title: Impact of different anticoagulants in obtaining reference profiles of exRNAs in healthy individuals (3)

status: Public on Jun 30 2023

city: Houston

first: exRNA

last: BRL

state: TX

address: One Baylor Plaza

department: Molecular & Human Genetics - Milosavljevic

country: USA

institute: Baylor College of Medicine

summary: Impact of different anticoagulants on profiles of exRNAs in healthy individuals

overall_design: "The study aimed to investigate the buosa indintriduced by the anticoagulant used in blood collextion in the expression levels of circulating miRNAs.  Eighty samples from 20 subjects, were colledced using 3 anticoagulant (C-Citrate, E-EDTA, H-Heparin) were used for each subject. As control we also used serum. Blodd was centrifuged at 500xg, 2500xg and 12,500xg for 20 mins, and the miRNA expression level from the resulting cell-free plasma was quantified by RT-PCR using TaqMan array microRNA kit (Platform GPL17853).

first: Ionita

last: Ghiran


title: A Novel Method for Visualizing In-Vivo Rates of Protein Degradation Provides Insight into how TRIM28 Regulates Muscle Size

city: Madison

first: Troy

middle: A

last: Hornberger

address: 2015 Linden Drive

institute: University of Wisconsin - Madison

type: Expression profiling by high throughput sequencing

summary: Skeletal muscle size is controlled by the balance between protein synthesis and protein degradation. Given the essential role of skeletal muscle in maintaining a high quality of life, understanding the mechanisms that modulate this balance are of critical importance. Previously, we demonstrated that muscle-specific knockout of TRIM28 reduces muscle size and function, and in the current study, we discovered that this effect is associated with an increase in protein degradation and a dramatic reduction in the expression of Mettl21c. Importantly, we also determined that overexpression of Mettl21c is sufficient to induce hypertrophy in both control TRIM28 knockout muscles. Moreover, we developed a simple pulse-chase biorthogonal non-canonical amino acid tagging technique that enabled us to visualize the in-vivo rate of protein degradation, and with this technique were able to conclude that the hypertrophic effect of Mettl21c is due, at least in part, to an inhibition of protein degradation.

overall_design:
RNA-seq of mouse plantaris muscles. Four replicates each of:
Wild Type Sham
TRIM28 mKO Sham
Wild Type MTE
TRIM28 mKO MTE


title: Inferring co-expression networks of Arabidopsis thaliana genes during their interaction with Trichoderma spp.

city: SAN LUIS POTOSI

first: Cesaré

last: Ovando-Vázquez

state: SAN LUIS POTOSI

address: Camino a la Presa de San José 2055. Lomas 4 sección

department: CNS

country: Mexico

institute: CONACyT IPICyT

summary: Tricoderma genus fungi are referred to as "biostimulants" because they promote plant development and provide disease resistance. In this study, utilizing a conventional transcriptome analysis and gene co-expression network analysis after conventionally stimulating Arabidopsis thaliana with Trichoderma atroviride or Trichoderma virens. We found by differential expression and functional enrichment analyses that the transcriptome analysis of the plant during interactions, T. atroviride and T. virens, were involved in the reduction of reactive oxygen species, defense mechanisms against pathogens, and hormone signaling pathways. T. virens, as opposed to T. atroviride, was more effective at downregulating genes related to terpenoid metabolism, root development, and chemical homeostasis. We were able to find functional gene modules through network analysis that closely link plant defense mechanisms with hypoxia mechanisms.   We discovered a transcription factor (locus AT2G47520) with two functional domains of interest: a DNA-binding domain and an N-terminal cysteine needed for protein stability under hypoxia. We discovered that the transcription factor can bind to the promoter sequence of the GCC-box gene that is connected to pathogenesis by positioned weight matrix analysis.

overall_design: Analysis of differential expression of Arabidopsis thaliana genes during its interaction with trichoderma. We used network analysis to investigate how the plant genes associated to respond to its colonization by trichoderma  samples of biological material were collected at 48, 72 and 96 hours after co-culture

first: Javier-David

last: Vega-Arroy

first: Alfredo

last: Herrera-Estrella

first: Sergio

last: Casas-Flores


title: Phase II Clinical Trial of Nab-Paclitaxel (NAB)Plus Cisplatin (PLA) Plus Gemcitabine (GEM) (NABPLAGEM) in Patients with Untreated Advanced Pancreatic Cancer.

city: Scottsdale

first: Michael

middle: Thomas

last: Barrett

state: AZ

address: 13400 East Shea Boulevard

department: Molecular Pharmacology and Experimental Therapeutics

institute: Mayo Clinic Arizona

summary: We applied DNA content flow cytometry to pancreatic ductal adenocarcinoma (PDAC) biopsies. We interrogated purified sorted tumor fractions with whole genome copy number variant (CNV) and next generation sequencing (NGS) analyses. These identified a variety of somatic genomic lesions targeting  genes and cellular pathways in PDAC. Of significant interest are lesions that may affect responses to therapies.

overall_design: We applied DNA content based flow sorting to isolate the nuclei of clonal populations from pancreas ductal adenocarcinoma (PDAC) tumor samples. We coupled this strategy with oligonucleotide array CGH (aCGH) and whole genome sequencing thereby obtaining high definition genomic profiles of clonal populations from each tumor.

first: Gayle

middle: S

last: Jameson

first: Peter

middle: J

last: Hosein

first: Erin

last: Pierce

first: Mandana

last: Kamgar

last: Gordon

first: Courtney

last: Snyder

first: Denise

last: Roe

first: Betsy

last: Wertheim

first: Marina

last: Davey

middle: T

first: Daniel

middle: D

last: Von Hoff

first: Erkut

last: Borazanci


title: Impact of circadian rhythm in obtaining reference profiles of exRNAs in healthy individuals (3)

first: exRNA

last: BRL

summary: Impact of circadian rhythm on profiles of exRNAs in healthy individuals

overall_design: " The goal of the project was to investigate the changes in the concetration of the circulating miRNAs during the timeof day (diurnal cycles). Blood from 16 donors was collected in the morning (8:30 am), afternoon (2:30 pm) and evening (70:30 pm). Blodd was centrifuged at 500xg, 2500xg and 12,500xg for 20 mins, and the concetration from the resulting cell-free plasma was quantified by RT-PCR using TaqMan array microRNA kit (Platform GPL17853).

first: Ionita

last: Ghiran


title: A handful of hybrid EMT cells are characterized as the origin from lung adenocarcinoma

city: Xi'an

first: Yang

last: Zhao

state: Shaanxi

address: No.157, fifth west road

department: Oncology

country: China

institute: Second affiliated hospital of Xi'an Jiaotong University

summary: EMT process resulted into tumor heterogeneity in lung adenocarcinoma.

overall_design: Through sing-cell sequencing, RNA-Mutect technique and spatial transcriptomics, a handful of hybrid EMT cells are characterized as the origin from lung adenocarcinoma


title: RNA-seq of Recombinant Mouse Cold-inducible RNA-binding protein(rmCIRP)-treated Naïve CD4+ T cells

city: Nanjing

first: Zongsheng

last: Wu

state: Jiangsu

address: No.87 Dingjiaqiao Road

department: Department of Critical Care Medicine,

institute: Jiangsu Provincial Key Laboratory of Critical Care Medicine,  Zhongda Hospital, School of Medicine, Southeast University

summary: Cold-inducible RNA-binding protein (CIRP) is a ubiquitous intracellular RNA chaperon, which serves as a damage-associated molecular pattern (DAMP) when released outside the cells upon stimulation by inflammation and infection. It has been shown that CIRP promotes splenic CD4+ and CD8+ T-cell activation in vivo and predisposes CD4+ T cells to a Th1 hyperinflammatory response profile in vitro. However, the effect and underlying mechanisms of CIRP on Th17/Treg differentiation is still unclear. This study reveals the transcriptomic changes of mouse Naïve CD4+ T cells induced by Recombinant Mouse CIRP (rmCIRP) in vitro.

overall_design: Mouse Naïve CD4+ T cells activated by plate-bound anti-CD3 (2 µg/ml) and anti-CD28(1 µg/ml). Then, Naïve CD4+ T cells were cultured in the presence of rmCIRP（1μg/ml）or equal volume PBS. Each group contained 3 replicates. After 24h, cells were collected, and subjected to RNA-seq.

first: Xu

last: Liu

first: Haibo

last: Qiu


title: Effect of C13 MOK-inhibitor on LPS-induced responses in primary microglial cells

city: Seville

first: Cintia

last: Roodveldt

address: CABIMER-Av. Americo Vespucio 24, Cartuja 93

country: Spain

institute: University of Seville

summary: To investigate the possible impact of MOK in microglial immune responses, we tested the effect of MOK-inhibition with the chemical compound C13, in LPS-stimulated microglial cells.

overall_design: Primary microglial cells from newborn mice were cultured and pre-treated with 10 uM AG2P145D/C13 (Garske et al., PNAS 2011; doi: 10.1073/pnas.1111239108) or DMSO (vehicle) for 1 h, and then stimulated with LPS (1 ug/ml) for 5h.

first: Jaime

middle: M

last: Franco

first: María

last: Gómez-Lima


title: Programmable envelopved delivery vehicels for human genome engineering in vivo

city: Berkeley

first: Marena

middle: Isabelle

last: Trinidad

state: CA

address: 2151 Berkeley Way

institute: Innovative Genomics Institute

summary: Viruses and virally-derived particles have the intrinsic capacity to deliver molecules to cells, but the difficulty of readily altering cell-type selectivity has hindered their use for therapeutic delivery. Here we show that cell surface marker recognition by antibody fragments displayed on membrane-derived particles encapsulating CRISPR-Cas9 protein and guide RNA can target genome editing tools to specific cells. These Cas9-packaging enveloped delivery vehicles (Cas9-EDVs), programmed with different displayed antibody fragments, confer genome editing in target cells over bystander cells in mixed cell populations both ex vivo and in vivo. This strategy enabled the generation of genome-edited chimeric antigen receptor (CAR) T cells in humanized mice, establishing a new programmable delivery modality with the potential for widespread therapeutic utility.

overall_design: RNA-seq-based T cell receptor repertoire analysis of primary human T cells isolated from humanized mice treated with Cas9-EDVs or lentivirus

first: Jennifer

middle: R

last: Hamilton

first: Evelyn

last: Chen

first: Barbara

last: Perez

first: Cindy

last: Sandoval Espinoza

first: Min

middle: H

last: Kang

first: Wayne

last: Ngo

last: Doudna


title: Effect of MOK in LPS-induced responses in microglial cells

summary: To investigate the possible impact of MOK in microglial immune responses, we tested the effect of LPS treatment in MOK-KO (H14) vs. WT SIM-A9 cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for MOK-KO (H14) or WT SIM-A9 cells in culture after LPS-treatment for 5h.

first: David

last: Pozo


title: Human stem cell-derived cardiomyocytes integrate into the heart of monkeys with surgically-created congenital-like cardiac defect

city: ROCHESTER

first: William

last: Sherman

state: MN

address: 200 1st St SW

department: Quantitative Health Sciences

institute: Mayo Clinic

summary: To investigate the transplantation of human induced pluripotent stem cell-derived cardiac lineage-cells into the heart of rhesus macaques with a surgical model of right ventricular pressure overload.

overall_design:
We study gene expression profiling of hiPSCs reprogrammed from human fibroblast cells and hiPSCs stem cell-derived cardiomyocytes
Comparative gene expression profiling analysis of bulk RNA-seq data for human induced pluripotent stem cell-derived cardiac lineage-cells

first: Minhwang

last: Chang

first: Frank

last: Secreto


title: Chromatin remodeling events associated with gARID are essential for gametocyte development in Plasmodium [RNA-seq]

city: tsu

first: masao

last: yuda

state: mie

address: edobashi 2-174

country: Japan

institute: mie university

summary: Plasmodium berghei transcriptomes of wild-type ANKA (WT) and garid knockout parasites [garid(-)] were analyzed at the gametocyte stage.

overall_design: WT and garid(-) were harvested after sulfadiazine treatment, and total RNA was extracted from the parasites. Libraries were constructed from the total RNA and then sequenced by the Next Generation Sequencing.

first: Tsubasa

last: Nishi

first: Izumi

last: Kaneko

first: Shiroh

last: Iwanaga

first: Masao

last: Yuda


title: Bisulfite-free base-resolution sequencing of oxidized cytosines (APOBEC-seq) reveals a ubiquitous role of thymine DNA glycosylase in active gene promoters and an interaction with MBD3/NuRD

city: Montreal

first: Moshe

last: Szyf

state: QC Quebec

address: 3655 Promenade Sir William Osler, Room 1309

department: Pharmacology & Therapeutics

country: Canada

institute: McGill University

type: Methylation profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: NanoDam Profiling of EGL-43 in the Anchor Cell

city: Stanford

first: Callista

last: Yee

state: California

address: 327 Campus Drive, Shen lab, Bass Biology 329

institute: Stanford University/HHMI

summary: Depending on the cellular context, TF expression can vary dramatically both spatially and temporally. These differences in expression patterns can result in tissue-specific differences in TF binding to downstream targets. To identify targets on a tissue-specific basis, Targeted DamID (TaDa) has been recently introduced to generate TF binding profiles in various models including C. elegans. However, TaDa suffers from portability such that a new promoter-TF fusion transgene must be constructed for every new experimental condition of interest. Here, we adapt NanoDam for usage in C. elegans, which relies on the use of endogenous TF-GFP knock-ins, a plethora of which have already been generated by the community. We report that NanoDam single copy transgenes consisting of lowly expressed, tissue-specific GFP nanobody-Dam fusions, when combined with endogenous GFP-tagged alleles of TFs, results in robust, tissue-specific profiling. Using an endogenous GFP-tagged allele of EGL-43/EVI1, we performed NanoDam profiling of two disparate tissue types, the anchor cell (AC) and dopaminergic neurons, and identify targets unique to each and shared by both cell types. We also identify two GATA TFs, ELT-6 and EGL-18, as novel regulators of AC invasion. Taken together, we demonstrate that NanoDam is capable of profiling endogenous GFP-tagged TFs to identify novel downstream targets in specific cell types of C. elegans.

overall_design: A single copy insertion of an Anchor Cell promoter driving expression of a GFP nanobody fused to Dam methylase was crossed together with animals carrying endogenous EGL-43::GFP. Dam methylase permanently methylated DNA in close proximity to regions of TF binding. DNA from L3 worms was extracted, digested with DpnI, amplified, and sequenced using the MinION Nanopore platform

first: Kang

last: Shen


title: SLAM-Seq analysis of early transcriptional changes by C13 MOK-inhibitor in microglial cells exposed to TDP-43-aggregates

city: Cambridge

first: Lajos

last: Kalmar

address: Tennis Court Road

country: United Kingdom

institute: MRC Toxicology Unit, University of cambridge

summary: To investigate the possible impact of MOK-inhibition in early transcriptional responses induced by TDP-43 aggregates, we tested the effect of AG2P145D/C13-pretreatment of SIM-A9 cells and subsequent exposure to TDP-43 (or sham) aggregates.

overall_design: Comparative transcriptional analysis of (nascent chain) SLAM-Seq data for SIM-A9 cells in culture treated with polymixin B for 1 h and then either with 10 uM AG2P145D/C13 (Garske et al., PNAS 2011; doi: 10.1073/pnas.1111239108)  or DMSO  for 1h. Subsequently, TDP-43- or sham-aggregates were added to 5 ug/mL final concentration (2.5 h), followed by addition of 4-thiouridine (S4U) to 100 uM final concentration and further incubation for a further 90 min.

first: Cintia

last: Roodveldt

first: Xin

middle: W

last: Yap

first: Ritwick

last: Sawarkar


title: CBF-beta mitigates PI3K-alpha specific inhibitor killing through PIM1 in PIK3CA mutant gastric cancer

city: Durham

first: Micah

last: Luftig

state: North Carolina

address: 213 Research Dr, 0045 CARL

institute: Duke University

summary: PIK3CA is the second most mutated gene in cancer leading to aberrant PI3K/AKT/mTOR signaling and increased translation, proliferation, and survival. Some 4-25% of gastric cancers display activating PIK3CA mutations including 80% of EBV-associated GCs. Small molecules including pan-PI3K and dual PI3K/mTOR inhibitors have shown moderate success clinically, due to broad on-target/off-tissue effects. Thus, isoform specific and mutant selective inhibitors have been of significant interest. However, drug resistance is a problem and has affected success of new drugs. There has been a concerted effort to define mechanisms of resistance and identify potent combinations in many tumor types, though gastric cancer is comparatively understudied. In this study we identified modulators of the response to the PI3Ka-specific inhibitor, BYL719, in PIK3CA mutant GCs. We found that loss of NEDD9 or inhibition of BCL-XL conferred hyper-sensitivity to BYL719, through increased cell cycle arrest and cell death, respectively. Additionally, we discovered that loss of CBFB conferred resistance to BYL719. CBFB loss led to up-regulation of the protein kinase PIM1, which can phosphorylate and activate several overlapping downstream substrates as AKT thereby maintaining pathway activity in the presence of PI3Ka inhibition. The addition of a pan-PIM inhibitor re-sensitized resistant cells to BYL719. Our data provide clear mechanistic insights into PI3Ka inhibitor response in PIK3CA mutant gastric tumors and can inform future work as mutant selective inhibitors are in development for diverse tumor types.

overall_design: To determine the mechanism of PI3Ka inhibitor resistance in PIK3CA mutant gastric cancer cells, we generated AGS cell lines with developed resistance to BYL719. We additionally generated AGS cells with genetic knockout of CBFB. We then performed gene expression profiling analysis using data obtained from RNA-seq of WT, CBFB KO, and BYL719-resistant cell lines basally and following 24 hour acute treatment with 1 uM BYL719.

first: Lyla

last: Stanland


title: Cellular Indexing of Transcriptomes and epitopes sequencing (CITE-seq) analysis to investigate the impact of granulocyte-colony stimulating factor on CRISPR/Cas9 gene edited human hematopoietic stem cell function

city: Bethesda

first: Daisuke

last: Araki

state: MD

address: 9000 Rockville Pike

institute: National Institutes of Health

summary: Our research has demonstrated that G-CSF impedes engraftment of CRISPR-Cas9 gene edited human hematopoietic stem cells (HSCs) by exacerbating p53-mediated DNA damage response. Results in this study suggest that the potential for G-CSF to exacerbate HSC toxicity mediated by DNA-damaging nucleases should be considered in autologous HSC gene therapy clinical trials.

overall_design: Human CD34+ cells edited with Cas9 alone (Cas9 group), Cas9+AAVS1-targeting gRNA (RNP group), or Cas9+AAVS1-targeting gRNA+GSE56 (RNP/GSE56 group) were transplanted into busulfan-conditioned NSG mice, and these mice subsequently received 3 days of PBS or G-CSF. Then, each mouse was euthanized and harvested for bone marrow cells and human CD34+cells were isolated using immunomagnetic beads. These CD34+ cells from a total of 6 mice were individually stained with Total seq B CITE-seq antibodies (CD38, CD45RA, CD90, CD49f) + hashtag oligo antibodies 1-6. Then, FACS sort was used to purify ~2,500 cells from each group, and subsequently pooled for CITE-seq library preparation/sequencing. Seurat was used to demultiplex data into 6 individual groups, and differential gene expression analysis was performed to evaluate the impact of G-CSF within Cas9, RNP and RNP/GSE56 groups.

first: Andre

last: Larochelle

first: Neelam

last: Redekar

first: Vicky

last: Chen


title: Transcriptomic analysis of long wavelength-sensing cones of zebrafish retina

city: St. Louis

first: Chi

last: Sun

state: MO

address: 4523 Clayton Ave.

department: Ophthalmology and Visual Sciences

institute: Washington University in St. Louis

summary: The tandemly duplicated zebrafish lws opsin genes and the human LWS/MWS opsin genes are evolved from a common ancestral long wavelength-sensing opsin gene. This dataset shows that LWS1 vs. LWS2 cone subtypes exhibit transcriptional differences beyond opsin expression.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for long wavelength-sensing cones and two subtypes. 3 replicates from FACS-sorted lws1 cone photoreceptor samples and 3 replicates of FACS-sorted lws2 cone photoreceptor samples. 3 replicates from FACS-sorted tdTomato+ cone photoreceptor samples and 3 replicates from FACS-sorted tdTomato- retinal cell samples.

first: Deborah

last: Stenkamp


title: Sugt1 loss skeletal muscle stem cells impairs muscle regeneration and causes premature muscle aging

city: Hong Kong

first: Gexin

last: Liu

state: Sha Tin

address: 503, Li Ka Shing Medical Science Building, PWH, Yin Cheng Street

country: Hong Kong

institute: Chinese University of Hong Kong

summary: Sugt1 RNA-seq in ASC cells from young and old mice are performed

overall_design: RNA-seq

first: Huating

last: Wang

first: Zhiming

last: He


title: Silencing of the Stat1-bcl2 axis accelerates efficient apoptosis of immature T lymphocytes with DNA damage in zebrafish mcm5 mutants

city: chengdu

first: Yong

last: Dong

state: sichuan

address: Xindu road 783, Xindu district

department: Immunology

institute: Chengdu medical college

summary: In this research, we found mcm5 mutation lead to  T cell deficiency and apoptosis in zebrafish. To reveal the molecular mechanism of mcm5 mutation in regulating T cell maturation, we performed RNA-Seq to discover the signal pathways regulated by mcm5.

overall_design: In order to reveal the downstream signals of mcm5 regulated in zebrafish, we performed transcriptome analysis of mcm5 mutants and wild type zebrafish. About 150 zebrafishes with 3.5dpf in each group were dived into three replicates, and then total RNA of wild type or mcm5  mutated zebrafish was extracted, and the cDNA library was constructed for sequencing. All the DNA libraries were sequenced by HiSeq X Ten. And the clean data were generated from the original raw data by removing the adapters.

first: Min

first: Sizhou

last: Huang


title: Bisulfite-free base-resolution sequencing of oxidized cytosines (APOBEC-seq) reveals a ubiquitous role of thymine DNA glycosylase in active gene promoters and an interaction with MBD3/NuRD [human ChIP-seq]

first: Moshe

last: Szyf

summary: Active DNA demethylation, the enzymatic removal of methyl groups from DNA initially triggered by their successive oxidation, is a fundamental process critical to regulating cellular identity. The major enzymes involved in this process have been recently elucidated, but other important components in this pathway and the independent contributions of oxidized 5-methylcytosine derivatives to the regulation of gene expression remain unclear. A major obstacle to the elucidation of this pathway is the low abundance of these derivatives and limited power of current detection technologies. Here, we first develop a technique for their detection with APOBEC3A conversion and sequencing (APOBEC-seq) to directly discriminate deamination-insensitive oxidized cytosines from methylated or unmethylated counterparts, which now facilitates robust DNA demethylation analysis suitable to interrogate the active DNA demethylation pathway by a comprehensive set of experiments. Our results demonstrate that APOBEC-seq is a powerful tool for the detection of oxidized cytosines, revealing insights about the relationship between oxidized gene re-activation and demethylation as a function of TDG, APEX1, and the MBD family of proteins. We also report a ubiquitous binding of TDG to all active unmethylated and unoxidized promoters – regardless of RNA polymerase subtype – suggesting that, together with TET family of enzymes, the presence of TDG at these regions may safeguard active genes from DNA hypermethylation-induced silencing and may explain the failures of CRISPR/dCas9-based DNA methylation editing tools to introduce persistent DNA hypermethylation at targeted promoters. We also report an interaction between MBD3/NuRD and TDG which recruits TDG to its targets and may shed light on the critical role of MBD3 in development. Finally, we apply APOBEC-seq to profile oxidation in vivo in the mouse cortex and report a dramatic tissue-specific pattern of oxidation in genes and enhancers.

overall_design: ChIP-sequencing of a flag-tagged catalytic domain of human TDG with a catalytic N140A mutation (3XFLAG-TDG-N140A-CD) and endogenous MBD3 in HEK293, HepG2, MCF-7, and IMR90 cell lines.

first: Daniel

last: Sapozhnikov


title: Bisulfite-free base-resolution sequencing of oxidized cytosines (APOBEC-seq) reveals a ubiquitous role of thymine DNA glycosylase in active gene promoters and an interaction with MBD3/NuRD [mouse ChIP-seq]

overall_design: ChIP sequencing of histone marks, RNA pol2 phosphoSer5, MBD3, and TDG in adult mouse cortex tissue.


title: Modeling the tumor microenvironment of anaplastic thyroid cancer: an orthotopic tumor model in C57BL/6 mice

city: Seoul

first: Yoo Hyung

last: Kim

address: Jongro-gu 101

country: South Korea

institute: Seoul national University Hospital

summary: Adapted TBP3743 cells were generated via in vivo serial passaging in C57BL/6 mice. Subsequently, the following orthotopic tumor models were established via intrathyroidal injection.

overall_design: B6129SF1 mice injected with original TBP3743 cells (SFOG), B6129SF1 mice injected with adapted cells (SFSC), and C57BL/6 mice injected with adapted cells (B6SC).

first: Zhen

last: Xu

first: Hyo

last: Shin

first: Yoo

first: Sun

last: Cho


title: Bisulfite-free base-resolution sequencing of oxidized cytosines (APOBEC-seq) reveals a ubiquitous role of thymine DNA glycosylase in active gene promoters and an interaction with MBD3/NuRD [human APOBEC-seq]

overall_design: APOBEC-sequencing of ChIP DNA of anti-FLAG ChIP for overexpressed TDG with a catalytic N140A mutation (3XFLAG-TDG-N140A-CD) in the HEK293 cell line and input control samples.


title: Transcriptomic and proteomic analysis reveals the potential role of RBMS1 in adipogenesis and adipocyte metabolism

city: Riyadh

first: Sameer

last: Mohammad

address: Ali Al Arini, Ar Rimayah, P.O. Box 3660, Mail code 1515

country: Saudi Arabia

institute: KAIMRC, KSAU-HS

summary: Knockdown of RBMS1 in pre-adipocytes impacted the differentiation process and reduced the expression of some of the key adipogenic markers. Transcriptomic and proteomic analysis indicated that RBMS1 depletion affected the expression of several genes involved in major metabolic processes, including carbohydrate and lipid metabolism.

overall_design: Comparative gene expression profiling of RBMS1 KD and scrambled control 3T3-L1 adipocytes

first: Ghida

last: Dairi

first: Abdulrahman

last: Alswaji

first: Mamoon

last: Rashid


title: DNA methylation profiling of zebrafish DNMT3aa and DNMT3ab mutants

city: Woods Hole

first: Neelakanteswar

last: Aluru

state: Massachusetts

address: 45 Water Street

department: Biology

institute: Woods Hole Oceanographic Institution

summary: Zebrafish embryos from the wildtype, dnmt3aa, dnmt3ab and double knockout (dnmt3aa, dnmt3ab) homozygous fish were collected at 10 hours post-fertilization and sampled for Reduced Representation Bisulfite Sequencing (RRBS).

overall_design: 10hpf embryos from four different genotypes were sampled and sequenced for RRBS profiling. Each genotype had 5 biological replicates with 20 embryos per replicate.

first: Jan

last: Engelhardt


title: METTL3-mediated m6A mRNA modification was involved in cadmium-induced liver disease

city: Guangzhou

first: Mingxue

last: Tan

address: North Campus, Sun Yat-Sen University, No. 74, 2nd Yat-Sen Street, Yuexiu District, Guangzhou City

department: Department of Toxicology

institute: School of Public Health, Sun Yat-sen University

summary:
Cadmium is an environmental pollutant that has extensive deleterious effects. However, the mechanisms underlying the hepatotoxicity induced by long-term exposure to cadmium remained undefined. In the present study, we explored the role of m6A methylation in the development of cadmium-induced liver disease. We showed a dynamic change of RNA methylation in liver tissue from mice administrated with cadmium chloride (CdCl2) for 3, 6 and 9 months, respectively. Particularly, the METTL3 expression was declined in a time-dependent manner, associated with the degree of liver injury, indicating the involvement of METTL3 in hepatotoxicity induced by CdCl2.
Moreover, we established a mouse model with liver-specific over-expression of Mettl3 and administrated these mice with CdCl2 for 6 months. Notably, METTL3 highly expressed in hepatocytes attenuated CdCl2-induced steatosis and liver fibrosis in mice. In vitro assay also showed METTL3 overexpression ameliorated the CdCl2-induced cytotoxicity and activation of primary hepatic stellate cells. Furthermore, transcriptome analysis identified 268 differentially expressed genes both in mice liver tissue treated with CdCl2 for 3 months and 9 months. Among them, 115 genes were predicted to be regulated by METTL3 determined by m6A2Target database. Further analysis revealed the perturbation of metabolic pathway, glycerophospholipid metabolism, ErbB signaling pathway, Hippo signaling pathway, and choline metabolism in cancer, and circadian rhythm, led to hepatotoxicity induced by CdCl2. Collectively, our findings reveal new insight into the crucial role of epigenetic modifications in hepatic diseases caused by long-term exposure to cadmium.

overall_design: Comparative gene expression analysis of RNA-seq data for mice with CdCl2 for 3 months and 9 months.

first: Liping

last: Chen

first: Huiqi

first: Wenxue

last: Li


title: Bisulfite-free base-resolution sequencing of oxidized cytosines (APOBEC-seq) reveals a ubiquitous role of thymine DNA glycosylase in active gene promoters and an interaction with MBD3/NuRD [mouse APOBEC-seq]

first: Moshe

overall_design: APOBEC-sequencing of ChIP DNA for histone marks, RNA pol2 phosphoSer5, and input.


title: Effects of Fmr1 gene mutations on sex differences in autism-like behavior and dendritic spine development in mice and transcriptomic studies

city: Shijiazhuang

first: zhao

last: Wang

address: 361 Zhongshan East Road, Yuca Street

institute: Hebei medical university

summary: Fragile X syndrome (FXS) is the most common single gene disorder contributing to autism spectrum disorder (ASD). Although significant sex differences are observed in FXS, few studies have focused on the phenotypic characteristics as well as the differences in brain pathological changes and gene expression in FXS by sex. Therefore, we analyzed sex differences in autism-like behavior and dendritic spine development in two-month-old male and female Fmr1 KO and C57 mice and evaluated the mechanisms at transcriptome level. Results suggest that Fmr1 KO mice display sex differences in autism-like behavior and dendritic spine density. Compared to females, male had more severe effects on anxiety, repetitive stereotype-like behaviors, and socializing, with higher dendritic spine density. Furthermore, two male-biased and five female-biased expressed genes were screened based on KEGG pathway enrichment and protein-protein interaction (PPI) analyses. In conclusion, our findings show mutations in the Fmr1 gene lead to aberrant expression of related genes and affect the sex-differentiated behavioral phenotypes of Fmr1 KO mice by affecting brain development and functional architecture, and suggest future studies should focus on including female subjects to comprehensively reflect the differentiation of FXS in both sexes and develop more precise and effective therapeutic strategies.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Fmr1 KO and C57 mice.

first: Zhao

first: Dan

last: Qiao

first: Huan

first: Shihua

last: zhang

first: Bohan

last: Zhang

first: Jingbao

first: Xiangting

last: Hu

first: Chang

first: Huixian

last: Cui

first: Xia

first: Sha


title: MicroRNA-1289 functions as a novel tumor suppressor in oral squamous cell carcinoma

city: Toon

first: Koh-ichi

last: Nakashiro

state: Ehime

address: 454 Shitsukawa

department: Oral and Maxillofacial Surgery

institute: Ehime University Graduate School of Medicine

summary:
Recently, a number of tumor suppressive microRNAs (TS-miRs) have been found in human ma-lignancies. In this study, we have attempted to identify a novel TS-miR in oral squamous cell carcinoma (OSCC) using function-based screening. First, we transfected human OSCC cells with 968 synthetic mimicking human mature miRs individually, and then the growth of these cells was evaluated. Five miRs significantly reduced the cell growth rate by less than 30%, and miR-1289 had the most potent growth inhibitory effect among these miRs. Next, miR-1289/atelocollagen complex administration significantly reduced the size of subcutaneously xenografted human OSCC tumors. Furthermore, the expression levels of miR-1289 were significant decreased in OSCC tissues compared to adjacent normal oral mucosa. Finally, we identified magnesium transporter 1 as a target gene of miR-1289. These results suggest that miR-1289 functions as a novel TS-miR in OSCC, and may be a useful therapeutic tool for the patients with OSCC.
We explored the target genes of miR-1289 in human oral squamous cell carcinoma cells using microarray analysis.

overall_design: We compared the gene expression profiles of 3 human oral squamous cell carcinoma cell lines treated with miR-1289 mimic and miR-non traget (NT).


title: Identifying a phenotypic spectrum in ALS patient-derived fibroblasts

city: San Francisco

first: Karl

last: Kumbier

address: 1700 4th Street, MC 2540

institute: University of California, San Francisco

summary: We sought to compare changes in gene expression levels and pathway-level dysregulation between FUS-ALS, sporadic ALS, and healthy control patient derived fibroblasts. Gene expression profiling analysis were performed on bulk RNA-seq data obtained from 12 FUS, 11 sporadic, and 13 healthy control cell lines.

overall_design:
Comparative gene expression profiling analysis of RNA-seq data for FUS-ALS, sporadic ALS, and healthy control patient-derived fibroblasts.
contributor: New York Genome Center ALS Consortium

first: Maike

last: Roth

first: Zizheng

first: Julia

last: Lazzari-Dean

first: Christopher

last: Waters

first: Ping

last: Huang

first: Vlad

last: Korobeynikov

first: Hemali

last: Phatnani

first: Neil

last: Shneider

first: Matthew

middle: P

last: Jacobson

first: Lani

middle: F

last: Wu

first: Steven

last: Altschuler

first: Capria

last: Rinaldi


title: Profiling of glycerol-induced models of muscle regeneration upon melatonin treatment for 14 days in mice

city: Hangzhou

first: Chen

last: Wentao

state: Zhejiang

address: No. 866 Yuhangtang Road

institute: Zhejiang University

summary: Intramuscular injection of glycerol (Gly) has been reported to lead to skeletal muscle regeneration and ectopic fat deposition. We utilized glycerol injections in the tibialis anterior muscles to investigate the effects of melatonin on skeletal muscle regeneration and intramuscular fat infiltration. We characterized genome-wide expression profiles of tibialis anterior muscles from wild-type mice injured by glycerol injection following melatonin intervention. Mice that were treated with melatonin exhibited improved muscle regeneration and reduced intramuscular fat deposition, which were associated with enhanced myogenesis, remodeled lipid metabolism and reduced immune cell infiltration.

overall_design: Transcriptomic profiling was performed on RNA derived from tibialis anterior muscle 14 days post glycerol injury following melatonin intervention. Tibialis anterior muscle of 12 week old wildtype C57BL/6J male mice were injected with glycerol were collected 14 days after injection. 3 biological replicates were used for each condition.

first: Wentao

last: Chen

first: Defeng

last: Ling

first: Liyi

last: Wang

first: Yanbing

last: Zhou

first: Yuqin

first: Shu

first: Wenjing

last: You

first: Yizhen

first: Tizhong

last: Shan


title: Transcriptomic profiling of mouse C2C12 myoblast  treated with recombinant protein GDF10 in vitro

summary: The purpose of this study is to investigate how GDF10 regulates early myoblast differentiation and fusion. We found that melatonin can enhance fibro-adipogenic progenitors (FAPs) paracrine signaling to support muscle regeneration. Through combining transcriptome analysis and single-cell transcriptome analysis, we identified GDF10 as a type of myogenic factor specifically secreted by FAPs, which plays a beneficial role in promoting muscle fiber development and regeneration. To determine the underlying mechanism by which GDF10 regulates myogenesis, we performed RNA-seq on myoblasts treated with GDF10 or vehicle for 6 hours in vitro. We found that GDF10 promoted myoblast fusion by regulating LKB1-AMPK-MYOG-MYMK signaling during differentiation. In summary, our study revealed novel insights into the mechanism by which melatonin promotes muscle regeneration by mediating the interplay between FAPs and muscle stem cells (MuSCs).

overall_design: Transcriptomic profiling was performed on RNA from mouse C2C12 myoblasts treated by GDF10 or vehicle for 6 hours in growth medium (2 biological replicates).

last: Zhang


title: mRNA expression quantitative Analysis of Kasumi-1 and NB4 treated with JOA compared with control

city: Weifang

first: Liuya

last: Wei

address: 7166 number, Baotong West Street

institute: Weifang Medical University

summary: The goals of this study are toevaluate the mRNA expressions of genes in Kasumi-1 and NB4 cell lines treated with JOA

overall_design: There are 6 samples for Kasumi-1 cell line ( control and JOA-treated) and 4 samples for NB4 cell line ( control and JOA-treated)

first: L

first: F

last: Li


title: β-Trcp and RSK2-mediated ubiquitination of FOXN3 facilitates BRCA1-dependent DNA damage repair in lung cancer

city: zhengzhou

first: XuDong

address: 40 North University Road

department: Academy of Medical Science

institute: zhengzhou university

summary: Radioresistance is one of the main factors that lead to the failure of radiotherapy in lung cancer patients. The mechanisms underlying these processes are, however, not fully understood. Here, we find that the low levels of FOXN3 protein is associated with poor prognosis of lung cancer patients. Furthermore, we show that depletion of FOXN3 promotes DNA damage repair and confers lung cancer radioresistance in a BRCA1-dependent manner. Mechanistically, we uncover that E3 ligase β-Trcp and protein kinase RSK2 bind to and cooperatively induce the ubiquitin-mediated degradation of FOXN3. More importantly, β-Trcp and RSK2-mediated ubiquitination of FOXN3 facilitate DNA damage repair in lung cancer. Thus, our findings reveal the molecular mechanism to control the abundance of FOXN3 in DNA damage repair, indicating that targeting β-Trcp/RSK2/FOXN3/BRCA-1 axis may be a novel radiosensitization strategy in lung cancer.

overall_design: RNA-seq analysis of negative control or siRNA(targeting FOXN3) H1299 cells

first: Xudong

first: Yulan

last: Zeng

first: Jingsong

first: Zhikun

last: Zheng

first: Zixuan

first: Huichan

last: Xue

first: Xiaorong

last: Dong

first: Gang

first: Shuangbing

last: Xu


title: Single cell RNA sequence reveals C5aR1 inhibition selectively targets pro-tumorigenic M2 macrophages reversing PARP inhibitor resistance

city: Portland

first: Xi

state: Oregon

address: 2730 SW Moody Ave

institute: Oregon Health & Science University

summary: Although Poly (ADP-ribose) polymerase (PARP) inhibitors (PARPi) have been approved in multiple diseases, including BRCA1/2 mutant breast cancer, responses are usually transient thus requiring the development of combination therapies that can capitalize on PARPi activity. We thus explored mechanisms underlying sensitivity and resistance to PARPi using two intrinsically sensitive and resistant syngeneic murine breast cancer models. Our data indicate that the PARPi sensitive tumor model has a high ratio of M1 anti-tumor/M2 pro-tumor macrophages with the M1/M2 ratio being increased by PARPi. In contrast the PARPi resistant tumor model had very low levels of M1 macrophages and thus a low M1/M2 ratio that was not altered by PARPi. Our data indicate that co-transplantation of the PARPi sensitive and the PARPi resistant tumor results in accumulation of M2 macrophages in the sensitive tumor, rendering the sensitive tumor PARPi resistant. C5aR1 and RPS19/C5aR1 signaling is selectively elevated in the M2 macrophages that are associated with PARPi resistance.  Strikingly C5aR1 targeting decreased M2 macrophages, while sparing M1 macrophages rendering PARPi resistant tumors sensitive to PARPi. Consistent with the murine data, human breast cancers with high C5aR1 levels have a poor response to immune checkpoint blockade. Thus targeting C5aR1 may represent a therapeutic approach to selectively deplete M2 macropahges and engender sensitivity to PARPi and potentially other therapeutic approaches.

overall_design: scRNA-seq by 10x genomics of two mouse-derived syngeneic transplant (LPA1-T22, and LPA1-T127) single strain transplanted or co-transplanted models treated with olaparib for 4 days, 8 days and 20 days

first: Grodon

middle: B

last: Mills


title: Transcriptomic profiling of mouse fibro/adipogenic progenitors (FAPs)  upon melatonin treatment in vitro

first: Chen

summary: The purpose of this study is to investigate how melatonin-influenced promyogenic factor secreted from fibro-adipogenic progenitors (FAPs) regulate muscle regeneration and muscle cell fusion during muscle repair. We highlighted the role of melatonin in regulating crosstalk between muscle stem cells and FAPs during muscle regeneration. Mice that were treated with melatonin exhibited improved muscle regeneration and reduced intramuscular fat deposition, which were associated with enhanced myogenesis, remodeled lipid metabolism and reduced immune cell infiltration. Notably, melatonin did not exert positive effects on cell fusion and myotube formation during differentiation. Interestingly, melatonin repressed fibro-adipogenic progenitor (FAP) adipogenesis in a dose-dependent manner in vitro. Furthermore, melatonin treatment enhanced the pro-myogenic effects of FAPs, which stimulated GDF10 secretion to promote muscle cell fusion and induce myotube hypertrophy.

overall_design: Transcriptomic profiling was performed on RNA from isolated FAPs treated by melatonin or vehicle for 24 hours in vitro. Fibro-adipogenic progenitors (FAPs) were isolated from uninjured tibialis anterior, gastrocnemius and quadriceps of wildtype C57BL/6J male mice. After 48 h, FAPs were treated with vehicle or melatonin for 24 h in vitro. 4 biological replicates were used for each condition.

first: Wentao

first: Defeng

first: Liyi

first: Yanbing

first: Yuqin

last: Huang

first: Shu

first: Wenjing

first: Yizhen


title: Molecular and functional features of synucleinopathy-associated astrocytes

first: Ho

last: Ko

address: 30-32 Ngan Shing Street, Shatin

department: Medicine and Therapeutics

institute: The Chinese University of Hong Kong

summary: Astrocyte (AC) involvement is a common neuropathological feature in human synucleinopathy-associated neurodegeneration. However, our understanding of the in vivo characteristics of reactive ACs in synucleinopathy remained limited. Here we report the transcriptomic and functional features of a unique synucleinopathy-associated AC (SAA) subtype in a mouse model. SAAs share a convergent transcriptomic state across synucleinopathy-laden brain regions, and are at least partially reliant on microglia for their phenotypic maintenance in vivo. Intravital imaging revealed that an upregulation of the excitatory amino acid transporter 2 (EAAT2) in synucleinopathy-affected ACs is associated with depressed neuronal activities. This is potentially mediated via increased AC glutamate uptake, as pharmacological induction of EAAT2 reproduced the same effect. With cross-species comparative analysis, we showed that the core SAA transcriptomic features are present in human aged and synucleinopathy-affected midbrain ACs, while important distinct characteristics also exist. Collectively, our results uncovered complex reactive AC changes that likely play important adaptive roles in synucleinopathy.

overall_design: Mouse brain frontal cortex and midbran two regions from Huα-Syn(A53T) and wildtype mice group(3 mice each group) were acquired to perform scRNAseq.

first: Zhongqi


title: Impact of cellular crosstalk on the cytochrome expression in an in vitro test system relevant for the alveolar barrier

city: Belvaux

first: Sebastien

last: Cambier

state: - select a state -

address: 41 rue du brill

department: ERIN

country: Luxembourg

institute: LIST - Luxembourg Institute of Science and Technology

summary:
Purpose: For humans, inhalation is considered as the main exposure route to chemicals, which is the reason why lung toxicity studies should be considered as a priority. Inhalation studies are often performed in vivo in rodents. Therefore, in vitro models may represent a valid and efficient alternative to predict the acute toxicity effects of inhaled chemicals on human health.  The models used in this study are really simple in vitro systems either constituted by THP1 alone or THP1 cocultured with A549. This special designed has the purpose to study the impact of cellular cross talk on the THP 1 immune cells when exposed to a chemical which is BaP in the present work.
Results: We describe the effects after 48 hours of exposure BaP in order to evaluate the importance of the cellular crosstalk in cell sensitivity toxicological effects of BaP. The set of parameters used to assess this cellular crosstalk included transcriptomics, cell imaging and enzymatic activity. The exposure did not cause any significant decrease of viability; all the parameters revealed the toxicity of the BaP. Regarding the global transcript, among differentially expressed genes (DEG) were found genes related to the enhancement of immune cells.
Conclusion: Coculture in the used of in vitro model drastically change the gene expression profile in THP1 cells, but similar effects were observed between the monoculture and the culture exposed to BaP. However the number of altered mechanism in the THP1 cocultured cells exposed to BaP was larger supporting the importance to take into account the cell interactions.

overall_design: THP1 mRNA profiles of 48h exposed mono and cocultured with A549 exposed to BaP in comparison to a negative control all in three biological replicates were analysed.

first: Sabina

last: Burla

first: Audrey

last: Jehanno

first: Jenny

last: Hennen

first: Tommaso

last: Serchi

first: Sylvain

last: Legay

first: Sebastian

middle: G

last: Klein

first: Carmen

last: Socaciu

first: Lucien

last: Hoffmann

first: Arno

middle: C

last: Gutleb


title: Global gene expression profiles of phoB and phoU mutants of X. citri pv. glycines 12-2 conducted under phosphate limitation conditions in vitro using RNA-seq

city: Bangkok

first: Tiyakhon

last: Chatnaparat

address: 50 Ngamwongwan Rd. Ladyao, Chatuchak

department: Plant Pathology

country: Thailand

institute: Kasetsart University

summary: RNAseq analysis of Xanthomonas citri pv. glycines 12-2 wild-type, phoB and phoU mutants under phosphate limited condition

overall_design: Sequencing was performed on cDNA prepared from mRNA isolated from the wild type, phoB and phoU mutants grown in MOPS minimal medium without added phosphate (0 Pi).


title: Reversing lysosome-mTORC1-ribosome axis dysregulations to mitigate C9FTD/ALS neurodegeneration

city: los angeles

first: Guoping

last: Fan

state: ca

address: 695 Charles E Young Drive South

department: Human Genetics

institute: university of california, los angeles

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

overall_design: Refer to individual Series


title: The administration of amnion-derived multipotent cell secretome ST266 protects against necrotizing enterocolitis in mice and piglets

city: Baltimore

first: David

middle: J.

last: Hackam

address: 733 North Broadway

department: Surgery

institute: Johns Hopkins University School of Medicine

summary: Necrotizing enterocolitis (NEC) is the leading cause of death from gastrointestinal disease in premature infants and is steadily rising in frequency. Patients who develop NEC have a very high mortality, illustrating the importance of developing novel prevention or treatment approaches. We and others have shown that NEC arises in part from exaggerated signaling via the bacterial receptor toll like receptor 4 (TLR4) on the intestinal epithelium, leading to widespread intestinal inflammation and intestinal ischemia. Strategies that limit the extent of TLR4 signaling, including the administration of amniotic fluid, can reduce NEC development in mouse and piglet models. We now seek to test the hypothesis that a secretome derived from amnion-derived cells can prevent or treat NEC in pre-clinical models of this disease via a process involving TLR4 inhibition. In support of this hypothesis, we show that the administration of this secretome, named ST266, to mice or piglets can prevent and treat experimental NEC. We further show that the protective effects of ST266 occurred in the presence of marked TLR4 inhibition in the intestinal epithelium of cultured epithelial cells, intestinal organoids, and human intestinal samples ex vivo. Strikingly, RNA-seq analysis of the intestinal epithelium in mice reveal the ST266 upregulates critical genes associated with gut remodeling, intestinal immunity, gut differentiation and energy metabolism. These findings show that the amnion-derived secretome ST266 can prevent and treat NEC, suggesting the possibility of novel therapeutic approaches for patients with this devastating disease.

overall_design: For RNAseq analysis, 16 samples from four experimental groups were collected from mouse ileum at age p11 with four replicates. Group 1: Breastfed control mice; Group 2: Mice with experimental NEC; Group 3: Mice with experimental NEC administered ST266 orally; Group 4: Mice with experimental NEC administered ST266 intraperitoneally.

first: Raheel

last: Ahmad

first: Chhinder

last: Sodhi


title: Reversing lysosome-mTORC1-ribosome axis dysregulations to mitigate C9FTD/ALS neurodegeneration [bulk RNA-Seq]

summary: We report the application of buld RNA-seq in the mouse cortex with C9FTD/ALS neurodegeneration

overall_design: Bulk RNA-seq were performed to identify what genes are dysregulated inC9orf72+/-;C9-BAC (3 biological replicates) mouse cortex compared to WT (2 biological replicates) controls, and what genes are changed by AAV-C9orf72- (2 biological replicated) or AAV-Smcr8- (1 biological replicates, we lost two samples during COVID mouse facility shut down) infected C9orf72+/-;C9-BAC mouse cortex.

first: Jing

last: Wang

first: Li

last: Ma


title: RNA-seq and ChIP-seq studies of cardiomyocyte differentiation from H1 hESCs

first: Weisheng

last: Cheng

address: 2nd Zhongshan Road

institute: Sun yat-sen University


title: CD4+ T cell subsets during LCMV infection

city: La Jolla

first: Ananda

last: Goldrath

address: 9500 Gilman Dr

institute: UCSD


title: RNA-seq of small cell lung cancer [circRNA-Seq]

city: Hefei

first: fengmei

last: chao

state: Anhui

address: East Huanhu road

institute: Anhui Provincial Cancer Hospital

type: Non-coding RNA profiling by high throughput sequencing

summary: We used CCK-8 experiment to determine the chemotherapy tolerance of small cell lung cancer cells, from which we found chemotherapy-sensitive cells (H446) and chemotherapy-tolerant cells (SHP77).By RNA-SEQ, we identified 401 circRNAs with abnormal expression associated with chemotherapy tolerance, including 212 up-regulated circRNAs and 189 down-regulated circRNAs. Through qRT-PCR verification, several circRNAs related to chemotherapy tolerance of small cell lung cancer were found, which helped us to further clarify the mechanism of chemotherapy tolerance of small cell lung cancer.

overall_design: CircRNA profiles of small cell lung cancer

first: Fengmei

last: Chao

first: Ming

last: Li


title: RNA-seq of small cell lung cancer


title: TimeChange: Topology inspired methods for the detection of differential dynamics in time-series data

city: Evanston

first: Ravi

last: Allada

state: Illinois

address: 2200 Campus Drive Room 2-201

institute: Northwestern University

summary: The circadian clock drives the oscillatory expression of thousands of genes across all tissues and bears significant implications for human health. RNA-seq time-series experiments interrogate the mechanistic links between transcriptional rhythms and phenotypic outcomes. Analysis methods must overcome the challenges of sparse temporal sampling, noisy data, and non-strictly periodic dynamics. Moreover, there remains a need for differential cycling analysis methods that can identify complex changes in rhythmicity for 2-sample comparisons across experimental conditions.    We present TimeChange -- a non-parametric and model-free method for the quantification of differential dynamics across experimental conditions. The method leverages a data transformation technique known as time-delay embedding to reconstruct the underlying state space for each gene-of-interest. Takens’ embedding theorem implies that rhythmic dynamics will exhibit circular patterns in the embedded space. TimeChange non-parametrically compares the distributions of points in the embedded space via the Fasano-Franceschini test to assess whether the topological structures differ significantly between phenotypes, thereby quantifying differences in transcriptional dynamics without requiring knowledge of the underlying model. Application of TimeChange to synthetic data shows that it accurately identifies changes in transcriptomic dynamics, including differences in amplitude/peaked-ness; changes in sawtooth asymmetries; and trending oscillatory drifts (e.g. linear, damped, and contractile). We further show that the method has potential utility beyond circadian dynamics. For instance, initial tests of TimeChange using erg rowing-machine data shows accurate classification of differential stroke dynamics in real time, suggesting potential uses of TimeChange in the field of sports science and medicine.

overall_design: Two independent replicates samplings were performed with a total of 24 (w1118: 2h interval) and 12 (Clk-Jrk: 4h interval) samples for each temperature condition (18 and 25).

first: Elan

last: Ness-Cohn

first: Dae-Sung

last: Hwangbo

first: James

last: Kwon

first: Marta

last: Iwanaszko

first: William

last: Kath

first: Rosemary

last: Braun


title: RNA-seq of small cell lung cancer [Small RNA-Seq]

summary: We used CCK-8 experiment to determine the chemotherapy tolerance of small cell lung cancer cells, from which we found chemotherapy-sensitive cells (H446) and chemotherapy-tolerant cells (SHP77).By RNA-SEQ, we found 99 miRNAs with abnormal expression associated with chemotherapy tolerance, including 69 up-regulated miRNAs and 30 down-regulated miRNAs. Several miRNAs related to chemotherapy tolerance of small cell lung cancer were found through qRT-PCR verification, which helped us to further clarify the mechanism of chemotherapy tolerance of small cell lung cancer.

overall_design: Small RNA profiles of small cell lung cancer


title: Comparative Transcriptome Analysis Reveals Insight into Exocarp Russeting  Pear Variety

city: Yangzhou

last: Zhang

address: 48 Wenhui Road

institute: Yangzhou university

summary: We carried out the transcriptome analysis to identify the key genes involved in pear fruit russet formation by comparing five pear varieties with distinct exocarp characteristics

overall_design: Transcriptome profiling of  five varieties of pear fruit skin, insights into pear fruit russet formation

first: Chunlei


title: Genome-wide transcriptomic profiling of cardiomyocyte differentiation from Wild-type and PERK-KO H1 hESCs [RNA-seq]

summary: Cardiac development involves large-scale rearrangements of the proteome. How the developing cardiac cells maintain the integrity of the proteome during the rapid lineage transition remains unclear. Here we show that proteotoxic stress visualized by the misfolded protein aggregates appears during early cardiac differentiation of human embryonic stem cells (hESCs) and is resolved by activation of the PERK branch of the unfolded protein response (UPR). PERK depletion increases misfolded protein accumulation, leading to pluripotency exit defect and impaired mesendoderm specification of hESCs. Mechanistically, we found that PERK safeguards cardiogenesis through its conserved downstream effector ATF4, which subsequently activates a novel transcriptional target WARS1, to cope with the differentiation-induced proteotoxic stress. Our results indicate that protein quality control represents a previously unrecognized core component of the cardiogenic regulatory network. Broadly, these findings provide a framework for understanding how UPR is integrated into the developmental program by activating the PERK-ATF4-WARS1 axis.

overall_design: Undifferentiated hESCs cultured in E8 medium were dissociated into single cell suspension by Accutase (Stem Cells Technology, 7920) and reseeded onto Matrigel-coated 24-well plate at a density of 105 cells/per well in E8 medium containing 10 μM Y-27632. When reached ~80% confluence 2-3 days after plating, CM differentiation was initiated by switching to the cardiac differentiation medium (DMEM/F-12 (Gibco, 11330032) supplemented with 50 U ml-1 Penicillin-Streptomycin (Gibco, 15070063), Chemically Defined Lipid Concentrate (1:100, Gibco, 11905031), 10.7 μg ml-1 holo-Transferrin human (Sigma, T0665), 71 μg ml-1 L-Ascorbic acid (Sigma, A8960), 14 ng ml-1 Sodium selenite (Sigma, S5261)) and renewed every day. 5 μM CHIR99021 (Selleck, S1263) and 3 μM IWP2 (Selleck, S7085) was added into the cardiac differentiation medium from days 0-1 and days 2-5, respectively. 3 μg ml-1 Heparin was added into the cardiac differentiation medium from days 1-7. 20 μg ml-1 Insulin (Sigma, 91077C) was added into the cardiac differentiation medium from day 7 onward. The medium was changed daily until day 7 and renewed every 2-3 days from day 7 onward. At day 0, 2 and 6 during the differentiation period, and cells were collected using using the NucleoZol reagent. mRNA libraries were prepared using the VAHTS® mRNA-seq V2 Library Prep Kit for Illumina from Vazyme and sequenced on an Illumina HiSeq 2000 with 150 bp paired-end reads by GENEWIZ.

last: Cao


title: RNA-seq of small cell lung cancer [PolyA RNA-Seq]

summary: We used CCK-8 experiment to determine the chemotherapy tolerance of small cell lung cancer cells, from which we found chemotherapy-sensitive cells (H446) and chemotherapy-tolerant cells (SHP77). By RNA-SEQ, we found 972 mRNAs with abnormal expression associated with chemotherapy tolerance, including 560 up-regulated mRNAs and 412 down-regulated mRNAs. Several miRNAs related to chemotherapy tolerance of small cell lung cancer were found through qRT-PCR verification, which helped us to further clarify the mechanism of chemotherapy tolerance of small cell lung cancer.

overall_design: RNA profiles of small cell lung cancer


title: Chromatin occupancy of ATF4 at day 1 of cardiomyocytes differentiation [ChIP-seq]

overall_design: Undifferentiated hESCs cultured in E8 medium were dissociated into single cell suspension by Accutase (Stem Cells Technology, 7920) and reseeded onto Matrigel-coated 24-well plate at a density of 105 cells/per well in E8 medium containing 10 μM Y-27632. When reached ~80% confluence 2-3 days after plating, CM differentiation was initiated by switching to the cardiac differentiation medium (DMEM/F-12 (Gibco, 11330032) supplemented with 50 U ml-1 Penicillin-Streptomycin (Gibco, 15070063), Chemically Defined Lipid Concentrate (1:100, Gibco, 11905031), 10.7 μg ml-1 holo-Transferrin human (Sigma, T0665), 71 μg ml-1 L-Ascorbic acid (Sigma, A8960), 14 ng ml-1 Sodium selenite (Sigma, S5261)) and renewed every day. 5 μM CHIR99021 (Selleck, S1263) and 3 μM IWP2 (Selleck, S7085) was added into the cardiac differentiation medium from days 0-1. Then samples were collected following the previously published protocol (Lee, T.I., Johnstone, S.E., and Young, R.A. (2006). Chromatin immunoprecipitation and microarray-based analysis of protein location. Nat Protoc 1, 729-748)


title: RNA-Seq of wild-type CD4+ T cell subsets during LCMV infection

state: CA

summary: Following an infection, CD4+ lymphocytes can differentiate into long-lived memory T cells, some of which circulate through the secondary lymphoid organs (SLOs) while a population lodges in non-lymphoid tissues. While CD4+ T cells in SLOs have been examined, the developmental origins and transcriptional regulation of tissue-resident memory T cells (TRM) remain largely undefined. Here, we investigated the phenotypic, functional, and transcriptional profile of virus-specific CD4+ TRM in the small intestine (SI) following acute lymphocytic choriomeningitis virus (LCMV) infection. LCMV-specific CD4+ TRM at day 7 of infection shared a gene-expression program and chromatin profile with TH1 cells and progressively acquired a mature TRM program by day 21 memory time point, supporting a developmental relationship between TRM and TH1 subsets. Furthermore, we demonstrated that TRM cells expressed genes associated with both effector and memory T cell fates, including the transcriptional regulators Blimp1, Id2, and Bcl6 which were necessary for CD4+ TRM differentiation. TH1-associated Blimp1 and Id2 were both required for early TRM formation, while TFH-associated Bcl6 initially inhibited TRM differentiation but was critical for development of long-lived TRM cells. Our results identify new significance for TFs previously associated with circulating CD4+ T cell populations and their roles in driving SI CD4+ TRM differentiation.

overall_design: 9 samples, 2-4 replicates per sample, naive or Day 7 or Day 21 LCMV infection CD4+ SMARTA T cells from spleen or small intestine subsets

first: Q

last: Nguyen

first: T

middle: Z

last: Deng

first: A


title: ATAC-Seq of CD4+ T cell subsets during LCMV infection

overall_design: 6 samples, 2 replicates each, Day 7 or Day 20 LCMV infection CD4+ T cell subsets


title: Human cytomegalovirus infection perturbs neural progenitor cell fate via the expression of viral microRNAs

city: OSLO

first: Xuan

last: Jiang

department: Department of Medical Genetics

country: Norway

institute: University of Oslo

summary:
Congenital human cytomegalovirus (HCMV) infection is the leading infectious cause of birth defects, including neurodevelopmental disorders. HCMV infection mainly targets neural progenitor cells (NPCs) in fetal brains, inducing abnormal differentiation by altering key regulatory pathways. HCMV expresses a series of viral miRNAs during infection, but their roles, particularly in NPCs, are not fully understood.
In this study, we characterized expression profiles of both cellular and viral miRNAs in HCMV-infected NPCs by microarray analysis during early infection time points and investigated the primary effects of these miRNAs on regulating NPC fate. While expression of most cellular miRNAs was unaffected by HCMV infection, one cellular miRNA was upregulated and six were downregulated from 2 to 24 h post infection. Moreover, of 17 HCMV miRNAs evaluated, six were differentially expressed in HCMV-infected NPCs during early infection time points.

platform_organism:
Homo sapiens
Human betaherpesvirus 5

overall_design: Primary human NPCs were mock-infected (mock) or infected with HCMV Towne strain at a multiplicity of infection (MOI) of 3 and investigated at early time points of 2, 4, 12 and 24 hpi. RNA samples were subjected to microarray analysis using miRNA microarray chips designed to detect both cellular and HCMV miRNAs based on the miRBase database annotation.

first: Ya-Ru

last: Fu

first: Si-Qing

last: Liu

first: Simon

last: Rayner

first: Min-Hua

last: Luo


title: Arbuscular mycorrhizal fungi and carrot demonstrate contrasting responses to drought stress as revealed through a dual transcriptomic approach

city: Spokane

first: Michelle

last: Pearson

state: WA

address: 3410 W Whistalks Way MS3280

department: Life Sciences

institute: Spokane Falls Community College

summary: To test the impacts of drought on the host and fungus, we inoculated carrots (Daucus carota cv. ‘Napoli’) with spores of Rhizophagus irregularis DAOM 197198. Carrots grew in a greenhouse, and at the beginning of taproot development, were exposed to a 10-day water restriction. We evaluated plant growth and physiological responses, colonization level, and plant and fungal gene expression.

sample_organism:
Daucus carota
Rhizophagus irregularis

platform_organism:
Daucus carota
Rhizophagus irregularis

overall_design: There were 4 treatment groups: non-mycorrhizal control, mycorrhizal control, non-mycorrhizal drought, and mycorrhizal drought. For each group, 4 replicates were sequenced and analyzed.

last: Keller-Pearson

first: Anthony

last: Bortolazzo

first: Luke

last: Willems

first: Brendan

last: Smith

first: Annika

last: Peterson

first: Jean-Michel

last: Ané

first: Erin

last: Silva


title: Single-cell RNA-Seq of wild-type and Bcl6KO CD4+ T cell subsets during LCMV infection

first: Ananda

last: Goldrath

overall_design: 13 samples, 1-2 replicates per sample, Day 7 or Day 21 LCMV infection of wild-type or Bcl6KO CD4+ SMARTA T cells from spleen or small intestine subsets


title: Next Generation Sequencing of si-NC and si-circFAM120A Transcriptomes

city: Jinan

first: Tingting

last: Zhou

address: 157 Jingliu Road

institute: Shandong

summary:
Purpose: to find the potential down-stream target gene of circFAM120A
Methods:  mRNA profiles of  decidualized human endometrial stromal cells (hESCs) after down-regulated FAM120A and control using siRNA were generated by NGS and compared by bioinformatics analysis
Results: we sequenced 26414 mRNAs in hESCs between the si-NC and si-circFAM120A groups and  identified 242 differentially expressed mRNAs, between which 161 were downregulated and 81 were up-regulated in si-circFAM120A group
Conclusions: Our study represents the  detailed analysis of decidualized hESCs transcriptomes between si-NC and si-circFAM120A groups.

first: Junhao

last: Yan


title: RNA-Seq of Bcl6-KO CD4+ T cell subsets during LCMV infection

overall_design: 3 samples, 2 replicates per sample, Day 7 LCMV infection of CD4+ SMARTA T cells from spleen or ssmall intestine subsets

first: Q

last: Nguyen

first: T

last: Deng


title: BMI Expression is Required for Pancreatic Cancer Progression

city: Ann Arbor

first: Filip

last: Bednar

address: 1500 E Medical Center Dr

institute: University of Michigan

summary: Pancreatic cancer is one of the deadliest human malignancies, with a survival rate less than 10%. Traditional modes of therapy have proven ineffective in the treatment of pancreatic cancer, highlighting the need to further understand the basic biology of the disease in order to identify new treatment modalities. Previously, our group showed that the epigenetic regulator Bmi1 is required for the initiation of pancreatic cancer in mice. In murine models of PDAC, mice lacking pancreatic Bmi1 expression do not develop precancerous lesions, despite oncogene expression. In this work, we sought to determine the role of Bmi1 in later stages of pancreatic tumor development. Using a CRISPR/Cas9 strategy, we deleted Bmi1 in primary human pancreatic caner cells and created clonal lines. When used in a subcutaenous tumor growth assay, those cells lacking BMI1 expression formed tumors that grew significantly smaller than controls. To query the mechanism of BMI1 action in pancreatic cancer growth, we used RNA sequencing to compare those pancreatic cancer cells with and without BMI1 expressed. This revealed that Bmi1 controls the gene expression of glycolysis and cell proliferation pathways, likely the reason for its requirement in pancreatic tumor growth. Overall, we found that Bmi1 is required in pancreatic tumor progression, and that it controls gene expression in both glycolysis and cell proliferation.

overall_design: Transcriptomic profiling of primary human pancreatic cancer cells with or without BMI1 expression

first: Heather

middle: K

last: Schofield

first: Zeribe

last: Nwosu


title: CHIP-seq analysis about H3K9me3 change after Zscan4 overexpression

city: Tianjin

first: Xuan

last: Zhao

state: Tianjin

address: No. 38 Tongyan Road, Haihe Education Park, Tianjin

department: State Key Laboratory of Medicinal Chemical Biology

institute: Nankai University

summary: Transcription factor Zscan4 was newly discovered to be a marker of the intermediate state of 2-cell like cells . In addition, WGCNA discovered a strong positive correlation between the expression of Zscan4 and that of MT2/MERVL. Hence, we examined the possibility for Zscan4 as an activator of MT2/MERVL.

overall_design: We overexpressed Zscan4 in J1. We performed CHIP-seq analysis in order to examine H3K9me3 change after Zscan4 overexpression

first: Weiyu

last: Zhang

first: Fuquan

last: Chen

first: Xinyi

last: Lu

first: Lin


title: Age prediction from human blood plasma using proteomic and small RNA data: a comparative analysis

city: Huddinge

first: Christian

middle: Günter

last: Riedel

state: Stockholm

address: Blickagången 16 (Neo Building, 6th floor)

department: Biosciences and Nutrition

country: Sweden

institute: Karolinska Institute

summary: Aging clocks, built from comprehensive molecular data, have emerged as promising tools in medicine, forensics, and ecological research. However, few studies have compared the suitability of different molecular data types to predict age in the same cohort and whether combining them would improve predictions. Here, we explored this at the level of proteins and small RNAs in 103 human blood plasma samples. First, we used a two-step mass spectrometry approach measuring 612 proteins to select and quantify 21 proteins that changed in abundance with age. Notably, proteins increasing with age were enriched for components of the complement system. Next, we used small RNA sequencing to select and quantify a set of 315 small RNAs that changed in abundance with age. Most of these were microRNAs (miRNAs), downregulated with age, and predicted to target genes related to growth, cancer, and senescence. Finally, we used the collected data to build age-predictive models. Among the different types of molecules, proteins yielded the most accurate model (R² = 0.59 ± 0.02), followed by miRNAs as the best-performing class of small RNAs (R² = 0.54 ± 0.02). Interestingly, the use of protein and miRNA data together improved predictions (R2 = 0.70 ± 0.01). Future work using larger sample sizes and a validation dataset will be necessary to confirm these results. Nevertheless, our study suggests that combining proteomic and miRNA data yields superior age predictions, possibly by capturing a broader range of age-related physiological changes. It will be interesting to determine if combining different molecular data types works as a general strategy to improve future aging clocks.

overall_design: Measurement of small RNA in 103 plasma samples from healthy individuals.

first: Jérôme

last: Salignon

first: Omid

last: Faridani

first: Tasso

last: Miliotis

first: Georges

middle: E

last: Janssens

first: Ping

first: Bader

last: Zarrouki

first: Rickard

last: Sandberg

first: Pia

last: Davidsson


title: The anti-fibrosis effect of iguratimod on skin tissues of systemic sclerosis patients

city: RTP

first: Xiaojiang

last: Xu

state: North Carolina

address: 111 T. W. Alexander Dr.,

institute: NIEHS

summary: To evaluate the possibility of iguratimod working on SSc patients in clinical practice, we collected skin biopsies from three early SSc patients. Three grafts were divided equally into two irradiated nude mice and treated with iguratimod or vehicle solution subcutaneously for five weeks. Total RNA from cultured fibroblasts or xenografts were extracted by TRIzol.Differential expression analysis of two groups was performed using the DESeq2 from R package. we find the ensemble of genes encoding extracellular matrix and ECM-associated proteins, which was termed as matrisome, was enriched at the top of the GSEA list.In the ensemble, there were pro-fibrotic cytokine genes such as TGFB1 and FGFs, and WNTs; ECM degradation enzymes genes such MMPs and CTSs; ECM-associated chemokine such CCL13 and CCL18; and notably, remarkable amount of glycoprotein/ proteoglycan genes such as LRG1, PRG4, HAPLN1 and PODNL1.

overall_design: Examation the difference of gene expression between the SSc skin biopesy treated with iguratimod or vehicle, there are three patients' biopsies

first: Qingran

last: Yan

first: Lichong

last: Shen


title: single cell RNA Sequencing of hippocampi of mice subjected or not to the learned helplessness paradigm

city: Miami

first: Eleonore

last: Beurel

state: FL

address: 1011 NW 15th Street Gautier room 415

department: Psychiatry

institute: University of Miami, Miller School of Medicine

summary: The goal of the study was to identify the hippocampal microenvironment asscoaited with stress, in particular stress-induced learned helplessness. By comparing chronic and acute induction of learned helplessness, we identified cell populations and genes associated with resilience.

overall_design: Mice were subjected or not to the learned helplessness paradigms (either acute: mice received footshocks and were tested the next day, or chronic: mice received the acute paradigm and are retested for 3 weeks, weekly), and hippocampal CD45+ live dead - cells were sorted, and 10X Genomics single cell RNA Sequencing was performed.


title: Transcriptional alterations of human HSCs in aging and MDS

city: Pamplona

first: Teresa

last: Ezponda

state: Navarra

address: Pio XII 55

department: Hematology/Oncology

institute: Center for Applied Medical Research

summary: RNA-seq analysis comparing the transcriptional landscape of normal young, normal aged and MDS-associated HSCs.

overall_design: HSCs were isolated from the bone marrow of young and aged healthy donors as well as MDS patients.

first: Felipe

last: Prosper Cardoso

last: Ezponda Itoiz


title: High temporal resolution transcriptomic profiling from fertilization through ZGA

city: Berkeley

last: He

address: Li Ka Shing Center

department: Dept of Molecular & Cell Biology

institute: University of California, Berkeley

summary: Single murine embryo RNA-seq covering fertilization through ZGA sampled every 2 hours after fertilization

overall_design: Female C57BL/6J mice were superovulated with PMSG and HCG 46hrs apart. Females were then paired with C57BL/6J stud mice. Sample collection began 12hrs post HCG from females that had been plugged at least 2hrs prior and was done every 2hrs spanning the 1C - 2C transition. Embryos were lysed and stored separately according to SMART-SEQ v4 manufacturer instructions. Once all samples were collected, cDNA synthesis and amplification and cleanup were done on the whole cohort according to manufacturer's instructions. Embryos from 0hrs post fertilization to late 2C were processed as a cohort. Oocyte and Morula samples were processed in separate batches.

first: Martin

last: Kinisu

first: Shibo

last: Jin

first: Hector

last: de Bezieux

first: Zhenyu

last: Xuan


title: Targetable programs of adult cancer are ontogenically rooted within early cell fate trajectories of human pluripotent state

city: Hamilton

first: Mickie

last: Bhatia

state: Ontario

address: 1200 Main Street West

department: Stem Cell and Cancer Research Institute (SCC-RI)

institute: McMaster University

summary: Recognized molecular similarities between pluripotency and cancer have recently been underscored with multi-omics campaigns revealing stemness networks that are shared between human pluripotent stem cells (hPSCs) and tumors, where tumors types cluster based on tissue origins. Informed by these in silico studies, we now demonstrate hPSCs serve as a source of networks that define properties of adult tissue oncogenesis. Single cell deconstruction of hPSCs allowed germ layer primed subsets to be identified that corresponded to lineage specified adult cancers. Chemical probes that induced germ layer differentiation of hPSCs also suppressed adult cancers, but were restricted to tumors of shared origin with germ layer specification. Metallothioneines induced mesoderm differentiation of hPSC with exclusive ability to overcome differentiation block of human leukemia. Our study provides causal evidence for a relationship between pluripotent state and human cancer that defines oncogenic reprogramming and thereby identify covert targets for cancer therapy

overall_design: Droplet-based single cell RNA sequencing of patient derived AML sample

first: Allison

middle: L

last: Boyd

first: Mio

last: Nakanishi

first: Luca

last: Orlando


title: Monocytes from peripheral blood from mouse with and without tumour

city: Edinburgh

first: Nizar

middle: N.

last: Batada

address: Crew Road

institute: Institute for Genetics and Molecular Medicine, University of Edinburgh

summary: Monocytes from peripheral blood of tumour-bearing (B6Tg(MMTV-PyMT)634Mul/Lellj) or non-tumor-bearing C57BL/6JCrl mice were FACS sorted and single cells analysed by SMARTseq2

overall_design: Single cell transcriptomic data are presented from CD11b+ CD45+ CD115+ Lineage- (CD3- CD19-NK1.1-) monocytes from 3 tumor-bearing B6Tg(MMTV-PyMT)634Mul/Lellj and 3 non-tumor-bearing C57BL/6JCrl mice.

first: Amy

last: Robinson

first: Jeffery

last: Pollard

first: Victor

last: Huicci

first: Katerina

last: Boufea


title: Bromocriptine reduces endometrial cell growth in women with adenomyosis by targeting glucose metabolism

city: Solna

first: Nageswara Rao

last: Boggavarapu

state: stockholm

address: Visionsgatan 4

department: Women and Children health

institute: Karolinska Institutet

summary: The primary aim of this study is to study the molecular changes in the endometrium of women with diffuse adenomyosis at baseline and after treatment with six months of vaginal bromocriptine, as a secondary outcome of a clinical trial.  Pictorial Blood Loss Assessment Chart (PBLAC) was used to assess the amount of menstrual bleeding. The results suggest an anti-proliferative effect of bromocriptine in the endometrium in women with adenomyosis achieved by regulating genes associated with glucose metabolism. We speculate that the above mechanism could explain the reduced bleeding and pain observed in women with adenomyosis after bromocriptine treatment.

overall_design:
The current study is a single arm, pre-post intervention study in a University-hospital initiated clinical trial.
Twelve women diagnosed with diffuse adenomyosis were administered for six months with a daily dose of 5mg vaginal bromocriptine.
Endometrial biopsies were collected at baseline and at the end of treatment.

first: Nageswara

last: Bogavarappu


title: MCM8 mediated mitophagy protects vascular health in response to nitric oxide signaling in a mouse model of Kawasaki disease

status: Public on Jun 29 2023

city: Guangzhou

first: Zhanghua

last: Chen

address: #9, Jinsui Road, Tianhe District

institute: Guangzhou Women and Children Medical Center

summary: Mitophagy is a major quality control pathway that removes unwanted or dysfunctional mitochondria, and plays an essential role in vascular health. Here we show that MCM8 expression is significantly decreased in children with Kawasaki disease (KD) who developed coronary artery aneurysms. Mechanistically, we discover that nitric oxide (NO) signaling promotes TRIM21 mediated MCM8 ubiquitination, which disrupts its interaction with MCM9 and promotes its cytosolic export. In the cytosol, MCM8 relocates to the mitochondria pore forming proteins and promotes their ubiquitination by TRIM21. In addition, MCM8 directly recruits LC3 via its LIR motif and initiates mitophagy. This suppresses mitochondrial DNA-mediated activation of type I interferon via cGAS and STING. Mice that are deficient in Mcm8, Trim21, Nos2, or reconstituted with the East-Asian specific MCM8-P276 variant develop more severe coronary artery vasculopathy in the Lactobacillus casei extract-induced KD model. Collectively, the data suggest that MCM8 protects vascular health in the KD setting.

overall_design: To investigate the role of MCM8 in protecting vascular health, we constructed wild type (Wt) and Mcm8-knock out mouse model of Kawasaki disease. Then we extracted total RNA from heart tissues and compared the transcriptomic differences of Wt and MCM8-/- mice under PBS or LCWE treatment.

first: Meng

last: Lin

first: Huifang

last: Xian

first: Yuxia

last: Zhang


title: Localized Prox1 regulates aortic valve endothelial cell diversity and extracellular matrix stratification

city: Cincinnati

first: Shreyasi

last: Mukherjee

state: OH

address: 3333 Burnet Ave

department: Developmental Biology

institute: Cincinnati Children's Hospital Medical Center

summary: We report CUT&RUN experiments to profile the genomic binding dynamics  of V5-tagged Prox1 in isolated aortic valve cells from 1 month old  NFATc1enCre Prox1 KI/+ mice or H3K27ac in isolated aortic valve endothelial cells from 1 month old wildtype mice.

overall_design: CUT&RUN experiments were performed on V5-tagged Prox1 in isolated aortic valve cells from 1 month old  NFATc1enCre Prox1 KI/+ mice or H3K27ac in isolated aortic valve endothelial cells from 1 month old wildtype mice.

first: Katherine

last: Yutzey

first: Anna

last: O'Donnell


title: miRNA profiles of natural recovery  in vitreous humor after NAION induction in rat

city: Hsinchu

first: YIHSUN

last: CHEN

address: Rm.201, Bldg. 27, No. 321, Sec. 2,  Kuang Fu Road, Hsinchu 300, Taiwan, R.O.C

country: Taiwan

institute: Biomedical Technology and Device Research Laboratories, ITRI

summary:
We collected some vitreous humors  from rat eyes through a photolabile paper based chip which experienced different natural recovery processes at day 0, 0.25, 1, 3, 7 day after eye stroke by laser induced in rat.  These mirs samples were collected from extracelluar vesicles of vitreous humor in rat.
We used microarray to find some new miRNAs that may participate in the natural recovery process after experience eye stroke.

overall_design: We used our established photolabile paper-based exosome collected chips to collect CD-63 exosomes from rare volume samples of vitreous humor in laser induced NAION model after 0, 0.25, 1, 3, 7day process of natural recovery. We observed and analysis these data, and try to find some novel miRNA may participate in natural recovery. And these miRNA maybe can be the diagnostic marker or treatment for eye stroke in the future .

first: Yihsun

first: Yaotseng

last: Wen


title: Decoding the pathogenesis of DBA by single-cell RNA-seq

first: Chenchen

last: Wang

address: Nanjing Road 288

institute: State key laboratory of Experimental Hematology

summary: Ribosomal protein dysfunction leads to diverse human diseases, including Diamond-Blackfan anemia (DBA). Despite the ubiquitous need for ribosomes in all cell types, the mechanisms underlying ribosomopathies manifesting with tissue-specific defects are still incompletely understood. In this study, at single cell resolution, we characterized the transcriptomes of highly-purified erythroid progenitors isolated from bone marrow (BM) of DBA patients, including non-treatment (NT), glucocorticoids (GC)-responsive (GCR) and GC-non-responsive (GCNR) patients. We uncovered that, rather than cell cycle arrest at G1 phase, erythroid progenitors in NT patients were compulsively entering cell cycle of S-phase, which triggered replication stress and consequently activated P53 pathway. In contrast, the cell cycle was restrained with compromised proliferation in GCR patients, but not GCNR counterparts, via elevating IFN pathway. More importantly, the combinational treatment of DEX and IFN exhibit a synergistic effect on erythrocytes from GCNR patients. Therefore, the innate cell cycle characteristics of erythroid progenitors is ascribed to the erythroid lineage specific defects of DBA. Controlling the cell cycle progression by IFN signaling underlies the GC clinical efficacy and combinational therapy of DEX and IFN holds great promise for GCNR patients.

overall_design: We sorted human BFU-E and CFU-E cells using flow cytometry from human bone marrow(healthy control, DBA patients), and then performed a modified single cell tagged reverse transcription protocol.

first: Bingrui


title: RA-dependent proximal and distal enhancers’ architecture promotes RA-induced early ESC differentiation

first: Niannian

last: Li

address: No. 94 Weijin Road, Nankai District, Tianjin

department: college of Life Sciences

summary: Retinoic acid (RA) plays a pivotal role in different biological processes including inducing differentiation of embryonic stem cells (ESCs).  We first knocked out one or both of RA receptors- Rarα and Rxrα to partially abolish the RA signaling, and then overexpressed one of them separately to hyper activation of RA signaling pathway.  By transcriptome analysis, we show that RA signaling effects multi-lineage differentiation, particularly the endoderm, and identify RA signaling target genes, interesting, there are two family cluster genes- Hoxb and Cyp26. Chromosome immunoprecipitation (ChIP-seq) shows that RA induces novel proximal and distal enhancers around the cluster target genes and these enhancers are dependent of RA receptors(Rarα/Rxrα). 4C-seq reveals enhancer-enhancer and enhancer-promoter interactions in their regions and shows a decrease in the relative frequency of contact relative to WT after Rarα/Rxrα-knockout, suggesting Rarα/Rxrα participate in mediating chromatin interaction. We also identify that enhancers significantly maintain expression of RA-induced Hoxb and Cyp26 family genes and regulate multi-lineage marker genes. At the same time, we reveal that disrupting RA-response elements (RAREs) in the enhancer affects the expression of the target gene. Our study provides mechanistic insight into RA-induced early ESC differentiation to endoderm and potential regular regulation of downstream target genes.

overall_design: 2 biological replicates were analyzed for WT (RARX), Rarα-KO, Rxrα-KO and RARX-DKO by RNA-seq in RA-treated  ESCs for 24 h, 2 biological replicates were analyzed for V-OE, Rarα-OE and Rxrα-OE by RNA-seq in RA-treated  ESCs for 24 h, 2 biological replicates of H3K27Ac ChIP-seq for WT in normal growth condition，2 biological replicates of H3K27Ac ChIP-seq  for WT (RARX), Rarα-KO, Rxrα-KO and RARX-DKO in RA-treated  ESCs for 24 h,  3 biological replicates were analyzed for WT(Cyp26), Cyp26-E1-KO and Cyp26-E2-KO by RNA-seq in RA-treated  ESCs for 24 h, 2 biological replicates were analyzed for WT (RARX), Rarα-KO, Rxrα-KO and RARX-DKO at Hoxb-E1,  Hoxb-E2,  Cyp26-E1 and Cyp26-E2 by 4C-seq in RA-treated  ESCs for 24 h

first: Wange

last: Lu

first: Xueyuan

last: Zhao

first: Guangsong

last: Su

first: Wenbin

first: Jian

last: Zheng

first: Lei


title: Changes in molecular profiles of the left ventricle during progressive dilated cardiomyopathy linked heart failure

city: Cleveland

first: Julian

middle: E.

last: Stelzer

address: 2109 Adelbert Rd.

department: Physiology and Biophysics

institute: Case Western Reserve University

summary:
To investigate molecular profiles of progressive heart failure, we studied mice that lack expression of the muscle LIM protein (MLPKO).
These mice showed dramatic HF progression between three and six weeks of age. We then performed gene expression profile analysis using data obtained from RNA-seq of mid wall left ventricular heart tissue from MLPKO mice and wild-type (WT) controls at three, six, and ten weeks of age (n=3 per group).

overall_design: Comparative gene expression profile analysis of RNA-seq data of heart tissue from three, six, and ten week MLPKO and age matched WT controls.

first: Joshua

last: Holmes


title: Chronic social defeat alters brain vascular-associated cell gene expression patterns leading to vascular dysfunction and immune system activation

city: Charlottesville

last: Samuels

state: Virginia

address: 409 Lane Road

department: Neuroscience

institute: University of Virginia

summary: Brain vascular integrity is critical for brain health, and its disruption is implicated in many brain pathologies, including psychiatric disorders. Brain-vascular barriers are a complex cellular landscape composed of endothelial, glial, mural, and immune cells. Yet currently, little is known about these brain vascular-associated cells (BVACs) in health and disease. Previously, we have demonstrated that 14 days of chronic social defeat (CSD), a mouse paradigm that produces anxiety and depressive-like behaviors, causes cerebrovascular damage in the form of scattered microbleeds. Here, we developed a technique to isolate barrier-related cells from the mouse brain and subjected the cells to single-cell RNA sequencing. Using this isolation technique, we found an enrichment in BVAC populations, including distinct subsets of endothelial and microglial cells. In CSD compared to home-cage control, differential gene expression patterns disclosed biological pathways involving vascular dysfunction, vascular healing, and immune system activation. Overall, our work demonstrates a unique technique to study rare BVAC populations from fresh brain tissue and suggests that neurovascular dysfunction is a key driver of psychosocial stress-induced brain pathology.

overall_design: Mouse neurovascular scRNAseq samples enriched via CD31-magnetic microbead isolation from chronic social defeat and home cage, non stress conditions

middle: D

first: Madison

last: Lotstein

first: Michael

last: Lehmann

first: Abdel

last: Elkahloun

first: Subhadra

last: Banerjee

first: Miles

last: Herkenham


title: Decoupled responses of the copepod Eurytemora affinis transcriptome and its microbiota to dissolved copper exposure

city: Le Havre

first: Caroline

last: Arcanjo

address: 25, rue Philippe Lebon

country: France

institute: UMR-I02 SEBIO

summary: Chemical contamination is a common threat to biota thriving in estuarine and coastal ecosystems. In particular, trace metals tend to accumulate and exert deleterious effects on small invertebrates such as zooplankton, which are essential trophic links between phytoplankton and higher-level consumers in aquatic food webs. Beyond the direct effects of the contamination, we hypothesized that metal exposure could also affect the zooplankton microbiota, which in turn might further impair host fitness. To assess this assumption, copepods (Eurytemora affinis) were sampled in the oligo-mesohaline zone of the Seine estuary and exposed to dissolved copper (25 µg.L-1) over a 72-hour time period. Copepod response to copper treatment was assessed by determining transcriptomic changes in E. affinis along with shifts in its microbiota. Unexpectedly, very few genes were differentially expressed in copper-treated copepods compared to controls, with most of the reported differences involving genes upregulated in males compared to females. In contrast, copper increased the taxonomic diversity indices of the microbiota and resulted in substantial compositional changes at both the phyla and genus levels. Phylogenetic reconstruction of the microbiota further suggested that copper mitigated phylogenetic relatedness of taxa at the basal tree structure of the phylogeny, whereas it strengthened it at the terminal branches. Increased terminal phylogenetic clustering in copper-treated copepods concurred with higher proportions of bacterial genera previously identified as copper resistant (e.g., Pseudomonas, Acinetobacter, and Alkanindiges) and a higher relative abundance of the copA gene encoding a periplasmic inducible multi-copper oxidase. Overall, these results revealed very contrasting responses of E. affinis and its microbiota to copper exposure. The enrichment in micro-organisms likely to perform copper sequestration and/or enzymatic transformation processes, underlines here the need to follow the microbial component during the evaluation of the vulnerability of the zooplankton to the metallic stress.

overall_design: Comparative gene expression analysis of RNA-seq data for adult male and female copepods Eurytemora affinis exposed to copper via the water. Triplicates were made for each condition (copper and control) and sex (male and female). Each sample correspond to a pool of 30 organisms.

first: Céline

last: Boulangé-Lecomte


title: RNA-seq analyses of mouse embryonic fibloblasts (MEFs) reprogrammed into induced pulmonary epithelial cell-like cells

city: New York

first: Hideo

last: Watanabe

state: NY

address: One Gustave L. Levy Place

department: Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine

institute: Icahn School of Medicine at Mount Sinai

summary:
RNA-seq analyses of MEFs obtained from GFP/SP-C transgenic mice on CBA/Ca x C57BL/6 mixed background were transduced sets of 3 or 4 combination factors (Nkx2-1/Foxa1/Gata, Nkx2-1/Foxa2/Gata, Nkx2-1/Foxa1/Foxa2/Gata6) into induced pulmonary epithelial cell-like cells 14 days after the transduction. Abstract is as follows: pneumocyte differentiation has been achieved previously using embryonic stem cells or induced pluripotent stem cells. However, direct reprograming of somatic cells into pulmonary epithelial cells has not been achieved. Here, we report that a combination of three or four transcription factors (i.e., Nkx2-1, Gata6, and [Foxa1 and/or Foxa2]) directly reprogrammed mouse tail-tip fibroblast or embryonic fibroblast into differentiated induced pulmonary epithelial cell-like cells (iPUL cells). iPUL cells had a global gene expression profile similar to various kinds of pulmonary epithelial cells. Some iPUL cells showed lamellar body-like structures and expressed SP-C, consistent with the features of alveolar epithelial type II cells. Interestingly, intratracheal administration of iPUL cells rescued influenza virus-induced acute lung injury in mice. These findings demonstrate that functional pulmonary epithelial cell-like cells can be directly reprogrammed from differentiated somatic cells by defined factors. Reprograming of fibroblasts might provide a source of pulmonary epithelial cells for regenerative medicine.
Publicly available raw RNA-seq data (GSE80101) representing whole mouse lung (SRR3353494, SRR3353497, SRR3353498) and alveolar type II cells (SRR3353495, SRR3353500, SRR3353510, SRR3353512) sorted in the basis of EpCAM+ and dTomato+ from SpcCreERT2;RosatdTomato mice were also simultaneously processed with our data.

overall_design: RNA-seq: 12 samples

first: Makoto

last: Ishii


title: Genome-wide methylation analysis of human breast cancer subtype group (Luminal A, Luminal B, HER2+ and TNBC)

city: Seoul

first: Jong Hoon

last: Park

address: Cheongpa-ro 47-gil 100, Yongsan-gu,

institute: Sookmyung Women's university

summary: To identify Differentially methylated regions (DMRs) in TNBCs, we performed methyl binding domain protein 2 enrichment of DNA followed by massively parallel sequencing (MBD-seq) using 10 breast tumors and 10 matched normal samples for each of the four subtypes (LumA, LumB, HER2, and TNBC), classified according to ER, PR, and HER2 expression. ~~. 468 genes were significantly hypomethylated and 353 genes were significantly hypermethylated in promoter and CDS regions in only TNBC.

overall_design: The sonicated genomic DNA was immunoprecipitated with human MBD2 protein. Next, MBD2-enriched DNA for each breast cancer subtype was used to construct DNA libraries according to the Illumina protocol.

first: Jong

first: Ye

middle: S

last: Kim

first: Woosung

last: Chung

first: Hyun

last: Kong


title: The effect of inhibition of receptor tyrosine kinase AXL on DNA damage response in ovarian cancer

status: Public on Jun 28 2023

city: Singapore

first: Tuan Zea

last: Tan

address: 14 Medical Drive, #11-01, Singapore

department: Cancer Science Institute Singapore

country: Singapore

institute: National University of Singapore

summary: To explore molecular alterations upon AXL inhibition and the functions that might be regulated by AXL and SAM68

overall_design:
Next, we performed RNA-sequencing on OV cells treated with DMSO or R428, OV cells with AXL knockout and OV cells with SAM68 KO to map out common biological processes distinctive to respective cell type and to compare their gene expression profile
We performed gene expression profiling analysis using data obtained from RNA-seq of 1 cell line treated with AXL inhibition at two time points, AXL knockout cell line and SAM68 knockout cell line

first: Xun

middle: H

last: Yeo

first: Wai

last: Tam

first: Ruby

middle: Y

last: Huang