title: IKZF1 gene deletions in BCP-ALL promote resistance to cytarabine treatment

status: Public on Aug 31 2023

city: Utrecht

first: Frank

middle: van

last: Leeuwen

address: Heidelberglaan 25

country: Netherlands

institute: Princess Maxima Center

type: Expression profiling by high throughput sequencing

summary: To obtain further insight into the pathways or specific genes that drive resistance to AraC upon loss of IKZF1, we performed RNAsequencing on samples from wildtype and IKZF1 knockout Sem cells treated with and without AraC

overall_design: SEM IKZF1 wildtype and SEM IKZF1 knockout cells were were either treated or untreated with 1uM AraC  for 16 hours, after which mRNA is isolated and transcriptome analyzed

first: Britt

middle: M

last: Vervoort

first: Kari

middle: J

last: Grunewald

first: Laurens

middle: T

last: van der Meer

middle: N

last: Van Leeuwen


title: Gene expression profile of latent metastatic (Lat-M) cells  from clear cell renal cell carcinoma (ccRCC)

city: DALLAS

first: KANGSAN

last: KIM

state: TX

address: 5323 Harry Hines Blvd

department: Pathology

country: USA

institute: UT Southwestern Medical Center

summary: Lat-M cells were derived using ccRCC cell line 769-P (Parental, PA) cells to investigate determinants of metatatic latency in ccRCCs. We profiled PA and LatM cells to understand gene expression in metastatic latency

overall_design: RNA-sequencing was performed using 3 PA replicates and 4 Lat-M replicates

first: Kangsan

last: Kim

first: Srinivas

last: Malladi


title: Comprehensive benchmarking of single cell RNA sequencing technologies for characterizing cellular perturbation systems

city: Ghent

first: Kaat

last: Durinck

address: Corneel Heymanslaan 10

department: Biomolecular Medicine

country: Belgium

institute: Center for Medical Genetics

summary: Technological advances in transcriptome sequencing of single cells provided an unprecedented view on tissue composition and cellular heterogeneity. While several studies have compared different single cell RNA-seq methods with respect to data quality and their ability to distinguish cellular  subpopulations, none of these comparative studies investigated the heterogeneity of the cellular transcriptional response upon a chemical perturbation. In this study, we evaluated the transcriptional response of NGP neuroblastoma cells upon nutlin-3 treatment using the C1, ddSeq and Chromium single cell systems. These systems and library preparation methods are representative for the wide variety of platforms, ranging from microfluids chips to droplet-based systems and from full transcript sequencing to 3’ end sequencing. In parallel, we used bulk RNA-seq for molecular characterization of the transcriptional response. Two complementary metrics to evaluate performance were applied: the first is the number and identification of differentially expressed genes as robustly assessed by two statistical models, and the second is enrichment analysis of biological signals, which is independent of sample size or number of cells evaluated. Where relevant, we downsampled sequencing library size, selected cell subpopulations based on specific RNA abundance features, or created pseudobulk samples to make the data more comparable. While the C1 detects the highest number of genes per cell and better resembles bulk RNA-seq, the Chromium identifies most differentially expressed genes, albeit still substantially fewer than bulk RNA-seq. Gene set enrichment analyses reveals that detection of the most abundant genes in single cell RNA-seq experiments is sufficient for molecular phenotyping. Finally, single cell RNA-seq reveals a heterogeneous response of NGP cells upon nutlin-3 treatment, pinpointing putative late-responders or resistant cells, hidden in bulk RNA-seq experiments.

overall_design: Samples were synchronized using serum starvation followed by treatment with Nutlin-3 or ethanol for 24 hours. Single cell RNA-seq was performed using the ddseq device.

first: Verboom

last: Karen

first: Alemu

last: Assefa

first: Nurten

last: Yigit

first: Jasper

last: Anckaert

first: Niels

last: Vandamme

first: Dries

last: Rombaut

first: Yvan

last: Saeys

first: Olivier

last: Thas

last: Speleman

first: Jo

last: Vandesompele


title: Within-species control reveals novel immune response genes in Caenorhabditis elegans

city: boston

first: Ayush

middle: Vasant

last: Ranawade

state: MA

address: 360 Huntington Ave

department: Bioengineering

institute: Northeastern University

summary: Used P. aeruginosa z11 strain as a control for P. aeruginosa PA14 infection studies in C. elegans

overall_design: RNAseq was performed in N2 wildtype at 22 hours after exposure to E. coli OP50, P. aeruginosa z11, and P. aeruginosa PA14

first: Erel

last: Levine


title: Decoding of translation-regulating entities reveals heterogeneous translation deficiency patterns in cellular senescence

city: Athens

first: Vassilis

middle: George

last: Gorgoulis

state: Athens

address: Mikras Asias 75

department: Medicine

country: Greece

institute: University of Athens

summary: Cellular senescence constitutes a generally irreversible proliferation barrier, accompanied by macromolecular damage and metabolic rewiring. Several senescence types have been identified based on the initiating stimulus, such as replicative (RS), stress-induced (SIS) and oncogene-induced senescence (OIS). Reduced protein synthesis is considered a senescence hallmark, but whether this trait pertains to various senescence subtypes and if distinct molecular mechanisms are involved remain largely unknown. Here, we analyze large published or experimentally produced RNA-seq and Ribo-seq datasets to determine whether major translation-regulating entities such as ribosome stalling, the presence of uORFs/dORFs and IRES elements may differentially contribute to translation deficiency in senescence subsets. We show that translation-regulating mechanisms may not be directly relevant to RS, however uORFs are significantly enriched in SIS. Interestingly, ribosome stalling, uORF/dORF patterns and IRES elements comprise predominant mechanisms upon OIS, strongly correlating with Notch pathway activation. Our study provides for the first time evidence that major translation dysregulation mechanisms/patterns occur during cellular senescence, but at different rates depending on the stimulus type. The degree at which those mechanisms accumulate directly correlates with translation deficiency levels. Our thorough analysis contributes to elucidating crucial and so far unknown differences in the translation machinery and ribosome biogenesis between senescence subsets.

overall_design: Translation efficiency changes upon different senescent stimuli versus normal proliferating conditions in IMR 90 cell line

first: Angelos

last: Papaspyropoulos

first: Orsalia

last: Hazapis

first: Abdullah

last: Altulea

first: Aikaterini

last: Polyzou

first: Panayotis

last: Verginis

first: Maria

last: Fousteri

first: Argyris

last: Papantonis

first: Marco

last: Demaria


title: Cenicriviroc reduces liver fibrosis by restoring the immune cell landscape via inactivating STAT1/NF&B/ERK signaling pathways [prevention_RNA-seq]

city: chengdu

first: chong

last: zhao

address: NO.1,4th Keyuan Road

country: China

institute: Lab of Gastroenterology and Hepatology

summary: This study depicts a novel mechanism by which CVC alleviates liver fibrosis by restoring the immune cell landscape. CVC can inhibit profibrotic gene transcription via inactivating the CCR2-STAT1/NF&B/ERK signaling pathways.

overall_design: One liver fibrosis model was induced by intraperitoneal injection of carbon tetrachloride (CCl4) with wild type for 6 weeks. For the prevention experiment, the wild-type mice were i.p. administered 4 doses of CVC and 2 doses of CCl4 per week for a total of 6 weeks. Control mice received the same volume of olive oil.

first: Jinhang

last: Gao


title: Serum tsncRNAs Reveals Novel Potential Therapeutic Targets of Salvianolic Acid B on Atherosclerosis

city: Shanghai

first: Yiru

last: Wang

address: Longhua Hospital, Shanghai University of Traditional Chinese Medicine, 725 South Wan-Ping Road, Shan

type: Non-coding RNA profiling by high throughput sequencing

summary: Objective: Salvianolic Acid B (SalB)  extracted from the roots and rhizomes of Salvia Miltiorrhiza Bunge  has been utilized to delay the progression of atherosclerosis (AS). Its therapeutic mechanisms remain unclear. Pre-transfer RNA and mature transfer RNA (tsncRNAs) is a novel class of short non-coding RNA  possessing potential regulating functions. In this study  the novel therapeutic targets of SalB by tsncRNAs-sequencing were explored.  Methods: Mice were randomly divided into three groups: control group (CON)  AS model group (MOD)  and SalB-treated group (SAB). The weight change  aortic sinus plaque  and inflammatory cytokines (IL-6  IL-10  TNF-) were assessed. Total RNA was extracted from serum to obtain tsncRNAs  followed expression profiling by the Illumina NextSeq instrument. Subsequently  tRNAscan and TargetScan were used to predict tsncRNAs targets. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway were used to predict the bioinformatics analysis. Quantitative real-time PCR (qPCR) was the method to validate potential tsncRNAs and related targets.  Results: A total of 8 tsncRNAs (fold change >1.5 and P-value <0.05) were significantly decreased in MOD group compared to CON group. Among them  tRNA-Glu-CTC-014 and tRNA-Gly-GCC-074 were markedly increased by SalB treatment and validated with quantitative real-time PCR. GO analysis revealed that the altered target genes of the selected tsncRNAs were most enriched in protein binding and cellular process. Moreover  KEGG pathway analysis demonstrated that altered target genes of tsncRNAs were most enriched in mitogen-activated protein kinase (MAPK) signaling pathway.  Conclusion: In conclusion  tRNA-Glu-CTC-014 and tRNA-Gly-GCC-074 were the potential therapeutic targets of SalB on AS treatment.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for blood of mice (control group  AS-model group  and SalB-intervention group).

first: Min

last: Du

first: Yifan

last: Zhang

first: Ping

last: Liu

first: Bing

last: Deng


title: RNA sequencing of left ventricle tissue two days after rHCI hydrogel injection in a mouse myocardial infarction model

city: Ottawa

first: Sarah

last: McLaughlin

state: ON

address: 40 Ruskin Street

country: Canada

institute: University of Ottawa Heart Institute

summary:
Purpose: rHCI hydrogel injection improves cardiac function within 2 days of treatment in a mouse model of myocardial infarction. The goal of this study was to determine the differences in gene expression with rHCI hydrogel injection post-myocardial infarction.
Methods: Total RNA was isolated from left ventricle tissue of samples and mRNA stranded libraries were prepared and sequenced in Illumina NovaSeq 6000 with a depth of 50 million reads per sample. Differential expression analysis of aligned reads was done to compared gene expression between PBS vs. rHCI, PBS vs. sham, and rHCI vs. sham comparisons.
Results: Differentially expressed genes between sham and PBS as well as rHCI and PBS showed known gene signatures of myocardial infarction. Seven differentially expressed genes were detected with rHCI hydrogel injection compared to PBS.
Conclusions: The target gene ERDR1 that is downregulated with rHCI injection led to discovery of changes in cardiomyocyte apoptosis and reduction of oxidative stress adducts with rHCI injection post-myocardial infarction.

overall_design: Left ventricle sample mRNA sequencing for mice with myocardial infarction injected with PBS (control) or rHCI hydrogel. An age-matched sham group was also included. There were 5 biological replicates per group for a total of 15 samples.

first: Erik

last: Suuronen


title: Microarray profiling of circRNA-associated-ceRNA networks in acne lesions

city: Nanjing

first: meng

last: zhou

address: Jiangwangmiao Street

institute: Chinese Academy of Medical Sciences and Peking Union Medical College

type:
Non-coding RNA profiling by array
Expression profiling by array

summary: To investigate the differential expression of circRNA in severe acne and its role in competitive endogenous RNA regulatory networks, we have employed RNA microarray technology as a discovery platform to identify genes

overall_design: Biopsy specimens were obtained from the lesions of six patients with severe acne and six healthy volunteers who had face plastic surgery.The different expression profiles of circRNAs,miRNA and mRNA between acne patients and normal controls were shown in Table S1, Table S2, and Table S3, respectively.

first: Meng

last: Zhou

first: Haoxiang

last: Xu


title: mRNA profiling on Axl inhibitor TP0903 treated CART19 compared to untreated CART19 produced from normal donors

city: Rochester

first: Saad

last: Kenderian

state: MN

address: 200 First Street SW

institute: Mayo Clinic

summary: RNA sequencing was performed on three biological replicates of  DMSO treated CART19 (control) and TP0903 treated CART19 produced from normal donors.

overall_design: T cells from normal donors were transduced with a replication-incompetent lentiviral vector expressing a second-generation chimeric antigen receptor (CAR) consisting of an anti-CD19 single chain variable fragment (FMC63) fused to 4-1BB and CD3ζ intracellular domains as previously described.  DMSO or TP-0903 treated CART19 were stimulated with CD19+ cell line Jeko-1 for 24 hours and CART19 were isolated with CD20 microbeads. After confirming CART19 isolation was performed successfully with flow cytometry (>99% purity), RNA was isolated from CART19.

first: Reona

middle: L

last: Sakemura

first: Carli

last: Stewart


title: FANCA deficiency promotes leukemic progression by allowing emergence of cells carrying oncogenic driver mutations

city: VILLEJUIF

first: Christel

last: GUILLOUF

address: 114 rue Edouard vaillant

country: France

institute: Gustave Roussy

summary:
Leukaemia is caused by the clonal evolution of a cell that accumulates mutations/genomic rearrangements, allowing unrestrained cell growth. However, recent identification of leukaemic mutations in the blood cells of healthy individuals revealed that additional events are required to expand the mutated clones for overt leukaemia. Here, we assessed the functional consequences of deleting the Fanconi anaemia A (Fanca) gene, which encodes a DNA damage response protein, in Spi1 transgenic mice that develop preleukaemic syndrome. Loss of FANCA increases SPI1-associated disease penetrance and favours leukaemic progression without increasing the global mutation load of leukaemic clones.
However, leukaemic FANCA-deleted cells display heterozygote activating mutations in known oncogenes, such as Kit or Nras, that are identified at low frequency in WT mice with preleukaemic syndrome, indicating that FANCA loss-of-function supports the emergence of oncogene mutated leukaemic cells. We show that a unique transcriptional deregulation is associated with the leukaemic status of cells devoid of FANCA activity, including MDM4, NOTCH and Wnt/-catenin pathways.
Our observations provide evidence that FANCA-deficient preleukaemic cells carrying oncogenic Kit or Ras mutations require a favourable intracellular environment to allow the emergence of leukaemic clones. The loss of FANCA may provide this mandatory cellular setup by allowing the simultaneous activation of several proliferative pathways.

overall_design: RNAseq of blasts maintained with EPO

first: Patrycja

last: Pawlikowska

first: Laure

last: Delestré

first: Sebastian

last: Gregoricchio

first: Alessia

last: Oppezzo

first: Michela

last: Esposito

first: M'Boyba

last: Diop

first: Filippo

last: Rosselli

last: Guillouf


title: Overactivation of ATP citrate lyase-H3K27 acetylation axis leads to maternal diabetes induced neural tube defect.

city: Beijing

first: Baoling

last: Bai

state: Beijing

address: Yabao Road2, Chaoyang District

institute: Capital institute of pediatrics

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Overactivation of ATP citrate lyase-H3K27 acetylation axis leads to maternal diabetes induced neural tube defect [ChIP-seq]

summary: Diabetes mellitus in early pregnancy is a non–genetic maternal risk factor for neural tube defects, which are associated with dysregulated gene expression and disruption of cellular behaviors. However, the key molecules linking high glucose metabolism to gene dysregulation remain unclear. Here, we report elevation of ATP citrate lyase (ACL), a metabolic enzyme of the glucose–related tricarboxylic acid cycle in brains of DM–induced mouse embryos with neural tube defects. Consistent with high glucose exposure, manipulation of ACL expression controlled the levels of acetyl-CoA and subsequent lysine 27 acetylation of histone H3 (H3K27ac). Inhibition of ACL activity significantly ameliorated diabetes mellitus–induced exencephaly in mouse embryos. Combinational analysis of H3K27ac ChIP-seq and RNA-seq data revealed a genome–wide synergistic dysregulation of 566 genes, among which the most highly upregulated gene was Txnip, which encodes a thioredoxin–interacting protein. Manipulation of ACL expression disrupted the levels of TXNIP protein, subsequent phosphorylation of apoptosis signal–regulating kinase 1 (ASK1) and neuroepithelial apoptosis. Such pathogenic pathway involving high glucose–induced ACL–H3K27ac, increased–TXNIP upregulation and excessive apoptosis was validated in human embryonic brain tissue affected by neural tube defects. Our study uncovers an intermediary role of ACL in linking high glucose metabolism to epigenetic alterations and neural tube defect formation.

overall_design: ChIP-seq for H3K27ac in mouse E9.5 brain tissue.

first: Huili

last: Li

first: Qin

last: Zhang


title: Enhanced STAT5a activation opposes Tox and rewires exhausted CD8 T cells towards a hybrid durable effector-like state during chronic stimulation [ATAC-Seq]

city: Philadelphia

first: E

middle: JOHN

last: WHERRY

state: PA

address: 421 Curie Blvd,354 BRB II/III

department: Systems Pharmacology       and Translational Therapeutics,Institute for Immunology

institute: University of Pennsylvania

summary:
Here, we discovered a reciprocal antagonism between Stat5a and Tox in TEX cells. Stat5a antagonized the Tox-mediated exhaustion program to achieve a durable and protective hybrid effector/NK-like differentiation state in settings that typically drive exhaustion. Stat5 also drove TEX progenitors to differentiate into the effector-like TEXint subset, a key developmental step for PD-1 blockade responsiveness.
Therapeutic enhancement of Stat5 activity in TEX cells using an orthogonal IL-2/IL2Rb pair system fostered TEXint cell accumulation and synergized with PD-L1 blockade. Finally, targeted delivery of Stat5-signals in TEX progenitors achieved partial epigenetic rewiring of these cells towards the effector/memory lineage and revived polyfunctionality. Together, these data highlight therapeutic opportunities of targeting Stat5 to antagonize the Tox-dependent epigenetic programming of TEX and provoke a hybrid program that exploits effector biology and durability for optimal therapeutic potential

overall_design: Three or more replicates from each sample were used for genomic DNA extraction and ATACseq assay was used to compare and analyse the open chromatin data to study the role of STAT5a in Tim3 postive CD8 subset cells

first: Jean

middle: C

last: Beltra

last: Wherry


title: Gene and allele specific expression during electric organ ontogeny in African weakly electric fish and hybrid

city: Potsdam

first: Feng

last: Cheng

address: Meistersingerstr., 5

country: Germany

institute: University of Potsdam

summary: Hybridization can act as a catalyst for rapid phenotypic evolution by introducing novel allelic combinations, which can affect hybrid phenotype through changes in gene expression. The African weakly electric fish use their muscle-derived electric organ to produce electric organ discharge (EOD) for electrocommunication and electrolocation. The EOD in genus Campylomormyrus and cross-species hybrids is usually species-specific and varies during ontogeny. We compared the gene expression patterns and allele specific expression between juvenile and adult individuals in C. compressirostris (EOD duration 0.4 ms in juvenile and 0.4 ms in adult), C. rhynchophorus (EOD duration 5 ms in juvenile and 40 ms in adult) and their hybrid (EOD duration 0.4 ms in juvenile and 4 ms in adult). Differentially expressed genes between juveniles and adults were highly enriched in “membrane”, “plasma membrane” and “cytoplasm” Go Ontogeny terms. We detected several potassium channel-related genes (e.g. KCNJ2, ADCYAP1) that are potentially involved in the EOD development during ontogeny. The alleles from C. compressirostris show dominant expression in the hybrid at juvenile and adult life stages. KCNJ2 is the only gene that exhibits allelic dominance of C. rhynchophorus allele, and has an increasing expression during ontogeny in this allele. This suggests that the EOD development in hybrids could be related to the increasing allelic expression of the C. rhynchophorus allele under the scenario of overall dominance of C. compressirostris alleles. Our study sheds light in the evolution of the electric organ discharge in electric fishes and on the role of introgressive hybridization in complex phenotypic traits.

sample_organism: Campylomormyrus compressirostris x Campylomormyrus rhynchophorus

overall_design: All juvenile samples were artifically bred and raised at the Univerrsity of Potsdam. Those fish were anesthetized by a lethal dose of clove oil, and dissected on cold 99% ethanol.  Electric organ tissue from each specimen were flash frozen in liquid nitrogen, and further preserved in -80°C.

first: Alice

middle: B

last: Dennis

first: Otto

last: Baumann

first: Marisol

last: Domínguez

first: Frank

last: Kirschbaum

first: Ralph

last: Tiedemann


title: Study on the effects of CD44 knockdown in glioblastoma multiforme cells in combination with Temozolomide

city: Guangzhou

first: Chongxian

last: Hou

state: Guangdong

address: Industrial Road No.253

department: Neurosurgery

institute: Zhujiang Hospital, Southern Medical University

summary: Our goal is to investigate the effects of CD44 knockdown alone and in combination with Temozolomide on glioblastoma multiforme cells. To achieve this, we treated U251 cells that had been transfected with either shCtrl lentivirus or shCD44 lentivirus with either DMSO or Temozolomide.

overall_design: U251 cells transfected with either shCtrl lentivirus or shCD44 lentivirus were treated with either DMSO or Temozolomide.

first: Shenbao

last: Shi

first: Jing'an

last: Ye

first: Yiquan

last: Ke


title: Transcriptional profiling of mouse small intestinal tissue with Eif4a1/4a2 mutation

city: Glasgow

first: Kathryn

last: Gilroy

address: Switchback Road

country: United Kingdom

institute: Cancer Research UK Scotland Institute

summary: Small intestinal tissue was collected for RNAseq analysis from mice with short term Apc inactivation or Apc inactivation with Kras mutation, in the presence or absence of Eif4a1 or Eif4a2 inactivaton.

overall_design: Expression data from mouse small intestine with the noted genotypes

first: Rachael

last: Smith

first: Owen

last: Sansom


title: Single-cell RNA transcriptomics of hypertensive nephropathy patients

city: CHANG SHA

first: YONG

last: ZHONG

address: XIANGYA ROAD

institute: XIANGYA HOSPITAL

summary: Hypertensive nephropathy (HTN) emerges as one of the leading causes of end-stage renal disease, yet the precise mechanisms and cell-specific gene expression changes are still unknown. This study used single-cell RNA sequencing (scRNA-seq) to explore novel molecular mechanisms and hub gene targets for HTN.Our data identifies a distinct cell-specific gene expression profile, pathogenic signaling pathways and potential cell-cell crosstalks in the progression of HTN. These findings will provide a promising novel landscape for mechanisms and treatment of HTN.

overall_design: We analyzed kidney samples from 3 patients with HTN  using single-cell RNA sequencing, compared with previous data of controls. We then identified distinct cell clusters through unsupervised clustering analysis of kidney specimens. Identification of the differentially expressed genes (DEGs) and enrichment analysis in different  cells as well as the interaction between cells were also performed. In addition, the differences of gene expression and enrichment pathway in patients with different levels of proteinuria were analyzed.

first: Rong

last: Tang

first: Wei

last: Lin

first: Yong

last: Zhong

first: Xiangcheng

last: Xiao


title: High throughput expression-based phenotyping and RNAi screening reveals novel regulators of planarian stem cells

city: Evanston

first: Christian

middle: Paul

last: Petersen

state: IL

address: 2205 Tech Drive, Hogan 2-100

department: Molecular Biosciences

institute: Northwestern University

summary: The complexity of cell types and states revealed by scRNAseq cell atlases presents a challenge for the systematic analysis of fate determinants using traditional screening methodologies. Differentiation in the planarian Schmidtea mediterranea exemplifies this problem, as these animals continuously produce over 100 differentiated cell types for homeostasis and regeneration using adult pluripotent stem cells termed neoblasts. The signaling factors enabling neoblast self-renewal and selective differentiation of these many fates are still incompletely understood. We developed a method using high-throughput expression profiling by qPCR and whole-animal RNAseq to simultaneously assess numerous cell fate markers as the phenotypic readout in large-scale RNAi screens. Applying this method, we performed an RNAi screen of 400 kinases, receptors, and other regulatory molecules to reveal specific functions for 30 previously unknown factors in neoblast biology. 17 genes were required for neoblast maintenance, including factors likely involved in cell-cycle regulation, nutrient sensing, and chromatin modification. Multidimensional expression information additionally revealed several specific regulators of other neoblast activities, including a mink1 kinase regulating global neoblast differentiation, the energy responsive kinase adenylate kinase-2 regulating intestine specification within the neoblast population, an RNA acetyl transferase nat10 regulating epidermal differentiation, and a pak1 kinase that restricts neoblast localization to prevent tissue outgrowths. These results identify several new regulators of neoblast activities and demonstrate the applicability of expression-based screening for systematic analysis of stem cell phenotypes in whole animals.

overall_design: Total RNA was isolated from whole planarian animals after 21 days following RNAi of a control gene (Photinus pyralis luciferase, Ppluc), PAPSS2,CSNK1A1,ANK1,MINK1,PRPF4B,piwi-2,PANK3,LPT,MNAT1,Rb,nat10,CDK7,AK2,ANAPC,STK39,PLK1,TRRAP,LAMTOR,PKN2,AKT,MARK2,repA1,zfp-1, and bruli.  3 biological replicates of 4 animals each were analyzed for each condition.  Worms were fed dsRNA every 2-3 days for 2 weeks and RNA harvested 7 days after the last feeding.

first: Erik

middle: G

last: Schad

middle: P


title: The main Transcription factor of Notch signalling RBPJ inhibits the formation of combined HCC-iCCA

first: Qiongxuan

last: Fang

address: NO.11, Xizhimen South Street

department: Department of Internal Medicine I

institute: Peking University People's Hospital

summary:
Background & Aims: Combined HCC-iCCA is a rare liver tumor type and is often not well separated from HCC and iCCA. In this study, we analyzed major differences between combined HCC-iCCA and iCCA.  Methods: We first characterized major differences between combined HCC-iCCA and iCCA by GSEA analysis. Consequently, we used CCl4 to induce chronic liver disease and subsequent liver carcinoma formation in mice. We forced the formation of combined HCC-iCCA through liver specific deletion of Rbpj, a key component of the Notch signaling pathway, in a Trp53 deficient background. Notch and p53 signaling pathways are involved in cellular differentiation processes and belong to the most affected pathways in liver carcinogenesis.  Results: We show that combined HCC-iCCA can be separated from iCCA through differences in development related pathways, metabolism, cell to cell interaction and immune related pathways in human patients and in mice. Dysregulation of Notch signaling through a hepatocyte-specific Rbpj knockout resulted in an increased tumor burden and a high frequency of combined HCC-iCCA formation. In addition, hepatocytic loss of Rbpj forced M2 macrophage polarization and a tumor promoting environment.  Conclusions: Dysregulation of Notch signaling is involved in tumor differentiation. Loss of Rbpj triggers the formation of combined HCC-iCCA which is associated by a pro-tumorigenic environment.
Our study highlights the importance of dysfunctional Notch signalling through Rbpj deletion in hepatocytes. Rbpj loss affects tumor differentiation and the tumor microenvironment which can be linked to a combined HCC-iCCA phenotype seen in human patients.

overall_design: Total RNA was isolated from murine whole tumor tissue, and the quality was analyzed by a bioanalyzer. Agilent Mouse Gene Expression Microarrays 8x60K were used.

first: Umesh

last: Tharehalli

first: André

last: Lechel


title: Identification of Pax7 target genes in muscle stem cells

city: Hiroshima-shi

first: Yasuo

last: Kitajima

state: Hiroshima

address: 1-2-3 Kasumi, Minami-ku

department: Graduate School of Biomedical and Health Sciences

country: Japan

institute: Hiroshima University

summary: Adult muscle stem cells, also known as muscle satellite cells, which are the resident tissue stem cells of skeletal muscle, provide myonuclei for postnatal muscle growth and for maintenance and regeneration in adults. Satellite cells specifically express the transcription factor pax7. The purpose of this study was to identify pax7 target genes and clarify the role of pax7 in muscle stem cell maintenance. We succeeded in generating Pax7-YFP knockin mice (Pax7-YFP KI) that can visualize endogenous pax7 expressed in satellite cells with YFP fluorescent protein. Novel pax7 target genes were identified by ChIP-sequencing (chromatin immunoprecipitation) analysis with muscle stem cells of Pax7-YFP KI mice.

overall_design: Examination of pax7 target genes in muscle stem cells.

first: Yusuke

last: Ono

first: Kazumitsu

last: Maehara

first: Yasuyuki

last: Ohkawa


title: IDHwt and IDHmut adult-type diffuse gliomas display distinct alterations in ribosome biogenesis and 2’O-methylation of ribosomal RNA

city: Lyon

first: Virginie

last: MARCEL

address: 28 rue Laennec

institute: Cancer Research Center of Lyon

summary: We simultaneously characterized alterations of both ribosome quality and quantity in high grade adult-type diffuse glioma. Unexpectedly, we uncovered that glioblastomas display the most prominent defects in ribosomal RNA chemical modifications (quality) while astrocytomas and oligodendrogliomas rather exhibit changes in ribosome biogenesis (quantity). Moreover, glioma cell lines exhibit distinct responses to clinically evaluated RNA Pol I inhibitors, CX5461 and BMH-21. This study highlights theranostic opportunities provided by the ribosome field to improve the management of glioma patients.

overall_design: ribosomal RNA 2'-O-ribose methylation profile in high grade adult-type glioma

first: Hermes

last: Paraqindes

last: Marcel

first: Sébastien

last: Durand

first: François

last: Ducray


title: Overactivation of ATP citrate lyase–H3K27 acetylation axis leads to maternal diabetes induced neural tube defect [RNA-seq]

first: Baoling

last: Bai

overall_design: To obtain the genetic expression profile in fetuses with neural tube defects caused by maternal diabetes, we collected three sets of brain tissue samples each from E9.5 normal group and NTD-afflicted fetus groups.

first: Huili

last: Li

first: Qin

last: Zhang


title: Single-nucleus transcriptomics and chromatin accessibility analysis of musk gland in Chinese forest musk deer

city: Yangling District，Xianyang City

first: Zhanjun

last: Ren

state: Shaanxi Province

institute: Northwest A&F University

summary: The Chinese forest musk deer (FMD; Moschus berezovskii) is an endangered artiodactyl mammal. Musk secreted by the musk gland of male FMD has extremely high economic and medicinal value. At present, little is known about the development of musk glands and the molecular mechanism of musk secretion. In the present research, using snRNA-seq and snATAC-seq association analysis performed on musk glands of forest musk deer, coupled with several bioinformatics analyses, the dynamic transcriptional cell atlas of musk gland development was revealed and the genes and transcription factors affecting musk secretion were determined. Based on uniform manifold approximation and projection (UMAP) analysis, we identified 12 cell types from musk glands, including two different acinar cells (clusters 0 and 10). In addition, the expression of core target genes and core transcription factors was verified by fluorescence in situ hybridization and immunohistochemistry. Combined with weighted gene co-expression network analysis (WGCNA), we obtained a deeper biological understanding of the relationship between core transcription factors, differentially expressed genes and musk secretion related pathways. This study lays a foundation for improving musk yield and meeting market demand. In the meantime, it also contributes to reducing the hunting and poaching of wild forest musk deer, protecting forest musk deer resources and maintaining ecological balance.

overall_design: Musk gland tissues were collected from young and adult male forest musk deer in the non-musk secretory period and musk secretory period, all of which died of woolball disease.

first: Chenmiao

last: Liu

first: Tingting

last: Hong

first: Tao

last: Xue


title: Direct reprogramming of human fibroblasts to expandable induced dopaminergic neuronal progenitors for Parkinson’s disease therapy [Array]

city: Daejeon

first: Minhyung

last: Lee

address: 125 Gwahak-ro

department: Stem Cell Convergence Research Center

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

summary: Personalized cell therapy is being explored as promising treatments for incurable diseases such as Parkinson’s disease (PD). Here, we directly reprogrammed human fibroblasts into induced dopaminergic neuronal progenitors (hiDPs) and assess their applicability for regenerative PD therapy. We found that hiDPs maintain progenitor characteristics over 20 passages and showed unaltered differentiation potential to midbrain dopaminergic neurons. By next-generation sequencing, we confirm that even long-term cultured hiDPs retain genomic stability, resulting in absence of tumorigenicity when transplanted, indicating preclinical safety. The hiDPs differentiate into highly pure dopaminergic neurons expressing markers associated with positive graft outcomes without unwanted serotonergic neurons known to cause graft-induced dyskinesia. The therapeutic effect and safety were confirmed by transplantation in rodent PD models. Because our optimized reprogramming conditions generate highly expandable hiDPs enabling scaled production of clonal cells and overcoming quality control issues, we propose that our hiDPs can become a preferred autologous therapy for aged and feeble PD patients vulnerable to immunosuppression regimens.

overall_design: Induced dopaminergic neuronal progenitors were directly reprogrammed from young and aged donors. Dopaminergic neuronal progenitors differentiated from human PSCs were used as reference samples. And Bulk RNA samples at day-0, 8, and 16 reprogramming cells were harvested to tracking changes during hiDP reprogramming.

first: Hwan

last: Choi

first: Jeongmin

last: Ha

first: Hyang-Ae

first: Areum

last: Baek

first: Hyuna

last: Sim

first: Sunhwa

last: Cho

first: Myungshin

last: Kim

first: Ilkyun

last: Im

first: Hyun-Soo

first: Mi-Yoon

last: Chang

first: Jeong

middle: Y

first: Young-Joo

last: Jeon

first: Myung

last: Son

first: Sang-Hun

first: Won-Ho

last: Shin

first: Cho-Rok

last: Jung

first: Ki-Suk

first: Jongpil

first: Mi-Young

first: Janghwan


title: Genome-wide mapping of epigenetic modification of 5-formylcytosine at single-base resolution by chemical labeling enrichment and deamination sequencing

city: 北京

first: li

middle: gao

last: jie

state: Alabama

address: Building 104, Yard 1, Beichen West Road, Chaoyang District, Beijing

institute: Beijing Institute of Genomics, Chinese Academy of Sciences

type: Methylation profiling by high throughput sequencing

summary: DNA cytosine methylation (5-methylcytosine, 5mC) is a predominant epigenetic modification that plays critical roles in a variety of biological and pathological processes in mammals. In active DNA demethylation, the ten-eleven translocation (TET) dioxygenases can sequentially oxidize 5mC to generate three modified forms of cytosine, 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC). Beyond being a demethylation intermediate, recent studies have shown that 5fC has regulatory functions in gene expression and chromatin organization. While some methods have been developed to detect 5fC, genome-wide mapping of 5fC at base resolution are still highly desirable. Herein, we propose a Chemical Labeling Enrichment and Deamination sequencing (CLED-seq) method for detecting 5fC in genomic DNA at single-base resolution. The CLED-seq method utilizes selective labeling and enrichment of 5fC-containing DNA fragments, followed by deamination mediated by A3A and sequencing. In the CLED-seq process, while all C, 5mC, and 5hmC are interpreted as T during sequencing, 5fC is still read as C, enabling the precise detection of 5fC in DNA. Using the proposed CLED-seq method, we accomplished genome-wide mapping of 5fC in mouse embryonic stem cells. The mapping study revealed that promoter regions enriched with 5fC overlapped with H3K4me1, H3K4me3, and H3K27ac marks. These findings suggest a correlation between 5fC marks and active gene expression in mouse embryonic stem cells. In conclusion, CLED-seq is a straightforward, bisulfite-free method that offers a valuable tool for detecting 5fC in genomes at a single-base resolution.

overall_design: In our current study, we have discovered that biotin-labeled 5fC exhibits notable resistance to deamination by A3A. Building on this finding, we propose a novel method, termed Chemical Labeling Enrichment and Deamination sequencing (CLED-seq), for the precise genome-wide mapping of 5fC at the single-base resolution. In the CLED-seq protocol, we employ biotin-ONH2 to selectively label the formyl group of 5fC in fragmented genomic DNA. Subsequently, streptavidin-coated magnetic beads are utilized to enrich the 5fC-containing DNA fragments. Treatment with A3A leads to the deamination of C, 5mC, and 5hmC, resulting in the formation of U, T, and 5hmU, respectively.

first: Bi-Feng

last: Yuan

first: Jiang-Hui

last: Ding

first: Gaojie

last: Li


title: Stat5 antagonizes Tox and CD8 T cell exhaustion to foster a durable effector-like state during chronic antigen exposure

first: E

last: WHERRY

summary:
Constitutive Stat5a activity antagonized Tox and rewired CD8 T cells away from exhaustion to acquire a durable effector/NK-like state with superior anti-tumor potential
Stat5 fostered TEXint, temporally re-engaging   the   Stat5   pathway,   partially   reprogrammed   the   epigenetic   landscape   of exhaustion and restored effector-like differentiation and function cell formation and partial re-acquisition of effector-biology during this TEXprog-to-TEXint transition,

overall_design: A replicate or two of each sample listed were used to compare the H3K27Ac binding occupancy using Cut and Run method along with IgG controls used as reference as listed

first: Jean

last: Beltra

last: Wherry


title: Methylation profile of latent metastatic (Lat-M) cells  from clear cell renal cell carcinoma (ccRCC)

city: DALLAS

first: KANGSAN

last: KIM

address: 5323 Harry Hines Blvd

institute: UT Southwestern Medical Center

summary: Lat-M cells were derived using ccRCC cell line 769-P (Parental, PA) cells to investigate determinants of metatatic latency in ccRCCs. We profiled methylation status of PA and LatM cells to understand epigenetic regulation of metastatic latency

overall_design: Whole genome bisulfite sequencing was performed using 2 PA replicates and 2 Lat-M replicates

first: Kangsan

first: Srinivas

last: Malladi


title: Direct reprogramming of human fibroblasts to expandable induced dopaminergic neuronal progenitors for Parkinson’s disease therapy

first: Minhyung

last: Lee

overall_design: Refer to individual Series


title: Enhancement of anti-tumor immunity by tertiary lymphoid structures in esophageal squamous cell carcinoma

city: Fukuoka

first: Shoichi

last: Nakamura

institute: Kyushu University

summary: Our study showed that TLS enhanced anti-tumor immunity in ESCC.

relation:
Reanalysis of: GSM5928062
Reanalysis of: GSM5928064
Reanalysis of: GSM5928066
Reanalysis of: GSM5928068
Reanalysis of: GSM5928069
Reanalysis of: GSM5928070
Reanalysis of: GSM5928071
Reanalysis of: GSM5928072
Reanalysis of: GSM5928075
Reanalysis of: GSM5928076
Reanalysis of: GSM5928077
Reanalysis of: GSM5928079
Reanalysis of: GSM5928081
Reanalysis of: GSM5928086

overall_design:
We used droplet-based single cell RNA sequencing (scRNA-seq) data of 14 samples, including 10 tumor samples, 4 normal samples.

***14 Samples were re-analyzed from Series GSE197677. The ESCC.integrated.rds processed data includes the re-analyzed 14 Sample data***

data processing step:
The sequence data were quantified and mapped to human reference genome (GRCh38) using the Cell Ranger toolkit by 10x Genomics.
The matrix data were imported using the Seurat R package (version 3.6.3).
To merge the data of all samples, we used the "SCTransform" package for the normalization and variance stabilization of molecular count data.

first: Kenoki

last: Ohuchida


title: Direct reprogramming of human fibroblasts to expandable induced dopaminergic neuronal progenitors for Parkinson’s disease therapy [ChIP-seq]

overall_design: Induced dopaminergic neuronal progenitors were directly reprogrammed from fibroblasts (Fb).  Samples at day-0, 16 of reprogramming cells, and isolated hiDP after reprogramming were harvested to track changes during hiDP reprogramming.

first: Hwan

last: Choi

first: Jeongmin

last: Ha

first: Hyang-Ae

first: Areum

last: Baek

first: Hyuna

last: Sim

first: Sunhwa

last: Cho

first: Myungshin

last: Kim

first: Ilkyun

last: Im

first: Hyun-Soo

first: Mi-Yoon

last: Chang

first: Jeong

first: Young-Joo

first: Myung

first: Sang-Hun

first: Won-Ho

first: Cho-Rok


title: Identification of HIV1-specific cascaded microRNA-mRNA regulatory relationships by parallel mRNA and microRNA expression profiling with AIDS patients after antiviral treatment

city: Shanghai

first: Xiaoqiang

last: Chai

state: Shanghai

address: No.130 Dongan Road

department: Institutes of Biomedical Sciences

institute: Fudan University

type:
Expression profiling by array
Non-coding RNA profiling by array

summary: The molecular pathogenesis of infection by HIV (human immunodeficiency virus) is extremely complex and is not clearly defined despite intensive research efforts. MiRNA as a class of regulators in cancer development can affect multiple gene pathways by targeting various mRNAs. Thus, studies aimed at transcription and regulation after antiviral treatment combined with beneficial researches related to miRNAs are required. With the purpose of identifying the cascaded miRNA-mRNA regulatory relationships related to infection of HIV in gene level, the parallel miRNA and mRNA expression profiles were analyzed in our study. The differential expressed miRNAs and mRNAs were selected primarily. The differentially regulated miRNA-mRNA interactions were further identified according to the Pearson correlation analysis of gene expression level. In our study, the calculation of the regulatory impact factors (RIF) was also conducted, and it revealed several essential regulators related to antiviral treatment with AIDS. To give a further insight into these TF (transcription factors) regulators, the co-expression gene modules were identified using a threshold-based hierarchical clustering method. Meanwhile, the regulatory network was generated during the computing process. Understanding these regulatory elements may bear significant implications on understanding the pathogenesis of AIDS occurrence.

overall_design:
The microarray profiles utilized in our study is derived from Chengdu University of TCM in Sichuan, China. All donors as experimental group are confirmed as AIDS clinical patients according to 1994 revised classification system for HIV infection in America using protein western blotting by local epidemic station. The diagnosis standards to patients were referred to the Guidelines for Diagnosis and Treatment of HIV/AIDS in China (2005). The patients were accepted if they conformed to the following criteria: (a) corresponding to the criteria for diagnosis and treatment of HIV/AIDS; (b) ranging in age from 4 to 78 years old; (c) agreeing to sign an informed consent form. In our study, there are fifty AIDS patients and seven healthy persons as control group donated blood samples. Controls were all healthy, HIV-1-negative donors. Whereas, two more representative groups named LVL and HVL were further defined according to the viral load of the patients in order to explore the relationship between virus load and gene expression level after antiviral therapy. The LVL group includes 14 samples from patients while HVL group includes 16 AIDS samples. In addition, a further 36 independent blood samples from 33 AIDS patients and 3 healthy donors were applied to test and verify the accuracy of the differential expression results. The clinical characteristics of the three groups (CON, LVL and HVL) were assumed in Table 6. The majority of HIV-positive carriers being treated with ART (antiretroviral therapy) as in-patients got improvements of the AIDS disease in our research.
mRNA and miRNA profiling of three groups: CON (n=7), LVL (n=14), HVL (n=16).

first: Quansheng

last: Feng

first: Xiao

last: Li


title: Compatibility of Calycosin-Tanshinone IIA improves Ang II-induced renal artery endothelial cell dysfunction through lncRNA-mRNA coexpression network

status: Public on Aug 30 2023

city: 济南市

first: 燕云

last: 江

state: 山东省

address: 山东省济南市长清区

institute: 山东中医药大学

summary: In the present investigation, an experimental model of endothelial cell injury was established by subjecting RRAECs to Ang II (5×10-7mol/L) for a duration of 24 h. Subsequently, this model was treated with a combination of Calycosin (3mg/L) and Tanshinone II (3mg/L). The changes in total ATP levels and autophagy function in RRAECs were evaluated using the ATP assay and dansylcadaverine (MDC) staining, respectively. Annexin V-FITC/PI staining and transwell assay were utilized to quantify the apoptosis rate and migration function of RRAECs. Moreover, the utilization of RNA-sequencing technology facilitated the identification of differentially expressed (DE) lncRNAs and mRNAs between various groups. Subsequently, a coexpression network between DE lncRNAs and mRNAs was constructed, followed by the implementation of GO and KEGG pathway enrichment analyses to elucidate the functional implications of the DE mRNAs interacting with lncRNAs within this network.

overall_design: Full transcriptome sequencing of 1 cell type

first: Liu

last: Yao

first: JiangYan

last: Yun


title: Targeting cancers with EGFR exon 20 insertion mutations by exploiting a dependency on parallel SRC signalling

city: London

first: Simon

last: Vyse

state: United Kingdom

address: 237 Fulham Rd

department: Molecular Pathology

institute: Institute of Cancer Research

summary: We performed RNAseq to compare differential gene expression between CUTO17, a human non-small cell lung cancer cell line which harbours an EGFR exon 20 insertion mutation, with CUTO17PozR, a cell line dervied from CUTO17 cells with acquired drug resistance to the EGFR inhibitor poziotinib through long-term drug exposure.

overall_design: Differential gene expression analysis between CUTO17 and CUTO17PozR cells

first: Paul

last: Huang


title: Gene expression in nucleus accumbens tissue of Foxp2 heterozygous mice (S321X/+) and wild-type littermates (WT) following single cocaine or saline injection

city: Paris

first: Matthias

last: Groszer

address: 17, rue du Fer à Moulin

department: Developmental Neuroscience

institute: INSERM U839

summary:
Foxp2 heterozygous mice and wildtype mice were injected with cocaine or saline, 1h post-injection nucleus acumbens RNA was extracted and analysed
We have tested a potential role for the transcription factor Foxp2 in dopamine signaling and reward associated synaptic plasticity and behavior. We found that Foxp2 is acutely downregulated in reward associated circuits in the nucleus accumbens following a single injection of cocaine. In Foxp2 heterozygous mutant mice, loss of transcriptional suppression by Foxp2 causes an increased constitutive expression of dopamine signaling related genes which corresponds with impairments in synaptic plasticity and reward associated behaviors.

overall_design: Nucleus accumbens tissue was extracted 1 hour after injection (i.p.)  of either saline or cocaine (15mg/kg). mRNA microarrays (Illumina MouseWG-6 v2) were used to analyzed gene expression in biological replicates (6 for WT cocain, 6 for WT saline, 5 for HET (S321X/+) saline, 6 for HET (S321X/+) cocain).

first: Cedric

last: Mombereau

first: Tanay

last: Ghosh


title: The Microbiome, Epigenome, and Diet in Adults with Obesity During Behavioral Weight Loss

city: Aurora

first: Sarah

middle: J.

last: Borengasser

state: Colorado

address: 12631 E. 17th Ave, Mailstop F-561

department: Pediatrics

institute: University of Colorado - Anschutz Medical Campus

summary: Whole blood, stool samples, and questionnaire data were collected from participants in the DRIFT2 trial at baseline and at a 3 month follow-up visit to analyze relationships between DNA methylation, gut microbes, and diet data. 128 total whole blood samples were collected .

overall_design: Bisulfite converted DNA from 128 samples were hybridised to the Illumina InfiniumEPIC Human Methylation Beadchip

first: Iain

middle: R

last: Konigsberg

first: Emily

last: Hill

first: Victoria

middle: A

last: Catenacci

first: Maggie

last: Stanislawski


title: miRNome Expression Analysis in Canine Diffuse Large B-Cell Lymphoma

city: West Lafayette

first: Nelly

last: Elshafie

state: Indiana

address: 625 Harrison St

institute: Purdue University

summary:
Introduction: Lymphoma is a common canine cancer with translational relevance to human disease. Diffuse large B-cell lymphoma (DLBCL) is the most frequent subtype, contributing to almost fifty percent of clinically recognized lymphoma cases. Identifying new biomarkers capable of early diagnosis and monitoring DLBCL is crucial for enhancing remission rates. This research seeks to advance our knowledge of the molecular biology of DLBCL by analyzing the expression of microRNAs, which regulate gene expression by negatively impacting gene expression via targeted RNA degradation or translational re-pression. The stability and accessibility of microRNAs make them appropriate biomarkers for the diagnosis, prognosis, and monitoring of diseases.
Methods: We extracted and sequenced microRNAs from ten fresh-frozen lymph node tissue samples (six DLBCL and four non-neoplastic). Results: Small RNA sequencing data analysis revealed 35 differently expressed miRNAs (DEMs) compared to controls. RT-qPCR confirmed that 23/35 DEMs in DLBCL were significantly upregulated (n = 14) or downregulated (n = 9). Statistical significance was determined by comparing each miRNA's average expression fold-change (2-Cq) between the DLCBL and healthy groups by applying the unpaired parametric Welch's 2-sample t-test and false discovery rate (FDR). The predicted target genes of the DEMs were mainly enriched in the PI3K-Akt-MAPK pathway. Discussion: Our data point to the potential value of miRNA signatures as diagnostic biomarkers and serve as a guideline for subsequent experimental studies to determine the targets and functions of these altered miRNAs in canine DLBCL.

overall_design: To  investigates the differentially expressed miRNAs in canine DLBCL using fresh frozen lymph node samples from six DLBCL dog patients and four normal healthy dogs  using small RNA sequencing data.

first: Ekramy

middle: E

last: Sayedahmed

first: Michael

last: Gribskov

first: Nathanael

middle: I

last: Lichti

first: Andrea

last: dos Santos

middle: O

last: Childress


title: ChIP-seq for histone H1.2 in A549

city: WuHan

first: Dong

last: Yang

address: No.5  HangKong Road

institute: Huazhong University of Science and Technology

summary: Our study represents the detailed analysis of whole-genome DNA-binding sites of linker histone variant H1.2 in human lung cancer cell line A549, with biologic replicates, generated by ChIP-seq technology

overall_design: DNA samples for histone H1.2 ChIP were  extracted from A549 cells. Two biological replicates of immunoprecipitated DNA samples were sent for sequencing.

first: Yuchen

last: Chen

first: Yangmian

last: Yuan

first: Ling

last: Zheng

first: Kun


title: Ezh2, Utx and Jmjd3 deletion on the H3k27me3 level in mouse chondrocytes

city: Xi'an

first: Feng

last: Zhang

address: Changle west Road

department: Department of Pathology

institute: Fourth Military Medical University

summary: The level of H3K27me3 were examined by conditional knockout Ezh2, Utx or Jmjd3 in mouse chondrocyte

overall_design: To compare with the level of H3K27me3 in wild type and Ezh2, Utx or Jmjd3 deleted mouse chondrocytes


title: Sex-Dependent Obesity Reduction from PPARa Activation by PDE9 Inhibition

city: Baltimore

first: Sumita

last: Mishra

state: MD

address: 720 Rutland Avenue

institute: Johns Hopkins University

summary: The ongoing pandemics of obesity and hypertension have increasingly impacted an aging population with heart disease creating a prevalent cardiometabolic syndrome (CMS). This affects many post-menopausal women and men and manifests by multi-organ adiposity, insulin desensitization and diabetes, impaired fat metabolism, and heart failure symptoms. Effective therapy countering these multiple defects remains lacking. Natriuretic peptides (NP) synthesized by the heart both protect against cardiac disease and reduce obesity by stimulating lipolysis, improving insulin signaling, and lowering appetite. However, their clinical translation remains stymied by blood pressure reduction and complex in vivo peptide pharmacology. Phosphodiesterase type 9 is expressed in myocardium and fat of mammals including humans and controls NP-coupled cyclic GMP hydrolysis. Its inhibition (PDE9-I) protects hearts against pressure-induced stress without changing blood pressure, though its impact on fat remains unknown. Here we show PDE9-I potently improves high-fat diet-induced severe obesity in mice with cardiometabolic syndrome without altering food intake or activity, but this only occurs in males and ovariectomized females. PDE9 localizes with mitochondria and its inhibition stimulates mitochondrial respiration, uncoupling, and fat oxidation in heart and adipose tissue to reduce abdominal and liver fat by activating peroxisome proliferator-activator receptor a (PPARa) signaling. ChIP-seq reveals that the sexual dimorphism relates to reduced PPARa DNA binding in genes regulating fatty acid metabolism due to estrogen-receptor activation. Human translation is revealed in obese patients with heart failure and preserved ejection fraction (HFpEF), in whom PDE9A and PPARA gene expression inversely correlate, and PPARA and fat metabolism regulated genes are reduced. This potent PDE9-PPARa regulated pathway has implications for treating obese post-menopausal females and males with cardiometabolic syndrome.  HFpEF accounts for half of all heart failure and is now commonly associated with class II (BMI>35 kg/m2) or greater obesity and CMS. The obesity is particularly hard to treat in these patients given that exercise capacity is quite limited, diet is rarely impactful at such weight, and surgical therapy poses greater risks. Despite having heart disease, NP levels are often low as hearts are less dilated and there is greater peripheral clearance with obesity. Loss of estrogen after menopause increases female risks for cardiovascular disease and stimulates visceral adiposity. Ovariectomy (OVX) mimics these changes, and when combined with a high-fat diet, exacerbates adiposity and adverse consequences of ischemic and hypertensive stress. These are reversed by exogenous estrogen but not therapies that require intact nitric oxide signaling, revealing an important role of estrogen-NO pathways. Estrogen treatment is largely abandoned due to adverse effects in humans. However, PDE9-I elevates cGMP-signaling by the NP pathway independent of NO-stimulation. We hypothesized that PDE9-I retains cardiac benefits in OVX female hearts subjected to pressure-induced stress and may also stimulate fat loss to improve CMS in concomitant diet induced obesity.

overall_design: We performed ChipSeq for PPARa DNA binding elements in HepG2 cells transfected with PPARa and stimulated with a selective PPARa agonist and contrasted the results to cells co-transfected with Era (Estrogen receptor alpha) or ERb (Estrogen receptor beta) and treated with corresponding selective agonists.


title: Pelvic floor muscle response after simulated birth injury and mechanisms of a skeletal muscle-derived ECM hydrogel (SKM)

city: La Jolla

first: Pamela

last: Duran

address: 2880 Torrey Pines Scenic Dr

institute: University of California, San Diego

summary: Time course of pelvic floor muscles response was investigated, together with the efficacy of an ECM hydrogel therapy.

overall_design: A custom codeset panel to investigate pathways known to regulate appendicular muscles’ response to injury: immune response, myogenesis, muscle anabolism and catabolism, ECM remodeling, neovascularization, and neuromuscular junction development and maturation

first: P

first: K

last: Christman

first: M

last: Alperin


title: Transcriptome profile of post-mortem ear and lung fibroblasts

city: Cleveland

first: Daniel

last: McGrail

state: Ohio

address: 9500 Euclid Avenue

department: Center for Immunotherapy and Precision Immuno-Oncology

institute: Cleveland Clinic

summary: Mouse ear and lung fibroblasts isolated from fresh tissue (0 hour) or 12 hour post-mortem tissue

overall_design: 2 samples for 0 hour and 12 hour lung fibroblasts, 3 samples for 0 hour and 12 hour ear fibroblasts

middle: J

first: Kathleen

middle: M

last: McAndrews

first: Raghu

last: Kalluri


title: Gene expression profiling of pancreatic cancer

city: Seoul

first: Sung Won

last: Kwon

address: 1 Gwanak-ro

department: Department of Pharmacy

institute: College of Pharmacy, Seoul National University

summary: We report the gene expression profiling of six paired samples (cancer and adjacent controls) in a Korean cohort.

overall_design: mRNA was extracted from the formalin-fixed paraffin-embedded tissues and profiled using Illumina HiSeq2500.

first: Soon-Sun

last: Hong


title: Influence of Vitamin D on Genome-Wide Expression in Natural Killer Cells

city: Homburg/Saar

first: Konstantinos

last: Christofyllakis

state: Saarland

address: Kirrbergerstrasse 100

department: Hematology Oncology Rheumatology and clinical Immunology

institute: Department of Oncology, Hematology, Rheumatology and Clinical Immunology, Saarland University Hospital

summary:
Vitamin D deficiency has been associated with decreased overall survival in patients with diffuse large B-cell lymphoma treated with rituximab. Natural killer cell-mediated antibody-dependent cytotoxicity is one of the main mechanisms of action of rituximab, and it has been shown to be enhanced after in vivo vitamin D supplementation.
We aimed to explore molecular mechanisms behind these findings using whole transcriptome analysis of natural killer cells after vitamin D supplementation

overall_design: Natural killer cells were isolated by magnetic depletion from eight otherwise healthy subjects with vitamin D deficiency before and after in vivo vitamin D supplementation. NK cell total RNA was extracted followed by whole transcriptome microarray analysis.

first: Frank

last: Neumann


title: The effect of plastic-related compounds on transcriptome-wide gene expression on CYP2C19-overexpressing HepG2 cells

city: Mainz

first: Federico

last: Marini

address: Obere Zahlbacher Strasse 69

department: Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI)

institute: University Medical Center - Mainz

summary: In recent years, plastic and especially microplastic in the oceans have caused huge problems to marine flora and fauna. Recently, such particles have also been detected in blood, breast milk, and placenta, underlining their ability to enter the human body presumably by the food chain and other yet unknown mechanisms. In addition, plastic contains plasticizers, antioxidants or lubricants, whose impact on human health is also under investigation. At the cellular level, the most important enzymes involved in the metabolism of xenobiotic compounds are the cytochrome P450 monooxygenases (CYPs). Despite their extensive characterization in the maintenance of cellular balance, their interaction with plastic and related products is elusive. In this study, the possible interactions between several plastic-related compounds and one of the most important cytochromes, CYP2C19, were analyzed. By applying virtual compound screening and molecular docking to more than 1000 commercially available plastic-related compounds, we identified candidates which are likely to interact with this protein. A growth inhibition assay confirmed their cytotoxic activity on a CYP2C19-transfected hepatic cell line. Subsequently, we studied the effect of selected compounds on the transcriptome-wide gene expression level by RNA-sequencing. Three candidate molecules, (i.e., 2,2'-methylene bis(6-tert-butyl-4-methylphenol; 1,1-bis(3,5-di-tert-butyl-2-hydroxyphenyl) ethane; 2,2'-methylene bis(6-cyclohexyl-4-methylphenol), which bound with high affinity to CYP2C19 in silico, exerted profound cytotoxicity in vitro, and interacted with several metabolic pathways of which the ‘cholesterol biosynthesis process’ was most affected. In addition, other affected pathways involving mitosis, DNA replication and inflammation have been identified, suggesting an increase of hepatotoxicity. These discoveries suggest that plastic-related compounds can damage the liver through their influence on several pathways.

overall_design: To examine whether plastic-related compounds may have a toxic effect on liver cells overexpressing cytochrome 2C19

first: Matteo

last: Rosellini

first: Alicia

last: Schulze

first: Ejlal

last: Omer

first: Jan-Heiner

last: Küpper

first: Thomas

last: Efferth


title: CUT & RUN analysis of H3K4me2 mark upon LSD1 inhibition

city: Ann Arbor

first: Karan

last: Bedi

state: MI

address: 1600 Huron Pkwy

department: Biostatistics

institute: University of Michigan

summary: Lysine-specific demethylase 1 (LSD1) is a histone demethylase that promotes stemness and cancer cell survival, including in prostate cancer. LSD1 has been shown to perfrom catalytic independent function sto promote prostate cancer survival. Here, we tested the levels of LSD1's canonical target H3K4me2 upon LSD1 inhibition with SP2509 across the genome using CUT and RUN analysis.

overall_design: LNCaP-N-Myc cells were treated with allsoteric LSD1 inhibitor SP2509 or vehicle (DMSO) in duplicates.

first: Anbarasu

last: Kumaraswamy

first: Zhi

last: Duan

first: Weisheng

last: Wu

first: Raymond

last: Cavalcante

first: Joel

last: Yates

first: Joshi

last: Alumkal


title: Atypical modes of CTCF binding facilitate tissue-specific and neuronal activity-dependent gene expression states.

city: Dalals

first: Morgan

last: Crewe

state: TX

address: 2201 Inwood Road

department: Psychiatry

institute: University of Texas Southwestern Medical Center

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

overall_design: Refer to individual Series


title: Atypical modes of CTCF binding facilitate tissue-specific and neuronal activity-dependent gene expression states [SMC1_ChIP-seq]

summary: The multivalent binding of CTCF to a variety of DNA sequences is thought to underlie its ability to mediate a large repertoire of cellular functions. CTCF is a 11 zinc-finger (ZF) protein that is anchored to a majority of its target sites via binding to a 20 base-pair core DNA sequence. Yet the diversity of CTCF binding sites (CBS) has not fully been characterized. Here we assessed CTCF occupancy in cultured mouse cortical neurons as a function of neuronal activity and observed that ~ 22 % of CBS lack the consensus CTCF motif. We report that sequence diversity at most of these atypical CBS is not random but involves degeneracy at specific nucleotide positions within the core CTCF position weight matrix (PWM) that likely affect the binding of ZFs 6 and 7. Surprisingly, degeneracy at the same nucleotides not only define most atypical CBS, but also CBS within most gene promoters, and CBS that are dynamically altered following neuronal stimulation, revealing how atypical CTCF binding could affect gene activity. Dynamic CBS across neural differentiation and neuronal stimulation are found both within and outside loop anchors and TADs, indicating that dynamic CBS could regulate gene activity independently of loop anchoring. Finally, we identified a second mode of atypical CTCF binding that defines most tissue-specific CBS. Unlike other atypical CBS, tissue-specific CBS largely bind sequences unrelated to the core CTCF motif and are enriched within the bodies of tissue-specific genes. Overall, these results indicate how CTCF binding at atypical CBS could allow it to dynamically regulate gene activity patterns during differentiation, development, and in response to environmental cues.

overall_design: SMC1 ChIP-seq in mouse cortical neruons

first: Amir

last: Segev

first: Richard

last: Rueda

first: Ram

last: Madabhushi


title: Atypical modes of CTCF binding facilitate tissue-specific and neuronal activity-dependent gene expression states [CTCF_ChIP-seq]

overall_design: CTCF ChIP-seq in mouse cortical neruons


title: Extracellular vesicles in young serum contribute to restoration of age-related brain transcriptomes and cognition in old mice

city: Pittsburgh

first: Iliya

last: Lefterov

address: 130 De Soto St

department: Environmental and Occupational Health

institute: University of Pittsburgh

summary: We have demonstrated that the circulating extracellular vesicles (EVs) are essential to the beneficial effect of young serum on the skeletal muscle regenerative cascade. Here, we show that infusions of young serum significantly improved age-associated memory deficits, and the effect was abolished after serum depletion of EVs. RNA-seq analysis of the choroid plexus demonstrated EV-mediated effects on genes involved in barrier function and trans-barrier transport. Comparing the differentially expressed genes to the recently published chronological aging clocks revealed a reversal of transcriptomic aging in the choroid plexus. The hippocampal transcriptome demonstrated a significant upregulation of the anti-aging gene Klotho following young serum treatment and an abrogated effect after EV depletion. Subsequent transcriptomic profiling of Klotho knockout and heterozygous mice showed downregulation of genes associated with transport, exocytosis, and lipid transport, while upregulated genes were associated with activated microglia. The results of our study indicate the significance of EVs as vehicles to deliver signals from the periphery to brain and the importance of Klotho in maintaining brain homeostasis.

overall_design: We performed RNA-seq on 1) dissected choroid plexus and hippocampus isoalted from aged mice infused with young serum; 2) 2-month-old α-Klotho knockout (Klko) and WT mice; 3) 9-month-old Klotho heterozygous (Klhet) and WT mice.

first: Nicholas

middle: F

last: Fitz

first: Amrita

last: Sahu

first: Yi

last: Lu

first: Fabrisia

last: Ambrosio

first: Radosveta

last: Koldamova


title: Differential ncRNAs of oxaliplatin-resistant versus parental HCT116 cells

city: Jinan

first: Xin

last: Zhang

state: Shandong

address: 107 Wenhua Xi Road

institute: Qilu Hospital, Shandong University

summary: Oxaliplatin resistance frequently leads to therapeutic failure in colorectal cancer (CRC). Increasing evidence has shown that noncoding RNAs (ncRNAs) play pivotal roles in chemoresistance of CRC. However, the roles and mechanisms of ncRNAs in oxaliplatin resistance are not well understood. In this study, to identify the ncRNAs induced by oxaliplatin, we profile the expression of ncRNAs in oxaliplatin-resistant HCT116 CRC cells (HCT116oxR) and parental HCT116 cells using next-generation sequencing technology.

overall_design: CRC cell line HCT116 was purchased from ATCC and cultured as recommended. HCT116 cells were exposed to an initial oxaliplatin concentration of 0.1 μmol/L in RPMI (Roswell Park Memorial Institute) 1640 (Thermo Fisher Scientific, Wilmington, DE, USA) containing 10% FBS (fetal bovine serum) , 100 U/ml penicillin, and 100 g/ml streptomycin. The surviving population of cells was grown to ~80% confluence and passaged twice to ensure viability. The concentration of oxaliplatin that the surviving population was exposed to was then sequentially increased to 0.5 μmol/L, 1.0 μmol/L, 2 μmol/L and finally to the concentration of 5 μmol/L for 1 year. PARALLEL study design with 6 samples, HCT116oxR versus parental HCT116 cell line biological replicates: 3 parental controls, 3 drug resistant, independently grown and harvested. Transcriptome sequencing was performed by next-generation sequencing technology.


title: Expression of expanded GGC repeats within NOTCH2NLC causes cardiac dysfunction in mouse models

city: Changsha

first: Yongcheng

last: Pan

state: Hunan

address: 87 Xiangya Rd

institute: Key Laboratory of Hunan Province in Neurodegenerative Disorders, Xiangya Hospital, Central South University

summary: Background: Neuronal intranuclear inclusion disease (NIID) is a rare neurodegenerative disorder characterized by widespread intranuclear inclusions in the nervous system as well as multiple visceral organs. In 2019, expanded GGC repeats within the 5’ untranslated region of the NOTCH2NLC gene was identified as the causative factor. Although NIID primarily affects the central and peripheral nervous systems, growing evidence suggests potential cardiac abnormalities in NIID. However, the link between expanded GGC repeats within NOTCH2NLC and cardiac dysfunction remains uncertain. Results: In this study, we utilized two transgenic mouse models, expressing NOTCH2NLC-(GGC)98 ubiquitously or specifically in cardiomyocytes, and identified p62-positive intranuclear NOTCH2NLC-polyG inclusions in cardiomyocytes in two mouse models. We observed that both models exhibited cardiac-related pathological and echocardiographic changes, albeit exhibiting varying degrees of severity. Transcriptomic analysis revealed shared downregulation of genes related to ion channels and mitochondria in both models, with the cardiomyocyte-specific mice showing a more pronounced downregulation of mitochondria and energy metabolism-related pathways. Further investigations revealed decreased expression of mitochondria-related genes and electron transport chain activity. At last, we conducted a retrospective review of cardiac-related examination results from NIID patients at our hospital and also identified some cardiac abnormalities in NIID patients.  Conclusions: Our study provided the first in vivo evidence linking GGC repeat expansions within NOTCH2NLC to cardiac abnormalities and highlighted the contribution of mitochondrial dysfunction in the development of cardiac abnormalities.

overall_design: To explore the underlying mechanisms leading to cardiac dysfunction upon the expression of NOTCH2NLC-(GGC)98 in cardiomyocytes, we performed RNA-seq analysis on heart tissues from the E2a-tg (ubiquitously expressed) mice at P30 (postnatal 30 days) and Myh6-tg (specifically expressed in cardiomyocytes after tamoxifen injection) mice at P90 (postnatal 90 days, 30 days after the first tamoxifen injection), along with age-matched control mice.

first: Qiong

last: Liu


title: Ancistrocladinium A modulates RNA splicing, cellular stress response and induces cell death in proteasome inhibi-tor-resistant multiple myeloma cells: A promising therapeutic agent candidate

city: Wuerzburg

first: Daniela

last: Bruennert

state: Bavaria

address: Josef-Schneider-Str. 4

department: Gynecology

institute: University Hospital Wuerzburg

summary:
Analysis of gene expression alterations and RNA splicing events after Ancistrocladinium A treatment of INA-6 multiple myeloma cell line
Ancistrocladinium A inan N,C-coupled naphthylisoquinoline alkaloid was analyzed for its ability to act as efficient anti-myeloma agent. The mode of action was unknown. We analyzed the effect of Ancistrocladinium A on the multiple myeloma cell line INA-6 on RNA level and identivied differentially regulated genes on the one hand and splicing events on the other hand gaining a first insight into the mode of action of Ancistrocladinium A.

overall_design: INA-6 cells were treated with PBS as solvent control or 3 µM Ancistrocladinium A followed by RNA extration and analysis using the Clariom D human array. Experiment was performed in quadruplicates. Analysis to determine differences between  PBS treated cells and Ancistrocladinium A treated cells was perfomed using the Transcriptome Analysis Console Software 4.0 (TAC4.0, Affymetrix).

last: Brünnert

first: Raina

last: Seupel

first: Pankaj

last: Goyal

first: Matthias

last: Bach

first: Heike

last: Schraud

first: Stefanie

last: Kirner

first: Eva

last: Köster

first: Doris

last: Feineis

first: Ralf

last: Bargou

first: Andreas

last: Schlosser

first: Gerhard

last: Bringmann

first: Manik

last: Chatterjee


title: Differentially expressed genes after transfection of miR-217 mimics in breast cancer cell line

city: zhengzhou

first: chenxi

last: ju

address: zhengzhou university, 100 science road

institute: zhengzhou university

summary: We report transcriptomic changes in human breast cancer cell lines after transfection of negative control mimic and hsa-miR-217 mimic.

overall_design: To investigate the function of miR-217 in breast cancer, RNA-seq was performed to compare the mRNA expression level between miR-217 mimics and mimics negative control-treated  MDA-MB-231.

first: Chenxi

last: Ju

first: Mingxia

last: Zhou

first: Dan

last: Du

first: Chang

last: Wang

first: Jieqiong

last: Yao

first: Hongle

last: Li

first: Fucheng

last: He

first: Jing


title: Gene expression in the liver and lungs of healthy, SIV-infected and ART-treated rhesus macaques

city: Québec

first: Jérôme

last: Estaquier

state: Québec

address: 2705 Boulevard Laurier

institute: Centre de Recherche du CHU de Québec-Université Laval

summary: Herein, we used rhesus macaques (RMs) infected with SIVmac251 to analyze the transcriptomic profiles of the liver and lungs of untreated and early antiretroviral therapy (ART)-treated RMs, compared to healthy uninfected RMs.

overall_design: RNA sequencing was performed in total liver and lung cells from healthy uninfected (n=3), high viremic SIVmac251-infected (n=4), low viremic SIVmac51-infected (n=4) and ART-treated (n=3) rhesus macaques using NovaSeq 6000 flowcell S1 at the Next-Generation Sequencing Platform, Genomics Center (CHU de Québec-Université Laval Research Center, Québec City, Canada).

first: Julien

last: Clain

first: Charles

last: Beauparlant

first: Arnaud

last: Droit


title: Transcriptome analysis reveals key genes and pathways that the ligand AA-14 acts on pituitary

city: jinan

first: Jun-Yan

state: Select one...

address: No. 44, West Culture Road, Lixia District, Jinan City, Shandong Province

institute: shandong university

summary: Our research is helpful to understand the physiological and pathological level changes caused by the ligand AA-14 acting on the receptor GPR101 on pituitary, to find the mechanism of the signaling pathway downstream of GPR101 under the action of the ligand, and to determine which signaling pathway is mediated by GPR101

overall_design: In this study, Cga-ctrlAAVGpr101fl/fl and Cga-creAAVGpr101fl/fl mice were treated with control vehicle or AA14 for one week before their pituitary tissues were collected. The pituitary was dispersed into single cells, then washed and subjected to flow cytometry analysis. The 2 control vehicle groups and the 2 ligand stimulation groups (3 samples each) were subjected to RNA sequencing.

first: J

last: Sun

first: Z

last: Yang


title: Mechanism of Thiotert in C6 cells

city: Hangzhou

first: Jianhong

last: Dong

state: 浙江

address: School of Pharmacy, Hangzhou Normal University

institute: Hangzhou Normal University

summary: Thiotert can induce the changes of gene expression in C6 cells

overall_design: The cells were treated with 15 μM Thiotert in the experimental group and compared with the control group.


title: CRISPR/dCas9 DNA methylation editing is heritable during human hematopoiesis and shapes immune progeny [RNA-seq]

city: London

first: Gabriella

last: Ficz

state: Rest of the World

address: Centre for Haemato-Oncology

institute: Barts Cancer Institute, Queen Mary University of London

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

overall_design: RNA-seq experiment monocytes and granulocytes harvested from engrafted mice. We sequenced 20 samples in total (5 controls and 5 p15 edited for both cell types; 1 control sample for granulocytes failed during low input Smart-seq2 preparation), therefore we have 19 samples in total. Monocytes and granulocytes harvested from mouse bone marrow were prepared for RNA-seq using a low input Smart-seq2 protocol (library preparation and sequencing by Novogene).

first: Emily

last: Saunderson


title: RNA-seq for gata1+ cells in add1 mutant zebrafish embryos and siblings at 22 hpf

city: Beijing

first: Shuyan

address: 2# Yabao Road

institute: Children's Hospital of Capital Institute of Pediatrics

summary: Adducin 1 (Add1) functions primarily as a membrane cytoskeletal protein, whereas Add1 contains a bipartite nuclear localization signal, implying its special nuclear function. However, the nuclear functional roles of Add1 apart from maintaining cytoskeletal stability remain unknown. Here, we created add1-deficient zebrafish using Tol2 transposon-mediated gene trapping and evaluated how add1 deficiency affected early hematopoiesis development. When add1 is lacking in zebrafish, both the primitive erythropoiesis and definitive hematopoiesis are compromised, and the primitive erythroblast cells are unable to develop into healthy erythrocytes. More significantly, the RNA sequencing results demonstrated that the p53 pathway is activated in the add1-depletion erythroblast cells, causing the erythroblasts to undergo apoptosis at the 14-somites stage and 24 hpf.  Additionally, the anemic phenotype and apoptosis in add1-deficient embryos can be partially rescued by p53 insufficiency. Taken together, our findings show that add1 is critical for zebrafish erythropoiesis partially through the p53-mediated apoptotic pathway, which expands the regulatory role of Add1 for nuclear function.

overall_design: To better understand the nuclear-specific function of add1, we used RNA-seq to analyze transcriptome changes in gata1-EGFP positive cells sorted from add1-deficient embryos and siblings at 22 hpf, when the differences in the number of erythrocytes were not yet evident in add1 mutant embryos. Comparative gene expression profiling analysis of RNA-seq data for erythroblast of add1 mutant and siblings.

first: Shaoguang

first: Quan


title: Differential expression analysis from autologous pair of epithelial and fibroblast cells established from oral tongue squamous cell carcinoma patients

city: Bangalore

first: Nehanjali

last: Dwivedi

state: Karnataka

address: MSCTR, 8th floor A block

country: India

institute: MSCTR

summary: In order to obtain differetially expressed genes between epithelial and fibrroblast cells, we established two autologous pair cell lines (MhCT12-F/E and MhCT08-F/E, where F - Fibroblast and E - Epithelial) from two non-habitual females diagnosed with squamous cell carcinoma of the tongue. After detailed characterization (PMID 35796014) of the cell lines, they were subjected to RNA-sequencing and the data was analysed further.

overall_design: Differential gene expression profiling analysis from RNA-seq data of autologous pair epithelial and fibroblast cells from a patient diagnosed with tongue squamous cell carcinoma.

first: Manjula

last: Das

first: Sujan

middle: K

last: Dhar


title: Dynamic transcriptome response of M. smegmatis to cold stress

city: Moscow

first: Artem

last: Grigorov

address: Ulitsa Miklukho-Maklaya, 16/10

department: Genomics and Postgenomic Technologies

country: Russia

institute: Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry

summary: The study was conducted to identify transcriptome changes in M. smegmatis during adaptation to low temperatures.

overall_design: The cell culture in triplicate was grown up to mid-log growth stage at 37 °C and then subjected to cold stress (15 °C). At time zero (before stress), and at 2, 5 and 24 hours, cell culture samples were taken, total and size-specific RNA was isolated and sequenced.

first: Tatyana

last: Azhikina


title: Effect of Misexpression of Sox9 on Gastric Differentiation

city: St. Louis

first: Spencer

middle: G.

last: Willet

state: MO

address: 660 S. Euclid Avenue, Campus Box 8103

department: Department of Developmental Biology

institute: Washington University in St. Louis

summary:
To determine if Sox9 was sufficient to drive mucous differentiation in the gastric epithelium, we bred mice carrying alleles for ROSA26rtTA.IRES.EGFP, TetO-Sox9, and Fgf20Cre.GFP. In these mice, cells expressing Cre will induce rtTA from the ROSA26rtTA.IRES.EGFP allele.
To explore transcriptional changes following adult misexpression of Sox9, we isolated RNA from the corpus of Fgf20Cre.GFP/Cre.GFP; ROSA26rtTA.IRES.EGFP/rtTA.IRES.EGFP; TetO-Sox9 pup (misexpression animals)  and ROSA26rtTA.IRES.EGFP/rtTA.IRES.EGFP; TetO-Sox9 pup (control) animals and performed RNA-sequencing.

overall_design: We gave 8-week-old control and miseexpression animals DOX for 2 weeks and isolated total RNA from the corpus.

first: Jason

last: Mills


title: Multi-omics analysis revealing the interplay between gut microbiome and the host following opioid use [ABX-RNA seq]

city: Miami

first: Udhghatri

last: Kolli

state: Fl

address: 1501 Nw 15th street

department: Surgery

institute: University of Miami

summary: To uncover the role of opioid induced dysbiosis in disrupting intestinal homeostasis, we conducted a multi-omics analysis with gut microbial, metabolite and intestinal transcriptomics data

overall_design: We  identified morphine-microbiome mediated changes in host gene expression changes in morphine treated and  microbiome depleted  morphine treatment (ABX_morphine) using RNA sequencing.

first: Richa

last: Jalodia

first: Shamsudheen

last: Moidunny

first: Praveen

last: Kumar Singh

first: Yuguang

last: Ban

first: Junyi

last: Tao

first: Gonzalo

middle: N

last: Cantu

first: Eridania

last: Valdes

first: Sundaram

last: Ramakrishnan

first: Sabita

last: Roy


title: Multi-omics analysis revealing the interplay between gut microbiome and the host following opioid use

overall_design: Refer to individual Series


title: Divergent Proteome Reactivity Influences Arm-Selective Activation of Pharmacological Endoplasmic Reticulum Proteostasis Regulators

city: La Jolla

first: Rockland

middle: Luke

last: Wiseman

state: CA

address: 10550 N Torrey Pines Rd

department: Molecular Medicine

institute: Scripps Research Isntitute

summary: Pharmacological activation of the activating transcription factor 6 (ATF6) arm of the Unfolded Protein Response (UPR) has proven useful for ameliorating proteostasis deficiencies in a variety of etiologically diverse diseases. Previous high-throughput screening efforts identified the small molecule AA147 as a potent and selective ATF6 activating compound that operates through a mechanism involving metabolic activation of its 2-amino- p -cresol substructure affording a quinone methide, which then covalently modifies a subset of ER protein disulfide isomerases (PDIs). Intriguingly, another compound identified in this screen, AA132, also contains a 2-amino- p -cresol moiety; however, this compound showed less transcriptional selectivity, instead globally activating all three arms of the UPR. Here, we show that AA132 activates global UPR signaling through a mechanism analogous to that of AA147, involving metabolic activation and covalent PDI modification. Chemoproteomic-enabled analyses show that AA132 covalently modifies PDIs to a greater extent than AA147. Paradoxically, activated AA132 reacts slower with PDIs, indicating it is less reactive than activated AA147. This suggests that the higher labeling of PDIs observed with activated AA132 can be attributed to its lower reactivity, which allows this activated compound to persist longer in the cellular environment prior to quenching by endogenous nucleophiles. Collectively, these results suggest that AA132 globally activates the UPR through increased engagement of ER PDIs. Consistent with this, reducing the cellular concentration of AA132 decreases PDI modifications and allows for selective ATF6 activation. Our results highlight the relationship between metabolically activatable-electrophile stability, ER proteome reactivity, and the transcriptional response observed with the enaminone chemotype of ER proteostasis regulators, enabling continued development of next-generation ATF6 activating compounds.

overall_design: HEK293T cells in 10cm plates were treated for 6 h with indicted treatment

first: Gabriel

last: Kline

first: Ryan

last: Paxman

first: Chung-Yon

last: Lin

first: Nicole

last: Madrazo

first: Julia

last: Grandjean

first: Kyunga

last: Lee

first: Karina

last: Nugroho

first: Evan

middle: T

last: Powers

first: R

middle: L

first: Jeffery

middle: W

last: Kelly


title: CIPN Nerve Biopsy RNA-Seq

city: Rochester

first: Surendra

last: Dasari

state: MN

address: 200 First Street SW

department: Quantitative Health Sciences Research

institute: Mayo Clinic

summary: Perpheral nerve biopsies from patients with chemotherapy induced peripheral nephropathy (CIPN) and controls were subjected to gene expression studu using RNA-Seq

overall_design: Three subjects with CIPN and three controls were utilized for this study.

first: Nathan

middle: P

last: Staff


title: Influence of in-vitro culture conditions and maternal metabolic status during embryonic genome activation on the Day-4 embryo transcriptome

city: Utrecht

first: Maria

middle: Belen

last: Rabaglino

address: Yalelaan 7

department: Population Health Science

institute: Utrecht University

summary: Milk production during the early postpartum in dairy cows can impact the circulating metabolites and negatively affects embryo survival. However, the molecular consequences for the embryo during its development in the oviduct are still unknown. The objective was to determine the impact of metabolic status on embryonic genome activation (EGA) using high-throughput sequencing to generate comprehensive transcriptome profiles of bovine 16-cell stage embryos which had undergone EGA in vitro or in the oviducts of primiparous postpartum dry or postpartum lactating Holstein Friesian cows.

overall_design: Two days after synchronized estrus, in vitro produced (IVP) 2- to 4-cell stage embryos were endoscopically transferred in pools of 50 into the oviduct ipsilateral to the corpus luteum of lactating (LACT, n=3) or nonlactating (i.e. dried off immediately at calving; DRY, n=3) dairy cows. On Day 4, the oviducts were flushed to recover the embryos. Pools of five Day-2 embryos (n=5) and Day 4 16-cell stage embryos obtained in vitro (n=3) or from LACT or DRY cows were subjected to RNAseq.

middle: B

first: Niamh

last: Forde

first: Urban

last: Besenfelder

first: Vitezslav

last: Havlicek

first: Helmut

last: Blum

first: Alexander

last: Graf

first: Eckhard

last: Wolf

first: Pat

last: Lonergan


title: Histone divergence in Trypanosoma brucei results in unique alterations in nucleosome structure

city: Edinburgh

first: Shaun

middle: Michael

last: Webb

address: 2.21 Swann Building, Kings Buildings

department: Wellcome Trust Centre for Cell Biology

institute: University of Edinburgh

summary: Eukaryotes have an array of diverse mechanisms for organising and using their genomes, but the histones that make up chromatin are highly conserved. Unusually, histones from Kinetoplastids are highly divergent. The structural and functional consequences of this variation are unknown. Here, we have biochemically characterised nucleosome core particles (NCPs) from the Kinetoplastid parasite Trypanosoma brucei. A structure of the T. brucei NCP reveals that global histone architecture is conserved, but specific sequence alterations lead to distinct DNA and protein interaction interfaces. The T. brucei NCP is unstable and has weakened DNA binding overall. However, dramatic changes at the H2A-H2B interface introduce local reinforcement of DNA contacts. The T. brucei acidic patch has altered topology and is refractory to known binders, indicating that the nature of chromatin interactions in T. brucei may be unique. Overall, our results provide a detailed molecular basis for understanding evolutionary divergence in chromatin structure.

overall_design: Sequencing fragments of Widom 601 145 bp DNA produced from limited miccrococcal nuclease digestion of Homo sapiens and Trypanosoma brucei nucleosome core particles

first: Gauri

last: Deak

first: Hannah

last: Wapenaar

first: Gorka

last: Sandoval

first: Ruofan

last: Chen

first: Mark

middle: R

last: Taylor

first: Hayden

last: Burdett

first: James

middle: A

last: Watson

first: Maarten

last: Tuijtel

first: Marcus

middle: D

last: Wilson


title: Multi-omics analysis revealing the interplay between gut microbiome and the host following opioid use [RNA-seq]

first: Udhghatri

last: Kolli

overall_design: We  identified changes in host gene expression changes following morphine treatment using RNA sequencing

first: Richa

last: Jalodia

first: Shamsudheen

last: Moidunny

first: Praveen

last: Kumar Singh

first: Yuguang

last: Ban

first: Junyi

last: Tao

first: Gonzalo

last: Cantu

first: Eridania

last: Valdes

first: Sundaram

last: Ramakrishnan

first: Sabita

last: Roy


title: hMENA isoforms regulate cancer intrinsic Type I IFN signaling and extrinsic mechanisms of resistance to immune checkpoint blockade in NSCLC [ATAC-seq]

city: Rome

first: Lorenzo

last: D'Ambrosio

address: Via Elio Chianesi 53

department: Dept. Of Research, Advanced Diagnostic, and Technological Innovation

country: Italy

institute: Regina Elena National Cancer Institute, IRCCS

summary: Understanding how cancer signaling pathways promote an immunosuppressive program which sustains acquired or primary resistance to immune checkpoint blockade (ICB) is a crucial step in improving immunotherapy efficacy. Among the pathways that can affect ICB response is the IFN pathway that may be detrimental rather than beneficial. Effects of hMENA11a down-regulation were tested by RNA-Seq, ATAC-Seq, flow cytometry and biochemical assays. ICB treated patient tumor tissues were profiled by Nanostring IO 360 Panel enriched with hMENA custom probes.

overall_design: The immune sensor retinoic acid-inducible gene I (RIG-I) induces IFN activation and secretion and is activated by actin cytoskeleton disturbance. The actin cytoskeleton regulatory protein hMENA, along with its isoforms, is a key signaling hub in different solid tumors, and recently its role as a regulator of transcription of genes encoding immunomodulatory secretory proteins has been proposed. When hMENA is expressed in tumor cells with low levels of the epithelial specific hMENA11a isoform, identifies NSCLC patients with poor prognosis. Aim was to identify cancer intrinsic and extrinsic pathways regulated by hMENA11a down-regulation as determinants of ICB response in NSCLC. Herein we present a novel mechanism of ICB resistance driven by hMENA11a down-regulation

first: Paola

last: Trono

first: Annalisa

last: Tocci

first: Giacomo

last: Corleone

last: D’Ambrosio

first: Francesca

last: De Nicola

last: Nisticò


title: hMENA isoforms regulate cancer intrinsic Type I IFN signaling and extrinsic mechanisms of resistance to immune checkpoint blockade in NSCLC [RNA-seq]


title: VEGF overexpressed mesoangioblasts enhance urethral and vaginal recovery following simulated vaginal birth in rats

city: Leuven

first: Bernard

middle: Klaas

last: van der Veer

state: Vlaams-Brabant

address: Herestraat 49 - box 804

department: Department of Development and Regeneration

institute: KU Leuven

summary: Background: Vaginal birth causes injury to the pelvic floor and may lead to urinary incontinence. Cell therapy has been proposed to assist in functional recovery. Objective: To assess if intra-arterial injection of mesoangioblasts (MABs) or Vascular Endothelial Growth Factor (VEGF)-overexpressed MABs, improves urethral and vaginal function recovery after simulated vaginal delivery (SVD). Results: All stem-cell injected rats had external urethral sphincteric and vaginal function recovery within 14d, as compared to half of controls. Functional recovery was paralleled by improved muscle regeneration and microvascularization. Recovery was not different between autologous and allogenic MABs. MABsallo-VEGF accelerated functional recovery and increased GAP-43 expression at 7d. We detected early on in the recovery major transcriptional changes in both MABsallo and MABsallo-VEGF. MABSallo upregulated transcripts that encode proteins involved in myogenesis and dendrite development, and downregulated pro-inflammatory processes MABsallo-VEGF upregulated transcripts that encode proteins involved neuron and dendrite development and downregulates genes involved in hypoxia and oxidative stress.  7d after injury, Later MABsallo-VEGF showed a decrease in oxidative and inflammatory response compared to  MABSallo treated urethras. These pathways are also downregulated in animals that have recovered at 7d, compared to non-recovered animals. Conclusion: Intra-arterial injection of MABsallo-VEGF enhances neuroregeneration and accelerates functional urethral and vaginal recovery after simulated vaginal delivery. Injection of stem cells induces faster recovery of urethral and vaginal function; cells overexpressing a factor increasing blood vessel formation, were even more effective.

overall_design: Female rats (n=24) were assigned to either injection of saline (control), allogeneic-MABs (MABsallo), or allogeneic-MABs overexpressing VEGF (MABsallo-VEGF).


title: cfDNA sequencing with TACS-TOPO scheme

city: Kashiwa

first: Fumihito

last: Miura

state: Chiba

address: Kashiwanoha 5-1-5

department: Graduate School of Frontier Sciences

institute: The University of Tokyo

summary: Human cfDNA was extracted from human serum, and served for sequencing library preparation with TACS-TOPO scheme.

overall_design: 1 sample

first: Osamu

last: Hisano

first: Miki

first: Yukiko

last: Shibata

first: Takashi

last: Ito