title: Highly cooperative chimeric super-SOX induces naïve pluripotency across species [ChIP-Seq]

city: Boston

first: Sergiy

last: Velychko

state: MA

address: 77 Avenue Louis Pasteur, Room 232

department: Genetics

institute: Harvard Medical School

summary: Our understanding of pluripotency remains limited: iPSC generation has only been established for a few model species, pluripotent stem cell lines exhibit inconsistent developmental potential, and germline transmission demonstrated only for mice and rats.  By swapping structural elements between Sox2 and Sox17, we built a chimeric super-SOX factor, Sox2-17, that enhanced iPSC generation in five tested species: mouse, human, cynomolgus monkey, cow, and pig. A swap of alanine to valine at the interface between Sox2 and Oct4 delivered a remarkable gain-of-function by stabilizing Sox2/Oct4 dimerization on DNA, enabling generation of high-grade OSKM iPSCs capable of supporting the development of healthy all-iPSC mice.  Sox2/Oct4 dimerization emerged as the core driver of naïve pluripotency with its levels diminished upon priming. Transient overexpression of Sox2-17 and Klf4 (S*K cocktail) restored the dimerization and boosted the developmental potential of pluripotent stem cells across species, providing a universal method for naïve reset in mammals.

overall_design: We performed chromatin immunoprecipitation with sequencing (ChIP-seq) to identify genome-wide binding sites early in reprogramming—48 hours after doxycycline induction of KS2 or KS2AV (Addgene #136617, containing Klf4 and Sox2 or Sox2AV) with or without addition of Oct4 or Oct6 (Addgene #136617 and 136611, O4KS  and O6KS cocktails) in Rosa26rtTA-Gof18 mouse embryonic fibroblasts (MEFs).

first: Vikas

last: Malik


title: Bacterial Protoplast-Derived Nanovesicles Carrying CRISPR/Cas9 Tools Efficiently Re-educate Tumor-Associated Macrophages for Cancer Immunotherapy

status: Public on Nov 27 2023

city: Nan Jing

first: pingwen

last: shao

address: 163 Xianlin Avenue, Qixia Distric

country: China

institute: Nanjing University

type: Expression profiling by high throughput sequencing

summary: To investigate the activation of tumor microenvirment, we used E.coli-derived nanovesicles to treat tumor-bearing mice and detected tumor tisssues  by RNA-Seq.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for PBS group and nanovesicle treatment group.

first: Mingming

last: Zhao

first: Xiaohui

last: Cheng

first: Pingwen

last: Shao

first: Yao

last: Dong


title: A comparison of bone microarchitectural and transcriptomic changes in murine long bones in response to hindlimb unloading and aging

city: Richmond

first: Steven

middle: Joshua

last: Meas

email: stevenmeas3@gmail.com, meass2@vcu.edu

state: VA

address: 70 S Madison St

country: USA

institute: Virginia Commonwealth University, Richmond

summary: Age and disuse-related bone loss both result in decreases in bone mineral density, cortical thickness, and trabecular thickness and connectivity. Disuse induces physiological changes in bone similar to those seen with aging. Animal studies used 6, and 22-month-old C57BL/6J male and female mice that were hindlimb unloaded (HLU) for 3 weeks. Ingenuity pathway analysis (IPA) included 4-month-old male mice unloaded for 3 weeks and a publicly available dataset (GLDS647) from 3-month female C57BL/6N mice unloaded for 7 days. There were age- and sex-dependent changes in bone structure and mechanical properties in response to HLU. The cortical bone and epiphyseal trabecular bone compartments were most affected. There were greater changes in bone mechanical properties due to age in males, and HLU in females.  RNA extracted from whole-bone marrow-flushed tibiae was sequenced and analyzed. Gene ontology analysis demonstrated that mitochondrial function was downregulated after HLU whereas cell-cycle transition was downregulated with aging. IPA was used to identify the leading canonical pathways and upstream regulators in each HLU age group. IPA identified “Senescence Pathway” as the third leading canonical pathway enriched in mice exposed to HLU. HLU induced activation of the senescence pathway in 3 month and 4-month-old mice, inhibited it in 6-month-old mice and did not change it in 22 month old mice. In conclusion, we demonstrate that hindlimb unloading initiates changes in bone microarchitecture and gene expression characteristic of aging, but with distinct differences.

overall_design: 6-month-old and 22-month-old male and female mice were subjected to hindlimb unloading (HLU) for a period of 3 weeks. RNA was extracted from marrow-flushed left tibias and sequenced.

first: Steve

first: Gabriella

last: Daire

first: Michael

last: Friedman

first: Rachel

last: DeNapoli

first: Preetam

last: Ghosh

first: Joshua

last: Farr

first: Henry

last: Donahue


title: Triptolide analogs induced apoptosis on pancreatic cancer patient-derived organoids

status: Public on Nov 24 2023

city: Chicago

first: Qiaomu

last: Tian

address: 5841 S. Maryland Ave

institute: University of Chicago

summary: Investigate the MOA of triptolide analog-CK21 in pancreatic cancer. Time course transcriptomic profiling of tumor organoids treated with CK21 in vitro revealed <10 differentially expressed genes (DEGs) at 3 h and ~8,000 DEGs at 12 h. Overall inhibition of general RNA transcription was observed, and Ingenuity pathway analysis together with functional cellular assays confirmed inhibition of the NF-κB pathway, increased oxidative phosphorylation and mitochondrial dysfunction, leading ultimately to increased reactive oxygen species (ROS) production, reduced B-cell-lymphoma protein 2 (BCL2) expression, and mitochondrial-mediated tumor cell apoptosis.

overall_design: A time-course transcriptomic profiling of tumor organoids treated with CK21 in vitro

first: Anita

last: Chong


title: Targeting DNA2 Overcomes Metabolic Reprogramming in Multiple Myeloma

city: Los Angeles

first: Feiyang

last: Ma

state: CA

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

institute: UCLA

summary: Targeting DNA2 is synthetically lethal in myeloma cells that undergo metabolic adaptation and rely on oxidative phosphorylation to maintain survival after DNA damage activation.

overall_design: To discover novel mechanisms through which MM cells overcome DNA damage, we investigated how MM cells become resistant to antisense oligonucleotide (ASO) therapy targeting ILF2, a DNA damage regulator that is overexpressed in 70% of MM patients whose disease has progressed after standard therapies have failed. Here, we show that MM cells undergo an adaptive metabolic rewiring and rely on oxidative phosphorylation to restore energy balance and promote survival in response to DNA damage activation. Using a CRISPR/Cas9 screening strategy, we identified the DNA repair protein DNA2, whose loss of function suppresses MM cells’ ability to overcome ILF2-ASOinduced DNA damage, as being essential to counteracting oxidative DNA damage and maintaining mitochondrial respiration.

first: Natthakan

last: Thongon

first: Simona

last: Colla


title: GPR15-mediated T cell recruitment during acute viral myocarditis facilitated virus elimination and improved outcome

city: Freiburg

first: Diana

last: Lindner

address: Hugstetter Straße 55

department: University Heart Center Freiburg-Bad Krozingen

country: Germany

institute: University Hospital Freiburg

summary: Viral myocarditis is characterised by infiltration of mononuclear cells essential for virus elimination. GPR15 has been identified as a homing receptor for regulatory T cells in inflammatory intestine diseases, but its role in inflammatory heart diseases is still elusive. Therefore, we investigated the role of GPR15 during coxsackievirus B3‑induced myocarditis utilizing GPR15‑deficient mice as well as using in vitro experiments. Here we show that GPR15 deficiency had no effect on susceptibility to virus infection, but virus elimination was scant leading to adverse cardiac remodelling and impaired cardiac function. Delayed recruitment of regulatory T cells was accompanied by prolonged persistence of cytotoxic T cells as well as regulatory T cells in GPR15-deficient mice. Further, RNA sequencing revealed prolonged inflammatory response and altered chemotaxis in GPR15-deficient mice. In line, we identified GPR15 and its ligand GPR15L as an important chemokine receptor-ligand pair for the recruitment of regulatory and cytotoxic T cells. In summary, the insufficient virus elimination might be caused by a delayed recruitment of T cells as well as delayed interferon-γ expression, resulting in a prolonged inflammatory response and an adverse outcome in GPR15-deficient mice.

overall_design: Heart tissue from GPR15 deficient and wildtype mice were investigated either with CVB3 induced myocarditis or controls


title: Effect of overexpression of IPW on RNA expression in fetal RPE

status: Public on Nov 26 2023

city: Nanjing

first: Ying

last: Wang

address: Guangzhou Road

institute: NanJing Medical University

summary: To reveal the clinical significance, pathological involvement and molecular mechanism of IPW in retinal pigment epithelium anomalies that contribute to age-related macular degeneration. Microarrays were performed to detect IPW expression under pathological conditions.

overall_design: RNA was extracted with its concentration and purity measured using a NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific), and its integrity assessed using the RNA Nano 6000 Assay Kit on the Agilent Bioanalyzer 2100 system (Agilent Technologies, Santa Clara, CA, USA). A total amount of 1 μg RNA was sent for sequencing library generation using the Hieff NGS Ultima Dual-mode mRNA Library Prep Kit for Illumina (Yeasen Biotechnology, Shanghai, China) following the manufacturer’s recommendations. The library fragments were then purified with the AMPure XP system (Beckman Coulter), and sequenced on an Illumina NovaSeq platform to generate 150 bp paired-end reads, according to the manufacturer’s instructions.

first: Xue

last: Chen

first: Qinghuai

last: Liu


title: Analysis of alternative exon-dependent interactome remodelling reveals multitasking functions of gene regulatory factors (Sap30bp RNA-Seq)

city: Toronto

first: Ulrich

last: Braunschweig

state: Ontario

address: 160 College Street

department: Donnelly Centre

country: Canada

institute: University of Toronto

summary: Alternative splicing is fundamental for the expansion of biological complexity, particularly in the vertebrate nervous system. Increasing evidence indicates that developmental stage and tissue-dependent alternative exons often control protein-protein interactions, yet only a minor fraction of these events has been characterized at the protein level. Using affinity purification-mass spectrometry (AP-MS) we show that approximately 60% of analyzed neural-differential exons in proteins previously implicated in transcriptional regulation result in the gain or loss of interaction partners. Focusing on Chtop and Sap30bp, the neural exons in these proteins unexpectedly remodel interactions with partners associated with mRNA processing and trafficking. Sap30bp additionally controls RNA localization by regulating the splicing of <100 nt ‘mini-introns’ that contribute to the nuclear retention of transcripts. These activities of Chtop and Sap30bp are linked to programs of transcriptomic regulation associated with development of the nervous system. AP-MS is thus a powerful approach for elucidating multifaceted functions of proteins imparted by context-dependent alternative exons.

overall_design: This dataset consists of 12 RNA-seq files associated with the manuscript "Analysis of alternative exon-dependent interactome remodelling reveals multitasking functions of gene regulatory factors" characterizing the effect of Sap30bp siRNA knockdown and neural/non-neural isoform rescue on gene expression and splicing in Neuro2a cell lines. For each isoform (with or without exon 3), a total of 6 samples were analyzed including non-targeting control (NTC), Sap30bp siRNA knockdown, and siRNA knockdown with Doxycycline-induced rescue with an siRNA-resistant Sap30bp cDNA performed in two biological replicates.

first: Jonathan

middle: F

last: Roth

first: Zhen-Yuan

last: Lin

first: Brett

last: Larsen

first: Robert

middle: J

last: Weatheritt

first: Anne-Claude

last: Gingras

first: Benjamin

last: Blencowe


title: Viral RNA-sequencing for the detection of the viruses replicating in humanized mice

city: Minato-ku

first: Kei

last: Sato

state: Tokyo

address: 4-6-1 Shiroganedai

department: Department of Microbiology and Immunology

country: Japan

institute: The Institute of Medical Science, The University of Tokyo

summary: The analysis of RNA-sequencing data reveals the proportion of the three viruses simultaneously inoculated into humanized mice.

overall_design: Three different HIV-1, CH185 wild-type, the CH185 delta PTAP1 mutant (i.e., CH185_dPATAP1), and the CH185 delta PTAP2 mutant (i.e., CH185_dPATAP2) were co-inoculated into nine humanized mice. At two weeks post-infection, the mice were sacrificed after anesthesia and plasma and spleen were collected. To analyze the proportion of the three different viruses in plasma and spleen samples prepared above, the RT-PCR amplicon sequencing that targets the p6 gag region in HIV-1 was performed. As RT-PCR primers, the CH269-PTAP-F  “TAGGGAAAATTTGGCCTTCC” and the CH269-PTAP-R “CCTCCAATTCCCCCTATCAT” were used.

first: Jumpei

last: Ito

first: Yorifumi

last: Satou

first: Naoko

last: Misawa


title: Analysis of alternative exon-dependent interactome remodelling reveals multitasking functions of gene regulatory factors (Chtop RNA-Seq)

overall_design: This dataset consists of 35 RNA-seq files associated with the manuscript "Analysis of alternative exon-dependent interactome remodelling reveals multitasking functions of gene regulatory factors" characterizing the effect of Chtop siRNA knockdown and neural/non-neural isoform rescue on transcript nuclear/cytoplasmic localization in Neuro2a cell lines. For each isoform (with or without exon 5), a total of 18 samples were analyzed including non-targeting control (NTC), Chtop siRNA knockdown, and Chtop siRNA knockdown with Doxycycline-induced rescue (using an siRNA-resistant Chtop cDNA) across total/nuclear/cytoplasmic fractions in two biological replicates.


title: TrkAWT and TrkAF592A animals at 14 d post-operative tendon injury for scRNA-Seq.

city: Baltimore

first: Aaron

last: James

state: Maryland

address: 720 Rutland Avenue, Ross Bldg., Room 529

department: Pathology

institute: Johns Hopkins University

summary: Peripheral afferent neurons terminate at the surfaces of tendons, yet their role after injury beyond nociceptive functions remain unclear.  Using transgenic animal models, sensory neurons were found to sprout after Achilles tendon injury in domains of Nerve growth factor (NGF) expression. Conditional deletion of Ngf in either myeloid or mesenchymal cell types led to tendon repair defects – findings phenocopied by inactivation of TrkA (Tropomyosin receptor kinase A) using a knockin mouse model. We sought to identify the signals modulated with neural TrkA inhibition. A combination of single cell and spatial transcriptomic analysis was performed on the Achilles injury site of TrkAF592A animals and compared them to TrkAWT.

overall_design: The injury site was dissected from TrkAWT (CONTROL) and TrkAF592A (INMPP1) animals at 14 d post-operative for scRNA-Seq. Pooled N=3 mice per genotype

first: Masnsen

last: Cherief

first: Zhao

last: Li


title: Quantitative analysis of transcription start site selection in Saccharomyces cerevisiae reveals control by DNA sequence, RNA Polymerase II activity, and NTP levels

city: Pittsburgh

first: Yunye

last: Zhu

state: PA

address: 4249 Fifth Avenue

department: Department of Biological Sciences

institute: University of Pittsburgh

summary: Transcription start site (TSS) selection is a key step in gene expression and occurs at many promoter positions over a wide range of efficiencies. Here, we develop a massively parallel reporter assay to quantitatively dissect contributions of promoter sequence, NTP substrate levels, and RNA polymerase II (Pol II) activity to TSS selection by "promoter scanning" in Saccharomyces cerevisiae (Pol II MAssively Systematic Transcript End Readout, "Pol II MASTER"). Using Pol II MASTER, we measure the efficiency of Pol II initiation at 1,000,000 individual TSS sequences in a defined promoter context. Pol II MASTER confirms proposed critical qualities of S. cerevisiae TSS -8, -1, and +1 positions quantitatively in a controlled promoter context. Pol II MASTER extends quantitative analysis to surrounding sequences and determines that they tune initiation over a wide range of efficiencies. These results enabled the development of a predictive model for initiation efficiency based on sequence. We show that genetic perturbation of Pol II catalytic activity alters initiation efficiency mostly independently of TSS sequence, but selectively modulates preference for initiating nucleotide. Intriguingly, we find that Pol II initiation efficiency is directly sensitive to GTP levels at the first five transcript positions and to CTP and UTP levels at the second position genome wide. These results suggest individual NTP levels can have transcript-specific effects on initiation, representing a cryptic layer of potential regulation at the level of Pol II biochemical properties. The results establish Pol II MASTER as a method for quantitative dissection of transcription initiation in eukaryotes.

sample_organism:
Escherichia coli
Saccharomyces cerevisiae

overall_design: We have constructed three massive promoter variant libraries ("AYR", "BYR", and "ARY") in E.coli and then transformed plasmid libraries into WT yeast and strains with altered Pol II catalytic activity (G1097D, E1103G, F1086S, and H1085Q). For each library, we applied DNA-seq on its E.coli sample and WT yeast samples. We also applied TSS-seq on WT yeast samples and Pol II mutant samples. All yeast samples contain three biological replicates.

first: Craig

middle: D

last: Kaplan


title: ITGB2 is a Central Hub-Gene Associated with Early  Fibro-Atheroma Development in A Swine Model of Atherosclerosis

city: Madison

first: Hasan

last: Khatib

state: WI

address: 1675 Observatory Dr

department: Animal and Dairy Sciences

institute: University of Wisconsin Madison

summary: Atherosclerosis is an inflammatory-driven disease involving complex mechanisms. Our study investigated the transcriptomic profile of swine abdominal aortic tissues with atherosclerotic lesions, identified pathways and biological processes that were enriched in DEGs, determined a set of hub genes central to atherosclerosis pathophysiology that may serve as potential therapeutic targets, and established a positive expression correlation between the top hub gene and its interconnecting genes upon in vitro manipulation. Our data showed that WMS FH exhibits immune and inflammation-related pathways. RNA-Seq result demonstrated distinct expression patterns between abdominal aortic tissue with atherosclerotic lesions (WMS FH) and lesion-free tissues (WMS normal) both at the gene and isoform levels. Ten hub genes were identified, including ITGB2, C1QA, LCP2, SPI1, CSF1R, CSF2RB, C5AR1, CTSS, MPEG1, C1QC. Moreover, manipulating the top-ranked gene (ITGB2) expression in porcine endothelial cells affected the expression of interconnecting genes.

overall_design: Total RNA was extracted from abdominal aortic tissues with atherosclerotic lesions (WMS FH n=11) and from abdominal aortic tissues that are lesion free (WMS normal n=11). Six RNA pools were constrcuted ( WMS FH n=3; WMS normal n=3). Pools were sequenced using RNA sequencing.

first: Hadjer

last: Namous

first: Christian

last: Krueger

first: Juan

last: Granada

first: Athanasios

last: Peppas

first: Maria

middle: P

last: Strillacci

first: Camila

middle: U

last: Braz

first: Jess

last: Reed

first: William

last: Soffregen


title: Suppression of IL-1β promotes beneficial accumulation of fibroblast-like cells in atherosclerotic plaques in clonal hematopoiesis [scRNA-Seq]

status: Public on Nov 25 2023

city: New York

first: Eunyoung

last: Kim

state: NY

institute: Columbia University

summary: Clonal hematopoiesis (CH) is an independent risk factor for atherosclerotic cardiovascular disease. Murine models of CH suggest a central role of inflammasomes and IL-1β in accelerated atherosclerosis and plaque destabilization. Here we show using scRNAseq in human carotid plaques that inflammasome components are enriched in macrophages, while the receptor for IL-1β is enriched in fibroblasts and smooth muscle cells (SMCs). To address the role of inflammatory crosstalk in features of plaque destabilization, we conducted SMC fate mapping in mice modeling Jak2VF or Tet2 CH treated with IL-1β antibodies. Unexpectedly, this treatment minimally affected SMC differentiation, leading instead to a prominent expansion of fibroblast-like cells. Depletion of fibroblasts from mice treated with IL-1β antibody resulted in thinner fibrous caps. Conversely, genetic inactivation of Jak2VF during plaque regression promoted fibroblasts accumulation and fibrous cap thickening. Our studies suggest that suppression of inflammasomes promotes plaque stabilization by recruiting fibroblast-like cells to the fibrous cap.

overall_design: 20% Jak2VF or cx3cr1-Cre Tet2 fl/fl bone marrow mixed with 80% WT bone marrow was tranplanted into Ldlr-/-  with a Myh11-Cre driven Zsgreen1 reporter. Mice were pulsed with tamoxifen, then put on a western diet for the last 6 weeks of diet mice were given IgG or IL-1b antibodies

first: Trevor

last: Fidler

first: Alan

last: Tall


title: Highly cooperative chimeric super-SOX induces naïve pluripotency across species [RRBS]

first: Sergiy

last: Velychko

type: Methylation profiling by high throughput sequencing

overall_design: To investigate the effects of SOX2AV and SOX2-17 on the fidelity of reprogramming, we generated and characterized 30 hiPSC lines using episomal reprogramming of new-born foreskin (young, Y) and 56-year-old male dermal (old, O, AG04148) fibroblasts. For episomal reprogramming 5x10^5 fibroblasts were nucleofected with 3 μg of plasmid DNA mix: pCXLE-SOX2-P2A-KLF4 (Addgene ID 193292), pCXLE-SOX2AV-p2a-KLF4 (Addgene ID193291) pCXLE-SOX2-17-P2A-KLF4 (Addgene ID 193290), pCXLE-L-MYC-F2A-LIN28 (ML, Addgene ID 27080), pCXLE-hOCT4-shTP53 (Addgene ID 27077), pCXWB-EBNA1 (Addgene ID 37624) using Lonza NHDF Nucleofector kit (U-23 program), and plated in ROCKi-containing fibroblast media on a CF1 feeder layer. All the selected clonal iPSC lines were integration-free with normal karyotypes. The hiPSC samples were collected at passage 10-12, at day 3 after plating on Matrigel (Cornig) in StemFlex media (Gibco).  We performed reduced representation bisulfite sequencing (RRBS) to analyze the methylome of hiPSCs.

first: Gal

last: Keshet


title: lncRNA expression profile in placenta of diabetic macrosomia and normal birth weight newborn

city: Shenyang

first: guiyu

last: song

state: Liaoning

address: Sanhao Street

institute: Shengjing Hospital affilited to China Medical University

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

summary: LncRNAs and mRNAs expression in placenta of diabetic macrosomia were detected by microarray profile.

overall_design: 4 patients were included in the microarray profile in each group (diabetic macrosomia and control group, respectively).

first: Song

last: Guiyu

first: Qiao

last: Chong

last: Quan


title: Suppression of IL-1β promotes beneficial accumulation of fibroblast-like cells in atherosclerotic plaques in clonal hematopoiesis

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

overall_design: Refer to individual Series


title: Effect of milk fat globules on growth and metabolism in rats fed an unbalanced diet

status: Public on Nov 23 2023

city: Rehovot

first: Jerome

last: Janssen

address: Herzl 229

country: Israel

institute: Hebrew University of Jerusalem

summary: We assessed the effects of supplementing milk fat globules (MFG) on the growth and development of the skeleton in rats fed a Western unbalanced diet (UBD). The UBD is high in sugar and fat, low in protein, fiber, and micronutrients, and negatively impacts health. The MFG—a complex structure secreted in milk—has a unique proteome and lipidome, and differs significantly from isolated dietary ingredients. Rats consuming the UBD exhibited growth retardation and disrupted bone structural and mechanical parameters; these were improved by supplementation with small MFG. The addition of small MFG increased the efficiency of protein utilization for growth, and improved trabecular and cortical bone parameters. Furthermore, consumption of UBD led to a decreased concentration of saturated fatty acids and increased levels of polyunsaturated fatty acids (PUFA), particularly omega-6 PUFA, in the serum, liver, and adipose tissue. The addition of small MFG restored PUFA concentration and the ratio of omega-6 to omega-3 PUFA in bone marrow and adipose tissue. Finally, large but not small MFG supplementation affected the cecal microbiome in rats. Overall, our results suggest that natural structure MFG supplementation can improve metabolism and bone development in rats fed an UBD, with the effects depending on MFG size, whereas the detrimental effects of an UBD on the microbiome were not mitigated by MFG supplementation.

overall_design: 3 week old Sprague-Dawley rats were fed for 6 weeks with a control diet, UBD or UBD+MFG. After the sacrifice, caecal stool samples were collected and used for 16S rRNA sequencing of the V4 region using 515F–806R primers.

first: Nurit

last: Argov-Argaman

first: Hodaya

last: Altman

middle: N

first: Seman

last: Daem

first: Chen

last: Raz

first: Ronit

last: Mesilati-Stahy

first: Svetlana

last: Penn

first: Efrat

last: Monsonengo-Ornan


title: Single cell RNA sequencing of PIM-silenced human Th17 cells

city: Turku

first: Riitta

last: Lahesmaa

address: Tykistökatu 6 A

country: Finland

institute: Turku Bioscience Centre, University of Turku

summary: The aim of this study was to investigate the transciptional mechanisms regulated by three PIM kinases at singel cell level during early human Th17 cell differentiation. PIM kinases were transiently silenced using RNAi (KD) approach followed by single cell RNA-seq to determine the gene expression profile of PIM negative Th17 cells.

first: Tanja

last: Buchacher

first: Ankitha

last: Shetty

first: Saara

middle: A

last: Koskela

first: Johannes

last: Smolander

first: Riina

last: Kaukonen

first: Antònio

middle: G

last: Sousa

first: Sini

last: Junttila

first: Asta

last: Laiho

first: Olof

last: Rundquist

first: Tapio

last: Lönnberg

first: Omid

last: Rasool

first: Alexander

last: Marson

first: Laura

middle: L

last: Elo


title: Functional T cells are capable of supernumerary cell division and longevity [ATAC-seq]

city: Minneapolis

first: David

last: Masopust

state: MN

address: 2101 6th St SE

department: Microbiology and Immunology

institute: University of Minnesota

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Differentiated somatic mammalian cells putatively exhibit species-specific division limits that impede cancer but may constrain lifespans. To provide immunity, transiently stimulated CD8 T cells undergo unusually rapid bursts of numerous cell divisions, then form quiescent long-lived memory cells that remain poised to reproliferate in response to subsequent immunological challenges. Here, we addressed whether T cells are intrinsically constrained by chronological or cell division limits. We activated mouse T cells in vivo using acute heterologous-prime-boost-boost vaccinations, transferred expanded cells to new mice, and then repeated that process iteratively. Over a period of 10 years (greatly exceeding the mouse lifespan) and 51 successive immunizations, T cells remained competent to respond to vaccination. Cells did require sufficient rest between stimulation events. Despite demonstrating the potential to expand the starting population at least 10^40-fold, cells did not show loss of proliferation control and results were not due to contamination with young cells. Persistent stimulation by chronic infections or cancer can result in a well-described transcriptional program that results in T cell proliferative senescence, functional exhaustion, and death. We found that while iterative acute stimulations also induced sustained expression and epigenetic remodeling of common exhaustion markers, including PD-1 and Tox, these cells retained the capacity to proliferate, execute antimicrobial functions, and form quiescent memory cells. These observations provide a model to better understand memory cell differentiation, exhaustion, and aging, and show that functionally competent T cells can retain the potential for extraordinary population expansion and longevity well beyond their organismal lifespan.

overall_design: Chromosomal accessibility profiles of sorted N-specific memory T cells upon 1,3,6,9,18,27,30,39, and 45 immunizations

first: Andrew

last: Soerens

first: Marco

last: Kuenzli


title: In vitro reconstitution of chromatin domains shows a role for nucleosome positioning in 3D genome organization

city: Göttingen

first: Elisa

last: Oberbeckmann

address: Justus-von-Liebig Weg 11

department: Molecular Biology

institute: University Medical Center Göttingen


title: Bulk RNA sequencing of PIM-silenced human Th17 cells

first: Riitta

last: Lahesmaa

summary: The aim of this study was to investigate the transciptional mechanisms regulated by three PIM kinases during early human Th17 cell differentiation. PIM kinases were transiently silenced using RNAi (KD) approach followed by RNA-seq to determine their global transciptional targets.

overall_design: Altogether 16 RNA-seq samples were analysed. The analysis was based on 4 biological replicates of each condition in Th17-polarized cells

first: Tanja

last: Buchacher


title: Global gene targets of PIM kinases in human Th17 cells


title: Analysis of alternative exon-dependent interactome remodelling reveals multitasking functions of gene regulatory factors (iCLIP-Seq)

first: Ulrich

last: Braunschweig

overall_design: This dataset consists of 9 iCLIP-seq files associated with the manuscript "Analysis of alternative exon-dependent interactome remodelling reveals multitasking functions of gene regulatory factors" comparing RNA-pulldown between Chtop isoforms with or without exon 5 in Neuro2a cell lines. Each isoform (with or without exon 5) was profiled in triplicates and compared to three size-matched input control samples.

first: Jonathan

last: Roth

first: Zhen-Yuan

last: Lin

first: Brett

last: Larsen

first: Robert

last: Weatheritt

first: Anne-Claude

last: Gingras

first: Benjamin

last: Blencowe


title: Transcriptome of human primary macrophages from healthy controls after long-term myelin phagocytosis

status: Public on Nov 22 2023

city: Vienna

first: Isabelle

last: Weinhofer

address: Spitalgasse 4

country: Austria

institute: Medical University of Vienna

summary: CD14+ monocytes were isolated from the blood of healthy human donors by Ficoll density-gradient centrifugation, magnetic cell sorting and LS column systems. CD14+ monocytes were in vitro differentiated to macrophages by culturing the cells for 7 days in RPMI medium containing 10% FCS, 1% penicillin/streptomycin, 1% glutamine, 1% Fungizone and supplemented with 50 ng/ml human macrophage-colony stimulating factor (M-CSF) in the presence or absence of myelin isolated from brain tissue of 6-8 week-old wild-type C57BL6/J mice.

overall_design: Comparative gene expression profiling analysis of human monocyte-derived macrophages differentiated in the absence or presence of myelin from brain tissue of wild-type C57BL6/J mice

first: Andrea

last: Villoria-González

first: Bettina

last: Zierfuss

first: Johannes

last: Berger


title: Low energy metabolism protects leukemia stem cells from chemotherapy and immunosurveillance via a SHP-1-PFKP axis

city: Guangzhou

first: Guo

last: Qiu

state: Guangdong

address: Guangzhou Avenue

institute: Nanfang Hospital, Southern Medical University

summary: To explore the effect of Shp-1 deletion on single-cell resolution, we profiled Shp-1f/f and Shp-1Δ/Δ AML cells from the BM of MLL-AF9 mice with or without chemotherapy using single-cell RNA sequencing (scRNA-seq).

overall_design: Primary bone marrow cells were collected from ML-AF9 mice and were examined under a microscope and counted using a hemocytometer.

first: Xi

last: Xu

first: Wenwen

last: Zhang

first: Yanhui

last: Yu

first: Xunlei

last: Kang

first: Linjia

last: Jiang

first: Meng

last: Zhao


title: ATGL deletion in castration-resistant prostate cancer cell line

city: Houston

first: Daniel

middle: E.

last: Frigo

state: TX

address: 1881 East Road - Unit 1907

institute: University of Texas MD Anderson Cancer Center

summary: Lipid metabolism plays a central role in prostate cancer. To date, the major focus on prostate cancer lipid metabolism has centered on the roles of de novo lipogenesis and lipid uptake with little consideration for how cancer cells access these lipids once they are created or taken up and stored. Analysis of patient-derived phosphoproteomics data identified adipose triglyceride lipase (ATGL), a rate-limiting enzyme in the breakdown of triglycerides and previously suspected tumor suppressor, as a target of calcium/calmodulin-dependent protein kinase kinase 2 (CAMKK2)-AMP-dependent protein kinase (AMPK) signaling that, conversely, promotes castration-resistant prostate cancer (CRPC) progression. Phosphorylation of ATGL by CAMKK2-AMPK signaling increased ATGL’s lipase activity, cancer cell proliferation, migration, and invasion. Shotgun lipidomics and imaging mass spectrometry demonstrated ATGL’s profound regulation of prostate cancer lipid metabolism in vitro and in vivo, remodeling membrane composition. Targeting ATGL using molecular, genetic, and/or pharmacological approaches impaired the growth of human and murine prostate cancer cells in culture and xenograft mouse models of CRPC as well as organoid models. The efficacy of ATGL inhibition occurs in a glucose concentration-dependent manner. Accordingly, pharmacological inhibition or depletion of ATGL induced metabolic plasticity with a shift towards glycolysis, which could be exploited therapeutically by co-targeting both metabolic pathways. Together, these data nominate ATGL and intracellular lipolysis as a potential therapeutic target for the treatment of CRPC and provide insights for future combination therapies.

overall_design: Comparative gene expression profiling analysis of RNA-seq data in isogenic ATGL knockout and addback cell lines, including wild type ATGL, a S404A mutant and a lipolytic-inactive S47A mutant. Cells were plated in RPMI1640 no glucose supplemented with 5mM glucose and 5% dialyzed FBS before harvesting for RNA sequencing. Three replicates per cell line were used.

first: Pham

last: Cao

first: Dominik

last: Awad

first: Jingjing

last: Liu


title: Highly cooperative chimeric super-SOX induces naïve pluripotency across species

city: Boston

first: Sergiy

last: Velychko

address: 77 Avenue Louis Pasteur, Room 232

institute: Harvard Medical School

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Nuclear export of circular RNA

city: Adelaide

first: Katherine

middle: Anne

last: Pillman

state: SA

address: North Terrace

department: Centre for Cancer Biology

country: Australia

institute: Adelaide University

summary: Circular RNAs (circRNAs), which are increasingly being implicated in a variety of functions in normal and cancerous cells1-5, are formed by back-splicing of precursor mRNAs in the nucleus6-10. circRNAs are predom¬inantly localized in the cytoplasm, indicating that they must be exported from the nucleus. Here, we uncover a pathway specific for nuclear export of circular RNA. This pathway requires Ran-GTP, Exportin-2 and IGF2BP1. Enhancing the nuclear Ran-GTP gradient by depletion or chemical inhibition of the major protein exporter, CRM1, selectively increases nuclear export of circRNAs, while reducing the nuclear Ran-GTP gradient selectively blocks circRNA export. Depletion or knockout of Exportin-2 specifically inhibits nuclear export of circRNA. Analysis of nuclear circRNA binding proteins reveals that interaction of IGF2BP1 with circRNA is enhanced by Ran-GTP.  Formation of circRNA export complexes in the nucleus is promoted by Ran-GTP through its interactions with IGF2BP1, Exportin-2 and circRNA. Our findings demonstrate that adaptors such as IGF2BP1 that bind directly to circular RNAs recruit Ran-GTP and Exportin-2 to export circRNAs in a mechanism analogous to protein export, rather than mRNA export.

overall_design: HITS-CLIP was performed on endogenous Ran from CAL51 cells using a Ran specific antibody.

first: B

middle: K

last: Dredge

first: Andrew

last: Bert

first: Gregory

last: Goodall


title: Exploratory pharmacogene variation in Ghanaian population

city: Cape Coast

first: Nicholas

middle: Ekow

last: Thomford

state: Central

address: PMB, University of Cape Coast School of Medical Sciences, Coast Coast, Ghana

department: Dept. of Med. Biochem.,SMS, CoHAS,

country: Ghana

institute: University of Cape Coast, Ghana

summary: Genetic variations in drug metabolising enzymes play a role in how individuals respond to drugs. Pharmacogene variation data in the Ghanaian population is limited and this study looks at exploring common variations that exist in our population for commonly used drugs. Samples were validated with PCR-RFLP for accuracy

overall_design: 100 samples were genotyped for pharmacogenes using the MassArrayiPLEX genotyping assay using the iPLEX Gold genotyping kit from Agena Bioscience. This requires an input of 40ng of DNA per sample. Samples are dispensed onto a SpectroCHIP Array and data acquired using MassARRAY analyzer. Data is automatically analyzed and acquired using Typer software version 3.99.105 for each sample.

middle: E

first: Robert

last: Biney


title: RNA sequencing reveals differential long noncoding RNA expression profiles in bacterial and viral meningitis in children

status: Public on Nov 21 2023

city: Shijiazhuang

first: Xin

last: Li

address: No.215 West Heping Street

institute: The Second Hospital of Hebei Medical University

summary: The aim of the present study was to investigate the alteration of lncRNAs in bacterial and viral meningitis in children.The differentially expressed mRNAs (DEmRNAs) and lncRNAs (DElncRNAs) were identified and the ceRNA network was characterized.

overall_design: Five patients with bacterial meningitis and five patients with viral meningitis were included in the study. Control group comprised five children. RNA sequencing was performed to obtain the differentially expressed mRNAs (DEmRNAs) and lncRNAs (DElncRNAs).

first: Suzhen

last: Sun

first: Huifeng


title: Highly cooperative chimeric super-SOX induces naïve pluripotency across species [RNA-Seq]

summary: Our understanding of pluripotency remains limited: iPSC generation has only been established for a few model species, pluripotent stem cell lines exhibit inconsistent developmental potential, and germline transmission demonstrated only for mice and rats.  By swapping structural elements between Sox2 and Sox17, we built a chimeric super-SOX factor, Sox2-17, that enhanced iPSC generation in five tested species: mouse, human, cynomolgus monkey, cow, and pig. A swap of alanine to valine at the interface between Sox2 and Oct4 delivered a remarkable gain-of-function by stabilizing Sox2/Oct4 dimerization on DNA, enabling generation of high-grade OSKM iPSCs capable of supporting the development of healthy all-iPSC mice.  Sox2/Oct4 dimerization emerged as the core driver of naïve pluripotency with its levels diminished upon priming. Transient overexpression of Sox2-17 and Klf4 (S*K cocktail) restored the dimerization and boosted the developmental potential of pluripotent stem cells across species, providing a universal method for naïve reset in mammals.

overall_design: To investigate the effects of SOX2AV and SOX2-17 on the fidelity of reprogramming, we generated and characterized 30 hiPSC lines using episomal reprogramming of new-born foreskin (young, Y) and 56-year-old male dermal (old, O, AG04148) fibroblasts. For episomal reprogramming 5x10^5 fibroblasts were nucleofected with 3 μg of plasmid DNA mix: pCXLE-SOX2-P2A-KLF4 (Addgene ID 193292), pCXLE-SOX2AV-p2a-KLF4 (Addgene ID193291) pCXLE-SOX2-17-P2A-KLF4 (Addgene ID 193290), pCXLE-L-MYC-F2A-LIN28 (ML, Addgene ID 27080), pCXLE-hOCT4-shTP53 (Addgene ID 27077), pCXWB-EBNA1 (Addgene ID 37624) using Lonza NHDF Nucleofector kit (U-23 program), and plated in ROCKi-containing fibroblast media on a CF1 feeder layer. All the selected clonal iPSC lines were integration-free with normal karyotypes. The hiPSC samples were collected at passage 10-12, at day 3 after plating on Matrigel (Cornig) in StemFlex media (Gibco).


title: Regulation, biogenesis and function of circDOCK1(2,27), an abundant epithelial-specific circRNA

summary: We describe the regulation, biogenesis and function of circDOCK1(2,27), a large, abundant EMT-regulated circular RNA whose formation is dependent on the epithelial-specific splicing regulator ESRP1. CircDOCK1(2,27) synthesis in epithelial cells represses cell motility both by diverting transcripts from DOCK1 mRNA production to circRNA formation and by direct inhibition of migration by the circRNA. HITS-CLIP analysis along with CRISPR-mediated deletions indicate ESRP1 controls circDOCK1(2,27) biosynthesis by binding a GGU-containing repeat region in intron 1 and detaining its splicing until Pol II completes its 157 kb journey to exon 27. Proximity-dependent biotinylation (BioID) assay suggests ESRP1 modifies the RNP landscape of intron 1 in a way that disfavours communication of exon 1 with exon 2, rather than physically bridging exon 2 to exon 27. The X-ray crystal structure of RNA-bound ESRP1 qRRM2 domain reveals it binds to GGU motifs, with the guanines embedded in clamp-like aromatic pockets in the protein.

overall_design: HITS-CLIP was performed on endogenous ESRP1 from 3 biological replicates of wt HMLE cells using an ESRP1 specific antibody and on 2 biological replicates each of N- and C-terminally 3XFLAG-tagged ESRP1 expressed in HMLE-i-ESRP1_FLAG cells after induction with 1 µg/ml doxycycline for 72 hours, using anti-FLAG antibody.


title: Tumor cell-intrinsic p38 MAPK signaling promotes IL1⍺-mediated stromal inflammation and therapeutic resistance in pancreatic cancer

city: Miami

first: Nipun

middle: B

last: Merchant

state: Florida

address: 1550 Northwest 10th Avenue, Fox 140

department: Surgery

institute: University of Miami/Jackson Memorial Hospital - Miami, FL

summary: Pancreatic ductal adenocarcinoma (PDAC) is characterized by a KRAS-driven inflammatory program and a desmoplastic stroma, which contribute to the profoundly chemoresistant phenotype. The tumor stroma contains an abundance of cancer-associated fibroblasts (CAFs), which engage in extensive paracrine crosstalk with tumor cells to perpetuate pro-tumorigenic inflammation. Interleukin-1α (IL1α), a pleiotropic, tumor cell-derived cytokine, plays a critical role in shaping the stromal landscape. We have identified p38 MAPK as a key regulator of IL1α gene expression and utilized single-cell RNA sequencing to study the role of p38 MAPK in PDAC

overall_design: Single-cell RNA sequencing of tumors derived from genetically-engineered Ptf1aCre/+; LSL-KrasG12D/+; Tgfbr2flox/flox (PKT) mice treated with either a p38 MAPK inhibitor (ARRY-614) or control vehicle. For 2.5 weeks, three PKT mice were treated with ARRY-614, and three PKT mice were treated with control vehicle. Upon sacrifice, tumors were harvested and three tumors from each treatment group were pooled for downstream sequencing. Single-cell RNA sequencing was performed using the 10X Genomics platform.

first: Samara

last: Singh

first: Austin

middle: R

last: Dosch

first: Siddharth

last: Mehra

first: Iago

last: De Castro Silva

first: Anna

last: Bianchi

first: Vanessa

last: Tonin-Garrido

first: Zhiqun

last: Zhou

last: Adams

first: Haleh

last: Amirian

first: Edmond

middle: W

last: Box

first: Xiaodian

first: Yuguang

last: Ban

first: Jashodeep

last: Datta

first: Nagaraj

middle: S

last: Nagathihalli


title: Secretion encoded single-cell sequencing (SEC-seq) uncovers gene expression signatures associated with high VEGF-A secretion in mesenchymal stromal cells

city: Los Angeles

first: Kathrin

last: Plath

address: 615 Charles E. Young Drive South

institute: University of California, Los Angeles

summary: Using secretion encoded single-cell sequencing (SEC-seq), which exploits hydrogel nanovials to capture individual cells and their secretions, we simultaneously measured the secretion of vascular endothelial growth factor A (VEGF-A) and the transcriptome for thousands of individual mesenchymal stromal cells (MSCs).

overall_design:
We combined the ability to capture cellular secretions with antibody-conjugated nanovials with a single cell sequencing workflow, which allows us to quantify VEGF-A protein secretion levels and whole transcriptome information from each single cell. We tested this SEC-seq workflow in MSCs, which can be induced to secrete more VEGF-A via hypoxic conditions.
Please note that processed data files generated from multiple samples are linked as Series supplementary files and are indicated in the corresponding sample description field.

first: Shreya

last: Udani

first: Justin

last: Langerman

first: Doyeon

last: Koo

first: Sevana

last: Baghdasarian

first: Brian

last: Cheng

first: Simran

last: Kang

first: Citradewi

last: Soemardy

first: Joseph

last: de Rutte

first: Dino

last: Di Carlo


title: Histone lactylation couples cellular metabolism with the activation of developmental gene regulatory networks

first: Marcos

last: Simoes-Costa

state: Massachusetts

address: 300 Longwood Ave

institute: Boston Children's Hospital


title: Choroid plexus mast cells drive tumor-associated hydrocephalus

city: Guangdong

first: Di

last: Can

address: Guangzhou

institute: Sun Yat-Sen university

summary: Tumor-associated hydrocephalus (TAH) is a common and lethal complication of brain metastases. Although other factors beyond mechanical obstructions have been suggested, the exact mechanisms are unknown. Using single-nucleus RNA-sequencing and spatial transcriptomics, we find that a distinct population of mast cells locate in the choroid plexus and dramatically increase during TAH. Genetic fate-tracing and intracranial mast cell-specific tryptase knockout showed that choroid plexus mast cells (CPMCs) disrupt cilia of choroid plexus epithelia via the tryptase-PAR2-FoxJ1 pathway and consequently increase cerebrospinal fluid production. Mast cells are also found in the human choroid plexus. Levels of tryptase in cerebrospinal fluid are closely associated with clinical severity of TAH. BMS-262084, an inhibitor of tryptase, can cross blood-brain-barrier, inhibits TAH in vivo and alleviates mast cell-induced damage of epithelial cilia in a human pluripotent stem cell-derived choroid plexus organoid model. Collectively, we uncover the function of CPMCs and provide an attractive therapy for TAH.

overall_design: 1. sn-seq: two exprimental groups: normal and EO771-VM-bearing mice, 3 independent replicates with 5 mice per group in each replicate. 2. ST, 3 brain sections from 3 EO771-VM mice. 3.RNA-seq: human choroid plexus epithelial cell line (HCPEpiC)  treated with or without tryptase (3 independent replicates per group).

first: Yiye

last: Li

first: Can

last: Di

first: Shijian

last: Song

first: Yubo

last: Zhang

first: Yiwen

last: Lu

first: Jianyou

last: Liao

first: Bingxi

last: Lei

first: Jian

last: Zhong

first: Kaihua

last: Guo

first: Nu

first: Shicheng

last: Su


title: Single-cell mRNA sequencing and TCR sequencing of CD4+ T cells in a mouse model of cutaneos B16 melanoma

city: Parkville

first: Jan

last: Schroeder

state: Victoria

address: Peter Doherty Institute Melbourne

department: DMI

institute: University of Melbourne

summary: This study sought to identify transcriptional states of CD4+ T cells from melanoma-challenged skin, primary tumours and tumour-draining lymph nodes. TCR sequencing was performed to identify expanded clonotypes to infer tumour-antigen specificity. This study identified heterogeneous populations of melanoma-specific CD4+ T cells that are distinct in the different anatomical locations.

overall_design: C57B/6 mice were challenged with B16.gD melanoma using the recently developed epicutaneous melanoma model (Park et al, Nature 2019). Melanoma-challenged skin and draining (brachial) lymph nodes from the same mice were harvested 8 days following inoculation. Primary tumours and tumour-draining (brachial) lymph nodes from tumour-bearing mice were harvested 20 days following inoculation. As a batch control, a brachial lymph node was harvested from a naive C57BL/6 mouse. Samples were stained simultaneously with antibodies for flow cytometry and TotalSeq-C hashtag antibodies (Biolegend). Samples were sorted on CD45.2+CD3+CD8-CD4+CD44+ cells except for the naïve lymph node (batch control) which was sorted on CD45.2+CD3+CD8-CD4+CD44-CD62L+. Day 8 skin and lymph node samples were pooled from 32 mice across two experiments. Day 20 tumour and lymph node samples were pooled from 4 mice in one experiment.

first: Emma

last: Bawden

first: Thomas

last: Gebhardt

last: Schröder


title: Runx1+ vascular smooth muscle cells are essential for hematopoietic stem and progenitor cell development in vivo

city: Edinburgh

first: Mihaela

last: Crisan

address: 5 Little France Drive

country: United Kingdom

institute: The University of Edinburgh

summary: We sequenced 4 sorted cell populations: ECs, HECs, Runx1+ IAHCs and Runx1- IAHCs.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for the 4 endothelial and hematopoetic stem cell populations.

first: Zaniah

last: Gonzalez

first: Alastair

middle: M

last: Kilpatrick

first: Madalena

last: Marques

first: Diana

last: Sá da Bandeira

first: Telma

last: Ventura

first: Mario

last: Gomez-Salazar

first: Lea

last: Bouilleau

first: Yvan

last: Marc

first: Ana

last: Barbosa

first: Fiona

last: Rossi

first: Mariana

last: Beltran

first: Harmen

last: van de Werken

first: Wilfred

last: van IJcken

first: Neil

middle: C

last: Henderson

first: Stuart

middle: J

last: Forbes


title: ERK-Mediated Phosphorylation of OLA1 Controls Adaptive Mitochondria to Nucleus Communication Regulating Cellular Homeostasis [CHIP-seq]

city: Milwaukee

first: Adeleye

middle: James

last: Afolayan

address: 8701 Watertown Plank road

department: Pediatrics

institute: Medical College of Wisconsin

summary: We found that changes in mitochondrial membrane potential or ROS generation trigger the translocation of OLA1 from mitochondria and cytoplasm to the nucleus, regulated by ERK1-mediated phosphorylation of OLA1 on Ser232/Tyr236. Subsequent phosphorylation of nuclear-OLA1 on Thre325 by ERK2 activates its function as a genetic factor regulating cellular homeostasis by modulating HDAC9 expression. Disruption of OLA1 phosphorylation blocks its nuclear translocation, compromised the expression of nuclear-encoded mitochondrial proteins, DNA damage response, and multiple stress-response-related-genes, leading to cellular dysfunction. Our findings reveal that OLA1 is a crucial component of mitonuclear response regulatory hubs essential for regulating cellular adaptation to stress.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) to define OLA1 interactions with DNA and identify putative OLA1 denovo binding motifs in the nucleus

first: Paul

last: Sidlowski


title: RNA sequencing of human pancreatic acinar and ductal cells

city: San Antonio

first: Pei

last: Wang

address: 7703 Floyd Curl Dr

department: Cell Systems & Anatomy

institute: University of Texas Health San Antonio

summary: Flow-sorted pancreatic acinar and ductal cells from fresh human pancreatic exocrine tissue were subjected to molecular characterization to identify lineage-specific expression and epigenetic properties. Cells of both lineages were cultured and transformed via lentiviral mutation to form pancreatic ductal adenocarcinoma.

overall_design: Flow-sorted pancreatic acinar and ductal cells from fresh human pancreatic exocrine tissue were subjected to RNAseq, before and after cell culture, for differential analysis of gene expression by lineage, condition, and genotype.

first: Yi

last: Xu

first: Michael

middle: H

last: Nipper

first: Zhengqing

last: Ye

first: Naoki

last: Akanuma

first: Kevin

last: Lopez

first: Janice

last: Deng

first: Aatur

middle: D

last: Singhi

first: Francis

last: Sharkey

first: Huamin

first: Luzhe

last: Sun

first: Yidong

last: Chen

first: Jun

last: Liu


title: Transcriptomic profiling of IDH-wt-hGICs-MGT#4-dEGFP cells upon overexpression of CRISPRa-screen predicted pro-mesenchymal phenotypic drivers.

city: Berlin

first: Gaetano

last: Gargiulo

address: Robert-Rössle-Straße 10

department: Molecular Oncology

institute: Max Delbrück Center for Molecular Medicine

summary: Functional validation of the genome-scale CRISPR-activation screen by transcriptomic profiling of MGT#4-reporter expressing IDH-wt human glioma initiating cells (hGICs) upon CRISPRa-mediated overexpression of the predicted pro-mesenchymal drivers.

overall_design: IDH-wt-hGICs, harboring a constitutively active dCas9-VPR system and the mesenchymal MGT#4-dEGFP reporter, were lentivirally transduced with constructs bearing four individual multiplexed sgRNAs targeting the respective screen hits (RELA, FOSL1, RAC1). Levels of MGT#4-reporter activation upon CRISPRa-mediated transcriptional amplification of the target genes were assessed via FACS at 6 and 14 days post-transduction. At the experimental end-point, guide-bearing reporter-high expressing cells were FACS-purified for subsequent whole transcriptome profiling alongside the unsorted parental IDH-wt-hGICs-MGT#4-dEGFP controls.

first: Yuliia

last: Dramaretska

first: Matthias

last: Schmitt

first: Michela

last: Serresi


title: Single cell-resolved study of advanced murine NASH reveals a homeostatic stellate cell signaling module [HSCc_fsk_3h_bulkRNA]

city: Odense M

first: Kim

last: Ravnskjaer

address: Campusvej 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

summary: Non-alcoholic steatohepatitis (NASH) is associated with hepatic steatosis, intralobular inflammation, and fibrosis. The degree of hepatic fibrosis, mainly caused by excessive production of extracellular matrix proteins, is the sole predictor of liver-related and overall mortality in NASH patients. The hepatic stellate cells (HSCs) are causally implicated in fibrogenesis during NASH development but as sinusoidal pericytes also vital for vascular homeostasis of the healthy liver. Using single-cell RNA-sequencing we have analyzed whole liver plasticity and interrogated the transition of HSCs from pericytes in the healthy liver to collagen-producing cells in a diet-induced murine model of advanced NASH. We show how postprandial cues are sensed and integrated by HSCs promoting their phenotypic stabilization and, through paracrine mediators, sinusoidal health. While dominant under healthy conditions the basis for this multimodal signaling through stellate cell-specific Gs protein-coupled receptors and the bile-acid receptor NR1H4/FXR deteriorates in activated HSCs of the NASH liver. Expression of key signaling components were validated in situ in human and murine liver tissue supporting the translatability of our findings and pharmacological relevance in treatment of chronic liver diseases as NASH.

overall_design: Here we performed gene expression profiling analysis of primary hepatic stellate cells (in vitro) using data obtained from RNA-seq of cells treated for 3 hours with either Foskolin (Fsk) or Dimethylsulfoxid (DMSO)

first: Sofie

last: Bendixen

first: Peter

last: Sørensen

first: Mike

last: Terkelsen

first: Daniel

last: Hansen

first: Kamilla

last: Hejn

first: Frederik

middle: A

last: Bjerre

first: Annemette

middle: P

last: Thulesen

first: Niels

middle: G

last: Eriksen

first: Philip

last: Hailenberg

first: Trine

middle: V

last: Dam

middle: T

last: Larsen

first: Charlotte

last: Wernberg

first: Janusa

last: Vijayathurai

first: Emma

last: Scott

first: Ann-Britt

last: Marcher

first: Sönke

last: Detlefsen

first: Lars

last: Grøntved

first: Henrik

last: Dimke

first: Mette

last: lauridsen

first: Alexander

last: Krag

first: Blagoy

last: Blagoev


title: Empagliflozin alleviates atherosclerotic calcification by inhibiting osteogenic differentiation of vascular smooth muscle cells

first: Junping

last: Li

address: 107 Yanjiang West Road, Yuexiu District, Guangzhou, Guangdong Province, China

institute: Sun Yat-sen Memorial Hospital, Sun Yat-sen University

summary: SGLT-2 inhibitors, such as empagliflozin, have been shown to reduce the occurrence of cardiovascular events and delay the progression of atherosclerosis. However, its role in atherosclerotic calcification remains unclear. In this research, ApoE-/- mice were fed with western diet and empagliflozin was added to the drinking water for 24 weeks. Empagliflozin treatment significantly alleviated arterial calcification assessed by alizarin red and von kossa staining in aortic roots and reduced the lipid levels, while had little effect on body weight and blood glucose levels in ApoE-/- mice. In vitro studies, empagliflozin significantly inhibits calcification of primary vascular smooth muscle cells (VSMCs) and aortic rings induced by osteogenic media (OM) or inorganic phosphorus (Pi). RNA sequencing of VSMCs cultured in OM with or without empagliflozin showed that empagliflozin negatively regulated the osteogenic differentiation of VSMCs. And further studies confirmed that empagliflozin significantly inhibited osteogenic differentiation of VSMCs via qRT-PCR.  Our study demonstrates that empagliflozin alleviates atherosclerotic calcification by inhibiting osteogenic differentiation of VSMCs, which addressed a critical need for the discovery of a drug-based therapeutic approach in the treatment of atherosclerotic calcification.

overall_design: To investigate the function of empagliflozin in the regulation of Osteogenic differentiation of primary vascular smooth muscle cells (VSMCs), we performed gene expression profiling analysis using data obtained from RNA-seq of VSMCs cultivated in osteogenic media (10mM β-GP plus 3.5mM CaCl2) treated with or without empagliflozin for 5 days.

first: Changping

first: Zhaoyu

last: Liu


title: ATAC-seq analysis for HPB-ALL cells overexprssing TAL1 and LMO1.

city: Singapore

first: Tze King

last: Tan

address: 14 Medical Drive

department: Cancer Science Institute

country: Singapore

institute: National University of Singapore

summary: ATAC-seq analysis was performed in a T-ALL cell line (HPB-ALL) which overexpresses TAL1 and LMO1 to analyze chromatin accessibility.

overall_design: The cells are incubated with Tn5 transposase. Tagmented DNA fragments are purified with Zymo DNA purification kit. ATAC libraries are purified and sequenced on Illumina NovaSeq at GENEWIZ Azenta Life Sciences Co. Ltd.

first: Jolynn

middle: Z

last: Ong

first: Tze

middle: K

first: Takaomi

last: Sanda


title: Transcriptome Analysis of Differentially Expressed Genes in the Wild-type and Fabp7 KO Mouse Inner Ear

city: Sendai

first: Jun

last: Suzuki

state: Miyagi

address: 1-1 Seiryo-machi, Aoba-ku

department: Department of Otorhinolaryngology-Head and Neck Surgery

institute: Tohoku University School of Medicine

summary: To reveal the function of FABP7 in the inner ear, we evaluated gene expressions between Wild-type and Fabp7 KO mice one day after noise exposure at 10 weeks, using RNA sequencing analysis. The read number was approximately 27–32 million paired-end reads per sample. A total of 24 and 23 genes were identified as upregulated and downregulated differentially expressed genes (DEGs), respectively in Fabp7 KO mice. The upregulation of genes related to nicotinamide-adenine dinucleotide (NADH) dehydrogenase (mt-Nd1, 2, 3, 4, and 6) and a glial high-affinity glutamate transporter (solute carrier family 1, member 2: Slc1a2) and downregulation of genes related to C/D box small nucleolar RNAs were observed in Fabp7 KO mice.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for inner ears of FABP7 KO  and control mice (FABP7KO, Control).

first: Takehito

last: Sugasawa


title: Hagfish genome elucidates vertebrate whole genome duplication events and their evolutionary consequences

city: Málaga

first: Juan

last: Pascual-Anaya

address: Campus de Teatinos, s/n

department: Departament of Animal Biology

country: Spain

institute: University of Málaga

summary: Polyploidy or whole genome duplication (WGD) is a major event that drastically reshapes genome architecture and is often assumed to be causally associated with organismal innovations and radiations. The 2R Hypothesis suggests that two WGD events (1R and 2R) occurred during early vertebrate evolution. However, the timing of the 2R event relative to the divergence of gnathostomes (jawed vertebrates) and cyclostomes (jawless hagfishes and lampreys) is unresolved and whether these WGD events underlie vertebrate phenotypic diversification remains elusive. Here we present the genome of the inshore hagfish, Eptatretus burgeri. Through comparative analysis with lamprey and gnathostome genomes, we reconstruct the early events in cyclostome genome evolution, leveraging insights into the ancestral vertebrate genome. Genome-wide synteny and phylogenetic analyses support a scenario in which 1R occurred in the vertebrate stem-lineage during the early Cambrian, and the 2R event occurred in the gnathostome stem-lineage, maximally in the late Cambrian-earliest Ordovician, after its divergence from cyclostomes. We find that the genome of stem-cyclostomes experienced at least an additional, independent genome triplication. Functional genomic and morphospace analyses demonstrate that WGD events generally contribute to developmental evolution with similar changes in the regulatory genome of both vertebrate groups. However, appreciable morphological diversification occurred only after the 2R event, questioning the general expectation that WGDs lead to leaps of bodyplan complexity.

overall_design: Genome-wide chromatin accessibilities were profiled in hagfish whole embryos at stages Dean 45 and 53  with an assay for transposase-accessible chromatin using sequencing (ATAC-seq).

first: Yong

last: Zhang

first: Masahiro

last: Uesaka

first: Jieyu

last: Shen


title: Profiles of Wnt pathway gene expression during tooth morphogenesis

city: Bethesda

first: Ryan

last: Dale

state: MD

address: Rm 10D39, 10 Center Drive

department: National Institute of Child Health and Human Development

institute: National Institutes of Health

summary: We used single-cell RNA sequencing (scRNA-seq) to profile Wnt signaling genes in maxillary and mandibular tooth organs from E15.5 and P1 stages

overall_design: Molar tooth organs from E15.5 embryos and P0/P1 mice pups (n=6) were used for single-cell dissociation and analyzed using scRNA-sequencing

first: Resmi

last: Raju

first: Jeremie

middle: O

last: Pina

first: Daniela

last: Roth

first: Parna

last: Chattaraj

first: Fahad

last: Kidwai

first: Fabio

last: Faucz

first: James

last: Iben

first: Gus

last: Fridell

first: Rena

middle: N

last: D’Souza


title: Glycosylation of queuosine in tRNAs contributes to optimal translation  and post-embryonic growth in vertebrates

city: Hirosawa Wako city, Saitama prefecture, Japan

first: Shintaro

last: Iwasaki

department: Cluster for Pioneering Research

institute: RIKEN

summary: Post-transcriptional modification of tRNAs is critical for protein synthesis. Queuosine (Q), a 7-deaza-guanosine derivative, is present at the first position of anticodons of several tRNA species. In vertebrate tRNAs for Tyr and Asp, Q is further glycosylated with galactose and mannose to generate galactosyl-queuosine (galQ) and mannosyl-queuosine (manQ), respectively. However, the biogenesis and physiological relevance of Q-glycosylation remain poorly understood. Here, we biochemically identified two RNA glycosylases, queuosine-tRNA galactosyltransferase (QTGAL) and queuosine-tRNA mannosyltransferase (QTMAN), and successfully reconstituted galQ and manQ formation on the respective tRNAs in the presence of nucleotide diphosphate sugars. Ribosome profiling analyses of human knockout (KO) cells of QTGAL and QTMAN revealed that Q-glycosylation slowed down elongation at the cognate codons, UAC and GAC (GAU), respectively. Furthermore, protein aggregates were significantly increased in both KO cell lines, indicating that Q-glycosylation contributes to proteostasis of nascent proteins. We determined atomic structures of human cytoplasmic tRNAs for Try and Asp bound to the ribosome A-site, providing the molecular basis of codon recognition regulated by galQ and manQ. Furthermore, zebrafish qtgal and qtman KO lines displayed shortened body length, suggesting Q-glycosylation is required for post-embryonic growth in vertebrates. These findings demonstrate that Q-glycosylation modulates codon-specific translation to optimize the decoding speed in protein synthesis, thereby maintaining correct folding of nascent proteins, proteome integrity, and normal growth of vertebrates.

overall_design: Ribosome profiling

first: Xuewei

last: Zhao

first: M

last: Ding

first: Kensuke

last: Ishiguro

first: Hironori

last: Saito

first: Ikuya

last: Matsuzawa

first: Mari

last: Mito

first: Toru

last: Irie

first: Kimi

last: Wakabayashi

first: Yuriko

last: Sakaguchi

first: Takeshi

last: Yokoyama

first: Yuichiro

last: Mishima

first: Mikako

last: Shirouzu

first: Takeo

first: Tsutomu


title: PREGNANCY-RESPONSIVE POOLS OF ADULT NEURAL STEM CELLS FOR TRANSIENT NEUROGENESIS IN MOTHERS

city: Basel

first: Jonas

middle: Alexander

last: Kretz

address: Schanzenstrasse 44

department: BSSE

country: Switzerland

institute: ETH

summary: Adult neural stem cells (NSCs) contribute to lifelong brain plasticity. In the adult mouse ventricular-subventricular zone, NSCs are heterogeneous and, depending on their location in the niche, give rise to different subtypes of olfactory bulb (OB) interneurons. Here we show that multiple regionally-distinct NSCs, including domains that are usually quiescent, are recruited on different gestation days during pregnancy. Synchronized activation of these adult NSC pools generates transient waves of short-lived OB interneurons, especially in layers with less neurogenesis under homeostasis. Using spatial transcriptomics, we identify molecular markers of pregnancy-associated interneurons, and show that some subsets are temporarily needed for own pup recognition. Thus, pregnancy triggers transient, yet behaviorally-relevant neurogenesis, highlighting the physiological relevance of adult stem cell heterogeneity.

overall_design: Comparative analysis between four mouse brain samples; (i) one mother during perinatal care, (ii) one mother at peri-weaning, (iii) two age-matched virgins, was performed with the 10x Genomics Visium platform for fresh frozen samples. Spatial transcriptome analysis focused on the differential gene expression across these states and was performed both globally and also stratified within the corresponding spot clusters.

first: Zayna

last: Chaker

first: Corina

last: Segalada

first: Ilhan

middle: E

last: Acar

first: Ana

last: Delgado

first: Valerie

last: Crotet

first: Andreas

last: Moor

first: Fiona

last: Doetsch


title: Nrf2 activation rescues stress-induced depression-like behaviour and inflammatory responses in male but not female rats

city: Vancouver

first: Ryan

middle: Thomas

last: McCallum

state: BC

address: 938 W 28th Ave

department: Faculty of Medicine

institute: University of British Columbia

summary:
Background: Major depressive disorder (MDD) is a recurring affective disorder that is two times more prevalent in females than males. Evidence supports immune system dysfunction as a major contributing factor to MDD, notably in a sexually dimorphic manner. Nuclear factor erythroid 2-related factor 2 (Nrf2), a regulator of antioxidant signaling during inflammation, is dysregulated in many chronic inflammatory disorders, however its role in depression and the associated sex differences have yet to be explored. Here we investigated the sex-specific antidepressant and immunomodulatory effects of the potent Nrf2 activator dimethyl fumarate (DMF), as well as the associated gene expression profiles.  Methods: Male and female rats were treated with vehicle or DMF (25 mg/kg) while subjected to 8 weeks of chronic unpredictable stress. The effect of DMF treatment on stress-induced depression- and anxiety-like behaviours, as well as deficits in recognition and spatial learning and memory were then assessed. Hippocampal (HIP) microglial activation and alterations in gene transcripts were also evaluated.  Results: DMF treatment during stress exposure had antidepressant effects in male but not female rats, with no anxiolytic effects in either sex. Recognition learning and memory and spatial learning and memory were impaired in chronically stressed males and females, respectively, however DMF treatment rescued these deficits. DMF treatment also prevented stress-induced HIP microglial activation in males. Conversely, females displayed no HIP microglial activation associated with stress exposure. Lastly, chronic stress elicited sex-specific alterations in HIP gene expression, many of which were normalized in animals treated with DMF. Of note, several differentially expressed genes in males were related to inflammatory or immune responses.  Conclusions: Collectively, these findings support a greater role of immune processes in males than females in a rodent model of depression. This suggests that pharmacotherapies that target Nrf2 have the potential to be an effective sex-specific treatment for depression.
Major depressive disorder is two times more prevalent in females than males. Further, immune system dysfunction has been shown to contribute to the development of depression, with previous studies consistently reporting chronic low-grade inflammation in depressed individuals. Not surprisingly, the immune system dysfunction associated with depression appears to be sex specific. As such, while anti-inflammatory drugs have shown antidepressant effects in preclinical studies, the sex differences in these effects are seldomly investigated.  Thus, this study sought to determine the sex-specific antidepressant and immune modulatory effects of dimethyl fumarate (DMF) treatment. DMF is a drug that activates the protein nuclear factor erythroid 2-related factor 2 to initiate anti-inflammatory signaling pathways. Here, male and female rats were exposed to 8 weeks of chronic stress while receiving daily DMF treatment. Subsequently, their expression of depression- and anxiety-like behaviours, as well as learning and memory deficits were assessed. Changes in the levels of an inflammatory marker in the brain and alterations in gene expression were also evaluated. DMF treatment had antidepressant effects in male rats only but did not have anti-anxiety effects in either sex.  The learning and memory deficits in both sexes were rescued with DMF treatment. Notably, chronic stress only increased inflammatory marker levels in male rats, which was prevented by DMF treatment. Additionally, DMF normalized several of the sex-specific gene alterations induced by chronic stress, with many of the male-specific genes relating to inflammatory processes. These data suggest that anti-inflammatory drugs may be an effective antidepressant treatment in males.

overall_design: 24 Total samples were analyzed

first: Rachel-Karson

last: Thériault

first: Joshua

last: Manduca

first: Isaac

middle: S

last: Russell

first: Angel

middle: M

last: Culmer

first: Janan

last: Doost

first: Tami

last: Martino

first: Melissa

middle: L

last: Perreault


title: Transcriptional changes on lymphatic endothelial cells upon co-culture with human melanoma cells

status: Public on Nov 20 2023

city: Helsinki

first: Päivi

last: Ojala

address: Haartmaninkatu 8

department: Department of Medicine

institute: University of Helsinki

summary: The aim was to study transcriptional changes on the primary human lymphatic endothelial cells when they have been in contact with a human melanoma cell line

overall_design: The data consists of two samples: the control samples consists of parental primary lymphatic endothelial cells and WM852 melanoma cells (1:10 mix). The co-cultured samples consists of LECs which were cultured for two days with melanoma cells before the cell sorting by FACS.

first: Sanni

last: Alve

first: Sinem

last: Karaman

first: Madeleine

middle: H

last: Lackman


title: Human Cerebellar Organoids with functional Purkinje Cells

first: Giorgia

last: Quadrato

state: CA

address: 1425 San Pablo Street, Rm 405

institute: Broad Institute, USC Stem Cell & Regenerative Medicine

summary: Research on human cerebellar development and disease has been hampered by the need for a human cell-based system that recapitulates the human cerebellum's cellular diversity and functional features. Here, we report a human organoid model (hCerOs) capable of developing the complex cellular diversity of the fetal cerebellum, including human-specific rhombic lip progenitor populations that have never been generated in vitro prior to this study. Two months old hCerOs form distinct cytoarchitectural features, including laminar organized layering and create functional connections between inhibitory and excitatory neurons that display coordinated network activity.  Long-term culture of hCerOs allows for healthy survival and maturation of Purkinje cells that display molecular and electrophysiological hallmarks of their in vivo counterparts, addressing a long-standing challenge in the field. This study therefore provides a physiologically relevant, all-human model system to elucidate the cell type specific mechanisms governing cerebellar development and disease.

overall_design: Human cerebellar brain organoids were generated and grown to a 2-month time point. Three organoids were each individually dissociated and analyzed by scRNA-seq.

first: Alexander

last: Atamian

first: Marcella

last: Birtele

first: Negar

last: Hosseini

first: Tuan

last: Nguyen

first: Anoothi

last: Seth

first: Ashley

last: Del Dosso

first: Sandeep

last: Paul

first: Neil

last: Tedeschi

last: Taylor

first: Marcelo

last: P Coba

first: Ranmal

last: Samarasinghe

first: Carlos

last: Lois


title: Circulating miR-let7a levels predict future development of chronic thromboembolic pulmonary hypertension

city: Hannover

first: Ke

last: Xiao

address: Carl-Neuberg-Straße 1

department: IMTTS

institute: Medizinische Hochschule Hannover (MHH)

summary: RNA was isolated from plasma of 20 healthy patients and 20 patients with acute pulmonary embolism. Dysregulated microRNA patterns were screened in these samples

overall_design: 20 plasma samples derived from healthy control patients and 20 plasma samples derived from patients wit pulmonary embolism

first: Franziska

last: Kenneweg

first: Thomas

last: Thum


title: An RNA-seq atlas of mouse brain areas during fasting and diet-induced obesity

city: Copenhagen

first: Lars

middle: Roed

last: Ingerslev

address: Blegdamsvej 3B

department: NNF Center for Basic Metabolic Research

institute: Copenhagen University

summary: Mammalian energy homeostasis is regulated by the hypothalamus and hindbrain, with the hippocampus, midbrain nuclei, and other regions implicated by evidence from human genetics studies. In order to understand how these brain regions respond to imbalances in energy homeostasis, we performed two experiments examining the effects of different diets in male C57BL6 mice. In our first study, groups of 6 pair-housed mice were given access to chow, high-fat diet or fasted for 16 hours. In our subsequent study, two groups of 10 mice were single-housed and given access to chow or fasted for 24h. We recorded food intake for each cage, the change in body weight for each animal, and collected hypothalamus, hippocampus, superior colliculus, inferior colliculus, prefrontal cortex, and zona incerta samples. We performed bulk RNA sequencing on 185 samples and validated them by a series of quality control assessments including alignment quality and gene expression profiling. We believe these studies capture the transcriptomic effects of acute fasting and high fat diet in the rodent brain and provide a valuable reference.

overall_design:
In the 16-hour study, 6 animals per group were pair housed and either fasted, kept on a chow diet, or switched to a HFD for 16 hours before being sacrificed. Hypothalamus, hippocampus, superior colliculus, inferior colliculus, and prefrontal cortex from each animal were sequenced
In the 24-hour study, 9 animals were kept on a chow diet and 10 animals were fasted. All animals were single housed and acclimatized for three days before the start of the experiment. After 24 hours of their respective diets, animals were sacrificed and the hypothalamus, hippocampus, superior colliculus, inferior colliculus, and zona incerta were sequenced

first: Petar

last: Todorov

first: Anders

middle: B

last: Klein

first: Kristoffer

last: Egerod

first: Christoffer

last: Clemmensen

first: Tune

last: Pers


title: ATI-1777 a topical JAK1/3 inhibitor may benefit atopic dermatitis without systemic drug exposure, results from preclinical development and Phase 2a randomized-control study ATI-1777-AD-201

city: St. Louise

first: CANXIN

last: XU

state: MO

address: 4340 Duncan Ave

department: Pharmacology

institute: Aclaris Therapeutics, Inc.

summary: Atopic dermatitis (AD), a chronic, pruritic skin disease, affects 10%-30% of children and up to 14% of adults in developed countries. Since current AD treatments may lead to systemic drug exposure and AD pathophysiology is partially mediated by JAK1/3 signaling, ATI-1777, a potent and selective JAK1/3 inhibitor, was designed with multiple sites of metabolism to deliver local efficacy in the skin and limit systemic exposure. In preclinical studies, ATI-1777 selectively inhibited JAK1/3 with limited systemic exposure and without any adverse effects. ATI-1777-AD-201 (NCT04598269), a Phase 2a, first-in-human, randomized, double-blind,vehicle-controlled, parallel-group study, evaluated the efficacy, safety, tolerability, and pharmacokinetics of ATI-1777 topical solution in 48participants with AD over 4 weeks. The primary outcome was reduction of a modified EASI score from baseline; reduction was significantly greater in the ATI-1777 group at Day28 compared to vehicle (percent reduction from baseline 74.45% [SE6.455] and 41.43% [SE6.189], respectively [p<0.001]). Average plasma  concentrations of ATI-1777 were <5% of the IC50 of ATI-1777 for inhibiting JAK1/3. No deaths or serious adverse events were reported. This demonstrates that topical ATI-1777 does not lead to pharmacologically relevant systemic drug exposure and may reduce clinical signs of AD.

overall_design: We developed a pharmacodynamic porcine topical model to assess the effects of ATI-1777 on JAK1/3 signaling and selected a suitable formulation for the compound. To select the most robustly induced genes by intradermal injection (ID) of IL-15 in the Yorkshire swine skin, we performed the RNA seq for 8 skin biopsy samples. For each of two pigs, two sites were injected with ID IL15 and two sites without injection, resulting in a total of 4 samples for IL-5 and 4 samples for control.  Biopsy samples of these sites were extracted for RNA, followed by RNA Seq and qPCR to determine the gene expression, and select optimal genes for the readouts.

first: Paul

last: Changelian

first: Canxin

last: Xu

first: Steve

last: Mnich


title: The Staphylococcus aureus CamS lipoprotein is a repressor of toxin production that shapes host-pathogen interaction

city: Leicester

first: Katrin

last: Schilcher

state: Leicestershire

address: University Road

department: Genetics and Genome Biology

institute: University of Leicester

summary: Lipoproteins of the opportunistic pathogen Staphylococcus aureus play a crucial role in various cellular processes and host interactions. Consisting of a protein and a lipid moiety, they support nutrient acquisition and anchor the protein to the bacterial membrane. Recently, we identified several processed and secreted small linear peptides that derive from the secretion signal sequence of S. aureus lipoproteins. Here, we show for the first time, that the protein moiety of the S. aureus lipoprotein CamS has a biological role that is distinct from its associated linear peptide staph-cAM373. The small peptide was shown to be involved in interspecies horizontal gene transfer, the primary mechanism for the dissemination of antibiotic resistance among bacteria. We provide evidence that the CamS protein moiety is a potent repressor of cytotoxins, such as α-toxin and leukocidins. The CamS-mediated suppression of toxin transcription was reflected by altered disease severity in in vivo infection models involving skin and soft tissue, as well as bloodstream infections. Collectively, we have uncovered the role of the protein moiety of the staphylococcal lipoprotein CamS as a previously uncharacterized repressor of S. aureus toxin production, which consequently regulates virulence and disease outcomes. Notably, the camS gene is conserved in S. aureus, and we also demonstrated the muted transcriptional response of cytotoxins in another S. aureus lineage. Our findings provide the first evidence of distinct biological functions of the protein moiety and its associated linear peptide for a specific lipoprotein. Therefore, lipoproteins in S. aureus consist of three functional components: a lipid moiety, a protein moiety, and a small linear peptide, with putative different biological roles that might not only determine the outcome of host-pathogen interactions but also drive the acquisition of antibiotic resistance determinants.

overall_design: RNA sequencing of S. aureus LAC wild type, mutant and complemented strains to determine differences in their gene expression profiles.

first: Morgan

last: Severn

first: Christian

last: Jenul

first: Young-Saeng

middle: C

last: Avina

first: Rebecca

middle: A

last: Keogh

first: Alexander

middle: R

last: Horswill


title: CRISPR-Cas immunity is repressed by the LysR-type transcriptional regulator PigU

city: Dunedin

first: Peter

middle: Charles

last: Fineran

state: Otago

address: 720 Cumberland Street

department: Department of Microbiology and Immunology

country: New Zealand

institute: University of Otago

summary: Bacteria protect themselves from infection by bacteriophages (phages) using different defence systems, such as CRISPR-Cas. Although CRISPR-Cas provides phage resistance, fitness costs are incurred, such as through autoimmunity. CRISPR-Cas regulation can optimise defence and minimise these costs. We recently developed a genome-wide functional genomics approach (SorTn-seq) for high-throughput discovery of regulators of bacterial gene expression. Here, we applied SorTn-seq to identify loci influencing expression of the two type III-A Serratia CRISPR arrays. Multiple genes affected CRISPR expression, including those involved in outer membrane and lipopolysaccharide synthesis. By comparing loci affecting type III CRISPR arrays and cas operon expression, we identified PigU (LrhA) as a repressor that co-ordinately controls both arrays and cas genes. By repressing type III-A CRISPR-Cas expression, PigU shuts off CRISPR-Cas interference against plasmids and phages. PigU also represses interference and CRISPR adaptation by the type I-F system, which is also present in Serratia. RNA sequencing demonstrated that PigU is a global regulator that controls secondary metabolite production and motility, in addition to CRISPR-Cas immunity. Increased PigU also resulted in elevated expression of three Serratia prophages, indicating their likely induction upon sensing PigU-induced cellular changes. In summary, PigU is a major regulator of CRISPR-Cas immunity in Serratia.

overall_design: To investigate the effects of a transposon insertion in the intergenic region between alaA and pigU in Serratia sp. ATCC 39006 strain LacA, RNA-seq was performed on the transposon mutant and the LacA (wildtype) control.

first: Leah

last: Smith

first: Hannah

middle: G

last: Hampton

first: Mariya

last: Yestigneyeva

first: Marina

last: Mahler

first: Zacharie

last: Paquet


title: A genome-wide relay of signalling-responsive enhancers drives hematopoietic specification

city: Birmingham

first: Benjamin

last: Edginton-White

address: Medical School

department: ICGS

institute: University of Birmingham

summary: Developmental control of gene expression critically depends on distal cis-regulatory elements including enhancers which interact with promoters to activate gene expression. Multiple genome-wide studies have mapped chromatin and genomic features of such elements. However, the enhancer definition is operational, and no global experiments have been conducted to date that identify their cell type and cell stage-specific transcription stimulatory activity in a chromatin context. Here, we describe a high-throughput method that identifies thousands of cis-elements capable of stimulating transcriptional activity from a minimal promoter using the blood progenitor differentiation from embryonic stem cells as model. We show that hematopoietic specification and blood cell-specific gene expression are controlled by the concerted action of thousands of differentiation stage-specific sets of cis-elements which respond to cytokine signals terminating at signalling responsive transcription factors. Our work presents a major advance in our understanding of developmental gene expression control in the hematopoietic system and beyond.

overall_design: Targeted DNA sequencing of fragment libraries cloned into an enhancer reporter cassette in the HPRT locus of HM-1 ES cells and their differentiated progeny. Populations of cells were sorted for Venus-YFP reporter activity into negative, low, medium and high.

first: Bejamin

last: Maytum

first: Sophie

last: Kellaway

first: Debbie

middle: K

last: Goode

last: Keane

first: Inti

last: Pagnuco

first: Salam

last: Assi

first: Luke

last: Ames

first: Mary

last: Clarke

last: Cockerill

first: Berthold

last: Göttgens

first: Jean-Baptiste

last: Cazier

first: Constanze

last: Bonifer


title: Single cell RNA seq analysis of the chicken basilar papilla following in vivo aminoglycoside induced hair cell ablation

city: Nashville

first: Taha

last: Jan

state: TN

address: 2220 Pierce Ave, PRB 752

department: Otolaryngology

institute: VUMC

summary: scRNAseq of chicken basilar papilla at P7 and P11 as controls, and 12, 16, 20, 24, 30, 38, 48, and 96 hours post sisomicin administration. Cells were isolated using FACS and underwent Smartseq-2 protocol for single cell RNA seq with paired-end sequencing. Processed data file contains SingleCellExperiment object with all metadata. The dataset has undergone quality control using scater package in R, normalized using SCnorm, and normalized counts were log2 transformed (found in RDS file here). Only genes expressed in at least 3 cells are included for a total of 16,302 genes. A total of 2,625 high quality cells are in the normalized dataset. Raw sequence data for all 3,831 sequenced cells pre-quality control is also included.

overall_design: Postnatal day 7 (P7) chicken inner ears were exposed to sisomicin with basilar papilla harvested at indicated timepoints post exposure. Cells underwent FACS sorting prior to library prep and single cell RNA sequencing using the Smartseq2 protocol.

first: Stefan

last: Heller

first: Nesrine

last: Benkafadar


title: METTL4-mediated N6-methyladenine DNA modification regulates thermotolerance in Arabidopsis thaliana

city: Changsha

first: Chongsheng

last: He

state: Hunan

address: 27 Tianma road

institute: Hunan university

summary:
Wild type and atdamt1 seedlings were heat treated for 2.5 hours, control and treated seedlings were collected to extract total RNA for mRNA-seq.
We then performed gene expression profiling analysis using data obtained from mRNA-seq.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for control and heat treated wild type and atdamt1 seedlings.

first: Linjun

last: Cai

first: Ancheng

last: Ma

first: Jiao

last: Lei


title: Gene regulatory network analysis predicts cooperating transcription factor regulons required for FLT3-ITD+ AML growth [scRNA-seq]

first: Peter

address: Vincent Drive

department: Institute for Cancer and Genomic Sciences

summary: AML is a heterogenous disease caused by different mutations. We have previously shown that each mutational sub-type develops its specific gene regulatory network (GRN) with transcription factors interacting with multiple gene modules, many of which are transcription factor genes themselves. Here we hypothesized that highly connected nodes within such networks comprise crucial regulators of AML maintenance. We tested this hypothesis using FLT3-ITD mutated AML as model and conducted an shRNA drop-out screen informed by this analysis. Our screen showed that AML-specific GRNs are predictive for identifying crucial regulatory modules required for AML but not normal cellular growth. Furthermore, our work shows that all modules are highly connected and regulate each other. The careful multi-omic analysis of the role of one (RUNX1) module by shRNA and chemical inhibition shows that this transcription factor and its target genes stabilize the GRN of FLT3-ITD AML and that its removal leads to GRN collapse and cell death

overall_design: Single-Cell RNA-Seq (3', 10x Genomics) of FLT3-ITD AML patient cells treated with CBFBi and untreated

first: Daniel

last: Coleman


title: Gene regulatory network analysis predicts cooperating transcription factor regulons required for FLT3-ITD+ AML growth [shRNA-seq]

last: Keane

overall_design: shRNA dropout screen of FLT3-ITD AML cell lines (MOLM14 and MV411) and healthy controls before and after shRNA induction with Doxycyline


title: Gene regulatory network analysis predicts cooperating transcription factor regulons required for FLT3-ITD+ AML growth [RNA-seq]

overall_design: Bulk RNA-Seq of FLT3-ITD AML patient cells treated with CBFBi, FLT3i, shRNA and controls


title: A multiscale 3D chromatin architecture that controls development of the humoral immune system is assembled by IKAROS [HiC_LpreB_Steadystate]

city: Charlestown

first: Katia

last: Georgopoulos

state: MA

address: 1st and 13th St

department: CBRC

institute: Harvard Medical School

summary: A generic level of chromatin organization generated by the interplay between cohesin and CTCF suffices to limit promiscuous interactions between regulatory elements, but a lineage-specific assembly of chromatin that supercedes these constraints is required to configure the genome to support the gene expression changes that guide faithful lineage progression. Using loss-of-function approaches in B cell precursors in vivo we show that IKAROS assembles interactions between sites often separated by megabase distances to configure a significant fraction of the genome in preparation for lymphoid development. Interactions emanating from IKAROS-bound enhancers override CTCF-imposed boundaries and assemble lineage-specific regulatory units built on a backbone of smaller invariant topological domains.In vitro deletion provides temporal resolution to changes in chromatin modifications, loops, and compartmental localization. Gain-of-function experiments in epithelial cells confirm IKAROS’ ability to reconfigure chromatin architecture at multiple scales.  While the compaction of the Igk locus required for genome editing represents a function of IKAROS unique to the lymphoid system, the more general function of this lineage-defining DNA binding protein to preconfigure the genome to support lineage specific gene expression and suppress activation of extra-lineage genes provides a paradigm for lineage restriction.

overall_design: We performed in situ Hi-C in wild-type and IkE5Δ/Δ large pre-B cells to understand IKAROS’ function in the genome organization in early B cell development.

first: Yeguang

last: Hu

first: Daniela

last: Salgado Figueroa

first: Zhihong

last: Zhang

first: Margaret

last: Vaselits

first: Sourya

last: Bhattacharyya

first: Marcus

last: Clark

first: Mariko

last: Kashiwagi

first: Bruce

last: Morgan

first: Ferhat

last: Ay


title: Gene regulatory network analysis predicts cooperating transcription factor regulons required for FLT3-ITD+ AML growth.

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

overall_design: Refer to individual Series


title: RNA and phosphoprotein profiles of TP53- and PTEN-knockouts in MCF10A at baseline and responding to DNA damage

city: Seattle

first: Amanda

last: Paulovich

state: WA

address: 1100 Fairview Ave. N.

institute: Fred Hutchinson Cancer Research Center

summary: A wealth of proteogenomic data has been generated using cancer samples to deepen our understanding of the mechanisms of cancer and how biological networks are altered in association with somatic mutation of tumor suppressor genes, such as TP53 and PTEN. To generate functional signatures of TP53 or PTEN loss, we profiled the RNA and phosphoproteomes of the MCF10A epithelial cell line, along with its congenic TP53- or PTEN-knockout derivatives, upon perturbation with the monofunctional DNA alkylating agent methyl methanesulfonate (MMS) vs. mock-treatment. To enable quantitative and reproducible mass spectrometry data generation, the cell lines were SILAC-labeled (stable isotope labeling with amino acids in cell culture), and the experimental design included label swapping and biological replicates. All data are publicly available and may be used to advance our understanding of the TP53 and PTEN tumor suppressor genes and to provide functional signatures for bioinformatic analyses of proteogenomic datasets.

overall_design: Cells from 3 MCF10A cell lines (WT, p53-KO, PTEN-KO) were treated with 0.5 mM methyl methanesulfonate and harvested after 3 hours of treatment. The experiment was repeated on three days. RNAs were extracted for RNAseq. More details about cell treatments and RNA extraction and sequencing are provided on the sample pages.

first: ChenWei

last: Lin

first: Regine

last: Schoenherr

first: Uliana

middle: J

last: Voytovich

first: Richard

last: Ivey

first: Jacob

last: Kennedy

first: Jeffrey

last: Whiteaker

first: Pei

last: Wang


title: Chemically defined and scalable culture system for intestinal stem cells derived from human intestinal organoids (RNA-Seq)

city: Daejeon

first: Mi-Young

last: Son

address: 111 Gwahangno, Yuseong-gu

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology (KRIBB)

summary: we established a human intestinal stem cell (ISC) culture method expanded under feeder-free and fully defined conditions through selective enrichment of ISC populations (ISC3D-hIO) within hIO derived from human pluripotent stem cells.

overall_design: Single cell RNA-sequencing of human intestinal stem cells (ISCs) derived from 3D human intestinal organoids (3D HIOs)

first: Ohman

last: Kwon


title: Effect of autologous fat grafting on Localized Scleroderma (morphea)

city: Guangzhou

first: Juzi

last: Liu

state: --- Select One ---

address: North Guangzhou Avenue 1838, Nanfang Hospital

country: China

institute: Southern Medical University

summary: Localized scleroderma (LoS), or morphea, refers to a group of rare autoimmune connective tissue diseases. Autologous fat grafting was able to correct volume loss in patients with LoS to improve facial disfigurement.However, whether it could exert a positive effect on reversing skin sclerosis remains unclear.

overall_design: 3 patients diagnosed with morphea received sequential fat grafting of autologous fat and cryopreserved stromal vascular fraction (SVF)-gel. Trancriptome analysis of lesional skin samples was compared before and 12 months after treatment.A total of 6 RNA-seqs were performed.

first: Jrunong

last: Cai

first: Jing

first: Qian

last: Zhang

first: Feng

last: Lu