title: An engineered model of metastatic colonization of human bone marrow reveals breast cancer cell remodeling of the hematopoietic niche

city: New York

first: Richard

last: Friedman

state: NY

address: 1130 St. Nicholas Av

department: Medicine

institute: Columbia University Irving  Medical Center

summary: Incomplete understanding of metastatic disease mechanisms continues to hinder effective treatment of cancer. Despite remarkable advancements toward the identification of druggable targets, treatment options for patients in remission following primary tumor resection remain limited. Bioengineered human tissue models of metastatic sites capable of recreating the physiologically relevant milieu of metastatic colonization may strengthen our grasp of cancer progression and contribute to the development of effective therapeutic strategies. We report the use of an engineered tissue model of human bone marrow (eBM) to identify microenvironmental cues regulating cancer cell proliferation and to investigate how triple-negative breast cancer cell lines influence hematopoiesis. Notably, individual stromal components of the BM niche (osteoblasts, endothelial cells, and mesenchymal stem/stromal cells) were each critical for regulating tumor cell quiescence and proliferation in the three-dimensional eBM niche. In this data set, we provide transcriptomic information from bulk RNA sequencing of MDA-MB-231 cancer cells that were pre-conditioned by being co-cultured on variations of eBM tissues. We envision that this human tissue model will facilitate studies of niche-specific metastatic progression and individualized responses to treatment.

overall_design: The transcriptome of MDA-MB-231 cells cultured in endosteal bone seeded with mesenchymal stem cells and endothelial cells (ME) was compared to that of MDA-MB-231 cells cultured in endosteal bone containing only osteoblasts (OB).

first: Ilaria

last: Baldassarri

first: Daniel Naveed

last: Tavakol

first: Pamela L.

last: Graney

first: Alan G.

last: Chramiec

first: Hanina

last: Hibshoosh

first: Gordana

last: Vunjak-Novakovic


title: Selective translation of nuclear mitochondrial respiratory proteins reprograms succinate metabolism in AML development and chemoresistance.[ATAC-seq]

status: Public on Sep 24 2024

city: wuhan

first: Haojian

last: Zhang

state: Hubei

address: Donghu Rd

department: Medical Research Institute

country: China

institute: Wuhan university

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Here we identify a novel RAS-responsive element binding protein 1 short isoform, RREB1S, as a key in governing mitochondrial complex II translation to promote stemness and drug resistance of cancer stem cells of acute myeloid leukemia

overall_design: This dataset contains ATAC-Seq experiments of leukemia stem cells isolated from WT or Rreb1-KO mice.leukemia stem cells were isolated from the bone marrow for ATAC-seq analysis with two biological replicates.

first: Guoqiang

last: Han


title: Valine-restricted diet regulates DNA methylation [ddC S1-END-Seq]

status: Public on Sep 23 2024

city: Shanghai

first: Yu

last: Yuanyuan

address: No. 1239, Siping Road, Shanghai

institute: Tongji University

type: Methylation profiling by high throughput sequencing

summary: The abundancy of intracellular amino acid (AA) levels is precisely sensed by complex machineries to regulate various signaling pathways and control cell functions. Insufficient intracellular AAs may block the release of tRNA molecules from the general control non-derepressible 2 (GCN2), and consequently activate GCN2-ATF4 pathways, which is an indirect mechanism for sensing general AAs levels. Additionally, the intracellular levels of some AAs can be sensed by direct binding to specific sensors. Nowadays, the sensors of arginine and leucine levels are most well-characterized, including CASTor1/2, SLC38A9, Sestrin2 and SAR1B, which regulate the mechanistic target of rapamycin complex 1 (mTORC1) pathway, and couple AA availability to cell growth and metabolism. However, it is still unclear whether and how other types of amino acids are directly sensed to regulate cellular functions except tRNA synthetases. Moreover, epigenetics is known to be regulated by the metabolism of amino acids, but it is incompletely understood how AA abundancy regulates the epigenetics, especially DNA methylation. The long-sought sensor of amino acids for epigenetic regulation has thus far been unknown. Here, we present evidence that valine sensor regulated DNA demethylation.

overall_design: ddC S1-END-seq in WT and TDG knockdown HCT116 cells upon valine deprivation

first: Jiali

last: Jin

first: Tong

last: Meng

first: Yuanyuan

last: Yu

first: Cizong

last: Jiang

first: Ping

last: Wang


title: Valine-restricted diet regulates DNA methylation [END-Seq, ddC S1-END-Seq]

overall_design: END-seq in HCT116 cell line upon valine deprivation and ddC-S1-END-seq in HCT116 cell line under valine deprivation


title: Valine-restricted diet regulates DNA methylation [H3K4me1 ChIP-Seq]

overall_design: Chromatin Immunoprecipitation sequencing (ChIP-seq) for H3K4me1 in WT HCT116 cells


title: Valine-restricted diet regulates DNA methylation [MAB-Seq]

overall_design: MAB-seq in WT HCT116 cell lines upon valine deprivation


title: Beta cell-specific PAK1 enrichment ameliorates diet-induced glucose intolerance by promoting insulin biogenesis and minimizing beta cell apoptosis [ChIP-Seq]

status: Public on Sep 25 2024

city: Duarte

first: Debbie

last: Thurmond

state: CA

address: City of Hope Beckman Research Institue

department: Molecular and Cellular Endocrinology

country: USA

institute: City of Hope

summary: Aims/ hypothesis: p21 (Cdc42/Rac1) activated Kinase 1 (PAK1) is depleted in type 2 diabetic human islets compared to non-diabetic (ND) human islets, and acute PAK1 restoration to type 2 diabetic human islets can restore insulin secretory function ex vivo. We hypothesized that beta cell specific PAK1 enrichment in vivo carries the capacity to mitigate high-fat diet-induced glucose intolerance by increasing the functional beta cell mass. Methods: Type 2 diabetic or ND human islets expressing exogenous PAK1 specifically in beta cells were used for bulk RNA-sequencing (RNA-seq). Human EndoC-

overall_design: Human EndoC-H1 cells overexpressing myc-tagged PAK1 were used for chromatin immunoprecipitation (ChIP) and ChIP-sequencing (ChIP-seq).

first: Miwon

last: Ahn

first: Sangeeta

last: Dhawan

first: Erika

middle: M

last: McCown

first: Pablo

middle: A

last: Garcia

first: Supriyo

last: Bhattacharya

first: Roland

last: Stein

middle: C


title: Valine-restricted diet regulates DNA methylation [NLS-HDAC6 TET2 ChIP-Seq]

overall_design: TET2 ChIP-seq in 6XNLS-HDAC6 expressing HDAC6 knockdown HCT116 cell line


title: Valine-restricted diet regulates DNA methylation [TET2 ChIP-Seq]

overall_design: Chromatin Immunoprecipitation sequencing (ChIP-seq) for TET2 in WT, HDAC6-KD HCT116 cells upon valine deprivation


title: Valine-restricted diet regulates DNA methylation [ACE-Seq]

overall_design: ACE-seq in WT, HDAC6 knockdown, TET2 knockdown cell lines upon valine deprivation


title: Valine-restricted diet regulates DNA methylation [Bisulfite-Seq]


title: Valine-restricted diet regulates DNA methylation [RNA-Seq]

type: Expression profiling by high throughput sequencing

overall_design: We used RNA-seq data obtained from WT, HDAC6-KD, TET2-KD HCT116 cells upon valine deprivation for gene expression profiling


title: EDC-3 and EDC-4 Regulate Embryonic mRNA Clearance and Biomolecular Condensate Specialization

city: Montreal

first: Alain

last: Pacis

state: QC

address: 1010 Sherbrooke #1800

country: Canada

institute: Canadian Centre for Computational Genomics (C3G)

summary: Animal development is dictated by the selective and timely decay of mRNAs in developmental transitions, but the impact of mRNA decapping scaffold proteins in development is unknown. This study unveils the roles and interactions of the DCAP-2 decapping scaffolds EDC-3 and EDC-4 in the embryonic development of C. elegans. EDC-3 facilitates the timely removal of specific embryonic mRNAs, including cgh-1, car-1, and ifet-1 by reducing their expression, and preventing excessive accumulation of DCAP-2 condensates in somatic cells. We further uncover a novel role for EDC-3 in defining the boundaries between P-bodies, germ granules, and stress granules. Lastly, we show that EDC-4 counteracts EDC-3 and engenders the assembly of DCAP-2 with the GID (CTLH) complex, a ubiquitin ligase involved in maternal-to-zygotic transition (MZT). Our findings support a model wherein multiple RNA decay mechanisms temporally partake in the clearance of maternal and zygotic mRNAs throughout embryonic development.

overall_design: To investigate the transcriptome-wide effect of EDC-3 and EDC-4, we performed RNA-seq on 4 biological replicates of RNA extracted from mixed-stage C. elegans embryos of WT (N2 strain), edc-3(ok1427) (RB1311 strain), edc-4(qe49) (FD135 strain), and edc-3(ok1427); edc-4(qe49) (FD135 strain). Differential gene expression and GSEA analyses were done to determine the differentially expressed genes and biological pathways in the mutants compared to WT.

first: Elva

last: Vidya

first: Thomas

middle: F

last: Duchaine


title: Mapping translation initiation sites by ribosome profiling in primary mouse cortical neurons treated with either DMSO or bicuculline

city: New Haven

first: Paul

last: Lee

state: CT

address: 100 College St Room 225

department: Neuroscience

institute: Yale University

summary: While previous studies suggest that many mRNAs containing more than one translation initiation site (TIS), the biological significance of most alternative TISs and their protein isoform (proteoform) products remains undetermined. Here we show that alternative translation initiation at a CUG and an AUG TIS in neuronal pentraxin receptor (NPR) mRNA produces two proteoforms, and their relative abundance is regulated by both neuronal activity as well as an adjacent RNA secondary structure. Downstream AUG initiation transformed the N-terminal transmembrane domain into a signal peptide, thereby converting NPR to a secreted factor sufficient to promote synaptic clustering of AMPA-type glutamate receptors. Changing the relative proteoform ratio, but not the overall NPR abundance reduces AMPA receptor in parvalbumin (PV)-positive interneurons and induces changes in learning behaviors in mice. In addition to NPR, N-terminal extensions of C1q-like synaptic organizers, mediated by upstream AUU start codons, anchor these otherwise secreted factors to the membrane. Thus, our results uncovered the plasticity of N-terminal signal sequences regulated by alternative TIS usage as a widespread mechanism to diversify protein localization and functions.

overall_design: Translation initiation sites mapping was done in day12 primary cortical neurons treated with either DMSO or bicuculline (40 μM) for 10 hours.

middle: J

last: Sun

first: Junjie

last: Guo


title: Managing the tradeoff between reproduction and survival requires flexibility in behavior and gene regulation in threespined stickleback

city: Urbana

first: Tina

last: Barbasch

address: 505 S Goodwin Ave

department: Evolution, Ecology, and Behavior

institute: University of Illinois Urbana Champaign

summary: Predators exert a powerful selective force, however predatoravoidance can conflict with other important activities such as attracting mates. Decisions over whether to court mates versus avoid predators are vital to fitness, yet the mechanistic underpinnings of how animals manage such tradeoffs are poorly understood. Here, we investigate flexibility of behavior and gene regulation in response to a tradeoff between avoiding predators (survival) and courting potential mates (reproduction) in threespined stickleback (Gasterosteus aculeatus). We compared behavioral and transcriptomic responses of male sticklebacks faced with a courtship opportunity and cues of a predator simultaneously to males faced with a courtship opportunity or cues of a predator alone, and found that males behaviorally compromised courtship in favor of predator avoidance when faced with a tradeoff between them. The need to manage this tradeoff elicited dynamic changes in brain gene expression, and sets of functionally-connected genes were organized into discrete modules based on co-expression. Additionally, we found that behavioral flexibility in response to tradeoffs corresponded to flexibility in gene regulatory network structure. Combined, these results uncover the coordinated response by the brain to a fundamental ecological tradeoff, providing insight into the structure and function of genetic networks underpinning how animals make fitness-influencing decisions.

overall_design: In this study, we presented male sticklebacks with a tradeoff between courtship and predation risk and compared their brain transcriptomic resposne to males faced with a courtship opportunity alone, cues of a predator alone, or a control.

first: V

middle: I

last: Abuwa

first: B

last: Carswell

first: Alison

last: Bell


title: Effect of ASB2 deletion on gene expression in non-stimulated and stimulated mouse Th2 lymphocytes

city: Toulouse

first: Isabelle

last: Lamsoul

address: CHU Purpan

country: France

institute: Inserm

summary: Because ASB2a-mediated degradation of filamin A and filamin B could be involved in the modulation of Th2 lymphocyte signaling and thus in the regulation of Th2-specific genes, the transcriptomic signatures of ctrl and ASB2a-deficient Th2 lymphocytes were established by RNA-seq. We here report no impact of ASB2a loss and filamin A/filamin B accumulation on the transcriptomic program of Th2 lymphocytes.

overall_design: Ctrl and ASB2 cKO mouse naive CD4+ cells were isolated from spleen of female Asb2fl/fl and VE-cadherin (VEC) -Cre;Asb2fl/fl transgenic mice (Metais et al., Circulation Research, 2018; Lamsoul et al., Blood, 2013), respectively, using a CD4+ T-cell Isolation Kit (BioLegend) and cultured for 3 days with plate-bound anti-CD3ε (5 µg/ml) in the presence of Th2 polarizing cytokines and antibody cocktails (10 ng/ml IL-2, 40 ng/ml IL-4, 1 µg/ml anti-CD28, and 10 µg/ml anti-IFNγ) in RPMI containing 10% FCS, 1% glutamine, 0.1% β-mercaptoethanol, and 1% penicillin/streptomycin in 24-well plates. Cells were then split across five noncoated plates and cultured for 3 additional days in fresh differentiating medium without antibodies (20 ng/ml IL-2 and 20 ng/ml IL-4). Th2 lymphocytes were stimulated at day 5 with 3µg/ml coated anti-CD3ε and 2µg/ml soluble anti-CD28 for 24h. RNA isolation was performed using the Nuclespin RNA kit (Macherey-Nagel).

first: Margot

last: Zahm

first: Adeline

last: Chaubet

first: Olivier

last: Joffre

first: Pierre

middle: G

last: Lutz


title: ACMSD inhibition corrects fibrosis, inflammation, and DNA damage in MASLD/MASH

city: Lausanne

first: Xiaoxu

last: Li

address: Station 15 - CH

country: Switzerland

institute: EPFL

summary: Recent findings reveal the importance of tryptophan-initiated de novo nicotinamide adenine dinucleotide (NAD+) synthesis in the liver, a process previously considered secondary to biosynthesis from nicotinamide. Here we show that inhibiting α-amino-β-carboxymuconate-ε-semialdehyde decarboxylase (ACMSD) promotes de novo NAD+ synthesis and reduces DNA damage ex vivo, in vivo and in human liver organoid (HLO) models. In mouse models of MASLD/MASH, de novo NAD+ biosynthesis is suppressed, and transcriptomic DNA damage signatures correlate with disease severity; In humans, Mendelian randomization-based genetic analysis suggests a notable impact of genomic stress on liver disease susceptibility. Therapeutic inhibiting ACMSD in mice elevates liver NAD+ and reverses MASLD/MASH, mitigating fibrosis, inflammation and DNA damage. Similar outcomes are recapitulated in HLO models of steatohepatitis and DNA damage. Our findings highlight the benefits of ACMSD inhibition for boosting hepatic NAD+ and genomic protection, indicating its therapeutic promise in liver diseases marked by NAD+ and genomic stress.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: To investigate the effect of ACMSD inhibition, mouse primary hepatocytes were treated with ACMSD inhibitor TLC-065 for 6, 12, and 24h. The effects of TLC-065 were tested in human liver organoid models of steatohepatitis.

first: Yasmine

last: Liu

first: Masaki

last: Kimura

first: Jonathan

last: Sulc

first: Sandra

middle: R

last: Lopez

first: Qi

last: Wang

first: Angelique

last: Scantlebery

first: Keno

last: Strotjohann

first: Hector

last: Gallart-Ayala

first: Archana

last: Vijayakumar

first: Robert

middle: P

last: Myers

first: Maroun

last: Bou-Sleiman

first: Julijana

last: Ivanisevic

first: Riekelt

middle: H

last: Houtkooper

first: G

last: Subramanian

first: Johan

last: Auwerx


title: Oral reovirus reshapes the gut microbiome and enhances antitumor immunity in colon cancer

city: Seongnam

first: WON SUK

last: LEE

address: 59 Yatap-ro

country: South Korea

institute: CHA Bundang Medical Center

summary: The results revealed differences between the RC402-treated and Control samples

overall_design: To elucidate the transcriptional changes upon RC402, we used the Nanostring PanCancer panel to compare 750 immune-related genes in tumors, lymph nodes, and peyer's patches in WT mice bearing CT26 tumors

first: Won Suk

last: Lee

first: Seung Joon

first: Hye Jin

first: Hong Jae

last: Chon

first: Chan

last: Kim


title: RNA-seq and ChIP-seq profiling of human iPSCs, derived NSCs and human fetal NSCs (RNA-Seq)

city: Segrate

first: Ingrid

last: Cifola

state: Milan

address: Via F.lli Cervi, 93

department: Institute for Biomedical Technologies (ITB)

country: Italy

institute: National Research Councill (CNR)

summary: Human iPSC-derived neural stem/progenitor cells (hiPSC-NSCs) are a promising source for cell/gene therapy approaches to target neurodegenerative and demyelinating disorders with unmet clinical needs. Despite the great effort in characterizing hiPSC-derived products in both in vitro and in vivo settings, we still lack a comprehensive study addressing hiPSC-NSC identity and safety at genome-wide level, an issue of paramount importance to establish accepted criteria for prospective clinical applications. Here, we evaluated the transcriptional (by poly-A+ RNA-seq) and epigenetic (by H3K27Ac ChIP-seq) signatures in hiPSCs and differentiated hiPSC-NSC progeny, keeping as reference a somatic clinically relevant human fetal NSC (hfNSCs) line. Overall, our comprehensive transcriptomic and epigenomic analysis coupled to a long-term functional in vivo characterization provided insight into the cell identity, safety profile, and therapeutic potential of hiPSC-NSCs, supporting the rationale for the continuous development of hiPSC-NSCs as an alternative source to somatic hfNSCs for treatment of neurodegenerative and demyelinating disorders.

overall_design: We performed the poly-A+ RNA-seq and ChIP-seq (for H3K27 Acetilation) profiling of three replicates of a human fetal neural stem cell (hfNSC) cell line, four replicates of human induced pluripotent stem cells (hiPSCs) obtained by reprogramming of healthy skin fibroblasts (two from adult fibroblasts and two from newborn fibroblasts), and four replicates of neural stem cells (NSCs) differentiated from hiPSCs (two from the adult hiPSCs and two from the newborn hiPSCs).

first: Luca

last: Petiti

first: Clelia

last: Peano

first: Annarita

last: Miccio


title: RNA-seq in SREBF1-deficient human iPSCs, hiPSC-NSCs and differentiated cells.

summary: Omics analyses and qRT-PCR time-course during the transition from hiPSC to hiPSC-NSC highlighted the up-regulation of SREBF1, a gene involved in cholesterol biosynthesis and lipid homeostasis, suggesting its potential role in NSC commitment/maintenance. To test this hypothesis, we generated SREBF1-deficient hiPSC lines by co-delivering ribonucleoprotein Cas9 with a pool of sgRNA targeting exon 5 of the SREBF1 gene. Upon isolation of three clones harboring the deletion we performed RNA-seq analysis in hiPSC, hiPSC-NSC and differentiated cultures at 7 and 14 days of differentiation, compared to control cells. This analysis will allow to identify the potential role of SREBF1 in affecting hiPSC-to-hiPSC-NSC transition, hiPSC-NSC maintenance and commitment toward differentiated cell populations.

overall_design: We performed the poly-A+ RNA-seq profiling in three clones of SREBF1-deficient human induced pluripotent stem cells (hiPSCs), neural stem cells (hiPSC-NSCs) and differentiated cells at d7 and d14. We also included three replicates of negative control for each  differentiation stage.

first: Marco

last: Luciani

first: Vasco

last: Meneghini


title: Dysfunction of exhausted T cells is enforced by MCT11-mediated lactate metabolism

city: Pittsburgh

first: Greg

last: Delgoffe

state: PA

address: 5115 Centre Ave.

institute: University of Pittsburgh

summary: CD8+ T cells are critical mediators of antitumor immunity but differentiate into a state of dysfunction, known as exhaustion, after experiencing persistent TCR stimulation and metabolic stress in the tumor microenvironment (TME). Exhausted T cells are characterized by the sustained upregulation of co-inhibitory molecules and reduced stemness and polyfunctionality. The TME also creates an immunosuppressive metabolic environment via reduced levels of vital nutrients and oxygen combined with increased catabolic waste products. Additionally, highly glycolytic tumor and stromal cells secrete lactic acid, acidifying the extracellular space. How exhausted T cells survive and function in the face of this altered metabolite balance remains unknown. Here we show terminally exhausted T cells in the TME upregulate a newly characterized, monocarboxylate transporter 11 (MCT11, encoded by Slc16a11), enabling uptake of monocarboxylates like lactic acid, which enforces their state of dysfunction. MCT11 expression requires both the core exhaustion program induced through chronic activation and metabolic stress signals, like hypoxia, originating within tissues. Overexpression of MCT11 in tumor-specific T cells accelerated exhaustion: increasing co-inhibitory marker expression and decreasing polyfunctionality. Conditional deletion of MCT11 in T cells reduced Texh cell lactic acid uptake and resulted in improved effector functions and improved response to immunotherapy. Further, a monoclonal antibody targeting MCT11 could block lactate uptake specifically in Texh cells, which, when used therapeutically in tumor-bearing mice, resulted in significantly reduced tumor growth, inducing complete regressions and immunologic memory. Our data support a model in which the exhaustion program upregulates MCT11, rendering Texh cells sensitive to toxic lactic acid present at high levels in the tumor microenvironment. MCT11 represents an attractive target to edit in therapeutic T cells or block using antibodies to render exhausted T cells impervious to lactic acid, allowing for tumor eradication.

overall_design: MCT11-KO (Slc16a11fl/fl x CD4Cre) mice (3 each) were inoculated with B16 melanoma tumors. At day +14, infiltrating CD8+ exhausted T cells were sorted (PD-1hiTim3+ fraction) from tumors and subjected to bulk RNA sequencing. For analysis, publicly available RNA-seq data from wild-type C57BL/6 CD8+ exhausted T cells isolated from B16 tumors in a similar fashion were used as controls (Ford et al., Sci Immunol 2022, PMID 35930654, GSE175408): samples GSM5333036, GSM5333037, and GSM5333038.

first: Ronal

last: Peralta

first: Bingxian

last: Xie

first: Konstantinos

last: Lontos

first: Hector

last: Nieves-Rosado

first: Kellie

last: Spahr

first: Rhodes

middle: B

last: Ford

first: Kevin

last: Quann

first: Andrew

last: Frisch

first: Victoria

last: Dean

first: Mary

last: Philbin

first: Tony

last: Cillo

first: Sebastien

last: Gingras

first: Amanda

last: Poholek

first: Lawrence

last: Kane

first: Dayana

last: Rivadeneira


title: RNA-seq and ChIP-seq profiling of human iPSCs, derived NSCs and human fetal NSCs (ChIP-Seq)

first: Ingrid

last: Cifola

first: Luca

last: Petiti

first: Clelia

last: Peano

first: Annarita

last: Miccio


title: Transcription processes compete with loop extrusion to homogenize promoter and enhancer dynamics

city: Illkirch

first: Tom

last: Sexton

address: 1 rue Laurent Fries

institute: IGBMC (Institute of Genetics and Molecular and Cellular Biology)

summary: The spatiotemporal configuration of genes with distal regulatory elements is believed to be crucial for transcriptional control, but full mechanistic understanding is lacking. We combine simultaneous live tracking of pairs of genomic loci and nascent transcripts with molecular dynamics simulations to assess the Sox2 gene and its enhancer. We find that both loci exhibit more constrained mobility than control sequences due to stalled cohesin at CTCF sites. Strikingly, enhancer mobility becomes constrained on transcriptional firing, homogenizing its dynamics with the gene promoter, suggestive of their co-transcriptional sharing of a nuclear microenvironment. Furthermore, we find transcription and loop extrusion to be antagonistic processes constraining regulatory loci. These findings indicate that modulating chromatin mobility can be an additional, underestimated means for effective gene regulation.

sample_organism: Mus musculus musculus x Mus musculus castaneus

overall_design: Allele-specific 4C-seq, with the Sox2 SCR as bait, for ESC lines, in duplicate (except for days 1, 2 and 3 of differentiation, which have one replicate)

first: Angeliki

last: Platania


title: Interplay between Two Paralogous Human Silencing Hub (HuSH) Complexes in Regulating LINE-1 Element Silencing [ChIP-seq]

city: Madison

first: Peter

last: Lewis

state: Wisconsin

address: 440 Henry Mall

department: Department of Biomolecular Chemistry

institute: University of Wisconsin-Madison

summary:
The Human Silencing Hub (HuSH) complex is a complex that silences retrotransposable elements in
vertebrates. Here, we identify a second HuSH complex, designated HuSH2, which is centered around
TASOR2, a paralog of the core TASOR protein in HuSH. Our findings reveal that HuSH and HuSH2 localize to
distinct and non-overlapping genomic loci. Specifically, HuSH localizes to and represses LINE-1
retrotransposons, whereas HuSH2 targets and represses KRAB-ZNFs and interferon signaling and response
genes. We use in silico protein structure predictions to simulate MPP8 interactions with TASOR paralogs,
guiding amino acid substitutions that disrupted binding to HuSH complexes. These MPP8 transgenes and
other constructs reveal the importance of HuSH complex quantities in regulating LINE-1 activity. Furthermore,
our results suggest that dynamic changes in TASOR and TASOR2 expression enable cells to finely tune
HuSH-mediated silencing. This study offers insights into the interplay of HuSH complexes, highlighting their
vital role in retrotransposon regulation.

overall_design: Chromatin Immunoprecipitation followed by DNA-sequenscing (ChIP-seq) for MPP8 and TASOR of the Human Silencing Hub (HuSH) complex. Completed in K-562 cells HuSH knockouts by CRISPR/Cas9 or cells overexpressing TASOR or TASOR2 transgenes.

first: Zena

last: Jensvold

first: Anna

last: Christenson

first: Julia

last: Flood


title: Interplay between Two Paralogous Human Silencing Hub (HuSH) Complexes in Regulating LINE-1 Element Silencing [RNA-seq]

overall_design: Total ribo-deplete RNA sequencing to assess differentially expressed genes and transposable elements. Completeed in K-562 cells HuSH knockouts by CRISPR/Cas9 or cells overexpressing TASOR or TASOR2 transgenes in two biological replicates.


title: Interplay between Two Paralogous Human Silencing Hub (HuSH) Complexes in Regulating LINE-1 Element Silencing

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

overall_design: Refer to individual Series

middle: D

middle: E

middle: W


title: RNA-seq and ChIP-seq profiling of human iPSCs, derived NSCs and human fetal NSCs


title: PD-L1 regulates dendritic cell ferroptosis during immunogenic chemotherapy

city: Beijing

first: Haidong

last: Tang

address: Shuangqing Road

institute: Tsinghua University

summary: Dendritic cells (DCs) express high levels of PD-L1 in the tumor microenvironment. However, the physiological functions of PD-L1 on DCs remain incompletely understood. Here, we explored the roles of PD-L1 signaling in dendritic cells. PD-L1 was knocked out in DC2.4 cells and transcriptional profiles were analyzed.

overall_design: Gene expression profiling analysis of RNA-seq data for DC2.4 cells and its PD-L1-knockout derivative.


title: Molecular profiling of mouse septal neurons with single nucleus RNA-seq

first: Xiaofei

last: Yu

address: 2005 Songhu Rd

institute: Fudan University

summary: To reveal functional diversity of neurons in the septal area of the forebrain, we isolated neuron nuclei from septal tissues of wild-type mice by FACS sorting and subjected them to single nucleus (sn)RNA sequencing with the 10x platform.

overall_design: NeuN+ nuclei from the septal area of adult C57BL6/J mice were purified and subjected to snRNA-seq

first: Lei

last: Chen

first: Zheyu

last: Jin


title: Fecal microbiota in mice before and after repeated mild stress

summary: To examine potential changes of the intestinal microbiota in mice caused by repeated mild stress, we profiled bacteria and fungi in the mouse feces by sequencing the 16s v3v4 region and the ITS1-2 region.

overall_design: Mice feces were collected before and after stress. Fecal microbial DNA were extracted by using QIAamp PowerFecal Pro DNA Kit (Cat. 51804). The 16s v3v4 regions and ITS1-2 regions were amplified by PCR with barcoded primers and sequenced with 2×300 paired-end reading. Data analysis were carried out with QIIME2(v2019.7)

first: Qingqing

last: Qi


title: Pooled CRISPR screens with joint single-nucleus chromatin accessibility and transcriptome profiling

status: Public on Sep 22 2024

first: Neville

last: Sanjana

state: New York

address: 101 Avenue of the Americas

institute: New York Genome Center

summary: MultiPerturb-seq is a high-throughput CRISPR screening platform with joint single nucleus chromatin accessibility, transcriptome, and guide RNA capture. It uses combinatorial indexing combined with droplet microfluidics to scale throughput and integrate all three modalities. We apply MultiPerturb-seq to identify key genes whose loss can trigger differentiation in a rare pediatric cancer, atypical teratoid/rhabdoid tumor (AT/RT), which is driven by loss of the SWI/SNF chromatin remodeling subunit SMARCB1.

overall_design: Single nucleus ATAC-seq, RNA-seq, and CRISPR guide RNA capture for BT16 cells transduced with an epigenomic remodeler library and a 20% spike-in of NIH3T3 cells transduced with non-targeting guides.

first: Rachel

last: Yan

first: Alba

last: Corman

first: Lyla

last: Katgara

first: Xiao

last: Wang

first: Xinhe

last: Xue

first: Zoran Z

last: Gajic

first: Richard

last: Sam

first: Michael

last: Farid

first: Samuel

last: Friedman

first: Jungwook

last: Choo

first: Ivan

last: Raimondi

first: Shridar

last: Ganesan

first: Eugene

last: Katsevich

first: Jeffrey

last: Greenfield

first: Nadia

last: Dahmane


title: PD-L1 regulates dendritic cell ferroptosis during immunogenic chemotherapy [scRNA-seq]

first: Haidong

last: Tang

summary: Dendritic cells (DCs) express high levels of PD-L1 in the tumor microenvironment and draining lymph nodes. Here, we explore the roles of PD-L1 signaling during immunogenic chemotherapy. DC-conditional PD-L1 knockout mice were inoculated with MC38-OVA tumors and treated with doxorubicin. T cells were isolated from draining lymph node for single cell RNA sequencing.

overall_design: DC-conditional PD-L1 knockout mice were inoculated with MC38-OVA tumor cells. After tumor established, mice were treated with doxorubicin. Draining lymph nodes were isolated and single cell suspensions were prepared. Live T cells were sorted by flow cytometry and single cell libraries were prepared.


title: Interferon subverts an AHR-JUN axis to promote CXCL13+ T cell in lupus [Time_coure_RNAseq]

city: Chicago

first: Calvin

last: Law

state: IL

address: 303 E Superior St Lurie 5-220

department: Dermatology

institute: Northwestern University

summary: Expansion of B cell-helper T cells including T follicular helper (Tfh) and T peripheral helper (Tph) cells is a prominent feature of systemic lupus erythematosus (SLE), a prototypical autoimmune disease with broad autoantibody production. Human Tfh and Tph cells are marked by high production of the B cell chemoattractant CXCL13, yet regulation of T cell CXCL13 production and the relationship between a CXCL13+ state and other differentiated T cell states remains largely undefined. Here, we identify a dramatic imbalance in CD4 T cell phenotypes in SLE patients, with expansion of PD-1+/ICOS+ CXCL13+ T cells and reduction of CD96hi IL-22+ T cells. Using CRISPR screens, we identify the aryl hydrocarbon receptor (AHR) as a potent negative regulator of CXCL13 production by human CD4 T cells. Transcriptomic, epigenetic, and functional studies demonstrate that AHR coordinates with AP-1 family member JUN to prevent CXCL13+ Tph/Tfh cell differentiation and promote an IL-22+ phenotype. Type I interferon (IFN), a pathogenic driver of SLE, opposes AHR and JUN to promote T cell production of CXCL13. These results place CXCL13+ Tph/Tfh cells on a polarization axis opposite from Th22 cells and reveal AHR, JUN, and IFN as key regulators of these divergent T cell states.

overall_design: Primary human CD4+ memory T cells treated with TGFβ + AHR inhibitor (n=3) and TGFβ + AHR agonist (n=3) with default settings, at each time point of Time course RNAseq experiment (Ext. Data Fig 6a.).

first: Jaehyuk

last: Choi

first: Deepak

last: Rao


title: Establishment of an ulcerative colitis model using colon organoids derived from human induced pluripotent stem cells

city: Kyoto

first: Kazuo

last: Takayama

state: Kyoto

address: Shogoin Kawaharacho 53, Sakyo-ku

department: Center for iPS Cell Research and Application

country: Japan

institute: Kyoto University

summary: The etiology of inflammatory bowel disease (IBD) is complex, with much room for a greater understanding and development of improved therapies. Therefore, establishing a reliable IBD model is crucial for future advancements. In this study, human induced pluripotent stem (iPS) cell-derived colon organoids (hiPSC-COs) were treated with a combination of TNF-α, IFN-γ, and IL-1β (3 cytokines: 3CK), known to elevate in the serum of IBD patients. Inflammatory responses in stromal cells and damage to intestinal epithelial cells were observed in the 3CK-treated hiPSC-COs. Comparison of molecular signatures of 3CK-treated hiPSC-COs with those of ulcerative colitis (UC) patient’s colon revealed that 3CK-treated hiPSC-COs resemble UC patient’s colon. Furthermore, the elevated production of inflammatory cytokines observed in 3CK-treated hiPSC-COs was attenuated by treatment with tofacitinib. Our UC model will be an essential tool to understand its pathologic mechanisms and identify effective therapeutic approaches.

overall_design: CNT and 3CK treated colon organoids derived from human iPS cells, 1383D6, were dissociated using trypsin treatment and analyzed by scRNA-seq.


title: ACMSD inhibition corrects fibrosis, inflammation, and DNA damage in MASLD/MASH

first: Yasmine

last: Liu

address: Station 19 CH-1015 Lausanne

department: Laboratory of intergrative systems physiology

overall_design: The therapeutic effect of TLC-065 was evaluated in a dietary mouse model of MASLD/MASH, where treatment commenced nine weeks after initiating a Western diet feeding regimen for 14 weeks. The same part of liver were collect from each mouse, snap freezed in liquid nitrogen and stored in -80 for mRNA extraction, purification and RNAseq.

first: Masaki

last: Kimura

first: Xiaoxu

last: Li

first: Jonathan

last: Sulc

first: Sandra

last: Rodriguez Lopez

first: Qi

last: Wang

first: Angelique

last: Scantlebery

first: Keno

last: Strotjohann

first: Archana

last: Vijayakumar

first: Robert

last: Myers

first: Maroun

last: Bou-Sleiman

first: Julijana

last: Ivanisevic

first: Riekelt

last: Houtkooper

first: G

last: Subramanian

first: Johan

last: Auwerx


title: Transcriptome analysis of pancreatic cancer cells with genetically modified Ptges or Ptger4

status: Public on Sep 21 2024

city: Philadelphia

first: Il-Kyu

last: Kim

state: Pennsylvania

address: 421 Curie Blvd.

department: Department of Medicine

institute: University of Pennsylvania

summary: Tumor cell-derived prostaglandin E2 (PGE2) is a tumor cell-intrinsic factor that supports immunosuppression in the tumor microenvironment (TME) by acting on the immune cells, but the impact of PGE2 signaling in tumor cells is unclear. We demonstrate that deleting the PGE2 synthesis enzyme or disrupting autocrine PGE2 signaling through EP4 receptors on tumor cells reverses the T cell-low, myeloid cell-rich TME, activates T cells, and suppresses tumor growth. Mechanistically, Ptges and Ptger4 KO tumor cells exhibited altered T and myeloid cell attractant chemokines, became more susceptible to TNF-a killing, and exhibited reduced adenosine synthesis. Our study reveals an unexpected finding – a non-redundant role for the autocrine mPGES1-PGE2-EP4 signaling axis in pancreatic cancer cells, further nominating mPGES-1 inhibition and EP4 blockade as immune-sensitizing approaches in cancer therapy.

overall_design: This project aims to identify the immunosuppressive mechanisms of the Ptges-PGE2-Ptger4 axis in pancreatic cancer. We utilized non-T cell-inflamed pancreatic cancer cell lines and genetically modified Ptges or Ptger4 gene in these cell lines and compared gene expression profiles between control and Ptges-deficient or Ptger4-deficient cell lines in vitro and in vivo.

first: Nune

last: Markosyan

first: Ben

middle: Z

last: Stanger

last: Vonderheide


title: Transcriptomic analysis of septal brain tissues of wild-type and TCRb-/- mice

first: Xiaofei

last: Yu

summary: To study immune influence on brain functions, we performed RNA-seq with brain septal tissues from stressed wild-type and TCRb-/- mice.

overall_design: The brain septal tissues were dissected 1.5 hours post restraint stressed and RNA were purified and sequenced.

first: Lei

last: Chen

first: Zheyu

last: Jin


title: Decoding the molecular, cellular, and functional heterogeneity of zebrafish intracardiac nervous system

city: New York

first: Caghan

last: Kizil

department: Neurology & TAUB Institute

institute: Columbia University

summary: In this project, we present a comprehensive taxonomy of the intracardiac nervous system (IcNS)  utilizing single-cell RNA sequencing, anatomical studies, and electrophysiological techniques.

overall_design: For single-cell sequencing experiments, 25 Tg(elavl3:eGFP (previously known as HuC:GFP)) of 5-month-old animal were used from both sexes for the first set and 25 Tg(elavl3:eGFP) of 11-month-old, and 10 Tg(nbt:DsRed) of 22-month-old animals from both sexes were used for the second set. Cells were dissociated sorted by FACS as described (Cosacak et al. 2019). The single-cell encapsulation and cDNA synthesis done by following 10X Genomics' workflows. The reads were aligned to zebrafish genome (GRChZ 11, v 105) was used for gene annotation and assigning reads to genes. Cellranger software version 6.1.2 was used to process the data.

first: Prabesh

last: Bhattarai

first: Elanur

last: Yilmaz

first: Kostantinos

last: Ampatzis


title: Epigenetic regulation by Polycomb Repressive Complex 1 promotes Cerebral Cavernous Malformations

status: Public on Sep 20 2024

city: Potsdam

first: Salim

last: Seyfried

address: Karl-Liebknecht-Str. 24-25

country: Germany

institute: University of Potsdam

summary: Cerebral cavernous malformations (CCMs) are anomalies that develop mainly in the cerebral vasculature. They result from mutations in CCM1/KRIT1, CCM2, or CCM3/PDCD10. Loss of CCM proteins triggers a MAPK-Krüppel-like factor 2 (KLF2) signaling cascade, which induces a pathophysiological pattern of gene expression within endothelial cells. The downstream target genes that are activated by KLF2 are mostly unknown. Here we show that Chromobox Protein Homolog 7 (CBX7), component of the Polycomb Repressive Complex 1, contributes to pathophysiological KLF2 signaling during zebrafish cardiovascular development. CBX7/cbx7a mRNA is strongly upregulated in lesions of CCM patients, and in human, mouse, and zebrafish CCM-deficient endothelial cells. The silencing or pharmacological inhibition of CBX7/Cbx7a suppresses pathological CCM phenotypes in ccm2 zebrafish, CCM2-deficient HUVECs, and in a pre-clinical murine CCM3 disease model. Whole-transcriptome datasets from zebrafish cardiovascular tissues and human endothelial cells reveal that CBX7/Cbx7a plays a role in the activation of KLF2 targets including genes encoding TEK, Angiopoietin1, WNT9, and endoMT proteins. Our findings uncover an intricate interplay in the regulation of Klf2-dependent biomechanical signaling by CBX7 in CCM. This work also provides insights for therapeutic strategies in the pathogenesis of CCM.

overall_design: In this experiment, we want to compare the RNA transcripts of different genetic background of zebrafish heart (which is considerred as enriched endothelial tissue). We have pooled heart samples from 56-59 hour post fertilized hour zebrafish embryos with 3 conditions (4 groups): wildtype (wt), ccm2 mutant (ccm2), double knockout mutant (DKOwBF). We prepared 4 biological samples for each group. Each sample consisting of 15-60 heart was RNA extracted, DNase treatment using Zymo Quick-RNA Microprep Kit. RNA later was checked integrity and concentration by D1000 Agilent ScreenTape. Samples with RIN values ranged from 7.2-9.3 were further librarized with NebNext Ultra II kit, with 30 ng of RNA as starting point.

first: Van-Cuong

last: Pham

first: Claudia

last: Rödel

first: Oliver

last: Dittrich


title: Thymic stromal lymphopoietin modulates T cell response to improve cardiac repair post-myocardial infarction

city: wuhan

first: wang

last: Xuhong

address: 1277 Jiefang Avenue

institute: Huazhong University of Science and Technology Tongji Medical College Affiliated Union Hospital

summary: The inflammatory response is associated with cardiac repair and ventricular remodeling after myocardial infarction (MI). The key inflammation regulatory factor thymic stromal lymphopoietin (TSLP) plays a critical role in various diseases. However, its role in cardiac repair after MI remains uncertain. In this study, we elucidated the biological function and mechanism of action of TSLP in cardiac repair and ventricular remodeling following MI. Wild-type and TSLP receptor (TSLPR)-knockout (Crlf2-/-) mice underwent MI induction via ligation of the left descending artery. TSLP expression was upregulated in the infarcted heart, with a peak observed on day 7 post-MI. TSLP expression was enriched in the cardiomyocytes of infarcted hearts, with the highest expression observed in dendritic cells. Crlf2-/- mice exhibited significantly reduced survival and worsened cardiac function, increased interstitial fibrosis and cardiomyocyte cross-sectional area, and reduced CD31+ staining, with no change in the proportion of apoptotic cardiomyocytes within the border zone. Mechanistically, a reduction in regulatory T cells and more innate immune cells and their subsets were observed in the infarcted hearts of Crlf2-/- mice, accompanied by a systemic reduction in T cell activation and proliferation. Simultaneously, RNA sequencing analysis of the infarcted hearts revealed significant downregulation of genes in Crlf2-/- mice. Our findings indicate that TSLP plays a pivotal role in regulating T cell responses, specifically T regulatory cells, thus promoting cardiac repair, which may provide a potential novel therapeutic approach for managing heart failure after MI.

overall_design: To investigate the differential gene expression in the heart tissue of mice 7 days after myocardial infarction caused by defects in the TSLP/TSLPR signaling pathway.

first: Xuhong

last: Wang

first: Tingting

last: Tang

first: Lingfeng

last: Zha

first: Xiang

last: Cheng


title: Combinations of HDAC inhibitor and PPAR agonist induce ferroptosis of leukemic stem cell-like cells in acute myeloid leukemia

city: Xiamen, China.

first: Jie

state: -- None selected --

address: Department of Hematology, The First Afﬁliated Hospital of Xiamen University, Xiamen, China.

institute: Xiamen University, Xiamen, China.

summary: Purpose: Leukemia stem cells (LSCs) are responsible for leukemia initiation, relapse, and therapeutic resistance. Therefore, the development of novel therapeutic approaches targeting LSCs is urgently needed for patients with AML. Methods: The LSCs-like cell lines (KG-1α and Kasumi-1), CD34+ primary AML cells purified from AML patients (n=23) treated with CS055 and/or chiglitazar and were analyzed for viability, death, and colony formation assay. We performed RNA-seq, Glutamate-Release, Intracellular-GSH, Lipid-ROS, transmission-electron-microscopy, Western-Blotting assay, and confirmed ferroptosis in LSCs-like cells. The luciferase-reporter, co-immunoprecipitation, HDAC3-shRNA/HDAC3/deacetylase-deficient LSCs-like cell lines, His-pull-down, and chromatin-immunoprecipitation assays performed to clarify the molecular mechanism of CS055/chiglitazar in LSCs-like cells. We also established CDX and PDX mouse models to evaluate the therapeutic efficacy of CS055/chiglitazar against-AML in vivo. Results: We report that the histone deacetylase inhibitor CS055, in combination with peroxisome proliferator-activated receptor (PPAR) pan-agonist (chiglitazar), synergistically targets leukemia stem-like cells from leukemia cell lines and patient samples, while sparing normal hematopoietic progenitor cells. Mechanistically, chiglitazar enhances the inhibitory effect of CS055 on HDAC3 and induces ferroptosis in LSCs-like cells by down-regulating the expression of ferroptosis suppressor SLC7A11. In fact, the inhibition of HDAC3 increases H3K27AC levels in the promoter region of activating transcription factor 3 (ATF3), a transcriptional repressor of the SLC7A11 gene, and upregulates the expression of ATF3. In contrast, ATF4, a SLC7A11 activator, is suppressed by HDAC3 inhibition. Conclusions: Our findings suggest that treatment with CS055 combined with chiglitazar, will target LSCs by inducing ferroptosis and may confer an effective approach for the treatment of AML.

overall_design:
To investigate the molecular mechanism by which the combination of CS055 and chiglitazar inhibits LSC-like cells. For this purpose, RNA-seq analyses were performed in KG-1α cells treated with DMSO,  (16 μM) chiglitazar and (4 μM) CS055 for 24 hours, respectively, all cells were collected and RNA-seq was performed by Seqhealth Technology Co., Ltd., (Wuhan, China).

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the raw data is no longer available due to the expiration of the company's data retention period
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first: Hui

last: Zhou

first: Dongmei

last: Qin

first: Chendi

last: Xie

first: Shuman

last: Jia

first: Ziwei

first: Yi

last: Qiu

first: Bing

last: Xu


title: Genetic charcterization of myeloproliferative neoplasms (MPN)

city: München

first: Torsten

last: Haferlach

address: Max-Lebsche-Platz 31

institute: MLL Munich leukemia laboratory

summary: Myeloproliferative neoplasms (MPN) are a heterogeneous group of clonal disorders characterized by aberrant hematopoietic proliferation and an intrinsic risk of progression to blast phase. The WHO classification 2022 identifies chronic myeloid leukemia and the BCR::ABL1 negative MPNs polycythemia vera, primary myelofibrosis and essential thrombocythemia as individual entities. However, overlaps, borderline findings or transitions between MPN subtypes occur and incomplete clinical data often complicates diagnosis. By conducting a thorough genetic analysis, we've developed a model that relies on 12 genetic markers to accurately stratify MPN patients. The model can be simplified into a decision tree for routine use. Comparing samples at chronic and blast phase revealed, that one third of patients lost their MPN driver-gene mutation, while mutations in splicing and chromatin modifying genes were stable, indicating a shared founder clone of chronic and blast phase with different driver mutations and therefore different progressing capacities. This was further supported by gain of typical de novo AML gene mutations, accompanied by gain of complex karyotypes and RAS pathway gene mutations. Our data suggest to perform a broader genetic screening at diagnosis and also at clinical progression, as driver mutations may change and the MPN driver mutations present at diagnosis may disappear.

overall_design: We performed gene expression profiling analyses based on RNA-Seq data from bone marrow or peripheral blood to obtain further insights into molecular mechanisms and classification of MPN patients.

first: Wencke

last: Walter

first: Niroshan

last: Nadarajah

first: Stephan

last: Hutter

first: Heiko

last: Müller

first: Wolfgang

last: Kern

first: Manja

last: Meggendorfer


title: Methylation and Transcriptomic Profiling Reveals Short Term and Long Term Regulatory Responses in Polarized Macrophages.

city: Tampere

first: Dario

last: Greco

address: Arvo ylpön Katu 34

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere University


title: Astrocytes Originated from Neural Stem Cells Drive Regenerative Remodeling of Pathologic CSPGs in Spinal Cord Injury

city: Winnipeg

first: Seyed Mojtaba

last: Hosseini

state: Manitoba

address: 745 Bannatyne Ave

institute: University of Manitoba

summary: Neural degeneration is a hallmark of spinal cord injury (SCI). Multipotent neural precursor cells (NPCs) have the potential to reconstruct the damaged neuron-glia network due to their tri-lineage capacity to generate neurons, astrocytes and oligodendrocytes. However, astrogenesis is the predominant fate of resident or transplanted NPCs in the SCI milieu adding to the abundant number of residents astrocytes in the lesion. How NPC-derived astrocytes respond to the inflammatory milieu of SCI, and the mechanisms by which they contribute to the post-injury recovery processes remain largely unknown. Here, we uncover that activated NPC-derived astrocytes exhibit distinct molecular signature that is immune modulatory and foster neurogenesis, neuronal maturity and synaptogenesis. Mechanistically, NPC-derived astrocytes perform regenerative matrix remodeling by clearing the inhibitory chondroitin sulfate proteoglycans (CSPGs) from the injury milieu through LAR and PTP- receptor mediated endocytosis and production of ADAMTS1 and ADAMTS9, while most resident astrocytes are pro-inflammatory and contribute to pathologic deposition of CSPGs. These novel findings unravel critical mechanisms of NPC-mediated astrogenesis in SCI repair.

overall_design: Conditions: 1)control NPC-derived astrocytes, 2)activated NPC-derived astrocytes, 3) control primary spinal astrocytes, 4) activated parimary spinal astrocytes


title: Transcriptomic Analysis Reveals Co-Regulation by PRMT5 and WDR77 in HSC-5 Cells

status: Public on Sep 19 2024

city: Cold Spring Harbor

first: Heng

last: Liang

address: 1 BUNGTOWN RD, MILLS LAB

institute: Cold Spring Harbor Laboratory

summary: CRISPR was utilized to deplete either PRMT5 or WDR77 in HSC-5 cells. Subsequently, RNA-seq was performed to identify changes in the transcriptome following the loss of PRMT5 or WDR77 in these cells. Critically, Gene Set Enrichment Analysis (GSEA) was conducted to screen and identify a list of genes co-regulated by PRMT5 and WDR77.

overall_design: To investigate the cooperative function PRMT5/WDR77 complex in the Squamous Cell Carcinoma, we established HSC5 cell lines in which each target gene has been knocked down by sgRNA.


title: Effects of ferroptosis inhibition on lung transcriptomics in monocrotaline rats

city: Minneapolis

first: Kurt

last: Prins

state: MN

address: 2231 6th St Se

institute: University of Minnesota

summary: We determined how ferroptosis inhibition with ferrostatin-1 modulated the lung transcriptomic signature

overall_design: Monocrotaline rats were treated with either vehicle or ferrostatin-1 for 10 days. End-point analysis was performed and whole lungs were collected and RNA was extracted for analysis


title: Effects of ferroptotic endothelial cell DAMPs on pulmonary artery smooth muscle cells

summary: We evaluated

overall_design: We took spent media from pulmonary artery endothelial cells treated with vehicle or erastin to determine how ferroptotic DAMPs affected PASMC gene regulation in vitro. RNA was then extracted from each experimental group and bulk RNAsequencing was performed


title: Itaconate transporter SLC13A3 impairs tumor immunity via endowing ferroptosis resistance [RNA-Seq]

city: Ann Arbor

first: Weiping

last: Zou

state: MI

address: 109 Zina Pitcher Pl

department: Surgery

institute: University of Michigan

summary: Immune checkpoint blockade (ICB) triggers tumor ferroptosis. However, most patients are unresponsive to ICB. Tumors might evade ferroptosis in the tumor microenvironment (TME). Here, we discovered SLC13A3 is an itaconate transporter in tumor cells and endows tumor ferroptosis resistance, diminishing tumor immunity and ICB efficacy. Mechanistically, tumor cells uptake itaconate via SLC13A3 from tumor-associated macrophages (TAMs), thereby activating the NRF2-SLC7A11 pathway and escaping from immune-mediated ferroptosis. Structural modeling and molecular docking analysis identified a functional inhibitor for SLC13A3 (SLC13A3i). Deletion of ACOD1 (an essential enzyme for itaconate synthesis) in macrophages, genetic ablation of SLC13A3 in tumors, or treatment with SLC13A3i sensitized tumors to ferroptosis, curbed tumor progression, and bolstered ICB effectiveness. Thus, we identify the interplay between tumors and TAMs via the SLC13A3-itaconate-NRF2-SLC7A11 axis as a previously unknown immune ferroptosis resistant mechanism in the TME and SLC13A3 as a promising immunometabolic target and disease indication for treating SLC13A3+cancer.

overall_design: Yumm5.2 cells underwent treatment with permeable itaconate or DMSO reagent control and were cultured for 20 hours.

last: Lin

first: Kole

last: Tison

first: Yuheng

last: Du


title: Microbial Dynamics and Pulmonary Immune Responses in COVID-19 Secondary Bacterial Pneumonia

city: San Francisco

first: Charles

last: Langelier

address: HSE 401, 513 Parnassus Ave

institute: University of California San Francisco

summary: Metatranscriptomic analysis identifies a state of pathogen dominance and suppressed pulmonary immune signaling in critically ill COVID-19 patients with secondary bacterial pneumonia.

overall_design:
Comparing host gene expression and microbiome differences in COVID-19 patients with secondary bacterial pneumonia vs those without.

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Submitter states that missing raw files are due to patient privacy concerns.
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title: Transcriptomic Cell Type Specificity of Local Cortical Circuits

city: LA JOLLA

first: Edward

middle: M.

last: Callaway

address: 10010 N Torrey Pines Rd

department: SNL-C

institute: Salk Institute

summary: The complex functions of the neocortex rely on networks of interconnected excitatory and inhibitory interneurons, each of which are composed of multiple neuron types. Prior studies have established rules of local connectivity between major subclasses of inhibitory and excitatory cortical neurons, but the advent of single-cell transcriptomic technologies has revealed a remarkable diversity in transcriptomic neuronal subtypes. Is there specificity of synaptic connections between cortical neurons classified at the level of transcriptomic subtypes, as might be expected if the different types mediate different functions? Here we present a novel method that links transcriptomic cell type to anatomical connectivity, “Single Transcriptome Assisted Rabies Tracing” (START). START combines monosynaptic rabies tracing and single-nuclei RNA sequencing (snRNA-seq) to identify the transcriptomic cell types providing monosynaptic inputs to defined populations of neurons. We employed START in conjunction with Cre driver mouse lines to transcriptomically characterize 35,717 neurons providing monosynaptic input to 5 different layer-specific excitatory cortical neuron populations in mouse V1. At the subclass level, we observed results consistent with findings from prior studies that resolve neuronal subclasses using antibody staining, Cre-expressing mouse lines, or morphological characterization. With improved neuronal subtype granularity achieved with START, we demonstrate transcriptomic subtype specificity of inhibitory inputs to various subclasses of excitatory neurons. These results establish local connectivity rules at the resolution of transcriptomic inhibitory cell types.

overall_design: Nuclei were collected from V1 of Cre-dependent mouse lines (Sepw1-Cre, Scnn1a-Cre, Tlx3-Cre, Npr3-Cre, and Ntsr1-Cre; n=4 per mouse for all lines except Npr3-Cre where n=5) following monosynaptic rabies tracing. V1 containing mCherry+ rabies-labeled nuclei was dissected and single-nucleus suspensions were prepared from dissected tissue for fluorescence-activated nuclei sorting (FANS) to collect mCherry+ nuclei. snRNA-seq of FANS sorted rabies-infected nuclei was performed using the 10X Genomics 3’ Kit v3.1.

first: Maribel

last: Patiño


title: Type II topoisomerases shape multi-scale 3D chromatin folding in regions of positive supercoils (HiC).

city: Mainz

first: Sergi

last: Sayols

address: Ackermannweg 4

institute: Institute of Molecular Biology, Mainz

summary: Type II topoisomerases (TOP2s) resolve torsional stress accumulated during various cellular processes and are enriched at chromatin loop anchors and TAD boundaries, where, when trapped, can lead to genomic instability promoting the formation of oncogenic fusions. Whether TOP2s relieve topological constraints at these positions and/or participate in 3D chromosome folding, remains unclear. Here, we combine 3D genomics, imaging and GapRUN, a method for the genome-wide profiling of positive supercoiling, to assess the role of TOP2s in shaping chromosome organization in human cells. Acute TOP2 depletion led to the emergence of new, large-scale contacts at the boundaries between active, positively supercoiled and lamina-associated domains. TOP2-dependent changes at the higher-order chromatin folding were accompanied by remodeling of chromatin-nuclear lamina interactions and of gene expression, while at the chromatin loop level, TOP2 depletion predominantly remodeled transcriptionally-anchored, positively supercoiled loops. We propose that TOP2s act as a fine-regulator of chromosome folding at multiple scales.

overall_design: Unsynchronised cells. We used colorectal carcinoma HCT116 cells in which the two endogenous TOP2A alleles were tagged with the mini auxin-inducible degron protein domain (mAID) allowing elimination of up to 95% of endogenous TOP2A after addition of auxin. We used this TOP2A-degron line to also generate a TOP2B knockout using CRISPR/Cas9 deletion, and thus be able to acutely degrade TOP2A in the presence or absence of TOP2B. 6 hours of auxin treatment sufficed for the  quantitative depletion of TOP2A protein. Cells in G1/G2. we arrested WT and TOP2DKO cells in the G1 or G2 stage of the cell cycle using a CDK4/6 (palbociclib) and CDK1 (RO3306) inhibitor, respectively, and degraded TOP2A via auxin treatment in arrested cells. 8 hours of auxin treatment sufficed for the  quantitative depletion of TOP2A protein.

first: Maria

last: Stefanova

first: Uira

last: Souto Melo

first: Vassilis

last: Roukos

first: Stefan

last: Mundlos


title: Itaconate transporter SLC13A3 impairs tumor immunity via endowing ferroptosis resistance

overall_design: Samples were fixed and dissociated using the Miltenyi Octo MACS according to 10X Demonstrated Protocol #CG000553. Dissociated cells were counted on Luna Fx7 (Logos Biosystems). Probes were hybridized, and samples were pooled and processed according to manufacturer instructions for 10X Genomics Chromium Fixed RNA Profiling Reagent Kits for Multiplexed Samples (PN 1000568). Final library quality was assessed using the Lab Chip GXII HT (PerkinElmer), and libraries were quantified by Qubit (Thermo Fisher). Pooled libraries were subjected to paired-end sequencing according to the manufacturer’s protocol (Illumina Nova-Seq X Plus). BCL Convert Software (Illumina) was used to generate de-multiplexed Fastq files, and the Cell Ranger Pipeline (10X Genomics) was used to align reads and generate count matrices.


title: ZmICE1a regulates the defence–storage trade-off in maize endosperm [RNA-seq]

city: Bei Jing

first: Wang

last: Qun

address: West Campus, China Agricultural University, 2 Yuanmingyuan West Road, Haidian District, Beijing

institute: China Agricultural University

summary: The endosperm of cereal grains feeds the entire world as major food supply, however little is known for its defense responses during endosperm development. Inducer of CBF Expression 1 (ICE1) is a known regulator of cold tolerance in plants. ICE1 has a monocot-specific homologue that is preferentially expressed in cereal grains but with an unclear regulatory function. Here, we characterized the function of monocot-specific ZmICE1 (ZmICE1a) in maize (Zea mays) kernel. mRNA in situ hybridization (ISH) revealed that ZmICE1a is predominantly expressed in the peripheral endosperm (AL, SAL, and BETL). Loss-of-function of ZmICE1a reduced starch content and kernel weight. RNA-seq analysis revealed contradicted expression patterns between starch synthesis genes and genes involved in defense and phytohormone synthesis in zmice1a developing endosperm. Coupled with CUT&Tag-seq analysis, we found that ZmICE1a positively regulates genes in starch synthesis, while negatively regulates genes in AL-specific defense and the synthesis of IAA and JA. Explant assays revealed that exogenous IAA or JA induces the expression of numerous defense genes. mRNA ISH assays revealed that the defense genes induced by IAA and JA, exhibit distinct spatial specific expression in BETL and SAL, respectively. Moreover, we dissected a JA-ZmJAZ9-ZmICE1a-MPI signaling axis involved in JA-mediated defense regulation. Overall, our study revealed ZmICE1a as a key regulatory for endosperm defense responses, and coordinates defense-storage tradeoffs during endosperm development.

overall_design: Identification of ZmICE1a regulatory functions using RNA-seq and CUT&Tag-seq during maize endosperm development


title: Type II topoisomerases shape multi-scale 3D chromatin folding in regions of positive supercoils (GapRUN).

overall_design: MutGapR-GFP and GapRWT-GFP in asynchronous HCT116 cells were harvested for CUT&RUN for GFP using the CUT&RUN Assay Kit (Cell signaling #86652).

first: Gabriel

last: Mello da Cunha Longo


title: Changes to the global transcriptome in human U2OS and BJ cell lines as a result of STING activation

city: Pittsburgh

first: Jay Xiaojun

last: Tan

address: Bridgeside Point 1, 4th Floor, 100 Technology Drive

institute: Aging Institute, University of Pittsburgh

summary: Activation of Stimulator of interferon genes (STING) is well known to upregulate inflammation through canonical TBK1 signaling. STING is recently found to activate noncanonical functions through its transmembrane proton channel. Whether STING stimulates any transcription programs through its channel is unknown. In this study, we identified the transcription factor EB (TFEB) as a downstream effector of the STING channel. TFEB is a transcriptional regulator of lysosomal biogenesis and autophagy. Using RNA sequencing approaches, we confirmed that STING activated transcriptional upregulation of lysosomal biogenesis and autophagy independently of TBK1.

overall_design: Two sets of experiments were performed. First, U2OS cells stably expressing mouse STING1-350, which cannot activate TBK1, were treated with or without DMXAA for 8 hours, and the total RNAs were isolated for sequencing. Second, BJ WT and STING-KO cells were treated with digitonin buffer with or without 1 uM cGAMP, and the total RNAs were isolated for sequencing.

first: Lyu

last: Bo

first: Dion

last: Will

first: Tan

last: Xiaojun


title: ZmICE1a regulates the defence–storage trade-off in maize endosperm [CUT&Tag]


title: Type II topoisomerases shape multi-scale 3D chromatin folding in regions of positive supercoils (Ttchem-seq).

overall_design: We used colorectal carcinoma HCT116 cells in which the two endogenous TOP2A alleles were tagged with the mini auxin-inducible degron protein domain (mAID) allowing elimination of up to 95% of endogenous TOP2A after addition of auxin. We used this TOP2A-degron line to also generate a TOP2B knockout using CRISPR/Cas9 deletion, and thus be able to acutely degrade TOP2A in the presence or absence of TOP2B. 8 hours of auxin treatment sufficed for the  quantitative depletion of TOP2A protein. Cells were synchronized in G1, TOP2A and/or TOP2B were perturbed and we pulsed cells with 4sU for TTChem-seq library preparation.


title: Type II topoisomerases shape multi-scale 3D chromatin folding in regions of positive supercoils

overall_design: Refer to individual Series


title: Type II topoisomerases shape multi-scale 3D chromatin folding in regions of positive supercoils (LaminB1 CnR).

overall_design: We used colorectal carcinoma HCT116 cells in which the two endogenous TOP2A alleles were tagged with the mini auxin-inducible degron protein domain (mAID) allowing elimination of up to 95% of endogenous TOP2A after addition of auxin. We used this TOP2A-degron line to also generate a TOP2B knockout using CRISPR/Cas9 deletion, and thus be able to acutely degrade TOP2A in the presence or absence of TOP2B. 8 hours of auxin treatment sufficed for the  quantitative depletion of TOP2A protein. Cells were synchronized in G1, TOP2A and/or TOP2B were perturbed and we proceeded with CUT&RUN for LaminB1..


title: ROSALIND protects the mitochondrial translational machinery from oxidative damage

city: Leuven

first: Eleonora

last: Leucci

address: Herestraat 49, bus 818 room 06.423

department: Oncology

country: Belgium

institute: KU Leuven

summary: Cancer therapy resistance, whether it is pre-existing, emerges after acquiring de novo mutations, or occurs through non-genetic adaptationwhether pre-existing or arising following the acquisition of de novo mutations and via non-genetic adaptation , is stillremains a clinical challenge. Multiple anticancer drugs are thought to cause cell death via increasing mitochondrial ROS which are a bioproduct of oxidative phosphorylation. However, when properly titrated, ROS can also promote cancer cell adaptation. In keeping line with this, upregulation of mitochondrial respiration coupled to high ROS-scavenging capacity is a characteristic shared by drug-tolerant cells in several cancers. Translational fidelity in the mitochondria and in the cytosol is essential for cell fitness and thus oxidative damage to the ribosomes should be prevented at all costs. While mechanisms for recognizing and repairing such damage exist in the cytoplasm, the status within mitochondria remains unclear.  By performing ascorbate peroxidase (APEX)-proximity ligation assay directed to the mitochondrial matrix followed by isolation and sequencing of RNA associated to mitochondrial proteins, we identified  the nuclear encoded lncRNA ROSALIND as a interacting partner of ribosomes. ROSALIND is upregulated in recurrent tumours and its expression can discriminate between responders and non-responders to immune checkpoint blockade in a melanoma cohort of patients. Featuring an unusually high G content, ROSALIND serves as a substrate for oxidation. Consequently, inhibiting ROSALIND leads to an increase in ROS and protein oxidation, resulting in severe mitochondrial respiration defects. This, in turn, impairs melanoma cell viability and immunogenicity both in vitro and ex vivo in preclinical humanized cancer models. These findings underscore the role of ROSALIND as a novel ROS buffering system, safeguarding mitochondrial translation from oxidative stress, and shed light on potential therapeutic strategies for overcoming cancer therapy resistance.

overall_design: Analysis of the RNA retrieved in the matrix upon block of mitochondrial translation as assessed by APEX-Seq


title: Type II topoisomerases shape multi-scale 3D chromatin folding in regions of positive supercoils (microC).

overall_design: We used colorectal carcinoma HCT116 cells in which the two endogenous TOP2A alleles were tagged with the mini auxin-inducible degron protein domain (mAID) allowing elimination of up to 95% of endogenous TOP2A after addition of auxin. We used this TOP2A-degron line to also generate a TOP2B knockout using CRISPR/Cas9 deletion, and thus be able to acutely degrade TOP2A in the presence or absence of TOP2B. 6 hours of auxin treatment sufficed for the  quantitative depletion of TOP2A protein. Cells in G1/G2. we arrested WT and TOP2DKO cells in the G1 or G2 stage of the cell cycle using a CDK4/6 (palbociclib) and CDK1 (RO3306) inhibitor, respectively, and degraded TOP2A via auxin treatment in arrested cells. 8 hours of auxin treatment sufficed for the  quantitative depletion of TOP2A protein.


title: Tbx1 haploinsufficiency induces bone-to-cerebellar deformity in 22q11.2 deletion syndrome

city: Memphis

first: Paul

middle: A.

last: Northcott

address: 262 Danny Thomas Place

department: Developmental Neurobiology

institute: St. Jude Children's Research Hospital

summary: 22q11.2 deletion syndrome (22q11DS) substantially increases the risk of cognitive decline and psychiatric disease. However, neuroanatomic changes in 22q11DS are of a subtle-to-moderate degree and their connection to brain function is not clear. Here we report a severe (~70%) and specific reduction (dysplasia) of two cerebellar lobules, paraflocculus and flocculus (PF/F) and associated deficits in vestibulo-ocular reflex (VOR) in mouse models of 22q11DS (22q11DS mice). A specific but less severe PF/F dysplasia was confirmed in humans with 22q11DS. Tbx1 haploinsufficiency recapitulated the PF/F and VOR deficits in 22q11DS mice. The 22q11DS-associated PF/F dysplasia was not due to altered neural composition or neurogenesis. Rather, a part of temporal bone called subarcuate fossa (SF), which encapsulates the PF/F, and semicircular canals of the inner ear, which connects to the SF were malformed in 22q11DS and Tbx1-deficientmice. Our single-nuclei RNA Sequencing and immunohistochemistry data revealed that Tbx1 haploinsufficiency caused precocious differentiation of chondrocyte to osteoblasts in the petrous bone, but no changes in cell type compositions in the PF/F. These data suggest a novel structure-function pathogenic interrelationship in 22q11DS, where Tbx1 haploinsufficiency causes a skeletal deformity occluding cerebellar development and resulting in motor learning deficiency.

overall_design: Transcriptome profiling by snRNA-seq in the developing petrous bone and paraflocculus/flocculus from the wild type and Tbx1+/- mouse at P5.5. The study included five mice in each group, with two replicates per group

first: Tae-Yeon

last: EOM

first: Stanislav

last: Zakharenko

first: Yiran

last: Li


title: Single-cell transcriptome analysis of the early immune response in the lymph nodes of Borrelia burgdorferi-infected mice

city: Turku

first: Varpu

last: Rinne

address: Kiinamyllynkatu 10, 20520

department: Institute of Biomedicine

institute: University of Turku

summary: Lyme borreliosis is a disease caused by Borrelia burgdorferi sensu lato bacteria. Borrelia burgdorferi is known to induce prolonged extrafollicular immune responses and abnormal germinal center formation. However, the mechanism behind this is poorly understood. The extrafollicular response is characterized by strong plasmablast induction and by an IgM, IgG3, and IgG2b dominant antibody production. These antibodies do not generate a neutralizing type of immunity, and the bacteria eventually establish a persistent infection. Here, we performed single-cell RNA sequencing to characterize the immune landscape of lymph node lymphocytes in the early Borrelia burgdorferi infection in a murine model.

overall_design: Four female mice (C3H/HeN, aged 4 weeks) were infected by administering 20 µl of the B. burgdorferi suspension (106bacteria/injection) subcutaneously into the hind-leg footpad. As a vehicle control, PBS (20 µl) was injected similarly into the other four mice. After four days, mice were sacrificed, and popliteal lymph nodes (draining lymph nodes for the hind leg) were harvested. Lymph nodes from infected mice were pooled into one sample and lymph nodes from control mice were pooled into another sample for lymphocyte isolation. Extracted lymphocytes were processed with the Chromium platform (10X Genomics) for library preparation, and the barcoded scRNA-seq libraries were constructed using 10XGenomics Chromium Next GEM Single Cell 3', Reagent Kit v3.1. Prepared libraries were sequenced using the Illumina Novaseq6000 Sequencing System.

first: Jukka

last: Hytönen

last: Alinikula

first: Annukka

last: Pietikäinen

first: Kirsi

last: Gröndahl-Yli-Hannuksela

first: Marko

last: Salmi

first: Pia

last: Rantakari

first: Ruth

last: Fair-Mäkelä

first: Tapio

last: Lönnberg


title: Distal chromosome 6q harbors a haploinsufficient tumor suppressor gene that regulates PI3K signaling in glioblastoma

city: Bethesda

first: Nicholas

middle: Klose

last: Nuechterlein

state: MD

address: 9000 Rockville Pike

institute: NIH

summary: Glioblastoma is a universally fatal disease characterized by remarkable molecular heterogeneity. Prognostic biomarkers in glioblastoma have implications for patient management and drug development but are currently limited. In this study, we analyzed exome-wide human glioblastoma somatic copy number alteration data and discovered cytoband 6q27 as an independent poor prognostic marker across multiple glioblastoma datasets. We then combined CRISPR-Cas9 data, human spatial transcriptomic data, and human and mouse RNA sequencing data to nominate PDE10A as a potential haploinsufficient tumor suppressor in the 6q27 region. Mouse glioblastoma modeling using the RCAS/tv-a system confirmed that Pde10a suppression induced an aggressive glioma phenotype in vivo. Cell culture analysis showed that decreased Pde10a expression led to increased Pi3k/Akt signaling, a response blocked by selective Pi3k inhibitors. Single nucleus RNA sequencing from our mouse gliomas in vivo, in combination with cell culture validation showed that Pde10a suppression was associated with a proneural to a mesenchymal transition that exhibited increased cell adhesion and decreased cell migration. PDE10A loss was associated with unmethylated MGMT promoter status in human glioblastoma and resistance to temozolomide and radiation therapy in vitro. Our results indicate that patients with glioblastoma harboring PDE10A loss have worse outcomes, increased resistance to standard-of-care therapy, and potentially increased sensitivity to PI3K inhibition.

overall_design: We targeted Pde10a with shRNAs in mouse neural stem cells deficient in Cdkn2a

first: Patrick

last: Cimino


title: RNA-Seq to decipher breast cancer-adipocytes reciprocal reprogramming: evaluating the impact of glucose

city: Maastricht

first: Michiel

last: Adriaens

address: Universiteitssingel 60

department: Maastricht Centre for Systems Biology - MaCSBio

country: Netherlands

institute: Maastricht University

summary: The tumor microenvironment, including adipocytes, is a critical element for breast cancer (BC) progression, also responding to metabolic stimuli characterizing obesity and/or diabetes. The reciprocal reprogramming established between BC cells and adipocytes remains to be deciphered. We investigated (i) the effect  of mammary adipocytes on BC cells and vice versa,  (ii) the impact  of glucose on BC cells, adipocytes and (iii) the impact of glucose on their cross-talk. We have identified adipocyte-modulated genes in BC cells and BC cell-modulated genes in adipocytes, dependently and independently of glucose levels. We identified the adipogenesis process as the most relevantly differentially regulated pathway both in cancer cells and in adipocytes upon exposure to high glucose concentration. Specifically, we observed that BC cells promote de-differentiation of adipocytes and re-shaping toward a fibroblast-like phenotype, particularly upon glucose lowering; the de-lipidation of adipocytes is paralleled by induction of adipogenesis genes in BC cells.

overall_design: To this end, we used a co-culture system in which mammary adipocytes and MCF7 BC cells were separated by an insert to allow the diffusion of soluble factors. Through RNA-Sequencing, the transcriptome of both cell types was determined, in co-cultures as well as a mono-cultures, while exposed to glucose concentrations resembling hyperglycemia or normoglycemia in humans.  We obtained evidence that adipocytes and BC cells reciprocally modify their transcriptome.

first: Maria

last: Ambrosio

first: Pietro

last: Formisano


title: Genetic Recording of Transient Endothelial Activation in Distinct Alveolar Capillary Cells during Pulmonary Fibrosis

status: Public on Sep 18 2024

city: Shanghai

first: Hongxin

address: Yueyang Road 320

department: Shanghai Institute of Biochemistry and Cell Biology

institute: University of Chinese Academy of Sciences

summary: Endothelial to mesenchymal transition (EndoMT) is essential for embryonic development. However, the contribution of ECs to fibroblasts through EndoMT remains highly controversial in adult pathological conditions. Here, our dual-recombinase genetic system precisely captured extensive mesenchymal gene activation events of alveolar capillary cells in chronic TAC-induced pulmonary hypertension and fibrosis. Moreover, this type of endothelial activation was specifically observed in Plvap+ gCap, but not CAR4+ aCap capillary cells. In addition, our genetic tool confirmed the contribution of resident fibroblasts to pulmonary fibrosis. Unraveling the process of endothelial activation provides novel insights into potential therapeutic strategies targeting heart failure-induced pulmonary fibrosis.

overall_design: In this study, we employed a dual-genetic approach to capture aSMA activation in pulmonary endothelial cells during transverse aortic constriction (TAC)-induced pulmonary fibrosis in mice. Endothelial cells (ECs) were labeled as ZsGreen+ and once aSMA activation occurred, even transiently, the cell was labeled as tdTomato+. To investigate the significance of aSMA activation in ECs, we compared the gene expression patterns of ZsGreen+ ECs and tdTomato+ ECs using bulk RNA-seq.

first: Shaohua

last: Zhang


title: Transcriptome data of HepaRG differentiation, de-differentiation, and re-differetiation.

city: Funabashi

first: Shinpei

last: Yamaguchi

state: Chiba

address: Miyama 2-2-1

department: Faculty of Science

institute: Toho University

summary: Primary hepatocytes are widely utilized for investigating drug efficacy and toxicity, yet variations between batches and limited proliferation capacity present significant challenges. HepaRG cells are versatile cells, capable of maintaining an undifferentiated state and differentiating through dimethyl sulfoxide treatment, allowing for molecular analysis of hepatocyte plasticity. To elucidate the underlying molecular mechanisms of HepaRG cell plasticity, we used CYP3A4G/7R HepaRG cells engineered to express DsRed under the control of the fetus-specific CYP3A7 gene and EGFP under the adult-specific CYP3A4 gene promoter. In time-lapse imaging of CYP3A4G/7R HepaRG cells, we observed CYP3A7-DsRed expression transitioning from negative to positive during proliferation period and CYP3A4-GFP expression activating during differentiation. The de-differentiation potency of differentiated CYP3A4G/7R HepaRG cells was assessed using inhibitors and cytokines. It was found that Y-27632 (Y), A-83-01 (A), and CHIR99021 (C) (collectively referred to as YAC), which are known to promote liver regeneration in mice, did not induce CYP3A7-DsRed expression. Instead, these inhibitors increased CYP3A4-GFP expressing population. Furthermore, CHIR99021 alone increased CYP3A4-GFP-positive cells, while Wnt3a treatment increased CYP3A7-DsRed-positive cells, suggesting that Wnt signaling plays distinct roles in HepaRG cells. It was apparent that de-differentiated cells had increased CYP3A4 activity after a second round of differentiation, compared to differentiated cells after the first round. Transcriptomic analysis of HepaRG cells revealed distinct profiles between proliferative, differentiated, and de-differentiated states, highlighting their robust plasticity. Notably, hepatoblastic cells de-differentiated by YAC or C displayed transcriptome patterns similar to undifferentiated cells, whereas CYP3A7-DsRed and CYP3A4-GFP exhibited expression patterns different from those of undifferentiated cells. These findings underscore the dynamic nature of HepaRG cells while cautioning against solely relying on CYP3 family gene expression as a marker of differentiation.

overall_design: This experimental design investigates the behavior of HepaRG cells under different culture conditions. Proliferating HepaRG cells are cultured in HepaRG medium for varying durations, with some transferred to small hepatocyte medium or treated with YAC. De-differentiated HepaRG cells are examined after differentiation by DMSO, followed by treatment with YAC, Y-27632, or A-83-01. Differentiated and re-differentiated CYP3A4G7R-HepaRG cells are also studied under various conditions, including treatments with DMSO, A-83-01, and Wnt3a. This setup provides a comprehensive analysis of the effects of different treatments and conditions on HepaRG cell differentiation and behavior.


title: Exposure to the antiretroviral drug dolutegravir impairs structure and neurogenesis in a forebrain organoid model of human embryonic cortical development

city: Philadelphia

first: Yijing

last: Su

address: Levy 326

department: Department of Oral Medicine

institute: University of Pennsylvania

summary: For many therapeutic drugs, including antiretroviral drugs used to treat people living with HIV-1 (PLWH), we have little data on the potential effects on the developing human brain due to limited access to tissue and historical constraints on the inclusion of pregnant populations in clinical trials. Human induced pluripotent stem cells (iPSCs) offer a new avenue to gain insight on how drugs may impact human cell types representative of the developing central nervous system. To prevent vertical transmission of HIV and promote the health of pregnant PLWH, antiretroviral therapy must be initiated and/or maintained throughout pregnancy. However, many antiretroviral drugs are approved for widespread use following clinical testing only in non-pregnant populations and there may be limited information on potential teratogenicity until pregnancy outcomes are evaluated.  The integrase strand transfer inhibitor dolutegravir (DTG) is a frontline antiretroviral drug that is effective in viral suppression of HIV but was previously reported to be associated with a slight increase in the risk for neural tube defects in one study, although this has not been replicated in other cohorts. To directly investigate the potential impact of DTG on human cortical neurogenesis, we measured the effects of daily drug exposure on the early stages of corticogenesis in a human iPSC-based forebrain organoid model. We observed deficits in organoid structure and impaired neurogenesis in DTG-treated organoids compared to vehicle-treated control organoids after 20 or 40 days in culture. Our highest dose of DTG (10µM) resulted in significantly smaller organoids with a reduced density of neural rosette structures compared to vehicle-treated controls. Mechanistically, RNA-sequencing and immunohistological analysis suggests dysregulated amino acid transport and activation of the integrated stress response in the DTG-treated organoids, and functionally, a small molecule integrated stress response inhibitor (ISRIB) could partially rescue increased expression of proteins related to cell cycle regulation. Together, these results illustrate the potential for human iPSC-based strategies to reveal biological processes during neurogenesis that may be affected by therapeutic drugs and provide complementary data in relevant human cell types to augment preclinical investigations of drug safety during pregnancy.

overall_design: To investigate the cellular processes that could be driving the reduction in size and rosette formation in the organoids, we performed bulk RNA-seq in the C1-2 iPSC line to identify differentially expressed genes following exposure to the highest dose of DTG.

first: Kimberly

last: Christian

first: Daniel


title: STAG2 loss in Ewing sarcoma alters enhancer-promoter contacts dependent and independent of EWS::FLI1

city: Madrid

last: Gimenez

address: Calle de Melchor Fernández Almagro, 3

country: Spain

institute: CNIO

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


title: CFTR Represses a PDX1 Axis to Govern Pancreatic Ductal Cell Fate [Bulk ATAC-seq]

city: Aurora

first: Kristen

last: Wells

state: CO

address: 1775 Aurora Ct,

department: Barbara Davis Center

institute: University of Colorado Anschutz

summary: Inflammation, acinar cell destruction, and ductal cell hyperplasia drive pancreatic remodeling in newborns with cystic fibrosis (CF) lacking a functional CFTR channel. In neonatal CF ferrets, these changes are associated with a transient phase of glucose intolerance that involves islet destruction and subsequent regeneration near hyperplastic ducts. Little is known about the phenotypic changes in CF ductal epithelium and its potential impact on islet function. Using bulk RNA-seq, scRNA-seq, and ATAC-seq on CF ferret models, we demonstrate that ductal CFTR protein constrains PDX1 expression by maintaining PTEN and GSK3b activation. In the absence of CFTR protein, centroacinar cells (or terminal ductal cells) adopted a bi-potent progenitor-like state associated with enhanced WNT/b-Catenin, TGFb and AKT signaling. Notably, using in vitro and in vivo hypomorphic models of mutant CFTR expression, we show that the level of CFTR protein, not its channel function, regulates PDX1 expression. Thus, this study has discovered a cell-autonomous CFTR-dependent mechanism by which CFTR mutations that produced little to no protein could impact pancreatic exocrine/endocrine remodeling in people with CF.

overall_design: Bulk ATAC-seq on differentiated WT and CF ferret PDE cultures grown at ALI

middle: L

first: Pavana

last: Rotti

first: John

last: Englehardt


title: CFTR Represses a PDX1 Axis to Govern Pancreatic Ductal Cell Fate [Bulk RNA-seq]

overall_design: RNA-seq on differentiated WT and CF ferret PDE cultures grown.


title: A SIRT7-dependent acetylation switch regulates early B-cell differentiation and lineage commitment through Pax5

city: Badalona

first: Alejandro

last: Vaquero

state: Barcelona

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

institute: Josep Carreras Leukemia Research Institute

summary: B lymphopoiesis is a key developmental event orchestrated by a complex combinatorial action of lineage-specific transcription factors. In early B cell progenitors, lineage commitment is directly mediated by the master regulator Pax5, whose deficiency is commonly associated with B cell Acute Lymphoblastic Leukemia (B-ALL). Despite its essential role in mammalian immunity, the regulatory mechanisms that control Pax5 function remain largely unknown. Here we show that NAD+-dependent enzyme SIRT7 coordinates B cell development progression through regulation of Pax5 function. We have identified a SIRT7-dependent regulatory switch based on dynamic deacetylation of a single Pax5 residue, which controls its activity and thereby B cell fate. While a PAX5K198 acetylated mimic is incapable of inducing both B cell development and identity due to reduced protein stability and impaired binding to chromatin, deacetylation of this residue boosts Pax5 activity, leading to massive gene repression and restoration of B cell commitment but not differentiation in vivo. These findings suggest an unexpected uncoupling of hematopoietic differentiation and lineage commitment. Further supporting the functional relevance of the SIRT7-PAX5 axis, the interplay between both factors is largely conserved in human B-ALL, where high SIRT7 expression is an independent good prognostic factor. Our findings unveil a crucial mechanism in the regulation of B-cell production based on the control of Pax5 function and underscore the key role of Sirtuins in the regulation of the immune system.

overall_design: Primary pro-B cells from Wt, Sirt7-/- or Pax5-/- mice were cultivated and transduced with transduction vectors expressing SIRT7Wt, SIRT7H187Y, PAX5Wt, PAX5K198Q or PAX5K198R and subjected to RNA expression profiling (RNA-Seq) and genome binding profiling (ChIP-Seq) by high-troughput sequencing.

first: Andres

last: Gamez-Garcia

first: Berta

middle: N

last: Vazquez

first: Alberto

last: Bueno-Costa

first: Joshua

last: Thackray


title: CFTR Represses a PDX1 Axis to Govern Pancreatic Ductal Cell Fate [scRNA-seq]

overall_design: Single cell RNA-seq on differentiated WT and CF ferret PDE cultures grown at ALI for 2, 5, 7, and 9 days

middle: F


title: Circumventing Resistance within the Ewing Sarcoma Microenvironment by Anti-MCAM Chimeric Antigen Receptor Modified Ex-vivo Expanded Natural Killer Cells Combinatorial Therapy

city: Columbus

first: Katherine

last: Miller

state: OH

address: 700 Children's Dr.

department: Institute for Genomic Medicine

institute: Nationwide Children's Hospital

summary: Pediatric patients with recurrent metastatic Ewing sarcoma (ES) have a dismal 5-year survival of < 30% largely secondary to treatment resistance in the tumor microenvironment (TME). Novel therapeutic approaches are desperately needed and represent an unmet need. Here, we developed a chimeric antigen receptor (CAR) expressing natural killer (NK) cell targeting melanoma cell adhesion molecule (MCAM) by electroporation of CAR mRNA into ex-vivo expanded NK cells. Expression of anti-MCAM CAR significantly and specifically enhanced NK cytotoxic activity compared to mock NK cells against MCAMhigh ES cells in vitro, and significantly reduced lung metastasis and extended animal survival in an orthotopic xenograft mouse model of ES. However, anti-MCAM CAR NK cells had minimal effects on decreasing primary tumor growth in vivo. We performed transcriptome profiling in patient-derived xenografts to identify the underlying mechanisms of NK cell resistance in ES TME.

overall_design: Luciferase expressing patient-derived ES A673 cells were orthotopically injected into NSG mice. When the tumors reach the size of 0.5 cm, PBS or ex vivo expanded NK cells were injected via tail vein. Tumors were harvested 24 hr after NK injection and dissected into peripheral and central tumor sections. Total RNA was extracted separately from the NK treated (T) or untreated (U) peripheral (P) or central (C) tumor sections and subjected to bulk RNA-Seq on NovaSeq 6000.

first: Wen

last: Luo

first: Mitchell

last: Cairo


title: Borrowing Transcriptional Kinases to Activate Apoptosis [RNA-seq]

city: Stanford

first: Sai

last: Gourisankar

state: CA

address: 240 Pasteur Dr, Rm 4700

department: Chemical Systems Biology

institute: Stanford

summary: Protein kinases are disease drivers whose therapeutic targeting traditionally centers on inhibition of enzymatic activity. Here chemically induced proximity is leveraged to convert kinase inhibitors into context-specific activators of therapeutic genes. Bivalent molecules that link ligands of the transcription factor B-cell lymphoma 6 (BCL6) to ATP-competitive inhibitors of cyclin-dependent kinases (CDKs) are developed to re-localize CDK to BCL6-bound loci on chromatin and direct phosphorylation of Pol II. The resulting BCL6-target proapoptotic gene expression translates into killing of diffuse large B-cell lymphoma (DLBCL) cells at 72h with EC50s of 0.9 – 10nM and specific ablation of the BCL6-dependent germinal center response in mice. The molecules exhibit 10,000-fold lower cytotoxicity in normal lymphocytes and are well tolerated in mice. Genomic and proteomic evidence corroborate a gain-of-function mechanism where, instead of global enzyme inhibition, a fraction of total kinase activity is borrowed and re-localized to BCL6-bound loci. The strategy demonstrates how kinase inhibitors can be used to context-specifically activate transcription, accessing new therapeutic space.

overall_design: SUDHL5 cells were plated at 1M/mL and treated with DMSO or CDK-TCIP1 at indicated concentrations at final 0.1% DMSO concentrations.

first: R

middle: C

last: Sarott

first: B

last: Karim

first: S

last: Nettles

first: H

last: Yang

last: Dwyer

first: J

middle: M

last: Simanauskaite

last: Tse

last: Abuzaid

first: A

last: Krokhotin

first: T

last: Hinshaw

first: M

last: Green

first: G

last: Crabtree

first: N

middle: S

last: Gray


title: Lysosomal integrity suppresses TIR-1/SARM1 aggregation to restrain toxic propagation of p38 innate immunity

city: Worcester

first: Read

last: Pukkila-Worley

state: MA

address: 364 Plantation Street

department: Medicine

institute: University of Massachusetts Medical School

summary: Innate immunity in bacteria, plants and animals requires the specialized subset of TIR-domain proteins that are NAD+ hydrolases. Aggregation of these TIR proteins engages their enzymatic activity, but it is not known how this protein multimerization is regulated. Here, we discovered that TIR oligomerization is exquisitely controlled to prevent immune toxicity. We found that p38 propagates its own activation by promoting the feedforward expression and aggregation of the lone enzymatic TIR protein in the nematode C. elegans, TIR-1/SARM1. We performed a forward genetic screen to determine how the p38 positive feedforward loop is regulated. We discovered that the integrity of the specific lysosomal sub-compartment that expresses TIR-1/SARM1 is actively maintained to limit inappropriate aggregation of this protein and restrain toxic p38 immune activation. Thus, innate immune defenses in intestinal epithelial cells are regulated by specific control of TIR-1/SARM1 multimerization.

overall_design: RNA-seq of C. elegans wild-type (T24B8.5p::gfp) animals exposed to Escherichia coli (OP50) or Pseudomonas aeruginosa (PA14) for 4 hours. RNA-seq of C. elegans wild-type (T24B8.5p::gfp) or rotr-1(ums53) mutants (rotr-1(ums53);T24B8.5p::gfp) grown on Escherichia coli (OP50).

first: Samantha

middle: Y

last: Tse-Kang


title: Borrowing Transcriptional Kinases to Activate Apoptosis [ChIP-seq]

overall_design: Cells were plated at 1M/mL and treated with DMSO or CDK-TCIP1 at indicated concentrations at final 0.1% DMSO concentrations.

middle: G

last: Zhang

middle: R


title: Effect of Gsdmc knockdown in murine KPC cells transcriptome

first: Christopher

last: Heeschen

address: 227 Chongqin South Rd.

department: Center for Single-Cell Omics

institute: Shanghai Jiao Tong University School of Medicine

summary: We identified that Gsdmc gene is important for pancreatic cancer in tumorigenesis and metastasis. Here we used  KPC mice (LSL-KrasG12D/+; p53f/f; Pdx1-Cre)-derived cancer cells, KPC cells in short, to check the effects of Gsdmc knockdown on primary tumor growth and metastasis. The results suggested that Gsdmc knockdown inhibited the expression of key genes in multiple pathways, including cell migration, epithelial-mesenchymal transition, immune cell recruitment, and so on. The data deposited here provides the transcriptomic alteration of KPC cells after Gsdmc knockdown with two shRNAs.

overall_design: KPC cells named CHX2000 was isolated from KPC tumors and cultured as stable cell line. Two shRNAs targeting Gsdmc gene were transfected to CHX2000 cells and produce CHX2000-shGC1 and CHX2000-shGC2 cells.

first: Renfei

last: Wu

first: Jingwei

last: Li

first: Ke

last: Jiang

first: Quan

last: Zheng

first: Siqi

last: Tang

first: Minchun

last: Chen

first: Zhenyang

last: Guo

first: Berina

last: Sabanovic

first: Serena

last: Tondi

first: Preeta

last: Ananthanarayanan

first: Lingxi

first: Chenlei

last: Wen

first: Baiyong

last: Shen

first: Alexandra

last: Aicher


title: BIGH3-induced Osteocyte Apoptosis and Gap Junction Failure Foster Osteolysis in Clear Cell Renal Cell Carcinoma (ccRCC) Bone Metastasis

city: Houston

first: Robert

last: Satcher

state: TX

address: 1515 Holcombe

department: Orthopaedic Oncology

institute: MD Anderson Cancer Center

summary: Metastatic progression in bone involves crosstalk between tumor cells and osteoblasts, osteoclasts, and osteocytes. Renal cell carcinoma bone metastases (RCCBM) are predominantly osteolytic and often treatment resistant. We previously reported that inhibition of osteoblast differentiation by BIGH3 (transforming growth factor-beta-induced protein ig-h3) secreted by colonizing 786-O RCC cells promotes tumor progression in bone. Here we report that BIGH3 induces osteocyte apoptosis in both human specimens and mice and inhibits gap junction (GJ) protein Cx43 expression and function, disrupting bone homeostasis. As proof-of-concept, lysosomal inhibitors, such as hydroxychloroquine (HCQ) and NH4Cl, reversed BIGH3-mediated GJ dysfunction in vitro; and inhibited tumor growth and reversed Bo-786 RCC-induced osteolysis in vivo. HCQ in combination with CBZ, but not alone, reversed the RCCBM-mediated decreases in bone mineral density and osteoblast numbers, and decreased osteocyte apoptosis and osteoclast recruitment. These BIGH3 associated impacts on the bone microenvironment comprise a noncanonical mechanism of metastasis progression.

overall_design: To evaluate the effects of BIGH3 treatment on Gja1, bulk RNA Seq was performed on BIGH3 treated MLO-Y4 osteocytes  and control MLO-Y4 osteocytes.

first: Tianhong

last: Pan

first: Fengshuo

last: Liu