title: Activation of polo-like kinase 1 correlates with selective motor neuron vulnerability in familial ALS

status: Public on Aug 27 2024

first: Andreas

last: Hermann

summary: Mutations in the Fused in Sarcoma (FUS) gene cause familial amyotrophic lateral sclerosis (ALS), characterized by selective degeneration of spinal motor neurons (sMNs) with relative sparing of cortical neurons (CNs). The mechanisms underlying this cell-type vulnerability remain unclear. Here, we compare CNs and sMNs derived from FUS-ALS models to assess differential responses to FUS mutations. We find that CNs are less affected than sMNs in DNA damage repair, axonal organelle trafficking, and stress granule dynamics. RNA sequencing (RNA-seq) reveals distinct transcriptomic signatures, with sMNs uniquely activating DNA damage responses involving cell cycle regulators, particularly polo-like kinase 1 (PLK1). PLK1 is highly expressed in sMNs but not CNs, correlating with greater nuclear FUS loss and splicing defects in sMNs. Cross-comparison with other familial ALS RNA-seq datasets highlights PLK1 upregulation as a shared molecular feature. These findings identify intrinsic differences between CNs and sMNs in FUS-ALS and suggest PLK1 as a potential driver of sMN vulnerability.

overall_design: Patient-derived isogenic spinal motoneurons (MN) or cortical neurons (CN) expressing either normal (FUS WT) or mutant P525L FUS-eGFP (FUS P525L) were matured for 21 DIV. The main cell model used in this study were neurons derived from FUS-WT-EGFP and FUS-P525L-EGFP that were generated as a part of previous study (Naumann, Pal et al. 2018). Briefly, fibroblasts carrying R521C FUS mutation obtained from a 58-year-old female were reprogrammed into iPSC using cDNA of OCT4, SOX2, KLF4 and cMYC delivered via retroviral vectors. Next, CRISPR/Cas9 genome editing was used to i) correct the R521C mutation into WT FUS and to tag it with EGFP to generate the FUS WT EGFP line or ii) replace the R521C mutation into P525L FUS mutation and to tag it with EGFP to generate FUS P525L EGFP line. Differentiation of hiPSC into spinal motor neurons (MNs) was carried out based on the protocol from Reinhardt et al. 2013. Differentiation of hiPSC into cortical neurons (CN) was based on the protocol published by Burkhardt et al.(Burkhardt, Martinez et al. 2013, Japtok, Lojewski et al. 2015).

first: Barbara

last: Szewczyk

first: Julia

last: Japtok

first: Banaja

middle: P

last: Dash

last: Petzold

first: Mathias

last: Lesche


title: A transient brain endothelial translatome response to endotoxin is associated with mild cognitive changes post-shock in young mice

status: Public on Aug 06 2024

city: Albany

first: Ramon

last: Bossardi Ramos

state: Ny

address: 43 New Scotland Avenue

department: Department of Molecular and Cellular Physiology

country: USA

institute: Albany Medical College

type: Expression profiling by high throughput sequencing

summary: Sepsis-associated encephalopathy (SAE) is associated with increased risk of long-term cognitive impairment. SAE is driven, at least in part, by brain endothelial dysfunction in response to systemic cytokine signaling. However, the mechanisms driving SAE and its consequences remain largely unknown. Here, we performed translating ribosome affinity purification and RNA-sequencing (TRAP-seq) from the brain endothelium to determine the transcriptional changes after an acute endotoxemic (LPS) challenge. LPS induced a strong acute transcriptional response in the brain endothelium that partially correlates with the whole brain transcriptional response and suggested an endothelial-specific hypoxia response. Consistent with a crucial role for IL-6, loss of the main regulator of this pathway, SOCS3, leads to a broadening of the population of genes responsive to LPS, suggesting that an overactivation of the IL-6/JAK/STAT3 pathway leads to an increased transcriptional response that could explain our prior findings of severe brain injury in these mice. To identify any potential sequelae of this acute response, we performed brain TRAP-seq following a battery of behavioral tests in mice after apparent recovery. We found that the transcriptional response returns to baseline within days post-challenge, but reductions in gene expression regulating protein translation and respiratory electron transport remained. We observed that mice that recovered from the endotoxemic shock showed mild, sex-dependent cognitive impairment, suggesting that the acute brain injury led to sustained effects. A better understanding of the transcriptional and non-transcriptional changes in response to shock is needed in order to prevent and/or revert the devastating consequences of septic shock.

overall_design: Performed translating ribosome affinity purification (TRAP) and RNA-sequencing (TRAP-seq) from the brain endothelium to determine the transcriptional changes after an acute endotoxemic (LPS) challenge

first: Alejandro

last: Adam

first: Shuhan

last: Lu


title: Context-Dependent Roles of Mitochondrial LONP1 in Orchestrating the Balance between Airway Progenitor versus Progeny Cells

status: Public on Aug 23 2024

city: San Diego

first: Le

last: Xu

state: CA

address: 8018 Regents Road Atp. 301

department: Pediatrics

institute: University of California, San Diego

summary: While all eukaryotic cells are dependent on mitochondria for function, in a complex tissue, which cell type and which cell behavior are more sensitive to mitochondrial deficiency remains unpredictable. Here we show that in the mouse airway, compromising mitochondrial function by inactivating mitochondrial protease gene Lonp1 led to reduced progenitor proliferation and differentiation during development; apoptosis of terminally differentiated ciliated cells and their replacement by basal progenitors and goblet cells during homeostasis; and failed airway progenitor migration into damaged alveoli following influenza infection. ATF4 and the integrated stress response (ISR) pathway are elevated and responsible for airway phenotypes. Such context dependent sensitivities are predicted by the selective expression of Bok, which is required for ISR activation. Reduced LONP1 expression is found in chronic obstructive pulmonary disease (COPD) airways with squamous metaplasia. These findings illustrate a cellular energy landscape whereby compromised mitochondrial function could favor the emergence of pathological cell types.

overall_design: Bulk RNA-seq from embryonic lungs at E13.5, including 3 controls and 4 Shhcre;Lonp1 mutants.  Single cell RNA-seq from purified adult airway epithelial cells of control and Sox2creER;Lonp1;tdTomato. scRNA-seq from control (PBS) and influenza infected lungs at D11 and D20.

first: Chunting

last: Tan

first: Justinn

last: Barr

first: Xin

last: Sun


title: mTOR activity paces human blastocyst stage developmental progression

status: Public on Sep 24 2024

city: Vienna

first: HEIDAR

last: HEIDARI KHOEI

address: Dr. Bohr-Gasse 3

country: Austria

institute: Institute of Molecular Biotechnology

summary:
Many mammals can temporally uncouple conception from parturition by pacing down their
development around the blastocyst stage. In mice, this dormant state is achieved by decreasing
the activity of the growth-regulating mTOR signaling pathway. It is unknown whether this ability
is conserved in mammals in general and in humans in particular. Here we show that decreasing
the activity of the mTOR signaling pathway induces human pluripotent stem cells (hPSCs) and
blastoids to enter a dormant state with limited proliferation, developmental progression, and
capacity to attach to endometrial cells. These in vitro assays show that, similar to other species,
the ability to enter dormancy is active in human cells around the blastocyst stage and is reversible
at both functional and molecular levels. The pacing of human blastocyst development has
potential implications for reproductive therapies

overall_design: To test the effect of mTOR inhibition on the developmental timeline and morphology of human blastoids, these were first formed and then further cultured in the presence of the mTOR inhibitor RapaLink-1 and to test whether Rapalink-1 treated blastoids are reversible, we reactivated blastoids after 3 days of Rapalink-1 treatment and further cultured them on matrigel-coated plates.

first: Heidar

last: Heidari Khoei

first: Saurabh

middle: J

last: Pradhan

first: Nicolas

last: Rivron


title: Mouse models for pancreatic ductal adenocarcinoma areaffected by the cre-driver used to promote KRASG12D activation

status: Public on Aug 20 2024

city: London

first: Christopher

middle: L

last: Pin

state: Ontario

address: 1151 Richmond St

country: Canada

institute: University of Western Ontario

summary: The fundamental biology of pancreatic ductal adenocarcinoma has been greatly impacted by the characterization of genetically engineered mouse models that allow temporal and spatial activation of oncogenic KRAS (KRASG12D). One of the most commonly used models involves targeted insertion of a cre-recombinase into the Ptf1a gene. However, this approach disrupts the Ptf1a gene, resulting in haploinsufficiency that likely affects sensitivity to oncogenic KRAS (KRASG12D). This study aims to determine if Ptf1a haploinsufficiency affected the acinar cell response to KRASG12D before and after induction of pancreatic injury. Taken together, our results suggest Ptf1a haploinsufficiency in Ptf1acreERT mouse models promotes KRASG12D priming of genes for promotion of PDAC.

overall_design: We performed morphological and molecular analysis of three genetically engineered mouse models that express a tamoxifen-inducible cre-recombinase to activate KRASG12D in acinar cells of the pancreas. The cre-recombinase was targeted to the acinar-specific transcription factor genes, Ptf1a or Mist1/Bhlha15, or expressed within a BAC-derived Elastase transgene. Histological and RNA-seq analyses were used to delineate differences between the models

first: Fatemeh

last: Mousavi

first: Joyce

last: Thompson

first: Justine

last: Lau

first: Nur

last: Renollet

first: Mickenzie

last: Martin

first: Jake

last: McGue

first: Timothy

last: Frankel

first: Parisa

last: Shooshtari

first: Filip

last: Bednar


title: Granulosa cells provide transcriptomic information on ovarian follicle dynamics in southern white rhinoceros

status: Public on Aug 25 2024

city: Escondido

first: Elena

last: Ruggeri

address: 15600 San Paqual Valley Rd.

institute: San Diego Zoo Wildlife Alliance

summary: Much remains unknown about the reproductive physiology of southern white rhinoceros (SWR) and the effect of ovarian stimulation prior to ovum pickup (OPU) have not been fully elucidated. Granulosa cells (GC) provide valuable insight into follicle growth and oocyte maturation status. The goals of this study were to evaluate transcriptomic changes in GC from three stages of follicle development and to identify biomarkers possibly associated with follicular growth and maturation as a result of ovarian stimulation. GC collected from SWRs following OPU were assigned stages based upon follicle size. Total RNA was isolated, and cDNA libraries were prepared and sequenced on a NovaSeq 6000. All bioinformatics analyses were performed utilizing the Galaxy web platform. Reads were aligned to CerSimCot1.0, and the manual curation was performed with EquCab3.0. Overall, 39,455 transcripts (21,612 genes) were identified across follicle stages, and manual curation yielded a 61% increase in gene identification from the original annotation. Granulosa cells from preovulatory follicles expressed the highest number of unique transcripts. The following seven biomarkers were determined based upon cluster analysis and patterns of expression: COL1A1, JMY, FBXW11, NRG1, TMPO, MACIR and COL4A1. These data can be used to potentially evaluate the effects of different ovarian stimulation protocols on follicle dynamics, improve OPU results, and support conservation efforts in this species.

overall_design: Transcriptomic of SWR GC from follicles in different stages of development.

first: Kristin

last: Klohonatz

first: Barbara

last: Durrant

first: Sirard

last: Marc-André


title: DeepRNA-Reg: A Deep-Learning Based Approach for Comparative Analysis of CLIP Experiments

status: Public on Aug 01 2024

city: San Francisco

first: K. Mark

last: Ansel

address: 513 Parnassus Ave. UCSF Box 0414

department: Microbiology & Immunology

institute: UCSF

summary: DeepRNA-Reg employs advances in deep learning to enable high-fidelity comparative analysis of paired datasets of high-throughput sequencing of RNA isolated by crosslinking immunoprecipitation (HITS-CLIP). In a HITS-CLIP experimental paradigm where Ago2 activity is precisely perturbed via gene knock-out of a microRNA cluster, DeepRNA-Reg offers a superior prediction set than the current best prescription for differential HITS-CLIP; furthermore, DeepRNA-Reg predictions adhere better to the ground-truth of the RNA primary and secondary structural motifs that enable miRNA-mediated targeting of RNA. DeepRNA-Reg uncovered novel mediators in the mechanism of microRNA-mediated restraint of type-2 immunity in T-Helper 2 cells. In a comparative analysis, DeepRNA-Reg predictions show greater translatability across distinct biological milieux, offering prediction sets with wide applicability for investigators.

overall_design: To investigate the ability of DeepRNA-Reg to identify differentially protein-bound loci between a pair of HITS-CLIP experiments, we  performed Ago2 HITS CLIP on mouse Th2 cells with the Mirc11 and Mirc22 clusters (miRNAs 23, 24, and 27) knocked-out and Th2 cells with a WT genotype.

first: Harshaan

last: Sekhon

first: Heather

middle: H

last: Pua

first: Eric

last: Wigton

first: Robin

last: Kageyama

first: K

middle: M


title: Effect of medication with Belinostat and Dasatinib on gene expression during MGG8, Glioblastoma Stem cell

city: Okayama-shi

first: Shuichiro

last: Hirano

address: kita-ku, shikata-cho, 2-5-1

country: Japan

institute: Okayama University

summary: To evaluate the effects of selected therapeutic drugs focusing on gene expression, we administered drugs to MGG8 GSCs, extracted RNA, and compared them.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for MGG8 treated with Belinostat, Dasatinib, Combination of both drugs and 0.1%DMSO(Control)

first: Atsuhito

last: Uneda

first: Yoshihiro

last: Otani


title: Elucidating the transcriptomic response of adult hypothalamic neuron cells to cannabidiol (CBD) exposure

city: Kraków

first: Artur

last: Gurgul

address: Rędzina 1C

department: Center for Experimental and Innovative Medicine

country: Poland

institute: University of Agriculture in Krakow

summary: Cannabidiol (CBD) actions in the brain are largely complex and not fully understood. One important brain structure that is a target for CBD, and for which health-beneficial CBD consequences can be seen is the hypothalamus. Given the fundamental role of gene expression in the hypothalamus's regulatory functions, this study undertook the analysis of changes arising in hypothalamic cells’ transcriptomes following various CBD treatments. For this purpose, we used a hypothalamic cellular model, namely we employ adult-derived mHypoA-2/12 mouse cell lines. In the course of the study, the neural cells were treated with different CBD doses (ranging from 0.325 to 3 µM) and vehicle as a control for 6 and 24 hours. The experiment setup allowed us to evaluate both the dosage and time-dependent effect of CBD on hypothalamic cells, particularly on their viability, apoptosis, and transcriptome profile.

overall_design: The adult mouse hypothalamic cell lines mHypoA-2/12 (Clu177) were purchased from Cedarlane (Canada) and cultured in recommended conditions. After culture stabilization, the cells were supplemented with CBD (0.325, 0.75, 1.5 and 3 µM) and cultured either for 6 hours (n = 3 for each concentration) or for 24 hours (n = 3 for each concentration). The vehicle control was 0.1% DMSO in the DMEM with GlutaMAX. When treatment time passed, cells were trypsinized, transferred to centrifuge tubes, and used for RNA isolation. Purified RNA was used for 3’mRNA-Seq to evaluate changes that arise in the transcriptome of the hypothalamic cells following different CBD treatments.

first: Igor

last: Jasielczuk

first: Tomasz

last: Szmatoła

first: Ewelina

last: Semik-Gurgul

first: Mirosław

last: Kucharski

first: Karolina

last: Mizera-Szpilka

first: Ewa

last: Ocłoń


title: Glioblastoma cell supermeres

status: Public on Jul 31 2024

city: NASHVILLE

first: Marisol

last: Ramirez

state: TENNESSEE

address: 2220 Pierce Avenue, 571 Preston Research Building

department: Center for Quantitative Sciences, Department of Biostatisticss

institute: Vanderbilt University Medical Center

type: Non-coding RNA profiling by high throughput sequencing

summary: To identify small RNAs coming out of glioblastoma cells in supermeres and other carriers

overall_design: 17 samples, 4 control and 13 experimental, replicates

first: Charest

last: Al

first: Vickers

last: Kasey

first: Franklin

last: Jeff

first: Massick

last: Clark

first: Michell

last: Danielle

first: Coffey

last: Robert


title: Galactin-3 regulation of CDC42 promotes neuronal autophagy following spinal cord injury

status: Public on Sep 01 2024

city: Xuancheng City

first: Zhiming

last: Cui

state: ANHUI

address: Anhui province

country: China

institute: The Second Affiliated Hospital of Nantong University

summary: Spinal cord injury (SCI) is a debilitating condition within the nervous system with a high disability rate and substantial economic burden. The functional recovery following SCI is enhanced by moderate levels of autophagy but hindered when autophagy becomes excessive. Galectin-3 (GAL3) has been recognized as an autophagy regulator; however, its role in SCI and its associated mechanism are largely unknown. Here we report that GAL3 was increased in spinal neurons and serum in SCI rats, and knockdown or inhibition of GAL3 promoted motor function recovery. The bioinformatics analysis showed that GAL3 is closely related to programmed cell death after SCI. Indeed, the knockdown of GAL3 resulted in a decrease in autophagy markers ATG7 and LC3 II/I ratio, along with an increase in P62 expression. Furthermore, GAL3 and cell division cycle 42 (CDC42) exhibited close associations with neuronal autophagy. Injection of CDC42 inhibitor ML141 effectively reduced GAL3-mediated enhancement of neuronal autophagy. Additionally, CDC42 was increased in spinal neurons post-SCI, and administration of ML141 decreased the expression of autophagy markers and improved motor function recovery. Importantly, elevated levels of GAL3 and CDC42 were observed in the serum of SCI patients. These findings suggest a potential interplay between GAL3 and CDC42 in regulating neuronal autophagy after SCI and indicate the therapeutic potential of targeting this pathway for enhancing recovery from spinal cord injuries.

overall_design: Total RNA was extracted from the spinal cord neurons of neonatal SD rats using Trizol reagent for subsequent sequencing. Sequencing was performed on an Illumina high-throughput sequencing platform (HiSeqTM2500/4000). There were a total of six samples, all of which were treated with high concentrations of glutamate to simulate a neuronal injury model. Among these, three samples were from neurons in the transfection control group, designated as Glu_1, Glu_2, and Glu_3, respectively. The other three samples were from neurons with GAL3 knocked out, designated as Glu_L_1, Glu_L_2, and Glu_L_3, respectively.

first: Lei

last: Yan

first: Chu

last: Chen

first: Hongxiang

last: Hong

first: Chunshuai

last: Wu

first: Guanhua

last: Xu

first: Yong-Jing

last: Gao


title: Gene expression changes in mouse breast cancer cells (4T1) after axitinib resistance and FACS isolation of SA-β-galHi (SM+) and SA-β-galLo (SM-) cells

city: Buffalo

first: Mark

middle: D

last: Long

state: NY

address: Elm & Carlton Streets

department: Bioinformatics & Biostatistics

institute: Roswell Park Comprehensive Cancer Center

summary: RNA sequencing analysis was used to identify changes in mouse breast cancer cells (4T1) after axitinib resistance and FACS isolation of SA-β-galHi (SM+) and SA-β-galLo (SM-) cells

overall_design: Mouse breast cancer cells (4T1) resistant to axitinib were derived in vivo after continuous treatment with 100mg/kg/day axitinib from post-surgical lesions. Resistant cells were maintained in vitro with 0.5µM axitinib for more than 2 months. Resistant cells were stained for fluorescent SA-β-gal substrate C12FDG and fractioned into SA-β-galHi (SM+) and SA-β-galLo (SM-) populations

first: Melissa

last: Dolan

first: John

last: Ebos


title: Zfp697 is an RNA-binding protein that regulates skeletal muscle inflammation and remodeling (Zfp697 transduced primary mouse myotubes ChIP-Seq)

status: Public on Jul 30 2024

city: Solna

first: Igor

last: Cervenka

address: Solnavägen 9

department: Physiology and Pharmacology

country: Sweden

institute: Karolinska Institutet

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Muscle atrophy is a morbidity and mortality risk factor that happens with disuse, chronic disease, and ageing. Recovery from atrophy involves changes in protein synthesis and different cell types such as muscle fibers, and satellite and immune cells. Here we show that the previously uncharacterized gene and protein Zfp697 is a damage-induced regulator of muscle regeneration. Zfp697/ZNF697 expression is transiently elevated during recovery from muscle atrophy or injury in mice and humans. Sustained Zfp697 expression in mouse muscle leads to a gene expression signature of chemokine secretion, immune cell recruitment, and extracellular matrix remodeling. Myofiber-specific Zfp697 ablation hinders the inflammatory and regenerative response to muscle injury, compromising functional recovery. We uncover Zfp697 as an essential mediator of the interferon gamma response in muscle cells that functions primarily as an ncRNA-binding protein, most notably the pro-regenerative miR-206. This work identifies Zfp697 as an integrator of cell-cell communication necessary for tissue regeneration.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for Flag and normal mouse IgG as a control in differentiated mouse myotubes transduced with Flag-Zfp697 adenovirus. Experiment was performed in triplicates.

first: Jorge

middle: C

last: Correia

first: Paulo

middle: R

last: Jannig

first: Maya

last: Gosztyla

first: Serge

last: Ducommun

first: Stine

last: Præstholm

first: Kyle

last: Dumont

first: Liu

last: Zhengye

first: Qishan

last: Liang

first: Daniel

last: Edsgärd

first: Olof

last: Emanuelsson

first: Paul

last: Gregorevic

first: Tomas

last: Venckunas

first: Marius

last: Brazaitis

first: Sigitas

last: Kamandulis

first: Johanna

middle: T

last: Lanner

first: Gene

middle: W

last: Yeo

last: Ruas


title: Upstream regulator of genomic imprinting in rice is a small RNA-associated chromatin remodeler [Bisulfite_seq]

status: Public on Jul 29 2024

city: Bangalore

first: Shivaprasad

last: Padubidri V.

address: UAS-GKVK Campus

country: India

institute: National Centre for Biological Sciences - TIFR

type: Methylation profiling by high throughput sequencing

summary: Knock down of CLSY3 in rice caused endosperm development defects. We investigated the molecular effects of loss of CLSY3 in rice  endosperm by profiling sRNA, targeted bisulfite PCR,whole genome bisulfite sequencing and mRNA transcriptomes .These analyses revealed the  roles of CLSY3 in Endosperm

overall_design: We have performed whole genome bisulfite sequencing to understand the methylation status of endosperm upon CLSY3 knockdown

first: Padubidri

middle: V

last: Shivaprasad

first: Avik

middle: K

last: Pal


title: Natural and non-natural cytokine receptors generate diverse cell states to enhance T cell therapy

city: Stanford

first: Yang

last: Zhao

address: Beckman B169B, 279 Campus Drive

department: MCP

institute: Stanford University

summary: Cytokines augment T cell function, but the nature of the optimal signals are not well defined. We deployed orthogonal cytokine-receptors to diversify the JAK/STAT signaling profiles elicited by orthogonal IL-2. We designed chimeric receptors consisting of the orthogonal IL-2 receptor extracellular domain (ECD) fused to intracellular domains (ICDs) from receptors for other common gamma chain cytokines as well as ICDs from interferon receptor, IL-10 receptor and homodimeric receptor families not expressed on T cells. Such non-natural pairings with the common gamma chain expand the JAK/STAT signaling space in T cells. Natural and non-natural orthogonal chimeric receptors led to distinct T cell fates in tumors, including naturally occurring states (Tc2 differentiation driven by orthogonal chimeric IL4R) and synthetic states (myeloid-like T cells driven by orthogonal chimeric granulocyte colony stimulating factor receptor). The orthogonal chimeric IL22R (o22R) potently activated STAT-1, -3, -4, and -5, imparting T cells with stem-like and effector properties. The pronounced anti-tumor functionality mediated by o22R and oGCSFR was linked to remodeling of the exhaustion-associated epigenome. Our study broadens the cytokine receptor repertoire, providing novel solutions to overcome barriers for using engineered T cells to treat cancer.

overall_design: NSG mice were inoculated s.c. with A375 cells (1 × 106) and received i.v. adoptive cell transfer of 3 × 106 NY-ESO-1 TCR-T cells (WT NY-ESO-1 TCR-T cells, or ho22R, or hoGCSFR expressing NY-ESO-1 TCR-T cells) on day 10 post-tumor inoculation followed by i.p. administration of MSA-hoIL-2 (2.5 × 104 unit  × 3 doses, 2.5 × 104 unit  × 3 doses) or PBS control every other day until day 20. On day 21, mice were sacrificed, tumors were minced and dissociated using a human tumor dissociation kit (Miltenyi Biotec) and a gentleMACS Octo Dissociator (Miltenyi Biotec). Tumor-infiltrating lymphocytes (TILs) were first enriched by density gradient centrifugation against Percoll (GE healthcare), and then stained with surface markers and DAPI (Sigma-Aldrich). CD3+ EGFR+ or CD3+ EGFR+YFP+ T cells were sorted using an Aria II sorter (BD Biosciences) at the Stanford Share FACS Facility for ATAC sequencing.

first: Masato

last: Ogishi

first: Chirs

last: Garcia


title: High-Throughput Transcriptomics Toxicity Assessment of Eleven Data-Poor Bisphenol A Alternatives

status: Public on Aug 26 2024

city: Ottawa

first: Matthew

last: Meier

address: 251 Sir Frederick Banting Driveway

department: Health Canada

institute: Government of Canada

summary: Bisphenol A (BPA), a widely used chemical in the production of plastics and epoxy resins, has garnered significant attention due to its association with adverse health effects, particularly its endocrine-disrupting properties. Regulatory measures aimed at reducing human exposure to BPA have led to a proliferation of alternative chemicals used in various consumer products. While these alternatives serve to reduce BPA exposure, concerns have arisen regarding their safety and potential toxicity as regrettable substitutes. Previous efforts have demonstrated that in vitro high-throughput transcriptomics (HTTr) studies can be used to assess the endocrine-disrupting potential of BPA alternatives, and this strategy produces transcriptomic points-of-departure (tPoDs) that are protective of human health when compared to the PODs from traditional rodent studies. In this study, we leveraged in vitro HTTr advancements to assess the toxicity of eleven data-poor legacy chemicals sharing structural similarities to BPA. Human breast cancer MCF-7 cells were exposed to BPA and 11 alternatives at concentrations ranging from (0.1 - 25 µM) to assess toxicity. Analysis of global transcriptomic changes and a previously characterized estrogen receptor alpha (ERα) biomarker signature revealed that 9/11 chemicals were bioactive. One of the chemicals (2,4’-Bisphenol A) activated the ERα biomarker at the same concentration as BPA (i.e., 4,4’-BPA) but was deemed to be more potent as it induced global transcriptomic changes at lower concentrations. These results are addressing data gaps in ongoing screening assessments to identify BPA alternatives with hazard potential and are helping to identify potential candidates to serve as safer alternatives.

overall_design: Three TempO-Seq plates were sequenced for this study to investigate the gene expression changes of BPA and 11 BPA alternatives on MCF-7 cells. Five concentrations of each chemical were tested in quadruplicate. In addition, technical controls (reference RNA; media only; cells with no treatment), solvent controls (dimethylsulfoxide, methanol), negatives controls (dexamethasone, Bis(4-chlorophenyl) sulfone), and positive controls (estradiol) were sequenced.

first: Marc

middle: A

last: Beal

first: Melanie

last: Coughlan

first: Andrée

last: Nunnikhoven

last: Gagné

first: Tara

middle: S

last: Barton-Maclaren

first: Lauren

last: Bradford

first: Andrea

last: Rowan-Carroll

first: Andrew

last: Williams


title: Zfp697 is an RNA-binding protein that regulates skeletal muscle inflammation and remodeling (Zfp697 skeletal muscle knockout RNA-Seq of unloading-reloading protocol)

first: Igor

last: Cervenka

overall_design: Comparative gene expression profiling analysis of RNA-seq data for mouse gastrocnemius muscle from model of hindlimb unloading/reloading comparing wild-type and Zfp697 conditional skeletal muscle knockout (mKO) animals. Control mice were kept in conventional cages throughout the entire protocol. Experiment was performed in three replicates per condition.

first: Jorge

last: Correia

first: Paulo

last: Jannig

first: Maya

last: Gosztyla

first: Serge

last: Ducommun

first: Stine

last: Præstholm

first: Kyle

last: Dumont

first: Liu

last: Zhengye

first: Qishan

last: Liang

first: Daniel

last: Edsgärd

first: Olof

last: Emanuelsson

first: Paul

last: Gregorevic

first: Tomas

last: Venckunas

first: Marius

last: Brazaitis

first: Sigitas

last: Kamandulis

last: Lanner

last: Yeo


title: Upstream regulator of genomic imprinting in rice is a small RNA-associated chromatin remodeler [targeted bisulfite PCR]

first: Shivaprasad

last: Padubidri V.

summary: Knock down of CLSY3 in rice caused endosperm development defects. We investigated the molecular effects of loss of CLSY3 in rice  endosperm by profiling sRNA, targeted bisulfite PCR and mRNA transcriptomes .These analyses revealed the  roles of CLSY3 in Endosperm

overall_design: We have performed targeted bisulfite PCR

first: Padubidri

last: Shivaprasad

first: Avik

last: Pal


title: Upstream regulator of genomic imprinting in rice is a small RNA-associated chromatin remodeler [ncRNA-Seq]

summary: Knock down of CLSY3 in rice caused endosperm development defects. We investigated the molecular effects of loss of CLSY3 in rice  endosperm by profiling sRNA and mRNA transcriptomes .These analyses revealed the  roles of CLSY3 in Endosperm development.

overall_design: We profiled sRNAs in the WT and clsy3 kd tissues from embryo and endosperm tissues to estimate the effect of loss of clsy3 the the sRNA transcriptome.


title: Upstream regulator of genomic imprinting in rice is a small RNA-associated chromatin remodeler [ChIP_seq]

overall_design: We have  performed ChIP-seq with C-terminal GFP tagged and C-terminal 2X myc tagged CLSY3 transgenic plants panicle.


title: Bulk RNA sequencing in SARS-CoV-2 infected patients

status: Public on Jul 27 2024

city: CHEONAN

first: Hyunkyung

last: Cha

state: Cheonan-si

address: Suncheonhyang 6-gil

department: Department of Otorhinolaryngology-Head and Neck Surgery

country: South Korea

institute: Soonchunhyang University Cheonan Hospital

summary: We report the application of bulk RNA sequencing technology for high-throughput profiling of SARS-CoV-2 infection in the human nasopharynx

overall_design: Examination of SARS-CoV-2-induced RNA expression in the nasopharynx of human

first: Hyun

last: Kim

first: Sujin

first: Chan

last: Lee


title: CDK7 is a novel therapeutic vulnerability in Fibrolamellar cancer

city: Madison

first: Sean

last: Ronnekleiv-Kelly

state: Wisconsin

address: K3/705 CSC, 600 Highland Avenue

department: Surgery

institute: University of Wisconsin Madison School of Medicine and Public Health

summary:
To identify targets in Fibrolamellar cancer (FLC), we introduced the FLC driver gene mutation (DNAJB1-PRKACA) into HepG2 cells to engineer FLC cell lines.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 6 different cell samples from HepG2, H33 (FLC cell line) and H12 (FLC cell line)

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HepG2 (control, n = 6) vs H33 (n = 6) and HepG2 (control, n = 6) vs H12 (n = 6)


title: Multi-omics datasets for finer-scale dissection of chromatin architecture alterations in radiation induced malignant transformation of bronchial epithelial cells [ATAC-Seq II]

status: Public on Jul 26 2024

city: Beijing

first: Yi

last: Hu

address: No. 28 Fuxing Rd， Haidian district，Beijing

institute: Chinese PLA General Hospital

summary: we generated CUT&Tag, ATAC-seq, RNA-seq, high-resolution Hi-C and Micro-C datasets for finer-scale dissection of chromatin architecture alterations in radiation induced malignant transformation of bronchial epithelial cells.

overall_design: ATAC-Seq profiles of normal control human bronchial epithelial cells, TP63 overexpressed human bronchial epithelial cells and radiation induced lung cancer cells

first: Z

last: pingkun

first: L

last: qiaowei


title: Upstream regulator of genomic imprinting in rice is a small RNA-associated chromatin remodeler

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

overall_design: Refer to individual Series


title: Zfp697 is an RNA-binding protein that regulates skeletal muscle inflammation and remodeling (Zfp697 transduced primary mouse myotubes RNA-Seq)

first: Igor

last: Cervenka

overall_design: Comparative gene expression profiling analysis of RNA-seq data from differentiated primary mouse myotubes infected with adenovirus endoding either Zfp697 gene or GFP as a control. Experiment contains three replicates for each condition

first: Jorge

last: Correia

first: Paulo

last: Jannig

first: Maya

last: Gosztyla

first: Serge

last: Ducommun

first: Stine

last: Præstholm

first: Kyle

last: Dumont

first: Liu

last: Zhengye

first: Qishan

last: Liang

first: Daniel

last: Edsgärd

last: Emanuelsson

first: Johanna

first: Gene

last: Ruas


title: Elucidating the mechanisms underlying H3K18la contributes to NSCLC progression

city: Zhengzhou

first: Cai

last: Zhang

address: 1#, Jianshedong Road

institute: The First Affiliated Hospital of Zhengzhou University

summary: Histone lactylation has been served as a novel epigenetic modification that directly stimulates gene transcription from chromatin. In order to study the regulatory mechanisms of H3K18la in non-small cell lung cancer (NSCLC), we performed ChIP-Seq to identify its target genes in NCI-H1299 cell lines.

overall_design: ChIP-Seq with anti-H3K18la in NCI-H1299 cells

first: Lu

last: Zheng


title: Cellular origin and clonal evolution of human dedifferentiated liposarcoma

status: Public on Jul 22 2024

city: Paris

first: Fabien

last: Quinquis

address: 26 rue d'Ulm

country: France

institute: Institut Curie

first: Nadège

last: Gruel

first: Chloé

last: Quignot

first: Sophie

last: El Zein

first: Laëtitia

last: Lesage

first: Sylvie

last: Bonvalot

first: Dimitri

last: Tzanis

first: Julien

last: Vibert

first: Nadine

last: El Tannir

first: Didier

last: Decaudin

first: Héloïse

last: Derrien

first: Ahmed

last: Dahmani

first: Odette

last: Mariani

last: Linares

first: Sylvain

last: Baulande

first: Joshua

last: Waterfall

first: Olivier

last: Delattre

first: Sarah

last: Watson


title: Multi-omics datasets for finer-scale dissection of chromatin architecture alterations in radiation induced malignant transformation of bronchial epithelial cells [Micro-C]

first: Yi

last: Hu

overall_design: Micro-C profiles of normal control human bronchial epithelial cells, TP63 overexpressed human bronchial epithelial cells and radiation induced lung cancer cells

first: Z

last: pingkun

first: L

last: qiaowei


title: Mechanism of homology search expansion during recombinational DNA repair

city: Lyon

first: Aurele

last: Piazza

address: 46 Allee d'Italie

institute: ENS Lyon

summary: Homology search is a central step of DNA double-strand break (DSB) repair by homologous recombination. How it operates in cells remains elusive. Here we developed a Hi-C-based methodology to map single-stranded DNA (ssDNA) contacts genome-wide in S. cerevisiae, which revealed two main homology search phases. Initial search conducted by short Rad51-ssDNA nucleoprotein filaments (NPFs) is confined in cis by cohesin-mediated chromatin loop folding. Progressive growth of stiff NPFs enables exploration of distant genomic sites. Long-range resection drives this transition from local to genome-wide search by increasing the probability of assembly of extensive NPFs. DSB end-tethering promotes coordinated homology search by opposite NPFs. Finally, an autonomous genetic element on chromosome III engages the NPF, which stimulates homology search in its vicinity. This work reveals the mechanism of the progressive expansion of homology search orchestrated by chromatin organizers, long-range resection, end-tethering, specialized genetic elements, and that exploits the stiff NPF structure conferred by Rad51 oligomerization.

overall_design: Hi-C and a Hi-C-based experiment enabling detection of ssDNA contacts were performed on S. cerevisiae cultures following site-specific formation of a DNA double-strand break on chr. V, in wild-type cells and various mutants and treatment conditions affecting homologous recombination and/or chromosome structure..

first: Agnès

last: Dumont

first: Nicolas

last: Mendiboure

first: Jérôme

last: Savocco

first: Aurèle


title: Multi-omics datasets for finer-scale dissection of chromatin architecture alterations in radiation induced malignant transformation of bronchial epithelial cells [CTCF CUT&Tag]

overall_design: CTCF CUT&Tag profiles of normal control human bronchial epithelial cells, TP63 overexpressed human bronchial epithelial cells and radiation induced lung cancer cells


title: Multi-omics datasets for finer-scale dissection of chromatin architecture alterations in radiation induced malignant transformation of bronchial epithelial cells [TP63 CUT&Tag]

overall_design: TP63 CUT&Tag profiles of normal control human bronchial epithelial cells, TP63 overexpressed human bronchial epithelial cells and radiation induced lung cancer cells


first: Fabien

last: Quinquis

summary: Dedifferentiated liposarcoma (DDLPS) is the most frequent high-grade soft tissue sarcoma subtype. It is characterized by a component of undifferentiated tumor cells coexisting with a component of well-differentiated adipocytic tumor cells. Both dedifferentiated (DD) and well-differentiated (WD) components exhibit MDM2 amplification, however their cellular origin remains elusive. Using single-cell RNA sequencing and functional assays in paired WD and DD components from primary DDLPS tumors, we characterized the cellular heterogeneity of DDLPS tumor and micro-environment. We identified a population of tumor adipocyte stem cells (ASC) showing striking similarities with adipocyte stromal progenitors found in white adipose tissue. We show that tumor ASC harbor the ancestral genomic alterations of WD and DD components, suggesting that both derive from these progenitors following clonal evolution. Last, we show that DD tumor cells keep important biological properties of ASC including pluripotency and that their adipogenic properties are inhibited by a TGF-β high immunosuppressive tumor micro-environment.

overall_design: Primary DDLPS, WDLPS, liposarcoma and peritumoral fat tissue of untreated patients were isolated and analyzed using RNAseq.

first: Nadège

last: Gruel

first: Chloé

last: Quignot

first: Sophie

last: El Zein

first: Laëtitia

last: Lesage

first: Sylvie

last: Bonvalot

first: Dimitri

last: Tzanis

first: Julien

last: Vibert

first: Nadine

last: El Tannir


title: Lineage specific canonical and non-canonical EZH2 activity in advanced prostate cancer subtypes [RNA-Seq]

status: Public on Jul 16 2024

city: Boston

first: Varadha Balaji

last: Venkadakrishnan

state: MA

address: 450 Brookline Ave

department: Department of Medical Oncology

institute: Dana-Farber Cancer Institute

summary: Inhibiting EZH2 using tazemetostat led to induction of lineage-specific genes

overall_design: Tazemetostat treated PRAD and NEPC samples.

first: Himisha

last: Beltran


title: Upstream regulator of genomic imprinting in rice is a small RNA-associated chromatin remodeler [bisulfite_PCR]

first: Shivaprasad

last: Padubidri V.

first: Padubidri

last: Shivaprasad

first: Avik

last: Pal


title: Lineage-specific canonical and non-canonical activity of EZH2 in advanced prostate cancer subtypes


title: ParBF DNA binding profiles over various supercoiling level and on linear DNA

status: Public on Jul 01 2024

city: Toulouse

first: Jean-Yves

last: Bouet

address: 169 avenue Marianne Grunberg-Manago

institute: CNRS

summary: We report the genome-wide analysis from chromatin immunoprecipitated DNA (ChIP-sequencing) of the DNA binding pattern of ParBF (SopB) of plasmid F. This study, performed in E. coli and Salmonella typhimurium, investigates the impact of DNA supercoiling on ParBF DNA binding profiles in vivo. We found that variation in DNA supercoiling does not significantly affect the ParB DNA binding profiles even on linear DNA.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

overall_design: Chromatin immunoprecipitation DNA-sequencing for ParB of plasmid F (ParBF) in bacterial strains exhibiting various DNA supercoiling level, and on linearized plasmid F at several positions relative to the centromere parSF. Biological replicates are labelled IP1 and IP2. Anti ParBF antibody is affinity purified before used.

first: Hicham

last: Sekkouri Alaoui

first: Jerome

last: Rech

first: Delphine

last: Labourdette


title: Epigenetic landscape of advanced prostate cancer

status: Public on Jul 20 2024

first: Kei

last: Mizuno

state: MASSACHUSETTS

address: 450 Brookline Avenue

institute: Dana-Farber Cancer institute

summary: Prostate cancer is characterized as being histologically and molecularly heterogeneous. Additionally, epigenetic changes play an important role in regulating the progression of prostate cancer. However, epigenetic intraindividual heterogeneity is largely unknown in advanced prostate cancer. Hence, the epigenetic profiles of advanced prostate cancer, including autopsy cases, were investigated.

overall_design: CUT&Tag analysis for histone modifications on samples from advanced prostate cancer patients

first: Varadha

middle: B


title: Multi-omics datasets for finer-scale dissection of chromatin architecture alterations in radiation induced malignant transformation of bronchial epithelial cells [STAG2 CUT&Tag]

first: Yi

last: Hu

overall_design: STAG2 CUT&Tag profiles of normal control human bronchial epithelial cells, TP63 overexpressed human bronchial epithelial cells and radiation induced lung cancer cells

first: Z

last: pingkun

first: L

last: qiaowei


title: Astrocyte morphology driven improvements to OCD phenotypes

status: Public on Jul 09 2024

city: Los Angeles

first: Riki

last: Kawaguchi

address: 760 Westwood Plaza, Room 37-420

department: Department of Psychiatry and Neurology Department of Psychiatry

institute: University of California, Los Angeles

summary: We investigated the consequences of striatal astrocyte Gi-GPCR activation in the SAPAP3 KO mouse model of OCD

overall_design: 16 whole striatum tissue samples for whole tissue bulk transcriptomics. 4 mice per experimental group, 4 experimental groups: wild-type + tdT, wild-type + hM4Di, KO + tdTomato, KO + hM4Di all treated with DCZ, the agonist of hM4Di.

first: Baljit

last: Khakh

first: Joselyn

last: Soto

first: Chiranjivi

last: Neupane

first: Muskan

last: Kaur

first: Vijaya

last: Pandey

first: James

last: Wohlschlegel


title: EZH2 knockout and rescue in WCM154 NEPC organoid model. [RNA-Seq]

first: Varadha Balaji

last: Venkadakrishnan

summary: EZH2 silencing led to further maturation of neuroendocrine terminal differentiation in NEPC.

overall_design: EZH2 was silenced in WCM154 NEPC organoids using 2 independent single-guide RNAs. EZH2 expression was rescued using a recombinant dTAG-EZH2.

first: Himisha

last: Beltran


title: Upstream regulator of genomic imprinting in rice is a small RNA-associated chromatin remodeler [PCR_product_deep_sequencing]

first: Shivaprasad

last: Padubidri V.

summary: Knock down of CLSY3 in rice caused endosperm development defects. We investigated the molecular effects of loss of CLSY3 in rice  endosperm by profiling sRNA, targeted bisulfite PCR,whole genome bisulfite sequencing and mRNA transcriptomes .These analyses revealed the  roles of CLSY3 in Endosperm

overall_design: We have performed deep sequencing of PCR products amplified from endosperm (WPxPB1) to check genomic imprinting status of CLSY3, ARF22 and SHH1 genes

first: Padubidri

last: Shivaprasad

first: Avik

last: Pal


title: Epigenetic profiling of prostate adenocarcinoma and neuroendocrine prostate cancer models to understand EZH2 activity. [Cut & Run]

summary: EZH2 has differential activity in prostate adenocarcinoma and neuroendocrine prostate cancer.

overall_design: Epigenetic profiling was performed in prostate cancer models upon EZH2 inhibiton or silencing.


title: Transcriptional remodeling by OTX2 directs specification and patterning of mammalian definitive endoderm [ATAC-seq]

status: Public on Jun 26 2024

city: New York

first: Ly-sha

last: Ee

address: 413 E 69th Street

institute: Weill Cornell Medicine

summary: We discovered a role for the transcription factor OTX2 in formation of mouse definitive endoderm (DE). We used ATAC-seq to identify open chromatin regions in OTX2-depleted definitive endoderm cells and identify sites with changed accessibility during DE differentiation

overall_design: Mouse EpiSCs were differentiated to DE with or without dTAG13 added at primitive streak stage to deplete OTX2 for 24hrs. Cells were harvested and live cells sorted by flow cytometry. Open chromatin regions were mapped by ATAC-seq on three technical replicates per sample.

first: Matthias

last: Stadtfeld

first: Daniel

last: Medina-Cano


title: small RNA-sequencing analysis of db/db mice exudate from subcutaneously implanted sponges

status: Public on Jun 30 2024

first: Nikolaos

last: Kalavros

state: Massachusetts

address: 330 Brookline Avenue

department: Pathology

institute: Beth Israel Deaconess Medical Center

summary: Dried polyvinyl alcohol (PVA) sponges were used for subcutaneous implantation in the mice dorsum, and were harvested on days 3, 5, 10, and 16 post-implantation.

overall_design: Male 16-week old db/db mice (stock # 000642) were obtained from Jackson Laboratories and were acclimated to the animal facility for at least one week before surgery. A vertical incision of 2 cm was created on depilated and disinfected dorsum and a pocket was formed by separating the skin from the muscle to insert 4-6 PVA sponges. Once insertions were completed, the incisions were sutured and dermabond was applied. On collection days, PVA sponges containing wound fluids were collected in empty 5 ml syringes, placed in 15 ml falcon tubes and centrifuged for fluid collection at 3,000 rpm for 10 minutes at 4 °C.

first: Georgios

last: Theocharidis


title: IL-13 decreases suceptibility to airway epithelial SARS-CoV-2 infection but increases disease severity in vivo

status: Public on Jun 28 2024

city: Iowa city

first: Alejandro

middle: Pezzulo

last: Colmenares

state: Iowa

address: 169 Newton Road

department: Internal medicine

institute: University of Iowa

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Transcriptional remodeling by OTX2 directs specification and patterning of mammalian definitive endoderm [CUT&RUN]

summary: We discovered a role for the transcription factor OTX2 in formation of mouse definitive endoderm (DE). We used CUT&RUN to map OTX2-bound genomic regions and identify OTX2-regulated genes during directed differentiation of EpiSCs to DE

overall_design: EpiSCs were converted to DE and live cells isolated by flow cytometry. OTX2 binding sites were mapped in mouse EpiSCs and definitive endoderm using CUT&RUN for HA in OTX2-HA tagged cell lines.

first: Alexander

last: Polyzos


title: Changes in tryptophan de novo NAD synthesis associated with chronic intestinal inflammation

first: Rhian

last: Stavely

address: 185 Cambridge Street, CPZN, 6100

department: Pediatric Surgery

institute: Massachusetts General Hospital

summary: Tryptophan metabolism and de novo NAD biosynthesis is associated with behavioural changes in IBD patients. The microbiota and tryptophan de novo syntheses of the distal colon, distal colon and brain of C57BL/6 control mice and Winnie mice littermates with chronic intestinal inflammation were compared using RNA-Seq. Differentially expressed genes were analysed using Micromon software. Changes in tryptophan and nicotinamide metabolism-associated gene expressions, metabolites, and abundance of gut microbiota associated with chronic intestinal inflammation and dysregulated tryptophan metabolism in the Winnie mouse distal colon and brain were apparent. Our findings shed light on the physiological alterations in tryptophan metabolism, specifically its diversion from the serotonergic pathway towards the kynurenine pathway and the consequential effects on de novo NAD+ synthesis, in the context of chronic intestinal inflammation

overall_design: To investigate Winnie mouse brains versus C57BL/6 mouse brains, 5 males and 5 females from each group were euthanised with pentobarb, their brains were extracted and immediately frozen in -80 degrees. Then RNA was extracted using Trizol and Qiagen RNA tissue extractor.

first: Jeannie

last: Devereaux

first: Kulmira

last: Nurgali

first: Ainsley

last: Robinson


title: IL-13 decreases suceptibility to airway epithelial SARS-CoV-2 infection but increases disease severity in vivo [Bulk RNA-seq]

summary: Human airway epithelia (HAE) undergo inflammation-induced remodeling in chronic lung diseases such as asthma and chronic bronchitis. The role of type 2 inflammation-induced epithelial remodeling in SARS-CoV-2 infection and the course of COVID-19 is unclear, moreover, there is discrepancy in the literature regarding the potential benefit of treatments that modulate type 2 inflammation. We investigated the role of IL-13-induced inflammation on SARS-CoV-2 binding/entry, replication, and host response in primary HAE cells in vitro and in a model of mouse-adapted SARS-CoV-2 in vivo. IL-13 protected airway epithelial cells from SARS-CoV-2 infection in vitro by decreasing the abundance of ACE2- expressing ciliated cells rather than by neutralization in the airway surface liquid or by interferon-mediated antiviral effects. In contrast, IL-13 worsened the severity of disease in mice in vivo; the effects were mediated by eicosanoid signaling and were abolished in mice deficient in the phospholipase A2 enzyme PLA2G2D. We conclude that IL-13-induced inflammation affects multiple steps of SARS-CoV-2-induced disease pathogenesis. Whereas IL-13-induced inflammation may be protective against initial infection at the airway epithelium, it enhances disease severity once infection progresses in vivo; blockade of IL-13 and/or eicosanoid signaling may be protective against progression to severe lung disease.

overall_design: To investigate the role of IL-13 induced inflammation on SARS-CoV-2 in vivo, we intranasally infected 4 mice by 1,000PFU of SARS2-N501YMA30 after a 4-day pretreatment of 2.5 μg/day intranasal IL-13 or vehicle. We harvested lungs  on the fifth day and then performed bulk RNA-seq.

first: Shreya

last: Ghimire

first: Biyun

last: Xue

first: Kun

last: Li

first: Ryan

last: Gannon

first: Christine

last: Wolford-Lenane

first: Andrew

last: Thurman

first: Huiyu

last: Gong

first: Grace

last: Necker

first: Jian

last: Zheng

first: David

last: Meyerholz

first: Stanley

last: Perlman

first: Paul

last: McCray

last: Pezzulo


title: Intermittent fasting alleviates photoreceptor degeneration and retina inflammation in oxidative stress-induced model of Age-Related Macular Degeneration

city: xu zhou

first: Jingzhen

address: huang shan road

department: Life science

institute: xuzhou medical university

summary: Age-related macular degeneration (AMD), a prevalent neurodegenerative disorder, remains the leading cause of vision loss among the elderly population. Despite the urgent need, effective treatments or preventive strategies for AMD are not available. Recent studies have highlighted the potential neuroprotective benefits of intermittent fasting (IF) in several models of aging and age-associated disorders. However, its efficacy in AMD has not been established. Our current research reveals that IF alleviated neurodegeneration  by reducing RPE and photoreceptor cell damage  in an oxidative stress-induced mouse model of AMD. The assessment of visual capabilities in mice through optomotor response (OMR) tests indicates that IF markedly preserved visual function in NaIO3-treated mice. To understand the mechanism by which IF exerts its protective effects, we performed transcriptome analyses and found that IF can counteract numerous transcriptional alterations induced by NaIO3, predominantly affecting genes involved in photoreceptor structure, inflammatory pathways and reactive oxygen species (ROS) process. Further, we demonstrated through multiple experiments that IF could effectively reduce ROS levels and restraining the hyperactivation of microglia and Müller cells within the RPE and retina. Moreover, we explored the initiation of IF at a later stage in an individual's lifespan and found that benefits were also obtained in the AMD model. Collectively, this study indicates IF exerts neuroprotective effects by reducing ROS production and inflammation in the retina, and is expected to become a new strategy for retinal degenerative diseases caused by oxidative damage, incluiding AMD.

overall_design: We examined the transcriptional profiles of IF-treated degenerative retina to explore the underlying mechanism. RNA was isolated from the RPE/choroid/sclera complex, which was either subjected to PBS or NaIO3 induction, with and without IF intervention, and subjected to RNA-seq analysis

first: Meng

first: Beibei

last: Wang


title: Cellular origin and clonal evolution of human dedifferentiated liposarcoma

first: Fabien

last: Quinquis

overall_design:
Primary DDLPS, WDLPS, liposarcoma and peritumoral fat tissue of untreated patients were isolated and analyzed using scRNAseq.

UPDATE [May-20-2025] The processed data files were updated.

first: Nadège

last: Gruel

first: Chloé

last: Quignot

first: Sophie

last: El Zein

first: Laëtitia

last: Lesage

first: Sylvie

last: Bonvalot

first: Dimitri

last: Tzanis

first: Julien

last: Vibert

first: Nadine

last: El Tannir

first: Didier

last: Decaudin

first: Héloïse

last: Derrien

first: Ahmed

last: Dahmani

first: Odette

last: Mariani

last: Linares

first: Sylvain

last: Baulande

first: Joshua

last: Waterfall

first: Olivier

last: Delattre

first: Sarah

last: Watson


title: A HigB-like toxin induces non-replicating Salmonella inside macrophages by inhibiting RNase III-dependent rRNA maturation [sehA_RNA-Seq]

status: Public on Jun 21 2024

city: Seoul

first: Yong-Joon

last: Cho

address: 1 Gwanak-ro, Gwanak-gu

institute: Seoul National University

summary: Many bacteria are often resistant to antibiotic treatment and drugs because, even if these drugs are effective, bacteria can slow down their growth rate and thus attenuate the effectiveness of the drug. A similar growth-rate control is detected in pathogenic bacteria that infect and persist inside their hosts. The bacterial growth rate within host cells can be regulated by multiple signaling pathways, most of which are still unknown. A toxin-antitoxin (TA) system is one of the candidates for controlling bacterial growth because the TA system could slow down growth by expressing a toxin component. The toxin protein can be neutralized by the antitoxin component, serving as a non-heritable phenotypic switch for growth rate. In this study, we investigated a type II toxin-antitoxin system from the intracellular bacterial pathogen Salmonella enterica serovar Typhimurium. We characterized residues required for toxin’s activity and a potential mechanism of the toxin by searching for its target via bacterial two-hybrid screening. Understanding the underlying mechanism of toxin-mediated persister formation and growth rate control within host cells will provide a new alternative to treat antibiotic resistant bacteria or intracellular bacteria surviving within host cells.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S

overall_design: We used RNA-seq to determine if the profile of mono-phosphated-OH and mono-phosphated mRNA differed between the sehA mutant and a strain that overexpressed sehA by arabinose induction.

first: Soomin

last: Choi

first: Seungwoo

last: Baek

first: Eunna

first: YoonKi

last: Kim

first: Eun-Jin

last: Lee


title: A HigB-like toxin induces non-replicating Salmonella inside macrophages by inhibiting RNase III-dependent rRNA maturation [sehB_RNA-Seq]

platform_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S

overall_design: We performed an RNA-Seq between the sehB mutant and wild type to analyze how the mRNA profile changed under the influence of overexpressed sehA as a result of sehB deletion.


title: Affinity maturation broadens influenza vaccine-induced antibody responses in humans

status: Public on Jun 13 2024

city: New Haven

first: Hailong

last: Meng

state: CT

address: 300 George Str

institute: Yale University

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

relation:
SuperSeries of: GSE211865
SuperSeries of: GSE211869


title: Affinity maturation broadens influenza vaccine-induced antibody responses in humans [bcr]

summary: Influenza virus vaccination remains the best strategy for combating virus infection, but vaccine efficacy is highly variable. An ideal influenza vaccine must have two attributes: one, it should be capable of inducing broadly cross-reactive antibodies that can neutralize diverse influenza virus strains; and two, it must induce long-lived antibody responses to maintain protective immunity for extended periods. Germinal center (GC) reactions are the major sites where diversification and affinity maturation of B cells occur. Whether a persistent GC response could expand the breadth of responding B cell clones following influenza vaccination in humans remains unknown. Here, we show that influenza virus vaccine-specific GC B cells persist for over nine weeks post vaccination in two out of seven individuals. These late vaccine-specific GC B cells exhibited increased somatic hypermutation (SHM) of their B cell receptors compared to early vaccine-specific GC B cells. After re-immunization with seasonal influenza virus vaccine, individuals with a persistent GC engaged vaccine-specific plasmablasts (PBs) with higher SHM frequency. Tracking the maturation of three clonally related GC B cell lineages over time revealed that late GC B cells had receptors that recognized and neutralized heterologous influenza virus strains. Thus, SHM induced by persistent GCs can broaden the antibody response to influenza virus vaccination. This indicates that seasonal influenza virus vaccination in humans can induce broadly cross-reactive antibodies that target diverse influenza virus strains.

overall_design: 128 samples from PBMC and lymph node were taken at multiple time points pre- and post-vaccination from 3 subjects. The samples were examined with bulk & single-cell BCR sequencing

first: Katherine

last: McIntire

first: Julian

middle: Q

last: Zhou

first: Steven

last: Kleinstein

first: Ali

last: Ellebedy


title: Transcriptional remodeling by OTX2 directs specification and patterning of mammalian definitive endoderm [scRNA-seq]

first: Ly-sha

last: Ee

summary: We discovered a role for the transcription factor OTX2 in formation of mouse definitive endoderm (DE). We determined the gene expression profiles during conversion of EpiSCs to DE using scRNA-seq. We used dTAG13 to deplete OTX2 at two timepoints of differentiation

overall_design: Mouse EpiSCs were differentiated to DE with or without dTAG13 added at primitive streak or 24hr DE stage to deplete OTX2 for further 24hrs. Cells were harvested and live cells sorted by flow cytometry.

first: Matthias

last: Stadtfeld

first: Daniel

last: Medina-Cano


title: Single-cell transcriptomic analysis of mouse lung cDC2s at various times post allergic sensitization

status: Public on Jun 05 2024

city: Research Triangle Park

first: Hideki

last: Nakano

state: NC

address: 111 TW Alexander Drive

department: Immunity, Inflammation and Disease Laboratory

institute: NIEHS

summary: Conventionaldendritic cells (cDCs) in the lung that drive effector T cell differentiation, and initiate allergic responses upon inhalation of allergens. CD11b+type 2 cDCs (cDC2s) are heterogeneous, but the relationship among  subpopulations has been elusive. To analyze their developmental pathways of cDC2 subpopulations, we performed single cell RNA-sequencing (scRNAS-Seq) of total lung cDC2s at various times following inhalation of house dust extracts, and detected multiple clusters based on their differential transcriptomes. The data of cDC2 transcriptome at steady state, early and later stages after activation will be applicable for the maturation pathway analysis of cDC2s.

overall_design: CD11b+cDC2s (CD45+ CD11c+ I-A+ Siglec-F– CD88– F4/80– CD103– Live/Dead–) from naive C57BL/6 mice, and mice 6 and 18 hours after inhalation house dust extract together with ovalbumin werepurified by flow cytometry sorting, and labeled with barcoded antibodies then loaded into the Single Cell Chip followed by forming single cell. The Gene Expression library and the ADT Library were prepared using the Chromium single cell 3′ v3 library and gel bead kit (10x Genomics) and additional reagents recommended in the protocol of Total A-seq (Biolegend). The two libraries were mixed at 10:1 molar ratio (Gene Expression library to ADT library) andsequenced by the NIEHS Epigenomics and DNA Sequencing Core Laboratory on NovaSeq 6000 (Illumina) with paired-end sequencing (Read 1: 28; Read 2: 90).

first: Donald

middle: N

last: Cook


title: Inhibiting macrophage-derived lactate transport restores cGAS-STING signaling and enhances anti-tumour immunity in glioblastoma

status: Public on Jun 01 2024

city: Chapel Hill

first: Daqi

last: Li

address: 450 West Dr

institute: Univerity of North Carolina at Chapel Hill

summary: Glioblastoma (GBM) is a malignancy with a complex tumour microenvironment (TME) dominated by GBM stem cells (GSCs) and infiltrated by tumour-associated macrophages (TAMs) and exhibits aberrant metabolic pathways. Lactate is a critical glycolytic metabolite that promotes tumour progression; however, the mechanisms of lactate transport and lactylation in the TME of GBM remain elusive. Here we show that lactate is transported from TAMs to GSCs via MCT4–MCT1. TAMs provide lactate to GSCs, promoting GSC proliferation and inducing lactylation of the non-homologous end joining protein KU70 at lysine 317 (K317), which inhibits cGAS–STING signalling and remodels the immunosuppressive TME. Inhibition of lactate transport or targeting the lactylation of KU70, in combination with the immune checkpoint blockade, demonstrates additive therapeutic benefits in immunocompetent xenograft models. This study unveils TAM-derived lactate and lactylation as critical regulators in GSCs to enforce an immunosuppressive microenvironment, opening avenues for developing combinatorial therapy for GBM.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for MES28 cell and its KD and rescued derivatives (shMCT1/shKU70/KU70-WT/KU70-MU).

first: Gaoyuan

last: Cui

first: Kailin

last: Yang

first: Chenfei

last: Lu

first: Yuhan

last: Jiang

first: Le

last: Zhang

first: Qiulian

last: Wu

first: Deobrat

last: Dixit

first: Zhe

last: Zhu

first: Ryan

last: Gimple

first: Danling

last: Gu

first: Jiancheng

last: Gao

first: Qiankun

last: Lin

first: Hang

last: Yu

first: Zhumei

last: Shi

first: Yun

last: Chen

first: Qianghu

last: Wang

first: Guangfu

last: Jin

first: Fan

first: Junfei

last: Shao

first: Qigang

first: Chong

last: Liu

first: Chaojun

first: Yongping

last: You

first: Nu

first: Junxia

first: Xu

last: Qian

first: Qian

first: Jeremy

last: Rich

first: Xiuxing


title: Affinity maturation broadens influenza vaccine-induced antibody responses in humans [gex]

first: Hailong

last: Meng

overall_design: 119 samples from PBMC, bone marrow plasma cells and lymph node were taken at multiple time points pre- and post-vaccination from 3 subjects. The samples were examined with single-cell RNA-seq.

first: Katherine

last: McIntire

first: Julian

last: Zhou

first: Steven

last: Kleinstein

first: Ali

last: Ellebedy


title: lncRNA-ZFAS1, an emerging gate-keeper in DNA damage-dependent transcriptional regulation [H3.3 ChIP-Seq]

status: Public on Jun 02 2024

city: Guangzhou

first: Yuming

state: Guangdong

address: Room 512, Anatomy Building

department: School of Basic Medical Science

institute: Guangzhou medical university

summary: Numerous long noncoding RNAs (lncRNAs) are generated in response to external stimuli, but the scope and functions of such activity are not known. Here, we provide insight into how the transcription of lncRNAs are connected to DNA damage response by identifying a lncRNA ZFAS1, which is required for cell cycle arrest, transcription regulation and DNA repair. Mechanistically, ZFAS1 facilitates the changing hyperphosphorylated forms of the large subunit of RNAPII around transcription initiation sites by directly targeting the regulated genes. We revealed extensive transcription shutdown and concomitant stimulated engagement of RNAPII-Ser2P are crucial for repair and cell survival upon genotoxic stress. Finally, ZFAS1 knockout in mice dampened transcription-coupled nucleotide excision repair (TC-NER) and led to kidney dysplasia. Our study extends the understanding of lncRNAs in DNA damage repair (DDR) and implies a protective role of lncRNA against DDR-deficient developmental disorders.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for H3.3 in the MRC5 cells with or without UV-C irradiation.

first: Jiena

first: Qing

last: Lu

first: Tingting

last: Zhu

first: Zixuan

last: Fan

last: He


title: lncRNA-ZFAS1, an emerging gate-keeper in DNA damage-dependent transcriptional regulation [CDK9 ChIP-Seq]

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for CDK9 in the WT and ZFAS1-depleted cells with or without UV-C irradiation.


title: The establishment of a DNA replication timing program in the early embryo.

status: Public on May 23 2024

city: København

first: Jason

last: Halliwell

address: Blegdamsvej 3B

country: Denmark

institute: The University of Copenhagen

summary: Single Embryo Repli-Seq was utilized to investigate the replication timing in zygotes and 2-cell cleavage stage embryos. The aim was to understand the temporal progression of DNA replication during the early stages of embryonic development in mammals.

overall_design: The replication timing of zygotes and 2-cell stage embryos was analyzed using Single Cell RepliSeq.

first: Eva

last: Hoffmann

first: Adnan

last: Hashim

first: John

last: Dahl

first: Javier

last: Gonzalez

first: Mads

last: Lerdrup


title: Single Cell Landscape of Left Atria Reveals Amphiregulin and Insulin-like Growth Factor 1 as Surrogate Markers in Patients with Atrial Fibrillation.

city: Kobe

first: Takuo

last: Emoto

state: Hyogo

address: 7-5-1 Kusunoki-cho, Chuo-ku

department: Division of Cardiovascular Medicine, Department of Internal Medicine

institute: Kobe University Graduate School of Medicine

summary: Atrial fibrillation (AF) is strongly associated with strokes, heart failure, and increased mortality. Inflammation plays a role in the pathophysiology of AF; however, how inflammation in AF is sustained and induces fibrosis is unclear. Therefore, this study aimed to identify the characteristic monocyte–macrophage heterogeneity and the cell–cell interactions between immune and non-immune cells at a single cell level in the left atrial (LA) tissues of patients with AF who underwent LA appendectomies. Myeloid cells were divided into five macrophage clusters, TNF+, two IL1B+, TREM2+, LYVE1+ resident macrophages, three monocyte clusters, five dendritic cell clusters, neutrophils, and mast cells. The CellChat analysis revealed that IL1B+ macrophages send epidermal growth factor (EGF) signalling to fibroblasts and resident macrophages send IGF1 singalling to cardiomyocytes. When compared to openly published control samples, Amphiregulin (AREG) was the most upregulated gene in monocytes and monocyte-derived IL1B+ macrophages in the AF group. We also found that AREG levels in serum were higher in patients with AF than controls. EGF signalling from IL1B+ macrophages could be therapeutic targets for AF, and AREG could be a functional biomarker for AF.

overall_design: CD45 positive cells of human left atium samples were isolated by Fluorescence-activated cell sorting and analyzed using scRNAseq, moreover, all cells of human left atium samples were analyzed using snRNAseq

first: Yuya

last: Suzuki


title: BALF single-cell landscape in CARDS and non-ARDS patients at two time points

status: Public on May 15 2024

city: Beijing

first: Longxiang

last: Su

state: Beijing

address: 1 Shuaifu Yuan

department: Department of Critical Care Medicine

institute: Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Science

summary: In this study, single-cell sequencing of the BALF of CARDS patients yielded the following results: (1) IL1B+ neutrophils were significantly increased in the BALF of CARDS patients with exacerbated disease, which was associated with poor prognosis of CARDS patients, and this type of neutrophils underwent fatty acid metabolism reprogramming in comparison with other types of neutrophils, which may be related to their high-inflammatory response. (2) IL1B+ neutrophils promoted TNF secretion from hyperinflammatory type M1 macrophages through a caspase-dependent pathway, suggesting that neutrophil-macrophage interactions play an important role in the mechanism of CARDS development.

overall_design: A total of 8 patients with severe ARDS, including 4 CARDS patients and 4 non-CARDS patients (2 bacterial pneumonia, 2 fungal pneumonia), were included in this study, of which 2 patients were treated with ECMO, and the rest of the patients received hormone therapy except for 1 patient who did not receive hormone therapy. BALF was retained in each patient at the time point of admission to the ICU (t1) and at the time point of development of an MS change value ≥1 point (t2).

first: Yingying

last: Yang

first: Haochen

last: Li

first: Peng

last: Liu

first: Yun

last: Long


title: Histone lactylation-mediated NSUN2 transcriptional activation dictates choroidal neovascularization through promoting AKAP2 mRNA expression [RNA-seq]

status: Public on May 19 2024

city: Shanghai

first: Sipeng

last: Zuo

state: Shanghai

address: No. 12, Lane 833, Zhizaoju Road, Huangpu District

institute: Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine

summary:
Background: As a widespread post-transcriptional RNA modification, N5-methylcytosine (m5C) is implicated in a variety of cellular responses and processes that regulate RNA metabolism. Despite this, a clear understanding of m5C modification’s role and mechanism in angiogenesis is still lacking.
Methods: Single-cell RNA sequencing data was analyzed to determine expression of m5C methylase NSUN2. m5C levels were determined by mRNA isolation and anti-m5C dot blot in both hypoxia-induced endothelial cells (ECs) and laser-induced choroidal neovascularization (CNV). In addition, endothelial cell and endothelium‐specific NSUN2‐knockout mouse model were used to investigate the effect of NSUN2 silence on angiogenic phenotype. Genome-wide multiomics analyses were performed to identify the functional target of NSUN2, including proteomic analysis, transcriptome screening and m5C-methylated RNA immunoprecipitation sequencing (m5C-meRIP-seq). CUT&Tag sequencing was performed to test the histone lactylation signal in the promoter region of NSUN2. Finally, AAV-mediated short hairpin RNAi knockdown of NSUN2 gene expression (AAV-shNSUN2) was constructed to investigate the effect of inhibiting CNV.
Results: First, we discovered that m5C methylase NSUN2 expression level and mRNA m5C level were significantly higher in CNV-ECs than in normal ECs. NSUN2 knockdown in ECs inhibited proliferative, migration, and tube formation activities of ECs. Moreover, compared with EC NSUN2flox/flox mice, EC-specific NSUN2-deficient (EC NSUN2-/-) mice displayed less retinal vascular leakage after laser induction. Through multiomics analyses, we subsequently identified A-kinase anchoring protein 2 (AKAP2), a scaffolding protein which isolate Protein kinase A (PKA) to specific subcellular locations through binding to its regulatory subunit, as a downstream candidate target of NSUN2 in ECs. Overexpression of exogenous AKAP2 markedly reversed the inhibitory phenotypes in NSUN2-deficient ECs. Interestingly, laser induced NSUN2 up-regulation was driven by lactate-mediated lactylation on histone H3K18. In CNV models, AAV-mediated repression of NSUN2 modulated highly retinal vascular leakage and choroidal thickness.
Conclusion: Overall, our findings indicate that NSUN2 is a novel therapeutic target for choroidal neovascularization.

overall_design: RNA-seq data related to gene NSUN2 in human umbilical vein endothelial cell

first: Lin

first: Linna

last: Lu

first: Xianqun


title: Mapping spatially resolved transcriptomes in human and mouse pulmonary fibrosis

status: Public on May 21 2024

city: Mölndal

first: Benjamin

last: Keith

address: Pepparedsleden 1

institute: AstraZeneca

summary: Idiopathic pulmonary fibrosis (IPF) is a progressive lung disease with poor prognosis and limited treatment options. Efforts to identify effective treatments are thwarted by limited understanding of IPF pathogenesis and poor translatability of available preclinical models. To address these limitations, we generated spatially resolved transcriptome maps of human IPF and bleomycin-induced mouse lung fibrosis.

overall_design: Female C57BL/6NCrl mice were challenged with 30 μl saline or bleomycin (Apollo Scientific, BI3543, Chemtronica Sweden; 40 µg/mouse) dissolved in saline via oropharyngeal route administration. Lungs were collected at day 7 (n=6 BLM, n=3 vehicle) or day 21 (n=6 BLM, n=3 vehicle) following administration. The mice were purchased from Charles River (Germany), and were 8 weeks + 5 days old at the time of study initiation. Animal handling conformed to standards established by the Council of Europe ETS123 AppA, the Helsinki Convention for the Use and Care of Animals, Swedish legislation, and AstraZeneca global internal standards. All mouse experiments were approved by the Gothenburg Ethics Committee for Experimental Animals in Sweden and conformed to Directive 2010/63/EU. The present study was approved by the local Ethical committee in Gothenburg (EA000680-2017) and the approved site number is 31-5373/11.

first: Lovisa

last: Franzén

first: Martina

last: Olsson Lindvall

first: Michael

last: Hühn

first: Victoria

last: Ptasinski

first: Laura

last: Setyo

middle: P

first: Astrid

last: Collin

first: Steven

last: Oag

first: Thomas

last: Volckaert

first: Annika

last: Borde

first: Joakim

last: Lundeberg

first: Julia

last: Lindgren

first: Graham

last: Belfield

first: Sonya

last: Jackson

first: Anna

last: Ollerstam

first: Marianna

last: Stamou

first: Patrik

last: Ståhl

first: Jorrit

middle: J

last: Hornberg


title: DNA methylation profiling of the Biomarkers of Aging Consortium Cohort

status: Public on May 29 2024

first: Jesse

last: Poganik

address: 77 Avenue Louis Pasteur

department: Medicine/Genetics

institute: Brigham and Women's Hospital, Harvard Medical School

type: Methylation profiling by genome tiling array

summary: We generated DNA methylation profiles of 500 diverse individuals to enable to construction and validation of DNA methylation biomarkers of aging.

overall_design: We selected 500 subjects to generate a cohort that was evenly divided between male and female, and represented a broad range of ages and race/ethnicity. DNA isolated from the blood of these subjects was profiled with the Illumina Infinium MethylationEPIC v2.0 array.

first: Mahdi

last: Moqri

first: Vadim

last: Gladyshev


title: lncRNA-ZFAS1, an emerging gate-keeper in DNA damage-dependent transcriptional regulation [OE CTD ChIP-Seq]

first: Yuming

last: Wang

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for RNAPII CTD Ser2P and Ser5P in the MRC5 cells overexpressing human ZFAS1 with or without UV-C irradiation.

first: Jiena

last: Liu

first: Qing

last: Lu

first: Tingting

last: Zhu

first: Zixuan

last: Fan

last: He


title: IL-8+ neutrophils drive inexorable inflammation in severe alcohol-associated hepatitis [scRNA-seq]

status: Public on May 13 2024

city: Rockville

first: Yukun

last: Guan

state: MD

address: 5625 Fishers Lane, Room 2S-30

institute: NIAAA

summary: Patients with alcohol-associated liver cirrhosis (AC) may develop severe alcohol-associated hepatitis (sAH), but the mechanisms underlying the transition from AC to sAH still remain unclear. We performed single cell RNA (scRNA) sequencing analysis of livers and peripheral white blood cells (WBC) from sAH and AC patients. We found that the significant difference between sAH and AC was that sAH livers had a markedly higher number of neutrophil subsets than AC livers. Thus, we further focused on the neutrophil cluster and found two distinct sAH-specific liver neutrophils are notably characterized by heightened expression of CXCL8 (IL-8) defined as IL-8+ neutrophils blood. Our current study has demonstrated that sAH had self-sustaining IL-8+ neutrophil accumulation that likely drives inexorable liver inflammation and failure in sAH. Based on our study, we believe targeting IL-8+ neutrophils is a promising therapeutic strategy for sAH.

overall_design: We performed scRNA sequencing analysis of 6 liver tissues and 7 peripheral white blood cells (WBC) from sAH and AC patients, including 5 sAH livers, 4 sAH WBCs; 1 AC liver, and 3 AC WBCs.

last: GUAN

first: Brandon

last: Peiffer

first: Dechun

last: Feng

first: Zhaoli

last: Sun

first: Bin

last: GAO


title: Histone lactylation-mediated NSUN2 transcriptional activation dictates choroidal neovascularization through promoting AKAP2 mRNA expression [CUT&Tag]

first: Sipeng

last: Zuo

overall_design: CUT&Tag-seq data related to gene NSUN2 in human umbilical vein endothelial cell

first: Lin

last: Li

first: Linna

first: Xianqun


title: MSA: Scalable DNA methylation BeadChip for human trait screening

status: Public on May 11 2024

city: Philadelphia

first: Wanding

last: Zhou

state: PA

address: 3501 Civic Center Blvd

department: Pathology and Lab Medicine

institute: Children's Hospital of Philadelphia

summary: We designed and introduced a new methylation array concentrating on human trait screening and discovery. The new MSA (Methylation Screening Array) leveraged the massive Infinium platform-based data from epigenome-wide association studies, combined with updated knowledge from the latest single cell and cell type-resolution whole genome methylome profiles, to achieve scalable screening of epigenetics-trait association in an ultra-high sample-throughput. Our design encompassed diverse human trait associations, including those with genetic, biological, and demographical variables, environmental exposures, and common human diseases such as neurodegenerative, genetic, cardiovascular, infectious, and immune diseases. We comprehensively evaluated this array's reproducibility, accuracy, and capacity in supporting 5-hydroxymethylation profiling and comprehensive cell-type deconvolution in diverse human tissues. Our first data using this platform uncovered dynamic chromatin and tissue contexts of DNA modification variations and genetic variants with human trait associations.

overall_design: Cell line (GM12878, K562, LNCaP, HeLa, Raji, MCF7, Jurkat, HCT116 and other Coriell cell lines), and 25 human tissue (Adrenal, Bladder, Cerebellum, Colon, Esophagus, Eye, Heart, Kidney, Larynx, Liver, Lung, Lymph Node, Motor cortex, Ovary, PBMC, Pancreas, Placenta, Prostate, Skin, Spinal Cord, Spleen, Stomach, Testis, Thymus, Thyroid, Trachea) and purified cell DNA (CD4+ T cells, CD8+ T cells, total T cell, NK cells, monocytes) and methylation titration control DNA is run on the MSA BeadChip to evaluate MSA reproducibility, accuracy, performance at low input ranges, and capability at capturing biological methylation variation. Tissues including cerebellum, motor cortex, colon, pancreas, skin, heart are additionally processed with bACE conversion to obtain 5hmC profiles.

first: David

last: Goldberg

first: Nicole

last: Renke


title: Analysis of gene expression in Mel Z cells grown on Matrigel (MM).

status: Public on May 10 2024

city: Moscow

first: Nickolai

last: Tchurikov

address: 32, Vavilova str.

department: Department of Epigenetic Mechanisms of Gene Expression Regulation

country: Russia

institute: Engelhardt Institute of Molecular Biology

summary: RNA-Seq procedure was used for analysis of expression in melanoma cells. Cells were separately lysed with Trizol reagent (Invotrogen). Total RNA was extracted from cell lysed with Trizol reagent and PureLink RNA Micro Kit (Invitrogen) according to manufacture instruction. RNA quality was checked with  BioAnalyser and  RNA 6000 Nano Kit (Agilent). Poly(A)+ RNA was purified with Dynabeads® mRNA Purification Kit (Ambion). Illumina library was prepared from poly(A)+RNA with NEBNextNEBNext® Ultra™II RNA Library Prep Kit for Illumina® (NEB) according to manual. Sequencing was performed on HiSeq1500 with 50 bp read length. At least 14.8 millions of reads were generated for each sample.

overall_design: Analysis of gene expression in Mel Z cells grown on plastic (MP), Matrigel (MM), and on Matrigel in the presence of inhibitor(MMI).

first: Yuri

last: Kravatsky

first: Amalia

last: Vartanian


title: Clinical and Immunological Responses to Combined JAK Inhibition and PD-1 immunotherapy for Lung Cancer Patients

status: Public on May 07 2024

first: Andy

last: Minn

state: Philadelphia

address: 421 Curie  Blvd

institute: University of Pennsylvania

summary: Persistent inflammation driven by cytokines like type-one interferon (IFN-I) can cause immunosuppression. We show that administration of the JAK1 inhibitor itacitinib after anti-PD1 immunotherapy improves immune function and anti-tumor responses in mice, and results in high response rates (67%) in a phase-2 clinical trial for metastatic non-small cell lung cancer. Patients who failed to respond to initial anti-PD1 immunotherapy but responded after addition of itacitinib had multiple features of poor immune function to anti-PD1 alone that improved after JAK inhibition. Itacitinib promoted CD8 T cell plasticity and therapeutic responses of exhausted- and effector-memory-like T cell clonotypes. Patients with persistent inflammation refractory to itacitinib showed progressive CD8 T cell terminal differentiation and progressive disease. Thus, JAK inhibition may improve the efficacy of anti-PD1 immunotherapy by pivoting T cell differentiation dynamics.

overall_design: Live CD8+ cells or Live CD45+ cells were sorted from PBMCs of Patients with NSCLC treated with anti-PD1 and JAKi or anti-PD1 alone during select timeponts in treatment

first: Divij

last: Mathew


title: Single-nucleus transcriptomic sequencing of aging hypothalamus treated with 17a-estradiol

status: Public on May 01 2024

city: Nantong

first: Yinchuan

state: Jiangsu

address: 16 wenfeng road, Chongchuan

department: Medical School

institute: Nantong University

summary: To dissect the role of 17a-estradiol in lifespan extending and its potential side effects for long-term administration, the pooled hypothalami from aging male Norway brown rats treated with 17a-estradiol for 6 months (O.T), aged male control (O), and young male control (Y) were subjected to single-nucleus transcriptomic sequencing (snRNA-seq).

overall_design: 24-month-old-male Norway brown rats were  fed freely with diet mixed with 17a-estradiol at a dose of 14.4 milligrams per kilogram diet (14.4 ppm) starting at 24 months of age for six months (O.T). 30-month-old-male rats and 4-month-old-male rats were used as aging control (O) and young sample control (Y) respectively. All rats had ad libitum access to food and water. The intact hypothalami in each group were pooled for nucleus isolation and snRNA-seq.

first: Shaoyang

last: Ji


title: Whole transcriptomic analysis of Korean osteoarthritis patients.

status: Public on Apr 30 2024

city: Busan

first: Jaewan

last: Jeon

address: 875, Haeun-daero, Haeundae-gu, Busan, Republic of Korea

institute: Jaewan Jeon

summary: A database of genes showing differences in expression in synovium tissues and normal synovium tissues of Korean patients with advanced osteoarthritis was established.

overall_design: Synovium tissue in osteoarthritis patients was secured when operating, and normal tissue was secured in patients requiring surgery due to sports damage. Confirmation of synovial tissue was performed by a pathologist and whole transcriptomic analysis was performed with the identified tissue.

first: Sang

last: Moon

first: Hwan-Kwon

last: Do


title: miRNA profiles in muscle of IUGR and normal weight pig fetuses

status: Public on May 24 2024

city: Roslin

first: F. Xavier

last: Donadeu

address: Easter Bush

country: United Kingdom

institute: University of edinburgh

summary: Intrauterine growth restriction (IUGR) is a leading cause of neonatal morbidity and mortality in humans and domestic animals. Developmental adaptations of skeletal muscle in IUGR lead to increased risk of premature muscle loss and metabolic disease later during life. Although transcriptome-wide profiles in muscle associated with IUGR have been reported, their regulation by miRNAs is not well understood. The aim of this study was to identify differences in miRNA expression in porcine skeletal muscle of IUGR and normal-weight (NW) littermates during late foetal development (day 90 of gestation).

overall_design: RNA sequencing was performed on a total of 8 semitendinous muscle samples collected from  4 pig litters at day 90 of gestation. Two male fetuses were collected from each litter, one with normal weight as defined by weight above the litter average (Large) and a IUGR fetus with weight >2 SD below the average litter weight (Small). Differentially expressed genes were identified from analyses taking account of 'litter'.

first: Yennifer

last: Cortes

first: Susanna

middle: E

last: Riley

first: Xavier


title: Effects of BPS and BPF on transcriptional networks of neuronal cells

status: Public on Apr 27 2024

city: Gainesville

first: Christopher

last: Martyniuk

state: FL

address: 8891 SW 79th Avenue

institute: University of Florida

summary: Over the past several years, replacement chemicals for bisphenol A have been manufactured and used as additives in sportswear, plastic bottles, food packaging, and in other products. More recently, replacement products for BPA are under investigation for toxicity, but there are little data on the potential for neurotoxicity. To address this gap, differentiated human SH-SY5Y cells were treated with a range of concentrations of BPS and BPF to better understand mechanisms of toxicity.

overall_design: Cell culture flasks were exposed to DMSO, or one dose of either BPS or BPF.  Cells were exposed in T75 flasks by removing all of the media and replacing it with 8 mL of differentiation media (DMEM:F12 containing 1% FBS, 1% antibiotic/antimycotic solution, and 10 µM retinoic acid) every 48 hours. On the 6th day, cells were exposed to media, 0.1 nM BPS, or 0.1 nM BPF (n=5-6) for 48 hours. Media was then removed and the remaining cells were trizoled and stored at -80°C for further processing.

first: Chris

last: Souders

first: Andrea

last: Guzman


title: lncRNA-ZFAS1, an emerging gate-keeper in DNA damage-dependent transcriptional regulation [GRO-seq]

first: Yuming

last: Wang

overall_design: WT and ZFAS1-knockdown MRC5 cells were treated with DRB (100 μM, 3.5 hrs), followed by 10 J/m2 UV-C irradiation or left untreated. Cells were washed with PBS to remove DRB immediately after UV-C treatment and incubated for 10 or 40 minutes, followed by cell lysis and nuclei isolation. Nuclei were subjected to GRO-Seq.

first: Jiena

last: Liu

first: Qing

last: Lu

first: Tingting

last: Zhu

first: Zixuan

last: Fan

last: He


title: Single cell sequencing data of zebrafish spinal cord injury

status: Public on May 03 2024

city: 南通

first: xing

middle: yi

last: song

state: 江苏

address: 江苏省南通市启秀路19号

department: 神经再生

institute: 南通大学

summary: After spinal cord injury in adult zebrafish, the spinal cord was taken out for single-cell data sequencing

overall_design: The spinal cord of adult zebrafish was taken for single cell sequencing

first: Lingyan

last: Xing

first: Jiaqi

first: Gang

last: Chen


title: In vitro reconstitution of epigenetic reprogramming in the human germ line [EM-Seq]

status: Public on Apr 24 2024

city: Kyoto

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

institute: Kyoto University, Graduate school of medicine

summary: Epigenetic reprogramming resets parental epigenetic memories and differentiates primordial germ cells (PGCs) into mitotic pro-spermatogonia or oogonia, ensuring sexually dimorphic germ-cell development for totipotency.  However, the mechanism of epigenetic reprogramming in humans remains unknown.  Here, we establish a robust strategy for inducing epigenetic reprogramming and differentiation of pluripotent stem cell (PSC)-derived human PGC-like cells (hPGCLCs) into mitotic pro-spermatogonia or oogonia, coupled with their extensive amplification (~>10(10)-fold).  Strikingly, bone morphogenetic protein (BMP) signaling is the key driver of these processes.  Mechanistically, BMP signaling attenuates the mitogen-activated protein kinase/extracellular-regulated kinase (MAPK/ERK) pathway and both de novo and maintenance DNA methyltransferase (DNMT) activities, promoting replication-coupled, passive DNA demethylation.  On the other hand, tens-eleven translocation (TET) 1, an active DNA demethylase abundant in human germ cells, plays a dual role in hPGCLC differentiation: safeguarding hPGCLCs against differentiation into amnion-like cells by repressing key genes with bivalent promoters, and facilitating coordinated activation of genes vital for spermatogenesis and oogenesis by demethylating their promoters.  Our study uncovers the principle of epigenetic reprogramming in humans, making a fundamental advance in human biology, and through the generation of abundant mitotic pro-spermatogonia and oogonia-like cells, represents a milestone for human in vitro gametogenesis (IVG) research and its potential translation into reproductive medicine.

overall_design: Whole genome EMseq analysis of human PGCLCs expanded with BMP signaling.

first: Yusuke

last: Murase

first: Ryuta

last: Yokogawa

first: Masahiro

last: Nagano

first: Yoshitaka

last: Katou

first: Manami

last: Mizuyama

first: Ayaka

last: Kitamura

first: Pimpitcha

last: Puangsricharoen

first: Chika

last: Yamashiro

first: Bo

last: Hu

first: Ken

last: Mizuta

first: Taro

last: Tsujimura

first: Takuya

last: Yamamoto

first: Kosuke

last: Ogata

first: Yasushi

last: Ishihama

first: Mitinori

last: Saitou


title: RoCK and ROI: a single-cell RNA-sequencing method with enhanced transcriptome information via targeted enrichment of transcripts and preselected, region-specific sequencing

city: Zürich

first: Giulia

middle: Arianna

last: Moro

address: Winterthurerstrasse 190

department: DMLS

country: Switzerland

institute: University of Zurich

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

overall_design: Refer to individual Series


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

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: Analysis of gene expression in Mel Z cells grown on MM, MP, and with MMI

first: Nickolai

last: Tchurikov


title: Bioinformatics and single-cell CRISPRi-based screen reveals effector genes and implicates multi-tissue etiology for BMD [bulk RNA-seq]

status: Public on Apr 17 2024

first: Mitchell

middle: L

last: Conery

address: 3615 Civic Center Blvd

department: Center for Spatial and Functional Genomics

summary: To nominate identify tissues relevant to the etiology of bone mineral density we generated ATAC-seq in pediatric hMSC-osteoblasts, hFOB 1.19 cells (hFOBs), osteoclasts, and primary chondrocytes. Leveraging the results of this experiment, we designed a CRISPRi screen in hFOBs with scRNA-seq expression read out. The targets selected for the screen were informed by newly generated Capture-C and bulk RNA-seq from hFOBs.

overall_design: hFOB 1.19 cells were differentiated at 39.5⁰C for 5 days prior to collection for sequencing.

first: James

last: Pippin

first: Matthew

middle: C

last: Pahl

first: Struan

middle: F

last: Grant


title: Bioinformatics and single-cell CRISPRi-based screen reveals effector genes and implicates multi-tissue etiology for BMD [scCRISPR screen]

overall_design: hFOBs constitutitively exprressing dCas9-CRISPRi-KRAB were transfected at a low MOI with a pool of 296 sgRNAs targeted to 89 sites. Cells with sgRNAs were selected for 9 days by puromycin and then differentiated for 5 days at 39.5⁰C prior to sequencing.


title: Bioinformatics and single-cell CRISPRi-based screen reveals effector genes and implicates multi-tissue etiology for BMD


title: Bioinformatics and single-cell CRISPRi-based screen reveals effector genes and implicates multi-tissue etiology for BMD [Capture-C]