title: First cleavage is a manifestation of the geometry of the unfertilized oocyte: implications for monozygotic twinning in mice.

city: Muenster

first: Wojciech

last: Makalowski

address: Niels Stensen Strasse 14

department: Faculty of Medicine

institute: University of Muenster

summary: A long-standing question in mammalian embryology is whether regional differences of oocyte composition matter for the properties of blastomeres receiving those regions after fertilization. A hitherto untested hypothesis is that allocation depends on the orientation of 1st cleavage. However, the orientation is influenced by the site of sperm entry in the oocyte, which can be almost anywhere on the membrane of oocytes when these are inseminated. Therefore, we harnessed the intracytoplasmic sperm injection to impose the site of fertilization in three specific ooplasmic regions (animal pole, vegetal pole, equator) of mouse oocytes. Notwithstanding this categorical distinction, the sister blastomeres of resultant 2-cell embryos differed from each other in the same way, as measured by gene expression and twin blastocysts formation following bisection. We reasoned that either the oocyte territories did not matter, or their effect was obscured by other factors. To shed light on these possibilities, we immobilized the oocytes on the micromanipulation stage during sperm injection and for 24 h thereafter. Imaging revealed that the orientation of 1st cleavage, instead of depending on the fertilization site, depended on the shorter diameter of the unfertilized oocyte. This even led to the segregation of animal and vegetal hemispheres in the blastomeres of 2-cell embryos. We conclude that 1stcleavage is a manifestation of the intrinsic organization of the oocyte prior to fertilization, and that oocyte geometry factors in to the patterning of mouse embryos more so than fertilization topology.

overall_design: The samples are monozygotic twin embryos of the mouse, at Theiler stages 2 and 5, generated as follows. Fertilized oocytes were produced by intracytoplasmic sperm injection (ICSI) of CD1 sperm into B6C3F1 oocytes, ensuring that the sperm head was deposited in the oocyte opposite the meiotic spindle (contralateral ICSI), or next to the meiotic spindle (isolateral ICSI) or half way in between (equatorial ICSI). Fertilization was followed by pool culture in KSOM medium containing aminoacids for one cell cycle. At the 2-cell stage, the sibling blastomeres were separated from each other (Theiler stage 2) and cultured individually to the blastocyst stage (Theiler stage 5), thereby producing twin blastocysts, as described (PMID 28811525). The samples used for RNA sequencing were the individual blastomeres (Theiler stage 2) or the individual blastocysts (Theiler stage 5), lysed keeping track of the type of ICSI (contralateral, Co; isolateral, Iso; equatorial, Equat), of the precursor embryo (e.g.embryo no.1, no.2, no.3, ..., no.132), and of the original pair association (e.g. blastomere 'a' and 'b'). Accordingly, the sample denomination "ICSI_Co_1a, blastomere" means that the blastomere 1a was obtained from an oocyte (no.1) that was fertilized opposite the meiotic spincle (contralateral), and that the blastomere was one ('a') of the two from the same 2-cell embryo. The sample denomination 'ICSI_Co_intact_76, blastocyst' means that blastocyst 76 was obtained from an oocyte (no.76) that was fertilized opposite the meiotic spindle (contralateral) and that the embryo was not bisected (intact). The sample denomination 'ICSI_Eq_twin_112a, blastocyst' means that the twin blastocyst 112a was obtained from an oocyte (no.112) that was fertilized at the equator and that was bisected at the 2-cell stage, so that twin blastocysts 112a and 112b arose from the in vitro culture of the sibling blastomeres.

first: Michele

last: Boiani

first: Georg

last: Fuellen

first: Reza

last: Halabian

first: Thomas

last: Nolte

first: Yutaka

last: Suzuki

first: Steffen

last: Israel


title: The Ribosome Assembly Factor Reh1 is Released from the Polypeptide Exit Tunnel in the Pioneer Round of Translation

status: Public on Jan 24 2024

city: Austin

first: Can

last: Cenik

state: TX

address: Moffett Molecular Biology Building 2.122 2500 Speedway

department: Molecular Biosciences

country: USA

institute: The University of Texas at Austin

summary: In S. cerevisiae, the ribosome assembly factor Reh1 binds to pre-60S subunits at a late stage during their cytoplasmic maturation. Unlike canonical assembly factors, which associate exclusively with pre-60S subunits, we observed that Reh1 sediments with polysomes in addition to free 60S subunits. We therefore investigated the intriguing possibility that Reh1 remains associated with 60S subunits after the release of the anti-association factor Tif6 and after subunit joining. Here, we show that Reh1-bound nascent 60S subunits associate with 40S subunits to form actively translating ribosomes.

overall_design: Selective ribosome profiling of  Reh1-bound ribosomes in S.cerevisiae.

first: Sharmishtha

last: Musalgaonkar

first: James

last: Yelland

first: Ruta

last: Chitale

first: Shilpa

last: Rao

first: Hakan

last: Ozadam

first: David

last: Taylor

first: Arlen

last: Johnson


title: Dual RNA-sequencing of Fusarium Head Blight resistance in winter wheat

city: Winnipeg

first: Philip

last: Walker

state: Manitoba

address: 104 Dunrobin Avenue

country: Canada

institute: Agriculture and AgriFood Canada

type: Expression profiling by high throughput sequencing

summary: In this study, we used dual RNA-sequencing to profile FHB-resistant AC Emerson, FHB-moderately AC Morley, and FHB-susceptible CDC Falcon winter wheat cultivars prior to and in response to Fusarium graminearum at 7 days post inoculation. Differential expression analyses revealed distinct defense responses between resistant and susceptible wheat cultivars including increased mechanical defense through lignin biosynthesis and increased deoxynivalenol (DON) detoxification through UDP-glycosyltransferase activity in resistant cultivars. Further, differential expression analysis in F. graminearum challenging these distinct cultivars revealed changes genes involved in trichothecene mycotoxin biosynthesis.

overall_design: FHB-resistant AC Emerson, FHB-moderately resistant AC Morley and FHB-susceptible CDC Falcon spikelets at 0 and 7 days post inoculation with Fusarium graminearum

first: Maria

middle: A

last: Henriquez


title: Nucleus-Translocated GCLM Promotes Chemoresistance in Colorectal Cancer through a Moonlighting Function

status: Public on Jan 28 2024

city: Shanghai

first: Haojie

last: Chen

state: Shanghai

address: Yueyang Road 320

department: PICB

country: China

institute: CAS

summary: Emerging evidence indicates that metabolic enzymes perform moonlighting functions during tumor progression, including the modulation of chemoresistance. However, the underlying mechanisms of these functions remain elusive. In this study, utilizing a genome-scale metabolic CRISPR-Cas9 knockout library screen, we observed that loss of Glutamate-cysteine ligase modifier subunit (GCLM), a rate-limiting enzyme in glutathione biosynthesis, noticeably heightens the sensitivity of colorectal cancer (CRC) cells to platinum-based chemotherapy. Mechanistically, we unveil a noncanonical mechanism through which nuclear GCLM competitively interacts with NF-kappa-B-repressing factor (NKRF), a known inhibitor of NF-κB signaling, to promote NF-κB activity and subsequently facilitate chemoresistance. In response to platinum drug treatment, P38 phosphorylates GCLM at T17, resulting in its recognition by importin a5 and subsequent nuclear translocation. Furthermore, elevated expression of nuclear GCLM is evident in CRC tissues and correlates with poor prognosis and heightened P38 activity. Overall, our findings shed light on the essential nonmetabolic role and posttranslational regulatory mechanism of GCLM in enhancing NF-κB activity and subsequent chemoresistance.

overall_design: The human metabolic enzyme sgRNA library, targeting 1773 metabolic enzyme-encoding genes with 4 sgRNAs per gene, was designed and synthesized by GENEWIZ (Suzhou, China) and was then packaged into lentiviruses as previously described. For the in vitro CRISPR-Cas9 knockout screenin the presence of oxaliplatin, 4×107 HCT116 cells were plated, transduced with the lentiviral library and selected with puromycin (0.8 µg/mL) as previously reported3. The selected cells were divided into 4 groups and treated with PBS or 10 µM oxaliplatin for 7 days. Thereafter, the remaining surviving cells were harvested, and their genomic DNA was isolated and amplified by 2-step PCR using NEBNext Ultra II Q5 Master Mix (M0544L, New England Biolabs, Ipswich, MA, USA) and the primers listed in Supplementary Table 4. The PCR products containing the sgRNA sequences were extracted from the gel, quantified, sequenced, and analyzed as previously described

first: Jin

last: Lin

first: Ze

last: Liu

first: Dong

first: Rui

last: Xu


title: Hypoxia increases the methylated histones to prevent histone clipping and redistribution of heterochromatin during Raf-induced senescence.

status: Public on Jan 22 2024

city: Seoul

first: Insoo

last: Yoon

address: 163 Seoulsiripdaero, Dongdaemun-gu

department: Department of Life Science

country: South Korea

institute: University of Seoul

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Hypoxia increases histone methylation by inhibiting O2- and a-ketoglutarate-dependent histone lysine demethylases (KDMs). This study is the first to demonstrate how the hypoxic increment of methylated histones cross-talks with other epigenetic changes, such as histone clipping, and heterochromatin redistribution (senescence-associated heterochromatin foci, SAHF) found during oncogene-induced senescence (OIS). Raf activation in primary human fibroblasts IMR90 increased cathepsin L (CTSL)-mediated clipping of histone 3 (H3), H2B and H4 at H3 A21/T22, H2B T19/K20, and H4 G11/K12, respectively. Hypoxia protected H3 from CTSL by increasing histone methylation, especially at H3K23me3 without reducing the activity of CTSL. The maintenance of methylated histones is sufficient for protecting histones from CTSL, not sufficient but necessary for inhibiting SAHFs. Expression of cleaved H3 induces senescence even under hypoxia, suggesting that hypoxia disrupts this positive feedback loop of OIS by increasing histone methylation. Thus, hypoxia protects histones and chromatin from dramatic epigenetic changes by increasing histone methylation. These observations suggest that the OIS process increases the accessibility of chromatin, which hypoxic conditions inhibited.

overall_design: To investigate how hypoxia affects chromatin accessibility in OIS, Assay for Transposase Accessible Chromatin with high-throughput sequencing (ATAC-seq) was used to profile the chromatin accessibilities for four conditions (Raf-inactivated normoxia sample, Raf-activated normoxia sample, Raf-inactivated hypoxia sample, Raf-activated hypoxia sample) including four replicates.

first: Soojeong

last: Chang

first: Hyunsung

last: Park

first: Dongsung

last: Lee


title: Chronic exposure to glucocorticoids amplifies inhibitory neuron cell fate during human neurodevelopment in organoids [scATAC-seq]

city: Munich

first: Elisabeth

last: Binder

address: Kraepelinstr. 2-10

department: Department Genes and Environment

country: Germany

institute: Max Planck Institute of Psychiatry

summary: Disruptions in the tightly regulated process of human brain development have been linked to increased risk for brain and mental illnesses. While the genetic contribution to these diseases is well established, important environmental factors have been less studied at molecular and cellular levels. In this study, we used single-cell and cell-type-specific techniques to investigate the effect of glucocorticoid (GC) exposure, a mediator of antenatal environmental risk, on gene regulation and lineage specification in unguided human neural organoids. We characterized the transcriptional response to chronic GC exposure during neural differentiation and studied the underlying gene regulatory networks by integrating single-cell transcriptomics- with chromatin accessibility data. We found lasting cell type-specific changes that included autism risk genes and several transcription factors associated with neurodevelopment. Chronic GCs influenced lineage specification primarily by priming the inhibitory neuron lineage through key transcription factors like PBX3. We provide evidence for convergence of genetic and environmental risk factors through a common mechanism of altering lineage specification.

overall_design: Single-cell ATAC sequencing (10x Genomics) was performed in neural organoids derived from the 409b2 iPSC line. Organoids were either chronically treated (Dexamethasone 100nM, Chr-Veh condition) or vehicle-exposed (DMSO, Veh-Veh condition) for 10 days (day 60 - 70) and collected at day 90 following a 20-day washout period and an additional 12 hour acute exposure to the treatment vehicle DMSO. Four biological replicates were collected for each condition.

first: Leander

last: Dony

first: Anthi

middle: C

last: Krontira

first: Lea

last: Kaspar

first: Ruhel

last: Ahmad

first: Ilknur

middle: S

last: Demirel

first: Malgorzata

last: Grochowicz

first: Tim

last: Schäfer

first: Fatema

last: Begum

first: Vincenza

last: Sportelli

first: Catarina

last: Raimundo

first: Maik

last: Koedel

first: Marta

last: Labeur

first: Silvia

last: Cappello

first: Fabian

middle: J

last: Theis

first: Cristiana

last: Cruceanu

middle: B


title: Chronic exposure to glucocorticoids amplifies inhibitory neuron cell fate during human neurodevelopment in organoids [scRNA-seq]

overall_design: Single-cell RNA sequencing (10x Genomics) was performed in neural organoids derived from two different iPSC lines (FOK4 and 409b2). Both chronically treated (Dexamethasone 100nM) and vehicle-exposed (DMSO) organoids were collected either immediately at day 70 after a 10 day exposure (Chr and Veh conditions) or at day 90 following a 20-day washout period and an additional 12 hour acute exposure to 100nM Dexamethasone (Chr-Acu and Veh-Acu conditions) or the treatment vehicle DMSO (Chr-Veh and Veh-Veh conditions). Four biological replicates were collected for each condition. Data from the Veh-Veh and Veh-Acu is available from the GEO ID GSE189534 (Veh-Veh and Veh-Acu conditions labelled Veh and Dex respectively; Line FOK4 and Line 409b2 labelled Line2 and Line3 respectively).


title: Chronic exposure to glucocorticoids amplifies inhibitory neuron cell fate during human neurodevelopment in organoids.

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

overall_design: Refer to individual Series


title: Tangeretin alleviates LPS-induced acute lung injury by inhibiting ferroptosis of macrophage via Nrf2 pathways

status: Public on Jan 20 2024

city: shanghai

first: Yunqian

last: Zhang

address: 1665 Kong Jiang Road, Yangpu District

institute: Xinhua Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China.

summary: Sepsis-induced acute lung injury (ALI) is a severe clinical condition with a high mortality rate. Tangeretin, widely found in citrus fruits, has been reported to exert antioxidant and anti-inflammatory properties. However, whether Tangeretin protects against sepsis-induced ALI and the potential mechanisms remain unclear.We established ALI model via intraperitoneally injected with 5 mg/kg lipopolysaccharides (LPS) for 12 h. Tangeretin was applied intraperitoneally 30 min before LPS treatment.  The lung tissue samples from both the LPS and LPS + TAN groups were subjected to RNA sequencing analysis, conducted by OE Biotech Co., Ltd. (Shanghai, China). We performed differential gene expression analysis using RNA-seq data between LPS and LPS/Tangeretin group.GSEA analysis between LPS and LPS/Tangeretin group showed that IL6_JAK_STAT3_SIGNALING, INFLAMMATORY_RESPONSE, TNFA_SIGNALING_VIA_NFKB were significantly enriched (Fig.3C-E). These results identified the anti-inflammatory effect of Tangeretin against sepsis-induced ALI.

overall_design: To induce a septic lung injury model, an intraperitoneal injection of lipopolysaccharide (LPS) extracted from Escherichia coli O111:B4 (L2630, Sigma-Aldrich, USA) was administered at a dosage of 5 mg/kg. Preceding this, tangeretin (Tan, HY-N0133, MCE corporation, USA) was given at 50 mg/kg intraperitoneally, 30 min prior to the LPS injection. The lung tissue samples from both the LPS and LPS + TAN groups were subjected to RNA sequencing analysis, conducted by OE Biotech Co., Ltd. (Shanghai, China). Briefly, Total RNA was extracted using TRIzol reagent (Invitrogen, USA), followed by an evaluation of its purity and quantification. RNA integrity was assessed via the Agilent 2100 Bioanalyzer (Agilent Technologies, USA). Subsequently, cDNA libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit, and the sequencing was executed on Illumina Novaseq 6000 platform. Approximately 50 M clean reads per sample were retained.

first: Hui

first: Yan

last: Wang

first: Siyuan

last: Li


title: Granulocytic myeloid-derived suppressor cell activity during biofilm infection is regulated by a glycolysis-HIF-1α axis

status: Public on Jan 23 2024

city: Omaha

first: Sankarasubramanian

last: Jagadesan

state: NE

address: 42end and Emile st

department: Department of Genetics, Cell Biology & Anatomy

institute: University of Nebraska Medical Center

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Decoupling the Biochemical and Mechanical Effects of Muscle Exercise on Motor Neurons with 2.5D Actuating Matrices [230828Ram_RNA-seq]

status: Public on Feb 25 2024

city: Cambridge

first: Vincent

last: Butty

state: MA

address: 77 Massachusetts Avenue Bldg 68-317A

department: Biology / Koch Institute / Bioengineering / CEHS

institute: Massachusetts Institute of Technology

summary: Muscles’ function as an endocrine organ is still poorly understood, but an emerging body of literature has provided evidence that myokines may aid in the development of surrounding tissues. Another outcome of muscle contraction in vivo is the localized mechanical forces produced. Current experimental techniques are not equipped to isolate and study the two effects independently. We have developed a system to culture contractile 2D optogenetic muscle long-term to provide a source for myokine secretion. We supplement our neuron monoculture with myokine secreted media and saw a 3X increase in total neurite length magnitude and a 3.2X increase in the rate of growth. As for mechanical stimulation, we optimize our Magnetic Matrix Actuation (MagMA) to provide localized stressors on the growing neurites. The mechanical stimulation regime results in a ~2.7X increase in both magnitude and rate of total neurite length. We validate our morphological findings with bulk RNA-sequencing analysis, the results show a large number of differentially expressed genes between the biochemical stimulation group and control. On the other hand, there was minimal difference between the mechanical stimulation group and control. Our study mechanistically unravels how repeated muscle contraction, or exercise, regulates motor neuron growth and maturation.

overall_design: HBG3 mESC neuron monoculture spheroids on day 8 of differentiation plated onto five different conditions. MC1-4 are magnetic controls, they contain the magnetically controlled silicone array but was never dynamically actuated. M1-4 consisted of are magnetically actuated samples. As for the biochemical stimulation portion, samples S1-6 were supplemented with myokine-infused media from optically stimulated muscle for 30 minutes at 1 Hz. The NE1-6 samples were infused with media that sat on the optogenetic muscle monolayer for 30 minutes, but it was not stimulated. C1-6 are the biological controls.

first: Bu

last: Angel

first: Raman

last: Ritu


title: Dose escalation of Wnt stimulation during the exit from pluripotency identifies tranilast as a small molecule regulator of cardiac mesoderm differentiation (RNA-Seq)

status: Public on Jan 19 2024

city: Birsbane

first: Nathan

middle: J.

last: Palpant

state: QLD

address: 306 Carmody Road

country: Australia

institute: University of Queensland

summary: Wnt signalling is a critical determinant of cell lineage development. This study used Wnt dose-dependent induction programs to gain insights into molecular regulation of stem cell differentiation. We performed single cell RNA-sequencing of cells responding to a dose-escalation protocol with Wnt agonist CHIR-99021 during the exit from pluripotency to identify cell types and genetic activity driven by Wnt stimulation. Results of activated gene sets and cell types were then used to build a multiple regression model that predicts the efficiency of cardiomyocyte differentiation. Cross-referencing Wnt-associated gene expression profiles to the Connectivity Map database, we identified a novel property of the small molecule drug, tranilast. We found that tranilast synergistically activates Wnt signalling to promote cardiac lineage differentiation which we validate in vitro and in vivo. Our study provides an integrated workflow that links experimental datasets, prediction models and small molecule databases to identify novel drug-like compounds that control cell differentiation.

overall_design: WTC-11 cells differentiated under different conditions were harvested for bulk RNA-seq on day 2. We then performed differential gene expression and gene ontology analysis to understand the mechanisms of tranilast on the regulation of cardiomyocyte differentiation.


title: An immune-inducible trihelix transcription factor suppresses bacterial resistance in Arabidopsis thaliana

status: Public on Feb 18 2024

city: Kyoto

first: Akira

last: Mine

state: Kyoto

address: Kitashirakawaoiwake-cho

department: Graduate School of Agriculture

country: Japan

institute: Kyoto university

summary: The plant innate immunity consists of the two interconnected mechanisms, pattern-triggered immunity (PTI) and effector-triggered immunity (ETI). Although much is known about how plants trigger immune responses upon pathogen recognition, the genetic program by which plants avoid an overshoot in pathogen-triggered immune responses remains largely unknown. Here, we discovered a trihelix transcription factor, GT-3a, as an immune-inducible negative regulator of bacterial resistance in Arabidopsis thaliana. Analysis of public RNA-seq data revealed that GT-3a is specifically induced by ETI activation not by PTI activation. Overexpression of GT-3a suppressed resistance against the bacterial pathogen Pseudomonas syringae pv. tomato DC3000 (Pto) and Pto-elicited expression of salicylic acid (SA)-responsive genes. Our results suggest that transcriptional induction of GT-3a circumvents the overshooting of SA-mediated defense responses during ETI.

overall_design:
We transformed Arabidopsis thaliana Col-0 (CS60000) to generate transgenic lines that express C-terminally GFP-fused GT-3a transcription factor under the control of cauliflower mosaic virus 35S promoter.
Col-0 and a selected transgenic line (GT3a-OE)  were grown on soil in a growth chamber at 22 °C and 60% relative humidity with a 10/14 hours light/dark cycle.
Leaves of 4- to 5-week-old Col-0  and GT3a-OE line were infiltrated with Pseudomonas syringae pv. tomato DC3000 (Pto) at OD600 0.001 using a needleless syringe. The infiltrated leaves were harvested 24 hours after infiltration.
To generate three biological replicates, three independent experimental trials were carried out.

first: Yuka

last: Sakata


title: Rapid and Functional Quantitative Interrogation of Human Enhancer Variants in Live Mice

status: Public on Jan 18 2024

city: Irvine

first: Evgeny

last: Kvon

state: CA

address: 4310 McGaugh Hall

department: Developmental and Cell Biology

institute: University of California, Irvine

summary: Functional characterisation of noncoding variants linked to human congenital disorders remains challenging due to the lack of efficient in vivo models. Here we introduce dual-enSERT, a robust two-color fluorescent reporter system which enables rapid comparative assessment of human enhancer variant activities in live mice. We use this new technology to examine the gain- and loss-of-function effects of enhancer variants previously linked to limb polydactyly, autism, and craniofacial malformation. By combining dual-enSERT with single-cell transcriptomics, we characterize variant enhancer allele activity at cellular resolution, revealing candidate molecular pathways implicated in pathogenic enhancer misregulation. We also use dual-enSERT to show that independent polydactyly-linked enhancer variants lead to ectopic expression in the same cell populations, indicating shared genetic mechanisms underlying noncoding variant pathogenesis. Finally, we streamline dual-enSERT for F0 analysis by placing both reporters on the same allele separated by an insulator. Our F0 dual-enSERT cuts the experimental time of noncoding variant selection to corresponding comparative in vivo activity in live embryos from three months to two weeks.

overall_design: Hindlimbs of two E11.5 transgenic embryos with two ZRS-reporters from dual-enSERT-1 and dual-enSERT-2 were independently dissected, dissociated into single cells, and scRNA-seq was performed.

first: Ethan

middle: W

last: Hollingsworth

middle: Z


title: Granulocytic myeloid-derived suppressor cell activity during biofilm infection is regulated by a glycolysis-HIF-1α axis II

status: Public on Feb 08 2024

summary: Staphylococcus aureus is a leading cause of biofilm-associated prosthetic joint infection (PJI). A primary contributor to infection chronicity is an expansion of granulocytic myeloid-derived suppressor cells (G-MDSCs) that are critical for orchestrating the anti-inflammatory biofilm milieu. Single-cell sequencing and bioinformatic metabolic algorithms were used to explore the link between G-MDSC metabolism and S. aureus PJI outcome. Glycolysis and the hypoxic response through hypoxia-inducible factor-1 alpha (HIF-1α) were significantly enriched in G-MDSCs. Interfering with both pathways in vivo, using a 2-deoxyglucose nanopreparation and granulocyte-targeted HIF-1α conditional knockout mice, respectively, attenuated G-MDSC-mediated immunosuppression and reduced bacterial burden in a mouse model of S. aureus PJI. In addition, scRNA-seq analysis of granulocytes from PJI patients also showed an enrichment in glycolysis and hypoxic response genes. These findings support the importance of a glycolysis/HIF-1α axis in promoting G-MDSC anti-inflammatory activity and biofilm persistence during PJI.

overall_design: Cells were collected from the blood and periprosthetic soft tissue of human subjects with prosthetic joint infection by FACS and prepared for single-cell sequencing using the 10X Genomics platform.

first: Chris

last: Horn

first: Prabhakar

last: Arumugam

first: Cortney

last: Heim

first: Tammy

last: Kielian


title: Extracellular Vesicle and Particle miRNAs in Maternal Plasma

status: Public on Jan 31 2024

city: Lebanon

first: Caitlin

middle: G

last: Howe

state: NH

address: 1 Medical Center Dr

department: Epidemiology

institute: Geisel School of Medicine at Dartmouth

summary: EVP miRNAs levels were measured in 54 plasma samples collected approximately 24-28 weeks gestation from individuals in New Hampshire using the NanoString nCounter Human v3 miRNA expression panel

overall_design: 54 plasma samples


title: Short-chain fatty acids propionate and butyrate control growth and differentiation linked to cellular metabolism [RNA-Seq]

status: Public on Jan 10 2024

city: Palo Alto

first: Michael

last: Nshanian

institute: Stanford University

summary: The short-chain fatty acids (SCFA) propionate and butyrate are produced in large amounts by microbial metabolism and have been identified as unique acyl lysine histone marks. In order to better understand the function of these modifications we used ChIP-Seq to map the genome-wide location of four short-chain acyl histone marks H3K18pr/bu and H4K12pr/bu in treated and untreated colorectal cancer (CRC) and normal cells, as well as in mouse intestines in vivo. We correlate these marks with open chromatin regions along with gene expression to access the function of the target regions. Our data demonstrate that propionate and butyrate act as promoters of growth, differentiation as well as ion transport. We propose a mechanism involving direct modification of specific genomic regions, resulting in increased chromatin accessibility, and in case of butyrate, opposing effects on the proliferation of normal versus CRC cells.

overall_design: Multiomic profiling (ChIP/ATAC/RNA-seq and CUT&Tag) was performed on short-chain fatty acids propionate and butyrate in colorectal cancer (CRC) and normal cell lines (SW480, CCD841, CT26) and on dietary fiber-supplemented (5% arabinoxylan) mouse intestines to determine their regulatory function. Cells were treated with 0 - 10 mM sodium propionate or sodium butyrate overnight and next-generation sequencing libraries were prepared according to individual sequencing type protocols. N = 2 experimental replicates were prepared per condition/IP for each histone mark and the corresponding control in ChIP-seq and CUT&Tag, plus n = 2 input for ChIP-seq. Tissues from two male CETP-ApoB-100 transgenic mice procured from Taconic Biosciences (New York, USA) were used per condition. N = 3 experimental replicates were prepared for ATAC/RNA-seq in SW480 cells. N = 4 experimental replicates were prepared for ATAC-seq in CT26 cells. For ChIP-seq and CUT&Tag genome-wide profiling of propionyl and butyryal histone marks in cells and in vivo, corresponding acetyl marks were used as controls for differential binding analysis. For ATAC/RNA-seq on treated cells (1 or 10 mM for propionate and butyrate, respectively) untreated (0 mM) conditions were used as controls. Next-generation sequencing was performed on Illumina HiSeq 4000 and NovaSeq 6000 SP platforms using paired-end, single index sequencing. Raw data was then analyzed for differential binding and accessibility, pathway and motif enrichment and differential expression to gain insight into the regulatory role of SCFA in the gut epithelium in the context of CRC and normal cells, as well as in relation to dietary fiber supplementation in vivo.

first: Benjamin

last: Geller

first: Joshua

last: Gruber

first: Faye

last: Chleilat

first: Jeannie

middle: M

last: Camarillo

first: Neil

middle: L

last: Kelleher

first: Yingming

last: Zhao

middle: P

last: Snyder


title: Targeting BRD4 Ameliorates Experimental Emphysema Via Suppressing both M1 and M2 alveolar macrophage polarization-1

status: Public on Jan 09 2024

city: Shenzhen

first: Difei

last: Li

address: No. 1017, Dongmen North Road, Luohu District

institute: Shenzhen People's Hospital

summary: BRD4 inhibition suppressed M2 macrophage polarization. Particularly, we deeply investigated the underlying molecular mechanism of how BRD4 regulate M2 genes expression. And finished this RNA-seq

overall_design: To investigate BRD4 inhibitors and degraders effect on the IL-4 induced M2 alveolar macrophage transcriptome, we finished the RNA-seq experiment.

first: Xing

last: Shi


title: Targeting BRD4 Ameliorates Experimental Emphysema Via Suppressing both M1 and M2 alveolar macrophage polarization-1[RNA-seq]

summary: BRD4 inhibition suppressed M1 macrophage polarization. Particularly, we deeply investigated the underlying molecular mechanism of how BRD4 regulate M1 genes expression. And finished this RNA-seq

overall_design: To investigate BRD4 inhibitors and degraders effect on the LPS/IFN-y induced M1 aveolar macrophage transcriptome, we finished the RNA-seq experiment.


title: Short-chain fatty acids propionate and butyrate control growth and differentiation linked to cellular metabolism [ChIP-Seq]


title: Targeting BRD4 Ameliorates Experimental Emphysema Via Suppressing both M1 and M2 alveolar macrophage polarization-3 [CUT&TAG]

summary: BRD4 inhibition suppressed M2 macrophage polarization. Particularly, we deeply investigated the underlying molecular mechanism of how BRD4 epigenetically regulate M2 genes expression. And finished the cut&tag experiment using BRD4, H3K27ac, IRF4 as antibody to find out the binding sites change in M2 macrophage treated with ARV825.

overall_design: To investigate BRD4 degraders effect on the binding sites change of BRD4, H3K27ac, IRF4 in IL-4 induced M2 aveolar macrophage , we finished the RNA-seq experiment.

first: Li

last: Difei

first: Shi

last: Xing


title: Short-chain fatty acids propionate and butyrate control growth and differentiation linked to cellular metabolism [CUT&Tag]


title: Characteristics and expression of lncRNA in Drosophila aneuploidy

status: Public on Jan 02 2024

city: Beijing

first: Lin

last: Sun

address: Xinjiekouwai Street

institute: Beijing Normal University

summary: Aneuploidy variation can widely affect the expression of the whole genome, which is detrimental to organisms.Long noncoding RNAs (lncRNAs) are defined as RNAs that are longer than 200 nucleotides and lack a significant open reading frame.Although only a few lncRNAs have been well described, and most of them are still functionally unknown, there is sufficient evidence that lncRNAs have important cellular functions.We provide a comprehensive description of the characteristics and expression profiles of lncRNAs in aneuploid Drosophila. It is found that lncRNAs are sensitive to aneuploidy.Several lncRNAs were investigated for their expression patterns during embryogenesis by fluorescence in situ hybridization.Our results suggest that lncRNAs are affected by genomic imbalance.

overall_design: Comapare the global expression of trisomy 2L, metafemale and wildtype Drosophila.


title: Ribosome profiling reveals conserved guanosine residues at ribosome pausing sites in Bacillus subtilis [Ribo-seq]

status: Public on Jan 01 2024

city: Amsterdam

first: Yaozu

last: Han

address: Science Park 904

country: Netherlands

institute: Unversity Of Amsterdam

summary: Ribosome pausing slows down translation and can affect protein synthesis. Improving translation efficiency can therefore be of commercial value. Here, we investigated the occurrence of ribosome pausing during amylase secretion by the industrial production organism Bacillus subtilis under semi fed-batch fermentation conditions. We first assessed our ribosome profiling setup by inducing ribosome stalling at isoleucine codons using the antibiotic mupirocin, and found a pause preference for isoleucine codons preceded by E and P site codons with guanosine residues in their first nucleotide position. Interestingly, when we applied standard ribosomal profiling conditions we found again an enrichment of guanosine residues in the E and P site of ribosome pause sites, but this time also upstream of the ribosome pause site. This sequence motif deviates from previously described ribosome pausing motifs. For the highly expressed amylase gene amyM several strong ribosome pausing sites were detected, which remained present during the 64-hour long fermentation, and were neither related to rare codons nor to secondary protein structures. When surveying the genome, an interesting finding was the presence of strong ribosome pausing sites in several toxins genes. These potential ribosome stall sites may function in preventing inadvertent activity in the cytosol.

overall_design: To analyze ribosome pausing in B. subtilis under repeated batch conditions, a simple fermentation setup was established by using rich medium to which 1% glucose was added after 16, 40 and 64 h. The culture was grown at 30 °C under continuous shaking, resulting in an OD600 of around 28 units after 64 h (Fig. 1). B. subtilis strain BY212 was used for amyM expression.

first: Biwen

last: Wang

first: Alberto

last: Agnolin

first: Gaurav

last: Dugar

first: Frans

last: Klis

first: Christopher

last: Sauer

first: Paul

middle: I

last: Costea

first: Max

middle: F

last: Felle

first: Mathis

last: Appelbaum

first: Leendert

last: Hamoen


title: Short-chain fatty acid metabolites propionate and butyrate are unique epigenetic regulatory elements linking diet, metabolism and gene expression

first: Michael

last: Nshanian


title: Ribosome profiling reveals conserved guanosine residues at ribosome pausing sites in Bacillus subtilis [RNA-seq]


title: Analysis of mouse antigen specific germinal centre B cell subset gene signatures in presence and absence of kidney disease during T dependent immunization

city: Wexford

first: PARTHA

middle: SARATHI

last: BISWAS

state: PA

address: 103 Blue Heron Dr

department: Medicine

institute: University of Pittsburgh

summary: Wild type or Aristolochic acid (AAI) nephropathy (AAN) mice were immunized with NP-KLH in Alum (100ug/mouse) On day 12  post-immunization, live NP-GcB cells were FACS-sorted from spleen according to B220+ GL7+ CD95+ NP+  expression directly into SmartSeq low-input RNA kit lysis buffer

overall_design: Intra-peritoneal AAI (7.5mg/kg body wt) induce AAN, on day 4 of AAN, mouse immunized with NP-KLH, on day 12 post-immunization, mice sacrificed for spleen harvest

first: Doureradjou

last: Peroumal

first: Chetan

last: Jawale

first: Partha

last: Biswas


title: Ribosome profiling reveals conserved guanosine residues at ribosome pausing sites in Bacillus subtilis


title: Spatial tumor immune heterogeneity facilitates subtype co-existence and therapy response via AP1 dichotomy in pancreatic cancer [RNA-seq]

status: Public on Dec 31 2023

city: Göttingen

first: Shiv

middle: K.

last: Singh

address: Robert-Koch-Straße 40

department: Gastroenterology, GI-Oncology and Endocrinology

institute: University Medical Center Göttingen

summary: Pancreatic ductal adenocarcinoma (PDAC) displays a high degree of spatial subtype heterogeneity. This intratumoral co-existence of classical and basal-like programs is evident in multi-scale transcriptomic and spatial analyses of resected, advanced-stage and chemotherapy-treated specimens and reciprocally linked to a diverse stromal immune microenvironment as well as worse clinical outcome. However, the underlying mechanisms of intratumoral subtype heterogeneity remain largely unclear. Here, by combining preclinical models, multi-center clinical, bulk and compartment-specific transcriptomic, proteomic, and bioimaging data from human specimens, we identified an interplay between neoplastic intrinsic AP1 transcription factor dichotomy and extrinsic CD68+ macrophages as a driver of intratumoral subtype co-existence along with an immunosuppressive tumor microenvironment with T cell exclusion. Our ATAC , ChIP-, and RNA-seq analyses revealed that JUNB/AP1- and HDAC-mediated epigenetic programs repress pro-inflammatory immune signatures in tumor cells, antagonizing cJUN/AP1 signaling to favor a therapy-responsive classical neoplastic identity. Through the tumor microenvironment, this dichotomous regulation was further amplified via regional macrophage populations. Moreover, CD68+/TNF-α+ cells associated with a reactive phenotype and reduced CD8+ T cell infiltration in human PDAC tumors. Consequently, combined anti-TNF-α immunotherapy and chemotherapy resulted in reduced macrophage counts and promoted CD3+/CD8+ T cell infiltration in basal-like PDAC, leading to improved survival in preclinical murine models. We conclude that tumor cell intrinsic epigenetic programs, together with extrinsic microenvironmental cues, facilitate intratumoral subtype heterogeneity and disease progression.

overall_design: To investigate the regulatory role of the JUNB/AP1 transcription factor in maintaining classical PDAC identity, we depleted JUNB in the established classical CAPAN1 cell line by siRNA. Further, the same CAPAN1 cell line was orthotopically implanted into the pancreas of nude mice and treated for three weeks with the cytokine TNF-alpha, in order to determine the potential effects of this treatment on inducing changes in the subtype identity and composition of the tumor microenvironment.


title: Histone N-tails modulate sequence-specific positioning of nucleosomes

status: Public on Jan 03 2024

city: Frederick

first: Wilfried

middle: Marie Francis

last: Guiblet

state: MD

address: 8560 Progress Drive

institute: Frederick National Laboratory for Cancer Research

summary: The precise mechanisms governing sequence-dependent positioning of nucleosomes on DNA remain unknown in detail. Existing algorithms, taking into account the sequence-dependent deformability of DNA and its interactions with the histone globular domains, predict rotational setting of only 65% of human nucleosomes mapped in vivo. To uncover novel factors responsible for the nucleosome positioning, we analyzed potential involvement of the histone N-tails in this process. To this aim, we reconstituted the H2A/H4 N-tailless nucleosomes on human BRCA1 DNA (~100 kb) and compared their positions and sequences with those of the wild-type nucleosomes. In the case of H2A tailless nucleosomes, the AT content of DNA sequences is changed locally at superhelical location (SHL) ±4, while maintaining the same rotational setting as their wild-type counterparts. Conversely, the H4 tailless nucleosomes display widespread changes of the AT content near SHL ±1 and SHL ±2, where the H4 N-tails interact with DNA. Furthermore, a substantial number of H4 tailless nucleosomes exhibit rotational setting opposite to that of the wild-type nucleosomes. Thus, our findings strongly suggest that the histone N-tails are operative in selection of nucleosome positions, which may have wide-ranging implications for epigenetic modulation of chromatin states.

overall_design: Reconstitution of BRCA1-TAR/YAC/BAC arrays of nucleosomes using Xenopus histone octamers with wild-type and H2A/H4 N-tailless histones.

first: Tatiana

last: Nikitina

first: Feng

last: Cui

first: Victor

last: Zhurkin


title: Chemical profiling of Jianwei Xiaoshi oral liquid and its potential mechanism of effect on high-calorie diet-induced dyspepsia in immature rats: gut flora, transcriptomics and network pharmacology

city: beijing

first: yan

last: zhang

state: Beijing

address: 16 Dongzhimen Inner South Street, Dongcheng District, Beijing

institute: China Academy of Chinese Medical Sciences

overall_design: The SD rats were divided into the control, model and high-dose group(n=4). Gene expression was detected using duodenal samples to identify the key regulatory genes for the treatment of dyspepsia with Jianwei Xiaoshi oral liquid

first: Haiyu

last: Zhao

first: Yan

last: Zhang


title: Dose escalation of Wnt stimulation during the exit from pluripotency identifies tranilast as a small molecule regulator of cardiac mesoderm differentiation

first: Nathan

last: Palpant

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

overall_design: Refer to individual Series


title: Tissue- and age-dependent gene expression signatures for ARE-Del homozygotes and heterozygotes

first: Heekyong

middle: R

last: Bae

address: Building 560, Room 31-23, NCI at Frederick

institute: National Cancer Institute

summary: Gene expression patterns specific to different tissues and ages were examined in mice with ARE-Del homozygotes and heterozygotes. The analysis covered 3, 6, and 12-week-old mice, considering samples from whole blood, kidney, spleen, and thymus. The experiments involved group sizes varying from 3 to 8 mice.

overall_design: Howard A. Young

first: Debora

last: Hodge


title: Genetic variation in IL-4 activated tissue resident macrophages alters the epigenetic state to determine strain specific synergistic responses to LPS [scATAC-seq]

status: Public on Dec 29 2023

city: Bethesda

first: Mingming

address: 9000 Rockville Pike

institute: national institutes of health

summary: IL-4 activates tissue resident macrophages (TRMs) to mediate tissue repair and clearance of nematode infections in mice, but most studies have been performed on the C57BL/6 background. The natural genetic variation between C57BL/6 and BALB/c mouse strains can result in differences in allergic responses, parasite resistance, monocyte to macrophage conversion and response to IL-4 activation. Here, we investigated in vivo IL-4 activation in TRMs of the peritoneal cavity from C57BL/6 and BALB/c mice and find that C57BL/6 TRMs are surprisingly more transcriptionally responsive to IL-4 stimulation, with greater association of induced genes with super enhancers, induced enhancers and topologically associating domains (TAD) boundaries. IL-4-directed epigenomic remodeling showed NF-κB motif enrichment only in C57BL/6 TRMs. This resulted in an enhanced synergistic response upon in vitro lipopolysaccharide (LPS) exposure in IL-4 activated C57BL/6 TRMs but not for BALB/c, despite unstimulated BALB/c TRMs having a stronger transcriptional response to LPS than C57BL/6 TRMs. Single cell RNA sequencing (scRNAseq) analysis of mixed bone marrow chimeric mice indicates that transcriptional differences between C57BL/6 and BALB/c TRMs is cell intrinsic within the same tissue environment. Hence, genetic variation alters IL-4-induced cell intrinsic epigenetic reprogramming between C57BL/6 and BALB/c TRMs to regulate the magnitude of synergistic responses to LPS exposure.

overall_design: Peritoneal cells were isolated from BL/6 and BALB/c mice alfter IL-4 treatment in vivo.

first: Katherine

last: Hornick

first: Justin

last: Lack

first: Verena

last: Link

first: Yasmine

last: Belkaid

first: Dragana

last: Jankovic

first: P’ng

last: Loke


title: Genetic variation in IL-4 activated tissue resident macrophages alters the epigenetic state to determine strain specific synergistic responses to LPS [scRNA-seq]

overall_design: Peritoneal cells were isolated from CB6F1/J (Jax no. 100007) mice alfter IL-4 treatment in vivo.


title: PI-5-P links the Hippo Pathway and PI5P4K signaling

city: La Jolla

first: Brooke

middle: M.

last: Emerling

address: 10901 North Torrey Pines Road

department: Cell and Molecular Biology of Cancer Program

institute: Sanford Burnham Prebys Medical Discovery Institute

summary: The phosphoinositide PI-5-P is a signaling lipid that mediates cellular responses to oxidative stress and DNA damage, however it is unclear how PI-5-P participates in these processes. Intracellular pools of PI-5-P are regulated by PI5P-Kinases (PI5P4Ks), but how PI5P4K activity is controlled has also remained elusive. Here, we used an unbiased screen to discover the core Hippo pathway kinases MST1/2 phosphorylate and inhibit PI5P4K signaling in vitro and in cells. We further show PI5P4Ks regulate several Hippo/YAP-related phenotypes in human cells, such as the interaction between the key Hippo proteins MOB1-LATS, and the genetic program governing epithelial-to-mesenchymal transition. Mechanistically, we show that MOB1 binds PI-5-P with high specificity and potency, providing a signaling connection between the Hippo Pathway and PI5P4Ks. These discoveries shed new light on how these two important evolutionary conserved signaling pathways are integrated to regulate metazoan development and human disease.

overall_design: Transcriptomics comparison of SCRin control versus ⍺-/-;βin MCF10A epithelial cells by RNA-seq

first: Lavinia

last: Palamiuc

first: Ryan

last: Loughran


title: Genetic variation in IL-4 activated tissue resident macrophages alters the epigenetic state to determine strain specific synergistic responses to LPS [RNA-seq]

overall_design: RNA-seq was performed after IL4, H. polygyrus or LPS treatment in Bl/6 and BALB/c mice.  Two or three replicates for each samples


title: RNA-seq in neurites and soma of primary hippocampal neurons isolated from P0 or P1 mice

status: Public on Jan 16 2024

city: Montreal

first: Celia

last: Alecki

state: QC

address: McIntyre Medical Sciences Building 3655 promenade Sir-William-Osler

institute: McGill University

summary: RNA-seq data on primary neurons isolated from P0 or P1 mice pups after stress using MG132 or under control conditions

overall_design: Neurons after 17 or 18 days of culture in vitro were stressed using 10 uM of MG132 for 7H. Soma and neurites were isolated and RNA were extracted from each compartment. Single-end RNA sequencing was performed.

first: Célia

first: Suleima

last: Jacob-Tomas

first: Maria

last: Vera


title: Short-chain fatty acids propionate and butyrate control growth and differentiation linked to cellular metabolism [ATAC-Seq]

first: Michael

last: Nshanian

overall_design: Multiomic profiling (ChIP/ATAC/RNA-seq and CUT&Tag) was performed on short-chain fatty acids propionate and butyrate in colorectal cancer (CRC) and normal cell lines (SW480, CCD841, CT26) and on dietary fiber-supplemented (5% arabinoxylan) mouse intestines to determine their regulatory function. Cells were treated with 0 - 10 mM sodium propionate or sodium butyrate overnight and next-generation sequencing libraries were prepared according to individual sequencing type protocols. N = 2 experimental replicates were prepared per condition/IP for each histone mark and the corresponding control in ChIP-seq and CUT&Tag, plus n = 2 input for ChIP-seq. Tissues from two male CETP-ApoB-100 transgenic mice procured from Taconic Biosciences (New York, USA) were used per condition. N = 3 experimental replicates were prepared for ATAC/RNA-seq in SW480 cells. N = 4 experimental replicates were prepared for ATAC-seq in CT26 cells. For ChIP-seq and CUT&Tag genome-wide profiling of propionyl and butyryal histone marks in cells and in vivo, corresponding acetyl marks were used as controls for differential binding analysis. For ATAC/RNA-seq on treated cells (1 or 10 mM for propionate and butyrate, respectively) untreated (0 mM) conditions were used as controls. Next-generation sequencing was performed on Illumina HiSeq 4000 and NovaSeq 6000 SP platforms using paired-end, single index sequencing. Raw data was then analyzed for differential binding and accessibility, pathway and motif enrichment and differential expression to gain insight into the regulatory role of SCFA in the gut epithelium in the context of CRC and normal cells, as well as in relation to dietary fiber supplementation in vivo.

first: Benjamin

last: Geller

first: Joshua

last: Gruber

first: Faye

last: Chleilat

first: Jeannie

last: Camarillo

first: Neil

last: Kelleher

first: Yingming

last: Zhao

last: Snyder


title: Genetic variation in IL-4 activated tissue resident macrophages alters the epigenetic state to determine strain specific synergistic responses to LPS [ChIP-seq]

first: Mingming

overall_design: ChIP-seq was performed on 4 samples, utilizing H3K27ac antibodies.  Two replicates for each samples

first: Katherine

last: Hornick

first: Justin

last: Lack

first: Verena

last: Link

first: Yasmine

last: Belkaid


title: Genetic variation in IL-4 activated tissue resident macrophages alters the epigenetic state to determine strain specific synergistic responses to LPS [Hi-C]

overall_design: Hi-C was performed on isolated tissue resident macrophages alter IL-4 treatment in vivo.

first: Dragana

last: Jankovic

first: P’ng

last: Loke


title: Comprehensive analysis of bioinformatics and system biology reveals the association between Girdin and hepatocellular carcinoma

status: Public on Dec 25 2023

city: chengdu

first: Tengda

last: Huang

state: Sichuan

address: gaopeng road

department: West China Hospital

institute: Sichuan University

summary: Introduction: Hepatocellular carcinoma stands as the most common cause of global cancer-related mortality. The actin-binding protein Girdin exhibits elevated expression in diverse tumors, fostering tumorigenesis and progression. Nevertheless, the precise mechanism by which Girdin regulates liver cancer remains elusive. Methods: This study comprehensively analyzed the expression level of Girdin in liver cancer and adjacent tissue, along with the correlation between Girdin expression and the clinical characteristics and prognosis of liver cancer. The analysis involved the integration of data from The Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO), Clinical Proteomic Tumor Analysis Consortium (CPTAC) database, and immunohistochemistry. Subsequently, the expression level of Girdin was knocked down to elucidate its role in the progression of liver cancer. Transcriptome sequencing was employed to investigate the mechanistic underpinnings of Girdin's regulatory impact on liver cancer. Additionally, the Comparative Toxicogenomics Database (CTD) was utilized to identify potential drugs or molecules for liver cancer treatment. Results: The findings revealed elevated Girdin expression in liver cancer tissues, and heightened Girdin expression correlated with adverse clinical features and prognosis. Silencing of Girdin markedly impeded the proliferation and migration of hepatocellular carcinoma cells. Moreover, transcriptome sequencing demonstrated that silencing Girdin led to differential expression of 176 genes and inhibition of the PI3K/Akt signaling pathway. Ultimately, we propose that Imatinib Mesylate, Orantinib, Resveratrol, Sorafenib, and Curcumin mayinteract with Girdin, potentially contributing to the treatment of liver cancer. Conclusion: This study reveals the association between Girdin and hepatocellular carcinoma, providing novel clues for future research and treatment of hepatocellular carcinoma.

overall_design: HepG2 cells were divided into 2 groups, including the negative control group (si-NC) and the si-Girdin group. RNA-seq was conducted.

first: Hongying

last: Chen

first: Hongyuan

last: Pan

first: Tian

last: Wu

first: Xiangyi

last: Ren

first: Liwen

last: Qin

first: Kefei

last: Yuan

first: Fang

last: He


title: Next Generation Sequencing Facilitates Analysis of Penfluridol Treatment and Control SamplesTranscriptomes

city: Shanghai

first: Song

middle: Ling

last: yi

address: Xuhui

institute: Lingyi Song

summary: Endometrial cancer (EC) is the most common cancer of the female reproductive tract and one of the few cancers for which survival has not substantially improved since the mid-1970s, reflecting few advances in treatment. The main therapeutic method of EC is surgical therapy assisted with radiotherapy and chemotherapy at present. Progesterone is the first-line drug for conservative treatment, but it faces the challenge of drug resistance and is ineffective for type II EC. There is an urgent clinical need to find new therapeutic targets and candidate drugs. Repurposing of existing drugs is a good strategy to discover new candidate drugs. Herein, 33 antipsychotics in our drug library were screened and penfluridol (PFD) was found to exhibit excelent anti-EC activity. Then the molecular target of PFD was revealed as the GTP-binding protein Septin7 using activity-based protein profiling (ABPP) techniques. Septin7 functioned as a tumor suppressor in EC and PFD exhibited weaker anticancer properties in Septin7 knockdown EC cells, indicating that Septin7 is essential for PFD biological activity. Notably, our investigations of PFD mechanism suggested that PFD binding with Septin7 inhibited the interaction of Septin7 with microtubules, thereby inhibiting microtubule polymerization and arresting the cell cycle in G1 phase. In addition, RNA-seq analysis and western blot showed that PFD could induce cell apoptosis by regulating Septin7-PIK3CA-AKT-Caspase3 pathway. Finally, PFD displayed significant in vivo antitumor efficacy in KLE endometrial cancer xenograft models without causing obvious side effects. Taken together, our findings revealed new target and mechanistic insights in EC therapeutic strategy and offer a potential candidate for the treatment of EC, especially progesterone resistance EC.

overall_design: Examination of Penfluridol treatment and control samples in ISK cells by RNA-seq, in triplicate.

first: Lingyi

last: Song

first: Huiwen

first: Xiao

last: Sun

first: Jian

last: Li

first: Fei

last: Mao


title: Alleviation of monocyte exhaustion by BCG derivative mycolic acid

status: Public on Dec 19 2023

city: Blacksburg

first: Blake

middle: Alexander

last: Caldwell

state: VA

address: 149 Life Sciences I Building, 970 Washington Street SW

department: Biological Sciences

institute: Virginia Tech

summary: Monocyte exhaustion characterized by sustained pathogenic inflammatory and immune-suppressive features underlies the pathogenesis of sepsis induced by systemic polymicrobial infections.  However, effective strategies in blocking monocyte exhaustion and restoring innate homeostasis are currently not available. In this study, we found that Methoxy-Mycolic Acid (M-MA), a branched mycolic acid derived from Mycobacterium Bovis Bacillus Calmette–Guérin (BCG), to be a potent agent in alleviating monocyte exhaustion and restoring immune homeostasis. Co-treatment of monocytes with M-MA can effectively block the expansion of exhausted Ly6Chi /CD38hi/PD-L1hi monocytes induced by repetitive LPS challenges, and restore the expression of immune-enhancing CD86 on co-treated monocytes.  Functionally, M-MA treatment restored mitochondrial functions of exhausted monocytes and alleviated their suppressive activities on co-cultured T cells. Mechanistically, M-MA exerts its protective effects independent of cellular receptor TREM2, and relieves cellular stress signaling through blocking Src-STAT1 mediated pathogenic inflammatory polarization as well as reducing the production of compensatory immune suppressors TAX1BP1 and PLAC8. Our whole genome methylation analyses further revealed that M-MA can effectively erase methylation memory of exhausted monocytes, with validated restoration of plac8 methylation by M-MA. Together, our data reveal M-MA as a potent agent in restoring monocyte homeostasis with future therapeutic potential for the treatment of sepsis.

overall_design: Genome-wide DNA methylation profiling was performed using Infinium Mouse Methylation BeadChip arrays. Based on variability observed in previous studies, a minimum of 4 biological replicates was determined to be sufficient for most BMMC culture experiments, which is sufficiently powered to detect differences in 5mC as low as 5%. All experiments were performed on at least two separate days and with mice from at least 3 separate litters.

first: Yajun

middle: A

first: Jing

last: Wang

first: Liwu


title: PUF partner interactions at a conserved interface shape the RNA binding landscape and cell fate

status: Public on Dec 22 2023

city: Madison

first: Brian

last: Carrick

state: WI

address: 433 Babcock Drive

department: Biochemistry

institute: University of Wisconsin-Madison

summary: Protein-RNA regulatory networks underpin much of biology. C. elegans FBF-2, a PUF RNA-binding protein, binds over 1000 RNAs to govern stem cells and differentiation. FBF-2 interacts with multiple protein partners via a key tyrosine, Y479. Here we investigate the in vivo significance of partnerships using a Y479A mutant. Y479A occupancy increases or decreases at specific sites across the transcriptome, varying with the RNA, and shifts from 3’UTRs to other regions. Germline development also changes in a very specific fashion: Y479A abolishes one FBF-2 function – the sperm to oocyte cell fate switch. Y479A changes to regulation of one mRNA, gld-1, are critical to this fate change, though other network changes are also important. FBF-2 switches from repression to activation of gld-1 RNA, likely by distinct FBF-2 partnerships. The role of partnerships in governing RNA regulatory networks will extend broadly, including for human health and disease, as protein partnerships pervade RNA control.

overall_design: Enhanced crosslinking and immunoprecipitation (eCLIP) followed by sequencing was used to determine the occupancy of wild-type FBF-2 and FBF-2(Y479A) on RNA targets in the germline of C. elegans. 4  biological replicates of each genotype were obtained (IP samples) as well as their corresponding size-matched input control (SMI).

middle: H

first: Fan

first: Sündüz

last: Keleş

first: Marvin

last: Wickens

first: Judith

last: Kimble


title: Centrosomal Localization of DNAJ-PKAc Fusion Heightens PLK1 Inhibitor Sensitivity in Fibrolamellar Cancer

city: Seattle

first: Taran

last: Gujral

state: WA

address: 1100 Fairview Ave N

institute: Fred Hutch Cancer Center

summary: Fibrolamellar carcinoma (FLC), a rare and fatal liver cancer lacking effective drug therapy, is driven by the DNAJ-PKAc fusion oncoprotein. However, the underlying mechanism of DNAJ-PKAc's role in FLC tumor growth remains enigmatic. Employing an unbiased systems-based approach, we uncovered a new role of DNAJ-PKAc oncoprotein in FLC and identified downstream kinases involved in this process. Functional screening, coupled with computational analysis, highlighted Polo-like kinase 1 (PLK1) as vital for FLC cell viability. Genetic and pharmacological PLK1 inhibition significantly reduced FLC cell growth, inducing apoptosis. Further studies showed DNAJ-PKAc's centrosomal presence and direct interaction with PLK1, revealing a novel mechanism that promotes PLK1 activation and mitotic progression. Clinical-grade PLK1 inhibitors effectively suppressed FLC tumor growth across multiple preclinical models, including patient-derived xenograft and an orthotopic model of FLC, suggesting promising therapeutic avenues. Our findings underscore the role of DNAJ-PKAc in rewiring signaling networks and highlight valuable clinical implications for PLK1-targeted therapies for FLC.

overall_design:
Bulk-RNA seq of Fibrolamellar tumors, non-tumor livers, patient-derived xenograft tumors, and cancer cells.

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Submitter states that missing raw files are due to file loss. Sample "FLC1, rep2".
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middle: S


title: Transcriptome analysis of the LPS response of BV-2 microglial cells displaying a CRISPR/Cas9-induced knockout of peroxisomal genes (Abcd1/Abcd2 or Acox1)

city: Dijon

first: Stéphane

last: Savary

address: 6 Bd Gabriel

country: France

institute: University of Bourgogne

summary: In X-linked adrenoleukodystrophy (X-ALD), the most common peroxisomal disorder, microglial defect is suggested to prime and amplify the neuroinflammatory process. By using CRISPR/Cas9 gene editing, we recently established BV-2 microglial cell models to study the impact of dysfunctional peroxisomal b-oxidation and demonstrated the emergence of a disease-associated microglial signature in these cell lines. Their transcriptomic analysis suggested consequences on immune response. To go further, we have used RNA-sequencing and functional assays related to immune response to compare the WT and mutant BV-2 cell lines in basal conditions or upon lipopolysaccharide (LPS) stimulation.

overall_design: Three genotypes were included in the study: WT BV-2 cells and 2 mutant BV-2 cells (Abcd1/Abcd2 double-deficient, Acox1-deficient). See Raas et al. 2019, PMID: 30769094 and PMID: 30312667 for the description of the mutant cell lines. Cells were incubated in the presence or absence of 1 µg/ml  LPS during 24 h.

first: Quentin

last: Raas

first: Catherine

last: Gondcaille

first: Céline

last: Keime

first: Romain

last: Kaiser


title: Gene expression by RNA-seq in purified paneth cells of WT and panetch cell specific  P55 KO mice 3 hours after TNF

status: Public on Dec 15 2023

city: Gent

first: Steven

last: Timmermans

address: Technologiepark 71

country: Belgium

institute: VIB-UGent

summary: The study of how gene expression in paneth cells changes 3 hours after TNF admistration in mice were the TNFR1 (P55) genes was deleted in paneth cells using Defa6-cre.

overall_design: To investigate the effects of TNF on paneth cell gene expression trough direct signalling via TNFR1 (P55), an RNA-seq was performed 3 hours after TNF or PBS (control) injection in P55 KO mice and P55 WT littermates

first: Charlotte

last: Wallaeys

first: Natalia

last: Garcia-Gonzalez

first: Jolien

last: Vandewalle

first: Tineke

last: Vanderhaeghen

first: Hester

last: Dufoo

first: Melanie

last: Eggermont

first: Riet

last: De Rycke

first: Serge

last: Verbanck

first: George

last: Kollias

first: Richard

last: Blumberg

first: Takao

last: Iwawaki

first: Claude

last: Libert


title: Temporal genomic analysis of melanoma rejection identifies regulators of tumor immune evasion

status: Public on Dec 12 2023

city: Stanford

first: Ansuman

middle: T

last: Satpathy

address: 240 Pasteur Drive

institute: Stanford University

overall_design: Refer to individual Series


title: Transcriptomic analysis of arginine- and leucine-starved mouse embryonic stem cells (Wild type and GCN2-deficient)

city: Martinsried

first: Assa

last: Yeroslaviz

state: Bavaria

address: Am Klopferspitz 18

department: computational Biology

institute: Max-Planck-Institute for biochemistry

summary: We analyzed the transcriptomes of Wild-type and GCN2-deficient mouse embryonic stem cells after 3h of arginine or leucine starvation.

overall_design: mRNA sequencing of Wild-type and GCN2-deficient E14 mouse embryonic stem cells after 3h of arginine or leucine starvation. Each starvation group were compared with the control group

first: Marion

last: Russier

first: Rinho

last: Kim

first: Peter

middle: J

last: Murray


title: The RNA sequencing of LSK from DIC mice

status: Public on Dec 10 2023

city: Chengdu

first: Xinyi

last: Kuang

address: No.34, Renmin South road

institute: West China Hospital of Stomatology

summary: To understand DIC-induced myeloid skewing of HSPCs, we profiled the transcriptome of LSK from DIC and control mice.

overall_design: Mice were divided into 2 groups (3 per group): DSS-induced colitis (DIC) and control. DIC mice received 2.5% DSS for 5 days. For bone marrow (BM) analysis, femurs were flushed with ice-cold PBSF and filtered to obtain a single-cell suspension. LSK (Lin- Sca1+ cKit+) cells from BM were sorted by FACS Aria II and resuspended in PBS with 0.04% BSA.

first: Xiaoyue

last: Jia

first: Xian

last: Peng

first: Xin

last: Zheng

first: Lei

last: Zhao

first: Liwei

last: Xu


title: Transcriptomic analysis of Rhipicephalus microplus hemocytes from female ticks infected with Babesia bovis or Babesia bigemina

city: Pullman

first: Massaro

middle: Wilson

last: Ueti

state: Washington

address: 3003 ADBF Washington State Univ, 3003 ADBF, Grimes Way

institute: USDA ARS Animal Disease Research Unit

summary: To understand the effect of Babesia infection on Rhipicephalus microplus hemocyte gene expression, we performed high throughput RNA-sequencing using samples collected from Rhipicephalus microplus uninfected tick hemolymph and infected with either Babesia bigemina or Babesia bovis. We evaluated gene expression differences that may be attributed to tick immune defense to babesial infection.

overall_design: Parasite mRNA isolated from 3 biological replicates for each of 1) uninfected tick hemolymph, 2) Babesia bigemina kinete stage parasites from infected tick hemolymph, and 3) Babesia bovis kinete stage parasites from infected tick hemolymph, were compared by RNAseq methodology using Illumina technology.

first: Rubikah

last: Vimonish

first: Janaina

last: Capelli-Peixoto

first: Lowell

last: Kappmeyer

middle: W


title: eIF3 Engages with 3’-UTR Termini of Highly Translated mRNAs in Neural Progenitor Cells [APA-Seq]

status: Public on Dec 08 2023

city: Berkeley

first: Marena

middle: Isabelle

last: Trinidad

address: 2151 Berkeley Way

institute: Innovative Genomics Institute

summary: Stem cell differentiation involves a global increase in protein synthesis to meet the demands of specialized cell types. However, the molecular mechanisms underlying this translational burst and the involvement of initiation factors remains largely unknown. Here, we investigate the roles of eukaryotic initiation factor 3 (eIF3) in early differentiation of human pluripotent stem cell (hPSC)-derived neural progenitor cells (NPCs). Using Quick-irCLIP and alternative polyadenylation (APA)-Seq, we show eIF3 crosslinks to many neurologically relevant mRNAs in NPCs. Our data reveal eIF3 predominantly interacts with 3’ untranslated region (3’-UTR) termini of multiple mRNA isoforms, adjacent to the poly(A) tail. High eIF3 crosslinking at 3’-UTR termini of mRNAs correlates with high translational activity, as determined by ribosome profiling. We identify the transcriptional regulator inhibitor of DNA binding 2 (ID2) mRNA as a case in which active translation levels and eIF3 crosslinking are dramatically increased upon early NPC differentiation. Furthermore, we find that eIF3 engagement at 3’-UTR ends is dependent on polyadenylation. The results presented here show that eIF3 engages with 3’-UTR termini in highly translated mRNAs, supporting a role of mRNA circularization in the mechanisms governing mRNA translation in NPCs.

overall_design:
To investigate the transcripts that eIF3 binds to in NPCs, we performed Quick-irCLIP in undifferentiated and early differentiated NPCs. We then performed alternative polyadenylation sequencing (APA-Seq) to validate our findings of eIF3 crosslinking at 3'-UTRs. Finally, we performed Ribosome profiling to determine that eIF3 crosslinking at 3'-UTRs in NPCs is correlated with high translation activity.
Grantee: Santi Mestre-Fos
Grant ID: EDUC4-12790
Funding Source: California Institute for Regenerative Medicine

first: Santi

last: Mestre-Fos

first: Lucas

last: Ferguson

first: Nicholas

last: Ingolia

first: Jamie

last: Cate


title: eIF3 Engages with 3’-UTR Termini of Highly Translated mRNAs in Neural Progenitor Cells

overall_design:
Refer to individual Series
Grantee: Santi Mestre-Fos
Grant ID: EDUC4-12790
Funding Source: California Institute for Regenerative Medicine


title: Temporal genomic analysis of melanoma rejection identifies regulators of tumor immune evasion [scc35]

first: Ansuman

last: Satpathy

summary: Decreased intra-tumor heterogeneity (ITH) correlates with increased patient survival and immunotherapy response. However, the mechanism underlying this association remains inconclusive since additional factors dictate tumor aggressiveness. Here, we study the mechanisms responsible for the immune escape of tumors bearing low ITH. We compare homogeneous, genetically similar single-cell clones that are rejected vs. non-rejected after transplantation. We followed the growth of these clone-derived tumors over time using single-cell RNA sequencing and immunophenotyping. Non-rejected clones show high infiltration of tumor-associated macrophages (TAM), increased Mif expression, lower T-cell infiltration, and increased T-cell exhaustion. Mif KO led to smaller tumors and reversed these immune phenotypes, validating its role in the growth of low ITH tumors. Mif secretion by these tumor cells causes TAM infiltration, thus contributing to an immunosuppressive environment that supports aggressive growth. We validated this result in melanoma patient data, confirming that high levels of MIF distinguish aggressive from non-aggressive ITHs.

overall_design: Live cells were sorted from tumor samples, hashed, and profiled with single-cell RNA-seq on the 10x Genomics platform.

first: Sapir

last: Cohen Shvefel

first: Joy

last: Pai

first: Yardena

last: Samuels


title: eIF3 Engages with 3’-UTR Termini of Highly Translated mRNAs in Neural Progenitor Cells [Quick-irCLIP]


title: A conserved transcriptional program for MAIT cells across mammalian evolution [Oaries_thymus_MAIT]

status: Public on Dec 04 2023

city: Paris

first: Martin

last: MESTDAGH

address: 26 rue d'ulm

institute: Institut Curie

summary: Mucosal-Associated Invariant T (MAIT) cells recognize the riboflavin pathway-derived metabolite 5-(2-oxopropylideneamino)-6-d-ribitylaminouracil (5-OP-RU) presented by the MHC-Ib molecule MR1. Both MR1 and the T cell receptor genes used by MAIT cells are under strong evolutionary pressure in mammals, suggesting an important role of 5-OP-RU-specific T cells across species. In humans and mice, MAIT cells acquire distinctive effector functions linked to the expression of the master transcription factor ZBTB16 (PLZF) during thymic development. Conservation of a unique differentiation program in 5-OP-RU-specific T cells from other species is unclear. Here, we used single-cell RNA sequencing to characterize the development of 5-OP-RU-specific T cells in 6 species spanning 110 million years of mammalian evolution. Cross-species comparative analyses revealed a conserved sequence of transcriptional events underlying the maturation of 5-OP-RU-specific thymocytes, marked by the early expression of ZBTB16 in all species. MAIT cells also co-expressed the transcription factors TBX21 (Tbet) and RORC (RORgt) in human, sheep, cattle and opossum. By contrast, Tbet and RORgt were expressed by distinct subsets of MAIT cells in the thymus of rodents, including pet mice and >30 genetically diverse mouse strains, dismissing a laboratory mouse artifact. In mice, RORgt+ MAIT cells further matured in the mesenteric lymph nodes and intestines to acquire a transcriptional program remarkably conserved in MAIT cells from non-rodent species and characterized by co-expression of type 1 and type 17 effector genes, but also genes associated with cytotoxicity and tissue repair. Thus, we define a deeply conserved transcriptional program for 5-OP-RU-specific T cells, which may help understand their functions.

first: François

last: Legoux

first: Olivier

last: Lantz

first: Yara

last: El Morr

first: Helene

last: Bugaut

last: Mestdagh


title: A conserved transcriptional program for MAIT cells across mammalian evolution [Mmusculus_MesLN_MAIT]


title: A conserved transcriptional program for MAIT cells across mammalian evolution [Mmusculus_Ileum_MAIT]


title: A conserved transcriptional program for MAIT cells across mammalian evolution [Mmusculus_Colon_MAIT]


title: A conserved transcriptional program for MAIT cells across mammalian evolution [Btaurus_thymus_MAIT]


title: A conserved transcriptional program for MAIT cells across mammalian evolution [Hsapiens_thymus_MAIT]

summary: Mucosal-Associated Invariant T (MAIT) cells recognize the riboflavin pathway-derived metabolite 5-(2-oxopropylideneamino)-6-d-ribitylaminouracil (5-OP-RU) presented by the MHC-Ib molecule MR1. Both MR1 and the T cell receptor genes used by MAIT cells are


title: A conserved transcriptional program for MAIT cells across mammalian evolution [Rnorvegicus_thymus_MAIT]


title: Shear stress promotes metabolic changes in endothelial cells

status: Public on Dec 01 2023

city: Leuven

first: Sandrine

last: Da Cruz

state: Flemish Brabant

address: ON 5 Herestraat 49

department: KU Leuven Department of Neurosciences

institute: VIB-KU Leuven Center for Brain and Disease Research

summary: Here we investigated how shear stress influences the metabolic behavior of endothelial cells (ECs) using a combination of transcriptomics, tracer metabolomics. Transcriptomics analysis of ECs under wall shear stress (WSS) showed an increase in the glutamine, asparagine, alanine, aspartate, and glutamate biochemical activity while the downregulated gene signature suggested a reduction of the glycolysis activity. Metabolomics analysis of the medium from static and WSS cultured ECs revealed that -upon WSS- changes in the nutritional preferences of ECs occurred. Using tracer metabolomics, we further evidenced that WSS promotes glutamine anaplerosis into the Krebs cycle and a decrease in the glycolytic metabolism of ECs in vitro. In conclusion, our findings elucidate the nutritional preferences of ECs and reveal the importance of a physical stimulus (WSS) in the regulation of EC metabolism in vitro.

overall_design: 4x4 design - 4 samples of HUVECs cultured under wall shear stress vs 4 samples of HUVECs cultured under static conditions

first: Max

last: Mazzone


title: A de novo Missense Mutation in PPP2R5D Alters Dopamine Pathways and Morphology of iPSC-derived Midbrain Neurons

status: Public on Nov 30 2023

city: Sacramento

first: Julian

last: Halmai

address: 2921 Stockton Blvd

department: Department of Neurology

institute: UC Davis

summary: Induced pluripotent stem cell (iPSC) models of neurodevelopmental disorders (NDDs) have promoted an understanding of commonalities and differences within or across patient populations by revealing the underlying molecular and cellular mechanisms contributing to disease pathology. Here, we focus on developing a human model for PPP2R5D-related NDD, called Jordan syndrome, which has been linked to Early-Onset Parkinson’s Disease (EOPD). This disease model includes patient-derived induced pluripotent stem cells (iPSCs) which were differentiated into neural stem cells (NSCs) and subsequently specified into a midbrain neural stem cell and neuronal state. We sought to understand the underlying molecular and cellular phenotypes across multiple cell states and neuronal subtypes in order to gain insight into Jordan syndrome pathology. Our work revealed that iPSC-derived midbrain neurons from Jordan syndrome patients display significant differences in dopamine-associated pathways and neuronal architecture.

overall_design: To develop a better understanding of the molecular consequence of mutant PPP2R5D pathology, RNA sequencing was performed across the four cell states of our disease model (iPSC, NSC, midbrain NSC and midbrain neuron) for isogenic and PPP2R5D E198K lines.

first: Jasmine

last: Carter

first: Kyle

last: Fink


title: A conserved transcriptional program for MAIT cells across mammalian evolution [Mdomestica_thymus_MAIT]


title: Gene expression by RNA-seq in purified paneth cells in antibiotics microbiome depleded mice

first: Steven

last: Timmermans

summary: The study of how gene expression in paneth cells changes after TNF admistration in mice were the microbiome has been depleted with broad spectrum antibiotics. The depletion of the microbiome excludes the occurence of indirect effects mediated through it by TNF on PC gene expression, only direct TNF effecs on crypt cells are measured

overall_design: To investigate the effects of TNF on PCs  without microbiome, PCs were purified from mice treated with antibiotics for 2 weeks and treated with 1µg/g TNF or PBS (control) by IP injection for 3 hours. A total of 4 biological replicates were used for each condition for a total of 8 samples

first: Charlotte

last: Wallaeys

first: Natalia

last: Garcia-Gonzalez

first: Jolien

last: Vandewalle

first: Tineke

last: Vanderhaeghen

first: Hester

last: Dufoo

first: Melanie

last: Eggermont

first: Riet

last: De Rycke

first: Serge

last: Verbanck

first: George

last: Kollias

first: Richard

last: Blumberg

first: Takao

last: Iwawaki

first: Claude

last: Libert


title: The cardioprotective effect of electrolyte solution Ringerfundin and a possible underlying mechanism

status: Public on Nov 16 2023

city: shanghai

first: min

last: chen

address: dongfang road 1678

institute: Shanghai children's Medical Center

summary: In order to study the protective effect of regardine on myocardial infarction, we injected regardine and physiological saline 1 hour before acute myocardial infarction, performed RNA seq, and compared their gene differential expression with each other, and compared them with the sham operation group.

overall_design: RNA-seq

first: Min

last: Chen


title: Multiomic analysis reveals cellular and epigenetic plasticity in intestinal pouches of ulcerative colitis patients

status: Public on Nov 15 2023

city: Chicago

first: Yu

last: Zhao

state: IL

address: 5841 S. Maryland Ave

department: Section of Genetic Medicine, Department of Medicine

institute: The University of Chicago

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


title: A conserved transcriptional program for MAIT cells across mammalian evolution

first: Martin

last: MESTDAGH

sample_organism:
Homo sapiens
Bos taurus
Ovis aries
Mus musculus
Rattus norvegicus
Monodelphis domestica


title: Multiomic analysis reveals cellular and epigenetic plasticity in intestinal pouches of ulcerative colitis patients [scRNA-seq]

summary: Total proctocolectomy with ileal pouch anal anastomosis (IPAA) is the standard treatment for patients with severe treatment resistant ulcerative colitis (UC). Despite significant improvements in patient outcomes, up to 50% of patients will develop inflammation of the pouch (pouchitis) within 1-2 years following surgery. The pathogenesis of pouchitis is not well understood. Functionalization of UC pouches is associated with histological changes, whether these reflect changes in cellular identity and metaplasia remains unclear. To address this question, we generated cellular atlases of single-cell transcriptomes and accessible chromatin to assess the cellular composition, transcriptomic and epigenetic profiles in UC pouches.

overall_design: We obtained scRNA-seq and scATAC-seq data from paired biopsy samples from the ileal pouch and ileal segment above the pouch (prepouch) of UC-IPAA patients (n=6) without symptoms.

first: Ran

last: Zhou

first: Anindita

last: Basu

first: Sebastian

last: Pott


title: Multiomic analysis reveals cellular and epigenetic plasticity in intestinal pouches of ulcerative colitis patients [scATAC-seq]


title: A new pipeline SPICE identifies novel JUN-IKZF1 composite elements

status: Public on Nov 05 2023

city: Bethesda

first: Peng

last: Li

address: 9000 Rockville Pike

department: NHLBI

institute: NIH

summary: Transcription factor partners can cooperatively bind to DNA composite elements to augment gene transcription. Here, we report a novel protein-DNA binding screening pipeline, termed Spacing Preference Identification of Composite Elements (SPICE), that can systematically predict protein binding partners and DNA motif spacing preferences. SPICE de novo predicted known composite elements, including AP1-IRF composite elements (AICE) and STAT5 tetramers, and also predicted a range of novel binding partners, including JUN-IKZF1 composite elements. We confirmed cooperative binding of JUN and IKZF1 to an upstream conserved noncoding region, CNS9, in the human IL10 gene, that contains a non-canonical IKZF1 site, and the activity of an IL10-luciferase reporter construct depended on both this site and the AP1 binding site within this composite element in primary B and T cells. Our findings reveal an unappreciated global association of IKZF1 and AP1, and establish SPICE as a valuable new pipeline for predicting novel transcription binding complexes.

overall_design: ChIP-Seq experiments with antibodies to IKZF1 and JUN in primary mouse B cells that were either untreated or treated with LPS or LPS + IL-21 for 3 hours.

first: Sree

last: Pulugulla

first: Sonali

last: Das

first: Jangsuk

last: Oh

first: Rosanne

last: Spolski

first: Jian-Xin

last: Lin

first: Warren

last: Leonard


title: β-adrenergic signaling triggers enteric glia reactivity and acute enteric gliosis during surgery

city: Bonn

first: Reiner

last: Schneider

address: Venusberg-Campus 1

department: Surgery Department

institute: University Clinics Bonn

summary:
BACKGROUND
Enteric glia contribute to the pathophysiology of various intestinal immune-driven diseases, such as postoperative ileus (POI), a motility disorder and common complication after abdominal surgery. Enteric gliosis of the intestinal muscularis externa (ME) has been identified as part of POI development. However, the glia-restricted responses and activation mechanisms are poorly understood. The sympathetic nervous system becomes rapidly activated by abdominal surgery. It modulates intestinal immunity, innervates all intestinal layers, and directly interfaces with enteric glia. We hypothesized that sympathetic innervation controls enteric glia reactivity in response to surgical trauma.
METHODS
Sox10iCreERT2/Rpl22HA/+ mice were subjected to a mouse model of laparotomy or intestinal manipulation to induce POI. Histological, protein, and transcriptomic analyses were performed to analyze glia-specific responses. Interactions between the sympathetic nervous system and enteric glia were studied in mice chemically depleted of TH+ sympathetic neurons and glial-restricted Sox10iCreERT2/JellyOPfl/+/Rpl22HA/+ mice, allowing optogenetic stimulation of β-adrenergic downstream signaling and glial-specific transcriptome analyses. A laparotomy model was used to study the effect of sympathetic signaling on enteric glia in the absence of intestinal manipulation. Mechanistic studies included adrenergic receptor expression profiling in vivo and in vitro and adrenergic agonism treatments of primary enteric glial cell cultures to elucidate the role of sympathetic signaling in acute enteric gliosis and POI.
RESULTS
With ~4000 differentially expressed genes, the most substantial enteric glia response occurs early after intestinal manipulation. During POI, enteric glia switch into a reactive state and continuously shape their microenvironment by releasing inflammatory and migratory factors. Sympathetic denervation reduced the inflammatory response of enteric glia in the early postoperative phase. Optogenetic and pharmacological stimulation of β-adrenergic downstream signaling triggered enteric glia reactivity. Finally, distinct adrenergic agonists revealed β-1/2 adrenoceptors as the molecular targets of sympathetic–driven enteric glial reactivity.
CONCLUSIONS
Enteric glia act as early responders during post-traumatic intestinal injury and inflammation. Intact sympathetic innervation and active β-adrenergic receptor signaling in enteric glia is a trigger of the immediate glial postoperative inflammatory response. With immune-activating cues originating from the sympathetic nervous system as early as the initial surgical incision, adrenergic signaling in enteric glia presents a promising target for preventing POI development.

overall_design: Examination of enteric glial cells during acute intestinal inflammation

first: Patrick

last: Leven

first: Linda

first: Shilpashree

last: Mallesh

first: Sven

last: Wehner


title: CLEC16A in astrocytes promotes mitophagy and limits pathology in a multiple sclerosis mouse model [bulk RNA-Seq]

status: Public on Nov 09 2023

city: Boston

first: Zhaorong

address: 60 Fenwood Road

institute: Dana Farber Cancer Institute

summary:
Astrocytes promote neuroinflammation and neurodegeneration in multiple sclerosis (MS) through cell-intrinsic activities and their ability to recruit and activate other cell types. Here, in a genome-wide CRISPR-based forward genetic screen investigating regulators of astrocyte proinflammatory responses, we identified the C-type lectin domain-containing 16A gene (CLEC16A), linked to MS susceptibility, as a suppressor of nuclear factor-κB (NF-κB) signaling. Gene and small-molecule perturbation studies in mouse primary and human embryonic stem cell-derived astrocytes in combination with mitochodrial, metabolic and multiomic analyses established that CLEC16A promotes mitophagy, limiting mitochondrial dysfunction and the accumulation of mitochondrial products that activate NF-κB, the NLRP3 inflammasome and gasdermin D. Astrocyte-specific Clec16a inactivation increased NF-κB, NLRP3 and gasdermin D activation in vivo, worsening experimental autoimmune encephalomyelitis, a mouse model of MS. Moreover, we detected disrupted mitophagic capacity and gasdermin D activation in astrocytes in samples from individuals with MS. These findings identify CLEC16A as a suppressor of astrocyte pathological responses and a candidate therapeutic target in MS.
Scheduled for publication in Nature Neuroscience
DOI: 10.1038/s41593-025-01875-9


title: Transcriptional dysregulation of BAHCC1 in melanoma [CUT&TAG_BAHCC1]

status: Public on Nov 04 2023

city: New York

first: Pietro

last: Berico

state: NY

address: 550 1st Ave

department: Pathology

institute: NYU Langone Health

summary: Transcriptional addiction of cancer cells for Super-Enhancer (SE) associated genes has been proven through an extensive use of transcriptional inhibitors against specific co-activators toward which SE are esponentially dependent compared to canonical enhancers. However, each cancer type displays different sensitivity against this new class of drugs whose efficacy may vary according to their transcriptomic profile including the expression of enzymatic proteins able to confer intrinsic tolerance or resistance. Moreover, SE has been observed as well in healthy cells which point a realistic concern toward the specificity of transcriptional inhibitors and their side effects on healthy tissues. Therefore, we looked at SE-associated genes specific for cancer using melanoma as a model. Here, we identified BAHCC1 whose activity is higher in melanoma compare to other cancer types and normal tissues. BAHCC1 is a protein involved both in gene expression and genomic stability. To explore BAHCC1 role in gene expression, we performed functional studies in melanoma cells in basal conditions or upon BAHCC1 silencing. Strikingly, BAHCC1 regulates an E2F-dependent subset of genes together with SWI/SNF chromatin remodelling complex.

overall_design: Cleavage Under Targets and Tagmentation (CUT&Tag) of BAHCC1 followed by deep sequencing

first: Frederic

last: Coin

first: Irwin

last: Davidson


title: A conserved transcriptional program for MAIT cells across mammalian evolution [Hsapiens_thymus_NKT]

first: Martin

last: MESTDAGH

first: François

last: Legoux

first: Olivier

last: Lantz

first: Yara

last: El Morr

first: Helene

last: Bugaut

last: Mestdagh


title: Post-transcriptional mechanisms modulate the consequences of adaptive copy number variation (RPF)

status: Public on Nov 01 2023

city: NEW YORK

first: Pieter

last: Spealman

address: 12 Waverly Pl.

institute: New York University

summary: Copy-number variants (CNVs) are large-scale amplifications or deletions of DNA that can drive rapid adaptive evolution and result in large-scale changes in gene expression. Whereas alterations in the copy number of one or more genes within a CNV can confer a selective advantage, other genes within a CNV can decrease fitness when their dosage is changed. Dosage compensation - in which the gene expression output from multiple gene copies is less than expected - is one means by which an organism can mitigate the fitness costs of deleterious gene amplification. Previous research has shown evidence for dosage compensation at both the transcriptional level and at the level of protein expression; however, the extent of compensation differs substantially between genes, strains, and studies. Here, we investigated sources of dosage compensation at multiple levels of gene expression regulation by defining the transcriptome, translatome and proteome of experimentally evolved yeast (Saccharomyces cerevisiae) strains containing adaptive CNVs. We quantified the gene expression output at each step and found evidence of widespread dosage compensation at the protein abundance (~47%) level. By contrast we find only limited evidence for dosage compensation at the transcriptional (~8%) and translational (~3%) level. We also find substantial divergence in the expression of unamplified genes in evolved strains that could be due to either the presence of a CNV or adaptation to the environment. Detailed analysis of 82 amplified and 411 unamplified genes with significantly discrepant relationships between RNA and protein abundances identified enrichment for upstream open reading frames (uORFs). These uORFs are enriched for binding site motifs for SSD1, an RNA binding protein that has previously been associated with tolerance of aneuploidy. Our findings suggest that, in the presence of CNVs, SSD1 may act to alter the expression of specific genes by potentiating uORF mediated translational regulation.

overall_design:
We grew four strains (DGY1726, DGY1735, DGY1741, DGY743) of CNV containing yeast, Saccharomyces cerevisiae, and their ancestor (DGY1657) in glutamine-limited media in chemostat conditions [as per PMID: 30562346] in replicate
DGY1726 (gln_ctrl02_c2); DGY1735 (gln_03_c1); DGY1741 (gln_05_c2); DGY1743 (gln_06_c2); DGY1657 (Anc). All strains are derived from FY4 / S288C. Genome sequencing of all strains: (ONT) PRJNA591579 (Illumina) PRJNA451489.

first: Carolina

last: de Santana

first: Titir

last: De

first: David

last: Gresham


title: Self-supervised learning for predicting transcriptomic groups on whole slides images in intrahepatic cholangiocarcinoma

city: CLICHY

first: Camille

last: PIGNOLET

address: 100 Bd du Général Leclerc

department: CRI U1149

institute: INSERM

summary: Backgrounds & Aims: Transcriptomic classification of intrahepatic cholangiocarcinoma (iCCA) has been recently improved from two classes to five classes, associated with pathological features, targetable genetic alterations and survival. Despite its prognostic and therapeutic value, the classification is not routinely performed due to technical limits such as insufficient material or the cost of molecular analyses. Our aim was to predict iCCA transcriptomic classes on whole-slide digital histological images (WSI) using a self-supervised learning (SSL) model. Methods: Gene expression was investigated using RNA sequencing to class samples in the five transcriptomic classes. We then used a SSL method called GigaSSL. We first trained our model on a discovery set of 769 slides (biopsy and surgical samples, 246 patients) in a 5-fold cross-validation scheme. We then validated the model in a TCGA (n= 29) and a French external validation set (n=32). Results: Our model showed good performance for predicting each transcriptomic class in the discovery set (Area under the curve, AUC: 0.55-0.81), particularly for the Hepatic stem-like class (most frequent group, 37% of cases), with AUC 0.81. The model generalised well for the prediction of four on five of the transcriptomic classes into the two validation sets with AUCs ranging from 0.76 to 0.80 in the TCGA set and from 0.62 to 0.92 in the French external set. Conclusion: We have developed and validated a SSL based model able to predict iCCA transcriptomic classes on routine histological slides (biopsy and surgical samples), which could have an impact on the management of patients.

overall_design: populational analysis

first: Aurélie

last: Beaufrère


title: VNN1 : a new biomarker of anorexia nervosa

status: Public on Oct 31 2023

last: Verebi

address: 102 rue de la Santé

institute: IPNP Inserm U1266

summary:
Anorexia nervosa (AN) is a psychiatric disorder with an estimated heritability of around 70%. Although the largest genome-wide association study meta-analysis on AN identified independent loci-conferring risk to the disorder, the molecular mechanisms underlying the genetic basis of AN remains to be elucidated.
To explore AN, we ran a transcriptome profiling in peripheral blood mononuclear cells of 15 AN subjects and 15 healthy controls. We validated our mean results in a mouse model of chronic food restriction mimicking several aspects of AN.
Through this exploratory study we identified 673 significantly differentially expressed genes in AN. Among these genes, we identified the Vanin-1 (Vnn1) gene that appears to play a major role in the regulation of multiple metabolic pathways. We confirmed an underexpression of Vnn1, especially in the liver, in a mouse model of chronic food restriction.
These results indicate that quantitative food restriction affects Vnn1 expression, suggesting that this gene may contribute to the anorexic phenotype in the chronic food restriction mouse model as well as in patients affected by AN. We believe that this report highlights promising candidate genes and gene pathways for AN and reveals Vnn1 as a biomarker that may be used as molecular targets to predict and/or to understand AN.

overall_design: All patients with AN were recruited through REMANO protocol. Diagnoses were made according to the criteria of the Diagnostic and Statistical Manual of Mental Disorders 5 (citation), screened through the Mini-International Neuropsychiatric Interview (MINI) during a face-to-face interview with a trained clinician. Exclusion criteria included other non-AN ED and potentially confounding psychiatric diagnoses such as psychotic disorders, and medical or neurological conditions causing weight loss.

first: Nicolas

last: Lebrun

first: Justine

last: Vily-Petit

first: Odile

last: Viltart

first: Philibert

last: Duriez

first: Benjamin

last: Saintpierre

first: Philip

last: Gorwood

last: Ramoz

first: Thierry

last: Bienvenu


title: Temporal genomic analysis of melanoma rejection identifies regulators of tumor immune evasion [scc]

first: Ansuman

last: Satpathy

address: 240 Pasteur Drive

institute: Stanford University

first: Sapir

last: Cohen Shvefel

first: Joy

last: Pai

first: Yardena

last: Samuels


title: A conserved transcriptional program for MAIT cells across mammalian evolution [Hsapiens_thymus_Tconv]

first: Martin

last: MESTDAGH

first: François

last: Legoux

first: Olivier

last: Lantz

first: Yara

last: El Morr

first: Helene

last: Bugaut

last: Mestdagh


title: lnc-PLCB1 is stabilized by METTL14 induced m6A modification and inhibits Helicobacter pylori mediated gastric cancer by degrading DDX21

status: Public on Oct 30 2023

city: Jinan

first: Mingjie

last: Chang

state: Shandong

address: WenHua XiLu

institute: Shandong University

summary: To determine the role of m6A modification in H.pylori-mediated gastric cancer, we performed RNA methylation immunoprecipitation sequencing (MeRIP-seq) after infecting gastric cancer cell line AGS with H. pylori standard strain Hp26695 at MOI=100 for 12h. The sequencing results include three parts: mRNA, lncRNA, and circRNA.

overall_design: M6A MeRIP-seq was performed after infection of gastric cancer cell line AGS with Hp26695 at MOI=100 for 12 h.

first: Wenjuan

last: Li


title: Gene expression analysis in canine epitheliotropic lymphoma - discovery cohort

status: Public on Oct 26 2023

city: North Grafton

first: Jillian

middle: M

last: Richmond

state: Massachusetts

address: 200 Westboro Road

department: Comparative Pathobiology

institute: Tufts Cummings School of Veterinary Medicine

summary: We performed targeted transcriptomic analysis on archival biopsies from client-owned dogs to examine immune and skin gene expression profiles in spontaneous canine epitheliotropic lymphoma (EL).

overall_design: Gene expression was analyzed using 160 custom Nanostring probes to analyze 6 canines with EL compared to 5 healthy controls (leg margin excisions).

first: Nicholas

last: Robinson

first: Ramon

last: Almela


title: Post-transcriptional mechanisms modulate the consequences of adaptive copy number variation (RNA)

first: Pieter

last: Spealman

first: Carolina

last: de Santana

first: Titir

last: De

first: David

last: Gresham