title: Combinatorial depletions of G-protein coupled receptor kinases (GRKs) in immune cells identify pleiotropic and cell type-specific functions

city: Freiburg im Breisgau

first: Katharina

last: Glaser

address: Stübeweg 51

institute: Max Planck Institute of Immunobiology and Epigenetics

summary: G-protein coupled receptor kinases (GRKs) participate in the regulation of chemokine receptors by mediating receptor desensitization. They can be recruited to agonist-activated G-protein coupled receptors (GPCRs) and phosphorylate their intracellular parts, which eventually blocks signal propagation and often induces receptor internalization. However, there is growing evidence that GRKs can also control cellular functions beyond GPCR regulation. Immune cells commonly express two to four members of the GRK family (GRK2, GRK3, GRK5, GRK6) simultaneously, but we have very limited knowledge about their interplay in primary immune cells. In particular, we are missing comprehensive studies comparing the role of this GRK interplay for (a) multiple GPCRs within one leukocyte type, and (b) one specific GPCR between several immune cell subsets. To address this issue, we generated mouse models of single, combinatorial and complete GRK knockouts in four primary immune cell types (neutrophils, T cells, B cells and dendritic cells) and systematically addressed the functional consequences on GPCR-controlled cell migration and tissue localization. Our study shows that combinatorial depletions of GRKs have pleiotropic and cell-type specific effects in leukocytes, many of which could not be predicted. Neutrophils lacking all four GRK family members show increased chemotactic migration responses to a wide range of GPCR ligands, whereas combinatorial GRK depletions in other immune cell types lead to pro- and anti-migratory responses. Combined depletion of GRK2 and GRK6 in T cells and B cells shows distinct functional outcomes for (a) one GPCR type in different cell types, and (b) different GPCRs in one cell type. These GPCR-type and cell-type specific effects reflect in altered lymphocyte chemotaxis in vitro and localization in vivo. Lastly, we provide evidence that complete GRK deficiency impairs dendritic cell homeostasis, which unexpectedly results from defective dendritic cell differentiation and maturation in vitro and in vivo. Together, our findings demonstrate the complexity of GRK functions in immune cells, which go beyond GPCR desensitization in specific leukocyte types. Furthermore, they highlight the need for studying GRK functions in primary immune cells to address their specific roles in each leukocyte subset.

overall_design: BMDCs from GM-CSF cultures, WT vs. 3xGRK KO, untreated and LPS-stimulated

first: Teresa

last: Tarrant

first: Tim

last: Lämmermann


title: PFK2/FBPase-2 is a potential target for metabolic engineering in the filamentous fungus Myceliophthora thermophila

status: Public on Sep 28 2022

city: Tianjin

first: Yongli

last: Zhang

address: 32 West 7th Avenue, Tianjin Airport Economic Area

country: China

institute: Chinese Academy of Sciences

type: Expression profiling by high throughput sequencing

summary: The PFK-2/ FBPase-2 are important regulatory enzymes in the glycolytic and are present in all major eukaryotic taxa. However, unlike the well-studied animal and plant PFK-2/ FBPase-2, their functions in filamentous fungi remain little investigated. As a typical filamentous fungus and industrial microorganisms, M. thermophila was choose to investigate the functions of this gene. At the same time, the application of regulating this gene in improving metabolites production was also studied.

sample_organism: Thermothelomyces thermophilus ATCC 42464

overall_design: There are three isomers of 6-phosphofructo-2-kinase/ fructose-2,6-bisphosphatase in M. thermophila, named pfk2-a(Mycth_71484), pfk2-b(Mycth_2301421), pfk2-c(Mycth_2312639), respectively.To learn more about the function of PFK-2/FBPase-2 in Myceliophthora thermophila. pfk2-a/b/c, single and triple gene knockouts were performed using the CRISPR/Cas9 system in M. thermophila wild-type strain (WT), respectively.Knockout of the above three genes and named koa, kob, and koc, respectively.While simultaneous knockout  three genes from wlid-type was named koabc. Mycelia for RNA isolation were harvested after 2 days and 4 days of cultivation.

first: Die

last: Hu


title: Bacterial transcription factors binding to coding regions regulate the internal cryptic promoters

city: Hong Kong

first: Xin

last: DENG

address: 1/F, Block 1, To Yuen Building, City University of Hong Kong, 31 To Yuen Street, Kowloon Tong

department: Department of Biomedical Sciences

country: Hong Kong

institute: City University of Hong Kong

summary: To analyze the antisense transcripts, we performed LM-seq for Pesudomonas aeruginosa ∆algR and Pesudomonas syringae ∆rhpS and their corresponding WT strain. Date-minging in ChIP-seq and HT-SELEX results from  public dataset, we got the TF binding sites (TFBS) across genome. Coupling analysis with LM-seq and these TFBS, our results revealed that the coding region binding TFs regulate antisense RNA transcription by regulating the activity of cryptic promoters.

sample_organism:
Pseudomonas aeruginosa
Pseudomonas syringae

overall_design: Pesudomonas aeruginosa ∆algR and Pesudomonas syringae ∆rhpS as well as their corresponding WT strain.

first: Canfeng

last: Hua

first: Jiadai

last: Huang

first: Tingting

last: Wang

last: Deng


title: Reduced microglial Trem2 levels is associated with abnormal synaptic pruning in the developing hippocampus of mice exposed to early life stress

city: NEW HAVEN

first: Arie

last: Kaffman

state: CT

address: 300 GEORGE ST. SUITE 901, SUITE 901

country: USA

institute: YALE UNIVERSITY

summary: The goal of this project was to assess the effects of two paradigms of early life stress on microglial gene expression in the developing hippocampus of 17-day old mice. Sixty thousands microglia  were isolated from the hippocampus of 17-day old mice pups exposed to control (CTL), limited bedding (LB) or unpredictable postnatal stress (UPS) conditions and were processed to assess gene expression using the mouse Glia panel (Nanostring, Cat # XT-Mm Glial profiling CSO).

overall_design: Microglia were isolated using Percoll gradient followed by flow cytometry from 17-day old pups exposed to CTL, LB and UPS condition (N=8 mice per rearing and sex for a total of 48 mice). Gene expression was assessed using the mouse Glia panel (Nanostring, Cat # XT- CSO-M-Glial-12) by running 4 separate batches with 2 mice per rearing group and sex in each batch. The effects of rearing (CTL, LB, UPS) and sex were initially assessed using a 3 X 2 MANOVA (N=8 mice per rearing and sex for a total of 48 mice) for expressed genes (> 20 counts). This analysis identified 87 differentially regulated genes (DRG) for rearing and only few DRG affected by sex (n=13) or interaction between sex and rearing condition (n=5). Based on the prominent rearing effect, advanced-analysis was conducted using the nSolver software to identify DRG between CTL and LB group, CTL and UPS, and LB and UPS with batch as a covariance.

first: Kiran

middle: K

last: Dayananda

first: Daniel

first: Sahabuddin

last: Ahmed

first: Baruh

last: Polis

first: Rafiad

last: Islam


title: The SPARC complex defines RNAPII promoters in Trypanosoma brucei [RNA-seq]

city: Edinburgh

first: Robin

last: Allshire

address: Max Born Crescent

country: United Kingdom

institute: Wellcome Centre for Cell Biology

summary: Kinetoplastids are a highly divergent lineage of eukaryotes with unusual mechanisms for regulating gene expression. We previously surveyed 65 putative chromatin factors in the kinetoplastid Trypanosoma brucei. Our analyses revealed that the predicted histone methyltransferase SET27 and the Chromodomain protein CRD1 are tightly concentrated at RNAPII transcription start regions (TSRs). Here we report that SET27 and CRD1 together with four biologically novel constituents form the SET27 promoter-associated regulatory complex (SPARC), which is specifically enriched at TSRs. SET27 loss leads to aberrant RNAPII recruitment to promoter sites, accumulation of polyadenylated transcripts upstream of normal transcription start sites, and conversion of some normally unidirectional promoters to bidirectional promoters. Transcriptome analysis in the absence of SET27 revealed upregulated  mRNA expression in the vicinity of SPARC peaks on chromosome cores in addition to derepression of genes encoding variant surface glycoproteins (VSGs) located in subtelomeric regions. These analyses uncover a novel chromatin-associated complex required to establish accurate promoter position and directionality.

overall_design: This RNA-seq dataset contains polyA selected transcripts from WT, set27D/+ (SKO), set27D/D (DKO), jbp2D/+ (SKO) and jbp2D/D (DKO) bloodstream form T. brucei cells.

first: Desislava

middle: P

last: Staneva


title: A REF6-dependent H3K27me3-depleted state facilitates gene activation during germination in Arabidopsis [RNA-Seq]

city: Beijing

first: Jie

last: Pan

address: No.1 West Beichen Road,Chaoyang District

institute: Institute of Genetics and Developmental Biology

summary: We report transcriptome changes and genome-wide dynamics of H3K27me3 during seed germination in Arabidopdsis, and investigate the impact of REF6-mediated H3K27 demethylation on germination. Compared with transcriptome changes, we discover delayed H3K27me3 reprogramming closely associated with the embryo to vegetative cell fate switch. REF6-mediated H3K27 demethylation promotes germination but does not significantly contribute to H3K27me3 dynamics during germination, but rather stably establishes an H3K27me3-depleted state permissive to transcription. By analyzing REF6 genomic binding, we show that it is absent from mature embryo chromatin and gradually establishes occupancy during the course of germination to counteract increased PRC2 activity.

overall_design: Examination of transcriptome, H3K27me3 and REF6 binding in germinating seeds and seedlings

first: Danhua

last: Jiang

first: Huairen


title: Simultaneous, cell-intrinsic downregulation of PD-1 and TIGIT can enhance effector function of CD19-targeting CAR T cells and promote early memory phenotype

city: Daejeon

first: YoungHo

last: Lee

address: 48, Yuseong-daero 1184beon-gil, Yuseong-gu

country: South Korea

institute: Curocell

summary: CD19-targeting chimeric antigen receptor (CAR) T cell have become an important therapeutic option for patients with relapsed and refractory B cell malignancies. However, according to the recent clinical data, a significant portion of patients still do not benefit from the therapy, due various resistance mechanisms including the high expression of multiple inhibitory immune checkpoint receptors on activated CAR-T cells. Studies of checkpoint blockade immunotherapy using monoclonal antibodies have shown that simultaneously targeting inhibitory receptors that are functionally non-redundant can synergistically enhance anti-tumor responses. Here we report a lentiviral two-in-one CAR T approach in which two checkpoint receptors can be downregulated simultaneously by a dual short-hairpin RNA (shRNA) cassette integrated into a CAR vector. Using this system, we evaluated CD19-targeting CAR T cells in the context of four different checkpoint combinations, PD-1/TIM-3, PD-1/LAG-3, PD-1/CTLA-4, and PD-1/TIGIT, and found that the CAR T with PD-1/TIGIT downregulation uniquely exhibited synergistic anti-tumor effect in mouse xenograft models compared to the single PD-1 downregulation and maintained cytolytic and proliferative capacity upon repeated antigen exposure. Importantly, functional and phenotypic analysis of CAR T cells as well as analysis of transcriptomic profiles suggests that downregulation of PD-1 enhances short-term effector function while downregulation of TIGIT is primarily responsible for maintaining a less-differentiated/exhausted state, providing a potential mechanism of the synergy. The PD-1/TIGIT downregulated CAR T cells generated from DLBCL patient-derived T cells following clinically applicable manufacturing process also showed a robust anti-tumor activity and significantly improved persistence in vivo compared to conventional CD19-targeting CAR T cells. Overall, our results demonstrate that the cell-intrinsic PD-1/TIGIT dual downregulation strategy may provide an effective way to overcome the immune checkpoint-mediated resistance in CAR T therapy.

overall_design: RNAseq profiling of  first and second restimulation CD19 specfic CAR T cells with GFP, PD-1, TIGIT, or PD-1/TIGIT downregualtion

first: Young-Ho

first: Hyeong

middle: J

first: Hyung

middle: C

last: Kim

first: Inkyung

last: Jung

first: Yujean

first: Chan

middle: H


title: BACH2 restricts NK cell maturation and function limiting immunity to cancer metastasis

status: Public on Sep 27 2022

city: Cambridge

first: Rahul

last: Roychoudhuri

address: Tennis Court Road

department: Department of Pathology

institute: University of Cambridge

summary: Natural killer (NK) cells are critical to immune surveillance against infections and cancer. Their role in immune surveillance requires that NK cells are present within tissues in a quiescent state. Mechanisms by which NK cells remain quiescent in tissues are incompletely elucidated. The transcriptional repressor BACH2 plays a critical role within the adaptive immune system, but its function within innate lymphocytes has been unclear. Here, we show that BACH2 acts as an intrinsic negative regulator of NK cell maturation and function. BACH2 is expressed within developing and mature NK cells and promotes the maintenance of immature NK cells by restricting their maturation in the presence of weak stimulatory signals. Loss of BACH2 within NK cells results in accumulation of activated NK cells with unrestrained cytotoxic function within tissues, which mediate augmented immune surveillance to pulmonary cancer metastasis. These findings establish a critical function of BACH2 as a global negative regulator of innate cytotoxic function and tumor immune surveillance by NK cells.

overall_design: WT or Bach2-deficient NK cells fractionated into subsets were sorted from spleens of cWT (Ncr1Cre) or cKO (Bach2flox/flox Ncr1Cre) animals and subjected to RNA-Seq (experiment CI0146). Bulk WT and Bach2-KO cells were sorted from spleens of mixed bone marrow chimeric animals reconstituted with ~1:1 mixtures of WT and Bach2-KO bone marrow cells (CI056). WT NK cell subsets were also sorted from spleens of WT animals (CI056). Total RNA extracted and sequenced. Experiments described in Imianowski et al, J Exp Med, 2022

first: Charlotte

last: Imianowski

first: Sarah

last: Whiteside

first: Teresa

last: Lozano


title: Surface-localized glycoproteins act through class C ARFs to fine-tune gametophore initiation in Physcomitrium patens

city: Nankang

first: Ooi-kock

last: Teh

state: Taipei

address: 128 Sec. 2, Academia Rd

department: Institute of Plant and Microbial Biology

country: Taiwan

institute: Academia Sinica

summary: To investigate transcriptomic profiles when auxin-dependent transcription factor ARFC2 from Physcomitrium patens is expressed, we established an inducible overexpressor line for PpARFC2. We then perform bulk RNA-seq on protonemata tissues that have been mock-treated or induced by beta-estradiol for 16 h.

overall_design: Two types of samples were analyzed Control and treatment using PpARFC2 overexpressor. The analyzed dataset includes two control samples, treated with DMSO and three treatment samples, treated with β-estradiol.

first: Fujita

last: Tomomichi


title: The SPARC complex defines RNAPII promoters in Trypanosoma brucei [ChIP-seq]

first: Robin

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: This ChIP-seq dataset shows the genomic association of YFP-tagged SPARC complex subunits in bloodstream form (BF) and procyclic form (PF) T. brucei, and the genomic association of YFP-RPB1 in WT, set27D/+ (SKO) and set27D/D (DKO) BF cells. There are three replicates for JBP2 (BF) and SET27 (PF), and two replicates for the remaining YFP-tagged proteins (BF and PF) and for the untagged control (PF).

first: Desislava


title: A REF6-dependent H3K27me3-depleted state facilitates gene activation during germination in Arabidopsis [REF6-HA ChIP-seq]

first: Jie

first: Danhua

last: Zhang


title: Chromatin status under knock-down of SNHG1  in neuroblastoma [ATAC-seq]

city: Taipei

first: Chia-Lang

last: Hsu

address: No. 7, Zhongshan S. Rd.

department: Department of Medical Research

institute: National Taiwan University Hospital

summary: The small nucleolar RNA host gene 1 (SNHG1) is a novel oncogenic long non-coding RNA (lncRNA) aberrantly expressed in different tumor types. We previously found highly expressed SNHG1 was associated with poor prognosis and MYCN status in neuroblastoma (NB). However, the molecular mechanisms of SNHG1 in NB are still unclear. Here, we disrupted endogenous SNHG1 in the MYCN-amplified NB cell line SK-N-BE(2)C using the CRISPR/Cas9 system, and demonstrated the proliferation and colony formation ability of SNHG1-knowndown cells were suppressed. The transcriptome analysis and function assays of SNHG1-knockdown cells revealed SNHG1 was involved in various biological processes including cell growth, migration, apoptosis, cell cycle, and reactive oxygen species (ROS). Interestingly, the expression of core regulatory circuitry (CRC) transcription factors in MYCN-amplified NB, including PHOX2B, HAND2, GATA3, ISL1, TBX1, and MYCN, were decreased in SNHG1-knockdown cells. The chromatin-immunoprecipitation sequencing (ChIP-seq) and transposase-accessible chromatin using sequencing (ATAC-seq) analyses show that chromatin status of these CRC members is altered, which may stem from interactions between SNHG1 and HDAC1/2. These findings demonstrate that SNHG1 plays a crucial role in maintaining NB identity via chromatin regulation and reveal the function of the lncRNA SNHG1 in NB.

overall_design: ATAC-seq in neuroblastoma cell SK-N-BE(2)C

first: H

middle: F

last: Juan

first: C

middle: L


title: Transcriptomics analysis of oligodendrocyte-enriched sorted cells with conditional deletion of Ral GTPases during development

city: Zurich

first: Jorge

middle: A.

last: Pereira

address: Otto-Stern-Weg 7

department: Dep. of Biology

country: Switzerland

institute: ETH Zurich

summary: RNA sequencing was performed to evaluate the transcriptome of oligodendrocyte-enriched sorted cells extracted from mice with conditional deletion of Ral GTPases in the oligodendrocyte-lineage during development.

overall_design: The dataset was generated with oligodendrocyte-enriched sorted cells extracted from spinal cords of 4 independent mice per genotype at 10 days of age (P10). The genotypes analyzed include controls, CnpCre:RalAflox/flox and CnpCre:RalAflox/flox:RalBflox/flox mutants, all of which also expressed the reporter gene TdTomato in oligodendrocyte-lineage cells.

first: Jonathan

last: DeGeer

first: Daniel

last: Gerber

first: Ueli

last: Suter


title: The loss of paraoxonase-2 activity aggravates lipid accumulation, mitochondrial dysfunction, and oxidative stress through the impaired autophagy pathway in in vitro fatty liver model

status: Public on Sep 26 2022

city: Suwon-si

first: Hyeong min

address: 304, Sinwon-ro

department: Reasearch

institute: Glaceum

summary: Non-alcoholic fatty liver disease (NAFLD) is an increasingly prevalent immunometabolic disease that can progress to hepatic cirrhosis and cancer. NAFLD pathogenesis is extremely complex and is associated with diverse features including oxidative stress, impaired mitochondrial function andlipid metabolism, and cellular inflammation. Thus, in-depth research on its underlying mechanisms and investigation into a potential drug target that has overarching effects on these features will provide benefits towards discovering effective treatments for NAFLD. Here, we examined the role of endogenous paraoxonase-2 (PON2), a membrane protein with reported antioxidant activity, in in vitro fatty liver model. We found that the hepatic loss of PON2 activity aggravated steatosis and oxidative stress under lipotoxic condition, and our transcriptome analysis revealed that PON2 deficiency disrupts the activation of numerous functional pathways closely related to NAFLD pathogenesis, including mitochondrial respiratory capacity, lipid metabolism, liver fibrosis, and hepatic inflammation. PON2 promoted the activation of overall autophagy pathway, especially mitophagy cargo sequestration, which may be considered as an underlying mechanism that contributed to the role of PON2 in alleviating oxidative stress, mitochondrial dysfunction, lipid accumulation, and inflammation. These results provide mechanistic foundation on the prospect of  targeting PON2 for the development of novel therapeutics for NAFLD in the future.

overall_design: Comparative gene expression profiling analysis of RNA-seq data in the PON2-deficient and control L02 cells

first: Kyun-Hwan

first: Gu-Choul

last: Shin

first: Hyeong

middle: M

middle: Y

first: Sang-Ku

last: Yoo

first: Hyung

middle: S

last: Park

first: Leo

last: Choi

first: Kwang-Pyo


title: Genome-wide transcriptome analysis of brain region (ventral part of telenchephalon, hypothalamus and pituitary) in grass puffer (Takifugu alboplumbeus)

city: Nagoya

first: Takashi

last: Yoshimura

address: Furo-cho, Chikusa-ku

country: Japan

institute: Nagoya University

summary: We compared the gene expression of ventral part of telenchephalon, hypothalamus and pituitary in grass puffer (Takifugu alboplumbeus) between the spring and neap tides during the breeding season using RNA-seq.

overall_design: To compare expression profile between the spring and neap tides, we collected wild male grass puffers (Takifugu alboplumbeus) at their spawning site, Minamichita, Japan every week (i.e., new, waxing, full and waning moons) for 2 months and performed RNA-seq analysis.


title: A giant virus genome is densely packaged by stable nucleosomes

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

summary: The doublet histones of Marseillevirus are distantly related to the four eukaryotic core histones and wrap DNA to form remarkably similar nucleosomes. By releasing Marseillevirus chromatin from virions into solution and performing genome-wide nuclease digestion and chemical cleavage assays, we find that the higher-order organization of Marseillevirus chromatin differs greatly from that of eukaryotes. Marseillevirus nucleosomes fully protect DNA within virions, without linker DNA or phasing along genes. Likewise, we observe that most nucleosomes reconstituted onto 3-copy tandem repeats of a nucleosome positioning sequence are tightly packed and fully wrapped. We also document repeat generation and instability during viral passage in amoeboid culture. Dense promiscuous packing of fully wrapped nucleosomes rather than “beads-on-a-string” with genic punctuation suggests a viral genome protection function for doublet histones.

sample_organism:
Drosophila melanogaster
synthetic construct
Marseillevirus marseillevirus

overall_design: We used MNase-seq and MPE-seq, nucleosome mapping strategies in which either an endo/exonuclease or a small molecule DNA cleavage reagent removes accessible DNA, followed by end-polishing and ligation of sequencing adapters to produce libraries for paired-end DNA sequencing.

first: Terri

middle: D

last: Bryson

first: Pablo

last: DeIoannes

first: Marco

middle: I

last: Valencia-Sanchez

first: Paul

middle: B

last: Talbert

first: Bernard

last: LaScola

first: Karim-Jean

last: Armache

first: Steven


title: RNA-seq analysis evaluating cell cycle specific gene expression and the effect of KRTAP2-3 gene inactivation in SAS cells expressing Fucci.

city: Tokyo

first: Daizo

last: Koinuma

address: Hongo 7-3-1, Bunkyo-ku

department: Pathology

institute: University of Tokyo

summary: Proliferation and migration of cancer cells are regulated by the stimuli from tumour microenvironment during its progression and metastasis. While transforming growth factor-β (TGF-β) increases migration and metastasis of various types of epithelial cancer cells via induction of epithelial-mesenchymal transition (EMT), it also decreases their proliferation by inducing G1 cell cycle arrest. However, the correlation of these tumour promoting and suppressing effects of TGF-β remains to be elusive because of the lack of analysis at a single cell level. Here, we showed that TGF-β confers the oral cancer cells residing in G1 phase with higher motility and mesenchymal phenotypes, suggesting a correlation between TGF-β-dependent cell cycle arrest and increased migration. We identified keratin-associated protein 2-3 (KRTAP2-3) as a regulator of these dual effects of TGF-β. Expression of KRTAP2-3 was associated with both TGF-β-induced cell cycle arrest and increased migration, and also was correlated with poor prognosis of head and neck cancer patients. We found that deletion of KRTAP2-3 gene decreased in vitro migration and in vivo metastasis of oral cancer cells via induction of mesenchymal-epithelial transition (MET). KRTAP2-3 also induces the expression of Regulator of G-protein signalling 4 (RGS4) and Zinc finger BED domain-containing protein 2 (ZBED2), which suppresses proliferation and increases migration of oral cancer cells, respectively. Present findings revealed novel mechanisms how TGF-β orchestrates proliferation and migration of cancer cells by inducing the expression of KRTAP2-3, and highlighted the importance of targeting the motile cancer cells under G1 cell cycle arrest to suppress metastasis.

overall_design: A total of 12 samples, 6 conditions (G1 and S/G2/M fractions, with/without TGF-b; KRTAP2-3 KO or control clones, no treatment), each in biological duplicate.

first: Kazuki

last: Takahashi

first: Katarzyna

middle: A

last: Inoue

first: Tetsuro

last: Watabe

first: Toru

last: Konishi

first: Kohei

last: Miyazono


title: RUNX1 Deficiency Cooperates with SRSF2 Mutation to Induce Multi-lineage Hematopoietic Defects Characteristic of Myelodysplastic Syndromes

city: San Diego

first: Dong-Er

last: Zhang

state: California

address: 3855 Health Sciences Dr

institute: UCSD

summary: Causal mutations in multiple classes of genes have been identified in MDS patients with some patients harboring more than one mutation. Interestingly, double mutations tend to occur in different classes, rather than the same classes of genes, as exemplified by frequent co-occurring mutations in the transcription factor RUNX1 and the splicing factor SRSF2. Here we report a mouse model in which Runx1 knockout was combined with the Srsf2 P95H mutation to cause multi-lineage hematopoietic defects. Besides their additive and synergistic effects, we also unexpectedly noted a degree of antagonizing activity of single mutations in specific hematopoietic progenitors. To uncover the mechanism, we further developed a cellular model using human K562 cells and performed parallel gene expression and splicing analyses in both human and murine contexts. We performed RNA-seq on sorted Lineage- c-Kit+ (LK) hematopoietic progenitors from bone marrow of mice from WT, runx1 KO ,  Srsf2 P95H knock in and  runx1  Srsf2 P95H double mutants.  We also performed RNA-seq on set of isogenic K562 cell lines: wild type (WT), SRSF2 P95H knock-in (SRSF2P95H/+/+), RUNX1 knockdown (RUNX1 KD), and SRSF2 P95H knock-in with RUNX1 knockdown (Double). Strikingly, while RUNX1 deficiency was responsible for altered transcription in both single and double mutants, it also induced dramatic changes in global splicing, as seen with mutant SRSF2, and only their combination induced mis-splicing of genes selectively enriched in the DNA damage response and cell cycle checkpoint pathways. Collectively, these data reveal the convergent impact of a prototypic MDS-associated double mutant on RNA processing and suggest that aberrant DNA damage repair and cell cycle regulation critically contribute to MDS development.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: RNA-seq of K562 and mouse LK cells with SRSF2 P95H, RUNX1 KO/KD, or both mutations. Performed differential gene expression analysis and alternative splicing analysis between indicated mutations and wildtype control. All samples collected in triplicate.

first: Yi-Jou

last: Huang

first: Jia-Yu

last: Chen

first: Xiang-Dong

last: Fu


title: RNA-Regulatory Exosome Complex Confers Erythroid Progenitor Cell Survival and Activity In Vivo

city: Madison

first: Colin

last: Dewey

address: 425 Henry Mall, 5420 Genetics/Biotechnology Center

institute: University of Wisconsin-Madison

summary: The RNA exosome complex (EC) confers post-transcriptional regulation by processing and degrading RNAs in a context-dependent manner. Although the EC functions in diverse cell types, its contributions to stem and progenitor cell development have not been widely studied.  Previously, we demonstrated that the transcriptional regulator of erythrocyte development GATA1 represses genes encoding EC subunits, and in vitro analyses implicated the EC in maintaining erythroid progenitors. EC loss promoted the transition of progenitors into differentiating erythroblasts. To determine if these mechanisms operate in vivo, we utilized a hematopoietic-specific Vav1-Cre mouse system to conditionally ablate Exosc3, encoding an EC structural subunit with a conserved RNA binding domain. Although Exosc3 fl/fl Cre+ embryos developed normally until E14.5, Exosc3 ablation was embryonic lethal, severely reduced erythro-myeloid progenitor activity and reduced immunophenotypic progenitors. Exosc3 ablation decreased Kit+ hematopoietic progenitors and the level of cell surface c-Kit. RNA-seq analysis of Exosc3-ablated BFU-E revealed elevated transcripts encoding pro-apoptotic factors, including BCL2 family members Bax, Puma and Noxa, the death receptor Fas, and p53 target genes. Exosc3-ablated BFU-E and CFU-E progenitors exhibited increased apoptosis. Although megakaryocyte-erythroid progenitor (MEP) levels were unaltered, they were functionally defective. We propose that the EC controls an ensemble of apoptosis-regulatory RNAs, thereby conferring erythroid progenitor survival and promoting developmental erythropoiesis in vivo.

overall_design: RNA-seq gene expression analysis of BFU-E sorted from E14.5 fetal livers (n = 6: 2 from each of 3 litters)

first: Isabela

last: Fraga de Andrade

first: Kirby

last: Johnson

first: Charu

last: Mehta

middle: N

first: Uttiya

last: Basu

first: Emery

last: Bresnick


title: INPP5D limits plaque formation and glial reactivity in the APP/PS1 mouse model of Alzheimer’s disease

city: New York

first: Philip

last: Hasel

address: 435 E 30th St

institute: NYU Langone Medical Centre

summary: Spatial Transcriptomics (Visium) of 12 coronal brain sections from 6 months old female Inpp5dfl/fl/Cx3cr1CreER/+ crossed to APPKM670/671NL/PSEN1Δexon9 (PSAPP) mice and treated with either cornoil or tamoxifen (75 mg/kg) at 3 months of age for 5 consecutive days

overall_design: Spatial Transcriptomics of Inpp5dfl/fl/Cx3cr1CreER/+ crossed to APPKM670/671NL/PSEN1Δexon9 (PSAPP) mice to study the transcriptomics, brain-region resolved effect of removing Inpp5d from microglia in an animal model of Alzheimer's disease

first: Shane

last: Liddelow

first: Emilie

last: Castranio

first: Michelle

middle: E

last: Ehrlich


title: Multiomic Evaluation of Metastasis Evolution, from Primary, CTC, to Metastatic Tumors

first: Ying Chih

last: Chang

state: Taipei City

address: 128 Academia Road, Section 2, Nankang

department: Genomics Research Center

summary: Metastasis is the most important cause of cancer-related death and it has been the most important issue both in basic and clinical cancer researches. Through in vivo spontaneous metastasis animal model, we successfully cultivated and expanded the metastasis lineage cells for genomic, methylomic, and transcriptomic analyses based on the high efficiency and excellent viability of a modified CTC-capturing system together with primary and metastasis tumors as well as parental 4T1-hHER2 breast cancer cell line.

overall_design: By using in vivo spontaneous metastasis animal model from NSG mice to harvest all metastatic lineages of cancer cells from primary tumor, circulating tumor cell, and metastasis tumor for following evaluation on cancer metastasis evolution.

first: Jia-Yang

first: Chun-Tsai

last: Su

first: Chien-Yi

last: Tung

first: Muh-Hwa

last: Yang

first: Ying-Chih


title: Enhancing Acsl4 in absence of mTORC2/Rictor drove β-cell dedifferentiation via inhibiting FoxO1 and promoting ROS production

city: Shanghai

first: canqi

last: cui

address: 197 Ruijin 2nd Road

institute: shanghai national reaearch center for endocrine and metabolic diseases

summary: We here identified Acsl4, a new target of mTORC2, could rescue the impaired β cell proliferation, but not deficient insulin secretion induced by loss of Rictor.

overall_design: ex vivo overexpression Acsl4 in βRicKO mice

first: Canqi

last: Cui

first: Yanyu

last: Gu


title: DNA methylation-based classification of sinonasal tumors

status: Public on Sep 25 2022

city: München

first: Philipp

last: Jurmeister

address: Thalkirchner Straße 36

department: Institute of Pathology

country: Germany

institute: Ludwig Maximilians University Hospital Munich

type: Methylation profiling by genome tiling array

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

overall_design: Refer to individual Series


title: TINCR lncRNA encodes a ubiquitin-like protein that activates CDC42, promotes epithelial differentiation and suppresses tumor growth

city: Barcelona

first: Camille

last: Stephan Otto Attolini

state: Select a State or Province

address: Baldiri Reixac 10

department: Biostatistics and bioinformatics Unit

country: Spain

institute: IRB Barcelona

summary: The human transcriptome contains thousands of small open reading frames (sORFs) that have been largely overlooked because of their small size. Some of these sORFs code for bioactive small proteins although none have been associated to the regulation of cell identity. Here, we show that TINCR lncRNA encodes pTINCR, an evolutionary conserved ubiquitin-like protein with a SUMO interacting motif (SIM) that is expressed in many epithelia. pTINCR binds to SUMO and modifies global cell SUMOylation patterns. One of its main targets is CDC42, a Rho-GTPase critical for actin cytoskeleton remodeling and for epidermal differentiation. pTINCR increases CDC42 SUMOylation and promotes its activation in a SIM-dependent manner. pTINCR is necessary and sufficient for epithelial cell differentiation in vitro, and promotes epidermal differentiation in vivo. Consistent with its pro-differentiation role, pTINCR expression is lost in human cutaneous squamous cell carcinomas (cSCC), and its overexpression reduces cSCC growth in vitro and in vivo. Moreover, pTINCR is a target of the tumor suppressor p53, and the expression of pTINCR in epithelial cancers correlates with better prognosis. Our results identify pTINCR as a novel regulator of epithelial differentiation with tumor suppressor activity. More generally, our findings suggest that the proteome encoded by previously assumed non-coding RNAs can indeed be a source of new regulators of cell identity relevant for cancer.

overall_design: hSCC10 cells were transduced with an inducible pTINCR overexpression vector or control vector. Expression of pTINCR was induced by doxycycline treatment (1ug/ml) and cells were collected at the specified timepoints (0h, 6h, 12h, 24h, 7 days, 14 days and 21 days). Doxycycline was changed every two days and cells splited every 4 days, when 80% of confluence was reached.

first: Maria

last: Abad

first: Olga

last: Boix

last: Stephan-Otto Attolini

first: Marion

last: Martinez


title: Single Cell RNA-Sequencing of Skeletal Muscle in Dystrophic Mouse Models

city: Los Angeles

first: Kholoud

middle: K.

last: Saleh

state: CA

address: 615 Charles E. Young Dr. S., BSRB 257

department: MIMG

institute: UCLA

summary: Duchenne muscular dystrophy (DMD) is caused by an out-of-frame mutation in the DMD gene that results in the absence of a functional dystrophin protein, leading to a devastating and progressive lethal muscle-wasting disease. Genetic modifiers have been shown to increase disease severity in DMD mouse models as well as in human patients. Little is known about cellular heterogeneity in skeletal muscle as disease severity increases. To address this, we explored skeletal muscle-resident cell populations in healthy (wt-NSG), dystrophic (mdx-NSG), and severely dystrophic (mdxD2-NSG) mouse models utilizing scRNA-seq. We found an increased frequency of activated fibroblasts, activated fibro-adipogenic progenitor cells, and proinflammatory macrophages in dystrophic and severely dystrophic gastrocnemius muscles. Moreover, in endothelial cells we found an upregulation of extracellular matrix and platelet aggregation genes in dystrophic and severely dystrophic muscles, indicating endothelial cell functional impairment. In summary, this work extends the understanding of the severe nature of DMD, which should be considered when developing regenerative therapeutic avenues for DMD.

overall_design: Gastrocnemius muscles were harvested from the right hindlimb of 8 weeks old wt-NSG, mdx-NSG, and mdxD2-NSG male mice each separately. The digested muscles were sorted for live cells, and 10X Chromium Single Cell 3' library construction was performed followed by Ilumina NovaSeq 6000 sequecning. Single cells were analyzed using R package Seurat V 3.1.5 for broad cell type identification (Butler et al., 2018). Further integration of all single cells from all mouse models was carried out using R package Harmony (Korsunsky et al., 2019). Cellular heterogenity between healthy (wt-NSG), dystrophic (mdx-NSG) and severly dystrophic (mdxD2-NSG) skeletal muscles were then investigated.

middle: K

first: April

last: Pyle


title: DNA methylation-based classification of sinonasal tumors [test set]

summary: The diagnosis of sinonasal tumors is challenging due to a heterogeneous spectrum of various differential diagnoses as well as poorly defined, disputed entities such as sinonasal undifferentiated carcinomas (SNUCs). In this study, we apply machine learning algorithm based on DNA methylation patterns to classify sinonasal tumors with clinical-grade reliability. We further show that sinonasal tumors with SNUC morphology are not as undifferentiated as their current terminology suggests but rather reassigned to four distinct molecular classes defined by epigenetic, mutational and proteomic profiles. This includes two classes with neuroendocrine differentiation, characterized by IDH2 or SMARCA4/ARID1A mutations with an overall favorable clinical course, whereas tumors that are driven by SMARCB1-deficiency and tumors that represent previously misclassified adenoid cystic carcinomas are highly aggressive. Our findings have the potential to dramatically improve the diagnostic classification of sinonasal tumors and will fundamentally change the current perception of SNUCs.

overall_design: 52 specimens were analyzed using the Illumina Infinium MethylationEPIC BeadChip

first: David

last: Capper


title: DNA methylation-based classification of sinonasal tumors [reference set]

summary: The histopathological diagnosis of sinonasal tumors is challenging as it encompasses a heterogeneous spectrum of various differential diagnoses as well as poorly defined, disputed entities such as sinonasal undifferentiated carcinomas (SNUCs). In this study, we show that a machine learning algorithm based on DNA methylation is able to classify sinonasal tumors with clinical-grade reliability. We further show that tumors with SNUC morphology are not as undifferentiated as their current terminology suggests, but can be assigned to four molecular classes defined by distinct epigenic, mutational and proteomic profiles. This includes two classes with neuroendocrine differentiation, characterized by IDH2 or SWI/SNF chromatin remodeling complex mutations and overall favorable clinical course, highly aggressive tumors that are driven by SMARCB1-deficiency and tumors that represent previously misclassified adenoid-cystic carcinomas. Our findings have the potential to dramatically improve the diagnostic of challenging sinonasal tumors and could fundamentally change the current perception of SNUCs.

overall_design: 461 specimens were analyzed using the Illumina Infinium HumanMethylation450 or MethylationEPIC BeadChip


title: A REF6-dependent H3K27me3-depleted state facilitates gene activation during germination in Arabidopsis [H3K27me3 ChIP-seq]

city: Beijing

first: Jie

last: Pan

address: No.1 West Beichen Road,Chaoyang District

institute: Institute of Genetics and Developmental Biology

summary: We report transcriptome changes and genome-wide dynamics of H3K27me3 during seed germination in Arabidopdsis, and investigate the impact of REF6-mediated H3K27 demethylation on germination. Compared with transcriptome changes, we discover delayed H3K27me3 reprogramming closely associated with the embryo to vegetative cell fate switch. REF6-mediated H3K27 demethylation promotes germination but does not significantly contribute to H3K27me3 dynamics during germination, but rather stably establishes an H3K27me3-depleted state permissive to transcription. By analyzing REF6 genomic binding, we show that it is absent from mature embryo chromatin and gradually establishes occupancy during the course of germination to counteract increased PRC2 activity.

overall_design: Examination of transcriptome, H3K27me3 and REF6 binding in germinating seeds and seedlings

first: Danhua

last: Jiang

first: Huairen

last: Zhang


title: Variation of DNA methylation on the IRX1/2 genes is responsible for the neural differentiation propensity in human induced pluripotent stem cells

status: Public on Sep 24 2022

city: Miyazaki

first: Koichiro

last: Nishino

state: Miyazaki

address: 1-1 Gakuen-Kibanadai-Nishi

department: Veterinary Medicine

institute: University of Miyazaki


title: Variation of DNA methylation on the IRX1/2 genes is responsible for the neural differentiation propensity in human induced pluripotent stem cells [Agilent SurePrint G3 Human GE v3 8x60K Microarray]

summary:
Human induced pluripotent stem cells (hiPSCs) are useful as a tool for reproducing neural development in vitro. However, each hiPSC line has a different ability to differentiate into specific lineages, as known as differentiation propensity, resulting in reduced reproducibility and increased time and cost requirements for research use. To overcome this issue, we searched for predictive signatures of neural differentiation propensity of hiPSCs using DNA methylation which is the main modulator of cellular properties.
We obtained 32 lines of hiPSC and its comprehensive DNA methylation data by Infinium MethylationEPIC beadchip. To assess the neural differentiation efficiency of these hiPSCs, we measured the percentage of PAX6-positive cells on day 7 of neural stem cell induction by the dual-SMAD inhibition protocol. Using DNA methylation data of undifferentiated hiPSCs and their measured differentiation efficiency into neural stem cells as the set of data, and HSIC Lasso, a machine learning-based nonlinear feature selection method, we attemted to identify neural differentiation associated differentially methylated sites.
Epigenome-wide unsupervised clustering could not distinguish between hiPSCs with varying differentiation efficiency. On the other hand, HSIC Lasso identified 62 probes that can explain the neural differentiation efficiency of hiPSCs. Selected features by HSIC Lasso were particularly enriched within the 3 Mbp on chromosome 5, harboring the IRX2, C5orf38, and IRX1 genes. Within this region, DNA methylation rates were correlated with neural differentiation efficiency particular to female hiPSCs and negatively correlated with gene expression of the IRX1/2 genes. In addition, forced expression of the IRX1/2 genes impaired the neural differentiation ability of hiPSCs.
We have shown for the first time that DNA methylation state on the IRX1/2 genes of hiPSCs is predictive biomarker of their ability for neural differentiation. The predictive markers for neural differentiation efficiency identified in this study can be useful for selection of suitable undifferetiated hiPSCs prior to differentiation induction.

overall_design: Total RNA were hybridised to the Agilent SurePrint G3 Human GE v3 8x60K Microarray

first: Asato

last: Sekiya

first: Ken

last: Takasawa

first: Yoshikazu

last: Arai

first: Shin-ichi

last: Horike

first: Hidenori

last: Akutsu

first: Akihiro

last: Umezawa


title: The Nematode Oscheius tipulae as A Genetic Model for Programmed DNA Elimination [RNA-seq]

city: Knoxville

first: Jianbin

last: Wang

state: TN

address: 1311 Cumberland Avenue

department: Biochemistry & Cellular and Molecular Biology

institute: University of Tennessee Knoxville

summary: Programmed DNA elimination (PDE) is a notable exception to the paradigm of genome integrity. In metazoa, PDE often occurs during early embryogenesis, coincident with germline to somatic cell differentiation. During PDE, portions of genomic DNA are lost, resulting in reduced somatic genomes. Recent studies have described the sequences lost and chromosome behavior in metazoa. However, a system for studying the mechanisms and consequences of PDE in metazoa is lacking. Here, we established a functional and genetic model for PDE in the free-living nematode Oscheius tipulae, a member of the Rhabditidae family, which includes Caenorhabditis elegans. O. tipulae was recently suggested to eliminate DNA. Using staged embryos, we show that O. tipulae PDE occurs during embryogenesis at the 2-16 cell stages, similar to the human/pig parasitic nematode Ascaris. We identified a conserved motif, named Sequence For Elimination (SFE), for all 12 break sites on the six chromosomes at the junction of retained and eliminated DNA. SFE mutants exhibit a “fail-to-eliminate” phenotype only at the modified sites. END-seq revealed that breaks can occur at multiple positions within the SFE, with extensive end resection followed by telomere addition to both retained and eliminated ends. We identified through END-seq in the wild-type embryos, genome sequencing of SFE mutants, and comparative genomics of 23 wild isolates a large number of functional SFEs at the chromosome ends. We suggest these alternative SFEs provide flexibility in the sequences eliminated and a fail-safe mechanism for PDE. These studies establish O. tipulae as a new, attractive model to study the mechanisms and consequences of PDE in a metazoan.

overall_design: RNA-seq from 20 Oscheius tipulae developmental stages including early embryogenesis with staged embryos during and after PDE, as well as samples from gastrulation, morphogenesis, staged larvae (L1 – L4), dauer, post-dauer larvae, young adults, mature adults and male adults

first: Jordan

last: Reed


title: Variation of DNA methylation on the IRX1/2 genes is responsible for the neural differentiation propensity in human induced pluripotent stem cells [Illumina Infunium MethylationEPIC]

overall_design: Bisulfite converted DNA were hybridised to the Illumina Infunium MethylationEPIC


title: The Nematode Oscheius tipulae as A Genetic Model for Programmed DNA Elimination [ATAC-seq]

overall_design: ATAC-seq of staged Oscheius tipulae embryos

first: James

middle: R

last: Simmons


title: Ferroptosis of tumor-associated neutrophils is immunosuppressive and promotes tumor growth

city: Cambridge

first: Gozde

last: Kar

address: Cambridge

institute: AstraZeneca

summary: Ferroptosis is a non-apoptotic form of regulated cell death triggered by the discoordination of regulatory redox mechanisms culminating in massive peroxidation of polyunsaturated phospholipids. The development of the concept of ferroptosis stemmed from an active search for alternatives to apoptosis in cancer cells. Ferroptosis inducers have shown remarkable effectiveness in killing tumor cells in vitro, yet with no obvious success in experimental animal models, with a notable exception of immune-deficient mice 1,2.  This suggests the potential poorly understood contribution of ferroptosis on immune cells.  Pathologically activated neutrophils (PMN), termed myeloid-derived suppressor cells (PMN-MDSC), are major negative regulators of anti-tumor immunity3-5.  Here, we found that PMN-MDSC in the tumor microenvironment (TME), spontaneously die by ferroptosis.  While decreasing the presence of PMN-MDSC, ferroptosis induces the release of oxygenated lipids and limits mouse and human T cell activity. In immune-competent mice, genetic and pharmacological inhibition of ferroptosis abrogates suppressive activity of PMN-MDSC, reduces tumor progression, and synergizes with immune checkpoint blockade (ICB) to suppress the tumor growth.  In contrast, induction of ferroptosis in immune-competent mice promotes tumor growth.  Thus, ferroptosis is a unique and targetable immunosuppressive mechanism of PMN-MDSC in the TME that can be pharmacologically modulated to limit tumor progression.

overall_design: CT26 TB mice were treated with liproxstatin-1 for 8 days. Tumors were collected and analyzed by scRNAseq.

first: Ayumi

last: Hashimoto


title: Spatial transcriptome analysis of brain region in grass puffer (Takifugu alboplumbeus)

first: Takashi

last: Yoshimura

summary: We have applied spatial transcriptomics on puffer brain using Visium Spatial Gene Expression platform (10X Genomics) to examine each genes expression level and site in the brain.

overall_design: We collected wild male grass puffers (Takifugu alboplumbeus) at their spawning site, Minamichita, Japan   and performed spatial transcriptome analysis.


title: The Nematode Oscheius tipulae as A Genetic Model for Programmed DNA Elimination [END-seq]

overall_design: END-seq on Oscheius tipulae early embryos

first: Brandon

last: Estrem


title: Identification of the cell subset generating crescents within human parietal epithelial cells (PECs)

city: Firenze

first: Roberto

last: Semeraro

address: Viale Pieraccini, 6

department: Medicina Sperimentale e Clinica

country: Italy

institute: Università degli studi di Firenze

summary: We generated a single-cell RNA sequencing (scRNAseq) dataset of primary cultures of human glomerular parietal epithelial cells. Comparing this dataset with an already available dataset obtained by scRNAseq of human renal progenitor cells (GSE137620), we identified an immature PEC subset characterized by the expression of stem cell markers and stratifin (SFN). Moreover, we analyzed the effect of treatment with the HDAC inhibitor panobinostat on PEC transcriptome demonstrating the upregulation of podocyte-specific markers in different PEC subsets including the stratifin-expressing subset.

overall_design: Identify and characterize an immature PEC subset and its response to panobinostat treatment

first: Maria

last: Melica

first: Laura

last: Lasagni

first: Paola

last: Romagnani


title: Multifarious translational regulation during replicative aging in yeast

city: Wako

first: Shintaro

last: Iwasaki

state: Saitama

address: 2-1, Hirosawa

department: Center for Pioneering Research

institute: RIKEN

summary: Protein synthesis is strictly regulated during replicative aging in yeast, but global translational regulation during replicative aging is poorly characterized. To conduct ribosomal profiling during replicative aging, we collected a large number of dividing aged cells using a miniature chemostat aging device. Translational efficiency, defined as the number of ribosome footprints normalized to transcript abundance, was compared between young and aged cells for each gene. We identified more than 700 genes with changes greater than twofold during replicative aging. Increased translational efficiency was observed in genes involved in DNA repair and chromosome organization. Decreased translational efficiency was observed in genes encoding ribosome components, transposon Ty1 and Ty2 genes, transcription factor HAC1 genes associated with the unfolded protein response, genes involved in cell wall synthesis and assembly, and ammonium permease genes. Our results provide a global view of translational regulation during replicative aging, in which the pathways involved in various cell functions are translationally regulated and cause diverse phenotypic changes.

overall_design: Ribosome profiling and RNA-Seq of Saccharomyces cerevisiae cells in the replicative aging using the MAD system

first: Tianyu

last: Zhao

first: Asaka

last: Chida

first: Yuichi

last: Shichino

first: Dongwoo

last: Choi

first: Masaki

last: Mizunuma

first: R

last: McIsaac

last: Ohya


title: Metabolic Characterization of Patient-derived Xenograft Models of Clear Cell Renal Cell Carcinoma Transcriptomic Analysis

city: STANFORD

last: Brooks

address: 300 PASTEUR DR

institute: STANFORD UNIVERSITY

summary: To investigate the metabolic characterization difference of patient-derived xenograft models in transcriptome level.

overall_design:
We performed gene expression profiling analysis using data obtained from RNA-seq of 47 different PDXs and XENs.
Comparative gene expression profiling analysis of RNA-seq data for different PDX and XEN models.

first: Dalin

last: Zhang

first: Hongjuan

first: Donna

last: Peehl


title: The Nematode Oscheius tipulae as A Genetic Model for Programmed DNA Elimination

first: Jianbin

last: Wang


title: Comparison of global DNA methylation analysis by whole genome bisulfite sequencing and the Infinium Mouse Methylation BeadChip using fresh and fresh-frozen mouse epidermis

status: Public on Sep 23 2022

city: Copenhagen

first: Olivia

last: Luxford Meyer

address: Frederik V's Vej 11

department: Department of Forensic Medicine

country: Denmark

institute: University of Copenhagen

type: Methylation profiling by high throughput sequencing


title: Stabilization of cell-cell adhesions prevents symmetry breaking and locks in pluripotency in 3D gastruloids

city: Baronissi

first: Giovanna

middle: Maria

last: Ventola

state: Salerno

address: Via S. Allende, 43/L


title: MiRNAs array after SH3BP2 silencing in Gastrointestinal stromal tumor cells

first: Margarita

last: Martin

state: Barcelona

address: Casanova 143

department: Biomedicine

institute: University of Barcelona

summary:
Silencing of the adaptor SH3BP2 impairs Gastrointestinal stromal tumors growth through miRNAs
We dissected SH3BP2 pathway in Gastrointestinal Stromal Tumor cells (GIST) performing a miRNA array in SH3BP2-silenced GIST cells

platform_organism:
Homo sapiens
Human alphaherpesvirus 1
Human alphaherpesvirus 2
Macacine alphaherpesvirus 1
Human betaherpesvirus 5
human gammaherpesvirus 4
Herpesvirus saimiri (strain 11)
JC polyomavirus
Human immunodeficiency virus 1
Human betaherpesvirus 6B
Human gammaherpesvirus 8
Merkel cell polyomavirus
Betapolyomavirus hominis
Betapolyomavirus macacae

overall_design: GIST cells lines :GIST 48 and GIST 882 were transduced with NTshRNA and SH3BP2 shRNA (seq21) lentivirus as described ( Serrano-Candelas, E. et al Mol. Oncol. 2018). MicroRNA array experiments were performed in triplicates and conducted by Exiqon, Services, Demark.

first: Eva

last: Serrano Candelas


title: Microarray of preadipocytes undergoing differentiation

city: Bronx

first: Ana

last: Cuervo

state: NY

address: 1300 Morris Park Avenue

institute: Albert Einstein College of Medicine

summary: Transcriptomics of 3T3L1 preadipocytes control or knocked down for lamp2a during adipocyte differentiation

overall_design: Microarray of preadipocytes control or knocked down for lamp2a at day 0 and day 2 of adipocyte differentiation

first: Susmita

last: Kaushik


title: Effect of panobinostat, givinostat and ruxolitinib treatment in the anti-GBM mouse model of crescentic glomerulonephritis.

first: Roberto

last: Semeraro

summary: We demonstrated that in anti-glomerular basement membrane (anti-GBM) glomerulonephritis, crescents derived from clonal amplification of an immature subset of parietal epithelial cells (PECs) and that following treatment of mice with 3 different drugs currently used in haematological stem cell disorders (panobinostat, givinostat and ruxolitinib), only panobinostat exerted beneficial effect. To establish the mechanism of action of panobinostat, we generated single-cell RNA sequencing (scRNAseq) datasets of kidney cells obtained from control mice with anti-GBM glomerulonephritis and of mice treated with the three drugs. The analysis demonstrated that the drugs exerted similar effects on clusters of cells of the immune system, suggesting that all the three drugs elicit similar anti-inflammatory and immunosuppressive properties.

overall_design: Establish the mechanism of the effect of panobinostat, givinostat and ruxolitinib treatment in the anti-GBM mouse model of crescentic glomerulonephritis

first: Melica

last: Maria Elena

first: Semeraro

last: Roberto

first: Lasagni

last: Laura

first: Romagnani

last: Paola


title: Establish the mechanism of the effect of panobinostat on murine Pax2+ renal progenitors.

summary: We generated single-cell RNA sequencing (scRNAseq) datasets of primary cultures of mouse Pax2+ renal progenitors isolated from healthy mice and treated in vitro with vehicle or the HDAC inhibitor panobinostat. Pax2+ cells expressed progenitor cells markers in absence of tubular and endothelial cell markers and following treatment with panobinostat, upregulated the expression of podocyte-specific markers.

overall_design: Identify and characterize the mechanism of action of panobinostat on renal progenitor cells.


title: Transciptome analysis of human aortic smooth muscle cells (HASMCs) with BAF60c knockdown

city: Ann Arbor

first: Guizhen

last: Zhao

state: MI

address: 2800 Plymouth Rd

department: Cardiovascular Center

institute: University of Michigan

summary: HASMCs were transfected with BAF60c siRNA (siBAF60c, 20um) or control siRNA (siControl) for 48 hours, and serum-starved for 24 hours , followed by RNA-sequencing

overall_design: HASMCs mRNA profiles of siControl (3 replicates) and siBAF60c (3 replicates) transfection were generated by RNA-sequencing

first: Jifeng

first: Eugene

last: Chen


title: Genome-wide maps of chromatin state changes in BAF60c deficient human aortic smooth muscle cells (HASMCs)

summary: We compared BRG1 binding and 4 histone modification states between siControl and siBAF60c transfected human aortic smooth muscle cells (HASMCs) through ChIP sequencing (ChIP-seq).

overall_design: Examination of BRG1 and 4 different histone modifications (H3K9ac, H3K27ac, H2K9me2 and H3K27me3) in siControl or siBAF60c transfected HASMCs.

first: Haocheng

last: Lu


title: Connexin 30 deficiency ameliorates the disease progression of amyotrophic lateral sclerosis model mice by suppressing glial inflammation.

city: Fukuoka

first: Ryo

last: Yamasaki

state: Fukuoka

address: 3-1-1 Maidashi, Higashi-Ku

department: Neurology

institute: Kyushu University

summary: Connexin (Cx)30, which forms gap junction interconnecting astrocytes, regulates cell adhesion and migration and modulates glutamate transport. The expression levels of Cx30 are known to be upregulated on the activated astroglia at CNS inflammation lesion, including mutant-SOD1 transgenic ALS model mice spinal cord lesion. We aimed to clarify the role of Cx30 in mSOD1-transgenic mice. Cx30 was highly expressed in the pre-clinical stage of mSOD1-Tg mice. Cx30-knockout mSOD1 mice showed a delayed onset and tended to extend the survival period (log-rank, p = 0.09). At the progressive and end stages, anterior horn cells were more preserved in Cx30-knockout mSOD1 mice. Additionally, dorsal horn cells were kept more in Cx30-knockout mSOD1 mice at all stages. In the lesion of Cx30-knockout mSOD1 mice, GFAP and C3 positive inflammatory astroglia were decreased. Further, in Cx30-knockout mSOD1 mice, the amount of NOS2 protein at the end stage and the amount of Cx43 protein at the pre-clinical stage were smaller than in mSOD1 mice. These findings indicated reduced expression of astroglial Cx30 in the early stage of ALS model mice protects neurons by the attenuation of glial inflammation.

overall_design: Gene expression in the mice spinal cord was mesured at the 8 weeks-old wild type mice, mutant SOD1 transgenic mice and connexin30-deficient mutant SOD1 transgenic mice.

first: Yu

last: Hashimoto

first: Senri

last: Ko

first: Yuko

last: Kobayakawa

first: Katsuhisa

last: Masaki

first: Noriko

last: Isobe


title: RNA-Seq analysis of Sfmbt depletion and ChIP-Seq analysis of Pho and Sfmbt-GFP binding in Drosophila ovaries

status: Public on Sep 22 2022

city: Caparica

first: Daniel

last: Sobral

address: Departamento Ciências da Vida, Faculdade de Ciências e Tecnologia - Universidade Nova de Lisboa, Campus de Caparica

department: Life Sciences

country: Portugal

institute: UCIBIO - FCT NOVA

summary: We analyzed the transcriptome of young ovaries by RNA sequencing (RNAseq) after germ line depletion of Sfmbt by RNAi. We determined the genomic binding sites for GFP-Sfmbt and Pho using ChIPseq.

overall_design: Drosophila ovaries were dissected from 2 days old females after pupae eclosion. For RNAseq, it was used the nanos-Gal4 driver for germ line-specific expression of, respectively, UAS-mCherry RNAi (negative control) or UAS-Sfmbt RNAi (Sfmbt RNAi-1; TRiP.HMS00473). Three biological replicas were used for each condition. For Pleiohomeotic (Pho) ChIPseq, it was used anti-Pho antibodies on chromatin prepared from yw ovaries. Two biological replicas. For Sfmbt ChIPseq, it was used anti-GFP antibodies on chromatin prepared from GFP-Sfmbt or untagged control (Oregon-R) ovaries. Two biological replicas for each condition.

first: Rui

middle: G

last: Martinho

first: Steven

last: DeLuca


title: Pyruvate and recombinant human basic fibroblast growth factor rescue the pluripotency and metabolism of bovine embryonic stem cells on low-density feeder layers

city: Hohhot

first: jing

last: wang

state: Nei Mongol

address: Zhaojun Road

institute: Inner Mongolia University

summary: Feeder cells still play an important role in the in vitro culture of bovine embryonic stem cells(bESCs). A suitable microenvironment or niche is essential for the self-renewal and pluripotency of stem cells cultured in vitro. Feeder cells participate in the construction of stem cell niches by secreting growth factors and extracellular matrix proteins. In this study, we used metabolomics and transcriptomics to investigate the effects of feeder layer deficiency on bESCs. bESCs co-cultured with low-density feeder cells experienced a decrease in pluripotent gene expression, cell differentiation, and central carbon metabolic activity. When cell-permeable pyruvate (Pyr) and recombinant human basic fibroblast growth factor (rhbFGF) were added to the culture system, the pluripotency of bESCs on low-density feeder layers was rescued, and acetyl-coenzyme A(AcCoA) synthesis and fatty acid de novo synthesis increased. rhbFGF enhances the effects of Pyr and activates the overall metabolic level of bESCs grown on low-density feeder layers.

overall_design: Pluripotent stem cells mRNA profiles in MC-F7,1/7MC-F7,1/7MC+Pyr-F7,1/7MC+Pyr+FGF-F7. Note,1M equal to MC, 1M-F7 equal to MC-F7, 1/7M-F7 equal to 1/7MC-F7.

first: Wenqiang

last: Xu

first: Jing

last: Wang

first: Wei

last: Li

first: Lingna

last: Gao

first: Ruifeng

last: Hao

first: Xuejie

last: Han

first: Chen

first: Hui

last: Zhang

first: Xueling


title: Reprograming of Proteasomal Degradation by Branched Chain Amino Acid Metabolism

city: Cologne

first: Thorsten

last: Hoppe

state: NRW

address: Joseph-Stelzmann-Str. 26

department: Institut für Genetik

institute: Universität zu Köln

summary: Branched‐chain amino acid (BCAA) metabolism is a central hub for energy production and regulation of numerous physiological processes. Controversially, both increased and decreased levels of BCAAs are associated with longevity. Using genetics and multi‐omics analyses in Caenorhabditis elegans, we identified adaptive regulation of the ubiquitin‐proteasome system (UPS) in response to defective BCAA catabolic reactions after the initial transamination step. Worms with impaired BCAA metabolism show a slower turnover of a GFP‐based proteasome substrate, which is suppressed by loss‐of‐function of the first BCAA catabolic enzyme, the branched‐chain aminotransferase BCAT‐1. The exogenous supply of BCAA‐derived carboxylic acids, which are known to accumulate in the body fluid of patients with BCAA metabolic disorders, is sufficient to regulate the UPS. The link between BCAA intermediates and UPS function presented here sheds light on the unexplained role of BCAAs in the aging process and opens future possibilities for therapeutic interventions.

overall_design: Analysis of the transcriptional profile of adult C. elegans branched chain amino acid mutants.

first: Sonia

last: Ravanelli

first: Prerana

last: Wagle


title: HSP70-driven molecular response to the proteasome machinery inhibition is a vulnerability in cancer

city: Warszawa

first: AKANKSHA

last: JAISWAR

address: ul. Adolfa Pawińskiego 5

country: Poland

institute: Mossakowski Medical Research Institute

summary: In this study we employed a label-free global proteomics approach, with a sensitivity of over 10k quantified proteins per sample, to determine contributions of different compensatory mechanisms upon the proteasome inhibition with carfilzomib - in cells of multiple myeloma, normal fibroblasts and cancers of lung, colon and pancreas. We identified several responding pathways, while the main HSP70 family stress inducible molecular chaperones HSPA1A and HSPA1B (often addressed jointly as HSPA1A/B or simply “Hsp70”, due to nearly identical protein sequences) were the most universal proteasome inhibition responders in proteomes of all the studied cell types. Further overlap of differential proteomics with RNA-seq analysis obtained at the same condions (DMSO control vs carfilzomib treatment) and a subsequent validation showed that the proteasome inhibition-dependent induction of HSPA1A/B and other chaperone proteins in cancer cells is in fact transcription-driven.

overall_design: Cell lines were either treated with carfilzomib (C) for 24h at concentrations at the IC50 of proteasome activity, or with DMSO (D) as a control, in biological triplicates (numbers 1-3). Total RNA was exracted from cells and subjected to mRNA sequencing.

first: Akanksha

last: Jaiswar

first: Magdalena

last: Oron

first: Dawid

last: Walerych


title: Whole genome bisulfite sequencing and Infinium Mouse Methylation BeadChip using fresh and fresh-frozen mouse epidermis (WGBS)

first: Olivia

last: Luxford Meyer

summary: We compared the global DNA methylation levels of hairless mouse epidermis using the Infinium Mouse Methylation BeadChip from Illumina and whole genome bisulfite sequencing (WGBS). We also studied the effect of sample storage conditions by using fresh and fresh-frozen epidermis. The DNA methylation levels of xxx,xxx CpG sites covered by both the BeadChip and WGBS were compared. DNA methylation levels obtained with WGBS and the BeadChip were strongly correlated (Pearson correlation r = 0.984). We applied a threshold of 15 reads for the WGBS methylation analysis. Even at a threshold of 10 reads, we observed no substantial difference in DNA methylation levels compared with that obtained with the BeadChip. The DNA methylation levels from the fresh and the fresh-frozen samples were strongly correlated when analysed with both the BeadChip (r = 0.996) and WGBS (r = 0.994). We conclude that the two methods of analysis generally work equally well for studies of DNA methylation of mouse epidermis and find that fresh and fresh-frozen epidermis can generally be used equally well. The choice of method will depend on the specific study’s aims and the available resources in the laboratory.

overall_design: Epidermal samples from six mice. Each sample was split in two (fresh-frozen and fresh). Samples were analysed with WGBS and BeadChip.

last: Meyer

first: Mikkel

last: Andersen

first: Claus

last: Børsting

first: Niels

last: Morling

first: Peter

last: Philipsen

first: Catharina

last: Lerche


summary: We compared the global DNA methylation levels of hairless mouse epidermis using the recently released Infinium Mouse Methylation BeadChip from Illumina and whole genome bisulphite sequencing (WGBS). We also studied the effect of sample storage conditions by using fresh and fresh-frozen epidermis. The DNA methylation levels of 123,851 CpG sites covered by both the BeadChip and WGBS were compared. DNA methylation levels obtained with WGBS and the BeadChip were strongly correlated (Pearson correlation r = 0.984). We applied a threshold of 15 reads for the WGBS methylation analysis. Even at a threshold of 10 reads, we observed no substantial difference in DNA methylation levels compared with that obtained with the BeadChip. The DNA methylation levels from the fresh and the fresh-frozen samples were strongly correlated when analysed with both the BeadChip (r = 0.999) and WGBS (r = 0.994). We conclude that the two methods of analysis generally work equally well for studies of DNA methylation of mouse epidermis and find that fresh and fresh-frozen epidermis can generally be used equally well. The choice of method will depend on the specific study's aims and the available resources in the laboratory


title: Stabilization of cell-cell adhesions prevents symmetry breaking and locks in pluripotency in 3D gastruloids [mRNASeq3prime]

first: Giovanna

last: Ventola

summary: We report the effect of Budesonode on embryonic stem-to-mesenchymal-like transition (esMT)  and 3D Gastruloids

overall_design: Examination of the transcriptional profile of 2D ESCs treated with Budesonide

first: Gabriella

last: Minchiotti

first: Eduardo

last: Patriarca

first: Cristina

last: D'Aniello


title: PCAT19 safeguards quiescent endothelial DNA by preventing uncontrolled phosphorylation of replication protein A2

city: Frankfurt am Main

first: Timothy

last: Warwick

state: Hesse

address: Theodor-Stern-Kai 7

department: Institute for Cardiovascular Physiology

institute: Goethe Universität Frankfurt am Main

summary: In healthy vessels, endothelial cells maintain a stable, differentiated and growth-arrested phenotype for years. Upon injury, a rapid phenotypic switch facilitates proliferation to restore tissue perfusion. Here we report the identification of the endothelial cell-enriched long noncoding RNA (lncRNA) PCAT19, which contributes to this process and acts as a safeguard for the endothelial genome during the quiescent phase. PCAT19 is enriched in confluent, quiescent endothelial cells. PCAT19 binds to the full replication protein A (RPA) complex in a DNA damage and cell cycle-related manner. PCAT19 limits phosphorylation of RPA2 on the serine 33 (S33) residue and thereby facilitates the DNA damage response at the expense of slower cell cycle progression. Reduction in PCAT19 levels, either in response to loss of cell contacts or knockdown, promoted endothelial proliferation and angiogenic function. Collectively, PCAT19 acts as a dynamic guardian of the endothelial genome, promotes cellular longevity and facilitates rapid switching to proliferation.

overall_design: RNA sequencing (n = 3) of human umbilical vein endothelial cells (HUVEC) treated with either control LNA gapmers or PCAT19 LNA gapmers, which knockdown PCAT19 expression.

first: James

last: Oo

first: Katalin

last: Pálfi

first: Ilka

last: Wittig

first: Cristian

last: Prieto-Garcia

first: Vigor

last: Matkovic

first: Ines

last: Tomašković

first: Frederike

last: Boos

first: Tom

last: Teichmann

first: Kirill

last: Petriukov

first: Lars

last: Maegdefessel

first: Zhiyuan

last: Wu

first: Minh

last: Duc Pham

first: Jaya

last: Krishnan

first: Andrew

middle: H

last: Baker

first: Stefan

last: Günther

first: Helle

last: Ulrich

first: Ivan

last: Dikic

first: Matthias

last: Leisegang

first: Ralf

middle: P

last: Brandes


title: RNA-seq analysis of human multiple myeloma cell line RPMI 8226 after HDAC1 knockdown

status: Public on Sep 21 2022

city: Tokushima

first: Takeshi

last: Harada

state: Tokushima

address: 3-18-15 Kuramoto-cho

department: Hematology, Endocrinology and Metabolism

institute: Tokushima University Graduate School of Biomedical Sciences

summary: Histone deacetylases (HDACs) have emerged as therapeutic targets in multiple myeloma (MM); however, the underlying roles of each class- or isoform-HDAC have not fully clarified. The present study delineates the effect of HDAC1 suppression or inhibition in MM cells. The RNA-seq analysis here revealed that HDAC1 suppression downregulated IRF4 and PIM2, which both play a crucial role in MM cell survival and proliferation. Mechanistically, HDAC1 inhibition dampens IRF4 transcription through histone hyperacetylation and hindrance of RNA polymerase II recruitment at IRF4 locus. PIM2 is transcriptionally under direct regulation by IRF4, thereby reducing PIM2 expression after HDAC1 inhibition. PIM2 is upregulated by the stimuli from bone marrow microenvironment including IL-6 independent of IRF4 regulation in MM cells. Although these stimuli reduce the cytotoxic effect of HDAC1 inhibition in MM cells, direct blockade of PIM2 overcomes the weak point of HDAC1 inhibition. The effect of the combination of class I HDAC inhibitors with PIM inhibitors is further confirmed in vivo mouse xenograft models. Our findings provoke clinical applications of class I HDAC inhibitors in combination with PIM inhibitors against MM.

overall_design: RPMI 8226 cells were transduced with control vector or HDAC1 shRNA in tripricate. After puromycin selection for 48 hr, the transduced cells were subject to RNA-seq.


title: RNA data of human FOP patients-derived iPSCs treated with ACVR1 R206H mutant-targeting AAVs

status: Public on Sep 20 2022

city: Worcester

first: JAE-HYUCK

last: SHIM

state: Massachusetts

address: 364 Plantation street

institute: University of Massachusetts Medical School

summary: We found that both A9 (amiR-RH6) and A10 (amiR-RH7)-AAVs significantly decrease osteogenic differentiation of FOP-iPSCs.  We also observed that A9 and A10-AAVs treatment changed the ratio of R206H mutant to wildtype of ACVR1 in FOP-iPSCs. To identify off-target effect of A9 or A10-AAVs, we compared RNA expression of FOP-iPSCs treated with control, A9, or A10-AAVs.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for human iPSCs treated with control, A9, or A10-AAVs.

first: Yeon-Suk

last: Yang

first: Jung-Min

last: Kim

first: Jun

last: Xie

first: Sachin

last: Chaugule

first: Chujiao

last: Lin

first: Hong

last: Ma

first: Edward

last: Hsiao

first: Jaehyoung

last: Hong

first: Hyonho

last: Chun

first: Eileen

last: Shore

first: Frederick

last: Kaplan

first: Guangping

last: Gao

first: Jae-Hyuck

last: Shim


title: CBFA2T3-GLIS2 oncogenic fusion is sufficient for leukemic transformation

city: Seattle

first: Soheil

last: Meshinchi

state: Washington

address: 1100 Fairview Ave N.

department: Clinical Research Division

institute: Fred Hutchinson Cancer Research Center

summary: Purpose: To investigate whether human cord blood CD34+ hematopoietic stem and progenitor cells (CB HSPCs) transduced with CBFA2T3-GLIS2 (C/G) expression construct recapitulates primary C/G acute myeloid leukemia (AML).     Methods:  CB HSPCs were transduced with either C/G fusion/GFP or GFP control contruct (C/G-CB or GFP-CB cells, respectively) and cultured in endothelial cell (EC) co-culture or myeloid promoting culture (MC) for 12 weeks. RNA from transduced cells were isolated at week 1, 6 and 12 in either culture condition. Whole transcriptome RNA-sequencing was conducted using 75bp strand-specific paired-end mRNA libraries and sequenced on the Illumina HiSeq 2000/2500.     Results: Unsurpervised clustering analysis of RNA-sequencing of C/G-CB cells cultured with ECs or in MC  demonstrated that the C/G-CB cells from weeks 6 and 12 in EC co-culture clustered with primary C/G-positive patient samples, but not C/G-CB cells cultured in MC nor GFP controls. In addition, EC C/G-CB cells had signficant enrichemnt of WNT, HEDGEHOG and TGF-beta pathways. However, both EC and MC cultures revealed up-regulation of ERG and BMP2, genes compared to GFP control, which are genes previously shown to be strongly upregulated in C/G AML, and concomitant down-regulation of the erythroid-megakaryocyte differentiation gene GATA1.    Conclusions: We find that lentiviral transduction of C/G fusion is sufficient to induce malignant transformation of human CB HSPCs that recapitulates the transcriptome of primary C/G AML.

overall_design: CB HSPCs engineered to express C/G fusion transcript were cultured with an endothelial co-culture system or in myeloid promoting conditions for 1, 6, and 12 weeks and underwent transcriptome profiling using ribodepleted (rRNA depleted) RNA-sequencing.

first: Quy

last: Le

first: Rhonda

last: Ries

first: Jenny

last: Smith

first: Amanda

last: Leonti


title: Stabilization of cell-cell adhesions prevents symmetry breaking and locks in pluripotency in 3D gastruloids [mRNASeq]

first: Giovanna

last: Ventola

overall_design: Examination of the transcriptional profile of 3D gastruloids treated with Budesonide

first: Gabriella

last: Minchiotti

first: Eduardo

last: Patriarca

first: Cristina

last: D'Aniello


title: Prolonged XPO1 inhibition is essential to achieve optimal antileukemic activity in NPM1-mutated acute myeloid leukemia

city: Perugia

first: Lorenzo

last: Brunetti

address: Piazzale Menghini 8/9

institute: University of Perugia

summary: NPM1-mutated acute myeloid leukemia (AML) accounts for one third of AML in adults. NPM1-mutated AML maintenance depends on the interaction between mutated NPM1 (NPM1c) and the nuclear exporter Exportin 1 (XPO1). In this work, we show that continous XPO1 inhibition is necessary to achieve stable disruption of the NPM1c-XPO1 interaction and to induce HOX downregulation and differentiation of AML cells with mutated NPM1. In contrast, intermittent XPO1 inhibition only results in minimal transcriptional perturbation and limited antileukemic activity.

overall_design: RNA-sequencing of OCI-AML3 cells treated with the XPO1 inhibitor Selinexor for either 24 or 72 hours and analyzed at 24 and 72 hours.

first: Giulia

last: Pianigiani

first: Giulio

last: Spinozzi


title: Hyperactive RAS/MAPK introduces cancer-specific mitotic vulnerabilities

city: Fort Collins

first: Erin

last: Osborne Nishimura

state: CO

address: 1870 Campus Delivery, 200 W. Lake St.

department: Biochemistry and Molecular Biology

institute: Colorado State University

summary: We performed tanscriptional profiling of ARPE19 and four isogenic transformed cells lines in which   Ras or two downstream pathways, MAPK or PI3K/mTOR, were up-regulated. The purpose of this study is to understand how Ras signaling impacts kinetochore function.

overall_design: mRNA-seq transcriptome profilng performed in triplicate on each of the five cell lines.

first: Jacob

last: Herman

first: Romario

last: Romain

first: Hazheen

last: Shirnnekhi

first: Keith

middle: F

last: DeLuca

first: Chad

last: Toled

first: Patrick

middle: J

last: Paddison

first: Jennifer


title: Arid1a loss potentiates pancreatic β-cell regeneration through activation of EGF signaling

city: Boston

first: Cigall

last: Kadoch

address: 450 Brookline Avenue

institute: Broad Institute of MIT and Harvard, Harvard Medical School, Dana-Farber Cancer Institute

summary: The dynamic regulation of β-cell abundance is poorly understood. Since chromatin remodeling plays critical roles in liver regeneration, these mechanisms could be generally important for regeneration in other tissues. Here we show that the ARID1A mammalian SWI/SNF complex subunit is a critical regulator of β-cell regeneration. Arid1a is highly expressed in quiescent β-cells but is physiologically suppressed when β-cells proliferate during pregnancy or after pancreas resection. Whole body Arid1a knockout mice are protected against streptozotocin induced diabetes. Cell-type and temporally specific genetic dissection show that β-cell specific Arid1a deletion can potentiate β-cell regeneration in multiple contexts. Transcriptomic and epigenomic profiling of mutant islets reveal increased Neuregulin-ERBB-NR4A signaling. Chemical inhibition of ERBB or NR4A1 was able to block increased regeneration associated with Arid1a loss. mSWI/SNF complex activity is a barrier to β-cell regeneration in physiologic and disease states.

overall_design: ChIP-Seq of the histone modification H3K27ac in MIN6 cells for wildtype, heterozygous ARID1A KO, and homozygous ARID1A KO samples.

first: Cemre

last: Celen

first: Clayton

last: Collings

first: Jordan

last: Otto

first: Hao

last: Zhu


title: ATF4-dependent fructolysis fuels brain tumorigenesis (WGS)

city: Beijing

first: Chao

last: Chen

address: Datun

department: CAS Key Laboratory of Infection and Immunity

institute: Institute of Biophysics, Chinese Academy of Sciences

summary: The goals of WGS (Whole Genome Sequencing) analysis in TJ46 cells derived from a GBM primary tissue  to obtain information on the genetic alterations that characterize this model.

overall_design: Sequencing libraries were prepared using the NEBNext DNA Library Prep Master Mix Set (Illumina) according to the manufacturer’s instructions. The libraries were paired-end sequenced on an Illumina NovaSeq 6000 (Annoroad Gene Technology Beijing Co. Ltd.).

first: Xinjian

last: Li


title: Genome-wide maps of Pol II pSer5 state in lung smooth muscle cells

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

summary: To examine the effects of Tet3-inactivation on genome-wide transcriptional initiation, we determined the binding profiles of Pol II pSer5, a specific form of Pol II that marks transcriptional initiation sites, by ChIP-seq after DRB-induced block of transcriptional elongation.

overall_design: Examination of control and Tet3-inactivation smooth muscle cells

first: Fan

last: Wu

last: Guenther


title: Infection of the murine placenta by Listeria monocytogenes induces sex-specific responses in the fetal brain

city: East Lansing

first: Jonathan

last: Hardy

state: Michigan

address: 775 Woodlot Drive

department: Microbiology and Molecular Genetics

institute: Michigan State University

summary: BACKGROUND: Epidemiological data indicate that prenatal infection is associated with an increased risk of several neurodevelopmental disorders in the progeny. These disorders display sex differences in presentation. The role of the placenta in the sex-specificity of infection-induced neurodevelopmental abnormalities is not well-defined. We used an imaging-based animal model of the bacterial pathogen Listeria monocytogenes to identify sex-specific effects of placental infection on neurodevelopment of the fetus. METHODS: Pregnant CD1 mice were infected with a bioluminescent strain of Listeria on embryonic day 14.5 (E14.5). Excised fetuses were imaged on E18.5 to identify the infected placentas. The associated fetal brains were analyzed for gene expression and altered brain structure due to infection. The behavior of adult offspring affected by prenatal Listeria infection was analyzed. RESULTS: Placental infection induced sex-specific alteration of gene expression patterns in the fetal brain and resulted in abnormal cortical development correlated with placental infection levels. Furthermore, male offspring exhibited abnormal social interaction, whereas females exhibited elevated anxiety. CONCLUSION: Placental infection by Listeria induced sex-specific abnormalities in neurodevelopment of the fetus. Prenatal infection also affected the behavior of the offspring in a sex-specific manner.

overall_design: Gene expression analysis of RNA-sequencing of Listeria monocytogenes exposed fetal mouse brains during pregnancy

first: Kun

last: Lee

first: Matti

last: Kiupel

first: Thomas

last: Woods

first: Prachee

last: Pingle


title: Anti-PD-1 re-navigates concealed IL-15 to rejuvenate tumor-specific PD-1+CD8+T cells inside the tumor microenvironment

first: Jiao

last: Shen

address: #15 Datun Rd., Chaoyang District

summary: The authors engineer an anti-PD-1-concealed sIL-15 fusion protein (αPD-1-IL-15-R), eliciting extraordinary antitumor immunity with negligible toxicity. αPD-1-IL-15-R largely expands tumor-specific CD8+T for effective tumor rejection through cis-delivery and further controls metastasis.

overall_design: TILs were isolated from MC38 tumor-bearing mice 48 hours after the 2nd injection of αPD-1-IL-15-R. Total RNA extraction, mRNA library construction, and sequencing were established by BGI (Beijing, China)


title: Ribosome profiling of Murine Embryonic Fibroblasts in the context of different Fbxo4 and hnRNPK status.

city: Cleveland

first: J Alan

last: Diehl

state: Ohio

address: 2109 Adelbert Rd. SOM Wood/W402

department: Department of Biochemistry

institute: Case Western Reserve University

summary: Background: SCF-Fbxo4 is suspected to regulate activity of RNA binding protein hnRNPK by non-degradive ubiquitylation. Research strategy: To determine the genomic output of SCF-Fbxo4 - hnRNPK interplay, murine embryonic fibroblasts (MEFs) with different status of hnRNPK/Fbxo4 were subjected to Ribosome profiling. Sequencing was performed on total RNA and RNA protected by ribosomes for each condition.

overall_design: Applying RNAi strategy hnRNPK was depleted in either wild type MEFs or MEFs Fbxo(-/-). MEFs conditioned in 4 different ways: wt- control (I), Fbxo4 knock-out (II), Fbxo4 knock-out + hnRNPK RNAi knock-down (III) and RNAi hnRNPK knock-down only (IV) were subjected to sequencing of total RNA and Ribosome protected fragment.

first: J

first: B

last: Mucha


title: RNA Sequencing of melanoma cell line (WM983B) upon Fbxo4 knock-down

summary: Fbxo4 is a member of Skip1-Cullin1-F-box protein E3 ubiquitin ligase complex that controls RNA biding proteins. We report that loss of Fbxo4 in melanoma contribute to altered gene expression leading to dysregulation pathways reponsible for cell-cell interaction, cell anocharege, invasion and motility.

overall_design: WM983B melanoma cell line were infected with empty lentiviral vector (control) or lentivirus encoding anti-Fbxo4 shRNA.

last: A Diehl


title: The histone variant macroH2A modulates inflammatory response in cancer [HepG2]

city: Badalona

first: Roberto

last: Malinverni

address: Josep Carreras Building, Ctra de Can Ruti,

institute: Josep Carreras Leukaemia Research Institute

summary: MacroH2A histone variants have a major role in nuclear organization and large-scale 3D chromatin architecture. How these alterations impinge on the behaviour of cancer cells is not known. Here, we describe the analysis of the total macroH2A loss of function phenotype in a model of hepatoblastoma, the main childhood liver cancer. Performing transcriptomic analyses in xenografts and cell cultures, we find that macroH2A modulated the response of cancer cells to paracrine inflammatory signalling. Specifically, ablation of macroH2A ablation neutralized the induction of a large subset of genes by TNFα and led to the hyperactivation of another subset of genes. Among the top macroH2A-sensitive genes we find the cancer-related gene DKK1 . Depletion of macroH2A rendered the DKK1 gene hypersensitive to TNFα signalling boosting the secretion of DKK1 protein. On the gene regulation level, this was mediated by an alteration of the local chromatin structure and facilitated activation of distal enhancer elements. The study of human samples of hepatoblastoma showed that DKK1 is strongly upregulated in tumors and associated with poor patient outcome. Taken together our results suggest that the regulation of 3D chromatin architecture by macroH2A histone variants has a central role in the response and regulation of paracrine signalling that might be relevant for the interaction of cancers with immune cells and other cells in their microenvironment.

overall_design: Transcriptomic profiling HepG2 cell lines stably expressing either control shRNAs (CTL) or shRNAs targeting macroH2A1 and macroH2A2 (DKD) and either untreated or treated with TNFα

first: David

last: Corujo

first: Marcus

last: Buschbeck


title: Reliable assessment of telomere maintenance mechanisms in neuroblastoma

status: Public on Sep 19 2022

first: Matthias

last: Fischer

address: Kerpener Str. 62

department: Department of Experimental Pediatric Oncology

institute: University Children’s Hospital of Cologne

summary:
Telomere maintenance mechanisms (TMM) are a hallmark of high-risk neuroblastoma, and are conferred by activation of telomerase or alternative lengthening of telomeres (ALT). However, detection of TMM is not yet part of the clinical routine, and consensus on TMM detection, especially on ALT assessment, remains to be achieved.
Based on our results we here propose a workflow to reliably detect TMM in neuroblastoma. We show that unambiguous classification is feasible following a stepwise approach that determines both, activation of telomerase and ALT. The workflow proposed in this study can be used in clinical routine and provides a framework to systematically evaluate telomere maintenance mechanisms in risk stratification and treatment allocation of neuroblastoma patients.

overall_design: Expression profiling and TERRA expression analysis by high throughput sequencing.

first: Meeser

last: Alina

first: Rosswog

last: Carolina

first: Fischer

last: Matthias


title: Next Generation Sequencing Facilitates Quantitative Analysis of control smooth muscle cells and Tet3-inactivation smooth muscle cells transcriptomes

first: Stefan

last: Günther

summary: Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived retinal transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis

overall_design: lung smooth muscle cells mRNA from control and Tet3-inactivation mice

first: Fan

last: Wu

last: Guenther


title: TRIM67 drives tumorigenesis in oligodendrogliomas through Rho GTPase-dependent membrane blebbing

city: Heidelberg

first: Sevin

last: Turcan

address: INF 460

institute: NCT

summary: The aim of this study is to characterize the mechanistic role of TRIM67 in glioma biogenesis. Towards this goal, here we utilized engineered human neural stem cells and patient-derived tumor sphere lines with or without IDH mutations and 1p/19q co-deletions to study the function of TRIM67 in gliomas. We found that upregulated TRIM67 induces membrane blebbing through Rho GTPase-mediated signaling, resulting in more advanced cell motility and tumor expansion.

overall_design: Analysis of total mRNA from human neural stem cells and 4 human glioma cell lines

first: Ruslan

last: Al-Ali

first: Julianna

last: Varga

first: Xueyuan

last: Sun


title: Gene expression profiling of melanoma cell lines (carrying NF1 loss-of-function) treated with DMSO (vehicle), MTX-216, MTX-211, trametinib, the combination of MTX-216 and trametinib, or pictilisib

city: Charlottesville

first: Mohammad

last: Fallahi-Sichani

state: VA

address: 415 Lane Rd

institute: University of Virginia

summary: In this study, we identified a multi-kinase inhibitor MTX-216 to be efficacious in blocking NF1 loss-of-function melanoma cells. To identify the mechansisms of action of MTX-216, we treated NF1 loss-of-function melanoma cell lines with MTX-216, MTX-211 (the structural analogue of MTX-216 that has no effect on melanoma cells) as well as commericial kinase inhibitors, trametinib and pictilisib, and compared their gene expression profiles.

overall_design: Three NF1 loss-of-function melanoma cell lines (MeWo, WM3918, SKMEL113) were treated with MTX-216 (1 uM), MTX-211 (1 uM), trametinib (0.1 uM), the combination of MTX-216 (1 uM) and trametinib (0.1 uM), pictilisib (1 uM), or DMSO (control) for 24 hours. Samples were treated in three independent replicates. Samples were enriched for polyA RNA prior to sequencing. Samples were run on Illumina NovaSeq 6000 (S4) using paired-end read with 150 cycles. In total, 1.4 billion reads were generated, including ~33 million reads per sample.

first: Cara

last: Abecunas


title: A microbiome-dependent gut–brain pathway regulates motivation for exercise

city: Philadelphia

first: Patrick

last: Lundgren

state: PA

address: 302 Johnson Pavilion, 3610 Hamilton Walk

institute: University of Pennsylvania

summary: Single nucleus RNA sequencing of mouse striatum at steady state and after exercise in mice treated and untreated with broad spectrum antibiotics.

overall_design: Nuclei were isolated and FACS sorted based on DAPI from mouse striatum at the given conditions and subsequently used in 10X Genomics pipeline.

first: Lenka

last: Dohnalova

first: Christoph

last: Thaiss


title: Ferroptosis of tumor-associated neutrophils is immunosuppressive and promotes tumor growth

first: Priyankara

last: Wickramasinghe

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

summary: Ferroptosis is a non-apoptotic form of regulated cell death triggered by the discoordination of regulatory redox mechanisms culminating in massive peroxidation of polyunsaturated phospholipids. The development of the concept of ferroptosis stemmed from an active search for alternatives to apoptosis in cancer cells. Ferroptosis inducers have shown remarkable effectiveness in killing tumor cells in vitro, yet with no obvious success in experimental animal models, with a notable exception of immune-deficient mice 1,2. This suggests the potential poorly understood contribution of ferroptosis on immune cells. Pathologically activated neutrophils (PMN), termed myeloid-derived suppressor cells (PMN-MDSC), are major negative regulators of anti-tumor immunity3-5. Here, we found that PMN-MDSC in the tumor microenvironment (TME), spontaneously die by ferroptosis. While decreasing the presence of PMN-MDSC, ferroptosis induces the release of oxygenated lipids and limits mouse and human T cell activity. In immune-competent mice, genetic and pharmacological inhibition of ferroptosis abrogates suppressive activity of PMN-MDSC, reduces tumor progression, and synergizes with immune checkpoint blockade (ICB) to suppress the tumor growth. In contrast, induction of ferroptosis in immune-competent mice promotes tumor growth. Thus, ferroptosis is a unique and targetable immunosuppressive mechanism of PMN-MDSC in the TME that can be pharmacologically modulated to limit tumor progression.

overall_design: RNA-seq of granulocytes with Alox15 WT and KO status

first: Dmitry

last: Gabrilovich

first: Rina

last: Kim


title: Caspase-8 and FADD prevent spontaneous ZBP1 expression and necroptosis

city: Memphis

first: Douglas

last: Green

state: United States

address: 262 Danny Thomas Pl

department: Immunology

institute: St Jude Children's Research Hospital

summary: Caspase-8 and FADD play key roles in the regulation of cell death by necroptosis. The absence of either protein results in early embryonic lethality due to the activation of the kinase RIPK3 and its phosphorylation of the necroptosis executioner, MLKL. We genetically engineered and characterized a mouse model to monitor MLKL phosphorylation in the absence of necroptosis in vivo. Ablation of caspase-8 or FADD resulted in the transcriptional upregulation in several tissues of ZBP1, a cytosolic nucleic acid sensor capable of activating RIPK3, and ZBP1 was required for spontaneous phosphorylation of MLKL. Our findings provide a novel mechanism by which the FADD-Caspase-8 complex prevents necroptosis.

overall_design: Here we performed RNAseq screening to identify gene expression in the absence or presence of Caspase-8 or FADD

first: Diego

last: Rodriguez

first: Bart

last: Tummer

first: Mark

last: Chen

first: Jeremy

middle: C

last: Crawford


title: Impact of KIF26A loss in human forebrain organoids

first: Christopher

last: Walsh

state: MA

address: 3 Blackfan Circle

department: Genetics and Genomics

institute: Boston Children's Hospital

summary: KIF26A is an unconventional kinesin that lacks motor activity. To characterize its role in brain development, we generated KIF26A knock-out iPSC lines and differentiated forebrain organoids. We performed single cell RNA sequencing at Day 60 and Day 80 to compare between control and KIF26A-deleted organoids at the molecular level, which revealed cell type-specific transcriptional changes in MAPK, MYC and E2F pathways.

overall_design: Control and KIF26A-deleted organoids were collected at Day 60 and 80, dissociated into single cells and captured using 10X Chromium platform.

first: Xuyu

last: Qian

first: Ellen

middle: M

last: DeGennaro

first: Maya

last: Talukdar