title: Prophage-encoded methyltransferase upregulates virulence to drive adaptation in an outbreak of community-acquired methicillin-resistant Staphylococcus aureus

city: New York

first: Alejandro

last: Pironti

state: NY

address: 430 East 29th Street

department: Microbiology

institute: NYU Langone Health

summary: To determine the effects of phage adenine methyltransferase (pamA) on gene expression in WT USA300 (LAC*)

overall_design: Comparative gene expression analysis of WT::pamA (USA300 LAC* containing a single copy of constituatively expressed pamA) and WT::EV control.

first: Robert

last: Ulrich

first: Bo

last: Shopsin


title: ACCELERATED CD8+ T CELL MATURATION IN INFANTS WITH PERINATAL HIV INFECTION

status: Public on Apr 16 2024

city: Miami

first: Akshay

last: Iyer

state: FL

country: USA

institute: University of Miami

type: Expression profiling by high throughput sequencing

summary: In perinatal HIV infection, early ART initiation is recommended but questions remain regarding infant immune responses to HIV and impact of HIV on immune development. Using single cell transcriptional and phenotypic analysis we evaluated the T cell compartment at pre-ART initiation of infants with perinatally acquired HIV from Maputo, Mozambique (TARA cohort). CD8+ T cell maturation subsets exhibited altered distribution in HIV exposed infected (HEI) infants relative to control infants (HIV exposed uninfected) with reduced naïve, increased effectors, higher frequencies of activated T cells, and lower frequencies of cells with markers of self-renewal. Additionally, a cluster of CD8+ T cells identified in HEI displayed gene profiles consistent with cytotoxic T lymphocytes (CTL) and showed evidence for hyper expansion. Longitudinal phenotypic analysis revealed accelerated maturation of CD8+ T cells was maintained in HEI despite viral control. The results point to a HIV directed immune response that is likely to influence reservoir establishment.

overall_design: Investigate gene expression profiles and T cell and B cell clonality in PBMC from 1 month old infants that aquired HIV perinatally.

first: Lesley

last: De Armas

first: Savita

last: Pahwa


title: Condensin I folds the C. elegans genome [RNA-seq]

status: Public on Apr 18 2024

city: Bern

first: Peter

last: Meister

state: Schweiz

address: Baltzerstrasse 4

department: Institute of Cell Biology

country: Switzerland

institute: University of Bern

summary: Structural Maintenance of chromosomes (SMC) complexes, cohesin and condensins, have been named after their roles during meiosis and mitosis. Recent data in mammalian cells and Drosophila have described the additional role of cohesin for genome folding into loops and domains during interphase. However, determinants of genome folding in holocentric species remain unclear. Using high resolution chromosome conformation capture, we show that overlapping large-scale nuclear localization and small-scale epigenomic states compartmentalize the C. elegans genome. By systematically and acutely inactivating each SMC complex, we observe that in contrast to other studied systems, cohesin creates small loops, while condensin I has a major role in genome folding: its inactivation causes genome-wide decompaction, chromosome mixing, loss of loops and TAD structures and reinforcement of fine-scale epigenomic compartments. Counter-intuitively, removal of condensin I and its X-specific variant condensin IDC from the X chromosomes led to the formation of a loop compartment coinciding with a subset of previously characterized loading sites for condensin IDC and bound by the X-targeting complex SDC. While transcriptional changes were limited for all autosomes upon cohesin and condensin II inactivation, removal of condensin I/IDC from the X chromosome led to transcriptional up-regulation of X-linked genes demonstrating that a sustained role for condensin IDC in gene regulation. Finally, while condensin I inactivation leads to reduced lifespan, we show that this reduction is due to X-specific gene upregulation rather than global genome decompaction.

overall_design: In this study, a total of 40 samples were analysed that comprise of 9 different strains in which different SMC complexes were inactivated and their controls. Each strain/condition has 3-4 biological replicates.

first: Moushumi

last: Das

first: Jennifer

last: Semple

first: Janik

last: Scotton

first: Ahrmad

last: Annan

first: Julie

last: Campos


title: Condensin I folds the C. elegans genome

status: Public on Apr 17 2024

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

overall_design: Refer to individual Series


title: High-Dimensional Single-Cell Multimodal Landscape of Human Carotid Atherosclerosis

status: Public on Apr 12 2024

first: Chenyi

last: Xue

institute: Columbia University


title: High-Dimensional Single-Cell Multimodal Landscape of Human Carotid Atherosclerosis [scRNA-seq]

summary:
Atherosclerotic plaques are complex tissues composed of a heterogeneous mixture of cells. However, our understanding of the comprehensive transcriptional and phenotypical landscape of the cells within these lesions is limited.
To characterize the landscape of human carotid atherosclerosis in greater detail, we combined cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) and single-cell RNA sequencing (scRNA-seq) to classify all cell types within lesions (n=21; 13 symptomatic) to achieve a comprehensive multimodal understanding of the cellular identities of atherosclerosis and their association with clinical pathophysiology.
We identified 25 cell populations, each with a unique multi-omic signature, including macrophages, T cells, NK cells, mast cells, B cells, plasma cells, neutrophils, dendritic cells, endothelial cells, fibroblasts, and smooth muscle cells (SMCs). Among the macrophages, we identified 2 proinflammatory subsets enriched in IL1B or C1Q expression, 2 TREM2 positive foam cells (one expressing inflammatory genes), and subpopulations with a proliferative gene signature and SMC-specific gene signature with fibrotic pathways upregulated. Further characterization revealed various subsets of SMCs and fibroblasts, including SMC-derived foam cells. These foamy SMCs were localized in the deep intima of coronary atherosclerotic lesions. Utilizing CITE-seq data, we developed a flow cytometry panel, using cell surface proteins CD29, CD142, and CD90, to isolate SMC-derived cells from lesions. Lastly, we observed reduced proportions of efferocytotic macrophages, classically activated endothelial cells, and contractile and modulated SMC-derived cells, while inflammatory SMCs were enriched in plaques of clinically symptomatic vs asymptomatic patients.
Our multimodal atlas of cell populations within atherosclerosis provides novel insights into the diversity, phenotype, location, isolation, and clinical relevance of the unique cellular composition of human carotid atherosclerosis. These findings facilitate both the mapping of cardiovascular disease susceptibility loci to specific cell types as well as the identification of novel molecular and cellular therapeutic targets for the treatment of the disease.

overall_design: Single-cell RNA sequencing (scRNA-seq) was performed on carotid athersclerotic plaques from 12 subjects (6 symptomatic).

first: Alexander

last: Bashore


title: Single cell atlas of the human retina

status: Public on Apr 25 2024

city: Palo Alto

first: Lattice

last: Data Coordination

state: CA

address: 3165 Porter Drive

department: Genetics

institute: Stanford University

type: Genome binding/occupancy profiling by high throughput sequencing

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

As the light sensing part of the visual system, the human retina is composed of five classes of neuron, including photoreceptors, horizontal cells, amacrine, bipolar, and retinal ganglion cells. Each class of neuron can be further classified into subgroups with the abundance varying three orders of magnitude. Therefore, to capture all cell types in the retina and generate a complete single cell reference atlas, it is essential to scale up from currently published single cell profiling studies to improve the sensitivity. In addition, to gain a better understanding of gene regulation at single cell level, it is important to include sufficient scATAC-seq data in the reference. To fill the gap, we performed snRNA-seq and snATAC-seq for the retina from healthy donors. To further increase the size of the dataset, we then collected and incorporated publicly available datasets. All data underwent a unified preprocessing pipeline and data integration. Multiple integration methods were benchmarked by scIB, and scVI was chosen. To harness the power of multiomics, snATAC-seq datasets were also preprocessed, and scGlue was used to generate co-embeddings between snRNA-seq and snATAC-seq cells. To facilitate the public use of references, we employ CELLxGENE and UCSC Cell Browser for visualization. By combining previously published and newly generated datasets, a single cell atlas of the human retina that is composed of 2.5 million single cells from 48 donors has been generated. As a result, over 90 distinct cell types are identified based on the transcriptomics profile with the rarest cell type accounting for about 0.01% of the cell population. In addition, open chromatin profiling has been generated for over 400K nuclei via single nuclei ATAC-seq, allowing systematic characterization of cis-regulatory elements for individual cell type. Integrative analysis reveals intriguing differences in the transcriptome, chromatin landscape, and gene regulatory network among cell class, subgroup, and type. In addition, changes in cell proportion, gene expression and chromatin openness have been observed between different gender and over age. Accessible through interactive browsers, this study represents the most comprehensive reference cell atlas of the human retina to date. As part of the human cell atlas project, this resource lays the foundation for further research in understanding retina biology and diseases.


title: XIST dampens X chromosome activity in a SPEN-dependent manner during early human development [GRO-seq]

status: Public on Apr 24 2024

city: Paris

first: Claire

last: Rougeulle

address: 35 rue Helene Brion

department: Epigenetics and Cell Fate

country: France

institute: Université Paris Cité, CNRS

summary: XIST long non-coding RNA is responsible for X chromosome inactivation (XCI) in placental mammals, yet it accumulates on both X chromosomes in human female pre-implantation embryos without triggering X chromosome silencing. The long non-coding RNA XACT co-accumulates with XIST on active Xs and may antagonize XIST function. Here we used human ES cells in a naïve state of pluripotency to assess the function of XIST and XACT in shaping the X chromosome chromatin and transcriptional landscapes during pre-implantation development. We show that XIST triggers the deposition of polycomb-mediated repressive histone modifications and attenuates transcription of most X-linked genes in a SPEN-dependent manner, while XACT deficiency does not significantly affect XIST activity or X-linked gene expression. Our study demonstrates that XIST is functional prior to XCI, confirms the existence of a transient process of X chromosome dosage compensation, and reveals that X chromosome inactivation and dampening rely on the same set of factors.

overall_design: Low input fastGRO-seq on 3 independent clones of XIST CRISPRi naïve hESCs treated with doxycyclin. Untreated clones were used as controls.

first: Charbel

last: Alfeghaly


title: High-Dimensional Single-Cell Multimodal Landscape of Human Carotid Atherosclerosis [CITE-seq]

overall_design: CITE-seq was performed on carotid atherosclerotic plaques from 6 subjects (5 symptomatic)


title: Condensin I folds the C. elegans genome [Ribo-Zero-seq]

overall_design: There are 4 samples analysed in this study which comprises of 4 different strains, including the control.


title: Merkel cell polyomavirus small tumor antigen contributes to immune evasion by interfering with type I interferon signaling [RNA-Seq]

status: Public on Apr 04 2024

city: Hamburg

first: Jiabin

last: Huang

address: Martinistr. 52

country: Germany

institute: University Medical Center Hamburg-Eppendorf

summary:
Merkel cell polyomavirus (MCPyV) is linked to Merkel cell carcinoma (MCC), a rare and aggressive skin cancer.
This study investigated the influence of MCPyV T antigens on the host genome using transcriptomics and epigenomics. Results revealed a role for the small Tumor (sT) antigen in subverting type I interferon response and immune evasion, contributing to persistent infection and tumor progression. These findings enhance our understanding of MCPyV pathogenesis and may inform new therapeutic strategies.

overall_design: Use of a lentiviral transduction system to overexpress MCPyV T antigens (large Tumor (LT), small Tumor (sT), and truncated LT (LTtr)) in primary human dermal fibroblasts. Transcriptional profiling to investigate the interaction of T antigens with host cellular gene regulatory processes, focusing on inflammatory cytokines and interferon-stimulated genes (ISGs). Analysis of transcriptional changes induced by T antigens, such as the induction of inflammatory cytokines by both sT and LT, the short-term induction of ISGs by LT, and the stable repression of ISG transcription by sT. Investigation of the balancing effect of sT on immune recognition during the initial phase of infection and its potential role in maintaining a persistent infection. Evaluation of the transcriptional changes when sT is co-overexpressed with LTtr, reflecting the immunogenic feature of MCCs and their ability to attract innate and adaptive immune cells.

first: Ohnezeit

last: Denise

first: Huang

last: Jiabin

first: Fischer

last: Nicole


title: Merkel cell polyomavirus small tumor antigen contributes to immune evasion by interfering with type I interferon signaling [ChIP-Seq]


title: Disruption of TGF-β signaling pathway is required to mediate effective killing of hepatocellular carcinoma by human iPSC-derived NK cells

status: Public on Apr 08 2024

city: San Diego

first: Dan

middle: S

last: Kaufman

state: California

address: 2880 Torrey Pines Scenic Dr

department: School of Medicine

institute: University of California San Diego

summary: Hepatocellular carcinoma (HCC) is the most common type of primary liver cancer. Transforming growth factor beta (TGF-β) is highly expressed in the liver tumor microenvironment and is known to inhibit immune cell activity. Here, we used human iPSCs to produce natural killer (NK) cells engineered to mediate improved anti-HCC activity. Specifically, we produced iPSC-NK cells with either knock out TGF-β receptor 2 (TGFBR2-KO) or expression of a dominant negative (DN) form of the TGF-β receptor 2 (TGFBR2-DN) combined with CARs that target either GPC3 or AFP. The TGFBR2-KO and TGFBR2-DN iPSC-NK cells are resistant to TGF-β inhibition and improved anti-HCC activity. However, expression of anti-HCC CARs on iPSC-NK cells did not lead to effective anti-HCC activity unless there was also inhibition of TGF-b activity. Our findings demonstrate that TGF-β signaling blockade is required for effective NK cell function against HCC and potentially other malignancies which express high levels of TGF-β.

overall_design: The WT, TGFBR2-KO and TGFBR2-DN iPSC deived NK cells are differentiated and expanded were cultured in standard and memory like conditions. The libraries were prepared for RNA samples using the Illumina Stranded mRNA Library Prep Kit, targeting mRNA via poly-A selection for strand-specific cDNA synthesis. The libraries were sequenced using Illumina Novaseq X+ in the IGM Genomics Center at UCSD.

first: Jaya

middle: L

last: Thangaraj

first: Michael

last: Coffey

first: Edith

last: Lopez


title: Whole-genome bisulfite sequencing of Mandarin fish ranavirus

status: Public on Apr 02 2024

city: Zhuhai

first: Mincong

last: Liang

state: Guangdong

address: No. 2 Daxue Road

department: School of Marine Sciences

country: China

institute: Sun Yat-sen University

type: Methylation profiling by high throughput sequencing

summary: To characterize the site-specific methylation landscape of the Mandarin fish ranavirus (MRV) genome, whole-genome bisulfite sequencing (WGBS) was conducted on an isolated MRV strain.

overall_design: After inoculating Mandarin fish fry (MFF-1) cells with MRV (MG941005.3) at 27°C and 5% carbon dioxide in Dulbecco's modified Eagle medium (DMEM) for 3 days, the sample was collected after repeated freeze-thaw cycles.  Virions were purified using a modified double sucrose gradient ultracentrifugation method.  Genomic DNA was extracted from the purified virions using the FastPure Cell/Tissue DNA Isolation Mini Kit (Vazyme, China), and whole-genome bisulfite sequencing (WGBS) was subsequently performed.

first: Weiqiang

last: Pan

first: Shaoping

last: Weng

first: Jianguo

last: He

first: Changjun

last: Guo


title: An interplay between extracellular matrix proteins and the cancer cell promotes the multistep process of in vitro vasculogenic mimicry formation.

status: Public on Apr 11 2024

city: Santiago

first: Gareth

last: Owen

state: Region Metropolitana

address: Avenida Libertador Bernardo O'Higgins 340

department: Department of Physiology

country: Chile

institute: Pontificia Universidad Catolica De Chile

summary: Cancer vasculogenic mimicry (VM) is the formation of vasculature structures in the absence of endothelial cells. We previously established an in vitro model that facilitates the formation of a lumen-containing and fluid-conducting tubular structures after 4 days cancer cell growth on Matrigel. Herein, we mechanistically characterize this model in breast and ovarian cancer cell lines demonstrating distinct phases of VM formation and the dependence of specific extracellular matrix proteins. We report that VM occurs in four distinct stages. Firstly, alignment, migration then clustering delineate the area of the future tubular structure. Secondly, contraction of aligned structures followed by loss of attachment of some cells and cellular blebbing. Thirdly, a phase of mass proliferation followed by the raising of specific areas of the cancer cell mass above the Matrigel (bridge). Finally, the formation of a cell monolayer closes the tubular structure, forms a glycoprotein-rich luminal lining, then elevates the structure. Only later stages of VM require AKT and FAK signaling. We demonstrate that the lining of the tubular lumen is rich in laminin. Laminin 111 (but not collagen I) must be presence in the extracellular matrix (Matrigel) for VM to occur and integrin β1, but not integrin β3, is required. RNASeq demonstrates that formation is principally post-transcriptional regulation, however, this technique together with siRNA knockdown identified the first and essential biological function for the protein SMIM11A. VM is associated with poor patient survival and thus an understanding of the mechanism of VM may bring to light novel anticancer targets.

overall_design: To understand if they were changes on the levels of transcripts during vasculogenic mimicry formation, RNA was obtained from HEY-A8 cell lines that were seeded on either Matrigel, which allows the formation of vasculogenic mimicry, or on denatured Matrigel, which only forms a monolayer of cells. RNA samples were obtained at different timepoints of formation: 2, 8, 24 and 48 hours after the cells were seeded on either of both conditions.

first: Gabriel

last: Mingo

first: Andres

last: Valdivia

first: Varina

last: Aldana


title: Studies on the photosynthetic characteristics and mechanism of the upland cotton virescent recessive genic male sterile line Yt30

status: Public on Apr 09 2024

city: nanjing

last: Yang

state: 选择一项...

address: 江苏省南京市卫岗一号南京农业大学

institute: Nanjing Agricultural university

summary: Clarified the relationship between the photosynthetic performance and photosynthetic pigment metabolism of Yt30.

overall_design: We performed transcriptome sequencing using the Virescent mutant (Yt30) and its green wild-type first true leaf.


title: Transfer learning enables identification of multiple types of RNA modification using nanopore direct RNA sequencing

status: Public on Mar 28 2024

city: Shanghai

first: Xiang

last: Yu

address: 800 Dongchuan Road

institute: Shanghai Jiao Tong University

summary: RNA internal modifications play critical role in development of multicellular organisms and their response to environmental cues. Using nanopore direct RNA sequencing (DRS), we constructed a large in vitro epitranscriptome (IVET) resource from plant cDNA library labeled with m6A, m1A and m5C respectively. Furthermore, after transfer learning, the pre-trained model was used to detect additional RNA internal modification such as m1A, hm5C, m7G and Ψ modification. Finally, we illustrated a global view of epitranscriptome with m6A, m1A, m5C, m7G and Ψ modification in rice seedlings under normal and high salinity environment. In summary, we provided a strategy for creating IVET resource from cDNA library and developed a computational method that use IVET-based transfer learning termed TandemMod for profiling epitranscriptome landscape with co-occupancy of multiple types of RNA modification in plants responsive to environmental signal.

sample_organism:
Oryza sativa
synthetic construct

platform_organism:
Oryza sativa
synthetic construct

overall_design: Comparative epitranscriptome profiling analysis of DRS data for rice seedings under normal and high salinity environment.

first: You

last: Wu

first: Wenna

last: Shao

first: Mengxiao

last: Yan

first: Hongxia

last: Wang


title: BAI1 localises AMPA receptors at the cochlear afferent postsynaptic density and is

status: Public on Mar 27 2024

first: Fiorella

last: Grandi

address: 105 Bld d'Hopital

department: Centre de Recherche de Myologie

institute: Sorbonne Universite

summary: Type I spiral ganglion neurons (SGNs) convey sound information to the central auditory pathway by forming axo-somatic synapses with inner hair cells (IHCs), the primary sensory receptors of the mammalian cochlea. Although IHC ribbon synapses have been extensively studied, the molecular mechanisms regulating the structure and function of the post-synaptic density (PSD) at the SGN afferent terminals are largely unknown. Using functional, morphological, and transcriptomic approaches, we demonstrate that brain-specific angiogenesis inhibitor 1 (BAI1), encoded by the Adgrb1 gene, is required for the clustering of the glutamate AMPA receptors GluR2-4 to the SGN post-synaptic density. Adult mice expressing BAI1 lacking the N-terminal thrombospondin type 1 repeats (TRS) have functional IHC synapses but fail to transmit acoustic information to the SGNs, leading to highly raised auditory thresholds. We also found that in adult Bai1-deficient mice, despite the almost complete absence of AMPA receptors, the SGN fibres innervating the IHCs did not degenerate. RNA sequencing and western blotting also indicate that AMPA receptors are expressed in the cochlea of Bai1-deficient mice, highlights that BAI1 is involved is trafficking or anchoring GluR2-4 to the PSDs. Moreover, these results have identified novel molecular and functional mechanisms required for sound encoding at cochlear ribbon synapses.

overall_design: The sensory epithelium and spiral ganglion neurons from 4 mice were micro dissected in DNase free ice-cold PBS 1X and immediately snap frozen in liquid nitrogen. Two batches of 3 and 4 replicates (P7) and one batch of 3 replicates (P22) from each genotype.

first: Adam

last: Carlton

first: Jing-Yi

last: Jeng

first: Walter

last: Marcotti


title: Mapping functional to morphological variation reveals the basis of regional extracellular matrix subversion and nerve invasion in pancreatic cancer [RNA-Seq2]

status: Public on Mar 25 2024

city: Milan

first: Pierluigi

last: Di Chiaro

address: Via Adamello 16

department: Department of Experimental Oncology

country: Italy

institute: European Institute of Oncology (IEO)

summary: Intratumor morphological heterogeneity of pancreatic ductal adenocarcinoma (PDAC) predicts clinical outcomes but is only partially understood at the molecular level. To elucidate the gene expression programs underpinning intratumor morphological variation in PDAC, we investigated and deconvoluted at single cell level the molecular profiles of histologically distinct clusters of PDAC cells. We identified three major morphological and functional variants that co-exist in varying proportions in all PDACs, display limited genetic diversity, and are associated with a distinct organization of the extracellular matrix: a glandular variant with classical ductal features; a transitional variant displaying abortive ductal structures and mixed endodermal and myofibroblast-like gene expression; and a poorly differentiated variant lacking ductal features and basement membrane, and showing neuronal lineage priming. Ex vivo and in vitro evidence supports the occurrence of dynamic transitions among these variants in part influenced by extracellular matrix composition and stiffness and associated with local, specifically neural, invasion.

overall_design: Total RNA from primary human pancreatic ductal adenocarcinoma cells was processed for multiparallel sequencing. Experiments were carried out in PATC69 cell line cultured on collagen-coated plates of 12kPa and 1kPa stiffness (2 replicates each).


title: Mapping functional to morphological variation reveals the basis of regional extracellular matrix subversion and nerve invasion in pancreatic cancer [DNA-seq]

overall_design: Gland forming (GL) and non-gland forming (NGL) tumor areas of 200-500 cells were collected from FFPE tissues in a cohort of 10 primary pancreatic ductal adenocarcinoma (PDAC) patients. Single or multiples areas were processed per patient for a total of 52 samples.


title: FER kinase governs invasive tumor growth through dynamic control of oncogenic growth factor receptor activity

status: Public on Mar 31 2024

city: Utrecht

first: Peter

last: Haughton

address: Heidelberglaan 100

department: Pathology

country: Netherlands

institute: UMCU

summary: EGFR antagonism using monoclonal antibodies remains the only approved and targeted first line treatment option for non-resectable head and neck squamous cell carcinoma (HNSCC), yielding a modest 13% response rate. While it is clear that alternative growth factor receptor (GFR) signals govern refractory behavior towards EGFR antagonism, it remains unknown which upstream mechanisms control subcellular GFR activation. Here, we show that FER, a non-receptor tyrosine kinase, controls invasive tumor growth through dynamic GFR activation and recycling. Using patient derived organoid (PDO) models HNSCC we demonstrate that FER is essential for invasive growth in collagen extracellular matrix (ECM) networks. We show that inactivation of FER impairs growth factor dependent phosphorylation of EGFR-Y1068 and MET-Y1234/5. Additionally, FER controls ligand dependent endocytic recycling, and endocytic velocity, implying multifactorial functional regulation of proximal receptors during HNSCC invasion. Loss of function experiments using either genetic intervention or a FER PROteolysis-TArgeting Chimera (PROTAC) strategy in PDO-based xenograft mouse models, demonstrate that FER is essential for invasive growth and metastasis of HNSCC. Finally, we demonstrate direct clinical relevance by showing that FER expression levels correlate with poor survival in HNSCC patients. In sum, we conclude that FER is a master regulator of HNSCC invasive growth and metastasis, and nominate FER as a prominent candidate for targeted clinical intervention in HNSCC patients.

overall_design: Single-cell mRNA sequencing was performed on a tongue squamous cell carcinoma patient derived organoid line (T4), cultured in a collagen type-I (invasive) matrix in the absence (dox neg) or presence of doxycyline to induce a FER knockdown (dox pos).

middle: D

first: Wisse

last: Haakma

first: Sandra

last: Tavares

first: Lotte

middle: N

last: Enserink

first: Garik

last: Galustjan

first: Sjors

last: Koppes

first: Else

last: Driehuis

first: Hans

last: Clevers

first: Yanchun

last: Zhang

first: Gaofeng

last: Fan

first: Stefan

last: Willems

first: Patrick

middle: W

last: Derksen


title: Merkel cell polyomavirus small tumor antigen contributes to immune evasion by interfering with type I interferon signaling

first: Jiabin

last: Huang


title: iPSC-based modeling of preeclampsia identifies defects in extravillous trophoblast differentiation

city: La Jolla

first: Robert

middle: E

last: Morey

institute: UCSD

summary: Preeclampsia (PE) is a hypertensive pregnancy disorder with increased risk of maternal and fetal morbidity and mortality. Abnormal extravillous trophoblast (EVT) development and function is considered to be the underlying cause of PE, but has not previously been modeled in vitro. We previously derived induced pluripotent stem cells (iPSC) from placentas of PE patients and characterized abnormalities in formation of syncytiotrophoblast and responses to changes in oxygen tension. In this study, we converted these primed iPSC to naïve iPSC, then derived trophoblast stem cells (TSC) and EVT to evaluate molecular mechanisms underlying PE. We found that primed (but not naïve) iPSC-derived PE-EVT have reduced surface HLA-G, blunted invasive capacity, and altered EVT-specific gene expression. These abnormalities correlated with promotor hypermethylation of genes associated with the epithelial-mesenchymal transition pathway, specifically in primed-iPSC derived PE-EVT. Our findings indicate that abnormal epigenetic regulation might play a role in the PE pathogenesis.

overall_design: To investigate the mechanisms underlying preeclampsia (PE) we used iPSC derived from the placentas of three PE patients (1932, 1933, 1981) and three control patients (1754, 1938, 1947), converted these primed iPSC to naive iPSC and then differentiated the primed and naive iPSC lines to  trophoblast stem cells (TSC) and extravillous trophoblast (EVT).  We then performed gene expression profiling on all of  these samples using RNA-seq. For each timepoint and patient, we sequenced 3 replicates.

first: Mariko

last: Horii


title: Optimization of a Mouse Model of Pancreatic Cancer to More Closely  Simulate the Human Phenotypes of Metastasis and Cachexia

status: Public on Apr 10 2024

city: Charleston

first: Stefano

last: Berto

state: SC

address: 68 President Street, BE208

institute: MUSC

summary: Experment1: To study the difference between the parental KPC line and the KPCML1 metastatic cell line Experiment2: To study the differentially regulated genes in cachectic mice, we RNA sequenced the TA muscles of different mouse models of cachexia and their respective controls

overall_design: Experiment 1(Design) - KPC mouse pancreatic cancer parental cells were injected orthtopically into mouse pancreas. Cells were extracted from liver metastases to generatetthe KPCML1.  Experiment 2(Design) - Mice were injected with C26 (colon cancer) cells subcutaneously, LLC (lung cancer) cells intramuscularly, KPC or KPCML1 (pancreatic cancer cells) cells orthotopically, or tamoxifen to induce the pancreatic cancer genetic tumor model. Muscle were taken from tumor bearing mice as well as aged matched controls in each experiment

first: Deinis

last: Guttridge


title: UBE2N function in skin homeostasis and immunity

status: Public on Apr 03 2024

city: Durham

first: Jennifer

middle: Yunyan

state: NC

address: 3 Genome Ct, rm4130

department: Dermatology

institute: Duke University

summary: Epidermal keratinoyctes consitute the primary physical and biological barrier of the skin. The goal of this study is to determine the functions of keratinocyte UBE2N in regulation of skin homeostasis and immunity.

overall_design: We subjected C57BL6 WT and Rosa26CreER:Ube2nFlox/Flox mice back skin with topical treatments of 4-hydroxytamoxifen, and then collected WT and mutant skin samples for single-cell RNA-sequencing analysis.

first: Min

middle: J

last: Lee

first: Wanying

last: Miao

first: Vaibhav

last: Jain

first: Simon

last: Gregory

middle: Y


title: Mapping functional to morphological variation reveals the basis of regional extracellular matrix subversion and nerve invasion in pancreatic cancer

first: Pierluigi

last: Di Chiaro

overall_design: Refer to individual Series


title: Evaluating the effects of PTEN loss-driven cell transformation

status: Public on Apr 01 2024

city: Boston

first: Cherubin

last: Manokaran

state: Massachusetts

address: 450 Brookline Ave

department: Cancer Biology

institute: Dana Farber Cancer Institute

summary: We developed a unique in vitro transformation model utilizing PTEN CRISPR in the MCF10A human mammary epithelial cell line to study PTEN loss-induced transformation and profiled genome-wide expression in these cells to understand how PTEN loss alters the transcription landscape. We also examined changes in gene expression following inhibition of the p110b catalytic subunit of PI3 kinase, which is activated in the transformed cells. In addition, we profiled gene expression in MCF10A cells ectopically expressing PD-L1 (CD274), which is suppressed in cells harboring PTEN CRISPR.

overall_design: Examination of the effects of PTEN loss-driven transformation in mammary epithelial cells

first: Yubao

last: Wang

first: Thomas

middle: M

last: Roberts


title: Refined mechanism of promoter Nucleosome-Depleted Regions resetting after replication

city: Geneva

first: Sevil

last: Zencir

address: 30, quai Ernest-Ansermet

department: Department of Molecular and Cellular Biology

institute: University of Geneva

summary: Replication disrupts chromatin organization. Thus, rapid resetting of nucleosome positioning is essential to maintain faithful gene expression. The initial step of this reconfiguration occurs at Nucleosome-Depleted Regions (NDRs). While studies have elucidated the role of Transcription Factors (TFs) and Chromatin Remodelers (CRs) in vitro or in maintaining NDRs in vivo, none has addressed their in vivo function shortly after replication. Through purification of nascent chromatin coupled with yeast genetics, we dissected the choreography of events governing the proper positioning of the -1/+1 nucleosomes flanking promoter NDRs. Our findings reveal that CRs are the primary contributors of -1/+1 repositioning post-replication, with RSC acting upstream of INO80. Surprisingly, while Reb1 and Abf1 TFs are not essential for NDR resetting, they are required for NDR maintenance via the promotion of H3 acetylations. Taken together, we propose a two-step model for NDR resetting in S. cerevisiae: first, CRs alone reset promoter NDRs after replication, while a combination of TFs and CRs is required for subsequent maintenance.

overall_design:
Nucleosome occupancy was measured by MNase-seq upon nuclear depletion of Abf1, Reb1, Rpo21, Sth1, Ino80 and Rsc3 in mature and nascent chromatin analyzing ‘Input’ and ‘Edu-labeled’ samples respectively. Edu labeling efficiency was measured by comparing G1-arrested and S-phase EdU labeled samples. Sth1 binding was measured by ChEC-seq upon nuclear depletion of Ino80. The binding of Ino80 was measured by ChEC-seq upon nuclear depletion of Sth1. The effect of the TSA treatment on nucleosome positioning was measured by MNase-seq upon depletion of Sth1, Ino80 and Reb1.
Please note that processed data file generated from both replicates is linked to the corresponding rep1 sample records.

first: Jatinder

middle: K

last: Gill

first: Françoise

last: Stutz

first: Julien

last: Soudet


title: Temporal constraints on enhancer usage and enhancer-promoter connectivity shape the regulation of limb gene transcription [scRNA-seq]

status: Public on Mar 22 2024

first: Guillaume

last: Andrey

address: Rue Michel-Servet 1

department: Department of Genetic Medicine and Development

summary: Repertoires of transcriptional enhancers orchestrate gene expression during embryonic development, thereby shaping the forms and functions of organs. Within these repertoires individual enhancers display spatially distinct or overlapping activities that collectively build up the expression domain of cognate genes. However, the temporal specificity of these enhancers - how their activities change over developmental time to dynamically influence gene expression - remains uncharacterized. Here, we observed that temporally restricted enhancer repertoires are embedded at numerous loci associated with mouse limb development. To monitor how such enhancer repertoires govern gene transcription in vivo across extensive developmental periods, we introduce the regulatory trajectory framework. This paradigm conceptually involves transcriptional initiation, marking the beginning of gene expression, followed by its maintenance over time, and ultimately decommissioning, leading to gene repression. To track and sort cells undergoing these distinct phases, we devised a transgenic recorder approach at the Shox2 model locus. Through this method, we discovered that cells maintaining Shox2 transcription in early and late limb development relies on distinct, temporally restricted enhancer repertoires. We demonstrate that eliminating early- or late-acting enhancers only transiently affects Shox2 expression indicating that these enhancer repertoires function independently. Additionally, we found that changes in the 3D topology of the locus associate with enhancer activities and that a rapid loss of enhancer-promoter contacts occurs during decommissioning. Finally, we show that the decommissioning of the Shox2 locus can be actively driven by Hoxd13, a gene which expression is known to antagonize Shox2. Overall, our work uncovers the dependency of developmental genes on enhancers with temporally restricted activities to generate complex expression patterns over time and shed light on the dynamics of enhancer-promoter interactions.

overall_design: We devised a dual-reporter system to monitor Shox2 regulatory trajectories and sort cells undergoing these distinct phases. First, we inserted in mouse embryonic stem cells (mESCs), 1kb upstream of the Shox2 transcriptional start site, a regulatory sensor cassette constituted by a minimal β-globin promoter, a mCherry reporter gene followed by a destabilized PEST sequence, a P2A self-cleavage sequence and a CRE recombinase gene. These cells cells were then retargeted to integrate, at the Rosa26 locus, a cassette with a splice acceptor followed by a floxed 3x SV40pA STOP signal and the EYFP gene open reading frame. We studied the transcriptional identity of these cells by scRNA-seq. We the profile the identity of sorted cells by RNA-seq and their regulatory profile by CHiC and ChIP-seq

first: Raquel

last: Rouco


title: Mapping functional to morphological variation reveals the basis of regional extracellular matrix subversion and nerve invasion in pancreatic cancer [RNA-Seq3]

overall_design: Tumor areas of 200-500 tumor cells invading perineurial structures (outside or inside of infiltrating nerves) were collected from FFPE pancreatic ductal adenocarcinoma (PDAC) tissues in a cohort of 14 patients. Single or multiples areas were processed per patient for a total of 42 samples.


title: Single nuclei gene expression profile for adult C. elegans and several longevity mutants

status: Public on Mar 21 2024

city: Ashburn

first: Shihong

middle: Max

last: Gao

address: 19700 Helix Dr

department: 4D Cellular Physiology

institute: Janelia Research Campus

summary: We presents a complete single-cell atlas of aging worms, encompassing both somatic and germ cell types. This atlas was built upon 241K nuclei across the worm lifespan at day 1, 6, 12, and 14 (100%, 99%, 61%, and 14% survival rates, respectively). The worms were aged under normal physiological conditions, without interfering with their reproductive processes.

overall_design: To perfom snRNAseq for wild-type and longevity worms, we harvested and homogenized ~2,000 worms for each genotype/condition. Nuclei were isolated using fluorescence-activated cell sorting (FACS) based on the DNA content signal and then proceed with 10x Chromium sequcing.

first: Yanyan

last: Qi

first: Hongjie

last: Li

first: Yusi

last: Fu

first: Meng


title: Temporal constraints on enhancer usage and enhancer-promoter connectivity shape the regulation of limb gene transcription [Caupture-HiC]

summary: The repertoire of enhancers orchestrating gene expression during embryonic development shapes the forms and functions of organs. Within regulatory landscapes, enhancers control their target genes through spatially distinct or overlapping activities. However, the temporal specificity of enhancers repertoires—how their activities change over time to dynamically influence gene expression—is less well characterized. In this study, we introduce the regulatory trajectory framework to monitor how enhancer landscapes govern gene transcription in vivo across extensive developmental periods. This paradigm conceptually involves transcriptional initiation, marking the beginning of gene expression, followed by its maintenance over time, and ultimately decommissioning, leading to gene repression. To track and sort cells undergoing these distinct phases, we devised a transgenic recorder approach at the Shox2 model locus. Through this method, we discovered that cells maintaining Shox2 transcription in early and late limb development relies on distinct, temporally restricted enhancer repertoires. We demonstrate that eliminating early- or late-acting enhancers only transiently affects Shox2 expression indicating that these enhancer repertoires function independently. Additionally, we found that changes in the locus' 3D topology associate with enhancer activities and that a rapid loss of enhancer-promoter contacts occurs during decommissioning. Finally, we show that the decommissioning of the Shox2 locus can be actively driven by Hoxd13, a gene which expression is known to antagonize Shox2. Overall, our work uncovers the dependency of developmental genes on enhancers with temporally restricted activities to generate complex expression patterns over time and shed light on the dynamics of enhancer-promoter interactions.


title: RNAseq for Young Old mouse liver hepatocytes with and without high fat diet

status: Public on Apr 17 2024

first: Xue

last: Lei

address: 10901 N Torrey Pines Rd

institute: SBP medical discovery institute

summary: Our Goal was to determine how hepatocytes of young and old mice differentially respond to 9-weeks of high fat diet vs normal chow.

overall_design: Upon receipt mice were rested for at least 2-weeks prior to initiation of experiment in which mice were maintained on either High fat diet (58y1, TestDiet) or  normal CHOW (Teklad global 18% protein) for 9-weeks prior to euthanasia and hepatocyte isolation.

first: Peter

last: Adams

first: Aaron

last: Havas


title: Autophagy regulates glucagon secretion via the beta2-adrenergic pathway

first: Hui

last: Pan

address: 1 Joslin Place

department: Bioinformatics and Biostatistics Core

institute: Joslin Diabetes Center

summary: Appropriate glucagon secretion from pancreatic alpha cells in response to hypoglycemia is an important component of maintaining glucose homeostasis. Dysregulated glucagon secretion leads to the delayed recovery from a hypoglycemic attack in type 1 diabetes patients which can be lethal. Although elucidating the precise mechanism of glucagon secretion in hypoglycemia is warranted, the underlying mechanism remains poorly understood.The present study provides evidence of the role of autophagy in glucagon secretion in hypoglycemia by demonstrating that autophagy regulates adrenergic stimulation of glucagon secretion downstream of beta2 adrenergic receptor. First, from the analyses of T1D human islets and the published database of scRNA-seq of T1D human alpha cells, we described autophagy pathways altered in T1D alpha cells.  Second, we generated alpha cell-specific Atg7KO mice (alphaAtg7KO) and clarified that the lack of autophagy in alpha cells impairs the reactive glucagon secretion in acute hypoglycemia. Third, to interrogate the molecular mechanism of autophagy-mediated glucagon regulation, we analyzed top genes downregulated inT1D and T2D alpha cells and found the expression of beta2 adrenergic receptor showed significant down-regulation in T1D alpha cells. We confirmed the decreased expression of  beta2 adrenergic receptor in alpha cells of the T1D pancreas section, the islets of alphaAtg7KO mice, and a murine alpha cell line with stable knockdown of Atg7. Furthermore, in vivo and ex vivo studies of alphaAtg7KO mice exhibited that lack of autophagy led to the loss of stimulatory effect of beta2-adrenergic signaling on glucagon secretion. Finally, we established the Atg7 knockdown model in sorted human alpha cells and confirmed the effect of autophagy on the expression of the beta2 adrenergic receptor. Together, our study provides novel insights into the regulatory role of autophagy in glucagon secretion in response to hypoglycemia and provides therapeutic options to achieve stable glycemic control in T1D patients.

overall_design: Freshly-isolated human pancreatic islets from nondiabetic subjects (n=4) and type 1 diabetes patients (n=3) were analyzed for RNA-seq. Samples were treated with or without ER stress inducer, thapsigargin (250 nM) for 24 hours.

first: Kimitaka

last: Shibue

first: Rohit

last: Kulkarni


title: Temporal constraints on enhancer usage and enhancer-promoter connectivity shape the regulation of limb gene transcription [RNA-seq]

overall_design:
We devised a dual-reporter system to monitor Shox2 regulatory trajectories and sort cells undergoing these distinct phases. First, we inserted in mouse embryonic stem cells (mESCs), 1kb upstream of the Shox2 transcriptional start site, a regulatory sensor cassette constituted by a minimal β-globin promoter, a mCherry reporter gene followed by a destabilized PEST sequence, a P2A self-cleavage sequence and a CRE recombinase gene. These cells cells were then retargeted to integrate, at the Rosa26 locus, a cassette with a splice acceptor followed by a floxed 3x SV40pA STOP signal and the EYFP gene open reading frame. We studied the transcriptional identity of these cells by scRNA-seq. We the profile the identity of sorted cells by RNA-seq and their regulatory profile by CHiC and ChIP-seq

***************************************************************
The table below lists GEO accessions reused/reanalyzed for this study.
***************************************************************


title: Mycobacterium tuberculosis induced interferon pathways distinguish responses of Human Alveolar Macrophages from Monocyte-Derived Macrophages

status: Public on Mar 20 2024

city: Seattle

first: Kimberly

middle: A

last: Dill-McFarland

state: WA

address: 750 Republican St

department: Allergy and Infectious Diseases

institute: University of Washington

summary: Alveolar macrophages (AMs) and recruited monocyte-derived macrophages (MDMs) mediate early lung immune responses to Mycobacterium tuberculosis (Mtb). Using paired human AMs and MDMs from 6 healthy volunteers, we investigated transcriptional profiles in responses to Mtb. We found 681 genes that were Mtb-dependent in AMs compared to MDMs, 107 that were induced in both cell types but in different directions, and 4538 that were Mtb-dependent in MDMs but not AMs (FDR < 0.05). We found that IFNA Response and IFNG Response were the top two gene sets selectively induced in Mtb-infected AM. Thus, a second experiment utilized MDMs treated with IFNA1, IFNA8, IFNE, or IFNL1 found that  IFNA8 modulated Mtb-induced pro-inflammatory cytokines and, compared to other interferons,stimulated unique transcriptional profiles.

overall_design: Using paired human AMs and 5-day MCSF-derived MDMs from 6 healthy volunteers, we infected cells for 6 hours with Mtb H37Rv, isolated RNA, and analyzed transcriptomic profiles with RNASeq. A second experiment utilized MDMs treated with IFNA1, IFNA8, IFNE, or IFNL1 for 6 hours.

first: Monica

last: Campo

first: Glenna

last: Peterson

first: Basilin

last: Benson

first: Shawn

last: Skerret

first: Thomas

middle: R

last: Hawn


title: Temporal constraints on enhancer usage and enhancer-promoter connectivity shape the regulation of limb gene transcription

first: Guillaume

last: Andrey


title: Temporal constraints on enhancer usage and enhancer-promoter connectivity shape the regulation of limb gene transcription [ChIP-seq]

first: Raquel

last: Rouco


title: Inheritance of miRNAs via Yolk Promotes Stress Resilience in Progeny [small RNA]

status: Public on Mar 12 2024

first: Germano

last: Cecere

address: Institut Pasteur, 28 Rue Du Docteur Roux, Batiment Monod, 5eme Etage

department: Development and stem cell biology

institute: Institut Pasteur

type: Non-coding RNA profiling by high throughput sequencing

summary: At the onset of reproduction, oviparous animals synthesize large amounts of yolk in somatic tissues to provide lipids and other nutrients to their progeny. However, whether the yolk transports other types of molecules, such as RNAs with gene regulatory functions, remains largely unexplored. Here, we have biochemically purified the yolk granules in the nematode Caenorhabditis elegans and show they contain microRNAs (miRNAs). We provide evidence that the yolk transports such miRNAs from the mother’s intestine to the embryos via the lipoprotein yolk receptor RME-2. These yolk-enriched miRNAs inherited by the embryos regulate the transcriptomes of developing larvae. Moreover, environmental stresses and maternal age modulate the transfer of yolk-enriched miRNAs, contributing to stress resilience benefits to progeny. This discovery establishes a novel paradigm in intergenerational gene regulation, where the gut-germline axis orchestrates the transmission of environmental cues through yolk-enriched miRNAs. Our work reveals a new mechanism underlying the soma-to-germline transfer of epigenetic information in animals.

overall_design:
small RNA sequencing profiles of sorted yolk by VIT-2::GFP and 2-cell embryos under different conditions of growth and genotypes.
RNA sequencing profiles of 2-cell embryos or freshly hatched L1 larvae.

first: Névé

last: Aupérin

first: Meetali

last: Singh

first: Loan

last: Bourdon

first: Almira

last: Chervova

first: Julie

last: Ovieve

first: Pierre-Henri

last: Commere

first: Hélène

last: Lopez-Maestre

first: Florent

last: Dingli

first: Damarys

last: Loew


title: A critical role for Hepatocyte Nuclear Factor 4 alpha in polymicrobial sepsis-associated metabolic reprogramming and death: effect of CLP/SHAM in Hnf4a WT and KO mice

city: Gent

first: Steven

last: Timmermans

address: Technologiepark 71

country: Belgium

institute: VIB-UGent

summary: In sepsis, limited food intake and increased energy expenditure induce a starvation response, which is compromised by a quick decline in expression of hepatic PPARα, a transcription factor essential in intracellular catabolism of free fatty acids. The mechanism upstream of this PPARα downregulation is unknown. We found that sepsis causes a progressive hepatic loss-of-function of HNF4α, which has strong impact on the expression of several important nuclear receptors, including PPARα. HNF4α depletion in hepatocytes dramatically increases sepsis lethality, steatosis and organ damage and prevents an adequate response towards IL6, which is critical for liver regeneration and survival. An HNF4α agonist protects against sepsis at all possible levels, irrespectively of bacterial loads, suggesting HNF4α is crucial in disease tolerance to sepsis. In conclusion, hepatic HNF4α fails in sepsis, causing PPARα downregulation and metabolic problems and a disturbed IL6-mediated acute phase response. The data open new insights and therapeutic options in sepsis.

overall_design: RNA-seq in WT mice and Hnf4a KO (inducible: induced by tamoxifen) mice sebjected to SHAM or CLP surgery, livers were isolated for transcripome profiling, using 4 biological replicates

first: Céline

last: Van Dender

first: Ville

last: Paakinaho

first: Tineke

last: Vanderhaeghen

first: Jolien

last: Vandewalle

first: Maarten

last: Claes

first: Bart

last: Roman

first: Jan

last: De Waele

first: Siska

last: Croubels

first: Karolien

last: De Bosscher

first: Jorma

last: Palvimo

first: Claude

last: Libert


title: Inheritance of miRNAs via Yolk Promotes Stress Resilience in Progeny

city: Paris

first: Germano

last: Cecere

overall_design: RNA sequencing profiles of 2-cell embryos or freshly hatched L1 larvae.

first: Névé

last: Aupérin

first: Meetali

last: Singh

first: Loan

last: Bourdon

first: Almira

last: Chervova

first: Julie

last: Ovieve


title: Herpesvirus remodel organization and function of mitochondria as infection proceeds

status: Public on Mar 18 2024

city: Kuopio

first: Henri

last: Niskanen

department: A.I. Virtanen Institute

country: Finland

institute: University of Eastern Finland

summary: During the infection, viruses target mitochondria to promote viral replication. Infection-induced stress during the progression of infection leads to the regulation of antiviral defenses and mitochondrial metabolism which are opposed by counteractions of viral factors. The precise structural and functional changes that underlie how mitochondria react to the infection remain largely unclear. Our multimodal integration of advanced imaging, genomics, and metabolomics draws a comprehensive picture of time-dependent changes in mitochondria as HSV-1 infection proceeds from early to late infection.

overall_design: Vero cells were infected with HSV1 and samples for GRO-Seq were collected 4 or 8 hours post infection.

first: Salla

last: Mattola

first: Minna

last: Kaikkonen

first: Elina

last: Mäntylä

first: Maija

last: Vihinen-Ranta


title: RNA-Seq Analysis Unraveling Novel Genes and Pathways Influencing Corneal Wound Healing

status: Public on Mar 11 2024

city: Columbia

first: Rajiv

last: Mohan

state: Missouri

address: 1520 East Rollins University of Missouri

department: Department of Veterinary Medicine and Surgery

institute: University of Missouri

summary: Transparent avascular cornea providing two third refraction to the eye. Restoration of corneal transparency and clear vision in a traumatic eye involves the action of many cytokines and signaling pathways. Out of several factors, stromal keratocytes/fibroblasts (CSFs) play a central role in corneal repair and wound healing. Post trauma, keratocytes/fibroblasts produce myofibroblasts to facilitate wound repair by synthesizing and secreting large extracellular matrix components, collagens, and alpha-smooth muscle actin stress fibers. This study aimed to perform RNASeq data analysis and pathway enrichments to gain a better understanding of gene regulation in corneal fibroblasts and myofibroblasts in corneal wound repair.

overall_design: To investigate differential gene expression, pathway enrichment, and gene regulation in corneal fibroblasts and myofibroblasts in corneal wound repair

first: Rajnish

last: Kumar

first: Ratnakar

last: Tripathi

first: Nishant

last: Sinha


title: 3D reconstruction of the mouse cochlea from scRNA-seq data suggests morphogen-based principles in apex-to-base specification

status: Public on Mar 04 2024

city: Ann Arbor

first: Joerg

last: Waldhaus

state: MI

address: Medical Sciences I Building, Rm. 5315A, 1150 West Medical Center Drive

department: Department of Otolaryngology–Head and Neck Surgery, Kresge Hearing Research Institute

institute: University of Michigan

summary: In the mammalian auditory system, frequency discrimination depends on numerous morphological and physiological properties of the organ of Corti that gradually change along the longitudinal (tonotopic) axis of the organ. For example, the basilar membrane stiffness changes tonotopically, thus affecting the tuning properties of individual hair cells. At the molecular level, those frequency-specific characteristics are mirrored by gene expression gradients; however, the molecular mechanisms controlling tonotopic gene expression in the mouse cochlea remain elusive. Through analyzing scRNA-seq data from two developmental time points, we predicted that morphogens, rather than a timing-associated mechanism, confer spatial identity in the cochlea. Subsequently, we reconstructed the developing cochlea in 3D space from scRNA-seq data to investigate the molecular pathways mediating tonotopic information. The retinoic acid and sonic hedgehog pathways were found to form opposing tonotopic gradients, and functional interrogation using mouse cochlear explants suggested that both pathways jointly specify the tonotopic axis during development.

overall_design: We investigated the transcriptional heterogeneity from the developing cochlear duct at embryonic day (E)12.5 and E14.5 via single-cell RNA sequencing (scRNA-seq). Inner ears samples were dissected from the Sox2-GFP mouse line and cochlea was separated from vestibular compartments. Cochlea samples were digested to single-cell level and subjected to fluorescence activated cell sorting of Sox2-GFP+ cells. For each time point, two independent libraries were generated using the 10x Genomics platform.

first: Shuze

last: Wang

first: Saikat

last: Chakraborty

first: Mary

middle: P

last: Lee


title: Transcription factor genomic occupancy is determined by multiple, overlapping DNA binding sites

status: Public on Mar 06 2024

first: Shubham

last: Khetan

state: MA

address: 77 Avenue Louis Pasteur

institute: Brigham and Women's Hospital

summary: Transcription factors (TFs) regulate gene expression by interacting with DNA in a sequence-specific manner. High-throughput in vitro technologies, such as PBMs and HT-SELEX, have revealed the DNA binding specificities of hundreds of TFs. However, they have limited ability to reliably identify lower affinity binding sites, which are increasingly recognized as important for precise spatial and temporal control of gene expression. To address this limitation, we developed a novel technology to measure protein affinity to DNA by in vitro transcription and RNA sequencing (PADIT-seq). Using PADIT-seq, we comprehensively assayed the binding preferences of four human and two yeast TFs to all possible 10-bp DNA sequences, detecting hundreds of novel lower affinity binding sites. The expanded repertoire of lower affinity binding sites unexpectedly revealed that nucleotides flanking high affinity DNA binding sites create overlapping lower affinity sites that together modulate TF genomic occupancy in vivo. We propose a model where TF binding is not determined by individual binding sites, but rather by the sum   of multiple, overlapping binding sites. Formation of such extended recognition sequences stems from an inherent property of TF binding sites to interweave each other. Consequently, competition between paralogous TFs for shared high-affinity binding sites is controlled by flanking nucleotides that create differential numbers of overlapping lower affinity binding sites. Noncoding variants alter multiple, overlapping binding sites to influence gene expression and human traits, including diseases.

overall_design: Binding preferences of 6 TFs to all possible 10-mers using PADIT-seq, a novel technology to detect TF-DNA interactions across the entire spectrum of affinities.

first: Brent

last: Carroll

first: Martha

last: Bulyk


title: Extensive and dynamic changes in the human blood transcriptome and its circadian organisation when lying in bed, head down, for 60 days

status: Public on Mar 09 2024

city: Guildford

first: Simon

last: Archer

address: Stag Hill

country: United Kingdom

institute: University of Surrey

summary: We investigated the human 24-h time series blood transcriptome in 20 individuals during a 90-day constant bed rest protocol.

overall_design: A total of 637 samples, involving 20 human subjects. Each subject contributed up to 36 samples, gathered across 24 hours over 6 different days.

first: Carla

last: Moller-Levet

first: Maria-Angeles

last: Bonmati-Carrion

first: Emma

last: Laing

first: Derk-Jan

last: Dijk


title: Aberrant non-canonical NF-κB signalling reprograms the epigenome landscape to drive oncogenic transcriptomes in multiple myeloma [RNA1]

status: Public on Mar 01 2024

city: Singapore

first: Yinghui

last: Li

state: Singapore

address: 60 Nanyang Drive

department: School of Biological Sciences

country: Singapore

institute: Nanyang Technological University

summary: In multiple myeloma, abnormal plasma cells establish oncogenic niches within the bone marrow by engaging the NF-κB pathway to nurture their survival while they accumulate pro-proliferative mutations. Under these conditions, many cases eventually develop genetic abnormalities endowing them with constitutive NF-κB activation. Here, we find that sustained NF-κB/p52 levels resulting from such mutations favours the recruitment of enhancers beyond the normal B-cell repertoire. Furthermore, through targeted disruption of p52, we characterise how such enhancers are complicit in the formation of super-enhancers and the establishment of cis-regulatory interactions with myeloma dependencies during constitutive activation of p52. Finally, we functionally validate the pathological impact of these cis-regulatory modules on cell and tumour phenotypes using in vitro and in vivo models, confirming RGS1 as a novel p52-dependent myeloma driver. We conclude that the divergent epigenomic reprogramming enforced by aberrant non-canonical NF-κB signalling potentiates transcriptional programs beneficial for multiple myeloma progression.

overall_design: RNA-sequencing (RNA-seq) of multiple myeloma cell lines KMS-11 and MM1.144 subjected to p52 knock down.

first: Daniel

last: Ang

first: Jean-Michel

last: Carter

first: Kamalakshi

last: Deka

first: Joel

middle: H

last: Tan

first: Jianbiao

last: Zhou

first: Qingfeng

last: Chen

first: Wee

last: Chng

first: Nathan

last: Harmston


title: Mouse Striatum scRNAseq:2months of age

status: Public on Feb 21 2024

city: Los Angeles

first: Kay

last: Linker

address: 10833 Le Conte Avenue, 53-263 CHS

department: Physiology

institute: UCLA

summary: The striatum is a functionally diverse brain region. We investigated astrocyte and glia diversity within this brain region.

overall_design: To investigate the functional heterogeneity of astrocytes from a defined brain region, we performed single cell RNA-seq of striatal cells from adult mice (8-9 weeks old).

first: Baljit

last: Khakh


title: An endosomal toll-like receptor inhibitor drug with therapeutic effects in autoimmune diseases

status: Public on Feb 29 2024

city: Suwon-si

first: Uisuk

last: Jeong

state: Gyeonggi-do

address: 206, World cup-ro

department: Molecular Science and Engineering

country: South Korea

institute: Ajou university

summary: Autoimmune disease is a systemic inflammatory response of immune blood cells caused by self-tolerance dysfunction, due to genetic or environmental factors or a combination thereof. Studies on autoimmune disease regarding the inhibition of toll-like receptor (TLR)7/9-MyD axis or the regulation of plasmacytoid dendritic cells (pDCs) and Th17 comprising an abundance of respective receptors have shown improvements in phenotypes or molecular markers, providing clues to the practicality of the inhibitors of endosomal TLRs. This study discovered several small-molecule compounds in endosomes exerting specific inhibitory effects on SITE1 shared among TLR 3, 7, 8, and 9, named endosomal TLR inhibitors (ETIs). The drug discovery process involved identifying lead compounds optimized to the receptors using a quantitative structure-activity relationship model and subsequent modification of the compounds to improve their binding affinity to target proteins. To propose a method of verifying the drug effects against side or placebo effect arising from false positives, the drug evaluation process converged from cellular response to signaling process to protein binding. Drug values on the inhibition of endosomal TLRs in autoimmune disease were assessed based on the onset of mild-to-life-threatening autoimmune disease including psoriasis, systemic lupus erythematosus, and multiple sclerosis. Complete healing was achieved for psoriasis through direct or indirect association with TLRs. Therapeutic potential of the novel ETIs for psoriasis was verified and is considered an effective drug for other autoimmune diseases associated with the TLR7/9-MyD axis.

overall_design: Gene expression profiling analysis of RNA-seq data to verify the effect of ETI41 or ETI60 treatment in TLR7 activation situation

first: Yangseon

last: Choi

first: Hongjun

first: Muhammad

last: Haseeb

first: Mahesh

last: Patra

first: Sangdun


title: Non-linear transcriptional responses to gradual modulation of transcription factor dosage

status: Public on Mar 02 2024

city: New York

first: Julia

last: Domingo

state: NY

address: 101 6th Av

institute: New York Genome Center

summary: Genomic loci associated with common traits and diseases are typically non-coding and likely impact gene expression, sometimes coinciding with rare loss-of-function variants in the target gene. However, our understanding of how gradual changes in gene dosage affect molecular, cellular, and organismal traits is currently limited. To address this gap, we induced gradual changes in gene expression of four genes using CRISPR activation and inactivation. Downstream transcriptional consequences of dosage modulation of three master trans-regulators associated with blood cell traits (GFI1B, NFE2, and MYB) was examined using targeted single-cell multimodal sequencing. We showed that guide tiling around the TSS is the most effective way to modulate cis gene expression across a wide range of fold-changes, with further effects from chromatin accessibility and histone marks that differ between the inhibition and activation systems. Our single-cell data allowed us to precisely detect subtle to large gene expression changes in dozens of trans genes, revealing that many responses to dosage changes of these three TFs are non-linear, including non-monotonic behaviours, even when constraining the fold-changes of the master regulators to a copy number gain or loss. We found that the dosage properties are linked to gene constraint and that some of these non-linear responses are enriched for disease and GWAS genes. Overall, our study provides a straightforward and scalable method to precisely modulate gene expression and gain insights into its downstream consequences at high resolution.

overall_design: ECCITE-seq experiments obtaining three different modalities from a single cell: Protein Hashes (HTO) to identify CRISPRi or CRISPRa cell line of origin, cDNA as measurement of RNA levels and sgRNAs (GDO) to ienditfy the unique loci perturbation

first: Júlia

first: Mariia

last: Minaeva

first: John

last: Morris

first: Marcello

last: Ziosi

first: Neville

last: Sanjana

first: Tuuli

last: Lappalainen


title: A critical role for Hepatocyte Nuclear Factor 4 alpha in polymicrobial sepsis-associated metabolic reprogramming and death: H3K27ac and H3K4me3 after CLP sepsis model

first: Steven

last: Timmermans

summary: Sepsis is a maladaptive host response towards an infection leading to tissue damage, organ failure, and ultimately death. In sepsis, limited food intake and increased energy expenditure induce a starvation response, which is hindered by hepatic disappearance of the key transcription factor PPARα. Since PPARα acts as a central player in intracellular catabolism of fatty acids (FAs), sepsis results in excess free FAs, which cause lipotoxicity. The mechanism upstream of the PPARα downregulation in sepsis is unknown. A potential mechanism resides in HNF4α, which regulates liver lipid metabolism directly by activating Ppara gene expression and indirectly by interacting with PPARα itself. A proper functioning of HNF4α is essential for maintaining liver identity. We here show that sepsis causes a progressive HNF4α loss-of-function in the liver, which impacts expression of several nuclear receptors, among which PPARα, and is characterized by a reduced HNF4α DNA binding. Specific HNF4α depletion in the liver dramatically worsens sepsis lethality, associated with increased steatosis and hepatocyte damage. HNF4α dysfunction also prevents an adequate response towards IL6, controlled by CEBPβ and STAT3, which is critical for a proper liver regeneration and survival. In addition, the HNF4α agonist NCT partially protects against sepsis by limiting hepatic steatosis and liver dysfunction. In conclusion, hepatic HNF4α fails in sepsis, causing PPARα downregulation and consequent metabolic problems on the one hand, and a disturbed IL6-mediated acute phase response and regeneration on the other hand. The data open new insights and therapeutic options in sepsis

overall_design: Chip-seq for histone modifications H3K27ac and H3K4me3 after in Sham and CLP conditions using 4biological replicates per group.

first: Céline

last: Van Dender

first: Ville

last: Paakinaho

first: Tineke

last: Vanderhaeghen

first: Jolien

last: Vandewalle

first: Maarten

last: Claes

first: Bart

last: Roman

first: Jan

last: De Waele

first: Siska

last: Croubels

first: Karolien

last: De Bosscher

first: Jorma

last: Palvimo

first: Claude

last: Libert


title: Comparing 10x Visium spatial transcriptomic technologies

status: Public on Feb 26 2024

city: Parkville

first: Matthew

last: Ritchie

state: Victoria

address: 1G Royal Parade

country: Australia

institute: The Walter and Eliza Hall Institute of Medical Research

summary: Spatial transcriptomics facilitates the understanding of gene expression within complex tissue contexts. Among the array of spatial capture technologies available is 10x Genomics’ Visium which provides whole tissue section profiling, enabling whole transcriptome spatial analysis. Our dataset comprises spleen tissue from mice infected with malaria, spanning multiple experiments and sample preparation protocols for tissue preservation, either as fresh frozen at optimal cutting temperature (OCT) or formalin-fixed paraffin-embedded (FFPE). Tissue placement was also considered, comparing direct tissue placement on the slide with the use of CytAssist (CA), which expands the Visium platform’s capabilities by allowing for the pre-selection of tissue sections and genes through a set of probes. We also include a matching scRNA-seq dataset that can be integrated with the spatial data.

overall_design: Samples were captured over 5 10x Genomics Visium fresh-frozen (FF) slides and 3 formalin-fixed paraffin-embedded (FFPE) slides and sequenced over 6 Illumina runs. A matching scRNA-seq sample of the 3 mouse spleens (708, 709, 713): 10x scRNA-seq with the large BioLegend panel of antibody derived tags (ADTs) was captured over 1 GEM wells and GEX, ADT, and HTO were sequenced over 1 Illumina run.

first: Mei

last: Du

first: Changqing

last: Wang

first: Charity

last: Law

first: Daniela

last: Amann-Zalcenstein

first: Casey

last: Anttila

first: Ling

last: Ling

first: Callum

last: Sargeant

first: Peter

middle: F

last: Hickey

first: Yunshun

last: Chen

first: Lisa

last: Ioannidis

first: Diana

last: Hansen

first: Rory

last: Bowden


title: Obesity-disrupted H3K4me3 in hematopoietic stem progentior cells in mice

status: Public on Mar 07 2024

city: Denver

first: Pluto

last: Bio

state: CO

address: 3575 Ringsby Ct Suite 414

institute: Pluto Bio

summary: Obesity alters long-term functions of hematopoietic stem cells (HSPCs), which are associated with myelopoitic bias and maladapted pro-inflammatory phenotype. H3K4me3 histone modification is generally considered an activating histone marks and is also liked with epigenetic programming for trained immunity. We aim to identify how obesity in mice alter H3K4me3 marks in HSPCs and study its impact on HSPC functions in vitro and in vivo.

overall_design: Comparative H3K4me3 marked peak analysis of ChIP-seq data for hematopoietic stem progenitor cells (Lin-Sca1+cKit+) obtained from the bone marrow of C57B6/J mice fed a high-fat diet or a normal-fat diet.

first: Norifumi

last: Urao

first: Kentaro

last: Takahashi


title: Nucleophosmin sustains WNT-driven cell proliferation and tumor initiation in vivo

status: Public on Feb 15 2024

city: Berlin

first: Chiara

last: Giacomelli

address: Robert-Rössle-Str. 10

institute: Max Delbrück Center for Molecular Medicine

summary: Nucleophosmin (NPM1) is a nucleolar protein frequently overexpressed in many solid tumours with little known about its functional role to support carcinogenesis. Here, we identify Npm1 as a commonly upregulated gene following Apc loss in highly proliferative tissues, and high expression correlates with increased proliferation in CRC patients. We show that NPM1 is dispensable for adult epithelial tissue homeostasis, however, it has a profound effect on WNT-driven intestinal and liver tumourigenesis, leading to reduced proliferation and extension of survival. Mechanistically, NPM1 depletion triggers integrated stress response (ISR) and p53 pathway activation. P53 deletion, or inhibition of the ISR effects, rescue proliferation following NPM1 loss. Overall, our results demonstrate that NPM1 supports WNT-driven cell proliferation and tumour initiation by attenuating p53 pathway activation or induction of ISR. Being dispensable for homeostasis, NPM1 presents as a promising target for cancer therapy in WNT-driven tumours with functional p53, including difficult to treat KRAS-mutant CRC and hepatic cancers.

overall_design: To investigate the role of Nucleophosmin (Npm1) on colorectal cancer, we conditionally deleted it in an APC null/KRAS mutant cancer model. Epithelial extracts three days post-KO were harvested from mice. Ribo-seq and total cytoplasmic RNA sequencing were performed to address the effects on translation as well as transcript levels. The experiment was performed in four independent mice. Replicates are indicated by _1/_2/_3/_4. CRUK Scotland Institute Mouse IDs are indicated.

first: Georgios

last: Kanellos

first: June

last: Munro

first: Owen

last: Sansom

first: Martin

last: Bushell


title: Long-Read Single-Cell RNA Sequencing Enables Cell Genotyping to Refine Subclone Detection in Chronic Lymphocytic Leukemia

city: Salt Lake City

first: Gabor

last: Marth

state: Utah

department: Human Genetics

institute: University of Utah

summary: Bruton's tyrosine kinase (BTK) inhibitors are effective treatments for chronic lymphocytic leukemia (CLL) due to BTK’s role in B-cell survival and proliferation. Though effective, resistance occurs most commonly due to a BTKC481S mutation that inhibits drug binding. Here, we sought to understand the impact of co-occurring BTK resistance mutations with known CLL driver mutations and the differential transcriptomic behavior of BTK-resistant CLL subclones in six patients who acquired BTKC481S mutations. We utilize MAS-seq, a long-read scRNAseq technology, to increase transcript coverage and expand the set of mutations that can be used to link cells to tumor subclones.

overall_design:
B-cells from pre- and post-treatment patient samples were isolated and sequenced using long-read scRNA-seq.

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Submitter states that missing raw data are being made available for controlled access in dbGaP.
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first: Gage

middle: S

last: Black

first: Xiaomeng

last: Huang

first: Yi

last: Qiao

first: Deborah

last: Stephens

first: Jennifer

last: Woyach

middle: T


title: Temporal gene expression changes and affected pathways in neurodevelopment of a mouse model of Smith-Lemli-Opitz syndrome

first: Libin

last: Xu

address: 1705 NE Pacific St

department: Medicinal Chemistry

summary: Smith-Lemli-Opitz syndrome is an autosomal recessive disorder that arises from mutations in the gene DHCR7, which encodes the terminal enzyme of cholesterol biosynthesis, leading to decreased production of cholesterol and accumulation of the cholesterol precursor, 7-dehydrocholesterol, and its oxysterol metabolites. The disorder displays a wide range of neurodevelopmental defects, intellectual disability and behavioral problems. However, an in-depth study on the temporal changes of gene expression in the developing brains of SLOS mice has not been done before. In this work, we carried out the transcriptomic analysis of whole brains from WT and Dhcr7-KO mice at four time points through postnatal day 0. First, we observed the expected downregulation of the Dhcr7 gene in the Dhcr7-KO mouse model, as well as gene expression changes of several other genes involved in cholesterol biosynthesis throughout all time points. Pathway and GO term enrichment analyses revealed affected signaling pathways and biological processes that were shared amongst time points and unique to individual time points. Specifically, the pathways important for embryonic development, including Hippo, Wnt, and TGF-β signaling pathways are the most significantly affected at the earliest time point, E12.5. Additionally, neurogenesis-related GO terms were enriched in earlier time points, consistent with the timing of development. Conversely, pathways related to synaptogenesis, which occurs later in development compared to neurogenesis, are significantly affected at the later time points, E16.5 and PND0, including the cholinergic, glutamatergic, and GABAergic synapses. The impact of these transcriptomic changes and enriched pathways is discussed in the context of known biological phenotypes of SLOS.

overall_design: Total RNA was sequenced for four replicates each of whole brains from WT and Dhcr7-KO mouse embryos/neonates at four different gestational time points, including three embryonic (E12.5, E14.5, and E16.5) and one postnatal time point (PND0).

first: Li

last: Amy

first: Tomita

last: Hideaki

first: Xu

last: Libin


title: Aberrant non-canonical NF-κB signalling reprograms the epigenome landscape to drive oncogenic transcriptomes in multiple myeloma

first: Yinghui

last: Li

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

overall_design: Refer to individual Series


title: Effects of PCB 52 Exposure Via Sub-Acute Nose-Only Inhalation on Gene Expression in Fat Depots of Adolescent Rats

city: Iowa City

first: Aloysius

middle: John

last: Klingelhutz

state: IA

address: 3-604 BSB, 51 Newton Road

department: Microbiology and Immunology

institute: University of Iowa

summary: Polychlorinated biphenyls (PCBs) are persistent environmental toxicants that pose a variety of health risks in humans. PCB 52 has been found in the indoor air of schools where adolescent students and staff are being actively exposed. This study examined the three different fat depots, namely, brown adipose tissue (BAT), subcutaneous adipose tissue (SAT), and visceral adipose tissue (VAT), of adolescent Sprague-Dawley rats after sub-acute exposure to PCB 52 via nose-only inhalation. Rats were exposed for 4 hours daily for 28 consecutive days. RNA extracted from both male and female fat depots were submitted for RNA sequencing to compare the effects of PCB 52 on the expression of genes in the fat depots.

overall_design: To determine the gene expression alterations following PCB 52 inhalation exposure in adolescent rats, samples from male and female fat depots (BAT, SAT, and VAT) were processed for RNA sequencing. (N = 6 per sex; Samples were excluded if RNA RINs were below 8).

first: Francoise

last: Gourronc

first: Amanda

last: Bullert

first: Hui

last: Wang

first: Brynn

last: Helm-Kwasny

first: Michael

last: Chimenti

first: Andrea

last: Adamcakova-Dodd

first: Xuefang

last: Jing

first: James

last: Ankrum

first: Peter

last: Thorne

first: Hans-Joachim

last: Lehmler


title: A human iPSC-derived multilineage liver organoid model containing Kupffer cells to study human sepsis-associated liver dysfunction [hiPSC-EMP-KC-pKC]

city: Minato

first: Yang

state: Tokyo

address: Shirokanedai 4-6-1

country: Japan

institute: The University of Tokyo

summary:
To incorporate Kupffer cells into hiPSC-LOs, we differentiated erythro-myeloid progenitors (EMPs) from hiPSCs.
We compares the gene expression profiles of hiPSC-EMPs with cord-blood hematopoietic stem and progenitor cells (CB-HSPCs); and EMP-generated Kupffer cells (EMP-KC) with human primary Kupffer cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for hiPSC, hiPSC-EMP, CB-HSPC, EMP-derived kupffer cells, and primary Kupffer cells.

first: Yunzhong

last: Nie

first: Hideki

last: Taniguchi


title: An MMSET inhibitor-induced changes in gene expression profile of multiple myeloma cells

city: Shimotsuke

first: Sae

last: Matsuoka

state: Tochigi

department: Center for Molecular Medicine

institute: Jichi  Medical  University

summary: We performed gene expression profiling to understand the mechansims of cytotoxic effects of an MMSET inhibitor on t(4;14)-positive multiple myeloma cells.

overall_design: We cultured the human myeloma cell line KMS34 with the MMSET inhibitor RK-552 and performed gene expression profiling using an Agilent GeneChip Array.

first: Jiro

last: Kikuchi


title: The Hxk1 protein of Candida albicans influences gene expression of both metabolic and virulence related genes

status: Public on Feb 13 2024

city: Merced

first: Clarissa

last: Nobile

state: California

address: 5200 N Lake road

department: Molecular and Cell Biology

institute: University of California MERCED

summary: The Hxk1 protein of Candida albicans is a moonlighting protein with a wide variety of functions. It phosphorylates N-acetylglucosamine (GlcNAc) which is necessary for different purposes in the cell including energy and chitin production. Further, this protein is a regulator for morphogenesis independent of its function during GlcNAc catabolism.To identify the regulatory role of Hxk1 and putative downstream regulator Hxk2, we performed CUT&RUN experiments for GFP-tagged Hxk1 strains and GFP-tagged Hxk2 strains.

overall_design: CUT&RUN for 3 biological replicates of GFP-tagged Hxk1, GFP-tagged Hxk2 and corresponding IgG negative controls.

first: Stefanie

last: Wijnants

first: Dimitrios

last: Sofras

first: Wouter

last: Van Genechten

first: Rudy

last: Vergauwen

first: Ashley

last: Valle Arevalo

first: Deepika

last: Gunasekaran

first: Craig

middle: L

last: Ennis

first: Sabrina

last: Jenull

first: Karl

last: Kuchler

first: Patrick

last: Van Dijck


title: Parallel tracking dosage compensation in the early mouse embryo

status: Public on Mar 15 2024

city: Boston

first: Chunyao

last: Wei

address: 185 Cambridge St.

department: Molecular Biology

institute: Massachusetts General Hospital

summary: We develop So-Smart-seq to interrogate a comprehensive transcriptome inclusive of coding, noncoding, and repetitive element transcription. We reveal that, surprisingly, de novo silencing pertains only to a subset of  paternal X (Xp) genes. In contrast, a set of evolutionarily older genes and LINEs demonstrate constitutive Xp silencing, adopt epigenetically distinct signatures, and do not require Xist to initiate silencing. On maternal X (Xm), however, these elements are hyperactivated. Thus, a significant subset of Xp elements appears to be inherited in a “pre-inactive” state. We also find that Xm-hyperactivation is timed to Xp silencing on an individual gene basis, giving rise to heterogeneity in the parallel track of dosage compensation as well. These conclusions have significant implications for the mechanism and evolution of imprinting in early mammals.

sample_organism:
Mus musculus
Mus musculus castaneus

platform_organism:
Mus musculus
Mus musculus castaneus

overall_design: Examining the full transcriptome of single preimplantation embryos at various stages from WT and Xist mutant mouse.

first: Barry

last: Kesner

first: Jeannie

last: Lee


title: Comparative analysis of gene expression in tumors responding and non-responding to anti-CTLA-4 in a preclinical study of melanoma

city: Bethesda

first: Teresa

last: Przytycka

state: MD

address: 8600 Rockville Pike

department: NLM

institute: NIH

summary: To investigate the diverse responses of the M4 mouse melanoma to immune checkpoint inhibitors, the tumors responding (R) and nonresponding (NR) to anti-CTLA-4 from a preclinical study of M4 melanoma were subjected to mRNA sequencing. The differentially expressed genes were analyzed to identify the signaling pathways that asscoiated with the therapeutic responses of the tumors.

overall_design: 40 C57BL/6 mice were implanted with the M4 melanoma cell line (B2905). When the tumors reached to average size of 75 mm^3, they were randomized to three groups: (1) 5 mice left untreated; (2) 5 mice treated with isotype control IgG2b; (3) 30 mice treated with anti-CTLA-4. The antibodies were given twice a week for two weeks. 20 tumors of the group (3) and 5 tumors of the group (2) were harvested for RNA sequencing. In the 10-11 days after the last dose of treatment, tumors were identified as nonresponders, responders, and stable disease if their sizes continued to increase, decrease, and remain stable, respectively.

first: Chi-Ping

last: Day

first: Eva

last: Guijarro

first: Glenn

last: Merlino


title: X inactivation regulates lymphocyte induced cardiac remodeling

status: Public on Feb 07 2024

city: Charleston

first: Stefano

last: Berto

state: SC

address: 68 President Street, BE208

institute: MUSC

summary: After menopause, women lose the protective effect of female hormones and experience increased risk of adverse cardiac remodeling following myocardial infarction (MI). This may be due in part to the deleterious effects of genes encoded on the X chromosome. On average, 15% of genes located on the X chromosome escape inactivation in women, resulting in over expression. We hypothesize that with age T-cells escape X-chromosome inactivation (XCI), thus exacerbating the inflammatory response and resulting in adverse post-MI remodeling in women. We will use 2 aims to delineate a mechanism defining age effects on XCI and how this in turn influences T-cell mediated post-MI remodeling. Aim 1 will test the hypothesis that older females have an increased number of T-cells that escape XCI and exacerbate monocyte recruitment and activation post-MI. Aim 2 will test the hypothesis that female mice with T-cells that have escaped XCI will have adverse remodeling and decreased post-MI survival. Our understanding of sex differences especially the influence of sex chromosomes during post-MI remodeling and development of heart failure is lacking. The information obtained from the proposed experiments will have direct implications for medical management of women post-MI.

overall_design: Myocardial infarction as induced in C57Bl6/J female mice by permanent occlusion of the left anterior descending artery ligation. At post-MI Day 5, cells were isolated from the infarct zone of young (3-5 months) and old (15-17 months old) and run for scRNA sequencing.

first: Bryan

last: Granger

first: Kristine

last: Deleon-Pennell


title: Comprehensive Transcriptomic Analysis of EWSR1::WT1 Targets Identifies CDK4/6 Inhibitors as a Novel Therapeutic for Desmoplastic Small Round Cell Tumor

status: Public on Feb 06 2024

city: New Orleans

first: Sean

middle: Bong

state: LA

address: 1700 Tulane Ave

department: Pathology

institute: Tulane University School of Medicine

summary: Desmoplastic small round cell tumor (DSRCT) is an aggressive, pediatric tumor characterized by the EWSR1::WT1 oncogene. Targeted therapies have not been developed and multimodal therapy is insufficient, leading to a 5-year survival rate of only 15-25%. Here, we deplete EWSR1::WT1 in DSRCT and for the first time establish its essentiality in vivo. Through transcriptomic analysis, we discover novel mechanistic insights into EWSR1::WT1 functionality including the uniqueness of its transcriptional alterations, the direct role of EWSR1::WT1 binding in gene upregulation, and the dominant role of the one of its two isoforms in transcription. We show that the dominant isoform binds to the CCND1 promoter and stimulates DSRCT growth through the Cyclin D-CDK4/6-RB axis. Treatment with the CDK4/6 inhibitor palbociclib successfully reduced growth in two DSRCT xenograft models. Given palbociclib’s previous approval by the FDA for the treatment of breast cancer, we advance palbociclib as an exciting DSRCT therapy that warrants urgent clinical investigation.

overall_design: DSRCT cell lines with doxycycline-indicuble shRNA against the EWSR1::WT1 fusion gene were cultured for 4-days  with or without doxycycline addition and harvested for analysis by RNA-seq.

middle: B

first: Justin

middle: W

last: Magrath


title: Ex vivo activation of the GCN2 pathway metabolically reprograms T cells leading to enhanced adoptive cell therapy

status: Public on Feb 17 2024

city: Toronto

first: Pamela

last: Ohashi

state: ON

address: 610 University Ave

department: Tumor Immunotherapy Program

country: Canada

institute: University Health Network

summary: The manipulation of T cell metabolism to enhance anti-tumor activity is an area of active investigation. Here, we report that activating the amino acid starvation response in effector CD8+ T cells ex vivo using the General Control Non-depressible 2 (GCN2) agonist halofuginone (halo) enhances oxidative metabolism and effector function. Further characterization revealed that halo-treated CD8+ T cells increased expression of the large neutral amino acid (LNAA) transporter CD98 as well as the co-stimulatory marker 4-1BB. Mechanistically, we identified autophagy coupled with the CD98-mTOR axis as key downstream mediators of the phenotype induced by halo treatment. The adoptive transfer of halo-treated CD8+ T cells into mice bearing well-established tumors led to robust tumor control and curative responses. Halo-treated T cells also synergized in vivo with a 4-1BB agonistic antibody to control tumor growth in a mouse model resistant to immunotherapy.  Importantly, treatment of human CD8+ T cells with halo resulted in similar metabolic and functional reprogramming. These findings demonstrate that activating the amino acid starvation response with the GCN2 agonist halofuginone can enhance T cell metabolism, effector function and anti-tumor activity, with the potential to augment existing clinical immunotherapeutic approaches.

overall_design: 12 CD8+ T-cell Samples profiled by RIBO-Seq: 3 Halofuginone (HALO)-treated samples, Ribosome-Protected RNA Fragments (RPF) profiled; 3 Control samples, RPF-profiled; 3 Halo-treated samples, total RNA profiled; 3 control samples, total RNA profiled.

first: St-Paul

last: Michael

first: Saibil

last: Samuel

first: Ohashi

last: Pamela

first: Sayad

last: Azin


title: A human iPSC-derived multilineage liver organoid model containing Kupffer cells to study human sepsis-associated liver dysfunction

first: Yang

last: Li


title: Identification of TREM1+CD163+ myeloid cells as a deleterious immune subset in HCC [Spatial Transcriptomics]

status: Public on Feb 04 2024

city: Laval

first: Maya

last: Saleh

state: Qc

address: 531 Boulevard des Prairies

department: Armand Frappier Santé Biotechnologie

institute: INRS

summary: Hepatocellular carcinoma (HCC) is an inflammation-associated cancer arising from viral and non-viral etiologies. Expansion of suppressive myeloid cells is a hallmark of chronic inflammation and cancer, but their heterogeneity in HCC is not fully resolved and might underlie immunotherapy resistance in the steatohepatitis setting. Here, we present a high resolution atlas of hepatic innate immune cells from patients with HCC that unravels a steatohepatitis contexture characterized by influx of inflammatory and immunosuppressive myeloid cells. A discrete myeloid cell population identified by selective expression of TREM1 and CD163 expands in steatohepatitis-HCC. We refer to this population as TREM1+ regulatory myeloid cells (Mreg), as it potently suppresses T cell effector functions, highly expresses TGFB1 and IL13RA1 and localizes to HCC fibrotic lesions.

overall_design: Single-cell RNA-seq (10x Genomics) on FACS-sorted CD45 + panTCRαβ - CD19 - innate immune cells freshly isolated from tumors (HCC) and adjacent non-tumoral (NT) liver sections were realized for 10 patients (10 HCC/CHC samples and 10 NT/TS samples). In parallel, we applied spatial transcriptomics (ST; Visium ® , 10x Genomics) on frozen tissue sections from two of the previous patients (2 CHC visium samples). Furthermore, bulk RNA-seq sequencing were performed on innate immunity cells that were isolated using the same sorting strategy designed for scRNAseq experiments, for six of the previous patients. Bulk RNA-seq sequencing were also realized on FACS-sorted cell population, namely THBS1_M (c0, c3 and c4) populations that were isolated according to specific sorting strategy. In summary, available data concerns 20 scRNA-seq samples, 2 visium spatial transcriptomics and 9 bulk RNA-seq.

first: Julie

last: Giraud

first: Domitille

last: Chalopin

first: Eloïse

last: Ramel

first: Thomas

last: Boyer

first: Atika

last: Zouine

first: Marie-Alix

last: Derieppe

first: Nicolas

last: Larmonier

first: Olivier

last: Adotevi

first: Brigitte

last: Le Bail

first: Jean-Frédéric

last: Blanc

first: Christophe

last: Laurent

first: Laurence

last: Chiche

first: Marc

last: Derive

first: Macha

last: Nikolski


title: Regulation of Spermatogenesis by Different Alternative Splicing Events of MEI1 Gene in Mongolian Horse

status: Public on Feb 02 2024

city: 呼和浩特市

first: 代玲

last: 宋

state: 内蒙古自治区

address: 内蒙古自治区呼和浩特市昭乌达路306号内蒙古农业大学新区

institute: lnner Mongolia Key Laboratory of Equine Science Research and Technology Innovation

summary: The Mongolian horse has the characteristics of cold resistance, rough feeding resistance, good endurance, strong disease resistance and strong gregariousness. The normal production of sperm in male mammals is the basis of reproduction, and spermatogenesis includes a mitosis, meiosis twice and metamorphosis of sperm cells. The MEI1 gene is involved in the meiosis cycle and is required for normal meiosis chromosome association. Previous studies have shown that alternative splicing of MEI1 gene can promote spermatogenesis in Mongolian horses. In this study, the expression of MEI1 gene was determined by immunofluorescence in the third generation Mongolian horse testicular sertoli cells. Two overexpressed lentiviral vectors with MXE and SE events of MEI1 gene were constructed and successfully infected into sertoli cells. CCK-8 was used to detect the proliferation and activity of infected cells, transcripomics and metabolomics were used to screen and annotate differential genes and differential metabolites in the two sertoli cells with MXE and SE events. After 72 h of virus infection, 193 differentially expressed genes and 11360 differentially expressed metabolites were screened, 109 up-regulated genes including MEI1 and 84 down-regulated genes, 7494 up-regulated metabolites and 3866 down-regulated metabolites. Differential genes and differential metabolites were mainly enriched in several pathways related to spermatogenesis. Differential genes such as IL31RA, ATP2B3, CASQ2 were highly expressed in SE events, IL11, PRLR, CCR7 were highly expressed in MXE events. Metabolites such as folic acid and spermine were highly expressed in SE events, citric acid and glutathione were highly expressed in MXE events. This suggested that both MXE and SE events of MEI1 gene can promote the activity of spermatogenesis signaling pathway, and the gene influences spermatogenesis by regulating the expression of metabolites. In summary, MXE and SE events of MEI1 gene can promote the expression of spermatogen-related genes and metabolites, and genes affect spermatogenesis by regulating the expression of metabolites. The results of this study laid a theoretical foundation for exploring the regulatory mechanism of different alternative splicing events on spermatogenesis in Mongolian horse.

overall_design: In this study, we constructed a MEI1 gene overexpression lentiviral vector with MXE and SE events and transfected it into supporting cells, respectively. With MXE group as the control group, CCK-8 was used to detect the proliferation and activity of infected cells. Transcriptomics and metabolomics were used to screen and annotate the differential genes and differential metabolites of the two supporting cells of MXE and SE events.

first: Dailing

last: Song

first: Yajuan

last: Weng

first: Baterin

last: Terigele

first: Guoqing

last: Wang

first: Dugarjaviin

last: Manglai

first: Bei


title: Gene expression analysis of murine wt and Nbeal2 -/- bone marrow derived mast cells (BMMCs) w/o IL-33 treatment

city: Jena

first: Marco

last: Groth

address: Beutenbergstraße 11

department: Core Facility - Next Generation Sequencing

institute: Leibniz Institute on Aging - FLI

summary: The Neurobeachin-like 2 (Nbeal2) protein is a BEACH (beige and chediak-higashi) family member. Loss of function mutations of the human NBEAL2 gene result in development of the gray platelet syndrome (GPS) a bleeding disorder characterized by macrothrombocytopenia, splenomegaly, and paucity of Î±-granules in megakaryocytes, platelets, mast cells (MCs), neutrophils and NK cells. We found that Nbeal2 deficiency in MCs leads to an enhanced resistance to growth factor deprivation, dysregulated distribution of c-Kit and of the multidrug resistant protein-1 (ABCB1), as well as to a pro-inflammatory MC-phenotype. These characteristics are caused by a defective protein degradation machinery resulting in accumulation of RSK and ribosomal proteins (RPS). These data demonstrate that Nbeal2 prevents oncogenic transformation by controlling protein homeostasis (proteostasis) in MCs.

overall_design: 16 samples in four groups: Nbeal2 -/- w/o IL-33: 4 samples; Nbeal2 -/- with IL-33: 4 samples; wildtype w/o IL-33: 4 samples; wildtype with IL-33: 4 samples.

first: Sebastian

last: Drube

first: Nico

last: Andreas