title: mRNA and lncRNA profiling of mice spleens inoculated with group ACYW135 meningococcal polysaccharide vaccine

first: Haiguang

last: Mao

state: Zhejiang

address: Yuhangtang Road 866

institute: Zhejiang University

summary: Group ACYW135 meningococcal polysaccharide vaccine (MPV-ACYW135) is a classical common vaccine used to prevent Neisseria meningitidis serogroup A, C, Y, W135. Although immunological research on MPV has been relatively complete in the past few decades, studies on the vaccine at the transcriptional levels are still limited. In the present study, mRNAs and lncRNAs related to immunity were screened from spleens of mice inoculated with MPV-ACYW135 and compared with the control group to identify the effect and mechanism of these mRNAs and lncRNAs on the immune response. A comprehensive analysis of mRNAs and lncRNAs between MPV group and control group was performed by RNA-seq with bioinformatics.

overall_design: The experiment was divided into 2 groups with 3 mice in each group. Mice in one group were injected with MPV-ACYW135, and the other group was the control group. The spleen is used for RNA sequencing. Comparative gene expression profiling analysis of RNA-seq data for MPV group (MPV_S_1, MPV_S_2, and MPV_S_3) and control group (Control_S_1, Control_S_2, and Control_S_3).

first: Mengting

last: Wang

last: Zhu

first: Jinbo


title: Haspin regulates mouse embryonic stem cell developmental potencies through Wnt5a mediated asymmetric cell division

status: Public on Aug 30 2023

city: shanghai

first: ying

middle: ying

last: Gao

address: Siping Road Street

country: China

institute: Tongji University

type: Expression profiling by high throughput sequencing

summary: To investigate the function of Haspin in the mouse embryonic stem cell, we established Haspin knockout cell lines.

overall_design: We performed gene expression profiling analysis using data obtained from RNA-seq from WT and Haspin knockout cells.

first: Yingying

first: Binbin

last: Ma

first: Yifan

last: Li

first: Xiangyu

last: Wu


title: Shared and organ-specific gene-expression programs during the development of the cochlea and the superior olivary complex

city: Tel Aviv

first: Karen

last: Avraham

country: Israel

institute: TAU

type: Non-coding RNA profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: MicroRNAs as predictors for postoperative outcome in patients with limited stage neuroendocrine carcinoma of the esophagus

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

country: Japan

institute: Toray Industries,Inc.

summary: Microarray analysis of 2630 miRNAs in 11 patients with sufficient quality RNA in pared tumor/normal specimens identified miRNAs that were differentially expressed between the patients with (n=6) and without (n=5) postoperative tumor relapse.

overall_design: The FFPE samples of the tumors (T) and their normal counterparts (N) were obtained for each case, sections (100 μm) were prepared, and total RNA was extracted. Extracted RNA samples were labeled and hybridized to a 3D-Gene Human miRNA Oligo chip (Toray Industries Inc., Tokyo, Japan) mounted with 2632 genes.

first: Tomoyuki

last: Okumura


title: CRISPR/dCas9 DNA methylation editing is heritable during human haematopoiesis and can impair differentiation in vivo [Targeted BS-seq]

city: London

first: Gabriella

last: Ficz

state: Rest of the World

address: Centre for Haemato-Oncology

country: United Kingdom

institute: Barts Cancer Institute, Queen Mary University of London

type: Methylation profiling by high throughput sequencing

summary: Ageing is associated with an abnormal increase of DNA methylation in human gene promoters, including in the bone marrow stem cells. DNA methylation patterns are further perturbed in haematological malignancies such as acute myeloid leukaemia (AML) but the physiological significance of such epigenetic changes is unknown. Using epigenetic editing of human stem/progenitor cells (HSPCs), we show evidence that p15 methylation affects haematopoiesis in vivo. We edited the CDKN2B (p15) promoter and ARF (p14) using dCas9-3A3L and observed DNA methylation spreading beyond the location of the gRNA. We find that despite a transient delivery system, DNA methylation is maintained during myeloid differentiation in vitro, and hypermethylation of the p15 promoter reduces gene expression. In vivo, edited human HSPCs can engraft the bone marrow of mice and targeted DNA methylation is maintained in HSPCs long term. Moreover, we identified how the epigenetic changes are conserved and inherited in both myeloid and lymphoid lineages. Although the proportion of myeloid (CD33+) and lymphoid (CD19+) cells is unaffected, monocyte (CD14+) populations decreased and granulocytes (CD66b+) increased in mice engrafted with p15 hypermethylated cells. We also observe significant changes in the proportions of multipotent and committed progenitor cells. This may have clinical relevance since we found that p15 promoter methylation is present in the peripheral blood of patients with clonal haematopoiesis. Our study shows DNA methylation can be targeted and maintained in human HSPCs and demonstrated functional relevance of aberrant DNA methylation on the p15 locus. As such, other ageing associated aberrant DNA methylation may impact haematopoiesis in vivo.

overall_design: Targeted bisulfite-sequencing data from the p15, p14 and p16 promoter after epigenetic editing or targeted-seq data at TET2 after genetic editing in haematopoetic stem and progenitor cells and in vitro experiments (colony forming unit assay) or in vivo engraftment into mice. Also targeted bisulfite sequencing of the p15 and p14 promoters in patients with Clonal Hematopoiesis

first: Emily

middle: A

last: Saunderson


title: Breast cancer prevention with liquiritigenin

city: Chicago

first: Atieh

last: Hajirahimkhan

state: Illinois

address: 303 E Superior, 4-220

country: USA

institute: Northwestern University

summary:
Breast cancer risk continues to increase post menopause. Anti-estrogen therapies are available to prevent postmenopausal breast cancer in high-risk women. However, their adverse effects have reduced acceptability and overall success in cancer prevention. Natural products such as hops (Humulus lupulus) and three pharmacopeial licorice (Glycyrrhiza) species have demonstrated estrogenic and chemopreventive properties, but little is known regarding their effects on aromatase expression and activity as well as pro-proliferation pathways in human breast tissue. We show that Gycyrrhiza inflata (GI) has the highest aromatase inhibition potency among these plant extracts. Moreover, phytoestrogens such as liquiritigenin which is common in all licorice species have potent aromatase inhibitory activity, which is further supported by computational docking of their structures in the binding pocket of aromatase. In addition, GI extract and liquiritigenin suppress aromatase expression in the breast tissue of high-risk postmenopausal women. Although liquiritigenin has estrogenic effects in vitro, with preferential activity through estrogen receptor (ER)-β, it reduces estradiol-induced uterine growth in vivo. It downregulates RNA translation, protein biosynthesis, and metabolism in high-risk women’s breast tissue. Finally, it reduces the rate of MCF-7 cell proliferation, with repeated dosing. Collectively, these data suggest that liquiritigenin has breast cancer prevention potential for high-risk postmenopausal women.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 4 different cells at two time points.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for breast tissue microstructures obtained from high-risk postmenopausal women and exposed to liquiritigenin for 24 h was performed.

first: Caitlin

last: Howell

first: Elizabeth

last: Bartom

first: Huali

last: Dong

first: Daniel

last: Lantvit

first: Xiaoling

last: Xuei

first: Shao-Nong

last: Chen

first: Guido

last: Pauli

first: Judy

last: Bolton

first: Susan

last: Clare

first: Seema

last: Khan

first: Birgit

last: Dietz


title: CRISPR/dCas9 DNA methylation editing is heritable during human haematopoiesis and can impair differentiation in vivo [methylation array]

type: Methylation profiling by genome tiling array


title: Shared and organ-specific gene-expression programs during the development of the cochlea and the superior olivary complex [RNA-seq]

first: Karen

last: Avraham

summary: To study and compare the genes and miRNA expression during the development of the Organ of Corti and the Superior Olivary complex, representing the peripheral and the central auditory systems.

overall_design: We extracted RNA and small RNA from these two organs at 3 important developmental time points and performed bioinformatical analysis of the expression and performed bioinformatical analysis of the expression.

first: Mor

last: Bordeynik-Cohen

first: Michal

last: Sperber

first: Ran

last: Elkon


title: exoRNA-mediated Cell-to-cell Communications in E. coli are Supported by Dps Mobility

city: Pushchino

first: Konstantin

middle: S.

last: Shavkunov

address: Institutskaya street, 3

country: Russia

institute: Institute of Cell Biophysics RAS

summary: Being a ferroxidase and a structural factor of the Escherichia coli nucleoid, Dps protein was recently encountered in the outer membrane and attracted attention as a potential partner for bacterial RNAs. Here, we show the first images visualizing Dps on the surface of bacteria and demonstrate that Dps produced by E. coli K-12 MG1655 or BL21(DE3) cells can cross bacteria-impermeable membrane and attach to the cell surface of a dps-null mutant. Using RNAseq and pull-down assays, we identified RNAs with specifically reduced secretion in the mutant and witnessed preferential interaction of Dps with tRNA and sRNA fragments. Upon analysis of their deviations from the genomic sequences, we selected one circular and six linear oligonucleotides with different folding as model RNAs and showed their ability to affect the growth of bacteria via Dps-dependent internalization by cells. This assumes Dps involvement in intercellular signal transduction within a bacterial population through participation in RNA secretion

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: Secretion of E.coli RNAs in the presence or absence of Dps was studied using RNA-seq and pull-down assays

first: Olga

middle: N

last: Ozoline

middle: S

first: Natalia

middle: Y

last: Markelova

last: Glazunova

first: Uliana

last: Shvyreva

first: Nikolay

middle: P

last: Kolzhetsov

middle: V

last: Alikina

first: Valery

last: Panyukov

first: Sergey

last: Antipov

first: Elena

last: Shilova

first: Eleva

last: Preobrazhenskaya


title: Shared and organ-specific gene-expression programs during the development of the cochlea and the superior olivary complex [miRNA-seq]

overall_design: We extracted RNA and small RNA from these two organs at 3 important developmental time points and performed bioinformatical analysis of the expression.


title: The LncRNA promotes vessel co-option mediated antiagiogenic therapies (AATs) resistance

city: guangzhou

first: wen

last: qing

state: State...

address: guangzhou

institute: jinan university

summary: To identify the lncRNAs that may participate in antiangiogenic therapy (AAT) resistance, the bevacizumab-resistant HCT116 CRCLM xenografts were established.

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of bevacizumab-sensitive HCT116 CRCLM and bevacizumab-resistant HCT116 CRCLM xenografts tissues. Comparative gene expression profiling analysis of RNA-seq data for bevacizumab-sensitive HCT116 CRCLM and bevacizumab-resistant HCT116 CRCLM xenografts tissues.

first: Dongmei

last: Zhang

first: Minfeng

last: Chen

first: Qing

last: Wen

first: Jingwen

last: Xie


title: Acidosis-induced gene expression regulation in human epithelial cells, fibroblasts and aortic vascular smooth muscle cells (in monoculture)

city: Halle (Saale)

first: Virginie

last: Dubourg

address: Magdeburger Str. 6

department: Julius Bernstein Institute for Physiology

country: Germany

institute: Martin Luther University - Halle-Wittenberg

summary: Acidic milieu induced gene expression regulation in HK2 cells (derived from the proximal tubule), CCD-1092SK (foreskin fibroblasts) and HAoSMC (primary human aortic smooth muscle cells)

overall_design: HK2, CCD-1092SK and HAoSMC were cultivated with an acidic milieu (pH 6.4 or 6.8) for 48h, before proceeding with RNAseq. pH 7.4 served as reference for all cell types.

first: Marie-Christin

last: Schulz

first: Stefanie

last: Ruhs

first: Philipp

last: Terpe

first: Michael

last: Kopf

first: Gerald

last: Schwerdt

last: Gekle


title: LSD1 inhibtion in NEPC cell line models.

city: Ann Arbor

first: Karan

last: Bedi

state: MI

address: 1600 Huron Pkwy

department: Biostatistics

institute: University of Michigan

summary: Lysine-specific demethylase 1 (LSD1) is a histone demethylase that promotes stemness and cancer cell survival, including in prostate cancer. Most prostate malignancies are adenocarcinomas with luminal differentiation. However, a subset of tumors undergoes cellular reprogramming to a more lethal neuroendocrine prostate cancer (NEPC) with neuronal differentiation. The frequency of NEPC is increasing since widespread use of potent androgen receptor signaling inhibitors. Currently, there are no effective treatments for NEPC. We previously determined that LSD1 promotes survival of prostate adenocarcinoma tumors. However, role of LSD1 in NEPC is largely unknown. We sought to identify key genes and molecular pathways controlled by LSD1 in NEPC. We therefore inhibited LSD1 with SP2509 and performed RNA-seq in LASCPC-01, LNCaP-N-Myc, and MR42D cell lines. The vast majority of differentially expressed genes after SP2509 treatment were upregulated, suggesting that LSD1 may primarily function as a transcriptional repressor in NEPC. RNA-seq analysis reveals that LSD1 represses pathways linked to luminal differentiation and TP53 is the top pathway reactivated after LSD1 suppression. Taken together, these data suggest that LSD1 may be an important regulator of TP53 function in prostate cancer.

overall_design: Three cell lines (LNCaP-NMyc, LASCPC-01 and MR42D) were treated with allsoteric LSD1 inhibitor SP2509 or vehicle (DMSO) in biological triplicates.

first: Anbarasu

last: Kumaraswamy

first: Zhi

last: Duan

first: Armand

last: Bankhead III

first: Zheng

last: Xia

first: Joel

last: Yates

first: Joshi

middle: J

last: Alumkal


title: CRISPR/dCas9 DNA methylation editing is heritable during human haematopoiesis and can impair differentiation in vivo.

first: Gabriella

last: Ficz


title: Acidosis-induced gene expression regulation in rat cells (in monoculture)

summary: Acidic milieu induced gene expression regulation in proximal tube cells (NRKE) and kidney fibroblasts (NRKF) from rats.

overall_design: NRKE and NRKF were cultivated (in monoculture) with pH 7.4 (control) or pH (6.0) for 48h, before proceeding with RNAseq.


title: Dna2 removes toxic RPA-ssDNA flaps generated from meiotic recombination-associated DNA synthesis

city: Jinan

first: liangran

last: zhang

state: Shandong

address: Jingshi Street

department: State Key Laboratory of Microbial Technology

institute: Shandong University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: During the repair of DNA double-strand breaks (DSBs), de novo synthesized DNA strand can displace the parental strand to generate single-strand DNA (ssDNA) flaps. Many programmed DSBs and thus many ssDNA flaps occur during meiosis. However, how these flaps are removed remains enigmatic. Here, we show that meiosis-specific depletion of Dna2 (dna2-md) in Saccharomyces cerevisiae causes an abundant accumulation of RPA-ssDNA flaps and an expansion of RPA from DSBs to broader regions. As a result, DSB repair is defective and spores are inviable, although the levels of crossovers/non-crossovers seem to be unaffected. Furthermore, inducing Dna2 expression at pachytene is highly effective in removing accumulated RPA and restoring spore viability. Moreover, the depletion of Pif1, an activator of polymerase δ required for meiotic recombination-associated DNA synthesis, and Pif1 inhibitor Mlh2 decreased and increased RPA accumulation in dna2-md, respectively. Together, our findings show that meiotic DSB repair requires Dna2 to remove RPA-ssDNA flaps generated from meiotic recombination-associated DNA synthesis. Additionally, we showed that Dna2 also regulates DSB-independent RPA distribution.

overall_design: Wild type, dna2-md, dna2-md spo11Y135F were analyzed. Cells were collected at SPM 4h and 7h, then Rfa1 antibody is used for ChIP experiment.

first: Binyuan

last: Zhai

first: Bo

last: Li

first: Jiaming

last: Zhang

first: Yingjin

last: Tan


title: Discovery of novel differentially expressed genes related to interstitial fibrosis and tubular atrophy among kidney transplantation recipients by mRNA-sequencing

city: Seoul

first: HyunKyung

last: Lee

address: 101, Daehak-ro

country: South Korea

institute: Seoul National University

summary:
Interstitial fibrosis and tubular atrophy (IF/TA) after kidney transplantation causes chronic deterioration of graft function. IF/TA can be diagnosed by graft biopsy; however, non-invasive diagnostic methods are unavailable. In this study, we identified IF/TA-related differentially expressed genes (DEGs) through next-generation sequencing using peripheral blood mononuclear cells (PBMCs)
PBMC samples from kidney transplantation recipients under standard immunosuppressive therapy (tacrolimus/mycophenolate mofetil or mycophenolate sodium/steroid) and diagnosed as IF/TA (n = 41) or normal (controls; n = 41) at their 1-year protocol biopsy were recruited between January 2020 and August 2020.

overall_design: DEGs were derived through mRNA-sequencing.

first: Hyun

middle: K

first: In-Wha

last: Kim

first: Jung

middle: M

last: Oh


title: HeberFERON distinctively targets Cell Cycle in the glioblastoma-derived cell line U-87MG

city: La Habana

first: Jamilet

last: Miranda

address: Ave. 31 No. 15802 between 158 and 190, Cubanacán, Playa

department: Bioinformatics

country: Cuba

institute: Center for Genetic Engineering and Biotechnology (CIGB)

summary:
Transcriptomic profile study comparing human glioblastoma derived cell line U-87MG treated with HeberFERON, alpha and gamma interferons.
HeberFERON is a co-formulation of alpha2b and gamma interferons, based on their synergism, that have shown its clinical superiority over individual interferons in basal cell carcinomas. In Glioblastoma (GBM), HeberFERON has shown promising preclinical and clinical results. This motivated us to design a microarray experiment aimed to identify the molecular mechanisms involved into the distinctive effect of HeberFERON compared with individual interferons.  Transcriptional expression profiling including a control (untreated) and three groups receiving alpha2b-interferon, gamma-interferon and HeberFERON was performed using an Illumina HT-12 microarray platform. Unsupervised methods for gene and sample grouping, identification of differentially expressed genes, functional enrichment and network analysis computational biology methods were applied to identify distinctive patterns of HeberFERON action. Validation of most distinctive genes was performed by qPCR. Cell Cycle analysis of cell treated by HeberFERON for 24h, 48h and 72h was carried out by flow cytometry. The three treatments show different behavior based on the gene expression profiles. Enrichment analysis identified several Mitotic Cell Cycle related events, in particular from Prometaphase to Anaphase, that are exclusively targeted by HeberFERON. FOXM1 transcription factor network which is involved in several Cell Cycle phases and is highly expressed in GBMs is significantly down regulated by HeberFERON. Flow cytometry experiments corroborated the action of HeberFERON over Cell Cycle in a dose and time dependent manner with a clear cellular arrest since 24h post-treatment. Despite the fact that p53 was not down-regulated by HeberFERON several genes involved in its regulatory activity were functionally enriched. Network analysis also revealed a strong relation of p53 with genes targeted by HeberFERON. We propose a mechanistic model to explain HeberFERON distinctive action, based on the simultaneous activation of PKR and ATF3, p53 phosphorylation changes as well as its reduced MDM2 mediated ubiquitination and export from nucleus to cytoplasm. PLK1, AURKB, BIRC5 and CCNB1 genes, all regulated by FOXM1, also play central roles in this model. These and other interactions could explain a G2/M arrest and the effect of HeberFERON over the proliferation of U-87MG. We proposed molecular mechanisms underlying the distinctive behavior of HeberFERON compared to individual interferon treatments, where Cell Cycle related events showed the highest relevance.

overall_design: Four groups or conditions with six biological replicates each, including cells: treated with IFNalpha2b, treated with IFNgamma, treated with HeberFERON co-formulation and a control untreated group.

first: Dania

last: Vázquez-Blomquist


title: A Spatial Transcriptome for Germinating Barley Grain

city: Bundoora

first: Mathew

middle: G

last: Lewsey

state: VIC

address: AgriBio, 5 Ring Rd

department: Animal, Plant and Soil Sciences

country: Australia

institute: La Trobe University

summary: A spatial resolved transcriptome for germinating barley grain was obtained for over 14,000 genes at 0, 1, 3 6 and 24 hours after imbibition. The spatial expression of a number of genes was validated using in-situ PCR, quantitative comparison to bulk RNA-seq reveal good correlations, despite the differences in the methodologies, and marker gene definition for tissues/clusters was consistent with previous gene specific studies. Targeted analysis of genes encoding aquaporins, crucial for water and ion movement during germination, revealed specific spatial expression patterns for gene members, and the tissue specific changes in gene members over time. Highly restricted spatial (and temporal) expression patterns were observed for genes encoding cell wall and transcription factors, e.g. one of the strongest expressed transcription factors was a bZIP family member that responds to germinating promoting Karrikin. It’s expression was restricted to the scutellum and the adjacent endosperm (0-3 HAI) and declined afterwards. Discovery-based bio-informatic approaches revealed thousands of genes displayed a spatially restricted pattern within tissues, with gene ontology revealing enriched categories such as auxin related functions of transport and response factors displaying distinct spatial expression patterns in tissues. This provides unprecedented spatial resolved cellular map for germination and specific genes to target for functional genomics to define cellular restricted processes in tissues during germination.

overall_design: Germinating barley grain were snap-frozened and longitudinal sectioned. The section of barley grains were sequenced and analysized using Visium protocol (10X Genomics). .

first: Marta

last: Peirats-Llobet

first: Changyu

last: Yi

first: Lim

middle: C

last: Liew

first: Oliver

last: Berkowitz

first: Reena

last: Narsai

first: James

last: Whelan


title: Transcriptional effects of extended opioid exposure in clear cell renal cell carcinomas.

city: Rockville

first: Alexis

middle: L

last: Norris

state: MD

address: 7500 Standish Place

institute: US FDA

summary: Opioids are commonly prescribed to patients with advanced clear cell renal cell carcinoma for extended periods of time in assistance for pain management. Because extended opioid exposure has been shown to affect the vasculature and to be immunosuppressive, we investigated how it may affect the metabolism and physiology of advanced clear cell renal cell carcinoma. RNA sequencing of archived patient’s specimens with extended opioid exposure or non-opioid exposure were peformed.

overall_design: The mRNA profiling of formalin-fixed paraffin-embedded (FFPE) section of clear cell kidney tumors from patients with "extended opioid exposure” (>=6 weeks), compared to those from patients with untreated (naïve) clear cell kidney tumors.

first: Mamatha

last: Garige

first: Carole

last: Sourbier


title: Effect of DHP and progesterone treatment on oocyte and egg transcriptomes of European eel (Anguilla anguilla)

city: Leiden

first: Ron

last: Dirks

address: Sylviusweg 74

country: Netherlands

institute: Future Genomics Technologies BV

summary: Since the identification of 17α,20β-dihydroxy-4-pregnen-3-one (DHP) as the main maturation-inducing hormone (MIH) in Japanese eel A. japonica, female European eels have been injected with this steroid to induce oocyte maturation and ovulation. However, the females injected with DHP need to ovulate rapidly following the DHP injection to release good quality eggs.  In this study, we compared treatment of progesterone (P) with DHP treatment as control, in vitro, to determine dose-response effects, and in vivo, at a single dose. Females were first matured by the routine protocol of weekly injections with carp pituitary extract (CPE at 20 mg kg-1) until a significant oocyte hydration response occurred as indicated by an increase of the body weight and oocytes displaying germinal vesicle migration. For the in vitro experiment, ovarian tissue was extracted and placed in culture plates containing hormone-free medium and media supplemented with the treatment (P: 10, 100, 1,000 ng.mL-1; DHP: 1, 10 and 100 ng.mL-1). Before and after incubation for 12 and 18 h, the folliculated  oocytes  were sampled for microscopy and gene expression analysis. For the in vivo experiment, females were either injected with P or DHP at a dose of 2 mg.kg-1 to assess their effects on ovulation and reproductive success. At the moment of stripping, eggs were sampled for RNA-sequencing to compare P vs. DHP stripped eggs with focus on genes marking gamete quality. Remaining eggs were fertilized and larval viability was recorded. Both P and DHP were able to induce germinal vesicle breakdown in vitro (P at 100 and 1,000 ng mL-1 ;DHP at 10 ng and 100 ng mL-1). RNAseq results reflected similar P and DHP effects on the expression of genes involved in egg quality aspects. Also expression of genes involved in oocyte maturation and ovulation was similar for both P and DHP treatment. Females injected with either P or DHP ovulated, released eggs and were equally able to produce larvae without any differences in reproductive success. Our results support the conclusion that P and DHP have similar competence as MIH which may be because P binds to the membrane progestin receptors  with similar capacity as DHP does. P is more attractive to apply as the price is 3,000 times lower than the price of DHP.

overall_design: Differential gene expression analysis of RNA-seq data (all samples in triplicate) for control oocytes before DHP and progesterone treatment and eggs harvested after either DHP or progesterone treatment.

first: Arjan

last: Palstra

first: Pauline

last: Jéhannet


title: Next Generation Sequencing For Quantitative Analysis Of Hepatic Transcriptomes In Response To Squalene in Swine model

city: Zaragoza

first: Roubi Hamid

middle: Ahmad

last: AbuObeid

state: Spain

address: calle de Miguel Servet, 177

country: Spain

institute: university of Zaragoza

summary:
Purpose: The goal of this study was to determine squalene effect on hepatic transcriptome by comparing high-throughput data for tested group vs. control group in male Large White x Landrace Large swine animals
Method: Study the Hepatic mRNA profile of swine animals in response to a steatotic diet supplied with 0.5% squalene over a month  by Transcriptome sequencing using DNBseq platform. Sequence reads that passed quality filters were mapped onto reference genome, followed by SNP & INDEL  variants calling and Gene expression detection.
Results:   Squalene intake did not significantly influence single nucleotide polymorphisms.   When alternative splicing events were tested, squalene administration had significant influence on splicing events including alternative 5' splicing, alternative 3' splicing , retained intron, skipped exons and mutually exclusive exons.  Splicing patterns led to variety of differentially splicing genes and a variety of different isoforms from one gene. Differentially expressed genes were 18,659 in the squalene group and 18,602 in control group.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Pig consuming a steatotic diet and their counterparts consuming the same diet enriched in 0.5% squalene

first: Roubi

middle: H

last: Abuobeid

first: Luis

last: Herrera

first: Roberto

last: Martínez-Beamonte

first: Jesus

last: Osada


title: Abstinence from Escalation of Cocaine Intake Changes the microRNA Landscape in the Cortico-Accumbal Pathway

city: Boston

first: Huiping

last: Zhang

state: MA

address: 72 East Concord Street

institute: Boston University

summary:
Cocaine administration alters the microRNA (miRNA) landscape in the cortico-accumbal pathway. These changes in miRNA can play a major role in the posttranscriptional regulation of gene expression during withdrawal. This study aimed to investigate the changes in microRNA expression in the cortico-accumbal pathway during acute withdrawal and protracted abstinence following escalated cocaine intake. Small RNA sequencing (sRNA-seq) was used to profile miRNA
transcriptomic changes in the cortico-accumbal pathway [infralimbic- and prelimbic-prefrontal cortex (IL and PL) and nucleus accumbens (NAc)] of rats with extended access to cocaine self-administration followed by an 18-h withdrawal or a 4-week abstinence. An 18-h withdrawal led to differential expression (fold-change > 1.5 and p < 0.05) of 21 miRNAs in the IL, 18 miRNAs in the PL, and two miRNAs in the NAc. The mRNAs potentially targeted by these miRNAs were enriched in the following pathways: gap junctions, neurotrophin signaling, MAPK signaling, and cocaine addiction. Moreover, a 4-week abstinence led to differential expression (fold-change > 1.5 and p < 0.05) of 23 miRNAs in the IL, seven in the PL, and five miRNAs in the NAc. The mRNAs potentially targeted by these miRNAs were enriched in pathways including gap junctions, cocaine addiction, MAPK signaling,
glutamatergic synapse, morphine addiction, and amphetamine addiction. Additionally, the expression levels of several miRNAs differentially expressed in either the IL or the NAc were significantly correlated with addiction behaviors. Our findings highlight the impact of acute and protracted abstinence from escalated cocaine intake on miRNA expression in the cortico-accumbal pathway, a key circuit in addiction, and suggest developing novel biomarkers and therapeutic approaches to prevent relapse by targeting abstinence-associated miRNAs and their regulated mRNAs.

overall_design: Compare miRNA transcriptome profiles among the three groups of rats (4-week abstinence vs. naïve; 16-hr withdrawal vs. naïve; and 4-week abstinence vs. 16-hr withdrawal)

first: Zhang

last: Huiping


title: RNA-sequencing data of HCT116-wild type (WT), HCT116-A20 knockout (KO) and HCT116-A20-KO-rescue (OE) cells

city: Guangzhou

first: Min

last: Luo

state: Guangdong

address: No.651,Dongdeng East Road

institute: Sun Yat-sen University Cancer Center

summary:
Purpose:  The goals of this study are to compare the transcriptome profiling (RNA-seq) of different A20 expression in HCT116 cells, to find potiential target genes for A20 mediated immnue escape.
Results: There were 352 genes altered after A20 was knocked out with the log-fold >2 or <-2 compared to WT cells, and p value<0.01 .  And 143 genes changed after rescued the expression of A20 in A20-KO cells compared to A20-KO cells.  Among these altered genes, 13 genes were changes consistently.
Conclusion:Gain- and loss-A20 functional studies proved that A20 could decrease the ¡°eat-me¡± signal calreticulin (CRT) protein on cell membranes via stabilizing stanniocalcin 1 (STC1).  Mechanistically, A20 inhibited the degradation of STC1 protein which could capture the CRT inside cell rather than to translocated to cell membrane.

overall_design: Methods:We used RNA-sequence assays to compare the expression of A20-related genes in HCT116-KO cells with A20-WT cells and A20-OE cells with A20-KO cells, respectively.

first: Xueping

last: Wang

first: Shaocong

last: Wu

first: Chuan

last: Yang

first: Qiao

last: Su

first: Lamei

last: Huang

first: Kai

last: Fu

first: Sainan

last: An

first: Fachao

last: Xie

first: Fang

first: Liwu


title: Selective enrichment of plasma cell-free messenger RNA in cancer-associated extracellular vesicles

city: PORTLAND

first: Hyun Ji

last: Kim

state: Oregon

address: 3181 SW Sam Jackson Park Rd.

institute: Oregon Health and Science University

summary: Cell-free messenger RNA (cf-mRNA) has shown promising diagnostic potentials. Unlike well-characterized extracellular miRNA, how cf-mRNA is protected and its potential biological significance remains unknown. To characterize the carriers of cf-mRNA in human plasma and their association with cancers, we performed transcriptome analysis of cf-mRNA in size-fractionated plasma from patients with lung cancer, liver cancer and multiple myeloma, and healthy donors. We found that the majority of cf-mRNA was enriched in extracellular vesicles (EVs) and was protected in EVs with remarkable stability in RNase-rich environments. We observed specific enrichment patterns of cf-mRNA in each vesicular and non-vesicular subpopulation in cancers. These EV-enriched differentiating genes are associated with specific biological pathways, such as immune systems, liver function, and oxygen transport in lung cancer, liver cancer, and multiple myeloma, respectively. Our results suggest that dissecting the complexity of EVs subpopulations illuminates their biological significance and becomes a promising approach for novel biomarker development.

overall_design: We sequenced total cell-free plasma RNA from 120 size-fractionated extracellular carriers (medium EVs, small EVs, non-EV particles, and soluble plasma protein fractions associated with early-, middle-, and late-eluting proteins) using lung cancer, liver cancer, multiple myeloma and healthy control sample set.

first: Thuy

middle: T

last: Ngo

first: Hyun


title: Elevated Dietary Non-Esterified Fatty Acid Levels Impact BeWo Trophoblast Metabolism and Lipid Processing: A Multi-OMICS Outlook

first: Timothy

middle: RH

last: Regnault

state: Ontario

address: Medical Sciences Building, Room 216

department: Physiology and Pharmacology

country: Canada

institute: Western University

summary: Maternal obesity and gestational diabetes mellitus (GDM) are associated with adverse intrauterine environments that are high in circulating nutrients. These adverse environments facilitate impairments in placental mitochondrial function and nutrient processing that ultimately leads to an increased risk of the exposed offspring developing non-communicable cardiometabolic health disorders (e.g. obesity, type 2 diabetes, metabolic syndrome). Analysis of fasting serum lipid levels in the third trimester has highlighted that Palmitate (PA) and oleate (OA) are the most abundance non-esterified fatty acids (NEFAs) in circulation. More importantly, these important NEFAs are elevated in both obese and GDM pregnancies. As PA and OA are the most abundant NEFAs in the typical “Westernized Diet” they elevated levels in obese and GDM pregnancies may highlight increased maternal consumption of these fats and could be a link between poor diet and abberant placental function. However, the independent and combined impacts of dietary PA and OA on mitochondrial function and nutrient processing in placental trophoblast cells remains poorly defined. Thus, in this study we sought to utilize a multi-omics approach (combining transcriptomics with untargeted metabolomics and lipidomics) to elucidate the underlying impacts of elevated NEFA levels on BeWo placental trophoblast cells. We highlighted a significant enrichment in the Wikipathways Fatty Acid Biosynthesis Pathway in BeWo cytotrophoblast cells treated with a combination of PA and OA (P/O; 50 µM each). Further, we identified differential expression of genes involved in lipid processing (e.g. ACADVL, ACACB, ACSL5, CREB3L3, PLIN2, and SCD) in BeWo cytotrophoblast cells treated with dietary NEFA species. Overall, these data highlighted that alterations in lipid processing, storage, and oxidation are implicated in the development of placental dysfunction in response to elevated lipid levels.

overall_design: 20 total BeWo cytotrophoblast samples cultured with dietary fats conjugated to BSA for 72 hours, 5 treated with F12K media supplemented with 0.3% Fatty Acid-Free BSA (BSA control); 5 treated with F12K media supplemented with 100 µM Palmitate (PA; 2:1 conjugation to BSA);  5 treated with F12K media supplemented with 100 µM Oleate (OA; 2:1 conjugation to BSA);  5 treated with F12K media supplemented with 50 µM each PA and OA (P/O; 2:1 conjugation to BSA)

first: Zachary

last: Easton

first: Xian

first: Liang

last: Li

middle: R


title: Cell type-specific attenuation of brassinosteroid signaling precedes stomatal asymmetric cell division

city: Ghent

first: Bert

last: De Rybel

address: Technologiepark 71

department: Center for Plant Systems Biology

country: Belgium

institute: VIB

summary: In Arabidopsis thaliana, brassinosteroid (BR) signaling and stomatal development are connected through the SHAGGY/GSK3-like kinase BR INSENSITIVE2 (BIN2). BIN2 is a key negative regulator of BR signaling but it plays a dual role in stomatal development. BIN2 promotes or restricts stomatal asymmetric cell division (ACD) depending on its subcellular localization, which is regulated by the stomatal lineage-specific scaffold protein POLAR. BRs inactivate BIN2, but how they govern stomatal development remains unclear. Mapping the single-cell transcriptome of stomatal lineages after triggering BR signaling with either exogenous BRs or the specific BIN2 inhibitor, bikinin, revealed that the two modes of BR signaling activation generate spatiotemporally distinct transcriptional responses. We established that BIN2 is always sensitive to the inhibitor but, when in a complex with POLAR and its closest homolog POLAR-LIKE1, it becomes protected from BR-mediated inactivation. Subsequently, BR signaling in ACD precursors is attenuated, while it remains active in epidermal cells devoid of scaffolds and undergoing differentiation. Our study demonstrates how scaffold proteins contribute to cellular signal specificity of hormonal responses in plants.

overall_design: Single-cell RNA-seq experiments were performed on protoplast cells extracted from the aerial tissue of 5 day old Arabidopsis thaliana seedlings.

first: Eun-Ji

first: Cheng

first: Boyu

last: Guo

first: Thomas

last: Eekhout

first: Anaxi

last: Houbaert

first: Jos

last: Wendrich

first: Niels

last: Vandamme

first: Yvan

last: Saeys

first: Manish

last: Tiwari

first: Claire

last: Simon-Vezo

first: Isabelle

last: Vanhoutte

first: Yuxian

last: Zhu

first: Kun

first: Eugenia

last: Russinova


title: Amphiregulin couples IL1RL1+ regulatory T cells and cancer-associated fibroblasts to inhibit antitumor immunity

city: PITTSBURGH

first: runzi

last: sun

state: PA

address: 203 Lothrop st

institute: university of pittsburgh

summary: We demonstrated that IL-33 induced strong CD8+ T cell antitumor immune responses characterized by robust clonal expansion and vigorous functional diversification. Nonetheless, IL-33 also produced intense regulatory T cell (Treg) accumulation in the TME, dominated by the IL1RL1+ Treg subset. We further showed that IL1RL1 signaling in Treg cells greatly dampened the antitumor activity of IL-33.

overall_design: Paired single cell RNA-seq and TCR-seq from FACS sorted T cells from mouse transplant melanoma B16 and IL-33 expressing B16-IL33 tumors.

first: Runzi

last: Sun

first: Binfeng

last: Lu


title: Adaptive Metabolic Response to Tyrosine Kinase Inhibition in Chronic Myelogenous Leukemia Stem Cells

city: Birmungham

first: Vipul

last: Sheth

state: AL

address: 2173 highland ave drive

institute: UAB

summary: Tyrosine kinase inhibitors (TKI) are highly effective in treating chronic myelogenous leukemia (CML), but primitive, quiescent CML stem cells persist as a source for recurrence. The effects of TKI treatment on CML stem cell metabolism, and the role of metabolic reprogramming in CML stem cell persistence after TKI treatment are not clear. Here we show that TKI treatment in a CML mouse model leads to acute inhibition of aerobic glycolysis, glutaminolysis, TCA cycle and oxidative phosphorylation (OXPHOS) in CML progenitor cells, but that these pathways are restored with continued TKI treatment. Single cell analysis reveals that primitive CML stem cell subpopulations characterized by lower OXPHOS, glycolysis, nucleotide metabolism, and MYC gene signatures are enriched after TKI treatment. TKI treatment initially results in broad inhibition of energy metabolism gene signatures, but continued treatment leads to metabolic reprogramming in persistent stem cells, with enhanced OXPHOS and MYC gene signatures. TKI treatment enhanced HIF-1 activity in quiescent CML stem cells, and addition of a HIF-1 inhibitor significantly depleted CML stem cells in TKI-treated mice. Our results identify mechanisms of metabolic adaptation in CML stem cells following TKI treatment, which can be targeted to deplete persistent quiescent CML stem cells.

overall_design: We studied changes in energy metabolism in CML stem and progenitor cells in response to TKI treatment using an inducible, transgenic SCL-tTA/BCR-ABL (BA) mouse model. In this model, tetracycline withdrawal leads to BCR-ABL expression in HSC and development of CML-like myeloproliferative disease. CML and normal mice were treated with the BCR-ABL TKI Nilotinib (50mg/kg daily by gavage) or vehicle. Bone marrow (BM) c-Kit+ cells were used for bioenergetics and metabolomics assays in order to have sufficient numbers of cells to conduct these analyses. However, this population is largely composed of progenitor cells and we therefore performed single cell gene expression analysis on BM Lin-FLT3-Sca-1+Kit+ (LSK) to study effects of TKI treatment on metabolism-related gene expression in primitive CML stem cells

first: Ravi

last: Bhatia

first: Shaowei

last: Qiu


title: OsPSTOL1 is prevalent in upland rice and enhances root growth and phosphate sufficiency in wheat

city: Riverside

first: Julia

last: Bailey-Serres

state: California

address: 900 University Ave

department: Department of Botany and Plant Sciences

institute: UC Riverside

summary: Improvement of phosphorus (P) uptake by crops is a prerequisite for sustainable agriculture. Rice (Oryza sativa L.) PHOSPHORUS-STARVATION TOLERANCE 1 (OsPSTOL1) increases root growth and total P uptake. Here, a biogeographic survey of rice demonstrates OsPSTOL1 loss in a subset of japonica rice after the temperate-tropical split and frequent absence in paddy varieties of east Asia. OsPSTOL1 absence or loss-of-function alleles prevail in landraces from regions with fertilizer use and controlled irrigation, suggesting it is an adaptive genetic variant in low nutrient rainfed ecosystems. OsPSTOL1 is a truncated member of a family of multi-module kinases associated with microbial interactions. We demonstrate that ectopic expression of OsPSTOL1 in wheat (Triticum aestivum L.) increases shoot and root growth under low P conditions, promotes root plasticity, and hastens induction of the low P response pathway. OsPSTOL1’s influence on adaptive root development in wheat validates its potential for broad utilization in crop improvement.

overall_design: Two independent transgenic lines ectopically ovexpressing OsPSTOL1 (PSTOL1.1 and PSTOL1.2) and their null segregants (Null) were grown under high (HP) and low (LP). phosphate conditions. Tissues from whole roots and crowns were sampled at 36 (E) and 50 (L) days after sowing (DAS).

first: Alek

last: Kettenburg

first: Miguel

middle: A

last: Lopez

first: Kalenahalli

last: Yogendra

first: Matthew

last: Prior

first: Teresa

last: Rose

first: Sabrina

last: Bimson

first: Sigrid

last: Heuer

first: Stuart

last: Roy


title: Obstructive sleep apnea is related to alterations in intestinal microbiome and impaired intestinal barrier function

first: Qianjun

last: Li

email: qqjun8@yeah.net, qqjun8@163.com

address: No. 1838, North Guangzhou Avenue

department: Sleep Medicine Center

institute: Nanfang Hospital, Southern Medical University

summary: Objectives: Obstructive Sleep Apnea (OSA) is related to repeated upper airway collapse, intermittent hypoxia, and intestinal barrier dysfunction. The resulting damage to the intestinal barrier may affect or be affected by the intestinal microbiota.  Methods: A prospective case-control was used, including 48 subjects from Sleep Medicine Center of Nanfang Hospital. Sleep apnea was diagnosed by overnight polysomnography. Fecal samples and blood samples were collected from subjects to detect intestinal microbiome composition (by 16S rDNA gene amplification and sequencing) and intestinal barrier biomarkers – intestinal fatty acid-binding protein (I-FABP) and D-lactic acid (D-LA) (by ELISA and colorimetry, respectively).  Results: The severity of OSA was related to differences in the structure and composition of the intestinal microbiome. Enriched Fusobacterium, Megamonasa, Lachnospiraceae_UCG_006, and reduced Anaerostipes was found in patients with severe OSA. Enriched Ruminococcus_2, Lachnoclostridium, Lachnospiraceae_UCG_006, and Alloprevotella was found in patients with high intestinal barrier biomarkers. Lachnoclostridium and Lachnospiraceae_UCG_006 were the common dominant bacteria of OSA and intestinal barrier damage. Fusobacterium and Peptoclostridium was independently associated with apnea-hypopnea index (AHI). The dominant genera of severe OSA were also related to glucose, lipid, neutrophils, monocytes and BMI. Network analysis identified links between the intestinal microbiome, intestinal barrier biomarkers, and AHI.  Conclusions: The study confirms that changes in the intestinal microbiota are related to intestinal barrier biomarkers among patients in OSA. These changes may play a pathophysiological role in the systemic inflammation and metabolic comorbidities associated with OSA, leading to multi-organ morbidity of OSA.

first: Ting

last: Xu

first: Chuan

last: Shao

first: Taoping


title: Fam172a deletion in brown adipose tissue protects against HFD-induced obesity by activating the BDH1-BHB pathway

status: Public on Aug 29 2023

city: Shanghai

first: Jiang-Feng

last: Ke

address: 600 Yishan Road

institute: Shanghai sixth people's hospital

summary: Family with sequence similarity 172 member A (FAM172A) protein acts as a key physiological repressor of brown adipose tissue (BAT) activity that plays a key role in energy metabolism. Its expression in BAT is suppressed by cold and other adrenergic stimulators. Mechanistically, FAM172A inhibits BAT activity and thermogenesis, in part, by binding to 3-hydroxybutyrate dehydrogenase 1 (BDH1), which subsequently affects the levels of beta-hydroxybutyrate (BHB), a ketone body metabolite closely involved in adipose mitochondrial biogenesis.

overall_design: RNA-binding protein immunoprecipitation (RIP)-sequencing was performed to identify the possible mRNAs that bind to the FAM172A protein in brown adipose tissue under cold exposure.

first: Jiangfeng

first: Zengkai

last: Wu

first: Ying

last: Yang

first: Lianxi


title: The RNA binding proteins TIA1 and TIAL1 protect germinal centre responses from apoptosis

city: Toulouse

first: Manuel

middle: D

last: Diaz-Munoz

address: CHU Purpan, BP3028

country: France

institute: INSERM

summary: Germinal centres (GC) are essential for the establishment of long-lasting antibody responses. In there, GC B cells rely on post-transcriptional RNA mechanisms for translating activation-associated transcriptional programs into functional changes in the cell proteome. However, we still lack knowledge about which are the critical proteins driving these key mechanisms. Here we show that the RNA binding proteins TIA1 and TIAL1 are required for the generation of long-lasting GC responses. TIA1 and TIAL1- deficient GC B cells fail to undergo antigen- mediated positive selection, expansion and differentiation into B cell clones producing high-affinity antibodies. Mechanistically, TIA1 and TIAL1 control the transcriptional identity of dark and light zone GC B cells and enable timely expression of the pro-survival molecule MCL1. Altogether, we demonstrate here that TIA1 and TIAL1 are key players in the post-transcriptional program that selects high-affinity antigen-specific GC B cells.

overall_design: Splenic germinal centre B cells from the dark zone (DZ) and the light zone (LZ) were sorted (by FACs) from Tia1fl/fl Tial1fl/fl (control) or Tia1fl/fl Tial1fl/fl AIDCre (Tia1 Tial1 double KO) mice at day 7 after immunization (ip) with NP-KLH in alum.

first: Ines

last: Osma-Garcia

first: Mailys

last: Mouysset

first: Dunja

last: Capitan-Sobrino

first: Yann

last: Aubert

first: Martin

last: Turner


title: The RNA binding proteins TIA1 and TIAL1 protect germinal centre responses from apoptosis [iCLIP]

summary: Germinal centres (GC) are essential for the establishment of long-lasting antibody responses. In there, GC B cells rely on post-transcriptional RNA mechanisms for translating activation-associated transcriptional programs into functional changes in the cell proteome. However, we still lack knowledge about which are the critical proteins driving these key mechanisms. Here we show that the RNA binding proteins TIA1 and TIAL1 are required for the generation of long-lasting GC responses. TIA1 and TIAL1- deficient GC B cells fail to undergo antigen-mediated positive selection, expansion and differentiation into B cell clones producing high-affinity antibodies. Mechanistically, TIA1 and TIAL1 control the transcriptional identity of dark and light zone GC B cells and enable timely expression of the pro-survival molecule MCL1. Altogether, we demonstrate here that TIA1 and TIAL1 are key players in the post-transcriptional program that selects high-affinity antigen-specific GC B cells.

overall_design: Individual cross-linking immunoprecipitation (iCLIP) and sequencing for TIA1 and TIAL1 in follicular B cells isolated from the spleen of C57BL/6 mice and stimulated with anti-IgM, anti-CD40 and rmIL4 for 48h.


title: NK cells engineered with a IL-15/IL-15Rα complex and CD19-targeted CAR show in vitro expansion and tumor regression in a murine xenograft model of B-cell leukemia in vivo

city: West Lafayette

first: Marxa

middle: Leao

last: Figueiredo

state: IN

address: 625 Harrison St

department: Basic Medical Sciences

institute: Purdue University

summary: Natural killer (NK) cells are an attractive therapeutic approach as alternative chimeric antigen receptor (CAR) carriers and unlike T cells, offer their use in allogeneic settings. The translation of NK cells into the clinic is still hampered by the inability of CAR-NK cells to expand in vitro and in vivo. Adoptive transfer of CAR-NK cells holds the promise of therapeutic benefit with a lower rate of adverse events due to the absence of GvHD and cytokine release syndrome. However, adoptive transfer of CAR-NK cells has not yet achieved breakthrough clinical results, and further improvement of CAR-NK cells is necessary. Here, we demonstrated that a fourth-generation CD19-targeted CAR (CAR.19) co-expressing IL-15 linked to its receptor IL-15/IL-15Rα (CAR.19-IL-15/IL-15Rα) significantly enhanced NK-92 cell proliferation, proinflammatory cytokine secretion, and cytotoxic activity against B-cell cancer cell lines in vitro and in a xenograft mouse model. Surprisingly, CAR construct comprising the IL-15/IL-15Rα was superior to CAR co-expressing the soluble form of IL-15 in terms of sustained proliferation, viability, but importantly also in their ability to control CD19+ B-cell lymphoma in a murine xenograft model. Together with the results of the systematic analysis of the transcriptome of activated NK-92 CAR variants, this supports the notion that IL-15/IL-15Rα comprising fourth-generation CARs may overcome the limitations of NK cell-based targeted tumor therapies in vivo by providing the necessary growth and activation signals

overall_design: Natural Killer 92 (NK-92) cells were maintained in serum free X-VIVO 10 media (Lonza, Cologne, Germany) containing 5% human heat inactivated AB plasma (Brazilian Blood Donation Service of Hemocentro de Ribeirao Preto), supplemented with 500 IU/ml IL-2 (Clinigen), as previously described (17,18) . Human leukemia cell lines K562, Raji and NALM-6 were cultured in RPMI medium (ThermoFisher Scientific) supplemented with 10% Fetal Bovine Serum (FBS). All cell lines were tested negative for mycoplasma using the MycoAlertPLUS Mycoplasma Detection Kit (Lonza) (reference value < 1.0).NK cells were cocultured with Raji cell 10:1 ratio (E:T) for 24h at 37°C, enough time to eliminate target cells. Total RNA from NK cells was isolated from two biological replicates. In short, RNA was isolated using RNeasy kit (Qiagen) according to manufacturer's protocol. Poly(A) RNA sequencing library was prepared following Illumina's TruSeq-stranded-mRNA protocol and conducted by LC Sciences (Houston, TX, USA). Poly(A) tail-containing mRNAs were purified using oligo-dT Briefly, magnetic beads with two rounds of purification, and fragmented using divalent cation buffer at elevated temperature. Quality control analysis and quantification of the sequencing library were performed using an Agilent Technologies 2100 Bioanalyzer High Sensitivity DNA Chip. Paired-ended sequencing was performed on Illumina’s NovaSeq 6000. For transcript assembly and estimating transcript expression levels, software is described by Figueiredo et al. (2020) (21). For differential expression analysis of mRNAs, StringTie was used by calculating fragments per kilobase million (FPKM). The differentially expressed mRNAs were selected with log2 (fold change) > 1.5 or log2 (fold change) < -1.5 and with statistical significance (p < 0.05) by edgeR.

first: Virginia

last: Picanco Castro

first: Renata

last: Silvestre


title: SARS-CoV-2 ORF3a expression in brain disrupts the autophagy-lysosomal pathway, impairs sphingolipid homeostasis and drives neuropathogenesis

city: Bethesda

first: Richard

last: Proia

address: 10 Center Drive Room 9D11

department: National Institute of Diabetes and Digestive and Kidney Diseases

institute: National Institutes of Health

summary:
Studied the neuropathological effects of SARS-CoV-2 open reading frame 3a (ORF3a) in mice.
Gene expression profiling analysis using data obtained from RNA-seq of 12 samples from AAV-Control (n=6) and AAV-ORF3a (n=6) transduced to express ORF3a.

overall_design: Compare gene expression profile with AAV treated and non- treated for pathway enrichment.

first: Hongling

last: Zhu

first: Colleen

last: Byrnes

first: Y. Terry

last: Lee

first: Galina

last: Tumetova

first: Hannah

last: Duffy

first: Jenna

middle: Y

last: Bakir

first: Sydney

middle: N

last: Pettit

first: Jabili

last: Angina

first: Maria

last: Allende

first: Mari

last: Kono


title: Immunomodulatory effects of hydrolyzed Debaryomyces hansenii in Atlantic salmon (Salmo salar L): From the in vitro model to a natural pathogen challenge after seawater transfer

city: Ås

first: Byron

last: Morales Lange

address: Arboretveien 6

country: Norway

institute: Norwegian University of Life Sciences

summary: Non-Saccharomyces yeast such as Debaryomyces hansenii or its cell wall-components are emerging candidates for novel functional aquafeeds, as they contain several microbe-associated molecular patterns (MAMPs) that can activate and modulate the host’s physiological responses and improve fish health and welfare. RNAseq results showed an upregulation in pathways associated with humoral immunity and complement activation in the liver. Considering these data, LAN6 could be a promising functional candidate for aquafeeds to achieve a more resilient salmon during fish farming.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for head kidney, liver and distal intestine from Atlantic salmon fed 0.1% hydrolyzed Debaryomyces hansenii.

first: B

last: Morales-Lange

first: M

last: Øverland


title: Gene expression analysis in canine diffuse large B cell lymphoma (DLBCL)

city: North Grafton

first: Jillian

last: Richmond

state: Massachusetts

address: 200 Westboro Road

department: Comparative Pathobiology

institute: Tufts Cummings School of Veterinary Medicine

summary: We performed a veterinary clinical oncology trial in client-owned dogs to determine if immune modulating drugs could be combined in rational approaches to treat spontaneous canine diffuse large B cell lymphoma (DLBCL).

overall_design:
Gene expression in lymph node aspirates at baseline and relapse from dogs enrolled in three different treatment arms was analyzed using the NanoString canine IO panel Sprint platform.
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Authors state, There are no processed data files, as I am providing raw count data and RCC files.

first: Cheryl

last: London

first: Heather

last: Gardner


title: Cdc73 protects Notch-induced T-cell leukemia cells from DNA damage and mitochondrial stress

city: Ann Arbor

first: Brian

last: Magnuson

address: 1500 East Medical Center Drive

institute: University of Michigan

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: Differential roles of FOXC2 in the trabecular meshwork and Schlemm’s canal in glaucomatous pathology

city: Chicago

first: Pieter

middle: Russell

last: Norden

state: IL

address: 303 E Superior Street

department: Feinberg Cardiovascular and Renal Research Institute

institute: Northwestern University Feinberg School of Medicine

summary: Impaired development and maintenance of Schlemm's canal (SC) are associated with perturbed aqueous humor outflow and intraocular pressure. The angiopoietin (ANGPT)/TIE2 signaling pathway regulates SC development and maintenance, whereas the molecular mechanisms of crosstalk between SC and the neural crest (NC)-derived neighboring tissue, the trabecular meshwork (TM), are poorly understood. Here, we show NC-specific forkhead box (Fox)c2 deletion in mice results in impaired SC morphogenesis, loss of SC identity, and elevated intraocular pressure. Visible-light optical coherence tomography analysis further demonstrated functional impairment of the SC in response to changes in intraocular pressure in NC-Foxc2 -/- mice, suggesting altered TM biomechanics. Single-cell RNA-sequencing analysis identified that this phenotype is predominately characterized by transcriptional changes associated with extracellular matrix organization and stiffness in TM cell clusters, including increased matrix metalloproteinase expression, which can cleave the TIE2 ectodomain to produce soluble TIE2. Moreover, endothelial-specific Foxc2 deletion impaired SC morphogenesis because of reduced TIE2 expression, which was rescued by deleting the TIE2 phosphatase VE-PTP. Thus, Foxc2 is critical in maintaining SC identity and morphogenesis via TM-SC crosstalk.

overall_design: The 10X Genomics Chromium platform was used to obtain single cell transcriptomes from the anterior eye segment of 4 week old wild-type and neural crest-specific Foxc2 knockout mice

first: Naoto

last: Ujiie

first: Raymond

last: Fang

first: Lisa

last: Beckmann

first: Zhen

last: Cai

first: Junghun

last: Kweon

first: Ting

last: Liu

first: Can

last: Tan

first: Megan

middle: S

last: Kuhn

first: W Daniel

last: Stamer

first: Kazushi

last: Aoto

first: Susan

middle: E

last: Quaggin

first: Hao

middle: F

last: Zhang

first: Tsutomu

last: Kume


title: Gene expression profile of human livers from patients with biliary atresia and controls (choledochocyst).

first: Junfeng

last: Wang

address: 399 Wanyuan Road

department: Department of Pediatric Surgery

institute: Chlidren's Hospital of Fudan University

summary: Gene expression profile of biliary atresia at time of Kasai portoenterostomy was evaluated by comparing gene expression profile in biliary atresia and controls (choledochocyst).

overall_design: Liver tissue RNA microarray was performed in 3 pairs of biliary atresia and control (choledochocyst) patients.

first: Min

last: Du

first: Lingdu

last: Meng

first: Shiwei

last: He

first: Ye

last: Zhu

first: Yifan

last: Yang

first: Xue

last: Ren

first: Yanlei

last: Huang

first: Song

last: Sun

first: Rui

last: Dong

first: Shan

last: Zheng

first: Gong

last: Chen


title: Transcriptomic analyses of joint tissues during osteoarthritis development in a rat model reveal dysregulated mechanotransduction and extracellular matrix pathways

city: La Jolla

first: Padma

last: Natarajan

state: CA

address: 10550 N.Torrey Pines Road

department: CCBB

institute: The Scripps Research Institute

summary: Transcriptomic changes in joint tissues during the development of osteoarthritis (OA) are of interest for the discovery of biomarkers and mechanisms of disease. The objective of this study was to use the rat medial meniscus transection (MMT) model to discover stage and tissue-specific transcriptomic changes. Sham or MMT surgeries were performed in mature rats. Cartilage, menisci and synovium were scored for histopathological changes at 2, 4 and 6 weeks post-surgery and processed for RNA-sequencing. Differentially expressed genes (DEG) were used to identify pathways and mechanisms. Published transcriptomic datasets from animal models and human OA were used to confirm and extend present findings. The total number of DEGs was already high at 2 weeks (723 in meniscus), followed by cartilage (259) and synovium (42) and declined to varying degrees in meniscus and synovium but increased in cartilage at 6 weeks. The most upregulated genes included tenascins. The 'response to mechanical stimulus' and extracellular matrix-related pathways were enriched in both cartilage and meniscus. Pathways that were enriched in synovium at 4 weeks indicate processes related to synovial hyperplasia and fibrosis. Synovium also showed upregulation of IL-11 and several MMPs. The mechanical stimulus pathway included upregulation of the mechanoreceptors PIEZO1, PIEZO2 and TRPV4 and nerve growth factor. Analysis of data from prior RNA-sequencing studies of animal models and human OA support these findings. These results indicate several shared pathways that are affected during OA in cartilage and meniscus and support the role of mechanotransduction and other pathways in OA pathogenesis.

first: Y

last: Hu

first: K

last: Li

first: H

last: Swahn

first: P

last: Ordoukhanian

first: S

last: Head

first: A

middle: K

last: Woods

middle: B

last: Joseph

last: Johnson

first: M

last: Lotz


title: miRNA sequencing analysis of miRNAs expression in peripheral blood from pediatric patients with β-thalassemia

status: Public on Aug 28 2023

city: Fuzhou

first: Hailong

state: Fujian

address: No.18 Daoshan Road, Gulou District

institute: Fujian Maternity and Child Health Hospital

summary: To explore the relationship between miRNAs expression and pediatric patients with β-thalassemia, we analyzed abnormal expressed miRNAs in peripheral blood of pediatric β-thalassemia by miRNA sequencing.

overall_design: 5 ml peripheral blood was collected from pediatric patients with β-thalassemia (n=5) and healthy controls (n=5). The mononuclear cells were collected from peripheral blood and used for total RNA isolation. After linker ligation, cDNA synthesis, and polymerase chain reaction amplification, miRNA sequencing was performed with an Illumina NextSeq 500 sequencer (Illumina).


title: SUMOylation inhibitor TAK-981 (Subasumstat) synergizes with 5-azacitidine in preclinical models of acute myeloid leukemia

city: Montpellier

first: Denis

last: Tempé

address: 1919 route de Mende

institute: CNRS

summary: Acute Myeloid Leukemias (AML) are severe hematomalignancies with dismal prognosis. The post-translational modification SUMOylation plays key roles in leukemogenesis and AML response to therapies. Here, we show that TAK-981 (subasumstat), a first-in-class SUMOylation inhibitor, is endowed with potent anti-leukemic activity in various preclinical models of AML. TAK-981 targets AML cell lines and patient blast cells in vitro and in vivo in xenografted mice with minimal toxicity on normal hematopoietic cells. Moreover, it synergizes with 5-azacitidine (AZA), a DNA-hypomethylating agent now used in combination with the BCL-2 inhibitor venetoclax to treat AML patients unfit for standard chemotherapies. Interestingly, TAK-981+AZA combination shows higher anti-leukemic activity than AZA+venetoclax combination both in vitro and in vivo, at least in the models tested. Mechanistically, TAK-981 potentiates the transcriptional reprogramming induced by AZA, promoting apoptosis, alteration of the cell cycle and differentiation of the leukemic cells. In addition, TAK-981+AZA treatment induces many genes linked to inflammation and immune response pathways. In particular, this leads to the secretion of type I interferon (IFN-I) by AML cells. Finally, TAK-981+AZA induces the expression of Natural Killer (NK)-activating ligands (MICA/B) and adhesion proteins (ICAM-1) at the surface of AML cells. Consistently, TAK-981+AZA-treated AML cells activate NKs and increase their cytotoxic activity. Targeting SUMOylation with TAK-981 may thus be a promising strategy to both sensitize AML cells to AZA and reduce their immune-escape capacities.

overall_design: Total RNA from U937 cells treated for 3 days with 10nM of either TAK-981, 5-azacitidine or the combination of TAK-981 + 5-azacitidine were sequenced in 3 biological replicates.

first: Guillaume

last: Bossis


title: Inhibition of HMOX1 alleviates diabetic cardiomyopathy by targeting ferroptosis

city: Chongqing

first: Huiping

last: Yang

address: 74 Linjiang Road

department: Cardiology

institute: Chongqing Medical University

summary: Diabetic cardiomyopathy (DCM) is an important complication of chronic diabetes mellitus (DM). However, its pathogenesis and pathologic process have not been fully elucidated. This study was aimed to investigate the role of ferroptosis in the pathogenesis of DCM and clarify the effect of HMOX1 on DCM by targeting ferroptosis. DCM mouse model was constructed by high fat diet (HFD) feeding and streptozotocin (STZ). injection.

overall_design: After 1 week of adaptive feeding, mice were randomly divided into two groups to receive a HFD (60% kcal% fat) or a normal chow for 8 weeks. At the age of 12 weeks, mice fed with HFD were intraperitoneal injected with a low-dose of streptozotocin (STZ, 40 mg/kg, dissolved in 0.1M of citrate acid buffer, # 60256ES80, YEASEN) for 3 consecutive days. Mice fed with normal diet were injected with only citrate acid buffer. Seven days after STZ administration, fasting blood glucose (FBG) were measured and only mice with blood glucose ≥ 11.1mM can be included in the DCM group. After that, mice were continually fed with HFD or normal diet until sacrificed at the age of 25 weeks.

first: Qiang

last: She


title: The effect of pressure on gene expression of blood and venous endothelial cells in humans

city: New York

first: Richard

last: Friedman

state: NY

address: 1130 St. Nicholas Av

department: Medicine

institute: Columbia University Irving  Medical Center

summary:
Two matched groups of Heart Failure with reduced ejection fraction
patients with no peripheral venous congestion were studied: with
recent prior heart failure hospitalization vs. without recent heart
failure hospitalization. Peripheral venous congestion was modeled
by inflating a cuff around the dominant arm, targeting an ~30mmHg
increase in venous pressure (venous stress test). Blood and
endothelial cells were sampled before and after 90 minutes of
venous stress test.

overall_design: hospitalization (n= 12 ) vs  no hospitalization (n= 11)

first: Paolo

middle: C

last: Colombo

first: Francesco

last: Castagna

first: Duygu

last: Onat

first: Ka

last: Wong

first: Ante

last: Harxhi

first: Yacki

last: Hayashi

first: Alberto

last: Pinsino

first: Annamaria

last: Ladanyi

first: Alexander

last: Mebazaa

first: Mattia

last: Arrigo

first: Thierry

last: LeJemtel

first: Panos

last: Papapanou

first: Hani

last: Sabbah

first: Ann

middle: M

last: Schmidt

first: Melana

last: Yuzefpolskaya

first: Ryan

last: Demmer


title: Mucosal CCL28 Chemokine Improves Protection against Genital Herpes through Mobilization of Antiviral Effector Memory CCR10+CD44+ CD62L-CD8+ T Cells and Memory CCR10+B220+CD27+ B Cells into the Infected Vaginal Mucosa

city: Irvine

first: Lbachir

last: BenMohamed

address: 843 Health Sciences Road, Hewitt Hall, 2nd Floor

institute: University of California Irvine

summary: Four major mucosal-associated chemokines, CCL25, CCL28, CXCL14, and CXCL17, play an important role in protecting mucosal surfaces from infectious pathogens. However, their role in protection against genital herpes remains to be fully explored. The CCL28 is a chemoattractant for the CCR10 receptor-expressing immune cells and is produced homeostatically in the human vaginal mucosa (VM). In this study, we investigated the role of the CCL28/CCR10 chemokine axis in mobilizing protective antiviral B and T cell subsets into the VM site of herpes infection. We report a significant increase in the frequencies of HSV-specific memory CCR10+CD44+CD8+ T cells, expressing high levels of CCR10, in herpes-infected asymptomatic (ASYMP) women compared with symptomatic women. Similarly, a significant increase in the CCL28 chemokine (a ligand of CCR10), was detected in the VM of herpes-infected ASYMP C57BL/6 mice, associated with the mobilization of high frequencies of HSV-specific effector memory CCR10+CD44+CD62L-CD8+ TEM cells and memory CCR10+B220+CD27+ B cells in the VM of HSV-infected ASYMP mice. Inversely, compared with wild-type C57BL/6 mice, the CCL28 knockout (CCL28-/-) mice (1) appeared to be more susceptible to intravaginal infection and reinfection with HSV type 2, and (2) exhibited a significant decrease in the frequencies of HSV-specific effector memory CCR10+CD44+CD62L-CD8+ TEM cells and of memory CD27+B220+ B cells in the infected VM. These findings suggest a critical role of the CCL28/CCR10 chemokine axis in the mobilization of antiviral memory B and T cells within the VM to protect against genital herpes infection and disease.

overall_design:
This study is supposed to investigate the functions and mechanisms asociated with mucosal chemokines in protecting mucosal surfaces from infectious pathogens. Their role in context to genital herpes is yet to be explored fully. This study investigated the role of CCL28/CCR10 chemokine axis in mobilizing protective antiviral B and T cell subsets into the VM site of herpes infection. In this study, we evaluated the potential use of the mucosal chemokine CCL28 to improve genital herpes immunity and protect against infection and disease caused by HSV and potentially other sexually transmitted viruses. We have studied the (i) genital infection of mice with HSV-2 by viral titration, (ii) monitored the genital herpes infection and disease scoring in mice, (iii) Bulk RNA sequencing on sorted CD81 T cells, (iv) Differential gene expression, (v) function of different immune cell markers by FACS, (vi) HSV-2 specific Ab secreting cell ELISPOT assay, (vii) immunohistochemistry for human VM tissue to see the immune cell infiltrations into the VM tissue sections.
We performed gene expression profiling analysis using RNA-Seq on 8 human samples. All samples were female herpes subjects categorised into Asymptomatic (n = 4), and Symptomatic (n = 4).

first: Nisha

last: Dhanushkodi

first: Swayam

last: Prakash


title: scRNA-seq analysis in kidney at 3 month of nephrotoxic nephritis model.

city: Seoul

first: Donghwan

last: YUN

state: Jongno-gu

address: 103 Daehakro

institute: Seoul National University Hospital

summary: One single-cell RNA transcriptomic dataset was originated from one wild-type mouse, which was harvested at 3 months after nephrotoxic nephritis model.

overall_design: Whole kidneys of C57BL/6 male mice were prepared for scRNA. For the model, mice were preimmunized with 200 μg of sheep immunoglobulin G in Freund’s complete adjuvant via the intraperitoneal route, followed by 5 μL/g sheep nephrotoxic serum (Probetex Inc.) via intravenous injection 4 days later. The mice were sacrificed at the indicated time points after reperfusion.

first: Yun

last: Donghwan

first: Hwang

last: Juhyeon

first: Han

last: Seung Seok


title: Maintenance of pluripotency signature in the entire ectoderm enables potential for neural crest formation

first: Laura

last: Kerosuo-Pahlberg

address: 30 Convent Dr

institute: NIDCR

summary: The ability of the pluripotent epiblast to contribute progeny to all three germ layers is thought to be lost after gastrulation. The later-forming neural crest (NC) rises from ectoderm and it remains poorly understood how its exceptionally high stem-cell potential to generate mesodermal- and endodermal-like cells is obtained. We monitored transcriptional changes from gastrulation to neurulation using single-cell-Multiplex-Spatial-Transcriptomics (scMST) complemented with RNA-sequencing. Unexpectedly, we find maintenance of undecided Nanog/Oct4-PouV/Klf4-positive pluripotent-like pan-ectodermal stem-cells spanning the entire ectoderm late in the neurulation process with ectodermal patterning completed only at the end of neurulation when pluripotency becomes restricted to NC, challenging our understanding of gastrulation. Furthermore, broad ectodermal pluripotency is found at all axial levels unrelated to the NC lineage the cells later commit to, suggesting a general role in stemness enhancement and proposing a mechanism by which the NC acquires its ability to form derivatives beyond “ectodermal-capacity” in chick and mouse embryos.

overall_design: Chicken embryos at HH4 were knocked down three genes Oct4/PouV, Nanog and Klf4, respectively, by electroporating a translation blocking morpholino on one side of the embryo (one MO per experiment). Then they were collected at HH7/HH8- for bulk rnaseq. The transcriprome of the knockdown side will be compared to the contralateral side treated with a control MO. Three embryos (3 halves) are pooled together per experiment (except for one gene that we already prepared 4 samples for). (10 samples)

first: Ceren

last: Pajanoja

first: Jenny

last: Hsin

first: Bradley

last: Olinger

first: Rita

last: Yazejian

first: Andrew

last: Schiffmacher

first: Shaun

last: Abrams

first: Arvydas

last: Dapkunas

first: Zarin

last: Zainul

last: Doyle

first: Daniel

last: Martin

last: Kerosuo


title: Ikzf1 lactylation regulates CD4 T cell differentiation

first: Wei

last: Fan

address: Youyi Road, No1

department: Urology

institute: The First affiliated hospital of Chongqing Medical University

summary: Dysregulation of Th17 differentiation was implicated in multiple inflammatory and autoimmune diseases including autoimmune uveitis. In the current study, we have provided evidence indicating that lactate-derived lactylation plays important roles in regulating Th17 differentiation. The lactylation level of CD4+ T cells was upregulated in EAU mice and inhibiting lactylation resulted in impaired EAU progression. We characterized the global lactylome of CD4+ T cells of normal and EAU mice. We found that the differentially lactylated proteins were enriched in pathways related to immune responses including leukocyte differentiation. Importantly, our results show that the lactylation level of Ikzf1 (K164) functions in regulating Th17 differentiation by differentially modulating gene expression patterns which are related to CD4+ T cell differentiation by CUT& Tag analysis. In view of the above mentioned well-documented evidence, Ikzf1 lactylation might represent an important regulator for Th17 differentiation in autoimmune uveitis.

overall_design: Naïve CD4+ T cells knocked down for endogenous Ikzf1 were transfected with Ikzf1 WT or K164R virus and then used for Th17 induction. 5 days after induction, the cells were harvested for CUT&Tag analysis.

first: Shengping

last: Hou


title: Comparison of gene expression profile between primary and bone metastasized cancers

city: Yokohama

first: Shinya

last: Sato

state: Kanagawa

address: 2-3-2, Nakao, Asahi-Ku

institute: Kanagawa Cancer Center Research Institute

summary: Bone metastasis occurs frequently in cancer patients. Conventional therapies have limited therapeutic outcomes, and thus, exploring the mechanisms of cancer progression in the bone metastasis is important to develop new effective therapies. In the bone microenvironment, adipocytes are the major stromal cells that interact with cancer cells during the bone metastasis. However, the comprehensive functions of bone marrow adipocytes in cancer progression are not yet fully understood. To address this, we investigated the role of bone marrow adipocytes on cancer cells, by focusing on an invasive front which reflects the direct effects of stromal cells on caner. In comprehensive histopathological and genetic analysis using bone metastasis specimens, we examined invasive fronts in bone metastasis and compared invasive fronts with adipocyte-rich bone marrow (adipo-BM) to those with hematopoietic cell-rich bone marrow (hemato-BM) as a normal counterpart of adipocytes. We found morphological complexity of invasive front with adipo-BM was significantly higher than that with hemato-BM. Based on immunohistochemistry, the invasive front with adipo-BM comparatively had significantly increased cancer-associated fibroblasts (CAFs) marker-positive area and lower density of CD8 positive lymphocytes compared to that with hemato-BM. RNA-seq analysis of primary and bone metastasis cancer reveals that bone metastasized cancer cells acquired drug resistance related gene expression phenotypes. Clearly, these findings indicate that bone marrow adipocytes provide favorable tumor microenvironment for cancer invasion and therapeutic resistance of bone metastasized cancers via CAF induction and immune evasion, providing a potential target for the treatment of bone metastasis.

overall_design:
Six samples of primary cancer tissues (group 1) and six samples of bone metastasized cancer tissues from same patients of group 1 (group 2) were used. We compared gene expression pattern between group 1 and group 2.
*** Raw data not provided due to Japan's personal information protection law. ***

first: Igor

last: Brodsky


title: Diploid and triploid Chinook salmon (Oncorhynchus tshawytscha) have altered microRNA responses in immune tissues after infection with Vibrio anguillarum

city: Waterloo

first: Ivan

middle: Gregory

last: Cadonic

address: 200 University Ave W, B1-171B

department: Biology

institute: University of Waterloo

summary: Production of sterile fishes through artificial retention of a third set of chromosomes (triploidy) is a sustainable alternative for aquaculture since it reduces pressure on wild populations. However, these fishes have reduced survival in stressful conditions and in response to pathogens. In this study, the impact of Vibrio anguillarum infection on diploid and triploid Chinook salmon (Oncorhynchus tshawytscha) was investigated to identify if there was any significant regulation by microRNAs (miRNA) in immune responsive tissues. Small RNAs from hindgut, head kidney, and spleen were sequenced to determine miRNA transcript abundance was altered due to ploidy and infection in nine-month old full-sibling diploids and triploids. Diploids had higher percent survival at the end of the infection, but no difference was found in mortality between the two ploidies.  All three tissues had differentially expressed miRNA prior to infection, indicating that subtle changes in epigenetic regulation due to increased ploidy. Additionally, miRNA were altered by infection, but only in spleen was there a difference in miRNA expression between diploids and triploids after three days of infection. Furthermore, one miRNA (ssa-miR-2188-3p) was confirmed as having an altered response to infection in triploids compared to diploids, implicating potential immune dysregulation due to increased ploidy. The miRNAs identified in this study are predicted to target immune pathways, providing evidence for their importance in regulating responses to pathogens. This study is the first to investigate how increased ploidy alters miRNA expression in response to infection. Additionally, it provides evidence for epigenetic dysregulation in triploid fishes, which may contribute to  their  poor performance in response to stress.

overall_design: Diploid and triploid full-sibling Chinook salmon hindgut, head kidney, and spleen were sampled before (Day0) and after (Day3) being exposed to Vibrio anguillarum

middle: G

first: John

middle: W

last: Heath

first: Brian

last: Dixon

first: Paul

last: Craig


title: Gene expression modification in lungs of rats exposed to Mitsui-7 and NM-403 by intratracheal instillation

city: Vandoeuvre les Nancy

first: Carole

last: Seidel

address: Rue du Morvan

institute: INRS

summary: In this work we study the pulmonary toxicological properties of Mitsui-7 and NM-403 using molecular toxicological approach. For this, we exposed Sprague Dawley rats by intratracheal instillation. Lung samples have been collected 3 days after the end of exposure and transcriptomics analysis were performed.

overall_design: 12 week old female Sprague Dawley rats were exposed by intratracheal instillation to Mitsui-7 and NM-403 (0.25 mg/rat). Mitsui-7 and NM-403-induced gene expression profile in Wild type and GMO [heterozygous for p53] rat lung was performed 3 days post exposure. Each group is composed of 6 control, 6 exposed rats (5 for GMO NM-403). A total of 35 samples (microarrays) was used.

first: Mylène

last: Lorcin

first: Hélène

last: Barthel

first: Sylvie

last: Sébillaud

first: Laurent

last: Gaté


title: Effect of Rinl deficiency on ex vivo isolated naïve and effector/memory CD4+ T cells

city: Vienna

first: Nicole

last: Boucheron

address: Lazarettgasse 19

country: Austria

institute: Institute of Immunology

summary: Rab GTPases are primarly involved in trafficking processes. Rinl belongs to the Ras-interaction/interference (Rin) proteins and is a guanine nucleotide exchange factor (GEF) for Rab5a and Rab22. By transcriptome analysis of naïve and effector CD4+ T cells we identify Rinl-regulated pathways in CD4+ T cells.

overall_design: To study the function of Rinl in CD4+ T cells, naïve (CD62L+CD44lo) and effector (CD62L-CD44hi) CD4+ T cells were isolated by fluorescence activated cell sorting from WT and Rinl-KO mice. RNA was isolated form the sorted cells and processed for RNA sequencing. We performed gene expression profiling by comparing WT and KO naïve CD4+ T cells as well as WT and KO effector CD4+ T cells.

first: Lisa

last: Sandner

first: Lina

last: Dobnikar

first: Michael

last: Schuster

first: Moritz

last: Madern


title: Regulatory T cells and CTLA4-mediated proliferative and functional paralysis suppress anti-tumor CD4 T cell responses and impede tumor control

city: Toronto

first: David

last: Brooks

address: 610, University Ave

institute: Princess Margaret Cancer Centre

summary: CD4 T cell help is critical for tumor control and the efficacy of immunotherapy. Yet, in contrast to CD8 T cells, CD4 tumor-specific T helper (Th) cell differentiation and function during cancer progression is unclear. We demonstrate that after priming, tumor-specific CD4 T cells in the draining lymph node (dLN) are rapidly frozen into a proliferatively paralyzed state, with concomitant immature Th-fate commitment, insufficient cellular metabolism and minimal tumor-infiltration. Overcoming these dysfunctions during tumor growth restarted T cell proliferation and differentiation to enable tumor control, identifying the requirement for tumor-induced CD4 T cell dysfunction to enable cancer progression. CD4 T cell dysfunction is regulated through an unlinked two-hit mechanism wherein natural (n)Treg modulation of antigen presentation and CTLA4 inhibited tumor-specific CD4 T cell-intrinsic signal integration diminish T cell activation to freeze the cells and prevent help. Targeting either nTreg or CTLA4 alone restored proliferation but failed to promote further effector T helper differentiation; only combination therapy fully restored anti-tumor CD4 T cells responses. Thus, our study demonstrates a complex regulatory system that restricts tumor-specific CD4 T cells in cancer and provides insight into therapeutic strategies for tumor control.

overall_design: SMARTA cells from day 8 tumor inguinal lymph nodes of WT or Treg-depleted mice treated with anti-CTLA4 or isotype antibody. Freshly isolated naive SMARTA cells were used as naive control

first: Mengdi

last: Guo

first: Diala

last: Abd-Rabbo

first: Bruna

last: Bertol

first: Madeleine

last: Carew

first: Sabelo

last: Lukhele

first: Laura

last: Snell

first: Wenxi

last: Xu

first: Giselle

last: Boukhaled

first: Heidi

last: Elsaesser

first: Marie

middle: J

last: Halaby

first: Tracy

middle: L

last: McGaha


title: Physical Exercise-induced Extracellular Vesicles Ameliorate Chronic Pancreatitis via Inhibiting STING-Interferon Signaling

city: Shanghai

first: Jie

last: Tong

address: Siping road

country: China

institute: Tongji University

overall_design: Prepare mouse pancreas as a single-cell suspension. BD Rhapsody system was used to capture the transcriptomic information of the single cells. All libraries were sequenced by Novaseq 6000 (Illumina, San Diego, CA) on a 150 bp paired-end run.

first: Dongjie

last: Li

first: Pei

last: Wang


title: Disruption of Multiple Overlapping Functions Following Step-Wise Inactivation of the Extended Myc Network

city: pittsburgh

first: Edward

middle: V.

last: Prochownik

address: 4401 Penn Avenue

department: Section of Hematology/Oncology

institute: Children’s Hospital of Pittsburgh

summary: Myc, a member of the Myc Network, supervises proliferation, metabolism and ribosomal function. The Mlx Network cross-talks with the Myc Network and regulates overlapping functions. We describe here the consequences of conditional Myc and/or Mlx gene knockouts (KOs) in primary and immortalized murine embryonic fibroblasts (MEFs). MycKO and MycKOxMlxKO “double KO” (DKO) primary MEFs, but not MlxKO MEFs, rapidly growth-arrested and displayed features of aging and senescence. In DKO MEFs, these were transient, indicating that Mlx was necessary to maintain them. KO MEFs deregulated transcripts pertaining to mitochondrial and ribosomal structure and function, cell cycle, aging, senescence and DNA damage. The expression of DNA damage-related proteins was also abnormal. Immortalized KO MEFs remained proliferation-competent but demonstrated differential sensitivities to genotoxic agents. Immortalized MycKO MEFs spontaneously developed tetraploidy that was Mlx-dependent. Different aspects of MEF aging, senescence and DNA damage responses are therefore differentially regulated by the Myc and Mlx Networks.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for MycKO, MlxKO, DKO(MycKO + MlxO) and WT in primary and immortalized MEF cells.

first: Huabo

middle: V


title: Oncogenic IDH mutations increase heterochromatin-related replication stress without impacting tumor mutation burden

first: Richard

last: Koche

state: New York

institute: Memorial Sloan Kettering Cancer Center

summary: Oncogenic mutations in the metabolic enzyme isocitrate dehydrogenase 1 and 2 (IDH1/2) have been found in a number of liquid and solid tumors. Their pathogenic mechanism of action involves production of 2-hydroxyglutarate (2HG), an oncometabolite that acts in part by inhibiting members of a family of dioxygenases that modulate chromatin dynamics. Recent work has suggested that mutant IDH (mIDH) and 2HG also impact sensitivity to inhibitors of poly-ADP ribose polymerases (PARP) but the molecular basis for this sensitivity is unclear. Unlike PARP inhibitor-sensitive BRCA1/2 tumors which exhibit impaired homologous recombination, IDH-mutant tumors have a silent mutational profile and lack mutational signatures associated with impaired homologous recombination. Instead, 2HG-producing IDH mutations lead to heterochromatin-dependent slowing of DNA replication and increased replication stress, resulting in DNA double strand breaks. This replicative stress manifests as replication fork slowing but the breaks are repaired without a significant increase in the cellular mutation burden. Faithful resolution of replicative stress in IDH-mutant cells is dependent on poly-ADP ribosylation. Treatment with PARP inhibitors restores replication fork speed but results in incomplete repair of DNA breaks. These findings provide evidence of a requirement for PARP in the replication of heterochromatin and further validate PARP as a potential therapeutic target in IDH-mutant tumors.

overall_design: Repli-seq in IDH2 wild type and R172K mutant U2OS and RKO cell lines.

first: Juan

last: Schvartzman

middle: P

first: Craig

last: Thompson


title: Tumor-intrinsic expression of the autophagy gene Atg16l1 suppresses anti-tumor immunity in colorectal cancer (single cell RNA-seq)

city: South San Francisco

first: Yasin

last: Senbabaoglu

address: 1 DNA Way

institute: Genentech

summary:
We utilized 10X single cell RNA sequencing to investigate in murine liver how Atg16l1 deletion in AKPS colorectal cancer organoids impacted phenotypic programming of organoid cells and myeloid cells in the tumor microenvironment.
Atg16l1 KO and Wt cells were inoculated into the liver of NSG mice via HTV injection. Tumors were harvested following ~3 weeks of growth and live Calcein blue+ 7ADD– cells were sorted into tumor (eGFP+CD45–) and immune (eGFP–CD45+) cells.

overall_design: Two mice each were inoculated with Atg16l1 wildtype and knockout organoids. Cells from each mouse were sorted into tumor and immune cells. Cells from two mice were then pooled to generate 4 samples (one each) for Atg16l1 wildtype tumor cells, Atg16l1 knockout tumor cells, immune cells from Atg16l1 wildtype tumor microenvironment, and immune cells from Atg16l1 knockout tumor microenvironment.

first: Lucia

last: Taraborrelli

first: Nathaniel

middle: R

last: West

first: Aditya

last: Murthy


title: IL-33–ST2 signaling promotes stemness in subtypes of myeloid leukemia cells through the Wnt and Notch pathways

city: Bern

first: Ramin

last: Radpour

address: Murtenstrasse 35

department: Department for BioMedical Research

country: Switzerland

institute: University of Bern

summary:
Purpose: The goal was to compare transcriptome profile of FACS-purified bone marrow AML1/ETO positive LSPCs from AML patients treated with rhIL-33 or controls (untreated).
Methods: The transcriptomic analysis of AML1/ETO positive LSPCs were assessed in biological replicates upon treatment treated rhIL-33 or controls using Illumina NextSeq 500.
Results: We mapped around 30 million sequence reads per sample to the human genome (GRCh38 - hg38) and identified differentially expressed transcripts in FACS-purified bone marrow AML1/ETO positive LSPCs from AML patients treated with rhIL-33 or controls (untreated). Differentially expressed genes between LSPCs treated with rhIL-33 or controls, were identified with a fold change ≥1.5 and FDR p-value <0.05.
Conclusions: Our study represents the first detailed RNA-seq analysis of FACS-purified bone marrow AML1/ETO positive LSPCs from AML patients treated with rhIL-33 or controls. Our results show that IL-33 treatment induces the regulation of metabolic process, cell cycle, regulation of NF-κΒ, MAPK and canonical Wnt signaling pathways, as well as the regulation of stem cell division and maintenance.

overall_design: mRNA of FACS-purified bone marrow derived AML1/ETO positive LSPCs from AML patients treated w/o rhIL-33 and profiled using Illumina NextSeq 500.

first: Pascal

last: Naef

first: Carsten

last: Riether

first: Adrian

last: Ochsenbein


title: Transcriptome analysis combined with metabolome analysis reveals the significant functions of CesA genes in cotton (Gossypium hirsutum) fiber length development

city: Zhengzhou

first: yanyong

last: cao

state: henan

address: No. 116, Huayuan Road

institute: Henan Academy of Agricultural Sciences

summary: Cotton (Gossypium hirsutum) is widely distributed worldwide, and improving the quality of its fiber is one of the most important tasks in cotton breeding. Cotton fibers are primarily composed of cellulose, which is synthesized and regulated by cellulose synthase (CesAs). However, the molecular mechanism of CesA genes in cotton is unclear. In this study, the cotton transcriptome and metabolome were used to investigate the significant function of CesA genes in fiber development. Finally, 321 metabolites were obtained, 84 of which were associated with the corresponding genes. Interestingly, a target gene named Gh_A08G144300, one of the CesA gene family members, was closely correlated with the development of cotton fibers. Then, identification and functional analysis were conducted. The target CesA gene Gh_A08G144300 was selected and analysed to determine its specific function in cotton fiber development. High-level gene expression of Gh_A08G144300 was found at different fiber development stages by RNA-seq analysis, and the silencing of Gh_A08G144300 visibly inhibited the growth of cotton fibers, showing that it is critical for their growth. This study provides an important reference for research on the gene function of Gh_A08G144300 and the regulatory mechanism of fiber development in cotton.

overall_design: There are 2 groups with 3 biological replicates in each group.

first: Guiqin

last: Sun

first: Quanzhi

last: Zhao


title: Tumor-intrinsic expression of the autophagy gene Atg16l1 suppresses anti-tumor immunity in colorectal cancer (bulk RNA-seq)

summary:
We utilized bulk RNA sequencing to assess intrinsic differences between wildtype and autophagy-defective (Atg16l1 deleted) AKPS colorectal cancer organoids in both untreated and IFN gamma treated conditions.
AKPS mutations consist of loss-of-function in tumor suppressors Apc, Trp53, Smad4, and gain-of-function in oncogenic Kras(G12D).

overall_design:
Examination of 2 clones from Atg16l1-wildtype and Atg16l1-deleted AKPS colorectal cancer organoids, with or without IFN gamma treatment.
There are two technical replicates from each clone for each one of the four conditions (WT untreated, WT treated, KO untreated, KO treated)


title: Myeloid MyD88 restricts CD8+ T cell response to radiation therapy in pancreatic cancer [Nanostring]

city: Portland

first: Michael

last: Gough

address: 4805 NE Glisan St

department: EACRI

institute: Providence Portland Medical Center

summary: Radiation therapy induces immunogenic cell death in cancer cells, whereby apoptotic cells release endogenous adjuvants that are sensed by immune cells to direct adaptive immune responses. Toll-like receptors (TLRs) expressed on several immune subtypes recognize these products to direct downstream responses in part via the adapter protein MyD88. Here we use lineage specific deletion of Myd88 to interrogate its contribution to the immune response to radiation therapy in distinct immune populations in pancreatic cancer. While Myd88 deletion in Itgax- and Lck-expressing immune populations had little discernable effects on response to radiation therapy, Lyz2-specific loss of Myd88 rendered tumors more susceptible to radiation therapy dependent on CD8+ T cells. scRNAseq revealed gene signatures in myeloid and dendritic cells indicative of enhanced type I and II interferon responses. Together, these data implicate MyD88 signaling in myeloid cells as a critical source of immunosuppression that hinders adaptive immune tumor control following radiation therapy.

overall_design: Nanostring analysis of whole tumor RNA isolated from Panc02-SIY tumors 7 days post-radiation therapy (16 Gy) in Myd88 fl/fl mice and Lyz2-Cre/Myd88 fl/fl mice , with 2 biological replicates in each group

first: Terry

last: Medler

first: Tiffany

last: Blair

first: Alejandro

last: Alice

first: Alexa

last: Dowdell

first: Brian

middle: D

last: Piening

first: Marka

last: Crittenden


title: Myeloid MyD88 restricts CD8+ T cell response to radiation therapy in pancreatic cancer [sequencing]

overall_design: Single cell RNA sequencing of CD45+ cells isolated from untreated PK5L1940 tumors or 3 days post-radiation therapy in Myd88 fl/fl mice and Lyz2-Cre/Myd88 fl/fl mice , with 4 biological replicates in each group


title: Myeloid MyD88 restricts CD8+ T cell response to radiation therapy in pancreatic cancer

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

overall_design: Refer to individual Series


title: RNA sequencing analysis of wild-type and Scd1-deficient CD4+ naïve T cells

city: Diepenbeek

first: Ibrahim

last: HAMAD

state: Yes

address: Agoralaan Building C

department: Hasselt University

summary: Analysis of differentially expressed genes in Scd1-deficient CD4+ naïve T cells. The goal of this study was to elucidate the underlying pathway of Scd1-deficiency leading to increased regulatory T cell differentiation.

overall_design: CD4+ T cells were purified from splenocytes (collected from 11-week-old wild-type and Scd1-deficient C57BL/6 mice) using magnetic separation. Subsequent fluorescence-activated cell sorted naïve T cells (CD4+ CD44med CD25- CD62L+) were lysed using QIAzol.

first: Jeroen

last: Bogie

first: Jerome

last: Hendriks

first: Elien

last: Grajchen