title: mRNA expression-based, potential mechanism of a herbal medicine formula HTG in treating dyslipidaemia rats

summary: mRNA expression in liver of rats(3, high fat diet group, 3, high fat diet + HTG treatment, 3) were detected, and differentially expressed mRNAs were analyzed to reveal potential mechanism of HTG in treating dyslipidaemia.

overall_design: 6 rats were divided into 2 group(high fat diet group:  high fat diet + 0.5% CMC-Na, HTG group: high fat diet + HTG treatment) and fed with different intervention for 12 weeks, at the end of the experiment, their liver tissues were harvested after anaesthetised for further detection.


title: Analysis of the transcriptomic profiles for HER2 CD8+ CAR T cells cultured under short-term resting conditions.

status: Public on Nov 21 2023

city: Shinjuku-ku

first: Makoto

last: Ando

state: Tokyo

address: 35 Shinanomachi

department: Department of Microbiology and Immunology

country: Japan

institute: Keio University School of Medicine

type: Expression profiling by high throughput sequencing

summary: T cell exhaustion and metabolic dysfunction induced by chronic antigen stimulation within the tumor microenvironment represent formidable obstacles in CAR T cell therapy for solid tumors. Previously, we developed a method to convert effector/exhausted CAR T cells that emerge from repeated antigen stimulation into stem cell memory-like CAR T (termed CAR-iTSCM) cells. These CAR-iTSCM cells exhibit expression of early memory markers and enhanced mitochondrial metabolism after quiescence under culture conditions containing IL-7, CXCL12, and the NOTCH-ligand. However, we noticed that this strategy was effective for CD19 CAR used for blood cancers, but not for HER2 CAR commonly used to treat solid tumors, due to tonic CAR signals. In this study, we developed a new culture condition for CAR iTSCM cells suitable for HER2 CAR and elucidated the mechanism of induction of stemness and mitochondrial fitness. We found that short-term resting condition with IL-7, CXCL12, and pan-tyrosine kinase inhibitor, Dasatinib can induce stem-like CAR T cells at the epigenetic level and enhance mitochondrial metabolism. We identified FOXO1 as a critical regulator in the process of epigenetic and metabolic reprogramming, and anti-tumor activity. We found that overexpression of FOXO1 leads to enhanced mitochondrial metabolism, efficient CAR T cell expansion, and potent anti-tumor effects through epigenetic modifications. These findings suggest that regulating the transcriptional activity of FOXO1 is a promising strategy for engineering effective CAR T cells for treating solid tumors. In this analysis, we aimed to investigate the effects of the resting conditions (IL-7+CXCL12+IGF-I +Dasatinib) on the transcriptomic profiles in 4-1BB-based HER2 CD8+ CAR T cells which exhibit tonic signals-induced exhaustion hallmarks.

overall_design: We performed bulk RNA-seq analysis using HER2 CD8+ CAR T cells under four different culture conditions (IL2, IL2.Das, 7.12.I, and 7.12.I.Das). Each CAR T cells were generated from different three healthy donors (n=3).


title: Potential mechanism of a herbal medicine formula HTG in treating dyslipidaemia rats

city: Changchun

first: Tongjian

last: Zhao

address: 1266 Fujin Road

country: China

institute: School of Pharmaceutical Sciences, Jilin University

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

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: Refer to individual Series


title: Analysis of the epigenetic profiles for HER2 CD8+ CAR T cells cultured under short-term resting conditions and overexpressing FOXO1WT

type: Genome binding/occupancy profiling by high throughput sequencing

summary: T cell exhaustion and metabolic dysfunction induced by chronic antigen stimulation within the tumor microenvironment represent formidable obstacles in CAR T cell therapy for solid tumors. Previously, we developed a method to convert effector/exhausted CAR T cells that emerge from repeated antigen stimulation into stem cell memory-like CAR T (termed CAR-iTSCM) cells. These CAR-iTSCM cells exhibit expression of early memory markers and enhanced mitochondrial metabolism after quiescence under culture conditions containing IL-7, CXCL12, and the NOTCH-ligand. However, we noticed that this strategy was effective for CD19-CAR used for blood cancers, but not for HER2 CAR commonly used to treat solid tumors, due to tonic CAR signals. In this study, we developed a new culture condition for CAR iTSCM cells suitable for HER2 CAR and elucidated the mechanism of induction of stemness and mitochondrial fitness. We found that short-term resting condition with IL-7, CXCL12, and pan-tyrosine kinase inhibitor, Dasatinib can induce stem-like CAR T cells at the epigenetic level and enhance mitochondrial metabolism. We identified FOXO1 as a critical regulator in the process of epigenetic and metabolic reprogramming, and anti-tumor activity. We found that overexpression of FOXO1 leads to enhanced mitochondrial metabolism, efficient CAR T cell expansion, and potent anti-tumor effects through epigenetic modifications. These findings suggest that regulating the transcriptional activity of FOXO1 is a promising strategy for engineering effective CAR T cells for treating solid tumors. In this analysis, we aimed to  investigate the effects of the resting conditions (IL-7+CXCL12+IGF-I +Dasatinib) and FOXO1 overexpression on the epigenetic profiles in 4-1BB-based HER2 CAR T cells which exhibit tonic signals-induced exhaustion hallmarks.

overall_design: We performed bulk ATAC-seq analysis using four different HER2 CAR T cells (Empty, FOXO1WT, 7/12/I, and 7/12/I + Das). Each CAR T cells were generated from different two healthy donors (n=2).


title: Exploring intrinsic variability between cultured nasal and bronchial epithelia in cystic fibrosis

city: Utrecht

first: Lisa

last: Rodenburg

address: Heidelberglaan 100

country: Netherlands

institute: University Medical Center Utrecht

summary: The nasal and bronchial epithelium are unified parts of the respiratory tract that are affected in the monogenic disorder cystic fibrosis (CF). Recent studies have uncovered that nasal and bronchial tissues exhibit intrinsic variability, including differences in mucociliary cell composition and expression of unique transcriptional regulatory proteins which relate to germ layer origin. In the present study, we explored transcriptomic differences between cultured nasal and bronchial epithelial cells from people with CF. Comparison of air-liquid interface-differentiated epithelial cells from subjects with CF revealed distinct mucociliary differentiation states of nasal and bronchial cultures. Moreover, using RNA sequencing we identified cell type-specific signature transcription factors in differentiated nasal and bronchial epithelial cells.

overall_design:
Comparative gene expression analysis of RNA-seq data for paired nasal and bronchial epithelial cells from 5 donors with CF. RNA was obtained from ALI-differentiated epithelial cells.

****Submitter declares that,  due to GDPR, only de-identified transcriptomic data (raw counts) can be provided***

middle: W

first: Jeffrey

middle: M

last: Beekman

first: Gimano

middle: D

last: Amatngalim


title: GCN2 is required to maintain core body temperature in mice during acute cold.

city: New Brunswick

first: Tracy

middle: G

last: Anthony

state: NJ

address: 59 Dudley Rd

department: Nutritional Sciences

country: USA

institute: Rutgers University

summary: Non-shivering thermogenesis in the brown adipose tissue (BAT) of rodents requires macronutrients to fuel the generation of heat during hypothermic conditions. Therefore, it is critical to identify signaling pathways which aid in nutrient delivery within this thermogenic tissue.To understand the contribution of the integrated stress response (ISR) in directing adaptive thermogenesis, we examined the role of the kinase activity of general control nonderepressible 2 (GCN2) within the BAT during acute cold exposure. We hypothesized that under hypothermic conditions, GCN2 maintains thermogenesis via ISR gene targets such as fibroblast growth factor 21 (FGF21), that triggers thermogenic uncoupling in BAT. In alignment with our hypothesis, both female and male mice either lacking GCN2 or administered a small molecule inhibitor of GCN2 were profoundly intolerant to acute cold stress. However, while GCN2 deletion in male mice impeded liver-derived FGF21 expression, it did not affect FGF21 levels in females, suggesting an alternative role for GCN2 in the maintenance of thermogenesis. Within the BAT, acute cold exposure increased ISR target genes and thermogenic genes regardless of GCN2 status and sex. RNA sequencing in BAT during cold exposure revealed a gene signature that identified actomyosin mechanics and transmembrane transport as the top two processes requiring GCN2. The top gene signature included cytoskeletal and class II myosin heavy chain genes critical for maximal thermogenesis during cold stress. The second gene signature included amino acid transporters which corresponded with higher circulating amino acids. In conclusion, we identify a novel role for GCN2 activation during acute cold exposure to facilitate mechanosensitive cell signaling and use of amino acids for adaptive thermogenesis.

overall_design: For this study, brown adipose tissue was collected from WT and whole body GCN2 KO mice held at room temperture or following 8-hours of cold exposure at 4C. Our comparisons look at changes in the BAT transcriptome with GCN2 deletion upon cold exposure by comparing the transcript abundance in cold treated GCN2 KO relative to WT Cold treated and WT room temperture held mice. In addition, we compare the transcript abundance in the brown adipose tissue of WT cold treated compared to WT room temperture held mice.

first: Jordan

middle: L

last: Levy

first: Emily

middle: T

last: Mirek

first: Esther

last: Rodriguez

first: Brian

last: Zalma

last: Burns

first: William

middle: O

last: Jonsson

first: Harini

last: Sampath

first: Kirk

middle: A

last: Staschke

first: Ronald

middle: C

last: Wek


title: Development of gene expression signatures for HCV infection

city: Wuhan

first: Haoran

last: Qu

state: Hubei

address: Wuhan University School of Basic Medical Sciences, Donghu Road 185#, Wuhan 430071, Hubei Province, P. R. China

institute: Wuhan University

summary: To further elucidate the gene expression profile alterations induced by HCV infection, we have employed the Arraystar Human LncRNA Microarray V3.0 as a discovery platform to identify genes associated with HCV infection. Human hepatocellular carcinoma cell line Huh7.5.1 was infected with HCVcc for 6 h. The gene expression pattern of HCVcc-infected Huh7.5.1 was compared with that of uninfected Huh7.5.1 to identify the differentially expressed genes induced by HCV infection.

overall_design: Gene expression profiling analysis of RNA-seq data for Huh7.5.1 cells infected with HCVcc for 6 h and uninfected Huh7.5.1 cells.

first: Xiao-Lian

last: Zhang

first: Tian

last: Xiang


title: Sulindac sulfide as a non-immune suppressive gamma-secretase modulator to target Triple-Negative Breast Cancer

city: New Orleans

first: Jovanny

last: Zabaleta

state: LA

address: 1700 Tulane Ave

department: Interdisciplinary Oncology

institute: LSUHSC

summary: Triple-negative breast cancer (TNBC) is defined as pathologically negative for estrogen receptor α (ER-), progesterone receptor (PR-), and human epidermal growth factor receptor 2 (HER2) amplification. TNBCs are a heterogeneous group of clinically aggressive tumors with high risk of recurrence and metastasis. Current pharmacological treatment options remain largely limited to chemotherapy, recently supplemented by immunotherapy [37296893]. There is strong evidence supporting the involvement of Notch signaling in TNBC progression. Expression of Notch1 and its ligand Jagged1 correlate with poor prognosis. Notch inhibitors, including gamma secretase inhibitors (GSIs), are quite effective in preclinical models of TNBC. However, the success of GSIs in clinical trials has been limited by their intestinal toxicity and potential for adverse immunological effects, since Notch plays key roles in T-cell activation, including CD8 T-cells in tumors. Our overarching goal is to replace GSIs with agents that lack their systemic toxicity and ideally, do not affect tumor immunity. We identified sulindac sulfide (SS), the active metabolite of FDA-approved NSAID sulindac, as a potential candidate to replace GSIs. We confirmed that SS, a known  gamma secretase modulator (GSM), inhibits Notch1 cleavage in TNBC cells. SS significantly inhibited mammosphere growth in all human and murine TNBC models tested. In a transplantable mouse TNBC tumor model (C0321), SS had remarkable single-agent anti-tumor activity and eliminated Notch1 protein expression in tumors. Importantly, the anti-tumor effects of SS were significantly enhanced when combined with α-PD1 immunotherapy in our TNBC organoids and in vivo. Our data support further investigation of SS for the treatment of TNBC, in conjunction with standard of care chemo- or -chemo-immunotherapy. Repurposing an FDA-approved, safe agent for the treatment of TNBC may be a cost-effective, rapidly deployable therapeutic option solution for a patient population in need of effective therapies.

overall_design: 1 million TNBC C0321 cells into syngeneic mice with 1:1 ratio of Matrigel to PBS into the mammary fat pad of 6-10-weeks old female FVB mice (Jackson Laboratory). Mice were treated with SS alone (60 mg/kg by PO) or saline daily for another 14 days and the RNA was extracted from the tumors for RNA sequencing.

first: Fokhrul

last: Hossain

first: Deniz

last: Ucar

first: Giulia

last: Monticone

first: Yong

last: Ran

first: Samarpan

last: Majumder

first: Kristina

last: Larter

first: Hanh

last: Luu

first: Dorota

last: Wyczechowska

first: Soroor

last: Heidari

first: Keli

last: Xu

first: Sudarvili

last: Shanthalingam

first: Margarite

last: Matossian

first: Yaguang

last: Xi

first: Matthew

last: Burow

first: Bridgette

last: Collins-Burow

first: Luis

last: Del Valle

first: Chindo

last: Hicks

first: Todd

middle: E

last: Golde

first: Barbara

last: Osborne

first: Lucio

last: Miele


title: Lactate as a major epigenetic carbon source for histone acetylation via nuclear LDH metabolism

city: Seoul

first: Yong Jin

last: An

address: 1, Gwanak-ro, Gwanak-gu

country: South Korea

institute: Seoul National University

summary: Histone acetylation involves the transfer of a two-carbon unit to nucleus as embedded in low-concentration metabolites. We find that lactate, a high-concentration metabolic by-product, can be a major carbon source for histone acetylation, through oxidation-dependent metabolism. Both in cells and in purified nucleus, 13C3-lactate carbons are incorporated into histone H4 (maximum incorporation: ~60%). In purified nucleus, this process depends on nucleus-localized lactate dehydrogenase (LDHA), the knockout of which abrogates the incorporation. Heterologous expression of nucleus-localized LDHA rescues the KO effect. Lactate itself increases histone acetylation, whereas inhibition of LDHA reduces the acetylation. In vitro and in vivo settings exhibit different lactate incorporation patterns, suggesting an influence of the microenvironment. Higher nuclear LDHA localization is observed in pancreatic cancer than in normal tissues, showing the disease relevance. Overall, lactate and nuclear LDHA can be major structural and regulatory players in the metabolism-epigenetics axis controlled by cell’s own or environmental status.

overall_design: Differences in ChIP peaks of histone acetyl H4 on chromosomes following 0 or 10 mM lactate treatment in PANC-1 cell

first: Yong

middle: J

first: Sihyang

last: Jo

first: Jin-Mo

last: Kim

first: Han-Sun

first: Hyun-Young

first: Sang-Min

last: Jeon

first: Dawool

last: Han

first: Jong-In

last: Yook

first: Keon-Wook

last: Kang

first: Sunghyouk

last: Park


title: Novel pan-ERR agonists ameliorate heart failure through enhancing cardiac fatty acid metabolism and mitochondrial function

city: Houston

first: Andrea

last: Wilderman

state: TX

address: One Baylor Plaza

institute: Baylor College of Medicine

summary: Cardiac metabolic dysfunction is a hallmark of heart failure. Estrogen related receptors ERRalpha and ERRgamma are essential regulators of cardiac metabolism. Therefore, activation of ERR could be a potential theraputic intervention for heart failure. However, in vivo studies demonstrating the potential utility of ERR agonists for heart failure treatment are lacking, as compounds with pharmackinetics appropriate for in vivo use have not been available. Using a structure-based design approach, we designed and synthesized two structurally distinct pan-ERR agonists, SLU-PP-332 (332) and SLU-PP-915 (915), which significantly improved ejection fraction, ameliorated fibrosis and increased survival associated with pressure overload-induced heart failure without affecting cardiac hypertrophy. Mechanistically, a broad spectrum of metabolic genes was transcriptionally activated by ERR agonists, particulary genes involved in fatty acid metabolism and mitochondrial function. Using both in vitro and in vivo genetic dependency experiments, we show that ERRgamma is the main mediatorof ERR agonism-induced transcriptional regulation and cardioprotection and definitively demonstrated target specificity. Additionally, ERR agonism also led to downregulation of cell cycle and development pathways, which was partially mediated by E2F1 in cardiomyocyte. In summary, ERR agonists maintain oxidative metabolism, which confers cardiac protection against pressure overload-induced heart failure in vivo. Our results provide direct pharmacological evidence supporting the further in vivo development of ERR agonists as novel heart failure theraputics.

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: To investigate ERR dependency in response to pan-ERR agonist 915, we used siRNA-targeted knockdown of ERRalpha and ERRgamma in neonatal rat ventricular myocytes (NRVM). As a control for the double-knockdown (DKD) NRVM we generated NRVM with non-targeting scramble siRNA (S). Gene expression of DKD and S lines were assessed when treated with 915 or vehicle control. To investigate the effect of ERR agonist 332 on cardiac function in a pressure-overload model, we performed TAC or sham surgery and treated mice with 332 (IP injection) for 6 weeks following surgery.

first: Weiyi

last: Xu

first: Lilei

last: Zhang

first: Thomas

last: Burris

first: Ronald

last: Evans


title: Structured wound angiogenesis instructs mesenchymal barrier compartments in the regenerating nerve [bulkRNASeq]

city: Milano MI

first: Aurora

last: Maurizio

state: Italy

address: Via Olgettina, 60

department: Center for Omics Sciences (COSR)

country: Italy

institute: IRCCS Ospedale San Raffaele

summary: Organ injury stimulates the formation of new capillaries to restore blood supply raising questions about the potential contribution of neoangiogenic vessel architecture to the healing process. With single-cell mapping we resolved the properties of endothelial cells that organize a polarized scaffold at the repair site of lesioned peripheral nerves. Transient reactivation of an embryonic guidance program is required to orient neovessels across the wound. Manipulation of this structured angiogenic response through genetic and pharmacological targeting of Plexin-D1/VEGF pathways within an early window of repair has long-term impact on configuration of the nerve stroma. Neovessels direct nerve-resident mesenchymal cells to mold a provisionary fibrotic scar by assembling an orderly system of stable barrier compartments that channel regenerating nerve fibers and shield them from the persistently leaky vasculature. Thus, guided and balanced repair angiogenesis enables the construction of a “bridge” microenvironment conducive for axon regrowth and homeostasis of the regenerated tissue.

overall_design: Endothelial cells genetically labeled with R26-TomatoLSL (Jax stock# 007914) reporter under the control of Cdh5(PAC)-CreERT2 (PMID: 20445537) were FACS-isolated from pooled uninjured sciatic nerves of adult mice or from the lesion site ("bridge" region) of sciatic neves at 7 or 14 days post-injury (dpi), and profiled by bulk RNA-seq. In a separate experiment, endothelial cells expressing Kdr-Cherry reporter (Jax stock# 018542) were FACS-isolated from the bridge region of sciatic nerves from control or Chd5::CreER; Plxnd1fl/fl mice (endothelial-specific deletion of Plexin-D1) at 7dpi.

first: Ganesh

middle: P

last: Bhat

first: Santo

last: Diprima

first: Stefano

last: Depretis

first: Dario

last: Bonanomi


title: The pelvic ganglion is a divergent outpost of the sympathetic chains

city: Paris

first: Olivier

last: Mirabeau

address: 25-28 rue du Docteur Roux

country: France

institute: Institut Pasteur

summary: The sacral autonomic outflow has been deemed parasympathetic and its ganglionic relay, the pelvic ganglion, common to the lumbar outflow, a mixed sympathetic/parasympathetic ganglion. Here we find that it is entirely and equally distinct from sympathetic and parasympathetic ganglia based on its transcriptome, but related to sympathetic ones by the criterion of its top genes. Thus, the pelvic ganglion appears as a divergent outpost of the sympathetic chains.

overall_design: The data was generated in two batches: the first batch consisting of the Stellate, Sphenopalatine and Pelvic_1, and the second batch consisting of Lumbar, Coeliac and Pelvic_2. The biological replicates Pelvic_1 and Pelvic_2 served for correcting the bias between the two batches.

first: J-F

last: Brunet

first: O

first: H

last: Rohrer

first: M

last: Sivori

first: S

last: Lameiras

first: F

last: Coulpier

last: Baulande


title: Structured wound angiogenesis instructs mesenchymal barrier compartments in the regenerating nerve


title: Modeling early-onset sporadic Alzheimer’s disease using iPSC-derived neurons

city: La Jolla

first: Shankar

last: Subramaniam

state: CA

address: 9500 Gilman Drive

department: Department of Bioengineering

institute: University of California, San Diego

summary: Non-familial Alzheimer’s disease (AD) occurring before 65 years of age is commonly referred to as early-onset Alzheimer’s disease (EOAD) and constitutes ~5-6% of all Alzheimer’s disease (AD) cases. While EOAD exhibits the same clinicopathological changes such as amyloid plaques, neurofibrillary tangles (NFTs), brain atrophy, and cognitive decline as observed in the more prevalent late-onset AD (LOAD), EOAD patients tend to have more severe cognitive deficits, including visuospatial, language, and motor dysfunction. Patient-derived induced pluripotent stem cells (iPSCs) have been used to model and study penetrative, familial AD (FAD) mutations in APP, PSEN1, and PSEN2, but have been seldom used for sporadic forms of AD that display more heterogeneous disease manifestation. In this study, we sought to characterize iPSC-derived neurons from EOAD patients via RNA-sequencing. A modest difference in expression profiles between EOAD patients and non-demented control subjects resulted in a limited number of differentially expressed genes (DEGs). Based on this analysis, we provide evidence that iPSC-derived neuron model systems, likely due to the loss of EOAD-associated epigenetic signatures during the iPSC reprogramming, are not an ideal model system to study sporadic AD.

overall_design: iPSC Neurons: The 4 non-demented control (NDC) subject iPSC neurons and the 4 early-onset Alzheimer's disease (EOAD) patient iPSC neurons were generated from reprogrammed iPSCs, originated from skin-derived fibroblasts. All neurons were differentiated from iPSCs using SMAD inhibition in neural maintenance media and converted to NPCs by bFGF. Neurons that were pelleted down and frozen per NDC subject or EOAD patient each contained roughly 150,000-2 million cells. RNA-seq data: Biological differentiation replicates (n=3) of neurons generated from NPCs derived from human iPSCs using paired-end sequencing runs orignating from 4 NDC subjects (n=24) and 4 EOAD patients (n=24).

first: Phoebe

last: Valdes

first: Kenneth

last: Henry

first: Michael

middle: Q

last: Fitzgerald

first: Koushik

last: Muralidharan

first: Andrew

middle: B

last: Caldwell

first: Srinivasan

last: Ramachandran

first: Lawrence

middle: S

last: Goldstein

first: William

last: Mobley

first: Douglas

middle: R

last: Galasko


title: Maternal RNA localization during early development of the axolotl

city: Vestec by Prague

first: Radek

last: Sindelka

address: Průmyslová 595

country: Czech Republic

institute: Institute of Biotechnology, Czech Academy of Science, v.v.i.

summary: The asymmetric localization of maternal biomolecules is critical for body plan development. One of the most popular model organisms for early embryogenesis studies is Xenopus laevis but there is a lack of information in other animal species. Here, we compare the early development of two amphibian species – the frog X. laevis and the axolotl Ambystoma mexicanum. This study aimed to identify asymmetrically localized RNAs along the animal-vegetal axis during the early development of A. mexicanum. For that purpose, we performed spatial transcriptome-wide analysis, which revealed dynamic changes along the animal-vegetal axis classified into the following categories: relocalization, de novo synthesis and degradation. Surprisingly, our results showed that many of the vegetally localized genes, which are important for germ cell development, are degraded during early development. Furthermore, we assessed the motif presence in UTRs of degraded mRNAs and revealed the enrichment of several motifs in RNAs of germ cell markers. Our results suggest novel reorganization of the transcriptome during embryogenesis of A. mexicanum to converge to the similar developmental pattern as the X. laevis.

overall_design: To assess the alterations of the transcriptome during embryogenesis, TOMOSeq was utilized on fertilized oocytes, 1-cell, 4-cells, 64-cells and 1000-cells. The experiment was performed using biological triplicates with each sample aligned from animal to vegetal regions and sectioned to produce 5 main sections (A to E) with “A” being the extreme animal region and “E” being the extreme vegetal region. The temporal and spatial changes in the transcriptome were then assessed to identify unique changes during the early stages of embryogenesis.

first: Kateřina

last: Šimková

first: Ravindra

last: Naraine

first: Pavel

last: Abaffy

last: Šindelka


title: Loss of SETD2 aggravates colorectal cancer progression caused by SMAD4 deletion through the RAS/MAPK pathway [RNA-seq]

city: Shanghai

first: Ma

last: Chunxiao

address: Huashan Road

institute: Ma Chunxiao

summary: To investigate the function of SETD2 in SMAD4-mutant colorectal cancer, we induced colorectal cancer in mice with intestinal epithelium-specific knockout of SMAD4 and SETD2 using AOM/DSS treatment.

overall_design: Comparative gene expression analysis was performed on RNA-seq data from mouse intestinal epithelial cells isolated from the intestine.


title: Loss of SETD2 aggravates colorectal cancer progression caused by SMAD4 deletion through the RAS/MAPK pathway


title: Loss of SETD2 aggravates colorectal cancer progression caused by SMAD4 deletion through the RAS/MAPK pathway [ChIP-seq]

overall_design: Chromatin immunoprecipitation followed by DNA sequencing (ChIP-seq) was used to detect H3K36me3 histone modification in the intestinal epithelial cells of SMAD4 knockout mice after AOM/DSS treatment.


title: Structured wound angiogenesis instructs mesenchymal barrier compartments in the regenerating nerve [scRNASeq_Pdgfrb]

first: Aurora

last: Maurizio

overall_design: Nerve-resident mesenchymal cells were genetically labeled R26-TomatoLSL (Jax stock# 007914) reporter under the control of Pdgfrb-cre/ERT2 (Jax stock# 029684), FACS-isolated from the intact sciatic nerve or from the bridge region at 7dpi and 21dpi and profiled by scRNA-seq.

first: Ganesh

last: Bhat

first: Santo

last: Diprima

first: Stefano

last: Depretis

first: Dario

last: Bonanomi


title: MicroRNA expression in mandibles of Wistar and Spontaneously Hypertensive rats with periodontal disease

city: Araçatuba

first: Victor Gustavo Balera

last: Brito

email: vgb.brito@unesp.br, brito@wustl.edu

state: SP

address: Marechal Rondon, km 527/8

department: Basic sciences

country: Brazil

institute: São Paulo State University

summary:
Periodontal disease (PD) is characterized by inflammation affecting the tissue surrounding the teeth, primarily affecting the soft tissues, like the gingiva. However, without proper treatment, the condition exacerbates and progresses to impact the deeper structures, as the alveolar bone. The periodontal inflammation leads to the alveolar bone resorption, that eventually results in the complete loss of tooth support. Given its potential consequences, periodontal disease is a significant public health concern, as one of the primary causes of tooth loss, contributing to issues such as impaired mastication, speech difficulties, low self-esteem, and quality of life. Notably, comorbidities, like hypertension, can exacerbate the progression and severity of periodontal disease. In addition, the coexistence of periodontal disease and hypertension is highly likely to occur due to sharing of several risk factors. A better understanding of the underling molecular mechanisms associated to the severity of periodontal disease in the context of hypertension would greatly contribute to the advancement of translational research in the field of periodontics. MicroRNAs, a class of small non-coding RNA molecules, have an important role in regulating gene expression at the post-transcriptional level. These molecules can regulate multiple mRNA targets through complementary base pairing between the miRNA 5' seed sequence and the mRNA 3' untranslated region (UTR). Therefore, microRNAs can potentially modulate a wide variety of cellular processes, in both normal and pathological contexts. Presently, most of the studies in the field concentrate on the periodontium soft tissues, while our understanding of microRNA modulation in the alveolar bone remains comparatively limited.
We used microarray analysis to evaluate the expression profiles of microRNAs in the mandibles of Wistar and SHR rats with periodontal disease, compared to their respective control groups. Our aim was to identify microRNAs of interest that could possibly be associated to the periodontal disease-induced alveolar bone loss.

overall_design: Age-matched 10-week-old Wistar and SHR rats underwent a 15-day periodontal disease induction by bilateral ligature placement on the first mandibular molars. The total RNA was extracted from the mandibular body (molar tooth region) and subsequently utilized for the microarray assays. The study comprised the following four groups (n=3/group): Wistar control (WC), Wistar with periodontal disease (WPD), SHR control (SC), and SHR rats with periodontal disease (SPD).

first: Sandra

middle: H

last: Oliveira


title: Time course CSE treatment of primary human bronchospheres

city: San Diego

first: John

last: Walker

address: 10675 John Jay Hopkins Dr

institute: NIBR

summary: Characterizing the effect of long-term cigarette smoke exposure on bronchospheres gene expression

overall_design: Bronchospheres were differentiated in 384-well plates on 50% Matrigel for two weeks, after which they were exposed to cigarette smoke extract (CSE) at the indicated percentages (diluted in HBEC differentiation media) for 7, 14, and 21 Days. Then they were lysed directly in the plate with Qiagen buffer RLT and then RNA was extracted from the cells using a Qiagen  RNeasy kit with the elution step done in water.

first: Pranjali

last: Beri

first: Young

middle: Y

last: Woo

first: Katie

last: Schierenbeck

first: Kaisheng

last: Chen

first: S.

middle: W

last: Barnes

first: Olivia

last: Ross

last: Krutil

first: Doug

last: Quackenbush

first: Bin

last: Fang

first: Erin

last: Toyama


title: Structured wound angiogenesis instructs mesenchymal barrier compartments in the regenerating nerve [scRNASeq_Cdh5]

first: Aurora

last: Maurizio

overall_design: Endothelial cells genetically labeled with R26-TomatoLSL (Jax stock# 007914) reporter under the control of Cdh5(PAC)-CreERT2 (PMID: 20445537) were FACS-isolated from pooled uninjured sciatic nerves of adult mice or from the lesion site ("bridge" region) of sciatic neves 7 days post-injury, and profiled with scRNA-seq.

last: Bhat


title: mRNA expression in WT and Fpt1 KO in glucose and ethanol (2h) [RNA-seq]

city: Amsterdam

first: Fred

last: van Leeuwen

address: Plesmanlaan 121

department: Gene Regulation

institute: Netherlands Cancer Institute

summary: Transcriptome analysis was performed on wild type and Fpt1 knockout cells in glucose and ethanol. Gene expression was compared between wild type and Fpt1 knockout samples to investigate the consequences of Fpt1 on cellular physiology.

overall_design: Examination of mRNA expression in Fpt1 knockout (4 biological replicates) and wild type cells (3 biological replicates) in glucose and ethanol (2h).

first: Maria

last: van Breugel

first: Ila

last: van Kruijsbergen


title: Genome-wide ChIP-exo profiling of Fpt1 in glucose

summary: Transcription of transfer-RNA genes (tDNAs) by RNA Polymerase III (RNAPIII) is tightly regulated upon nutrient and stress signaling. However, identical tDNAs across the genome are differentially regulated, suggesting regulation at the chromatin-level plays a crucial role. This study aimed to identify such mechanisms by decoding the chromatin proteome of a native tDNA locus in yeast using Epi-Decoder. The tDNA proteome showed dynamic binding of both known and unknown factors upon nutrient stress, including Ykr011c (Fpt1), a protein of unknown function. Decoding the tDNA proteome in the absence of Fpt1 revealed a role in the eviction of RNAPIII during repressed transcription. Fpt1 exclusively occupied RNAPIII-regulated genes, but cells without Fpt1 also showed impaired shutdown of RNAPII-transcribed ribosome biogenesis genes in changing nutrient conditions. These findings provide support for a novel chromatin-associated regulator required for proper RNAPIII assembly that also tunes an integrated physiological response to changing metabolic conditions.

overall_design: Genome-wide ChIP-exo binding profiles of Fpt1 were determined using high throughput paired-end sequencing using ChIP-exo 5.0.

first: Chitvan

last: Mittal

first: Franklin

last: Pugh


title: Genome-wide profiling of Fpt1, Rpb2, Rpo31 and Rpl13a in glucose [ChIP-seq]

summary: Genome-wide profiling of Fpt1, Rpb2, Rpo31 and Rpl13a was performed to compare Fpt1 binding sites with RNAPIII and RNAPII regulated sites.

overall_design: Genome binding/profiling by high-throughput sequencing of three biological replicates. Two input samples were taken along as controls.

first: Teun

last: van den Brand


title: Long-read direct RNA sequencing of the mitochondrial transcriptome of Saccharomyces cerevisiae

city: Delft

first: Marcel

last: van den Broek

address: Van der Maasweg 9

institute: Delft University of Technology

summary: Mitochondria fulfil many essential roles in eukaryotic cells, yet some of their molecular mechanisms are still unexplored. Although 99% of the mitochondrial proteins are imported from the cytosol, mitochondria have their own DNA, transcription and translation machinery. The Saccharomyces cerevisiae mitochondrial DNA contains 11 polycistronic transcripts that encode 2 ribosomal subunits, 24 tRNAs and 9 genes, which can be spliced in alternative ways to yield different proteins. There are still many unresolved questions about mitochondrial genes and their splicing, including how gene expression and splicing is affected by different growth conditions and what role introns play in mitochondrial physiology. In the present study, we aimed to elucidate this by developing an RNA-sequencing method for mitochondrial RNA using Nanopore technology.

overall_design: Comparision of transcription between the mitochondrial transcriptomes of cells grown on glucose versus cells grown on ethanol. All data is derived from mitchondria isolated from biological triplicate cultures and sequenced with Nanopore Direct RNA sequencing

first: Charlotte

last: Koster

first: Askar

last: Kleefeldt

first: Marijke

last: Luttik

first: Jean-Marc

last: Daran

first: Pascale

last: Daran-Lapjuade


title: A regulator of RNA Polymerase III at tRNA genes revealed by locus-specific proteome decoding

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

overall_design: Refer to individual Series


title: Hepatitis B/C viruses manipulate TNNT1 expression to induce epithelial-mesenchymal transition and hepatocellular carcinogenesis

first: Haoran

last: Qu

summary: Infection with hepatitis B and C viruses (HBV and HCV) is a major cause of hepatocellular carcinoma (HCC). While troponin T (TNNT1) is essential for actin thin filament function, little is known about its role in HBV/HCV-associated HCC. Here, we found TNNT1 expression was significantly upregulated in HBV/HCV-infected hepatoma cells, HCC tissues, and mouse models. HBV/HCV-induced c-Myc acts as a transcription factor for TNNT1 induction. HBV/HCV-induced TNNT1 binds metastasis-associated protein 2 (MTA2) and activates the PI3K-AKT-mTOR-TNNT1 loop, causing lysosomal dysfunction and autophagy suppression. This leads to increased proliferation and epithelial-mesenchymal transition (EMT) of liver cancer cells marked by Vimentin and ZEB2. Four amino acid residues (R110A, E112A, R115A, and E119A) within the TNNT1 troponin domain are required for TNNT1-MTA2 binding and mediate TNNT1’s suppression of autophagy and promotion of proliferation/EMT. Importantly, liver-specific TNNT1 deficiency in mice attenuates HBV/HCV-induced c-Myc-driven HCC EMT properties in vivo. This study reveals for the first time that hepatitis virus-induced TNNT1 can induce EMT and hepatocellular carcinogenesis. TNNT1 may be a promising target for viral HCC therapy.

overall_design: To detect the mechanism of TNNT1 in hepatocellular carcinoma progression, we knocked down TNNT1 in the hepatocellular carcinoma cell line Huh7.5.1 by Crispr-cas9 technology, and then performed RNA-seq sequencing together with wild-type Huh7.5.1.

first: Yan

last: Xie

first: Min

last: Liu

first: Xiaolian

last: Zhang


title: Natural product Shi-Bi-Man ameliorates psoriasis via inhibiting IL-23/Th17 axis and CXCL16-mediated endothelial activation

city: Nanjing

first: zhang

last: zhang chenyang

address: 163 Xianlin Avenue

institute: Nanjing University

summary:
Purpose: We aimed to find a potential for psoriasis and to explore the mechanism of SBM to relieve psoriasis-like skin inflammation in mice.
Methods: Supplementation with smear administration of SBM in the imiquimod-induced murine model, record the weight change and psoriasis Area and Severity Index (PASI) score during the whole process. Using hematoxylin-eosin staining to obverse to skin structure. Performing single-cell RNA sequencing to explore the mechanism of SBM in influencing psoriasis-like phenotype. Immunofluorescence were conducted for verification.
Results: SBM remarkably alleviated the psoriasis-like phenotype. Single-cell RNA sequencing analysis shown the expression of Il17 and Il23 was diminished in keratinocytes and T cells, accompanied by a reduction in the proportion of Th17 cells. Meanwhile, endothelial cell activation was inhibited along with the expression of Cxcl16.
Conclusion: In this work, we found that natural product SBM inhibited the IL-23/Th17 axis and CXCL16-mediated endothelial activation and had a good therapeutic effect on psoriasis in mice model. This work suggests the potential therapeutic value of SBM in psoriatic patients.

overall_design: Molecular mechanism of SBM in improving psoriasis.

first: Yang

last: Sun

first: Chenyang

first: Haojie

last: Du

first: Jiao


title: Single cell-resolved study of advanced murine MASH reveals a homeostatic pericyte signaling module

city: Odense M

first: Kim

last: Ravnskjaer

address: Campusvej 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

summary: Non-alcoholic steatohepatitis (NASH) is associated with hepatic steatosis, intralobular inflammation, and fibrosis. The degree of hepatic fibrosis, mainly caused by excessive production of extracellular matrix proteins, is the sole predictor of liver-related and overall mortality in NASH patients. The hepatic stellate cells (HSCs) are causally implicated in fibrogenesis during NASH development but as sinusoidal pericytes also vital for vascular homeostasis of the healthy liver. Using single-cell RNA-sequencing we have analyzed whole liver plasticity and interrogated the transition of HSCs from pericytes in the healthy liver to collagen-producing cells in a diet-induced murine model of advanced NASH. We show how postprandial cues are sensed and integrated by HSCs promoting their phenotypic stabilization and, through paracrine mediators, sinusoidal health. While dominant under healthy conditions the basis for this multimodal signaling through stellate cell-specific Gs protein-coupled receptors and the bile-acid receptor NR1H4/FXR deteriorates in activated HSCs of the NASH liver. Expression of key signaling components were validated in situ in human and murine liver tissue supporting the translatability of our findings and pharmacological relevance in treatment of chronic liver diseases as NASH.

overall_design: 10x Genomics single-cell transcriptomic data of isolated liver cells from healthy (52w chow diet) and diseased (52w Western Diet) mice.

first: Sofie

middle: M

last: Bendixen

first: Peter

last: Sørensen

first: Mike

middle: K

last: Terkelsen

first: Daniel

last: Hansen

first: Kamilla

last: Hejn

first: Frederik

last: Bjerre

first: Annemette

last: Thulesen

first: Niels

last: Eriksen

first: Philip

last: Hailenberg

first: Trine

middle: V

last: Dam

last: Larsen

last: Wernberg

first: Janusa

last: Vijayathurai

first: Emma

last: Scott

first: Ann-Britt

last: Marcher

first: Sönke

last: Detlefsen

first: Lars

last: Grøntved

first: Henrik

last: Dimke

first: Mette

last: lauridsen

first: Alexander

last: Krag

first: Blagoy

last: Blagoev


first: Kim

last: Ravnskjaer

overall_design: Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) for investigation of chromatin accesibilty of Hepatic Stellate Cells

first: Sofie

last: Bendixen

first: Peter

last: Sørensen

first: Mike

last: Terkelsen

last: Hansen

last: Hejn

middle: G

middle: T

first: Charlotte


overall_design: Here we performed gene expression profiling analysis of primary hepatic stellate cells (in vitro) using data obtained from RNA-seq of cells treated with Foskolin (Fsk) for 3 hours and then 21 hours DMSO or Dimethylsulfoxid (DMSO) for 24 hours

first: Daniel

first: Kamilla

first: Frederik

middle: A

last: Bjerre

first: Annemette

last: Thulesen

first: Niels

last: Eriksen

last: Hailenberg

last: Dam

last: Larsen


summary: Here we profile the transcripts of app. 32.000 single cells isolated from livers of healthy mice fed with a chow diet and diseased mice fed with a western diet for 52 weks.  We analyzed the fibrogenic transition of HSCs from pericytes to collagen-producing cells, interrogated the NASH-associated rerouting of mononuclear phagocytes and uncovered novel aspects of cellular palsticity during more advanced stages of NASH. We reveal Stellate cell-specific Gs-protein-coupled receptors and the bile-acid receptor NR1H4/FXR seemingly dominated HSC biology in the healthy liver, forming the basis for multimodal diurnal signaling, but deteriorated in activated HSCs in advanced NASH. In addition to two emerging populations of Trem2-expressing monocyte-derived macrophages we found a population of CD207-positive macrophages significantly expanded in advanced NASH and likely derived from both incoming monocytes and Kupffer cells. Our work illustrates the emmense plasticity liver cells undergo upon induction of NASH, and potentially map novel treatment targets

overall_design: Here we performed gene expression profiling analysis of primary hepatic stellate cells (in vitro) using data obtained from RNA-seq of cells treated with a combination of either Obeticholic acid (OCA) (3h)  + Vasoactive intestinal peptide (VIP) (3 hour), or DMSO (3 hour) + VIP (3 hour)

first: Philip

first: Trine

last: Wernberg

first: Janusa

last: Vijayathurai

first: Emma

last: Scott

first: Ann-Britt

last: Marcher

last: Detlefsen

last: Grøntved


last: Ravnskjaer

overall_design: Here we performed gene expression profiling analysis of primary hepatic stellate cells (in vitro) using data obtained from RNA-seq of cells treated with obeticholic acid (OCA) or Dimethylsulfoxid (DMSO)

last: Bendixen

first: Sönke

first: Lars

first: Henrik

last: Dimke

first: Mette

last: lauridsen

first: Alexander

last: Krag

last: Blagoev


title: Mapping and quantifying transcriptomes of MTSS1 overexpressed in the wild type nasopharyngeal carcinoma cells by RNA-Seq

city: Stockholm

first: Ingemar

last: Ernberg

address: Solnavagen 9 C8

department: Department of Microbiology, Tumor and Cell Biology

country: Sweden

institute: Karolinska Institutet

summary: Metastasis suppressor 1 (MTSS1) is frequently lost in metastatic tissues, which correlates with advanced tumor stages and poor patient prognosis across a variety of cancers. The anti-metastatic mechanisms of MTSS1 are not well understood. We applied RNAseq technology to map the transcriptomes of wild type and MTSS1 overexpressed nasopharyngeal carcinoma cells.

overall_design: Comparisons of the gene expression between the Myc-tagged empty vector and Myc-MTSS1 samples were carried out to determine the differentially regulated genes.

first: Shixing

last: Zheng


title: Self-assembled hyaluronic acid nanomedicine as a topical therapeutic agent for targeted modulation of dysregulated skin barrier and immune responses in a mouse model of psoriasis

first: Jung-Woong

last: Kim

address: 84 Heuksuk-ro Dongjak-ku

department: Life Science

institute: Chung-Ang University

summary:
Purpose: profiling the differential transcripts usage in HACN treated macrophage polarization toward proinflammatory M1 polarization
Methods: transcriptome analysis by the RNA-seq via mRNA pull-down
Results: The mRNA profiles by RNA sequencing in bone marrow-derived macrophages showed that the whole gene expression patterns altered by lipopolysaccharide (LPS) were restored by HACN pre-treatment, and most of those genes were related to the inflammatory response including M1 polarization
Conclusions: The inhibitory effects of HA-NPs on LPS-induced M1 polarization are attributed to the presence of self-assembled HA shell, not the hydrophobic constituents and the free HAs.

overall_design: N: control group, P: LPS treaed group, X LPS+HACA treated group

first: Wook


title: Identification of circRNA-miRNA-mRNA network and primary blast lung injury-related circRNAs in mouse

city: Tianjin

first: QIanying

last: Lu

address: No. 92, Weijin Road, Nankai District

institute: Tianjin University

type: Non-coding RNA profiling by high throughput sequencing

summary: Background. Primary blast lung injury (PBLI) was the main cause of death for blast injury patients, however, there is no diagnosis and effective treatment for PBLI in clinical practice. Circular RNAs (circRNAs) is becoming new regulators of various diseases, and the performance of circRNAs in PBLI remain largely unknown. This study aimed to investigate the PBLI-related circRNA, to provide a new idea for the PBLI diagnosis and treatment. Methods. The differentially expressed (DE) circRNAs and mRNAs profile were screened by transcriptome high throughput sequencing. The differentially expressed circRNA linear transcripts and mRNAs were used to performed GO and KEGG pathway enrichment to investigate the potential function. The circRNA-miRNA-mRNA network was based on DE circRNA-miRNA pairs and PBLI-related mRNAs-miRNA pairs. Results. A total of 117 circRNAs and 681 mRNAs were aberrantly expressed in PBLI, including 64 up-regulated and 53 down-regulated circRNAs, and 315 up-regulated and 366 down-regulated mRNAs. GO and KEGG analysis revealed that the up-regulated circRNAs might involve MAPK signaling pathways, and down-regulated circRNAs might involve in the TGF-β signaling pathway. And the differentially expressed mRNAs might involve TNF signaling pathway and fanconi anemia pathway. A total of 89 PBLI-related circRNAs and 156 circRNAs-miRNA-mRNA interactions were predicted, these circRNAs might involve in the inflammation, oxidative stress or DNA damage repair in PBLI. Conclusion. This study reveals the circRNA-miRNA-mRNA network based on altered expression of circRNAs and mRNA in PBLI. Our results may provide information about the occurrence of PBLI and new ideas for diagnosing and treating PBLI.

overall_design: twelve mice were randomly divided into two groups: the control group and the PBLI group. After anesthesia, the chest of the mice in the PBLI group was exposed to blast waves with an overpressure of 0.5 bar. Animals in the control group were anesthetized in the same manner but were not exposed to blast overpressure. Six hours post-blast, the mice were sacrificed and their lung was harvested. Part of the lung tissue of each mouse were cut and place in liquid nitrogen for subsequent sequencing, and the rest were stored in -80℃ refrigerator. Every two tissues used for sequencing are mixed into one sample, that is, 3 samples each in the control group and the PBLI group for sequencing

first: Qianying

first: Junfeng

last: Li

first: Yanmei

last: Zhao

first: Jianfeng

last: Zhang

first: Mingyu

last: Shi

first: Sifan

last: Yu

first: Siyu

last: Huang

first: Xiangyan

last: Meng

first: Haojun

last: Fan


title: Fam46a is a regulator for gene expression in secretory tissues and plays an important role in development and homeostasis [FAM46A-shRNA]

city: Kyoto

first: Toshiyasu

last: Suzuki

address: Sakyo-ku

department: Department of Cell and Developmental Biology, Graduate school of Biostudies

institute: Kyoto University

summary: In early embryonic development, the organiser functions in multiple developmental processes, including neural induction, dorsoventral patterning of the mesoderm, and formation of the axial mesoderm. Chordin is a central molecule for the activity of the Spemann’s organiser and abundantly secreted from the Spemann’s organiser in Xenopus laevis. However, so far, a whole picture of the gene expression profile regulated by Chordin has not been examined. Here, we perform microarray analysis of chordin overexpression and identify fam46a as an upregulated gene. We demonstrate that fam46a is essential for Xenopus laevis early embryonic development as well as gene induction during cell differentiation in mammalian cell culture models. fam46a is preferentially expressed in tissues with high secretory ability. In Xenopus laevis, fam46a is required for normal neural tube closure and expression of epidermal markers, neural markers and mesodermal markers. In the human Caco-2 cell model, FAM46A is localised in the nucleus and cytoplasm, and regulates gene induction during cell differentiation. In the mouse intestinal organoid model, Fam46a is required for survival of organoids as well as enterocyte differentiation. These results indicate that fam46a is a regulator for gene expression in secretory cells during cell differentiation in early embryonic development and adult homeostasis.

overall_design:
To analyse which genes were affected by FAM46A depletion in Caco-2 cells, we performed microarray analysis on Caco-2 cells infected with shRNA-expressing lentivirus.
Caco-2 cells were infected with lentivirus expressing scramble shRNA, FAM46A-shRNA#2 or FAM46A-shRNA#4.

first: Chie

last: Shintani

first: Tetsuro

last: Araki

first: Koichi

last: Miyatake

first: Morioh

last: Kusakabe


title: Characterization of the cutaneous tumor microenvironment of advanced-stage mycosis fungoides using single-cell RNA sequencing

city: Pittsburgh

first: Patrizia

last: Fuschiotti

state: PA

address: 200 Lothrop St

institute: University of Pittsburgh

summary: Malignant T lymphocyte proliferation in mycosis fungoides (MF) is largely restricted to the skin, implying that malignant cells are dependent on their specific cutaneous tumor microenvironment (TME), including interactions with non-malignant immune and stromal cells, cytokines, and other immunomodulatory factors. To explore these interactions, we performed a comprehensive transcriptome analysis of the TME in advanced-stage MF skin tumors by single-cell RNA sequencing. Our analysis identified cell-type compositions, cellular functions, and cell-cell interactions in the MF TME that were distinct from those from healthy skin and benign dermatoses. While patterns of gene expression were common amongst patient samples, high transcriptional diversity was also observed in immune and stromal cells, with dynamic interactions and crosstalk between these cells and malignant T lymphocytes. This heterogeneity mapped to processes such as cell trafficking, matrix interactions, angiogenesis, immune functions, and metabolism that affect cancer cell growth, migration and invasion, as well as anti-tumor immunity. By comprehensively characterizing the transcriptomes of immune and stromal cell within the cutaneous microenvironment of individual MF tumors, we have identified patterns of dysfunction common to all tumors that represents a resource for identifying candidates with therapeutic potential as well as patient-specific heterogeneity that has important implications for personalized disease management.

overall_design: 7 CTCL samples and 9 normal skin samples were analyzed. MF17,MF18,MF21, and MF21 were reused from GSE182861.

first: Alyxzandria

last: Gaydosik

first: Connor

last: Stonesifer

first: Tracy

last: Tabib

first: Robert

last: Lafyatis

first: Larisa

last: Geskin


title: Identification and profiling of microRNAs in Zea mays in response to Spodoptera frugiperda feeding

status: Public on Nov 20 2023

city: Jinan

first: jianhua

last: zhang

address: gongyebei street No. 23788

institute: Shandong Academy of Agricultural Sciences

summary: MicroRNAs (miRNAs) are endogenous small noncoding RNAs (18–25 nt) that are involved in many physiological processes including development, cancer, immunity, apoptosis and host-microbe interactions through posttranscriptional regulation of gene expression. In this study, we measured the profile of small RNAs in Zea mays after one day and three days of Spodoptera frugiperda feeding. We identified 500 miRNAs, including 449 known and 51 novel miRNAs. In addition, we identified the miRNAs differentially expressed in Z. mays after one day and three days of S. frugiperda feeding, and the possible target genes were identified. This study identified critical miRNAs involved in the Z. mays during S. frugiperda feeding, thus providing a useful resource for exploring the regulatory role of miRNAs during plant-insect interactions.

overall_design: The microRNAs expression profile in Zea mays during Spodoptera frugiperda feeding


title: Citrulline supplementation leads to increased immune suppression and more severe outcomes in infected newborn piglets

city: Copenhagen

first: Jingren

last: Zhong

state: Frederiksberg

address: Dyrlægevej 68 DK-1870

institute: University of Copenhagen

summary: Background: Preterm infants are at high risk of infection and sepsis, which is associated with arginine (ARG) deficiency. Optimal nutrition for preterm newborns suspected with infection is critical to prevent sepsis development. Citrulline (CIT) supplementation is known to prevent sepsis in adult rodents, by maintaining sufficient blood ARG levels and vascular stabilization. We hypothesized that CIT therapy improve sepsis outcomes in infected preterm newborns via CIT and ARG metabolism.Results: After infection, oral CIT supplementation led to higher mortality, blood bacterial load, and circulating and hepatic inflammation, compared with the infected controls. Intravenous CIT administration also showed increased inflammation and bacterial burdens without increased mortality. Liver transcriptomics and data from in vitro blood stimulation indicated that CIT induces enhanced immunosuppression, which may impair resistance response to bacteria at early stage of infection and later cause excessive inflammation and tissue damage. Conclusion: Early stage of CIT supplementation exacerbates sepsis severity in infected preterm pigs, likely via induced enhanced systemic immunosuppression.

overall_design: Caesarean-delivered, parentally nourished preterm pigs were treated with CIT (1g/kg) via an oral bolus (ORA_CIT) or continuous intravenous supplement (IV_CIT), then inoculated with Staphylococcus epidermidis or saline (SE/CON) and cared for 14h. Clinical outcomes were monitored, while blood, liver and spleen samples were collected for analysis. Liver RNA was used for RNAseq.

first: Ole

last: Bæk

first: Sebastian

last: Høj Johansen

first: Duc

last: Ninh Nguyen


title: Fam46a is a regulator for gene expression in secretory tissues and plays an important role in development and homeostasis [Chordin]

overall_design: To screen novel genes which are important for neural induction in Xenopus laevis, we performed microarray analysis and compared gene expression profiles between untreated animal cap explants and chordin-overexpressing animal cap explants.


title: Expression Data from Brucella abortus strain 2308 and isogenic mavR mutant cells

city: Pittsford

first: Paul

last: M Dunman

state: NY

address: 695 W. Bloomfield Rd

institute: University of Rochester

summary:
MavR is a 160 nucleotide regulatory RNA molecule that is produced during B. abortus strain 2308 growth in nutrient-replete broth.
We used custom-made Affymetrix B. abortus strain 2308 derived GeneChips to compare the gene expression properties of wild type and isogenic mavR mutant cells.

overall_design: B. abortus strain 2308 or mavR mutant cells were grown to late exponential growth phase in brucella broth , total bacterial RNA was isolated and subjected to GeneChip hybridization and analysis.  We sought to determine the regulatory effects of abcR1 and abcR2 RNA species.

last: Dunman

first: Clayton

last: Caswell


title: Fam46a is a regulator for gene expression in secretory tissues and plays an important role in development and homeostasis

first: Toshiyasu

last: Suzuki

sample_organism:
Xenopus laevis
Homo sapiens

platform_organism:
Xenopus laevis
Homo sapiens

overall_design: Refer to individual Series


title: The RNA binding proteins ZFP36L1 and ZFP36L2 modulate transcriptional and post-transcriptional genome wide effects of glucocorticoids

city: Edinburgh

first: Jennifer

last: Rynne

email: jrynne@ed.ac.uk, jenrynne@gmail.com

address: QMRI, Edinburgh BioQuarter, Little France Crescent

country: United Kingdom

institute: University of Edinburgh

summary: To investigate the genome-wide role of RNA binding proteins ZFP36L1 and ZFP36L2 in glucocorticoid mechanisms of action in bronchial epithelial cells

overall_design:
Primary BECs were depleted of ZFP36L1 and ZFP36L2 and stimulated with dexamethasone overnight. Frac-seq was performed to allow comparison of total mRNA to monosomal (80S) and polyribosomal (poly) bound mRNAs
RNA-seq was performed for each fraction (total, 80S, poly) comparing the effects of knockdown and of dexamethasone (DEX)

first: Rocio

last: Martinez-Nunez


title: Transcriptional regulation of amino acid metabolism by KDM2B, in the context of ncPRC1.1 and in concert with MYC and ATF4 [RNA-Seq]

city: Columbus

first: Alessandro

last: La Ferlita

state: OH

department: The James Comprehensive Cancer Center

institute: The Ohio State University

summary: KDM2B encodes a JmjC domain-containing histone lysine demethylase, which functions as an oncogene in several types of tumors, including TNBC. This study was initiated to address the cancer relevance of the results of our earlier work, which had shown that overexpression of KDM2B renders mouse embryonic fibroblasts (MEFs) resistant to oxidative stress by regulating antioxidant mechanisms.  Methods We mainly employed a multi-omics strategy consisting of RNA-Seq, quantitative TMT proteomics, Mass-spectrometry-based global metabolomics, ATAC-Seq and ChIP-seq, to explore the role of KDM2B in the resistance to oxidative stress and intermediary metabolism. These data and data from existing patient datasets were analyzed using bioinformatic tools, including exon-intron-split analysis (EISA), FLUFF and clustering analyses. The main genetic strategy we employed was gene silencing with shRNAs. ROS were measured by flow cytometry, following staining with CellROX and various metabolites were measured with biochemical assays, using commercially available kits. Gene expression was monitored with qRT-PCR and immunoblotting, as indicated.  Results The knockdown of KDM2B in basal-like breast cancer cell lines lowers the levels of GSH and sensitizes the cells to ROS inducers, GSH targeting molecules, and DUB inhibitors. To address the mechanism of GSH regulation, we knocked down KDM2B in MDA-MB-231 cells and we examined the effects of the knockdown, using a multi-omics strategy. The results showed that KDM2B, functioning in the context of ncPRC1.1, regulates a network of epigenetic and transcription factors, which control a host of metabolic enzymes, including those involved in the SGOC, glutamate, and GSH metabolism. They also showed that KDM2B enhances the chromatin accessibility and expression of MYC and ATF4, and that it binds in concert with MYC and ATF4, the promoters of a large number of transcriptionally active genes, including many, encoding metabolic enzymes. Additionally, MYC and ATF4 binding sites were enriched in genes whose accessibility depends on KDM2B, and analysis of a cohort of TNBCs expressing high or low levels of KDM2B, but similar levels of MYC and ATF4 identified a subset of MYC targets, whose expression correlates with the expression of KDM2B. Further analyses of basal-like TNBCs in the same cohort, revealed that tumors expressing high levels of all three regulators exhibit a distinct metabolic signature that carries a poor prognosis.  Conclusions The present study links KDM2B, ATF4, and MYC in a transcriptional network that regulates the expression of multiple metabolic enzymes, including those that control the interconnected SGOC, glutamate, and GSH metabolic pathways. The co-occupancy of the promoters of many transcriptionally active genes, by all three factors, the enrichment of MYC binding sites in genes whose chromatin accessibility depends on KDM2B, and the correlation of the levels of KDM2B with the expression of a subset of MYC target genes in tumors that express similar levels of MYC, suggest that KDM2B regulates both the expression and the transcriptional activity of MYC. Importantly, the concerted expression of all three factors also defines a distinct metabolic subset of TNBCs with poor prognosis. Overall, this study identifies novel mechanisms of SGOC regulation, suggests novel KDM2B-dependent metabolic vulnerabilities in TNBC, and provides new insights into the role of KDM2B in the epigenetic regulation of transcription.

overall_design: RNA samples were sequenced in triplicates. RNAseq was performed in Empty Vector (control) and KDM2B-Knockdown (shKDM2B) MDA-MB-231 triple-negative breast cancer cells.

first: Evangelia

last: Chavdoula

first: Vollter

last: Anastas

first: Julian

last: Aldana

first: Giuseppe

last: Carota

first: Mariarita

last: Spampinato

first: Burak

last: Soysal

first: Ilaria

last: Cosentini

first: Sameer

last: Parashar

first: Anuvrat

last: Sircar

first: Giovanni

last: Nigita

first: Lalit

last: Sehgal

first: Michael

last: Freitas

first: Philip

last: Tsichlis


title: Transcriptional regulation of amino acid metabolism by KDM2B, in the context of ncPRC1.1 and in concert with MYC and ATF4. [ATAC-Seq]

overall_design: Comparative study of chromatin accessibility (ATAC-seq) between the Empty Vector (control) and KDM2B Knockdown (shKDM2B) MDA-MB-231 triple-negative breast cancer cells. ATAC samples were sequenced in triplicates.


title: TDP1 gene knockout effect on transcriptome

city: Novosibirsk

first: Maxim

last: Ri

address: Lavrenteva st. 6

country: Russia

institute: LLC AcademGene

summary: TDP1 is an enzyme that in humans is encoded by the TDP1 gene.[5][6][7]  TDP1 is the protein involved in repairing stalled topoisomerase I-DNA complexes.  We evaluated the effect of Tdp1 knockout in HEK293A cells on the gene expression.

overall_design: Knockout HEK293A cell line was generated using the CRISPR/Cas9 method. gRNA were designed against region with constitutive protein-encoding exons of Tdp1 gene. Then, we performed comparative gene expression profiling analysis of RNA-seq data for HEK293A wild type cells and Tdp1-KO under influence of DMSO, topotecan, OL9-119 and its combination (topotecan+OL9-119). Wild type control samples fastq files were uploaded under GSE218871.

first: Nadezhda

last: Dyrkheeva

first: Anastasia

last: Malakhova

first: Aleksandra

middle: L

last: Zakharenko

first: Larisa

last: Okorokova

first: Dmitriy

middle: N

last: Shtokalo

first: Sophia

last: Pavlova

first: Sergey

last: Medvedev

first: Suren

last: Zakian

first: Anna

last: Nushtaeva

first: Marsel

last: Kabilov

first: Alexey

last: Tupikin

first: Olga

last: Luzina

first: Nariman

middle: F

last: Salakhutdinov

middle: I

last: Lavrik


title: Transcriptional regulation of amino acid metabolism by KDM2B, in the context of ncPRC1.1 and in concert with MYC and ATF4 [ChIP-seq]

first: Alessandro

last: La Ferlita

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for the epigenetic factor KDM2B, the transcription factors ATF4 and MYC, and the histone modifications H3K4me3, H3K27me3, H2AK119ub, H3K27ac in MDA-MB-231 triple-negative breast cancer cells. ChIP samples were sequenced in duplicates.

first: Evangelia

last: Chavdoula

first: Vollter

last: Anastas

first: Julian

last: Aldana

first: Giuseppe

last: Carota

first: Mariarita

last: Spampinato

first: Burak

last: Soysal

first: Ilaria

last: Cosentini

first: Sameer

last: Parashar

first: Anuvrat

last: Sircar

first: Giovanni

last: Nigita

first: Lalit

last: Sehgal

last: Freitas


title: Transcriptional regulation of amino acid metabolism by KDM2B, in the context of ncPRC1.1 and in concert with MYC and ATF4


title: Transcriptome Analysis Between Green Cabbage (Brassica oleracea var. capitata) and Savoy Cabbage (Brassica oleracea var. sabauda)

city: Anseong-si

first: Peter

last: Choi

state: Gyeonggi-do

address: 4726, Seodong-daero, Daedeok-myeon,

department: plant biotechnology

summary: We found several candidate genes might be involved in the crinkled leaf phenotype of savoy cabbage.

overall_design: Cabbage (B. oleracea L. subsp. capitata) cultivar ‘Daebakna (DBN)’ and savoy type cabbage (B. oleracea L. subsp. Sabauda) cultivar ‘Serpentine (ser)’ were obtained from Asia Seed Company and used in this study. After seed sterilization, sterilized seeds were incubated at 22℃ under the long day light condition in growth room. 2 weeks old seedling were transplanted to soil pots and grown in the greenhouse located in the Anseong campus of Chung-Ang University at South Korea.

first: Dong

last: Kim


title: Full inactivation of DYRK1A in heterozygous embryonic forebrain at E15.5

city: ILLKIRCH

first: Yann

last: HERAULT

address: 1 rue Laurent Fries

institute: IGBMC/PHENOMIN-ICS

summary: we analyzed gene expression in E15.5 Dyrk1a<+/-> forebrains and compared it to control littermates.

overall_design: Forebrains from control (wt) and mutant (Dyrk1a<+/->) mice (n=3 per genotypes) were microdissected at the age of 15.5 days post coitum (E15.5) from the Dyrk1a<+/-> line.

last: Herault

first: Aline

last: Dubos

first: Maria

last: del Mar Muniz Moreno

first: Valerie

last: Nalesso


title: conditional inactivation of DYRK1A in the Dlx5 domain at embryonic forebrain at E15.5

summary: we analyzed gene expression in E15.5 Dyrk1aDlxcre/+ forebrains and compared it to control littermates.

overall_design: Forebrains from control (wt) and mutant (Dyrk1a<DlxCre/+>) mice (n=3 per genotypes) were microdissected at the age of 15.5 days post coitum (E15.5) from the Dyrk1a<DlxCre/+> line. Then RNA was extracted using Trizol and Qiagen RNeasy Minikit following the manufacturer protocol, and sent for single-end bulk RNA-Seq sequencing. The preparation of the libraries was done by the GenomEast platform, using the TruSeq Stranded Total RNA Sample Preparation Guide PN 15031048. Total RNA-Seq libraries were generated from 150-300 ng of total RNA using TruSeq Stranded Total RNA LT Sample Prep Kit with Ribo-Zero Gold (Illumina, San Diego, CA), according to manufacturer's instructions. Following purification, the depleted RNA was fragmented into small pieces using divalent cations at 94oC for 2 minutes. Cleaved RNA fragments were then copied into first strand cDNA using reverse transcriptase and random primers followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. Strand specificity was achieved by replacing dTTP with dUTP during second strand synthesis. The double stranded cDNA fragments were blunted using T4 DNA polymerase, Klenow DNA polymerase and T4 PNK. A single 'A' nucleotide was added to the 3' ends of the blunt DNA fragments using a Klenow fragment (3' to 5'exo minus) enzyme. The cDNA fragments were ligated to double stranded adapters using T4 DNA Ligase. The ligated products were enriched by PCR amplification (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 12 cycles; 5 min at 72oC). Surplus PCR primers were further removed by purification using AMPure XP beads (Beckman-Coulter, Villepinte, France) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis. The molecule extracted from the biological material were polyA RNA. The sequencing was performed by the platform using Illumina Hiseq 4000.  The alignment was performed on the mouse GRCm38 release 93 using HISAT2 87 with the options -p 8 –dta, -t –summary-file –no-unal, --no-hd. Samtools version 1.9 (http://www.htslib.org/) was used to generate the bam file and index and the counts were generated using HTSeq-Count 0.9.1 88. Using RseQC 89 we checked that the percentage of mapped reads distributed in each genomic feature followed an optimal distribution (exon, 5’UTR exon, 3’ UTR exon, Intron, Intergenic…). Then differential expression analysis was done using FCROS 90. Representation of protein-protein interaction network was obtained from mysregulated genes using Cytoscape 91.


title: Thyroid Hormone T4 Mitigates Traumatic Brain Injury by Dynamically Remodeling Cell Type Specific Genes, Pathways, and Networks in Hippocampus and Frontal Cortex

city: Los Angeles

first: Xia

last: Yang

state: California

address: 610 Charles E. Young Drive East

department: Integrative Biology and Physiology

institute: University of California, Los Angeles

summary: The complex pathology of traumatic brain injury (TBI) is a main contributor to the difficulties in achieving a successful therapeutic regimen. Previously, we showed that thyroxine (T4) administration prevented the cognitive impairments induced by TBI in mice. To understand the underlying mechanism, we carried out a systems level single cell transcriptomic study to investigate the spatiotemporal effects of T4 on individual cell types in the hippocampus and frontal cortex at three post-injury stages. Our multi-tissue multi-stage results showed that acute T4 treatment within 6 hours of injury altered the transcriptome in numerous cell types across tissues and timepoints, in particular in astrocytes, microglia, oligodendrocytes, and endothelial cells. We also identified key TBI-affected genes such as Mbp and Plp1 as well as numerous pathways such as oxidative phosphorylation, immune response, and nervous system related pathways to be reversed after T4 treatment. Within- and between-cell-type network modeling revealed that certain dynamic shifts in subnetworks related to cell cycle, stress response, and RNA processing in both tissues that were affected by TBI and were mitigated by T4. Integration of the genes altered by TBI and/or T4 with candidate genes from human genome-wide association studies (GWAS) of various diseases support the relevance of T4 treatment in alleviating cognitive, psychiatric and neurodegenerative disorders related to TBI. Our systems-level approach elucidated the temporal and spatial dynamic reprogramming of cell-type specific genes, pathways, and networks, as well as cell-cell communications through which T4 mitigates cognitive dysfunction induced by TBI.

overall_design: Nine groups of mice (n=7/group) including sham, mTBI, and mTBI+T4 treatments across 24hr, 7-day, and 21-day timepoints were investigated. Mice from the 7-day timepoint underwent spatial learning and memory evaluation using the Barnes Maze. The hippocampus and frontal cortex tissues of a subset of mice from each of the 9 groups (n=3/group) were then subject to scRNAseq analysis.

first: Zhang

last: Guanglin

first: Diamante

last: Graciel

first: Ahn

last: In Sook

first: Ying

last: Zhe

first: Yang

last: Xia


title: Loss of p73 contributes to COPD

city: Nashville

first: Jessica

last: Blackburn

address: 1611 21st Ave MCN

institute: VUMC

summary:
Rationale: Multiciliated cell (MCC) loss/dysfunction is common in the small airways of patients with COPD but it is unclear if this contributes to COPD lung pathology.
Objectives: To determine whether loss of MCCs causes a COPD-like phenotype in mice and explore a potential role for the transcription factor p73 in COPD.
Methods: p73floxE7-E9 mice were crossed with Shh-Cre mice to generate mice lacking MCCs in the airway epithelium. The resulting p73airway mice were analyzed using electron microscopy, flow cytometry, morphometry, forced oscillation technique, and single-cell RNA sequencing. Further, the effects of cigarette smoke on p73 transcript and protein expression were examined using in vitro and in vivo models and in studies including airway epithelium from smokers and COPD patients.
Measurements and Main Results: Loss of functional p73 in the respiratory epithelium resulted in a near-complete absence of MCCs in p73airway mice. In adulthood, these mice spontaneously developed neutrophilic inflammation and emphysema-like lung remodeling and had progressive loss of secretory cells. Exposure of normal airway epithelium cells to cigarette smoke rapidly and durably suppressed p73 expression in vitro and in vivo. Further, TP73 mRNA expression was reduced in the airways of current smokers (n=82) compared to former smokers (n=69) and p73-expressing MCCs were reduced in the small airways of COPD patients (n=11) compared non-COPD controls (n=12).
Conclusions: Loss of functional p73 in murine airway epithelium results in the absence of MCCs and promotes COPD-like lung pathology. In smokers and patients with COPD, loss of p73 may contribute to MCC loss or dysfunction.

overall_design: We used PARSE to perfom SPLiT-seq on the pooled lungs of six  2 month-old C57Bl6/J mice Shh.Cre+/Flox-p73 at E7-E9 (Cre_Pos), in addition to the pooled lungs of six 2 month-old C57Bl6/J mice Shh.Cre-/Flox-p73 that are littermates homozygous for the p73 flox E7-E9 allele(Cre_Neg). We used the Evercode WT kit to sequence a total of 20,000 cells pooled between the two conditions. The pooled cells were divided into 4 sublibraries.  In the Parse WT kit, the Cre_Pos sample corresponds to barcoding wells A1-B12 and the Cre_Neg sample corresponds to wells C1-D12.

first: Bradley

last: Richmond


title: A multiscale 3D chromatin architecture that controls development of the humoral immune system is assembled by IKAROS [ChIP-Seq 3]

city: Charlestown

first: Katia

last: Georgopoulos

state: MA

address: 1st and 13th St

department: CBRC

institute: Harvard Medical School

summary: A generic level of chromatin organization generated by the interplay between cohesin and CTCF suffices to limit promiscuous interactions between regulatory elements, but a lineage-specific assembly of chromatin that supercedes these constraints is required to configure the genome to support the gene expression changes that guide faithful lineage progression. Using loss-of-function approaches in B cell precursors in vivo we show that IKAROS assembles interactions between sites often separated by megabase distances to configure a significant fraction of the genome in preparation for lymphoid development. Interactions emanating from IKAROS-bound enhancers override CTCF-imposed boundaries and assemble lineage-specific regulatory units built on a backbone of smaller invariant topological domains.In vitro deletion provides temporal resolution to changes in chromatin modifications, loops, and compartmental localization. Gain-of-function experiments in epithelial cells confirm IKAROS’ ability to reconfigure chromatin architecture at multiple scales.  While the compaction of the Igk locus required for genome editing represents a function of IKAROS unique to the lymphoid system, the more general function of this lineage-defining DNA binding protein to preconfigure the genome to support lineage specific gene expression and suppress activation of extra-lineage genes provides a paradigm for lineage restriction.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for histone modifications and transcription factors in wildtype and IkE5Δ/Δ large preB cells

first: Yeguang

last: Hu

first: Daniela

last: Salgado Figueroa

first: Zhihong

last: Zhang

first: Margaret

last: Vaselits

first: Sourya

last: Bhattacharyya

first: Marcus

last: Clark

first: Mariko

last: Kashiwagi

first: Bruce

last: Morgan

first: Ferhat

last: Ay


title: A multiscale 3D chromatin architecture that controls development of the humoral immune system is assembled by IKAROS [RNA-Seq 3]

overall_design: We performed in situ Hi-C in wild-type and IkE5Δ/Δ large pre-B cells to understand IKAROS’ function in the genome organization in early B cell development.


title: A longitudinal single-cell atlas of treatment response in pediatric AML (scATAC-Seq)

city: Vancouver

first: Marco

last: Marra

state: BC

address: 675 West 10th Avenue

department: Genome Sciences Centre

country: Canada

institute: BC Cancer Research Centre

summary: Pediatric acute myeloid leukemia (pAML) is a disease characterized by heterogeneous cellular composition, driver alterations and prognosis. Characterization of this heterogeneity and how it affects treatment response remains relatively understudied in pediatric patients. We therefore used single-cell RNA sequencing and single-cell ATAC sequencing to profile 684,031 diagnosis, remission and relapse cells from 28 patients representing different pAML subtypes. Analysis revealed that at diagnosis, cellular compositions differed between distinct subgroups. Upon relapse, cellular hierarchies transitioned towards a more primitive state regardless of subtype. These primitive cells were distinct compared to cells at diagnosis, having underrepresentation of transcriptional programs involved in myeloid differentiation while programs commonly found in other lineages were overrepresented. In a subset of patients, this appeared to accompany the appearance of a B-lymphoid-like hierarchy. Together, our data reveal the emergence of apparent subtype-specific plasticity upon treatment and inform on potential novel therapeutic angles to target these cell populations.

overall_design:
Single cell ATAC sequencing from 28 matched patient tumors enrolled in the study. Biopsies were taken from bone marrow or peripheral blood at diagnosis, remission and relapse and Ficoll-enriched.
-----------------------------------
Authors state:
Raw data have not been uploaded as it concerns sequencing data from patients. These data are in the process of being uploaded to the protected environment of EGA under accession number EGAS00001007323.

first: Sander

last: Lambo

first: Diane

last: Trinh

first: Rhonda

middle: E

last: Ries

first: Dan

last: Jin

first: Audi

last: Setiadi

first: Michelle

last: Ng

first: Veronique

last: Leblanc

first: Mike

last: Loken

first: Lisa

last: Broderson

first: Fangyan

last: Dai

first: Laura

last: Pardo

first: Xiaotu

last: Ma

first: Suzanne

last: Vercauteren

first: Soheil

last: Meschinchi


title: Fam46a is a regulator for gene expression in secretory tissues and plays an important role in development and homeostasis [Fam46a-MO1]

first: Toshiyasu

last: Suzuki

overall_design:
To analyse which genes were affected by fam46a depletion in the Xenopus laevis embryo, we performed microarray analysis on fam46a depleted embryos.
CoMO (10 ng/cell), Fam46a-MO1 (10 ng/cell) or Fam46a-MO2 (7 ng/cell) plus Fam46-MO3 (7 ng/cell) was injected into the animal pole of all blastomeres at the four-cell stage.

first: Chie

last: Shintani

first: Tetsuro

last: Araki

first: Koichi

last: Miyatake

first: Morioh

last: Kusakabe


title: A longitudinal single-cell atlas of treatment response in pediatric AML (scRNA-Seq)

first: Marco

last: Marra

overall_design:
Single cell RNA sequencing  from 28 matched patient tumors enrolled in the study. Biopsies were taken from bone marrow or peripheral blood at diagnosis, remission and relapse and Ficoll-enriched.
-----------------------------------
Authors state:
Raw data have not been uploaded as it concerns sequencing data from patients. These data are in the process of being uploaded to the protected environment of EGA under accession number EGAS00001007323.

first: Sander

last: Lambo

first: Diane

last: Trinh

first: Rhonda

last: Ries


title: Steroid Receptor Coactivator-2 Drives Epithelial Reprogramming That Enalbles Murine Embryo Implantation

city: HOUSTON

first: Vineet

middle: Kumar

last: Maurya

address: ONE BAYLOR PLAZA

department: Molecular & Cell Biology

institute: BAYLOR COLLEGE OF MEDICINE

summary: Using conditional knockout technology, we demonstrate that steroid receptor coactivator-2 (SRC-2) is essential for development of the receptive uterus for embryo implantation.  Through bulk RNA-seq analysis, we reveal that endometrial SRC-2 is required for not only the induction of the expression of established genes associated with uterine receptivity but also for the expression of genes involved in endometrial epithelial changes that enable attachment and invasion of the embryo into the underlying stroma.  Together, these RNA-seq results underscore the importance of SRC-2 as a transcriptional coregulator in the endometrium during the periimplantation period.

overall_design: To investigate the SRC-2 gene signature in regulation of embryo implantation, the mouse gestation day 5 uterine tissue from 3 different SRC-2f/f and SRC-2d/d mice were used. Total RNA was isolated from control (SRC-2f/f) and mutant (SRC-2d/d) GD 5 uterus and subjected to the RNAseq assay.

first: John

middle: P

last: Lydon


title: Tumor cell-derived CTSZ mediates macrophage recruitment and M2 polarization to promote castration-resistant prostate cancer progression through the TRA2A/IL-32/ITGA5 axis

city: Chongqing

first: Saipeng

last: Chen

address: Gaotan Yan Street

institute: The First Affiliated Hospital of the Army Medical University

summary: Castration-resistant prostate cancer (CRPC) is a lethal stage of prostate cancer after androgen deprivation therapy (ADT). However, most studies have focused on the autonomous alterations of CRPC cells, and the specific contribution of CRPC cells to the metastatic microenvironment remains less well understood. Here, we report that cathepsin Z (CTSZ) was overexpressed in CRPC cells, enhancing macrophage infiltration and promoting M2 polarization, ultimately leading  to the metastasis of CRPC. Mechanistically, CTSZ facilitates the maturation of IL-32 mRNA by directly degrading the alternative splicing factor TRA2A in CRPC cells, thereby increasing the secretion of IL-32. Subsequently, elevated IL-32 directly binds to ITGA5 in macrophages and activates the PI3K/AKT/mTOR pathway in macrophages, thus promoting the recruitment and polarization of macrophages. Furthermore, treatment with an ITGA5 inhibitor blocked the effect of CTSZ overexpression and suppressed CRPC development. These findings uncover a novel mechanism wherein CTSZ involvement in cell‒cell interactions within the tumor microenvironment contributes to the progression of CRPC and provide new therapeutic strategies for CRPC.

overall_design:
To investigate the mechanism of CTSZ regulating cytokine secretion in prostate cancer cells, we established a stable knockdown of CTSZ in PC3 cells using shRNA.
Subsequently, we collected RNA from the experimental and control groups. Compare gene expression profile analysis in the RNA-seq data.


title: A multiscale 3D chromatin architecture that controls development of the humoral immune system is assembled by IKAROS [RNA-seq LpreB]

first: Katia

last: Georgopoulos

overall_design: We performed RNA-seq in wild-type and IkE5Δ/Δ large pre-B cells to understand IKAROS’ function in the genome organization in early B cell development.

first: Yeguang

last: Hu

first: Daniela

last: Salgado Figueroa

first: Zhihong

last: Zhang

first: Margaret

last: Vaselits

first: Sourya

last: Bhattacharyya

first: Marcus

middle: R

last: Clark

first: Mariko

last: Kashiwagi

first: Bruce

last: Morgan

first: Ferhat

last: Ay


title: A multiscale 3D chromatin architecture that controls development of the humoral immune system is assembled by IKAROS [ChIP-seq LpreB cell]


title: Early senescence-induced immunosuppressive β-cell secretome prevents type 1 diabetes

city: Madison

first: Hugo

last: Lee

state: WI

address: 440 Henry Mall

institute: University of Wisconsin-Madison

summary: During the progression of type 1 diabetes (T1D), β-cells are exposed to significant stress and therefore require adaptive responses to survive. The adaptive mechanisms that can preserve β-cell function and survival in the face of autoimmunity remain unclear. Here we show that deletion of the unfolded protein response genes, Atf6α or Ire1α, in β-cells of NOD mice prior to insulitis generates a p21-driven early senescence phenotype and altered β-cell secretome that significantly enhances leukemia inhibitory factor-mediated recruitment of M2 macrophages to the islets. Consequently, M2 macrophages promote anti-inflammatory responses and immune surveillance that cause resolution of islet inflammation, removal of terminally senesced β-cells, reduction of β-cell apoptosis, and prevention of T1D. We further demonstrate that p21-mediated early senescence signature is conserved in residual β-cells of T1D patients. Our findings reveal a previously unrecognized link between β-cell UPR and senescence that, if leveraged, may represent a novel therapeutic strategy for T1D.

overall_design: mRNA sequencing of 6-week-old Atf6fl/fl (WT) and Atf6β-/- (KO) mice were done with n=3-4 per group

first: Gulcan

middle: S

last: Sahin

first: Chien-Wen

first: Shreyash

last: Sonthalia

first: Sandra

last: Cañas

first: Hulya

middle: Z

last: Oktay

first: Alexander

last: Duckworth

first: Gabriel

last: Brawerman

first: Peter

middle: J

last: Thompson

first: Maria

last: Hatzoglou

first: Decio

last: Eizirik

first: Feyza

last: Engin


title: A multiscale 3D chromatin architecture that controls development of the humoral immune system is assembled by IKAROS [RNA-seq HaCaT]

first: Katia

last: Georgopoulos

overall_design: We performed RNA-seq in HaCaT keratinocyte cells.  Doxycycline (Dox) was added into the culture medium to a final concentration of 0.1μg/ml to induce the expression of IKAROS (HaCaT_Tet-on_Ik1) or Luciferase (HaCaT_Tet-on_Luc).

first: Yeguang

last: Hu

first: Daniela

last: Salgado Figueroa

first: Zhihong

last: Zhang

first: Margaret

last: Vaselits

first: Sourya


title: A multiscale 3D chromatin architecture that controls development of the humoral immune system is assembled by IKAROS [ChIP-seq HaCaT]

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for histone modifications and transcription factors in HaCaT cells that express IKAROS or Luciferase

last: Bhattacharyya

first: Marcus

last: Clark

first: Mariko

last: Kashiwagi

first: Bruce

last: Morgan

first: Ferhat

last: Ay


title: A multiscale 3D chromatin architecture that controls development of the humoral immune system is assembled by IKAROS [Hi-C_HaCaT]

overall_design: We induced IKAROS expression in HaCaT cells using a Tet-on strategy and performed in situ Hi-C at different time points to investigate the impact of IKAROS on genome organization in human skin epithelial cells which normally do not express IKAROS.


title: A multiscale 3D chromatin architecture that controls development of the humoral immune system is assembled by IKAROS [HiChIP_HaCaT]

overall_design: We induced ectopic IKAROS expression in HaCaT cells using a Tet-on strategy and performed HiChIPs for H3K27ac and CTCF at different time points to investigate the impact of IKAROS on regulatory and structural chromatin interactions in human skin epithelial cells which normally do not express IKAROS.


title: A multiscale 3D chromatin architecture that controls development of the humoral immune system is assembled by IKAROS [HiChIP_LpreB steady state]

overall_design: We performed HiChIPs for H3K27ac, CTCF, SMC1a and IKAROS in wild-type and IkE5Δ/Δ large pre-B cells to understand IKAROS’ function in the regulatory and structural genomic interactions in early B cell development.


title: A multiscale 3D chromatin architecture that controls development of the humoral immune system is assembled by IKAROS [HiC_LpreB_Inducible_deletion]

overall_design: We induced IkE5 deletion in established large pre-B cell culture and performed in situ Hi-C at different time points to investigate the temporal changes in genome organization upon IkE5 deletion.


title: A multiscale 3D chromatin architecture that controls development of the humoral immune system is assembled by IKAROS [HiChIP_LpreB_Inducible]

overall_design: We induced IkE5 deletion in established large pre-B cell culture and performed HiChIPs for H3K27ac, SMC1a and CTCF at different time points to investigate the temporal change in regulatory and structural interactions upon IkE5 deletion.


title: H3K27ac Hi-ChIP analysis in TAL1-FKBP12 Jurkat cells

city: Singapore

first: Tze King

last: Tan

address: 14 Medical Drive

department: Cancer Science Institute

country: Singapore

institute: National University of Singapore

summary: H3K27ac Hi-ChIP analysis was performed in TAL1-FKBP12 Jurkat cells to analyze active chromatin-chromatin interactions after DMSO or dTAG-13 treatment.

overall_design: The cells were crosslinked with formaldehyde for 10 min.  DNA was enriched by chromatin-immunoprecipitation (ChIP), tagmented with Tn5, subjected for library construction, and sequenced by the DNBseq platform.  Hi-ChIP was performed using an antibody against H3K27ac (Abcam: ab4729).

first: Jolynn

last: Ong

first: Tze

first: Takaomi

last: Sanda


title: 4C-seq analysis in TAL1-FKBP12 Jurkat cells

summary: 4C analysis was performed in TAL1-FKBP12 Jurkat cells to analyze chromatin-chromatin interactions after DMSO or dTAG-13 treatment.

overall_design: Restriction enzyme digestion was performed with N1aIII (NEB) followed by overnight ligation and subsequent reverse crosslinking. DNA fragments were purified to yield the 3C template. 3C template was then subjected to a second restriction enzyme digestion by DpnII (NEB), overnight ligation and sample purification were repeated to yield the 4C template. Library preparation involved two PCR steps to amplify the fragments ligated to the sequence of interest followed by a second PCR to incorporate sequencing adapters.


title: ChIP-seq analysis for TAL1-FKBP12 Jurkat cells

summary: ChIP-seq analysis was performed in a Jurkat cell line to analyze DNA bindings of TAL1-FKBP12 protein using an anti-HA antibody after DMSO or dTAG-13 treatment.

overall_design: The cells were crosslinked with formaldehyde for 10 min.  DNA was enriched by chromatin-immunoprecipitation (ChIP), subjected for library construction, and sequenced by the DNBSEQ platform.  A sample of whole cell extract (input) was sequenced and used as the background to determine enrichment.  ChIP was performed using an antibody against HA (Cat#3724, Cell Signalling Technology).


title: Cut&Run analysis for transcription factors in TAL1-FKBP12 Jurkat cells

summary: Cut&Run analysis was performed in TAL1-FKBP12 Jurkat cells to analyze DNA bindings of GATA3 and RUNX1 after DMSO or dTAG-13 treatment.

overall_design: Jurkat cells were incubated with CUTANA pA/G-Mnase. Chromtin fragments were purified utilizing a Cutana DNA purification kit. Libraries were generated using a NEBNext Ultra II DNA library prep kit and analyzed on Illumina NovaSeq at GENEWIZ Azenta Life Sciences Co. Ltd.


title: RNA-seq analysis in TAL1-FKBP12 Jurkat cells after the treatment with DMSO, dTAG-13, GSI or combination drugs

summary: RNA-seq analysis was performed in a TAL1-FKBP12 Jurkat cells to analyze gene expression changes after drug treatment.

overall_design: TAL1-FKBP Jurkat cells were treatd with DMSO, dTAG-13, GSI or combination of dTAG-13 and GSI. Total RNA was harvested at 24 hours after drug treatment.  RNA-seq analysis was performed.


title: Regulatory mechanisms and context-dependent roles of TAL1 in TALL

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

overall_design: Refer to individual Series


title: IL-17A and IL-17F producing cells

city: Slough

first: Andrew

middle: James

last: Skelton

address: 208 Bath Road

department: Translational Bioinformatics

institute: UCB


title: RNA-seq analysis after the treatment with DMSO or dTAG-13 in TAL1-FKBP12 Jurkat cells

summary: RNA-seq analysis was performed in a TAL1-FKBP12 Jurkat cell line to analyze gene expression changes after dTAG-13 treatmentat at various time points (1h, 2h, 4h, 6h, 8h, 16h, 24h, 48h and 72h).

overall_design: TAL1-FKBP12 Jurkat cells were treated with DMSO or dTAG-13 for 1h, 2h, 4h, 6h, 8h, 16h, 24h, 48h or 72h. Total RNA was harvested and RNA-seq analysis was performed.

middle: K


title: RNA-seq analysis after TAL1 and LMO1 overexpression in HPB-ALL cells

summary: RNA-seq analysis was performed in a T-ALL cell line (HPB-ALL) to analyze gene expression changes after TAL1/LMO1 overexpression.

overall_design: Lentiviral transduction was carried out in HPB-ALL cells to overexpress TAL1/LMO1. Total RNA was harvested after TAL1/LMO1 overexpression and RNA-seq analysis was performed.


title: ChIP sequencing of IL-17A and IL-17F producing cells

summary: IL-17A has emerged as a pivotal driver of tissue pathology in many immune-mediated inflammatory diseases. Despite sharing 50% sequence homology and the same signalling pathway, the role of IL-17F remains less clear. ChIP sequencing of human IL-17 popualtions isolated using a cytokine capture technique identified clear epigenetic differences in IL-17A and IL-17F producing cells.

overall_design: Memory CD4+ T cells were isolated from PBMCs and activated with anti-CD3/CD28, IL-1b and IL-23 for 72 hours from n=6 individual donors. IL-17 secreting cells were captured using bispecific antibodies: CD45/IL-17A or CD45/IL-17F. Live cells were then washed and stained with fluorochrome conjugated antibodies towards IL-17A or IL-17F and FACS sorted.

first: Suzanne

last: Cole

first: Ash

last: Maroof


title: RNA-seq analysis after TP73 exons 2-3 deletion in TL-Om1 cells

summary: RNA-seq analysis was performed in an adult T-cell leukemia/lymphoma cell line (TL-Om1) to analyze gene expression changes after TP73 exons 2-3 deletion

overall_design: Lentiviral infection was carried out on TL-Om1 cells to stably express Cas9 protein. Subseqeunt infection with doxycycline (dox)-inducible sgRNA was done to guide Cas9 protein to specified TP73 exons 2-3 region. Total RNA was harvested from the cells from independent culture or sorted cells after 8 weeks of co-culture. RNA-seq analysis was performed.

first: Rui

last: Yokomori


title: FGF19 facilitates colorectal cancer metastasis through FGFR4-ERK-NF-κB signaling pathway

city: Jinan

first: Tianli

last: Chen

state: Shandong

address: 107 West Wenhua Road

department: Department of General Surgery

institute: Qilu Hospital of Shandong University

summary: Globally, colorectal cancer(CRC) is the third most common malignancy. In recent years, despite the emergence of new screening and treatment strategies, the prognosis of CRC remains poor and distant metastasis remains a major obstacle to the treatment of CRC. Therefore, it is significant to explore new diagnostic and prognostic markers and therapeutic targets. Fibroblast growth factor 19(FGF19) has been reported to promote tumor invasion of CRC. However, the exact mechanism is still unclear.

overall_design: HCT116 cells were stimulated with hFGF19(100 ng/ml) for 72 hours and subjected to differential gene expression studies by RNA-seq.


title: Skeletal muscle gene expression from P301L tau expressing mice using NanoString

status: Public on Nov 19 2023

city: Gainesville

first: Bryan

last: Alava

state: FL

institute: University of Florida

summary: We analyzed gene expression in regions from tibialis anterior cross sections of P301L tau expressing mice and controls. The regions were: standard myofibers, regions containing centrally nucleated myofibers, myofibers proximal to nerve bundle, and myofibers proximal to vasculature

overall_design: Male and female P301L tau expressing mice and their sex and age matched controls. N=3 biological replicates per sex/treatment

first: Gabriela

last: Hery


title: Bulk RNA-seq of Sertoli cell treated with cell debris and ML-SA1

city: Zhuhai

first: Liangyu

last: Zhao

state: Guangdong

address: 52th Meihua Road, Zhuhai, China

institute: Shanghai Jiao Tong University School of Medicinethe Fifth Affiliated Hospital of Sun Yat-sen University

summary: Transcriptom changes in Sertoli cells after phagocyting debis and the effect of ML-SA1 on this process

overall_design: SCNC group was Sertoli cell come from aged men,  SC_G group was Sertoli cell come from aged men treated with debris, and SC_ML group was Sertoli cell come from aged men treated with debris and ML-SA1.