title: Cancer-specific miRNAs Extracted from Tissue-exudative Ex-tracellular Vesicles in Ovarian Clear Cell Carcinoma

city: Takatsuki

first: Hiroshi

last: Maruoka

state: Osaka

address: 2-7 Daigakumachi

institute: Department of Obstetrics and Gynecology, Educational Foundation of Osaka Medical and Pharmaceu-tical University

summary:
Ovarian clear cell carcinomas (OCCs) arise from endometriotic cysts that many women develop. Because the prognosis for OCC is poor, there is a need to identify biomarkers for early detection of OCC. Extracellular vesicles have attracted attention as biomarker carriers. This study aimed to identify cancer-specific miRNAs as novel OCC biomarkers using tissue-exudative extracellular vesicles (Te-EVs). Te-EVs were collected from patients with OCC on one side and a normal ovary on the other side. RNA sequencing was performed to identify cancerspecific miRNAs in Te-EVs.
We identified tissue-specific miRNAs in the EVs secreted by OCC tissues. These EV miRNAs can be used as biomarkers for the early diagnosis and detection of OCC.

overall_design: Specimens were collected from four patients with Ovarian Clear Cell Carcinomas (OCCs); all four had OCCs on one side and normal ovaries on the other side. miRNAs extracted from EVs secreted from OCCs were compared with those extracted from EVs secreted from normal tissue.

first: Tomohito

last: Tanaka


title: Function-specific IL-17A and dexamethasone interactions in primary human airway epithelial cells

status: Public on Oct 01 2022

city: Groningen

first: Reinoud

last: Gosens

address: Antonius Deusinglaan 1

department: Molecular Pharmacology

country: Netherlands

institute: University of Groningen

type: Expression profiling by high throughput sequencing

summary: Asthmatics have elevated levels of IL-17A compared to healthy controls. IL-17A is likely to contribute to reduced corticosteroid sensitivity of human airway epithelium. Here, we aimed to investigate the mechanistic underpinnings of this reduced sensitivity in more detail. Differentiated primary human airway epithelial cells (hAECs) were exposed to IL-17A in the absence or presence of dexamethasone. Cells were then collected for RNA sequencing analysis or used for barrier function experiments. Mucus was collected for volume measurement and basal medium for cytokine analysis. 2861 genes were differentially expressed by IL-17A (Padj<0.05), of which the majority was not sensitive to dexamethasone (<50% inhibition). IL-17A did inhibit canonical corticosteroid genes, such as HSD11B2 and FKBP5 (p<0.05). Inflammatory and goblet cell metaplasia markers, cytokine secretion and mucus production were all induced by IL-17A, and these effects were not prevented by dexamethasone. Dexamethasone did reverse IL-17A-stimulated epithelial barrier disruption, and this was associated with gene expression changes related to cilia function and development. We conclude that IL-17A induces function-specific corticosteroid-insensitivity. Whereas inflammatory response genes and mucus production in primary hAECs in response to IL-17A were corticosteroid-insensitive, corticosteroids were able to reverse IL-17A-induced epithelial barrier disruption.

overall_design: Differentiated primary human airway epithelial cells (hAECs) were exposed to IL-17A (10 ng/ml) in the absence or presence of dexamethasone (100 nM). Cells were then collected for RNA sequencing analysis or used for barrier function experiments.

first: Siti

middle: F

last: Rahmawati

first: Remon

last: Vos

first: Huib

middle: A

last: Kerstjens

first: Loes

middle: E

last: Kistemaker


title: RNA sequencing for one patient with acute lymphoblastic leukemia.

city: Dalian

first: Jinsong

last: Yan

state: Liaoning

address: 467 Zhongshan Road, Dalian 116027, Liaoning, P. R. China

department: Department of Hematology

country: China

institute: the Second Hospital of Dalian Medical University

summary: Acute lymphoblastic leukemia (ALL) is a type of heterogeneous hematopoietic malignancy that accounts for approximately 20% of adult ALL. Although ALL complete remission (CR) rate has increased to 85%–90% after induction chemotherapy, 40%–50% of patients eventually relapsed. Therefore, it is necessary to improve the outcomes of ALL via accurate diagnosis and individualized treatments,which benefits in part from molecular biomarkers. Here, we identified a new fusion gene,Acyl-CoA Thioesterase 7–Nephrocystin 4 (ACOT7–NPHP4), in a 34-year-old patient with ALL. The fusion gene contributed to chemoresistance to doxorubicin and acted as a new molecular marker.

overall_design: Examination of fusion genes in one patient with acute lymphoblastic leukemia.


title: Hi-TrAC reveals fine-scale chromatin structures organized by transcription factors

status: Public on Oct 02 2022

city: Bethesda

first: Yaqiang

last: Cao

state: Maryland

address: 9000 Rockville Pike

department: System Biology Center

country: USA

institute: NHLBI

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The three-dimensional genomic structure plays a critical role in gene expression, cellular differentiation, and pathological conditions. Previous studies have extensively investigated the structures including A/B compartments and topologically associating domains (TADs) at a scale from hundreds of kilobases (kb) to megabases (Mb). However, fine-scale chromatin architectures, particularly enhancer-promoter interactions, which are often within 100 kb and critical for the temporospatial regulation of expression, remain to be fully characterized due to technical limitations. In this study, we report Hi-TrAC as a proximity ligation free, robust, and sensitive technique to profile genome-wide chromatin interactions at high-resolution among accessible regulatory elements. Hi-TrAC detects chromatin looping among accessible chromatin regions at single nucleosome resolution. We observed that cell-specifically expressed genes are harbored in active sub-TADs. With almost half million identified loops, we constructed a comprehensive interaction network of regulatory elements across the genome. After integrating chromatin binding profiles of transcription factors (TFs), we discovered that cohesin complex and CTCF are responsible for organizing long-range chromatin loops, which are related with domain formation, whereas ZNF143 and HCFC1 are involved in structuring short-range chromatin loops between regulatory elements, which directly regulate gene expression.  Thus, here we developed a new methodology to identify a delicate and comprehensive network of cis regulatory elements, revealing the complexity and a division of labor of TFs in chromatin looping for genome organization and gene expression.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: The genome structure of GM12878, K562 and mESC cells was studied by a newly developed technique Hi-TrAC. Chromatin binding profiles of architectural proteins CTCF, RAD21, HCFC1 and ZNF143 were studied by ChIP-seq. The effect of these four proteins on gene expression was investigated by RNA-seq, accessbility changes were studied by ATAC-seq, changes of chromatin interactions were also validated by Hi-C.

first: Shuai

last: Liu

first: Kairong

last: Cui

first: Qingsong

last: Tang

first: Keji

last: Zhao


title: Transcriptome analysis of activated CD4+ T cells deficient for Zfp36 or Zfp36l1

city: Cambridge

first: Louise

last: Matheson

address: Babraham Research Campus

department: Laboratory of Lymphocyte Signalling and Development

country: United Kingdom

institute: The Babraham Institute

summary: Characterisation of the effects on the transcriptome of deleting the Zfp36 or Zfp36l1 genes in activated CD4+ T cells

overall_design: mRNA sequencing libraries from Zfp36-/- and Zfp36l1-/- activated CD4+ T cells, and corresponding floxed controls. 2-3 replicate libraries were generated for each genotype.

first: Sebastian

last: Łukasiak

middle: S

first: Martin

last: Turner


title: Loss of the Nuclear Envelope Protein LAP1B Disrupts Myogenic Differentiation of Patient-Derived Fibroblasts

city: Ankara

first: Pervin

last: Dinçer

address: Hacettepe, Merkez Kampüs, A kapısı, 4. kat

department: Dept. of Medical Biology

country: Turkey

institute: Hacettepe University

summary: Lamina-associated polypeptide 1 (LAP1) is a ubiquitously expressed inner nuclear membrane protein encoded by TOR1AIP1, and present as two isoforms in humans, LAP1B and LAP1C. While loss of both isoforms results in a multisystemic progeroid-like syndrome, specific loss of LAP1B causes muscular dystrophy and cardiomyopathy, suggesting that LAP1B has a critical role in striated muscle. To gain more insight into the molecular pathophysiology underlying muscular dystrophy caused by LAP1B, we established a patient-derived fibroblast line transdifferentiated into myogenic cells with inducible MyoD expression. Compared to controls, we observed strikingly reduced myogenic differentiation and fusion potentials. Similar defects were observed in C2C12 myoblasts carrying loss-of-function LAP1A/B mutations. Using RNA sequencing, we showed that despite MyoD overexpression and efficient cell cycle exit, transcriptional reprogramming of LAP1B-deficient cells into the myogenic lineage was impaired with delayed activation of myogenin and muscle-specific downstream genes. Gene set enrichment analysis suggested dysregulation of protein metabolism, extracellular matrix and chromosome organization. Finally, we found that LAP1B-deficient cells exhibit nuclear deformations such as increased micronuclei and altered morphometric parameters. This study reports the phenotypic and transcriptomic changes during myoconversion of patient-derived fibroblasts and provides a useful resource to gain new insights into the mechanisms implicated in LAP1B-associated nuclear envelopathies.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for control and LGMD2Y patient-derived immortalized myoconverted fibroblasts.

first: Aybar

middle: C

last: Acar

first: Gülsüm

last: Kayman Kürekçi


title: Effect of NCOA4-depletion on the transcriptome profile of J774 mouse macrophage cells

status: Public on Sep 30 2022

city: Seoul

first: Moon-Suhn

last: Ryu

address: 50 Yonsei-ro, Seodaemun-gu

department: Food and Nutrition

country: South Korea

institute: Yonsei University

summary:
To determine the physiological roles of NCOA4 and ferritinophagy in macrophages, NCOA4 was depleted via liposome-mediated siRNA delivery into cells.
Cells were treated with siRNA for NCOA4 depletion and then the transcriptome profiles acquired from RNA-seq were compared with those of control (scramble siRNA-treated) cells.

overall_design: Comparative gene expression profiling of control J774 cells and those deficient in NCOA4 (n = 3 biological replicates per group)

first: Cole

last: Guggisberg


title: Canine Polarized Macrophages Express Distinct Functional and Transcriptomic Profiles

city: Fort Collins

first: Steven

last: Dow

state: CO

address: 300 W Drake Rd

department: Clinical Sciences

institute: Colorado State University

summary: in the present study we investigate polarized canine macrophages using transcriptome sequencing, a larger panel of flow cytometry markers, and antimicrobial functional assays. Transcriptome analysis of primary canine monocyte-derived macrophages revealed unique, previously unreported signatures for polarized M1 and M2 macrophages.

overall_design: canine monocyte derived macrophages were differentiated into inflamtory or anti-inflmatory phenotypes then subjected to bulk RNA sequencing

first: Lyndah

last: Chow

first: Sirikul

last: Soontararak


title: NOMe-Seq analysis of fixed budding yeast nuclei with two DNA methyltransferases II

city: Kashiwa

first: Fumihito

last: Miura

state: Chiba

address: Kashiwanoha 5-1-5

department: Graduate School of Frontier Sciences

country: Japan

institute: The University of Tokyo

type: Methylation profiling by high throughput sequencing

summary: NOMe-Seq analysis was performed with two cytosine C-5 DNA methyltransferases recognizing GC and CC dinucleotides were performed

overall_design: Spheroplasts were prepared with treating S288C cells with Zymolyase 100T. Then, 1% formaldehyde was added to fix the cells. After washing the cells with 1 M sorbitol, the yeast nuclei were prepared with a solution containing 0.1% NP-40. The nuclei were suspended in methylation buffer, and cytosine C-5 DNA methyltransferase was added. The solution was incubated at 37°C for 1 hr and collected nuclei. Then genomic DNA was extracted, and library preparation was performed with tPBAT protocol (Miura F et al., NAR, 2019)


title: NOMe-Seq analysis of IMR-90 cell line II

summary: NOMe-Seq analysis was performed with GC-recognizing cytosine DNA methyltransferase

overall_design: The IMR-90 nuclei were prepared with a solution containing 0.1% NP-40. Then, the nuclei were suspended in methylation buffer, and cytosine C-5 DNA methyltransferase recognizing GC dinucleotide was added. The solution was incubated at 37°C for 1 hr and collected nuclei. Then genomic DNA was extracted, and library preparation was performed with tPBAT protocol (Miura F et al., NAR, 2019)


title: TGFB in bone marrow dysfunction in diabetes

city: London

first: Jina

last: Kum

state: ON

address: 1151 Richmond Street

country: Canada

institute: Western University

summary:
We performed a microarray analysis to understand the mechanisms of TGFB1-mediated inhibition of adipogenesis on cultured human primary bone marrow-derived mesenchymal progenitor cells (bm-MPCs).
Our goal was to identify targetable pathways that mediate the effect of TGFB1.

overall_design: Human bone marrow-derived mesenchymal progenitor cells were cultured at a density  of 40,000 cells/cm^2. We cultured bm-MPCs in normal growth media (Control), adipogenic differentiation media (ADP), adipogenic differentiation media with TGFB1 (10 ng/mL), and adipogenic differentiation media with TGFB1 + TAK1 inhibitor (10 umol/L).  Total RNA was purified and transcriptome-wide analysis of gene expression was performed by Clariom S Assay.

middle: J

first: Christopher

last: Howlett

first: Zia

last: Khan


title: NOMe-Seq analysis of fixed budding yeast nuclei with two DNA methyltransferases

summary: NOMe-Seq analysis was performed with two cytosine C-5 DNA methyltransferases recognizing GC and CC dinucleotides


title: C. elegans L4 hypodermal RNA polymerase DamID

city: Seville

first: Peter

last: Askjaer

address: Universidad Pablo de Olavide, Carretera de Utrera, km 1

country: Spain

institute: Andalusian Centre for Developmental Biology

summary: To adapt RNA polymerase DamID (RAPID) for FLP-mediated spatial control in Caenorhabditis elegans, we inserted a Dam::rpb-6 fusion gene downstream of a FRT-flanked mCh::his-58 cassette and under control of the hsp-16.41 promoter. We introduced a single copy of this construct into the C. elegans genome and crossed the resulting line with a dpy-7p::FLP driver to enable basal Dam::rpb-6 expression in the hypodermis. Nematodes were cultured at 20 degrees Celcius to ensure low levels of Dam::RPB-6 expression in the hypodermis and total genomic DNA was purified from L4 larvae. DNA from animals expressing GFP::Dam was used to control for unspecific methylation. The genome-wide association profile of Dam::RPB-6 was determined by deep sequencing, which revealed a list of 2331 protein coding genes with FDR < 0.05. Original RAPID reference: Gomez-Saldivar et al (2020) Tissue-Specific Transcription Footprinting Using RNA PoI DamID (RAPID) in Caenorhabditis elegans. Genetics 216, 931–945. doi:10.1534/genetics.120.303774

overall_design: Two replicas of control strain BN561 (GFP::Dam in hypodermis) and two replicas of strain BN1414 (Dam::RPB-6 in hypodermis).

first: Adrián

last: Fragoso-Luna

first: Raquel

last: Romero-Bueno


title: NOMe-Seq analysis of IMR-90 cell line

summary: NOMe-Seq analysis was performed with CC-recognizing cytosine DNA methyltransferase

overall_design: The IMR-90 nuclei were prepared with a solution containing 0.1% NP-40. Then, the nuclei were suspended in methylation buffer, and cytosine C-5 DNA methyltransferase recognizing CC dinucleotide was added. The solution was incubated at 37°C for 1 hr and collected nuclei. Then genomic DNA was extracted, and library preparation was performed with tPBAT protocol (Miura F et al., NAR, 2019)


title: RNAseq analysis of A549 cells depleted of RPS19 using siRNAs

city: Canberra

first: Ross

last: Hannan

state: ACT

address: John Curtin School of Medical Research

department: John Curtin School of Medical Research

country: Australia

institute: Australian National University

summary: Gene expression profiling analysis of RNA-seq data for A549 cells transfected with non-targeting siRNA (siOTP) and KD derivatives (siRPS19) to ascertain relative gene expression (reads per kilobase per million, RPKM) for use to intersect with high-throughput RNA interference screening (siRNA) data to assess baseline expression of candidates being screened in these assays.

overall_design: A549 cells transfected with either non-targeting siRNA (siOTP, reference) or RPS19 (siRPS19) siRNAs for 72 hours were subjected to RNAseq analysis (50bp paired-end sequencing) as outlined in the treatment protocol. Samples were transfected and harvested as biological replicates (3 replicates per treatment).

first: Amee

last: George


title: Parkin Regulates Adiposity by Coordinating Mitophagy with Mitochondrial Biogenesis in White Adipocytes

status: Public on Sep 29 2022

city: Los Angeles

first: Zhengyi

last: Zhang

address: Westwood

institute: UCLA

summary: Parkin, an E3 ubiquitin ligase, plays an essential role in mitochondrial quality control. However, the mechanisms by which Parkin connects mitochondrial homeostasis to cellular metabolism in adipose tissue remain unclear. Here, we demonstrate that Park2 gene (encodes Parkin) deletion specifically from adipose tissue protects mice against high-fat diet and aging-induced obesity. Despite a mild reduction in mitophagy, mitochondrial DNA (mtDNA) content and mitochondrial function are significantly increased in Park2 deficient white adipocytes. Moreover, Park2 gene deletion robustly elevates mitochondrial biogenesis by increasing Pgc1α protein stability through mitochondrial superoxide-activated Nqo1. Both in vitro and in vivo studies show that Nqo1 overexpression elevates Pgc1α protein level and mtDNA content and enhances mitochondrial activity in mouse and human adipocytes. Taken together, our findings indicate that Parkin regulates mitochondrial homeostasis by balancing mitophagy and Pgc1α-mediated mitochondrial biogenesis in white adipocytes, suggesting a potential therapeutic target in adipocytes to combat obesity and obesity-associated disorders.

overall_design: We studied adipose-specific Parkin knock out mouse model and AAV drived adipose Nqo1 transgenic mouse model.

first: Timothy

middle: M

last: Moore

first: Lijing

last: Cheng

first: Dane

last: Wolf

first: Jennifer

last: Ngo

first: Mayuko

last: Segawa

first: Xiaopeng

last: Zhu

first: Alexander

middle: R

last: Strumwasser

first: Yang

last: Cao

first: Bethan

middle: L

last: Clifford

first: Alice

last: Ma

first: Philip

last: Scumpia

first: Orian

last: Shirihai

first: Thomas

middle: Q

last: de Aguiar Vallim

first: Markku

last: Laakso

first: Aldons

last: Lusis

first: Andrea

last: Hevener

first: Zhenqi

last: Zhou


title: Gene expression in manganese-pretreated DNA-stimulated human macrophages

status: Public on Sep 27 2022

city: Frederick

first: Jun

last: Yang

state: MD

address: P. O. Box B

institute: Leidos Biomedical

summary: A total of 1,302 genes with greater than two-fold increase or decrease and p value less than 0.05 were included in the analysis. 582 genes (cluster 1) were downregulated by Mn2+, and 587 genes (cluster 2) were upregulated by Mn2+. A total of 133 genes (cluster 3) were upregulated by DNA transfection alone. The Venn diagram showed that 351 genes are upregulated in DNA-mediated responses and 247 genes were upregulated by Mn2+ treatment. Of note, the expression of 104 genes were initiated by DNA stimulation alone and then enhanced by Mn2+ treatments. Using a functional enrichment analysis resource (Metascape ), the set of 247 genes (Mn2+-treatment-mediated upregulation) was significantly enriched for the genes involved in multiple biological processes, such as innate immune response and inflammatory cytokines, which include IL-10, IL-4, and IL-13 signaling and the Toll-like receptor signaling pathway. Meanwhile, we noticed that Mn2+ treatment significantly enhanced the responses of the host cells to external stimuli. Similarly, the set of 104 genes was significantly enriched for cytokine signaling in the immune system and for responses to tumor necrosis factor (TNF) or IFN-γ. More interestingly, we found that both functional enrichment analyses for the 247 and 104 genes shared a common category: 38 genes in the 247 genes and 20 genes of the 104 genes were involved in the positive regulation of protein phosphorylation.

overall_design: Macrophages were pretreated with MnCl2 at 25 µM, then transfected with DNA. The gene expression profiles in untreated, Mn2+-treated, DNA-transfected, and a combination of Mn2+- and DNA-treated cells were compared

first: Hongyan

last: Sui

first: Qian

last: Chen

first: Tomozumi

last: Imamichi


title: Changes in mRNA transcripts in retina of miR-29a knockout mice

status: Public on Oct 19 2022

city: Wenzhou

first: Dewei

last: Peng

address: No.270, Xueyuanxi Road

institute: Wenzhou Medical University

summary: The mature mammalian retina results from a complex series of developmental events. A lot of work now exists on the organization, function, and development of mouse retina, and the high-throughput technologies for gene expression analyses have helped us to obtain deep insight into the mechanism about the genes that control the retinal neurogenesis and vasculogenesis.

overall_design: mRNA profiles of retinas from miR-29a KO mice and wild type mice of eight-week-old were generated by deep sequencing.

first: Zai

last: Chi

first: De

middle: W

first: Chun

last: Lan


title: Sexually Dimorphic Estrogen Sensing in Skeletal Stem Cells Controls Skeletal Regeneration

city: PALO ALTO

first: yuting

last: wang

state: California

address: 265 campus drive, lokey stem cell research building, RM-G3105-SIM1

institute: Stanford University

summary: Sexually dimorphic tissues are formed by cells that are regulated by sex hormones. While a number of systemic hormones and transcription factors are known to regulate proliferation and differentiation of osteoblasts and osteoclasts, the mechanisms that determine sexually dimorphic differences in bone regeneration are unclear. To explore how sex hormones regulate bone regeneration, we compared bone fracture repair between adult male and female mice. We find that skeletal stem cell (SSC) mediated regeneration in female mice is dependent on estrogen signaling but SSCs from male mice do not exhibit similar estrogen responsiveness. Mechanistically, we found that estrogen acts directly on the SSC lineage in mice and humans by up-regulating multiple skeletogenic pathways and is necessary for the stem cell’s ability to self- renew and differentiate. Our results also suggest a clinically applicable strategy to accelerate bone healing using localized estrogen hormone therapy.

overall_design: fracture callus SSC and BCSP were FACs isolated from sham female /ovx female/ovx+e2 mice.

first: Tom

last: Andrew

first: Charles

last: Chan


title: Saturated Fat Impairs Circadian Transcriptomics through Histone Modification of Enhancers

city: Stockholm

first: Carolina

last: Nylén

address: Karolinska University Hospital

country: Sweden

institute: Karolinska Institutet

summary: Aims/hypothesis: Obesity and elevated circulating lipids may impair metabolism by disrupting the molecular circadian clock. We tested the hypothesis that lipid-overload may interact with the circadian clock and alter the rhythmicity of gene expression through epigenetic mechanisms.  Methods: We determined the effect of the saturated fatty acid palmitate on circadian transcriptomics and examined the impact on histone H3 lysine K27 acetylation (H3K27ac) and the regulation of circadian rhythms in primary human skeletal muscle myotubes. Total H3 abundance and histone H3K27ac was assessed in vastus lateralis muscle biopsies from men with either obesity or normal weight.  Results: Palmitate reprogrammed the circadian transcriptome in myotubes without altering the mRNA rhythm of core clock genes. Genes with enhanced cycling in response to palmitate were associated with post-translational modification of histones. Cycling of histone 3 lysine 27 acetylation (H3K27ac), a marker of active gene enhancers, was modified by palmitate treatment in myotubes. Chromatin immunoprecipitation and sequencing confirmed that palmitate altered the cycling of DNA regions associated with H3K27ac. Overlap of mRNA and DNA regions associated with H3K27ac and pharmacological inhibition of histone acetyl transferases revealed novel cycling genes associated to lipid exposure in human myotubes.  Conclusion/interpretation: Palmitate disrupts transcriptomic rhythmicity and modifies histone H3K27ac in circadian manner, suggesting acute lipid-overload alters the circadian chromatin landscape and reprograms circadian gene expression of skeletal muscle.

overall_design: Human primary skeletal myotubes were synchronized with serum shock and exposed to 0.4 mM of palmitate of BSA-conjugated palmitate. DNA was extracted 24h, 32h, 40h and 48h after the beginning of treatment and analyzed by ChIPseq for histone 3 lyzine 27 acetylation.

first: Laura

last: Puig

first: Ali

last: Altıntaş

first: Prasad

middle: G

last: Kamble

first: Salvador

last: Casaní-Galdón

first: Brendan

last: Gabriel

first: Romain

last: Barrès

first: Ana

last: Conesa

first: Alexander

middle: V

last: Chibalin

first: Erik

last: Näslund

first: Anna

last: Krook

first: Nicolas

last: Pillon

first: Juleen

last: Zierath


title: Sodium Butyrate(SB) mediates Histone Crotonylation and Alleviated Neonatal Rats Hypoxic -Ischemic Brain Injury Through Gut-Brain Axis

city: beijing

first: shan

address: 2yabao road

institute: Capital Institute of Pediatrics

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

overall_design: Refer to individual Series


title: Runx1 is a central regulator of osteogenesis for bone homeostasis by orchestrating BMP and WNT signaling pathways

status: Public on Sep 26 2022

city: New Orleans

first: Yi-Ping

last: Li

state: LA

address: 1441 Canal St, Room 318

department: Pathology and Laboratory Medicine

institute: Tulane University School of Medicine

summary:
Runx1 is highly expressed in osteoblasts, however, its function in osteogenesis is unclear. We generated mesenchymal progenitor-specific (Runx1f/fTwist2-Cre) and osteoblast-specific (Runx1f/fCol1α1-Cre) conditional knockout (Runx1 CKO) mice. The mutant CKO mice with normal skeletal development displayed a severe osteoporosis phenotype at postnatal and adult stages. Runx1 CKO resulted in decreased osteogenesis and increased adipogenesis. RNA-sequencing analysis, Western blot, and qPCR validation of Runx1 CKO samples showed that Runx1 regulates BMP signaling pathway and Wnt/β-catenin signaling pathway. ChIP assay revealed direct binding of Runx1 to the promoter regions of Bmp7, Alk3, and Atf4, and promoter mapping demonstrated that Runx1 upregulates their promoter activity through the binding regions. Bmp7 overexpression rescued Alk3, Runx2, and Atf4 expression in Runx1-deficient BMSCs. Runx2 expression was decreased while Runx1 was not changed in Alk3 deficient osteoblasts. Atf4 overexpression in Runx1-deficient BMSCs did not rescue expression of Runx1, Bmp7, and Alk3. Smad1/5/8 activity was vitally reduced in Runx1 CKO cells, indicating Runx1 positively regulates the Bmp7/Alk3/Smad1/5/8/Runx2/ATF4 signaling pathway. Notably, Runx1 overexpression in Runx2-/- osteoblasts rescued expression of Atf4, OCN, and ALP to compensate Runx2 function. Runx1 CKO mice at various osteoblast differentiation stages reduced Wnt signaling and caused high expression of C/ebpα and Pparγ and largely increased adipogenesis. Co-culture of Runx1-deficient and wild-type cells demonstrated that Runx1 regulates osteoblast−adipocyte lineage commitment both cell-autonomously and non-autonomously. Notably, Runx1 overexpression rescued bone loss in OVX-induced osteoporosis. This study focused on the role of Runx1 in different cell populations with regards to BMP and Wnt signaling pathways and in the interacting network underlying bone homeostasis as well as adipogenesis, and has provided new insight and advancement of knowledge in skeletal development. Collectively, Runx1 maintains adult bone homeostasis from bone loss though up-regulating Bmp7/Alk3/Smad1/5/8/Runx2/ATF4 and WNT/β-Catenin signaling pathways, and targeting Runx1 potentially leads to novel therapeutics for osteoporosis.
Using unbiased genome-wide RNA-seq data from Runx1f/fCol1α1-Cre, Runx1ffTwist2-cre, Runx1f/f;Col2α1-Cre and their control osteoblasts, we examined Runx1-mediated transcriptional targets that could account for osteoblast differentiation defects and increased adipocytes.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for mice WT, Runx1f/fCol1α1-Cre, and Runx1ffTwist2-cre osteoblasts; and Runx1f/f;Col2α1-Cre and WT cartilage

first: Wei

last: Chen

first: Diep

last: Edwards


title: Sodium Butyrate mediates Histone Crotonylation and Alleviated Neonatal Rats Hypoxic -Ischemic Brain Injury Through Gut-Brain Axis [RNA-seq]

last: wang

summary: CurrentNeonatal hypoxic-ischemic encephalopathy (HIE) refers to nervous system damage caused by perinatal hypoxia, which is the major cause of long-term neuro-developmental disorders in surviving infants. However, the mechanisms still require further investigation. In this study, we found that the butanoate metabolism pathway exhibited significantly decreased and short chain fatty acid (SCFAs)-producing bacteria, especially butyrate-producing bacteria, were significantly decreased in fecal of neonatal hypoxic-ischemic brain damage (HIBD) rats. Surprisingly, Sodium butyrate (SB) treatment could ameliorate pathological damage both in the cerebral cortex and hippocampus and facilitate recovery of SCFAs-producing bacteria related to metabolic pathways in neonatal HIBD rats. Moreover, we found that in samples from SB treatment neonatal HIBD rats cortex with high levels of butyrate acid along with aberrant key crotonyl-CoA-producing enzymes ACADS levels was observed compared HIBD rats. We also demonstrated that a decrease in histone 3-lysine 9-crotonylation (H3K9cr) downregulated expression of the HIE-related neurotrophic genes Bdnf, Gdnf, Cdnf, and Manf in HIBD rats. Furthermore, SB restored H3K9cr binding to HIE-related neurotrophic genes. Collectively, our results indicate that SB contributes to ameliorate pathological of HIBD by altering gut microbiota and brain SCFAs levels subsequently affecting histone crotonylation-mediated neurotrophic-related genes expression. This may be a novel microbiological approach for preventing and treating HIE.

overall_design: RNA-seq

first: Shan

last: Wang

first: Xuejia

last: He

first: Ing

last: Zhang


title: Transcriptome sequencing of transgenic Nicotiana benthamiana producing moth pheromones [2]

city: Ljubljana

first: Mojca

last: Juteršek

address: Večna pot 111

department: Department of Biotechnology and Systems Biology

country: Slovenia

institute: National Institute of Biology

summary: Insect sex pheromones are an important resource in integrated pest management. Encouraging steps have been made towards their sustainable production in plant biofactories, but important obstacles remain to be resolved. We have used transcriptomic analysis to determine the molecular perturbations behing growth penalty associated with high pheromone production in transgenic Nicotiana benthamiana lines with constitutive expression of genes for biosynthesis of moth sex pheromones - SexyPlants v1.2. We analyzed two lines with high production of pheromones as well as wt N. benthamiana.

overall_design: Transgenic Nicotiana benthamiana lines with constitutive expression of moth pheromone biosynthesis genes as well as wt plants were grown in controlled conditions and sampled at the same growth stage, determined by the number of fully developed leaves (35 days in soil). We sampled 2nd and 3rd fully developed leaf from each plant. Four biological replicates (plants) per plant line were sampled. We inclued two different lines with high production phenotype and wt plants.

first: Juteršek

last: Mojca

first: Petek

last: Marko

first: Mateos-Fernández

last: Rubén

first: Gianoglio

last: Silvia


title: HIF1α-AS1 is a DNA:DNA:RNA triplex-forming lncRNA interacting with the HUSH complex

status: Public on Sep 23 2022

city: Frankfurt am Main

first: Timothy

last: Warwick

state: Hesse

address: Theodor-Stern-Kai 7

department: Institute for Cardiovascular Physiology

country: Germany

institute: Goethe Universität Frankfurt am Main

summary: To investigate the effect of HIF1a-AS1 on chromatin accessibility, a number of ATAC-sequencing experiments were performed after perturbation of the lncRNA.

overall_design: ATAC-sequencing following CRISPRi, CRISPRa or LentiCRISPR of HIF1a-AS1.

first: Matthias

last: Leisegang

first: Jasleen

last: Kaur Bains

first: Sandra

last: Seredinski

first: James

last: Oo

first: Nina

last: Krause

first: Chao-Chung

last: Kuo

first: Stefan

last: Günther

first: Nevcin

last: Sentürk Cetin

first: Can

last: Cao

first: Frederike

last: Boos

first: Judit

last: Izquierdo Ponce

first: Rebecca

last: Bednarz

first: Chanil

last: Valasarajan

first: Dominik

last: Fuhrmann

first: Jens

last: Preussner

first: Mario

last: Looso

first: Soni

last: Pulamsetti

first: Marcel

middle: H

last: Schulz

first: Flavia

last: Rezende

first: Ralf

last: Gilsbach

first: Beatrice

last: Pflüger-Müller

first: Ilka

last: Wittig

first: Ingrid

last: Grummt

first: Teodora

last: Ribarska

first: Ivan

last: Costa

first: Harald

last: Schwalbe

middle: P

last: Brandes


title: Sodium Butyrate(SB) mediates Histone Crotonylation and Alleviated Neonatal Rats Hypoxic -Ischemic Brain Injury Through Gut-Brain Axis [ChIP-seq]

first: shan

last: wang

summary: Neonatal hypoxic-ischemic encephalopathy (HIE) refers to nervous system damage caused by perinatal hypoxia, which is the major cause of long-term neuro-developmental disorders in surviving infants. However, the mechanisms still require further investigation. In this study, we found that the butanoate metabolism pathway exhibited significantly decreased and short chain fatty acid (SCFAs)-producing bacteria, especially butyrate-producing bacteria, were significantly decreased in fecal of neonatal hypoxic-ischemic brain damage (HIBD) rats. Surprisingly, Sodium butyrate (SB) treatment could ameliorate pathological damage both in the cerebral cortex and hippocampus and facilitate recovery of SCFAs-producing bacteria related to metabolic pathways in neonatal HIBD rats. Moreover, we found that in samples from SB treatment neonatal HIBD rats cortex with high levels of butyrate acid along with aberrant key crotonyl-CoA-producing enzymes ACADS levels was observed compared HIBD rats. We also demonstrated that a decrease in histone 3-lysine 9-crotonylation (H3K9cr) downregulated expression of the HIE-related neurotrophic genes Bdnf, Gdnf, Cdnf, and Manf in HIBD rats. Furthermore, SB restored H3K9cr binding to HIE-related neurotrophic genes. Collectively, our results indicate that SB contributes to ameliorate pathological of HIBD by altering gut microbiota and brain SCFAs levels subsequently affecting histone crotonylation-mediated neurotrophic-related genes expression. This may be a novel microbiological approach for preventing and treating HIE.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for histone modifications H3K9cr in rat brain tissue.

first: Shan

last: Wang

first: Meirong

last: Bi

first: Xuejia

last: He


title: Loss of Mst1/2 activity promotes non-mitotic hair cell generation in the neonatal organ of Corti

status: Public on Sep 25 2022

city: Shanghai

first: Luo

last: Guo

address: 83# fenyang road, 9# building, room 613

institute: Fudan University

summary: We used in vitro RNA-sequencing to show that the Hippo signaling pathway is involved in HC damage and self-repair processes. Turning off Hippo signaling through Mst1/2 inhibition or Yap overexpression induces YAP nuclear accumulation, especially in supporting cells, which induces supernumerary HC production and HC regeneration after injury. Mechanistically, these effects of Hippo signaling work synergistically with the Notch pathway.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for C3H10T1/2 cells and its KD derivatives (shKDM4D, shNFIB, and shMLL1).

first: Xiaoling

last: Lu

last: Sun


title: Single cell transcriptomic of murine pancreatic tumor model by treatment of PD-L1-directed PlGF/VEGF blockade

first: Duk Ki

last: Kim

address: Daehakro 103

institute: Seoul National University of Hospital

summary: We developed a multi-paratopic VEGF decoy receptor (Ate-Grab) by fusing the scFv of atezolizumab to VEGF-Grab to target PD-L1 expressing cells in tumor microenvironment. We compared the single-cell transcriptomes of gemcitabine-treated and Ate-Grab with Gemcitabine-treated Pan02 tumors. We confirmed the subtype of cancer-associated fibroblasts(CAFs) that modulates the collagen inside the tumor microenvrionment. In the Ate-Grab+Gemcitabine group, it was confirmed that new CAFs were regulated.

overall_design: Orthotopic murine pancreatic cancer models using Pan02 cells were generated. They were treated by Gemcitabine alone or Ate-Grab with Gemcitabine for 5 times every 3 days. Five gemcitabine-treated tumors and four tumors treated with Ate-Grab + gemcitabine were pooled and subjected to single-cell RNA sequencing (scRNA-seq) analysis

first: Duk

middle: K

first: Juhee

last: Jeong

first: Dong

last: Lee

first: Do

middle: Y

last: Hyeon

first: Suwan

last: Jeon

first: Daehee

last: Hwang

first: Ho

first: Keehoon

last: Jung


title: Visium spatial transcriptomics analysis of lacrimal gland during chronic inflammation progression.

city: La Jolla

first: Helen

last: Makarenkova

state: CA

address: 10550 N Torrey Pines Rd, MB-218

department: Molecular Medicine

institute: The Scripps Research Institute

summary: To identify the transcriptomic alterations within the different cellular compartments of the lacrimal gland during chronic inflammation, we analyzed the lacrimal glands of NOD.B10.H2b vs BALB/cJ with 10X Visium technology

overall_design: We sequenced RNA from lacrimal glands cryosections (10μm) of BALB/cJ (control) and NOD.H2b (disease) mice aged of 4 months in duplicates.

first: Olivier

last: Mauduit

first: Vanessa

last: Delcroix

first: Takeshi

last: Umazume

first: Cintia

last: de Paiva

first: Darlene

last: Dartt


title: Inactivation of LATS1/2 drives luminal-basal plasticity to initiate basal-like mammary carcinomas

city: BOSTON

first: Boting

last: Ning

state: Massachusetts

address: 72 E Concord St

institute: BOSTON UNIVERSITY

summary: Basal breast cancers, an aggressive breast cancer subtype that has poor treatment options, are thought to arise from luminal mammary epithelial cells that undergo basal-like plasticity through poorly understood mechanisms. Using genetic mouse models and ex vivo primary organoid cultures, we show that conditional co-deletion of the LATS1 and LATS2 kinases, key effectors of Hippo pathway signaling, in mature mammary luminal epithelial cells promotes the development of basal-like carcinomas that metastasize over time. Genetic co-deletion experiments revealed that phenotypes resulting from the loss of LATS1/2 activity are dependent on the transcriptional regulators YAP/TAZ. Notably, transcriptional analyses of LATS1/2-deleted mammary epithelial cells revealed a gene expression program that associates with human basal breast cancers. Our study demonstrates in vivo roles for the LATS1/2 kinases in mammary epithelial homeostasis and luminal-basal fate control and implicates signaling networks induced upon the loss of LATS1/2 activity in the development of basal breast cancers.

overall_design: Lineage-traced mammary cells from control (lsl-EYFP; K8CreERT2), LATS1/2-KO (LATS1/2f/f; lsl-EYFP; K8CreERT2), and LATS1/2-Sox9-KO (LATS1/2f/f; Sox9f/f; lsl-EYFP; K8CreERT2) mice were isolated and transcriptionally profiled. Each condition had three replicates.

first: Joseph

last: Kern

first: Xaralabos

last: Varelas


title: Expression data from human induced Pluripotent Stem Cel (iPSC) and Embryoid Body (EB)

status: Public on Sep 24 2022

city: Kashihara

first: Tsutomu

last: Nakazawa

state: Nara

address: 840, Shijo-cho

institute: Nara medical university

summary: We analyzed the comprehensive gene expression of human iPSC and EB. EB was induced for 7days.

overall_design: 2 samples


title: Transcriptome sequencing of transgenic Nicotiana benthamiana producing moth pheromones [1]

first: Mojca

last: Juteršek

summary: Insect sex pheromones are an important resource in integrated pest management. Encouraging steps have been made towards their sustainable production in plant biofactories, but important obstacles remain to be resolved. We have used transcriptomic analysis to determine the molecular perturbations behing growth penalty associated with high pheromone production in transgenic Nicotiana benthamiana lines with constitutive expression of genes for biosynthesis of moth sex pheromones - SexyPlants v1.0. We analyzed lines with high production (homozygous lines) and strong growth penalty as well as lines with low production (heterozygous lines) and negligible growth penalty.

overall_design: Transgenic Nicotiana benthamiana lines with constitutive expression of moth pheromone biosynthesis genes as well as wt plants were grown in controlled conditions and sampled at the same growth stage, determined by the number of fully developed leaves (35 days in soil for wt and low producer plants and 54 days in soil for high producer plants). We sampled 2nd and 3rd fully developed leaf from each plant. Four biological replicates (plants) per plant line were sampled. We inclued two different lines with high production phenotype, two lines with  low production phenotype and wt plants.

first: Juteršek

last: Mojca

first: Petek

last: Marko

first: Moreno

last: Elena

first: Vázquez-Vilar

last: Marta

first: Fernandez-Del-Carmen

last: Asun


title: Mechanosensing brain tumor cells construct blood-tumor barrier to mask chemosensitivity

status: Public on Sep 22 2022

city: Changsha

first: Siyi

last: Wanggou

state: Hunan

address: Xiangya Road, No.87

department: Departmeng of Neurosurgery

institute: Xiangya Hospital, Central South University

summary: This dataset includes the raw single-cell RNAseq data from Math1-Cre;SmoM2 and Math1-Cre;SmoM2;Piezo2 fl/fl mouse medulloblastoma model. In this project, we focused on transcriptomic alteration caused by Piezo2 knockout in Sox2 positive MB initiation cells.

overall_design: Single-Cell RNAseq from Piezo2 wildtype vs Piezo2 knockout in mouse SHH medulloblastoma model

first: Xi

last: Huang


title: Hepatic thyroid hormone signalling modulates glucose homeostasis through the regulation of GLP-1 production via bile acid-mediated FXR antagonism

first: ying

last: yan

address: 320 Yueyang Road, Shanghai

institute: Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences

summary: A greater understanding of the glucose homeostasis mediated by glucagon-like peptide-1 (GLP-1) will facilitate the development of novel glucose-lowering treatments. Here we show that improved glucose metabolism in hypothyroid mice after treatment of T3, the active form of thyroid hormone (TH), is accompanied with increased GLP-1 production and insulin secretion. Treatment of a GLP-1 receptor antagonist is able to attenuate the observed T3 effect on insulin and glucose levels, suggesting that GLP-1 is critically involved in the regulation of glucose homeostasis by T3. By using a mouse model lacking hepatic TH receptor β (TRβ) and a liver-specific TRβ-selective agonist, we demonstrate that TRβ-mediated hepatic TH signalling is not only required for the regulation of GLP-1 production by T3 but also the insulinotropic and glucose-lowering effects of T3. Accordingly, administration of the liver-targeted TRβ-selective agonist is capable of increasing GLP-1 and insulin levels and alleviating hyperglycemia in diet-induced obesity. Mechanistically, through suppressing CYP8B1 expression, T3 shapes the bile acid (BA) composition and increases the levels of Farnesoid X receptor (FXR)-antagonistic BAs, thereby potentiating the GLP-1 production and insulin secretion by repressing intestinal FXR signalling. Consistently, correlations between the T3 levels and either GLP-1 or FXR-antagonistic BA levels can be observed in euthyroid human subjects. Thus, our study reveals a previously undescribed role of hepatic TH signalling in glucose homeostasis through the regulation of GLP-1 production via BA-mediated FXR antagonism, which will underpin the development of novel therapeutics.

overall_design: There are two groups, fasting and feeding, one sample per group, and each sample is the pool of livers of three mice treated the same.

first: Wei

last: Liu

first: Ying

last: Yan

first: Zhoumin

last: Niu

first: Chao

last: Sun

first: Peng

last: Li

last: Shen

first: Shengnan

first: Yuying

first: Zhong-Ze

last: Fang

first: Lin

last: Zhao

first: Changtao

last: Jiang

first: Jingjing

first: Hao

last: Ying


title: V-ATPase/TORC1-mediated ATFS-1 translation directs mitochondrial UPR activation in C. elegans

city: Lausanne

first: Terytty Yang

address: EPFL SV IBI-SV LISP AI 1145

country: Switzerland

institute: EPFL

summary: To adapt mitochondrial function to the ever-changing intra- and extra-cellular environment, multiple mitochondrial stress response (MSR) pathways, including the mitochondrial unfolded protein response (UPRmt), have evolved. However, how the mitochondrial stress signal is sensed and relayed to UPRmt transcription factors, such as ATFS-1 in Caenorhabditis elegans, remains largely unknown. Here, we show that a panel of vacuolar H+-ATPase (v-ATPase) subunits and the target of rapamycin complex 1 (TORC1) activity are essential for the cytosolic relay of mitochondrial stress to ATFS-1, and for the induction of the UPRmt. Mechanistically, mitochondrial stress stimulates v-ATPase/Rheb-dependent TORC1 activation, subsequently promoting ATFS-1 translation. Increased translation of ATFS-1 upon mitochondrial stress furthermore relies on a set of ribosomal components, but is independent of GCN-2/PEK-1 signaling.  Finally, the v-ATPase and ribosomal subunits are required for mitochondrial surveillance and mitochondrial stress-induced longevity. These results reveal a v-ATPase-TORC1-ATFS-1 signaling pathway that links mitochondrial stress to the UPRmt through intimate crosstalks between multiple organelles.

overall_design: N2 worms carrying a hsp-6::GFP reporter fed with control, vha-1, vha-4, vha-16, vha-19, atfs-1 and cco-1 RNAi

first: Terytty

first: Arwen

last: Gao

first: Xiaoxu

first: Amelia

last: Lalou

first: Adrienne

last: Mottis

first: Minho

last: Shong

first: Kristina

last: Schoonjans

first: Johan

last: Auwerx


title: Hepatic thyroid hormone signalling modulates glucose homeostasis through the regulation of GLP-1 production via bile acid-mediated FXR antagonism [RNA-seq]

first: ying

last: yan

overall_design: There are three groups, MMI, MMI+T3, and CT, three sample per group

first: Ying

first: Zhoumin

first: Chao

first: Peng

first: Siyi


title: DNA methyltransferase 3A controls intestinal epithelial barrier function and regeneration in the colon

status: Public on Sep 21 2022

city: Kiel

first: Neha

last: Mishra

address: Rosalind-Franklin-Str. 12

institute: Institute of Clinical Molecular Biology

type: Methylation profiling by genome tiling array


title: The 3D enhancer network of the developing T cell genome is controlled by SATB1 [ATAC-seq]

city: Tampa

first: Tomas

last: Zelenka

state: Florida

address: 12902 Magnolia Drive

department: Immunology

institute: H. Lee Moffitt Cancer Center & Research Institute

summary: Mechanisms of tissue-specific gene expression regulation, particularly via spatial coordination of gene promoters and their regulatory elements are poorly understood. Here we investigated the 3D genome organization of developing murine T cells. We identified a tissue-specific genome organizer SATB1 as a factor enriched at the anchors of promoter-enhancer chromatin loops. To unravel its functions in T cells, we generated Satb1fl/flCd4-Cre+ (Satb1 cKO) conditional knockout animals. Satb1 cKO animals suffer from severe autoimmunity so we sought to investigate a potential link between the autoimmunity and putatively deregulated nuclear architecture caused by SATB1 depletion.  This series of ATAC-Seq experiments is a part of SuperSeries including also RNA-Seq, Hi-C and HiChIP experiments to fully understand the deregulation of Satb1 cKO thymocytes and to unravel the roles of SATB1 in T cell chromatin organization. ATAC-Seq experiments supported the repressive nature of Satb1 cKO nuclear environment and together with the other datasets it showed that SATB1 functions primarily as an activator. SATB1 mediates promoter-enhancer chromatin loops affecting a number of master regulator genes whose deregulation in knockout animals may comprise a cell-intrinsic mechanism of the autoimmunity. Our findings indicate a possible existence of a special class of genome organizers controlling tissue and/or time-specific transcriptional programs via spatial chromatin arrangements that are complementary to the function of conventional and ubiquitously expressed genome organizers.

overall_design: Three biological replicates from each wild type and conditional knockout Satb1fl/flCd4-Cre+ mice were analyzed. ATAC-Seq libraries were prepared from viable thymocytes using the Omni-ATAC protocol.

first: Antonios

last: Klonizakis

first: Charalampos

last: Spilianakis


title: DNA methyltransferase 3A controls intestinal epithelial barrier function and regeneration in the colon [RNA-seq]

summary: Genetic variants in the DNMT3A locus have been associated with inflammatory bowel disease (IBD). DNMT3A is part of the epigenetic machinery physiologically involved in DNA methylation. We show that DNMT3A plays a critical role in maintaining intestinal homeostasis and gut barrier function. DNMT3A expression is downregulated in intestinal epithelial cells (IECs) from IBD patients and upon TNF treatment in murine intestinal organoids. Ablation of DNMT3A in Caco-2 cells results in global DNA hypomethylation, which is linked to impaired regenerative capacity, transepithelial resistance and intercellular junction formation. Genetic deletion of Dnmt3a in IECs (Dnmt3aΔIEC) in mice confirms the phenotype of an altered epithelial ultrastructure with shortened apical-junctional complexes, reduced Goblet cell numbers and increased intestinal permeability in the colon in vivo. Dnmt3aΔIEC mice suffer from increased susceptibility to experimental colitis, characterized by reduced epithelial regeneration. These data demonstrate a critical role for DNMT3A in orchestrating intestinal epithelial homeostasis and response to tissue damage and suggest an involvement of impaired epithelial DNMT3A function in the etiology of IBD.

overall_design: For the in vitro experiment with Caco-2 cells, 4 groups have been analyzed with 4 replicates each. For in vivo experiment using purified intestinal epithelial cells from Dnmt3a △IEC in steady state, 4 wild type mice and 4 Dnmt3a △IEC mice were used.

first: Antonella

last: Fazio

first: Dora

last: Bordoni

first: Philip

last: Rosenstiel


title: Rescue of Down syndrome related deficits by Brwd1 copy number restoration

city: New York

first: Aarthi

last: Ramakrishnan

state: New York

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

summary: Trisomy 21 [Down syndrome/DS] is the most common genetic cause of intellectual disability worldwide. Despite much progress in the genetic characterization of DS, the genes encoded from chromosome 21 (HSA21) that directly contribute to intellectual disability remain incompletely understood. Here, we found that a largely uncharacterized chromatin effector protein, BRWD1, is triplicated in DS neurons and brain of trisomic mice. We demonstrated that selective copy number restoration of Brwd1 in DS animals rescues transcriptional, synaptic and cognitive deficits. We showed that Brwd1 binds to the neuronal BAF chromatin remodeling complex, and that such interactions promote BAF’s genomic mistargeting in DS-like brain. Brwd1 renormalization in trisomic animals rescues these aberrant chromatin events. These findings thus establish BRWD1 as a critical epigenomic mediator of DS related phenotypes.

overall_design: RNA-seq performed in E16 forebrain-derived primary neuronal cultures mouse brain, and embryonic forebrain (mixed male female) and adult hippocampus (male and female), and ChIP-seq for Smarca2/4 and neuronal ATAC-seq were performed in adult male hippocampus to examine the impact of Brwd1 copy number restoration in DS-like (Ts65Dn) mice on transcriptional patterning, BAF complex recruitment and chromatin accessibility. Three genotypes were compared: euploid vs. Ts65Dn vs. Ts65Dn; Brwd1+/-.

first: Ashley

last: Lepack

first: Wendy

last: Wenderski

first: Sasha

last: Fulton

first: Andrew

last: Eagle

first: Li

last: Shen

first: Robert

middle: D

last: Blitzer

first: Alfred

last: Robison

first: Gerald

last: Crabtree

first: Ian

last: Maze


title: Human primed and naïve PSCs are equally potent in differentiating into bona fide trophoblast stem cells (ATAC-Seq)

city: Rehovot

first: Noa

last: Novershtern

address: Weizmann Institute

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

summary: Cells of the trophoblast lineage constitute the major part of placental tissues in higher mammals. Recent derivation of human trophoblast stem cells (TSC) from placental cytotrophoblasts (CT) and from blastocyst opens new opportunities for studying development and function of human placenta. Here we report that inhibition of TGF pathway leads to direct and robust conversion of primed human pluripotent stem cells into TSC. The resulting cell lines exhibit self-renewal, are able to differentiate into the main trophoblast lineages, and present RNA and epigenetic profiles that are indistinguishable from the TSC lines derived from placenta or blastocyst. Furthermore, activation of YAP pathway is necessary and sufficient for this conversion.

overall_design: ATAC-Seq

first: Sergey

last: Viukov

first: Tom

last: Shani

first: Jacob

last: Hanna


title: Saturated Fat Impairs Circadian Transcriptomics through Histone Modification of Enhancers

city: Copenhagen

first: Ali

last: Altintas

address: Blegdamsvej 3B

department: NNF Center for Basic Metabolic Research

country: Denmark

institute: Copenhagen University

summary: Aims/hypothesis: Obesity and elevated circulating lipids may impair metabolism by disrupting the molecular circadian clock. We tested the hypothesis that lipid-overload may interact with the circadian clock and alter the rhythmicity of gene expression through epigenetic mechanisms.  Methods: We determined the effect of the saturated fatty acid palmitate on circadian transcriptomics and examined the impact on histone H3 lysine K27 acetylation (H3K27ac) and the regulation of circadian rhythms in primary human skeletal muscle myotubes. Total H3 abundance and histone H3K27ac was assessed in vastus lateralis muscle biopsies from men with either obesity or normal weight.  Results: Palmitate reprogrammed the circadian transcriptome in myotubes without altering the mRNA rhythm of core clock genes. Genes with enhanced cycling in response to palmitate were associated with post-translational modification of histones. Cycling of histone 3 lysine 27 acetylation (H3K27ac), a marker of active gene enhancers, was modified by palmitate treatment in myotubes. Chromatin immunoprecipitation and sequencing confirmed that palmitate altered the cycling of DNA regions associated with H3K27ac. Overlap of mRNA and DNA regions associated with H3K27ac and pharmacological inhibition of histone acetyl transferases revealed novel cycling genes associated to lipid exposure in human myotubes.  Conclusion/interpretation: Palmitate disrupts transcriptomic rhythmicity and modifies histone H3K27ac in circadian manner, suggesting acute lipid-overload alters the circadian chromatin landscape and reprograms circadian gene expression of skeletal muscle.

overall_design: Skeletal muscle biopsies were obtained from healthy men. Primary myotubes cultures were prepared, synchronized, exposed to palmitate and harvested every 6 hours over 42 hours and the transcriptome was analyzed by RNA-sequencing. Control samples in this study were previously uploaded in GSE182117.

first: Nicolas

last: Pillon

first: Laura

last: Puig

last: Altıntaş

first: Prasad

last: Kamble

first: Salvador

last: Casaní-Galdón

first: Brendan

last: Gabriel

first: Romain

last: Barrès

first: Ana

last: Conesa

first: Alexander

last: Chibalin

first: Erik

last: Näslund

first: Anna

last: Krook

first: Juleen

last: Zierath


title: Rescue of Down syndrome related deficits by Brwd1 copy number restoration in Ts65Dn mice

first: Sasha

middle: Leilani

last: Fulton

state: NY

address: 3227 Broadway

institute: Columbia University

summary: With an astounding incidence of ~1 in 800 births, Down syndrome (DS) is the most common chromosomal condition linked to intellectual disability worldwide. While the genetic basis of DS has been identified as a triplication of chromosome 21 (HSA21), the genes encoded from HSA21 that directly contribute to cognitive deficits remain incompletely understood. Here, we found that the HSA21-encoded chromatin effector, BRWD1, was upregulated in Down syndrome neurons and brain of trisomic mice. We showed that selective copy number restoration of Brwd1 in trisomic animals rescued deficits in hippocampal LTP, cognition and gene expression. We demonstrated that Brwd1 tightly binds the BAF chromatin remodeling complex, and that increased Brwd1 expression promotes BAF genomic mistargeting. Importantly, Brwd1 renormalization rescued aberrant BAF localization, along with associated changes in chromatin accessibility and gene expression. These findings establish BRWD1 as a key epigenomic mediator of normal neurodevelopment and an important contributor to DS-related phenotypes.

overall_design: In order to confirm relevance of Ts65Dn to human DS etiology, we first performed bulk RNA-seq profiling on E17.5 Ts65Dn vs. euploid forebrain tissues. Furthermore, in order to further evaluate the effects of Brwd1 rescue within the context of adult brain, we performed bulk RNA-seq on hippocampal tissues from 6-week-old male and female animals, comparing Ts65Dn vs. euploid and Ts65Dn;Brwd1+/– genotypes .

first: Ian

last: Maze


title: Post-ICB treatment PDAC infiltrating T cells gene expression

city: Atlanta

first: Edmund K.

last: Waller

state: Georgia

address: 1365 Clifton Rd Building C

department: Hematology and Medical Oncology

institute: Emory University School of Medicine

summary: For the subcutaneous model, 5x105 KPC-Luc cells were injected subcutaneously near the right flank of female C57BL/6 mice. For the MT5 or Panc02 models, 5x105 were injected subcutaneously near the right flank of female C57BL/6 mice. For the orthotopic KPC-Luc model, mice were anesthetized, and the KPC-Luc cells were suspended in Matrigel and injected in the tail of the pancreas following laparotomy. 6-7 days after tumor implantation mice were randomized into 4 treatment groups and treatedwith VIP-R antagonist and/or anti-PD-1. While scram+IgG control mice received scrambled peptide and isotype IgG, the VIP-R antagonist, anti-PD-1 and VIP-R antagonist and anti-PD-1 groups received VIP-R antagonist and IgG; scrambled peptide and anti-PD-1; and VIP-R antagonist and anti-PD-1, respectively. The treatment regimen involved administering 10μg of scrambled or VIP-R antagonist: ANT008 or ANT308, subcutaneously every day and 200μg of IgG or anti-PD-1 intraperitoneally once every three days, for a total of 10 days.

overall_design: 4 groups: control, aPD-1, Ant008, aPD-1+Ant008. 3 samples per each group. 12 samples are analyzed.

first: Sruthi

last: Ravindranathan

first: Tenzin

last: Passang

first: Hanwen

last: Zhang

first: Edmund


title: Real-time quantitative PCR analysis of rainbow trout immune related gene expressed during exposure to Diplostomum pseudospathaceum

city: Frederiksberg

first: Per

middle: Walter

last: Kania

address: Stigbojlen 7

department: Department of Veterinary and Animal Sciences

institute: University of Copenhagen

summary:
Marker-assisted selective breeding of fish with higher levels of resistance towards specific pathogens has shown successful, but. However, the impact of host genotype on multiple pathogen infections are is still poorly investigated. This study examined the resistance in rainbow trout (Oncorhynchus mykis) towards infection with the eye fluke Diplostomum pseudospathaceum. We used genetically selected rainbow trout, carrying SNPs associated with resistance towards the parasitic ciliate Ichthyophthirius multifiliis, and exposed the fish to eye fluke cercariae. We showed that fish partly resistant to I. multifiliis were more susceptible to eye fluke invasion. Expression The expression of immune relevant genes (encoding innate and adaptive factors) was also affected as these genotypes responded less strongly to a secondary fluke infection. The complexity of genome architecture in disease resistance towards multiple pathogens is discussed.
A total of 200 rainbow trout (body weight 14.3-17.7 g, body length 10.2-11.5 cm) were used for the study. Two groups of rainbow trout with high (QTL fish) and low (non-QTL fish) frequency of SNPs associated with I. multifiliis resistance, were hatched from eyed eggs at the disease free recirculated Bornholm Salmon Hatchery, Nexø, Denmark  and subsequently reared to the fingerling stage. For this purpose, the first group (QTL-fish) was produced by using sperm from three male genotyped parents carrying SNPs AX-89947214 (Omy17) and AX-89960822 (Omy16), and the other group (non-QTL fish) was produced by using sperm from three other male parents negative for these SNPs. In both cases, sperm was used to fertilize a common pool of eggs stripped from a total of 30 outbred females. Processes of hatching and subsequent rearing of fry to the fingerling stage did not differ between groups of QTL fish and non-QTL fish.   From each group (QTL and non-QTL fish) we randomly gathered 100 rainbow trout and transported them (3 h duration) from the hatchery to the infection facility at the University of Copenhagen. Fish  were then accommodated and acclimatized 14 d in identical aerated glass tanks with internal biofilters (25 fish per 60 L water, total tank volume 80 L), which were placed in a temperature temperature-controlled room (water temperature constant at 12°C, pH 7.6). We used 30% water change per day to maintain ammonia levels below 0.25. Fish were fed by pelleted feed (1% of fish biomass per day).  All fish were genotyped with respect to the two relevant QTLs, one on chomosome 16 and one on chromosome 17.  Fish being double heterozugous were excluded from qPCR analysis.

overall_design: Exposure of fish to cercariae was conducted in duplicate for each group (QTL fish and non-QTL fish).   Group 1. A total of 100 fish (50 QTL and 50 non-QTL fish) was exposed to 240 cercariae/fish during a 48 h period starting from day 0.   Group 2. Fish (10 QTL and 10 non-QTL) were kept un-infected until exposure on day 10, at which time the previously exposed fish (Group 1) also were exposed (re-exposure, see below). This group was considered as a control for second exposure in Group 1.   Group 3. A total of 80 fish (40 QTL-fish and 40 non-QTL fish) were kept as uninfected time-point control (not exposed) throughout the experiment.  Re-exposure (lasting 72 h) to cercariae (480 cercariae/fish) was initiated on day 10 on Group 1 and Group 2.   Samples comprised 2x5 fish per group per time-point, comprising eyes for enumeration of metacercariae, gill and spleen for gene expression and fins for genotyping.   Time-points were 5h post exposure (5hpe), 4, 7, 20 days post exposure (dpe) (Group 1 and 3) and 20 dpe for Group 2.   An additional sampling was done for group 1 at 27 dpe (for enumeration of metacercaria only). Thus, these samples were not subjected to Real-time quantitative PCR analysis.

first: Asma

last: Karami

first: Kurt

last: Buchmann


title: HMG20B stabilizes interaction of LSD1 with GFI1 on chromatin to confer transcription repression and leukemia cell differentiation block [ChIP-seq I]

status: Public on Oct 06 2022

city: Manchester

first: Tim

last: Somervaille

address: Wilmslow Rd

department: Manchester Institute

institute: Cancer Research UK

summary: Pharmacologic inhibition of LSD1 induces molecular and morphologic differentiation of blast cells in acute myeloid leukaemia (AML) patients harboring MLL gene translocations. In addition to its demethylase activity, LSD1 has a critical scaffolding function at genomic sites occupied by the SNAG domain transcription repressor GFI1. Importantly, inhibitors block both enzymatic and scaffolding activities, in the latter case by disrupting the protein:protein interaction of GFI1 with LSD1. To explore the wider consequences of LSD1 inhibition on the LSD1 protein complex we made use of mass spectrometry approaches. We discovered that the interaction of the HMG-box protein HMG20B with LSD1 was also disrupted by LSD1 inhibition. Downstream investigations revealed that HMG20B is colocated on chromatin genome-wide with GFI1 and LSD1; the strongest HMG20B binding colocates with the strongest GFI1 and LSD1 binding. Functional assays demonstrated that HMG20B depletion induces leukaemia cell differentiation and further revealed that HMG20B is required for the transcription repressor activity of GFI1 through stabilizing the interaction on chromatin of LSD1 with GFI1. Interaction of HMG20B with LSD1 is through its coiled-coil domain. Thus, HMG20B is a critical component of the GFI1:LSD1 transcription repressor complex which contributes to leukaemia cell differentiation block.

overall_design: Human THP1 AML cells were infected with lentivirus to induce doxycycline-induced expression of Flag-tagged full HMG20B, or a fusion protein containing the GFI1 DNA binding domain (GFI1-ZNF) fused with the full HMG20B. Cells were grown in the presence or absence of doxycycline for 48 hr. and subsequently ChIP-sequencing for LSD1, GFI1, Flag-HMG20B/GFI1-ZNF-HMG20B or H3K27ac was done.


title: CST6 suppresses osteolytic bone disease in multiple myeloma by blocking osteoclast differentiation

city: little rock

first: Dongzheng

last: Gai

state: AR

address: 4301 W Markham St

institute: UAMS

summary: To further determine how CST6 influence the myeloma bone disease.

overall_design: scRNA sequencing were performed on bone marrow mononuclear cells from tumor bearing mice treated with and without CST6.

first: Fenghuang

last: Zhan


title: Human primed and naive PSCs are equally potent in differentiating into bona fide trophoblast stem cells (RNA-Seq)

first: Noa

last: Novershtern

overall_design: RNA-seq

first: Sergey

last: Viukov

first: Tom

last: Shani

first: Jacob

last: Hanna


title: Expanding the genetic tool kit helps dissect a global stress response in the early-branching species Fusobacterium nucleatum

status: Public on Sep 20 2022

city: Würzburg

first: Falk

last: Ponath

address: Josef-Schneider-Straße 2

institute: Helmholtz Institute for RNA-based Infection Research (HIRI)

summary: We elucidated the global regulatory network of sigma E in Fusobacterium nucleatum. For this, we developed new genetic tools for the anaerobic bacterium. This uncovered a conserved regulon of the sigma factor including a noncoding arm of the sRNA FoxI. In this process, FoxI serves as a negative regulator of sigma E to downregulate several outer membrane proteins as well as the putative galactose transporter mglBAC.

sample_organism: Fusobacterium nucleatum subsp. nucleatum ATCC 23726

overall_design:
Samples were treated with anhydrotetracycline (100ng/ml) or left untreated for 20min (FoxI) or 30min (rpoE) at mid-exponential phase.
Samples marked with "shock" were either treated with polymyxin B or exposed to atmospheric oxygen for 20min at mid-exponential phase.
Isolated RNA was used for cDNA library generation following the RNA-seq protocol.

first: Yan

last: Zhu

first: Valentina

last: Cosi

first: Jörg

last: Vogel


title: DNA methyltransferase 3A controls intestinal epithelial barrier function and regeneration in the colon [Array]

first: Neha

last: Mishra

overall_design: 4 groups of Caco-2 cells were analyzed, each comprising 4 replicates. For baseline condition analysis, purified intestinal epithelial cells from steady state Dnmt3afl/fl (n=3) and Dnmt3a△IEC (n=4) were used. For in vivo DSS experiment, intestinal crypts were obtained from Dnmt3afl/fl  and Dnmt3aΔIEC mice at day 5 (peak of disease:n=5 vs 5), and at day 12 (recovery phase: 7 days after DSS treatment:n=8 vs 7)

first: Antonella

last: Fazio

first: Dora

last: Bordoni

first: Philip

last: Rosenstiel


title: m6A methylome in WT- and K177Q-METTL3 reconstituting MDA-MB-231 cells as well as in METTL3-deficient MDA-MB-231 cells.

city: Taiyuan

first: Xiaoniu

last: He

address: No.99 Longcheng Street

institute: Shanxi Bethune Hospital

summary: We report the application of MeRIP sequencing technology for high-throughput profiling of m6A methylome in breast cancer cells. Comparison of m6A methylome between METTL3-WT and METTL3-K177Q reconstituting cells revealed the following findings: 1) Significant global alteration of methylation sites due to K177Q mutation (termed as KQ-m6A signature).  2) GO analysis of the differential m6A-MeRIP candidates enriched pathways involved in chromatin modification, RNA splicing, DNA damage, cell cycle, and autophagy, consistent with a critical role of m6A-mediated nuclear biological activities and highlighted generally recognized cellular events associated with tumorigenesis. 3) we dissected potential mechanistic clues explaining the attenuated invasive phenotype in METTL3K177Q reconstituting cells.

overall_design: Examination of different m6A modification levels and gene expressions in WT- and K177Q-METTL3 reconstituting MDA-MB-231 cells as well as in METTL3-deficient MDA-MB-231 cells.

first: Yuanpei

last: Li


title: polysome profiling RNA seq experiments on extracts from METTL3-WT and METTL3-K177Q reconstituting cells

summary: Given the overall steady-state mRNA abundance between these two groups displayed negligible differences, these data implied an increased translational efficiency in cells bearing K177Q mutation.

overall_design: Using sucrose gradient centrifugation, collected fractions were pulled into sub-polysome fraction and polysome fraction. Then, sub-polysome and polysome samples were subjected to RNA-seq.


title: Diversity of astrocytes across the mouse CNS [scRNA-seq]

status: Public on Sep 19 2022

city: Los Angeles

first: Riki

last: Kawaguchi

address: 760 Westwood Plaza, Room 37-420

department: Department of Psychiatry and Neurology Department of Psychiatry

institute: University of California, Los Angeles

summary: We assessed astrocyte diversity in the cortex, hippocampus, and striatum using sing cell RNA-seq (scRNA-seq). We also assessed cortical astrocytes in wild type control and transgenic APP/PS1dE9 mice using scRNA-seq.

overall_design: Total of 34 10X Genomics Chromium samples from cortical, hippocampal, and striatal tissues of C57BL/6 mice and cortical tissues of APP/PS1dE9 mice were used for this dataset. Single cell suspension was prepared according to the protocol of Act-seq.

first: Fumito

last: Endo

first: Fuying

last: Gao

first: Baljit

last: Khakh


title: METTL3-WT and METTL3-K177Q

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

overall_design: Refer to individual Series


title: TYK2 regulates human pancreatic beta-cell development and its responses to interferon-alpha [tyk2_scRNAseq]

city: Helsinki

first: Jouni

middle: Antero

last: Kvist

state: Uusimaa

address: Haartmaninkatu 8

department: Research Program for Molecular Neurology

country: Finland

institute: University of Helsinki

summary: Type 1 diabetes (T1D) is an autoimmune disease that results in the destruction of insulin producing pancreatic b-cells. One of the genes associated with T1D is TYK2, which encodes a Janus kinase with critical roles in type-I interferon (IFN) mediated intracellular signalling. To study the role of TYK2 in human pancreatic b-cell development and response to IFNa, we generated TYK2 knockout human iPSCs and directed them into the pancreatic endocrine lineage. Unexpectedly, loss of TYK2 compromised the emergence of endocrine precursors by regulating KRAS expression, however, mature b-cell function was not affected. In the mature stem cell-derived islets, the loss or inhibition of TYK2 prevented IFNa-induced antigen processing and presentation, including MHC Class I expression, enhancing their survival against T-cell cytotoxicity. These results identify an unsuspected role for TYK2 on b-cell development and support TYK2 inhibition in adult b-cells as a potent therapeutic target to halt T1D progression.

overall_design: We performed single cell RNA-seq in two stages (S5 & S6) of pancreatic differentiation for CRISPR/Cas9 generated TYK2 KO hiPSC lines and non-edited negative control (WT) samples. We also performed scRNA-seq on same samples (in S6) treated with IFNa.

first: Vikash

last: Chandra

first: Hazem

last: Ibrahim

first: Clémentine

last: Halliez

first: Rashmi

last: Prasad

first: Federica

last: Vecchio

first: Om

last: Dwivedi

first: Diego

last: Balboa

first: Jonna

last: Saarimäki-Vire

first: Hossam

last: Montaser

last: Barsby

first: Väinö

last: Lithovius

first: Isabella

last: Artner

first: Swetha

last: Gopalakrishnan

first: Leif

last: Groop

first: Roberto

last: Mallone

first: Decio

last: Eizirik

first: Timo

last: Otonkoski


title: TYK2 regulates human pancreatic beta-cell development and its responses to interferon-alpha

first: Jouni

last: Kvist


title: Diversity of astrocytes across the mouse CNS

first: Riki

last: Kawaguchi


title: TYK2 regulates human pancreatic beta-cell development and its responses to interferon-alpha [tyk2_bulkseq]

overall_design: We employed CRISPR/Cas9 engineering to generate TYK2 KO hiPSC lines (HEL46.11). We performed pancreatic differentiation using a seven-stage protocol and compared the KO to a non-edited negative clone serving as a wildtype (WT) control. The genotypes were compared to each other across developmental stages (iPSC, S4, S5 & S6) using bulk-RNA-seq (with three biological replicates per stage).

first: Vikash

last: Chandra

first: Hazem

last: Ibrahim

last: Halliez

first: Tom


title: The role of hepatic XBP1 in FXR null mice

city: Chicago

first: Xiaoying

last: Liu

state: IL

address: 240 E Huron St., McGaw M-319

institute: Northwestern University

summary: X-box binding protein 1 (XBP1) is a key component of the unfolded protein response that is activated in response to ER stress. Farnesoid X receptor (FXR) null (Fxr-/-) mice have elevated bile acid levels and progressive liver injury. Hepatic XBP1 pathway is activated in older Fxr-/- mice. This project is to investigate the role of liver XBP1 in Fxr-/- mice.

overall_design: We generated mice with FXR and liver-specific XBP1 double knockout (DKO, Fxr-/-Xbp1LKO) and Fxr-/-Xbp1fl/fl single knockout (SKO) mice. Liver RNA was extracted from chow-fed male 8-10 weeks old SKO and DKO mice.

first: Richard

last: Green


title: RNA sequencing (RNA-seq) of BUD31 knockdown or overexpression in ovarian cancer cells

city: Jinan

first: Zixiang

last: Wang

state: Shandong

address: No.44 Wenhuaxi Road

department: Cheeloo College of Medicine

institute: Shandong University

summary: Mis-regulation of splicing factors are thought to activate cancer specific splicing programs that contribute to cancer development and progression. However, it remains a major challenge to identify the key splicing variants caused by aberrant expression of splicing factors in cancer. Here we report that splicing factor BUD31 is commonly overexpressed in high-grade serous ovarian carcinoma (HGSOC) and high level of BUD31 is associated with poor prognosis. RNA-seq analysis reveals that BUD31 inhibition predominantly results in alternation of exon skipping and intron retention. We further identify binding motif and preferred genome-wide binding pattern of BUD31 by CLIP-seq analysis. In particular, we demonstrate that BUD31 overexpression drives an oncogenic splicing switch of BCL2L12 (an anti-apoptotic BCL2 family member) to produce a full-length isoform (BCL2L12-L) which in turn increased the survival, proliferation and anti-apoptosis ability of ovarian cancer cells. Our data indicate that BUD31 is a critical oncogenic splicing factor in ovarian cancer and might act as a potential therapeutic target.

overall_design: Dox-inducible BUD31 knockdown or overexpression cell lines were constructed in HEYA8, A2780, SKOV3 cells. The assay was performed on three biological triplicates.

first: Zhaojian


title: BUD31 in ovarian cancer cells


title: Transcriptome profiling (RNA-seq) of chemotherapy treated CRC organoids

status: Public on Sep 16 2022

city: Barcelona

first: Camille

last: Stephan Otto Attolini

state: Select a State or Province

address: Baldiri Reixac 10

department: Biostatistics and bioinformatics Unit

institute: IRB Barcelona

summary: The main goal of this study was to analyze transcriptional differences between AKP CRC organoids treated or not with chemotherapy (FOLFIRI) by RNA-seq.

overall_design: AKP organoids were treated or not with FOLFIRI (5FU+SN38) for 2 days. Total RNA was extracted using PureLink RNA mini kit. RNA libraries were prepared for sequencing using the kits NEBNext® Poly(A) mRNA Magnetic Isolation Module and NEBNext® Ultra™ II RNA Library Prep Kit for Illumina®.

last: Stephan-Otto Attolini

first: Adrià

last: Cañellas-Socias

first: Eduard

last: Batlle

first: Laura

last: Novellasdemunt


title: Enterococci enhance Clostridioides difficile pathogenesis

status: Public on Sep 17 2022

city: Philadelphia

first: Joseph

last: Zackular

state: Pennsylvania

address: 3615 Civic Center Blvd

institute: University of Pennsylvania

summary: Clostridioides difficile is one of the most common nosocomial pathogens and a global public health threat. Upon colonization of the gastrointestinal tract, C. difficile is exposed to a rapidly changing polymicrobial environment and a dynamic metabolic milieu. Despite the link between the gut microbiota and susceptibility to C. difficile, the impact of synergistic interactions between the microbiota and pathogens on the outcome of infection is largely unknown. Here, we show that microbial cooperation between C. difficile and Enterococcus has a profound impact on the growth, metabolism, and pathogenesis of C. difficile.. Through a process of nutrient restriction and metabolite cross-feeding, E. faecalis shapes the metabolic environment in the gut to enhance C. difficile fitness and increase toxin production. These findings demonstrate that members of the microbiota, such as Enterococcus, have a previously unappreciated impact on C. difficile behavior and virulence.

sample_organism:
Enterococcus faecalis
Clostridioides difficile

overall_design: RNA-sequencing of Clostridioides difficile CD196 and Enterococcus faecalis OG1RF in monoculture and in coculture with three biological replicates per sample

first: Alexander

middle: B

last: Smith

first: Chao

last: Di


title: RNA sequencing of CRC tumor organoids engineered with key driver mutations

summary: We profiled CRC organoids engineered with different combinations of driver mutations. All organoids were derived from one mouse and then mutations were sequentially introduced by CRISPR Cas9

overall_design: Organoids were grown in full medium and harvested when they reached confluence.

middle: S

last: Attolini


title: A Novel Biological Role for von Willebrand Factor in Linking Primary Hemostasis and Innate Immunity

status: Public on Sep 18 2022

city: Dublin

first: Karsten

last: Hokamp

address: College Green

department: Smurfit Institute of Genetics

country: Ireland

institute: Trinity College Dublin

summary: The plasma multimeric glycoprotein von Willebrand factor (VWF) plays a critical role in primary hemostasis by tethering platelets to exposed collagen at sites of vascular injury. Recent studies have identified additional biological roles for VWF, and in particular suggest that VWF may play an important role in regulating inflammatory responses. Critically however, the molecular mechanisms through which VWF exerts its immuno-modulatory effects remains poorly understood. In this study, we report for the first time that VWF binding to macrophages triggers direct downstream MAPkinase signaling leading to NF-kB activation and production of pro-inflammatory cytokines and chemokines. In keeping with these observations, VWF binding also promotes macrophage M1 polarization and shifts macrophage metabolism towards glycolysis in a p38 dependent manner. Cumulatively, our findings define an entirely new biological role for VWF in modulating macrophage function, and thereby establish a novel link between primary hemostasis and innate immunity.

overall_design: Comparative gene expression profiling analysis of RNA-seq data on BMDMs after incubation in the presence of pd-VWF, LPS or PBS control for 3.5 hours or 16 hours.

first: James

last: O'Donnell

first: Padraic

last: Fallon

first: Fiona

last: Roche

first: Frederick

last: Sheedy


title: TYK2 regulates human pancreatic beta-cell development and its responses to interferon-alpha [ultradeep]

first: Jouni

last: Kvist

overall_design: To identify candidate genes of pancreatic development that are also associated with the development of T1D in humans, we performed deep RNA-seq at specific stages (S1, S4, S7 & graft) of human induced pluripotent stem cells (hiPSCs) pancreatic differentiation (with 5 biological replicated per stage).

first: Vikash

last: Chandra

first: Hazem

last: Ibrahim

first: Clémentine

last: Halliez

first: Rashmi

last: Prasad

first: Federica

last: Vecchio

first: Om

last: Dwivedi

first: Diego

last: Balboa

first: Jonna

last: Saarimäki-Vire

first: Hossam

last: Montaser

first: Tom

last: Barsby

first: Väinö

last: Lithovius

first: Isabella

last: Artner

first: Swetha

last: Gopalakrishnan

first: Leif

last: Groop

first: Roberto

last: Mallone

first: Decio

last: Eizirik

first: Timo

last: Otonkoski


title: Expression profiling of AKTP primary tumors cells with high or low expression of Emp1

first: Adria

last: Caballe

address: C/ Baldiri Reixac 10

department: biostatistics

institute: IRB

summary: We sorted Emp1-tdTomato high and low cells from primary tumors grown in 4 different mice for 4 weeks

overall_design: High and low samples are paired, they come from the same tissue sample. 4 biological replicates

first: Adrià

last: Cañellas

first: Eduard

last: Batlle


title: Profiling of AKTP MTOs alone or coculture with colon fibroblasts

summary: This array was performed  to investigate the effect that colon fibroblasts have on gene expression in mouse tumor organoids.

overall_design: MTOs were cultured in BME alone or in combination with colon fibroblast for 7 days. Tumor cells were then FACS sorted and profiled.


title: The rearing environment persistently modulates mouse phenotypes from the molecular to the behavioural level

status: Public on Sep 15 2022

city: Bern

first: Ivana

last: Jaric

address: Länggassstrasse 120

department: Animal Welfare Division

institute: Vetsuisse Faculty, University of Bern

summary: The phenotype of an organism results from its genotype and the influence of the environment throughout development. Even when using animals of the same genotype, independent studies may test animals of different phenotypes, resulting in poor replicability due to genotype-by-environment interactions. Thus, genetically defined strains of mice may respond differently to experimental treatments depending on their rearing environment. However, the extent of such phenotypic plasticity and its implications for the replicability of research findings have remained unknown. Here, we examined the extent to which common environmental differences between animal facilities modulate the phenotype of genetically homogeneous (inbred) mice. We conducted a comprehensive multi-center study, whereby inbred C57BL/6J mice from a single breeding cohort were allocated to and reared in five different animal facilities throughout early life and adolescence, before being transported to a single test laboratory. We found persistent effects of the rearing facility on the composition and heterogeneity of the gut microbial community. These effects were paralleled by persistent differences in body weight and in the behavioural phenotype of the mice. Furthermore, we show that environmental variation among animal facilities is strong enough to influence epigenetic patterns in neurons at the level of chromatin organization. We detected changes in chromatin organization in the regulatory regions of genes involved in nucleosome assembly, neuronal differentiation, synaptic plasticity and regulation of behaviour. Our findings demonstrate that common environmental differences between animal facilities may produce facility-specific phenotypes, from the molecular to the behavioural level. Furthermore, they highlight an important limitation of inferences from single-laboratory studies and thus argue that study designs should take environmental background into account to increase the robustness and replicability of findings.

overall_design: Nine-week-old, time-mated, primiparous pregnant C57BL/6JRj female mice in the last third of pregnancy, all from a single breeding population (Janvier Labs, Le Genest-Saint-Isle, France) were randomly allocated and transported to five independent rearing facilities (RF), where their offspring were born and reared until eight weeks of age. In order to assess the effect of the rearing environment independent of genotype and test conditions, both male and female offspring from all five RF were then transported to a single laboratory that was new for all mice to test for phenotypic differences. Specifically, we examined the extent and persistence of variation in the composition of the gut microbiota associated with the different rearing facilities and measured differences in phenotypic traits such as body weight, adrenal weight, neuroendocrine stress reactivity, and behavior. In addition, we assessed differences in neural chromatin accessibility to explore the potential biological basis of behavioral differences. The ATAC-seq analysis was performed on ventral hippocampi isolated from male mice at TP1 and TP2. For this, test-naïve male mice were used to avoid effects of testing on the chromatin profile. Five cages per rearing facility were selected randomly from all cages containing 3 male littermates after weaning. One mouse from the selected cages was sacrificed in the rearing facility at TP1 (total n=25, i.e. 5 biological replicates per rearing laboratory), while its test-naïve littermate was sacrificed in the testing laboratory at the end of the experiment (TP2; total n=25, i.e. 5 biological replicate per rearing facility). The analysis has been restricted to males because they showed the most pronounced phenotypic differences in behavior.

first: Bernhard

last: Voelkl

first: Melanie

last: Clerc

first: Marc

last: Schmid

first: Janja

last: Novak

first: Marianna

last: Rosso

first: Reto

last: Rufener

first: Vanessa

middle: T

last: von Kortzfleisch

first: Helene

last: Richter

first: Manuela

last: Büttner

first: André

last: Bleich

first: Irmgard

last: Amrein

first: David

last: Wolfer

first: Chadi

last: Touma

first: Shinichi

last: Sunagawa

first: Hanno

last: Würbel


title: Identification of topologically associated domains (TADs) in peripheral blood CD34+ cells

city: Miami

first: Qin

last: Yang

state: FL

address: 1501 NW 10th Avenue

department: Sylvester Comprehensive Cancer Center

institute: University of Miami Miller School of Medicine

summary: We performed a Hi-C experiment on CD34+ cells isolated from peripheral blood and identifed topologically associated domains (TADs).

overall_design: Two replicates of mobilized peripheral blood CD34+ cells were purchased from Fred Hutchinson Hematopoietic Cell Procurement Services. Hi-C was performed in replicate on CD34+ cells.

first: Hsuan-Ting

last: Huang

first: Maria

middle: E

last: Figueroa


title: Human Core Nucleoporin Selectively Regulates Gene Transcription but is Dispensable for 3D Genome Organization

city: HOUSTON

first: chuangye

last: Qi

state: Texas

address: One plaza

department: Huffington Center

institute: Baylor College of Medicine

summary: NUPs have been shown to be important in transcriptional regulation and in three-dimensional (3D) genome organization. However, evidence in support of their direct roles remains limited, and their action mechanisms are elusive.here,we take advantage of a few advanced techniques including Cut&Run, auxin-induced rapid degron, PRO-Seq, dCas9 chromatin tethering, in situ Hi-C and HiChIP to directly address these outstanding questions in human cells, and our results provide new insights into the direct but also specific roles of core NUPs in gene transcription, while revealing their dispensity for the overall organization of 3D genome architecture.

overall_design: the role of core human nucleoporins in human cells

first: Wenbo

last: Li


title: RNA transcriptomics analysis on transfected k562 cells at different feeding regimes

status: Public on Sep 14 2022

city: London

first: Benjamin

last: Schumann

address: 80 Wood Lane

institute: Imperial College London

summary: We developed a chemical precision tool that allows cell-type specific labelling of glycoproteins. Cells are endowed with an artificial biosynthetic pathway that allows the synthesis of modified UDP-GalNAc when cells are fed with modified GalNAc precursor (Ac4GalN6yne). The aim of this RNA-seq analysis is to establish if the transfection of cells with the artificial biosynthetic pathway (NahK and AGX1-F383A enzymes) and/or the feeding treatment (DMSO or Ac4GalN6yne or Ac4GalNAc) have a substantial effect on the RNA transcriptomics.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for k562 cells transfected with either empty or Nahk/AGX1_F383A plasmid at different feeding regimes.

first: Anna

last: Cioce

first: Beatriz

last: Calle

first: Tatiana

last: Rizou

first: Sarah

middle: C

last: Lowery

first: Victoria

middle: L

last: Bridgeman

first: Keira

last: Mahoney

first: Andrea

last: Marchesi

first: Ganka

last: Bineva-Todd

first: Zhen

first: Omur

last: Tastan

first: Chloe

last: Roustan

first: Pablo

last: Soro-Barrio

first: Mahmoud-Reza

last: Rafiee

first: Acely

last: Garza-Garcia

first: Aristotelis

last: Antonopoulos

first: Thomas

middle: M

last: Wood

first: Tessa

last: Keenan

first: Peter

last: Both

first: Kun

first: Fabio

last: Parmeggiani

first: Ambrosius

last: Snijders

first: Mark

last: Skehel

first: Svend

last: Kjaer

first: Martin

middle: A

last: Fascione

first: Carolyn

middle: R

last: Bertozzi

first: Stuart

last: Haslam

first: Sabine

last: Flitsch

first: Stacy

last: Malaker

first: Ilaria

last: Malanchi


title: Myocardial TRPC6-mediated Zn2+ influx induces beneficial positive inotropy through b-adrenoceptors

city: Setagaya

first: Takuya

last: Kuroda

state: Tokyo

address: 1-18-1 Kamiyoga

department: Division of cell-based therapeutic products

institute: National Institute of Health and Sciences

summary: Baroreflex control of cardiac contraction (positive inotropy) through sympathetic nerve activation is important to maintain cardiocirculatory homeostasis. Transient receptor potential canonical subfamily (TRPC) channels are responsible for alfa1-adrenoceptor (alfa1AR)-stimulated cation entry and their upregulation is reportedly associated with pathological cardiac remodeling, but whether TRPC channels participate in physiological pump functions remains unclear. Here, we demonstrate that TRPC6-specific Zn2+ influx potentiates alfa-adrenoceptor (alfaAR)-stimulated positive inotropy in rodent cardiomyocytes. Deletion of the trpc6 gene impairs sympathetic nerve-activated positive inotropy, but not chronotropy in mice. TRPC6-mediated Zn2+ influx boosts alfa1AR-stimulatedalfaAR/Gs-dependent signaling in rat cardiomyocytes by inhibiting alfa-arrestin-mediated alfaAR internalization. Replacing two TRPC6-specific amino acids in the pore region with those of TRPC3 diminishes the alfa1AR-stimulated Zn2+ influx and positive inotropic response. Pharmacological enhancement of TRPC6-mediated Zn2+ influx prevents the progression of heart failure in dilated cardiomyopathy mice. Our data provide evidence that TRPC6-mediated Zn2+ influx with α1AR stimulation enhances baroreflex-induced positive inotropy, which may be a new therapeutic strategy for chronic heart failure.

overall_design: WT, TRPC3(-/-) and TRPC6(-/-) mouse hearts analyzed by microarray. n=3 each group.

first: Yoji

last: Sato

first: Motohiro

last: Nishida


title: Transcriptome Sequencing Reveals Pathways Related to Proliferation and Differentiation of Shitou Goose Myoblasts

city: guangzhou

first: Shuai Zhang

last: Shuai Zhang

address: Wushan Street, Tianhe District

country: China

institute: South China Agricultural University

summary: In this study, we cultured lion-headed goose myoblasts and induced their differentiation, followed by RNA-seq extraction of total RNA from proliferative and differentiated cells, respectively. The identified lncRNAs and mRNAs were analyzed, including enrichment analysis, alternative splicing, and construction of interaction networks.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for the Proliferative and differentiated myoblasts of Shitou Goose.

first: Jiahui

last: CHEN

first: Shuai

last: ZHANG

first: Xianqi

last: DENG

first: Danlu

first: Genghua

first: Huaqiang

last: WEN

first: Yunqian

last: YIN

first: Zetong

last: LIN

first: Xiquan

first: Wen

last: LUO


title: Identification of genes associated with bortezomib-based treatment in multiple myeloma patients through bone marrow single-cell RNA-Seq

city: seoul

first: SeungHyun

last: Jung

state: seoul

address: catholic university, medical college, banpo-dong

department: Department of Biochemistry

institute: Catholic University of Korea

summary: In this study, we performed scRNA-seq analyses of bone marrow mononuclear cells (BM-MNCs) in patients with MM receiving bortezomib-based treatments to investigate following questions; (i) the compositional differences in BM-MNCs between normal control and MM patients, and between good and poor responder groups, and (ii) the genes and the cell-to-cell communication networks associated with the treatment responsiveness.

overall_design: For scRNA-seq, we used baseline bone marrow aspirates (treatment-naïve) from 18 MMs, who treated with bortezomib-melphalan-prednisolone. The single-cell library preparation relied on a commercially available droplet method using the 10x Genomic Chromium System and Single Cell 3' v3 Reagent Kit according to the manufacturer’s protocol.

first: Seung-Hyun

first: Sung-Soo

last: Park

first: SugHyung

last: Lee

first: Yeun-Jun

last: Chung

first: Chang-Ki

last: Min


title: DNA replication timing directly regulates the frequency of oncogenic chromosomal translocations

city: Vienna

first: Tobias

last: Neumann

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP

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

overall_design: Refer to individual Series


title: Post-ICB treatment PDAC infiltrating T cells TCR profile

city: Atlanta

first: Edmund K.

last: Waller

address: 1365 Clifton Rd Building C

country: USA

institute: Emory University School of Medicine

summary: For the subcutaneous model, 5x105 KPC-Luc cells were injected subcutaneously near the right flank of female C57BL/6 mice. 6-7 days after tumor implantation mice were randomized into 4 treatment groups and treatedwith VIP-R antagonist and/or anti-PD-1. While scram+IgG control mice received scrambled peptide and isotype IgG, the VIP-R antagonist, anti-PD-1 and VIP-R antagonist and anti-PD-1 groups received VIP-R antagonist and IgG; scrambled peptide and anti-PD-1; and VIP-R antagonist and anti-PD-1, respectively. The treatment regimen involved administering 10μg of scrambled or VIP-R antagonist: ANT008, subcutaneously every day and 200μg of IgG or anti-PD-1 intraperitoneally once every three days, for a total of 10 days.

overall_design:
4 groups: control, aPD-1, Ant008, aPD-1+Ant008. 4 samples per each group. 16 samples are analyzed.
Sequencing of TCR-β CDR3 V and J sequences performed by Adaptive Biotechnologies (Seattle, WA).

>>>Submitter states: Adaptive Biotechnologies does not provide raw data files<<<

first: Sruthi

last: Ravindranathan

first: Tenzin

last: Passang

first: Hanwen

last: Zhang

first: Edmund