title: Next Generation Sequencing Facilitates Quantitative Analysis of transcriptomes in CTR-KD ARP-1 cells and LILRB1-KD ARP-1 cells sorted from the bone marrow of NSG mice transplanted with these cells

city: houston

first: Miao

last: Xian

state: TX

address: 6560 Fannin St.

institute: houston methodist hospital

summary: To determine what signalling pathways are affected by LILRB1 in MM cells, ARP-1 MM cell lines were transfected with lentivirus to knockdown LILRB1, injected to nsg mice, sorted from the bone marrow of NSG mice and sent for RNA-seq. Total RNAs of 2 x 10^6 CTR-KD ARP-1 cells or LILRB1-KD ARP-1 cells were extracted by RNeasy Mini Kit (Qiagen). 5-10 µg RNA samples were sent to Cancer Genomics Center at The University of Texas  (Houston, TX) for RNA-seq followed by data analysis.  We use the RNA-seq data to determine differential expression of genes in CTR-KD ARP-1 cells and LILRB1-KD ARP-1 cells.

overall_design: Examination of gene-profiling data in CTR-KD ARP-1 cells and LILRB1-KD ARP-1 cells.

first: Qiang

last: Wang


title: Chromatin interaction of Cebpa during adipocyte differentiation (4C-Seq)

status: Public on Mar 07 2024

city: Chengdu

first: Xiaokai

last: Li

state: Sichuan

address: Huiming road #211

country: China

institute: Sichuan Agricultural University

summary:
Cebpa is a critical transcription factor gene for adipocyte differentiation and adipose tissue development. However, mechanisms controlling Cebpa expression during adipogenic differentiation remain largely unknown. Here, we generated the high-resolution chromatin interaction maps of Cebpa in 3T3-L1 preadipocytes (3T3-L1) and 3T3-L1 adipocytes (3T3-L1-AD) using circularized chromosome conformation capture coupled with next-generation sequencing (4C-seq), and characterized differences in their chromatin interactomes and chromatin status of the interaction sites during adipogenic differentiation.
We performed a 4C-seq experiment on inguinal white adipose tissue (iWAT) to evaluate whether chromatin interaction between Cebpa-L1-AD-En2 and Cebpa promoters in 3T3-L1 adipocytes also exists in mouse adipose tissue.

overall_design: We performed gene expression profiling analysis using data obtained from 4C-seq of 3T3-L1 preadipocytes (3T3-L1) and 3T3-L1 adipocytes (3T3-L1-AD) cells on days 7 of differentiation

first: Sha

last: Zeng

first: Yu

last: Zhang


title: CAPN3 depletion causes continuously activated innate immune response in zebrafish

city: Charlottesville

first: Delai

last: Huang

state: VA

address: University of Virginia

country: USA

institute: UVA

type: Expression profiling by high throughput sequencing

summary: Capn3 is responsible for human disease LGMD2B, but the mechanism is largely unknown. We generated two capn3b-/- mutant zebrafish alleles and found that p53 is highly enriched in the hepatocyte nucleoli of capn3b knock-out fish. Although homozygous capn3b knock-out mutants are viable and fertile, they display shorter length and lateral curvature phenotype in adulthood, which is similar to the limb-girdle muscular dystrophy type 2A (LGMD2A) patients caused by capn3 mutation. Using RNA-seq analysis of adult liver, we identified differentially expressed genes in capn3b-/- mutants. Genes involved in innate immune response pathways were highly enriched in the mutants' livers. This study presents the connection between capn3 deficiency and immune defects and provides new insights into LGMD2B therapy.

overall_design: Identification of differentially expressed genes between capn3b-/- mutant and wild type zebrafish livers.

first: Yayue

last: Chen

first: Jinrong

last: Peng


title: Induction of Immortal-like CAR-T Cells by Defined Factors (scRNA_seq)

city: Beijing

first: Gang

last: Jin

address: Zhongguancun North street

department: Institute for Immunology

institute: Tsinghua University

summary: In order to investigate the population heterogeneity of CAR19TIF, we determined to profile the single cell RNA transcriptional status of CAR19TIF cells derived from spleens of recipient mice at 2-month post cell transfer. Furthermore, we determined to examine potential subsets among the CAR19TIF cells and critical gene expression levels.

overall_design: Thy1.1+ CAR19TIF cells derived from spleen of one recipient mouse were isolated and purified on 2-month post cell transfer. After sample preparation, scRNA seq was performed.

first: Lixia

first: Min


title: Induction of Immortal-like CAR-T Cells by Defined Factors (bulk RNA-seq)

summary: In order to investigate the underlying mechanism, we determined to profile the transcriptional status of CAR19TIF cells and sgZcsh12a CAR T cells derived from spleens of recipient mice at Day-10 post cell transfer and CAR19TIF cells and endogenous CD8 T cells derived from spleens of recipient mice at 3-month post cell transfer.

overall_design: Thy1.1+ CAR19TIF and sgZc3h12a CAR19T cells derived from recipient mice were isolated and purified on Day-10 post cell transfer. And Thy1.1+ CAR19TIF and endogenous CD8 T cells derived from recipient mice were processed by same procedure on 3-month post cell transfer.


title: Identifying functional enhancers regulating Cebpa expression and adipocyte differentiation (mRNA-Seq)

summary: To explore the effect of enhancer repression on adipocyte differentiation in a transcriptome-wide manner, we infected cells  with 1 mL lentiviruses medium containing dCas9-KRAB-En2-sgRNAs (Experimental group) or dCas9-KRAB (Control group) at the multiplicity of infection (MOI) of 100 for 12 h. We performed transcriptional profiling by RNA sequencing (RNA-seq) for dCas9-KRAB-En2 and dCas9-KRAB cells at day 7 of differentiation.

overall_design: Gene expression profiling analysis of mRNA-seq data for  dCas9-KRAB cells and dCas9-KRAB-En2 cells on days 7 of differentiation.


title: Single cell RNA sequencing of human pluripotent stem cells directed toward the amnioblast lineage.

city: Cambridge

first: Irina

last: Mohorianu

address: Puddicombe Way

department: Wellcome-MRC Cambridge Stem Cell Institute

country: United Kingdom

institute: University of Cambridge

summary: A newly developed condition to induce human amniotic and surface ectoderm lineages from pluripotent stem cells was analysed at the single cell resolution over 24-hour time points up to three days in aim to understand the molecular mechanisms regulating these lineage commitment.

overall_design: Human induced pluripotent stem cells were sparsely seeded and cultured in the ABCP condition to generate a heterogenous population of ectodermal progenitors, and were collected on day 0, 1, 2 and 3 to depict the fate transitions toward amnioblast-like cells.

first: Shota

last: Nakanoh

first: Ilias

last: Moutsopoulos

first: Ludovic

last: Vallier


title: Next Generation Sequencing Facilitates Quantitative Analysis of Ocular Adnexal Lymphoma and inflammation Transcriptomes

city: Shanghai

first: Jiahao

last: Shi

state: Shanghai

address: No. 12, Lane 833, Zhizaoju Road, Huangpu District,

department: Department of Ophthalmology

institute: Shanghai 9th Peoples Hospital Affiliated to Shanghai Jiaotong University School of Medicine

summary: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to describe NGS-derived  transcriptome profiling (RNA-seq)  of ocular adnexal lymphomas (OALs). Gene expression profiling of RNA was performed on OAL and inflammation samples to identify  pathway alterations and expression changes affected by clinical traits

overall_design: OAL mRNA profiles of  20 samples, idiopathic orbital inflammation mRNA profiles of 4 samples, and reactive lymphoid hyperplaisa mRNA profiles of 6 samples from patients were generated by deep sequencing using Illumina Novaseq 6000 according to the manufacturer's direction. RNA was extracted from cryopreserved lymphoma tumor specimens. The sequence reads that passed quality filters were analyzed at the transcript isoform level.

last: Zhou

first: Renbing

last: Jia

first: Yixiong

first: Xianqun

last: Fan


title: Induction of Immortal-like CAR-T Cells by Defined Factors

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

overall_design: Refer to individual Series


title: TMPRSS4 promotes cell proliferation and inhibits apoptosis in pancreatic ductal adenocarcinoma by activating ERK1/2 signaling pathway

city: Guangzhou

first: Jianyou

middle: No

last: Gu

state: Guangdong

address: 253 Gongye Middle Avenue, Haizhu District

department: No

institute: Zhujiang Hospital, Southern Medical University

summary: Transmembrane protease serine 4 (TMPRSS4) is upregulated in various kinds of human cancers, including pancreatic cancer. However, its biological function in pancreatic ductal adenocarcinoma (PDAC) remains unclear. In the current study, real-time qPCR, immunohistochemical staining, Western blotting, and database (Cancer Genome Atlas and Gene Expression) analysis revealed remarkable overexpression of TMPRSS4 in PDAC tissue as compared to non-tumor tissue. The TMPRSS4 overexpression was associated with poor prognosis of PDAC patients. Moreover, multivariate analysis revealed that TMPRSS4 serves as an independent risk factor in PDAC. We performed gain-and loss-of-function analysis and found that TMPRSS4 promotes cellular proliferation and inhibits apoptosis of PDAC cells both in vitro and in vivo. Furthermore, we showed that TMPRSS4 might promote cell proliferation and inhibit apoptosis through activating ERK1/2 signaling pathway in pancreatic cancer cells. These findings were validated by using ERK1/2 phosphorylation inhibitor SCH772984 both in vitro and in vivo. Taken together, this study suggests that TMPRSS4 is a proto-oncogene, which promotes initiation and progression of PDAC by controlling cell proliferation and apoptosis. Our findings indicate that TMPRSS4 could be a promising prognostic biomarker and a therapeutic target for the treatment of pancreatic cancer.

overall_design: RNA-seq analysis was performed in three shTMPRSS4-treated cells along with the control samples

first: Wenjie

first: Junfeng

first: Xianxing

first: Tian

last: Tao

first: Ludi

last: Yang

first: Yao

last: Zheng

first: Songsong

last: Liu

first: Jiali

first: Liwei

last: Zhu

first: Huaizhi

first: Yingfang


title: RNA expression of human naive B cells either unstimulated or  activated with CD40L in presence or absence of transient Fas engagement

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

country: Germany

institute: University clinics Freiburg

summary: Fas signaling has been previously associated with induction of gene expression. The goal of this study is to characterize the role of short-term Fas engagement on the transcriptome of activated human B cells.

overall_design: Isolated B cells were stimulated with CD40L overnight or left unstimulated. CD40L-stimulated B cells were then treated with FasL or FasL+Q-VD for 4h.   Total RNA was isolated and subjected to NextSeq 500 (Illumina) uni-directional sequencing in triplicates.

first: Melanie

last: Boerries

first: Julian

last: Staniek

first: Marta

last: Rizzi


title: Artesunate inhibits the cell viability of diffuse large B cell lymphoma cells by  increasing the susceptibility to ferroptosis (RNA-seq).

status: Public on Mar 06 2024

first: Chengjie

last: Geng

state: 广东

address: 广东省广州市天河区黄埔道西601

department: Life and Science Department

institute: Jinan University

summary: Comparing  the effects of artesunate versus DMSO in three DLBCL cell lines, we found a decrease in cell viability to 80%-60%. Over increasing artesunate dosage,we found increasing ROS generation and lipid peroxidation. In combination with the Ferrostatin-1 rescue experiment, we conclude that cell death induced by artesunate is ferroptotic. We compared the transcriptome of the U2932 cell line with and without 100µm artesunate in triplicate. A ferroptosis gene signature is shown to be enriched among the upregulated genes of this comparison. GPX4 protein expression was shown to be downregulated after artesunate in U2932 cells, but not in the rescue experiment with Ferrostatin-1. MT1G gene expression was identified as required for artesunate-mediated ferroptosis via targeted suppression by shRNAs. We present significantly decreased cell viability when combining artesunate with doxorubicin, suggesting a potential translation into clinic for treatment of ABC and GCB DLBCL.

overall_design: To investigate the genes regulated by artesunate-induced cell death phenotype in diffuse large B-cell lymphoma（DLBCL），we extracted total RNA from U2932 cells treated with or without 100 μM artesunate and performed transcript sequencing.

first: Xiaohui

first: Liyi

last: Zeng

first: Lan

last: Zhang


title: Chemotherapy-induced dynamic remodeling of tumor microenvironment and cellular program in tongue squamous cell carcinoma

first: Siyuan

last: Huang

state: Beijing

address: No.5 Yiheyuan Road Haidian District, Beijing, P.R.China

institute: Peking University

summary: Tongue squamous cell carcinoma (TSCC)

overall_design: Two patients were diagnosed with tongue squamous cell carcinoma and received chemotherapy

first: Junyan

first: Wenjie

last: Wu


title: Cellular atlas of the human ovary using morphologically guided spatial transciptomics and single-cell sequencing [NanoString GeoMx]

city: Ann Arbor

first: Jun

last: Li

state: Michigan

address: 1141 Catherine St

department: Human Genetics

institute: University of Michigan

summary: The reproductive and endocrine functions of the human ovary involve spatially defined interactions among highly specialized cell populations. Despite the importance of the ovary in female fertility and overall endocrine health, the functional attributes of ovarian cells and the complex structures in which they reside are largely uncharacterized, limiting our understanding of the key mechanisms of follicle development such as steroid hormone production and somatic-germ cells interactions. In this study we profiled the expression of >18,000 protein genes in 257 spatially defined human ovary samples to examine major types of functional units in the ovary, including areas enriched for oocytes, theca cells, and granulosa cells. To complement the spatial data, we generated single-cell RNA sequencing data for 21,198 past-QC cells from three additional donors and identified four major cell types and four immune cell subtypes. Custom selection of sampling areas and antibody-guided targeting of known cell types led to transcriptional profiles that are spatially highly specific, revealing distinct gene activities for early-stage oocytes and for theca and granulosa cells, respectively, all collected from their native tissue sites. These data significantly expanded the knowledge of molecular programs driving follicle development, contributing to a panel of 76 oocyte-specific genes including novel markers PADI6, UCHL1, ZFAND2A, and REC114, and similarly a 96- and 45-gene panel for granulosa and theca cells, respectively. Serial samples in follicle rings and across consecutive layers of the cortex and medulla uncovered spatial gradients in antral follicles and in the cortex surface, as well as previously unappreciated diversity of local gene expression patterns, reflecting regional variations of hormone signaling (NR4A1, CEBPD, STAR, and ADAMTS4) and extracellular matrix remodeling (VIM, COL1/8/12/14/16/18, and TIMP1/2). The combined spatial and single-cell human ovary atlas reported here serves as a resource for developing next-generation reagents for cell enrichment, high-resolution imaging, lineage analysis, and perturbation.

overall_design: Two healthy donors sequenced using nanoString GeoMx and three healthy donors sequenced using 10x Chromium


title: Cellular atlas of the human ovary using morphologically guided spatial transciptomics and single-cell sequencing [scRNA-seq]


title: Low-dose exposure to microplastics retards meiotic maturation via HDACs insufficiency

city: 33-浙江省

first: Ming

last: Zong

address: University Town, Chashan, Wenzhou

institute: Wenzhou Medical University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Microplastics (MPs) are considered as one of the main reasons for male and female infertility. However, the reproductive toxicity and its related mechanisms are understood by animal models with acute exposure to MPs at present. In the study, we show the low-dose polystyrene microplastics (PSMPs) exposure results in severely abnormal reproduction in female, but not male in mouse model, exhibiting failed oocyte meiotic maturation. Mechanistically, the PSMPs exposure induces the over-activation of cell metabolism pathways, insufficient HDACs and H4K16 hyperacetylation in oocytes in vivo and in vitro. By addition of HDAC3 inhibitor, the failed oocyte maturation, over-activation of cell metabolism pathways and H4K16 hyperacetylation are recapitulated, and the overexpression of HDAC3 can rescue the defects of meiotic maturation induced by PSMPs. Our observations suggest a direct link of the maturation defects induced by PSMPs to HDAC3 insufficiency. Thus, we propose the potential treatments for therapy of the failed meiotic maturation of oocyte from women highly exposed to MPs by activating or supplying HDAC3.

overall_design: We illustrated the PSMPs exposure induces the over-activation of cell metabolism pathways, insufficient HDACs and H4K16 hyperacetylation in oocytes. In the RNA-seq analysis on oocytes, 5 embryos were used for per reaction and two or three replicates were performed for each group. In the CUT&Tag on oocytes, 20 embryos were used for per reaction and two or three replicates were performed for each group.

first: Qi

last: Zhao

first: Entong

last: Song

first: Hongye

last: Linghu

first: Xuanwen

first: Songling

last: Xiao

first: Baicui

last: Wang

first: Wanchun

last: Guan

first: Jianzhong

last: Su

first: Jiaming

first: Shaorong

last: Gao

first: Qingran

last: Kong


title: Immunotherapy-resistant acute lymphoblastic leukemia cells exhibit reduced CD19 and CD22 expression and BTK pathway dependency [RNA-seq]

city: Bronx

first: Kith

last: Pradhan

state: ny

address: 1300 Morris Park Ave

institute: Einstein College of Medicine

summary: While therapies targeting CD19 by antibodies, CAR-T cells and T cell engagers have improved the response rates in B-cell malignancies; the emergence of resistant cell populations with low CD19 expression can lead to relapsed disease. We developed an in vitro model of adaptive resistance facilitated by chronic exposure of leukemia cells to a CD19-immunotoxin. Single-cell (sc) RNAseq showed increase in transcriptionally distinct CD19low populations in resistant cells. Mass cytometry demonstrated that CD22 was also decreased in these CD19low resistant cells. ATAC-seq showed decreased chromatin accessibility at promoters of both CD19 and CD22 in the resistant cell populations. Combined loss of both CD19 and CD22 antigens was validated in samples from pediatric and young adult patients with B-ALL that relapsed after CD19 CAR-T targeted therapy. Functionally, resistant cells were characterized by slower growth and lower basal levels of MEK activation. CD19low resistant cells exhibited preserved B cell receptor signaling and were more sensitive to both BTK and MEK inhibition. These data demonstrate that resistance to CD19 immunotherapies can result in decreased expression of both CD19 and CD22 and can result in dependency on BTK pathways.

overall_design: The objective of this experiment was to compare transcription in parental and resistant REH cells. REH resistant cells were established by ongoing tretement of REH parental cells with anti-cd19 immunotoxin.

first: Sarah

last: Aminov

first: Amit

last: Verma

first: Shahina

last: Maqbool

first: Yongmei


title: Immunotherapy-resistant acute lymphoblastic leukemia cells exhibit reduced CD19 and CD22 expression and BTK pathway dependency [ATAC-seq]

overall_design: The objective of this experiment was to compare chromatin accessibility in parental and resistant REH cells. REH resistant cells were established by ongoing tretement of REH parental cells with anti-cd19 immunotoxin.


title: Finasteride delays atherosclerosis progression in mice and is associated with a reduction in plasma cholesterol in men

city: Urbana

first: Jaume

last: Amengual

state: IL

address: 905 S Goodwin Ave

department: Food Science and Human Nutrition

institute: University of Illinois at Urbana Champaign

summary: Finasteride is commonly prescribed to treat benign prostate hyperplasia and male-pattern baldness in cis men and, more recently, trans individuals. However, the effect of finasteride on cardiovascular disease remains elusive. We evaluated the role of finasteride on atherosclerosis using low-density lipoprotein (LDL) receptor-deficient (Ldlr-/-) mice. Next, we examined the relevance to humans by analysing the data deposited between 2009 and 2016 in the National Health and Nutrition Examination Survey (NHANES). We show that finasteride reduces total plasma cholesterol and delays the development of atherosclerosis in Ldlr-/- mice. Finasteride reduced monocytosis, monocyte recruitment to the lesion, macrophage lesion content, and necrotic core area, the latter of which is an indicator of plaque vulnerability in humans. RNA sequencing analysis revealed a downregulation of inflammatory pathways and an upregulation of bile acid metabolism, oxidative phosphorylation, and cholesterol pathways in the liver of mice taking finasteride. Men reporting the use of finasteride showed lower plasma levels of cholesterol and LDL-cholesterol than those not taking the drug. Our data unveil finasteride as a potential treatment to delay cardiovascular disease in people by improving the plasma lipid profile.

overall_design: Male Ldlr-/- were fed Western diet without finasteride or the same diet supplemented with 1000 mg finasteride/kg for 12 weeks. After 12 weeks on a diet, mice were fasted overnight and euthanized. Upon harvesting, tissues were immediately placed in liquid nitrogen and stored at -80ºC. Liver RNA was isolated using a Zymo Research mini prep tissue kit (Irvine, CA), following a DNaseI treatment, according to the manufacturer's instructions.

first: Patrick

last: McQueen

first: Ivan

last: Pinos

first: Donald

last: Molina


title: Divergent composition and transposon-silencing activity of small RNAs in mammalian oocytes II

first: Wei

last: Liu

address: 320 Yueyang Road

department: Institute of Biochemistry and Cell Biology

institute: Chinese Academy of Sciences

type: Non-coding RNA profiling by high throughput sequencing

summary: We found piRNAs with different lengths represented the predominant small RNA species in oocytes from the 12 explored species, except mouse. We found endo-siRNAs resulted from the truncated Dicer isoform were mouse-specific, and os-piRNAs associating with PIWIL3 in human oocytes are widespread in mammals and are typically with low levels of the 2’-3’-O-methylation. The sequences of many highly expressed piRNA clusters are fast-evolving compared with their syntenic genomic locations, and the TE families distributing in the conserved piRNA clusters are various between species.

overall_design: Profiling small RNAs and mRNA in oocytes from 12 animals.

first: Li

last: Hou

first: Ligang

last: Wu


title: Transcriptomics and metabolomics reveal the underlying mechanism of drought treatment on anthocyanin accumulation in postharvest blood orange fruit

city: Changsha

first: Ling

last: Sheng

address: Donghu

institute: Hunan Agricultural University

summary:
Background: Anthocyanins are the most important compounds for nutritional quality and economic values of blood orange. However, there are few reports on the pre-harvest treatment accelerate the accumulation of anthocyanins in postharvest blood orange fruit. Here, we performed a comparative Transcriptome and metabolomics analysis to elucidate the underlying mechanism involved in seasonal drought (SD) treatment during fruit expansion stage on anthocyanin accumulation in postharvest ‘Tarocco’ blood orange fruit.
Results: Our results showed that SD treatment slowed down the fruit enlargement and increased the sugar accumulation during fruit development and matured period. Obviously, under SD treatment, the accumulation of anthocyanin in blood orange fruit during postharvest storage was significantly accelerated and markedly higher than that in CK. Meanwhile, the total flavonoids and phenols contents and antioxidant activity in SD treatment fruit were also sensibly increased during postharvest storage. Based on metabolome, we found that substrates required for anthocyanin biosynthesis, such as amino acids and their derivatives, and phenolic acids, have significantly accumulated and higher in SD treated mature fruit compared with that of CK. Further according to the results of transcriptome data and weighted gene coexpression correlation network analysis (WGCNA) analysis, phenylalanine ammonia-lyase (PAL3) was considered key structural gene. qRT-PCR analysis verified that the PAL3 was highly expressed in SD treated postharvest stored fruit and was significantly positively correlated with the anthocyanin content. Moreover, we found that other structural genes in anthocyanin biosynthesis pathway were also upregulated under SD treatment through transcriptome data and qRT-PCR analysis.
Conclusions: The findings suggest that SD treatment promotes the accumulation of substrates necessary for anthocyanin biosynthesis during fruit ripening process, and activates the expression of anthocyanin biosynthesis pathway genes during postharvest storage period, especially PAL3, co-contributed to the rapid accumulation of anthocyanin. The present study provides a theoretical basis for postharvest quality control and water-saving utilization of blood orange fruit.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for drought treated and control postharvest ‘Tarocco’ Blood orange

first: Hongbing

first: Yan

last: Jin

first: Le

last: Huang

first: Chouyu

last: Miao

first: Jiayi

last: Tang

first: Huimin

last: Zhang

first: Haojie

last: Yin

first: Xiaopeng

last: Lu

last: Li

first: Suming

last: Dai

first: Alessandra

last: Gentile


title: Insights into selective action of microsecond pulsed electric fields on healthy and cancer stem cells

city: padova

first: silvia

last: bresolin

state: padova

address: via giustiniani 3

department: department of women's and children's health

country: Italy

institute: università di padova


title: YfmR is a translation factor that prevents ribosome stalling and cell death in the absence of EF-P

city: Ithaca

first: Heather

last: Feaga

state: NY

address: 123 Wing Dr

institute: Cornell University

summary: Protein synthesis is performed by the ribosome and a host of highly conserved elongation factors. Elongation factor P (EF-P) prevents ribosome stalling at difficult-to-translate sequences, particularly  polyproline tracts. In bacteria, phenotypes associated with efp deletion range from modest to lethal, suggesting that some species encode an additional translation factor that has similar function to EF-P. Here we identify YfmR as a translation factor that is essential in the absence of EF-P in B. subtilis.  YfmR is an ABCF ATPase that is closely related to both Uup and EttA, ABCFs that bind the ribosomal E-site and are conserved in more than 50% of bacterial genomes. We show that YfmR associates with actively translating ribosomes, and that depleting YfmR from ∆efp cells causes severe ribosome stalling at a polyproline tract in vivo. YfmR depletion from ∆efp cells was lethal, and caused reduced levels of actively translating ribosomes. Our results therefore identify YfmR as an important translation factor that is essential in B. subtilis in the absence of EF-P.

sample_organism: Bacillus subtilis subsp. subtilis str. 168

overall_design: Magellan 6x in vitro transposed gDNA prepared from wild-type B. subtilis 168 (40) was transformed into wild type or ∆efp B. subtilis. Transposon insertions were sequenced on the Illumina MiSeq platform (v3 150 bp kit) at the Cornell University Biotechnology Resource Center.


title: The neutrophil–osteogenic cell axis promotes bone destruction in periodontitis

city: Tokyo

first: Masayuki

last: Tsukasaki

state: --None--

address: 7-3-1, Hongo, Bunkyo-ku

country: Japan

institute: The University of Tokyo

summary: We performed single-cell RNA-sequencing analysis on mouse periodontal lesions to analyze the detailed mechanism underlying immune–bone cell interactions in periodontitis.

overall_design: Periodontal tissues were obtained from five control mice and five ligature-induced periodontitis (LIP) mice by stripping the gingival mucosa and scraping the surface of the alveolar bone. After enzymatic digestion, periodontal cells were collected, and single-cell RNA sequencing analysis was performed using the 10x Genomics Chromium system. In this study, data from control and LIP mice were initially combined and analyzed using the integration function, and then separated using the split function to show data from LIP mice.

first: Yutaro

last: Ando


title: A vagal reflex evoked by airway closure

city: Boston

first: Michael

last: Schappe

address: 240 Longwood

institute: Harvard Medical School

summary: Airway integrity must be continuously maintained throughout life. Sensory neurons guard against airway obstruction and on a moment-by-moment basis, enact vital reflexes to maintain respiratory function. Decreased lung capacity is common and life-threatening across many respiratory diseases, and lung collapse can be acutely evoked by chest wall trauma, pneumothorax, or airway compression. Here, we characterize a neuronal reflex of the vagus nerve evoked by airway closure that leads to gasping. In vivo vagal ganglion imaging revealed dedicated sensory neurons that detect airway compression but not airway stretch. Vagal neurons expressing PVALB mediate airway closure responses, and innervate clusters of lung epithelial cells called neuroepithelial bodies (NEBs). Stimulating NEBs or vagal PVALB neurons evoked gasping in the absence of airway threats, while ablating NEBs or vagal PVALB neurons eliminated gasping to airway closure. Single-cell RNA sequencing revealed that NEBs uniformly express the mechanoreceptor PIEZO2, and targeted knockout of PIEZO2 in NEBs also eliminated responses to airway closure. NEBs are dispensable for the Hering-Breuer inspiratory reflex, indicating that discrete terminal structures detect airway closure and inflation. Like Merkel cells involved in touch sensation, NEBs are PIEZO2-expressing epithelial cells, and moreover, are critical for an aspect of lung mechanosensation. These findings expand our understanding of neuronal diversity in the airways, and reveal a dedicated vagal pathway that detects airway closure to help preserve respiratory function.

overall_design: Lung neuroendocrine cells, which comprise neuroepithelial bodies (NEBs), were isolated from Ascl1-CreER; Ai14 and Calca-Egfp mice. Reporter expressing cells were enriched by fluorescence-activated cell sorting (FACS) and analyzed using scRNAseq.

middle: S

first: Philip

middle: A

last: Brinn

first: Narendra

middle: R

last: Joshi

first: Rachel

last: Greenberg

first: Soohong

last: Min

first: AbdulRasheed

last: Alabi

first: Chuchu

first: Stephen

middle: D

last: Liberles


title: Effects of cinnamic acid on the hair growth ability of dermal papilla cells

city: Kawasaki

first: Tatsuto

last: Kageyama

state: Kanagawa

address: Life Innovation Center, 3-25-22 Tonomachi

institute: Kanagawa Institute of Industrial Science and Technology

summary: We examined effects of cinnamic acid on the hair growth ability of dermal papilla cells. Treatment with cinnamic acid led to upregulation of G-protein coupled receptor signaling pathway and neuroactive ligand-receptor interaction in human DP cells.

overall_design: We annalysed gene expression of human dermal papilla cells with/without 100 μg/mL treatment for 3 days.

first: Junji

last: Fukuda


title: Epigenetic regulation in small intestinal epitheliel cells with butyrate exposure

city: Cincinnati

first: Theresa

last: Alenghat

state: Ohio

address: 3333 Burnet Avenue

department: Division of Immunobiology

institute: Cincinnati Children's Hospital Medical Center

summary: H3K9Ac enrichment in intestinal epithelial cells from the intestine of WT mice treated with vehicle or buytrate for 7 days. Intestinal epithelial cells were harvested from the terminal ileum of vehicle or butyrate treated mice. Chromatin immunoprecipitation was performed with anti-H3K9Ac. Sequencing was performed using the Illumina and reads were mapped to mm10 genome using STAR Aligner.

overall_design: Characterization of histone acetylation in intestinal epithelial cells from vehicle and buytrate treated mice.

first: Emily

last: Eshleman


title: Targeting of mitochondrial fission through natural flavonones elicits anti-myeloma activity

city: Catanzaro

first: Claudia

last: Veneziano

address: Viale Europa, Località Germaneto

department: Department of Experimental and Clinical Medicine

institute: "Magna Graecia" University of Catanzaro

summary:
Background
Mitochondrial alterations, often dependent on unbalanced mitochondrial dynamics, feature in cancer pathobiology, making mitochondria-targeting therapies a promising avenue for the treatment of several cancers, including multiple myeloma (MM). Flavonones are natural flavonoids endowed with mitochondrial-targeting activities. Herein, we investigated the capability of two flavonones, Hesperetin (Hes) and Naringenin (Nar), to selectively target Drp1, a pivotal regulator of mitochondrial dynamics, prompting anti-MM activity.
Results
Hes and Nar were found to accommodate within the GTPase binding site of Drp1, and to inhibit Drp1 expression and activity, leading to hyperfused mitochondria with reduced OXPHOS. In vitro, Hes and Nar reduced MM clonogenicity and viability, even in the presence of patient-derived bone marrow stromal cells, triggering ER stress and apoptosis. Interestingly, Hes and Nar rewired MM cell metabolism through the down-regulation of master transcription activators (SREBF-1, c-MYC) of lipogenesis genes. An extract of Tacle, a Citrus variety rich in Hes and Nar, was capable to recapitulate the phenotypic and molecular perturbations of each flavonone, triggering anti-MM activity in vivo.
Conclusion
Hes and Nar inhibit proliferation, induce apoptosis and rewire the metabolism of MM cells via the targeting of the mitochondrial fission pathway.

overall_design: RNA samples extracted from AMO1 myeloma cell line after 48h of Hes and Nar or vehicle treatment and were profiled for RNA seq analysis.

first: Carmela

last: De Marco

first: Roberta

last: Torcasio

first: Cantafio

middle: M

last: Gallo

first: Amodio

last: Nicola


title: Brain and Blood Transcriptome Profiles Delineate Common Genetic Pathways across Suicidal Ideation and Suicide II

city: New York

first: Fatemeh

last: Haghighi

address: 1425 Madison Ave, 9-20D

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

summary: Human genetic studies indicate that suicidal ideation and behavior are both heritable. Most studies have examined associations between aberrant gene expression and suicide behavior, but behavior risk is linked to severity of suicidal ideation. Through a gene network approach, this study investigates how gene co-expression patterns are associated with suicidal ideation and severity using RNA-seq data in peripheral blood from 46 live participants with elevated suicidal ideation and 46 with no ideation. Associations with presence of suicidal ideation were found within 18 co-expressed modules (p<0.05), as well as in 3 co-expressed modules associated with suicidal ideation severity (p<0.05, not explained by severity of depression). Suicidal ideation presence and severity-related gene modules with enrichment of genes involved in defense against microbial infection, inflammation, and adaptive immune response were identified, and investigated using RNA-seq data from postmortem brain that revealed gene expression differences with moderate effect sizes  in suicide decedents vs. non-suicides in white matter, but not gray matter. Findings support a role of brain and peripheral blood inflammation in suicide risk, showing that suicidal ideation presence and severity are associated with an inflammatory signature detectable in blood and brain, indicating a biological continuity between ideation and suicidal behavior that may underlie a common heritability.

overall_design: Prefrontal cortical regions, specifically the ventral white matter (BA 47), from frozen brain sections were used for RNA-seq assays. The cohort consisted of 15 suicide decedents, and 9 non-psychiatric non-suicide controls who died of accidental causes and were all free of gross neuropathology.

first: Sun

last: Shengnan

first: Liu

last: Qingkun

first: Wang

last: Zhaoyu

first: Huang

last: Yung-yu

first: Sublette

last: Elizabeth

first: Dwork

last: Andrew J.

first: Rosklija

last: Gorazd

first: Ge

last: Yongchao

first: Galfalvy

last: Hanga

first: Mann

last: J John

first: Haghighi

last: Fatemeh


title: Insights into selective action of microsecond pulsed electric fields on healthy and cancer stem cells (NHA)

first: silvia

last: bresolin

summary:
In the last few years, pulsed electric fields have emerged as promising clinical tools for tumor treatments. This study highlights the distinct impact of a specific pulsed electric field protocol named PEF-5 (0.3 MV/m, 40 µs, 5 pulses) on astrocytes (NHA), medulloblastoma (D283) and gli-oblastoma (U87 NS) cancer stem-like cells. We pursued this goal performing ultrastructural analyses corroborated by molecular/omics approaches to understand the vulnerability or re-sistance mechanisms triggered by PEF-5 exposure in the different cell types. Electron microscopic analyses showed that, independently of exposed cells, the main targets of PEF-5 were the cell membrane and the cytoskeleton, presenting indiscriminate filopodia disappearance on the cell surface accompanied by a rapid cell swelling. Nevertheless, cells activated different responses stemming from intracellular organelles. NHA triggered a protective mechanism to recover from the damaged membranes and eliminated the detrimental ROS to maintain cell vital functions. Conversely, PEF-5 induced a different action on mitochondria of cancer stem-like cells, more prominent on D283 compared to U87 NS cells, in correlation with a higher basal level of CD133 protein in D283 cells. In this case, a complete mitochondrial dysfunction was demonstrated, inhibiting the recovery of D283 vital processes, while a mild perturbation was observed in mito-chondria of U87 NS cells, not sufficient to impair their cell functions. Altogether, these results suggest the possibility to use PEF-based technology as a novel strategy to target selectively mi-tochondria of CSCs, preserving healthy cells.
Ultrastructural analysis, supported by transcriptomic characterization in microsecond pulsed electric field exposed normal brain and brain tumor cells

overall_design: Gene expression was measured using Affymetrix platform in control and PEF-5 exposed NHA cells 24h after exposure.

first: Silvia

last: Bresolin

first: Luca

last: Persano


title: Nuclear receptor coactivator SRC-1 promotes colorectal cancer immune escape by enhancing PD-L1 transcription and protein stability

city: Xiamen

first: Yilin

last: Hong

address: Xiang'an South Road

institute: Xiamen University

summary: mRNA expression of Ctrl and KOSRC-1 MC38 cells were detected, and differentially expressed mRNAs were analyzed to reveal potential mechanism of SRC-1 in up-regulating PD-L1 expression.

overall_design: To investigate the potential mechanism of SRC-1 in up-regulating PD-L1 expression, we established SRC-1-knockout MC38 cells. We then peformed gene expression profiling analysis using data obtained from RNA-seq. Comparative gene expression profiling analysis of RNA-seq data for Ctrl and SRC-1-knockout MC38 cells.

first: Qiang

last: Chen


title: Protein S-nitrosylation Restricts Xenobiotic Receptor PXR Hyperactivity and Ameliorates Acetaminophen-induced Liver Injury in Mice

city: DaLian

first: qi

last: cui

state: LiaoNing

address: DaLian

institute: 大连医科大学

summary: Drug-induced liver injury (DILI), especially acetaminophen overdose, is the leading cause of acute liver failure. Pregnane X receptor (PXR) is a nuclear receptor and the master regulator of drug metabolism. Aberrant activation of PXR plays a pathogenic role in the acetaminophen hepatotoxicity. Here, we aimed to examine the PXR S-nitrosylation (SNO) in response to acetaminophen. We found that PXR was S-nitrosylated in hepatocytes and the mouse livers after exposure to acetaminophen or S-nitrosoglutathione (GSNO). Mass-spectrometry and site-directed mutagenesis identified the cysteine 307 as the primary residue for SNO-modification. In hepatocytes, SNO suppressed both agonist (rifampicin and SR12813)-induced and constitutively active PXR (VP-PXR) activations. Furthermore, in acetaminophen overdosed mouse livers, PXR protein was decreased at the centrilobular regions overlapping with increased SNO. In PXR-deficient (PXR-/-) mice, replenishing the livers with the SNO-deficient PXR significantly aggravated hepatic necrosis and apoptosis, increased HMGB1 release, and exacerbated liver injury and inflammation. Particularly, we demonstrated that S-nitrosoglutathione reductase (GSNOR) inhibitor N6022 promoted hepatoprotection by increasing the levels of PXR S-nitrosylation. In conclusion, PXR is post-translationally modified by S-nitrosylation in hepatocytes in response to acetaminophen. This modification mitigated the acetaminophen-induced PXR hyperactivity. It may serve as a new target for therapeutical intervention.

overall_design: Mice were fasted for 12 h and intraperitoneal injected with freshly made acetaminophen solution (300 mg/kg) or saline. Mice were injected with acetaminophen 12 h, 24 h, 48 h, 72 h and 96 h prior to their sacrifice. Blood was collected under isoflurane anesthesia by retro-orbital bleeding. The livers were collected for protein extraction or for histopathological and immunohistological studies.

first: Qi

last: Cui

first: Lei

last: Xiao

first: Nanping

last: Wang


title: Dissection of a CTCF insulator and its impact on chromosome topology and oncogene expression in gastrointestinal stromal tumor (RNA-Seq)

first: Kyung Lock

last: Kim

state: MA

address: 450 Brookline Avenue

department: Cancer Biology

institute: Dana-Farber Cancer Institute

summary: Enhancer-Promoter communication is dependent on the topological organization of genomic DNA, including topologically-associated domains (TADs) and boundaries enforced by the CTCF insulator protein. Here, we characterized the structure and function of the FGF3/4 locus and the boundary element that insulates the region from an enhancer in the adjacent TAD.

overall_design: To investigate the impact of CTCF insulator disruptions in SDH-intact cells, we established derivatives of the GIST-T1 cell line. We then performed gene expression profiling analysis between WT and insulator KO cell lines using data obtained from RNA-seq.

first: Kyung

middle: L

first: Bradley

middle: E

last: Bernstein


title: Dissection of a CTCF insulator and its impact on chromosome topology and oncogene expression in gastrointestinal stromal tumor (micro-C)

overall_design: To investigate the topological impact of CTCF insulator disruptions, we established derivatives of the GIST-T1 cell line. We then performed region-capture micro-C assay in GIST-T1 WT and insulator KO cells.


title: CLIP (NOVA1 & AGO) and RNAseq (control & NOVA1KD) in human GBM cells

first: Yuhki

last: Saito

address: 1230 York Ave

institute: Rockefeller University

summary: GBM cells derived from a patient were subjected to CLIP and RNAseq assays to for transcriptome analysis (CLIP and RNAseq).

overall_design: GBM cells derived from a patinet were UV-irradiated and subjected to CLIP with  anti-NOVA1 antibody (ab183024 from Abcam) and anti-AGO antibody (2A8: from Dr. Zissimos Mourelatos) and RNAseq (shControl vs shNOVA1KD1 & 2). mRNA abundance and translation efficiency profiles by deep sequencing using Illumina Novaseq. Detailed desription in accompanying paper.

first: Robert

middle: B

last: Darnell


title: Pediatric Neoplastic and Normal Brain RNAseq Data

city: Aurora

first: Andrew

last: Donson

state: CO

department: Pediatrics

institute: CU Anschutz Medical Campus

summary: RNAseq analysis across the spectrum of childhood brain tumors and normal brain tissue.

overall_design: We performed RNAseq on a patient samples obtained from routine surgical resection and autopsy in order to identify differentially expressed genes between tumors.


title: Dissection of a CTCF topological boundary uncovers principles of enhancer-oncogene regulation

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

overall_design: Refer to individual Series


title: Insights into selective action of microsecond pulsed electric fields on healthy and cancer stem cells (D283)

summary:
In the last few years, pulsed electric fields have emerged as promising clinical tools for tumor treatments. This study highlights the distinct impact of a specific pulsed electric field protocol named PEF-5 (0.3 MV/m, 40 µs, 5 pulses) on astrocytes (NHA), medulloblastoma (D283) and gli-oblastoma (U87 NS) cancer stem-like cells. We pursued this goal performing ultrastructural analyses corroborated by molecular/omics approaches to understand the vulnerability or re-sistance mechanisms triggered by PEF-5 exposure in the different cell types. Electron microscopic analyses showed that, independently of exposed cells, the main targets of PEF-5 were the cell membrane and the cytoskeleton, presenting indiscriminate filopodia disappearance on the cell surface accompanied by a rapid cell swelling. Nevertheless, cells activated different responses stemming from intracellular organelles. NHA triggered a protective mechanism to recover from the damaged membranes and eliminated the detrimental ROS to maintain cell vital functions. Conversely, PEF-5 induced a different action on mitochondria of cancer stem-like cells, more prominent on D283 compared to U87 NS cells, in correlation with a higher basal level of CD133 protein in D283 cells. In this case, a complete mitochondrial dysfunction was demonstrated, inhibiting the recovery of D283 vital processes, while a mild perturbation was observed in mito-chondria of U87 NS cells, not sufficient to impair their cell functions. Altogether, these results suggest the possibility to use PEF-based technology as a novel strategy to target selectively mi-tochondria of CSCs, preserving healthy cells.
Ultrastructural analysis, supported by transcriptomic characterization in microsecond pulsed electric field exposed normal brain and brain tumor cells.

overall_design: Gene expression was measured using Affymetrix platform in control and PEF-5 exposed D283_Med cells 24h after exposure.


title: Novel mouse model of Weaver syndrome displays overgrowth and excess osteogenesis reversible with KDM6A/6B inhibition

city: Baltimore

first: Christine

middle: W

last: Gao

state: MD

address: 733 N. Broadway, Rm 406

institute: Johns Hopkins University School of Medicine

summary: Weaver syndrome is a Mendelian disorder of the epigenetic machinery (MDEM) caused by germline variants in EZH2, which encodes the predominant H3K27 methyltransferase and key enzymatic component of Polycomb repressive complex 2 (PRC2). Weaver syndrome is characterized by striking overgrowth and advanced bone age, intellectual disability, and distinctive facies. We generated a mouse model for the most common Weaver syndrome missense variant, EZH2 p.R684C. Ezh2R684C/R684C mouse embryonic fibroblasts (MEFs) showed global depletion of H3K27me3. Ezh2R684C/+ mice had abnormal bone parameters indicative of skeletal overgrowth, and Ezh2R684C/+ osteoblasts showed increased osteogenic activity. RNA-seq comparing osteoblasts differentiated from Ezh2R684C/+ and Ezh2+/+ bone marrow mesenchymal stem cells (BM-MSCs) indicated collective dysregulation of the BMP pathway and osteoblast differentiation. Inhibition of the opposing H3K27 demethylases Kdm6a/6b substantially reversed the excessive osteogenesis in Ezh2R684C/+ cells both at the transcriptional and phenotypic levels. This supports both the ideas that writers and erasers of histone marks exist in a fine balance to maintain epigenome state, and that epigenetic modulating agents have therapeutic potential for the treatment of MDEMs.

overall_design: In the first experiment, we differentiated Ezh2R684C/+ and Ezh2+/+ bone marrow mesenchymal stem cells (BM-MSCs) to osteoblasts for 14 days (D14), then collected RNA for transcriptomic profiling. For the second experiment, we treated Ezh2R684C/+ and Ezh2+/+ BM-MSCs with either DMSO (vehicle) or 2 μM of GSK-J4 for the first 7 days of osteoblast differentiation, then continued the differentiation process through day 21 (D21), when RNA samples were collected for transcriptomic profiling.

first: WanYing

last: Lin

first: Leandros

last: Boukas

first: Kasper

last: Hansen

first: Jill

last: Fahrner


title: Multiple mechanisms activate GCN2 eIF2 kinase in response to diverse stress conditions

city: Indianapolis

first: Ronald

middle: C

last: Wek

state: IN

address: 635 N. Barnhill Dr. MS4067

department: Biochemistry and Molecular Biology

institute: Indiana University School of Medicine

summary: Diverse environmental insults induce the integrated stress response (ISR), which features eIF2 phosphorylation and translational control that serves to restore protein homeostasis. The eIF2 kinase GCN2 is a first responder in the ISR that is activated by amino acid depletion and other unrelated stresses. Two processes are suggested to trigger an ordered process of GCN2 activation during stress: GCN2 monitoring stress via accumulating uncharged tRNAs or by stalled and colliding ribosomes. Our results suggest that while ribosomal collisions are indeed essential for GCN2 activation in response to translational elongation inhibitors, conditions that trigger deacylation of tRNAs activate GCN2 via its direct association with affected tRNAs. Both process require the GCN2 regulatory domain related to histidyl tRNA synthetases. GCN2 activation by UV irradiation features lowered amino acids and increased uncharged tRNAs and ribosome collisions are dispensable. We conclude that there are multiple mechanisms that activate GCN2 during diverse stresses.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: tRNA Charge-Seq was applied to MEF cells treated with Halofuginone (HF) and human NTERT cells treated with UV irradiation to study the mechanisms by which uncharged tRNA accumulation and ribosome stalling active Gcn2 and trigger the Integrated Stress Response (ISR)

first: Jagannath

last: Misra

first: Kenneth

last: Carlson

first: Dan

middle: F

last: Spandau


title: Brain and Blood Transcriptome Profiles Delineate Common Genetic Pathways across Suicidal Ideation and Suicide

first: Fatemeh

last: Haghighi

overall_design: Peripheral blood RNA-seq of adults 20-65 years old from three groups including: Healthy controls; participants with a major depressive disorder diagnosis (MDD) with no history of suicide attempt; and participants with MDD diagnosis with history of suicide attempt were assayed.

first: Shengnan

last: Sun

first: Qingkun

last: Liu

first: Zhaoyu

first: Yung-yu

last: Huang

first: M

last: Sublette

middle: J

last: Dwork

first: Gorazd

last: Rosklija

first: Yongchao

last: Ge

first: Hanga

last: Galfalvy

first: J

last: Mann


title: iPSC-derived microglia carrying the TREM2 R47H/+ mutation are pro-inflammatory and promote synapse loss.

city: Cambridge

first: Jay

last: Penney

address: 77 Massachusetts Avenue

department: Picower Institute

institute: Massachusetts Institute of Technology

summary: Genetic findings have highlighted key roles for microglia in the pathology of neurodegenerative conditions such as Alzheimer’s disease (AD). A number of mutations in the microglial protein TREM2 (triggering receptor expressed on myeloid cells 2) have been associated with increased risk for developing Alzheimer’s disease (AD), most notably the R47H/+ substitution. We employed gene editing and stem cell models to gain insight into the effects of the TREM2 R47H/+ mutation on human iPSC-derived microglia. We found transcriptional changes affecting numerous cellular processes, with R47H/+ cells exhibiting a pro-inflammatory gene expression signature. TREM2 R47H/+ also caused impairments in microglial movement and the uptake of multiple substrates, as well as rendering microglia hyper-responsive to inflammatory stimuli. We developed an in vitro laser-induced injury model in neuron-microglia co-cultures, finding an impaired injury response by TREM2 R47H/+ microglia. Furthermore, mouse brains transplanted with TREM2 R47H/+ microglia exhibited reduced synaptic density, with upregulation of multiple complement cascade components in TREM2 R47H/+ microglia suggesting inappropriate synaptic pruning as one potential mechanism. These findings identify a number of potentially detrimental effects of the TREM2 R47H/+ mutation on microglial gene expression and function likely to underlie its association with AD.

overall_design:
CRISPR/Cas9 gene editing was performed to generate TREM2 R47H/+ and control iPSC lines (2 clones of each). Cell lines were differentiated to iPSC-derived microglia and RNA-seq was performed to determine the effect of the TREM2 R47H/+ mutation under baseline conditions.
A subsequent experiment involved treatment of the iPSC-derived microglia with pro-inflammatory compounds (LPS and IFNgamma) followed by RNA-seq to determine whether TREM2 R47H/+ microglia respond differently to pro-inflammatory stimuli than wild-type controls.

first: William

middle: T

last: Ralvenius

first: Anjanet

last: Loon

first: Oyku

last: Cerit

first: Vishnu

last: Dileep

first: Blerta

last: Milo

first: Ping-Chieh

last: Pao

first: Hannah

last: Woolf

first: Li-Huei

last: Tsai


title: Higher SLC7A2 expression is associated with abnormal neuroinflammatory response and nitrosative stress in Huntington’s disease

city: Boca Raton

first: Jianning

last: Wei

state: FL

address: 777 Glades Road

department: Biomedical Science

institute: Florida Atlantic University

summary:
Background: We previously identified solute carrier family 7 member 2 (SLC7A2) as one of the top up-regulated genes when normal huntingtin was deleted. SLC7A2 has a high affinity for Arginine. Arginine is implicated in inflammatory responses and SLC7A2 is an important regulator of innate and adaptive immunity in macrophagy. Although neuroinflammation is clearly demonstrated in HD animal models and patients, the question of whether neuroinflammation actively participates in HD pathogenesis is a topic of ongoing research and debate. Here we study the role of SLC7A2 in mediating neuroinflammatory stress response in HD cells.
Methods: RNA sequencing, quantitative RT-PCR and datamining of publicly available RNA-seq datasets of human patients were performed to assess the levels of SLC7A2 mRNA in different HD cellular models and patients. Biochemical studies were then conducted on cell lines and primary mouse astrocytes to investigate Arginine metabolism and nitrosative stress in response to neuroinflammation. The CRISPR-Cas9 system was used to knockout SLC7A2 in STHdhQ7 and Q111 cells to investigate its role in mediating the neuroinflammatory response. Live-cell imaging was used to measure mitochondrial dynamics. Finally, exploratory studies were performed using Enroll-HD periodic human patient datasets to analyze the effect of Arginine supplement on HD progression.
Results: We found that SLC7A2 is selectively up-regulated in HD cellular models and patients. HD cells exhibit an overactive response to neuroinflammatory challenges including abnormally high iNOS induction and NO production, leading to increased protein nitrosylation. Depleting extracellular Arg or knocking out SLC7A2 can block the iNOS induction and NO production in STHdhQ111 cells. We further examined the functional impact of protein nitrosylation on a well-documented protein target, DRP-1 and found that more mitochondria were fragmented in challenged STHdhQ111 cells. Lastly, analysis of Enroll-HD datasets suggested that HD patients taking Arginine supplement progressed more rapidly than others.
Conclusions: Our data suggest a novel pathway that links Arginine uptake to nitrosative stress via up-regulation of SLC7A2 in the pathogenesis and progression of HD. It further implicates that Arginine supplement may potentially pose a greater risk to HD patients.

overall_design: To investigate the global transcriptomal changes in STHdhQ7/Q7 and STHdhQ111/!111 cells in response to neuroinflammation. Neuroinflammation was induced with a combination of 100ng/ml IFNg and 5ug/ml LPS.


title: MY-COMP, an inhibitor of the transcriptional activity of YAP-B-MYB, identifies NEK2 as a novel mediator of YAP oncogenesis in uveal melanoma cells [CUT&RUN]

city: Wuerzburg

first: Carsten

middle: P

last: Ade

address: Am Hubland

department: Lehrstuhl Biochemie und Molekularbiologie

institute: University of Wuerzburg

summary:
Activation of YAP is frequently observed in cancer and is associated with poor outcomes, making it an attractive target for therapeutic intervention. Previous studies have mainly focused on blocking the interaction of YAP with TEAD transcription factors. Here we took a different approach by interfering with the binding of YAP to the transcription factor B-MYB using MY-COMP, a fragment of B-MYB containing the YAP binding domain fused to a nuclear localization signal. We found that expression of MY-COMP inhibited the binding of B-MYB to YAP, resulting in growth defects, nuclear abnormalities and polyploidization in HeLa cells.
Additionally, MY-COMP interfered with normal cell cycle progression of YAP-dependent uveal melanoma cells, but its effects were much weaker in YAP-independent cutaneous melanoma cell lines. MY-COMP antagonized the YAP-dependent expression of MMB-regulated cell cycle genes, providing an explanation for the observed phenotypes. We identified NIMA-related kinase (NEK2) as a candidate target downstream of YAP and B-MYB, contributing to the transformation of YAP-dependent uveal tumor cell lines. Overall, our findings suggest that targeting selected YAP-MMB regulated genes such as NEK2 or inhibiting the WW-domains of YAP to suppress YAP-regulated cell cycle genes could provide a novel mechanism to antagonize the pro-tumorigenic functions of YAP.

overall_design: CUT&RUN sequencing was done with uveal melanoma cells (92.1) without further treatment in order to identify chromatin bound proteins YAP, H3K4me1, H3K4me3, H3K27ac and H4ac. For CUT&Run sequencing samples, the immunoprecipitation of digested DNA was done for YAP, H3K4me1, H3K4me3, H3K27ac and H4ac, using th below listed antibodies. As control, DNA was sequenced following immunoprecipitation with an unspecific IgG antibody.

first: Doerthe

last: Gertzmann

first: Franziska

last: Liss

first: Marco

last: Gruendl

first: Laura

last: Baehner

first: Victoria

last: Schoeffler

first: Björn

last: von Eyss

first: Stefan

last: Gaubatz


title: MY-COMP, an inhibitor of the transcriptional activity of YAP-B-MYB, identifies NEK2 as a novel mediator of YAP oncogenesis in uveal melanoma cells


title: Dissection of a CTCF insulator and its impact on chromosome topology and oncogene expression in gastrointestinal stromal tumor (ChIP-Seq)

first: Kyung Lock

last: Kim

overall_design: To investigate the impact of CTCF insulator disruptions, we established derivatives of the GIST-T1 cell line. We then performed chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for CTCF, H3K27ac and H3K27me3 in GIST-T1 WT and insulator KO cell lines.

first: Kyung

first: Bradley

last: Bernstein


title: RNAseq analysis of mutants in coding and non-coding transcription of phosphate genes in the yeast Saccharomyces cerevisiae.

city: Leiden

first: Paul

last: van Heusden

address: Sylviusweg 72

department: Institute of Biology

country: Netherlands

institute: Leiden University

summary: This study addresses the effect of mutations related to sense and antisense transcription of Saccharomyces cerevisiae phosphate genes using strand-specific RNAseq. Replacement of the transcriptional terminator of PHO84 by that of CYC1 resulted, unexpectedly, in an increased antisense transcription and a strongly reduced sense transcription of PHO84. Also RNA levels of  SPL2 were strongly reduced. Deletion of the PHO84 coding region did not markedly affect the expression of SPL2, suggesting that antisense transcription of PHO84 and not the Pho84 transporter affects the expression of SPL2. Deletion of the two putative binding sites for the transcriptional regulator Ume6 in the SPL2 promoter resulted in a slightly increased level of SPL2 RNA, whereas deletion of the UME6 gene resulted in a decreased level of SPL2 and PHO84 RNA. These results suggests that Ume6 is involved in the regulation of SPL2 by a mechanism different from a simple binding to the putative Ume6 binding sites.

overall_design: Samples were analyzed in two series. In the first series three independent cultures of BY4741, three independent cultures of BY4741ΔP and three independent cultures of BY4741Tpho84-Tcyc1 were used. In the second series two independent cultures of BY4741,  three independent cultures of BY4741ΔU, three independent culture of ume6Δ, two independent culture of pho4Δ and two independent culture of pho84Δ were used.

first: P


title: Highly functional intestinal monolayer through organoids derived from human iPS cells for drug discovery research

city: Suita

first: Tatsuya

last: Inui

state: Osaka

institute: Osaka university

summary: Human induced pluripotent stem (iPS) cell-derived enterocyte-like cells (ELCs) are expected to evaluate intestinal absorption and metabolism of orally administered drugs. However, it was difficult to generate large amounts of ELCs with high quality because they cannot proliferate and be passaged. In this study, we established the organoids from ELCs (ELC-org), which could be passaged and maintained for more than a year. When ELC-org were dissociated into single cells and seeded on cell culture inserts (ELC-org-mono), they formed a tight monolayer in 3 days. Both ELC-org and ELC-org-mono were composed exclusively of epithelial cells, being nearly 100% of EpCAM-positive. Gene expressions of many drug-metabolizing enzymes and drug transporters were enhanced in ELC-org-mono compared to those in ELCs and ELC-org. Their levels were similar to those in human adult intestine. The CYP3A4 activity level in ELC-org-mono was comparable or higher than that in primary cryopreserved human small intestinal cells and their expression level was up-regulated by inducers such as rifampicin. ELC-org-mono had the efflux activities of P-gp and BCRP. Importantly, ELC-org-mono cultured for more than a year maintained high intestinal functions. Even when the cryopreserved organoid-derived cells were directly seeded and cultured on cell culture inserts, they maintained high intestinal functions similar to the cells without cryopreservation. RNA-seq analysis showed that ELC-org-mono were more mature as intestinal epithelial cells than ELC and ELC-org. Therefore, we have successfully improved the function and convenience of ELCs by utilizing organoid technology.

overall_design: Human iPS cell-derived enterocyte-like cells (ELCs), ELC-derived intestinal organoids (ELC-org) and ELC-org-derived monolayers

first: Yusei

last: Uraya

first: Jumpei

last: Yokota

first: Tomoki

last: Yamashita

first: Kanae

last: Kawai

first: Yukiko

last: Ueyama-Toba

first: Hiroyuki

last: Mizuguchi


title: Splicing targeting approaches highlight actionable vulnerabilities in advanced prostate cancer [22Rv1]

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

country: France

institute: GenoSplice technology

summary: To investigate if pharmacological inhibition of splicing could uncover novel actionable vulnerabilities in CRPC, we profiled the genome-wide transcriptional changes elicited in 22Rv1 cells by treatment with three drugs that inhibit the splicing through different molecular targets: i. Pladienolide B, that impairs the activity of SF3B1; ii.  Indisulam that promote degradation of the splicing factor RBM39; iii. THZ531 inhibits the cyclin dependent kinases (CDK) 12 and 13.

overall_design: Poly-A plus RNA-sequencing of 22Rv1 cells treated with Indisulam (3.3µM, 12hrs), or Pladienolide B (10nM, 6hrs) or THZ531 (200nM, 6hrs) or DMSO as control.

first: Ambra

last: Antonioni

first: Cinzia

last: Caggiano

first: Chiara

last: Naro

first: Ariane

last: Jolly

first: Maria

last: Paronetto

first: Claudio

last: Sette


title: NOTUM-MEDIATED WNT SILENCING DRIVES EXTRAVILLOUS TROPHOBLAST CELL LINEAGE DEVELOPMENT [Notum knockdown]

city: Stillwater,

first: Khursheed

last: Iqbal

state: OK

address: 310 N Monroe St,

institute: Oklahoma state university

summary: WNT activated signal transduction is a conserved regulator of morphogenesis of many organ systems, including the placenta.  In human trophoblast stem (TS) cells, activation of canonical WNT signaling is a key to maintenance of the TS cell stem state. NOTUM, a negative regulator of canonical WNT signaling, was prominently expressed in first trimester EVT cells developing in situ and upregulated in EVT cells derived from human TS cells. Furthermore, NOTUM was required for human TS cell differentiation to EVT cells. Canonical WNT signaling is essential for maintaining human trophoblast cell stemness and prevention of human TS cell differentiation. Downregulation of canonical WNT signaling via the actions of NOTUM is required for EVT cell differentiation.

overall_design: NOTUM was knocked down in human trophoblast stem cells using lentiviral delivery of shRNA. Following selection by puromycin, cells were differentiated for eight days (Okae et al.) into extravillous trophoblast (EVT). On day eight of differentiation, cells treated with either control shRNA or NOTUM-specific shRNA were collected and RNA was isolated.

first: Vinay

last: Shukla

first: Michael

last: Soares


title: Effect of OCT4 overexpression on the neural induction of human dental pulp stem cells

city: Adelaide

first: James

last: Breen

state: SA

address: 108 North Terrace (Ground Floor)

department: John Curtin School of Medical Research

country: Australia

institute: Australian National University

summary: Stem cell-based therapy is an alternative strategy for brain repair. Various cell types have been investigated and dental pulp stem cells (DPSC) have been identified as promising candidates. These multipotent stem cells are found in the dental pulp tissue of molar teeth. They are clinically easily obtained, have a high proliferative rate, and possess neurogenic potential due to their mesoectodermal origin. Here, overexpression of octamer-binding transcription factor 4 (OCT4) in combination with neural conditions was used to reprogram human DPSC along the neural lineage. Transcriptomic analysis of differentially-expressed genes highlighted the expression of genes associated with neural and neuronal functions in the OCT4-overexpressing DPSC following neural induction.

overall_design: Human dental pulp stem cells were transduced with either an empty lentiviral vector or a lentiviral vector encoding for OCT4, and were cultured in neural inductive conditions. RNA-sequencing was performed on one biological sample, with four replicates in each of three groups; untransduced DPSC in standard growth conditions (DPSC), empty vector-transduced DPSC following neural induction (DPSC-EV), and OCT4 vector-transduced DPSC following neural induction (DPSC-OCT4).

last: Gancheva

first: Karlea

last: Kremer

first: Agnes

last: Arthur

first: Anne

last: Hamilton-Bruce

first: Paul

last: Thomas

first: Stan

last: Gronthos

first: Simon

last: Koblar


title: Neonatal CD8+ T cells resist terminal exhaustion during chronic infection

city: Ithaca

first: Andrew

last: Grimson

address: 445 Biotechnology Building

department: Molecular Biology & Genetics

institute: Cornell University


title: COP1 controls light-dependent chromatin remodeling in Arabidopsis [RNA-Seq]

city: Austin

first: Wenli

last: Wang

state: Texas

department: Molecular Biosciences

institute: university of Texas at Austin

summary:
Light is an environmental factor that influences various aspects of plant development. Phytochromes (phys) as light sensors regulate myriads of downstream genes in response to changes in environmental factors. VIL1 (VIN3-LIKE 1)/VERNALIZATION  5 (VRN5), a Polycomb Repressive Complex 2 (PRC2) - associated protein, mediates vernalization pathway. VIL1 directly interacts with phyB and regulates photomorphogenesis through the formation of repressive chromatin loops at downstream growth-promoting genes in response to light. CONSTITUTIVELY PHOTOMORPHOGENIC 1 (COP1) is an E3 ligase for a number of substrates in light signaling, acting as a central repressor of photomorphogenesis. Here, we show that VIL1 is a substrate of COP1 and COP1 degrades VIL1 through the ubiquitin/26S proteosome system (UPS) in the dark. Our study illustrates that COP1 controls light-dependent formation of chromatin loop by regulating the stability of VIL1 and limits a repressive histone modification to fine-tune expressions of growth-promoting genes during photomorphogenesis.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 4 different genotypes at two time points (ZT0 and ZT6).

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Col-0, vil1-1, cop1-4, vil1-1cop1-4 and hy5-215 mutants.

first: Junghyun

last: Kim

first: Teresa

last: Martinez

first: Enamul

last: Huq

first: Sibum

last: Sung


title: NOTUM-MEDIATED WNT SILENCING DRIVES EXTRAVILLOUS TROPHOBLAST CELL LINEAGE DEVELOPMENT [CHIR99021]

last: Iqbal

overall_design: Glycogen synthase kinase 3 (GSK3) inhibitor, CHIR99021 was added as a supplement to the standard EVT cell differentiation culture conditions of CT27 human TS cells (Okae et al.). On day eight of differentiation, cells treated with either control or CHIR992021 02µM were collected and RNA was isolated.


title: COP1 controls light-dependent chromatin remodeling in Arabidopsis


title: COP1 controls light-dependent chromatin remodeling in Arabidopsis [ChIP-Seq]

summary:
Light is an environmental factor that influences various aspects of plant development. Phytochromes (phys) as light sensors regulate myriads of downstream genes in response to changes in environmental factors. VIL1 (VIN3-LIKE 1)/VERNALIZATION  5 (VRN5), a Polycomb Repressive Complex 2 (PRC2) - associated protein, mediates vernalization pathway. VIL1 directly interacts with phyB and regulates photomorphogenesis through the formation of repressive chromatin loops at downstream growth-promoting genes in response to light. CONSTITUTIVELY PHOTOMORPHOGENIC 1 (COP1) is an E3 ligase for a number of substrates in light signaling, acting as a central repressor of photomorphogenesis. Here, we show that VIL1 is a substrate of COP1 and COP1 degrades VIL1 through the ubiquitin/26S proteosome system (UPS) in the dark. Our study illustrates that COP1 controls light-dependent formation of chromatin loop by regulating the stability of VIL1 and limits a repressive histone modification to fine-tune expressions of growth-promoting genes during photomorphogenesis.
We performed Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for histone modifications H3K27me3 in five Arabidopsis genotypes (Col-0, vil1-1, cop1-4, vil1-1cop1-4 and hy5-215).


title: Transcriptomics driven metabolic pathway analysis reveals similar metabolic alterations in diet- and chemical-induced mouse NASH model and human

city: Bern

first: Mojgan

last: Masoodi

address: Freiburgstrasse 18

department: Institute of Clinical Chemistry

country: Switzerland

institute: Inselspital, Bern University Hospital

summary: Non-alcoholic fatty liver disease (NAFLD) is the most common chronic liver disease worldwide, and can rapidly progress to non-alcoholic steatohepatitis (NASH). Accurate preclinical models and robust methodologies need to be established to understand the underlying metabolic mechanisms and develop treatment strategies. Based on our meta-analysis of currently available data on several mouse models, we hypothesized a diet- and chemical-induced NASH model closely resembles metabolic alteration in human.  We developed an already established WD+CCl4-induced NASH model. We developed and performed transcriptomics driven metabolic pathway analysis (TDMPA) using differentially expressed genes in mouse NASH liver compared to control. We compared the altered metabolic pathways and enzymatic reactions to human NASH. We performed functional assays and lipidomics to confirm our findings related to metabolic alterations.   Numerous metabolic pathways were altered in human NASH and mouse model. De novo triglyceride biosynthesis, fatty acid beta-oxidation, bile acid biosynthesis, cholesterol metabolism, and oxidative phosphorylation were the most influenced pathways. We confirmed significant reduction in mitochondrial functions and bioenergetics in NASH model, and in acylcarnitines. We identified a wide range of lipid species within the most perturbed pathways predicted by TDMPA. Triglycerides, phospholipids and bile acids were increased significantly in NASH, confirming our initial observations.    We identified several metabolic pathways that typify NASH pathophysiology in human. By comparing human and mouse metabolic signatures, we evaluated metabolic resemblance of mouse model to human and its suitability for the study of the disease and potential usage for drug discovery and testing. We also presented TDMPA, a novel methodology to evaluate metabolic pathway alterations in metabolic disorders and a valuable tool for defining metabolic space to aid experimental design for lipidomics and metabolomics approaches.

overall_design: Comparative gene expression analysis of RNA sequencing data for various mouse interventions. Liver tissue of mouse was analyzed from mice belonging to one of four groups: Control (18 weeks standard chow diet), NASH (18 weeks western diet supplemented by weekly CCl4 injection), Placebo (22 weeks western diet supplemented by weekly CCl4 injection and placebo treatment), and TGC (22 weeks western diet supplemented by weekly CCl4 injection and drug treatment).

first: Sofia

last: Tsouka

first: Pavitra

last: Kumar

first: Patcharamon

last: Seubnooch

first: Katrin

last: Freiburghaus

first: Marie

last: St-Pierre

first: Jean-François

last: Dufour


title: MY-COMP, an inhibitor of the transcriptional activity of YAP-B-MYB, identifies NEK2 as a novel mediator of YAP oncogenesis in uveal melanoma cells [RNA-seq]

first: Carsten

last: Ade

overall_design: The RNA-seq was done with MCF10A cells that stably express a tamoxifen (4-OHT) inducible ER-YAP2SA fusion construct for the constitutively active YAP mutant YAP2SA. Furthermore, these MCF10A cells also contain a doxycycline-inducible MY-COMP construct. In addition, a RNA-seq was done with 92-1 cells that stably express MY-COMP or a control (GFP) and that were transfected with a control siRNA or a siRNA targeting YAP/TAZ.

first: Doerthe

last: Gertzmann

first: Franziska

last: Liss

first: Marco

last: Gruendl

first: Laura

last: Baehner

first: Victoria

last: Schoeffler

first: Björn

last: von Eyss

first: Stefan

last: Gaubatz


title: Single Center Randomized Trial of Orca-T alone versus Orca-T Plus Tacrolimus Prophylaxis in the Prevention of Acute Graft Versus Host Disease

city: Stanford

first: Cameron

middle: Scott

last: Bader

state: California

address: 269 Campus Drive, CCSR Room 2250

department: BMT and Cell Therapy

institute: Stanford University

summary: Twenty-four patients were randomized to receive Orca-T alone (n=12) or Orca-T plus single-agent GVHD prophylaxis (n=12) to determine if Orca-T alone was non-inferior in preventing acute GVHD.

overall_design: Bulk RNA-seq differential expression analysis of day +14 post-transplant sorted CD4+ T conventional cells and CD4+ Tregs between Orca-T alone, Orca-T + GVHD prophylaxis, and standard-of-care.

first: Everett

middle: H

last: Meyer


title: Stat5 induces androgen receptor (AR) gene transcription in prostate cancer and offers a druggable pathway to target androgen receptor signaling

city: Minneapolis

first: Stephen

last: Jameson

state: MN

address: Wallin Medical Biosciences Bldg, MMC 641

department: Lab Medicine and Pathology

institute: University of Minnesota

summary: The goal of this study was to compare the global transcriptomic effects of knockdown of AR vs inhibition of STAT5 via treatment with IST5-002 in the prostate cancer cell line CWR22Rv1. We knocked down AR with 2 independent shRNAs (or shCtrl). We treated cells for 72 hrs with 0.8 µM IST5-002 (or DMSO control).

overall_design: Comparative gene expression profiling in CWR22Rv1 cells between five groups total. CWR22Rv1 cells with AR knocked down via shRNA (shAR-574, shAR-847 and control shCtrl) or treated for 72 hours with 0.8 uM IST5-002 (or DMSO control).

first: Samuel

last: Pitzen

first: Braedan

last: McCluskey

first: Scott

last: Dehm


title: CENP-A chaperone Scm3HJURP contains a cysteine-rich domain required for centromere targeting and kinetochore integrity

city: Bethesda

first: Shiv

last: Grewal

address: 9000 Rockville Pike

department: National Cancer Institute

institute: National Institutes of Health

summary: Centromeric chromatin is crucial for supporting kinetochore assembly and chromosome segregation. To specify centromeres, the histone H3 variant CENP-A is loaded by the conserved chaperone Scm3/HJURP. The amino-terminus of Scm3/HJURP interacts with CENP-A, while the carboxyl-terminus contains a small domain that interacts with the Mis18 holocomplex, which facilitates centromere localization. Fungal Scm3 proteins contain an additional conserved cysteine-rich domain (CYS) with unknown function.  In this study, we found that CYS is essential for the localization and function of fission yeast Scm3. Disrupting CYS prevents Scm3 from localizing to the centromere and results in cell lethality. Moreover, introducing point mutations in a predicted zinc-binding motif within CYS hinders Scm3 centromere targeting and kinetochore integrity, consistent with structural evidence that CYS binds zinc. We find that expressing only the Scm3 carboxyl-terminus is harmful as it localizes to centromeres and causes defective kinetochores. Remarkably, mutating the CYS zinc-binding motif in this construct eliminates the observed centromere localization and toxicity. Together, our findings establish this cysteine-rich domain with predicted zinc-binding capability as an essential feature of fungal Scm3 proteins and shed new light on the molecular mechanism for targeting Scm3 to centromeres.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for CENP-A chaperone Scm3, as well as a Scm3-∆CYS mutants and untagged control in fission yeast Schizosaccharomyces pombe.

first: H

last: Folco

first: Hua

last: Xiao

first: David

last: Wheeler

first: Hanqiao

last: Feng

first: Yawen

last: Bai

middle: I


title: Identification of the mesenchymal signals regulating embryonic mammary gland development

city: Bristol

first: Qiang

last: Lan

address: Biomedical Sciences Building, University Walk

department: School of Cellular and Molecular Medicine

institute: University of Bristol

summary: The development of branched organs like mammary and salivary glands is regulated by tissue interactions between the epithelial and mesenchymal tissues. Mammary gland consists of a branched epithelial ductal network embedded in a mammary specific mesenchyme. In order to uncover the molecular mechanisms regulating embryonic mammary gland development, we compared the transcriptomes of mesenchymes from different development stages and tissues by RNA-sequencing

overall_design: E13.5 submandibular gland mesenchyme, E13.5 mammary gland mesenchyme, E13.5 ventral skin mesenchyme, E16.5 mammary gland mesenchyme and E16.5 fat pad from C57Bl/6JOlaHsd embryos were manually microdissected from the tissues after enzymatic treatment (Dispase II and Pancreatic-Trypsin consecutively). The mesenchymes isolated from 2-3 embryos from the same litter were pooled together as one sample. Altogether, five biological replicates were collected from 3 different litters.

first: Q

first: E

last: Trela

first: M

last: Mikkola


title: Transcript isoform switching occurs in the murine synaptic transcriptome during aging

city: Lausanne

first: Martino

last: Ugolini

state: Vaud

address: Genopode

department: CIG

institute: UNIL

summary: Preliminary Summary: In this study, we set to specifically analyze effects of aging on differential splicing in the local synaptic proteome. To this end, we analyzed the RNA extracted from synaptosomes obtained from cerebral cortices of C57BL/6 mice of 3 weeks, 5 months and 19 months of age. Synaptosomes are artificial, membranous sacs that contain synaptic components and are generated by subcellular fractionation of homogenized or ground-up nerve tissue. We employ RNA-seq using paired long-reads to obtain comprehensive sequence information on synaptic transcripts and two different bioinformatic methods (DIEGO and LeafCutter) to quantify differential splicing. Finally, the change in the usage of the selected junctions was validated through RT-qPCR and RT-PCR using an independent set of samples.

overall_design: rRNA-depleted RNA of cortex-derived synaptosomes of 3-weeks, 5-months and 19-months old mice (C57BL/6, 4 biological replicates for each age) were sequenced using Illumina HiSeq 2500 System (paired-end). Total Homogenate samples from 5-months old mice were used for reference.

first: Cinzia

last: Caterino

first: Marco

last: Groth

first: Konstantin

last: Riege

first: Steve

last: Hoffmann

first: Alessandro

last: Cellerino


title: Regulation of gene expression in enteroids by butyrate and IL-13

city: Cincinnati

first: Theresa

last: Alenghat

address: 3333 Burnet Avenue

department: Division of Immunobiology

institute: Cincinnati Children's Hospital Medical Center

summary: Expression in organoids dervied from the ileum of WT C57Bl/6 mice stimulated with butyrate, IL-13, or butyrate + IL-13. Intestinal organoids were stimulated with butyrate for 48hrs, then IL-13 for 72 hrs. RNA was isolated using RNeasy Kit (Qiagen). Sequencing was performed using the Illumina HiSeq2500. Reads were mapped to the mm10 genome using Bowtie.

overall_design: Characterization of differential gene expression in intestinal organoids treated with IL-13 +/- buytrate.

first: Emily

last: Eshleman


title: RNA-seq for bone marrow cells of CLP-induced septic mice

city: Shanghai

first: Wang

last: yaodong

address: Wanyuan Road

institute: Children's hospital of fudan university

summary: To investigate the differentially expressed genes in bone marrow cells of septic mice at different stage

overall_design: Comparative gene expression profiling analysis of RNA-seq data for 4 group (conctrol, CLP d1, CLP d3, Clp d6, 2 different mice respectively).

last: Yaodong

first: Zhang

last: Caiyan

first: Lu

last: Guoping

first: Zhou

last: Yufeng


title: Effects of RYGB on liver health in obese mice.

city: Baton Rouge

first: Jaroslaw

last: Staszkiewicz

state: LA

address: 6400 Perkins Rd

department: Genomics Core Facility

institute: Pennington Biomedical Research Center

summary: We investigated the effects of RYGB compared to a sham surgery or caloric restriction on hepatic function. For that, the goals of this study is to identify changes in the liver transcriptome profiling (RNA-seq) that could explain improvements in liver health and function with RYGB compared to other treatment methods.

overall_design: Mice underwent RYGB bariatric surgery, sham surgery, or were weight-matched to the RYGB group via calorie restriction. Mice were euthanized 20 weeks post-surgery and liver tissue was collected.

first: Christopher

last: Axelrod

first: Elizabeth

last: Heintz

first: Wagner

middle: S

last: Dantas

first: John

last: Kirwan


title: BET Bromodomain Degradation Disrupts Function but Not 3D Formation of RNA Pol2 Clusters

status: Public on Mar 05 2024

city: Cleveland

first: Hyunmin

last: Kim

address: 10900 Euclid Ave.

department: Department of Genetics and Genome Sciences

institute: Case Western Reserve University

summary: Fusion-positive rhabdomyosarcoma (FP-RMS) is driven by a translocation that creates the chimeric transcription factor PAX3-FOXO1 (P3F), which assembles de novo super enhancers to drive high levels of transcription of other core regulatory transcription factors (CRTFs). P3F recruits co-regulatory factors to super enhancers such as BRD4, which recognizes acetylated lysines via BET bromodomains. In this study, we demonstrate that inhibition or degradation of BRD4 leads to global decreases in transcription, and selective downregulation of CRTFs. We also show that the BRD4 degrader ARV-771 halts transcription while preserving RNA Polymerase II (Pol2) loops between super enhancers and their target genes, and causes the removal of Pol2 only past the transcriptional end site of CRTF genes, suggesting a novel effect of BRD4 on Pol2 looping. We finally test the most potent molecule, inhibitor BMS-986158, in an orthotopic PDX mouse model of FP-RMS with additional high-risk mutations, and find that it is well tolerated in vivo and leads to an average decrease in tumor size. This effort represents a partnership with an FP-RMS patient and family advocates to make preclinical data rapidly accessible to the family, and to generate data to inform future patients who develop this disease.

overall_design: In the present study, we test ARV-771, is a small-molecule proteolysis-targeting chimera (PROTAC) that links BET bromodomain proteins to an E3 ubiquitin ligase von Hippel Lindau, triggering ubiquitination and proteasomal degradation [23]. The BET-targeting arm of ARV-771 has a similar structure to JQ1 (ref. [23]). We also test BMS-986156, a BET bromodomain inhibitor with a carboline-based structure that showed favorable pharmacokinetics and anticancer activity against many different PDX models [24]. An advantage of degraders over inhibitors is that inhibitors must remain bound to exert their effect, while a single degrader molecule is released once degradation is complete, allowing for molecular recycling and potential gains in potency, and safety.

first: Berkley

last: Gryder

first: Diana

last: Chin


title: NOTUM-MEDIATED WNT SILENCING DRIVES EXTRAVILLOUS TROPHOBLAST CELL LINEAGE DEVELOPMENT

first: Khursheed

last: Iqbal

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

overall_design: Refer to individual Series


title: Effect of TUDCA on the artery which suffered from the atherosclerosis in ApoE-/- mice

city: 杭州

first: 张

last: 越晟

address: 浙江大学

institute: 浙江大学

summary: Cholesterol efflux capacity dysfunction in macrophages is thought to be important in atherosclerosis. However, the molecular mechanism underlying this dysfunction remains unclear. Our previous analysis found that the increase of endoplasmic reticulum stress in macrophages during atherosclerotic plaque formation. Here we extended our analysis to ApoE-/- mice fed a high fat diet, some of which were treated with tauroursodeoxycholic acid (TUDCA) and collected the arteries of mice among these three groups (NFD, HFD and HFD+TUDCA) to perform the Bulk-RNA sequencing. There was significantly high expression of matrix metalloproteinase family (MMP9, MMP25, MMP8, MMP12, MMP13 and MMP3), CD68, inflammasome (IL1b, IL18bp, ifi44, ifi204 and Nlrp3), ER stress (Hspa5) and cholesterol transporters (ABCA1 and ABCG1) in the HFD group compared with the NFD group, however, TUDCA rescued the high expression of the above DEGs to different degrees. As shown by the expression levels of ifi204, Nlrp3, Il1b, and Il18, inflammasome activation was evident in the arteries of the HFD group compared to the NFD group. The ER stress inhibitor TUDCA not only decreased expression of the ER stress-related gene Hspa5 but also down-regulated inflammasome activation (as seen with the expression levels of ifi204, ifi44, NLRP3 and IL1b) in the artery of TUDCA treated mice compared with mice without drugs.

overall_design: Male ApoE-/- mice (8 weeks old, n =60) were obtained from HFK Bioscience Company (Beijing, China). All the ApoE-/- mice were randomly divided into 3 groups: Group 1: control group (normal fat diet, NFD); Group 2: high-fat diet (HFD); Group 3: HFD + TUDCA. A random number table was used for mouse randomization. Group 1 mice were fed with a diet of 5% fat without cholesterol, whereas the other groups were fed with an HFD (16% fat and 0·25% cholesterol). After 8 weeks of HFD feeding, one group of HFD-treated mice was intragastric administration with 1000 mg/kg of TUDCA once daily (HFD+TUDCA group) for 4 weeks, whereas the NFD-treated mice and other group of HFD-treated mice were treated with an equal volume of saline (NFD or HFD group) for 4 weeks. After 4 weeks of TUDCA or saline treatment, the mice were anaesthetized intraperitoneally with 3% pentobarbital sodium (40 mg/kg) and sacrificed. The aortic tissues from the ascending aorta to the ileal bifurcation were immediately gathered for bulk-RNA sequencing.

first: Xuyang

last: Wang

first: Luping

last: Du

first: Xiaogang

last: Guo


title: pTAC3 and pTAC14 are required for binding of Plastid Encoded RNA Polymerase to DNA

city: Coyoacan

first: V Miguel

last: Palomar

state: Mexico City

address: Circuito Exterior SN

department: Biochemistry

country: Mexico

institute: School of Chemistry, UNAM

summary:
Plastid Encoded RNA Polymerase (PEP) is a bacterial type multisubunit RNA polymerase responsible for the bulk of transcription in chloroplasts. It contains four core subunits, which are orthologs of their cyanobacterial counterparts. In Arabidopsis thaliana PEP associates with 12 PEP-associated proteins (PAPs), which serve as peripheral subunits of the RNA polymerase. The exact contributions of PAPs to PEP function remain poorly understood. We show that a peripheral subunit of PEP, PAP1 (pTAC3), binds the same genomic loci as RpoB, a core subunit of PEP. PAP1 (pTAC3) and another peripheral PEP subunit, PAP7 (pTAC14), are required for RpoB binding to DNA. RpoB and another core PEP subunit, RpoC1, are expressed in pap1 (ptac3) and pap7 (ptac14) mutants. We propose that the peripheral subunits of PEP are required for the recruitment of core PEP subunits to DNA.
pTAC3, binds the same genomic loci as RpoB, a core subunit of PEP. PAP1
pTAC3 and another peripheral PEP subunit, PAP7

overall_design: The data consists of 3 replicates of RpoB ChIP-seq in Col0 wt, ptac3 and ptac14 mutants, and pTAC3 ChIP on Col0 wt and ptac3 mutant

first: V

first: Andrzej

last: Wierzbicki


title: Effect of cardiac SRPK3 overexpression in adult mice

city: Wuhan

first: Saiyang

last: Xie

address: Jiefang Road 238

institute: Wuhan university

summary: Pathological cardiac hypertrophy is unequivocally identified as an ominous escalation of hemodynamically stressful overload, ultimately heighten risk of sudden death as heart failure (HF) ensues. Here, we explored how dysregulated mitochondrial RNA (mtRNA) metabolism remodels mitochondrial bioenergetics and controls hypertrophic-phenotype cardiopathy in mice and humans. Utilizing targeted genetic approaches and in vivo functional imaging, we describe a potent cardiac pro-hypertrophic role for serine arginine protein kinase 3 (SRPK3), which is highly induced in myocardium upon hypertrophic stimuli. Adult extended expression of SRPK3 in cardiomyocytes (CMs) leads to spontaneously concentric hypertrophy and eventuates sudden cardiac death in mice.

overall_design: To clarify the specific mechanisms by which SRPK3 regulates cardiac hypertrophy, we generated cardiac Srpk3 transgenic (Srpk3-cTg) mouse.

first: Qizhu

last: Tang


title: Diminished arachidonate 5-lipoxygenase perturbs phase separation and transcriptional response of Runx2 to reverse pathological ventricular remodeling

summary: Untargeted metabolomics showed that serum 5-HETE (a primary product of Alox5) levels were little changed in patients with cardiac hypertrophy, while Alox5 expression was significantly upregulated in murine hypertensive cardiac samples and human cardiac samples of hypertrophy, which prompted us to test whether high Alox5 levels under hypertensive stimuli were directly associated with pathologic myocardium in an enzymatic activity-independent manner. Herein, we revealed that Alox5 deficiency significantly ameliorated transverse aortic constriction (TAC)-induced hypertrophy. Cardiomyocyte-specific Alox5 depletion attenuated hypertensive ventricular remodeling. Conversely, cardiac-specifical Alox5 overexpression showed a pro-hypertrophic cardiac phenotype. Ablation of Alox5 in bone marrow-derived cells did not affect pathological cardiac remodeling and heart failure.

overall_design: To clarify the specific mechanisms by which Alox5 regulates cardiac hypertrophy, we generated cardiac Alox5 deficient mouse.


title: The plant POLYMERASE-ASSOCIATED FACTOR1 complex links transcription and H2B monoubiquitination genome wide

city: Valencia

first: Jaime

last: Pérez

address: Calle del Ingeniero Fausto Elio, s/n

country: Spain

institute: IBMCP

sample_organism:
Arabidopsis thaliana
Drosophila melanogaster


title: Common modes of ERK induction resolve into context specific signalling via a combination of signal duration and cell type specific transcriptional repression [E5.5_RNA]

city: Copenhagen

first: Josh

last: Brickman

address: 3B Blegdamsvej

department: reNEW

country: Denmark

institute: Copenhagen University

summary: Fibroblast Growth Factor (FGF) signalling via ERK exerts diverse roles in development and disease. In mammalian preimplantation embryos and naïve pluripotent stem cells ERK promotes differentiation, whereas in primed pluripotent states closer to somatic differentiation ERK sustains self-renewal. How can the same pathway produce different outcomes in two related cell types? To explore context-dependent ERK signalling in embryonic development and differentiation we generated cell and mouse lines that allow for tissue- and time-specific cell intrinsic ERK activation. Using these tools, we find variations in response to ERK are mostly mediated by repression of transcriptional targets that occur in tandem with reductions in chromatin accessibility at regulatory regions. Furthermore, immediate early ERK responses are largely shared by different cell types but become refined producing cell-specific programs as increasing durations of signalling interface with cell specific gene regulatory networks. Induction in naïve pluripotency is accompanied by chromatin changes, whereas in later stages it is not, suggesting that chromatin context doesn’t shape signalling response. Altogether, our data suggest that cell-type specific responses to ERK signalling exploit the same immediate early response, but then sculpt it to specific lineages via repression of distinct cellular programs and downstream indirect stimulation of available enhancer networks.

overall_design:
To map the transcriptional response to ERK in pluripotent cell types, we targeted mESCs with a version of the cRAF inducible model in Hamilton et al., 2019. The construct allows for rapid and homogeneous ERK induction upon tamoxifen supplementation.
We then created a mouse line by injecting ESCs with this construct to morulas. We collected samples for RNA-seq from post-implantation Epiblast (E5.5), before (0h) and after 4h of ERK.
For each condition, 2 replicates were collected from 2 biological clones (clone 4 and 8), as a total of 4 replicates per condition.

first: Marta

last: Perera

first: Joshua


title: Common modes of ERK induction resolve into context specific signalling via a combination of signal duration and cell type specific transcriptional repression [RSC_RNA]

overall_design:
To map the transcriptional response to ERK in pluripotent cell types, we targeted mESCs with a version of the cRAF inducible model in Hamilton et al., 2019. The construct allows for rapid and homogeneous ERK induction upon tamoxifen supplementation.
We differentiated targeted ESC towards RSC and collected samples for RNA-seq before induction (0h), after 2h and 4h of ERK induction, and then treated for an additional 2h with MEK inhibitor (rev), to explore reversion of ERK targets.
For each condition, 2 replicates were collected from 2 biological clones (clone 4 and 8), as a total of 4 replicates per condition.