title: Transcriptomic changes during skeletal muscle atrophy [RNA-seq]

status: Public on Aug 24 2023

summary: To investigate the possible changes of genes expression during muscle atrophy, we performed bulk RNA-seq of skeletal muscle from C57 BL/6 mice with or without denervation (2 weeks).

overall_design: Bulk RNA-seq of gastrocnemius muscle from 3 normal and 3 denervated mice.

first: Meijun

last: Si

first: Hongchun

last: Lin

first: Hui

last: Peng

first: Sandhya

last: Thomas

first: William

last: Mitch


title: ETV6 Represses Inflammatory Response Genes and Regulates HSPC Function During Stress Hematopoiesis in Mice [scRNA-seq]

city: Memphis

first: Kim

last: Nichols

state: TN

address: 262 Danny Thomas Pl

department: Oncology

country: USA

institute: St. Jude Children's Research Hospital

type: Expression profiling by high throughput sequencing

summary: ETS Variant 6 (ETV6) encodes an essential transcriptional repressor abundantly expressed in hematopoietic stem and progenitor cells (HSPCs), where it is required for adult hematopoiesis. Heterozygous pathogenic germline ETV6 variants are associated with Thrombocytopenia 5 (T5), a poorly-understood genetic condition predisposing to thrombocytopenia and hematologic malignancies. To elucidate how germline ETV6 variants impact the HSPC compartment and contribute to disease, we generated a knock-in mouse harboring an Etv6R355X loss-of-function variant, which represents the mouse equivalent to the T5-associated variant ETV6R359X. All HSPC subpopulations are present in the bone marrow (BM) of Etv6R355X/+ mice under homeostatic conditions; however, these animals exhibit subtle shifts in the proportions and/or numbers of specific progenitor subtypes. To examine whether the Etv6R355X/+ mutation impacts HSPC function, we carried out serial competitive transplantation and observed that Etv6R355X/+ lineagesca1+cKit+ (LSK) cells exhibit significantly impaired reconstitution, with near complete failure to repopulate irradiated-recipients by the tertiary transplant. Mechanistic studies incorporating CUT&RUN, ATAC-Seq and Hi-C identify ETV6 binding at inflammatory gene loci, including those within the TNF pathway in Etv6+/+ HSPCs, the mouse BM-progenitor derived HPC5 cell line, and G-CSF-mobilized human CD34+ cells. Further, single-cell RNA sequencing of mouse LSK cells isolated six-weeks post-competitive transplantation reveals upregulation of inflammatory gene pathways. Corroborating these findings, we observe significantly increased production of TNF by Etv6R355X/+ versus Etv6+/+ HSPCs post-transplantation. From these studies, we conclude that ETV6 represses inflammatory response genes within HSPCs under conditions of hematopoietic stress, and that this mechanism may be critical to sustain HSPC function.

overall_design:
To elucidate how germline ETV6 variants impact the HSPC compartment and contribute to disease, we generated a knock-in mouse harboring Etv6R355X, the murine equivalent to a T5-associated variant ETV6R359X. Young Etv6R355X/+ mice retained normal frequencies of lineage-sca1+cKit+ (LSK) cells but LSK frequencies were significantly decreased in 12-month-old animals.
Single cell RNAseq of post-transplant LSK enriched bone marrow from Etv6R355X/+ and Etv6 +/+ mice.

first: Mackenzie

last: Bloom

first: Ninad

last: Oak

middle: E


title: Plasma exosomes lncRNA-miRNA-mRNA network construction and its diagnostic efficacy identification in first-episode schizophrenia

status: Public on Aug 30 2023

city: Taiyuan City

first: Xinzhe

last: Du

state: Shanxi Province

address: Jiefang Road

country: China

institute: Shanxi Medical University

type: Non-coding RNA profiling by high throughput sequencing

summary:
This study examined the miRNA expression level in exosomal derived from the plasma of first episode schizophrenia (FOS) patients and Healthy controls (HC), and explored the the potential of exosomes as biomarkers for schizophrenia.
This study examined the lncRNA expression level in exosomal derived from the plasma of first episode schizophrenia (FOS) patients and Healthy controls (HC), and explored the the potential of exosomes as biomarkers for schizophrenia.
This study examined the mRNA expression level in exosomal derived from the plasma of first episode schizophrenia (FOS) patients and Healthy controls (HC), and explored the the potential of exosomes as biomarkers for schizophrenia.

overall_design:
we recruited 10 FOS patients and healthy controls (HCs) respectively, examined the miRNA expression level of plasma exosome by high throughput sequencing
we recruited 10 FOS patients and healthy controls (HCs) respectively, examined the lncRNA expression level of plasma exosome by high throughput sequencing
we recruited 10 FOS patients and healthy controls (HCs) respectively, examined the mRNA expression level of plasma exosome by high throughput sequencing

first: Yao

last: Gao

first: Sha

last: Liu

first: Yong

last: Xu


title: RBM33 Acts as an m6A Reader Essential for ALKBH5-mediated m6A Demethylation and Head and Neck Squamous Carcinoma Tumorigenesis [PAR-CLIP]

status: Public on Sep 05 2023

city: Chicago

first: Allen

last: Zhu

state: Illinois

address: 929 E 57th St, Room E331

institute: University of Chicago

summary: Head and neck squamous cell carcinoma (HNSC) is one of the most common malignant cancers worldwide. However, it is always detected at an advanced stage because of a lack of biomarkers for early diagnosis. Here, we identify the RNA binding motif protein 33 (RBM33) is commonly up-regulated in HNSC and it is essential for tumorigenesis. Mechanistically, RBM33 is an m6A reader protein and forms a complex with ALKBH5. RBM33 plays crucial roles in ALKBH5-mediated mRNA m6A demethylation not only by recruitment ALKBH5 to substrate but also activation its demethylase activity through inhibition it’s SUMOylation. Moreover, global transcriptomic and epitranscriptomic analyses identify that DDIT4 is a functional downstream target gene for RBM33 in HNSC and RBM33-mediated HNSC tumorigenesis by inhibition the mTOR pathway through the inhibition of m6A-dependent DDIT4 mRNA decay. Taken together, our study uncovers a novel molecular mechanism that RBM33/ALKBH5/m6A/DDIT4/mTOR axis regulates HNSC progression through the inhibition of mTOR pathway and targeting RBM33 may be a promising strategy for HNSC treatment.

overall_design: Two ALKBH5 replicates from wild type HEK293, two ALKBH5 replicates from RBM33 knock-out HEK293, two RBM33 replicates from wild type HEK293, two ALKBH5 replicates from wild type UM-SCC-1 and two RBM33 replicates from wild type UM-SCC-1 samples were collected for high-throughput sequencing.

first: Fang

last: Yu

first: Shun

first: Chuan

last: He

first: Zhijian

last: Qian


title: ETV6 Represses Inflammatory Response Genes and Regulates HSPC Function During Stress Hematopoiesis in Mice [CUT&RUN]

type: Genome binding/occupancy profiling by high throughput sequencing

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Cut&Run sequencing of Etv6R355X/+ and Etv6+/+ mouse bone marrow (BM) LSKs cells, HPC5 cell line, and human CD34 cells.


title: The E2 SUMO-conjugating enzyme UBE2I is essential for chromatin dynamics and transcriptional silencing in mouse oocytes

status: Public on Aug 23 2023

city: Houston

first: Peixin

last: Jiang

state: TX

address: One Baylor Plaza

institute: Baylor College of Medicine

summary: In mammals, meiotically competent oocytes develop cyclically during ovarian folliculogenesis. During their development, prophase I arrested oocytes are highly  transcriptionally active in preparation for the resumption of meiosis  and early stages of embryogenesis prior to the maternal to zygotic transition. Defective oocyte development during folliculogenesis leads to meiotic defects, aneuploidy, follicular atresia, or non-viable embryos. SUMOylation, a dynamic post-translational protein modification, is essential for oocyte development during folliculogenesis and to regulate meiotic maturation in mice. We generated a novel oocyte-specific knockout of Ube2i, the sole SUMO E2 ligase, to test its role growing ovarian follicles using Zp3-cre. Ube2i Zp3-cre+ female mice are sterile with oocytes with defects in meiotic progression but not meiotic resumption. Importantly, fully grown oocytes do not silence transcription and prematurely activate the zygotic transcriptional program. This work uncovers unknown functions of UBE2i as a key orchestrator of chromatin and transcriptional regulation in oocytes.

overall_design: We performed RNA-sequencing analysis on 17 individual control and 17 individual Ube2i cKO oocytes

first: Stephanie

middle: A

last: Pangas

first: Shawn

middle: M

last: Briley


title: ETV6 Represses Inflammatory Response Genes and Regulates HSPC Function During Stress Hematopoiesis in Mice [ATAC-seq]

overall_design: ATACseq of Etv6+/+ HPC5 cell line.


title: ETV6 Represses Inflammatory Response Genes and Regulates HSPC Function During Stress Hematopoiesis in Mice

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

ETS Variant 6 (ETV6) encodes an essential transcriptional repressor abundantly expressed in hematopoietic stem and progenitor cells (HSPCs), where it is required for adult hematopoiesis. Heterozygous pathogenic germline ETV6 variants are associated with Thrombocytopenia 5 (T5), a poorly understood genetic condition predisposing to thrombocytopenia and hematologic malignancies. To elucidate how germline ETV6 variants impact the HSPC compartment and contribute to disease, we generated a knock-in mouse model harboring an Etv6R355X loss-of-function variant, which is equivalent to the T5-associated variant ETV6R359X. Under homeostatic conditions, all HSPC subpopulations are present in the bone marrow (BM) of Etv6R355X/+ mice; however, these animals display subtle shifts in the proportions and/or numbers of specific progenitor subtypes. To examine whether the Etv6R355X/+ mutation impacts HSPC function, we carried out serial competitive transplantation and observed that Etv6R355X/+ lineage-sca1+cKit+ (LSK) cells exhibit significantly impaired reconstitution compared to Etv6+/+ LSK cells with near complete failure to repopulate irradiated-recipients by the tertiary transplant. Mechanistic studies incorporating CUT&RUN, ATAC-Seq and Hi-C identify ETV6 binding at inflammatory gene loci, including those within the TNF signaling pathway, in Etv6+/+ HSPCs, mouse BM-progenitor-derived HPC5 cells, and human CD34+ cells. Further, single-cell RNA-Seq of BM cells isolated post-competitive transplantation reveals upregulation of inflammatory genes in Etv6R355X/+ compared to Etv6+/+ progenitors. Corroborating these findings, Etv6R355X/+ HSPCs produce significantly more TNF than Etv6+/+ cells post-transplantation. From these studies, we conclude that ETV6 is required to repress inflammatory gene expression in HSPCs under conditions of hematopoietic stress and this mechanism may be critical to sustain HSPC function.

relation:
SuperSeries of: GSE213593
SuperSeries of: GSE213594
SuperSeries of: GSE213595
SuperSeries of: GSE213596
SuperSeries of: GSE233968

overall_design: Refer to individual Series


title: The Cul5 E3 Ligase Complex Is a Key Negative Feedback Regulator of TCR/IL2 Signaling and Anti-Tumor Activity in CD8+ T Cells

status: Public on Sep 01 2023

city: New Haven

first: jingjing

last: Ren

state: Connecticut

address: 200 S Frontage Rd, #0618: Hunter Building

institute: Yale University

summary: To help advancing cancer immunotherapies, we developed a step-wise CRISPR knockout (KO) screening strategy under the selection of TGF-beta, and identified Cul5 as a core negative-feedback regulator of CD8+ T cell differentiation and persistence.

overall_design: To comprehensively identify gene candidates regulating functional CD8+ T cell subgroups, we performed single-cell CRISPR KO screening with tumor-infiltrating CD8+ T cells by single-cell RNA sequencing in parallel with single-cell sgRNA sequencing.

first: Xiaofeng

last: Liao

first: Jingjing

first: Dianqing

last: Wu


title: Rat deconvolution as knowledge miner for immune cell trafficking from toxicogenomics databases

status: Public on Aug 15 2023

city: Bunkyo

first: Tadahaya

last: Mizuno

state: Tokyo

address: 7-3-1, Hongo, Pharmaceutical Sciences, Sogo-kenkyuto 8th floor, Dotai

department: Pharmaceutical Sciences

country: Japan

institute: The University of Tokyo

summary: Toxicogenomics databases are useful for understanding biological responses in individuals because they are derived from well-controlled experiments and include a diverse spectrum of biological responses. Although these databases contain no information regarding immune cells in the liver, which are important in the progression of liver injury, deconvolution that estimates cell-type proportions from bulk transcriptome could add information regarding immune cell trafficking to the database. However, deconvolution has been mainly applied to humans and mice and less often to rats, which are the main target of toxicogenomics databases. Here, we developed a deconvolution method for rats and established a methodology to obtain information regarding immune cells from toxicogenomics databases. The contributions of this work are three-fold. First, we obtained the gene expression profiles of various rat immune cells necessary for deconvolution and constructed a dataset; second, we compared the accuracy of models based on human and mouse datasets and showed the impact of species differences on deconvolution; third, we showed that rat deconvolution could retrieve information regarding immune cell trafficking from toxicogenomics databases. Correspondence: Tadahaya Mizuno

overall_design: To establish and validate a rat-specific deconvolution, RNA-sequencing analysis was performed on 6 types of sorted immune cells obtained from the spleen and the blood, the whole blood cells, the spleen, and the liver of rats.

first: Katsuhisa

last: Morita

first: Iori

last: Azuma


title: RNA-seq and scRNA-seq gene expression of breast tumors with mutant p53 or mutant p53 deleted

status: Public on Aug 18 2023

first: Yuan

last: Qi

address: 1400 Pressler St

department: Bioinformatics & Computational Biology

institute: University of Texas M.D. Anderson Cancer Center

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


title: ETV6 Represses Inflammatory Response Genes and Regulates HSPC Function During Stress Hematopoiesis in Mice [RNA-seq]

first: Kim

last: Nichols

summary:
ETS Variant 6 (ETV6) encodes an essential transcriptional repressor abundantly expressed in hematopoietic stem and progenitor cells (HSPCs), where it is required for adult hematopoiesis. Heterozygous pathogenic germline ETV6 variants are associated with Thrombocytopenia 5 (T5), a poorly-understood genetic condition predisposing to thrombocytopenia and hematologic malignancies. To elucidate how germline ETV6 variants impact the HSPC compartment and contribute to disease, we generated a knock-in mouse harboring an Etv6R355X loss-of-function variant, which represents the mouse equivalent to the T5-associated variant ETV6R359X. All HSPC subpopulations are present in the bone marrow (BM) of Etv6R355X/+ mice under homeostatic conditions; however, these animals exhibit subtle shifts in the proportions and/or numbers of specific progenitor subtypes. To examine whether the Etv6R355X/+ mutation impacts HSPC function, we carried out serial competitive transplantation and observed that Etv6R355X/+ lineagesca1+cKit+ (LSK) cells exhibit significantly impaired reconstitution, with near complete failure to repopulate irradiated-recipients by the tertiary transplant. Mechanistic studies incorporating CUT&RUN, ATAC-Seq and Hi-C identify ETV6 binding at inflammatory gene loci, including those within the TNF pathway in Etv6+/+ HSPCs, the mouse BM-progenitor derived HPC5 cell line, and G-CSF-mobilized human CD34+ cells. Further, single-cell RNA sequencing of mouse LSK cells isolated six-weeks post-competitive transplantation reveals upregulation of inflammatory gene pathways. Corroborating these findings, we observe significantly increased production of TNF by Etv6R355X/+ versus Etv6+/+ HSPCs post-transplantation. From these studies, we conclude that ETV6 represses inflammatory response genes within HSPCs under conditions of hematopoietic stress, and that this mechanism may be critical to sustain HSPC function.
Functionally, Etv6R355X/+ bone marrow (BM) cells exhibited reduced colony formation in later rounds of serial replating, while Etv6R355X/+ LSKs exhibited significantly impaired engraftment in serial competitive transplantation. RNA-seq of Etv6R355X/+ LSKs and/or sort-purified HSPCs revealed upregulation of genes associated with an active stem cell phenotype and pro-inflammatory signaling, including increased expression of the cytokine Tnf. CUT&RUN of Etv6+/+ LSKs and HPC5 hematopoietic progenitors showed that ETV6 binds to the Tnf locus at regions of open chromatin, while CUT&RUN of human CD34+ cells identified ETV6 targets enriched in TNF signaling. In line with these findings, Etv6R355X/+ HSPCs exhibited increased cell-cycling and TNF expression post-transplantation. Finally, genetic deletion of Tnf restored the serial replating capacity of Etv6R355X/+ BM cells.

overall_design: Bulk RNAseq of Etv6R355X/+ mouse bone marrow (BM) LSKs cells.

first: Mackenzie

last: Bloom

first: Ninad

last: Oak


title: Systems metabolic engineering of Streptomyces albus for advanced production of the reverse antibiotic nybomycin

status: Public on Aug 10 2023

city: Bielefeld

first: Christian

last: Ruckert-Reed

address: Sequenz 1

department: Medical School OWL

country: Germany

institute: Bielefeld University

summary: Time series data for several S. albus strains engineered to produce nybomycin.

overall_design: Whole transcriptomes of nybomycin production strains derived from three time points (growth phase, early production phase, and late production phase) and five strains (Del14-4N24, NYB-2B, NYB-3B, NYB-4B, and NYB-4C) using 3 biological replicates each.

first: Julian

last: Stegmüller

first: Marta

middle: R

last: Estévez

first: Wei

last: Shu

first: Lars

last: Gläser

first: Maksym

last: Myronovskyi

last: Rückert-Reed

first: Jörn

last: Kalinowski

first: Andriy

last: Luzhetskyy

first: Christoph

last: Wittmann


title: GPNMB+Gal-3+ Hepatic Parenchymal Cells Promote Immunosuppressive Microenvironment Formation and Hepatocellular Carcinogenesis

city: Shanghai

first: qiudong

last: zhao

address: 225 Changhai Road

department: Tumor Immunology and Gene Therapy Center

institute: Shanghai Eastern Hepatobiliary Surgery Hospital

summary: Hepatocellular carcinoma (HCC) involves a multistep pathological process in which heterogenous cells are evolved to shape an immunosuppressive microenvironment. Yet it remains largely unknown regarding the specific cell populations and their evolving routes essential for HCC development. Here, we created a rat model mimicking human HCC and generated a single-cell resolution atlas to HCC development. Specifically, we identified three populations of hepatic parenchymal cells during HCC progression, i.e., metabolic hepatocyte (HC Meta ), hepatic progenitor cell-like population with differentiation potential (HPC-like Diff ) and immunosuppressive malignant transformation subset (H-M Immu ). These three distinct subpopulations formed an oncogenic trajectory depicting a dynamic landscape of hepatocyte carcinogenesis, with signature genes reflecting the transition from HPC-like Diff to H-M Immu . Cross-species comparative analysis further revealed the H-M Immu subset to be highly conserved. Importantly, the H-M Immu (GPNMB + Gal-3 + ) cells exhibit both malignant and immunosuppressive properties. Moreover, SOX18 was found to be required for the generation of GPNMB + Gal-3 + H-M Immu cells and for their ability to form tumors. Enrichment of GPNMB + Gal-3 + H-M Immu subset was found to be associated with poor prognosis and higher rate of recurrence for HCC patients. Collectively, we unraveled the single-cell evolving mechanism of HCC and uncovered GPNMB + Gal-3 + H-M Immu cells as a major subset contributing to the immunosuppressive microenvironment and HCC malignance

overall_design: Rats treated with DEN up to 16 weeks.

first: Yan

last: Meng

first: Qiudong

last: Zhao

last: Sang

first: Jianping

last: Liao

first: lixin

last: Wei


title: Transcriptomic profile of multiple sclerosis patients treated with dimethyl fumarate and their age and sex-matched healthy controls

status: Public on Aug 08 2023

city: Madrid

first: Alicia

last: Sanchez

address: Joaquín Rodrigo, 2 Majadahonda

country: Spain

institute: Instituto de Investigación Sanitaria Puerta de Hierro-Segovia de Arana

summary: Dimethyl fumarate (DMF) is an immunomodulatory drug approved for the therapy of multiple sclerosis (MS). The identification of response biomarkers to DMF is a necessity in the clinical practice. With this aim, we studied the transcriptomic changes produced by DMF in peripheral blood mononuclear cells (PBMCs) and its association with clinical response. DMF induced a mild transcriptional effect, with only 328 differentially expressed genes (DEGs) after 12 months of treatment. The overall effect was a downregulation of pro-inflammatory genes, chemokines, and activators of the NF-kB pathway. At baseline, no DEGs were found between responders and non-responders. During DMF treatment a differential transcriptomic response was observed, with responders presenting a higher number of DEGs (902 genes) compared to non-responders (189 genes). Responder patients to DMF exhibit a distinguishable transcriptomic response compared to non-responders that should be further studied for the validation of biomarkers of treatment response to DMF.

overall_design: We extracted blood from 10 multiple sclerosis patients (5 responders to DMF and 5 non-responders to DMF) immediately before starting treatment and at 12 months of therapy with DMF. Blood was also extracted from 10 healthy donors, which were matched for age and sex with the patients, at a single timepoint. Peripheral blood mononuclear cells (PBMCs) were isolated from the blood using Ficoll density gradient centrifugation. Total RNA from PBMCs was extracted using the Maxwell 16 LEV simply RNA Cells kit (Promega Biotech Ibérica) on the Maxwell 16 instrument, according to the manufacturer’s instructions. The quality and quantity of the RNA was determined in Bioanalyzer 2100 (Agilent Technologies) and Qubit 3.0 (Thermo Fisher Scientific), respectively. Poly(A)+ mRNA fraction was isolated from total RNA and cDNA libraries were obtained following Illumina’s recommendations. Briefly, poly(A)+ RNA was isolated on poly-T oligo-attached magnetic beads and chemically fragmented prior to reverse transcription and cDNA generation. The cDNA went through an end repair process, addition of a single “A” base to the 3’ end and ligation to the adapters. Finally, the products were purified and enriched with PCR to create the indexed final double stranded DNA library. The quality and quantity of the libraries were analysed in tapeStation 4200, using the High Sensitivity assay (Agilent Technologies). The pool of libraries was sequenced by pair-end sequencing (150x2) in Novaseq 6000 (Illumina) at a sequencing depth of 40 million reads per sample.

last: Sánchez-Sanz

first: Antonio

last: García-Merino

middle: J

last: Sánchez-López


title: the profiles of m6A modification in villous tissues with embryo damage

status: Public on Aug 06 2023

city: Shenzhen

first: Jiajie

last: She

address: huafu street

institute: Shenzhen Second people's hospital

summary: A growing number of studies have demonstrated that N6 methyladenine (m6A) acts as an important role in the pathogenesis of reproductive diseases, which makes it essential to profile the genome-wide m6A modifications in embryo damage. In this study, due to the microscopicity of early villous tissue, we performed high-throughput sequencing for villous tissues from three patients with embryo damage and three patients with painless abortion. Based on meRIP-seq data, we identified 18,568 m6A peaks from these two samples. These m6A peaks were mainly located in the coding region near the stop codon and were mainly characterized by AUGGAC and UGGACG motif. Compared with the normal group, the embryo damage group had 2,159 significantly upregulated m6A peaks and 281 downregulated m6A peaks. Genes with altered m6A peaks were mainly involved in Hippo and Wnt signaling pathways. Based on RNA-seq data, we found that differentially expressed genes were mainly involved in Th17 cell differentiation, TNF signaling pathway, and ECM-receptor interaction. Based on the conjoint analysis of meRIP-seq and RNA-seq data, we identified 36 genes with differentially methylated m6A peaks and synchronously differential expression. These genes were mainly involved in the Wnt signaling pathway, phosphatase activity regulation, protein phosphatase inhibitor activity, and transcription inhibitor activity. In general, our study revealed the transcriptome-wide m6A methylome in early embryonic development, which may provide novel insights into the pathogenesis and treatment of embryo damage.

overall_design: the profiles of m6A modification in villous tissues from three patients with embryo damage and three patients with painless abortion

first: Kaifen

last: Tan


title: Effect of N-glycosylated of SIDT1 on gene expression of human embryonic kidney (HEK293T) cells

status: Public on Aug 09 2023

city: Nanjing

first: Tingting

last: Yang

state: Jiangsu

address: No. 163 Xianlin Road

institute: Nanjing University

summary: The mammalian SID-1 transmembrane family member 1 (SIDT1), are multi-pass transmembrane proteins that mediate the cellular uptake and intracellular trafficking of nucleic acids, playing important roles in the immune response and tumorigenesis. We here report N-glycosylation as a key regulator of SIDT1-mediated RNA transport activities. To identify regulators whose expression was induced by N-glycan-deficient SIDT1, we further performed gene expression analysis on wild-type SIDT1 and non-N-glycosylated SIDT1overexpression HEK293F cells. Samples were subjected to RNA sequencing (RNA-seq) to reveal genes differences in SIDT1 overexpressing cells versus SIDT1N-glycan overexpressing cells. Our results indicate that the non-N-glycosylated SIDT1 is severely misfolded. These severely misfolded non-N-glycosylated SIDT1 may cause ER stress, leading to the induction of the unfolded protein response (UPR) and regulated by the ERQC system.

overall_design: To identify regulators whose expression was induced by N-glycan-deficient SIDT1, we performed gene expression analysis on empty vector pcDNA3.1(+), wild-type SIDT1, and non-N-glycosylated SIDT1 (SIDT1DN-glycan) overexpression HEK293F cells.

first: Haonan

last: Xiao

first: Le

last: Zheng


title: Unveiling the effect of the Parkinson's disease related Miro1R272Q mutation in the transcriptome of human iPSC-derived dopaminergic neurons

status: Public on Aug 31 2023

city: Belvaux

first: Claudia

last: Saraiva

state: Luxembourg

address: 6, avenue du Swing

department: Luxembourg Centre for Systems Biomedicine

country: Luxembourg

institute: University of Luxembourg

summary: Over the past decade evidences have been pointing in a role of RhoT1 gene (Miro1) in Parkinson's disease (PD). Miro 1 is an important part of the motor/adaptor complex and an essencial regulator of mitochondrial transport and homeostasis in neurons. In fact, our group have identify a few PD patiens carrying heterozygous mutations in the RhoT1 gene. One specific mutation, Miro1 R272Q , seems to play a important role in the pathology development. To better understand the role of Miro1 R272Q mutation in PD we used iPSC-derived doapminergic neurons. Three different cell lines, one coming from a PD patient harboring the Miro1 R272Q mutation, its respective isogenic control and a healthy individual (age- and sex- matched) were used in the study to generate dopaminergic neurons (most affected cellular population in PD). At day 30 of culture, gene expression changes caused by the Miro1 R272Q mutation were unveil using bulk RNA sequencing. The data showed a clear separation between the PD Miro1 R272Q cells and isogenc and helthy control at the PC1. Also, deregulated Go Terms such as axon, neuron projection, vesicle release, among other support the role of Miro1 R272Q mutant as important in PD pathogenecity.

overall_design: 30 day old iPSC-derived dopaminergic neurons from 3 different cell lines - 1 PD patient with Miro1 R272Q mutation, 1 isogenic control, 1 healthy individual (aged- and sex-matched) - were used to assess total RNA. A total of 4 independ derivations of dopaminergic neurons for each cell line were sent to RNA-seq analysis. This allow to comprove the robustness of the model and assess the specific contribution of Miro1 R272Q mutant on the PD phenotypes observed.

first: Axel

last: Chemla

first: Jochen

last: Ohnmacht

first: Cláudia


title: A role for BCL6 in maintaining CX3CR1+ CD4+ T cells during helminth infection

status: Public on Aug 12 2023

city: NYC

first: Denis

last: Loredan

state: NY

address: 550 1st Ave

department: Microbiology

institute: New York University Grossman Medical school

summary: Distinct subsets of T lymphocytes express CX3CR1 under inflammatory conditions, but little is known about CX3CR1+ CD4+ T cells during Type 2 inflammation in helminth infections. Here, we used a fate-mapping mouse model to characterize CX3CR1+ CD4+ T cells during both acute Nippostrongylus brasiliensis and chronic Schistosoma mansoni helminth infections, revealing CX3CR1+ CD4+ T cells to be an activated tissue homing subset with varying capacity for cytokine production. Tracking these cells over time revealed that maintenance of CX3CR1 itself along with a TH2 phenotype conferred a survival advantage in the inflamed tissue. Single-cell RNA-sequencing analysis of fate-mapped CX3CR1+ CD4+ T cells from both the peripheral tissue and the spleen revealed a considerable level of diversity and identified a distinct population of BCL6+ TCF-1+ PD1+ CD4+ T cells in the spleen during helminth infections. Conditional deletion of BCL6 in CX3CR1+ cells result in fewer CX3CR1+ CD4+ during infection, indicating a role in sustaining CD4+ T cell responses to helminth infections. Overall, our studies revealed the behavior and heterogeneity of CX3CR1+ CD4+ T cells during Type 2 inflammation in helminth infections and identified BCL6 to be important in their maintenance

overall_design: Single cell suspensions were obtained from livers and spleens .  For both tissues, cells were sorted on singlet cells, live cells, CD45+ cells, DumpNEG (CD11b+, CD11c+, CD49b+, CD19+, CD8+) cells, CD3+ cells, CD4+ cells. Cells were isolated from 2 mice and pooled together, with equal numbers of cells pooled from each animal used. 12,000 cells from each tissue were loaded on a 10X Genomics Next GEM chip and single-cell GEMs were generated on a 10X Chromium Controller

middle: G

first: Joseph

middle: C

last: Devlin

first: Kamal

last: Khanna

first: P’ng

last: Loke


title: Sigle-cell transcriptome analysis of EpiSC-derived neural stem cell lines derived from EpiSCs under different Wnt signal inputs

status: Public on Aug 01 2023

city: Takatsuki

first: Hisato

last: Kondoh

state: Osaka

address: 1-1 Murasaki-cho

institute: Biohistory Research Hall

summary: The four neural stem cell lines, XN4, XN1, KN1, and CN4, were derived from EpiSCs under different Wnt signal inputs (Nakamura et al., to be submitted). Microarray analysis of the transcripts indicated that these cells have different anteroposterior regional characteristics of the embryonic CNS from the forebrain to the thoracic spinal cord. However, each cell line has a relatively broad anteroposterior regional coverage. For instance, the XN1 line expressed midbrain-characteristic genes and hindbrain-characteristic genes. Single-cell transcriptome analysis of the four cell lines was performed to confirm that the broad anteroposterior specificity is intrinsic to individual cells of the cell line rather than the cell lines are composite of separable subpopulations with narrower anteroposterior specificities.

overall_design: The NSC lines, XN4, XN1, KN1, and CN4, in a growing phase, were dissociated using Accutase, passed through a 20 µm cell strainer, suspended in 10x volumes of CellCover (Anacyte Laboratories), and stored at 4º C, up to 2 weeks, until cells were processed for the single-cell transcriptome library preparation. After washing in 50% DMEM /50% Neurobasal Medium with 0.004% BSA, the cells were loaded on a BD Rhapsody cartridge (BD Biosciences) to capture mRNAs of cells on isolated magnetic beads. Single-cell RNA sequencing libraries were prepared for each NSC line using a BD Rhapsody WTA Amplification kit (633801) using the manufacturer-supplied protocol. The libraries were sequenced using Hi-SeqX (Illumina) for 150 b paired-end reads to gain Fastq data. The sequence data were processed using the BD Rhapsody WTA pipeline on the Seven Bridge Genomics platform. R1 reads were used to gain transcript data in individual cells and R2 to align them on the mouse mm10 (GRCm38) genome sequence.The single-cell transcriptome analysis was performed for the two purposes: (1) to show that a significant fraction of cells simultaneously express genes representing different CNS regions and (2) to show that the cells in a cell line form an inseparable cell group in the UMAP projection of the data. For the first purpose, the reads per cell spreadsheet data (RPC.csv) were directly analyzed. For the second purpose, transcript reads of ribosomal and mitochondrial proteins were omitted from the analysis because the cells were nearly homogeneous, and the reads of these transcripts were found to erroneously contribute to sub-clustering the cells. Then 4000 cells for each line were randomly selected, normalized, and scaled according to the standard procedure of Seurat (v. 4.3.0) (Satija et al., 2015).

first: Kae

last: Nakamura

first: Yusaku

last: Watanebe


title: The landscape of abiotic and biotic stress-responsive splice variants with deep RNA-seq datasets in hot pepper

status: Public on Aug 07 2023

city: Jinju

first: Seon-In

last: Yeom

address: 501, Jinjou-daero

country: South Korea

institute: Gyeongsang National University

summary: Alternative splicing (AS) is a widely observed phenomenon in eukaryotes that plays a critical role in development and stress responses. In plants, the large number of RNA-seq datasets in response to different environmental stressors can provide clues for identification of condition-specific and/or common AS variants for preferred agronomic traits. We report RNA-seq datasets (350.7 Gb) from Capsicum annuum inoculated with one of three bacteria, one virus, or one oomycete and obtained additional existing transcriptome datasets. In this study, we investigated the landscape of AS in response to environmental stressors, signaling molecules, and tissues from 425 total samples comprising 841.49 Gb. In addition, we identified genes that undergo AS under specific and shared stress conditions to obtain potential genes that may be involved in enhancing tolerance to stressors. We uncovered 1,642,007 AS events and identified 4,354 differential alternative splicing (DAS) genes related to environmental stressors, tissues, and signaling molecules. This information and approach provide useful data for basic-research focused on enhancing tolerance to environmental stressors in hot pepper or establishing breeding programs.

overall_design: The normalization criteria of RNA-seq sets for different pathogens were performed identically to study the resistance response of pepper and to minimize bias in the analysis.

first: Nayoung

last: Kim

first: Junesung

last: Lee


title: ETV6 Represses Inflammatory Response Genes and Regulates HSPC Function During Stress Hematopoiesis in Mice [Hi-C]

first: Kim

last: Nichols

summary: ETS Variant 6 (ETV6) encodes an essential transcriptional repressor abundantly expressed in hematopoietic stem and progenitor cells (HSPCs), where it is required for adult hematopoiesis. Heterozygous pathogenic germline ETV6 variants are associated with Thrombocytopenia 5 (T5), a poorly-understood genetic condition predisposing to thrombocytopenia and hematologic malignancies. To elucidate how germline ETV6 variants impact the HSPC compartment and contribute to disease, we generated a knock-in mouse harboring an Etv6R355X loss-of-function variant, which represents the mouse equivalent to the T5-associated variant ETV6R359X. All HSPC subpopulations are present in the bone marrow (BM) of Etv6R355X/+ mice under homeostatic conditions; however, these animals exhibit subtle shifts in the proportions and/or numbers of specific progenitor subtypes. To examine whether the Etv6R355X/+ mutation impacts HSPC function, we carried out serial competitive transplantation and observed that Etv6R355X/+ lineagesca1+cKit+ (LSK) cells exhibit significantly impaired reconstitution, with near complete failure to repopulate irradiated-recipients by the tertiary transplant. Mechanistic studies incorporating CUT&RUN, ATAC-Seq and Hi-C identify ETV6 binding at inflammatory gene loci, including those within the TNF pathway in Etv6+/+ HSPCs, the mouse BM-progenitor derived HPC5 cell line, and G-CSF-mobilized human CD34+ cells. Further, single-cell RNA sequencing of mouse LSK cells isolated six-weeks post-competitive transplantation reveals upregulation of inflammatory gene pathways. Corroborating these findings, we observe significantly increased production of TNF by Etv6R355X/+ versus Etv6+/+ HSPCs post-transplantation. From these studies, we conclude that ETV6 represses inflammatory response genes within HSPCs under conditions of hematopoietic stress, and that this mechanism may be critical to sustain HSPC function.

overall_design: Hi-C sequencing of  Etv6+/+ HPC5 cell line

first: Mackenzie

last: Bloom

first: Ninad

last: Oak


title: Germ granule association drives small RNA specificity for a nuclear Argonaute protein [sRNA-seq]

city: Los Angeles

first: Carolyn

middle: Marie

last: Phillips

state: CA

address: 1050 Childs Way, RRI 201

department: Biological Sciences

institute: University of Southern California

summary: RNA interference (RNAi) is a conserved gene silencing process that exists in diverse organisms to protect genome integrity and regulate gene expression. In C. elegans, majority of RNAi components are located in phase-separated perinuclear germ granules, including P granule, Mutator foci, Z granule, and SIMR foci. However, the protein components and function of the newly discovered SIMR foci are unknown. Here we identified HRDE-2 as a SIMR foci component, which interacts with the germline nuclear RNAi Argonaute HRDE-1. We found that unloaded HRDE-1 localizes to SIMR foci and this localization depends on HRDE-2. In addition, HRDE-2 contributes to HRDE-1 small RNAs binding specificity and, in the absence of HRDE-2, HRDE-1 exclusively loads CSR-class 22G-RNAs rather than WAGO-class 22G-RNAs, promotes H3K9me3 deposition on CSR-targets, but does not silence these CSR-target genes. Thus, our study demonstrates that HRDE-2 is critical to ensure correct small RNAs are used to guide nuclear RNA silencing in the C. elegans germline.

overall_design: FLAG::HRDE-1 immunoprecipitation from whole worm extract followed by small RNA purification, library preparation, and sequencing

first: Shihui

last: Chen


title: Germ granule association drives small RNA specificity for a nuclear Argonaute protein [mRNA-seq]

overall_design: PolyA-selected RNA from whole worms (from wild-type, hrde-1(tm1200), and hrde-2(qe20)) was used to make mRNA-seq libraries


title: Microenvironmental Stiffness Induces Metabolic Reprogramming in Glioblastoma

status: Public on Aug 02 2023

city: Austin

first: Alireza

last: Sohrabi

address: 2501 speedway, EER building, Room 5.646_Seidlits Lab, EER building_Seidlits Lab

institute: UT Austin

summary: The mechanical properties of solid tumors influence tumor cell phenotype and ability to invade into surrounding tissues. Using bioengineered scaffolds to provide a matrix microenvironment for patient-derived glioblastoma (GBM) spheroids, this study demonstrates that a soft, brain-like matrix induces GBM cells to shift to a glycolysis-weighted metabolic state which supports invasive behavior.  We first show that orthotopic murine GBM tumors are stiffer than peri-tumoral brain tissues, but tumor stiffness is heterogenous where tumor edges are softer than the tumor core. Then, we developed three-dimensional scaffolds with µ-compressive moduli resembling either stiffer, tumor core or softer, peri-tumoral brain tissue. We demonstrate that the softer matrix microenvironment induces a shift in GBM cell metabolism toward glycolysis which manifests in lower proliferation rate and increased migration activities. Finally, we show that these mechanical cues are transduced from the matrix via CD44 and integrin receptors to induce metabolic and phenotypic changes in cancer cells.

overall_design: To investigate the role of stiffness on glioblastoma , patient derived cells were encapsulated in hydrogels with mechanical properties mimicking the tumor stiffness and the peritumoral brain tissue

first: Austin

last: Lefebvre

first: Mollie

last: Harrison

first: Michael

last: Condro

first: Talia

last: Sanazzaro

first: Gevick

last: Safarians

first: Itay

last: Solomon

first: Soniya

last: Bastola

first: Shadi

last: Kordbacheh

first: Nadia

last: Toh

first: Harley

middle: I

last: Kornblum

first: Michelle

last: Digman

first: Stephanie

middle: K

last: Seidlits


title: RNA-Sequencing Predicts a Role of Androgen Receptor and Aldehyde Dehydrogenase 1A1 in Osteosarcoma Lung Metastases

city: Pittsburgh

first: Kurt

last: Weiss

state: PA

address: 5117 Centre Avenue

institute: University of Pittsburgh

summary:
To identify OS-specific gene alterations, 38 tumor samples were collected from 29 unique patients with osteosarcoma.
We performed RNA-sequencing on 28 primary osteosarcoma tumors and 10 metastatic osteosarcoma tumors. We compared the primary and metastatic genomic signatures of all 38 samples to discover differentially expressed genes.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for 14 samples from primary tumor sites in patients that never developed lung metastases, 14 samples from primary tumor sites in patients that did develop lung metastases, and 10 metastatic lung tumors. This group of samples includes 4 sets of matched primary osteosarcoma and metastatic lung tumors.

first: Tanya

last: Heim


title: Targeting Pancreatic Cancer Metabolic Dependencies through Glutamine Antagonism

city: New York

first: Joel

last: Encarnacion-Rosado

state: New York

address: 550 First Avenue

department: Radiation Oncology

institute: NYU Grossman School of Medicine

summary: Pancreatic ductal adenocarcinoma (PDAC) is one of the deadliest types of cancer. A factor that contributes to the poor prognosis of the disease is the complex tumor microenvironment (TME). The PDAC TME is composed of excessive fibrosis and desmoplasia, which creates a harsh environment resulting in hypoxia and altered nutrient availability. To promote survival and proliferation in this environment, PDAC cells can reprogram glutamine (Gln) metabolism. Previous studies have demonstrated that PDAC cells use Gln to support proliferation and redox balance. However, earlier attempts to inhibit Gln metabolism using glutaminase inhibitors resulted in rapid metabolic reprogramming and ultimately therapeutic resistance.  Here, we hypothesized that using a Gln analogue, such as 6-Diazo-5-oxo-L-norleucine (DON), could broadly target Gln metabolism in PDAC and prevent rapid adaptation. Indeed, DON treatment led to a significant decrease in PDAC proliferation in a dose-dependent manner, as well as a profound reduction of various metabolites involved in central carbon and nucleotide metabolism, suggesting that DON creates a metabolic crisis. In addition, we observed a significant decrease in tumor growth in various in vivo models (syngeneic, immunodeficient) using DRP-104 (sirpiglenastat), a novel pro-drug version of DON that was designed to circumvent DON associated GI toxicity and allow the therapeutic exploration of broad Gln antagonism.  Mechanistically, we found that ERK signaling is increased as a compensatory mechanism through the increased activity of receptor tyrosine kinases (RTKs). Combinatorial treatment of DRP-104 and Trametinib (MEK1/2) inhibitor led to a significant increase in survival in a syngeneic model PDAC. Taken together, these pre-clinical results suggest that broadly targeting Gln metabolism could provide a new therapeutic avenue for PDAC and that the combination with an ERK signaling pathway inhibitor could further improve the therapeutic outcome.

overall_design: Total  RNA was extracted from tumor and tumor cells using PuTotal RNA from cell cultures and tumors were obtained using TRizol (Thermo, 15596026) and PureLink RNA Midi Kit (Thermo, 12183025) kit according to the manufacturer’s instructionsreLink RNA Minit Kit (Thermo Scientific)


title: Metabolic control in VAT by Tregs through OSM-mediated suppression of adipogenesis

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

summary: Regulatory T cells (Tregs) play diverse roles in tissue homeostasis. In visceral adipose tissue (VAT), resident Tregs, enriched with PPARγ, are clonally expanded in a IL-33 dependent manner. However, the tissue-specific functions of VAT Tregs, with unique transcriptome compared to spleen or other peripheral tissues, remain largely unknown. We identified two PPARγ+ mesenchymal stromal cells in VAT (VmSCs), named VmSC4s (PPARγ+Thy1-) and 5s (PPARγ+Thy1+). Lineage-tracing and transcriptome analysis revealled that VmSC4s contain precursors for VmSC5s. We also demonstrated that VAT Tregs directly suppress adipogenic differentation of VmSC5s through Oncostain M (OSM) to promote insulin sensitivity and glucose tolerance. Thus, VAT-Treg-derived OSM and VmSCs-displayed OSMR maintain tissue homeostasis via limiting the differentiation of dysfunctional adipocytes, which provide therapeutic targets for treating obesity and diabetes.

overall_design: To determine if there is a transition between VmSC4s and 5s, the two populations were adoptive-transferred into a Kaeda recipient mice. VmSC4s and 5s before transfer, VmSC4-derived VmSC4s as well as 5s, and VmSC5-derived VmSC5s were double-sorted. To study if VAT Tregs control adipogenesis, Tregs were puctually depleted via diphtheria toxin (DT) injections into Foxp3-DTR+ and littermate Foxp3-DTR- controls. Then the floating cells from VAT were digested in QIAzol for RNA extraction. To verify whether inhibition of adipogenesis from VAT Tregs is direct, conditioned medium from VAT Tregs was incubated with VmSC5s. VmSC5s were also treated with 10ng/mL OSM to further investigate the mediators from VAT Tregs to control adipogenic differentiation.

first: Gang

last: Wang

first: Raul

last: Spallanzani

first: Diane

last: Mathis


title: Investigation of the usefulness of liver-specific deconvolution method toward legacy data utilization

status: Public on Jul 31 2023

first: Tadahaya

last: Mizuno

summary: Deconvolution is a methodology for estimating the immune cell proportions from the transcriptome. It is mainly applied to blood-derived samples and tumor tissues. However, the influence of tissue-specific modeling on the estimation results has rarely been investigated. In this study, we constructed a system to evaluate the performance of the deconvolution method on liver transcriptome data. Correspondence: Tadahaya Mizuno

overall_design: To evaluate and optimize the reference-based deconvolution method against liver tissue samples, RNA-seq analysis was performed on a total of 57 samples extracted from various mouse liver injury models.

first: Iori

last: Azuma

first: Katsuhisa

last: Morita


title: Cell-Free RNA Signature for Noninvasive Diagnosis of Hepatocellular Carcinoma Using MOF to Enrich Circulating Nucleic Acids

city: wuhan

first: shuang

last: peng

address: wuhan university

institute: wuhan university

summary:
We developed a new method to extract cfNA (containing cfDNA, cfRNA and viral RNA) from serum/plasma based on the adsorption of nucleic acids by MOF materials (Co-IRMOF-74-IV), and compared the extraction capability with commercial kit method.
We conducted a comprehensive characterization of the cell-free RNA in a small number of clinical samples, including patients with HCC (n=14), CHB (n=17) and normal individuals (n=8). And then we build a model with 6 cfRNA signature to diagnose liver cancer, and indicated high diagnostic efficiency (AUC=0.905) in the independent validation cohort (HCC n=7, CHB n=4 and normal individuals n=8)

overall_design: We sequenced cfRNA extracted from 0.5 ml of plasma obtained from 39 training set plasma samples (14 HCC, 17 CHB and 8 normal individuals), and we build a model with 6 cfRNA signature to diagnose HCC, which was verified high diagnostic efficiency (AUC=0.905) in the independent validation cohort (HCC n=7, CHB n=4 and normal individuals n=8).

first: Peng

last: Shuang

first: Han

last: Shaoqin

first: Yu

last: Haixin

first: Liu

last: Songmei

first: Zhou

last: Xiang


title: The DYRK1A protein kinase is recruited to a subset of ribosomal protein gene promoters in human and mouse cells [HeLa RNA-seq]

city: Barcelona

first: Chiara

last: Di Vona

state: Spain

address: Carrer Dr. Aiguader 88

department: Gene Regulation, Stem Cells and Cancer

institute: CRG

summary: Ribosomal protein genes (RPGs) coding sequences are highly conserved along evolution; however, promoter features and the machinery involved in their transcriptional regulation are not. In eukaryotes, the main genomic elements and players involved in RPG transcriptional regulation have been mostly characterized in Saccharomyces cerevisiae. However, given the lack of evolutionary conservation of the yeast factors, studies in higher eukaryotes have focused on searching for differential enrichment of transcription factor-binding motifs within the RPG promoters. Among them, the palindromic motif TCTCGCGAGA, which is currently acknowledged as a ZBTB33/KAISO motif, also matches the genomic sequence bound by the protein kinase DYRK1A. DYRK1A, a member of the human family of DYRK kinases, fulfills many diverse functions by phosphorylating a broad set of proteins involved in different cellular processes. One of such functions is to be a chromatin-associated kinase capable of regulating gene expression. Here, we analyze in-depth the presence of DYRK1A at the promoters of human and mouse RPGs and explore its functional consequences. Our results indicate that DYRK1A is a positive regulator of RPGs’ expression at the transcriptional level, and further expand the functional spectrum of the kinase as a contributor to the regulation of cell growth in mammalian cells.

overall_design: Expression profiling by high throughput sequencing. mRNA profiles of HeLa cells treated with shControl (control) or shDYRK1A, were generated by deep sequencing.

first: C

first: S

last: De la Luna


title: The DYRK1A protein kinase is recruited to a subset of ribosomal protein gene promoters in human and mouse cells

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

overall_design: Refer to individual Series


title: c-Myb upregulation stimulates antitumor immunity in a murine colorectal cancer model

status: Public on Jul 28 2023

city: Brno

first: Lucia

last: Knopfova

address: Kamenice 5

department: Department of Experimental Biology

country: Czech Republic

institute: Faculty of Science, Masaryk University

summary: While the transcription factor c-Myb is overexpressed in different types of solid tumors, including colorectal cancer, its exact role in tumorigenesis is unclear. In this study, we show that tumor-intrinsic c-Myb expression in mouse models of colon cancer and melanoma suppresses tumor growth. While no difference in proliferation, apoptosis, and angiogenesis of tumors were evident, we observed changes in intratumoral immune cell infiltrates. MC38 tumors with upregulated c-Myb expression showed increased counts of CD103+ dendritic cells and eosinophils, but decreased tumor-associated macrophages (TAMs). Concomitantly, an increase in cytotoxic CD8+ T cells upon c-Myb upregulation was observed, which correlated with a pro-inflammatory tumor microenvironment and increased numbers of M1 polarized TAMs. Mechanistically, c-Myb upregulation in immunogenic MC38 colon cancer cells resulted in enhanced expression of immunomodulatory genes, including b2-microglobulin, interferon-β and decreased expression of the chemokine receptor CCR2. The observed increased counts of cytotoxic CD8+ T cells contributed to tumor growth attenuation. In poorly immunogenic CT26, LLC and B16-BL6 tumor cells, c-Myb upregulation did not affect immune responses. Interestingly, c-Myb upregulation has led to a reduced B16-BL6 tumor growth but it did not affect tumor growth of CT26 and LLC tumors. Altogether, we postulate that c-Myb functions as a tumor suppressor in a tumor cell-type specific manner and modulates anti-tumor immunity.

overall_design: MC38T/O (doxycycline inducible c-Myb, 5x105 cells) tumor cells were subcutaneously injected in the right flank of a mouse. Mice were fed doxycycline containing or control chow for 21 days. GFP+CD45- tumor cells were sorted from excized tumors and RNA was isolated using RNeasy Plus Mini Kit (Qiagen). RNAseq of DOX-treated (c-Myb induced expression) and control tumor cells was analyzed.

first: Merel

last: van Gogh

first: Petr

last: Benes

first: Lubor

last: Borsig


title: Data of RNA-seq transcriptomes of gastrocnemius muscle and epididymal adipose tissue in obese rats changes in hypoxic exercise environments

status: Public on Jul 25 2023

city: Jinan

first: Qinglu

last: Wang

state: Shandong

address: 10600 Century Avenue

institute: Shandong Sport University

summary: With the economic development and the change of people's lifestyle, the incidence of obesity in China is increasing year by year, and obesity has become a major public health problem that endangers global health. At present, the average obesity rate in China is about 12%, and the total number of obesities ranks first in the world. Obesity is a metabolic disorder caused by excessive accumulation of white adipose tissue, which can further induce metabolic syndrome such as insulin resistance, type 2 diabetes, and cardiovascular and cerebrovascular diseases. Studies have shown that altitude hypoxic exercise can not only improve muscle buffering capacity and body performance, but also reduce body weight and body fat more significantly. In many countries, it has been used as a treatment program for obesity diseases. Hypoxic exercise can improve lipid metabolism, reduce blood lipid levels, inhibit fatty acid synthesis, and promote fatty acid decomposition and oxidation, which is the mechanism of hypoxic exercise to significantly reduce weight and fat. However, the mechanism of the cross-talk between muscle and fat tissue is not well understood under hypoxia exercise and normoxia exercise conditions. We performed RNA sequence analysis of mRNA isolated from epididymal adipose tissue and gastrocnemius muscle tissue in obese rats. The data contained changes in four different states: normoxic quiet, normoxic exercise, hypoxic quiet, and hypoxic exercise. RNA-seq data will provide insights into the cross-talk between muscle and fat, and the mechanisms of fat metabolism. The data of this study have not been published and are hereby published on this platform to study the cross talk between muscle tissue and adipose tissue in rats under different oxygen content and exercise environment.

overall_design: 3-week-old healthy male SD rats were used in this experiment. We constructed an obese rat model and randomly divided the rats into normoxic quiet training, normoxic exercise training, hypoxic quiet training, and hypoxic exercise training. Gastrocnemius muscle tissue and epididymal adipose tissue were isolated for RNA-seq transcriptomes analysis. The data changes of rats in different exercise environments were collected.

first: Wen

last: Ma

first: Youhan

last: Liu

first: Chang

last: Meng


title: Heterogeneity in the gene regulatory landscape of leiomyosarcoma

city: Heidelberg

first: Nicola

last: Biondi

state: Baden-Württemberg

address: Im Neuenheimer Feld 581

department: Functional and Structural Genomics

institute: German Cancer Research Center (DKFZ)

summary: Soft-tissue sarcomas are group of rare, tremendously heterogeneous, and highly aggressive malignancies. Characterizing inter-tumor heterogeneity is crucial for selecting suitable sarcoma therapy, as the presence of diverse molecular subgroups of patients can be associated with disease outcome or response to treatment. While cancer subtypes are often characterized by differences in gene expression, the mechanisms that drive these differences are generally unknown. We therefore set out to model the regulatory mechanisms driving sarcoma heterogeneity. We subtyped soft-tissue sarcomas based on patient-specific, genome-wide gene regulatory networks and found pronounced regulatory heterogeneity in leiomyosarcoma—one of the most common soft-tissue sarcomas subtypes that arises in smooth muscle tissue.

overall_design: ATAC-seq was performed on four leiomyosarcoma cell lines, including SK-UT-1, SK-UT1-B, MES-SA and SK-LMS-1. Each cell lines had three replicates.

first: Tatiana

last: Belova

first: Ping-Han

last: Hsieh

first: Pavlo

last: Lutsik

first: Priya

last: Chudasama

first: Marieke

middle: L

last: Kuijjer


title: HOXA3 functions as the on-off switch to regulate the development of hESC-derived third pharyngeal pouch endoderm through EPHB2-mediated Wnt pathway

status: Public on Jul 24 2023

city: Guangzhou

first: Yingjie

last: Fu

address: No.381, Wushan Road, Tianhe District

institute: South China University of Technology

summary: Normal commitment of the endoderm of the third pharyngeal pouch (3PP) is essential for the development and differentiation of the thymus. The aim of this study was to investigate the role of transcription factor HOXA3 in the development and differentiation of the third pharyngeal pouch endoderm from human embryonic stem cells (hESCs). 3PP endoderm (3PPE) was differentiated from hESC-derived definitive endoderm (DE) by mimicking developmental queues with Activin A, WNT3A, retinoic acid and BMP4. The function of 3PPE was assessed by further differentiating into functional thymic epithelial cells. The effect of HOXA3 inhibition on cells of 3PPE was subsequently investigated. A highly efficient approach for differentiating 3PPE cells has been developed and these cells expressed 3PPE related genes HOXA3, SIX1, PAX9 as well as EpCAM. 3PPE cells had a strong potential to develop into thymic epithelia which expressed both the cortical epithelial cell markers K8 and CD205, and the medullary epithelial cell markers K5 and AIRE, and also promoted T cell maturation. More importantly, transcription factor HOXA3 not only regulated the differentiation of 3PPE, but also had a crucial role for the proliferation and migration 3PPE cells. Our further investigation revealed that HOXA3 controlled the commitment and function of 3PPE through the regulation of the Wnt signaling pathway by EPHB2. Our results demonstrated that HOXA3 functioned as the on-off switch to regulate the development of hESC-derived 3PPE through EPHB2-mediated Wnt pathway, and our findings will provide new insights into studying the development of the third pharyngeal pouch and thymic organ in vitro and in vivo.

overall_design: We compared the gene expression profiling changes of RNA-seq data before and after the inhibition of HOXA3 in the third pharyngeal pouch endoderm cells derived from human embryonic stem cells.

first: Xueyan

last: Zhang

first: Haibin

last: Wu

first: Pingping

first: Shoupei

first: Tingting

last: Guo

first: Huanhuan

last: Shan

first: Yan

last: Liang

first: Honglin

last: Chen

first: Jinghe

last: Xie

first: Yuyou

last: Duan


title: Germ granule association drives small RNA specificity for a nuclear Argonaute protein [CUT&Tag]

first: Carolyn

last: Phillips

overall_design: CUT&Tag libraries for H3K9me3 and IgG control were generated from purified germline nuclei from wild-type, hrde-1(tm1200), and hrde-2(qe20)

first: Shihui


title: Germ granule association drives small RNA specificity for a nuclear Argonaute protein


title: Inactivation of the tumor suppressor gene Apc synergizes with H. pylori to induce DNA damage and replication stress in murine gastric stem and progenitor cells [scRNA-seq]

city: Zurich

first: Genome

last: Informatics

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich (FGCZ)

country: Switzerland

institute: ETH ZURICH / University of Zurich

summary: Helicobacter pylori infection is a major risk factor for the development of gastric cancer. The bacteria reside in close proximity to gastric surface mucous as well as stem and progenitor cells. Here, we take advantage of wild type and genetically engineered murine gastric organoids and organoid-derived monolayers to study the cellular targets of H. pylori-induced DNA damage and replication stress, and to explore possible interactions with preexisting gastric cancer driver mutations. We find using alkaline comet assay, single molecule DNA fiber assays and immunofluorescence microscopy of DNA repair factors that H. pylori induces transcription-dependent DNA damage in actively replicating, Lgr5-positive antral stem and progenitor cells and their Troy-positive corpus counterparts, but not in other gastric epithelial lineages. Infection-dependent DNA damage is aggravated by Apc inactivation, but not by Trp53 or Smad4 loss, or Erbb2 overexpression. Our data suggest that H. pylori induces DNA damage in stem and progenitor cells, especially in settings of hyperproliferation due to constitutively active Wnt signaling.

overall_design:
C57BL/6J-ApcMin/J (Strain #:002020) and C57BL/6JRj (WT) were obtained from the Jackson laboratory.
scRNA-seq of corpus and antrum cells, infected or not with H. pylori.

first: Jiazhuo

last: He

first: Anne

last: Müller

first: Peter

last: Leary


title: A KDPG sensor RccR governs Pseudomonas aeruginosa carbon metabolism and aminoglycoside antibiotic tolerance

status: Public on Jul 20 2023

city: shanghai

first: yujuw

last: wang

state: shanghai

address: 199 huanke road

institute: shanghaitech university

summary: Pseudomonas aeruginosa harbors sophisticated transcription factor (TF) networks to coordinately regulate cellular metabolic states for rapidly adapting to changing environments. The superior capacity in fine-tuning the metabolic states enables its success in tolerance to antibiotics and evading host immune defenses. However, the linkage among transcriptional regulation, metabolic states, and antibiotic tolerance in P. aeruginosa remains largely unclear. By screening the P. aeruginosa TF mutant library constructed by CRISPR/Cas12k-guided transposase, we identify that rccR (PA5438) is a major genetic determinant in aminoglycoside antibiotic tolerance, the deletion of which substantially enhances bacterial tolerance. We further reveal the inhibitory roles of RccR in pyruvate metabolism (aceE/F) and glyoxylate shunt pathway (aceA and glcB), and overexpression of aceA or glcB enhances bacterial tolerance. Moreover, we identify that 2-keto-3-deoxy-6-phosphogluconate (KDPG) is a signal molecule that directly binds to RccR. Structural analysis of the RccR/KDPG complex reveals the detailed interactions. Substitution of the key residues R152, K270, or R277 with alanine abolishes KDPG sensing by RccR and impairs bacterial growth with glycerol or glucose as the sole carbon source. Collectively, our study unveils the connection between aminoglycoside antibiotic tolerance and RccR-mediated central carbon metabolism regulation in P. aeruginosa, and elucidates the KDPG sensing mechanism by RccR.

overall_design: P. aeruginosa PAO1 wild-type and rccR-deletion mutant strains were cultured in LB medium at 37℃ and harvested at the exponential phase and stationary phase, respectively. The total RNAs were extracted using the MiniBEST Universal RNA Extraction Kit (Takara) and used as templates for reverse transcription to cDNA using the TransScript® One-Step gDNA Removal and cDNA Synthesis SuperMix (TransGen Biotech Co) according to the manufacturer’s instructions. The cDNA products were subjected to transcriptome sequencing by Majorbio (Shanghai).

first: Yujue

last: Wang


title: Mineralized collagen induces phenotypic changes in MDA-MB-231

status: Public on Jul 19 2023

city: Ithaca

first: Claudia

last: Fischbach

address: 237 Tower Road

institute: Cornell University

summary: We examine the transcriptional alterations induced by in vitro culture of MDA-MB-231 cells on microfabricated hydroxyapatite-mineralized collagen devices that simulate bone matrix (PMID 29759731). As a control, we additionally characterize the transcriptional activity of cells cultured on a collagen substrate. We find that mineralized collagen increases the expression of genes associated with stemness and metastasis while culture on collagen increased expression of genes associated with cell cycle progression.

overall_design: MDA-MB-231 were seeded onto collagen or mineralized collagen microwells and routinely cultured for 7 days. Cells were harvested using collagenase and RNA was isolated from each sample using an RNA isolation kit accourding to manufacturer's protocols. Library prep was done with Illumina TruSeq RNA stranded kit and samples were sequenced as 1 x 86 bp single-end reads on the NextSeq500.

first: Siyoung

last: Choi

first: Matthew

last: Whitman

first: Adrian

last: Shimpi


title: Biofilm transcriptional pathways in the model symbiont Vibrio fischeri

status: Public on Jul 17 2023

city: Madison

first: Jacob

middle: Alan

last: Vander Griend

state: Wisconsin

address: 1550 Linden Drive

department: Medical Microbiology and Immunology

institute: University of Wisconsin - Madison

summary: Beneficial microbial symbionts are often horizontally acquired by their animal hosts from environmental sources, requiring the symbionts to complete a lifestyle transition from free-living in the environment to association with host tissues. In the model symbiosis between the Hawaiian bobtail squid and its microbial symbiont Vibrio fischeri, one mechanism used to make this transition during host colonization is the formation of biofilm-like aggregates on host mucosa. Extensive work has previously been conducted to isolate the critical factors controlling V. fischeri biofilm formation, yet much remains unknown regarding the full breadth of the biofilm-associated regulon. Here, we probed in vitro models of biofilm formation using transcriptomics, to identify novel regulatory pathways active within biofilms of the V. fischeri type strain ES114. Through comparing the gene-sets which became differentially regulated in multiple biofilm models, we discovered a shared set of 232 genes which demonstrated similar patterns in expression relative to uninduced controls. These genes contained representatives of multiple exopolysaccharide loci, genes involved in flagellar motility, and a diverse collection of other genes. Follow-up analysis suggested that these transcriptomic changes reflected true phenotypic effects, including changes in motility and cyclic-di-GMP production in biofilm-induced backgrounds. Beyond characterizing the shared biofilm response, we additionally profiled the regulatory activity of the sensor kinase RscS. This sensor kinase has previously been characterized to function as a phospho-donor within an established biofilm-inducing phospho-relay, yet our data suggests that RscS moonlights in at least one other phospho-relay that integrates downstream signaling from a homolog of the Vibrio cholerae response regulator VpsR, without a need for its established signaling partners. Overall, this study adds to our understanding of the genes involved in V. fischeri biofilm regulation, while revealing new regulatory pathways branching from previously characterized signaling networks.

overall_design: To investigate the biofilm transcriptome of the symbiont Vibrio fischeri, we collected total RNA from multiple biofilm induced mutants and the wild-type strain.

first: Mark

last: Mandel


title: Expression data of AsPC-1 and MIA Paca-2 cell lines cultured in nutrient deprivation

city: Columbus

first: Gian Luca

last: Rampioni Vinciguerra

state: OH

address: 460W 12th Avenue

department: Cancer Biology and Genetics

institute: The Ohio State University

summary:
Pancreatic ductal adenocarcinoma (PDAC) aggressiveness largely relies on its capability to thrive and progress in a highly desmoplastic microenvironment with limited nutrients.
We used microarrays to identify genes potentially dysregulated by nutrient deprivation in two different PDAC cell lines

overall_design: AsPC-1 and MIA PaCa-2 cell lines were cultured in Normal serum (10% FBS, Ns) or in nutrient deprivation (0% FBS, N-dep) for 72 hours

first: Gian-Luca

first: Francesca

last: Lovat

first: Carlo

last: Croce


title: Gene expression profiles of EpiSC-derived neural stem cell lines in comparison with EpiSC and embryonic CNS

city: Takatsuki

first: Hisato

last: Kondoh

address: 1-1 Murasaki-cho

institute: Biohistory Research Hall

summary: Epiblast stem cells (EpiSCs) maintained in the medium with activin were freed from activin to elicit neural development, exposed to various strengths of Wnt signals, which may provide the initial stage of anteroposterior regional specificities, and placed in the culture condition to arrest neural development but expand cells as neural stem cells (NSCs) with epidermal growth factor (EGF) and fibroblast growth factor 2 (FGF2).

overall_design: Duplicate cultures of original EpiSCs, the neural stem cell lines, XN4, XN1, KN3, KN1, CN1, and CN4, in the order of Wnt signal input levels from lower, were processed for total RNA extraction using TRIzol™ Plus (Thermo Fisher Scientific) and analyzed. Also, the forebrain (FB), midbrain (MB), hindbrain (HB), and cervical spinal cord (SC) tissues of E10.5 mouse embryos were processed for RNA extraction similarly to compare the expression of the central nervous system (CNS) portion landmark genes. Two litters, each with 5~6 embryos, were used as biological duplicates.

first: H

first: K

last: Nakamura

first: Y

last: Watanabe


title: Single-cell analysis of immune and stroma cell remodeling in renal cell carcinoma primary tumors and bone metastatic lesions

first: Shenglin

last: Mei

address: 10 Shattuck Street

institute: Harvard medical school (DMBI)

summary: Cancer metastasis in the bone represents an incurable disease. About one-third of patients with advanced renal cell carcinoma (ccRCC) have bone metastasis at the time of diagnosis making it a life-threatening disease. The bone metastatic niche, including immune and stroma microenvironment, has not been defined. Here, we created a human single-cell transcriptome cell-atlas of ccRCC bone metastases, contrasted with normal bone marrow immune cells and stroma.

overall_design: We collected fresh patient samples directly from the operating room and performed single-cell transcriptomic profiling of solid metastatic tissue (Tumor fraction), liquid bone marrow at the vertebral level of spinal cord compression (Involved), as well as liquid bone marrow from a different vertebral body distant from the tumor site but within the surgical field (Distal). In addition, we enriched immune and stroma cells from patients undergoing hip replacement surgery (Benign) as extra control. Bone marrow were disaggregated and profiled by 10X Genomics Single cell 3 gene expression V2.


title: Genome-wide analysis of replication fork locations in hydroxyurea-treated Saccharomyces cerevisiae by TrAEL-seq

status: Public on Jul 23 2023

city: Cambridge

first: Laura

last: Biggins

address: Babraham Research Campus

department: Bioinformatics

country: United Kingdom

institute: The Babraham Institute

summary: TrAEL-seq was performed on hydroxyurea-blocked and then released yeast cells to track replication fork stalling and replication fork restart, in wild-type and replisome mutant strains.

overall_design: Wild type and replisome mutant cells were synchronized in G1 phase, released into 200mM HU to arrest all forks (T0 Timepoint) and then released the cells into normal media to analyze fork recovery 20 min (T1 timepoint) and 40 min (T2 timepoint) after the removal of hydroxyurea.

first: Andreas

last: Hadjicharalambous

first: Alex

last: Whale

first: Geylani

last: Can

last: Skehel

first: Jonathan

last: Houseley

first: Philip

last: Zegerman


title: Deep Spatial Profiling of Venezuelan Equine Encephalitis Virus Reveals Increased Genetic Diversity Amidst Neuroinflammation and Cell Death During Brain Infection

status: Public on Jul 21 2023

city: Memphis

first: Evan

middle: Peter

last: Williams

state: TN

address: 858 Madison Ave

department: Dept. of Microbiology, Immunology, and Biochemistry

institute: University of Tennessee Health Science Center

summary: Venezuelan equine encephalitis virus (VEEV) causes a febrile illness that can progress to neurological disease with the possibility of death in human cases. The evaluation and optimization of therapeutics that target brain infections demands knowledge of the host’s response to VEEV, the dynamics of infection, and the potential for within-host evolution of the virus. We hypothesized that selective pressures during infection of the brain may differ temporally and spatially and so we investigated the dynamics of the host response, viral transcript levels, and genetic variation of VEEV TC-83 in eight areas of the brain in mice over 7 days post-infection (dpi). Viral replication increased throughout the brain until 5-6 dpi and decreased thereafter with neurons as the main site of viral replication. Low levels of genetic diversity were noted on 1 dpi, and was followed by an expansion in the genetic diversity of VEEV and nonsynonymous mutations (Ns) that peaked by 5 dpi. The proinflammatory response and the influx of immune cells mirrored the levels of virus and correlated with substantial damage to neurons by 5 dpi and increased activation of microglial cells and astrocytes. The prevalence and dynamics of Ns mutations suggests that the VEEV is under selection within the brain and that progressive neuroinflammation may play a role in acting as a selective pressure.

overall_design:
Gene expression profiles by RNA-Seq of the brains of C3H/NeN mice intranassally infected with VEEV-TC or mock-infected on 1-,3-,5-,6-, and 7-days post-infection.

Definitions:
MOB - main olfactory bulb
PIR - piriform cortex
STR - striatum
MTX - motor cortex
HIP - hippocampus
STX - sensory cortex
THA - thalamus
CBX - cerebellum

middle: P

first: Xue

last: Yi

first: Jasper

last: Lee

first: Colleen

middle: B

last: Jonsson


title: The DYRK1A protein kinase is recruited to a subset of ribosomal protein gene promoters in human and mouse cells [RNA-seq]

first: Chiara

last: Di Vona

overall_design: Expression profiling by high throughput sequencing. mRNA profiles of T98G cells treated with shControl (control) or shDYRK1A, were generated by deep sequencing.

last: Barba

first: Susana

last: de la Luna


title: Effect of the Regnase-1/3-Nfkbiz axis on the epigenomic profile in mouse Flt3–CD48–Lin–Sca1+Kit+ (LSK) cells

city: Kyoto

first: Takuya

last: Uehata

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Graduate School of Medicine

institute: Kyoto university

summary: Regulation of lineage biases in hematopoietic stem and progenitor cells (HSPCs) is pivotal for balanced hematopoietic output. However, little is known about the mechanism behind lineage choice in HSPCs. Here, we show that mRNA decay factors Regnase-1 (Zc3h12a) and Regnase-3 (Zc3h12c) are critical for induction of myeloid lineage priming, restricting lymphoid differentiation in HSPCs. Regnase-1- and Regnase-3-mediated control of mRNA encoding Nfkbiz, a transcriptional and epigenetic regulator, was essential for balancing lymphoid/myeloid lineage output in HSPCs in vivo. Furthermore, single cell-assay for transposase-accessible chromatin sequencing (scATAC-seq) analysis revealed that Regnase-1 and Regnase-3 control the epigenetic landscape on myeloid-related gene loci in hematopoietic stem cells (HSCs) via Nfkbiz. Consistently, an antisense oligonucleotide designed to inhibit Regnase-1- and Regnase-3-mediated Nfkbiz mRNA degradation primed HSCs toward myeloid lineages by enhancing Nfkbiz expression. Collectively, the collaboration between post-transcriptional control and chromatin remodeling by the Regnase-1/Regnase-3-Nfkbiz axis governs lineage priming, instructing HSC lineage specification.

overall_design: Flt3–CD48–LSK cells were isolated by Fluorescence-activated cell sorting (FACS) from CreERT2+Regnase-1fl/flRegnase-3–/–, CreERT2+Regnase-1fl/flRegnase-3–/–Nfkbizfl/fl, CreERT2+Nfkbizfl/fl, or control mice, and analyzed using scATAC-seq.

first: Osamu

last: Takeuchi


title: Transcriptomic analysis of the liver from control sibling and mutant uhrf1-hi272 zebrafish larvae at 120 hpf treated with DMSO or Palbociclib (PD)

city: Abu Dhabi

first: Kirsten

last: Sadler Edepli

state: Abu Dhabi

department: Biology

country: United Arab Emirates

institute: New York University Abu Dhabi

summary: This study was carried out to compare the changes in gene expression in livers of 120 hpf control sibling and mutant uhrf1-hi272 zebrafish larvae in response to treatment with  DMSO or Palbociclib (PD)

overall_design: 48 hpf embryos from an incross of uhrf1-hi272+/-  zebrafish adults with Tg(fabp10a:CAAX-EGFP) to mark the livers  were treated with either 0.5% DMSO or 20 microM PD in 0.5% DMSO in 6 well plates. At  120 hpf, 15- 20 livers from were dissected from larvae treated with PD or DMSO treated and individual livers were immediately placed in TRIzol and stored at -80 while the carcass of each larvae was genotyped. The individual livers from uhrf1hi272-/-  mutants and from WT in each treatment batch were pooled RNA was extracted per standard TRIzol/Chloroform method and concentrated, DNAse 1 treated and resuspended in DNase/RNase free water. For library preparation, high quality RNA was identified based on bioanalyzer analysis and quantified so that 100 ng of total RNA was used to initiate the library preparation using Ribo-Zero rRNA Removal Kit (Human/Mouse/Rat). The RNA sample was chemically fragmented and random primed for reverse transcription using Illumina TruSeq V2 RNA sample Prep Kit and first-strand cDNA reverse transcribed using random primers. Following second-strand cDNA synthesis, and end repair. TrueSeq adapter-index was ligated to cDNA libraries, and PCR amplification of 12 cycles was done for enrichment, producing a 350-400 bp fragment including adapters. The fragment sizes and purity of the libraries were confirmed by analyzing on a Bioanalyzer 2100 and were sequenced using the Illumina NextSeq 550 system with a Paired-end HO V2.5 kit, 150 cycles.

first: Bhavani

last: Pranesh

middle: S

last: Edepli


title: Imetelstat is effective in Acute Myeloid Leukemia (AML) patient xenografts.

status: Public on Jul 14 2023

city: Brisbane

first: Jasmin

last: Straube

state: QLD

address: 300 Herston Rd

country: Australia

institute: QIMR Berghofer

summary: Imetelstat is a covalently lipidated 13-mer thiophosphoramidate oligonucleotide that competitively inhibits telomerase activity. Here, we show that imetelstat effectively diminishes AML burden and prolongs survival in a comprehensive, randomized Phase II-like preclinical trial in AML patient-derived xenografts (PDX).

overall_design: RNA profiles of splenic hCD45+ cells from NRGS mice transplanted with AML patient samples (8 individual models), generated after treatment with vehicle or imetelstat, in duplicate.

first: Claudia

last: Bruedigam

first: Steven

middle: W

last: Lane


title: Acute Myeloid Leukemia (AML) patient xenografts

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

overall_design: Refer to individual Series


title: A Legionella toxin mimics tRNA and glycosylates the translation machinery to trigger a ribotoxic stress response.

city: San Francisco

first: Mark

last: Voorhies

address: 513 Parnassus, S472

department: Microbiology and Immunology

institute: University of California

summary: Pathogens often secrete proteins or nucleic acids that mimic the structure and/or function of molecules expressed within their host counterparts. Such molecular mimicry empowers pathogens to subvert critical host processes and helps establish infection. We report here that the intracellular bacterium Legionella pneumophila (L.p.) secretes a toxin named SidI (substrate of icm/dot transporter I) which possesses a transfer RNA (tRNA) like fold and functions as a mannosyl transferase . The 3.1 Å cryo-EM structure of SidI reveals an N-terminal domain that exhibits a characteristic ‘inverted L-shape’ and charge distribution that is present in two known protein mimics of tRNAs, the bacterial elongation factor EF-G and the mammalian release factor eRF1. In addition, SidI’s C-terminal domain adopts a glycosyl transferase B fold and shares considerable homology to a known mannosyl transferase. This molecular coupling of fold and enzymatic function allows SidI to bind and glycosylate components of the host translational apparatus, including the ribosome, resulting in a robust block of protein synthesis that is comparable to the potency exhibited by the toxin ricin. Additionally, we uncovered that the translational pausing activated by SidI elicits a stress response signature reminiscent to the ribotoxic stress response activated by elongation inhibitors that induce ribosome collisions. SidI mediated perturbations to the ribosome activates the stress kinases ZAKα and p38, that in turn drive the accumulation of the protein activating transcription factor 3 (ATF3). Intriguingly, ATF3 escapes the translation block imposed by SidI, translocates to the nucleus, and subsequently orchestrates the transcription of stress-inducible genes that culminates in the activation of a cell death program. Thus, using Legionella and its effectors as tools, we have unravelled the role of a ribosome to nuclear signaling pathway that regulates cell fate.

overall_design: Expression profiling by RNA-seq of HEK293-FcgR cells infected with either WT or ΔdotA Legionella (as a time course) and HEK293T cells treated with ansiomycin or didemnin-B (for 4 hours) with two bioreps for each condition.

first: Advait

last: Subramanian

first: Lan

last: Wang

first: Tom

last: Moss

first: Smriti

last: Sangwan

first: Erica

last: Stevenson

first: Ernst

middle: H

last: Pulido

first: Samantha

last: Kwok

first: Danielle

last: Swaney

first: Nevan

last: Krogan

first: Stephen

last: Floor

first: Anita

last: Sil

first: Peter

last: Walter

first: Shaeri

last: Mukherjee


title: Generation of a unique, comprehensive and representative Acute Myeloid Leukemia (AML) patient-derived xenograft (PDX) resource.

first: Jasmin

last: Straube

summary: Randomized Phase II-like preclinical trials in patient-derived xenografts (PDX) provide an attractive option to define the efficacy of drugs that act via cell-intrinsic mechanisms, and to identify biomarkers of response and resistance across genetically diverse subtypes of leukemia. Here, we generated a unique, comprehensive and representative AML PDX resource that reflects the genetic abnormalities that are found in large clinical trials.

overall_design: RNA profiles of AML patient samples that successfully engrafted in NSGS and NRGS recipients.


title: The DYRK1A protein kinase is recruited to a subset of ribosomal protein gene promoters in human and mouse cells [ChIP-seq]

city: Barcelona

first: Chiara

last: Di Vona

address: Carrer Dr. Aiguader 88

institute: CRG

summary: Ribosomal protein genes (RPGs) coding sequences are highly conserved along evolution; however, promoter features and the machinery involved in their transcriptional regulation are not. In eukaryotes, the main genomic elements and players involved in RPG transcriptional regulation have been mostly characterized in Saccharomyces cerevisiae. However, given the lack of evolutionary conservation of the yeast factors, studies in higher eukaryotes have focused on searching for differential enrichment of transcription factor-binding motifs within the RPG promoters. Among them, the palindromic motif TCTCGCGAGA, which is currently acknowledged as a ZBTB33/KAISO motif, also matches the genomic sequence bound by the protein kinase DYRK1A. DYRK1A, a member of the human family of DYRK kinases, fulfills many diverse functions by phosphorylating a broad set of proteins involved in different cellular processes. One of such functions is to be a chromatin-associated kinase capable of regulating gene expression. Here, we analyze in-depth the presence of DYRK1A at the promoters of human and mouse RPGs and explore its functional consequences. Our results indicate that DYRK1A is a positive regulator of RPGs’ expression at the transcriptional level, and further expand the functional spectrum of the kinase as a contributor to the regulation of cell growth in mammalian cells.

overall_design: Profiling the occupancy of DYRK1A, RNAPOLII and ZBTB33/KAISO in different cell lines and tissues

first: Laura

last: Barba

first: Roberto

last: Ferrari

first: Susana

last: de la Luna


title: Preservation of orphan ribosomal proteins during stress in chaperone-stirred condensates

status: Public on Jul 27 2023

city: Chicago

first: Asif

last: Ali

state: Illinois

address: 929 E 57th St

department: Molecular Genetics and Cell Biology

institute: University of Chicago

summary: Ribosome biogenesis is among the most resource-intensive cellular processes, with ribosomal proteins accounting for up to half of all newly synthesized proteins in eukaryotic cells. During stress, cells shut down ribosome biogenesis in part by halting rRNA synthesis, potentially leading to massive accumulation of aggregation-prone “orphan” ribosomal proteins (oRPs). Here we show that during heat shock in yeast and human cells, oRPs accumulate as reversible condensates at the nucleolar periphery recognized by the Hsp70 co-chaperone Sis1/DnaJB6. oRP condensates are liquid-like in cell-free lysate but solidify upon depletion of Sis1 or inhibition of Hsp70. When cells recover from heat shock, oRP condensates disperse in a Sis1-dependent manner, and their ribosomal protein constituents are incorporated into functional ribosomes in the cytosol, enabling cells to efficiently resume growth.

overall_design: Total RNA was extracted from S. cerevisiae before and after anchor away of Ifh1.

first: Rania

last: Garde

first: David

last: Pincus


title: EZH2 inhibition sensitizes IDH1R132H mutant gliomas to Panobinostat

status: Public on Jul 12 2023

city: New York

first: Dr. Liang

last: Lei

state: NY

address: 1130 St. Nicholas Ave

department: Pathology and Cell Biology

institute: Columbia University

summary: Isocitrate Dehydrogenase-1 (IDH1) is commonly mutated in lower grade diffuse gliomas. The IDH1R132H mutation is an important diagnostic tool for tumor diagnosis and prognosis, however its role in glioma development, and its impact on response to therapy, is not fully understood. We developed a murine model of proneural IDH1R132H mutated glioma that shows elevated production of 2-Hydroxyglutarate (2-HG) and increased tri-methylation of lysine residue K27 on histone H3 (H3K27me3) compared to IDH1 wild-type tumors. We found that using Tazemetostat to inhibit the methyltransferase for H3K27, Enhancer of Zeste 2 (EZH2), reduced H3K27me3 levels and increased acetylation on H3K27. We also found that, although the histone deacetylase inhibitor (HDACi) Panobinostat was less cytotoxic in IDH1R132H mutated cells (either isolated from murine glioma or oligodendrocyte progenitor cells infected in vitro with a retrovirus expressing IDH1R132H) compared to IDH1-wildtype cells, co-treatment with Tazemetostat is synergistic in both mutant and wildtype models. These findings indicate a novel therapeutic strategy for IDH1-mutated gliomas that targets the specific epigenetic alteration in these tumors.

overall_design:
To determine the effect of IDH1 R132H mutation on gliomagenesis, we established an in vivo and in vitro model for both mutant and wildtype IDH1 murine gliomas initated by targeting glial progenitors of the subcortical white matter.
We performed transcriptional profiling by RNA-seq on the IDH1R132H mutant and wildtype tumors to determine if these tumors would recapitulate the molecular profile of human proneural gliomas from the Verhaak et al. subtype classifers gene signatures.
We compared the expression profile of the wildtype (N=5) and IDH1R132H (n=6) endstage murine tumors to the TCGA database using Gene Set Enrichment Analysis (GSEA),

first: Sprinzen

last: Lisa

first: Godinez

last: Franklin

first: Mela

last: Angeliki

first: Lei

last: Liang

first: Upadhyayula

last: Pavan

first: Mahajan

last: Aayushi

first: Humala

last: Nelson

first: Manier

first: Caprioli

last: Richard

first: Quinones-Hinojosa

last: Alfredo

first: Casaccia

last: Patrizia

first: Canoll

last: Peter


title: NSD1 deposits Histone H3 lysine 36 dimethylation to pattern non-CG DNA methylation in neurons

status: Public on Jul 07 2023

city: Saint Louis

first: Nicole

last: Hamagami

state: MO

address: 4487 McPherson Ave. Unit C

department: Neuroscience

institute: Washington University in St. Louis

type: Methylation profiling by high throughput sequencing


title: NSD1 deposits Histone H3 lysine 36 dimethylation to pattern non-CG DNA methylation in neurons [WGBS in vitro]

summary: During postnatal development the DNA methyltransferase DNMT3A deposits high levels of nonCG cytosine methylation in neurons. This unique methylation is critical for transcriptional regulation in the mature mammalian brain, and loss of this mark is implicated in DNMT3Aassociated neurodevelopmental disorders (NDDs). The mechanisms determining genomic nonCG methylation profiles are not well defined however, and it is unknown if this pathway is disrupted in additional NDDs. Here we show that genome topology and gene-expression converge to shape Histone H3 lysine 36 dimethylation (H3K36me2) profiles, which in turn recruit DNMT3A and pattern neuronal non-CG methylation. Brain-specific deletion of NSD1, the H3K36 methyltransferase mutated in the NDD Sotos syndrome, disrupts megabase-scale H3K36me2 patterns, causing alterations in non-CG methylation and transcription that overlap models of DNMT3A disorders. Our findings indicate that H3K36me2 deposited by NSD1 is an important determinant of neuronal non-CG DNA methylation and implicates disruption of this methylation in Sotos syndrome.

overall_design: Hi-depth whole genome bisulfite sequencing (WGBS) of DIV18 primary culture neurons.

first: Dennis

last: Wu

first: Adam

last: Clemens

first: Sabin

last: Nettles

first: Aidan

last: Li

first: Harrison

last: Gabel


title: NSD1 deposits Histone H3 lysine 36 dimethylation to pattern non-CG DNA methylation in neurons [RNA-seq]

overall_design: Comparative gene expression profiling analysis of total RNA-seq data from 8-week NSD1 cKO and control mouse cerebral cortex


title: NSD1 deposits Histone H3 lysine 36 dimethylation to pattern non-CG DNA methylation in neurons [WGBS in vivo]

overall_design: Hi-depth whole genome bisulfite sequencing (WGBS) of mouse cerebral cortex from 8-week NSD1 cKO and control mice.


title: Nutrient-restriction activated Fra-2 promotes tumor progression in Mir15aKO pancreatic cancer

first: Gian Luca

last: Rampioni Vinciguerra

summary:
We used microarrays to identify genes dysregulated in cellular stress response to nutrient deprivation in an inducible mouse model of Mir15aKO PDAC
Expression data of pancreatic cancer collected from genetic mouse model KrasLSL-G12D/Ptf1aCre-ERTM/Ptenflox (named KPP mouse) and KrasLSL-G12D/Ptf1aCre-ERTM/Ptenflox/Mir15aKO (named GL mouse) fed with Control diet (C-diet, 20% protein) and isocaloric, low-protein diet (LP-diet, 5% protein)

overall_design: once tumors were induced by tamoxifen, KPP and GL mice were randomly distributed in two different cohorts, fed with C-diet or LP-diet. Mice were sacrificed after 60 days and PDAC collected and analyzed

first: Gian-Luca

first: Francesca

last: Lovat

first: Carlo

last: Croce


title: NSD1 deposits Histone H3 lysine 36 dimethylation to pattern non-CG DNA methylation in neurons [ChIP-seq vitro]

overall_design: Chromatin immunoprecipitation DNA sequencing (ChIP-seq) for histone histone modifications H3K36me2 and DNA methyltransferase DNMT3A in  DIV12 primary cultured neurons


title: Analysis of gene expression in pancreatic beta-cells of NOD mice

status: Public on Jul 03 2023

city: Saga City

first: Keiichiro

last: Mine

state: Saga

address: 5-1-1 Nabeshima

institute: Saga university

summary: Pancreatic beta-cells were purified by FluoZin-3-AM and TMRE from at least eight mice to minimize the individual heterogeneity on diabetes progression, and devoted to transcriptome analysis.

overall_design: 6-week-old wild type beta-cell data was used as control sample.


title: NSD1 deposits Histone H3 lysine 36 dimethylation to pattern non-CG DNA methylation in neurons [ChIP Rx]

overall_design: Chromatin immunoprecipitation with reference exogenous genome (ChIP-Rx) for histone histone modifications H3K36me2, H3K36me3, and DNA methyltransferase DNMT3A in mouse cerebral cortex from 2-week NSD1 cKO and control mice.


title: The dual GGDEF/EAL domain enzyme PA0285 is a Pseudomonas species housekeeping phosphodiesterase regulating early attachment and biofilm architecture

status: Public on Jul 01 2023

city: Singapore

first: Xianghui

last: Liu

address: 60 Nanyang Drive, SBS-01N-27

country: Singapore

institute: Nanyang Technological Univ. of Singapore

summary: Bacterial lifestyles are dictated by the conditions encountered during colonization of a specific ecological niche or host. A wide range of environmental stimuli triggers sensory modules, that modify activity of proteins, or/and initiate a transfer of information in complex regulatory networks, which modulate gene expression, and therefore adaptation. The transition between planktonic and biofilm growth is dependent on the homeostasis of the intracellular second messenger c-di-GMP. High c-di-GMP levels driven by diguanylate cyclase (DGC) activity favor biofilm while low levels maintained by phosphodiesterase (PDE) enzymes encourage planktonic style or biofilm dispersal. In Pseudomonas aeruginosa over 40 PDE/DGC are involved in c-di-GMP homeostasis, including 16 dual enzymes possessing both canonical DGC and PDE motifs, i.e. GGDEF and EAL, respectively. It has been previously reported that the deletion of the PDE/DGC dual enzyme PA0285, one of 5 c-di-GMP-related enzymes conserved across all Pseudomonas species, impacts biofilms and causes elevated c-di-GMP levels in P. aeruginosa. Here we confirm that this role is conserved in various P. aeruginosa (PAO1, PA14 and PAK) and Pseudomonas putida strains. Deletion of PA0285 has the highest impact during the early stage of surface colonization, and RNA-seq analysis in biofilm context indicates that it may be associated with upregulation of cupA fimbrial genes. We demonstrate that the C-terminal portion of PA0285 encompassing the GGDEF and EAL domains binds the respective GTP (GGDEF) and c-di-GMP (EAL) substrates but only exhibits PDE activity in vitro. Both GGDEF and EAL domains are important for PA0285 PDE activity in vivo as suggested by site-directed mutants in each of the key motifs. Complementation of the PA0285 mutant strain with the C-terminal GGDEF/EAL portion in trans is not as effective as with the full-length gene suggesting that the transmembrane region and PAS domains contained in PA0285’s N-terminal portion influence its PDE activity in vivo. We speculate that the transmembrane portion or/and PAS domains of PA0285 impede its PDE activity in vivo through modulating the conformation of the enzyme, as shown for P. aeruginosa RbdA, in response to an unknown stimulus.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Pseudomonas aeruginosa wild-type PAO1 and PA0285 mutant in both biofilm and planktonic growth conditions.

first: Kira

last: Eiler

first: Joey

last: Yam

first: Richard

last: Morton

first: Jaime

last: Brizuela

first: Adeline

last: Yong

first: Michael

last: Givskov

first: Sven-Andreas

last: Freibert

first: Gert

last: Bange

first: Scott

last: Rice

first: Wieland

last: Steinchen

first: Alain

last: Filloux


title: Gestational diabetes augments group B Streptococcus perinatal infection through disruptions in maternal immunity and the vaginal microbiota

status: Public on Jul 05 2023

city: Houston

first: Vicki

last: Mercado-Evans

state: TX

address: One Baylor Plaza

institute: Baylor College of Medicine

summary: Group B Streptococcus (GBS) is a pervasive perinatal pathogen, yet factors driving GBS dissemination in utero are poorly defined. Gestational diabetes mellitus (GDM), a complication marked by dysregulated immunity and maternal microbial dysbiosis, increases risk for GBS perinatal disease. We interrogated host-pathogen dynamics in a novel murine GDM model of GBS colonization and perinatal transmission. GDM mice had greater GBS in utero dissemination and subsequently worse neonatal outcomes. Dual-RNA sequencing revealed differential GBS adaptation to the GDM reproductive tract, including a putative glycosyltransferase (yfhO), and altered host responses. GDM disruption of immunity included reduced uterine natural killer cell activation, impaired recruitment to placentae, and altered vaginal cytokines. Lastly, we observed distinct vaginal microbial taxa associated with GDM status and GBS invasive disease status. Our translational model of GBS perinatal transmission in GDM hosts recapitulates several clinical aspects and enables discovery of host and bacterial drivers of GBS perinatal disease.

overall_design: To understand GBS-host interactions in the gestational diabetic host, we challenged pregnant control and gestational diabetic mice with GBS (Strain A909) on E14.5 and E15.5, and performed dual RNAseq of GBS and vaginal or uterine tissues 3 days after initial challenge.