title: Differences in the Aroma Profiles of Seedless-treated and Nontreated ‘Shine Muscat’ Grape Berries Decrease with Ripening

city: Nishitokyo

first: Chikako

last: HONDA

state: Tokyo

address: Midoricho

institute: The University of Tokyo

summary: In the production of seedless table grapes, it is conventional to use plant growth regulators including gibberellins. Little is known about the differences in aroma volatiles between seedless-treated grapes and nontreated (seeded) grapes. Therefore, in this study, the aroma volatile profiles of seedless-treated and nontreated ‘Shine Muscat’ grape berries during ripening were compared using gas chromatography-mass spectrometry. Measurements of volatiles during ripening showed 202 peaks in the seedless-treated and nontreated whole grape berries. According to two-way analysis of variance, the number of volatiles with differences between seedless-treated and nontreated berries and/or between ripening stages was 123, whereas those with no differences between treatments and between ripening stages was 79. Two-way hierarchical clustering analysis for the 123 volatiles showed that seedless-treated berries at the early ripening stages were separated from the other berries, and the seedless-treated and nontreated berries at the post-ripening stage were classified into the same cluster. At the early ripening stage, more lipoxygenase-pathway volatiles were produced in the seedless-treated berries than in the non-treated ones. Linalool compounds increased in both seedless-treated and nontreated berries with ripening. Gene expression profile comparisons using principal component analysis of RNA-sequencing data showed that the seedless-treated berries ripened earlier than the nontreated berries at the early ripening stage. The number of differentially expressed genes in the seedless-treated berries decreased during ripening. Using weighted gene co-expression network analyses, 12 modules and 24 modules were detected in berry skin and flesh, respectively. The correlation analysis revealed that 33 volatiles correlated with four modules in the skin and 50 volatiles correlated with nine modules in the flesh. Most of the volatiles correlated with these modules were those that showed significant differences between treatments and/or ripening stages by two-way analysis of variance. The differences in the aroma volatile profiles between seedless-treated and nontreated berries decreased as harvest was delayed, suggesting that delaying the harvest may make it possible to bring the aroma of seedless-treated ‘Shine Muscat’ berries closer to the original aroma of the seeded berries.

overall_design: Volatiles profiles in the seedless- and non-treated 'Shine Muscat' grape berries were compared using GC/MS. RNA-sequencing and weighted gene co-expression network analyses were conducted to identify the specific modules correlated with the volatile profiles.

last: Honda

first: Fukuyo

last: Tanaka

first: Yoshihiro

last: Ohmori

first: Atsushi

last: Nagano


title: Specialized post-arterial capillaries facilitate adult bone remodeling

status: Public on Aug 22 2024

city: Muenster

first: Hyun-Woo

last: Jeong

state: NRW

department: Dept. Tissue Morphogenesis

country: Germany

institute: Max-Planck-Institute for Molecular Biomedicine

type: Expression profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Specialized post-arterial capillaries for adult bone remodeling [BoneEC]

summary: A single cell transcriptomic profile of bone endothelial cells of the murine femur and tibia.

overall_design: GFP+ tdTomato+ double positive cells were FACS-isolated from Cdh5-mTnG femur and tibia. Cells were loaded onto 10X Genomics Chromium Single Cell Expression Solution V2/V3 platform. cDNA was sequenced by Illumina NextSeq 500.

first: Vishal

last: Mohanakrishnan

first: Ralf

middle: H

last: Adams

first: Kishor

middle: K

last: Sivaraj


title: Development and IND-enabling studies of a novel Cas9 genome-edited autologous CD34+ cell therapy to induce fetal hemoglobin for sickle cell disease [scRNA]

status: Public on Aug 21 2024

city: Memphis

first: Shengdar

last: Tsai

state: TN

address: 262 Danny Thomas Pl

department: Department of Hematology

country: USA

institute: St Jude Children's Research Hospital

summary: To determine the heterogeneity of fetal hemoglobin induction at a single-cell level, CD235a+ erythroid cells were extracted from mouse BM after 17 weeks xenotransplantation. Single-cell RNA-sequencing (10x Genomics) showed 82% of the cells  more than 30% g-globin expression in edited cells compared to unedited controls (26.7%).

overall_design: Single-cell RNA-sequencing analysis of CD235a+ cells from transplanted NBSGW mice bone marrow (BM) derived from three SCD donors at 17 weeks.

first: Varun

last: Katta

first: Yichao

last: Li


title: scRNA of the immune infiltrate of TRAMP-C1 allografts upon different androgen-deprivation therapeutic combinations

city: Bellinzona

first: Andrea

last: Alimonti

address: Via vela 6

department: Molecular Oncology

country: Switzerland

institute: Institute of oncology research

summary: Prostate cancer (PCa) is the second most frequent cancer diagnosis made in men and the fifth leading cause of death worldwide. Since PCa initiation and disease progression are driven by androgen receptor (AR) signaling, several effective AR signaling inhibitors (ARSIs) have been developed in the last few years. However, despite initial clinically significant therapy responses, secondary resistance to these treatments eventually emerges. Therapy resistance in prostate cancer is commonly associated with inflammation and accumulation of immunosuppressive neutrophils in the tumor microenvironment, also secreting oncogenic factors.

overall_design: To characterize the immune infiltrate of TRAMP-C1 allografts treated with different androgen-deprivation therapy approaches, scRNA seq was performed on FACS-sorted intratumor CD45+ cells. Surgically castrated mice were treated with 1) enzalutamide alone, 2) enzalutamide + Anti-IL-23 antibody, 3) enzalutamide + aCXCR2. Mice were sacrificed either at the early or the late phase of response to treatment. Based on tumor growth curves, early phase of therapy response was defined as the first two weeks of treatment.

first: Martina

last: Troiani


title: Development and IND-enabling studies of a novel Cas9 genome-edited autologous CD34+ cell therapy to induce fetal hemoglobin for sickle cell disease [sgRNA]

summary: To identify potential single-guide RNA (sgRNAs) contaminants in the GMP HBG-sgRNA, we performed SMARTer smRNA-sequencing (Takara). 80.79% of the 5' spacer sequence perfectly matched the targeting sgRNA sequence and no evidence of contaminants sgRNAs that could target other genomic regions.

overall_design: Single guide-RNA (sgRNA) sequencing of GMP HBG-sgRNA using the SMARTer smRNA-seq technology.


title: Specialized post-arterial capillaries for adult bone remodeling [Dach1OE]

summary: A single cell transcriptomic profile of bone stromal cells of the murine femur at postnatal day 30 (P30), Tamoxifen injected at Postnatal day 1 and 2.

overall_design: scRNA sequencing of non-hematopoietic bone stromal cells using BD Rhapsody Express


title: Bulk RNA-seq of castration-resistant tumors from Ptenpc-/- mice reconstituted with either F10fl/fl or F10fl/fl; LysM-Cre+ mice

summary: PTEN is one of the most altered tumor suppressor genes in human prostate cancer (PCa). Prostate specific-Pten-deficient mouse models develop prostate cancer eventually progressing to castration-resistant prostate cancer (CRPC), also due to alterations of the tumor immune infiltrate. By using single-cell RNA-seq, we report the identification of a subset of CD84+; CD11b+; Ly6G+; Ly6Clow immunosuppressive neutrophils that secreted the coagulation factor X (FX) into the prostate TME to directly promote PCa growth.

overall_design: To characterize the impact of F10 immune cells, bulk-RNA seq was performed on Ptenpc-/- mice reconstituted with either F10fl/fl or F10fl/fl; LysM-Cre+ mice


title: Bulk RNA-seq of IVD-hMDSCs treated upon CD84 ligation

summary: CD84 is a key marker of PMN-MDSCs in multiple mouse models and patients tumor samples. Increased CD84 expression levels were found in pathophysiological conditions associated with thrombo-inflammation

overall_design: To investigate the effect of CD84 ligation in PMN-MDSCs biology, bulk RNA-seq of in vitro-derived human MDSCs (IVD-hMDSCs) stimulated with human recombinant CD84 for 48 hours was performed.


title: Thyroid hormone remodels cortex to coordinate body-wide metabolism and exploration

city: Cambridge

first: Evan

last: Macosko

state: MA

address: 75 Ames St

institute: Broad Institute

summary: Animals adapt to environmental conditions by modifying the function of their internal organs, including the brain. To be adaptive, alterations in behavior must be coordinated with the functional state of organs throughout the body. Here we find that thyroid hormone--a regulator of metabolism in many peripheral organs--directly activates cell-type specific transcriptional programs in frontal cortex of adult male mice. These programs are enriched for axon-guidance genes in glutamatergic projection neurons, synaptic regulatory genes in both astrocytes and neurons, and pro-myelination factors in oligodendrocytes, suggesting widespread plasticity of cortical circuits. Indeed, whole-cell electrophysiology revealed that thyroid hormone alters excitatory and inhibitory synaptic transmission, an effect that requires thyroid hormone-induced gene regulatory programs in presynaptic neurons. Furthermore, thyroid hormone action in frontal cortex regulates innate exploratory behaviors and causally promotes exploratory decision-making. Thus, thyroid hormone acts directly on cerebral cortex in males to coordinate exploratory behaviors with whole-body metabolic state.

overall_design: To identify transcriptional programs that may mediate thyroid-dependent changes in exploratory behaviors, we conducted single-nucleus RNA sequencing (snRNAseq) of dorsal frontal cortex, centered on the secondary motor cortex, of control male mice or those exposed to systemic thyroid hormone (T3) treatment for 2.5 days. To address whether the T3-regulated transcriptional programs are a cell-autonomous response to T3 in cortical neurons, we also performed snRNAseq on a cohort of mice expressing either a mutant thyroid receptor derived from an individual with generalized thyroid resistance (DN-THR) or overexpression of the wild-type thyroid receptor (WT-THR). Datasets were analyzed to identify thyroid hormone-induced, cell-type specific transcriptional programs in the male mouse frontal cortex.

first: Daniel

middle: R

last: Hochbaum

first: Lauren

last: Hulshof

first: Amanda

last: Urke

first: Wengang

last: Wang

first: Alexandra

middle: C

last: Dubinsky

first: Hannah

last: Farnsworth

first: Richard

last: Hakim

first: Sherry

last: Lin

first: Giona

last: Kleinberg

first: Kiera

last: Robertson

first: Canaria

last: Park

first: Alyssa

last: Solberg

first: Yechan

last: Yang

first: Caroline

last: Baynard

first: Naeem

middle: M

last: Nadaf

first: Celia

last: Beron

first: Allison

middle: E

last: Girasole

first: Lynne

last: Chantranupong

first: Marissa

last: Cortopassi

first: Shannon

last: Prouty

first: Ludwig

last: Geistlinger

first: Alexander

last: Banks

first: Thomas

last: Scanlan

first: Sandeep

last: Datta

first: Michael

last: Greenberg

first: Gabriella

middle: L

last: Boulting

middle: Z

first: Bernardo

last: Sabatini


title: Alcohol and fear conditioning produce strain-specific changes in the dorsal hippocampal transcriptome of adolescent C57BL/6J and DBA/2J mice

city: University Park

first: Laurel

last: Seemiller

state: PA

address: 314 Mueller Laboratory

institute: Pennsylvania State University

summary: Adolescent sensitivity to alcohol is predictive of later alcohol use and is influenced by genetic background. Data from our laboratory suggested that adolescent C57BL/6J and DBA/2J inbred mice differed in susceptibility to dorsal hippocampus-dependent contextual fear learning deficits after acute alcohol exposure. To investigate the biological underpinnings of this strain difference, we examined dorsal hippocampus gene expression via RNA-sequencing after alcohol and/or fear conditioning across male and female C57BL/6J and DBA/2J adolescents. Strains exhibited dramatic differences in dorsal hippocampal gene expression. Specifically, C57BL/6J and DBA/2J strains differed in 3526 transcripts in males and 2675 transcripts in females. We identified pathways likely to be involved in mediating alcohol’s effects on learning, including networks associated with Chrna7 and Fmr1. These findings provide insight into the mechanisms underlying strain differences in alcohol’s effects on learning and suggest that different biological networks are recruited for learning based on genetics, sex, and alcohol exposure.

overall_design: We conducted RNA-sequencing to compare dorsal hippocampus gene expression from male and female adolescent mice (C57BL/6J and DBA/2J strains) after an acute EtOH (1.5 g/kg) or saline injection and fear conditioning (FC) or no fear conditioning control (noFC) conditions.

first: Lisa

last: Goldberg

first: Aswathy

last: Sebastian

first: Sue

last: Rutherford Siegel

first: Craig

last: Praul

first: Dana

last: Zeid

first: Istvan

last: Albert

first: Jacob

last: Beierle

first: Camron

last: Bryant

middle: J

last: Gould


title: Alzheimer’s disease-linked risk alleles elevate microglial cGAS-associated senescence and neurodegeneration in a tauopathy model [bulk_RNAseq]

city: New York

first: Li

last: Gan

state: NY

address: 413 East 69th Street, 9th Floor BB904

department: Helen and Robert Appel Alzheimer’s Disease Research Institute

institute: Weill Cornell Medicine

summary: The strongest risk factors for Alzheimer’s disease (AD) include the 4 allele of apolipoprotein E (APOE), the R47H variant of triggering receptor expressed on myeloid cells 2 (TREM2), and female sex. Here, we combine APOE4 and TREM2R47H (R47H) in female P301S tauopathy mice to identify the pathways activated when AD risk is the strongest, thereby highlighting disease-causing mechanisms. We find that the R47H variant induces neurodegeneration in female APOE4 mice without impacting hippocampal tau load. The combination of APOE4 and R47H amplified tauopathy-induced cell-autonomous microglial cGAS-STING signaling and type-I interferon response, and interferon signaling converged across glial cell types in the hippocampus. APOE4-R47H microglia displayed cGAS- and BAX-dependent upregulation of senescence, showing association between neurotoxic signatures and implicating mitochondrial permeabilization in pathogenesis. By uncovering pathways enhanced by the strongest AD risk factors, our study points to cGAS-STING signaling and associated microglial senescence as potential drivers of AD risk.

overall_design: Bulk RNA sequencing of primary microglia isolated from mouse line expressing the human TREM2 common variant CV/CV or R47H/CV on the APOE4/APOE4 or APOE3/APOE3 homozygous background (n=3).

first: Gillian

last: Carling

last: Fan

first: Nessa

last: Foxe

first: Kendra

last: Norman

first: Pearly

last: Ye

first: Man

middle: Y

last: Wong

first: Daphne

last: Zhu

first: Fangmin

last: Yu

first: Jielin

last: Xu

first: Allan

last: Yarahmady

first: Hao

last: Chen

first: Yige

last: Huang

first: Sadaf

last: Amin

first: Emmanouil

last: Zacharioudakis

first: Xiaoying

first: David

last: Holtzman

first: Sue-Ann

last: Mok

first: Evripidis

last: Gavathiotis

first: Subhash

last: Sinha

first: Feixiong

last: Cheng

first: Wenjie

last: Luo

first: Shiaoching

last: Gong


title: Secreted factors from M1 macrophages drive prostate cancer stem cell plasticity by upregulating NANOG, SOX2 and CD44 through NFκB signaling [LNCaP-C42B]

city: Kuopio

first: Einari

middle: A

last: Niskanen

address: Yliopistonranta 8

department: School of Medicine

country: Finland

institute: University of Eastern Finland

summary: The inflammatory tumor microenvironment (TME) is a key driver of tumor-promoting pro-cesses. Tumor-associated macrophages are one of the main immune cell types in the TME and their increased density is related to poor prognosis in prostate cancer. Here, we investigated the influence of pro-inflammatory (M1) and immunosuppressive (M2) macrophages on pros-tate cancer lineage plasticity. Our findings reveal that M1 macrophage secreted factors up-regulate genes related to stemness while downregulating genes associated with androgen re-sponse in prostate cancer cells. The expression of cancer stem cell plasticity markers NANOG, KLF4, SOX2, OCT4 and CD44 was stimulated by the secreted factors from M1 macrophages. Moreover, AR and its target gene KLK3 were observed to be suppressed in LNCaP cells treated with secreted factors from M1 macrophages. Inhibition of NFκB signaling using the IKK16 inhibitor resulted in downregulation of NANOG, SOX2 and CD44 and cancer stem cell plasticity. Our study highlights that the secreted factors from M1 macrophages drive prostate cancer cell plasticity by upregulating the expression of cancer stem cell plasticity markers through NFκB signaling pathway.

overall_design: To investigate the effects of secreted factors from pro-inflammatory (M1) and immunosuppressive (M2) macrophages on LNCaP-C42B prostate cancer cells, we treated LNCaP-C42B cells with conditioned medium (CM) from M0, M1 or M2 polarized THP-1 macrophages for 48 hours. We established RNA-seq for control (RPMI medium), M0 CM, M1 CM and  M2 CM.

first: Kirsi

last: Ketola

first: Sanna

last: Pasonen-Seppänen

last: Kainulainen


title: Secreted factors from M1 macrophages drive prostate cancer stem cell plasticity by upregulating NANOG, SOX2 and CD44 through NFκB signaling [LNCaP]

summary: The inflammatory tumor microenvironment (TME) is a key driver of tumor-promoting processes. Tumor-associated macrophages are one of the main immune cell types in the TME and their density increases during cancer progression. Here, we investigated the influence of pro-inflammatory (M1) and immunosuppressive (M2) macrophages on prostate cancer lineage plasticity. Our findings reveal that M1 macrophage secreted factors upregulate genes related to stemness while downregulating genes associated with androgen response in LNCaP prostate cancer cells. Cancer stem cell plasticity markers NANOG, KLF4, SOX2, OCT4 and CD44 were stimulated by the secreted factors from M1 macrophages. Moreover, AR and its target gene KLK3 were observed to be suppressed in LNCaP cells treated exposed to secreted factors from M1 macrophages. Inhibition of NF-κB signaling using the IKK16 inhibitor resulted in downregulation of NANOG, SOX2 and CD44. Our study highlights that the secreted factors from M1 macrophages drive prostate cancer cell plasticity by upregulating the expression of cancer stem cell plasticity markers through NF-κB signaling pathway.

overall_design: To investigate the effects of secreted factors from pro-inflammatory (M1) and immunesuppressive (M2) macrophages on LNCaP prostate cells, we treated LNCaP cells with conditioned medium (CM) from M0, M1 or M2 polarized THP-1 macrophages for 48 hours. In addition, we combined M1 CM with DMSO or NFκB inhibitor IKK16 to study the role of NFκB signaling on M1 CM -induced gene expression. We established RNA-seq for control (RPMI medium), M0 CM, M1 CM and  M2 CM as well as M1 CM with DMSO and M1 CM with IKK16 -treated LNCaP cells.


title: PINX1 loss confers susceptibility to PARP inhibition in pan-cancer cells

city: Shanghai

first: Mei

address: 393 Middle Huaxia Road

country: China

institute: ShanghaiTech University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: PARP inhibitors have exhibited efficacy in BRCA-proficient patients, further highlighting the necessity for a deeper understanding of PARP1 function and its inhibition in cancer therapy. Here, we unveil PIN2/TRF1-interacting telomerase inhibitor 1 (PINX1) as an uncharacterized PARP1-interacting protein that synergizes with PARP inhibitors upon its depletion across various cancer cell lines. Loss of PINX1 compromises DNA damage repair capacity upon etoposide treatment. The vulnerability of PINX1-deficient cells to etoposide and PARP inhibitors could be effectively restored by introducing either a full-length or a mutant form of PINX1 lacking telomerase inhibitory activity. Mechanistically, PINX1 is recruited to DNA lesions via PARP1, facilitating the downstream recruitment of the DNA repair factor XRCC1. In the absence of DNA damage, PINX1 constitutively binds to PARP1, promoting PARP1-chromatin association and transcription of specific DNA damage repair proteins, including XRCC1, and transcriptional regulators, including GLIS3. Collectively, our findings identify PINX1 as a multifaceted partner of PARP1, crucial for safeguarding cells against genotoxic stress and emerging as a potential candidate for targeted tumor therapy.

overall_design: To investigate the specific alterations in the presence of PINX1 on the binding of PARP1 to chromatin, we conducted the chromatin immunoprecipitation (ChIP) sequencing analysis. We enriched PARP1-bound chromatin using lysates from WT, PINX1KO, or PINX1-reconstituted KO cells with an anti-PARP1 antibody and subjected them to sequencing.


title: scRNA of either HSPC or CRPC Ptenpc-/- mouse prostate cancers

first: Andrea

last: Alimonti

summary: PTEN is one of the most altered tumor suppressor genes in human prostate cancer. Prostate specific-Pten-deficient mouse models develop prostate cancer eventually progressing to CRPC, also due to alterations of the tumor immune infiltrate.

overall_design: To characterize the tumor microenvironment of Ptenpc-/- mice developing castration-resistant prostate cancer, scRNA seq was performed on tumors from 24-week-old Ptenpc-/-mice.

first: Martina

last: Troiani


title: Altered enhancer-promoter interaction leads to MNX1 expression in pediatric acute myeloid leukemia with t(7;12)(q36;p13) [HiC]

city: Heidelberg

first: Christoph

last: Plass

address: Im Neueneimer Feld 280

department: Division of Cancer Epigenomics

institute: DKFZ (German Cancer Research Center)

summary: Acute myeloid leukemia (AML) with translocation t(7;12)(q36;p13) is a subgroup that occurs only in infants or very young children and is characterised by a poor outcome. Deep molecular characterization has been hampered by the rarity of this AML subtype and the lack of model systems. Approximately 50% of AML with t(7;12)(q36;p13) express an MNX1::ETV6 oncofusion transcript, but there is no evidence for the presence of an oncofusion protein. However, a universal feature is the strong RNA and protein expression of MNX1, a homeobox transcription factor that is normally not transcribed in haematopoietic cells. Here we use whole genome sequencing data to precisely map the translocation breakpoints on chromosomes 7 and 12 in these pediatric AML patients to a region downstream of MNX1 on chromosome 7 and either introns 1 or 2 of ETV6 on chromosome 12. We confirm the tight correlation of MNX1 overexpression in t(7;12)(q36;p13) AML in our own samples and three additional cohorts of pediatric AML. Using a CRISPR-engineered iPSC cell line, ChiPSC22t(7;12), harbouring the t(7;12)(q36;p13) translocation, we unravel an enhancer-hijacking event leading to MNX1 overexpression. Identification of hematopoietic enhancer regions in hematopoietic stem and progenitor cells derived from differentiated ChiPSC22t(7;12) cells allowed us to demonstrate their importance for MNX1 expression in knock-out experiments and by measuring the promoter-enhancer distance in confocal microscopy. In contrast to the prevailing dogma in AML, suggesting that translocations lead to the creation of oncofusion genes, t(7;12)(q36;p13) AML is characterized by an enhancer-hijacking event driving MNX1, a novel leukemia oncogene and the haploinsufficiency of ETV6.

overall_design: We used the iPSC line CHIPSC22  (Cellartis/Takara Bio Europe AB, Gothenburg, Sweden), both WT and with a t(7;12)(q36;p13) translocation. We included both the iPSC CHIPSC22 and CHIPSC22 differentiated into hematopoietic stem and progenitor cells (HSPC).

first: Dieter

last: Weichenhan


title: Altered enhancer-promoter interaction leads to MNX1 expression in pediatric acute myeloid leukemia with t(7;12)(q36;p13) [ACT-Seq]

overall_design: We used the iPSC line CHIPSC22  (Cellartis/Takara Bio Europe AB, Gothenburg, Sweden), both WT and with a t(7;12)(q36;p13) translocation. We included both the iPSC CHIPSC22 and CHIPSC22 differentiated into hematopoietic stem and progenitor cells (HSPC). We used antibodies against H3K4me1, H3K27ac and IgG. For each condition, 3 replicates were used.


title: Altered enhancer-promoter interaction leads to MNX1 expression in pediatric acute myeloid leukemia with t(7;12)(q36;p13) [ATAC-Seq]

overall_design: We used the iPSC line CHIPSC22  (Cellartis/Takara Bio Europe AB, Gothenburg, Sweden), both WT and with a t(7;12)(q36;p13) translocation. We included both the iPSC CHIPSC22 and CHIPSC22 differentiated into hematopoietic stem and progenitor cells (HSPC). For each condition, 3 replicates were used.


title: Altered enhancer-promoter interaction leads to MNX1 expression in pediatric acute myeloid leukemia with t(7;12)(q36;p13)

overall_design: Refer to individual Series


title: Altered enhancer-promoter interaction leads to MNX1 expression in pediatric acute myeloid leukemia with t(7;12)(q36;p13) [4C-Seq]

overall_design: We used the iPSC line CHIPSC22  (Cellartis/Takara Bio Europe AB, Gothenburg, Sweden), both WT and with a t(7;12)(q36;p13) translocation. We included both the iPSC CHIPSC22 and CHIPSC22 differentiated into hematopoietic stem and progenitor cells (HSPC). For each condition, 2 replicates and included for the t(7;12) case, 1 for the WT case.


title: Dormancy-inducing 3D engineered matrix uncovers mechanosensitive and drug-protective FHL2-p21 signaling axis

city: Regensburg

first: Xin

last: Lu

address: Universitätsstraße 31

institute: University of Regensburg

summary: Solid cancers frequently relapse with distant metastasis, despite local and systemic treatment. Cellular dormancy has been identified as an important mechanism underlying drug resistance enabling late relapse. Therefore, relapse from invisible, minimal residual cancer of seemingly disease-free patients call for in vitro models of dormant cells suited for drug discovery. Here, we explore dormancy-inducing 3D engineered matrices, which generate mechanical confinement and induce growth arrest and survival against chemotherapy in cancer cells. We characterized the dormant phenotype of solitary cells by P-ERKlow:P-p38high dormancy signaling ratio, along with Ki67− expression. As underlying mechanism, we identified stiffness-dependent nuclear localization of the four-and-a-half LIM domain 2 (FHL2) protein, leading to p53-independent high p21Cip1/Waf1 nuclear expression, validated in murine and human tissue. Suggestive of a resistance-causing role, cells in the dormancy-inducing matrix became sensitive against chemotherapy upon FHL2 down-regulation. Thus, our biomaterial-based approach will enable systematic screens for previously unidentified compounds suited to eradicate potentially relapsing dormant cancer cells.

overall_design: mRNA profiles of MDA-MB-231 triple negative breast cancer cell line retrieved from 3D covalently-crosslinked alginate hydrogels with two different stiffness (stiff vs soft) and 3D Matrigel

first: Sadra

last: Bakhshandeh

first: Unai

last: Heras

first: Hubert

last: Taïeb

first: Adithi

last: Varadarajan

first: Susanna

last: Lissek

first: Sarah

last: Hücker

first: Daniela

middle: S

last: Garske

last: Young

last: Abaurrea

first: Maria

last: Caffarel

first: Ana

last: Riestra

first: Paloma

last: Bragado

first: Jörg

last: Contzen

first: Manfred

last: Gossen

first: Stefan

last: Kirsch

first: Jens

last: Warfsmann

first: Kamran

last: Honarnejad

last: Klein

first: Amaia

last: Cipitria


title: Topical Application of Nano-sized Graphene Oxide Cream Ameliorates Acute Skin Inflammation in Mice

status: Public on Aug 20 2024

city: Wonju-si

first: Sung Won

last: Lee

state: Gangwon-do

address: 83 Sangjidae-gil

country: South Korea

institute: Sangji university

summary: We have previously shown that nano-sized graphene oxide (NGO) displays anti-inflammatory activities against natural killer T (NKT) cell-mediated sepsis. To address whether NGO could be applied to treat acute skin inflammation. We developed a conventional skin Cetaphil® cream containing NGO (NGO cream) for topical application to skin lesions and investigated its therapeutic efficacy by employing the tape-stripping-induced acute skin inflammation model. Topical application of NGO cream to the wounded area significantly reduced skin lesions compared with the control cream. Moreover, NGO cream treatment prevented the tape-stripping-elicited infiltration of and IL1β production by skin neutrophils and dendritic cells (DCs). Furthermore, such anti-inflammatory effects of NGO cream were attributed to decreased infiltration of IL12-producing DCs and IFNγ-producing cells (e.g., CD4+ T, CD8+ T, γδ T, NK, and NKT cells) into the skin. In addition, topical NGO cream administration enhanced the expression of suppressive molecules such as FR4 on skin regulatory T cells. Through RNA sequencing analysis, we found that the preventive effect of NGO cream on acute skin inflammation may be correlated with the activation of keratinocytes located in the epidermis. Our results support NGO cream as a therapeutic option to control acute skin inflammation.

overall_design: Either control cream- or NGO cream was applied topically to the tape-stripped dorsal skin of B6 mice. Subsequently, the skin were harvested.

first: Hyun Jung

last: Park

first: Tae-Cheol

last: Kim

first: Yun Hoo

first: Keun Soo

first: Luc

last: Van Kaer

first: Suklyun

last: Hong

first: Seokmann


title: ZIC2 and ZIC3 promote SWI/SNF recruitment to safeguard progression towards human primed pluripotency [ATAC-Seq]

city: Montreal

first: William

middle: A.

last: Pastor

state: Quebec

address: 3655 Promenade Sir-William-Osler

department: Biochemistry

country: Canada

institute: McGill University

summary: ZIC2 and ZIC3 are essential for acquisition and maintenance of primed pluripotency. In this study, we conducted ATAC-seq in single and compound knockout of ZIC2, ZIC3 and ZIC5 primed hESCs, naïve hESCs lacking ZIC3 that inducibly express ZIC2, naive hESCs that inducible express ZIC2 or ZIC3, ZIC3-depleted primed hESCs that were cultured in 5iLAF medium for six days and undergoing reversion to a naive state, naive hESCs expressing ectopic ZIC2 in the presence of a BRG1 PROTAC.

overall_design: ATAC-seq from single and compound knockout of ZIC2, ZIC3 and ZIC5 primed hESCs, naïve hESCs lacking ZIC3 that inducibly express ZIC2, naive hESCs that inducible express ZIC2 or ZIC3, ZIC3-depleted primed hESCs that were cultured in 5iLAF medium for six days and undergoing reversion to a naive state, naive hESCs expressing ectopic ZIC2 in the presence of a BRG1 PROTAC. ATAC-seq from naive hESCs sorted for CD75hi cells cultured in PXGL medium are also included.

first: Ishtiaque

last: Hossain


title: ZIC2 and ZIC3 promote SWI/SNF recruitment to safeguard progression towards human primed pluripotency [CUT&Tag]

summary: ZIC2 and ZIC3 are essential for acquisition and maintenance of primed pluripotency. In this study, we profiled chromatin occupancy of  BRG1, EZH2, H3K27ac and H3K4me3 upon concomitant loss of ZIC2 and ZIC3 in primed hESCs, and of BRG1 upon ectopic expression of ZIC2 for increasing periods of time in naïve hESCs.

overall_design: Chromatin profiling of BRG1, EZH2, H3K27ac and H3K4me3 upon concomitant loss of ZIC2 and ZIC3 in primed hESCs. Chromatin profiling of BRG1 upon ectopic expression of ZIC2 for increasing periods of time in naïve hESCs.


title: ZIC2 and ZIC3 promote SWI/SNF recruitment to safeguard progression towards human primed pluripotency [RNA-seq]

summary: ZIC2 and ZIC3 are essential for acquisition and maintenance of primed pluripotency. In this study, we conducted next generation sequencing of polyA-enriched bulk RNA in single and compound knockouts of ZIC2, ZIC3 and ZIC5 primed hESCs, naïve hESCs lacking ZIC3 that inducibly express ZIC2, and primed hESCs that were cultured in 5iLAF medium for six days and undergoing reversion to a naive state.

overall_design: Bulk RNA-seq of polyA-enriched RNA from single and compound knockout of ZIC2, ZIC3 and ZIC5 primed hESCs, naïve hESCs lacking ZIC3 that inducibly express ZIC2, and primed hESCs lacking ZIC3 that were cultured in 5iLAF medium for six days and undergoing reversion to a naive state.


title: ZIC2 and ZIC3 promote SWI/SNF recruitment to safeguard progression towards human primed pluripotency [ChIP-seq]

summary: The primed epiblast acts as a transitional stage between the relatively homogeneous naïve epiblast and the gastrulating embryo. Its formation entails coordinated changes in regulatory circuits driven by strict epigenetic mechanisms. Using a multi-omic approach in human embryonic stem cell models across the spectrum of peri-implantation development, we demonstrate that the transcription factors ZIC2 and ZIC3 have overlapping but essential roles in opening primed-specific enhancers. Together they are essential to facilitate progression to and maintain primed pluripotency. ZIC2/3 achieve their function by recruiting SWI/SNF to chromatin and loss of ZIC2/3 or degradation of SWI/SNF both prevent enhancer activation. Loss of ZIC2/3 results in transcriptome changes consistent with perturbed Polycomb activity and a shift towards the expression of genes linked to mesendoderm differentiation. Additionally, we find an intriguing dependency on the transcriptional machinery for sustained recruitment of ZIC2/3 over a subset of primed-hESC specific enhancers. Taken together, ZIC2 and ZIC3 regulate highly dynamic lineage-specific enhancers and collectively act as key regulators of human primed pluripotency.

overall_design: Profiling of genome-wide chromatin occupancy dynamics of ZIC2 and ZIC3 in primed hPSCs, and the effect on BRG1 and H3K27me3 occupancy upon loss of ZIC2 and ZIC3 or upon gain of ZIC2 in primed hESCs and naïve hESCs respectively.


title: Transcriptomic changes in the PacC transcription factor deletion mutant of the plant pathogenic fungus Botrytis cinerea

city: Villeurbanne

first: Nathalie

last: Poussereau

address: 10, rue Dubois

country: France

institute: University Lyon1

summary: Botrytis cinerea, the causal agent of gray mold, is a necrotrophic fungus that can infect a wide variety of plant species and plant tissues. During infection, this pathogen modulates the pH of its environment by secreting organic acids or ammonia. Deletion of the gene encoding the pH-responsive transcription factor PacC revealed the importance of this regulator in different steps of the infection process and particularly in the secretion of organics acids, reactive oxygen species and plant cell wall degrading enzymes. This study aimed to identify the regulatory networks controlled by this fungus-specific transcription factor when the fungus is placed under acidic or alkaline conditions.

overall_design:
Botrytis cinerea WT and DBcpacC mutant strains were grown on solid MANG medium for 3 days on the surface of cellophane membranes. The membranes were then transferred for 4 h onto the surface of 2 ml of liquid Gamborg medium buffered at pH 5.0 or 7.0
Three independent biological replicates were performed for each condition
The 12 total-RNA samples were used for RNA-SEQ sequencing.

first: Christine

last: Rascle

first: Bastien

last: Malbert

first: Isabelle

last: Goncalves

first: Mathias

last: Choquer

first: Christophe

last: Bruel


title: Global Lactylation Profiling Reveals Lactate-Driven Regulatory Mechanisms Promoting Tumor Progression in Oral Squamous Cell Carcinoma [RNA-seq]

city: Beijing

first: Fengyang

last: Jing

address: xueyuan road #38

institute: Peking university

summary: Cancer cells often rely on aerobic glycolysis for metabolism, and lactylation, a newly discovered post-translational modification, significantly impacts molecular processes. This study comprehensively analyzes lactylation's role in oral squamous cell carcinoma (OSCC), providing initial insights into its impact on progression. Oral squamous cell carcinoma cell lines, before and after lactate treatment, underwent CUT&TAG, ATAC, and transcriptomic sequencing. ChIP-qPCR and RT-qPCR validated results in OSCC tissues. Integrated analysis identified 217 genes with increased expression driven by lactylation in OSCC. Lactylation broadly impacted pathways in cancer, notably regulating PI3K/AKT and MAPK signaling. This pioneering study analyzes lactylation in OSCC, providing a global map of its regulation in oral squamous cell carcinoma from the perspective of chromatin-driven gene expression.

overall_design: Treating CAL27 cells with 10mM lactate for 24 hours, we conducted CUT&TAG-seq on lactylation modification and ATAC-seq, along with downstream RNA-seq.

first: Tiejun

last: Li


title: Global Lactylation Profiling Reveals Lactate-Driven Regulatory Mechanisms Promoting Tumor Progression in Oral Squamous Cell Carcinoma

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


title: Global Lactylation Profiling Reveals Lactate-Driven Regulatory Mechanisms Promoting Tumor Progression in Oral Squamous Cell Carcinoma [CUT&TAG]


title: Global Lactylation Profiling Reveals Lactate-Driven Regulatory Mechanisms Promoting Tumor Progression in Oral Squamous Cell Carcinoma [ATAC-seq]


title: Gpx4 regulates iNKT cell homeostasis and function by preventing lipid peroxidation and ferroptosis

city: Oklahoma City

first: Sophia

middle: P. M.

last: Sok

address: 825 NE 13th St

institute: Oklahoma Medical Research Foundation

summary: Invariant natural killer T (iNKT) cells are a group of innate like T cells that plays important roles in immune homeostasis and activation. We found that iNKT cells, compared to CD4+ T cells, have significantly higher levels of lipid peroxidation in both mice and humans. Proteomic analysis also demonstrated that iNKT cells express higher levels of Glutathione peroxidase 4 (Gpx4), a major antioxidant enzyme that reduces lipid peroxidation and prevents ferroptosis. T cell specific deletion of Gpx4 reduces iNKT cell population, most prominently the IFNg producing NKT1 subset. RNAseq analysis revealed IFNg signaling, cell cycle regulation, as well as mitochondrial function are perturbed by Gpx4 deletion in iNKT cells. Consistently, we detected impaired cytokine production, elevated cell proliferation and cell death, and accumulation of lipid peroxides and mitochondrial ROS in Gpx4 KO iNKT cells. Ferroptosis inhibitor, iron chelator, vitamin E and vitamin K2 can prevent ferroptosis induced by Gpx4 deficiency in iNKT cells and ameliorate the impaired function of iNKT cells due to Gpx4 inhibition. Lastly, vitamin E rescued iNKT cell population in Gpx4 KO mice. Altogether, our findings reveal the critical role of Gpx4 in regulating iNKT cell homeostasis and function, through controlling lipid peroxidation and ferroptosis.

overall_design: Splenic iNKT cells from WT and Gpx4-cKO mice were flow sorted, and transcriptomes were analyzed by RNAseq.

first: Kaitlyn

last: Pipkin

first: Narcis

middle: I

last: Popescu

first: Megan

last: Reidy

first: Bin

first: Holly

last: Van Remmen

first: Mike

last: Kinter

first: Xiao-Hong

last: Sun

first: Zhichao

last: Fan

first: Meng

last: Zhao


title: Time-Course Analysis of Hepatic Single-Nuclei RNA-Sequencing in Mice Treated with  2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD)

city: East Lansing

first: Timothy

last: Zacharewski

state: MI

address: 603 Wilson Rd., BCH Building RM#212

department: Biochemistry and Molecular Biology

institute: Michigan State University

summary: 2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) is a persistent environmental contaminant that disrupts normal hepatic function. This disruption leads to the development and progression of non-alcoholic fatty liver disease (NAFLD) pathologies, including steatosis, steatohepatitis, and fibrosis. TCDD exerts hepatotoxic effects through activation of the aryl hydrocarbon receptor (AHR) eliciting transcriptional changes. Although diverse liver cell types contribute to TCDD-induced hepatotoxicity, cell-specific transcriptional changes in response to acute TCDD exposure remain unclear. The objective of this project was to elucidate the cell-specific outcomes of AHR activation following acute TCDD exposure. We conducted liver single-nuclei RNA-sequencing from male C57BL/6 mice administered 30 μg/kg of TCDD or sesame oil and sacrificed at 2, 4, 8, 12, 18, 24, or 72 hours post-oral gavage. Leiden clustering and annotation identified 10 major liver cell types, and 2 macrophage and 8 endothelial cell (EC) subtypes. While most cell types maintained their relative abundance, neutrophils exhibited an increase at 72 hours in response to TCDD. Hepatocytes, ECs, and hepatic stellate cells (HSCs) were the only cell types with cell-specific gene expression changes with known AHR binding sites (1,550, 102, and 40, respectively). Functional enrichment analysis in response to TCDD revealed disruptions in the metabolism of steroids, primary bile acids, vitamins, retinols, and glutathione in addition to one-carbon metabolism. EC differential gene expression was associated with PI3-AKT signaling, as well as protein processing and transport pathways. HSCs were enriched in protein processing, ABC transporters, and the dysregulation of tryptophan and linoleic acid metabolism.  Altogether, these results suggest that early responses to TCDD trigger cell-specific changes in gene expression in the liver, contributing to hepatotoxicity and the emergence of hepatic pathologies related to NAFLD.

overall_design: Male C57BL/6mice at postnatal day 28 (n = 3) were administered either sesame oil vehicle or 30 μg/kg TCDD through oral gavage. Liver samples were collected following 2, 4, 8, 12, 18, 24, and 72 hours post-administration. Immediately upon collection, these liver samples were snap-frozen in liquid nitrogen and subsequently stored at -80°C. Nuclei were isolated from the frozen liver samples and stained with DAPI, afterwhich a single-nuclei suspension was generated through FACS. Libraries were prepared using the 10X Genomics Single Cell 3' v3.1 Dual Index kit.

first: Giovan

middle: N

last: Cholico

first: Rance

last: Nault

first: Tim


title: Erasure of DNA methylation in rat fetal germ cells is sex-specific and sensitive to maternal high-fat diet.

city: Laval

first: Geraldine

last: Delbes

address: 531 Boul des Prairies

department: Biology

institute: INRS Centre Armand-Frappier Santé Biotechnologie

type: Methylation profiling by high throughput sequencing

summary: we tested the impact of a maternal HFD on embryonic germline DNAme erasure using a rat strain that expresses green fluorescent protein specifically in germ cells. DNAme was analysed by methyl-seq capture in germ cells collected from male and female F1 gonads at gestational day 16.

overall_design:
After running the classic pipeline of DNA methylation data processing, DNA methylation was extracted for each samples and each mapped locus, then this data were segmented into segments with at least 50bp and finally we performed DMR search and explored the segments.
Re-analysed Samples PRJNA909769:
GSM6801700 SAMN32093467 SRX18528715
GSM6801701 SAMN32093466 SRX18528716
GSM6801702 SAMN32093465 SRX18528717
GSM6801703 SAMN32093464 SRX18528718

first: Rhizlane

last: El omri-Charai

first: Arlette

last: Rwigemera

first: Isabelle

last: Gilbert

first: Alexandra

last: Langford

first: Claude

last: Robert

first: Deborah

last: Sloboda

first: Géraldine


title: DNA cytosine methylation suppresses meiotic recombination at the sex-determining region (RNA-Seq)

first: Xiuqi

last: Gui

address: 320 Yue Yang Rd

institute: Shanghai Institute of Nutrition and Health

summary: In sexual organisms, random meiotic recombination between homologous chromosomes is vital to maximize genetic variation among offspring. The sex-determining region (SDR), however, does not undergo recombination, as required for the maintenance of distinct alleles. The contribution of epigenetic versus genetic mechanisms to suppress recombination in SDRs and how the suppression mechanisms evolve remain poorly understood. Here we describe the mechanistic control of meiotic recombination at the mating-type locus (MT) in the green alga Chlamydomonas reinhardtii. We identify a maintenance DNA methyltransferase, DNMT1, mutation of which leads to the depletion of 95% of 5-methylcytosines (5mCs) in the nuclear genome. While the 5mC deficiency causes no discernible alteration in haploid vegetative growth or sexual differentiation, the dnmt1 homozygotes display substantially reduced spore viability and 4-progeny-tetrad frequency. Strikingly, in dnmt1 homozygotes, anomalous meiotic recombination takes place at MT, generating haploid progenies with mixed mating-type harboring both plus and minus markers. Although the repressive histone methylation H3K9me1 at MT is lost concurrently in dnmt1 strains, loss of histone methylation alone by gene deletion of the responsible histone methyltransferase SET3p does not lead to anomalous recombination at MT. Thus, DNA methylation, rather than histone modification, mediates the recombination suppression at MT in C. reinhardtii. This finding suggests that in early eukaryotes, which likely lacked histone-based chromatin modification, DNA methylation may have been co-opted to suppress meiotic recombination between alleles responsible for separate sexes.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for WT (CC-5155/CC-5325) strains and dnmt1 strains.

first: Tong

last: Ge


title: Memory B cells dominate the early antibody-secreting cell response to  SARS-CoV-2 mRNA vaccination in naïve individuals independently of their antibody affinity

first: Anna

last: Obraztsova

address: Im Neuenheimer Feld 280

department: B Cell Immunology

institute: German Cencer Research Center (DKFZ)

summary: Memory B cells (MBCs) formed over the individual’s lifetime constitute nearly half of the adult peripheral blood B cell repertoire in humans. To assess their response to novel antigens, we tracked the origin and followed the differentiation paths of MBCs in the early anti-S response to mRNA vaccination in SARS-CoV-2-naïve individuals on single-cell and monoclonal antibody level. Newly generated and pre-existing MBCs differed in their differentiation paths despite similar levels of SARS-CoV-2 and common corona virus S-reactivity. Pre-existing highly mutated MBCs showed no signs of germinal center re-entry and rapidly developed into mature antibody secreting cells (ASCs). In contrast, newly generated MBCs derived from naïve precursors showed strong signs of antibody affinity maturation before differentiating into ASCs. Thus, although pre-existing human MBCs have an intrinsic propensity to differentiate into ASCs, the quality of the anti-S antibody and MBC response improved through the clonal selection and affinity maturation of naïve precursors.

overall_design: Blood from five healthy volunteers (V1-5) was collected directly before and one, two, and three weeks (1w, 2w, 3w) after the first (I) and second (II) vaccination with BNT162b2. Donor V5 was excluded from analysis due to rapid anti-S IgG response indicating previous SARS-CoV-2 exposure. S-reacitve B cells (S+), activated B cells (CD71+) and plasmablasts (CD27+CD38+) were isolated from PBMC samples by fluorescence-activated cell sorting (FACS) and analyzed using scRNAseq

first: Zhe

last: Li

first: Hedda

last: Wardemann


title: DNA cytosine methylation suppresses meiotic recombination at the sex-determining region (Bisulfite-Seq)

overall_design: Whole-genome bisulfite sequencing (WGBS) analysis for WT, dnmt1 and set3 strains.


title: Genome-wide chromatin binding of ERRα and ERRγ in SH-SY5Y cells

city: Tokyo

first: Kaoru

last: Sato

address: 35-2 Sakae-cho, Itabashi-ku

country: Japan

institute: Tokyo Metropolitan Institute of Gerontology

summary: The SH-SY5Y Human neuroblastoma cell line was subcloned from the SK-N-SH cell line, which has been isolated from a bone marrow biopsy of a 4 year-old female patient. To examine the transcriptional regulation by ERRα and ERRγ in human neuronal cells, we investigated chromatin binding  regions of  ERRαlpha and ERRγ genome-wide in the SH-SY5Y cells. We detected thier target genes, which were largely overlap.

overall_design: ChIP-seq of ERRα and ERRγ in SH-SY5Y cells

first: Ken-ichi

last: Takayama

first: Satoshi

last: Inoue


title: Transcriptomes in Human neuroblastoma cell line SH-SY5Y depleted with ERRαlpha and ERRgamma

summary: The SH-SY5Y Human neuroblastoma cell line was subcloned from the SK-N-SH cell line, which has been isolated from a bone marrow biopsy of a 4 year-old female patient. To examine the overall distribution of gene expression under stress condition in human neuronal cells, we investigated changes in the transcriptome profiles in the SH-SY5Y cells depleted  with ERRαlpha and ERRgamma by gene knockdown. We detected changes in the expression levels for several genes.

overall_design: RNA-seq of control and ERRα- or ERRγ-depleted SH-SY5Y cells


title: Soluble Mesothelin-Related Peptide as a Prognosticator in Pleural Mesothelioma Patients Receiving Checkpoint Immunotherapy

status: Public on Aug 19 2024

city: Houston

first: Sung Wook

last: Kang

state: TX

address: one plaza

department: Surgery

institute: Baylor college of medicine

summary:
Objective: Immune checkpoint therapy (ICT) has significantly impacted malignant pleural mesothelioma (MPM) treatment. Despite some promising results from combination therapies, nearly half of MPM patients do not benefit, underscoring the urgent need for reliable predictive biomarkers. This study assesses the prognostic value of serum soluble mesothelin-related peptide (SMRP) and PD-L1 levels in MPM patients receiving ICT.
Results: Seventy-seven patients (62%) were treated with either anti-PD-(L)1 monotherapy, while the remaining 38% were given combination ICT. Higher pre-ICT SMRP levels were notably observed in epithelioid versus non-epithelioid MPM. Serum PD-L1 levels did not show significant differences between the groups. Univariable analysis identified durable clinical benefits, development of immune-related adverse events, and SMRP levels as significantly associated with OS. Multivariable analysis confirmed SMRP as an independent prognostic factor, with lower levels (≤1.35 nmol/L) correlating with improved OS (median survival: 23 months vs. 13 months). This finding was further validated in the prospective ICT clinical trial cohort.
Conclusions: SMRP emerges as a promising serum biomarker for predicting survival in MPM patients treated with ICT, warranting further prospective investigation.

overall_design: Methods: We conducted a retrospective analysis of 125 MPM patients treated with ICT by measuring pre-ICT serum levels of SMRP and PD-L1 using the MESOMARK and Luminex assays, respectively. We also examined the correlation of these serum levels with tumor mRNA expressions of MSLN and PD-L1. Both univariable and multivariable Cox regression analyses were used to determine independent prognosticators for overall survival (OS). A prospective ICT clinical trial and our historical cohort were included for validation.

first: Hyun-Sung

last: Lee

first: Bryan

last: Burt


title: GLUT1 overexpression in CAR-T cells induces metabolic reprogramming and enhances potency

city: Stanford

first: Yiyun

last: Chen

state: California

address: 265 Campus Dr Room G2105

department: Stanford Cancer Institute

institute: Stanford University

summary: The intensive nutrient requirements needed to sustain T cell activation and proliferation combined with competition for nutrients within the tumor microenvironment raise the prospect that glucose availability may limit CAR T cell function. Here, we sought to test the hypothesis that stable overexpression (OE) of the glucose transporter GLUT1 in primary human CAR-T cells would improve their function and antitumor potency. We observed that GLUT1OE in CAR-T cells increased glucose consumption, glycolysis, glycolytic reserve and oxidative phosphorylation and these effects were associated with decreased T cell exhaustion and increased Th17 differentiation. GLUT1OE also induced broad metabolic reprogramming associated with increased glutathione41 mediated resistance to reactive oxygen species, and increased inosine accumulation. When challenged with tumors, GLUT1OE CAR-T cells secreted more proinflammatory cytokines and mediated enhanced cytotoxicity in vitro and demonstrated superior tumor control and persistence in vivo. Our collective findings support a model wherein glucose availability is rate limiting for optimal effector CAR-T cell function and demonstrate that enhancing glucose availability via GLUT1OE provides a new approach to augment antitumor immune function.

overall_design: On days 14-16 control cells or GLUT1 overexpressing CAR-T cells were collected and total mRNA was isolated using Qiagen RNEasy Plus mini isolation kit. Bulk RNAseq was performed by Novogene using the NovaSeq platform.

first: Justin

last: Guerrero

first: Dorota

middle: D

last: Klysz

first: Elena

last: Sotillo

first: Crystal

last: Mackall


title: Set6: ERCC bulk short-read RNA-seq by Element Biosciences AVITI platform, additional samples

city: Pittsburgh

first: Shuchang

last: Liu

address: 203 Lothrop Street

institute: University of Pittsburgh

summary: DNA sequencing is a critical tool in modern biology. Over the last two decades, it has been revolutionized by the advent of massively parallel sequencing, leading to significant advances in genome and transcriptome sequencing of various organisms. Nevertheless, challenges such as accuracy, lack of competitive options and prohibitive costs associated with high throughput parallel short-read sequencing persist. Here, we conduct a comparative analysis between the Element Biosciences AVITI platform and its counterpart the Illumina NextSeq platform, testing DNA and RNA short-read sequencing, as well as synthetic long-read sequencing for single cells and RNA transcripts.

overall_design: Bulk short-read RNA-seq on Universal Human Reference with ERCC spike-in samples (Mix 1) by Element Biosciences AVITI platform, with four repeats

first: Silvia

first: Caroline

last: Obert

first: Yan-Ping

last: Yu

first: Junhua

last: Zhao

first: Bao-Guo

last: Ren

first: Kelly

last: Blease

first: Benjamin

last: Krajacich

first: Wenjia

last: Wang

first: Kyle

last: Metcalfe

first: Mat

last: Smith

first: Tuval

last: Ben-Yehezkel

first: Jian-Hua

last: Luo


title: DNA cytosine methylation suppresses meiotic recombination at the sex-determining region (ChiP-Seq)

first: Xiuqi

last: Gui

overall_design: Chromatin immunoprecipitation sequencing (ChIP-seq) for histone modifications H3K4me1, H3K9me1, H3K4me3 and H3K9me3 in WT, dnmt1 and set3 strains.

first: Tong

last: Ge


title: DNA cytosine methylation suppresses meiotic recombination at the sex-determining region

overall_design: Refer to individual Series


title: DFF-ChIP: a method to detect and quantify complex interactions between RNA polymerase II, transcription factors, and chromatin

city: Iowa City

first: David

last: Price

state: Iowa

address: 500 Newton Road, 260 EMRB

institute: University of Iowa

summary: Recently, we introduced a chromatin immunoprecipitation (ChIP) technique utilizing the human DNA Fragmentation Factor (DFF) to digest the DNA prior to immunoprecipitation (DFF-ChIP) that provided the precise location of transcription complexes and their interactions with neighboring nucleosomes. Here we expand the technique to new targets and provide useful information concerning purification of DFF, digestion conditions, and the impact of crosslinking. DFF-ChIP analysis was performed individually for subunits of Mediator, DSIF, and NELF that that do not interact with DNA directly, but rather interact with RNA polymerase II (Pol II). We found that Mediator was associated almost exclusively with preinitiation complexes (PICs) and that DSIF and NELF were associated with engaged Pol II and, in addition, potential intermediates between PICs and early initiation complexes. DFF-ChIP was then used to analyze the occupancy of a tight binding transcription factor, CTCF, and a much weaker binding factor, glucocorticoid receptor (GR), with and without crosslinking and to compare these results to those from standard ChIP-Seq that employs sonication and CUT&RUN which utilizes MNase to fragment the genomic DNA. The results presented indicate that DFF-ChIP reveals details of occupancy that are not available using other methods including information revealing pertinent protein:protein interactions.

overall_design: Nuclei from SUB-B15 were rapidly isolated following no treatment or treatment with 1 µM dexamethasone. After 1 hour of dexamethasone, both untreated and treated nuclei were either immediately isolated or crosslinked with 1% formaldehyde for 10 minutes followed by immediate quenching with 1M Tris. The resulting nuclei were then digested with DNA fragmentation Factor (DFF), an endonuclease with reduced intra-nucleosomal cutting as compared to Micrococcal nuclease (MNase), to generate primarily mono-nucleosomes. After release of chromatin from the nucleus following light sonication, transcription factors were then immunoprecipitated from the released chromatin. SUP-B15 DFF-ChIP was spiked in with 2% mouse nuclei (4T1) cells. HeLa nuclei were similarly prepared without treatment with dexamethasone or nuclei spike-in. Finally, SUP-B15 and B1 nuclei were prepared for ChIP-Seq as described in the methods section utilizing different crosslinking, sonication, and library prep conditions.

last: Spector

first: Juan

middle: F

last: Santana

first: Miles

last: Pufall

middle: H


title: High-throughput transposon mutagenesis in the family Enterobacteriaceae reveals core essential genes and rapid turnover of essentiality

city: Würzburg

first: Lars

last: Barquist

state: Bayern

address: Josef-Schneider-Straße 2 / Bau D15

institute: Helmholtz Institute for RNA-based Infection Research

summary: The Enterobacteriaceae are a scientifically and medically important clade of bacteria, containing the gut commensal and model organism Escherichia coli, as well as several major human pathogens including Salmonella enterica and Klebsiella pneumoniae. Essential gene sets have been determined for several members of the Enterobacteriaceae, and the E. coli Keio single-gene deletion library is often regarded as a gold standard for gene essentiality studies. However, it remains unclear how much essential genes vary between strains and species. To investigate this, we have assembled a collection of thirteen sequenced high-density transposon mutant libraries from five genera of the Enterobacteriaceae. We first benchmark a number of gene essentiality prediction approaches, investigate the effects of transposon density on essentiality prediction, and identify biases in transposon insertion sequencing data. Based on these investigations we develop a new classifier for gene essentiality. Using gene essentiality defined by this new classifier, we define a core essential genome in the Enterobacteriaceae of 201 universally essential genes, and reconstruct an ancestral essential gene set of 296 genes. Despite the presence of a large cohort of variably essential genes, we find an absence of evidence for genus-specific essential genes. A clear example of this sporadic essentiality is given by the set of genes regulating the σE extracytoplasmic stress response, which appears to have independently become essential multiple times in the Enterobacteriaceae. Finally, we compare our essential gene sets to the natural experiment of gene loss in obligate insect endosymbionts closely related to the Enterobacteriaceae. This isolates a remarkably small set of genes absolutely required for survival, and uncovers several instances of essential stress responses masked by redundancy in free-living bacteria.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium

sample_organism: Salmonella enterica subsp. enterica serovar Enteritidis

overall_design: Comparison of gene essentiality measurements generated by transposon insertion sequencing

first: Gemma

last: Langridge

first: Amy

middle: K

last: Cain

first: Christine

last: Boinett

first: Moataz

last: Abd El Ghany


title: Butyrate and propionate are microbial danger signals that activate the NLRP3-inflammasome in human macrophages in the presence of TLR stimulation

city: Badalona

first: LUCIA

last: LORENZI

state: Barcelona

address: Ctra de Can Ruti, Camí de les Escoles s/n

country: Spain

institute: Josep Carreras Research Institute

summary: Short chain fatty acids (SCFAs) are immunomodulatory compounds produced by the microbiome through fermentation of dietary fibre. Although they are generally considered beneficial for gut health, patients suffering from inflammatory bowel disease (IBD) have shown poor tolerance to fibre-rich diets, suggesting that SCFAs may have contrary effects under inflammatory conditions. To investigate this, we examined the effect of SCFAs on human macrophages in the presence of toll-like receptor agonists. In contrast to their anti-inflammatory effects under steady state conditions, we observed that the SCFAs butyrate and propionate triggered the activation of the NLRP3 inflammasome when added in conjunction with TLR agonists. Mechanistically, butyrate and propionate activated NLRP3 by inhibiting HDACs 1-3 and 10, leading to an uneven distribution of histone hyperacetylation that resulted in alterations in the transcriptome. Specifically, there was a lack of hyperacetylation at the loci of the CFLAR and IL10 genes, two important inhibitors of NLRP3 inflammasome activation. The concurrent loss of transcription and protein expression of cFLIP and IL-10 enabled caspase-8-dependent NLRP3-inflammasome activation. SCFA-driven NLRP3 activation did not require potassium efflux and did not result in cell death but rather triggered hyperactivation and IL-1b release. Our findings demonstrate that butyrate and propionate are bacterially-derived, viability-dependent danger signals (vita-PAMPs) that regulate NLRP3 inflammasome activation through epigenetic modulation of the inflammatory response.

overall_design: To assess the effect of SCFAs on the LPS-mediated transcriptome in hMDM, we conducted RNA-seq in hMDM treated with butyrate, propionate or acetate in the presence of LPS for 16h. NaCl was included as the vehicle alone control, and TSA was included to define the effect of HDAC inhibition on the LPS response.

first: Matthew

last: Mangan

first: Eicke

last: Latz

first: Sergi

last: Cuartero

first: Lucía

last: Lorenzi


title: High mechanical conditioning by tumor extracellular matrix stiffness is a predictive biomarker for anti-fibrotic therapy in HER2-negative breast cancer

city: Madrid

first: Leonardo

middle: Daniel

last: Garma

state: Madrid

address: Melchor Fernández Almagro 3

institute: Spanish National Cancer Research Center

summary:
Background
Tumor progression has been linked to stiffening of the extracellular matrix (ECM) caused by fibrosis. Cancer cells can be mechanically conditioned by stiff ECM, exhibiting a 1004-gene signature (MeCo score). Nintedanib has demonstrated anti-fibrotic activity in idiopathic pulmonary fibrosis. This study explores nintedanib’s anti-fibrotic effect on breast cancer outcomes.

Methods
We present long-term follow-up and analysis of a neoadjuvant randomized Phase 2 trial in early HER2-negative breast cancer. Patients (N = 130) underwent a baseline biopsy and received 12 paclitaxel courses alone (control arm) or in combination with nintedanib (experimental arm). Tumor MeCo score was determined by RNAseq. The primary aim was to assess nintedanib's impact on event-free survival (EFS) based on MeCo scores.

Results
Follow-up data were retrieved from 111 patients; 75 baseline and 24 post-run-in phase samples were sequenced. After median follow-up of 9.67 years, median EFS was not statistically different between arms (P = 0.37). However, in the control arm, High versus Low MeCo patients had a statistically higher relapse risk: hazard ratio (HR) = 0.21; P = 0.0075. This risk was corrected by nintedanib in the experimental arm: HR = 0.37; P = 0.16. Nintedanib demonstrated pharmacodynamic engagement, reducing the MeCo score by 25% during the run-in phase (P<0.01). Patients with Low MeCo after run-in had the best long-term prognosis (HR = 0.087; P = 0.03).

Conclusions
High MeCo is predictive of poor outcomes in HER2-negative early breast cancer, although this risk can be mitigated by nintedanib, which is able to specifically reduce mechanical conditioning.

overall_design: Collected tumor samples from NCT01484080 clinical trial were used for retrospective gene expression analysis on breast cancer patients before and after treatment with the antiangiogenic drug bevacizumab. Total RNA from tumors embedded in paraffined blocks was isolated using RNeasy FFPE it (Quiagen, #73504) according to the manufacturer’s protocol. RNA quality was determined by Agilent's 2100 Bioanalyzer Lab-Chip technology.

first: Miguel

last: Quintela-Fandino

first: Begoña

last: Bermejo

first: Esther

last: Zamora

first: Fernando

last: Moreno

first: Adam

last: Grant

last: Watson

first: Ramón

last: Colomer

first: Ghassan

last: Mouneimne


overall_design: Chromatin immunoprecipitation sequencing (ChIP-seq) of the histone mark H3K27ac (with Drosophila spike-in chromatin form normalization) in human GM-MDMs.


title: Set5: HCC single-cell Loop-seq long-read RNA-seq by Element Biosciences AVITI platform

first: Shuchang

last: Liu

overall_design: HCC samples and benign liver samples were freshly dissected from a patient who underwent liver transplantation. Long-read single-cell transcriptome sequencing was performed by LoopSeq, Element Biosciences. Each library (tumor or benign) was sequenced by four runs and eventually pooled together. Same sample as we did in GSE223743, but sequenced with Element Biosciences AVITI machine.

first: Silvia

first: Caroline

last: Obert

first: Yan-Ping

last: Yu

first: Junhua

last: Zhao

first: Bao-Guo

last: Ren

first: Kelly

last: Blease

first: Benjamin

last: Krajacich

first: Wenjia

last: Wang

first: Kyle

last: Metcalfe

first: Mat

last: Smith

first: Tuval

last: Ben-Yehezkel

first: Jian-Hua

last: Luo


title: Set3: ERCC bulk Loop-seq long-read RNA-seq by Element Biosciences AVITI platform

overall_design: Bulk long-read RNA-seq on ERCC spike-in samples by Element Biosciences AVITI platform. Data for all the long reads and data only for full-length transcripts.


title: Set4: ERCC bulk Loop-seq long-read RNA-seq by Illumina NovaSeq platform


title: Set2: ERCC bulk short-read RNA-seq by Illumina NextSeq platform

overall_design: Bulk short-read RNA-seq on ERCC spike-in samples by Illumina NextSeq platform


title: An IDR-dependent mechanism for nuclear receptor control of mediator interaction with RNA polymerase II

city: bethesda

first: Seolkyoung

last: Jung

state: MD

address: 10 Center Dr

department: NIAMS

institute: NIH

summary: We investigated modulation of metazoan MED interaction with RNA polymerase II (Pol II) by antagonistic effects of the MED26 subunit and the Cdk8 kinase module (CKM), both of which associate dynamically with MED. Results from in vivo studies point to a general and important role of MED26 in transcription, connected to Pol II recruitment. Analysis of CKM-MED and MED26-MED complexes by cryo-EM and crosslinking-mass spectrometry showed that CKM and MED26 have opposite effects on mMED association with Pol II (blocking and facilitating it, respectively), and revealed that the structural basis for their antagonistic interaction with MED relates to extended intrinsically-disordered regions (IDRs) in MED26 and the CKM subunit MED13 competing for interaction with MED. We found CKM-MED to be the preferred target of nuclear receptors (NRs), whose binding can initiate rearrangements of the MED13 IDR that allow MED26-dependent interaction of CKM-MED with the Pol II carboxy-terminal domain (CTD). Our results suggest that activators might play a critical role independent of MED recruitment, instead “activating” CKM-MED for CTD interaction in a MED26-dependent manner and, thus, controlling the start of preinitiation complex assembly. The presence of an intermediate state in which MED26 and the CTD II can interact with CKM-MED suggests a mechanism for fast, recruitment-independent activation connected to promoter-proximal Pol II pausing, with an activator enabling interaction between the originally inactive CKM-MED and a paused Pol II poised to initiate transcription. We found that CTD interaction with CKM-MED influences the subunit composition of the Tail module and this allostery suggests that the mechanism we propose could apply to non-NR activators targeting Tail subunits.

overall_design: spike-in control mRNAseq, chipseq, CUT&RUN

first: Haiyan

first: Jiaqin

last: Li

first: Yufei

last: Xiang

first: Sohail

last: Malik

first: Supriya

last: Vartak

first: Natalie

last: Young

first: McKayla

last: Ryner

first: Andrea

last: Conte

first: Robert

middle: G

last: Roeder

first: Yi

last: Shi

first: Rafael

last: Casellas

first: Francisco

last: Asturias


title: Type 2 cytokine-dependent skin barrier regulation in personalized 2D- and 3D skin models of atopic dermatitis: A pilot study

city: Kiel

first: Matthias

last: Hübenthal

state: SH

address: Rosalind-Franklin-Str. 9

department: Dermatology, Venereology and Allergy

institute: University Hospital Schleswig-Holstein

summary: Keratinocytes from healthy donors stimulated with type 2 cytokines are often used to experimentally study atopic dermatitis (AD) inflammatory responses. Due to potential intrinsic alterations, it seems favorable to use keratinocytes from AD patients. Keratinocytes isolated from hair follicles offer a non-invasive approach to investigate AD-derived keratinocytes. To evaluate whether such AD-derived keratinocytes are suitable to mimic AD inflammatory responses we compared hair follicle-derived keratinocytes from healthy donors and AD patients in a type 2 cytokine environment. Stimulation of AD-derived keratinocytes with IL-4 and IL-13 induced higher expression changes of AD-associated markers as compared to healthy keratinocytes. The combination of IL-4 and IL-13 generally induced highest expression changes, but IL-13 alone also induced significant changes of AD-specific markers. Similar to the 2D cultures, IL-4/IL-13 stimulation of 3D skin models generated with AD-derived keratinocytes modulated the expression of several AD-relevant factors. Whole transcriptome analysis revealed that IL-4 and IL-13 acted similarly on these 3D skin models. Histologically, IL-13 alone and in combination with IL-4 increased epidermal spongiosis, a histological hallmark of AD skin. Taken together, our pilot study suggests that hair follicle-derived keratinocytes from AD patients represent a useful model system to study AD-related inflammation in a personalized in vitro model.

overall_design: Organotypic 3D skin models generated from hair follicle-derived human keratinocytes from two atopic dermatitis patients were left unstimulated or stimulated with Th2 cytokines IL-4, IL-13 and IL-4+IL-13. Two stimulations were done for each donor and each condition.

first: Hila

last: Emmert

first: Franziska

last: Rademacher

first: Regine

last: Gläser

first: Hanne

last: Norsgaard

first: Stephan

last: Weidinger

first: Jürgen

last: Harder


title: RNA-Seq of Nothobranchius furzeri brain of male fishes of two strains (MZM_A41 and MZM-0410) of age 39/35 dph (days post hatch)

city: Jena

first: Marco

last: Groth

address: Beutenbergstraße 11

department: Core Facility - Next Generation Sequencing

institute: Leibniz Institute on Aging - FLI

summary: A vast body of studies is available that describes age-dependent gene expression in relationship to aging in a number of different model species. These data were obtained from animals kept in conditions with reduced environmental challenges, abundant food and deprivation of natural sensory stimulation. Here we compared wild- and captive-aging in the short-lived turquoise killifish (Nothobranchius furzeri). These fish inhabit temporary ponds in the African savannah and when the ponds are flooded eggs hatch synchronously enabling a precise timing of the population age. We collected brains for wild fish of different ages and quantified the global age-dependent regulation of transcripts using RNAseq. A major difference between captive and wild population is that wild population reach larger sizes and cease their growth rapidly, enabling the analysis of age-dependent gene expression without the confounding effect of adult brain growth.We found that the majority of differentially-expressed genes show the same direction of regulation in wild- and captive-population. However, a number of genes were regulated in opposite direction. Genes down-regulated in the wild and up-regulated in captivity were enriched for terms related to neuronal communication. Genes up-regulated in the wild and down-regulated in captive conditions were up-regulated in terms related to DNA replication. Finally, the rate of age-dependent gene regulation was higher in the wild animals suggesting a phenomenon of accelerated aging.

overall_design: 8 samples (sex: males, tissue: whole brain): MZM_A41 (4 samples, age: 39 dph), MZM-0410 (4 samples, age: 35 dph)

first: Mario

last: Baumgart

first: Mariateresa

last: Mazzetto

first: Martin

last: Reichard

first: Alessandro

last: Cellerino


title: Optimization of the Irf8 +32 kb enhancer disrupts dendritic cell lineage segregation [scRNA-seq]

status: Public on Aug 18 2024

city: St. Louis

first: Feiya

last: Ou

state: MO

address: 4939 Children's Place

department: Pathology & Immunology

institute: Washington University in St. Louis

summary: Autoactivation of lineage-determining transcription factors (TFs) mediates bistable expression to generate distinct cell phenotypes essential for complex body plans. Classical dendritic cells type 1 (cDC1) and type 2 (cDC2) provide non-redundant functions required for defense against distinct immune challenges. Interferon Regulatory Factor 8 (IRF8), the cDC1 lineage-determining TF, undergoes autoactivation in cDC1 progenitors to establish cDC1 identity, yet its expression is downregulated during cDC2 differentiation by an unknown mechanism. This study reveals that the Irf8 +32 kb enhancer, responsible for IRF8 autoactivation, has been tuned to possess low-affinity IRF8 binding sites. Incorporation of multiple high-affinity IRF8 binding sites into the Irf8 +32 kb enhancer induces erroneous IRF8 autoactivation in specified cDC2 progenitors, causing their redirection towards cDC1 and a novel hybrid DC subset with mixed lineage phenotypes. These developmental alterations critically impair both cDC1- and cDC2-dependent arms of immunity. Collectively, our findings underscore the significance of enhancer suboptimization in the developmental segregation of classical dendritic cells required for normal immune function.

overall_design: BM and spleens were harvested from two WT and two Irf8 +32H/H mice. The BM samples were depleted of lin+ cells expressing CD3e, CD8b, CD11b, CD19, B220, ly-6G, TER-119, and NK1.1. Each sample was stained with fluorochrome-conjugated antibodies and labeled with a unique Antibody Capture TotalSeq B antibody (Biolegend) before sorting for lin- Flt3+ Kitint-lo cells. Two samples from each genotype were pooled and resuspended in PBS with 0.04% BSA at a final concentration of approximately 1,000 cells/mL. The spleen samples were enriched for CD11c-expressing cells, similarly stained with fluorochrome-conjugated antibodies and labeled with a unique Antibody Capture TotalSeq B antibody (Biolegend), before further sort-purification for CD11c+ cells. All four samples were pooled and resuspended in PBS with 0.04% BSA at approximately 1,000 cells/mL. These were loaded on a 10× Genomics Chromium Single Cell Controller at GTAC@MGI at Washington University School of Medicine. Library preparation was performed using the 10× Genomics Next GEM Single Cell 3’ Reagents Kit v3. Libraries were sequenced using an Illumina Novaseq 6000 sequencer, producing 150 bp paired-end reads. Sequencing targeted depths of 1B reads for the gene expression (GEX) library and 100M reads for the hashtag oligo (HTO) library, respectively. The Cell Ranger pipeline v8.0.0 was used for aligning reads to the mm10 reference genome, single cell counting, barcode processing, and sample demultiplexing. scRNA-seq downstream analysis was conducted using Seurat v5.0.3 in R. After removing unwanted cells, UMI counts in each cell were normalized using log transformation with a scale factor of 10,000. For each dataset, 2,000 highly variable genes were identified and used for PCA. For the BM dataset, cell cycle phase scores were calculated, and the difference between G2M and S phase scores was regressed out. Dimensional reduction and clustering were performed using the FindNeighbors, RunUMAP, and FindClusters functions, utilizing the top 30 PCs. The clustering resolution was set at 0.6 for the BM dataset and 0.5 for the spleen dataset.

first: Kenneth

middle: M

last: Murphy


title: Set1: ERCC bulk short-read RNA-seq by Element Biosciences AVITI platform

first: Shuchang

last: Liu

overall_design: Bulk short-read RNA-seq on ERCC spike-in samples by Element Biosciences AVITI platform

first: Silvia

first: Caroline

last: Obert

first: Yan-Ping

last: Yu

first: Junhua

last: Zhao

first: Bao-Guo

last: Ren

first: Kelly

last: Blease

first: Benjamin

last: Krajacich

first: Wenjia

last: Wang

first: Kyle

last: Metcalfe

first: Mat

last: Smith

first: Tuval

last: Ben-Yehezkel

first: Jian-Hua

last: Luo


title: Transcription factor cascades during fasting amplify gluconeogenesis and instigate a secondary wave of ketogenic gene transcription.

city: Rehovot

first: Ido

last: Goldstein

address: POB 12

department: Institute of Biochemistry, Food Science and Nutrition

country: Israel

institute: The Hebrew University of Jerusalem

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


title: Transcription factor cascades during fasting amplify gluconeogenesis and instigate a secondary wave of ketogenic gene transcription. [ChIP-Seq]

summary: During fasting, bodily homeostasis is maintained due to hepatic production of glucose (via gluconeogenesis) and ketone bodies (via ketogenesis). The major hormones governing hepatic fuel production are glucagon and glucocorticoids who initiate a complex transcriptional program aimed at supporting gluconeogenesis and ketogenesis. Here, we found that in addition to the known metabolic genes induced by glucagon and glucocorticoids, these hormones each induce a set of genes encoding transcription factors (TFs) thereby initiating transcriptional cascades. Glucocorticoids activate the glucocorticoid receptor (GR) that induces the genes encoding two TFs - C/EBPβ and PPARα. Transcriptomic analysis combined with gene silencing revealed the role of C/EBPβ as an amplifier of hormone-induced gluconeogenesis. In contrast, the GR-PPARα cascade initiated a secondary transcriptional wave of genes supporting ketogenesis. We show that a dual treatment of glucocorticoids with a PPARα agonist leads to synergistic induction of ketogenic genes and that this induction is dependent on protein synthesis. Genome-wide analysis of enhancer dynamics revealed numerous enhancers activated by the GR-PPARα cascade. These enhancers are proximal to ketogenic genes, are enriched for the PPARα binding motif and show increased PPARα binding as profiled by ChIP-seq. In summary, this study reveals abundant TF cascades occurring during fasting. These cascades serve two separated purposes: the amplification of the primary gluconeogenic transcriptional program and the induction of a secondary gene program aimed at enhancing ketogenesis.

overall_design: Primary hepatocytes were isolated from male, 8-10 weeks-old mice (strain C57BL/6JOlaHsd). Three hours after plating, media was changed to Williams E media. After 18h, the hepatocytes were treated with hormones (corticosterone 1 µM, Wy14643 10 µM or a dual treatment) for 8h.

first: Dana

last: Goldberg


title: Genetic and developmental divergence in the neural crest programme between cichlid fish species

city: Basel

first: Grégoire

last: Vernaz

address: Vesalgasse 1

institute: University of Basel

summary: Neural crest (NC) is a vertebrate-specific embryonic progenitor cell population at the basis of important vertebrate features such as the craniofacial skeleton and pigmentation patterns. Despite the wide-ranging variation of NC-derived traits across vertebrates, the contribution of NC to species diversification remains underexplored. Here, leveraging the adaptive diversity of African Great Lakes' cichlid species, we combined comparative transcriptomics and population genomics to investigate the evolution of the NC genetic program in the context of their morphological divergence. Our analysis revealed substantial differences in transcriptional landscapes across somitogenesis, an embryonic period coinciding with NC development and migration. This included dozens of genes with described functions in the vertebrate NC gene regulatory network, several of which showed signatures of positive selection. Among candidates showing between-species expression divergence, we focused on teleost-specific paralogs of the NC-specifier sox10 (sox10a and sox10b) as prime candidates to influence NC development. These genes, expressed in NC cells, displayed remarkable spatio-temporal variation in cichlids, suggesting their contribution to interspecific morphological differences, such as craniofacial structures and pigmentation. Finally, through CRISPR/Cas9 mutagenesis, we demonstrated the functional divergence between cichlid sox10 paralogs, with the acquisition of a novel skeletogenic function by sox10a. When compared with teleost models zebrafish and medaka, our findings reveal that sox10 duplication, although retained in most teleost lineages, had variable functional fates across their phylogeny. Altogether, our study suggests that NC-related processes—particularly those controlled by sox10s—are involved in generating morphological diversification between species and lays the groundwork for further investigations into the mechanisms underpinning vertebrate NC diversification.

sample_organism:
Astatotilapia calliptera
Rhamphochromis sp. 'chilingali'

overall_design: Comparative transcriptomics analysis across somitogenesis using RNAsequencing between two Lake Malawi cichlid species, i.e., A. calliptera 'Mbaka' and Rhamphochromis sp. 'chilingali'. The main steps include gene mapping (A.calliptera reference genome assembly), quantification (using STAR and HTSeq - output is DESeq2-normalised gene count) and differential expression analysis (using DESeq2).

first: M. Emília

last: Santos

first: Aleksandra

last: Marconi


title: Colibactin-driven colon cancer requires adhesin-mediated epithelial binding

city: Gent

first: Lars

last: Vereecke

address: Technologiepark-Zwijnaarde 927

department: IRC

country: Belgium

institute: VIB

summary: Various bacteria are suggested to contribute to colorectal cancer (CRC) development, including pks+ E. coli, which produces the genotoxin colibactin that induces characteristic mutational signatures in host epithelial cells. However, it remains unclear how the highly unstable colibactin molecule is able to access host epithelial cells to cause harm. Using the microbiota-dependent ZEB2-transgenic mouse model of invasive CRC, we demonstrate that the oncogenic potential of pks+ E. coli critically depends on bacterial adhesion to host epithelial cells, mediated by the type-1 pilus adhesin FimH and the F9-pilus adhesin FmlH. Blocking bacterial adhesion using a pharmacological FimH inhibitor attenuates colibactin-mediated genotoxicity and CRC exacerbation. We also show that allelic switching of FimH strongly influences genotoxic potential of pks+ E. coli and can induce a genotoxic gain-of-function in the probiotic strain Nissle 1917. Adhesin-mediated epithelial binding subsequently allows the production of the genotoxin colibactin in close proximity to host epithelial cells, which promotes DNA damage and drives CRC development. These findings present promising therapeutic avenues for the development of anti-adhesive therapies aimed at mitigating colibactin-induced DNA damage and inhibiting the initiation and progression of CRC, particularly in individuals at risk for developing CRC.

overall_design: To investigate the effect of pks+ E. coli 11G5 infection (compared to the commensal E. coli Nissle) on colorectal cancer, we infected healthy (wildtype, WT) and Zeb2IEC-Tg/+ mice (model of microbiota-dependent invasive colorectal carcinoma) with either E. coli Nissle or E. coli 11G5 and isolated immune (CD45+) and epithelial (Epcam+) cells to evaluate their transcriptome.

first: Maude

last: Jans

first: Magdalena

last: Kolata

first: Gillian

last: Blancke

first: Aline

last: D’Hondt

first: Claudia

last: Gräf

first: Maarten

last: Ciers

first: Mozes

last: Sze

first: Alexandra

last: Thiran

first: Ioanna

last: Petta

first: Vanessa

last: Andries

first: Sara

last: Verbandt

first: Engy

last: Shokry

first: David

last: Sumpton

first: Johan

last: Vande Voorde

first: Geert

last: Berx

first: Sabine

last: Tejpar

last: van Loo

first: Iliyan

last: Iliev

first: Han

last: Remaut


title: De-phosphorylation of bZIP59 by PP2A ensures appropriate shade avoidance response in Arabidopsis

city: Shanghai

first: Lin

last: Li

address: 2005 Songhu Road, Yangpu Distric

department: school of life science

institute: Fudan university

summary: Shade can trigger the shade avoidance syndrome (SAS) in shade-intolerant species, which cause exaggerated growth and affect crop yield. We report that Arabidopsis transcription factors bZIP59 negatively regulate SAS. To identify direct targets of bZIP59 at the genome-wide level, we performed ChIP-Seq using ProbZIP59::bZIP59-GFP/bzip59 transgenic plants under white light or transferred to shade conditions for 2 hours. Our results indicated shade light dramatically increased the DNA binding ability of bZIP59, and shade-enhanced binding of bZIP59 majorly located around transcriptional start site (TSS) of genes.

overall_design: 7-day-old white-light-grown ProbZIP59::bZIP59-GFP/bzip59 seedlings were treated 2 hr shade before harvesting for DNA extraction.

first: Fengquan


title: Effect of bZIP59 on transcriptional regulation during shade avoidance responses in Arabidopsis

summary: Shade can trigger the shade avoidance syndrome (SAS) in shade-intolerant species,which cause exaggerated growth and affect crop yield.We report that Arabidopsis transcription factors bZIP59 negatively regulate SAS. To investigate the function of bZIP59 during SAS, we performed RNA-Seq of wild type Col-0 and a T-DNA insertion line bzip59 (SALK_024459) in while light and shade.

overall_design: 7-day-white-light grown seedlings (Col-0 and bzip59) treated with 2h shade before RNA extraction.


title: Transcription factor cascades during fasting amplify gluconeogenesis and instigate a secondary wave of ketogenic gene transcription. [RNA-Seq 1]

first: Ido

last: Goldstein

overall_design: primary hepatocytes were isolated from male, 8-10 weeks-old mice (strain C57BL/6JOlaHsd). Three hours after plating, media was changed to Williams E media and the PMH were infected with adenovirus: Ad-ShCebpb. After 12 h, hormones (Glucagon 100 nM , corticosterone 1 µM or a dual treatment)  were added for 8h.

first: Dana

last: Goldberg


title: Transcriptome data of compatible soybean host inoculated with Sinorhizobium fredii with variants of NopP and NopI

city: Hong Kong

first: Hon-Ming

last: Lam

state: Hong Kong

address: The Chinese University of Hong Kong

country: Hong Kong

institute: The Chinese University of Hong Kong

summary: Nodulation Outer Protein P (NopP) and NopI of the type 3 secretion system (T3SS) of the rhizobium determine host specificity. Sinorhizobium fredii CCBAU25509 (R2) and CCBAU45436 (R4) have different NopP and NopI variants, affecting their respective symbiotic compatibilities with the cultivated soybean C08 and the wild soybean W05. Swapping the NopP variants between R2 and R4 has been shown to switch their compatibility with C08 with the rj2/Rfg1 genotype. To understand the effects of Nops on host compatibility, analyses on the transcriptomic data of W05 roots and nodules inoculated with S. fredii strains containing Nop variants uncovered many differentially expressed genes related to nodulation and nodule functions, providing important information on the effects of Nops on hosts and nodules.

overall_design: To investigate the function of Nops in the regulationg of soybean inocualtion and nitrogen fixation, we swapped the NopP and NopI between Sinorhizobium fredii CCBAU25509 and CCBAU45436 and used these strains to infect soybean W05.

first: Kejing

last: Fan

first: Zhixia

last: Xiao

first: Liping

last: Wang

first: Wai-Lun

last: Cheung

first: Fuk-Ling

last: Wong

first: Feng

last: Zhang

first: Man-Wah


title: Chromatin Remodelling in Damaged Intestinal Crypts Orchestrates Redundant TGFβ and Hippo Signalling to Drive Regeneration

city: Toronto

first: Jeff

last: Wrana

state: Ontario

address: 600 University Avenue

institute: Lunenfeld-Tanenbaum Research Institute

summary: Regenerative cell state dynamics are under-characterized.  Intestinal damage prompts reprogramming into revival stem cells (revSCs) that reconstitute Lgr5+ intestinal stem cells (ISCs). Here, single nuclear multiomics of crypts regenerating from irradiation shows revSC epigenetic profiles overlap with ISCs and differentiated lineages.  RevSC genes themselves are accessible throughout homeostatic epithelia, while damage-induced crypt remodelling converges on the Hippo and TGFβ pathway that is transiently activated in the crypt and directly induces functional revSCs.  Combinatorial analysis of gene expression suggests multiple sources of revSCs, and we show TGFb can reprogram Enterocytes, Goblet, and Paneth cells into revSCs, further demonstrating individual revSCs form organoids.  Despite this, loss of TGFβ signalling yielded mild regenerative defects, whereas interference in both Hippo and TGFβ led to rapid intestinal collapse with no detectable revSCs or ISCs. Regenerative signalling is thus poised for activation by a compensatory system of crypt-localized, transient morphogen cues that support robust intestinal regeneration.

overall_design: Mouse small intestine at 0, 1, and 2 days following 12Gy irradiation

first: Mardi

last: Fink

first: Kizito

last: Njah

first: Shyam

last: Patel

first: David

middle: P

last: Cook

first: Vanessa

last: Man

first: Francesco

last: Ruso

first: Arsheen

last: Rajan

first: Masahiro

last: Narimatsu

first: Andreea

last: Obersterescu

first: Melanie

last: Pye

first: Daniel

last: Trcka

first: Kin

last: Chan

first: Arshad

last: Ayyaz

first: Jeffrey

middle: L


title: Butyrate and propionate are microbial danger signals that activate the NLRP3-inflammasome in human macrophages in the presence of TLR stimulation

first: LUCIA

last: LORENZI

overall_design: Refer to individual Series


title: Transcription factor cascades during fasting amplify gluconeogenesis and instigate a secondary wave of ketogenic gene transcription. [RNA-Seq 2]

first: Ido

last: Goldstein

overall_design: Primary hepatocytes were isolated from male, 8-10 weeks-old mice (strain C57BL/6JOlaHsd). Three hours after plating, media was changed to Williams E media. After 18 h, hormones (corticosterone 1 µM, Wy14643 10 µM or a dual treatment)  were added for 8h.

first: Dana

last: Goldberg


title: Rnf20 levels modulate the VEGF-Notch signaling circuits during sprouting angiogenesis [ChIP-seq]

city: Mannheim

first: Gergana

last: Dobreva

state: Baden Württemberg

address: Ludolf-Krehl-Str. 7-11

department: Cardiovascular Genomics and Epigenomics

institute: Medical Faculty Mannheim/University of Heidelberg

summary: Tight control of cell fate choices is crucial for proper vessel development. Here we show that Rnf20, the major E3 ubiquitin ligase of histone H2B, plays a key role in the tight control of VEGF-Notch signaling, which is crucial for proper vessel growth and patterning, as well as for the dynamic tip-stalk cell fate at the vascular front. We demonstrate that Rnf20 is dynamically expressed in the developing retina and controls vessel growth through two distinct modes of action. On the one hand, it restricts gene activation by the endothelial transcription factor ERG and on the other, it orchestrates large-scale mRNA processing events, which change the bioavailability and function of critical pro-angiogenic factors. We show that Rnf20 plays a key role for the upregulation of both VEGFR2 through alternative polyadenylation and VEGFA through intron inclusion, as well as for suppressing the ability of Notch1 to bind to chromatin. Interestingly, perturbations of RNF20 have been associated with complex cardiovascular malformations in human patients, suggesting that delineating the mechanisms that control Rnf20 expression and activity may provide new insights into diseases caused by vascular dysfunction.

overall_design: HUVEC cells were transfected with SiCTR or siRNF20 to follow ChIP-seq with Pol 2 antibody following the protocol for ChiP-seq described in (PMID: 32065070)

first: Nalan

last: Tetik-Elsherbiny

first: Julio

last: Cordero


title: RNF20-mediated transcriptional pausing and alternative splicing of pro-angiogenic genes orchestrate vessel growth [05H2Bub_siRNF20_ChIP_seq_HUV]

summary: Signal-responsive gene expression is essential for vascular growth and patterning, yet the mechanisms allowing the integration of signaling inputs and transcriptional activities are largely unknown. Here we show that RNF20, the major E3 ubiquitin ligase of histone H2B, plays a key role during sprouting angiogenesis by mediating Pol II promoter-proximal pausing at pro-angiogenic genes. Furthermore, it orchestrates large-scale mRNA processing events, which change the bioavailability and function of critical pro-angiogenic factors, such as VEGFA. Mechanistically, we show that RNF20 restricts ERG-dependent gene activation through the VEGF-ERK1/2 axis while enabling Notch1 to bind to chromatin, thereby modulating the VEGF-Notch signaling circuits. Since perturbations of RNF20 are associated with cardiovascular malformations in human patients, our work may provide novel therapeutic avenues for diseases caused by vascular dysfunction.

overall_design: HUVEC cells were transfected with siCtr or siRNF20. 60h after transfection, cells were harvested to perform ChIP-seq.

last: Tetik


title: Rnf20 levels modulate the VEGF-Notch signaling circuits during sprouting angiogenesis [03ATAC_seq-Retina]

overall_design: Around 2000 cells from P7 Retina Pups were collected  to perform ATAC-seq


title: Rnf20 levels modulate the VEGF-Notch signaling circuits during sprouting angiogenesis [02RNF20_Huvec]

overall_design: P7 Retina  EC were collected  to perform polyA RNA-seq


title: Rnf20 levels modulate the VEGF-Notch signaling circuits during sprouting angiogenesis [Rnf20_CD31_RNA_seq]

overall_design: P7 Retina  EC were collected  to perform low-Input of RNA-seq


title: Single-cell RNA sequencing reveals the impact of CD34+ cells during heart failure in the hypertrophic heart with hyperlipidemia

status: Public on Aug 17 2024

city: Hangzhou

first: Qingbo

last: Xu

state: Zhejiang

address: 79 Qingchun Road

department: Department of Cardiology

institute: First Affiliated Hospital, Zhejiang University School of Medicine

summary: Hyperlipidemia and hypertension might play a role in cardiac fibrosis, in which a heterogeneous population of fibroblasts seems important. However, it is unknown whether CD34+ cells are involved in the pathogenesis of cardiac fibrosis. This study aimed to investigate the mechanism of CD34+ cell differentiation in cardiac fibrosis during hyperlipidemia. By analyzing the transcriptomes of single cells from the Cd34-CreERT2;R26-tdTomato&ApoE-/- heart, we also demonstrated the dynamics of cell landscape during cardiac fibrosis in the hypertrophic heart with hyperlipidemia.

overall_design: scRNA-seq for total non-cardiomyocytes and CD34+ cells from Cd34-CreERT2;R26-tdTomato&ApoE-/- mice hearts

first: L

last: Du

first: Q


title: Single-cell RNA sequencing for heart failure with a history of coronary heart disease and hypertension

summary: Hyperlipidaemia and hypertension might play a role in cardiac fibrosis, in which a heterogeneous population of fibroblasts seems important. The study aimed to explore the mechanism of fibroblasts in cardiac fibrosis during hyperlipidaemia.

overall_design: Human hearts tissue were first digested, and then the nucleated live cells were sorted by FACS, followed by single-cell RNA sequencing.

first: Luping

first: Xuyang

last: Wang

first: Yan

last: Guo