title: Global cellular metabolic rewiring adapts Corynebacterium glutamicum to efficient non-natural substrate utilization

city: Tianjin

first: Xi

last: Sun

address: Yaguan road 135

institute: Tianjin university

summary: Efficient assimilation of renewable feedstocks is the cornerstone for achieving sustainable and economical microbial production of commodity chemicals. Unfortunately, most renewables are foreign to the cellular metabolism of classical industrial workhorses, resulting in unsatisfactory biomanufacturing performance. Here, Corynebacterium glutamicum was systematically engineered for rapid non-natural xylose metabolism and the underlying adaptations were elucidated by combining metabolic engineering, adaptive laboratory evolution and systems biology techniques. A plasmid-free, stable and efficient xylose-utilizing chassis strain, named CGS15, was reconstructed with both a rapid specific growth rate of 0.341 h-1 on xylose and an excellent co-utilization of glucose and xylose at a ratio of about 2:1. For the first time, we revealed a novel xylose regulatory mechanism by the endogenous transcription factor IpsA with global regulatory effects on C. glutamicum core carbon and energy metabolism. The coordination between the heterologous xylose metabolism and the endogenous carbon/energy metabolism both endowed cells with accelerated growth and released carbon catabolite repression. Finally, this chassis demonstrated great promise for lignocellulosic biorefinery applications by producing 97.1 g/L of the platform compound succinate from corn stalk hydrolysate with an average productivity of 8.09 g/L/h. This work provides an elegant paradigm to understand and engineer the metabolism of renewable substrates for sustainable biomanufacturing.

overall_design: Here, we applied integrated multidisciplinary strategies including metabolic engineering, evolutionary engineering and systems biology to systematically investigate rapid non-natural substrate (xylose) metabolism in Corynebacterium glutamicum.

first: Yufeng

last: Mao

first: Zhiwen

last: Wang


title: Next Generation Sequencing of macrophages cocultured with tumor cell

status: Public on Oct 02 2022

city: Beijing

first: Xuefei

last: Guo

state: Bejing

address: Xueyuan road, haidian district

department: Institute of Systems Biomedicine

country: China

institute: Peking university health science center

type: Expression profiling by high throughput sequencing

summary: To systematically examine the effect of tumor cells on macrophages, the RAW264.7 cells after a 24-hour coculture with CT26 cells were subjected to RNA sequencing, the complete medium of CT26 cells were used as control.

overall_design: mRNA profiles of macrophages cocultured with or without tumor cells

first: Xiao


title: IL-17 cytokines preferentially act on naïve CD4+ T cells

status: Public on Oct 03 2022

city: Iowa City

first: Nitin

last: Karandikar

state: Iowa

address: C673 General Hospital

department: Pathology

country: USA

institute: University of Iowa

summary: CD4+ Th17 T cells are a key helper population in the regulation of both protective immunity during infection and in self-tolerance. Through the secretion of IL-17, Th17 cells act in promotion of inflammation and thus a major therapeutic target for autoimmune disorders. Recent reports have brought to light that the IL-17 family cytokines, IL-17A, IL-17F and IL-17AF, can directly act on CD4+ T-cells, both in murine and human systems. Here we show that this action is preferentially targeted toward naïve, but not memory, CD4+ T-cells. Moreover,  IL-17A, IL-17F and IL-17AF led to reduction in immune signaling genes, but an increase in interferon responsive genes across all treatments. In addition, IL-17A, IL-17F and IL-17AF treatment possessed differences in downstream transcriptional signaling, with IL-17AF heterodimer conferring both the greatest transcriptional change and suppressed phenotype. Detailed transcriptome analysis provides important functional insights into the genes and pathways that are modulated as a result of IL-17-mediated signaling.

overall_design: mRNA profiles of ex vivo-purified bulk CD4+CD25- CD45RO+ memory T-cells were activated in vitro for 48 or 168 hours in the presence of media alone (controls), or 10 ng/ml of IL-17A, IL-17F or IL-17AF

first: Michael

middle: P

last: Crawford

first: Nicholas

last: Borcherding

middle: J


title: Inhibition of the CtBP complex and FBXO11 enhances MHC class II expression and anti-cancer immune responses [RNA-Seq]

city: Melbourne

first: Mark

last: Dawson

address: 305 Grattan Street

department: Cancer Research

country: Australia

institute: Peter MacCallum Cancer Centre

summary: There is increasing recognition of the prognostic significance of tumor cell major histocompatibility complex (MHC) class II expression in anti-cancer immunity. Relapse of acute myeloid leukemia (AML) following allogeneic stem cell transplantation (alloSCT) has recently been linked to MHC class II silencing in leukemic blasts; however, the regulation of MHC class II expression remains incompletely understood. Utilizing unbiased CRISPR-Cas9 screens, we identify that the C-terminal binding protein (CtBP) complex transcriptionally represses MHC class II pathway genes, while the E3 ubiquitin ligase complex component FBXO11 mediates degradation of CIITA, the principal transcription factor regulating MHC class II expression. Targeting these repressive mechanisms selectively induces MHC class II upregulation across a range of AML cell lines. Functionally, MHC class II+ leukemic blasts stimulate antigen-dependent CD4+ T cell activation and potent anti-tumor immune responses, providing fundamental insights into the graft-versus-leukemia effect. These findings establish the rationale for therapeutic strategies aimed at restoring tumor-specific MHC class II expression to salvage AML relapse post-alloSCT and also potentially to enhance immunotherapy outcomes in non-myeloid malignancies.

overall_design: RNAseq of OCI-AML3 cells after CRISPR KO of FBXO11 or RREB1, with or without IFN-gamma stimulation.

first: Kah

middle: L

last: Chan

first: Marian

last: Burr

middle: A


title: Inhibition of the CtBP complex and FBXO11 enhances MHC class II expression and anti-cancer immune responses [CUT&TAG]

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: CUT&Tag chromatin profiling for H3K9me2 and H3K27me3 in MV4-11 AML cells.


title: Inhibition of the CtBP complex and FBXO11 enhances MHC class II expression and anti-cancer immune responses [Epigenetic CRISPRscreen]

overall_design: CRISPR screen for MHC-II high cells using custom targeted epigenetic library.


title: Inhibition of the CtBP complex and FBXO11 enhances MHC class II expression and anti-cancer immune responses [Whole-genome CRISPRscreen]

overall_design: CRISPR screen for MHC-II high cells using whole genome library.


title: Glucocorticoid imprints a low glucose metabolism onto CD8 T cells and induces the persistent suppression of the immune response

city: Toon

first: Junpei

last: Suzuki

address: Shitukawa

department: Graduate School of Medicine

country: Japan

institute: Ehime University

summary: To elucidate the effect of predonisolone on CD8 T cell differentiation, we have measured gene expression in predonisolone-treated CD8  cells.

overall_design: Gene expression of vehicle control (Ctrl) or Prednisolone (PSL; 1 uM)-treated CD8 T cells was measured at five days after TCR stimulation.

first: Amane

last: Konishi


title: Single cell RNAseq reveal covid19 vaccine response difference

city: los angeles

first: Changfu

last: Yao

state: Ca

address: 8700 Beverly Blvd. AHSP Room A9401

department: Lung and Regenerative Medicine Institutes

institute: cedars-sinai medical center

summary: Single cell RNAseq was performed on PBMC isolated from health workers who received two doses of Pfizer COVID19 vaccine and determined as either normal responders or low responders by antibody test. Each group has 4 patients. Cells from each patient were labeled with Totalseq C hashing antibodies and mixed 1:1:1:1 for each group. Single cells were further captured using 10x chromium Next GEM 5 prime kit.

overall_design: We isolated PBMCs from health workers with either normal reponse or low reponse to COVID19 vaccine

first: Peter

last: Chen


title: The whole transcriptome regulation as a function of mitochondrial polymorphisms and age in C. elegans

city: Xuzhou

first: Zuobin

last: Zhu

state: Jiangsu

address: Tongshan road 209

department: Department of Genetics

institute: Xuzhou Medical University

summary: The complex IV polymorphisms in mitochondria not only affected the mitochondria mass but also miRNA, lncRNA, mRNA and circRNA profiles. Furthermore, Most of genes that associated with mitochondria, showed age-related expression feature (P = 3.62156E-37). Next, we constructed a differentially expressed circRNA-lncRNA-miRNA-mRNA-ceRNA regulatory networks to determine functional interactions affected by the mitochondria variation. We also selected top 10 candidates ceRNA with the most correlation among the RNA. In addition, KEGG pathway analyses showed that the genes affected by the mitochondria variation were an enrichment of metabolic activity. Finally, we examined the metabolic changes in the old worms and analyzed the association between the metabolites and genes. The construction of multi-omics regulation network is great value for the research of nuclear genes mitochondria and aging. Here, we constructed a multi-level regulatory network with aging which affected by the mitochondria variation in C. elegans and the interaction between these genes are great value for further aging research. Thus, our finding provides new evidence for understanding the molecular mechanisms of how mitochondria influence on aging.

overall_design: lncRNA and mRNA profiles of 0-day, 6-day, 9-day, 12-day old N2 strain and the transnuclear CN30 worms were generated by deep sequencing, using Illumina  HiSeq Xten platform.

first: Ying

last: Li


title: Bulk RNAseq analysis of Ecsit-deficient skeletal progenitors

city: Worcester

first: Rui

state: Massachusetts

address: 364 Plantation Street, LRB

department: MCCB

institute: University of Massachusetts Medical School

summary: Whole transcriptome analysis showing differential gene expression in Ecsit sufficient vs deficient skeletal progenitors.

overall_design: Skeletal progenitors were obtained from digested hindlimbs of EcsitPrx1;Rosa26mTmG and Ecsitfl/fl;Rosa26mTmG pups at postnatal day 1, and DAPI- live cells were FACS sorted using a FACSAria II SORP cell sorter (Becton Dickinson). Total RNA isolated from Prx1+CD45-Tie2-Ter119- skeletal progenitors was subjected to RNA seq.

first: Chujiao

last: Lin

first: Qiyuan

last: Yang

first: Dongsheng

first: Jun

last: Xie

first: Yeon-Suk

first: Sachin

last: Chaugule

first: Ngoc

last: DeSouza

first: Won-Taek

last: Oh

first: Zhihao

first: Aijaz

last: John

first: Qiang

last: Qiu

first: Lihua

first: Matthew

last: Greenblatt

first: Sankar

last: Ghosh

first: Shaoguang

first: Guangping

last: Gao

first: Cole

last: Haynes

first: Charles

last: Emerson

first: Jae-Hyuck

last: Shim


title: NGS-based miRNome profile in cardiac muscle tissue of congenital heart disease patients

city: Bangalore

first: madavan

last: vasudevan

state: Karnataka

address: Kasturi Nagar

country: India

institute: Theomics International Private Limited

type: Non-coding RNA profiling by high throughput sequencing

summary: The goal of this study was to explore the miRNome profile in three frequently occurring Congenital Heart Disease (CHD) types, namely Atrial Septal Defect (ASD), Ventricular Septal Defect (VSD) and Tetralogy of Fallot (TOF). For this purpose, we extracted total RNA from the cardiac tissues of patients with CHD and non-CHD, which was subjected to high-throughput sequencing technology to profile the miRNAs. The small RNA sequencing data was analyzed using the nf-core bioinformatic analysis pipeline. There were 40 up-regulated and 8 down-regulated miRNAs identified to be differentially expressed. These miRNAs are predicted to target several genes involved in regulatory pathways such as cell proliferation, differentiation, cell survival, etc. The results from this study are expected to expand the existing knowledge on molecular basis of CHD. Functional validation can throw insights on molecular epidemiology and therapy for heart diseases.

overall_design: Investigation of the microRNA expression profile in 3 types of Congenital Heart Disease (CHD) cases against non-CHD controls

first: Anandan

last: Balakrishnan

first: Madavan

last: Vasudevan


title: expression data from colon cancer

city: Bronx

first: Elena

last: Tosti

address: 1301 Morris park avenue

institute: Albert Einstein College of Medicine

summary:
expression analysis in colon cancer from  Msh2 and Tgfbr2 intestinal epithelium inactivated mouse model
detailed gene expression analysis in colon cacer developed in mouse model with  Msh2 and Tgfbr2  inactivated eary n  from Villin Cre recombnase exclusively in the intestine

overall_design: Gene expression analysis of RNA isolated from bulk tissue was performed using the Mouse Gene ST 1.0 Array System (Affymetrix). colon cancer tissue amd matched tumor free muosa were used for RNA extraction

first: Winfried

last: Edelmann

first: Pilib

middle: O

last: Broin

first: Mariel

middle: B

last: Silva


title: KDM6B protects T-ALL cells from NOTCH1-induced oncogenic stress [Mouse RNAseq]

status: Public on Oct 01 2022

city: St Louis

first: Grant

last: Challen

state: MO

address: 660 Euclid Avenue

department: Medicine

institute: Washington University School of Medicine

summary: Kdm6b mutant cells are at a survival disadvantage in NOTCH1- induced T-ALL

overall_design: T-ALL cells were sorted from peripheral blood of Vav-CRE:Control and Vav-CRE:Kdm6b-KO mice for RNA-seq to determine gene expression changes

first: Nancy

last: Issa

first: Aishwarya

last: Krishnan

first: Hassan

last: Bjeije

first: Hamza

last: Celik

first: Saranajith

last: Dunuwille

first: Won

middle: K

last: Kyuh

first: Andrew

last: Young

first: Sammi

last: Burkart

first: Jason

last: Arand


title: Colon cancer

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

overall_design: Refer to individual Series


title: Inhibition of the CtBP complex and FBXO11 enhances MHC class II expression and anti-cancer immune responses

first: Mark

last: Dawson


title: KDM6B protects T-ALL cells from NOTCH1-induced oncogenic stress

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Targeting MLL methyltransferases enhance the anti-tumor effects of PI3K inhibition in hormone receptor-positive breast cancer [RNA-Seq]

city: Atlanta

first: Jennifer

middle: Marie

last: Spangle

state: Georgia

address: 1365C Clifton Rd NE

institute: Emory University

summary: The high frequency of aberrant PI3K pathway activation in hormone receptor-positive (HR+) breast cancer has led to the development, clinical testing, and approval of the p110a-selective PI3K inhibitor alpelisib. The limited clinical efficacy of alpelisib and other PI3K inhibitors is partially attributed to the functional antagonism between PI3K and estrogen receptor (ER) signaling, which is mitigated via combined PI3K inhibition and endocrine therapy. We and others have previously demonstrated chromatin-associated mechanisms by which PI3K supports cancer development and antagonizes ER signaling through the modulation of the H3K4 methylation axis; inhibition of KDM5A promoter H3K4 demethylation and KMT2D/MLL4-directed enhancer H3K4 methylation. Here we show that inhibition of the H3K4 histone methyltransferase MLL1 in combination with PI3K inhibition impairs HR+ breast cancer clonogenicity and cell proliferation. While combined PI3K/MLL1 inhibition reduces PI3K/AKT signaling and H3K4 methylation, MLL1 inhibition increases PI3K/AKT signaling and dysregulates the expression of processes that lead to AKT activation. These data reveal a feedback loop between MLL1 and AKT whereby MLL1 inhibition reactivates AKT. We show that combined PI3K and MLL1 inhibition synergizes to cause cell death in in vitro and in vivo models of HR+ breast cancer, which is enhanced by the additional genetic ablation of the H3K4 methyltransferase and AKT target KMT2D/MLL4. Together, our data provide evidence of a feedback mechanism connecting histone methylation with AKT and may support the preclinical development and testing of pan-MLL inhibitors.

overall_design: Comparative gene expression analysis of RNA-seq data in T47D cells treated with the MLL1 inhibitor MI503 or DMSO for 24h.

first: J

last: Farhi

first: K

last: Parwani

middle: M


title: Transcriptome profiling of Arabidopsis seedlings upon hyperosmotic stress

city: Shenzhen

first: Yinpeng

last: Xie

state: Guangdong

address: 1088 Xueyuan Avenue

institute: Southern University of Science and Technology

summary: We examined the possible effect of hyperosmotic stress on Arabidopsis transcriptome using mRNA-seq. We found that the transcriptome is reprogrammed in response to hyperosmotic stress, in a DCP5-dependent.

overall_design: High-throughput sequencing of mRNA from Col-0 and dcp5-1 Arabidopsis seedlings with 0 min or 60 min of hyperosmotic stress mediated by 150 mM NaCl

first: Zhenyu

last: Wang


title: Single-cell atlas of patient-derived trophoblast organoids (TO) in on-going pregnancies.

city: Rotterdam

first: Olivier

last: Schäffers

address: Dr. Molenwaterplein 40

country: Netherlands

institute: Erasmus Medical Center

summary: Trophoblast organoids (TOs) hold great promise for elucidating human placental development and function. By deriving TOs in on-going pregnancies using chorionic villus sampling (CVS), we established a platform to study trophoblast differentiation and function in early pregnancy, including pregnancies with different fetal genetic abnormalities. We addressed cellular heterogeneity of CVS-derived TOs by providing a single-cell transcriptomic atlas and show that CVS-TOs recapitulate key aspects of the human placenta, including syncytial fusion and hormone synthesis. This study demonstrates the utility of trophoblast organoids for investigating genetic defects in the placenta and describes an experimental platform for future personalized placental medicine approaches, including genotype-phenotype mapping.

overall_design: TOs derived from chorionic villi (10-14 weeks of gestation) were dissociated into single-cell suspensions and subsequently processed on the 10X Genomics Chromium Platform using the Next GEM Single Cell 3' Reagent kit (v3.1) with Dual Index Kit following the manufacturer's protocol.

first: Joost

last: Gribnau

first: Bas

last: van Rijn


title: Acute deletion of TET enzymes results in aneuploidy in mouse embryonic stem cells through decreased expression of Khdc3 (Whole Genome Sequencing [Low Coverage])

city: SAN DIEGO

first: Anjana

last: Rao

state: CALIFORNIA

address: 9420 Athena CIRCLE, LA JOLLA

institute: LA JOLLA INSTITUTE

summary:
Low coverage whole genome sequencing (lc-WGS) from inducible Tet TKO (Tet iTKO) and control (Ctrl) mouse ESCs (mESC), as well as for germline Dnmt TKO mESCs.
mESCs were sorted to isolate the Live/Dead dye and Thy1.2 negative CD326+GFP+ population representing the mESCs populations responsive to the tamoxifen treatment. The cells were resuspended in FACS buffer and filtered with a 70 µM filter before sorting. These bulk-population samples were analyzed by using low coverage Whole Genome Sequencing (lc-WGS).

overall_design: Low coverage Whole Genome Sequencing (WGS) from bulk Ctrl and Tet iTKO mESC populations under three different conditions: pre-treatment, tamoxifen treated and long-term culture after tamoxifen treatment. Dnmt TKO (germline Knock-out [non-inducible]) mESC were included as part of the long-term effects comparison.

first: Romain

last: Georges

first: Hugo

last: Sepulveda

first: Carlos

last: Angel


title: Transcriptomic analyses reveal regional signatures in lung allograft recipients

city: Perth

first: Patricia

last: Agudelo-Romero

state: WA

address: Northern Entrance, Perth Children's Hospital, 15 Hospital Ave, Nedlands

department: Chronic and Severe Diseases

institute: Telethon Kids Institute

summary: Background and objective: Long term outcomes of allograft recipients are compromised by the development of chronic lung allograft dysfunction (CLAD) or bronchiolitis obliterans syndrome (BOS) which initiates in the lung periphery. We established baseline transcriptomic profiles of both the large and small airway epithelial cells (referred as LAEC and SAEC, respectively) to identify regional differences irrespective of initiating disease.  Methods: We obtained matched primary LAEC and SAEC from lung allograft recipients (n=4, 42.5±4.2 years) and established primary cultures. Bulk RNA sequencing was performed to determine differentially expressed genes.  Results: We observed differences in the transcriptional program between LAEC and SAEC Transcription factors (TF) were ranked within the top ten differentially regulated genes. The most abundant TF families included C2H2-ZF, homeobox and bHLH. Upstream regulator analyses identified homeobox genes being significantly in LAEC. Protein-protein interaction network analysis emphasised the role of TFs (ISL1, MSX1, HOXA1, GATA6, ZNF423) in airway modulation. Additionally, functional enrichment analysis revealed the activation of chemotaxis, metalloendipeptidase/metallopeptidase activity and pro-inflammatory signatures (IL17 signalling and RAGE), in LAEC, while SAEC were characterised by elevated expression of surfactant metabolism related genes. Moreover, alveolar and club cells-related genes were expressed in SAEC, suggesting a lower airway-specific signature.  Conclusion: Our analysis shows robust transcriptional differences between LAEC and SAEC. We suggest a potential role for homeobox TF family as well as the activation of the immune system in the biology of LAEC. Conversely, we observed an alveoli-like transcriptional signature in SAEC, including gas-exchange signals and surfactant metabolism; pathways involved in lung homeostasis.

overall_design: Matched samples from proximal and distal lung biopsies were obtained from lung allograft recipients during the routine surveillance bronchoscopy. Patients did not present symptomatology indicative of bronchiolitis obliterans syndrome (BOS), transplant rejection or infections at the time of sample collection. Specimens were obtained from four patients (3 females, age range 38-47) that underwent double lung transplantation. The reasons for lung transplantation were cystic fibrosis (CF; 3 cases), and congenital heart disease (CHD; 1 case). Both, large and small airway epithelial cells (referred as LAEC and SAEC) were grown as a monolayer to confluency and cells then harvested for transcriptomics analysis.

first: Kak-Ming

last: Ling

first: Melanie

last: Lavender

first: Jeremy

last: Wrobel

first: Michael

last: Musk

first: Stephen

last: Stick

first: Anthony

last: Kicic


title: Transcriptomic analysis of cardiac gene expression associated to RAGE deletion and aging

city: Milano

first: Gualtiero

middle: Ivanoe

last: Colombo

address: Via Carlo Parea, 4

country: Italy

institute: Centro Cardiologico Monzino IRCCS

summary:
Cardiac aging is characterized by increased cardiomyocyte hypertrophy, myocardial stiffness and fibrosis, which enhance the cardiovascular risk. The receptor for advanced glycation end-products (RAGE) is involved in several age-related diseases. Rage knockout (Rage-/-) mice show an acceleration of cardiac dimensions changes and interstitial fibrosis with aging. This study identifies the age-associated cardiac gene expression signature induced by RAGE deletion.
We analyzed the left ventricle transcriptome of 2.5- (Young), 12- (Middle age, MA) and 21- (Old) month-old female Rage-/- and C57BL/6 (WT) mice. By comparing Young, MA and Old Rage-/- versus age-matched WT mice, we identified 122, 192 and 11 differently expressed genes, respectively. Functional inference analysis showed that RAGE deletion is associated with: (i) a down-regulation of genes involved in antigen processing and presentation of exogenous antigen, adaptive immune response, cytokine and type I- and gamma-interferon mediated pathway in Young animals; (ii) an up-regulation of genes related to fatty acid oxidation, cardiac structure remodeling and impaired response to hypoxia in MA mice; (iii) an up-regulation of few genes belonging to complement activation and triglyceride biosynthetic process in Old animals.
Our findings show that the age-dependent cardiac phenotype of Rage-/- mice is mainly associated to alterations of genes related to adaptive immunity and cardiac stress pathways.

overall_design: A total of 29 mice of different ages (i.e. ten-week-old, twelve-month-old or twenty-one-month-old (Young, MA and Old, respectively)), and genotypes (i.e. Wild type and Rage-/-) were used. RNA was extracted from left ventricle of frozen mouse hearts and used for microarray assays. An additive linear model for a multilevel experiment, which includes mouse age and genotype factors, was designed.

first: Luca

last: Piacentini

middle: I

first: Angela

last: Raucci


title: Protein Kinase C Delta Regulates Mononuclear Phagocytes by Repressing Type I and II Interferon Signaling and Hinders Response to Immunotherapy in Cancer

city: Memphis

first: Liza

last: Makowski

state: Tennessee

address: 19 South Manassas St

department: Medicine- Heme Onc

institute: UTHSC

summary: Mononuclear phagocytes (MPs) comprise monocytes, macrophages and dendritic cells and play a crucial role in tissue homeostasis. However, accumulating evidence suggests that mononuclear phagocytes contribute to tumor progression and resistance to checkpoint blockade. Protein kinase C delta (PKCδ) is a serine/threonine kinase that plays a crucial role in regulating the immune response by preventing autoimmunity. However, the role of PKCδ in antitumor immunity is unknown. In this study, we found that PKCδ is abundantly expressed by MPs in several human and mouse tumors. PKCδ-/- mice were more resistant to growth of various cancers compared to wild-type mice and were more responsive to anti-PD-1 immunotherapy. Furthermore, we found that tumors from PKCδ-/- mice harbor a Th-1-skewed immune response including increased antigen cross-presentation and T cell activation. Depletion of MPs in vivo altered tumor growth in wild-type mice, but not in PKCδ-/- mice. In addition, co-injection of PKCδ-/- M2-like macrophages with cancer cells into wild-type mice markedly delayed tumor growth and significantly increased intratumoral T cell activation compared to wild-type M2-like macrophages co-injected with cancer cells. Finally, intrinsic loss of PKCδ functionally reprogrammed macrophages and dendritic cells by promoting their antigen presenting and cross-presenting capacity and triggered Type I and II interferon signaling. Our results suggest that PKCδ can be targeted to reprogram mononuclear phagocytes and augment checkpoint blockade efficacy.

overall_design: RNA-seq data from PKC delta wildtype or knockout bulk tumors, bone marrow-derived macrophages, dendritic cells or immature myeloid cells.

first: David

middle: N

last: Hayes


title: Molecular and anatomical roadmap of stroke pathology in immunodeficient mice

city: Schlieren, Zurich

first: Ruslan

last: Rust

state: Zurich

address: Wagistrasse 12

country: Switzerland

institute: University of Zurich

summary: Here, we assessed the stroke pathology of popular genetic immunodeficient mouse models using NOD scid gamma (NSG) and recombination activating gene 2 (Rag2–/–) mice as well as pharmacologically immunosuppressed mice and compared them to immune competent, wildtype (WT) C57BL/6J mice three weeks after injury.

overall_design: We compared gene expression differences after photothrombotic stroke at 21 days after injury in the injured brain regions of NSG, Rag2, WT-Tacrolimus, WT mice.

first: Rebecca

last: Weber

first: Christian

last: Tackenberg


title: RNA-seq on LX-2 cells treated with conditioned medium from either HCT116Vector or HCT116FGFBP1 cells

city: Guangzhou

first: Minfeng

last: Chen

address: Huangpu road 601

institute: Jinan University

summary: To define the global effects of tumor cell-derived FGFBP1 on the phenotype modifications of HSCs

overall_design: We performed gene expression profiling analysis using data obtained from RNA-seq of 2 different condition mediums cultured LX-2 cells.

first: Dongmei

last: Zhang

first: Ming

last: Qi

first: Shuran

last: Fan


title: Targeting MLL methyltransferases enhance the anti-tumor effects of PI3K inhibition in hormone receptor-positive breast cancer [Cut & Run]

first: Jennifer

last: Spangle

overall_design: Comparative genomic localization of H3K4me3 and MLL1 from CUT&RUN-seq data in T47D cells treated with the MLL1 inhibitor MI503 for 24h

first: G

last: Cooper

first: K

last: Parwani

first: J


title: Targeting MLL methyltransferases enhance the anti-tumor effects of PI3K inhibition in hormone receptor-positive breast cancer


title: FOXM1-mediated regulation of reactive oxygen species and radioresistance in oral squamous cell carcinoma cells

city: Kumamoto

first: Ryoji

last: Yoshida

state: Kumamoto

address: Honjo 1-1-1, Chu-o-ku

department: Oral and Maxillofacial Surgery

institute: Kumamoto University

summary: Radioresistance is a major obstacle to the successful treatment of oral squamous cell carcinoma (OSCC). To help overcome this issue, we have developed clinically relevant radioresistant (CRR) cell lines, generated by irradiating parental cells over time, which are useful for OSCC research. In the present study, we conducted gene expression analysis using CRR cells and their parental lines to investigate the regulation of radioresistance in OSCC cells. Based on gene expression changes over time in CRR cells and parental lines subjected to irradiation, forkhead box M1 (FOXM1) was selected for further analysis in terms of its expression OSCC cell lines, including CRR cell lines, and clinical specimens. We suppressed or upregulated the expression of FOXM1 in OSCC cell lines, including CRR cell lines, and examined radiosensitivity, DNA damage, and cell viability under various conditions. The molecular network regulating radiotolerance was also investigated, especially the redox pathway, and the radiosensitizing effect of FOXM1 inhibitors was examined as a potential therapeutic application. We found that FOXM1 was not expressed in normal human keratinocytes but was expressed in several OSCC cell types. The expression of FOXM1 was upregulated in CRR cells compared with that detected in the parental cell lines. In clinical specimens, FOXM1 expression was upregulated in cells that survived irradiation. FOXM1-specific siRNA treatment increased radiosensitivity, whereas FOXM1 overexpression decreased radiosensitivity, and DNA damage was altered significantly under both conditions as well as the levels of redox-related molecules and reactive oxygen species production. Treatment with the FOXM1 inhibitor thiostrepton had a radiosensitizing effect and overcame radiotolerance in CRR cells. According to these results, the FOXM1-mediated regulation of reactive oxygen species could be a novel therapeutic target for the treatment of radioresistant OSCC; thus, treatment strategies targeting this axis might overcome radioresistance in this disease.

overall_design: SAS and SAS-R cells were irradiated with X-rays at 2 Gy per day for 5 days, and total RNA was collected 1, 3, 6, and 12 h after irradiation. Total RNA was also extracted from nonirradiated SAS and SAS-R cells that were cultured for use as control samples.

first: Hisashi

last: Takeshita

first: Junki

last: Inoue

first: Mayumi

last: Hirayama

first: Toru

last: Oyama

first: Ryuta

last: Kubo

first: Keisuke

last: Yamana

first: Yuka

last: Nagao

first: Shunsuke

last: Gohara

last: Sakata

first: Masatoshi

first: Kenta

last: Kawahara

first: Nozomu

last: Takahashi

first: Akiyuki

last: Hirosue

first: Yoshikazu

last: Kuwata

first: Manabu

last: Fukumoto

first: Ryo

last: Toya

first: Ryuji

last: Murakami

first: Hideki

last: Nakayama


title: Long non-coding RNAs are markers of Schistosoma mansoni single-cell populations

city: Sao Paulo

first: Ana

middle: Carolina

last: Tahira

state: São Paulo

address: Avenida Vital Brasil, 1500 prédio 55

department: Parasitologia

country: Brazil

institute: Instituto Butantan

summary: Schistosoma mansoni is a flatworm that causes schistosomiasis, a neglected tropical disease that affects over 200 million people worldwide. New therapeutic targets are needed with only one drug available for treatment and no vaccine. Long non-coding RNAs (lncRNAs) are transcripts longer than 200 nucleotides with low or no protein-coding potential. In other organisms, they have been shown as involved with reproduction, stem cell maintenance and drug resistance, and they tend to exhibit tissue-specific expression patterns. S. mansoni expresses thousands of lncRNA genes; however, the cell type expression patterns of lncRNAs in the parasite remain uncharacterized. Here, we have re-analyzed public single-cell RNA-sequencing (scRNA-seq) data obtained from adult S. mansoni to identify the lncRNAs signature of adult schistosome cell types. A total of 8023 lncRNAs (79% of all lncRNAs) was detected. Analyses of the lncRNAs expression profiles in the cells using statistically stringent criteria were performed to identify 74 lncRNA gene markers of cell clusters. Male gamete and tegument lineage clusters contained most of the cluster-specific lncRNA markers. We also identified lncRNA markers of specific neural clusters. Whole-mount in situ hybridization (WISH) and double fluorescence in situ hybridization were used to validate the cluster-specific expression of 13 out of 16 lncRNA gene markers (81%) in the male and female adult parasite tissues; for one of these 16 gene loci, probes for two different lncRNA isoforms were used, which showed differential isoforms usage in testis and ovary. An atlas of the expression profiles across the cell clusters of all lncRNAs detected in our analysis is available as a public website resource. The results presented here give strong support to a tissue-specific expression and to a regulated expression program of lncRNAs in S. mansoni. This will be the basis for further exploration of lncRNA genes as potential therapeutic targets.

overall_design:
We reanalyzed the scRNA-seq from Wendt et al. (2020) SRA project PRJNA611777 to measure gene expression of lncRNAs described in  Maciel et al. (2019)  from a gtf file downloaded from http://verjolab.usp.br/public/schMan/schMan3/macielEtAl2019/files/, along with the genome assembly Smansoni_v7 from WormBase (Howe et al., 2017).

DATA PROCESSING SUMMARY:
We reanalyzed the scRNA-seq from Wendt et al. (2020) SRA project PRJNA611777, gene expression was calculated using Starsolo version 2.7.9a (Kaminow et al., 2021) along with a merged gene annotation file containing protein-coding genes, pseudogenes (Schistosoma mansoni WormBase gene annotation version 16 (Howe et al., 2017) ) and lncRNA genes (Maciel et al., 2019) from a gtf file downloaded from http://verjolab.usp.br/public/schMan/schMan3/macielEtAl2019/files/ , along with the genome assembly Smansoni_v7 from WormBase (Howe et al., 2017) with the following parameters “-- soloType CB_UMI_Simple --soloCellFilter EmptyDrops_CR --soloFeatures Gene Velocyto GeneFull --soloMultiMappers EM --soloCBwhitelist barcodes_whitelist”.  For all samples except SRX7888067, we used the barcode whitelist from Cell Ranger chemistry V2; for sample SRX7888067, we used the barcode whitelist from chemistry V3. Filtered count matrices for all samples were imported into R (Team, 2018) using Seurat v4.0.6.9900 (Hao et al., 2021) and cells were further removed from each matrix when the number of features was less than 500, number of counts less than 1000 and greater than 20000, and percentage of mitochondrial genes greater than 3%. Matrices from all samples were normalized using the NormalizeData function, and variable features were identified using FindVariableFeatures with the following parameters “selection. Method = ‘vst’, nfeatures = 2000”. Additionally, we scaled the matrices and found principal components using the functions ScaleData, and RunPCA with the parameters “npcs = 100”. To generate the count matrix of all samples, we used the scRNA-seq integration approach from Seurat (Stuart et al., 2019).  For that, we first identified integration features using the function SelectIntegrationFeatures, then the integration anchors were identified using the function FindIntegrationAnchors with the following parameters “k.anchor = 20,dims = 1:78, anchor.features = features, reduction = ‘rpca’” and finally integrated the matrices using IntegrateData function. Then, the integrated matrix was scaled using the function ScaleData, and principal components were identified using the function runPCA with the following parameters “npcs = 100”. A final sparse matrix with 48094 cells was obtained containing expression data for protein-coding genes, pseudogenes, and lncRNAs; and it was used for the following procedures.

Grant Number: 18/23693-5
Grant Title: Mechanisms of action of long non-coding RNAs involved with gene activation programs in eukaryotes.
Funding source: FAPESP - The São Paulo research Foundation
Grantee: Sergio Verjovski-Almeida

first: David

last: Morales-Vicente

middle: C

first: Sergio

last: Verjovski-Almeida


title: miRNA expression profiles of EVs from control and MDS mice

city: Tokyo

first: Yasutaka

last: Hayashi

address: 4-6-1 Shirokanedai, Minato-ku

department: Division of Cellular Therapy, Advanced Clinical Research Center

institute: Institute of Medical Science, The University of Tokyo

summary: To identify the mechanism by which miRNAs in EVs derived from MDS cells suppressed the osteolineage differentiation of MSCs and disrupted normal hematopoiesis, we comprehensively explored the miRNAs encapsulated in EVs by miRNA-array. Consistent with the heterogeneous nature of MDS, the hypoplastic Abcg2-MDS/AML model and the hyperplastic NHD13Tg model share few elevated miRNAs. However, it is noteworthy that the pathways targeted by each upregulated miRNA are mutually shared, such as the pathways associated with MSC differentiation and survival, including axon guidance and MAPK signaling.  These results suggest that miRNAs play an essential role in the MSC impairment observed in MDS.

overall_design: Experiments using BM cells derived EVs from two MDS model mice, Nup98-HoxD13 (WT and Tg) and Abcg2(Control and Abcg2).

first: Yusuke

last: Yoshioka

first: Daichi

last: Inoue

first: Takahiro

last: Ochiya

first: Toshio

last: Kitamura


title: Gene expression profiles of mesenchymal stromal cells in MDS mice.

summary: To characterize the dysregulated MSCs in the murine MDS models, we performed a single-cell RNA sequence (scRNA-seq) analysis of FACS-sorted MSCs. The proportions of subclusters comprising MSCs were discrete between controls and MDS, and Osteolineage population was reduced in MDS compared with the control. In addition, Lepr+ mesenchymal population in MDS mice exhibited the remarkable reduction of skeletal stem marker Grem1 and MSC marker genes. This transcriptome analysis suggested that the osteolineage differentiation of MSCs is suppressed in vivo in the presence of MDS cells.

overall_design: Experiments using MSCs from two MDS model mice, Nup98-HoxD13 (WT_A1 and Tg_A2) and Abcg2(Control and Abcg2).

first: Koichi

first: Akira

last: Nishiyama

first: Yo

last: Mabuchi

first: Tomohiko

last: Tamura


title: Sc-RNA seq for intrinsic mechanisms of distinct axonal growth capacity in different peripheral sensory neuron subtypes

city: Beijing

first: Xi-Yin

last: Zhang

address: College Road

department: Neuroscience Research Institute

institute: Peking University

summary: Dorsal root ganglion neurons are the primary neurons of the sensory afferent pathway and are a heterogeneous population. Dorsal root ganglion neurons exhibit a wide range of terminal morphologies, complex central projection patterns, and different physiological properties, which allow them to adapt to various sensory stimulation modalities and transmit the corresponding sensory information to the central nervous system. Here, we used single-cell sequencing technology to explore the mechanisms behind the differences in axonal lengths in DRG neurons cultured in vitro. The single-cell sequencing data grouped by axon length were compared and analyzed to find core genes that may be closely related to axon length in a list of differentially expressed genes that significantly change with axon length; as well as to explore whether these genes also play an important role in the process of axon regeneration after peripheral nerve injury.

overall_design: Single-cell RNA sequencing was performed on acute-dissociated dorsal root ganglia neurons from male SD Rat by mouth pipette, total 1080 sc-RNA seq cell data in 17 batches.

first: Yu-Pu

last: Wang

first: Yun


title: Loss of SNAI1 induces cellular plasticity in invasive triple-negative breast cancer cells

city: Uppsala

first: Mohamad

middle: Moustafa

last: Ali

state: Uppsala län

address: husargatan 3, Biomedical Center

department: IMBIM

country: Sweden

institute: Uppsala University

summary:
To investigate the effect of SNAI1 Knockout on development and growth of triple-negative human breast cancer cells
The transcription factor SNAI1 mediates epithelial-mesenchymal transition, fibroblast activation and controls inter-tissue migration. High SNAI1 expression characterizes metastatic triple-negative breast carcinomas, and its knockout by CRISPR/Cas9 uncovered establishment of an epithelio-mesenchymal phenotype accompanied by reduced signaling by the cytokine TGF-β. The SNAI1 knockout cells exhibited plasticity in differentiation, drifting towards the luminal phenotype, gained stemness potential and could differentiate into acinar mammospheres in 3D culture. Loss of SNAI1 derepressed the transcription factor FOXA1, a pioneering factor of mammary luminal progenitors. FOXA1 induced a specific gene program, including the androgen receptor (AR). Inhibiting AR via a specific antagonist regenerated the basal phenotype and blocked acinar differentiation. Thus, loss of SNAI1 in the context of triple-negative breast carcinoma cells promotes an intermediary luminal progenitor phenotype that gains differentiation plasticity, based on the dual transcriptional action of FOXA1 and AR. This function of SNAI1 provides means to separate cell invasiveness from progenitor cell de-differentiation as independent cellular programs.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for MDA-MB-231 wildtype and SNAI1 knockout cells(WT, CS16 and CS19).

first: Chrysoula

last: Tsirigoti

first: Varun

last: Maturi

first: Carl-Henrik

last: Heldin

first: Aristidis

last: Moustakas


title: RNA-seq on primary human kidney epithelial cells with oleate treatment and PLIN2 knockdown

city: New Haven

first: Haikuo

last: Li

state: CT

address: 55 Prospect St

institute: Washington University in St. Louis

summary: Here we investigated the transcriptomic changes induced by oleic acid treatment on human Primary Renal Proximal Tubule Epithelial Cells (RPTECs) with RNA-seq. We also profiled cells with oleic acid treatment after PLIN2 gene knockdown with siRNA treatment.

overall_design: There are a total of 15 samples derived from 5 groups with 3 replicates per group.  Sample 1-3: RPTECs treated with non-targeting control siRNA (NTsiRNA).  Sample 4-6: RPTECs treated with NTsiRNA and processed for 6-hour oleate-BSA stimulus.  Sample 7-9: RPTECs treated with PLIN2 siRNA and processed for 6-hour oleate-BSA stimulus.  Sample 10-12: RPTECs treated with NTsiRNA and harvested at 2 days after 6-hour oleate-BSA stimulus.  Sample 13-15: RPTECs treated with PLIN2 siRNA and harvested at 2 days after 6-hour oleate-BSA stimulus.  Libraries were generated with the poly-A selection method and sequenced with the NovaSeq 6000 S4 platform (2×150 bp) at a target of 30 million reads per library.

first: Benjamin

middle: D

last: Humphreys


title: GIP acts on multiple signaling pathways to uncouple bone resorption and formation

city: Odense

first: Alexander

last: Rauch

address: Campusvej 55

department: Department of Clinical Research

country: Denmark

institute: University of Southern Denmark and Odense University Hospital

summary: Clinical investigations show that short-term treatment with gastric inhibitory polypeptide (GIP) acutely decreases serum markers of bone resorption and may increase bone formation. We report that the GIP receptor (GIPR) is expressed in human osteoclasts. Furthermore, GIP inhibits osteoclastogenesis, delays and inhibits bone resorption, and increases osteoclast apoptosis by acting upon multiple signaling pathways to impair nuclear translocation of nuclear factor of activated T cells 1 (NFATc1) and nuclear factor-κB (NFκB). Human osteoblasts also express GIPR. Although GIP improves osteoblast survival via cAMP and Akt-mediated pathways, expression of osteoblast-specific genes including RUNX2 and BGLAP and bone formation is not changed by GIP. Treatment of co-cultures of osteoclasts and osteoblasts with GIP decreased bone resorption but did not change formation. Antagonizing the GIPR with GIP(3-30)NH2 abolished the effects of GIP on osteoblasts and osteoclasts. Clinical studies are needed to determine if longer-term GIPR activation uncouples bone resorption and formation and improves bone mass

overall_design: Osteoclasts differentiated in vitro from CD14 positive peripheral blood cells of 8 anonymous donors were stimulated  with GIP (10nM) or not for 4 hours.

first: Morten

middle: S

last: Hansen

first: Kent

last: Søe

first: Line

last: Chistensen

first: Paula

last: Fernandez-Guerra

first: Nina

middle: W

first: Rachael

last: Wyatt

first: Claire

last: Martin

first: Rowan

last: Hardy

first: Thomas

last: Andersen

first: Jacob

last: Olesen

first: Bolette

last: Hartmann

first: Mette

last: Rosenkilde

first: Moustapha

last: Kassem

first: Caroline

last: Gorvin

last: Frost


title: Low-dose exposure to PBDE disrupts genomic integrity and innate immunity in mammary tissue

city: Los Angeles

first: Donald

middle: M.

last: Lamkin

state: CA

address: 300 UCLA Medical Plaza, Room 3160

department: Semel Institute for Neuroscience

institute: UCLA

summary: RNAseq results were generated from the normal mammary tissues of nude mice in a simple 2-group experiment (BDE-47 exposure vs. Vehicle-only exposure) after 16 weeks of exposure from subcutaneous osmotic minipumps

overall_design: Total RNA was purified from normal mouse mammary tissues of nude mice after 16 weeks of exposure to BDE-47 (n = 7) or vehicle-only (n = 8)


title: Effects of short-term starvation on the transcriptome and lipid metabolism of epididymal white adipose tissue in mice

first: Yuan

last: Chu

address: No. 38, kexueyuan Road, Changping District

institute: Beijing Institute of Lifeomics

summary: Beneficial effects have been reported in individuals undergoing fasting to treat excessive weight gain and obesity. To better understand the effects of starvation on the transcriptome and lipid metabolism of white adipose tissue, we established a mouse model of 24-hour fasting using wild type C57BL/6J mice, and performed RNA-seq analysis of the white adipose tissue from the epididymis of fasted mice and control mice. Compared with the control fed mice, these fasted mice showed suppressed lipid synthesis and inhibited insulin signaling, while the lipolysis and gluconeogenesis were enhanced to maintain blood sugar stability. Specifically, the fasted mice had reduced volume of adipose tissues, increased levels of serum NEFA and ANP. In epididymal white adipose tissue, starvation increased the NEFA content, up-regulated the mRNA levels of Atgl, Adrb2, Anp, and Npr1, and promoted the phosphorylation of Hsl. Notably, bioinformatics analysis of the RNA-seq data showed that 24-hour fasting-induced alterations in lipid metabolism was associated with suppressed AMPK signaling and enhanced PPAR signaling in white adipose tissue, which was verified by quantitative PCR. Collectively, these findings supported that starvation promoted the conversion of energy-supplying substrates from glucose to fat. Our work sheds new light on harnessing the plasticity of adipose tissues and the AMPK/PPAR signaling pathways to develop potential strategies to combat obesity and other glucose/lipid metabolisms-associated human diseases.

overall_design: After 16-week-old wild-type mice were starved for 24 h, RNA from white adipose tissue in the epididymis of the mice was extracted and transcriptome sequencing was performed. Normal feeding WT mice served as controls. There were 3 biological replicates for each treatment group.

first: Song-Hui

last: Yao

first: Xiao-Fang

last: Wang

first: Yue

last: Wan

first: Dian-Dian

last: Dong

first: Hui

last: Chen

first: Miao

last: Yu

first: Xiao-Ming

last: Yang


title: Expression from L4/5 DRGs after oral administration of LBP

city: Guildford

first: Ngan Pan

middle: Bennett

last: Au

state: Surrey

address: Vet School Main Building (VSM), Daphne Jackson Road

country: United Kingdom

institute: University of Surrey

summary:
Current study found that oral administration markedly increased the growth capacity of DRG neurons.
In this dataset, we identified genes that were differentially expressed in L4/5 DRGs after oral administration of LBP

overall_design: Adult male mice were received oral administration of LBP for 13 consecutive days. L4/5 DRGs wer harvested for microarray analaysis. A total of 6 samples were analyzed.

first: Chi Him Eddie

last: Ma

first: Ngan Pan Bennett

first: Giovanni

last: Coppola

first: Dan

last: Geschwind


title: Probiotic supplementation with Lactiplantibacillus plantarum 299v modulates ER and oxidative stress pathways in ?-cells and prevents Type 1 diabetes in gluten-free BioBreeding Rats

city: Milwaukee

first: Martin

last: Hessner

state: WI

address: 8701 Watertown Plank Road

department: Pediatrics

institute: Medical College of Wisconsin

summary:
Type 1 diabetes (T1D) is an autoimmune disease characterized by destruction of the pancreatic β-cells. T1D pathogenesis has a strong genetic basis. However, in recent decades, the prevalence of high-risk HLA haplotypes among new diagnoses has declined, the age of onset has decreased, and T1D incidence has increased. These changes are consistent with increased environmental pressure and coincide with introduction of the Western diet, widespread antibiotic use and reduced breast feeding. These factors are thought to drive intestinal dysbiosis, increased gut permeability and systemic inflammation. Notably, our studies of T1D families and the BioBreeding (BB) rat have identified a peripheral inflammatory state associated with diabetes susceptibility that is consistent with microbial antigen exposure and pattern recognition receptor ligation. Lactiplantibacillus plantarum 299v (Lp299v), a probiotic strain, is reported to increase plasma and stool levels of anti-inflammatory short chain fatty acids (SCFA) and promote IL-10 signaling in colonic derived macrophages and T-cells.
Here we investigated the effect of Lp299v supplement on T1D progression and inflammatory phenotypes in diabetes prone BB DRlyp/lyp rats. Rats were weaned at 21 days onto a normal cereal diet (ND) or a gluten-free hydrolyzed casein diet (HCD), with and without daily Lp299v supplementation. All DRlyp/lyp ND rats developed T1D by day 83 (mean time to onset of 62.8+/-7.9 days). DRlyp/lyp ND+Lp299v rats exhibited an insignificant delay in T1D onset (62.6+/-6.5 days), however 8% remained diabetes-free to day 130. Providing DRlyp/lyp rats HCD prevented T1D in 17% of rats (to age 130 days) and significantly delayed onset (mean time to onset 72.8+/-7.3 days, p<0.001). Providing DRlyp/lyp rats HCD+Lp299v prevented T1D in 25% of rats and more robustly delayed onset (mean time to onset 84.9 +/-14.3 days, p<0.001). While multiplex ELISA failed to detect significantly altered plasma cytokine/chemokine levels at 40 days of life, plasma induced transcription revealed greatest normalization of systemic inflammation in the HCD+Lp299v group. Plasma SCFA levels (propionate and butyrate, p<0.01) were elevated in the HCD+Lp299v group compared to the ND group. Global gene expression analysis of pancreatic islets was conducted at 40 days, prior to insulitis. Endoplasmic reticulum (ER) stress has been implicated in the formation of islet neoantigens that may underlie the initial loss of immune tolerance in T1D. Under one or both diets, Lp299v favorably modulated islet expression levels of pathways and transcripts related to inflammation and innate immunity (Cxcl9, Cxcl10), oxidative stress (Gsta1, Gsta4, Gstp1, Gstk1), as well as ER stress and unfolded protein response (Cirbp, Edem1, Hspa1a, Atf4). These ongoing studies add to a growing understanding that inherited susceptibility can be modulated by diet and microbiota.

overall_design: Pancreatic islets were isolated from 40 day old rats of BB DRlyp/lyp ND, DRlyp/lyp ND+Lp299v, DRlyp/lyp HCD, DRlyp/lyp HCD+Lp299v, and Flyp/lyp ND and run global gene expression analysis.

first: Pinar

last: Sargin

first: Mark

middle: F

last: Roethle

first: Shuang

last: Jia

first: Kristen

last: Dew

first: Tyler

last: Laib

first: Samantha

last: Atkinson

first: Ru-Jeng

last: Teng

first: Marty


title: A novel long noncoding RNA SNHG3 promotes osteoblast differentiation through BMP2 upregulation in calcific aortic valve disease

first: Long

address: No. 167 North Lishi Road, Xich

institute: Fuwai hospital

summary: The role of long noncoding RNAs (lncRNAs) in calcific aortic valve disease (CAVD) remains largely elusive. This study aims to report a novel therapeutic lncRNA, SNHG3, and elucidate its role in CAVD. Based on high-throughput transcriptomic sequencing of human aortic valves, SNHG3 is among the most highly expressed lncRNAs in CAVD. Furthermore, SNHG3 upregulation is verified in human calcified aortic valves, osteoblastic human aortic valve interstitial cells (hVICs), and aortic valve tissues in CAVD mice. Moreover, knockdown of SNHG3 with antisense oligonucleotide markedly ameliorates aortic valve calcification in high cholesterol diet-treated ApoE-/- mice, as evidenced by reduced calcium deposition in the aortic valve leaflets, improved echocardiographic parameters, and decreased osteogenic differentiation markers (RUNX2, osteopontin, and osteocalcin) in aortic valves. Consistent with these in vivo findings, SNHG3 overexpression aggravates the calcification of hVICs, while knockdown of SNHG3 alleviates the process of differential calcification. Transcriptomics sequencing, gene set enrichment analyses, RNA-pull down, RNA immunoprecipitation and chromatin immunoprecipitation-qPCR show that SNHG3 physically interacts with polycomb repressive complex 2 to suppress the H3K27 tri-methylation BMP2 locus, which in turn activates BMP2 expression and signaling pathways. Taken together, SNHG3 promotes aortic valve calcification by upregulating BMP2, which might be a novel therapeutic target in human CAVD.

overall_design: lncRNA sequencing on 10 patients with calcific aortic valve disease and 12 controls (non-mineralized aortic valves)

first: Sun

last: cheng

first: Chen

last: Long

first: Liu

last: Hangning

first: Zheng

last: Zhe


title: High-throughput RNA sequencing of transcriptomes expressed in Oral squamous cell carcinoma (OSCC) and human oral keratinocytes (HOK)

city: Rourkela

first: Dr. Bibekanand

last: Mallick

state: Odisha

address: NIT Rourkela

department: Department of Life Science

institute: National Institute of Technology

summary: Next-generation sequencing (NGS) has transformed systems-based analysis in the molecular landscapes of various cancer types. The goals of this study are to obtain transcriptomes expressed in human oral squamous cell carcinoma (OSCC) cell lines. The transcriptome profiles of OSCC cell lines (H357, KB and Hep-2) and normal Human oral keratinocytes (HOK) were obtained from the high throughput RNA sequencing sequencing using Illumina Hiseq2500 platform. We obtained 10160, 10251, 10191, 10201 transcripts expressed in HOK, H357, KB, and Hep-2 respectively, which include protein coding genes (PCGs), lncRNAs, pseudogenes and others. Our results showed a set of transcripts that are dysregulated in OSCC, which might be playing some key roles in tumorigenesis process. Further in-depth analysis might provide clues for better understanding of gene function in OSCC.

overall_design: 1 µg of total RNA obtained from above all cell lines were used as the starting material for library preparation as prescribed by Illumina Hiseq transcriptome library protocol. The mRNA libraries were sequenced on Illumina HiSeq2500 platform. Upon de-multiplexing, reads are obtained and then analyzed after QC.

first: Pooja

last: Gupta

first: Trisha

last: Chattopadhyay

first: Bibekanand


title: Prognostic Values of Immune Landscape in Ras-Mutant Colorectal Cancer Peritoneal Metastases

first: Dong

last: Yan

state: Beijing

address: 82th South Xinhua Road, Tongzhou District

department: Oncology Department

institute: Beijing Luhe Hospital,Capital Medical University

summary: The peritoneal metastasis (PM) in patients with colorectal cancer (CRC) associated with poor survival, especially in those with Ras mutations. However, knowledge on the mechanism of molecular biology in CRC peritoneal metastasis (CRCPM) is limited, and the impact of tumor immune microenvironment (TME) on PM pathogenesis and the prognosis of CRCPM remains unclear. Therefore, we characterized the TME of CRCPM and evaluated its potential diagnostic and prognostic values. This study involved 21 patients with metastatic CRC (mCRC), of whom 11 with CRCPM were classified into the experimental group and 10 with mCRC without PM (noCRCPM) were classified into the control group. Formalin-fixed and paraffin-embedded tissue of primary tumors from all patients was examined using the NanoString RNA sequencing system. The clinicopathological variables and TME biomarkers were compared using the chi-square test and Cox regression analysis. According to the results of multivariate analysis, a prognostic nomogram was generated, and its prediction ability was measured using the concordance index (C-index). Survival curves were generated using the Kaplan–Meier method, and survival comparison between groups was conducted using the log-rank test.

first: Jiandong

last: Yang

first: Xuyang

last: Zhang

first: Xia

last: You

first: Jing

first: Ruofan

last: Li

first: Yurong

last: Cheng

first: Yingying

last: Tong

first: Yanping

last: Hu

first: Tingting

last: Sun

first: Chuang

last: Qi

first: Wenjing

last: Xi

first: Xiaomin

first: Wanglong

last: Deng

first: Lixin


title: Genome-wide profiling of small RNAs in human Oral squamous cell carcinoma (OSCC) cell lines

first: Dr. Bibekanand

summary: To elucidate the potential role of small ncRNAs, such as piRNAs and miRNAs in oncogenesis of Oral squamous cell carcinoma (OSCC), we performed genome wide profiling in three human OSCC cell lines, H357 (tongue squamous cell carcinoma), KB (mouth cancer), Hep-2 (laryngeal cancer), and HOK (Normal human oral keratinocyte) using high-throughput RNA sequencing (RNA-Seq) of small RNAs. We discovered 4854 piRNAs in H357, 5184 in KB, 8340 in Hep-2, and 4735 in HOK, while miRNAs in H357, KB, Hep-2, and HOK were 1538, 1533, 1257, and 1468, respectively. This is the first study to identify both piRNAs and miRNAs in OSCCs, which will serve as a future resource for understanding the molecular mechanisms underlying the complex neoplastic events mediated by these small RNAs. Furthermore, these piRNAs and miRNAs have the potential to be used as biomarkers for OSCC.

overall_design: Total RNA was isolated from above three cell lines for library preparation as prescribed by NEB Next Small RNA Sample Preparation protocol. The small RNA libraries (ranging up to 50 bp) were sequenced on Illumina HiSeq 2500. The reads are obtained and analysed after QC to predict both known, novel piRNAs and miRNAs.

first: Trisha

first: Pooja


title: Characterization and function of transcriptional elongation during zygotic genome activation in mouse embryos  [RNA-seq]

city: Munich

first: Tamas

last: Schauer

address: Feodor-Lynen-Straße 21

department: Institute of Epigenetics and Stem Cells

country: Germany

institute: Helmholtz Zentrum München

summary: The work associated to these datasets focuses on the investigation of transcriptional regulation during the earliest stages of mammalian embryogenesis. In particular, ChILseq and RNAseq datasets were generated to study the process of zygotic genome activation in mouse embryos. After fertilisation, the mouse embryo activates its own genome for the first time in a process known as zygotic genome activation, which occurs primarily on two main waves. The first wave occurs in zygotes, and the second one at the late 2-cell stage. To understand how the RNA Polymerase II functions during these waves, we have implemented a ChILseq approach to generate genome-wide maps of Ser5 and Ser2 phosphorylated forms of RNA Polymerase II in zygotes, 2- and 8-cell stage embryos. In addition, we have investigated how elongation factors, such as NELF and DSIF regulate major ZGA by performing single embryo RNAseq using SMART-seq2 in 2-cell stage embryos upon depletion of Spt5, NELFE and upon chemical inhibition of Cdk9.

overall_design: RNA-seq experiments upon Cdk9 inhibition, Spt5, NELF-E depletion by Trim-Away as well as IgG Trim-Away and no injection control in single 2-cell stage embryos.

first: Kenichiro

last: Abe

first: Maria-Elena

last: Torres-Padilla


title: Characterization and function of transcriptional elongation during zygotic genome activation in mouse embryos [ChIL-seq]

overall_design: ChIL-seq experiments using Pol II Ser5P, Ser2P and IgG antibody in 3 biological replicates


title: Characterization and function of transcriptional elongation during zygotic genome activation in mouse embryos [ChIP-seq]

overall_design: ChIP-seq experiments using Pol II Ser5P, Ser2P and IgG antibody in 3 biological replicates


title: Thyroidal gene expression changes in tamoxifen inducible Foxe1 knockout mouse at two weeks post-treatment

city: Sydney

first: Martyn

last: Bullock

state: NSW

address: Cnr Reserve Rd  and Westbourne St, Royal North Shore Hospital, St Leonards

department: Kolling Institute

institute: Univeristy of Sydney

summary: To directly examine the role of Foxe1 in the adult thyroid we generated a model of tamoxifen-inducible Cre mediated Foxe1 deletion in mice of C57BL/6J background (Foxe1flox/flox/Cre). Tamoxifen (0.05g/kg) was administered intraperitoneally to Foxe1flox/flox/Cre mice or Cre control mice aged 6-8 weeks, once daily for five consecutive days. Thyroids were harvested two weeks post-treatment, total RNA extracted and transcriptomic analysis performed using Clariom S Mouse arrays.

overall_design: Foxe1flox/flox/Cre (n=3) versus Cre control (n=3) mice


title: Large-scale multiplexed profiling of mouse kidney fibrogenesis with sci-RNA-seq3

first: Haikuo

summary: We employed single-cell combinatorial indexing RNA-seq (sci-RNA-seq), a scRNA-seq technology with high throughput, high sample multiplexing capacity and low costs, to decipher the molecular events involved in mouse kidney fibrogenesis. With the hypothesis that different types of kidney insults may lead to distinct cellular injury responses, we leveraged sci-RNA-seq to profile mouse kidneys collected from two mouse kidney fibrogenesis models, unilateral ischemia-reperfusion injury (uni-IRI) and unilateral ureteral obstruction (UUO), at multiple stages. We described an atlas of kidney fibrogenesis (available at http://humphreyslab.com/SingleCell/) with a total of 309,666 cells profiled from 11 biological conditions and 24 samples in one experiment. We discovered that uni-IRI and UUO produced two types of early-stage injured PT cells with different transcriptomic signature. Further investigation on the two cell states highlighted their distinct mechanisms of metabolic regulation. Analysis of other structures of TECs revealed a common cellular response to injury and repair. In addition, we described the heterogeneity within kidney stroma and the dynamics of cell-cell communications in kidney fibrogenesis.

overall_design: We induced uni-IRI and UUO surgeries on wild-type adult male mice, which were euthanized at multiple timepoints as the disease progresses (0, 6 hours and 2, 7, 14, 28 days post uni-IRI or 0, 2, 4, 6, 10, 14 days post UUO; n = 2 for each timepoint). For each sample mentioned above, nuclei were extracted from the kidney tissue, fixed and snap-frozen. We generated a sci-RNA-seq3 (current version of sci-RNA-seq) library based on a previously demonstrated protocol, including nuclei permeabilization, three-level combinatorial indexing composed of reverse transcription (RT), hairpin ligation and indexed PCR, and library purification. In this experiment, we also introduced a species-mixing control by spiking a nuclei mixture collected from human HEK-293T and mouse C3H/10T1/2 cultured cells.

first: Benjamin

last: Humphreys


title: Transcriptomic effects of forced expression of FOXO3, PRDM1⍺ and PRDM1β in pre-B ALL cell line 697 [exp1]

city: Newcastle Upon Tyne

first: Paul

last: Sinclair

state: Tyne and Wear

address: Level 6, Herschel Building, Newcstle university

department: Translational and Clinical Research Institute

institute: Newcastle University

summary: Lentiviral constructs expressing candidate tumoure suppressor genes were transduced into 697 cells. Of the candidates FOXO3, two isoforms of PRDM1 (⍺ and β) suppressed growth in-vitro and in-vivo. To indentify tumour suppressor mechanisms we extracted RNA from triplicate 697 cultures four days after transduced with empty vector (SIN-SIEW) or constructs expressing FOXO3, PRDM1⍺ or PRDM1β.  Approximately 90 million 100bp paired-end reads were generated per sample by illumina sequencing.

overall_design: mRNA profiles of 697 cells transduced with control vector, or constructs expressing FOXO3, PRDM1⍺ or PRDM1β c-DNA.


title: Dual targeting of TGF-β and PD-L1 with bifunctional anti-PD-L1 /TGF-β RII agents in recurrent cervical cancer

city: Jinan

first: Wenxiong

address: No.107 West Wenhua Road, Jinan, 250001, China

institute: Qilu Hospital, Cheeloo College of Medicine, Shandong University

summary:
Purpose: To find out the patients who are most sensitive and effective to the anti-PD-L1 and TGF-β bifunctional fusion protein in the treatment of recurrent cervical cancer.
Patients and methods: We report two cases of recurrent cervical cancer treated with the anti-PD-L1 and TGF-β bifunctional fusion protein. We described the clinical course, clinical characteristics, and genetic characteristics of the two patients, and analyzed the changes of gene expression in the two patients after treatment.
Results: Although PD-L1 expression and HPV status were same in the two patients, the treatment effect of two patients with recurrent cervical cancer was different, according to the evaluation of enhanced computed tomography (CT), one was partial response (PR) and the other was progressive disease (PD), which may indicate that PD-L1 expression and HPV status of patients is not enough to predict the effectiveness of the anti-PD-L1 and TGF-β bifunctional fusion protein treatments. Then, we demonstrated that the changes of peripheral blood lymphocytes of two patients during the treatment had different trends. Moreover, number of alterable genes in PR patient is much greater than that in PD patient, indicating PR patient may be more sensible to the anti-PD-L1 and TGF-β bifunctional fusion protein treatments. Total 4844 genes changing-fate gene set selected which is believed conducting anti-cancer function during the anti-PD-L1 and TGF-β bifunctional fusion protein treatments. Furthermore, we identified that changing-fate genes were correlated with female reproductive organ cancer, infectious disease, inflammatory disease, immune system, indicating these genes may conducting anti-cancer, anti-inflammation and immune function.
Conclusion: Anti-PD-L1 and TGF-β bifunctional fusion protein is feasible for the treatment of recurrent cervical cancer. Multi-center, large-sample prospective clinical studies are still needed to further explore the efficacy of anti-PD-L1 and TGF-β bifunctional fusion protein in recurrent cervical cancer and screen appropriate patients, so as to achieve the maximum survival benefit of patients.

overall_design: Examination the changes of gene expression in the two patients after anti-PD-L1 and TGF-β bifunctional fusion protein treatment.

first: Jin

last: Peng


title: Transcriptome analysis revealed altered response to hypoxia, inflammation and immune regulation in Pdcd10-depleted endothelial cells

city: Santander

first: Lucio

last: Di Filippo

state: Cantabria

address: PCTCAN - Cl. Albert Einstein, 22

country: Spain

institute: IBBTEC

summary: Here we provided novel insights on the physiological functions of PDCD10 by RNA-Seq analysis, profiling Pdcd10-silenced mouse endothelial cells (ECs). We identified 53645 differentially expressed genes (DEGs) in Pdcd10-ECs compared to the respective control cell line, of which 94 reported a p-value Adjusted (pAdj) <0.05. A functional clustered dendogram generated by using ReviGO Gene ontology resource  showed that the DEGs were clustered in cell proliferation, oxidative stress, vascular processes, extra-endothelial cell environment, and immune response gene ontology functions. Moreover, the major cluster of significant genes resulted to significantly enrich specific interesting signaling playing a fundamental role in inflammation and pathogen recognition, such as Hypoxia inducible factor-1 (HIF1α) and Nos2 signaling suggesting the importance of Pdcd10 in these unexplored molecular mechanisms. A validation analysis performed on wild type, Pdcd10-null and Pdcd10-null reconstituted cell lines, were found to be consistent with the sequencing data, revealing that the prioritized genes linked to the mainly meaningful pathways, have a direct functional relation with Pdcd10 expression level modulation.

first: Carmela

last: Fusco

first: Grazia

last: Nardella

last: Difilippo

first: Davide

last: Cacchiarelli

first: Antonio

last: Petracca

first: Lucia

last: Micale

first: Matteo

last: Malinverno

first: Marco

last: Castori


title: Whole-transcriptome analysis of serum L1CAM-captured extracellular vesicles related to autism spectrum disorder

city: Xi'an

first: Yannan

last: Qin

address: West Road Yanta

institute: Xi'an Jiaotong University

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

summary: L1CAM-captured extracellular vesicles (LCEVs) were isolated and characterized meticulously. Whole-transcriptome of LCEVs was analyzed by lncRNA microarray and RNA-Sequencing. RNAs expressed differently in LCEVs from ASD sera vs. TD sera were screened, analyzed, and further validated.

overall_design: Serum samples were collected from 100 ASD children and 60 age-matched typically developed (TD) children.To tolerate individual variation, 25 μL of each serum sample was collected and every 20 samples were pooled into one subgroup. Altogether, we got 5 ASD subgroups and 3 TD subgroups (n=20). To avoid bias caused by gender difference, proportion of males in each subgroup was the same (90%). LCEVs in the pooled sera in each group were isolated. Total RNA in LCEVs was isolated using the Exosomal RNA isolation kit and further analyzed using LC Biotech Human lncRNA Microarray 4×180 K (Agilent Technologies; Santa Clara, CA).

first: Li

last: Cao


title: Pharmacologic Reduction of Mitochondrial Iron Triggers a Noncanonical BAX/BAK-Dependent Cell Death

city: Melbourne

first: Mark

last: Dawson

address: 305 Grattan Street

department: Cancer Research

institute: Peter MacCallum Cancer Centre

summary: Cancer cell metabolism is increasingly recognized as providing an exciting therapeutic opportunity. However, a drug that directly couples targeting of a metabolic dependency with the induction of cell death in cancer cells has largely remained elusive. Here we report that the drug-like small-molecule ironomycin reduces the mitochondrial iron load, resulting in the potent disruption of mitochondrial metabolism. Ironomycin promotes the recruitment and activation of BAX/BAK, but the resulting mitochondrial outer membrane permeabilization (MOMP) does not lead to potent activation of the apoptotic caspases, nor is the ensuing cell death prevented by inhibiting the previously established pathways of programmed cell death. Consistent with the fact that ironomycin and BH3 mimetics induce MOMP through independent nonredundant pathways, we find that ironomycin exhibits marked in vitro and in vivo synergy with venetoclax and overcomes venetoclax resistance in primary patient samples.

overall_design: MV4-11 cell line (Biphenotypic B Myelomonocytic Leukemia) was treared with Ironomycin (AM5) for 6 and 24 hours in triplicate. MV4-11 with HK2 and PGP KO was treated with Ironomycin (AM5) for 24 hours in triplicate. Controls were cells treated with DMSO in triplicate

middle: A

first: Sylvain

last: Garciaz


title: Transcriptomic Characterization of PRP5 knockdown in HEK293T cells

city: Hangzhou

first: Xiaofeng

last: Zhang

state: Zhejiang

address: Westlake University

institute: Westlake University

summary: Splicing abnormality has been observed in various types of SF3B1-mutated tumors. Aberrant usage of 3’SS has been established as the most frequent splicing defect and is attributed to altered BS selection. In this study, we examined whether reduced PRP5 expression would phenocopy the splicing defects of SF3B1 cancer mutations.

overall_design: Analysis of alternative splicing induced by PRP5 knockdown in HEK293T cells, each experimental group has 3 replicates

first: Pan

last: Li

first: Fenghua

last: Yang

first: Yigong

last: Shi


title: Next generation sequencing facilitates quantitative analysis of tissue-specific molecular signatures in lupus mice

city: Athens

first: Αnastasia

last: Filia

address: Soranou Efessiou 4

country: Greece

institute: BRFAA

summary: Purpose: Next-generation sequencing (NGS) technology was used to map expression profiles of effector (spleen) and key target tissues (kidney and brain) in mouse model of Systemic Lupus Erythematosus (SLE). Methods: Total RNA was extracted from total brain, total kidney and total spleen using Trizol and mRNA libraries were generated using the Illumina TruSeq Sample Preparation kit v2. Paired-end 37-bp mRNA sequencing was performed on Illumina HiSeq2000 platform. Quality of sequencing was assessed using FastQC software. Raw reads in fastq format were collected and aligned to the mouse genome (mm10 version) using STAR 2.6 algorithm. Gene quantification was performed using HTSeq and differential expression analysis was performed using edgeR package. Results: We defined kidney-specific molecular signatures of the murine lupus transcriptome that mirrors nephritis-specific transcriptome alterations in human SLE. Conclusions: By the use of the mouse kidney-specific transcriptome and through training of a large whole-blood RNA-sequencing dataset of SLE patients, we developed and validated an algorithm that predicts patients with active LN from SLE patients without LN and suggest vigilance in the monitoring of these patients and potential enrollment in LN prevention studies.

overall_design: New Zealand Black (NZB) female mice were crossed with New Zealand White (NZW) male mice. Female hybrids NZB/W-F1 (n=3 at each time-point) were sacrificed with perfusion with PBS at the pre-puberty stage (1 month), pre-autoimmunity stage (3 months)  and nephritic stage (6 months old where proteinuria is more than 200 mg/dl for 3 consecutive days) of the disease. Spleen, kidneys and brain were extracted. Age-matched female C57BL/6 mice (n=3) were used as controls.

first: Anastasia

first: Eleni

last: Frangou

first: Aggelos

last: Banos

first: Maria

last: Grigoriou


title: RNASeq of human bronchial epithelial (HBE) cells with cGAS-siRNA transfected

first: Wenqi

last: Diao

address: 88 JieFang Road

department: Department of Respiratory and Critical Care Medicine

institute: Second Affiliated Hospital of Zhejiang University School of Medicine

summary: Cyclic guanosine monophosphate (GMP)-adenosine monophosphate (AMP) synthase (cGAS) is a newly discovered sensor that detects cytosolic DNA as a universal danger-associated molecular pattern (DAMP). Here, we used RNA-seq to analyze transcriptomic expression difference between control-siRNA and cGAS-siRNA cells to find out what genes involved in the regulation of inflammation and injury.

overall_design: This dataset contains mRNA levels from 3 control-siRNA treated and 3 cgas-siRNA treated HBE cell lines. The samples were disposed and analyzed by BGI.

first: Zhangchu

last: Jin

first: Anyi

last: Guo

first: Shiyi

first: Yinling

last: Han

first: Yinfang

last: Wu

first: Yun

last: Zhao

first: Yanping

first: Jiaxin

last: Shen

first: Songmin

last: Ying

first: Wen

first: Huhao

first: Zhihua

last: Chen

first: Fugui

last: Yan


title: GM-CSF-induced CD40high human blood dendritic cells promote Tfh1 polarization

city: Paris

first: Melissa

last: Saichi

address: 1 avenue Claude Vellefaux

country: France

institute: Human Immunology Pathophysiology Immunotherapy (HIPI)- Inserm

summary: Using single-cell RNA sequencing  (10X technology) on CD4+T cells, we report that GM-CSF-activated human blood CD1c+ dendritic cells (DC) (cDC2) drive the differentiation of naïve CD4+ T cells into Tfh1. These Tfh1 cells displayed typical Tfh molecular features, including high levels of PD-1, CXCR5, and ICOS. They co-expressed Bcl6 and T-bet, and secreted large amounts of IL-21 and IFN-γ.

overall_design: We performed single cell RNA sequencing using 10X Chromium technology on CD4+ T cells previously co-cultured with three different DC activation conditions (GM-CSF-activated-DC, LPS-activated-DC and Medium-activated-DC). The protocol is detailed below.

first: Sarantis

last: Korniotos


title: The protein kinase activity of NME7 activates one-carbon metabolism through positively regulating wnt/β-catenin signaling

city: Shanghai

first: Xiaoyu

last: Liu

state: Shanghai

address: 180 Yue-yang road

department: Department of Interventional Radiology

institute: Ruijin Hospital, Shanghai Jiao Tong University School of Medicine

summary: Metabolic reprogramming by oncogenic signaling is a hallmark of cancer. Hyperactivation of Wnt/β-catenin signaling has been reported in hepatocellular carcinoma (HCC). However, the molecular mechanisms linked to hyperactivation of Wnt/β-catenin signaling and the strategy for targeting this pathway in HCC are incompletely understood. In this study, a screen of the potential kinases regulating Wnt/β-catenin signaling revealed that NME7 is a positive regulator of this pathway. NME7 was upregulated in HCC, and its expression was positively correlated with the clinical features of patients with HCC. Knockdown of NME7 inhibited the growth and tumorigenesis of HCC cells, while overexpression of NME7 cooperated with c-Myc to drive tumorigenesis in a mouse model of HCC established by hydrodynamic injection and promote the growth of tumor-derived organoids. Mechanistically, GSK3β was identified as the substrate of NME7, and their interaction was strengthened upon Wnt3a stimulation. NME7 exerts protein kinase activity and phosphorylates serine 9 of GSK3β in vitro and in vivo. Through further study, MTHFD2, the key enzyme in one-carbon metabolism, was found to be the target gene of β-catenin and to mediate the biological functions of NME7. Moreover, mouse tumor-derived organoids with NME7 overexpression exhibited increased sensitivity to the MTHFD2 inhibitor LY345899. Additionally, the expression levels of NME7, β-catenin and MTHFD2 correlated well in HCC, and higher expression of all three predicted poor prognosis. Taken together, the results of this study emphasize the crucial roles of NME7 protein kinase activity in activating one-carbon metabolism and Wnt/β-catenin signaling, suggesting that NME7 and MTHFD2 are therapeutic targets for HCC.

overall_design: PVTT hepatoma carcinoma cell into experimental group that was added DOX (induced NME7 knockdown) and control group did not add DOX (control). Each group was prepared for two samples.The NME7 gene was knocked down in DOX treated cells.

first: Yuezhen

last: Deng

first: Xinxin

last: Ren


title: Identification of Drug Candidates Rescuing SARS-CoV-2 Infection Induced Dopaminergic Neuron Senescence

city: New York

first: Shuibing

state: NY

address: A 827B, 1300 York Ave

department: Surgery

institute: Weill Cornell Medical College

summary: RNA-seq analysis was applied to examine the mock or SARS-CoV-2 infected DA neurons.We found SARS-CoV-2 infection caused DA neurons senescence.We also found several drug candidates block SARS-CoV-2 infection caused senescence of hPSC-derived DA neurons. RNA-seq was applied to analyze the drug candidates or DMSO treated DA neurons upon SARS-CoV-2 infection. The genes involved in senescence pathway were rescued in riluzole, metformin or imatinib treated DA neurons.

overall_design: Examination of day 40-50 hPSC-derived DA neurons.

first: Yuling

first: Liuliu

last: Yang


title: Transcriptomic effects of forced expression of FOXO3 and FOXO1 in pre-B ALL cell line 697 [exp2]

first: Paul

middle: B

last: Sinclair

summary: To investigate diferences in function  between the related transcription factors FOXO1 and FOXO3 in pre-B acute lymphocytic leukaemia (ALL) cells we extracted RNA from triplicate 697 cultures four days after transduced with empty vector (SIN-SIEW) or constructs expressing FOXO1 or FOXO3.  Approximately 30 million 70bp paired-end reads were generated per sample by illumina sequencing.

overall_design: mRNA profiles of 697 cells transduced with control vector, or constructs expressing FOXO1 or FOXO3 c-DNA.


title: AOS10-FMT could rescure the adverse effects induced by high fat diet & STZ on the small intestinal [16S-intestinal]

city: Qingdao

first: Yong

state: Shandong

address: 700 Changcheng Road

department: College of Life Sciences

institute: Qingdao Agricultural University

summary: We reported the side-effects of High fat diet & STZ on the small intestinal, and foud that the AOS10-FMT could rescure the side-effect of High fat diet & STZ in many factors

overall_design: Exploration of the FMT effects on the damaged small intestinal induced by High fat diet & STZ

first: Yanan

last: Hao


title: JQ1 promotes invasion in a BET protein independent manner in prostate cancer

city: houston

first: Ming-Jer

last: Tsai

state: Texas

address: One Baylor Plaza

institute: baylor college of medicine

summary: Recent findings have shown that inhibitors targeting BET (bromodomain and extraterminal domain) proteins, such as the small molecule JQ1, are potent growth inhibitors of many cancers and hold promise for cancer therapy. However, some reports also have revealed that JQ1 can activate additional oncogenic pathways and may affect EMT (epithelial mesenchymal transition). Therefore, it is important to address the potential unexpected effect of JQ1 treatment, such as cell invasion and metastasis. Here, we showed that in prostate cancer, JQ1 inhibited cancer cell growth but promoted invasion and metastasis in a BET protein independent manner. Multiple invasion pathways including EMT, BMP (bone morphogenetic protein) signaling, chemokine signaling and focal adhesion pathway were activated by JQ1 to promote invasion. Notably, JQ1 induced upregulation of invasion genes through inhibition of FOXA1, an invasion suppressor in prostate cancer. JQ1 directly interacted with FOXA1, inactivated FOXA1 binding to its interacting repressors, TLE3, HDAC7 and NFIC, thus blocking FOXA1 repressive function and activating the invasion genes. Our finding indicates that JQ1 has an unexpected effect of promoting invasion in prostate cancer. Thus, the ill effect of JQ1 or its derived therapeutic agents could not be ignored during cancer treatment, especially in FOXA1 related cancers.

overall_design: mRNA profiles of LNCaP cells treated with JQ1 for 3 days with or without BRD4 knockdown. RNA-sequencing and analysis was performed by EA | Q² Solutions, Morrisville, NC 27560.

first: Leiming

last: Wang


title: Mechanisms and treatment of cold-storage-induced microvascular obstructions in normothermic machine perfusion of human kidney

city: Cambridge

first: John

middle: Robert

last: Ferdinand

address: Department of Medicine

institute: University of Cambridge

summary: Human kidneys which were accepted for transplantation and subsequently not used were subjected to ex vivo normothermic machine perfusion. During perfusion it was found the tubular epithelia synthesized fibrinogen which led to red blood cell aggregation and pathologic plugging of renal microvasculature. Sequential ex vivo delivery of plasminogen and tissue plasminogen activator (tPA) during normothermic machine perfusion effectively lyses these fibrinogen-mediated plugs.

overall_design: Pairs of human kidneys were subjected to ex vivo normothermic perfusion. One kidney in each pair was treated and the other not. Samples were taken pre- and post-perfusion for RNASeq.

first: J

middle: R

last: DiRito

first: M

last: Clatworthy

middle: L

last: Nicholson

first: G

middle: T

last: Tietjan


title: AOS10-FMT could rescure the adverse effects induced by high fat diet & STZ on the Colon [16S-colon]

last: Zhao

summary: We reported the side-effects of High fat diet & STZ on the colon, and found that the AOS10-FMT could rescure the side-effect of High fat diet & STZ in many factors

overall_design: Exploration of the FMT effects on the damaged colon induced by High fat diet & STZ


title: Gene expression profile of VCaP_ctrl and VCaP_enz stimulated by DHT and enzalutamide

first: Zemin

last: Hou

address: 320 Yueyang Road

department: Shanghai Institutes of Biochemistry and Cell biology

institute: Chinese Academy of Sciences

summary: VCaP_ctrl (Vc) and VCaP_enz (Ver) cells were starved for 2 days and stimulated with 1 nM DHT or 1 μM enzalutamide or both treatment. Gene expression profiles were examined to distinguish the difference of Vc and Ver.

first: Zejie

last: Mei

first: Jingjie

last: Tang


title: Insights into the mechanism underlying the therapeutic effects of raspberry ketone on human colorectal carcinoma cells revealed by RNA sequencing and bioinformatics analysis

city: Harbin

first: Haopeng

last: Zhang

state: Heilongjiang

address: No. 37 Yiyuan Street

department: Department of General Surgery & Bio-Bank of General Surgery

institute: The Fourth Aﬃliated Hospital of Harbin Medical University

summary: Colorectal cancer (CRC) is the most commonly diagnosed cancer of the digestive system. Bioactive substances from plants are of particular research interest, due to their chemopreventive or chemotherapeutic properties against tumors. Raspberry ketone (RK), one of the major aromatic compounds in red raspberries, is widely used as a flavoring agent in foodstuffs, and for nutritional and medicinal purposes. In the present study, we found that RK inhibited the growth of DLD-1 CRC cells and identified differentially expressed genes (DEGs) by RNA sequencing in DLD-1 cells treated with RK. Transcriptome analyses indicated significant changes in the mRNA levels of 901 genes according to P - values < 0.01 (609 up- and 292 down-regulated) after treatment of DLD-1 cells with 400 μg/mL RK for 72 h. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that various cellular functions were involved in RK treatment. Interaction network analysis of GO terms and KEGG pathways revealed details of their interactions and predicted the key RK target pathways. These results provide evidence applicable to the prevention and therapy of CRC.

overall_design: Identified differentially expressed genes (DEGs) by RNA sequencing in DLD-1 cells treated with RK

first: Hao

middle: P

first: Ming

last: Liu


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and ASIC1a-/- Hypothalamus Transcriptomes

city: Lausanne

first: zhong

last: peng

state: Vaud

address: Rue du Bugnon 27

department: Department of Biomedical Sciences

institute: University of Lausanne

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare circadian gene expression in WT and ASIC1a-/- mice hypothalamusl transcriptome profiling at ZT1 and ZT13
Methods: hypothalamus mRNA profiles of 3-month-old wild-type (WT) and Acid-sensing ion channel 1a knockout (ASIC1a−/−) mice were generated by deep sequencing, in triplicate, using Illumina GAIIx.
Results: Using an optimized data analysis workflow, we mapped about 46 to 56 millions sequence reads per sample to the mouse genome and identified about 15,000 transcripts in the hypothalamus of WT and ASIC1a−/− mice. 3 genes expression changed at ZT1 and 13 genes expreesion changed at ZT13
Conclusions: Our study represents the first detailed analysis of retinal transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that ASIC1a-/- mice only change 16 genes expression

overall_design: Hypothalamus mRNA profiles of 3-month old male wild type (WT) and ASIC1a-/- mice

first: Zhong

last: Peng

first: Stephan

last: Kellenberger


title: DNA Methylation assessment of GLO1-depleted MDA-MB-231 breast cancer cells and mouse xenografts

city: Brussels

first: Gaurav

last: Dube

state: Brussels Capital Region

address: 808 Route de Lennik

department: Faculty of Medicine

country: Belgium

institute: UCRC-ULB

type: Methylation profiling by genome tiling array

summary: Oncometabolites are of the utmost importance to our understanding of tumor initiation, progression and resistance to therapy. We previously demonstrated that methylglyoxal (MG), a reactive dicarbonyl spontaneously formed in glycolytic cancer cells, unexpectedly enhanced their metastatic potential. Here, using genome-wide DNA methylation analysis, we report that MG stress induced DNA methyltransferases (DNMTs) expression resulting in DNA hypermethylation in triple negative breast cancer cells. Interestingly, we observed that DNMT3B protein was stabilized upon MG stress. Consistently, MG stressed cells demonstrated a significant loss of tumor suppressor genes as assessed using integrated analysis of methylome and RNASeq data. Both 5-AZA demethylating agent and MG scavengers triggered the re-expression of representative silenced genes. We have delineated an epigenomic signature of MG stress that effectively provided survival stratification in breast cancer patients. This study emphasizes the importance of MG stress, occurring downstream of the Warburg effect, as a major epigenetic regulator and proposes MG scavengers to reverse altered patterns of gene expression associated with MG stress pro-cancer effects.

overall_design: Total genomic DNA of 3 biological replicates of 2 clones of GLO1-silenced (shGLO1) cells and 1 control (shNT) clone, from MDA-MB-231 cells and mouse xenografts, were analysed using Infinium 850K array.

last: DUBE

first: Assia

last: TIAMIOU

first: Martin

last: BIZET

first: Justine

last: BELLIER

first: Y

last: BOUMAHD

first: Marie-Julie

last: NOKIN

first: Emilie

last: CALONNE

first: Rachel

last: DEPLUS

first: T

last: WISSOCQ

first: F

last: AGIRMAN

first: N

last: MALOUJAHMOUM

first: O

last: PEULEN

first: Vincent

last: CASTRONOVO

first: François

last: FUKS

first: Akeila

last: BELLAHCÈNE


title: Profiling the retinal microRNA (miRNA) transcriptomes in a rat model of oxygen-induced retinopathy (OIR) by next-generation sequencing

city: Dublin

first: vikrant

last: singh

state: Ireland

address: 31 York Street

country: Ireland

institute: Royal college of Surgeons in Ireland

summary:
Purpose: The study aimed to determine the transcriptome profile of retinal miRNA in a Sprague Dawley (SD) rat model of oxygen-induced retinopathy
Methods: The newborn rats in OIR group were subjected to daily cycles of 80% oxygen for 21 hours and room air for 3 hours in a customised chamber for 14 days (postnatal day 14, P14), then return to room air for 15 days (postnatal day 29, P29). The newborn rats in sham group were housed in room air for 14 days. Retinal miRNA expression profiles of OIR or sham rats at P14 or OIR rats at P29 were generated by deep sequencing, in triplicate, using Illumina Hiseq-2500 RNA-seq platform. Briefly, the sequence reads from all samples were analysed for overall quality, screened for the presence of any contaminants and trimmed accordingly. The cleaned sequence reads were then processed through the quantification modules miRDEEP2 ver2.0.0.7 pipeline for known miRNA expression profiling. Rat miRNAs from miRBASE release21 were used for mapping and quantification. Differential miRNA expression analysis was undertaken using voom bioconductor package (https://www.bioconductor.org/packages/release/bioc/vignettes/limma/inst/doc/usersguide.pdf).
Results: A total of 465 miRNAs were identified in the rat retina. The miRNAs with significantly altered levels (P<0.05) were identified in OIR rats at P14 compared with the sham controls or OIR rats at P29. Among those altered miRNAs, seven miRNAs were down-regulated in OIR rats at P14 with Log2 (Fold Change) < -1 fold, and no miRNAs were up-regulated.  Additionally, the expression of these down-regulated miRNAs in OIR rats at P14 was restored at P29 after they were exposed to room air.
Conclusion: Our study represents the first detailed analysis of retinal miRNA expression profile in rat model of OIR by miRNA-NGS technology.

overall_design: The expression profiles of retinal miRNA from OIR or sham rats were generated by deep sequencing, in triplicate, using Illumina Hiseq-2500 RNA-seq platform.

first: Jiang-Hui

last: Wang

first: Damien

last: Ling

first: Leilei

last: Tu

first: Vikrant

last: Singh

first: Moeen

last: Riaz

first: Guei-Sheung

last: Liu


title: Profiling the retinal microRNA (miRNA) expression in rodents by Next-Generation Sequencing

summary:
Purpose: The study aimed to determine the expression profiles of retinal miRNA from adult Sprague Dawley (SD) rat and C57BL/6 mice.
Methods: The profile of retinal miRNA transcriptom from rat (8 weeks old) and mice (8 weeks old) were generated by deep sequencing, in triplicate, using Illumina Hiseq-2500 RNA-seq platform. The sequence reads from all samples were analysed for overall quality, screened for the presence of any contaminants and trimmed accordingly. The cleaned sequence reads were then processed through the quantification modules miRDEEP2 ver2.0.0.7 pipeline for known miRNA expression profiling. Rat or mice miRNAs from miRBASE release21 were used for mapping and quantification.
Results: We identified a total of 643 and 1294 miRNAs, that were expressed in the retina of rat and mouse, respectively. Moreover, with a readcount cutoff of >0.5, 475 and 614 miRNAs were identified in the retina of rat and mouse, respectively.
Conclusion: Our study represents the first detailed analysis of retinal miRNA profile in adult rat and mouse. Our results also suggested that both species have a similar expression patterns of retinal miRNAs.

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: The expression profiles of retinal miRNAs in the rat and mice were generated by deep sequencing, in triplicate, using an Illumina Hiseq-2500 RNA-seq platform.


title: ARID1A Loss Promotes Lung Adenocarcinoma by Remodeling Chromatin Accessibility and Activating Glycolytic Reprogramming

first: Xiaoyu

country: China

summary: This study demonstrated that ARID1A loss markedly promotes lung tumorigenesis in genetic mice models. RNA sequencing reveals significant enrichment of the glycolytic pathway in ARID1A-deficient tumors, which is characterized by the upregulation of PGAM1, PKM2, and PGK1. Besides, ARID1A depletion increases chromatin accessibility and enhances the binding ability of Hif-1a to the promoter regions of Pgam1, Pkm, and Pgk1. In patients with lung cancer, ARID1A status is negatively correlated with mRNA level of PGAM1, PKM, and PGK1.

overall_design: RNA-Seq; ATAC-seq and ChIP-seq

first: Liu

last: Xiaoyu

first: Wang

last: Xiaojing

first: Deng

last: Yuezhen

last: Zhongmin


title: miRNA transcriptome profiling of Chlorella sorokiniana and Chlorella zofingiensis under normal and stress condition

city: Serdang

first: Siti Nor Ani

last: Azaman

state: Selangor

address: Jalan UPM

country: Malaysia

institute: Universiti Putra Malaysia

summary:
Purpose: The purpose of this study are to identify the miRNA involved in regulating the production of metabolites in Chlorella sorokiniana and Chlorella zofingiensis under normal and stress-induced condition through RNA-sequencing technique.
Methods: miRNA transcriptome profile from normal and stress sample of C. sorokiniana and C. zofingiensis were generated, in triplicate, using Illumina Miseq.  The sequence reads that passed quality filters were analysed using CLC genomic workbench and OmiRas.
Results: The known and predicted novel miRNAs were identified. Although most of the identified miRNAs were not functionally determined, this study suggests that they were species-specific, which may have roles in regulating genes during stress related condition.

sample_organism:
Chlorella sorokiniana
Chromochloris zofingiensis

overall_design: miRNA transcriptome profile of C. sorokiniana and C. zofingiensis under normal and stress conditions were generated in triplicates by deep sequencing using NEBNext Multiplex Small RNA Library Prep for Illumina.

first: Siti-Nor-Ani

first: Swee-Keong

last: Yeap

first: Sheau-Wei

last: Tan

first: Dilan

last: Satharasinghe

first: Woan

last: Liew

first: Fatimah

last: Mohd Yusoff

first: Norio

last: Nagao

first: Hyunh

last: Ky

first: David

last: Hornby

first: Qaiser

middle: I

last: Sheikh