title: mRNA profiling of injured mouse livers with MycER activation

city: Cambridge

first: Luca

last: Pellegrinet

address: 80 Tennis Court Road

department: Biochemistry

institute: University of Cambridge

summary: This study explore the role of the Myc oncogene  in liver injury, in particular for the determination of the cellular programme involved in tissue repair and normalization after injury, a process that is blocked by Myc deregulation. The first objective of this study is to define the transcriptional profile of mouse livers 12 days after injury with or without MycER activation. The second objective is to determine the trancriptionl signature at 1,2,3,7 days after MycER was inactivated in pre injured liver to monitor its normalization.

overall_design: 3 mice per time points where used. The first analysis is done comparing samples "12" with "12ON", for the second ojective the 4 OFF time points (1,2,3,7) where compared to the "12ON" samples.

first: Gerard

last: Evan

first: Sabine

last: Dietmann


title: Next Generation Sequencing Facilitates Quantitative Analysis of control and AOM+DSS mouse model Transcriptomes

status: Public on Mar 05 2022

city: Shanghai

first: Jianfeng

last: Chen

state: Shanghai

address: 270 Dong'an Road

country: China

institute: Fudan University Shanghai Cancer Center

type: Expression profiling by high throughput sequencing

summary: The goal of this study is to screen the differential genes between control and AOM+DSS mouse model, then analyze the significant pathways.

overall_design: The total RNA of each group was pooled from 6 individuals separately. RNA-seq was performed using the proton sequencing process.

first: Peipei

last: Ding

first: Weiguo

last: Hu


title: Variability in energy metabolism enzymes in tumor cells.

city: Barcelona

first: Gustavo

last: Rodriguez-Esteban

state: Catalonia

address: C. Baldiri Reixac, 4; Barcelona Science Park

department: Development

country: Spain

institute: Centro Nacional de Análisis Genómico

summary:
Variability in gene expression is an important and largely unknown phenomenon responsible of tumor resistance to chemotherapy. Here, we show that energy metabolism proteins are highly variable, specially Glut1, G6PD, PKM2 and SDHA. In contrast, the variability of housekeeping proteins was low. We identified the PI3K/Akt/mTor pathway as the source of variability for PKM2.Variability was independent of the energy source used. However, cells grown on glucose down-regulate G6PDH and SDHA, promoting oxidative stress.

Variability and chemotherapy plasticity were directly related, and the combination of drugs with opposite effect on the expression of plastic proteins resulted in positive synergy. Human solid tumor cells displayed higher variability in metabolic enzymes than cultured cells. The most aggressive tumors showed higher variability than less aggressive ones. This suggests that variability in energy metabolism enzymes could be a biomarker for tumor stratification and therapy election.

overall_design: In order to reveal the origin of the variability of metabolic enzymes, we performed single-cell transcriptomic analysis of HeLa cells. 96 cells were sorted and sequenced for this study.

first: Holger

last: Heyn

last: Rodríguez-Esteban


title: In-vivo Transcriptomic Profiling of Systemic Aging using Stem Cell Encapsulation

city: Lausanne

first: Jerome

last: Feige

address: EPFL Innovation Park, Building H

department: Musculo-Skeletal Health

country: Switzerland

institute: Nestle Institute Of Health Sciences

summary: Sustained exposure to a young systemic environment rejuvenates aged tissues and promotes stem cell function. However, due to the intrinsic complexity of tissues it remains challenging to pinpoint direct effects of circulating factors on specific cell populations. Here we describe a method for the encapsulation of human stem cells in highly diffusible polyethersulfone hollow fiber capsules that can be used to profile systemic aging independent of physical cellular interactions in-vivo.

sample_organism:
Homo sapiens
Mus musculus
unidentified

overall_design: Microarrays from encapsulated human myoblasts subcutaneously implanted into young and aged mice for ten days. Control microarrays were performed using mouse connective tissue surrounding implanted capsules in the young and aged conditions.

first: Omid

last: Mashinchian

first: Xiaotong

last: Hong

first: Eugenia

last: Migliavacca

first: Christophe

last: Boss

first: Frederic

last: Raymond

first: Sylviane

last: Metairon

first: C

middle: F

last: Bentzinger

middle: N


title: Disruption of serine/threonine protein kinase STK-12 increases cellulase expression in Neurospora crassa

city: Tianjin

first: liangcai

last: lin

address: 32 West 7th Avenue, Tianjin Airport Economic Area

institute: Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences

summary: In this work, we reported that STK-12 functions as a novel repressor of cellulase expression. The stk-12 disruption strain not only displayed enhanced cellulase production but also retained a steady state, with high expression levels of cellulase genes, for longer than the wild type strain.

overall_design: Conidia of △stk-12 and wild-type (WT) strains were separately inoculated into Avicel medium (1×Vogel's salt, 2% w/v crystalline cellulose) and batch cultured for 5 days. Total RNA from frozen samples was extracted and treated.

first: Liangcai

last: Lin

first: Chaoguang

last: Tian


title: Exosomes from MSC facilitate diabetic wound healing by promoting angiogenesis

status: Public on Mar 04 2022

city: Yiwu

first: Qiang

last: Sun

state: Zhejiang

address: No. N1, Shangcheng Avenue

institute: Zhejiang University

type: Non-coding RNA profiling by genome tiling array

summary: Mesenchymal stem cell (MSC)-derived exosomes had been reported to be a prospective candidate in accelerating diabetic wound healing. Hence, this study intended to explore whether exosomes originating from the human umbilical cord MSC (hucMSC) could display a superior proangiogenic effect on diabetic wound repair and its underlying molecular mechanism.

overall_design: The conditioned medium of MSCs was collected to isolate Exos.

last: Li

first: Guo

last: lei


title: High-dose isoproterenol induced cardiac immune responses

city: Muenster

first: Hyun-Woo

last: Jeong

state: NRW

department: Dept. Tissue Morphogenesis

country: Germany

institute: Max-Planck-Institute for Molecular Biomedicine

summary: Cardiac CD45+ cells sorted from isoproterenol treated mice

overall_design: WT female mice were injected intraperitoneally with 200 mg/kg isoproterenol (ISO). After 24h, hearts were harvested, digested and flow corted for CD45+ cells. 15K CD45+ cells were subjected to 10Xgenomics and NGS. Cells from 3 mice were pooled.

first: Xudong

last: Liao

first: Mukesh

middle: K

last: Jain


title: LRG1 is an adipokine that mediates obesity-induced hepatosteatosis and insulin resistance [liver_RNA-seq]

city: SAN ANTONIO

first: Sijia

last: He

state: Texas

address: 7703 Floyd Curl Dr.

country: USA

institute: uthealth sa

summary: Dysregulation in adipokine biosynthesis and function contributes to obesity-induced metabolic diseases. However, the identities and functions of many of the obesity-induced secretory molecules remain unknown. This study identified Leucine-rich alpha-2-glycoprotein 1 (LRG1) as an obesity-associated adipokine. The effects of LRG1 deficiency on liver tissue gene expression were tested in current assay.

overall_design: To test the effects of LRG1 deficiency on gene expression profile of liver tissue in mouse, liver samples from wild type and Lrg1 knockout mice were used for analysis.

first: Jiyoon

last: Ryu

first: Juanhong

last: Liu

first: Hairong

last: Luo

first: Ying

last: Lv

first: Paul

middle: R

last: Langlais

first: Jie

last: Wen

first: Feng

last: Dong

first: Zhe

first: Wenjuan

last: Xia

first: Jane

middle: L

last: Lynch

first: Ravindranath

last: Duggirala

first: Bruce

middle: J

last: Nicholson

first: Mengwei

last: Zang

first: Yuguang

last: Shi

first: Fang

last: Zhang

first: Juli

last: Bai

first: Lily

middle: Q


title: sAPPa, a neuroprotective protein in the brain has widespread effects on the transcriptome and proteome of human iPSC-derived glutamatergic neurons related to memory mechanisms.

city: Dunedin

first: Katie

last: Peppercorn

state: Otago

address: 710 Cumberland Street

country: New Zealand

institute: University of Otago

summary: Secreted amyloid precursor protein alpha (sAPPa) processed from a parent human brain protein, APP, can modulate learning and memory. It has potential for development of a therapy preventing, delaying, or even reversing Alzheimer’s disease. In this study a comprehensive analysis to understand how it affects the transcriptome and proteome of the human neuron was undertaken. Human iPSC-derived glutamatergic neurons in culture were exposed to 1 nM sAPPa over a time course and changes in the transcriptome and proteome were identified with RNA sequencing and SWATH-MS respectively. A large subset (~30%) of differentially expressed transcripts and proteins were functionally involved with the molecular biology of learning and memory, consistent with reported links of sAPPa to memory enhancement, as well as neurogenic, neurotrophic and neuroprotective phenotypes in previous studies. Differentially expressed proteins included those encoded in previously identified Alzheimer’s risk genes, APP processing related proteins, proteins involved in synaptogenesis, neurotransmitters, receptors, synaptic vesicle proteins, cytoskeletal proteins, proteins involved in protein and organelle trafficking, and proteins important for cell signalling, transcriptional splicing, and functions of the proteosome and lysosome. We have identified a complex set of genes affected by sAPPa, which may aid further investigation into the mechanism of how this neuroprotective protein affects memory formation and how it might be used as an Alzheimer’s disease therapy.

overall_design: Human iPSC derived glutamatergic neurons (n=3 per time point) were treated with 1 nM sAPPa in a reverse time course (2 h, 0.5 h or 0 h) and subject to RNA sequencing. Neurons were cultured on a 6 well plates (3 wells per time point) and sAPPa was added to the cell culture media at 2 h, 30 min or 0 h prior to addition of lysis buffer (Norgen total RNA extraction kit). The Otago Genomics Facility (University of Otago) performed two lanes of paired end RNA sequencing for each of the 9 RNA samples. Differential analysis compared the differential expression between 30 min/0 h and 2 h/0 h.

first: Warren

last: Tate

first: Stephanie

last: Hughes

first: Elizabeth

last: Permina


title: RNA-sequencing of PAD patient derived myotubes under hypoxia cycling conditions

city: Waco

first: Panagiotis

last: Koutakis

state: TX

address: 101 Bagby Ave

department: Biology

institute: Baylor University

summary: Peripheral Artery Disease (PAD) is a disease characterized by atherosclerosis of the arteries supplying the lower extremities. In PAD, atherosclerotic occlusions restrict the delivery of blood to the skeletal muscles of affected extremities. As a result, the muscles which are supplied by the affected arteries can experience ischemia/reperfusion (I/R) injuries. This can lead to an altered metabolomics profile, increased oxidative damage to those muscles, and the degeneration of myofibers. In our study, we modeled I/R injuries by culturing differentiated skeletal muscle derived cells (skMDCs), also known as myotubes, under cyclic conditions of hypoxia and hyperoxia. These conditions mimic those that PAD patient muscles experience. Our results show an altered transcriptomic profile in PAD patient derived myotubes and explore the contribution of I/R injuries to those transcriptomic changes.

overall_design: Examination of gene expression differences between healthy control and PAD patient myotubes as well as comparisons between hypoxia cycling conditions.

first: Andrew

last: Ring


title: Alterations in Retrotransposition, Synaptic Connectivity, and Myelination Implicated by Transcriptomic Changes Following Maternal Immune Activation in Nonhuman Primates

city: Los Angeles

first: Katherine

last: Eyring

state: CA

address: 695 Charles E. Young Dr. South

institute: UCLA

summary: BACKGROUND: Maternal immune activation (MIA) is a proposed risk factor for multiple neuropsychiatric disorders,  including schizophrenia. However, the molecular mechanisms through which MIA imparts risk remain poorly un-  derstood. A recently developed nonhuman primate model of exposure to the viral mimic poly:ICLC during pregnancy  shows abnormal social and repetitive behaviors and elevated striatal dopamine, a molecular hallmark of human  psychosis, providing an unprecedented opportunity for studying underlying molecular correlates.  METHODS: We performed RNA sequencing across psychiatrically relevant brain regions (prefrontal cortex, anterior  cingulate, hippocampus) and primary visual cortex for comparison from 3.5- to 4-year-old male MIA-exposed and  control offspring—an age comparable to mid adolescence in humans.  RESULTS: We identify 266 unique genes differentially expressed in at least one brain region, with the greatest number  observed in hippocampus. Co-expression networks identified region-specific alterations in synaptic signaling and  oligodendrocytes. Although we observed temporal and regional differences, transcriptomic changes were shared  across first- and second-trimester exposures, including for the top differentially expressed genes—PIWIL2 and  MGARP. In addition to PIWIL2, several other regulators of retrotransposition and endogenous transposable  elements were dysregulated following MIA, potentially connecting MIA to retrotransposition.  CONCLUSIONS: Together, these results begin to elucidate the brain-level molecular processes through which MIA  may impart risk for psychiatric disease

overall_design: Bulk RNAseq analysis of 4 non-human primate brain regions following materal immune activation

first: Nicholas

last: Page

first: Michael

last: Gandal

first: Myka

last: Estes

first: Scott

last: Cameron

first: Jessie

last: Buth

first: Sepideh

last: Parhami

first: Gokul

last: Ramaswami

first: Karl

last: Murray

first: David

middle: G

last: Amaral

first: Judy

middle: A

last: Van de Water

first: Cynthia

middle: M

last: Schumann

first: Cameron

middle: S

last: Carter

first: Melissa

middle: D

last: Bauman

first: A

last: McAllister

first: Daniel

middle: H

last: Geschwind


title: Development of gene expression signatures for high salt treated RAW264.7 macrophages

city: Regensburg

first: Patrick

last: Neubert

address: Franz-Josef-Strauß-Allee 11

department: Department of Clinical Microbiology and Hygiene

institute: University Hospital Regensburg

summary: Identification of high salt-modified gene expression changes after 24h with and without LPS stimulation

overall_design: RAW264.7 macrophages were exposed to +40 mM NaCl +/- 10 ng/ml LPS for 24h

first: Stefan

last: Tomiuk


title: The nephrotxin Puromycin aminonucleoside induces injury in kidney organoids differentiated from human urine SIX2-positive stem cell derived induced pluripotent stem cells.

city: Düsseldorf

first: Wasco

last: Wruck

address: Moorenstr. 5

institute: Universitätsklinikum Düsseldorf

summary: Kidney diseases including acute kidney injury (AKI) and chronic kidney disease (CKD), which can progress to end stage renal disease (ESRD), are a worldwide health burden. Organ trans-plantation or kidney dialysis are the only effective available therapeutic tools. Therefore, in vitro models of kidney diseases and the development of prospective therapeutic means are highly demanded. Within the kidney, the glomeruli are involved in blood filtration and waste excre-tion, and are easily affected by changing cellular conditions. Puromycin aminonucleoside (PAN) is a nephrotoxin, which can be harnessed for imitating acute glomerular damage and modelling of glomerular disease. For this reason, we generated kidney organoids from three iPSC lines and treated these with PAN in order to induce kidney injury. Morphological observations re-vealed disruption of glomerular and tubular structures within the kidney organoids upon PAN treatment, which were confirmed by transcriptome analyses. Subsequent analyses revealed an upregulation of immune response as well as inflammatory and cell death-related processes. We concluded that treatment of iPSC-derived kidney organoids with PAN induces kidney injury mediated an intertwined network of inflammation, cytoskeletal re-arrangement, DNA damage, apoptosis and cell death. Furthermore, urine stem cell-derived kidney organoids can be used for modelling of kidney-associated diseases and drug discovery.

overall_design: The transcriptomes of iPSC-derived spheroids and kidney organoids with and without Puromycin aminonucleoside (PAN) treatment were compared by microarray analysis (PrimeView Human Gene Expression Array, Affymetrix, Thermo Fisher Scientific).

first: Wruck

last: Wasco

first: Nguyen

last: Lisa

first: Adjaye

last: James


title: Next Generation Sequencing Facilitates Quantitative Analysis of MM cell line Transcriptomes

city: Chengdu

first: Fangfang

last: Wang

address: Guoxuexiang NO.37

institute: West China Hospital, Sichuan University

summary: We discovered that the activated-leukocyte-cell-adhesion-molecule (ALCAM)  regulated myelomagenesis. ALCAM was a negative regulator of myeloma clonogenicity. To determine what signalling pathways are affected by ALCAM in MM cells, we established CTR-KD and ALCAM-KD RPMI8226 MM cell lines. Hoechst33342 staining was performed on CTR-KD and ALCAM-KD RPMI8226 MM cell. Then flow cytometry was used to separate MP and SP cells of the two types of cells. Total RNA of each sample was extracted using TRIzol Reagent (Invitrogen). Next generation sequencing library preparations were constructed  using NEBNext®  Ultra™ RNA Library Prep Kit for Illumina (Vazyme, Cat No. NR603, China).RNA-seq was performed by GENEWIZ (Suzhou, China) on an Illumina Hiseq platform.

overall_design: Examination of mRNA profiles in CTR-KD MP, CTR-KD SP,  ALCAM-KD MP and ALCAM-KD SP RPMI8226 cell.

first: Wang

last: Fangfang

first: Luo

last: Hongmei

first: Zhang

last: Dan

first: Zheng

last: Yuhuan


title: LRG1 is an adipokine that mediates obesity-induced hepatosteatosis and insulin resistance [array]

first: Sijia

last: He

summary:
Dysregulation in adipokine biosynthesis and function contributes to obesity-induced metabolic diseases. However, the identities and functions of many of the obesity-induced secretory molecules remain unknown. In this study, microarray was used to identify genes that are differentially expressed during adipocyte differentiation, further screening based on microarray result identified Leucine-rich alpha-2-glycoprotein 1 (LRG1) as an obesity-associated adipokine.
Expression data of pre-adipocytes and  mature adipocytes

overall_design: 4 groups of cells were used in this assay: brown pre-adipocyte (n=3), differentiated brown adipocyte (n=3), 3T3-L1 white pre-adipocyte (n=3), differentiated 3T3-L1 white adipocyte (n=3)

first: Jiyoon

last: Ryu

first: Juanhong

last: Liu

first: Hairong

last: Luo

first: Ying

last: Lv

first: Paul

last: Langlais

first: Jie

last: Wen

first: Feng

last: Dong

first: Zhe

last: Sun

first: Wenjuan

last: Xia

first: Jane

last: Lynch

first: Ravindranath

last: Duggirala

first: Bruce

last: Nicholson

first: Mengwei

last: Zang

first: Yuguang

last: Shi

first: Fang

last: Zhang

first: Juli

last: Bai

first: Lily


title: Whole genome DNA methylation profiling of D2 medium spiny neurons in mouse nucleus accumbens using two independent library preparation methods

city: Tallahassee

first: Jian

last: Feng

state: FL

address: 319 Stadium Dr

department: biological science

institute: Florida State University

type: Methylation profiling by high throughput sequencing

summary: We isolated genomic DNA from adult male mouse nucleus accumbens (NAc) D2 medium spiny neurons (D2-MSN) by fluorescence-activated cell sorting. We performed the whole genome methylation profiling using two independent library preparation methods, namely the sodium bisulfite-based Accel-NGS Methyl-Seq (AM-seq) of Swift biosciences and the enzymatic conversion-based method Enzymatic Methyl-seq (EM-seq) from New England Biolabs, on two identical samples. We mapped about 400 million paired-end reads to the mouse genome (build mm10) and assessed measures of each methylome by two methods. This study provided a side-by-side comparison of two independent whole genome profiling methods for low-input neuronal samples.

overall_design: Whole genome DNA methylation profiling of NAc D2-MSN of adult male C57BL/6J mice.

first: Yuxiang

last: Li

first: Haiyang

last: Xu

first: Javed

last: Chitaman


title: Arabinogalactan enhanced Mycobacterium virulence through reprogramming phagocyte oxidative metabolism and inducing cell death

first: Hanmei

last: Liu

address: D507, School of Life Sciences, Fudan University, Yangpu District, Shanghai

department: School of Life Sciences

institute: Fudan University

summary: Arabinogalactan (AG) participates in forming the cell wall core of mycobacteria which is known as mAGP complex. Few studies on effects of AG on real-world virulence revealed its interaction with the host immune system, especially when taking the whole mycobacterial conditions into account.  By CRISPRi, conditional mutant strains were constructed with low-expression of embA or glfT2 which involved in AG biosynthesis. HPGPC and HPLC confirmed EmbA_KD strain had a remarkable decrease in AG content with fragmentary arabinose chains, and GlfT2_KD strain displayed a modest reduction in content with dramatically cut-down galactose chains. Loose and thickened cell wall structure occurred with AG loss, and extracellular leakage happened from decreased arabinose under TEM and SEM. Phenotypes of EmbA_KD strain including spreading motility, biofilm formation and ethambutol resistance altered.  When murine Tr4A.1 macrophages and human Gal9 KO cells were infected, EmbA_KD/GlfT2_KD strains displayed limited proliferation. Through transcriptome profiling, phagocytes infected by EmbA_KD/GlfT2_KD strains showed enhanced oxidative metabolism, and macrophages trended to survival when exposed to EmbA_KD strain. Secretion of proinflammatory cytokines such as IL-6/MCP-1/MIP-1α/MIP-1β were induced by EmbA_KD strain via the TLR2 - C/EBPβ signaling pathway, which benefited the bactericidal effect. The onset progressions of knock-down strains in larvae zebrafish and murine tail infection models significantly delayed with attenuate inflammatory infiltrate in murine tail, further confirmed that AG was an important virulence factor at the whole bacterial level. In adult zebrafish, EmbA_KD showed decreased CFU/granulomas counts and restricted formation and distribution of granulomas.  In conclusion, AG restrained host innate immune responses to enhance proliferation through reprogramming oxidative metabolism and cell death, and inhibiting phagocytes migration possibly. Arabinose chains contribute more to AG virulence, and cause easier recognition and removal of Mycobacterium by the host immune cells, which mimics the ethambutol inhibition process.

overall_design: Transcriptome profling of murine J774A.1 macrophage which infected by embA/glfT2 knock-down Mycobacterium marium

first: Yeyu

first: Lu

first: Haipeng

first: Jun


title: LRG1 is an adipokine that mediates obesity-induced hepatosteatosis and insulin resistance.

first: Sijia

last: He

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

overall_design: Refer to individual Series


title: LRG1 is an adipokine that mediates obesity-induced hepatosteatosis and insulin resistance [heaptocyte_RNA-seq]

summary: Dysregulation in adipokine biosynthesis and function contributes to obesity-induced metabolic diseases. However, the identities and functions of many of the obesity-induced secretory molecules remain unknown. This study identified Leucine-rich alpha-2-glycoprotein 1 (LRG1) as an obesity-associated adipokine. The effects of LRG1 protein treatment on primary hepatocyte gene expression was tested in current assay.

overall_design: To test effects of LRG1 protein treatment on gene expression profile in primary hepatocytes, total of 6 samples were analyzed (3 control vs 3 LRG1 treated).

first: Jiyoon

last: Ryu

first: Juanhong

first: Hairong

last: Luo

first: Ying

last: Lv

first: Paul

last: Langlais

first: Jie

last: Wen

first: Feng

first: Zhe

first: Wenjuan

first: Jane

first: Ravindranath


title: Medulloblastoma cerebrospinal fluid reveals hypoxic indicators (metabolites and lipids) and cancer-specific RNAs

city: St. Petersburg

first: Rudrmani

last: Pokhrel

state: United States

address: 600 Fifth Street S.

department: Oncology

institute: Johns Hopkins All Children’s Hospital

summary: Medulloblastoma (MB) is the most common malignant brain tumor in children.  There remains an unmet need for diagnostics to sensitively detect the disease, particularly recurrences. Cerebrospinal fluid (CSF) provides a window into the central nervous system, and liquid biopsy of CSF could provide a relatively non-invasive means for disease diagnosis. CSF samples from patients with or without medulloblastoma (MB) were subjected to RNA-sequencing to identify differentially expressed transcripts. Although the transcriptomic signatures in CSF to differentiate MB subgroup separation was challenging, we were able to identify a group of gene signatures that could separate cancer from normal CSF. Our approach provides several candidate signatures that deserve further validation, including the novel circular RNA circ_463, and insights into the impact of MB on the CSF microenvironment.

overall_design: CSF samples from patients with (n=40) or without (n=11; no cancer) MB were subjected to RNA-sequencing. RNAs were purified from 0.2 mL CSF and library was made Ovation SoLo system (NuGen). Libraries were subjected to RNA-sequencing using a NextSeq550 (illumina).

first: Bongyong

last: Lee

first: Rudramani

first: Ranjan

last: Perera


title: Distinct adipogenic and fibrogenic differentiation capacities of mesenchymal stromal cells from pancreas and white adipose tissue

city: Nuthetal

first: Heike

last: Vogel

state: BRB

address: Arthur-Scheunert-Allee 114-116

department: Department of Experimental Diabetology

institute: German Institute of Human Nutrition Potsdam-Rehbruecke

type: Non-coding RNA profiling by high throughput sequencing


title: Distinct adipogenic and fibrogenic differentiation capacities of mesenchymal stromal cells from pancreas and white adipose tissue [miRNA-Seq]

summary: Distinctive characteristics between iWAT and pancreas MSCs from 10-week old B6 mice was investigated via transcriptomics and miRNome

overall_design: Comparison of two distinctive species (iWAT and pancreas) of mesenchymal stromal cells (MSCs) from mice.

first: Annette

last: Schürmann

first: Tim

last: Schulz

first: Heja

last: Aga

first: Mandy

last: Stadion

first: Francisco

last: Garcia

first: George

last: Soultoukis

first: Markus

last: Jähnert

first: Pascal

last: Gottmann


title: Distinct adipogenic and fibrogenic differentiation capacities of mesenchymal stromal cells from pancreas and white adipose tissue [RNA-Seq]


title: Comprehensive transcriptional and clonotypic analysis of peripheral blood constituents in Sézary syndrome.

city: Iowa City

first: Ali

last: Jabbari

state: IA

address: 500 Newton Road

department: Dermatology

institute: University of Iowa

summary: Although central to the diagnosis of cutaneous T cell lymphoma (CTCL) is the malignant clonal proliferation of skin-tropic T cells the diagnosis represents a spectrum of diseases and clinical courses. Most patients have an indolent disease course with cycling of therapies, while others, especially in advanced stages of disease, have aggressive progression and poor median survival. Adding to the difficulty of treatment, Sézary syndrome (SS), a leukemic variant of CTCL, lacks highly characteristic phenotypic and genetic markers that would aid in not only the diagnosis of the malignancy, but also response to therapies. Using single-cell mRNA and T-cell-receptor sequencing, of peripheral blood immune cells in SS, we extensively mapped the transcriptomic variations of nearly 50,000 T cells of both malignant and nonmalignant origins. We identified potential diverging SS cell populations, including quiescent and proliferative populations shared across multiple patients.

overall_design: CD45+ immune cells were isolated from peripheral blood of patients with Sezary Syndrome. Single-cell suspensions were processed with the Chromium Single Cell 5-prime Library & Gel Bead Kit and the 10x Genomics TCR Immunprofiling kit.

first: Nicholas

last: Borcherding


title: Next Generation Sequencing analysis of IL-2 induced OT-I wild-type and OT-I Themis cKO cells for three days.

city: Xiamen

first: Yongchao

last: Liu

address: School of life sciences, Xiamen Univesity, Xiamen, Fujian. 361102, P.R.China

institute: Xiamen University

summary: Thymocyte-expressed molecule involved in selection (Themis) was identified as a T cell-specific protein for T cell development. Recently, Themis was found to be required for T cell homeostasis by orchestrating TCR signaling and cytokine, especially γc family cytokine IL-7 signaling in peraphrial CD8+ T cells. Here, our study identifies Themis as a regulator for another γc family cytokine IL-2-induced proliferation. Transcriptomics and metabolomics reveal that Themis regulates Jak-Stat, Akt-mTOR as well as the downstream metabolic pathways. Moreover, how Themis regulates Shp1 phosphatase activity is still controversial. We further demonstrate that Themis negatively regulates Shp1 phosphatase activity on Jak1 and Jak3 to facilitate downstream signaling and subsequently metabolic reprograming, highlighting the importance of Themis in metabolic responses of CD8+ T cells.

overall_design: Fresh enriched naïve OT-I wild-type and OT-I Themis cKO cells were cultured with IL-2 (1μg/ml) for three days. mRNA profiles of the culturing cells were generated by deep sequencing in triplicate.


title: Single cell mRNA-Seq of developing stem-borne roots in tomato

city: Rehovot

first: Idan

last: Efroni

address: POB 12

department: Plant Sciences

country: Israel

institute: Hebrew University

summary: Plants adjust their growth in response to environmental cues by forming new organs in different development contexts. Underground lateral roots initiate from prepatterned cells in the main root, but cells can also bypass the root/shoot trajectory separation and generate shoot-borne-roots through an unknown mechanism. Here, we mapped tomato (Solanum lycoperiscum) shoot-borne-roots development at single-cell resolution and show that they initiate from differentiated phloem-associated cells via a unique transitional stem-cell-like state. This state required the activity of a transcription factor which we named SHOOTBORNE ROOTLESS (SBRL), a function that was deeply conserved in angiosperms. Phylogenetic analysis revealed that SBRL arose in angiosperms as an ancient duplicated superlocus with its paralogs showing root-type-specific transient expression in wound-induced and lateral root initiation. Mutants in all SBRL-like genes completely lost post-embryonic roots. We propose that the activation of a common transition state by context-specific regulators underlies the plasticity of plant root systems.

overall_design: DR5:VENUS or DR5:mScarleti-NLS TCSn:mNeonGreen tomato plants were grown in growth chamber. At ~4 weeks after germination, stem-borne root primordia were collected from sections of internode 1 under a fluorescent stereoscope. Microdissection sections were transferred to cell wall digestion solution and protoplasts were isolated, sorted using FACS followed by mRNA sequencing.

first: Moutasem

last: Omary

first: Naama

last: Gil

first: Evyatar

last: Steiner

first: Chen

last: Yahav

first: Anat

last: Hendelman


title: Developmental series of tomato lateral root development

summary: The purpose of this dataset is to generate a transcriptomic series of staged non-induced lateral root intiation in M82 tomato. Sections of the primary roots containing lateral roots at 5 different developemental stages (staged by their anatomy and expression of the auxin response marker DR5) were collected.

overall_design: Experiment was performed in duplicates. A section of the primary root containing no lateral roots was used as control


title: Transcriptomic analysis of of SNX-5422-treated human primary tracheobronchial epithelial (TBE) cells.

city: Durham

first: Ria

last: Goswami

state: NC

address: 2 Genome Ct. MSRBII

department: Duke Human Vaccine Institute

institute: Duke University

summary:
Purpose: In addition to developing antivirals targeting specific SARS-CoV-2 viral proteins, there has been a growing effort in developing therapeutics targeting host proteins exploited by SARS-CoV-2 for their replication or implicated in viral pathogenesis. As such therapeutics can impair normal functioning of host proteins, a clear understanding of their impact on cellular mechanisms is critically important. Here, we characterized the interactions of a host-targeted anti-SARS-CoV-2 therapeutic, SNX-5422, with the cellular machinery using a physiologically relevant ex vivo human primary tracheobronchial epithelial (TBE) cell model.
Methods: Fully differentiated human TBE cells (EpiAirwayTM) from 3 independent donors with no reported respiratory disease or smoking history were obtained from MatTek (Ashland, MA). The cells were cultured at the air-liquid interface in 1 ml of AIR-100-MM culture medium (MatTek) in 6 well plates at 37°C in 5% CO2. Upon receipt of cells, the cultures were acclimated for 16-24hr prior to the start of experiments. Human TBE cells from each donor were treated with 1µM SNX-5422 or 0.1% DMSO added to the media on the basolateral side of the culture, in three biological replicates. After 48hrs, cells were resuspended in TRIzol reagent (Thermo Fisher) and total RNA from the cells was extracted by phase separation with chloroform and subsequently using the RNeasy Mini Kit (Qiagen). RNA-Seq libraries were prepared using TruSeq RNA library Prep Kit v2 (Illumina, Inc. USA). Before pooling and sequencing, fragment length distribution and library quality were assessed on a TapeStation 2200 (Agilent Technologies), and the libraries were validated by Qubit Fluorometers (Thermo Fisher). All libraries were then pooled in a concentration at 4nM and sequenced in quadruplets on a NextSeq 500 Illumina sequencing platform system using NextSeq 500/550 High Output Kit v2.0 (150 cycles) (Illumina, Inc. USA).
Conclusion: This study identified differentially expressed genes between DMSO-treated and SNX-5422-treated human TBE cells.

overall_design: Bulk RNA-seq analysis of human TBE cells from 3 independent donors with no reported respiratory disease or smoking history treated with 1μM SNX-5422 or 0.1%DMSO (drug-vehicle)

first: Veronica

last: Russell

first: Joshua

last: Tu

first: Philip

last: Hughes

first: Francine

last: Kelly

first: Stephanie

last: Langel

first: Justin

last: Steppe

first: Scott

last: Palmer

first: Timothy

last: Haystead

first: Maria

last: Blasi

first: Sallie

last: Permar


title: Single cell transcriptome profiling of mouse pancreatic β-lineage cells and hESC-derived β-like cells

city: Suita

first: Shugo

last: Sasaki

state: Osaka

address: 2-2 Yamadaoka, Suita-shi

department: Metabolic Medicine

country: Japan

institute: Osaka University

summary: While pancreatic β cells have been shown to originate from endocrine progenitors in ductal regions, it remains unclear precisely where β cells emerge and which transcripts define newborn β cells. Here, we used a mouse model “Ins1-GFP;Timer” that provides spatial information during β-cell neogenesis with high temporal resolution. Fluorescent imaging demonstrated that, as expected, some newborn β cells arise close to the ducts; unexpectedly, all the others arise away from the ducts and adjacent to blood vessels. Single-cell RNA-sequencing (scRNA-seq) demonstrated five distinct populations of newborn β cells, confirming the spatial heterogeneity of β-cell neogenesis, and integration analysis with scRNA-seq of hESC-derived β-like cells uncovered transcriptional similarity with the data in mouse β cells. Thus, the combination of time-resolved histological imaging with single-cell transcriptional mapping demonstrated novel features of spatial and transcriptional heterogeneity in β-cell neogenesis, which will lead to a better understanding of β-cell differentiation for future cell therapy.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
This study characterizes the single-cell transcriptomes of mouse pancreatic β-lineage cells and hESC-derived β-like cells
Cellranger aggr was used to combine data from multiple samples (Green1, Green2 and Red);
Aggregation file of Green1 and Green2: Green_aggr.barcodes.tsv.gz, Green_aggr.genes.tsv.gz, Green_aggr.matrix.mtx.gz
Aggregation file of Green1,  Green2 and Red: Green_Red_aggr.barcodes.tsv.gz, Green_Red_aggr.genes.tsv.gz, Green_Red_aggr.matrix.mtx.gz
Aggregation file of ES1 and ES2: ES_aggr.barcodes.tsv.gz, ES_aggr.genes.tsv.gz, ES_aggr.matrix.mtx.gz

first: Michelle

middle: Y

last: Lee

first: Yuka

last: Wakabayashi

first: Luka

last: Suzuki

first: Helena

last: Winata

first: Miwa

last: Himuro

first: Taka-aki

last: Matsuoka

first: Iichiro

last: Shimomura

first: Hirotaka

last: Watada

first: Francis

middle: C

last: Lynn

first: Takeshi

last: Miyatsuka


title: Histone Hypoacetylation Impairs the Plasticity of Human Hepatocytes with Aging

city: YOKOHAMA

first: Yun-Zhong

last: NIE

state: Kanagawa

address: 3-9, Fukuura, Kanazawa-ku

department: Department of Regenerative Medicine

institute: Yokohama City University Graduate School of Medicine


title: Histone Hypoacetylation Impairs the Plasticity of Human Hepatocytes with Aging [FigS3]

summary: Although aging associated decline of liver regeneration was discovered half a century ago, how aging contributes to the decline of liver regenerative capacity and how to improve this capacity in the elderly is still unknown. Hepatocyte plasticity is known to play a central role in the maintenance of liver regeneration; hence, we describe a strategy to explore the mechanisms underlying the relation between aging and hepatocyte plasticity: experiments with human induced-pluripotent-stem-cell–derived hepatocytes (hiPSC-Heps). Here, we established a simple and convenient method for generation of hiPSC-Heps that can maintain hepatic function for a long time with gradual accumulation of aging related markers and characteristics. We found that in contrast to rodent hepatocytes, FGF2 is essential for the plasticity of human hepatocytes, and the FGF2-activated MAPK–EZH2 axis can help to reprogram hiPSC-Heps into proliferative hepatic cells with a bipotential differentiation ability. Notably, our results showed the plasticity of hiPSC-Heps decreases with aging and this phenomenon strongly correlates with histone acetylation. Moreover, we found that selective inhibition of histone deacetylases can markedly improve the plasticity of old hiPSC-Heps and primary human hepatocytes and surprisingly increases the repopulation capacity of old PHHs in a liver injury model. Therefore, we can conclude that aging-associated histone hypoacetylation impairs hepatocyte plasticity.

overall_design: Transcriptome profiling of hiPSC derived Heptocyte (D22-Hep, D52-Hep and D72-Hep), D22-pHC, PHHs and PHH-pHC

first: Yun-Wen

last: Zheng

first: Hideki

last: Taniguchi


title: Histone Hypoacetylation Impairs the Plasticity of Human Hepatocytes with Aging [Fig4]


title: Histone Hypoacetylation Impairs the Plasticity of Human Hepatocytes with Aging [Fig1, FigS1 and Fig3]


title: Expression data from PrimeView human gene expression array

status: Public on Mar 03 2022

city: Nanjing

first: Pengfei

last: Shao

address: 300 Guangzhou Road

institute: The First Affiliated Hospital of Nanjing Medical University

summary:
Gene expression in A498 cells infected with shCtrl and shMCM8 was detected with a PrimeView human gene expression array.
We performed Affymetrix Human Gene Chip Prime View analysis on  shCtrl and shMCM8  A498 cells. Of the 2415 differentially expressed genes (DEGs) found in  shMCM8 and shCtrl A498 cells, 1263 were up-regulated and 1152 were down-regulated based on the threshold of absolute fold change ≥ 2 and FDR < 0.05

overall_design: The total RNA of A498 cells infected with shCtrl and A498 was extracted. The RNA sequencing was performed with Affymetrix human GeneChip PrimeView and the outcomes were scanned by Affymetrix Scanner 3000. The statistical significance of raw data was completed by a Welch t-test with Benjamini-Hochberg FDR (|Fold Change| ≥ 2 and FDR < 0.05 as significant).

first: Kai

last: Guo


title: Abdominal Aortic Aneurysm in C57BL/6J Mice - Male and Female PPE vs. Sham Day 7

city: Stanford

first: Joshua

middle: M.

last: Spin

address: 300 Pasteur Drive

institute: Stanford University

summary:
Transcriptional profiling of infrarenal aorta from male and female mice (10-weeks old, C57BL/6J), treated with either porcine pancreatic elastase (PPE) local infusion or sham operation (saline infusion). Samples harvested 7 days after treatment.
Goal was to examine gene expression in AAA in this model in both genders. Surgical protocol is as described in PMCID: PMC3148686/PMID: 19629030.

overall_design: Two condition experiment, each in male and female, one infrarenal aorta per array. Sham vs. PPE at 1 time point (Day 7). Total arrays 19:  female sham 7d (3), female PPE 7d (4), male sham 7d (5), male PPE 7d (7).


title: The transcription factor, α1ACT, acts through a microRNA network to regulate neurogenesis and cell death during neonatal cerebellar development

city: Chicago

first: Christopher

last: Gomez

state: IL

address: 5812 S Ellis Ave Room J219

department: Neurology

institute: University of Chicago

summary: To investigate whether α1ACT acts through a microRNA network, we studied α1ACT-associated simultaneous miRNA:mRNA expression transcriptome profiles during cerebellar development in a context-dependent manner, using miRNA-seq paired with previously reported RNA-seq.

overall_design: Examination the miRNA-seq results between pc12 cell lines stably expressing blank vector and α1ACT; pairing the differentially expressed miRNA with previously reported DEGs via miRWALK to investigate the α1ACT mediated miRNA regulation network. All outcomes were validated via qRT-PCR

first: Cenfu

last: Wei

first: Xiaofei

last: Du


title: Transcriptomic expression of A549 cells treated with palbociclib and indisulam or PF-06873600 and SUM159 cells treated with PF-06873600

city: Amsterdam

first: Rodrigo

last: Leite de Oliveira

address: De Boelelaan 1118

country: Netherlands

institute: Amsterdam UMC / location VUmc

summary: Inducing senescence in cancer cells is emerging as a new therapeutic strategy. We tested the senescence induction of palbociclib and indisulam or PF-06873600 in A549 and  PF-06873600 in SUM159 cells, and profiled these for senescence associated gene signatures.

overall_design: Transcriptomic analysis of A549 cells treated with palbociclib and indisulam or PF-06873600  and SUM159 cells treated with PF-06873600 and controls. The experiment was performed in technical duplicates. A549 cells were treated with 2µM Palbociclib,  0.5µM of indisulam and the combniation for 10 days. A549 and SUM159 were treated with 0.5µM PF-06873600  for 7 days.

first: Ziva

last: Pogacar

first: Jackie

last: Johnson

first: Lenno

last: Krenning

first: Fleur

last: Jochems

first: Giulia

last: DeConti

first: Cor

last: Lieftink

first: Arno

last: Velds

first: Leyma

last: Wardak

first: Kelvin

last: Groot

first: Arnout

last: Schepers

first: Liqin

last: Wang

first: Ji-Ying

last: Song

first: Marieke

last: vandeVen

first: Olaf

last: vanTellingen

first: Rene

last: Medema

last: Bernards

last: LeitedeOliveira


title: Transcriptomic expression of A549 and SUM159 cells treated with palbociclib and indisulam

last: Leite de Oliveira

summary: Indisulam is a molecular glue targeting a splicing factor RBM39 for degradation. To assess splicing errors when treating the cells with indisulam, palbociclib and the combination we perform RNA sequencing and analyze splicing errors.

overall_design: Transcriptomic analysis of A549 ans SUM159 cells treated with palbociclib and indisulam and controls. The experiment was performed in technical duplicates. The cells were treated with 2µM Palbociclib, 3µM of indisulam and the combniation for 16h.

last: Pogacar


title: Transcriptomic expression of A549 CDK2 KO cells treated or untreated with palbociclib

summary: Inducing senescence in cancer cells is emerging as a new therapeutic strategy. We tested the senescence induction of palbociclib in CDK2 KO cells, and profiled these for senescence associated gene signatures. This was a CRISPR generated CDK2 KO clone in A549 cells.

overall_design: Transcriptomic analysis of A549 CDK2 KO cells treated with palbociclib and control. The experiment was performed in technical duplicates.

last: Johnson

last: Krenning


title: Transcriptomic expression of SUM159 cells treated with palbociclib and indisulam

summary: Inducing senescence in cancer cells is emerging as a new therapeutic strategy. We tested the senescence induction of palbociclib and indisulam in SUM159 cells, and profiled these for senescence associated gene signatures.

overall_design: Transcriptomic analysis of  SUM159 cells treated with palbociclib and indisulam and controls. The experiment was performed in technical duplicates. The cells were treated with 2µM Palbociclib, 3µM of indisulam and the combniation for 16h.

last: Jochems

last: DeConti


title: The Dynamic Proteome in Arabidopsis Thaliana Early Embryogenesis

city: HONG KONG

first: Dianjing

last: GUO

address: G94, South Block, Science Center, CUHK

institute: CUHK

summary: Using nanoproteomics,we profiled the dynamics of proteome and found potentially important proteins in Arabidopsis thaliana early embryogenesis. Combining with RNAs-seq, we unveiled the relationship of protein and mRNA during Arabidopsis embryogenesis.

overall_design: mRNA profile of six distinct stages in Arabidopsis early embryogenesis

first: Yingzhang

last: HUANG

first: Limeng

last: Zhou

last: Guo


title: Discovery and functional interrogation of the virus and host RNA interactome of SARS-CoV-2 proteins [eCLIP]

status: Public on Mar 09 2022

city: La Jolla

first: Gene

last: Yeo

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

summary: The coronavirus disease 2019 (COVID-19) pandemic was caused by severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2). Understanding the molecular functions of SARS-CoV-2 proteins is thus imperative to developing effective antiviral treatments. Here, we use enhanced crosslinking and immunoprecipitation to investigate SARS-CoV-2 protein interactions with viral and host RNAs. SARS-CoV-2 proteins, NSP8 and NSP12, are found to specifically bind to untranslated regions of the RNA viral genome, with NSP12 additionally binding to all transcription regulatory sequences. This provides evidence for their central roles in replication and transcription. Moreover, we discovered a potential site of NSP12 mediated genome recombination, which could explain the genetic diversity found in coronaviruses. SARS-CoV-2 proteins exogenously expressed in human lung epithelial cells bind to 4,281 unique host RNAs. Nine SARS-CoV-2 proteins upregulate target gene expression, including NSP12 which upregulates mitochondrial electron transport and N-linked glycosylation proteins. Furthermore, siRNA knockdown of NSP12-targeted proteins in human lung organoid cells demonstrates substantial antiviral effects. Conversely, NSP9 inhibits host gene expression via blocking mRNA export and dampens antiviral inflammation response such as interleukin 1α (IL1α) production. Our extensive viral protein-RNA interactome provides a catalog of potential therapeutic targets and offers insight into the etiology of COVID-19 as a safeguard against future pandemics.

sample_organism:
Homo sapiens
Chlorocebus sabaeus

platform_organism:
Homo sapiens
Chlorocebus sabaeus

overall_design: Crosslinking and immunoprecipitation of SARS-CoV-2 protein bound RNA and sequencing from 2 technical replicates.

first: Xiang

last: Joy

first: Mueller

last: Jasmine

first: Luo

last: En-Ching

first: Yee

last: Brian

first: Schafer

last: Danielle

first: Schmok

last: Jonathan

first: Tan

last: Frederick

first: Her

last: Hsuan-Lin

first: Chen

last: Chun-Yuan

first: Brannan

last: Kristopher

first: Jones

last: Krysten

first: Park

last: Samuel

first: Jin

last: Wenhao

first: McVicar

last: Rachael

first: Kwong

last: Elizabeth

first: Le

last: Phuong

first: Eric

last: Kofman

first: Vu

last: Anthony

first: Li

last: Yan-Hua

first: Dong

last: Kevin

first: Tankka

last: Alexandra

first: Song

last: Yan

last: Van Nostrand

first: Leibel

last: Sandra

middle: W


title: Synergistic Action of WDR5 and HDM2 inhibitors in SMARCB1-deficient cancer cells

city: Nashville

first: Jing

last: Wang

state: TN

address: 2220 Pierce Avenue

institute: Vanderbilt University Medical Center

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Rhabdoid tumors (RT) are rare and aggressive pediatric tumors that are driven by the loss the tumor suppressor SNF5 (SMARCB1). Here we examine how RT cells respond to small molecule-mediated inhibitors of the “WIN” site of WDR5, a chromatin-associated protein that regulates a specific set of genes linked to protein synthesis. We characterize WDR5 binding in RT cell lines via ChIP-Seq and show that WIN site inhibitor rapidly and comprehensively displaces WDR5 from chromatin in these cells. Using Precision Run On-sequencing (PRO-Seq) we show that WDR5-bound protein synthesis genes are early and direct transcriptional targets of WIN site inhibitor. We also use RNA-Seq to characterize the persistent transcriptional changes in RT lines treated with WIN site inhibitor, and compare these transcriptional effects with those of the HDM2 inhibitor nutlin-3a.

overall_design: G401 scr shRNA, G401 p53 shRNA, or WT TTC549, cells were treated with DMSO or WIN site inhibitor C16. ChIP-Seq was used to track interaction of WDR5 with chromatin and RNA-Seq was used to monitor long-term transcriptional changes.

first: William

middle: P

last: Tansey

first: Andrea

last: Wojciechowski

first: Qi

last: Liu


title: Human gene expression microarray analysis in CEM cells overexpressing HTLV-1 Rex

city: Tokyo

first: Kazumi

last: Nakano

state: Kanto

address: 4-6-1, Shirokanedai, Minatoku

department: Department of Computational Biology and Medical Sciences

institute: Grad. Sch. Frontier Sci., The University of Tokyo

summary: HTLV-1 is an onco-retrovirus that infects human T cells and causes poor prognosis leukaemia/lymphoma, ATL. The viral RNA binding protein, Rex, intervenes in host cell regulation of gene expression, splicing and translation mechanisms to promote viral particle replication, but the detailed mechanism of its function has not been elucidated. In the present study, we stably overexpressed HTLV-1 Rex in the human T-cell-derived cell line, CEM, and investigated effect of Rex on gene expression profiles in CEM cells by gene expression microarray analysis.

overall_design: The Retrovirus expression system was used to express HTLV-1 Rex in CEM cells. CEM cells infected with a retrovirus not expressing Rex were prepared as a negative control. Retrovirus expression was performed four times and CEM-Rex and CEM-Emp (negative control) were prepared n=4 each. Total RNA was extracted from these cells and subjected to gene expression microarray (Whole Human GenomeMicroarray Kit, #G4845A, Agilent Technologies, Inc).

first: Koichi

last: Yokoyama

first: Toshiki

last: Watanabe


title: Microglia influence neurofilament deposition in ALS iPSC-derived motor neurons

city: Milwaukee

first: Allison

last: Ebert

state: WI

address: 8701 Watertown Plank Rd

institute: Medical College of Wisconsin

summary: Utilizing bulk RNA sequencing, we analyzed differences in the the transcriptomes of motor neurons originating from ALS-discordant, twin patient induced pleuripotent stem cells (iPSCs). Our goal with this study is to determine differentially-affected genes that may play a role in the development of Amyotrophic Lateral Sclerosis in the affected twin.

overall_design: Evaluate mRNA profiles in day 21 iPSC-derived motor neurons from ALS-discordant twins

first: Reilly

last: Allison

first: Jacob

last: Adelman

first: Jenica

last: Abrudan

first: Raul

last: Urrutia

first: Michael

middle: T

last: Zimmermann

first: Angela

last: Mathison


title: Protein kinase inhibitor-mediated immunoprophylactic and immunotherapeutic control of colon cancer

city: DIJON

first: François

last: Ghiringhelli

address: 1 rue du Professeur Marion

country: France

institute: UMR INSERM 1231

summary: An innovative multikinase inhibitor (H89)-based antitumor immunotherapy in colorectal cancer (CRC) is presented. The study was designed to evaluate the effect of H89 on colon tumor growth and carcinogenesis through in vivo analyses. Syngeneic mouse models of CRC cancer in BALB/c mice and chemically colon tumorigenesis, reveals that H89 delays colon oncogenesis, related to a preventive effect, and prevents tumor growth, underlying an antitumor effect respectively. Using immunodeficient and monoclonal antibody-specific immunosuppression, we identified immune cell populations involved in the preventive (NK-cell dependent) and antitumor activity of H89 (T-cell dependent). Flow cytometry analysis showed that the antitumor effect of H89 was correlated with an increase in the tumor microenvironment of CD4+ Th1 cells and CD8+ cytotoxic T cells and a decrease of CD4+ Treg cells infiltration. Furthermore, qRT-PCR revealed that H89 can promote naïve CD4+ T cells differentiation into Th1, decreases Treg differentiation and increases ex vivo CD8+ T cell-mediated killing of cancer cells. An RNAseq profiling experiment showed that H89 induces an overexpression of genes involved in antitumor immune response, such as IL-15RA, whose inhibition counteracts the antitumor effect of H89. In conclusion, our findings identify H89 as a potential strategy for the prevention and treatment of CRC.

overall_design: RNA profiles of CT26-tumor bearing Balb/c mice treated or not by the kinase inhibitor H89

first: Silvia

last: Ghione

first: Cindy

last: Racoeur

first: Nesrine

last: Mabrouk

first: Jingxuan

last: Shan

first: Emma

last: Groetz

first: Elise

last: Ballot

first: Caroline

last: Truntzer

first: Lotfi

last: Chouchane

first: Frédérique

last: Vegran

first: Catherine

last: Paul

first: Stéphanie

last: Plenchette

first: Ali

last: Bettaieb


title: Genome-wide sequencing of cultured  MDSCs obtained from bone marrow of lnc57Rik ko , lncGM1082 ko and WT mice.

city: Tianjin

first: Ya

last: Wang

address: Weijin South Road, Nankai District

institute: Nankai University

summary: To fully elucidate the effects of long non-coding RNA 5730403I07Rik (lnc57Rik) and lncGM1082 on myeloid-derived suppressor cell (MDSCs), we generated lnc57Rik knockout (KO) and lncGM1082 ko mice. Then bone marrow cells were obtained from the femurs of C57BL/6, lnc57Rik KO,  or lncGM1082 ko mice and cultured in RPMI-1640 medium supplemented with GM-CSF plus IL6 for 4 days. We further performed a high-throughput sequencing analysis in cultured MDSCs obtained from bone marrow of lnc57Rik ko, lncGM1082 ko and wild type (WT) mice.

overall_design: Two MDSCs samples from wild type (WT), lnc57Rik-/-, lncGM1082-/- mice


title: Next Generation Sequencing Facilitates Quantitative Analysis of cultured  coding mRNA in human lnc57Rik knockdown and overexpressing MDSCs. Human MSDCs were isolated from peripheral blood and then exposed to human GM-CSF.

summary: Bio-informatics showed that human lnc57Rik was highly homologue to mouse lnc57Rik, we therefore examined whether human lnc57Rik was similar in function to murine lnc57Rik. Generation Sequencing Facilitates Quantitative Analysis showed differences in the gene expression in ln57Rik knockdown or exogenous lnc57Rik overexpressed MDSCs as compared with their controls


title: Senescence associated gene signatures

first: Rodrigo

last: Leite de Oliveira

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

overall_design: Refer to individual Series


title: Human exon microarray analysis in CEM cells overexpressing HTLV-1 Rex

first: Kazumi

last: Nakano

summary: HTLV-1 is an onco-retrovirus that infects human T cells and causes poor prognosis leukaemia/lymphoma, ATL. The viral RNA binding protein, Rex, intervenes in host cell regulation of gene expression, splicing and translation mechanisms to promote viral particle replication, but the detailed mechanism of its function has not been elucidated. In the present study, we stably overexpressed HTLV-1 Rex in the human T-cell-derived cell line, CEM, and investigated effect of Rex on splicing patterns in CEM cells by exon microarray analysis.

overall_design: The Retrovirus expression system was used to express HTLV-1 Rex in CEM cells. CEM cells infected with a retrovirus not expressing Rex were prepared as a negative control. Retrovirus expression was performed four times and CEM-Rex and CEM-Emp (negative control) were prepared n=4 each. Total RNA was extracted from these cells and subjected to exon microarray (SureScript Whole Human Genome Exon Microarray 2x400K).

first: Koki

last: Uchida

first: Kaoru

last: Uchimaru

first: Toshiki

last: Watanabe


title: Search for macrophage-derved factors related to angiogenesis and wound healing

city: Toon

first: Yukihiro

last: Kohrara

state: Ehime

address: Sitsukawa

institute: Ehime University

summary: Macrophages are progenitors of osteoclasts, but macrophages themselves also regulates bone metabolism.  Macrophages mediate not only bone formation by osteoblasts in physiological conditions, but also regeneration after fracture.  However, the mechanisms how macrophages control bone formation and regeneration remain unclear.  Here we demonstrate that liposome-encapsulated Clodronate (Clod-lip) model with targeted depletion of phagocytic macrophages exhibits impaired angiogenesis of type H vessels, which couple angiogenesis and osteogenesis, in mouse cortical bone defect model by drill-hole injury.  Additionaly, we identify Tgfbi (encoding TGF, beta-induced protein), Plau (encoding uPA), and Tgfb1 (encoding TGF-β1) as genes of macrophage-secreted factors mediating angiogenesis and wound healing by RNA-seq analysis.  These mRNAs were highly expressed in bone marrow-derived macrophages among bone cells by qRT-PCR.  Finally, we show that treatment with uPA inhibitor or TGF-β Receptor I, Receptor II inhibitor impaired bone regeneration after injury, confirming importance of uPA and TGF-β1 for bone repair.  Therefore, we proposed that these factors may be potential for therapeutic targets for delayed union, or non-union patients.  Our findings reveal a novel mechanism of bone regeneration mediated by macrophages.

overall_design: Repair tissue mRNA profiles of Empty-lip or Clod-lip injected mice

last: Kohara


title: Identification of axillary lymph node metastasis-related circRNAs in breast cancer using transcriptome sequencing

city: Jinan

first: Peng

last: Su

address: Wen Hua Xi Road 107

institute: Qilu Hospital of Shandong University

summary: Circular RNAs (circRNAs) play critical roles in the initiation and progression of cancer. Emerging evidence shows that circRNAs may function as potential markers for cancer diagnosis and treatment. However, the roles of circRNAs in breast cancer axillary lymph node metastasis (ALNM) remain need to be determined. Transcriptome sequencing was performed to screen the differentially expressed circRNAs in three breast cancer tissues with ALNM and three without ALNM.

overall_design: For transcriptome sequencing, breast cancer tissues were collected from six patients, including three with axillary lymph node metastasis (ALNM) and three without ALNM. Transcriptome high‐throughput sequencing was performed. Raw junction reads for all samples were normalized by total reads number and log2 transformed. Differentially expressed circRNAs were identified between two groups (P < 0.05, fold change > 2). Totally, 31 circRNAs were found to be differentially expressed in breast cancer with ALNM versus without ALNM (fold change > 2, P < 0.05). Among the 31 circRNAs, 21 were upregulated and 10 were downregulated in breast cancer with ALNM compared with those without ALNM.

first: Ya-Wen


title: Placenta and fetal brain share a neurodevelopmental disorder DNA methylation profile in a mouse model of prenatal PCB exposure [RNA]

city: South San Francisco

first: Benjamin

middle: I

last: Laufer

state: California

address: 1 DNA Way

institute: Genentech

summary: Polychlorinated biphenyls (PCBs) are developmental neurotoxicants implicated as environmental risk factors for neurodevelopmental disorders (NDD). We examined the effects of prenatal exposure to a human-relevant mixture of PCBs on the DNA methylation profiles of fetal mouse brain and placenta. We found thousands of differentially methylated regions (DMRs) distinguishing placentas and brains from PCB-exposed embryos from sex-matched vehicle controls. In both placenta and brain, PCB-associated DMRs were enriched for functions related to neurodevelopment and cellular signaling and enriched within regions of bivalent chromatin. The placenta and brain PCB DMRs overlapped significantly and mapped to a shared subset of genes enriched for Wnt signaling, Slit/Robo signaling, and genes differentially expressed in NDD models. PBC DMRs also significantly overlapped with DMRs from the brains of humans with Rett syndrome and Dup15q syndrome. These results demonstrate that placenta can be used as a surrogate for embryonic brain DNA methylation changes relevant to an NDD.

overall_design: Pregnant C57BL/6J mice were continuously exposed to 1.0 mg/kg/d mixture of a polychlorinated biphenyls (PCBs). The exposed dams and vehicle matched control dams were sacrificed on gestational day 18 and brain and placenta were harvested from 44 embryos. DNA methylation was assayed by low-pass whole genome bisulfite sequencing (WGBS) and RNA expression was assayed by RNA sequencing (RNA-seq).


title: Placenta and fetal brain share a neurodevelopmental disorder DNA methylation profile in a mouse model of prenatal PCB exposure [WGBS]

overall_design: Pregnant C57BL/6J mice were continuously exposed to 1.0 mg/kg/d mixture of a polychlorinated biphenyls (PCBs). The exposed dams and vehicle matched control dams were sacrificed on gestational day 18 and brain and placenta were harvested from 44 embryos. DNA methylation was assayed by low-pass whole genome bisulfite sequencing (WGBS).


title: Placenta and fetal brain share a neurodevelopmental disorder DNA methylation profile in a mouse model of prenatal PCB exposure


title: miR-22 and miR-205 drive tumor aggressiveness of mucoepidermoid carcinomas of salivary glands [miRNA]

city: Sao Paulo

first: Fabio

middle: Albuquerque

last: Marchi

address: Av Dr Arnaldo

department: CTO

country: Brazil

institute: ICESP

summary: We used miRNA expression arrays and integrated analysis to study mucoepidermoid carcinomas (MEC) to identify potential drivers involved with its pathogenesis. Normal salivary glands were used as controls.

overall_design: 25 MECs and 06 normal salivary glands (controls) were studied using Agilent Sure-Print G3 Human miRNA 8x60K microarrays for miRNA expression analysis. Tumor samples were compared to nornal salivary gland samples

first: Fabricio

last: Passador-Santos

first: Silvia

middle: R

last: Rogatto


title: Genome-wide epigenome mapping in human induced pluripotent cells in WT and KDM6AKO cells.

city: St Louis

first: Todd

last: Druley

state: Missouri

address: 660 South Euclid Ave

department: Department of Pediatrics

institute: Washington University In St Louis


title: miR-22 and miR-205 drive tumor aggressiveness of mucoepidermoid carcinomas of salivary glands

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


title: miR-22 and miR-205 drive tumor aggressiveness of mucoepidermoid carcinomas of salivary glands [mRNA]

summary: We used mRNA expression arrays and integrated analysis to study mucoepidermoid carcinomas (MEC) to identify potential drivers involved with its pathogenesis. Normal salivary glands were used as controls.

overall_design: 34 MECs and 05 normal salivary glands (controls) were studied using Agilent Two-color SurePrint G3 Human Gene Expression Microarray 8x60K for gene expression analysis. Tumor samples were compared to nornal salivary gland samples


title: Genome-wide epigenome mapping in human induced pluripotent cells in WT and KDM6AKO cells. [RNA-Seq]

summary: KDM6A is a histone demethylase that remove H3K27me3 lysine. This study compares the transcriptomic profile between WT and KDM6A KO cells and further evaluates their functional validation by applying the invitro hematopoietic differentiation protocol.

overall_design: Examination of transcriptomic profile in WT and KDM6A KO cells.

first: T


title: Next Generation Sequencing Facilitates Quantitative Analysis of Chenopodium quinoa Transcriptomes

city: Shanghai

first: Moyang

last: Liu

address: dongchuan road 800

department: School of Agriculture and Biology

institute: Shanghai Jiao Tong University

summary: We generated 70.9 Gb of high-quality sequencing data (~7.88 Gb per sample) and catalogued the expression profiles of 54，238 annotated Chenopodium quinoa genes in each sample. These genes have known or potential roles in the roots, stems, and leaves of quinoa. Therefore, we are appealing candidates for further investigation of the gene expression and associated regulatory mechanisms.

overall_design: mRNA profiles of roots, stems and leaves of yellow bitter quinoa were generated by deep sequencing, in triplicate, using Illumina HiSeq4000.


title: Genome-wide epigenome mapping in human induced pluripotent cells in WT and KDM6KO cells. [ChIP-Seq]

summary: KDM6A is a histone demethylase that remove H3K27me3 lysine. This study compares the histone modification pattern between WT and KDM6A KO cells.

overall_design: Examination of 4 different histone modifications in KDM6AKO hIPSCs cells.


title: MiRNA Profiling of Colorectal Tumors by Next Generation Sequencing

city: Kaunas

first: Rokas

last: Lukosevicius

address: Eiveniu str. 4

department: Institute for Digestive Research

country: Lithuania

institute: Lithuanian University of Health Sciences

summary: Colorectal tumors have an impaired gene expression. As microRNAs (miRNAs) are involved in post-transcriptional regulation of gene expression we performed high-troughput miRNA profiling of 20 Adenomatous Polyp, 20 CRC and 32 healthy control formalin-fixed and paraffin-embedded samples using small RNA sequencing approach.

overall_design: MiRNA profiling of colorectal cancer, adenomatous polyps and healthy colon fresh-frozen biopsy samples

first: Jurgita

last: Skieceviciene

first: Simonas

last: Juzenas


title: Human biliary epithelial cells from discarded donor livers rescue bile duct structure and function in a mouse model of biliary disease

city: Edinburgh

first: Stuart

last: Forbes

address: 5 Little France Drive

department: Centre for Regenerative Medicine

country: United Kingdom

institute: The University of Edinburgh

summary:
Biliary diseases can cause inflammation, fibrosis, bile duct destruction and eventually liver failure. There are no curative treatments for biliary disease except for liver transplantation. New therapies are urgently required.
We have purified human Biliary Epithelial Cells (hBEC) from discarded human livers. hBECs were tested as a cell therapy in a mouse model of biliary disease where the conditional deletion of Mdm2 in cholangiocytes causes senescence, biliary strictures and fibrosis.
hBEC are expandable, phenotypically stable and help restore biliary structure and function, highlighting their regenerative capacity and a potential alternative to liver transplantation for biliary disease.

overall_design: Differential expression of CD133+ and CD133- human biliary epithelial cells from healthy (n=2) and steatotic (n=3) livers; Gene expression at different cell passages of CD133+ human biliary epithelial cells grown in vitro in two dimension-GMP compatible conditions (2D; n=4) and three dimensions (3D, organoids; n=5)

first: John

last: Hallett

first: Sofia

last: Ferreira-Gonzalez

first: Tak

last: Man

first: Alastair

last: Kilpatrick

first: Hannah

last: Esser

first: Kayleigh

last: Thirlwell

first: Mark

last: MacMillan

first: Daniel

last: Rodrigo-Torres

middle: J

last: Dwyer

first: Victoria

middle: L

last: Gadd

first: Candice

last: Ashmore-Harris

first: Wei-Yu

last: Lu

last: Thomson

first: Maurits

last: Jansen

first: Eoghan

last: O'Duibhir

first: Philip

last: Starkey Lewis

first: Lara

last: Campana

first: Rhona

last: Aird

first: Thomas

last: Bate

first: Alasdair

last: Fraser

last: Campbell

first: Gabriel

last: Oniscu

first: David

last: Hay

first: Antony

last: Callanan


title: RUVBL1 promotes enzalutamide resistance of prostate tumors through the PLXNA1-CRAF-MAPK pathway

status: Public on Mar 02 2022

first: Fei

middle: fei

last: Sun

state: Shandong

address: WENHUAXI road

institute: Department of Pathology, Qilu Hospital, Shandong University

summary: The aim of this research was to confirm the regulatory effect of RUVBL1 on gene expression in castration resistant prostate cancer.

overall_design: In this research, there were six samples examined including samples of negative control cells (C4-2B-ENZR-NC) and samples of RUVBL1 knocked-down cells (C4-2B-ENZR-siRUVBL1).

first: Feifei

first: Bo

last: Han


title: Gene expression changes in NCU10K cells lacking Nedd4

city: Adelaide

first: Quenten

last: Schwarz

state: South Australia

address: Bradley Building, North Terrace

country: Australia

institute: University of South Australia

summary: Nedd4 is an E3 ubiquitin ligase that has essential roles in neural crest cell development. This study aimed to detect the gene expression changes induced by removing Nedd4 in the neural crest cell line, NCU10K, to define the molecular pathways regulated by Nedd4.

overall_design: This study compared 3 independent biological replicates consisting of RNA collected from NCU10K cells treated with control siRNAs for 48 hrs (3 separate experiments run in a 10cm plate) or Nedd4 siRNAs for 48 hrs to knock down Nedd4 (3 separate experiments run in a 10cm plate).


title: Whole transcriptome analysis of liver tissue in CLP mice and alpha-lactose treated mice

city: Wuhan

first: Zhaohui

last: Tang

state: Hubei

address: no.1095 Jiefang Avenue

department: Division of Trauma & Surgical Critical Care, Department of Surgery

institute: Tongji Hospital

summary: Sepsis is a syndromic response to infection and is frequently a final common pathway to death from many infectious diseases worldwide. The global burden of sepsis is difficult to ascertain, although a recent scientific publication estimated that there were 48.9 million cases and 11 million sepsis-related deaths worldwide, which accounted for almost 20% of all global deaths.In this experiment, we systematically studied the gene expression changes in the liver of sepsis using septic mice and contributed to the rationalization of the immune to sepsis in mice. Administration of α-lactose to block Tim-3 signaling pathway significantly improved the survival of septic mice. In order to figure out the mechanisms of the α-lactose, we explored the immune changes in mice after α-lactose interference, rationalizing sepsis in mice, and exploring the potential of a-lactose to treat sepsis.

overall_design: We divided the mice into CLP group, control group, and alpha-lactose and obtained liver samples after 24h, respectively.

first: Jingzhi

last: Yang

first: Teding

last: Chang

first: Liangsheng

first: Hai

last: Deng

first: Deng

last: Chen


title: Anti-obesity Effects of Polymethoxyflavone-Rich Fraction from Jinkyool (Citrus sunki Hort. ex Tanaka) Leaf on Obese Mice Induced by High-Fat Diet

city: Jeju

first: Mi Gyeong

last: Jang

address: 102 Jejudaehakno

country: South Korea

institute: Jeju National University

summary: Polymethoxyflavones (PMFs) are flavonoids exclusively found in certain citrus fruits and have been reported to be beneficial to human health. Most studies have been conducted with PMFs isolated from citrus peels, while there is no study on PMFs isolated from leaves. In this study, we prepared PMF-rich fraction (PRF) from leaf of Citrus sunki Hort ex. Tanaka (Jinkyool) and investigated whether PRF can improve metabolic decline in obese mice induced by high-fat diet (HFD) for five weeks. HFD induced obese mice were assigned into HFD, OR (HFD + orlistat 15.6 mg/kg of body weight/day), and PRF (HFD + 50, 100, 200 mg/kg of body weight/day) groups. Orlistat and PRE were orally administrated for 5 weeks. At the end of experiment, serum biochemical parameters, histology and protein expression profiles were investigated in the tissues of each group. The body weight gain of obese mice was significantly reduced after orlistat and PRF administration for five weeks. PRE effectively improved HFD-induced insulin resistance and dyslipidemia. Histological analysis in liver demonstrated that PRF potentially improved the liver function as it inhibited the incidence of fatty liver. Moreover, PRF increased the phosphorylation of activated AMP-activated protein kinase (AMPK), acetyl-CoA carboxylase (ACC), and hormone-sensitive lipase (HSL) in HFD-induced obese mice. Moreover, the liver transcriptome analysis revealed that PRE administration enriched the genes, which were mainly fatty acid metabolism. Overall, these results indicated that PRF exert anti-obesity effect by modulation of lipid metabolism.

overall_design: Liver RNA profiles of C57BL/6J mice were generated by mRNA sequencing, using Illumina NovaSeq 6000.

first: Se

last: Kim

first: Mi

middle: G


title: Identify the regulatory network of LncRNA HAR1A in neurological development by RNA-Sequencing and bioinformatics analysis.

city: GUANGZHOU

first: kayleigh

last: huang

state: Not Applicable

address: 6F BLDG D 188 KAIYUAN AVE HUANGPU DISTRICT

institute: GUANGZHOU MENDEL GENES

summary: LncRNA HAR1A, which is explicitly expressed in Cajal-Retzius neurons (CRs), has been reported to be related to the development of the human brain. As one of the human accelerated regions (HARs) gene, it plays an important role in Central neural evolution. Dysregulation of lncRNA HAR1A was associated with central nervous system diseases. This study confirmed that overexpressed HAR1A would improve memory and cognitive ability. We provided RNA sequencing results of brain tissue of the transgene mice (overexpress HAR1A) and normal mice.

overall_design: RNA-seq of brain tissue of transgene mice (overexpress HAR1A) and normal mice

first: Shengmou

last: Lin

first: Luting

last: Zhang

first: Kailing

last: Huang

first: Zhouxia

last: Zheng

first: Xiaoshun

last: Shi

first: Allen

middle: m

first: Jimei

last: Li

first: JingYin

last: Kong

first: Min


title: CAF from metastatic ovarian cancer (mCAF) vs  CAF from non-metastatic ovarian cancer (nmCAF)

city: Seongnam-si

first: Daun

last: Jung

state: Gyeonggi-do

address: Bundang-gu, 삼평동 689

department: Department of Pathology

institute: CHA Bundang Medical Center

summary: we performed microarray to employ an unbiased approach to identify the altered gene expression involved in metastasis, and transcriptionally compared mCAFs and nmCAFs

overall_design: mRNA profiles of mCAF and nmCAF

first: Hee

last: An


title: RnaSeq of Basal Epithelial Cell Subsets From Naïve C57BL/6 Mice

city: Boston

first: Nora

last: Barrett

address: 60 Fenwood Rd

institute: BWH

summary: Low-input RNA seq of sorted BCAMhi and BCAMlo basal cells

overall_design: Low-input RNA seq analysis of sorted ex-vivo airway epithelial cells from mouse

first: Xin

last: Wang

first: Nils

last: Hallen


title: Transcriptome profile in SULF2 knockdown pancreatic tumor cells

first: Ruizhe

last: He

address: No. 639, Zhizaoju Road

summary: We constructed the SULF2 knockdown cell lines and its controls in CFPAC-1 cells using CRISPR-cas9 system, followed by transcriptome sequencing.

overall_design: SULF2 knockdown cell lines in CFPAC-1 cells and the controls

first: He

last: Ruizhe

first: Sun

last: Yongwei


title: A Fungal Effector Suppresses the Nuclear Export of AGO1-miRNA Complex to Promote Infection in Plants

first: Chen

last: Zhu

address: 300 Feng Lin Road, Shanghai 200032, China

institute: CAS Center for Excellence in Molecular Plant Sciences

summary: Communication between interacting organisms via bioactive molecules is widespread  in nature and plays key roles in diverse biological processes. Small RNAs (sRNAs) can  travel between host plants and filamentous pathogens to trigger trans-kingdom RNA  interference (RNAi) in recipient cells and modulate plant defense and pathogen  virulence. However, how trans-kingdom RNAi is regulated has rarely been reported. Here, we show that the secretory protein VdSSR1 (secretory silencing repressor 1) from Verticillium dahliae, a soil-borne phytopathogenic fungus that causes wilt diseases in a  wide range of plant hosts, is required for fungal virulence in plants through the  suppression of trans-kingdom RNAi.

overall_design: Two col-0 samples，Two SSR1 overexpression samples and two alys samples were sequenced for mRNA and sRNA


title: Transcriptomic profiles of jejunum, liver, spleen and  jejunal Peyer's patches in piglets exposed to Fumonisin B1

city: Toulouse

first: Yannick

last: Lippi

address: 180 chemin de tournefeuille

department: GeT-TRiX facility

institute: INRAE

type:
Expression profiling by array
Third-party reanalysis

summary: Fumonisin B1 (FB1) is a mycotoxin produced by Fusarium species. In mammals, this toxin causes multiple organ-specific damages. Among its multiple effects, FB1 promotes hepatotoxicity, is immunotoxic and alters the intestinal functions. Despite its inhibitory effect on de novo ceramide synthesis, the molecular mechanism of FB1 action and toxicity remain unclears. In order to explore the mechanism of FB1 toxicity in multiple tissues, we analyzed the transcriptome of the jejunal section,  liver, spleen and  jejunal Peyer's patches which are targeted by FB1.

overall_design: Ten weeks old pigs were sacrificed after 4 weeks feeding with control diet (6 pigs) or feeding with control diet artificially contaminated with 10 ppm Fumonisin B1 (6 pigs). After sacrifice Jejunal section,  liver, spleen and  jejunal Peyer's patches  samples from each of 12 pigs are collected and used for microarray gene expression study.

first: Nicolas

last: Loiseau

first: Pascal

last: Gourbeyre

first: Joëlle

last: Laffitte

first: Julien

last: Fayet

first: Anne-Marie

last: Cossalter

first: Philippe

last: Pinton

first: Isabelle

last: Oswald


title: Identification of the potential genes regulating seed germination speed in maize

city: Beijing

first: Zhang

last: Huairen

address: No. 1 West Beichen Road

institute: Institute of Genetics and Developmental Biology, Chinese Academy of Sciences

summary:
Purpose: To identify the potential genes that regulate seed germination speed in maize, we performed a time-series transcriptome analysis with two inbred maize lines (72-3 fast germination, F9721 slow germination) during the seed germination and compared the differentially expressed genes (DEGs) in transcriptome with genes identified by GWAS
Methods: Methods: mRNA profiles of two maize inbred lines 72-3 and F9721 showing divergent seed germination at six stages during germination were generated by deep sequencing, in triplicate, using Illumina Hiseq2500. The sequence reads that passed quality filters were analyzed at the gene level. Hisat2 was used to align clean reads to maize B73 reference genome, and HTSeq was used to count transcript abundance. DESeq2 models were used to compare DEGs at each germination stage within or between samples
Results: Comparative transcriptome study identified 12 hours after imbibition (HAI) as the critical stage responsible for the variation of germination speed. The DEGs between 72-3 and F9721 were mainly enriched in metabolic pathways, biosynthesis of secondary metabolites, oxidoreductase activity pathways, hormone signal transduction, and amino acid transporter activity pathways
Conclusions: Combined with evidence from gene expression data, GWAS, and gene synteny with other model species, we finally anchored three genes as the likely candidate genes regulating germination speed in maize

overall_design: RNAseq for two inbred maize lines with divergent seed germination speed and compare the DEGs at critical germination stage with candidate genes identified using GWAS

first: Huairen

last: Zhang

first: Jie

last: Zang

first: Juan

last: Liu


title: A mixture of endocrine disrupting chemicals associated with lower birth weight in children induces adipogenesis and DNA methylation changes in human mesenchymal stem cells

city: Uppsala

first: Polina

last: Lizunkova

address: Norbyvägen 18A

department: Organismal Biology

country: Sweden

institute: Uppsala University

type: Methylation profiling by genome tiling array

summary: Endocrine disrupting chemicals (EDCs) are man-made compounds that alter functions of the endocrine system. Environmental mixtures of EDCs might have adverse effects on human health, even though their individual concentrations are below regulatory levels of concerns. However, studies identifying and experimentally testing adverse effects of real-life mixtures are scarce. In this study, we aimed at evaluating an epidemiologically identified EDC mixture in an experi-mental setting to delineate its cellular and epigenetic effects. The mixture was established using data from Swedish Environmental Longitudinal Mother and child Asthma and allergy (SELMA) study where it was associated with lower birth weight, an early marker for prenatal metabolic programming. This mixture was then tested for its ability to change metabolic programming of human mesenchymal stem cells. In these cells, we assessed if the mixture induced adipogenesis and genome-wide DNA methylation changes. The mixture increased lipid droplet accumulation already at concentrations corresponding to levels measured in the pregnant women of the SELMA study. Furthermore, we identified differentially methylated regions in genes important for adipogenesis and thermogenesis. This study shows that a mixture reflecting human real-life exposure can induce molecular and cellular changes during development that could underlie adverse outcomes.

overall_design: hMSCs were treated with 3 concentrations of Mix G1 and control (DMSO), genomic DNA was collected from triplicate samples of hMSCs from both donors, bisulphite converted and standard Illumina EPIC array was run.

first: Elin

last: Engdahl

first: Gábor

last: Borbély

last: Rüegg


title: Gene expression profile of breast cancer cell line MDA-MB-231 xenograft - validation set

city: Milan

first: Matteo

last: Dugo

address: via Olgettina 60

department: Department of Medical Oncology

country: Italy

institute: IRCCS Ospedale San Raffaele

summary: Progression to stage IV disease remains the main cause of breast cancer-related deaths. Increasing knowledge of the hematogenous phase of metastasis is key for exploiting the entire window of opportunity to interfere with early dissemination and to achieve a more effective disease control. On the hypothesis that the distinguishing molecular features of circulating tumor cells (CTCs) reveal useful information on metastasis biology and disease outcome, we compared the transcriptomes of CTCs and solid primary/secondary lesions of the MDA-MB-231 xenograft model and provided evidence that blood-borne dissemination is regulated by numerous genes. Our new CTC-specific signature improved CTC detection and outcome prognostication in early-stage breast cancer patients compared to conventional CTC markers, and shed light on the metastatic process by highlighting the role of two genes.

overall_design: We injected MDA-MB-231 breast cancer cells in the mammary fat pad of NOD scid female mice and ran two independent gene expression profile experiments using tissues from three animals each. Sample profiling was carried out through the Whole-Genome DASL HT Assay. We first demonstrated that query oligos detect human and not murine RNA sequences, and compared the transcriptomes of (i) frozen sections of primary tumor nodules, lymph-nodes and lungs (solid lesions), (ii) circulating tumor cells isolated from blood samples (CTC), (iii) tumor cells disseminated to bone marrow flushed out from femur bones (DTC), and (iv) in vitro cultured MDA-MB-231 cells (parental cell line). A universal Mouse RNA reference was used as negative control (EI29_UMR).

first: Emanuela

last: Fina

first: Vera

last: Cappelletti


title: Comparative Transcriptome Analysis of callery pear (Pyrus calleryana Decne) seeds at three different stages of cold stratification

city: Yangzhou

first: Jing

address: 48 Wenhui Road

country: China

institute: Yangzhou university

summary: We carried out the transcriptome analysis to  explore expression profiles differences and identify the key genes involved in pear seed dormancy release, by comparing callery pear (Pyrus calleryana Decne) seeds at three different stages of cold stratification

overall_design: Transcriptome profiling of callery pear seeds with 0 d, 20 d and 50 d stratification, insights into seed dormancy release regulation

first: Chunlei

last: Wang


title: Gene expression profile of breast cancer cell line MDA-MB-231 xenograft

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

overall_design: Refer to individual Series


title: Olfactomedin-4 supports cutaneous wound healing by promoting skin cell proliferation and migration

city: Tartu

first: Mariliis

last: Klaas

address: Riia 23

department: Institute of Molecular and Cell Biology

country: Estonia

institute: University of Tartu

summary: Olfactomedin-4 (OLFM4) is an olfactomedin-domain containing glycoprotein that acts as an important regulator of cell adhesion, proliferation, gastrointestinal inflammation, innate immunity and cancer metastasis. In the present study we aimed to elucidate its role in skin regeneration and wound healing. We found that OLFM4 expression is transiently upregulated in the proliferative phase of cutaneous wound healing in humans as well as in mice. Moreover, a significant increase in OLFM4 expression was detected in the skin of lesional psoriasis, a disease characterized by keratinocyte hyperproliferation. In vitro experiments demonstrated that OLFM4 can selectively stimulate keratinocyte proliferation and increase both keratinocyte and fibroblast migration ability. Using proteotransciptomic pathway analysis we revealed that transcription factors POU5F1/OCT4 and ESR1 acted as hubs for OLFM4-dependent signalling in keratinocytes.

overall_design: Changes in human primary skin keratinocyte and fibroblast RNA profiles in response to stimulation with recombinant OLFM4 protein

first: Viljar

last: Jaks


title: Histone H3 lysine 4 and 27 trimethylation signatures associated with human Alzheimer’s disease

city: PADOVA

first: GIUSEPPE

last: PERSICO

state: PD

address: VIA UGO BASSI 58/B

institute: UNIVERSITA' DI PADOVA

summary:
Background: Epigenetic remodeling is emerging as a critical process for both onset and progression of Alzheimer's disease (AD), the most common form of neurodegenerative dementia. However, it is not clear to what extent the distribution of histone modifications is involved in AD
Methods: To investigate histone H3 modifications in AD, we compared the genome-wide distributions of H3K4me3 and H3K27me3 in entorhinal cortices from severe sporadic AD patients and from age-matched healthy individuals of both sexes.
Conclusions: The signature of H3K4me3 and H3K27me3 identified in AD patients validates the role of epigenetic chromatin remodeling in neurodegenerative disease and sheds light on genomic adaptive mechanisms involved in AD.

overall_design: Frozen human entorhinal cortex (n°= 15) tissues generously provided by the Medical Research Council Brain Bank for Dementia Research, Oxford (UK) are analyzed throught ChIP-seq approach to investigate the genome-wide distributions of H3K4me3 and H3K27me3.

first: Giuseppe

last: Persico

first: Francesca

last: Casciaro

first: Stefano

last: Amatori

first: Martina

last: Rusin

first: Francesco

last: Cantatore

first: Amalia

last: Perna

first: Lavinia

last: Alberi Auber

first: Mirco

last: Fanelli

first: Marco

last: Giorgio


title: Cell surface nucleolin is a novel ADAMTS5 receptor mediating endothelial cell apoptosis

city: Sigapore

first: Jong Huat

last: Tee

state: Singapore

address: Blk S3 level 6, Science Dr 4

department: Biological Sciences

country: Singapore

institute: National University Singapore

summary: This study demonstrates that TS5-p45 induces endothelial cell (EC) apoptosis in a caspase-dependent manner via its cell surface receptor Nucleolin (NCL). To unravel how this apoptosis mechanism is induced in ECs, we performed RNA-seq using TS5-p45-treated ECs. Transcriptional changes under TS5-p45 treatment was further evaluated to highlight some of the caspase-dependent apoptosis-inducing and -suppressing genes which are altered in favor of apoptosis.

overall_design: Total RNA samples from (12 h) TS5-p45-treated ECs and control ECs, in triplicates

first: Dogan

last: Kirman

first: Neslihan

middle: A

last: Kaya

first: Ruowen

last: Ge


title: Methyl-lysine readers PHF20 and PHF20L1 define two distinct NSL complexes

city: Houston

first: Margarida

last: Albuquerque Almeida Santos

state: TX

address: 1515 Holcombe Blvd

institute: MD Anderson Cancer Center

summary: The methyl lysine readers PHF (plant homeodomain finger) 20 (PHF20) and its homolog PHF20 Like 1 (PHF20L1) are known components of the NSL (non-specific lethal) complex that regulates gene expression through its histone acetyltransferase activity. In the current model, both PHF homologs coexist in the same NSL complex although this was not formally tested; nor have the functions of PHF20 and PHF20L1 regarding NSL complex integrity and transcriptional regulation been investigated. Here we perform an in-depth biochemical and functional characterization of PHF20 and PHF20L1 in the context of the NSL complex. We identify the existence of two distinct NSL complexes that exclusively contain either PHF20 or PHF20L1; the two PHF homologs do not complex together in the same NSL species. Our data show that the C-terminal domains are essential for PHF20 and PHF20L1 to complex with NSL and the Tudor 2 domains of PHF20 and PHF20L1 are required for chromatin binding. The genome-wide landscape of PHF20/PHF20L1 binding to chromatin shows that they bind mostly to the same genomic regions, at promoters of highly expressed/housekeeping genes. Yet, deletion of PHF20 and PHF20L1 does not abrogate gene expression of the identified targets or impact the recruitment of NSL to the promoters of those genes, suggesting the existence of an alternative mechanism that compensates for the transcription of genes whose sustained expression is important for critical cellular functions.

overall_design: Examination of chromatin landscape of PHF20 and PHF20L1 binding genome-wide in U2OS cells.

last: Santos

first: Hieu

last: Van

first: Peter

last: Harkins

first: Avni

last: Patel

first: Abhinav

middle: K

last: Jain

first: Yue

last: Lu

first: Mark

last: Bedford


title: Time-course transcriptome analysis-guided identification of a four-component system, SbrH1-R that regulates milbemycin biosynthesis by influencing gene cluster expression, precursor supply, and antibiotic efflux

city: Harbin

first: Lan

last: Ye

address: No. 59 Mucai Street

institute: Northeast Agricultural University

summary: Streptomyces bingchenggensis is a soil bacterium that produces milbemycins, which have been applied widely as insecticides and anthelmintics in agricultural and veterinary field. To gain further insights into the regulatory mechanisms in Streptomyces bingchenggensis and mine useful targets for future metabolic engineering to improve milbemycin production, we have compared two strains（the parental strain and high-yielding strain）by comparative transcriptome analysis.This work provides beneficial targets and corresponding engineering methods to facilitate high-production of milbemycins and other polyketide pesticides.

overall_design: 2 time points were designed at 3 and 6 day in two strains. The samples were collected at each time point named W1,W2,H1,H2

first: L

first: Y

last: Zhang

first: S

last: Li

first: W

last: Xiang


title: Modeling Down syndrome AML by introducing disese-specific mutations in iPSCs

city: Wilmington

first: Anilkumar

last: Gopalakrishnapillai

state: DE

address: 200 Powder Mill road

institute: Nemours Children's Health

summary: Down syndrome AML is characterized by the presence of the pathgnonomic mutation in GATA1, which cooperates with other somatic mutations. In this study, we utilzed iPSCs derived from Down syndrome individuals bearing trisomy 21 and introduced disease-specific mutations using CRISPR-Cas9. Hematopoeitic stem and progenitor cells (HSPCs) obtained by hematopoeitic differentiation of these iPSCs, and megakaryocytes generated from the HSPCs (by culturing in megakaryocyte-specific media) were used for RNA sequencing analysis.

overall_design: Transcriptome profiles in HSPCs and megakaryocytes from trisomic iPSCs with or without disease-specific mutations.

first: Sonali

last: Barwe

first: E

last: Kolb

first: Aimy

last: Sebastian


title: SHMT2 drives the progression of colorectal cancer by regulating UHRF1 expression

city: guiyang

first: guanghui

last: wang

address: zhongshan road

institute: hospital

summary: Introduction: Serine hydroxymethyltransferase 2 (SHMT2) has a critical role in serine-glycine metabolism to drive cancer cell proliferation. Yet, the function of SHMT2 in tumorigenesis, especially in human colorectal cancer (CRC) progression, remains largely unclear.   Materials and Methods: CRC and paired normal samples were collected in the Department of Colorectal Surgery, XinHua Hospital, Shanghai Jiao Tong University School of Medicine and assessed by real-time polymerase chain reaction (qPCR) analysis, Western blot (WB), and immunohistochemistry (IHC). Moreover, SHMT2 expression in human CRC cells was identified by qPCR and WB. The CRC cell proliferation, migration, and invasion after SHMT2 knockdown were explored through in vitro and in vivo assays. mRNA-seq assays were used to investigate the underlying mechanisms behind the SHMT2 function.   Results: It was found that SHMT2 mRNA and protein were over-expressed in CRC tissue compared to the levels in normal mucosa. Positive expression of SHMT2 was significantly correlated with TNM stage and lymph node metastasis, and elevated expression of SHMT2 resulted as an independent prognostic factor in patients with CRC. SHMT2 knockdown impaired proliferation of CRC in vitro and in vivo and induced cell cycle arrest by regulating UHRF1 expression.  Conclusion: Taken together, our findings reveal that UHRF1 is a novel target gene of SHMT2, which can be used as a potential therapeutic strategy for CRC therapy.

overall_design: mRNA profile of SHMT2 knockdown CRC cell line (SW620 AND SW480)

first: XIMAO

last: Cui

first: GUANGHUI

last: Wang


title: RNA sequencing analysis in ESCC cells with Drp1 overexpression or TFAM deficiency

city: Kaifeng

first: Dengke

last: Bao

state: Henan

address: Jinming Road

department: School of Pharmacy

institute: Henan University

summary: Mitochondrial homeostasis is important for cell metabolism, growth, proliferation, and immune responses. The critical regulator for mitochondrial homeostasis, Drp1 and TFAM are frequently abnormal expression in many cancers and is closely implicated in tumorigenesis. Here, we found that Drp1 high expression or TFAM low expression is correlated with poor overall survival of ESCC patients. However, the underling mechanism by Drp1 or TFAM influence tumor progression is largely unknown, especially in esophageal squamous cell carcinoma (ESCC). To investigate the underling mechanisms of Drp1 overexpression or TFAM deficiency-mediated ESCC progression, transcriptome profiling was performed by RNA sequencing analysis in ESCC cells with Drp1 overexpression or TFAM knockdown.

overall_design: Human ESCC cell lines KYSE-30 with Drp1 overexpression or TFAM deficiency were established by stable transfection with pcDNA3.1(+)-Drp1 or pSilencer3.1-H1 neo-shTFAM.  Differential gene expression analysis after Drp1 overexpression or TFAM knockdown are performed by RNA sequencing analysis in ESCC cells when compared to control KYSE-30 cell lines.

first: Yujia

first: Yanming