title: Impact of SOCS1 inactivation on Marilyn adoptive cell transfer in MB49 female C57BL/6 bearing mice

summary: In vivo, the expansion of antigen experienced CD4+ T cells is limited by intrinsic factors. Using an in vivo genome-wide CRISPR-Cas9 screen, we identified SOCS1 as a major non-redundant checkpoint imposing a brake on antigen experienced CD4+ T-cell proliferation upon antigen challenge. Although SOCS1 has been previously described as an inhibitor of CD8+ T-cell effector function, we highlight here that it is abrogating the CD4+ T-cell response. SOCS1 integrates several cytokines receptor signals to actively silence TCR-induced polycytokine signaling pathways, restraining CD4+ T cell proliferation and functions. Targeting SOCS1 in mouse and human CD4+ and CD8+ T cells improved the therapeutic efficacy of antitumor adoptive T-cell therapies, enhancing intra-tumor T cell accumulation, persistence and effector functions. SOCS1 deletion in CAR-T cells enhances CD4+ CAR T-cell proliferation/survival and polyfunctionality in vivo, promoting long term rejection of established tumors. These findings identify SOCS1 as a major intracellular checkpoint inhibitor of re-stimulated CD4+ T cells, opening new possibilities to optimize adoptive T cell therapies.

overall_design: Female C57BL6 mice bearing MB49 male bladder tumors were adoptively transferred with Marilyn Mock or Marilyn sgSOCS1. Marilyn CD4 T cells were extracted from draining lymph node at day 7 after transfer


title: Molecular Signatures of HFpEF: Systems Biology in a Cardiac-Centric Large Animal Model

status: Public on Sep 01 2021

city: Philadelphia

first: Andrew

last: Gibb

state: PA

address: 3500 N. Broad St.

country: USA

institute: Temple University

type: Expression profiling by high throughput sequencing

summary: In this study the authors used systems biology to define progressive changes in metabolism and transcription in a large animal model of heart failure with preserved ejection fraction (HFpEF). Transcriptomic analysis of cardiac tissue, 1 month post-banding, revealed loss of electron transport chain components, and this was supported by changes in metabolism and mitochondrial function, altogether signifying alterations in oxidative metabolism. Established HFpEF, 4 months post-banding, resulted in changes in intermediary metabolism with normalized mitochondrial function. Mitochondrial dysfunction and energetic deficiencies were noted in skeletal muscle at early and late phases of disease, suggesting cardiac-derived signaling contributes to peripheral tissue maladaptation in HFpEF. Collectively, these results provide insights into the cellular biology underlying HFpEF progression.

overall_design: Examination of overall changes during the progression of HFpEF in feline model

middle: A

first: Emma

middle: K

last: Murray

first: John

middle: W

last: Elrod


title: Expression data from mouse kidney intraperitoneally administered with LPS and Stx

city: Fukushima

first: Yohei

last: Kume

state: Fukushima

address: 1, Hikarigaoka

department: Pediatrics

country: Japan

institute: Fukushima Medical University

summary: Mice intraperitoneally administered with LPS and Stx exhibit HUS-like pathology. While mouse and human Gb3 localization is different, LPS and  Stx induced kidney injury models in mice have been used to confirm responsiveness to various stx-related inflammatory pathways and treatments. In order for this mouse model to apply tHUS in humans, more detailed and exhaustive comprehension of this animal model is needed. Although molecular studies have been conducted on this mouse model before, we consider that there is still scope for further investigation of molecular pathways and studies on kidney damage segments. Overall, Biological pathways, upstream regulators, and downstream biological activities occurring in the kidney after LPS/Stx administration were identified through Ingenuity Pathway Analysis ™   using the result of microarray. In addition, we identified the detailed damaged site in the renal tubule from the down-regulation gene revealed by microarray.

overall_design: Quality of the RNA was analyzed by a Bioanalyzer 2100.  We performed gene expression microarray analysis of kidney from mice treated with Stx and LPS, and control mice

first: Hayato

last: Go

first: Kazuhide

last: Suyama


title: Impact of SOCS1 inactivation on OT1 adoptive cell transfer in B16-OVA melanoma C57BL/6 bearing mice

status: Public on Sep 02 2021

city: Paris

first: Aurélien

last: Sutra del Galy

address: 26 rue d'Ulm

country: France

institute: Institut Curie

summary: Role of SOCS1 inactivation on OT1 transferred T cells anti-tumor activity in B16-OVA melanoma tumoirs

overall_design: C57BL6 mice bearing B16OVA established melanoma tumors were adoptively transferred with OT1 Mock or OT1 sgSOCS1 and extracted from tumors at day 14 after transfer

first: Laurie

last: Menger

last: Sutra Del Galy


title: Key Super Enhancers Drive Tumor-Suppressing Transcription Feedback Programs in Mature B Cell Cancers

city: Memphis

first: Jared

last: Andrews

state: Tennessee

address: 262 Danny Thomas Pl

department: Developmental Neurobiology

institute: St. Jude Children's Research Hospital

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: Integration of clinical and multi-omics data identifies changes in the composition and activity of autologous-conditioned plasma that correlate with outcomes in patients with knee osteoarthritis

city: New york

first: Yurii

last: Chinenov

state: New York

address: 535 E 71 str, Hospital for Special Surgery

department: Research Division

institute: Hospital for special surgery

summary: Autologous blood-derived products such as platelet-rich plasma (PRP) or autologous-conditioned plasma (ACP) have been used for managing symptoms of knee osteoarthritis (OA); however, the outcomes are highly variable due to limited information about the characteristics of these products, and how they impact clinical responses. We hypothesized that the clinical response ACP in patients with knee OA will correlate with the biologic activity and composition of the ACP administered. To test our hypothesis, we enrolled 51 patients with mild-moderate knee OA.  We collected clinical information at baseline, and patient reported outcomes at 6 weeks and 6 months after ACP injection. We evaluated the composition of ACP by multiplex ELISA, and the biologic activity of the same aliquots using an in vitro biologic assay paired with gene expression analyses. Patients were stratified as responders and non-responders to ACP based on achievement of minimal clinically important differences in patient reported outcomes collected at 6 weeks and 6 months. RNA sequencing revealed that ACP modulates inflammatory responses in a co-culture of macrophages and fibroblast-like synoviocytes (fibroblasts); using this data, we selected specific genes to evaluate the biologic activity of ACP in vitro. Comparison of ACP from responders and non-responders revealed differences in the composition and activity of ACP between these groups.  By integrating clinical and multi-omics data, we uncovered changes in the composition and biologic activity of ACP that may correlate with outcomes in knee OA patients.

overall_design: Macrophages (n=4) and fibroblasts (n=4) were co-cultured in a 0.4 mm polyester trans-well system. The co-cultured cells were left untreated (control, medium) or incubated with 10% v:v of activated ACP, 20ng/ml of recombinant human TNF, or ACP+TNF for an additional 24 hours. At 24 h, RNA was isolated for RNA-seq.

first: Habib

last: Zahir

first: Bijan

last: Dehghani

first: Xiaoning

last: Yuan

first: Christine

last: Kim

first: Alissa

last: Burge

first: Reyna

last: Bandhari

first: Daniel

last: Nemirov

first: Patrick

last: Fava

first: Peter

last: Moley

first: Hollis

last: Potter

first: Joseph

last: Nguyen

first: Brian

last: Halpern

first: Laura

last: Donlin

first: Lionel

last: Ivashkiv

first: Scott

last: Rodeo

first: Miguel

last: Otero


title: Regulation of P53 signaling in breast cancer by the E3 ubiquitin ligase RNF187

city: Xinxiang

first: Ting

last: Zhuang

state: Henan

address: Jinsui Road 601

country: China

institute: Xinxiang Medical University

summary: The tumor suppressor P53 plays critical roles in prohibiting cancer. P53 is rarely mutated and still functional in luminal types of breast cancer. According to current knowledge, wild type P53 function is tightly controlled by post-translational modification, such as ubiquitination. Several ubiquitin ligases were shown to regulate P53 ubiquitination and protein stability. Here, we report RNF187, a RING family ubiquitin ligase, facilitates breast cancer growth and inhibits apoptosis via modulating P53 signaling. RNF187 is elevated in breast cancer and correlates with breast cancer survival only in P53 wild type groups. The bio-informatics analysis shows that RNF187 negatively correlates P53 target gene expression, such as IGFBP3 and FAS in breast cancer. RNF187 depletion inhibits breast cancer growth and facilitates cell death. RNA sequencing analysis indicates that RNF187 could be an important modifier for P53 signaling. Further experiments show that RNF187 interacts with P53 and promotes P53 degradation via facilitating P53 poly-ubiquitination in breast cancer cells. Interesting, the in vitro ubiquitin assay shows that RNF187 could directly ubiquitinate P53, which is independent of MDM2. These finding reveals a novel direct P53 regulator and a potential therapeutic target for breast cancer.

overall_design: Breast cancer cell mRNA samples were summarized in six samples, divided into two groups, siControl and siRNF187

first: Jian

last: Zhu

first: Xin

last: Li

first: Shu

last: Zhuo

first: Zhiguo

last: Niu


title: Impact of SOCS1 inactivation on CAR19 antitumor activity againt Nalm6 ALL (leukemia) in NSG mice

first: Aurélien

last: Sutra del Galy

summary: SOCS1 is a new intracellular checkpoint abrogating CD4 T cells response with translational value in improving CAR T cells therapies

overall_design: NSG mice bearingNalm6-luc leukemia were adoptively transferred with CD4 CAR CD8 CAR Mock orsgSOCS1 and extracted from bone marrow at day 7 and and day 28 after transfer

first: Laurie

last: Menger

last: Sutra Del Galy


title: RNA Sequencing of heart from near term fetuses (E18.5)  of control and obese dams

city: Aurora

first: Amy

last: Kelly

state: Colorado

address: 12700 East 19th Avenue, Mail Stop 8613, P.O. Box 6511

institute: University of Colorado

summary: The study objective was to determine differentially expressed mRNA transcripts in cardiac tissues from E18.5 fetal mice e born to obese dams fed a high fat/high sugar diet and control  dams fed normal diet.

overall_design: Twelve-week-old C57BL/6J female mice were fed either a control diet (D12489, 10% calories from fat) or an obesogenic diet (Western Diet D12089B; Research Diets, 40% of calories from fat). Female mice fed the obesogenic diet had ad libitum access to 20% sucrose solution supplemented with micronutrients. Females were mated following a 25% gain in weight over the initial body weight in the obesogenic diet. All males were fed control diet. At E18.5, animals were euthanized and hearts were flash frozen. Following RNA isolation, RNAseq was performed.

first: Owen

middle: R

last: Vaughan

first: Fredrick

middle: J

last: Rosario

middle: C

last: Cox

first: Jeannie

middle: E

last: Chan

first: Theresa

middle: L

last: Powell

first: Thomas

last: Jansson


title: Transcriptional response by murine microglia in Alzheimer's disease

city: Madison

first: Daniel

last: Shippy

address: 1111 Highland Avenue

institute: UW-Madison

summary: Murine N9 microglial cells were treated with LPS (1µg/ml) for 6 hours. Comparing LPS treated vs. untreated microglial cells will expand upon our previous study comparing the microgial transcriptional reponse from wild-type vs. 5XFAD mice in an effort to further understand the transcriptional response in Alzheimer's disease progression

overall_design: RNA profiles comparing untreated vs. LPS treated microglia

first: Tyler

last: Ulland


title: Ontogeny and function of the circadian clock in intestinal organoids [mouse]

city: Cincinnati

first: Andrew

last: Rosselot

state: OH

address: 231, Albert Sabin way

department: Department of Pharmacology and Systems Biology

institute: University of Cincinnati, College of Medicine

summary: Circadian rhythms regulate diverse aspects of gastrointestinal physiology ranging from the composition of microbiota to motility. However, development of the intestinal circadian clock and detailed molecular mechanisms regulating circadian physiology of the intestine remain largely unknown. The lack of appropriate human model systems that enable organ- and/or diseasespecific interrogation of clock functions is a major obstacle hindering advancements of translational applications using chronotherapy. In this report, we show that both pluripotent stem cell-derived human intestinal organoids engrafted into mice and patient-derived human intestinal enteroids (HIEs) possess robust circadian rhythms, and demonstrate circadian phase-dependent necrotic cell death responses to Clostridium difficile toxin B (TcdB). Intriguingly, mouse and human enteroids demonstrate anti-phasic necrotic cell death responses. RNA-Seq data show ~4% of genes are rhythmically expressed in HIEs. Remarkably, we observe anti-phasic gene expression of Rac1, a small GTPase directly inactivated by TcdB, between mouse and human enteroids. Importantly, the observed circadian time-dependent necrotic cell death response is abolished in both mouse enteroids and human intestinal organoids (HIOs) lacking robust circadian rhythms. Our findings uncover robust functions of circadian rhythms regulating critical clock-controlled genes (CCGs) in human enteroids governing organism-specific, circadian phasedependent necrotic cell death responses. Our data highlight unique differences between mouse and human enteroids, and lay a foundation for human organ- and disease-specific investigation of clock functions using human organoids for translational applications.

overall_design: Mouse enteroids were isolated from the tamoxifen-inducible Bmal1f/f-EsrCRE mouse. Circadian rhythms of Bmal1f/f-EsrCRE enteroids were synchronized using dexamethasone, and 10ng/mL of TcdB was added to the growth media at 24- (D24) and 36-hour (D36) post-dexamethasone treatment.

first: Miri

last: Park

first: Toru

last: Matsu-Ura

first: Gang

last: Wu

first: Danilo

last: Flores

first: Krithika

last: Subramanian

first: Suengwon

last: Lee

first: Nambirajan

last: Sundaram

first: Taylor

last: Broda

first: Heather

last: McCauley

first: Jennifer

last: Hawkins

first: Kashish

last: Chetal

first: Nathan

last: Salomonis

first: Noah

middle: F

last: Shroyer

first: Michael

last: Helmrath

first: James

middle: M

last: Wells

first: John

middle: B

last: Hogenesch

first: Sean

last: Moore

first: Christian

middle: I

last: Hong


title: Gene expression profile of mouse hematopoieitic progenitor cell lines with inducible loss of Ddx41 expression

first: Kwangmin

last: Choi

state: Ohio

address: 333 Burnet Avenue

department: Experimental Hematology & Cancer Biology

institute: Cincinnati Children's Hospital Medical Center

summary: Germline mutations in the RNA Helicase gene DDX41 cause inherited predisposition to Myelodysplastic Syndrome and other myeloid blood malignancies. We characterized the effect of loss of one or both copies of the Ddx41 gene on the gene expression profile of immortalized hematopoietic progenitor cells.

overall_design: To determine the role effect of loss of Ddx41 on hematopoietic progenitor cells, we generated immortalized hematopoietic cell lines from Ddx41-floxed; Rosa-CreERT mice. This approach allows for the inducible deletion of Ddx41 and timecourse analysis of the cellular response to loss of Ddx41. Since loss of both alleles of Ddx41 causes cell death by 72hours post-excision, we characterized the gene expression of the cells at the 48 hour timepoint after induction of Cre activity by treatment with tamoxifen.

first: Timothy

last: Chlon

first: Daniel

middle: T

last: Starczynowski


title: Physical Activity Moderates Inflammatory Gene Expression in Rheumatoid Arthritis

city: San Francisco

first: Marina

last: Sirota

state: CA

address: 490 Illinois St, Floor 2

department: Bakar Computational Health Sciences Institute

institute: UCSF

summary:
Background/Purpose: Prior studies show an independent association between greater physical activity and lower inflammatory markers among adults in the general population, but the impact of physical activity on systemic inflammation in people with rheumatoid arthritis (RA) hasn’t been thoroughly investigated. We therefore aimed to determine whether physical activity behavior associates with differential expression of inflammatory genes in RA.
Methods: Data derive from baseline assessments for a prospective observational cohort of patients with RA. At each study visit, we obtained detailed clinical information, collected peripheral whole blood for subsequent RNA sequencing (RNA-seq), and provided participants with actigraphs (GT9X ActiGraph Link device) to objectively measure physical activity by wearing the device at home for 7 consecutive 24-hour periods. Participants were categorized into three physical activity groups based on the highest (“active”), middle (“intermediate”), and lowest (“inactive”) tertiles for percentage of time spent in moderate/vigorous physical activity (metabolic equivalent (MET) level ≥2.00) across the sample.
Results: There were 35 patients with complete clinical, actigraphy, and transcriptomic data available for analysis. The participants had a mean age of 56 years, were 90% female, and self-reported the following racial/ethnic identities: 32% white, 11% African American, 8% Asian, 40% Hispanic. Participants spent 48%, 41%, and 12% of time awake in sedentary, light, and moderate physical activity, respectively. None of the participants achieved vigorous activity. The patients in the most active group were younger but did not otherwise significantly differ by clinical and demographic characteristics compared to the other physical activity groups. However, in the differential gene expression analysis comparing the highest versus lowest physical activity tertiles, there were 365 up- and 402 down-regulated genes at an adjusted P value < 0.1. Gene set enrichment analysis revealed that the most physically active patients exhibited downregulation of diverse innate and adaptive immune signaling pathways. Assessment of upstream cytokine activation states demonstrated inhibition of type I, II and III interferons and activation of EPO in the highest physical activity tertile patients.
Conclusion: Among a racially and ethnically diverse RA cohort, participants who spent more time in moderately intense physical activity had down-regulation of genes involved in both innate and adaptive immune signaling compared to those who were more sedentary. These findings provide mechanistic evidence to support a disease-modifying effect of physical activity in RA.

overall_design: The most active (top tertile) versus least active (bottom tertile) RA patients were analyzed.

first: Sarah

last: Patterson

first: Shenghuan

last: Sun

first: Dmitry

last: Rychkov

first: Alexandra

last: Tsitsiklis

first: Paula

middle: H

last: Serpa

first: Patricia

last: Katz

first: Charles

last: Langelier


title: Expression data from Arabidopsis plants overexpressing CLE３ in roots

city: Tokyo

first: Dichao

last: Ma

address: 1-1-1 Yayoi, Bunkyo-ku

department: Graduate School of Agricultural and Life Sciences

institute: The University of Tokyo

summary: Plant hormones and small secretory peptides often function as environmental stress mediators. Some recent reports indicate that small secretory peptides, such as CLAVATA3/EMBRYO SURROUNDING REGION-RELATED (CLE), also function as mediators of environmental stimuli. CLE３ is induced in roots by defense elicitor treatment. Plants without functional CLE3 showed compromized defense gene responses in shoots when plant roots were treated with NaSA.  Here, we identified specific genes downstream of CLE3 in roots and shoots with transformed Arabidopsis plants.

overall_design: To identify specific genes downstream of CLE3, GeneChip analyses were performed using roots and shoots separately collected from arabidopsis seedlings, roots of which were treated with estrogen or DMSO for 24h.


title: Genetic responses of metabolically active Limnospira sp. PCC 8005 exposed for one lifecycle to high-dose gamma radiation

city: Mol

first: Mohamed

last: Mysara

state: Belgium

address: Boeretang 200

country: Belgium

institute: Belgian nuclear research center (SCK-CEN)

summary:
Two morphotypes of Limnospira indica (formerly Arthrospira sp.) strain PCC 8005, denoted as P2 (straight trichomes) and P6 (helical trichomes), were subjected to chronic gamma radiation from spent nuclear fuel (SNF) rods at a dose rate of ca. 80 Gy.h-1 for one mass doubling period under continuous light with photoautotrophic metabolism fully active. Samples were taken for post-irradiation growth recovery and RNAseq transcriptional analysis at approximate time in-tervals of 15, 40, and 71.5 hrs corresponding to cumulative doses of ca. 1450, 3200, and 5700 Gy, respectively. Both morphotypes, which were previously reported to display different antioxidant capacities and differ at the genomic level in 168 SNPs, 48 indels and 4 large insertions (Yadav et al., 2019), recovered equally well from 1450 and 3200 Gy. However, while the P2 straight type recov-ered from 5700 Gy by regaining normal growth within 6 days, the P6 helical type took about 13 days to recover from this dose, indicating differences in their radiation tolerance and response. To investigate these differences, P2 and P6 cells exposed to the intermediate dose of gamma radiation (3200 Gy) were analyzed for differential gene expression by RNAseq analysis. A total of 1553 genes (887 and 666 of P2 and P6, respectively, with 352 genes in common) were selected based on a two-fold change in expression and a false discovery rate FDR smaller or equal to 0.05. About 85% of these 1553 genes encoded products of yet unknown function. Of the 229 remaining genes, 171 had a defined function while 58 genes were transcribed into non-coding RNA including 21 tRNAs (all downregulated). From PCC 8005-P2 and PCC 8005-P6 expression patterns it emerges that although the cellular routes used by the two sub strains to cope with ionizing radiation do overlap to a large extent, both strains displayed a distinct preference of priorities likely brought about by marginal differences in their genetic backgrounds.
Small inoculants (1 mL) of irradiated and non-irradiated L. indica cultures were grown in 30 mL of fresh Zarrouk media in T-75 tissue flasks (Thermofisher Scientific). All cultures were grown in triplicates per exposed dose with their respective non-irradiated cultures under standard laboratory conditions. Recovery was followed at OD750 every alternate day for a period of 30 days. The proliferation curve was plotted as OD750 versus time using Graphpad Prism v7 (GraphPad Software, La Jolla, California, USA – https://www.graphpad.com/)
Triplicates of a non-irradiated control per dose were kept at otherwise analogous conditions in the lab. The L. indica P2 and P6 culture samples were collected in time in-tervals at three prechosen time points T1 to T3 of exposure (~15, ~40, and ~71.5h) corresponding to approximate cumulative doses of respectively 1450, 3200, and 5700 Gy, with the actual doses for the individual samples determined by dosimetry using Harwell Amber-3042 radiation-sensitive polymethylmethacrylate dosimeters attached to the cul-ture tubes.
Genes were considered as being differentially expressed if they abided to the selection criteria: -1 >= log2FC >= 1, with an FDR equal or below 0.05 for both options.

overall_design: Two morphotypes of Limnospira indica (formerly Arthrospira sp.) strain PCC 8005, denoted as P2 (straight trichomes) and P6 (helical trichomes), were subjected to chronic gamma radiation from spent nuclear fuel (SNF) rods at a dose rate of ca. 80 Gy.h-1 for one mass doubling period under continuous light with photoautotrophic metabolism fully active. A control sample is provided which was not irradiated. Samples were prepared in triplicates, and were taken for post-irradiation growth recovery and RNAseq transcriptional analysis at approximate time in-tervals of 15, 40, and 71.5 hrs corresponding to cumulative doses of ca. 1450, 3200, and 5700 Gy, respectively.


title: The ZMM protein Zip4 directly couples meiotic crossover formation to synaptonemal complex assembly

city: PARIS

first: Valerie

last: Borde

summary: Meiotic crossover recombination is triggered by the formation of programmed double strand breaks (DSBs) catalyzed by the conserved Spo11 protein. Only a subset of these DSBs are repaired as crossovers, promoted by a group of eight evolutionarily conserved proteins, named ZMM. The synaptonemal complex (SC) that assembles between homologous chromosomes  is composed of two axial elements, from which chromatin loops emanate, held together by a central region, composed of the central element and a transverse filament protein. In budding yeast, crossover formation is functionally linked to the formation of the SC, but the underlying mechanism is unknown. Here we found that the SC central element protein, Ecm11, mainly localizes on both DSB sites and sites that attach chromatin loops to the chromosome axis, in a way that strictly requires the ZMM protein Zip4. We further show that Zip4 directly interacts with Ecm11 and that point mutants that specifically abolish the Zip4-Ecm11 interaction loose Ecm11 binding to chromosomes and exhibit defective SC assembly. Interestingly, SC assembly can be partially rescued by artificially tethering interaction-defective Ecm11 to Zip4. This direct connection that ensures SC assembly from CO sites could be a way for the meiotic cell to shut down further DSB formation once enough recombination sites have been selected for crossovers, thereby preventing excess crossovers.  Finally, we found that the mammalian ortholog of Zip4, TEX11, interacts with the SC central element TEX12, raising the possibility that this may be a general mechanism.

overall_design: 4 samples total: each comes from two independent replicates each of anti-FLAG ChIP in untagged, Ecm11-His6FLAG3, zip4∆ Ecm11-His6FLAG3 and zip1∆ Ecm11-His6FLAG3 S. cerevisiae cells at 5 h in meiosis combined with 10% of spike-in S. mikatae Ecm11-His6FLAG3 cells at 4h in meiosis

first: Valérie


title: A role for Elongin in Mediator recruitment at ATF6α regulated genes [RNA-Seq]

city: Kansas City

first: Shiyuan

middle: (Cynthia)

last: Chen

state: MO

department: Computational Biology

institute: Stowers Institute for Medical Research

summary: The bZIP transcription factor ATF6α is a master regulator of endoplasmic reticulum (ER) stress response genes. In this report, we identify the multifunctional RNA polymerase II transcription factor Elongin as a cofactor for ATF6α-dependent transcription activation. Biochemical studies reveal that Elongin functions at least in part by facilitating ATF6α-dependent loading of Mediator at the promoters and enhancers of ER stress response genes. Depletion of Elongin from cells leads to impaired transcription of ER stress response genes and to defects in the recruitment of Mediator and, in particular, its CDK8 kinase subunit. Taken together, these findings bring to light a new role for Elongin as a loading factor for Mediator during the ER stress response.

overall_design: RNA-seq of polyA-selected libraries prepared from HCT116 cells

first: Yanfeng

last: He

first: Joan

last: Conaway

first: Ron


title: Comprehensive genome wide analysis of Satb2 function during vertebrate embryogenesis

city: Pune

first: Sanjeev

last: Galande

state: Maharashtra

address: Dr. Homi bhabha road, Pashan

department: Biology

country: India

institute: IISER Pune

summary: In this study, we have addressed the involvement of chromatin organizer SATB2 in orchestrating zygotic genome activation and neural crest specification during zebrafish embryogenesis. Integrative analysis of transcriptome, genome-wide occupancy and chromatin accessibility reveals contrasting molecular activities of maternally deposited and zygotically synthesized Satb2. Comparative analysis with mouse embryos highlighted conserved molecular mechansisms for Satb2 during neural crest specification.

sample_organism:
Danio rerio
Mus musculus

platform_organism:
Danio rerio
Mus musculus

overall_design: To obtain insights into evolutionary conserved and zebrafish specific functions of Satb2, we performed stage dependent 3' mRNA analysis (80  % epiboly, 6 somite and 14 somites) on Wild type and Satb2 mutants in zebrafish (atleast in duplicates). We also performed stage dependent ChIPseq with anti-zebrafish Satb2  (512 cell, Dome stage, 80  % epiboly, 6 somite and 14 somites)  in zebrafish and anti-human antibodies generated in this study (atleast in duplicates) in mouse embryos (E9.5 head, E9.5 trunk and E13.5 dorsal telencephalon) respectively. To get insights into chromatin modification status and accessibility upon loss or gain of function of Satb2, we performed ChIPseq for histone modifications (Dome stage) and ATAC-seq (Dome and 14 somites stage). Tg: SOX10:egfp line were utilized to isolate neural crest population and perform Satb2 ChIPseq (14 somites) to obtain neural crest specific occupancy of Satb2. scRNAseq analysis were utilized to understand cell autonomous regulation of Satb2 during ZGA (Dome stage) and neural crest specific function of Satb2 during organogenesis (14 somites).

first: Saurabh

last: Pradhan


title: Paired-end RNA Sequencing on Madin-Darby Canine Kidney (G-MDCK) epithelial cells infected or not with Listeria monocytogenes and residing on varying stiffness substrates.

city: Tübingen

first: Effie

last: Bastounis

state: Baden-Württemberg

address: Auf der Morgenstelle 28/E7

department: Interfaculty Institute of Microbiology and Infection Medicine

country: Germany

institute: University of Tübingen

summary:
Purpose: When we infect MDCK epithelial cells we low dosage of Listeria monocytogenes, we observe that at late times (24 h) post-infection the infected cells pertaining in infection foci get collectively extruded out of the epithelial monolayer forming a 3D mound. The formation of the infection mound results from the competition between two populations: the uninfected cells ("surrounders") that eventually squeeze and extrude the infected cells ("mounders") in the infected wells. The extracellular matrix where the host cells adhere appears to impact the formation of infection mounds with more mounding on glassr as opposed to soft 3 kPa substrata, as evidenced by confocal 3D microscopy. Here we built poalyacrylamide hydrogels of varing stiffness (3 kPa soft or 70 kPa stiff) and coated them with collagen I rat tail. We also placed host cells on glass collagen I-coated surfaces. We then infected for 24 h (or not) the host cells with Listeria monocytogenes to infer how matrix stiffness-dependent gene expression of MDCK cells in monolayers changes in uninfected versus infected wells, through RNA-Sequencing. Our goal was to understand how matrix stiffness impacts transcriptional regulation of host cells and whether that could modulate the collective extrusion of infected epithelial cells triggered by surrounding uninfected cells.
Methods and Results: By analyzing the differentially expressed genes between all conditions we find a significant number of up- or down-regulated genes between all groups, other than between cells residing on soft versus stiff polyacrylamide hydrogels that behave similarly in terms of gene expression. Through pathway enrichement analysis, we find that cells residing on polyacrylamide hydrogels as opposed to cells residing on glass show higher upregulation of a number of innate immune signaling related pathways (e.g. MAPK, TNF) even when infection is not involved. When comparing infected versus not wells, the relative differences in gene expression for cells residing on glass are higher than for cells residing on hydrogels. However certain specific innate immune signaling pathways that regulate mound formation (https://www.sciencedirect.com/science/article/abs/pii/S1534580721000708), show higher upregulation in infection for cells on hydrogels as opposed to glass (e.g. IL-17, TNF, NF-κΒ; evidenced by pathway enrichement analysis). Finally, through pathway enrichement analysis we find that the relative change based on enrichement score when comparing uninfected versus infected settings for cells residing on glass versus on polyacrylamide hydrogels is lower for the former (i.e. for cells residing on glass) for NF-κB, TNF and IL17. However, with regards to the MAPK pathway the enrichment score of cells from infected versus uninfected wells, is much higher for cells residing on glass as opposed to polyacrylamide hydrogles.
Conclusions: Infection of MDCK epithelial cells with Listeria monocytogenes significantly alters the transcriptome of the infected host cells when those are examined 24 h post infection and compared to uninfected cells on all different  substrata. Compared to cells residing on glass substrates cells residing on polyacrylamide hydrogels (irrespective of whether the stiffness is low i.e. 3 kPa or high i.e. 70 kPa) show significant differences both when uninfected settings and when infected ones are compared.

overall_design: Epithelial cell mRNA profiles of cells previously residing in confluency on glass substrates or polyacrylamide hydrogels (of 3 KPa or 70 kPa) coated with 0.25 mg/mL collagen  where either (1) uninfected; or (2) infected with low dosage of Listeria monocytogenes (MOI=200) at 24 h post-infection and compared. Sampled were generated in quadruplicate, using Illumina NovaSeq 6000 using the NovaSeq 6000 S4 Reagent Kit with 2x150 read length and 40 million reads per sample.


title: Small RNA sequencing of NlCSP1-infiltrated Nicotiana benthamiana

city: Shanghai

first: Li

last: Wan

state: Shanghai

address: 300 Feng Lin Road

department: CAS Center for Excellence in Molecular Plant Sciences

institute: Chinese Academy of Sciences

type: Non-coding RNA profiling by high throughput sequencing

summary: In order to find the miRNAs, target genes and signaling pathways related to the dwarf phenotype induced by NlCSP1, 35S-NlCSP1 and 35S-GFP control were infiltrated into Nicotiana benthamiana. We analyzed the differentially expressed miRNAs in the infiltrated leaves (NlCSP1_Z/GFP_Z) and the upper uninfiltrated leaves (NlCSP1_O/GFP_O) of N. benthamiana. A total of 106 and 97 differentially expressed miRNAs were identified in NlCSP1_Z/GFP_Z and NlCSP1_O/GFP_O, respectively. KEGG annotation revealed a large number of differentially expressed miRNAs involved in plant hormone signal transduction, indicating that NlCSP1 changed the hormone signal pathway in N. benthamiana.

overall_design: In order to find the miRNAs, target genes and signaling pathways related to the dwarf phenotype induced by NlCSP1, 35S-NlCSP1 and 35S-GFP control were infiltrated into the infiltrated leaves (NlCSP1_Z/GFP_Z) and the upper uninfiltrated leaves (NlCSP1_O/GFP_O) of Nicotiana benthamiana.

first: Weiwei

last: Rao


title: RNA sequencing of cell-specific profile of wild type and unc-4 VAs

city: Nashville

first: Sierra

middle: D

last: Palumbos

state: TN

address: 2201 West End Ave, Nashville

department: Cell and Developmental Biology

institute: Vanderbilt University

summary: We report the transcriptome profile of the VA neuron in L2 wild type and unc-4 mutant C. elegans

overall_design: VA neurons were isolated using FACS sorting

first: Rebecca

last: McWhirter


title: Gene expression profiling of newly-diagnosed DLBCL samples with RNA sequencing

city: Fukuoka

first: Yuichiro

last: Semba

address: 3-1-1 Maidashi

institute: Kyushu University

summary: Diffuse large B-cell lymphoma (DLBCL) is the most common B-cell malignancy with varying prognosis after the gold standard rituximab, cyclophosphamide, doxorubicin, vincristine, and prednisone (R-CHOP). Several prognostic models have been established by focusing primarily on characteristics of lymphoma cells themselves, including cell-of-origin, genomic alterations, and gene/protein expressions. However, the prognostic impact of the lymphoma microenvironment and its association with characteristics of lymphoma cells are not fully understood. Using highly-sensitive transcriptome profiling of untreated DLBCL tissues, we here assess the clinical impact of lymphoma microenvironment on the clinical outcomes and pathophysiological, molecular signatures in DLBCL. The presence of normal germinal center (GC)-microenvironmental cells, including follicular T cells, macrophage/dendritic cells, and stromal cells, in lymphoma tissue indicates a positive therapeutic response. Our prognostic model, based on quantitation of transcripts from distinct GC-microenvironmental cell markers, clearly identified patients with graded prognosis independently of existing prognostic models. We observed increased incidences of genomic alterations and aberrant gene expression associated with poor prognosis in DLBCL tissues lacking GC-microenvironmental cells relative to those containing these cells. These data suggest that the loss of GC-associated microenvironmental signature dictates clinical outcomes of DLBCL patients reflecting the accumulation of “unfavorable” molecular signatures.

overall_design: In the study presented here, we  performed a pilot screen to identify genes correlated with specific patient outcomes by analyzing FFPE samples obtained at initial diagnosis from 30 DLBCL patients: 15 showing favorable outcomes (>4 years in remission) and 15 showing poor prognosis (primary refractory or early relapse disease). Nineteen samples were subject to analysis due to data quality.

first: Kohta

last: Miyawaki

first: Takeshi

last: Sugio


title: Mapping of pseudouridine residues on cellular and viral transcripts using a novel antibody-based technique

city: Taipei

first: Kevin

last: Tsai

address: 128 Sec. 2, Academia Rd. Nankang

department: Institute of Biomedical Sciences

country: Taiwan

institute: Academia Sinica

summary: Pseudouridine (ψ) is the most common non-canonical ribonucleoside present on mammalian non-coding RNAs (ncRNAs), where is contributes ~10% of the total uridine level. However, ψ constitutes only ~0.3% of the uridines present on mRNAs and its effect on mRNA function remains unclear. Ψ residues have however been shown to inhibit the detection of exogenous RNA transcripts by host innate immune factors, thus raising the possibility that viruses might have subverted the addition of ψ residues to mRNAs by host pseudouridine synthase (PUS) enzymes as a way to inhibit antiviral responses in infected cells. Here, we describe and validate a novel antibody-based ψ mapping technique called photo-crosslinking assisted ψ sequencing (PA-ψ-seq) and then use it to map ψ residues on not only multiple cellular RNAs but also the mRNAs and genomic RNA encoded by HIV-1. We also describe several 293T-derived cell lines in which human PUS enzymes previously reported to add ψ residues to mRNAs, specifically PUS1, PUS7 and TRUB1/PUS4, were individually inactivated by gene editing. Surprisingly, while this allowed us to assign several sites of ψ addition on cellular mRNAs to each of these three PUS enzymes, the ψ sites present on HIV-1 transcripts remained unaffected. However, loss of PUS1 function did significantly reduce HIV-1 gene expression by a presumably indirect mechanism.

overall_design: Photoactivated UV crosslinking of pseudouridine antibody to pseudouridilated RNA, followed by immunoprecipitation and sequencing (PA-Ψ-Seq). RNA from 293T or CEM cells, WT or pseudouridine synthatase (Pus) knockout cells

first: Cecilia

last: Campos

first: Bryan

last: Cullen


title: Gene expression profiling of human neuroblastoma cell line SK-N-AS_tetoff_MYCN cultured in the presence (D+) or absence (D-) of 1 µg/ml doxycycline for 6 days

city: Birmingham

first: Han-Fei

last: Ding

state: Alabama

address: WTI 602D, 1824 6th Avenue South

department: Pathology

institute: University of Alabama at Birmingham

summary: Microarray gene expression profiling reveals that MYCN reprograms cellular metabolism by transcriptional activation of metabolic pathways critical for cancer cell growth and proliferation

overall_design: Affymetrix microarray assays were performed according to the manufacturer's directions on total RNA isolated from three independent samples of SK-N-AS_tetoff_MYCN cells cultured in the presence (D+) or absence (D-) of 1 µg/ml doxycycline for 6 days

first: Jane


title: The RNA-seq analysis of rice roots colonized by the endophytic bacterium Azoarcus olearius BH72 after one-, three- and seven-days post inoculation and after three days of boosted colonization.

city: Bremen

first: Barbara

last: Reinhold-Hurek

state: Bremen

address: Leobener Str. 5

department: Microbe-Plant Interactions

institute: University of Bremen

summary:
Purpose: Transcriptional profiling of Oryza sativa japonica Nipponbare roots after one, three and seven days post inoculation with Azoarcus olearius BH72 (vs. non-inoculated controls) to understand the changes in transcriptomic response of rice roots to colonization by bacterial endophyte at initial stages of interaction; Additional set-up was included in which bacterial growth was boosted (through increasing 20-times carbon source - malic acid in the plant's hydroponic medium) to study rice roots transcriptome during enhanced colonization by the endophyte after three days post inoculation.
Methods: Rice root mRNA profiles after one day, three days (including additional set-ups for boosted colonization), and seven days post inoculation with Azoarcus olearius BH72 and corresponding non-inoculated controls were generated by RNA sequencing, in triplicates, using Illumina NextSeq 500. Raw reads were then filtered, trimmed (PHRED > 33) and mapped  onto IRGSP-1 version of Oryza sativa ssp. japonica cv. Nipponbare genome using CLC Genomics Workbench 8.5.1 (Qiagen, Germany). Expression of 17 selected genes was confirmed via RT-qPCR.
Results: Using the RNA-Seq technology we obtained transcriptomic data from 24 sequencing libraries, with an average 46,181,160 clean reads per library, of which 87% or more were mapped onto the Oryza sativa ssp. japonica cv. Nipponbare IRGSP-1.0 genome (Fig. S3). We considered genes as differentially regulated (DEG) that exhibited at least 1.5-fold-change in expression level between Azo-colonized and non-colonized roots and FDR<0.05.
Conclusions: Bacteria appeared to short-circuit the initial root defense responses for a compatible interaction during endophytic establishment, involving previously unknown putative rice candidate genes.

overall_design: Experiments included generating Oryza sativa japonica Nipponbare roots mRNA profiles at three time points (one, three and seven days post inoculation with Azoarcus olearius BH72), which were either subjected or not subjected to treatment (inoculated with endophytic bacterium Azoarcus olearius BH72 or non-inoculated), in three independent biological replicates (18 samples in total). Additional root mRNA profiles were obtained from plants subjected to boosted colonization by the endophyte or non-inoculated plants at one time point (three days post inoculation) also in three independent biological replicates (6 samples in total).

first: Marta

last: Marszalkowska


title: The effects of SNAI2 overexpression on the transcriptional program in HaCaT cells

first: Hatta

last: Mitsutoki

state: Fukuoka

address: 2-15-1 Tamura,Sawara-ku

department: Physiological Science and Molecular Biology

institute: Fukuoka Dental College

summary: Investigation of the transcriptional profile of SNAI2-overexpressing HaCaT cells.

overall_design: TY1-tagged SNAI2 expressing HaCaT cells were generated by retroviral transduction. TY1-tag expressing cells were used for comparison.

first: Mitsutoki

last: Hatta

first: Yoshiyuki

last: Nagaoka

first: Yukimasa

last: Takeishi

first: Yuki

last: Miyake


title: Transcriptomic  analysis  of the marine diatom Nitzschia laevis during glucose-induced trophic transition

city: Shenzhen

first: Xuemei

last: Mao

address: Baishi Road

department: IAS

institute: Shenzhen University

summary: RNA sequencing (RNA-seq) experiment was performed on 18 samples of Nitzschia laevis cells collected at 3 h, 6 h and 12 h after inoculation in treated medium with glucose addition (+G) and control group (-G) respectively. The de novo assembly totally generated 16650 unigenes.

overall_design: mRNA profiles of 18 samples collected at 3 h, 6 h and 12 h with (+G) or without (-G, as control) glucose addition (refered as +G3h, +G6h, +G12h, -G3h, -G6h, -G12h, with 3 replicates respectively)


title: The effect of dietary methionine restriction using different protein sources on the transcriptome of mouse livers

city: Baton Rouge

first: Thomas

last: Gettys

state: LA

address: 6400 Perkins Road

department: Nutrient Sensing and Adipocyte Signaling

institute: Pennington Biomedical Research Center

summary: Dietary Methionine restriction (MR) has been demonstrated to induce a set of hepatic responses, including activation of hepatic stress response and suppression of hepatic lipogenesis. In the current study, we used two different protein sources to achieve MR. Casein was used in normal protein (NP, 20% casein) and low protein (LP, 5% casein) diet. Soy protein was used in 20Soy (20% soy), 20Soy+SAA (20% soy, Met and Cys was added back to match their concentration in NP diet), and 10Soy (11.5% soy, the Met concentration matches LP diet). Results show that mice that were fed LP and 10Soy diet have lower body weight and adiposity and increased food and water intake, energy expenditure, and serum FGF21 levels compared to their relative controls. The RNAseq experiment was conducted to compare the effect of MR using these two protein sources on the hepatic transcriptome.

overall_design: Comparison of the effects of MR implemented in two intact protein sources, casein (each 6 samples from NP and LP fed mice) and soy (each 6 samples from 20Soy, 20Soy+SAA, and 10Soy diets). The additonal control soy diet (20Soy+SAA) is designed to isolate the effect of Methinone restriction from protein restriction.

first: Han

last: Fang

first: Kirsten

last: Stone

first: Jaroslaw

last: Staszkiewicz

first: Jasleen

last: Kaur

first: Richard

middle: P

last: Carmouche

first: Sara

last: Webb

first: Sujoy

last: Ghosh


title: Establishment of an intradermal ear injection model of IL-17A and IL-36γ as a tool to investigate the psoriatic cytokine network

city: Cologne

first: Ali

last: Abdallah

address: Joseph Stelzmann Str. 26

department: Medical Faculty

institute: University of Cologne

summary: The aim of this study was to establish an intradermal ear injection model to evaluate the effects of IL-36γ and IL-17A in psoriasis.The cytokines IL-36γ and IL-17A were injected intradermally alone or in combination into the ear pinnae of C57BL/6 mice. Ear thickness measurement was performed daily. After 4 days mice were euthanized and a gene expression profiling was conducted.

overall_design: 12 samples were analyzed: Comparison between a PBS control group and groups that were treated with either IL-17A, IL-36γ or the combination of both (3 samples of each group were analyzed).

first: David

last: Kluwig

first: Sebastian

last: Huth

first: Carolina

last: Pfaff

first: Katharina

last: Fietkau

first: Laura

first: Yvonne

last: Marquardt

first: Jens

last: Baron

first: Bernhard

last: Lüscher


title: Roles of Zfp36l1 and Zfp36l1 in retinal development

city: Buffalo

first: Xiuqian

last: Mu

state: NY

address: 701 Ellicott Street

department: Ophthalmology

institute: University at Buffalo

summary: We report our study of the function of two members of the TTP (tristetraprolin) mRNA binding protein family, Zfp36l1 and Zfp36l2, in retinal development. We found that Zfp36l1 and Zfp36l2 were expressed in retinal progenitor cells during development and Müller glial cells and photoreceptors in the mature retina. Our analysis of the mutant retinas showed that, whereas the single knockout retinas appeared largely normal, the double knockout (DKO) retina manifested decreased RPC proliferation and increased differentiation of multiple retinal cell types. RNA-seq analysis not only confirmed the imbalance of proliferation and differentiation in the DKO retina but also revealed Zfp36l1 and Zfp36l2 interact with multiple signaling pathways including the sonic hedgehog pathway and the Notch pathway, to regulate this process.

overall_design: Zfp36l1 and Zfp36l2 were conditionally knocked out by crossing two floxed alleles (Zfp36l1F and Zfp36l2F) with the retinal specific Cre line Vsx2-Cre. Transcriptomic profiles of the double knockout (Zfp36l1/F/F;Zfp36l2F/F; Vsx2-Cre) retina and  control retina (Zfp36l1/F/F;Zfp36l2F/F) from different stages (E14.5, E17.5, P0, P5 and P16) were compared by RNA-seq.

first: Jie

last: Wang

first: Tao

last: Liu

first: Fuguo

last: Wu


title: Ontogeny and function of the circadian clock in intestinal organoids [human]

city: Cincinnati

first: Andrew

last: Rosselot

address: 231, Albert Sabin way

department: Department of Pharmacology and Systems Biology

institute: University of Cincinnati, College of Medicine

summary: Circadian rhythms regulate diverse aspects of gastrointestinal physiology ranging from the composition of microbiota to motility. However, development of the intestinal circadian clock and detailed molecular mechanisms regulating circadian physiology of the intestine remain largely unknown. The lack of appropriate human model systems that enable organ- and/or diseasespecific interrogation of clock functions is a major obstacle hindering advancements of translational applications using chronotherapy. In this report, we show that both pluripotent stem cell-derived human intestinal organoids engrafted into mice and patient-derived human intestinal enteroids (HIEs) possess robust circadian rhythms, and demonstrate circadian phase-dependent necrotic cell death responses to Clostridium difficile toxin B (TcdB). Intriguingly, mouse and human enteroids demonstrate anti-phasic necrotic cell death responses. RNA-Seq data show ~4% of genes are rhythmically expressed in HIEs. Remarkably, we observe anti-phasic gene expression of Rac1, a small GTPase directly inactivated by TcdB, between mouse and human enteroids. Importantly, the observed circadian time-dependent necrotic cell death response is abolished in both mouse enteroids and human intestinal organoids (HIOs) lacking robust circadian rhythms. Our findings uncover robust functions of circadian rhythms regulating critical clock-controlled genes (CCGs) in human enteroids governing organism-specific, circadian phasedependent necrotic cell death responses. Our data highlight unique differences between mouse and human enteroids, and lay a foundation for human organ- and disease-specific investigation of clock functions using human organoids for translational applications.

overall_design: Samples were collected every two hours for 48-hours starting at 24-hours post circadian synchronization using dexamethasone.

first: Miri

last: Park

first: Toru

last: Matsu-Ura

first: Gang

first: Danilo

last: Flores

first: Krithika

last: R Subramanian

first: Suengwon

last: Lee

first: Nambirajan

last: Sundaram

first: Taylor

last: Broda

first: Heather

middle: A

last: McCauley

first: Jennifer

last: Hawkins

first: Kashish

last: Chetal

first: Nathan

last: Salomonis

first: Noah

last: Shroyer

first: Michael

last: Helmrath

first: James

last: Wells

first: John

last: Hogenesch

first: Sean

last: Moore

first: Christian

last: Hong


title: Single-cell sequencing unveils distinct immune microenvironment in human chronic pancreatitis

city: Stanford

first: Bomi

address: 1291 Welch Road

institute: Stanford University

summary:
Purpose: Chronic pancreatitis (CP) is considered an irreversible fibroinflammatory pancreatic disease with no active FDA approved therapy. Due to difficulty in accessing pancreas tissues, little is known about local immune responses in human CP. Here we attempted to uncover the disease-specific immune responses in pancreata from two different etiologies of CP (hereditary and idiopathic CP) compared with those from non-diseased controls by using CITE-seq and scTCR-seq.
Methods: We performed cellular indexing of transcriptomes and epitopes by sequencing (CITE-Seq) and T cell receptor sequencing of pancreatic immune cells isolated from organ donors (n=3) and CP patients (Hereditary CP, n=5; Idiopathic CP, n=4) who underwent total pancreatectomy.
Results: Deep single-cell sequencing revealed distinct immune characteristics and a significantly enriched CCR6+ CD4+ T cells in hereditary compared with idiopathic CP. In hereditary CP, a reduction in T cell clonality was observed due to the increased CD4+ T (Th) cells that replaced tissue resident CD8+ T cells. Lineage tracing analysis with scRNA/TCR-seq data also unveiled unique interactions between CCR6+ Th and Th1 subsets, and TCR clustering analysis showed unique common antigen binding motifs in hereditary CP. In addition, we observed a significant upregulation of the CCR6 ligand (CCL20) among monocytes in hereditary CP as compared with those in idiopathic CP. The functional significance of the CCR6 expression in CD4+ T cells was confirmed by flow cytometry and migration assay.
Conclusions: Our approaches with integrative single-cell analyses unveiled distinct pancreatic immune signatures and pathways between different etiologies of CP. Our study specifically unveiled pancreas-specific immune crosstalks through a CCR6-CCL20 axis that might be leveraged as a potential future target in human hereditary CP

overall_design: Simultaneous single-cell profiles of 13 feature protein expressions, transcriptomes, and TCR repertoires in pancreatic immune cells from humam donors and CP patients.

first: Hong

last: Namkoong

first: Yan

last: Yang

first: Huang

last: Huang

first: David

last: Heller

first: Gregory

last: Szot

first: Mark

last: Davis

first: Stephen

last: Pandol

first: Melena

last: Bellin

first: Aida

last: Habtezion


title: The effects of TGF-β1-induced EMT on the transcriptional program in HaCaT cells

first: Hatta

last: Mitsutoki

summary: Investigation of the transcriptional profile of TGF-β1-induced EMT in HaCaT cells.

overall_design: HaCaT cells grown in DMEM supplemented with 10% fetal bovine serum were treated with TGF-β1 for 48h to induce an EMT program. Non-treated cells were used for comparison.

first: Mitsutoki

last: Hatta

first: Yoshiyuki

last: Nagaoka

first: Yukimasa

last: Takeishi

first: Yuki

last: Miyake


title: Concordance of PAM50 molecular subtyping between oligonucleotide microarray and NanoString nCounter assay for Taiwanese breast cancer

city: New Taipei

first: Chih-Cheng

last: Chien

address: No 2, Ln 59, Jian-Cheng Rd, Sijhih Dist

institute: Sijhih Cathay General Hospital

summary:
Five molecular subtypes have been identified according to intrinsic genes transcription. Microarrays have been adopted for molecular subtyping in addition to the original NanoString nCounter assay. This study aimed to evaluate subtyping consistency among Taiwanese breast cancers.
Our study showed that fundamental discrepancy exists between distinct gene expression measuring approaches, and cross platform equivalence should not be overemphasized with too much extrapolation.

overall_design: A total of 109 Taiwanese breast cancers (24 with adjacent normal breast) were assayed with Affymetrix microarrays and 96 were assayed with NanoString Codeset BCeCSig, which also investigated academic PAM50. Sixty-one patients were assayed for both platforms. Subtyping was called for each patient with the nearest centroid.

first: Yen-Jen

last: Chen

first: Ching-Shui

first: Tzu-Pin

last: Lu

first: Chih-Yi

last: Liu

first: Chi-Jung

first: Jen-Hwey

last: Chiu

first: Ling-Ming

last: Tseng

first: Chi-Cheng


title: Escherichia coli alpha-hemolysin HlyA induces host cell polarity changes, epithelial barrier dysfunction and cell detachment in human colon carcinoma Caco-2 cell model via PTEN-dependent dysregulation of cell junctions

city: Berlin

first: Oliver

last: Nagel

address: Hindenburgdamm 30

department: Department of Gastroenterology, Rheumatology and Infectious Diseases

institute: Charité - Universitätsmedizin Berlin

summary: Escherichia coli  of the B2 phylotype reside in human and animal intestines. We addressed the questions which host cell processes were dysregulated by E. coli HlyA that can potentiate intestinal diseases. The colon carcinoma cell line Caco-2 was infected by HlyA+ E. coli. Cell polarity regulation was analyzed by live cell imaging for the localization of phosphatidylinositol-4,5-bisphosphate (PIP2) abundance in the plasma membrane. In Caco-2 monolayers, transepithelial electrical resistance was measured to determine barrier function. Cell morphologyproliferation and dissemination was assessed microscopically. Cell signaling and polarity regulation was analyzed by RNA-Seq.

overall_design: mRNA profiles from infected Caco-2 cells and controls were generated by paired-end sequencing using Illumina NovaSeq 6000

first: Emanuel

last: Schulz

first: Michael

last: Schumann

first: Martina

last: Schneemann

first: Violaine

last: Dony

first: Anja

last: Fromm

first: Jörg-Dieter

last: Schulzke

first: Roland

last: Bücker


title: A role for Elongin in Mediator recruitment at ATF6α regulated genes [Cut&Tag]

city: Kansas City

first: Shiyuan

institute: Stowers Institute for Medical Research

summary: The bZIP transcription factor ATF6α is a master regulator of endoplasmic reticulum (ER) stress response genes. In this report, we identify the multifunctional RNA polymerase II transcription factor Elongin as a cofactor for ATF6α-dependent transcription activation. Biochemical studies reveal that Elongin functions at least in part by facilitating ATF6α-dependent loading of Mediator at the promoters and enhancers of ER stress response genes. Depletion of Elongin from cells leads to impaired transcription of ER stress response genes and to defects in the recruitment of Mediator and, in particular, its CDK8 kinase subunit. Taken together, these findings bring to light a new role for Elongin as a loading factor for Mediator during the ER stress response.

overall_design: Cut&Tag in HCT116 cells with siRNA targeting Elongin A (siELOA) or control non-targeting siRNA (nonT), followed by induction of ER stress with 300 nM thapsigargin (Tg).

first: Yanfeng

last: He

first: Joan

last: Conaway

first: Ron


title: Transcriptome sequencing of human brain tissue after intracerebral hemorrhage

city: Tianjin

first: Qiang

state: Tianjin

address: No.154 Anshan Road, Heping District

department: Neurology

institute: Tianjin Medical University General Hospital

summary: We used tissue bulk RNA-seq to analyze gene expression profile in the brain after intracerebral hemorrhage.

overall_design: Peri-hematomal tissue from basal ganglia areas was collected within 24h after ICH in ICH patients who were subjected to craniotomy surgery, and tissue mRNAs were prepared to process RNA-seq.

first: Zilong

last: Zhu

first: Zhiguo

last: Li


title: Whole transcriptome analysis of hypoxic pulmonary hypertension

city: Kunming

first: xiqian

last: xing

state: Yunnan

address: No. 176, Qingnian Road

department: Department of Respiratory Medicine

institute: The Affiliated Hospital of Yunnan University, The Second People's Hospital of Yunnan Province

summary: Non-coding RNA plays an important regulatory role in the occurrence and development of hypoxic pulmonary hypertension (HPH). Therefore, we use high-throughput RNA sequence and bioinformatics methods to analyze the whole transcriptome HPH rats in lung tissue.

overall_design: Two-group experiment (Con = normal atmospheric conditions (control) vs HPH = atmospheric hypoxia). Three biological replicas of each group in rat lung tissue.

first: Xiqian

last: Xing

first: Jiao

last: Yang

first: Shuanglan

last: Xu

first: Jie


title: Spatial transcriptomics of fixed tissue micro-regions using Pick-Seq [tonsil]

city: Boston,

first: Ajit Johnson

last: Nirmal

state: MA

address: 200 Longwood Avenue

department: Harvard Program in Therapeutic Science

institute: Harvard Medical School

summary: Spatial transcriptomics and multiplexed imaging are complementary methods for studying tissue biology. Here we describe a simple method for transcriptional profiling of formalin fixed histology specimens based on mechanical isolation of tissue micro-regions containing 5-20 cells. Sequencing micro-regions from an archival melanoma specimen having multiple distinct histologies reveals significant differences in transcriptional programs associated with tumor invasion, proliferation, and immunoediting and parallel imaging confirms changes in immuno-phenotypes and cancer cell states.

overall_design: mRNA from 40μm regions of interest were collected from two histological sites in human FFPE tonsil sections, sequenced and gene expression profiles were analyzed.

first: Ajit

first: Zoltan

last: Maliga

first: Nolan

middle: G

last: Ericson

first: Peter

middle: K

last: Sorger


title: Metformin and leucine combination increase satellite cell abundance and extracellular matrix remodeling during disuse and recovery in aged mice

city: Salt Lake City

first: Micah

last: Drummond

state: Utah

address: 520 Wakara Way

department: Physical Therapy and Athletic Training

institute: The University of Utah

summary: Loss of muscle mass and strength following disuse followed by impaired muscle recovery likely contribute to sarcopenia in older adults. Metformin and leucine individually have shown positive effects in skeletal muscle during atrophy conditions but have not been evaluated in combination nor under the conditions of disuse atrophy and recovery in aging. The purpose of this study was to determine if a dual treatment of metformin and leucine (MET+LEU) would prevent disuse-induced atrophy and/or promote muscle recovery in aged mice (22-24 mo). We were also interested if these muscle responses correspond to changes in satellite cells and ECM abundance. Aged mice were subjected to 14 days of hindlimb unloading (HU) followed by 7 or 14 days of reloading (7 or 14d RL). Metformin (MET), leucine (LEU), or MET+LEU was administered via drinking water and were compared to Vehicle-treated mice. We observed that MET+LEU increased whole body grip strength, muscle specific force and satellite cell abundance during HU but did not alter muscle size during HU or RL. Moreover, MET+LEU treatment increased ECM turnover driven by a decrease in collagen IV   content during 7 and 14d RL. Transcriptome analysis revealed that MET+LEU altered Gene Set Enrichment Analysis hallmark pathways related to inflammation and myogenesis during HU. Together  , MET+LEU was able to improve muscle quality during disuse and recovery in aging possibly by increasing muscle satellite cell content and reducing excessive ECM accumulation.

overall_design: 52 total samples, 4 treatment groups with 3 timepoints each. N=4/group. Reference samples used were ambulatory control or vehicle treated mice.

first: Jonathan

last: Petrocelli

first: Ziad

middle: S

last: Mahmassani

first: Chris

last: Stubben


title: Sex-specific effects of in vitro fertilization on adult metabolic phenotypes and hepatic transcriptomic and proteomic pathways in mouse

city: Philadelphia

first: Yemin

last: Lan

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

summary: Although in vitro fertilization (IVF) is associated with adverse perinatal outcomes, an increasing concern is the long-term health implications. We augmented our IVF mouse model to longitudinally investigate cardiometabolic outcomes in offspring from optimal neonatal litter sizes. We found that IVF-conceived females had higher body weight and cholesterol levels compared to naturally-conceived females, whereas IVF-conceived males had higher levels of triglycerides and insulin, and increased body fat composition. Through transcriptomics and proteomics of adult liver, we identified sexually-dimorphic dysregulation of the sterol regulatory element binding protein (SREBP) pathways that contribute to the sex-specfic phenotypes. We also found that global loss of DNA methylation in placenta was linked to higher cholesterol levels in IVF-conceived females. Our findings indicate that IVF procedures have long-lasting sex-specific effects on metabolic health of offspring and lay the foundation to utilize the placenta as a predictor of long-term outcomes.

overall_design: RNA-seq of natural born or IVF mouse liver, that is male or female with 3 replicates each.

first: Laren

last: Narapareddy

first: Marisa

last: Bartolomei


title: Exon level expression profile of submandibular glands in female MyD88+/+ and MyD88−/− NOD mice.

city: Mizuho

first: Taiki

last: Mori

address: 1851 Hozumi

institute: Asahi University School of Dentistry

summary:
Transcriptome analysis of submandibular glands in female MyD88+/+ and MyD88−/− NOD mice.
Sjögren's syndrome (SS) is an autoimmune disease characterized by dysfunction of salivary glands (SGs) and lacrimal glands, which is caused by chronic inflammation associated with autoantibody and autoreactive lymphocyte infiltration. The pathogenic mechanism of SS has not been fully elucidated. Infiltrated lymphocytes form regularized structures similar to lymphoid follicles of secondary lymphoid organs, such as T/B cell compartments, high endothelial venules (HEVs), lymphatic vessels, and germinal centers, therefore being believed as an ectopic lymphoid tissue called tertiary lymphoid organs (TLO). We previously found that deletion of the Toll-like receptor/IL-1 receptor (TLR/IL-1R) adaptor molecule gene Myd88 in SS model mice NOD reduced the frequency of lymphocyte infiltration and HEV formation in SGs. In this study, we analyzed the effect of MyD88 deficiency on lymphoid follicle formation in SGs of NOD mice. Microarray analysis showed decreased expression of genes related to TLO, such as Cxcl13 and Cxcr5, in Myd88-deficient SGs. These results indicate that deficiency of TLR/IL-1R signaling decrease gene expression ot chemokines in SGs, suggesting MyD88-dependent signaling is directly involved in formation of lymphoid follicles in SS.

overall_design: We analyzed submandibular glands from 3 female MyD88+/+ and  3 MyD88−/− NOD mice using the Clariom S platform. Array data was processed by Transcriptome Analysis Console Tool. No techinical replicates were performed.

first: Hideo

last: Kataoka

first: Takeshi

last: Into


title: Spatial transcriptomics of fixed tissue micro-regions using Pick-Seq [breast]

overall_design: mRNA from 40μm regions of interest were collected from three histological sites in human breast cancer sections (Fresh Frozen), sequenced and gene expression profiles were analyzed.

middle: J


title: Spatial transcriptomics of fixed tissue micro-regions using Pick-Seq

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

overall_design: Refer to individual Series


title: Bcor deficiency perturbs erythro-megakaryopoiesis and cooperates with Dnmt3a loss in acute erythroid leukemia onset in mice

city: Houston

first: Margaret

last: Goodell

state: TX

address: One Baylor Plaza, N1030

institute: Baylor College of Medicine

summary: Recurrent loss-of-function mutations of BCL6 co-repressor (BCOR) gene are found in about 4% of AML patients with normal karyotype and are associated with DNMT3a mutations and poor prognosis. Therefore, new anti-leukemia treatments and mouse models are needed for this combinatorial AML genotype. For this purpose, we first generated a Bcor-/- knock-out mouse model characterized by impaired erythroid development (macrocytosis and anemia) and enhanced thrombopoiesis, which are both features of myelodysplasia/myeloproliferative neoplasms. We then created and characterized double Bcor-/-/Dnmt3a-/- knock-out mice. Interestingly, these animals developed a fully penetrant acute erythroid leukemia (AEL) characterized by leukocytosis secondary to the expansion of blasts expressing c-Kit+ and the erythroid marker Ter119, macrocytic anemia and progressive reduction of the thrombocytosis associated with loss of Bcor alone. Transcriptomic analysis of double knock-out bone marrow progenitors revealed that aberrant erythroid skewing was induced by epigenetic changes affecting specific transcriptional factors (GATA1-2) and cell-cycle regulators (Mdm2, Tp53). These findings prompted us to investigate the efficacy of demethylating agents in AEL, with significant impact on progressive leukemic burden and mice overall survival. Information gained from our model expands the knowledge on the biology of AEL and may help designing new rational treatments for patients suffering from this high-risk leukemia.

overall_design: RNA-seq analysis on LSK and MEP BM cells of Bcor-/-Dnmt3a-/- mice.

first: P

last: Sportoletti

first: M

first: B

last: Falini


title: Large-scale genomic alterations identified in cancer patients on the course of cancer recovery with complementary Huaier treatment identified by total RNA- and small non-coding RNA-sequencing.

city: Kanagawa

first: Manami

last: Tanaka

address: 2-22-9 Hiratsuka, Kanagawa 259-1211, Japan

institute: Bradeion Institute of Medical Sciences

summary: Tremetes robiniophila Murr (Huaier), has been well known by many literatures as a significant cancer complementary therapy.  We have proved that a broad spectrum of anti-cancer effect of Huaier is based on the rescue of the disrupted Hippo signalling pathway, especially through the recovery in transcriptional dysregulation.  We have further investigated the systematic molecular mechanism of cancer recovery as clinical research, using a systematic transcriptome analysis using genome-scale mRNA and small non-coding RNA sequencing.

overall_design: The obtained peripheral blood samples (from cancer patients as well as normal controls) were designated to be used for RNA extraction, construction of whole transcriptome library for sequencing on DNBSeq Platform, followed by whole transcriptome mapping.  We have also performed total non-coding small RNAs sequencing on the same DNBSeq Platform, and the length of small RNAs were found to be between 18 to 30 nucleotides.  Total 91 samples from 32 cancer patients were sequenced and analysed.

first: Tomoo

first: Fei

last: Teng

first: Hong

last: Lin

first: Chenying

last: Xu

first: Ning

last: Li

first: Zhu

last: Luo

first: Ding

last: Wei

first: Zhengxin

last: Lu


title: Transcriptome Profiling of Longissimus Dorsi Muscle of Donkeys with High and Low Intramuscular Fat Content

city: Jinzhong

first: wufeng

last: li

state: Shanxi provence

address: 1 Mingxian South Road, Taigu District

department: college of Life Sciences

institute: Shanxi Agricultural University

summary: The content of intramuscular fat (IMF) is closely related to meat quality traits. In this study, in order to explore the candidate genes related to IMF content, the longissimus dorsi muscle of Guangling donkey was measured for intramuscular fat content. According to its intramuscular fat content, it was divided into two groups, the low fat group (L , N=3) and high-fat group (H, n=3), using RNA-seq to identify differentially expressed genes (DGEs) on the longissimus dorsi muscle tissue of Guangling donkey with high and low intramuscular fat content to reveal the possibility Gene network and metabolic pathways that help increase intramuscular fat content. A total of 167 DEGs (|log2Fold Change|>=1 and FDR<0.05) were detected in the high (H) and low (L) groups of Guangling donkeys, of which 64 were up-regulated genes and 103 were down-regulated genes. The GO enrichment and KEGG pathway analysis showed that these differential genes were enriched in several biological processes and pathways related to adipocyte differentiation, lipid biosynthesis, and neutral lipid metabolism. These results will help to further explore the molecular mechanism of IMF deposition in donkeys and provide a theoretical basis for the molecular breeding of Guangling donkeys.

overall_design: Illumina Nova seq was used to sequence the high and low intramuscular fat content in longissimus muscle of Guangling donkey, and the mRNA profiles of high (H) and low (L) intramuscular fat content of of Guangling donkey longissimus dorsi muscle were obtained

first: Wufeng

first: Jingwei

last: Zhao

first: Yutong

last: Sun


title: Effects of SGLT2 inhibition with ertugliflozin on myocardial remodeling, energetics and gene expression in the presence and absence of diabetes in mice

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

summary: Background: Inhibitors of sodium glucose linked transporter 2 (SGLT2i) improve heart failure (HF) outcomes in patients independent of diabetes. While animal studies suggest SGLT2i improve cardiac metabolism, the effect of SGLT2i on mitochondrial function in the heart is not known. Our goal was to assess the effects of SGLT2i on mitochondrial function, high energy phosphates and genes encoding mitochondrial proteins in hearts of mice with and without diet-induced diabetes.  Methods & Results: Ertugliflozin (Ertu; formulated to 0.5 mg/g of diet) was given for 4 months to mice fed a high fat, high sucrose (HFHS) diet that causes diabetic cardiomyopathy or control diet (CD). Mitochondrial function was measured in isolated cardiac mitochondria. Myocardial energetics were assessed by NMR spectroscopy simultaneously with systolic function in isolated beating hearts. Myocardial gene expression was assessed by RNA seq using gene set enrichment analysis. HFHS diet caused myocardial hypertrophy and diastolic dysfunction, mitochondrial dysfunction (decreased ATP production, increased reactive oxygen species release) and an impaired energetic response to increased work demand - all of which were prevented by Ertu. Conctractile function, as reflected by the rate x pressure product (RPP), was super-normalized to a value 124% of CD hearts at high work demand.  In control mice, Ertu had no effect on isolated mitochondria function or high energy phosphates, but similar to HFHS hearts, caused super-normalization of RPP to 125% of CD hearts. By GSEA the highest scoring gene set for Ertu treatment was oxidative phosphorylation (OXPHOS), which was up-regulated across all groups while controlling for diet with a Normalized Enrichment Score (NES) of +3.71, and was similarly up-regulated in HFHS-fed mice (NES, +3.32) and in CD-fed mice (NES, +3.34). Fatty acid metabolism (FAM) was the second-highest scoring gene set for Ertu, and, like OXPHOS, was up-regulated independent of diet (NES, +2.82).  Conclusion: The super-normalization of contractile function and induction of the OXPHOS and FAM gene sets by Ertu are independent of diabetic status. Pro-metabolic remodeling of the myocardium by Ertu may support increased contractile function and contribute to the beneficial actions of Ertu in states such as heart failure that are associated with impaired cardiac mitochondrial function.

overall_design: 4 representative left ventriclar cardiac tissue samples per group (out of 12 total available samples per group in the study) were assessed, for a total of 16 samples in the RNAseq. The reference group is the control diet (CD) group without Ertugliflozin treatment.

first: Dominique

last: Croteau

first: Wilson

last: Colucci

first: Ivan

last: Luptak


title: The function of intragenic tRNA R-loop

city: Beijing

first: QIANWEN

last: SUN

address: Zhongguancun Street

department: School of life sciences

institute: Tsinghua University

summary: Intragenic tRNAs-promoted R-loops formation orchestrate Arabidopsis oxidative stress survival

overall_design: ssDRIP-seq, RNA-seq and ChIP-seq in Arabidopsis

first: Kunpeng

last: Liu

first: Qianwen


title: Flow upregulates glycocalyx-related genes and makes surface charge more negative of a human blood-brain barrier co-culture model in an organ-on-a-chip device

city: Szeged

first: Ana Raquel

last: Santa-Maria

address: Temesvári krt. 62

department: Biological Barriers Research Group

country: Hungary

institute: Biological Research Centre (BRC)

summary: The highly negatively charged endothelial surface glycocalyx (ESG) functions as mechano-sensor detecting shear forces generated by the blood flow on the luminal side of brain endothelial cells (ECs) and contributes to the physical barrier of the blood-brain barrier (BBB). Despite the importance of ESG in the regulation of BBB permeability in physiological conditions and in diseases, this is an underresearched area. Microfluidic lab-on-a-chip (LOC) devices allow the study of BBB properties in dynamic conditions. We studied a BBB model, human endothelial cells derived from hematopoetic stem cells in co-culture with brain pericytes, in an LOC device to understand the role of fluid flow in the regulation of ESG-related genes and surface charge. The MACE gene sequencing study showed differentially expressed core protein genes of the ESG after fluid flow, as well as enriched pathways for the extracellular matrix molecules. We observed increased barrier properties, a higher intensity glycocalyx staining and a more negative surface charge of human brain ECs in dynamic conditions. Our study is the first to provide data on ESG of human ECs in an LOC device under dynamic conditions and confirm the importance of fluid flow for BBB culture models.

overall_design: 8 samples were analysed by genome-wide gene expression profiling of endothelial cells cultured in microfluidic lab-on-a-chip devices under static or dynamic conditions  (3 and 5 biological replicates, respectively) using the Rapid MACE-seq method to identify differentially expressed genes upon fluid flow.

first: Ana

middle: R

first: Fruzsina

last: Walter

first: Ricardo

last: Figueiredo

first: András

last: Kincses

first: Marjolein

last: Heymans

first: Maxime

last: Culot

first: Peter

last: Winter

first: Fabien

last: Gosselet

last: Dér

first: Maria

last: Deli


title: Follicular helper T cells express a metabolic and cell signaling gene signature in a lupus-prone murine model

city: Gainesville

first: Minghao

last: Gong

state: Florida

address: 1395 Center Drive, D6-18c

department: Pathology

institute: University of Florida

summary: Systemic lupus erythematosus (SLE) is an autoimmune disease in which autoreactive follicular helper T (Tfh) cells license high-affinity autoantibody production. Strikingly, the frequency of circulating Tfh is correlated with disease activity in SLE patients. As such, understanding the molecular mechanisms responsible for the aberrant Tfh cell generation and activation in lupus is of fundamental significance. We previously demonstrated that expanded Tfh cells in the B6.Sle1.Sle2.Sle3 (TC for triple congenic) lupus model exhibit high glycolysis and oxidative metabolism, which can be constrained by inhibiting glycolysis with 2-deoxyglucose (2DG). We performed RNA-seq analyses of splenic Tfh and naïve CD4+ T cells (Tn) comparing between TC and B6 mice. First, data revealed a large number of shared gene signatures in Tfh and Tn comparing between TC and B6 group, implicating that the aberrant development of Tfh initiates as early as Tn state. Further alignment of the Tfh transcriptome obtained from RNA-seq and earlier microarray assays demonstrated concerted alterations in numerous gene signatures of overactivation of T cells including dysregulated tyrosine kinase signaling and MAPK signaling pathways. Gene set enrichment analyses (GSEA) further revealed altered metabolic pathways (e.g., oxidative phosphorylation and pyruvate metabolism) among splenic TC Tfh cells.

overall_design: Splenic CD4+CD44+CD162lo/-PD-1+ Tfh cells and CD4+CD44- Tn cells  from B6.NZM-Sle1NZM2410/AegSle2NZM2410/AegSle3NZM2410/Aeg/LmoJ (TC) congenic mice and B6 control at the matched ages of 8 months old were sorted for RNA-seq analysis.

first: Gong

last: Minghao

first: Cornaby

last: Caleb

first: Morel

last: Laurence


title: RNAseq  and TCRseq analysis of entinostat treated bladder tumors

city: Chapel Hill

first: William

last: Kim

state: NC

address: 450 West Dr

department: Lineberger Comprehensive Cancer Center

institute: UNC Chapel Hill

type: Genome variation profiling by high throughput sequencing

summary: We present transcriptome profiling, TCR repertoire and WES of mouse bladder tumors with and without entinostat treatment, which is a HDAC inhibitor

overall_design: BBN963 cells were injected subcutaneously in C57BL/6 mice at 3.0 x 10^6 cells. Once tumors reached 200mm3 in tumor volume, mice were randomized and treated with chow containing entinostat (12mg/kg). Entinostat treated tumors were collected at 100mm3

first: Andrew

last: Truong

first: Mi

last: Zhou

first: Bhavani

last: Krishnan

middle: Y


title: Human embryonic stem cell-derived neural crest model for neuroblastoma

city: HONG KONG

first: Zhihui

last: WENG

address: Lo Kwee-Seong Integrated Biomedical Sciences  Building, Area 39, The Chinese University of Hong  Kong

country: Hong Kong

institute: CUHK

summary: Neuroblastoma is a common childhood malignant tumor of neural crest origin with remarkable heterogeneity in outcomes. Amplification of the oncogene MYCN is strongly associated with highly malignant behaviour and poor prognosis. Here, we used human ESC-derived neural crest model to recapitulate the initiation of MYCN-driven neuroblastoma and to identify MYCN downstream effectors. Our results show that induced deregulation of MYCN in human neural crest progenitor cells is sufficient to induce tumors that recapitulate the pathological and molecular features of human MYCN-amplified neuroblastoma(MNA-NB). By using this platform, we are able to identify a group of 28 genes that are associated with MYCN expression level only in MNA-NB.

overall_design: RNA-sequencing of control NCSCs and NCSCs+MYCN

last: Weng


title: Synchronization and interaction of proline, ascorbate and oxidative stress pathways under abiotic stress combination in tomato plants

city: Davis

first: Barbara

last: Blanco-Ulate

state: CA

address: One Shields Avenue

department: Plant Sciences

institute: University of California, Davis

summary: Adverse environmental conditions, such as salinity, heat waves, or water scarcity have a devastating impact on plant productivity. In nature, multiple abiotic stresses occur simultaneously and plants evolved unique responses to cope against combination stress that are not induced under a single stress condition. Here we coupled genome-wide transcriptional profiling and untargeted metabolomics with physiological and biochemical analyses to characterize the effect of salinity and heat applied jointly in the metabolism of tomato plants. Our results demonstrate that combination of salinity and heat causes unique reprogramming of tomato metabolic pathways, including changes in the expression of 1,388 genes and accumulation of 568 molecular features. Pathway enrichment analysis of transcript and metabolite data indicated that the proline and ascorbate pathways act synchronously to maintain cellular redox homeostasis, which was supported by measurements of enzymatic activity and oxidative stress markers. We also identified key transcription factors from the basic Leucine Zipper Domain (bZIP), Zinc Finger Cysteine-2/Histidine-2 (C2H2) and Trihelix families that are likely regulators of the identified up-regulated genes under salinity and heat combination.  Our results expand the current understanding of how plants acclimate to environmental stresses in combination and unveiled the synergism between key cellular metabolic pathways for effective reactive oxygen species detoxification. Our study opens the door to elucidating the different signaling mechanisms for stress tolerance.

overall_design: Genome-wide transcriptional profiling to characterize the effect of salinity and heat applied jointly in the metabolism of tomato plants.

first: María

last: Lopez-Delacalle

first: Christian

last: Silva

first: Teresa

middle: C

last: Mestre

first: Vicente

last: Martinez

first: Rosa

last: Rivero


title: Gene expression profiling of TET1 KO induced pluripotent stem cells (iPSCs) reprogrammed from WT mouse embryonic fibroblasts (MEFs)

city: Leuven

first: Kian

middle: Peng

last: Koh

state: Select...

address: Herestraat 49, O&N IV - box 804

institute: KULeuven

summary: The generation of induced pluripotent stem cells (iPSCs) involves activation of the endogenous pluripotency circuitry and global DNA demethylation late in reprogramming, but temporal resolution of these events are insufficient using existing stage markers. Here, we generated murine transgenic lines harboring dual fluorescent reporters reflecting cell-state specific expression of the master pluripotency factor Oct4 and the 5-methylcytosine dioxygenase Tet1. By assessing reprogramming intermediates based on dual reporter patterns, we identified a sequential order of Tet1 and Oct4 gene activation at proximal and distal regulatory elements following pluripotency entry. A transient phase of global gene repression accompanies full activation of Tet1, precedes activation of meiotic and gametogenesis genes, and distinguishes phases of global DNA demethylation reminiscent of germ-line reprogramming. Loss of Tet1 is compatible with reprogramming towards full Oct4 gene activation, but generates iPSCs with epigenetic defects. Therefore, the transcriptional logic of Tet1 expression signals an epigenetic roadmap towards efficient reprogramming.

overall_design: Transcriptome analysis of Cas9 TET1 KO and non-targeted iPSCs all in biological triplicates by RNA-seq.

first: Michela

last: Bartoccetti

first: Ben

last: van der Veer


title: RNA-Sequencing analysis of control and SORBS2 knockdown cardiac progenitor cells derived from human stem cells in vitro

city: Shanghai

first: Fei

last: Liang

state: Shanghai

address: 1678 Dong Fang Road

department: Shanghai Children's Medical Center

institute: Shanghai Jiao Tong University School of Medicine

summary: Chromosome 4q deletion syndrome is one of the most frequently detected genomic imbalance events in congenital heart disease (CHD) patients. However, a portion of terminal 4q deletions with CHD do not include known CHD genes. Here in a target sequencing of a panel of known and candidate CHD genes, we showed that the detrimental rare variants of SORBS2 in 4q35.1 are significantly enriched in CHD patients. Examination of Sorbs2-/- mouse hearts revealed two types of atrial septal defects (ASD), atrial hypoplasia/aplasia and double atrial septum. In vitro human cardiogenesis indicated a dual role of SORBS2 in maintaining sarcomeric integrity of cardiomyocytes and specifying the fate of cardiac progenitors. Mechanistically, SORBS2 promotes the commitment of the second heart field (SHF) over the first heart field (FHF) fate through c-ABL/NOTCH/SHH axis. Taken together, our data demonstrate that SORBS2 is a novel CHD gene within deleted 4q interval. The presence of double atrial septum in Sorbs2-/- mouse reveals the first molecular etiology of the rare anomaly linked to paradoxical thromboembolism.

overall_design: Examination of mRNA profiles of control and SORBS2 knockdown cardiac progenitor cells

first: Xiaoqing

last: Zhang

first: Bo

last: Wang

first: Zhen

first: Qihua

last: Fu


title: Spatial transcriptomics of fixed tissue micro-regions using Pick-Seq [melanoma]

first: Ajit Johnson

last: Nirmal

summary: Spatial transcriptomics and multiplexed imaging are complementary methods for studying tissue biology. Here we describe a simple method for transcriptional profiling of formalin fixed histology specimens based on mechanical isolation of tissue micro-regions containing 5-20 cells. Sequencing micro-regions from an archival melanoma specimen having multiple distinct histologies reveals significant differences in transcriptional programs associated with tumor invasion, proliferation, and immunoediting and parallel imaging confirms changes in immuno-phenotypes and cancer cell states.

overall_design: mRNA from 40μm regions of interest were collected from multiple histological sites in FFPE melanoma tissue sections, sequenced and gene expression profiles were analyzed.

first: Ajit

first: Zoltan

last: Maliga

first: Nolan

last: Ericson

first: Peter

last: Sorger


title: lncRNA expression alterations in mesothelial cells treated with exosomes

city: Hangzhou

first: Conghui

state: China

address: No.1 Xueshi Road

institute: Zhejiang University

summary: To investigate whether exosomes from ovarian cancer cell lines could change lncRNA expression in mesothelial cells, exosomes from ovarian cancer cells (SKOV3 cells, A2780 cells) were added to MeT-5A cells, PBS treatment was set as blank control. Total RNAs of MeT-5A cells treated with exosomes were extracted, and then lncRNA sequencing was performed.

overall_design: Treatment of exosomes from SKOV3 and A2780 cells induced lncRNA expression in human mesothelial cell lines was measured at 48 hours after exposure to dose of 50ug.


title: DNA methylation profiling across six histological states of prostate cancer

city: Dublin

first: Antoinette

last: Perry

address: Science West, University College Dublin, Belfield, Dublin, Ireland

country: Ireland

institute: University College Dublin

summary: In spite of its prevalence as one of the world’s leading malignancies, prostate cancer (PCa) continues to evade molecular taxonomic sub-classification. However, gross clinical differences are observed within the umbrella term ‘prostate adenocarcinoma’; the majority of tumors appear indolent in nature, whilst a subset manifest aggressively. Contributing factors towards this resistance to molecular classification are an atypically low mutation frequency and a poorly delineated pathobiology. Conversely, epigenetic changes are evidenced to be amongst the earliest and most-widespread aberrations in PCa . We thus hypothesized that delineating epigenomic alterations during the stepwise progression of PCa would improve our understanding of the disease pathobiology and the molecular underpinning of indolent and aggressive tumors. Herein, we report the first epigenomic roadmap of prostate tumorigenesis, in which we dissected DNA methylation and microRNA expression in enriched epithelial cells across the entire trajectory of PCa, through tumor initiation, primary disease and metastatic dissemination.   												Infinium Human Methylation450K Beachip (Illumina) technology was employed to assess the methylation status of >485,000 CpG sites throughout the genome across six histological stages of prostate cancer (PCa) tumorigenesis: benign (n=10), proliferative inflammatory atrophy (PIA; n=7), high grade prostatic intra-epithelial neoplasia (HGPIN; n=6), indolent PCa (PCI, n=7), agressive PCa (PCA; n=8) and lethal metastatic PCa (PCM; n=6). Three peripheral blood lymphocytes (PBL) samples were also included for control purposes.

overall_design: Bisulfite converted DNA for 47 samples was profiled by the Illumina Infinium Human Methylation450K array

first: R

first: C

last: O'Rourke

first: A


title: Overexpression of the cytokinesis regulator PRC1 activates the p53 pathway due to cytoplasmic microtubule-bundling resulting in senescence of A549 lung cancer cells

city: Wuerzburg

first: Carsten

last: Ade

address: Am Hubland

department: Lehrstuhl Biochemie und Molekularbiologie

institute: University of Wuerzburg

summary: Protein regulator of cytokinesis 1 (PRC1) is a microtubule-bundling protein with essential roles in mitosis and cytokinesis. In this study we investigated the potential nuclear functions of PRC1 and the consequences of overexpression of PRC1 by using lung cancer cell lines stably expressing inducible expression constructs for PRC1. Ectopically expressed PRC1 resulted in proliferation defects, multi-nucleation and enlargement of cells which were directly linked to microtubule-bundling within the cytoplasm. Genome wide expression profiling by RNA sequencing revealed that the p53 pathway is activated upon overexpression of PRC1 resulting in cellular senescence. A mutant of PRC1 unable to enter into the nucleus induced the same gene sets as wildtype PRC1, suggesting that PRC1 has no nuclear-specific functions in lung cancer cells. The depletion of p53 switched the response to PRC1 overexpression or depletion from senescence to apoptosis. In addition, treatment with cisplatin, a commonly used chemotherapeutic drug, enhanced the proliferation defects due to deregulated PRC1, implicating PRC1 as a possible therapeutic target for cancer. Taken together, PRC1 needs to be tightly regulated to allow unperturbed proliferation of lung cancer cells.

overall_design: RNA-seq analysis of A549 lung cancer cells after overexpression of PRC1 or PRC1-NLS3A.

first: Steffen

last: Hanselmann

first: Woo

last: Shin

first: Stefan

last: Gaubatz


title: Muscle transcriptome from active and hibernating brown bears (Ursus arctos)

city: Saint-Genès Champanelle

first: Etienne

last: Lefai

address: INRA Auvergne Rhône -Alpes

institute: INRA

summary:
Male and female 2- and 3-years old brown bear from the region of Tackasen (Sweden) were captured in summer and winter. Muscle biopsies from vastus lateralis were collected in february (hibernation state) and june (active period).
Total RNA were extracted from muscle tissue and full transcriptome analysis (RNA Seq) were performed.
Statistical analysis were performed to winter versus summer comparison from matched paired samples

overall_design: mRNA profiles of six individual bears at the two season were generated

first: Fabrice

last: Bertile

first: Lydie

last: Combaret


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and non-antibiotic pharmaceuticals stressed E. coli K-12 LE392, P. putida KT2440, and RP4 plasmid Transcriptomes [experiment 1]

city: Brisbane

first: Jianhua

last: Guo

address: Research Road, Level 4 Gehrmann Building

department: Australian Centre for Water and Environmental Biotechnology

country: Australia

institute: University of Queensland

summary: The goals of this study are to use Next-generation sequencing (NGS) to detect bacterial mRNA profiles of wild-type E. coli K-12 LE392, P. putida KT2440 and IncPα RP4 plasmid, and their mRNA response under the exposure of six non-antibiotic pharmaceuticals, including ibuprofen, naproxen, gemfibrozil, diclofenac, propanolol, and iopromide. The concentrations were 0.5 mg/L for ibuprofen, naproxen, gemfibrozil, diclofenac, propanolol, and 1.0 mg/L for iopromide. The group without dosing pharmaceutical was the control group. Each concentration was conducted in triplicate. By comparing the mRNA profiles of experimental groups and control group, the effects of these six non-antibiotic pharmaceuticals on transcriptional levels can be revealed. Illumina HiSeq 2500 was applied. The NGS QC toolkit (version 2.3.3) was used to treat the raw sequence reads to trim the 3’-end residual adaptors and primers, and the ambiguous characters in the reads were removed. Then, the sequence reads consisting of at least 85% bases were progressively trimmed at the 3’-ends until a quality value ≥ 20 were kept. Downstream analyses were performed using the generated clean reads of no shorter than 75 bp. The clean reads of each sample were aligned to the E. coli reference genome (NC_000913), P.putida reference genome (NC_002947), and IncPα plasmid reference genome (NC_00) using SeqAlto (version 0.5). Cufflinks (version 2.2.1) was used to calculate the strand-specific coverage for each gene, and to analyze the differential expression in triplicate bacterial cell cultures. The statistical analyses and visualization were conducted using CummeRbund package in R (http://compbio.mit.edu/cummeRbund/). Gene expression was calculated as fragments per kilobase of a gene per million mapped reads (FPKM, a normalized value generated from the frequency of detection and the length of a given gene.

sample_organism:
Plasmid RP4
Escherichia coli K-12
Pseudomonas putida KT2440

overall_design: Bacterial mRNA profiles of wild-type E. coli K-12 LE392, P. putida KT2440, and IncPα RP4 plasmid in response to 0.5 mg/L ibuprofen, 0.5 mg/L naproxen, 0.5 mg/L gemfibrozil, 0.5 mg/L diclofenac, 0.5 mg/L propanolol, and 1.0 mg/L  iopromide for 2 hours, bacteria and plasmid without dosing pharmaceutical are the control group, in triplicate, using Illumina HiSeq 2500

first: Yue

first: Ji

last: Lu

first: Likai

last: Mao


title: Expression data from human hematopoietic stem cells with different culture systems

city: Taoyuan City

first: TSAI

middle: CHI

last: LIU

address: No. 300, Zhongda Rd., Zhongli District,

department: Department of Biomedical Sciences and Engineering

institute: National Central University

summary: To date, different experimental strategies have been developed for the ex vivo expansion of human hematopoietic stem (HSCs) in clinical application. However, it is still unclear to what difference in genomic function in HSCs expansion under different culture systems. In this study, we compared gene-expression profile of ex vivo expanded serum (10% FBS, fetal bovine serum) and serum-free culture systems, and then analyze molecular function of differentially expressed gene using microarray chips.

overall_design: human hematopoietic stem cells from 2 different expanded culture systems

first: Tsai-Chi

last: Liu

first: Yi-Chiung

last: Hsu