title: Emergent metastatic heterogeneity of primary tumor cells is restricted by the Ig-transmembrane protein VSIG III

overall_design: RNAseq of 2 clones derived from heterogeneous primary Colon Cancer cell culture, in triplicates


title: Emergent metastatic heterogeneity of primary tumor cells is restricted by the Ig-transmembrane protein VSIG I

status: Public on Nov 09 2020

city: Geneva

first: Celine

last: Delucinge

address: 1 rue Michel Servet

department: iGE3 Genomics Platform

country: Switzerland

institute: University of Geneva

type: Expression profiling by high throughput sequencing

summary: Our study prompeted us to assign, through spiked single cell RNAseq, metastatic  function to transcriptomic cluster of colon cancer cells. Interactions between clones also uncover a restrictive anti metastatic influence that act intrinsically and non-cell automomously. We identify VSIG1 as critical mediator of this influence.

first: Carolina

last: Bernal

first: Marianna

last: Silvano

first: Yann

last: Tapponnier

first: Santosh

last: Anand

first: Cecilia

last: Angulo

first: Ariel

last: Ruiz i Altaba


title: Transcriptome analysis of CD45-CD31+ endothelial cells in ischemic hindlimb muscle after IL-35 injection

city: Philadelphia

first: Xiaofeng

last: Yang

state: PA

address: 3500 North Broad Street

department: Cardiovascular Research Center

country: USA

institute: Temple University

summary: We report the first time of the transcriptome difference between IL35- and PBS-injected ischemic muscle after hindlimb ischemia, specifically in isolated CD45-CD31+ endothelial cell

overall_design: After single cell suspension, we specifically isolated CD45-CD31+ bona fide EC from the ischemic muscle at day 0, and 14 after hindlimb ischemia surgery using fluorescence-activated cell sorting (FACS). About 0.1 million cells were collected for RNA extraction and deep-sequencing. Single-end reads at 75 bp with 30 million reads per sample were generated for bioinformatic analysis.

first: Fu

last: Hangfei

first: Sun

last: Yu

first: Yang

last: Xiaofeng


title: OncoSig: a new algorithm for the accurate and systematic de novo prediction of Oncoprotein-centric Signaling networks

status: Public on Nov 11 2020

city: San Francisco

first: David

last: Simpson

state: California

address: 1550 4th Street

institute: UCSF

summary: We introduce a new algorithm, OncoSig, to address the deficiencies of canonical pathways through the accurate, context-specific prediction of proteins representing both known and novel functional members of Oncoprotein-centric Signaling networks. OncoSig performs systematic, de novo elucidation of Protein-Centric molecular interaction maps (PC-maps), which include upstream modulators, cognate binding partners, and downstream effectors. The reconstructed KRAS PC-Map in lung adenocarcinoma (LUAD) demonstrates the recapitulation of known biology and, critically, the discovery of novel KRAS effectors that elicit synthetic lethality in LUAD organoid cultures. To illustrate the generalizability of OncoSig, the methodology is applied to elucidate the PC-maps of ten recurrently mutated oncoproteins and oncopathways in LUAD as well as KRAS PC-Maps across three tumor contexts. OncoSig thus reveals tumorigenic architecture to an unprecedented degree and provides a unique mechanistic perspective on how the flow of information in cells is dysregulated in support of tumor homeostasis. To validate predicted KRAS effectors in primary tumor organoid cultures, this study includes a pooled RNAi screening approach (shRNA-seq) in primary lung tumors from a mouse model driven by mutant Kras and p53 loss.

overall_design: We analyze shRNA abundance at two different timepoints of 27 sample pools using 3-6 biological replicates for genes predicted to play a functional role in KRAS driven tumorigenesis (2 sample pools x 6 replicates) and compare these results to over 500 genes not predicted to be important for KRAS function (25 sample pools x 3 replicates).

middle: R


title: RNAseq of Axin2pos and Axin2neg cell populations derived from differentiated bile duct organoids treated with Rspo1

city: Cardiff

first: Eider

last: Valle-Encinas

state: Cardiff

address: Sir Martin Evans Building, Museum Avenue

department: Biosciences

country: United Kingdom

institute: Cardiff University

summary:
Purpose: The goal of this study was to compare the transcriptome profiling (RNAseq) of two cell populations (Axin2pos and Axin2neg) that in differentiated bile duct-derived organoids (Axin2CreERT2+/-; R26-LSL-tdTom+/-) that aroused following 24h Rspo1 treatment. The transcriptome of these two cell populations was additionally compared with cells isolated from differentiated control organoids, which were all negative for Axin2 expression.
Methods: Single-end 75bp sequencing of Axin2pos and Axin2neg cells isolated by FACS from differentiated bile duct organoids (Axin2CreERT2+/-; R26-LSL-tdTom+/-)  organoids at three different passages (P5, P6 and P10) based on tdTom expression levels  was performed with 100ng of total RNA input. To label Axin2 expressing cells, organoids treated with 500nM of 4-OHT for the last 24h of culture. Rspo1-treated organoids were exposed to 100ng/ml of Rspo1 during the last 24h of culture.
Results: The addition of Rspo1 to the cultures caused an overall decrease of BEC lineage markers (Hnf1b, Muc1, Krt19, Krt7) in both Axin2pos and Axin2neg cells when compared to untreated cells, indicating that exposure to Rspo1 promoted escape from biliary fate. Axin2pos isolated from Rspo1-treated organoids were enriched in proliferation and hepatic progenitor cell markers when compared to Axin2neg cells isolated from Rspo1 treated organoids
Conclusions: Our study uncover a possible role for the Wnt signalling pathway in BEC regenerative biology and cellular plasticity.

overall_design: mRNA profiles of cells isolated from control (untreated_Axin2neg) or Rspo1 treated (Rspo1_Axin2neg and Rspo1_Axin2pos) differentiated bile duct organoids originated from a single Axin2CreERT2+/-; R26-LSL-tdTom+/- animal at three different passages (P5, P6 and P10).

first: Robert

last: Andrews

first: Sumukh

last: Deshpande

first: Angela

middle: M

last: Marchbank

first: Georgina

middle: E

last: Smethurst


title: FACSorting cell population depending on their relative expression of VSIG1

first: Celine

last: Delucinge

summary: We Immunostained C11 colon cancer cellular clone cells to FACSort 4 cell-populations depending on their relative level of expression of VSIG1

overall_design: RNA seq of 4 populations expressing different level of VISG1 (Neg-Low-Mid-High) on 3 independant replicates


title: Transcriptomic profiling of circulating T follicular helper cells (cTFH) and activated memory B cells (ABC) in kidney transplant recipients

city: Pittsburgh

first: Uma

last: Chandran

address: 5150 Center Ave

department: BioMedical Informatics

institute: University of Pittsburgh

summary: We compared the transcriptomic profile between patients without donor-specific HLA antibodies (DSA-), patients with donor-specific HLA antibodies without antibody-mediated rejection (DSA+ ABMR-) and patients  with donor-specific HLA antibodies and antibody-mediated rejection (DSA+ ABMR+). We found that patient with DSA+ ABMR+ had a distinct transcriptomic profile compared to DSA- and DSA+ ABMR-, characterized by upregulation of genes encoding for germinal center T follicular helper cells function, T-B cell interaction and costimulatory molecules.

overall_design:
We analysed N=3 cTFH and N=3 ABC samples per group of patients (DSA-, DSA+ABMR-, DSA+ ABMR+), without replicates, sequencing was done using the Illumina NextSeq 500 as the platform, and RNA extraction method was Total RNA using the miRNeasy Mini kit

**Raw data not provided due to patient privacy concerns**

first: Kevin

last: Louis

first: Diana

last: Metes

first: Alexander

last: Chang


title: Maternal Immune Activation Disrupts Proteostasis in the Fetal Brain

city: Boston

first: Brian

last: Kalish

state: MA

address: 220 Longwood Ave

department: Neurobiology

institute: Boston Children's Hospital

summary: Maternal infection and inflammation during pregnancy is associated with neurodevelopmental disorders in offspring, but little is understood about the molecular mechanisms underlying this epidemiologic phenomenon. We leveraged single-cell RNA sequencing to profile transcriptional changes in the rodent fetal brain in response to maternal immune activation (MIA) and identified perturbations in cellular pathways associated with mRNA translation, ribosome biogenesis, and stress signaling. We found that MIA specifically activated the integrated stress response (ISR) in male, but not female, MIA offspring, thereby reducing global mRNA translation and altering nascent proteome synthesis. Moreover, genetic blockade of ISR activation rescued the social behavior phenotype in MIA male offspring. Our data suggest that therapeutic targeting of the ISR may be beneficial in reducing maternal inflammation-associated neurodevelopmental disorders.

overall_design:
Two timepoints (E14 and E18), each with two bioreplicates of the following: PBS control male, PBS control female, maternal immune activation male, maternal immune activation female.

RNA-seq and ribosome profiling of one timepoint (E18) with replicates of the following conditions: PBS control male, PBS control female, maternal immune activation male, maternal immune activation female.

middle: T

first: Michael

last: Greenberg


title: Three-dimensional bioprinting enables creation of tissue-informed glioblastoma microenvironments for modeling complex cellular interactions

city: San Diego

first: Jeremy

last: Rich

state: CA

address: 9500 Gilman Drive #0695

institute: University of California, San Diego

summary: Brain tumors are dynamic complex ecosystems with multiple cell types. To model the brain tumor microenvironment in a reproducible and scalable system, we developed a rapid three-dimensional (3D) bioprinting method to construct clinically relevant biomimetic tissue models. In recurrent glioblastoma, macrophages/microglia prominently contribute to the tumor mass. To parse the function of macrophages in 3D, we compared the growth of glioblastoma stem cells (GSCs) alone or with astrocytes and neural precursor cells (NPCs) in a hyaluronic acid (HA)-rich hydrogel, with or without macrophages. Bioprinted constructs integrating macrophage recapitulate patient-derived transcriptional profiles predictive of patient survival, maintenance of stemness, invasion, and drug resistance. Whole genome CRISPR screening with bioprinted complex systems identified unique molecular dependencies in GSCs, relative to sphere culture. Multicellular bioprinted models serve as a scalable and physiologic platform to interrogate drug sensitivity, cellular crosstalk, invasion, context-dependent functional dependencies, as well as immunologic interactions in a species-matched neural environment.

overall_design: RNA sequencing of 8 samples with 2 replicates for each sample

first: Min

last: Tang

first: Qi

last: Xie

first: Ryan

middle: C

last: Gimple

first: Zheng

last: Zhong

first: Briana

last: Prager

first: Zhixin

last: Qiu

first: Shaochen

last: Chen

middle: N


title: Emergent metastatic heterogeneity of primary tumor cells is restricted by the Ig-transmembrane protein VSIG VI

overall_design: RNAseq of clone E3 FACS sorted for GFP and previously co-coltured with different cells

first: Carolina

last: Bernal

first: Marianna

last: Silvano

first: Yann

last: Tapponnier

first: Santosh

last: Anand

first: Cecilia

last: Angulo

first: Ariel

last: Ruiz i Altaba


title: Mechanism of tolerance improvement of Escherichia coli W against 3-hydroxypropionic acid by deletion of a less characterized transcription factor yieP   (RNA-seq data seq)

city: Ulsan

first: Donghyuk

last: Kim

address: 50 UNIST-gil, Eonyang-eup, Ulju-gun

department: Department of Chemical Engineering

country: South Korea

institute: UNIST

summary: The mechanism of 3-HP tolerance related to YieP was elucidated. The genome-wide analysises were carried out to find out the genes reponsible for 3-HP tolerance.

overall_design: E. coli W strains (wild-type and yieP deletion) were cultured in modified M9 minimal medium with 100 mM glycerol as the carbon source. Genome-wide transcription of these strains was compared in the presence and absence of 3-HP.

first: Thuan

middle: P

last: Nguyen-Vo

first: Seyoung

last: Ko

first: Jung

first: Sunghoon

last: Park


title: Skeletal glucocorticoid signaling determines aging-related leptin resistance and obesity

city: Sydney

first: Ruby

middle: CY

last: Lin

state: NSW

address: 176 Hawkesbury Road, Westmead

country: Australia

institute: The Westmead Institute for Medical Research

summary: Aging contributes to many chronic conditions, including central obesity, insulin resistance and osteoporosis, which are also critical features of glucocorticoid excess. To investigate tissue-specific sites of glucocorticoid (GC) action during aging, we disrupted GC signalling in mouse osteoblasts via transgenic overexpression of the GC-inactivating enzyme, 11β-hydroxysteroid-dehydrogenase type 2 (11β-HSD2). Wild-type mice with intact osteoblastic GC signalling developed leptin resistance, obesity and insulin resistance with aging. In contrast, transgenic (HSD2OB-tg) mice remained lean and leptin-sensitive, and were protected against aging-related hyperinsulinaemia, blunted sympathetic responses and loss of thermogenic adipose tissue. These salutary effects were independent of the osteoblast-derived factors osteocalcin and lipocalin-2. Gene expression analysis of bones from HSD2OB-tg mice indicated an early induction of pro-osteogenic and anti-adipogenic factors, and activation of a local pro-inflammatory TLR4-ZBTB16-NR1H3 network in osteoblastic cells. These findings reveal a critical role for skeletal glucocorticoid signaling in central leptin action, and in impaired metabolic function with aging

overall_design: Wild-type and HSD2^OB-tg mice were housed under standard laboratory conditions at 24°C on a 12:12 h light–dark cycle with free access to standard chow and water. Mice were sacrificed at 3, 6, 12 and 18 m of age for females and 3 and 18 m of age for males. Food intake was determined every 4 to 6 wks. Total RNA extracted from tibiae and femur of 3, 6, 12, and 18 months old WT vs HSD2^ob-tg mice were interrogated using Affymetrix Mouse GeneChip Gene 2.1 ST arrays. Biological triplicates were investigated.

first: Holger

last: Henneicke

first: Michael

last: Swarbrick

first: Hong

last: Zhou

first: Markus

middle: J

last: Siebel


title: Emergent metastatic heterogeneity of primary tumor cells is restricted by the Ig-transmembrane protein VSIG V

first: Celine

last: Delucinge

overall_design: RNAseq of clone E3 infected with lentivirus for ectopic expression of VSIG1V1 and VSIGV2 cDNA and PTWEEN


title: WT and inv(16)/KITD816Y granulocyte macrophage progenitor (GMP) cells [mouse]

city: Copenhagen

first: Kim

last: Theilgaard-Mönch

address: Ole Maaløes Vej 5

country: Denmark

institute: Rigshospitalet/National Univ. Hospital and Biotech Research and Innovation Centre

type:
Expression profiling by array
Third-party reanalysis

summary: WT GMPs (Lin- IL7R- Sca1- ckit+ FcgRhiCD34+) and inv(16)/KITD816Y GMPs (Lin- Sca1- ckit+ CD41- FcgR+ CD150-) were FACS sorted as described in material and methods from supplementary data (Estruch M et al 2020)

overall_design:
Targeted inhibition of cooperative mutation- and therapy-induced AKT activation in AML effectively enhances response to chemotherapy
This series includes re-analyzed samples from GSE15907.

first: Montserrat

last: Estruch

first: Kristian

last: Reckzeh

first: Camilla

last: Vittori

first: Anders

last: Centio

first: Mina

last: Ali

first: Sophia

last: Engelhard

first: Ling

last: Zhao

first: Kyoung

last: Won

first: Paul

last: Liu

first: Bo

last: Porse


title: RNA-binding protein quaking (Qk) promotes switching from neurogenesis to gliogenesis of neural stem cells during brain development [P7 cortex]

city: Higashi-Osaka

first: Kei

last: IIDA

state: Osaka

address: Kowakae 3-4-1

country: Japan

institute: Kindai University

summary: During mammalian brain development, neural stem cells (NSCs) initially produce only neurons and subsequently shift to glial production, while it is still unknown what regulates this drastic fate change. Here we discovered RNA-binding protein (RBP) of quaking (Qk) is selectively expressed in NSCs and is essential for switching from neurogenesis to gliogenesis. Using CNS-specific KO mice for Qk, we found that gliogenesis, but not neurogenesis, was specifically disrupted in Qk-/- brains. In glial differentiating condition, Qk-/- NSCs failed to enter gliogenesis but caused ectopic neurogenic gene expression. Pathway analysis of Qk-/- NSCs identified endocytosis as the regulatory functional cluster of Qk which has been shown to facilitate extra-cellular signaling receptors replacement and promote NSC differentiation. Mechanistically, Qk regulates endocytosis pathway genes through stabilizing their mRNAs via Qk binding sequences in 3’UTR. These results uncovered the cell fate determination mechanism of NSCs through mRNA regulation.

overall_design: We analyzed mRNA expression in cerebral cortices from 3 control & 3 Qk-/- P7 mouse brains

first: Akihide

last: Takeuchi

last: Iida

first: Masatoshi

last: Hagiwara


title: RNA-binding protein quaking (Qk) promotes switching from neurogenesis to gliogenesis of neural stem cells during brain development [Dif_NSCs]

overall_design: We analyzed mRNA expression in glial progenitors from 2 control & 2 Qk-/- neural stem cells


title: Maternal Brown Fat Thermogenesis Programs Glucose Tolerance in the Male Offspring

city: Lübeck

first: Rebecca

last: Oelkrug

address: Ratzeburger Allee 160

country: Germany

institute: University of Lübeck

summary:
We tested if minor changes in environmental temperature during pregnancy can severely alter the phenotype of the offspring already in the next generation. Genome-wide expression profiling of liver samples obtained from adult male mice offspring identified several alterations in the hepatic transcriptomic landscape, thus demonstrating that even minor differences in the demand for maternal thermogenesis profoundly and permanently alter hepatic gene activity in the adult offspring.

Liver gene expression data of offspring from dams that were kept at different ambient temperatures (30°C, 23°C, 18°C, 10°C) only during pregnancy.

overall_design: Five adult male mice per maternal condition (30°C, 23°C, 18°C, 10°C) were analysed (4 group comparison).

first: Jens

last: Mittag


title: Emergent metastatic heterogeneity of primary tumor cells is restricted by the Ig-transmembrane protein VSIG IV

first: Celine

last: Delucinge

overall_design: RNAseq of clone C11 infected with lentivirus for shVSIG1 and PLKO

first: Carolina

last: Bernal

first: Marianna

last: Silvano

first: Yann

last: Tapponnier

first: Santosh

last: Anand

first: Cecilia

last: Angulo

first: Ariel

last: Ruiz i Altaba


title: The N6-methyadenosine (m6A) levels in HaCaT-T cells and control HaCaT cells

status: Public on Nov 08 2020

city: Chengdu

first: Zunzhen

last: Zhang

address: West China School of Public Health and West China Fourth Hospital, Sichuan University

country: China

institute: Sichuan University

summary: Human m6A-mRNA&lncRNA Epitranscriptomic  Microarray of arsenite-transformed human keratinocytes (HaCaT-T cells, 1 μM arsenite exposure for 50 passages) compared to its control HaCaT cells (passed for 50 passages without arsenic exposure).

overall_design: Two-condition experiment, HaCaT-T vs. HaCaT cells. Biological replicates: 1 control replicate, 1 transformed replicates.

first: Tianhe

last: Zhao


title: The Msi1-mTOR pathway drives the pathogenesis of Paget's disease

status: Public on Nov 12 2020

city: Irvine

first: Maksim

middle: V

last: Plikus

address: 845 Health Sciences Road

department: Developmental and Cell Biology

institute: University of California, Irvine

summary: We report the single cell transcriptomes of normal and Extramammary Paget Disease (EMPD) human scrotal skin epidermal cells; as well as the single cell transcriptomes of normal and Krt14-rtTA;TRE-Msi1 double transgenic (DTG) mouse dorsal skin epidermal cells.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Examination of epidermal cell heteregeneity in human EMPD and a mouse model for Paget disease. Characterization of Paget cells in human EMPD and Paget-like cells in DTG mice.

first: Yongli

last: Song

first: Christian

middle: F

last: Guerrero-Juarez

first: Nie

last: Nie

first: Zhengquan

last: Yu


title: Chromatin accessibility analysis uncovers TFAP2A as a regulator on pro-angiogenesis of acquired resistance to anlotinib

city: Shanghai

first: Le

middle: Le

address: 241 Huaihai West Rd

department: Shanghai chest hospital

institute: Shanghai Jiaotong university

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Anlotinib, a multitarget agent a multi-target agent that inhibits tumor proliferation and angiogenesis, has been demonstrated to be effective for non-small cell lung cancer (NSCLC) at third-line or over third-line. However, the underlying mechanisms of anlotinib acquired-resistance is still unclear. Here we performed chromatin accessibility profiling on anlotinib-resistant NCI-H1975 and wild-type NCI-H1975. By integrating with transcriptome analysis, we found that anlotinib resistance was due to increased angiogenic capacity, and revealed that TFAP2A was involved in anlotinib resistance. Next, TFAP2A was knock-down in anlotinib-resistant cells and RNAseq was performed to see down-regulated genes with TFAP2A KD.

overall_design: Anlotinib-resistant and wild-type NCI-H1975 cells were used for ATAC-seq and RNA-seq,  TFAP2A KD anlotinib-resistant cells were used for RNAseq.

first: Lele

first: Jun

last: Lu

first: Ruiqi

last: Liu


title: Aspirin Suppresses Age-Related Methylation Drift in Healthy Colon by Targeting Epigenetic Regulators

city: Basel

first: Faiza

last: Noreen

address: Mattenstrasse 28

department: Department of Biomedicine

institute: University of Basel

type: Methylation profiling by genome tiling array

summary: DNA of 124 normal mucosa biopsies from cecum (proximal) and sigmoid (distal) colon obtained at baseline (t1) and after 10years (t2) from 31 screening females was subjected to measure DNA methylation profiles by Illumina Infinium EPIC Human Methylation BeadChip across approximately 850,000 CpGs.

overall_design: Bisulphite converted DNA from the 124 samples were hybridised to the Illumina Infinium EPIC Human Methylation BeadChip. Methylation score of each CpG is represented as beta value.

first: Kaspar

last: Truninger

first: Primo

last: Schär


title: YTHDF2 mediates the mRNA degradation in prostate cancer in m6A-dependent way

city: Hangzhou

first: Jiangfeng

last: Li

address: Qingchun Road 79

institute: First Affiliated Hospital, School of medicine, Zhejiang University

type: Methylation profiling by high throughput sequencing

summary: As the crucial m6A reader, YTHDF2 usually degrades the target mRNAs by recognizing the m6A modified sites, consequently altering m6A levels of each mRNA. In this study, we used m6A MeRIP sequencing to detect the m6A modification alterations in prostate cancer (PCa) cell line after knocking down YTHDF2 and identify how YTHDF2 promote the PCa progression by mediating the mRNA degradation in m6A-dependent way.

overall_design: M6A MeRIP sequencing was used to detect the m6A modification alterations in two groups (PC-3 cell line, shNC and shYTHDF2).

first: Xiao

last: Wang


title: Comprehensive analysis of circRNA expression profiles and circRNA associated competing endogenous RNA networks in IgA nephropathy

city: Changsha

first: Hong

state: Hunan

address: Renmin Road 139#

department: Nephrology

institute: The Second Xiangya Hospital, Central South University

summary:
Purpose: Immunoglobulin A nephropathy (IgAN) is immune-mediated primary glomerulonephritis, which is the most common reason leading to renal failure worldwide, the exact pathogenesis of IgAN is not well defined. Accumulating evidence indicates that circular RNAs (circRNAs) play crucial roles in the immune disease by involving in the competing endogenous RNA (ceRNA) network mechanism. At present, the studies of the circRNA profiles and circRNA-associated ceRNA networks in the IgAN are still scarce. This study aimed to elucidate the potential roles of circRNA, microRNA (miRNA), and messenger RNA (mRNA) ceRNA network in peripheral blood mononuclear cells (PBMCs) of IgAN.
Methods: CircRNA sequencing was used to identify the differential expressed circRNAs (DEcircRNAs) of PBMCs in IgAN and healthy controls. A circRNA-miRNA-mRNA ceRNA network was constructed to further investigate the mechanisms of IgAN.
Results: A total of 145 circRNAs were differentially expressed in IgAN compared with controls (|log2 (FC)|>1 and P-value <0.05). Combined with the data from GSE73953 and GSE25590 in GEO database, a ceRNA network was constructed which contained 16 DEcircRNAs, 72 differential expressed mRNAs (DEmRNAs) and 11 differential expressed miRNAs (DEmiRNAs).
Conclusion: Our study identified a novel circRNA-mediated ceRNA regulatory network mechanisms in the pathogenesis of IgAN.

overall_design: circRNA from IgAN patients and control subjects were generated by deep sequencing, in triplicate.

first: Haiyang

first: Di

first: Yexin

first: Liyu

last: He


title: Brain pathology and cerebellar Purkinje cell loss in a mouse model of chronic neuronopathic Gaucher disease

city: Rehovot

first: Yael

last: Pewzner-Jung

address: 234 Herzl St.

country: Israel

institute: Weiamann Institute of Science

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

overall_design: Refer to individual Series


title: Loop Extrusion Mediates Physiological Locus Contraction for V(D)J Recombination (3C-HTGTS)

first: Frederick

middle: W

last: Alt

address: 1 Blackfan Circle

department: PCMM

summary: Immunoglobulin heavy chain locus (Igh) VH, D, and JH gene segments are developmentally assembled into V(D)J exons. RAG endonuclease initiates V(D)J recombination by binding a JH-recombination signal sequence (RSS) within a chromatin-based recombination center (RC) and then, in an orientation-dependent process, scans upstream D-containing chromatin presented by cohesin-mediated loop extrusion for convergent D-RSSs to initiate DJH-RC formation. In primary pro-B cells, 100s of upstream VH-associated RSSs, embedded in convergent orientation to the DJH-RC-RSS, gain proximity to the DJH-RC for VH-to-DJH joining via a mechanistically-undefined VH-locus contraction process.  Here, we report that a 2.4 mega-base VH locus inversion in primary pro-B cells nearly abrogates rearrangements of normally convergent VH-RSSs and cryptic RSSs, even though locus contraction per se is maintained. Moreover, this inversion activated rearrangement of both cryptic VH-locus RSSs normally in the opposite orientation and, unexpectedly, of normally-oriented cryptic RSSs within multiple, sequential upstream convergent-CBE domains. Primary pro-B cells had significantly reduced transcription of Wapl, a cohesin-unloading factor, versus levels in v-Abl pro-B lines that lack marked locus contraction or distal VH rearrangements. Correspondingly, Wapl depletion in v-Abl lines activated VH-locus contraction and orientation-specific RAG-scanning across the VH-locus. Our findings indicate that locus contraction and physiological VH-to-DJH joining both are regulated via circumvention of CBE scanning impediments.

overall_design: We performed 3C-HTGTS in BM pro-B cells and v- Abl transformed pro-B cells and its various mutant derivatives to study orientation-dependent linear RAG scanning and locus contraction in long-range cohesin-driven V(D)J recombination.

first: Hai-qiang

last: Dai

first: Hongli

last: Hu


title: Loop Extrusion Mediates Physiological Locus Contraction for V(D)J Recombination (ChIP-Seq)

overall_design: We performed ChIP-Seq in BM pro-B cells and v- Abl transformed pro-B cells and its various mutant derivatives to study orientation-dependent linear RAG scanning and locus contraction in long-range cohesin-driven V(D)J recombination.

first: Haiqiang


title: Loop Extrusion Mediates Physiological Locus Contraction for V(D)J Recombination (GRO-Seq)

overall_design: We performed GRO-Seq in BM pro-B cells and v- Abl transformed pro-B cells and its various mutant derivatives to study orientation-dependent linear RAG scanning and locus contraction in long-range cohesin-driven V(D)J recombination.


title: Brain pathology and cerebellar Purkinje cell loss in a mouse model of chronic neuronopathic Gaucher disease [whole brain]

summary: Gaucher disease (GD) is currently the focus of considerable attention due primarily to the association between the gene that causes GD (GBA) and Parkinson’s disease. Mouse models exist for the systemic (type 1) and for the acute neuronopathic forms (type 2) of GD. Here we report the generation of a mouse that phenotypically models chronic neuronopathic type 3 GD. Gba-/-;Gbatg mice, which contain a Gba transgene regulated by doxycycline, accumulate moderate levels of the offending substrate in GD, glucosylceramide, and live for up to 10 months, i.e. significantly longer than mice which model type 2 GD. Gba-/-;Gbatg mice display behavioral abnormalities at ~4 months, which deteriorate with age, along with significant neuropathology including loss of Purkinje neurons. Gene expression is altered in the brain and in isolated microglia, although the changes in gene expression are less extensive than in mice modeling type 2 disease. Finally, bone deformities are consistent with the Gba-/-;Gbatg mice being a genuine type 3 GD model. Together, the Gba-/-;Gbatg mice share pathological pathways with acute neuronopathic GD mice but also display differences that might help understand the distinct disease course and progression of type 2 and 3 patients.

overall_design: RNA was isolated from whole brain homogenates of C57BL/6 6-9 months old Gba-/-;GbaTg Chronic Gaucher disease mouse model and littermate control Gba+/-;GbaTg and Gba+/+ mice after administration of doxycycline for ~4-7 months. In addition, RNA was isolated from whole brain homogenates of C57BL/6 wildtype mice, injected with conduritol B-epoxide (CBE) from P8-P21 to induce acute Gaucher disease, or control mice injected in parallel with PBS were examined on P21.

first: Noa

last: Wigoda

first: Anthony

middle: H

last: Futerman


title: Tracheal aspirate transcriptomic and miRNA signatures of extreme premature birth with bronchopulmonary dysplasia

city: Hershey

first: Yuka

last: Imamura Kawasawa

address: 500 University Dr.

department: College of Medicine, Pharmacology

institute: Penn State University

summary: We analyzed mRNA profiles in tracheal aspirates from 53 newborns receiving invasive mechanical ventilation. Twenty-six infants were extremely preterm diagnosed with BPD and twenty-seven were term babies receiving invasive mechanical ventilation for elective procedure. Specific mRNA signatures in TAs may serve as potential biomarkers for extreme prematurity and BPD pathogenesis.

overall_design: We extracted RNA from 0.5 mL of tracheal aspirates from neonates without lung disease or with bronchopulmonary dysplasia. Transcriptomic analysis was performed by RNAseq. Raw data is not provided due to the agreement by Institutional Review Board (IRB).

first: Christiana

last: Oji-Mmuo

first: Roopa

last: Siddaiah

first: Patricia

last: Silveyra


title: RNA-binding protein quaking (Qk) promotes switching from neurogenesis to gliogenesis of neural stem cells during brain development

first: Kei

last: IIDA


title: Loop Extrusion Mediates Physiological Locus Contraction for V(D)J Recombination (LAM-HTGTS)

overall_design: We performed LAM-HTGTS in BM pro-B cells and v- Abl transformed pro-B cells and its various mutant derivatives to study orientation-dependent linear RAG scanning and locus contraction in long-range cohesin-driven V(D)J recombination.


title: The role of AIB1D4 cistrome in early breast cancer progression

city: Washington

first: Ghada

last: Sharif

state: DC

address: 3970 Reservoir Rd NW NRB E311

institute: Georgetown University

summary: We report the global occupancy by ChIP-seq of AIB1 in MCF10A, MCF10A-D4, MCFDCIS and MCFDCIS-D4 cells. We performed ChIP and library preparation with the ActiveMotif Low Cell ChIP-seq kit. Data was aligned to hg19 with rsubread, data was sorted and de-duplicated with SAMTOOLS, and peaks were called with CSAW. Analysis was done with ChIP-seeker in R.

overall_design: Examination of ChIP-seq of AIB1 isoforms binding to the genome in MCFDCIS vs. MCFDCIS-D4 cell lines in triplicate, normalized to cell lysate input. And, MCF10A vs. MCF10A-D4 cell lines in triplicate, normalized to cell lysate input.

first: Anna

last: Riegel


title: Development of New Therapeutic Combinations for Ovarian Cancer Using Genetically Defined, Syngeneic Organoid Platform

city: New York

first: Igor

last: Dolgalev

state: New York

address: 550 1st Ave

institute: NYU Grossman School of Medicine

summary: The paucity of genetically informed, immune-competent tumor models impedes evaluation of conventional, targeted, and immune therapies. By engineering mouse fallopian tube (FT) organoids using lentiviral gene transduction and/or CRISPR/Cas9 mutagenesis, we generated multiple high grade serous ovarian carcinoma (HGSOC) models exhibiting combinations of mutations seen in patients. Detailed analysis of homologous recombination (HR)-proficient (Tp53-/-;Ccne1OE;Akt2OE ;KrasOE), HR-deficient (Tp53-/-;Brca1-/-;MycOE ) and unclassified (Tp53-/-;Pten-/-;Nf1-/-) examples revealed differences in in vitro properties and tumorigenicity/metastasis. Tumorigenic organoids had differential sensitivity to HGSOC chemotherapeutics and evoked distinct immune microenvironments. These findings enabled development of a chemotherapy/immunotherapy regimen that yielded durable, T-cell dependent responses in Tp53-/-;Ccne1OE;Akt2OE;Kras HGSOC; by contrast, Tp53-/-;Pten-/-;Nf1-/- tumors failed to respond. Genotype-informed, syngeneic organoid models could provide an improved platform for rapid evaluation of tumor biology and therapeutics.

overall_design: mRNA profiles of 4 independent tumors derived from organoid injection of Tp53-/-;Ccne1OE;Akt2OE;KrasOE, Tp53-/-;Pten-/-;Nf1-/- and Tp53-/-;Brca1-/-;MycOE, respectively.

first: Shuang

last: Zhang

first: Benjamin

middle: G

last: Neel


title: Natural variation analysis of perennial ryegrass in response to abiotic stress highlights LpHSFC1b as a positive regulator of heat stress

city: Wuhan

first: Zhulong

last: Chan

state: Hubei Province

address: No. 1, Shizishan St, Nanhu

department: College of Horticulture and Forestry Sciences

institute: Huazhong Agricultural University

summary:
Purpose: We aimed to dissect response of Perennial_ryegrass to drought, heat and cold stresses and identify stress responsive genes in Perennial_ryegrass.
Methods: The sequencing libraries was constructed using NEBNext® UltraTM RNA Library Prep Kit for Illumina®, sequenced on an Illumina Hiseq platform and 125 bp/150 bp paired-end reads were generated. Clean data (clean reads) were obtained after removing reads containing poly-N or adapter, and low quality reads from raw data. Transcriptome assembly was accomplished based on the left.fq.gz and right.fq.gz using Trinity.  Gene function was annotated based on the following databases: NR (NCBI non-redundant protein sequences), Pfam (Protein family), KOG/COG/eggNOG (Clusters of Orthologous Groups of proteins), Swiss-Prot (A manually annotated and reviewed protein sequence database), KEGG (Kyoto Encyclopedia of Genes and Genomes) and GO (Gene Ontology). Differential expression analysis of two groups was performed using the DESeq R package (1.10.1). Genes with an adjusted P-value<0.05 and fold change>2 found by DESeq were assigned as differentially expressed.
Results:In total, four samples with two biological replicates per genotype/treatment combination were used for RNA sequencing analysis. At least 5 G clean bases were generated for each sample.After sequencing quality control, a total 137822219 clean reads and 41.05 G clean bases were generated. The Q30 base percentage of each sample was higher than 91.0% (Table S1). A total of 32840 unigenes were obtained after transcriptome assembly. Comparative analysis identified genes modulated by  drought, heat and cold stresses

overall_design: For cold and heat treatments, 14-day-old seedlings were treated at 4 and 42 oC for 12 hours, respectively. For drought treatment, 7-day-old seedlings were withheld water for 7 days. Stress-treated and control seedlings were collected for RNA isolation with 30 seedlings for each treatment or control replicate.

first: Tianxiao

last: Sun


title: An H3K4me3 reader, BAP18 as an adaptor of COMPASS-like core subunits co-activates ERa action to confer to tamoxifen resistance in breast cancer

first: Ge

state: Hubei

address: Shizi Mountain Street No.1

institute: Huazhong Argriculture University

summary: Estrogen receptor alpha (ERalpha signaling pathway is essential for ERalpha positive breast cancer progression and endocrine therapy resistance. BPTF associated protein of 18kDa (BAP18) has been recognized as a crucial H3K4me3 reader. However, the whole genomic occupation of BAP18 and its biological function in breast cancer are still elusive. Here, we found that higher expression of BAP18 in ERalpha positive breast cancer is positively correlated with poor prognosis. ChIP-seq analysis further demonstrated that the half estrogen response elements (EREs) and the CCCTC binding factor (CTCF) binding sites are the significant enrichment sites found in estrogen-induced BAP18 binding sites. In addition, we provide the evidence to demonstrate that BAP18 as a novel co-activator of ERalpha is required for the recruitment of COMPASS-like core subunits to cis-regulatory element of ERalpha target genes in breast cancer cells. BAP18 is recruited to the promoter regions of estrogen-induced genes, accompanied with the enrichment of the lysine 4-trimethylated histone H3 tail (H3K4me3) in the presence of E2. Furthermore, BAP18 promotes cell growth and confers to ERalpha antagonist tamoxifen resistancein ERalpha positive breast cancer. Our data suggest that BAP18 facilitates the association between ERalpha  and COMPASS-like core subunits, which might be an essential epigenetic therapeutic target for breast cancer.

overall_design: Examination of BAP18 global enrichment on chrmatin in MCF7 cell.

first: Chunyu

last: Wang


title: RNA-seq analysis of transcriptomes in control and LAMP2A-overexpressed D3 ES cells

city: Philadelphia

first: Xiaolu

last: Yang

address: BRB2/3,421 curie blvd

institute: University of Pennsylvania

summary: The role of autophagy and metabolism in regulating the pluripotency of stem cells is not well understood. LAMP2A is a key gene in CMA. Here we compared transcriptomic changes in LAMP2A-overexpressed D3 versus control cells, as well as changes in LAMP2A-overexpressed cells with versus without DM-αKG treatment (4mM, 72 hrs). We found that overexpression of LAMP2A leads to decreased expression of genes related to stem cell differentiation, and this can be largely restored by DM-αKG supplement. This study provides a promising link for autophagy, metabolism, and pluripotency of stem cells.

overall_design: RNA-Seq was performed to measure transcriptomes of D3 ES cells under three conditions: 1) cells stably expressed pCDH-control vector (VT), 2) LAMP2A overexpressed cells without (LAMP2A), and 3) with DM-αKG treatment (4 mM, 72 hrs) (LAMP2A+ DM-αKG).

first: Yi

last: Xu


title: Brain pathology and cerebellar Purkinje cell loss in a mouse model of chronic neuronopathic Gaucher disease [microglia]

first: Yael

last: Pewzner-Jung

overall_design: RNA was isolated from sorted microglia of C57BL/6 7 months old Gba-/-;GbaTg Chronic Gaucher disease mouse model and littermate control Gba+/-;GbaTg, Gba+/- and Gba+/+ mice after administration of doxycycline for ~5.5 months. In addition, RNA was isolated from sorted microglia of C57BL/6 wildtype mice, injected with conduritol B-epoxide (CBE) from P8-P21 to induce acute Gaucher disease, or control mice injected in parallel with PBS were examined on P21.

first: Noa

last: Wigoda

first: Anthony


title: Terminal B cell differentiation

city: Oullins

first: Fabrice

last: Chatonnet

address: 165 Chemin du Grand Revoyet

country: France

institute: INSERM


title: Chromatin accessibility profiling of terminal B cell differentiation [ATAC-Seq]

summary: The terminal differentiation of B cells into antibody-secreting cells (ASCs) is a critical component of adaptive immune responses. Using our in vitro differentiation system, we combined RNA sequencing with ATAC-seq to characterize genomic events driving the ASC differentiation of human primary naive B cells. After an initial response to IL-4, cells that committed to an ASC fate downregulated the CD23 marker and IL-4 signaling, whereas cells that maintained IL-4 signaling did not differentiate. As demonstrated in the mouse, downregulation of the human ubiquitin ligase CBLB was required to free IRF4 from proteasomal degradation and produce levels needed for ASC differentiation. Our results evidenced two previously undocumented mechanisms driving human terminal B cell differentiation. Lastly, we showed that CD23-negative cells (i) carried the imprint of their previous activated B-cell status, (ii) were precursors of plasmablasts, and (iii) had a similar phenotype to in vivo pre-plasmablasts.

overall_design: Four cell populations of in vitro differentiating B cells were analyzed by ATAC-seq after cell sorting on 50,000 cells. No replicates.

first: Amandine

last: Pignarre

first: Gersende

last: Caron

first: Thierry

last: Fest


title: Nuclear peripheral chromatin-lamin B1 interaction is required for global integrity of chromatin architecture and dynamics in human cells

city: Beijing

first: Mengfan

last: Li

address: No.5 Yiheyuan Road

institute: Peking University

summary:
Background: The eukaryotic genome is folded into higher-order conformation accompanied with constrained dynamics for coordinated genome functions. However, the molecular machinery underlying these hierarchically organized three-dimensional (3D) chromatin architecture and dynamics remains poorly understood.
Results: Here by combining imaging and sequencing, we studied the role of lamin B1 in chromatin architecture and dynamics. We found that lamin B1 depletion leads to chromatin redistribution and decompaction. Consequently, lamina-associated domains (LADs) are detached from the nuclear periphery. The inter-chromosomal interactions and overlap between chromosome territories are increased. Moreover, Hi-C data revealed that lamin B1 is required for the integrity and segregation of chromatin compartments but not for the topologically associating domains (TADs). Using live cell single molecule tracking, we further proved that depletion of lamin B1 leads to increased chromatin dynamics, owing to chromatin decompaction and redistribution toward nucleoplasm.
Conclusions: Taken together, our data suggest that lamin B1 and chromatin interactions at the nuclear periphery promote LAD maintenance, genomic compartmentalization into chromosome territories and A/B compartments and confine chromatin dynamics, supporting its crucial role in chromatin higher-order structure and chromatin dynamics.

overall_design: Analysis of chromatin 3D structure, lamina associated domains and gene expression data in wild-type and LMNB1-knockout MDA-MB-231 breast cancer cell lines. There are 2 replicates for each Hi-C sample, 3 replicates for each lamin A ChIP-seq sample and 3 replicates for each RNA-seq sample.

first: Lei

last: Chang


title: Expression profiling of terminal B cell differentiation [RNA-Seq]

overall_design: Four cell populations of in vitro differentiating B cells were analyzed by RNA-seq in triplicates.


title: SYK activity modulates the EGFR-dependent transcriptome

city: Baltimore

first: Yu

last: Yu

state: MD

address: CRB-2, Rm 376, 1550 Orleans St

department: Department of Pathology

institute: Johns Hopkins School of Medicine

summary:
Background: Among all gynecologic malignancies, epithelial ovarian cancer has the highest case-to-fatality ratio. Most patients are diagnosed at advanced stages and recurrence is common and accounts for disease-related mortality. Spleen tyrosine kinase (SYK) is an emerging cancer-associated kinase upregulated in recurrent tumors and is amenable for inhibition using small compounds that have been studied in clinical trials for autoimmune diseases. Our previous proteomic analysis identified several novel SYK substrates including EGFR and ERBB2. Here, we investigated the cross-talk between these pathways in ovarian carcinomas.

Methods: Immunohistochemistry and immunoblotting were utilized to assess SYK and EGFR phosphorylation in ovarian serous carcinomas. Association with survival was determined by Kaplan-Meier analysis and the log-rank test. To study its role in EGFR signaling, SYK activity was modulated using a small molecule inhibitor, a syngeneic knockout, and an active kinase inducible system. We applied RNA-seq to investigate the SYK-regulated EGF-induced transcriptome.

Results: Intense immunoreactivity of active pSYK(Y525/526) correlated with poor overall survival in two independent ovarian cancer cohorts. SYK directly phosphorylated EGFR and ERBB2, while knockout of SYK reduces their phosphorylation. Phosphorylation levels of SYK(Y525/526) positively correlated with EGFR(Y1187) and STAT3(Y705). Active SYK reduced sensitivity to the EGFR/ERBB2 inhibitor, lapatinib, and SYK non-phosphorylatable EGFR mutant was more sensitive to paclitaxel. SYK modulated the EGF-induced transcriptome, supporting its involvement in EGFR/ERBB2-regulated transcriptional activity.

Conclusions: Our findings suggest an upstream role of SYK in regulating the EGFR/ERBB2 signaling, and provide a biological rationale for targeting SYK in ovarian cancer therapy.

overall_design: RNA-seq on wildtype and SYK KO cells with no treatment or treated with EGF (50 ng/ml) for 24 h

first: Y

first: T-L

first: I-M

last: Shih


title: Differential transcriptomes of developing zebrafish embryos from commencement to completion of gastrulation

city: Fukuoka

first: Yasuyuki

last: Ohkawa

address: 3-1-1 Maidashi

institute: Medical Institute of Bioregulation

summary: We report differential transcriptomes of zebrafish embryos at 6 and 10 hours post fertilization. Specifically, we note a dramatic shift in the expression of genes involved in cellular metabolism from 6 to 10 hours post fertilization. This result may explain at least in part why metabolic demand of developing embryos at the examined stage is sharply increased.

overall_design: Comparison of mRNA profiles of zebrafish embryos between 6 and 10 hour post fertilization by deep sequencing

first: Seong-Kyu

last: Choe

first: In-Koo

last: Nam

first: Yong-Il

last: Kim

first: Sushil

last: Bhandari

first: Jumpei

last: Nogami


title: AML patient granulocyte macrophage progenitor (GMP) cells [human]

city: Copenhagen

first: Kim

last: Theilgaard-Mönch

address: Ole Maaløes Vej 5

institute: Rigshospitalet/National Univ. Hospital and Biotech Research and Innovation Centre

summary: AML patient GMPs or CMPs were FACS sorted as described in material and methods from supplementary data (Estruch M et al 2020)

overall_design:
Targeted inhibition of cooperative mutation- and therapy-induced AKT activation in AML effectively enhances response to chemotherapy
This series includes re-analyzed data from GSE11864,GSE19599 and GSE42519. Also re-analyzed were two samples from EMBL ArrayExpress: E-MEXP-1242:
Immcon2cd14poscd16neg241104.CEL
Immcont1cd14poscd16neg241104.CEL

first: Montserrat

last: Estruch

first: Kristian

last: Reckzeh

first: Camilla

last: Vittori

first: Anders

last: Centio

first: Mina

last: Ali

first: Sophia

last: Engelhard

first: Ling

last: Zhao

first: Kyoung

last: Won

first: Paul

last: Liu

first: Bo

last: Porse


title: Mifepristone-induced tumor regression in C4-HD tumors

status: Public on Nov 07 2020

city: Jacksonville

first: Derek

middle: Charles

last: Radisky

state: Florida

address: 4500 San Pablo Road

department: Cancer Biology

institute: Mayo Clinic

summary:
Comparison of gene expression data between control and MFP-treated C4-HD tumors.
The role of active antitumor immunity in hormone receptor positive (HR+) breast cancer has been historically underlooked. The aim of this study was to determine the contribution of the immune system to antiprogestin-induced tumor growth inhibition using a hormone-dependent breast cancer model. BALB/c-GFP+ bone marrow (BM) cells were transplanted into immunodeficient NSG mice to generate an immunocompetent NSG/BM-GFP+ (NSG-R) mouse model. Treatment with the antiprogestin Mifepristone (MFP) inhibited growth of 59-2-HI tumors with similar kinetics in both animal models. Interestingly, MFP treatment reshaped the tumor microenvironment, enhancing the production of proinflammatory cytokines and chemokines. Tumors in MFP-treated immunocompetent mice showed increased infiltration of F4/80+ macrophages, NK, and CD8 T cells, displaying a central memory phenotype. Mechanistically, MFP induced immunogenic cell death in vivo and in vitro, as depicted by the expression and subcellular localization of the alarmins calreticulin and HMGB-1 and the induction of an immunogenic cell death gene program. Moreover, MFP-treated tumor cells efficiently activated immature dendritic cells, evidenced by enhanced expression of MHC-II and CD86, and induced a memory T cell response, attenuating tumor onset and growth after re-challenge. Finally, MFP treatment increased the sensitivity of HR+ 59-2-HI tumor to PD-L1 blockade, suggesting that antiprogestins may improve immunotherapy response rates. These results contribute to a better understanding of the mechanisms underlying the antitumor effect of hormonal treatment and the rational design of therapeutic combinations based on endocrine and immunomodulatory agents in HR+ breast cancer.

overall_design: Gene expression profiling of control and MFP-treated C4-HD tumors (12-24-48hs). The gene expression profiles of two independent replicates per condition were compared by microarray analysis. For this analysis, we used C4-HD tumors growing in MPA treated BALB/c mice. When tumors reached 50 mm , MPA pellets were removed by surgery and replaced by a sc. MFP pellet (10 mg/kg/day). Two days later, tumors were excised and fixed in formalin. RNA was extracted from formalin-fixed paraffin-embedded (FFPE) tumors using the RNeasy FFPE kit (Qiagen; Germantown, MD). RNA integrity was assessed with an Agilent Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA, USA). RNA was then labeled and hybridized to Gene Chip Mouse Genome 430 2.0 (Affymetrix, Santa Clara, CA, USA) according to the manufacturer’s instructions

first: Gonzalo

last: Sequeira

first: Ana

last: Sahores

first: Tomás

last: Dalotto-Moreno

first: Ramiro

last: Perrotta

first: Gabriela

last: Pataccini

first: Silvia

middle: I

last: Vanzulli

first: María

middle: L

last: Polo

first: Carol

middle: A

last: Sartorius

first: Virginia

last: Novaro

first: Caroline

last: Lamb

first: Gabriel

last: Rabinovich

first: Mariana

last: Salatino

first: Claudia

last: Lanari


title: Reshaping Circadian Metabolism in the Suprachiasmatic Nucleus and Prefrontal Cortex by Nutritional Challenge

city: Irvine

first: Muntaha

middle: Fatima

last: Samad

address: Campus Dr

department: CS

institute: UC Irvine

summary: We compared the transcriptome of Suprachiasmatic Nucleus in C57BL/6J mice fed a high-fat diet or normal chow through an entire circadian cycle: 6 time points (TP) every four hours.

overall_design: RNA-seq analysis of the Suprachiasmatic Nucleus of mice fed high-fat diet versus normal chow fed mice.

first: Paola

last: Tognini

first: Kenichiro

last: Kinouchi

first: Yu

first: Pierre

last: Baldi

first: Paolo

last: Sassone-Corsi


title: Transcritome profiling of plp-1-mutant Caenorhabditis elegans

city: Chennai

first: Kuppuswamy

last: Subramaniam

state: Tamil Nadu

address: Room#301, Block-2

department: Department of Biotechnology

country: India

institute: Indian Institute of Technology Madras

summary: Through high-throuhgput RNA-sequencing, this study identifies mRNAs that are differentially expressed between plp-1(ok2155) and wild-type C. elegans. Analysed results are published in Development. 2020 Oct 13:dev.195578. doi: 10.1242/dev.195578. PMID: 33051256  Abstract of the publication: The germ line genome is guarded against invading foreign genetic elements by small RNA-dependent gene-silencing pathways. Components of these pathways localize to, or form distinct aggregates in the vicinity of, germ granules. These components and their dynamics in and out of granules are currently being intensively studied. Here, we report the identification of PLP-1, a C. elegans protein related to the human single-stranded nucleic acid-binding protein called Pur-alpha, as a component of germ granules in C. elegans We show that PLP-1 is essential for silencing different types of transgenes in the germ line, and for suppressing the expression of several endogenous genes controlled by the germline gene-silencing pathways. Our results reveal that PLP-1 functions downstream of small RNA biogenesis during initiation of gene silencing. Based on these results and the earlier findings that Pur-alpha proteins interact with both RNA and protein, we propose PLP-1 couples certain RNAs with their protein partners in the silencing complex. Its orthologs localized on RNA granules may similarly contribute to germline gene silencing in other organisms.

overall_design: Samples: Wild-type strain N2 (Sample A) and plp-1(ok2155) (Sample B).  Replicates: Three biological replicates (A1, A2, A3 and B1, B2 and B3)  Developmental stage: Mixed-stage hermaphrodites grown at 20C

first: Rajaram

last: Vishnupriya


title: miR-106b-5p is a key player in adaptive response to drug-induced liver injury and liver regeneration by targeting vimentin

first: Lingqi

last: Yu

address: Yuhangtang Road No.388

institute: Zhejiang University

summary:
The key exosomal miRNAs in adaptive response to drug-induced liver (DILI) and liver regeneration were investigated and proved.
This study aimed to decipher the mechanism of restorative events in the adaptive response to DILI by investigating circulating exosomal miRNAs. Using toosendanin-induced liver injury model, exosomal miR-106b-5p was identified as a robust driver in the adaptive response of TILI.

overall_design: Serum exosomal miRNAs were prepared on 3, 9, and 21 days of 80 mg/kg toosendanin exposure. Each group (TSN-3day，TSN-9day, TSN-21day, con-3day, can-9day, con-21day）contains 4 samples.

first: Xiaoyan

last: Lu

first: Jie

last: Zheng

first: Junying

last: Li

first: He

last: Lou

first: Wentao

last: Zhang

first: Hui

last: Guo

first: Yuzhen

last: Wang

first: Xuemei

first: Xiaohui

last: Fan

first: Yue

last: Gao

first: Jürgen

last: Borlak


title: The histone H3-lysine 4-methyltransferase Mll4 governs the development of growth hormone-releasing hormone-producing neurons

city: Seoul

first: Sujeong

last: Lim

address: 369 Sangdo-ro, Dongjak-gu, Seoul, Republic of Korea

institute: Soongsil University

summary: In humans, inactivating mutations in MLL4, which encodes a histone H3-lysine 4-methyltrasferase, lead to Kabuki syndrome (KS). While dwarfism is a cardinal feature of KS, the underlying etiology remains unclear. Here we report that Mll4 is a critical regulator of the development of growth hormone-releasing hormone (GHRH)-producing neurons in the hypothalamus. The two distinct Mll4 mutant mouse models exhibited dwarfism, accompanied by impairment of developmental programs for GHRH-neurons. Our genome-wide studies revealed that, in the developing hypothalamus, Mll4 collaborates mainly with the transcription factor Nrf1 to trigger the expression of GHRH-neuronal genes. Interestingly, the deficiency of Mll4 resulted in a marked reduction of transcriptionally active histone marks in the embryonic hypothalamus, which was rescued by treatment with the histone deacetylase inhibitor AR-42. Further, AR-42 treatment restored GHRH-neuronal production in Mll4 mutant mice. Together, our results suggest that the dysregulation of MLL4-directed epigenetic control of GHRH-neuronal genes is a substantial contributing factor to dwarfism in human KS.

overall_design: ChIP-seq samples from wild-type hypothalamus were prepared for sequencing according to the Illumina protocol, and sequenced on the Illumina Hiseq 2500. We will then identified that Mll4 and Nrf1 cooperate to regulate the gene transcription in the development of GHRH-neurons in the hypothalamic arcuate nucleus.

first: Su

first: Sung

middle: M

last: Youn

first: Sangsoo

last: Kim

first: Jae

last: Lee


title: The role AIB1D4 cistrome in early breast cancer progression

first: Ghada

last: Sharif

summary: We report the global occupancy by ChIP-seq of the histone marks (H3K4me1, H3K4me3, H3K427ac) in MCFDCIS and  MCFDCIS-D4 cells. DNA sequencing libraries were prepared using the Kapa Hyper DNA library prep (Roche). ChIP-Seq data were aligned to hg19 using Rsubread and the differential genomic binding was established using csaw

overall_design:
Examination of ChIP-seq of histone marks status in MCFDCIS vs MCFDCIS-D4 cell lines in triplicate, normalized to cell  lysate input.

AIB1-Delta4 is a naturally occurring AIB1 isoform missing exon 4. The resulting protein lacks the first 223 amino acids from the N-terminus, yet the rest of the sequence is in frame similar to the full length protein.

first: Anna

middle: T

last: Riegel


title: A type 2C protein phosphatase activates high-affinity nitrate uptake by directly dephosphorylating NRT2.1 in Arabidopsis

status: Public on Nov 06 2020

city: Nagoya

first: Yoshikatsu

last: Matsubayashi

state: Aichi

address: Chikusa

department: Graduate School of Science

institute: Nagoya University

summary:
Nitrate transporter NRT2.1, which plays a central role in high-affinity nitrate uptake in roots, is activated at the post-translational level in response to nitrogen (N) starvation. However, critical enzymes required for post-translational activation of NRT2.1 remain to be identified. Here, we show that a type 2C protein phosphatase, designated CEPD-induced phosphatase (CEPH), activates high-affinity nitrate uptake by directly dephosphorylating S501 of NRT2.1, a residue that functions as a negative phospho-switch. CEPH is predominantly expressed in epidermal and cortex cells in roots and up-regulated by N starvation via a CEPDL2/CEPD1/2-mediated long-distance signaling from shoots. Loss of CEPH leads to a marked decrease in high-affinity nitrate uptake, tissue nitrate content, and plant biomass. Collectively, our results identify CEPH as a crucial enzyme in N starvation-dependent activation of NRT2.1, providing molecular and mechanistic insights into how plants regulate high-affinity nitrate uptake at the post-translational level in response to the N environment.
We prepared total RNA from roots of wild type, CEPD1ox, CEPD2ox and CEPDL2ox plants grown on N-replete vertical plates for 14 d, and used a microarray analysis to identify genes specifically induced by CEPD family peptides.

overall_design: Total RNA isolated from the roots were subjected to microarray analysis. Labeled complementary RNA was hybridized with an Affymetrix Genechip Arabidopsis Gene 1.0 ST array.

first: Yuri

last: Ohkubo

first: Keiko

last: Kuwata


title: Scalable pooled CRISPR screens with single cell chromatin accessibility profiling.

first: Neville

last: Sanjana

address: 101 Avenue of the Americas

institute: New York Genome Center

summary: A scalable, cost-effective method that combines CRISPR perturbations with a single-cell indexing assay for transposase-accessible chromatin (CRISPR-sciATAC). This method links genome-wide chromatin accessibility to genetic perturbations through simultaneous capture of ATAC-seq fragments and CRISPR guide RNAs from single cells using a 96-well plate combinatorial indexing approach.

overall_design: Single cell ATAC-seq and CRISPR sgRNA capture for K562 cells and a mixture of NIH3T3 cells and HEK293T cells.

first: Noa

last: Liscovitch-Brauer

first: Antonino

last: Montalbano

first: Jiale

last: Deng

first: Alejandro

last: Méndez-Mancilla

first: Hans-Hermann

last: Wessels

first: Nicholas

last: Moss

first: Chia-Yu

last: Kung

first: Akash

last: Sookdeo

first: Xinyi

first: Evan

last: Geller

first: Suma

last: Jaini

first: Peter

last: Smibert

middle: E


title: Next Generation Sequencing Facilitates Quantitative Analysis of  Osteoblast Mineralization Transcriptomes

city: Zibo

first: Lianqing

last: Wang

state: Shandong

address: Gongqingtuan West Street 54#

department: Center of Translational Medicine

institute: Zibo Central Hospital

type: Non-coding RNA profiling by high throughput sequencing

summary: We report the application of next generation sequencing technology for high-throughput profiling of mRNA, circRNA and lncRNA in hFOB 1.19 cells during the mineralization. Osteoblast RNA profiles in different process of mineralization, which is day 0, day 3, day 6 and day 9, respectively. The transcriptome sequencing on an Illumina HiSeq X Ten platform were carried out at Novogene Bioinformatics Technology Co., Ltd. (Beijing, China). Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. In the process of osteoblast mineralization, a total of 8464 dysregulated circRNAs were identified, of which 6332 circRNAs were upregulated and 2132 circRNAs were downregulated. In addition, 1633 differentially expressed mRNAs were also identified, with 1027 mRNAs upregulated and 606 mRNAs downregulated.  This study provides a framework for the application of NGS profiling towards characterization of osteoblast mineraliztion.

overall_design: osteoblast mRNA, circRNA and lincRNA profiles of 0, 3, 6 and 9 day induction by deep sequencing.

first: Qiaoli

last: Zhai


title: Function of the porcine TRPC1 gene in myogenesis and muscle growth

first: Yu

last: Fu

address: Yuanmingyuan West Road 2#,Haidian District

department: college of animal science and technology

institute: China agricultural university

summary: Muscle growth is a quantitative trait controlled by multiple genes in animals. Previously, we showed that transient receptor potential channel 1 (TRPC1) was a differentially expressed gene in muscle tissues between pig breeds with divergent growth traits using RNA-seq. In this study, we characterized the expression profiles of TRPC1 in different tissues and various pig breeds, and found that TRPC1 is highly expressed in muscle. We found two effective single nucleotide polymorphism (SNP) sites (C-1763T and C-1604T) in TRPC1 that could affect the activity of the promoter region and regulate the growth rate of pigs. Functionally, we used RNAi and overexpression to illustrate that TRPC1 promotes myoblast proliferation, migration, differentiation, fusion, and muscle hypertrophy, while inhibiting muscle degradation, and that these processes may be mediated by activating the Wnt signaling pathways. Taken together, our results revealed that TRPC1 may be a promoter of muscle growth and development and it plays a role in Wnt-mediated myogenesis.

overall_design: mRNA profiles of control and TRPC1-overexpressed C2C12 cells, three replicates in each group

first: Rui

middle: X

last: Nie

first: Bo

last: Zhang

first: Hao


title: Loop Extrusion Mediates Physiological Locus Contraction for V(D)J Recombination

city: Boston

first: Frederick

last: Alt

address: 1 Blackfan Circle

institute: Boston Children's Hospital

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

overall_design: Refer to individual Series


title: Expression profile of early and mid-secretory human endometrium revealed by RNA-seq: a paired-sample cohort study

city: Tartu

first: Viktorija

last: Kukushkina

address: Riia 23b

country: Estonia

institute: Estonian Genome Center, University of Tartu

summary: Inner uterine lining or endometrium is a unique constantly self-renewed adult tissue that is vital for embryo implantation. As the footrace for universal endometrial receptivity markers continues, RNA-seq remains the most powerful tool for transcriptomic marker discovery. In this study, we aimed to elucidate endometrial maturation mechanisms at transcriptomic level and identify novel robust biomarker candidates for endometrial receptivity in a multicentre study. Additionally, we compared mid-secretory transcriptome profiles from healthy women with profiles of women with repeated IVF failure to find transcriptome changes related to problems with endometrial receptivity.

overall_design: The differential gene expression profiles of early secretory and mid-secretory phase endometrial biopsies obtained from 15 healthy fertile women across one menstrual cycle were analysed using paired sample study design, followed by meta-analysis and gene expression profile deconvolution. Additionally, mid-secretory transcriptome profiles of healthy women were compared to those from women with repeated IVF failure (n=39)

first: Marina

last: Suhorutshenko

first: Agne

last: Velthut-Meikas

first: Reedik

last: Mägi

first: Maire

last: Peters

first: Signe

last: Altmäe

first: Kaarel

last: Krjutškov

first: Juan

last: Martinez-Blanch

first: Francisco

last: Codoñer

first: Felipe

last: Vilella

first: Carlos

last: Simon

first: Andres

last: Salumets

first: Triin

last: Laisk-Podar


title: SARS-CoV-2 infection of primary human lung epithelium for COVID-19 modeling and drug discovery

city: los angeles

first: Changfu

last: Yao

state: Ca

address: 8700 Beverly Blvd. AHSP Room A9401

department: Lung and Regenerative Medicine Institutes

institute: cedars-sinai medical center

summary: Coronavirus disease 2019 (COVID-19) is the latest respiratory pandemic resulting from zoonotic transmission of severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2). Severe symptoms include viral pneumonia secondary to infection and inflammation of the lower respiratory tract, in some cases causing death. We developed primary human lung epithelial  infection models to understand responses of proximal and distal lung epithelium to SARS-CoV-2 infection. Differentiated air-liquid interface cultures of proximal airway epithelium and 3D organoid cultures of alveolar epithelium were readily infected by SARS-CoV-2 leading to an epithelial cell-autonomous proinflammatory response. We validated the efficacy of selected candidate COVID-19 drugs confirming that Remdesivir strongly suppressed viral infection/replication. We provide a relevant platform for studying COVID-19 pathobiology and for rapid drug screening against SARS-CoV-2 and future emergent respiratory pathogens.

overall_design: We isolated primary lung alveolar AT2 cells and cultured in 3D, then infected with SARS-CoV2. RNA isolated from infected organoid for RNA-seq

first: Barry

last: Stripp

first: Aproova

last: Mulay


title: Identifying differentially expressed genes in Zmat3 knockout cells

city: Stanford

first: Kathryn

last: Bieging-Rolett

state: California

address: CCSR-South, Rm 1240, 269 Campus Drive

department: Radiation Oncology

institute: Stanford University School of Medicine

summary: The goal of the study was to identify genes whose expression is Zmat3 depedent using RNA-seq.

overall_design: We used CRISPR/Cas9 to knockout Zmat3 in Cas9+ E1A;HrasG12V mouse embryonic fibroblasts (MEFs).  After selection for Zmat3 or negative control sgRNAs, cells were cultured for 10 days, and then RNA was collected for RNA-seq, using Illumina TruSeq v2.

first: Laura

middle: D

last: Attardi


title: Modeling Cellular Crosstalk and Organotypic Vasculature Development with Human iPSC-Derived Endothelial Cells (iPS-EC) and Cardiomyocytes (iPS-CM) [RNA-seq]

city: HELSINKI

first: Emmi

last: Helle

address: Haartmaninkatu 8

country: Finland

institute: University of Helsinki

summary: The aim was to study the effect of shear stress on iPS-derived endothelial cells (iPS-EC). iPS-ECs were grown in static conditions and in flow in the Ibidi Pump system. The transcriptional landscapes of cells grown in these 2 conditions were compared.

overall_design: RNA sequencing (RNA-seq) analysis of four iPS-EC cellines grown in static conditions and in flow (15DYN) for 24h.

first: Riikka

last: Kivelä


title: Whole-genome RNA-deep sequencing of pancreatic islets of congenic Nidd/DBA mice

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

summary: Here, we describe the QTL Nidd/DBA, a diabetogenic allele which was contributed by DBA and enhanced hyperglycemia and β-cell loss. In order to re-address the issue of which variants on chromosome 4 are responsible for this trait, Nidd/DBA recombinant congenic lines were generated on an NZO background. Gene expression profiles of pancreatic islets were generated from congenic mice carrying the initial 13.6 Mbp fragment (RCS-I) of the Nidd/DBA locus. Six genes within the critical region were differentially expressed in pancreatic islets of homozygous Nidd/DBAD/D mice compared to homozygous Nidd/DBAN/N controls.

overall_design: Analysis of pancreatic islets of 6-week old mice

first: Heja

last: Aga

first: Annette

last: Schürmann


title: Heparin Binding Epidermal Like Growth Factor-Mediated Marrow Adipocyte Ablation Induces Profound Bone Formation

first: Ruteja

last: Barve

state: MO

address: 4515 McKinley Ave

department: Genetics

institute: Washington University

summary: Products of adipocytes control bone cells and may therefore lead to new anti-osteoporosis therapies. To address this issue we mated mice expressing the primate diphtheria toxin receptor (DTR), which is equivalent to Heparin Binding Epidermal Like Growth Factor (HB-EGF), under control of a Stop-flox cassette, to those expressing adiponectin-Cre (ADQ-Cre). Injected diphtheria toxin (DT) completely eliminates white and brown adipose tissue in these DTRADQ mice and ablates marrow adipocytes. Medullary bone of DTRADQ mice begins to accumulate, due to stimulated osteoblast recruitment and differentiation, within 4 days of injected DT. By 10-14 days of DT administration to DTRADQ mice, trabecular bone has increased 1000%. Two months after fat ablation, cortical thickness has markedly increased as has bone strength. To gain insight into the signaling events by which DT/DTRADQ adipocyte ablation promotes osteogenesis we performed RNAseq analysis of marrow prior to and after 1-3 days of DT injection. This exercise confirms ablation of marrow adipocytes, as adiponectin expression is markedly reduced while enhanced expression of Col1a1 and Col1a2 genes is in keeping with stimulated osteogenesis. RNAseq analysis also indicates that DT/DTRADQ-induced osteogenesis is mediated by the BMPR pathway. For example, there is suppressed genetic expression of the specific BMPR inhibitors, chordin-like1 (CHRDL1) and gremlin1 (GREM1). This adipocyte ablation-mediated increase in bone mass is due to cooperative activation of BMP and EGF receptor signaling as adipocyte-produced inhibitors are suppressed and downstream targets activated or expressed. Medicinal inhibition of either signaling pathway prevents induction of the osteosclerotic phenotype. DTR-induced post-natal osteogenesis does not represent the products of peripheral fat depots and is more likely due to those of marrow adipocytes. Thus, anabolic drugs activating both BMP and EGF receptor signaling may be a means of profoundly increasing bone mass and treating osteoporosis.

overall_design: Examination of transcriptional profiles of whole bone marrow from DTRADQ and Cre negative littermate control mice prior to and after 1-3 days of DT injection. 4 mice per group.

first: Wei

last: Zou

first: Steven

last: teitelbaum


title: Expression profiling of Setleis vs Control lymphoblastoid cells

city: San Juan

first: Carmen

middle: Lydia

last: Cadilla

state: PR

address: University of Puerto Rico Medical Sciences Campus, Area of Medical Center

department: Biochemistry

country: Puerto Rico

institute: University of Puerto Rico School of Medicine

summary: Background: Setleis Syndrome (SS) is a rare focal facial dermal dysplasia frequently found in Puerto Ricans, presenting with bilateral temporal skin lesions, eyelash abnormalities and absent meibomian glands. SS is caused by homozygous mutations in the TWIST2 gene, which codes for a transcription factor of the bHLH family known to be involved in skin and facial development.   Methods: We obtained gene expression profiles by microarray analyses from control and Setleis Syndrome patient primary skin fibroblast and lymphoblastoid cell lines.  Results: Out of 983 differentially regulated genes in fibroblasts, 479 were down-regulated and 504 were up-regulated, while in lymphoblasts a greater number of differentially regulated genes (1248  down-regulated and 73 up-regulated) were found after microarray analysis. Real time PCR reactions confirmed altered expression of several differentially regulated genes.   Conclusion: TWIST2 is described as a repressor, but expression profiling indicates it has a role in gene activation, as evidenced by the much higher proportion of down-regulated genes in cells from SS patients, including cytokine genes, in fibroblasts, the top three networks involved genes that function in Cancer, Nervous System Development and Function, Lipid Metabolism, Molecular Transport and Organismal Injury and Abnormalities. In Lymphoblastoid cells, the top three networks involved genes in Endocrine System Disorders, Cell Cycle, Cellular Assembly and Organization, Cardiovascular Disease and Developmental Disorders

overall_design: We used lymphoblastoid cell lines generated by Epstein Barr virus transformation, grown in RPMI 1640 supplemented media, from Puerto Rican controls (unaffected, wild type for TWIST2) and a Puerto Rican Setleis Syndrome patient homozygous for the Q119X TWIST2 mutation. The two women whose blood was used to generate the lymphoblastoid cell lines were sisters.


title: Mechanistic basis and efficacy of targeting Beta Catenin-TCF7L2-JMJD6-MYC Axis to overcome resistance to BET inhibitors

city: Houston

first: Kapil

last: Bhalla

state: TX

address: 1515 Holcombe Blvd

department: Leukemia

institute: MD Anderson Cancer Center


title: Mechanistic basis and efficacy of targeting Beta Catenin-TCF7L2-JMJD6-MYC Axis to overcome resistance to BET inhibitors [no drug]

summary: Promising activity of BET protein inhibitors (BETis) is compromised by adaptive or innate resistance in AML. Here, modeling of BETi-  persister/resistance (BETi-P/R) in human post-MPN secondary AML (sAML) cells demonstrated accessible and active chromatin in specific    super-enhancers/enhancers, which was associated with increased levels of nuclear β-catenin, TCF7L2, JMJD6, and c-Myc in BETi-P/R sAML  cells. Following BETi treatment, c-Myc levels were rapidly restored in BETi-P/R sAML cells. CRISPR/Cas9-mediated knockout of TCF7L2 or JMJD6  reversed BETi-P/R, whereas ectopic overexpression conferred BETi-P/R in sAML cells; confirming the mechanistic role of the β-catenin-TCF7L2-  JMJD6-MYC axis in BETi-resistance. Patient-derived, post-MPN, CD34+ sAML blasts exhibiting relative resistance to BETi, as compared to  sensitive sAML blasts, displayed higher mRNA and protein expressions of TCF7L2, JMJD6 and c-Myc, and following BETi washout exhibited rapid  restoration of c-Myc and JMJD6. CRISPR/Cas9 knockout of TCF7L2 and JMJD6 depleted their levels, inducing loss of viability of the sAML blasts.  Disruption of co-localization of nuclear β-catenin with TBL1 and TCF7L2 by the small molecule inhibitor BC2059 combined with depletion of BRD4  by BET-PROTAC reduced c-Myc levels and exerted synergistic lethality in BETi-P/R sAML cells. This combination also reduced leukemia burden    and improved survival of mice engrafted with BETi-P/R sAML cells or with patient-derived AML blasts innately resistant to BETi. Therefore, multi-  targeted disruption of β-catenin-TCF7L2-JMJD6-MYC axis overcomes adaptive and innate BETi-resistance, exhibiting pre-clinical efficacy against    human post-MPN sAML cells.

overall_design: Secondary AML SET2  cells and their OTX persister resistant derivatives (SET-2-OTX P/R ) were isolated as biologic replicates (SET-2 and SET-2 OTX P/R n=3) and RNA Sequencing was performed

middle: N

first: Warren

last: Fiskus


title: Identifying Zmat3-bound RNAs

summary: The goal of the study was to identify RNAs bound by Zmat3 using eCLIP.

overall_design: Three lines of sgNC Cas9+ E1A;HrasG12V MEFs and one Zmat3 knockout MEF sample expressing E1A and HrasG12V  were used for the experiment. Briefly, 20 million cells were UV crosslinked, lysed, sonicated, and treated with Rnase.  Then the samples were immunoprecipitated with anti-Zmat3 antibodies.  After washes, samples were run on a NuPAGE gel, transferred to nitrocellulose membrane, and the region from 35 to 110 kDa was isolated and treated with Proteinase K.  RNA was isolated, reverse transcribed, and sequenced on an Illumina HiSeq4000.


title: Mechanistic basis and efficacy of targeting Beta Catenin-TCF7L2-JMJD6-MYC Axis to overcome resistance to BET inhibitors [OTX015]

overall_design: Secondary AML HEL92.1.7  cells and their OTX persister resistant derivative (HEL OTX P/R) were treated for 8 hours with 1000 nM of OTX015 to determine the effects of BET inhibitor treatment on the global transcriptome profile in parental and persister-resistant cells. Cells were treated independently and RNA was isolated from biologic replicates (HEL92.1.7 and HEL-OTX P/R untreated [n=2 each]; HEL92.1.7 and HEL-OTX P/R OTX015-treated [n=2 each]) and RNA Sequencing was performed.


title: Differential gene expression profiles of human efferent ducts and epididymis

city: Quebec

first: Ezequiel

last: Calvo

state: Quebec

address: 2705 Boul. Laurier

department: Molecular Endocrinilogy

country: Canada

institute: CRCHUL

summary: Mammalian spermatozoa acquire their fertilizing ability during epididymal transit. Gene expression patterns along the epididymis are established by specific transcription factor networks that coordinate region-specific functions. The epididymis is usually divided into 3 segments: caput, corpus, and cauda. The human epididymis anatomy does not allow clear distinction between these three segments. To determine to which extent gene expression is segmented along the human epididymis, transcriptome profiling was performed on 8 distinct epididymal regions from 3 donors. Microarray analysis was performed on a Gene Chip Human Clariom S (Affymetrix®) array representing 337 100 transcriptional variants encoded by 20 800 genes. Proximal segments 1 to 3 were distinguishable from the distal epididymal segments (4 to 8) as shown by unsupervised Principal Component Analysis. Transcripts from each segment with differentially expressed genes (DEGs) > 2-fold change and FDR < 0.05 were clustered in relation to their intensity profiles. While no DEGs were detected between segments 1–3 corresponding to the efferent ducts, 1140 DEGs were detected between efferent ducts (1–3) and the epididymis (4–8), 400 between caput (4–6) vs. corpus/cauda (7–8) and none between corpus (7) and cauda (8). Gene Ontology annotation revealed that up-regulated DEGs in the efferent ducts (1–3) were predominantly related to cilium assembly/movement and cell differentiation. The biological process terms fertilization, defense and immune responses were associated with caput epididymis (4–6) while spermatogenesis and protein binding were found all along the epididymis (4–8). In conclusion, the proximal human epididymis is exclusively occupied by efferent ducts with a distinct DEG profile compared with the downstream epididymal segments. Moreover, gene expression profiling revealed two regions in the human epididymis; the caput and the distal corpus/cauda region. Taken together, analysis of the human epididymal transcriptome reveals a limited DEG profile.

overall_design: Human epididymides were obtained through our local organ transplantation program after obtaining written consent from the families as previously described. Donors were 37, 50 and 52 years of age with no known medical pathologies that could affect reproductive function. Epididymides anatomically defined as an organ found on the surface of the testis, were dissected into 8 sections as illustrated in Figure 1A. According to human epididymal histology, sections 1–3 correspond to efferent ducts.  The caput, corpus and cauda segments are less well defined and are referred to sections 4–6, 7 and 8, respectively. Each section was dissected into small tissue pieces that were snap-frozen in liquid nitrogen and stored at −80°C until use.

first: Christine

last: Legaré

first: Robert

last: Sullivan


title: Mechanistic basis and efficacy of targeting Beta Catenin-TCF7L2-JMJD6-MYC Axis to overcome resistance to BET inhibitors [ChIP-seq]

overall_design: Examination of Acetylated K27  histone H3 modification and BRD4  occupancy by ChIP-Seq analysis in secondary AML SET2 and HEL92.1.7  cells and their OTX persister resistant derivatives (SET-2-OTX P/R and HEL OTX P/R).


title: Combination of iron deprivation and chemotherapies treatments in breast cancer xenografts

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

institute: GenoSplice technology

summary: To ensure their high proliferation rate, tumor cells display an iron metabolic disorder with increased iron needs, making them more susceptible to iron deprivation. This vulnerability could be a therapeutic target. In breast cancers, the development of new therapeutic approaches is urgently needed for patients with triple negative tumors which frequently relapse after chemotherapy and suffer from a lack of targeted therapies. Anticancer activity of iron chelator deferasirox (DFX) assessed in monotherapy do not appear to be effective enough to treat breast cancer progression. In this work, we demonstrated that DFX synergizes with standard chemotherapeutic agents such as with doxorubicin, cisplatin and carboplatin to inhibit cell proliferation and induce apoptosis and autophagy in TNBC cell lines. Moreover, the combination of DFX with doxorubicin and cyclophosphamide allowed to delay or avoid recurrences in breast cancer patient-derived xenografts without increasing the side-effects of chemotherapies alone or altering global iron storage of mice. Antitumor synergy of DFX and doxorubicin involves down-regulation of PI3K and NF-κB pathways. Furthermore, as TNBC patients with low iron tumor dynamic in their tumor present a good prognosis, we thought that iron deprivation mediated by iron chelators may all the more increase the effectiveness of conventional chemotherapies for TNBC treatments.

overall_design: comparison of tumors group treated with different drugs

first: Sandrine

last: Tury

first: Franck

last: Assayag

first: Florian

last: Bonin

first: Sophie

last: Chateau-Joubert

first: Jean-Luc

last: Servely

last: Vacher

first: Véronique

last: Becette

first: Martial

last: Caly

first: Audrey

last: Rapinat

first: David

last: Gentien

first: Anne

last: Schnitzler

first: François

last: Lallemand

first: Elisabetta

last: Marangoni

first: Ivan

last: Bièche

first: Céline

last: Callens


title: Transcriptomic analysis of human varicose veins

city: Shanghai

first: Bin

last: Zhou

state: Shanghai

address: No.150, Jimo Road, Pudong

department: Vascular Surgery

institute: Shanghai East Hospital affiliated to Tongji University School of Medicine

summary: tRNA-derived fragments (tRFs) with a size of 15-50 nt are derived from mature or precursor tRNAs and associated with a variety of pathological conditions. However, the roles of tRFs in varicose veins (VVs) are largely unknown. The aim of this study was to identify the tRFs involved in VVs and predict their potential biological functions. We first performed small RNA-seq to investigate the expression profiles of tRFs in vascular tissue of VVs patients and healthy controls. In total, 13,789 tRFs were obtained, accounting for 4 % of the total small RNA. Moreover, 45 tRFs were remarkably changed, of which 14 were up-regulated and 31 were down-regulated. Gene Ontology analysis showed that the target genes of these differently expressed tRFs are mainly involved in transcriptional functions, DNA-template and nervous system development. Kyoto Encyclopedia of Genes and Genomes  analysis revealed that target genes of these differently expressed tRFs were significantly enriched the wnt signaling pathway and the calcium signaling pathway which regulate local hypoxia and degradation of extracellular matrix(ECM) processes, which play an important role in the development of VVs. Furthermore, differentially expressed mRNA-tRF-non coding RNA regulatory network was constructed which revealed that tRFs may play a central role in this interaction network and correlate with many mRNAs and ncRNAs. Additionally, two up-regulated tRFs (tRF-36-F900BY4D84KRIME and tRF-23-87R8WP9IY) and one down-regulated tRFs (tRF-40-86J8WPMN1E8Y7Z2R)) were identified and verified. These results show that tRFs are aberrantly expressed in vascular tissue of patients with VVs and might play important roles in the development of VVs.

overall_design: small RNA-Seq profiles of control healthy, B1-B4; RNA-Seq profiles of case, A1-A4

first: Chong

last: Xu

first: Xiang

last: Wang

first: Yi

last: Hong

first: Guojun

last: Chen

first: Jin

last: Ge


title: Comparative microRNA expression profiles of Schistosoma japonicum from SCID mouse and BALB/c mouse

city: Wuhan

first: Rong

last: Liu

address: 185 East Lake Road

department: School of Basic Medical Sciences

institute: Wuhan University

summary:
Background: In immunodeficient mice, the growth and reproduction of schistosome were significantly retarded, and their virulence on the host was also weakened. Some studies have suggested that host factors including endocrine and immune signals can modulate the parasite’s development and maturation. However, it is still not clear for the molecular mechanisms underlying the growth and maturation regulation of schistosome.
Methods: We isolated the total RNAs of female and male schistosome from immunodeficient SCID mice and immunocompetent BALB/c mice (labeled as S_F, S_M, B_F and B_M) obtained at five weeks post infection with cercariae, and constructed cDNA libraries of small RNAs using small RNA sample pre kit for small RNA deep sequencing on an Illumina (Solexa) platform.
Results: Of the 122 (75 known and 47 novel) identified S. japonicum-specific miRNAs, statistical analysis revealed that 33 miRNAs (17 miRNAs were up-regulated and 16 were down-regulated, P<0.05) in female schistosome and 33 miRNAs (13 miRNAs were up-regulated and 20 were down-regulated, P<0.05) in male schistosome from SCID mice were differentially expressed when compared with those from BALB/c mice. The Venn diagram of the differentially expressed miRNAs shows 21 miRNAs were common between S_F vs B_ F and S_M vs B_M, 12 miRNAs were specific in female comparison, and other 12 were specific in male comparison.
Conclusions: This study provides a comparative microRNAs expression profiles of schistosomes derived from SCID mice and immunocompetent BALB/c mice. A number of microRNAs were identified to potentially participate in regulating the development of schistosomes. These findings lay the foundation for schistosomiasis research in regulation of the development of schistosomes and provide a valuable resource for screening antischistosomal intervention targets or vaccine candidates.

overall_design: Examination of Schistosoma japonicum worms from SCID mouse and BALB/c mouse

first: Hui-fen

last: Dong


title: Transcriptional profiling of embryo cryotolerance

city: São Carlos

first: Mateus

middle: José

last: Sudano

state: SP

address: Rod. Washington Luis - Km 235

department: Department of Genetics and Evolution

country: Brazil

institute: Federal University of São Carlos

summary: The cryosurvival of embryos is a complex process involving dynamic and integrated morphological, functional, and molecular changes. Here, we evaluated the transcriptional profiling of bovine embryos possessing high and low cryotolerance (HC and LC, respectively) by assessing the resumption of development. Embryos were produced in vitro (N = 1137) and cryopreserved (N = 894). Blastocysts samples possessed pronounced group individualization at RNA sequencing. A total of 114 genes were differentially expressed, and 27 and 84 genes were upregulated in HC and LC, respectively. Among the over‐represented biological functions, cellular growth and proliferation, cell death and survival, and organismal survival were predicted to be activated, while cellular movement and cell‐to‐cell signaling were predicted to be inhibited in HC embryos. Enriched canonical pathways and upstream regulators related to cellular proliferation and survival (HC), inflammatory processes, and cell death (LC) were predicted to represent two embryonic molecular profiles present during the resumption of development after cryopreservation. The marked contrast in transcriptional profiles between HC and LC strongly suggests the influence of embryonic competence after cryopreservation on its respective transcriptome and indicated that HC and LC presented two different molecular strategies to overcome cryopreservation‐related stress and resume postcryopreservation development.

overall_design: Examination of the transcriptional profiles of bovines embryos possessing  high and low cryotolerance


title: Brd2/4 and Myc regulate alternative cell lineage programs during early osteoclast development

status: Public on Nov 05 2020

city: London

first: Anastasios

last: Karadimitris

address: Hammersmith Campus, Du Cane Road

department: Department of Immunology and Inflammation

institute: Imperial College London

overall_design: Refer to individual Series


title: Brd2/4 and Myc regulate alternative cell lineage programs during early osteoclast development [H3K27ac ChIP-seq]

summary: Osteoclast development in response to RANKL is critical for bone homeostasis in health and in disease e.g., osteoporosis and cancer. The early and direct chromatin regulatory changes imparted by BET proteins Brd2-4 and osteoclast-affiliated transcription factors (TF) during osteoclastogenesis are not known. Here we show that as early as 4h post-RANKL, osteoclast development entails regulation of two alternative cell fate transcriptional programs, osteoclast vs. macrophage, with repression of the latter following activation of the former. Pharmacological inhibition shows that this requires increased chromatin binding in a non-redundant manner of Brd2 at promoters and Brd4 at enhancers/super-enhancers. Myc, the top RANKL-induced TF, is predicted to regulate early regulatory events in co-operation with Brd2/4 and Max and by establishing negative and positive regulatory loops with other lineage-affiliated TF. These novel insights into the transcriptional regulation of osteoclastogenesis suggest the clinical potential of selective targeting of Brd2/4 to abrogate aberrant OC activation.

overall_design: Monocyte-derived cell line induced to differentiate to OC by addition of RANKL (50ng/ml). The effect of the BET inhibitor (Ibet-500nM) was studied alone or in combination with RANKL. ChIP-seq was performed in crosslinked cells after 4 hrs.

first: Valentina

middle: S

last: Caputo

first: Nikolaos

last: Trasanidis

first: Xiaolin

last: Xiao

first: Mark

last: Robinson

first: Alexia

last: Katsarou

first: Kanagaraju

last: Ponnusamy

first: Rab

middle: K

last: Prinjha

first: Nicholas

last: Smithers

first: Aristeidis

last: Chaidos

first: Holger

last: Auner


title: Brd2/4 and Myc regulate alternative cell lineage programs during early osteoclast development [ATAC-seq]

overall_design: Monocyte-derived cell line induced to differentiate to OC by addition of RANKL (50ng/ml). The effect of the BET inhibitor (Ibet-500nM) was studied alone or in combination with RANKL. ATAC libraries were produced after 4 hrs incubation.

middle: W


title: Brd2/4 and Myc regulate alternative cell lineage programs during early osteoclast development [RNA-seq]

overall_design: Monocyte-derived cell line induced to differentiate to OC by addition of RANKL (50ng/ml). The effect of the BET inhibitor (Ibet-500nM) was studied alone or in combination with RANKL. For RNA-seq, samples were taken at 0/4/14 and 24hrs and RNA-seq libraries.


title: Transcriptomic and metabolomic responses of rice plants to Cnaphalocrocis medinalis caterpillar infestation

city: Xinyang

first: Qingsong

state: Henan

address: No. 237, Nanhu road

institute: Xinyang Normal University

summary: We compared the transcriptomic differences in rice leaves after being fed by C. medinalis using RNA sequencing. Global transcriptome changes in rice leaves responding to 1, 6, 12 and 24 h of such feeding were quantified by examining mRNAs of 20 libraries (four biological replicates at each of five sampling times) that collectively included 164.04 Gb of clean reads. Each of these samples contained at least 7.36 Gb of data with Q30 quality scores  90.70%. The GC content accounted for 53.16-53.71% of these reads. A total of 44.84-56.19 million reads were mapped uniquely to the rice IRGSP-1.0 reference genome, with unique mapping rates ranging from 89.73% to 91.36%. Using absolute value of log2(fold change) > 0 and FDR adjusted P value (padj) ≤ 0.05 as threshold for recognizing differentially expressed genes between any two treatments, a total of 6,372 DEGs were identified in rice leaves at different time points (1, 6, 12, and 24 h) of C. medinalis infestation.

overall_design: We compared the transcriptomic in rice leaves after 0, 1, 6,12, and 24 h of being fed by rice leaf roller Cnaphalocrocis medinalis.

first: Yunhe

last: Li


title: Requirement of Drosha in developmental hematopoiesis

city: San Francisco

first: Giorgio

last: Lagna

state: CA

address: 555 Mission Bay Blvd South

department: CVRI

institute: UCSF

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


title: Brd2/4 and Myc regulate alternative cell lineage programs during early osteoclast development [BRD ChIP-seq]


title: Next Generation Sequencing of control and knockout erythroblasts transcriptomes

summary: Purpose: Use next generation sequencing to analyze the cellular pathway change in erythroblasts upon Drosha deletion

overall_design: Erythroblasts were sorted from five E10.5 peripheral blood of Drosha cKO embryos or control embryos and pooled for to RNA prep and next generation sequencing.

first: Xuan

last: Jiang


title: The Transcriptome of over expressed SLAMF6 isoform-3 in activated Jurkat cell line

city: Jerusalem

first: Elad

last: Zisman

address: Kalman Ya'akov Man

institute: The Hebrew University

summary: SLAMF6 is a homotypic receptor of the Ig-superfamily associated with progenitor exhausted T cells. In humans, SLAMF6 has three splice isoforms involving its V-domain.We KO isoform 1 of SLAMF6 in a Jurkat cell line and harvest this cell line RNA using Bulk-RNA-Seq after activation in 5 time points. Comparing the results to WT Jurkat cell line, we analyzed the transcriptional landscape and showed that after activation SLAMF6 isoform 3 is the prominent expressed isoform, and that the KO Jurkat cells have a stronger cytotoxic phenotype.

overall_design: RNA-Seq from WT Jurkat cell line and SLAMF6 isoform 1 KO, after activation on five timepoints: 0,6,12,24,36

first: Emma

last: Hajaj

first: Michal

last: Lotem

first: Moshe

last: Sade-Feldman

first: Nir

last: Hacohen


title: Targeting the HuR oncogenic role with a new class of inhibitors of HuR dimerization

city: Birmingham

first: Louis

middle: Burt

last: Nabors

state: AL

address: 510 20th Street South, FOT 1020

department: Neurology

institute: University of Alabama at Birmingham

summary: Comprehensive meta-analysis and target screening confirmed that the mRNA-binding protein of ELAV-family HuR is oncogenic and universally upregulated in brain tumors, which highlight HuR as an universal chemotherapeutic target. HuR functionality in cancer cells is strictly dependent on HuR nuclear/cytoplasmic shuttling and dimerization; therefore, we developed a new class of inhibitors of HuR protein dimerization by utilizing medicinal chemistry techniques and reporter cell-based assay of HuR dimerization. The therapeutic potentials of lead compound (SRI-42127) were evaluated in five primary patient-derived glioma xenolines of classic, proneural, and mesenchymal subtypes, in vitro, and in mouse glioma model, in vivo. The Illumina global RNA-Sequencing was performed on PDGx-derived glioma neurospheres of different subtypes after treatment with DMSO (control) or SRI-42127 (3 uM) for 12 h to analysis transcripts and cell-signaling pathways affected by new inhibitor of HuR dimerization.

overall_design: Two biological replicates were analyzed for each of  five PDGx cell lines in two different conditions: i) afte treatment with inhibitor of HuR dimerization SRI-42127, 3 uM for 12 hours; ii) after treatment with corresponding DMSO concentration for 12 hours.

first: Xiuhua

last: Yang

first: Natalia

last: Filippova

first: David

last: Crossman

first: L

middle: B


title: Next Generation Sequencing of Ctrl and K562 DROSHA knockdown cells

summary: Purpose: Use next generation sequencing to analyze the cellular pathway change inK562 cells upon Drosha deletion

overall_design: DROSHA crispr or non-specific crispr V2 lenti-virus were used to infect K562 cells to generate ctrl or drosha KD K562 cells.  RNA prep and next generation sequencing.

first: Srivats

last: Venkataramanan

first: Lorenzo

last: Calviello