title: MDA-MB-231 small spheroids and capsules.

status: Public on Jun 30 2024

city: Albany

first: Ramon

last: Bossardi Ramos

state: Ny

address: 43 New Scotland Avenue

department: Department of Molecular and Cellular Physiology

country: USA

institute: Albany Medical College

type: Expression profiling by high throughput sequencing

summary: MDA-MB-231 triple-negative breast cancer cells were each grown into aggregates using two fabrication approaches, (1) liquid overlay with a low (8,000 cell) seeding density, and (2) via microencapsulation with subsequent microcapsule processing. Upon sample maturation, RNA from these samples was extracted and sequenced to help identify differences in model gene expression.

overall_design: RNA-Seq

first: Cassandra

last: Roberge

first: Barroso

last: Margarida

first: Christopher

last: James


title: A mechanically regulated liquid-liquid phase separation of the transcriptional regulator Tono instructs muscle development

city: Marseille

first: Bianca

middle: Hermine

last: Habermann

address: Avenue de Luminy 163

country: France

institute: IBDM UMR7288

summary: Muscle morphogenesis is a multi-step program, starting with myoblast fusion, followed by myotube-tendon attachment and sarcomere assembly, with subsequent sarcomere maturation, mitochondrial amplification and specialisation. The correct chronological order of these steps requires precise control of the transcriptional regulators and their effectors. How this regulation is achieved during muscle development is not well understood. In a genome-wide RNAi screen inDrosophila, we identified the BTB-zinc finger protein Tono (CG32121) as a muscle-specific transcriptional regulator.tonomutant flight muscles display severe deficits in mitochondria and sarcomere maturation, resulting in uncontrolled contractile forces causing muscle atrophy during development. Tono protein is expressed during sarcomere maturation and localises in distinct condensates in flight muscle nuclei. Interestingly, internal pressure exerted by the maturing sarcomeres deforms the muscle nuclei into elongated shapes and changes the Tono condensates, suggesting that Tono senses the mechanical status of the muscle cells. Indeed, external mechanical pressure on the muscles triggers rapid liquid-liquid phase separation of Tono utilising its BTB domain. Thus, we propose that Tono senses high mechanical pressure to in turn adapt muscle transcription specifically at the sarcomere maturation stage. Consistently,tonomutant muscles display specific defects in a transcriptional switch that represses early muscle differentiation genes and boosts late ones. We hypothesise that a similar mechano-responsive regulation mechanism may control the activity of related BTB-zinc finger proteins that, if mutated, can result in uncontrolled force production in human muscle.

overall_design: Design 1: tono[1]; Mef2-Gal4, UAS-GFP-Gma IFM at 30 h APF versus control Mef2-Gal4, UAS-GFP-Gma IFM at 30 h APF; Design 2: tono[1]; Mef2-Gal4, UAS-GFP-Gma IFM at 48 h APF versus control Mef2-Gal4, UAS-GFP-Gma IFM at 48 h APF; Design 3: tono[1];Mef2-Gal4, UAS-GFP-Gma IFM at 48 h APF versus tono[1]; Mef2-Gal4, UAS-GFP-Gma IFM at 30 h APF;  Design 4: control Mef2-Gal4, UAS-GFP-Gma IFM at 48 h APF versus control Mef2-Gal4, UAS-GFP-Gma IFM at 30 h APF

first: Xu

last: Zhang

first: Jerome

last: Avellaneda

first: Maria

middle: L

last: Spletter

first: Sandra

last: Lemke

first: Pierre

last: Mangeol

middle: H

first: Frank

last: Schnorrer


title: A novel small molecule derived from Lentinula edodes targets PRDX1 to inhibit RANKL-induced osteoclast differentiation and rescues the osteoporotic phenotype [Denatonium]

city: Cheongju

first: Kyunghwan

last: Kim

address: Rm #202a, Bldg. S1-5, 1 chungdae-ro

country: South Korea

institute: Chungbuk National University

summary: Bone remodeling, crucial for skeletal integrity, involves osteoclasts and osteoblasts. Osteoclastogenesis, regulated by NFATc1, is activated by c-Fos and NF-κB signaling in response to RANKL. Excessive RANKL signaling contributes to bone loss pathology. Here we reveal denatonium as an inhibitor of RANKL-induced osteoclast differentiation through the p65 pathway. RNA-seq identified downregulated osteoclast-related genes. Affinity chromatography pinpointed 35 denatonium-interacting proteins, with PRDX1 showing specificity. PRDX1 deficiency led to osteoporosis with increased osteoclast activity and enhanced RANKL-induced osteoclast formation. Denatonium blocked PRDX1 lysosomal degradation, stabilizing PRDX1. Through transcription factor binding site analysis, p65 emerged as a major target suppressed by the denatonium-PRDX1 interaction. Chromatin immunoprecipitation confirmed that the denatonium-PRDX1 complex inhibited p65 enrichment at promoter regions critical for osteoclast differentiation. In an osteoporosis animal model, denatonium treatment restored bone health. This study uncovers denatonium's novel role in bone formation regulation by selectively targeting PRDX1, suggesting its potential in osteoporosis treatment.

overall_design: To explore the impact of denatonium on osteoclast differentiation, bone marrow macrophages (BMMs) were exposed to RANKL (100ng/ml) for 72 hours, with or without the presence of denatonium.


title: Comparative gene expression profiling analysis of RNA-seq data for WT (Nipponbare) and OsEXPA7 overexpression.

city: Shanghai

first: xinwei

state: Shanghai

address: No. 2005, Songhu Road, Yangpu District

department: State Key Laboratory of Genetic Engineering

country: China

institute: Fudan University

summary: Yield and quality are the two most important traits in crop breeding. Exploring the regulatory mechanisms that affect both yield and quality traits is of great significance for understanding the molecular genetic networks controlling these key crop attributes. Expansins are cell wall loosening proteins that play important roles in regulating rice grain size. We investigated the effect of OsEXPA7, encoding an expansin, on rice grain size and quality. OsEXPA7 overexpression resulted in increased plant height, panicle length, grain length, and thousand-grain weight in rice. OsEXPA7 overexpression also affected gel consistency and amylose content in rice grains, thus affecting rice quality. Subcellular localization and tissue expression analyses showed that OsEXPA7 is localized on the cell wall and is highly expressed in the panicle. Hormone treatment experiments revealed that OsEXPA7 expression mainly responds to methyl jasmonate, brassinolide, and gibberellin. Transcriptome analysis and RT-qPCR experiments showed that overexpression of OsEXPA7 affects the expression of OsJAZs in the jasmonic acid pathway and BZR1 and GE in the brassinosteroid pathway. In addition, OsEXPA7 regulates the expression of key quantitative trait loci related to yield traits, as well as regulates the expression levels of BIP1 and bZIP50 involved in the seed storage protein biosynthesis pathway. These results reveal that OsEXPA7 positively regulates rice yield traits and negatively regulates grain quality traits by involving plant hormone pathways and other trait-related pathway genes. These findings increase our understanding of the potential mechanism of expansins in regulating rice yield and quality traits and will be useful for breeding high-yielding and high-quality rice cultivars.

first: Xinwei

first: Ying

last: Wang

first: Mingyu

last: Liu

first: Peiwen

last: Yan

first: Fuan

last: Niu

first: Fuying

last: Ma

first: Jian

last: Hu

first: Shicong

last: He

first: Jinhao

last: Cui

first: Xinyu

last: Yuan

first: Jinshui

last: Yang

first: Liming

last: Cao

first: Xiaojin

last: Luo


title: A novel small molecule derived from Lentinula edodes targets PRDX1 to inhibit RANKL-induced osteoclast differentiation and rescues the osteoporotic phenotype [PRDX KO]

overall_design: To investigate the effect of Prdx1 on osteoclast differentiaion, BMMs depleted of mock or Prdx1 were treated with or without RANKL (100ng/ml) for 48 h.


title: Surufatinib increases cholangiocarcinoma cells radiosensitivity by anti-tumor proliferation and inhibition of macrophage M2 polarization

city: Wuhan

first: Ningyu

state: Hubei

address: JIEFANG ROAD1277#

department: Cancer Center, Union Hospital

institute: Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China

summary: This study confirmed the radiosensitizing effects of surufatinib on cholangiocarcinoma. The mechanism is that surufatinib can activate TLR3, up-regulate the expression of TRIF protein, increase DNA damage and apoptosis after radiation, and up-regulate NF- κB signal pathway to inhibit M2 polarization of tumor-associated macrophages, thus enhance radiosensitivity.

overall_design: In order to investigate the mechanism of surufatinib in enhancing radiotherapy sensitivity of cholangiocarcinoma, we used a cholangiocarcinoma cell line TFK1, and set up a blank control group, a radiotherapy group (6Gy), a chemotherapy group  (surufatinib 4.33ng/ml), and a combination treatment group (surufatinib 4.33ng/ml+RT 6Gy). After 24 hours of treatment, total RNA was extracted for transcriptome sequencing in different treatment groups.

first: Wang

last: Ningyu

first: Huang

last: Ai

first: Mei

last: Xiangping

first: Ma

last: Hong


title: Whole transcriptome analysis of Acinetobacter calcoaceticus Aca13 induced by n-hexadecane or naphthalene

city: Changchun city

first: Tingdi

last: Zhang

state: Jilin Province

address: 2519 Jiefang Road

department: college of new energy and environment

institute: Jilin University

summary: Petroleum hydrocarbons are recalcitrant contaminants, which has caused most serious environmental problems. Acinetobacter calcoaceticus Aca13 was isolated from petroleum polluted soil for petroleum biodegradation. Hexadecane and naphthalene were used to incubate with Acinetobacter calcoaceticus Aca13. After incubation, the whole transcriptome was obtained from treated groups and control groups, and then used for RNA sequence and analysis. Obtained data in this project will help us understand the biodegradation mechanism of hexadecane and naphthalene, and will be helpful for the bioremediation of petroleum hydrocarbons.

overall_design: 3 Groups: Hexadecane group (named as AcaH1, AcaH2, AcaH3, respectively), naphthalene group (named as AcaN1, AcaN2, AcaN3, respectively) and control group (named as Aca1, Aca2, Aca3, respectively). Each group has three replicates.

first: Hongchu

last: Chen

first: Ze

first: Sishuo

first: Zhixing

first: Yongxiao

first: Chuanyu

last: Qin


title: SMXL4/5-HsfA2 regulatory loop orchestrates plant growth-thermotolerance trade-off

city: Shenzhen

first: Yan

last: wei

address: shenzhenxueyuanroad

institute: Southern University of Science and Technology

summary: Heat stress (HS) is often a recurring and constant threat to crop productivity worldwide. For optimal crop survival, a sensitive and dynamic balance between stress-response and growth-control is required. Previous studies have demonstrated unique properties of 22-nt siRNAs in plant adaptation to environmental stresses, yet much less is known about how DCL2 regulate mechanisms under stresses in detail. Here, we demonstrate that the production of 22-nt siRNAs, particularly from SMXL4/5, might be crucial for plants to adapt to HS.

overall_design: High-throughput sequencing of total mRNA from Col-0 (co), ski2 dcl4 (sd), ski2 dcl4 dcl2 (sdd), smxl4 smxl5 (s45), and smxl6 smxl7 smxl8 (s678) Arabidopsis seedlings with or without 44 ℃ 85 min heat stress

first: Yajie

last: Pan


title: Oxidative burst causes loss of tapetal Ubisch body and male sterility in rice

first: Chuanlin

last: Shi

address: Dapeng

institute: Chinese Academy of Agricultural Sciences

summary: We identified the nup1 mutant rice that exhibited specific male sterility due to the absence of Ubisch body formation and pollen grain production. We cloned the causal gene and demonstrated that NUP1, a class III peroxidase predominantly expressed in the anther wall, mediated ROS scavenging. The loss-of-function of NUP1 resulted in ROS burst in anthers, which disrupted the oxidation-reduction process and carbohydrate and lipid metabolisms, and thereby led to loss of tapetal Ubisch bodies and ultimately resulted in male sterility in rice. Our study expands the understanding of the molecular mechanisms by which ROS homeostasis regulates cell metabolism, tapetal Ubisch body formation and male fertility in plants.

overall_design: Anthers at stages of 10 (S10) and 11 (S11) from wild-type and nup1 mutant were collected with three biological replicates. Total RNA was isolated and used for poly(A) RNA isolation with oligo(dT) beads, and were then used for RNA-seq library construction using the NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs), based on the manufacturer’s instructions. RNA-seq libraries were sequenced (paired-end 150-bp) on an Illumina NovaSeq 6000 platform at Novogene, China. After quality control and adapter trimming, reads were mapped to the Oryza sativa v.7.0 genome sequences (MSU Rice Genome Annotation Project) using Hisat2 (Kim et al., 2019). Gene expression level quantification and differential expression analysis (FDR < 0.01, FC > 2) were conducted using Cufflinks (Trapnell et al., 2010).

last: shi

first: Lianguang

last: Shang


title: A scalable, GMP-compatible, autologous organotypic cell therapy for Dystrophic Epidermolysis Bullosa

city: Stanford

first: Anthony

last: Oro

state: CA

address: 269 Campus Drvie

department: Dermatology

institute: Stanford University

summary: Gene editing in induced pluripotent stem (iPS) cells has been hailed for enabling new cell therapies for various monogenetic diseases including dystrophic epidermolysis bullosa(DEB). However, manufacturing, efficacy, and safety roadblocks have limited the development of genetically corrected, autologous iPS cell-based therapies. We developed Dystrophic Epidermolysis Bullosa Cell Therapy (DEBCT), a new generation GMP-compatible (cGMP), reproducible, and scalable platform to produce autologous clinical-grade iPS cell-derived organotypic induced skin composite (iSC) grafts to treat incurable wounds of patients lacking type VII collagen (C7).

overall_design: 4 samples, 2 replicates of each from iPSC derived keratinocytes sorted based on CD49f/ITGA6.

first: Jessica

last: Torkelson

first: Sadhana

last: Gaddam


title: Divergent roles for caspase-8 and MLKL in high-fat diet induced obesity and NAFLD in mice

city: New York

first: Isabella

last: Kong

state: New York

address: 1300 York Ave

institute: Weill Cornell Medicine

summary: Cell death frequently occurs in the pathogenesis of obesity and non-alcoholic fatty liver disease (NAFLD). However, the exact contribution of core cell death machinery to disease manifestations remains ill defined. Here, we show via the direct comparison of mice genetically deficient in apoptotic caspase-8 in myeloid cells, or the essential necroptotic regulators, Receptor-interacting protein kinase-3 (RIPK3) and Mixed lineage kinase domain-like (MLKL), that RIPK3-caspase-8 signaling regulates macrophage inflammatory responses and drives adipose tissue inflammation and NAFLD upon high-fat diet feeding. In contrast, MLKL, divergent to RIPK3, contributes to both obesity and NAFLD in a manner largely independent of inflammation. We also uncover that MLKL regulates the expression of molecules involved in lipid uptake, transport and metabolism and, congruent with this, we discover a shift in the hepatic lipidome upon MLKL deletion. Collectively, these findings highlight MLKL as an attractive therapeutic target to combat the growing obesity pandemic and metabolic disease.

overall_design: Eight- to nine-week old Wild-type and Mlkl-/- mice were fed either a high-fat diet (HFD; 36% fat, 59% of total energy from lipid; Specialty Feeds, WA, Australia) or a normal chow diet (ND) ad libitum for 16-25 weeks. Liver RNA was extracted from fed animal (selected based on mean organ weights) using Trizol RNA Isolation Reagents and purified using RNeasy Mini Kit (QIAGEN).

first: Stephanie

last: Conos

first: Hazel

last: Tye

first: Tirta

last: Djajawi

first: Kate

last: Lawlor


title: A novel small molecule derived from Lentinula edodes targets PRDX1 to inhibit RANKL-induced osteoclast differentiation and rescues the osteoporotic phenotype

first: Kyunghwan

last: Kim

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

overall_design: Refer to individual Series


title: A gene regulatory network of the endothelial-to-hematopoietic transition [ATAC-seq]

city: Oxford

first: Marella

last: de Bruijn

address: MRC MHU, WIMM, John Radcliffe Hospital

department: Radcliffe Department of Medicine

country: United Kingdom

institute: University of Oxford

type: Genome binding/occupancy profiling by high throughput sequencing

summary: In vertebrate embryos, hematopoietic stem cells (HSCs) are generated from a subset of the aortic endothelium, the hemogenic endothelium (HE), via a process called endothelial-to-hematopoietic transition (EHT). The transcriptional mechanisms by which EHT is controlled, and how HE initiates hematopoietic differentiation, are not fully understood. In this study, we generated mini-bulk RNA-seq and ATAC-seq datasets from EHT populations in the E8.5 to E10.5 mouse embryonic dorsal aorta, and integrated these data to construct a predictive gene regulatory network underlying EHT.

overall_design: ATAC-seq data generated from pools of 1500 cells. Data generated from EHT cell populations from E8.5, E9.5, and E10.5 mouse dorsal aorta. Biological replicates are included. EC - endothelial cell; HE - Hemogenic endothelium, HPC - hematopoietic progenitor cell.

first: Joe

middle: R

last: Harman

first: Lucas

last: Greder

first: Gemma

last: Swiers

middle: F


title: Knockdown of EIF3G inhibits the intracellular protein translation of H1299 cells

city: Beijing

first: Shuohua

last: Chen

address: Haidian District

institute: Tsinghua University

summary: eIF3 is the largest translation initiation factor in mammalian cells, consisting of 13 subunits. This translation initiation factor is involved in multiple processes of protein translation in cells, including translation initiation, termination, and ribosome recycling. Several studies have reported that multiple subunits of eIF3 exhibit abnormal expression in tumor cells and play an important role in the occurrence and development of tumors. In this study, it was found that changes in the expression level of EIF3G significantly affected the growth of non-small cell lung cancer. Knockdown of EIF3G inhibited the intracellular protein translation process of non-small cell lung cancer cells H1299. Through the study of translatome, it was found that knockdown of EIF3G significantly affected the cell cycle processes in H1299 cells. In vitro cell experiments also showed that changes in the expression level of EIF3G influences the cell cycle distribution of H1299 cells. This study is the first to explore the impact of knockdown of EIF3G on the translatome of H1299 cells.

overall_design: The H1299 cells treated with siEIF3Gs or siCtrl were lysed, and the cell supernatants were collected after centrifugation. Ten percent of the total lysate was taken as input control. The cell lysate supernatants were then subjected to sucrose density gradient centrifugation, and the resulting products were separated using Gradient108 and Fractionator (BIOCOMP, Canada). The centrifuged products of the polysomal fraction were collected for RNA extraction. Subsequently, both the input control and the mRNA bound to the polysomes were extracted and sequenced.

first: Yan

last: Fu

first: Yongzhang

last: Luo


title: Learning-Associated Astrocyte Ensembles Regulate Memory Recall

city: Houston

first: Yeunjung

last: Ko

address: 1 Baylor Plz

institute: Baylor College of Medicine

summary: The physical manifestations of memory formation and recall are fundamental questions that remain unresolved. At the cellular level, ensembles of neurons called engrams are activated by learning events and control memory recall. Astrocytes are in close proximity to neurons and engage in a range of activities that support neurotransmission and circuit plasticity. Moreover, astrocytes exhibit experience dependent plasticity; however whether specific ensembles of astrocytes participate in memory recall remains obscure. Here we show that learning events induce c-Fos expression in a subset of hippocampal astrocytes, which subsequently regulates hippocampal circuit function. Intersectional, c-Fos based labeling of these astrocyte ensembles after learning events reveals that they are closely affiliated with engram neurons, while re-activation of these astrocyte ensembles stimulates memory recall. At the molecular level, these astrocyte ensembles exhibit elevated expression of NFIA and its selective deletion from this population suppresses memory recall. Together, our studies identify learning-associated astrocyte ensembles as a new form of plasticity that is sufficient to provoke memory recall, while implicating astrocytes as a reservoir for the storage of memories.

overall_design: To further examine the molecular properties of learning-associated astrocytes, we employed the Fos-Flex-Flp AAV viral injection into a dual reporter mouse line (Aldh1l1-CreER; Aldh1l1-GFP; Rosa-CAG-FSF-tdTomato), in which all astrocytes express GFP, and Flp-expressing astrocytes additionally express tdTomato. With this system, we were able to uniquely label learning-associated astrocytes (GFP+, tdTomato+) and non-learning-associated astrocytes (GFP+, tdTomato-). After tamoxifen treatment and fear conditioning, we used FACS to purify the respective populations and performed transcriptomic RNA-sequencing.

first: Ukbong

last: Kwon

first: Michael

last: Williamson

first: Deneen

last: Benjamin


title: Persistent alterations in glucose metabolism, gut microbiome, and adipose tissue transcriptome after two-week sleep recovery in chronically sleep-fragmented female mice

first: Ling

last: Zhong

address: Wangfujing Street

department: Department of Endocrinology

institute: Peking Union Medical College Hospital

summary: Introduction: Chronic sleep fragmentation (SF) is prevalent in contemporary human society, highlighting detrimental effects on glucose metabolism and adipose tissue morphology, which is closely linked to gut microbiota composition. However, it remains unclear whether sleep recovery (SR) after prolonged SF can ameliorate glucose metabolism, influence the transcriptome of inguinal white adipose tissue (iWAT), and whether these effects align with alterations in the gut microbiota.  Methods: Mice were subjected to 8 weeks of SF and subsequently allowed 2 weeks of SR. We assessed glucose tolerance through intraperitoneal glucose tolerance tests (ipGTT), analyzed gut microbiota via 16s rDNA amplicon sequencing, and examined transcriptomic alterations in iWAT using RNA sequencing.  Results: Despite the two-week SR following chronic SF, significant glucose intolerance persisted, accompanied by subtle shifts in the gut microbiota and alterations in gene expression within iWAT. The top hub genes Ncapg, Cenpe, and Tik were identified from the protein-protein interaction network.  Conclusion: Even followed by a brief period of SR, prolonged SF still led to ongoing glucose intolerance and alterations in the adipose tissue transcriptome in mice. These changes were intertwined with modifications in the gut microbiome. The shifts in gut microbiota may play a pivotal role in understanding the sustained negative effects of SF.

overall_design: RNA sequencing was conducted on 15-week-old female C57BL/6N mice who were subjected to  8 weeks of sleep fragmentation and subsequently allowed 2 weeks of sleep recovery.


title: Differentially expressed genes between the bone metastatic subpopulations and lung metastatic subpopulations of lung adenocarcinoma

city: Suzhou

first: zhao

last: WANG

address: No. 199 Ren'ai Road

department: Suzhou Medical College

institute: Soochow University

summary: To define the molecular underpinning of LUAD bone metastasis, we performed high-throughput transcriptome sequencing (RNA-seq) using total RNA from LuM and BoM cell subpopulations. Afterwards, differentially expressed genes were used for further analysis.

overall_design: We established a mouse model for multi-organ metastases of A549 cells, which generated four bone-metastatic subpopulations (A549-BoM-1, 2, 3, and 4) and lung-metastatic subpopulations (A549-LuM-1, 2, and 3). All of them were used for RNA-seq, and the LuM group was used as negative control.

first: Zhao

last: Wang

first: Zhe

last: Lei


title: A chromatin-driven mechanism of transcription in ammonia-oxidizing archaea under environmental stress [RNA-seq]

summary: Ammonia-oxidizing archaea (AOA) play a significant role in global nitrogen and carbon cycling. AOA can survive under fluctuating environmental conditions by modulating gene expression. Little is known about how AOA regulate gene expression to adapt environmental stress. Here, we report a chromatin-driven mechanism of transcription in Nitrososphaera Viennensis (EN76) to adapt to temperature stress. Using computational and biochemical assays, we found EN76 contains an archaeasome structure. We found that several residues, including G20, K57, and T58 of histone, are important to form archaea chromatin structures. In vitro transcription assays revealed that AOA chromatin efficiently controls gene expression, similar to eukaryote chromatin. Furthermore, we identified AOA histone acetylation, which activates gene expression. Moreover, by integrating chromatin-based gene expression analyses, we revealed that AOA differentially regulate gene expression in response to temperature stress by altering archaeasome occupancy. Our study provides unprecedented documentation that AOA fine-tunes gene expression through a chromatin-driven epigenetic mechanism.

overall_design: To investigate the effect of thermal stress on archaea, N. viennensis was cultured in 5 L of artificial freshwater medium at two different temperatures (33 °C and 42 °C) in the dark


title: Glutamine inhibition combined with CD47 blockade enhances radiotherapy-induced ferroptosis in head and neck squamous cell carcinoma [RNA-Seq]

first: An

last: Song

address: Luoyu Road 237

institute: Wuhan University

summary:
To investigate the glutamine inhibition combined with CD47 blockade regulation of ferroptosis in HNSCC.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 3 different cells at two time points.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for SCC7 cells and cells received radiotherapy.

first: Lei

last: Wu

first: Bo-Xin

last: Zhang

first: Qi-Chao

last: Yang

first: Yuan-Tong

last: Liu

first: Hao

last: Li

first: Liang

last: Mao

first: Dian

last: Xiong

first: Hai-Jun

last: Yu

first: Zhi-Jun

last: Sun


title: Male MEIKIN mutations cause sperm chromosome chaos and recurrent blastulation failure afteriIntracytoplasmic sperm injection

city: Changsha

first: Xueqin

last: Chen

state: Hunan

address: Medical College of Xiangya, No.172 Tongzipo Road, Changsha City, Hunan Prov, China

department: SCHOOL OF BASIC MEDICAL SCIENCES

institute: Central South of University

summary: We describe a unique phenotype, blastulation failure, in three primary infertile males with oligoasthenoteratozoospermia (OAT) who underwent intracytoplasmic sperm injection (ICSI), resulting in multiple good-quality cleavage embryos that repeatedly failed to achieve blastulation or implantation. Single-cell analysis revealed that the arrested embryos had complex spermatozoa-derived chromosomal abnormalities, major embryonic genome activation failure, and overactivation of stress and apoptosis pathways at the transcriptional level. We further identified mutations in the meiosis-specific kinetochore factor MEIKIN gene in these males, causing OAT and chromosomal chaos in the spermatozoa. This study is the first to establish a connection between the genetic etiology of OAT and a novel embryo development arrest phenotype, indicating potenial risks of ICSI for OAT patients and providing a new explanation for recurrent implantation failure.

overall_design: Arrested embryos from patients with MEIKIN gene mutations were separated into single blastomeres for smart-seq2 sequencing to explore alterations in gene expression.

first: Wenbin

last: He

first: Weina

first: Gang

first: Yueqiu

last: Tan

first: Ge

last: Lin


title: Lymphatic-derived 25-hydroxycholesterol promotes immunity in melanoma by inhibiting PPAR-γ in tumor associated macrophages and monocytes

city: Geneva

first: Natacha

last: Civic

address: Rue Michel-Servet 1

department: iGE3 Genomics Platform

country: Switzerland

institute: University of Geneva

summary: In melanoma, lymphangiogenesis correlates with metastasis and poor prognosis and promotes immunosuppression. However, it also potentiates immunotherapy by supporting trafficking of immune cells. Lymphatic endothelial cells (LECs) are highly plastic cells that shape their phenotype according to distinct microenvironments, which likely define their functional properties, such as immunomodulation. Here, we show in a lymphangiogenic murine melanoma model that LECs upregulate the enzyme Ch25h, which catalyzes the formation of 25-hydroxycholesterol (25-HC) from cholesterol and plays important roles in regulating lipid metabolism, gene expression, and immune activation. LECs represent the main source of extracellular 25-HC in tumors, leading to the inhibition of PPAR- in intra-tumoral macrophages and monocytes. This prevents their immunosuppressive phenotype and instead promotes their conversion into proinflammatory myeloid cells that support effector T cell functions. We identify here in mechanistic detail a novel LEC function that supports anti-tumor immunity, which can be therapeutically exploited in combination with immunotherapy.

overall_design: mRNA profiles of lymphatic endothelial cells derived from lymphangiogenic mouse melanoma cell line B16-OVA-VEGFC which transplanted in Ch25h lymphatic-specific knock-out mice or littermate control.

first: Mengzhu

first: Dale

last: Brighouse

first: Stéphanie

last: Hugues


title: A gene regulatory network of the endothelial-to-hematopoietic transition

first: Marella

last: de Bruijn


title: Characterization of the mutational landscape of high-grade gliomas in a Latin American cohort

city: Temuco

first: Mauricio

middle: A.

last: Saez

address: Manuel Montt 56

country: Chile

institute: Universidad Catolica de Temuco

summary: We conducted a targeted genomic analysis using next-generation sequencing techniques in 70 Chilean patients with high-grade gliomas from a national single-center referral institution. We focused on relevant molecular markers such as mutations in isocitrate dehydrogenase 1/2 (IDH), telomerase reverse transcriptase promoter (TERTp), histone 3 (H3) gene family, TP53 and PTEN, epidermal growth factor receptor (EGFR) gene amplification, and cyclin-dependent kinase inhibitor 2A (CDKN2A) deletions. Survival analyses were performed to assess the clinical relevance and their impact on patient prognosis. Additionally, we explored the endoplasmic reticulum stress-related gene ERN1 due to its potential role in high-grade gliomas. This study underscores the importance of glioblastoma research in underrepresented populations, providing insights into high-grade gliomas molecular characteristics within Latin America. Our findings contribute to the growing evidence suggesting molecular diversity across glioblastoma populations, offering a foundation for future international comparative studies.

overall_design: We conducted an observational retrospective cohort study, which included 70 patients aged 18 and above  with a confirmed diagnosis of high-grade glioma based on the current WHO classification system for CNS tumors at the time. Patients who underwent total or partial resection surgery at the Asenjo Neurosurgery Institute between January 2014 and January 2020 were included in the study. 5 patients who underwent anterior temporal lobectomy for epilepsy treatment were prospectively included in the analysis as non-tumor tissue controls. We utilized the AmpliSeq™ for Illumina tool to create a customized amplicon panel covering specific genomic regions of interest of several neuro-oncology related genes.

first: Rodrigo

last: Fernandez-Gajardo

first: Hery

last: Urra

first: David

last: Rojas

first: Jose

middle: M

last: Matamala

first: Claudio

last: Hetz


title: Neuroligin 3 promotes functional recovery of spinal cord injury through coordinating with Sar1a and Hspa8 at synapses

city: Guangzhou city

first: Mangmang

last: Li

state: Guangdong province

address: 1838 N Guangzhou Ave

department: Department of Cell Biology School of Basic Medical Sciences

institute: Southern Medical University

summary: The recovery of locomotor function following incomplete spinal cord injury (SCI) primarily relies on the precise reconstruction of synaptic communications between spared corticospinal tract (CST) axons and propriospinal neurons. However, components capable of rebuilding synaptic machinery after injury remain elusive.  Here, using RNA-Seq of human umbilical cord-derived MSCs (hUC-MSCs) before and after transplantation in SCI rats, along with in vitro and in vivo functional screenings, we identified Neuroligin 3 (NLGN3) as a spinal cord microenvironment (SCE)-activated cell adhesion molecule (CAM) in hUC-MSCs, promoting MSC-mediated functional recovery of SCI. Importantly, spinal neuron-specific activation of Nlgn3 led to significant functional improvement in SCI rats, resembling the effects of hUC-MSC transplantation. We elucidated the protein interactome of Nlgn3, enriched with proteins involved in synaptic transmission. Specifically, Nlgn3 interacted with synaptic vesicle (SV)-associated proteins, Sar1a and Hspa8, modulating their recruitment at synapses. Remarkably, restoring either of these two proteins in injured spinal neurons improved locomotor recovery of SCI, with further enhancement when combined with Nlgn3. Thus, our results not only reveal the previously unknown therapeutic effect of Nlgn3 in SCI repair but also propose a novel approach for treating SCI by targeting protein complexes centered around Nlgn3. This study also suggests that MSCs can serve as a stem cell platform for identifying innovative therapeutic targets and mechanisms to reestablish corticospinal-spinal relay circuits after SCI.

overall_design:
In this study, 10-mm spinal cord segments centered at the epicenter were collected from rats subjected to different treatments for total RNA extraction.
A total of 20 sequencing libraries were prepared, encompassing three biological replicates for MSC-in vitro, four replicates for the MSC-SCI-1d, MSC-sham-1d and MSC-sham-3d groups, and five replicates for the MSC-SCI-3d groups

first: Weiwei

last: Zou

first: Musheng


title: Determine the role of ALK5 signaling in murine brain pericytes at embryonic day E13.5

city: New Haven

first: Jui

last: Dave

state: CT

address: 300 George St

department: Cardiovascular Research Center

institute: Yale University

summary: Pericytes (PCs) are microvascular mural cells which constituent the embryonic blood brain barrier (BBB) along with endothelial cells (ECs). During brain development, germinal matrix (GM) - a highly vascularized region rich in neuronal-glial precursors, is selectively vulnerable to hemorrhage in premature infants. The transforming growth factor β (TGFβ) pathway plays a crucial role in barrier development by regulating cellular cross talk between PCs and ECs. Indeed, murine embryos lacking TGFβ receptor activin receptor-like kinase 5 (Alk5) in brain PCs (mutants) develop gross germinal matrix hemorrhage-intraventricular hemorrhage (GMH-IVH) and culminate in perinatal lethality. Mutant GM vessels display reduced PC and collagen coverage, abnormal vessel dilation and EC hyperproliferation. However, the mechanistic link between PC-specific deletion of ALK5 and aberrant EC behavior remains elusive. Herein, using bulk RNA sequencing from human brain PCs lacking ALK5 (siALK5) as well as murine vascular cells [PCs and ECs] isolated from embryonic brain at embryonic days E11.5 and  E13.5 we establish that angiopoietin 2 (ANGPT2), a secreted angiogenic growth factor, is robustly repressed by the TGFβ pathway in PCs. Conversely, mutants lacking PC-ALK5 secrete higher levels of ANGPT2 resulting in overactivation of tyrosine protein kinase receptor (TIE2) and culminating in EC hyperproliferation, vessel dilation, BBB breakdown and GMH. PC-specific Angpt2 deletion or pharmacological inhibition in mutants improves GM vessel morphology, reduces EC proliferation and attenuates GMH pathogenesis. Taken together, we demonstrate that loss of TGFβ-mediated ANGPT2 repression in PCs is detrimental for BBB integrity and identify ANGPT2 as an important pathological target for GMH-IVH.

overall_design: To evaluate ALK5-mediated differential gene expression in percityes during cerebrovascular development at E13.5, perciytes were isolated from murine embryonic brains of Pdgfrb-Cre, Alk5(flox/+) [control] and Pdgfrb-Cre, Alk5(flox/flox) [mutant] mice also bearing ZS green by flow cytometry. Total RNA was isolated and subjected to bulk RNA sequencing.

first: Daniel

last: Greif


title: RNA Sequencing of Ishikawa Cell Line with NCF2 Knockdown Using Small Interfering RNA

city: Jinan

first: Yao

last: Liu

state: Shandong

address: Wenhuaxi Road 107#

institute: Qilu Hospital of Shandong University

summary: Progestin therapy is one of the preferred treatment modalities for early-stage endometrial cancer patients wishing to retain fertility and for conservatively managing advanced endometrial cancer. However, a significant number of patients currently do not benefit from progestin therapy due to issues such as progestin resistance. In the past, we established a medroxyprogesterone acetate-resistant Ishikawa cell line. From this, we identified the NCF2 gene, which was highly expressed in the resistant group. Functional validation experiments revealed that knocking down NCF2 can effectively reverse progestin resistance. To explore its mechanism, we performed RNA sequencing post-NCF2 knockdown.

overall_design: Sequencing samples were divided into two groups, with three replicates each. The control group was transfected with negative control small interfering RNA (siRNA), while the experimental group was transfected with siRNA targeting the knockdown sequence. Samples were collected 72 hours post-transfection for RNA sequencing.

first: Shourong

last: Wang

first: Jie

last: Jiang


title: A gene regulatory network of the endothelial-to-hematopoietic transition [RNA-seq]

overall_design: RNA-seq gene expression data generated from pools of 100 cells. Data generated from EHT cell populations from E8.5, E9.5, and E10.5 mouse dorsal aorta. Biological replicates are included. EC - endothelial cell; HE - Hemogenic endothelium, HPC - hematopoietic progenitor cell.

first: Joe

last: Harman

first: Lucas

last: Greder

first: Gemma

last: Swiers


title: Capture of germ-line competent stem cells between rosette-stage and formative pluripotent states

city: Hefei

first: shoudong

last: ye

address: No 111, Jiu Long Road

department: Cell Biology

institute: Anhui University

summary: The establishment of stem cells with varying pluripotency potentials is crucial for understanding the developmental progression of pre- and post-implantation embryos. Despite the advancement through the proposal of the formative pluripotent state, the model of pluripotent development remains incomplete. Here, we derived a novel type of pluripotent stem cells from mouse embryonic stem cells and sustained them in vitro through the application of MEK inhibitor PD0325901, Tankyrase inhibitor IWR1, and adenylate cyclase activator Forskolin. These cells exhibit distinct transcriptome and epigenetic profiles, resembling the epiblasts of E5.0-E5.5, and reside between rosette-like stem cells and formative stem cells. We refer to them as rfISCs (Intermediate stem cells between RSCs and FSCs). rfISCs can differentiate into germ cells in vitro and form blastocyst chimeras in vivo. Additionally, the formation of rfISCs is governed by distinct signaling pathways and transcription factors. Specifically, IWR1-mediated inhibition of Wnt signaling enhances Tcf7l1-mediated Otx2 expression, essential for rfISCs generation yet prone to inducing neural differentiation, whereas Forskolin induces Id1 transcription, suppressing neural lineage gene expression via the PKA pathway. Hence, co-overexpression of Id1 and Otx2 is sufficient to sustain rfISCs stability. The emergence of rfISCs aids in comprehending early embryo development.

overall_design: ESCs cultured in 2i conditions as control and rfISCs cultured in PIF conditions were collected by using Trizol. Two repeat groups were set for each treatment group. These samples were sent to MajorBIO (Shanghai, China) company to do deep sequencing.


title: Determine the role of ALK5 signaling in human brain pericytes treated with TGFβ.

overall_design: To evaluate ALK5-mediated differential gene expression in percityes, cultured human brain perciytes were trasnfecetd with Scr (control siRNA)or siALK5 (siRNA targeting ALK5) and then treated with or without TGFβ. Total RNA was isolated and subjected to bulk RNA sequencing.


title: Effect of miR-27a-5p on SGBS adipogenesis

city: Ulm

first: Julian

last: Roos

department: Department of Pediatrics and Adolescent Medicine

country: Germany

institute: Ulm University Medical Center

summary: We have recently confirmed miR-27a-3p as a crucial regulator of human adipogenesis (Wu H, Pula T, Tews D, Amri E-Z, Debatin K-M, Wabitsch M, Fischer-Posovszky P, Roos J. microRNA-27a-3p but Not -5p Is a Crucial Mediator of Human Adipogenesis. Cells. 2021; 10(11):3205. https://doi.org/10.3390/cells10113205 ). MiR-27a-5p did not impair human adipogenesis. However, since several publications state that miR-27a ist also a crucial regulator of UCP1, we were interested if miR-27a-3p or miR-27a-5p regulatas UCP1 and other thermogenesis related genes. We found a strong regulation of UCP1 with functional relevance for the cellular metabolism by miR-27a-5p.To asesse the mRNA gene expression pattern, mRNA sequencing was performed.

overall_design: For mRNA Sequencing RNA samples from SGBS cells transfected two days prior adipogenic induction with either 20 nM Syn-hsa-miR-27a-5p or non-target control were harvested on day 8 of adipogenesis and sent for sequencing to Eurofins Genomics (Ebersberg, Germany).  Further analysis was performed by the Core Unit Bioinformatics and Datamanagement of Ulm University.

first: Hang

last: Wu

first: Pamela

last: Fischer-Posovszky


title: RNA-seq in Black and White Sesame

city: Xuzhou

first: Tao

last: Xu

state: Jiangsu

address: Shanghai Road 101

institute: Jiangsu Normal University

summary: Sesame seeds is an important traditional crop with high oil content and other abundant nutrients which are very beneficial for diet and health of human being. However, the molecular mechanism for metabolite accumulation, especially for oil and phenylpropanoid biosynthesis, is still not very clear in sesame. In this study, the transcriptome profiles of black and white sesame seeds were compared by RNA-sequencing. Transcriptome analysis showed that the expression patterns of genes encoding phenylpropanoid pathway enzymes were different between the two sesame cultivars. Compared with white sesame, most of genes involved in oil biosynthesis were significantly down-regulated in black sesame.

overall_design: Transcriptome sequencing was performed on sesame seeds from white and black sesame cultivars, and each cultivar contained 3 biological repeats. The clean data of each library were mapped to the S. indicum genome.


title: RNA-seq of LS180 cells

city: Debrecen

first: Beáta

last: Scholtz

address: Nagyerdei krt. 98

department: Department of Biochemistry and Molecular Biology

country: Hungary

institute: University of Debrecen, Faculty of Medicine

summary: A combination of ribosome profiling and RNA-seq was used to analyze the translatome of LS180 colon adenocarcinoma cells

overall_design: 2 biological replicates were prepared from LS180 cell cultures, at 60-80% confluency, under standard culture conditions. PolyA+ RNA and ribosome-protected RNA fragments were isolated from each replicate.

first: Miklós

last: Geiszt

first: Anna

last: Orient

first: Veronika

last: Pape

last: Pató

first: Gábor

last: Sirokmány


title: Ribosome profiling of LS180 cells


title: Suppression of reactive oxygen species formation in the human colon through post-transcriptional mechanisms

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

overall_design: Refer to individual Series


title: EED mediates epigenetic repression of developmental genes in growing oocytes and modulates neural and skeletal development in offspring [Bone Samples]

city: Clayton

first: Patrick

middle: S

last: Western

state: VIC

address: 27-31 Wright Street

department: Centre for Reproductive Health

country: Australia

institute: Hudson Institute of Medical Research

summary: Epigenetic modifications regulate transcriptional access to unique cell-type-specific gene sets, which define cell differentiation and tissue development. Cell-to-cell heritability of this information provides long-term molecular memories that define cell lineage identities. Germline epigenetic programming, including genomic imprinting, can substantially alter offspring development, but the mechanisms are poorly understood. In this study we demonstrate that the essential polycomb complex gene, Eed, regulates histone methylation in a large cohort of non-imprinted developmental genes in mouse and human oocytes. Using a model that facilitates the separation of genetic and epigenetic inheritance, we show that Eed establishes H3K27me3 during a unique widow of early oocyte growth and is essential in mouse oocytes for mediating a complex program that controls fetal growth and co-ordinated development of multiple tissues in late-stage fetal offspring, including bone, brain and placenta. Our study defines a new role for Eed in epigenetic inheritance that profoundly affects offspring growth and development.

overall_design: Examination of the impact of EED deletion in oocytes on oocyte epigenetic programming and offspring development

first: Ellen

middle: G

last: Jarred

first: Ruby

last: Oberin

first: Sigrid

last: Petautschnig

first: Zhipeng

last: Qu

first: Tesha

last: Tsai

first: Heidi

last: Bildsoe

first: Stephen

last: Pederson

first: Thi

middle: T

last: Truong

first: Qing-hua

last: Zhang

first: Jessica

last: Stringer

first: John

last: Carroll

first: Marteen

last: van den Buuse

first: David

middle: K

last: Gardner

first: Natalie

middle: A

last: Sims

last: Adelson


title: High throughput gene expression data of fibroblast growth factor 19-overexpressing SK-MES-1 cells and control cells

city: shanghai

first: Yanshuang

state: China

address: 1954 Huashan Road, Shanghai Jiao Tong University, Shanghai 200030, PR China

institute: Shanghai Jiao Tong University

summary: The lung squamous cell carcinoma cell line SK-MES-1 was used to construct fibroblast growth factor 19-overexpressing stable cells and control cells, and then the mRNA levels of the two cells were detected by high-throughput sequencing

overall_design: Lung squamous cell carcinoma cell line SK-MES-1 was transfected with LV-NC or LV-FGF19, and then high-throughput sequencing was performed.

first: Tingyu

last: WU

first: Weiliang

last: Xia


title: Proteogenomic integration of single-cell RNA and protein analysis identifies novel tumour-infiltrating lymphocyte phenotypes in breast cancer

city: Darlinghurst

first: Alexander

last: Swarbrick

state: New South Wales

address: 384 Victoria Street

department: Cancer

institute: Garvan Institute of Medical Research

summary: High-throughput single-cell RNA sequencing (scRNA-Seq) has become a routine platform for the dissection of solid tumours into their cellular components. The development of methods to incorporate detection of cellular protein epitopes via barcoded antibodies has enabled advances in immunophenotyping, but its application to investigating tissue immunology has been limited. We applied joint single cell RNA and epitope analysis to a cohort of 6 breast cancer samples to improve resolution of the tumour microenvironment (TME). We detect cell types unidentifiable by analysis of RNA or protein alone, and reveal novel markers for resting and activated tissue infiltrating lymphocytes (TILs). We further identify two distinct states of activated CD4+ T follicular helper (Tfh) cells in breast cancers – one associated with markers of tissue residency and exhaustion (CD103+ Tfh), and a previously-undescribed phenotype marked by the expression of IGFL2 and NMB (IGFL2+ Tfh). The two Tfh cell subsets occupy distinct TME niches, with CD103+ Tfh cells uniquely co-localizing with and signalling to macrophages. This Tfh cell stratification is clinically important, as the increased ratio of CD103 Tfh to IGFL2+ Tfh cells associates with improved disease outcome and response to checkpoint immunotherapy. Collectively, we provide a framework for improved phenotyping of TILs and showcase how proteogenomics more robustly catalogues the emergence of novel cellular states with clinical significance in tissue contexts such as the TME.

overall_design: We performed CITE-seq on 6 primary breast cancer tumours using 10X Genomics.

first: Ghamdan

last: Al-Eryani


title: RNA-Seq analysis of kidney transcriptome profiles in young spontaneously hypertensive rats and revealing the protective effects and potential therapeutic targets of SGLT2 inhibitors in early hypertensive nephropathy

city: 重庆

first: Jianlin

last: Du

state: 重庆

address: 74 Lin Jiang Road

institute: Department of Cardiology, The Second Affiliated Hospital of Chongqing Medical University

summary: Hypertensive nephropathy is a common complication of hypertension that places a heavy burden on society. SGLT2 inhibitors are a new class of hypoglycemic agents that have been shown to have specific protective effects on the kidneys. This study aimed to investigate the early changes in renal transcription spectrum in spontaneously hypertensive rats and the effects of DAPA, a sodium-glucose cotransporter 2 inhibitor, on the remission of hypertensive nephropathy and its underlying molecular mechanisms. We furthermore show thatSGLT2 inhibitors may reduce inflammation and improve energy metabolism by regulating the expression of SLC9a3, Zbtb20, Trim50 and Ccnl2.

overall_design: In this study, three-month-old rats were randomly divided into three groups: Wistar-Kyoto (WKY; normal control), spontaneously hypertensive (SHR), and dapagliflozin-treated SHR (SGLT2) groups. After eight weeks, kidney tissues were extracted, the mRNA expression profiles were identified with RNA-Seq.

first: Xin

last: Yuan

first: Jing

last: Wang

first: JIangjun

last: Wei


title: Transcriptome and microbiome profile of nasopharyngeal samples among COVID-19 patients with different levels of severity revealed through RNA-seq analysis

city: Bandung

first: Miftahul

last: Faridl

state: Jawa barat

address: Jalan Ganeca No. 12, Dago, Coblong, Bandung, Jawa Barat, Indonesia

department: School of Life Sciences and Technology

country: Indonesia

institute: Bandung Institute of Technology

summary: Differences in symptom manifestation among COVID-19 patients are caused mainly by the host factors. Gene expression profiles from nasopharyngeal samples might provide a clue to dysregulated biological processes, causing a variety of severity levels. The metagenomic profile from nasopharyngeal tissue might also provide details of coinfection that might contribute to the severity. Hence, we performed total RNA sequencing from asymptomatic patients and patients with mild and severe illnesses. Severe groups were characterized by the upregulation of the complement gene MASP1, inflammatory cytokines CXCL5 and CXCL12, and the fibrosis markers COL1A1 and COL3A1. On the contrary, the lack of activation of the B cell immune response, T cell immune response, and the cell-surface antigen recognition and signaling process were found in this severe group.

overall_design: Total RNA sequencing of nasopharyngeal swabs from COVID-19 patients with different levels of severity (5 negative controls, 2 asymptomatic patients, 5 mildly symptomatic patients, 8 severely symptomatic patients, and 5 controls).

first: Muhammad

last: Dewantara

first: Karlina

last: Mellyani

first: Rudi

last: Wisaksana

first: Yovita

last: Hartantri

first: Karimatu

last: Khoirunnisa

first: Ihsan

last: Fauzan

first: Agust

last: Siregar

first: Findy

last: Ashgi

first: Ema

last: Rahmawati

first: Rifky

middle: W

last: Rachman

first: Cut

middle: N

last: Alamanda

first: Rini

last: Robiani

first: Hadiana

last: Hadiana

first: Ryan

middle: B

last: Ristandi

first: Popi

last: Septiani

first: Azzania

last: Fibriani


title: Estrogen alleviates acute and chronic itch in mice

city: Beijing

first: jinhua

last: jin

state: Beijing

address: 33 Ba-Da-Chu Road, Shi-Jing-Shan District

institute: Plastic Surgery Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College

summary: RNAseq analysis showed that estrogen-treatment caused significantly reduced expression level of itch-related molecules

overall_design: female mice ovariectomized ,then  a slow–release pellet of 17β-estradiol and their placebo were placed back to its ovary position in estrogen or placebo group respectively.   Placebo group displayed significantly increased itch signaling moleculars,

first: Jinhua

last: Jin

first: Li

last: Li

first: Yuhui

last: Wang

first: Keyan

first: Weiou

first: Qing

last: Liu

first: Chao

last: Wen

first: Quanle

first: Guanghai

last: Yan

first: Fushan

last: Xue


title: RNA sequencing analysis of VCaP cells resistant to abiraterone

city: Göttingen

first: Oliver

last: Hahn

address: Robert-Koch-Str. 40

department: Department of Urology

institute: University Medical Center Göttingen

summary: Here, we analyze gene expression of prostate cancer cell line VCaP (VCaP WT) and VCaP after long time treatment with abiraterone (VCaP AA) in order to investigate possible resistance mechanisms to second-generation antiandrogens.

overall_design: VCaP WT vs. VCaP AA cells after long time treatment with increasing concentrations of abiraterone (up to 5 µM). Analysis done in 2 biological replicates

first: Paul

last: Thelen

first: Johanna

middle: C

last: Becker

first: Marina

last: Bertlich


title: Analysis of m6A in NB cell line (miCLIP)

city: Trento

first: Erik

last: Dassi

state: TN

address: Via Sommarive, 9

department: CIBIO

country: Italy

institute: University of Trento

summary: miCLIP of control, METTL14-overexpressed and ALKBH5-rescued CHP-212 cells

overall_design: 3 biological samples per condition were used, for a total of 14 samples: 3 control IP, 1 control input, 3 METTL14oe IP, 1 METTL14oe input, 3 ALKBH5rc IP, 1 ALKBH5rc input, 1 igG, 1 H2O

first: Alessandro

last: Quattrone

first: Giulia

last: Montuori

first: Eliana

last: Destefanis


title: Cytoskeleton alteration regulates cardiomyocyte cell cycle activity and histone modification via Sirt1-NFAT axis

city: Shanghai

first: Rui

last: Jiang

address: 1239 Siping Road, Shanghai, P.R. China

department: Department of life science and technology

institute: Tongji university

summary: The acquisition of knowledge pertaining to the molecular mechanisms that govern cardiomyocyte (CM) proliferation would enable the creation of novel approaches to promote cardiac regeneration in adult individuals, a crucial therapeutic objective that has yet to be accomplished. The limited regenerative response observed in adult myocardium may be attributed, in part, to the relatively low proliferative capacity of cardiomyocytes. The comprehension of cardiomyocyte division is a complex undertaking, as cardiomyocytes are capable of entering the cell cycle but are unable to complete cell division. Our research revealed that the induction of cardiac cytoskeleton changes by Blebbistatin result in the entry of cardiomyocytes entry into the cell cycle but, followed by cell cycle arrest at the G2/M phase. Sirt1 is identified as a potential mediator of the binucleation process in neonatal rat cardiomyocytes, which is regulated by the cardiomyocyte cytoskeleton. Furthermore, the distribution of H3K9me3 in cardiomyocytes with varying nuclear numbers and treatments indicates a significant involvement in the formation of binucleated cardiomyocytes.

overall_design:
To investigate what mediate the cytoskeleton alters epigenetics in cardiomyocytes,we treated neonatal rat ventricular cardiomyocytes with 25μm blebbistatin or DMSO for 0.5h.
RNA-seq analysis of NRVCs treated with 0.25μm Blebb or DMSO; ChIP-Seq analysis of H3K9me3 in NRVCs treated with 0.25μm Blebb or DMSO(3 replicates per group).

first: Ke

last: Wei


title: Effect of TAFA4 on Human macrophage M2c polarization

city: Marseille

first: Bertrand

last: Escaliere

address: 163 avenue de Luminy

institute: CIML

summary: We aimed to decipher the effect of the neuropeptide TAFA4 on human M2c macrophage polarization. We used monocytes isolated from peripheral blood of three independant donors and generated different polarisations in the presence or absence of TAFA4. Monocytes were cultured with M-CSF for six days to induce their differentiation in macrophages (Mφ). On day six, the cells were left untreated or were treated for two days with dexamethasone to induce their M2c polarization. After differentiation and polarization, 100,000 cells from each condition and donor were sorted to remove debris and dead cells, then used for the sequencing.

overall_design: Total RNA was then extracted with the RNeasy Plus Micro Kit (Qiagen) and stored at -80°C until use. We used the Smart-seq v4 Ultra Low Input RNA Kit and the Nextera XT DNA Sample Preparation Kit for library construction. Sequencing was performed with HiSeq 4000 technology (Illumina).

first: Jordi

last: Gouilly

first: Sophie

last: Ugolini


title: RNA-seq analysis of mRNA expression profiles upon NAT10 depletion

city: GUANGZHOU

first: Min

last: Deng

state: GUANGDONG

address: Affiliated Cancer Hospital & Institute of Guangzhou Medical University, NO.78, Hengzhigang Road.

summary: NAT10 (N-acetyltransferase-like protein) regulates N4-acetylcytidine formation in RNA. However, the biological function and mechanisms of NAT10 were poorly defined. To understand the molecular mechanism by which NAT10 affect GC progression, we performed RNA sequencing (RNA-seq) in AGS cells with NAT10 knockout and in BGC823 cells with shNAT10, with independent biological replicates.

overall_design: Examination of RNA-seq in 2 cell types.


title: Expression profile of transcripts associated with Apcin-induced growth inhibition and apoptosis in endometrial carcinoma

city: Wuhan

first: Fang

last: Fang

address: 1277 Jiefang Avenue

department: Department of Obstetrics and Gynecology

institute: Union Hospital, Tongji Medical College, Huazhong University of Science and Technology

summary: Background: Endometrial carcinoma (EC) is a common gynecological malignancy with increasing incidence and death rate during the past years. In order to obtain better prognosis, it is necessary to develop novel therapy strategies for EC, especially for molecular targeted therapy. CDC20 is an Anaphase promoting complex/cyclosome (APC/C) activator and has been reported to exhibit an oncogenic function. Thus, CDC20 could be a promising therapeutic target for EC.  Methods: The expression of CDC20 was analyzed based on TCGA databases and Human Protein Atlas and verified in EC cell lines by western blotting. We evaluated the anti-tumor effects of CDC20 inhibitor Apcin on proliferation, apoptosis, cell cycle and mobility of EC cell lines, AN3CA and KLE, by CCK8 assay, flow cytometer analysis, wound healing and transwell assay respectively. Furthermore, we performed RNA-sequencing on EC cells with or without Apcin treatment and conducted bioinformatics analysis to explore the molecular mechanism. The differentially expressed genes were verified by PCR and western blotting.  Results: TCGA data reveal that the expression level of CDC20 is higher in EC tissue than in nonmalignant tissue. Stable and high expression of CDC20 was also detected in EC cell lines. Treatment with CDC20 inhibitor Apcin inhibited proliferation and induced apoptosis while did not influence mobility ability of EC cells. The effects of Apcin treatment on cell cycle distribution were different between these two EC cell lines. The percentage of G2/M phase cells was increased in Apcin-treated KLE cells but did not change significantly in Apcin-treated AN3CA cells. Bioinformatics analysis of RNA-seq data identified that apoptosis, P53 pathway and TNF signaling pathway were activated in EC cells after Apcin treatment, indicating the potential mechanisms through which Apcin exerted its antitumor function. Furthermore, the anti-tumor effects of Apcin are related to the regulation of BBC3 and P21 expression in EC cells.  Conclusions: CDC20 is a promising molecular target and Apcin may be a potential pharmaceutics for EC treatment. CDC20 is a novel molecular target in EC, which highlights Apcin as a candidate drug in targeted therapy of EC.

overall_design: RNA-sequencing on EC cell lines (AN3CA and KLE) with or without Apcin treatment

first: Ni

last: Ke


title: miRNA expression of kidney samples of DKD patients and controls

city: zhengzhou

first: Guo

last: Jia

address: 1 Jianshe Dong Lu, Erqi District,

institute: The First Affiliated Hospital of Zhengzhou University

summary: In order to find out the different expression of miRNA in DKD patients and controls, the kidney tissues of DKD and controls were used to do the miRNA mircroassy.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: three samples of DKDpatients and three samples of controls were performed the mircoassay analysis.

first: Jia

last: Guo


title: ALK1/Smad4 signaling is required for the identity of Kupffer cells and prevention of bacterial infection.

first: Dianyuan

last: Zhao

address: 38 Life Science Park Road

institute: National Center for Protein Sciences

summary: RNA Sequencing of liver Kupffer cells and and monocyte-derived macrophages (MoMs) to assess role of ALK1 and Smad4.

overall_design: RNA-seq for Clec4F+ Tim4+ and Clec4F- Tim4+ Kupffer cells from Alk1 fl/fl Cx3cr1-Cre mice; Kupffer cells from Smad4 fl/fl and Smad4 fl/fl Vav1-Cre mice; Monocyte-derived macrophages from Alk1 fl/fl and Alk1 fl/fl Vav1-Cre mice infected with Listeria monocytogenes 3d post infection.

first: Li

last: Tang


title: A phase 2 Randomized Controlled Trial of Adjuvant Tumor-Infiltrating Lymphocytes for Pretreatment Epstein-Barr Virus DNA-selected High-Risk Nasopharyngeal Carcinoma Patients

city: Guangzhou

first: jiang

last: li

address: 651 Dongfeng East Road, Yuexiu District, Guangzhou

institute: Sun yat-sen university

summary: 420 locoregionally advanced NPC patients underwent pEBV DNA screening. 156 patients (37.1%) who had pEBV DNA ≥4000 copies/mL were included and randomly assigned to CCRT plus TIL infusion group (n=78) and CCRT alone group (n=78). Outcomes were classified as patients with a poor outcome (nonresponders) and patients with a favorable outcome (responders). Single cell RNA sequencing (scRNA-seq) for infused TIL products in responder and non-responder.

overall_design: We profiled 4 TIL infusion products from patient with Epstein-Barr Virus DNA-selected High-Risk Nasopharyngeal Carcinoma treated with CCRT and TIL (responder, n=2; nonresponder, n=2), using single-cell transcriptomics.

first: Yu-Jing

last: Liang

first: Qiu-Yan

last: Chen

first: Jing-Xiao

last: Xu

first: Xiu-feng

last: Liu

first: Jian-Chuan

last: Xia

first: Li-Ting

first: Shan-Shan

first: Bin

last: Song

first: Pan

last: Wang

first: Ji-Bin

last: Li

first: jianhui

last: yue

first: Qing

first: Hao-Yuan

last: Mo

first: Ling

last: Sun

first: Dong-Hua

last: Luo

first: Chong

first: Sai-Lan

first: Qing-Nan

first: Xue-Song

first: Jin-Jie

last: Yan

first: Xiao-Yun

last: He

first: Yi-Na

first: Cai-Ping

last: Nie

first: Zhen-Chong

last: Yang

first: Xi

last: Zhang

first: Lin-Quan

first: Yi-Xin

last: Zeng

first: Jiang

first: Hai-Qiang

last: Mai


title: Single cell RNA-Seq of patient derived kidney organoids as a model of Fanconi renotubular syndrome

city: Parkville

first: Belinda

last: Phipson

address: 1G Royal Parade

department: Bioinformatics

institute: WEHI

summary: Three pooled iPSC-derived human kidney organoids from three different cell lines were derived from one kidney disease patient and cultured in parallel. The three cell lines represent (1) heterozygous HNF4A mutation present in the patient, (2) CRISPR-Cas9 gene corrected line, and (3) a null line that has two indels in HNF4A. The cells from the organoids were isolated and processed for single cell sequencing using 10x Genomics technology.

overall_design: High resolution single cell analysis of patient derived kidney organoids as a model of Fanconi renotubular syndrome.

first: B

first: H

last: Spijker

first: M

last: Little


title: “Bench-to-Bedside and Back” analysis of NAFLD model reveals common transcriptomic shifts between mouse and human during disease progression

city: Singapore

first: Zun Siong

last: Low

address: 11 Mandalay Rd

country: Singapore

institute: Lee Kong Chian School of Medicine

summary: Transcriptomics of mice in NAFLD progression

overall_design: Mice fed NAFLD-inducing diet for duration of weeks 1, 4, 8, 12, 16, 32, 48 compared with mice fed on purified control diet of respective duration

first: Zun

last: LOW

first: Nguan

last: TAN

first: Walter

last: WAHLI

first: Damien

last: Chua


title: RNA SEQ STEC FHI96 Type III mod

city: Gold Coast

first: John

middle: Michael

last: Atack

state: QLD

address: Gold Coast Campus

department: Institute for Glycomics

institute: Griffith University

summary: Comparison of RNA expression profiles from STEC strain FHI96 expressing methyltransferase mod (ON; 52reps) or not (OFF; 51reps).

overall_design: RNA isolated from triplicate cultures of each strain (STECmod ON 52reps and STECmod OFF 51reps) grown in LB to mid-log; comparison of gene expression profiles by comparing STECmod ON 52reps vs. STECmod OFF 51reps to determine differential gene expression influenced by Mod methylation differences due to phase-variation of mod.

first: Michael

middle: P

last: Jennings


title: Mevastatin Promotes Healing by Targeting Caveolin-1 to Restore EGFR Signaling

city: Miami

first: Marjana

last: Tomic-Canic

state: Fl

address: 1600 NW 10th Ave

institute: University of Miami

summary: We performed RNA-seq on primary human keratinocytes treated with mevastatin to identify the molecular mechanisms by which statins promote wound healing. Our results identified a mevastatin gene signature that activated and modulated the EGF signaling to trigger an anti-proliferative and pro-migratory phenotype. In addition, EGFR signaling is downregulated in chronic non-healing wounds and mevastatin was able to restore EGFR signaling by downregulating caveolin proteins, a known inhibitor of EGFR signaling and wound healing. These results demonstrate that statins may have considerable therapeutic potential for patients with chronic wounds that can be rapidly translated to clinical use.

overall_design: Transcriptome profiles from primary human keratinocytes treated with mevastatin generated by deep sequencing using Illumina NextSeq500.


title: Alcohol-Induced Alterations in Sperm Noncoding RNAs Persist After One Month Cessation and Correlate with Indicators of Epididymal Mitochondrial Dysfunction II

status: Public on Jun 29 2024

city: College Station

first: MICHAEL

middle: C.

last: GOLDING

state: Texas

address: 4466 TAMU

department: Physiology

institute: Texas A&M UNiversity

type: Non-coding RNA profiling by high throughput sequencing

summary: Background Chronic preconception paternal alcohol use modifies the sperm epigenome, inducing fetoplacental growth defects in the offspring of exposed males. A crucial outstanding question in the field of paternal epigenetic inheritance concerns the resilience of the male reproductive tract and the germline's capacity to recover and correct sperm-inherited epigenetic errors after stressor withdrawal. Objectives We set out to determine if measures of the sperm-inherited epigenetic program revert to match the control treatment one month after withdrawing daily alcohol treatments. Materials and Methods Using a voluntary access model, we exposed C57Bl6/J males to 10% alcohol for ten weeks, withdrew alcohol treatment for four weeks, and used RNA sequencing to examine gene expression patterns in the caput section of the epididymis. We then compared the abundance of sperm small RNA species between treatments. Results In the caput section of the epididymis, chronic alcohol exposures induced changes in the transcriptional control of genetic pathways related to mitochondrial function, oxidative phosphorylation, the generalized stress response (EIF2 signaling), and Sirtuin signaling. Subsequent analysis identified region-specific, alcohol-induced changes in mitochondrial DNA copy number across the epididymis, which correlated with increases in the mitochondrial DNA content of alcohol-exposed sperm. Notably, in the corpus section of the epididymis, increases in mitochondrial DNA copy number persisted one month after alcohol cessation. Analysis of sperm noncoding RNAs between Control and Alcohol-Exposed males one month after alcohol withdrawal revealed a ~100-fold increase in mir-196a, a microRNA induced as part of the Nuclear Factor Erythroid 2-Related Factor 2 (Nrf2)-driven cellular antioxidant response. Discussion and Conclusion Our data reveal that alcohol-induced epididymal mitochondrial dysfunction and differences in sperm noncoding RNA content persist after alcohol withdrawal. Further, differences in mir-196a and sperm mitochondrial DNA copy number may serve as viable biomarkers of adverse alterations in the sperm-inherited epigenetic program.

overall_design: Small RNA seq of alcohol cessation sperm between control and ethanol treatments

first: S

last: Bhadsavle


title: Age-dependent heat shock hormesis to HSF-1 deficiency suggests a compensatory mechanism mediated by the unfolded protein response and innate immunity in young Caenorhabditis elegans

city: Budapest

first: Janos

last: Barna

state: Budapest

address: ELTE Egyetem tér 1-3.

department: Genetics

institute: Eotvos Lorand University

summary: The goal of this RNA-Seq analysis was to identify genes differentially expressed in wild type (N2) and a hypomorphic mutant of the gene encoding heat shock factor 1 {hsf-1(sy441)} at normal conditions and upon heat shock. This study aimed to identify genes that are up- or downregulated when HSF-1  activity is impaired at 20 ºC. We also aimed to identify gene that are regulated by HSF-1 upon heat stress by comparing differentially expressed genes upon heat shock in wild type and in hsf-1(sy441) mutant background.

overall_design: We found that thermotolerance of 1 day old adult hsf-1(sy441) mutants is increased compared to the wild type (N2). To identify genes which possibly contribute to this phenotype we performed an RNA-seq analysis of wild type [N2] and hsf-1(sy441) at 20 ºC and determined differentialy expressed genes in hsf-1(sy441) mutant compared to the wild type.   To identify HSF-1 dependent transcriptional changes upon heat shock we performed an RNA-seq analysis of  wild type [N2] and hsf-1(sy441) animals after heat shock at 35 ºC for 30 minutes.

first: János

first: Dániel

last: Kovács


title: RNA sequencing analysis of A549 cells under glutamine deprivation

city: hefei

first: Liu

last: Kaiyue

state: anhui

institute: University of Science and Technology of China

summary: We performed RNA-seq ananlysis to idendity lncRNAs regulated by glutamine deprivation in A549 cells.

overall_design: RNA-seq was performed on A549 cells cultured in complete medium(ctrl) or glutamine-depleted medium(QD) for 24 hours, and then we compared gene expression profiling analysis of ctrl and QD RNA-seq data.

first: Kaiyue

last: Liu


title: Gomisin G inhibits pancreatic cancer cell growth through the Hippo-YAP signaling pathway

city: wenzhou

first: Changrui

last: Qian

state: zhejiang

address: wenzhou medical university

institute: wenzhou medical university

summary: Purpose: The purpose of this study was to investigate the effect of Gomisin G on the transcription level of pancreatic cancer cells SW1990.

overall_design: Methods: The pancreatic cancer cell SW1990 were treated with vehicle or Gomisin G.

first: Lan

last: Li

first: Guang

last: Wu


title: Tumor-secreted FGF21 acts as an immune suppressor by rewiring cholesterol metabolism of CD8+ T cells

first: Hu

last: Cegui

address: 160 Pujian Road, Pudong New Area, Shanghai

institute: Ren Ji Hospital

summary: Tumors use various strategies for immune evasion. Understanding the mechanisms by which tumors suppress anti-tumor immunity facilitates the development of immunotherapies. Here we have identified tumor-secreted fibroblast growth factor 21 (FGF21) as an essential immune suppressor. We show that FGF21 is upregulated in multiple types of tumors and promotes tumor progression. FGF21 significantly disrupts CD8+T anti-tumor immune response by rewiring cholesterol metabolism of CD8+ T cells. We further reveal that FGF21 activates AKT-mTORC1- sterolregulatoryelementbindingprotein 1 (SREBP1) signal axis to enhance cholesterol biosynthesis in CD8+T cells. FGF21 knockdown or blockade of FGF21 by a neutralizing antibody attenuates AKT-mTORC1 signaling and subsequently decreases cholesterol content in CD8+T cells, thus restoring CD8+T cytotoxic function and robustly suppressing tumor growth. Our findings uncover FGF21 as a “secreted immune checkpoint” to restrict anti-tumor immunity and suggest its inhibition is a useful strategy for improving the efficacy of cancer immunotherapy.

overall_design: To investigate the effect of FGF21 on CD8+T cells, we constructed shNC/shFgf21 tumor cell lines and sorted shNC/shFgf21 MC38 tumor-infiltrating T cells for RNA seq.

first: Cegui

last: Hu

first: Wen

last: Qiao

first: Xiang

first: Zhi-kun

last: Ning

first: Jiang

first: Sumiya

last: Dalangood

first: Hanjun

last: Yu

first: Zhen

last: Zong

first: Zhenke

last: Wen

first: Jun

last: Gui


title: PARP15 promotes vascular barrier integrity in inflammation

city: Bethesda

first: Kirk

middle: M.

last: Druey

state: MD

address: 10 Center Drive Room 11N238A

department: NIAID

institute: National Institutes of Health

summary: The vascular endothelial barrier, which supports balanced plasma solute and macromolecule composition, controls hemostasis, and limits leukocyte extravasation at homeostasis, is frequently disrupted in inflammation associated with sepsis and other critical illness. Monoclonal gammopathy-associated idiopathic systemic capillary leak syndrome (ISCLS, Clarkson disease) is a rare and devastating disorder characterized by relapsing-remitting episodes of spontaneous, profound microvascular hyper-permeability. A loss of function (LOF) mutation (G628R) in the mono ADP-ribosyltransferase PARP15, a protein of unknown function that is absent in mice, is associated with ISCLS and correlates with clinical markers of severe vascular leakage. In vascular endothelial cells, PARP15 suppresses cytokine-induced barrier disruption by ADP-ribosylating the scaffold protein JNK-interacting protein 3 (JIP3) and inhibiting p38 MAP kinase activation. Mice expressing human wild type (WT) PARP15 have curtailed inflammation-associated vascular leakage compared to mice expressing PARP15(G628R) in a p38-dependent fashion. Thus, PARP15 is essential for vascular endothelial barrier function under inflammatory stress.

overall_design: To investigate the functional effects of PARP15 G268R mutation on endothelial cell function, we conducted RNAseq on mutant and control microvascular endothelial cells, both stimulated and unstimulated.

first: Eunice

last: Chan

first: Ararat

middle: J

last: Ablooglu

first: Chandra

last: Ghosh

first: Abhishek

last: Desai

first: Niccole

last: Schaible

first: Xiuying

last: Chen

first: Ming

last: Zhao

first: M

last: Olano

first: Sundar

last: Ganesan

first: Justin

last: Lack

first: Ramaswamy

last: Krishnan

first: Samir

last: Parikh


title: Human blastoid from primed human embryonic stem cells

city: Abu Dhabi

first: Ken-ichiro

last: Kamei

address: Saadiyat Campus, #C1-032

country: United Arab Emirates

institute: New York University Abu Dhabi

summary: A human blastoid, which is an artificial human blastocyst, and has a potential as great tool to investigate fundamentals during the development and establish in vitro models to study the pregnancy failure and birth deficiency, without the use of a human embryo. In 2021, although some methods to generate blastoids have been reported, they used human naïve pluripotent stem cells, which often show genomic instability during in vitro culture. Here, we introduce the simple, robust and scalable method to generate human blastoids from more stable human primed embryonic stem cells. By using non-cell-adhesive hydrogel, hESC aggregates received the chemophysical cellular environment, and forming the asymmetric blastoid structure with the cellular distribution like a human blastocyst. The obtained blastoids also showed the capability the implantation in vitro. This model will enable to elucidate the underlying mechanisms of human pre- and post-implantation process, leading to assisted reproductive technology.

overall_design: We analyzed cDNA profiles StepOnePlus from RNAs in individual KhES1 human embryonic stem cells and human blastoids generated from KhES1 cells using Illumina Next seq 500.

first: Satoshi

last: Imamura

first: Xiaopeng

first: Shiho

last: Terada

first: Akihisa

last: Yamamoto

first: Kaori

last: Mutsuda-Zapater

first: Kyoko

last: Sawada

first: Koki

last: Yoshimoto

first: Motomu

last: Tanaka

first: Kamei

last: Ken-ichiro


title: Glucosamine Mediated Hexosamine Biosynthesis Pathway Activation Utilizes ATF4 to Promote “Exercise-Like” Angiogenesis and Perfusion Recovery in Peripheral Arterial Disease

city: Augusta

first: Brian

last: Annex

state: Georgia

address: 1120 15th Street

department: VBC

institute: Augusta university

summary: Background: Endothelial cells (ECs) use glycolysis to produce energy. In pre-clinical models of peripheral arterial disease (PAD), the further activation of EC glycolysis was ineffective and/or deleterious in promoting hypoxia-dependent angiogenesis while pentose phosphate pathway (PPP) activation was effective. Hexosamine biosynthesis pathway (HBP), PPP, and glycolysis are closely linked. Glucosamine directly activates HBP.Methods:Hind-limb ischemia (HLI)ineNOS-/-and Balb/c mice was used. Glucosamine (600 ug/g/day)  was injected intraperitoneally. Blood flow recovery was assessed using laser Doppler perfusion imaging (LDPI), angiogenesis was studied by CD31immunostaining.In-vitro: human umbilical vein ECs (HUVECs) and mouse microvascular EC with glucosamine, L-glucose or vascular endothelial growth factor (VEGF165a), were tested underhypoxiaand serum starvation (HSS). Cell counting kit-8 (CCK-8), tube formation, intracellular reactive oxygen species (ROS), Electric Cell-substrate Impedance Sensing (ECIS) and FITC dextran permeability were assessed. Glycolysis and oxidative phosphorylation were assessed by seahorse assay. Gene expression was assessed using RNA sequencing, real-time qPCR, and western blot. Human muscle biopsies from patients with PAD were assessed for EC O-GlcNAcylation before and after supervised exercise vs. standard medical care. Results: Day-3 post-HLI,glucosamine vs. control-treated eNOS-/-had less necrosis.Beginning Day-7 post-HLI, glucosamine vs. control-treated Balb/chad higherblood flowthat persisted to Day-21whereischemic musclesshowed greaterCD31 staining/muscle fiber. In-vitro,glucosamine vs. L-glucoseshowedimproved EC survival and tube formation. RNA-sequencing of glucosamine vs. L-glucose showed increased amino acid metabolism. That resulted in increased oxidative phosphorylation and serine biosynthesis pathway (SBP) without an increase in glycolysis or PPP genes. This was associated with better barrier function and less ROS compared to activating glycolysis by VEGF165a. These effects were mediated by activating transcription factor 4 (ATF4); a driver of exercise-induced angiogenesis. Finally, in muscle biopsies from humans with PAD,EC/O-GlcNAcylation was increased by 12 weeks of supervised exercise vs. standard medical care. Conclusion: In-cells, mice, and humans activation of HBP by glucosamine in PAD inducesan “exercise-like” angiogenesis and offers a promising novel therapeutic pathway to treat this challenging disorder.

overall_design: To examine what gene expression that mediate the glucosamine induced hypoxia dependent angiogenesis in HUVECs under HSS conditions

first: Suhib

last: Alhusban

first: Mohamed

last: Nofal

first: Anita

last: Kovacs-Kasa

first: Taylor

last: Kress

first: Murat

last: Koseoglu

first: Abdelrahman

last: Zaied

first: Eric

last: Belin de Chantemele

middle: H


city: Kyoto

first: Ken-ichiro

last: Kamei

state: Kyoto

address: Yoshida-Ushinomiya-cho, Sakyo-ku

department: iCeMS

country: Japan

institute: Kyoto University

first: Satoshi

last: Wen


title: RNAseq comparison of lung fibroblasts from Pteropus alecto (PaLung cell line) and Homo sapiens (WI-38 cell line)

first: Koji

last: Itahana

address: 8 College Road

institute: Duke-NUS Medical School

summary: The transcriptome of PaLung cells and WI-38 cells were compared to identify differences in central metabolism

sample_organism:
Pteropus alecto
Homo sapiens

platform_organism:
Pteropus alecto
Homo sapiens

overall_design: Comparative gene expression profiling analysis of RNA-seq data for PaLung and WI-38 cell lines.

first: Javier

last: Koh

first: Aaron

last: Irving

first: Yoko

first: Younghwan

last: Lee

first: Lin-Fa

last: Wang

first: N

last: Suhas Jagannathan

first: Lisa

last: Tucker-Kellogg


title: Single-Nucleus Transcriptomic Atlas of Goat (Capra hircus) Ovarian Prolificacy

city: Nanning

first: Sanbao

last: Zhang

address: No.100,Daxue East Road

institute: Guangxi University

summary: Molecular mechanisms of follicular atresia and prolificacy of mammal remain unclear. We surveyed the single-cell transcriptomic landscape of ovaries from single and prolificacy goat and identified seven ovarian cell types with distinct gene-expression, transcriptional factor networks and reciprocal interactions signatures. In-depth dissection of gene-expression dynamics of granulosa cells (GCs) that displayed development stage-specific expression patterns and specific gene signatures were identified that may reflect developmental competency and ovarian reserve. what’s more, we revealed the origin of theca cells.  Further analysis of cell-type-specific prolificacy-associated transcriptional changes uncovered apoptosis, anabolism and response to hormone stimulation as are crucial factor in dominant follicle development and ovulation. Additionally, differentially expressed genes (DEGs) of SERPINE2 can interact with CYP19A1 to promote cell proliferation, inhibit apoptosis and promoting the anabolism were observed in mouse granulosa cells. Thus, our work provides a comprehensive understanding of the cell-type-specific mechanisms underlying goat ovarian prolificacy at single-cell resolution, provides key insights into offers important clues for improving follicle recruitment in vivo and revealing new diagnostic biomarkers and potential therapeutic targets for ovulation disorder.

overall_design: Granulosa cells were isolated from C57BL/6J mouse ovarian tissue 3 days after PMSG induction. SV40 gene was transfected into cells by lentivirus transfection to obtain immortalized function. Briefly, the GCs were isolated from the follicular fluid using density gradient centrifugation at 2000 rpm for 30 min. Following centrifugation, the sediments layer was collected and washed with Dulbecco phosphate-buffered saline (GIBCO). After a brief exposure to 0.2% hyaluronidase (Sigma) at 37℃, the cell suspensions were centrifuged at 3000 rpm for 5 min. Then, the purity of isolated GCs was assessed by immunofluorescence for GC markers. All cells were cultured in DMEM/F12 medium (GIBCO) supplemented with 10% FBS (GIBCO), 100 U/ml penicillin, and 100 mg/ml streptomycin (GIBCO) at 37℃ in 5% CO2. All the cell cultures were tested negative for myco- plasma contamination.

first: Qinyang

last: Jiang

first: Yanna

last: Huang


title: AOS10-FMT could rescure the adverse effects induced by high fat diet & STZ on the testis [testis_RNA-seq]

city: Qingdao

first: Yong

last: Zhao

state: Shandong

address: 700 Changcheng Road

department: College of Life Sciences

institute: Qingdao Agricultural University

summary: We report the side-effects of High fat diet & STZ on the testis, and foud that the AOS10-FMT could rescure the side-effect of High fat diet & STZ in many factors,such as spermatogenesis,lipid metabolism and oxidative stress

overall_design: Exploration of the FMT effects on the damaged testis induced by High fat diet & STZ

first: Yanan

last: Hao


title: AOS10-FMT could rescure the adverse effects induced by high fat diet & STZ on the Spleen [spleen_RNA-seq]

summary: We report the side-effects of High fat diet & STZ on the spleen, and foud that the AOS10-FMT could rescure the side-effect of High fat diet & STZ in many factors,such as inflammation

overall_design: Exploration of the FMT effects on the damaged spleen induced by High fat diet & STZ


title: Gene expression profiles of p63 knockout mouse

city: Houston

first: Frank

last: McKeon

state: TX

address: 3455 Cullen Blvd

department: Biology and Biochemistry

institute: University of Houston

summary: p63 is essential for the self-renewal of stem cells of all stratified epithelial tissues, including mammary and prostate glands as well as all squamous epithelia. In p63 null embryos, stratified epithelial tissues are lost or eroded several days after stratification due to the loss of regenerative cell populations. Here we show that p63 null embryos rapidly develop intestine-like metaplasia with gene expression profiles similar to Barrett’s metaplasia in a proximal stomach region.  Also, we found that deletion of p63 cells in bladder leads to an expansion of columnar epithelial cells along the basement membrane and their rapid transition to a metaplastic phenotype similar to Barrett’s esophagus. It is likely that bladder carcinogens recapitulate this entire metaplastic transition.

overall_design: Tissues including proximal stomach (PS), distal stomach (DS), small intestine (SI), large intestine (LI) and bladder (BL) were collected from p63 knockout (KO) and wild type (WT) mice.  BL were collected on three time points (embryo (E) 15, 18 and 19).  PS, DS, SI and LI were collected from E18 fetus.  We used Affymetrix mouse 430 2.0 array chip to hybridize 2 samples from each of tissues (p63 knockout and wild types).

first: Yue

last: Hong

first: Christopher

last: Crum

first: Yusuke

last: Yamamoto

first: Xia

first: Wa

last: Xian


title: Chromatin accessibility of genomic regions in human mesenchymal stem cells cultured in sliding hydrogels (SGs) and chemical hydrogels (CGs) undergoing chondrogenesis.

city: Palo Alto

first: Fan

last: Yang

state: California

address: Orthopedic Surgery, 240 Pasteur Drive, Biomedical Innovation Building 1200

institute: Stanford University

summary: Cells can deform their local microenvironment by exerting forces through pushing and pulling. Such interactions result in behaviors such as cell spreading, cell migration, or cell volume expansion, which occur on timescales of hours to days. However, whether cells can deform local niches at shorter timescales and how such interactions impact long-term cell fates remain largely unknown. Here we report “cell dancing”- a previously unknown cell behavior characterized by seconds-to-minutes scale deformation of the pericellular niche and enhanced cytoskeletal and nuclear dynamics. Using hydrogels that allow cells to deform their local 3D niche and mesenchymal stem cell chondrogenesis as a model system, we identify early-stage cell dancing essential for enhancing stem cell differentiation in 3D. This is mediated through nuclear mechanotransduction pathways that repress global chromatin accessibility, which is necessary for cell dancing-enhanced differentiation. We further demonstrate that cell dancing induces nuclear deformations and phospholipase A2 (PLA2) signaling, and small molecules targeting this pathway can further boost stem cell chondrogenesis. Finally, we validate that cell dancing can enhance stem cell differentiation towards multiple lineages and occurs in other commonly used hydrogel systems. These results establish cell dancing as a novel cell behavior in 3D that may be broadly applied to promote desirable cell fates and tissue outcomes.

overall_design: ATAC-seq analysis was conducted for two conditions (SG and CG) at two time points (16 hours and 48 hours)

first: Manish

last: Ayushman

first: Eunice

last: Lopez-Fuentes

first: Alejandro

last: Sweet-Cordero


title: Single-cell sequencing highlights increased atypical AT2 interacting with M1 macrophage in COPD

status: Public on Jun 28 2024

city: Seoul

first: Jihwan

last: Moon

address: gangnam-gu irwon-ro 81

department: Department of Digital Health

institute: Sungkyunkwan University

summary: We have constructed a transcriptomic map of airways using lung tissues from three COPD (GOLD grade I) who underwent surgical resection for lung cancer. We performed 5' single-cell RNA sequencing (scRNA-seq) on three COPD and three control matched lung tissue, as well as the organoid samples.

overall_design: COPD and control lung tissues were obtained from the surgical specimens of patients with primary lung cancer while non-cancer tissue was obtained from lung periphery as distal to the cancer site as possible. COPD was diagnosed on the Global Initiative for Chronic Obstructive Lung Disease criteria. We performed single-cell RNA sequencing (scRNA-seq) on three COPD and three control matched lung tissue, as well as the organoid samples. All three COPD patients had GOLD grade1, with two showing evidence of emphysema on the chest CT scans. Except for one control participant, all participants had a history of smoking.

first: Hye

last: Park

first: Sang-Won

last: Um

first: Woong-Yang


title: Transcriptome comparison of wild-tyle (w1118) vs. actβ mutants (act80/act4E) Drosophila larvae

city: Minneapolis

first: Michael

last: O'Connor

state: MN

address: 321 Church St SE

department: Genetics Cell Biology and Development

institute: University of Minnesota

summary: TGFβ/Activin subfamilies of ligands.  In Drosophila the TGFβ/Activin branch includes three ligands, Myoglianin (Myo), Activin-β (Actβ) and Dawdle (Daw). All three ligands signal through the same type I receptor, Baboon, in conjunction with a type II receptor, Punt or Wit.  Baboon has three distinct splice isoforms, termed Babo A, Babo B and Babo C, that differ only in exon 4, which encodes the ligand binding domain. This difference enables each ligand to potentially signal through a single splice isoform39. Formation of the ligand receptor complex stimulates phosphorylation of the receptor-Smad, dSmad2/Smox, which translocates to the nucleus as a complex with the co-Smad Medea where it serves as a transcriptional transducer. In order to gain insight into the genes regulated by Actβ we carried out a transcriptomic analysis comparing Actβ mutants to wild-type controls.

overall_design: Animals were raised on apple juice plates supplemented with yeast paste until the early L3 time point (approximately 68 hours AEL). RNA was extracted 8 larvae of each biological repliacte and a minimum of five biological replicates were submitted for each genotype: wild-type control (w1118) and actβ mutants (act80/act4E).  The Actβ80 allele is an EMS-induced substitution leading to a premature stop codon and presumed to be a null mutation.  Actβ4E was generated using the clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 system. Two guide RNAs were cloned into the BbsI site of the pU6-BbsI-chiRNA plasmid (obtained from Addgene) and injected by Best Gene into w1118; PBac{y[+mDint2]=vas-Cas9}VK00027 on chromosome 3 (#51324; BDSC).Total RNA (3 μg per sample) was submitted to the University of Minnesota Genomics Center (UMGC) for quality assessment and Illumina next-generation sequencing.  2 x 150bp fastq.gz paired-end reads for samples (n=30.3 Million average reads per sample) were trimmed using Trimmomatic (v 0.33) enabled with the “-q” option; 3bp sliding-window trimming from 3’ end requiring minimum Q30.  Quality control on raw sequence data for each sample was performed with fastq.gzC. Read mapping was performed via Hisat2 (v2.1.0) using the Drosophila genome (Drosophila melanogaster (BDGP6.28) as a reference. Gene quantification was done via Feature Counts for raw read counts.

first: Heidi

last: Bretscher


title: Human blastoid from primed human incuded pluripotent stem cells

first: Ken-ichiro

last: Kamei

summary: A human blastoid, which is an artificial human blastocyst, and has a potential as great tool to investigate fundamentals during the development and establish in vitro models to study the pregnancy failure and birth deficiency, without the use of a human embryo. In 2021, although some methods to generate blastoids have been reported, they used human naïve pluripotent stem cells, which often show genomic instability during in vitro culture. Here, we introduce the simple, robust and scalable method to generate human blastoids from more stable human primed pluripotent stem cells. By using non-cell-adhesive hydrogel, hPSC aggregates received the chemophysical cellular environment, and forming the asymmetric blastoid structure with the cellular distribution like a human blastocyst. The obtained blastoids also showed the capability the implantation in vitro. This model will enable to elucidate the underlying mechanisms of human pre- and post-implantation process, leading to assisted reproductive technology.

overall_design: We analyzed cDNA profiles StepOnePlus from RNAs in individual 585A1 human induced pluripotent stem cells and human blastoids generated from 585A1 hiPSCs using Illumina Next seq 500.

first: Satoshi

last: Imamura

first: Xiaopeng

last: Wen

first: Shiho

last: Terada

first: Akihisa

first: Kaori

last: Mutsuda-Zapater

first: Kyoko

last: Sawada

first: Koki

last: Yoshimoto

first: Motomu

last: Tanaka

first: Kamei

last: Ken-ichiro


title: Dynamic impacts of stock enhancement on wild Amur sturgeon (Acipenser schrenkii): New protection insight into intestinal microbe and gene expression mode

city: Changchun

first: Yutao

last: Li

address: Jingyue Street

institute: Northeast Normal University

summary: On October 9th,2023, one thousand Amur sturgeon with similar genetic background were released to Songhua River after artificial breeding in Harbin. Before re-wilding to river,they were bred in the net cages. To explore whether feeding Limnodrilus before stock enhancement would affect the gene expression mode, we set two groups, one group was fed with commerial feed , another was fed with fresh Limnodrilus. After 30 d breeding, we collected the gut samples to perform transcriptome sequencing project.

overall_design: On October 9th,2023, one thousand Amur sturgeon with similar genetic background were released to Songhua River after artificial breeding in Harbin. Before re-wilding to river,they were bred in the net cages. To explore whether feeding Limnodrilus before stock enhancement would affect the gene expression mode, we set two groups, one group was fed with commerial feed (Q), another was fed with fresh Limnodrilus (H). After 30 d breeding process, we collected the gut samples to perform transcriptome sequencing project.In addition, Limnodrilus was bred in the fish-breeding water source to allow Limnodrilus to carrry the environmental microbe.


title: Organoid Culture Promotes Dedifferentiation of Mouse Myoblasts into Stem Cells Capable of Complete Muscle Regeneration

city: Cambridge

first: Kristina

last: Holton

state: MA

address: 7 Divinity Ave

department: HSCRB

institute: Harvard University

summary: Experimental cell therapies for skeletal muscle conditions have shown little success, primarily because they used committed myogenic progenitors rather than true muscle stem cells, known as satellite cells. Here we present a method to generate in vitro–derived satellite cells (idSCs) from skeletal muscle tissue. When transplanted in small numbers into mouse muscle, mouse idSCs fuse into myofibers, repopulate the satellite cell niche, self-renew, support multiple rounds of muscle regeneration, and improve force production on par with freshly isolated satellite cells. in damaged skeletal muscle. We profiled the epigenomic and transcriptional differences between idSCs and satellite cells, and used these differences to identify core signaling pathways and genes that confer idSC functionality. Finally, fromhuman muscle biopsies we successfully generated satellite cell–like cells in vitro. After further development, idSCs may provide a scalable source of cells for the treatment of genetic muscle disorders, trauma-induced muscle damage and age-related muscle weakness.

overall_design: ATAC-seq was performed on mouse satellite cells, myoblasts, and in vitro-derived satellite cells at 10, 20, and 30 days of generation.

first: Lee

middle: L

last: Rubin

first: Feodor

middle: D

last: Price

first: Andrew

middle: R

last: Gehrke


title: AOS10-FMT could rescure the adverse effects induced by high fat diet & STZ on the kidney [kidney_RNA-seq]

first: Yong

last: Zhao

summary: We report the side-effects of High fat diet & STZ on the liver, and foud that the AOS10-FMT could rescure the side-effect of High fat diet & STZ in many factors,such as lipid metabolism and oxidative stress

overall_design: Exploration of the FMT effects on the damaged kidney induced by High fat diet & STZ

first: Yanan

last: Hao