title: Combined blockade of B7-H3 and CD47 immune checkpoints is a new therapeutic strategy for β-catenin driven melanomas [single cell CD45+ YUMM 2.1]

overall_design:
To identify the composition of the immune cell infiltrate within the tumor milieu, we analyzed the major immune cell subsets and functional categories (i.e. CD4+ T cells, CD8+ T cells, NK cells, dendritic cells, B cells, and macrophages) from the dissected tumors in mice treated with isotype control, anti-B7-H3 antibody, anti-PD1, and the combination of both antibodies using CD45+ sorted RNA-sequencing experiments.

Each sample (GSM) is multiplexed and can be demultiplexed using the information in the HTO sample.  Each replicate is represented by two processed data archives appended with either '_1' or '_2'. The sequencing library was run in two separate lanes to reach a higher number of cells and reads sequenced.  Each lane of data was used to produce one archive of processed data per replicate.


title: ChIRP-seq of Hoxc4-au in epidydimal white adipose tissue (eWAT)-derived preadipocytes.

status: Public on Oct 30 2023

city: Cambridge

first: Mengxi

last: Jiang

state: MA

address: 455 Main Street

country: USA

institute: Whitehead Institute

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We report the genome-wide occupancy of Hoxc4-au by using chromatin isolation after RNA purification (CHIRP) in eWAT-derived preadipocytes

overall_design: Profiling of genome-wide binding sites of Hoxc4-au by ChIRP-seq in eWAT-derived preadipocytes.

first: Bingbing

last: Yuan


title: Combined blockade of B7-H3 and CD47 immune checkpoints is a new therapeutic strategy for β-catenin driven melanomas [YUMM 2.1]

city: New York

first: Tiphaine

middle: Christiane

last: Martin

address: 1470 Madison Ave

department: Oncological Sciences

institute: Icahn School of Medicine at Mount Sinai, Tisch Cancer Institute

type: Expression profiling by high throughput sequencing

summary: In melanoma, immune cell infiltration into the tumor is associated with better patient outcomes and response to immunotherapy. T cell non-inflamed tumors (‘cold tumors’) are associated with tumor cell intrinsic Wnt/β-catenin activation, and are resistant to anti-PD-1 alone or in combination with anti-CTLA-4 therapy. Reversal of the ‘cold tumor’ phenotype and identifying new effective immunotherapies are challenges in melanoma. In a well-established preclinical melanoma model driven by β-catenin, we found that immune checkpoint molecule B7-H3 confers a suppressive tumor microenvironment by modulating antiviral signals and matricellular proteins. Its inhibition primes the microenvironment, and together with blockade of the macrophage checkpoint CD47, but not with anti-PD-1, results in synergistic anti-tumor responses. This study brings B7-H3 to the forefront as inducing a suppressive microenvironment when overexpressed, and it’s co-targeting with CD47 as a novel combination of immune checkpoint inhibitors in melanoma that calls for testing in clinical trials.

overall_design: To identify the composition of the immune cell infiltrate within the tumor milieu, we analyzed the major immune cell subsets and functional categories (i.e. CD4+ T cells, CD8+ T cells, NK cells, dendritic cells, B cells, and macrophages) from the dissected tumors in mice treated with isotype control, anti-B7-H3 antibody, anti-PD1, and the combination of both antibodies using CD45+ sorted RNA-sequencing experiments.

first: Min

last: Hsu

middle: C

first: Julide

middle: T

last: Celebi


title: Novel mouse cell lines and in vivo models for human high-grade neuroendocrine lung carcinoma SCLC and LCNEC

status: Public on Oct 29 2023

city: Madrid

first: Ramon

last: Garcia-Escudero

state: Madrid

address: Avda Complutense 40, Ed 70A

department: Biomedical Innovation

country: Spain

institute: CIEMAT

summary: There is a clear need to expand the toolkit of adequate mouse models and cell lines available for preclinical studies of high-grade neuroendocrine lung carcinoma (Small Cell Lung Carcinoma, SCLC and Large Cell Neuroendocrine Carcinoma, LCNEC), two highly aggressive tumor types with dismal prognosis and few therapeutic options. Actually, paucity is extreme in the case of LCNEC.  Given the lack of murine cell lines and transplant models of LCNEC the need is imperative/unmet. In this study, we have generated and examined new models of LCNEC and SCLC transplantable cell lines derived from our previously developed primary mouse LCNEC and SCLC tumors. RNA-seq analysis demonstrated that our cell lines and syngeneic tumors maintained the transcriptome program from the original transgenic primary tumor, and display strong similarities to human SCLC or LCNEC. Importantly, the SCLC transplanted cell lines show the ability of metastasize, mimicking this characteristic of the human condition. In summary, we have generated mouse cell line tools that allow further basic and translational research, as well as preclinical testing of new treatment strategies for SCLC and LCNEC, as they retain important features of their human counterparts and address the lack of LCNEC disease models.

overall_design: Gene expression profiling analysis of RNA-seq data for mouse cancer cell lines, mouse allograft tumors, and normal lung from mice.

first: Mirentxu

last: Santos

first: Corina

last: Lorz


title: Genome-wide identification of transcriptional targets for H2AK119ub and H3K36me2 in LP-1 control and PSMD14 knockdown cells

city: Beijing

first: Lin

last: He

address: Xueyuan Road 38

country: China

institute: Peking University

summary: To investigate the PSMD14-NSD2 complex track with H2AK119ub or H3K36me2, CUT&Tag was performed in LP-1 cells infected with lentiviruses carrying control shRNA or PSMD14 shRNA using antibodies against H2AK119ub or H3K36me2. Following CUT&Tag,  DNAs were amplified using non-biased conditions, labeled, and sequenced with Illumina NovaSeq 150PE.

overall_design: Examination of transcriptional targets for H2AK119ub and H3K36me2 in LP-1 control and PSMD14 knockdown cells

first: Chunyu

last: Yu

first: Xinhua

last: Liu


title: RNA-seq analysis after MIR4435-2HG knockdown in HemECs

city: Jinan

first: Zhiyu

last: Li

address: Jingwu Road

department: Department of Plastic and Aesthetic Surgery

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

summary: Infantile hemangiomas (IHs) are commonly observed benign tumors that can cause serious complications.In this study, we investigated the role of M2 macrophage-derived exosomal lncRNA MIR4435-2HG in IHs. Exosomes derived from M2 polarized macrophages were extracted. Next, using cell co-culture or transfection, we investigated whether M2 polarized macrophage-derived exosomes (M2-exos) can transport MIR4435-2HG to regulate the proliferation, migration, invasion, and angiogenesis of hemangioma-derived endothelial cells (HemECs). RNA-seq and RNA pull-down assays were performed to identify targets and regulatory pathways of MIR4435-2HG. We explored the possible mechanisms through which MIR4435-2HG regulates the biological function of HemECs.We found that M2-exos significantly enhanced the proliferation, migration, invasion, and angiogenesis of HemECs. Thus, HemECs uptake M2-exos and promote biological functions through the inclusion of MIR4435-2HG. RNA-seq and RNA pull-down experiments confirmed that MIR4435-2HG regulates of HNRNPA1 expression and directly binds to HNRNPA1, consequently affecting the NF-κB signal pathway.In conclusion, MIR4435-2HG of M2-exos promotes the progression of IHs and enhances the proliferation, migration, invasion, and angiogenesis of HemECs by directly binding to HNRNPA1. This study not only reveals the mechanism of interaction between M2 macrophages and HemECs, but also provides a promising therapeutic target for IHs.

overall_design: In our further investigation of the biological role of MIR4435-2HG in HemECs, lentiviral vectors with MIR4435-2HG knock down were constructed and successfully transfected into HemECs. We performed RNA-seq analysis of cells with shMIR4435-2HG and shNC.


title: Genome-wide identification of transcriptional targets for PSMD14 and NSD2 in LP-1 cells

summary: To investigate the genome-wide transcription targets of PSMD14-NSD2 complex and to explore the gain-of-function of PSMD14-NSD2 complex in multiple myeloma, cleavage under targets and tagmentation (CUT&Tag) was performed in LP-1 cells using antibodies against PSMD14 or NSD2. Following CUT&Tag,  DNAs were amplified using non-biased conditions, labeled, and sequenced with Illumina NovaSeq 150PE.

overall_design: Examination of transcriptional targets for PSMD14 and NSD2 in LP-1 cells


title: 昼夜时钟蛋白NR1D1通过调节线粒体生物合成和脂质运输来控制颗粒细胞内分泌功能

city: Guangzhou

first: Ou

last: Xiang-Hong

address: Guangzhou

institute: Guangdong Second Provincial General Hospital

summary: With rapid economic and social development, people's living habits have changed dramatically. Long-term exposure to artificial light, shift work and staying up late have been found to seriously disrupt people's normal biological rhythms and impair female reproductive function, leading to increased rates of infertility and abortion. In this study, we established a mouse model of continuous light exposure to explore the effects of long-term environmental circadian disturbances on the reproductive endocrine function and related mechanisms in females. We found that continuous light exposure caused reproductive and endocrine metabolic abnormalities in female mice, including estrous cycle disorders, ovarian changes of increased unruptured luteinized cystic follicles, LH elevation and hyperandrogenism. Moreover, the circadian rhythm genes expression in follicular granulosa cells was disrupted, in particular the expression of Nr1d1 showed a significant increase at night. We further showed that the up-regulation of NR1D1 promoted the expression of mitochondrial biosynthesis protein PGC1α and lipid transport related proteins such as SLC27A6, CPT1α, etc, in granulosa cells, and activated the PTEN/PI3K/AKT signaling pathway, leading to premature luteinization of granulosa cells. In addition, the gap junctions between cumulus and oocytes were prematurely closed in COCs treated with NR1D1 agonist GSK4112, which impaired oocyte quality, resulting in reduced maturation, disordered spindle assembly and chromosome arrangement, mitochondrial dysfunction. In conclusion, the circadian clock protein NR1D1 plays an essential role in maintaining granulosa cell endocrine function and oocyte quality. The findings may provide fresh insights into how circadian rhythm disturbances caused by staying up late and continuous exposure to artificial light sources can damage female reproductive function.

overall_design: To further investigate how elevated expression levels of NR1D1 are involved in affecting endocrine function in granulosa cells, we selected the NR1D1 agonist GSK4112 to treat follicular granulosa cells of female mice in vivo.


title: Loss of L-cells due to acute graft-versus-host disease leads to Paneth cell defects which can be compensated by glucagon like peptide-2

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

country: Germany

institute: University clinics Freiburg

summary: Paneth cells are targets of allo-reactive T cells during acute graft-versus-host disease (GVHD). GVHD-related loss of Paneth cells is connected to intestinal dysbiosis and a decline of antimicrobial peptides. Glucagon-like-peptide-2 (GLP-2) is an enteroendocrine tissue hormone, produced by the intestinal L-cells, that leads to expansion of Paneth cells. Microarray-based analysis of the intestinal tract revealed upregulation of a host-defense gene signature, increased Reg3-γ and Defensin-α-4 in the teduglutide treated group compared to the vehicle treated group. these results indicate that treatment of GVHD mice the GLP-2 analogue, teduglutide, restores intestinal homeostasis with increased Paneth cells and antimicrobial peptides

overall_design: BALB/c mice were pre-treated with theduglutide or vehicle twice a day for three days (d-3 to d-1). On d0 mice were lethal irradiated with 1000 cGy using a 137Cs source divided into two equal doses at 4 hours apart. After the second irradiation, mice were injected intravenously (i.v.) with 5x10e6 bone marrow cells together with 0.3 x 10e6 CD4+/CD8+ T cells from a C57BL/6 donor. Recipients were next treated with teduglutide or vehicle twice a day for 10 days after the allo-HCT. 4h after the last treatment the mice were sacrificed and Ileum samples were collected and processed to abtain RNA. RNA samples were further processed to perform microarray analysis, where we aim to obtain signifficant differences bwteen groups in relation to host defense gene sets.

first: Johana

last: Norona

first: Robert

last: Zeiser

first: Melanie

last: Boerries


title: Expression profiling by high throughput sequencing to evaluate the effect of aroylated phenylenediamine HO53 on autophagy induction in mature human bronchial epithelial cells (BCi-NS1.1 cell line)

city: Reykjavik

first: Iwona

middle: Teresa

last: Myszor

address: Vatnsmyrarvegur 16

country: Iceland

institute: University of Iceland

summary: We used RNA sequencing to exploit molecular mechanisms behind HO53 induced autophagy in mature human bronchial epithelial cells (BCi-NS1.1 cell line). We performed transcriptome analysis of mature bronchial epithelial cells (BCi-NS1.1 cell line) treated with aroylated phenylenediamine HO53 for different time points 4 h, 8 h and 24 h and compared it to transcriptome of untreated cells collected at the same time points. A broad effect of HO53 on the gene expression in mature human lung epithelial cells (BCi-NS1.1) shows molecular signature for pathways involved in autophagy regulation. The expression pattern for selected genes was reconfirmed by qRT-PCR using SYBR Green reagent.

overall_design: Expression profiling by high throughput sequencing of HO53 treated vs untreated differentiated in air-liquid intephase (ALI) culture human bronchial epithelial cells (BCi-NS1.1 cell line)

first: Snaevar

last: Sigurdsson

first: Gudmundur

middle: H

last: Gudmundsson


title: RNA-seq analysis of macrophages after rGAS6 stimulation

first: Zhenxing

last: Liang

state: Guangdong

address: 26 Yuancun Erheng Rd

institute: The Sixth Affiliated Hospital, Sun Yat-sen University

summary: We performed RNA-seq analysis of macrophages treated with rGAS6 to identify the differentially expressed genes.

overall_design: RNA-seq analysis to find the change of gene expression after rGAS6 stimulation.

first: Ping

last: Lan


title: Metagenomics assessment of WKY and SHR rodents

city: Gainesville

first: Christopher

last: Martyniuk

state: FL

address: 8891 SW 79th Avenue

institute: University of Florida

summary: The microbiome plays a significant role in gut brain communication and is linked to several animal and human diseases. Hypertension is characterized by gut dysbiosis, and this study aimed to determine how the gut microbiome differed between male and female normotensive and hypertensive rodents. WKY is a genetic control for spontaneous hypertensive rats or SHR which is well documented to have elevated blood pressure at approximately 8 to 10 weeks. We compared the microbiome of normotensive and hypertensive rodents using a meta-genomics approach.

overall_design: Male and female rats from two strains were housed at University fo Florida. Cecal fecal matter was collected from both male and female rats at 14-15 weeks. Blood pressure, feces, and weights were collected throughout the experiment and at endpoint plasma, colons, brains, and cecal fecal contents were collected. Feces were processed as below for metagenomics. Samples sizes were the following: male WKY (n=7), male SHR (n=7), female WKY (n=9), female SHR (n=10)

first: Basak

last: Ajaz

first: Wendi

last: Malphurs

first: Kit

last: Souders

first: Chris

first: Jasenka

last: Zubcevic


title: Combined blockade of B7-H3 and CD47 immune checkpoints is a new therapeutic strategy for β-catenin driven melanomas [transfection]

first: Tiphaine

last: Martin

summary: In melanoma, immune cell infiltration into the tumor is associated with better patient outcomes and response to immunotherapy. T cell non-inflamed tumors (‘cold tumors’) are associated with tumor cell intrinsic Wnt/β-catenin activation, and are resistant to anti-PD-1 alone or in combination with anti-CTLA-4 therapy. Reversal of the ‘cold tumor’ phenotype and identifying new effective immunotherapies are challenges in melanoma. In a well-established preclinical melanoma model driven by β-catenin, we found that immune checkpoint molecule B7-H3 confers a suppressive tumor microenvironment by modulating antiviral signals and matricellular proteins. Its inhibition primes the microenvironment, and together with blockade of the macrophage checkpoint CD47, but not with anti-PD-1, results in synergistic anti-tumor responses. This study brings B7-H3 to the forefront as inducing a suppressive microenvironment when overexpressed, and co-targeting with CD47 as a novel combination of immune checkpoint inhibitors in melanoma that calls for testing in clinical trials.

overall_design: To gain insight into its functions and examine the downstream effectors of B7-H3, we selected two human metastatic melanomacell lines, Hs. 688(A)T and Hs. 839T, with the highest levels of B7-H3 expression. Cells were transfected with either scrambled or B7-H3 specific siRNAs in triplicates (total 12 samples), and transcriptomes were analyzed via RNA-sequencing.

first: Min

last: Hsu

first: Alexander

last: Solovyov

first: Julide

last: Celebi


title: Combined blockade of B7-H3 and CD47 immune checkpoints is a new therapeutic strategy for β-catenin driven melanomas

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Characterization of Mmp3 positive and negative cells from SVF of subcutaneous adipose tissue

status: Public on Oct 28 2023

city: Bronx

first: Kosaku

last: Shinoda

state: NY

address: 1301 Morris Park Ave

institute: Albert Einstein College of Medicine

summary: RNA sequencing from isolated MMP3+ cells in subcutaneous WAT SVF showed higher expression of genes associated with beige progenitors.

overall_design: Charactarize Mmp3 positive and negative cells from SVF of subcutaneous adipose tissue by RNA-seq

first: Aoi

last: Satoh


title: Effect of overexpression A20 on gene expression during of TM3 Leydig cells

city: Nanjing

first: Dong

last: Xing

state: Jiangsu

address: Dingjiaqiao street

institute: Southeast university

summary: To investigate the impact of A20 on testosterone synthesis in the context of age-related inflammation, we employed lentiviral constructs to establish TNFAIP3-overexpressing TM3 cell lines. Subsequently, we conducted gene expression profiling analysis using RNA-seq data obtained from both normal TM3 cells and TNFAIP3-overexpressing TM3 cells.

overall_design: Comparative gene expression profling analysis of RNA-seg data for TM3 cells and its overexpression derivative (O/E A20)


title: Comprehensive Transcriptional Profiling of the Cell Envelope Stress Response of Bacillus subtilis

city: Dresden

first: Thorsten

last: Mascher

address: Zellescher Weg 20b

department: Institute of Microbiology

institute: Technische Universität Dresden

summary: Bacterial cell envelope is the first and the major line of defense against threats from the environment. Because of its crucial roles in bacterial cell life, cell envelope is a prime target for numerous antibiotics. In this study, by treating Gram-positive model strain Bacillus subtilis with numbers of cell wall targeted antibiotics, we aimed to obtain a global comprehensive transcriptional profile of cell envelope stress response in B. subtilis via transcriptomic study using high-throughput RNA sequencing approach. This knowledge will then be subject to a series of comparative genomics analyses to get detailed information of the distribution and conservation of cell envelope stress-sensing regulatory systems in B. subtilis.

overall_design: Wild type Bacillus subtilis W168 cells at exponential phase of growth were treated with cell wall-targeted compounds, bacitracin, vancomycin, tunicamycin, phophomycin, penicillin G, flavomycin and lysozyme, respectively. With 10 min of induction, all samples were processed to undergo total RNA extraction, cDNA library preparation and then high-throughput RNA sequencing. The resulting sequencing raw data were analyzed in silico to reveal the differential gene expression in different treatments relative to non-treatment control.

first: Qian

last: Zhang

first: Diana

last: Wolf


title: Profiling of mRNA localization of nuclear-encoded mitochondrial proteins in zebrafish.

city: Warsaw

first: Cecilia

middle: Lanny

last: Winata

state: Masovia

address: 4 Ks. Trojdena Street

department: Zebrafish Developmental Genomics Laboratory

country: Poland

institute: International Institute of Molecular and Cell Biology in Warsaw

summary: Current evidence suggests that nuclear-encoded mitochondrial proteins can be locally translated at the mitochondrial surface and co-translationally or post-translationally imported into mitochondria. mRNA localization on the mitochondrial membrane, a prerequisite for localized translation, remains uncharacterized in higher eukaryotic organisms. We employed fractionation-sequencing to profile mitochondria-associated mRNAs in zebrafish larvae. Our transcriptome-wide analysis reveals the localization of mRNAs of only 12% of the nuclear-encoded mitochondrial proteins to the mitochondrial surface, which suggests that post-translational import is the dominant mode of protein import to mitochondria. Additionally, the mRNAs which were localized to the mitochondrial membrane consisted mostly of those encoding proteins involved in mitochondrial dynamics, suggesting their site-specific translation. Finally, we show that the loss of function of the MIA pathway responsible for the post-translational import of a subclass of mitochondrial proteins, triggers mitochondrial localization of mRNAs encoding proteins that are imported to mitochondria via other pathways. Thus, our study suggests that mRNA targeting and localized translation could be relevant in higher eukaryotes to combat stress conditions affecting mitochondrial biogenesis in general.

overall_design: Biochemical fractionation of WT (AB) and chchd4abns292/bns292  5dpf zebrafish larvae was perfomed to obtain MARS and HSF fractions. Three replicates each of whole unfractionated RNA samples, as well as RNA isolated from MARS, HSF, and PNS were sequenced on Illumina Nextseq platform using paired end sequencing. Differential enrichment analysis was performed by comparing the fractions against whole unfractionated sample.

first: Sreedevi

last: Sugunan

first: Rohit

last: Suratekar

first: Agnieszka

last: Chacinska


title: Lineage selection and self-renewal in a murine multipotent hematopoietic precursor

city: New Haven

first: Rolando

last: Garcia-Milian

state: CT

address: 333 Cedar St

department: CWML

institute: Yale University

summary: EML cells are a multipotent murine hematopoietic cell line derived in a simple process from normal bone marrow.  These cells offer a model system with several advantages for the study of the early steps in hematopoietic differentiation. Cultured EML cells

overall_design:
14.5 day C57BL/6 fetal liver cells or EML cells were isolated, the apoptotic cells were excluded using Annexin V Apoptosis Detection Kit eFluor® 450 (ebioscience), and only Annexin V negative cells were used to sort pure live cell populations for further

Raw data were not provided for this submission. If you are interested in the raw data for this study, please contact the submitter directly.

first: Sherman

last: Weissman


title: Regulation of Endogenous Retroviruses and Cellular Genes by HIV-1 Rev [RNA-seq]

status: Public on Oct 31 2023

city: Charlottesville

first: Lou

last: Hammarskjold

state: VA

address: 1340 Jefferson Park Avenue

institute: University of Virginia

summary: A combination of bioinformatics, RNAseq, and cell-based functional assays were used to study the changes in host cell gene expression when HIV-1 Rev, Tat, Tat and Rev or HERV-K Rec was expressed. These results suggest that HIV Rev is capable of modulating gene and mRNA isoform expression, during HIV-1 infection.

overall_design: Investigation into host cell gene expression when HIV-1 Rev is expressed in T-lymphocyte cells.

first: Laurie

middle: R

last: Gray

first: David

last: Rekosh


title: Engineered hydrogel reveals contribution of matrix mechanics to esophageal adenocarcinoma and identifies matrix-activated therapeutic targets

status: Public on Oct 27 2023

first: Spyros

last: Karaiskos

department: Herbert Irving Cancer Center

institute: Columbia University

type: Genome variation profiling by high throughput sequencing


title: Characterization of microRNAs in spent culture medium associated with human embryo quality and development

first: Shanshan

last: Wang

state: JiangSu

address: No. 53, Zhongshan North Road, Nanjing, Jiangsu 210028

institute: The Affiliated Drum Tower Hospital of Nanjing University Medical School

type: Non-coding RNA profiling by high throughput sequencing

summary: Purpose: Given implantation failure limited the improvement of the in vitro fertilization (IVF) success rate, it was urgent to identify potential biomarkers for embryo quality and predicting the outcomes of IVF-ET.  Methods: The expression profiles of 16 spent culture media (SCM) collected from embryos at the cleavage on Day 3 (D3 cleavage) and blastocyst stages on Day 5 (D5 blastocyst) during IVF cycles were determined with RNA-sequencing. Differentially expressed miRNAs (DEmiRNAs) were identified with p-value < 0.05 and |log2FC|> 1. Then, the miRNA-mRNA interaction networks were constructed by using Cytoscape software. Finally, the GO and KEGG pathway analysis of target genes of DEmiRNAs were conducted.  Results: Compared with pregnant groups, 29 DEmiRNA were detected in non-pregnant groups at D3 cleavage, and 26 DEmiRNA were detected in non-pregnant group at D5 blastocyst. Among them, a total of six known miRNAs, including hsa-miR-199a-3p>hsa-miR-199b-3p, hsa-miR-199a-5p, hsa-miR-379-5p, hsa-miR-432-5p, hsa-miR-99a-5p and hsa-miR-483-5p, were identified. The results of GO and KEGG pathway analysis indicated that these target genes of DEmiRNAs were associated with various biological processes.  Conclusion: In conclusion, we identified three miRNAs, including hsa-miR-199a-5p, hsa-miR-483-5p and hsa-miR-432-5p, may serve as biomarkers for embryo quality during IVF cycles.

overall_design: The miRNA expression profiles of 16 spent culture media (SCM) collected from embryos at the cleavage on Day 3 (D3 cleavage) and blastocyst stages on Day 5 (D5 blastocyst) during IVF cycles were obtained based on Illumina X-ten platform.

first: Weihua

last: Jiang


title: Engineered hydrogel reveals contribution of matrix mechanics to esophageal adenocarcinoma and identifies matrix-activated therapeutic targets [WES]

summary: Increased extracellular matrix (ECM) stiffness has been implicated in esophageal adenocarcinoma (EAC) progression, metastasis, and resistance to therapy. However, the underlying pro-tumorigenic pathways are yet to be defined. Additional work is needed to develop physiologically relevant in vitro 3D culture models that better recapitulate the human tumor microenvironment and can be used to dissect the contributions of matrix stiffness to EAC pathogenesis. Here, we describe a modular, tumor ECM-mimetic hydrogel platform with tunable mechanical properties, defined presentation of cell-adhesive ligands, and protease-dependent degradation that supports robust in vitro growth and expansion of patient-derived EAC 3D organoids (EAC PDOs). Hydrogel mechanical properties control EAC PDO formation, growth, proliferation, and activation of tumor-associated pathways that elicit stem-like properties in the cancer cells, as highlighted through in vitro and in vivo environments.

overall_design: We also demonstrate that the engineered hydrogel serves as a platform to identify potential therapeutic targets to disrupt the contribution of pro-tumorigenic matrix mechanics in EAC. Together, these studies show that an engineered PDO culture platform can be used to elucidate underlying matrix-mediated mechanisms of EAC, and inform the development of therapeutics that target ECM stiffness in EAC.

first: Ricardo

last: Cruz-Acuna

first: Secunda

middle: W

last: Kariuki

first: Anil

middle: K

last: Rustgi


title: RNA-Sequencing analysis of control and UXS1 KO A549 cells

city: Worcester

first: Rui

last: Li

state: Massachusetts

address: 364 Plantation Street, LRB

department: MCCB

institute: University of Massachusetts Medical School

summary: The mRNA profiles of A549 cell line were analyzed by RNA-sequencing under control and UXS1 KO conditions to identify gene expression changes induced by disruption of UXS1.

overall_design: Compare the mRNA profiles of A549 cancer cells under CTRL (non-targeting guide) and UXS1 KO mediated by CRISPR-cas9. Each condition was analyzed in biological triplicate for a total of 6 samples.

first: Mihir

middle: B

last: Doshi

first: Dohoon

last: Kim

first: Lihua

middle: J

last: Zhu


title: Engineered hydrogel reveals contribution of matrix mechanics to esophageal adenocarcinoma and identifies matrix-activated therapeutic targets [RNA-seq]

summary:
Increased extracellular matrix (ECM) stiffness has been implicated in esophageal adenocarcinoma (EAC) progression, metastasis, and resistance to therapy. However, the underlying pro-tumorigenic pathways are yet to be defined. Additional work is needed to develop physiologically relevant in vitro 3D culture models that better recapitulate the human tumor microenvironment and can be used to dissect the contributions of matrix stiffness to EAC pathogenesis. Here, we describe a modular, tumor ECM-mimetic hydrogel platform with tunable mechanical properties, defined presentation of cell-adhesive ligands, and protease-dependent degradation that supports robust in vitro growth and expansion of patient-derived EAC 3D organoids (EAC PDOs). Hydrogel mechanical properties control EAC PDO formation, growth, proliferation, and activation of tumor-associated pathways that elicit stem-like properties in the cancer cells, as highlighted through in vitro and in vivo environments.
We also demonstrate that the engineered hydrogel serves as a platform to identify potential therapeutic targets to disrupt the contribution of pro-tumorigenic matrix mechanics in EAC. Together, these studies show that an engineered PDO culture platform can be used to elucidate underlying matrix-mediated mechanisms of EAC, and inform the development of therapeutics that target ECM stiffness in EAC.

overall_design: Samples are patient-derived 3D esophageal adenocarcinoma (EAC) organoids grown in 4 different hydrogel conditions. Only one organoid line was used. Each hydrogel condition was performed in triplicates, for a total of 12 samples. Samples 4, 8 and 12 are the reference group, as triplicates, which are EAC organoids grown in Matrigel of 100 Pa of storage modulus. Samples 3, 7 and 11 are EAC organoids grown in NorHA hydrogels of 100 Pa of storage modulus, in triplicates. Samples 2, 6 and 10 are EAC organoids grown in NorHA hydrogels of 350 Pa of storage modulus, in triplicates. Samples 1, 5 and 9 are EAC organoids grown in NorHA hydrogels of 1000 Pa of storage modulus, in triplicates.

last: Cruz Acuna

first: Kariuki

last: Secunda


title: Effect of nicotinamide mononucleotide on gene expression of CD4+ T cells with HIV-1 infection or mock infection

city: Hong Kong

first: Ming

last: Yue

address: 21 Sassoon Road, Pokfulam

institute: The University of Hong Kong

summary:
To investigate the effect of nicotinamide mononucleotide (NMN) on CD4+ T cells, primary human CD4+ T cells purified from peripheral blood mononuclear cells of healthy donors were treated without or with NMN.
Expression profiling analysis on either host gene or viral gene was performed using data obtained from bulk RNA-seq of NMN-treated and untreated (control) CD4+ T cells at 48 hours post treatment and/or post infection.

overall_design: Gene expression profiling analysis of RNA-seq data compared between NMN-treated and untreated (control) CD4+ T cells, or viral gene expression profiling analysis compared among NMN-treated and untreated CD4+ T cells with HIV infection using mock infection as control.

first: Yufei

last: Mo

first: Youqiang

last: Song

first: Zhiwei

last: Chen


title: Identification of miR-203a target genes [RIP-seq]

first: Junhui

address: 364 Plantation St

summary: To identify targets of miR-203a we coupled RNA-seq and AGO2-RNA immunoprecipitation (RIP-seq) in MCF10A cells expressing a control pre-miR-203a or control, empty vector

overall_design: RNA from AGO2 immunoprecipitates from MCF10A cells expressing either pre-miR-203a or empty vector control were analyzed using RNAseq.  Downstream analysis was compared to RNA-seq dataset.

first: Tessa

middle: M

last: Simone

first: Michael

last: Green


title: Unbiased transcription factor CRISPR screen identifies ZNF800 as master repressor of enteroendocrine differentiation [screen]

city: Utrecht

first: Jeff

last: DeMartino

address: Heidelberglaan 25

country: Netherlands

institute: Princess Maxima Center

summary: Enteroendocrine cells (EECs) are hormone-producing cells residing in the epithelium of stomach, small intestine (SI) and colon. EECs regulate various aspects of metabolic activity including insulin levels, satiety, gastrointestinal secretion and motility. The generation of different EEC lineages of the SI is incompletely understood. We now report a TFome-wide CRISPR knockout screen in adult human intestinal organoids to identify dominant transcription factors controlling EEC differentiation. ZNF800 is discovered as a master repressor for endocrine lineage commitment, which particularly restricts enterochromaffin cell differentiation by directly controlling an endocrine TF network centered on PAX4. Thus, organoid models allow unbiased functional SCRISPR screens for genes that program cell differentiation.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: TFome-wide CRISPR knockout screen in human small intestinal organoids

first: Lin

last: Lin


title: Unbiased transcription factor CRISPR screen identifies ZNF800 as master repressor of enteroendocrine differentiation [scRNA-seq]

overall_design: Single-cell RNA-sequencing of WT and ZNF800-KO human small intestinal organoids


title: Extracellular molecular response of bovine oviductal organoids to thermal stress.

city: Fort Collins

first: Ahmed

last: Gad

state: Colorado

address: 3107 Rampart Rd

department: Biomedical Sciences

institute: Colorado State University

summary: The mammalian oviduct is a complex, fibromuscular organ known for its role in orchestrating a series of timely and dynamic changes to suitably support early embryogenesis. Establishing successful reproductive outcomes are largely determined through effective and cohesive communication systems between the transient embryo and the maternal environment. Climate change-induced, Heat stress (HS), is one of the largest single stressors compromising reproductive function. Systemic changes in the redox status of the maternal environment, adversely affect fertilization and early embryonic development, negative causation of HS. Oviductal organoids represent a 3-dimensional, biomimetic model to study the physiological impact of HS on the physiology of the oviduct and the subsequent developing embryo. In this study, we aimed to generate a robust bovine oviductal organoid culture system to decrypt the oviducts' differential response to HS in terms of secreted EV-miRNome, to elucidate the impact of thermal stress on oviductal physiology with subsequent potential impacts on early embryo development.

overall_design: The proposed research utilized the bovine species as a large animal model to study EV-mediated response of oviductal organoids to thermal stress. Bovine reproductive tissues, readily obtained from a local slaughterhouse were utilized to establish a BOEC organoids for the production of extracellular vesicles to study the physiology of the oviduct under HS and the potential embryo-maternal signals shuttled through the oviduct microenvironment. Oviductal organoids cultured under normal (37 °C) or heat stress (42 °C) conditions and EVs were isolated from the culture media for RNA isolation and small-RNA sequencing.

first: Nico

middle: G

last: Menjivar

first: Riley

middle: E

last: Thompson

first: Melinda

middle: A

last: Meyers

first: Fiona

last: Hollinshead

first: Dawit

last: Tesfaye


title: Tsc1a knockdown and Mycobacterium marinum infection

status: Public on Oct 26 2023

city: Camperdown

first: RENHUA

last: SONG

state: NSW

address: Charles Perkins Centre - D17, Level 4 West. The University of Sydney Johns Hopkins Drive

country: Australia

institute: Centenary Institute

summary: We identify a putative link between miR-126 and the tsc1a signalling pathway resulting in the suppression of permissive macrophage accumulation at early zebrafish-M. marinum granulomas. Mechanistically, we find a detrimental effect of tsc1a expression that renders zebrafish embryos susceptible to higher bacterial burden and increased cell death via mTOR inhibition.

overall_design: Whole zebrafish embryo RNAseq of scram and tsc1a gRNA/Cas9-injected, with and without Mycobacterium marinum infection

first: Wright

last: Kathryn

first: Song

last: Renhua

first: Wong

last: Justin

first: Oehlers

last: Stefan


title: Transcriptomic response of bovine oviductal organoids to thermal stress.

summary: The mammalian oviduct is a complex, fibromuscular organ known for its role in orchestrating a series of timely and dynamic changes to suitably support early embryogenesis. Establishing successful reproductive outcomes are largely determined through effective and cohesive communication systems between the transient embryo and the maternal environment. Climate change-induced, Heat stress (HS), is one of the largest single stressors compromising reproductive function. Systemic changes in the redox status of the maternal environment, adversely affect fertilization and early embryonic development, negative causation of HS. Oviductal organoids represent a 3-dimensional, biomimetic model to study the physiological impact of HS on the physiology of the oviduct and the subsequent developing embryo. In this study, we aimed to generate a robust bovine oviductal organoid culture system to decrypt the oviducts' differential transcriptomic response to HS, to elucidate the impact of thermal stress on oviductal physiology with subsequent potential impacts on early embryo development.

overall_design: The proposed research utilized the bovine species as a large animal model to study the transcriptomic chnags in oviductal organoids as a response to thermal stress. Bovine reproductive tissues, readily obtained from a local slaughterhouse were utilized to establish a BOEC organoids to study the physiology of the oviduct under HS. Oviductal organoids were cultured under normal (37 °C) or heat stress (42 °C) conditions and then used for RNA isolation and sequencing.


title: Lactate Reprograms Glioblastoma Immunity through CBX3-regulated Histone Lactylation [RNA-seq]

city: New York

first: Shuai

last: Wang

address: 550 First Avenue

institute: NYU Grossman School of Medicine

summary: Glioblastoma (GBM), an aggressive brain malignancy with a cellular hierarchy dominated by GBM stem cells (GSCs), evades anti-tumor immunity through mechanisms that remain incompletely understood. Like most cancers, GBMs undergo metabolic reprogramming towards glycolysis to generate lactate. Here, we show that lactate production by patient-derived GSCs and microglia induces tumor cell epigenetic reprogramming through histone lactylation, an activating modification that leads to immunosuppressive transcriptional programs and suppression of microglial phagocytosis via transcriptional upregulation of CD47, a “don’t eat me” signal, in GBM cells. Leveraging these findings, pharmacologic targeting of lactate production augments efficacy of anti-CD47 therapy. Mechanistically, lactylated histone interacts with the heterochromatin component chromobox protein homolog 3 (CBX3). Although CBX3 does not possess direct lactyltransferase activity, CBX3 binds histone acetyltransferase (HAT) P300 to induce increased P300 substrate specificity toward lactyl-coA and a transcriptional shift toward an immunosuppressive cytokine profile. Targeting CBX3 inhibits tumor growth by both tumor cell-intrinsic mechanisms and increased tumor cell phagocytosis. Collectively, these results suggest that lactate mediates a metabolism-induced epigenetic reprogramming in GBM that contributes to CD47-dependent immune evasion, which can be leveraged to augment efficacy of immune-oncology therapies.

overall_design: To investigate the role of lactate-regulated hsitone lactylation in GBM cells, GSC23 and CW468 were treated with 10 mM sodium lactylate for 48 hours. To reveal the role of CBX3 in GBM cells, we established CBX3 knockdown cell lines in GSC23 and CW468 by using shRNA

first: Jeremy

middle: N

last: Rich


title: Lactate Reprograms Glioblastoma Immunity through CBX3-regulated Histone Lactylation

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

overall_design: Refer to individual Series


title: Mouse skin CD45 cells in house dust mite dermatitis

city: San Francisco

first: Marlys

last: Fassett

state: CA

address: 35 Medical Center Way Rm 1026

department: Dermatology

institute: UCSF-Parnassus

summary: Despite robust literature associating IL-31 with pruritic inflammatory skin diseases, its influence on cutaneous inflammation and on the interplay between inflammatory and neurosensory pathways remain unmapped. Here, we examined the consequences of disrupting Il31 and its receptor Il31ra in a mouse model of house dust mite (HDM) allergic dermatitis. Il31-deficient mice displayed an increased number and proportion of cutaneous type 2 cytokine-producing CD4 T cells and serum IgE in response to HDM. Single cell RNA-sequencing analysis of skin CD45+ populations from HDM-treated skin revealed that Il4ra+ monocytes and macrophages capable of fueling a feedforward type 2 inflammatory loop were selectively enriched in Il31ra-deficient HDM dermatitis skin. Thus, IL-31 is not strictly a pro-inflammatory cytokine, but rather an immunoregulatory factor that limits the magnitude of type 2 inflammatory responses in skin.

overall_design:
To determine the contribution of IL-31 to skin inflammation in dust mite-induced dermatitis, we epicutaneously challenged WT C57Bl/6 (B6_HDMw3) and IL31RAKO (B6_IL31RAKO_HDMw3) with Biostir HDM ointment.
HDM-treated skin pooled from 4 mice per group (B6_WT or B6_IL31RAKO) was harvested and digested with liberase, hyaluronidase, and DNAse. Viable CD45+ skin cells from each experimental group (WT_HDM and IL31RAKO_HDM) were isolated by FACS-sorting in preparation for RNA sequencing.

first: K

last: Ansel

first: Andrew

last: Schroeder


title: MUCOSAL EXPRESSION OF GENES PI3, ANXA1, AND VDR DESCRIMINATES CROHN’S DISEASE FROM ULCERATIVE COLITIS IN INFLAMMATORY BOWEL DISEASE PATIENTS

city: Herlev

first: Jaslin

middle: P

last: James

address: Borgmester Ib Juuls vej 1

department: Department of Pathology

country: Denmark

institute: Herlev hospital

summary: Differential diagnosis in inflammatory bowel disease (IBD) patients from the start of the diagnosis is challenging. In this study we tried to discriminate two subtypes of IBD such as Chron's disease(CD) and Ulcerative colitis (UC) using differential expression of genes from formalin-fixed paraffin-embedded mucosal biopsies of 33 IBD patients and 10 healthy controls.

overall_design:
Whole transcriptome RNA sequencing was performed using AmpliSeq human gene expression panel on FFPE colonic mucosal biopsies of IBD patients (CD, n=16, UC, n=17) and non-IBD controls (n=10) to study differential gene expression between CD and UC samples.
NOTE FROM SUBMITTER: Raw data generated during the current study can not be made publicily available, which is in accordance with the rules concerning processing of personal data set out in the EU General Data Protection Regulation (GDPR) and the Danish Data Protection Act. Nonetheless, may a researcher have an interest in our data they are welcome to contact us and collaborate. The data that support the findings of this study can be requested from The National Secretariat for Bio- and Genome Bank Denmark, RBGB.sekretariat.herlev-og-gentofte-hospital@regionh.dk, Herlev Hospital, Borgmester Ib Juuls Vej 73, 2730 Herlev, Denmark.

first: Boye

middle: S

last: Nielsen

first: Ib

last: Christensen

first: Ebbe

last: Langholz

first: Mikkel

last: Malham

first: Tim

last: Poulsen

first: Lene

last: Riis

first: Estrid

last: Høgdall


title: Unbiased transcription factor CRISPR screen identifies ZNF800 as master repressor of enteroendocrine differentiation [CHIP-seq]

first: Jeff

last: DeMartino

overall_design: ChIP-seq to determine genome-wide binding of ZNF800 in human small intestinal organoids

first: Lin

last: Lin


title: Next-Generation Sequencing Facilitates Quantitative Analysis of Wild Type and SNORD12B  Knock Down Expression of ESCC Transcriptomes.

city: Jinan

first: Tian

middle: Bao

last: Qing

address: Jiyan ROAD

institute: Shandong Cancer Hospital and Institute

summary: We aimed to detect the mRNA expression levels in KYSE30 cells after stable knock down SNORD12B expression with shRNA or vector.

overall_design: Totally, three samples were examined: KYSE30 stable knock down SNORD12B cell lines (sh12B-#1 and sh12B#2) versus pLKO.1.

first: Ming

last: Yang

first: Baoqing

last: Tian


title: MSP-induced Transcriptional Signature in Mouse Primary Colonic Epithelial Cells

city: Cambridge

first: Ramnik

last: Xavier

address: 415 Main Street

institute: Broad Institute of MIT and Harvard

summary: Ron (Mst1r), the receptor for MSP is highly expressed in colonic epithelial cells, especially in immature cell types, such as stem cells, TA cells and immature enterocytes. To identify genes that can be induced by MSP in mouse colonic epithelial cells, we performed bulk RNA-seq using day2 colon spheroids.

overall_design: To define MSP-induced transcriptional signature on mouse primary colonic epithelial cells, day2 colonic spheroids cells were treated with PBS or recombinant mouse MSP protein (100 ng/ml) for 0, 2, 4, 6h.

first: Toru

last: Nakata

first: Bihua

last: Li

first: Chenhao

first: Daniel

last: Graham


title: Spatial Transcriptomic profiling of day2 wounds and intact tissues of Hgfac WT and KO mice

summary: Wound healing is orchestrated by a spatial and temporal network of intercellular communication between epithelial cells, the stromal compartment, and the immune system. Our scRNA-seq analysis of Hgfac WT and KO wounds reveals that Aldh1a3 is downstream of the HGFAC system and Aldh1a3 is highly upregulated in wound-asociated epithelial (WAE) cells in responce to endoscopic wounding, suggesting WAE cells can potentially secrete retinoic acid into wound bed. To dissect the healing responce in the intestinal mucosa, we peformed spatial transcriptomics analysis.

overall_design: Day2 colonic wounds and intact colon samples from Hgfac WT and KO mice embedded into O.C.T. were used for Visium spatial transcriptomics.

first: Åsa

last: Segerstolpe


title: Lactate Reprograms Glioblastoma Immunity through CBX3-regulated Histone Lactylation [ChIP-seq]

first: Shuai

last: Wang

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-Seq) for total histone lactylation in GSC23 cells.

first: Jeremy

last: Rich


title: Single-Cell Transcriptomic Profiling of colonic wounds and intact tissues in Hgfac WT and KO mice

summary: Wound healing is orchestrated by a spatial and temporal network of intercellular communication between epithelial cells, the stromal compartment, and the immune system. We found that Hgfac KO mice showed delayed wound healing in an endoscopic wound model. To dissect the celluar and molecular mechanisms of tissue healing, we collected tissues from day2 wounds or intact tissues from Hgfac WT and KO mice using a skin biopsy punch and dissociated cells for scRNA-seq analysis.

overall_design: To identify transcriptional programs associated with wound healing in various cell types and to analyze whether there is a differenbe betwween Hgfac WT and KO mice.

first: Toufic

last: Mayassi


title: Dimethyl alpha-ketoglutarate inhibits proliferation in diffuse intrinsic pontine glioma by reprogramming epigenetic and transcriptional networks

city: Cheongju

first: Kyunghwan

last: Kim

address: Rm #202a, Bldg. S1-5, 1 chungdae-ro

country: South Korea

institute: Chungbuk National University

summary: Diffuse intrinsic pontine glioma (DIPG) is a highly aggressive pediatric brain tumor with limited therapeutic options. Here, we investigated the potential of dimethyl alpha-ketoglutarate (DMKG) as an anti-proliferative agent against DIPG and unraveled its underlying molecular mechanisms. DMKG exhibited robust inhibition of DIPG cell proliferation, colony formation, and neurosphere growth. Transcriptomic analysis revealed substantial alterations in gene expression, with upregulated genes enriched in hypoxia-related pathways and downregulated genes associated with cell division and the mitotic cell cycle. Notably, DMKG induced G1/S phase cell cycle arrest and downregulated histone H3 lysine 27 acetylation (H3K27ac) without affecting H3 methylation levels. The inhibition of AKT and ERK signaling pathways by DMKG coincided with decreased expression of the CBP/p300 coactivator. Importantly, we identified the c-MYC-p300/ATF1-p300 axis as a key mediator of DMKG's effects, demonstrating reduced binding to target gene promoters and decreased H3K27ac levels. Depletion of c-MYC or ATF1 effectively inhibited DIPG cell growth. These findings highlight the potent anti-proliferative properties of DMKG, its impact on epigenetic modifications, and the involvement of the c-MYC-p300/ATF1-p300 axis in DIPG, shedding light on potential therapeutic strategies for this devastating disease.

overall_design: Transcriptome profiles of DMKG-treated DIPG cells were generated in duplicate using Hiseq2500.


title: Haploid androgenetic development of bovine embryos reveals imbalanced WNT signaling and impaired cell fate differentiation.

city: Québec

first: Ricardo

middle: Perecin

last: Nociti

state: Québec

address: 2425, Rue de l'Agriculture

department: Animal Science

country: Canada

institute: Université Laval

summary: Haploid embryos have contributed significantly to our understanding of the role of parental genomes in development and can be applied to important biotechnology for human and animal species. However, development to the blastocyst stage is severely hindered in bovine haploid androgenetic embryos (hAE). To further our understanding of such developmental arrest, we performed a comprehensive comparison of the transcriptomic profile of morula-stage embryos, which were validated by qRT-PCR of transcripts associated with differentiation in haploid and biparental embryos. Among numerous disturbances, results showed that pluripotency pathways, especially the wingless-related integration site (WNT) signaling, were particularly unbalanced in hAE. Moreover, transcript levels of KLF4, NANOG, POU5F1, SOX2, CDX2, CTNNBL1, AXIN2, and GSK3B were noticeably altered in hAE, suggesting disturbance of pluripotency and canonical WNT pathways. To evaluate the role of WNT on hAE competence, we exposed early day-5 morula stage embryos to the GSK3B inhibitor CHIR99021. Although no alterations were observed in pluripotency and WNT-related transcripts, exposure to CHIR99021 improved their ability to reach the blastocysts stage, confirming the importance of the WNT pathway in the developmental outcome of bovine hAE.

overall_design: Bovine embryos at morula stage being Haploid Androgenotes, Haploid Parthenote and ICSI.

first: Luis

last: Paredes

first: Lawrence

middle: C

last: Smith


title: Genetic vulnerability to healing reveals a spatially resolved epithelial restitution program


title: Retinoic acid-induced Transcriptional Signature in Mouse Fibroblast cells

summary: During intestinal wound healing process, wound-associated epithelial (WAE) cells are differentiated from neighboring crypts and migrate to cover the wound bed. We found that WAE cells can produce retinoic acid via aldh1a3 and secrete it into wound bed. WAE cells and fibroblasts are highly colocalized in wound bed, suggesting fibroblasts can potenlially receive RA signal from WAE cells. To identify genes that can be induced by retinoic acid in mouse fibroblast, we performed bulk RNA-seq using NIH3T3 cells.

overall_design: To define an inducible RA transcriptional signature on mouse fibroblast, NIH3T3 cells were treated with DMSO or 1uM ATRA for 0h, 8h, 16h.


title: Abl depletion via autophagy mediates the beneficial effects of quercetin against Alzheimer pathology across species

city: Düsseldorf

first: Natascia

last: Ventura

address: Auf'm Hennekamp 50

institute: Heinrich Heine University  and the IUF- Leibniz Research Institute for Environmental Medicine

summary: Alzheimer's disease is the most common age-associated neurodegenerative disorder and the most frequent form of dementia in our society. Aging is a complex biological process concurrently shaped by genetic, dietary and environmental factors and natural compounds are emerging for their beneficial effects against age-related disorders such as cancer or cardiovascular diseases. Besides their antioxidant activity often described in simple model organisms, the molecular mechanisms underlying the beneficial effects of different dietary compounds remain largely unknown. Here, we exploited widely established C. elegans models for AD to test the effects of different natural compounds in vivo and focused on mechanistic aspects of one of them, quercetin, using complementary systems and assays. We show that quercetin has evolutionarily conserved beneficial effects against AD pathology: it prevents Aβ-induced detrimental effects in different C. elegans AD models and it reduces Aβ-secretion in mammalian cells. Mechanistically, we found that the beneficial effects of quercetin are mediated by autophagy-dependent reduced expression of Abl tyrosine kinase. In turn, autophagy is required upon Abl suppression to mediate quercetin’s protective effects against Aβ toxicity. Our data support the power of C. elegans as an in vivo model to investigate therapeutic options for Alzheimer disease.

overall_design: Worms were collected on day 3 after  birth, with 5 independent replicates performed for both control and  quercetin treated groups, while 4 independent replicates were performed for  lutein.

first: Alfonso

last: Schiavi

first: Claudia

last: Cirotti

first: Lora

last: Gerber

first: Giulia

middle: D

last: Lauro

first: Silvia

last: Maglioni

first: Patrick

last: Petzsch

first: Karl

last: Köhrer

first: Roel

last: Schins

first: Tina

last: Wahle

first: Daniela

last: Barilà


title: Whole-transcriptome analyses identify critical differentially expressed mRNAs, miRNAs, lncRNAs, and circRNAs during the process of oral carcinogenesis

city: Chengdu

first: Shouyi

last: Tang

state: Sichuan

address: Chengdu, Sichuan, P. R. China.

institute: Sichuan  University

summary: Oral carcinogenesis is a multi-step process involving normal mucosa progressing to oral precancerous lesions and finally to oral squamous cell carcinoma (OSCC). This complex process encompasses various molecules, including non-coding RNAs (ncRNAs). In this study, we performed whole-transcriptome analyses on adjacent normal tissues, oral leukoplakia tissues, and OSCC tissues, with the goal of identifying key differentially expressed circRNAs, lncRNAs, miRNAs, and mRNAs associated with different stages of oral carcinogenesis.  In our study, numerous differentially expressed circRNAs, lncRNAs, miRNAs, and mRNAs were identified in adjacent normal, oral leukoplakia, and OSCC tissues. Subsequently, we constructed two regulatory competitive endogenous RNA (ceRNA) networks and identified some potential critical molecules involved in oral carcinogenesis. In conclusion, based on the whole-transcriptome analyses, we mapped the molecular feathers at RNA level during the process of oral carcinogenesis and revealed certain ncRNAs with great research potential.

overall_design: In this study, we conducted whole-transcriptome sequencing on OSCC tumors, oral leukoplakia tissues, and adjacent normal tissues to screen for driver genes with significant alterations, desiring to reveal the underlying regulatory mechanism during the process from normal mucosa to oral leukoplakia and finally to OSCC at the transcriptional level.

first: Luyao

last: Cai

first: Yuting

last: Hu

first: Ying

last: Li

first: Xin

last: Zeng

first: Qianming

last: Chen

first: Yingqiang

last: Shen

first: Yu

last: Zhou


title: The DUF3715 domain has a conserved role in RNA-directed transposon silencing

city: Edinburgh

first: Theresa

last: Schöpp

address: 5 Little France Drive

country: United Kingdom

institute: University of Edinburgh

summary: RNA-directed transposon silencing operates in the mammalian soma and germline tosafeguard genomic integrity. The piRNA pathway and the HUSHcomplex identify activetransposons through recognition of their nascent transcripts, but mechanisticunderstanding of how these distinct pathways evolved is lacking. TASOR is anessential component of the HUSH complex. TASOR’s DUF3715 domain adopts apseudo-PARP structure and is required for transposon silencing in a mannerindependent of complex assembly. TEX15, an essential piRNA pathway factor, alsocontains the DUF3715 domain. Here, we show that TASOR’s and TEX15’s DUF3715domain share extensive structural homology. We found that the DUF3715 domain arosein early eukaryotes and that in vertebrates it is restricted to TEX15, TASOR, andTASORB orthologues. While TASOR-like proteins are found throughout metazoa,TEX15 is vertebrate specific. The branchingof TEX15 and TASOR-like DUF3715 domainlikely occurred in early metazoan evolution. Remarkably, despite this vast evolutionarydistance, the DUF3715 domain from divergent TEX15 sequences can functionallysubstitute for the same domain in TASOR and mediates transposon silencing. We havethus termed this domain of unknown function as the RNA-directed pseudo-PARPtransposon silencing (RDTS) domain. In summary, we show an unexpected functionallink between these critical transposon silencing pathways.

overall_design: To investigate the conservation of the DUF3715 domain between TEX15 and TASOR we established Tasor-deficient mouse ES cell lines which were subsequently reconstituted with mutant and chimeric TASOR constructs.


title: Expression profiling of STAT3-regulated genes in U937-derived macrophages

city: San Antonio

first: Tim

middle: Hui-Ming

last: Huang

state: TX

address: 7703 Floyd Curl Dr

institute: University of Texas Health at San Antonio

summary: We used RNA-Seq assay to characterize STAT3-regulated gene expression patterns in U937-derived macrophages. We wanted to determine how STAT3 activation involves in function, differentiation, cytokine secretion of macrophages.

overall_design: Vehicle control and STAT3 knockdown U937-derived macrophages were used for RNA-Seq assays in order to compare the transcriptional profiles that are regulated by STAT3.

first: Josephine

last: Taverna

first: Zhao

last: Zhang

first: Catherine

last: Limboy

first: Chia-Nung

last: Hung


title: miR-199a and miR-199b facilitate diffuse gastric cancer progression by targeting Frizzled-6

city: Cheonan

first: Keunsoo

last: Kang

state: Chungnam

address: Dandae-ro 119

department: Microbiology

institute: Dankook University

summary: Pathological markers that can monitor the progression of gastric cancer (GC) may facilitate the diagnosis and treatment of patients with diffuse GC (DGC). To identify microRNAs (miRNAs) that can differentiate between early and advanced DGC in the gastric mucosa, miRNA expression profiling was performed using the NanoString nCounter method in human DGC tumors. Ectopic expression of miR-199a and miR-199b (miR-199a/b) in SNU601 human GC cells accelerated the growth rate, viability, and motility of cancer cells and increased the tumor volume and weight in a mouse xenograft model. To study their clinicopathological roles in patients with GC, miR-199a/b levels were measured in human GC tumor samples using in situ hybridization. High miR-199a/b expression level was associated with enhanced lymphovascular invasion, advanced T stage, and lymph-node metastasis. Using the 3′-untranslated region (UTR) luciferase assay, Frizzled-6 (FZD6) was confirmed to be a direct target of miR-199a/b in GC cells. siRNA-mediated depletion of FZD6 enhanced the motility of SNU601 cells, and addback of FZD6 restored cancer cell motility stimulated by miR-199a/b. In conclusion, miR-199a/b promotes DGC progression by targeting FZD6, implying that miR-199a/b can be used as prognostic and diagnostic biomarkers for the disease.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for SNU601 cells and their derivatives (miR-199a and miR-199b overexpression).

first: Soon

last: Hong

first: Yoon

middle: H

last: Ko

first: Young-Ho

last: Ahn


title: Unbiased transcription factor CRISPR screen identifies ZNF800 as master repressor of enteroendocrine differentiation.

first: Jeff

last: DeMartino

overall_design: Refer to individual Series


title: miRNA-seq of grapefruit exosomes and fusion vesicles

city: Shenzhen

first: Rufan

address: No.66,Gongchang Road,Guangming District

institute: Sun Yat-sen University

summary:
miRNA-sequencing of grapefruit-derived extracellular vesicles and fusion nanovesicles derived from grapefruit-derived extracellular vesicles and gingival mesenchymal stem cell-derived vesicles.
We then performed gene expression profiling analysis  to explore the miRNAs derived from grapefruit-derived extracellular vesicles, and the retention rate of miRNAs after membrane fusion

overall_design: Comparative gene expression profiling analysis of miRNA-seq data for grapefruit exosomes and fusion vesicles derived from grapefruit exosomes, each group had three biological replicates.

first: Fang

last: Cheng

first: Hongbo


title: Changes in gene expression in mouse prostate in response to genetic activation of AMPK

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

institute: MRC London Institute of Medical Sciences

summary: Emerging evidence indicates that metabolic dysregulation drives prostate cancer (PCa) progression and metastasis. AMPK is a master regulator of metabolism although its role in PCa remains unclear. Here we show that genetic and pharmacological activation of AMPK provides a dramatic protective effect on PCa progression in vivo. We show that AMPK activation induces PGC1a expression leading to a catabolic metabolic reprogramming of PCa cells. This catabolic state is characterised by increased mitochondrial gene expression, increased fatty acid oxidation, decreased lipogenic potential, decreased cell proliferation and decreased cell invasiveness. Together, these changes inhibit PCa disease progression. Additionally, we identify a gene network that is inhibited by AMPK activation involved in cell cycle regulation. We show correlation between this gene network and PGC1a expression in human PCa. Taken together our findings strongly support the use of AMPK activators for clinical treatment of PCa.

overall_design: RNA from six replicate mouse whole prostate tissue from prostate-specific Pten null and prostate-specific Pten null with AMPK gain-of-function (GoF) mutation was sequenced using NextSeq 500.

first: Lucy

last: Penfold

first: David

last: Carling


title: miRNA-seq of cell membrane-based vesicles derived from gingiva-derived mesenchymal stem cells

summary:
miRNA-sequencing of cell membrane-based vesicles derived from gingiva-derived mesenchymal stem cells and fusion nanovesicles.
We then performed gene expression profiling analysis  to explore the miRNAs  of cell membrane-based vesicles derived from gingiva-derived mesenchymal stem cells , and the retention rate of miRNAs after membrane fusion

overall_design: Comparative gene expression profiling analysis of miRNA-seq data for cell membrane-based vesicles derived from gingiva-derived mesenchymal stem cells and fusion vesicles , each group had three biological replicates.

last: Chen


title: Trancriptomic characterization of labetuzumab effect on IL13-treated human bronchial epithelial cells

city: Macclesfield

first: Carlos

middle: Lopez

last: Garcia

state: Cheshire

address: Alderley Park, Congleton Rd, Alderley Edge, West Didsbury

department: TLCB

institute: CRUK-MI

summary: We have characterized the effect of the CEACAM5 targeting monoclonal antibody labetuzumab (2 µg/mL) on the transcriptional response to interleukin-13 (IL-13) treatment (10ng/mL) of air-liquid interface (ALI) cultures generated from primary human bronchial epithelial cells. ALI cultures were treated with IL-13 and labetuzumab during the last 7 days of ALI development and the transcriptomes analyzed by RNA-seq.

overall_design: We analyzed the transcriptomes of 12 ALI cultures divided in 3 experimental groups: untreated control ALIs ( no IL-13, no labetuzumab), IL-13 treated ALIs and ALIs treated with both IL-13 and labetuzumab.

last: Lopez-Garcia


title: scRNA seq of the oral squamous cell carcinoma gingivo-buccal (OSCC-GB)

city: Kalyani

first: Arindam

last: Maitra

state: West Bengal

address: PO: NSS

country: India

institute: National institute of Biomedical Genomics

summary: Intra-tumor cellular diversity plays an important role in cancer progression, recurrence, and overall survival of cancer patients. We used scRNA-seq to characterize the cell type and cell state diversity in the tumor ecosystem of OSCC-GB

overall_design: Single-cell was isolated from primary tumors of OSCC-GB and scRNA-seq was performed using 10x Genomics Chromium platform

first: Partha

last: Majumder


title: Mechanical forces direct the cell fate of inner ear organoids in a stage-dependent manner

city: Shanghai

first: Mingyu

last: Xia

state: Shanghai

address: No. 83, Fenyang Road, Xuhui District

department: ENT Institute and Otorhinolaryngology Department of the Affiliated Eye and ENT Hospital, Sta

institute: Fudan University

summary: During the development, mechanical force plays an important role in shaping the inner ear and establishing regular cellular patterns, however, the effects of ubiquitous mechanical cues on cellular fate determination are not clear. Here we developed stiffness adjustable hydrogels for three-dimensional (3D) cochlear organoid culture, which could precisely simulate the mechanical force from the extracellular matrix (ECM) during the expansion of cochlear progenitor cells (CPCs) and organoid formation. Within a certain range, suitable stiffness can stimulate CPC proliferation through a mechanism requiring integrin/cytoskeleton/YAP signaling. Surprisingly, increasing stiffness could inhibit the proliferation of CPCs and induce the differentiation of organoids, which was mediated by the increased intracellular Ca2+ signaling in CPCs, and further activated Klf2 to promote the differentiation of HCs with bundles. Furthermore, this chemical-defined hydrogel is also suitable for 3D bioprinting, and we printed the spiral-like structure with CPCs and HCs, which provided a promising way for cochlear organoids to further improve our understanding of the organization of the inner ear and contribute to developing new therapeutic approaches for HCs regeneration.

overall_design: We establish a chemically defined GelMA-HA-RGD hybrid hydrogel-based 3D culture system for cochlear organoid formation from cochlear progenitor cells. We compared the cells cultured in gels with different degrees of stiffness. Highly resembling the dynamic force pattern from the extracellular matrix in the developmental microenvironment in which inner ear progenitors reside in vivo, the tunable mechanical force in the hybrid hydrogel system manipulated CPC proliferation and differentiation.

first: Huawei

last: Li

first: Wenyan

first: Mingxuan

last: Wu


title: DNA methylation of fibroblasts from one HGPS patient

city: Bologna

first: Maria Giulia

last: Bacalini

address: Via Altura 3

department: Brain Aging Laboratory

country: Italy

institute: IRCCS Istituto delle Scienze Neurologiche di Bologna

summary: DNAm profiling of fibroblasts from one HGPS patient (6 years; 3 replicates assessed) and two healthy controls (12 and 15 years, each assessed in 2 replicates)

overall_design: 1 µg of DNA was bisulfite-converted using the EZ DNA Methylation kit (Zymo Research) and analysed using the HumanMethylationEPIC BeadChip (Illumina) following manufacturer's instructions

first: Giovanna

last: Lattanzi

first: Maria

first: Paolo

last: Garagnani


title: Investigating the NRAS 5’ UTR as a Target for Small Molecules

city: Groningen

first: Danny

last: Incarnato

state: Netherlands

address: Nijenborgh 7

department: Molecular Genetics

institute: University of Groningen

summary: Neuroblastoma RAS (NRAS) is an oncogene that is deregulated and highly mutated in cancers including melanomas and acute myeloid leukemias. Constitutively activated NRAS induces the MAPK and AKT signaling pathways and leads to uncontrolled proliferation and cell growth, making it an attractive target for small molecule inhibition. Like all RAS-family proteins, it has proven difficult to identify small molecules that directly inhibit the protein. An alternative approach would involve targeting the NRAS mRNA. The 5′ untranslated region (5′ UTR) of the NRAS mRNA is reported to contain a G-quadruplex (G4) that regulates the translation of NRAS mRNA. Stabilizing the G4 structure in NRAS by small molecules could reduce NRAS protein expression in cancer cells by impacting translation. Here we report a novel class of small molecule that binds to the G4 structure located in the 5′ UTR of the NRAS mRNA. We used a small molecule microarray (SMM) screen to identify molecules that selectively bind to the NRAS-G4. Biophysical studies demonstrated that compound 18 binds reversibly to the NRAS-G4 structure with submicromolar affinity. A Luciferase based reporter assay indicated that 18 inhibits the translation of NRAS via stabilizing the NRAS-G4 in vitro but showed only moderate effects on the NRAS levels in cellulo. Rapid Amplification of cDNA Ends (RACE), RT-PCR analysis on 14 different NRAS-expressing cell lines, coupled with analysis of publicly available CAGE seq experiments, revealed that predominant NRAS transcript does not possess the G4 structure. Further analysis of published rG4 and G4 sequencing data indicated the presence of G4 structure in the promoter region of NRAS gene (DNA) but not in the mRNA. Thus, although the NRAS transcript lacks a G4 in many cell lines the broader concept of targeting folded regions within 5’ UTRs to control translation remains a highly attractive strategy.

overall_design: RNA-seq, SHAPE-MaP.

first: Sumirtha

last: Balaratnam

first: Zachary

last: Torrey

middle: R

last: Calabrese

first: Michael

middle: T

last: Banco

first: Kamyar

last: Yazdan

first: Xiao

last: Liang

first: Adrian

last: Ferré-D'Amaré

first: John

last: Schneekloth Jr


title: Amplification of Oocytes through Parthenogenesis [RRBS]

city: Munich

first: Chenglei

last: Tian

address: Ingolstädter Landstraße 1

institute: Helmholtz Munich

type: Methylation profiling by high throughput sequencing

summary: We asked whether oocyte number could be amplified through parthenogenesis of mouse oocytes, without requiring creation of a paternal genome and a genetically unique genome. Parthenotes develop to a blastocyst-like stage, and from this parthenogenetic ESCs (pESCs) can be derived with high efficiency. Like ESCs, pESCs maintain unlimited self-renewal and pluripotency, as well as germline competence. Further, we demonstrate that their expression pattern of imprinted maternal genes resembles that observed in oocytes. pESCs can be directed to differentiate into primordial germ cell-like cells (PGCLCs) and form oocytes that produce fertile pups and reconstitute ovarian endocrine functions. The transcriptome and imprinting pattern of PGCLCs differentiated from pESCs more closely approximate those of in vivo produced embryonic PGCs, than PGCLCs produced from ESCs. Parthenogenesis offers a promising route for deriving PGCLCs and amplifying oocytes by faithfully maintaining maternal genes, without fertilization.

overall_design: We performed RRBS assay to analysis the DNA methylation between female ESC and pESC, and also analysis the DNA methylation among PGC, female ESC-PGCLC and pESC-PGCLCs


title: Genome-wide maps of SBNO2 target transcripts and RNA-seq of SBNO2 deficient cells

city: Bethesda

first: Markus

last: Hafner

state: MD

address: 50 South Drive

department: NIAMS

institute: NIH

summary: DExD/H box helicases are ATPases that govern key biochemical events of host RNA metabolism including unwinding or annealing RNA, facilitating the formation or remodeling of ribonucleoprotein complexes, and controlling transcriptional or translational RNA pools essential for normal human neurodevelopment1-6. Some helicases also recognize foreign RNAs of infectious agents during immune responses but how they govern host genes essential for immunity is unknown. Here we describe a previously undiscovered genetic immunodysregulatory syndrome, due to Strawberry Notch Homolog 2 (SBNO2) deficiency, that highlights a new function of these helicases in binding to nascent transcripts of host cytokine and immune response genes near the transcription start site and increasing their expression.

overall_design: Integrating photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation (PAR-CLIP) and RNA-seq data to reveal the function of SBNO2.

first: Kazuyuki

last: Meguro

first: Dimitrios

last: Anastasakis


title: Single-Cell Decoding of the Clinical Outcome-Associated Diversification and Dynamic  Changes of CAR-T Cells in Patients with B-cell ALL

city: Beijing

first: Zongcheng

last: Li

address: No. 8 East Street, Fengtai District

institute: Fifth Medical Center of Chinese PLA General Hospital

summary: Cellular evolution and molecular programs of chimeric antigen receptor-engineered  (CAR)-T cells post-infusion are pivotal for developing better treatment strategies. Here,  we constructed a high-precision single-cell transcriptional dynamic landscape of 7,578  CAR-T cells from 26 B-ALL patients and evaluated their long-term therapeutic efficacy.  We demonstrated that the cytotoxic profile rather than memory property was a  favorable biomarker for long-term remission. At the single-cell resolution, we  uncovered the vast heterogeneity of CAR-T cells in vivo and identified eight CAR-T  cell subtypes. Remarkably, the dominance of cytotoxic subtypes was coincident with  long-term remission, while the emergence of subtypes with B-cell transcriptional  features could be detected early and predict relapse. Furthermore, we defined  transcriptional hallmarks of distinct CAR-T cell populations and revealed molecular  changes along computationally-inferred cellular evolution of CAR-T cells in vivo .  Collectively, these results illuminated intrinsic properties for durable response and  provided molecular cues for improving CAR-T immunotherapy.

overall_design: Herein, we comprehensively dissected the dynamical changes in the transcriptomic profile of CAR-T cells enriched from IPs and paired peripheral blood samples longitudinally, collected at serial time points post-infusion for up to 15 months, and explored their clinical implications in the long-term response or resistance in 26 B-ALL patients.   In order to obtain highly reliable CAR-T cells, a two-step purification procedure was adopted to purify CAR-T cells from infusion products and peripheral blood samples. Firstly, immunophenotypic CAR-T cells (CD3+ CAR+) were isolated and individually sorted into 96-well plates by Moflo XDP (Beckman Coulter). Then, sorted CAR-T cells were further validated by the amplification of CAR sequence in single-cell polymerase chain reaction (scPCR) before library preparation.

first: Liang

last: Huang

first: Lei

last: Zhao

first: Lilin

last: Ye

first: Yu

last: Lan

first: Jianfeng

last: Zhou


title: RNA Sequencing Facilitates Quantitative Analysis of Parkinson's patients (PD) and non-PD control (NC) Plasma Tanscriptomes

city: Nanjing

first: Han

last: Xiaojuan

state: Jiangsu

address: Zhongshan Road 321

institute: Nanjing Drum Tower Hospital,  The Affiliated Hospital of Nanjing University Medical School

summary: Despite extensive investigation of Parkinson's disease (PD), rending oxidative stress, mitochondrial dysfunction, altered proteostasis, and abnormal insulin signaling as potential mechanisms, however, etiology of most cases remains undefined. To reveal the underlying mechanism and determine the correlation of SH2B1 expression and Parkinson’s disease, we monitored the related gene levels during PD progress in humans and mice. For human subjects, we collected plasma from Parkinson’s patients (PD, diagnosed by clinicians and non-PD controls (NC, because brain samples are not available) and performed whole-transcriptome gene expression analysis. The transcriptome microarray enabled detection of the differential expression of 3229 transcripts (FPKM >= 0.1; cutoff of 2.0-fold change; p < 0.05) and further filtering of 952 transcripts (588 up-, 364 down-regulated transcripts in PD; reads > 5, p < 0.05).Based on the unbiased analysis, we revealed that SH2B1, but not SH2B2 or SH2B3, was reduced in PD patients’ plasma. Real-time quantitative polymerase chain reaction (qPCR) confirmed that there was decreased expression of SH2B1 in PD patients’ plasma as well as in plasma from MPTP/p induced murine PD model. SH2B1 is an intracellular adaptor protein that assists signal transduction of several receptor-tyrosine-kinases and elicits beneficial metabolic effects in obesity. Here, we show that SH2B1 is a key component of molecular chaperone autophagy (CMA) that preserves dopaminergic neuron health and counters MPTP/p-induced PD in mice. Sh2b1 deficiency accelerated neuron apoptosis in PD mouse. In contrast, transgenic expression of Sh2b1 in neurons alleviated MPTP/p-induced injury. SH2B1 attenuated neuron apoptosis by binding HSC70 to promote CMA degradation of PLIN4, a lipid droplets (LDs) surrounding protein, thus suppressed PLIN4/LDs mediated lipid peroxidation stress in PD mice brain. Adeno-associated virus–mediated (AAV-mediated) rescue of neuron HSC70 expression in wildtype not Sh2b1-deficent mice functionally restored the neuropathology of PD. Thus, neuronal SH2B1 serves as an assistant in CMA rather than insulin signaling by promoting a CMA substrate degradation to counter MPTP/p-induced neurodegeneration.

overall_design: RNA sequencing(including circRNA ,LncRNA,mRNA) in serum from control(NC) persons and Parkinson's patients, in quadruplication.

first: M

last: Lu

first: X

last: Han

first: J

last: Tang


title: The eukaryotic translation initiation factor eIF4E regulates flowering and circadian rhythm in Arabidopsis

status: Public on Oct 25 2023

city: FuZhou

first: Jing

last: Zhang

state: Fujian Province

address: No.15 Shangxiadian Road, Cangshan District, Fuzhou City, Fujian Province, China

institute: Fujian Agriculture and Forestry University

summary: Translation initiation is a rate-limiting step in protein synthesis. The eukaryotic translation initiation factor 4E (eIF4E) plays an essential role in the translation initiation process. However, how eIF4E-dependent translation initiation regulates plant growth and development remains not fully understood. In this study, we have found that Arabidopsis eIF4E proteins distribute both in the nucleus and cytoplasm, and only cytoplasmic eIF4E is implicated in the control of flowering time. Results of profiling the genome-wide translation by Ribo-tag sequencing further reveal that eIF4E may regulate plant flowering by affecting homeostatic translation of flowering-time genes, including the Central Oscillator Genes (COGs). Consistent with the hypothesis that transcription-translation feedback loop is the core mechanism to drive the oscillation of circadian clock, we show that the eIF4E-dependent translation modulates the rhythmic oscillation of protein abundance of the clock-related genes (CCGs). Together, our study provides mechanistic insights into how the protein translation regulates multiple developmental processed in Arabidopsis including circadian clock and photoperiodic flowering.

overall_design: The differences of transcriptomes and  translatomes between wild type and eif4e mutant were compared and analyzed

first: Lianfeng

last: Gu

first: Guifang

last: Lin

first: Qin

last: Wang


title: A bacteria-derived tetramerized protein ameliorates nonalcoholic steatohepatitis (NASH) in mice via binding and relocating acetyl-coA carboxylase

city: wuhan

first: Yan

address: 299 Bayi Road, Wuchang District, Wuhan City, Hubei Province

department: Department of Medical Genetics

institute: Wuhan University

summary: Increased de novo lipogenesis (DNL) is a major feature of nonalcoholic steatohepatitis (NASH). None of the drug targeting the catalytic activity of acetyl-CoA carboxylase (ACC), the rate-limiting enzyme in the DNL process, has been approved by FDA. Whether cytosolic ACC1 can be regulated spatially is unknown. Herein, we found that streptavidin, which is a bacterium derived tetrameric protein, forms cytosolic condensates and efficiently induce a spatial re-localization of ACC1 in liver cells, concomitant with inhibited lipid accumulation. Both SA tetrameric structure and multivalent protein interaction are required for condensates formation. Interestingly, the condensates are further characterized as gel-like membraneless organelle (SAGMO) and significantly restrict the cytosolic dispersion of ACC1 and fatty acid synthase (FASN). Notably, AAV mediated delivery of SA partially blocks mice liver DNL and ameliorate NASH without eliciting hypertriglyceridemia. In summary, our study demonstrates that insulating lipogenesis-related proteins by SAGMO might be effective for NASH treatment.

overall_design: To establish a fatty liver model, mice were fed a HFD diet (protein, 20%; fat, 60%; carbohydrates, 20%; #D12492, SYSE Bio-tech Co., LTD, Changzhou, China) for 24 weeks. To induce NASH, mice were fed a HFHC diet (protein, 14%; fat, 42%; carbohydrates, 44%; cholesterol, 0.2%; #TP26304, TROPHIC Animal Feed High-Tech Co. Ltd, Nantong, China) with free access to a mixture of 23.1% fructose and 18.9% sucrose in water solution for 16 weeks. Mice in the control group were fed a normal chow (NC) diet (protein, 20.6%; fat, 12.0%; carbohydrates,67.4 %; XIETONG BIO-ENGINEERING CO., LTD. Nanjing, China). AAV2/9-SA or AAV2/9-Ctrl (4.8X10^10vg per mouse, via tail vein) were administered to mice after 7 weeks of feeding.

first: Mingkun

last: Yang

first: Li

first: Fan

first: Jiachen

last: Fan

first: Yulong

last: Qiang

first: Yuting

last: Chang

first: Wenjie

first: Leilei

last: Yan

first: Jie

last: Xiong

last: Ping

first: Shizhen

last: Chen

first: Dong

last: Men

first: Feng


title: MicroRNA-1 protects the endothelium in acute lung injury

city: West Haven

first: Francesc

last: Lopez

state: CT

department: Department of Genetics

institute: Yale University

summary: Acute lung injury (ALI) and its most severe form, acute respiratory distress syndrome (ARDS), cause severe endothelial dysfunction in the lung and vascular endothelial growth factor (VEGF) is elevated in ARDS. We have found that the levels of a VEGF-regulated microRNA, microRNA-1 (miR-1) is reduced in the lung endothelium after acute injury. Pulmonary endothelial cell (EC)-specific overexpression of miR-1 protects the lung against cell death and barrier dysfunction in both murine and human models and increases the survival of mice after pneumonia-induced ALI. MiR-1 has an intrinsic protective effect in pulmonary and other types of ECs; it inhibits apoptosis and necroptosis pathways and decreases capillary leak by protecting adherens and tight junctions. Comparative gene expression analysis and RISC recruitment assays identified miR-1 targets in the context of injury, including  phosphodiesterase 5A (PDE5A), angiopoetin-2 (ANGPT2), connector enhancer of kinase suppressor of ras 3 (CNKSR3) and TNF alpha induced protein 2 (TNFAIP2). We validated miR-1-mediated regulation of ANGPT2 in both mouse and human ECs and found that in a 119-patient pneumonia cohort, miR-1 correlated inversely with ANGPT2. These findings illustrate the novel role of miR-1 as a cytoprotective orchestrator of endothelial response to acute injury with prognostic and therapeutic potential.

overall_design: Whole genome transcriptome of HPMECs with and without treatment with TNF alpha, with three replicates of per condition

first: Asawari

last: Korde

first: Maria

last: Haslip

first: Prachi

last: Pednekar

first: Alamzeb

last: Khan

first: Maurizio

last: Chioccioli

first: Sameet

last: Mehta

last: Lopez-Giraldez

first: Santos

last: Bermejo

first: Mauricio

last: Rojas

first: Charles

last: Dela Cruz

first: Michael

last: Matthay

first: Jordan

last: Pober

first: Richard

last: Pierce

first: Shervin

last: Takyar


title: The Gene Profile of Senescent Conjunctival Cells

city: Kyoto

first: Akifumi

last: Matsumoto

state: Kyoto

address: 465 Kajii-cho, Kawaramachi-Hirokoji, Kamigyo-ku

department: Department of Ophthalmology

country: Japan

institute: Kyoto Prefectural University of Medicine

summary: To investigate the gene profiles of senescent conjunctival cells by X-ray exposure.

overall_design: Three biological replicates were analyzed for each of 2 conditions (untreated, irradiation)

first: Koji

last: Kitazawa

first: Kosaku

last: Numa


title: Tissue morphology influences the temporal program of human cerebral organoids

city: Cambridge

first: Madeline

last: Lancaster

state: Cambridgeshire

address: Cambridge Biomedical Campus, Francis Crick Avenue

department: Cell Biology Division

institute: MRC Laboratory of Molecular Biology

summary: Organs are the ensemble of different cell types in a complex architectural milieu. It is well-known that progression through fate decisions sets up the complex cellular makeup and architecture of an organ, but how that same architecture may impact on cell fate is less clear. We sought to examine this by taking advantage of the unique capabilities of organoids as a tractable in vitro model to interrogate how fate and form interact during organ development. Screening methodological variations encountered in the literature revealed that common protocol adjustments, such as small molecule patterning and exposure to exogenous extracellular matrix, impacted various aspects of morphology, from macro structure to tissue architecture. We demonstrated that overall morphology is a predictor of tissue architecture and that perturbing morphology results in changes in cytoarchitecture. Vice-versa, perturbing cytoarchitecture by mechanically redistributing cells in a random spatial conformation resulted in a simplified overall morphology. We next examined the impact of these morphological perturbations on cell fate through integrated snRNA-seq and spatial transcriptomics within the phenotypic landscape. Regardless of the specific protocol, organoids with more complex morphology better mimicked in vivo human fetal brain development than organoids with simplified morphology. Further, organoids with perturbed tissue architecture profiled with scRNA-seq over a time course experiment displayed aberrant temporal progression in cell fate, with cells being intermingled in both space and time. Finally, imparting a simplified morphology through physical encapsulation led to disrupted tissue cytoarchitecture and a similar abnormal temporal progression. These data not only point to the importance of tissue morphology in organoid fidelity compared to in vivo, but also demonstrate that cells require proper spatial coordinates in order to undergo the proper temporal trajectory of events.

overall_design: Single organoids were incubated in 1 mL Accumax solution (Merck, A7089) supplemented with DNase I (Sigma, 04716728001) 1.25 U/mL. Organoids were incubated in the solution at 37°C for 20 minutes on a shaker followed by gentle agitation and pipetting. The enzymatic activity of Accumax was stopped by adding IDM+A or FBS (fetal bovine serum Merck, F2442) 1:10. The solution was filtered through 70 µm cell strainer prior to cell counting. The solution was centrifuged at 200g for 10 minutes at 4°C and the pellet resuspended in cell prefixation buffer (Parse Biosciences). Sample fixation and split-seq were performed according to the Evercode Fixation v3 Parse Biosciences protocol. Control (COs) were collected at day 45, 55, 70 for sequencing. Dissociated (DISS) organoids were collected for sequencing at day 48, 55, 70, and Constrained (CONS) organoids were collected at day 55. Parse Biosciences Evercode whole transcriptome WT was used for COs, CONS, and DISS single cells.  For nuclear split-seq, nuclei were isolated as described above, and sample fixation and split-seq were performed according to the Evercode Fixation v3 Parse Biosciences protocol for single nuclei. Nuclei were sequenced with Parse Biosciences Evercode whole transcriptome WT Mini. 20,000 total nuclei and 60,000 total cells were loaded for split-seq. Single cells were sequenced on a S2 Novaseq lane (4 billion reads depth). Single nuclei were sequenced on a SP Novaseq lane (400 million reads depth). N=2 organoids per batch (3 batches) per condition per time point exception made for day48 (2 batches), day55 COs (5 batches), day55 DISS (2 batches), day55 CONS (3 batches, 5 organoids). For further details see attached metadata excel spredsheats and Parse Biosciences computational pipe line output (submitted as suplmentary files).

first: Ivan

last: Imaz-Rosshandler

first: Ilaria

last: Chiaradia


title: Atractylenolide III Ameliorated Autophagy Dysfunction via EpidermalGrowth Factor Receptor-Mammalian Target of Rapamycin Signals and Alleviated Silicosis Fibrosis in Mice

city: Changsha

first: Hanqin

last: Wang

address: Tongzipo road No.371

institute: Hunan Normal University

summary: Atractylenolide III (ATL-III) is a major active constituent of the natural plant Atractylodes rhizome. Our previous study has shown that ATL-III may alleviate alveolar macrophage apoptosis via the inhibition of the mammalian target of rapamycin (mTOR)-mediated autophagy of human silicosis. Therefore, we aimed to further explore the function of ATL-III in autophagy, apoptosis, and pulmonary fibrosis by establishing the ATL-III-intervened silicosis mouse model in this study. Meanwhile, we sought and then verified potential autophagy-related signaling pathways by matching differentially expressed genes (attained by RNA sequencing) and the autophagy database. In this study, RNA-sequencing results implied that the epidermal growth factor receptor, the crucial upstream activator of mTOR, was seen as a potential autophagy-regulatory molecule in the ATL-IIIeintervened silicosis mouse model. The finding of this study was that ATL-III might improve the disorder of autophagic degradation via the activation of epidermal growth factor receptor-mTOR signals in the pulmonary tissue of the silicosis mouse model. ATL-III also alleviated cell apoptosis and silicotic fibrosis. Overall, we supposed that ATL-III might be a potential protective medicine, which had a regulatory effect on autophagy, for the intervention of silicotic fibrosis. In the future, the therapeutic drugs for silicosis should be further focused on the development and application of such natural autophagy agents.

overall_design: Male C57BL/6J mice (6 to 8 weeks old, 20 to 25g), were housed in an air-conditioned room under light-controlled conditions (twelve-hour light/twelve-hour dark cycle) with standard laboratory food and water ad libitum. A total of 60 mice were randomly divided into 3 groups as follows (n = 20 for every group): the Ctrl group, which was instilled intratracheally with 50 mL of saline; the Silica group, which was instilled intratracheally with 50 mL of saline containing 5 mg of silica; and the Silica þ ATL-III group, which was injected intraperitoneally with 0.2 mL of saline containing 30 mg/kg/d of ATL-III on the basis of the Silica group..  Mice were executed with pentobarbital sodium anesthesia on the 28th day after instillation, and lung tissues were extracted for RNA sequencing.

first: Shiyi

last: Tan

first: Shi

last: Chen

first: Huimin

last: Kang

first: Ke

last: Zhou

first: Shang

last: Yang


title: Cohesin mediates DNA loop extrusion and sister chromatid cohesion by distinct mechanisms [Hi-C]

city: Vienna

first: Roman

last: Stocsits

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP - Research Institute of Molecular Pathology

summary: Cohesin connects CTCF binding sites and other genomic loci in cis to form chromatin loops, and replicated DNA molecules in trans to mediate sister chromatid cohesion. Whether cohesin uses distinct or related mechanisms to perform these functions is unknown. Here we describe a cohesin hinge mutant, which can extrude DNA into loops but is unable to mediate cohesion. Our results suggest that the latter defect arises during cohesion establishment. The observation that cohesin’s cohesion and loop extrusion activities can be separated indicates that cohesin uses distinct mechanisms to perform these two functions. Unexpectedly, the same hinge mutant can also not be stopped by CTCF boundaries as well as wildtype cohesin. This suggests that cohesion establishment and cohesin’s interaction with CTCF boundaries depend on related mechanisms and raises the possibility that both require transient hinge opening to entrap DNA inside the cohesin ring.

overall_design: Hi-C to analyze the effect of mutations on chromatin architectures in different conditions

first: Kota

last: Nagasaka

first: Gordana

last: Wutz


title: Effect of Card9 knockout on gene expression in cardiac tissues of mice post myocardial infarction

first: Yan

last: Liu

address: 2 Anzhen Road, Chaoyang District

institute: Beijing Institute of Heart Lung and Blood Vessel Diseases, Beijing Anzhen Hospital, Capital Medical University

summary: Immune cell infiltration in response to myocyte death contributes to extracellular matrix (ECM) remodeling and scar formation after myocardial infarction (MI). Caspase-recruitment domain protein 9 (CARD9) which belongs to CARD family acts as an adapter that mediate the transduction of proinflammatory signaling cascades in innate immunity. To investigate the role of CARD9 in cardiac injury and repair post ischemia, we subjected Card9 knockout mice to myocardial infarction (MI) , and then performed RNA-seq and gene expression profiling analysis using the ischemic cardiac tissues at 3 days post-MI, to identify key genes and pathways regulated by CARD9.

overall_design: 12-week-old male WT and Card9 KO mice were subjected to MI by ligation of left coronary artery. Cardiac tissues below the ligature from MI and Sham mice at 3 days post-MI were harvested and used for total RNA extraction and RNA-seq (n=2 for each group).

first: Jie

last: Du

first: Yulin

last: Li


title: Impaired Branched-Chain Amino Acid Catabolism is Associated with Chemotherapy-Induced Heart Failure and Rescued by Metformin

city: Cleveland

first: Feixiong

last: Cheng

state: Ohio

address: 9500 Euclid Ave

department: Genomic Medicine

institute: Cleveland Clinic

summary:
To investigate the cooperative function KDM4D/NFIB/MLL1 complex in the regulation of adipogenic differentiation, we established 10T1/2 cell lines in which each target gene has been knocked down by shRNA.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 3 different drug treatments.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for hiPSC-cardiomyocyte cells treated with doxorubicin versus DMSO, and doxorubicin and metformin co-treatment versus DMSO

first: Jessica

last: Castrillon Lal


title: Ribosomal dysregulation: A conserved pathophysiological mechanism in human depression and mouse chronic stress

city: Toledo

first: Rammohan

last: Shukla

state: OH

address: 3000 Arlington Avenue

department: Department of Neurosciences

institute: University of Toledo

summary: The biological underpinnings of major depressive disorder (MDD) heterogeneity are unknown, in part due to the poor association between MDD models and clinical endpoints. We compared transcriptomic profiles of human postmortem MDD brain tissue and chronic variable stress (CVS)-exposed mice to identify orthologous genes. A downregulation of ribosomal protein genes (RPGs) and upregulation of associated RP pseudogenes in the prefrontal cortex of several independent cohorts from both human MDD and mouse CVS tissue prompted a seeded gene co-expression analysis using the RPGs altered in both groups. Downregulated RPGs were found to regulate synaptic changes in human MDD and mouse CVS through a RP pseudogene-driven mechanism. In vitro and in silico analysis further suggested that the inverse RPG/RP pseudogene association was a glucocorticoid-driven response and reversed during MDD remission. Thus, stress-induced alterations in RPGs may contribute to synaptic dysregulation in MDD, providing a mechanism for the variability in depression presentation.

overall_design: Comparative analysis of molecular data (mRNA) from different experimental systems of chronic stress and major depressive disorder (MDD).

first: Xiaolu

last: Zhang

first: Mahmoud

last: Eladawi

first: William

last: Ryan

first: Xiaoming

last: Fan

first: Stephen

last: Prevoznik

first: Trupti

last: Devale

first: Barkha

last: Ramnani

first: Krishnamurthy

last: Malathi

first: Etienne

last: Sibille

first: Robert

last: Mccullumsmith

first: Toshifumi

last: Tomoda