title: RNA Seq analysis of tolerant (BPT5204) and susceptible (TN1) variety of Oryza sativa cv. Indica under drought, pathogen, and combined stress

city: Faridabad

first: Ramu

last: Vemanna

address: NCR Biotech Science Cluster, Faridabad

institute: Regional Centre for Biotechnology

summary: Climate change is affecting the unprecedented drought scenario and frequent occurrence of pathogen infection in rice. Simultaneous occurrence of these stresses could lead to more crop loss. Transcription response of genes involved in combined stress would provide relevant candidate gene to develop climate resilient rice. We report individual drought, Xoo infection and combined stress on rice. RNA Seq of contrasting genotypes BPT5204 and TN1 has revealed many candidate genes. A meta-analysis further filtered out some candidate genes which could be used for breeding programme. Several genes identified were already characterized by other groups for individual stress condition. However the genes involved in drought and pathogen infection could be further used for genetic manipulation studies in future.

overall_design: Samples from four categories: control, drought, pathogen, and drought + pathogen were analysed from both BPT5204 and TN1 variety. Each sample was run in duplicate. Total number of sample analysed is 16.

first: Garima

last: Pal

first: Rahul

last: Bakade

first: Sanjay

last: Deshpande

first: Swathi

last: Patil

first: Akashata

last: Dawane

first: Subham

last: Agarwal

first: Vidya

last: Niranjan

first: M

last: Prasannakumar


title: Annotation of estrogen-regulated enhancer RNAs [PRO-cap]

status: Public on Jun 16 2022

city: Dallas

first: W. Lee

last: Kraus

state: TX

address: 5323 Harry Hines Blvd.

country: USA

institute: UT Southwestern Medical Center

summary: To annotate estrogen-regulated eRNAs in MCF-7 breast cancer cells, we used precision nuclear run-on and sequencing of capped RNA (PRO-cap) to determine the transcription start sites of eRNAs.

overall_design: PRO-cap in MCF-7 treated with either DMSO or 45 min 17-b-estradiol.

first: Tim

middle: Y

last: Hou

first: W

middle: L


title: A functional circuit formed by the autonomic nerves and myofibroblasts controls mammalian alveolar formation for gas exchange

city: San Francisco

first: Pao-Tien

last: Chuang

address: 555 Mission Bay Blvd. South

institute: University of California, San Francisco

type: Expression profiling by high throughput sequencing

summary: Alveolar formation increases the surface area for gas exchange. A molecular understanding of alveologenesis remains incomplete. Here, we show that the autonomic nerve and alveolar myofibroblast form a functional unit in mice. Myofibroblasts secrete neurotrophins to promote neurite extension/survival, whereas neurotransmitters released from autonomic terminals are necessary for myofibroblast proliferation and migration, a key step in alveologenesis. This establishes a functional link between autonomic innervation and alveolar formation. We also discover that planar cell polarity (PCP) signaling employs a Wnt-Fz/Ror-Vangl cascade to regulate the cytoskeleton and neurotransmitter trafficking/release from the terminals of autonomic nerves. This represents a new aspect of PCP signaling in conferring cellular properties. Together, these studies offer molecular insight into how autonomic activity controls alveolar formation. Our work also illustrates the fundamental principle of how two tissues (e.g., nerves and lungs) interact to build alveoli at the organismal level.

overall_design: Gene expression profile of lung cells at P3

first: Kuan

last: Zhang

first: Erica

last: Yao

first: Shao-An

last: Wang

first: Ethan

first: Julia

last: Wong

first: Liliana

last: Minichiello

first: Andrew

last: Schroeder

first: Walter

last: Eckalbar

first: Paul

middle: J

last: Wolters


title: Expression data from SMA fibroblasts treated with amiloride or EIPA

city: Philadelphia

first: Matthew

middle: E R

last: Butchbach

state: PA

address: 1020 Locust St

institute: Thomas Jefferson University

summary: Spinal muscular atrophy (SMA) is an autosomal recessive, pediatric-onset disorder caused by the loss of spinal motor neurons thereby leading to generalized muscle atrophy. SMA is caused by the loss of or mutations in the survival motor neuron 1 (SMN1) gene. SMN1 is duplicated only in human to give rise to the paralogous SMN2 gene. These paralogs are nearly identical except for a cytosine to thymine (C-to-T) transition within an exonic splicing enhancer (ESE) element within exon 7. As a result, the majority of SMN2 transcripts lack exon 7 (SMNΔ7) which produces a truncated and unstable SMN protein. Since SMN2 copy number is inversely related to disease severity, it is a well-established target for SMA therapeutics development. 5-(N-ethyl-N-isopropyl)amiloride (EIPA), an inhibitor of sodium/proton exchangers (NHEs), has previously been shown to increase exon 7 inclusion and SMN protein levels in SMA cells. In this study several different types of NHE inhibitors were evaluated for their ability to modulate SMN2 expression. EIPA as well as 5-(N,N-hexamethylene)amiloride (HMA) increase exon 7 inclusion in SMN2 splicing reporter lines as well as in SMA fibroblasts. The EIPA-induced exon 7 inclusion occurs via a mechanism unique from that used by RG7800, another SMN2 splicing modulator, and does not involve previously identified splicing factors. Transcriptome analysis identified novel targets, including TIA1 and FABP3, for further characterization. EIPA and HMA are more selective at inhibiting the NHE5 isoform, which is expressed in fibroblasts as well as in neuronal cells. These results show that NHE5 inhibition increases SMN2 expression and may be a novel target for therapeutics development.

overall_design: Type II SMA fibroblasts (GM03813) were treated (n=3/treatment) with either 10 microM amiloride, 10 microM EIPA or DMSO for 5 days. Total RNA was isolated from each sample, labeled with biotin and then hybridized on Affymetrix Clariom D human arrays.

middle: E


title: Th2/Th1 cytokine imbalance is associated with higher COVID-19 risk mortality

city: New York

first: Ana

last: Pavel

state: NY

address: One Gustave L. Levy Place

department: Dermatology

institute: Icahn School of Medicine at Mount Sinai

summary: In this study we profiled 288 new serum proteomics samples measured at admission from patients hospitalized within the Mount Sinai Health System with positive SARS-CoV-2 infection. We first computed Th1 and Th2 pathway enrichment scores by gene set variation analysis and then compared the differences in Th2 and Th1 pathway scores between patients that died compared to those that survived.

overall_design: We evaluated 288 new serum samples from hospitalized patients with a positive SARS-CoV-2 polymerase chain reaction (PCR) test in the Mount Sinai Health System from 03/01/20 to 06/07/20. Serum cytokines were profiled by Proseek Multiplex OLINK Proteomics as previously decribed. We computed enrichment scores for Th1 and Th2 immune pathways by gene set variation analysis, and modeled the Th2/Th1 balance as the difference between Th2 and Th1 enrichment scores.

middle: B

first: Jacob

middle: W

last: Glickman

first: James

middle: R

last: Michels

first: Seunghee

last: Kim-Schulze

first: Rachel

last: Miller

first: Emma

last: Guttman-Yassky


title: Transcriptional impact of EGFR-AT1R-TP receptor crosstalk in mouse aortic vascular smooth muscle cells

city: Halle (Saale)

first: Virginie

last: Dubourg

address: Magdeburger Str. 6

department: Julius Bernstein Institute for Physiology

country: Germany

institute: Martin Luther University - Halle-Wittenberg

summary: The impact EGFR, AT1R and TP receptor individual or simultaneous activations on the gene expression was investigated in mouse aortic vascular smooth muscle cells (aVSMC)

overall_design: RNAsequencing of aVSMC incubated for 24h or 48h with EGF and/or Angiotensin II and/or U46619.

first: Michael

last: Gekle

first: Gerald

last: Schwerdt

first: Barbara

last: Schreier

first: Sindy

last: Rabe

first: Ralf

middle: A

last: Benndorf


title: Genome-wide analysis of KSHV splicing regulation by ORF57

city: Frederick

first: Zhi-Ming

last: Zheng

state: Maryland

department: Center for Cancer Research

institute: National Cancer Institute

summary: Kaposi's sarcoma-associated virus (KSHV) ORF57 is a viral RNA-binding protein required for proper posttranscriptional processing of viral transcripts including RNA splicing. To identify the viral splicing events regulated by ORF57 we performed a genome-wide analysis of RNA splicing of viral RNAs in wild type (WT) versus ORF57 knock-out (57KO) primary effusion lymphoma cells line BCBL-1 after induction of KSHV lytic replication by 24h treatment with valproic acid (VA).

overall_design: The obtained reads were mapped to human/KSHV chimeric genome by STAR aligner to identify KSHV splicing events. To detemine ORF57 activity on viral RNA splicing, we compared the number of splice reads mapped to unique splicing junction in WT versus 57KO BCBL-1 cells.

first: Vladimir

last: Majerciak

first: Alexei

last: Lobanov


title: Adoptively transferred in vitro-generated MDSCs improve T cell function and antigen-specific immunity after blunt chest trauma-induced lung injury

city: Ulm

first: Karlheinz

last: Holzmann

address: Helmholtzstreet 8/1

department: Medical Faculty

institute: Ulm University

summary:
Does the adoptive transfer of MDSCs modulate lymphocyte (T cell) functions?
Microarray expression analysis of T cells from MDSC-treated mice after Blunt chest trauma (TxT)

overall_design: 1) doptive transfer of MDSCs 24h after TxT, 2) isolation of spleen cells 7/14 days after TxT, 3) sorting of CD3+ CD4+ and CD3+ CD8+ Tcells, 4) isolation of RNA, 5) Microarray analysis

first: Monika

last: Kustermann

first: Linda

last: Wolf

first: Gudrun

last: Strauß


title: Annotation of estrogen-regulated enhancer RNAs [RNA-seq]

first: W. Lee

last: Kraus

summary: To annotate estrogen-regulated eRNAs in MCF-7 breast cancer cells, we used RNA-sequencing of polyA-depleted and polyA-enriched RNA fractions to assemble the gene bodies of eRNAs.

overall_design: RNA-seq libraries from polyA-depleted and polyA-enriched fractions in MCF-7 treated with either DMSO or 45 min 17-b-estradiol.

first: Tim

last: Hou

first: W


title: Transcriptional response to PORCN inhibition using an in vivo model of RNF43 mutant pancreatic adenocarcinoma (HPAF-II) in EP300 knockout and WT cells

city: Cardiff

first: NATHAN

last: HARMSTON

address: Museum Avenue

country: United Kingdom

institute: Cardiff University

summary: RNF43-mutant pancreatic tumors are driven by Wnt signaling and sensitive to Wnt inhibition, e.g. PORCN inhibitors. However, some RNF43-mutant pancreatic cancers are intrinsically resistant to Wnt inhibition. We identified that EP300 mutations confer resistance to PORCN inhibitors in RNF43-mutant pancreatic cancers. We found that EP300 knockout down-regulated GATA6 expression and GATA6-regulated differentiation program, making the anti-differentiation roles of Wnt signaling dispensable.

overall_design: To decipher the underlying drug resistance mechanisms, we performed transcriptome analysis in EP300 wildtype and knockout HPAF-II orthotopic xenografts treated with vehicle or PORCN inhibitor ETC-159 (5 mg/kg q.d. x 3 days or 15 mg/kg q.d. x 3days). Orthotopic tumors were harvested 8 hours post the last dose (56 hours of treatment). Total RNAs were extracted and subjected to RNA-seq.

first: Zheng

last: Zhong

first: Nathan

last: Harmston

first: David

middle: M

last: Virshup


title: Annotation of estrogen-regulated enhancer RNAs

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Genome Methylation in Wild Beluga Whales

city: Los Angeles

first: Steve

last: Horvath

state: CA

address: 695 Charles E. Young Drive South, Box 708822

department: Human Genetics

institute: University of California, Los Angeles

type: Methylation profiling by genome tiling array

summary:
An Infinium microarray platform (GPL28271, HorvathMammalMethylChip40) was used to generate DNA methylation data from skin samples of beluga whales, Maui's dolphin, and humpback whale.
Tissue: Skin

sample_organism:
Delphinapterus leucas
Physeter macrocephalus
Balaenoptera musculus
Megaptera novaeangliae
Cephalorhynchus hectori maui

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: N=143 skin samples. Mainly from beluga but also Maui dolphin and 1 humpback whale. Profiled on the mammalian methylation array platform (GPL28271). The characteristic variable CanBeUsedForAgingStudies.

first: Ellie

last: Bors

first: Scott

last: Baker


title: Spatial centrosome proteome of human neural cells uncovers novel interactors and disease hubs

status: Public on Jun 15 2022

city: shanghai

first: sirui

last: zhang

address: yueyang road

country: China

institute: CAS

summary: Despite the crucial importance of the centrosome in brain development and disease, its comprehensive proteome remains uncharacterized in neural cells. Here, we used spatial proteomics to elucidate protein interaction networks at the centrosome of iPSC-derived human neural stem cells (NSCs) and neurons. Centrosome-associated proteins were largely cell-type specific, with protein hubs involved in RNA-dynamics. Analysis of neurodevelopmental disease cohorts identified a significant overrepresentation of NSC centrosome proteins with variants in patients with periventricular heterotopia (PH). Expressing the PH-associated mutant splicing factor PRPF6 reproduced the periventricular misplacement in the developing mouse brain, highlighting mis-splicing of transcripts of the MAP-kinase SAD-A at centrosomal location as essential for the phenotype. Collectively, cell-type specific centrosome interactomes explain how genetic variants in ubiquitous proteins may convey brain-specific phenotypes.

overall_design: RNA from FACS sorted electroporated (GFP+) cells was isolated in Extraction Buffer (Arcturus), heated to 42 and stored at -80 cDNA was synthesized from 300 pg of total RNA using SMART‐Seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech), according to the manufacturer's instructions. Prior to generating the final library for Illumina sequencing, the Covaris AFA system was used to perform the cDNA shearing, resulting in 200‐ to 500‐bp‐long cDNA fragments. The quality and concentration of the sheared cDNA were assessed on Agilent 2100 Bioanalyzer before proceeding to library preparation using MicroPlex Library Preparation kit v2 (Diagenode). Final libraries were evaluated and quantified using an Agilent 2100 Bioanalyzer, and the concentration was measured additionally with Quant‐iT PicoGreen dsDNA Assay Kit (InvitrogenTM) before sequencing. The uniquely barcoded libraries were multiplexed onto one lane and 150‐bp paired‐end deep sequencing was carried out on HiSeq 4000 (Illumina) that generated ~ 30 million reads per sample.

first: Adam

middle: C

last: O’Neill

first: Fatma

last: Uzbas

first: Giulia

last: Antognolli

first: Florencia

last: Merino

first: Sirui

last: Zhang

first: Zefeng

last: Wang

first: Magdalena

last: Götz


title: Single Cell Transcriptomic Profiling of Cardiac Tissues and Surrounding Tissues During Early Cardiac Development

city: New York City

first: Nicole

last: Dubois

address: 1470 Madison Avenue, 8th Floor, Room 301

institute: Icahn School of Medicine of Mount Sinai

summary: The specification of distinct cardiac lineages during development is thought to occur prior to the morphogenetic events that lead to chamber formation and acquisition of bona fide atrial or ventricular identity. However, the mechanisms underlying these dynamic early specification events remain poorly understood. In this study, we performed single cell analysis across the time window of progenitor specification, namely at the cardiac crescent (E8.25), primitive heart tube (E8.75) and heart tube (E9.25) stages to uncover the transcriptional heterogeneity of early progenitor cells ,as well as mechanisms underlying differentiation of atrial and ventricular cardiomyocytes and associated cardiac cell types.

overall_design: Cells of the early cardiac lineages and surrounding structures were dissected from early Foxa2Cre;mTmG mouse embryos, where expression of EGFP labels Foxa2-lineage traced cells. Cells were dissociated into single-cells for scRNAseq without the need for cell sorting.

first: D

last: Gonzalez

first: N


title: MicroRNA-sequencing Analysis of Plasma-derived Exosomes Provides Novel Insights into the Disease Mechanism of Childhood Atopic Dermatitis

city: Beijing

first: Teng

last: Zhu

address: 56 South Lishi Road

institute: Beijing Children's Hospital

type: Non-coding RNA profiling by high throughput sequencing

summary: To investigate the expression pattern of exosomal miRNAs in pediatric atopic dermatitis patients, we performed miRNA-Seq of plasmal exosome from 5 patients and 5 healthy controls. We identify 40 differentially expressed exosomal miRNAs (DEPEMs) and found their target genes were involved in multiple functions and pathways associated with AD through  GO and KEGG pathway analysis.

overall_design: Comparative gene expression profiling analysis of miRNA-seq data for pediatric atopic dermatitis patients and healthy controls.

first: Jing

last: Sun

last: Tian

first: Yuan

last: Liang

first: Lin

last: Ma


title: A gastruloid model of the interaction between embryonic and extra-embryonic cell types

city: Leiden

first: Stefan

last: Semrau

state: Zuid-Holland

address: Einsteinweg 55

department: Physics

country: Netherlands

institute: Leiden University

summary: Single-cell RNA sequencing of extra-embryonic endoderm enhanced gastruloids (XEGs) and gastruloids

overall_design: 10X Single-Cell Gene Expression

first: Noémie

last: Bérenger-Currias

first: Maria

last: Mircea

first: Esmée

last: Adegeest

first: Patrick

last: van den Berg

first: Marleen

last: Feliksik

first: Mazène

last: Hochane

first: Timon

last: Idema

first: Sander

last: Tans


title: Spontaneous Endometritotic Lesions Compared to Eutopic Endometrium in the Baboon

city: Grand Rapids

first: Gregory

last: Burns

state: MI

address: 400 Monroe Ave NW

department: Obstetrics, Gynecology and Reproductive Biology

institute: Michigan State University

summary: The development and progression of endometriotic lesions are poorly understood, but immune cell dysfunction and inflammation are closely associated with the pathophysiology of endometriosis. A lack of suitable 3D in vitro models permitting the study of interactions between cell types and the microenvironment is a contributing factor. To address this limitation, we developed endometriotic organoids (EO) to explore the role of epithelial-stromal interactions and model peritoneal cell invasion associated with lesion development (GSE202661). These organoids were compared to spontaneous endometriotic lesions from baboons (Papio anubis).

overall_design: Endometriotic lesion tissues (n=4) were compared to eutopic endometrium (n=3).

first: Yong

last: Song

first: Niraj

last: Joshi

first: Ripla

last: Arora

first: J

last: Kim

first: Asgerally

middle: T

last: Fazleabas


title: RNA-seq of CAFs grown on different substrates

city: Urbana

first: Taher

last: Saif

state: IL

address: 105 S Mathews Ave

department: Grainger College of Engineering

institute: University of Illinois at Urbana-Champaign

summary: Almost all solid tumors become stiff with progression of cancer. Cancer Associated Fibroblasts (CAFs), most abundant stromal cells in the tumor microenvironment (TME), are known to mediate the stiffening. While the biochemical crosstalk between CAFs and cancer cells have been widely investigated, it is yet not clear whether CAFs in stiffer TME promote metastatic progression, and if so, how. To address this question, here we explore the role of mechanical stiffness and cell traction force in regulating human colorectal CAF (CAF05 cell line) gene expressions that are relevant to metastatic progression. We cultured CAFs on 2D polyacrylamide hydrogels with increasing elastic modulus (E) of 1, 10 and 40 kPa, and quantified corresponding cell spreading area and cytoskeletal force. We performed genome-wide transcriptome analyses in these cells to identify differentially expressed genes on 40 KPa compared to those on 1 kPa substrate. The latter represents normal tissue stiffness of colon.

overall_design: CAFs were grown on polyacrylamide hydrogel (PA gel) substrates of 1 kPa, 10 kPa and 40 kPa elastic modulus. Fibronectin coating were applied on the substrates. Cell were also grown on plastic dish that has an elastic modulus of 3.4 GPa. After 48 hrs of culture, RNA was extracted using Trizol reagent and then processed for RNAseq.

first: Bashar

last: Emon

first: You

first: Prasanth

middle: K

last: Kannanganattu

first: M


title: Iron-overloaded follicular fluid increases the risk of endometriosis-related infertility by triggering granulosa cell ferroptosis and oocyte dysmaturity [miRNA-seq]

city: Shanghai

first: Yangshuo

last: Li

address: 168 Changhai Road

institute: Navy Medical University

summary: To explore the differences of miRNAs from exosomes of granulosa cell in different groups, we extracted exosomes from mouse granulosa cells intervened by different reagents.

overall_design: Mouse granulosa cells were acclimated in DMEM / F12 without exosomes for 24 h, and then subjected to different interventions. No special treatment was provided to the control group (CON). The ferric citrate (FAC) group was treated with 100 μM ferric citrate. The deferoxamine mesylate (DFO) group was treated with ferric citrate (100 μM) and deferoxamine mesylate (100 μM). VE group was treated with ferric citrate (100 μM) and VITE (200 μM). All groups were cultured for 48 h. After termination of incubation, centrifugation was carried out in steps at 4 °C and 300 ×g for 10 min to remove cells and 3 000 ×g for 10 min to remove large cell debris. After centrifugation at 10 000 ×g for 40 min, the supernatant was filtered through a 0.22 μM PVDF filter (Millipore, USA). Finally, centrifugation at 100 000 ×g for 90 min, the supernatant was removed and resuspended in 200 μL of PBS to obtain the cell supernatant exosomes precipitation.The integrity was confirmed using Agilent 2100 TapeStation (Agilent). Small RNA sequencing was conducted using Illumina HiSeq 2500 with read lengths of 15–41 bp.

first: Zhexin

last: Ni

first: Chaoqin

last: Yu


title: Chronic chemogenetic activation of the superior colliculus in glaucomatous mice: local and retrograde molecular signature

city: Leuven

first: Lieve

last: Moons

state: Vlaams-Brabant

address: Naamsestraat 61

department: Biology

country: Belgium

institute: KU Leuven

summary: One important facet of the glaucoma pathology is axonal damage, which ultimately disrupts the connection between the retina and its postsynaptic targets. The concurrent loss of retrograde support interferes with the functionality and survival of the retinal ganglion cells (RGCs). Con-versely, previous research has shown that stimulation of neuronal activity in a primary retinal target area—i.e., the superior colliculus— promotes RGC survival in an acute mouse model of glaucoma. To build further on this observation, we applied repeated chemogenetics in the superior colliculus of a more chronic model of glaucoma—i.e., the microbead occlusion model—and per-formed bulk RNA sequencing on collicular lysates and isolated RGCs. Our study revealed that chronic target stimulation upon glaucomatous injury phenocopies the a priori expected molecular response: growth factors were pinpointed as essential transcriptional regulators both in the locally stimulated tissue and in distant, unstimulated RGCs. Strikingly, and although the RGC tran-scriptome revealed an enrichment of pro-survival signaling pathways, functional rescue of injured RGCs was not achieved.

overall_design: In this experiment, we FACsorted retinal ganglion cells and collected lysates of superior colliculi of adult mice (+- 10 weeks old). Per tissue, 10-11 biological samples were used per experimental groups. Experimental groups included sham mice, mice subjected to ocular hypertension (microbead occlusion model), mice subjected to chronic DREADD (hM3Dq) stimulation in the colliculus and mice subjected to ocular hypertension and chronic DREADD stimulation in the colliculus. Libraries for the RGC samples were prepared with SmarSeq2, collicular samples with Lexogen Quantseq.

first: Marie

last: Claes

first: Alvaro

last: Cortés-Calabuig


title: A novel strategy for regulating mRNA’s degradation via interfering the AUF1’s binding to mRNA [RIP-seq]

city: Guangzhou

first: KUNTAO

last: LI

address: College of Pharmacy, Sun Yat-sen University, Panyu District, Guangzhou city, Guangdong Province

institute: Sun Yan-Sen University

summary:
Purpose: To verify the relationship between AUF1 and tumor cells proliferation, we detected the function of AUF1 in Hela cells using RIP-seq analysis.
Methods: Genomic alignment (version from UCSC genome browser) was using Tophat (version:2.0.13) to get uniquely mapping reads. p value <0.05 considered as significantly modulated, were retained for further analysis. This choice is motivated by the decision to maximize the sensitivity of this analysis, in order to perform a massive screening and identify candidate genes to be validated with a wider sample population with real-time PCR analysis
Results: The quantity of gene expression was calculated by FPKM (Fragments Per Kilobase of transcript per Million fragments mapped).50% of the binding region of AUF1 was in the exon region, and others were mainly in the 3’-UTR regions (29.6%). AUF1’s targeted genes were related to metabolic and single-organism processes. AUF1’s targeted genes were mainly concentrated in the protein synthesis process of the endoplasmic reticulum and cancer pathway.
Conclusions: AUF1 might be involved in the regulation of translation and participated in the regulation of tumorigenesis and development through its target genes.

overall_design: Fragment of RNA binding to AUF1 antibody in Hela cells

first: Zhi-Yin

last: Sun

first: Kun-Tao


title: A novel strategy for regulating mRNA's degradation via interfering the AUF1's binding to mRNA


title: Iron-overloaded follicular fluid increases the risk of endometriosis-related infertility by triggering granulosa cell ferroptosis and oocyte dysmaturity

summary: To investigate the different function of endometriosis-related infertile patients follicular fluid (EMFF) and follicular fluid in control group (COFF), follicular fluid was collected and used for RNA sequencing.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for follicular fluid in endometriosis-related infertile patients and in control group.

first: Di


title: Severe infection constitutively upregulates TIMP1 in the bone marrow hematopoietic niche to support long-term enhanced myelopoiesis

city: Manhasset

first: Yong-Rui

last: Zou

address: 350 Community Drive

department: The Institute of Molecular Medicine

institute: Feinstein Institutes for Medical Research

summary: Infection is able to elicit innate immunological memory by enhancing a long-term myeloid output even after the inciting infectious agent has been cleared. However, mechanisms underlying such a regulation are not fully understood. Using a mouse polymicrobial peritonitis (sepsis) model, we show that severe infection leads to increased, sustained myelopoiesis after the infection is resolved. The infection experience is imprinted in the bone marrow (BM) stromal cells, in the form of a constitutive upregulation of the tissue inhibitor of metalloproteinases 1 (TIMP1). TIMP1 antagonizes the function of ADAM10, an essential cleavage enzyme for the activation of Notch which in turn suppresses myelopoiesis. While TIMP1 is dispensable for myelopoiesis under the steady state, increased TIMP1 enhances myelopoiesis post infection. Thus, our data reveal that infection could establish an inflammatory memory in the BM niche to support a long-term enhanced output of innate immune cells.

overall_design: Adult C57BL/6 mice were subjected to sham or cecal ligation and puncture (CLP) surgery. At week 12 after surgery, lineage marker-negative Kit+ Sca1+ (LSK) hematopoietic stem and progenitor cells were sorted for scRNA-seq.

first: Tengfei


title: Long-term high-fat high-fructose diet induces type 2 diabetes in rats through oxidative stress

first: Yue

last: Zhao

address: No. 1 Dahua Road, Beijing 100730, China

institute: Beijing Hospital

summary: Long-term consumption of a western diet is a major cause of type 2 diabetes mellitus (T2DM). However, the effects of diet on pancreatic structure and function remain unclear. Rats fed a high-fat, high-fructose (HFHF) diet were compared with rats fed a normal diet for 3 and 18 months. Plasma biochemical parameters and inflammatory factors were used to reflect metabolic profile and in-flammatory status. The rats developed metabolic disorders, and the size of the islets in the pancreas increased after three months of HFHF treatment but decreased and became irregular after 18 months. Fasting insulin, C-peptide, proinsulin, and intact proinsulin levels were significantly higher in the HFHF group than those in the age-matched controls. Plasma oxidative parameters and nucleic acid oxidation markers (8-oxo-Gsn and 8-oxo-dGsn) elevated before inflammatory factors, suggesting that the HFHF diet increased the degree of oxidative stress before affecting in-flammation. Single-cell RNA sequencing also verified that the transcriptional level of oxidoreduc-tase changed differently in islet sub-populations with aging and long-term HFHF diet. We demonstrated that long-term HFHF diet and aging-associated structural and transcriptomic changes that underlie pancreatic islet functional decay is a possible underlying mechanism of T2DM, and our study could provide new insights to prevent the development of diet-induced T2DM

overall_design: Pancreatic cells of two Wistar rats per group (aged 2 months, high-fat high fructose diet and normal diet groups after 18 months of feeding) were subjected to scRNA-seq.

first: QingYu

last: Wang

first: JianPing

last: Cai


title: Endometriotic Organoids: A Novel In Vitro Model of Endometriotic Lesion Development

first: Gregory

last: Burns

summary: The development and progression of endometriotic lesions are poorly understood, but immune cell dysfunction and inflammation are closely associated with the pathophysiology of endometriosis. A lack of suitable 3D in vitro models permitting the study of interactions between cell types and the microenvironment is a contributing factor. To address this limitation, we developed endometriotic organoids (EO) to explore the role of epithelial-stromal interactions and model peritoneal cell invasion associated with lesion development. Using a non-adherent microwell culture system, spherical organoids were generated with endometriotic epithelial cells (12Z) combined with immortalized endometriotic stromal cells (iEc-ESC) or immortalized uterine stromal cells (iHUF). Organoids self-organized with stromal cells occupying the center and epithelial cells on the periphery of the organoid. Endometriotic organoids (EO), containing iEc-ESC, resulted in the development of stratified 12Z epithelial cells compared to those with iHUF where the 12Z cells developed as a single layered epithelium. Transcriptomic analysis found 4,522 differentially expressed genes (DEG) between EO and 12Z/iHUF organoids, and the top DEG included increased expression of interleukins and prostaglandin synthase enzymes. An overlap of the EO DEG with baboon endometriotic lesions was highly significant. Finally, to mimic invasion of endometrial tissue into the peritoneum, a model was developed using EO and extracellular matrix containing human peritoneal mesothelial cells (LP9). Invasion of EO into the extracellular matrix-LP9 layer was increased in presence of estrogen or THP1-derived proinflammatory macrophages. Taken together, our results strongly support the concept that EO are an appropriate model for dissecting mechanisms that contribute to endometriotic lesion development.

overall_design: We completed RNA-sequencing of organoids containing ectopic stromal and epithelial cell lines (iEc-ESC/12Z) and compared the profile to normal stromal and ectopic epithelial organoids (iHUF/12Z) to identify the effect of ectopic stromal cells on the organoids.

first: Yong

last: Song

first: Niraj

last: Joshi

first: Ripla

last: Arora

first: J

last: Kim

first: Asgerally


title: METTL18-mediated histidine methylation on RPL3 modulates translation elongation for proteostasis maintenance.

city: Bunkyo-ku

first: Eriko

last: Matsuura

state: Tokyo

address: Yayoi

department: IQB

country: Japan

institute: The University of Tokyo

summary: Protein methylation occurs predominantly on lysine and arginine residues, but histidine also serves as a substrate for the modification. However, a limited number of enzymes responsible for this modification have been reported. Moreover, the biological role of histidine methylation has remained poorly understood. Here, we report that human METTL18 is a histidine methyltransferase for the ribosomal protein RPL3 and that the modification specifically slows ribosome traverse on tyrosine codons, allowing the proper folding of synthesized proteins. By performing an in vitro methylation assay with a methyl donor analog and quantitative mass spectrometry, we found that His245 of RPL3 is methylated at the τ-N position by METTL18. Structural comparison of the modified and unmodified ribosomes showed stoichiometric modification and suggested a role in translation tuning. Indeed, genome-wide ribosome profiling revealed suppressed ribosomal translocation at tyrosine codons by RPL3 methylation. Because the slower elongation provides enough time for nascent protein folding, RPL3 methylation protects cells from the cellular aggregation of Tyr-rich proteins. Our results reveal histidine methylation as an example of a “ribosome code” that ensures proteome integrity in cells.

overall_design: Ribosome profiling

last: Matsuura-Suzuki


title: scRNAseq of RA and PsA patient synovial tissue single cell suspensions

city: DUBLIN, IRELAND

first: Achilleas

last: Floudas

address: Pearse street 152 - 160

country: Ireland

institute: Trinity Biomedical Sciences Institu

summary: To investigate the cell composition and cell-cell interaction in RA and PsA patient inflamed joints

overall_design: Following arthrotsopic surgery, single cell suspension of ~15 biopsies per patient were generated. 4 RA and 5 PsA synovial tissue samples are analysed.


title: Understanding the underlying molecular mechanisms of meiotic arrest in organotypic culture of prepubertal rat testicular tissues

city: Rennes

first: Frédéric

last: Chalmel

state: France

address: 9 avenue du Pr. Léon Bernard

department: Physiology and physiopathology of the urogenital tract

country: France

institute: Inserm U1085-Irset

summary: We report the use of the Bulk RNA-sequencing technology on in vivo and in vitro cultured prepubertal testicular tissues. The goal of this study is to identify the origin of the maturation arrest observed in rat prepubertal testicular tissue cultured with the organ culture system with a transcriptomic approach. We compared the gene expression of 14.5 dpp rat testicular tissues cultured up to 6, 16, 22 and 28 days. The statistical filtration revealed 600 differentially expressed genes showing significant differential abundances in all three comparisons. This study uncovered for the first time several mechanisms that could explain the meiotic arrest observed in cultures of rat prepubertal testicular tissues.

overall_design: Testicular mRNA profiles of 14.5 day old rat and 6, 16, 22 and 28 days cultured tissues

first: Justine

last: Saulnier


title: Single-cell RNA Sequencing of Human Esophageal Epithelium in Homeostasis and Allergic Inflammation

city: Cincinnati

first: Hee-Woong

last: Lim

state: Ohio

address: 3333 Burnet Ave. MLC 7024

department: Division of Biomedical Informatics

institute: Cincinnati Children's Hospital Medical Center

summary: To investigate gene expression signature of the human esophageal epithelium at the homeostatic and inflammatory conditions we performed scRNAseq on the human  esophageal biopsies obtained from the healhy patients, patients with active eosinophilic esophagitis (EoE) and patients in the remission.

overall_design: Esophageal biopsies from obtained from the healhy patients, patients with active EoE and patients in the remission were collected, processed to generate single cell suspension and subjected to 10X scRNAseq

first: Mark

last: Rochman

first: Ting

last: Wen

first: Marc

last: Rothenberg


title: Bulk RNA Sequencing of Human Esophageal Epithelium in Homeostasis and Allergic Inflammation

summary: To investigate gene expression signature of the human esophageal epithelium we performed FACS sorting of the basal and the suprabasal layers from the esophageal biopsies based on the expression of podoplanin and E-cadherin.

overall_design: We then performed bulk RNA sequencing on gene expression analysis of the basal (podoplanin high) and the suprabasal (podoplanin low) populations


title: Comprehensive identification of RNA transcripts and construction of RNA networks in chronic obstructive pulmonary disease

city: Hefei

first: Dahai

last: Zhao

state: Anhui

address: Furong Road, 678

department: Respiratory and Critical Care Medicine

institute: The Second Affiliated Hospital, Anhui Medical University

summary: Here, we report a comprehensive analysis of dysregulated mRNAs, lncRNAs, miRNAs and circRNAs in peripheral blood of COPD patients with high-throughput RNA sequencing. We mapped about 50~80 million sequence reads per sample to the human genome. GSEA analysis showed that these dysregulated RNAs correlate with several critical biological processes such as RNA modification, and RNA metabolism. RT-qPCR (SYBR Green assays) with more clinical COPD samples were used for the validation of some dysregulated RNAs. We have also constructed the co-expression network between lncRNA and mRNA, and established the circRNA-miRNA-mRNA in CAC based on this data. This study provides valuable insights to understand the RNA involvement and regulation in COPD, assisting future COPD investigations.

overall_design: Examination of mRNAs, lncRNAs, miRNAs and circRNAs in peripheral blood of COPD patients

first: Yucong


title: A novel strategy for regulating mRNA’s degradation via interfering the AUF1’s binding to mRNA [RNA-seq]

first: KUNTAO

last: LI

summary:
Purpose:To explore how JNJ-7706621 affected the cellular processes and the possible relationship between AUF1 functions, we analyzed global transcriptome alterations of SK-MEL-2 cells at certain time points (48 h) after JNJ-7706621 treatment using RNA-seq analysis.
Methods: Differential expression analysis for mRNA was performed using R package edgeR. Differentially expressed RNAs with |log2(FC)| value >1 and q value <0.05, considered as significantly modulated, were retained for further analysis. This choice is motivated by the decision to maximize the sensitivity of this analysis, in order to perform a massive screening and identify candidate genes to be validated with a wider sample population with real-time PCR analysis
Results: The quantity of gene expression was calculated by FPKM (Fragments Per Kilobase of transcript per Million fragments mapped). Genes with log2 (Fold change) >1 and P value < 0.05 were considered as differentially expressed genes (DEGs).  There were 146 upregulated genes and 158 downregulated genes for a total of 304 DEGs that were results are shown in Fig. 8A. Furthermore, the enriched KEGG pathways were analyzed and the top 30 pathways involved in these 304 DEGs between the two groups are shown in Figure SI. Among the top 30 pathways, 9 pathways related to mitochondrial function had significant effects. 37 DEGs in KEGG pathway associated with mitochondrial function was conducted and analyzed.
Conclusions: 70% gene was up-regulated by  JNJ-7706621 and up-regulated genes mainly affect cancer and inflammatory factors according the RNA-seq analysis

overall_design: mRNA profiles of SK-MEL-2 cells (ctrl) and SK-MEL-2 cells (treated by JNJ-7706621)

first: Kun-Tao

last: Li


title: A plant-specific splicing factor RS33 regulates abiotic stress responses in rice

city: Jeddah

first: Haroon

last: Butt

state: Makkah

address: King Abdullah University of Science and Technology (KAUST) Thuwal, 23955-6900

department: BESE

country: Saudi Arabia

institute: KAUST

summary: Here, we investigated the function of the plant-specific SR protein RS33 in pre-mRNA splicing regulation and abiotic stress responses in rice. The loss-of-function mutant, rs33, showed increased sensitivity to salt and low-temperature stress. Genome-wide analyses of gene expression and splicing in seedlings subjected to these stresses identified multiple splice isoforms from stress-responsive genes dependent on RS33. The number of RS33-regulated genes is much higher under low-temperature stress as compared to salt stress. Our results suggest that this plant-specific splicing factor plays crucial and distinct roles during plant adaptation to abiotic stresses.

overall_design: 7-day-old seedlings of rs33 mutant, and WT are treated for 3hours and 6hours with 200mM NaCl, 4ºC and mock treatments.

first: Jeremie

last: Bazin

first: Kasavajhala

middle: V

last: Prasad

first: Martin

last: Crespi

first: Anireddy

middle: S

last: Reddy

first: Magdy

last: Mahfouz


title: lncRNA SCIRT in hypoxia/reoxygenation.

city: Zhanjiang

first: Zhe

last: Hu

state: Guangdong

address: 57 Renmin Avenue South, Xiashan District

institute: Guangdong Medical University

summary: To know effects of long noncoding RNA (lncRNA) SCIRT in hypoxia/reoxygenation (H/R). We compared expression profiles of human umbilical vein endothelial cells (HUVECs) under normal condition, H/R condition without SCIRT knockdown, and H/R condition with SCIRT knockdown.

overall_design: Two biological replicates from each condition were used for comparison.

first: Jihong

last: Yang


title: Differential mRNA Expression Profiling Reveals the Role of MiR-375 in Inflammation of Bovine Mammary Epithelial Cells

city: Yinchuan

first: Xing-Ping

last: Wang

state: Ningxia

address: No. 489, Helan Shanxi Road, Xixia District

department: College of animal science and technology

institute: Ningxia University

summary: Purpose: to detect expression profile of differentially expressed mRNAs during bovine mammary epithelial cells (MAC-T) transfected with miR-375 inhibitor or negative control (NC) inhibitor in vitro.  Methods: bovine mammary epithelial cells were transfected with miR-375 inhibitor or negative control (NC) inhibitor to assess the expression profiles of mRNAs using RNA-seq.  Results:  silencing miR-375 down-regulated and upregulated the expression of 48 and 15 mRNAs, respectively, in bovine mammary epithelial cells.  Conclusion: miR-375 silencing dysregulated the expression of 63 mRNAs in bMECs. Also, miR-375 silencing increased the expression of NR4A1 and PTPN5 genes, all anti-inflammatory genes, via the MAPK signaling pathway. Given the negative correlation between miR-375 expression and NR4A1 and PTPN5 genes, miR-375 potentially promotes inflammation in the mammary gland through the MAPK signaling pathway. The findings of this study provide a new perspective of treating mastitis in cows.

overall_design: Bovine mammary epithelial cells were seeded and cultured in 6-well plates. When the cells reached 60-70% confluence, they were transfected with miR-375 or negative control (NC) (final concentration 100nM). The experiment was performed in triplicate. Subsequently, all samples were used to perform the RNA-seq.

first: Yu-Hang

first: Qi-Chao

first: Zhuo-Ma

last: Luoreng

first: Jian

first: Yun

last: Ma

first: Da-Wei

last: Wei


title: Differential Expression of Calcium Channels and Signaling Pathways in Hematologic Cancers

city: Vancouver BC

first: Christian

last: Steidl

state: British Columbia

address: 675, West 10th Ave

department: Department of Lymphoid Cancer Research

country: Canada

institute: BC Cancer

summary: Cell surface calcium (Ca2+) channels permit Ca2+ ion influx, with Ca2+ taking part in cellular functions such as proliferation, survival, and activation. The expression of voltage-dependent Ca2+ (CaV) channels may modulate the growth of hematologic cancers. Profile analysis of Ca2+ channels, with a focus on the L-type CaV channels, was performed on RNA sequencing data from lymphoma and leukemia cell lines and samples derived from patients with diffuse large B cell lymphoma (DLBCL). CaV1.2 expression was found to be elevated in classical Hodgkin lymphoma (CHL) cell lines when compared to other B cell lymphoma cell lines. In our analysis comparing activated B cell-like DLBCL (ABC-DLBCL) and germinal centre B cell-like DLBCL (GCB-DLBCL) patient samples, ABC-DLBCL revealed stronger expression of CaV1.3, whereas CaV1.1, CaV1.2, and CaV1.4 showed greater expression levels in GCB-DLBCL. As Ca2+ is known to bind to calmodulin, leading to calcineurin activation and the passage of nuclear factor of activated T cells (NFAT) to the cell nucleus, pathways for calcineurin, calmodulin, NFAT, and Ca2+ signaling were also analyzed by gene set enrichment analysis. The NFAT and Ca2+ signaling pathways were found to be upregulated in the CHL cell lines relative to other B cell lymphoma cell lines. Furthermore, the calmodulin and Ca2+ signaling pathways were shown to be downregulated in the ABC-DLBCL patient samples. The findings of this study suggest that L-type CaV channels and Ca2+-related pathways could serve as differentiating components for biologic therapies to target hematological cancers.

overall_design: RNASeq analysis of 44 cell lines derived from lymphoma samples.

first: Shawna

last: Stanwood

first: Lauren

last: Chong

first: Wilfred

last: Jefferies


title: miRNA-200b - A potential biomarker identified in a porcine model of cardiogenic shock and mechanical unloading

city: Birmingham

first: Sayan

last: Bakshi

state: Alabama

department: Department of Pathology

institute: University of Alabama at Birmingham

summary:
Cardiogenic shock (CS) alters whole body metabolism and circulating biomarkers serve as prognostic markers in CS patients. Percutaneous ventricular assist devices (pVADs) unload the left ventricle by actively ejecting blood into the aorta. The goal of the present study was to identify alterations in circulating metabolites and transcripts in a large animal model that might serve as potential prognostic biomarkers in acute CS and additional left ventricular unloading by Impella® pVAD support.
Methods: CS was induced in a preclinical large animal model by injecting microspheres into the left coronary artery system in six pigs. After the induction of CS, mechanical pVAD support was implemented for 30 minutes total. Serum samples were collected under basal conditions, after the onset of CS, and following additional pVAD unloading. Circulating metabolites were determined by metabolomic analysis, circulating RNA entities by RNA sequencing.
Results: CS and additional pVAD support alter the abundance of circulating metabolites involved in Aminoacyl-tRNA biosynthesis and amino acid metabolism. RNA sequencing revealed decreased abundance of the hypoxia sensitive miRNA-200b following the induction of CS, which was reversed following pVAD support.
Conclusions: The hypoxamir miRNA-200b is a potential circulating marker that is repressed in CS and is restored following pVAD support. The early transcriptional response with increased miRNA-200b expression following only 30 minutes of pVAD support suggests that mechanical unloading alters whole body metabolism. Future studies are required to delineate the impact of serum miRNA-200b levels as a prognostic marker in patients with acute CS and pVAD unloading.

overall_design: Circulating RNA expression profiles of pigs under basal conditions, after the onset of CS, and following additional pVAD unloading.

last: Riehle


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Adar1 B Cell Conditional Knockout Activated B Cells Transcriptomes

city: Shenzhen

first: Yuxing

last: Li

address: No. 1088 Xueyuan Avenue

institute: Southern University of Science and Technology

summary:
Purpose: to compare the gene expression differences between wild-type activated B cells and Adar1 knockout activated B cells
Methods: In vitro activated B cells were sorted using a BD FACSAira sorter, and total RNA was extracted using RNeasy Mini Kit (Qiagen) and poly(A) mRNA was isolated with the poly(A) mRNA Magnetic Isolation Module (NEB). Libraries were prepared using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB) and sequenced on an Illumina Hiseq instrument (Illumina). Sequence reads were filtrated using Cutadapt (V1.9.1), and then mapped to the reference genome sequences (GRCm38.98) using Hisat2 (V2.0.1).

overall_design: Mouse splenic B cells from wild-type and Adar1 B cell conditional knockout mice were purified using anti-CD43 microbeads and cultured 36 hours at the concentration of 2 million cells per ml in DMEM medium supplemented with 10% FBS, 1% penicillin/streptomycin, 1% non-essential amino acids, 1 μg/ml anti-CD40 and 10 μg/ml anti-IgM at 37℃ with 5% CO2.

first: Xijun

last: Ou


title: Cohesin-dependent chromosome loop extrusion is limited by transcription and stalled replication forks [RNA-seq]

first: Ryuichiro

last: Nakato

address: 1-1-1 Yayoi

department: Institute for Quantitative Biosciences

summary: Genome function depends on regulated chromosome folding, and loop extrusion by the protein complex cohesin is essential for this multilayered organization. The chromosomal positioning of cohesin is controlled by transcription, and the complex also localizes to stalled replication forks. However, the role of transcription and replication in chromosome looping remains unclear. Here, we show that reduction of chromosome-bound RNA polymerase weakens normal cohesin loop extrusion boundaries, allowing cohesin to form new long-range chromosome cis interactions. Stress response genes activated by transcription inhibition are also shown to act as new loop extrusion boundaries. Furthermore, cohesin loop extrusion during early S-phase is jointly controlled by transcription and replication units. Together, the results reveal that replication and transcription machineries are chromosome folding regulators that block the progression of loop-extruding cohesin, opening for new perspectives on cohesin’s roles in genome function and stability.

overall_design: Spike-in RNA-seq of G2/M-arrested, untreated and thiolutin-treated wild type Saccharomyces cerevisiae cells.

first: Kristian

last: Jeppsson

first: Toyonori

last: Sakata

first: Stefina

last: Milanova

first: Katsuhiko

last: Shirahige

first: Camilla

last: Björkegren


title: Peritoneal Metastases from Colorectal Cancer belong to Consensus Molecular Subtype 4 and are sensitized to oxaliplatin by inhibiting reducing capacity

city: Utrecht

first: Onno

last: Kranenburg

address: Heidelberglaan 100

institute: UMC Utrecht

summary:
Background: Peritoneal metastases (PM) in colorectal cancer (CRC) are associated with therapy resistance and poor survival. Oxaliplatin monotherapy is widely applied in the intraperitoneal treatment of PM, but fails to yield clinical benefit. We aimed to identify the mechanism(s) underlying PM resistance to oxaliplatin and to develop strategies overcoming such resistance.
Experimental design:  We generated a biobank consisting of 35 primary tumor regions and 59 paired PM from 12 patients. All samples were analyzed by RNA sequencing. We also generated a series of PM-derived organoid (PMDO) cultures and used these to design and test strategies to overcome resistance to oxaliplatin
Results: PM displayed various hallmarks of aggressive CRC biology. The vast majority of PM and paired primary tumors belonged to the Consensus Molecular Subtype 4 (CMS4). PMDO cultures were resistant to oxaliplatin and expressed high levels of glutamate-cysteine ligase (GCLC) causing detoxification of oxaliplatin through glutathione synthesis. Genetic or pharmacological targeting of GCLC sensitized PMDOs to a 1-hour exposure to oxaliplatin, through increased platinum-DNA adduct formation
Conclusions: These results link oxaliplatin resistance of colorectal PM to their CMS4 status and high reducing capacity. Inhibiting the reducing capacity of PM may be an effective strategy to overcome PM resistance to oxaliplatin

overall_design: RNA sequncing of 113 snap frozen tissue samples of primary tumor and metastasis

first: Jamila

last: Laoukili

first: Alexander

last: Constantinides

first: Emma

last: Wassenaar

first: Djamila

last: Boerma


title: RNAseq of irradiated and non-irradiated hemichordate larvae and juveniles

city: Pacific Grove

first: Christopher

last: Lowe

address: 120 Oceanview Bvld

institute: Hopkins Marine Station of Stanford University

summary: To further characterize the molecular characteristics of proliferative cells in Schizocardium californicum, we exploited the sensitivity of proliferative cells to irradiation. To do this, we treated larvae and juveniles with irradiation. Three days after treatment animals looked morphologically the same as controls, but EdU incorporation was eliminated in both larvae and juveniles. We extracted total RNA from this same stage of three days post-irradiation from 5 pooled individuals in three independent biological replicates and made RNA sequencing libraries.

overall_design: 5 individuals at each stage, larva or juvenile, were treated with 120gy and 200gy respectively. RNA was extracted for three biological replicates.

first: Paul

last: Bump


title: Alveolar basal cells differentiate towards secretory epithelial and aberrant basaloid cells in vitro

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel

summary: We performed a single-cell transcriptome analysis of alveolar basal cells from peripheral lung tissue of patients with idiopathic pulmonary fibrosis (IPF), cultured in DMEM or Cnt-PR-A growth medium.

overall_design:
Single-cell suspensions were generated from cells from cultured peripheral lung tissue biopsies from 3 IPF patients grown for 5 days in DMEM groth medium. An additional cell suspension from one of the IPF patients originates from cells transferred from DMEM to Cnt-PR-A growth medium for 5 additional days. The 4 cell suspensions were loaded on separate wells of a 10X Genomics Chromium Single Cell Controller on 2 different batches.

**RAW data not provided due to lack of patient consent**

first: Petra

last: Khan

first: Katrin

last: Hostettler

first: Julien

last: Roux


title: EPAJ: Effect of mares' parity and age

city: PALAISEAU

first: Emilie

last: Derisoud

state: Essonne

address: 26 Rue des Prés,

institute: INRAE

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

overall_design: Refer to individual Series


title: Triple-helix potential of the mouse genome

city: Kyoto

first: Shintaro

last: Yamada

state: --- Select a state ---

address: Yoshida Konoe, Sakyo-ku

department: Graduate School of Medicine

institute: Kyoto University

summary: Certain DNA sequences, including mirror-symmetric polypyrimidine/polypurine runs, are capable of folding into a triple-helix-containing non-B-form DNA structure called H-DNA. Such H-DNA-forming sequences are frequent in many eukaryotic genomes, including in mammals, and multiple lines of evidence indicate that these motifs are mutagenic and can impinge on DNA replication, transcription, and other aspects of genome function. In this study, we show that the triplex-forming potential of H-DNA motifs in the mouse genome can be evaluated using S1-sequencing (S1-seq), which uses the single-stranded DNA (ssDNA)-specific nuclease S1 to generate deep-sequencing libraries that report on the position of ssDNA throughout the genome. When S1-seq was applied to genomic DNA isolated from mouse testis cells and splenic B cells, we observed prominent clusters of S1-seq reads that appeared to be independent of endogenous double-strand breaks, that coincided with H-DNA motifs, and that correlated strongly with the triplex-forming potential of the motifs. Fine-scale patterns of S1-seq reads, including a pronounced strand asymmetry in favor of centrally-positioned reads on the pyrimidine-containing strand, suggested that this S1-seq signal is specific for one of the four possible isomers of H-DNA (H-y5). By leveraging the abundance and complexity of naturally occurring H-DNA motifs across the mouse genome, we further defined how polypyrimidine repeat length and the presence of repeat-interrupting substitutions modify the structure of H-DNA. This study provides a new approach for studying DNA secondary structure genome wide at high spatial resolution.

overall_design: Detection of single-stranded DNA in the genome in mouse testis cells and B cells

first: Kaku

last: Maekawa

first: Rahul

last: Sharma

first: Jayanta

last: Chaudhuri

first: Scott

last: Keeney


title: MicroRNA-3622 family at 8q21 locus exerts oncogenic effects by regulating the p53-downstream gene network in prostate cancer progression

first: Lizhong

last: Wang

address: 740 20th St S

institute: UAB

summary: The chromosome 8q21 locus, which contains NKX3.1 and microRNA (miR)-3622 family (miR-3622a/b), is a frequently deleted region in human prostate cancer. Thus, miR-3622 is proposed as a tumor suppressor in various cancers, including prostate cancer, but its role remains debatable. In the present study, we found that mature miR-3622b-3p expression was higher in human prostate cancer than in normal prostate, while expression of miR-3622a was downregulated in human prostate cancer. Also, miR-3622b-3p facelifted cell proliferation, migration and invasion, whereas miR-3622a-3p inhibited cell migration and invasion but not proliferation in human prostate cancer cells. To address the role of miR-3622 locus, we knockout (KO) endogenous miR-3622, including both miR-3622a/b, in various human prostate cancer cell lines. Our data showed that miR-3622 KO reduced cell proliferation, migration, and invasion in vitro and tumor growth and metastasis in vivo. Functional analysis revealed that miR-3622 regulated p53 downstream gene network, including p21, c-MYC, and AIFM2, to control the cell cycle and apoptosis. Furthermore, using CRISPR interference, miRNA/mRNA immunoprecipitation assay, and dual-luciferase assay, we identified AIFM2, a direct target gene of miR-3622b-3p, that is responsible for miR-3622 KO-induced apoptosis. Also, we established a miR-3622-AIFM2 axis that contributes to oncogenic function during tumor progression. In addition, miR-3622 KO inhibited the epithelial-mesenchymal transition via upregulation of vimentin involved in prostate cancer metastasis. Our results suggest that miR-3622b-3p is overexpressed in human prostate cancer and plays an oncogenic role in tumor progression and metastasis via repression of p53 signaling, especially through a miR-3622-AIFM2 axis. On the other hand, deletion of miR-3622 at 8q21 locus in human prostate cancer may reduce oncogenic effects on tumor progression and metastasis.

overall_design: total RNA expression by deep-sequencing in LNCaP sorted for different levels of miR-3622 family activity

first: Runhua

last: Liu


title: Inflammation associated gene expression in the mammary gland of lactating mothers who delivered preterm and were randomly assigned to DHA supplementation.

first: Rebekah

last: Karns

state: OH

address: 3333 Burnet Ave

department: Gastroenterology, Hepatology, & Nutrition

summary:
Background: This is a transcriptome analysis of specimens obtained from a randomized trial of lactating mothers assigned to 200mg/day DHA, STD or 1000mg/day DHA, EXP.
Methods: High quality extracellular mammary epithelial cell mRNA was isolated from fresh milk fat and submitted for RNA-sequencing in n=6 EXP and n=4 STD samples.
Results: There were 409 DEG. In the EXP group, up-regulation of inflammation-inbibiting genes was seen and down-regulation of pro-inflammatory genes. Ontological analysis revealed 5 clusters of up-regulated gene sets in the EXP group, including immune regulation and management of oxidative stress associated clusters.
Conclusion: Findings reveal that increased DHA supplementation during lactation can modulate the expression of inflammation-associated genes within the mammary gland.

overall_design: RNA-seq of mammary epithelial cell mRNA isolated from fresh milk fat globule.

first: Joselyn

last: Adams

first: Christina

last: Valentine

first: Lynette

last: Rogers

first: Masahiko

last: Murase

first: Grace

last: Fowler

first: Laurie

last: Nommsen-Rivers


title: lncRNA and mRNA expression of HUVECs under H/R and normal conditions

first: Zhe

last: Hu

summary:
To have a global view of transcriptional change of hypoxia/reoxygenation (H/R) condition compared with normal condition, we collected human umbilical vein endothelial cells (HUVECs) from both conditions.
The expression profiles of HUVECs were detected by microarray, and two conditions were compared to detect significantly changed lncRNAs and mRNAs.

overall_design: Three biological replicates from each condition were used for comparing H/R vs control condition.

first: Jihong

last: Yang


title: Tumor FAK Orchestrates Immunosuppression in Ovarian Cancer via the CD155/TIGIT axis

city: La Jolla

first: Duygu

last: Ozmadenci

state: CA

address: Moores Cancer Center 3855 Health Sciences Drive

department: OBGYN

institute: UC San Diego

summary:
An immune profiling of  cells recovered from the peritoneal cavity of mice seeded with KMF ovarian cancer cells with FAK knockout reconstituted with FAK or a kinase dead FAK
An immune profiling of  cells recovered from the peritoneal cavity of mice seeded with KMF ovarian cancer cells with FAK kockout reconstituted with FAK, then treated with FAKi VS4716 (100mg/kg) or vehicle by gavage twice daily.

overall_design: In the study presented here, a panel of 770 genes was evaluated by Nanostring Immune Profiling on cells isolated from the peritoneal cavity of mice 21 days after being seeded with the KMF cells listed above.

first: Dwayne

last: Stupack

first: David

last: Schlaepfer


title: Ccr4-Not complex reduces transcription efficiency in heterochromatin

city: Memphis

first: Mario

last: Halic

state: Tennessee

address: 262 Danny Thomas Place

department: Structural Biology

institute: St. Jude Children’s Research Hospital

summary: Heterochromatic silencing is thought to occur through a combination of transcriptional silencing and RNA degradation, but the relative contribution of each pathway is not known. In this study we analyzed RNA Polymerase II (RNA Pol II) occupancy and levels of nascent and steady-state RNA in different strains of fission yeast, in order to quantify the contribution of each pathway to heterochromatic silencing. We found that transcriptional silencing consists of two components, reduced RNA Pol II accessibility and, unexpectedly, reduced transcriptional efficiency. Heterochromatic loci showed lower transcriptional output compared to euchromatic loci, despite the presence of comparable amounts of RNA Pol II in both types of regions. We determined that the Ccr4-Not complex and H3K9 methylation are required for reduced transcriptional efficiency in heterochromatin and that a subset of heterochromatic RNA is degraded more rapidly than euchromatic RNA. Finally, we quantified the contribution of different chromatin modifiers, RNAi and RNA degradation to each silencing pathway. Our data show that several pathways contribute to heterochromatic silencing in a locus-specific manner and reveal transcriptional efficiency as a new mechanism of silencing.

overall_design: pA-RNA , total-RNA, ChIP and RIP sequencing in wild type cells and different mutants of S.pombe with at least two replicates per condition.

first: Pablo

last: Monteagudo

first: Cornelia

last: Brönner

first: Parastou

last: Kohvaei

first: Haris

last: Amedi

first: Stefan

last: Canzar


title: Nucleome programming is required for the foundation of totipotency in mammalian germline development [ATAC-Seq]

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

institute: Kyoto University, Graduate school of medicine

summary: Germ cells are unique in engendering totipotency, yet the mechanisms underlying this capacity remain elusive. Here, we perform comprehensive and in-depth nucleome analysis of mouse germ-cell development in vitro, encompassing pluripotent precursors, primordial germ cells (PGCs) before and after epigenetic reprogramming, and spermatogonia/spermatogonial stem cells (SSCs). Although epigenetic reprogramming, including genome-wide DNA de-methylation, creates broadly open chromatin with abundant enhancer-like signatures, the augmented chromatin insulation safeguards transcriptional fidelity. These insulatory constraints are then erased en masse for spermatogonial development. Notably, despite distinguishing epigenetic programming, including global DNA re-methylation, the PGCs-to-spermatogonia/SSCs development entails further euchromatization. This accompanies substantial erasure of lamina-associated domains, generating spermatogonia/SSCs with a minimal peripheral attachment of chromatin except for pericentromeres—an architecture conserved in primates. Accordingly, faulty nucleome maturation, including persistent insulation and improper euchromatization, leads to impaired spermatogenic potential. Given that PGCs after epigenetic reprogramming serve as oogenic progenitors as well, our findings elucidate a principle for the nucleome programming that creates gametogenic progenitors in both sexes, defining a basis for nuclear totipotency.

overall_design: Nucleome profiling of various cell types along murine germ-cell development using ATAC-seq

first: Masahiro

last: Nagano

first: Bo

first: Shihori

last: Yokobayashi

first: Akitoshi

last: Yamamura

first: Fumiya

last: Umemura

first: Mariel

last: Coradin

first: Hiroshi

last: Ohta

first: Yukiko

last: Ishikura

first: Ikuhiro

last: Okamoto

first: Hiroki

last: Ikeda

first: Naofumi

last: Kawahira

first: Yoshiaki

last: Nosaka

first: Sakura

last: Shimizu

first: Yoji

last: Kojima

first: Ken

last: Mizuta

first: Tomoko

last: Kasahara

first: Yusuke

last: Imoto

first: Killian

last: Meehan

first: Roman

last: Stocsits

first: Gordana

last: Wutz

first: Yasuaki

last: Hiraoka

first: Yasuhiro

last: Murakawa

first: Takuya

last: Yamamoto

first: Kikue

last: Tachibana

first: Jan-Michel

last: Peters

first: Leonid

last: Mirny

first: Benjamin

last: Garcia

first: Jacek

last: Majewski

first: Mitinori

last: Saitou


title: Nucleome programming is required for the foundation of totipotency in mammalian germline development [NET-CAGE]

first: Yukihiro

last: Yabuta

overall_design: Nucleome profiling of various cell types along murine germ-cell development using NET-CAGE

first: Masahiro

last: Nagano

first: Bo

last: Hu

first: Shihori

last: Yokobayashi

first: Akitoshi

last: Yamamura

first: Fumiya

last: Umemura

first: Mariel

last: Coradin

first: Hiroshi

last: Ohta

first: Yukiko

last: Ishikura

first: Ikuhiro

last: Okamoto

first: Hiroki

last: Ikeda

first: Naofumi

last: Kawahira

first: Yoshiaki

last: Nosaka

first: Sakura

last: Shimizu


title: Targeting metabolic adaptations in the breast cancer–liver metastatic niche using dietary approaches to improve endocrine therapy efficacy

city: Urbana

first: Zeynep

last: Madak Erdogan

state: IL

address: 1201 S Goodwin Ave

department: FSHN

institute: UIUC

summary: Estrogen receptor-positive (ER+) metastatic tumors contribute to nearly 70% of breast cancer-related deaths. Most patients with ER+ metastatic breast cancer (MBC) undergo treatment with the estrogen receptor agonist fulvestrant (Fulv) as standard of care. Yet, among such patients, metastasis in liver is associated with reduced overall survival compared to other metastasis sites. The factors underlying the reduced responsiveness of liver metastases to ER agonists remain unknown, impeding the development of more effective treatment approaches to improve outcomes for patients with ER+ liver metastases. We therefore evaluated site-specific changes in MBC cells and determined the mechanisms through which the liver metastatic niche specifically influences ER+ tumor metabolism and drug resistance. We characterized ER activity of MBC cells both in vitro, using a novel system of tissue-specific extracellular matrix hydrogels representing the stroma of ER+ tumor metastatic sites (liver, bone), and in vivo, in liver and lung metastasis mouse models. ER+ metastatic liver tumors and MBC cells grown in liver hydrogels displayed upregulated expression of glucose metabolism enzymes in response to Fulv. Furthermore, differential ERαERα activity, but not expression, was detected in liver hydrogels. In vivo, increased glucose metabolism led to increased glycogen deposition in liver metastatic tumors, while a fasting-mimicking diet increased efficacy of Fulv treatment to reduce the metastatic burden. Our findings identify a novel mechanism of endocrine resistance driven by the liver tumor microenvironment. These results may guide the development of dietary strategies to circumvent drug resistance in liver metastasis, with potential applicability in other metastatic diseases.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: In this study, we focused on tumor-intrinsic metabolic mechanisms that arise specifically in the liver metastatic niche. We used tissue-specific hydrogels to partially mimic metastatic niches and liver-specific cell line xenograft (CLX) models to delineate ER+ MBC metabolic adaptations in a liver metastatic tissue context. We used metabolomics, flux analysis, transcriptomics, and cistromics to associate metabolic pathway changes with ER activity.

last: Madak-Erdogan

first: Qianying

last: Zuo

first: Yu-Jeh

last: Liu


title: Population genomics of variegated toad-headed lizard Phrynocephalus versicolor and its adaptation to the colorful sand of the Gobi Desert

city: Berkeley

first: Diana

last: Aguilar Gomez

address: 4th floor VLSB, University of California Berkeley

department: Center for Computational Biology

institute: University of California Berkeley

summary: Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of melanic variation. The goals of this study are to  evaluate population evolutionary genetics associated with dark and light color variation in a lizard.

overall_design: RNA for from different tisues of the ssmple female was extracted to generate a comprehensive transcriptome. Additionally 3 individuals from melanic population HSK were sequenced to be compared in differential expression analysis against non-melanic population GZ

first: Yuanting

last: Jin

last: Aguilar-Gómez

first: Débora

last: Brandt

first: Rasmus

last: Nielsen


title: Nucleome programming is required for the foundation of totipotency in mammalian germline development

first: Yukihiro

last: Yabuta


title: Nucleome programming is required for the foundation of totipotency in mammalian germline development [ChIP-Seq]

overall_design: Nucleome profiling of various cell types along murine germ-cell development using ChIP-seq against histone modifications, transcription factors, and architectural proteins

first: Masahiro

last: Nagano

first: Bo

last: Hu

first: Shihori

last: Yokobayashi

first: Akitoshi

last: Yamamura

first: Fumiya

last: Umemura

last: Coradin

last: Ohta

first: Yoji

last: Kojima

first: Ken

last: Mizuta

first: Tomoko

last: Kasahara

first: Yusuke

last: Imoto

first: Killian

last: Meehan

first: Roman

last: Stocsits

first: Gordana

last: Wutz

first: Yasuaki

last: Hiraoka

first: Yasuhiro

last: Murakawa

first: Takuya

last: Yamamoto

first: Kikue

last: Tachibana

first: Jan-Michel

last: Peters

first: Leonid

last: Mirny

first: Benjamin

last: Garcia

first: Jacek

last: Majewski

first: Mitinori

last: Saitou


title: The balance between protective and pathogenic immune responses to pneumonia in the neonatal lung enforced by the gut microbiota

city: Cincinnati

first: Hitesh

last: Deshmukh

address: 3333 Burnet Ave.

department: Neonatology and Pulmonary Biology

institute: Cincinnati Childrens Hospital Medical Center

summary: Although modern clinical practices such as cesarean sections and perinatal antibiotics have improved infant survival, treatment with broad-spectrum antibiotics alters intestinal microbiota and causes dysbiosis. Infants exposed to perinatal antibiotics have an increased likelihood of life-threatening infections, including pneumonia. Here, we investigated how the gut microbiota sculpt pulmonary immune responses, promoting recovery and resolution of infection in newborn rhesus macaques. Early-life antibiotic exposure interrupted the maturation of intestinal commensal bacteria and disrupted the developmental trajectory of the pulmonary immune system, as assessed by single-cell proteomic and transcriptomic analyses. Early-life antibiotic exposure rendered newborn macaques more susceptible to bacterial pneumonia, concurrent with increases in neutrophil senescence and hyperinflammation, broad inflammatory cytokine signaling, and macrophage dysfunction. This pathogenic reprogramming of pulmonary immunity was further reflected by a hyperinflammatory signature in all pulmonary immune cell subsets coupled with a global loss of tissue-protective, homeostatic pathways in the lungs of dysbiotic newborns. Fecal microbiota transfer was associated with partial correction of the broad immune maladaptations and protection against severe pneumonia. These data demonstrate the importance of intestinal microbiota in programming pulmonary immunity and support the idea that gut microbiota promote the balance between pathways driving tissue repair and inflammatory responses associated with clinical recovery from infection in infants. Our results highlight a potential role for microbial transfer for immune support in these at-risk infants.

overall_design: scRNAseq of pulmonary immune (CD326-CD31-CD45+) cells in antibiotic-treated, no-antibiotic-control-, and fecal-transplant neonatal rhesus macaques after infection with Streptococcus pneumoniae; plus, pulmonary immune cells from control neonatal rhesus macaque (No ABX, no infection).

first: Joseph

last: Stevens


title: METTL18-mediated histidine methylation on RPL3 modulates translation elongation for proteostasis maintenance

city: Bunkyo-ku

first: Eriko

last: Matsuura

state: Tokyo

address: Yayoi

department: IQB

institute: The University of Tokyo

summary: In addition to predominant protein methylation on lysine and arginine residues, histidine also serves as a substrate for the modification. However, a limited number of enzymes responsible for this modification has been reported. Moreover, the biological mission of the histidine methylation has remained poorly understood. Here, we reported that human METTL18 is a histidine methyltransferase for ribosomal protein RPL3 and that the modification specifically slows ribosome traverse on tyrosine codons, allowing proper folding of synthesized proteins. Harnessing in vitro methylation assay with methyl-donor analogue and quantitative mass spectrometry, we identified that His245 of RPL3 is methylated at τ-N position by METTL18. Structural comparison of the modified and unmodified ribosomes showed the stoichiometric modification and suggested its role in translation tuning. Indeed, genome-wide ribosome profiling revealed the suppressed ribosomal translocation at tyrosine codons by RPL3 methylation. Because the slower elongation provides enough time for nascent protein folding, RPL3 methylation protects cells from cellular aggregation of Tyr-rich proteins. Our results reveal histidine methylation as an example of “ribosome code”, which ensures proteome integrity in cells.

overall_design: Ribosome profiling

last: Matsuura-Suzuki


title: A Mesenchymal Tumor Cell State Confers Increased Dependency on the Bcl-xL Anti-apoptotic Protein in Kidney Cancer

city: Cleveland

first: Treg

last: Grubb

email: grubbt@ccf.org, grubbt4@ccf.org

address: 9500 Euclid Avenue

department: Cancer Biology

institute: Cleveland Clinic Foundation

summary: Genome-wide genetic screens have identified cellular dependencies in many cancers. Using Novartis’ DRIVE and the Broad Institute’s Achilles shRNA screening datasets, we mined for targetable dependencies in kidney lineage cancer cells. Our studies identified a dependency, preferentially in kidney cancer cells versus cells of other lineages, on the BCL2L1 gene, which encodes the Bcl-xL anti-apoptotic protein. Genetic and pharmacological inactivation of Bcl-xL, but not its paralog BCL2, led to fitness defects in renal cancer cells, and also sensitized them to chemotherapeutics. Expression levels of Bcl-xL, VHL status, and p53 mutation status were insufficient to predict Bcl-xL dependence. Instead, analyzing the transcriptional hallmarks of response to Bcl-xL blockade identified an elevated mesenchymal cell state signature in Bcl-xL dependent lines. Functional studies to address if these cell state differences drive Bcl-xL dependence showed that maintaining mesenchymal characteristics was necessary to confer sensitivity to Bcl-xL loss; and, conversely, that promoting mesenchymal transition was sufficient to increase sensitivity to Bcl-xL inhibition in resistant cells. This mesenchymal signature was also observed in almost a third of human renal tumors, and is associated with worse clinical outcomes. Detachment from an organized epithelium incites protective apoptotic responses in normal cells (e.g. anoikis); however, our findings suggest that, in mesenchymal kidney cancer cells Bcl-xL activity counteracts this protective mechanism and enables tumor cell survival. Altogether, our studies uncover an unexpected link between cellular cell state and dependence on anti-apoptotic proteins, and justify the use of Bcl-xL blockade to target a clinically aggressive subset of human kidney cancers.

overall_design: A498, CAKI2, OSRC2, and UMRC2 cells were transcriptionally profiled at baseline (untreated) and following acute treatment with the Bcl-xl inhibitor, A-1331852. Profiling was performed in duplicate for a total of 16 samples.

first: Smruthi

last: Maganti

first: Abhishek

last: Chakraborty


title: A simple strategy effectively improves glucose homeostasis and prevents loss of islet beta cells in diabetic mice

city: Shanghai

first: Yan

last: Chen

address: 320 Yueyang Road

department: Shanghai Institute of Nutrition and Health

institute: Chinese Academy of Sciences

summary: Single cell sequencing revealed that the composition of islets cells were changed significantly in db/db mice, indicating diet intervention can shape islets cells and restore the function of endocrine cells in pancreases islets.

overall_design: Examination of pancreas islets cells  in 4 different groups of mice.

first: Siying

last: Wei


title: Cabozantinib enhances anti-PD1 efficacy and elicits a neutrophil-based immune response in murine models: implications for human HCC II

city: Barcelona

first: Roger

last: Esteban-Fabró

state: Barcelona

address: Rosselló, 149-153

country: Spain

institute: IDIBAPS

summary: Background & Aims: Immune checkpoint inhibitors combined with anti-angiogenic agents produces benefits in the treatment of advanced hepatocellular carcinoma (HCC). We investigated the efficacy and immunomodulatory activity of cabozantinib alone and combined with anti-PD1 in experimental models of HCC, and explored the potential target population that might benefit from this combination. Approach & Results: C57BL/6J mice bearing subcutaneous Hepa1-6 or Hep53.4 tumours received cabozantinib, anti-PD1, their combination or placebo. Tumour and blood samples were analysed by flow cytometry, immunohistochemistry, transcriptome and cytokine profiling. Cabozantinib-related effects were validated in a colorectal cancer PDX model. Transcriptomic data from three human HCC cohorts (Cohort 1: n=167, Cohort 2: n=57, TCGA: n=319) were used to cluster patients according to neutrophil features, and assess their impact on survival. The combination of cabozantinib and anti-PD1 showed increased anti-tumour efficacy compared to monotherapy and placebo (P<0.05). Cabozantinib alone significantly increased neutrophil infiltration and reduced CD8+PD1+ T cell proportions in the tumour, while the combination with anti-PD1 further stimulated both effects and significantly decreased T regulatory cell infiltration (all P<0.05). In blood, cabozantinib and especially combination increased the proportions of overall T cells (P<0.01) and memory/effector T cells (P<0.05), while lowering the neutrophil-to-lymphocyte ratio (P<0.001 for combination). Unsupervised clustering of human HCCs revealed that high tumour enrichment in neutrophil features observed with the treatment combination was linked to less proliferative phenotypes, and well-differentiated HCC with better prognosis. Neutrophil recruitment in both humans and mice was linked to CXCR2 ligands and CXCL12 (P<0.05). Conclusions: Cabozantinib in combination with anti-PD1 enhanced anti-tumour immunity by bringing together innate neutrophil-driven and adaptive immune responses, a mechanism of action which favours this approach for the treatment of HCC.

overall_design: C57BL/6 mice bearing subcutaneous HCC tumours were randomly assigned to receive a) Placebo; b) Cabozantinib; c) Anti-PD1; or d) Combination of cabozantinib with anti-PD1. Animals were culled at day 14 and tumours were extracted and processed for the transcriptomic assessment through a microarray platform.

first: Josep

last: Llovet

first: Catherine

last: Willoughby


title: Maternal age affects D8 embryo gene expression both in trophoblast and inner cell

first: Emilie

last: Derisoud

summary: The aim of the study was to compare the effects of maternal age on embryos in horses. For that, 11 embryos were collected at 8 days post ovulation (expanded blastocyst stage) from 2 groups of multiparous mares of different age: 5 from young mares (<10 years old) and 6 from old mares (10-17 years old).  Embryos collected were cut in 2 parts: one hemi-embryo containing pure trophoblast and the other one containing trophoblast + inner cell mass. ARN extractions were performed for all samples using PicoPure RNA isolation kit (Applied Biosystem). Five nanograms of both parts of each embryo were sequenced in paired-end with a length of 30-50bp separately using Illumina NextSeq 500 High. Data were trimmed using Cutadapt. Sequences with less than 10bp were removed.

overall_design: 11 embryos cut in ICM and TE parts analyzed according to maternal age (Old or young mares)

first: Luc

last: Jouneau

first: Cédric

last: Dubois

last: Archilla

first: Yann

last: Jaszczyszyn

first: Rachel

last: Legendre

first: Nathalie

last: Daniel

last: Peynot

first: Michele

last: Dahirel

first: Laurence

last: Wimel

first: Véronique

last: Duranthon

first: Pascale

last: Chavatte-Palmer


title: Cell type inference in human lung tissue by domain adaptation of single-cell and spatial transcriptomic data

city: Seoul

first: Hongyoon

last: Choi

address: 101, Daehak-ro, Jongno-gu

department: Department of Nuclear Medicine

country: South Korea

institute: Seoul National University Hospital

summary: We developed a method, CellDART, which estimates the spatial distribution of cells defined by single-cell level data using domain adaptation of neural networks, and applied to the spatial mapping of human lung tissue. The neural network that predicts the cell proportion in a pseudospot, a virtual mixture of cells from single-cell data, is translated to decompose the cell types in each spatial barcoded region. CellDART elucidated the cell type predominance defined by the human lung cell atlas across the human lung tissue compartments and it corresponded to the known prevalent cell types.

overall_design: Two normal lung samples were acquired from lung specimen from one patient who underwent surgical resection for lung cancer. The samples were cryosectioned and processed for Visium Spatial Transcritpomic analysis.

first: Kwon

first: Young

last: Kim


title: Cohesin-dependent chromosome loop extrusion is limited by transcription and stalled replication forks [ChIP-seq]

first: Ryuichiro

last: Nakato

address: 1-1-1 Yayoi

summary: Genome function depends on regulated chromosome folding, and loop extrusion by the protein complex cohesin is essential for this multilayered organization. The chromosomal positioning of cohesin is controlled by transcription, and the complex also localizes to stalled replication forks. However, the role of transcription and replication in chromosome looping remains unclear. Here, we show that reduction of chromosome-bound RNA polymerase weakens normal cohesin loop extrusion boundaries, allowing cohesin to form new long-range chromosome cis interactions. Stress response genes activated by transcription inhibition are also shown to act as new loop extrusion boundaries. Furthermore, cohesin loop extrusion during early S-phase is jointly controlled by transcription and replication units. Together, the results reveal that replication and transcription machineries are chromosome folding regulators that block the progression of loop-extruding cohesin, opening for new perspectives on cohesin’s roles in genome function and stability.

overall_design: Analysis of cohesin and RNA pol II chromosome association by ChIP-seq in Saccharomyces cerevisiae cells

first: Kristian

last: Jeppsson

first: Toyonori

last: Sakata

first: Stefina

last: Milanova

first: Katsuhiko

last: Shirahige

first: Camilla

last: Björkegren


title: Study of transcriptional effects of FOXS1 silencing and TGF-beta treatment in SNU-449 hepatocellular carcinoma cell line

city: Rennes

first: Cedric

last: Coulouarn

address: CLCC Eugène Marquis, Rue de la Bataille Flandres Dunkerque, Bat D, 1er étage

institute: INSERM

summary: Background & aims: Transforming Growth Factor beta (TGFβ) is a pleiotropic cytokine which controls fundamental cellular processes associated with tumor onset and progression. In hepatocellular carcinoma (HCC), we previously highlighted TGFβ signatures recapitulating its functional duality (i.e. cytostatic versus pro-metastatic features) to discriminate patients with good and poor prognosis. Here, we aimed at characterizing Forkhead Box S1 (FOXS1), a predicted transcription factor that we hypothesize to mediate pro-metastatic properties of TGFβ. Methods: FOXS1 expression was profiled in well-characterized HCC cell lines. Transient loss of function of FOXS1 (siRNA) was combined with functional assays and analysis of epithelial-mesenchymal transition (EMT) markers by western blot and immunofluorescence. Clinical relevance of FOXS1 was determined by integrative genomics. Results: Our data show that FOXS1 is a novel canonical SMAD-dependent TGFβ target. Its expression correlates with a mesenchymal phenotype. FOXS1 mediates pro-metastatic properties of TGFβ by inducing EMT and cell migration. In human HCC, FOXS1 correlates with VIM expression and is highly expressed in specific molecular subtypes associated with a poorer differentiation and no CTNNB1 mutation. FOXS1 expression predicts a poor prognosis (e.g. reduced patient survival) in liver, colon, stomach and kidney cancer. Conclusions: FOXS1 is a novel TGFβ target and a key mediator of EMT. Its induction in cancer is associated with a poor prognosis. Thus, determining the expression of FOXS1 in advanced tumors in which the pro-metastatic arm of TGFβ is activated could help to identify patients who may benefit from targeted therapies using TGFβ inhibitors.

overall_design: SNU-449 cells (ATCC® CRL-2234, grade II-III/IV)  were grown in a MEM medium (Sigma, M2279) supplemented with 100U/ml penicillin, 100μg/ml streptomycin (Gibco, 15070-063), 2mM L-Gluta and 10% fetal bovine serum (HyClone). Cultures were performed at 37°C in a 5% CO2 atmosphere. Overnight serum starvation was performed before each treatment. Cells were treated with 1ng/mL recombinant human TGFβ1 (R&D system, Minneapolis, USA) versus BSA control for 72hrs. FOXS1 loss of function was performed by using two different small interfering RNAs (siRNA) purchased from Ambion: siFOXS1#1 (s5256, 5’-AAUCGGCCCAUGAUGUAGCgg-3’) and siFOXS1#2 (s107325, 5’-CAUGCAAAAAUUCAGUGCCgg-3’). FAM-labeled negative control siRNA No.1 (Ambion AM4620) was used as control (siNC). Cells were transfected at 70% confluency with 50nM siRNA using lipofectamine RNAiMAX reagent and Opti-MEM medium according to manufacturer’s instructions (Invitrogen). Experiments were performed in triplicates.


title: Global analysis reveals large scale dynamics of protein-RNA interaction and RNA secondary structure characteristics of Physcomitrella patens ABA response  (mRNA)

city: Philadelphia

first: Mengge

last: Shan

state: PA

address: 433 South University Avenue

department: Biology

institute: University of Pennylsvania

summary: Eukaryotic RNA molecules undergo multiple regulatory steps prior to being translated as proteins. Two features of post-transcriptional regulation are RNA secondary structure and RNA-binding protein (RBP) interactions with mRNAs. Here we reveal the global landscape of RBP-RNA interactions the bryophyte Physcomitrella patens undergoes as part of its response to the phytohormone abscisic acid (ABA). We show that P. patens undergoes large scale shifts in RNA secondary structure and RBP-RNA interactions as well as identify sites of RBP-RNA interaction and describe enriched motifs, among which are two purine rich sequences. We further elucidate the collection of proteins that bind to these sequences, among which are P. patens cold shock containing proteins. Together, the data suggest that P. patens undergoes a large-scale change in RNA secondary structure and RBP binding as a response to ABA and also identifies CSPs as well as several other proteins as possible regulators of that response.

overall_design: mRNA-seq of 2 biological replicates of P. patens protonema treated with 10 uM ABA for 0, 30, or 60 minutes

first: Matthew

last: Willmann

first: Brian

middle: D

last: Gregory


title: WTAP-mediated m6A modification profiling in human nasopharyngeal carcinoma cell lines

city: Guangzhou

first: Zhi-Xuan

last: Li

address: No. 651 Dongfeng east road, Yuexiu district, Guangzhou

institute: Sun Yat-sen University Cancer Center

summary: N(6)-methyladenosine (m6A) plays an important role in the tumorigenesis and progression of cancers. However, the clinical significance of m6A and their regulatory mechanisms in nasopharyngeal carcinogenesis (NPC) remain largely unknown. In this study, we used the microarray analysis to study WTAP-mediated m6A modification profiles in human nasopharyngeal carcinoma cell line, HONE-1, by comparing 3 pairs of samples with or without WTAP knockdown.

overall_design: RNA before and after m6A immunoprecipitation from 3 pairs of scrambled control or WTAP-silencing HONE-1 NPC cells were used to acquire different expression profiles of m6A modification and mRNA. In this way, this study provided the basis for further studying the roles and functions of WTAP-mediated m6A modification in NPC.

first: Zi-Qi

last: Zheng

first: Ying

last: Sun


title: Next Generation Sequencing Facilitates Quantitative Analysis of different developmental stage pEGFP-N1 injected zebrafish embryos and untreated group transcriptomes

city: Nanjing

state: Jiangsu

address: No.12, Xuefu Road

institute: Qingshun Zhao

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare the early stage of pEGFP-N1 injected zebrafish embros transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis
Methods: we injected the plasmid pEGFP-N1 into zebrafish zygotes by microinjection, and then when the embryos to develop to 1 hour-post-fertilization (hpf), 6 hpf and 12 hpf, these groups was collected respectively by deep sequencing, in triplicate, using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays
Results: Bioinformatics analysis of the transcriptome sequencing found that the expression levels of genes related to the apoptosis process (Fig.1A), endogenous immune response and tumor necrosis factor-mediated signaling pathways were abnormal up-regulation, mainly including isg15, foxo3b, phlda3, cdkn1a, zgc:136826, and si:dkey-204l11.1, compared with the non-injected group at 6hpf. These genes are found in somatic cells to deal with foreign plasmids invasion.

overall_design: Zebrafish embryos in 1hpf, 6hpf and 12hpf mRNA profiles of pEGFP-N1 injected and untreated group

first: Qingshun

last: Zhao

first: Dongya

last: Jiang

first: Yunyun

last: Yue

first: Luqingiqing

last: He

first: Shuang

last: Wang

first: YunFeng

last: Zhang


title: Global analysis reveals large scale dynamics of protein-RNA interaction and RNA secondary structure characteristics of Physcomitrella patens ABA response  (PIP-Seq)

overall_design: 2 replicates per timepoint of protein interaction profile sequencing (PIP-seq) in P. patens protonema after 00, 30, or 60 minutes of 10 uM ABA treatment. Each rep is crosslinked with formaldehyde and split into structure-only and protein-bound libraries and then further split based on RNAse treatment (i.e. ssRNAse or dsRNAse)


title: Single-cell RNA Sequencing Facilitates Quantitative Analysis of  Fbxw11 overexpressed hematopoietic stem/progenitor cells

city: Tianjin

first: Lina

address: 288 nanjing Road

institute: institute of blood disease

summary: We compared the transcriptomic changes in hematopoietic stem/progenitor cells (LSK) when Fbxw11 overexpressed.  In order to study the function of Fbxw11 in hematopoietic stem/progenitor cells.

overall_design: Hematopoietic stem/progenitor cells were infected with Fbxw11 expressed lentivirus, and compare the transcriptomics changes at single cell level

first: Guoguang

first: Yongjun

last: Piao


title: Cohesin-dependent chromosome loop extrusion is limited by transcription and stalled replication forks [Hi-C]

first: Ryuichiro

last: Nakato

overall_design: Analysis of chromosome conformation by Hi-C in Saccharomyces cerevisiae cells.

first: Kristian

last: Jeppsson

first: Toyonori

last: Sakata

first: Stefina

last: Milanova

first: Katsuhiko

first: Camilla


title: Anti CD20 increases PD-L1 protein expression in a cell line of primary mediastinal B cell lymphoma through immunogenetic and micro RNA signaling

status: Public on Jun 14 2022

city: Syracuse

first: Frank

last: Middleton

state: NY

address: 505 Irving Avenue

department: Neuroscience and Physiology

institute: SUNY Upstate Medical Univ

summary: Cell lines of mediastinal lymphomas, one each of primary mediastinal (thymic) large B cell lymphoma (PMBL), classic Hodgkin lymphoma (CHL), B-cell lymphoma, unclassifiable, with features intermediate between diffuse large B-cell lymphoma and CHL, and T-cell lymphoma were treated with rituximab (RmAb), brentuximab vedotin (BV), ibrutinib (IBR), prednisone (PRED) or untreated (UT) for 48 hours. Flow cytometry for PD-L1 protein was performed, and differential expression (DE) analysis of mRNA and miRNA performed by RNAseq. B-cell lines exhibited 2- fold increase in PD-L1 protein (p<.05) with RmAb compared to UT. Others showed no effect of RmAb, however, the T-cell line showed 2-fold increase on treatment with BV (P<.05). DE performed by limma showed no genomic level changes. ANOVA analysis of PMBL treated with RmAb, however, showed physiologic level DE involving >3000 genes involving multiple pathways associated with cell death and survival, protein degradation, mRNA translation, mRNA degradation, immunologic functions, and PD-1/PD-L1 immunotherapy. In the B cell lines, DE of CD274 (PD-L1) was decreased or not significant. MiRNA DE showed upregulation of 7 miRNAs, including miR-155-5p.

overall_design: Multiple cell lines were treated with rituximab (RmAb), brentuximab vedotin (BV), ibrutinib (IBR), and prednisone(PRED) prior to differential expression (DE) analysis of mRNA and miRNA performed by bulk RNAseq.

first: Robert

last: Hutchison

first: Karen

last: Gentile


title: Effect of c-Jun on gene expression of bone metastatic luminal breast cancer cell line

city: Tokyo

first: Yuxuan

last: Han

address: 2-2 Wakamatsu-cho, Shinjuku-ku

department: department of advanced science and engineering

institute: Waseda Univ.

summary:
To investigate the function c-Jun in the regulation of  bone metastasis, we established MCF7-BM02-TAM67 cell lines in which expressed dominant negative c-Jun
We then performed gene expression profiling analysis using data obtained from RNA-seq of 3 different cells

overall_design: Comparative gene expression profiling analysis of RNA-seq data for MCF7 bone metastatic cells and its c-Jun deficient derivatives (TAM67).