title: Pharmacological HDAC inhibition impairs pancreatic β-cell function through a genome-wide epigenomic reprogramming [RNA-seq]

city: Lille

first: Frederik

last: Oger

address: Faculté de Médecine - Pôle Recherche - 2eme etage - 1 place de Verdun

institute: Université de Lille

summary: Histone deacetylases (HDAC) enzymes are chromatin modifiers which directly regulate gene expression through deacetylation of lysine residues within specific histone and non-histone proteins. A cell-specific gene expression pattern defines the identity of insulin-producing pancreatic b cells, yet molecular networks driving this transcriptional specificity are not fully understood. Here, we investigated the HDAC-dependent molecular mechanisms controlling pancreatic b-cell identity and function using trichostatin A (TSA), a pan-HDAC inhibitor. We observed that TSA alters insulin secretion associated with b-cell specific transcriptome programming in both mouse and human b-cell lines, as well as on human pancreatic islets. We also demonstrated that this alternative b-cell transcriptional program in response to HDAC inhibition is related to an epigenome-wide remodeling at both promoters and enhancers. Our data indicate that full HDAC activity is required to safeguard the epigenome, to protect against loss of β-cell identity with unsuitable expression of genes associated with alternative cell fates.

overall_design: Transcriptomic profiling of TSA-treated Min6 cells, mouse beta cell sorted, EndoCbH1 cells and human islets of Langerhans

first: Frédérik

first: Maeva

last: Moreno

first: Mehdi

last: Derhourhi

first: Bryan

last: Thiroux

first: Lionel

last: Berberian

first: Cyril

last: Bourouh

first: Emmanuel

last: Durand

first: Souhila

last: Amanzougarene

first: Alaa

last: Badreddine

first: Etienne

last: Blanc

first: Olivier

last: Molendi-Coste

first: Laurent

last: Pineau

first: Gianni

last: Pasquetti

first: Laure

last: Rolland

first: Charlène

last: Carney

first: Florine

last: Bornaque

first: Emilie

last: Courty

first: Céline

last: Gheeraert

first: Jérôme

last: Eeckhoute

first: David

last: Dombrowicz

first: Julie

last: Kerr-Conte

first: François

last: Pattou

first: Bart

last: Staels

first: Philippe

last: Froguel

first: Amélie

last: Bonnefond

first: Jean-Sébastien

last: Annicotte


title: Responses of microglia in the mouse brain after ischemic stroke

status: Public on Aug 08 2023

city: Pittsburgh

first: Yejie

last: Shi

state: PA

address: S-510 Biomedical Science Tower, 3500 Terrace Street

department: Neurology

country: USA

institute: University of Pittsburgh

type: Expression profiling by high throughput sequencing

summary: This project investigated responses of microglia in the mouse brain after an ischemic stroke. Mice were subjected to transient focal cerebral ischemia induced by 1 hour of left middle cerebral artery (MCA) occlusion followed by reperfusion. Control mice were subjected to sham surgery without the occlusion of the MCA. Three days after MCA occlusion or sham surgery, microglia were enriched from the brain by fluorescence-activated cell sorting and subjected to bulk RNA-seq. This project was closely related to our previously published dataset GSE141972; therefore, the animals had the same genetic background for comparison purposes. The animals used in this study were hemizygouse for CX3CR1(CreER), so that they can serve as wild-type controls for any conditional knockout driven by the CX3CR1(CreER) promoter.

overall_design:
Hemizygous CX3CR1(CreER/WT) mice on C57BL/6 background were used. To serve as wild-type controls to other conditional knockout mice driven by the CX3CR1(CreER) promoter, these mice received intraperitoneal injections of tamoxifen (75 mg/kg/day for 4 days).  Forteen days after the initial tamoxifen injection,mice (8-10 weeks old, male) were subjected to transient focal cerebral ischemia induced by occlusion of the left middle cerebral artery for 1 hour, followed by reperfusion, or control sham surgery. The CD11b+CD45low (microglia) cell population was collected by fluorescence-activated cell sorting from the left (ipsilesional) brain hemisphere 3 days after ischemic stroke or sham operation. In each group there were 2-3 biological replicates. Each sample was from 1 mouse brain. The sorted cells were subjected to mRNA sequencing.

Re-used Samples in GSE141972/PRJNA595477:
GSM4217272      SRX7366406     SAMN13556317    WT microglia 1
GSM4217273      SRX7366407     SAMN13556316    WT microglia 2
GSM4217274      SRX7366408     SAMN13556315    WT microglia 3

first: Jun

last: Chen


title: CUT&RUN seq of HSF4 and COIL after UV stimulation of NIH-3T3 cells

city: Tianjin

first: Heng

last: Zhang

address: 38 Rd.Tongyan

country: China

institute: Nankai University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Intense ultraviolet (UV) exposure can cause phototoxic reactions, such as skin inflammation, resulting in injury. UV is believed to be the direct cause of DNA damage, but the mechanisms of transcriptional regulation within cells after DNA damage are unclear. The bioinformatic analysis of transcriptome sequencing data from UV-irradiated and non-UV-irradiated skin showed that transcription-related proteins, such as HSF4 and COIL, mediate the cellular response to UV irradiation. HSF4 and COIL could form a complex under UV irradiation, and the preference for binding target genes changed. This is due to the presence of a large number of R-loops in the cells under UV irradiation and the ability of COIL to recognize the R-loops. The regulation of target genes was altered by the HSF4-COIL complex, and the expression of inflammation and aging-related genes, such as ATG7, TFPI, and LIMS1, were enhanced. A drug screen was performed for the recognition sites of COIL and R-loop. N6-(2-hydroxyethyl)-adenosine (HEA) could competitively bind COIL and inhibit the binding of COIL to R-loop. Thus, the activation of downstream inflammation-related genes and inflammatory skin injury were inhibited.

first: Yiqian

last: Feng

first: Tao

last: Sun


title: Prolonged Kaposi's Sarcoma-associated Herpesvirus vIL-6 Exposure Enhances Inflammatory Responses by Epigenetic Reprogramming (CUT&RUN)

city: Sacramento

first: Clifford

middle: G.

last: Tepper

state: CA

address: 4645 2nd Avenue, Room 2300A

department: Biochemistry and Molecular Medicine

institute: UC Davis School of Medicine

summary: Kaposi sarcoma-associated herpesvirus (KSHV) inflammatory cytokine syndrome (KICS) is a newly described chronic inflammatory disease condition caused by KSHV infection and is characterized by high KSHV viral load and sustained elevations of serum KSHV-encoded IL-6 (vIL-6) and human IL-6 (hIL-6). KICS has significant immortality and possesses greater risks of having other complications, which include malignancies. Although prolonged inflammatory vIL-6 exposure by persistent KSHV infection is expected to have key roles in subsequent disease development, the biological effects of prolonged vIL-6 exposure remain elusive. Using thiol(SH)-Linked Alkylation for the Metabolic Sequencing (SLAM-seq) and Cleavage Under Target & Release Using Nuclease (CUT&RUN) analysis, we studied the effect of prolonged vIL-6 exposure in chromatin landscape and resulting cytokine production. The studies showed that prolonged vIL-6 exposure increased Bromodomain containing 4 (BRD4) and histone H3 lysine 27 acetylation (H3K27Ac) co-occupancies on chromatin, and the recruitment sites were frequently co-localized with poised RNA polymerase II with associated enzymes. Increased BRD4 recruitment on promoters was associated with increased and prolonged p65 (RelA) binding after the LPS stimulation. The p65 binding resulted in quicker and sustained transcription bursts from the promoters; this mechanism increased total amounts of hIL-6 and IL-10 in tissue culture. Pretreatment with the BRD4 inhibitor, OTX015, eliminated the enhanced inflammatory cytokine production. These findings suggest that persistent vIL-6 exposure may establish a chromatin landscape favorable for the reactivation of inflammatory responses in monocytes. This epigenetic memory may explain the greater risk of chronic inflammatory disease development in KSHV-infected individuals.

overall_design: The goal of these studies was to utilize CUT&RUN in order to define changes in the chromatin landscape mediated by prolonged vIL-6 exposure. For this CUT&RUN was performed for BRD4, RNA polymerase II, two active histone modification marks (H3K27Ac, H3K4me3), and CTCF.

first: Yoshihiro

last: Izumiya

first: Tomoki

last: Inagaki

middle: G


title: Prolonged Kaposi's Sarcoma-associated Herpesvirus vIL-6 Exposure Enhances Inflammatory Responses by Epigenetic Reprogramming.

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

overall_design: Refer to individual Series


title: Gene expression analysis in recurrent BPPV: a prelimary study

city: Yangsan

first: Jae-Hwan

last: Choi

address: Kumo-ro 20, Beomo-ri, Mulgum-eup

country: South Korea

institute: Pusan National University Yangsan Hospital

summary:
Benign paroxysmal positional vertigo (BPPV) is the most common cause of recurrent vertigo, but the exact pathogenesis still remains unknown.
This study aimed to provide novel insights into a pathophysiology of recurrent BPPV using gene expression profiling combined with bioinformatics analysis.

overall_design: Total RNAs were extracted from peripheral whole blood cells of four AUV patients and four normal controls. Using the Affymetrix Human Clariom S Assay, the differentially expressed genes (DEGs) between BPPV and normal control samples were screened by the cut-off criteria (|fold changes| > 2 and p-value < 0.05). Functional enrichment analysis for DEGs was performed using Gene Ontology (GO)  analysis, and the protein-protein interaction (PPI) network was constructed using the STRING database.

first: Eun

middle: H

last: Oh

first: Jin-Ok

last: Lee


title: Single cell RNA sequencing of sorted NK, CD8+ T, γδ T, and KIR3DL3+ cells from PBMC

city: Aurora

first: Liyen

last: Loh

state: Colorado

address: 12800 E 19th Ave, Research 1 North, P18-8401K

institute: University of Colorado

summary: NK cells stochastically express a range of inhibitory and activating receptors that balance their effector functions. Of these receptors, the KIRs are the most polymorphic, with KIR3DL3 present at two copies in every individual. The distribution and biology KIR3DL3 remain understudied. We used single cell RNA sequencing (scRNA-seq) to analyze the transcriptome of KIR3DL3+ lymphocytes in the blood.

overall_design: KIR3DL3+ lymphocytes were enriched from Peripheral Blood Mononuclear cells and purified by Fluorescence-activated cell sorting (FACS) and analyzed using scRNAseq.

first: Paul

last: Norman

first: William

last: Palmer


title: Characterization of a barley (Hordeum vulgare L.) mutant with Multiple Stem Nodes and Spikes and Dwarf (msnsd) and fine-mapping of its causal gene

city: Wuhan

first: Dan

last: Qin

address: Nanhu Avenue No.3

institute: Hubei Academy of Agricultural Universtiy

summary: Abstract: Multiple nodes and dwarf mutants in barley are a valuable resource for identifying genes that control shoot branching, vegetative growth, and development. In this study, physiological, microscopic and genetic analylsis were conducted to characterize and fine-map the underling gene of A a barley mutant with Multiple Stem Nodes and Spikes and Dwarf (msnsd) , which was selected from EMS- and 60Co-treated barley cv. Edamai 934 (E934) to characterize the mutant and fine-map its underlying gene. The msnsd mutant had more stem nodes and , lower plant height and a shorter plastochron than Edamai 934the wild type. Moreover, the mutant had two or more spikes on each tiller., emerging from the lower nodes or the base of the top spike, and a shorter plastochron.  Microscopic analysis showed that the dwarf phenotype of msnsd resulted from reduced cell lengths and cell numbers in the stem. Further physiological analysis showed that msnsd was GA3-deficient, with its plant height increasing after external GA3 application. Genetic analysis revealed that a single recessive nuclear gene, namely, HvMSNSD, controlled the msnsd phenotype. Using a segregating population derived from Harrington and the msnsd mutant, HvMSNSD was fine-mapped on chromosome 5H in a 200 kb interval using bulked segregant analysis (BSA) coupled with RNA-sequencing (BSR-seq), with a C-T substitution in the exon of HvTCP25 co-segregating with the msnsd phenotype. RNA-seq analysis showed that a gene encoding gibberellin 2-oxidase 8, a negative regulator of GA biosynthesis, was upregulated in the msnsd mutant. Transcriptomic analysis identified several Several known genes related to inflorescence development that were also upregulated and enriched in the msnsd mutant. Collectively, we propose that HvMSNSD regulates the plastochron and morphology of reproductive organs, likely by coordinating GA homeostasis and changed expression of floral development related genes in barley. this This study offers valuable insights into the molecular regulation of barley plant architecture and inflorescence development

overall_design: Immature spikes of msnsd and E934 from the glume primordium to the lemma primordium stages, approximately 0.5–1 cm in length, were collected and frozen in liquid nitrogen, with three biological replicates for each sample. Total RNA extraction, library construction, and RNA-seq were performed at Beijing Novogene Bioinformatics Technology Co. Ltd, Beijing, China. Clean reads of each sample were mapped to the reference Morex V3 assembly (Mascher et al., 2021). Transcript quantification from RNA-seq data was performed using the Salmon software package (1.9.0). Expression levels of mapped reads were quantified based on transcripts per kilobase of exon per million mapped reads (TPM) (Patro et al., 2017).

first: Dandan

first: Rui

last: Liu

first: Fuchao

last: Xu

first: Guoqing

last: Dong

first: Qing

first: Yanchun

last: Peng

first: Le

first: Hongna

last: Cheng

first: Ganggang

last: Guo

first: Jing

first: Chengdao

last: Li


title: METTL1 promotes tumorigenesis through tRNA-derived fragment biogenesis in prostate cancer

city: Derio

first: Ana

middle: Maria

last: Aransay

state: BIZKAIA

address: Parque tecnologico de Bizkaia, Building 801-A

department: Genome Analysis Platform

country: Spain

institute: CIC bioGUNE

type: Non-coding RNA profiling by high throughput sequencing

summary: Newly growing evidence highlights the essential role that epitranscriptomic marks play in the development of cancer; however, little is known about the role and implications of altered epitranscriptome deposition in prostate cancer. Here, we show that the transfer RNA N7-methylguanosine (m7G) transferase METTL1 is highly expressed in primary and advanced prostate tumours. Mechanistically, we find that METTL1 depletion causes the loss of m7G tRNA methylation and promotes the biogenesis of a novel class of small non-coding RNAs derived from 5’tRNA fragments. 5′ tRNA-derived small RNAs steer translation control to favour the synthesis of key regulators of tumour growth suppression, interferon pathway, and immune effectors. Knockdown of Mettl1 in prostate cancer preclinical models increases intratumoural infiltration of pro-inflammatory immune cells and enhances responses to immunotherapy, leading to decreased tumour progression. Collectively, our findings reveal a therapeutically actionable role of METTL1-directed m7G tRNA methylation in cancer cell translational control and tumour biology.

overall_design: Sequences of RNAs bound to METTL1 in prostate cancer cell lines PC3. Photoactivatable-ribonucleoside-enhanced cross-linking immunoprecipitation (PAR-CLIP) was applied to PC3 cells  expressing HA-METTL1.Empty vector was used as control. METTL1 was IP using anti-HA antibodies. RNAs bound to METTL1 were extracted and sequenced.

first: Sandra

last: Blanco

first: Angelika

last: Merkel

first: Sonia

last: Guil


title: Pharmacological HDAC inhibition impairs pancreatic beta cell function through an epigenome-wide reprogramming [ChIP-seq]

first: Frederik

last: Oger

country: France

overall_design: Epigenomic profiling of TSA-treated Min6 cells

first: Frédérik

first: Maeva

last: Moreno

first: Mehdi

last: Derhourhi

first: Bryan

last: Thiroux

first: Lionel

last: Berberian

first: Cyril

last: Bourouh

first: Emmanuel

last: Durand

first: Souhila

last: Amanzougarene

first: Alaa

last: Badreddine

first: Etienne

last: Blanc

first: Olivier

last: Molendi-Coste

first: Laurent

last: Pineau

first: Gianni

last: Pasquetti

first: Laure

last: Rolland

first: Charlène

last: Carney

first: Florine

last: Bornaque

first: Emilie

last: Courty

first: Céline

last: Gheeraert

first: Jérôme

last: Eeckhoute

first: David

last: Dombrowicz

first: Julie

last: Kerr-Conte

first: François

last: Pattou

first: Bart

last: Staels

first: Philippe

last: Froguel

first: Amélie

last: Bonnefond

first: Jean-Sébastien

last: Annicotte


title: Organoid modeling of lung-resident immune responses to SARS-CoV-2 infection

city: Fremont

first: Shannon

last: Choi

state: California

address: 44126 Paseo Padre Parkway

institute: Stanford School of Medicine

summary: We sought to understand the effect of SARS-CoV-2 infection on transcriptomes of human lung organoids at various time points during infection.

overall_design: We performed differential gene expression analysis using data obtained from bulk RNA-sequencing of 4 mock and 4 infected time points (3, 7, 10, 14 days post-infection). We also took samples 48 hours post-infection with or without the presence of the antiviral drug remdesivir.

first: Calvin

last: Kuo


title: Neuronal mimicry mechanisms promote the growth of small-cell lung cancer in the brain [human SCLC cell RNA seq]

status: Public on Aug 09 2023

city: Stanford

first: Fangfei

last: Qu

state: CA California

address: SIM1 G2065, 265 Campus Drive

institute: Stanford University

summary: Small cell lung cancer (SCLC) is a fatal form of cancer that frequently metastasizes to the brain. Here we investigated the mechanisms allowing SCLC cells to grow in the unique brain microenvironment. We found that neuronal programs upregulated in SCLC cells during tumor progression and upon growth in the brain are critical for SCLC growth in the brain. Mechanistically, the presence of SCLC cells in the brain re-activates astrocytes, which in turn promote the survival of SCLC cells by secreting neuronal pro-survival factors such as SERPINE1. We also identified Reelin, a molecule produced by developing neurons to recruit astrocytes, as a molecule secreted by SCLC cells to recruit astrocytes to the tumor site and promote SCLC growth in the brain. Thus, SCLC cells co-opt mechanisms normally at play between astrocytes and neurons to promote SCLC growth in the brain. Targeting such developmental neuronal programs may help treat brain metastases.

overall_design: 6 samples were analyzed: NCI-H82 cultured alone (2) or co-cultured with human astrocytes (3). SUBr1 cell line (1)

first: Juliens

last: Sage


title: Prolonged Kaposi's Sarcoma-associated Herpesvirus vIL-6 Exposure Enhances Inflammatory Responses by Epigenetic Reprogramming (SLAM-seq)

first: Clifford

last: Tepper

overall_design: The goal of these studies was to utilize thiol(SH )-linked alkylation for the metabolic sequencing of RNA (SLAM-seq) in order to define the direct transcriptional effects in response to cytokine stimulation. This was performed in the context of the parental THP-1 and vIL-6/THP-1 cell line models. Replicate cultures from each cell line were treated with either vehicle control, viral IL-6 (vIL-6), human IL-6 (hIL-6), transforming growth factor-B (TGF-B), the lipopolysaccharide (LPS). Additionally, sequential treatments of vIL-6 -> vIL-6 restimulation,  vIL-6 -> hIL-6 stimulation, and vIL-6 -> TGF-B stimulation were performed. Subsequently, the cells were incubated for an additional 1 hour in the presence of 4-Thiouridine (s4U; 300 uM) in order to label nascent transcripts. Following treatment, the cells were harvested for isolation of total RNA (containing s4Uracil-labeled transcripts) and followed by library preparation and next-generation sequencing (NGS).

first: Yoshihiro

last: Izumiya

first: Tomoki

last: Inagaki


title: Prolonged Kaposi's Sarcoma-associated Herpesvirus vIL-6 Exposure Enhances Inflammatory Responses by Epigenetic Reprogramming (RNA-seq)

overall_design: The goal of this study was to define the effects of prolonged vIL-6 exposure on the transcription of KSHV genes. Parental THP-1 and vIL-6/THP-1 cells were either infected with r219.KSHV for 72 hours or mock-infected. Cells were harvested at the completion of the treatment and followed by total RNA isolation and RNA-sequencing.


title: scRNA sequencing of BM hematopoietic cells under CA colonization

city: Philadelphia

first: Ken

last: Cadwell

address: 421 Curie Boulevard

institute: University of Pennsylvania Perelman School of Medicine

summary: Fungal colonization leads to enhanced granulopoiesis in the bone marrow. The purpose of the study is to understand the alteration of cell compostions and transcriptional profile under CA colonization.

overall_design: Laboratory mice (C57BL/6J) under antibiotic treatment were orally innoculated with PBS or Candida albicans SC3514 (4 mice per group). After 3 weeks, BM hematopoietic cells were harvested. Cells from each mouse were then hashtagged following RBC lysis process.

first: Ying-Han

last: Chen

first: Kimberly

last: Zaldana


title: Landscape of Double-Stranded DNA Breaks in Postmortem Brains from Alzheimer’s Disease and Non-Demented Individuals  Journal of Alzheimer’s Disease

city: Kansas City

first: Sumedha

middle: S

last: Gunewardena

state: Kansas

address: 2146 West 39th Avenue

department: Dept. of Molecular and Integrative Physiology

institute: University of kansas medical center

summary: Background: Alzheimer’s disease (AD) brains accumulate DNA double-strand breaks (DSBs), which could contribute to neurodegeneration and dysfunction. The genomic distribution of AD brain DSBs is unclear. Objective: To map genome-wide DSB distributions in AD and age-matched control brains. Results: The AD brains contained 18 times more DSBs than the control brains and the pattern of AD DNA DSBs differed from the control brain pattern. In conjunction with published genome, epigenome, and transcriptome analyses, our data revealed aberrant DSB formation correlates with AD-associated single-nucleotide polymorphisms (SNPs), increased chromatin accessibility, and upregulated gene expression. Conclusion: This study is the first to characterize the AD brain DSB landscape. Our data suggest in AD, an accumulation of DSBs at ectopic genomic loci could contribute to an aberrant upregulation of gene expression.

overall_design: Methods: We obtained autopsy brain tissue from 3 AD and 3 age-matched control individuals. The donors were men between the ages of 78 to 91. Nuclei extracted from frontal cortex tissue were subjected to Cleavage Under Targets & Release UsingNuclease (CUT&RUN) assay with an antibody against g-H2AX, a marker of DSBformation. g-H2AX-enriched chromatins were purified and analyzed via high-throughput genomic sequencing.

first: Xiaoyu

last: Zhang

first: Yan

last: Liu

first: Ning

last: Wang


title: WT and CXCR6KO OT1 T cells

city: New York

first: Amanda

last: Lund

state: New York

address: 522 First Ave

institute: NYU Langone Health

summary: WT and KO OT1 T cells were isolated from vaccinia-OVA infected ears 21 days post infection

overall_design: WT and KO OT1 T cells were MACS enriched, then flow sorted on CD8+, CD44+, Live, CD45 IV- (extravascular). Enriched cells were then submitted to NYU genomics center for single cell RNA sequencing

first: Heim

last: Taylor

first: Lin

last: Ziyan

first: Lund

last: Amanda


title: Cardiac Myofibrillogenesis 1 is Spatiotemporally Modulated by the Molecular Chaperone UNC45B

city: Miaoli County

first: Paul

middle: Wei-Che

last: Hsu

state: Taiwan

address: Zhunan: 35, Keyan Road, Zhunan Town

department: National Health Research Institutes

country: Taiwan

institute: National Health Research Institutes

summary: Sarcomeres are fundamental to cardiac muscle contraction. Their impairment can elicit cardiomyopathies, leading causes of death worldwide. However, the molecular mechanism underlying sarcomere assembly remains obscure. We used human embryonic stem cell (hESC)-derived cardiomyocytes (CMs) to reveal step-wise spatiotemporal regulation of core cardiac myofibrillogenesis-associated proteins. We found that the molecular chaperone UNC45B is highly co-expressed with KINDLIN2 (KIND2), a marker of protocostameres, and later its distribution overlaps with that of muscle myosin MYH6. UNC45B-knockout CMs display essentially no contractility. Our phenotypic analyses further reveal that: 1) binding of Z-line anchor protein ACTN2 to protocostameres is perturbed due to impaired protocostamere formation, resulting in ACTN2 accumulation; 2) F-ACTIN polymerization is suppressed; and 3) MYH6 becomes degraded, so it cannot replace non-muscle myosin MYH10. Our mechanistic study demonstrates that UNC45B mediates protocostamere formation by regulating KIND2 expression. Thus, we show that UNC45B modulates cardiac myofibrillogenesis by interacting spatiotemporally with various proteins.

overall_design: Overexpression of UNC45B and KIND2 in UNC45B-knockout or wild-type hESC lines

first: Su-Yi

last: Tsai


title: Targeting polyploid giant cancer cells potentiates a therapeutic response and overcomes resistance to PARP inhibitors in ovarian cancer

city: Houston

first: Haoqiang

last: Ying

state: Texas

address: 1515 Holcombe Blvd

institute: M. D. Anderson Cancer Center

summary: PARP inhibitor olaparib induces the formation of polyploid giant cancer cells (PGCCs) in ovarian and breast cancer cell lines, human high-grade serous ovarian cancer (HGSC)–derived organoids, and HGSC patient-derived xenografts (PDXs). Time-lapse tracking of ovarian cancer cells revealed that PGCCs primarily developed from endoreplication of cancer cells after exposure to sublethal concentrations of olaparib. PGCCs exhibited features of senescent cells but, after olaparib withdrawal, could escape senescence via restitutional multipolar endomitosis and other modes of cell division to generate mitotically competent resistant daughter cells. The contraceptive drug mifepristone blocked PGCC formation and daughter cell production. Mifepristone/olaparib combination therapy substantially reduced tumor growth in PDX models without previous olaparib exposure, while mifepristone alone decreased tumor growth in PDX models with acquired olaparib resistance. Thus, targeting PGCCs may represent a promising approach to potentiate the therapeutic response to PARPi and overcome PARPi-induced resistance.

overall_design: Ovarian cancer cell lines and organoids were treated with olaparib and cells are harvested at different time points to perform RNAseq

first: Xudong

first: Jun

last: Yao

first: Xiaoran

last: Li

last: Niu

first: Richard

middle: A

last: Hajek

first: Guang

last: Peng

first: Shannon

last: Westin

first: Anil

middle: K

last: Sood

first: Jinsong


title: Assessment of colorectal cancer risk factors through the application of network-based approaches in a biracial cohort of colon organoid stem cells

city: Charlottesville

first: Matthew

last: Devall

state: Virginia

address: 1335 Lee Street

institute: University of Virginia

summary: Numerous demographic factors have been associated with colorectal cancer (CRC) risk, with age, body mass index, smoking history, sex, and differences in ancestry, among the most consistent. However, biological mechanisms underlying these associations remain unclear. Limitations of traditional cancer models, such as animal models and CRC cell lines, and the large data dispari-ty between European American and minority groups present challenges in relating mechanisms to the average-risk population. There is a need for studies to be performed in a racially diverse pop-ulations and in cells relevant to CRC initiation. Colon crypt stem cells are believed to be the pri-mary cells of origin for CRCs. In this study, we enriched for stem cell populations in organoids derived from the healthy colon of seven European Americans and eight African Americans. Weighted gene co-expression network analysis was performed following RNA sequencing to identify modules of gene co-expression that were differentially associated with these five CRC risk factors. Candidate driver genes of CRC risk were identified through analysis of module structure and overlaid with data derived from publicly available CRC tumors and genome-wide association studies. We identified several genes that represent putative targets of CRC risk factors and warrant further investigation

overall_design: RNA-sequencing protocols were performed on healthy African American and European American stem cell enriched colon organoids derived from right colon at the time of colonoscopy.

first: Stephen

last: Eaton

first: Cynthia

last: Yoshida

first: Steven

middle: M

last: Powell

first: Graham

last: Casey

first: Li


title: Transcriptomic Regulations of Heat Stress Response in the liver of Lactating Dairy Cows

city: Ithaca

first: Guangsheng

state: NY

address: 507 Tower Rd.

department: Animal Science

institute: Cornell

summary: Heat stress (HS) has become a major challenge in the dairy industry around the world. Although numerous measures have been taken to alleviate the HS impact on milk production, the cellular level response to HS remains unclear in dairy cows. The objective of this study was to dissect functional alterations based on transcriptomic dynamics in the liver of cows under HS. Dairy cows exposed to HS exhibited both decreased feed intake and milk yield. Through liver transcriptomic analysis, differentially expressed genes were identified among three experimental conditions, including heat stress (HS), pair-fed (PF), and thermoneutral (TN) groups. We observed the upregulation of protein folding and inflammation-related genes in the HS group, while the mitochondrial genes were downregulated. Gene functional enrichment also revealed that mitochondria function and oxidative phosphorylation were dysregulated under HS. The liver transcriptome analysis generated a comprehensive gene expression regulation network upon HS in lactating dairy cows. Overall, this study provides novel insights into molecular and metabolic changes of cows conditioned under HS. Our results could facilitate the development of efficient biomarkers to mitigate the negative effect of HS on dairy cow health and productivity.

overall_design: RNA-seq was to detect the differential expression genes across three environmental conditions: Heat stress, thermoneutrality, and pair-fed

first: Xingtan

last: Yu

first: A

middle: B

last: Fontoura

last: Javaid

first: V

last: Sáinz de la Maza-Escolà

first: N

last: Salandy

first: S

middle: L

last: Fubini

first: E

last: Grilli

first: J

middle: W

last: McFadden

middle: E

last: Duan


title: Phosphorylated nuclear DICER1 promotes open chromatin state and gastric cell fate in lung adenocarcinomas [Nanostring]

first: Raisa

last: Reyes-Castro

address: 6767 Bertner Ave

department: Genetics

institute: UT Health MD Anderson Cancer Center

summary: DICER1 canonically regulates micro(mi)RNA-mediated epithelial-to-mesenchymal transition (EMT) in lung adenocarcinomas (LUADs). We discovered that KRAS/ERK pathway phosphorylates DICER1 causing its nuclear translocation; phosphomimetic Dicer1 contributes to tumorigenesis in mice. Mechanisms through which phospho-DICER1 regulates tumor progression remain undefined. Here, we show that phospho-DICER1 is expressed in invasive human LUADs and promotes late-stage tumor progression in mice with oncogenic Kras, independent of miRNAs and EMT. Strikingly, in mice, we observed that the AT2 tumor cells with phospho-DICER1 express endodermal (gastric) genes and display an open chromatin state such that there are sub-populations of tumors cells with alveolar-endodermal or only endodermal identity. Importantly, we also observed expression of gastric genes in human LUADs with phospho-DICER1. Mechanistically, we identify a chromatin-DICER1 nuclear complex comprised of Mediator complex subunit 12, CBX1, MACROH2A.1 and transcriptional regulators. Together, we propose that phosphorylated-nuclear DICER1 leads to lineage reprogramming of AT2 tumor cells to mediate lung cancer progression.

overall_design: For miRNA expression assay, lung tumors from KrasLA1/+;Dicer1S2D/+ mice (n=5)  were compared to lung tumors from Kras LA1/+ mice (n=4). KrasLA1 mouse model have an oncogenic Kras G12D mutation. And KrasLA1/+;Dicer1S2D/+ have  a heterozygous phosphomimetic Dicer1 in where serienes 1712 and 1836 were replaced to aspartic acid, in a heterozygous Kras LA1 oncogenic background. For this experiment, 30 to 37 weeks old mice from both genotypes were used. A total of 50mg of lung tumors per mouse was used and 577 miRNAs were analyzed using Nanostring nCounter mouse miRNA array..

first: Shin-Yu

last: Chen

first: Jacob

last: Seemann

first: Guillermina

last: Lozano

first: Swathi

last: Arur


title: An ATP-sensitive phosphoketolase regulates carbon fixation in cyanobacteria

city: Taipei

first: James

middle: C.

last: Liao

address: 128 Academia Road, Section 2, Nankang, Taipei 11529, Taiwan

institute: Academia Sinica

summary: Regulation of CO2 fixation in cyanobacteria is important both for the organism and the global carbon balance. Here we show that phosphoketolase in Synechococcus elongatus PCC7942 (SeXPK) possesses a distinct ATP sensing mechanism, which upon ATP drops, allows SeXPK to divert precursors of the RuBisCO substrate away from the Calvin-Benson-Bassham (CBB) cycle. Deleting the SeXPK gene increased CO2 fixation particularly during light-dark transitions. In high-density cultures, the xpk strain showed a 60% increase in carbon fixation, and unexpectedly resulted in sucrose secretion without any pathway engineering. Using cryo-EM analysis, we discovered that these functions were enabled by a unique allosteric regulatory site involving two subunits jointly binding two ATP, which constantly suppresses the activity of SeXPK until the ATP level drops. This magnesium-independent ATP allosteric site is present in many species across all three domains of life, where it may also play important regulatory functions.

overall_design: Compare WT and del(xpk) transciptome of Synecococcus elongatus PCC7942 in different light conditions

first: Kuan-Jen

last: Lu

first: Chiung-Wen

last: Chang

first: Chun-Hsiung

last: Wang

first: Frederic

middle: Y

first: Irene

last: Huang

first: Pin-Hsuan

first: Cheng-Han

last: Yang

first: Hsiang-Yi

last: Wu

first: Wen-Jin

first: Kai-Cheng

last: Hsu

first: Meng-Chiao

last: Ho

first: Ming-Daw

last: Tsai

middle: C


title: Role of Cterminal FGF23 peptide in inflammation

city: Chicago

first: Valentin

last: David

state: Illinois

address: 320 E Superior Street

department: Medicine

institute: Northwestern University

summary: RNAseq of liver of mice with a conditional  overexpression of Cterminal FGF23 peptide in osteoblasts and osteocytes  and WT littermates 6 hours post-injection of 250ng/g of recombinant murine Il-1B or saline.

overall_design: These R26-stop-CterFgf23 mutant mice have a loxP-flanked STOP sequence followed by the Cterminal peptide of FGF23 inserted into the Gt(ROSA)26Sor locus. When bred to mice expressing Dmp1-Cre recombinase, the STOP sequence is deleted and CterFgf23 expression is observed in mature osteoblasts and osteocytes in the bone of the double mutant offspring (CterTg). At 6 weeks, WT and CterTg mice were injected with a single dose of 250ng/g recombinant murin IL-1B or saline as Ctr and sacrificed 6 hours post-injection, and Liver was collected. Total RNA was isolated and submitted for RNAsequencing.

first: Aline

last: Martin


title: Transcriptional analysis of different tylosin high-producing strains.

city: Shanghai

first: Penghui

last: Dai

address: 800 Dongchuan Road

department: School of Life Sciences and Biotechnology

institute: Shanghai Jiao Tong University

summary:
To investigate gene expression differences of different tylosin high-producing strains, transcriptomes of three tylosin high-producing engineered strains (TLPH08-2, TLPH11 and TLPH17) and the vector control strain TLSET152  were analyzed by RNA-Seq.
Different strains (TLSET152, TLPH08-2, TLPH11 and TLPH17) were harvested at 96 h of fermentationat and then RNA isolation, transcriptome sequencing and data analysis were conducted.

overall_design: Comparative gene expression profiling analysis of  different genes overexpression strains at 96 h of fermentation .

first: Meifeng

last: Tao


title: Engineered exosomes reprogram Gli1+ cells in vivo to prevent calcification of vascular grafts and autologous pathological vessels

city: 重庆

first: 浩然

last: 肖

state: other

address: 重庆市沙坪坝区高滩岩正街30号

institute: 学校

summary: Engineered exosomes reprogrammed Gli1+ cells to promote SMC reconstruction and inhibit calcification in TEVBs and autologous pathological vessels.

overall_design: After engineered exosome therapy in rats with chronic renal disease, comparative gene expression profiling analysis of RNA-seq data for aorta and thoracic aorta

first: Juan

last: Yan

first: Haoran

last: Xiao

first: Xin

last: Zhou

first: Wen

last: Zeng


title: Exosomal microRNA profiling in aqueous humor of the patients with Central Serous Chorioretinopathy by Next-Generation Sequencing

city: Seoul

first: Junyeop

last: Lee

address: 88, Olympic-ro 43gil, Sonpa-gu

department: Ophthalmology

institute: Asan Medical Center, Seoul

summary: We report the aqueous humor-derived exosomal miRNA expression profiles from CSC patients and cataract patients as control, and with analysis by anti-VEGF treatment responders (CSC-R) and non-responders (CSC-NR).

overall_design: miRNA expression profiling analysis of miRNA-seq data for human aqueous humor-derived exosomes of CSC patients.

first: Jee

first: Soo

middle: J

last: Kim


title: Next-generation sequencing analysis of ginseng transcriptomes in response to Colletotrichum panacicola infection

city: Changchun

first: Shouan

last: Liu

address: Xi-An-Da Road 5333

institute: Jilin University

summary: Next-generation sequencing (NGS) was performed to identify genes changed in ginseng upon Colletotrichum panacicola infection. The goal of the work is to find interesting genes involved in ginseng in response to fungi induction. The object is to reveal the molecular mechanism of ginseng disease development caused by Colletotrichum panacicola.

overall_design: mRNA profiling of ginseng in response to Colletotrichum panacicola infection.


title: Transcriptome in Rat liver, 3 months after 7 weeks of control diet, high fat diet or heat-mositure-treated high fat diet

city: Tokyo

first: Sihui

last: Ma

address: Yayoi 1-1-1

country: Japan

institute: The university of Tokyo

summary:
In the present study, we designed a 7-week rat model,  consuming high-fat diet or heat-misture-treated high fat diet. The liver was used for microarray analyses.
Transcriptome profiling reveal that high-fat diet with or with out heat-moisture treatment induced different transcriptome changes, mainly on lipid metabolism and inflammation.

overall_design: High-fat diet, or heat-moisture-treated high-fat diet were administrated to rats, the livers were used for RNA extraction and hybridization on Affymetrix microarrays.

first: Huijuan

last: Jia

first: Hisanori

last: Kato


title: Phosphorylated nuclear DICER1 promotes open chromatin state and gastric cell fate in lung adenocarcinomas [scRNA-seq]

first: Raisa

last: Reyes-Castro

overall_design: scRNA-sequencing of lung tumors from KrasLA1/+ and KrasLA1/+;DicerS2D/+ mice. scRNA-Seq was performed  to study and compare tumor cell population between both mice genotype.

first: Shin-Yu

last: Chen

first: Jacob

last: Seemann

first: Guillermina

last: Lozano

first: Swathi

last: Arur


title: TGFß in the microenvironment induces a physiologically occurring immune-suppressive senescent state

city: Charlestown

first: Shyamala

last: Maheswaran

state: MA

address: 149 13th Street

department: Cancer Center

institute: Massachusetts General Hospital

summary: To define the molecular mechanism responsible for promoting Early- and Deep-senescence, we performed RNA-sequencing of the ß-gal-high E- and D-senescent populations.

overall_design:
ß-gal-high cells sorted from TGFß-treated (5 ng/ml, 15 days) hypoxic and normoxic A549 cultures were compared using non-treated cells under normoxic condition.
The E and D senescent populations represent Nd15BgH and Hd15BgH.

first: Satoru

last: Matsuda

first: Robert

last: Morris


title: Transcriptonal response of mammalian cells lacking FLVCR1 to choline depleted or replete media conditions

first: Kivanc

last: Birsoy

address: 1230 York Avenue, The Rockefeller University  Box 225 Tim Kenny/Kivanc Birsoy

institute: The Rockefeller University

summary: Integrative genetic analysis identified FLVCR1 as a choline transporter in mammalian cells. We profilied the transcriptional response of HeLa cells with and without FLVCR1 to choline depeleted or replete conditions.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from FLVCR1 knockout HeLa cells complemented with FLVCR1 cDNA or vector control after culture in choline depelted or replete conditions for 24 hours.

first: Timothy

last: Kenny


title:  T cells control murine subcutaneous adipose wasting during chronic Trypanosoma brucei infection

city: Manchester

first: Juan

middle: Fernando

last: Quintana

address: 2.18c CTF, Grafton Street

department: Lydia Becker Institute of Immunology and Inflammation

country: United Kingdom

institute: University of Manchester

summary: African trypanosomes have been recently shown to colonise the skin in a process critical for parasite transmission. However, the tissue responses to infection, especially in the lead to parasite transition from the host skin to the vector remain unresolved. Here, using a combination of spatial and single cell transcriptomics, coupled with imaging mass cytometry and genetic models, we investigated the local immune response of the skin in both a murine model of infection and in human samples from the Democratic Republic of Congo (DRC). Our results provide several novel key findings previously unappreciated in the context of parasitic infections in the skin. Firstly, we identified that the skin stromal cells, in particular interstitial preadipocytes located in the subcutis, upregulate several genes involved in inflammatory signalling and antigen presentation, including several molecules involved in T cell activation and survival. Secondly, we detected a significant expansion of a population of IL-17 producing Vg6 gdT cells in the infected murine skin compared to naïve controls, that occur mainly in the subcutis, that we further validated at the protein level by flow cytometry. In silico cell-cell communication analyses between adipocytes and T cells suggests that adipocytes trigger T cell activation locally via Il6, Il10, and Tnfsf18 signalling, amongst others. Thirdly, mice deficient of Vg6 gdT cells show extensive inflammation, increased IFNg-producing CD4+ T cells, and tissue parasite burden compared to naïve controls, indicating that Vg6 gdT cells are important to limit skin inflammation and parasite replication. Based on these observations, we proposed a model whereby interstitial preadipocytes (and potentially adipocytes) as well as Vg6 gdT cells act concertedly in the subcutis to limit tissue damage and parasite load, thus imposing an immunological barrier for transmission. These studies shed light into the mechanisms of gdT cells-mediated immunity in the skin in the context of African trypanosomes infection, as well as a potential role of immature and mature adipocytes as homeostatic regulators on the skin during chronic infection.

overall_design: Single cell and spatial transcriptomics of murine skln infected with Trypanosoma brucei

middle: F

first: Matthew

last: Sinton

first: Praveena

last: Chandrasegaran

first: Agatha

last: Nabilla Lestari

first: Bachar

last: Cheaib

first: John

last: Ogunsola

first: Rhiannon

last: Heslop

first: Nono

last: Kuispond

first: Anneli

last: Cooper

first: Seth

last: Coffelt

first: Annette

last: MacLeod


title: Gene expression profile at single cell level of adipocyte progenitors from subcutaneous inguinal adipose depots

city: San Francisco

first: Min

last: Chen

address: Fourth St.

institute: University of California

summary: Stromal vascular fraction (SVF) derived from adipose tissue is enriched for adipocyte progenitor cells, it is composed of aheterogeneous populations of cells and cell types. We use single-cell RNA-Sequencing (scRNA-Seq) to deconvolution of cell types in adipocyte progenitors and a general hierarchical structure is emerging.

overall_design: Adipocyte progenitors (CD31- CD45- SVF) of C57BL/6J mouse were isolated by Fluorescence-activated cell sorting (FACS) according to the presence or absence of CD31 and CD45 and analyzed using scRNAseq.

first: Brian

last: Feldman


title: Phosphorylated nuclear DICER1 promotes open chromatin state and gastric cell fate in lung adenocarcinomas

first: Raisa

last: Reyes-Castro

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

overall_design: Refer to individual Series


title: Phosphorylated nuclear DICER1 promotes open chromatin state and gastric cell fate in lung adenocarcinomas [ATAC-seq]

overall_design: Chromatin accessibility across the genome of KrasLA1/+;Dicer1S2D/+ lung tumors was determined by ATAC sequencing.

first: Shin-Yu

first: Jacob

last: Seemann

first: Guillermina

last: Lozano

first: Swathi

last: Arur


title: EHD1-dependent traffic of IGF-1 receptor to the cell surface is essential for Ewing sarcoma tumorigenesis and metastasis

city: Omaha

first: Jordan

last: Rowley

state: NE

address: 3828 Jones St, Apt 202

institute: University of Nebraska Medical Center

summary: EHD1-dependent RTK traffic regulation is a pro-oncogenic mechanism that impinges on IGF-1R in Ewing Sarcoma.

overall_design: mRNA profiles of human Ewing Sarcoma cell line TC71 with doxycycline inducible EHD1 knockdown and non-targeting control.

first: Sukanya

last: Chakraborty

first: Achyuth

last: Kalluchi

first: Hamid

last: Band


title: CAF-1 deposits newly synthesized histones during DNA replication using distinct mechanisms on the leading and lagging strands

city: Copenhagen

first: Anja

last: Groth

address: Blegdamsvej 3B

country: Denmark

institute: Novo Nordisk Foundation Center for Protein Research

summary: During every cell cycle, both the genome and the associated chromatin must be accurately replicated. Chromatin Assembly Factor-1 (CAF-1) is a key regulator of chromatin replication, but how CAF-1 functions in relation to the DNA replication machinery is unknown. Here, we reveal that this crosstalk differs between the leading and lagging strand at replication forks. Using biochemical reconstitution, we show that DNA and histones promote CAF-1 recruitment to its binding partner PCNA and reveal that two CAF-1 complexes are required for efficient nucleosome assembly under these conditions. Remarkably, in the context of the replisome, CAF-1 competes with the leading strand DNA polymerase epsilon (Pole) for PCNA binding. However, CAF-1 does not affect the activity of the lagging strand DNA polymerase Delta (Pold). Yet, in cells, CAF-1 deposits newly synthesized histones equally on both daughter strands. Thus, on the leading strand, chromatin assembly by CAF-1 cannot occur simultaneously to DNA synthesis, while on the lagging strand these processes may be coupled. We propose that these differences may facilitate distinct parental histone recycling mechanisms and accommodate the inherent asymmetry of DNA replication.

overall_design: SCAR-seq (Sister Chromatids After Replication) time-series measuring histone partition in nascent chromatin of H3K27me3, H4K20me0 in CAF-1 dTAG mouse embryonic stem cells (1 clone, DMSO and dTAG treatment,  3 replicates for calculating total reads, 2 replicates for histone partition scores, includes stranded input controls).

first: Clément

last: Rouillon

first: Bruna

middle: V

last: Eckhardt

first: Leonie

last: Kollenstart

first: Fabian

last: Gruss

first: Alexander

last: Verkennis

first: Inge

last: Rondeel

first: Peter

middle: H

last: Krijger

first: Giulia

last: Ricci

first: Alva

last: Biran

first: Theo

last: van Laar

first: Charlotte

last: Delvaux de Fenffe

first: Georgiana

last: Luppens

first: Pascal

last: Albanese

first: Koichi

last: Sato

first: Richard

last: Scheltema

first: Wouter

last: de Laat

first: Puck

last: Knipscheer

first: Nynke

last: Dekker

first: Francesca

last: Mattiroli


title: Lenvatinib recruits cytotoxic GZMK+CD8 T cells in hepatocellular carcinoma

city: Tsu city

first: Naoto

last: Fujiwara

state: Mie

address: 2-174 Edobashi

institute: Mie University

summary: Lenvatinib targets multiple oncogenic kinases including vascular endothelial growth factor receptors (VEGFRs) and showed longer median progression-free survival than sorafenib, the only approved treatment for >10 years. With the successful combination therapy of anti-PD-L1 pembrolizumab and anti-VEGF bevacizumab for advanced HCC as well as encouraging experimental findings, lenvatinib was also expected to enhance anti-tumor effects by combining anti-PD-1 pembrolizumab compared to lenvatinib alone; however, the phase III clinical trial failed to show their synergetic survival benefits, highlighting the need for elucidating its mode of action in human HCC specimens after lenvatinib treatment. We performed multi-layer transcriptome analyses of surgically resected human HCC samples after lenvatinib treatment as a neo-adjuvant therapy using RNA-sequencing. Molecular pathway analyses and immunohistochemistry revealed that VEGF-mediated aberrant vascularity and cytotoxic GZMK+CD8 T cells infiltration were significantly improved in lenvatinib-treated HCC; however, the majority of these cytotoxic T cells were trapped in the intratumor fibrotic stroma, suggesting that lenvatinib-treated HCC is in the so-called excluded condition. Excluded tumors are generally believed to be less responsive to immune checkpoint inhibitors, which might be the reason the combination therapy failed to show the additive benefits.

overall_design: HCC tumor tissues were obtained from 5 patients who underwent surgical resection neo-adjuvant lenvatinib treatement and 10 matched control patients and used for RNA isolation and genome-wide transcriptome profiling by RNA-Seq.

first: Tomoharu

last: Yamada

first: Hayato

last: Nakagawa


title: Effect of hPNPase on Escherichia coli transcritome after addition of rifampicin

city: Milano

first: Federico

last: Zambelli

address: Via Giovanni Celoria 26

department: Department of Biosciences

country: Italy

institute: University of Milan

summary: We replaced the natural pnp locus with the human cDNA and studied the transcriptomes of 3 strains, namely the wt pnp+ (C-1a), the mutant with pnp ORF deletion (C-5691) and the strain with the substitution of the bacterial ORF with the human one (C-6001), before and 4 minutes after the addition of rifampicin to inhibit transcription.

overall_design: Comparative RNA stability analysis of RNA-seq data for C-1a cells and its  derivatives C-5691 and C-6001

first: Federica

last: Briani

first: Giulio

last: Pavesi

last: Forti


title: Macrophage-Endothelial Cell Crosstalk Orchestrates Neutrophil Recruitment in Inflamed Mucosa RNA-Seq

first: Connor

last: Lantz

state: IL

address: 303 E. Chicago Ave. Ward 4-075

summary: Rapid neutrophil (PMN) mobilization to sites of insult is critical for host defense and requires crossing of the vascular wall. PMN transendothelial migration (TEM) involves several well-studied sequential adhesive interactions with vascular ECs, however what initiates or terminates this process is not well-understood. Our findings identified a new mechanism where mucosal interstitial macrophages are recruited to interact with the vascular wall and locally prime endothelial cell (EC) responses to accommodate PMN TEM. Using real-time intravital microscopy (IVM) on lipopolysaccharides (LPS)-inflamed intestines in CX3CR1-EGFP macrophage-reporter mice, complemented by whole-mount tissue imaging and flow cytometry, we demonstrate that macrophage presence was critical for the initiation of PMN-EC adhesive interactions and subsequent PMN TEM and accumulation in the intestinal mucosa. Anti CSFR-1 antibody-mediated macrophage depletion in the lamina propria and at the vessel wall significantly reduced PMN adhesion and TEM in inflamed intestines. Vessel associated macrophages (VAMs) were found to trigger localized upregulation of EC ICAM-1 expression and their removal resulted in elimination of the ICAM-1 “hot spots”, impeding PMN-EC interactions. Further mechanistic studies using human clinical specimens, TNFa knockout macrophage chimeras, TNFa/TNF receptor (TNFR) neutralization and multi-cellular macrophage-EC-PMN cocultures revealed a new role for macrophage TNFa and EC TNFRII axis in regulating EC adhesion molecule expression and PMN TEM. As such, our findings identify new, clinically relevant mechanism by which macrophage regulate PMN trafficking in inflamed mucosa.

overall_design: CD45-/Live1-/CD31+ ECs were flow-sorted from LPS-stimulated colon lamina propria with and without macrophage depletion and subjected to mRNA sequencing.

first: Xingsheng

last: Ren

first: Ronen

last: Sumagin


title: Targeted transcriptional analysis of IgA vasculitis, IgA nephropathy, and IgA dominant infection related glomerulonephritis

city: Portland

first: Vanderlene

last: Kung

state: OR

address: 3181 SW Sam Jackson Park Rd.

department: Department of Pathology & Laboratory Medicine

institute: Oregon Health & Science University

summary: This study identifies immune transcript signatures that may predict IgAV nephritis in skin biopsies and distinguish IgA-IRGN from IgAN and IgAV in kidney biopsies

overall_design: RNA was extracted from 24 formalin-fixed paraffin-embedded tissue specimens (16 kidney, 8 skin) from 21 patients with IgAV nephritis (n=7), IgAN (n=5), and IgA-IRGN (n=4), and IgAV skin biopsies from patients with (n=3) and without (n=5) IgAV nephritis.  Differential gene expression and gene set enrichment analysis were performed on a total of 594 transcripts (Nanostring immunology panel) profiled using the nCounter system


title: Bankable human iPSC-derived Retinal Progenitors as a New Source of Multipotent Cells

city: Saclay

first: Jerome

middle: Eric

last: Roger

state: Please select

address: 151 Route de la Rotonde, Campus CEA Saclay - Bat 151

department: CERTO

institute: CNRS-Universite Paris Sud

summary: Retinal progenitor cells (RPCs) are the source of all retinal cell types during retinogenesis. Until now, the isolation and expansion of RPCs has been at the expense of their multipotency. Here, we report simple methods and media for the generation, expansion, and cryopreservation of human induced pluripotent stem-cell derived-RPCs (hiRPCs). Thawed and passed hiRPCs maintained biochemical and transcriptional RPC phenotypes and their ability to differentiate into all retinal cell types. Specific conditions allowed the generation of large cultures of photoreceptor precursors enriched up to 90% within a few weeks and without a purification step. Combined RNA-seq analysis between hiRPCs and retinal organoids identified genes involved in developmental or degenerative retinal diseases. Thus, hiRPC lines could provide a new source of retinal cells for cell-based therapies or drug discovery and could be an advanced cellular tool to better understand retinal dystrophies.

overall_design: Comparative gene expression analysis of retinal progenitor cells using RPC-dedicated medium (RPCM) allowing the amplification of hiPSC-derived RPCs (hiRPCs)

first: Sandy

last: Gozlan

first: Vivien

last: Batoumeni

first: Tara

last: Fournier

first: Céline

last: Nanteau

first: Anais

last: Potey

first: Marilou

last: Clémençcon

first: Gaël

last: Orieux

first: Jose-Alain

last: Sahel

first: Olivier

last: Goureau

first: Jérôme

first: Sacha

last: Reichman


title: Super-enhancer-driven MLX mediates redox balance maintanance via SLC7A11 in osteosarcoma

city: Shenzhen

first: Xin

last: Wang

state: Guangdong

address: 1068, Xueyuan Road

department: Institute of Synthetic Biology

institute: Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences

summary: A systematic analysis of super-enhancers identified MLX as a potential oncogene in osteosarcoma. Knockdown of MLX impaired tumor aggressiveness in vitro and in vivo, suggesting oncogenic properties of MLX. Mechanistically, silencing of  MLX downregulates SLC7A11, a key gene encoding glutamate/cystine antiporter, to attenuate the uptake of cystine and interrupt the redox balance, leading to ferroptotic cell death. Pharmacological inhibition of SLC7A11 triggered massive ferroptosis and caused impaired tumor growth, providing a promising approach for osteosarcoma treatment.

overall_design: We performed shRNA-mediated knock-down of MLX in 143B cells. RNA isolation and unstranded RNA-seq library preparation were carried out using RNeasy Mini Kit (Qiagen) and NEBNext UltraTM RNA Library Prep Kit for Illumina, respectively.

first: Weitang

last: Guo

first: Bing

last: Lu

first: Wei

last: Zhao


title: Osteoblast-Endothelial Transition Contributes to Glucocorticoid-Induced Bone Loss

city: Los Angeles

first: Xiuju

last: Wu

state: CA

address: 650 Charles Young Dr East, CHS A2-237

institute: University of California, Los Angeles

summary:
To investigate the transition of osteoblast to endothelial-like cell in glucocorticoid induced osteoporosis.
We performed gene expression profiling analysis using data obtained from RNA-seq of dexamethasone treated vs control.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for dexamethasone treated vs control with three biological replicates included in each group.

first: Qiao

last: Xiaojing

first: Wu

last: Xiuju


title: RNA-seq of NPs and NP-IDO-APT treated lymphocytes

city: Beijing

first: Zhenyu

last: Zhu

state: Beijing

address: 38 Xueyuan Road, Haidian

institute: Peking University

summary: To explore the effect of IDO-APT on T cell function, we conducted RNA transcriptome profiling of NPs, named as NP-Scr-APT in article, and NP-IDO-APT treated lymphocytes.

overall_design: In vitro culture of lymphocytes with NPs or NP-IDO-APT for 6 days

first: Zeliang

last: Yang


title: A meet-up of AcP and c-di-GMP modulates BldD activity for  development and antibiotic production in actinobacteria

city: Shanghai

first: Di

last: You

address: Meilong Road 130

institute: East China University of Science & Technology

summary: Actinobacteria are ubiquitous bacteria undergoing complex developmental transition coincided with antibiotics production in response to stress or nutrients starvation. This transition is mainly controlled by the interaction between the second messenger c-di-GMP and the master repressor BldD. To date, the upstream factors and the global signal networks that regulate this intriguing cell biological processes still remained unknown. In Saccharopolyspora erythraea, we found that acetyl phosphate (AcP) accumulation resulting from environmental nitrogen stress participated in the regulation of BldD activity through cooperation with c-di-GMP. AcP-induced acetylation of BldD at K11 caused the BldD dimer to fall apart and dissociate from the target DNA, as well as disrupted the signal transduction of c-di-GMP, thus governed both developmental transition and antibiotics production. Meanwhile, practical mutation of BldDK11R bypassing the acetylation regulation could enhance the positive effect of BldD on antibiotics production. Our finding represents an entirely different role of the covalent modification caused by AcP, which integrated with c-di-GMP signal in modulating the activity of BldD for development and antibiotic production coping with environmental stress. This coherent and highly conserved regulatory network might offer new insight into the direct connections from specific regulator to the actinobacteria biological process associated with major morphogenetic event

overall_design: ChIP-Seq

first: Yu

last: Fu

first: Yu-Qi

last: Dong

first: Jin-Long

last: Shen

first: Bin-Cheng

last: Yin

first: Bang-Ce

last: Ye


title: Generalized low levels of serum N-glycans associates with young biological age and good physical condition

first: Jiteng

last: Fan

state: Shanghai

address: 130 Dongan Road

institute: Fudan university

summary: Caloric restriction (CR) can prolong life and ameliorate age-related diseases, thus its molecular basis might provide new insights for finding biomarker and intervention for aging and age-related disease. Glycosylation is an important post-translational modification, which can timely reflect the changes of intracellular state. Serum N-glycosylation was found changed with aging in humans and mice. CR is widely accepted as an effective anti-aging intervention in mice and could affect mouse serum fucosylated N-glycans. However, the effect of CR on the level of global N-glycans remains unknown. In order to explore whether CR affect the level of global N-glycans, we performed a comprehensive serum glycome profiling in mice of 30% calorie restriction group and ad libitum group at 7 time points across 60 weeks by MALDI-TOF-MS. At each time point, the majority of glycans, including galactosylated and high mannose glycans, showed a consistent low level in CR group. Interestingly, the minority of glycans which have O-acetylated sialic acid modification primarily on α2,6-linked sialic acid showed a consistent high level in CR group. Liver transcriptome analysis further revealed a decreased transcripts level of genes involved in N-glycan biosynthesis while increased level of acetyl-CoA production. This finding is consistent with changes in serum N-glycans and O-acetylated sialic acids. Therefore, we provided one possible molecular basis for the beneficial effect of CR from N-glycosylation perspective.

overall_design: The calorie restriction was initiated at 12 weeks of age and liver tissues were collected from male mice at 30 weeks of age. There were 3 control-fed mice and 4 calorie restricted mice in the analysis.

first: Jichen

last: Sha

first: Shuhui

last: Zhang

first: Huijuan

first: Xiaoyun

last: Niu

first: Yong

last: Gu

first: Shifang

last: Ren

first: Jianxin


title: Comparsion of TCR-CDR3 sequencing of WT, STAT3ko, STAT3koPD-1ko  donor T cells in the Liver and Gut of allogenetic HCT mouse recepients

city: Duarte

first: Defu

last: Zeng

address: 1500 E Duarte Rd

department: Immunology & Theranostics

institute: City of Hope National Medical Center

summary: We injected  Thy1.2+ T cells from WT or STAT3ko or STAT3koPD-1ko C57BL/6 mice with T cell-depleted bone marrow cells from WT C57BL/6 mice into WT BALB/c recipients to establish acute GVHD model.

overall_design: We measured TCR repertoire of WT, STAT3ko, STAT3koPD-1ko C57BL/6donor CD4+ and CD8+ T cells before HCT and in the GVHD target tissues liver and gut at 6 days after HCT.

first: Xiwei

last: Wu

first: Qinjian

last: Li

first: Hanjun

last: Qin

first: Wei

last: Chen


title: Comparison of gene profile of WT, STAT3 KO and STAT3koPD-1ko donor T cells in the liver of allogenetic HCT mouse recepients

overall_design: We isolated donor CD4+ or CD8+ T cells from liver on day 6 after HCT, then performed RNA-Seq to compare gene profiling of T cells from WT, STAT3 KO or STAT3koPD-1ko donors.

first: Xiwe


title: PD-1 instructs a tumor suppressive metabolic program to restrain AP-1 activity in T cell lymphoma [ATAC-seq]

city: Munich

first: Tim

last: Wartewig

address: Einsteinstrasse 25

department: Clinical Chemistry

country: Germany

institute: TUM

summary:
To dissect T cell lymphoma pathogenesis, we previously engineered a genetically controllable murine model of human T-NHL based on tamoxifen-inducible irreversible expression of the T-NHL oncogene ITK-SYK, which enforces strong oncogenic TCR signaling.
Three days after ITK-SYK expression, we purified the oncogene-expressing cells by fluorescence-activated cell sorting (FACS) for Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq).

overall_design: Comparative footprint analysis of ATAC-seq data for ITK-SYK expressing T cells with and without PD-1 deletion (ex vivo and in presence of the ACLY inhibitor BMS-303141).

first: Juergen

last: Ruland


title: Organoid modeling of lung-intrinsic immune responses to SARS-CoV-2 infection

city: Leiden

first: Vincent

last: van Unen

state: ZH

address: Albinusdreef 2

department: Immunology

country: Netherlands

institute: Leiden University

summary: Current study of the mechanistic underpinnings of infectious disease is limited by an absence of human in vitro model systems which recapitulate the full spectrum of epithelial and immune responses induced by host-pathogen interactions. To address this gap, we describe a holistic, three-dimensional, air-liquid interface (ALI) lung organoid method from adult tissue comprising epithelial and stromal architecture along with a full complement of resident innate and adaptive immune cells. This novel system allows the study of the intrinsic tissue-resident immune function of the lung without requiring additional immune reconstitution from lung-extrinsic sources. Using SARS-CoV-2 infection of these 3D human lung ALI organoids, we demonstrate the ability of the endogenous immune system of the lung to mount a coordinated response including cytokine production, chemotaxis, adaptive CD4+ and CD8+ T-cell responses, and antibody production. Further, this immune response is dampened by inhibitors of viral replication and augmented in vaccinated individuals. Together, we describe the successful generation of human lung organoids that preserve the diversity of stromal and tissue-resident immune populations and SARS-CoV-2 infection thereof. This en bloc system demonstrates the sufficiency of lung to independently initiate anamnestic responses without a peripheral lymphoid component, as applicable to physiologic modeling of immune responses to SARS-CoV-2 and the broad study of pulmonary disease.

overall_design: Organoids were harvested either from collagen or suspension, digested into single-cell suspensions, and sorted on a BD FACSAria II SORP for singlet discrimination, followed by live/dead gating, then CD45-/+gating, and analyzed using scRNAseq.

first: Shannon

middle: S

last: Choi

first: Calvin

last: Kuo


title: Transcriptomic effects of an o2-sensing diguanylate cyclase in the phytopathogen Pectobacterium carotovorum

city: University Park

first: Emily

last: Weinert

state: PA

address: 306 Althouse Lab

department: Department of Biochemistry and Molecular Biology

institute: Penn State University

summary: The transcriptinal effect of the diguanylate cyclase domain-containing globin coupled oxygen senor protein PccDgcO was examined in Pectobacterium carotovrum bacteruia grown aerobically and anaerobically. RNA sequencing and differential expression analysis showed that PccDgcO plays a role in transisitioning from aerobic to anaerobic metabolism, and controls various functions, such as metal homeostasis, virulence factor expression, bacterial communication, and motility. inductively coupled plasma - mass spectrometry revealed decreased cellular concentrations of 6 important metals in the PccDgcO deletion strain, showing that globin coupled sensors can affect cellular metal homeostasis.

sample_organism: Pectobacterium carotovorum subsp. carotovorum

overall_design: Global transcript levels in WT and a 'dgcO' deletion strain of P. carotovorum were compared when grown both aerobically and anaerobically in order to identify cellular processes modulated by PccDgcO.

first: Florian

last: Fekete


title: PD-1 instructs a tumor suppressive metabolic program to restrain AP-1 activity in T cell lymphoma

summary:
To dissect T cell lymphoma pathogenesis, we previously engineered a genetically controllable murine model of human T-NHL based on tamoxifen-inducible irreversible expression of the T-NHL oncogene ITK-SYK, which enforces strong oncogenic TCR signaling.
Three days after ITK-SYK expression, we purified the oncogene-expressing cells by fluorescence-activated cell sorting (FACS) for RNA sequencing.

overall_design: Comparative gene expression analysis of RNA-seq data for ITK-SYK expressing T cells with and without PD-1 deletion.


title: Characterization of the effects of Runx1 KO in the mouse adult ovary

city: Durham

first: Humphrey

middle: Hung-Chang

last: Yao

state: NC

address: 111 TW Alexander Drive

institute: NIEHS/NIH

summary: In this study, we investigated the effects of Runx1 loss on ovarian pathogenesis in mice. Conditional loss of Runx1 in the somatic cells of the ovary led to an increased prevalence of ovarian tumors in aged mice. While ovaries from4.5 months old mice did not display tumors, they all contained abnormal follicle-like lesions. RNA-Sequencing analysis on 4.5 month old ovaries identified differentially expressed genes in Runx1 KO ovaries, including genes involved in metaplasia, ovarian cancer, epithelial cell development, tight junctions, cell-cell adhesion, and Wnt/beta-catenin pathway.

overall_design: RNA-seq on control and Runx1 KO ovaries at 4.5 months of age

first: Kamiya

last: Bridges

first: Barbara

last: Nicol


title: Selective IL-27 production by intestinal regulatory T cells permits gut-specific regulation of Th17 immunity [scRNA-Seq]

city: La Jolla

first: Li-Fan

last: Lu

address: 9500 Gilman Dr., NSB 5314

department: Biological Sciences

institute: University of California, San Diego

summary: Regulatory T (Treg) cells are instrumental in establishing immunological tolerance. However, the precise effector mechanisms by which Treg cells control a specific type of immune response in a given tissue remains unresolved. By simultaneously studying Treg cells from different tissue origins under systemic autoimmunity, here we show that IL-27 is specifically produced by intestinal Treg cells to regulate Th17 immunity. Selectively increased intestinal Th17 responses in mice with Treg cell-specific IL-27 ablation led to exacerbated intestinal inflammation and colitis-associated cancer, but also helped protect against enteric bacterial infection. Furthermore, single-cell transcriptomic analysis has identified a CD83+TCF1+ Treg cell subset that is distinct from previously characterized intestinal Treg cell populations as the main IL-27 producers. Collectively, our study uncovers a novel Treg cell suppression mechanism crucial for controlling a specific type of immune response in a particular tissue, and provides further mechanistic insights into tissue-specific Treg cell-mediated immune regulation.

overall_design: cells isolated from large intestine lamina propia of mice 10 days post Citrobacter rodentium infection and enriched for CD45+ cells by Miltenyi beads

first: Rasika

last: Patkar

first: Chia-Hao

last: Lin


title: Isotoosendanin exerts inhibition on triple-negative breast cancer through abrogating TGF-β-induced EMT via directly targeting TGFβR1

city: shanghai

first: zhangjingnan

middle: zhangjinnan

last: zhangjinnan

address: cailunroad 1200

institute: Shanghai University of Traditional Chinese medicine

summary: In this study, analysis of mRNA sequencing was used to identify potential biological signalling pathways involved in the inhibition of triple negative breast cancer metastasis by ITSN.

overall_design: In the study here we collected 6 breast samples from 2 groups (control, 1mg/kg and ITSN groups), each containing 3 replicates, and used them to obtain mRNA expression profiles.

first: Jingnan

last: Zhang

first: Lili

last: Ji


title: Comparison of gene profile of WT, STAT3 KO  donor T cells in the spleen of allogenetic HCT mouse recepients

first: Defu

last: Zeng

summary: We injected  Thy1.2+ T cells from WT or STAT3ko C57BL/6 mice with T cell-depleted bone marrow cells from WT C57BL/6 mice into WT BALB/c recipients to establish acute GVHD model.

overall_design: We isolated donor CD4+ or CD8+ T cells from spleen on day 6 after HCT, then performed RNA-Seq to compare gene profiling of T cells from WT, STAT3KO donors.

first: Xiwei

last: Wu

first: Shijie

last: Yang

first: Xiaoqi

last: Wang


title: Consequences of depleting core RNAi factors on miRNA profiles

city: DALLAS

first: David

middle: Reid

last: Corey

state: TX

address: 6001 Forest Park Road

department: Pharmacology

institute: UT-Southwestern Medical Center at Dallas

summary: In this study, we used CRISPR/Cas9 to deplete HCT116 cells of DROSHA, AGO1, AGO2, AGO1/2, AGO1/2/3, TNRC6A/B, TNRC6/B + siTNRC6C,  TNRC6A/B-/- + siGL2, WT, WT + siGL2, WT + siTNRC6C. Then, we used these KO and siRNA KD cell lines to measure resulting miRNA profiles.

overall_design: Comparative gene expression profiling analysis of small-RNA-seq data for HCT116 cells and its KO derivatives (DROSHA-/-, AGO1-/-, AGO2-/-, AGO1/2-/-, AGO1/2/3-/-, TNRC6A/B-/-, TNRC6/B-/- + siTNRC6C, TNRC6A/B-/- + siGL2, WT, WT + siGL2, WT + siTNRC6C).

first: Krystal

last: Johnson

first: Samantha

middle: T

first: Jing

last: Liu

first: Yongjun

last: Chu

middle: R


title: Siginificance of Saccharomyces cerevisiae Cdc55p on gene expression at initial stage of alcoholic fermentation

city: Ikoma

first: Daisuke

last: Watanabe

state: Nara

address: 8916-5 Takayamacho

institute: Nara Institute of Science and Technology

summary: Our previous report revealed that protein phosphatase 2A (PP2A), complexed with the B55delta-type regulatory subunit (i.e. Cdc55p), is solely responsible for the outstanding glycolytic activity of sake yeast strains (Watanabe et al., Appl. Environ. Microbiol. 85, e02083-18 (2019). However, how PP2A mediates yeast alcoholic fermentation remains elusive. Thus, RNA-seq analysis of S. cerevisiae cdc55-delta cells at the initial fermentation stage was performed to identify the downstream effector targeting the glycolytic control.

overall_design: Cdc55p-deficient cells (cdc55-delta) and their control (wild type) of S. cerevisiae BY4741 strain at 6 h after inoculation in YPD20 medium were collected and subjected to RNA-seq analysis.


title: Induced differentiation of large yellow croaker muscle satellite cells

city: Hangzhou

first: 劳

last: 霁晖

state: Zhejiang

address: 866 Yuhangtang Road, Xihu District

department: College of life sciences

institute: Zhejiang University

summary:
Traditional differentiation of myoblasts is usually induced by serum starvation method, in which 2%HS is used to induce myoblasts to differentiate into myotubes. But, traditional serum starvation method is difficult to differentiate large yellow croaker muscle satellite cells efficiently. Although myotubes were induced within 2-3 days with medium containing 2% horse serum (HS), they detached shortly and died soon after. To improve differentiation efficiency and survival rate, different combinations of basal medium, serum ratios and myogenic factors were evaluated. Finally, the F12 medium containing 8% HS, 10 ng/ml IGF-1, 50 nM necrosulfonamide and 200 μM ascorbic acid was identified as an effective recipe for myogenic differentiation. On day 3 of culture in this differentiation medium, elongated myotubes began to appear, and on day 6, striations similar to skeletal muscle were observed in some of myotubes. But it is still inefficient, the fusion index (the proportion of nuclei in multinucleated myotubes) was 6.39% on day 3 and 1.30% on day 6 (1.30%) .Therefore, we need to find a more efficient method to induce myogenic differentiation.
We then performed gene expression profiling analysis using data obtained from RNA-seq of Large yellow croaker muscle satellite cells during differentiation at three time points(day0,day3,day6).

overall_design: differential expression analysis of RNA-seq data for  Large yellow croaker muscle satellite cells during differentiation at three time points(day0,day3,day6)

first: Jun

last: Chen

first: Xiao

last: Huang

first: Jihui

last: Lao

first: Yijian

first: Yuyan

last: Jiang


title: Effect of hPNPase on Escherichia coli transcritome

city: Milano

first: Federico

last: Zambelli

address: Via Giovanni Celoria 26

institute: University of Milan

summary: We replaced the natural pnp locus with the human cDNA and studied the transcriptomes of 3 strains, namely the wt pnp+ (C-1a), the mutant with pnp ORF deletion (C-5691) and the strain with the substitution of the bacterial ORF with the human one (C-6001).

overall_design: Comparative gene expression profiling analysis of RNA-seq data for C-1a cells and its  derivatives C-5691 and C-6001

first: Federica

last: Briani

first: Giulio

last: Pavesi

first: Francesca

last: Forti


title: Transcriptome data of MHCII-high and MHCII-low hematopoietic stem cells of middle-aged mice

city: Chongqing

first: Weinian

last: Liao

address: Gaotanyan street 30

institute: Army Medical University

summary: Analysis of MHCII-high (MHCII-hi) and MHCII-low (MHCII-lo) hematopoietic stem cells  (Lineage-Sca-1+c-Kit+CD150+Flt3-CD48-). The two population of hematopoietic stem cell (HSC) were purified from the bone marrow of 12 months old (12 mo) mice. Results provide insight into the role of MHCII in HSC.

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of MHCII-hi and MHCII-lo HSCs of mice at 12 mo.

first: Changhong

last: Du

first: Junping


title: Transcriptome data of MHCII-high and MHCII-low hematopoietic stem cells of mice exposed to irradiation

summary: Analysis of MHCII-high (MHCII-hi) and MHCII-low (MHCII-lo) hematopoietic stem cells  (Lineage-Sca-1+c-Kit+CD150+Flt3-CD48-). The two population of hematopoietic stem cell (HSC) were purified from the bone marrow of mice at 3 months post 5 Gy total body irradiation (IR). Results provide insight into the role of MHCII in HSC.

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of MHCII-hi and MHCII-lo HSCs of mice with IR.

last: Wang


title: CircAFF1 is a circRNA with a role in alveolar rhabdomyosarcoma cell cycle migration

city: Roma

first: Alessio

last: Colantoni

state: RM

address: Piazzale Aldo Moro, 5

department: Dipartimento di Biologia e Biotecnologie "Charles Darwin"

institute: "Sapienza" University of Rome

summary: Circular RNAs (circRNAs), a new division of covalently closed RNA formed by a back-splicing reaction, have been involved in the regulation of diverse processes including those that occur in the development and pathologic processes such as cancer. In this manuscript, we describe circAFF1, a circular RNA overexpressed in representative rhabdomyosarcoma cell lines. We demonstrated that circAFF1 is a cytoplasmatic circRNA and its depletion in alveolar rhabdomyosarcoma cells impacts cell homeostasis favouring cell migration, pointing to this non-coding RNA as a novel regulator of the alveolar rhabdomyosarcoma progression and as a putative future therapeutic target.

overall_design: High-throughput sequencing of Poly-A+ RNA from alveolar rhabdomyosarcoma cells transfected with a siRNA targeting circAFF1 back-splicing junction (si-circAFF1). The raw data produced from cells treated with a control siRNA (si-SCR) were previously deposited in GEO with the accession code GSE174397.

first: Álvaro

last: Centrón-Broco

last: Rossi

first: Dario

last: Dattilo

first: Andrea

last: Giuliani

first: Gaia

last: Di Timoteo

first: Manuel

last: Beltran

first: Irene

last: Bozzoni


title: Characteristic impairment of progesterone response in the cultured cervical fibroblast obtained from patients with refractory cervical insufficiency

city: Chiba

first: Ichiro

last: Manabe

address: 1-8-1 Inohana, Chuo

institute: Chiba University

summary: We compared the gene expression in response to progesterone (1μM) in human cervical fibroblasts.

overall_design: Comparative RNA-seq profiling of effects of progesterone on cervical fibroblast in cervical insufficiency and normal pregnancy

first: Yumiko

last: Oishi


title: Donor T cell STAT3 deficiency enables tissue PD-L1-dependent prevention of GVHD while preserving GVL effect activity

first: Defu

last: Zeng

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

overall_design: Refer to individual Series


title: Transcriptome data of MHCII-high and MHCII-low hematopoietic stem cells of mice under homeostasis

summary: Analysis of MHCII-high (MHCII-hi) and MHCII-low (MHCII-lo) hematopoietic stem cells  (Lineage-Sca-1+c-Kit+CD150+Flt3-CD48-). The two population of hematopoietic stem cell (HSC) were purified from the bone marrow of 5 months old WT mice (Ctrl). Results provide insight into the role of MHCII in HSC.

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of MHCII-hi and MHCII-lo HSCs of mice at 5 mo.


title: Transcriptome data of MHCII-high and MHCII-low hematopoietic stem cells of mice


title: Multi-scale epigenomic priming of inflammatory genes enables rapid recall in human memory T helper cells [ChIP-seq]

city: Rotterdam

first: Ralph

last: Stadhouders

address: Dr. Molewaterplein 50

department: Pulmonary Medicine

institute: Erasmus Medical Center

summary: Memory T cells provide long-lasting defense responses through their ability to rapidly reactivate. How memory T cells efficiently ‘recall’ an inflammatory transcriptional program remains unclear. Here, we show that primary human CD4+ memory T helper (Th) cells carry three distinct activation-inducible recall gene modules that drive metabolic adaptation, T cell activation and inflammatory cytokine production. Enhancer elements controlling recall genes were epigenetically primed through the local maintenance of transcription-permissive chromatin in resting memory Th cells. At the three-dimensional level, recall genes clustered in transcriptionally permissive subnuclear compartments and resided in topologically associating domains (‘memory TADs’), in which activation-associated promoter-enhancer interactions were pre-formed. This primed epigenomic landscape was exploited by AP-1 transcription factors - including MAF - to promote rapid transcriptional activation. Finally, recall genes and their enhancers were linked to memory Th cell dysfunction in chronic inflammatory disease. Together, our results implicate multi-scale epigenomic priming - comprising a specialized three-dimensional chromatin organization - as a key mechanism underlying immunological memory.

overall_design: ChIP-Seq (n=2-3 biological replicates, independent donors) was performed on primary human naive or memory T helper cells.

first: Anne

last: van Schoonhoven


title: Transcriptome data of bone marrow hematopoietic stem cells (HSCs) with premature aging

summary: Recent advances have taken advantage of various animal models in HSC aging research, including certain gene mutations, chemicals, and ionizing radiation (IR). To identify the underlying mechanisms and phenotype switching in HSC aging,  we employed IR-induced premature HSC aging model and performed RNA-seq of HSCs from the bone marrow (BM) of mice at three months post IR and their age-matched control mice (Ctrl).

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of BM HSCs (Lineage-Sca-1+c-Kit+CD150+Flt3-CD48-) of control or IR mice.


title: Multi-scale epigenomic priming of inflammatory genes enables rapid recall in human memory T helper cells [RNA-seq]

overall_design: RNA-Seq (n=3 biological replicates, independent donors) was performed on primary human naive or memory T helper cells, both in a resting state and after in vitro stimulation.


title: Regulation of acetate tolerance by unannotated small open reading frame (smORF) polypeptides in Methylomonas sp. DH-1

city: Seoul

first: Yong-Joon

last: Cho

address: 1 Gwanak-ro, Gwanak-gu

institute: Seoul National University


title: Determination of WatR binding site in Methylomonas sp. DH-1 after lactate adaptive evolution

summary: JHM80 strain was obtained by adaptive evolution of Methylomonas sp. DH-1 strain against 8.0 g/L of lactate. The tolerance against lactate of JHM80 was obtained by the overexpression of watR (weak acid tolerance regulator). In order to discover the target genes of WatR, FLAG epitope tag was added to WatR of JHM80 strain and ChIP-seq was performed.

overall_design: In order to discover the target genes and binding consensus of WatR, ChIP-seq was performed in the normal growth condition.

first: Seungwoo

last: Cha

first: Yong

first: Ji

last: Hahn


title: IS-Seq: a novel bioinformatics pipeline for integration sites analysis

city: Cambridge

first: Aimin

last: Yan

state: MA

address: One Kendall Square Building 300 Suite 201

institute: AVROBIO, Inc.

summary: IS-Seq pipeline is developed,and 4 data sets are used to compare different abundance estimation methods of this pipeline

overall_design: HL60 cell line are transduced with a lentiviral vector, ddPCR is used to measure their average VCN, the gDNA from clone CL6 with average VCN=1 was diluted into gDNA from the transduced polyclonal HL60 bulk population at different relative contributions (100%, 75%, 50%, 10%, 1% and 0%)

first: Cristina

last: Baricordi

first: Anthony

last: Nguyen

first: Luigi

last: Barbarossa

first: Mariana

last: Loperfido

first: Luca

last: Biasco


title: Transcriptome analysis of Methylomonas sp. DH-1 wild-type and ΔwatR strain according to acetate treatment

summary: WatR (weak acid tolerance regulator) was discovered to contribute to the tolerance against several organic acids. Generally, deletion of watR gene caused decreased tolerance. However, in the case of acetate, the tolerance has been increased according to the absence of watR. In order to determine the relationship between WatR and acetate, we tried to discover the acetate responsive genes in wild-type and ΔwatR strain.

overall_design: To discover the target genes which are directly regulated by WatR upon acetate stress, the gene expression of wild-type was analyzed before/after acetate treatment and compared to the result of ΔwatR strain.


title: Plasma small-extracellular vesicles enriched in miR-122-5p promote disease aggressiveness in pediatric Anaplastic Large Cell Lymphoma

city: Padova

first: Stefania

last: Bortoluzzi

state: PD

address: Via U.Bassi 58/ B

department: Molecular Medicine

institute: University of Padova

summary: Emerging evidence shows that small extracellular vesicles (S-EVs) play a critical role in cancer biology. However, the role of S-EVs in pediatric anaplastic large cell lymphoma (ALCL) is still largely unknown. Small RNA sequencing of plasma S-EVs revealed a peculiar microRNA profile in pediatric ALCL patients compared to healthy donors (HD). In particular, the liver-specific miR-122-5p was more abundant in ALCL plasma S-EVs compared to HD. Elevated levels of miR-122-5p correlated with advanced stage disease and impaired hepatic function in ALCL patients. In vitro experiments demonstrated that miR-122-5p inhibits glucose consumption in stromal cells, and the increased glucose availability enhances ALCL cell aggressiveness. Moreover, miR-122-5p promoted tumor dissemination in vivo. This study identified a new molecular factor promoting ALCL cell dissemination. This finding sets the ground for investigating the clinical use of miR-122-5p antagonists in ALCL patients to potentially improve the clinical outcome.

overall_design: Comparative gene expression profiling analysis of small RNA-seq data for plasma small extracellular vesicle (S-EV) samples and paired tumor biopsies at diagnosis from 20 paediatric ALCL patients. Patient follow-up resulted in 14 complete remission and 6 relapsed patients. Plus, five samples from healthy donor plasma S-EVs (HD), and S-EVs from Karpas299, MAC2A, SR786, SUDHL1, and SUPM2 cell lines.

first: Carlotta

last: Damanti

first: Lavinia

last: Ferrone

first: Enrico

last: Gaffo

first: Anna

last: Garbin

last: Tosato

first: Giorgia

last: Contarini

first: Ilaria

last: Gallingani

first: Roberta

last: Angioni

first: Barbara

last: Molon

first: Giulia

last: Borile

first: Elisa

last: Carraro

first: Federico

last: Scarmozzino

first: Angelo

middle: P

last: Dei Tos

first: Marco

last: Pizzi

first: Marta

last: Pillon

first: Francesco

last: Ciscato

first: Andrea

last: Rasola

first: Ionica

last: Masgras

first: Alessandra

last: Biffi

first: Federica

last: Lovisa

first: Lara

last: Mussolin


title: Blockage of retinoic acid signaling via RARγ suppressed the proliferation of pancreatic cancer cells by arresting the cell cycle progression of the G1-S phase

city: Kobe

first: Kohei

last: Yamakawa

address: 7-5-1 Kusunoki-Cho, Chuo-Ku

institute: Kobe University Graduate School of Medicine

summary: Blockage of RARγ signaling broadly downregulated the gene expression associated with the cell cycle progression of the G1-S phase and DNA synthesis in PDAC cells

overall_design: Comparison of the gene expression profiles between control and RARγi-treated cells using PDAC cell lines (PK-1 and Panc-1)

first: Michiyo

last: Koyanagi-Aoi

first: Takashi

last: Aoi


title: Short-term smoking cessation leads to a universal downregulation of DNA methylation in patients with a smoking history

city: Zhengzhou

first: yong

last: qi

state: Henan

address: Weiwu Road

department: Department of Respiratory and Critical Care Medicine

institute: Henan Provincial People’s Hospital

type: Methylation profiling by genome tiling array

summary:
Background: Epigenetics is involved in various human diseases. Smoking is one of the most common environmental factors causing epigenetic changes. The DNA methylation changes and mechanisms after quitting smoking have not yet been defined. The present study examined the changes in DNA methylation level before and after short-term smoking cessation and explored the potential mechanism.
Methods: Whole blood and clinical data were collected in 8 patients before and after short-term smoking cessation, DNA methylation was assessed, and differentially methylated sites were analyzed, followed by a comprehensive analysis of the differentially methylated sites with clinical data. GO/KEGG enrichment and protein-protein interaction (PPI) network identified the hub genes. The differentially methylated sites were detected by GEO2R between former smoking and current smoking in GSE50660 from the GEO database. Then, a Venn analysis was carried out using the differentially methylated sites. GO/KEGG enrichment analysis was performed on the genes corresponding to the common DNA methylation sites, the PPI network was constructed, and hub genes were predicted. The enriched genes associated with the cell cycle were selected, and the gene expression was analyzed in pan-cancer based on the TCGA database.
Results: Most of the DNA methylation levels were decreased after short-term smoking cessation; a total of 694 hypermethylated CPG sites and 3184 hypomethylated CPG sites were identified. The DNA methylation levels altered according to the clinical data (body weight, expiratory, and tobacco dependence score). Enrichment analysis, construction of PPI network, and pan-cancer analysis suggested that smoking cessation may be involved in various biological processes.
Conclusions: Smoking cessation leads to epigenetic changes, mainly observed in the decline of most DNA methylation levels. Bioinformatics further identified the biologically relevant changes after short-term smoking cessation.

overall_design: Whole blood samples from 8 subjects before and after smoking cessation intervention were collected to extract genomic DNA.

first: Junyi

last: Shang

first: Xinran

last: Nie

first: Yanan

last: Qi

first: Jing

last: Zhou

first: Yong


title: Anthocyanin-treated osteoblast cells [miRNA-seq]

city: Chicago

first: Gail

middle: B

last: Mahady

state: Il

address: 833 S Wood St

department: Pharmacy Practice

institute: University of Illinois

summary: Our preliminary data shows that dietary ACNs increased osteoblast differentiation and function in human osteoblasts, as well as increased osteoblast differentiation and reduced bone resorption in transgenic medaka. In cultured human osteoblasts, ACNs and resveratrol enhanced growth, reduced apoptosis and increased the expression of HDACs and PGC-1, suggesting that ACNs alter epigenetic regulation and mitochondrial biogenesis

overall_design: miRNA-seq

first: Pinal

last: Kanabar


title: RNAseq of mouse corpus callosum from WT or TRPA1-KO animals under chronic cerebral hypoperfusion

city: Kyoto

first: Kazuki

last: Nagayasu

address: 46-29 Yoshidashimoadachicho, Sakyo

department: Graduate School of Pharmaceutical Sciences

institute: Kyoto University

summary: Chronic cerebral hypoperfusion is manifested in various CNS diseases accompanied by cognitive impairment, such as dementia, however the precise mechanism of chronic cerebral hypoperfusion-induced cognitive impairment remains unknown. Recently, transient receptor potential ankyrin 1 (TRPA1), activated by oxidative stress, was reported to be involved in the cerebrovascular diseases, therefore we investigated the pathophysiological role of TRPA1 in chronic cerebral hypoperfusion using a mouse bilateral common carotid artery stenosis (BCAS) model. Early cognitive impairment and white matter injury was induced by BCAS in TRPA1-knockout (TRPA1-KO) but not wild-type (WT) mice. For further investigation into the involvement of TRPA1 in chronic cerebral hypoperfusion, we conducted RNA sequence (RNAseq) in the corpus callosum from sham- and BCAS-operated WT and TRPA1-KO mice.

overall_design: Corpus callosum mRNA profiles of BCAS- or sham-operated WT or TRPA1-KO mice.

first: Masashi

last: Kakae

first: Hisashi

last: Shirakawa

first: Shuji

last: Kaneko


title: USP7 represses lineage differentiation genes of mouse embryonic stem cells through both catalytic and non-catalytic activity

first: Chao

last: Liu

state: State...

address: Zhejiang University

summary: USP7, a ubiquitin-specific peptidase (USP), plays an important role in many cellular processes through its catalytic deubiquitination of various substrates. However, its nuclear function to regulate gene expression in mouse embryonic stem cells (mESCs) remains largely unknown. Here, we report that USP7 maintains mESCs identity through both catalytic activity-dependent and -independent repression of lineage differentiation genes. Usp7 depletion attenuates SOX2 level and derepresses lineage differentiation genes thereby compromising mESCs identity. Mechanistically, USP7 deubiquitinates and stabilizes SOX2 to repress mesoendodermal (ME) lineage genes. Moreover, USP7 assembles into RYBP-variant polycomb repressive complex 1 (vPRC1) and contributes to Polycomb chromatin domain-mediated repression of ME lineage genes in a catalytic activity-dependent manner. However, USP7 deficient in its deubiquitination function is able to maintain RYBP binding on chromatin to represses primitive endoderm-associated genes in mESCs. Overall, our study demonstrates that USP7 harbors both catalytic and non-catalytic scaffold activity to repress lineage differentiation genes thereby revealing a previously unrecognized role in controlling gene expression and maintaining mESCs identity.

overall_design:
mRNA profiles of mESCs with auxin inducible degradation to rapidly deplete Usp7 protein, and overexpressed a Usp7 with HA-C224S enzyme catalytic center mutation (HA-C224S) and a HA-Usp7 wild type full length (HA-Usp7-FL)  after IAA addition for 3 days
mRNA profiles of mESCs transfected with shRNA lentiviruses for Usp7 and vector (Negtive control) after 7 days.

first: Junfeng

last: Ji


title: A histone deacetylase network regulates epigenetic reprogramming and viral silencing in HIV infected cells

city: Boston

first: Jeremy

last: Simon

address: 450 Brookline Ave

department: Department of Data Science

institute: Dana-Farber Cancer Institute

summary: During HIV infection, a latent viral reservoir is formed that persists during antiretroviral therapy (ART) and is maintained by a heritable state of transcriptional repression. Recent findings indicate that much of the reservoir originates from infections occurring in the weeks near the time of ART initiation, raising the important possibility that interventions during this period might prevent reservoir seeding and substantially reduce reservoir size. Based on this concept, we tested the ability of compounds that target epigenetic machinery to prevent the establishment of latent HIV infection in primary CD4 T cells. We identified class 1 histone deacetylase inhibitors (HDACi) as potent agents of latency prevention, an activity distinct from latency reversal. Inhibiting HDACs in productively infected cells caused extended maintenance of HIV expression, even after HDACi withdrawal, and this activity was associated with persistently elevated H3K9 acetylation and reduced H3K9 methylation at the viral LTR promoter region. HDAC inhibition in HIV-infected CD4 T cells during effector-to-memory transition led to a striking change in the memory subset distribution indicating reprogramming of cell identity. Through knockout of individual HDACs and use of HDAC-selective inhibitors, we determined that HDAC1 and HDAC3 play crucial and distinct roles in proviral silencing initiation. Overall, this work indicates that a network of HDACs regulate a critical gateway process for HIV latency establishment and are required for the development of CD4 T-cell memory subsets that preferentially harbor long-lived, latent provirus. Epigenetic reprogramming by clinical targeting of HDACs during ART initiation may represent a novel way to prevent seeding of the HIV reservoir in vivo

overall_design: CUT&RUN profiling of H3K4me3, H3K27ac, H3K9ac, H3K9me3 and H3K27me3 histone marks in infected cells that had been cultured with or without vorinostat (SAHA). We similarly profiled total RNA Polymerase II (RPD1 subunit, tPol2) and RNA Polymerase II phosphorylated on Ser 2 of the heptameric repeat region (P-S2, Pol2s2)

middle: M

first: Jackson

last: Peterson

first: Edward

last: Browne


title: Anthocyanin-treated osteoblast cells