title: Differential regulation by CX3CR1 ligands CX3CL1 and CCL26 on mouse bone marrow-derived macrophages

status: Public on Jan 29 2023

city: Chicago

first: Gye Young

last: Park

state: IL

address: 909 S. Wolcott Avenue CMRB 3080

department: Medicine

institute: University of Illinois at Chicago

summary: We studied the effect of ligation on chemokine receptor CX3CR1 in the mouse bone marrow-derived macrophages (BMDM). We compared transcriptional profiles of BMDM treated with CX3CL1 and those of CCL26 to test if these two CX3CR1 ligands regulate differently.

overall_design: BMDM mRNA profiles of 6-week-old wild type mice treated with BSA, CX3CL1 or CCL26.

first: Hyung

last: Moon

first: Seung-jae

last: Kim

first: Gye

middle: Y


title: Epigenome-Wide Analysis of Aging Effects on Liver Regeneration

status: Public on Jan 28 2023

city: Houston

first: Xiaoqin

last: Liu

state: TX

address: 2121 W. Holcombe Blvd., Room 511

department: Center for translational cancer research

country: USA

institute: Texas A&M University IBT

type: Methylation profiling by high throughput sequencing

summary: This project aims to identify DNA methylation changes that occur during liver aging and regeneration using a whole-genome single nucleotide resolution approach and determine the genes and pathways associated with the differentially methylated genomic regions (DMRs) that are co-regulated by aging and regeneration

overall_design: Comparative DNA methylation profiling analysis of WGBS data for mouse livers during aging and regeneration.

first: Junying

last: Wang

first: Wen

last: Zhang

first: Minjee

first: Ke

first: Robert

last: Tsai


title: AoSte12 is required for mycelial development, conidiation, trap morphogenesis, and secondary metabolism by regulating hyphal fusion in nematode-trapping fungus of Arthrobotrys oligospora [DAP-seq]

city: Kunming

last: Bai

address: No. 2, Cuihu North Road

country: China

institute: Yunnan University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: DAP-Seq analysis revealed that AoSte12 was involved in cellular growth and diverse metabolic processes.

overall_design: The cDNA sequence encoding protein AoSte12 is constructed in Halo Tag plasmid, the construct vector pAoSte12-halo was identified by sequencing, then the vector and the genome DNA of A. oligospora were send to Genedenovo Biotechnology (Guangzhou, China) for DAP-seq analysis. The AoSte12 protein binds to the target genome fragment, thus the DNA fragment of the genome bound by the target protein can be enriched. Through the combination with high-throughput sequencing technology, DNA products after DAP were sequenced and analyzed, DNA binding sites of target proteins were searched from the whole genome, and high-throughput data results were obtained by efficient sequencing methods. The DNA libraries were sequenced on the Illumina sequencing platform by Genedenovo Biotechnology Co., Ltd (Guangzhou, China).

first: Meihua

last: Xie

first: Qianqian

first: Wenjie

first: Yankun

first: Jinkui

last: Yang


title: Network Pharmacology-based analysis of Resinacein S against non-alcoholic fatty liver disease by modulating lipid metabolism

city: Shanghai

first: Feifei

last: Mao

address: 301 Yanchang Middle Road

institute: Shanghai Tenth People’s Hospital

type: Expression profiling by high throughput sequencing

summary: In order to investigate the hub regulated genes of Resinacein S against NAFLD in human liver cells, we treated the normal human hepatic cell line L02 with Resinacein S and detected the gene expression profiles by RNA-Seq.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Resinacein S treated human-normal-liver-cell line L02 compared to DMSO groups.

first: Shanshan

last: Gao

first: Yanjie

last: Huang


title: Bacterial droplet-based single-cell RNA-seq reveals antibiotic-associated heterogeneous cellular states

status: Public on Jan 27 2023

city: Cambridge

first: Peijun

last: Ma

state: MA

address: 415 Main Street

department: Infectious Disease and Microbiome program

institute: The Broad Institute of MIT and Harvard

summary: In this study, we introduce BacDrop, a bacterial droplet-based high throughput scRNA-seq technology that can be applied to large cell numbers. We applied BacDrop to study Klebsiella pneumoniae clinical isolates and elucidated their critical, genome-wide heterogeneity in the absence and presence of antibiotic perturbations.

sample_organism:
Pseudomonas aeruginosa
Escherichia coli
Klebsiella pneumoniae
Enterococcus faecalis

overall_design: An antibiotic-susceptible K. penumoniae isolate, MGH66, was treated separately with three different antibiotics, including meropenem, ciprofloxacin, and gentamicin. BacDrop was applied to these three samples as well as the untreated control. We profiled the within population heterogeneity in these 4 samples. In addition, we also applied BacDrop to a multi-drug resistant K. pneumoniae BIDMC35, and demonstrated the within population heterogeneity in this strain.

first: Deborah

middle: T

last: Hung


title: Contribution of variant subunits and associated factors to genome-wide distribution and dynamics of cohesin [RNA-seq]

status: Public on Jan 26 2023

city: Madrid

first: Daniel

last: Gimenez

address: Calle de Melchor Fernández Almagro, 3

country: Spain

institute: CNIO

summary: The cohesin complex organizes the genome forming dynamic chromatin loops that impact on all DNA-mediates processes. There are two different cohesin complexes in vertebrate somatic cells, carrying the STAG1 or STAG2 subunit, and two versions of the regulatory subunit PDS5, PDS5A and PDS5B. Mice deficient for any of the variant subunits are embryonic lethal, which indicates that they are not functionally redundant. However, their specific behavior at the molecular level is not fully understood. The genome-wide distribution of cohesin provides important information with functional consequences. Here, we have characterized the distribution of cohesin subunits and regulators in mouse embryo fibroblasts (MEFs) either wild type or deficient for cohesin subunits and regulators by chromatin immunoprecipitation and deep sequencing. We identify non-CTCF cohesin binding sites in addition to the commonly detected CTCF cohesin sites and show that cohesin-STAG2 is the preferred variant at these positions. Moreover, this complex has a more dynamic association with chromatin as judged by fluorescent recovery after photobleaching (FRAP), associates preferentially with WAPL and is more easily extracted from chromatin with salt than cohesin-STAG1. We observe that both PDS5A and PDS5B are exclusively located at cohesin-CTCF positions, that ablation of a single paralog has no noticeable consequences for cohesin distribution, while double knocked out cells show decreased accumulation of cohesin at all its binding sites. With the exception of a fraction of cohesin positions in which we find binding of all regulators-including CTCF and WAPL-, the presence of NIPBL and PDS5 is mutually exclusive, consistent with results of immunoprecipitation reactions in mammalian cells, as suggested previously from results in vitro. Our findings support the idea that non-CTCF cohesin binding sites represent sites of cohesin loading or pausing and are preferentially occupied by the more dynamic cohesin-STAG2. PDS5 proteins redundantly contribute to arrest cohesin at CTCF sites, possibly by preventing binding of NIPBL, but are not essential for this arrest. These results add important insights towards understanding how cohesin regulates genome folding and the specific contributions of the different variants that coexist in the cell.

overall_design: RNA-seq of MEFs.

last: Gimenez-Llorente

first: Ana

last: Cuadrado

first: Magali

last: De Koninck

first: Miguel

last: Ruiz-Torres

last: Losada

first: Aleksandar

last: Kojic

first: Miriam

last: Rodríguez-Corsino


title: A Zeb1/Mitochondrial Creatine Kinase Metabolic Axis Controls Osteoclast Activation and Skeletal Remodeling

city: Ann Arbor

first: Lingxin

last: Zhu

state: Michigan

address: 210 Washtenaw Ave, Life Sciences Institute, Room 5008

institute: Univeristy of Michigan in Ann Arbor

summary: To begin identifying potential Zeb1 targets capable of regulating bone resorbing activity, we conducted a transcriptome analysis comparing the expression profiles of wild-type versus Zeb1ΔM/ΔM osteoclasts.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for control and Zeb1-deleted bone marrow-derived macrophages and osteoclasts.

first: Stephen

middle: J

last: Weiss


title: High throughput analysis of binding of E. coli Lrp mutants

status: Public on Jan 31 2023

first: Lydia

last: Freddolino

state: MI

address: 1150 W. Medical Center Dr., MSRB 3 room 3315

department: Biological Chemistry

institute: University of Michigan

summary: Feast-Famine Response Proteins are a widely conserved class of global regulators in prokaryotes, the most highly studied of which is the E. coli leucine-responsive regulatory protein (Lrp). Lrp senses environmental nutrition status and subsequently regulates up to one-third of the genes in E. coli, either directly or indirectly. Lrp exists predominantly as octamers and hexadecamers (16mers), where leucine is believed to shift the equilibrium towards the octameric state. In this study, we analyzed the effects of three oligomerization state mutants of Lrp in terms of their ability to bind to DNA and regulate gene expression in response to exogenous leucine. We find that oligomerization beyond dimers is required for Lrp’s regulatory activity, and that contrary to prior speculation, exogenous leucine modulates Lrp activity at its target promoters exclusively by inhibiting Lrp binding to DNA. We also find evidence that Lrp binding bridges DNA over length scales of multiple kilobases, revealing a new range of mechanisms for Lrp-mediated transcriptional regulation.

overall_design:
Examination of the effects of Lrp mutants on DNA binding and changes in gene expression in Min or LIV media at Log or Stationary Phase. Two lineages of each strain were generated independently (Lineage A or B), and two biological replicates of each condition were performed on separate days (1 and 2).
Please note that each processed data file was generated from multiple samples as indicated in the corresponding sample description field.

first: Christine

middle: A

last: Ziegler

first: Peter

middle: L


title: Transcriptional profiling of human cardiomyocytes and endothelial cells derived from NOTCH1 knockout induced pluripotent stem cells (iPSCs)

city: Memphis

first: Zhaohui

last: Xu

state: TN

address: 262 Danny Thomas Place

department: Infectious Diseases

institute: St. Jude Children's Research Hospital

summary: Pathogenic NOTCH1 mutations are linked to congenital heart defects. To pinpoint how NOTCH1 deficiency affects cardiac development, we generated homozygous NOTCH1 knockout (N1KO) human induced pluripotent stem cells (iPSCs). We then performed high-throughput RNA-seq to profile differential gene expression in cardiomyocytes (iPSC-CMs) and endothelial cells (iPSC-ECs) derived from wild type (WT) and N1KO iPSCs.

overall_design: Transcriptomic profiling of cardiomyocytes (iPSC-CMs) and endothelial cells (iPSC-ECs) derived from WT and N1KO iPSCs.

first: Ming-Tao

last: Zhao

first: Shiqiao

last: Ye


title: Genome Wide Binding profile and transcriptome of STAT3 and STAT3 Mutant Y640F in STAT3 Wildtype and STAT3 Mutant Y640F hematopoietic progenitor cell lines

status: Public on Jan 25 2023

city: Vienna

first: Veronika

last: Sexl

address: Veterinaerplatz 1

department: Pharmacology / Toxikology

country: Austria

institute: University of Veterinary Medicine Vienna

summary: In many human cancers the transcription factor STAT3 is constitutively active and contributes to oncogenesis, tumour growth and progression. Recently, gain-of-function mutations of STAT3 have been identified in patients suffering from various haematopoietic malignancies and are postulated to enhance the transcriptional activity of STAT3. We investigated the gene expression and binding profile of the most common STAT3 mutant Y640F compared to wild-type STAT3, describing it's mechanism of action and pinpointing to novel therapeutic intervention sites.

overall_design: (RNA-Seq) mRNA from HPC7 or HPCLSK transduced with retroviral vectors encoding empty vector, STAT3 or STAT3Y640F (3 technical replicates) were prepared using the Lexogen SENSE mRNA-Seq library preparation kit. Single-end, 50bp sequencing was performed on an Illumina HiSeq 3000/4000  sequencer. Reads were mapped to the GENECODE M13 genome. (ChIP Seq) HPC7 expressing empty vector, STAT3, STAT3Y640F ) linked to a C-terminal V5 tag were used for V5-ChIP (3 technical replicates). After V5-pull down genomic regions were subjected to sequencing library preparation and sequencing was performed using the Illumina HiSeq3000/4000 platform in 50-base-pair single-end mode.

first: Tania

last: Brandstoetter

first: Barbara

last: Maurer

first: Reinhard

last: Grausenburger


title: AoSte12 is required for mycelial development, conidiation, trap morphogenesis, and secondary metabolism by regulating hyphal fusion in nematode-trapping fungus of Arthrobotrys oligospora [gene expression]

last: Bai

summary: Transcriptomic analysis revealed that differentially expressed genes in the absence of AoSte12 were involved in mycelial growth, development process,conidiation, cell nucleus and trap formation.

overall_design: WT (represented by A) and ΔAoste12 (represented by B) strains grown on cellophane-overlaid CMY plates at 28°C for 5 and 7 days, three replicates were used for each sample. After collecting the samples, RNA was extracted with the AxyPrep Multisource RNA Miniprep Kit (Axygen, Jiangsu, China), and then sent to Majorbio Bio-Pharm Technology Co., Ltd. (Shanghai, China) to construct the transcriptome of WT and ΔAoste12 strains. The final cDNA library was sequenced on an Illumina Novaseq 4000 platform.

first: Meihua

last: Xie

first: Qianqian

last: Liu

first: Wenjie

last: Wang

first: Yankun

first: Jinkui

last: Yang


title: Contribution of variant subunits and associated factors to genome-wide distribution and dynamics of cohesin

first: Daniel

last: Gimenez

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

overall_design: Refer to individual Series


title: Genome-wide transcriptome analysis of Esrrb wt and KO  mouse embryonic stem cells, differentiated towards FS cells with AloXR protocol (Kinoshita et al., 2021)

city: Pozzuoli

first: Margherita

last: Mutarelli

address: Via Campi Flegrei 34

department: ISASI

country: Italy

institute: CNR

summary: We report the application of genome-wide RNA-sequencing analysis for Esrrb WT and Esrrb KO mES cells after differentiation towards Formative Stem cells (FS cells). We find that expression of some formative genes was reduced in Esrrb KO cells compared to WT, and that lineage markers were significantly upregulated in Esrrb KO cells. This indicates that transition toward the formative state is impaired in Esrrb KO cells.

overall_design: mRNA profiles of WT or Esrrb KO mES during transition towards Formative State.

first: Martina

last: Chieregato

first: Linda

last: Diamante


title: Genome-wide transcriptome analysis of Esrrb WT and conditional Esrrb KO mouse embryonic stem cells

summary: We report the application of genome-wide RNA-sequencing analysis for Esrrb WT and conditional Esrrb KO mES cells after differentation for 48 hours. Global transcriptome profiling revealed impaired induction of formative genes in conditional KO cells compared to WT cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for E14 and Esrrb KO cells  stably transfected either with an inducible Empty vector or with an inducible vector expressing Esrrb. Cells were maintained with DOX and 2iL and subsequently differentiated for 48 hours in absence of 2iL and DOX.

first: Elena

last: Guerzoni

first: Francesco

last: Panariello


title: Genome-wide transcriptome analysis of pluripotent (2iL or 2i) and differentiated mES cells

summary: We report the application of genome-wide RNA-sequencing analysis for pluripotent mouse ES cells maintained in 2iL or 2i and differentiated for 12, 24, 36, 48, 60, 72, 84, 96 hours. We find that cells differentiating from both 2iL and 2i follow a similar trajectory with 2i samples accelerated by 24 hours. Moreover we performed unsupervised hierarchical clustering on cells differentiating from 2iL and defined 6 groups of genes (gene signatures) based on their transcriptional behaviour during differentiation. Finally we reported that only after activation and dissolution of the formative signatures cells are fully committed. The same behaviour is true for cells differentiating from 2i.

overall_design: mRNA profiles of mES cells cultured in 2iL or 2i and during dfferentiation (24,36, 48, 60, 72, 84,96 hours after 2iL withdrawal or 12, 24, 36, 48, 60, 72, 84 hours after 2i withdrawal)

last: Carbognin

first: Annamaria

last: Carissimo


title: Contribution of variant subunits and associated factors to genome-wide distribution and dynamics of cohesin [ChIP-seq]

overall_design: ChIP-seq for cohesin subunits (SMC1A, STAG1 and STAG2) was performed in mouse embryonic fibroblasts either wild type or deficient for cohesin subunits cohesin regulators. For the different genotypes, each replicate corresponds to MEF extracted from a different embryo. Input samples are an equimolar mix of chromatin from the two clones. WT clones for each condition come from littermates in the case of constitutive KOs (Pds5A KO, Pds5B KO, Stag1 KO) or from the same clone without exposure to Cre (Pds5 DKO, Stag2 KO, Ctcf KO).

last: Gimenez-Llorente

first: Ana

last: Cuadrado

first: Magali

last: De Koninck

first: Miguel

last: Ruiz-Torres

last: Losada

first: Aleksandar

last: Kojic

first: Miriam

last: Rodríguez-Corsino


title: Genome-wide transcriptome analysis of pluripotent (2iL), differentiated (2iL withdrawal) or re-induced (2iL re-application during differentiation) mES cells

summary: We report the application of genome-wide RNA-sequencing analysis for pluripotent mouse ES cells maintained in 2iL, differentiated for 24, 48, 96 and 120 hours or treated with 2iL for 24hours after 48 or 96 hours of differentiation. We find that after 48h of differentiation cells respond to 2iL reinduction by upregulating naïve markers and downregulating formative markers, while cells that underwent 96 hours of differentiation failed to do so. This indicates that committment is associated with a change in the transcriptional response to external signals.

overall_design: mRNA profiles of mES cells cultured in 2iL, during dfferentiation (24, 48, 96 and 120 hours after 2iL withdrawal) or re-induced by 24 hours treatment with 2iL at 48 and 96 hours (48_24, 96_24).


title: Genome-wide transcriptome analysis of pluripotent (2iL) or differentiated (2iL withdrawal) wild-type or Esrrb KO mES cells.

summary: We report the application of genome-wide RNA-sequencing analysis for pluripotent wild-type or Esrrb KO mouse ES cells, maintained in 2iL or differentiated for 24, 48 or 72 hours. We find an anticipated progression of Esrrb KO cells as compared to wild-type cells and a massive downregulation of formative genes in multiple Esrrb KO clones, confirming the role of Esrrb as an inducer of the formative program. Such Esrrb KO cells also show upregulation of committed genes and activation of the Mesendoderm program.

overall_design: mRNA profiles of wild-type and Esrrb KO mES cells cultured in 2iL or after 24, 48 or 72 hours of differentiation.


title: Genome-wide transcriptome analysis of pluripotent (2iL) and differentiated (2iL withdrawal) mES cells, overexpressing a DOX-inducible Esrrb

summary: We report the application of genome-wide RNA-sequencing analysis for pluripotent mouse ES cells transfected with DOX-inducible Esrrb and maintained in 2iL, or differentiated for 96 hours with or without Doxycycline. We find that Esrrb expression is sufficient to confer reversibility and activates both naive and formative genes.

overall_design: mRNA profiles of mES cells transfected with DOX-inducible Esrrb and cultured in 2iL or after 96 hours of differentiation with or without Doxycycline treatment.


title: Esrrb conveys naive pluripotent cells through the formative transcriptional program


title: Genome-wide maps of chromatin accessible regions in pluripotent (2iL) and differentiated (48h, 96h) mES cells

summary: We report the application of sequencing technology for profiling of genome-wide chromatin accessible regions in mouse ES cells. We generated genome-wide chromatin-state maps of mouse embryonic stem cells maintained in pluripotent state (2iL) and differentiated for 48 and 96 hours (48 and 96). We find that the large majority of ESRRB motif-cointaining regions are found in 2iL and at 48 hours and that several formative genes contain time-specific oper regions at 48h, but not at earlier or later time-points.

overall_design: Examination of genome-wide chromatin accessible regions in pluripotent and differentiated mES cells

first: Antonio

last: Grimaldi


title: Mechanistic insights into anti-cancer properties of Curcumin and Andrographis in colorectal cancer

status: Public on Jan 21 2023

city: Monrovia

first: Ajay

last: Goel

state: California

address: 1218 S. Fifth Avenue

department: Molecular Diagnostics and Experimental Therapeutics

institute: Beckman Research Institute of City of Hope

summary: Colorectal cancer (CRC) remains the major leading cause of cancer-related deaths worldwide. The limitations of current chemotherapeutic drugs in CRC include their toxicity, side effects, and exorbitant costs. To assess these unmet needs in CRC treatment, several naturally occurring compounds, including Curcumin and Andrographis, have gained increasing attention due to their multi-targeted functionality and safety vs. conventional drugs. In the current study, we revealed that a combination of Curcumin and Andrographis exhibited superior anti-tumor effects by inhibiting cell proliferation, invasion, colony formation, and induction of apoptosis. Genomewide transcriptomic expression profiling analysis revealed that Curcumin and Andrographis activated the ferroptosis pathway.

overall_design: Identify differentially expressed genes in Curcumin or Andrographis treated cells compared to non-treated cells

first: Katsuki

last: Miyazaki


title: Injured Mus and Acomys ear tissues at day0 were analyzed using 10X single-cell rna-seq

status: Public on Jan 23 2023

city: Cincinnati

first: Mike

last: Adam

state: Ohio

address: 240 Albert Sabin Way

department: CBDI

institute: Cincinnati Children's Hospital Research Foundation

summary: Macrophages play an essential role in tissue regeneration. However, the ability to dissect the role of macrophages in regeneration from their role in wound healing with scar has been hampered by a lack of comparative systems. In this study, we use a mammalian model of tissue regeneration and scar formation to contrast the role of macrophages in both wound healing paradigms. The African Spiny mouse (A. cahirinus) can regenerate tissue of the external ear pinnae after 4mm biopsy punch. The common lab mouse (M. musculus) forms a scar after the same injury. We test the potential of bone marrow derived macrophages from both species to activate local ear fibroblasts and find macrophages from A. cahirinus are able to induce a matrix turnover phenotype in fibroblasts from both species. We identify growth factors and cytokines specific to macrophages derived from A. cahirinus, and using single cell RNAseq and screening with these factors, we identify populations of macrophages unique to a regenerating injury compared to scar forming injury. Finally we test how macrophage populations change over time in a regenerating injury and how they differ from each stage in a scar forming system

sample_organism:
Acomys cahirinus
Mus musculus

platform_organism:
Acomys cahirinus
Mus musculus

overall_design: Injured Mus and Acomys ear tissues were analyzed using 10X single-cell rna-seq

first: Ashley

last: Seifert

first: Steve

last: Potter


title: Improving anti-tumor efficacy of low-dose Vincristine in rhabdomyosarcoma via the combination therapy with FOXM1 inhibitor RCM1.

status: Public on Jan 18 2023

first: Jose

last: Gomez-Arroyo

address: 3333 Burnet Ave

department: Pulmonary and Critical Care Medicine

institute: University of Cincinnati

summary: Rhabdomyosarcoma (RMS) is a highly metastatic soft-tissue sarcoma that often develops resistance to current therapies, including vincristine. Since the existing treatments have not significantly improved survival, there is a critical need for new therapeutic approaches for RMS patients. FOXM1, a known oncogene, is highly expressed in RMS, and is associated with the worst prognosis in RMS patients. In the present study, we found that the combination treatment with specific FOXM1 inhibitor RCM1 and low doses of vincristine is more effective in increasing apoptosis and decreasing RMS cell proliferation in vitro compared to single drugs alone. Since RCM1 is highly hydrophobic, we developed innovative nanoparticle delivery system containing poly-beta-amino-esters and folic acid (NPFA), which efficiently delivers RCM1 to mouse RMS tumors in vivo. The combination of low doses of vincristine together with intravenous administration of NPFA nanoparticles containing RCM1 effectively reduced RMS tumor volumes, increased tumor cell death and decreased tumor cell proliferation in RMS tumors compared to RCM1 or vincristine alone. The combination therapy was non-toxic as demonstrated by liver metabolic panels using peripheral blood serum. Using RNA-seq of dissected RMS tumors, we identified Chac1 as a uniquely downregulated gene after the combination treatment. Knockdown of Chac1 in RMS cells in vitro recapitulated the effects of the combination therapy. Altogether, combination treatment with low doses of vincristine and nanoparticle delivery of FOXM1 inhibitor RCM1 in a pre-clinical model of RMS has superior anti-tumor effects and decreases CHAC1 while reducing vincristine toxicity

overall_design: Dissected Rd76-9 tumors from control (treated with empty nanoparticle and saline), 0.25mg/kg VCR, 8μg RCM1 and 0.25mg/kg VCR + 8μg RCM1 groups were snap frozen in liquid nitrogen 16 days post tumor inoculation. RNA was extracted from bulk tumor samples and were sent for sequencing.

first: Johnny

last: Donovan

first: Zicheng

last: Deng

first: Fenghua

last: Bian

first: Samriddhi

last: Shukla

first: Donglu

last: Shi

first: Vladimir

middle: V

last: Kalinichenko

first: Tanya

last: Kalin


title: Genome-wide transcriptome analysis of Epiblast Like Cells (EpiLC), early Primordial Germ Cells (PGCLCd3) and late Primordial Germ Cells (PGCLCd5) with WT or EsrrbKO background

first: Margherita

last: Mutarelli

summary: We report the application of genome-wide RNA-sequencing analysis for WT or EsrrbKO mES cells after transition towards EpiLC and subsequent differentiation in early (d3) or late (d5) PGCLC. We find that formative early and formative late gene signatures were significantly reduced in EsrrbKO EpiLC compared to WT EpiLC. Furthermore, both early and late PGC gene sets were significantly downregulated in EsrrbKO PGCLC, while  somatic markers were robustly increased. This indicates that the developmental program is not properly activated during transition towards PGCLC in EsrrbKO cells.

overall_design: mRNA profiles of WT or EsrrbKO mES during transition towards EpiLC and subsiquent differentiation in early (d3) or late (d5) PGCLC.

first: Valentina

last: Carlini

first: Jamie

last: Hackett


title: Loss of H3K9 tri-methylation alters mitotic chromosome compaction and transcription factor retention during mitosis

status: Public on Jan 17 2023

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

country: United Kingdom

institute: MRC London Institute of Medical Sciences

summary: Recent studies have shown that repressive chromatin machinery, including DNA methyltransferases (DNMTs) and Polycomb Repressor Complexes (PRCs), bind to chromosomes throughout mitosis and their depletion results in increased chromosome size. Enzymes that catalyse H3K9 methylation, such as Suv39h1, Suv39h2, G9a, GLP are also retained by mitotic chromosomes. Surprisingly however, mutants lacking H3K9me3 have unusually small and compact mitotic chromosomes that are associated with increased H3S10ph and H3K27me3 levels. Despite these differences, chromatin accessibility, as measured by ATAC-seq, was broadly similar between genotypes. Chromosome size and centromere compaction in these mutants was rescued by providing exogenous Suv39h1, or inhibiting Ezh2 activity. Quantitative proteomic comparisons of native mitotic chromosomes isolated from wildtype versus Suv39h1,2 double null ESCs revealed that H3K9me3 was essential for the efficient retention of bookmarking factors such as Esrrb. These results highlight an unexpected role for repressive heterochromatin domains in preserving transcription factor binding through mitosis, and underscore the importance of H3K9me3 for sustaining chromosome architecture and epigenetic memory during cell division.

overall_design: ATAC-seq was performed in duplicate on wild-type (WT26) and Suv39h dn (DN57) mouse embryonic stem cells (ESCs) for asynchronous cells, mitotic cells and flow-cytometry purified mitotic chromosomes.

first: Andrew

last: Dimond

first: Dounia

last: Djeghloul

first: Yi-Fang

last: Wang

first: Amanda

middle: G

last: Fisher


title: MME+ fibro-adipogenic progenitors are the dominant adipogenic population during fatty infiltration in human skeletal muscle

city: Zurich

first: Genome

last: Informatics

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich (FGCZ)

country: Switzerland

institute: ETH ZURICH / University of Zurich

summary: Fatty infiltration, the ectopic deposition of adipose tissue within skeletal muscle, is mediated via the adipogenic differentiation of fibro-adipogenic progenitors (FAPs). We used single-nuclei and single-cell RNA sequencing to characterize FAP heterogeneity in patients with fatty infiltration. We identified an MME+ FAP subpopulation which, based on ex vivo characterization as well as transplantation experiments, exhibits high adipogenic potential. MME+ FAPs are characterized by low activity of WNT, known to control adipogenic commitment, and are refractory to the inhibitory role of WNT activators. Using preclinical models for muscle damage versus fatty infiltration, we show that many MME+ FAPs undergo apoptosis during muscle regeneration and differentiate into adipocytes under pathological conditions, leading to their depletion. Finally, we utilized the varying fat infiltration levels in human hip muscles to show the depletion of MME+ FAPs in fatty infiltrated human muscle. Altogether, we have identified the dominant adipogenic FAP subpopulation in skeletal muscle.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: For bulk RNAseq, mRNA from sorted skeletal muscle FAPs (PDGFRA/eGFP+ MME+/-). 5 biological replicates per group. For human sn- and scRNA-seq, we harvested muscles from fatty (GM) and non-fatty infiltrated (RF) muscles. One sample per condition (scRNAseq), and pooled muscles (n=5) in 2 technical replicates (snRNAseq). For mouse scRNAseq, we harvested muscles from WT mouse. One biological sample.

first: Gillian

last: Fitzgerald

first: Guillermo

last: Turiel

first: Tatiane

last: Gorski

first: Ines

last: Soro-Arnaiz

first: Jing

last: Zhang

first: Nicola

middle: C

last: Casartelli

first: Evi

last: Masschelein

last: Maffiuleti

first: Reto

last: Sutter

first: Michael

last: Leunig

first: Jean

last: Farup

first: Katrien

last: DeBock


title: Congenital heart disease associated bronchopulmonary dysplasia and its underlying mechanisms

first: Debao

last: Li

address: No. 1678 Dongfang Road, Tangqiao Street

institute: Shanghai Children's Medical Center

summary: We reported the RNAseq analyses of lungs tissues in neonatal SD rats with or without reduced pulmonary blood flow(RPF). RPF was induced by causing the supravalvular pulmonary stenosis through pulmonary artery banding within 24 hours postnatally (P1). RNAseq analyses of the upper lobe of the right lung tissues was generated at P14 from 5 sham-operated rats and 5 PAB rats. The results revealed that there were 2013 differentially expressed genes between PAB and sham group at P7, among which 936 were upregulated and 1077 were downregulated. GO and KEGG pathway analysis of downregulation of DEGs indicated that abundantly enriched terms of cell migration and metabolism.

overall_design: RNAseq analyses of the upper lobe of the right lungs tissues in PAB and sham-operated neonatal rats.

first: Lijun

last: Chen

first: Lincai

last: Ye

first: Qi

last: Sun


title: Identification of TEAD4 target genes in the colorectal cancer cells

city: shanghai

first: Zhenyu

last: Huang

address: NO. 1665 kongjiang RD.

institute: Colorectal Cancer Research Center of Shanghai

summary: Transcription factor TEAD4 is overexpressed in CRC. To explore the potential new pro-tumorigenic function of TEAD4 in CRC, we performed RNA-seq analysis to identify new target genes of TEAD4 in HCT116 and SW620 cells

overall_design: RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.

first: Yu

last: Tong


title: CRISPR-Cas9 editing of the TNPO3 mutation causing Limb-Girdle Muscular Dystrophy type D2 in a muscle cell model

city: Burjassot

first: Ruben

last: Artero

state: Valencia

address: C/ Doctor Moliner, 50

department: Genetics

institute: Universidad de Valencia

summary: A single nucleotide deletion in the stop codon of the nuclear import receptor transportin 3 (TNPO3), also involved in HIV infection, causes the ultrarare autosomal dominant disease limb-girdle muscular dystrophy D2 (LGMDD2) by adding 15 extra amino acids to the wild-type protein. Here, we generated the first patient-derived in vitro model of LGMDD2 as an immortalized myoblast cell line carrying the TNPO3 mutation. The cell model reproduced critical molecular alterations observed in patients, including TNPO3 overexpression, defects in terminal muscle markers, and autophagy overactivation. Correction of the LGMDD2 mutation by means of CRISPR-Cas9 edition produced a significant reversion of the pathological phenotypes in edited cells, including a complete absence of mutant TNPO3 protein using a polyclonal antibody specific against the abnormal 15 amino acid peptide. Transcriptomic analysis identified that 15% of the transcriptome was differentially expressed in model myotubes. CRISPR-Cas9 corrected cells showed that 44% of the alterations were rescued towards normal levels, including pathways involved in cell signalling and extracellular matrix structure. Globally, this work provides proof-of-concept of the potential of CRISPR-Cas9-mediated gene editing of TNPO3 as a therapeutic approach and describes critical reagents in LGMDD2 research.

overall_design: RNA-seq comparison between control, LGMDD2 and LGMDD2 treated with CRISPR samples

first: Águeda

last: Blázquez-Bernal

first: Javier

last: Poyatos-Garcia

first: Marta

last: Selva-Giménez

first: Ariadna

last: Bargiela

first: Jorge

last: Espinosa-Espinosa

first: Rafael

middle: P

last: Vázquez-Manrique

first: Anne

last: Bigot

first: Juan

last: Vilchez


title: Response to oxaliplatin in CCD-18Co

status: Public on Jan 16 2023

city: Barcelona

first: Alexandre

last: CALON

address: Dr. Aiguader, 88

institute: Hospital del Mar Medical Research Institute (IMIM)

summary: We obtained the gene expression signature from oxaliplatin-treated fibroblasts and quantified the association of oxaliplatin-activated fibroblasts with disease progression in colorectal cancer.

overall_design: CCD-18Co cells were treated with oxaliplatin (100 µM) for 6 days. Gene expression profiles from treated and control cells were measured in duplicate using Affymetrix PrimeView human gene expression arrays.

last: Calon


title: Response to TGF-Beta in CCD-18Co

summary: We obtained the gene expression signature from TGF-beta-treated fibroblasts and quantified the association of TGF-beta-activated fibroblasts with disease progression in colorectal cancer.

overall_design: CCD-18Co cells were treated with recombinant human TGF-β1 (5ng/mL) for 8 hours in DMEM supplemented with 0.2% FBS. Gene expression profiles from treated and control cells were measured in duplicate using Affymetrix HT_HG-U133_Plus_PM human gene expression arrays.


title: A genome-wide screen in macrophages defines host genes regulating the uptake of Mycobacterium abscessus

status: Public on Jan 13 2023

city: East Lansing

first: Andrew

last: Olive

address: 567 Wilson Rd

department: Microbiology and Molecular Genetics

institute: Michigan State University

summary: The initial interactions between a host cell and a pathogen can dictate disease outcomes and are important targets for host-directed therapies. Mycobacterium abscessus (Mab) is a highly antibiotic resistant, rapidly growing non-tuberculous mycobacterium that infects patients with chronic lung diseases, like cystic fibrosis. Mab can infect host immune cells, such as macrophages, which contribute to its pathogenesis. However, our understanding of host genes that modulate the initial host-Mab interactions remains unclear. Here, we developed a functional genetic approach by coupling a Mab fluorescent reporter with a genome-wide knockout library in murine macrophages. We used this approach to conduct a forward genetic screen to uncover host genes that contribute to the uptake of Mab by macrophages. We identified known regulators of phagocytosis, such as the integrin Itgb2, and uncovered a key requirement for glycosaminoglycan (sGAG) synthesis for macrophages to efficiently bind to Mab. CRISPR-Cas9 targeting of three key sGAG biosynthesis regulators, UGDH, B4GALT7 and B3GAT3 resulted in reduced uptake of both smooth and rough Mab variants by macrophages. Mechanistic studies suggest that sGAGs function upstream of pathogen engulfment and are required for uptake of Mab but not Escherichia coli or latex beads. Further investigation found that the loss of sGAGs reduces the surface expression, but not the mRNA expression, of key integrins, suggesting a key role for sGAGs in modulating surface receptor availability. Together these studies globally defined and characterized important regulators of macrophage-Mab interactions and are a first step better understand important host genes that contribute to Mab pathogenesis and disease.

overall_design: Genome-wide CRISPR knockout screen in murine iBMDMs for regulators of M. abscessus uptake

first: Haleigh

middle: N

last: Gilliland


title: Genome-wide maps of ESRRB binding in pluripotent (2iL) and differentiated (48h, 96h) mES cells

first: Margherita

last: Mutarelli

summary: We report the application of sequencing technology for profiling of genome-wide ESRRB binding in mouse ES cells. We generated genome-wide chromatin-state maps of mouse embryonic stem cells maintained in pluripotent state (2iL) and differentiated for 48 and 96 hours (48 and 96). We find that the large majority of ESRRB binding occurs in 2iL and at 48 hours and that several formative genes promoters are bound by ESRRB in 2iL and at 48h. Moreover ESRRB peaks on naïve genes (e.g. Tfcp2l1, Nanog) decrease as soon as cells start differentiating while peaks on formative genes are present in 2iL and the signal is maintained (or increased) at 48 hours, further endorsing the concept of Esrrb as a direct activator of the formative gene program during the Reversible phase.

overall_design: Examination of ESRRB binding in pluripotent and differentiated mES cells

first: Elena

last: Carbognin

first: Marcella

last: Cesana

first: Francesco

last: Panariello


title: NANOGP1, a tandem duplicate of NANOG, exhibits partial functional conservation in human naïve pluripotent stem cells

first: Simon

middle: Richard

last: Andrews

state: Cambs

address: Babraham Research Campus

department: Science Services

institute: The Babraham Institute

summary: Gene duplication events are important drivers of evolution by providing genetic material for new gene functions. They also create opportunities for diverse developmental strategies to emerge between species. To study the contribution of duplicated genes to human early development, we examined the evolution and function of NANOGP1, a tandem duplicate of the key transcription factor NANOG. We found that NANOGP1 and NANOG have overlapping but distinct expression profiles, with high NANOGP1 expression restricted to early epiblast cells and naïve-state pluripotent stem cells. Sequence analysis and epitope-tagging of the endogenous locus revealed that NANOGP1 is protein-coding with an intact homeobox domain. NANOGP1 has been retained only in great apes, whereas Old World monkeys have disabled the gene in different ways including point mutations in the homeodomain. NANOGP1 is a strong inducer of naïve pluripotency, however, unlike NANOG, it is not required to maintain the undifferentiated status of human naïve pluripotent cells. By retaining expression, sequence and partial functional conservation with its ancestral copy, NANOGP1 exemplifies how gene duplication and subfunctionalisation can contribute to transcription factor activity in human pluripotency and development.

overall_design: We performed RNA-seq for two different lines (NANOG knockdown and NANOGP1 knockdown) at four to five timepoints with three biological replicates.

first: Katsiaryna

last: Maskalenka

first: Gökberk

last: Alagöz

first: Felix

last: Krueger

first: Joshua

last: Wright

first: Maria

last: Rostovskaya

first: Asif

last: Nakhuda

first: Adam

last: Bendall

first: Aylwyn

last: Scally

first: Peter

last: Rugg-Gunn


title: Pan-cancer analysis revealed H3K4me1 at bivalent promoters premarks DNA hypermethylation during tumor development and identified the regulatory role of DNA methylation in relation to histone modifications [RRBS]

status: Public on Jan 12 2023

city: Shenzhen

first: Cao

last: Qiang

address: No. 66 Gongchang Road, Guangming District, Shenzhen

department: School of Medicine

institute: Sun Yat-sen University

summary:
Background: DNA hypermethylation at promoter CpG islands (CGIs) is a hallmark of cancers and could lead to dysregulation of gene expression in the development of cancers, however, its dynamics and regulatory mechanisms remain elusive. Bivalent genes, that direct development and differentiation of stem cells, are found to be frequent targets of hypermethylation in cancers.

Results: Here we performed comprehensive analysis across multiple cancer types and identified that the decrease in H3K4me1 levels coincides with DNA hypermethylation at the bivalent promoter CGIs during tumorigenesis. Removal of DNA hypermethylation leads to increment of H3K4me1 at promoter CGIs with preference for bivalent genes. Nevertheless, the alteration of H3K4me1 by overexpressing or knockout LSD1, the demethylase of H3K4, doesn't change the level or pattern of DNA methylation. Moreover, LSD1 was found to regulate the expression of a bivalent gene OVOL2 to promote tumorigenesis. Knockdown of OVOL2 in LSD1 knockout HCT116 cells restored the cancer cell phenotype.

Conclusion: In summary, our work identified a universal indicator that can pre-mark DNA hypermethylation in cancer cells, and dissected the interplay between H3K4me1 and DNA hypermethylation in detail. Current study also reveals a novel mechanism underlying the oncogenic role of LSD1, providing clues for cancer therapies.

overall_design: HCT116 and NCM460

first: Yang

last: Lu

first: Qiang

last: Cao

first: Xuan

last: Jiang

first: Xin

last: Li


title: Pan-cancer analysis revealed H3K4me1 at bivalent promoters premarks DNA hypermethylation during tumor development and identified the regulatory role of DNA methylation in relation to histone modifications[RNA-seq]

overall_design: Human colorectal carcinoma HCT116 cell line WT and LSD1 knockout


title: Pan-cancer analysis revealed H3K4me1 at bivalent promoters premarks DNA hypermethylation during tumor development and identified the regulatory role of DNA methylation in relation to histone modifications [ChIP-seq]

overall_design: we performed comprehensive analysis across multiple cancer types and identified that DNA hypermethylation in cancers can be predicated by enriched unimodal pattern of Histone H3 lysine 4 mono-methylation (H3K4me1) in corresponding normal tissues.


title: METTL16 drives leukemogenesis and leukemia stem cell self-renewal by reprogramming BCAA metabolism

first: Jianjun

last: Chen

state: CA

department: Systems Biology

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

overall_design: Refer to individual Series


title: Pan-cancer analysis revealed H3K4me1 at bivalent promoters premarks DNA hypermethylation during tumor development and identified the regulatory role of DNA methylation in relation to histone modifications

status: Public on Jan 11 2023


title: LncRNAs and mRNAs of sugar beet in response to drought stress

city: Taigu

first: Chunlei

last: Zou

address: No.1 Mingxian Road

institute: Shanxi Agricultural University

summary: We analyzed lncRNAs and mRNAs from sugar beet leaves under water control treatment using high-throughput sequencing technology and bioinformatic approaches to explore the genome-wide quantity of lncRNAs and mRNAs and their potential function in the regulation of drought responses.

overall_design: Sugar beet seedlings were divided into two groups: (1) well-watered (CK), (2) drought stress (DR).


title: Elements of divergence in germline determination in closely related sea urchin species

status: Public on Jan 19 2023

city: Providence

first: Nathalie

last: Oulhen

state: RI

address: 185 meeting street

institute: Brown university

summary: Evolutionary transitions enable the wide diversity in life histories of plants and animals. This is particularly germane in the development of the germline in which fitness is a direct readout of evolutionary change. Here, we focused on two distinct sea urchin species who shared a common ancestor 50 million years ago. Even though they both rely on inherited mechanisms to specify their germ line, the integration of stage-matched scRNA seq datasets from these two sea urchins revealed, amongst others, a broader expression of Nanos2 in Lytechinus variegatus (Lv) compared to Strongylocentrotus purpuratus (Sp). In Sp, Nanos2 mRNA expression is highly restricted to the PGCs by a lability element in its 3’UTR. This element is lacking in Lv Nanos2, explaining how this mRNA more broadly accumulates in the Lv embryos. We discovered that the Lv Nanos2 3’UTR instead leads to a germline specific translation of the protein. The results emphasize that regulatory mechanisms resulting in germline diversity rely less on transcriptional regulation and more on post-transcriptional and post-translational restrictions of key gene products, such as Nanos2.

overall_design: Developmental time points in the sea urchin Lytechinus variegatus and integration with the sea urchin Strongylocentrotus purpuratus dataset

first: Morita

last: Shumpei

first: Oulhen

last: Nathalie

first: Foster

last: Stephany

first: Wessel

last: Gary


title: Convergent coexpression of autism associated genes suggests some novel risk genes may not be detectable in large-scale genetic studies

status: Public on Jan 10 2023

city: Boston

first: Serkan

last: Erdin

address: 185 Cambridge Street

department: Center for Genomic Medicine

institute: Massachusetts General Hospital

summary: Autism spectrum disorder (ASD) is a highly heritable neurodevelopmental disorder characterized by deficits in social interactions and communication. Protein function altering variants in many genes have been shown to contribute to ASD risk; however, understanding the biological convergence across so many genes has been difficult and genetic studies depending on presence of deleterious variation may be limited in implicating highly intolerant genes with shorter coding sequences. Here, we demonstrate that coexpression patterns from human post-mortem brain samples (N = 993) are significantly correlated with the transcriptional consequences of CRISPR perturbations (gene editing, interference and activation) in human neurons (N = 17). Across 71 ASD risk genes, there is significant tissue-specific transcriptional convergence that implicates synaptic pathways. Tissue specific convergence of risk genes is a generalizable phenomenon, shown additionally in schizophrenia (brain) and atrial fibrillation (heart). The degree of this convergence in ASD is significantly correlated with the level of association to ASD from sequencing studies (rho = -0.32, P = 3.03 ×10−65) as well as differential expression in post-mortem ASD brains (rho = -0.23, P = 2.39×10−43). After removing all genes statistically associated with ASD, the remaining positively convergent genes showed intolerance to functional mutations, had shorter coding lengths than the ASD genes and were enriched for genes with clinical reports of potential pathogenic contribution to ASD. These results indicate that leveraging convergent coexpression can identify potentially novel risk genes that are unlikely to be discovered by sequencing studies. Overall, this work provides a simple approach to functionally proxy CRISPR perturbation, demonstrates significant context-specific transcriptional convergence among known risk genes of multiple diseases, and proposes novel ASD risk gene candidates.

overall_design: Bulk RNAseq based transcriptomic analyses of  human iPSC-derived induced neuron cell lines with CRISPR/Cas9-edited SCN2A heterozygous deletion and wild-type SCN2A.

first: Calwing

last: Liao

first: Mariana

last: Moyses-Oliveira

first: Celine

middle: E

last: De Esch

first: Riya

last: Bhavsar

first: Xander

last: Nuttle

first: Aiqun

first: Alex

last: Yu

first: Nicholas

middle: D

last: Burt

first: Jack

middle: M

last: Fu

first: Minghui

last: Wang

first: Theodore

last: Morley

first: Lide

last: Han

first: CommonMind

last: Consortium

first: Patrick

last: Dion

first: Guy

last: Rouleau

first: Bin

last: Zhang

first: Kristen

last: Brennand

first: Michael

last: Talkowski

first: Douglas

last: Ruderfer


title: Molecular Profiling Provides Clinical Insights into Targeted and Immunotherapies as well as Prognosis for Colorectal Cancer

status: Public on Jan 09 2023

city: Shanghai

first: Xin

last: Hu

address: 688 Hongqu Road

department: Precision Medicine

institute: Fudan University Shanghai Cancer Center

summary: We performed single cell sequencing to validate the genomic-guided predictive efficacy of immunotherapy and comprehend the interactions between tumor cells and immune-system cells in cases of wtih complete response and progressive disease.

overall_design: Two treatment-naive colorectal cancer patients (one MSI-high/TIB-high and one POLE-mutant/TMB-UH) were recruited and received a single dose of pembrolizumab. Paired endoscopic biopsies of the tumor and adjacent normal tissue were collected for single cell sequencing at baseline and after two courses of neoadjuvant therapy.

first: Linwei

last: Guo

first: Yunjin

first: Chenchen

first: Tian'an


state: --- Select a state ---

address: 270 Dongan Road

summary: Background and aims  Tumor genetic testing is indispensable in the management of primary and advanced colorectal cancer, with one-third of patients progressing despite standard care. We aimed to refine the indications for genomics-guided precision therapy.  Methods  We prospectively sequenced 869 tumors from Chinese patients with colorectal cancer and performed a comprehensive analysis of clinical and genomic profiles. The clinical significance of single mutation and co-occurring events was assessed in metastatic colorectal cancer (mCRC). The tumor immune microenvironment was evaluated by Immunoscore assay and single-cell sequencing.  Results  Single gene somatic mutations in BRAF and RBM10 were associated with shorter progression-free survival (PFS) in treatment-naive mCRC patients (BRAF: hazard ratio [HR] = 2.2 [95% CI, 1.1-4.4]; RBM10: HR= 6.8 [95% CI, 2.6-17.3]), and RBM10 remained a risk factor irrespective of the addition of bevacizumab to the chemotherapy regimens. KRAS mutations coexisting with those in AMER1 or APC were enriched in the metastatic cohort (26.23%), which had poor PFS and did not benefit from bevacizumab. 40 patients (4.6%) carried pathogenic or likely pathogenic germline alterations in the DNA damage repair pathway and 30% of them had double-hit events in the tumor with higher MSI scores. High tumor indel burden with MSI-high suggested a large number of tumor-infiltrating lymphocytes, whereas POLE-mutant with TMB-ultrahigh indicated a relatively quiescent immunophenotype. The heterogeneous genomic-immunological ecosystem was reflected in the divergent antigen presentation, immune checkpoint protein expression and responses of T cells to pembrolizumab treatment.  Conclusion  Integrated analysis of the clinical, genomic, and immunological profiles of colorectal cancer provides insights into prognostic stratification, drug response and potential clinical trials.

overall_design: mRNA sequencing was performed on 12 MSI-high/TIB-high and 6 POLE-mutant/TMB-UH individuals to elucidate the significance of genetic indicators on the immune contexture.


title: Amniotes co-opt intrinsic genetic instability to protect germ-line genome integrity

status: Public on Jan 24 2023

city: Yiwu

first: Jiafei

last: Shen

address: N1 Shangcheng Road

institute: International Institutes of Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine

type: Non-coding RNA profiling by high throughput sequencing

type: Genome variation profiling by high throughput sequencing

summary: We applied high-throughput sequencing on rooster testis samples.

overall_design: High-throughput sequencing data including RNAseq, small-RNA seq and ONT of rooster testis. All sequencing data were sequenced on Illumina platform and Oxford Nanopore Technologies.

first: Yu

middle: H

last: Sun

middle: Z

last: Li


title: Pharmacological inhibition of G9a ameliorates pulmonary vascular remodeling in PAH

status: Public on Jan 20 2023

city: Spring House

first: Vinod

last: Krishna

state: Pennsylvania

address: 1400 McKean Road

institute: Janssen R&D LLC

summary:
Background:Pulmonary arterial hypertension (PAH) is a severe condition characterized by progressive vascular remodeling of small pulmonary arteries (PAs) causing sustained elevation of PA pressure, right ventricular failure and death. Similar to cancer cells, PA smooth muscle cells (PASMCs), which play a key role in pulmonary vascular remodeling, have adopted multiple mechanisms to sustain their survival and proliferation in the presence of stress. The histone methyltransferase G9a has been shown to exert oncogenic effects and to serve as a buffer against an exaggerated transcriptional response. Therefore, we hypothesized that G9a up-regulation in PAH plays a pivotal role in pulmonary vascular remodeling by maintaining the abnormal phenotype of PAH-PASMCs.
Methods: G9alevels were measured in PAs and isolated PASMCs of PAH patients and animal models. Selective G9a pharmacological inhibitors were used in human PAH-PASMCs and in rodent PAH models (i.e.Fawn-Hooded rats and Sugen/Hypoxia-exposed mice).
Results: We present evidence of increased expression of G9a in PASMCs from PAH patients as well as in remodeled PAs from animal models. We found that pharmacological inhibition of G9a activity using BIX01294 and UNC0642significantly reduces the prosurvival and proproliferative potentials of cultured PAH-PASMCs. Using RNA sequencing, further exploration revealed that G9a promotes extracellular matrix production and affords protection against the negative effects of an overactive stress response. Finally, we found that therapeutic treatment with BIX01294 reduced pulmonary vascular remodeling and lowered mean PA pressure in Fawn-Hooded rats. Treatment of Sugen/hypoxia-challenged mice with BIX01294 also improved pulmonary hemodynamics and right ventricular function.
Conclusions:These findings suggest that G9a inhibition may represent a new therapeutic approach in PAH.

overall_design: RNASeq of 3 treated and 5 Vehicle cell lines from PAH samples

first: Charifa

last: Awada

first: Alice

last: Bourgeois

first: Sarah

last: Eve-Lemay

first: Yann

last: Grobs

first: Tetsuro

last: Yokokawa

first: Sandra

last: Breuils-Bonnet

last: Martineau

first: Francois

last: Potus

first: Jey

last: Jeyaseelan

first: Steeve

last: Provencher

first: Sebastien

last: Bonnet

first: Olivier

last: Boucherat


title: Genome-wide effects of enterolactone on gene expression in MCF-7 cells

status: Public on Jan 06 2023

city: Guwahati

first: Anil

middle: Mukund

last: Limaye

state: Assam

address: IIT Guwahati

department: Department of Biosciences and Bioengineering

country: India

institute: Indian Institute of Technology Guwahati

summary: Application of next generation sequencing technology to identify genes modulated by enterolactone in MCF-7 cells

overall_design: MCF-7 cells were treated with 10 µM enterolactone or vehicle (DMSO) for 72 h.

first: Juana

last: Hatwik


title: Cell and sub-compartment specific proteomics reveals astrocyte contributions in a mouse model of OCD

city: Los Angeles

first: Riki

last: Kawaguchi

address: 760 Westwood Plaza, Room 37-420

department: Department of Psychiatry and Neurology Department of Psychiatry

institute: University of California, Los Angeles

summary: We investigated the sub-proteomes of different functional compartments in astrocyte and neurons in the striatum. We compared the proteomes to the cell-specific RNA profiles of neurons and astrocytes from these analyses. We found one gene and protein that was highly expressed in neurons and astrocytes called SAPAP3. Knockout of this gene product results in an OCD-like phenotype in mouse. RNA-seq of astrocytes and bulk RNA-seq analyses of this mouse model revealed very low DEGs.

overall_design: 40 samples from 24 adult mice. Astrocyte RiboTag AAV and Neuron RiboTag AAV was injected into the striatum to extract RNA specifically from astrocytes or neurons. We used wildtype mice and used an OCD mouse model (SAPAP3 KO). After tissue homogenization, RNA was purified from the cleared lysate as the input sample and astrocyte or neuron specific ribosome-associated RNA was immunoprecipitated with a hemagglutinin (HA) tag as the IP sample.

first: Joselyn

last: Soto

first: Yasaman

last: Jami

first: Jakelyn

last: Chacon

first: Blanca

last: Diaz-Castro

first: Stefanie

last: Moye

first: James

last: Wohlschlegel

first: Baljit

last: Khakh


title: microRNA expression in fibroblastic foci within idiopathic pulmonary fibrosis lungs reveals novel disease relevant pathways.

city: Newcastle upon Tyne

first: Laura

last: Sabater

state: Newcastle Upon Tyne

address: 4th Floor, William Leech Building

department: Biosciences institute

institute: Newcastle University

summary: MicroRNAs (miRs) are a class of non-coding RNAs of ~22nt long that play an important role in regulating gene expression at a post-transcriptional level. Aberrant levels of miRs have been associated with profibrotic processes in idiopathic pulmonary fibrosis (IPF). However, the majority of these studies used whole IPF tissue or in vitro monocultures in which fibrosis has been artificially induced. In this study, we used laser microdissection to collect fibroblastic foci (FF), the key pathological lesion in IPF, then isolate miRs and compare their expression levels to those found in whole IPF lung tissue and/or in vitro cultured fibroblast from IPF or normal lungs. Methods – LCM was utilised on formalin embedded IPF tissue to isolate multiple FF and isolate miRs. Libraries were generated and sequenced; data were bioinformatically analysed and Ingenuity Pathway Analysis (IPA) used for integration. Results - Our analysis revealed a total of 49 miRs differentially expressed in FF, of which only 7 were also differentially expressed in in vitro cultured fibroblast. This approach uncovered novel miRs that could be related to IPF. Conclusion - miR expression analyses in LCM isolated FF were able to identify up to 40 miRs not previously described in IPF. Differential expression of these miRs could potentially contribute to IPF development and progression.

overall_design: Differential miRNAs expression was analysed in Fibrotic Foci cut with a Laser Microdissection Microscope from IPF tissue sections, whole IPF tissue sections, isolated fibroblasts from IPF lung and control normal lungs.

first: Jean

middle: B

last: Gossard

first: Inmaculada

last: Hernandez

first: Daniel

last: Rico

first: Andy

last: Blanchard

first: Lee

last: Borthwick

first: Andrew

last: Fisher

first: Fiona

last: Oakley

first: Derek

last: Mann

first: Jelena


title: MeRIP sequencing for CSPC vs CRPC samples

status: Public on Jan 03 2023

city: Tianjin

first: Yang

last: Li

state: Tianjin

address: Pingjiang Road 23th

institute: the Second Hospital of Tianjin Medical University

summary: To investigate if there is a difference of N6-methyladenosine(m6A) modification between castration-resistant prostate cancer (CRPC) and castration-sensitive prostate cancer (CSPC), we collected 30 specimens, including 15 CRPC and 15 CSPC, to perform RNA-seq and MeRIP-seq. All specimens were postoperative tissues and each 5 CRPC or CSPC specimens were mixed into 1 sample to meet the RNA dosage of RNA-seq and MeRIP-seq.

overall_design: 3 CSPC VS 3 CRPC

first: Zhiqun

last: Shang


title: Regulation of endogenous retrovirus-derived regulatory elements by GATA2/3 and MSX2 in human trophoblast stem cells (RNA-seq)

status: Public on Jan 01 2023

city: Bethesda

first: Mingan

last: Sun

state: Maryland

address: Building 6B, 6 Center Drive

department: Eunice Kennedy Shriver National Institute of Child Health and Human Development

institute: National Institute of Health

summary: The placenta is an organ with extraordinary phenotypic diversity in eutherian mammals. Recent evidence suggest that numerous human placental enhancers are evolved from lineage-specific insertions of endogenous retroviruses (ERVs), yet the transcription factors (TFs) underlying their regulation remain largely elusive. Here, by first focusing on MER41, a primate-specific ERV family previously linked to placenta and innate immunity, we uncover the binding motifs of multiple crucial trophoblast TFs (GATA2/3, MSX2, GRHL2) in addition to innate immuninty TFs STAT1 and IRF1. Integration of ChIP-Seq data confirms the binding of GATA2/3 and MSX2 on the majority of MER41-derived enhancers in human trophoblast stem cells (TSCs). Notably, the usb-family composition of MER41-derived enhancers that are active in human TSCs are distinct from those activated  upon interferon stimulation, which is determined by the binding of trophoblast TFs. We further demonstrate that GATA2/3 and MSX2 have prevalent binding on numerous other ERV families – indicating their broad impact on ERV-derived placental enhancers. Functionally, the derepression of many syncytiotrophoblast genes after disruption of MSX2 is likely to be mediated by enhancers derived from ERVs – suggesting ERVs are also important for mediating transcriptional repression in human TSCs. Overall, this study characterized the prevalent binding of GATA2/3, MSX2 and their co-factors on ERV-derived enhancers in human TSCs and provided mechanistic insights into the importance of ERVs in human trophoblast regulatory network.

overall_design: ChIP-Seq (H3K27ac) and RNA-Seq data are generated for human trophoblast stem cells with or without interferon-gamma stimulation, respectively.

first: Cui

last: Du

first: Jing

last: Jiang

first: Yuzhuo

first: Miao

last: Yu

first: Jian

last: Jin

first: Todd

middle: S

last: Macfarlan

first: Bin

last: Cao

first: Ming-an


title: Placental Inflammation Significantly Correlates with Reduced Risk for Retinopathy of Prematurity

city: SLC

first: Leah

last: Owen

state: UT

address: 65 N. Mario Capecchi Dr

department: Ophthalmology

institute: John Moran Eye Center

summary: Retinopathy of prematurity (ROP), a blinding condition affecting preterm infants, accounts for up to 40% of all childhood blindness worldwide. ROP is an interruption of retinal vascular maturation, which is physiologically complete at full term and thus ongoing at the time of preterm birth. Although ROP demonstrates delayed onset following preterm birth, representing a window for therapeutic intervention, we cannot cure or prevent this disease.  The in-utero environment, including placental function, is increasingly recognized for contributions to preterm infant disease risk. Herein, we examine the clinical associations between presence and severity of acute placental inflammation to ROP risk. Using logistic regression, we find a protective relationship between presence and severity of acute placental inflammation and preterm infant development of ROP. This is most significant for infants born in the absence of maternal preeclampsia. Further, we examine the underlying molecular mediators that may inform this protective paradigm. Adopting a candidate approach analyzing proteins with described ROP risk associations, we find that placental HTRA1 and FABP4 protein expression is significantly decreased within placental tissues characterized by acute inflammation. Additionally, HTRA1 and VEGFA demonstrate inverse longitudinal trends within the peripheral circulation for infants born in the presence compared to absence of acute placental inflammation. An agnostic approach, including whole transcriptome and differential methylation placental analysis, identifies novel mediators and pathways that may underly protection. Taken together, these data build on emerging literature showing disparate associations between acute placental inflammation and ROP development within preeclamptic or non-preeclamptic preterm infant populations and identifies novel placental mechanisms that may inform postnatal risk associations in preterm infants.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for human placental tissue relative to retinopathy of prematurity clinical outcomes.

first: Charles

last: Zhang

first: Kinsey

last: Shirer

first: Lara

last: Carroll

first: Blair

last: Wood

first: Kathryn

last: Szczotka

first: Colette

last: Cornia

first: Chris

middle: J

last: Stubben

first: Lakshmi

last: Katikaneni

first: Margaret

last: DeAngelis

first: Jessica

last: Comstock


title: Prions induce an early Arc response in the hippocampus of prion-infected mice

city: La Jolla

first: Christina

last: Sigurdson

address: 9500 Gilman Dr

institute: UC San Diego

summary: Synapse dysfunction and synaptic loss are a central feature of neurodegenerative disorders, including prion disease. The cellular prion protein (PrPC) binds prion, amyloid-β, tau, and α-synuclein oligomers, resulting in the activation of macromolecular complexes and signaling at the post-synapse, yet the initial signaling events are unclear. Here we used a transcriptomic approach focused on the early-stage, prion-infected hippocampus of male wild type mice, and identify immediate early genes, including the synaptic activity response gene, Arc/Arg3.1, as significantly upregulated. In a longitudinal study of the prion-infected hippocampus, Arc/Arg-3.1 protein increased, from early to terminal disease. Notably, metabotropic glutamate receptor levels (mGluR5 dimers) were markedly reduced over time, while phosphorylated AMPA receptors (pGluA1-S845) levels increased. Sporadic Creutzfeldt-Jakob disease (sCJD) post-mortem cortical samples also showed low levels of mGluR5 dimers. Together, these findings suggest that prions trigger a chronic Arc response, an increase in phosphorylated GluA1, and a reduction in mGluR5 receptors beginning in early disease.

overall_design: RNA-seq for prion (22L strain)- or mock-inoculated C57/BL6J male mice at 63 days post inoculation  or 40% in disease progression to terminal disease

first: Daniel

last: Ojeda-Juarez

last: Lawrence

first: Katrin

last: Soldau

first: Donald

last: Pizzo

first: Emily

last: Wheeler

first: Patricia

last: Aguilar-Calvo

first: Helen

last: Khuu

first: Joy

last: Chen

first: Adela

last: Malik

first: Gail

last: Funk

first: Thu

last: Nam

first: Henry

last: Sanchez

first: Michael

last: Geschwind

first: Chengbiao

last: Wu

first: Gene

middle: W

last: Yeo

first: Xu

first: Gentry

last: Patrick


title: Effect of depletion of Ctr9, Pcgf6 and Tbx3 on gene expression in embryonic stem cells(ESCs)

city: Chongqing

first: Chen

last: Zhang

address: 30# Gaotanyan Rd, Shapingba District

institute: Army Medical University

summary: For validating the newly defined PAF, PCGF and TBX3 modules, the major transcriptional factor of each module (Ctr9, Pcgf6 and Tbx3) was knocked down individually by RNAi in a Nanog-GFP reporter ESC line. We then performed gene expression profiling analysis using data obtained from RNA-seq of 4 different cells at one time points.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for ESCs and its KD derivatives (shCtr9, shPcgf6, and shTbx3).

first: Yan

last: Ruan

first: Jiaqi

last: Wang


title: Regulation of endogenous retrovirus-derived regulatory elements by GATA2/3 and MSX2 in human trophoblast stem cells (ChIP-seq)

first: Mingan

last: Sun

first: Cui

last: Du

first: Jing

last: Jiang

first: Yuzhuo

last: Li

first: Miao

last: Yu

first: Jian

last: Jin

first: Todd

last: Macfarlan

first: Bin

last: Cao

first: Ming-an


title: Transcriptome analysis of AoPEX14/17 in nematode-trapping fungus Arthrobotrys oligospora

city: Kunming City, Yunnan Province

first: Liu

last: Qianqian

address: No.2 Cuihu North Road, Wuhua District

institute: Yunnan University

summary: Transcriptomic analysis revealed that differentially expressed genes in the absence of AoPEX14/17 were involved in  TCA cycle, fatty acid degradation, oxidative phosphorylation.

overall_design: Examination of differential genes in the WT and ΔAopex14/17 mutant strains and prediction of multiple cytological processes that may affect trap formation in Arthrobotrys oligospora.

first: Qianqian

last: Liu

first: Jinkui

last: Yang


title: CRISPR deletion of ELAVL1 (HuR) in MIA PaCa-2 in vitro cells and in vivo tumors

city: Portland

first: Grace

middle: Anne

last: McCarthy

state: Oregon

address: 2730 S Moody Ave

department: Department of Surgery

institute: Oregon Health & Science University

summary: To investigate the impact of the mRNA stabilty factor HuR on the pancreatic cancer transcriptome in MIA PaCa-2 in vitro cell line and in vivo tumors at multiple time points of tumor growth

overall_design: CRISPR-mediated deletion of ELAVL1 (HuR) in MIA PaCa-2 PDAC cells. HuR wildtype (WT) or HuR knockout (KO) cells in culture (in vitro) were collected at 70% confuency for RNA extraction. HuR WT and HuR KO orthotopic tumors (in vivo) were harvested 2, 3, and 4 weeks post-injection for RNA extraction.

middle: A

first: Jonathan

middle: R

last: Brody


title: An unbiased AAV-STARR-seq screen revealing the enhancer activity map of genomic regions in the mouse brain in vivo.

city: Mainz

first: Simon

last: Rumpel

state: Rheinland-Pfalz

address: Hanns-Dieter-Hüsch Weg 19

department: Institute of Physiology

country: Germany

institute: Universitätsmedizin Mainz

summary: Enhancers are important cis-regulatory elements controlling cell-type specific expression patterns of genes. Furthermore, combinations of enhancers and minimal promoters are utilized to construct small, artificial promoters for gene delivery vectors. Large-scale functional screening methodology to construct genomic maps of enhancer activities has been successfully established in cultured cell lines, however, not yet applied to terminally differentiated cells and tissues in a living animal. Here, we transposed the Self-Transcribing Active Regulatory Region Sequencing (STARR-seq) technique to the mouse brain using adeno-associated-viruses (AAV) for the delivery of a highly complex screening library tiling entire genomic regions and covering in total 3 Mb of the mouse genome. We identified 483 sequences with enhancer activity, including sequences that were not predicted by DNA accessibility or histone marks. Characterizing the expression patterns of fluorescent reporters controlled by nine candidate sequences, we observed differential expression patterns also in sparse cell types. Together, our study provides an entry point for the unbiased study of enhancer activities in organisms during health and disease.

overall_design: STARR-seq screen performed in vivo in mouse brain with six biological replicates.

first: Ya-Chien

last: Chan

first: Eike

last: Kienle

first: Martin

last: Oti

first: Antonella

last: di Liddo

first: Maria

last: Mendez-Lago

first: Dominik

middle: F

last: Aschauer

first: Manuel

last: Peter

first: Michaela

last: Pagani

first: Cosmas

last: Arnold

first: Andreas

last: Vonderheit

first: Christian

last: Schön

first: Sebastian

last: Kreuz

first: Alexander

last: Stark


title: An IL6-STAT3-MR-FGF21 Axis Mediates Heart-Liver Crosstalk after Myocardial Infarction

first: Jianyong

last: Sun

address: 115 Jinzun Road, Pudong New District

department: Laboratory of Oral Microbiota and Systemic Diseases

institute: Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine

summary: The liver plays a protective role in myocardial infarction (MI). However, very little is known about the mechanisms. Here, we identify mineralocorticoid receptor (MR) as a pivotal nexus that conveys communications between the liver and the heart during MI. On one hand, hepatocyte MR deficiency and MR antagonist spironolactone both improve cardiac repair after MI through regulation on hepatic fibroblast growth factor 21 (FGF21), illustrating an MR/FGF21 axis that underlies the liver-to-heart protection against MI. On the other hand, an upstreaming acute interleukin-6 (IL6) / signal transducer and activator of transcription 3 (STAT3) pathway transmits the heart-to-liver signal to suppress MR expression after MI. Hepatocyte IL6 receptor (IL6R) deficiency and STAT3 deficiency both aggravate cardiac injury through their regulation on the MR/FGF21 axis. Therefore, we have unveiled an IL6/STAT3/MR/FGF21 signaling axis that mediates heart-liver crosstalk during MI. Targeting the signaling axis and the crosstalk may provide novel strategies to treat MI and heart failure.

overall_design: Liver mRNA profiles of wild type and HMRKO mice 1 day after MI or sham operation, and liver mRNA profiles of wild type 12 hours after MI or sham operation

first: Jian-Yong

first: Lin-Jun

last: DU

first: Sheng-Zhong

last: Duan


title: Exosomal miR-128-3p reversed fibrinogen-mediated inhibition of oligodendrocyte progenitor cell differentiation and remyelination after cerebral ischemia by targeting BMP signaling (miRNA-Seq)

status: Public on Dec 31 2022

city: Beijing

first: Huiqing

last: Hou

state: Beijing

address: No.119, South 4th Ring West Road, Fengtai District

department: Neurology

institute: Beijing Tiantan Hospital

summary:
To understand the mechanism by which fibrinogen inhibits OPC differentiation after ischemia and identify the precise target for reversing fibrinogen’s effects, OPCs were used for miRNA sequencing analysis.
We then performed gene expression profiling analysis using data obtained from miRNA-seq.

overall_design: Comparative gene expression profiling analysis of miRNA-seq data for control OPCs and fibrinogen tretment OPCs.


title: A network of small RNAs regulates sporulation initiation in C. difficile

city: Wuerzburg

first: Franziska

last: Faber

state: Bavaria

address: Josef-Schneider-Straße 2

department: Institute for Molecular Infection Biology

institute: University of Wuerzburg

summary: The obligate anaerobic, enteric pathogen Clostridioides difficile persists in the intestinal tract by forming antibiotic resistant endospores that contribute to relapsing and recurrent infections. Despite the importance of sporulation for C. difficile pathogenesis, environmental cues, and molecular mechanisms regulating sporulation initiation remain ill defined. Here, using RIL-seq to capture the Hfq-dependent RNA-RNA interactome, we discovered a network of small RNAs that bind to mRNAs encoding sporulation-related genes. We show that two of these small RNAs, SpoX and SpoY, regulate translation of the master regulator of sporulation, Spo0A, in an opposing manner, which ultimately leads to altered sporulation rates. Infection of antibiotic-treated mice with SpoX and SpoY deletion mutants revealed a global effect on gut colonization and intestinal sporulation. Our work uncovers an elaborate RNA-RNA interactome controlling the physiology and virulence of C. difficile and identifies a complex post-transcriptional layer in the regulation of spore formation in this important human pathogen.

overall_design: RIL-seq was performed to capture the RNA-RNA interactome mediated by the RNA chaperone Hfq in C. difficile

first: Manuela

last: Fuchs

first: Vanessa

last: Lamm-Schmidt

first: Tina

last: Lenče

first: Johannes

last: Sulzer

first: Arne

last: Bublitz

first: Janet

last: Wackenreuter

first: Milan

last: Gerovac

first: Till

last: Strowig


title: Tumor and immune remodeling following radiotherapy in human renal cell carcinoma

city: Buffalo

first: Jianmin

last: Wang

state: NY

address: Elm and Carlton Streets

department: Bioinformatics and Biostatistics

institute: Roswell Park Comprehensive Cancer Center

summary: We performed single-cell analysis of renal cell carcinoma tumors from patients treated with or without radiotherapy to address how treatment shapes the immune compartment and interactions with cancer cells.  We identified increased transition from stem-like T cell populations to effector and exhausted T cells in irradiated tumors.

overall_design: Single cell comparisons of radiotherapy treated resected RCC tumors and nephrectomy only controls.

first: Jacky

last: Chow

first: Thomas

last: Schwaab

first: Scott

last: Abrams

first: Anurag

last: Singh

first: Jason

last: Muhitch


title: The endogenous repertoire harbors self-reactive CD4+ T cell clones that adopt a T follicular helper-like phenotype at steady state

city: Chicago

first: Peter

last: Savage

state: IL

department: Pathology

institute: University of Chicago

summary: The T cell repertoire of healthy mice and humans harbors self-reactive CD4+ conventional T (Tconv) cells capable of inducing autoimmunity. Using T cell receptor (TCR) profiling paired with in vivo clonal analysis of T cell differentiation, we identified Tconv cell clones that are recurrently enriched in non-lymphoid organs following ablation of Foxp3+ regulatory T cells. A subset of these clones were highly proliferative in the lymphoid organs at steady state and exhibited overt reactivity to self-ligands displayed by dendritic cells, yet were not purged by clonal deletion. These clones spontaneously adopted numerous hallmarks of T follicular helper (Tfh) cells, including expression of Bcl6 and PD-1, yet failed to produce common effector cytokines at baseline. The homeostasis of polyclonal Tconv cells displaying similar features was critically dependent on B cells. Our work identifies a naturally occurring population of self-reactive Tfh-like cells and delineates a previously unappreciated fate for self-specific Tconv cells.

overall_design: Examination of differential gene expression by 2 TCR "retrogenic" CD4+ T cell clones. Cells of interest were FACS sorted from pooled spleen and lymph nodes of C57BL/6J mice that received bone marrow progenitors retrovirally transduced with a TCRa expression construct.

first: Victoria

last: Lee

first: Donald

last: Rodriguez

first: Sharon

last: Zeng

first: Jaime

middle: L

last: Chao

first: Matthew

middle: T

last: Walker

first: Christine

last: Miller

first: David

last: Klawon

first: Mary

last: Schoenbach

first: Junting

last: Ai

first: Domenick

last: Kennedy

first: Mark

last: Maienschein-Cline

first: Nicholas

last: Socci

first: Marcus

last: Clark


title: Exosomal miR-128-3p reversed fibrinogen-mediated inhibition of oligodendrocyte progenitor cell differentiation and remyelination after cerebral ischemia by targeting BMP signaling

first: Huiqing

last: Hou

summary: To understand the mechanism by which fibrinogen inhibits OPC differentiation after ischemia and identify the precise target for reversing fibrinogen’s effects, OPCs were used for mRNA sequencing analysis.

overall_design:
We then performed gene expression profiling analysis using data obtained from RNA-seq.
Comparative gene expression profiling analysis of RNA-seq data for control OPCs and fibrinogen tretment OPCs.


title: H3K27me3 demethylases maintain the transcriptional and epigenomic landscape of the intestinal epithelium.

city: Philadelphia

first: Klaus

last: Kaestner

state: PA

address: University of Pennsylvania, 12-126 Smilow Center for Translational Research, 3400 Civic Center Boulevard

department: Department of Genetics and Institute for Diabetes Obesity and Metabolism, Perelman School of Medicine

institute: University of Pennsylvania

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

overall_design: Refer to individual Series


title: H3K27me3 demethylases maintain the transcriptional and epigenomic landscape of the intestinal epithelium [CHIP-seq]

summary:
To determine the contribution of H3K27me3 demethylases to intestinal homeostasis, an inducible mouse model was used to simultaneously ablate Kdm6a and Kdm6b expression from the intestinal epithelium.
We then performed RNA-Seq gene expression analysis at two timepoints (7 days and 5 months) following induction of Kdm6a and Kdm6b ablation. Differential H3K27me3 regions were also identified using ChIP-Seq at one time point (7 days) following gene ablation.

overall_design: Chromatin-immunoprecipitation followed by sequencing (ChIP-Seq) for H3K27me3 in crypt intestinal epithelial cells collected from control and "double knock out" ("DKO") samples seven days after induction of Kdm6a and Kdm6b ablation

first: Hannah

last: Kolev

first: Elisabetta

last: Manduchi


title: Neuronal HLH-30/TFEB modulates muscle mitochondrial fragmentation to improve thermoresistance in C. elegans

city: Providence

first: Louis

last: Lapierre

address: 185 Meeting St.

institute: Brown

summary: RNA-seq performed for studying transcriptomic changesmodulated by neuronal HLH-30 during heat stress

overall_design: Comparison of transcript expression between Day 1 animals incubated at 20C or 37C


title: Transcriptomic data of Bevacizumab-adapted colorectal adenocarcinoma cells HCT116

status: Public on Jan 02 2023

city: Firenze

first: Annarosa

last: Arcangeli

state: FI

address: Viale Morgagni 50

institute: University of Firenze

summary: Determination of the ion channel and transporters gene expression profile of  Bevacizumab-adapted colorectal adenocarcinoma cells HCT116

overall_design: Gene expression of Bevacizumab-adapted colorectal adenocarcinoma cells HCT116. It has been compared with that of WT HCT116

first: Elena

last: Lastraioli

first: Tiziano

last: Lottini

first: Cesare

last: Sala

first: Federico

last: Ruffinatti

first: Luca

last: Visentin


title: Genetic and environmental contribution to DNA methylation in intercross populations in Arabiodopsis thaliana

city: Vienna

first: Rahul

last: Pisupati

address: Dr. Bohrgasse 3

institute: Gregor Mendel Institute

summary: DNA methylation is one of the important epigenetic marks conserved across both plants and animals. Recent work in Arabidopsis thaliana has demonstrated the existence of large geographic variation in DNA methylation, which must reflect genetic differences and/or an epigenetic memory of local environments. Here we investigate the cause of these differences in a genetic cross between a southern Swedish line with low DNA methylation and a northern Swedish line with high DNA methylation,  carried out at two different temperatures. Using bisulfite-sequencing data with nucleotide-level resolution on hundreds of individuals, we find genetic and environmental factors regulating DNA methylation variation.

overall_design: F2 intercross design. Plants were grown on soil at 4C and 16C

first: Magnus

last: Nordborg


title: Galectin-1 regulates expression and alternative splicing of angiogenic genes by interacting with their RNAs in HUVECs

status: Public on Dec 23 2022

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

summary: Background: Angiogenesis is an essential step for tissue development and its dysregulation is associated with various diseases, including moyamoya disease. Among the regulators of angiogenesis, galectin-1 encoded by LGALS1, plays essential roles, but the underlying mechanisms need to be further expounded. In this study, we systematically investigated the potential targets of galectin-1 by silencing LGALS1 (siLGALS1) in human umbilical vein endothelial cells (HUVECs) and performing whole transcriptome sequencing (RNA-seq) experiments. We also integrated galectin-1-interacting RNA data to explore how galectin-1 regulates gene expression and alternative splicing.   Results: By systematical analysis, we found siLGALS1 treatment significantly regulated 1451 differentially expressed genes (DEGs), including 604 up-regulated DEGs and 847 down-regulated DEGs. The down-regulated DEGs were significantly enriched in angiogenesis and inflammatory response pathways. The involved genes included CCL2, GJA5, CALCRL, ACKR3, HEY1, AQP1, CD34, ECM1, RAMP2, and SELP, which were also validated by RT-qPCR experiment. We also analyzed the dysregulated alternative splicing (AS) profile by siLGALS1, and found siLGALS1 had obvious bias for dysregulated AS types, preferring to promote exon skipping and intron retention, and inhibit cassette exon events. Interestingly, we found the regulated AS genes (RASGs) were enriched in focal adhesion and VEGF signaling pathway, which were highly related to angiogenesis. Finally, we found hundreds of RASGs were also bound by galectin-1 using the published iRIP-seq data of galectin-1, including RASGs from angiogenesis pathway.   Conclusions: In summary, our results demonstrated that galectin-1 could regulate angiogenesis-related genes at transcriptional and post-transcriptional levels, which is associated its RNA binding ability in HUVECs. The discovery extends our understanding on the functions and molecular mechanisms of galectin-1 during the development of angiogenesis, which could be served as a therapeutic option in anti-angiogenic treatment in future.

overall_design: We silenced LGALS1 expression in human umbilical vein endothelial cells (HUVECs) in this study, and then performed whole transcriptome sequencing experiment (RNA-seq) to extensively explore the regulated expression and alternative splicing levels.

first: Jiajun

last: Wei

first: Yunfei

last: Wu

first: Yue

last: Sun


title: Temporal single-cell transcriptomic profiling of cardiac differentiation in human induced pluripotent stem cells with NOTCH1 mutations

status: Public on Dec 21 2022

city: Columbus

first: Cankun

last: Wang

state: OH

address: 281 W Lane Ave, Columbus, OH 43210

institute: The Ohio State University Wexner Medical Center

summary: Pathological variants in NOTCH1 have been implicated in multiple types of congenital heart defects including bicuspid aortic valve and hypoplastic left heart syndrome (HLHS). To probe how NOTCH1 deficiency affects cardiac development, we generated homozygous NOTCH1 knockout (N1KO) human induced pluripotent stem cells (iPSCs). We then ran single-cell RNA-seq to temporally profile transcriptomic changes during cardiac differentiation in wild type (WT) and N1KO iPSCs. We collected differentiating cells at multiple time points corresponding to different development stages, i.e., Day 0 (D0: pluripotent stem cell), D2 (mesoderm), D5 (cardiac mesoderm), D10 (cardiac progenitor), D14 (early cardiomyocyte), and D30 (fetal cardiomyocyte). Single-cell transcriptomics analysis reveals that NOTCH1 disruption impairs human ventricular cardiomyocyte differentiation and proliferation through balancing cell fate determination of cardiac mesoderm toward the first heart field, second heart field, and epicardial lineages.

overall_design: Single-cell transcriptomic analysis of differentiating cells collected at different time points (D0, D2, D5, D10, D14 and D30) during cardiac differentiation of WT and N1KO human iPSCs.

first: Ming-Tao

last: Zhao

first: Shiqiao

last: Ye


title: A member of transcription/export complex (TREX), THOC5 controls elongation rate by recruiting CDK12.

city: Hannover

first: Doan Duy Hai

last: Tran

state: Niedersachsen

address: Carl-Neubergsstr. 1

department: Institut of physiological Chemistry

institute: Hannover Medical School

summary: THOC5, a member of the THO complex that is a subcomplex of Transcription/export complex (TREX) 1, is essential for 3´processing of slow kinetics IEGs, and for export of only a subset of genes. Applying nanopore mRNA-sequence technology, we show here that upon depletion of THOC5, 50% of mRNAs showed alteration of 3´end cleavage sites. Moreover, polymerase-II (Pol II)-CHIP-sequencing data reveals that upon depletion of THOC5 Pol II density was increased at gene body and 3´UTR.  THOC5 is recruited near to Pol II high density sites except promotor regions, suggesting that THOC5 is involved in transcription elongation. Indeed, 385 THOC5 independent genes in fast Pol II cells became THOC5 dependent in slow Pol II cells. Chromatin associated THOC5 in slow Pol II cells interacts with CDK12, RNA helicases DDX5 and DDX, and THOC6, but not with other members of THO complex. Notably, THOC5 did not form this complex in fast poly II cells. CDK12 was recruited to R-loop (DNA:RNA hybrid)  in THOC5/THOC6 dependent manner. Here, THOC6, but not THOC5 directly interacts with R-loop then, recruited DDX5 resolves R-loop and then CDK12 enhances further transcription elongation.   These data show for the first time the novel function of THOC5/THOC6 complex during transcription elongation.

overall_design: Cells expressing fast (E1129G) and slow (R749H) RNA Polymerase II mutants were infected with shRNA control and shTHOC5 for 5 days. Total RNAs were isolated and subjected to transcriptome analysis.

first: Doan

first: Mareike

last: Polenkowski

first: Aldrige

last: Allister

first: Andrew

last: Pierce

first: Lutz

last: Wiehlmann

first: Andrea

last: Hoffmann

first: Anthony

last: Whetton

first: Teruko

last: Tamura


title: H3K27me3 demethylases maintain the transcriptional and epigenomic landscape of the intestinal epithelium [RNA-seq]

first: Klaus

last: Kaestner

overall_design: Comparative gene expression analysis of RNA-Seq data obtained from crypt intestinal epithelial cells from control and "double knock out" ("DKO") samples at two timepoints following induction of gene ablation.

first: Hannah

last: Kolev

first: Yemin

last: Lan


title: mRNA/miRNA profiling of peripheral blood samples in PCOS patients

city: Thiruvananthapuram

first: Malini

last: Laloraya

state: Kerala

address: Thycaud PO, Poojappura

department: Department of Molecular Reproduction,

institute: Rajiv Gandhi Centre for Biotechnology,

type:
Expression profiling by array
Other


title: Long RNA profiles of human brain extracellular vesicles in  Alzheimer's disease

first: Wei

last: Ge

state: State...

address: 5 Dong Dan San Tiao, Dongcheng District

department: Department of Immunology

institute: Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences

summary: Alzheimer's disease (AD) is the most common neurodegenerative disorder. Extracellular vesicles (EVs) are carriers of nucleic acids, lipids and proteins, and are known to play a significant role in neurodegenerative pathogenesis. The goals of this study are to compare long RNA (exLR) profiling of EVs in normal human brains with which in AD human brain. EVs were isolated from frontal cortex of normal control (n=10) and AD (n=8) donors.

overall_design: Examination of  long RNA (exLR) profiling in normal human brain-derived EVs and AD human brain-derived EVs.

first: Dan

last: Luo

first: Haotian

last: Liu

first: Chao

last: Ma


title: A cysteine-rich secretory protein involves in phytohormone melatonin mediated plant resistance to CGMMV

status: Public on Dec 30 2022

city: henan

first: Xue

last: Yang

address: henan

institute: henan agricultrial university

summary: Background: Melatonin is considered to be a polyfunctional master regulator in animals and higher plants. Exogenous melatonin inhibits plant infection by multiple diseases; however, the role of melatonin in cucumber green mottle mosaic virus (CGMMV) infection remains unknown. Results: In this study, we demonstrated that exogenous melatonin treatment can effectively control CGMMV infection. The greatest control effect was achieved by 3 days of root irrigation at a melatonin concentration of 50 µM. Exogenous melatonin showed preventive and therapeutic effects against CGMMV infection at early stage in tobacco and cucumber. We utilized RNA sequencing technology to compare the expression profiles of mock-inoculated, CGMMV-infected, and melatonin+CGMMV-infected tobacco leaves. Defense-related gene CRISP1 was specifically upregulated in response to melatonin, but not to salicylic acid (SA). Silencing CRISP1 enhanced the preventive effects of melatonin on CGMMV infection, but had no effect on CGMMV infection. We also found exogenous melatonin has preventive effects against another Tobamovirus, pepper mild mottle virus (PMMoV) infection. Conclusions: Together, these results indicate that exogenous melatonin controls two Tobamovirus infection and inhibition of CRISP1 enhanced melatonin control effects against CGMMV infection, which may lead to the development of a novel melatonin treatment for Tobamovirus control.

overall_design: N. benthamiana plants were irrigated daily with 50 µM melatonin for 3 days; ddH2O was used as a control. On day 4, CGMMV was inoculated onto plant leaves. Leaves were collected for RNA-Seq analysis at 9 dpi. Three replicate leaf samples were collected for each treatment (CGMMV_MEL, CGMMV_CK, and WT) and each sample contained leaves from at least eight plants. At 7 dpi with CGMMV, tobacco leaves were collected for total RNA extraction.

first: Yan

last: Shi


title: Alteration of LncRNA expression in mice placentae after frozen embryo transfer is associated with increased fetal weight.

status: Public on Dec 22 2022

city: China

first: Yuan

last: Zhu

address: Hankou Road 22, Nanjing 210008

institute: Nanjing University medical school

summary: Background: Frozen embryo transfer (FET) significantly upregulates fetal weight compared with fresh embryo transfer. However, the mechanism of FET increasing fetal weight remains unclear.   Methods: We transferred blastocysts which had been vitrifified and warmed or fresh blastocysts into individual pseudopregnant recipients (n=11 mice each group) produced by natural mating to eliminate the influence of superovulation. The fetal weight, placental weight, placental efficiency and placenta architecture were compared. We performed placental lncRNA sequencing and mRNA sequencing to study the placental transcriptoms changes. And 15 selected differentially expressed lncRNAs and 15 mRNAs was checked.  Findings: Enhanced birthweight (1.513 g vs. 1.685 g, P <0.001) was found in FET mice, with increased placental efficiency (11.355 vs. 10.312, P =0.045) and proportion of labyrinth zone area (59.78% vs. 53.19%, P = 0.034), indicating FET might change the placental function and morphology architecture. A total of placental 97608 mRNAs and 103339 lncRNAs were obtained, among which 1012 mRNAs and 554 lncRNAs showed significantly different expression between two groups. KEGG and GO enrichment analyses showed that the differentially expressed lncRNAs and their targeted mRNAs were related to labyrinth zone formation and maternal-fetal interface vascular remodeling. qRT-PCR, Western blotting and correlation analysis demonstrated that suppressed Lncenc1 to elevate Gjb5 might play a role in increased fetal weight of FET.   Interpretation: FET changes the placental function and architecture resulting in higher mouse fetal weight, potentially via the network diagram of Lncenc1-miRNA-Gjb5.

overall_design: lncRNA and mRNA transcriptomes of FET and fresh ET mouse placentas

first: Yunni

last: Cai

first: Bo

last: Zhen

first: Yuting

last: Zhang

first: Jianjun

last: Zhou


title: SNP rs9277336 Controls the ACTN4-HLA-DPA1 Axis and Pulmonary Endothelial Pathophenotypes in Pulmonary Arterial Hypertension

status: Public on Dec 19 2022

city: Pittsburgh

first: Neha

last: Hafeez

address: E1240 BST, 200 Lothrop Street

institute: University of Pittsburgh

summary:
HLA-DPA1-related SNP rs9277336 is linked to increased PAH risk and binds ACTN4 in an allele-specific fashion. HLA-DPA1 transcript is decreased in PAH lung endothelial cells and controlled by ACTN4. ACTN4 differential binding may cause HLA-DPA1-mediated immune dysfunction.
The purpose of this specific experiment is to determine the downstream effects of ACTN4 and HLA-DPA1 downregulation, specifically looking at overlaps between the two conditions.

overall_design: Human PAECs were treated with siRNA against ACTN4, HLA-DPA1, or a negative control.

first: Stephen

middle: Y

last: Chan


title: Next Generation Sequencing of Wild Type and OsMIR393b Transcriptomes

city: Hangzhou

first: Fu

last: Guo

address: Yuhangtang Road 866

institute: Zhejiang University

summary: Acquiring the gene network required for somatic embryogenesis by comparing the differentially expressed genes.

overall_design: mRNA profiles of  mature embryos of wild type (NIP) and OsMIR393b (OEB)

first: Hongwu

last: Bian

first: Lin

last: Xu

first: Peijing