title: Comparative transcriptome analysis of T lymphocyte subpopulations from porcine thymus and lymph nodes

city: Wuhan

first: Pingping

last: Han

state: Hubei

address: Shizishan Street, Hongshan District

institute: Huazhong Agricultural University

summary: The development and migration of T cells in the thymus and peripheral tissues are crucial for maintaining adaptive immunity in mammals. However, the regulatory mechanisms underlying T cell development and thymocyte identity formation in pigs remain largely underexplored. Here, by integrating bulk and single-cell RNA-sequencing data, we investigated regulatory signatures of porcine thymus and lymph node T cells. The comparison of T cell subpopulations derived from porcine thymus and lymph nodes revealed that their transcriptomic differences were influenced more by tissue origin than by T cell phenotypes, and that lymph node cells exhibited greater transcriptional diversity than thymocytes. Through weighted gene co-expression network analysis (WGCNA), we identified the key modules and candidate hub genes regulating the heterogeneity of T cell subpopulations. Further, we integrated the porcine thymocyte dataset with peripheral blood mononuclear cell (PBMC) dataset to systematically compare transcriptomic differences between T cell types from different tissues. Based on single-cell datasets, we further identified the key transcription factors (TFs) responsible for maintaining porcine thymocyte identity and unveiled that these TFs coordinately regulated the entire T cell development process. Finally, we performed GWAS of cell type-specific differentially expressed genes (DEGs) and 30 complex traits, and found that the DEGs in thymus-related and peripheral blood-related cell types, especially CD4_SP cluster and CD8-related cluster, were significantly associated with pig productive and reproductive traits. Our findings provide an insight into T cell development and lay a foundation for further exploring the porcine immune system and genetic mechanisms underlying complex traits in pigs.

overall_design:
Fresh thymic and mesenteric lymph node tissues were obtained 3 healthy Large White pigs from the experimental farm of Huazhong Agricultural University (Wuhan, China)
Porcine thymocytes were initially were divided into CD3-positive and CD3-negative fractions using FACS. The CD3-positive fraction was subjected to FACS gating based on forward scatter (FSC) and side scatter (SSC) parameters, further divided into 3 distinct populations according to CD4 and/or CD8 marker expression, namely, CD4-CD8+ (Q1), CD4+CD8+ (Q2), and CD4+CD8- (Q4) T cells. The CD4-CD8- (Q3) cell population was enriched through negative sorting.Using the above-mentioned sorting strategy, we divided porcine mesenteric lymph node cells into 3 cell populations including CD4-CD8- (Q3), CD4+CD8- (Q4), and CD4-CD8+ (Q1) T cells
To investigate the transcriptomic differences of T lymphocyte across different tissues, we conducted RNA-seq of a total of 7 distinct T cell subpopulations isolated from porcine thymus and lymph nodes.

first: Wei

last: Zhang

first: Daoyuan

last: Wang

first: Yalan

last: Wu

first: Xinyun

last: Li

first: Shuhong

last: Zhao

first: Mengjin

last: Zhu


title: Factors governing the transcriptome changes and chronological lifespan of fission yeast during phosphate starvation

status: Public on Jan 27 2024

city: New York

first: Angad

last: Garg

state: New York

department: Molecular Biology

country: USA

institute: Memorial Sloan Kettering Cancer Center

type: Expression profiling by high throughput sequencing

summary: This RNA-Seq analysis compares gene expression of the pho7∆ fission yeast (Schizosaccharomyces pombe) strain prior to phosphate starvation (0 HR), i.e. in phosphate replete conditions, and at various times after phosphate starvation (4, 8, 12, 24, 36, and 48 HR) contrasting to the WT fission yeast S. pombe cells grown in phosphate replete conditions (WT 0HR)

overall_design: 7 test samples and 1 control sample was processed (each sample has 3 replicate experiments)

first: Ana

last: Sanchez

first: Beate

last: Schwer

first: Stewart

last: Shuman


title: CD151 expression indicates the subtype specification of human induced pluripotent stem cell-derived atrial and ventricular cardiomyocytes

status: Public on Jan 29 2024

city: Kyoto

first: Yoshinori

last: Yoshida

address: 53, Kawahara-cho, Shogoin, Sakyo-ku

country: Japan

institute: Kyoto University

summary: Current differentiation protocols for human pluripotent stem cells produce a heterogeneous population of cardiomyocytes (CMs). Here, we identified CD151 as a marker of ventricular CMs (VCMs) and atrial CMs (ACMs) from 212 different cell surface markers. In the VCM induction, CD151high CMs were a homogeneous population of mature VCMs, including binuclear VCMs, and showed enriched cell cycle-related genes based on RNA-seq analysis. As for the ACM induction, CD151low CMs expressed high levels of atrial-related genes and exhibited atrial-type electrophysiological properties. According to RNA-seq analysis, CD151high CMs from the ACM induction had molecular signatures for cell-cell interactions and NOTCH signaling. When treated with a NOTCH signal inhibitor, the same cells showed mature electrophysiological properties consistent of ACMs with an increasing expression of atrial-related genes. Altogether, we found that CD151 is an indicator of subtype specification with distinct mechanisms between VCM and ACM differentiation and that NOTCH signaling inhibition enhances atrial specification.

overall_design: mRNA profiles of hiPSC-CMs sorted by CD151 were generated by deep sequencing, in triplicate, using Illumina Nextseq 500.

first: Koakutsu-Nakanishi

last: Misato

first: Miki

last: Kenji

first: Sasaki

last: Masako

first: Okubo

last: Chikako

first: Yoshida

last: Yoshinori


title: P53-P21-RB pathway promotes BRD4 degradation in liver cancer through decreasing USP1 transcription

status: Public on Jan 26 2024

first: LI

last: NENG

address: 13 Hangkong Road

department: Biochemistry and Molecular Biology

country: China

institute: Huazhong University of Science and Technology

summary: Liver cancer claims over 800,000 human deaths each year. Liver cancer is notoriously refractory to conventional therapeutics. Further insight into the etiology carries promise for innovative diagnostics and therapeutics. Tumor progression is governed by interplay between tumor promoting genes and suppressor genes. BRD4, an acetyl-lysine binding protein, plays a critical role in development and human diseases. In many cancer types, BRD4 is overexpressed and promotes activation of a pro-tumor gene network. But the underlying mechanism for BRD4 overexpression remains elusive. As BRD4 has risen as a promising therapeutic target, to understand the mechanism regulating BRD4 protein level will shed insight into BRD4-targeting therapeutics. In this study, we find BRD4 protein level in liver cancer is significantly regulated by P53, the most frequently dysregulated tumor suppressor. We identify a strong negative correlation between protein levels of P53 and BRD4 in liver cancer. We then show P53 promotes BRD4 protein degradation. Mechanistically, P53 represses the transcription of USP1, a deubiquitinase, through P21-RB. We show USP1 is a deubiquitinase of BRD4, which increases its stability. We show the pro-tumor role of USP1 is partially mediated by BRD4 and the USP1-BRD4 axis upholds expression of a group of cancer-related genes. In summary, we identify a functional P53-P21-RB-USP1-BRD4 axis in liver cancer.

overall_design: To examine the effect on transcriptome by USP1 and BRD4, we introduce tetracycline-inducible shRNA of USP1 and BRD4 respectively into HepG2 cells. Doxycycline was used to induce knockdown.

first: Li

last: Neng

first: Lidong

last: Sun


title: The helicase domain of human Dicer prevents RNAi-independent activation of antiviral and inflammatory pathways

city: Strasbourg

first: Sébastien

last: Pfeffer

address: 2 allée Konrad Roentgen

department: UPR 9002 - Architecture et Réactivité de l'ARN

country: France

institute: CNRS - Institut de Biologie Moléculaire et Cellulaire (IBMC)

summary: In mammalian somatic cells, the relative contribution of RNAi and the type I interferon response during viral infection is unclear. The apparent inefficiency of antiviral RNAi might be due to self-limiting properties and mitigating co-factors of the key enzyme Dicer. In particular, the helicase domain of human Dicer appears to be an important restriction factor of its activity. Here, we study the involvement of several helicase-truncated mutants of human Dicer in the antiviral response. All deletion mutants display a PKR-dependent antiviral phenotype against certain viruses, and one of them, Dicer N1, acts in a completely RNAi-independent manner. Transcriptomic analyses show that many genes from the interferon and inflammatory response pathways are upregulated in Dicer N1-expressing cells. We show that some of these genes are controlled by NF-kB and that blocking this pathway abrogates the antiviral phenotype of Dicer N1. Our findings highlight the crosstalk between Dicer, PKR, and the NF-kB pathway, and suggest that human Dicer may have repurposed its helicase domain to prevent basal activation of antiviral and inflammatory pathways.

sample_organism:
Homo sapiens
Sindbis virus

platform_organism:
Homo sapiens
Sindbis virus

overall_design: Refer to individual Series


overall_design: NoDice FHA:DICER WT #4 or N1 #6 cells were infected with a modified version of Sindbis virus expressing GFP at an MOI of 2 for 12 h or 0.02 for 24 h. RNAs were isolated and sequenced. The experiment was done in 3 biological replicates. The uninfected samples (mock) and Sindbis infected samples (MOI of 2 at 12 hpi and MOI of 0.02 at 24 hpi) were analyzed for both cell lines. Total mRNA sequencing aimed to investigate differential transcriptomics according to the Dicer isoform with or without Sindbis virus infection.

first: Morgane

last: Baldaccini

first: Léa

last: Gaucherand

first: Béatrice

last: Chane-Woon-Ming

first: Mélanie

last: Messmer

first: Floriane

last: Gucciardi


overall_design: NoDice FHA:DICER WT #4 or N1 #6 cells were infected with a modified version of Sindbis virus expressing GFP at an MOI of 0.02 for 24 h. To enrich in small RNAs, Argonautes-IPs (AGO-IP) were done using the TNRC6B peptide in Sindbis infected cells followed by small RNA extraction. In parallel, a control IP (CTL IP) was performed. The experiment was done in 3 biological replicates. RNAs coming from AGO IP for the 3 replicates or from the CTL IP for one replicate in Sindbis infected samples (MOI of 0.02 at 24 hpi) were analyzed for both cell lines. Small RNA sequencing aimed to investigate an RNAi pattern for the Dicer isoform in the context of Sindbis virus infection.


title: RIPSeq analysis (CoIP) of CcaF1 from R. sphaeroides 2.4.1 under phototrophic growth conditions

city: Gießen

first: Gabriele

last: Klug

address: Heinrich-Buff-Ring 26-32

department: Molecular- and Microbiology

country: Germany

institute: Justus-Liebig University Gießen

summary: In previous studies we identified the small RNA-binding protein CcaF1 that is involved in sRNA maturation and RNA turnover in Rhodobacter sphaeroides under microaerobic growth conditions (Grützner et al., 2021, Nucleic Acids Res. 49(6), doi: 10.1093/nar/gkab146). In this study we analysed the the small RNA-binding protein CcaF1 under phototrophic growth condtions to identify new RNA binding partners.

overall_design: The CcaF1 protein was overexpressed with an 3xFLAG (pRKccaF1FLAG) in R. sphaeroides under phototrophic growth condtions

first: Julian

last: Grützner

first: Janek

last: Börner


title: Lineage-tracing revealed transient phenotypic adaption of tubular cells during acute kidney injury

city: Aachen

first: Mingbo

last: Cheng

state: North Rhine-Westphal

address: Pauwelsstr. 19

institute: Uniklinik RWTH Aachen

summary: we performed lineage tracing of injured proximal tubule cells by single cell profiling in acute kidney injury. Single-cell sequencing profiles were generated 8, 24, 48 hours and 6 and 12 days after unilateral ischemia-reperfusion in a unique transgenic mouse.

overall_design: Mice were euthanized at 8, 24, 48 hours and 6 and 12 days after unilateral Ischemia-Reperfusion injury

first: Eleni

last: Stamellou

first: Ivan

middle: G

last: Costa

first: Marcus

middle: J

last: Moeller


title: Scd-1 deficiency promotes the differentiation of CD8+ T effector

status: Public on Jan 25 2024

city: Shanghai

first: Yiwei

last: Lin

address: No.1630 Dongfang Road, Shanghai

institute: Renji Hospital, Shanghai Jiao Tong University School of Medicine

summary: The impact of various fatty acid types on adaptive immunity remains uncertain, and their roles remain unelucidated. In this study, we showed that the enzyme stearoyl-CoA desaturase-1 (Scd-1) and its resulting compound, oleic acid (OA), have a substantial impact on the transformation of CD8+ naïve T cells into effector T cells. Inactivation of Scd-1 triggers the specialization of CD8+ T cells into the Teff subset, enhancing the effector function and mitochondrial metabolism of Teff cells, and OA can partially counteract this.

overall_design:
To further explore the influence of Scd-1 on the differentiation and functional status of Teffs, we isolated CD8+ T cells from the spleens of both WT and Scd-1-/- mice using MojoSort Mouse CD8 T Cell Isolation Kit (BioLegend), which were then induced to differentiate into Teff cells using IL-2 after three days of stimulation with CD3/28.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 2 different cells.
Comparative gene expression profiling analysis of RNA-seq data for CD8+ Teff cells from WT and Scd-1-/- mice.

first: Xushuo

last: Li


title: The chromatin factors SET-26 and HCF-1 oppose the histone deacetylase HDA-1 in longevity and gene regulation in C. elegans [CUT&RUN]

city: Ithaca

first: Siu

middle: Sylvia

last: Lee

state: NY

address: 520 Campus road

institute: Cornell University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: SET-26, HCF-1, and HDA-1 are highly conserved chromatin factors with key roles in development and aging. Here we present mechanistic insights into how these factors regulate gene expression and modulate longevity in C. elegans. We show that SET-26 and HCF-1 cooperate to regulate a common set of genes, and both antagonize the histone deacetylase HDA-1 to limit longevity. We propose a model in which SET-26 recruits HCF-1 to chromatin in somatic cells, where they stabilize each other at the promoters of a subset of genes, particularly mitochondrial function genes, and regulate their expression. HDA-1 opposes SET-26 and HCF-1 on the regulation of a subset of their common target genes and in longevity. Our findings suggest that SET-26, HCF-1, and HDA-1 comprise a mechanism to fine-tune gene expression and longevity and likely have important implications for the mechanistic understanding of how these factors function in diverse organisms, particularly in aging biology.

overall_design: CUT&RUN chromatin binding profiles of C. elegans proteins SET-26, HCF-1, and HDA-1 at day 1 of adulthood in somatic-only or whole worm samples, in set-26(tm2467) or hcf-1(pk924) mutant backgrounds. Profiles were obtained using CRISPR knock-in strains for each factor. Two replicates are included for each experiment, and normalization tracks (either antibody background or H3 immunoprecipitated in parallel) are included for each experiment.

first: Felicity

last: Emerson


title: Rapid unleashing of macrophage efferocytic capacity via transcriptional pause release (RNA-Seq)

city: Saint Louis

first: Kodi

middle: S

last: Ravichandran

state: Missouri

address: 660 Euclid Ave

department: Pathology and Immunology

institute: Washington University School of Medicine

summary: Macrophages can adjust their phenotype and function in response to environmental cues, such as encountering apoptotic cells or pathogens. After tissue injury or inflammation, macrophages must successively engulf and process multiple apoptotic corpses (via efferocytosis) to achieve tissue homeostasis. How macrophages may rapidly adapt their transcription to achieve continued corpse uptake is incompletely understood. Transcriptional pause/release is an evolutionarily conserved process wherein RNA polymerase II (Pol II), after initiating transcription for 20-60 nucleotides, gets ‘paused’ for seconds to hours; paused Pol II then gets ‘released’ to complete transcription to make full-length mRNA. Here we show that macrophages, within minutes of corpse encounter, use transcriptional pause/release as a mechanism to unleash a rapid transcriptional response. For human and murine macrophages, the Pol II pause/release was crucial for continued efferocytosis of corpses in vitro and in vivo. Interestingly, blocking Pol II pause/release did not impede FcR-mediated phagocytosis, yeast uptake, or bacterial phagocytosis. Integrating data from three complementary genomic approaches of PRO-seq, RNA-seq, and ATAC-seq on efferocytic macrophages at different time points, we found that Pol II pause/release controls expression of select transcription factors and downstream target genes. Further mechanistic studies on transcription factor Egr3, one of the genes prominently affected by pause/release, uncovered Egr3-related reprogramming of macrophage genes involved in cytoskeleton and corpse processing. Via lysosomal probes and a newly designed genetic fluorescent reporter, we identify a key role for pause/release in phagosome acidification during efferocytosis. Further, microglia from egr3-deficient zebrafish embryos displayed reduced phagocytosis of apoptotic neurons and fewer maturing endosomes, supporting a defect in corpse processing. Collectively, these data advance a novel concept that macrophages use Polymerase II pause/release as a mechanism to rapidly alter their transcriptional programs for efficient processing of the ingested apoptotic corpse and for successive efferocytosis.

overall_design: Hoxb8-derived macrophages were incubated with apoptotic cells for 45min, 90min and 180min efferocytosis.

first: Turan

last: Tufan

first: Gamze

last: Comertpay

first: Ambra

last: Villani

first: Geoffrey

middle: M

last: Nelson

first: Marina

last: Terekhova

first: Shannon

last: Kelley

first: Pavel

last: Zakharov

first: Rochelle

last: Ellison

first: Oleg

last: Shpynov

first: Michael

last: Raymond

first: Jerry

last: Sun

first: Yitan

last: Chen

first: Enno

last: Bockelmann

first: Marta

last: Stremska

first: Lance

middle: W

last: Peterson

first: Laura

last: Boeckaerts

first: Seth

middle: R

last: Goldman

first: J

middle: I

last: Etchegaray

first: Maxim

middle: N

last: Artyomov

first: Francesca

last: Peri


title: Rapid unleashing of macrophage efferocytic capacity via transcriptional pause release

first: Kodi

last: Ravichandran

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


first: Ana

last: Sanchez

address: 430 E 67th Street, RRL-865

summary: RNA-seq analysis compares gene expression of the ecl3∆ and ecl123∆ mutants to the wild-type fission yeast (Schizosaccharomyces pombe).

overall_design: 2 test samples and 1 control sample were processed (each sample has 3 replicate experiments).

first: Angad

last: Garg

first: Beate

last: Schwer

first: Stewart

last: Shuman


title: Rapid unleashing of macrophage efferocytic capacity via transcriptional pause release (ATAC-Seq)

overall_design: Hoxb8-derived macrophages were incubated with apoptotic cells for 15min, 30min, and 45min efferocytosis.

first: Turan

last: Tufan

first: Gamze

last: Comertpay

first: Ambra

last: Villani

first: Geoffrey

last: Nelson

first: Marina

last: Terekhova

first: Shannon

last: Kelley

first: Pavel

last: Zakharov

first: Rochelle

last: Ellison

first: Oleg

last: Shpynov


title: Rapid unleashing of macrophage efferocytic capacity via transcriptional pause release (PRO-Seq)

overall_design: Hoxb8-derived macrophages were incubated with apoptotic cells for 45min and 90min efferocytosis.

first: Michael

last: Raymond

first: Jerry

last: Sun

first: Yitan

last: Chen

first: Enno

last: Bockelmann

first: Marta

last: Stremska

first: Lance

last: Peterson

first: Laura

last: Boeckaerts

first: Seth

last: Goldman

first: J

last: Etchegaray


title: Patient derived organoid established under hypoxic is preferrentially enriched for Moffitt, basal like subtype that corresponse to the dedifferentiate portion of the tumour section.

city: Oxford

first: Pakavarin

last: Louphrasitthiphol

address: Old Road Campus Research Building (off Roosevelt Drive)

department: Nuffield Department of Clinical Medicine

country: United Kingdom

institute: Ludwig Institute for Cancer Research

summary: It is widely accepted that the desmoplastic feature of pancreatic ductal adenocarcinoma (PDAC) and the associated hypoxic microenvironment strongly correlate with a more malignant phenotype that is more resistance to conventional-, targeted- and immuno-therapies. Whether chronic hypoxia in the PDAC stromal gives rise to distinct populations driven by genetics diversity or adoption of distinct phenotypic states in response to low oxygen-tension is poorly understood.  To overcome potential selection bias during the establishment of primary 3D organoids lines, single cell dissociated from each surgically resected tumour were split and established directly in 20% O2 (normoxia) and 1% O2 (hypoxia), yielding cystic and solid organoid morphology respectively. Organoid established under hypoxia (HYPO-PCO) displayed higher expression of EMT-related proteins, a Moffitt basil-like subtype transcriptomes and higher resistance to 5-FU than organoid established under normoxia (NORMO-PCO). Strikingly, while NORMO-PCO subjected to hypoxia displayed the expected gene signatures enriched including inflammatory response, mTORC1 signalling and glycolysis, these signatures were also enriched when compared to HYPO-PCO under hypoxia. This indicates that the two organoid lines captured distinct population from the same tumour which they were derived from.  Given recent appreciation for the better understanding of and the ability to target hypoxia to improve PDAC therapeutic responses, this study highlights the importance of our approach to study hypoxic population over the more conventional model which study hypoxic response in organoids established under normoxia.

overall_design: Dissociated clinical specimens were split into half, and subjected to identical establishment protocol with the exception of oxygen level being at either 20% (normoxia) or 1% (hypoxia). A total of three passages were performed in medium without EGF for the purpose of enriching pancreatic cancer organoids. Following establishment respective RNA samples were collected before switching to the opposite oxygen concentrations and cultured for a total of three passages before further RNA samples were collected.

first: Tatsuya

last: Oda

first: Koichiro

last: Kumano

first: Hiromitsu

last: Nakahashi


title: NFAT signaling is indispensable for persistent memory responses of MCMV-specific CD8+ T cells

city: Brisbane

first: M. Zeeshan

last: Chaudhry

state: Queensland

address: 37 Kent Street

country: Australia

institute: The University of Queensland

summary: Cytomegalovirus (CMV) induces a uniquely robust and persistent T cell response, where the size of the antigen-specific population does not contract, but rather inflates during viral latency. It has been proposed that intermittent engagements of T cell receptors (TCRs) by viral antigens upon subclinical episodes of virus reactivation feed the inflation of CMV-specific memory cells, but evidence of TCR engagement has remained lacking. Nuclear factor of activated T cells (NFAT) is a family of transcription factors, where NFATc1, NFATc2 and NFATc3 are expressed in mature T lymphocytes, of which NFATc1 and NFATc2 are the dominating family members. In an in vivo model of mouse CMV (MCMV) infection of mice with genetic ablation of NFAT signaling, we show a selective impact of this defect in TCR signaling on the long-term inflation of MCMV-specific CD8 T cell responses, while the initial responses to acute infection remain largely maintained. NFATc1 ablation had an immediate effect, while ablation of both NFATs had the most profound influence. In presence of other lymphocytes, NFAT deficiency in T cells had no effect on virus replication or latency, but in adoptive immunotherapy of RAG2-deficient recipient mice, the lack of both NFAT molecules in solely transplanted CD8+ T cells uncovered their decreased antiviral efficacy. We characterized CD8 responses in absence of either or both NFAT molecules by transcriptome analyses and demonstrate that T cell-intrinsic NFAT is not necessary for CD8 T cell priming, but rather for their maturation towards effector memory and in particular the effector cells, which dominate the pool of inflationary cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for WT and NFATc1, NFATc2 and NFAT-DKO CD8+ T cells isoalted from MCMV infected animals.

first: Zeeshan


title: ERG and c-MYC Co-regulate a Critical Gene Network in BCR-ABL1 B-cell Acute Lymphoblastic Leukemia

city: Melbourne

first: Ashley

middle: P

last: Ng

state: VIC

address: 1G Royal Parade, Parkville

institute: The Walter and Eliza Hall Institute of Medical Research

summary: Philadelphia chromosome-positive B-cell acute lymphoblastic leukaemia (Ph+B-ALL), characterised by the BCR-ABL1 fusion gene, remains a poor prognosis cancer that needs new therapeutic approaches. Transcriptomic profiling and pathway analysis identified up-regulation of the oncogenic transcription factors ERG and c-MYC,  with enrichment of genes involved in metabolic processes including ribosome biogenesis.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from defined cell populations. ChIP-seq from C57BL/6 proB cells and Rag1CreT/+;ErgΔ/Δ preproB cells.


title: miRNA microarray data of drug-resistant breast cancer cell lines after chemotherapy

city: Seoul

first: MINWOO

last: KIM

state: Seoul

address: 50-1 Yonsei-ro, Seodaemum-gu

country: South Korea

institute: Yonsei University College of Medicine

summary: The impact of three different chemodrugs (Adriamycin, Taxotere, Cytoxan) on the breast cancer cell lines (MDA-MB-231, MDA-MB-468, HCC1395) was analyzed compared to the parental cell by Affymetrix microarray

first: Min

last: Kim

first: Jee

middle: Y

first: Seung


title: Proinflammatory phenotype of iPS cell-derived JAK2 V617F megakaryocytes induces fibrosis in 3D in vitro bone marrow niche

first: Martin

last: Zenke

address: Pauwelsstrasse 30

department: Hematology, Oncology and Stem Cell Transplantation

institute: RWTH Aachen University

summary: In this dataset, we determine the global gene expression in human induced pluripotent stem (iPS) cell-derived CD61+ megakaryocytes carrying homozygous JAK2 V617F mutation or the JAK2 wildtype gene.

overall_design: 6 samples; Three biological replicates were analyzed per genotype. Hom - homozygous JAK2 V617F; WT - JAK2 Wildtype gene.

first: N

last: Flosdorf

last: Böhnke

first: M

middle: A

last: de Toledo

last: Lutterbach

first: V

last: Gomez Lerma

last: Graßhoff

first: K

last: Olschok

first: S

last: Gupta

last: Tharmapalan

first: H

last: Schüler

first: A

last: Maurer

last: Sontag

first: C

last: Küstermann

last: Sere

first: W

last: Wagner

first: I

last: Costa

first: T

middle: H

last: Brümmendorf

last: Koschmieder

last: Chatain

last: Castilho

first: R

middle: K

last: Schneider


title: BHLHE40/41 regulate microglia and peripheral macrophage responses associated with Alzheimer’s disease and other disorders of lipid-rich tissues [THP1_BHLHE40_41KD]

status: Public on Jan 24 2024

first: Anna

last: Podlesny-Drabiniok

address: 1425 Madison Avenue

institute: Icahn School of Medicine at Mount Sinai

summary: Genetic and experimental evidence suggests that Alzheimer’s disease (AD) risk alleles and genes may influence disease susceptibility by altering the transcriptional and cellular responses of macrophages, including microglia, to damage of lipid-rich tissues like the brain. Recently, sc/nRNA sequencing studies identified similar transcriptional activation states in subpopulations of macrophages in aging and degenerating brains and in other diseased lipid-rich tissues. We collectively refer to these subpopulations of microglia and peripheral macrophages as DLAMs. Using macrophage sc/nRNA-seq data from healthy and diseased human and mouse lipid-rich tissues, we reconstructed gene regulatory networks and identified 11 strong candidate transcriptional regulators of the DLAM response across species. Loss or reduction of two of these transcription factors, BHLHE40/41, in iPSC-derived microglia and human THP-1 macrophages as well as loss of Bhlhe40/41 in mouse microglia, resulted in increased expression of DLAM genes involved in cholesterol clearance and lysosomal processing, increased cholesterol efflux and storage, and increased lysosomal mass and degradative capacity. These findings provide novel targets for therapeutic modulation of macrophage/microglial function in AD and other disorders affecting lipid-rich tissues

overall_design: We performed bulk RNA-seq of THP-1 macrophges treated with siRNA to reduce expression of BHLHE40 (40KD), BHLHE41 (41KD) and BHLHE40/41 (DKD). We used scrambled (SCR) cells with unchanged level of BHLHE40 and/or BHLHE41 as a control. RNAseq was performed on samples harvested from 4 independent THP-1 macrophage differentiation amd siRNA treatment.

first: Yiyuan

last: Liu

first: Edoardo

last: Marcora

first: Alison

last: Goate


title: Spatially-resolved transcriptomics reveal macrophage heterogeneity and prognostic significance in diffuse large B-cell lymphoma

city: Singapore

first: Min

address: 13-02, 14 Medical Drive, Singapore

country: Singapore

institute: National University of Singapore

summary: Macrophages are abundant immune cells in the microenvironment of diffuse large B-cell lymphoma (DLBCL). Macrophage phenotyping by immunohistochemistry has varying prognostic significance across studies in DLBCL and does not provide a comprehensive analysis of macrophage subtypes. We hypothesized that whole-transcriptomic analysis (WTA) of macrophage in-situ would identify new macrophage subsets of biological and clinical significances.

overall_design: Using digital spatial profiling with whole transcriptome analysis of CD68+ cells, we characterized macrophages in distinct spatial niches of reactive lymphoid tissues (RLTs) and DLBCL. We reveal previously unrecognized transcriptomic differences between macrophages populating in RLTs (light zone (LZ)/ dark zone (DZ), germinal center (GC)/ interfollicular (IF) regions), and in between disease states (RLTs and DLBCL). And we also captured the CD20+ cells in the same way, which was used for validation.

first: Patrick

last: Jaynes

first: Susan

last: Hue

first: Siok-Bian

last: Ng

first: Claudio

last: Tripodo

first: Anand

middle: D

last: Jeyasekharan


title: BHLHE40/41 regulate microglia and peripheral macrophage responses associated with Alzheimer’s disease and other disorders of lipid-rich tissues.

status: Public on Jan 23 2024

overall_design: We performed bulk RNA-seq of iPSC-derived microglia (iMGLs) with genetic inactivation of BHLHE40 (40KO), BHLHE41 (41KO) and BHLHE40/41 (DKO). We used wild type (WT) cells with unchanged level of BHLHE40 and/or BHLHE41 as a control. RNAseq was performed on samples harvested from 5 independent iMGLs differentiation.


title: Differential impact of high-salt levels in vitro and in vivo on macrophage core functions

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

summary: We analyzed the gene expression differences in RNA-seq data of murine bone-marrow derived macrophages (BMDM) in response to treatment with NaCl. RNA of 3 samples differentiated in vitro for 8 days using M-CSF and treated with RPMI medium or RPMI medium containing additional 62mM NaCl, respectively, was isolated with trizol and miRNeasy micro kit (Qiagen) according to the manufacturer’s protocol and 100 ng of RNA was converted into cDNA libraries using the TruSeq RNA library preparation kit v2 for 75 bp single read sequencing performed on a HiSeq1500. We aligned the reads using STAR and performed downstream expression analysis in R using DESeq2.

overall_design: Examination of NaCl-induced gene expression differences in RNA-seq data of 3 NaCl-stimulated BMBM samples compared to 3 unstimulated murine BMDM samples.

first: Linda

last: Müller

first: Aya

last: Nasr

first: Susanne

middle: V

last: Schmidt

first: Jonas

last: Schulte-Schrepping

middle: L

first: Waldemar

last: Kolanus

first: Eliva

last: Mass


title: Interleukin 13 Signaling to Macrophages Promotes Functional Recovery after Myocardial Infarction

city: Milwaukee

first: Santiago

last: Alvarez Argote

state: WI

address: 8701 Watertown Plank Rd, Physiology, Medical College of Wisconsin

department: Physiology

institute: The Medical College of Wisconsin, Inc.

summary: Adult mice were subjected to surgical myocardial infarction (MI), and daily  injected with recombinant IL13 or PBS as a control following MI. Mice were euthanized at 4 or 7 days post injury and live leukocytes were isolated from the heart and subjected single cell RNA sequencing.

last: Alvarez-Argote

first: Samantha

last: Paddock

first: Michael

last: Flinn

first: Caelan

last: Moreno

first: Makenna

middle: C

last: Knas

first: Victor

last: Almeida

first: Sydney

last: Buday

first: Amirala

last: Bakhshian Nik

first: Michaela

last: Patterson

first: Yi-Guang

last: Chen

first: Chien-Wei

last: Lin

first: Caitlin

last: O'Meara


title: Regulation of YAP Promotor Accessibility in Endothelial Mechanotransduction

city: Stockholm

first: Lars

last: Holmgren

state: Stockholm

address: Solnavägen 30

department: Oncology Pathology

country: Sweden

institute: Karolinska Institute

summary: Endothelial cells (ECs) are constantly exposed to mechanical forces in the form of fluid shear stress, extracellular stiffness, and cyclic strain. How mechanical forces are transduced to the nucleus to drive transcriptional reprogramming in ECs is poorly understood. The mechanoresponsive activity of Yes associated protein (YAP) and its role in vascular development are well described, however, whether changes to transcription or epigenetic regulation of YAP are involved in these processes remains unanswered. Our results reveal that mechanical forces sensed at cell-cell junctions by the YAP target gene, Angiomotin-like 2 (AmotL2), are directly intervened into changes in global chromatin accessibility and EZH2 activity leading to modulation of YAP-promotor activity. Functionally, shear stress induced proliferation of ECs in vivo were reliant on AmotL2 and YAP/TAZ endothelial expression. Mechanistically, uncoupling of the nuclear-cytoskeletal connection from junctions and focal adhesions led to altered nuclear morphology, chromatin accessibility and suppression of YAP-promotor activity. Our findings reveal a role for AmotL2 and nuclear-cytoskeletal force transmission in modulating the epigenetic and transcriptional regulation of YAP to maintain a mechanoenforced positive-feedback loop of vascular homeostasis.

overall_design: Bulk ATAC-seq from HUVEC and HUAEC cells transduced with shScr or shAmotL2 lentivirus with 4 replicates per condition to investigate the role of AmotL2 in regulating chromatin accessibility

first: Aarren

middle: J

last: Mannon


title: Management of Pediatric Gigantism Caused by the TADopathy, X-Linked Acrogigantism

city: Pieve Emanuele

first: Giampaolo

last: Trivellin

state: Lombardy

address: Via Rita Levi Montalcini 4

country: Italy

institute: Humanitas University

summary: X-linked acrogigantism (X-LAG) is a rare form of pituitary gigantism that is associated with growth hormone (GH) and prolactin-secreting pituitary adenomas/pituitary neuroendocrine tumors (PitNETs) that develop in infancy. It is caused by a duplication on chromosome Xq26.3 that leads to misexpression of the gene GPR101, a constitutively-active stimulator of pituitary GH and prolactin secretion. GPR101 normally exists within its own topologically associating domain (TAD) and is insulated from surrounding regulatory elements. X-LAG is a TADopathy in which the duplication disrupts a conserved TAD border, leading to a neoTAD in which ectopic enhancers drive GPR101 over-expression causing gigantism. Here we trace the full diagnostic and therapeutic pathway of a female patient with X-LAG from 4C-seq studies demonstrating the neoTAD through to medical and surgical interventions and detailed tumor histopathology. The complex nature of treating young children with X-LAG is illustrated, including the achievement of hormonal control using a combination of neurosurgery and adult doses of first-generation somatostatin analogs.

overall_design: Human 4C-seq profiles derived from blood-derived cells of one individual with a Xq26.3 duplication affected by X-linked acrogigantism (S17) and one wild-type control.

first: Manuela

last: Caruso

first: Diego

last: Mazzatenta

first: Sofia

last: Asioli

first: Giuseppe

last: Costanza

first: Martin

last: Franke

first: Dayana

last: Abboud

first: Julien

last: Hanson

first: Veronique

last: Raverot

first: Patrick

last: Petrossians

first: Albert

last: Beckers

first: Marco

last: Cappa

first: Adrian

middle: F

last: Daly


title: Nigral Transcriptomic Profiles in Engrailed-1 Hemizygous Mouse Models of Parkinson’s Disease Reveal Upregulation of Oxidative Phosphorylation-Related Genes Associated with Resistance to Dopaminergic Neurodegeneration

city: Lund

first: Lautaro Francisco

middle: Francisco

last: Belfiori Carrasco

state: Skåne

address: Sölvegatan 19, BMC A10

institute: Lund University

summary: Engrailed 1 (EN1) is a conserved transcription factor essential for programming, survival, and maintenance of midbrain dopaminergic neurons. En1-hemizygosity (En1+/-) leads to a spontaneous Parkinson’s disease-like (PD-like) progressive nigrostriatal degeneration as well as motor impairment and depressive-like behavior in SwissOF1 (OF1-En1+/-) mice. This phenotype is absent in C57Bl/6j (C57-En1+/-) mice. Here we studied PD-like phenotypes and early transcriptome profiles in OF1 wild-type (WT) and OF1-En1+/- male mice and compare to that of C57 WT and C57-En1+/- male mice. To detect transcriptional changes prior to dopaminergic cell loss, we performed RNA-seq of 1-week old mice substantia nigra pars compacta (SNpc). Histology and stereology were used to assess dopaminergic nigrostriatal pathology in 4 and 16 weeks old mice. OF1-En1+/- mice showed an increase (79%) in dopaminergic striatal axonal swellings from 4 to 16 weeks and a loss (23%) of dopaminergic neurons in the SNpc at 16 weeks compared to OF1 WT. Axonal swellings were also present in C57-En1+/- mice but did not increase over time. 52 differentially expressed genes (DEGs) were observed between the C57-WT and the C57-En1+/- mice, while 198 DEGs were observed in the OF1 strain. Enrichment analysis revealed that the neuroprotective phenotype of C57-En1+/- mice was associated with an upregulation of oxidative phosphorylation-related genes compared to both C57 WT and to OF1- En1+/- mice. These results highlight the importance of considering genetic background in PD models and provide valuable insight on how expression of mitochondrial proteins before the onset of neurodegeneration is associated to vulnerability of nigrostriatal dopaminergic neurons.

overall_design: Laser microdissected substantia nigra from SwissOF1 and C57Bl/6j mice both Wild type and Engrailed 1 hemizygous. 3 male mice per group. Total 12 mice

first: Lautaro

last: Belfiori

first: Alfredo

last: DueñasRey

first: Dorottya

last: Ralbovszki

first: Itzia

last: Jimenez-Ferrer

first: Filip

last: Bäckström

first: Sagar

middle: S

last: Balikai

first: Dag

last: Ahrén

first: Kajsa

last: Atterling Brolin

first: Maria

last: Swanberg


title: Deep phenotyping of Post-infectious Myalgic Encephalomyelitis/Chronic Fatigue Syndrome [Protein plasma]

city: Bethesda

first: Avindra

last: Nath

state: Maryland

address: 10 Center Drive

institute: NIH/NINDS

summary: Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a disabling disorder that may occur following an infection, yet the clinical phenotype is poorly defined, the pathophysiology is unknown, and no disease-modifying treatments are available. We used rigorous criteria to recruit a cohort of post-infectious ME/CFS (PI-ME/CFS) volunteers (n=17) with matched healthy controls (n=21) to conduct deep clinical and biological phenotyping using an extensive battery of tests. Among the many physical and cognitive complaints, one defining feature of PI-ME/CFS was an alteration of effort preference, rather than physical or central fatigue, due to dysfunction of integrative brain regions potentially associated with central catechol pathway dysregulation, with consequences on autonomic functioning and physical deconditioning. Immune profiling suggested chronic antigenic stimulation with increase in naïve and decrease in switched memory B-cells. Alterations in gene expression profiles of peripheral blood mononuclear cells and metabolic pathways were consistent with cellular phenotypic studies and demonstrated differences according to sex. Together these clinical abnormalities and biomarker differences provide unique insight into the underlying pathophysiology of PI-ME/CFS, which may guide future intervention.

overall_design: The proteome for 42 separate Plasma samples were profiled using the SOMAscan human proteomic assay. Samples included 21 individuals diagnosed with Chronic Fatigue Syndrome (9 Male, 12 Female) and 21 Controls (10 Male, 11 Female).

first: Brian

last: Walitt

first: Komudi

last: Singh

first: Mark

last: Hallett

first: Steve

last: Jacobson

first: Kong

last: Chen

first: Yoshimi

middle: E

last: Akahata

first: Richard

last: Apps

first: Jennifer

last: Barb

last: Bedard

first: Robert

last: Brychta

first: Ashura

middle: W

last: Buckley

first: Peter

last: Burbelo

first: Brice

last: Calco

first: Brianna

last: Cathay

first: Li

first: Jinguo

first: Foo

last: Cheung

first: Snigdha

last: Chigurupati

first: Lisa

middle: M

last: Chin

first: Benjamin

last: Coleman

first: Amber

middle: B

last: Courville

first: Madeleine

last: Deming

first: Bart

last: Drinkard

last: Feng

first: Luigi

last: Ferrucci

first: Scott

last: Gabel

first: Angelique

last: Gavin

first: David

last: Goldstein

first: Shahin

last: Hassanzadeh

first: Sean

last: Horan

first: Silvina

middle: G

last: Horovitz

first: Kory

last: Johnson

first: Anita

last: Govan

first: Kristine

last: Knutson

first: Joy

last: Kreskow

first: Samuel

last: LaMunion


title: Homeodomain-only protein (HOPX) negatively regulates CD8+ T cell proliferation and affects differentiation and aging

city: Baltimore

first: Supriyo

last: De

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

summary: HOPX is an atypical homeodomain-containing protein lacking DNA-binding capacity. Via interaction with transcription factors, particularly SRF, it has critical functions in the development of various tissues. Here we unveil an essential regulatory role of HOPX in human T lymphocytes. Human CD8+ T cells expressed all three isoforms (a, b, and c) of HOPX wherein HOPXb was the predominant one. HOPX expression was induced by TCR activation and increased from TN to TEM cells. Overexpression of HOPX constrained the proliferation of TN cells while knockdown of HOPX promoted the proliferation of TEM cells upon TCR activation. Mechanistically, HOPX/SRF bound to the promoters and repressed expression of MYC and NR4A1, the key regulators of T cell proliferation and activation. Importantly, CD8+ T cells from the elderly had elevated levels of HOPX, correlated with their blunted TCR-induced proliferation. Knockdown of HOPX rescued the proliferative capacity of T cells from the elderly. Our results support that HOPX is a molecular switch that balances CD8+ T cell proliferation across subsets and with age.

overall_design: Micrarrray-based transcriptome profiling of RNA from tdTom+ cells derived from HOPXb transduced and control CD8+ human naïve  T cells (TN) cells three days after HOPXb or control lentivirus transduction (N= four individuals per condition).

first: Qian

last: Yang

first: Michael

last: Patrick

first: Jian

last: Lu

first: Joseph

last: Chen

first: Yongqing

last: Zhang

first: Humza

last: Hemani

first: Elin

last: Lehrmann

first: Nan-ping

last: Weng


title: N6-methyladenosine modification is not a general trait of viral RNA genomes [Dengue]

city: Barcelona

first: Juana

last: Diez

address: Dr. Aiguader, 88

country: Spain

institute: Pompeu Fabra University

summary: N6-methyladenosine (m6A), the most common internal RNA modification in eukaryotic mRNAs, is described to be abundantly present in the genomes of cytoplasmic-replicating RNA viruses. Yet, how the host nuclear m6A writer has access to the viral RNAs in the cytoplasm and what are the associated biological consequences remain unknown. Here, we comprehensively addressed these questions by combining antibody-dependent (m6A-seq) and antibody-independent (SELECT and nanopore direct RNA sequencing) methods on the cytoplasmic-replicating Chikungunya virus (CHIKV) RNA, and found no evidence of m6A modifications. Moreover, depletion of m6A modification machinery components did not affect CHIKV infection, and CHIKV infection did not alter their cellular localization. Consistent with these observations, no m6A modifications were found in the RNA genome of the dengue virus (DENV), another cytoplasmic-replicating virus. Our results challenge the idea that m6A modification is a general trait of cytoplasmic-replicating RNA viruses and stress the need of confirming antibody-dependent detection of m6A modifications with orthogonal antibody-independent methods.

sample_organism:
Homo sapiens
Dengue virus

platform_organism:
Homo sapiens
Dengue virus

overall_design: m6A-RIP on Dengue-infected HEK293T cells, made up of two input and two IP samples, used to perform downstream peakcalling analysis.

first: Belinda

last: Baquero-Perez

first: Ivaylo

last: Yonchev

first: Anna

last: Delgado-Tejedor

first: Rebeca

last: Medina

first: Mireia

last: Puig-Torrents

first: Ian

last: Sudbery

first: Oguzhan

last: Begik

first: Stuart

last: Wilson

first: Eva

last: Novoa


title: N6-methyladenosine modification is not a general trait of viral RNA genomes [CHIKV]

sample_organism:
Homo sapiens
Chikungunya virus

platform_organism:
Homo sapiens
Chikungunya virus

overall_design: m6A-RIP on CHIKV-infected HEK293T cells, made up of two input and two IP samples, used to perform downstream peakcalling analysis.


title: N6-methyladenosine modification is not a general trait of viral RNA genomes.

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

sample_organism:
Homo sapiens
Dengue virus
Chikungunya virus

overall_design: Refer to individual Series


title: ChREBP ChIP-seq data from primary cultured hepatocytes

city: Pars

first: Renaud

last: Dentin

address: 24 rue du Faubourg Saint Jacques

department: Endocrinology, Metabolism and Diabetes

institute: INSERM U1016

summary: Identification by Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) of ChREBP binding sites in primary cultured mouse hepatocytes cultured for 24h with 25 mM glucose and 100 nM insulin.

overall_design: Chromatin immunoprecipitation DNA sequencing (ChIP-seq) for ChREBP, RNA polII and H3K4Me3 in primary cultured mouse hepatocytes

first: Emmanuel

last: Benichou

first: Marie-Clotilde

last: Alves-Guerra


title: Single-cell and spatial multi-omics highlight effects of anti-integrin therapy across cellular compartments in ulcerative colitis [biopsy CITE-seq]

status: Public on Jan 22 2024

city: San Francisco

first: Michael

middle: George

last: Kattah

state: CA

address: 513 Parnassus Ave

department: Medicine-Gastroenterology

institute: UCSF

summary: Ulcerative colitis (UC) is a chronic inflammatory condition of the colon, driven by mucosal immune and stromal subsets, culminating in epithelial injury. Vedolizumab (VDZ) is an anti-integrin monoclonal antibody that is effective for treating UC. VDZ is known to inhibit lymphocyte trafficking to the intestine, but its broader effects on other cell subsets are less defined. To identify the inflammatory cells that contribute to colitis and are affected by VDZ, we performed a single-cell and spatial transcriptomic and proteomic analysis of peripheral blood and colonic biopsies in healthy controls (HC) and patients with UC on VDZ or other therapies. We identified significant effects of VDZ on mononuclear phagocyte (MNP) subsets, in addition to modest effects on lymphocyte populations. Spatial transcriptomics and proteomics of formalin-fixed, paraffin-embedded (FFPE) biopsies at single-cell resolution demonstrated trends towards increased abundance and proximity of activated MNP and fibroblast subsets in active colitis compared to HC, with inhibition by VDZ. Spatial transcriptomics of archived FFPE specimens pre-treatment identified epithelial-, MNP-, and fibroblast-enriched genes related to VDZ response versus non-response, and these were validated in an external, publicly accessible bulk transcriptomic dataset. Single cell and spatial multi-omics highlight important roles for myeloid, stromal, and epithelial subsets in UC.

overall_design:
Healthy control (HC), ulcerative colitis (UC) patients on 5-ASA therapy, and UC patients on Vedolizumab (VDZ) blood scRNA-seq, biopsy sc-RNA-seq, biopsy CITE-seq. Samples were pooled and subsequently deconvoluted with freemuxlet/demuxlet

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Submitter states that missing raw files are due to patient privacy concerns.
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first: Elvira

last: Mennillo

first: Gabriela

last: Fragiadakis

first: Alexis

last: Combes


title: Single-cell and spatial multi-omics highlight effects of anti-integrin therapy across cellular compartments in ulcerative colitis


title: Single-cell and spatial multi-omics highlight effects of anti-integrin therapy across cellular compartments in ulcerative colitis [biopsy scRNA-seq]


title: Single-cell and spatial multi-omics highlight effects of anti-integrin therapy across cellular compartments in ulcerative colitis [blood scRNA-seq]


title: Profiling of microglia nodules in multiple sclerosis reveals propensity for lesion formation

city: Amsterdam

first: Aletta

last: van den Bosch

address: Meibergdreef 47

country: Netherlands

institute: Netherlands institute of Neuroscience

summary: Microglia nodules (HLA-DR+ cell clusters) are associated with brain pathology. In this post-mortem study, we investigated whether they represent the first stage of multiple sclerosis (MS) lesion formation. We show that microglia nodules are associated with more severe MS pathology. Compared to microglia nodules in stroke, those in MS show enhanced expression of genes previously found upregulated in MS lesions. Furthermore, genes associated with lipid metabolism, presence of T and B cells, production of immunoglobulins and cytokines, activation of the complement cascade, and metabolic stress are upregulated in microglia nodules in MS. Compared to stroke, they more frequently phagocytose oxidized phospholipids and possess a more tubular mitochondrial network. Strikingly, in MS, some microglia nodules encapsulate partially demyelinated axons. Taken together, we propose that activation of microglia nodules in MS by cytokines and immunoglobulins, together with phagocytosis of oxidized phospholipids, may lead to a microglia-phenotype prone to MS lesion formation.

overall_design: MS and stroke subcortical (normal appearing) white matter tissue was stained for HLA-DR and microglia nodules as well as non-nodular (normal appearing) white matter was collected with laser capture microscopy. At least 80 microglia nodules were collected per sample.

first: Marlijn

last: van der Poel

first: Nina

last: Fransen

first: Maria

last: Vincenten

first: Anneleen

last: Bobeldijk

first: Aldo

last: Jongejan

first: Hendrik

last: Engelenburg

first: Perry

last: Moerland

first: Joost

last: Smolders

first: Inge

last: Huitinga

first: Jörg

last: Hamann


title: Transcriptomic profiling in NUAK1 KO neurons

city: Lyon

first: Hélène

last: Polvèche

address: 46 allée d'italie

institute: LBMC - ENS de Lyon

summary: The project focuses on the protein kinase NUAK1, which controls the development of brain cortical connectivity in mice. Recent data suggest that NUAK1 is involved in the regulation of the spliceosome and more broadly of mRNA biology. The aim of this project is to test whether inactivation of NUAK1 (constitutive KO) in primary neuronal cultures affects the expression level of genes relevant for cortical and axon development. We prepared primary cultures of mouse neurons at the embryonic developmental stage E15.5. The samples were either KO or WT (controls). We collected the samples from 4 individual cultures performed blind to genotype, then selected the samples based on PCR to identify sex and genotype. Cultures were thus performed under the same conditions but not performed the same day nor from the same litter for each sample.

overall_design: We collected the neurons after 5 days of culture in vitro, when axon development is ongoing. Since neurons were grown in serum-free medium, there was limited astrocytic growth, allowing to focus our analysis more specifically onto glutamatergic cortical neurons. Collection conditions: Samples were scrapped in PBS, flash-frozen, and total RAN was extracted using a commercial kit from SIGMA

first: Damien

last: Plassard

first: Evelyne

last: Goillot

first: Julien

last: Courchet

first: Cyril

last: Bourgeois


title: Effect of extracellular RNase digestion on cellular RNA from neutrophils and GlycoRNA sequences of neutrophils

city: New Haven

first: Jun

last: Lu

state: CT

address: 10 Amistad St.

department: Yale Stem Cell Center

institute: Yale University

type: Non-coding RNA profiling by high throughput sequencing

summary:
These data are used to determine whether extracellular RNase A treatment affects cellular RNA levels.
GlycoRNAs were sequenced in both primary bone marrow neutrophils as well as an in vitro neutriphil differentiation cell line (HOXB8).

overall_design:
For RNAseq, primary mouse bone marrow neutrophils were harvested, and subjected to extracellular RNase A treatment or mock treatment. Total RNAs were prepared using TRIzol extraction. Two biological replicates were prepared.
Libraries were prepared using polyA selection, followed by Illumina sequencing, all performed by Yale Center of Genomic Analysis.

For small RNA seq, primary mouse bone marrow neutrophils, HOXB8 cells or differentiated HOXB8 cells were harvested. Total RNAs were prepared using TRIzol extraction. Total RNAs were subjected to glycoRNA purification using either streptavidin beads or WGA beads.
Small RNA libraries were prepared, followed by Illumina sequencing by Yale Center of Genomic Analysis.

first: Ningning

last: Zhang

first: Xujun

last: Wang


title: Single-cell RNA-sequence of the skin lesion of IgE-dependent skin allergic inflammation (IgE-CAI) model

city: Bunkyo-ku

first: Kensuke

last: Miyake

state: Tokyo

address: 1-5-45, Yushima

department: Institute of Integrated Research

institute: Institute of Science Tokyo

summary: Basophils play critical roles in the development of mouse delayed-onset skin allergic inflammation (IgE-CAI model). Importantly, they also contribute to the resolution of allergic inflammation by promoting the generation of pro-resolving macrophages. However, it remains unclear how pro-resolving macrophages suppress excess inflammation. To address this, we conducted single-cell RNA-seq (scRNA-seq) analysis of the IgE-CAI skin lesion at days 3 and 5 post-challenge of allergens. scRNA-seq analysis identified two distinct classical monocyte-derived macrophage (CMDM) populations, namely early and late CMDMs, in IgE-CAI skin lesion. The former population was preferentially observed at the peak of inflammation (day 3), whereas the latter one at the termination phase of inflammation (day 5). Gene ontology analysis revealed that genes associated with phagocytosis were enriched in late CMDMs. In particular, late CMDMs displayed upregulated expression of Gas6 and Mertk, key genes for phagocytic clearance of apoptotic cells. Taken together, scRNA-seq identified CMDMs that display high capacity of dead cell clearance and contribute to the resolution of IgE-CAI.

overall_design: Cells isolated from IgE-CAI skin lesions of WT and Ccr2-/- mice on day 3 and 5 post-antigen challenge were analyzed by scRNA-seq.

first: Junya

last: Ito

first: Kazufusa

last: Takahashi

last: Nakabayashi

first: Shigeyuki

last: Shichino

first: Soichiro

last: Yoshikawa

first: Hajime

last: Karasuyama


title: The neural-progenitor/stem-cell (NPSC) properties of hindbrain boundary cells

status: Public on Jan 21 2024

city: Jerusalem

first: Yuval

last: Nevo

address: Ein Kerem Campus

country: Israel

institute: The Hebrew University of Jerusalem

summary: Hindbrain boundary cells of st. 18 HH chick embryo express the ECM molecule Chondrotin sulphate proteoglycan (CSPG). To determine whether the ventricular zone of hindbrain boundaries act as reservoirs of NPSCs, we separated between hindbrain boundary cells and the rest of hindbrain cells based on the expression pattern of CSPG which seemed membrane-bound. FACS approach was used to isolate CSPG-positive cells and CSPG-negative cells. 4-6 biological replicates, each composed of cells from 30 hindbrains, underwent RNA-sequencing. These RNA-sequencing results were used for gene expression profiling analysis and functional characterization of the different cell groups.

overall_design: Comparative gene expression profiling analysis of RNA-seq data obtained from CSPG-positive cells and CSPG-negative cells collected from st. 18 HH chick embryonic hindbrains. 6 biological replicates of CSPG-negative cells and 4 biological replicates of CSPG-positive cells were included in the analysis.

first: Sela-Donenfeld

last: Dalit


title: Modular Tissue-in-a-CUBE platform to model blood-brain barrier (BBB) and brain interaction

status: Public on Jan 18 2024

city: Kobe

first: Masaya

last: Hagiwara

state: Hyogo

address: 6-7-1 Minatojima-minamimachi Chuo-ku

institute: RIKEN BDR

summary: With the advent of increasingly sophisticated organoids, there is growing demand for technology to replicate the interactions between multiple tissues or organs. This is challenging to achieve, however, due to the varying culture conditions of the different cell types that make up each tissue. Current methods often require complicated microfluidic setups, but fragile tissue samples tend not to fare well with rough handling. Furthermore, the more complicated the human system to be replicated, the more difficult the model becomes to operate. Here, we present the development of a multi-tissue chip platform that takes advantage of the modularity and convenient handling ability of a CUBE device. We first developed a blood-brain barrier-in-a-CUBE by layering astrocytes, pericytes, and brain microvascular endothelial cells in the CUBE, and confirmed the expression and function of important tight junction and transporter proteins in the blood-brain barrier model. Then, we demonstrated the application of integrating Tissue-in-a-CUBE with a chip in simulating the in vitro testing of the permeability of a drug through the blood-brain barrier to the brain and its effect on treating the glioblastoma brain cancer model. We anticipate that this platform can be adapted for use with organoids to build complex human systems in vitro by the combination of multiple simple CUBE units.

overall_design: To investigate the effect of primary astrocytes and pericytes on BBB functionality, RNA-seq was conducted. Samples were prepared with and without astrocytesand pericytes at day 2, 4 and 6 respectively.

first: Isabel

last: Koh


title: Monocyte-mediated thrombosis linked to circulating tissue factor and immune-paralysis in COVID-19

city: Ann Arbor

first: Sascha

last: Goonewardena

state: Michigan

address: 1500 E Medical Center Dr

department: Department of Internal Medicine

institute: University of Michigan

summary: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections cause coronavirus disease 2019 (COVID-19) and are associated with inflammation and coagulopathy and high incidence of thrombosis. Myeloid cells (Mϕ) help coordinate the initial immune response in COVID-19. Although we appreciate that Mϕ lie at the nexus of inflammation and thrombosis, the mechanisms that unite the two in COVID-19 remain largely unknown. In this study, we employed systems biology approaches including proteomics, transcriptomics, and mass cytometry to define the circulating proteome and circulating immune cell phenotypes in subjects with COVID-19. In a cohort of COVID-19 subjects (n=35), circulating markers of inflammation (CCL23, IL-6) and vascular dysfunction (ACE2, tissue factor [TF]) were elevated in subjects with severe compared with mild COVID-19. Additionally, although the total white blood cell (WBC) counts were similar between COVID-19 groups, CD14+ monocytes from severe COVID-19 subjects expressed more TF. At baseline, transcriptomics demonstrated increased IL-6, CCL3, ACOD1, C5AR1, C5AR2, and TF in severe COVID-19 subjects compared with controls. Using “stress” transcriptomics, we found that circulating immune cells from severe COVID-19 subjects had evidence of profound immune paralysis with greatly reduced transcriptional activation and release of inflammatory markers in response to Toll-like receptor (TLR) activation. Finally, sera from severe (but not mild) COVID-19 subjects activated human monocytes and induced TF expression. Taken together, these observations further elucidate the pathological mechanisms that underlie immune dysfunction and coagulation abnormalities in COVID-19, contributing to our growing understanding of SARS-CoV-2 infections that could also be leveraged to develop novel diagnostic and therapeutic strategies.

overall_design:
To investigate if the circulating immune cells from Severe COVID-19 subjects are primed and hyperresponsive to inflammatory stimuli.  To define the baseline activation state and circulating immune cell responses to stress, we obtained PBMC from severe COVID-19 subjects and age-matched controls  and stimulated them with the TLR4 ligand LPS (1 ug /ml for 2 hours).
After TLR-4 ligand stimulation RNA was isolated and and processed for RNA-seq

middle: N

first: Qinzhong

last: Chen

first: Ashley

last: Tate

first: Olga

last: Grushko

first: Dilna

last: Damodaran

first: Pennelope

last: Blakely

first: Salim

last: Hayek

first: David

last: Pinsky

first: Robert

last: Rosenson


title: VEGF-C prophylaxis promotes lymphatic drainage, microglia modulation, and neuroprotection in response to stroke injury

first: Jean

last: Bouchart

address: 300 Georges Street

department: Neurology

summary: Meningeal lymphatic vessels (MLVs) promote tissue clearance and immune surveillance in the central nervous system (CNS). Vascular endothelial growth factor-C (VEGF-C) regulates MLV development and maintenance and has therapeutic potential for treating neurological disorders. Herein, we investigated the effects of VEGF-C overexpression on brain fluid drainage and ischemic stroke outcomes in mice. Intra-cerebrospinal administration of an adeno-associated virus expressing mouse full-length VEGF-C (AAV-mVEGF-C) increased CSF drainage to the deep cervical lymph nodes (dCLNs) by enhancing lymphatic growth, and upregulated neuroprotective signaling pathways identified by single nuclei RNA sequencing of brain cells. In a mouse model of ischemic stroke, AAV-mVEGF-C pretreatment reduced stroke injury and ameliorated motor performances in the subacute stage, associated with mitigated microglia-mediated inflammation and increased BDNF signaling in brain cells. Neuroprotective effects of VEGF-C were lost upon ligation of the dCLN afferent lymphatics, and not mimicked by acute post-stroke VEGF-C injection. We conclude that VEGF-C prophylaxis promotes multiple vascular, immune, and neural responses that culminate in a protection against neurological damage in acute ischemic stroke.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Male C57BL/6J mice AAV-mVEGF-C and AAV-CTRL brain cells nuclei.

first: Ligia

last: Braga Boisserand

first: Luiz

middle: H

last: Geraldo

first: Marie-Renee

last: El Kamouh

first: Seyoung

last: Lee

first: Jean-Leon

last: Thomas


title: A single nuclear transcriptomic characterization of mechanisms responsible for impaired angiogenesis and blood-brain barrier function in Alzheimer’s disease

status: Public on Jan 20 2024

city: London

first: Paul

last: Matthews

address: White City

institute: Imperial College London

summary: Brain perfusion and blood-brain barrier (BBB) integrity are reduced early in Alzheimer’s disease (AD). We performed single nucleus RNA sequencing of vascular cells isolated from AD and non-diseased control brains to characterize pathological transcriptional signatures responsible for this. We found that endothelial cells (EC) are enriched for expression of genes associated with susceptibility to AD. Increased β-amyloid is associated with BBB impairment and a dysfunctional angiogenic response related to a failure of increased pro-angiogenic HIF1A to increased VEGFA signalling to EC. This is associated with vascular inflammatory activation, EC senescence and apoptosis. Our genomic dissection of vascular cell risk gene enrichment provides evidence for a causal role of EC pathology in AD and suggests that reducing vascular inflammatory activation and restoring effective angiogenesis could reduce vascular dysfunction contributing to the genesis or progression of early AD.

overall_design:
Samples from the prefrontal cortex were processed for microvessel single nuclei isolation. All steps were carried out on ice or at 4oC. Tissue was processed to first isolate microvessels and then to release single nuclei for sequencing. Tissue was dounce homogenized and then centrifuged at 1000g for 3 min. Pellets were re-suspended in 5.3% dextran and overlayed on a pre-prepared dextran gradient (4%, 12%, 16%). After centrifugation the bottom layer was subject to a second dextran gradient spin, 4200g for 20 min. The pellets were resuspended and passed through a 100um filter and then a 40um filter. The 40um filter was inverted and centrifuged at 800g for 8 minutes. The isolated microvessels were incubated with Collagenase for 20 minutes and nuclei released by grinding with a pestle and filtering through a 20um filter.

***************************************************************
Submitter states that raw files are not in SRA due to patient privacy concerns.
For raw files, visit the project space in https://www.synapse.org/#!Synapse:syn36812517/wiki/619350 ***************************************************************

first: Stergios

last: Tsartsalis

first: Hannah

last: Sleven

first: Nurun

last: Fancy

first: Frank

last: Wessely

first: Amy

last: Smith

first: Nanet

last: Willumsen

first: Dorcas

last: Cheung

first: Michal

last: Rokicki

first: Vicky

last: Chau

first: Eseoghene

last: Ifie

first: Combiz

last: Khozoie

first: Olaf

last: Ansorge

first: Xin

last: Yang

first: Marion

last: Jenkins

first: Karen

last: Davey

first: Aisling

last: McGarry

last: Muirhead

first: Stephanie

last: Debette

first: Johanna

last: Jackson

first: Axel

last: Montagne

middle: R

last: Owen

first: Scott

last: Miners

first: Seth

last: Love

first: Caleb

last: Webber

first: Zameel

last: Cader


title: Molecular correlation between mouse retina and striatum in HD

city: Alicante

first: Luis

last: Valor

state: Alicante

address: Av. Pintor Baeza, 12

institute: ISABIAL

summary: Huntington’s disease (HD) is a devastating disorder caused by an aberrant expansion of CAG repeats in the HTT gene. Striatal dysfunction has been widely studied in HD mouse models as part of the basal ganglia, the main brain areas affected in patients that explain the most evident symptomatology. However, cumulative evidence indicates that the retina can also be functionally altered with consequences for visual function and circadian rhythms. Moreover, the retina is the most exposed part of the CNS that can be used for monitoring the health status of patients using non-invasive techniques and for treatment screenings in preclinical models. To establish the retina as an appropriate tissue for HD studies, it is first required to link retinal alterations at the cellular and molecular levels with those of the inner brain. In this work, we confirmed that the retinas of R6/1 mice were functionally and morphologically affected, and suffered a rearrangement of its transcriptome as extensive as in the striatum. Tissue-enriched genes were downregulated in both areas, but a neuroinflammation signature was specific to the R6/1 retina through the glial activation that was apparently absent in the striatum of the same animals. These phenomena were confirmed in the zQ175 strain, and were accompanied by a differential impairment of the autophagy system between both tissues that may have implications for autophagic-based therapies in HD. Overall, these results demonstrated the suitability of the retina as a research model for HD and general neurodegeneration.

overall_design: Comparison of the gene expression profile in the retina and striatum of the same R6/1 and wild-type littermates.


title: KRAB zinc finger proteins ZNF587/ZNF417 protect lymphoma cells from replicative stress-induced inflammation [RNA_D6]

city: Lausanne

first: Filipe

last: Martins

address: Station 19

country: Switzerland

institute: Epfl

summary: Heterochromatin loss and genetic instability enhance cancer progression by favoring clonal diversity, yet uncontrolled replicative stress leads to mitotic catastrophe and inflammatory responses promoting immune rejection. KRAB-containing zinc finger proteins (KZFPs) contribute to heterochromatin maintenance at transposable elements (TEs). Here, we describe how upregulation of a cluster of primate-specific KZFPs is associated with poor prognosis, increased copy number alterations, and suppression of immune responses in diffuse large B cell lymphoma (DLBCL). Depleting two of these KZFPs targeting evolutionarily recent TEs, ZNF587 and ZNF417, impairs proliferation of cells derived from DLBCL and several other tumor types. This correlates with heterochromatin redistribution, replicative stress, and cGAS-STING-mediated induction of an interferon/inflammatory response leading to enhanced susceptibility to macrophage-mediated phagocytosis, increased surface expression of HLA-I and presentation of a neo-immunopeptidome. Thus, cancer cells can subvert KZFPs to dampen TE-originating surveillance mechanisms, which likely facilitates clonal expansion, diversification, and immune evasion.

overall_design: RNA-Seq performed on four shZNF587/417 and four control samples in OCI-Ly7 and U2932 cells, 6 days after lentiviral transduction.

first: Joana

last: Carlevaro-Fita


title: KRAB zinc finger proteins ZNF587/ZNF417 protect lymphoma cells from replicative stress-induced inflammation [TrAEL-seq]

overall_design: TrAEL-Seq performed on one shZNF587/417 and one control sample, 72h after lentiviral transduction.


title: Roles of the kinase NUAK1 on spliceosome in the mouse cortex

first: Hélène

last: Polvèche

summary: The project focuses on the protein kinase NUAK1, which controls the development of brain cortical connectivity in mice. Recent data suggest that NUAK1 is involved in the regulation of the spliceosome and more broadly of mRNA biology. The aim of this project is to test whether inactivation of NUAK1 (constitutive KO) affects the expression level of genes relevant for cortical development in the embryonic brain. We collected the cortex of embryos (littermates) at the late embryonic developmental stage (E18.5, i.e. just before birth). The samples will be either KO or WT (controls). We collected the samples on the same day, under the same conditions, and as far as possible we made homogeneous groups: same litter, same proportion of males/females.

overall_design: We collected the cortex of embryos from a constitutive NUAK1 KO line, at the E18.5 embryonic stage. At this stage the cortex is mainly composed of maturing neurons (70X), migrating interneurons (10X) and progenitors/glial cells/endothelial cells (15-20X).  Collection conditions: Samples were obtained from microdissected embryos. The females were mated at the same time and the embryos were from 4 litters.

first: Evelyne

last: Goillot

first: Julien

last: Courchet

first: Cyril

last: Bourgeois


title: Progranulin–glucocerebrosidase complex regulates tau and alpha-synuclein inclusions to alter phenotypes in tauopathy

first: Hideyuki

last: Takahashi

state: Connecticut

address: 295 Congress Ave.  BCMM431

department: Neuroscience

summary: Many neurodegenerative disorders including Alzheimer’s disease (AD) and frontotemporal lobar degeneration (FTLD) are characterized by abnormal protein deposition and frequently show comorbid pathology. Progranulin (PGRN) is implicated not only in TDP-43 but in tau and alpha-synuclein proteinopathies. However, the underlying mechanisms are unknown. Here, we generated P301S tau transgenic mice with PGRN haploinsufficiency and loss and found that those mice exhibit exacerbated disinhibition phenotype while showing attenuated memory impairment, hippocampal atrophy, and transcriptomic changes. Remarkably, the phenotypic alteration was accompanied by an increase in tau inclusions, which are positive for alpha-synuclein, a PGRN binding partner beta-glucocerebrosidase (GCase), and its substrate glucosylceramide. GCase inhibition or PGRN deficiency enhanced tau aggregation induced by AD-derived tau seeds in neurons.  In vitro, GCase and glucosylceramide promoted P301S tau aggregation. Similar co-pathology was observed in AD and FTLD-GRN patients.

overall_design: 18 samples (hippocampus) from 6 genotypes with 3 biological replicates were individually processed and sequenced.  Nuclei were isolated from hippocampi using Nuclei EZ Prep Kit (SIGMA #NUC-101). Libraries were prepared using Chromium Single Cell 3” Reagent Kits v3 (10X Genomics) . The libraries underwent HiSeq paired-end sequencing with a sequence depth of 200 million reads per sample using NovaSeq instrument (Ilumina).

first: Sanaea

last: Bhagwagar

first: Sarah

last: Nies

first: Marius

middle: T

last: Chiasseu

first: Guilin

last: Wang

first: Ian

last: Mackenzie

first: Stephen

last: Strittmatter


title: KRAB zinc finger proteins ZNF587/ZNF417 protect lymphoma cells from replicative stress-induced inflammation [RNA_72h]

overall_design: RNA-Seq performed on three shZNF587/417 and three control samples, 72h after lentiviral transduction.


title: Bulk RNA-sequence of four monocyte-macrophage subpopulations isolated from the IgE-dependent skin allergic inflammation (IgE-CAI) skin lesion

first: Kensuke

last: Miyake

summary: Basophils play critical roles in the development of mouse delayed-onset skin allergic inflammation (IgE-CAI model). Importantly, they also contribute to the resolution of allergic inflammation by promoting the generation of pro-resolving macrophages. However, it remains unclear how pro-resolving macrophages suppress excess inflammation. To address this, we conducted single-cell RNA-seq (scRNA-seq) analysis of the IgE-CAI skin lesion at days 3 and 5 post-challenge of allergens. scRNA-seq analysis identified four distinct monocyte-macrophage subpopulations, namely classical monoytes, early CMDMs, late CMDMs and resident-like macrophages. Based on the gene expression profiles, classical monoytes, early CMDMs, late CMDMs and resident-like macrophages corresponded to Ly6ChiPD-L2lo, Ly6ChiPD-L2hi, Ly6CloPD-L2hi, and Ly6CloPD-L2lo, respectively.

overall_design: IgE-CAI model was elicited to BALB/c WT mice.  Cells isolated from IgE-CAI skin lesions of WT mice on day 5 post-antigen challenge were subjected to cell sorting. Four monocyte-macrophage subpopulations, namely Ly6ChiPD-L2lo, Ly6ChiPD-L2hi, Ly6CloPD-L2hi, and Ly6CloPD-L2lo were isolated from the IgE-CAI skin lesion and subjected to bulk RNA-seq analysis.

first: Junya

last: Ito

first: Kazufusa

first: Jun

last: Nakabayashi

first: Shigeyuki

last: Shichino

first: Soichiro

last: Yoshikawa

first: Hajime

last: Karasuyama


title: Bulk RNA-seq comparison of TYA018 HDAC6 inhibition vs vehicle after a single dose treatment in Mus Musculus to treat heart failure with preserved ejection fraction

status: Public on Jan 17 2024

city: South San Francisco

first: Farshad

last: Farshidfar

address: 171 Oyster Point Blvd Ste 500

institute: Tenaya Therapeutics Inc.

summary: Heart failure with preserved ejection fraction (HFpEF) is a prevalent health condition associated with high morbidity and mortality, but currently, there are few effective therapies. Our previous research showed that inhibiting histone deacetylase 6 (HDAC6) had a beneficial effect on a genetic cardiomyopathy model. The overlapping underlying mechanisms involving inflammation and metabolism between cardiomyopathy and HFpEF prompted us to explore the role of HDAC6 in HFpEF. The results showed that inhibiting HDAC6 with TYA-018 reversed preexisting cardiac hypertrophy and diastolic dysfunction, and improved lung congestion and exercise capacity in mouse models of HFpEF, including a newly developed model that combines moderate trans-aortic constriction and high-fat diet to mimic the systemic and cardiovascular features of human HFpEF. Moreover, mice with genetic Hdac6 deletion delayed the development of HFpEF and were resistant to the effects of TYA-018. The efficacy of TYA-018 was comparable to a SGLT2 inhibitor, and the combination showed increased effects. Mechanistically, TYA-018 restored expression of gene sets associated with hypertrophy, fibrosis, and mitochondrial energy production in heart tissue from HFpEF mice. TYA-018 also inhibited activation of human cardiac fibroblasts and increased mitochondrial respiratory capacity in induced pluripotent stem cell–derived cardiomyocytes. These findings support the direct role of HDAC6 on HFpEF pathophysiology in the heart and that inhibiting HDAC6 may be a promising approach to treating HFpEF.

overall_design: RNA sequencing on 3 groups of C57BL6 mice with wild-type background: Control (non-failing, n=4), HFD/L-NAME HFpEF model (n=4), HFpEF+TYA-018 (n=4).

first: Sara

last: Ranjbarvaziri

first: Aliya

last: Zeng

first: Iris

last: Wu

first: Amara

last: Greer-Short

first: Farshidfar

last: Farshad

first: Ana

last: Budan

first: Emma

last: Xu

first: Reva

last: Shenwai

first: Matthew

last: Kozubov

first: Cindy

last: Li

first: Melissa

last: Van Pell

first: Francis

last: Grafton

first: Charles

last: Mackay

first: Xiaomei

last: Song

first: James

last: Priest

first: Gretchen

last: Argast

first: Mohammad

middle: A

last: Mandegar

first: Timothy

last: Hoey

first: Jin

last: Yang


title: KRAB zinc finger proteins ZNF587/ZNF417 protect lymphoma cells from replicative stress-induced inflammation.

first: Filipe

last: Martins

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

overall_design: Refer to individual Series


title: Targeting HDAC6 to treat heart failure with preserved ejection fraction (HFpEF)

first: Farshad

last: Farshidfar


title: sFANS ATACseq profiling of cortical cell types from human control samples

city: New York

first: Christina

last: Pressl

state: NY

address: 1230 York Avenue

institute: The Rockefeller University

summary: To reveal gene expression programs altered in the deep layer neuron cell classes of Huntington's Disease samples, we first filtered the cell-type specific differential gene expression lists from our DESeq2 analyses based on the cell-type specific accessible promotor peaks revealed through ATACseq of control deep layer nuclei. This step allowed us to focus our gene lists for the following GO analyses to those genes that were truly accessible in the specific cell-types.

overall_design: We have employed serial fluorescence activated nuclear sorting (sFANS) protocols to isulate nuclei from deep layer cortical cell types, followed by ATACseq profiling.

first: Nathaniel

last: Heintz


title: Methylone is a rapid-acting neuroplastogen with less off-target activity than MDMA

first: Jennifer

last: Warner-Schmidt

address: 220 5th Ave 17th Floor

institute: Transcend Therapeutics

summary:
Background: Post-traumatic stress disorder (PTSD) is a highly prevalent psychiatric disorder that can become chronic and debilitating when left untreated. Available pharmacotherapies are limited, take weeks to show modest benefit and remain ineffective for up to 40% of patients. Methylone is currently in clinical development for the treatment of PTSD. Preclinical studies show rapid, robust and long-lasting antidepressant-like and anxiolytic effects. The mechanism of action underlying these effects is not yet fully understood. This study investigated the downstream gene expression changes and signaling pathways affected by methylone in key brain areas linked to PTSD and MDD. It also sought to determine whether neuroplasticity-related genes were involved. We compared effects of methylone with MDMA to explore similarities and differences in their brain effects because MDMA-assisted psychotherapy has recently shown benefit in clinical trials for PTSD and methylone is a structural analog of MDMA.
Methods: We used RNA sequencing (RNA-seq) to probe drug-induced gene expression changes in the amygdala and frontal cortex, two brain areas responsible for emotional learning that are affected by PTSD and MDD. Rats were treated with methylone or MDMA (both 10 mg/kg, IP), and their responses were compared with controls.
Results: RNA-seq results revealed significant regulation of myelin-related genes in the amygdala, confirmed by immunohistochemistry. In the frontal cortex, methylone significantly upregulated genes implicated in neuroplasticity.
Conclusions: Results suggest that (1) methylone is a rapid-acting neuroplastogen that affects key brain substrates for PTSD and MDD and that (2) methylone appears to exhibit higher specificity and fewer off-target effects than MDMA. Together, these results are consistent with the reported clinical experiences of methylone and MDMA and bolster the potential use of methylone in the treatment of PTSD and, potentially, other neuropsychiatric disorders.

overall_design: Frontal cortex or amygdala were dissected from rats treated with methylone (10 mg/kg, IP), MDMA (10 mg/kg, IP) or vehicle and RNAseq was performed. There were six animals per treatment group. We compared gene expression in methylone or MDMA-treated animals with vehicle-treated controls.


title: sFANS RNAseq profiling of deep layer cortical cell types from human control and Huntington's Disease samples

summary: The properties of the cell types that are most vulnerable in the Huntington's disease (HD) cortex have not been delineated. Here we have employed serial fluorescence activated nuclear sorting (sFANS) and deep molecular profiling to demonstrate that layer 5a pyramidal neurons are selectively vulnerable in primary motor cortex and other cortical areas.

overall_design:
Nuclei from neuronal cell populations from the deep layers of cortex (layers 5 and 6) were isolated from post-mortem human brain samples. Nuclei were labeled with fluorescent antibodies and sorted into cell-type specific populations by FACS. RNA was extracted, libraries were generated for RNA sequencing, and analyses of cell-type specific nuclear gene expression transcript levels were performed.
Genotyping information is listed for patient samples and for a select set of control samples.


title: Efect of Arpp21 deficiency on TCR repertoire diversity

city: Ulm

first: Marcin

last: Lyszkiewicz

address: Eythstr. 24

department: Dpt. of  Pediatrics and Adolescent Medicine

institute: Ulm University Medical Center

summary: To assess the impact of Arpp21 deficiency on the TCR repertoire, we generated Arpp21-deficient mice from which we isolated CD4 T cells and subjected them to NGS sequencing.

overall_design: From the spleens of age-matched mice, 7 of which were WT and 7 of which were Arpp21 KO, 6.8 million CD4 T cells were purified by FACS.   Technical details:  - Library preparation kit: Takara SMARTer Mouse TCR alpha-beta Profiling Kit  - Sample QC method: Qubit and Tapestation  - Library QC method: Qubit and Tapestation  - Instrument: Illumina MiSeq  - Read length: PE300

first: Meng

last: Xu

first: Viggo

last: Heissmeyer


title: Single nucleus RNA-seq comparison of TYA018 HDAC6 inhibition and Empagliflozin SGLT2 inhibition to treat heart failure with preserved ejection fraction

overall_design: Single nucleus RNA sequencing on 4 groups of C57BL6 mice with wild-type background: Control treated with vehicle  (n=2), HFD/L-NAME HFpEF model treated with vehicle (n=2), HFpEF treated with TYA-018 HDAC6 inhibitor (n=2), HFpEF treated with empagliflozin SGLT2 inhibitor (n=2).

first: Sara

last: Ranjbarvaziri

first: Aliya

last: Zeng

first: Iris

last: Wu

first: Amara

last: Greer-Short

first: Farshidfar

last: Farshad

first: Ana

last: Budan

first: Emma

first: Reva

last: Shenwai

first: Matthew

last: Kozubov

first: Cindy

last: Li

first: Melissa

last: Van Pell


title: A SWI/SNF-dependent transcriptional regulation mediated by POU2AF2/C11orf53 at enhancer

status: Public on Jan 19 2024

city: Chicago

first: Lu

last: Wang

state: Illinois

address: 303 E. Superior Street Simpson Querrey 7-414

department: Biochemistry and Molecular Genetics

institute: Northwestern University

summary: Recent studies have identified a previously uncharacterized protein C11orf53 (now named POU2AF2/OCA-T1), functions as a new co-activator of POU2F3, the master transcription factor which is critical for both normal and neoplastic tuft cell identity and viability. Here, we demonstrated that POU2AF2 functions as an “Yin-Yang” factor which mediates both transcriptional activation and repression at distal enhance elements. Loss of POU2AF2 led to an inhibition of active enhancer nearby genes, such as tuft cell identity genes, and a derepression of Polycomb-dependent poised enhancer nearby genes, which are critical for cell viability and differentiation. Mechanistically, depletion of POU2AF2 leads to a global redistribution of the chromatin occupancy of SWI/SNF complex, resulting in a significant 3D genome structure change and a subsequent transcriptional reprogramming. Genome wide CRISPR screen further demonstrated that POU2AF2 depletion or SWI/SNF inhibition led to a PTEN-dependent cell growth defect, which revealed a potential role of POU2AF2-SWI/SNF axis in small cell lung cancer pathogenesis. Finally, pharmacological inhibition of SWI/SNF phenocopied POU2AF2 depletion in terms of gene expression alteration and cell viability decease in SCLC-P subtype cells. Therefore, impeding POU2AF2 mediated SWI/SNF function represents a potential therapeutic approach for human SCLC therapy.

overall_design: To determine the transcriptional repression function of POU2AF2, we depleted POU2AF2 by two distinct sgRNAs in different SCLC cell lines and conducted RNA-seq experiments. To study the potential mechanisms, we determined the chromatin occupancy of BRG1 and PRC2 in POU2AF2 wild type and depleted cells by ChIP-seq. To understand how POU2AF2 impacts chromatin accessibility, we performed ATAC-seq in cells transduced with either non-targeting sgRNA or two distinct POU2AF2 sgRNAs. To study the high chromatin structure change, we employed Hi-C experiments.

first: Zibo

last: Zhao


title: Molecular reframing of fibroblasts during resolution of arthritis [Visium]

status: Public on Jan 16 2024

city: Erlangen

first: Hashem

last: Mohammadian

address: Ulmenweg 18

department: Department of Medicine 3 - Rheumatology and Immunology

institute: University of Erlangen-Nürnberg

summary: Fibroblasts are key orchestrators of inflammation. Little is known whether these cells change phenotype during resolution of inflammation. We adopted a method to visualise fibroblast activation during inflammation in humans in vivo, which is based on a fibroblast activation protein (FAP) tracer detected by positron emission tomography (PET). While tracer accumulation was high in active arthritis, it decreased significantly after TNF- and IL-17A inhibition. Biopsy-based scRNA-seq analyses in experimental arthritis demonstrated that FAP signal reduction reflected a phenotypic switch from pro-inflammatory MMP3+/IL6+ fibroblasts (high FAP internalisation) to pro-resolving CD200+DKK3+ fibroblasts (low FAP internalisation). Spatial transcriptomics of human joints revealed that pro-resolving niches of CD200+DKK3+ fibroblasts clustered with innate lymphoid cells (ILC)2, whereas MMP3+/IL6+ fibroblasts were co-localised with inflammatory immune cells. CD200+DKK3+ fibroblasts stabilised the ILC2 phenotype and induced resolution of arthritis via CD200/CD200R1 pathway. Taken together, these data suggest a dynamic molecular regulation of the mesenchymal compartment during resolution of inflammation.

overall_design: Synovial biopsies from two active Psoriatic Arthritis patient and two healthy individuals were analyzed using spatial transcriptomics

first: Simon

last: Rauber

first: Juan

middle: D

last: Cañete

first: Andreas

last: Ramming


title: KRAB zinc finger proteins ZNF587/ZNF417 protect lymphoma cells from replicative stress-induced inflammation [CUT&Tag]

first: Filipe

last: Martins

overall_design: CUT & Tag for H3K9me3 and gH2AX performed on two shZNF587/417 and two control samples for each mark, 72h after lentiviral transduction.

first: Joana

last: Carlevaro-Fita


title: Molecular reframing of fibroblasts during resolution of arthritis

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: RNA-seq comparison of HFD-mTAC model of heart failure with preserved ejection fraction vs control heart tissue in Mus Musculus

first: Farshad

last: Farshidfar

overall_design: RNA sequencing on 2 groups of C57BL6 mice with wild-type background: Control (non-failing, n=5), HFD/mTAC HFpEF model (n=5). Both treated with vehicle.

first: Sara

last: Ranjbarvaziri

first: Aliya

last: Zeng

first: Iris

last: Xu

first: Francis

last: Grafton

first: Charles

last: Mackay

first: Xiaomei

last: Song

first: James

last: Priest

first: Gretchen

last: Argast

first: Mohammad

last: Mandegar

first: Timothy

last: Hoey

first: Jin

last: Yang


title: Bulk RNA-seq comparison of TYA-018 HDAC6 inhibition vs SGLT2 inhibition vs vehicle after a 3-months long-term treatment in Mus Musculus to treat heart failure with preserved ejection fraction

overall_design: RNA sequencing on 4 groups of C57BL6 mice with wild-type background: Control (non-failing, n=8), HFD/L-NAME HFpEF model (n=8), HFpEF+TYA-018 (n=11), HFpEF+Empagliflozin (n=11).

last: Wu

first: Amara

last: Greer-Short

first: Farshidfar

last: Farshad

first: Ana

last: Budan

first: Emma

first: Reva

last: Shenwai

first: Matthew

last: Kozubov

first: Cindy

last: Li

first: Melissa

last: Van Pell


title: Increased Antibody Titers but Induced T-Cell AICD and Apoptosis Response in COVID-19 Convalescents by Inactivated Vaccine Booster

status: Public on Jan 15 2024

city: Shanghai

first: Yuxuan

last: Zheng

address: 825 Zhangheng Rd.

institute: Fudan University

summary: It is urgently needed to evaluate the necessity and benefits of booster vaccination to facilitate clinical decision-making for recovered COVID-19 patients. In this study, we conducted a multicentre, prospective clinical trial of the earliest COVID-19 patients with a definitive history of direct or indirect exposure to SARS-CoV-2 through Hubei Province from three Chinese hospitals to evaluate the efficiency, safety and immune response of CoronaVac (an inactivated COVID-19 vaccine). Convalescent patients with high titres (≥ 1:96) or non-severe also exhibited higher frequency of long COVID-19 symptoms. One booster dose in convalescent patients with antibody titres below 1:96 significantly induced neutralizing antibodies against prototypic SARS-CoV-2 and the Delta variant by 13.03- and 9.27-fold, respectively. Transient adverse events occurred in three out of the twenty-eight immunized participants (10.71%). In addition, the ratio of naïve T cells increased dramatically, and TEMRA and TEM cells gradually decreased post vaccination. The expression levels of activation-induced cell death and apoptosis-related genes were significantly elevated after vaccination in all T-cell subtypes in convalescent patients. Our results indicate that vaccine-mediated T-cell consumption and regeneration patterns may be detrimental to the antiviral response.

overall_design: We generated a single-cell combined transcriptome (single-cell RNA-seq [scRNA- seq], T-cell receptor [TCR] and B-cell receptor [BCR]) for three convalescent patients who experienced the most apparent increases in naïve T cells before (day 0) and after vaccination (day 28) using 10× Genomics platform.

first: Jingmin

last: Zhao

first: Han

last: Zhang

first: Lina

last: Jiang

first: Fang

last: Cheng

first: Wei

first: Zihao

last: Wang

first: Hongyang

last: Liu

first: Shaohua

first: Yiyun

first: Meiling

first: Yan

first: Shuhong

first: Min

last: Fang

first: Xuyu

last: Zhou

first: Xin

last: Ye

first: Shousong

first: Songdong

last: Meng


title: sFANS enriched snRNAseq profiling of deep layer cortical cell types from human control and Huntington's Disease samples

first: Christina

last: Pressl

summary: The properties of the cell types that are most vulnerable in the Huntington’s disease (HD) cortex have not been delineated. Here we have employed serial fluorescence activated nuclear sorting (sFANS) and deep molecular profiling to demonstrate that layer 5a pyramidal neurons are selectively vulnerable in primary motor cortex and other cortical areas.

overall_design: Nuclei from neuronal cell populations from the deep layers of cortex (layers 5 and 6) were isolated from post-mortem human brain samples. Nuclei were labeled with fluorescent antibodies and sorted into cell-type specific populations by FACS and further processed through the 10X platform for the generation of single nuclei RNA sequencing (snRNAseq) datasets.

first: Nathaniel

last: Heintz


title: sFANS RNAseq profiling of cortical cell types from human control samples

summary: To study the properties of the major cell types of human cortex we have employed serial fluorescence activated nuclear sorting (sFANS) and deep molecular profiling.

overall_design: Nuclei from neuronal and non-neuronal cell populations were isolated from post-mortem human brain samples. Nuclei were labeled with fluorescent antibodies and sorted into cell-type specific populations by FACS. RNA was extracted, libraries were generated for RNA sequencing, and analyses of cell-type sopecific nuclear gene expression transcript levels were performed.


title: KRAB zinc finger proteins ZNF587/ZNF417 protect lymphoma cells from replicative stress-induced inflammation [RNA_D10]

first: Filipe

last: Martins

overall_design: RNA-Seq performed on three shZNF587/417 and three control samples, 10 days after lentiviral transduction.

first: Joana

last: Carlevaro-Fita


title: Inhalation of ACE2-expressing lung spheroid cell exosomes provides prophylactic protection against SARS-CoV-2

status: Public on Jan 13 2024

city: Raleigh

first: Zhenzhen

state: North Carolina

address: 1060 William Moore Dr

institute: North Carolina State University

summary: Continued emergence of SARS-CoV-2 variants of concern that are capable of escaping vaccine-induced immunity pose the urgency for developing new COVID-19 therapeutics. An essential mechanism for SARS-CoV-2 infection begins with the viral spike protein binding to the human ACE2. Consequently, inhibiting this interaction is a highly promising therapeutic strategy against COVID-19. Herein, we demonstrate that ACE2-expressing human lung spheroid cells (LSC)-derived exosomes (LSC-Exo) could function as a prophylactic agent to bind and neutralize SARS-CoV-2 and protect the host against SARS-CoV-2 infection. Inhalation of LSC-Exo facilitates their deposition and biodistribution throughout the whole lung in a female mouse model. We show that LSC-Exo blocks the interaction of SARS-CoV-2 with host cells in vitro and in vivo by neutralizing the virus. LSC-Exo treatment protected hamsters from SARS-CoV-2-induced disease and reduced viral loads. Furthermore, LSC-Exo intercept the entry of multiple SARS-CoV-2 variant pseudoviruses in female mice and show comparable or equal potency against the wild-type strain, demonstrating that LSC-Exo may act as broad-spectrum protectant against existing and emerging virus variants.

overall_design: To To elucidate the underlying protection mechanisms of LSC-Exo against SARS-CoV-2 infection, the bulk RNA sequencing (RNA-seq) analysis on lung tissues of infected hamsters that received PBS or LSC-Exo treatment was performed.