by pushing cohesin along transcription units, extends chromatin loops and defines their ultimate positions. Our results necessitate a re-evaluation of the loop extrusion hypothesis and point to an alternative mechanism for cohesin-dependent chromatin organisation. Loop formation by DNA-DNA capture, akin to sister chromatid cohesion establishment at replication forks, unifies cohesin’s two roles in chromosome segregation and interphase genome organisation.

overall_design: Cohesin calibrated ChIP sequencing and Micro-C. Two independent replicates are provided

last: Guérin

first: Christopher

last: Barrington

first: Georgii

last: Pobegalov

first: Maxim

middle: I

last: Molodtsov

first: Frank

last: Uhlmann


title: Pharmacological Repositioning of the transcription factor PU.1 [PRO-seq]

summary: This study aims to investigate the effects of PU.1 binding-site inhibitors/redistributors (DB2115) upon nascent transcription in AML cell lines

overall_design: The MOLM-13 cell line were treated with 5uM of DB compound for 0,1, 4 & 12hr, before cells were harvested for Precision nuclear run on and sequencing (PRO-seq).


title: Pharmacological Repositioning of the transcription factor PU.1 [ChIP-seq]

summary: To investigate the effects of DB2115 (PU.1 binding-site inhibitor/redistributor) upon PU.1 genomic localization, the transcriptome and chromatin accessibility.

overall_design: MOLM-13 cells grown in 10% FBS, 1% Pen Strep, RPMI media were treated with 5uM of DB2115 for 12hr before cells were harvested and Classical PU.1 ChIP was performed