title: The Link between Osteoporosis and Frozen Shoulder: Exploring the Therapeutic Effect of TAK715 on Reversing Fibrosis and Protecting against Osteoporosis via the p38 MAPK Signaling Pathway

status: Public on Apr 27 2024

city: Guangzhou

first: Xinhao

last: Li

address: Yanjiang street

institute: Sun Yat-sen Memorial Hospital

summary: The global incidence of frozen shoulder (FS) and osteoporosis (OP) is high. Although FS patients may experience localized OP in the shoulder, there is still insufficient strong evidence to confirm the relationship between FS and OP. The main objective of this current research is to investigate the pathogenesis mechanism of FS and explore the connection between FS and OP.We obtained FS and OP datasets from GEO and identified crosstalk genes. We screened the p38 MAPK signaling pathway and its specific inhibitor, TAK715. We conducted flow cytometry, western blot, and PCR analyses to assess the treatment effect of TAK715 on FS synovium fibroblasts at concentrations of 1μM, 5μM, and 10μM. Additionally, we employed SD rats to validate the treatment effects of TAK715 in vivo. TAK715 was found to also intervene in the activation of osteoclasts. We successfully established a FS and OP rat model, with the FS with OP rat displaying more severe symptoms. Results demonstrated that TAK715 effectively corrected both fibrosis and osteoporosis simultaneously in vivo.The frozen shoulder with osteoporosis may exhibit more severe symptoms, and TAK715 is effective in protecting fibrosis and osteoporosis both in vitro and vivo. The therapy to correct FS and OP simultaneously by TAK715 provides novel approach in FS treatment and study.

overall_design: Comparative gene expression profiling analysis of RNA-seq data of human shoulder synouvium fibroblasts with TAK715 at 5 uM

first: Yan

last: Yan

first: Yi

last: Long


title: Mesoscale chromatin confinement facilitates target search of pioneer transcription factors in live cells

status: Public on Apr 28 2024

city: Beijing

first: Wulan

last: Deng

address: Beijing Haidian District Yiheyuan Road #5

department: BIOPIC

country: China

institute: Peking University

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Expression data from human Bladder cancer cell line J82 with control or overexpression of SQLE

city: Tianjin

first: Guangming

state: Tianjin

address: No. 22 Qixiangtai Road

department: Pathogen

institute: Tianjin Medical University

summary: Several reports showed that SQLE was upregulated in some types of cancer, and it is essential for cancer development. Herein, to uncover the role of SQLE in BCa, we performed the RNA-seq to detect the gene expression levels in BCa cell line J82 with overexpression of SQLE.

overall_design: SQLE overexpression in bladder cancer cell line J82 was performed by transfection with SQLE overexpressing plasmid and named this cell line as SQLE. Meanwhile, control J82 cell line was named as Vector-NC. Replicate RNA are obtained from SQLE and Vector-NC, respectively, named SQLE_1, SQLE_2, SQLE_3, Vector-NC_1, Vector-NC_2, Vector-NC_3. We sought to obtain the expression profiles of WT and OE SQLE in J82 , and found the downstream genes and pathways, which influenced by SQLE.

first: Liang

last: Dai

first: Yimin

last: Wang

first: Wangteng

last: Ma


title: CDK5RAP3 is activated by master TFs and regulates ER-Phagy in neuroblastoma

city: Suzhou

first: Zimu

last: Zhang

state: Jiangsu

address: Zhongnan Street

institute: Children’s Hospital of Soochow University

summary: Cyclin-dependent kinase 5 regulatory subunit associated protein 3(CDK5RAP3) is regulated by master TFs in neuroblastoma, and its functions in neuroblastoma are yet unclear. Herein, we observed a significantly elevated CDK5RAP3 expression level in neuroblastoma, which was associated with a poor prognosis in patients.  CDK5RAP3 promotes the growth of neuroblastoma cells both in vitro and in vivo. Mechanistically, defective CDK5RAP3 interferes with UFMylation system, thereby triggering endoplasmic reticulum(ER)-Phagy. Additionally, we provide evidence that CDK5RAP3 maintains stability of MEIS2, a master TF in neuroblastoma, and in turn contributes high expression of CDK5RAP3. Overall, our findings shed light on the molecular mechanisms through which CDK5RAP3 promotes tumor progression and suggest that its inhibition may represent a novel therapeutic strategy in neuroblastoma.

overall_design: mRNA profiles of SK-N-BE(2) cells transfected with control shRNA (sh-NC) or sh-CDK5RAP3 were generated by RNA sequencing, in double, using Illumina NovaSeq6000.

first: Ran

last: Zhuo

first: Jian

last: Pan


title: Therapeutic vaccine induced plasma cell differentiation is defective upon persistent HBsAg stimulation

city: Xiamen

first: Jinhang

last: He

state: Fujian

address: No.4221, South Xiang'an Road

institute: Xiamen University


title: RNA-seq analysis on organoids derived from metastatic tumor patients

city: shanghai

first: shaoxuan

last: wang

address: 138 Yi xue yuan Road

institute: fudan university

summary: To evaluate the efficiency of apatinib on vascularized patient-derived tumor organoids (PDTOs)-on-a-chip derived from patients with metastatic tumors, we conducted RNA-seq analysis on organoids derived from patients whom had metastatic tumors. Specifically, we extracted RNA for sequencing from tumor cells of organoids either cultured alone or co-cultured with MVs with or without apatinib treatment

overall_design: RNA-Seq from tumor cells of organoids either cultured alone or co-cultured with MVs with or without apatinib treatment

first: Shaoxuan

first: Yan-Jun

last: Liu


title: Effects of dichloroacetate on transcriptional networks in rat Schwann cells and primary sensory neurons

city: Gainesville

first: Christopher

last: Martyniuk

state: FL

address: 8891 SW 79th Avenue

country: USA

institute: University of Florida

summary: Peripheral neuropathy (PN) is a debilitating side effect of many pharmaceutical agents and is among the most common reasons why patients stop their treatment early. Dichloroacetate (DCA) is a therapeutic drug that inhibits the pyruvate dehydrogenase complex (PDC), thereby modulating metabolic flux in cells. Despite success in improving outcomes of disease, reversible PN has been the single factor limiting the therapeutic potential for DCA. As a result, clinical trials for the drug have been halted prematurely. Establishing toxicity pathways in cells of the peripheral nervous system (PNS) that are involved in DCA-induced PN would provide new opportunities to intervene and mitigate adverse side effects associated with DCA. We investigated the molecular mechanisms underlying DCA-induced injury to both glial and neuronal cells. It was hypothesized that SCs would show activated transcriptional responses associated with oxidative damage and apoptosis at therapeutic doses while these responses will be absent or reduced in DRGs. Experiments were expected to pinpoint molecular mechanisms underlying DCA-induced neurotoxicity, and to reveal the window of therapeutic intervention to reduce side effects associated with DCA in clinical settings.

overall_design: RNA-seq profiling of dichloroacetate on transcriptional networks in rat Schwann cells and primary sensory neurons

first: Chris


title: RNA-seq for liver tissue in mice

city: Guiyang

first: Gongzhen

last: Chen

address: Dongqing South-Road 4#

institute: Guizhou University of Traditional Chinese Medicine

summary: This study aims to investigate genes regulated by liver tissue from the mice treated with water extract of Emilia sonchifolia.

overall_design: Liver tissues from the mice treated with phosphate buffer saline or water extract of Emilia sonchifolia were subjected to RNA-seq. Liver tissues from the mice treated with phosphate buffer saline were used as control group.

first: Xin


title: The allosteric landscape of the Src kinase

city: Barcelona

first: Antoni

last: Beltran

address: Dr Aiguader, 88

country: Spain

institute: CRG Barcelona

summary: Enzymes catalyze the reactions of life and are the targets of nearly all small molecule drugs. Most drugs inhibit enzymes by binding to conserved active sites, causing problems of specificity and toxicity. Targeting regulatory allosteric sites can increase specificity, overcome drug resistance and tune or activate activity.However, the vast majority of enzymes have no known allosteric sites and methods do not exist to globally identify or predict them.Here we present a general and fast method to globally chart allosteric communication in enzymes and apply it to the Src protein kinase to produce the first comprehensive map of negative and positive allosteric control of enzymatic activity. Allosteric control of Src is pervasive, anisotropic and distance dependent, but fairly predictable from simple sequence and structural features. The comprehensive allosteric map enables unbiased identification of all the allosterically active surface pockets of the Src kinase for the development of activatory and inhibitory drugs.This general approach can be used to chart global allosteric maps of many kinases, enzymes, and other biochemical activities important for medicine and biotechnology.

sample_organism:
Saccharomyces cerevisiae
Homo sapiens

platform_organism:
Saccharomyces cerevisiae
Homo sapiens

overall_design: We designed a variant library covering the kinase domain of the human tyrosine kinase Src. The library is split in 5 blocks of ~60 aa residues, and each block consists of all single substitutions in 10 genetic backgrounds (54,455 genotypes in total across the full kinase domain). Each block was cloned into a Src kinase domain alone construct (KD), and a full-length Src construct (FL), and each of these was selected in triplicate in activity and protein abundance assays in yeast. The data files here correspond to the amplicon-seq libraries of the population of variants in each block before and after selection (inputs and outputs).

first: Ben

last: Lehner


title: Effects of BPS and BPF on transcriptional networks of neuronal cells

summary: Over the past several years, replacement chemicals for bisphenol A have been manufactured and used as additives in sportswear, plastic bottles, food packaging, and in other products. More recently, replacement products for BPA are under investigation for toxicity, but there are little data on the potential for neurotoxicity. To address this gap, differentiated human SH-SY5Y cells were treated with a range of concentrations of BPS and BPF to better understand mechanisms of toxicity.

overall_design: Cell culture flasks were exposed to DMSO, or one dose of either BPS or BPF.  Cells were exposed in T75 flasks by removing all of the media and replacing it with 8 mL of differentiation media (DMEM:F12 containing 1% FBS, 1% antibiotic/antimycotic solution, and 10 µM retinoic acid) every 48 hours. On the 6th day, cells were exposed to media, 0.1 nM BPS, or 0.1 nM BPF (n=5-6) for 48 hours. Media was then removed and the remaining cells were trizoled and stored at -80°C for further processing.

last: Souders

first: Andrea

last: Guzman


title: Next-generation sequencing analysis of 7-month-old SRSF2 flox/flox and SRSF2-PKO mice pancreatic islet transcriptome

city: 上海

first: WENJU

last: QIAN

state: 上海

address: 徐汇区岳阳路

institute: 上海中科院

summary: We report insulin secretion defects in SRSF2 Ins2-Cre mice, in which SRSF2 is ablated in pancreatic β cells.

overall_design: The control and SRSF2 Ins2-Cre gene in pancreatic β cells mRNA profiles were generated by deep sequencing, using Illumina novaseq 6000.

first: Wenju

last: Qian

first: Ying

last: Feng


title: RNA-seq of E0771-Vector control and E0771-Malt1-WT at basal condition

status: Public on Apr 26 2024

first: Hanqiu

last: Zheng

address: Haidian District

institute: Tsinghua university

summary: To reveal the downstream signal change induced by Malt1, we collected mRNA samples from Vector control- and WT-Malt1-expressing E0771 cancer cells, and performed RNA-seq analysis.

overall_design: E0771 cells expressing either -Vector control or wild type-Malt1 (M-WT) were lysed by TRIZOL for RNA extraction,  perform reverse transcription and cDNA library for RNA-Seq analysis.

first: Yuwei

last: Tao

first: Chen

last: Tian


title: Cancer cell genetics shaping of the tumor microenvironment reveals myeloid cell-centric exploitable vulnerabilities in hepatocellular carcinoma [WES]

city: Amsterdam

first: Masami

last: Ando-Kuri

address: Plesmanlaan 121

country: Netherlands

institute: Netherlands Cancer Institute (NKI)

summary: Hepatocellular carcinoma (HCC) is a highly heterogenous disease associated with an equally dynamic tumor microenvironment (TME).  We generated somatic HCC mouse models bearing clinically-relevant oncogenic driver combinations that faithfully recapitulated different human HCC subclasses. Using WES data, we explored the tumor mutation frequencies between models and compared them with human datasets.

overall_design: WES profiles of bulk tumors from genetically-distinct HCC mouse models. 3 biological replicates were pooled.

first: Christel

middle: F

last: Ramirez

first: Serena

last: Vegna

first: Daniel

last: de Groot


title: Double-stranded RNA triggers a distinct integrated stress response in the early embryo [RNA-seq, Ribo-seq]

city: Qingdao

first: tong

last: lu

address: 72, binghai rd

institute: ShanDong University

summary: Double-stranded RNA (dsRNA) is associated with virus infections and is present as by-products during the transcription of synthetic mRNA, which has been widely used in gene gain-of-function studies and serves as a core component in emerging mRNA-based therapies1-4. The presence of dsRNA in host cells induces an integrated stress response that functions to prevent virus replication and infection5,6. Unlike differentiated cells, undifferentiated cells adopt a distinct defense strategy against RNA virus infection7, but the mechanism is unclear. We show a previously unidentified response triggered by dsRNA in the early embryo. Although dsRNA causes a global protein translation inhibition in a PKR-eIF2α independent manner and leads to developmental delay and cell necrosis, it also strongly induces p53 activation, which then upregulates Interferon Stimulated Genes independently of interferon ligands. Importantly, we demonstrate that the burst of p53 signaling dose not result in cell death but functions as a protective mechanism against deleterious translation blockage by slowing down global protein degradation via ISGylation. Our work has identified a distinct dsRNA-induced stress response in the embryo, reflecting an ancient innate immune memory before the establishment of the IFN system. It also raises the provocative question as to the original protective role of p53 during evolution.

overall_design: To characterize the distribution of ribosomes on mRNA, we performed Ribosome profiling (Ribo-seq) analysis with RNA-seq on dsRNA-injected embryos.

first: Tong

last: Lu

first: Ming

last: Shao


title: Understanding resistance to polymyxin and amikacin in Klebsiella pneumoniae

city: Brasília

first: Camila

middle: Maurmann

last: de Souza

state: Distrito Federal

address: QS 07, Lote 01, Taguatinga Sul

department: Biotechnology

country: Brazil

institute: Universidade Católica de Brasília

summary: Klebsiella pneumoniae poses a significant global health threat primarily attributable to its pronounced resistance. Here, we report an in vitro acquired resistance analyses of K. pneumoniae to the combination of amikacin and polymyxin B. We found some differentially expressed genes associated with the resistome of K. pneumoniae. The main differences were found in the genes aphA, asmA, phoP, and in the arn operon. Once these genes are related to modification in lipopolysaccharides, aminoglycosides and in the membrane structure, the mechanisms associated with them can justify the resistance acquisition to amikacin and polymyxin b.

overall_design: To investigate the resistance mechanism against amikacin and polymyxin B, we compare a resistant lineage (E6) and a control lineage (C1) after growing in subinhibitory concentrations of polymyxin B and amikacin for 1 hour. Subsequently, we conducted gene expression analysis utilizing RNA-seq data acquired from both lineages. Hence, a comparative gene expression profile of RNA-seq data for C1 and E6 lineages was obtained.

first: Octavio

last: Franco


title: Characterization of premature cell senescence in Alzheimer’s disease using single nuclear transcriptomics

city: London

first: Paul

middle: M

last: Matthews

address: White City

country: United Kingdom

institute: Imperial College London

summary: Aging is associated with cell senescence and is the major risk factor for AD. We characterized premature cell senescence in post mortem brains from non-diseased controls (NDC) and donors with Alzheimer’s disease (AD) using imaging mass cytometry (IMC) and single nuclear RNA (snRNA) sequencing (>200,000 nuclei). We found increases in numbers of glia immunostaining for galactosidase beta (>4-fold) and p16INK4A (up to 2-fold) with AD relative to NDC. Increased glial expression of genes related to senescence was associated with greater -amyloid load. Prematurely senescent microglia downregulated phagocytic pathways suggesting reduced capacity for -amyloid clearance. Gene set enrichment and pseudo-time trajectories described extensive DNA double-strand breaks (DSBs), mitochondrial dysfunction and ER stress associated with increased β-amyloid leading to premature senescence in microglia. We replicated these observations with independent AD snRNA-seq datasets. Our results describe a burden of senescent glia with AD that is sufficiently high to contribute to disease progression. These findings support the hypothesis that microglia are a primary target for senolytic treatments in AD.

overall_design:
This study was carried out in accordance with the Regional Ethics Committee and Imperial College Use of Human Tissue guidelines. Cases were selected based first on neuropathological diagnosis from UK brain banks (London Neurodegeneration [King’s College London] and Parkinson’s UK [Imperial College London] Brain Bank). We then excluded cases with clinical or pathological evidence for small vessel disease, stroke, cerebral amyloid angiopathy, diabetes, Lewy body pathology (TDP-43), or other neurological diseases.  Where the information was available, cases were selected with a post-mortem delay of less than 60 h. Samples included EC, MTG and SSC cortices from a final set of 17 cases including 8 NDC donors (Braak stage 0–II) and 9 neuropathologically defined AD (Braak stage III–VI) donors (total of 49 brain samples).

***************************************************************
Submitter states that missing raw files are due to patient privacy concerns.
For raw files, visit the project space in https://www.synapse.org/#!Synapse:syn36812517/wiki/619350
***************************************************************

first: Nurun

last: Fancy

first: Amy

last: Smith

first: Alessia

last: Caramello

first: Stergios

last: Tsartsalis

first: Karen

last: Davey

first: Robert

middle: C

last: Muirhead

first: Aisling

last: McGarry

first: Marion

last: Jenkins

first: Eleonore

last: Schneegans

first: Vicky

last: Chau

first: Michael

last: Thomas

first: Sam

last: Boulger

first: To

middle: K

last: Cheung

first: Emily

last: Adair

first: Marianna

last: Papageorgopoulou

first: Nanet

last: Willumsen

first: Combiz

last: Khozoie

first: Diego

last: Gomez-Nicola

first: Johanna

last: Jackson


title: Atlas of Cynomolgus Macaque Hematopoiesis

city: Japan

first: Ryo

last: Yamamoto

state: Kyoto

address: Yoshidakonoecho, Sakyo-ku

department: ASHBi

country: Japan

institute: Kyoto Univerisity

summary: Self-renewal and differentiation are inherent properties of hematopoietic stem cells that are necessary to support hematopoiesis. However, the underlying mechanisms, especially in human, remain unclear. Here, using the cynomolgus macaque as a surrogate model, we develop a new gating strategy to isolate with high purity transplantable cynomolgus HSCs and generated a single-cell transcriptomic map of cynomolgus HSCs and progenitor cells, that covers the gestational period not analyzed in human. We show that hematopoietic cells from the late-1st to early-3rd trimester fetal liver and late-2nd trimester and thereafter bone marrow has repopulating potential, closely mimicking humans. Unexpectedly however, we found unlike in human, cynomolgus HSCs express CD38 but not CD33, indicating that these cellular counterparts are molecularly distinct. Our transcriptomic analysis reveals the presence of a direct differentiation pathway from HSCs to megakaryocyte lineages, lineage-primed multipotent progenitors and also identified putative HSC surface markers. Taken together, our comprehensive dataset highlights not only the utility of cynomolgus monkeys as model systems to study hematopoiesis but also their potential for translational applications.

overall_design: To obtain transcriptomic landscape of cynomolgus macaque hamatopoiesis across developmental stages, we analyzed CD34 positive hematopoietic cells of early 2nd FL, late 2nd FL, early 3rd FL, late 2nd FBM, early 3rd FBM and ABM using 10X Genomics 5’ chemistry based single-cell RNA-sequencing.

first: Shinichiro

last: Oshima

first: Rahul

last: Sinha

first: Kazuhiro

last: Takeuchi


title: GPAT3 is a novel inflammatory protein promoting gastric bacterial colonization and gastritis in Helicobacter pylori infection

city: Chongqing

first: yuan

last: zhuang

address: Gaotanyan Street

institute: Third Military Medical University

summary: Bacterial-modulated gastric epithelial cells (GECs) play key roles in H. pylori-associated pathology. Here we demonstrate a pro-colonization and pro-inflammation role of GEC-expressed glycerol-3-phosphate acyltransferase 3 (GPAT3), a lipid metabolism-associated protein, in H. pylori infection. GPAT3 expression was elevated in gastric mucosa of both patients and mice infected with H. pylori. GPAT3 in GECs was synergistically induced by H. pylori and IL-22 in a cagA-dependent manner. Human gastric GPAT3 correlated with H. pylori colonization and the severity of gastritis, and mouse GPAT3 from non-bone marrow-derived cells promoted bacteria colonization and inflammation. Importantly, H. pylori colonization and inflammation were attenuated in Il22-/-, Gpat3-/- and Il22-/-Gpat3-/- mice. Mechanistically, GPAT3 directly interacted with CCAR1 and activated IKKγ, subsequently promoted NF-κB phosphorylation whereby NF-kB directly bound to the promoters of MMP1, CXCL11 and IL-33 to activate their transcription, which not only led to decreased E-cadherin and zonula occludens-1 proteins by MMP1, thereby resulting in gastric mucosal damage and increased H. pylori colonization; but also resulted in increased gastric influx of CD8+ T cells via CXCL11-dependent migration and their subsequent IL-33-dependent IFN-γ production, thereby promoting H. pylori-associated gastritis. Overall, we propose a model in which GPAT3 collectively ensures H. pylori persistence and promotes gastritis.

overall_design: To investigate the function of GPAT3 in gastric epithelial cells, AGS cells were pre-treated with GPAT3 siRNA or non-specific control siRNA (NC) (40 nM) for 24 h

first: Geng-Yu

last: Yue

first: Xiao-Lin

last: Xu

first: Wen-Qing

last: Tian

first: Peng

last: Zhu

first: Yu-Gang

last: Liu

first: Jiang-Bo

last: Wu

first: Wan-Yan

last: Chen

first: Pan

last: Wang

first: Jing-Yu

first: Si-Xu

first: Mu-Han

last: Lü

first: Sheng-Qian

last: Yang

first: Tao

first: Ping

last: Cheng

first: Fang-Yuan

last: Mao

first: Yong-Sheng

last: Teng

first: Shou-Lu

last: Luo

first: Jin-Yu

last: Zhang

first: Liu-Sheng

last: Peng

first: Quan-Ming

last: Zou

first: Ya-Ling

last: Liao

first: Shi-Ming

first: Yong-Liang

last: Zhao

first: Hong

last: Zhou

first: Weisan

last: You

first: Rui

last: Xie

first: Yuan

last: Zhuang


title: Effect of expression of ZEBRA on gene expression in Ramos cells [CUT-Tag]

city: Lanzhou

first: caiyue

last: que

state: 甘肃

address: 天水南路222号

institute: 兰州大学

summary: EBV immediate early protein ZEBRA was corroborated to interact with Pax5 which controls the fate of B cells. Ramos cells were infected with ZEBRA-expression lentivirus and positively infected cells were sorted, which were named Ramos-Lv-ZEBRA.

overall_design: CUT&Tag analysis of H3K9me2-binding in control Ramos cells (Ramos), the lentivirus vector infected Ramos cells (Ramos-Lv-Vector) and Ramos-Lv-ZEBRA.

first: Junfei

last: Wu

first: Caiyue

last: Que

first: Huanqin

last: Liu

first: Mengdan

last: Hou

first: jing

first: Guohui

last: Chen

first: Huazheng

last: Jiang

first: Yongheng

last: Shao

first: Zijian

last: Qin

first: Haozhen

last: Chang


title: DRAIC mediates hnRNPA2B1 stability and m6A-modified IGF1R instability to inhibit tumor progression

city: Nanjing

first: Shan

last: Gao

address: No. 2 Sipailou, Xuanwu District

institute: Southeast University

summary: Both N6-methyladenosine (m6A) mediates RNA fates and ubiquitin mediates protein fates play an important role in either physiology or pathology including cancer, yet how long noncoding RNAs (lncRNAs) are involved in a link of molecular fate between m6A and ubiquitin remains unknown. Here, we reveal a role for a lncRNA Downregulated RNA in Cancer (DRAIC) to suppress tumor growth and metastasis in clear cell Renal Carcinoma (ccRCC). Mechanistically, DRAIC physically interacts with heterogeneous nuclear ribonucleoprotein A2B1 (hnRNPA2B1) and enhances its protein stability by blocking E3 ligase F-box protein 11 (FBXO11)-mediated ubiquitin and proteasome-dependent degradation. Subsequently, hnRNPA2B1 destabilizes m6A modified-type 1 insulin-like growth factor receptor (IGF1R) to lead to inhibition of ccRCC progression. Moreover, four m6A modification sites of IGF1R are identified and results in its mRNA degradation. Collectively, our findings reveal that DRAIC/hnRNPA2B1 axis regulates IGF1R mRNA expression in an m6A-dependent manner and highlights an important mechanism of IGF1R fate. These findings shed light on DRAIC/hnRNPA2B1/FBXO11/IGF1R axis as potential therapeutic targets in ccRCC and build a link of molecular fate between m6A-modified RNA and ubiquitin-modified protein.

overall_design: RIP assay was performed using m6A antibody in 786-0 cells and the enriched RNA was sequenced with input sample

first: Ya

last: Wen

first: Xiwang

last: Yang

first: Yifei

last: Li

first: Xueqing

first: Liqiang

last: Duan

first: Shuwen

last: Chenge

first: Bo

last: Peng

first: Xiaofeng

last: Zhua

first: Xiaoli

first: Chang

last: Zhang

first: Tianyou

last: Cheng

first: He

last: Wang

first: Yibi


title: Identifying differences in differentiation between adherent and suspension culture for iPSC derived beta cells

city: Beachwood

first: Trailhead

last: Biosystems

state: Ohio

address: 23215 Commerce Park Rd

institute: Trailhead Biosystems Inc

summary: Stage 3 cells from a suspension environment and adherent culture were compared and evaluated through RNA sequencing. RNA sequencing data in heatmap and volcano plot evaluation of core endocrine genes showed that expression levels in adherent cells were lower than those expressed in 3D environment. Several genes that are essential for insulin transcription such as NEUROD1, MAFA, PPARGC1A and NKX2.2 along with INS were expressed with higher transcript levels in bioreactor samples. It was observed that genes usually expressed in earlier stages such as FOXA2 and HNF1b had higher expression levels in adherent culture indicating that 2D environment differentiation might be lagging.

overall_design: To investigate the impact of cell culture platform on iPSC differentiation into pancreatic beta cells.

first: Haneen

last: Yehya

first: Roshan

last: Padmanabhan

first: Michael

middle: A

last: Bukys


title: Neuroendocrine cells initiate protective upper airway reflexes

city: San Francisc

first: David

last: Julius

state: CA

institute: UCSF

summary: Airway neuroendocrine (NE) cells have been proposed to serve as specialized sensory epithelial cells that modulate respiratory behavior by communicating with nearby nerve endings. However, their functional properties and physiological roles in the healthy lung, trachea and larynx remain largely unknown. Here, we show that NE cells in these compartments possess distinct biophysical properties, but share sensitivity to the commonly aspirated noxious stimuli, water and acid. Moreover, we found that tracheal and laryngeal NE cells protect the airways by releasing ATP to activate purinoreceptive sensory neurons that initiate swallowing and expiratory reflexes. Our work uncovers striking molecular and biophysical diversity of NE cells across the airways and reveals mechanisms by which these specialized excitable cells serve as sentinels for activating a critical nociceptive circuit.

overall_design: Compare expression between neuroenodcrine cells and epithelial cells in the lung, lower trachea, upper trachea, larynx. Cells were dissociated and FACs sorted from Ascl1-CreERT2;lsl-tdTomato mice with neuroendocrines cells defined as tdTomato+ and epithelial cells defined as EpCam+/tdTomato-. For a given tissue, NE and epithelial cells were FACs sorted in parallel (n=3 biological replicates). Lung cells were dissociated from one set of mice and tracheal/laryngeal NE cells were dissociated from another set.

first: Laura

last: Seeholzer


title: Effect of expression of ZEBRA on gene expression in Ramos cells [ChIP-Seq]

first: caiyue

last: que

overall_design: ChIP-seq analysis of H3K9me2-binding in control Ramos cells (Ramos), the lentivirus vector infected Ramos cells (Ramos-Lv-Vector) and Ramos-Lv-ZEBRA.

first: Junfei

last: Wu

first: Caiyue

last: Que

first: Huanqin

last: Liu

first: Mengdan

last: Hou

first: jing

last: Zhao

first: Guohui

last: Chen

first: Huazheng

last: Jiang

first: Yongheng

last: Shao

first: Zijian

last: Qin

first: Haozhen

last: Chang


title: Natural killer cell receptor expressing B cells: a distinct but rare subset of innate immune cells in rhesus macaques

city: Atlanta

first: Gregory

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

summary: Natural killer-like B (NKB) cells are unique innate immune cells that express both natural killer (NK) and B cell markers. They act as first responders by secreting IL-18 upon infection, thus inducing the critical cascade of innate and adaptive immune cell infiltration and activation. However, limited research exists on the role of NKB cells in homeostasis, and infection in primates. Therefore, we investigated the signaling and trafficking proteome, in situ localization and transcriptome of NKB cells in comparison to conventionally defined NK and B cells. Intracellular signaling proteins and trafficking markers were expressed differentially on naïve NKB characterized by high expression of CD62L and Syk, and low expression of CD69, a4b7, FcRg, Zap70, and CD3z which were more similar to B cells than NK cells. CD20+NKG2a/c+ NKB cells were identified in spleen, mesenteric lymph nodes (MLN), colon, jejunum, and liver of naïve RM by tissue imaging with NKB cell counts concentrated in spleen and MLN. Transcriptomic analysis of naïve splenic NKB cells by scRNAseq  showed that NKB cells undergo somatic hypermutation and express Ig receptors, similar to B cells. While only 15% of sorted NKB population showed transcript expression of both KLRC1 (NKG2A) and MS4A1 (CD20), cells expressing KLRC1, MS4A1and IgH/IgL transcripts were only 5%. However, we observed expanded NKB frequencies in gut mucosa as early as 35 days and in buccal mucosa as early as 14 days post-SIV infection using an RM model of HIV infection, thus indicating NKB cells, though infrequent, could have potential roles to play in mucosal infections.

overall_design: Sorted NK, B and NK cells from three SIV-negative rhesus macaques


title: Characteristics of medial prefrontal cortex during retrieval of METH-associated CPP memory

city: Guangzhou

first: Yubo

last: Hu

address: 74 Zhongshaner Rd

institute: Sun Yat-sen University

summary: To investigate the candidate molecular mechanisms underlies methamphetamine-associated CPP memory retrieval and reconsolidation, we compared the transcriptional profling changes in the mPFC between mice that underwent retrieval and non-retrieval after methamphetamine-paired CPP training.

overall_design: We collected mPFC tissue 1 hour post-CPP test ended in male C57BL/6 adult mice. 2-3 mice were mixed as 1 biological sample pool.

first: Zhenjie

last: Gao

first: Xin

last: Cheng

first: Hu


title: The prenatal nicotine exposure leads to epigenetic alterations in nervous system signaling genes in the rat

city: Rennes

first: Fatima

last: SMAGULOVA

address: 9 av. Prof. Léon Bernard

country: France

institute: Irset - U1085

type: Methylation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Germ cell specific high level of H3K9me3 in chicken PGCs: distribution and role in gene expression control [RNA-Seq]

city: Bron

first: Clémence

last: Kress

address: 18 avenue du Doyen Lépine

institute: INRAE, Inserm

summary: Chicken primordial germ cells (PGCs) have an epigenetic signature which differs from the one that mammalian PGCs acquire with their epigenome reprogramming during early embryonic development. In particular, chicken PGCs display a high global amount of histone H3 lysine 9 trimethylation (H3K9me3) compared to somatic cell types. We performed the genome-wide profiling of H3K9me3 and the transcriptome analysis on chicken PGCs compared to embryonic stem cells (ESCs) as a closely related, non germinal cell type.

overall_design:
Comparative gene expression profiling analysis of RNA-seq data for chicken PGCs and ESCs.
Re-analyzed Sample: PGC rep1 SAMN07460473 SRX3070410
Re-analyzed Sample: ESC rep1 SAMN07460476 SRX3070407

first: Luc

last: Jouneau

first: Bertrand

last: Pain


title: Germ cell specific high level of H3K9me3 in chicken PGCs: distribution and role in gene expression control [ChIP-Seq]

overall_design: Chromatin immunoprecipitation followed by DNA sequencing (ChIP-seq) for H3K9me3 in chicken PGCs and ESCs.


title: Transcriptomic Profiling of Lactotroph Pituitary Neuroendocrine Tumors via RNA Sequencing and Ingenuity Pathway Analysis

city: Bunkyo-ku

first: Yujiro

last: Hattori

state: Tokyo

address: 1-1-5 Sendagi

institute: Nippon Medical School

summary: Background: Lactotroph pituitary neuroendocrine tumors (PitNETs) are common pituitary tumors, but their underlying molecular mechanisms remain unclear. This study aimed to investigate the transcriptomic landscape of lactotroph PitNETs and identify potential molecular mechanisms and therapeutic targets through RNA sequencing and ingenuity pathway analysis (IPA). Methods: Lactotroph PitNET tissues from five surgical cases without dopamine agonist treatment underwent RNA sequencing. Normal pituitary tissues from three patients served as controls. Differentially expressed genes (DEGs) were identified, and the functional pathways and gene networks were explored by IPA. Results: Transcriptome analysis revealed that lactotroph PitNETs had gene expression patterns that were distinct from normal pituitary tissues. We identified 1,172 upregulated DEGs, including nine long intergenic noncoding RNAs (lincRNAs) belonging to the top 30 DEGs. IPA of the upregulated DEGs showed that the estrogen receptor signaling, oxidative phosphorylation signaling, and EIF signaling were activated. In gene network analysis, key upstream regulators, such as EGR1, PRKACA, PITX2, CREB1, and JUND, may play critical roles in lactotroph PitNETs.

overall_design:
We studied five patients with lactotroph PitNETs who had markedly elevated prolactin levels and subsequently underwent endoscopic transsphenoidal surgery without preoperative medications such as cabergoline and other dopamine agonists, with rapid postoperative normalization of prolactin levels.
As for the control, three normal pituitary gland tissues were obtained from other patients undergoing endoscopic transsphenoidal surgery through legitimate reasons (e.g., ensuring intraoperative visual field for complete removal of suprasellar tumor) and having normal pituitary hormone sampling values, including hormone stimulation test, preoperatively.
After extracting RNA from the tissue, we constructed the transcriptome landscapes of these PitNETs using RNA-seq data and compared them to normal pituitary tissues to analyze functional pathways and gene networks.

first: Shigeyuki

last: Tahara

first: Hitoshi

last: Ozawa

first: Akio

last: Morita

first: Hirotaka

last: Ishii


title: Germ cell specific high level of H3K9me3 in chicken PGCs: distribution and role in gene expression control


title: The initial age-associated decline in early T-cell progenitors reflects fewer pre-thymic progenitors and altered signals in the bone marrow and thymus microenvironments

city: Austin

first: Lauren

last: Ehrlich

state: TX

address: Neural and Molecular Sciences building

institute: University of Texas at Austin

summary: To identify candidatemechanisms underlying the early decline in CLPs and MPPs by 3MO.

overall_design: We carried out bulk RNA-seq on 1MO v 3MO CLPs and MPPs (N=3 independent experimental repeats) using 150bp paired-end sequencing with a target of 20 million reads per sample.

middle: I

first: Ellen

middle: R

last: Richie

first: Jayashree

last: Srinivasan

first: Anusha

last: Vasudev


title: Trim2b mediates protection against SVCV infection by degrading NLRP12-like and viral SVCV-N/SVCV-G proteins

city: wuhan

first: wu

middle: xiao

last: man

address: Donghu South Road

institute: Institute of Hydrobiology, Chinese Academy of Sciences

summary: In the present study, we report the functional characterization of zebrafish trim2b. we show that zebrafish trim2b plays a protective role in the host defense against SVCV infection. During SVCV infection, the in vivo studies revealed that trim2b overexpression led to the decreased virus loads and increased survival rate. Zebrafish trim2b deficiency led to the increased virus loads and decreased survival rate. In addition, Zebrafish trim2b deficiency leads higher numbers of immune related DEGs and signaling pathways enriched during the SVCV infection or uninfection. Among them, NOD-like receptor signaling pathway was significantly enriched. The present study characterized two NLRs degraded by trim2b plays a negative role in the host defense against SVCV infection.

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of  WT and trim2b-/- zebrafish larvae at  6 days post fertilization and 48 hours post SVCV infection

first: Ming

middle: X

last: Chang

first: Hong

last: Fang


title: Single-cell RNA-seq analysis of Mettl14d/d mouse uterus compared to Mettl14f/f mouse uterus on gestational day 4

status: Public on Apr 25 2024

first: Ji-Long

last: Liu

address: 483 Wushan Rd

institute: South China Agricultural University

summary: We specifically deleted Mettl14 in mouse uterus using the Pgr-Cre driver. To portray the molecular mechanism for Mettl14 function in mouse uterus, uterine tissues were collected from Mettl14f/f and Mettl14d/d mice on gestational day 4 and subjected to single-cell RNA-seq analysis.

overall_design: Uterine tissues were collected from Mettl14f/f and Mettl14d/d mice on gestational day 4 and subjected to single-cell RNA-seq analysis.


title: Alzheimer’s disease neuroinflammatory risk genes can be targeted with RNase-H active antisense oligonucleotides in human microglia

city: Leuven

first: Ivana

last: Geric

address: O&N4 Herestraat 49,

country: Belgium

institute: KU Leuven, Department of Neurosciences

summary: Microglia play important roles in maintaining brain homeostasis. The discovery of genetic variants in the genes encoding Apolipoprotein E (APOE) and triggering receptor expressed on myeloid cells 2 (TREM2) as the strongest risk factors for Alzheimer’s disease (AD) highlights the importance of microglial biology in the brain. The sequence, structure and function of microglial proteins are poorly conserved across species, and this hampered the development of APOE and TREM2 targeting therapeutic strategies. One way to target APOE and TREM2 is to modulate their expression using antisense oligonucleotides (ASOs). In this study, we identified ASOs that selectively and potently reduce human APOE and TREM2 levels in human myeloid cells including iPSC-derived microglia. We demonstrated that a single bolus delivery of the ASOs in the mouse cerebrospinal fluid (CSF) is sufficient for the ASO to be pharmacologically active and modify the phenotype of xenografted human microglia throughout the mouse brain for at least 4 weeks. This study is the first proof-of-concept that the expression of microglial genes can be modulated using ASOs in a dose-dependent manner in order to manipulate human microglia phenotypes in vivo, and demonstrates the utility of these ASOs both as research and therapeutic tools to modulate neuroinflammation.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Bulk RNA sequencing on FACS-sorted CD11b+/hCD45+ xenotransplanted human microglia, examining App-NL-G-F mice (xenotrasplanted with human-embrionic-stem-cell-derived microglia) treated for 1 or 4 weeks with APOE- and TREM2-targeting antisense oligonucleotides compared to vehicle treatment, at 6-7 month of age (6 groups in total; 4 mice per experimental group).

first: Lina

last: Vandermeulen

first: Mohamed

last: Kreir

first: Ashley

last: Lu

first: Annelies

last: Nonneman

first: Leen

last: Wolfs

first: Rafaela

last: Policarpo

first: Nicola

last: Fattorelli

first: An

last: De Bondt

first: Ilse

last: Van Den Wyngaert

first: Mark

last: Fiers

first: Bart

last: De Strooper

first: Constantin

last: d’Ydewalle

first: Renzo

last: Mancuso


title: The human cumulus cell transcriptome provides poor predictive value for embryo transfer outcome

city: Madrid

first: Leopoldo

last: González-Brusi

state: Madrid

address: Avda Puerta de Hierro, 12

department: Animal Reproduction

institute: Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria

summary: Is the transcriptome of cumulus cells a good predictor of the embryo’s developmental competence? The objective of this study was to analyze the transcriptional differences between cumulus cells from oocytes exhibiting different developmental potentials following individual in vitro embryo production and transfer by RNA‐seq. Cumulus cells were allocated into three groups according to the developmental potential of their enclosed oocyte: (1) not able to develop to the blastocyst stage (Bl–), (2) able to develop to the blastocyst stage but failing to establish a pregnancy (P–), or (3) able to develop to the blastocyst stage and to establish a clinical pregnancy (P+).

overall_design: RNAseq analysis was performed on 5 samples  of cumulus cells surrounding oocytes of different developmental ability corresponding to three groups (Bl-, P- and P+)

first: A

last: Martínez-Moro

first: L

first: I

last: Lamas-Toranzo

first: P

last: González-Dosal

first: F

last: Rodríguez-Juarez

last: Bermejo-Álvarez


title: A complete map of affinity and specificity encoding for a partially fuzzy protein interaction

city: Barcelona

first: Taraneh

last: Zarin

address: C/Dr. Aiguader 88

institute: Centre for Genomic Regulation

summary: Thousands of protein domains encoded in the human genome function by binding up to a million short linear motifs embedded in intrinsically disordered regions of other proteins. How affinity and specificity are encoded in these binding domains and the motifs themselves is not well understood. The evolvability of binding specificity - how rapidly and extensively it can change upon mutation - is also largely unexplored, as is the contribution of ‘fuzzy’ dynamic residues to affinity and specificity in protein-protein interactions. Here we produce the first global map of affinity and specificity encoding in a globular protein domain. Quantifying >200,000  energetic interactions between the domain and ligand allows us to identify 20 major energetically coupled pairs of sites. These are organised into six modules, with the vast majority of mutations in each module only reprogramming specificity for a single position in the ligand. Nine of the major energetic couplings encoding specificity are direct structural contacts and 11 have an allosteric mechanism of action. The dynamic tail of the ligand is more robust to mutation than the structured portion but contributes additively to binding affinity and communicates with structured residues to enable changes in specificity. Our results present how affinity and specificity are encoded in a globular protein domain interacting with a disordered peptide and a direct comparison of the encoding of affinity and specificity in structured and dynamic molecular recognition.

overall_design: Input and output samples of DNA amplicons from libraries of variants used to quantify fitness/protein binding scores of different variants of PSD95-PDZ3 and CRIPT proteins. Libraries were transformed into yeast and subjected to a protein complementation assay with or without a selective drug.


title: The effect of high or low fat diet on the miRNA composition of exosomes derived from adipose tissue

city: Shanghai

first: Yunkai

last: Lin

address: Qianju Road 366

department: National Center for Liver Cancer

institute: Second Military Medical University

type: Non-coding RNA profiling by high throughput sequencing

summary: Exosomes are nanosized extracellular vesicles with lipid bilayer membranes and contain various contents, including lipids, miRNAs and proteins, all of which are widely involved in signaling pathways and genetic information processes. Exosomes derived from adipose tissues (AT-Exos) have been identified as a crucialmedium in the transmission of information from adipose tissue to itself and to other organs, including exosomes derived from inguinal white adipose tissue (iWAT-Exos), visceral white adipose tissue (vWAT-Exos) and brown adipose tissue (BAT-Exos). Here we reported that dietary conditions and tissue origins of exosome can affect the composition and function of miRNAs in AT-Exos, mainly including lipid metabolism and inflammatory signaling pathways associated with metabolic imbalance.

overall_design: To describe the miRNA profiles of AT-Exos under diet-induced obesity, we isolated WAT-Exos and BAT-Exos from 6 weeks wild-type C57BL/6 (B6) mice fed a high-fat diet (HFD) or low-fat diet (LFD) over 4 months. We then performed miRNA profiling analysis using data obtain from miRNA-seq of 4 different AT-Exos. Comparative miRNA profiling analysis of miRNA-seq data for LFD-WAT-Exos and HFD-WAT-Exos, LFD-BAT-Exos and HFD-BAT-Exos, LFD-WAT-Exos and LFD-BAT-Exos, HFD-WAT-Exos and HFD-BAT-Exos.


title: Effect of exosomes dervied from different adipose tissue on gene expression in 3T3L1 cells under high-low fat diet conditions

summary: Exosomes derived from adipose tissues (AT-Exos) have been identified as a crucialmedium in the transmission of information from adipose tissue to itself and to other organs, including exosomes derived from inguinal white adipose tissue (iWAT-Exos), visceral white adipose tissue (vWAT-Exos) and brown adipose tissue (BAT-Exos). However, the functional differences in depot-specific AT-Exos under obese conditions remain elusive. Here we reported that AT-Exos participated in regulating adipocyte inflammation and metabolic homeostasis. Notably, vWAT-Exos play a critical role in promoting lipid accumulation and inflammation in the development of obesity. Although both are derived from “energy storage” WAT, the biological effects exhibited by iWAT-Exos are far different from those vWAT-Exos. Especially under diet-induced obesity conditions, iWAT-Exos appeared to be BAT-Exo-like, exhibiting an “energy expending” type. Altogether, our data indicated that AT-Exos from different depots have distinct functions and effects on adipocytes metabolism.

overall_design:
To verify the effects of AT-Exos on metabolic homeostasis in adipocytes, we isolated iWAT-Exos, vWAT-Exos and BAT-Exos from (High fat diet) HFD-fed or (low fat diet) LFD-fed mice and stimulated mature 3T3-L1 adipocytes.
We then performed gene expression profiling analysis using data obtain from RNA-seq of 7 different cells.
Comparative gene expression profiling analysis of RNA-seq data for 3T3L1 cells control group and its treatment group (LFD-iWAT-Exos, LFD-vWAT-Exos, LFD-BAT-Exos, HFD-iWAT-Exos, HFD-vWAT-Exos and HFD-BAT-Exos).
Comparative gene expression profiling analysis of RNA-seq data for 3T3L1 cells treated with LFD-AT-Exos and 3T3L1 cells treated with HFD-AT-Exos.


title: Lipid droplet-mediated danger signaling balances Trem2+ macrophage induction and NLRP3 inflammasome activation in NASH

city: Ann Arbor

first: Xiaoxue

last: Qiu

state: MI

address: 210 Washtenaw

department: Life Sciences Institute

institute: University of Michigan

summary: Macrophages are exquisitely capable of sensing danger-associated molecular patterns (DAMPs) and orchestrating inflammatory response during tissue injury. Nonalcoholic steatohepatitis (NASH) represents an advanced stage of metabolic fatty liver disease that increases the risk for cirrhosis and liver cancer. Pathogenic mechanisms of NASH center on hepatocyte injury and the ensuing immune response within the liver microenvironment. However, the nature of DAMPs released by injured hepatocytes and how they shape the liver immune milieu remain largely unknown. Here we show that lipid droplets (LDs) released by injured fatty hepatocytes provide a potent signal that triggers monocyte infiltration and maturation into Trem2+ macrophages, recently described as NASH-associated macrophages (NAMs) or lipid- associated macrophages. LD treatment exacerbated liver injury in mice with diet-induced NASH. We identified Membrane spanning 4-domains a7 (Ms4a7) as a NAM-specific pathogenic factor that was strongly induced in mouse and human NASH. Ms4a7 inactivation ameliorated key aspects of diet-induced NASH pathologies in mice. At the mechanistic level, Ms4a7 physically interacts with NLR family pyrin domain containing 3 (NLRP3) and is required for endosomal NLRP3 inflammasome activation. These findings illustrate a crucial role of Ms4a7 in driving pro-inflammatory signaling in NASH liver. Surprisingly, LD treatments attenuated Ms4a7 expression and NLRP3 inflammasome activation in cultured macrophages. As such, LDs serve as a DAMP signal that balances the induction of Trem2+ macrophages and NLRP3 inflammasome activation in NASH liver

overall_design: Bulk RNA-seq on nonalcoholic steatohepatitis (NASH) mouse liver in WT and Ms4a7 KO; Bulk RNA-seq on healthy mouse liver treated with either lipid droplets (LD) or PBS; Single-nucleus RNA-seq on NASH mouse liver in different genotypes

first: Linkang

last: Zhou

first: Tongyu

last: Liu

first: You

last: Lu

first: Siming

last: Li

first: Jiandie

middle: D


title: LIX1L aggravates NASH-HCC progression by reprogramming of hepatic Metabolism and microenvironment via CD36

city: 南京市

first: 映蓉

last: 冷

state: 江苏省

address: 江苏省南京市江宁区龙眠大道639号中国药科大学

institute: 中国药科大学

summary: Limb expression 1-like protein (LIX1L) plays important role in various liver disorders, but its role and underlying mechanism in nonalcoholic hepatitis (NASH) and HCC progression remains obscure. Here, we report that LIX1L functions as a key integrative regulator linking lipid metabolism and inflammation, adipose tissue dysfunction and hepatic microenvironment reprogramming which promotes NASH progression. LIX1L significantly upregulated in NAFLD/NASH patients, mouse models and palmitic acid-stimulated hepatocytes. Lix1l deletion inhibits lipid deposition, inflammatory response and fibrosis in liver as well as adipocyte differentiation by downregulation of fatty acid translocase CD36 expression, alleviating NASH and associated HCC progression. In contrast, adeno-associated virus (AAV)-mediated LIX1L overexpression exacerbates NASH progression in mice. Mechanistically, metabolic stress promotes PARP1 mediated poly-ADP-ribosylation (PARylation) of LIX1L, subsequently increasing the stability and RNA binding ability of LIX1L protein. LIX1L binds to AU-rich element (ARE) in the 3’ untranslated region (UTR) of CD36 mRNA, thus attenuating CD36 mRNA decay. In NASH and associated HCC mouse models, LIX1L deficiency-mediated downregulation of CD36 suppresses adipogenesis, hepatic lipid uptake, and reprograms the tumor-prone liver microenvironment with increased cytotoxic T lymphocytes (CTLs), reduced immunosuppressive cell proportions. These data indicate a systematic function of LIX1L in the pathogenesis of NASH and underscore the PARP1/LIX1L/CD36 axis as a potential target for treatment of NASH and associated HCC.

overall_design: To investigate how LIX1L affects NASH, we conducted RNA sequencing (RNA-seq) on the livers of LIX1L KO and WT mice that were subjected to a high-fat diet (HFD).

first: Yingrong

last: Leng

first: Yanqiu

last: Zhang

first: Yang

last: Cheng

first: Shengtao

last: Ye

first: Ying

last: Zheng

first: Mengmeng

last: He

first: Enyi

last: Wu

first: Hao

first: Lingyi

last: Kong


title: KCTD proteins have redundant functions in controlling cellular growth.

city: Montreal

first: Terence

last: Hébert

state: Quebec

address: 3655 Promenade Sir William Osler

department: Pharmacology and Therapeutics

country: Canada

institute: McGill University

summary: We explored functional redundancy of three structurally related KCTD proteins, KCTD2, KCTD5 and KCTD17 by progressively knocking them out in HEK 293 cells using CRISPR/Cas9 genome editing. After validating knockout, we assessed the effects of progressive knockout on cell growth and gene expression. We noted progressive effects of knockout of KCTD isoforms on cell growth were most pervasive when all three isoforms were deleted suggesting some functions were conserved between them. This was also reflected in progressive changes in gene expression. Our previous work indicated that Gb1 was involved in transcriptional control of gene expression, so we compared gene expression patterns between GNB1 and KCTD KO. Knockout of GNB1 lead to numerous changes in the expression levels of other G protein subunit genes while knockout of KCTD isoforms, had the opposite effect, presumably because of their role in regulating levels of Gb1. Our work demonstrates a unique relationship between KCTD proteins and Gb1 and a global role for this subfamily of KCTD proteins in maintaining the ability of cells to survive and proliferate.

overall_design: To explore the redundancy among KCTD proteins 2, 5, and 17 in the regulation of G-proteins and cellular growth, we conducted sequential CRISPR-KO targeting these proteins in HEK293 cells.

first: Robert

last: Rizk

first: Dominic

last: Devost

first: Darlaine

last: Pétrin

middle: E


title: Gene expression profile of in-vitro differentiated Dendritic Cells (DCs) from induced pluripotent stem cell (iPSC) and cord blood sources

city: Parkville

first: Stemformatics

state: VIC

address: 30 Royal Parade

country: Australia

institute: The University of Melbourne

summary: Dendritic cells (DCs) are rare innate immune cells that are essential regulators of anti-tumour, anti-viral and vaccine responses by the adaptive immune system. We established a protocol to differentiate human dendritic cells from iPSCs and compare their behaviour with cord blood_derived equivalents. We used bulk RNA-seq analysis to characterise the different subsets of in vitro-generated DCs including DC1, DC2A and DC2B.

overall_design: In vitro-differentiated DC subsets from iPSC and cord blood CD34+ progenitors were isolated by Fluorescence-activated cell sorting (FACS) as Live HLADR+ CD11c+ CD141+ CLEC9A+ DC1,  HLADR+ CD11c+ CD1c+ CD14- DC2A and HLADR+ CD11c+ CD1c+ CD14+ DC2B subsets and were analysed by bulk RNA sequencing.

first: Zahra

last: Elahi

first: Christine

last: Wells

first: Suzanne

last: Butcher


title: Single-cell RNA sequencing reveals diverse cell populations and transcriptional differences during skeletal muscle development in Megalobrama amblycephala

city: Wuhan City

first: Qi

last: Liu

address: Huazhong Agricultural University, Hongshan District, Wuhan City, Hubei Province

institute: Huazhong Agricultural University

summary: Fish skeletal muscle plays a crucial role in various physiological functions, and providing an important source of meat for human consumption. Therefore, understanding the molecular genetic regulation of muscle development and growth can benefit in enhancing the efficacy of aquaculture. Morphological and skeletal muscle histological analysis of Megalobrama amblycephala at 14 development stages ranging from 5-240 days post-hatching (d) revealed that 30 d and 45 d are the crucial stages for postembryonic muscle fibers hyperplasia and hypertrophy in M. amblycephala, respectively. Then we utilized single cell RNA sequencing (scRNA-seq) to investigate the regulation mechanism of postembryonic muscle development in M. amblycephala skeletal muscle at 30 d and 45 d. Here, scRNA-seq obtained 45,572 cells and identified a total of 13 distinct cell types in the skeletal muscle tissue. We reconstructed the cell differentiation events using all the cell clusters by single cell pseudo time trajectories, and the differentiation trajectory indicates that skeletal muscle cells derive from mesenchymal stem cells (MSCs). Furthermore, we analyzed the cell-specificity of skeletal muscle-related cells and their differences at different developmental stages, and identified a total of 51 crucial genes for muscle development, including 9 genes from muscle progenitors, 35 genes from myoblasts, and 7 genes from skeletal myocytes. Cell-cell communication analysis indicated that IGF, VEGF, and SEMA3 signaling pathways serve as important incoming signaling pathways for MSCs at 30 d. Skeletal myocytes (SMs) and tendon cells etc., might influence the differentiation of MSCs into myogenic lineages via Igf2b - Igf1ra and Igf1 - Igf1ra ligand - receptor interaction. This study revealed a list of new genes involved in M. amblycephala postembryonic myogenesis, and will provide the information for the molecular breeding of muscle mass trait in M. amblycephala.

overall_design: The rapid period (30 days and 45 days) of hyperplasia and hypertrophy of the dorsal skeletal muscle of Megalobrama amblycephala was analyzed using scRNA-seq.

first: Lusha

first: Zexia

last: Gao


title: Deep transcriptional profiling of the two cancer stem cell populations present in the SW480 cell line as presented in "Colorectal Cancer Stem Cell Subtypes Orchestrate Distinct Tumor Microenvironments"  [bulk RNA-seq]

city: Irvine

first: Linzi

last: Hosohama

address: 839 Health Sciences Court

institute: University of California Irvine

summary: Tumor heterogeneity derives from diverse populations of cancer cells that contribute unique properties to the microenvironment and tumor progression. While multiple classification systems have been developed to define tumor subtypes in colorectal cancer (CRC), the lack of single cell resolution has prohibited a better understanding of how these distinct cancer cell subtypes influence the overall tumor phenotype. Here were report that two cancer stem cell subtypes that are oncogenic versions of the intestinal Crypt Base Columnar (CBC) and Regenerative Stem Cell (RSC) populations, are commonly co-present in human CRC. We develop subtype-specific xenograft models utilizing a heterogeneous patient cell line (SW480) that contains CBCs and RSCs, and we define their tumor microenvironments at high resolution via single cell RNA sequencing. RSCs create differentiated, inflammatory, slow growing tumors. CBCs create proliferative, immune-suppressive, invasive tumors. With this enhanced resolution, we unify current CRC patient classification schema with TME phenotypes and organization.

overall_design:
Two subtype populations from the human colorectal cancer cell line SW480 (SW480-CBC and SW480-RSC) were isolated by Fluorescence-activated cell sorting (FACS) using the cell surface receptor ROBO1 (clone: MAB7118). Five replicates each of ROBO1pos (SW480-CBC) and ROBO1neg (SW480-RSC) cells were obtained and directly submitted for bulk RNA-sequencing.
We then performed DESeq2 analysis to compare gene expression in each subtype.

first: Amber

middle: N

last: Habowski

first: Marian

middle: L

last: Waterman


title: Putting the STING back into BH3-mimetic drugs for TP53 mutant blood cancers

first: Sarah

middle: T

last: Diepstraten

address: 1G Royal Pde

institute: The Walter and Eliza Hall Institute

summary: TP53-mutant blood cancers remain a major clinical challenge. BH3-mimetic drugs inhibit BCL-2 pro-survival proteins to promote cancer cell apoptosis. Despite acting downstream of TP53, functional TP53 is required for maximal cancer cell killing by BH3-mimetics through an unknown mechanism. Here, we report TP53 can be activated following BH3-mimetic induced mitochondrial outer membrane permeabilization, which leads to induction of BH3-only proteins, thereby potentiating the pro-apoptotic signal. TP53-deficient lymphomas lack this feed-forward loop, providing opportunities for survival and disease relapse after BH3-mimetic treatment. The therapeutic barrier imposed by defects in TP53 could be overcome by direct activation of the cGAS/STING pathway, which promotes apoptosis of blood cancer cells through TP53-independent BH3-only protein upregulation. Combining clinically relevant STING agonists with BH3-mimetics efficiently killed TP53-mutant mouse B lymphoma, human NK/T lymphoma and acute myeloid leukemia cells. This represents a promising therapy regime that can be fast-tracked to tackle TP53-mutant blood cancers in the clinic.

overall_design: To examine the downstream efffects of apoptosis-inducing drugs, mouse Eu-Myc lymphoma cells were treated with the MCL-1 inhibitor S63845 and/or the STING agonist diABZI for 24 h in the presence of caspase inhibitors and RNAseq performed. For STING agonist comparisons, 2 independent Eu-Myc lymphoma cell lines were included. For MCL-1 inhibitor (S63845) comparisons, 3 independent Eu-Myc lymphoma cell lines were included. The study includes parental lymphomas (control, containing Cas9 and a non-targeting sgRNA (hBim)), as well as Trp53 KO and Sting KO derivatives, generated by CRISPR/Cas9.

first: John

last: La Marca

first: Gemma

last: Kelly


title: ZBTB16 inhibits DNA replication and induces cell cycle arrest by targeting WDHD1 transcription in lung adenocarcinoma [ChIP-seq]

city: jinan

first: Deyu

last: Guo

state: Shandong Province

address: Science and Education Park

department: Shandong Provincial Hospital

institute: Shandong University

summary: Lung adenocarcinoma is a malignant tumor with high morbidity and mortality. ZBTB16 plays a double role in various tumors; however, the potential mechanism of ZBTB16 in the pathophysiology of lung adenocarcinoma has yet to be elucidated. We herein observed a decreased expression of ZBTB16 mRNA and protein in lung adenocarcinoma and a significantly increased DNA methylation level of ZBTB16 in patients with lung adenocarcinoma. Analysis of public databases and patients’ clinical data indicated a close association between ZBTB16 and patient survival. Ectopic expression of ZBTB16 in lung adenocarcinoma cells significantly inhibited cell proliferation, invasion, and migration. It also induced cell cycle arrest in the S phase. Meanwhile, mitotic catastrophe was induced, and DNA damage and apoptosis occurred. In line with these findings, the overexpression of ZBTB16 in xenograft mice resulted in the inhibition of tumor growth. Comprehensive analysis showed that WDHD1 was a potential target for ZBTB16. The overexpression of both isoforms of WDHD1 significantly reversed the ZBTB16-mediated inhibition of lung adenocarcinoma proliferation and cell cycle. These studies suggest that ZBTB16 impedes the progression of lung adenocarcinoma by interfering with WDHD1 transcription, making it a potential novel therapeutic target in the management of lung adenocarcinoma.

overall_design: Chromatin Immunoprecipitation DNA-sequencing (ChIP-seq) was performed to detect the target genes of ZBTB16 in A549 cell line.

first: Jiajun

last: Du

first: Kai

last: Wang

first: Tao

last: Yan

first: Shijie

last: Sun

first: Yadong

first: Haotian

last: Zheng

first: Guanghui


title: Tissue-resident trained immunity in hepatocytes protects septic-liver injury in zebrafish

first: dahai

last: Yang

address: No.130, Meilong Road, Xuhui District

institute: East China University of Science and Technology

summary: Trained immunity is classically characterized by long-term epigenetic reprogramming of innate immune cells to combat infectious diseases. Infection-induced organ injury is a common clinical severity phenotype of sepsis. However, whether the induction of trained immunity plays a role in protecting septic-organ injury remains largely unknown. Here, through establishing an in vivo β-glucan training and secondary LPS challenge-induced organ injury model in zebrafish larvae, we observe that induction of trained immunity could inhibit the pyroptosis of hepatocytes to alleviate septic-liver injury, with an elevated epigenetic modification of trimethylation at histone 3 lysine 4 (H3K4me3) that targets mitophagy activation. Moreover, we identify a novel C-type lectin domain receptor in zebrafish, named DrDectin-1, which is revealed as the orchestrator in gating H3K4me3 rewiring-mediated mitophagy activation and alleviating the pyroptosis-engaged septic-liver injury in vivo. Taken together, our results uncover a tissue-resident trained immunity in maintaining tissue homeostasis at a whole animal level, and offer a facile in vivo model to efficiently integrate trained immunity for immunotherapies.

overall_design: ChIP-Seq for H3K4me3 in zebrafish liver (ZFL)  cells after β-glucan treatment

first: Zhuang

first: Yuanyuan

first: Dahai


title: Single-cell ATAC-seq analysis of human plasma cell differentiation

city: Montpellier

first: Elina

last: Alaterre

address: 141 Rue de la Cardonille

institute: Institute of Human Genetics

summary: We performed single-cell ATACseq on the four populations (MBC, prePB, PB and PC) generated during normal plasma cell differentiation

overall_design: prePB, PB and PC were generated in vitro from MBC and isolated by Fluorescence-activated cell sorting (FACS)

first: Sara

last: Ovejero

first: Jérôme

last: Moreaux


title: Telomerase is essential for cardiac differentiation and sustained metabolism of human cardiomyocytes

city: Hannover

first: Maximilian

last: Fuchs

address: Carl-Neuberg-Str. 1

department: IMTTS

country: Germany

institute: Hanover Medical School

summary: The scRNA seq was performed on day 12 of hiPSC-cardiomyocyte differentiation protocol with 3 different conditions of telomere length at the hiPSC stage, namely- long telomeres, intermediate telomeres and short telomeres. The analysis showed expected clusters of the mesodermal lineage but a shift of clusters was observed depending upon the telomere legth status of the parent CRISPRi TERT hiPSCs used for differentiation

overall_design: The scRNA seq was performed on day 12 of hiPSC-cardiomyocyte differentiation protocol with 3 different conditions of telomere length at the hiPSC stage, namely- long telomeres, intermediate telomeres and short telomeres. This was performed in a doxycycline inducible CRISPRi TERT hiPSC line.


title: KIS counteracts PTBP2 and regulates alternative exon usage in neurons

first: Carme

last: Gallego

state: Catalonia

address: Baldiri Reixac 15 3-A16

institute: IBMB-CSIC

summary: Alternative RNA splicing is an essential and dynamic process in neuronal differentiation and synapse maturation, and dysregulation of this process has been associated with neurodegenerative diseases. Recent studies have revealed the importance of RNA-binding proteins in the regulation of neuronal splicing programs. However, the molecular mechanisms involved in the control of these splicing regulators are still unclear. Here we show that KIS, a kinase upregulated in the developmental brain, imposes a genome-wide alteration in exon usage during neuronal differentiation. KIS contains a protein-recognition domain common to spliceosomal components and phosphorylates PTBP2, counteracting the role of this splicing factor in exon exclusion. At the molecular level, phosphorylation of unstructured domains within PTBP2 causes its dissociation from two co-regulators, Matrin3 and hnRNPM, and hinders the RNA-binding capability of the complex. Furthermore, KIS and PTBP2 display strong and opposing functional interactions in synaptic spine emergence and maturation. Taken together, our data uncover a post-translational control of splicing regulators that link transcriptional and alternative exon usage programs in neuronal development.

overall_design: To analyze the role of KIS in genome-wide exon usage during neuronal differentiation in vitro we infected cortical neurons at 7DIV with lentiviral constructs co-expressing GFP and a shRNA targeted against KIS or a control shRNA, and collected them at 18DIV to obtain total RNA from triplicate samples for deep sequencing analysis.

first: Marcos

last: Moreno-Aguilera


title: The molecular basis of scale development highlighted by a single-cell atlas of Bicyclus anynana butterfly pupal forewings

city: Sheffield

first: Anupama

last: Prakash

address: Firth Court

institute: University of Sheffield

summary: Butterfly wings display a diversity of cell types, including large polyploid scale cells, yet the molecular basis of such diversity is poorly understood. To explore scale cell diversity at a transcriptomic level, we employ single-cell RNA sequencing of ∼5,200 large cells (>6 μm) from 22.5- to 25-h male pupal forewings of the butterfly Bicyclus anynana. Using unsupervised clustering, followed by in situ hybridization, immunofluorescence, and CRISPR-Cas9 editing of candidate genes, we annotate various cell types on the wing. We identify genes marking non-innervated scale cells, pheromone-producing glandular cells, and innervated sensory cell types. We show that senseless, a zinc-finger transcription factor, and HR38, a hormone receptor, determine the identity, size, and color of different scale cell types and are important regulators of scale cell differentiation. This dataset and the identification of various wing cell-type markers provide a foundation to compare and explore scale cell-type diversification across arthropod species.

overall_design: Large cells (>6 µm) from 22.5-25-hour male pupal forewings of the butterfly Bicyclus anynana were isolated using Fluorescence Activated Cell Sorting (FACS) and analyzed using scRNA-seq


title: Multiome in the same cell revealed the impact of osmotic stress on Arabidopsis root tip development at single-cell level [ATAC]

city: Baoding

first: Qing

last: LIU

state: Hebei

address: Lingyusi Street

department: College of Horticulture, College of Life Sciences

country: Afghanistan

institute: Hebei Agricultural University

summary: Cell-specific transcriptional regulatory networks (TRNs) play vital roles in plant development and response to environmental stresses. However, traditional single-cell mono-omics techniques are unable to fully capture the relationships and dynamics of molecular information within cells. While data integration algorithm facilitates the merging of single-cell RNA-seq and single-cell ATAC-seq data, ensuring the accuracy of the integration process remains a challenge, particularly when investigating cell-type-specific TRNs. In this study, we aimed to elucidate the TRNs of Arabidopsis under osmotic stress at the single-cell level by employing single-cell multi-omics technology to simultaneously examine gene expression and chromatin accessibility of 16,670 Arabidopsis root tip nuclei. We performed 12,968 peak-to-gene linkage at bona fide single-cell level, instead of previous computational integration at cell type level, which enabled us to obtain an unprecedented resolution to reconstruct transcriptional regulation. Pseudotime developmental trajectories revealed that osmotic stress led to shift the developmental status of Suberin synthetic endodermis (Suberin-endo) and trichoblast cells. We identified candidate stress-related cell-specific enhancers and cis-regulatory elements as well as potential target genes, and uncovered large cellular heterogeneity. We also found that cis-regulatory elements became accessible prior to gene expression and these cis-regulatory elements could form a positive feedback loop with epigenetic modification H3K4me3 in response to osmotic stress in columella cells.

overall_design: In this study, we used the 10x Chromium Single Cell Multiome ATAC + Gene Expression platform to simultaneously perform transcriptome and chromatin accessibility sequencing within the same cell in Arabidopsis root tips. This approach enabled us to more precisely dissect the transcriptional regulatory network of Arabidopsis gene expression under osmotic stress at the single-cell level.


title: Telomerase is essential for cardiac differentiation and sustained metabolism of human cardiomyocytes II

summary: In this study, we employed an inducible CRISPRi human induced pluripotent stem cell (hiPSC) line to silence TERT expression enabling the generation of hiPSCs and hiPSC-derived cardiomyocytes with long and short telomeres. Reduced telomerase activity and shorter telomere lengths of hiPSCs strongly hampered their differentiation potential towards cardiomyocytes

overall_design: The bulk RNA seq was performed on CRISPRi TERT hiPSC line with 4 different conditions in a doxycycline inducible CRISPRi TERT hiPSC line. The telomerase activity and telomere length were altered at the hiPSC stage to give rise to - long telomeres (C2 group, no doxycycline), intermediate telomeres (D2 group- 2 passages with doxycycline) and short telomeres (D5 group-5 passages with doxycycline) and reversed (R2 group-2 passages without doxycycline from the D5 group).

first: Shambhabi

last: Chatterjee


title: Single-cell RNA-seq analysis of human plasma cell differentiation

summary: We performed single-cell RNAseq on the four populations (MBC, prePB, PB and PC) generated during normal plasma cell differentiation


title: Effect of depletion of KDM4D, NFIB, and MLL1 on gene expression during adipogenic differentiation of C3H10T1/2 mesenchymal stem cells

city: San Diego

first: April

middle: Elizabeth

last: Williams

state: California

address: 10010 N Torrey Pines Rd

department: IGC

institute: Salk Institute for Biological Studies

summary: The limited efficacy of currently approved immunotherapies in EGFR-mutant lung adenocarcinoma (LUAD) underscores the need to better understand alternative mechanisms governing local immunosuppression to fuel novel therapies. Elevated surfactant and GM-CSF secretion from the transformed epithelium induces tumor-associated alveolar macrophages (TA-AM) to proliferate and support tumor growth by rewiring inflammatory functions and lipid metabolism. TA-AM properties are driven by increased GM-CSF—PPARγ signaling and inhibition of airway GM-CSF or PPARγ in TA-AMs suppresses cholesterol efflux to tumor cells, which impairs EGFR phosphorylation and restrains LUAD progression. In the absence of TA-AM metabolic support, LUAD cells compensate by increasing cholesterol synthesis, and blocking PPARγ in TA-AMs simultaneous with statin therapy further suppresses tumor progression and increases T cell effector functions. These results reveal new therapeutic combinations for immunotherapy resistant EGFR-mutant LUADs and demonstrate how such cancer cells can metabolically co-opt TA-AMs through GM-CSF—PPARγ signaling to provide nutrients that promote oncogenic signaling and growth.

overall_design: Single-cell RNA sequencing of lungs from EGFR-mutant LUAD tumors with WT and PPARγ-/- macrophages or their littermate healthy controls.

first: Alexandra

last: Kuhlmann-Hogan

first: Susan

last: Kaech


title: Integrative Gene Regulatory Network Analysis Discloses Key Driver Genes of Fibromuscular Dysplasia in Females: the DEFINE-FMD study

city: Aurora

first: Mary

last: Weiser-Evans

state: CO

address: 12700 East 19th Avenue, C281

department: Renal Diseases & Hypertension

institute: University of Colorado Anschutz Medical Campus

summary: Fibromuscular dysplasia (FMD) is poorly understood but relatively common vascular disease affecting 3-5% of adult females. 1-3 The pathobiology of FMD involves arterial lesions of stenosis, dissection, tortuosity, dilation and aneurysm which can lead to hypertension, stroke, heart attack and even death. 3-7 While a limited number of gene variants have been associated with FMD,8-12  there are no animal models and few insights as to why this disease occurs. 3,13 By integrating DNA genotype and RNA sequence data from primary fibroblasts of 83 FMD patients and 71 matched healthy controls from the DEFINE-FMD study, we inferred 18 gene co-expression networks, of which four were found to act together as an FMD-associated supernetwork in the arterial wall. After in vivo perturbation of this gene co-expression supernetwork by selective knockout of a top network key driver, mice developed arterial dilation/aneurysm; a hallmark of FMD. Molecular studies indicated that this supernetwork governs multiple aspects of vascular cell physiology and functionality, including collagen/matrix production. Using linkage disequilibrium score regression to determine genetic contribution to disease, 14-16 we found that this supernetwork accounts for 45.4% of FMD heritability (H2 ). These studies illuminate the complex causal mechanisms of FMD and suggest a potential therapeutic avenue to address this challenging disease.

overall_design: Aortic and carotid arteries tissue were harvest from female Sm22α-Ubr4KO and Sm22α-Ubr4WT mice 8-9 months after tamoxifen treatment.

first: Valentina

last: d'Escamard

first: Sizhao

last: Lu

first: Jason

last: Kovacic


title: Maternal Circulating Exosomal miR-185-5p as Non-invasive Biomarker for the Prediction of Recurrent Pregnancy Loss.

city: xi'an

first: yujing

last: xiong

state: Shaanxi

address: Xinyi Road, Baqiao District

department: Obstetrics and Gynecology

institute: Tangdu Hospital of Air Force Medical University

summary: Pregnancy losses usually happening suddenly and are irreversible, this study aims to find a predictive biomarker of the upcoming pregnancy loss. We collected serum exosomes from pregnant women prospectively from 6 to 8 weeks gestation and divided the patients into ongoing pregnancy (OP) group, sporadic pregnancy loss (SPL) group, and recurrent pregnancy loss (RPL) group according to the pregnancy progress and pregnancy history. Then we performed genome-wide miRNA expression profiling by small RNA sequencing to identify differences between patients who are going to lose pregnancy and who would not. The results showed there were 68 miRNAs differently expressed among three groups. When comparing RPL group with OP group, there was a set of 43 miRNAs differentially expressed including 25 miRNAs up-regulated in the RPL group and 18 miRNAs down-regulated. Compared SPL group with OP group, there was a set of 76 miRNAs differentially expressed including 24 miRNAs up-regulated in the SPL group and 52 miRNAs down-regulated. Moreover, we combined RPL group and SPL group into PL group, and then compared PL group with OP group, there were 81 miRNAs expressed differently while 60 were up-regulated and 21 were down-regulated. Our study found that there were significant differences in the expression levels of exosomal miRNAs in peripheral blood between patients who continued pregnancy and those who were about to miscarriage, suggesting that maternal peripheral blood exosomal miRNAs could be used as predictive molecular markers for miscarriage.

overall_design: Maternal serum exosomal miRNAs expression profile in early pregnancy.

first: Yujing

last: Xiong

first: Xiaohong

last: Wang

first: Zheng

last: Fang


title: FABP4 deficiency ameliorates alcoholic steatohepatitis in mice

status: Public on Apr 24 2024

city: Nan ning

first: Hao

last: Xing

address: zhongshan Street

institute: Guangxi Key Laboratory of Immunology and Metabolism for Liver Diseases, Nanning

summary: Fatty acid-binding protein 4 (FABP4) plays an essential role in metabolism and inflammatory. However, the role of FABP4 in alcoholic steatohepatitis (ASH) remains unclear. This study aimed to investigate the function of FABP4 and the underlying mechanisms in the progression of ASH.

overall_design: To further investigate the mechanisms of Fabp4 in the development of ASH, we performed transcriptional profiling of the liver tissues of ASH mice.


title: Effects of mir-483 and mir-663a knockout in human cancer cell lines

city: Tübingen

first: Daniel

middle: J.

last: Merk

address: Otfried-Müller-Str. 27

institute: Hertie-Institute for Clinical Brain Research

summary: CRISPR/Cas9 knockout screens were performed to identify core fitness miRNA gene in human cancer cell lines.

overall_design: Gene expression profiling of human cancer cell lines with knockout of either mir-483 or mir-663a.

middle: J

first: Ghazaleh

last: Tabatabai


title: Multiome in the same cell revealed the impact of osmotic stress on Arabidopsis root tip development at single-cell level [Cut&Tag]


city: Taiyuan

first: Liqin

last: Yan

address: Jiefang Road

institute: Shanxi Medical University

summary:
Gene expression in NCI-H1299 cells infected with shCtrl and shRPL35A was detected with a PrimeView human gene expression array.
Gene expression profiling of shCtrl and shRPL35A NCI-H1299 cells was acquired and analyzed. Differentially expressed genes were identified based on fold change of mean of expression (fold change ≥ 1.3) and FDR (< 0.05) from P value calculated based on linear model of empirical Bayesian distribution. Finally, 2055 upregulated genes and 1559 downregulated genes were characterized.

overall_design: Gene expression in shRPL35A NCI-H1299 cells and control NCI-H1299 cells was detection using Human gene expression array. Firstly, total RNA was extracted and RNA quality and integrity was determined by Nanodrop 2000 (Thremo Fisher Scientific) and Agilent 2100 and Agilent RNA 6000 Nano Kit (Agilent). Then, RNA sequencing was performed with Affymetrix human GeneChip PrimeView According to the instructions. The outcomes were scanned by Affymetrix Scanner 3000. Raw Data filtering was completed by using a Welch t-test with Benjamini-Hochberg FDR (|Fold Change| ≥ 1.3 and FDR < 0.05 as significant). Finally, Ingenuity Pathway Analysis (IPA) (Qiagen, Hilden, Germany) was executed and |Z - score| ≥ 2 is considered valuable.

first: Xinri

last: Zhang


title: Single cell profiling of SW480 subtype-specific subcutaneous and orthotopic xenografts (SW480-CBC and SW480-RSC) as presented in "Colorectal Cancer Stem Cell Subtypes Orchestrate Distinct Tumor Microenvironments" [scRNA-seq]

first: Linzi

last: Hosohama

summary: Tumor heterogeneity derives from diverse populations of cancer cells that contribute unique properties to the microenvironment and tumor progression. While multiple classification systems have been developed to define tumor subtypes in colorectal cancer (CRC), the lack of single cell resolution has prohibited a better understanding of how these distinct cancer cell subtypes influence the overall tumor phenotype. Here were report that two cancer stem cell subtypes that are oncogenic versions of the intestinal Crypt Base Columnar (CBC) and Regenerative Stem Cell (RSC) populations, are commonly co-present in human CRC. We develop subtype-specific xenograft models utilizing a heterogeneous patient cell line (SW480) that contains CBCs and RSCs, and we define their tumor microenvironments at high resolution via single cell RNA sequencing. RSCs create differentiated, inflammatory, slow growing tumors. CBCs create proliferative, immune-suppressive, invasive tumors. With this enhanced resolution, we unify current CRC patient classification schema with TME phenotypes and organization.

overall_design:
SW480-subtype specific (CBC or RSC) and mixed parental SW480 xenograft tumors were generated in NSG mice by left and right rear flank injections (i.e. subcutaneous tumors; n=2 per subtype and SW480 parental) or by injecting cells into the submucosal space of the NSG mouse cecum (i.e. orthotopic tumors; n=4 per subtype only). Tumors developed for 21-28 days before excision and tissue dissociation for 10X Genomics single cell RNA-sequencing. "C2" and "pos" sample names refer to CBC xenografts; "E11" and "neg" sample names refer to RSC xenografts.
We then performed Cell Ranger alignment and Seurat clustering to identify cells corresponding to the human tumor and mouse tumor microenvironment compartments. We provide compiled R objects (.rds) containing all of the mouse and human cells that passed quality control in subcutaneous tumors (subQ_xenografts combined) and orthotopic tumors (ortho_xenografts combined).

first: Delia

middle: F

last: Tifrea

first: Marian

last: Waterman


title: Identification of cambium stem cell factors and their positioning mechanism

city: Helsinki

first: Xixi

address: Pläsinpellonkuja 4 B 50

country: Finland

institute: University of Helsinki

summary: Wood constitutes the majority of terrestrial biomass.Composed of xylem, it arises from one side of the vascular cambium, a bifacial stem cell niche that also produces phloem on the opposing side. It is currently unknown which molecular factors endowcambium stem cell identity. Here we show that TDIF ligand-activated PXY receptors promote the expression of CAMBIUM AINTEGUMENTA-LIKE (CAIL) transcription factors to define cambium stem cell identity inthe Arabidopsisroot. By sequestrating the phloem-originated TDIF, xylem-dependent PXY confines the TDIF signaling front, resulting in the activation of CAIL expression and stem cell identity in only a narrow domain. Our findings show how signals emanating from cells on opposing sides ensure robust yet dynamically adjustable positioning of a bifacial stem cell.

overall_design: There are 2 groups (Mock, Induced), made up of 3 biological replicates with 2 time points (8hours, 24hours) totalling 12 samples. For each sample, 1.5cm of root segments below the root-hypocotyl junction were collected from 15 individuals, and visible lateral roots were removed.

first: Gugan

last: Eswaran

first: Jing

first: Tiina

last: Blomster

first: Ari

middle: P

last: Mähönen


title: Differential expression analysis connects knock-downs of eIF3e and eIF3d with the MAP kinase signaling pathway

city: Prague

first: Anna

last: Herrmannová

address: Vídeňská 1083

country: Czech Republic

institute: Institute of Microbiology of the Czech Academy of Sciences

summary: A prominent hallmark of cancer is deregulated protein synthesis. It is well established that various translation initiation factors (eIFs) are either overexpressed or under-expressed in numerous types of cancer. Recent studies suggest that rather than representing an indirect consequence of neoplasia, imbalanced expression of eIFs significantly contributes to cellular transformation, tumor development, cancer cell survival, metastasis and tumor angiogenesis. Among them, eIF3 stands out as the largest complex composed of 12 subunits with a modular assembly, where aberrant expression of one subunit leads to partially functional subcomplexes. Here we took advantage of well-established knockdowns of subunits d, e and h of human eIF3, all implicated in cancer, and investigated their impact on differential gene expression translatome-wide by Ribo-Seq. We demonstrate that eIF3e and eIF3d knock-downs result in reduced translation efficiency of numerous components of the MAPK signaling pathway, a pathway often upregulated in cancer, and pathways preventing genotoxic stress. Concurrently, depletion of eIF3d increased translation of proteins associated with membrane organelles, whereas eIF3e depletion increased expression of numerous ribosomal proteins, implicating eIF3e in controlling the balanced production of mature ribosomes. Overall, our data illustrate that individual eIF3 subunits exert specific translational control over a broad range of cellular transcripts.

overall_design: Ribo-Seq and RNA-Seq data for HeLa cells and its KD derivatives (eIF3d, eIF3e, eIF3h)

first: Jan

last: Jelínek

first: Farkas

last: Kerényi

first: Klára

last: Pospíšilová

first: Susan

last: Wagner

last: Brábek

first: Leoš

middle: S

last: Valášek


title: Effect of expression of ZEBRA on gene expression during Ramos cells

city: Lanzhou

first: caiyue

last: que

state: 甘肃

address: 天水南路222号

institute: 兰州大学

summary: EBV immediate early protein ZEBRA was corroborated to interact with Pax5 which controls the fate of B cells. Ramos cells were infected with ZEBRA-expression lentivirus and positively infected cells were sorted, which were named Ramos-Lv-ZEBRA.

overall_design: In order to investigate the transcription differentiation among the control Ramos cells (Ramos), the lentivirus vector infected Ramos cells (Ramos-Lv-Vector) and Ramos-Lv-ZEBRA, total RNA was extracted from these three cells to perform mRAN-seq.

first: Junfei

last: Wu

first: Caiyue

last: Que

first: Huanqin

last: Liu

first: Mengdan

last: Hou

first: jing

last: Zhao

first: Guohui

last: Chen

first: Huazheng

last: Jiang

first: Yongheng

last: Shao

first: Zijian

last: Qin

first: Haozhen

last: Chang


title: Expression data from  Tieghemelin and Maslinic acid-treated C3H mice

city: Tsukuba,

first: Meriem

last: Bejaoui

state: Ibaraki

address: 1 Chome-1-1 Tennodai

institute: University of Tsukuba

summary:
Gene expression profiling reveals a potential role of Tieghemelin and Maslinic acid in stimulating hair growth in C3H mice.
C3H male mice are a model for hair growth, treated with 1% Tieghemelin, 1% Maslinic acid and 1% Minoxidil for 20 days. Microarray gene expression profiling was conducted for two biological replicates

overall_design: Collected mice skin samples were subjected to DNA microarray analysis. Template RNA was extracted using ISOGEN solution (Nippon Gene, Japan) as described above. The GeneChip WT PLUS Reagent Kit (ThermoFisher Scientific, Waltham, MA, USA) and GeneChip™ Hybridization, Wash and Stain Kit (ThermoFisher Scientific, Waltham, MA, USA) were utilized following the manufacturer's protocol to generate a purified, fragmented, and labeled aRNA.  The Clariom S array Mouse (ThermoFisher Scientific, Waltham, MA, USA) was used for hybridization in the GeneChip™ Fluidics Station (ThermoFisher Scientific, Waltham, MA, USA). The arrays were scanned using the GeneChip Scanner (ThermoFisher Scientific, Waltham, MA, USA), generating raw signal intensity values (CEL files). The CEL files were normalized using the Transcriptome Analysis Console (TAC) Software (version 4.0.1). Genes with fold change ≥ 1.7 (in linear space) and p-value ≤ 0.05 were considered differentially expressed genes (DEGs) and were used for further analysis.


title: Enteric nervous system injury and intestinal dysmotility after West Nile virus infection is mediated by perforin and Fas-ligand dependent T cell effector functions

city: St. Louis

first: Hana

last: Janova

state: MO

address: 425 S. Euclid Ave

institute: Washington University in St. Louis

summary: Intestinal dysmotility syndromes have been linked to antecedent bacterial and viral infections. For example, infection of mice with the neurotropic flavivirus, West Nile Virus (WNV), leads to intestinal transit defects. Here, we find that within one week of WNV infection, enteric neurons and glia become damaged, resulting in a permanent reduction in their network density. Using cell-depleting antibodies, adoptive transfer experiments, and mice lacking specific immune cells or immune functions, we show that infiltrating WNV-specific CD4+ and CD8+ T cells damage the enteric nervous system (ENS) and glia, which leads to intestinal dysmotility; these T cells use multiple and redundant effector functions including perforin and Fas ligand. In comparison, WNV-triggered ENS injury and intestinal dysmotility occurs independently of infiltrating monocytes, whereas resident muscularis macrophages prevent excessive damage to the ENS and glia. Overall, our experiments establish that antigen specific T cell subsets and their effector molecules responding to WNV infection cause an immune pathology directed against neurons and supporting glia that results in intestinal dysmotility.

overall_design:
Translating ribosomal affinity purification (TRAP) of the muscularis externa of West Nile virus (WNV) and mock-infected Snap25l10a GFP mice was performed at 6 days post infection to identify factors regulating response of enteric neurons in distal part of small intestine to WNV.
Isolated immunopreciptated ribosome-bound mRNA from enteric neurons was used for high-throughput sequencing.

first: Michael

last: Diamond

first: Fang

first: Thaddeus

last: Stappenbeck


title: Transcriptomic changes in SUDHL6 cells upon treatment with S63845 in the presence or abscence of active caspases

city: Frankfurt am Main

first: Meike

last: Vogler

address: Komturstrasse 3a

department: Institute for Experimental Pediatric Hematology and Oncology

institute: Goethe University Frankfurt

summary: We identified a novel form of caspase-independent cell death (CICD) induced by BH3-mimetics. To characterize the transcriptional changes during CICD and compare these to apoptotic changes, we performed RNA Seq analysis on SUDHL6 lymphoma cells treated with the MCL1 inhibitor S63845 in the presence or abscence of the broad spectrum caspase inhibitor zVAD.fmk.

overall_design: RNA Seq analaysis was performed on biological duplicates (sample 1 and sample 2). "Control" are untreated SUDHL6 cells, "S63845" were treated with  300 nM of S63845 for 8h, and "S63845+zVAD" were treated with 300 nM S63845 and 20 uM zVAD.fmk for 8 hours.


title: Human CD34+/dim neutrophil-committed progenitors do not differentiate into neutrophil-like CXCR1+CD14+CD16- monocytes in vitro

city: Verona

first: Francisco

middle: Miguel Angel

last: Bianchetto-Aguilera

state: VR

address: Strade le Grazie, 8

department: Department of Medicine

country: Italy

institute: University of Verona

summary: The advent of recent cutting-edge technologies has allowed the discovery and characterization of novel hematopoietic progenitors, including SSCloCD66b+CD15+CD11b-CD49dhiproNeu1s and SSChiCD66b+CD15+CD11b-CD49dintproNeus2s, CD66b+CD15+CD11b+CD49d+CD101-preNeus and Lin-CD66b+CD117+CD71+eNePs along human neutropoiesis process. In this research field, we recently identified CD66b-CD38+CD64dimCD115-, CD34+ and CD34dim/-cells exclusively committed to the neutrophil lineage [which we renamed as CD34+ and CD34dim/- neutrophil-committed progenitors (NCPs)], representing the earliest neutrophil precursors identifiable and sorted by flow cytometry. Moreover, based on their differential CD34 and CD45RA expression, we could identify four populations of NCPs, namely: CD34+CD45RA-/NCP1s, CD34+CD45RA+/NCP2s, CD34dim/-CD45RA+/NCP3s and CD34dim/-CD45RA-/NCP4s. This said, a very recent study by Ikeda and coworkers (PMID: 36862552) reported that neutrophil precursors termed either neutrophil progenitors (NePs) or “early neutrophil-committed progenitors” would generate immunosuppressive neutrophil-like CXCR1+CD14+CD16-monocytes. Hence, presuming that NePs/alias “early neutrophil-committed progenitors” correspond to NCPs, the selective neutrophil-commitment that we attributed to NCPs is contradicted by Ikeda and coworkers’ paper. In this study, by performing a more analytical reevaluation at the phenotypic and molecular levels of the cells generated by NCP2s and NCP4s (selected as representatives of NCPs), we categorically exclude that NCPs generate neutrophil-like CXCR1+CD14+CD16-monocytes. Rather, we provide substantial evidence indicating that the cells generated by NePs/alias “early neutrophil-committed progenitors” are neutrophilic cells at different stage of maturation, displaying moderate levels of CD14, instead of neutrophil-like CXCR1+CD14+CD16-monocytes as pointed by Ikeda and coworkers. Hence, the conclusion that NePs/alias “early neutrophil-committed progenitors” aberrantly differentiate into neutrophil-like monocytes derives, in our opinion, from data misinterpretation

overall_design:
To assess their differentiation potential,  sorted NCP2s (PMID: 35484408) were cultured on MS-5 stromal cell line (ACC 441,  Leibniz-Institut DSMZ,  Braunschweig,  Germany),  according to established protocols (PMID:26292072)
• After 6 days in culture, CD66b+ cells generated by NCP2s cells were then prepared for RNA sequencing studies. The bulk RNA-seqs obtained were then compared with other retrieved from published studies: The bulk RNA-seqs obtained were then compared with others retrieved from published studies. • GSE113182:  GSM3099240, GSM3099244 • GSE175880:  GSM5772725, GSM5772727, GSM5772728, GSM5772729, GSM5772730, GSM5772731, GSM5772732, GSM5772733, GSM5772734, GSM5772735, GSM5772736, GSM5772737, GSM5772738, GSM5772739, GSM5772740, GSM5772741, GSM5772742, GSM5772743, GSM5772744, GSM5772747, GSM5772748, GSM5772749, GSM5772751, GSM5772752, GSM5772753, GSM5772756, GSM5772757, GSM5772758, GSM5772761, GSM5772762, and GSM5772763) • GSE136107:  GSM4041235, GSM4041236, GSM4041237, GSM4041243, GSM4041244, GSM4041245, GSM4041246, GSM4041247, GSM4041248. • GSE224101: GSM7011869, GSM7011870, GSM7011871, GSM7011872, and GSM7011873)

first: Nicola

last: Tamassia

first: Marco

last: Cassatella