title: Circadian reprogramming of lipid metabolism in early diabetic nephropathy.

first: Xiao-Qian

last: Li

state: Henan

address: No. 1, East of Jianshe Street, Erqi District

department: Nephrology Hospital

institute: the First Affiliated Hospital of Zhengzhou University

summary: Circadian clock is a highly conserved regulatory system which could coordinate many physiological processes with external stimuli, displaying oscillation with a periodicity of ~24 hour. Dysfunction of circadian clock has been involved in the pathogenesis of a broad spectrum of diseases such as metabolic diseases and chronic kidney disease. However the role of circadian clock in diabetic nephropathy remains largely unknown.

overall_design: In this study, we performed the RNA sequencing on renal cortex collected every 4 hour across the day from control and diabetic mice with three biological duplicates for each zeitgeber time

first: Zhan-Zheng

last: Zhao


title: Generation of thymus reconstituting T cell progenitors from genetically unmodified human pluripotent stem cells

status: Public on May 04 2023

city: Dolgoprudny

first: Eugene

last: Albert

address: Institutskiy Pereulok, 9

country: Russia

institute: MIPT

type: Expression profiling by high throughput sequencing

summary: Derivation of transplantable T cell progenitors from human pluripotent stem cells is the key step towards regenerative therapy of hereditary and acquired immunodeficiencies. Here, we describe an original methodology for differentiation of genetically non-modified human pluripotent stem cells (hPSCs) that yields T cell progenitors capable for direct and unmediated reconstitution of mouse thymus. The hPSC-derived T cell progenitors exhibited a strong thymus and spleen homing potential and developed into single positive human T cells that could enter circulation. Detailed single cell transcriptome analysis confirmed the similarity of hPSC-T cell progenitors with their in vivo counterparts. The transcription profiling attested the emergence of cells that displayed the transcription signature of early T cell progenitors.

overall_design: Invitro differentiation of hPSCs into T cell progenetors

first: Elena

last: Filonenko


title: Slowing prion disease via M1 muscarinic receptors is associated with reduced neuroinflammation and down-regulation of neurodegenerative disease markers

city: Bearsden

first: Pawel

last: Herzyk

address: Wolfson Wohl Cancer Research Centre, Garscube Estate

department: College of Medical, Veterinary and Life Sciences

country: United Kingdom

institute: University of Glasgow

summary:
Purpose: evaluation of the neuroprotective effects of VU846 compound, a positive allosteric modulator highly specific for the M1 muscarinic receptor, using the Next-generation sequencing (NGS) technology in a context of neurodegeneration induced by prion disease.
Methods: Tg37 hemizygous mice at 3 to 4 weeks were inoculated with either the Rocky Mountain Laboratory (RML) scrapie prion brain homogenate, causative of the neurodegeneration, or normal brain homogenate for control purposes. Mice were also daily injected with either the M1 specific positive allosteric modulator VU836 or vehicle. The drug treatment started at 7week post brain homogenate inoculations (wpi) and 11wpi. The hippocampi from 3 mice of each group (control + vehicle, control + VU846, prion + vehicle and prion + VU846) were subject to tot RNA extraction. Raw reads were then converted into Fastq format, mapped to the “mouse-mm10” genome using HISAT2 (Galaxy Version 2.1.0) and processed with the StringTie (Galaxy Version 1.3.3.2) for assembling and quantification.  Differential gene expression comparisons were performed with DESeq2 statistical tool (Galaxy Version 2.11.40.2) and data further analysed with two online software suites, Gene Ontology Panther (http://www.pantherdb.org/) and Pathway Studio (www.pathwaystudio.com).
Results: we use the bioinformatic tool Pathway Studio (www.pathwaystudio.com) to quantitatively assesses the changes in the transcriptome with gene functions reported in the literature to assign an actication score. Strikingly, up and down regulation of genes changed by prion disease promote neuroinflammation and Alzheimer’s disease (AD) (positive activation scores), whereas the M1R specific positive allosteric modulator VU846 treatment modified the expression of genes to inhibit the neuroinflammatory and neurodegenerative processes directly associated with AD (negative activation score). Among these are genes associated with the complement system, microglia and astrocyte activation. Furthermore, consistent with the notion that neuroinflammatory pathways were activated in prion disease and diminished by VU846, the GO Pathway analysis revealed enrichment of genes in pathways such as the complement cascade and chemokine/cytokine signalling. Conversely, a group of genes that were down-regulated in prion disease were transcribed at significantly higher levels in the prion-effect of animals treated with VU846. These genes were strongly associated with synaptic plasticity, learning and memory, cognition and synaptic transmission by the GO Pathway analysis.
Conclusions: These data point to the possibility that specific features of neuroinflammation and disease-adaptation may be directly regulated by M1-receptor activity strongly reinforcing the concept that pharmaceutically targeting M1 muscarinic receptor is neuroprotective and it might lead to the development of new treatments of Alzheimer’s like neurodegenerative diseases.

overall_design: Gene expression profiles of hippocampi from each group (control + vehicle, control + VU846, prion + vehicle and prion + VU846) were generated by RNAseq using NextSeq500 instrument (Illumina) sequencer.

first: Mario

last: Rossi

first: Andrew

last: Tobin


title: ACSS2 inhibitors act as metabo-immunomodulators in triple negative breast cancer [scRNA-Seq]

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

country: USA

institute: The Wistar Institute

summary: Acetate metabolism is an important metabolic pathway in many types of cancers and is primarily controlled by acetyl-CoA synthetase 2 (ACSS2), an enzyme that catalyzes the conversion of acetate to acetyl-CoA. However, the consequences of inhibiting tumor acetate metabolism on the tumor microenvironment and anti-tumor immunity are unknown. Herein we demonstrate that the growth of ACSS2 deficient triple negative breast cancer is severely impaired when host immunity is intact and, in many instances, ACSS2 deficient tumors are fully cleared by the immune system. Pharmacological inhibition of ACSS2 using a potent small molecule inhibitor reproduces these effects and enhances the efficacy of standard of care chemotherapy for TNBC. Single cell RNA sequencing of vehicle versus ACSS2 inhibitor treated tumors indicates differentiation and activation of T cells suggesting a crosstalk between acetate metabolism and immune cells in the tumor microenvironment. Our data suggest that blocking ACSS2 and acetate metabolism in tumors increases the availability of acetate in the tumor microenvironment. Tumor infiltrating T cells can then use acetate as a fuel source due to the relatively high expression of acetyl-CoA synthetase 1 (ACSS1), which is impervious to ACSS2 inhibitors. In this manner, ACSS1-driven oxidation of acetate in T cells helps to metabolically bolster anti-tumor immune responses. Based on our findings, we propose a completely novel paradigm for ACSS2 inhibitors as metaboimmunomodulators that dually act as inhibitors of tumor cell metabolism and modulators of tumor immunity.

overall_design: RNA-seq of different Bmal1 status

first: Katelyn

last: Miller

first: Zachary

last: Schug


title: ACSS2 inhibitors act as metabo-immunomodulators in triple negative breast cancer

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

overall_design: Refer to individual Series


title: ACSS2 inhibitors act as metabo-immunomodulators in triple negative breast cancer [RNA-Seq]


title: Cell State Dependent Alteration of Melanoma Plasticity and Immunity by the Circadian Transcription Factor Bmal1 [RNA-Seq]

summary: The circadian transcription factor Bmal1 accelerates melanoma tumorigenesis through initial cell state dependent mechanisms in which Hif1??, Sox9 or Myh9, MRTF-SRF, AP-1 are involved and modulate tumor microenvironment to favor tumor growth

first: Chi

last: Dang

first: Xue

last: Zhang


title: Genome wide CRISPR screen for CG-806 resistance in OCI-LY3 cells using Y. Kosuke library

city: Portland

first: Alexey

last: Danilov

state: OR

address: 3181 SW Sam Jackson Pk Rd

institute: Oregon Health and Science Univeristy

summary: OCI-LY3 cells were infected with CRISPR/Cas9 library, selected for puromycin resistance for integration events and exposed to CG-806  or vehicle, DMSO, at 1 microMolar concentrations.  Cells were collected at time 0 (post puromycin selection) and day 7. DNA was extracted and sgRNA barcodes were amplified. PCR library was deep sequenced using highthroughput Illumina platform Novaseq 6000.

overall_design: Performed comparisons of sgRNA read counts between DMSO and CG-806  treated cells at corresponding time points.

first: Daniel

last: Bottomly

first: Tingting

last: Liu

first: Tamilla

last: Nechiporuk


title: Periostin+ stromal cells guide lymphovascular invasion by cancer cells

status: Public on May 03 2023

city: Charlottesville

first: Anwaruddin

last: Mohammad

state: VA

address: Pinn Hall

department: Bioinformatics Core

institute: University of Virginia

summary: Cancer cell dissemination to sentinel lymph nodes associates with poor patient outcomes, particularly in breast cancer. The process by which cancer cells egress from the primary tumor upon interfacing with the lymphatic vasculature is complex and driven by dynamic interactions between cancer cells and stromal cells, including cancer associated fibroblasts (CAFs). The matricellular protein periostin can distinguish CAF subtypes in breast cancer and is associated with increased desmoplasia and disease recurrence in patients. However, since periostin is secreted, periostin-expressing CAFs are difficult to characterize in situ, limiting our understanding of their specific contribution to cancer progression. Here, we used in vivo genetic labeling and ablation to lineage trace periostin+ cells and characterize their functions during tumor growth and metastasis. Periostin-expressing CAFs were spatially found at periductal and perivascular margins, were enriched at lymphatic vessel peripheries, and were differentially activated by highly-metastatic cancer cells versus poorly-metastatic counterparts. Surprisingly, genetically depleting periostin+ CAFs slightly accelerated primary tumor growth but impaired intratumoral collagen organization and inhibited lymphatic, but not lung, metastases. Periostin ablation in CAFs impaired their ability to deposit aligned collagen matrices and inhibited cancer cell invasion through collagen and across lymphatic endothelial cell monolayers. Thus, highly-metastatic cancer cells mobilize periostin-expressing CAFs in the primary tumor site that promote collagen remodeling and collective cell invasion within lymphatic vessels and ultimately to sentinel lymph nodes.

overall_design: Primary human breast cancer-associated fibroblasts (CAFs) from culture were treated with si-Scr (si-Control) or si-POSTN with 4 replicates each.

middle: C

last: Dudley

first: Jamie

middle: L


title: Bcl-xL is required to protect endothelial cells latently infected with KSHV from virus induced intrinsic apoptosis

city: Seattle

first: Michael

last: Lagunoff

state: WA

address: 750 Republican St.

department: Microbiology

institute: University of Washington

summary: An sgRNA sub-pool derived from hits and controls in a whole genome screen (PMID: 33122441) was used to investigate genes which are essential during latent KSHV infection of human endothelial cells. The initial pool of library transduced cells was used to confirm efficient transduction of the library and effective selection against sgRNAs targeting generally essential genes over the course of the 8 day experiment. Two replicate experiments were done and comparisons between mock infected and KSHV infected cells was used to identify KSHV infection-specific essential genes.

first: Lyndsey

middle: N

last: Moore

last: Holmes

first: Joselyn

last: Vinueza

first: Anjali

last: Sharma


title: Direct neuronal reprogramming by temporal identity factors

city: Montreal

first: Awais

last: Javed

state: Quebec

address: 110 Avenue des Pins

country: Canada

institute: IRCM

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Temporal identity factors are sufficient to reprogram developmental competence of neural progenitors and shift cell fate output, but whether they can also reprogram the identity of terminally differentiated cells is unknown. To address this question, we designed a conditional gene expression system that allows rapid screening of potential reprogramming factors in mouse retinal glial cells combined with genetic lineage tracing. Using this assay, we found that co-expression of the early temporal identity transcription factors Ikzf1 and Ikzf4 is sufficient to directly convert Müller glial cells into cells that translocate to the outer nuclear layer (ONL), where photoreceptor cells normally reside. We name these “induced ONL (iONL)” cells. Using genetic lineage tracing, histological, immunohistochemical, and single-cell transcriptome and multiome analyses, we show that expression of Ikzf1/4 in Müller glia in vivo, without retinal injury, mostly generate iONL cells that share molecular characteristics with bipolar cells, although a fraction of them stain for Rxrg, a cone photoreceptor marker. Furthermore, we show that co-expression of Ikzf1 and Ikzf4 can reprogram mouse embryonic fibroblasts to induced neurons (iN) in culture by rapidly remodeling chromatin and activating a neuronal gene expression program. This work uncovers general neuronal reprogramming properties for temporal identity factors in terminally differentiated cells.

overall_design: ScRNA-seq and joint cell scRNA/ATAC-seq analysis of reprogrammed Muller glia and RNA-seq/ATAC-seq analysis of reprogrammed MEFs

first: Camille

last: Boudreau-Pinsonneault

first: Luke

middle: A

last: David

first: Jose

last: Lourenço Fernandes

first: Michel

last: Fries

first: Pierre

last: Mattar

last: Cayouette


title: Biallelic null variants in PNPLA8 cause microcephaly through the reduced abundance of basal radial gliaナカセンセイキニュウ

city: Nagoya

first: Yuji

last: Nakamura

address: Kawasumi 1, Mizuho-cho, Mizuho-ku

department: Department of Pediatrics and Neonatology

country: Japan

institute: Nagoya City University Graduate School of Medical Sciences

summary: PNPLA8, one of the calcium-independent phospholipase A2 enzymes, is involved in various physiological conditions through the maintenance of membrane phospholipids. However, little is known about its role in brain development. Here, we report 14 individuals from 12 unrelated families with biallelic ultra-rare variants in PNPLA8 presenting with a wide spectrum of clinical features ranging from developmental and epileptic-dyskinetic encephalopathy (DEDE) to progressive movement disorders and no phenotype depending on the variants and their positions. Complete loss of PNPLA8 was associated with the severe end of the spectrum showing DEDE manifestations and congenital or progressive microcephaly. Using cerebral organoids generated from human induced pluripotent stem cells (iPSCs), we found that loss of PNPLA8 reduces the abundance of basal radial glial cells (bRGCs) and upper-layer neurons. By spatial transcriptomic analysis targeting apical radial glial cells (aRGCs), we found the downregulation of bRGC-related gene sets in patient-derived cerebral organoids. Lipidomic analysis revealed a decrease in the amount of lysophosphatidic acid, lysophosphatidylethanolamine, and phosphatidic acid, indicative of the disturbed phospholipid metabolism in PNPLA8 knockout neural progenitor cells. Our data suggest that PNPLA8 has a critical role in the bRGC-mediated expansion of the developing human cortex by regulating the fate commitment of aRGCs.ナカセンセイキニュウ

overall_design: We performed PIC analysis to isolate expression profiles of apical radial glial cells of cerebral organoids derived from patient and control induced pluripotent stem cells.

first: Issei

middle: S

last: Shimada

first: Reza

last: Maroofian

first: Masanori

last: Fujimoto

first: Emi

last: Sato

first: Hiroshi

last: Takase

first: Shiho

last: Aoki

first: Akihiko

last: Miyauchi

first: Eriko

last: Koshimizu

first: Satoko

last: Miyatake

first: Yuko

last: Arioka

first: Mizuki

last: Honda

first: Takayoshi

last: Higashi

first: Fuyuki

last: Miya

first: Yukimune

last: Okubo

first: Isamu

last: Ogawa

first: Mohammad

last: Miryounesi

first: Sahar

last: Alijanpour

first: Farzad

last: Ahmadabadi

first: Peter

last: Herkenrath

first: Hormos

last: Dafsari

first: Mohammed

last: Balwi

first: Antonio

last: Vitobello

first: Anne-Sophie

last: Denommé-Pichon

first: Médéric

last: Jeanne

first: Antoine

last: Civit

first: Maha

last: Zaki

first: Hossein

last: Darvish

first: Somayeh

last: Bakhtiari

last: Kruer

first: Christopher

last: Carroll

first: Ehsan

middle: G

last: Karimiani

first: Rozhgar

last: Khailany

first: Talib

last: Abdulqadir

last: Bauer

first: Giovanni

last: Zifarelli

first: Mina

last: Zamani

first: Tahere

last: Seifi

first: Chadi

last: Alam

first: Henry

last: Houlden

first: Kazuhiro

last: Haginoya

first: Tamihide

last: Matsunaga

first: Hitoshi

last: Osaka


title: scATAC on palm and hip

city: Ann Arbor

first: Lam

last: Tsoi

state: MI

address: Medical Sciences 1 Bldg. 1301 E. Catherine

institute: University of Michigan

summary: We aim to investigate chromatin accessibility in the keratinocytes of hip and palm

overall_design: single cell ATAC experiments conducted on palm and hip, focusing on epidermal layer

first: Mrinal

last: Sarkar

first: Johann

middle: E

last: Gudjonsson


title: Heterozygous midnolin knockout attenuates severity of nonalcoholic fatty liver disease in mice fed a Western-style diet high in fat, cholesterol, and fructose

city: Duarte

first: Keane

last: Lai

state: CA

address: 1500 E Duarte Rd

department: Molecular Medicine BRI

institute: City of Hope National Medical Center

summary: We found that global heterozygous midnolin knockout attenuated the severity of nonalnonalcoholic fatty liver disease (NAFLD) in mice fed a Western-style diet, high in fat, cholesterol, and fructose. This attenuation in disease was associated with significantly reduced levels of large lipid droplets, hepatic free cholesterol, and serum LDL, with significantly differential gene expression involved in cholesterol/lipid metabolism.

overall_design: In order to investigate the role of midnolin in NAFLD, we generated midnolin (Midn) global knockout (KO) mice. Global homozygous Midn KO mice, however, were largely embryonic lethal, thus, heterozygous (hemizygous) mice were used for this study. To establish the NAFLD heterozygous Midn KO mouse model, two groups of mice heterozygous (het) and wild-type (wt) were fed with a Western-style diet, high in fat, cholesterol, and fructose ad libitum for 25 weeks. During the special diet feeding, mice were monitored regularly and 5 h-fasting blood was also collected for further serum analysis. At terminal stage, mice's liver tissues were collected and processed for biochemical analysis and histology.

first: Soo-Mi

last: Kweon

first: Jose

last: Irimia-Dominguez

first: Gayeoun

last: Kim

middle: K


title: Combined single-sample metabolomics and RNAseq reveals a hepatic pyrimidine metabolic response to acute viral infection

city: Grand Rapids

first: Zach

middle: B

last: Madaj

address: 333 Bostwick Ave NE

department: Bioinformatics and Biostatistics Core

institute: Van Andel Research Institute

summary: In-depth analysis of the usefulness of single-sample metabolite/RNA extraction for multi-‘omics readout.

overall_design: Using pulverized frozen livers of mice injected with lymphocytic choriomeningitis virus (LCMV) or vehicle (Veh) we isolated RNA prior (RNA) or following metabolite extraction (MetRNA). RNA sequencing (RNAseq) data was evaluated for differential expression analysis and dispersion, and differential metabolite abundance was determined.

first: Zachary

first: Michael

last: Dahabieh

first: Vijayvardhan

first: Brejnev

last: Muhire

first: Dean

last: Pettinga

first: Rebecca

last: Siwicki

first: Abigail

last: Ellis

first: Christine

last: Isaguirre

first: Martha

last: Escobar Galvis

first: Lisa

last: DeCamp

first: Russel

last: Jones

first: Scott

last: Givan

first: Marie

last: Adams

first: Ryan

middle: D

last: Sheldon


title: Subcutaneous adipose tissue transcriptome highlights specific expression profiles in pediatric severe obesity: a pilot study

city: Milan

first: Letizia

last: Messa

address: Piazza Leonardo Da Vinci 32

department: Electronics, Informatics and Bioengineering

country: Italy

institute: Politecnico di Milano

summary: Pediatric obesity prevalence is rapidly rising worldwide and “omic” approaches are helpful in obesity molecular pathophysiology investigation. This work aimed at the identification of transcriptional differences in subcutaneous adipose tissue (scAT) of children with overweight (OW), obesity (OB) or severe obesity (SV) respect those with normal weight (NW). Periumbilical scAT biopsies were collected from 20 male children aged 1-12 years. Considering BMI z-score, chil-dren were stratified into 4 groups: SV, OB, OW, NW. scAT RNA-Seq analyses were performed, differential expression analysis was achieved using the DESeq2 R package. Pathways analysis was performed to gain biological insights on gene expression. Our data highlight the significant deregulation in both coding and non-coding transcripts in the SV group when compared to NW, OW, and OB. KEGG pathway analysis showed involvement for coding transcripts mainly in li-pid metabolism. GSEA analysis revealed upregulation of lipid degradation and metabolism in SV vs OB and SV vs OW. Bioenergetic processes and the catabolism of branched-chain amino acids resulted upregulated in SV when compared to OB, OW, NW. In conclusion, we report for the first time that a significant transcriptional deregulation occurs in periumbilical scAT of children with severe obesity with respect to normal weight, overweight or mild obesity.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for subcutaneous adipose tissue (scAT) of children with overweight (OW), obesity (OB) or severe obesity (SV) respect those with normal weight (NW)

first: Clarissa

last: Berardo

first: Valeria

last: Calcaterra

first: Alessia

last: Mauri

first: Stephana

last: Carelli

first: Francesca

last: Destro

first: Federica

last: Rey

first: Erika

last: Cordaro

first: Gloria

last: Pelizzo

first: Gianvincenzo

last: Zuccotti

first: Cristina

last: Cereda


title: Resveratrol attenuates the mitochondrial RNA-mediated cellular response to immunogenic stress

city: Daejeon

first: Doyeong

last: Ku

address: Daehak-ro, 291

country: South Korea

institute: Korea Advanced Institute of Science and Technology

summary: To investigate the gene expression upon mitochondrial stress, oligomycin A or ER stress, tunicamycin treatment, we established HCT116 cell lines after 24h treatment of oligomycin A or tunicamycin.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HCT116 cells after 24h from oligomycin A or tunicamycin treatment.

first: Namseok

last: Lee

first: Yoosik

last: Kim


title: Knockdown of MRPL35 promotes cell apoptosis and inhibits cell proliferation in non-small-cell lung cancer

city: Bengbu

first: Lei

last: Chen

state: Anhui Province

address: Anhui Province Key Laboratory of Clinical and Preclinical Research in Respiratory Disease, Department of Pulmonary and Critical Care Medicine, First Affiliated Hospital of Bengbu Medical College, Bengbu 233004, China

country: China

institute: The First Affiliated Hospital of Bengbu Medical College

summary:
Background: Non-small cell lung cancer (NSCLC) is a major pathological type of lung cancer. However, its pathogenesis remains largely unclear. MRPL35 is a regulatory subunit of the mitoribosome, which can regulate the assembly of cytochrome c oxidases and play an important role in the occurrence of NSCLC.
Methods:The expression of MRPL35 in NSCLC was detected by tissue microarray and immunohistochemistry. H1299 cells were infected with lentivirus to knockdown MRPL35, and the cells were subjected to crystal violet staining to assess the results of colony formation assays. A549 cells were infected by lentiviral particles-expressing shMRPL35 or shControl, and then subcutaneously injected into nude mice. Tumorigenesis in mice was detected by in vivo imaging. The potential pathway of MRPL35 in NSCLC was assessed by Western blotting.  Results:MRPL35 was over-expressed in NSCLC tissue compared to para-cancerous and normal tissues. Knockdown of MRPL35 suppressed cell proliferation and decreased NSCLC progression both in vitro and in vivo. The possible molecular mechanisms were also clarified, which indicated that MRPL35 could be involved in cell apoptosis and proliferation by modulating the expression levels of CDK1, BIRC5, CHEK1, STMN1 and MCM2. Knockdown of MRPL35 activated p53 signaling pathway and inhibited cell cycle regulation.   Conclusions:The oncogenic role of MRPL35 in NSCLC was potentially mediated through the cell cycle regulatory genes such as BIRC5, STMN1, CDK1, CHEK1 and MCM2, as well as activation of P53 signaling pathway.

overall_design: A549 cells were transfected with lentivirus shctrl and shMRPL35 for RNA extraction and hybridization on Affymetrix microarrays.

first: Chengling

last: Zhao


title: Metformin restrains ZIKV replication and alleviates virus-induced inflammatory responses in microglia

city: Galveston

first: Lynn

last: Soong

state: TX

address: 301 University Blvd

department: Microbiology and Immunology

institute: University of Texas Medical Branch

summary:
C20 were pre-treated with metformin at specified concentration (5 mM) for 2 h, followed by ZIKV infection at MOI 3. After infection of 1.5 h, cells were washed three times with PBS. Medium containing metformin was again supplemented and maintained during the culture. The total RNA of samples at 16 and 48 h were extracted for RNA-seq analysis.
We then performed differential expression analysis using data obtained by RNA-seq of ZIKV infection and metformin treatment (16 h and 48 h).

overall_design: C20 were infected by ZIKV infection and cultured in the presence of metformin for 16 and 48 h, C20 were collected  and analyzed using RNAseq.

first: Xiaofang

last: Wang

first: Liang

last: Yuejin

first: Jiaren

last: Sun


title: Transcriptomics reveals molecular differences in equine oocytes vitrified before and after in vitro maturation

city: Merelbeke

first: Katrien

last: Smits

address: Salisburylaan 133

department: Internal Medicine, Reproduction and Population Medicine

country: Belgium

institute: Ghent University

summary: The aim of this study was to analyze transcriptome profiles with RNA sequencing (RNA-seq) in metaphase II horse oocytes after vitrification before and after in vitro maturation (IVM). To do so, transcriptome profile of three groups were compared: (1) oocytes vitrified immature, warmed, and in vitro matured (VGV), (2) in vitro matured and vitrified (VMAT), and (3) fresh oocytes (CONTROL).

overall_design: Examining the effects vitrification before and after in vitro maturation  on the transcriptomic level of the mature oocyte.

first: Daniel

last: Velez

first: Krishna

last: Pavani

first: Tim

last: Meese

first: Filip

last: Van Nieuwerburgh

first: Ann

last: Van Soom


title: Transcriptome changes in the retinal pigment epithelial cells of Microtubule-Associated Protein 1 Light Chain 3B gene knockout mouse (LC3b-/-)

first: Kathleen

last: Boesze-Battaglia

address: 240 South 40th St

institute: University of Pennsylvania

summary:
RPE cells from WT and Total RNA was isolated from WT and LC3b-/- mice were isolated by enzymatic treatment and gentle dissociation, followed by RNA extraction.
RNA-sequencing by the Next-Generation Sequencing Core of the University of Pennsylvania.

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of 4 wild type and 3  LC3b-/-

first: Anuradha

last: Dhingra

first: John

middle: W

last: Tobias


title: Characterization of methionine dependence in melanoma cells [HumanMethylationEPIC]

city: Little Rock

first: Allen

last: Gies

state: AR

address: 4301 W. Markham

department: Biochemistry and Molecular Biology

institute: University of Arkansas for Medical Sciences

type: Methylation profiling by genome tiling array

summary: Dietary methionine restriction is associated with a reduction in tumor growth in preclinical studies and an increase in lifespan in animal models. The mechanism by which methionine restriction inhibits tumor growth while sparing normal cells is incompletely understood, except for the observation that normal cells can utilize methionine or homocysteine interchangeably (methionine independence) while most cancer cells are strictly dependent on methionine availability. Here, we compared a typical methionine dependent and a rare methionine independent melanoma cell line. We show that replacing methionine, a methyl donor, with homocysteine generally induced hypomethylation in gene promoters. This decrease was similar in methionine dependent versus methionine independent cells. There was only a low level of pathway enrichment, suggesting that the hypomethylation is generic rather than gene specific. Whole proteome and transcriptome were also analyzed. This analysis revealed that contrarily to the effect on methylation, the replacement of methionine with homocysteine had a much greater effect on the transcriptome and proteome of methionine dependent cells than methionine independent cells. Interestingly, the methionine adenosyltransferase 2A (MAT2A), responsible for the synthesis of s-adenosylmethionine from methionine, was equally strongly upregulated in both cell lines. This suggests that the absence of methionine is equally detected but trigger different outcomesin methionine dependent versus independent cells. Our analysis reveals the importance of cell cycle control, DNA damage repair, translation, nutrient sensing, oxidative stress and tight junctions in the cellular response to methionine stress in melanoma.

overall_design: In this study, we sought to understand the many ramifications of the replacement of methionine with homocysteine in cell culture media. We compared the methylome and proteome of two human melanoma cell lines. One, A101D, is a prototypical cancer cell line displaying methionine dependence. The second, MeWo, has long been described as methionine independent, i.e. rescued by homocysteine.

first: Sarita

last: Garg

first: Lauren

last: Morehead

first: Jordan

last: Bird

first: Stefan

last: Graw

first: Aaron

last: Storey

first: Alan

last: Tackett

first: Rick

last: Edmondson

first: Samuel

last: Mackintosh

first: Stephanie

last: Byrum

first: Isabelle

middle: R

last: Miousse


title: Assessing kidney injury induced by mercuric chloride in guinea pigs with in vivo and in vitro experiments [in vitro]

city: Frederick

first: Himanshu

last: Goel

state: MD

address: 2405 Whittier Drive, Suite 200

institute: Biotechnology HPC Software Applications Institute (BHSAI)

summary: In this study we tested the ability to predict organ injury from in vitro transcriptomics data  at early time points after exposure to mercury chloride (12 and 24 hours). We selected mercury chloride, a compound extensively used in animal studies for its ability to cause acute kidney damage.

overall_design: We isolated the renal proximal tubules epithelial cells from 6- to 8-week-old guinea pigs and were exposed to vehilce or mercuric chloride dose of 30 and 40 µM as the low and high doses. RNA-seq data were collected 12 and 24 hours after application of vehicle or mercuric chlroide.

first: Venkat

last: Pannala

first: Mohamed

last: AbdulHameed

first: Richard

last: Printz

first: Chiyo

last: Shiota

first: Shanea

last: Estes

first: Masakazu

first: Anders

last: Wallqvist


title: ZFP750 regulates skin lipid metabolism and cutaneous barrier

city: Rome

first: Lorenzo

last: D'Ambrosio

address: Via Elio Chianesi 53

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

institute: Regina Elena National Cancer Institute, IRCCS

summary: A life-essential function of the epidermis is to provide a physical barrier that prevents the loss of water and electrolytes. Essential mediators of this permeability barrier function include ceramides, cholesterol and very long chain fatty acids. Accordingly, their alteration may lead to distinct human conditions, including psoriasis or atopic dermatitis. Recently, a frameshift mutation in the human ZNF750 gene, that encodes for a zinc finger transcription factor, causing a seborrhea-like dermatitis with psoriasiform element, has brought ZNF750 as a key element for the maintenance of the epidermal tissue homeostasis. To clarify this hypothesis, with its underlying molecular mechanism, we generated a novel mouse knockout by deleting exon 2. Here, we show that genetic deletion of the mouse homolog ZFP750 results in loss of epidermal permeability barrier function. ZFP750-/- mice die shortly after birth, within 12 hours. In the stratum corneum of ZFP750-/- mice levels of ceramides, nonpolar lipids and intercellular lipid lamellae are significantly reduced. The alteration of the epidermal lipid homeostasis is directly linked to the transcriptional activity of ZFP750. Indeed, in addition to epidermal differentiation genes, ZFP750 directly and/or indirectly regulates the expression of nearly 50 crucial enzymes in the biosynthesis of ceramides, such as SPTLC1, DGAT2, SMPD3, ELOVL7 and DEGS2. Overall, our study identifies the transcription factor ZFP750 as a master regulator of lipid biosynthesis and epidermal homeostasis and may contribute to our understanding of the pathogenesis of several human skin diseases.

overall_design: Comparative gene expression profiling analysis of RNA-seq data of ZFP750-/- vs Wild-type mice.

first: Alessio

last: Butera

first: Matteo

last: Cassandri

first: Francesca

last: De Nicola

last: D’Ambrosio

first: Maurizio

last: Fanciulli

first: Massimiliano

last: Agostini

first: Gerry

last: Melino


title: Assessing kidney injury induced by mercuric chloride in guinea pigs with in vivo and in vitro experiments [in vivo]

summary: In this study we tested the ability to predict organ injury from in vivo transcriptomics data in male Hartley guinea pigs at early time points after exposure to mercury chloride (9 and 33 hours). We selected mercury chloride, a compound extensively used in animal studies for its ability to cause acute kidney damage.

overall_design: We treated male Hartley guinea pigs with saline solution (control), 1.00 mg/kg (low dose), and 1.50 mg/kg (high dose) to produce different degrees of injury. RNA samples for gene expression analysis were collected from the kidney at 9 and 33 hours. Number of repicates were five.


title: Highly-conserved regulatory activity of the ANR family in the virulence of diarrheagenic bacteria through interaction with Master and Global regulators

first: Araceli

last: Santiago

address: 409 Lane Road

department: Pediatrics

summary: To gain mechanistic insights into this phenomenon, we characterized the regulatory role of Rnr in the virulence of prototype EPEC strain E2348-69 by genetic, biochemical, and human organoid-based approaches. Accordingly, RNA-seq analysis revealed more than 500 genes differentially regulated by Rnr, including the type-3 secretion system (T3SS).

overall_design: RNA was extracted from EPEC E2348/69 derivatives (WT EPEC,  EPECrnr, and EPECrnr(pRnr) grown in DMEM-HG


title: Comparision of RNA expression profile between early and late postpartum breast cancer

city: Bangalore

first: Jyothi

last: Prabhu

state: Karnataka

address: Koramangala, 4th Block

department: Division of Molecular Medicine

country: India

institute: St. John's Research Institute

summary:
To evaluate differentially regulated pathways contributing  to poor prognosis in ealy postpartum breast cancer (PPBC)
RNA sequncing was performed on early PPBC  (PPBC1 samples (duration between last child birth and diagnosis of breast cancer ≤5years), n=3) and late PPBC tumors (PPBC2 samples  (duration between last child birth and diagnosis of breast cancer 6-10 years), n=3) and PPBC3 samples  (duration between last child birth and diagnosis of breast cancer >10 years), n=4).

overall_design: Differentially regulated pathways between early and late PPBC tumors were analyzed

first: Vidya

middle: P

last: Nimbalkar

first: V

last: Snijesh

first: Savitha

last: Rajarajan

first: Annie

last: Alexander

first: Rohini

last: Kaluve

first: Rakesh

last: Ramesh

first: Srinath

last: BS


title: Assessing kidney injury induced by mercuric chloride in guinea pigs with in vivo and in vitro experiments

first: Himanshu

last: Goel

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

overall_design: Refer to individual Series


title: Characterization of methionine dependence in melanoma cells [RNA-seq]

first: Allen

last: Gies

first: Sarita

last: Garg

first: Lauren

last: Morehead

first: Jordan

last: Bird

first: Stefan

last: Graw

first: Aaron

last: Storey

first: Alan

last: Tackett

first: Rick

last: Edmondson

first: Samuel

last: Mackintosh

first: Stephanie

last: Byrum

first: Isabelle

last: Miousse


title: Characterization of methionine dependence in melanoma cells


title: Inducible MLL-AF9 expression drives an AML program during human pluripotent stem cell-derived hematopoietic differentiation [ATAC-Seq]

city: Nijmegen

first: Joost

last: Martens

state: Nederland

address: Geert Grooteplein 28

department: RIMLS

country: Netherlands

institute: Radboud University

summary: The t(9; 11) (p22; q23) translocation produces the MLL-AF9 fusion protein, which is found in up to 25% of de novo AML cases in children. Despite major advances, a comprehensive understanding of context-dependent MLL-AF9-mediated gene programs during early hematopoiesis is challenging. Here, we generated a human inducible pluripotent stem cell (hiPSC) model with doxycycline dose-dependent MLL-AF9 expression. We exploit MLL-AF9 expression as an oncogenic hit to uncover epigenetic and transcriptomic effects on iPSC-derived hematopoietic development and the transformation into (pre-) leukemic states. In doing so, we observed disruption of early myelomonocytic development and expansion of a CD34+ early hematopoietic progenitor compartment upon MLL-AF9 activation. Indeed, we identified gene profiles consistent with primary MLL-AF9 AMLs. We exploit this system to uncover a highly confident MLL-AF9-associated gene core set that faithfully represent primary MLL-AF9 AMLs, including known and thus far unknown factors in MLL-AF9 AMLs. Our system allows for careful chemically controlled and stepwise in vitro iPSC-derived differentiation under serum-free and feeder-free conditions. For a disease that currently lacks effective treatments, our system provides a novel entry-point into exploring potential novel biomarkers and targets for personalized therapeutic strategies.

overall_design: ATAC-seq data for MLL-AF9 induced (myeloid) differentiated iPS cells and its untreated counterpart.

first: B

middle: M

last: Heuts

first: S

last: Arza-Apalategi

last: Alkema

first: E

last: Tijchon

first: L

last: Jussen

last: Bergevoet

last: van der Reijden

first: J

middle: H


title: Survey of microbiota composition differences between obese subjects before and after Lactiplantibacillus plantarum probiotic treatment

city: Firenze

first: Matteo

last: Ramazzotti

address: viale Morgagni 50

department: Experimental and Clinical Biomedical Sciences

institute: University of Florence

summary: The study evaluates the effect of Lactiplantibacillus plantarum IMC 510® supplementation on anthropometric and biochemical parameters, GM composition and gastrointestinal and general symptoms of overweight/obese subjects.

overall_design: Total DNA was extracted from the stool of the patients, amplified to collect amplicons of variable V3–V4 regions (primers 341F and 805R) of the bacterial 16s rRNA gene and sequenced with MiSeq (2x300bp) Illumina platform.

first: Amedeo

last: Amedei


title: Transcriptomic profiles of Beauveria bassiana exposed to linoleic acid stress

city: Hangzhou

first: Shenghua

last: Ying

state: Zhejiang

address: Yu-hang-tang Road 688

institute: Zhejiang University

summary: The entomopathogenici fungus B. bassiana is of great imporatnce in biological control of insect pests. In integrated pest management (IPM) program, unsaturated fatty acids and their derivatives are used as fungicides. The compatibility of mycoinsecticides with fungicides has attracted more and more attention. The genome-wide exprssion analysis involved in fungal resonse to unsaturated fatty acids was analyzed by using high throughput sequencing (RNA-Seq) at different concentrations of  linoleic acid. Our transcriptional profiles revealed that numerous differentially expressed genes (DEGs), of which involved in metabolism, cell transport and cell rescue, were significantly involved in the tolerance of  B. bassiana to linoleic acid stress.

overall_design: Comparison was conducted among total RNA obtained from B. bassiana stressed with different concentrations of linoleic acid.

first: Sheng-Hua


title: Novel RNA-binding Proteins Bind U1 snRNA to Promote Splicing of Weak 5' Splice Sites

city: Basel

first: Fabio

last: Mohn

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

summary: Removal of introns during pre-mRNA splicing, which is central to gene expression, initiates by base pairing of U1 snRNA with a 5' splice site (5'SS). In mammals, many introns contain weak 5'SSs that are not efficiently recognized by the canonical U1 snRNP, suggesting alternative mechanisms exist. Here, we develop a cross-linking immunoprecipitation coupled to a high-throughput sequencing method, BCLIP-seq, to identify NRDE2 (Nuclear RNAi defective-2) and CCDC174 (Coiled-Coil Domain-Containing 174) as novel RNA-binding proteins in mouse ES cells that associate with U1 snRNA and unspliced 5'SSs. Both proteins bind directly to U1 snRNA independently of canonical U1 snRNP specific proteins, and they are required for the selection and effective processing of weak 5'SSs. Our results reveal that mammalian cells use non-canonical splicing factors bound directly to U1 snRNA to effectively select suboptimal 5'SS sequences in hundreds of genes, promoting proper splice site choice and accurate pre-mRNA splicing.

overall_design: All BCLIP-seq, RNA-seq and Ribo-seq experiments were performed in two independent replicates for each sample. BCLIP-seq was done with proteins endogenously tagged with a composite 3xFLAG+AviTag (3A tag). Nrde2 and Mtrex knockout were induced by treating the conditional knockout mES cells with 100 nM 4-hydroxytamoxifen for 4 and 3 days, respectively. Depletion of all the proteins fused to FKBP12F36V degron was achieved by treating the cells with 500 nM dTAG-13 compound for 24 hours. The indicated RNA-seq samples were treated for 4 hours with 0.1 mg/ml cycloheximide (CHX).

first: Matyas

last: Flemr

first: Michaela

last: Schwaiger

first: Marc

last: Bühler


title: The BbLar1-mediated transcriptome in Beauveria bassiana exposed to linoleic acid stress

summary: Fungal tolerance is important for B. bassiana in biological control of insect pests. BbLar1 plays important roles in fungal resistance to linoleic acid stress. The genome-wide exprssion analysis involved in fungal resonse to unsaturated fatty acids was analyzed by using high throughput sequencing (RNA-Seq) at different concentrations of  linoleic acid. Our analyese revealed that BbLar1 mediated numerous differentially expressed genes (DEGs), of which involved in metabolism, cell transport and cell rescue, were significantly involved in the tolerance of  B. bassiana to linoleic acid stress.

overall_design: Comparison was conducted between the ΔBblar1 mutant strains at the indicated concentration of linoleic acid.


title: MOUSE peritoneal macrophages  treated with C498 or LPS

city: qingdao

first: jing

last: Xv

address: East Hong Kong Road

institute: Ocean  University of China

summary: Mouse peritoneal macrophages were isolated and treated with vehicle or C498 (15 μM) for 0.5 h, followed by LPS (100 ng/ml) challenge for an additional 4 h.

first: xv

last: jing

first: song

last: qiaoling

first: zhao

last: chenyang

first: yang

last: jinbo


title: Surges in biosynthetic gene cluster transcription are accompanied by bursts in natural compound production in the myxobacterium Sorangium sp. So ce836

city: Oldenburg

first: Janina

last: Leinberger

address: Ammerländer Heerstraße 114-118

department: Institute for Chemistry and Biology of the Marine Environment

country: Germany

institute: University of Oldenburg

summary: An improved understanding of the genome-wide regulation of natural compound biosynthesis in bacterial producers may accelerate the discovery of novel biologically active molecules and facilitate their production. To this end, we have investigated the time course of genome-wide transcription in the myxobacterium Sorangium sp. So ce836 in relation to its production of natural compounds. Time-resolved RNA sequencing revealed the dynamic temporal variation of transcriptional activity, indicating that core biosynthesis genes from 48 biosynthetic gene clusters (BGCs; 92% of all BGCs encoded in the genome) were actively transcribed at specific time points in a batch culture. The majority (80%) of polyketide synthase and nonribosomal peptide synthetase genes displayed distinct peaks of transcription during exponential bacterial growth. Strikingly, these surges in BGC transcriptional activity were associated with boosts in the production of known natural compounds, indicating that their biosynthesis was crucially regulated at the transcriptional level. In contrast, BGC read counts from single time points had limited predictive value about biosynthetic activity, since transcription levels varied >100-fold among BGCs with detected natural products. Taken together, our time-course data provided unique insights into the dynamics of natural compound biosynthesis and its regulation in a wild-type myxobacterium, challenging the commonly cited notion of preferential BGC expression under meager conditions for bacterial growth. The close association between BGC transcription and compound production suggested that the molecular manipulation of transcriptional activity may be a viable strategy to increase compound yields from myxobacterial producer strains, warranting increased efforts to develop genetic engineering tools for these organisms.

overall_design: Time course gene expression analysis of RNA-seq data of Sorangium sp. So ce836 grown at 5 different time points with 3 to 5 replicates.

first: Judith

last: Boldt

first: Laima

last: Lukoševičiūtė

first: Chengzhang

last: Fu

first: Matthias

last: Steglich

first: Boyke

last: Bunk

first: Vera

last: Junker

first: Aileen

last: Gollasch

first: Birte

last: Trunkwalter

first: Kathrin

middle: I

last: Mohr

first: Michael

last: Beckstette

first: Joachim

last: Wink

first: Nestor

last: Zaburannyi

first: Jörg

last: Overmann

first: Rolf

last: Müller

first: Ulrich

last: Nübel


title: BCR-ABL triggers a glucose-dependent survival program during leukemogenesis through the suppression of TXNIP

city: xi'an

first: Liangliang

last: Shen

address: West changle road 169

institute: The fourth military medical university

summary: Imatinib is highly effective in the treatment of chronic myelogenous leukemia (CML), but the primary and acquired imatinib resistance remains the big hurdle. Molecular mechanisms for CML resistance to tyrosine kinase inhibitors, beyond point mutations in BCR-ABL kinase domain, still need to be addressed. Here, we demonstrated that TXNIP is a novel BCR-ABL target gene. Suppression of TXNIP is responsible for BCR-ABL triggered glucose metabolic reprogramming and mitochondrial homeostasis. Mechanistically, Miz-1/P300 complex transactivates TXNIP through the recognition of TXNIP core promoter region,  responding to the c-Myc suppression by either imatinib or BCR-ABL knockdown. TXNIP restoration sensitizes CML cells to imatinib treatment and compromises imatinib resistant CML cell survival, predominantly through the blockage of both glycolysis and glucose oxidation which results in the mitochondrial dysfunction and ATP production. In particular, TXNIP suppresses expressions of the key glycolytic enzyme, HK2 and LDHA, potentially through Fbw7-dependent c-Myc degradation. In accordance, BCR-ABL suppression of TXNIP provides a novel survival pathway for the transformation of mouse BM cells. Combination of drug inducing TXNIP expression with imatinib synergistically kills CML cells from patients and further extends the survival of CML mice. Thus, the activation of TXNIP represents an effective strategy for CML treatment to overcome resistance.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for K562 cells,  K562 cells with TNXIP knockdown and imatinib resistant K562 cells

first: Lin

last: Feng


title: Controlled MLL-AF9 Expression in Human Induced Pluripotent Stem Cells Reveals MLL-AF9-specific Oncogene Program [hiMLLAF9_scRNAseq]

first: Joost

last: Martens

summary: A t(9;11)(p22;q23) translocation produces the MLL-AF9 fusion protein, which is found in up to 25% of de novo AML cases in children. Despite major advances, obtaining a comprehensive under-standing of context-dependent MLL-AF9-mediated gene programs during early hematopoiesis is challenging. Here, we generated a human inducible pluripotent stem cell (hiPSC) model with a doxycycline dose-dependent MLL-AF9 expression. We exploited MLL-AF9 expression as an onco-genic hit to uncover epigenetic and transcriptomic effects on iPSC-derived hematopoietic develop-ment and the transformation into (pre-)leukemic states. In doing so, we observed a disruption in early myelomonocytic development. Accordingly, we identified gene profiles that were consistent with primary MLL-AF9 AML and uncovered high-confidence MLL-AF9-associated core genes that are faithfully represented in primary MLL-AF9 AML, including known and presently unknown factors. Using single-cell RNA-sequencing, we identified an increase of CD34 expressing early hematopoietic progenitor-like cell states as well as granulocyte-monocyte progenitor-like cells upon MLL-AF9 activation. Our system allows for careful chemically controlled and stepwise in vitro hiPSC-derived differentiation under serum-free and feeder-free conditions. For a disease that cur-rently lacks effective precision medicine, our system provides a novel entry-point into exploring po-tential novel targets for personalized therapeutic strategies.

overall_design: Comparative single-cell RNA-seq analysis using MLL-AF9 induced (myeloid) differentiated iPS cells and its untreated counterpart.

first: B

last: Heuts

first: S

last: Arza-Apalategi

last: Alkema

first: E

last: Tijchon

first: L

last: Jussen

last: Bergevoet

last: van der Reijden

first: J


title: Inducible MLL-AF9 Expression Drives an AML Program during Human Pluripotent Stem Cell-Derived Hematopoietic  Differentiation

overall_design: Comparative gene expression profiling analysis (RNA-seq) using MLL-AF9 induced (myeloid) differentiated iPS cells and its untreated counterpart.


title: Comparing the microbiota composition of stool, intestinal biopsy and saliva between patients with Adenoma and Adenocarcinoma

first: Matteo

last: Ramazzotti

summary: Increasing importance in the onset and progression from colonic adenomatous polyps (AP) to colorectal cancer (CRC) has been attributed to the gut microbiota and the oncometabolites they may produce. To comprehensively study the microbial spatial variations and role of microbiota in CRC progression, multiple niches from the gastrointestinal system have to be investigated. We collected saliva, tissue and stool samples from 61 patients, including 46 CRC patients and 15 AP patients, well matched in age and sex, who were undergoing surgery in 2018 at the Careggi University Hospital (Florence, Italy).  For all samples and locations we surveyed microbial composition through 16S ribosomal RNA and metabolites using NMR, and compared them across tissues and disease state, also considering CRC TNM staging. Our result suggest the importance of microbiota communities and derived oncometabolites in CRC development. Such association can be a forerunner for future studies on CRC/AP management.


title: Conserved transcriptional connectivity of regulatory T cells in the tumor microenvironment informs novel combination cancer therapy strategies [visium]

city: New York

first: Dana

last: Pe'er

state: NY

address: 417 E 68th St

department: Computational and Systems Biology

institute: Memorial Sloan Kettering Cancer Center

summary: While regulatory T (Treg) cells are traditionally viewed as professional suppressors of antigen presenting and effector T cells in both autoimmunity and cancer, recent findings of distinct Treg functions in tissue maintenance suggest that their regulatory purview extends to a wider range of cells and is broader than previously assumed. To elucidate tumoral Treg “connectivity” to diverse tumor-supporting accessory cell types, we explored immediate early changes in their single cell transcriptomes upon punctual Treg depletion in experimental lung cancer and injury-induced inflammation. Prior to any notable T cell activation and inflammation, fibroblasts, endothelial and myeloid cells exhibited pronounced changes in their gene expression in both cancer and injury settings. Factor analysis revealed shared Treg-dependent gene programs, foremost, prominent upregulation of VEGF signaling-related genes upon Treg deprivation in either setting, as well as in Treg-poor vs Treg-rich human lung adenocarcinomas. Accordingly, punctual Treg depletion combined with short-term VEGF blockade showed markedly improved control of PD-1 blockade-resistant lung adenocarcinoma progression in mice compared to the corresponding monotherapies, highlighting a promising factor-based querying approach to elucidating novel rational combination treatments of solid organ cancers.

overall_design: Lungs were collected from  KrasLSL-G12D/WTTrp53fl/fl  Foxp3GFP-DTR  (KP-DTR) mice harboring ~3 months old Adenicarcinomas, following 48 hr treatment with Diphteria toxin (DT) to deplete Tregs, or PBS as control. Lungs were perofused and snap-frozen in OCT. All samples were sections with a Cryostat to a thickness of 10um.

first: Ariella

last: Glasner

first: Samuel

last: Rose

first: Roshan

last: Sharma

first: Herman

last: Gudjonson

first: Jesse

last: Green

first: Sham

last: Rampersaud

first: Isabella

last: Valdes

first: Michail

last: Schizas

first: Stanislav

last: Dikiy

first: Alejandra

last: Mendoza

first: Wei

last: Hu

first: Zhong-min

last: Wang

first: Alexander

middle: Y

last: Rudensky


title: Reversible epigenetic alterations mediate PSMA expression heterogeneity in advanced metastatic prostate cancer.

city: Seattle

first: Brian

last: Hanratty

address: 1100 Fairview Avenue

department: Division of Human Biology

institute: Fred Hutchinson Cancer Cancer

type: Methylation profiling by high throughput sequencing

summary: Purpose: Prostate-specific membrane antigen (PSMA) is a cell surface protein expressed in prostate cancer. PSMA targeted imaging and therapeutic approaches have shown clinical benefit, but there are limited data on the heterogeneity of PSMA tissue expression in metastatic castration-resistant prostate cancer (mCRPC) and the mechanisms involved in regulating PSMA expression are not well understood. Results: PSMA expression differed across molecular subtypes of CRPC. In a rapid autopsy cohort in which multiple metastatic sites per patient were sampled, we found that 13/52 (25%) of cases had no PSMA detected and 24/52 (46%) showed heterogeneous PSMA expression between individual metastases. Of these 52 cases, 35 (67%) cases harbored at least one PSMA negative metastatic site. Transcriptomic analyses of PSMA negative tumors revealed distinct differences relative to PSMA-positive tumors including expression of several drug targets. DNA methylation studies showed a tight correlation between CpG methylation and PSMA expression. Treatment with histone deacetylase (HDAC) and DNA methyl transferase (DNMT) inhibitors restored of PSMA expression in vitro and in vivo. Conclusions: Here, we document the extent of PSMA expression diversity in CRPC, highlight novel targeting approaches for PSMA-negative tumors and propose strategies to overcome resistance to PSMA-directed therapies. Collectively, these data can help to guide the clinical development of PSMA targeting agents for diagnosis and therapy.

overall_design: Experimental Design: Genome wide methylation changes were determined by whole genome bisulfite sequencing in prostate cancer patient derived xenografts (LuCaP 77,78, 93).

first: Erolcan

last: Sayar

first: Radhika

last: Patel

first: Ilsa

last: Coleman

first: Martine

last: Roudier

first: Ailin

last: Zhang

first: Jin-Yih

last: Low

first: Lisa

last: Ang

first: Vipul

last: Bhatia

first: Mohamed

last: Adil

first: Hasim

last: Bakbak

first: David

last: Quigley

first: Michael

middle: T

last: Schweizer

first: Jessica

last: Hawley

first: Lori

last: Kollath

first: Lawrence

last: True

first: Felix

last: Feng

first: Neil

last: Bander

first: Eva

last: Corey

first: John

last: Lee

first: Colm

last: Morrissey

first: Roman

last: Gulati

first: Peter

last: Nelson

middle: C

last: Haffner


title: Exposure to a bacterial metabolite induces specific transcriptional signature of DAF-16 regulated genes, xanthine oxidase, and Phase I detoxification enzymes in C. elegans

city: Tuscaloosa

first: Guy

last: Caldwell

state: AL

address: 300 Hackberry Lane

department: Biological Sciences

institute: The University of Alabama

summary:
RNA-seq analysis of the effect of a secondary metabolite produced by Streptomyces venezuelae that enhanced oxidative stress, mitochondrial dysfunction, and neurodegeneration in Caenorhabditis elegans.
Nearly all DEGs had previous evidence of an association with DAF-16 (FOXO). DEGs were also enriched for Phase I (CYP) and Phase II (UGT) detoxification genes.
DEGs representing several non-CYP Phase I enzymes were identified, including down-regulation of xdh-1. XDH-1 is interconvertible with XO and S. ven metabolite exposure enhanced XO activity.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for C. elegans exposed to the S.ven metabolite or an ethyl acetate solvent control, 5 biological replicates.

first: Jennifer

middle: L

last: Thies

first: Karolina

last: Willicott

first: Maici

last: Craig

first: Madeline

last: Greene

first: Cassandra

middle: N

last: DuGay

first: Kim


title: Conditioned media from Cancer cell lines regulate mRNAs in differentiated human muscle stem cells

city: Indianapolis

first: Harikrishna

last: Nakshatri

state: IN

address: 980 W. Walnut St. R3C218C

department: General Surgery

institute: Indiana University School of Medicine

summary: To investigate whether conditioned medium (CM) from cancer cell culture impacts dynamic changes of the transcriptome in myotubes differentiated from hMuSC, we ran RNA sequencing from differentiated hMuSC that were treated by multiple breast cancer cell lines-conditioned medium. Among 14208 readable mRNAs, MCF-7 CM treatment induced significant changes in 2680 genes, MB-468 CM caused significant changes in 2674 genes, and SKBR-3 CM resulted in significant changes in 1823 genes in myotubes from differentiated hMuSC, compared to control group, respectively. Among them, 961 genes had significant upregulation or downregulation presented in differentiated myotubes over all 3 breast cancer cell lines CMs

overall_design: Examination of mRNA changes with treatment of conditioned media from Cancer cell lines

first: Ruizhong

last: Wang


title: Epigenomic and transcriptomic changes associate with skeletal muscle stem cells to myotube differentiation.

summary: It is well established that differentiation of muscle stem cells to myotubes is associated with significant changes in transcriptional landscape orchestrated by distinct transcription factor networks and such a dramatic change is likely coincident with changes in chromatin accessibility. We utilized this technique to map chromatin accessibility and transcriptome changes at single cell upon differentiation of human muscle stem cells. Results of these studies showed that integrated ATAC-seq and RNA-seq identified 18 subclusters of cells. Subclusters 0, 2-5, 7, 9, 12 and 18 are part of one group of cells, whereas subclusters 1, 6, and 17 formed another subgroup.  Subclusters 14 and 10 formed another group, whereas 11, 13 and 15 formed another group. Subcluster 8 formed another distinct group. Thus cells in hMuSCs could be subgrouped into five major clusters. These studies demonstrate heterogeneity in skeletal muscle cell population.

overall_design: Map chromatin accessibility and transcriptome changes at single cell upon differentiation of human muscle stem cells.

first: Hongyu

last: Gao

first: Yunlong

last: Liu


title: Metabolic engineering of the acid-tolerant yeast Pichia kudriavzevii for efficient L-malic acid production at low pH

city: Tianjin

first: Feiyu

last: Fan

state: Tianjin

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

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

summary: Soluble pyridine nucleotide transhydrogenase (EcSthA) derived from Escherichia coli was introduced into the L-malic acid producing strain MA009-5 of Pichia kudriavzevii to obtain strain MA009-10. It was found that MA009-10 was superior to MA009-5 in terms of L-malic acid titer, glucose consumption rate, and glucose/L-malic acid conversion rate. To elucidate the effect of EcSthA expression on L-malic acid synthesis, we analyzed the RNA-seq data of both strains.

overall_design: Comparative gene expression profiling of RNA-seq data from strains MA009-5 and MA009-10.

first: Yongyan

last: Xi

first: Hongtao

last: Xu

first: Tao

last: Zhan

first: Ying

last: Qin

first: Xueli

last: Zhang


title: Regulation of inulin and sucrose utilization by Aspergillus niger AmyR and InuR

city: Utrecht

first: Ronald

last: de Vries

address: Uppsalalaan 8

department: fungal physiology

institute: Centre of fungal biodiversity

summary: The aim of this study was to investigate the regulatory role of Aspergillus niger AmyR and InuR during growth on inulin and sucrose

overall_design: We comapred the transcriptome data of Aspergillus niger reference strain (ku70 mutant) and single/double deletion mutant strains of AmyR and InuR during growth on inulin and sucrose

first: Roland

middle: S

last: Kun

first: Mao

last: Peng


title: A single-cell RNA-seq survey of the action profile of general anaesthetics on the human prefrontal cortex cells

city: ZhengZhou city

first: Enqiang

last: Chang

state: Henan

address: No.7, Weiwu Road, ZhengZhou city, HeNan province, China

institute: Henan Provincial People’s Hospital

summary: The cellular and molecular actions of general anaesthetics to induce anaesthesia state and also cellular signalling changes for subsequent potential “long term” effects remain largely elusive although great efforts have been made to study these in vitro, ex vivo and in vivo settings. General anaesthetics were reported to act on voltage-gated ion channels and ligand-gated ion channels. Here we used single-cell RNA-sequencing complemented with whole-cell patch clamp and calcium transient techniques to examine the gene transcriptome and ion channels profiling of sevoflurane and propofol, both commonly used clinically, on human embryonic primary prefrontal cortex (PFC) mixed cell cultures. Both propofol and sevoflurane at clinically relevant dose/concentration promoted “microgliosis” but only sevoflurane changed microglia cell similarity. Propofol and sevoflurane each extensively but transiently altered transcriptome profiling 2 hours after anaesthetics exposure across microglia, excitatory neurons, interneurons, astrocytes and oligodendrocyte progenitor cells. Within the excitatory neurons and microglia, exemplary ion-gated and ligand-gated ion channels related genes response to either anaesthetic included SCN1A, CACNAB2, KCNA1, GABRR2 and GRINA1 amongst many others. Utilising scRNA-seq as a robust and high-throughput tool, our work may provide a comprehensive blueprint for future mechanistic studies of general anaesthetics in clinically relevant settings.

overall_design: Single-cell RNA-sequencing complemented with whole-cell patch clamp and calcium transient techniques to examine the gene transcriptome and ion channels profiling of sevoflurane and propofol, both commonly used clinically, on human embryonic primary prefrontal cortex (PFC) mixed cell cultures.

first: Daqing

last: Ma

first: Jiaqiang

first: Yangyang


title: Epigenetic remodeling during monolayer cell expansion reduces regeneration potential

city: Boulder

first: Eduard

last: Casas

state: Colorado

address: Porter Biosciences, CU Campus

department: MCDB

institute: CU Boulder

summary: The purpose of this study was to understand the how the supression of H3K9me3 impacts the phenotype of chondrocytes during a monolayer expansion process which causes chondrocyte dedifferentiation. Therefore, we compared the mRNA expression profiles of chondrocytes isolated from H3K9M (inducible histone H3.3 lysine-to-methionine mutant) and H3WT (inducibly expressed wild-type H3.3) after 16 population doublings.

overall_design: Compared mRNA profiles of H3K9M (inducible histone H3.3 lysine-to-methionine mutant (H3K9M)) and H3WT (inducibly expressed wild-type H3.3) chondrocyte cells cultured for 16 population doublings on standard tissue culture plastic.

first: Adrienne

last: Scott

first: Stephanie

last: Schneider

first: Alison

last: Swearingen

first: Benjamin

last: Seelbinder

first: Justin

last: Brumbaugh

first: Corey

last: Neu


title: Limiting Mrs2-Dependent Mg2+ Uptake Induces Metabolic Programming in Prolonged Dietary Stress

city: San Antonio

first: Travis

last: Madaris

state: Texas

address: 7703 Floyd Curl

department: Medicine

institute: University of Texas Health San Antonio

summary: MANUSCRIPT ABSTRACT: The most abundant cellular divalent cations, Mg2+ (mM) and Ca2+ (nM-µM), antagonistically regulate divergent metabolic pathways with several orders of magnitude affinity preference, but its physiological significance of this competition remains largely unknown. In mice consuming a Western diet, genetic ablation of the mitochondrial Mg2+ channel Mrs2 prevents weight gain, enhances mitochondrial activity, decreases fat accumulation in the liver, and causes prominent browning of white adipose. Mrs2 deficiency further restrains citrate efflux from the mitochondria, making it unavailable to support de novo lipogenesis. As citrate is an endogenous Mg2+ chelator, this may represent an adaptive response to a perceived deficit of the cation. Transcriptional profiling of liver and white adipose reveals higher expression of genes involved in glycolysis, b-oxidation, thermogenesis, and HIF-1a-targets, in Mrs2-/- mice that are further enhanced under Western diet-associated metabolic stress. Thus, lowering mMg2+ is sufficient to promote metabolism and dampens diet induced obesity and metabolic syndrome.

overall_design: Investigate the role of mitochondrial magnesium in regulating metabolism and mitochondrial function. WT and Mrs2 KO mice were utilized to examine this, and an obesogenic diet called Western Diet (control diet called chow diet). Gene expression studies were conducted on the liver and iWAT tissues as described to examine the metabolic reprogramming induced by the chronic Western diet. N=3 biological replicates (mice) per group.

first: Manigandan

last: Venkatesan

first: Madesh

last: Muniswamy


title: The impact of remote solid tumors on bone marrow ecosystem at single-cell resolution

city: Houston

first: Xiang

address: One Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

summary: The bone marrow (BM) environment (BME) is inhabited by hematopoietic stem and progenitor cells (HSPCs) and niche cells, which are sources of bone homeostasis, hematopoiesis and immune response. The BM senses many pathological insults, including solid cancers. However, a comprehensive understanding of BM ecosystem response to solid cancer is lacking. Herein, by single-cell RNA sequencing, we characterized the BM landscape in tumor-bearing models prior to metastasis. We found that remote tumors induce dramatic systemic BM niche remodeling that drives HSPC reprogramming and dysfunctional hematopoiesis, which is distinct from innate immune responses.

overall_design: To identify the changes of  hematopoietic stem and progenitor cells (HSPCs) and the bone marrow (BM) niche cells in the context of tumor burden, we isolated  BM Lin-cKit+ cells (enriched with HSPCs) and CD45-Ter119- cells (niche compartment) from tumor-free (Sham-operated) and mammary tumor (PyMT-N)-bearing mice, then subjected to 3' single-cell RNA sequencing

first: Xiaoxin

last: Hao

first: Yichao

last: Shen


title: DNA demethylating agents and EZH2 inhibitors for Adult T cell leukemia [Affymetrix]

city: saga

first: yuki

last: kurahashi

state: saga

address: nabeshima 5-1-1

institute: saga university

summary: Adult T-cell leukemia/lymphoma (ATL) is a malignancy of mature CD4+ T-cells caused by human T-cell lymphotropic virus type 1 (HTLV-1). Recently, it has been noted that some epigenome abnormalities including DNA methylation and tri-methylation at histone H3Lys27 (H3K27me3) contribute to malignant transformation of ATL. Hence, we investigate the combined effect of DNA demethylating agents and enhancer of zeste homolog 2 (EZH2), which catalyze H3K27me3, inhibitors in ATL. Gene expression microarray analyses revealed that the combination changes gene expressions stronger than the single treatment.

overall_design: To investigate the combined effect of a DNA demethylating agent (OR21) and an EZH2 inhibitor (EPZ-6438), comparing the gene expressions between OR21 and/or EPZ-6438 treated cells and untreated cells.

first: Y

last: Kurahashi

first: T

last: Watanabe

last: Yamamoto

first: H

last: Ureshino

first: K

last: Kamachi

first: N

last: Yoshida-Sakai

last: Fukuda-Kurahashi

first: S

last: Yamashita

last: Hattori

last: Nakamura

first: A

last: Kawaguchi

last: Ushijima

first: E

last: Sueoka

last: Kimura


title: Total RNA expression in extracellular vesicles (EVs) derived from untreated and lipid nanoparticle(LNP) treated cells: lung epithelial, umbilical vein endothelial, and cardiac progenitor cells

city: Skövde

first: Jane

last: Synnergren

address: Högskolevägen 1

country: Sweden

institute: University of Skövde

summary: The study used next-generation sequencing to compare mRNA content of EVs from 3 different cell origins which are untreated control or treated with LNP containing VEGFA mRNA. Our goal is to carry out functional and pathway analysis of the differentially expressed genes. The RNA profiles of EV content from treated and untreated cells; lung epithelial (HTB-177) , umbilical vein endothelial (HUVEC), and cardiac progenitor cells(CPC), were generated by RNA-Seq using Illumina NovaSeq6000. Differentially expressed genes were identified using the DESeq2 package. We found that the VEGFA mRNA was among the most upregulated genes in EVs from LNP treated cells. We also identified multiple genes and pathways associated with angiogenesis and cardiac conditions that were activated in the EVs derived from treated cells. The result suggests that VEGFA-LNP were processed by the cells and certain portions of the mRNA were packaged into EVs and released into the cell culture medium.

overall_design: mRNA profiles of EVs derived from HTB-177 (n = 4) , HUVEC (n = 4) or CPC (n = 3) cells which were untreated or treated with LNP containing VEGFA mRNA

first: Muhammad

last: Nawaz

first: Sepideh

last: Hagvall

first: Benyapa

last: Tangruksa

first: Yujia

last: Jing

first: Marco

last: Maugeri

first: Azadeh

last: Reyahi

first: Elena

last: Garre

first: Alessandro

last: Camponeschi

first: Jonas

last: Christoffersson

first: Ola

last: Grimsholm

first: Lennart

last: Lindfors

first: Hadi

last: Valadi


title: Maturation of hiPSC-derived cardiomyocytes in tri-cellular cardiac microtissues promotes adult alternative splicing of SCN5A revealing effects of mutations in cardiac disease

city: Padova

first: Milena

last: Bellin

state: PD

address: Via Ugo Bassi 58/B

department: Department of Biology

institute: University of Padova

summary: Human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) are used to examine in vitro the effect of mutations in the cardiac sodium channel gene SCN5A, associated with cardiac arrhythmias. Postnatally SCN5A undergoes a fetal-to-adult isoform switch, but hiPSC-CMs in conventional 2-dimensional cultures are fetal-like. This impedes evaluation of mutations in the adult isoform. Here, we derived hiPSC-CMs from a patient carrying compound mutations in the adult SCN5A exon 6B and in exon 4 and generated isogenic corrected lines. In hiPSC-CM 2-dimensional culture, exon 6B mutation did not affect single-cell electrophysiology because of its limited expression. CRISPR/Cas9-mediated excision of the fetal exon 6A with did not promote adult SCN5A expression, rather it impaired the splicing. By maturing hiPSC-CMs in three-dimensional tri-cell type cardiac microtissues, SCN5A underwent isoform switch and revealed the functional effect of exon 6B mutation. Upregulation of the splicing factor MBNL1 in hiPSC-CMs either by culture in microtissues or by overexpression was sufficient to promote exon 6B inclusion. Our results support the ability to study developmentally regulated cardiac genes and postnatal cardiac arrhythmias using hiPSC cardiac cells.

overall_design: We derived hiPSC-CMs from a patient carrying compound mutations in the adult SCN5A exon 6B and in exon 4 and generated isogenic corrected lines we sequenced.

first: Giulia

last: Campostrini

first: Georgios

last: Kosmidis

first: Dorien

last: Ward-van Oostwaard

first: Richard

last: Davis

first: Loukia

last: Yiangou

first: Daniele

last: Ottaviani

first: Christiaan

last: Veerman

first: Hailiang

last: Mei

first: Valeria

middle: V

last: Orlova

first: Arthur

middle: A

last: Wilde

first: Connie

last: Bezzina

first: Arie

middle: O

last: Verkerk

first: Christine

last: Mummery


title: DNA demethylating agents and EZH2 inhibitors for Adult T cell leukemia [Illumina]

first: yuki

last: kurahashi

summary: Adult T-cell leukemia/lymphoma (ATL) is a malignancy of mature CD4+ T-cells caused by human T-cell lymphotropic virus type 1 (HTLV-1). Recently, it has been noted that some epigenome abnormalities including DNA methylation and tri-methylation at histone H3Lys27 (H3K27me3) contribute to malignant transformation of ATL. Hence, we investigate the combined effect of DNA demethylating agents and enhancer of zeste homolog 2 (EZH2), which catalyze H3K27me3, inhibitors in ATL. Methylaome analyse revealed that OR21 and the combination changes DNA methylation.

overall_design: To investigate the combined effect of a DNA demethylating agent (OR21) and an EZH2 inhibitor (EPZ-6438), comparing the methylation status between OR21 and/or EPZ-6438 treated cells and untreated cells.

first: Y

last: Kurahashi

first: T

last: Watanabe

last: Yamamoto

first: H

last: Ureshino

first: K

last: Kamachi

first: N

last: Yoshida-Sakai

last: Fukuda-Kurahashi

first: S

last: Yamashita

last: Hattori

last: Nakamura

first: A

last: Kawaguchi

last: Ushijima

first: E

last: Sueoka

last: Kimura


title: DNA demethylating agents and EZH2 inhibitors for Adult T cell leukemia

type:
Expression profiling by array
Methylation profiling by array

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

overall_design: Refer to individual Series


title: Galnt17 loss-of-function leads to developmental delay, abnormal coordination, activity, and social interactions, with cerebellar vermis pathology

first: Christopher

last: Seward

state: WA

address: Stubbs Lab, Rm 404, 720 Broadway

institute: Pacific Northwest Research Institute

summary: GALNT17 encodes a N-acetylgalactosaminyltransferase (GalNAc-T) protein specifically involved in mucin-type O-linked glycosylation of target proteins, a process important for cell adhesion, cell signaling, neurotransmitter activity, neurite outgrowth, and neurite sensing. GALNT17, also known as WBSCR17, is located at the edge of the Williams-Beuren Syndrome (WBS) critical region and adjacent to the AUTS2 locus, genomic regions associated with neurodevelopmental phenotypes that are thought to be co-regulated. Although previous data have implicated Galnt17 in neurodevelopment, the in vivo functions of this gene have not been investigated. In this study, we have analyzed behavioral, brain pathology, and molecular phenotypes exhibited by Galnt17 knockout (Galnt17-/-) mice. We show that Galnt17-/- mutants exhibit developmental neuropathology within the cerebellar vermis, along with abnormal activity, coordination, and social interaction deficits. Transcriptomic and protein analysis revealed reductions in both mucin type O-glycosylation and heparan sulfate synthesis in the developing mutant cerebellum along with disruption of pathways central to neuron differentiation, axon pathfinding, and synaptic signaling, consistent with the mutant neuropathology. These brain and behavioral phenotypes and molecular data confirm a specific role for Galnt17 in brain development and suggest new clues to factors that could contribute to phenotypes in certain WBS and AUTS2 syndrome patients.

overall_design: RNA Sequencing was performed on RNA samples collected from individual cerebellums of male, 14-day old (P14), mice.  Two mouse strains were sampled in biological triplicate, Wbscr17-/- and B6C3 w/t control.  Paired end RNA Libraries were prepared and sequenced on a Hiseq 4000 sequencer with a read length of 2x150bp.

first: Chih-Ying

last: Chen

first: Huimin

last: Zhang

first: Jennifer

last: Yoo

first: Weii-Chun

last: Kao

first: Hanna

last: Pawlowski

first: Lisa

middle: J

last: Stubbs


title: Complementies strategies encoded by DBD and IDRs direct TF binding

city: Rehovot

first: Naama

last: Barkai

state: --- Select a state ---

address: Herzl St 234

department: Molecular Genetics

country: Israel

institute: Weizmann Institute

summary: Profiling TF sequence variants to map their specificity determinants

overall_design: 49 Transcription factors were tagged with MNAse, sequence variants constructed using CRIPSR and profiled using ChEC-Seq

first: Divya

last: Kumar

first: Felix

last: Jonas


title: Transcriptional profiling of a patient-matched cohort of glioblastoma (IDH-wildtype) for therapeutic target and repurposing drug identification

city: Belfast

first: AIdeen

last: Roddy

address: 97 Lisburn Road

department: Patrick G Johnston Centre for Cancer Research

institute: Queen's University Belfast

summary: Cohort of patient matched initial and recurrent IDH-wt Glioblastoma GBM. Profiled using Clariom D Human array.

last: Prise


title: Single-cell and spatial transcriptomic analysis of homeostatic adult human skin

first: Andrew

last: Ji

address: 1428 Madison Ave.

institute: Icahn School of Medicine at Mount Sinai

summary: Epidermal homeostasis is governed by a balance between keratinocyte proliferation and differentiation with contributions from cell-cell interactions, but conserved or divergent mechanisms governing this equilibrium across species, and how an imbalance contributes to skin disease, are largely undefined. To address these questions, human skin single-cell RNA-sequencing (scRNA-seq) and spatial transcriptomics (ST) data were integrated and compared to mouse skin data. Human skin cell type annotation was improved by using matched ST data, highlighting the importance of spatial context in cell type identity, and ST refined cellular communication inference. In cross-species analyses, we identified a human spinous keratinocyte subpopulation that exhibited proliferative capacity and a heavy-metal processing signature, which was absent in mouse and may account for species differences in epidermal thickness. This human subpopulation was expanded in psoriasis and zinc-deficiency dermatitis, attesting to disease relevance and suggesting a paradigm of subpopulation dysfunction as a hallmark of disease. To assess additional potential subpopulation drivers of skin diseases, we performed cell-of-origin enrichment analysis within genodermatoses, nominating pathogenic cell subpopulations and their communication pathways, which highlighted multiple potential therapeutic targets. This integrated dataset is encompassed in a publicly available web resource to aid mechanistic and translational studies of normal and diseased skin.

overall_design: Human skin samples were fresh frozen and sectioned at 10um thickness onto spatial transcriptomics (ST) slides for mRNA capture, followed by library preparation and sequencing


title: RNA sequencing data from patients with drug reaction with eosinophilia and systemic symptoms to antibiotics

city: Southampton

first: Marta

middle: Ewa

last: Polak

state: Hampshire

address: Southampton General Hospital, Mailpoint 813, LE59,

department: Clinical and Experimental Sciences

institute: University of Southampton

summary: Drug reaction with eosinophilia and systemic symptoms (DRESS) is a cutaneous drug hypersensitivity reaction (DHR) with internal organ involvement and associated mortality, often caused by antibiotics. Despite the risk of severe systemic involvement, no robust diagnostic test to identify causative drug exists. To identify potential biomarkers, we evaluated changes in gene expression following exposure of PBMCs to a culprit antibiotic (cefoxitin, teicoplanin, vancomycin, dapsone) and developed a molecular assay test (MAT).

overall_design: Transcriptome profile comparisons of drug-stimulated PBMCs against media control from 5 antibiotic-DRESS cases 24-hour in vitro  exposure to culprit drug (culprit drugs: cefoxitin, teicoplanin, vancomycin, dapsone)

middle: E

first: William

last: Haw

first: Ying

last: Teo

first: Michael

last: Ardern-Jones


title: The consequences of selection bias in analysis of pre-mRNA splicing

city: Ithaca

first: Jeffrey

last: Pleiss

address: 453 Biotech

institute: Cornell University

summary: Investigating the consequences of selection bias in analysis of pre-mRNA splicing

overall_design: pre-mRNA splicing profiles of wild type and prp2 mutant S. cerevisiae were generated by MPE-seq in triplicate

first: Zachary

middle: W

last: Dwyer


title: RNA-seq analysis of proximal tubule specific Fan1 knockout transgenic kidneys subjected to cisplatin injury

city: Pittsburgh

first: Rannar

last: Airik

address: 4401 Penn Avenue

institute: University of Pittsburgh

summary: FAN1 is a DNA endonuclease that we have previously identified as the underlying genetic cause of karyomegalic interstitial nephritis (OMIM: 614817) in humans. In order to deduce the molecular function of FAN1 in the setting of acute kidney injury and progression to chronic kidney disease, we generated a proximal tubule specific Fan1 knockout mouse model and subjected these mice to cisplatin injury. RNA-seq of the transgenic mice kidneys revealed dysregulation of the DNA damage repair pathway as well as cell cycle associated genes. Together, the data supports for a role of Fan1 in DNA damage repair, and that in its absence results in dysfunctional proximal tubule repair and regeneration upon cisplatin injury.

overall_design: 2X150 bp standard RNA-seq was performed using an Illumina HiSeq platform

first: Merlin

first: Yu

last: Phua


title: CD45 is sufficient to initiate EndMT in human endothelial cells

city: Boston

first: Joyce

last: Bischoff

state: MA

address: One Blackfan Circle

institute: Boston Children's Hospital

summary: Bulk RNA-Seq revealed that activation of the endogenous CD45 promoter induced expression of several genes implicated in EndMT. CD45-positive endothelial cells showed significantly increased migration, a hallmark of EndMT, increased collagen gel contraction, a hallmark of mesenchymal cells, and decreased cell-cell barrier integrity, indicating reduced endothelial function.

overall_design: We activated the endogenous CD45 promoter in human endothelial colony forming cells (ECFCs) using a CRISPR/inactive Cas9 transcriptional activation system.  Bulk RNA-Seq was carried out on control ECFCs and CD45-positive ECFCs (5 biological replicates for each) to identify transcriptomic changes.


title: Conserved transcriptional connectivity of regulatory T cells in the tumor microenvironment informs novel combination cancer therapy strategies

city: New York

first: Dana

last: Pe'er

address: 417 E 68th St

institute: Memorial Sloan Kettering Cancer Center


title: KDM4C silencing inhibits cell migration and enhances radiosensitivity by upregulating CXCL2 in hepatocellular carcinoma

city: Wuhan

first: Zhen

last: Zeng

address: Xinhua Road

institute: Huazhong University of Science and Technology

summary: KDM4C, a histone lysine demethylase, has been proposed to participate in malignant transformation and progression in several types of cancer. However, its roles in hepatocellular carcinoma (HCC) remain poorly understood. In this study, we report that KDM4C protein level is upregulated and KDM4C silencing inhibits cell growth, proliferation and migration in HCC. Furthermore, we provide evidence that depletion of KDM4C leads to defective G2/M checkpoint, increases radiation-induced DNA damage and impairs DNA repair, and enhances radiosensitivity in HCC cells. Using RNA sequencing, we uncover that chemokine CXCL2 is a downstream effector of KDM4C. KDM4C knockdown upregulates the expression of CXCL2 and promotes the secretion of CXCL2 in HCC cells. Importantly, the observed effects caused by KDM4C depletion in HCC cells can be partially rescued by CXCL2 silencing. Thus, our findings demonstrate that KDM4C is involved in the cell migration and radiosensitivity via modulating CXCL2, indicating that KDM4C may be a potential therapeutic target in HCC.

overall_design: Huh7 cells transfected with Scrambled or SiRNAs targeting KDM4C for 48 hours were analyzed by RNA-seq.

first: Shuangbing

last: Xu


title: Inhibitory effect of microRNA on carcinogenesis of colorectal cancer using CDX2P-NLS Cre;Apc+/loxP (CPC-Apc) mice (mRNA)

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

summary: To observe the process of carcinogenesis, CPC-Apc mice were used as a mouse model of spontaneous colorectal cancer. MiRNAs (miR-200c, miR-302 (-a,-b,-c,-d), and miR-369 (-3p, -5p)) or negative control miRNA were intravenously injected to CPC-Apc mice from 8 weeks of age 3 times per week for 8 weeks with super carbonate apatite as drug delivery system. To know the therapeutic effect alive, endoscopic study was performed at 9 and 13 weeks. It revealed that tumor incidence was suppressed in mice with miRs compared to control. Mice were sacrificed at 15 weeks of age.

overall_design: Gene expression analysis of colorectal normal tissues were performed using Sure Print G3 Mouse GE 8×60K (G4852A) as one color experiments.Each sample was classified as follows;   (1) normal tissue of mice injected microRNAs (n=2), (2) tumor tissue of mice injected microRNAs (n=2), (3) normal tissues of CPC-Apc mice (n=2), and (4) tumor tissues of CPC-Apc mice (n=7)

first: Tsuyoshi

last: Hata

first: Hirofumi

last: Yamamoto


title: Expression data of CIS-deleted NK cells

status: Public on May 02 2023

city: Kashihara

first: Tsutomu

last: Nakazawa

state: Nara

address: 840, Shijo-cho

institute: Nara medical university

summary: Genome editing human NK cells expanded from human peripheral blood.

overall_design: Human CD3-depleted PBMC cultured for 14 days.


title: Inhibitory effect of microRNA on carcinogenesis of colorectal cancer using CDX2P-NLS Cre;Apc+/loxP (CPC-Apc) mice

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


title: Mast cell tolerance in the skin microenvironment to commensal bacteria is controlled by fibroblasts [triplicates]

city: San Diego

first: Anna

last: Di Nardo

address: 9500 Gilman Drive

department: Dermatology ACTRI

institute: UCSD

summary:
To investigate the cooperative function of dermal fibroblast and mast cell in inducing mast cell tolerance to commensals
We then performed gene expression profiling analysis using data obtained from RNA-seq of mast cells, and mast cells conditioned by dermal fibroblasts before and after treatments with commensal bacteria supernatants.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for conditioned and not conditioned mast cells

first: Yu-Ling

last: Chang

first: Shahrzad

last: Alimohammadi

first: Kana

last: Masuda-Kuroki

first: Zhenping

last: Wang

first: Krishna

last: Sriram

first: Paul

last: Insel


title: Mast cell tolerance in the skin microenvironment to commensal bacteria is controlled by fibroblasts


title: Brain-wide Correspondence Between Neuronal Epigenomics and Long-Distance Projections [5]

status: Public on May 06 2023

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

summary: Single-cell genetic and epigenetic analyses parse the brain’s billions of neurons into thousands of “cell-type” clusters, each residing in different brain structures. Many of these cell types mediate their unique functions by virtue of targeted long-distance axonal projections to allow interactions between specific cell types. Here we have used Epi-Retro-Seq to link single cell epigenomes and associated cell types to their long-distance projections for 33,034 neurons dissected from 32 different source regions projecting to 24 different targets (225 source→target combinations) across the whole mouse brain. We highlight uses of this large data set for interrogating both overarching principles relating projection cell types to their transcriptomic and epigenomic properties and for addressing and developing specific hypotheses about cell types and connections as they relate to genetics. We provide an overall synthesis of the data set with 926 statistical comparisons of the discriminability of neurons projecting to each target for every dissected source region. We integrate this dataset into the larger, annotated BICCN cell type atlas composed of millions of neurons to link projection cell types to consensus clusters. Integration with spatial transcriptomic data further assigns projection-enriched clusters to much smaller source regions than afforded by the original dissections. We exemplify these capabilities by presenting in-depth analyses of neurons with identified projections from the hypothalamus, thalamus, hindbrain, amygdala, and midbrain to provide new insights into the properties of those cell types, including differentially expressed genes, their associated cis-regulatory elements and transcription factor binding motifs, and neurotransmitter usage.

overall_design: In Epi-Retro-Seq, the retrograde viral tracer rAAV2-retro-Cre is injected in the target region in an INTACT mouse, turning on Cre-dependent nuclear-GFP expression in neurons that project to the injected target, throughout the mouse brain. The brain is then sectioned into eighteen 600-micron coronal slices, and the brain regions of interest are mannually dissected from each slice. Nuclei are sampled from 4 mice (2 male and 2 female) for each projection target. Nuclei from each of the dissected source regions are prepared, from which GFP+/NeuN+ nuclei (the GFP-labeled projection neurons) are isolated as single nuclei using fluorescence activated nuclei sorting (FANS) and assayed using snmC-Seq2/3 to profile their genome-wide DNA methylation signatures. Low-quality nuclei were removed.

first: Jingtian

last: Zhou

first: Zhuzhu

last: Zhang

first: May

last: Wu

first: Hanqing

last: Liu

first: Yan

last: Pang

last: Bartlett

first: Angeline

last: Rivkin

first: Will

last: Lagos

first: Elora

last: Williams

first: Cheng-Ta

last: Lee

first: Paula

last: Assakura Miyazaki

first: Andrew

last: Aldridge

first: Qiurui

first: J

last: Salinda

first: Naomi

last: Claffey

first: Michelle

last: Liem

first: Conor

last: Fitzpatrick

first: Lara

last: Boggeman

first: Jordan

last: Altshul

first: Mia

last: Kenworthy

first: Cynthia

last: Valadon

last: Nery

first: Rosa

middle: G

last: Castanon

first: Neelakshi

last: Patne

first: Minh

last: Vu

first: Mohammad

last: Rashid

first: Matthew

last: Jacobs

first: Tony

last: Ito-Cole

first: Julia

last: Osteen

first: Sharon

last: Huang

first: António

last: Pinto-Duartec

first: Bertha

last: Dominguez

first: Jared

middle: B

last: Smith

first: Carolyn

last: O'Connor

first: Kuo-Fen

first: Eran

last: Mukamel

first: Xin

last: Jin

first: M

last: Behrens


title: Implications of the SRP72 p.R124S mutation on signal recognition particle functions [K562_SRP72]

city: Hong Kong

first: Margaret HL

last: Ng

address: Prince of Wales Hospital

department: Department of Anatomical and Cellular Pathology

country: Hong Kong

institute: The Chinese University of Hong Kong

summary: To investigate the functional significance of the SRP72 p.R124S mutation, we overexpressed the mutant protein in K562 myeloid leukemia cells and analysed global gene expression changes using RNA-seq.

overall_design: Differential gene expression profiling analysis of RNA-seq data for K562 cells expressing SRP72 p.R124S mutant and wild-type SRP72.

first: Margaret

first: Chi-Keung

last: Cheng

first: Yuk-Lin

last: Yung


title: Genomic analysis of pediatric AML by whole transcriptome sequencing [pediatric AML patients]

summary: Pediatric AML is an aggressive hematological malignancy associated with distinctive genomic features. We employed RNA-seq to study fusion genes and clinically relevant gene expression patterns in pediatric AML patients.

overall_design: Whole transcriptome sequencing was employed to study genome-wide changes in leukemic blasts from pediatric AML patients.


title: Deep genomic characterisation of pediatric acute myeloid leukemia


title: Targeted DNA demethylation of the Arabidopsis genome using the SunTag-dCpf1-TET1cd system

city: Nanchang

first: Reqing

last: He

state: Jiangxi

address: No.999 Xuefu Avenue, Honggutan District

department: College of Life Science

institute: Nanchang University

summary: DNA methylation is a stable and heritable epigenetic mark, and it plays an important role in regulation of gene expression and transposon silencing. Here we developed a CRISPR/dCpf1-based targeted demethylation system using the catalytic domain of the human demethylase TEN-ELEVEN TRANSLOCATION1 (TET1cd) and a SunTag system. The SunTag-dCpf1-TET1cd system is able to achieve targeted DNA demethylation and ur-regulate gene expression when guided to the FWA or CACTA1 loci in Arabidopsis thaliana. Our study provides tools for targeted removal of DNA cytosine methylation, and activation of protein-coding genes or transposons expression.

overall_design: Methylation profiling by high throughput sequencing

first: Yunxi

last: Zheng


title: Inhibitory effect of microRNA on carcinogenesis of colorectal cancer using CDX2P-NLS Cre;Apc+/loxP (CPC-Apc) mice [miRNA]

first: Daisuke

last: Okuzaki

overall_design: miRNA microarray analysis of colorectal normal tissues (n=3) and and tumor tissues (n=2) were performed using Mouse miRNA (8 x 60K) ver.19 (G4872A) as one color experiments.Each sample was classified as follows;   (1) normal tissue of mice injected microRNAs, as “tumor-supprresed mucosa”   (2) normal tissues of CPC-Apc mice, as “tumor-potential mucosa”

first: Tsuyoshi

last: Hata

first: Hirofumi

last: Yamamoto


title: Effect of gene POX07948 deletion on gene expression of Penicillium oxalicum

city: zhengzhou

first: Li

last: Xudong

address: No. 1, Jianshe East Road, Erqi District

institute: The First Affiliated Hospital of Zhengzhou University

summary: To explore the effect of phosphokinase POX07948 on the transcription levels of cellulase-encoding genes and xylanase-encoding genes

first: Shuai

last: Zhao

first: Ma

last: Bo


title: Gene expression and clonotypes of T cells cultured in extracellular matrices of different viscoelasticies

first: Kwasi

last: Adu-Berchie

state: Massachusetts

address: 3 Blackfan Circle

institute: Harvard University

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

overall_design: Refer to individual Series