title: Transcriptome analysis in B16F10 and 4T1 cell lines with decitabine treatment [RNA-seq]

summary: The goal of RNA-seq is to identify the differential expressed genes in the B16F10 and 4T1 cells after Decitabine treatment.  Three biological replicates were assigned for each group and in total 12 groups were prepared for RNA-seq libraries with 300 ng mRNA as starting materials using NEXTflex Illumina qRNA-Seq Library Prep Kit (Bioo Scientific). We mapped over 60 million reads per sample to mouse genome (mm10) with RSEM workflow. P-values of differential expression were adjusted for multiple-hypothesis testing using False Discovery Rate (FDR) method.

overall_design: Messenger RNA from B16F10 and 4T1 cell lines were extacted and cDNA libraries were generated for deep sequencing, in triplicate, using HiSeq 4000 or NovaSeq S4


title: Macrophage-mediated myelin recycling fuels brain cancer malignancy (RNA-Seq in vivo)

status: Public on Jun 30 2024

city: Amsterdam

first: Daan

middle: Juri

last: Kloosterman

address: Plesmanlaan 121

department: Tumor Biology & Immunology

country: Netherlands

institute: The Netherlands Cancer

type: Expression profiling by high throughput sequencing

summary: Tumors growing in metabolically-challenged environments, such as glioblastoma in the brain, are particularly reliant on cross-talk with their tumor microenvironment (TME) to satisfy their high energetic needs. However, the intricacies of this metabolic interplay and the consequences on immune cell subset diversity and function remain largely unexplored. We interrogated the heterogeneity of the glioblastoma TME using single cell multi-omics analyses in preclinical glioblastoma mouse models and patient samples, and identified metabolically-rewired tumor-associated macrophage (TAM) subpopulations that fuel glioblastoma malignancy. These TAM subsets, termed lipid-laden macrophages (LLMs) to reflect their increased lipid metabolism activity and cholesterol storage, are epigenetically rewired, display immunosuppressive features and are enriched in the aggressive mesenchymal glioblastoma subtype. In response to TME-derived cues triggering liver-X-receptor (LXR) expression, macrophages increase engulfment of cholesterol-rich myelin debris and acquire an LLM phenotype. Subsequently, LLMs directly transfer myelin-derived lipids to cancer cells in an LXR/Abca1-dependent manner, thereby fueling the heightened metabolic demands of mesenchymal glioblastoma. Furthermore, LLM content predicts clinical outcomes and immune checkpoint blockade response in glioblastoma patients and other cancer types. Our work provides an in-depth understanding of the immune-metabolic interplay during glioblastoma progression in a subtype- and microanatomical niche-dependent manner, thereby laying a framework for the discovery of targetable metabolic vulnerabilities in glioblastoma.

overall_design: To reveal the reciprocal interactions between macrophages and tumor cells that fuel glioblastoma malignancy, we investigated the dynamic contexture of the glioblastoma TME at the single cell and spatial transcriptomic levels, in two genetically-engineered mouse models (GEMMs) that recapitulate key characteristics of human gliomagenesis and therapeutic response. Both GEMMs involve enforced expression of platelet-derived growth factor-b in Nestin-positive progenitor cells, either in an Ink4a/ArfKO background (herein termed PDG-Ink4a), or in combination with a short-hairpin-mediated knockdown of p53 in tumor cells (herein termed PDG-p53). Orthogonally, publicly available transcriptional datasets of glioblastoma patients enabled the validation of our murine models’ clinical relevance. We explored the dynamic heterogeneity of macrophage subsets in relation to their local microenvironment, employing multi-omics approaches and a wide range of functional ex vivo and in vitro assays to unveil novel pro-tumorigenic interactions underlying macrophage and tumor cell co-evolution in the glioblastoma TME.

middle: J

first: Johanna

last: Erbani

first: Menno

last: Boon

first: Martina

last: Farber

first: Shanna

middle: M

last: Handgraaf

first: Masami

last: Ando-Kuri

first: Bauke

last: Fontein

first: Elena

last: Sánchez-López

first: Marjolijn

last: Mertz

first: Marja

last: Nieuwland

first: Ning

middle: Q

last: Liu

first: Gabriel

last: Forn-Cuni

first: Nicole

middle: N

last: van der Wel

first: Anita

middle: E

last: Grootemaat

first: Luuk

last: Reinalda

first: Sander

middle: I

last: van Kasteren

first: Elzo

last: de Wit

first: Brian

last: Ruffel

first: Ewa

last: Snaar-Jagalska

first: Kevin

last: Petrecca

first: Dieta

last: Brandsma

first: Alexander

last: Kros

first: Martin

last: Giera

first: Leila

last: Akkari


title: Chromatin accessibility in B16 and 4T1 cell lines with decitabine treatment [ATAC-seq]

city: Boston

first: Eric

last: Greer

state: MA

address: 320 Longwood Avenue

department: Newborn Medicine/Department of Pediatrics

country: USA

institute: Boston Children's Hospital/Harvard Medical School

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The goal of ATAC-seq is to identify the open chromatin regions in the B16 and 4T1 cells after Decitabine treatment.  Three biological replicates were assigned for each group and in total 12 groups were prepared for ATAC-seq libraries. We mapped about 30-100 million reads per sample to M.musculus (mm10) with bowtie2 workflow.  Open chromatin regions were deducted by ChIPseeker with corrected p < 0.05. Our results showed M.Musculus have dispartate chromatin accessibility after Decitabine treatment

overall_design: Nuclei from B16 and 4T1 cells were extacted and transposed, and cDNA libraries were generated for deep sequencing, in triplicate, using HiSeq 4000 or NovaSeq S4

first: Ying

last: Zhang

first: Simon

middle: Y

last: Wang


title: Endogenous opioid signalling regulates spinal ependymal cell proliferation

status: Public on Jun 29 2024

city: San Francisco

first: David

last: Julius

state: CA

address: Genentech Hall Room N-276, 600 16th Street

department: Physiology

institute: UCSF

summary: After injury, mammalian spinal cords develop scars to confine the lesion and prevent further damage. However, excessive scarring can hinder neural regeneration and functional recovery. These competing actions underscore the importance of developing therapeutic strategies to dynamically modulate scar progression. Previous research on scarring has primarily focused on astrocytes, but recent evidence has suggested that ependymal cells also participate. Ependymal cells normally form the epithelial layer encasing the central canal, but they undergo massive proliferation and differentiation into astroglia following certain injuries, becoming a core scar component. However, the mechanisms regulating ependymal proliferation in vivo remain unclear. Here we uncover an endogenous κ-opioid signalling pathway that controls ependymal proliferation. Specifically, we detect expression of the κ-opioid receptor, OPRK1, in a functionally under-characterized cell type known as cerebrospinal fluid-contacting neuron (CSF-cN). We also discover a neighbouring cell population that expresses the cognate ligand prodynorphin (PDYN). Whereas κ-opioids are typically considered inhibitory, they excite CSF-cNs to inhibit ependymal proliferation. Systemic administration of a κ-antagonist enhances ependymal proliferation in uninjured spinal cords in a CSF-cN-dependent manner. Moreover, a κ-agonist impairs ependymal proliferation, scar formation and motor function following injury. Together, our data suggest a paracrine signalling pathway in which PDYN+ cells tonically release κ-opioids to stimulate CSF-cNs and suppress ependymal proliferation, revealing an endogenous mechanism and potential pharmacological strategy for modulating scarring after spinal cord injury.

overall_design: We characterized the transcriptomic profile of cerebrospinal fluid-contacting neurons (CSF-cNs) in the mouse spinal cord to study their physiological role. We expressed tdTomato in CSF-cNs of 4 wildtype C57BL6/J mice by intracerebroventricular injection of AAV2-CAG-tdT. Sagittal slices of the spinal cord containing the ependymal region were enzymatically dissociated and tdTomato+ cells were captured by fluorescence-activated cell sorting (FACS). Each sample contains 50 cells collected from a single mouse.

first: Wendy

middle: S

last: Yue

first: Kouki

middle: K

last: Touhara

first: Kenichi

last: Toma

first: Xin

last: Duan


title: Macrophage-mediated myelin recycling fuels brain cancer malignancy (RNA-Seq in vitro)

first: Daan

last: Kloosterman

first: Johanna

last: Erbani

first: Menno

last: Boon

first: Martina

last: Farber

first: Shanna

last: Handgraaf

first: Masami

last: Ando-Kuri

first: Bauke

last: Fontein

first: Elena

last: Sánchez-López

first: Marjolijn

last: Mertz

first: Marja

last: Nieuwland

first: Ning

last: Liu

first: Gabriel

last: Forn-Cuni

first: Nicole

last: van der Wel

first: Anita

last: Grootemaat

first: Luuk

last: Reinalda

first: Sander

last: van Kasteren


title: Macrophage-mediated myelin recycling fuels brain cancer malignancy (ATAC-Seq)

first: Elzo

last: de Wit

first: Brian

last: Ruffel

first: Ewa

last: Snaar-Jagalska

first: Kevin

last: Petrecca

first: Dieta

last: Brandsma

first: Alexander

last: Kros

first: Martin

last: Giera

first: Leila

last: Akkari


title: Expression data from patient-derived pancreatic cancer organoids with gene engineering

city: Tokyo

first: Masayuki

last: Fujii

address: 35, Shinanomachi, Shinjuku-ku

country: Japan

institute: Keio University

summary:
Lineage plasticity often emerges in human cancer along with clinical progression and exposure to chemotherapy. Although lineage transition is evident in an aggressive subtype of human pancreatic cancer characterized by the loss of the ductal identity and manifestation of squamous cell-like features, the drivers of these processes have remained elusive. We here harmonized organoid technology, molecular profiling and gene engineering and found that the H3K27me3-mediated erasure of the ductal identity and lineage specifiers, and hijacking of the TP63-driven squamous-cell program provide environmental fitness. Induction and fixation of the squamous-cell identity was dependent on Wnt-deficient environment, whereas KDM6A loss or a hypoxic niche licensed tumor cells for squamous reprogramming. EZH2 inhibition counterbalanced the epigenetic bias and curbed the growth of pancreatic cancer organoids with squamous features. Our results demonstrate how adversarial microenvironment dictates the molecular and histological evolution of human pancreatic cancer, and provide insights into the principles and significance of lineage conversion in human cancer.
We used microarray gene expression analysis to study the effect of delta-Np63 overexpression and TP63 knockout in patient-derived pancreatic cancer organoids or genetically engineered organoids.

overall_design: Delta-Np63 was overexpressed in a patient-derived classical pancreatic cancer organoid line and a genetically engineered duct organoids with KRAS, TP53, CDKN2A and GATA6 engineering. TP63 was knocked out in an patient-derived adenosquamous carcinoma line. Gene expression profiles were obtained from the parental organoid lines and these p63-engineered organoid lines using microarray.

first: Toshiro

last: Sato


title: Shared and redundant proteins coordinate signal cross-talk between MAPK pathways in yeast

city: Chapel Hill

first: Henrik

middle: Gunnar

last: Dohlman

address: 120 Mason Farm Rd

institute: UNC Chapel Hill

summary: All cells must detect, interpret and adapt to multiple and concurrent stimuli. While signaling pathways are highly specialized, different pathways often share components or have components with overlapping functions. In the yeast Saccharomyces cerevisiae, the high osmolarity glycerol (HOG) pathway has two seemingly redundant branches, mediated by Sln1 and Sho1. Both branches are activated by osmotic pressure, leading to phosphorylation of the MAPKs Hog1 and Kss1. The mating pathway is activated by pheromone, leading to phosphorylation of the MAPKs Fus3 and Kss1. Given that Kss1 is shared by the two pathways, we investigated its role in signal coordination. We activated both pathways with a combination of salt and pheromone, in cells lacking the shared MAPK and in cells lacking either of the redundant branches of the HOG pathway. By systematically evaluating MAPK activation, translocation, and transcription programs, we determined that Sho1 mediates cross talk between the HOG and mating pathways and does so through Kss1. Further, we show that Kss1 initiates a transcriptional program that is distinct from that induced by Hog1 and Fus3. Our findings reveal how redundant and shared components coordinate concurrent signals and thereby adapt to sudden environmental changes.

overall_design: To investigate if the yeast (s.cerevisiae) HOG pathway Sln1 (sho1𝛥𝛥) and Sho1 (ssk1sho1𝛥) branches have distinct transcriptome under 350 mM KCl. Also to look at transcriptome changes of the MAPK Kss1. Each sample has 3 biological repeats.

first: Shu

last: Zhang


title: Macrophage-mediated myelin recycling fuels brain cancer malignancy

first: Daan

last: Kloosterman

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

overall_design: Refer to individual Series


title: In vivo CRISPR screens identify a dual function of MEN1 in regulating tumor-microenvironment interactions

city: Shanghai

first: Yin

last: Liu

state: Shanghai

address: Building #2, 507 Zhengmin Road

department: Department of Laboratory Medicine

country: China

institute: Shanghai Pulmonary Hospital, Tongji University School of Medicine

summary: Functional genomic screen in 2D cell culture is limited in identifying therapeutic targets that modulates tumor-microenvironment interaction. Through comparison of targeted CRISPR-Cas9 screens in 2D cell culture and cell line derived xenografts of lung cancer A549, we identified MEN1 as the top hit that confers differential essentialities in vitro and in vivo. Knockout of MEN1 in multiple solid cancer types does not impact cell proliferation in vitro, but significantly promotes and inhibits tumor growth in immunodeficient and immunocompetent mice, respectively. Mechanistically, knockout of MEN1 leads to redistribution of its interaction partner MLL1, a histone methyltransferase, to repetitive genomic regions that produce double stranded RNA. This resulted in MARV and cGAS-STING dependent activation of viral mimicry response, which induces tumor promoting neutrophil and tumor suppressing CD8+ T cell infiltrations in immunodeficient and immunocompetent mice, respectively. Consistently, multiple immune cell infiltrations are negatively correlated with MEN1 abundance and positively correlated with that of MLL1 in patient tumors of a broad range of cancer types. Pharmacological inhibition of MEN1-MLL1 interaction reduces tumor growth in CD8+ T cell dependent manner, and synergizes with anti-PD-L1 treatment. These findings reveal tumor microenvironment dependent oncogenic and tumor suppressive function of MEN1 and provide rationale for therapeutic targeting of MEN1 alone or in combination with immunotherapy in multiple solid cancer types.

overall_design: Examination of immune cell infiltration in Men1 knockout CT26 tumor samples

first: Peiran

last: Su

first: Housheng

middle: H

last: He

first: Ming-Sound

last: Tsao

first: Tianyi

last: Chen


title: Splicing regulatory network of master regulator RNA Binding Protein Multiple Splicing (RBPMS) in human Embryonic stem cell derived Vascular Smooth Muscle Cells.

city: Cambridge

first: Irina

last: Mohorianu

address: Puddicombe Way

department: Wellcome-MRC Cambridge Stem Cell Institute

country: United Kingdom

institute: University of Cambridge

summary: We report the splicing and gene expression regulation by RBPMS In hES-VSMCs. We have used a Doxycycline inducible over-expression system to examine the splicing networks controlled by RBPMS in VSMCs; a protein that is highly expressed in native arterial tissue VSMCs. Previously, we have described its splicing regulatory functions in rat VSMCs (Nakagaki-SIlva et al, 2019). Here we report human VSMC specific interactions using VSMCs differentiated from human ES cells via a neural crest lineage. These cells do not endogenously express RBPMS; however, over-expression drives splicing patterns characteristic of mature tissue VSMCs evenin the in  vitro differentiated cells.

overall_design: Examination of transcriptomics upon over-expression of a splicing regulator in in vitro differentiated VSMCs.

first: Aishwarya

middle: G

last: Jacob

first: Ilias

last: Moutsopoulos

first: Chris

last: Smith

first: Sanjay

last: SInha


title: Augmenting fibronectin levels in injured adult CNS promotes axon regeneration in vivo [scRNA-seq]

status: Public on Jun 28 2024

city: Farmington

first: Ephraim

middle: F

last: Trakhtenberg

state: CT

address: 263 Farmington Ave. RM L4005

department: Neuroscience

institute: University of Connecticut School of Medicine

summary: In an attempt to repair injured central nervous system (CNS) nerves/tracts, immune cells are recruited into the injury site, but endogenous response in adult mammals is insufficient for promoting regeneration of severed axons. Here, we found that a portion of retinal ganglion cell (RGC) CNS projection neurons that survive after optic nerve crush (ONC) injury are enriched for and upregulate fibronectin (Fn)-interacting integrins Itga5 and ItgaV, and that Fn promotes long-term survival and long-distance axon regeneration of a portion of axotomized adult RGCs in culture. We then show that, Fn is developmentally downregulated in the axonal tracts of optic nerve and spinal cord, but injury-activated macrophages/microglia upregulate Fn while axon regeneration-promoting zymosan augments their recruitment (and thereby increases Fn levels) in the injured optic nerve. Finally, we found that Fn’s RGD motif, established to interact with Itga5 and ItgaV, promotes long-term survival and long-distance axon regeneration of adult RGCs after ONC in vivo, with some axons reaching the optic chiasm when co-treated with Rpl7a gene therapy. Thus, experimentally augmenting Fn levels in the injured CNS is a promising approach for therapeutic neuroprotection and axon regeneration of at least a portion of neurons.

overall_design:
We generated 10x Genomics 3’-droplet based scRNA-seq dataset of macrophage/microglia from adult (10 weeks old) uninjured and injured (2 weeks after ONC) optic nerves from mice  of both sexes using methods we previously described (Rheaume et al 2018; Xing et al, 2023). ONC injury was performed at 8 weeks. Cells from were loaded for capture onto the Chromium System using the v2 single cell reagent kit (10X Genomics). Following capture and lysis, cDNA was synthesized and amplified (12 cycles) as per manufacturer's protocol (10X Genomics). After demultiplexing and aligning to the mouse genome and transcriptome (mm10) using the CellRanger pipeline and merging/integration in Rstuduio, 778 macrophage/microglia passed quality control (including filters of a minimum of 200 genes and a maximum of 6500 genes). Batches were merged, normalized and scaled using Seurat.
Each  bam file is comprised of a single paired end fastq files. After each is aligned to the mm10 genome using Cell Ranger Count, batches were merged, normalized and scaled using Seurat with default parameters.  Seurat's RunUmap function was performed with parameters "dims = 1:4" and all other parameters as default.

first: Agnieszka

last: Lukomska

first: Matthew

middle: P

last: Frost

first: Bruce

middle: A

last: Rheaume


title: B16 and 4T1 cell lines with decitabine treatment

first: Eric

last: Greer

type: Methylation profiling by high throughput sequencing


title: Augmenting fibronectin levels in injured adult CNS promotes axon regeneration in vivo


title: In vivo CRISPR screens for Toxoplasma hyperLOPIT-unassigened proteins_2

city: Suita

first: Yuta

last: Tachibana

state: Osaka

address: 3-1, Yamadaoka

department: Research Institute for Microbial Diseases (RIMD)

institute: Osaka University

summary: We performed in vivo CRISPR screens of Toxoplasma targeting hyperLOPIT-unassigened genes during mouse infection.

overall_design: This Unassigned_2 library targeting 295 genes which consisted 2949 gRNAs targeting hyperLOPIT-unassigened genes together with dispensable and essential control genes.

first: Masahiro

last: Yamamoto


title: Stem cells tightly regulate dead cell clearance to maintain tissue fitness [scRNA-seq]

city: New York City

first: Katherine

last: Stewart

state: NY

address: 1230 York Avenue

department: Laboratory of Mammalian Cell Biology and Development

institute: The Rockefeller University

summary: Macrophages and dendritic cells have long been appreciated for their ability to migrate to and engulf dying cells and debris, including some of the billions of cells that are naturally eliminated from our body daily. However, a substantial amount of these dying cells are cleared by local tissue cells, so-called ‘non-professional phagocytes’, critical to preserve organismal fitness. How non-professional phagocytes are able to sense and digest nearby apoptotic corpses while still performing their normal tissue functions is unclear. Here, we explore the molecular mechanisms underlying this balancing act.  Exploiting the cyclical bouts of tissue regeneration and degeneration during the hair cycle, we show that stem cells can transiently become non-professional phagocytes when confronted with dying cells. Adoption of this phagocytic state requires not only local lipids produced by apoptotic corpses, which are necessary for RXRα activation, but also tissue-specific retinoids able to activate RARg. The dual factor dependency enables tight regulation of the genes requisite to activate phagocytic apoptotic clearance. The tunable phagocytic program we describe here offers an attractive mechanism to offset phagocytic duties against the primary stem cell function of replenishing differentiated cells to preserve tissue integrity during homeostasis. Our findings have broad implications for other non-motile stem or progenitor cells which experience cell death in an immune-privileged niche.

overall_design: For each hair cycle stage, wild type hair follicle stem cells (HFSCs) from 3-6 wild type animals were pooled and FACS sorted directly into SMARTSeq2 lysis buffer in 96-well plates and snap frozen. SMART-Seq2 was performed as described in Picelli, S. et al. Full-length RNA-seq from single cells using Smart-seq2. Nature Protocols 9, 171-181 (2014). Modifications were made as in Yang, H., Adam, R. C., Ge, Y., Hua, Z. L. & Fuchs, E. Epithelial-Mesenchymal Micro-niches Govern Stem Cell Lineage Choices. Cell 169, 483-496.e413 (2017).

first: Elaine

last: Fuchs


title: Stem cells tightly regulate dead cell clearance to maintain tissue fitness [CUT&Run]

overall_design: 500,000 cultured hair follicle stem cells per sample were trypsinized, washed with PBS and pelleted. Cut-&-Run-seq was performed as described before in Skene, P. J. & Henikoff, S. An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites. Elife 6 (2017). Briefly, HFSCs were cross-linked in cross-linking buffer with rotation for 10 min, quenched with glycine, washed and resuspended in NE1 buffer and rotated for 10min at 4oC. Nuclei were washed with CNR binding buffer and incubated with concanavalin-A beads or 10 min at 4 °C. ConA-bead bound nuclei were incubated overnight at 4 °C in CNR antibody buffer and 1:50 RXRa antibody (Cell Signaling Technologies, clone D6H10, #3085). ConA-bead bound nuclei were washed with CNR Triton wash buffer. then resuspended and incubated at 4 °C for 60 min in CUT&RUN antibody buffer and 2.5 μl pAG-MNase (EpiCypher). Following this, ConA-bead bound nuclei were washed twice with CUT&RUN Triton wash buffer, resuspended in 100 μl of Triton wash buffer and incubated on ice for 5 min before 2ul of 100mM CaCl2 was added per sample. Samples were incubated on ice for 30 min and the reaction was then stopped by adding 100ul of 2× stop buffer (340 mM NaCl, 20 mM EDTA, 4 mM egtazic acid, 0.1% Triton X-100 and 50 μg ml−1 RNaseA) and incubated at 37 °C for 10 min. ConA-bound nuclei were captured on a magnet, and supernatant containing Cut-and-Run DNA fragments was collected. Supernatant was incubated at 70 °C for 4 h with 2 μl 10% sodium dodecyl sulfate and 2.5 μL 20 mg ml−1 proteinase K, prior to DNA purification using PCI reagent (phenol:chloroform:isoamyl alcohol, Millipore). DNA fragments were precipitated overnight with ethanol and glycogen at -20 oC before resuspension in elution buffer (1 mM Tris–HCl pH 8.0 and 0.1 mM EDTA). CNR sequencing libraries were generated using NEBNext Ultra II DNA Library Prep Kit for Illumina and NEBNext Multiplex Oligos for Illumina. PCR-amplified libraries were purified using 1X ratio of SPRI beads (Beckman) and eluted in 15 μl EB buffer (Qiagen). All CNR libraries were sequenced on Illumina NextSeq using 40 bp paired-end reads.


title: Stem cells tightly regulate dead cell clearance to maintain tissue fitness [ATAC-seq]

overall_design: Hair follicle stem cells were FACS-sorted directly into PBS. ATAC-seq was performed as described before in Buenrostro et al., 2013. Briefly, FACS sorted HFSCs were lysed with ATAC lysis buffer on ice for 1 minute. Lysed cells were then tagmented with Tn5 transposase (Illumina) at 37C for 30min. Cleaned up fragments were PCR amplified (NEB) and size selected with 1.8X SPRI beads (Beckman Coulter). All libraries were sequenced on Illumina NextSeq 500 with 40-bp paired-end settings.


title: Gestational Ozone Inhalation Elicits Maternal Cardiac Dysfunction and Transcriptional Changes to Placental Pericytes and Endothelial Cells

city: Albuquerque

last: Campen

state: NM

address: 2502 Marble Ave NE

department: Pharmaceutical Sciences

institute: University of New Mexico Health Sciences Center

summary: To investigate the effects of gestational exposure to ozone, we performed single-cell RNA-sequencing on murine placental tissues.

overall_design: Pregnant dams were exposed to 1ppm ozone or filtered air controls on gestational day 10, placental tissue was dissociated and libraries were prepped 8 days post exposure on gestational day 18.

first: Russell

last: Hunter

first: Andrew

last: Ottens

first: Melissa

last: Suter

first: William

last: Hines


title: Fibrin drives thromboinflammation and neuropathology in COVID-19 [Lung]

first: Zhaoqi

last: Yan

address: 1650 Owen St

institute: Gladstone Institutes

summary: Life-threatening thrombotic events and neurological symptoms are prevalent in COVID-19 and are persistent in patients with long COVID experiencing post-acute sequelae of SARS-CoV-2 infection1,2,3,4. Despite the clinical evidence1,5,6,7, the underlying mechanisms of coagulopathy in COVID-19 and its consequences in inflammation and neuropathology remain poorly understood and treatment options are insufficient. Fibrinogen, the central structural component of blood clots, is abundantly deposited in the lungs and brains of patients with COVID-19, correlates with disease severity and is a predictive biomarker for post-COVID-19 cognitive deficits1,5,8,9,10. Here we show that fibrin binds to the SARS-CoV-2 spike protein, forming proinflammatory blood clots that drive systemic thromboinflammation and neuropathology in COVID-19. Fibrin, acting through its inflammatory domain, is required for oxidative stress and macrophage activation in the lungs, whereas it suppresses natural killer cells, after SARS-CoV-2 infection. Fibrin promotes neuroinflammation and neuronal loss after infection, as well as innate immune activation in the brain and lungs independently of active infection. A monoclonal antibody targeting the inflammatory fibrin domain provides protection from microglial activation and neuronal injury, as well as from thromboinflammation in the lung after infection. Thus, fibrin drives inflammation and neuropathology in SARS-CoV-2 infection, and fibrin-targeting immunotherapy may represent a therapeutic intervention for patients with acute COVID-19 and long COVID.

overall_design: We performed bulk RNA-seq analysis from SARS-CoV-2 B.1.351 (beta variant) infected lung tissues isolated from wildtype (WT) C57BL6/L (n = 4) and Fga-/- (n = 5) mice three days post-infection. Uninfected lung samples from WT (n = 4) and Fga-/- (n = 3) mice were used as control.

first: Katerina

last: Akassoglou


title: Adipose cDC1s contribute to obesity-associated white adipose tissue inflammation and metabolic dysfunction through STING-dependent IL-12 production

city: Los Angeles

first: Joey

middle: Han Tang

last: Li

address: 615 Charles E. Young Dr S

institute: UCLA

summary: Obesity is associated with chronic low-grade white adipose tissue (WAT) inflammation that can contribute to the development of insulin resistance in mammals. Previous studies have identified interleukin (IL)-12 as a critical upstream regulator of WAT inflammation and metabolic dysfunction during obesity, however, the cell types and mechanisms that initiate WAT IL-12 production remain unclear. Analysis of mouse and human WAT single cell transcriptomic datasets, IL-12 reporter mice, and IL-12p70 protein levels by ELISA identified activated conventional type 1 dendritic cells (cDC1s) as the cellular source of WAT IL-12 during diet-induced obesity. cDC1s were required for the development of obesity-associated inflammation by increasing group 1 innate lymphocyte interferon (IFN)-γ production and inflammatory macrophage accumulation. Inducible depletion of cDC1s increased WAT insulin sensitivity and systemic glucose tolerance during diet-induced obesity. Endocytosis of apoptotic bodies containing self-DNA by WAT cDC1 drove STING-dependent IL-12 production. Together, these results suggest that WAT cDC1s act as critical regulators of adipose tissue inflammation and metabolic homeostasis during obesity.

overall_design: Bulk RNA-seq analysis of adipose cDC1s of 4-week LFD- or 60% HFD-fed WT mice

middle: D

last: Hildreth

first: Eddie

middle: T

last: Padilla

first: Meha

last: Gupta

first: Yung

last: Yu Wong

first: Akshara

middle: R

last: Legala

first: Timothy

last: O'Sullivan


title: Fibrin drives thromboinflammation and neuropathology in COVID-19 [NK_Fibrin_in_vitro]

overall_design: NK cells were purified from the splenocytes of C57BL/6 mice and stimulated with IL-15 (50 ng/ml, Biolegend) for 4 days with or without fibrin. Viable CD45+CD3-NK1.1+ cells were isolated by fluorescence-activated cell sorting (FACS) and used for bulk RNA-seq. See the Methods section of the publication for details.


title: Cytokines drive the formation of memory-like NK cell subsets via epigenetic rewiring and transcriptional mechanisms [scRNA-seq]

city: Saint Louis

first: Todd

last: Fehniger

state: Missouri

address: 660 South Euclid Avenue, Campus Box 8007

department: Medicine

institute: Washington University School of Medicine

summary: NK cells are innate lymphoid cells that protect the host against malignant and infected cells. Activation with the cytokines IL-12, IL-15, and IL-18 induces NK cells to differentiate into memory-like NK cells that have enhanced function compared to conventional NK (cNK) cells. However, mechanisms governing their biology and whether all cNK cells become memory-like are unclear. We identified that IL-12/15/18 activation results in two main fates: reprogramming into enriched memory-like (eML) or priming into effector (eff)cNK cells. eML NK cells have distinct epigenetics, phenotype, and enhanced function (IFNγ, cytotoxicity) compared to cNK and effcNK cells. In contrast, effcNK cells transcriptionally and epigenetically resemble cNK cells. Furthermore, we identify that within cNK cells CD56bright and CD56dim NK cells are the origin of distinct subsets of eML NK cells. Moreover, these two subsets of eML NK cells persist within patients receiving ML NK cell therapy for several months. Thus, IL-12/15/18 activation of NK cells results in multiple cell fates, with epigenetic and transcriptional mechanisms orchestrating eML NK cell differentiation and function. These mechanistic insights provide new strategies to enhance NK cellular therapy.

overall_design: Peripheral blood NK were isolated from healthy human donors, activated with IL-12/15/18 overnight, and differentiated for 6-7 days in vitro in 1 ng/mL IL-15. Cells were submitted for scRNA-seq, CITE-seq, or ATAC-seq after overnight activation or differentiation.

first: Jennifer

last: Foltz

last: Tran

first: Evelyn

last: Schmidt

first: Changxu

last: Fan

first: Pamela

last: Wong


title: Whole lung gene expression in Tcrd-/- mice after Burkholderia thailandensis infection

city: Seattle

first: Sina

last: Gharib

state: WA

address: 850 Republican St.

institute: University of Washington

summary: Neutrophil recruitment appears critical to the pulmonary defense to B. pseudomallei. Therefore, we hypothesized that γδ T cells are critical regulators of pulmonary bacterial clearance given their proposed regulation of neutrophil recruitment to the lung. To investigate this hypothesis, we leveraged multiple in vivo models of pulmonary melioidosis to further understand the mechanisms by which γδ T cells regulate inflammation early in severe pulmonary infection. Included in this investigation, we assessed whole lung bulk RNA-sequencing data in mice with and without γδ T cells after infection with Burkholderia thailandensis.

overall_design: We infected 8-12 week old female wild type C57BL/6 mice and Tcrd-/- mice on a C57BL/6 background with whole body aerolozide B. thailandensis. At 24 hours after infection, we procured whole lungs, extracted RNA and then performed bulk RNA-sequencing. Uninfected control mice of both backgrounds also had their whole lungs procured, RNA extracted and bulk RNA-sequencing performed concurrently.

first: Shelton

last: Wright


title: Effect of PI3K/mTOR dual-target inhibitor WX390 on adipose-derived stem cells isolated from facial infiltrating lipomatosis

first: Hongrui

last: Chen

address: 639 Zhizaoju Road, Shanghai 200011, P.R.China.

department: Plastic and reconstruction surgery

institute: Shanghai ninth people's hospital

summary: Facial infiltrating lipomatosis (FIL) is a congenital disorder characterized by unilateral facial enlargement. Although next-generation sequencing has revealed that the pathogenesis of FIL is associated with phosphatidylinositol 3-kinase catalytic subunit alpha (PIK3CA) mutations, the underlying molecular mechanisms remain undetermined. We found that the adipose tissue in FIL patients demonstrated tissue infiltration accompanied by adipocytes hypertrophy and increased lipid accumulation. All FIL-ADSCs harboured PIK3CA mutations. Compared to ADSCs obtained from normal subcutaneous adipose tissue, FIL-ADSCs exhibited a greater capacity for adipogenesis. Suppression of PIK3CA resulted in a reduction in the adipogenic potential of FIL-ADSCs. Furthermore, WX390, a novel dual-target PI3K/mTOR inhibitor, was found to impede PIK3CA-mediated adipogenesis both in vivo and in vitro. RNA-seq revealed that the expression of transient receptor potential vanilloid subtype 1 (TRPV1) was upregulated after PI3K pathway inhibition, and overexpression and activation of TRPV1 both inhibited adipogenesis of FIL-ADSCs. Our study showed that PIK3CA mutations promoted adipogenesis in FIL-ADSCs and that this effect was achieved by suppressing the expression of TPRV1. Pathogenesis experiments suggested that WX390 may serve as an agent for the treatment of FIL.

overall_design: To explore the gene expression alterations in FIL-ADSCs after WX390 treatment, we applied WX390 to FIL-ADSCs isolated from three different patients. By utilizing RNA sequencing, we compared the gene expression profiles between WX390-treated and untreated FIL-ADSCs.

first: Bin

last: Sun

first: Chen

last: Hua

first: Xiaoxi

last: Lin


title: Stem cells tightly regulate dead cell clearance to maintain tissue fitness

first: Katherine

last: Stewart


title: Fibrin drives thromboinflammation and neuropathology in COVID-19

first: Zhaoqi

last: Yan


title: Harmine and Exendin-4 Combination Therapy Safely Expands Human Beta Cell Mass In Vivo

city: Duarte

first: Adolfo

middle: Garcia

last: Ocana

state: California

address: 1500 E Duarte Rd

department: Molecular and Cellular Endocrinology

institute: City of Hope Beckman Research Center

summary: 537 million people globally suffer from diabetes. Insulin-producing beta cells are reduced in number in most people with diabetes, but the majority still have some residual beta cells. Disappointingly, none of the many diabetes drugs in common use can increase human beta cell numbers. Recently, small molecules that inhibit the kinase, Dual Tyrosine-Regulated Kinase 1A (DYRK1A), have been shown to induce immunohistochemical markers of human beta cell replication, and this is enhanced by drugs that stimulate the GLP1 receptor (GLP1R) on beta cells. However, it remains to be demonstrated whether these immunohistochemical findings translate into an actual increase in human beta cell numbers in vivo. It is also unknown whether DYRK1A inhibitors together with GLP1R agonists (GLP1RAs) affect human beta cell survival. Here, we demonstrate for the first time that combination of a DYRK1A inhibitor with exendin-4 increases actual human beta cell mass in vivo by 400-700% in diabetic and non-diabetic mice over three months, reverses diabetes in vivo, without significant alteration in human alpha cell mass. The augmentation in human beta cell mass occurs through mechanisms that include enhanced human beta cell proliferation, function, and survival. The increase in human beta cell survival is mediated in part by the islet prohormone, VGF. Taken together, these findings demonstrate the remarkable therapeutic potential and safety profile of the DYRK1A inhibitor-GLP1RA combination for diabetes treatment.

overall_design: To address the mechanism involved in the human beta cell protective action of the harmine-exendin-4 combination, we performed RNAseq analysis on human islet grafts following one week of treatment.

last: Garcia-Ocana

first: Carolina

last: Rosselot

first: Yansui

last: Li

first: Randy

last: Kang


title: Next Generation Sequencing Facilitates Quantitative Analysis of GSL1 function

city: Atlanta

first: Liwei

last: Lang

state: GA

address: 1701 Uppergate Drive

institute: Emory University

summary: The aim of this study is to investigate the influence of GLS1 on the transcriptome profile of human head and neck squamous cell carcinoma (HNSCC)

overall_design: Investigation of mRNA profiles in human head and neck squamous cell carcinoma with or without GLS1 knockdown

first: Yong

last: Teng


title: Precise in-vivo RNA base editing with a wobble-enhanced circular CLUSTER guide RNA

status: Public on Jun 27 2024

city: Tübingen

first: Philipp

last: Reautschnig

address: Auf der Morgenstelle

country: Germany

institute: University of Tübingen

summary: Adenosine-to-inosine RNA base editing is a strategy developed to safely manipulate genetic information at the RNA level. Particularly promising for clinical implementation is the use of the ubiquitously expressed endogenous editing enzyme ADAR (adenosine deaminase acting on RNA) with tailored guide RNAs. However, the precision of editing could be compromised by global off-target events that can potentially occur throughout the transcriptome. In this study, we introduce a novel circular CLUSTER guide RNA design that recruits endogenous ADAR in vivo. The goals of the whole transcriptome sequencing experiment were to evaluate the A-to-G RNA editing index and the global editing precision of this novel design. To achieve this, Rett syndrome mice harboring a Mecp2 W104Amber mutation were treated either with a circular CLUSTER guide RNA targeting the mutant Mecp2 transcript or a scrambled and thus non-targeting control guide RNA. Both the targeting and the non-targeting guide RNA were encoded as AAV and delivered via retro-orbital injection of 4x10^12 viral genomes per mouse. The used AAV serotype PHP.eB allows cargo delivery to the mouse brain after systemic administration. Four weeks after injection the thalamus was isolated for NGS analysis. Whole transcriptome sequencing showed that the A-to-G RNA editing index was unaffected by treatment with the targeting guide RNA compared to the scrambled non-targeting control. We were unable to identify any global off-target events, excluding mouse to mouse variability, which suggests a very high precision of our approach on the transcriptome-wide level. Harnessing endogenous ADAR with permanent, AAV-driven CLUSTER guide RNAs in the CNS is an important next step towards the development of novel drug modalities that fight neurological diseases.

overall_design: Four weeks post injection, brains were dissected in 5 mM HEPES in HBSS and total RNA was isolated from individual brain regions using QIAzol reagent (Qiagen, #79306) and the Qiagen miRNeasy Kit reagent (Qiagen, #217004) according to the manufacturer’s instructions. Purified RNA was delivered to CeGaT for total RNA‐seq. The library was prepared with the KAPA RNA HyperPrep Library Prep Kit with RiboErase (HMR) and KAPA Globin Depletion Hybridization Oligos (Roche) and sequenced with a NovaSeq 6000 (50 M reads, 2 × 100‐bp paired‐end; Illumina).

first: Carolin

last: Fruhner

first: Nicolai

last: Wahn

first: Charlotte

last: Wiegand

first: Sabrina

last: Kragness

first: John

last: Yung

first: Daniel

last: Hofacker

first: Jenna

last: Fisk

first: Michelle

last: Eidelman

first: Nils

last: Waffenschmidt

first: Maximilian

last: Feige

first: Laura

last: Pfeiffer

first: Annika

last: Schulz

first: Yvonne

last: Füll

first: Erez

last: Levanon

first: Gail

last: Mandel

first: Thorsten

last: Stafforst


title: Transcriptome analysis reveal novel gene fusions in early onset sporadic rectal cancers

city: Hyderabad

first: Murali

middle: Dharan

last: Bashyam

address: Inner ring road, Uppal

country: India

institute: Centre for DNA Fingerprinting and Diagnostics

summary: Gene fusions (GFs) represent a distinct class of structural variants identified consistently in cancer genomes across multiple cancer types. Several GFs exhibit gain of oncogenic function, and thus, have been the focus for development of efficient targeted therapies. Here, we present a comprehensive landscape of GFs in early-onset sporadic rectal cancer (EOSRC), a poorly studied colorectal cancer (CRC) subtype prevalent in developing countries from the transcriptome analysis of 37 EOSRC samples. Gene Ontology analysis revealed enrichment of unique biological process terms associated with 5’- and 3’- fusion partner genes. An extensive network analysis highlighted several promiscuous genes participating in GF formation. Further, an in-depth evaluation revealed significant association of these promiscuous genes with chromosome fragile sites.

overall_design: To identify all GF events in EOSRC samples, RNA-Seq on 37 EOSRC tumor samples, collected in-house, was performed.

first: Pratyusha

last: Bala

first: Padmavathi

last: Kavadipula

first: Asmita

last: Gupta


title: Mechanisms of response and tolerance to active RAS inhibition in KRAS-mutant NSCLC

city: Redwood City

first: Ximo

last: Pechuan-Jorge

address: 700 Saginaw Drive

institute: Revolution Medicines

summary: Resistance to inactive state-selective RASG12C inhibitors frequently entails accumulation of RASGTP, rendering effective inhibition of active RAS potentially desirable. Here, we evaluated the anti-tumor activity of the RAS(ON) multi-selective tri-complex inhibitor RMC-7977 and dissected mechanisms of response and tolerance in KRASG12C-mutant NSCLC. Broad-spectrum, reversible RASGTP inhibition with or without concurrent covalent targeting of active RASG12C yielded superior and differentiated antitumor activity across diverse co-mutational KRASG12C-mutant NSCLC mouse models of primary or acquired RASG12C(ON) or (OFF) inhibitor resistance. Interrogation of time-resolved single cell transcriptional responses established an in vivo atlas of multi-modal acute and chronic RAS pathway inhibition in the NSCLC ecosystem and uncovered a regenerative mucinous transcriptional program that supports long-term tumor cell persistence. In patients with advanced KRASG12C-mutant NSCLC, the presence of mucinous histological features portended poor response to sotorasib or adagrasib. Our results have potential implications for personalized medicine and the development of rational RAS inhibitor-anchored therapeutic strategies.

overall_design: Lung tumor cell lines derived from KRAS G12C mutated C57/BL6 mice mice were grown in vivo and treated with either vehicle or RAS inhibitors. Tumors were processed isolate cells for scRNAseq.

first: Haniel

last: Araujo

first: Teng

last: Zhou

first: Minh

last: Truong Do

first: Xin

last: Hu

first: Frank

last: Rojas Alvarez

first: Maria

middle: E

last: Salvatierra

first: Heladio

last: Ibarguen

first: Richard

last: Lee

first: Rashi

last: Raghulan

first: Harshit

last: Shah

first: Mariela

last: Moreno Ayala

first: Shuhong

last: Wu

first: Luisa

middle: M

last: Solis Soto

first: Marcelo

middle: V

last: Negrao

first: Don

middle: L

last: Gibbons

first: David

last: Hong

first: Jack

last: Roth

last: Heymach

first: Jianjun

last: Zhang

first: Jingjing

last: Jiang

first: Mallika

last: Singh

first: Jacqueline

last: Smith

first: Elsa

last: Quintana

first: Ferdinandos

last: Skoulidis


title: Candida auris-macrophage cellular interactions and transcriptional response

city: Houston

first: Michael

last: Lorenz

state: TX

address: 6431 Fannin

institute: UTHealth Houston

summary: The pathogenic yeast Candida auris represents a global threat of the utmost clinical relevance. This emerging fungal species is remarkable in its resistance to commonly used antifungal and its persistence in the nosocomial settings. The innate immune system is one the first lines of defense preventing the dissemination of pathogens in the host. C. auris is susceptible to circulating phagocytes, namely neutrophils. However, some gaps of knowledge remain regarding the cellular and transcriptional responses towards other phagocytic lineages. In this work, we examined the interactions of this yeast with macrophages. We found that macrophages avidly phagocytose C. auris, however intracellular replication is not inhibited, indicating that C. auris is able to resist the killing mechanisms imposed by the phagocyte. Intracellular replication does not induce macrophage lysis, however. The transcriptional response of C. auris to macrophage phagocytosis is very similar to other members of the CUG clade (C. albicans, C. tropicalis, C. parapsilosis, C. lusitaniae), i.e., downregulation of transcription/translation and upregulation of alternative carbon metabolism pathways, transporters and induction of oxidative stress response and proteolysis. Gene family expansions are common in this yeast, and we found that many of these genes are induced in response to macrophage co-incubation. Among these, amino acid and oligopeptide transporters, as well as lipases and proteases are upregulated. Thus, C. auris shares key transcriptional signatures shared with other fungal pathogens and capitalizes on the expansion of gene families coding for potential virulence attributes that allow its survival, persistence, and evasion of the innate immune system.

overall_design: RNA was harvested from Candida auris incubated for 1 hour in the presence or absence of murine bone marrow-derived macrophages. Three biological replicates were obtained for each condition.

first: Pedro

last: Miramón

first: Andrew

last: Pountain


title: Age-related epithelial defects limit thymic function and regeneration [bulk]

first: Anastasia

middle: I

last: Kousa

department: Hematology / HCT

institute: City of Hope

summary: The thymus is essential for establishing adaptive immunity yet undergoes age-related involution that leads to compromised immune responsiveness. The thymus is also extremely sensitive to acute insult and although capable of regeneration, this capacity declines with age for unknown reasons. We applied single-cell and spatial transcriptomics, lineage-tracing and advanced imaging to define age-related changes in non-hematopoietic stromal cells and discovered the emergence of two atypical thymic epithelial cell (TEC) states. These age-associated (aa)TECs formed high-density peri-medullary epithelial clusters that were devoid of thymocytes; an accretion of non-productive thymic tissue that worsened with age, exhibited features of epithelial-to-mesenchymal transition (EMT), and was associated with downregulation of FOXN1. Interaction analysis revealed that the emergence of aaTEC drew tonic signals from other functional TEC populations at baseline acting as a sink for TEC growth factors. Following acute injury, aaTEC expanded substantially, further perturbing trophic regeneration pathways and correlating with defective repair of the involuted thymus. These findings therefore define a unique feature of thymic involution linked to immune aging and could have implications for developing immune boosting therapies in older individuals.

overall_design: Bulk RNA-seq profiles of CD45- thymic cells from 2-month-old at steady state (PBS) and at days 1 (d1), 4 (d4) and 7 (d7) after sublethal total body irradiation (TBI).

first: Lorenz

last: Jahn

first: Kelin

last: Zhao

first: Angel

last: Flores

first: Dante

last: Acenas II

first: Emma

last: Lederer

first: Kimon

last: Argyropoulos

first: Andri

last: Lemarquis

last: Granadier

first: Kirsten

last: Cooper

last: D’Andrea

first: Julie

last: Sheridan

first: Jennifer

last: Tsai

first: Lisa

last: Sikkema

first: Amina

last: Lazrak

first: Katherine

last: Nichols

first: Nichole

last: Lee

first: Romina

last: Ghale

first: Florent

last: Malard

first: Hana

last: Andrlova

first: Enrico

last: Velardi

first: Salma

last: Youssef

first: Marina

last: Burgos da Silva

first: Melissa

last: Docampo

first: Roshan

last: Sharma

first: Linas

last: Mazutis

first: Verena

middle: C

last: Wimmer

first: Kelly

last: Rogers

first: Susan

last: DeWolf

first: Brianna

last: Gipson

first: Antonio

last: Gomes

first: Manu

last: Setty

first: Dana

last: Pe'er

first: Laura

last: Hale

first: Nancy

last: Manley

first: Daniel

last: Gray

first: Marcel

last: van den Brink

first: Jarrod

last: Dudakov


title: Multiparametric atlas of the pre-metastatic liver for prediction of metastatic outcome in early-stage pancreatic cancer

city: New York

first: Linda

last: Bojmar

address: 413 E 69th St, Belfer Research Bldg

department: Department of Pediatrics

institute: Weill Cornell Medicine

summary: Metastasis occurs frequently after resection of pancreatic cancer (PaC). We hypothesized that multiparametric analysis of pre-metastatic liver biopsies will classify patients according to their metastatic risk, timing, and organ site. Liver biopsies obtained during pancreatectomy from 49 patients with localized PaC and 19 control patients with non-cancerous pancreatic lesions were analyzed combining metabolomic, tissue and single cell transcriptomics, and multiplex imaging approaches. Patients were followed prospectively (median three years) and classified into four recurrence groups; early (<6 months post resection) or late (>6 months post resection) liver metastasis (LiM), extrahepatic (EHM) metastasis, and disease-free survivors (NED). Overall, PaC livers exhibited signs of augmented inflammation, compared to controls. Enrichment of neutrophil extracellular traps (NETs), Ki-67 upregulation, and decreased liver creatine significantly distinguished those with future metastasis from NED. Patients with future LiM were characterized by scant T cell lobular infiltration, less steatosis, and higher levels of citrullinated H3, compared to patients who developed EHM metastasis, who had overexpression of interferon target genes (MX1, NR1D1) and an increase of CD11B+ NK cells. Upregulation of sortilin-1 and prominent NETs, together with the lack of T cells and a reduction in CD11B+ NK cells, differentiated patients with early-onset from those with late-onset LiM. Liver profiles of NED closely resembled those of controls. Using the above parameters, a machine learning-based model was developed that successfully predicted the metastatic outcome at the time of surgery with 78% accuracy. Therefore, multiparametric profiling of liver biopsies at the time of PaC diagnosis may determine metastatic risk and organotropism, and guide clinical stratification for optimal treatment selection.

overall_design: Single cell RNA seq of hepatic non-parenchymal cells (isolated by density gradient centrifugation; predominantly CD45+) from the pre-metastatic liver of patients with localized pancreatic cancer (PaC), compared with the liver of patients with non-cancerous (peri-)pancreatic lesions (PanIN, retention cysts, duodenal adenoma, IPMN without dysplasia, low-grade pancreatic neuroendocrine neoplasm).

first: Constantinos

last: Zambirinis

first: David

last: Lyden

first: William

last: Jarnagin

first: Robert

last: Schwartz

first: Jonathan

last: Hernandez


title: Age-related epithelial defects limit thymic function and regeneration

first: Anastasia

last: Kousa

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

overall_design: Refer to individual Series


title: Age-related epithelial defects limit thymic function and regeneration [single cell; Foxn1LacZ]

overall_design: Single cell RNA-seq profiles of CD45- thymic cells from Foxn1 LacZ mock and mutant 6-month-old mice at steady state.

first: Lorenz

last: Jahn

first: Kelin

last: Zhao

first: Angel

last: Flores

first: Dante

last: Acenas II

first: Emma

last: Lederer

first: Kimon

last: Argyropoulos

first: Andri

last: Lemarquis

last: Granadier

first: Kirsten

last: Cooper

first: Michael

last: D’Andrea

first: Julie

last: Sheridan

first: Jennifer

last: Tsai

first: Lisa

last: Sikkema

first: Amina

last: Lazrak

first: Katherine

last: Nichols

first: Nichole

last: Lee

first: Romina

last: Ghale

first: Florent

last: Malard

first: Hana

last: Andrlova

first: Enrico

last: Velardi

first: Salma

last: Youssef

first: Marina

last: Burgos da Silva

first: Melissa

last: Docampo

first: Roshan

last: Sharma

first: Linas

last: Mazutis

first: Verena

last: Wimmer

first: Kelly

last: Rogers

first: Susan

last: DeWolf

middle: H


title: A network of acetyl phosphate-dependent modification supports c-di-AMP homeostasis in Actinobacteria

first: Di

last: You

address: Meilong Road 130

institute: East China University of Science & Technology

summary: K78 acetylation inhibits the global outcome of DasR binding to its targeted genes in vivo.

overall_design: Saccharopolyspora erythraea WT and K78Q strains grown in TSB medium are used for ChIP-seq

first: Yu

last: Fu

first: Liu-Chang

last: Zhao

first: Jin-Long

last: Shen

first: Shi-Yu

last: Zhou

first: Bin-Cheng

last: Yin

first: Bang-Ce

last: Ye


title: Effect of iodide ions on gene expression during M1 polarization of RAW264.7 macrophages.

city: Beijing

first: Xin

last: Zhang

state: Beijing

address: 38 Xueyuan Road

department: Institute of Systems Biomedicine

institute: Peking University

summary: To study the effect of iodide ions on the M1 polarization of macrophages, we chose the RAW264.7 cell line. We then performed gene expression profiling analysis using data obtained from RNA-seq of 3 different groups.

overall_design: Comparative gene expression profiling of RNA-seq data from Mock group cells, M1 polarized group cells and M1 polarized plus iodide ion group cells.

first: Dan

last: Lu

first: Wenyu

last: Tian


title: Cytokines drive the formation of memory-like NK cell subsets via epigenetic rewiring and transcriptional mechanisms [ATAC-seq]

first: Todd

last: Fehniger

first: Jennifer

last: Foltz

last: Tran

first: Evelyn

last: Schmidt

first: Changxu

last: Fan

first: Pamela

last: Wong


title: Age-related epithelial defects limit thymic function and regeneration [visium]

first: Anastasia

last: Kousa

overall_design: Spatial transcriptomic profiles of thymus from 2-month-old and 18-month-old mice at steady state (day 0; d0).

first: Lorenz

last: Jahn

first: Kelin

first: Angel

last: Flores

first: Dante

last: Acenas II

first: Emma

last: Lederer

first: Kimon

last: Argyropoulos

first: Andri

last: Lemarquis

first: David

last: Granadier

first: Kirsten

last: Cooper

first: Michael

last: D’Andrea

first: Julie

last: Sheridan

last: Tsai

first: Lisa

last: Sikkema

first: Amina

last: Lazrak

first: Katherine

last: Nichols

first: Nichole

last: Lee

first: Romina

last: Ghale

first: Florent

last: Malard

first: Hana

last: Andrlova

first: Enrico

last: Velardi

first: Salma

last: Youssef

first: Marina

last: Burgos da Silva

first: Melissa

last: Docampo

first: Roshan

last: Sharma

first: Linas

last: Mazutis

first: Verena

last: Wimmer

first: Kelly

last: Rogers

last: DeWolf

first: Brianna

last: Gipson

first: Antonio

last: Gomes

first: Manu

last: Setty

first: Dana

last: Pe'er

first: Laura

last: Hale

first: Nancy

last: Manley

first: Daniel

last: Gray

first: Marcel

last: van den Brink

first: Jarrod

last: Dudakov


title: Transcriptional profiling of embryos lacking Flvcr1

city: Rancagua

first: Nicolas

last: Santander

address: Libertador Bernardo O'Higgins 611

country: Chile

institute: Universidad de O´Higgins

summary: Flvcr1 is a heme transporter involved in multiple processes. Here we invetigated the role of this transporter in brain development in mice. Deletion of Flvcr1 in nerual progenitors leads to metabolic collapse of neural progenitors and cortical disruption. Using transcriptional profiling, we show that brains of these embryos expressed reduced levels of electron transport chain components and increased levels of heme metabolic genes. These results implicate Flvcr1 in brain development through control of the metabolic state in neural progenitors.

overall_design: We inactivated Flvcr1 in neural progenitors using Nestin-Cre and isolated brains from 3 control and 3 mutant embryos at E14.5.

first: Thomas

last: Arnold

first: Emanuela

last: Tolosano

first: Deborah

last: Chiabrando


title: Cytokines drive the formation of memory-like NK cell subsets via epigenetic rewiring and transcriptional mechanisms [CITE-seq]

first: Todd

last: Fehniger

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Peripheral blood NK were isolated from healthy human donors, activated with IL-12/15/18 overnight, and differentiated for 6-7 days in vitro in 1 ng/mL IL-15. Cells were submitted for scRNA-seq, CITE-seq, or ATAC-seq after overnight activation or differentiation.

first: Jennifer

last: Foltz

last: Tran

first: Evelyn

last: Schmidt

first: Changxu

last: Fan

first: Pamela

last: Wong


title: Physiologic media renders human iPSC-derived macrophages permissive for M. tuberculosis by rewiring organelle function and metabolism

city: London

first: Rachel

last: Lai

address: Du Cane Road

department: Infectious Disease

institute: Imperial College London

summary: In vitro studies are crucial for our understanding of the human macrophage immune functions. However, traditional in vitro culture media poorly reflect the metabolic composition of blood, potentially affecting the outcomes of these studies. Here, we analysed the impact of a physiological medium on human induced pluripotent stem cell (iPSC)-derived macrophages (iPSDM) function. Macrophages cultured in a human plasma-like medium (HPLM) were more permissive to Mycobacterium tuberculosis (Mtb) replication and showed decreased lipid metabolism with increased metabolic polarisation. Functionally, HPLM-differentiated macrophages showed different metabolic organelle content and activity. Specifically, HPLM-cultured macrophages displayed reduced lipid droplet and peroxisome content, increased lysosomal proteolytic activity, and increased mitochondrial activity and dynamics. Inhibiting or inducing lipid droplet formation revealed that lipid droplet content is a key factor influencing macrophage permissiveness to Mtb. These findings underscore the importance of using physiologically relevant media in vitro for accurately studying human macrophage function.

overall_design: Human iPSc derived macrophages in 6 conditions with 3 technical replicates each. The conditions are: M-CSF and GM-CSF differentiation using XVIVO15, OXM and HPLM media.

first: Claudio

last: Bussi

first: Max

last: Gutierrez


title: Single-cell analysis reveals a novel regulatory mechanism of endothelial-to-mesenchymal transition

city: Aarhus

first: Lin

last: Lin

address: Høegh-Guldbergs Gade 10

department: Department of Biomedicine

country: Denmark

institute: Aarhus University

summary: The transdifferentiation of endothelial cells (ECs) towards a mesenchymal-like phenotype, referred to as endothelial-to-mesenchymal transition (EndMT), is critical for embryonic development, and in adults it is one of the major contributors to the onset of diseases, including cancer, fibrosis and a number of cardiovascular disorders. Here we identified mitochondrial calcium signaling as a  key regulator of EndMT in three in vitro EndMT models, as well as in physiopathological conditions in vivo. Pharmacological inhibition of the mitochondrial calcium uniporter (MCU) prevents EndMT. Deletion of MCU in ECs confirms loss of EndMT during cardiac embryo development as well as in a hind limb ischemia mouse model. Together, our data provide evidence of a novel regulatory mechanism of endothelial transdifferentation, thus potentially allowing for the development of new therapeutic interventions for EndMT-related diseases.

overall_design: To identify novel regulators of EndMT, we single cell profiled three in vitro EndMT models. EndMT was induced in freshly isolated human umbilical vein endothelial cells (HUVECs) by: 1) long-term TGF-b treatment, 2) ERG silencing (shERG) and 3) SNAI1 overexpression (SNAIOE). Each experimental condition was compared to control HUVECs (untreated, pLKO-empty and pRRL-empty, respectively). For each model, a pooled sample of two HUVEC donors was subjected to scRNA-seq. We then perfomed gene expression profiling analysis of each model individually and combined.

first: Anna

last: Cantelmo

first: Jermaine

last: Goveia

first: Aleksandar

last: Beatovic

first: Job

last: Van Kerckhove


title: Multi-parametric atlas of the pre-metastatic liver for prediction of metastatic outcome in early-stage pancreatic cancer

first: Linda

last: Bojmar

summary: Metastasis occurs frequently after resection of pancreatic cancer (PC). We hypothesized that multiparametric analysis of pre-metastatic liver biopsies will classify patients according to their metastatic risk, timing, and organ site. Liver biopsies obtained during pancreatectomy from 49 patients with localized PC and 18 control patients with non-cancerous pancreatic lesions were analyzed combining metabolomic, tissue and single cell transcriptomics, and multiplex imaging approaches. Patients were followed prospectively (median three years) and classified into four recurrence groups; early (<6 months post resection) or late (>6 months post resection) liver metastasis (LM), extrahepatic (EH) metastasis, and disease-free survivors (NED). Overall, PC livers exhibited signs of augmented inflammation, compared to controls. Enrichment of neutrophil extracellular traps (NETs), Ki-67 upregulation, and decreased liver creatine significantly distinguished those with future metastasis from NED. Patients with future LM were characterized by scant T cell lobular infiltration, less steatosis, and higher levels of citrullinated H3, compared to patients who developed EH metastasis, who had overexpression of interferon target genes (MX1, NR1D1) and an increase of CD11B+ NK cells. Upregulation of sortilin-1 and prominent NETs, together with the lack of T cells and a reduction in CD11B+ NK cells, differentiated patients with early-onset from those with late-onset LM. Liver profiles of NED closely resembled those of controls. Using the above parameters, a machine learning-based model was developed that successfully predicted the metastatic outcome at the time of surgery with 78% accuracy. Therefore, multiparametric profiling of liver biopsies at the time of PC diagnosis may determine metastatic risk and organotropism, and guide clinical stratification for optimal treatment selection.

overall_design: comparative RNA-seq analysis of the pre-metastatic liver of patients with localized pancreatic cancer (PC), with the liver of patients with non-cancerous (peri-)pancreatic lesions (PanIN, retention cysts, duodenal adenoma). Additionally, PC patients were followed prospectively and classified into recurrence groups (early or late liver metastasis, extrahepatic metastasis, or disease free over median follow-up of 3 years) and these were also compared.

first: Constantinos

last: Zambirinis

first: David

last: Lyden

first: William

last: Jarnagin

first: Robert

last: Schwartz

first: Jonathan

last: Hernandez


title: Pre-clinical proof of principle for orally delivered Th17 antagonist miniproteins

status: Public on Jun 26 2024

last: Baker

address: Molecular Engineering and Sciences, Box 351655

summary: Interleukin (IL)-23 and IL-17 are well-validated therapeutic targets in autoinflammatory diseases. Antibodies targeting IL-23 and IL-17 have shown clinical efficacy but are limited by high costs, safety risks, lack of sustained efficacy, and poor patient convenience as they require parenteral administration. Here, we present designed miniproteins inhibiting IL-23R and IL-17 with antibody-like, low picomolar affinities at a fraction of the molecular size. The minibinders potently block cell signaling in vitro and are extremely stable, enabling oral administration and low-cost manufacturing. The orally administered IL-23R minibinder shows efficacy better than a clinical anti-IL-23 antibody in mouse colitis and has a favorable pharmacokinetics (PK) and biodistribution profile in rats. This work demonstrates that orally administered de novo-designed minibinders can reach a therapeutic target past the gut epithelial barrier. With high potency, gut stability, and straightforward manufacturability, de novo-designed minibinders are a promising modality for oral biologics.

overall_design: In the related work, proteins were computationally designed to bind IL-23R or IL-17A. Site-directed saturation mutagenesis libraries were generated based on the sequences of sub-optimal minibinders, transformed into yeast for surface display, and selected for high-affinity binding to each target, optionally after pre-treatment of the library with simuated intestinal fluid. Next generation sequencing analysis of the naive and selected pools was used to determine the fitness of each mutation for affinity and stability.

first: Stephanie

last: Berger

first: Franziska

last: Seeger

first: Ta-Yi

last: Yu


title: RNAseq of patient-derived colon organoids treated with 3PO for 24h

city: Goettingen

first: Tiago

last: De Oliveira

state: NI

address: Robert-Koch-Str. 40

department: Department of Surgery

institute: University Medical Center Göttingen

summary: To evaluate 3PO-induced changes on cellular transcriptomes in a more advanced in vitro model, patient-derived organoids (PDOs) of three different patients were treated with 30 ¬µM 3PO for 24h and their RNA was extracted and sequenced. Next, the resulting gene expression data were interpreted by Gene Set Enrichment Analysis (GSEA).

overall_design: compound treatment design

first: Lena

last: Conradi

first: Natasa

last: Josipovic

first: Karly

last: Conrads

first: Dorothee

last: Sartorius


title: Age-related epithelial defects limit thymic function and regeneration [single cell]

first: Anastasia

last: Kousa

overall_design: Single cell RNA-seq profiles of CD45- thymic stroma cells from 2-month-old and 18-month-old mice at steady state (day 0; d0) and at days 1 (d1), 4 (d4) and 7 (d7) after sublethal total body irradiation (TBI).

first: Lorenz

last: Jahn

first: Kelin

last: Zhao

first: Angel

last: Flores

first: Dante

last: Acenas II

first: Emma

last: Lederer

first: Kimon

last: Argyropoulos

first: Andri

last: Lemarquis

last: Granadier

first: Kirsten

last: Cooper

first: Michael

last: D’Andrea

first: Julie

last: Sheridan

first: Jennifer

last: Tsai

first: Lisa

last: Sikkema

first: Amina

last: Lazrak

first: Katherine

last: Nichols

first: Nichole

last: Lee

first: Romina

last: Ghale

first: Florent

last: Malard

first: Hana

last: Andrlova

first: Enrico

last: Velardi

first: Salma

last: Youssef

first: Marina

last: Burgos da Silva

first: Melissa

last: Docampo

first: Roshan

last: Sharma

first: Linas

last: Mazutis

first: Verena

last: Wimmer

first: Kelly

last: Rogers

first: Susan

last: DeWolf

first: Brianna

last: Gipson

first: Antonio

last: Gomes

first: Manu

last: Setty

first: Dana

last: Pe'er

first: Laura

last: Hale

first: Nancy

last: Manley

first: Daniel

last: Gray

first: Marcel

last: van den Brink

first: Jarrod

last: Dudakov


title: Discovery of an embryonically derived bipotent population of endothelial-macrophage progenitor cells in postnatal aorta

city: Adelaide

first: Peter

middle: James

last: Psaltis

state: South Australia

address: North Terrace

department: Adelaide Medical School

country: Australia

institute: University of Adelaide

summary: Converging evidence indicates that extra-embryonic yolk sac is the source of both macrophages and endothelial cells in adult mouse tissues. Prevailing views are that these embryonically derived cells are maintained after birth by proliferative self-renewal in their differentiated states. Here we identify clonogenic endothelial-macrophage (EndoMac) progenitor cells in the adventitia of embryonic and postnatal mouse aorta, that are independent of Flt3-mediated bone marrow hematopoiesis and derive from an early embryonic CX3CR1+ and CSF1R+ source. These bipotent progenitors are proliferative and vasculogenic, contributing to adventitial neovascularization and forming perfused blood vessels after transfer into ischemic tissue. We establish a regulatory role for angiotensin II, which enhances their clonogenic and differentiation properties and rapidly stimulates their proliferative expansion in vivo. Our findings demonstrate that embryonically derived EndoMac progenitors participate in local vasculogenic responses in the aortic wall by contributing to the expansion of endothelial cells and macrophages postnatally.

overall_design: Haematopoietic colony forming unit- macrophages cultured from freshly prepared cell suspecsions of postnatal mouse aorta were harvested and FACS-purified viable cells analysed using scRNA-seq.

first: Anna

last: Williamson

middle: J


title: U4 inhibits premature cleavage and polyadenylation of pre-mRNAs [mRNA-seq]

city: guangzhou

first: chengguo

last: yao

address: No. 74 zhongshan 2rd road

department: school of medicine

institute: sysu

summary: To understand how U4 snRNP regulates premature cleavage and polyadenylation of pre-mRNAs at the transcriptome wide, we conducted mRNA-seq analysis on control, U1 and U4-AMO treated HeLa cells

overall_design: We carried standard mRNA-seq analysis in NC AMO, U1 and U4 AMO-treated HeLa cells

first: Qiumin

last: Feng

first: Zejin

last: Lin

first: Danhui

last: Zhao

first: Congting

last: Ye

first: Chengguo

last: Yao


title: Spatial transcriptome gene expression profile in 2 patients with Hashimoto's thyroiditis and 2 patients with papillary thyroid cancer combined with Hashimoto's thyroiditis.

first: Xin

last: Zhang

summary: Hashimoto's thyroiditis and papillary thyroid cancer are the most common thyroid disorders. We used spatial transcriptome sequencing (ST-seq) to investigate their potential relationship.

overall_design: Specimens were collected from patients with Hashimoto's thyroiditis and papillary thyroid cancer and analyzed using ST-seq.

first: Dan

last: Lu

first: Limei

last: Guo

first: Wenyu

last: Tian


title: U4 inhibits premature cleavage and polyadenylation of pre-mRNAs


title: U4 inhibits premature cleavage and polyadenylation of pre-mRNAs [mRNA 3'-seq]

summary: To understand how U4 snRNP regulates premature cleavage and polyadenylation of pre-mRNAs at the transcriptome wide,  we conducted 3'-seq analysis on control, U1 and U4-AMO treated samples using the Lexogen mRNA 3'-seq kit (Cat. 016.24), which enables accurate quantification of global PAS usage.

overall_design: We carried mRNA 3'-seq analysis in NC AMO, U1 and U4 AMO-treated HeLa/HEK-293/Neuro-2A/NIH-3T3 cells


title: Wound induced small-peptide mediated signalling cascade dictates growth vs defense decision in rice

city: Bangalore

first: Shivaprasad

last: Padubidri V.

address: UAS-GKVK Campus

institute: National Centre for Biological Sciences - TIFR

overall_design: Refer to individual Series


title: Glucocorticoid Receptor Signaling is Critical for Mouse Corneal Development, Inhibition of Inflammatory Response and Neovascularization of the Cornea

city: RTP

first: Xiaojiang

last: Xu

state: North Carolina

address: 111 T. W. Alexander Dr.,

institute: NIEHS

summary: Synthetic glucocorticoids are widely prescribed in the treatment of ocular infections and disorders. The actions of glucocorticoids are mediated by the glucocorticoid receptor (GR); however, the molecular and physiological functions of GR signaling in the cornea are poorly understood. To understand the direct role of GR signaling in the cornea, we developed mice with conditional knockout of GR in the corneal epithelium. Global transcriptomic approaches revealed that loss of GR signaling in the cornea resulted in the dysregulation of a large cohort of genes strongly associated with an enhanced immune response.

overall_design: To generate mice lacking GR in the cornea epithelium (corneaGRKO mice), mice homozygous for the floxed GR allele (GRflox) were crossed with mice expressing Cre recombinase driven by the P0 promoter of Pax6 gene.   Male corneaGRKO mice that were 3 months of age and their age-matched control (GRflox) littermates were euthanized, eyes removed, and total RNA was isolated from the whole cornea. The control GRflox and corneaGRKO groups each had 4 replicates, where each replicate had 4-6 corneas pooled into one sample.  Indexed samples were sequenced using the 75bp pair-end protocol using the Illumina NextSeq500 sequencer as per the manufacturer’s protocol. Reads greater than 40 million reads per sample were aligned to the reference genome UCSC mm9.

first: Mahita

last: Kadmiel

first: Robert

last: Oakley

first: John

last: Cidlowski


title: Loss of Inpp5d has disease-relevant and sex-specific effects on glial transcriptomes

city: Indianapolis

first: Luke

middle: Child

last: Dabin

state: Indiana

department: Medical and Molecular Genetics

institute: Indiana University

summary: INTRODUCTION: INPP5D is genetically associated with Alzheimer’s disease risk. Loss of Inpp5d alters amyloid pathology in models of amyloidosis. Inpp5d is predominantly expressed in microglia but its function in brain is poorly understood. METHODS: We performed single-cell RNA-sequencing to study the effect of Inpp5d loss on wild-type mouse brain transcriptomes. RESULTS: Loss of Inpp5d has sex-specific effects on the brain transcriptome. Affected genes are enriched for multiple neurodegeneration terms. Network analyses reveal a gene co-expression module centered around Inpp5d in female mice. Inpp5d loss alters PTN, PSAP, and VEGFA signaling probability between cell types. DISCUSSION: Our data suggest Inpp5d’s normal function is entangled with mechanisms involved in neurodegeneration. We report the effect of Inpp5d loss without pathology and show that this has dramatic effects on gene expression. Our study provides a critical reference for researchers of neurodegeneration, allowing separation of disease-specific changes mediated by Inpp5d in disease from baseline effects of Inpp5d loss.

overall_design: Data contains single-cell RNA-sequencing data from two female and male wildtype, two female and male Inpp5d hetereozygous knockout, two female and male Inpp5d homozygous knockout mice, all six weeks of age.

first: Holly

last: Kersey

first: Byungwook

last: Kim

first: Dom

last: Acri

first: Ahmad

last: Sharify

first: Audrey

last: Lee-Gosselin

first: Cristian

last: Lasagna-Reeves

first: Adrian

last: Oblak

first: Bruce

last: Lamb

first: Jungsu


title: Phosphorylation of PABPN1 during mitosis protects mRNA from hyperadenylation and maintains transcriptome dynamics.

city: New Haven

first: Jackson

last: Gordon

address: 333 Cedar St

department: MB&B

institute: Yale University

summary: Polyadenylation controls mRNA biogenesis, nuclear export, translation, and decay. These processes are interdependent and coordinately regulated by poly(A)-binding proteins (PABPs), yet how PABPs are themselves regulated is not fully understood. Here, we show that human PABPN1, the nuclear PABP, is phosphorylated by mitotic kinases at four specific sites during mitosis, a time when nucleoplasm and cytoplasm mix. Phospho-inhibitory mutations decreased human cell proliferation. We therefore employed long-read sequencing to determine how PABPN1 phospho-site mutants affected poly(A) tails lengths of individual mRNAs, and TimeLapse-seq to monitor mRNA synthesis and decay. Phospho-inhibitory PABPN1 mutants lengthened poly(A) tails on both spliced and unspliced transcripts. In contrast, expression of phospho-mimetic PABPN1 resulted in shorter poly(A) tails and reduced transcriptome stability, indicating reduced polyadenylation activity of PABPN1 and targeting of long-tailed transcripts for decay. Thus, PABPN1 phosphorylation confers transcriptome instability that is associated with resetting the gene expression program as cells passage through cell cycle.

overall_design: To investigate the role of PABPN1 phosphorylation in mRNA processing, we constructed HEK293T cell lines with Doxycycline-inducible expression of WT PABPN1, 4SA PABPN1 (S19, S150, S197, and S304 to A), or 4SD PABPN1 (S19, S150, S197, and S304 to D).

first: David

last: Phizicky

first: Leonard

last: Schärfen

first: Courtney

last: Brown

first: Dahyana

last: Arias Escayola

first: TuKiet

last: Lam

first: Jean

last: Kanyo

first: Matthew

last: Simon

first: Karla

last: Neugebauer


title: Wound induced small-peptide mediated signalling cascade regulated by a receptor like kinase- OsLRR-RLK1 dictates growth vs defense decision in rice

first: Shivaprasad

last: Padubidri V.

summary: We identified the involvement of OsPSKR, a receptor like kinase in wound responses in rice. OsPSKR regulates balance between growth and defense responses by suppressing exaggerated defense responses and promoting growth responses.

overall_design: We performed RNA-sequencing to identify transcriptional dynamics upon wounding and differential regulation of gene expression upon perturbation of OsLRR-RLK1.

first: V

middle: P

last: Shivaprasad

first: C

middle: Y

last: Harshith


title: Epigenomic profile of bladder cancer cell line HT1376  treated with CPI-0209

city: Cambridge

first: Patrick

last: Trojer

state: Massachusetts

address: 215 First Street, Suite 200

institute: Constellation Pharmaceuticals

summary: Advanced bladder cancer remains a difficult cancer to treat, and for the majority of patients, current standard treatments ultimately prove ineffective.  These tumors frequently harbor mutations in the BAF complex subunit ARID1A, which has been reported to confer sensitivity to EZH2 inhibition in several tumor types.  Here we describe the generation of CPI-0209, a best-in-class, orally available EZH2 inhibitor.  We show that mutant bladder cancer lines harboring ARID1A loss of function (LOF) mutations are preferentially sensitive to inhibition of EZH2. Treatment with CPI-0209 not only elicits a significant monotherapeutic response in ARID1A mutant models, it also outperforms cisplatin and improves response in chemo-resistant models. These findings shine light on new therapeutic opportunities for patients with advanced urothelial carcinoma.

overall_design: Bladder cancer cell line HT1376 was treated with or without EZH2 inhibitor CPI-0209 for 8 days before subject to ChIP-seq.

first: Patricia

last: Keller

first: Elizabeth

last: Adams

first: Rentian

last: Wu


title: Transcriptomic change of bladder cancer cell lines treated with CPI-0209 [2]

summary: Advanced bladder cancer remains a difficult cancer to treat, and for the majority of patients, current standard treatments ultimately prove ineffective.  These tumors frequently harbor mutations in the BAF complex subunit ARID1A, which has been reported to confer sensitivity to EZH2 inhibition in several tumor types.  Here we describe the generation of CPI-0209, a best-in-class, orally available EZH2 inhibitor.  We show that mutant bladder cancer lines harboring ARID1A loss of function (LOF) mutations are preferentially sensitive to inhibition of EZH2. Treatment with CPI-0209 not only elicits a significant monotherapeutic response in ARID1A mutant models, it also outperforms cisplatin and improves response in chemo-resistant models. These findings shine light on new therapeutic opportunities for patients with advanced urothelial carcinoma.

overall_design: Bladder cancer cell lines were treated with or without EZH2 inhibitor CPI-0209 for 4 days before subject to RNA-seq.


overall_design: Xenograft of bladder cancer cell line HT1376 were treated with or without EZH2 inhibitors before subject to RNA-seq.


first: Xiaojiang

last: Xu

summary: Synthetic glucocorticoids are widely prescribed in the treatment of ocular infections and disorders. The actions of glucocorticoids are mediated by the glucocorticoid receptor (GR); however, the molecular and physiological functions of GR signaling in the cornea are poorly understood. In this study, we show that treatment of mice with glucocorticoid eye drops led to a profound regulation of the corneal transcriptome.  To determine the global transcriptional profile of GR activity in the cornea, we treated adult wild-type male mice with dexamethasone (a synthetic glucocorticoid) eye drops or vehicle eye drops for 6 hours and then performed RNA sequencing on RNA extracted from whole corneas. All the animals used for this study were adrenalectomized to remove endogenous glucocorticoids.  These data demonstrate that a short exposure of glucocorticoids to the cornea results in major changes in the gene expression landscape.

overall_design: Male wild-type C57BL/6J mice that were 8 weeks old were adrenalectomized (ADX) to remove endogenous glucocorticoids.  Approximately 4 weeks after the surgery, mice were treated with dexamethasone eye drops or vehicle eye drops for 6 hours.  Mice were euthanized, eyes removed, and total RNA was isolated from the whole cornea. Each experimental group had 4 replicates, where each replicate had 4-6 corneas pooled into one sample.  Indexed samples were sequenced using the 75bp pair-end protocol using the Illumina NextSeq500 sequencer as per the manufacturer’s protocol. Reads greater than 40 million reads per sample were aligned to the reference genome UCSC mm9.

first: Kadmiel

last: Mahita

first: Oakley

last: Robert

first: Xu

last: Xiaojiang

first: Cidlowski

last: John


title: Epigenomic change of ARDI1A mutant bladder cancer cell line treated with CPI-0209 or induced ARID1A expression

overall_design: HT1376-TetON control cells and a clonal HT1376-TetON-ARID1A cell line were induced with 50 ng/ml doxycycline for 24 hours and then treated for 4 days with DMSO or 250 nM CPI-0209.


title: Genetic and epigenetic driven variation contribute to adaptation and evolution under endocrine treatment

city: Vienna

first: Iros

last: Barozzi

address: Borschkegasse 8a

country: Austria

institute: Medical University Vienna

summary: Comprehensive profiling of hormone-dependent breast cancer (HDBC) has identified hundreds of protein-coding alterations contributing to cancer initiation, but only a handful have been linked to endocrine therapy resistance, potentially contributing to 40% of relapses. If other mechanisms underlie the evolution of HDBC under adjuvant therapy is currently unknown. In this work, we employ integrative functional genomics to dissect the contribution of cis-regulatory elements (CREs) to cancer evolution by focusing on 12 megabases of non-coding DNA, including clonal enhancers, gene promoters, and boundaries of topologically associating domains. Massive parallel epigenetic perturbation (CRISPRi) in vitro reveals context-dependent roles for many of these CREs, with a specific impact on dormancy entrance and endocrine therapy resistance. Profiling of CRE somatic alterations in a unique, longitudinal cohort of patients treated with endocrine therapies identifies non-coding changes potentially involved in therapy resistance. Overall, our data uncover how endocrine therapies triggers the emergence of transient features which could ultimately be exploited to hinder the adaptive process.

sample_organism:
Homo sapiens
mixed DNA library

platform_organism:
Homo sapiens
mixed DNA library

overall_design: CRISPRi screens performed in MCF7 (in either presence or absence of oestrogen), derived resistant cells (LTED), and in T47D (in either presence or absence of oestrogen), targeting non-coding regions of the genome (putateive enhancers, putative insulators, and promoters)

first: I

first: N

last: Slaven

first: E

last: Canale

first: R

last: Lopes

middle: A

last: Monteiro Barbosa

first: D

last: Ivanoiu

last: Pacini

first: M

last: Bleu

last: Mensa

first: A

last: Chambers

first: S

last: Bravaccini

last: Ravaioli

last: Dieci

first: G

last: Pruneri

middle: G

last: Galli

first: L

last: Magnani


title: Gene expression profiling of sorted primary human bronchial epithelial cell populations

city: Minneapolis

first: Frances

last: Shepherd

state: MN

address: 689 23rd Ave SE

institute: University of Minnesota

summary: Influenza viruses pose a significant burden on global human health. Influenza has a broad cellular tropism in the airway, but how infection of different epithelial cell types impacts replication kinetics and burden in the airways is not fully understood. Using primary human airway cultures, which recapitulate the diverse epithelial cell landscape of the human airways, we investigated the impact of cell type composition on virus tropism and replication kinetics. Cultures were highly diverse across multiple donors and 30 independent differentiation conditions and supported a range of influenza replication. Although many cell types were susceptible to influenza, ciliated and secretory cells were predominantly infected. Despite the strong tropism preference for secretory and ciliated cells, which consistently make up 75% or more of infected cells, only ciliated cells were associated with increased virus production. Surprisingly, infected secretory cells were associated with overall reduced virus output. These data highlight the heterogeneous outcomes of influenza virus infections in primary human airway cultures and the disparate impacts of infected cell identity on burst size, even among preferentially infected cell types.

overall_design: NHBE cells were grown at air-liquid interface for 3 weeks in Pneumacult media. Single cell suspensions were filtered and counted and 10,000 cells per condition were used to generate Gel Bead-in Emulsions (GEMs). The 10X Chromium 3' GEX Capture kit and the 10X Chromium controller were used to generate GEMs and barcoding per manufacturers protocol (10X Genomics, Pleasanton, CA, USA). GEMs generated were used for cDNA synthesis and library preparation using the Chromium Single Cell 3' Library Kit and run on a NovaSeq S2. 2x100 PE Run.

first: Shanley

middle: N

last: Roach

middle: K

first: Clayton

last: Mickelson

first: Jessica

last: Fiege

first: Beth

last: Thielen

first: Lauren

last: Pross

first: Autum

last: Sanders

first: Mason

last: Robertson

first: Ryan

last: Langlois


title: Targeting fatty acid metabolism to abrogate differentiation block in pre-leukemia induced by AML1-ETO

city: Tianjin

first: Yu

last: Liu

state: -- None selected --

address: 288 Nanjing Road

institute: Chinese Academy of Medical Sciences & Peking Union Medical College

summary: To gain the underlying insight into the functional impact of AML1-ETO expressed in HSPCs, RNA-seq was performed on purified LT-HSCs and GMPs from the bone marrow (BM) of both AML1-ETO expressed (AML1/ETO) and Wild-Type (control) C57 mice. Our work suggested that AML1-ETO resulted in impaired hematopoietic reconstitution and increased self-renewal ability.The oxidative phosphorylation and glycolysis decreased significantly in AML1/ETO LT-HSCs accompanied by increased HSC quiescence and reduced cell cycling. Furthermore, it was observed that HSCs expressing AML1-ETO exhibited an increased requirement for fatty acids when they differentiated.

overall_design: Expression profiling by high throughput sequencing of LT-HSC cells and GMP cells for AML1/ETO mice and control mice

first: Jianxiang

last: Wang

first: Shaowei

last: Qiu

first: Xiaoyu


title: PHF6 suppresses self-renewal of leukemic stem cells in AML

status: Public on Jun 25 2024

city: Philadelphia

first: Vikram

middle: R

last: Paralkar

state: PA

address: 421 Curie Boulevard

department: Division of Hematology and Oncology, Department of Medicine

institute: University of Pennsylvania Perelman School of Medicine

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

first: Subin

middle: S

last: George

first: Aishwarya

last: Pawar

first: Sapana

last: Jalnapurkar


title: Study of CPI-0209 in patients with advanced tumors.

first: Patrick

last: Trojer

overall_design: The patients were from the phase 1 portion of the phase 1/2 study of CPI-0209 in patients with advanced tumors (clinicaltrials.gov identifier: NCT04104776).  Phase 1 was a 7-cohort dose escalation study in patients receiving CPI-0209 once daily at doses between 50 and 375 mg. All patients gave informed consent and the trial was conducted in accordance with the Declaration of Helsinki.

first: Patricia

last: Keller

first: Elizabeth

last: Adams

first: Rentian

last: Wu


title: Wound induced small-peptide mediated signalling cascade regulated by OsPSKR, dictates balance between growth and defense in rice

first: Shivaprasad

last: Padubidri V.

summary: We identified the involvement of OsPSKR in perceiving PSK as KO plants were almost insensitive to PSK treatment

overall_design: We performed RNA-sequencing to check the transcriptional response of rice plants (both WT and OsPSKR KO)  to PSK treatment

first: V

last: Shivaprasad

first: C

last: Harshith


title: Transcriptome analysis to investigate the role of ACLY pathway in senescent cells.

city: Kumamoto

first: Mitsuyoshi

last: Nakao

address: 2-2-1 Honjo, Chuo-ku

department: Institute of Molecular Embryology and Genetics

institute: Kumamoto University

summary: Transcriptome analysis revealed that the inhibition of ACLY pathway supressed the expression of proinflammatory SASP

overall_design: Examination of the role of ACLY pathway in oncogene-induced senescent cells and in aged tissues

first: Kan

last: Etoh


title: BirthSeq, a new method to isolate and analyze dated cells in different vertebrates

city: Leioa

first: Fernando

last: García-Moreno

state: Bizkaia

address: Barrio Sarriena s/n Edificio Sede

country: Spain

institute: Achucarro BCN

summary: Embryonic development is a complex and dynamic process that unfolds over time and involves the production and diversification of increasing numbers of cells. The impact of developmental time on the formation of the central nervous system is well-documented, with evidence showing that time plays a critical role in establishing the identity of neuronal subtypes. However, the study of how time translates into genetic instructions driving cell fate is limited by the scarcity of suitable experimental tools. We introduce BirthSeq, a new method for isolating and analyzing cells based on their birth date. This innovative technique allows for in vivo labeling of cells, isolation via FACS, and analysis using high-throughput techniques. We tuned up BirthSeq in developmental organs across three vertebrate species (mouse, chick, and gecko), and fully made use of it for single-cell RNA sequencing and novel spatially resolved transcriptomic approaches in mouse and chick, respectively. Overall, BirthSeq provides a versatile tool for studying virtually any tissue in different vertebrate organism, helping to fill the necessity in developmental biology research by targeting cells and their temporal cues.

overall_design: Single cell RNA sequencing of birthdated cells from chicken and mouse were obtained by Birth-seq protocol published in this article. Birthdated cells with fluorescence EdU were FAC-Sorted and then droplet captured with 10X Genomics Chronium V3 pipeline. Libraries were sequenced with Novaseq 6000 for 50000 reads.

first: Eneritz

last: Rueda-Alaña

first: Marco

last: Grillo

first: Enrique

last: Vázquez

first: Sergio

last: Marco-Salas

first: Rodrigo

last: Senovilla-Ganzo

first: Laura

last: Escobar

first: Ana

last: Quintas-Gorozarri

first: Alberto

last: Benguría

middle: M

last: Aransay

first: Nora

last: Bengoa-Vergniory

last: Dopazo

first: Juan

last: Encinas

first: Mats

last: Nilson


title: Enrichment of various epigenetic histone marks in human myoblasts

city: Madison

first: Jeffrey

last: Dilworth

state: Wisconsin

address: 1111 Highland Ave

institute: University of Wisconsin

summary: WS234 cells are an immortalized human cell line. Here we have explored the distribution of histone marks (H3K27me3, H3K27ac, H3K4me3, H3K4me1, and  H3K9me3) across the genome in proliferative conditions.

overall_design: WS234 cells were grown in culture media for 48 hours and cells were trypsinized, counted and used for CUT&Tag studies. Two biological replicates per groups (total 12 samples) were subjected to CUT&Tag analysis using H3K27me3, H3K27ac, H3K4me3, H3K4me1, and  H3K9me3 or IgG antibodies. Accumulation of modified histones across the genome was analyzed.

first: Sarah

last: Hachmer

first: Matthew

last: Wong

first: Eric

last: Arezza

first: Lynn

last: Megeney

first: F


title: U4 inhibits premature cleavage and polyadenylation of pre-mRNAs [ChIP-seq]

first: chengguo

last: yao

summary: To understand how U4 snRNP regulates premature cleavage and polyadenylation of pre-mRNAs at the transcriptome wide,  we conducted RNAPII ChIP-seq analysis on control, U1 and U4-AMO treated samples.

overall_design: We carried RNAPII ChIP-seq analysis in NC AMO, U1 and U4 AMO-treated HeLa cells using an antibody targeting RNAPII CTD (santa cruz  sc-47701-X)

first: Qiumin

last: Feng

first: Zejin

last: Lin

first: Danhui

last: Zhao

first: Congting

last: Ye

first: Chengguo

last: Yao


title: The primitive endoderm supports lineage plasticity to enable regulative development [scRNA-Seq]

city: Copenhagen

first: Josh

last: Brickman

address: 3B Blegdamsvej

department: reNEW

institute: Copenhagen University

summary: Mammalian blastocyst formation involves the specification of trophectoderm followed by differentiation of the inner cell mass into embryonic epiblast and extra-embryonic primitive endoderm (PrE). During this time, the embryo maintains a window of plasticity and can redirect its cellular fate when challenged experimentally. In this context, we found that the PrE alone was sufficient to regenerate a complete blastocyst and continue postimplantation development. We identify an in vitro population similar to the early PrE in vivo that exhibits the same embryonic and extra-embryonic potency and can form complete stem cell-based embryo models termed blastoids. Commitment in the PrE is suppressed by JAK/STAT signalling, collaborating with OCT4 and the sustained expression of a subset of pluripotency-related transcription factors that safeguard an enhancer landscape permissive for multi-lineage differentiation. Our observations support the notion that transcription factor persistence underlies plasticity in regulative development and highlights the importance of the PrE in perturbed development.

overall_design: scRNA-seq of mouse 2iLIF ESCs, naïve extra-embryonic endoderm (nEnd), 3D nEnd and nEnd differentiated is trophoblast stem cell medium (TSC)

first: Madeleine

last: Linneberg-Agerholm

first: Alba

last: Redó-Riveiro

first: Annika

last: Charlotte Sell

first: Marta

last: Perera

first: Martin

last: Proks

first: Teresa

middle: E

last: Knudsen

first: Antonio

last: Barral

first: Miguel

last: Manzanares

first: Joshua


title: The primitive endoderm supports lineage plasticity to enable regulative development [CUT&Tag H3K4me3]

overall_design: Cleavage Under Targets & Tagmentation (CUT&Tag) of naïve extra-embryonic endoderm (nEnd) subpopulations


title: H3K27Ac ChIP-seq to investigate the role of ACLY pathway in senescent cells.

first: Mitsuyoshi

last: Nakao

summary: H3K27Ac ChIP-seq analysis revealed that the inhibition of ACLY pathway supressed the expression of proinflammatory SASP

overall_design: Examination of H3K27Ac occupancy in proliferative (Pro), oncogene-induced senescent (Sen), and ACLY-knockdowned Sen IMR-90 cells.

first: Kan

last: Etoh


title: The influence of TFEB on gene expression in primary murine germinal center and non-germinal center B cells

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

summary: To investigate TFEB-dependent mRNA expression in murine B cells, FACS-sorted germinal center and non-germinal center B lymphocytes of B-cell-specific conditional TFEB KO mice and control littermates were subjected to RNA sequencing analysis

overall_design: Comparative gene expression profiling analysis of RNA-seq data for FACS-sorted germinal center (CD19+GL7+CD95+) and non-germinal center (CD19+GL7-CD95-) B cells of conditional TFEB KO mice (Tfeb fl/fl Mb1-Cre +/-) and control littermates (Tfeb fl/fl Mb1-Cre -/-)

first: Matthias

last: Münchhalfen

first: Richard

last: Görg

first: Michael

last: Haberl