title: RNA-binding protein RPS27 and gene expression regulation in human umbilical vein endothelial cells (HUVECs)

status: Public on Mar 31 2024

city: Urumqi

first: Jingzhan

last: Zhang

state: Xinjiang

address: NO. 91, Tianchi Road, Tianshan District

department: Dermatology

country: China

institute: People’s Hospital of Xinjiang Uygur Autonomous Region

type: Expression profiling by high throughput sequencing

summary: RPS27, a significantly down-regulated and validated RBP in kaposi's sarcoma (KS), and known to be associated with viral infection. As KS is an endothelial cell cancer, we used HUVECs as the cell model to explore the functions of RPS27. RNA-seq technology was used to investigate the differentially expressed genes in HUVECs. By using small interference RNAs (siRNAs) to silence the expression of RPS27 (siRPS27), we detected significant decrease of RPS27 expression in RNA levels comparing with the negative control (siNC) samples.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for RPS27 gene silent HUVECs. The experiment was divided into two groups, each with three replicates. NC group: HUVECs transfection 0.1μM RPS27 siRNA NC; RPS27 siRNA group: HUVECs transfection 0.1μM RPS27 siRNA.


title: Dendrite intercalation between epidermal cells tunes nociceptor sensitivity to mechanical stimuli in Drosophila larvae

city: Seattle

first: Jay

middle: Z

last: Parrish

state: WA

address: 3747 W Stevens Way NE

country: USA

institute: University of Washington

summary: An animal’s skin provides a first point of contact with the sensory environment, including noxious cues that elicit protective behavioral responses. Nociceptive somatosensory neurons densely innervate and intimately interact with epidermal cells to receive these cues, however the mechanisms by which epidermal interactions shape processing of noxious inputs is still poorly understood. Here, we identify a role for dendrite intercalation between epidermal cells in tuning sensitivity of Drosophila larvae to noxious mechanical stimuli. In wild-type larvae, dendrites of nociceptive class IV da neurons intercalate between epidermal cells at apodemes, which function as body wall muscle attachment sites, but not at other sites in the epidermis. From a genetic screen we identified miR-14 as a regulator of dendrite positioning in the epidermis: miR-14 is expressed broadly in the epidermis but not in apodemes, and miR-14 inactivation leads to excessive apical dendrite intercalation between epidermal cells. We found that miR-14 regulates expression and distribution of the epidermal Innexins ogre and Inx2 and that these epidermal gap junction proteins restrict epidermal dendrite intercalation. Finally, we found that altering the extent of epidermal dendrite intercalation had corresponding effects on nociception: increasing epidermal intercalation sensitized larvae to noxious mechanical inputs and increased mechanically evoked calcium responses in nociceptive neurons, whereas reducing epidermal dendrite intercalation had the opposite effects. Altogether, these studies identify epidermal dendrite intercalation as a mechanism for mechanical coupling of nociceptive neurons to the epidermis, with nociceptive sensitivity tuned by the extent of intercalation.

overall_design: Control (w1118) or miR-14 mutant (w1118; miR-14Δ1) larvae with cytoplasmic GFP expressed in the cells of interest (apodemes, UAS-2x-EGFP/+; sr-GAL4/+; epidermal cells, UAS-2x-EGFP/+; R38F11-GAL4/+) were microdissected and dissociated in collagenase type I (Fisher 17-100-017) into single cell suspensions. Pools of 10 cells of interest were isolated using manual aspiration, transferred into lysis buffer, and used for library preparation.

first: K

middle: P

last: Luedke

first: J

last: Yoshino

first: C

last: Yin

first: N

last: Jiang

middle: M

last: Huang

last: Huynh


title: Cell Rejuvenation Signal Activations via Microfluidic Cell Stretch (passage 7)

city: Seoul

first: Tak-il

last: Jeon

address: 120 Neungdong-ro

department: Department of Stem Cell and Regenerative Biotechnology

country: South Korea

institute: Konkuk University

type: Non-coding RNA profiling by high throughput sequencing

summary: MiR modulated the rejuvenation signaling-related genes by applying a physical force on the cell.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for 3 groups (passage7-EP, -MiR, and -control).

first: Geun-Ho

last: Gang

first: Soo

middle: B

last: Jang

first: Tak-Il

first: Ssang-Goo

last: Cho


title: Expression profiles of E4BP4 knockout RAW264.7 cells [RAW_KOvsWT_RNA-seq]

city: Ube

first: Akihiko

last: Taguchi

state: Yamaguchi

address: 1-1-1 minamikogushi

country: Japan

institute: Yamaguchi University

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to evaluate the gene expression of E4BP4 knockout (KO) RAW264.7 cells.
Methods: We generated E4BP4-KO RAW264.7 Cell Line using CRISPR-CAS9 system. Control plasmid was encoding the Cas9 nuclease without gRNA sequence. Total RNA of E4BP4-KO and Control (CTRL) RAW264.7 cells was extracted. RAW264.7 cells RNA profiles were generated by deep sequencing for two groups (E4BP4-KO versus CTRL RAW264.7 cells) with three samples each.
Results: There were significant differences between E4BP4-KO and CTRL RAW264.7 cells.
Conclusions:  Deletion of E4BP4 in RAW264.7 cells induced various changes at the transcription level.

overall_design: E4BP4 knockout RAW264.7 Cell Line profiles.

first: Yasuko

last: Kajimura

first: Yukio

last: Tanizawa


title: Expression profiles of M1-polarized RAW264.7 cells [RAW_M1vsM0_RNA-seq]

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to evaluate the gene expression of M1-polarized RAW264.7 cells compared with M0 RAW264.7 cells.
Methods: RAW264.7 cells were polarized toward M1 using LPS and IFN-γ. M0 RAW264.7 cells were maintained in culture without LPS and  IFN-γ. Total RNA of M1 and M0 RAW264.7 cells was extracted. RAW264.7 cells RNA profiles were generated by deep sequencing for two groups (M1 versus M0 RAW264.7 cells) with three  samples each.
Results: There were significant differences between M1 and M0 RAW264.7 cells.
Conclusions:  Polarization of RAW264.7 cells from M0 to M1 induces various changes at the transcription level.

overall_design: M1-polarized RAW264.7 Cell Line profiles.


title: Hit-and-run silencing of endogenous DUX4 by targeting DNA hypomethylation on D4Z4 repeats in facioscapulohumeral muscular dystrophy [RNA-seq]

city: Kyoto

first: Mitsuru

last: Sasaki-Honda

address: Shogoin, Sakyoku

department: Dept. of Clinical Application

institute: CiRA

summary: Facioscapulohumeral muscular dystrophy (FSHD), a progressive skeletal muscle disorder, is epigenetically characterized with DNA hypomethylation of D4Z4 repeats in 4q35 region, allowing aberrant DUX4 expression. Sustainable DUX4 suppression is a promising therapeutic clue to prevent disease progression, but most of the supposed methods depend on expression of their mediator biochemical entity, potentially narrowing QoL of individuals with FSHD in the clinical context. In this study, we report that by applying hit-and-run silencing with dCas9-mediated epigenetic editing targeting DNA hypomethylation on D4Z4 repeats, we could achieve suppression of endogenous DUX4 in our FSHD patients-derived iPSC model. Notably, DNA methylation was significantly upregulated in FSHD cells and suppression effect was observed at least two weeks after intervention, which was not the case by transient treatment of typical dCas9-KRAB alone. Off-target analysis showed that despite the potential genome-wide risk in DNA methylation, the impact on transcriptome was limited. We propose that hit-and-run silencing can be a promising option to prevent disease progression with minimum intervention for individuals with FSHD, motivating further study for clinical development.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for myogenic differentiated FSHD2 iPSC with or without transient induction of hit-and-run silencing

first: Hidetoshi

last: Sakurai


title: Bioengineering of a human innervated cardiac muscle model

city: Göttingen

first: André

last: Fischer

state: Niedersachsen

address: Von-Siebold-Str. 3a

department: Epigenetics and Systems Medicine in Neurodegenerative Diseases

country: Germany

institute: Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE)

summary: Cardiac autonomic neurons control cardiac contractility. Dysregulation of the autonomic nervous system can lead to sympathetic overdrive resulting in heart failure and an increased incidence of fatal arrhythmias. Here, we introduce innervated engineered human myocardium (iEHM), a novel model of neuro-cardiac junctions, constructed by fusion of a bioengineered neural organoid (BENO) patterned to autonomic nervous system and engineered human myocardium (EHM). Projections of sympathetic neurons into engineered human myocardium formed presynaptic terminals in close proximity to cardiomyocytes and an extensive vascular network co-developing in the tissues. Contractile responses to optogenetic stimulation of the accordingly engineered neuronal component demonstrated functionality of the engineered neuro-cardiac junctions in iEHM. This model will serve as a human surrogate system to delineate neuron and cardiac cell contribution to brain and heart diseases and is an important step towards engineering a human brain to heart axis in a dish.

overall_design: Sympathetic neuronal organoids (SNO) were generated by culturing human induced pluripotent stem cells (hiPSC) in a 3D collagen matrix and step-wise addition of growth factors and small molecules to direct them toward an autonomic, predominantly sympathetic neuronal fate. The medium used for the SNO was based on neuron-specific Neurobasal-A medium. EHM were engineered by combining human foreskin fibroblasts and hiPSC-derived cardiomyocytes with bovine collagen and casting this mixture into a ring-shaped mold. EHM were matured for four weeks in an EHM-specific medium on auxotonic stretchers. After 40 days of culture, SNO were fused with EHM by placing the SNO in the center of the muscle ring to generate iEHM. From this day, iEHM were cultured in a mixture of neuron- and EHM-specific medium in a 1:1 ratio. At this time, SNO were transitioned to the same medium mixture to examine changes in the neuronal tissues unspecific neuro-cardiac interaction. At 6 weeks after fusion (SNO were 12 weeks old), one iEHM sample was snap-frozen, single nuclei were isolated, and RNA was sequenced as described.

first: Lennart

middle: V

last: Schneider

first: Guobin

last: Bao

first: Aditi

last: Methi

first: Ole

last: Jensen

first: Kea

middle: A

last: Schmoll

first: Michael

middle: G

last: Setya

first: Sadman

last: Sakib

first: Aminath

middle: L

last: Fahud

first: Jürgen

last: Brockmöller

first: Norman

middle: Y

last: Liaw

first: Wolfram-Hubertus

last: Zimmermann

first: Maria-Patapia

last: Zafeiriou


title: Transcriptome analysis of C1q-administrated murine lungs

city: Noda

first: Tatsuro

last: Ogawa

address: 2641, Yamasaki

institute: Tokyo University of Science

summary: Pulmonary fibrosis (PF) is a progressive fibrotic disease with a poor prognosis and suboptimal therapeutic options.  The complement molecule C1q, which plays an important role in the phagocytic capacity of macrophages, has recently been reported to exacerbate several fibrosis-related diseases. On the other hand, there are still no reports in PF. Here, we analyzed gene expression changes of C1q-administrated murine lungs.

overall_design: To clarify transcriptomic landscape of C1q-administrated murine lungs, we intratracheally administered with C1q (20 µg/mouse) to WT mice and lungs were harvested. Lung cells were performed transcriptome analysis by 5′sequence using Illumina Novaseq 6000 sequencer.

first: Shigeyuki

last: Shichino

first: Satoshi

last: Ueha

first: Kouji

last: Matsushima


title: KDM5A epigenetically orchestrates MHC-I associated anti-tumor immunity of immunotherapy [DC RNA-seq]

city: Beijing

first: Tantan

last: Wang

address: Haidian  District

institute: Tsinghua University

summary: Immune checkpoint blockade (ICB) therapy revolutionized cancer treatment, but many patients with impaired MHC-I expression remain refractory. Histone methylation was involved in anti-tumor immunity of ICB. However, the link between histone methylation and MHC-I regulation and the related mechanisms are poorly understood. Here we show that KDM5A, an H3K4 demethylase that is critical for MHC-I expression and associated antigen presentation capacity, induces robust immune response and enhances ICB efficacy. Mechanistically, KDM5A upregulates IFN-gamma/STAT1-mediated MHC-I expression via directly binding and suppressing Scos1 in tumor cells. The genes encoding the lysosomal cathepsins are recognized and up-regulated by KDM5A, resulting in enhanced antigen-presentation abilities of both tumor cells and dendritic cells. Furthermore, pharmacological enhancing KDM5A improves response to anti-PD-1 therapy. These investigations demonstrate that enhancing KDM5A triggers MHC-associated antigen presentation of both tumor cells and DCs simultaneously to boost antitumor immunity, thus represents a candidate ICB sensitizer.

overall_design: RNA-seq for the mouse  WT cDC1s and KDM5A knock out cDC1s were carried out .

first: Dan

last: Li


title: Hit-and-run silencing of endogenous DUX4 by targeting DNA hypomethylation on D4Z4 repeats in facioscapulohumeral muscular dystrophy

first: Mitsuru

last: Sasaki-Honda

type: Methylation profiling by genome tiling array

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

overall_design: Refer to individual Series


title: Assay for Transposase-Accessible Chromatin in E4BP4 overexpressed RAW264.7 cells

first: Akihiko

last: Taguchi

type: Genome binding/occupancy profiling by high throughput sequencing

summary: ATACseq was performed by overexpressing E4BP4 in RAW264.7 cells using lentivirus.

overall_design: Lentivirus expressing mCherry(control) or E4BP4 were produced by Vector Builder.RAW264.7 cells were plated at a density of 1x105 cells/well (non-treated 24-well plate). 24 hours　after incubation, RAW cells were infected with lentiviruses expressing mCherry or E4BP4 at 100 MOI. After infection, the cells were replaced with a fresh medium, and 48 hours later, the cells were collected and used for ATAC-seq.

first: Yoichi

last: Asaoka

first: Yuko

last: Nagao


title: AMPK activation in response to hepatitis E virus infection inhibited viral replication by attenuating autophagosome and promoting innate immunity

city: shenzhen

first: Chunling

address: 广东省深圳市南山区学苑大道1088号

institute: southern university of science and technology

summary:
Background & Aims: Other than hepatitis B or C virus infection, Hepatitis E virus (HEV) infection is generally asymptomatic or leads to acute and self-limiting hepatitis. However, the mechanism of host cell defense against HEV is unclear. Viruses are known to perturb host cellular metabolism to enable their replication and spread. AMP-activated protein kinase (AMPK) activation is crucial for the regulation of cell homeostasis. We thus investigated the role of AMPK in HEV infection.
Methods: Huh7, THP1 and HepG2 cells inoculated with infectious HEV viral particle or Huh7 and organoids transfected with in vitro generated subgenomic or full-length GT3 (Kernow-C1 p6 strain) HEV RNA, namely, p6Luc or p6 were used to model HEV infection. Viral replication and genes expression were quantified. Activation of AMPK, innate immune response and autophagy process were assessed.
Results: We found HEV infection can trigger AMPK activation by phosphorylation of AMPK at threonine 172 by transfecting HEV viral RNA into host cells or inoculating host cells with infectious HEV viral particle. The activation of AMPK is associated with HEV induced mitochondrial damage and ATP deficiency. Pharmacological activation of AMPK using 5-aminoimidazole-4-carboxamide ribonucleotide (AICAR) attenuated HEV replication, which was reversed by an AMPK inhibitor (compound C). Lentivirus-mediated knockdown of AMPK provided further evidence that AMPK has an antiviral effect on HEV replication. These results suggested that AMPK activation is a potent strategy of host cells for HEV clearance. Consistent with its antiviral effect, AMPK activation potentiated the expression of genes with antiviral properties (e.g., IFNs, ISG15, and IRF9) and inhibited inflammatory response (e.g., NF-KB NLRP3 and IL-1β). Meanwhile, HEV and activated AMPK also decreased autophagosome accumulation by decreasing induction of autophagy and autophagic degradation. Consistently, we found inhibition of AMPK efficiently augmented HEV induced autophagosome accumulation, evidenced by a marked increase in LC3II. Our previous study showed that rapamycin, an activator of autophagic induction by inhibiting mTOR, and Bafilomycin A1, an inhibitor of autophagic degradation, has a potent pro-HEV effect under AICAR treatment. Moreover, Wortmannin inhibiting autophagic induction recover AMPK inhibitor induced HEV replication. Together, these results suggested that HEV induced AMPK activation can serve to protect HEV infected cells from HEV infection by attenuating autophagosome and promoting innate immunity.
Conclusions: Here we show that HEV infection can activate AMPK phosphorylation, which attenuates autophagosome accumulation and increases innate immune signaling. Thus, the AMPK activation in response to HEV infection is critical in host cells for rapid viral clearance by coordinating autophagic process and establishing persistent antiviral immunity.

overall_design: AMPK activation depends on nutrient depravation, calcium fluctuations, and increased ADP/ATP ratios in concert with AMP/ATP and. In attempt to study if the metabolic changes upon HEV infection are responsible for the phosphorylated activation of AMPK, we compared  gene expression by RNA sequencing in acute HEV infected and mock cells.

first: Yijin


title: Gene expression profile of hair follicle stem cells (HFSCs) isolated from wild type and homozygous Dab2 cKO (Dab2 Fl/Fl) mice at postnatal day 68

city: Navi Mumbai

first: SANJEEV

middle: K

last: WAGHMARE

state: MAHARASHTRA

address: Sector 22, Kharghar

department: STEM CELL BIOLOGY GROUP

country: India

institute: ACTREC, TATA MEMORIAL CENTRE

summary: Disabled 2 is an endocytic adaptor protein known to regulate various signaling pathways such Wnt , BMP, TGF and Ras/MAPK. In the present study, we observed that Dab2 is expressed in all the compartments of the hair follicle. K14 Cre specific homozygous Dab2 knockout resulted in delayed activation of HFSCs and delayed Ist hair follicle cycle initiation. At PD68, both WT and Dab2 cKO mice were at telogen. In addition, loss of Dab2 also led to reduced HFSCs pool extended quiescence, and reduced self renewal capacity of HFSCs at PD68. We performed expression profiling of HFSCs isolated from WT and Dab2 cKO mice at PD68 to check for the differentially regulated genes involved in HFSCs activation. The expression analysis helped us to elucidate the detailed molecular mechanisms involved in Dab2 mediated regulation of HFSCs activation and quiescence.

overall_design: To understand the detailed molecular mechanisms involved in Dab2 mediated regulation of HFSCs, we performed expression profiling on HFSCs isolated from dorsal skin sections of WT and Dab2 cKO mice at PD68 using total RNA sequencing.

first: S

last: waghmare


title: Transcriptome analysis of C1q treated lung fibroblasts

summary: Pulmonary fibrosis (PF) is a progressive fibrotic disease with a poor prognosis and suboptimal therapeutic options.  The complement molecule C1q, which plays an important role in the phagocytic capacity of macrophages, has recently been reported to exacerbate several fibrosis-related diseases. On the other hand, there are still no reports in PF. Here, we analyzed the effect of C1q treatment on lung fibroblasts.

overall_design: To clarify transcriptomic landscape of C1q treated lung fibroblasts, we purified lineage (CD45, CD31, EpCAM, CD146, and Ter119)–  lung fibroblasts by AutoMACS separator from WT mice. Cultured fibroblasts stimulated with C1q (1, 10, and 100 µg/ml, MilliporeSigma) for 2, 24, 48, and 72h and performed transcriptome analysis by 5′sequence using Illumina Novaseq 6000 sequencer.


title: Expression profiles of colon macrophages from macrophage-specific E4BP4 transgenic mouse [ColonMac_RNA-seq]

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to evaluate the effects of macrophage-specific E4BP4 overexpression under c-fms gene  promoter on colon macrophages during the recovery phase of Dextran Sodium Sulfate (DSS)-induced colitis.
Methods: We generated transgenic mice (TG) with macrophage-specific E4BP4 overexpression. Colon macrophages were isolated at Zeitgeber Time (ZT) 0 from TG mice and WT littermates and total RNA was extracted. Colon macrophage RNA profiles were generated by deep sequencing for two groups with three mouse samples each.
Results: There were significant differences between TG and WT mice.
Conclusions:  Colon macrophages from the E4BP4 transgenic mice during the recovery phase of DSS-induced colitis might be altered at the transcription level.

overall_design: Colon macrophage mRNA profiles of 8-week old wild type mice and transgenic mice with macropahge-specific E4BP4 overexpression.

first: Yasuko

last: Kajimura

first: Yukio

last: Tanizawa


title: A single-arm trial of guselkumab in the treatment of adults with pityriasis rubra pilaris (PRP)

city: Portland

first: Connie

last: Shao

state: OR

address: 3303 S Bond Ave Building 1

institute: Oregon Health & Science University

summary: Importance: There is no FDA-approved treatment for pityriasis rubra pilaris and it is common for patients to fail several systemic options. Involvement of IL-23 pathway suggests a potential therapeutic target.   Objective: To determine whether guselkumab, an IL-23p19 inhibitor, provides clinical improvement for subjects with PRP.   Design: Single-arm, investigator-initiated trial from October, 2019 to August, 2022. Primary outcome was observed at 24 weeks, and additional patient follow-up occurred at 36 weeks.   Participants: 14 adult subjects with moderate-to-severe pityriasis rubra pilaris were enrolled; 12 completed the trial. Age- and sex-matched healthy controls provided skin and blood for proteomic and transcriptomic studies.   Intervention: Guselkumab is a humanized IgG1 lambda antibody that selectively binds and inhibits the p19 subunit of interleukin-23. Subcutaneous injections were performed at the  FDA-approved dosing schedule for psoriasis over a 24-week period.   Main Outcomes and Measures: The primary outcome was mean change in psoriasis area and severity index (PASI) at week 24. Secondary outcomes included improvement in body surface area, quality of life, time to improvement, sustained remission at 36 weeks, and correlation to germline mutations and cytokine expression.   Results: An intention-to-treat analysis was performed for our cohort of ten males and six females, with a median age of 59.5 years. The mean improvement in psoriasis area and severity index, body surface area, and dermatology life quality index (DLQI) were 18.9 ± 12.5 (p<0.001), 40.5 ± 36.5 (p=0.003), and 12.2 ± 7.8 (p<0.001), respectively. 11 subjects showed sustained remission off therapy, evidenced by decreased PASI scores between week-24 and week-36. No subjects had CARD14 gene variations. There was one serious adverse event, unrelated to study drug. Proteomics and gene expression profiles improved with clinical improvement.   Conclusion and Relevance: Guselkumab appears to be efficacious in the treatment of refractory PRP.

overall_design: Single-arm, investigator-initiated trial from October, 2019 to August, 2022. Primary outcome was observed at 24 weeks, and additional patient follow-up occurred at 36 weeks. 14 adult subjects with moderate-to-severe pityriasis rubra pilaris were enrolled; 12 completed the trial. Age- and sex-matched healthy controls provided skin and blood for proteomic and transcriptomic studies.

first: Teri

last: Greiling

first: Rose

middle: C

last: Velasco

first: Brett

last: Cutler

first: Gail

last: Kent

first: Pamela

last: Cassidy

first: Keith

last: Choate


title: Sex Differences in the Skeletal Muscle Response to a High Fat, High Sucrose Diet in Rats

city: Oklahoma City

first: Michael

middle: C.

last: Rudolph

state: OK

address: 975 NE 10th St. BRC North rm 364

department: Biochemistry and Physiology

institute: OUHSC

summary: Men are diagnosed with type 2 diabetes at lower body mass indexes than women; the role of skel-etal muscle in this sex difference is poorly understood. Type 2 diabetes impacts skeletal muscle, particularly in females who demonstrate a lower oxidative capacity compared to males. To ad-dress mechanistic differences underlying this sex disparity, we investigated skeletal muscle mito-chondrial respiration in female and male rats in response to chronic high-fat, high-sugar (HFHS) diet consumption. Four-week-old Wistar Rats were fed a standard chow or HFHS diet for 14 weeks to identify sex-specific adaptations in mitochondrial respirometry and characteristics, transcrip-tional patterns, and protein profiles. Fat mass was greater with the HFHS diet in both sexes when controlled for body mass (p < 0.0001). Blood glucose and insulin resistance were greater in males (p = 0.01) and HFHS-fed rats (p < 0.001). HFHS-fed males had higher mitochondrial respiration compared with females (p < 0.01 sex/diet interaction). No evidence of a difference by sex or diet was found for mitochondrial synthesis, dynamics, or quality to support the mitochondrial respi-ration sex/diet interaction. However, transcriptomic analyses indicate sex differences in nutrient handling. Sex-specific differences occurred in PI3K/AKT signaling, PPARα/RXRα, and triacyl-glycerol degradation. These findings may provide insight into the clinical sex differences in body mass index threshold for diabetes development and tissue-specific progression of insulin re-sistance.

overall_design: Differential gene expression profiling analysis of RNA-seq data for gastronemius of male and female Wistar rats given chow or high fat/high sugar diet

first: Nicholas

last: Hulett

first: Rebecca

last: Scalzo

first: Kartik

last: Shankar


title: Expression profiles of CD45+ cells in colon lamina propria from macrophage-specific E4BP4 transgenic mouse

first: Akihiko

last: Taguchi

summary:
Purpose: The goals of this study are to confirm the hypothesis that E4BP4 regulates colon specific anti-inflammatory macrophage.
Methods: We generated transgenic mice (TG) with macrophage-specific E4BP4 overexpression. CD45+ cells in colon lamina propria were isolated at Zeitgeber Time (ZT) 0 from TG mice and WT littermates during the recovery period of dextran sulfate sodium (DSS)-induced colitis, and total RNA was extracted.  CD45+ cells in colon lamina propria RNA profiles were generated by deep sequencing for two groups with one mouse sample each.
Results: There were significant differences between TG and WT mice.
Conclusions:  E4BP4 increased the number of M2 macrophage population and upregulated anti-inflammatory genes.

overall_design: The mRNA profiles of individual CD45+ cells in colon lamina propria of 8-week old wild type mice and transgenic mice with macrophage-specific E4BP4 overexpression during the recovery period of DSS-induced colitis.


title: Hit-and-run silencing of endogenous DUX4 by targeting DNA hypomethylation on D4Z4 repeats in facioscapulohumeral muscular dystrophy [EPIC Methylation]

first: Mitsuru

last: Sasaki-Honda

overall_design: Bisulphite converted DNA from the 7 samples were hybridised to the Infinium Methylation EPIC BeadChip

first: Hidetoshi

last: Sakurai


title: Time-series single-cell RNA sequencing analysis of C1q-administrated murine lungs

first: Tatsuro

last: Ogawa

summary: Pulmonary fibrosis (PF) is a progressive fibrotic disease with a poor prognosis and suboptimal therapeutic options.  The complement molecule C1q, which plays an important role in the phagocytic capacity of macrophages, has recently been reported to exacerbate several fibrosis-related diseases. On the other hand, there are still no reports in PF. Here, we analyzed detailed gene expression changes of each cell population in C1q-administrated murine lungs.

overall_design: To clarify transcriptomic landscape of C1q-administrated murine lungs, we intratracheally administered with C1q (20 µg/mouse) to WT mice and lungs were harvested at day0, 1, and 3.  scRNA-seq was performed using Illumina Novaseq 6000 sequencer.

first: Shigeyuki

last: Shichino

first: Satoshi

last: Ueha

first: Kouji

last: Matsushima


title: mRNA-seq data during learning and memory in mice

city: Shanghai

first: Domgmin

last: Yin

state: Shanghai

address: No.3663, Zhongshan North Road

institute: Shanghai Key Laboratory of Brain Functional Genomics

summary: RNA was extracted from homogenates (HOM) and synapses (SYN) of mice on days 1, 6, and 20 after Morris water maze (MWM) training. Regular RNA sequencing was performed using the NovaSeq 6000 system (Illumina). Our protocol yielded reliable input for SYN using hippocampal RNA from ten mice. In contrast, we generated input libraries for HOM using hippocampal RNA from three mice per three biological replicates

overall_design: RNA-seq profiling of mRNA in hippocampus tissues (homogenates or synapse)

first: Hai-qian

last: Zhou

first: Jia-wei

last: Zhang

first: Zhen

last: Zhu

first: Dong-sheng

last: Chen

first: Dong-min


title: Cell Rejuvenation Signal Activations via Microfluidic Cell Stretch (passage 18)

first: Tak-il

last: Jeon

summary: MiR modulated the rejuvenation signaling-related genes by applying a physical force on the old cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for 3 groups (passage18-EP, -MiR, and -control).

first: Geun-Ho

last: Gang

first: Soo

last: Jang

first: Tak-Il

first: Ssang-Goo

last: Cho


title: Single-Cell Atlas of a Rat Model of Vaginal Birth Injury induced Stress Urinary Incontinence

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: Stress urinary incontinence (SUI) greatly affects the daily life of numerous women and is closely related to a history of vaginal delivery and aging. We used vaginal balloon dilation to simulate vaginal birth injury in young and middle-aged rats to produce a SUI animal model, and found that young rats restored urethral structure and function well, but not the middle-aged rats. To identify the characteristics of cellular and molecular changes in the urethral microenvironment during the repair process of SUI. We profiled 51,690 individual female rat urethra cells from 24 and 48 weeks old, with or without simulated vaginal birth injury.

overall_design: Fourteen female Sprague-Dawley rats, aged 24 and 48 weeks, were procured from Charles River Laboratories (Wilmington, MA, USA). These rats were randomly assigned to two cohorts: (A) Young (24 weeks) and (B) middle-aged (48 weeks). Each cohort was subdivided into 3 groups: sham control (SHAM group), vaginal balloon dilation and ovariectomy (VBDO group), VBDO + BAPN (BAPN group).  Each group consists of 7 rats: 6 for functional study and 1 for single cell RNA sequencing.


title: Expression profiles of macrophages

first: Akihiko

last: Taguchi


title: Expression profiles of E4BP4 overexpression RAW264.7 cells

summary: E4BP4 was overexpressed in RAW264.7 cells using lentivirus and RNAseq was performed.

overall_design: Lentivirus expressing mCherry(control) or E4BP4 were produced by Vector Builder.RAW264.7 cells were plated at a density of 1x105 cells/well (non-treated 24-well plate). 24 hours　after incubation, RAW cells were infected with lentiviruses expressing mCherry or E4BP4 at 100 MOI. After infection, the cells were replaced with a fresh medium, and 48 hours later, the cells were collected and used for RNA-seq.

first: Yuko

last: Nagao


title: Balanced spatiotemporal arrangements of Histone H3 and H4 post-translational modifications are necessary for meiotic prophase I chromosome organization

city: Hyderabad

first: Lava

middle: Kumar

last: Surarapu

state: Telangana

address: NIAB, Gowlidoddi, Gachiboli, Hyderabad, Telangana

institute: National Institute of Animal Biotechnology

summary: Dynamic nuclear architecture and chromatin organizations are the key features of the mid- prophase I in mammalian meiosis. Where the chromatin undergoes major changes, including meiosis-specific spatiotemporal arrangements and remodelling, the establishment of chromatin loop–axis structure, pairing, and crossing over between homologous chromosomes, any deficiencies in these events may induce genome instability, subsequently leading to failure to produce gametes and infertility. Despite the significance of chromatin structure, little is known about the location of chromatin marks and the necessity of their balance during meiosis prophase I. Here, we show a thorough cytological study of the surface-spread meiotic chromosomes of mouse spermatocytes for H3K9,14,18,23,27,36, H4K12,16 acetylation, and H3K4,9,27,36 methylation. Active acetylation and methylation marks on H3 and H4, such as H3K9ac, H3K14ac, H3K18ac, H3K36ac, H3K56ac, H4K12ac, H4K16ac, and H3K27me3 and H3K36me3 exhibited pan-nuclear localization away from heterochromatin. In comparison, repressive marks like H3K9me3 are localized to heterochromatin. In addition, we found that the intensities of H3K23ac, H3K27ac, and H3K9me3 enhanced during meiotic prophase I. Further, taking advantage of the delivery of small-molecule chemical inhibitors Methotrexate (MTX; heterochromatin enhancer), HMS-I1 (heterochromatin inhibitor), Anacardic acid (AA; histone acetyltransferase inhibitor), Trichostatin A (TSA; histone deacetylase inhibitor), IOX1 (JmjC demethylases inhibitor), and AZ505 (methyl transferase inhibitor) in seminiferous tubules through the rete testis route, revealed that alteration in histone modifications enhanced the centromere mislocalization, chromosome breakage, altered meiotic recombination and reduced sperm count. Notably, an imbalance in the histone modifications influences the chromosome axis length and chromatin loop size via transcriptional regulation of meiosis- specific genes. Our findings highlight the importance of balanced chromatin modifications in meiotic prophase I chromosome organization and instability.

overall_design: whole testes transcriptome analysis of triplicate samples for control and other 4 different treatmnets (MTX, HMS-I1, AA and TSA).

first: Aradhana

last: mohanthy

first: anjali

last: kumari

first: ajith

last: kumar

first: ranjiht

first: mohd

last: Athar

first: R

last: Gandham

first: H

last: Prasada Rao


title: Applications of zebrafish embryo models to predict developmental toxicity for agrochemical product development

city: Indianapolis

first: Shreedharan

last: Sriram

address: 9330 Zionsville Road

institute: Corteva Agriscience

summary: Development of safe crop protection products is a complex process that traditionally relies on intensive animal use for hazard identification. Methods that capture toxicity at early stages of agrochemical discovery programs enable a more efficient and sustainable product development pipeline. Here we have explored whether the zebrafish model can be leveraged to identify mammalian-relevant toxicity. We used transgenic zebrafish to assess developmental toxicity following exposures to known mammalian teratogens, and captured larval morphological malformations, including bone and vascular perturbations. We further applied toxicogenomics to identify common biomarker signatures of teratogen exposure. The results show that the larval malformation assay predicted teratogenicity with 82.35% accuracy, 87.50% specificity, and 77.78% sensitivity. Slightly lower accuracy was obtained with the vascular and bone assays. A set of 20 biomarkers were identified that efficiently segregated teratogenic chemicals from non-teratogens. In conclusion, zebrafish are valuable, robust, and cost-effective models for toxicity testing at early stages of product development.

overall_design: RNAseq transcriptomics profiling on zebrafish embryos after treatments with a set of agrochemicals, with known developmental toxicity endpoints, at multiple doses

first: Enrica

last: Bianchi

first: Maria

last: Bondesson

first: Beas

last: Bhattacharya


title: Comparative MicroRNA Sequencing Analysis in Late L1 Larvae of C. elegans: Wild Type N2 Versus myrf-1(ju1121) Mutants

first: LIFANG

last: WANG

address: 393 Middle Huaxia Road

institute: SHANGHAITECH

summary: Our research revealed that the transmembrane transcription factors MYRF-1 and MYRF-2 are crucial for activating the microRNA lin-4 at the end of the first larval stage in C. elegans. To determine whether MYRF regulates other microRNA genes during this period, we conducted a microRNA sequencing analysis to compare microRNA expression in late L1 larvae of wild type and myrf-1(ju1121) mutants. The myrf-1(ju1121) mutation causes a loss of function in both MYRF-1 and MYRF-2. Our analysis identified a subset of microRNAs that were differentially expressed between the wild type and the myrf-1(ju1121) mutants.

overall_design: Late L1 larvae from both wild type and myrf-1(ju1121) mutants, each harboring the transgene marker Phlh-8-GFP(ayIs6), were gathered. RNA was subsequently extracted from these samples and subjected to microRNA sequencing and analysis.

first: Zhimin

last: Xu

first: Zhao

last: Wang

first: Lifang

first: Yingchuan

last: Qi


title: Expression profiles of M2-polarized RAW264.7 cells [RAW_M2vsM0_RNA-seq]

first: Akihiko

last: Taguchi

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to evaluate the gene expression of M2-polarized RAW264.7 cells compared with M0 RAW264.7 cells.
Methods: RAW264.7 cells were polarized toward M2 using IL-4. M0 RAW264.7 cells were maintained in culture without IL-4. Total RNA of M2 and M0 RAW264.7 cells was extracted. RAW264.7 cells RNA profiles were generated by deep sequencing for two groups (M2 versus M0 RAW264.7 cells) with three  samples each.
Results: There were significant differences between M2 and M0 RAW264.7 cells.
Conclusions:  Polarization of RAW264.7 cells from M0 to M2 induces various changes at the transcription level.

overall_design: M2-polarized RAW264.7 Cell Line profiles.

first: Yasuko

last: Kajimura

first: Yukio

last: Tanizawa


title: ChIP_seq for E4BP4 in RAW264.7 cells [RAW_ChIP-seq]

summary: Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to evaluate the effects of liver-specific E4BP4 overexpression under mouse albumin promoter on the liver glucose and lipid metabolism.

overall_design: E4BP4 ChIP-Seq in RAW264.7 cells


title: Expression profiles of M2-polarized bone marrow-derived macrophage from wild type mouse [BMDM_RNA-seq]

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to evaluate the gene expression of M2-polarized bone marrow-derived macrophages (BMDM) compared with M0-BMDMs from wild type (WT) mouse.
Methods: BMDMs were obtained from WT mice and polarized toward M2-BMDMs using IL-4 and M-CSF. M0-BMDMs were maintained in culture with M-CSF only. Total RNA of M2- and M0-BMDMs was extracted. BMDM RNA profiles were generated by deep sequencing for two groups (M2- versus M0-BMDM) with three mouse samples each.
Results: There were significant differences between M2- and M0-BMDMs.
Conclusions:  Polarization of BMDMs from M0 to M2 induces various changes at the transcription level.

overall_design: M2-polarized BMDM mRNA profiles of 8-week old wild type mice.


title: m6A epitranscriptomic changes in response to hypoxic condition or ALKBH5 knock-down in U87

city: Tianjin

first: xudong

last: Wu

address: Qixiangtai Road

institute: Tianjin medical university

summary: Compared with the normoxia control, 174 m6A peaks from 58 m6A-modified transcripts are significantly increased while 2032 m6A peaks from 556 m6A-modified transcripts are significantly decreased in hypoxia. Among the downregulated m6A peaks in hypoxia compared with normoxia condition, ALKBH5 depletion leads to 847 increased m6A peaks in 276 transcripts (fold change≥1.5).

overall_design: The m6A profiles of U87 WT-Normoxia, U87 WT-Hypoxia, U87 shScr-Hypoxia and U87 shALKBH5-Hypoxia

first: Xudong

first: Feng

last: Dong

first: Xiaoyang

last: Qin


title: Autophagy regulates glucagon secretion via the beta2-adrenergic pathway

city: Boston

first: Hui

last: Pan

address: 1 Joslin Place

department: Bioinformatics and Biostatistics Core

institute: Joslin Diabetes Center

summary: Appropriate glucagon secretion from pancreatic alpha cells in response to hypoglycemia is an important component of maintaining glucose homeostasis. Dysregulated glucagon secretion leads to the delayed recovery from a hypoglycemic attack in type 1 diabetes patients which can be lethal. Although elucidating the precise mechanism of glucagon secretion in hypoglycemia is warranted, the underlying mechanism remains poorly understood.The present study provides evidence of the role of autophagy in glucagon secretion in hypoglycemia by demonstrating that autophagy regulates adrenergic stimulation of glucagon secretion downstream of beta2 adrenergic receptor. First, from the analyses of T1D human islets and the published database of scRNA-seq of T1D human alpha cells, we described autophagy pathways altered in T1D alpha cells.  Second, we generated alpha cell-specific Atg7KO mice (alphaAtg7KO) and clarified that the lack of autophagy in alpha cells impairs the reactive glucagon secretion in acute hypoglycemia. Third, to interrogate the molecular mechanism of autophagy-mediated glucagon regulation, we analyzed top genes downregulated inT1D and T2D alpha cells and found the expression of beta2 adrenergic receptor showed significant down-regulation in T1D alpha cells. We confirmed the decreased expression of  beta2 adrenergic receptor in alpha cells of the T1D pancreas section, the islets of alphaAtg7KO mice, and a murine alpha cell line with stable knockdown of Atg7. Furthermore, in vivo and ex vivo studies of alphaAtg7KO mice exhibited that lack of autophagy led to the loss of stimulatory effect of beta2-adrenergic signaling on glucagon secretion. Finally, we established the Atg7 knockdown model in sorted human alpha cells and confirmed the effect of autophagy on the expression of the beta2 adrenergic receptor. Together, our study provides novel insights into the regulatory role of autophagy in glucagon secretion in response to hypoglycemia and provides therapeutic options to achieve stable glycemic control in T1D patients.

overall_design: Freshly-isolated human pancreatic islets from nondiabetic subjects (n=4) and type 1 diabetes patients (n=3) were analyzed for RNA-seq. Samples were treated with or without ER stress inducer, thapsigargin (250 nM) for 24 hours.

first: Kimitaka

last: Shibue

first: Rohit

middle: N

last: Kulkarni


title: Hypoxia and ALKBH5 in U87 cells

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

overall_design: Refer to individual Series


title: Global epigenome analysis reveals the role of histone modifications in the chilling-regulated gene expressions in dormant apple flower buds [RNA-seq]

city: Wuhan

first: Wenxing

last: Chen

address: No.1, Shizishan Street, Hongshan District

institute: Huazhong Agricultural University

summary: Bud dormancy – the repeated phase of rest that punctuates periods of growth in the life cycles of many perennial species. In temperate fruit trees, fulfillment of chilling requirement and subsequent heat requirement enable dormant buds to have uniform blooming in field. However, effects of environmental factors such as chilling underlying dormancy release and bud break has not been fully understood. Histone modification is an important epigenetic regulation system which plays an important role in gene expression in various developmental and adaptive processes. Taking advantage of next-generation sequencing, we generated epigenome and transcriptome profiling at different stages before chilling, after chilling and just before bud break in apple (Malus x domestica). We found H3K27me3 may play dominant role during chilling and the genes involved in lignin and lipid metabolic process showed histone modifications. Interestingly, the higher ratio of genes in chilling-associated network exhibited histone modifications, suggesting crucial epigenetic roles in regulating gene expressions in response to chilling during dormancy. Furthermore, H3K4me3 may play more important role during bud break and the genes related to cell wall modification/organization were strongly modified. Taken together, this study provides important insights into the chromatin-based gene regulation underlying chilling-mediated dormancy release and bud break in apple.

overall_design: We conducted RNA-seq using terminal buds at three stages, buds before chilling exposure (sample “BC”) and after chilling exposure (sample “AC”), buds after chilling exposure then under forcing condition before bud break (sample “BB”).

first: Hisayo

last: Yamane

first: Yosuke

last: Tamada

first: Miwako

last: Matsushita

first: Yutaro

last: Osako

first: Mei

last: Gao-Takai

first: Zhengrong

last: Luo

first: Ryutaro

last: Tao


title: The differential gene expression of the lung cancer cell line HCC827 before and after resistance to osimertinib

status: Public on Mar 30 2024

city: wuhan

first: wei

last: lin

state: 否

address: Luo Yu Road 1037，Hongshan District

institute: Huazhong University of Science and Technology

summary: Osimertinib, as a third-generation epidermal growth factor receptor-tyrosine kinase inhibitor (EGFR-TKI), has been approved as a first-line therapy in advanced non–small-cell lung cancer (NSCLC) patients with EGFR-activating or T790M resistance mutations. However, the efficacy of osimertinib is limited due to acquired resistance. In order to search for the mechanism of resistance to osimertinib, we screened on significantly upregulated genes encoding protein kinases in osimertinib-resistant NSCLC cells via RNA-sequence.In summary, our data elucidate the alterations in gene expression within lung cancer cells before and after resistance to osimertinib, aiding in the analysis and identification of key molecules influencing osimertinib resistance.

overall_design: To establish resistant cell lines to osimertinib, the parent cells (HCC827) were exposed to gradually increasing concentrations of osimertinib, including 10nM, 50nM, 100nM, 500nM, 1μM, and 5μM. Each concentration gradient was cultured for 1 month. Ultimately, the cells that could grow normally in a culture environment with a concentration of 5μM of osimertinib were defined as osimertinib-resistant cell line (HCC827OR)

first: Yongde

last: Liao

first: Wei

last: Lin

first: Yunchong

last: Meng


title: Global epigenome analysis reveals the role of histone modifications in the chilling-regulated gene expressions in dormant apple flower buds

overall_design: We conducted ChIP-seq using terminal buds at three stages, buds before chilling exposure (sample “BC”) and after chilling exposure (sample “AC”), buds after chilling exposure then under forcing condition before bud break (sample “BB”), using antibodies against H3K27me3 and H3K4me3, and both H3 and Input were used as standard control. All sample were did with two biology replicates (_rep1 and _rep2).


title: The use of plasma microRNAs (miRs) as diagnostic and prognostic biomarkers of chronic kidney disease (CKD)

city: Belfast

first: David

middle: Arthur

last: Simpson

state: N. Ireland

address: The Wellcome – Wolfson Institute for Experimental Medicine, 97 Lisburn Road

department: Wellcome-Wolfson Institite for Experimental Medicine

country: United Kingdom

institute: Queen's University Belfast

summary: MicroRNAs (miRs) have the potential to be employed as diagnostic and prognostic biomarkers of chronic kidney disease (CKD) and are functionally important in disease pathogenesis. To identify novel miR biomarkers we performed small RNA-sequencing (sRNA-Seq) to detect miRs that were quantitatively altered in the circulation of individuals with type 2 diabetes (T2D) with CKD compared to those with normal kidney function. MiR-190a-5p abundance was significantly lower in the circulation of T2D patients with reduced kidney function compared to those with normal kidney function. To validate if the loss of circulating miR-190a-5p was associated with reduced kidney function we measured miR-190a-5p in an unselected cohort of CKD patients and determined if dysregulated miR-190a-5p could predict kidney outcomes. In individuals with no or moderate albuminuria (<300mg/mmol), serum miR-190a-5p levels predicted CKD progression (reaching end-stage kidney disease or >30% reduction from baseline eGFR, independent of age, sex, baseline eGFR, urinary albumin excretion, or blood pressure (adjusted HR 0.80, 95% CI: 0.66-0.96, p=0.015). To identify the kidney source of miR-190a-5p we utilised transcriptomic data from mouse models of kidney injury and single nuclear (sn) RNA-Seq from human kidney, finding that miR-190a-5p is enriched in the proximal tubule (PT) but down-regulated following injury. Bioinformatic analysis highlighted ADAM10as a potential miR-190a-5p target and we validated this in human PT cell line. Our analyses suggest that miR-190a-5p is a biomarker of tubular cell health and low circulating levels may predict CKD progression in patients with low or moderate proteinuria independent of existing risk factors.

overall_design: This study applied a miRNA next generation sequencing (NGS) approach to measure DKD-related differential expression of plasma miRNAs. The discovery cohort comprised individuals with type 2 diabetic kidney disease (T2DKD, n = 9), age and gender matched patients with type 2 diabetes mellitus and normal renal function (T2DNRF, n = 13) and non-diabetic with normal renal function (NDNRF, n = 11). Libraries were successfully prepared from the low yields of plasma-derived RNA and sequenced to reveal global miRNA expression.


title: Geneship analysis of porcine femoral arteries after minimally invasive repair by different means of closure

city: guangzhou

first: wenxuan

last: Wu

address: xiaoguwei Street

institute: South China University of Technology

summary: After observing the surgical wounds on the 28th postoperative day, the experimental animals were put to death. Vascular tissues from the surgical site were taken and subjected to gene microarray analysis. This was used to examine the effect of TAG repair in the experimental group and Exoseal repair in the control group.

overall_design: Three Exoseal treated samples and three TAG treated samples were analyzed. Exoseal is a commercially available vascular closure device and TAG is the vascular glue used in the experiment.

first: Wenxuan

first: Chengkai

last: Xuan

first: Shengtao

last: Yan

first: Haotian

last: Lu

first: Xuetao

last: Shi


title: miRNA transcriptomic data of Jining gray goat ovarian and uterine tissues during sexual maturation

city: Tai’an

first: Chao

last: Tianle

state: Shandong

address: Daizong street, no. 61, 6/5000 Shandong Agricultural University

institute: 6/5000 Shandong Agricultural University

summary: Ovarian and uterine tissues from five female Jining Gray goats were collected at the following time points: after birth (D1), 2-month-old (M2), 4-month-old (M4), and 6-month-old (M6). All samples were utilized for the construction of small RNA-seq libraries and subsequent small RNA sequencing. We explored the role of small RNAs in regulating reproductive processes in the ovary and uterus during sexual maturation.

overall_design: We collected uterine and ovarian tissues from female goats at 1 day, 2 months, 4 months, and 6 months after birth, all of which came from the same farm and were raised under the same conditions.

first: Yanyan

last: Wang

first: Qing

last: Li

first: Tianle

last: Chao

first: Jianmin


title: PEGboIFN-lambda as a FMD preexposure prophylactic and vaccine adjuvant in cattle—ISG and adaptive immunity gene expression

city: Rockville

first: Fayna

last: Diaz San Segundo

state: MD

address: 5601 Fisher Ln

department: NIAID-DMID-OBRRTR

institute: NIH

summary: Foot-and-mouth disease (FMD) is a vesicular disease of cloven-hoofed animals with devastating economic implications. The current FMD vaccine, routinely used in enzootic countries, requires at least 7 days to induce protection. However, FMD vaccination is typically not recommended for use in non-enzootic areas, underscoring the need to develop new fast-acting therapies for FMD control during outbreaks. Interferons (IFNs) are among the immune system’s first line of defense against viral infections. Bovine type III IFN delivered by a replication defective adenovirus (Ad) vector has effectively blocked FMD in cattle. However, the limited duration of protection—usually only 1-3 days post-treatment (dpt)—diminishes its utility as a field therapeutic. Here we test whether polyethylene glycosylation (PEGylation) of recombinant bovine IFNλ3 (PEGboIFNλ3) can extend the duration of IFN-induced prevention of FMDV infection in both vaccinated and unvaccinated cattle. We treated groups of heifers with PEGboIFNλ3 alone or in combination with an adenovirus-based FMD O1Manisa vaccine (Adt-O1M) at either 3 or 5 days prior to challenge with homologous wild type FMDV. We found that pre-treatment with PEGboIFNλ3 was highly effective at preventing clinical FMD when administered at either time point, with or without co-administration of Adt-O1M vaccine. PEGboIFNλ3 protein was detectable systemically for >10 days and antiviral activity for 4 days following administration. Furthermore, in combination with Adt-O1M vaccine, we observed a strong induction of FMDV-specific IFNγ+ T cell response, demonstrating its adjuvanticity when co-administered with a vaccine. Our results demonstrate the promise of this modified IFN as a pre-exposure prophylactic therapy for use in emergency outbreak scenarios.

overall_design: 112 Samples, 3 biological replicates per treatment condition and time point and two technical replicates per sample.

first: Sarah

middle: E

last: Attreed

first: Christina

last: Silva

first: Monica

last: Rodriguez-Calzada

first: Aishwarya

last: Mogulothu

first: Sophia

last: Abbott

first: Paul

last: Azzinaro

first: Peter

last: Canning

first: Lillian

last: Skidmore

first: Jay

last: Nelson

first: Nick

last: Knudsen

first: Gisselle

last: Medina

first: Teresa

last: de los Santos

last: Díaz-San Segundo


title: Cortical and hippocampal gene expression after transcranial focal stimulation and a single seizure in rats

city: CDMX

first: Iris

middle: Angélica

last: Feria

state: CDMX

address: Cuauhtemoc 330, Doctores

department: UIMEN

country: Mexico

institute: Instituto Mexicano del Seguro Social

summary:
Transcranial Electrical Stimulation has therapeutic effects on different diseases, including epilepsy. Particularly, Transcranial Focal Stimulation (TFS) has anticonvulsive and antiepileptogenic effects.
Nevertheless, the mechanisms and therapeutic targets that induced these effects remain ellusive. We aimed to screen the genetic expression in the cerebral cortex and the hippocampus of rats after a single seizure and TFS to identify potential targets.

overall_design: We analyzed 15 rat brain samples  (9 cortical and 6 hippocampal) using the Affymetrix Clariom S Rat Chip. Raw data was analyzed using Bioconductor. No technical replicated were performed.

first: Daniel

last: Perez-Perez

last: Feria-Romero

first: Walter

last: Besio

first: Luisa

last: Rocha

first: Luis

last: Bautista-Orozco

first: Sandra

last: Orozco-Suarez


title: Cortical and hippocampal gene expression after transcranial focal stimulation in healthy rats

summary:
Transcranial Electrical Stimulation has therapeutic effects on different diseases, including epilepsy. Nevertheless, previous evidence also suggest that TFS could modify protein expression in the healthy brain of rats.
We aimed to screen genetic expression in the cerebral cortex and the hippocampus of healthy rats to identify potential targets of therapeutic or adverse effects of TFS.

overall_design: We analyzed 9 rat brain samples  (3 cortical and 6 hippocampal) using the Affymetrix Clariom D Rat Chip. Raw data was analyzed using Bioconductor. No technical replicated were performed.


title: Macrophage WEE1 promotes atherosclerosis via directly phosphorylating NF-κB p65 subunit and inducing inflammatory response

city: Wenzhou

first: Guang

last: Liang

address: Chashan Street

institute: Wenzhou Medical University

summary: Background: Atherosclerosis leads high mortality, highlighting an urgent need for new therapeutic strategies. Protein kinases orchestrate multiple cellular events in atherosclerosis and may provide new therapeutic targets for atherosclerosis. Here, we identified a protein kinase, WEE1 G2 checkpoint kinase (WEE1), promoting inflammatory response in atherosclerosis.  Methods: The ApoE-/- mice without macrophage-specific WEE1 deletion (ApoE-/-WEE1f/f) and ApoE-/- mice with macrophage-specific WEE1 deletion (ApoE-/-WEE1MCKO) were generated using bone marrow transplantation. These mice and WEE1 inhibitor MK1775 were used in a high-fat diet (HFD)-induced atherosclerotic model. Human atherosclerotic tissues, mouse primary peritoneal macrophages (MPMs), 293T cells, and recombinant proteins were utilized to investigate the pathogenic role and underlying mechanisms of WEE1. Results: We identified up-regulated p-WEE1 in macrophages in atherosclerotic lesions of HFD-fed ApoE-/- mice. Transcriptome sequencing analysis indicated that WEE1 promotes oxLDL-induced inflammation in macrophages. We then demonstrated that macrophage-specific deletion or pharmacological inhibition of WEE1 attenuates atherosclerosis by reducing inflammation both in vivo and in vitro. The overexpression of wild-type WEE1 or activating-mutant WEE1, but not inactivating-mutant WEE1, exacerbates inflammation in macrophages. Mechanistically, transcriptome sequencing analysis and co-immunoprecipitation followed by quantitative proteomics analysis identified p65 as a binding protein of WEE1. We confirmed that WEE1 directly interacts with the RHD domain of p65 via kinase domain and phosphorylates p65 at S536, thereby facilitating subsequent NF-κB activation and inflammatory response in macrophages.  Conclusions: Our findings demonstrated that macrophage WEE1 promotes inflammatory atherosclerosis by directly binding to p65 and phosphorylate it at S536. This study provides WEE1 as a new p65 regulator in inflammation and a potential therapeutic target for atherosclerosis.

overall_design: Total RNA from the cells was collected using RNAiso Plus and subjected to genome-wide transcriptomic analysis using LC-Bio (Hangzhou, China).

first: Zhuqi

last: Huang


title: PEAR1 is a potential regulator of early hematopoiesis of human pluripotent stem cells

city: 天津市西青区

first: Shuo

last: Zhang

address: 西青区梅苑路12号

institute: 血液病医院

summary: Human pluripotent stem cells (hPSCs) provide a potential resource for the generation of functional blood cells in vitro. However, it remains largely unknown about the mechanism underlying hPSC-derived hematopoiesis. Here, we identified platelet endothelial aggregation receptor-1 (PEAR1) as a potential regulator of early hematopoietic development of hPSCs. We found that the expression of PEAR1 was gradually increased during endothelial and hematopoietic development. The hematopoietic potential was enriched in PEAR1+ population and PEAR1 could be used as a potential marker to enrich hemogenic endothelium. Moreover, knockout of PEAR1 impaired the hematopoietic potential of hPSCs.  Collectively, our findings demonstrate that PEAR1 is required for early hematopoiesis and can be potentially used for establishing new strategies to produce more functional blood cells from hPSCs.

overall_design: 1.We performed bulk-RNA sequencing (RNA-seq) of the PEAR1+ population and the PEAR1- population on Day5, to gain more molecular insights into the effect of PEAR1 on early hematopoietic development. 2. We performed RNA-seq analysis of the Day 5 cells differentiated from BC1-PKO or BC1, to compare the molecular changes of PEAR1 knockout in hematopoiesis

first: Kengyuan

last: Qu


title: A spatiotemporal dynamic atlas of circular RNAs unraveled extensive intraspecific and developmental variation in maize

city: WuHan

first: Qixiao

last: Jin

address: No. 1, Shizishan Street, Hongshan District, Wuhan City, Hubei Province

institute: Hua Zhong Agricultural University

summary: We assembled a complete transcriptomic landscape integrating both linear and circRNAs across 26 different tissues and stages in a classic maize hybrid triplet - B73, Mo17, and their hybrid F1.

overall_design: We performed the mRNA-seq and circRNA-seq on 26 different tissues or developmental stages of two maize inbred lines, B73 and Mo17, as well as their F1 hybrid. These large-scale datasets provided opportunities to monitor the mRNA and circRNA developmental dynamics of differential expression and regulatory variation.

first: Jia

last: Qian

first: Zi

last: Luo


title: POLB regulates proliferation and apoptosis of bovine primary myocytes

status: Public on Mar 29 2024

city: Zhengzhou

first: Geyang

state: Henan

address: 116 Huayuan Road, Jinshui District

department: Animal husbandry institute

institute: Henan Academy of Agricultural Sciences

summary: DNA polymerase β (DNA polymerase beta, POLB) belongs to a member of the DNA polymerase X family, mainly involved in various biological metabolic processes such as eukaryotic DNA replication, DNA damage repair, gene recombination and cell cycle regulation. In this study, the muscle development-related gene POLB was screened by selection signature and RNA-seq analysis, and then validated for the proliferation and apoptosis of bovine primary myocytes. It was also found that overexpression of the POLB gene had a pro-apoptosis effect, but interfering with the expression of the gene had no significant effect on cells. Then the analysis of related apoptotic genes revealed that POLB overexpression affected CASP9 gene expression.

overall_design: In order to identify candidate genes affecting muscle development of Jiaxian Red Bull by transcriptome analysis, the longissimus dorsi muscle of five Jiaxian Red cattle at 18 month of age were sequenced by RNA-seq.

first: Jiamei

last: Wang

first: Yulong

last: Li

first: Zijing

first: Xiangnan


title: Trichoderma atroviride small RNA1 targets the Arabidopsis PRIM2 gene to establish a mutualistic relationship

city: Irapuato

middle: F.

last: Garcia-Ortega

state: Guanajuato

address: Km 9.6 Libramiento Norte

department: Department of Genetic Engineering

institute: Center for Research and Advanced Studies of the National Polytechnic Institute (Cinvestav)

summary: This study investigates the multifaceted defense mechanisms of plants in response to beneficial fungi Trichoderma atroviride. The researchers focus on a small RNA, Ta_sRNA1, produced by T. atroviride during its interaction with Arabidopsis thaliana.

sample_organism:
Arabidopsis thaliana
Trichoderma atroviride

overall_design: A. thaliana roots inoculation with T. atroviride was performed and then collected from the interaction zone at 24, 48, 72, and 96 h of coculture. Total RNA was extracted and sRNA-seq libraries were generated according to the sRNA cloning protocol provided by Solexa.

first: Erya

middle: J

last: Hernández-Hernández

first: Mitzuko-Dautt

last: Castro

first: Fernanda

last: Padrón-Rodríguez

middle: F

last: García-Ortega

first: María

last: González-López

first: Magnolia

last: Estrada-Rivera

first: Saúl

last: Jijón-Moreno

first: Sergio

last: Casas-Flores


title: Next Generation Sequencing Facilitates Quantitative Analysis of U87 Transcriptomes to define the ALKBH5-dependent hypoxia-induced genes

first: xudong

last: Wu

summary: Among 720 hypoxia-induced genes (at least 2 folds of upregulation in Hypoxia-treated U87 WT or shScr cells compared with Normoxia), the expression of 35 genes is significantly suppressed by ALKBH5 depletion (U87 Hypoxia shALKBH5/shScr)

overall_design: The mRNA profiles of U87 WT-Normoxia, U87 WT-Hypoxia, U87 shScr-Hypoxia and U87 shALKBH5-Hypoxia

first: Xudong

first: Feng

last: Dong

first: Xiaoyang

last: Qin


title: Multi-omics analysis of sarcospan overexpression in mdx skeletal muscle reveals compensatory remodeling of cytoskeleton-matrix interactions that promote mechanotransduction pathways

city: Los Angeles

first: Hafsa

last: Mamsa

state: CA

address: 610 Charles E. Young Drive East

department: Integrative Biology & Physiology

institute: University of California Los Angeles

summary: Background: The dystrophin-glycoprotein complex (DGC) is a critical adhesion complex of the muscle cell membrane, providing a mechanical link between the extracellular matrix (ECM) and the cortical cytoskeleton that stabilizes the sarcolemma during repeated muscle contractions. One integral component of the DGC is the transmembrane protein, sarcospan (SSPN). Overexpression of SSPN in the skeletal muscle of mdx mice (murine model of DMD) restores muscle fiber attachment to the ECM in part through an associated increase in utrophin and integrin adhesion complexes at the cell membrane, protecting the muscle from contraction-induced injury. In this study, we utilized transcriptomic and ECM protein-optimized proteomics data sets from wild-type, mdx, and mdx transgenic (mdxTG) skeletal muscle tissues to identify pathways and proteins driving the compensatory action of SSPN overexpression.  Methods: The tibialis anterior and quadriceps muscles were isolated from wild-type, mdx, and mdxTG mice and subjected to bulk RNA-Seq and global proteomics analysis using methods to enhance capture of ECM proteins. Data sets were further analyzed through the ingenuity pathway analysis (QIAGEN) and integrative gene set enrichment to identify candidate networks, signaling pathways, and upstream regulators.  Results: Through our multi-omics approach, we identified 3 classes of differentially expressed genes and proteins in mdxTG muscle, including those that were (1) unrestored (significantly different from wild type, but not from mdx), (2) restored (significantly different from mdx, but not from wild type), and (3) compensatory (significantly different from both wild type and mdx). We identified signaling pathways that may contribute to the rescue phenotype, most notably cytoskeleton and ECM organization pathways. ECM-optimized proteomics revealed an increased abundance of collagens II, V, and XI, along with β-spectrin in mdxTG samples. Using ingenuity pathway analysis, we identified upstream regulators that are computationally predicted to drive compensatory changes, revealing a possible mechanism of SSPN rescue through a rewiring of cell-ECM bidirectional communication. We found that SSPN overexpression results in upregulation of key signaling molecules associated with regulation of cytoskeleton organization and mechanotransduction, including Yap1, Sox9, Rho, RAC, and Wnt.  Conclusions: Our findings indicate that SSPN overexpression rescues dystrophin deficiency partially through mechanotransduction signaling cascades mediated through components of the ECM and the cortical cytoskeleton.

overall_design: Expression profiling of tibialis anterior muscle from wild type (WT), mdx (DMD murine model), and mdxTG (mdx mice transgenically expressing SSPN) to determine the molecular pathways evoked by SPPN in ameilorating pathology in mdx.

first: Jackie

last: McCourt

first: Kristen

middle: M

last: Stearns-Reider

first: Rachelle

middle: H

last: Crosbie


title: Transcriptomic data of Jining gray goat ovarian and uterine tissues during sexual maturation

first: Chao

last: Tianle

summary: Ovarian and uterine tissues from five female Jining Gray goats were collected at the following time points: after birth (D1), 2-month-old (M2), 4-month-old (M4), and 6-month-old (M6). All samples were applied for rRNA-depleted RNA-seq libraries construction and transcriptome sequencing. We investigated the transcriptomic mechanisms involved in reproductive regulation in the ovary and uterus during sexual maturation.

first: Yanyan

last: Wang

first: Qing

last: Li

first: Tianle

last: Chao

first: Jianmin


title: Identification of YAP-TEAD gene signatures in metastatic melanoma

city: Cambridge

first: Charles

last: Whittaker

state: MA

institute: Koch Institute

summary: YAP1 (Yes-associated protein 1) is transcriptional co-activator that partners with the TEAD family of transcription factors to regulate gene expression. Increased YAP-TEAD activity is strongly implicated in the development, progression, and metastasis of several cancer types including melanoma, but the YAP-TEAD target genes that are responsible for YAP-TEAD-dependent melanoma progression and metastasis are largely unknown. To identify YAP-TEAD regulated genes in metastatic melanoma cells we used RNA-sequencing to compare gene expression in control A375 human melanoma cells to A375 cells expressing mutant forms of YAP with increased transcriptional activity due to the mutation of LATS inhibitory phosphorylation sites (YAPS127A or YAPS127A,S381A). To determine which YAP-dependent gene expression changes are mediated by TEADs we also included a mutant form of YAP that is unable to bind TEADS (YAPS94A,S127A).

overall_design: A375 human melanoma cells were infected with the retrovirus that delivers either a control empty vector (MSCV-IRES-Hygro) or the indicated mutants of human YAP (YAPS127A, YAPS94A,S127A, or YAPS94A,S127A,S381A). Stably transduced cells were selected with hygromycin and then cells were plated tissue culture plastic in growth media (DMEM+ 10% fetal bovine serum, 2 mM L-glutamine) at ~60% confluence. Three individual biological replicates were plated for each cell line. Twenty-four hours later, cells were lysed with TRIzol and RNA was isolated according to the manufacturer's protocol. cDNA was generated as described and used for RNA-sequencing.

first: Emily

last: Norton

first: Ryan

last: Kanai

first: Patrick

last: Stern

first: Richard

middle: O

last: Hynes

first: John

last: Lamar


title: MLKL preserves the splenic microenvironment to repress hematopoiesis during atherosclerosis

city: Ottawa

first: Katey

last: Rayner

state: ON

address: 40 Ruskin Street, Room H-4211A

country: Canada

institute: University of Ottawa Heart Institute

summary: Dysregulation of the hematopoietic niche during hyperlipidemia facilitates pathologic leukocyte production, driving atherogenesis. While definitive hematopoiesis primarily occurs in the bone marrow, during atherosclerosis this also occurs in the spleen. Cells of the bone marrow niche, in particular endothelial cells, have been studied in atherosclerosis, while little is known about how splenic endothelial cells respond to the atherogenic environment. Here we show unique dysregulated pathways in splenic compared to bone marrow endothelial cells during atherosclerosis, including perturbations of lipid metabolism and endocytic trafficking pathways. As part of this response, we identified MLKL as a repressor of splenic, but not bone marrow, myelopoiesis. Silencing MLKL in splenic endothelial cells results in inefficient endosomal trafficking and lipid accumulation, ultimately promoting the production of myeloid cells that participate in plaque development. These studies identify endocytic trafficking by MLKL as a key mechanism of splenic endothelial cell maintenance, splenic hematopoiesis, and subsequently atherosclerosis.

overall_design: RNA-Seq was performed on splenic endothelial cells derived from Apoe-knockout mice after 8 weeks of control or MLKL-targeting ASO and high cholesterol diet feeding.

first: Adil

last: Rasheed


title: NINJ2 inhibition increased chemo-sensitivity by decreasing CICs in chemotherapy-resistant gastric cancer

city: Suwon

first: Jae-Il

last: Choi

address: 164, World cup-ro, Yeongtong-gu

department: Pathology

institute: Ajou University School of Medicine

summary: One of the first-line chemotherapy regimes for gastric cancer is a combination treatment of epirubicin, cisplatin, and 5-fluorouracil (ECF). Chemoresistance remains the major obstacle to achieving successful results from gastric cancer treatment. Understanding acquired or pre-existing resistance to anticancer drugs is essential to the development of a therapeutic modality for gastric cancer. In this study, we established ECF-resistant (ECF-R) gastric cancer cell lines. We found that nerve injury–induced protein 2 (Ninjurin2, NINJ2) functioned as a biomarker for ECF-R in both gastric cancer cells. We also investigated the NINJ2 binding molecule and downstream pathway using both LC-MS/MS and phospho-antibody arrays.

overall_design: Examination of parental and ECF-resistant (ECF-R) MKN-28/74 gastric cancer cells (N=1).

last: Rim

first: Joon

last: Park

first: Beom

last: Lim

first: Hye

last: Chung

first: Jong-Baeck


title: Effects of the treatment with pegIFNa, Azacytidine or pegIFNa+Azacytidine in LT-HSCs from JAK2-V617F MPN mice or JAK2-V617F;Dnmt3a-KO MPN mice.

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel

summary: Pegylated interferon alpha (pegIFNα) can induce molecular remissions in JAK2-V617F-positive myeloproliferative neoplasms (MPN) patients by targeting long-term hematopoietic stem cells (LT-HSCs). Additional somatic mutations in genes regulating LT-HSC self-renewal, such as DNMT3A, have been reported to have poorer responses to pegIFNα. We investigated if DNMT3A loss leads to alterations in JAK2-V617F LT-HSCs functions conferring resistance to pegIFNα treatment in a mouse model of MPN and in hematopoietic progenitors from MPN patients. Long-term treatment with pegIFNα normalized blood parameters, reduced splenomegaly and JAK2-V617F-chimerism in single-mutant JAK2-V617F (VF) mice. However, pegIFNα in VF;Dnmt3aΔ/Δ (VF;DmΔ/Δ) mice worsened splenomegaly and failed to reduce JAK2-V617F-chimerism. Furthermore, LT-HSCs from VF;DmΔ/Δ mice compared to VF were less prone to accumulate DNA damage and exit dormancy upon pegIFNα treatment. RNA-sequencing showed that IFNα induced stronger upregulation of inflammatory pathways in LT-HSCs from VF;DmΔ/Δ compared to VF mice, indicating that the resistance of VF;DmΔ/Δ LT-HSC was not due to failure in IFNα signaling. Transplantations of bone marrow from pegIFNα treated VF;DmΔ/Δ mice gave rise to more aggressive disease in secondary and tertiary recipients. Liquid cultures of hematopoietic progenitors from MPN patients with JAK2-V617F and DNMT3A mutation showed increased percentages of JAK2-V617F-positive colonies upon IFNα exposure, whereas in patients with JAK2-V617F alone the percentages of JAK2-V617F-positive colonies decreased or remained unchanged. PegIFNα combined with 5-azacytidine only partially overcame resistance in VF;DmΔ/Δ mice. However, this combination strongly decreased the JAK2-mutant allele burden in mice carrying VF mutation only, showing potential to inflict substantial damage preferentially to the JAK2-mutant clone.

overall_design: A cohort of MPN mice was generated by transplanting bone marrow (BM) cells from either JAK2-V617F transgenic mice (VF) or JAK2-V617F;Dnmt3a-KO mice (VFDM) into WT mice in competition with 10-fold excess BM from WT donor mice. Once the mice developed MPN phenotype (4 weeks after transplantation), they were treated with vehicle, pegIFNa (IFN), 5-azacytidine (Aza) or the combination (COMBO) of both drugs (n=4). After 8 weeks of treatment, LT-HSCs were sorted (lin- ckit+ Sca1+ CD150+ CD48-) and RNA was extracted and sequenced.

first: Marc

last: Usart

first: Radek

last: Skoda

first: Athimed

last: El Taher


title: RNA sequencing of chronic and acute coxsackievirus B3 (CVB3) infection

status: Public on Mar 28 2024

city: Charlottesville

first: Kevin

middle: A.

last: Janes

state: VA

address: Box 800759 Health System

department: Department of Biomedical Engineering

institute: University of Virginia

summary: The goal of this study was to examine gene expression changes associated with CVB3 infection in cell culture. Induced pluripotent stem cell (iPSC)-derived cardiomyocytes and AC16 cells were used to study acute infection. AC16 cells expressing low levels of CVB3 RNA were used to study chronic infection.

overall_design:
iPSC-derived cardiomyocytes (iCell Cardiomyocytes²) were differentiated for two or four days before infection with wildype CVB3 (MOI 10 for 8 hours) or encapsidation-deficient CVB3 (VP4 A67G - MOI of 3 for 16 hours).
AC16 cells with ectopic CXADR overexpression (AC16-CAR) were infected with wildype CVB3 (MOI 10 for 8 hours) or encapsidation-deficient CVB3 (VP4 A67G - MOI of 3 for 16 hours). The uninfected AC16-CAR cell RNA-seq is in GSE155312.
AC16 cells were stably transfected with encapsidation-deficient pSLIK CVB3 (VP4 A67G) under the control of a tetracycline-inducible promoter that permits only leaky expression in the absence of tetracycline. 12 clones were then isolated.
9 of the CVB3+ AC16 clones were genetically perturbed with constitutively active MKK6 (MKK6-EE), constitutively active IKK2 (IKK2-EE), or degradation resistant IκBα (IκBα-SR) or pharmacologically perturbed using BIRB796 (p38 inhibitor).

first: Griffiths

middle: D

last: Cameron

first: Shah

last: Millie

first: Janes

middle: A

last: Kevin


title: Distinct features of the regenerating heart uncovered through comparative single-cell profiling

city: SALT LAKE CITY

first: Clayton

last: Carey

state: UT

address: 1390 President's Circle

department: Biology

institute: University of Utah

summary: Adult humans respond to heart injury by forming a permanent scar, yet other vertebrates are capable of robust and complete cardiac regeneration. Despite progress towards characterizing the mechanisms of cardiac regeneration in fish and amphibians, the large evolutionary gulf between mammals and regenerating vertebrates complicates deciphering which cellular and molecular features truly enable regeneration. To better define these features, we compared cardiac injury responses in zebrafish and medaka, two fish species that share similar heart anatomy and common teleost ancestry but differ in regenerative capability. We used single-cell transcriptional profiling to create a time-resolved comparative cell atlas of injury responses in all major cardiac cell types across both species. With this approach, we identified several key features that distinguish cardiac injury response in the non-regenerating medaka heart. By comparing immune responses to injury, we found altered cell recruitment and a distinct pro-inflammatory gene program in medaka leukocytes, and an absence of the injury-induced interferon response seen in zebrafish. In addition, we found a lack of pro-regenerative signals, including nrg1 and retinoic acid, from medaka endothelial and epicardial cells. Finally, we identified alterations in the myocardial structure in medaka, where they lack primordial layer cardiomyocytes and fail to employ a cardioprotective gene program shared by regenerating vertebrates. Our findings reveal notable variation in injury response across nearly all major cardiac cell types in zebrafish and medaka, demonstrating how evolutionary divergence influences the hidden cellular features underpinning regenerative potential in these seemingly similar vertebrates.

sample_organism:
Danio rerio
Oryzias latipes

platform_organism:
Danio rerio
Oryzias latipes

overall_design: scRNA-seq of dissected ventricles from zebrafish and medaka fish before injury, 3 days, and 14 days post-injury

first: Hailey

middle: L

last: Hollins

first: Alexis

middle: V

last: Schmid

first: James

last: Gagnon


title: IL-17C is a driver of damaging inflammation duringNeisseria gonorrhoeaeinfection of human Fallopian tube

city: Madison

first: Joseph

last: Dillard

state: WI

institute: University of Wisconsin-Madison

summary: The human-restricted pathogenNeisseria gonorrhoeaeascends into the upper female reproductive tract to cause damaging inflammation within the Fallopian tubes (salpingitis) and pelvic inflammatory disease (PID), increasing the risk of infertility and life-threatening ectopic pregnancy. The loss of ciliated cells from the epithelium is thought to be both a consequence of inflammation and a cause of the associated adverse sequelae. However, the links between infection, inflammation, and ciliated cell extrusion remain unresolved. With the use ofex vivocultures of human Fallopian tube paired with RNA sequencing we defined the tissue response to gonococcal challenge, identifying cytokine, chemokine, cell adhesion, and apoptosis related transcripts not previously recognized as potentiators of gonococcal PID. Unexpectedly, the cytokine IL-17C was one of the most highly induced genes. Yet, this cytokine has no previous association with gonococcal disease nor any sexually transmitted infection and thus it was selected for further characterization in our model. We show that human Fallopian tubes express the IL-17C receptor (IL-17RE) on the epithelial surface and that treatment with purified IL-17C induces pro-inflammatory cytokine secretion in addition to sloughing of the epithelium and generalized tissue damage. These results demonstrate a previously unrecognized but critical role of IL-17C in the damaging inflammation induced by gonococci in a human explant model of PID.

overall_design: We performed gene expression profiling analysis using data obtained from RNA-seq of 4 different donor tissues for each treatment (mock, WT Neisseria gonorrhoeae supernatant, and ldcA mutant supernatant) and time point (6 and 24 hours)

first: Erin

last: Garcia

first: Jonathan

last: Lenz

first: Ryan

last: Schaub

first: Kathleen

middle: T

last: Hackett

first: Wilmara

last: Salgado-Pabón

middle: P


title: Esophageal Squamous Cell Carcinoma tumors from Indian patients: nuclear-stabilized p53 (NS+) versus unstable p53 (NS-) protein

city: Hyderabad

first: Murali

middle: Dharan

last: Bashyam

address: Inner ring road, Uppal

institute: Centre for DNA Fingerprinting and Diagnostics

summary: Transcriptional profiling of Esophageal Squamous Cell Carcinoma (ESCC) tumors comparing samples harbouring nuclear-stabilized p53 (NS+) versus unstable p53 (NS-) protein, determined through immunohistochemistry (IHC) staining of the tumor sections. The goal was to identify the genes that were differentially regulated between NS+ and NS- ESCC samples.

overall_design: Two-condition experiment, NS+ versus NS- esophageal tumors. NS+ tumors: 17, NS- tumors: 19.

first: Sara

last: George


title: Spatial transcriptomics of brains from tumor-bearing C57BL/6 mice

city: Salamanca

first: Arantxa

last: Tabernero

address: Pintor Fernando Gallego 1

department: INCyL

country: Spain

institute: Universidad de Salamanca

summary: GL261-derived glioblastoma stem cells (GSCs) form aggressive tumors when implanted into the brains of C57BL/6 mice. We used spatial transcriptomics to analyze brain sections of tumor-bearing C57BL/6 mice at 28 days post-implantation

overall_design: GL261-GSCs were intracranially implanted into C57BL/6 mice and sagittal sections of the brains were taken 28 days post-implantation.

first: Laura

last: García-Vicente

first: Neff

last: Norma


title: Single-nucleus RNA-sequencing (snRNA-Seq) of brain cells from tumor-bearing C57BL/6 mice

summary: GL261-derived glioblastoma stem cells (GSCs) form aggressive tumors when implanted into the brains of C57BL/6 mice. We used snRNA-Seq to analyze GL261 and GL261-GSCs as well as tumor samples of 7 and 28 days of development.

overall_design: Samples containing tumor cells and surrounding tissue were taken and analyzed using snRNA-Seq

first: Norma

last: Neff


title: Single-cell RNA-sequencing (scRNA-Seq) of GL261 and GL261-GSCs

summary: GL261 cells are one of the most common mouse glioblastoma cells used for in vivo studies in a immunocompetent model. We analyze GL261 and stem cells derived from them (GL261-GSCs) using scRNA-Seq.

overall_design: GL261 cells and GSCs derived from them were analyzed using scRNA-Seq


title: Nucleotide metabolism in cancer cells fuels a UDP-driven macrophage cross-talk promoting immunosuppression and immunotherapy resistance [RNAseq_Panc02_sgNT_sgCda_invitro]

city: Leuven

first: Sandrine

last: Da Cruz

state: Flemish Brabant

address: ON 5 Herestraat 49

department: KU Leuven Department of Neurosciences

country: Belgium

institute: VIB-KU Leuven Center for Brain and Disease Research

summary:
Purpose: To study the effects of CDA depletion on PancO2 cell line. Here, we used RNA sequencing to understand if sgCda can alter cancer cell immunogenicity by looking at mutational burden.
Methods: PancO2  cancer cells were transduced with a doxycycline-inducible Cas9 nuclease (Edit-R Inducible Lentiviral Cas9, Dharmacom) and selected with blasticidin (Bio-Connect). Cells expressing the doxycycline-inducible Cas9 nuclease were transduced with a target specific gRNA for CDA and a control non-targeting NT gRNA, and selected with puromycin (Sigma-Aldrich). After selection, cells were treated for seven days with or without doxycycline (2.5ug/mL, Sigma-Aldrich) to induce Cas9 expression and grown for seven more days without doxycycline before being used. Then RNA was isolated using TRIzol (Life Technologies). Starting from total RNA, poly-adenylated fragments were isolated, reverse transcribed and converted into indexed sequencing libraries using the KAPA stranded mRNA-seq kit (Sopachem, Eke, Belgium). The first 50 bases of these libraries were sequenced on a HiSeq 2500 system (Illumina, San Diego, CA). These raw reads were mapped after removal of the sequencing adapters to the reference transcriptome and genome (GRCm38/mm10) using the Bowtie TopHat pipeline (Langmead and Salzberg, 2012). Mapped reads were assigned to ensemble gene IDs by HTSeq. Variants were identified following GATK's best practice and only variants unique in one sample were retained.
Results. Mapped reads were on average 35,159,030 ± 6,605,340 assigned counts per sample and 1,132 ± 266 mutations.

overall_design:
CDA manipulation in PancO2 cancer cells did not alter their immunogenicity. No differences in mutational burden were observed between sgNT and sgCda PancO2 cell line.
5x5 design in C57BL/6J mice with tumor tissue RNA sequencing conducted

first: Massimiliano

last: Mazzone


title: Nucleotide metabolism in cancer cells fuels a UDP-driven macrophage cross-talk promoting immunosuppression and immunotherapy resistance [RNAseq_meta_analysis]

summary:
The project aims to identify metabolic genes and pathways associated with immunotherapy resistance.
Methods: 4x10e6 Panc02, 1x10e6 MC38 or 2x10e6 CT26 cells were injected subcutaneously (s.c.) in the right flank of the mouse in a final suspension of 200μl PBS. Tumor volumes were measured at least three times per week. At the indicated time points, mice were randomized and treated intraperitoneally (i.p.) with 10 mg/kg α-PD-1 (BioXcell) or α-CTLA4 or control IgG from rat serum (Sigma-Aldrich). At end-stage, tumor-bearing mice were sacrificed by cervical dislocation and RNA was isolated from tumor tissue using TRIzol (Life Technologies). Starting from total RNA, poly-adenylated fragments were isolated, reverse transcribed and converted into indexed sequencing libraries using the Illumina TruSeq RNA sample preparation kit V2 according to the manufacturer’s instructions. The first 50 bases of these libraries were sequenced on a HiSeq 2500 system (Illumina, San Diego, CA). Raw sequencing reads were mapped to the transcriptome and the mouse reference genome (GRCm38/mm10) using TopHat 2.0 and Bowtie2.0 (Langmead and Salzberg, 2012). Mapped reads were assigned to ensemble gene IDs with the HTSeq software package.
Transcriptome profiling was performed in three different murine cancer models (MC38, CT26 and panc02) treated with PD-1, CTLA-4 or vehicle
Our bulk tumor transcriptomic profiles of responsive (MC38), low responsive (CT26) and non-responsive (PancO2) murine tumor models were integrated with publicly available pretreatment transcriptomic datasets of patients responding and resistant to immune checkpoint inhibitors, such as α-CTLA-4 and α-PD-1 (Van Allen- et al., Science 2015; Hugo et al., Cell 2016; Ascierto et al., Cancer Imm Research 2016). All these datasets were interpreted by using our in-house BIOMEX platform (Goveia et al., EMBO Mol Med 2016), which focuses on metabolic profiles. Metabolic genes were ranked, prioritizing the most consistently upregulated genes associated with resistance to immuno checkpoint inhibitors (ICIs).

overall_design: Bulk tumor transcriptomic profile data from PancO2, MC38 and CT26 murine tumor models after α-PD-1, α-CTLA4 or vehicle treatment.


title: Nucleotide metabolism in cancer cells fuels a UDP-driven macrophage cross-talk promoting immunosuppression and immunotherapy resistance

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

overall_design: Refer to individual Series


title: Three-Dimensional Matrix Stiffness Modulates Mechanosensitive and Phenotypic Alterations in Oral Squamous Cell Carcinoma Spheroids

city: Cincinnati

first: Claire

last: Chougnet

state: OH

address: 240 Albert Sabin Way

department: Immunobiology

institute: Cincinnati Children's Hospital Medical Center

summary: Extracellular biophysical cues such as matrix stiffness are key stimuli tuning cell fate and affecting tumor progression in vivo. However, it remains unclear how spheroids in a 3D microenvironment perceive matrix mechanical stiffness stimuli and translate them into intracellular signals driving cancer. Mechanosensitive Piezo1 and TRPV4 ion channels, upregulated in many malignancies, are major transducers of such physical stimuli into biochemical responses. Most mechanotransduction studies probing the reception of changing stiffness cues by cells are, however, still limited to 2D culture systems or cell-extracellular matrix models which lack the major cell-cell interactions prevalent in 3D cancer tumors. Here, we engineered a 3D spheroid culture environment with varying mechanobiological properties to study the effect of static matrix stiffness stimuli on mechanosensitive and malignant phenotypes in oral squamous cell carcinoma spheroids. We find that spheroid growth is enhanced when cultured in stiff extracellular matrix. Using flow cytometry, we show that the expression of mechanoreceptor Piezo1 and stemness marker CD44 is upregulated in stiff matrix. We also report the upregulation of a selection of genes with associations to mechanoreception, ion channel transport, extracellular matrix organization, and tumorigenic phenotypes in stiff matrix spheroids. Together, our results indicate that cancer cells in 3D spheroids utilize mechanosensitive ion channels Piezo1 and TRPV4 to sense changes in static extracellular matrix stiffness and that stiffness drives pro-tumorigenic phenotypes in oral squamous cell carcinoma.

overall_design: Cal27 spheroids were cultured in soft (3 mg/mL Matrigel) and stiff (12 mg/mL Matrigel) using the liquid overlay technique. Spheroids cultured in both conditions were harvested on day 14 and total RNA was isolated and sequenced.

first: Maulee

last: Sheth

first: Manju

last: Sharma

first: Leyla

last: Esfandiari


title: Nucleotide metabolism in cancer cells fuels a UDP-driven macrophage cross-talk promoting immunosuppression and immunotherapy resistance [RNAseq_Panc02_sgNT_sgCda_tumor]

summary:
Purpose: Here we use Here, we used RNA sequencing to identify trascriptictomic profile of sgNT and sgCda PancO2 tumor bearing-mice.
Methods: 4x10e6 sgNT and sgCda Panc02 cells were injected subcutaneously (s.c.) in the right flank of the C57BL/6J mouse in a final suspension of 200 μL PBS. Tumor volumes were measured at least three times per week. At day 16 after injection, tumor-bearing mice were sacrificed by cervical dislocation and RNA was isolated from tumor tissue using TRIzol (Life Technologies). Starting from total RNA, poly-adenylated fragments were isolated, reverse transcribed and converted into indexed sequencing libraries using the KAPA stranded mRNA-seq kit (Sopachem, Eke, Belgium). The first 50 bases of these libraries were sequenced on a HiSeq 4000 system (Illumina, San Diego, CA). These raw reads were mapped after removal of the sequencing adapters to the reference transcriptome and genome (GRCm38/mm10) using the Bowtie 2.0 and TopHat 2.0 pipeline (Langmead and Salzberg, 2012).

overall_design:
Transcriptome profiling was performed in sgNT and sgCda Panc02 tumor murine models.
5x5 design in C57BL/6J mice with tumor tissue RNA sequencing conducted


title: BAI1 localises AMPA receptors at the cochlear afferent postsynaptic density and is

status: Public on Mar 27 2024

city: Paris

first: Fiorella

last: Grandi

address: 105 Bld d'Hopital

department: Centre de Recherche de Myologie

country: France

institute: Sorbonne Universite

summary: Type I spiral ganglion neurons (SGNs) convey sound information to the central auditory pathway by forming axo-somatic synapses with inner hair cells (IHCs), the primary sensory receptors of the mammalian cochlea. Although IHC ribbon synapses have been extensively studied, the molecular mechanisms regulating the structure and function of the post-synaptic density (PSD) at the SGN afferent terminals are largely unknown. Using functional, morphological, and transcriptomic approaches, we demonstrate that brain-specific angiogenesis inhibitor 1 (BAI1), encoded by the Adgrb1 gene, is required for the clustering of the glutamate AMPA receptors GluR2-4 to the SGN post-synaptic density. Adult mice expressing BAI1 lacking the N-terminal thrombospondin type 1 repeats (TRS) have functional IHC synapses but fail to transmit acoustic information to the SGNs, leading to highly raised auditory thresholds. We also found that in adult Bai1-deficient mice, despite the almost complete absence of AMPA receptors, the SGN fibres innervating the IHCs did not degenerate. RNA sequencing and western blotting also indicate that AMPA receptors are expressed in the cochlea of Bai1-deficient mice, highlights that BAI1 is involved is trafficking or anchoring GluR2-4 to the PSDs. Moreover, these results have identified novel molecular and functional mechanisms required for sound encoding at cochlear ribbon synapses.

overall_design: The sensory epithelium and spiral ganglion neurons from 4 mice were micro dissected in DNase free ice-cold PBS 1X and immediately snap frozen in liquid nitrogen. Two batches of 3 and 4 replicates (P7) and one batch of 3 replicates (P22) from each genotype.

first: Adam

last: Carlton

first: Jing-Yi

last: Jeng

first: Walter

last: Marcotti


title: High-throughout sequencing of triple negative breast cancer cells treated with Lespedeza bicolor root

city: Wenzhou

first: Kejie

last: Chen

state: Zhejiang

address: Chashan

institute: Wenzhou Medical University

summary: The high-throughput sequencing technology was performed after the treatment of human triple negative breast cancer cells MDA-MB-231 and BT549 with Lespedeza bicolor root extracted by ourselves, to explore the expression of genes related to cell proliferation, adhesion, migration and invasion of human triple negative breast cancer cells MDA-MB-231 and BT549 after the treatment of Lespedeza bicolor root changes, and to find an interesting target gene.

overall_design: Human triple negative breast cancer cells MDA-MB-231 and BT549 were treated with Lespedeza bicolor root at the concentration of 5 µg/mL for 48 hours.

first: Namki

last: Cho

first: Zijun

last: Li


title: Chemically induced expansion of type 2 alveolar epithelial cell  promotes regenerative lower airway repair

city: Hangzhou

first: Sida

last: Shao

address: 18 Shilongshan Rd, Xihu District

institute: Westlake University

summary: To evaluate the effect of DPP4 inhibitor on regenerative repair of the lung upon injury, we carried out a single cell RNA sequencing study. In this study, orally administered sitagliptin was tested in LPS-induced lung injury model, followed by longitudinal single cell transcriptomic analysis with lung cells harvested at indicated time points.

overall_design: We evaluated the effects of DPP4 inhibitors on AEC2 expansion by RNA sequencing and single cell RNA sequencing methods. An RNA sequencing experiment was performed to characterize the human small airway epithelial cells. Then we compared the transcriptomes of human small airway epithelial cells treated with DMSO, IGF1, sitagliptin, saxagliptin, NVP-728 and TGFβ1. To gain further insights into the effects of DPP4 inhibitor on lung damage repair, orally administered sitagliptin was tested in LPS-induced lung injury model, followed by longitudinal single cell transcriptomic analysis with lung cells harvested at indicated time points.

last: Zhang

first: Gregory

last: Specht

first: Shaochen

last: You

first: Shuangwei

first: Van

last: Nguyen-Tran

first: Sean

middle: B

last: Joesph

first: Arnab

middle: K

last: Chatterjee

first: Jeffrey

first: Peter

middle: G

last: Schultz

first: Michael

last: Bollong


first: Arantxa

last: Tabernero

summary: GL261 cells are one of the most common mouse glioblastoma cells used for in vivo studies in a immunocompetent model.

first: Laura

last: García-Vicente

first: Neff

last: Norma