title: Effects of DDX18 on chromatin characteristics

summary: Hs766T cell line of pancreatic ductal adenocarcinoma (PDAC) highly expressed DDX18, and the effects of DDX18 on chromatin characteristics of PDAC cells were examined

overall_design: Pancreatic cancer cell lines with stable high expression of DDX18 were constructed, and the only the expression stable vector were used as the control.


title: TRIM27 mediates protective immunity against tuberculosis by activating host autophagy flux

status: Public on Jul 03 2024

city: beijing

first: lu

last: z

state: - 选择 -

address: beijing

country: China

institute: institution of microbology

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Infectious diseases, such as Mycobacterium tuberculosis (Mtb)-caused tuberculosis (TB), remain a global health threat exacerbated by increasing drug resistance. Host-directed therapy (HDT) is a complementing strategy for infection treatment through targeting host immune mechanisms. However, the limited understanding of the host factors and their regulatory mechanisms involved in host immune defense against infections has impeded HDT development. Here, we identify the E3 ubiquitin ligase tripartite motif-containing 27 (TRIM27) elicits host protective immunity against Mtb. Mechanistically, TRIM27 enters host cell nucleus upon Mtb infection to function as a transcription activator of transcription factor EB (TFEB). TRIM27 binds to TFEB promoter and the TFEB transcription factor cAMP responsive element binding protein 1 (CREB1), thus enhancing CREB1-TFEB promoter binding affinity and promoting CREB1 transcription activity towards TFEB, eventually leading to autophagy activation and pathogen clearance. Thus, TRIM27 contributes to host anti-Mtb immunity and targeting TRIM27/CREB1/TFEB axis serves as a promising HDT-based TB treatment.

overall_design: Chromation immunoprecipitation DNA-sequencing(ChIP-seq) for TRIM27 in healthy Peripheral blood mononuclear cells uninfected and infected with Mtb.

first: Cui-Hua

last: Liu

first: Jing

last: Wang

first: Dongdong

last: Zhao


title: The miRNA profiles of amniotic fluid-derived extracellular vesicles of congenital diaphragmatic hernia patients.

city: Nagoya

first: Kosuke

last: Yoshida

state: Aichi

address: 65 Tsuruma-cho

country: Japan

institute: Nagoya University

type: Non-coding RNA profiling by high throughput sequencing

summary: Congenital diaphragmatic hernia (CDH) is a life-threatening anomaly with high morbidity and mortality. To investigate the pathogenesis of CDH, miRNA sequencing was performed using amniotic fluid-derived extracellular vesicles (AF-EVs) of CDH patients.

overall_design: Amniotic fluid samples were collected during cesarean delivery from women who provided written informed consent from January 2012 to October 2017 at Nagoya University Hospital. Twenty-one CDH cases born at late and full term (between 37 0/7 and 41 6/7 gestational weeks) and those who born at late and full term at the same time without congenital malformations or neonatal intensive care unit (NICU) admission (control cases: n = 24) were included. CDH cases were divided into two groups; the good prognosis group (CDH-Good) and the poor prognosis group (CDH-Poor). Cases who required extracorporeal membrane oxygenation (ECMO) and neonatal deaths were defined as the CDH-Poor group (n = 5), and the others were defined as the CDH-Good group (n = 16).

first: Seiko

last: Matsuo

first: Akira

last: Yokoi

first: Masami

last: Kitagawa


title: The miRNA profiles of amniotic fluid-derived extracellular vesicles and fetal lung tissue of nitrofen-induced congenital diaphragmatic hernia rat model.

summary: Congenital diaphragmatic hernia (CDH) is a life-threatening anomaly with high morbidity and mortality. To investigate the pathogenesis of CDH, miRNA sequencing was performed using amniotic fluid-derived extracellular vesicles (AF-EVs) and fetal lung tissue of nitrofen-induced CDH rat model.

overall_design: We used three pregnant Sprague-Dawley rats in this study. On day 9 of the pregnancy, two rats received 100 mg of nitrofen dissolved in 1 mL of olive oil, and two rats received olive oil alone. On day 21, the rats were sacrificed, and AF-EVs of each fetus were collected using cellulose nanofiber-based EV sheets. Then, we checked the presence of CDH. In this study, we used six nitrofen-treated fetuses with CDH, six nitrofen-treated fetuses without CDH, and three olive oil-treated control fetuses. Total RNAs were extracted from the lung and corresponding AF-EVs, and miRNA sequencing was performed.


title: Carbon source competition within a wound can significantly influence infection progression.

city: Uxbridge

first: Ronan

last: McCarthy

address: Kingston Ln

country: United Kingdom

institute: Brunel University London

type: Expression profiling by high throughput sequencing

summary: It is becoming increasingly apparent that commensal skin bacteria have an important role in wound healing and infection progression. However, the precise mechanisms underpinning many of these probiotic interactions remain to be fully uncovered. In this work, we demonstrate that the common skin commensal Cutibacterium acnes can limit the pathogenicity of the prevalent wound pathogen Pseudomonas aeruginosa in vivo. We show that this impact on pathogenicity is independent of any effect on growth, but occurs through a significant down regulation of the Type Three Secretion System (T3SS), the primary toxin secretion system utilized by P. aeruginosa in eukaryotic infection. We also show a down regulation in glucose acquisition systems, a known regulator of the T3SS, suggesting that glucose availability in a wound can influence infection progression. This suggests that introducing carbon source competition within the wound microenvironment may be an effective way to prevent or limit wound infection.

overall_design:
P. aeruginosa PA14 was grown in the overnight tube at 37°C at 180 rpm. Cultures were then adjusted to OD=0.1 with LB and added in proportion 1:1 to TSB or the supernatant of C. acnes CCUG 38584 to be grown to OD600=0.6-0.7 at 37°C at 180 rpm. Upon reaching the desired optical density, 1 ml of the cultures was aliquoted and spun down at 5000 rpm for 10 mins, the supernatant was discarded, and the pellets were resuspended in the RNAlater buffer (ThermoFischer). The resuspended cells were stored in the buffer at 4°C overnight. RNA extraction procedure was performed with RNeasy Mini Kit (Qiagen). Extracted RNA was quantified using Nanodrop. The quality of the extraction was assessed with Bioanalyser. Samples were stored at -20°C until shipment to the sequencing facility. Illumina sequencing was performed by Microbial Genome Sequencing Centre (MiGS).
Raw fastq files were obtained from the sequencing facility. Adapter and quality trimming was performed by MiGS using bcl2fastq. Reads and their quality was assessed with fastqc and visualised through multiqc (Andrews S, 2010, Ewels et al., 2016). Read mapping was performed with hisat2 with ‘--very-sensitive’ parameter (Kim et al., 2019). Read quantification was performed with featureCounts available within the Subread package (Liao et al., 2014). Read normalisation was performed using the edgeR package in R with the Trimmed Mean of M values algorithm (Robinson et al., 2010). Differential expression analysis was performed using edgeR’s Quasi-Linear F-Test (qlfTest) functionality against treatment groups. All quantified genes were subset by log-fold change (logFC) > |1| and p-value < 0.05 to create a list of differentially expressed genes. All quantified genes were visualised in a volcano plot in ggplot2 R package.

first: Evgenia

last: Maslova

middle: R


title: Tumor-derived kynurenine induces Siglec-15 expression and promotes CD8+T cell exhaustion in oral squamous cell carcinoma

city: Shanghai

first: Hailong

last: Ma

address: Zhizaoju Rd

institute: Shanghai Ninth People’s Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine

summary: Metabolic deregulation and immune escape are pivotal hallmarks of cancer; however, the profile of metabolic reprogramming in oral squamous cell carcinoma (OSCC) and how it drives immune escape remain unclear. We identified significant metabolic disorders in OSCC. Amino acid metabolism, especially tryptophan/kynurenine metabolism, was altered. Here, we found that kynurenine promotes migration, invasion, and proliferation in vitro and in vivo. In addition, most immune checkpoints were upregulated in patients with high kynurenine levels. We then identified that kynurenine can promote Siglec-15 expression via AhR activation. Furthermore, tumor-derived kynurenine can directly exhaust CD8+ T cells, whereas blocking of kynurenine transporters reversed this effect. Moreover, we found that ectopic expression of Siglec-15 can promote immune escape in tumor microenvironment (TME) by suppressing T cell infiltration and inducing CD8+ T cell exhaustion in vivo, while targeting AhR reduces kynurenine-mediated immune escape. Finally, we design NH2-MSNs nanoparticles to deliver Siglec-15 small interfering RNA, which successfully remodels the TME and enhances anti-PD-1 efficacy in tumor-bearing immunocompetent mice. Clinically, Siglec-15 expression is correlated with AhR expression and high infiltration of exhausted CD8+ T cells. These findings reveal that the Kyn/AhR/Siglec-15 signaling pathway is a novel immunometabolism mechanism in OSCC, thus opening a new therapeutic avenue for metabolic immunotherapy.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for 69 pairs of oral squamous cell carcinoma and paracancerous tissues

first: Xinyu

last: Zhang

first: Jianbo

last: Shi

first: Shufang

last: Jin

first: Ruijie

first: Mingyu

last: Li

first: Zhiyuan

first: Xi

last: Yang


title: The difference of chromatin between tumor tissue and adjacent tissue in patients with pancreatic cancer

city: Jinan

first: Guoying

last: Dong

state: Shandong

address: Jinan lixia district Wenhua west road no. 44

department: Cheeloo College of Medicine

institute: Shandong University

summary: In order to better study the differences between pancreatic cancer patients' tumor tissues and their adjacent tissues, we compared chromatin accessibility of pancreatic cancer tumor tissues and adjacent tissues of the same patient from the whole genome, in an effort to find meaningful research targets related to pancreatic cancer patients

overall_design: The tumor tissue of pancreatic cancer patients was compared with its adjacent tissue

first: Yunshan

first: Guangwei

last: Wei

first: Qin

last: dong


title: Explore the gene sets modulated by alterations in lactate levels.

city: Wuhan

first: Kaixiang

last: Feng

address: No.169, Donghu Road

institute: Wuhan University

summary: Lactate is an end product of glycolysis and a signaling factor involved in important physiological functions in triple-negative breast cancer. 2-deoxyglucose inhibits glucose metabolism and reduces lactate production. To explore these regulated gene sets, we performed genome-wide transcriptional analysis.

overall_design: MDA-MB-231 cells were incubated with different concentrations of 2-deoxy-glucose (0,10mM,20mM) for 24 hours, and then harvested for total RNA extraction.


title: Chromatin Remodeling Drives Immune-Fibroblast Cell Communication in Heart Failure (ChIP-Seq)

city: San Francisco

first: Michael

last: Alexanian

state: CA

address: 1650 Owens Street

country: USA

institute: Gladstone Institutes

summary: Chronic inflammation and tissue fibrosis are common stress responses that worsen organ function, yet their crosstalk is poorly understood. Here, we show that conditional deletion of the transcription co-activator Brd4 in Cx3cr1-positive myeloid cells ameliorates heart failure and is associated with a dramatic reduction in fibroblast activation. We identified a specific BRD4-occupied enhancer in Cx3cr1-positive cells that controls expression of Interleukin-1 beta (Il1b), and show that secreted IL1B activates a p65/RELA-dependent enhancer downstream of MEOX1, driving a profibrotic response in human cardiac fibroblasts. In vivo, antibody-mediated IL1B neutralization prevented stress-induced expression of MEOX1, inhibited fibroblast activation, and improved cardiac function in heart failure. The elucidation of BRD4-dependent crosstalk between a specific immune cell subset and fibroblasts through IL1B provides new therapeutic strategies for heart disease and other disorders of chronic inflammation and maladaptive tissue remodeling.

overall_design: Single cell or nuclei RNAseq from adult heart in the context of BET bromodomain inhibition, BRD4 genetic deletion and neutralization of the cytokine IL1B

first: Angelo

last: Pelonero

first: Pawel

middle: F

last: Przytycki

first: Tomohiro

last: Nishino


title: Chromatin Remodeling Drives Immune-Fibroblast Cell Communication in Heart Failure (Cut & Run)


title: Chromatin Remodeling Drives Immune-Fibroblast Cell Communication in Heart Failure (scATAC-Seq)


title: Effect of MOTS-c treatment on cast immobilization-induced skeletal muscle atrophy

city: Los Angeles

first: Hiroshi

last: Kumagai

address: 3715 McClintock Ave

institute: University of Southern California

summary:
To understand the effect of MOTS-c treatment on cast immobilization-induced skeletal muscle atrophy, we injected MOTS-c into casted mice.
We then performed gene expression profiling analysis using data obtained from RNA-seq of three groups: non-immobilization group, immobilization control group, and immobilization and MOTS-c treated group.

overall_design: Male C57BL/6J mice at 10 wk of age were obtained and assigned to one of the three experimental groups: non-immobilization control group (sterilized water injection for eight days, twice a day intraperitoneal injection, n = 8), immobilization control group (sterilized water injection for eight days, twice a day intraperitoneal injection, n = 8), and immobilization and MOTS-c treated group (15 mg/kg/day MOTS-c injection for 8 days, twice a day intraperitoneal injection, n = 8). Hindlimb immobilization was performed by using casting and the casting material was attached to both hinds. After eight days of hindlimb immobilization, mice were euthanized and gastrocnemius muscle was collected under anesthesia with isoflurane for RNA-seq.

first: Pinchas

last: Cohen


title: Chromatin Remodeling Drives Immune-Fibroblast Cell Communication in Heart Failure

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Chromatin Remodeling Drives Immune-Fibroblast Cell Communication in Heart Failure (scRNA-Seq)


title: Chromatin Remodeling Drives Immune-Fibroblast Cell Communication in Heart Failure (Bulk RNA-Seq)

overall_design: Bulk RNA-seq on Human induced pluripotent stem cell derived cardiac fibroblasts (iPSC-FBs) with IL1B and TGFB stimulation


title: Genome-wide quantification of RNA flow across subcellular compartments reveals determinants of the transcript life cycle

city: Boston

first: Brendan

middle: Michael

last: Smalec

state: MA

address: 77 Avenue Louis Pasteur, Rm 356

department: Genetics

institute: Harvard Medical School


title: Genome-wide quantification of RNA flow across subcellular compartments reveals determinants of the transcript life cycle [RNA-seq]

summary: Series of regulatory mechanisms control eukaryotic mRNAs, from their production on chromatin to their eventual degradation. Dissecting these pathways requires quantitative measurements of mRNA flow across the cell. We developed subcellular TimeLapse-seq to measure the rates at which RNAs are released from chromatin, exported from the nucleus, loaded onto polysomes, and degraded within the nucleus and the cytoplasm. All rates displayed substantial variability genome-wide, and transcripts from genes with related functions flowed across subcellular compartments with similar kinetics. For some genes, most transcripts were rapidly degraded within the nucleus, while the remaining molecules were exported and persisted with stable lifespans. With compartment-specific measurements of poly(A) tail lengths, we found that relationships between tail length and stability differ across the cell. The targets of RNA binding proteins experience distinct RNA flow kinetics, and we found that two, DDX3X and PABPC4, act by controlling the nuclear export of their targets. Finally, we developed a machine learning model to propose additional molecular features that underlie the diverse life cycle of mammalian mRNAs.

overall_design: Subcellular TimeLapse sequencing in human K562 and mouse NIH-3T3 cells.

first: Robert

last: Ietswaart

middle: M

first: Albert

last: Xu

first: Karine

last: Choquet

first: Erik

last: McShane

first: Ziad

last: Jowhar

first: Chantal

middle: K

last: Guegler

first: Autum

last: Baxter-Koenigs

first: Emma

last: West

first: Becky Xu

last: Hua Fu

first: Luke

last: Gilbert

first: Stephen

middle: N

last: Floor

first: L Stirling

last: Churchman


title: HRCT1 promotes tumor metastasis and growth via Her2-MAPK pathway in gastrica cancer

first: Hou

last: Feng

address: Wenhuaxi Road 44

summary: HRCT1 gene and protein was overexpressed in primary gastric cancer samples with lymphatic metastasis compared to samples with no metastasis.High expression of HRCT1 was also found to be associated with advanced clinical stage, poor overall survival and disease free survival. Overexpression of HRCT1 dramatically enhanced the migration, invasion, and metastatic ability of gastric cancer cells both in vitro and in vivo. HRCT1 was further demonstrated to promote the progression of gastric cancer by activating the HER2-MAPK passway.

overall_design: Microarray assay was used to screen the differentially expressed genes between metastatic sample and non-metastatic samples. The level of HRCT1 mRNA in gastric cancer and gastric cancer cells was quantified by RT-qPCR. Immunohistochemistry and Western blot were performed to detect the expression of HRCT1 protein. Transwell assay，MTS and EDU were performed to detect the migration，invasion and proliferation ability of gastric cancer cells in vitro.Tumor-bearing mice experiment was performed to detect the migration，invasion and proliferation ability of gastric cancer cells in vivo.Microarray assay was used to screen the signal pathway regulated by HRCT1

first: Feng

last: Hou

first: Peng

last: Gao


title: Neurofilament accumulations in Amyotrophic Lateral Sclerosis patients’ motor neurons impair structural axonal initial segment integrity

city: Paris

first: Noémie

last: Robil

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

country: France

institute: GenoSplice technology

summary: Neurofilament (NF) accumulation is a pathological hallmark observed in motor neurons (MNs) of patients with Amyotrophic Lateral Sclerosis (ALS) and levels of NF in fluids is becoming the prime biomarker of ALS progression. However, the underlying mechanisms linking NF accumulations and MN degeneration are not elucidated. Here, we show that integrity of the axonal initial segment (AIS), the region of action potential initiation and of polarized trafficking, is impaired by NF accumulations in human MNs carrying mutations in the two main causal ALS genes: C9ORF72 and SOD1. We show that in mutant MNs derived from induced pluripotent stem cells, both light (NF-L) and phosphorylated heavy chains (pNF-H) accumulated progressively with MN aging and that pNF-H accumulation in the AIS region led to significant structural and molecular alterations. In parallel, ALS MNs acquired altered excitability with aging. Focusing on axonal organization appears as an effective readout for MN cell death and preserving AIS integrity could have important therapeutic implications.

overall_design: Comparisons of RNA expression in MN from ALS patients compared to control MNs at different time-points of their maturation in cultures

first: Cynthia

last: Lefebvre-Omar

first: Elise

last: Liu

first: Carine

last: Dalle

first: Boris

last: Lamotte d'Incamps

first: Stéphanie

last: Bigou

first: Clément

last: Daube

first: Marc

last: Davenne

first: Stéphane

last: Blanchard

first: Guillaume

last: Tournaire

first: Charles

last: Nicaise

first: François

last: Salachas

first: Lucette

last: Lacomblez

first: Danielle

last: Seilhean

first: Christian

middle: S

last: Lobsiger

last: Millecamps

first: Séverine

last: Boillée

first: Delphine

last: Bohl


title: Transcriptomic analysis revealed genes involved in response to cold stress in Prunus sibirica

city: Shenyang

first: Shengjun

last: Dong

address: No.120 Dongling Road, Shenhe District, Shenyang, Liaoning Province, P.R.China.

institute: Shenyang Agricultural University

summary: Through transcriptome sequencing analysis of clones with strong freezing resistance (338) and weak freezing resistance (28) of Prunus sibirica，a total of 6001 significantly differentially expressed genes were obtained. Among them, there are 2070 up-regulated genes and 3,931 down-regulated genes. Differential genes are compared and screened, and WRKY, NAC, bHLH, MADS, MYB, Homeobox, F-box, ZEP, SBT, ERF, CAMTA, MDH, etc. Freeze-related gene family.

overall_design: Using Prunus sibirica flower organs with strong frost resistance clone No. 338(treatment group) and weak frost resistance clone No. 28(control group) as the test materials, flowers were collected  when the flower organs were subjected to frost (-4 °C). The clones were repeated 3 times, placed in liquid nitrogen, stored in an ultra-low temperature refrigerator (-80 °C), and transcriptome sequencing was completed by Nuovo Zhiyuan (Beijing) Co., Ltd.

first: Quangang

first: Jianhua

last: Chen

first: Wenying

last: Li


title: The mechanism of circ-ARAP2 regulation of tumor EMT and stem cell differentiation affecting proliferation, invasion and chemotherapy resistance of Esophageal Squamous Cell Carcinoma

first: Xu

last: Pei

address: Jiangpu Road 1665

institute: Xinhua Hospita;

summary: Circular RNAs (circRNAs) belong to a novel class of noncoding RNA that gained more attention in human cancer pathogenesis. The circRNA roles in esophageal squamous cell carcinoma (ESCC) is unknown. Present investigation was to characterize new circRNAs regulating ESCC progression and explore the regulatory mechanisms in ESCC. In this study, circRNAs differentially expressed in ESCC and adjacent normal tissues were characterized via high-throughput sequencing. We then investigated the effects of the differentially expressed circRNA ARFGAP with RhoGAP domain, ankyrin repeat and PH domain 2 (circ-ARAP2) on tumor progression in vivo and in vitro. We used luciferase reporter assays to identify the relationships between circ-ARAP2, its target microRNA (miR)-761 and the cell cycle regulator Forkhead Box M1 (FOXM1). Expression profile analyses regarding human circRNAs in ESCC demonstrated that circ-ARAP2 was up-regulated significantly in ESCC tissues and cell lines. The circ-ARAP2 down-regulation suppressed ESCC proliferation, tumor growth and metastasis in vivo and in vitro. The data also suggested that miR-761 and FOXM1 were circ-ARAP2 downstream targets which were confirmed through luciferase reporter analysis. Overexpression of FOXM1 or inhibiting miR-761 slowed ESCC cell proliferation and invasion after silencing circ-ARAP2. circ-ARAP2 also influenced the endothelial-mesenchymal transition (EMT) and cancer stem cells differently by regulating miR-761/FOXM1. In one word, the results demonstrated that abnormal circ-ARAP2 expression promoted ESCC progression by regulating miR-761/FOXM1 axis-mediated stemness and EMT.

overall_design: Examination of 4 ESCC tumor tissues

first: Pei

last: Xu

first: Lei

last: Wang


title: Mesenchymal stem cells derived exosomes (MSCs-Exo) attenuate neuropathic pain by modulating microglial autophagy and neuroinflammation

first: Zheyu

last: Zhang

address: Yueyang Road

institute: CAS

summary: The study aimed to investigate how MSCs-Exo regulate neuroinflammation and neuropathic pain through vitro and in vivo studies.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for BV-2 cells treated with MSCs-Exo or lipopolysaccharide (LPS)

last: Gao

first: Long-fei

first: Xiang-qing

last: Kong

first: Chun-yang

last: Meng


title: Expression data from control-knockdown (CTR-KD) and MAST4-KD human multiple myeloma (MM) cell lines

city: chengdu

first: Yushan

last: Cui

address: Guo Xue Xiang #37 Chengdu, Sichuan Province,  P.R.China

department: Department of Hematology

institute: West China Hospital, Sichuan University

summary: We found that estrogen cell signaling played a regulatory role in MM bone disease (MMBD), and the estrogen-responsive gene microtubule-associated serine/threonine kinase family member 4 (MAST4) was a critical factor. To determine what signalling pathways are affected by MAST4 in MM cells, we established CTR-KD and MAST4-KD ARD MM cell lines. Total RNA of each sample was extracted using TRIzol Reagent (Invitrogen). Next generation sequencing library preparations were constructed  using NEBNext®  Ultra™ RNA Library Prep Kit for Illumina (Vazyme, Cat No. NR603, China).RNA-seq was performed by GENEWIZ (Suzhou, China) on an Illumina Hiseq platform.

overall_design: Examination of mRNA profiles in CTR-KD and MAST4-KD MM cell lines

first: Y

first: F

last: Zheng


title: Comprehensive transcriptome analysis of CIAV infected MDCC-MSB1 cells [RNA-seq]

status: Public on Jul 02 2024

city: 广州

first: Mengyue

address: 广东省广州市天河区五山483号

department: College Of Animal Science Of South China Agricultural University

institute: South China Agricultural University

summary: Chicken infectious anaemia (CIA) is an immunosuppressive disease caused by chicken infectious anaemia virus (CIAV). Due to immunosuppression, the disease is often leads to mixed infections and secondary infections, exacerbating viral, bacterial, and fungal infections, which can be highly detrimental. Therefore, it is imperative to identify the immune genes involved in regulating CIAV infection. In this study, comprehensive transcriptome sequencing was employed to determine the expression levels of regulated immune genes including mRNAs, microRNAs, lncRNAs, and circRNAs in CIAV-infected MDCC-MSB1 cells. A total of 2590 differentially expressed genes were identified in CIAV-infected MDCC-MSB1 cells, of which 526 were up-regulated. There were 539 differentially expressed mRNAs, including 166 up-regulated mRNAs, 38 differentially expressed microRNAs, including 22 up-regulated microRNAs, 1957 differentially expressed lncRNAs, including 295 up-regulated lncRNAs, and 56 differentially expressed circRNAs, including 43 up-regulated circRNAs. Subsequently, we selected the top 20 significantly up-regulated differentially expressed genes (GEM, ODF1, ARHGEF12, DOC2B, ZP2, gga-miR-1306-5p_L-1R-2, gga-miR-6615-3p, gga-mir-3535-p5, gga-miR-726-5p_1ss4AG, gga-miR-458a-3p, ENSGALG00010010181, ENSGALG00010002366, ENSGALG00010019353, ENSGALG00010029120, ENSGALG00010026718, circMAP3K5, ENSGALG00010015867, circGALNT1, circMCTP2, circPTEN) among the 526 up-regulated differentially expressed genes for Gene Ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, and we found that those 20 genes were significantly enriched in key pathways such as apoptosis, transcriptional regulation, MAPK signaling pathway, p53 signaling pathway and phosphatidylinositol signaling system. qRT-PCR was used to further verify the accuracy of RNA sequencing at the transcriptional level. In summary, this study provides a theoretical foundation for future prevention and control strategies against CIAV, while further investigation is required to elucidate the functions and mechanisms underlying these significantly differentially expressed genes.

overall_design: CIAV-infected MDCC-MSB1 cells VS CIAV-uninfected MDCC-MSB1 cells


title: Comprehensive transcriptome analysis of CIAV infected MDCC-MSB1 cells []

address: 广东省广州市天河区五山483号


title: Transcriptomic profile of Mycobacteriophage Adephagia

city: Pittsburgh

first: Krista

middle: G.

last: Freeman

state: PA

address: 4249 Fifth Avenue

department: Biological Sciences

institute: University of Pittsburgh

summary: The gene expression during early (30min) and late (210 minutes) infection of Mycobacteriophage Adephagia was analyzed, as well as in a Adephagia lysogen.

overall_design: Total RNA was isolated, depleted of rRNA and prepped for sequencing (Illumina) during early and late infection of Adephagia and a lysogen.

middle: G

first: Michael

middle: J

last: Lauer

first: Graham

last: Hatfull

first: Rebecca

last: Garlena


title: A single-cell atlas deconstructs heterogeneity across multiple models in murine traumatic brain injury and identifies novel cell-specific targets

first: Dhivyaa

last: Rajasundaram

address: 4401 Penn Avenue

department: Pediatrics

summary: The problem of traumatic brain injury (TBI) heterogeneity has been a critical barrier to successful translation of therapies in the field. TBI heterogeneity exists in the patient substrate pre-injury (genetics, sex, comorbidities), external injury characteristics (severity, mechanism), and resultant post-injury host response that is responsible for deleterious secondary injury processes (seizures, neuroinflammation, neurodegeneration) and repair/regeneration. Identification of final common molecular pathways and signatures that integrate this vast heterogeneity could be valuable for guiding biomarkers, therapeutic targets, and predictive enrichment. In this study, we present the first large-scale searchable murine single-cell atlas of the transcriptomic response to TBI in 339,357 cells as a foundational step in molecularly deconstructing TBI heterogeneity. We identify 23 cell types with massive heterogeneity in the single-cell response across extrinsicand intrinsic factors, that has been underestimated. Majority of response to TBI was unique to individual cell populations with minimal overlap even within a single injury-model thus highlighting the importance of cell-level resolution. Through this effort, we report novel cell-specific targets and a previously unrecognized role for specific microglial and ependymal subtypes in post-TBI pathophysiology that is highly variable depending on the extrinsic and intrinsic factors studied. One ependymal subtype was a hub of neuroinflammatory signaling after contusional-TBI, particularly related to Il-1b. A single microglial-lineage along pseudotime (comprising 3 microglial subtypes) was a key mediator of host-response after TBI, and shared features with disease associated microglia noted in Alzheimer’s disease and other neurodegenerative disorders, potentially providing a link between TBI and accelerated neurodegeneration. One microglial subtype within this lineage emerged as a key target – it was the only cell type of all 23 that retained persistent and marked gene expression changes 6 months post contusional-TBI. We identify sexually dimorphic gene expression and pathway vulnerabilities with cell-specific differences in both immune and non-immune biological processes. These likely contribute to sex-based outcome and warrant further study to facilitate discovery of cell- and sex-specific druggable targets. Active changes in brain regions distal from the site of primary TBI impact included infiltration of specific microglial populations as well as cell-specific transcriptomic changes in several genes and inflammatory processes distinct from both the peri-contusional and naïve signatures. This atlas validates several known contributors in TBI pathophysiology, and also identifies previously unrecognized targets and avenues for further research. Beyond our presented exemplar analyses (including pathways of clinical interest like sulfonylurea-receptor-1), the companion searchable atlas serves as a foundation for countless future efforts to understand cell-specific heterogeneity after TBI (https://shiny.crc.pitt.edu/cerebri/) as well as numerous other neurological diseases with overlapping pathophysiology.

overall_design: We isolated and dissociated fresh tissue from naïve or injured cortex  post-TBI in three clinically-relevant mouse models across a spectrum of TBI. Experiments were performed individually without hashing. Our established translational models included repetitive-Closed-Head-Injury TBI (rCHI, mimicking sports injuries), controlled cortical impact (CCI, mimicking cerebral contusion), and CCI with hemorrhagic-shock (devastating polytrauma frequently seen in critically ill TBI). Workflow of injury models/conditions and sampling locations from naïve and injured brain are described in the manuscript- briefly tissue was isolated from left pericontusional or naïve brain 24h post-injury (rCHI, CCI or CCI+HS), and 7d and 6mo post-CCI (Allen-Mouse Brain bregma values -0.755 to -2.75). Tissue was also obtained from females (ipsilateral) and male contralateral mirror-image brain-tissue 24h post-CCI in separate experiments. Tissue was micro-dissected, single-cells were isolated, sequenced and computationally analyzed. There are extensive publications on outcome implications in these models as cited in the paper. In CCI (the most common preclinical TBI-model), cells were isolated from both sexes, the ipsilateral/peri-contusional and mirror-image contralateral cortex, and multiple timepoints. After generating a single-cell gene-expression matrix that integrated naïve and injured cells we defined cell-cluster specific markers and identified ten umbrella cell-types with 23 transcriptomically distinct cell populations.

first: Ruchira

last: Jha

first: Dennis

last: Simon

first: Patrick

last: Kochanek

first: Gary

last: Kohanbash


title: Loss of skeletal muscle Bmal1 chromatin accessibility

city: Gainesville

first: Mark

middle: Robert

last: Viggars

state: Alachua

address: University of Florida, M531

department: Physiology & Aging

institute: University of Florida

summary: Investigate the effects loss of skeletal muscle Bmal1 has on gastrocnemius chromatin accessibility via ATAC-seq.

overall_design: Gastrocnemius muscles were collected at 6 months of age from vehicle treated and iMSBmal1KO mice. Two whole gastrocnemius muscle (~300-350mg) were diced and then homogenized using a Polytron homogenizer in homogenization buffer (Homogenization buffer (10mM HEPES, pH 7.5, 10mM MgCl2, 60mM KCl, 300mM sucrose, 0.1mM EDTA, 0.1% Triton, 1mM DTT, complete with mini protease inhibitor mix). Homogenates were spun at 300rpm for 3 minutes and supernatant containing nuclei moved to a new tube. This was repeated 3 times. The supernatant was then filtered through a 40µm cell strainer before centrifugation at 1000g for 10 minutes. The nuclei pellet was then resuspended in 1.2ml of homogenization buffer, gently triturated and 200µl loaded on top of several 2.15M sucrose cushions (10mM HEPES, pH 7.5, 10mM MgCl2, 60mM KCl, 2.15M sucrose, 0.1mM EDTA, 0.1% Triton, 1mM DTT, complete with mini protease inhibitor mix). Nuclei samples were centrifuged at 13,500g at 4°C for 1.5 hours. Samples were aspirated and washed leaving a nuclei pellet, mainly free of cytoplasmic fragments. Nuclei were quality checked using light microscopy (intact nuclei, no blebbing, free of cytoplasmic fragments) and then counted. 50,000 nuclei were used for input into a commercially available ATAC-seq kit which includes library preparation (#53150, Active Motif, Inc., CA, USA).

first: Karyn

middle: A

last: Esser


title: Loss of skeletal muscle Bmal1 +/- Acute Exercise

summary: Investigate the effects loss of skeletal muscle Bmal1 has on the acute transcriptional response to exercise in gastrocnemius muscle.

overall_design: Mouse gastrocnemius muscles were collected +/- 1-hour post 30-minute treadmill exercise +/- skeletal muscle BMAL1


title: Unraveling the molecular mechanisms of fish physiological response to freshwater salinization: A comparative multi-tissue transcriptomic study in a river polluted by potash mining

city: Cologne

first: Camilo

last: Escobar Sierra

state: NRW

address: Zülpicher Strasse 47b

department: Institute of Zoology

country: Germany

institute: University of Cologne

summary: Freshwater salinization is an escalating global environmental issue that threatens freshwater biodiversity, including fish populations. This study aims to uncover the molecular basis of salinity physiological responses in a non-native minnow species (Phoxinus septimaniae x P. dragarum) exposed to saline effluents from potash mines in the Llobregat River, Barcelona, Spain. Employing high-throughput mRNA sequencing and differential gene expression analyses, brain, gills, and liver tissues collected from fish at two stations (upstream and downstream of saline effluent discharge) were examined. Salinization markedly influenced global gene expression profiles, with the brain exhibiting the most differentially expressed genes, emphasizing its unique sensitivity to salinity fluctuations. Pathway analyses revealed the expected enrichment of ion transport and osmoregulation pathways across all tissues. Furthermore, tissue-specific pathways associated with stress, reproduction, growth, immune responses, methylation, and neurological development were identified in the context of salinization. Rigorous validation of RNA-seq data through quantitative PCR (qPCR) underscored the robustness and consistency of our findings across platforms. This investigation unveils intricate molecular mechanisms steering salinity physiological response in non-native minnows confronting diverse environmental stressors. This comprehensive analysis sheds light on the underlying genetic and physiological mechanisms governing fish physiological response in salinity-stressed environments, offering essential knowledge for the conservation and management of freshwater ecosystems facing salinization.

overall_design: This study investigates the ecological consequences of freshwater salinization caused by potash mining activities near the Llobregat River in Barcelona, Spain, focusing on the molecular underpinnings of salinity adaptation in the invasive minnow (Phoxinus septimaniae x P. dragarum). The research aims to uncover tissue-specific responses in the brain, gills, and liver by employing high-throughput mRNA sequencing and differential gene expression analyses. Minnows were sampled from two stations along the Llobregat River: the "Salt" station near a potash mine, exhibiting extreme salinity (18.1 ppt), and a "reference station" upstream with significantly lower salinity. Six fish samples (three from each station) were immediately fixed and stored. RNA extraction and sequencing were performed on the brain, liver, and gill tissues. A de novo transcriptomic analysis assessed differential gene expression and gene ontology variation between the “salt” and “reference” tissues.

last: Escobar-Sierra

first: Miguel

last: Cañedo-Argüelles

first: Dolors

last: Vinyoles

first: Kathrin

middle: P

last: Lampert


title: Loss of skeletal muscle Bmal1 +/- Exercise Training [Mouse liver, heart, inguinal white adipose and lung tissues

summary:
Investigate the effects loss of skeletal muscle Bmal1 has on systemic transcriptomes +/- exercise training.

Mouse liver, heart, white adipose and lung tissues were collected 47 hours post their last exercise bout, with or without 6-weeks of daily treadmill training. +/- Skeletal muscle Bmal1

overall_design: Mouse liver, heart, white adipose and lung tissues were collected 48 hours post their last exercise bout, with or without 6-weeks of daily treadmill training. +/- Skeletal muscle Bmal1


title: Analysis of the heterogeneity and complexity of murine extraorbital lacrimal gland via single-cell RNA sequencing

city: Zhengzhou

first: Zhijie

last: Li

state: Henan

address: Weiwu Road No. 7

institute: Department of Ophthalmology, Zhengzhou University People's Hospital, Henan Provincial People's Hospital

summary: Purpose: The lacrimal gland is essential for maintaining ocular surface health and avoiding external damage by secreting an aqueous layer of the tear film. However, a healthy lacrimal gland’s inventory of cell types and heterogeneity remains understudied. Methods: Here, 10X Genome-based single-cell RNA sequencing was used to generate an unbiased classification of cellular diversity in the extraorbital lacrimal gland (ELG) of C57BL/6J mice. From 43,850 high-quality cells, we produced an atlas of cell heterogeneity and defined cell types using classic marker genes. The possible functions of these cells were analyzed through bioinformatics analysis. Additionally, the CellChat was employed for a preliminary analysis of the cell-cell communication network in the ELG. Results: Over 37 subclasses of cells were identified, including seven types of glandular epithelial cells, three types of fibroblasts, ten types of myeloid-derived immune cells, at least eleven types of lymphoid-derived immune cells, and five types of vascular-associated cell subsets. The cell-cell communication network analysis revealed that fibroblasts and immune cells play a pivotal role in the dense intercellular communication network within the mouse ELG.  Conclusions: This study provides a comprehensive transcriptome atlas and related database of the mouse ELG.

overall_design: Two ELGs from each male mouse were pooled to form a single sample, resulting in six samples from six adult mice for scRNA-seq.

first: Duliurui

last: Huang

first: Xinwei

last: Jiao

first: Shenzhen

first: Jiangman

last: Liu

first: Hongli

last: Si

first: Di

last: Qi

first: Xiaoting

last: Pei

first: Dingli

last: Lu

first: Yimian

last: Wang


title: Discerning the immune profile of the cervical cancer microenvironment

city: Barcelona

first: Lara

last: Nonell

address: C/ NATZARET, 115-117

department: VHIOinformatics

country: Spain

institute: Vall d'Hebron Institute of Oncology (VHIO)

summary: Customized gene expression profiling of a cohort of 24 cervical cancer samples

overall_design: Custom gene expression analysis of 24 fixed-paraffin embeded cervical cancer samples, being the sample name Px_1

first: Joan

last: Seoane

first: Ester

last: Bonfill-Teixidor


title: Gene expression changes associated with acquired resistance to anti-EGFR therapy (cetuximab) in colorectal cancer cells

city: Woluwé

first: Jérôme

last: Ambroise

address: Avenue Hippocrate 54

department: Institut de Recherche Expérimentale et Clinique

country: Belgium

institute: Université catholique de Louvain

summary: Despite the implementation of personalized medicine, patients with metastatic CRC (mCRC) still have a dismal overall survival due to the frequent occurrence of acquired resistance mechanisms thereby leading to clinical relapse. Understanding molecular mechanisms that support acquired resistance to anti-EGFR targeted therapy in mCRC is therefore clinically relevant and key to improving patient outcomes. Here, we observe distinct metabolic changes between cetuximab-resistant CRC cell populations, with in particular an increased glycolytic activity in KRAS-mutant cetuximab-resistant LIM1215 but not in KRAS-amplified resistant DiFi cells. We show that cetuximab-resistant LIM1215 cells have the capacity to recycle glycolysis-derived lactate to sustain their growth capacity. This is associated with an upregulation of the lactate importer MCT1 at both transcript and protein levels. Pharmacological inhibition of MCT1, with AR-C155858, reduces the uptake and oxidation of lactate and impairs growth capacity in cetuximab-resistant LIM1215 cells. This study identifies MCT1-dependent lactate utilization as a clinically actionable, metabolic vulnerability to overcome KRAS-mutant-mediated acquired resistance to anti-EGFR therapy in CRC.

overall_design:
To study the metabolic adaptation of CRC cells upon acquired resistance to cetuximab treatment, we used two human colon cancer cell lines LIM1215 and DiFi, initially cetuximab-sensitive (denoted as -S), and for which populations with acquired resistance (-R1 and -R2) had been previously established upon chronic exposure for several months with the drug (Misale et al Nature 2012). While DiFi-R cells harbored EGFR gene copy number reduction and KRAS gene amplification, LIM1215-R cells were reported to display KRAS activating mutations.
We then carried out gene expression profiling analysis using RNA-seq data obtained from cetuximab-resistant (-R1 and -R2) and cetuximab-sensitive (-S) DiFi and LIM1215 CRC cells.

first: Elena

last: Richiardone

first: Romain

last: Boidot

first: Alberto

last: Bardelli

first: Sabrina

last: Arena

first: Cyril

last: Corbet


title: Facile Osteoimmunomodulatory Nanoparticles Augment 3D-Printed Scaffold-Mediated Bone Regeneration

city: Rochester

first: Hani

last: Awad

state: NY

address: 601 Elmwood Avenue

department: Biomedical Engineering

institute: University of Rochester

summary: Regenerating critical-sized long bone defects poses substantial challenges due to limitations of autografts and processed allografts. Biomaterial scaffolds offer versatile alternatives, yet their effectiveness is often constrained by their limited innate osteoinductivity. While growth factors and cells can enhance osteoinduction, the inclusion of biologics in biomaterial scaffolds creates regulatory challenges for clinical translation. To address this, here we describe three-dimensional (3D) printed polycaprolactone (PCL) scaffolds for temporally controlled delivery of osteoimmunomodulatory amorphous calcium phosphate-chitosan nanoparticles (ACPC-NP).  In vitro, the ACPC-NP exhibit concentration dependent effects on osteoblasts, monocytes, and osteoclasts. At increasing concentrations up to 500 μg/ml, these nanoparticles stimulate osteogenesis, modulate M2/M1 macrophage polarization, and inhibit osteoclast maturation and activity. Leveraging these concentration-dependent effects in vivo through temporally controlled release of ACPC-NP from 3D-printed PCL scaffolds, we observe the complete regeneration and the restoration of biomechanical strength of critically sized radial defects in rats. Such healing is absent in defects implanted with bare PCL scaffolds or those loaded with calcium-phosphate microparticles. The tunable osteoimmunomodulation by the NP underscore the translational potential of this technology to yield structurally sound and functionally robust bone regeneration outcomes.

overall_design: Three types of scaffolds were fabricated using 3D printing techniques, including PCL scaffolds containing  amorphous calcium phosphate chitosan nanoparticles (ACPC-NP), calcium phosphate microparticles (CaP), and bare PCL. We then set out to test their effects in vivo using a rat radius critical-sized bone defect model. To gain mechanistic insights on the osteogenic capacity of the ACPC-NP scaffold compared to CaP and PCL scaffolds, bulk RNA sequencing was performed on mRNA from cells released from the bone tissues extending 1mm proximal and distal to the scaffolds at weeks 2 and 6 post-implantation.

first: Ming

last: Yan

first: Baixue

last: Xiao

first: Anthony

last: Yosick

first: Bei


title: COL10A1 expression distinguishes a subset of cancer-associated fibroblasts present in the stroma of high-risk basal cell carcinoma

city: Schlieren

first: Gaetana

last: Restivo

address: Wagistrasse 18

department: Department of Dermatology

country: Switzerland

institute: University Hospital Zurich

summary: Basal cell carcinoma (BCC) is the most frequently diagnosed skin cancer and the most common malignancy in humans. Different morphological subtypes of BCC are associated with low- or high-risk of recurrence and aggressiveness, but the underlying biology of how the individual subtypes arise remains largely unknown. Because the majority of BCCs appear to arise from mutations in the same pathway, we hypothesized that BCC development, growth and invasive potential is also influenced by the tumor microenvironment and in particular by cancer-associated fibroblasts (CAFs) and their secreted factors. In this work, we aimed to characterize the stroma of the different BCC subtypes with a focus on CAF populations. To investigate the stromal features of the different BCC subtypes, we applied laser-capture microdissection (LCM) followed by RNA sequencing. A cohort of 15 BCC samples from 5 different “pure” subtypes (superficial, nodular, micronodular, sclerosing and basosquamous; n=3 each) were selected and included in the analysis. Healthy skin was used as a control (n=6). We show that the stroma of the different BCC subtypes have distinct gene expression signatures. Nodular and micronodular seem to have the most similar signatures, while superficial and sclerosing the most different. By comparing low- and high-risk BCC subtypes, we observed that Collagen 10A1 (COL10A1) is overexpressed in the stroma of sclerosing/infiltrative and basosquamous but not micronodular high-risk subtypes. Those findings were confirmed by immunohistochemistry in a cohort of 89 different BCC and 13 healthy skin samples. Moreover, scRNAseq analysis of BCCs of two independent datasets showed that the COL10A1-expressing population of cells is associated with the stroma adjacent to invasive BCC and shows extracellular matrix remodeling features.

overall_design: In order to investigate the stromal features characterizing the different BCC morphological subtypes, we selected FFPE specimens of superficial, nodular, micronodular, sclerosing/infiltrating and basosquamous BCC subtypes. Healthy skin samples were included as controls. To specifically analyze stromal cell populations and extracellular matrix components directly adjacent to tumor cells or healthy epidermis, we applied Laser-Capture Microdissection (LCM) followed by RNA sequencing.

first: Mauro

last: Esposito


title: Gene expression of Cancer-associated fibroblasts from orthotopically engrafted murine colon tumors on the single cell level (Sort-Seq)

city: Erlangen

first: Harald

last: Schuhwerk

address: Glückstrasse 6

summary: The EMT-transcription factor ZEB1 is heterogeneously expressed in tumor cells and in cancer-associated fibroblasts (CAFs) in colorectal cancer (CRC). While ZEB1 in tumor cells regulates metastasis and therapy resistance, its role in CAFs is largely unknown. Combining fibroblast-specific Zeb1 deletion with immunocompetent mouse models of CRC, we observe that inflammation-driven tumorigenesis is accelerated, whereas invasion and metastasis in sporadic cancers is reduced upon fibroblast-specific loss of Zeb1.  Single-cell transcriptomics, histological characterization and in vitro modelling reveal a crucial role in CAF polarization, promoting myofibroblastic features by restricting inflammatory activation. Zeb1 deficiency impairs collagen deposition and CAF barrier function but increasesd NFκB-mediated cytokine production, jointly promoting lymphocyte recruitment and immune checkpoint activation.

overall_design: We used single cell RNA sequencing (scRNA-seq) via SORT-Seq to analyze the transcriptome of orthotopically engrafted murine colon cancer organoids. Cell types within whole tumors were isolated by FACS (following colon tumor digestion) using marker combinations (Epcam, CD45 and CD31).

first: Marc

last: Stemmler

first: Henner

last: Farin

first: Constantin

last: Menche


title: Gene expression of Cancer-associated fibroblasts from AOM/DSS autchthonous murine tumors on the single cell level (Sort-Seq)

overall_design: We used single cell RNA sequencing (scRNA-seq) via SORT-Seq to analyze the diversity of murine AOM/DSS CAFs enriched by FACS (following colon tumor digestion) by gating for absence of Epcam, CD45 and CD31 immunoreactivity.


title: Hypoxia and inflammation induce synergistic transcriptome turnover in macrophages

city: Boulder

first: Edward

last: Courvan

address: 3415 Colorado Ave

institute: University of Colorado

summary: Macrophages are effector immune cells that experience substantial changes to oxygenation when transiting through tissues, especially when entering tumors or infected wounds. How hypoxia alters gene expression and macrophage effector function at the post-transcriptional level remains poorly understood. Here we use TimeLapse-seq to measure how inflammatory activation modifies the hypoxic response in primary macrophages. Nucleoside recoding sequencing allows derivation of steady-state transcript levels, degradation rates, and transcriptional synthesis rates from the same dataset. We find that hypoxia produces distinct responses from resting and inflammatory macrophages. Hypoxia induces destabilization of mRNA transcripts, though inflammatory macrophages substantially increase mRNA degradation compared to resting macrophages. Increased RNA turnover results in upregulation of ribosomal protein genes and downregulation of extracellular matrix components in inflammatory macrophages. Hypoxia induces gene expression changes similar to tumorigenic macrophages in solid tumor biopsies, including increased ribosomal protein expression, implying that post-transcriptional control contributes to translation regulation in tumorigenic macrophages.

overall_design: Samples are triplicate TimeLapse-seq transcriptome libraries prepared from human macrophages that are either left resting, inflammatory activated in normoxia, or inflammatory activated in hypoxia.

first: Courvan

last: Edward

first: Parker

last: Roy


title: Loss of skeletal muscle Bmal1 +/- Exercise Training

first: Mark

last: Viggars

summary: Investigate the effects loss of skeletal muscle Bmal1 has on exercise training via transcriptional analysis (RNA-sequencing).

overall_design: Mouse gastrocnemius muscles, +/- BMAL1 were collected 47 hours post their last exercise bout, with or without 6-weeks of daily treadmill training.

first: Karyn

last: Esser


title: Genome-wide quantification of RNA flow across subcellular compartments reveals determinants of the transcript life cycle [Nanostring]

first: Brendan

last: Smalec

address: 77 Avenue Louis Pasteur, Rm 356

summary: Series of regulatory mechanisms control eukaryotic mRNAs, from their production on chromatin to their eventual degradation. Dissecting these pathways requires quantitative measurements of mRNA flow across the cell. We developed subcellular TimeLapse-seq to measure the rates at which RNAs are released from chromatin, exported from the nucleus, loaded onto polysomes, and degraded within the nucleus and the cytoplasm. All rates displayed substantial variability genome-wide, and transcripts from genes with related functions flowed across subcellular compartments with similar kinetics. For some genes, most transcripts were rapidly degraded within the nucleus, while the remaining molecules were exported and persisted with stable lifespans. With compartment-specific measurements of poly(A) tail lengths, we found that relationships between tail length and stability differ across the cell. The targets of RNA binding proteins experience distinct RNA flow kinetics, and we found that two, DDX3X and PABPC4, act by controlling the nuclear export of their targets. Finally, we developed a machine learning model to propose additional molecular features that underlie the diverse life cycle of mammalian mRNAs.

overall_design: Verification of subcellular TimeLapse-seq estimation of fraction of newly synthesized RNA per gene. Here we used a custom NanoString assay to estimate the fraction of 4sU-labeled RNAs following 5 different 4sU pulses across 3 RNA populations (total, nuclear, and cytoplasm RNA) for 20 genes.

first: Robert

last: Ietswaart

first: Albert

last: Xu

first: Karine

last: Choquet

first: Erik

last: McShane

first: Ziad

last: Jowhar

first: Chantal

last: Guegler

first: Autum

last: Baxter-Koenigs

first: Emma

last: West

first: Becky Xu

last: Hua Fu

first: Luke

last: Gilbert

first: Stephen

last: Floor

first: L Stirling

last: Churchman


title: Pan-cancer mapping of single CD8+ T cell profiles reveals a TCF1:CXCR6 axis regulating CD28 co-stimulation and anti-tumor immunity III

first: The Gene Lay Institute of

last: Immunology and Inflammation

address: 60 Fenwood Road,

institute: Brigham and Women's Hospital

summary: Cytotoxic CD8+ T cells need to persist and function in diverse tumor microenvironments to exert their effects. Here, we developed Generalizable Matrix Decomposition Framework (GMDF), a matrix factorization algorithm that recovers both shared and tumor type-specific transcriptional programs from diverse data sets, and applied it to a scRNA-seq compendium of 38,852 CD8+ T cells from 141 patients spanning nine different human cancers. Our meta-single-cell analyses uncovered a pan-cancer T cell dysfunction program that was predictive of clinical responses to checkpoint blockade in melanoma and highlighted CXCR6 as a pan-cancer marker of chronically activated T cells. CXCR6 transcription was activated by AP-1 factors and repressed by TCF1. In mouse models, CXCR6 expression increased with tumor progression and upon checkpoint blockade. CXCR6 deletion in CD8+ T cells increased apoptosis of PD1+Tim3+ cells and compromised tumor growth control due to suppressed expression of survival factors and CD28 co-stimulation, revealing a role for CXCR6 in opposing PD1-mediated suppression of CD28 signaling. Our application of GMDF led us to discover a TCF1:CXCR6 axis that counterbalances PD1-mediated suppression of CD8+ cell responses and is essential for effective anti-tumor immunity.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for in vitro activated OTI wildtype (WT 1,2,3) and OTI CXCR6 KO (KO 1,2,3) CD8+ T cells post co-culture with ova-pulsed bone marrow-derived dendritic cells

first: Ana

middle: C

last: Anderson

first: Katherine

last: Tooley


title: Pan-cancer mapping of single CD8+ T cell profiles reveals a TCF1:CXCR6 axis regulating CD28 co-stimulation and anti-tumor immunity I

overall_design: Comparative gene expression profiling analysis of RNA-seq data for different timepoints after in vitro activation of CD8+ T cells isolated from 3 OTI wildtype (E8i-cre-, Tcf7FL/FL, OTI+) (Mice 4-6) and 3 OTI Tcf7 cKO (E8i-cre+, Tcf7FL/FL, OTI+) (Mice 1-3)


title: Endometrial adhesion G protein-coupled receptors are dynamically expressed across the menstrual cycle and expression is altered by ovarian stimulation

city: Newark

first: Alexander

last: Lemenze

state: New Jersey

address: 185 South Orange Ave

institute: Rutgers

summary: Approximately 10% of women of reproductive age in the United States suffer from infertility3 and a large number of these women will undergo in vitro fertilization (IVF) with the intent to conceive a child. Ovarian stimulation (OS), utilized for the development of multiple ovarian follicles for IVF, induces supraphysiologic levels of E2 and an early rise in P4. These hormonal changes disrupt endometrial differentiation that decreases implantation rates or result in placental insufficiency and pregnancy complications. To improve pregnancy rates and reduce the risk of pregnancy complications associated with IVF, it is crucial to advance our molecular understanding of the molecular regulation of endometrial differentiation. Previous studies from our laboratory suggest G protein-coupled receptors (GPCRs) are important regulators of endometrial differentiation. To investigate this further, using a retrospective dataset, we identified all GPCRs expressed across the proliferative and secretory phase of the menstrual cycle and found that many members of the adhesion G protein-coupled receptor (ADGR) family are dynamically expressed. This suggests these ADGRs are E2- and/or P4-regulated genes.  We therefore hypothesized that for these ADGR genes, mRNA expression would be disrupted in an OS cycle. This hypothesis was tested on endometrial biopsies collected in the secretory phase from prospective cohorts of women in natural and OS cycles. Consistent with the retrospective dataset, our data revealed that members of the ADGR gene family are expressed in the secretory phase of the natural menstrual cycle and for the first time, we show that their expression is altered by ovarian stimulation.

overall_design: Endometrial biopsies were performend  on women in natural and ovarian stimulation cycles . In natural cycles, endometrial biopsies were performed 2 or 9 days after detection of a urine LH surge, (hCG2 and hCG9). In ovarian stimulation cycles,  endometrial biopsies were performed 2 or 9 days after administration of the 10K unit hCG ovulation trigger. Total RNA was extracted from each sample.

first: Andy

middle: V

last: Babwah

first: Nataki

last: Douglas

last: Dubin

first: Xusheng

last: Zhang

first: Nischelle

last: Kalakota


title: Pan-cancer mapping of single CD8+ T cell profiles reveals a TCF1:CXCR6 axis regulating CD28 co-stimulation and anti-tumor immunity II

overall_design: Intratumoral immune cells from wildtype (WT, E8i-cre-, Tcf7 FL/FL) and Tcf7 cKO (KO, E8i-cre+, Tcf7 FL/FL) mice were isolated by Fluorescence-activated cell sorting (FACS) and analyzed using scRNAseq.

first: Asaf

last: Madi


title: Short-term cold exposure induces persistent epigenomic memory in brown fat

city: Philadelphia

first: Mohit

middle: K.

last: Midha

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

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

overall_design: Refer to individual Series


title: Transcriptome m6A sequencing (MeRIP-seq)of human pancreatic cancer cells

city: hangzhou province

first: chaojie

last: huang

state: zhejiang

address: shangtang road No158, Hangzhou city, zhejiang province china

institute: Zhejiang provincial people’s Hospital

summary: We analyze  Global M6A Abundance in PANC-1 cells treated with fisetin by MeRIP-seq

overall_design: 3 matched  replicates samples in DMSO and 80nM fisetin treatment

first: Liping

last: Cao

first: Shengnan

last: Jia

first: Chaojie

last: Huang


title: Pan-cancer mapping of single CD8+ T cell profiles reveals a TCF1:CXCR6 axis regulating CD28 co-stimulation and anti-tumor immunity

city: Boston


title: Single cell view of tumor microenvironment gradients in pleural mesothelioma

city: New York

last: Tsankov

state: New York

address: 1 Gustave L. Levy Pl

department: Genetics and Genomics

institute: Icahn School of Medicine at Mount SInai

summary: Immunotherapies have shown great promise in pleural mesothelioma (PM), yet most patients still do not achieve  significant clinical response, highlighting the importance of improving understanding of the tumor  microenvironment (TME). Here, we utilized high-throughput, single-cell RNA-sequencing to de novo identify 54  expression programs and construct a comprehensive cellular catalogue of the PM TME. We found four cancer-  intrinsic programs associated with poor disease outcome and a novel fetal-like, endothelial cell population that  likely responds to VEGF signaling and promotes angiogenesis. Throughout cellular compartments, we observe  substantial difference in the TME associated with a cancer-intrinsic sarcomatoid signature, including enrichment in  fetal-like endothelial cells, CXCL9+ macrophages, cytotoxic, exhausted, and regulatory T cells, which we validated  using imaging and bulk deconvolution analyses on two independent cohorts. Finally, we show, both  computationally and experimentally, that NKG2A-HLA-E interaction between NK and tumor cells represents an  important new therapeutic axis in PM, especially for epithelioid cases.

overall_design: Patient-matching primary tumor resections and blood samples were collected from 13 MPM patients. Dissociated single cells from the tumor samples were profiled using the Chromium platform (10x Genomics, Pleasanton, CA) with the 3′ gene expression (3′ GEX) V3 kit or 5' gene expression (5' GEX) kits according to manufacturer instructions. Cells from the blood samples were profiled with the 10x Chromium Next GEM Chip K Kit and TCR CDR3 sequences were enriched using the human V(D)J T cell enrichment.

first: Bruno

last: Giotti

first: Komal

last: Dolasia

first: William

last: Zhao

first: Peiwen

last: Cai

first: Robert

last: Sweeney

first: Elliot

last: Merritt

first: Evgeny

last: Kiner

first: Grace

last: Kim

first: Atharva

last: Bhagwat

first: Samarth

last: Hegde

first: Bailey

last: Fitzgerald

first: Sanjana

last: Shroff

first: Travis

last: Dawson

first: Monica

last: Garcia-Barros

first: Rachel

last: Chen

first: Sacha

last: Gnjatic

first: Jamshid

last: Abdul-Ghafar

first: Alan

last: Soto

last: Brody

first: Seunghee

last: Kim-Schulze

first: Zhihong

first: Kristin

last: Beaumont

first: Miriam

last: Merad

first: Raja

last: Flores

first: Rpbert

last: Sebra

first: Amir

last: Horowitz

first: Thomas

middle: U

last: Marron

first: Anna

last: Tocheva

first: Andrea

last: Wolf


title: IMPACT OF NEAR-CONTINUOUS LOW DOSE-RATE NEUTRON IRRADIATION ON PREGNANCY OUTCOMES IN MICE

status: Public on Jul 01 2024

city: Aurora

first: Andrew

last: Goodspeed

state: CO

address: 12801 E 17th Ave, Mail Stop 8303

institute: University of Colorado Anschutz Medical Campus

summary: The effects of galactic cosmic radiation on reproductive physiology remain largely unknown. We determined the impact of near-continuous low-dose-rate Californium-252 neutron irradiation (1 mGy/day) as a space-relevant analog on litter size and number of resorptions at embryonic day (E) 12.5 (n=19 radiated dams, n=20 controls) and litter size, number of resorptions, fetal growth, and placental signaling and transcriptome (RNA sequencing) at E18.5 (n=21 radiated dams, n=20 controls) in pregnant mice. A significantly increased early resorption rate and decreased placental weight was observed in irradiated mice. There were no statistically significant differences in litter size, fetal weight, length, or malformation rate between the groups. Near-continuous radiation had no significant effects on mechanistic target of rapamycin (mTOR), endoplasmic reticulum stress or inflammatory signaling, rate of double-stranded DNA breaks, and had minimal effects on gene expression in the placenta. These data suggest that near-continuous, low-level galactic cosmic radiation has a limited impact on pregnancy outcomes.

overall_design: RNA sequencing was performed on one randomly selected placenta from each of 15 irradiated E18.5 litters and 15 control litters. The RNA from each of the 30 individual placentas was isolated using a Qiagen RNeasy mini kit following the manufacturer’s instructions. Next, a reverse transcriptase reaction was performed using the Qiagen Quantitect RT kit according to manufacturer’s instructions (Qiagen, Hilden, Germany). The resulting cDNA was then subjected to quantitative PCR. RNA purity, quantity and integrity was determined with NanoDrop (ThermoFisher Scientific, Waltham, MA) and TapeStation 4200 (Agilent, Santa Clara, CA) analysis prior to RNA-seq library preparation. The Universal Plus mRNA-Seq library preparation kit with NuQuant was used (Tecan, Männedorf, Switzerland) with an input of 200ng of total RNA to generate RNA-Seq libraries. Paired-end sequencing reads of 150bp were generated on NovaSeq 6000 (Illumina, San Diego, CA) sequencer and de-multiplexed using bcl2fastq.  Illumina adapters and the first 12 base pairs of each read were trimmed using BBDuk (BBMAP; www.sourceforge.net/projects/bbmap) and reads <50bp post-trimming were discarded. Reads were aligned and quantified using STAR (2.6.0a)54 against the Ensembl mouse transcriptome (mg38.p6 genome release 96). Ensembl IDs were mapped to gene names and counts of genes with multiple IDs were aggregated. Low expression genes were removed if mean raw count <1 or mean counts per million (CPM) <1 for the dataset. Reads were normalized to CPM using the edgeR R package (Bioconductor; Boston, MA)55. Differential expression was calculated using the voom function in the limma R package with RNA integrity numbers as a covariate56. Gene set enrichment analysis (GSEA) was performed using the full ranked list of genes by fold change for the indicated comparison and the fgsea R package57 using Hallmark, Gene Ontology Biological Processes, and KEGG gene sets from the Molecular Signatures Database58-59. A heatmap was generated with the ComplexHeatmap R package58 following z-score transformation. Additional plots were generated using the ggplot2 R package61.

first: Jon

last: Steller

first: Rebecca

last: Blue

first: April

last: Ronca

first: Theresa

last: Powell

last: Jansson


title: Repeated exposure to lidocaine induces hippocampal synaptic and cognitive impairment in aged mice by activating microglia and neurotoxic A1astrocytes

city: Fuzhou

first: Xiaochun

last: Zheng

state: Fujian

address: Dong street

department: Anesthessia

institute: Fujian Provincial Hospital

summary: To investigate changes in hippocampal genes mice after lidocaine injections

overall_design: Young and old mice were randomly divided into control groups and lidocaine groups. Multiple injections of lidocaine were administered to both young and old mice, followed by RNA sequencing of the hippocampus to observe the effects of lidocaine on hippocampal gene expression


title: Activated SKN-1 alters the longevity trajectory of long-lived C. elegans mutants

city: Los Angeles

first: Chris

last: Turner

address: 3715 McClintock Ave

institute: University of Southern California

summary: In the presence of stressful environments, the SKN-1 cytoprotective transcription factor is activated to induce the expression of gene targets that can restore homeostasis. However, constitutive activation of SKN-1 results in diminished health and a reduction of lifespan.  Here we demonstrate the necessity to regulate the activity of SKN-1 for maintaining the longevity promoting responses associated with impaired daf-2/insulin receptor signaling, the eat-2 model of caloric restriction, and glp-1-dependent loss of germ cell proliferation.  A hallmark of animals with constitutive SKN-1 activation is the age-dependent loss of somatic lipids and this phenotype is linked to the general reduction in survival in animals harboring the skn-1gf allele, but surprisingly, daf-2lf; skn-1gf double mutant animals do not redistribute somatic lipids which suggests the insulin signaling pathway functions downstream of SKN-1 in the maintenance of lipid distribution. As expected, eat-2lf; skn-1gf double mutant animals, which independently activate SKN-1, continue to display somatic lipid depletion in older ages with and without the skn-1gf activating mutation but animals lacking a proliferating germline do not redistribute somatic lipids, which supports a genetic model where SKN-1 activity is an important regulator of lipid mobilization in response to food availability to fuel the developing germline by engaging the daf-2/insulin receptor pathway.

overall_design: Differential expression analysis to undestand the transcriptome differences between daf-2lf mutnats and daf-2lf;skn-1gf double mutants

middle: D

first: Sean

last: Curran


title: Molecular regulation of photoinduced seasonal changes in Japanese Quail (Coturnix japonica) energy rheostasis.

city: Glasgow

first: Sayantan

last: Sur

address: University of Glasgow, Vet School, Garscube Campus, Bearsden Road

department: School of Biodiversity, One Health & Veterinary Medicine

institute: University of Glasgow

summary: The neuroendocrine regulation of seasonal energy homeostasis and rheostasis are widely studied. However, the molecular pathways underlying tissue-specific adaptations remain poorly described. We conducted an experiment to examine long-term rheostatic changes in energy stability using the well-characterized photoperiodic response of the Japanese quail. We exposed quails to photoperiodic transitions simulating the annual photic cycle and examined the morphology and fat deposition in liver, and white adipose tissue. To identify molecular substrates during the vernal transition in lipid accumulation, we conducted transcriptomic analyses of white adipose and liver tissues. We identified transcripts involved in adipocyte growth (Cysteine Rich Angiogenic Inducer 61, Very Low Density Lipoprotein Receptor) and obesity-linked disease resistance (Insulin-Like Growth Factor Binding Protein 2, Apolipoprotein D) increase expression in anticipation of body mass gain. In the liver, under long photoperiods, transcripts involved in fatty acid (FA) synthesis (Fatty Acid Synthase, Fatty Acid Desaturase 2) were down-regulated. Parallel upregulation of hepatic Fatty Acid Translocase and Pyruvate Dehydrogenase Kinase 4 expression suggests increased circulatory FA uptake and a switch from glucose to FA utilization. Overall, we have identified tissue-specific biochemical and molecular changes that drive photoperiod-induced adipogenesis in quails. These findings can be use to determine conserved pathways that enable animals to accumulate fat without developing metabolic diseases.

overall_design: To investigate seasonal changes in liver and white adipose tissue transcriptome, male quails (N=12 samples) housed in the long photoperiod (16L:8D) were subjected to 8 hours short photoperiod (N=4, 8L), 12 hours long photoperiod (N=4,12v) and 16 hours long photoperiod (N=4, 16v). Birds were killed by cervical dislocation followed by exsanguination via severing the jugular vein. The liver,  and abdominal white adipose tissue were rapidly collected and stored at −80°C. We then performed RNA sequencing of RNA extracted (RNEasy plus mini kit) from the liver (N=12) and adipose tissue (N=12) using GridION Mk1 (Oxford Nanopore Technologies).

first: Tyler

last: Stevenson


title: Gene expression profile of liver obtained from liver-specific  Me1-deficient mice challenged with high-fat diet

city: hangzhou

first: Jiawei

last: Zhang

address: NO.2318, Yuhangtang Rd, Yuhang District, 311121, Hangzhou, Zhejiang, P.R.China

institute: Hangzhou Normal university

summary: Nonalcoholic fatty liver disease (NAFLD) has grown from a relatively unknown disease to the leading chronic liver disease globally. Malic enzyme 1 (ME1) is a cytosolic NADP+-dependent enzyme involved in the oxidative decarboxylation of malate to pyruvate while concomitantly generating nicotinamide adenine dinucleotide phosphate (NADPH) from NADP+. Previous genome-wide association studies have identified ME1 as a susceptibility gene for obesity and diabetes. This analysis was performed to understand the transcriptomic changes associated with hepatic Me1 loss in male mice challenged with high-fat diet.

overall_design: To investigat the function of ME1 in NAFLD, we constructed Me1 hepatocyte-specific knockout mice (HKO) and wild-type littermates (Flox). We then performed gene expression profiling analysis using data obtained from RNA-seq of the livers of HKO and Flox, which were fed for 16 weeks with high-fat diet.

first: Zhang

last: Jiawei

first: Fang

last: Xuexian


title: Analysis of striatal zinc finger protein (ZFP) repression of mutant Huntingtin (HTT) in the zQ175DN knock-in mouse model of Huntington's disease (snRNA-seq)

city: Princeton

first: Jeff

last: Aaronson

address: 155 Village Boulevard, Suite 200

department: Discovery & Systems Biology

institute: CHDI

summary: We assessed the relative efficacy of selectively lowering mHTT in the striatum at different intervention times in a human HTT exon 1  knock-in mouse model of Huntington’s disease, zQ175DN KI, using a virally delivered zinc finger protein transcriptional repressor directed against the expanded CAG repeat of the mutant HTT gene (Zeitler et al. Nat Med. 2019 Jul;25(7):1131-1142).

overall_design: Simultaneous bilateral striatal stereotactic injections were performed in zQ175DN heterozygous (zQ175) or wild type (WT) littermates at either 2 or 6 months of age. The zQ175 knock-in (zQ175 KI) mouse has the mouse Htt exon 1 replaced by the human HTT exon 1 sequence with a ~190 CAG repeat tract (JAX ID: B6.129S1-Htttm1.1Mfc/190ChdiJ, CHDI ID: CHDI-80003019). One striatal hemisphere of each mouse was injected with purified, endotoxin free AAV2/2+1 virus expressing C-terminally HA-tagged mutant Huntingtin (mHTT) zinc finger repressor protein (ZFP30645, AAV-SWB, HA), under control of the human synapsin (hsyn) promotor (CHDI-90003731, “nZFP”). This ZFP targets expanded CAG repeats in the mutant Htt DNA, resulting in robust and selective abrogation of mHTT production (>80%) in striatal neurons. The other striatal hemisphere of each mouse was injected with either a control (inactive) AAV2/2+1 virus expressing C-terminally HA-tagged  mutant huntingtin ZFP repressor protein lacking the DNA binding domain, under the control of hsyn (CHDI-90003732; “DBD”) or with an alternative AAV2/2+1 control virus containing a non-protein encoding, non-mRNA encoding plasmid with a stuffer sequence between the inverted terminal repeats (transcription blocker (TB) / stop-EGFP nucleotide sequence (EstopB) / transcription blocker reverse complement (TBrc) and bovine growth hormone poly A (bGHpA)); (CHDI-90003959; “Estop”). Mice injected at 2 months were maintained for a further 4 or  6 months prior to humane euthanasia and focal striatal tissue (separate left and right hemisphere) collection at 6 months (2M_6M treatment group) or 8 months (2M_8M treatment group) of age respectively. Mice injected at 6 months were maintained for a further 2, 4 or 6 months prior to humane euthanasia and striatal tissue (separate left and right hemisphere) collection at 8 months (6M_8M treatment group), 10 months (6M_10M treatment group) or 12 months (6M_12M treatment group) of age respectively. Tissues were maintained at -80 C until processing. This culminated in 30 sample groups (5 treatment paradigms x  3 viral treatments per paradigm, applied to 2 genotypes (WT and zQ175)). Each of the 30 sample groups consisted of 4 striatal samples from an equally balanced proportion of injected male and female mice. Striatal samples were subjected to RNA isolation and single nucleus RNA sequencing.

first: Jian

last: Chen

first: Vahri

last: Beaumont


title: Analysis of striatal zinc finger protein (ZFP) repression of mutant Huntingtin (HTT) in the zQ175DN knock-in mouse model of  Huntington's disease


title: Analysis of striatal zinc finger protein (ZFP) repression of mutant Huntingtin (HTT) in the zQ175DN knock-in mouse model of  Huntington's disease (bulk RNA-seq)

summary: We assessed the relative efficacy of selectively lowering mHTT in the striatum at different intervention times in a human HTT exon 1 knock-in mouse model of Huntington’s disease, zQ175DN KI, using a virally delivered zinc finger protein transcriptional repressor directed against the expanded CAG repeat of the mutant HTT gene (Zeitler et al. Nat Med. 2019 Jul;25(7):1131-1142).

overall_design: Simultaneous bilateral striatal stereotactic injections were performed in zQ175DN heterozygous (zQ175) or wild type (WT) littermates at either 2 or 6 months of age. The zQ175 knock-in (zQ175 KI) mouse has the mouse Htt exon 1 replaced by the human HTT exon 1 sequence with a ~190 CAG repeat tract (JAX ID: B6.129S1-Htttm1.1Mfc/190ChdiJ, CHDI ID: CHDI-80003019). One striatal hemisphere of each mouse was injected with purified, endotoxin free AAV2/2+1 virus expressing C-terminally HA-tagged mutant Huntingtin (mHTT) zinc finger repressor protein (ZFP30645, AAV-SWB, HA), under control of the human synapsin (hsyn) promotor (CHDI-90003731, “nZFP”). This ZFP targets expanded CAG repeats in the mutant Htt DNA, resulting in robust and selective abrogation of mHTT production (>80%) in striatal neurons. The other striatal hemisphere of each mouse was injected with either a control (inactive) AAV2/2+1 virus expressing C-terminally HA-tagged  mutant huntingtin ZFP repressor protein lacking the DNA binding domain, under the control of hsyn (CHDI-90003732; “DBD”) or with an alternative AAV2/2+1 control virus containing a non-protein encoding, non-mRNA encoding plasmid with a stuffer sequence between the inverted terminal repeats (transcription blocker (TB) / stop-EGFP nucleotide sequence (EstopB) / transcription blocker reverse complement (TBrc) and bovine growth hormone poly A (bGHpA)); (CHDI-90003959; “Estop”). Mice injected at 2 months were maintained for a further 4 or  6 months prior to humane euthanasia and focal striatal tissue (separate left and right hemisphere) collection at 6 months (2M_6M treatment group) or 8 months (2M_8M treatment group) of age respectively. Mice injected at 6 months were maintained for a further 2, 4 or 6 months prior to humane euthanasia and striatal tissue (separate left and right hemisphere) collection at 8 months (6M_8M treatment group) 10 months (6M_10M treatment group) or 12 months (6M_12M treatment group) of age respectively. Tissues were maintained at -80oC until processing. This culminated in 30 sample groups (5 treatment paradigms x  3 viral treatments per paradigm, applied to 2 genotypes (WT and zQ175)). Each of the 30 sample groups consisted of 7 – 8 striatal samples from an equally balanced proportion of injected male and female mice. Striatal samples were subjected to RNA isolation and sequencing (Illumina, stranded mRNAseq: 40-50M reads, Paired End, 100-150bp).


title: mRNA gene expression of colon fibroblasts isolated from mouse colon

first: Marc

middle: P.

last: Stemmler

address: Glückstr. 6

department: Experimental Medicine 1

institute: Friedrich-Alexander University of Erlangen-Nürnberg

overall_design: Established fibroblast cultures from Zeb1 flox/flox (Fib-Ctrl) and Zeb1 del/del (Fib-ΔZeb1) were cultured regularly and RNA was harvested by Qiagen RNeasy

first: Harald

last: Schuhwerk

first: Isabell

last: Armstark

first: Yussuf

last: Hajjaj

first: Ruthger

last: van Roey

first: Constantin

last: Menche

first: Henner

last: Farin


title: Transcriptomic analysis of short term melanoma cell culture

city: Nice

first: Robert

last: Ballotti

state: Alpes maritimes

address: Hopital Archet2, Bat Archimed, 151, Rt de St Antoine de Ginestiere

institute: INSERM U1065, Team1  Bat Archimed, Hopîtal Archet2

summary: Melanoma cell isolated from melanoma tumors were cultured for less than 20 passages. RNAs were extracted and analysed on Agilent One-Color Gene Expression arrays

overall_design: Description of gene expression in different melanoma short term culture, no replicat. Agi_Hsa-v2_8x60K

last: BALLOTTI

first: Pascal

last: BARBRY

first: Kevin

last: LEBRIGAND


title: Transcriptome analyses of Arabidopsis lines overexpressing distinct PLC genes to explore their contribution to drought tolerance

city: Amsterdam

first: Max

last: van Hooren

state: Noord Holland

address: Science park 904

department: Plant Cell biology

country: Netherlands

institute: University of Amsterdam

summary: Overexpression (OE) of phospholipase C (PLC) promotes drought stress tolerance in various plant species. How PLC contributes to this phenotype is unknown. To investigate this, transcriptomic analyses of drought-stressed Arabidopsis plants were performed in wild type (WT) and four distinct PLC-OE backgrounds. To be able to measure the earliest responses in both root- and shoot tissues, a vermiculite-based assay was developed. Subsequent transcriptomics analyses revealed that WT plants responded relatively strongly to the drought, whereas all PLC-OEs lines responded to a lesser extent. Changes in various pathways were observed that were differentially regulated in WT. These include, i) several phospholipid metabolism genes, which may counteract the overexpression of PLC activity, ii) genes involved in the circadian rhythm, shifting to a more night-like expression pattern for the PLC-OE lines, iii) downregulation of several light reaction-related genes, and iv) upregulation of genes involved in the brassinosteroid signalling pathway. In the PLC-OE lines, a subset of genes involved in auxin signalling was found to be differently regulated under drought. Similarly, genes upstream of H2O2 production were found upregulated, while ROS-induced genes were downregulated. Though unable to pin point the primary cause of the drought tolerant phenotype in PLC-OE plants, several novel connections were identified, which are highlighted and discussed in more detail.

overall_design: RNAseq of Arabidopsis WT and PLC OEs. Plants were first grown 9 days on agar, followed by 12 days of growth on vermiculite with growth media. After 7 days of either remaining in contact with growth media, or no contact with media (drought) whole roots systems and whole shoots were harvested between 1 and 5 pm, cycling between the different samples before returning to the replicates. 4 replicates were used for all WT and PLC5-OE samples, 3 replicated were used for all other PLC-OEs. A single plant was used per replicate. Samples were frozen, ground up with mortar and pestle in liquid nitrogen. RNA was isolated using RNeasy Plant Mini Kit from qiagen. Quality was checked by RIN measurements. with all root samples scoring at least 6.5 and all shoot samples at least 9. RNA was mixed with ERCC RNA spike-in Control mix 1, afterwards a poly-A enrichment was performed using Dynabeads mRNA DIRECt micro purification kit. Total RNA-Seq kit v2 and the Ion Xpress RNA-Seq barcoding kit, bar-coded RNA libraries were generated. The 2200 TapeStation was used with Agilent D1000 ScreenTapes to assess the size distribution and yield. On the Ion Chef System sequencing templates were prepared, with the Ion PI Hi-Q Chef kit. Finally, sequencing was performed using an Ion PI Chip v3 on the Ion Proton platform by the ‘Dutch Genomics Service and Support Provider’ (MAD, SILS, University of Amsterdam, The Netherlands)

first: Teun

last: Munnik


title: Sex differences in metabolic adaptation in infants with cyanotic congenital heart disease

city: Houston

first: Tina

middle: Oak

last: Findley

state: TX

address: 6431 Fannin Street, MSB 3.224

institute: University of Texas Health Science Center at Houston

summary: Background:Femaleinfantswith congenital heart disease (CHD)facesignificantlyhigherpostoperativemortality ratesafter adjusting for cardiac complexity.Sex differences in metabolic adaptation to cardiac stressors maybe an earlycontributor tocardiac dysfunction.In adult diseases, hypoxic/ischemic cardiomyocytesundergo acardioprotectivemetabolicshift fromoxidative phosphorylation to glycolysiswhichappears to be regulated in a sexually dimorphic manner.We hypothesizesex differences incardiacmetabolismare presentincyanotic CHDand detectable asearly as theinfantperiod. Methods:RNA sequencingwas performedon blood samples(cyanotic CHD cases,n=11;controls,n=11)andanalyzedusinggene set enrichment analysis (GSEA). Global plasma metaboliteprofiling(UPLC-MS/MS)was performedusinga larger representative cohort(cyanotic CHD,n = 27;non-cyanotic CHD,n = 11;unaffectedcontrols,n = 12). Results:Hallmark gene sets in glycolysis, fatty acid metabolism, and oxidative phosphorylationwere significantly enrichedincyanotic CHDfemales compared to malecounterparts, which was consistent withmetabolomicdifferences between sexes.Minimalsex differencesinmetabolicpathwayswereobservedinnormoxicpatients(bothcontrols and non-cyanotic CHDcases). Conclusion:These observationssuggestunderlying differences inmetabolicadaptationtochronic hypoxiabetween males and females withcyanotic CHD.

overall_design:
RNA sequencing was performed on blood samples (cyanotic CHD cases, n=11; controls, n=11) and analyzed using gene set enrichment analysis (GSEA). Global plasma metabolite profiling (UPLC-MS/MS) was performed using a larger representative cohort (cyanotic CHD, n = 27; non-cyanotic CHD, n = 11; unaffected controls, n = 12).
Hypoxic = Cyanotic CHD cases; Control = Controls

middle: O

first: Ana

last: Palei

first: Kyung

last: Cho

first: Zhongming

last: Zhao

first: Caleb

last: Shi

first: Gouri

last: Mahajan

first: Antonio

middle: F

last: Corno

first: Jorge

last: Salazar

first: Louise

last: McCullough


title: Comparative transcriptomic profiling between two radiologic phenotypes in lungs from patients with pulmonary disease caused by Mycobacterium avium complex

city: Seoul

first: Su-Young

last: Kim

address: 81, Irwon-ro, Gangnam-gu

country: South Korea

institute: Samsung Medical Center

summary: The incidence of Mycobacterium avium complex (MAC)-induced pulmonary disease (PD) has been increasing in South Korea, posing considerable challenges in treatment. Treatment guidelines recommend initiating therapy after serial computed tomography (CT) monitoring. While drug treatment often improves outcomes in patients with the nodular bronchiectatic (NB) form, those with the fibrocavitary (FC) form may continue to experience persistence despite treatment. Our objective was to classify type-specific and common genes based on radiological phenotypes (NB and FC) using RNA sequencing to analyze the cellular landscape of 11 NB sections, 10 FC sections, and 21 unaffected sections from 21 MAC-PD cases. Predictive in silico analysis indicated a significant role for genes related to B cell proliferation and regulation in both forms. Additionally, NB patients exhibited predominantly regulated antimicrobial immune responses, whereas FC patients showed enrichment in genes related to extracellular matrix structure. These target genes identified through genetic analysis could potentially serve as predictive biomarkers for type-specific biological processes and cellular pathways, necessitating further validation studies.

overall_design: To examine biological variances between two distinct clinical phenotypes (NB or FC forms) based on unaffected sections, lung tissue was procured in pairs from each patient. Then, one sample originated from an affected lesion, and the other was extracted from an unaffected region. Resection criteria included consideration of the cavity lesion in FC form or the bronchiectasis lesion in NB form, along with the unaffected area.

first: Byung

middle: W

last: Jhun

first: Seong

middle: M

last: Moon

first: Sung

last: Shin

first: Ju

last: Lee


title: Experimental menopause in 3xTg-AD mice triggers metabolic and cognitive dysfunction aligned with Alzheimer's disease processes

city: Stirling

first: James

last: Timmons

address: Bridge of Allan

institute: Augur Precision Medicine LTD

summary: There is a compelling link between menopause and Alzheimer's disease (AD), with few established molecular mechanisms. A lack of experimental models limits validation of causal drivers of these interactions. Here, we characterize the accelerated ovarian failure (OF) model of menopause in the triple-transgenic AD (3xTg-AD) mouse. Ovotoxin, 4-vinylcyclohexene diepoxide accelerated follicular loss, ablating circulating progesterone. OF resulted in decreased performance in the Y-maze, Novel Object Recognition, and Barnes Maze, consistent with accelerated AD. OF aggravated age-related impaired glucose tolerance and caused insulin resistance and these alterations correlated with the degree of cognitive impairment. Transcriptomic analyses of the mouse hippocampus identified 19 differentially regulated genes in OF mice, including some linked to AD, including C4b, Ifit3b, Cxcl13 and Gabrg2. We produced new transcriptomic profiles of dementia-free human entorhinal cortex (n=99) and remodeled entorhinal cortex profiles from patients (n=64; Braak scores 0-6). Analyses of our 19 OF genes, identified that C4B expression was upregulated with both age and Braak score, while several revealed novel co-expression relationships, including between Shootin (SHTN1) and GABA receptor subunit (GABRG2). In summary, accelerated ovarian failure presents key cognitive, metabolic and molecular changes associated with age-related decline in cognitive function, indicating that it can be useful for the identification of novel therapeutic targets

overall_design: Female triple-transgenic AD (3xTg-AD)(26) mice were purchased through The Jackson Laboratory and the NIH supported Mutant Mouse Resource and Research Center (MMRRC). Mice were housed four animals per cage in an AAALAC-accredited animal facility at the University of Miami Miller School of Medicine. Ovotoxin vinylcyclohexene dioxide (VCD; Sigma, cat. #94956) was diluted in sesame oil (Fisher Scientific, cat #18-606-186). Animals were administered 160 mg/kg VCD (n = 19) to induce OF or sesame oil vehicle (n = 20) at a final volume of 100µL intraperitoneal (i.p.) starting at 4 months of age. Mice were injected 5 days a week for 3 weeks, for a total of 15 days. Mice representing peri-OF (Ctrl n = 9; VCD n = 8) were euthanized 90-100 d.p.i., when mice were 30-32 weeks old. Mice representing post-OF (Ctrl n = 10; VCD n = 10) were euthanized 217-224 d.p.i., approximately 48 weeks old. 28 RNA samples were successfully processed to completed CEL files passing QC.

first: Jamie

first: Jessica

last: Dennison


title: Analysis of genes in human entorhinal cortext samples by age (selected from a pre-clinical study of experimental menopause in 3xTg-AD mice)

summary: We produced new transcriptomic profiles of dementia-free human entorhinal cortex (n=99) and remodeled entorhinal cortex profiles from patients (n=64; Braak scores 0-6).   There is a compelling link between menopause and Alzheimer's disease (AD), with few established molecular mechanisms. A lack of experimental models limits validation of causal drivers of these interactions. Here, we characterize the accelerated ovarian failure (OF) model of menopause in the triple-transgenic AD (3xTg-AD) mouse. Ovotoxin, 4-vinylcyclohexene diepoxide accelerated follicular loss, ablating circulating progesterone. OF resulted in decreased performance in the Y-maze, Novel Object Recognition, and Barnes Maze, consistent with accelerated AD. OF aggravated age-related impaired glucose tolerance and caused insulin resistance and these alterations correlated with the degree of cognitive impairment. Transcriptomic analyses of the mouse hippocampus identified 19 differentially regulated genes in OF mice, including some linked to AD, including C4b, Ifit3b, Cxcl13 and Gabrg2. Analyses of our 19 OF genes, identified that C4B expression was upregulated with both age and Braak score, while several revealed novel co-expression relationships, including between Shootin (SHTN1) and GABA receptor subunit (GABRG2). In summary, accelerated ovarian failure presents key cognitive, metabolic and molecular changes associated with age-related decline in cognitive function, indicating that it can be useful for the identification of novel therapeutic targets

overall_design: Nineteen genes were identified in an analysis of female triple-transgenic AD (3xTg-AD)(26) mice treated with Ovotoxin vinylcyclohexene dioxide (VCD; Sigma, cat. #94956) to induce menopause. Two hundred and twenty Human samples from NIH funded brain banks (see metadata) were shipped to University of Miami and RNA extracted (TRIZOL), and processed on Affymetrix Clariom D arrays. 190 samples passed QC, with a subbatch of samples from Icahn School of medicine being reject for having the wrong molecular sex (XIST expression). From these a subset of 99 were recorded to be free of evidence of dementia (histopathology). The CEL files from these 99 donors were processed using a custom CDF (provided), the data was adjusted using updated COMBAT, for biobank location and our candidate genes were subsetted and analysed with respect to donor age.


title: Effects of envelope- or membrane-protein segments of SARS-CoV-2 on gene expression of HUVEC cells

city: Suzhou

first: Yiqiang

last: Wang

state: Jiangsu

address: 111 Renai Road

institute: Xi'an Jiaotong-Liverpool University

summary: Exterior segments of E-proteins bound onto and modulated gene expression in human vascular endothelial cells in vitro The finding that EC38 segment laid out of SARS-CoV-2 virus envelope prompted us to wonder if this segment would bind onto and impact the biology of host cells.   Bearing the viremia during severe COVID-19 in mind, more attention was paid to the circulation system.   Cultured human umbilical vein endothelial cells (HUVECs) were used to test the binding of EC38 and MN19 peptides and the potential consequence in terms of gene expression upon such binding.  To check if the binding of interest peptides onto HUVEC concurred functional consequences in the cells, HUVECs were treated with EC38 and MN19 peptides (5μM) for 24 hours, and their transcriptome was measured via RNA sequencing.

overall_design: To check if the interested peptides corresponding to segments of envelope (E-) or membrane (M-) proteins of SARS-CoV-2 would stimulate changes of transcriptome in HUVEC cells. HUVECs were treated with EC38 and MN19 peptides (5μM) for 24 hours, and their transcriptome was measured via RNA sequencing.

first: Jie

last: Xu


title: SWI/SNF chromatin-remodeling factor BAF60b restrains inflammatory diseases by affecting regulatory T cells migration [RNA-Seq]

city: Hangzhou

first: Xiaoqian

last: Liu

address: 866 Yuhangtang Road, Xihu District

institute: Zhejiang University

summary: Regulatory T (Treg) cells play a critical regulatory role in the immune system by suppressing excessive immune responses and maintaining immune balance. The effective migration of Treg cells is crucial for controlling the development and progression of inflammatory diseases. However, the epigenetic mechanisms responsible for directing Treg cells into the inflammatory tissue remain incompletely elucidated. In this study, we identified BAF60b, a subunit of SWI/SNF chromatin remodeling complexes, as a positive regulator of Treg cells migration that inhibits the progression of inflammation in experimental autoimmune encephalomyelitis (EAE) and colitis animal models. Mechanistically, transcriptome and genome-wide chromatin landscaped analyses demonstrated that BAF60b interacts with the transcription factor RUNX1 to promote the expression of CCR9 on Treg cells, which in turn affects their ability to migrate to inflammatory tissues. Our work provides insights into the essential role of BAF60b in regulating Treg cells migration and its impact on inflammatory diseases.

overall_design: To investigate the role of BAF60b in Treg cells, we established conventional BAF60b knockout mice. We isolated GFP+Treg cells from spleen of wild-type and BAF60b-deficient mice for RNA-Seq

first: Kuai

first: Lie


title: SWI/SNF chromatin-remodeling factor BAF60b restrains inflammatory diseases by affecting regulatory T cells migration [CUT&Tag]

overall_design: To investigate the role of BAF60b in Treg cells, we established conventional BAF60b knockout mice. We isolated GFP+Treg cells from spleen of wild-type and BAF60b-deficient mice for CUT&Tag