title: Integrated transcriptomics and metabolomics reveal tolerance mechanisms to hypoxia stress in Yesso scallop, Mizuhopecten yessoensis

city: Dalian

first: Zhongming

last: Fu

state: Liaoning

address: Heishijiao Street

institute: Dalian Ocean University

summary: Global warming and human activities have led to an increased frequency of hypoxia in coastal regions. Hypoxia not only affects the growth and development of scallops but can also cause death, posing a significant challenge to the health and sustainability of aquaculture. Its effects on scallop growth and immune system have been widely reported, but studies on the effects of hypoxic stress on the metabolism of Yesso scallop Mizuhopecten yessoensis are not fully understood. Additionally, the molecular mechanisms of hypoxic stress on damage to the Yesso scallop are still limited. In this study, we deploy high-throughput RNA sequencing (RNA-Seq) and non-targeted liquid chromatography-mass spectrometry (LC-MS) based metabolomics analysis to investigate the alterations in key genes and metabolites in scallops after 24 hours of hypoxia stress (DO: 1 ± 0.1 mg/L). A total of 704 differentially expressed genes (DEGs) and 302 differentially expressed metabolites (DEMs) were identified in the gill tissues of Yesso scallops under hypoxic conditions, respectively. DEGs and DEMs were involved in energy metabolism, antioxidant responses, immune responses, and inflammatory responses, as well as processes of cell apoptosis and cell proliferation. KEGG enrichment analysis shows that the mTOR signaling pathway is a significantly enriched pathway shared by DEGs and DEMs. These findings suggest that Yesso scallops cope with acute hypoxic stress by changing energy metabolism, inhibiting cell apoptosis and proliferation, and increasing immune defense strategies. Overall, the results of this study provide a new understanding of how Yesso scallops respond to hypoxia and provide target genes for the selection and breeding of low-oxygen-tolerant scallops.

overall_design: To study the molecular mechanisms of scallops responding to hypoxia, we conducted transcriptome sequencing analysis on scallops after hypoxia treatment. A total of 60 scallops individuals were randomly divided into two groups and used in the hypoxia experiment. The control group had a dissolved oxygen (DO) level set at 9.0 ± 0.9 mg/L, whereas the DO level for the group under hypoxia stress was maintained at 1.0 ± 0.1 mg/L. After 24 hours of treatment,  three scallops were randomly selected from each group, dissected to obtain gill tissue, quickly frozen in liquid nitrogen, and then stored in a -80°C freezer.

first: Chenge

last: Fan

first: Yaqing

last: Chang

first: Xubo


title: AAGGG repeat expansions trigger repeat-dependent synaptic dysregulation in human CANVAS Neurons [CANVAS_Control_Isogenic]

status: Public on Sep 01 2024

city: Ann Arbor

first: Connor

middle: J

last: Maltby

state: MI

address: 109 Zina Pitcher Place

department: Neurology

country: USA

institute: University of Michigan

type: Expression profiling by high throughput sequencing

summary: Cerebellar ataxia with neuropathy and vestibular areflexia syndrome (CANVAS) is a late onset, recessively inherited neurodegenerative disorder caused by a biallelic, non-reference pentameric CCCTT(AAGGG) repeat expansion within the second intron of replication factor complex subunit 1 (RFC1). While rare compound heterozygous CANVAS cases harbor RFC1 loss-of-function mutations alongside monoallelic repeat-expansions, RFC1 expression is maintained at normal levels in the presence of biallelic expanded repeats. To investigate how these pentameric repeats cause disease, we generated CANVAS patient iPSC derived neurons and utilized calcium imaging and transcriptomic analysis to define repeat elicited gain-of-function and loss-of-function contributions to neuronal toxicity. AAGGG repeat expansions do not alter neuronal RFC1 splicing, expression, or DNA repair pathway functions. In reporter assays, AAGGG repeats are translated into pentapeptide repeat proteins that selectively accumulate in patient brains. However, neither these proteins nor repeat RNA foci were detected in iNeurons and overexpression of these repeats in isolation did not induce neuronal toxicity. CANVAS iNeurons exhibit defects in neuronal development and diminished synaptic connectivity that is rescued by CRISPR deletion of a single expanded allele. Importantly, these deficits were not replicated by knockdown of RFC1 in control neurons and showed incomplete or no rescue upon over-expression of RFC1. These findings support a repeat-dependent and RFC1-independent mechanism as the underlying cause of neurodegeneration in CANVAS, with important implications for therapeutic development in this currently untreatable condition.

overall_design:
To assess global dysregulation of gene expression in CANVAS, we generated multiple Control, CANVAS, and Isogenic corrected patient iPSC lines. These were differentiated to forebrain glutamatergic neurons by modified Dual-SMAD inhibition protocol.
Neurons were aged to 10-weeks in vitro and were analyzed by paired-end RNASequencing of Control (n=3x2), CANVAS (n=3x2), Isogenic (n=1x2) patient iPSC-derived neurons.
RNASeq data were analyzed for differential expression, differential exon usage, and circRNA expression.

first: Samantha

last: Grudzien


title: Cell and state-specific eQTL analysis in human endometrial mesenchymal cells uncovers candidate susceptibility genes for reproductive diseases and traits

city: Herston

first: Sally

last: Mortlock

state: QLD

address: School of Public Health

department: School of Public Health

country: Australia

institute: University of Queensland

summary: The functional consequence of genetic variants and how they contribute to disease remains elusive. Studying genetic variants in disease-relevant cells captures variations in effects in cell types and states. The endometrium is a heterogenic tissue with critical reproduction roles considered complex genetic traits. We assessed the association between genetic variants and gene expression in purified endometrial mesenchymal cells using both bulk and single-cell RNA-sequencing data from patients with endometria-driven reproductive disorders. We compared these to those identified in whole endometrium and to reproductive disease-associated genetic loci. We identified cis-eQTLs for 947 unique eGenes in isolated endometrial mesenchymal cells of which 50% had not previously been identified in whole endometrium. Single-cell RNA-sequencing data stratifying by differentiation state we found a further 25 and 26 unique eGenes in stem and mature mesenchymal cells respectively. Comparison with reproductive disease-associated variants identified overlaps with COG6 and AC012313.10 with age of menarche and HELB with age of menopause. Summary Mendelian Randomisation (SMR) identified potential causal effects of RPS2 on age of menarche and KANSLI on age at first birth, as well as a mesenchymal stem cell state-specific influence of GATD3A on uterine fibroid formation. Identifying functional consequences of genetic variants critical to disease can be enhanced with disease-relevant, purified cells. We provide evidence for critical roles for COG6 and HELB in age-related traits of reproduction and a causal role for GATD3A on uterine fibroid formation during early cell development supporting that genetic influences on early stem cell state and subsequent differentiation can contribute to disease pathology.

overall_design: Endometrial stromal cells were isolated from endometrial biopsies and cultured. RNA was extracted from the cultured primary cells and RNA-sequencing perofrmed.

first: Brett

last: McKinnon

first: Samuel

last: Lukowski

first: Joanna

last: Crawford

first: Michael

last: Mueller

first: Grant

last: Montgomery


title: AAGGG repeat expansions trigger repeat-dependent synaptic dysregulation in human CANVAS Neurons [RFC1_Addition]

overall_design:
To assess global dysregulation of gene expression in CANVAS, we generated multiple Control, CANVAS, and Isogenic corrected patient iPSC lines. These were differentiated to forebrain glutamatergic neurons by modified Dual-SMAD inhibition protocol.
Neurons were aged to 10-weeks in vitro and were analyzed by paired-end RNASequencing of Control+GFP (n=3), Control+RFC1 (n=3), CANVAS+GFP (n=3), and CANVAS+RFC1 (n=3) iPSC-derived neurons. Neurons were treated with the respective lentivirus particles at DIV5 and continued expressing the integrated shRNA's throughout the 10-week differentiation before analysis.

RNASeq data were analyzed for differential expression, differential exon usage, and circRNA expression.


title: D53 is a dual-function transcription repressor of strigolactone signaling in cotton

city: Xi`an

first: Chen

middle: Hao

last: Ren

state: Shannxi

address: No. 620, West Chang'an Street, Chang'an District, Xi'an City

department: College of Life Sciences

country: China

institute: Shannxi Normal University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Strigolactones (SLs), a class of phytohormones, play a pivotal role in governing critical aspects of plant development, including shoot branching and root development. DWARF53 (D53) is a key repressor in the SL signaling. Nevertheless, its involvement and regulatory mechanisms in cotton fiber development—a representative single-cell model, has remained elusive. In this study, we unveil GhD53 represses the transcription of SL-inducible genes GhFAD3-2 and GhFAD3-4, which are involved in linolenic acid biosynthesis—a stimulant of cell elongation, thus inhibiting cotton fiber elongation. We demonstrate that GhD53's inhibitory influence on cotton fiber elongation is relieved in the presence of SLs, as GhD53 undergoes degradation. This alleviation of GhD53 repression triggers the activation of GhFAD3 expression, promoting fiber cell elongation. Remarkably, GhD53 serves as a dual-function transcription repressor, impeding SLs’ role in fiber elongation. Firstly, as a transcription factor, GhD53 directly binds to GhFAD3 promoters, suppressing their transcription. Secondly, GhD53 physically interacts with GhSLRF, a bHLH-type transcription factor, preventing it from binding to GhFAD3 promoters and repressing its transcription activation activity. GhD53 emerges as a pivotal component in the regulatory network governing SL signaling transduction. Overall, our findings provide novel insights into D53’s role in SL signaling and delineate a comprehensive framework for transmitting SL signals to modulate plant cell elongation behavior.

overall_design: Using an in vitro expressed transcription factor (TF) to probe bare genomic DNA fragments, in order to establish binding sites (peaks) and sequence motifs.

first: Huiqin

last: Wang


title: Investigation of PSF and p53 binding sites in prostate ccancer cells

city: Itabashi-ku

first: Ken-ichi

last: Takayama

address: Sakaecho

country: Japan

institute: Tokyo Metropolitan Institute of Gerontology

summary: Proline- and glutamine-rich (PSF) has been identified as an important driver of aggressive cancers, in which PSF-RNA interactions promotes the expression of numerous oncogenic transcripts by modulating epigenetic and splicing systems. To develop small compounds targeting PSF as next generation therapeutic agents for hormone therapy refractory cancers, we performed small molecule library screen and identified the compound designated as No.10-3 as a potent PSF inhibitor. We further describe another small molecule C-30, an improved analog of No.10-3. PSF inhibits p53 epression in prostate cancer cells by epigenetic regulation.  We then  performed ChIP-seq analysis to determined PSF and p53 binding regions.

overall_design: Identification of binding sites of PSF, and p53 in prostate cancer cell line, 22Rv1. In addition, PSF binding sites in DU145 prostate cancer cells bearing mutated p53 protein.


title: Intestinal lamina propria CD45+ immune cells sequencing of WT and AhR-deficient mice

city: Shanghai

first: Yajing

last: Gao

address: Minhang district

institute: Fudan University

summary: We used scRNAseq to identify potential effector cells contributing to the exacerbated inflammatory responses in AhR deficient mice.

overall_design: Intestinal lamina propria CD45+ immune cells were isolated by positive selection with anti-mouse CD45 magnetic beads according to manufacturer's instructions and analyzed using scRNAseq.


title: Insulin controls hepatic bile acid metabolism by the spatial repatterning of gene expression

city: Ithica

first: Praveen

last: Sethupathy

state: NY

address: Cornell University College of Veterinary Medicine, Box 17

institute: Cornell University

summary: Insulin regulation of hepatic gene expression is critical for controlling metabolism and preventing diabetes, atherosclerosis and NAFLD; yet, how insulin regulates gene expression in the spatial context of the liver lobule is largely unexplored.  Here, we find that insulin regulates bile acid metabolism by segregating CYP8B1, the enzyme that catalyzes the 12α-hydroxylation of bile acids, from the other enzymes required for bile acid synthesis.  When insulin signaling is disrupted, Cyp8b1 and the other bile acid synthesis genes become co-localized within the same zone, and 12α-hydroxylated bile acids, which drive atherosclerosis and NAFLD, are increased. Novel zone-specific genetic manipulations of Cyp8b1 that mimic the effects of insulin result in a more benign bile salt profile. Mechanistically, the zonal effects of insulin are not due to gradients of insulin concentration or signaling, but through insulin crosstalk with positional Wnt signals: Wnt and insulin act together to determine the complement of transcription factors active in the pericentral hepatocytes and thereby regulate Cyp8b1 zonation.  Taken together, these data show that by repatterning gene expression in the liver lobule, insulin can transcriptionally regulate the outputs of a metabolic pathway.  The spatial dimension of transcriptional regulation represents a novel lens with which to view the control of metabolism that may ultimately lead us to more precise therapies.

overall_design: Single nuclei sequencing of liver tissue from mus musculus following a 16-24 hour fast and compared to a fed control.

first: Sudha

last: Biddinger

first: Matt

last: Kanke


title: PiRNA DQ571591 regulated the function of non-small cell lung cancer cells

first: Chuandong

address: 320 Yueyang Road

institute: SJTU

type: Non-coding RNA profiling by high throughput sequencing

summary: In-depth study of the pathogenesis of NSCLC is of great significance, for the discovery of new early clinical diagnosis strategies and treatment targets for NSCLC. Epigenetics has become a research hotspot in the field of life science in recent years, and research on noncoding RNAs including PIWI-interacting RNAs (piRNAs) is an important part of this field. An increasing number of studies have shown that piRNAs play an important role in silencing transposons and regulating messenger RNA (mRNA) and long noncoding RNA (lncRNA). In the field of cancer research, piRNAs may become new molecular markers and therapeutic targets.

overall_design: PiRNAs related to NSCLC were found by small noncoding RNA sequencing and qPCR detection.  The target of piRNA DQ571591 was found by mRNA sequencing.

first: Ling

last: Zhou

first: Guochao

last: Shi

first: Yun

last: Feng


title: Codon Specific Readthrough as a Mechanism of BRCA2 Restoration in Acquired PARP Inhibitor and Chemotherapy Resistance [WES]

city: Rochester

first: Cristina

last: Correia

state: Minnesota

address: Kellen Bld 3 th Floor, 200 1st street SW

institute: Mayo Clinic

summary: Deleterious alterations of the gene encoding BRCA2, a protein involved in homologous recombination (HR), contribute to the pathogenesis of a subset of ovarian, breast, prostate and pancreatic cancers as well as their increased sensitivity to platinating agents and poly(ADP-ribose) polymerase inhibitors (PARPis). While secondary mutations that restore a functional BRCA2 protein are detected in a fraction of cases that become drug resistant, the causes of resistance in other cases are poorly understood. Here we characterized clones derived from the BRCA2-mutant ovarian cancer line PEO1 by PARPi selection. Colony forming assays demonstrated cross-resistance of these clones to multiple PARPis, cisplatin and doxorubicin. Despite persistence of the signature 4965C>G (p.Y1655X) BRCA2 nonsense mutation, HR was restored in the resistant cells. Immunoprecipitation followed by immunoblotting or mass spectrometry demonstrated expression of low levels of BRCA2 protein, including peptides distal to the premature termination codon. Reporter assays demonstrated readthrough selective for the UAG stop codon in the resistant clones but not parental PEO1 cells. Mass spectrometry and immunoblotting provided evidence for readthrough of stop codons, particularly UAGs, in additional proteins in the resistant clones. BRCA2 gene interruption either 5’ or 3’ to the stop codon restored sensitivity of the resistant clones to PARPis and cisplatin, implicating the low level BRCA2 expression in resistance. Accordingly, the present results identify low level readthrough of nonsense codons as a potential mechanism of drug resistance that might need to be considered when assessing the impact of BRCA2 nonsense mutations.

overall_design: RNAseq data of 15 samples (PEO1 parental or and veliparib resistant ABTR clones (n=4) ) in three independent experiments. PEO1 resistant clones (ABTR) were generated by continuous exposurse to veliparib (ABT888) 40 uM.

first: Scott

last: Kaufmann

first: Hu

last: Li


title: TEX264 drives selective autophagy of DNA lesions  to promote DNA repair and cell survival

city: Oxford

first: Pauline

last: Lascaux

address: The MRC Weatherall Institute of Molecular Medicine

department: Department of Oncology

country: United Kingdom

institute: University of Oxford

summary: DNA repair and autophagy are distinct biological processes vital for cell survival. Although autophagy helps maintain genome stability, there is no evidence of its direct role in the repair of DNA lesions. We discovered that in human cells, lysosomes process Topoisomerase 1-cleavage complexes (TOP1cc) DNA lesion. Selective degradation of TOP1cc by autophagy directs DNA damage repair and cell survival at clinically relevant doses of Topoisomerase 1 inhibitors. TOP1cc are exported from the nucleus to lysosomes through transient alteration of the nuclear envelope, and independent of the proteasome. Mechanistically, the autophagy receptor TEX264 acts as a TOP1cc sensor at DNA replication forks, triggering TOP1cc processing by the p97 ATPase and mediating TOP1cc delivery to lysosomes dependent on MRE11 nuclease and ATR kinase. We found an evolutionary conserved role for selective autophagy in DNA damage repair that enables cell survival, protects genome stability, and is clinically relevant for colorectal cancer patients.

overall_design: Sequencing of DNA fragments purified from the lysosomes vesicles of HeLa cells by LysoIP from 2 biological replicates (LysoIP-Seq). Cells were treated for 6 hours with CPT and BAF.

first: Camilla

last: Trugenberger

first: Annamaria

last: Ruggiano

first: Gwendoline

last: Hoslett

first: Wei

last: Song

first: James

last: Bancroft

first: Errin

last: Johnson

first: Iolanda

last: Vendrell

first: Roman

last: Fischer

first: Sara

last: Tribble

first: Ivan

last: Anticevic

first: Cecile

last: Otten

first: Ignacio

last: Torrecilla

first: Stelios

last: Koukouravas

first: Yichen

last: Zhao

first: Hongbin

last: Yang

first: Ftoon

last: Aljarbou

first: Cristiano

last: Peron

first: Giulio

last: Deangeli

first: Enric

last: Domingo

first: Loic

last: Carrique

first: Alvin Wei

last: Tian Ng

first: Joanne

last: Ngeow

first: Vincenzo

last: D'Angiolella

first: Nuno

last: Raimundo

first: Tim

last: Maughan

first: Marta

last: Popovic

first: Ira

last: Milosevic

first: Kristijan

last: Ramadan


title: Transcriptomic Response of Adult Fruit Flies to Arsenite Exposure II

city: Bloomington

first: Jason

middle: M

last: Tennessen

email: tennessenlab@gmail.com, tennlab@iu.edu, jtenness@iu.edu, tourigny@iu.edu

state: IN

address: 1001 E 3rd St

department: Biology

institute: Indiana University

summary: As part of our exploration into alternative model systems for toxicology, we exposed male and female adult D. melanogaster to varying concentratios of arsenite over the course of two days and profiled their response via RNA-seq

overall_design:
Male and female starved adult flies were exposed to zero (control), 0.25mM, or 1mM sodium arsenite in their food for the alotted time (0, 1, 2, 4, 8, 12, 24, 48h), before collection and proccessing for RNA-seq
These data stem from an in-house re-run of experimental samples initially profiled in GSE235705, which was missing several male timepoints and had a high variance of read depth
A few samples were re-run for increased depth; the concatenated fastq files are identified by their "S00" sample numbers
raw fastq files are coded with the schema: "[NaAsO2 (soduium arsenite)]- [M/F (male or female)  0/1/2/4/8/24/48 (time of treatment in hours)  A/B/C (0, 0.25, or 1mM arsenite, respectively)]-[1/2/3/4 (replicate number)]

first: Shannon

last: Smoot

middle: P

last: Tourigny

first: Thomas

last: Kaufman


title: The impact of ART-relevant in vitro maturation on active translation in oocytes and zygotes

city: Libechov

first: Michal

last: Dvoran

address: Rumburska 89

country: Czech Republic

institute: Institute of Animal Physiology and Genetics, CAS

summary: Assisted reproductive technology (ART) has become an indispensable tool in fertility treatment. Most ART patients respond normally to controlled ovarian stimulation, however some may benefit from the alternative method of oocyte in vitro maturation (IVM), recognized but still underdeveloped method with limited results. As oocytes undergo the transcriptionally silent phase of meiosis, protein synthesis is an important regulator of oocyte development. Here, we have modelled and compared the clinically relevant IVM simulation with in vivo conditions in mouse oocytes and zygotes.

overall_design:
We apply clinically relevant conditions on the mouse model system with aim to uncover the differences in selective recruitment of stored maternal transcripts by the oocyte and zygote translation machinery.
Every sample type was collected in quadruplicates: (in vitro matured denuded oocytes=IVM, in vitro matured cumulus-oocyte complexes=COC, in vivo matured oocytes=IVO, in vitro matured and fertilized pronuclear zygotes=IMZ, in vivo matured and fertilized pronuclear zygotes=IVZ)
We performed total RNA isolation followed by polysome fractionation as well as collected unfractionated total RNA in respective samples.
We performed differential gene expression analysis between in vitro and in vivo maturation conditions from obtained RNA-seq data in oocytes and zygotes

first: Rajan

last: Iyyappan

first: Tomas

last: Masek

first: Martin

last: Pospisek

last: Kubelka

first: Andrej

last: Susor


title: Determining the DNA-binding targets of NFATc2 in the AML cell line THP-1

city: Glasgow

first: Shaun

middle: David

last: Patterson

address: University Avenue

institute: University of Glasgow

summary: Based on previous work on the KDM histone demethylase family in AML, the transcription factor NFATC2 was identified as a regulatory target of KDM4A in MLL-AF9-rearrangement THP-1 cells. Our existing work examined the elements of the transcriptome regulated by NFATC2 in THP-1 cells and so, to further this work, we aimed to characterise the DNA-binding targets of NFATc2 in these cells. In this study, we used NFATc2 immunoprecipitation for ChIP-seq in untreated THP-1 cells, in order to determine these.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for NFATc2 vs input DNA, in lysates from untreated THP-1 cells; three experimental replicates.

middle: D

first: Matthew

middle: E

last: Massett

first: Xu

last: Huang

first: Heather

middle: G

last: Jørgensen

first: Alison

last: Michie


title: Aging and senescence-associated signatures of aged kidney glomerular cells [bulk RNA-seq]

city: South San Francisco

first: Andrey

last: Shaw

state: California

address: 1 DNA Way

institute: Genentech

summary: The kidney governs many physiological factors of the body, and the glomerulus is its core filtration unit. Glomeruli comprise of less than 1.5% of the kidney’s volume and thus are underrepresented in many analyses of the kidney, and require particular isolation methods. Aging is a major risk factor for kidney disease, yet despite the importance of proper glomerular function, we have limited knowledge of the changes that glomerular cells undergo during aging. Here we interrogate the aged mouse kidney, glomerulus and glomerular cells using various approaches, including single cell RNA sequencing (scRNA-Seq), to identify age and senescence associated changes at the tissue and cellular level. We show that the aged kidney and glomerulus undergo structural changes, including increased fibrosis, glomerulonephritis and expression of injury and senescence-associated markers. Lastly, we utilized our method for high-throughput analysis of mouse glomeruli to characterize cell-specific and age-related changes in glomerular cells. This analysis revealed a senescence-associated phenotype in aged mesangial cells, and emphasized the potential importance of mesangial cells and macrophages in this niche. Our study provides insights into the molecular and cellular changes of the aging glomerulus that suggest therapeutic targets for age-related renal dysfunction.

overall_design: Isolated kidney glomeruli were isolated from young and old mice for bulk RNA sequencing.

first: Ben

last: Korin

first: Shimrit

last: Avraham

first: Andrew

last: McKay

first: Steffen

last: Durinck

first: Reuben

last: Moncada

first: Hari

last: Menon

first: Spyridon

last: Darmanis

first: Yuxin

last: Liang

first: Zora

last: Modrusan

first: Joshua

last: Webster

middle: S


title: The effect on gene expression in filamentous haploid of sugarcane smut fungus Sporisorium scitamineum

city: Nanning

first: Shan

last: Lu

state: --- Select One ---

address: No.100,Daxue East Road

institute: Guangxi University

summary: There are two mating types, “+” and “-” strains in S. scitamineum. Generally, dikaryote cells are formed after fussion of the germ turbs from both mating type strains and filamentation (filamentous growth) with infection potential occur afterward. By introducing bE2 gene and/or orther related genes, derived from the opposite mating type strain JG36, haploid mutants with filamentation characteristics were generated,  including M6,M8,M9 and M10. Among these are 446 genes that were found in both filamentous haploid strains, including 237 genes up-regulated and 209 genes down-regulated. The up-regulated genes were mainly enriched in amino acid biosynthesis, starch and sucrose metabolism, secondary metabolite biosynthesis, and pentose phosphate pathways. Down-regulated expression genes are mainly enriched in fatty acid synthesis and metabolism, homologous recombination, peroxides, biosynthesis of unsaturated fatty acids, ubiquitin-mediated protein hydrolysis and other metabolic pathways. Several MAP kinases and protein kinases were up- or down-regulated in the filamentous haploid.

overall_design: We generated filamentous haploids by ATMT. We then performed gene expression profiling analysis using data obtained from RNA-seq of wild type strain and filamentous haploids. Comparative gene expression profiling analysis RNA-seq data for wild type strain and filamentous haploids.

first: Baoshan

last: Chen


title: Aging and senescence-associated signatures of aged kidney glomerular cells

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

overall_design: Refer to individual Series


title: Aging and senescence-associated signatures of aged kidney glomerular cells [scRNA-seq]

overall_design: Kidney glomeruli were extracted from young and old mice and characterized using single cell RNA sequencing.


title: Transcriptomic analysis of 30dpp ovaries and 35dpp testes exposed to the cocktails of pharmaceuticals ibuprofen (IBU), 2hydroxyIBU (2hIBU), diclofenac (DCF) and 17a ethinyl-estradiol (EE2) in mice

city: Montpellier

first: Brigitte

last: Boizet Bonhoure

address: 141 rue de la Cardonille

department: Human Genetic Institute

country: France

institute: CNRS UMR9002

summary: The endocrine disrupting pharmaceuticals, non-steroidal anti-inflammatory drugs (NSAIDs) and 17α-ethinyl-estradiol (EE2), are among the most relevant molecules found in aquatic ecosystems, surface and drinking water due to their incomplete removal by wastewater treatment plants. Exposure to therapeutic doses has a negative impact on gonadal development and fertility in rodent models; however, the effects of their chronic exposure at lower doses are not known. In this study, we investigated the impact of chronic exposure to a mixture containing ibuprofen, 2hydroxy-ibuprofen, diclofenac, and EE2 at two environmentally relevant doses (added to the drinking water from fetal life, 8.5 dpc, until puberty) on the reproductive tract in F1 exposed mice and their F2 offspring. In F1 animals, exposure delayed male puberty and accelerated female puberty. In post-pubertal F1 testes and ovaries, differentiation/maturation of the different gonad cell types was altered, and some of these modifications were observed also in the non-exposed F2 generation. Transcriptomic analysis of post-pubertal testes and ovaries of F1 (exposed) and F2 animals revealed significant changes in gene expression profiles and enriched pathways, particularly the inflammasome, metabolism and extracellular matrix pathways, compared with controls (non-exposed). This suggested that exposure to these drug cocktails has an inter-generational impact (Int. J. Mol. Sci. 2023, 24, 5890. /doi: 10.3390/ijms24065890)

overall_design: Two mixtures containing environmentally relevant doses of IBU/2hIBU + DCF + EE2 (D1 and D2) were added or not (control; C) to the drinking water of pregnant mice and their progeny from 8.5 days post-coitum (dpc) until animal sacrifice (30 days post-partum, dpp, for females and 35 dpp for males): F0 males and females from different litters were mated to minimize inbreeding and mated females were divided in three groups: control (no exposure), IBU/2hIBU+DCF+EE2 dose 1 (D1), and IBU/2hIBU+DCF+EE2 dose 2 (D2) (n= 6-7 females per exposure group). The IBU, 2hIBU, DCF and EE2 doses were calculated on the basis of their mean concentrations (5, 40, 10 and 1-2 ng/L, respectively) and maximum concentrations (50-100, 85-100, 50 and 20-50 ng/L, respectively) found in environmental drinking water samples. Thus, the calculated doses in the animal drinking water were: i) D1: IBU 11.3 ng/L/2hIBU 90 ng/L + DCF 22.5 ng/L + EE2 2.25 ng/L; and ii) D2: IBU 113 ng/L/2hIBU 225 ng/L + DCF 112 ng/L + EE2 45 ng/L. The control group was exposed to diluted ethanol (0.001%). Animals were reared in polyphenylsulfone (PPSU) cages in controlled environmental conditions (light/darkness: 12h/12h, 23°C) and drinking water was put in PPSU bottles wrapped in aluminum foil, and were fed with SAFE D131 that does not contain fish proteins, soy and alfalfa. Municipal tap water was provided ad libitum.

last: Boizet-Bonhoure

first: Pascal

last: Philibert


title: Expression data from lung resident mesenchymal stem cells from idiopathic pulmonary fibrosis patients and control subjects

city: Palma

first: Josep

last: Muncunill Farreny

address: Carretera de Valldemossa, 79. Hospital Universitario Son Espases

country: Spain

institute: IdISBa

summary:
Lung resident mesenchymal stem cells exert a pivotal role in tissue repair. Idiopathic pulmonary fibrosis is characterized by an aberrant tissue repair.
We performed a transcriptomic analysis to characterize lung resident mesenchymal stem cells from idiopathic pulmonary fibrosis patients

overall_design: Lung resident mesenchymal stem cells were isolated from idiopathic pulmonary fibrosis patients and control subjects. RNA was isolated from cultured cells and transcriptomic analysis were performed by using the GeneChip® Gene 1.0 ST Array System (Affymetrix)

first: J

last: Mercader-Barceló

first: V

last: Asensio-Landa


title: Immunophenotyping peripheral blood mononuclear cells in human HFpEF

city: Nashville

first: Charles

middle: Duncan

last: Smart

address: 2201 West End Ave

department: Molecular Physiology and Biophysics

institute: Vanderbilt University

summary: Immune cell activation in heart failure is poorly understood. We profiled circulating leukocytes in humans with heart failure with preserved ejection fraction and non heart failure controls to identify novel changes associated with HFpEF diagnosis

overall_design: We performed multiomic profiling of PBMCs from non heart failure controls and patients with heart failure with preserved ejection fraction to identify novel transcriptomic changes in circulating immune cells

first: C

first: D

last: Dixon

last: Fehrenbach

middle: W

last: Wassenar

first: E

last: Dillon

middle: K

last: Gupta

first: M

last: Madhur


title: Single-cell transcriptomes for paired uninflamed and inflamed mucosal tissues of CD patients

city: Nanjing

first: Peizhao

last: Liu

state: Jiangsu

address: Zhongshan East Road 305#

institute: Jingling Hospital, Medical School of Nanjing University

summary: The single-cell transcriptomes were performed from paired uninflamed and inflamed mucosal biopsies obtained from surgically resected colonic samples from 3 CD patients.

overall_design:
The fresh colon tissues were stored in the sCelLiveTM Tissue Preservation Solution (Singleron) on ice after the surgery within 30 min. After digesting with sCelLiveTM Tissue Dissociation Solution (Singleron) and incubating with GEXSCOPE red blood cell lysis buﬀer (RCLB, Singleron), the samples were stained with Trypan Blue and the cell viability was evaluated microscopically. Single-cell suspensions (2×10^5 cells/ mL) were loaded onto microwell chip using the Singleron Matrix Single Cell Processing System. Barcoding Beads were subsequently collected from the microwell chip, followed by reverse transcription of the mRNA captured by the Barcoding Beads and to obtain cDNA, and PCR amplification. The scRNA-seq libraries were constructed according to the protocol of the GEXSCOPE Single Cell RNA Library Kits (Singleron). Individual libraries were diluted to 4 nM, pooled, and sequenced on Illumina novaseq 6000 with 150 bp paired end reads. Raw reads from scRNA-seq were processed to generate gene expression matrixes using CeleScope (https://github.com/singleron-RD/CeleScope) v1.5.2 pipeline. Briefly, raw reads were first processed with CeleScope to remove low quality reads with Cutadapt v1.17 to trim poly-A tail and adapter sequences. Cell barcode and UMI were extracted. UMI counts and gene counts of each cell were acquired with featureCounts v2.0.1 software, and used to generate expression matrix files for subsequent analysis.
The 3 uninflammed samples are: DTJ-C, LWF-C, and TJY-C
The 3 inflammed samples are: DTJ-D, LWF-D, and TJY-D

first: Wenbin

last: Gong

first: Xiuwen

last: Wu

first: Yun

last: Zhao

first: Jianan

last: Ren


title: Effect of Rad knockout on heart failure improvement

city: Lexington

first: Jonathan

last: Satin

state: KY

address: 741 S. Limestone St.

department: Physiology

institute: University of Kentucky

summary: To investiage the ability of positve inotropism from myocardial Rad reduction we induced Rad knockout after onset of pressure overload to reverse or compensate progression of heart failure

overall_design: We performed RNAseq from hearts of sham and TAC mice in wild-type or Rad knockout, hearts harvested >2months after TAC and >1month after Rad knockout

first: Douglas

last: Andres

first: Brooke

last: Ahern

first: Garrett

last: Elmore


title: RNA-Seq based gene expression profiling of mouse Meis1-Meis2 double KO or wild-type atria and ventricles (Adult).

city: Madrid

first: Manuel

last: Gomez

state: Madrid

address: Melchor Fernández Almagro, 3

institute: CNIC

summary: The goal of this study was to compare the gene expression profile, using RNA-seq technology, of mouse Meis1-Meis2 double KO or wild-type fetal or adult hearts.

overall_design: RNA-seq was performed in four different conditions, atria and ventricles from fetal hearts at E15.5 and from adult hearts to compare Meis1 and Meis2 double deletion (constitutive or inducible) with control littermates. In all cases, 4 replicates were used for each condition.

last: Torres


title: Atherosclerotic process regulates arterial damage, abdominal aortic aneurysm (AAA) formation and rupture

city: Kobe

first: Takuo

last: Emoto

state: Hyogo

address: 7-5-1 Kusunoki-cho, Chuo-ku

department: Division of Cardiovascular Medicine, Department of Internal Medicine

institute: Kobe University Graduate School of Medicine

summary: By modeling interaction of cigarette smoke and hypercholesterolemia, we provide experimental evidence that atherosclerotic disease directly contributes to AAA formation and rupture; AAA progression is mediated by inflammatory Mφ residing within associated atherosclerotic plaque.

overall_design: Single cell transcreptome of human AAA


title: The Transcriptome Analysis Reveals the Underlying Mechanism of Low Fetal Weight due to Prenatal High Estradiol Exposure in Mice

first: Xiaoguo

last: Zheng

address: 145 Guangyuan Road

institute: Shanghai Jiaotong University

summary:
To reveal differences in transcriptome profiles of mouse placentas between HE placentas and NC placentas, aiming to identify the important genes and critical pathways associated with the underlying mechanism for the risk of low birth weight induced by high maternal serum E2 levels.
We used the mouse model of high E2 prenatal exposure or pure core oil exposure and collect the pups and placentas. In total, 12 samples were sequenced, including 3 placentas derived from male pups and 3 placentas obtained from female pups in both control and E2-treated groups.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for 12 samples including 3 placentas derived from male pups and 3 placentas obtained from female pups in both control and E2-treated groups.

first: Xiaojun

last: Chen

first: Hefeng

last: Huang

first: Jing

last: Lin

first: Yuchuan

last: Zhou

first: Huihui

last: Wang

first: Chengliang

first: Xinmei


title: mRNA seq of MOSAICS based Irs1 KO, Srebf1 KO, Tbx3 KO, Bcl6 KO, Smyd2 KO and control (sgGFP and sgLacZ) livers

city: Dallas

first: Hao

last: Zhu

address: 5323 Harry Hines Blvd

institute: UTSW

summary:
To investigate expression changes of the KO vs. control livers under 3 months of Western Diet.
We then performed mRNA seq analysis on MOSAICS based single-gene whole-liver KO samples and control samples

overall_design: Comparative gene expression profiling analysis of RNA-seq data for KO vs. control livers

first: Zixi

first: Yunguan

first: Yuemeng

last: Jia


title: Doxorubicin and protective inhibitor treated iPSC derived cardiomyocytes

city: palo alto

first: Chun

last: Liu

state: CA

address: 1291 Welch Road BMI building, 3200-CVI Rm

institute: stanford

summary: Investigation of drug and gene rescues doxorubicin induced alterations of transcriptomic and metabolic profiles

overall_design: RNA-seq analysis on 1) WT and CA12 KO iCMs treated with vehicle or doxorubicin (0.5 µM) and 2) WT iCMs treated with doxorubicin plus indisulam to gain a comprehensive understanding of their genome-wide transcriptomic changes.

first: Mengcheng

last: Shen


title: Effect of SLC7A9 on gene expression in AGS gastric cancer cells

city: shanghai

first: Haoran

last: Feng

address: ruijin 2 road. NO.197

institute: shanghai ruijin hospital

summary: To investigate the function of SLC7A9 in gastric cancer, vector and SLC7A9 lentiviruses were transferred to AGS

overall_design: Comparative gene expression profiling analysis of RNA-seq data for AGS/vector and AGS/SLC7A9.

first: Junxian

last: Yu


title: Gene expression profiling of stress-induced senescence and paracrine senecence in human hepatocytes

city: Stockholm

first: Xiangyu

last: Li

address: Tomtebodavägen 23, Solna

department: Science for life laboratory

country: Sweden

institute: KTH-Royal Institute of Technology

summary: Hepatocytes undergo senescence during development and progression of NAFLD. In order to better understand the phenotype of these senescent cells we generated an in vitro model of stress-induced senescence in IHH cells. To further understand the dynamic regulation of paracrine senescence, IHH cells were exposed to conditioned medium generated by an inducible model of stress-induced senescence.

overall_design: mRNA expression proflles were obtained from IHH (immortalized human hepatocyte) cells exposed to (1) doxorubicin (DOX; 2 µM) for 2h  and (2) conditioned media from ctrl-and DOX-treated IHH cells.

first: Ulf

last: Smith

first: Ritesh

last: Baboota


title: Expression profile of ATF2 knockdown in gastric cancer cell line MGC803 and genome-wide maps of  ATF2 binding sites in gastric cancer cell line AGS [ChIP-Seq]

city: Hefei

first: xiang

middle: yong

state: Anhui

address: JiXi Avenue

department: Department of General Surgery

institute: The First Affiliated Hospital of Anhui Medical University

summary:
Activation transcription factor 2 (ATF2), a member of the ATF/CREB family of transcription factors, is implicated in a broad spectrum of cancer-related biological functions, such as cell proliferation, apoptosis and DNA repair. Growing evidence indicates ATF2 act as an oncogene or a tumor suppressor in different cancer types depending on its expression level and subcellular localization.
In this study, RNA-seq and ChIP-seq were performed for identification of genome-wide DNA binding sites and potential transcription targets for ATF2.

overall_design: The ChIP assay and high through-put sequencing were conducted in AGS cells stably overexpressing ATF2.

first: Xin

last: Xu

first: Yongxiang


title: Expression profile of ATF2 knockdown in gastric cancer cell line MGC803 and genome-wide maps of  ATF2 binding sites in gastric cancer cell line AGS


title: Expression profile of ATF2 knockdown in gastric cancer cell line MGC803 and genome-wide maps of  ATF2 binding sites in gastric cancer cell line AGS [RNA-Seq]

overall_design: Comparative gene expression profiling analysis of RNA-seq data for control and ATF2 knockdown MGC803 cells.


title: Heteronemin and Tetrac Induce Anti-proliferation by Blocking EGFR-mediated Signaling in Colorectal Cancer Cells

city: Taipei City

first: Sukanya

last: Unson

address: No. 250, Wuxing Street, Xinyi District

department: Cancer biology and drug discovery

country: Taiwan

institute: Taipei medical university

summary:
Heatmap, pathway scores and significant modulation of genes induced by heteronemin, tetrac, and their combination versus the control in HCT 116 cells were performed.
(abstract) Overexpression of EGFR accounts for 60-80% of colorectal cancer patients. Anti-EGFR monoclonal antibodies are ineffective in colorectal cancer patients due to KRAS mutation. To discover new therapeutic strategies urgently need for colorectal cancer patients. Sponge extract, heteronemin, has been shown to induce anti-proliferation in different types of cancer. Tetrac shows to inhibit Ras-mutant cancer cell proliferation. Cell viability was evaluated in the HT-29 and HCT-116 cell lines to determine the antitumor effects of heteronemin and its combination with tetrac. Gene expressions were determined by NanoString technology and a quantitative RT-PCR. Protein expressions and cell cycle distributions were respectively assessed by Western blotting and flow cytometry. Heteronemin or its combination with tetrac inhibited cancer cell growth in both mutant and KRAS wild-type CRC. Combined treatment altered the cell cycle in both cell lines at the sub-G1 and S phases. Moreover, their combination induced inactivation of EGFR signaling via downregulating the phosphorylated and total extracellular signal-regulated kinase 1/2 (ERK1/2) protein in both cell lines. The programmed death ligand 1 (PD-L1) protein was reduced in HCT-116 cells, while HT-29 cells showed downregulation of the phosphorylated and total phosphatidylinositol 3-kinase (PI3K) protein. In KRAS mutant cells, heteronemin or its combination with tetrac showed significant modulation of genes associated with cancer progression by NanoString technology. Therefore, tetrac improved the anticancer effect of heteronemin and may be an alternative strategy to effective overcome KRAS mutation-acquired resistance to anti-EGFR therapy.
1. To investigate whether heteronemin combined tetrac induce the antitumor effect in different KRAS statuses of CRC via blocking of EGFR signaling cascades.
2. To assess gene expression profiling in KRAS-mutant CRC cells by nanostring technology.

overall_design: In this study, NanoString was used for the gene expression analyses of the HCT-116 cell line.Technical and biological normalization of the raw counts of each gene was performed using nSolver Software vers. 4.0. For technical normalization, a positive control factor was calculated for each sample.

first: Bella

last: Tsai


title: RNA-Seq based gene expression profiling of mouse epicardial-cells with Meis1-Meis2 double KO or wild-type genotypes.

first: Manuel

last: Gomez

summary: The goal of this study was to compare the gene expression profile, using RNA-seq technology, of mouse epicardial-cells with Meis1-Meis2 double KO or wild-type genotypes.

overall_design: Epicardial cells, isolated from WT or Meis1-Meis2 double KO mice, were used to extract poly A RNA with the aim of studying the effect of the mutations on gene expression profiles, using RNA-Seq technology.

first: M

last: Torres


title: Genome-wide identification of ZCCHC10 targets in acute myeloid leukemia cells

city: Changsha

first: Jianlin

state: Hunan

address: 36 Lushan road

department: College of Life Science

institute: Hunan Normal University

summary: To explore which pathways ZCCHC10 is involved in acute myeloid leukemia (AML), we constructed ML-2 cells stably expressing ZCCHC10 (ML2-Zh10) or empty vector (ML2-Vec). Then, RNA-seq was performed to compare the mRNA profilings of ML2-ZH10 and ML2-Vec cells.

overall_design: Comparing the mRNA profilings of ML-2 cells stably expressing ZCCHC10 (ML2-Zh10) and empty vector (ML2-Vec)

first: Yichong

last: Ning

first: Hao


title: Activity-dependent history in hippocampal neurons dictates temporal dynamics of homeostatic synaptic scaling

city: Ann Arbor

first: Shigeki

last: Iwase

address: 1241 E. Catherine St.

institute: University of Michigan

summary: Neural circuits utilize a host of homeostatic plasticity mechanisms, including synaptic scaling, to maintain stability in circuits undergoing experience-dependent remodeling necessary for information processing. During synaptic scaling, compensatory adaptations in synaptic strength are induced after chronic manipulations in neuronal firing, but our understanding of this process is largely limited to its initial induction. How these homeostatic synaptic adaptations evolve when activity renormalizes and their impact on subsequent homeostatic compensation are both poorly understood.  To examine these issues, we investigated whether a previous history of homeostatic scaling in networks of cultured hippocampal neurons altered their subsequent homeostatic responses to chronic activity manipulations. Unexpectedly, we found that a history of synaptic scaling strongly suppressed future scaling to the same, and even opposite, activity challenges. This history-dependent suppression was specific for future homeostatic compensation, as networks with a prior scaling history showed no deficits in the chemical induction of long-term potentiation (cLTP), a Hebbian form of synaptic plasticity. Hippocampal neurons with a prior scaling history exhibited normal engagement of activity-dependent signaling during subsequent activity challenges (as assessed by examination of the ERK/MAPK pathway) but demonstrated widespread alterations in activity-dependent transcriptional

overall_design: To examine transcriptional dynamics directly, we employed bromouridine RNA sequencing (BrU-seq) to monitor newly generated transcripts over the first 4hrs of activity silencing. This genome-wide nascent transcript profiling technique provides an unbiased account of newly transcribed genes during TTX silencing of neurons. We prepared primary hippocampal and cortical neuron co-cultures from brain tissue isolated from P1-P2 rats and allowed them to mature for 14 days in vitro (DIV). We adopted the same paradigm we have used in functional studies, where neurons are treated with either vehicle or TTX from 0-24hrs, followed by a 48hr washout period, then either vehicle or TTX again for 4hrs. During the last 30mins of this second TTX treatment, we added BrU to the culture medium to label newly synthesized transcripts which are then isolated using magnetic beads coated with anti-BrU antibody and processed for next-generation sequencing.

first: Alex

last: Chen

first: Patricia

last: Garay

first: Michael

last: Sutton


title: Insight into the epigenetic regulation of gene expression in the bloodstream and procyclic forms of Trypanosoma brucei through the involvement of G-Quadruplexes

status: Public on Aug 31 2024

city: Groningen

first: Anne

middle: de

last: Jong

address: Nijenborgh 7

department: Molecular Genetics

country: Netherlands

institute: university of Groningen

summary: The study investigates the epigenetic role of G-quadruplexes (G4s) in the differentiation of Trypanosoma brucei brucei, specifically between its bloodstream form (BF) and procyclic form (PC). An in silico analysis identified 115,126 potential G4 sequences (PQSs) across the genome, with 63% having a high probability of G4 formation. These PQSs are unevenly distributed, with notable enrichment in regions associated with antigenic variation, such as variant surface glycoproteins and bloodstream expression sites. The differential distribution of PQSs correlates with regions of high densities of differentially expressed genes, suggesting a regulatory role in morphological transitions. The study assessed the effects of G4-ligands (AQ1, Pt-TTPY, and pyridostatin) on gene expression, revealing significant downregulation of DEGs and highlighting their therapeutic potential. Functional analysis using Gene Ontology indicated that G4-ligands impact various biological processes differently in BF and PC forms. These findings underscore the epigenetic complexity of T. brucei and the potential of G4 structures as key regulators of gene expression and differentiation, offering novel insights into therapeutic strategies targeting the parasite's adaptive mechanisms.

overall_design: T. brucei parasites in logarithmic phase were incubated with 2X of the half-maximal inhibitory concentration of AQ1 (BSF: 0,24 uM and PCF: 9), Pt-TTPY (BSF: 0,26 uM and PCF: 48,46 uM) and pyridostatin (BSF: 11,04 uM and PCF: 18,18 uM) for 18 h at 37ºC or 28 ºC,  5% CO2 and 100% of humidity. Then, the parasites were washed twice in phosphate buffered saline and processed by RNA isolation. Total RNA was purified using a total RNA isolation kit (Qiagen, Germany) according to the manufacturer’s instructions. The RiboCop for Bacteria (Lexogen) was used to deplete 800 ng of the extracted total RNA for rRNA. The NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (New England Biolabs, UK) was used to prepare the library preps for Illumina sequencing. Samples were sequenced on the Illumina NexSeq 1000 to generate 100 bases single-end reads (100SE) with an average read-depth of 10M reads per sample. The quality of the resulting fastq reads were checked using FastQC v0.11.9 (Babraham Bioinformatics, Cambridge) and mapped on the reference genome using STAR v2.7.10b (default setting with following changes; --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNoverReadLmax 0.04). The resulting SAM files were converted to BAM using SAMtools 1.1171 , and featuresCounts 2.0.1 72 was used to obtain the gene counts. Each sample was performed in duplicate

first: Efres

last: Belmonte-Reche

first: Marta

last: Martínez-García

last: de Jong

first: Oscar

last: Kuipers

first: Rubén

last: Cebrián


title: Transcriptome analysis of Citrus reticulata ovule early development based on laser capture microdissection

city: Wuhan

first: Liqing

last: Lu

state: Hubei

address: No.1 of Shizishan street, Hongshan District

institute: Huazhong Agricultural University

summary: Ovule developmental arrest is one of the early phenotypes of seed abortion. However, the molecular mechanism underlying ovule developmental arrest of citrus is still unclear. In this study, laser capture microdissection (LCM) was used to accurately divide the ovules of seedless Ponkan ‘Huagan NO.4’ (Citrus reticulata) (MT) and seeded Ponkan ‘Egan NO.1’ (Citrus reticulata) (WT) into nucellus and integument tissues. The captured tissues were used for subsequent RNA-seq. Moreover, single-molecule real-time (SMRT) sequencing was used to generate full-length transcripts of WT, which were used as reference transcripts for RNA-seq. These data can be utilized to analyse the causes of citrus seedlessness formation and the molecular regulatory network in the process of ovule abortion.

overall_design: Based on the LCM strategy, we collected 12 samples from three development stages (18 DAP (day after pollening),28 DAP,32 DAP), and two tissues of citrus ovule for RNA-seq. Three biological replicates were designed for each sample. Citrus leaves and ovaries at different development stages were mixed for SMRT sequencing.

first: Juxun

last: Wu

first: Hualin

last: Yi


title: Multi-omics data analysis for the JGOG3025-TR2 ovarian cancer cohort [OncoScan_CNV]

city: Kyoto

first: Shiro

last: Takamatsu

address: 54 Shogoin Kawahara, Sakyo, Kyoto

department: Gynecology and Obstetrics

institute: Kyoto University Graduate School of Medicine

type:
Genome variation profiling by SNP array
SNP genotyping by SNP array

summary: The JGOG3025 study was conducted by the Japanese Gynecologic Oncology Group (JGOG) on 710 patients with epithelial ovarian cancer (NCT03159572). In the JGOG3025-TR2 study, fresh frozen tumor tissues from 274 and 15 cases diagnosed as stage II or higher high-grade serous carcinoma (HGSC) or high-grade endometrioid carcinoma (HGEC) in the central pathological review were submitted to SNP array, total RNA-sequencing, and DNA methylation array analyses.

overall_design: Genomic DNA from 287 ovarian cancer samples were subjected to Affymetrix (Thermo Fisher Scientific) OncoScan CNV assay

first: Kosuke

last: Yoshihara

first: Tsukasa

last: Baba

first: Muneaki

last: Shimada

first: Hiroshi

last: Yoshida

first: Hiroaki

last: Kajiyama

first: Katsutoshi

last: Oda

first: Masaki

last: Mandai

first: Aikou

last: Okamoto

first: Takayuki

last: Enomoto

first: Noriomi

last: Matsumura


title: Multi-omics data analysis for the JGOG3025-TR2 ovarian cancer cohort [RNA-seq]

overall_design: Total RNA extracted from 291 ovarian cancer samples were processed based on SMART-Seq protocol and sequencied using Illumina NovaSeq 6000 system


title: Cancer-associated DNA Hypermethylation of Polycomb Targets Requires DNMT3A Dual Recognition of histone H2AK119 Ubiquitination and the Nucleosome Acidic Patch [EM-Seq]

city: New York City

first: Kristjan

middle: H.

last: Gretarsson

state: New York

institute: Columbia University

type: Methylation profiling by high throughput sequencing

summary: During tumor development, promoter CpG islands (CGIs) that are normally silenced by Polycomb repressive complexes (PRCs) become DNA hypermethylated. The molecular mechanism by which de novo DNA methyltransferase(s) catalyze CpG methylation at PRC-regulated regions remains unclear. Here we report a cryo-EM structure of DNMT3A long isoform (DNMT3A1) N-terminal region in complex with nucleosome carrying PRC1-mediated histone H2A lysine 119 mono-ubiquitination (H2AK119Ub). We identify regions within the DNMT3A1 N-terminus that bind H2AK119Ub and the nucleosome acidic patch. This bidentate interaction is specifically required for effective DNMT3A1 engagement with H2AK119Ub-modified chromatin in cells. Furthermore, aberrant redistribution of DNMT3A1 to Polycomb target genes inhibits their transcriptional derepression during cell differentiation and recapitulates the cancer-associated DNA hypermethylation signature, an effect rescued by disruption of DNMT3A1-acidic patch interaction. Together, our analyses reveal a binding interface critical for countering promoter CGI DNA hypermethylation, a major molecular hallmark of cancer.

overall_design: DNA methylation analysed in DNMT1/3A/3B/3L (QKO) mESC expressing different DNMT3A1 mutants using  EnzymaticMethyl-seq (EM-seq)

middle: H

first: Chao


title: Effect of hydroxy vs amino complex in zinc uptake, in WT and Zip4-/- mice

city: Nashville

first: James

last: West

state: TN

address: 4200 E 9TH Ave, Box B133

department: Medicine

institute: Vanderbilt University

summary: Amino complexed zinc has superior uptake to hydroxy-complexed zinc, in both WT mice, and particularly in ZIP4 (zinc transporter) knockout mice.

overall_design: Gut mRNA profiles of wild type (WT), ZIP4 +/-, and Zip4-/- mice fed 15 ppm zinc in organic complexes, with the zinc attached at either hydroxy or amino terminus


title: Multi-omics data analysis for the JGOG3025-TR2 ovarian cancer cohort

type: Methylation profiling by genome tiling array

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

relation:
SuperSeries of: GSE263083
SuperSeries of: GSE263434
SuperSeries of: GSE263437

overall_design: Refer to individual Series


title: Cancer-associated DNA Hypermethylation of Polycomb Targets Requires DNMT3A Dual Recognition of histone H2AK119 Ubiquitination and the Nucleosome Acidic Patch [RNA-Seq]

overall_design: To investigate the role of DNMT3A1 induced hypermethylation in differentiation we generated 10T cell lines expressing different DNMT3A1 mutants. Comparative gene expression analysis at different timepoints during adipocyte differentiation for all DNMT3A1 mutants.


title: Cancer-associated DNA Hypermethylation of Polycomb Targets Requires DNMT3A Dual Recognition of histone H2AK119 Ubiquitination and the Nucleosome Acidic Patch [ChIP-seq]

overall_design: Comparative gene expression analysis at different timepoints during adipocyte differentiation for all DNMT3A1 mutants.


title: Lymph node stromal cells support the maturation of pre-DCs into cDCs via colony stimulating factor 1

city: Braunschweig

first: Carolin

last: Wiechers

state: Niedersachsen

address: Inhoffenstraße 7

department: Experimental Immunology

country: Germany

institute: Helmholtz Centre for Infection Research

summary: Conventional dendritic cells (cDCs) arise from committed precursor dendritic cells (pre DCs) in the bone marrow that continuously seed the periphery. Pre-DCs and other upstream progenitors proliferate and mature in response to Fms-related receptor tyrosine kinase 3 ligand (FLT3L), which is considered the most important cytokine for cDC development. However, other cytokines such as stem cell factor (SCF) and colony stimulating factor 1 (CSF1) were also shown to induce pre-DC maturation into DC-like cells. It is not completely understood which cells contribute to cDC development once pre-DCs arrive in peripheral tissues. Here, we analyzed the impact of lymph node (LN) fibroblastic stromal cells (FSCs) on the maturation of pre-DCs into cDCs. We could demonstrate that ex vivo isolated LN FSCs co-cultured with pre-DCs induce precursor maturation into DC-like cells, which were capable of efficiently promoting the proliferation of naïve CD4+ T cells. Interestingly, FSCs isolated from mesenteric lymph nodes (mLNs) or peripheral LNs (pLNs) induced DC-like cells with highly comparable transcriptomes, showing similarity to both ex vivo isolated DCs and macrophages based on characteristic signature genes. Finally, by performing supplementation and receptor blocking studies we could demonstrate that CSF1 is a driving factor for LN FSC-mediated pre-DC maturation into DC-like cells. In summary, we could identify CSF1 as a novel stromal cell-derived factor that supports the maturation of pre-DCs into cDCs within secondary lymphoid organs.

overall_design: RNA-seq with 3 replicates per condition for cultured DC-like cells

first: Joern

last: Pezoldt

first: Michael

last: Beckstette

first: Jochen

last: Huehn


title: Cancer-associated DNA Hypermethylation of Polycomb Targets Requires DNMT3A Dual Recognition of histone H2AK119 Ubiquitination and the Nucleosome Acidic Patch [RRBS]

overall_design: DNA methylation analysis using RRBS of 10T cells, TKO mESC, and Normal and SCC Esophogus Organoids with different DNMT3A1 mutations

last: Lu


title: Long term effects of CCR2+ myeloid cell depletion on islet cell populations identified by scRNA-seq

city: Seattle

first: Sina

last: Gharib

state: WA

address: 850 Republican St.

institute: University of Washington

summary: Pancreatic islets were isolated from 1 month and 6 months old CCR2-DTR+/- and wild type mice, previously treated with diphtheria toxin to transiently deplete CCR2+ myeloid cells during the first 10 days of life.

overall_design: Islet tissue was then processed for scRNA-seq to derive gene expression profiles of islet cells at  two time points.

first: Laura

last: Crisa

first: Vincenzo

last: Cirulli


title: Frizzled5 Maintains Homeostasis of Adult Intestinal Epithelium Through Organization of Chromatin Accessibility

city: Kansas City

first: Shiyuan

middle: (Cynthia)

last: Chen

state: MO

department: Computational Biology

institute: Stowers Institute for Medical Research

summary: Analyze the gene profiles and chromatin accessibility change upon Fzd5 knockout in mouse intestinal epithelium

overall_design: ScRNA-seq of Intestinal epithelial cells, ScRNA-seq of Intestinal Lgr5 positive cells, ScRNA-seq of Ctrl and Fzd5KO Intestinal epithelial cells, and ScATAC-seq of Ctrl and Fzd5KO Intestinal nuclei

first: Lu

last: Deng

first: Linheng

last: Li


title: Epididymal acquired sperm microRNAs modify post-fertilization embryonic gene expression

city: Philadelphia

first: Natalie

middle: Alyce

last: Trigg

state: Pennsylvania

address: 421 Curie Blvd

institute: Children's Hospital of Philadelphia

summary: Sperm small RNAs have emerged as important non-genetic contributors to embryogenesis and offspring health. A subset of sperm small RNAs are thought to be acquired during epididymal transit. However, the transfer of RNAs from the somatic epididymis to the sperm has been questioned, and the identity of the specific small RNAs transferred remains unclear. Here, we employ Cre/Lox genetics to generate germline- and epididymal-specific Dgcr8 conditional knockout mice to investigate the dynamics of sperm microRNAs and their function in the early embryo. Interestingly, sperm from germline specific Dgcr8 knockout males restored the levels of 58 of the 98 (59%) miRNAs that were lost in testicular sperm during epididymal transit. Conversely, sperm from epididymal Dgcr8 knockouts displayed a 5-fold reduction in 25 miRNAs. This substantial loss of epididymal miRNAs in sperm was accompanied by transcriptomic changes in the embryo which was rescued by microinjection of epididymal miRNAs. These findings ultimately demonstrate the acquisition of miRNAs by sperm during epididymal transit and their regulation of post-fertilization embryonic gene expression.

overall_design: To examine the impact of ablation of the miRNA pathway  on male fertility and the regulation of gene expression in the male reproductive tract we sequenced the small RNA fraction of testicular and cauda sperm from 2 Dgcr8 conditional knockout mice and their respective controls and performed RNA-seq on epididymal tissue from these mice. Additionally, in examining the impact of altered sperm miRNA levels on gene expression in the early embryo we sequenced single embryos  (4-cell and morula stage) fertilized by control and mutant male mice.

middle: A

first: Colin

middle: C

last: Conine


title: Genome-wide AR chromatin association in human lung adenocarcinoma cancer cells

city: Worcester

first: Junhui

state: MA

address: 364 Plantation St

institute: University of Massachusetts Medical School

summary: AR is a transcription factor that functions in maintenance and development of prostate and various tissues. By performing AR ChIP-seq analysis, we show that AR binds to the promoter, intron, and enhancer regions of the KRAS and various AR target genes in human lung KRAS mutant cancer cells.

overall_design: Examination of genome-wide mapping of AR binding in human lung KRAS mutant cancer cells

first: Dong-Hwan

last: Kim

middle: R

last: Green


title: The Effect of a Novel Preclinical Agent, SpiD3, on Drug-resistant Chronic Lymphocytic Leukemia

status: Public on Aug 30 2024

city: Omaha

first: Dalia

last: ElGamal

state: Nebraska

department: Eppley Institute for Research in Cancer and Allied Diseases

institute: University of Nebraska Medical Center

summary: B-cell receptor (BCR) signaling is a central driver in chronic lymphocytic leukemia (CLL), along with activation of pro-survival pathways (e.g., NF- κB) and aberrant anti-apoptotic (e.g., BCL2), culminating to CLL cell survival and drug-resistance. Front-line targeted therapies such as ibrutinib (IBR) and venetoclax (VEN) have radically improved CLL management. Yet, persisting CLL cells lead to relapse in ~20% of patients, signifying the need for alternative therapeutics with novel approaches to CLL cell elimination and overcoming resistance mechanisms. SpiD3 is a novel spirocyclic dimer of analog 19 displaying NF-κB inhibitory activity. Recently, we have shown that SpiD3 inhibits CLL proliferation and induces cytotoxicity, by promoting futile activation of the unfolded response pathway (UPR) and generation of reactive oxygen species (ROS), resulting in insurmountable endoplasmic reticulum stress. RNA-sequencing analysis of IBR- and VEN-resistant CLL cell lines revealed ferroptosis, UPR signaling, and oxidative stress among the top pathways modulated by SpiD3 treatment. By examining SpiD3 induced protein aggregation, ROS production, and ferroptosis in preclinical models of CLL, our data demonstrates marked SpiD3-induced anti-leukemic properties and CLL cell cytotoxicity, including in cell lines resistant to current front-line therapeutics, substantiating the development of SpiD3 as a novel therapeutic approach to management of relapse/refractory CLL disease.

overall_design:
To investigate the gene changes in ibrutinib-resistant HG-3 CLL cell line compared to their wild-type counterpart. Additionally, assess how SpiD3 modulated those genes in both the wild-type and resistant cells.
We then performed gene expression analysis on wild-type HG-3 CLL cells and ibrutinib-resistant HG-3 CLL cells treated in triplicate with either vehicle, SpiD3, or ibrutinib.

first: Alexandria

middle: P

last: Eiken


title: Stably incorporated ribonucleotides in murine tissues: quantitation, base identity and distribution in nuclear and mitochondrial DNA

city: Göteborg

first: Anders R.

last: Clausen

address: Box 440

institute: University of Gothenburg

summary: Ribonucleotides are estimated to be the most common non-canonical nucleotides transiently incorporated in DNA. Their presence or failure of their removal can affect genome stability and mutations in factors involved in dNTP pool maintenance or ribonucleotide removal can cause Aicardi-Goutières syndrome or promote certain human cancers. Here, we have mapped and quantitated ribonucleotides genome-wide, in nine tissues of wild-type mice. We observed tissue-specific variation in number and base identity of incorporated ribonucleotides and present evidence that a number of genomic features, such as tRNA genes, transcription start sites and G-quadruplexes, can increase the frequency of stably incorporated ribonucleotides in their proximity. Moreover, we present the non-random distribution of incorporated ribonucleotides in mtDNA and identified ribonucleotide hotpots. The study presents a framework to understand the physiological role of ribonucleotides in mammalian DNA.

overall_design: We used HydEn-seq to investigate the genome-wide distribution of ribonucleotides in organs isolated from mice.

first: Katrin

last: Kreisel

first: Josephine

last: Kalm

first: Sashidhar

last: Bandaru

first: Chandu

last: Ala

first: Levent

last: Akyürek

first: Anders


title: Single-Cell RNA Sequencing Analysis of the Early Postnatal Mouse Lens Epithelium

status: Public on Aug 29 2024

city: Stony Brook

first: David

last: McKinnon

address: Nichols Rd

institute: Stony Brook University

summary: Single-cell RNA sequencing (scRNA-seq) was used to assess transcriptional heterogeneity between cells in the postnatal day 2 lens epithelium and identify distinct epithelial cell subtypes.

overall_design: scRNA-seq on P2 mouse lenses was performed using the 10x Genomics Chromium Single Cell 3' Kit (v3.1) and short-read Illumina sequencing.

first: Adrienne

last: Giannone

first: Caterina

last: Sellitto

first: Barbara

last: Rosati

first: Thomas

last: White


title: Transcriptome profiling and Co-expression networks of longissimus dorsi muscle in Gayal（Bos frontalis）and Banna cattle（Bos taurus） with different beef qualities

city: Yangling

first: Zehui

last: Wei

address: No.3 Taicheng Road

institute: Northwest A&F University

summary: The Gayal (Bos frontalis) is a rare semi-domesticated cattle in China. Gayal has typical beef body shape and good meat production performance. Compared with other cattle species, it has the characteristics of tender meat and extremely low fat content. To explore the underlying mechanism responsible for the differences of meat quality between different breeds, the longissimus dorsi muscle (LM) from Gayal and Banna cattle (Bos taurus)  were investigated using transcriptome analysis. The gene expression profiling identified 638 differentially expressed genes (DEGs) between LM muscles from Gayal and Banna cattle. Gene Ontology (GO) enrichment of biological functions and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that the gene products were mainly involved in the PPAR signaling pathway, lipid metabolism and amino acid metabolism pathway. Protein-protein interaction（PPI） network analysis showed APOB, CYP7A1, THBS2, ITGAV, IGFBP1 and IGF2R may have great impact on meat quality characteristics of Gayal. Moreover, three transcription factors, FOXA2, NEUROG2, and RUNX1, which may affect meat quality by regulating the expression of genes related to muscle growth and development have also been found. In summary, our research reveals the molecular mechanisms that cause Gayal meat quality characteristics. It will contribute to improving meat quality of cattle through molecular breeding.

sample_organism:
Bos taurus
Bos frontalis

platform_organism:
Bos taurus
Bos frontalis

overall_design: The gene expression profiling of the longissimus dorsi muscle (LM) from Gayal and Banna cattle

first: Fang

last: Wang

first: Xiaoyan

last: Kong

first: Jiannan

last: Xue

first: Xiaolin

last: Dong

first: Li

last: Zhu

last: Zhang

first: Huan

last: Teng

first: Cunling

last: Jia

first: Xiao

last: Gou


title: Gene expression profiling of human livers during normothermic machine perfusion

city: Innsbruck

first: Theresa

last: Hautz

address: Anichstr. 45

department: Department of Visceral, Transplant and Thoracic Surgery

country: Austria

institute: Medical University of Innsbruck

summary: Normothermic machine perfusion (NMP) has been successfully implemented in clinical routine of liver transplantation over the past years. However, little is known about the mechanisms how NMP impacts on the transcriptome of a human donor liver. We herein examined gene expression profiles in transplanted and non-transplanted livers over NMP time. 50 livers subjected to NMP were included in this study. 30 were transplanted after a maximum of 20 hours (h) perfusion, while 15 were discarded due to poor performance. Biopsies were collected befor eNP (PRE), 1h, 6h, 12h, 20h of NMP and after reperfusion. Next-generation sequencing was applied in liver biopsies to assess differential gene expression over perfusion time. Perfusate samples were collected regularly to monitor liver function. Comparison in differential gene expression between PRE and 20h NMP showed 415 upregulated and 727 downregulated genes. Most significantly upregulated genes were associated with extra cellular matrix organization, cell growth/differentiation processes and cytokine signaling. A set of genes were identified which were significantly differentially expressed and important for classification of  non-transplanted vs transplanted biopsies, especially at 12 and 20h of NMP. A 7-gene-signature showed good separation already at 6H NMP, thereby CD274 (PD-L1) expression was  ponted out as most important.

overall_design: Gene expression profiling of human livers were performed at several timepoints during normothermic machine perfusion (NMP) (PRE (baseline before NMP), 1H, 6H, 12H,20H, POST (post transplant)) using RNA sequencing analyses. Differentially expressed genes were identified at each timepoint compared to baseline (PRE) in paired analyses and at each timepoint between nontransplanetd livers (NTP) and transplanted livers (TP).

first: Hubert

last: Hackl

first: Raphael

last: Gronauer

first: Hendrik

last: Gottschling

first: Stefan

last: Schneeberger


title: Single-cell transcriptomic analysis of retinal immune regulation and blood-retinal barrier function during experimental autoimmune uveitis

city: Oxford

first: Kanmin

address: Nuffield Department of Clinical Neurosciences, Level 6, West Wing, John Radcliffe Hospital

institute: University of Oxford

summary: Uveitis is characterised by breakdown of the blood-retinal barrier (BRB), allowing infiltration of immune cells that mediate intraocular inflammation, which can lead to irreversible damage of the neuroretina and the loss of sight. Treatment of uveitis relies heavily on corticosteroids and systemic immunosuppression due to limited understanding of the molecular immune interactions that underpin ocular immune homeostasis. By performing single-cell transcriptomic analysis of whole dissociated mouse retinas with experimental autoimmune uveitis (EAU) versus healthy control, we gained an unbiased appreciation of the immune interactions that drive retinal inflammation in a model of posterior uveitis.

overall_design: 1 healthy C57BL/6J mouse retina and 2 C57BL/6J retinas from mice with experimental autoimmune uveitis were dissociated and analysed by single cell RNA-seq.

first: Joel

last: Quinn

first: Ahmed

last: Salman

first: Christopher

last: Paluch

first: Matthew

last: Jackson-Wood

first: Michelle

last: McClements

first: Jian

last: Luo

first: Simon

middle: J

last: Davis

first: Richard

last: Cornall

first: Robert

last: MacLaren

first: Calliope

last: Dendrou


title: Multi-omics data analysis for the JGOG3025-TR2 ovarian cancer cohort [Infinium MethylationEPIC]

first: Shiro

last: Takamatsu

overall_design: Bisulfite converted DNA from 285 ovarian cancer samples were subjected to the Infinium MethylationEPIC BeadChip assay

first: Kosuke

last: Yoshihara

first: Tsukasa

last: Baba

first: Muneaki

last: Shimada

first: Hiroshi

last: Yoshida

first: Hiroaki

last: Kajiyama

first: Katsutoshi

last: Oda

first: Masaki

last: Mandai

first: Aikou

last: Okamoto

first: Takayuki

last: Enomoto

first: Noriomi

last: Matsumura


title: Transcriptomic changes in bronchoalovelar derived macrophages after expsoure to whole body cigarette smoke exposure (8 weeks)

status: Public on Aug 28 2024

city: Santa Cruz

first: Susan

last: Carpenter

address: 1156 High St

department: MCD Biology

institute: University of California Santa Crtuzz

summary: Chronic obstructive pulmonary disease (COPD) is an inflammatory airway disease characterized by emphysema and chronic bronchitis and a leading cause of mortality worldwide. COPD is commonly associated with several comorbid diseases which contribute to worse patient outcomes. Cigarette smoke (CS) is the most prominent risk factor for COPD development and progression and is known to be detrimental to numerous effector functions of lung resident immune cells, including phagocytosis and cytokine production.  Methods: C57BL/6 mice were exposed to 8 weeks of CS as an experimental model of COPD.  Airspace macrophages (AMs) were isolated from  CS-exposed and RA mice and bulk RNA-Seq performed. The functional role of differentially expressed genes was assessed through gene ontology analyses. Ingenuity Pathway Analysis was used to determine the activation states of canonical pathways and upstream regulators enriched in differentially expressed genes in AMs. Results:  CS induced decreased expression of genes involved in pathogen response, phagosome formation, and immune cell trafficking in AMs.  Conclusions: CS exposure can induce transcriptomic remodelling in  AMs. Our study highlights the ability of CS exposure to affect immune cell populations distal to the lung and warrants further investigation into the functional effects of these changes and the ensuing role in driving multimorbid disease.

overall_design: C57BL/6J wild type mice (Stock No. 000664) were purchased from The Jackson Laboratory and were maintained under specific pathogen-free conditions at Weill Cornell Medicine. Sex and age-matched mice aged between 6-12 weeks of age were exposed to whole-body CS using the Teague Enterprises TE-10 inhalation exposure apparatus and 3R4F cigarettes acquired from the University of Kentucky Centre for Reference Products. Mice were exposed to CS (average total particulate matter (TPM) of 150 mg/m3) for a minimum of 2 hours per day for 5 days a week, for an 8-week period.

first: Suzanne

last: Cloonan


title: 5-formylcytosine is an activating epigenetic mark for RNA Pol III during zygotic reprogramming

city: Mainz

first: Emil

last: Karaulanov

address: Ackermannweg 4

institute: Institute of Molecular Biology

summary: 5-methylcytosine (5mC) is an established epigenetic mark in vertebrate genomic DNA, but whether its oxidation intermediates formed during TET-mediated DNA demethylation possess an instructive role of their own that is also physiologically relevant remains unresolved. Here, we reveal a 5-formylcytosine (5fC) nuclear chromocenter, which transiently forms during zygotic genome activation (ZGA) in Xenopus and mouse embryos. We identify this chromocenter as the perinucleolar compartment, a structure associated with RNA Pol III transcription. In Xenopus embryos, 5fC is highly enriched on Pol III target genes activated at ZGA, notably at oocyte-type tandem arrayed tRNA genes. By manipulating Tet and Tdg enzymes, we show that 5fC is required as a regulatory mark to promote Pol III recruitment as well as tRNA expression. Concordantly, 5fC modification of a tRNA transgene enhances its expression in vivo. The results establish 5fC as an activating epigenetic mark during zygotic reprogramming of Pol III gene expression.

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


title: IL-9 secreted by leukemia stem cells induces Th1-skewed CD4+ T cells, which promote their expansion

city: Bern

first: Ramin

last: Radpour

address: Murtenstrasse 35

department: Department for BioMedical Research

country: Switzerland

institute: University of Bern

summary: We performed a comprehensive transcriptomic profiling of BM-infiltrating CD4+ T cells of AML patients from different AML patients and controls. This analysis revealed that BM-infiltrating CD4+ T cells are activated and skewed towards Th1 polarization.

overall_design: We characterized the molecular signature of BM-infiltrating CD4+ T cells in patients with acute myeloid leukemia (AML) compared to control subjects.

first: Adrian

middle: F

last: Ochsenbein


title: Cancer-associated DNA Hypermethylation of Polycomb Targets Requires DNMT3A Dual Recognition of histone H2AK119 Ubiquitination and the Nucleosome Acidic Patch [Cut&Tag]

first: Kristjan

last: Gretarsson

summary: During tumor development, promoter CpG islands (CGIs) that are normally silenced by Polycomb repressive complexes (PRCs) become DNA hypermethylated. The molecular mechanism by which de novo DNA methyltransferase(s) catalyze CpG methylation at PRC-regulated regions remains unclear. Here we report a cryo-EM structure of DNMT3A long isoform (DNMT3A1) N-terminal region in complex with nucleosome carrying PRC1-mediated histone H2A lysine 119 mono-ubiquitination (H2AK119Ub). We identify regions within the DNMT3A1 N-terminus that bind H2AK119Ub and the nucleosome acidic patch. This bidentate interaction is specifically required for effective DNMT3A1 engagement with H2AK119Ub-modified chromatin in cells. Furthermore, aberrant redistribution of DNMT3A1 to Polycomb target genes inhibits their transcriptional derepression during cell differentiation and recapitulates the cancer-associated DNA hypermethylation signature, an effect rescued by disruption of DNMT3A1-acidic patch interaction. Together, our analyses reveal a binding interface critical for countering promoter CGI DNA hypermethylation, a major molecular hallmark of cancer.

overall_design: Cut&Tag of H3K27me3, H2AK119Ub and H3K4me3 in Normal and SCC Esophogus Organoids

first: Chao

last: Lu


title: Cancer-associated DNA Hypermethylation of Polycomb Targets Requires DNMT3A Dual Recognition of histone H2AK119 Ubiquitination and the Nucleosome Acidic Patch [CUT7Run]

overall_design: Cut&Run of IgG, H3K36me2, H3K27me3, H2AK119Ub and H3K4me3 in 10T cells and QKO mESC

first: Danielle

last: Maryanski

first: Jamie

last: McCuiston

first: Michael-Christopher

last: Keogh


title: Chromatin assessibility detection in the absence of Fzd5 gene in intestinal epithelium [Cut & Tag]

first: Shiyuan

last: Chen

summary: Using CUT&TAG to assess Fzd5 knockdown effect on epithelial chromatin assessiblity change, using anitbodies targeting PoII2, H3K4trime3, and Beta-catenin.

overall_design: Two groups: Ctrl and Fzd5KO. Replicates for each antibody of each group.

first: Lu

last: Deng

first: Linheng

last: Li


title: Elevated GRHL2 imparts plasticity in estrogen receptor positive breast cancer cells [RNA-seq]

status: Public on Aug 25 2024

city: Madison

first: Elaine

last: Alarid

state: WI

address: 111 Highland Avenue

institute: University of Wisconsin Madison

summary: Estrogen receptor (ER) positive breast cancer is characterized by a late recurrence following initial treatment. The epithelial cell fate transcription factor Grainyhead-like protein 2 (GRHL2) is amplified in ER positive breast cancers and is indicative of poorer prognosis as compared to ER negative breast cancer. To understand how GRHL2 contributes to progression, GRHL2 was overexpressed in ER positive cells. To examine gene expression changes from elevated GRHL2 levels, RNA-sequencing was performed to better comprehend how high GRHL2 may change its transcriptional activity.

overall_design: To investigate the long-term effects of elevated GRHL2, a tetracycline-inducible cell line capable of expressing GRHL2-GFP upon exposure to doxycycline hyclate (Dox) was treated with 1 μg/mL for 72 hours, with media changes every 24 hours. A Biosciences FACSAria™Cell Sorter was used to sort Dox treated cells for GFP expression. Control cells without Dox treatment remain unsorted. All samples included were analyzed with 5 biological replicates. RNA sequencing was performed by AZENTA Life Sciences Next Generation Sequencing. Gene expression profiling analyses were conducted using RNA-seq data.

first: Christy

last: Zheng

first: Kaelyn

middle: O

last: Allen

first: Phillipos

last: Tsourkas

first: Sean

last: McIlwain

first: Jessica

middle: M

last: Vera

middle: T


title: Elevated GRHL2 imparts plasticity in estrogen receptor positive breast cancer cells [ChIP-Seq]

summary: Estrogen receptor (ER) positive breast cancer is characterized by a late recurrence following initial treatment. The epithelial cell fate transcription factor Grainyhead-like protein 2 (GRHL2) is amplified in ER positive breast cancers and is indicative of poorer prognosis as compared to ER negative breast cancer. To understand how GRHL2 contributes to progression, GRHL2 was overexpressed in ER positive cells. To determine how GRHL2 overexpression affects GRHL2 binding to DNA, ChIP sequencing was conducted to evaluate binding intensity and location.

overall_design: To investigate the long-term effects of elevated GRHL2, a tetracycline-inducible cell line capable of expressing GRHL2-GFP upon exposure to doxycycline hyclate (Dox) was treated with 1 μg/mL for 24, 48, or 72 hours, with media changes every 24 hours. Cells were fixed, sonicated, and immunoprecipitated with an anti-GRHL2 antibody prior to library preparation. All samples included were analyzed with 3 biological replicates. ChIP sequencing was performed by AZENTA Life Sciences Next Generation Sequencing. Differential gene expression and motif analyses were conducted using ChIP-seq data.


title: Frizzled5

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

overall_design: Refer to individual Series


title: Effect of male sex-category on gene expression in the m. longissimus dorsi (LD) and m. semispinalis capitis (SSC)

status: Public on Aug 23 2024

city: Ljubljana

first: Klavdija

last: Poklukar Žnidaršič

state: Ljubljana

address: Hacquetova ulica 17

department: Animal Science department

country: Slovenia

institute: Agricultural Institute of Slovenia

summary: RNA- sequencing was performed to compare the effect of male sex category, i.e. entire males (EM), surgical castrates (SC), and immunocastrates (IC) on differential gene expression in LD and SSC muscles. Extracted RNA from 6 randomly selected animals of each sex category and muscle were pooled together and used for library preparation and sequencing. A total of 71 and 36 differentially expressed genes (DEGs) were detected in LD and SSC, respectively (|log2(fold change) >1| and -log10(q-value) <0.005). In LD, 36 DEGs were detected between EM and IC. 29 DEGs were detected between EM and SC and only 6 DEGs were detected when comparing IC and SC. In SSC, the number of DEGs was lower compared to LD. Only 8 DEGs were detected when either EM and IC or EM and SC were compared. The number of DEGs between IC and SC was higher for SCC than for LD (20 vs. 6). In LD, downregulated genes predominated in EM compared to either IC or SC and were mainly associated with skeletal muscle tissue development, skeletal cell differentiation, and negative regulation of biological/cellular processes. When comparing IC and SC, predominantly upregulated genes were observed, and the enriched GO terms were related to various biological processes, including regulation of fibrinolysis, apoptosis, energy homeostasis, fatty acid oxidation, and behaviour. In SSC, significantly enriched GO terms were found only for predominantly upregulated genes in IC compared to SC and were related to the regulation of energy homeostasis and fatty acid oxidation, response to hormones/stimuli, and regulation of cellular ketone metabolic process.

overall_design: Pigs originating from one slaughter batch (12 entire males (EM), 12 immunocastrated (IC) and 12 surgically castrated (SC) pigs) of the commercial Landrace x Pietrain crosses were used. Surgically castrated pigs were castrated within the first week of life, while immunocastrated pigs were vaccinated at the age of 12 and 21 weeks with a vaccine against GnRH (Improvac® vaccine, Zoetis). At the age of 26 weeks, animals were slaughtered and at the end of the slaughterline (45 min post mortem), approx. 1 cm3 muscle samples were taken from the central part of LD at the level of the last rib and from the SSC i.e., from the central part of its m. biventer cervicis, at the level of the 4th cervical vertebra.  Muscles were sampled at the right side of the carcass, snap-frozen in liquid nitrogen and stored at –80°C until subsequent analysis

first: Milka

last: Vrecl

first: Gregor

last: Fazarinc

last: Poklukar


title: HDAC6 Inhibition Disrupts HDAC6-P300 Interaction Reshaping the Cancer Chromatin Landscape (ChIP-Seq)

status: Public on Aug 19 2024

city: Rome

first: daniele

last: santoni

address: via dei taurini 19

country: Italy

institute: IASI - CNR

summary: Histone deacetylases (HDACs) are crucial regulators of gene expression, DNA synthesis, and cellular processes, making them essential targets in cancer research. HDAC6, specifically, influences protein stability and chromatin dynamics. Despite HDAC6's potential therapeutic value, its exact role in gene regulation and chromatin remodeling needs further clarification. This study examines how HDAC6 inactivation influences lysine acetyltransferase P300 stabilization and subsequent effects on chromatin structure and function in cancer cells. We employed the HDAC6 inhibitor ITF3756, siRNA, or CRISPR/Cas9 gene editing to inactivate HDAC6 in different epigenomic backgrounds. Constantly, this inactivation led to significant changes in chromatin accessibility, particularly increased acetylation of histone H3 lysines 9, 14, and 27 (ATAC-seq and H3K27Ac ChIP-seq analysis). Transcriptomics, proteomics, and gene ontology analysis revealed gene changes in cell proliferation, adhesion, migration, and apoptosis. Significantly, HDAC6 inactivation altered P300 ubiquitination, stabilizing P300 and leading to downregulating genes critical for cancer cell survival. Our study highlights the substantial impact of HDAC6 inactivation on the chromatin landscape of cancer cells and suggests a role for P300 in contributing to the anticancer effects. The stabilization of P300 with HDAC6 inhibition proposes a potential shift in therapeutic focus from HDAC6 itself to its interaction with P300. This finding opens new avenues for developing targeted cancer therapies, improving our understanding of epigenetic mechanisms in cancer cells.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for H3K27ac in B16F10 cells WT vs KO_HDAC6.

first: Michela

last: Gottardi Zamperla

first: Barbara

last: Illi

first: Veronica

last: Barbi

first: Chiara

last: Cencioni

first: Daniele

last: Santoni

first: Stella

last: Gagliardi

first: Maria

last: Garofalo

first: Gabriele

last: Zingale

first: Irene

last: Pandino

first: Diego

last: Sbardella

first: Lina

last: Cipolla

first: Simone

last: Sabbioneda

first: Antonella

last: Farsetti

last: Ripamonti

first: Gianluca

last: Fossati

first: Christian

last: Steinkühler

first: Carlo

last: Gaetano

first: Sandra

last: Atlante


title: Simulated Microgravity Impairs Human NK Cell Cytotoxic Activity Against Space Radiation-Relevant Leukemic Cells

status: Public on Aug 22 2024

city: Winston-Salem

first: Kimberly

middle: D

last: Reeves

state: North Carolina

address: Medical Center Blvd

institute: Wake Forest School of Medicine

summary: Natural killer (NK) cells are important effectors of the innate immune system. Unlike T cells, NK cells do not require antigen-priming, making them an important first-line of defense against malignant cells. Because of the potential for increased cancer risk as a result of astronaut exposure to space radiation, we performed studies to determine whether conditions of microgravity present during spaceflight affects the body’s natural defenses against leukemogenesis. Human NK cells were cultured for 48 hours under normal gravity and simulated microgravity (smG), and cytotoxicity against K-562 (CML) and MOLT-4 (T-ALL) cell lines was measured using standard methodology or under continuous conditions of smG. Even this brief exposure to smG markedly reduced NK cytotoxicity against both leukemic cells using standard assay procedures, and these deleterious effects were even more pronounced in continuous smG. RNA-seq performed on NK cells from two healthy donors provided insight into the mechanism(s) by which smG reduced cytotoxicity. Given our prior report that human HSC exposed to simulated space radiation gave rise to T-ALL in vivo, the reduced cytotoxicity against MOLT-4 is striking and raises the possibility thatmG may add to astronaut risk of leukemogenesis during prolonged missions beyond LEO.

overall_design: Gene expression profiling analysis of RNA-Seq data for NK cells isolated from two healthy donors. The cells were exposed to normal gravity or smG to determine gene expression alterations, providing insight into the mechanisms by which smG reduces cytotoxicity.

first: Bradford

last: Kuhlman

first: Jonathan

last: Diaz

first: Trang

last: Simon

first: Stephen

last: Walker

first: Anthony

last: Atala

first: Graca

last: Almeida-Porada

first: Christopher

last: Porada


title: Molecular Signatures of CB-6644 inhibition of the RUVBL1/2 complex in Multiple Myeloma [RNA-seq]

city: Morgantown

first: Gangqing

last: Hu

state: West Virginia

address: 64 Medical Center Drive

department: MicroBiology, Immunology, and Cell Biology

institute: West Virginia University

summary: Multiple Myeloma is the second most hematological cancer. RUVBL1 and RUVBL2 forms a subcomplex of many chromatin remodeling complexes implicated in cancer progress. As an inhibitor specific to the RUVBL1/2 complex, CB-6644 exhibits remarkable anti-tumor activity in xenograft models of Burkitt’s lymphoma and multiple myeloma (MM). In this work, we defined transcriptional signatures corresponding to CB-6644 treatment in MM cells and determined underlying epigenetic changes in terms of chromatin accessibility.CB-6644 upregulated biological processes related to interferon response and downregulated those linked to cell proliferation in MM cells. Transcriptional regulator inference identified ATF4/CEBP and E2Fs as regulators for downregulated genes and MED1 and MYC as regulators for upregulated genes. CB-6644-induced changes in chromatin accessibility occurred mostly in non-promoter regions. Footprinting analysis identified transcription factors implied in modulating chromatin accessibility in response to CB-6644 treatment, including ATF4/CEBP and IRF4. Lastly, integrative analysis of transcription responses to various chemical compounds of the molecular signature genes from public gene expression data identified CB-5083, a p97 inhibitor, as a synergistic candidate with CB66-44 in MM cells, but experimental validation refuted this hypothesis.

overall_design: To characterized the transcriptome (gene expression) signatures of CB-6644 treatment in MM cells. We determined transcriptional pathways affected by CB-6644 through RNA-Seq data analysis in two MM cell linesm MM.1S and RPMI 8226, treated with 120nm and 40 nm CB-6644, respectively, in 72 hours and compared to DMSO-treated control cells.

first: Weijun

last: Yi

first: Sebastian

last: Dziadowicz

first: Rachel

last: Mangano

first: Lei

last: Wang

first: Joseph

last: McBee

first: Steven

last: Frisch

first: Lori

last: Hazlehurst

first: Donald

last: Adjeroh


title: Helminth protein enhances wound healing by inhibiting fibrosis and promoting tissue regeneration

city: Newark

first: Alexander

last: Lemenze

state: New Jersey

address: 185 South Orange Ave

institute: Rutgers

summary: Skin wound healing due to full thickness wounds typically results in fibrosis and scarring, where parenchyma tissue is replaced with connective tissue. A major advance in wound healing research would be to instead promote tissue regeneration.  Helminth parasites express excretory/secretory (ES) molecules, which can modulate mammalian host responses.  One recently discovered ES protein, TGF-β mimic (TGM), binds the TGF- receptor, though likely has other activities. Here we demonstrate that topical administration of TGM under a Tegaderm bandage enhanced wound healing and tissue regeneration in an in vivo wound biopsy model. Increased restoration of normal tissue structure in the wound beds of TGM-treated mice was observed during mid- to late-stage wound healing. Both accelerated re-epithelialization and hair follicle regeneration were observed.  Further analysis showed differential expansion of myeloid populations at different wound healing stages, suggesting recruitment and reprogramming of specific macrophage subsets. This study indicates a role for TGM as a potential therapeutic option for enhanced wound healing.

overall_design: Immune cells were obtained as CD45+ cells from a full thickness skin biopsy.  Each sample of one treatment contained a unique Hashtag and were pooled before analyzed using scRNAseq

first: Katherine

last: Lothstein

first: William

last: Gause


title: Development and IND-enabling studies of a novel Cas9 genome-edited autologous CD34+ cell therapy to induce fetal hemoglobin for sickle cell disease

status: Public on Aug 21 2024

city: Memphis

first: Shengdar

last: Tsai

address: 262 Danny Thomas Pl

department: Department of Hematology

institute: St Jude Children's Research Hospital

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct