title: Dynamic regulation of chromatin accessibility during melanocyte stem cell activation

city: La Jolla

first: Seoyeon

last: Lee

state: California

address: 9500 Gilman Dr.

institute: University of California, San Diego

summary: We sorted melanocyte nuclei from quiescent (telogen) skin, skin actively producing hair shafts (anagen), and skin exposed to UVB. With these sorted nuclei, we then utilized single-nucleus assay for transposase-accessible chromatin with high-throughput sequencing (snATAC-seq) and characterized three melanocyte lineages: quiescent McSCs (qMcSCs), activated McSCs (aMcSCs), and differentiated melanocytes (dMCs) that co-exist in all three skin conditions. Furthermore, we successfully identified differentially accessible genes and enriched transcription factor binding motifs for each melanocyte lineage. Our findings reveal potential gene regulators that determine these melanocyte cell states and provide new insights into how aMcSC chromatin states are regulated differently under divergent intrinsic and extrinsic cues. We also provide a publicly available online tool with a user-friendly interface to explore this comprehensive dataset, which will provide a resource for further studies on McSC regulation upon natural or UVB-mediated stem cell activation.

overall_design: snATAC-seq library was generated from GFP+ nuclei from dorsal skin of 7-week-old Dct-rtTa; Tre-H2B-GFP mice in telogen phase or treated with Nair cream or UVB after providing drinking water containing doxycycline.

first: Paul

last: Soloway

first: Luye

last: An

first: Andrew

last: White


title: Transcriptional profiling of young and old mouse macrophages interacting with nanoparticles

status: Public on Jul 18 2023

city: Houston

first: Wen

last: Jiang

state: TX

address: 1515 Holcombe Blvd

country: USA

institute: MD Anderson Cancer Center

type: Expression profiling by high throughput sequencing

summary: This SuperSeries is composed of the SubSeries listed below.Nanomedicines have been approved to treat multiple human diseases. However, clinical adoption of nanoformulated agents is often hindered by concerns about hepatic uptake and clearance, a process that is not fully understood. Here we show that the antitumour efficacy of cancer nanomedicine exhibits an age-associated disparity. Tumour delivery and treatment outcomes are superior in old versus young mice, probably due to an age-related decline in the ability of hepatic phagocytes to take up and remove nanoparticles. Transcriptomic- and protein-level analysis at the single-cell and bulk levels reveals an age-associated decrease in the numbers of hepatic macrophages that express the scavenger receptor MARCO in mice, non-human primates and humans. Therapeutic blockade of MARCO is shown to decrease the phagocytic uptake of nanoparticles and improve the antitumour effect of clinically approved cancer nanotherapeutics in young but not aged mice. Together, these results reveal an age-associated disparity in the phagocytic clearance of nanotherapeutics that affects their antitumour response, thus providing a strong rationale for an age-appropriate approach to cancer nanomedicine.

overall_design: Refer to individual Series


title: Transcriptional profiling of young and old mouse macrophages interacting with nanoparticles [scRNA-seq]

type: Expression profiling by genome tiling array

summary: The mononuclear phagocytic system is integral to the clearance of nanotherapeutics. However, the precise mechanisms involved in the phagocytic clearance of nanotherapeutics, and how age-associated changes in innate immune cells affect this clearance, are poorly understood. We found that the ability of professional phagocytes to take up nanoparticles diminishes with age. Bulk RNA sequencing of bone marrow derived macrophages and single cell RNA sequencing of liver macrophages derived from young and old mice was carried out to investigate the gene expression changes that may be assiciated with the changed ability of macrophages to uptake nanoparticles.

overall_design: We extracted RNA from bone marrow derived macrophages of young and old C57BL6 background mice and perfrom bulk RNA sequencing to compare the gene expression differences. We injected nanoparticles intravenously to young and old C57BL6 background mice and perform single-cell RNA sequencing of the enriched liver macrophages.

first: Hongmei

last: Wang

first: Betty

middle: Y

last: Kim


title: miRNAs screening in small extracellular vesicles (sEVs) from patients with primary antiphospholipid syndrome  (PAPS)

city: Barcelona

first: Cristina

last: Sole Marce

address: Pg Vall Hebron 119-129

country: Spain

institute: Vall Hebron Institute Research

type: Non-coding RNA profiling by high throughput sequencing

summary: To discover miRNAs implicate in PAPS pathogenesis, we isolated sEVs from plasma of PAPS patients, aPL patients (patients with positive antiphospholipid antibodies without thrombotic or obstretic complications) and control. Then, we extracted RNA total and we performed miRNA-sequencing.

overall_design:
We then performed gene expression profiling analysis using data obtained from miRNA-seq of PAPS patients (N=8), control patients (N=8) and aPL patients (N=8). aPL patients are patients with antiphospholipid antibodies without associated thrombotic or obstretic complications.
Comparative gene expression profiling analysis of miRNA-seq data for APS, aPL and control groups.

first: Josefina

last: Cortés-Hernández

last: Solé


title: Transcriptional profiling of young and old mouse macrophages interacting with nanoparticles [Bulk RNA-seq]


title: Chromatin profiling of zebrafish spinal cord tissue at 2 week post injury

city: Madison

first: jianhong

last: ou

state: WI

address: 330 N Orchard Street

institute: Morgridge institute for research

type: Genome binding/occupancy profiling by high throughput sequencing

summary: To identify regulatory tissue regeneration enhancer elements (TREEs) relevant during spinal cord regeneration, we  performed ATAC sequencing datasets of zebrafish spinal cord at 2 weeks after sham injury and after transection.

overall_design: Spinal cord chromatin profiles 1week after spinal cord transection and in sham injured controls.

first: Valentina

last: Cigliola

first: Adam

last: Shoffner

first: Nutishia

first: Jianhong

last: Ou

first: Clay

last: Becker

first: Jiaul

last: Hoque

first: Trevor

last: Gonzalez

first: Yanchao

last: Han

first: Grace

last: Sheng

first: Timothy

last: Faw

first: Muhammad

last: Abd-El-Barr

first: Shyni

last: Varghese

first: Aravind

last: Asokan

first: Kenneth

middle: D

last: Poss


title: Genome-wide maps of chromatin state in HCT116 cells expressing Flag-tagged VCP

city: Guangzhou

first: Youwei

last: Huang

state: Guangdong

address: West Huangpu Avenue no.601

department: Department of pharmacology

country: China

institute: Jinan University

summary: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for VCP and Flag in HCT116 cells expressing Flag-tagged VCP.

overall_design: Examination of VCP-Flag overexpression HCT116 cells.

first: Haipeng

last: Zhang


title: Inulin-induced differences on serum extracellular vesicles derived miRNAs in dairy cows suffering from subclinical mastitis

city: Beijing

first: Wanjie

last: Yu

address: No. 2 Yuanmingyuan West Road

institute: Institute of Animal Science, Chinese Academy of Agricultural Sciences

summary: MicroRNA (miRNA) profiles vary with the nutritional and pathological conditions of cattle. In this study, we aimed to investigate the effects of inulin supplement on miRNA profiles derived from serum extracellular vesicles (EVs). Our goal was to determine the differences in miRNA expressions and analyse the pathways in which they are involved. Based on the results of California mastitis test and milk somatic cell counts, ten lactating cows with subclinical mastitis were randomly divided into two groups: an inulin group and a control group (n = 5 in each group). The inulin group received a daily supplement of 300 g of inulin while the control group did not receive any supplementation. After a 5-week treatment period, serum-derived EV-miRNAs from each cow were isolated. High-throughput sequencing was conducted to identify differentially expressed miRNAs. GO and KEGG bioinformatics analysis was performed to examine the target genes of these differentially expressed miRNAs. The EV-RNA concentration and small RNA content were not affected by the inulin treatment. A total of 162 known miRNAs and 180 novel miRNAs were identified from 10 samples in the two groups. Among the known miRNAs, 23 miRNAs were found to be differentially expressed between the two groups, with 18 upregulated and five downregulated in the inulin group compared to the control group. Pathway analysis revealed the involvement of these differentially expressed miRNAs in the regulation of cell structure and function, lipid oxidation and metabolism, immunity and inflammation, as well as digestion and absorption of nutrients. Overall, our study provides a molecular-level explanation for the reported beneficial health effects of inulin supplementation in cows with subclinical mastitis.

overall_design: Ten cows that were suffering from subclinical mastitis were selected and randomly divided into two groups, supplement with or without inulin (control and inulin group, respectively; n=5). Blood samples were collected from each cow after 6 weeks. miRNAs were seperated from serum EVs, and small RNA sequencing was conducted by company.

first: Xuemei

first: Martine

last: Schroyen

first: Yue

last: Wang

first: Beihai

last: Xiong


title: Zebrafish spinal cord tissue at 1 week post injury

first: jianhong

last: ou

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


title: RNA sequencing of zebrafish spinal cord tissue at 1 week post injury

summary: To identify regulators of spinal cord regeneration, we  performed RNA sequencing of zebrafish spinal cord at 1 week after sham injury and after transection.

overall_design: Spinal cord RNA profiles 1week after spinal cord transection and in sham injured controls.

first: Valentina

last: Cigliola

first: Adam

last: Shoffner

first: Nutishia

last: Lee

first: Jianhong

last: Ou

first: Clay

last: Becker

first: Jiaul


title: Chromatin profiling of zebrafish spinal cord tissue at 1 week post injury

summary: To identify regulatory tissue regeneration enhancer elements (TREEs) relevant during spinal cord regeneration, we  performed ATAC sequencing datasets of zebrafish spinal cord at 1 week after sham injury and after transection.

last: Hoque

first: Trevor

last: Gonzalez

first: Yanchao

last: Han

first: Grace

last: Sheng

first: Timothy

last: Faw

first: Muhammad

first: Shyni


title: Genotoxic effects of base and prime editing in human hematopoietic stem cells [BARseq_BaseE]

city: Milan

first: Stefano

last: Beretta

address: Via Olgettina, 60

country: Italy

institute: San Raffaele Telethon Institute for Gene Therapy

summary: Emerging base and prime editing may provide safer and more precise genetic engineering than nuclease-based approaches bypassing the dependence on DNA double strand breaks (DSBs). However, little is known about cellular responses and genotoxicity. Here, we comparatively assessed state-of-the-art base and prime editors (B/PE) versus Cas9 in human hematopoietic stem/progenitor cells (HSPCs). BE and PE induced detrimental transcriptional responses constraining editing efficiency and/or HSPC repopulation in xenotransplants, albeit to a lesser extent than Cas9. DNA DSBs and their genotoxic byproducts, including deletions and translocations, were less frequent but not abrogated by BE and PE, particularly for cytidine BE due to suboptimal inhibition of base excision repair. Tailoring timing and B/PE expression enabled highly efficient and precise editing of long-term repopulating HSPCs. However, we uncovered a genome-wide effect of BEs on the mutational landscape of HSPCs, raising concerns for a potential genotoxic impact and calling for further investigations and improvements in view of clinical application.

overall_design: BAR-Seq clonal tracking performed on samples from a pool of 6 CB donors, treated with different editing conditions, namely, mock electroporation (mock electro), Cas9, BE4max, and ABE8.20-m, in different organs and lineages.

first: Martina

last: Fiumara

first: Samuele

last: Ferrari

first: Ivan

last: Merelli

first: Luigi

last: Naldini


title: Genotoxic effects of base and prime editing in human hematopoietic stem cells [RNAseq_BaseEd]

summary: Emerging base and prime editing may provide safer and more precise genetic engineering than nuclease-based approaches bypassing the dependence on DNA double strand breaks (DSBs). However, little is known about cellular responses and genotoxicity. Here, we comparatively assessed state-of-the-art base and prime editors (B/PE) versus Cas9 in human hematopoietic stem/progenitor cells (HSPCs). BE and PE induced detrimental transcriptional responses constraining editing efficiency and/or HSPC repopulation in xenotransplants, albeit to a lesser extent than Cas9. DNA DSBs and their genotoxic byproducts, including deletions and translocations, were less frequent but not abrogated by BE and PE, particularly for cytidine BE due to suboptimal inhibition of base excision repair. Tailoring timing and B/PE expression enabled highly efficient and precise editing of long-term repopulating HSPCs. However, we uncovered a genome-wide effect of BEs on the mutational landscape of HSPCs, raising concerns for a potential genotoxic impact and calling for further investigations and improvements in view of clinical application.and/or HSPC repopulation in xenotransplants, albeit to a lesser extent than Cas9. DNA DSBs and their genotoxic byproducts, including deletions and translocations, were lower but not abrogated by BE and PE, particularly for cytidine BE upon suboptimal base excision repair inhibition. Tailoring timing and B/PE expression enabled highly efficient and precise editing of long-term repopulating HSPCs. However, we uncovered a genome-wide effect of cytidine BE on mutational landscape of hematopoietic grafts, raising concerns for its prospective clinical application. Conversely, the superior efficiency and precision of adenine BE built confidence on its entry into clinical arena.

overall_design: Whole transcriptomic analyses on human HSPC cells from a pool of 6 CB donors, comparing untreated (UT) cells with different editing conditions, namely, mock electroporation (mock electro), Cas9, BE4max, and ABE8.20-m, edited at day 1 and 3.


title: Loss of fatty acid oxidation in mitochondria promotes epigenetic control of cardiomyocyte maturation status

city: Bad Nauheim

first: Carsten

last: Kuenne

address: Ludwigstrasse 43

department: Bioinformatics

country: Germany

institute: Max Planck Institute for Heart and Lung Research


title: Gene Expression Analysis of NK cells after co-culture with Liver Sinusoidal Endothelial Cells (LSECs)

status: Public on Jul 17 2023

city: Mannheim

first: Carolina

last: Delatorre

address: Theodor-Kutzer-Ufer 1-3

institute: University Heidelberg

summary: The liver is enriched in innate lymphocytes, including Natural Killer (NK) cells, that can continuously interact with Liver Sinusoidal Endothelial Cells (LSECs) within liver sinusoids. NK cells provide the early defence against infections and malignancies by exerting cytotoxicity and by secreting pro-inflammatory cytokines. To decipher how LSECs affect NK cell phenotype and function, we co-cultured NK cells with LSECs and used microarray technology to identify transcriptomic changes.

overall_design:
co-cultured NK cells with LSECs
Please note that the chips used are 'Clariom D Mouse', previously labeled as GeneChip Mouse Transcriptome Array (MTA) but later changed to 'Clariom_D_Mouse', and thus the chp information (included in the CEL files, generated before renaming) reads MTA-1_0.

first: Ana

last: Stojanovic


title: Regulation of human germline commitment by DMRT1 [RNA-seq and Cut&Run]

city: Cambridge

first: SUN MIN

last: LEE

state: Cambridgeshire

address: Gurdon Institute, Tennis Court Road

country: United Kingdom

institute: Gurdon Institute

summary: Nascent human primordial germ cell-like cells (PGCLCs) can be specified with BMP2 or BMP4 together with SCF and EGF from germline competent embryonic stem cells which are maintained in the presence of inhibitors for GSK3, MEK, p38 and JNK together with FGF2, TGFβ and LIF (4i ESC). Here we discovered that Activin A and retinoic acid treatment after PGC specification induced genes expressed in migrating and gonadal PGCs in vivo, including DMRT1 and CDH5. Ectopic expression of DMRT1 and SOX17 resulted in repression of pluripotent genes as well as induction of DAZL and a subset of mitotic arrest PGC genes. Our findings provide novel insights on the roles of DMRT1 for the transition from nascent PGCs towards germline determination and molecular mechanisms of early human germline development.

overall_design: RNA profiles of 4i ESC, NANOS3+ PGCLCs, DMRT1+ PGCLCs, and DAZL+ PGCLCs. Cut-And-Run-sequencing targeting DMRT1 in DAZL+ PGCLCs.

first: Naoko

last: Irie

first: Sun

first: Azim

last: Surani


title: Genome-wide maps of H3K4me3 deposition comparing Ctrl and Fatty acid oxidation restricted (Cpt1b-deficiency) adult cardiomyocyte

summary: In the heart, metabolic profile switches from glycolysis to fatty acid oxidation (FAO) rapidly after birth accompanied by chromatin reconfiguration, cell cycle exit and cardiomyocyte (CM) maturation, suggesting a synergistic rewiring of transcriptional networks regulated by epigenetic mechanisms in accordance with environmental and metabolic signals. To gain a better insight into the interconnection between epigenetic processes and metabolic pathways during cardiac development, maturation and heart regeneration, we induced a metabolic reprogramming by depleting CPT1b, a crucial enzyme for FAO, specifically in CM.  Cpt1b inactivation led to cardiomegaly and attenuated cardiac damage in response to myocardial injury primarily attributed to augmented CM proliferation and enhanced resistance to ischemic injury.

overall_design: Examination of H3K4me3 genome-wide deposition comparing Ctrl and Cpt1b-deficient adult CM

first: Xiang

last: Li

first: Stefan

last: Guenther

first: Thomas

last: Braun


title: Early clonal extinction in glioblastoma progression revealed by genetic barcoding

city: Genoa

first: Paolo

last: Malatesta

address: Largo Rosanna Benzi 10

institute: IRCCS Ospedale Policlinico San Martino


title: The VCAM1–ApoE pathway directs microglial chemotaxis and alleviates Alzheimer’s disease pathology

city: Hong Kong

first: Nancy

last: Ip

address: Room 6313, Academic Building The Hong Kong University of Science and Technology Clear Water Bay, Kowloon

summary: In Alzheimer’s disease (AD), sensome receptor dysfunction impairs microglial danger-associated molecular pattern (DAMP) clearance and exacerbates disease pathology. While extrinsic signals including interleukin-33 (IL-33) can restore microglial DAMP clearance, it remains largely unclear how the sensome receptor(s) is regulated and interacts with DAMP during phagocytic clearance. Here, we show that IL-33 induces VCAM1 in microglia, which promotes microglial chemotaxis toward amyloid-beta (Aβ) plaque-associated ApoE, and leads to Aβ clearance. We show that IL-33 stimulates a chemotactic state in microglia, characterized by Aβ-directed migration. Functional screening identified that VCAM1 directs microglial Aβ chemotaxis by sensing Aβ plaque-associated ApoE. Moreover, we found that disrupting VCAM1–ApoE interaction abolishes microglial Aβ chemotaxis, resulting in decreased microglial clearance of Aβ. In patients with AD, higher cerebrospinal fluid levels of soluble VCAM1 were correlated with impaired microglial Aβ chemotaxis. Together, our findings demonstrate that promoting VCAM1–ApoE-dependent microglial functions ameliorates AD pathology.

overall_design: FACS-isolated microglia in IL-33-treated AD transgenic mice

first: Shun-Fat

last: Lau


title: Fatty acid oxidation restriction triggered by Cpt1b deficiency specific in adult cardiomyocyte (CM) with aMHC-MCM promotes CM dedifferentiation [RNA-seq II]

overall_design: Transcriptome profiles of adult CM isolated from Ctrl and Cpt1b-deficient mice 4 weeks after TAM injection


title: Fatty acid oxidation restriction triggered by Cpt1b deficiency specific in cardiomyocyte (CM) with Myh6-Cre benefits heart regeneration [RNA-seq I]

overall_design: Transcriptome profiles of adult CM isolated from Ctrl and Cpt1b-deficient mice. CRE-driver was aMHC-Cre.


title: Transcriptome analysis of Chi3l1-deficient TFH cells

status: Public on Jul 19 2023

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

summary: To better understand how Chi3l1 regulates the TFH response, we analyzed the transcriptome of CXCR5+PD1+CD4+Lin- TFH cells from msLNs of WT and Chi3l1-/- mice on D14 post H. pylori infection.

overall_design: RNA-seq on wildtype and Chi3l1-deficient TFH cells after H. pylori infection with 9 replicates per group.

first: C

first: F

middle: E

last: Lund

first: M

middle: L

last: Curtiss


title: Nanostring transcriptomic analysis of lungs from antiChemR23 treated and untreated 4T1-bearing mice

city: NANTES

first: Isabelle

last: Girault

state: PAYS-DE-LA-LOIRE

address: 22 BOULEVARD BENONI GOULIN

country: France

institute: OSE IMMUNOTHERAPEUTICS

summary: Macrophages are a major component of the tumor environment and their accumulation often correlates with poor prognosis and resistance to anticancer treatments. In this study, we thus investigated the therapeutic interest to target ChemR23, a receptor of the resolution of inflammation, in cancers using an agonist monoclonal antibody, antiChemR23. In vitro experiments on M2-like macrophages treated by antiChemR23 agonist decreased their inflammatory phenotype. In vivo, treatment with antiChemR23 agonist increased mouse survival and decreased metastasis occurrence in a model of triple-negative breast cancer in correlation with modulation of TAM phenotype in the metastatic niche.

overall_design: 4T1-luc2 cells (0.25x106/mouse in PBS) were injected into the fat pad of mammary gland of 8-week-old BALB/c female mice (day 0). Mice were treated with antiChemR23a agonist (n=7) or hIgG1 (n=4) mAbs intraperitoneally at 1mg/kg 3 times a week for 3 weeks from day 7 to day 28. At day 13, primary tumors were surgically removed from mammary glands. Tumor spreading was analyzed by overall survival and by in vivo bioluminescence on lungs every week using a bioimager.

first: Vanessa

last: Gauttier


title: Reductive carboxylation epigenetically instructs effector T cell differentiation

city: Lausanne

first: Tania

last: Wyss

address: Rue du Bugnon 25A

country: Switzerland

institute: SIB Swiss Institute of Bioinformatics

overall_design: Refer to individual Series


title: Targeting ChemR23, a receptor of the resolution of inflammation, in cancers using an agonist monoclonal antibody

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Effect of overexpression of VCP on gene expression during colorectal cancer progression of HCT116 cells

first: Youwei

last: Huang

summary:
To investigate the function of VCP in the colorectal cancer progression, we established HCT116 cell lines overexpressing VCP.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 3 different cells overexpressing VCP and control vector.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HCT116 cells overexpressing VCP and control vector.

first: Haipeng

last: Zhang


title: Reductive carboxylation epigenetically instructs effector T cell differentiation [ATAC-Seq]

summary:
The differentiation into effector and memory CD8+ T cell subsets was recently associated with specific metabolic pathways to sustain their diverse bioenergetics needs. Clonally expanding T cells rely strongly on glucose and glutamine utilization to maintain high cell proliferation and effector functions.
We found that proliferating effector CD8+ T cells, in addition to oxidizing, also reductively carboxylate glutamine, to maintain rapid lipid synthesis for cell proliferation. Interfering with reductive carboxylation by genetic deletion of isocitrate dehydrogenase 2 (IDH2), the enzyme mediating this reaction in the mitochondria, surprisingly did not impair proliferation and effector function upon infection, but skewed the CD8+ T cell response towards enhanced memory differentiation. Pharmacological IDH2 inhibition during in vitro CAR T cell manufacturing also induced memory features and thus strongly enhanced their antitumor activity and persistence upon adoptive cell transfer into murine melanoma tumour models.
Mechanistically, IDH2 inhibition caused a disequilibrium in metabolites regulating histone-modifying enzymes, which altered the epigenetic landscape, increasing chromatin accessibility at genes required for memory differentiation. Restoring this metabolite balance or preventing the epigenetic modifications abrogated the enhanced CD8+ T cell memory differentiation and anti-tumour activity induced by IDH2 inhibition.
These findings suggest that reductive carboxylation of glutamine in activated CD8+ T cells is dispensable for their effector function, but instead primarily instructs a metabolite composition that epigenetically locks them in a terminal effector differentiation program. Blocking this metabolic route allows for increased memory formation, which can be exploited to optimize CAR T cell production for adoptive cell transfer immunotherapy against cancer.

overall_design: Chromatin accessibility analysis by ATAC sequencing was performed on activated CD8+ T cells that were conditioned for 7 days with DMSO or AG-221 5µM (an IDH2 inhibitor).

first: Alison

last: Jaccard

first: Pedro

last: Romero

first: Mathias

last: Wenes


title: Regulation of human germline commitment by DMRT1

first: SUN MIN

last: LEE

type: Methylation profiling by high throughput sequencing


title: Nanostring transcriptomic analysis of M(M-CSF) (M2-like) macrophages treated with antiChemR23 agonist or untreated.

overall_design: Monocytes were treated in vitro with M-CSF at 50ng/ml (Isokine, 01-A0220) to obtain M(M-CSF) (M2-like) macrophages.After 3 days in culture, macrophages were incubated with 10µg/ml of antiChemR23 or hIgG1 antibodies for 24h. Then, cells were stimulated with 200ng/ml lipopolysaccharide (LPS) (Sigma-Aldrich) for 6h and cells were lysed using the RLT buffer (Qiagen) supplemented by 1% β-mercaptoethanol (Sigma-Aldrich). Total RNA was isolated using the RNeasy Mini Kit according to the manufacturer’s protocol (Qiagen).


title: RNA-sequencing of PD-1+ CD8 T cells following two week PD-1 blockade (stem-like and terminally-differentiated subsets).

first: William

last: Hudson

address: 1 Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

summary: The goal of this study is to characterize the transcriptional profile of PD-1+ stem-like (Tim-3-CD73+) versus terminally-differentiated (Tim-3+CD73-) CD8 T cells following two week αPD-1 blockade.

overall_design: Splenocytes were isolated from mice >45 days post-LCMV Clone 13 infection (2×106 pfu, i.v. after CD4 T cell depletion). Mice received isotype or αPD-1 blockade for two weeks. Cells were stained with extracellular antibodies (CD4, CD8, CD19, PD-1, Tim-3, and CD73 from Biolegend) for 30 minutes. Cell viability was determined with the Live/Dead fixable aqua dead cell stain kit (Invitrogen). Cells were washed and sorted on a FACSAria II (BD Biosciences). Two populations of PD-1+ CD8 T cells were sorted in duplicate from αPD-1 or isotype-treated samples: stem-like (Tim-3-CD73+) and terminally-differentiated (Tim-3+CD73-). CD44loCD62Lhi CD8 T cells were also sorted in duplicate from naïve mice as controls. RNA was isolated from each sample using the All-Prep DNA/RNA Micro Kit (Qiagen) and then submitted for sequencing.

first: Amanda

last: Gill


title: Whole transcriptome RNAseq analysis of adult Inha WT and KO normal testis (N), tumour associated tubules (TAT) and tumour regions (TM).

status: Public on Jul 16 2023

city: Giessen

first: Daniela

last: Fietz

address: Frankfurter Straße 98

department: Institute for Veterinary Anatomy,  Histology and Embryology

institute: Justus Liebig University Giessen

summary: We performed bulk RNA-Seq on testes from adult Inha WT and KO mice (lacking the inhibin a gene).

overall_design: Inha KO mice develop stromal tumours and the aim of this experiment was to examine the differences in the KO normal (N), tumour associated tubules (TAT) and tumour regions (TM) compared to Inha WT. In some instances, multiple tumours were analysed within a single testis and between testes from the same animal.

first: P

last: Whiley

first: B

last: Nathaniel

last: Stanton

first: R

middle: M

last: Hobbs

first: K

last: Loveland


title: Effect of WNT hyperactivation by CTNNB1 overexpression or APC knockdown on gene expression in HT29 cells

first: Sellers

last: Lab

state: MA

address: 415 Main St

institute: Broad Institute

summary: To investigate effect of  WNT hyperactivation by CTNNB1 overexpression or APC knockdown on gene expression and probe possible mechanism of cell viability effect, we overexpressed GFP/CTNNB1, or induce knockdown of APC by shNT1 (non-targeting) and shAPC

overall_design: 4 experimental conditions (GFP overexpression, CTNNB1 overexpression, shNT1 ctr, shRNA-APC), in triplicate, of human HT29 tumor cells.

first: Liang

last: Chang


title: Neuroblastoma RAS viral oncogene homolog (N-RAS) deficiency aggravates liver injury and fibrosis

status: Public on Jul 15 2023

city: Madrid

first: Francisco

middle: Javier

last: Cubero

address: c/Doctor Severo Ochoa, 9

department: Department of Immunology, Ophthalmology & ENT

institute: Complutense University School of Medicine

summary:
To gain insight into the differential signaling pathways triggered in N-RAS-/-  versus N-RAS+/+ mice during liver injury and fibrosis, we performed microarray analyses of livers 28 days after CCl4 treatment and BDL surgery, respectively. Our findings suggested that increased cell proliferation and matrix deposition as well as loss of cell homeostasis were characteristic of N-RAS-/- after experimental fibrosis.
We used microarrays to detail the global programme of gene expression underlying CCl4 and BDL challenge,

overall_design: CCl4 and BDL induced gene expression in livers of N-RAS-/-  and N-RAS+/+ mice was measured at 28 days after challenge. Three livers from each group were analyzed in both CCl4 and BDL experiments.

middle: J

first: Kang

last: ZHENG


title: Multi-transcriptomics reveals brain cellular responses to peripheral infection in Alzheimer's disease model mice

city: Pittsburgh

first: Iliya

last: Lefterov

state: PA

address: 130 De Soto St

department: Environmental and Occupational Health

institute: University of Pittsburgh

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


title: Multi-transcriptomics reveals brain cellular responses to peripheral infection in Alzheimer's disease model mice [spatial transcriptomics]

summary: Peripheral inflammation has been associated with various neurodegeneration, including Alzheimer's Disease (AD). In this study, we employed an AD mouse model nasally infected with Staphylococcus aureus to assess the impact of chronic or acute peripheral inflammation on brain transcriptome and amyloid pathology. The chronic exposure increased the diffuse and compact amyloid plaques and blood cytokine levels. Following a short-term exposure, single-cell and spatial transcriptomics uncovered cell type- and spatial-specific transcriptional changes indicating a dysregulation of the brain barriers, including the blood-brain and the blood-cerebrospinal fluid barriers. Brain macrophages exhibited increased Apoe expression and macrophage-specific genes were upregulated at ventricular areas of infected mice. In addition, we report an increase of disease associated microglia genes around the A plaques, together with disbalances in neuronal expression in response to peripheral inflammation. Overall, results enlighten the mechanisms linking peripheral inflammation to AD.

overall_design: We used an AD mouse model nasally infected with Staphylococcus aureus. mRNA-seq for whole brain was conducted following long-term treatment (16 weeks) , and scRNA-seq and visium spatial transcriptomics were peformed after 1-week acute peripheral inflammation.


title: Multi-transcriptomics reveals brain cellular responses to peripheral infection in Alzheimer's disease model mice [RNA-seq]


title: C. elegans germ granules regulate both germline and somatic RNAome [miRNA-Seq]

status: Public on Jul 20 2023

city: Columbus

first: Wen

last: Tang

state: Ohio

address: 1060 Carmack Rd

department: Department of Biological Chemistry and Pharmacology

institute: The Ohio State University

summary: Germ granules are membrane-less organelles essential for small RNA biogenesis and germline development. Among the conserved properties of germ granules is their association with the nuclear membrane. Recent studies demonstrated that LOTUS domain proteins, EGGD-1 and EGGD-2 (also known as MIP-1 and MIP-2 respectively), promote the formation of perinuclear germ granules in C. elegans. This finding presents a unique opportunity to evaluate the significance of perinuclear localization of germ granules. Here we show that loss of eggd-1 causes the coalescence of germ granules and formation of abnormal cytoplasmic aggregates. Impairment of perinuclear granules affects certain germline classes of small RNAs including Piwi-interacting RNAs. Transcriptome profiling reveals overexpression of spermatogenic and cuticle-related genes in eggd-1 hermaphrodites. We further demonstrate that disruption of germ granules activates HLH-30-mediated transcriptional program in somatic tissues. Collectively, our findings underscore the essential role of EGGD-1 in germ granule organization and reveal an unexpected germ granule-to-soma communication.

overall_design: Small RNA expression and analysis of small RNAs isolated from wild type and eggd-1 C. elegans mutants by small RNA sequencing

first: Ian

middle: F

last: Price

first: Jillian

last: Wagner

first: Benjamin

last: Pastore

first: Hannah

last: Hertz


title: Multi-transcriptomics reveals brain cellular responses to peripheral infection in Alzheimer's disease model mice [scRNA-seq]


title: Reductive carboxylation epigenetically instructs effector T cell differentiation [RNA-Seq]

first: Tania

last: Wyss

overall_design: mRNA profiles of DMSO or AG-221-treated CD8+ T cells

first: Alison

last: Jaccard

first: Pedro

last: Romero

first: Mathias

last: Wenes


title: The PTPN2/PTPN1 inhibitor ABBV-CLS-484 unleashes potent anti-tumour immunity

status: Public on Jul 14 2023

first: Robert

last: Manguso

address: 415 Main Street


title: The PTPN2/N1 inhibitor ABBV-CLS-484 unleashes potent anti-tumour immunity [TIL_ATACseq]

summary: Immune checkpoint blockade is effective for some cancer patients, but most are refractory to current immunotherapies and new approaches are needed to overcome resistance. The protein tyrosine phosphatases PTPN2 and PTPN1 are central regulators of inflammation, and their genetic deletion in either tumour or immune cells promotes anti-tumour immunity. However, phosphatases are challenging drug targets and in particular, the active site has been considered undruggable. Here, we present the discovery and characterization of ABBV-CLS-484 (AC484), a first-in-class, orally bioavailable, potent PTPN2/N1 active site inhibitor. AC484 treatment in vitro amplifies the response to interferon and promotes the activation and function of several immune cell subsets. In murine cancer models resistant to PD-1 blockade, AC484 monotherapy generates potent anti-tumour immunity. We show that AC484 inflames the tumour microenvironment and promotes NK and CD8+ T cell function by enhancing JAK-STAT signaling and reducing T cell dysfunction. PTPN2/N1 inhibitors offer a promising new strategy for cancer immunotherapy and are currently being evaluated in patients with advanced solid tumours (NCT04777994). More broadly, our study shows that small molecule inhibitors of key intracellular immune regulators can achieve efficacy comparable to or exceeding antibody-based immune checkpoint blockade in preclinical models. Finally, to our knowledge, AC484 represents the first active-site phosphatase inhibitor to enter clinical evaluation for cancer immunotherapy and may pave the way for additional therapeutics targeting this important class of enzymes.

overall_design: CD8+ T cells were isolated from subcutaneous B16 tumors and separated into progenitor exahusted or terminally exhausted pools by Fluorescence-activated cell sorting (FACS). We utilized ATAC-seq to analyze the epigenetic changes of tumour-infiltrating T cells upon AC484 treatment

first: Ashwin

last: V Kammula

first: Audrey

last: Muscato

first: Omar

middle: I

last: Avila

first: Hakimeh

last: Ebrahimi-Nik

first: Kathleen

middle: B

last: Yates

middle: T


title: Vaccine Infection T cell Comparison

city: Aurora

first: Ross

last: Kedl

state: CO

address: 12800 E. 19th Avenue

department: Immunology and Microbiology

institute: University of Colorado Anschutz Medical Campus

summary: Protection from pathogens relies on both humoral (antibody-mediated) and cellular (T cell-mediated) responses. While infections robustly elicit both of these types of immunity, currently approved vaccine adjuvants largely fail to induce significant T cell responses. However, recent work by our lab and others suggests that the mechanisms governing vaccine-elicited T cells (Tvac) may be substantially different than those governing infection-elicited T cells (Tinf). We have recently demonstrated that optimal subunit vaccine-elicited T cell responses rely on different cytokine signals (IL-27 and 15) and metabolic function (oxidative phosphorylation vs. aerobic glycolysis) leading to phenotypically and functionally different outcomes (memory vs. effector). Our goal was to investigate the transcriptional programming that promotes Tvac formation. Using a bulk RNAsequencing approach we compared WT Tvac at day 3 post immunization to Tvac where IL-27 or IL-15 signaling was absent, to Tinf at day 4 post infectious challenge, or to naive OT-1 T cells.

overall_design: A small number (20000) of congenically marked (CD45.1) WT or IL27R KO OT-I T cells were adoptively transferred into WT or IL-15KO naïve B6 recipients (CD45.2). These recipients were then immunized intravenously (i.v.) against OVA using our combined adjuvant vaccine (poly I:C, anti-CD40) or infection with LM-OVA ) or Vaccinia Virus-OVA (VV). OT-I T cells were isolated on day 3 (adjuvant samples) or day 4(infectious samples) post immunization using FACS sorting of CD45.1+ CD8+ cells.

first: Scott

last: Thompson


title: Multi-omics and 3D-imaging reveal bone heterogeneity and unique calvaria cells in neuroinflammation

city: Munich

first: Louis

last: Kuemmerle

address: Ingolstädter Landstraße 1

institute: Helmholtz Centre Munich

summary: The bone marrow in the skull is important for shaping immune responses in the brain and meninges, but its molecular makeup in comparison to other bones in mice and humans remains unclear. Here, we show that the skull has the most distinct transcriptomic profile compared to other bones in states of health and injury, characterized by a late-stage neutrophil phenotype. In humans, proteome analysis reveal that the skull marrow is the most distinct, with differentially expressed neutrophil-related pathways and a unique synaptic protein signature. 3D imaging demonstrates the structural and cellular details of human skull-meninges connections compared to veins. Lastly, using TSPO-PET imaging, we show that the skull bone marrow reflects inflammatory brain responses with a disease-specific spatial distribution in patients with various neurological disorders. The unique molecular profile, anatomical, and functional connections of the skull show its potential as a new site for diagnosing, monitoring, and treating brain diseases.

overall_design: A single-cell RNA sequencing experiment was conducted using 10x Genomics technology on samples from three distinct groups, which included six bones, meninges, and the brain. The study comprised three groups: those that underwent MCAo surgery, those that underwent sham surgery, and a group of naive animals. Each sample consisted of cells pooled from three animals, with a total of 32 samples utilized. The MCAo surgery group contributed 2 samples, each consisting of cells pooled from 3 different animals. The sham and naive groups served as control groups. In addition to the single-cell RNA sequencing, bulk RNA sequencing experiments were conducted using the Illumina ligation stranded mRNA preparation kit. These experiments involved samples from the six bones under the three conditions (naive, sham, and MCAo). Separate measurements were taken for 4-6 animals per condition, yielding a total of 95 samples. Furthermore, bulk RNA sequencing was carried out using Smart-seq2 for mini-bulks of about 50 CD45+/Cd11b+ sorted immune cells each from the skull and femur. These samples were taken from wildtype animals (5 in total) and 5xFAD animals (3 in total), amassing 168 samples overall, with approximately 20 samples per animal.

first: Zeynep

last: Kolabas

last: Perneczky

last: Förstera

first: Selin

last: Ulukaya

first: Mayar

last: Ali

first: Saketh

last: Kapoor

first: Laura

last: Bartos

first: Maren

last: Büttner

first: Ozum

middle: S

last: Caliskan

first: Zhouyi

last: Rong

first: Hongcheng

last: Mai

first: Luciano

last: Höher

first: Denise

last: Jeridi

first: Muge

last: Molbay

first: Igor

last: Khalin

first: Ioannis

middle: K

last: Deligiannis

first: Moritz

last: Negwer

first: Kenny

last: Roberts

first: Alba

last: Simats

first: Olga

last: Carofiglio

first: Mihail

last: Todorov

first: Izabela

last: Horvath

first: Furkan

last: Ozturk

first: Selina

last: Hummel

first: Gloria

last: Biechele

first: Artem

last: Zatcepin

first: Marcus

last: Unterrainer

first: Johannes

last: Gnörich

first: Jay

last: Roodselaar

first: Joshua

last: Shrouder

first: Pardis

last: Khosravani

last: Tast

first: Lisa

last: Richter

last: Díaz-Marugan

first: Doris

last: Kaltenecker

first: Laurin

last: Lux

first: Ying

last: Chen

first: Shan

last: Zhao

first: Boris-Stephan

last: Rauchmann

first: Michael

last: Sterr

first: Ines

last: Kunze

first: Karen

last: Stanic

first: Simon


title: Ezh2 promotes mammary tumor initiation through the epigenetic regulation of the Wnt and mTORC1 signaling pathways (RNA-Seq)

city: Montreal

first: William

last: Muller

state: Quebec

address: 1160 Av des Pins O

department: Biochemistry

country: Canada

institute: McGill University

summary: The regulation of gene expression through histone post-translational modifications plays a crucial role in breast cancer progression. However, the molecular mechanisms underlying the contribution of histone modification to tumor initiation remain unclear. To gain a deeper understanding of the role of the histone modifier Enhancer of Zeste homology 2 (Ezh2) in the early stages of mammary tumor progression, we employed an inducible mammary organoid system bearing conditional Ezh2 alleles that faithfully recapitulates key events of Luminal B breast cancer initiation. We showed that the loss of Ezh2 severely impairs oncogene-induced organoid growth, with Ezh2-deficient organoids maintaining a polarized epithelial phenotype. Transcriptomic profiling showed that Ezh2-deficient mammary epithelial cells upregulated the expression of negative regulators of Wnt signaling and downregulated genes involved in mTORC1 (mechanistic target of rapamycin complex 1) signaling. We identified Sfrp1, a Wnt signaling suppressor, as an Ezh2 target gene that is de-repressed and expressed in Ezh2-deficient epithelium. Furthermore, an analysis of breast cancer data revealed that Sfrp1 expression was associated with favorable clinical outcomes in Luminal B breast cancer patients. Finally, we confirmed that targeting Ezh2 impairs mTORC1 activity through an indirect mechanism that upregulates the expression of the tumour suppressor Pten. These findings indicate that Ezh2 integrates the mTORC1 and Wnt signaling pathways during early mammary tumor progression, arguing that inhibiting Ezh2 or therapeutically targeting Ezh2-dependent programs could be beneficial for the treatment of early-stage Luminal B breast cancer.

overall_design: To investigate the differentially expressed genes across EZH2 wildtype and knockout mouse strain during early tumor initiation phase, we cultured organoids obtained from mammary glands of both MIC/EZH2wt/wt and MIC/EZH2fl/fl mouse strains. These organoids were treated with doxycycline for a duration of 8 days to induce oncogene expresion (polyomavirus middle-T antigen) and deletion of conditional Ezh2 alleles. Following this, we harvested cells and extracted RNA. Subsequently, we subjected the RNA samples to RNA-sequencing analysis to analyze gene expression.

first: Linshan

last: Liu

first: Alain

last: Pacis


title: The PTPN2/PTPN1 inhibitor ABBV-CLS-484 unleashes potent anti-tumour immunity [SK_RNAseq]

first: Robert

last: Manguso

summary: AC484 is a first-in-class, orally bioavailable, potent PTPN2/N1 active site inhibitor. In order to investigate the response of AC484 and IFNg treatment on wild type and PTPN2/N1 dual deletion B16F10 cells, these tumours were transcriptionally profiled.

overall_design: Control and PTPN2/N1 dual deletion B16F10 tumours were treated with either AC484, IFNg, or a combination of the two. RNA was isolated from these cells and sequenced.

first: Omar

last: Avila

first: Sarah

last: Kim

first: Hakimeh

last: Ebrahimi-Nik

first: Kathleen

last: Yates


title: Single-cell comparison of day 7 vaccine, listeria and vaccinia virus elicited CD8 T cells

first: Ross

last: Kedl

summary: Protection from pathogens relies on both humoral (antibody-mediated) and cellular (T cell-mediated) responses. While infections robustly elicit both of these types of immunity, currently approved vaccine adjuvants largely fail to induce significant T cell responses. However, recent work by our lab and others suggests that the mechanisms governing vaccine-elicited T cells (Tvac) may be substantially different than those governing infection-elicited T cells (Tinf). We have recently demonstrated that optimal subunit vaccine-elicited T cell responses rely on different cytokine signals (IL-27 and 15) and metabolic function (oxidative phosphorylation vs. aerobic glycolysis) leading to phenotypically and functionally different outcomes (memory vs. effector). Our goal was to investigate the transcriptional programming that promotes Tvac formation. Using a single-cell RNA-seq approach, we compared Tvac and Tinf at day 7 post-immunization or infectious challenge to determine the heterogenity of CD8 T cell responses at this peak timepoint.

overall_design:
A small number (500) of congenically marked (CD45.1) OT-I T cells were adoptively transferred into a naïve B6 recipient (CD45.2). These recipients were then immunized intravenously against OVA using our combined adjuvant vaccine (poly I:C, anti-CD40), infection with Listeria monocytogenes-OVA (LM) or Vaccinia Virus-OVA (VV). T cells were isolated on day 7 post immunization using FACS sorting of CD45.1+ CD8+ cells. Cells from an individual condition (adjuvant, LM or VV) were stained with an unique oligo-tagged anti-CD45 “hashtag” antibody (Biolegend) and then combined into one sample.
-------------------
HTO barcode sequence hashtagged sample
TotalSeq-A0301 anti-mouse Hashtag 1 Antibody ACCCACCAGTAAGAC Adjuvant
TotalSeq-A0302 anti-mouse Hashtag 2 Antibody GGTCGAGAGCATTCA Listeria monocytogenes
TotalSeq-A0303 anti-mouse Hashtag 3 Antibody CTTGCCGCATGTCAT Vaccinia Virus

first: Scott

last: Thompson


title: Ezh2 promotes mammary tumor initiation through the epigenetic regulation of the Wnt and mTORC1 signaling pathways

overall_design: Refer to individual Series


title: Transcriptome analysis on postmortem brain of patients with schizophrenia

city: Sendai

first: Kazusa

last: Miyahara

address: Seiryo-machi 2-1

country: Japan

institute: Tohoku University

summary: Gene expression levels were evaluated using microarray. By correlation analyses, Genes which are significantly correlated with quality indicators, tissue pH and RNA integrity number, were identified.

overall_design: Total RNA were obtained from human postmortem occipital lobe, and correlation between each gene expression levels and quality indicators were investigated.  日野案　Total RNA was obtained from the cortex of the occipital lobe of the postmortem human brain. The mRNA expression levels were analyzed, and the correlation between each gene expression level and quality indicators was investigated.  國井　Total RNA was obtained from the occipital cortex of the postmortem human brain. The mRNA expression levels were analyzed, and the correlation between each gene expression level and quality indicators was investigated.

first: Mizuki

last: Hino

first: Zhiqian

last: Yu

first: Chiaki

last: Ono

first: Atsuko

last: Nagaoka

first: Masataka

last: Hatano

first: Risa

last: Shishido

first: Hirooki

last: Yabe

first: Hiroaki

last: Tomita

first: Yasuto

last: Kunii


title: Secreted NS1 proteins of tick-borne encephalitis virus and West Nile virus block dendritic cell activation and effector functions

city: Hannover

first: Imke

last: Steffen

address: Buenteweg 17

institute: University of Veterinary Medicine Hannover

summary: Flavivirus non-structural protein 1 (NS1) is secreted from cells in infected individuals and in cell culture and levels correlate with disease severity. Treatment of murine bone marrow–derived dendritic cells (BMDCs) with recombinantly produced solube NS1 (sNS1) of tick-borne encephalitis virus (TBEV) or West Nile virus (WNV) prior to poly(I:C) stimulation revealed two gene clusters that were downregulated by TBEV or WNV sNS1 and that were associated with innate and adaptive immune responses. Especially co-stimulatory molecules and pro-inflammatory cytokines as well as chemokines were found to be downregulated in sNS1 pre-treated BMDCs prior to poly(I:C) stimulation.

overall_design: BMDCs were left untreated, or stimulated with poly(I:C), or pre-treated with TBEV or WNV sNS1 for 16 h and stimulated with poly(I:C) for 24 h. RNA from 3 replicates in each condition was extracted using Trizol and the Directzol Miniprep Plus Kit, and sequenced on Illumina NovaSeq platform with 100 bp paired-end read configuration.

first: António

middle: A

last: R. Camarão

first: Olivia

last: Gern

first: Felix

last: Stegmann

last: Mulenge

first: Bibiana

last: Costa

first: Babak

last: Saremi

first: Klaus

last: Jung

first: Bernd

last: Lepenies

first: Ulrich

last: Kalinke


title: Gene expression profile at single cell level from the whole brain of two tree shrew fetus

city: Kunming

first: Xiao-Lin

last: Zhuang

address: Longxin Road

institute: ology, Kunming Institute of Zoology, Chinese Academy of Sciences

summary: Although continual expansion of the brain during primate evolution accounts for our enhanced cognitive capabilities, the drivers of brain evolution have scarcely been explored. Tree shrews are closely related to primates that comparing their brains to primate brains at the single-cell level will provide new insights into the evolution of the primate brain.

overall_design: Whole brains of tree shrew embryos were collected from 2 two-thirds-gestation embryos (4-5 post-conceptional weeks) for single cell RNA-sequencing. The 10x library was constructed using 10x Chromium Controller and Chromium Single Cell 3’ Reagent Kits (v3 chemistry CG000183) following the detailed protocol of the manufacturer. Libraries were sequenced using an Illumina NovaSeq 6000 sequencer with 150-bp paired-end reads.

first: Jin-Jin

last: Zhang

first: Yong

last: Shao

first: Dong-Dong

last: Wu


title: Molecular profiling of Ebf2+ and Ebf2- PαS  mesenchymal stem cells from mouse dorsal skin

city: Huddinge

first: HONG

last: QIAN

state: Stockholms Lan

address: Neo, HERM, Floor 7, Hälsovägen 7,

department: Department of Medicine

country: Sweden

institute: Karolinska Institute

summary: While extensive efforts have been on understanding bone marrow (BM) niche contribution to normal and malignant hematopoiesis, the role of extramedullary niches has been largely ignored. Evidence suggests a BM mesenchymal stem cell (MSC) counterpart exists in skin. However, their native identity and role in hematopoiesis remain unexplored. Here, we demonstrated that mouse skin harbors MSC subsets that are phenotypically and molecularly similar to BM MSCs, including a primitive MSC population marked by Early B-cell Factor 2 (Ebf2) and downstream MSCs lacking Ebf2. Functionally, skin MSCs not only support acute myeloid leukemia (AML) stem cells but also protect them from chemotherapy. This persistence of AML cells in skin were further amplified in AML-promoting microenvironment lacking Lama4. Our study demonstrated the features of extramedullary niches in skin and their previously unrecognized role in supporting AML stem cells during chemotherapy, opening a new path for understanding the extramedullary manifestation of AML in patients.

overall_design: Examination of mRNA profiles in skin mesenchymal stem cells  sorted from 3 mice and bone marrow mesenchymal stem cells sorted  from 4 mice.

first: Hong

last: Qian

first: Lskshmi

last: Sandhow

first: Huan

last: Cai

first: Pingnan

last: Xiao

first: Makoto

last: Kondo


title: The PTPN2/N1 inhibitor ABBV-CLS-484 unleashes potent anti-tumour immunity [PTPN2i-MS-TCRseq]

city: Cambridge

first: Robert

last: Manguso

summary: To assess TCR diversity in AC484-treated tumors we profiled the TCRβ chain repertoire from untreated, anti-PD-1-treated, or AC484-treated B16 tumours

overall_design: We performed TCR profiling analysis on RNA extracted from subcutaneous B16 bulk tumor tissue to analyze the TCR repertoire upon AC484 treatment.

first: James

middle: C

last: Patti

first: Mitchell

last: Yeary

first: Arvin

last: Iracheta-Vellve

first: Kira

last: Olander

first: Sarah

last: Kim

first: Kathleen

last: Yates


title: Proviral location affects cognate peptide-induced virus production and immune recognition of 2 HIV-1-infected T cell clones

city: Baltimore

first: Kellie

last: Smith

address: 1550 Orleans St

institute: Johns Hopkins University

summary: In this study, we determined the effect of proviral inducibility on CD8+ T cell recognition of HIV-infected clones. We showed that a T cell clone containing a provirus integrated in relatively transcriptionally inactive site was much less recognized by CD8+ T cells than a  T cell clone containing a provirus that was integrated into a trancriptionally active site.

overall_design:
We compared the peripheral  T cell receptor repertoire before and after chemoradiation in an elite controller with lung cancer. We also perfomed the functional expansion of specific T cells (FEST) assay to determine the repertoire of CD4+ T cells that responded to an HIV Gag peptide.
*** Raw data files not provided due to sensitive nature of the data. ***

first: Filippo

last: Dragoni

first: Francesco

last: Simonetti

first: Joel

last: Blankson


title: Expression data from white matter astrocytes of wild-type or GnT-IX-deficient mice after cuprizone administration

city: Fukushima City

first: Shinobu

last: Kitazume

state: Fukushima

address: 1 Hikariga-oka

institute: Fukushima Medical University

summary: Multiple sclerosis (MS) is an immune-based demyelinating disease. Currently available therapeutics target inflammation but have little impact on promoting remyelination. Furthermore, MS diagnosis is sometimes challenging. Using a demyelination model mice, we previously found that protein tyrosine phosphatase receptor type zeta (PTPRZ) receives abnormal glycosylation, a branched O-mannosyl (O-Man) glycan and that branched O-Man glycosylated PTPRZ specifically occurs in reactive astrocytes of demyelinated lesions. Furthermore, by genetically deleting the branching enzyme, GnT-IX (also known as GnT-Vb), astrogliosis was attenuated and remyelination enhanced. To characterize the PTPRZ expressing astrocytes, microarray analysis was performed using astrocytes from mice after short and long term-cuprizone administration.

overall_design: Astrocytes were isolated from white matters of wild-type and GnT-IX-deficient mice after 0, 3, or 12 weeks of cuprizone administration and used for microarray analysis. Three independent biological replicates were performed.

first: Kanoko

last: Sakuda


title: Ezh2 promotes mammary tumor initiation through epigenetic regulation of the Wnt and mTORC1 signaling pathways (ChIP-Seq)

first: William

last: Muller

overall_design: MIC/EZH2wt/wt organoids derived from mouse mammary epithelial cells were grown in culture medium for 6 days followed by 8 days of doxycycline treatment. ChIP sequencing with H3K27me3 antibody was performed.

first: Linshan

last: Liu

first: Alain

last: Pacis


title: Long-read transcriptome profiling of human lung cancer cell lines

city: Parkville

first: Matthew

last: Ritchie

state: Victoria

address: 1G Royal Parade

country: Australia

institute: The Walter and Eliza Hall Institute of Medical Research

summary: Purpose: The aim of this study is to compare the transcriptome profiles using a mixture design that allows the relative changes of the majority of the genes profiled to be estimated.   Methods - Cell Culture: Lung adenocarcinoma cell lines NCI-H1975 and HCC827 were grown in Roswell Park Memorial Institute (RPMI) 1640 medium with 10% fetal calf serum and 1% penicillin-streptomycin.  Methods - RNA preparation: mRNA was extracted using a Qiagen RNA miniprep kit and purified using the NEBNext® Poly(A) mRNA Magnetic Isolation Module (E7490).  Purified mRNA spiked with sequins was used for the cRNA-PCR Barcoding (SQK-PCS109 with SQK-PBK004) kit (ONT). Completed libraries were sequenced on PromethION (ONT). Reads were mapped to known genomic features of the GrCh38 reference transcriptome and RNA sequin transcriptome combined sequences at the transcript-level and single reads were then summarized into transcript-level counts using salmon software (Patro et al. 2017).

overall_design: Total RNA was extracted from lung adenocarcinoma cell lines NCI-H1975 and HCC827. Total RNA transcriptome from these samples was profiled by RNA-seq (Oxford Nanopore Technologies PromethION).

first: Xueyi

last: Dong

first: Jafar

last: Jabbari

first: Quentin

last: Gouil

first: Mei

last: Du


title: The PTPN2/N1 inhibitor ABBV-CLS-484 unleashes potent anti-tumour immunity [TIL_RNAseq]

first: Robert

last: Manguso

overall_design: CD8+ T cells were isolated from subcutaneous B16 tumors and separated into progenitor exahusted or terminally exhausted pools by Fluorescence-activated cell sorting (FACS). We utilized RNAseq to analyze the gene expression profile of tumour-infiltrating T cells upon AC484 treatment

first: Ashwin

middle: V

last: Kammula

first: Omar

last: Avila

first: Audrey

last: Muscato

first: Hakimeh

last: Ebrahimi-Nik


title: Activin E controls body fat distribution via suppression of adipose lipolysis in mice

city: Tarrytown

first: Yuanqi

last: Zhao

address: 777 Old Saw Mill River Road

institute: Regeneron Pharmaceuticals

summary: Body fat distribution is a heritable risk factor for cardiovascular and metabolic disease. In humans, rare Inhibin beta E (INHBE, activin E) loss-of-function variants are associated with lower waist-to-hip ratio and protection from type 2 diabetes. Hepatic fatty acid sensing promotes INHBE expression during fasting and in obese individuals, yet it is unclear how the hepatokine activin E governs body shape and energy metabolism. Here, we uncover activin E as a negative feedback regulator of adipose lipolysis that restrains excessive fat breakdown during fasting. By suppressing β-agonist-induced lipolysis, activin E promotes visceral fat accumulation, adipocyte hypertrophy and contributes to adipose dysfunction in mice. Mechanistically, we demonstrate that activin E elicits its effect on adipose tissue through ACVR1C, activating SMAD2/3 signaling and suppressing PPARG target genes. Conversely, loss of activin E or ACVR1C increases fat utilization, lowers adiposity and drives gene signatures indicative of healthy adipose function. Our studies identify activin E-ACVR1C as metabolic rheostat promoting liver-adipose crosstalk to preserve fat mass during prolonged fasting, a mechanism that is maladaptive in obese individuals.

overall_design: All mice are on 100% C57BL/6NTac background. For over-expression studies on chow diet, mice were transduced with AAV8 constructs driving either GFP control or mInhbe expression in livers (where Inhbe is endogenously expressed). n=10 for control and Inhbe over-expression groups.  For loss of function, we have phenotyped WT vs Inhbe KO mice on chow vs. high fat diet (4 groups in total). Due to limited availability of KO animals, we have n=8 for all groups, except n=7 for Inhbe KO on chow diet. We have the same treatment groups for both subcutaneous adipose and epididymal adipose tissues.

first: Joseph

last: Song

first: Nicole

last: Negron

first: Shuo

last: Li


title: The PTPN2/N1 inhibitor ABBV-CLS-484 unleashes potent anti-tumour immunity[PTPN2i-MS-scRNAseq]

summary: To examine the effect of AC484 inhibition on the tumor immune microenvironment, we performed scRNA-seq on CD45+ cells from B16 and KPC tumors from mice treated with vehicle, anti-PD-1, or AC484.

overall_design: CD45+ cells were isolated from subcutaneous B16 or KPC tumors. We used scRNAseq to analyze the response of immune cells in the tumor microenvironment to AC484 treatment

first: Sarah

last: Kim

first: Kathleen

last: Yates


title: Metabolic responses of normal rat kidneys to a high salt intake

city: Milwaukee

first: Satoshi

last: Shimada

address: 8701 Watertown plank road

department: Physiology

institute: Medical College of Wisconsin

summary: Determine changes in the Sprague-Dawley rats' kidney cortex (Cx) and outer medulla (OM) tissue metabolomic and mRNAseq profiles before and following the switch from a 0.4% to a 4.0% NaCl diet.

overall_design: mRNAseq for Cx and OM tissues before and 14 and 21 days following the switch from a 0.4% to a 4.0% NaCl diet.

first: Brian

last: Hoffmann

first: Chun

last: Yang

first: Theresa

last: Kurth

first: Andrew

last: Greene

first: Mingyu

last: Liang

first: Ranjan

last: Dash

first: Allen

last: Cowley Jr


title: scNanoHi-C: a single-cell long-read concatemer sequencing method to reveal high-order structures within individual cells

city: Beijing

first: Jiansen

last: Lu

address: No. 5 Yiheyuan Road, Haidian District

department: Biomedical Pioneering Innovation Center (BIOPIC)

institute: Peking University

summary: High-order three-dimensional (3D) organization of regulatory elements provide a topological basis for genes regulation, but it remains unclear that how multiple regulatory elements interact across mammalian genome in a single cell. To address this, herein, we developed scNanoHi-C, which applies Nanopore sequencing to explore genome-wide proximal high-order chromatin contacts within individual cells. Evaluation of the method suggested that scNanoHi-C reliably and effectively profiled chromosome structure and distinguished structure subtype among single cells, which could also be used to detect genomic variations including CNVs and SVs, as well as scaffold the de novo assembly of single cell genomes. Importantly, our results suggested that high-order structures were extensively existed in active transcription chromatin across the genome, and multiway interactions between enhancers and their target promoters were observed in the first time within single cells. Taken together, scNanoHi-C sparked new insights of high-order 3D genome structure at the single-cell level.

overall_design: single-cell 3D genomic struture  profiling by scNanoHi-C

first: Wen


title: Widespread regulatory specificities between transcriptional corepressors and enhancers in Drosophila

city: Vienna

first: Jelle

last: Jacobs

address: Campus-Vienna-Biocenter 1

department: VBC

country: Austria

institute: Institute of molecular Pathology

summary: Animal development and homeostasis critically depend on the accurate regulation of gene expression, which includes the silencing of genes that should not be active. Silencing or repression of transcription is mediated by a specific class of transcription factors termed repressors that, typically via the recruitment of co-repressors (CoRs), can dominantly suppress transcription, even in the presence of activating cues. Here, we used functional genomics to discover previously unknown regulatory specificities between CoRs and enhancers. Enhancers can typically be repressed by only a subset of CoRs. Enhancers classified by CoR sensitivity also show distinct biological functions and endogenous chromatin features. Moreover, enhancers that are sensitive or resistant to silencing by specific CoRs differ in TF motif content. Strikingly, we identified TF motifs that are necessary and sufficient for resistance to specific CoRs, and can predict enhancer sensitivity to CoRs based on TF motif content.

overall_design: We evaluted the direct effect of 5 CoRepressors on the activity of enhancers in Drosophila S2 cells using a modified version of STARR-seq termed repressor-STARR-seq. The repressors CoRest, CtBP, Rbf, Rbf2 and Sin3A are fused to the Gal4-DNA-binding domain and recruited next to the enhancer library through 4xUAS sites. Additionally we also tested the effect of recruiting CtBP and Rbf upstream of the promoter or upstream of the enhancers. We performed genome-wide and BAC screens (~750bp) and desigend oligonucleotide (250bp) screens, each sample with biological replicate. Reads were internally normalized, using a spike-in control of D. Pseudoobscura enhancers, lacking the 4xUAS binding sites.

first: Michaela

last: Pagani

first: Christoph

last: Wenzl

first: Alexander

last: Stark


title: Single-cell transcriptome profiling of mouse colonic mucosa in colitis

city: Chicago

first: Cambrian

middle: Yangshao

last: Liu

state: IL

address: 5841 S Maryland Ave

institute: The University of Chicago

summary: Chronic injury and inflammation pose high risks for epithelial dysplasia and cancer. In the “field cancerization” model, spontaneous mutations confer a stem-cell fitness advantage and promote gradual clonal expansion. Here, through 3d imaging, fate-mapping, biophysical modeling, and single-cell transcriptomics in a mouse model of acute colitis, we define an alternate, rapid mechanism for clonal expansion: the neutral activation of metabolically reprogrammed “founder progenitor cells” (FPCs) during wound healing. FPCs leverage the breakdown of normal crypt regenerative boundaries to expand multiplicatively into new crypts patterned from a zone of cellular mixing and plasticity. FPCs represent relatively generic proliferative cells probabilistically emerging from a background of fetal-reprogrammed epithelium and derive from both surface and basal zones of the injured colonic mucosa. Acute wound healing activates spatial and lineage plasticity to generate clonal fields without significant mutational burden. These results suggest that hallmark pre-neoplastic changes may arise from a punctuated pattern of injury and healing rather than gradual field cancerization.

overall_design: Single-cell RNA sequencing of mucosal cells from colons of uninjured mice or mice with DSS-induced or Il10-/- colitis.

first: D

last: Polk


title: Distinct layers of BRD4-PTEFb reveal bromodomain-independent function in transcriptional regulation

first: Ali

last: Shilatifard

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

summary: The BET family protein BRD4, which forms the CDK9-containing BRD4-PTEFb complex, is considered to be a master regulator of RNA polymerase II (Pol II) pause release. Because its tandem bromodomains interact with acetylated histone lysine residues, it has long been thought that BRD4 requires these bromodomains for its recruitment to chromatin and transcriptional regulatory function. Here, using rapid depletion and genetic complementation with domain deletion mutants, we demonstrate that BRD4 bromodomains are dispensable for Pol II pause release. A minimal, bromodomain-less C-terminal BRD4 fragment containing the PTEFb-interacting C-terminal motif (CTM) is instead both necessary and sufficient to mediate Pol II pause release in the absence of full-length BRD4. Although BRD4-PTEFb can associate with chromatin through acetyl recognition, our results indicate that a distinct, active BRD4-PTEFb population functions to regulate transcription independently of bromodomain-mediated chromatin association. These findings may enable more effective pharmaceutical modulation of BRD4-PTEFb activity.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) and comparative expression profiling of RNA-seq for BRD4 and its domains mutants to investigate their role in Pol II pause-release.

first: Bin

last: Zheng

first: Marta

last: Iwanaszko

first: Benjamin

last: Howard


title: CRISPR-ChIP to identify mechanisms of chromatin regulation [ChIP-seq]

city: Melbourne

first: Mark

last: Dawson

address: 305 Grattan Street

department: Cancer Research

institute: Peter MacCallum Cancer Centre

summary: The regulation of all chromatin-templated processes involves the selective recruitment of chromatin factors to facilitate DNA repair, replication, and transcription. Chromatin immunoprecipitation (ChIP) is a critical experimental method used to provide spatiotemporal evidence for the coordination of these chromatin-based events including the dynamic regulation of chromatin modifications at cis-regulatory elements. However, getting a global appreciation of all the factors that influence a specific chromatin event has remained challenging. Here, as a proof of concept we demonstrate the utility of coupling unbiased functional genomics with ChIP to identify the factors associated with active transcription. Specifically, we use this method to identify the major chromatin factors associated with recruitment of RNA polymerase 2 and the catalysis of two evolutionarily conserved histone modifications; H3K4me3 present at the transcriptional start site and H3K79me2 present through the gene body of actively transcribed genes. With CRISPR-ChIP we identify all the non-redundant COMPASS complex members required for H3K4me3 and the major components of mediator and TFIID required for Pol II recruitment during the maintenance of gene expression. Importantly, using CRISPR-ChIP in leukaemia cells driven by MLL-translocations we uncover a functional partitioning of H3K79 methylation into two distinct regulatory units. An oncogenic DOT1L complex, where the malignant driver directs the catalytic activity of DOT1L at MLL-fusion target genes which is separate from the endogenous DOT1L complex where catalytic activity is directed by MLLT10 at actively expressed genes not controlled by the MLL-fusion protein. This functional demarcation has therapeutic implications and explains why Menin inhibition surprisingly controls methylation of H3K79 at a critical subset of genes that sustain MLL-fusion leukaemia.

overall_design: ChIP-seq for H3K4me3, H3K79me2, H3K27ac, Pol II and FLAG-MLLAF9

first: Omer

last: Gilan


title: CRISPR-ChIP to identify mechanisms of chromatin regulation [CRISPR-ChIP]

overall_design: Coupling CRISPR screen with Chromatin immunoprecipitation (ChIP)


title: scRNA-seq of murine bone and marrow cells

status: Public on Jul 13 2023

city: Rochester

first: Madison

last: Doolittle

state: MN

address: 200 1st St SW

institute: Mayo Clinic

summary: To investigate heterogeneity of senescence at the single-cell level, we performed scRNA-seq analysis on bone and marrow mesenchymal cells from aged mice

overall_design: We isolated bone and marrow cells from the femurs and tibias of 3 24-month-old mice, depleted of immune cells Lin- by MACS and enriched for live mesenchymal cells (CD45-SyTOX-) by FACS, and performed 10X Genomics single-cell RNA-sequencing. Samples were pooled and run across two lanes.

first: Sundeep

last: Khosla


title: CRISPR-ChIP to identify mechanisms of chromatin regulation [RNA-seq]

overall_design: RNA-seq in MLLAF9 Cas9 cells with KO of DOTCOM complex members


city: Shinjuku-ku

first: Tsukasa

last: Sanosaka

state: Tokyo

address: 35 Shinanomachi

department: Department of Physiology

institute: Keio University School of Medicine

summary: Single cell RNA sequencing for bone marrow CD31+CD45- cells from diaphysis, metaphysis or epiphysis of mouse femurs

overall_design: mRNA profiles of bone marrow CD31+CD45- cells. One experiment for each fragment (epiphysis, metaphysis, diaphysis).


title: Dioxin Disrupts Dynamic DNA Methylation Patterns in Genes that Govern Cardiomyocyte Maturation [BiSulfite-seq]

city: Cincinnati

first: Mario

last: Medvedovic

state: OH

address: 3223 Eden Av. ML 56

department: Department of Environmental Health

institute: University of Cincinnati

summary: To test the hypothesis that the disruption caused by TCDD in cardiomyocytes results from changes in DNA methylation and gene expression patterns, we established a stable mouse embryonic stem cell line expressing a puromycin resistance selectable marker under the control of the cardiomyocyte-specific Nkx2.5 promoter. Differentiation of these cells in the presence of puromycin induces the expression of a large suite of cardiomyocyte specific markers. To assess the consequences of TCDD treatment on gene expression and DNA methylation in these cardiomyocytes, we subjected them to transcriptome and methylome analyses in the presence of TCDD. Unlike control cardiomyocytes maintained in vehicle, the TCDD-treated cardiomyocytes showed extensive gene expression changes, with a significant correlation between differential RNA expression and DNA methylation in 122 genes, many of which are key elements of pathways that regulate cardiovascular development and function. Our findings provide an important clue towards the elucidation of the complex interactions between genetic and epigenetic mechanisms, and environmental factors that may contribute to CHD incidence.

overall_design: To analyze gene expression and DNA methylation changes across time, we compared  Nkx2-5- positive cells treated with vehicle (control) with a) untreated ES cells, and b) Nkx2-5- positive cells treated with 5 nM TCDD for 24, 72, and 96 hours.

first: Matthew

last: de Gannes

first: Chia-I

last: Ko

first: Xiang

last: Zhang

first: Jacek

last: Biesiada

first: Liang

last: Niu

first: Sheryl

last: Koch

first: Jack

last: Rubinstein

first: Alvaro

last: Puga


title: miRNA sequencing profile of colonic mucosa in global mir-10b KO and WT mice

city: Reno

first: Seungil

last: Ro

state: Nevada

address: 1664 N. Virginia St

department: Physiology and Cell Biology

institute: University of Nevada Reno

summary:
Background/ Aim: Diabetes has substantive co-occurrence with disorders of gut-brain interactions (DGBIs). The pathophysiological and molecular mechanisms linking diabetes and DGBIs are unclear. miRNAs are key regulators of diabetes and gut dysmotility. We investigated whether impaired gut barrier function regulated by a key miRNA, miR-10b-5p, links diabetes and gut dysmotility.
Methods: We created a new mouse line using the Mb3Cas12a/Mb3Cpf1 endonuclease to knock out mir-10b globally. Loss of function studies were conducted to characterize diabetes, gut dysmotility, and gut barrier dysfunction phenotypes in these mice. Gain of function studies were conducted by injecting these mice with a miR-10b-5p mimic. Further, we performed miRNA-sequencing analysis from colonic mucosa from mir-10b KO, WT, and miR-10b-5p mimic injected mice to confirm 1) deficiency of miR-10b-5p in KO mice, and 2) restoration of miR-10b-5p expression after the mimic injection.
Results: Congenital loss of mir-10b in mice led to the development of hyperglycemia, gut dysmotility, and gut barrier dysfunction. We found increased gut permeability and reduced expression of the tight junction protein Zonula occludens-1 (ZO-1), in the colon of mir-10b KO mice. We further confirmed that patients with diabetes or IBS-C, a known DGBI that is linked to leaky gut, had significantly reduced miR-10b-5p expression. Injection of a miR-10b-5p mimic in mir-10b KO mice rescued these molecular alterations and phenotypes.
Conclusion: Our study uncovered a potential pathophysiologic mechanism of gut barrier dysfunction that links both the diabetes and gut dysmotility phenotypes in mice lacking miR-10b-5p. Treatment with a miR-10b-5p mimic reversed the leaky gut, diabetic, and gut dysmotility phenotypes, highlighting the translational potential of miR-10b-5p mimic.

overall_design: Global transcriptomic profiling of miRNA produced in colonic mucosa in global mir-10b KO and WT

first: Rajan

last: Singh


title: Transendothelial migration of human B cells: chemokine versus antigen

city: New Haven

first: Thomas

middle: David

last: Manes

state: CT

address: 10 Amistad St.

department: Immunobiology

institute: Yale University School of Medicine

summary: B cells, like T cells, can infiltrate sites of inflammation, but the processes and B cell subsets involved are poorly understood. Using human cells and in vitro assays, we find only a very small number of B cells will adhere to TNF-activated (but not to resting) human microvascular endothelial cells (ECs) under conditions of venular flow and do so by binding to ICAM-1 and VCAM-1. CXCL13 and to a lesser extent CXCL10 bound to the ECs can increase adhesion and induce transendothelial migration (TEM) of adherent naïve and memory B cells in 10-15 minutes through a process involving cell spreading, translocation of the microtubule organizing center (MTOC) into a trailing uropod and interacting with EC ALCAM. Engagement of the BCR by EC-bound anti-κ light chain antibody also increases adhesion and TEM of κ+ but not λ+ B cells. BCR-induced TEM takes 30-60 minutes, requires Syk activation, is initiated by B cell rounding up and translocation of the MTOC to the region of the B cell adjacent to the EC and also utilizes EC ALCAM for TEM. BCR engagement reduces the number of B cells responding to chemokines and preferentially stimulates TEM of CD27+ B cells that co-express IgD, with or without IgM, as well as CD43.  RNA Seq analysis suggests peripheral blood CD19+CD27+CD43+IgD+ cells have increased expression of genes that support BCR activation as well as innate immune properties in comparison to total peripheral blood CD19+ cells.

overall_design: To further characterize a rare population of human peripheral blood CD19+CD27+CD43+IgD+ cells, we prepared RNA from total CD19+ cells and isolated CD19+CD27+CD43+IgD+ cellsand compared their transcriptional profiles by RNA Seq.

first: Vivian

last: Wang

first: Jordan

last: Pober


title: Consensus molecular subtype transition during progression of colorectal cancer [NanoClassifier Gene Set]

city: Amsterdam

first: Arezo

last: Torang

address: Meibergdreef 9

country: Netherlands

institute: Amsterdam UMC

summary: The consensus molecular subtype (CMS) classification divides colorectal cancer (CRC) into four distinct subtypes based on RNA-expression profiles. The biological differences between CMSs are already present in CRC precursor lesions, but not all CMSs pose the same risk of malignant transformation. To fully understand the path to malignant transformation and to determine whether CMS is a fixed entity during progression, genomic and transcriptomic data from two regions of the same CRC lesion were compared: the precursor and carcinoma region. In total, 24 patients that underwent endoscopic removal of T1-2 CRC were included. Regions were subtyped for CMS and DNA mutation analysis was performed. Additionally, a set of 85 benign adenomas was CMS subtyped. This analysis revealed that almost all benign adenomas were classified as CMS3 (91.8%). In contrast, CMS2 was the most prevalent subtype in precursor regions (66.7%), followed by CMS3 (29.2%). CMS4 was absent in precursor lesions and originated at the carcinoma stage. Importantly, CMS switching occurred in a substantial number of cases and almost all (6 out of 7) CMS3 precursor regions showed a shift to a different subtype in the carcinoma part of the lesion, which in 4 cases was classified as CMS4. In conclusion, our data indicate that CMS3 is related to a more indolent type of precursor lesions that less likely progresses to CRC and when this occurs it often associates with a subtype change that includes the more aggressive mesenchymal CMS4. In contrast, an acquired CMS2 signature appeared to be rather fixed during early CRC development. Combined our data shows that subtype changes occur during progression and that CMS3 switching is related to changes in the genomic background through acquisition of a novel driver mutation (TP53) or selective expansion of a clone, but also occurred independent of such genetic changes.

overall_design: This study retrospectively selected patients who underwent endoscopic resection for early-stage colorectal cancer (CRC) at the Amsterdam University Medical Centers, location AMC, between 2016 and 2021. Exclusions were made for patients with hereditary CRC predisposition, inflammatory bowel disease history, neoadjuvant treatment evidence, or piecemeal resection. Informed consent was obtained, and the study followed the guidelines of the Declaration of Helsinki and the Netherlands Code of Conduct. Pathology review involved collecting haematoxylin-eosin (H&E) slides and formalin-fixed paraffin-embedded (FFPE) tumor tissue blocks, which were reviewed by two expert pathologists. The amount of carcinoma and precursor tissue was assessed, and specimens with sufficient tissue for RNA and DNA extraction were selected. The precursor adenoma region was categorized based on dysplasia level and morphology. RNA and DNA were extracted from the same tissue sections using the AllPrep FFPE DNA/RNA kit (Qiagen, Hilden, Germany) according to manufacturer’s instructions. RNA quantity and quality were measured using NanoDrop2000 (Thermo Fisher Scientific, Waltham, MA, USA) and Tapestation (Agilent Technologies, Santa Clara, CA, USA). DNA quantity was assessed with a Qubit Fluorometer (Thermo Fisher Scientific, Waltham, MA, USA).

first: Simone

last: Weerd

first: Jan

middle: P

last: Medema


title: Consensus molecular subtype transition during progression of colorectal cancer

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

overall_design: Refer to individual Series


title: Lgr5-expressing secretory cells form a Wnt inhibitory niche in cartilage critical for chondrocyte identity

city: New York

first: Ikue

last: Tosa

state: New York

department: College of Dental Medicine

institute: Columbia University

summary: We performed gene expression profiling analysis using data obtained from RNA-seq of condylar cartilage cells from post-traumatic temporomandibular joint osteoarthritis model to investigate the signaling pathways critical for cellular functions during  temporomandibular joint osteoarthritis pathology.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for control and osteoarthritis model in condylar cartilage cells from temporomandibular joints.

first: Angela

last: Ruscitto

first: Peng

last: Chen

first: Ziyi

first: Gan

last: Zhou

first: Mallory

last: Morel

first: Alia

first: Gwendolyn

last: Reeve

first: Michael

last: Lecholop

first: Marshall

last: Wilson

first: Daniel

last: Bonthius

first: Mo

first: Mitsuaki

last: Ono

first: Timothy

first: Hai

last: Yao

first: Mildred

last: Embree


title: Role of Atg16L1 in skin biology

city: Zwijnaarde

first: VIB

last: Single Cell Core

address: Technologiepark-Zwijnaarde 71

department: VIB Single cell core

country: Belgium

institute: VIB

summary: In order to unravel the functional role of autophagy in skin homeostasis, we performed single-cell RNA-sequencing on total skin of 10-weeks-old male mice lacking ATG16L1 selectively in keratinocytes. Keratinocyte-specific ATG16L1 knock-out (KO) mice do not show an overt skin phenotype. By performing single-cell analysis on total skin of control mice and mice lacking ATG16L1 in keratinocytes, we could identify a crucial role for keratinocyte autophagyin mediating the timing of hair follicle stem cell activation in hair growth.

overall_design: The purpose of this study was to delineate the cellular and molecular changes that occur in the skin when ATG16L1 is absent in keratinocytes. Total skin was harvested from wild-type (WT) and keratinocyte-specific ATG16L1 knock-out (KO) mouse skin. We FACS sorted live cells from single-cell suspensions of total skin.

first: Esther

last: Hoste

first: Lisette

last: Van Hove

first: Jana

last: Roels

first: Niels

last: Vandamme


title: Positive regulation of oxidative phosphorylation by nuclear myosin 1 protects cells from metabolic reprogramming and tumorigenesis in mice

city: Abu Dhabi

first: Piergiorgio

last: Percipalle

state: Abu Dhabi

address: Saadiyat Campus, Abu Dhabi

department: Biology Department, Science Division

country: United Arab Emirates

institute: New York University Abu Dhabi

summary: Metabolic reprograming is one of the hallmarks of tumorigenesis. Using a combination of multi-omics, here we show that nuclear myosin 1 (NM1) serves a key regulator of cellular metabolism. As part of nutrient-sensing PI3K/Akt/mTOR pathway, NM1 forms a positive feedback loop with mTOR, and directly affects mitochondrial oxidative phosphorylation via transcriptional regulation of mitochondrial transcription factors TFAM and PGC1α. NM1 depletion leads to a suppression of PI3K/Akt/mTOR pathway, underdevelopment of mitochondria inner cristae and redistribution of mitochondria within a cell,  which is associated with reduced expression of oxidative phosphorylation genes, decreased mitochondrial DNA copy number, and deregulated mitochondrial dynamics. This leads to a metabolic reprogramming of NM1 KO cells from oxidative phosphorylation to aerobic glycolysis and with that associated metabolomic profile typical for cancer cells, namely, increased amino acid-, fatty acid-, and sugar metabolism, and increase in glucose uptake, lactate production and intracellular acidity. We show that NM1 KO cells are able to form solid tumors in a nude mouse model even though they have supressed PI3K/Akt/mTOR signalling pathway suggesting that the metabolic switch towards aerobic glycolysis provide a sufficient signal for carcinogenesis. We suggest that NM1 plays a key role as tumor suppressor and that NM1 depletion may be partly responsible for the Warburg effect at the early onset of tumorigenesis.

overall_design: RNA seq of tumors derived from NM1 KO mouse embryonic fibroblasts and tumors derived from NM1 KO mouse embryonic fibroblast with reintroduced NM1 (KO+NM1)

first: Tomas

last: Venit

first: Nizar

last: Drou


title: CITE-seq of murine bone and marrow cells

first: Madison

last: Doolittle

summary: To investigate heterogeneity of CD24 osteolineage cells at the single-cell level, we performed CITE-seq analysis with the CD24 antibody on bone and marrow mesenchymal cells from mouse femurs and tibias

overall_design: We isolated bone and marrow cells from the femurs and tibias of 2 mice (n=1 24-month-old, n=1 6-month-old), stained with CD24 TotalSeq antibody, depleted of immune cells (Lin-) by MACS and enriched for live mesenchymal cells (CD45-SyTOX-) by FACS, and performed 10X Genomics CITE- and single-cell RNA-sequencing

first: Sundeep

last: Khosla


title: Consensus molecular subtype transition during progression of colorectal cancer [Tumor Signaling 360™ Panel]

first: Arezo

last: Torang

first: Simone

last: Weerd

first: Jan

last: Medema


title: MCPIP1 functions as a safeguard of early embryonic development

city: Warsaw

first: Michal

last: Mikula

address: Roentgena 5

department: Experimental Oncology

country: Poland

institute: Maria Skłodowska-Curie National Research Institute of Oncology

summary: Expression of zc3h12a encoding Mcpip1 is tightly controlled within first cell divisions of zebrafish. Overexpression of Mcpip1 leads to the profound transcriptomic changes in the developing embryos and impairs early embryonic development of zebrafish.

overall_design: RNA-seq was performed to analyse transcriptome of zebrafish embryos overexpressing Mcpip1 (wild type and catalytically inactive mutant).

first: Agata

last: Lichawska-Cieslar

first: Weronika

last: Szukala

first: Tomasz

last: Prajsnar

first: Niedharsan

last: Pooranachandran

first: Maria

last: Kulecka

first: Michalina

last: Dabrowska

first: Krzysztof

last: Rakus

first: Magdalena

last: Chadzinska

first: Jolanta

last: Jura


title: Targeting Metabolic Adaptations in the Breast Cancer–Liver Metastatic Niche Using Dietary Approaches to Improve Endocrine Therapy Efficacy

city: Urbana

first: Zeynep

last: Madak Erdogan

address: 1201 S Goodwin Ave

department: FSHN

country: USA

institute: UIUC

summary: Estrogen receptor–positive (ERþ) metastatic tumors contribute to nearly 70% of breast cancer–related deaths. Most patients with ERþ metastatic breast cancer (MBC) undergo treatment with the estrogen receptor antagonist fulvestrant as standard of care. Yet, among such patients, metastasis in liver is associated with reduced overall survival compared with other metastasis sites. The factors underlying the reduced responsiveness of liver metastases to ER targeting agents remain unknown, impeding the development of more effective treatment approaches to improve outcomes for patients with ERþ liver metastases. We therefore evaluated site specific changes in MBC cells and determined the mechanisms through which the liver metastatic niche specifically influences ERþ tumor metabolism and drug resistance. We characterized ER activity of MBC cells both in vitro, using a novel system of tissue-specific extracellular matrix hydrogels representing the stroma of ERþ tumor metastatic sites (liver, lung, and bone), and in vivo, in liver and lung metastasis mouse models. ERþ metastatic liver tumors and MBC cells grown in liver hydrogels displayed upregu lated expression of glucose metabolism enzymes in response to fulvestrant. Furthermore, differential ERa activity, but not expres sion, was detected in liver hydrogels. In vivo, increased glucose metabolism led to increased glycogen deposition in liver metastatic tumors, while a fasting-mimicking diet increased efficacy of fulves trant treatment to reduce the metastatic burden. Our findings identify a novel mechanism of endocrine resistance driven by the liver tumor microenvironment.

overall_design: 1x106 MCF7 Y537S cells resuspended in 1% PBS were injected to ovariectomized, NOD SCID gamma (NSG) immunodeficient female mice via tail vein. Fulvestrant (Sigma) was dissolved in 10% DMSO and 90% corn oil and administrated via intramuscular injection (100 mg/kg) twice a week (Monday, Friday) for four weeks. After six weeks, mice were euthanized and organs were harvested.

first: Qianying

last: Zuo

first: Ayca

middle: N

last: Mogol

first: Yu-Jeh

last: Liu

first: Ashlie

last: Santaliz Casiano

first: Christine

last: Chien

first: Jenny

last: Drnevich

first: Ozan

last: Imir

first: Eylem

last: Kulkoyluoglu-Cotul

first: Nicole

middle: H

last: Park

first: David

last: Shapiro

first: Ben

first: Yvonne

last: Ziegler

first: Benita

last: Katzenellenbogen

first: Evelyn

last: Aranda

first: John

middle: D

last: O’Neill

first: Akshara

last: Raghavendra

first: Debu

last: Tripathy

last: Madak-Erdogan


title: Prerenal azotemia triggers the hepatic acute response in a novel, clinically-defined, acute murine model

city: Aurora

first: Mary

last: Weiser-Evans

address: 12700 East 19th Avenue, C281

department: Renal Diseases & Hypertension

institute: University of Colorado Anschutz Medical Campus

summary: Prerenal azotemia (PRA) is a major cause of acute kidney injury (AKI) and uncommonly studied in preclinical models. Using a reverse translational approach, we developed a novel model of PRA that meets the clinical definition. 6 hours after furosemide administration to induce volume loss in wild type (WT) mice, measured GFR was 25% of baseline and returned to baseline after saline resuscitation at 48 hours. At 6 hours of PRA, plasma IL-6 was significantly increased, renal and liver histology were normal, renal and liver lactate were normal, and renal KIM-1 immunofluorescence was negative; 327 differentially regulated genes were upregulated in the  liver and the acute phase response was the most significantly upregulated pathway; 25% of upregulated genes were reduced in IL-6-/-, and the acute phase response was the most significantly downregulated pathway. Three significantly upregulated genes were further investigated: NGAL, CXCL1, and haptoglobin; hepatic gene expression and plasma protein levels were all increased in WT PRA and were all reduced in IL-6-/- PRA. This work demonstrates previously unknown systemic effects of prerenal azotemia that includes systemic inflammation and IL-6 mediated upregulation of the hepatic acute phase response; we anticipate that these effects will have significant clinical consequences.

overall_design: Using RNA-seq to profile the transcriptomes of hepatic tissues in wild type (WT) and IL-6-/- mice subjected to vehicle (Veh, 4 WT replicates, 4 IL-6-/- replicates) or furosemide-induced pre-renal azotemia (PRA, 4 WT replicates, 3 IL-6-/- replicates) treatments. Non-injected mice (normal, 4 replicates) were used examined as control.

first: Kayo

last: Okamura

first: Sizhao

last: Lu

first: Zhibin

last: He

last: Montford

first: Scott

last: Lucia

last: Orlicky

first: Sarah

last: Faubel


title: FBL promotes cancer cell proliferation and DNA damage repair via YBX1

city: baoding

first: chen

last: wu

state: hebei

address: wusidong road

institute: hebei university

summary:
To further investigate the underlying function and molecular mechanism of FBL in DNA damage response, we conducted RNA sequencing analysis (RNA-seq) and detected the genome-wide transcriptomic changes in HCT116 cells and shFBL-HCT116 cells following MMC treatment.
Together, these data indicate that the activation of the FBL/YBX1 signaling axis upon DNA damage regulates the transcriptional activation of genes directly involved in the repair of DNA DSBs, such as BRCA1 and contributes to promoting the resistance of cells to DNA-damaging agents.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HCT116 cells and its KD derivatives (shFBL).

first: xiaorui

last: sun


title: RNA-seq of NIC+,CdGAPwt/wt and NIC+,CdGAPfx/fx tumors

city: Boston

first: Marie-Anne

last: Goyette

address: 450 Brookline avenue

institute: DFCI

summary: CdGAP/ARHGAP31 is a molecular target of TGFb-mediated EMT and required for Her2-positive breast cancer growth and metastasis  Metastasis is the leading cause of death in breast cancer patients. The epithelial-to-mesenchymal transition (EMT) has a crucial role in metastasis and is highly critical for tumor cell dissemination. CdGAP/ARHGAP31 is highly expressed in breast cancer tissues and is associated with poor clinical outcome in breast cancer patients. CdGAP cooperates in a GAP-independent manner with the transcriptional repressor Zeb2 to function as a critical modulator of breast cancer through repression of E-cadherin transcription. In this study, we used a murine model of Her2+ breast cancer to investigate further the role of CdGAP in breast tumorigenesis. We found that CdGAP was essential for tumor formation and metastasis to the lungs in the Her2+ mouse breast cancer model. We determined that CdGAP is required for intravasation and growth at the metastatic sites. By using global gene expression approaches, we found that CdGAP depletion in Her2+ primary tumors was associated with an EMT signature, including a decreased expression of the metastatic factor claudin-2 and an increase in E-cadherin expression.  In Her2+ breast cancer cells, CdGAP expression is positively regulated by the TGFb canonical pathway in a smad-dependent manner and regulates cell proliferation, migration, invasion, and adhesion. CdGAP was found to interact with the focal adhesion protein Talin and regulates focal adhesion dynamics in breast cancer cells. Collectively, CdGAP appears as a potential anti-metastatic target for the treatment of Her2+ breast cancer.

overall_design: Differential gene expression profile between tumors from NIC+,CdGAPwt/wt mice and NIC+,CdGAPfx/fx mice (Illumina HiSEq 2000)

first: Jean-François

last: Côté

first: Nathalie

last: Lamarche


title: Prognostic marker of DNA methylation and NGS sequencing in progressive glioblastoma from the EORTC-26101 trial

status: Public on Jul 12 2023

city: Heidelberg

first: Tobias

last: Kessler

address: Im Neuenheimer Feld 280

institute: DKFZ

summary: The data contains Illumina 450k array methylation files from 380 patients with diffuse IDH wild-type glioma from the EORTC-26101 trial

overall_design: FFPE tissue from 280 patients with glioblastoma was analyzed with Illumina 450k methylation arrays. Subsequent analyses included methylation classification, CNV profiling and MGMT promotor status (see https://www.molecularneuropathology.org/mnp/

first: Wolfgang

last: Wick


title: Exportin 1 inhibition prevents neuroendocrine transformation through SOX2 downregulation in lung and prostate cancers

first: Yingqian

middle: Ada

last: Zhan

address: 430 East 67th Street

department: EPIGENETICS RESEARCH CENTER

institute: MSKCC


title: CRISPR-ChIP to identify mechanisms of chromatin regulation

first: Mark

last: Dawson

institute: Peter MacCallum Cancer Centre