title: Exportin 1 inhibition prevents neuroendocrine transformation through SOX2 downregulation in lung and prostate cancers [RNA-seq]

summary: In lung and prostate adenocarcinomas, neuroendocrine (NE) transformation to an aggressive derivative resembling small cell lung cancer (SCLC) is associated with poor prognosis. We previously described dependency of SCLC on the nuclear transporter exportin 1. Here we explored the role of exportin 1 in NE transformation. We observed upregulated exportin 1 in lung and prostate pre-transformation adenocarcinomas. Exportin 1 was induced upregulated following genetic inactivation of TP53 and RB1 in lung and prostate adenocarcinoma cell lines, accompanied by increased sensitivity to the exportin 1 inhibitor selinexor in vitro. Exportin 1 inhibition prevented NE transformation and extended response to targeted therapies in both lung anddifferent TP53/RB1-inactivated prostate adenocarcinoma xenograft models that acquire NE features upon treatment with the AR inhibitor enzalutamide, and extended response to the EGFR inhibitor osimertinib in a lung cancer transformation patient-derived xenograft (PDX) model exhibiting combined adenocarcinoma/SCLC histology. Ectopic SOX2 expression restored the enzalutamide-promoted NE transformationNE phenotype on adenocarcinoma-to-NE transformation xenograft models despite selinexor treatment. Selinexor sensitized NE-transformed lung and prostate small cell carcinoma PDXs tumors after NE transformation to standard cytotoxics.   Together these data nominate exportin 1 inhibition as a novel  potential therapeutic approach target to constrain lineage plasticity and prevent or treat NE transformation in lung and prostate adenocarcinoma.

overall_design:
4-10 female 6-week-old NOD.Cg-Prkdc<scid> Il2rg<tm1Wjl>/SzJ (NSG) mice were subcutaneously engrafted per treatment arm and until tumors reached 100-150 mm3. At that point, mice were randomized into groups and treated with either vehicle, cisplatin (2 mg/kg intraperitoneally (i.p.) once/week), etoposide (3 mg/kg i.p. QDx3), selinexor (10 mg/kg p.o. QDx3), enzalutamide (10 mg/kg per os (p.o). QDx5), osimertinib (25 mg/kg p.o. QDx5) or the combinations of cisplatin + etoposide, cisplatin + selinexor, enzalutamide + selinexor or osimertinib + selinexor at the previously mentioned doses. 3-4 tumors per treatment group were collected at day 56 (day 31 for the control condition). Mice weights and tumor volumes were measured twice a week and mice were sacrificed when tumors reached humane endpoint (volume = 1000 mm3). The number of mice per treatment arm were selected according to previous experience with the models and response to treatments. Blinding was not performed. All animal experiments were approved by the Memorial Sloan Kettering Cancer Center (MSKCC) Animal Care and Use Committee (#13-07-007). Frozen tissues were weighed and homogenized in RLT and nucleic acids were extracted using the AllPrep DNA/RNA Mini Kit (QIAGEN, #80204) according to the manufacturer’s instructions. RNA was eluted in nuclease-free water.

**Raw data not provided due to accidental deletion of files**

first: Alvaro

last: Quintanal-Villalonga

first: Charles

middle: M

last: Rudin

first: Richard

last: Koche


title: Exportin 1 inhibition prevents neuroendocrine transformation through SOX2 downregulation in lung and prostate cancers [ATAC-seq]

status: Public on Jul 12 2023

city: New York

first: Yingqian

middle: Ada

last: Zhan

state: New York

address: 430 East 67th Street

department: EPIGENETICS RESEARCH CENTER

country: USA

institute: MSKCC

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: 4-10 female 6-week-old NOD.Cg-Prkdc<scid> Il2rg<tm1Wjl>/SzJ (NSG) mice were subcutaneously engrafted per treatment arm and until tumors reached 100-150 mm3. At that point, mice were randomized into groups and treated with either vehicle, cisplatin (2 mg/kg intraperitoneally (i.p.) once/week), etoposide (3 mg/kg i.p. QDx3), selinexor (10 mg/kg p.o. QDx3), enzalutamide (10 mg/kg per os (p.o). QDx5), osimertinib (25 mg/kg p.o. QDx5) or the combinations of cisplatin + etoposide, cisplatin + selinexor, enzalutamide + selinexor or osimertinib + selinexor at the previously mentioned doses. 3-4 tumors per treatment group were collected at day 56 (day 31 for the control condition). Mice weights and tumor volumes were measured twice a week and mice were sacrificed when tumors reached humane endpoint (volume = 1000 mm3). The number of mice per treatment arm were selected according to previous experience with the models and response to treatments. Blinding was not performed. All animal experiments were approved by the Memorial Sloan Kettering Cancer Center (MSKCC) Animal Care and Use Committee (#13-07-007). Frozen tissues were weighed and homogenized in RLT and nucleic acids were extracted using the AllPrep DNA/RNA Mini Kit (QIAGEN, #80204) according to the manufacturer’s instructions. RNA was eluted in nuclease-free water.

middle: A

middle: P


title: Single-cell analysis of conventional dendritic cells in an immunogenic murine melanoma model

status: Public on Jul 13 2023

city: Freising

first: Gustavo

middle: P.

last: de Almeida

state: Bavaria

address: Liesel-Beckmann-Str. 1

department: Division of Animal Physiology and Immunology

country: Germany

institute: Technical University of Munich

type: Expression profiling by high throughput sequencing

summary: Single-cell RNA sequencing was used to show the heterogeneity of conventional dendritic cells in the immunigenic murine melanoma BRAFV600E Ptgs1/Ptgs2-/-. Our analysis shows that on day 6 of tumor growth, 3 distinct populations of cDC1 and 2 distinct populations of cDC2 can be found in the tumor microenvironment. The differentially expressed genes of these populations indicate a functional heterogeneity.

overall_design: Analysis of heterogeneity of the conventional dendritic cell population within an immunogenic murine melanoma model.

first: J

last: Böttcher

first: P

last: Meiser

first: G


title: Hemizygous deletion of the autism-associated gene CHD8 impairs synaptic function through widespread changes in gene expression and chromatin compaction

first: Alba

last: Corman

address: 101 Avenue of the Americas

institute: New York Genome Center

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

overall_design: Refer to individual Series


title: Hemizygous deletion of the autism-associated gene CHD8 impairs synaptic function through widespread changes in gene expression and chromatin compaction (RNA-Seq)

summary: In this study, we developed two isogenic haploinsufficient CHD8+/– human embryonic stem cell lines (hESCs) that we induced into neurons (iNs) upon doxycycline-inducible overexpression of Neurogenin 2 and Neurogenin 1 (NEUROG2/1), and we profiled the key molecular alterations in chromatin accessibility (ATAC-seq) and expression (RNA-seq) resulting from the loss of CHD8, the most recurrently mutated gene in autism spectrum disorders (ASD).

overall_design: We examined transcriptome profiles using RNA-seq and chromatin structure using ATAC-seq in 3 cell types, two clonal CHD8+/–  hESCs HUES66 lines (CHD8-A and CHD8-B) and the isogenic control (H66), which were differentiated into neurons (iNs) after 9 days of doxycycline-inducible overexpression of Neurogenin 2 and Neurogenin 1 (NEUROG2/1) (Ngn, Day9).  For the RNA-seq experiment, three biological triplicates of induced neurons (Ngn, Day9) for each line (H66, CHD8-A, and CHD8-B) were analyzed.

first: Xi

last: Shi

first: Congyi

last: Lu

first: Alexandra

last: Nikish

first: Yang

last: Zhou

first: Randy

middle: J

last: Platt

first: Ivan

last: Iossifov

first: Feng

last: Zhang

first: Jen

middle: Q

last: Pan

first: Neville

middle: E

last: Sanjana


title: LuxR402 of Novosphingobium sp. HR1a regulates the correct configuration of cell envelopes

city: Little Rock

first: Zulema

last: Udaondo

state: AR

address: 501 Jack Stephens Drive

department: Biomedical Informatics

institute: UAMS

summary: In this work, we report that the knockout mutant in other of this  luxR-like genes (named luxR402) in Novosphingobium sp. HR1a; floculated faster than the wild-type when cultures are in repose. Transcriptomic analysis allowed us to determine the LuxR402 regulon; we have identified that the carbohydrate assimilation pathway and TCA cycle are affected in the mutant. Accordingly, the mutant presented poorer growth than the wild-type when growing in different carbon sources. At stationary phase of growth the pili biosynthesis, trehalose utilization and capside-related proteins were affected in the mutant strain. Microscopy assays determined that the mutant strain cultures presented cells aggrupations and that the extracellular matrix is less abundant than in the wild-type cultures.

overall_design: Gene expression profiling analysis using data obtained from RNA-seq of a HR1a mutant

first: Ana

last: Segura

first: Lazaro

last: Molina


title: IGF2BP family of RNA-binding proteins regulate innate and adaptive immune responses in cancer cells and tumor microenvironment

city: Hershey

first: Irina

last: Elcheva

state: Pennsylvania

address: 500 University Drive, C7743

department: Pediatrics

institute: Penn State College of Medicine

summary: Insulin-like growth factor 2 mRNA-binding proteins (IGF2BP1, IGF2BP2, and IGF2BP3) are a family of RNA-binding proteins that play an essential role in the development and disease by regulating mRNA stability and translation of critical regulators of cell division and metabolism. Genetic and chemical inhibition of these proteins slows down cancer cell proliferation, decreases invasiveness, and prolongs life span in a variety of animal models. The role of RNA-binding proteins in the induction of tissues’ immunogenicity is increasingly recognized, but, the impact of the IGF2BPs family of proteins on the induction of innate and adaptive immune responses in cancer is not fully understood. Here we report that downregulation of IGF2BP1, 2, and 3 expression facilitates the expression of interferon beta-stimulated genes. IGF2BP1 has a greater effect on interferon beta and gamma signalings compared to IGF2BP2 and IGF2BP3 paralogs. We demonstrate that knockdown or knockout of IGF2BP1, 2, and 3 significantly potentiates inhibition of cell growth induced by IFNβ and IFNγ. Mouse melanoma cells with Igf2bp knockouts demonstrate increased expression of MHC I (H-2) and induce intracellular Ifn-γ expression in syngeneic T-lymphocytes in vitro. Increased immunogenicity, associated with Igf2bp1 inhibition, “inflames” mouse melanoma tumors microenvironment in SM1/C57BL/6  and SW1/C3H mouse models measured by a two-fold increase of NK cells and tumor-associated myeloid cells. Finally, we demonstrate that the efficiency of anti-PD1 immunotherapy in the mouse melanoma model is significantly more efficient in tumors that lack Igf2bp1 expression. Our retrospective data analysis of immunotherapies in human melanoma patients indicates that high levels of IGF2BP1 and IGF2BP3 are associated with resistance to immunotherapies and poor prognosis. In summary, our study provides evidence of the role of IGF2BP proteins in regulating tumor immunogenicity and establishes those RBPs as immunotherapeutic targets in cancer.

overall_design: To assess the role of IGF2BP proteins on response to interferon beta, the expression of IGF2BP1, 2, or 3 was silenced by constitutive expression of short hairpin RNA (shRNA) or non-targeitng shRNA control. Human recombinant interferon beta, hrIFN-β, was routinely applied at concentrations 10 ng/mL. For gene expression analysis, hrIFN-β was added into a standard growth media (DMEM high glucose, 10% FBS, 1% P/s), and incubated for 12 hours prior to the collection of an experiment. RNA was extracted using the RNeasy Mini Kit (Qiagen, Germantown, MD), followed by DNase I treatment with DNA-free DNA Removal Kit (Invitrogen, Carlsbad, CA).

first: Yasin

last: Uzun

first: Vladimir

last: Spiegelman


title: GABA regulates electrical activity and tumor initiation in melanoma

first: Richard

last: White

state: NY

department: Cancer Biology and Genetics

institute: Memorial Sloan Kettering Cancer Center

summary: Oncogenes can only initiate tumors in certain cellular contexts, which is referred to as oncogenic competence. In melanoma, whether cells in the microenvironment can endow such competence remains unclear. Using a combination of zebrafish transgenesis coupled with human tissues, we demonstrate that GABAergic signaling between keratinocytes and melanocytes promotes melanoma initiation by BRAFV600E. GABA is synthesized in melanoma cells, which then acts on GABA-A receptors on keratinocytes. Electron microscopy demonstrates specialized cell-cell junctions between keratinocytes and melanoma cells, and multi-electrode array analysis shows that GABA acts to inhibit electrical activity in melanoma/keratinocyte co-cultures. Genetic and pharmacologic perturbation of GABA synthesis abrogates melanoma initiation in vivo. These data suggest that GABAergic signaling across the skin microenvironment regulates the ability of oncogenes to initiate melanoma.

overall_design: To identify differentially expressed genes between monocultured, co-cultured and switched keratinocytes, we performed RNA-sequencing of the parental keratinocyte populations in monoculture and co-culture and the co-cultured keratinocyte populations that had undergone Cre mediated switching. Each condition was analyzed using three biological replicates for each of the three conditions (9 samples total).

first: Mohita

last: Tagore


title: Prdm16 mutation determines sex-specific cardiac metabolism and identifies two novel cardiac metabolic regulators

city: Berlin

first: Markus

last: Landthaler

address: Hannoversche Str. 28

department: Berlin Institute for Medical Systems Biology

institute: Max Delbrueck Center

summary:
Background: Mutation of the PRDM16 gene causes human dilated and noncompaction cardiomyopathy. The PRDM16 protein is a transcriptional regulator that affects cardiac development via Tbx5 and Hand1, thus regulating myocardial structure. The biallelic inactivation of Prdm16 induces severe cardiac dysfunction with postnatal lethality and hypertrophy in mice. The early pathological events that occur upon Prdm16 inactivation have not been explored.
Methods: This study performed in-depth pathophysiological and molecular analyses of male and female Prdm16csp1/wt mice that carry systemic, monoallelic Prdm16 gene inactivation. We systematically assessed early molecular changes through transcriptomics, proteomics, and metabolomics. Kinetic modelling of cardiac metabolism was performed in silico with CARDIOKIN.
Results: Prdm16csp1/wt mice are viable up to 8 months, develop hypoplastic hearts, and diminished systolic performance that is more pronounced in female mice. Prdm16csp1/wt cardiac tissue of both sexes showed reductions in metabolites associated with amino acid as well as glycerol metabolism, glycolysis, and the tricarboxylic acid cycle. Prdm16csp1/wt cardiac tissue revealed diminished glutathione (GSH) and increased inosine monophosphate (IMP) levels indicating oxidative stress and a dysregulated energetics, respectively. An accumulation of triacylglycerides exclusively in male Prdm16csp1/wt hearts, suggests a sex-specific metabolic adaptation. Metabolic modelling using CARDIOKIN identified a reduction in fatty acid utilization in males as well as lower glucose utilization in female Prdm16csp1/wt cardiac tissue. On the level of transcripts and protein expression, Prdm16csp1/wt hearts demonstrate an upregulation of pyridine nucleotide-disulphide oxidoreductase domain 2 (Pyroxd2) and the transcriptional regulator pre B-cell leukemia transcription factor interacting protein 1 (Pbxip1). The strongest concordant transcriptional upregulation was detected for Prdm16 itself, probably through an autoregulatory mechanism.
Conclusions: Monoallelic, global Prdm16 mutation diminishes cardiac performance in Prdm16csp1/wt mice. Metabolic alterations and transcriptional dysregulation in Prdm16csp1/wt affect cardiac tissue. Female Prdm16csp1/wt mice develop a more pronounced phenotype, indicating sexual dimorphism at this early pathological window. This study suggests that metabolic dysregulation is an early event in the PRDM16 associated cardiac pathology.

overall_design: Four groups of Prdm16_csp1/wt mice were compared: male Prdm16_wt/wt (wt) vs. male Prdm16_csp1/wt (het); female Prdm16_wt/wt (wt) vs. female Prdm16_csp1/wt (het).

first: Jirko

last: Kühnisch

first: Benedikt

last: Obermayer


title: The role of SARS-CoV-2 nucleocapsid protein in effecting immune cells and insights on its molecular mechanisms

city: Nanchong

first: Yan

last: Lu

address: 1 Shida Road, Nanchong, Sichuan 637009, P.R. China

country: China

institute: China West Normal University

summary: The study aims were to explore the immune regulatory function of SARA-CoV-2 Nucleocapsid (N protein) and the related mechanisms. In a series of protein activity experiments, the SARA-CoV-2 Nucleocapsid showed the proliferation effect on three immune cell lines (Raw264.7, Jurkat and Raji) in a dose-dependent manner. N protein(10μg/mL) could significantly change cell cycle progressing of these three immune cell lines and could promote Raw264.7 cells quickly entering G2/M phase from the S phase to achieve rapid growth. Additionally, N protein((10μg/mL) also could stimulate Raw264.7 cells to secrete a large number of proinflammatory factors such as TNFα, IL6 and IL10. The RNA sequencing analysis indicated that N protein changed the expression of some certain genes  significantly in immune related function and four important signaling pathways including JAK-STAT signaling pathway, TNF signaling pathway, NF-kappa B signaling pathway and MAPK signaling pathway, which suggested that N protein could not only regulate the expression of genes involved in the process of resisting virus infection in macrophages of immune system, but also change the cellular signal processing.

overall_design: To investigate the effect of SARS-CoV-2 nucleocapsid protein on immune cells .Raw264.7 cells were planted in 75 cm2 cell culture tanks and treated with 10µg/mL N protein of SARS-CoV-2 or Con A (as positive control) for 24 hours. Untreated cells as blank control. Each experiment with three Biological replicates.

first: Yiling

last: Hou


title: RAS-stilumated release of exosomal miR-494-3p promotes osteolytic bone metastasis of breast cancer cells

city: chuncheon

first: okhwa

last: kim

country: South Korea

institute: kangwon national university

summary: This study provides a novel mechanism that RAS activation of breast cancer cells induces osteolytic bone metastasis by stimulating the exosome-mediated transfer of osteoclastogenic miRNAs including miR-494-3p to bone cells

overall_design: 2 samples


title: Trimannose-coupled antimiR-21 for macrophage-targeted inhalation treatment of acute inflammatory lung damage [transcriptome_human_COVID]

city: Munich

first: Stefan

last: Engelhardt

address: Biedersteiner Str. 29

department: Institute of Pharmacology and Toxicology

institute: Technical University Munich

summary: Recent studies of severe acute inflammatory lung disease including COVID-19 have identified macrophages to drive pulmonary hyperinflammation and long-term damage such as fibrosis. Here, we report on the development of a first-in-class, carbohydrate-coupled inhibitor of microRNA-21 (RCS-21), as a therapeutic means against pulmonary hyperinflammation and fibrosis. MicroRNA-21 was among the strongest upregulated microRNAs in COVID-19 and in mice with acute inflammatory lung damage and was the strongest expressed microRNA in pulmonary macrophages. Chemical linkage of an oligonucleotide inhibitor of microRNA-21 to trimannose achieved rapid and specific delivery to macrophages upon inhalation in mice. RCS-21 reversed pathological activation of macrophages and prevented pulmonary dysfunction and fibrosis after acute lung damage in mice.  In human lung tissue infected with SARS-CoV-2 ex vivo, RCS-21 effectively prevented the exaggerated inflammatory response. Our data imply trimannose-coupling for effective and selective delivery of inhaled oligonucleotides to pulmonary macrophages and report on a first mannose-coupled candidate therapeutic for COVID-19.

overall_design: Here, we sequenced human post mortem lungs (COVID-19 and controls) and fresh human lungs infected with SARS-CoV-2 (+Treatment with RCS-21).

first: Christina

last: Beck

first: Deepak

last: Ramanujam


title: Trimannose-coupled antimiR-21 for macrophage-targeted inhalation treatment of acute inflammatory lung damage [transcriptome_mouse]

overall_design: Here, we sequenced human post mortem lungs and fresh human lungs in a COVID-19 context.

first: Paula

last: Vaccarello


title: Trimannose-coupled antimiR-21 for macrophage-targeted inhalation treatment of acute inflammatory lung damage [mirnome_mouse]

type: Non-coding RNA profiling by high throughput sequencing

overall_design: Here, we sequenced a) total lungs from bleomycin and control mice and b) different pulmonary cell types from WT mice.


title: Trimannose-coupled antimiR-21 for macrophage-targeted inhalation treatment of acute inflammatory lung damage [mirnome_human_basal]

overall_design: Here, we sequenced fresh lungs from humans.


title: Trimannose-coupled antimiR-21 for macrophage-targeted inhalation treatment of acute inflammatory lung damage [mirnome_human_COVID]


title: Trimannose-coupled antimiR-21 for macrophage-targeted inhalation treatment of acute inflammatory lung damage [scRNA-seq]

overall_design:
Here, we carried out Single cell sequencing on primary lung cells isolated from RCS-21 and control-treated mice 14 days after bleomycin.
Wild type mice were subjected to acute lung injury by bleomycin, and a single inhaled dose of RCS-21 or control oligo was administered using a nebulizer at 4 days after injury. 10 days later lungs were harvested, digested and the pulmonary cells were sorted into leukocytes and non-leukocytes using magnetic activated cell sorting. Cells were multiplexed from three different animals in each group and the proportion of CD45+ cells were reduced to 50% to avoid oversampling


title: High expression of circRNAs in muscle and stromal cell confound bulk tissue analyses in cancer research [NanoString]

city: Aarhus

first: Juan Luis

last: Garcia-Rodriguez

address: Høegh-Guldbergs Gade 10

department: Biomedicine

country: Denmark

institute: Aarhus University

summary: Circular RNAs (circRNAs) are covalently closed molecules that are likely to play important roles in cancer development and progression. Hundreds of differentially expressed circRNAs between tumors and adjacent normal tissues have been identified in studies using RNA-sequencing or microarrays, emphasizing a strong translational potential. However, previous studies were performed using RNA from bulk tissues and the spatial expression patterns of most circRNAs are unknown. Here, we show that the majority of differentially expressed circRNAs from bulk tissue analyses of colon tumors relative to adjacent normal tissues are, surprisingly, not differentially expressed when comparing cancer cells directly with normal epithelial cells. By manipulating the proliferation rates of cells grown in culture, we find that these discrepancies are explained by circRNAs accumulating to high levels in quiescent muscle cells due to their high stability and, on the contrary, circRNAs are diluted to low levels in the fast-proliferating cancer cells due to their slow biogenesis rates. Thus, we observed striking changes in circRNA expression patterns within different sub-compartments of colon tumors and adjacent normal tissues. Likewise, we find that the high circRNA content in muscle cells can be a strong confounding factor in bulk analyses of circRNAs in bladder and prostate cancer. Together our findings emphasize the limitations of using bulk tissues for studying differential circRNA expression in cancer and highlight a particular need for spatial analysis in this field of research.

overall_design: This study included five stage II (TNM classification) colon cancer patients with tumors classified as T3 or T4. Paired normal tissues were also collected for all patients. Laser capture microdissection was performed for each of the five patient's tissues to separate two different sub-compartments from each cancer or normal tissue type. Cancer cells and tumor stroma were the two sub-compartments from the cancer tissues. Normal epithelium and muscularis propria were the two sub-compartments dissected from the adjacent normal tissues. RNA was extracted from the resulting samples. In addition, RNA was extracted from bulk cancer tissues and paired normal tissues. Finally, from the Caco-2 adenocarcinoma cell line, RNA was extracted and either treated with RNase R or mock-treated. In addition, RNA was extracted from three other colon adenocarcinoma cell lines. These samples were then interrogated for the 70 top high-abundance circRNA present in the colon. A list of housekeeping and tissue specific marker linear genes was also included in the panel.

first: Juan

middle: L

last: García-Rodríguez

first: Ulrik

last: Korsgaard

first: Henrik

last: Hager

first: Lasse

middle: S

last: Kristensen


title: High expression of circRNAs in muscle and stromal cell confound bulk tissue analyses in cancer research


title: High expression of circRNAs in muscle and stromal cell confound bulk tissue analyses in cancer research [RNA-Seq]

overall_design: In this study, 2 cell lines (Caco2 and hASMC) were interrogated for their circRNA levels before and after starvation. Four different timepoints: 24h: 24h after seeding with complete media; 96h: 24h of seeding with complete media follwed by 72h in starvation (no FBS in media); 120h: 24h of seeding with complete media followed by 96h in starvation (no FBS in media); 168h: 24h of seeding with complete media followed by 96h in starvations and followed by 48h with complete media (Recovered).


title: NFAT5 induction by the tumor microenvironment enforces CD8 T cell exhaustion

city: Lausanne

first: Tania

last: Wyss

address: Rue du Bugnon 25A

country: Switzerland

institute: SIB Swiss Institute of Bioinformatics

summary: To decipher if NFAT5 controls CD8 T cell exhaustion during chronic infection on a molecular level, we performed scRNA sequencing on sorted P14 WT and NFAT5 KO CD8 from the spleen of a chronic LCMV-infected mouse.

overall_design: Vb5 transgenic mice (CD45.1) were adoptively  transferred with  NFAT5 KO or wild-type (WT) P14 CD8 T cells from naive mice (CD45.2) and infected LCMV clone 13 (cl13). Total P14 cells were flow sorted from the spleen on day 28 post infection  and processed for scRNAseq analysis.

first: Grégory

last: Verdeil

first: Held

last: Werner

first: Cropp

last: Daniela

first: Mélanie

last: Charmoy

first: Wyss

last: Tania


title: Trimannose-coupled antimiR-21 for macrophage-targeted inhalation treatment of acute inflammatory lung damage

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Endothelial sensing of AHR ligands regulates intestinal barrier immunity [LEC_SI]

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

country: United Kingdom

institute: MRC London Institute of Medical Sciences

summary: The blood and lymphatic vasculature is lined by functionally specialised endothelial cells (ECs). In the intestine, ECs act as an essential physical barrier, controlling nutrient transport, facilitating tissue immunosurveillance, and coordinating angiogenesis and lymphangiogenesis to ensure appropriate tissue perfusion and drainage. Conversely, endothelial maladaptation can lead to pathological angiogenesis and the perpetuation of inflammation in chronic inflammatory diseases. However, whether enteric ECs actively engage in the regulation of intestinal homeostasis and pathology through integration of environmental cues is currently unknown. Here, we show that the aryl hydrocarbon receptor (AHR), a ligand-activated transcription factor, acts as critical node for EC-sensing of dietary and microbial metabolites.  We first established a comprehensive single-cell endothelial atlas of the mouse small intestine uncovering the cellular complexity and functional heterogeneity of blood and lymphatic ECs, identifying transcriptional networks and putative biological roles across endothelial subtypes. Analyses of AHR mediated responses at single-cell resolution identified tissue-protective transcriptional signatures and regulatory networks promoting quiescence and vasculoprotection. Endothelial AHR-deficiency in mice resulted in cellular activation, proliferation, and initiation of angiogenic pathways disrupting tissue homeostasis. In human ECs, AHR signalling promoted quiescence through cell cycle arrest and tempered endothelial inflammatory responses. Together, our data provide a comprehensive dissection of the impact of environmental sensing across the spectrum of enteric endothelia, demonstrating that endothelial AHR signalling serves to promote homeostasis and prevent aberrant inflammatory responses at the intestinal barrier.

overall_design: Examination of AHR-deficient (VeciCre x AHR flfl x NuTRAP) vs control (VeciCre x NuTRAP) mice small intestinal lymphatic endothelial cell transcriptomes by bulk RNA sequencing.

first: Benjamin

middle: G

last: Wiggins

first: Yi-Fang

last: Wang

first: Catherine

last: Chahrour

first: Chris

last: Schiering


title: Endothelial sensing of AHR ligands regulates intestinal barrier immunity [AHR KO RNA-seq]

overall_design: Examination of small intestinal tissue-wide changes between endothelial-AHR deficient mice and littermate controls at steady state by RNA sequencing.


title: LncRNA AGPG confers endocrine resistance in breast cancer by promoting E2F1 activity

city: yangzhou

first: Yu

last: Shiyi

state: Jiangsu

address: hanjiang district jiangyangzhonglu136, Hanjiang district, Jiangyangzhonglu 136

institute: yangzhou university

summary: Resistance to endocrine therapy represents a major threat to patients with estrogen receptor α positive (ERα+) breast cancer. The development of resistance is mainly through activating E2F signaling. However, the mechanisms that govern E2F1 activity in these resistant cells remain poorly understood. Here, we identify Actin Gamma 1 Pseudogene 25 (AGPG) as a lncRNA whose expression is driven by epigenomic activation of enhancer in endocrine resistant breast cancer cells. High expression of AGPG is associated with poor survival of ERα+ breast cancer, especially in patients receiving endocrine therapy. Stable knockdown and overexpression of AGPG demonstrate that AGPG promotes endocrine resistance, cell cycle progression, cell proliferation in vitro and in vivo. AGPG functions by direct binding purine rich element binding protein α (PURα), a transcription factor repressing E2F1 signaling and sensitized ERα+ breast cancer cells to endocrine therapy. Via binding to the region responsible for PURα/E2F1 interaction in PURα protein, AGPG releases E2F1 from PURα, leading to activation of E2F1 signaling in ERα+ breast cancer cells. Clinically, E2F1 target genes are strongly correlated with AGPG and PURα expression. Thus, our study reveals AGPG as a promising biomarker and potential therapeutic target in breast cancer.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for MCF7 cells, its knockdown derivatives (shAGPG1, shAGPG2, shPURA1, shPURA2) and derivative with AGPG overexpression(AGPG_OE).

first: Shiyi

last: Yu

first: Haibo

last: Sun


title: RNA markers revealed by transcriptomic analyses represent informative approaches for desired phenotypic traits in plant breeding

city: Villeneuve d'Ascq

first: Anca

last: Lucau-Danila

address: Cité Scientifique SN2 303

department: Biology

country: France

institute: University of Lille

summary: Results suggest that the observed differences in morphometric parameters between the studied varieties have a background in differently expressed genes involved in different biochemical pathways.

overall_design: Seven flax cultivars (Diane, Hermes, Drakkar, Belinka, Adelie, Violin, and Oliver) were grown under field conditions and their gene expression profiles were compared each other.

first: Malika

last: Chabi

first: Sandrine

last: Arribat


title: Endothelial sensing of AHR ligands regulates intestinal barrier immunity [BEC_SI]

overall_design: Examination of AHR-deficient (VeciCre x AHR flfl x NuTRAP) vs control (VeciCre x NuTRAP) mice small intestinal blood endothelial cell transcriptomes by bulk RNA sequencing.


title: Endothelial sensing of AHR ligands regulates intestinal barrier immunity [scRNAseq]

overall_design: Using single-cell RNA sequencing to examine a) small intestinal endothelial cellular heterogeneity, and b) impact of ligand-stimulated aryl hydrocarbon receptor pathway activation across these populations.


title: Hemizygous deletion of the autism-associated gene CHD8 impairs synaptic function through widespread changes in gene expression and chromatin compaction (ATAC-Seq)

first: Alba

last: Corman

overall_design: We examined transcriptome profiles using RNA-seq and chromatin structure using ATAC-seq in 3 cell types, two clonal CHD8+/–  hESCs HUES66 lines (CHD8-A and CHD8-B) and the isogenic control (H66), which were differentiated into neurons (iNs) after 9 days of doxycycline-inducible overexpression of Neurogenin 2 and Neurogenin 1 (NEUROG2/1) (Ngn, Day9).  For the ATAC-seq characterization, two biological replicates of induced neurons (Ngn, Day9) for each line (H66, CHD8-A, and CHD8-B) were deeply sequenced and analyzed.

first: Xi

last: Shi

first: Congyi

last: Lu

first: Alexandra

last: Nikish

first: Yang

last: Zhou

first: Randy

last: Platt

first: Ivan

last: Iossifov

first: Feng

last: Zhang

first: Jen

last: Pan

first: Neville

last: Sanjana


title: Endothelial sensing of AHR ligands regulates intestinal barrier immunity

first: LMS

last: Bioinformatics Core

overall_design: Refer to individual Series


title: Endothelial sensing of AHR ligands regulates intestinal barrier immunity [Hg bulkRNAseq]

overall_design: Using RNA sequencing to examine the impact of FICZ treatment on HUVEC transcriptomes

first: Alice

last: Burke

first: Marian

middle: H

last: Dore

first: Chris

last: Schiering


title: Revealing and harnessing CD39 for the treatment of colorectal cancer and liver metastases by engineered T cells [NanoString]

city: Milan

first: Chiara

last: Balestrieri

address: Via Olgettina 58

department: Center for Omics Sciences

country: Italy

institute: IRCCS San Raffaele Scientific Institute

summary: Colorectal tumors are often densely infiltrated by immune cells that have a role in surveillance and modulation of tumor progression but are burdened by exhaustion mechanisms fueled by the tumor microenvironment, which must be counteracted to achieve control. Here, we deployed a multidimensional approach to unravel the T cell functional landscape in tumor and peritumoral tissues from primary colorectal cancers and liver metastases. We found that T-cells are mainly localized at the front edge and that tumor-infiltrating T cells co-express multiple inhibitory receptors and highlighted CD39 as the major driver of exhaustion in both primary and metastatic colorectal tumors. By CRISPR/Cas9 genome editing tools, we simultaneously redirected T-cell specificity employing a novel T-cell receptor targeting the HER-2 antigen, and disrupted CD39, thus generating triple-knockout engineered lymphocytes. We showed that the absence of CD39 confers HER2-specific T cells a functional advantage in eliminating HER2+ patient-derived organoids, starring the relevance of the CD39 axis for further exploitation in adoptive T-cell therapy strategies to treat primary and metastatic colorectal cancer.

overall_design: 58 samples derived from peritumoral and tumoral areas of 33 patients diagnosed with liver Colorectal Cancer metastasis were analyzed.

first: A

last: Potenza

first: C

first: E

last: Ruggiero

last: Bonini


title: Transcriptomic analysis of the ocular posterior segment completes a cell atlas of the human eye

city: Cambridge

first: Wenjun

last: Yan

state: MA

address: 52 Oxford Street

department: Department of Molecular  and Cellular Biology

institute: Harvard University

summary: Although the visual system extends through the brain, most vision loss originates from defects in the eye. Its central element is the neural retina, which senses light, processes visual signals, and transmits them to the rest of the brain through the optic nerve (ON). Surrounding the retina are numerous other structures, conventionally divided into anterior and posterior segments. Here we used high-throughput single nucleus RNA sequencing (snRNA-seq) to classify and characterize cells in the extraretinal components of the posterior segment: ON, optic nerve head (ONH), peripheral sclera, peripapillary sclera (PPS), choroid, and retinal pigment epithelium (RPE). Defects in each of these tissues are associated with blinding diseases – for example, glaucoma (ONH and PPS), optic neuritis (ON), retinitis pigmentosa (RPE), and age-related macular degeneration (RPE and choroid). From ~151,000 single nuclei, we identified 37 transcriptomically distinct cell types, including multiple types of astrocytes, oligodendrocytes, fibroblasts, and vascular endothelial cells. Our analyses revealed a differential distribution of many cell types among distinct structures. Together with our previous analyses of the anterior segment and retina, the new data complete a “Version 1” cell atlas of the human eye. We used this atlas to map the expression of >180 genes associated with the risk of developing glaucoma, which is known to involve ocular tissues in both anterior and posterior segments as well as neural retina. Similar methods can be used to investigate numerous additional ocular diseases, many of which are currently untreatable.

overall_design: single nucleus RNA-seq was performed on nuclei isolated from frozen human oculartissues. Fluorescence-activated cell sorting was used to collect DAPI-positive nuclei. For each tissue, three or more biological samples were used. Approximately 8000 (for some samples less) nuclei were recovered for each sample, and each nucleuswas sequenced to a depth of~40000 reads.

first: Aboozar

last: Monavarfeshani

first: Gregory

last: Hageman

first: Joshua

middle: R

last: Sanes


title: Revealing and harnessing CD39 for the treatment of colorectal cancer and liver metastases by engineered T cells [mCRC]

overall_design: Total 42 OCT-embedded samples of liver Colorectal Cancer metastasis were analyzed


title: Transcriptional changes by short- and long-term IFNγ in cancer cell lines

status: Public on Jul 11 2023

first: Mario

last: Niepel

address: 35 Cambridgepark Dr Suite 300

institute: Ribon Therapeutics, Inc.

summary: Chronic interferon-gamma (IFN-γ) exposure to tumour cells drives resistance to immune checkpoint blockade therapy (ICBT) has been characterised as one of the resistance mechanisms.  However, the detailed mechanistic insight remains unknown to which interactor promoting this phenomenon.  We found out that chronic IFN-γ to tumour cells was fundamentally different and those genes upregulated only during chronic IFN-γ has shown to a lower survival of cancer patients treated with ICBT.

overall_design: Chronic interferon-gamma (IFN-γ) exposure to tumour cells has been reported to be one of the key drivers to one of the resistance mechanisms in immune checkpoint blockade therapy (ICBT).  This study aimed to study the transcriptomic difference between untreated, short-term IFN-γ-treated, and long-term IFN-γ-treated tumour cells (YUMM2.1 and CT26 cell lines).

first: Chun

middle: W

last: Wong

first: Roma

last: Kaul

first: Chang

last: Liu

first: Adam

last: Hurlstone


title: Synchronized response of CD4+ T cells to short-term dietary changes - Tissue RNA sequencing diet change (baseline)

city: Hamburg

first: Babett

last: Steglich

address: Martinistrasse 52

institute: Universitätsklinikum Hamburg-Eppendorf

summary: Omnivorous animals, including mice and humans, tend to prefer energy-dense nutrients rich in fat over plant-based diets, especially for short periods of time. The health consequences of this short-term consumption of energy-dense nutrients remain still unclear. We found that every short-term, reiterated switches to feast diets mimicking our social eating behavior, breached the potential buffering effect of the intestinal microbiota and deeply reorganized the immunological architecture of mucosa-associated lymphoid tissues. The first dietary switch was sufficient to induce transient mucosal immune depression and suppress systemic, antigen-specific immunity leading to higher susceptibility to Salmonella Typhimurium and Listeria monocytogenes infections. This was explained by a reduction of CD4+ T cell metabolic fitness and cytokine production due to impaired mTOR activity in response to withdrawal of microbial provision of fiber metabolites. Reintroducing dietary fiber efficiently rewired T cell metabolism and restored both mucosal and systemic CD4+ T cell functions and immunity. Finally, dietary intervention study in human volunteers confirmed the impact of short-term dietary switches on human CD4+ T cell functionality. This work reveals that short-term nutritional changes cause a drastic yet transient depression of both mucosal and systemic immunity, creating windows of opportunities for pathogenic infections.

overall_design: RNA sequencing of total tissue from Ileum - baseline (3, 6, and 9 days of regular diet) and diet change (3d RD + 3d FD, 3d RD + 3d FD + 3d RD)

first: Francesco

last: Siracusa

first: Nicola

last: Schaltenberg

first: Yogesh

last: Kumar

first: Till

last: Lesker

first: Eran

last: Elinav

first: Samuel

last: Huber

first: Joerg

last: Heeren

last: Gagliani


title: Effect of MPC309 (AR-targeting Multivalent Peptoid Conjugate) treatment on gene expression in LNCaP-ABL cells (castration-resistant prostate cancer cell line) in comparison to Vehicle control and another AR ligand, Ethisterone (partial agonist): ATAC-Seq

first: Michael

last: Garabedian

address: 500 First Ave

institute: NYU School of Medicine

summary: We conducted ATAC-seq on LNCaP-abl cells treated overnight with either vehicle (DMSO), MPC309, Backbone, DHT or Enzalutamide to reveal areas of accessible chromatin. Our results indicated that the vast majority of peaks (>46,000) were shared among all groups. Notwithstanding, MPC309 incited some chromatin restructuring, as evidenced by the unique 8,750 open chromatin sites seen in cells treated with MPC309 as opposed to those treated with the vehicle. Analysis of transcription factor (TF) binding-motifs around regions of chromatin exclusively open in MPC309-treated cells exposed NR-binding motifs (GRE, PRE, ARE, AR-half sites). This indicates the potential for MPC309-bound AR to interact with chromatin at AR-specific locations.

overall_design: LNCaP-abl cells were cultured under androgen deprivation and treated with vehicle (DMSO), 1μM backbone, 1μM MPC309, 10nM DHT, or 10μM enzalutamide overnight, and ATAC-seq performed. Accessible chromatin profiling analysis was performed using the Rosalind software.

first: Justine

last: Habault


title: Revealing and harnessing CD39 for the treatment of colorectal cancer and liver metastases by engineered T cells [CRC]

first: Chiara

last: Balestrieri

overall_design: 37 tissues derived from non-neoplastic, peritumoral and tumoral areas of 13 patients diagnosed with primary Colorectal Cancer were dissociated to obtain a single cell suspension using GentleMacs dissociator (Miltenyi).

first: A

last: Potenza

first: C

first: E

last: Ruggiero

last: Bonini


title: Effect of MPC309 (AR-targeting Multivalent Peptoid Conjugate) treatment on gene expression in LNCaP-ABL cells (castration-resistant prostate cancer cell line) in comparison to Vehicle control and another AR ligand, Ethisterone (partial agonist): RNA-Seq

summary: Prostate cancers evolve to resist androgen receptor (AR) pathway inhibitors, such as enzalutamide, leading to castration resistance due to sustained AR expression and function. In response, we have designed a novel strategy to regulate the AR and suppress castration-resistant prostate cancer (CRPC) by employing multivalent peptoid conjugates (MPCs). These conjugates comprise multiple copies of the AR-targeting ligand ethisterone attached to a peptidomimetic framework. To pinpoint the genes and pathways impacted by MPC309, we performed RNA-sequencing on LNCaP-abl cells, which were treated overnight with various agents: vehicle (DMSO), peptoid backbone, MPC309, dihydrotestosterone (an AR activator), or enzalutamide (an AR inhibitor commonly used clinically). Our findings revealed unique gene expression patterns (transcriptomes) in cells exposed to each compound, indicating that MPC309 may be a new AR ligand influencing the AR transcriptional response.

overall_design: LNCaP-abl cells were cultured under androgen deprivation and treated with vehicle (DMSO), 1μM peptoid backbone lacking the ethisterone moieties, 1μM MPC309, 10nM DHT, or 10μM enzalutamide overnight, and RNA-seq performed. The experiment was performed in duplicate.  Gene expression profiling analysis was performed and analyzed.


title: SOCS3 deletion in effector T cells confers an anti-tumorigenic role of IL-6 to the pro-tumorigenic cytokine [scATAC-Seq]

city: Shinjuku-ku

first: Setsuko

last: Mise-Omata

state: Tokyo

address: 35 Shinanomachi

department: Department of Microbiology and Immunology

country: Japan

institute: Keio University

summary: Interleukin (IL)-6 is abundantly expressed in the tumor microenvironment and is associated with poor patient outcomes. Here, we demonstrate that the deletion of the suppressor of cytokine signaling 3 (SOCS3) in T cells potentiates anti-tumor immune responses by conferring the anti-tumorigenic function of IL-6 in mouse and human models. In Socs3-deficient CD8+ T cells, IL-6 upregulates the expression of type I interferon (IFN)-regulated genes and enhances the anti-tumor effector function of T cells, while also modifying mitochondrial fitness to increase mitochondrial membrane potential and reactive oxygen species (ROS) levels and to promote metabolic glycolysis in the energy state. Furthermore, Socs3 deficiency reduces regulatory T cells and increases T helper 1 (Th1) cells. SOCS3 knockdown in human chimeric antigen receptor T (CAR-T) cells exhibits a strong anti-tumor response in humanized mice. Thus, genetic disruption of SOCS3 offers an avenue to improve the therapeutic efficacy of adoptive T cell therapy.

overall_design: MC38 cells, murine colon adenocarcinoma cells, were subcutaneously injected in the flanks of WT Socs3f/f or Cd4Cre Socs3f/f mice. CD3e+ TCRb+ T cells were isolated from tumor mass 12 days after tumor inoculation for scATACseq analysis.

first: Makoto

last: Ando

first: Tanakorn

last: Srirat

first: Kensuke

last: Nakagawara

first: Taeko

last: Hayakawa

first: Mana

last: Iizuka-Koga

first: Hiroshi

last: Nishimasu

first: Osamu

last: Nureki

first: Minako

last: Itho

first: Akihiko

last: Yoshimura


title: Synchronized response of CD4+ T cells to short-term dietary changes - Tissue RNA sequencing diet change

first: Babett

last: Steglich

overall_design: RNA sequencing of total tissue from Peyer's patches and Ileum on day 0, 3, 6, 9 and 12 after initial diet change

first: Francesco

last: Siracusa

first: Nicola

last: Schaltenberg

first: Yogesh

last: Kumar

first: Till

last: Lesker

first: Eran

last: Elinav

first: Samuel

last: Huber

first: Joerg

last: Heeren

last: Gagliani


title: Effect of MPC309 (AR-targeting Multivalent Peptoid Conjugate) treatment on gene expression in LNCaP-ABL cells (castration-resistant prostate cancer cell line) in comparison to Vehicle control and another well-known AR ligand, Ethisterone (partial agonist)

city: New York

first: Michael

last: Garabedian

summary:
Effect of MPC309 (an AR-targeting Multivalent Peptoid Conjugate) treatment on gene expression in LNCaP-ABL cells (a castration-resistant prostate cancer cell line) in comparison to Vehicle control and another well-known AR ligand, Ethisterone (partial agonist).
Prostate cancers adapt to androgen receptor (AR) pathway inhibitors and progress to castration resistance due to ongoing AR expression and function. To counter this, we developed a new approach to modulate the AR and inhibit castration-resistant prostate cancer (CRPC) using multivalent peptoid conjugates (MPCs) that contain multiple copies of the AR-targeting ligand ethisterone attached to a peptidomimetic scaffold. To determine if the effects of MPC309 differ from those of ethisterone alone, we conducted RNA-seq analysis on LNCaP-abl cells. These cells were treated overnight with either a control vehicle (DMSO), MPC309, or ethisterone. Our analysis revealed that there was minimal overlap in the genes regulated by MPC309 and ethisterone alone.

overall_design: LNCaP-abl cells were cultured under androgen deprivation and treated with vehicle (DMSO), 1μM MPC309 or 10μM ethisterone overnight, and RNA-seq was performed. Experiments were performed in duplicate. Gene expression profiling analysis was performed by RNA seq and analyzed using the Rosalind software.

first: Justine

last: Habault


title: SOCS3 deletion in effector T cells confers an anti-tumorigenic role of IL-6 to the pro-tumorigenic cytokine [scRNA-seq]

first: Setsuko

last: Mise-Omata

overall_design: MC38 cells, murine colon adenocarcinoma cells, were subcutaneously injected in the flanks of WT Socs3f/f or Cd4Cre Socs3f/f mice. CD3e+ TCRb+ T cells were isolated from tumor mass 12 days after tumor inoculation for scRNAseq analysis.

first: Makoto

last: Ando

first: Tanakorn

last: Srirat

first: Kensuke

last: Nakagawara

last: Hayakawa

last: Ito


title: Persistent and transient olfactory deficits in COVID-19 are associated to inflammation and zinc homeostasis

city: Padova

first: Cristiano

last: De Pitta

address: Via U. Bassi, 58/B

institute: University of Padova

summary: The Coronavirus Disease 2019 (COVID-19) is mainly a respiratory syndrome that can affect multiple organ systems, causing a variety of symptoms. Among the most common and characteristic symptoms are deficits in smell and taste perception, which may last for weeks/months after COVID-19 diagnosis owing to mechanisms that are not fully elucidated. In order to identify the determinants of olfactory symptom persistence, we obtained olfactory mucosa (OM) from 21 subjects, grouped according to clinical criteria: i) with persistent olfactory symptoms; ii) with transient olfactory symptoms; iii) without olfactory symptoms; and iv) non-COVID-19 controls. Cells from the olfactory mucosa were harvested for transcriptome analyses. RNA-Seq assays showed that gene expression levels are altered for a long time after infection. The expression profile of micro RNAs appeared significantly altered after infection, but no relationship with olfactory symptoms was found. On the other hand, patients with persistent olfactory deficits displayed increased levels of expression of genes involved in the inflammatory response and zinc homeostasis, suggesting an association with persistent or transient olfactory deficits in individuals who experienced SARS-CoV-2 infection.

overall_design: miRNA expression profiles were carried out using the “Agilent SurePrintG3 Human miRNA v.21 (8x60K)” microarrays (Agilent Technologies, Santa Clara, CA, USA)” (Agilent Technologies), that allows the detection of 2.549 known human (miRBase Release 21.0) and 76 viral miRNAs. We analysed miRNA expression profiles of 13 subjects grouped in in three clinical groups, according to their olfactory symptoms after the infection by SARS-CoV-2. The first group is composed by the patients with long-lasting olfactory disturbances (G1); the third  one is represented by patients without olfactory disturbances (G3) and the fourth group is composed by healthy controls (G4).

first: Lorenzo

last: Lupi

first: Anna

last: Bordin

first: Gabriele

last: Sales

first: Davide

last: Colaianni

first: Adriana

last: Vitiello

first: Alberto

last: Biscontin

last: Reale

first: Alfredo

last: Garzino-Demo

first: Angelo

last: Antonini

first: Giancarlo

last: Ottaviano

first: Carla

last: Mucignat

first: Cristina

last: Parolin

first: Arianna

last: Calistri

last: De Pittà


title: Pairwise multiplex CRISPR/Cas9 screen of mitophagy receptors in acute myeloid leukemia

city: Frankfurt am Main

first: Martin

last: Wegner

state: Hessen

address: Theodor-Stern-Kai 7

department: Institute of Biochemistry II

institute: University Hospital Frankfurt am Main, Germany

summary: The selective autophagic degradation of mitochondria via mitophagy is essential for preserving mitochondrial homeostasis and thereby disease maintenance and progression in acute myeloid leukemia. The process of mitophagy is orchestrated by a variety of mitophagy receptors whose interplay in AML is not well understood. Here, we established a dual multiplexed CRISPR screen targeting mitophagy receptors to elucidate redundancies and individual contributions of mitophagy receptors and gain a deeper understanding of the functional interactome governing mitophagy in AML.

sample_organism:
Escherichia coli
Homo sapiens

platform_organism:
Escherichia coli
Homo sapiens

overall_design: Pairwise multiplex CRISPR/Cas9 screen of mitophagy receptors for proliferation and DFP- or OA-induced mitophagy flux  in acute myeloid leukemia cell line MV4-11

first: Laura

last: Meyer

first: Christian

last: Brandts


title: Targeting N-glycosylation of 4F2hc mediated by glycosyltransferases B3GNT3 sensitizes ferroptosis of pancreatic ductal adenocarcinoma

city: Beijing

first: HENG

last: MA

address: NO.1 Shuaifu Gardern

department: Pothology

institute: Peking Union Medical College Hospital

summary: Aberrant glycosylation involves multifaceted pathological and pathophysiological changes in pancreatic ductal adenocarcinoma (PDAC), including but not limited to conferring tumor cells the ability to resist cell death. Ferroptosis driven by lethal lipid peroxidation provides a targetable vulnerability to PDAC. However, the crosstalk between glycosylation and ferroptosis remains unclear. Here, we identified 4F2hc, a subunit of the glutamate-cystine antiporter system Xc–, its N-glycosylation is involved in PDAC ferroptosis by N- and O-linked glycoproteomics. Knockdown of SLC3A2 (gene name of 4F2hc) or blocking the N-glycosylation of 4F2hc potentiates ferroptosis sensitization of PDAC cells by impairing the activity of system Xc– manifested by a marked decrease in intracellular glutathione. To identify which glycosyltransferases are critical for glycosylation initiation during ferroptosis execution. We collected 207 glycosyltransferase genes (GTGs) and performed parallel RNA-seq to reveal that the glycosyltransferase B3GNT3 catalyzes the glycosylation of 4F2hc, which stabilizes the 4F2hc protein as well as its interaction with xCT. Additionally, upon the combination with a ferroptosis inducer, treatment with the classical N-glycosylation inhibitor tunicamycin (TM) markedly triggered the overactivation of lipid peroxidation and enhanced the sensitivity of PDAC cells to ferroptosis. Notably, we confirmed that genetic perturbation of SLC3A2 or combination treatment with TM markedly increased ferroptosis sensitivity in the orthotopic PDAC model. Clinically, high expression of 4F2hc and B3GNT3 contributes to the progression and poor survival of PDAC patients. Collectively, our findings reveal a previously unappreciated function of N-glycosylation of 4F2hc in ferroptosis and suggest that targeting glycosylated 4F2hc can induce susceptibility to ferroptosis in PDAC.

overall_design: Gene expression profiling was obtained from RNA-seq of PANC-1 cells treated with 0.8 μM RSL3 for 12 hours

first: Heng

last: Ma

first: Shuangni

last: Yu

first: Jie

last: Chen


title: Effect of MPC309 (AR-targeting Multivalent Peptoid Conjugate) treatment on gene expression in LNCaP-ABL cells (castration-resistant prostate cancer cell line) in comparison to Vehicle control and another AR ligand, Ethisterone (partial agonist): ChIP-Seq

first: Michael

last: Garabedian

summary: To establish wehther the genes stimulated or inhibited by MPC309 are directly influenced by the AR, we conducted ChIP-seq of AR from LNCaP-abl cells that had been treated with vehicle (DMSO), MPC309, Backbone, DHT, or Enzalutamide overnight. Our results revealed a more pronounced AR presence in cells exposed to MPC309 and DHT as compared to control groups and those treated with enzalutamide, reinforcing the idea that MPC309 facilitates distinct AR interactions with chromatin. Genes linked with AR occupancy mirrored similar GO terms as those seen in RNA-seq experiments. Out of the 251 genes repressed by MPC309 compared to controls (vehicle and backbone), 246 (98%) had an AR binding site within 15 kb upstream or downstream of the gene promoter. Similarly, of the 405 genes stimulated by MPC309, 387 (96%) had an AR binding site within 15 kb of the gene promoter. These observations suggest that the gene regulation driven by MPC309 stems from AR interactions with chromatin, resulting in varying impacts on gene expression compared to DHT or enzalutamide, consequently inhibiting the growth of prostate cancer cells.

overall_design: LNCaP-abl cells were cultured under androgen deprivation and treated with vehicle (DMSO), 1μM backbone, 1μM MPC309, 10nM DHT, or 10μM enzalutamide overnight, and AR ChIP-seq performed. AR occupancy profiling analysis was performed using the Rosalind software.

first: Justine

last: Habault


title: Synchronized response of CD4+ T cells to short-term dietary changes - CD4+ T cell RNA sequencing

first: Babett

last: Steglich

overall_design: RNA sequencing of FACS sorted CD4+ T cells from Peyer's patches and draining lymph nodes after OVA challenge

first: Francesco

last: Siracusa

first: Nicola

last: Schaltenberg

first: Yogesh

last: Kumar

first: Till

last: Lesker

first: Eran

last: Elinav

first: Samuel

last: Huber

first: Joerg

last: Heeren

last: Gagliani


title: SOCS3 deletion in effector T cells confers an anti-tumorigenic role of IL-6 to the pro-tumorigenic cytokine

first: Setsuko

last: Mise-Omata

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

overall_design: Refer to individual Series


title: Astroglial Hmgb1 regulates postnatal astrocyte morphogenesis and cerebrovascular maturation

status: Public on Jul 10 2023

city: Ottawa

first: Baptiste

last: Lacoste

state: Ontario

address: 451 Smyth Rd, Roger Guindon Hall

department: Cellular and Molecular Medicine

country: Canada

institute: University of Ottawa

summary: Astrocytes are intimately linked with brain blood vessels, a relationship critical for neuronal function. However, astroglial factors driving these physical and functional associations during postnatal brain development have yet to be identified. By characterizing structural and transcriptional changes in mouse cortical astrocytes during the first two postnatal weeks, we find that high-mobility group box 1 (Hmgb1), normally upregulated with injury and involved in adult cerebrovascular repair, is highly expressed in astrocytes at birth and then decreases rapidly. Astrocyte-selective ablation of Hmgb1 at birth affects astrocyte morphology and endfoot placement, alters distribution of endfoot proteins connexin43 and aquaporin-4, induces transcriptional changes in astrocytes related to cytoskeleton remodeling, and profoundly disrupts endothelial ultrastructure. While lack of astroglial Hmgb1 does not affect the blood-brain barrier or angiogenesis postnatally, it impairs neurovascular coupling and behavior in adult mice. These findings identify astroglial Hmgb1 as a key player in postnatal gliovascular maturation.

overall_design: We performed spatial gene expression profiling of astrocytes and microvessels on tissue sections from the developing postnatal mouse cerebral cortex, using the NanoString platform. Three postnatal time points were chosen (P0, P5 and P14) for comparisons. Only wild-type mice were used.

first: Moises

last: Freitas-Andrade

first: Cesar

last: Comin

first: Peter

last: Van Dyken

first: Julie

last: Ouellette

first: Joanna

last: Raman-Nair

first: Nicole

last: Blakeley

first: Qing

middle: Y

last: Liu

first: Sonia

last: Leclerc

first: Youlian

last: Pan

first: Ziying

first: Micaël

last: Carrier

first: Karan

last: Thakur

first: Alexandre

last: Savard

first: Gareth

last: Rurak

first: Marie-Ève

last: Tremblay

first: Natalina

last: Salmaso

first: Luciano

last: Da F Costa

first: Gianfilippo

last: Coppola


title: T cell intrinsic STAT1 signaling prevents aberrant Th1 responses during acute toxoplasmosis

city: Bethesda

first: Stephen

last: Brooks

state: MD

address: 50 SOUTH DR, RM 1140

department: Biodata Mining and Discovery Section

institute: NIAMS/NIH

summary: Infection-induced T cell responses must be properly tempered and terminated to prevent immuno-pathology. Using transgenic mice, we demonstrate that T cell intrinsic STAT1 signaling is required to curb inflammation during acute infection with Toxoplasma gondii. Specifically, we report that mice lacking STAT1 selectively in T cells expel parasites but ultimately succumb to lethal immuno-pathology characterized by aberrant Th1-type responses with reduced IL-10 and increased IL-13 production. We also find that, unlike STAT1, STAT3 is not required for induction of IL-10 or suppression of IL-13 during acute toxoplasmosis. Each of these findings was confirmed in vitro and ChIP-seq data mining showed that STAT1 and STAT3 co-localize at the Il10 locus, as well as loci encoding other transcription factors that regulate IL-10 production, most notably Maf and Irf4. These data advance basic understanding of how infection-induced T cell responses are managed to prevent immuno-pathology and provide specific insights on the anti-inflammatory properties of STAT1, highlighting its role in shaping the character of Th1-type responses.

overall_design: mRNA-seq analysis of IFN-g-producing CD4+ T cells from spleens of WT and STAT1 T-KO mice infected with Toxoplasma gondii for 7 days

first: Aaron

middle: B

last: Schultz

first: David

last: Kugler

first: Luis

last: Nivelo

first: Nicolas

last: Vitari

first: Laura

last: Doyle

first: Svetlana

last: Ristin

first: Lothar

last: Hennighausen

first: John

last: O’Shea

first: Dragana

last: Jankovic

first: Alejandro

middle: V

last: Villarino


title: Polycomb Repressive Complex 1 subunit Cbx4 positively regulates effector responses in CD8 T cells

city: Rio de Janeiro

first: Renata

last: Meirelles Pereira

state: RJ

address: Av. Carlos Chagas Filho, 373, Sala D1-035

department: Instituto de Microbiologia Paulo de Goes

country: Brazil

institute: Universidade Federal do Rio de Janeiro

summary: Cytotoxic T lymphocyte (CTL) differentiation is controlled by the crosstalk of various transcription factors and epigenetic modulators. Fully uncovering this process is fundamental to improving immunotherapy and designing novel therapeutic approaches. Here, we show that Polycomb Repressive Complex (PRC)1 subunit Chromobox (Cbx)4 favors effector CTL differentiation in murine model. Cbx4 deficiency in CTLs induced transcriptional signature and phenotype of memory cells, increasing the memory CTL population during acute viral infection. It has been previously shown that besides binding to H3K27me3 through its chromodomain, Cbx4 function as a SUMO E3 ligase in a SUMO interacting motifs (SIM)-dependent way. Overexpression of Cbx4 mutants in distinct domains showed that this protein regulates CTL differentiation primarily in a SIM-dependent way and partially through its chromodomain. Our data revealed a novel role of a Polycomb group protein Cbx4 controlling CTL differentiation and indicates the SUMOylation as a key molecular mechanism connected to chromatin modification in this process.

overall_design: To investigate the contribution of Cbx4 to the regulation of CD8 T cell transcriptional profile, in vitro-activated P14 Thy1.1+ CD8 T cells transduced with retrovirus expressing control shRNA or shRNA targeting Cbx4 were adoptively transferred to congenic receptor mice subsequently infected in acute LCMV infection model. Adoptively transfered transduced P14 CD8 T cells were sort-purified (Thy1.1+Ametrine+) by FACS on day 8 post-infection from the spleen of receptor mice and total RNA was extracted for RNA-Seq.

middle: M

last: Pereira

first: Gustavo

last: Martinez

first: Guilherme

last: Melo


title: Single cell analysis of CD1a-restricted Group A streptococcus (GAS)-reactive peripheral and cutaneous T cells

city: Oxford

first: Yi-Ling

last: Chen

state: Oxfordshire

address: Old Road Campus

department: Nuffield Department of Medicine

institute: CAMS Oxford Institute (COI)

summary: Skin and blood single cell RNA sequencing datasets of IL-22- and IFNγ-secreting CD1a-reactive GAS-responsive T cells were generated from four healthy skins, five healthy PBMCs and three psoriatic PBMCs. Using cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq), we measured T cell specific functional states at both protein and transcriptome levels.

overall_design: We deployed CD1a-expressing K562 cells as antigen presenting cells. K562-CD1a were infected with GAS, and were recognized by ex vivo cutaneous and blood T cells in a CD1a-dependent manner leading to production of IL-22 or IFNγ, detected using Cytokine Secretion assays. FACS-isolated CD3+ T cells with or without prior K562 co-culture were included to establish the dataset. CITE-seq antibodies against the fluorochromes PE or APC on the detection antibodies were included to further characterise cytokine-producing T cells.

first: Jeongmin

last: Woo

first: Prathiba

last: Kurupati

first: Lea

last: Nussbaum

last: Duncan

first: Hashem

last: Koohy

first: Graham

last: Ogg

first: Rosana

middle: O

last: Babu


title: 3D Landscape of Regulatory Elements and Transcription Factors for Transcriptional Regulation in Arabidopsis

city: Wuhan

first: Li

last: Deng

address: Shizishan 1

institute: Huazhong Agricultural University


title: 3D Landscape of Regulatory Elements and Transcription Factors for Transcriptional Regulation in Arabidopsis [ChIA-PET]

summary: Analyses of the regulatory repertoire showed that distal active cis-regulatory elements (CREs) are linked to their target genes through long-range chromatin interactions with increased expression, and poised CREs are linked to their target genes through long-range chromatin interactions with depressed expression. Furthermore, we demonstrated that transcription factor MYC2 is critical for chromatin spatial organization, and proposed that MYC2 occupancy and MYC2-mediated chromatin interactions coordinately facilitate transcription within the framework of 3D chromatin architecture. An analysis of functionally related gene-defined chromatin connectivity networks revealed that genes implicated in flowering-time control are functionally compartmentalized into separate subdomains via their spatial activity in the leaf or shoot apical meristem, linking active mark- or H3K27me3-associated chromatin conformation to coordinated gene expression. The results showed that the guiding principle for modulating gene transcription in Arabidopsis includes not only the linear juxtaposition, but also the long-range chromatin interactions.

overall_design: Here, using the improved chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) approach, we mapped chromatin interactions associated with H3K4me3 in Col-0 and myc2.

first: L

last: Zhao

first: Q

last: Zhou


title: 3D Landscape of Regulatory Elements and Transcription Factors for Transcriptional Regulation in Arabidopsis [ChIP-seq]

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for the histone modification H3K4me3 in myc2 mutant.


title: 3D Landscape of Regulatory Elements and Transcription Factors for Transcriptional Regulation in Arabidopsis [ATAC-seq]

overall_design: Here, we generated the assay for transposase-accessible chromatin using sequencing (ATAC-seq) data to define the accessible chromatin regions.


title: Immature leaves are the dominant volatile sensing organs of maize

city: Bern

first: Matthias

last: Erb

address: Altenbergrain 21

department: Institute of Plant Sciences

institute: University of Bern

summary: Plants perceive herbivory induced volatiles and respond to them by upregulating their defenses. So far, the organs responsible for volatile perception remain poorly described. Here, we show that responsiveness to the herbivory induced green leaf volatile (Z)-3-hexenyl acetate (HAC) in terms of volatile emission, transcriptional regulation and jasmonate defense hormone activation is largely constrained to younger maize leaves. Older leaves are much less sensitive to HAC. In a given leaf, responsiveness to HAC is high at immature developmental stages and drops off rapidly during maturation. Responsiveness to the non-volatile elicitor ZmPep3 shows an opposite pattern, demonstrating that this form of hyposmia (i.e. decreased sense of smell) is not due to a general defect in jasmonate defense signaling in mature leaves. Neither stomatal conductance nor leaf cuticle composition explain the unresponsiveness of older leaves to HAC, suggesting perception mechanisms upstream of jasmonate signaling as driving factors. Finally, we show that hyposmia in older leaves is not restricted to HAC, and extends to the full blend of herbivory induced volatiles. In conclusion, our work identifies immature maize leaves as dominant stress volatile sensing organs. The tight spatiotemporal control of volatile perception may facilitate within-plant defense signaling to protect young leaves, and may allow plants with complex architectures to explore the dynamic odor landscapes at the outer periphery of their shoots

overall_design: This experiment is to test the effect of (Z)-3-hexenyl acetate (HAC) and ZmPep3 on the gene expression in mature and immature maize leaves. Detached mature leaves (leaf 4) and immatue leaves ( leaf 5 and leaf 6) from V4 stage B73 maize seedlings were used as plant materials for treatment with HAC supplied as disenser and ZmPep3 supplied in solution.

first: Lei

last: Wang


title: Choline metabolism underpins macrophage IL-4 polarization and RELMα up-regulation in helminth infection

first: Alexandre

last: Blais

state: ON

address: 451 Smyth Road

summary: Type 2 cytokines like IL-4 are hallmarks of helminth infection and activate macrophages to limit immunopathology and mediate helminth clearance. In addition to cytokines, nutrients and metabolites critically influence macrophage polarization. Choline is an essential nutrient known to support normal macrophage responses to lipopolysaccharide; however, its function in macrophages polarized by type 2 cytokines is unknown. Using murine IL-4-polarized macrophages, targeted lipidomics revealed significantly elevated levels of phosphatidylcholine, with select changes to other choline-containing lipid species. These changes were supported by the coordinated upregulation of choline transport compared to naïve macrophages. Pharmacological inhibition of choline metabolism significantly suppressed several mitochondrial transcripts and dramatically inhibited select IL-4-responsive transcripts, most notably, Retnla. We further confirmed that blocking choline metabolism diminished IL-4-induced RELMα (encoded by Retnla) protein content and secretion and caused a dramatic reprogramming toward glycolytic metabolism. To better understand the physiological implications of these observations, naïve or mice infected with intestinal helminths Heligmosomoides polygyrus or Nippostrongylus brasiliensis were treated with the choline kinase α inhibitor, RSM-932A, to limit choline metabolism in vivo. Pharmacological inhibition of choline metabolism lowered RELMα expression across cell-types and tissues and led to the disappearance of peritoneal macrophages and B-1 lymphocytes and an influx of infiltrating monocytes. The impaired macrophage activation was associated with some loss in optimal immunity to H. polygyrus with increased egg burden, but there were no differences in intestinal worm count nor differences in N. brasiliensis parasite burden. Together, these data demonstrate that choline metabolism is required for macrophage RELMα induction, metabolic programming, and peritoneal immune homeostasis, which could have important implications in the context of other models of infection or cancer immunity.

overall_design: To investigate the requirement for choline metabolism during macrophage polarization, we treated bone marrow-derived macrophages with inhibitors of choline uptake or choline kinase and polarized with IL-4. We used cells grown in DMEM with L929 culture supernatant at day 7 from three female 12-week-old C57BL/6J mice. Samples were sent to Novogene for RNA-seq.

first: Peyman

last: Ghorbani

first: Sang

last: Kim

first: Meera

last: Nair

first: Morgan

middle: D

last: Fullerton


title: Synchronized response of CD4+ T cells to short-term dietary changes - Tissue RNA sequencing after Salmonella infection

first: Babett

last: Steglich

summary: Omnivorous animals, including mice and humans, tend to prefer energy-dense nutrients rich in fat over plant-based diets, especially for short periods of time. The health consequences of this short-term consumption of energy-dense nutrients remain still unclear. We found that every short-term, reiterated switches to feast diets mimicking our social eating behavior, breached the potential buffering effect of the intestinal microbiota and deeply reorganized the immunological architecture of mucosa-associated lymphoid tissues. The first dietary switch was sufficient to induce transient mucosal immune depression and suppress systemic, antigen-specific immunity leading to higher susceptibility to Salmonella Typhimurium and Listeria monocytogenes infections. This was explained by a reduction of CD4+ T cell metabolic fitness and cytokine production due to impaired mTOR activity in response to withdrawal of microbial provision of fiber metabolites. Reintroducing dietary fiber efficiently rewired T cell metabolism and restored both mucosal and systemic CD4+ T cell functions and immunity. Finally, dietary intervention study in human volunteers confirmed the impact of short-term dietary switches on human CD4+ T cell functionality. This work reveals that short-term nutritional changes cause a drastic yet transient depression of both mucosal and systemic immunity, creating windows of opportunities for pathogenic infections.

overall_design: RNA sequencing of total tissue from Peyer's patches isolated on day 4 after Salmonella Typhimurium infection

first: Francesco

last: Siracusa

first: Nicola

last: Schaltenberg

first: Yogesh

last: Kumar

first: Till

last: Lesker

first: Eran

last: Elinav

first: Samuel

last: Huber

first: Joerg

last: Heeren

last: Gagliani


title: Efficacy of abemaciclib in palbociclib-resistant hormone receptor positive organoids derived from patient derived xenografts from patients who progressed on palbociclib

city: Houston

first: Khandan

last: Keyomarsi

state: Texas

address: 1515 Holcombe Blvd

department: Experimental Radiation Onc

institute: University of Texas - MD Anderson Cancer Center

summary:
Resistance to CDK4/6 inhibitors plus endocrine therapy, standard of care for HR+/HER2-neg metastatic breast cancer (MBC) patients, remains as a clinical problem with limited therapeutic options after disease progression. Treatment with abemaciclib after progression on a prior CDK4/6i has received increasing interest. However, molecular predictors of cross-resistance and unique mechanism of resistance to each CDK4/6i are unknown. In this study, multiomics analyses revealed ≥30 differentially altered pathways between palbociclib and abemaciclib resistant models.
Mechanistic, preclinical and retrospective clinical evidence showed that HR+/HER2-neg MBC tumors refractory to palbociclib still may be responsive to abemaciclib. Based on the unique mechanisms of resistance to each CDK4/6i, we propose that patients who would benefit from abemaciclib treatment post progression on palbociclib could be selected based on the Hallmark gene set enrichment of G2/M pathway, while those who most probably would be refractory could be identified base on the gene set enrichment of OXPHOS pathway.

overall_design: Gene expression profiling analysis of RNA-seq data for Tumor Organoids derived from palbociclib-resistant PDXs.

first: Juliana

last: Navarro-Yepes

first: Nicole

last: Kettner

first: Xiayu

last: Rao

first: Cassandra

last: Bishop

first: Tuyen

last: Bui

first: Yan

first: Akshara

last: Raghavendra

first: Jing

first: Aysegul

last: Sahin

first: Funda

last: Meric-Bernstam

first: Senthil

last: Damodaran

first: Debasish

last: Tripathy

first: Kelly

middle: K

last: Hunt


title: Efficacy of abemaciclib in palbociclib-resistant hormone receptor positive breast cancer cell lines: MCF-7 and T47D

overall_design: Comparative gene expression profiling analysis of RNA-seq data for palbociclib vs abemaciclib resistant cells. In total 11 resistant cell lines were analyzed by triplicate. MCF7 parental cell line included 6 replicates.

last: Wang


title: 3D Landscape of Regulatory Elements and Transcription Factors for Transcriptional Regulation in Arabidopsis [RNA-seq]

first: Li

last: Deng

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Col-0 and myc2.

first: L

last: Zhao

first: Q

last: Zhou


title: Organization and replicon interactions within the highly segmented Borrelia burgdorferi genome

city: Bloomington

first: Xindan

state: IN

address: 1001 E 3rd St

institute: Indiana University at Bloomington

summary: Borrelia burgdorferi, a causative agent of Lyme disease, contains the most segmented bacterial genome known to date, with one linear chromosome and over twenty plasmids. How this unusually complex genome is organized, and whether and how the different replicons interact are unclear. We recently demonstrated that B. burgdorferi is polyploid and the copies of the chromosome and plasmids are regularly spaced in each cell, which is critical for faithful segregation of the genome to daughter cells. Regular spacing of the chromosome is regulated by two separate partitioning systems (parBS and parAZ) and the structural maintenance of chromosomes (SMC) protein. Here, using chromosome conformation capture (Hi-C), we characterized the conformation of the B. burgdorferi genome and the interactions between the replicons. We uncovered that although the linear chromosome lacks contacts between the two replication arms, the two telomeres are in frequent contact. Moreover, several plasmids specifically interact with the chromosome oriC region, and a subset of plasmids interact with each other more than with others. We found that SMC and the SMC-like MksB protein mediate long-range interactions on the chromosome, but they minimally affect plasmid-chromosome or plasmid-plasmid interactions. Finally, we found that disruption of the two partition systems leads to chromosome restructuring, correlating with the mis-positioning of chromosome oriC. Altogether, this study revealed the conformation of a complex genome and analyzed the contribution of the partition systems and SMC family proteins to this organization. This work expands the understanding of the organization and maintenance of multipartite bacterial genomes.

overall_design: Hi-C experiments were performed on wild type and mutant cells of Borrelia burgdorferi S9 growing in BSK-II.

first: X


title: Synchronized response of CD4+ T cells to short-term dietary changes leads to windows of mucosal and systemic immune depression

first: Babett

last: Steglich


title: LRRC10 regulates mammalian cardiomyocyte cell cycle exit and heart regeneration

city: La Jolla

first: Rebecca

middle: J.

last: Salamon

state: CA

address: 9500 Gilman Drive

department: Pediatrics

institute: University of California, San Diego

summary: Bulk RNA expression profiles were captured from hearts of Leucine-rich repeat containing protein 10 (Lrrc10) knockout (KO) and wild type (WT) mice that underwent myocardial infarction (MI) or sham (SH) surgery at postnatal day 1 and full ventricle collection at 7 days post-surgery

overall_design:
Heart ventricle mRNA profiles were generated from Lrrc10 KO and WT neonatal mice by high throughput sequencing, in quadruplicates and sex-balanced groups, using Illumina HiSeq.
contributor: University of Wisconsin-Madison Biotechnology Center (UWBC) Gene Expression Center

first: Megan

middle: C

last: McKeon

first: Xiaoya

last: Zhang

first: Ahmed

middle: I

last: Mahmoud


title: Sequential early life infections alter peripheral blood transcriptomics in aging female mice but not the response to de novo infection with influenza virus or M. tuberculosis

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

summary:
The experimental mouse model is important for understanding the impact of aging on immune function. Humans are exposed to multiple pathogens during their lifetime, which has a significant effect on immune function as they age, while laboratory mice are aged under specific pathogen-free (SPF) conditions, reducing their exposure to pathogens throughout life. To determine the impact of accumulating antigen exposure on immunity in the aging mouse, and to develop a more relevant model, we sequentially infected young female mice with four distinct pathogens, a murine g-herpesvirus (gHV68), Sendai virus, murine cytomegalovirus (mCMV) and Heligmosomoides polygyrus (H. poly) at eight-week intervals, while mock-infected mice received PBS. After aging the mice to 18-20 months, we analyzed multiple immune parameters, compared to control, mock-infected mice maintained under SPF conditions. We assessed transcriptional activity in peripheral blood, T cell phenotype, CD8 T cell repertoire, and the response of the animals to infection with influenza virus and M. tuberculosis. Our data show enhanced
transcriptional activation in sequentially infected aged mice, with changes in some CD8 T cell subsets. However, there was no measurable difference in the response of mock and sequentially infected aged mice to de novo infection with either influenza virus or M. tuberculosis at 18-20 months. Unexpectedly, undertaking a similar influenza challenge in 25-month-old female mice revealed a significantly higher survival rate for serially infected (80%) versus mock infected (20%) mice. These data suggest that while exposure to a variety of pathogen challenges in the mouse model does not overtly impact cellular markers of immunity in aged female mice following de novo respiratory infection, subtle changes may emerge in other compartments or with increasing age.

overall_design: A microarray gene expression analysis of peripheral blood from 42 aged C57/BL6 female mice (18-22 months), which were given four different inoculations with PBS (mock-infected (MI, N =2`)), or a sequentially infected (SI, N = 2`) with a murine -herpesvirus (HV68), Sendai virus, murine cytomegalovirus (mCMV) and Heligmosomoides polygyrus (H. poly) at 8 week intervals, with no interventions or re-infections until sacrifice.

first: Kathleen

last: Lanzer

first: Tres

last: Cookenham

first: Elin

last: Lehrmann

first: Yongqing

first: Debbie

last: Duso

first: Carol

last: Xie

first: William

last: Reiley

first: Kevin

last: Becker

first: Marcia

middle: A

last: Blackman


title: Coronary Plaque Sampling Reveals Molecular Insights into Coronary Artery Disease

city: Tucson

first: Yong

last: Liu

state: AZ

address: The University of Arizona

department: Physiology

institute: University of Arizona

summary: We developed a coronary plaque sampling approach that could be applied broadly in live patients with coronary artery disease (CAD) to obtain molecular and cellular insights into human coronary atherosclerosis.  Our approach combined RNA retrieval directly from balloons used in percutaneous coronary interventions (PCI) and inexpensive, low-input RNA-Seq using SMART-seq. We generated SMART-Seq libraries from coronary samples from 27 patients. Of the 27 patients, 13 were confirmed to have stable CAD (sCAD) and 14 confirmed to have been performed on lesions causing acute coronary syndrome (ACS). We applied CIBERSORTx to analyze the SMART-seq data from each of the 27 samples. We found fibroblasts and fibromyoctes were enriched, while smooth muscle cells were reduced, in samples from ACS compared with sCAD patients. We identified 371 genes as significantly differential expressed (q<0.05) between sCAD and ACS patients.

overall_design: Total RNA were extracted directly from human coronary plaques in live patients.  RNA profiles were compared betweeen 13 sCAD patients and 14 ACS patients.

first: Widlansky

middle: E

last: Michael

first: Liu

last: Yong

first: Tumusiime

last: Shakirah

first: Hofeld

last: Benjamin

first: Khan

last: Nabeel

first: Aljadah

first: Wang

last: Jingli

first: Anger

last: Amberly

first: Qiu

last: Qiongzi

first: Therani

last: Bhavika

last: Pengyuan

first: Liang

last: Mingyu


title: Unreprogrammed H3K9me3 prevents minor zygotic genome activation and lineage commitment in SCNT embryos

city: Shanghai

first: Qianshu

last: Zhu

state: Shanghai

address: Siping Road

department: School of Life Science and Technology

institute: Tongji University

summary: Somatic cell nuclear transfer (SCNT) can be used to reprogram differentiated somatic cells to a totipotent state but has poor efficiency in supporting full-term development. H3K9me3 is considered to be an epigenetic barrier to zygotic genomic activation in 2-cell SCNT embryos. However, the mechanism underlying the failure of H3K9me3 reprogramming during SCNT embryo development remains elusive. Here, we perform genome-wide profiling of H3K9me3 in cumulus cell-derived SCNT embryos. We find redundant H3K9me3 marks are closely related to defective minor zygotic genome activation. Moreover, SCNT blastocysts show severely indistinct lineage-specific H3K9me3 deposition. We identify MAX and MCRS1 as potential H3K9me3-related transcription factors and are essential for early embryogenesis. Overexpression of Max and Mcrs1 significantly benefits SCNT embryo development. Notably, MCRS1 partially rescues lineage-specific H3K9me3 allocation, and further improves the efficiency of full-term development. Importantly, our data confirm the conservation of deficient H3K9me3 differentiation in Sertoli cell-derived SCNT embryos, which may be regulated by alternative mechanisms.

overall_design: Cut&Run in somatic cell nuclear transfer (NT) 6-hpa wild type and knock down (siRNA treatment) Suv39h2 .

first: Ruiming

last: Xv


title: Dendritic cell ICAM-1 strengthens synapses of CD8 T cells and dendritic cells but is dispensable for effector and memory responses

city: Rehovot

first: Ester

last: Feldmesser

state: Rehovot

address: POB 25

department: Life Science Core Facilities

country: Israel

institute: Weizmann Institute

summary: Single cell RNAseq analysis was employed to compare CD8 T cells  generated in vaccinated LNs normally expressing or deficient in DC ICAM-1.

overall_design: OT-1 CD8 cells were isolated from control (2 mice) or DC-specific ICAM-1 KO (2 mice) 72 hr after vaccination with aDEC205-OVA plus aCD40 (samples 1-4) or with MVA:OVA (samples 5-8). Samples were processed for  scRNA-seq analysis on hashed-tagged single channel of 10x genomics

first: Anita

last: Sapoznikov

first: Moshe

last: Biton

first: Noa

last: Wigoda


overall_design: Smart-seq in somatic cell nuclear transfer (NT) embryos and morpholino knock down Max and Mcrs1 in fertilized blastocyst embryos.


overall_design:
The specific pathogen-free grade mice (SPF) grade mice, including
C57BL/6j,DBA/2 and B6D2F1 mice,were housed in the animal facility at
Tongji University, Shanghai, China. Mice were housed in individually
ventilated cages with an environment with temperature ranging from
23 to 27°C, humidity of 30–45%, and a light cycle with 12 h of light and
12 h of darkness. All the mice had free access to food and water. All
experiments were performed in accordance with the University of
Health Guide for the Care and Use of Laboratory Animals and were
approved by the Biological Research Ethics Committee of Tongji
University (TJAB04021104).
The B6D2F1 hybrid mice (8–10 weeks old) were obtained from
mating female C57BL/6j mice with male DBA/2 mice.


title: Single-cell multi-omics sequencing reveals the epigenomic landscapes in human spermatogenesis [Bisulfite-Seq]

status: Public on Jul 09 2023

city: Guangzhou

first: Xinyan

last: Yang

state: Guangdong

address: No.1023,South Shatai Road, Baiyun District

department: Developmental Biology

institute: Southern Medical University

type: Methylation profiling by high throughput sequencing

summary: Human spermatogenesis is a well-ordered dynamic process, which ensures the long-term production of functional spermatozoa; however, the roles of DNA methylation and chromatin accessibility in this process remain largely unknown. Here, by simultaneously investigating the chromatin accessibility, DNA methylome and transcriptome landscapes of human spermatogenesis using the modified single-cell chromatin overall omic-scale landscape sequencing approach (Modified scCOOL-seq), we revealed that the transcriptional changes throughout human spermatogenesis were correlated with the dynamic alternations of chromatin accessibility; particularly, several potential transcription factors and a set of regulatory elements involved in such process were identified. Remarkably, a round of DNA demethylation was uncovered upon meiosis initiation in human spermatogenesis, which was associated with male meiotic recombination and conserved between human and mouse. And aberrant DNA hypermethylation at recombination hotspots could be detected in leptotene spermatocytes of certain nonobstructive azoospermia patients. Functionally, the intervention of DNA demethylation affected male meiotic recombination. Collectively, this study provides multi-omics landscapes of human spermatogenesis at single-cell resolution, and offers insights into the association between DNA demethylation and male meiotic recombination.

overall_design:
Here, we sequenced DNA methylation of DMSO- and Deci-treated HEK293T cells, and DNA methylation of spermatocytes from Uhrf1 cKO and control mice at PND 20.

Submitters declare that raw data related to human is submitted to the National Genomics Data Center, China National Center for Bioinformation (CNCB-NGDC) due to the Regulations of the People's Republic of China on the Management of Human Genetic Resources.

*** All the raw fastq data have been uploaded to GSA for Human as access controlled data under accession HRA004922 and CRA011561:
https://ngdc.cncb.ac.cn/gsa-human/browse/HRA004922
https://ngdc.cncb.ac.cn/gsa/browse/CRA011561

NOTE:
Part of the data of GSE235322 and all the data of GSE235323 are stored in HRA004922.
Another part of GSE235322 data is stored in CRA011561.

first: Xiao-Yang

last: Zhao

first: Shuai

last: Gao

first: Gang

last: Chang

first: Yaping

last: Huang

first: Lin

last: Li


title: Single-cell multi-omics sequencing reveals the epigenomic landscapes in human spermatogenesis [CUT&Tag]

overall_design:
To evaluate if DNA demethylation could affect the binding of PRDM9, the binding sites of PRDM9 were examined in HEK293T cells with DNA methylation inhibitor (Decitabine) treatment followed by transfection of hPRDM9-Flag.

Submitters declare that raw data related to human is submitted to the National Genomics Data Center, China National Center for Bioinformation (CNCB-NGDC) due to the Regulations of the People's Republic of China on the Management of Human Genetic Resources.

*** All the raw fastq data have been uploaded to GSA for Human as access controlled data under accession HRA004922:
https://ngdc.cncb.ac.cn/gsa-human/browse/HRA004922


title: Apolipoprotein E deficiency potentiates macrophage resistance to staphylococcus aureus osteomyelitis via regulating cholesterol metabolism

first: Mincheng

last: Lu

address: No. 1838 Guangzhou Dadao Bei

institute: 南方医院

summary:
To explore how APOE functions in the mechanism of regulation of cholesterol metabolism during S. aureus osteomyelitis, we established S. aureus osteomyelitis models in WT mice and APOE knockout  mice.
We then performed gene expression profiling analysis using data obtained from RNA-seq of bone marrow from mice mentioned above at day 7 after operation.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for WT and APOE knockout mice with or without S. aureus osteomyelitis.


title: 3D Landscape of Regulatory Elements and Transcription Factors for Transcription in Arabidopsis

first: Qiangwei

last: Zhou

state: Hubei

address: Hongshan district, shizishan #1

institute: Huazhong Agricultural university

summary: Whereas spatial genome organization at large scale of compartments and topologically associating domains (TADs) is relatively well studied, the spatial organization of regulatory elements at finer scales is poorly understood in plants. Here, using high-resolution chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) approach, we mapped histone modification-marked DNA elements-associated and RNA polymerase II (RNAPII)-tethered chromatin interactions involving in transcriptionally active, inactive and Polycomb-repressed states in Arabidopsis. Analysis of the regulatory repertoire showed that both active proximal and distal cis-regulatory elements (CREs) promote the transcription of their nearest and long-range connecting genes; poised CREs act as transcriptional repressors to repress their interacting genes’ expression, indicating that the linear juxtaposition is not the only guiding principle modulating gene transcription. Chromatin connectivity networks revealed that genes implicating in flowering-time control are functionally compartmentalized into separate subnuclear domains, linking active mark- and H3K27me3-associated chromatin conformation to coordinated gene expression. Our study uncovers fine-scale Arabidopsis genome organization and their roles in orchestrating transcription and development.

first: L

first: Q

last: Deng


title: A group of WRKY transcription factors form a protein complex with PHD-containing proteins to repress the transcription of stress responsive genes [RNA-Seq]

first: xinjian

last: He

address: No. 7, zhongguancun life science park road, changping district

institute: National Institute of Biological Sciences

summary: In higher plants, WRKY is a large transcription factor family involved in multiple biological processes by mediating either transcriptional activation or repression. Although the conserved WRKY domain is known to mediate the binding of WRKY transcription factors to DNA, little is known about how the other domains are involved in the regulation of transcription. We find that the group IId WRKY transcription factors interact with PHD-containing OBE proteins and form redundant WRKY-OBE complexes in Arabidopsis thaliana. We find that a conserved coiled-coil motif in the group IId WRKY transcription factors functions as an OBE-interacting domain (OID), which is involved in transcriptional repression and target gene selection. The WRKY-OBE complexes mediate transcriptional repression at a large number of stress responsive genes and are required for maintaining normal plant growth and development. While the growth of high order of wrky mutants is retarded at the early seedling stage, the low order of wrky mutants show reduced plant height and increased drought tolerance, which is consistent with the increased expression of stress responsive genes, including DREB1A, DREB1B, and DREB1C. Moreover, we found that the expression levels of most of group IId WRKY genes are markedly reduced in drought stress conditions relative to non-stress conditions. These results together suggest that the WRKY-OBE repress the transcription of stress responsive genes primarily under non-stress conditions, thereby coordinating plant growth and drought stress tolerance under variable environmental conditions.

overall_design: Examination of the mRNA expression of 11-day-old wild type and three mutants in Arabidopsis

first: Xin-Jian


title: A group of WRKY transcription factors form a protein complex with PHD-containing proteins to repress the transcription of stress responsive genes [ChIP-Seq]

overall_design: Examination of protein binding levels in transgenic plants