title: Simultaneous targeting of peripheral and brain tumors with a therapeutic nanoparticle to disrupt metabolic adaptability at both sites

city: Miami

first: Shanta

last: Dhar

state: Florida

address: 1011 NW 15th Street, Room 437

department: Biochemistry

institute: University of Miami

summary: Brain metastasis of advanced breast cancer often results in deleterious consequences. Metastases to the brain lead to significant challenges in treatment options, as the blood– brain barrier (BBB) prevents conventional therapy. Thus, we hypothesized that creation of a nanoparticle (NP) that distributes to both primary tumor site and across the BBB for secondary brain tumor can be extremely beneficial. Here, we report a simple target- ing strategy to attack both the primary breast and secondary brain tumors utilizing a single NP platform. The nature of these mitochondrion-targeted, BBB-penetrating NPs allow for simultaneous targeting and drug delivery to the hyperpolarized mitochondrial membrane of the extracranial primary tumor site in addition to tumors at the brain. By utilizing a combination of such dual anatomical distributing NPs loaded with therapeu- tics, we demonstrate a proof-of-concept idea to combat the increased metabolic plasticity of brain metastases by lowering two major energy sources, oxidative phosphorylation (OXPHOS) and glycolysis. By utilizing complementary studies and genomic analyses, we demonstrate the utility of a chemotherapeutic prodrug to decrease OXPHOS and glycolysis by pairing with a NP loaded with pyruvate dehydrogenase kinase 1 inhibitor. Decreasing glycolysis aims to combat the metabolic flexibility of both primary and sec- ondary tumors for therapeutic outcome. We also address the in vivo safety parameters by addressing peripheral neuropathy and neurobehavior outcomes. Our results also demonstrate that this combination therapeutic approach utilizes mitochondrial genome targeting strategy to overcome DNA repair–based chemoresistance mechanisms.

overall_design:
We treated the MDA-MB-231-BR cells cells with cisplatin or T-Platin-M-NP and then we performed RNA sequencing analysis to understand the expression profiles of OXPHOS, nucleotide excision pathway and nuclear encoded mitochondrial genes.
A primary  xenoraft tumor model was generated using MDA-MB-231-BR cells in BALB/c nude mice and treated with cisplatin, 2-DG, T-Platin-M-NP or T-Platin-M-NP+2-DG. Tumor samples were harvested at the end of the study and then performed expression profiling analysis using the data obtained from the RNA -seq of tumor samples and study  expression of genes related OXPHOS, glycolysis and execision repair pathways.
A dual tumor model was generated using MDA-MB-231-BRLuc cells in BALB/c nude mice and treated with cisplatin or T-Platin-M-NP+T-Mito-DCA-NP. Tumor samples were harvested at the end of the study and then performed expression profiling analysis using the data obtained from the RNA -seq of tumor samples and study expression of genes related to OXPHOS, glycolysis, Fatty acid oxidation, apoptosis and various repair pathways.

first: A

last: Ashokan

first: S

last: Sarkar

first: M

middle: Z

last: Kamran

first: B

last: Surnar

last: Kalathil

last: Spencer


title: The heterogeneous sensitivity of pediatric brain tumors to different oncolytic viruses is predicted by unique gene molecular profiles

status: Public on Apr 28 2024

city: Utrecht

first: Konstantinos

last: Vazaios

address: Heidelberglaan 25

country: Netherlands

institute: Princess Maxima Center for Pediatric Oncology

type: Expression profiling by high throughput sequencing

summary: Despite decades of research, the prognosis of high-grade pediatric brain tumors (PBTs) remains dismal, however, recent cases of favorable clinical responses were documented in clinical trials using oncolytic viruses (OVs). Therefore, we employ four different species of OVs: adenovirus Delta24-RGD, herpes simplex virus rQNestin34.5v1, reovirus R124 and the non-virulent Newcastle Disease Virus rNDV-F0-GFP against three entities of PBTs (high-grade gliomas, atypical teratoid/rhabdoid tumors and ependymomas) to determine their in vitro efficacy. These four OVs were screened on 14 patient-derived spheroids and the degree of oncolysis was assessed using an ATP-based assay. Subsequently, the observed viral efficacies were correlated to whole transcriptome data and Gene Ontology analysis was performed. Although no significant tumor type-specific OV efficacy was observed, whole transcriptome analysis revealed the intrinsic biological processes that associated with OV efficacy. The predictive power of those molecular profiles was further validated by screening the OV in vitro efficacy on additional PBTs. In summary, our results demonstrate OV susceptibility of multiple patient-derived PBT entities and the ability to predict in vitro responses to OVs using unique molecular profiles. Those profiles  highlight the cellular intrinsic factors for potent oncolysis, that could potentially allow stratification of patients and lead to improved OV responses.

overall_design:
To investigate the intrinsic factors that relate to Oncolytic virus (OV) oncolysis we used a panel of 14 patient derived pediatric brain tumor cell cultures (PBTs) which were infected with 4 different OVs: Delta24-RGD, rQNestin34.5v1, R124 and rNDV-F0-GFP.
We then performed gene expression profiling using RNA seq data obtained from the 14 uninfected PBTs.
The gene expression of the PBTs was correlated (using spearman correlation) with the concentration of each OV needed to kill 50% per PBT 5 days post infection (EC50s).
Gene Ontology enrichment was performed using as input the significantly correlated genes to link specific factors to OV sensitivity and resistance.
Additional PBTs were used for phenotypic profiling using the significantly correlating genes in order to predict their response to the OVs and those profiles were further validated through in vitro testing.

first: Eftychia

last: Stavrakaki

first: Lisette

middle: B

last: Vogelezang

first: Jie

last: Ju

first: Piotr

last: Waranecki

first: Dennis

middle: S

last: Metselaar

first: Michael

middle: H

last: Meel

first: Vera

last: Kemp

first: Bernadette

middle: G

last: van den Hoogen

first: Rob

middle: C

last: Hoeben

first: Antonio

middle: E

last: Chiocca

first: William

middle: F

last: Goins

first: Andrew

last: Stubbs

first: Yunlei

last: Li

first: Marta

middle: M

last: Alonso

first: Friso

last: Calkoen

first: Esther

last: Hulleman

first: Jasper

last: van der Lugt

first: Martine

last: Lamfers


title: Zika Virus Non-Coding RNAs Antagonize Antiviral Responses by PKR-Mediated Translational Arrest (Ribo-Seq)

city: Ciudad de Buenos Aires

first: Horacio Martín

last: Pallarés

address: Av patricias argentinas 435

country: Argentina

institute: Fundación instituto leloir

summary: Zika virus (ZIKV) is an emerging mosquito-borne flavivirus that causes severe outbreaks in human populations. ZIKV infection leads to the accumulation of small non-coding viral RNAs (known as sfRNAs) that are crucial for evasion of antiviral responses and for viral pathogenesis. However, the mechanistic understanding of how sfRNAs function remains incomplete. Here, we use recombinant ZIKVs and ribosome profiling of infected human cells to show that sfRNAs block translation of antiviral genes. Mechanistically, we demonstrate that specific RNA structures present in sfRNAs trigger PKR activation, which instead of limiting viral replication, enhances viral particle production. Although ZIKV infection induces mRNA expression of antiviral genes, translation efficiency of type I interferon and interferon stimulated genes were significantly downregulated by PKR activation. Our results reveal a novel viral adaptation mechanism mediated by sfRNAs, where ZIKV increases its fitness by repurposing the antiviral role of PKR into a proviral factor.

overall_design: To investigate the effect of sfRNAs accumulation on the translation landscape of the cell host, we created a recombinant ZIKV incapable of producing sfRNAs (ZIKV sfRNAnull) by introducing mutations into the full-length cDNA of ZIKV ARCB116141 (pZIKVAr). Subsequently, we infected the A549 human cell line with both ZIKV WT and ZIKV sfRNAnull at an MOI=10. Ribosome Profiling and RNA-seq analyses were then performed on mock-infected and ZIKV-infected cells at 20 hours post-infection, utilizing data obtained from 2 replicates for each condition.

first: Horacio

first: María

last: González López Ledesma

first: Santiago

last: Oviedo Rouco

first: Luciana

middle: A

last: Castellano

first: Guadalupe

last: Costa Navarro

first: Ana

middle: J

last: Fernández-Alvarez

last: D’Andreiz

first: Victor

middle: D

last: Aldas-Bulos

first: Diego

last: Alvarez

first: Ariel

last: Bazzini

first: Andrea

middle: V

last: Gamarnik


title: Zika Virus Non-Coding RNAs Antagonize Antiviral Responses by PKR-Mediated Translational Arrest (RNA-Seq)


title: New insights into benzo[⍺]pyrene osteotoxicity in zebrafish

status: Public on Apr 29 2024

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

country: Germany

institute: MPI for heart and lung research

summary: Persistent and ubiquitous organic pollutants, such as the polycyclic aromatic hydrocarbon benzo[⍺]pyrene (BaP), represent a major threat to aquatic organisms and human health. Beside some well-documented adverse effects on the development and reproduction of aquatic organisms, BaP was recently shown to affect fish bone formation and skeletal development through mechanisms that remain poorly understood. In this work, several bone-related in vivo assays were used in zebrafish to evaluate the osteotoxic effects of BaP during bone development and regeneration. Exposure to BaP for 3 days induced a dose-dependent reduction of the size of the opercular bone in 6 days post-fertilization (dpf) larvae, and affected osteoblast maturation as observed by the expression of the mature marker, osteocalcin. Exposure to BaP for 27 days affected the development of the axial skeleton and increased the incidence and severity of skeletal deformities. During bone regeneration, BaP affected the mineralization of newly formed fin rays and scales, while it impaired fin ray patterning and scale shape, through mechanisms that may involve an imbalance of bone remodeling. Transcriptomic and gene expression analyses indicate that BaP induced the activation of xenobiotic and metabolic pathways, while negatively impacting extracellular matrix formation and organization. Interestingly, BaP exposure positively regulated inflammation markers in 6 dpf larvae and increased neutrophil recruitment. A direct interaction between neutrophils and bone extracellular matrix or bone forming cells was observed in vivo, suggesting a role for neutrophils in the mechanisms underlying BaP osteotoxicity. Our work provides novel data on the cellular and molecular players involved in BaP osteotoxicity and brings new insights into a possible role for neutrophils in inflammatory bone reduction.

overall_design: Whole-larvae mRNA profiles of 6 day post fertilization (dpf) wild type zebrafish strain AB, treated either with DMSO 0.1% or benzo(α)pyrene 1 μM from 3 to 6 dpf

first: Marco

last: Tarasco

first: João

last: Cardeira da Silva

first: Didier

middle: Y

last: Stainier

first: M

middle: L

last: Cancela

first: Vincent

last: Laizé


title: The prenatal nicotine exposure leads to epigenetic alterations in nervous system signaling genes in the rat [RNA-seq]

status: Public on Apr 26 2024

city: Rennes

first: Fatima

last: SMAGULOVA

address: 9 av. Prof. Léon Bernard

country: France

institute: Irset - U1085

summary: Background. Prenatal exposure to nicotine has been documented to impose numerous deleterious effects on fetal development. However, the epigenetic changes promoted by nicotine exposure on germ cell are still not well understood. Objectives. In this study, we focused on elucidating the impact of prenatal nicotine exposure on regulatory epigenetic mechanisms important for the germ cells development.  Objectives. In this study, we focused on elucidating the impact of prenatal nicotine exposure on regulatory epigenetic mechanisms important for the germ cells development.

overall_design: Methods. Sprague-Dawley rats were exposed to nicotine during pregnancy and male progeny was analyzed at age of 11 weeks. Testis morphology was analyzed using frozen testis sections and expression of germ cell markers was examined by RT-qPCR; regulatory histone modifications were assessed by WB. A genome-wide DNA methylation was analyzed using MEDIP-seq. We also carried out transcriptomics analysis in pituitary gland with RNA-seq.

last: Smagulova


title: EHF is an essential regulator of mammary alveolar lineage differentiation and putative suppressor of breast tumorigenesis

city: Clayton

first: Wei

last: Shi

state: VIC

address: 15 Innovation Walk

department: Department of Biochemistry and Molecular Biology

country: Australia

institute: Monash University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The Ets homologous factor (Ehf) is highly expressed in the mammary gland in pregnancy and lactation. Mothers with Ehf deletion fail to lactate due to impaired lobuloalveolar development. ATACseq profiling of luminal mammary epithelial cells at late pregnancy (18.5dP) demonstrated that loss of Ehf results in significant chromatin remodelling.

overall_design: ATAC sequencing of luminal mammary epithelial cells (Ter119–CD31−CD45–CD24+CD29Lo) from mice with and without deletion of Ehf at late pregnancy (18.5 days pregnant)

first: Yang

last: Liao

first: Rebecca

last: Nightingale

first: Camilla

last: Reehorst

first: François

last: Vaillant

first: Jane

last: Visvader

first: Bhupinder

last: Pal

first: John

last: Mariadason


title: The prenatal nicotine exposure leads to epigenetic alterations in nervous system signaling genes in the rat [MeDIP]

type: Methylation profiling by high throughput sequencing

summary: Background. Prenatal exposure to nicotine has been documented to impose numerous deleterious effects on fetal development. However, the epigenetic changes promoted by nicotine exposure on germ cell are still not well understood. Objectives. In this study, we focused on elucidating the impact of prenatal nicotine exposure on regulatory epigenetic mechanisms important for the germ cells development. s important for the germ cells development

overall_design: Sprague-Dawley rats were exposed to nicotine during pregnancy and male progeny was analyzed at age of 11 weeks. A genome-wide DNA methylation was analyzed using MEDIP-seq.


title: Zika Virus Non-Coding RNAs Antagonize Antiviral Responses by PKR-Mediated Translational Arrest

first: Horacio Martín

last: Pallarés

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

overall_design: Refer to individual Series


title: Meningioma transcriptomic landscape demonstrates novel subtypes with regional associated biology and patient outcome

city: Seattle

first: Eric

last: Holland

state: WA

address: 1100 Fairview Ave. N

department: Human Biology

country: USA

institute: Fred Hutch Cancer Center

summary: Meningiomas are the most common primary intracranial tumors in humans. While most of these tumors are benign, some are malignant, rapidly recur after multimodal treatment with surgery and radiotherapy, and can ultimately be fatal. The current WHO grade system does not always identify high risk meningiomas, therefore better characterizations of the biology of aggressive tumors are needed. In order to address these challenges, we combined 13 bulk RNA-Seq datasets, corrected for batch effects, and applied Uniform Manifold Approximation and Projection (UMAP) to create a reference landscape of ~1300 meningioma tumors. Our analyses revealed multiple distinct meningioma subtypes with specific biological signatures. Clinical metadata, mutations, copy number alterations, and gene-fusion data effectively correlated with regions of the UMAP. Notably, regional distribution of time to recurrence identified major clusters as well as intra-cluster differences of meningiomas with varying patient outcomes. The most aggressive subtype, characterized by an enrichment of higher WHO grades, frequent tumor recurrences, and shorter time to recurrence, exhibited elevated proliferation rates and RNA expression resembling muscle development. To facilitate clinical applications, we developed a cross-validated nearest-neighbors-based algorithm that accurately maps new patients onto this UMAP landscape. Our study highlights the utility of transcriptomic analysis in discerning meningioma heterogeneity as well as successful combination of multiple datasets from various sources. We provide a valuable tool for understanding the disease, predicting tumor biology and patient prognosis. This resource is accessible via the open source, interactive online tool Oncoscape, where the scientific community can explore the landscape and mine clinical and genomic metadata.

overall_design: We collected meningioma tumor samples, extracted total RNA and sequenced. Then we combined the in-house sequenced dataset with other publicly available meningioma RNA-Seq datasets that we collected to generate a UMAP. Clinical and genomic metadata was overlaid on to the UMAP and meningioma subtypes were analyzed.

first: H. Nayanga

last: Thirimanne

first: Sonali

last: Arora

first: Damian

last: Almiron Bonnin

first: Carolina

last: Parada

first: Manuel

last: Ferreira


title: CDC7 inhibition impairs neuroendocrine transformation in lung and prostate tumors through MYC degradation

status: Public on May 01 2024

city: New York

first: Yingqian

middle: Ada

last: Zhan

state: New York

address: 430 East 67th Street

department: EPIGENETICS RESEARCH CENTER

institute: MSKCC


title: Grainyhead-like-2, an epithelial master programmer, promotes interferon induction and suppresses breast cancer recurrence [RNA-Seq]

city: Morgantown

first: Gangqing

last: Hu

state: West Virginia

address: 64 Medical Center Drive

department: MicroBiology, Immunology, and Cell Biology

institute: West Virginia University

summary: Type-I and -III interferons play a central role in immune rejection of pathogens and tumors, thus promoting immunogenicity and suppressing tumor recurrence.  Differentiation of embryonic stem cells to pluripotent epithelial cells activates the interferon response during development, raising the question of whether epithelial vs. mesenchymal gene signatures in cancer potentially regulate the interferon pathway as well.  Here we show that Grainyhead-like-2 (GRHL2), a master programmer of epithelial cell identity, promotes the type-I and -III interferon responses to double-strand RNA, an important ligand for immune rejection of tumors via interferons. The positive effects of GRHL2 were mediated by enhanced IRF3 and relA/NF-kB activation, upregulation of IRF1, and a functional GRHL2 binding site identified in the IFNL1 promoter. In addition, time to recurrence in breast cancer correlated positively with GRHL2 protein expression, indicating that GRHL2 is a tumor recurrence suppressor, consistent with its enhancement of interferon responses.  These observations demonstrate that epithelial cell identity supports interferon responses in the context of cancer.

overall_design: To investigate the transcriptome change affected by GRHL2 in the presence or absence of polyIC induction, we established GRHL2 knockdown cells derived from MCF10aneoT. We then perfomed gene expression profiling analysis using data obtained from RNA-seq 9 different cells in  the presence or absence of polyIC induction.Comparative gene expression profilling analysis of RNA-seq data for MCF10A cells and its KO detrivatives.

first: Ian

last: MacFawn

first: Joshua

last: Farris

first: Phillip

last: Pifer

first: Naira

last: Margaryan

first: Halima

last: Akhter

first: Sebastian

last: Dziadowicz

first: Lei

last: Wang

first: James

last: Denvir

first: Steven

last: Frisch


title: Expression data from leaves of tomato (Solanum lycopersicum L. cv. MicroTom) plants subjected to 1000 Hz sound vibration (at 90 dB for 2 h for 3 consecutive days) and/or inoculated with Pst DC300.

city: Cartagena

first: Antonio

last: Calderón

state: Outside North America

address: Paseo Alfonso XIII, 48

country: Spain

institute: Universidad Politécnica de Cartagena

summary:
As mechanical stimuli, sound vibrations are known to influence various molecular and physiological processes that can ultimately improve crop performance and yield.
Microarray analyses were carried out to investigate the global gene expression changes in MicroTom plants subjected to 1000 Hz sound vibration prior to infection with Pst DC300 to test the effectiveness of sound as a priming agent. Data revealed that 1000 Hz pretreatment is effective in eliciting a transcriptional reprogramming in tomato plants grown under normal conditions, but particularly after Pst DC3000 infection. The protective effect of 1000 Hz pretreatment against Pst DC3000 appeared to be mediated by the upregulation of both unique differentially expressed genes (DEGs) involved in cell wall reinforcement, phenylpropanoid pathway and defensive proteins as well as common DEGs associated with boosting plant basal immunity.

overall_design: Gene expression was analyzed in leaves of Micro-Tom plants subjected to 1000 Hz sound vibration and/or inoculated with Pst DC300 in comparison to untreated controls. Leaves were harvested after 1 day and 3 days of sound treatment and immediately frozen in liquid N2 for subsequent RNA extraction. Three biological replicates (each one including four plants) were considered for each treatment, resulting in a total of 24 samples. Microarrays analysis was performed using the GeneChip® Tomato Gene 1.1 ST Array Strip (Affymetrix).

last: Calderon

first: Maria

last: Ferrer

first: Lorena

last: Almagro

first: Andres

last: Martinez-Calderon


title: Copanlisib Microarray Data

city: st louis

first: Cynthia

last: Ma

state: Missouri

address: 4515 Mckinley, 4515 Mckinley

department: Medical Oncology

institute: Washington University

summary: Chemotherapy is the mainstay treatment stragety for triple negative breast cancer (TNBC). However resistance to chemotherapy is common, leading to disease progression and death. Strategies that improve chemotherapy efficacy has the potential to reduce TNBC mortality. In this research, we demonstrated that the pan-PI3K inhibitor copanlisib, which is already in clinic to treat hematologic malignancies, enhanced the cytotoxicity of eribulin, a common chemotherapy used to treat taxane-resistant TNBC, in a panel of TNBC patient-derived xenograft (PDX) models. The improved tumor growth inhibition was irrespective of PI3K pathway alteration and was corroborated by the enhanced apoptotic induction observed in PDX tumors post combination therapy compared to each drug alone. The combination therapy inhibited eribulin-induced PI3K pathway activation, providing an underlying mechanism of action for its enhanced anti-tumor effect. Based on these results, a Phase I/II trial of this combination in patients with metastatic TNBC was initiated and is ongoing.

overall_design: 27 mRNA microarray experiments were analyzed for 8 different HIM lines.  5 of these lines had data from a patient biospy as well as multiple passages from a mouse xenograft.  3 tumors had data from mouse xenograft passages but no data from the patient biopsy.  Each representative patient tumor sample and mouse xenograft passage was amplified, labeled, and co-hybridized with a reference sample.

first: Jeremy

middle: W

last: Hoog


title: TNF-NFkB-p53 axis restricts in vivo survival of hPSC-derived dopamine neuron (RNA-Seq)

first: Hyein

middle: Sophia

last: Cho

state: NY

address: 430 E 67th St

department: Developmental Biology

institute: Memorial Sloan Kettering Cancer Center

summary: Cas9 screen to enhance survival of postmitotic dopamine neurons in vivo. We identified TP53-mediated apoptotic cell death as major contributor to dopamine neuron loss and uncovered a causal link of TNFa-NFκB signaling in limiting cell survival. A surface marker screen enabled the purification of midbrain dopamine neurons obviating the need for genetic reporters. Combining cell sorting with adalimumab pretreatment, a clinically approved TNFa inhibitor, enabled efficient engraftment of postmitotic dopamine neurons leading to extensive re-innervation and functional recovery in a preclinical PD mouse model. Thus, transient TNFa inhibition may present a clinically relevant strategy to enhance survival of human PSC-derived lineages in PD and beyond.

overall_design: Bulk RNA-seq study of TP53 WT dopamine neurons, in vitro and in vivo

first: Fayzan

last: Chaudhry

first: Doron

last: Betel

first: Lorenz

last: Studer


title: Grainyhead-like-2, an epithelial master programmer, promotes interferon induction and suppresses breast cancer recurrence

first: Gangqing

last: Hu


title: Grainyhead-like-2, an epithelial master programmer, promotes interferon induction and suppresses breast cancer recurrence [ATAC-seq]

overall_design: Assays for chromatin accessibility (ATAC-seq) for GRHL2 KO and control cells with and without PolyIC treatment

first: Ian

last: MacFawn

first: Joshua

last: Farris

first: Phillip

last: Pifer

first: Naira

last: Margaryan

last: Akhter


title: Bradykinin promotes immune responses in differentiated embryonic neurospheres carrying APP swe and PS1 dE9 mutations

status: Public on Apr 30 2024

city: São Paulo

first: Eduardo

middle: Moraes

last: Reis

state: SP

address: Av. Prof. Lineu Prestes, 748

country: Brazil

institute: University of São Paulo

summary: Neural stem cells (NSCs) can be cultivated from developing brains, reproducing many of the processes that occur during neural development. They can be isolated from a variety of animal models, such as transgenic mice carrying mutations in amyloid precursor protein (APP) and presenilin 1 and 2 (PSEN 1 and 2), characteristic of familial Alzheimer’s Disease (AD). Modulating the development of these cells with inflammation-related peptides, like bradykinin (BK) and its antagonist HOE-140, enables the understanding of the impact of such molecules on the genetic load of treated neurospheres. To facilitate an understanding of the wider biological processes in the context of neuroinflammation, we performed a global gene expression analysis on the transgenic neurospheres treated with BK and HOE-140. To validate the microarray data, quantitative real-time reverse-transcription polymerase chain reaction (RT-PCR) was performed on 8 important genes related to the immune response in AD. We then performed a comparative analysis of the transcriptional profiles between treatments, including gene ontology and reactome enrichment, construction and analysis of protein-protein interaction networks and, finally, comparing our data with human datasetd from AD patients. We observed that the treatments modulated the expression of genes mainly related to neuroinflammation mediated by microglia, with BK promoting an increase in the expression of genes that enrich processes, pathways, and cellular components related to immune impairment, neurodegeneration and cell cycle. B2 receptor inhibition by HOE-140 acting on reduction of AD-related anomalies caused in this system. Our results reinforce that BK is an important modulating agent and enhances the immunological changes identified in transgenic neurospheres that carry the genetic load of AD.

overall_design: Four condition experiment, APPswe/PS1dE9 (APP_WT) vs. WT cells, APPswe/PS1dE9 vs. APPswe/PS1dE9 treated with BK (BK_APP) and  APPswe/PS1dE9 vs. APPswe/PS1dE9 treated with HOE-140 (HOE_APP). Biological replicates: 4 APP, 4 WT, 4 BK replicates, 4 HOE-140.

first: Guilherme

last: Juvenal

first: Carine

last: Meinerz

first: Ana

last: Ayupe

first: Henrique

last: Campos

first: Beatriz

last: Longo

first: Micheli

last: Pillat

first: Henning

last: Ulrich


title: TNF-NFkB-p53 axis restricts in vivo survival of hPSC-derived dopamine neuron (CRISPR screen)

first: Hyein

last: Cho

summary: First-in-human clinical trials illustrate the feasibility and translational potential of human pluripotent stem cell (hPSC)-based cell therapy in Parkinson’s disease (PD). However, a major unresolved challenge is the extensive cell death following transplantation with <10% of grafted dopamine neurons surviving. Here, we performed a pooled CRISPR/Cas9 screen to enhance survival of postmitotic dopamine neurons in vivo. We identified TP53-mediated apoptotic cell death as major contributor to dopamine neuron loss and uncovered a causal link of TNFa-NFκB signaling in limiting cell survival. A surface marker screen enabled the purification of midbrain dopamine neurons obviating the need for genetic reporters. Combining cell sorting with adalimumab pretreatment, a clinically approved TNFa inhibitor, enabled efficient engraftment of postmitotic dopamine neurons leading to extensive re-innervation and functional recovery in a preclinical PD mouse model. Thus, transient TNFa inhibition may present a clinically relevant strategy to enhance survival of human PSC-derived lineages in PD and beyond.

overall_design: CRISPR screen study of TP53 WT dopamine neurons, in vitro and in vivo

middle: S

last: Chaudhry


title: Novel spirocyclic dimer, SpiD3, targets critical tumor survival pathways and displays potent preclinical activity in B-cell chronic lymphocytic leukemia

city: Omaha

first: Jordan

last: Rowley

state: NE

address: 3828 Jones St, Apt 202

institute: University of Nebraska Medical Center

summary: Chronic lymphocytic leukemia (CLL) cell survival and growth is fueled by aberrant activation of various pro-survival signaling pathways within tumor niches. Specifically, B-cell receptor (BCR) signaling, toll-like receptor signaling, and supportive cellular interactions drive constitutive activation of NF-κB signaling and transcription of proliferative/pro-survival genes. Directly targeting the NF-κB pathway has been a challenge, however, herein, we investigated SpiD3, a spirocyclic dimer and novel NF-κB pathway inhibitor in preclinical models of CLL. Through cross-linking NF-κB proteins, SpiD3 attenuated NF-κB signaling in CLL cells independent of microenvironmental signals. Our integrated multi-omics and functional analyses revealed BCRNF-κB signaling, endoplasmic reticulum stress, oxidative stress, and activation of the unfolded protein response among the top pathways modulated by SpiD3 treatment. This was accompanied by marked inhibition of global protein synthesis, cumulating in profound anti-tumor properties in CLL cells. SpiD3 also modulated tumor microenvironment interactions shown by decreased chemokine and cytokine gene expression as well as decreased CLL chemotaxis towards CXCL-12 and CXCL-13. Moreover, SpiD3 induced apoptosis of stroma-protected primary CLL cells comparable to the BCR-targeting agent, ibrutinib. SpiD3 strikingly demonstrated selective cytotoxicity towards CLL cells compared to healthy lymphocytes, synergized with ibrutinib, and retained its anti-tumor effects in ibrutinib-resistant CLL cells. Altogether, our findings provide preclinical evidence for SpiD3 as an attractive therapeutic agent for CLL, especially in the context of relapsed/refractory disease.

overall_design: mRNA profiles of OSU-CLL cell line with SpiD3 treatment (1 uM, 2 uM) and vehicle (DMSO) control.

first: Alexandria

middle: P

last: Eiken

first: Achyuth

last: Kalluchi

first: Dalia

last: El-Gamal


title: TNF-NFkB-p53 axis restricts in vivo survival of hPSC-derived dopamine neuron (scRNA-Seq)

overall_design: Single cell RNA-seq study of TP53 WT and KO dopamine neurons, in vitro and in vivo

first: Fayzan

first: Doron

last: Betel

first: Lorenz

last: Studer


title: Position-dependent function of human sequence-specific transcription factors

city: La Jolla

first: Christopher

last: Benner

state: California

address: 9500 Gilman Dr. MC 0640

department: Medicine

institute: University of California, San Diego (UCSD)

summary: Patterns of transcriptional activity are encoded in our genome through regulatory elements such as promoters or enhancers that, paradoxically, often contain similar assortments of sequence-specific transcription factor (TF) binding sites. Knowledge of how these sequence motifs encode multiple, often overlapping gene expression programs is central to understanding gene regulation and how mutations in non-coding DNA manifest in disease. Exploiting natural genetic variation, perturbation of endogenous TF protein levels, and analysis of synthetic regulatory elements using a novel transcription start site (TSS) capturing massively parallel reporter assay approach, here we show that the outcome of TF binding on transcription initiation is position dependent. Analyzing TF motif occurrences relative to the TSS, we identified several motifs with highly preferential and superhelical positioning. We show that these patterns are a combination of a TF's distinct functional profiles: many TFs, including canonical activators like NRF1, NFY, Sp1 or YY1, activate or repress transcription initiation depending on their precise position relative to the TSS. As such, TFs can collectively guide the site and frequency of transcription initiation. More broadly, these findings reveal how similar assortments of TFs, but with different spatial relationships, can result in distinct gene regulatory outcomes and underscore a critical role for TSS data in decoding the regulatory information of our genome.

sample_organism:
Homo sapiens
Mus musculus
Chlorocebus sabaeus

overall_design: Profiling transcription initiation in the genome using csRNA-seq or from massively parallel reporter assays using TSS-MPRA, stable RNA levels by RNA-seq, TF occupany by ChIP-seq.

first: Sascha

middle: H

last: Duttke

first: Carlos

last: Guzman

first: Max

last: Chang

first: Jialei

last: Xie

first: Nathaniel

last: Delos Santos

first: Aaron

last: Carlin

first: Sven

last: Heinz


title: miR-7 controls glutamatergic transmission and neuronal connectivity in a Cdr1as-dependent manner

city: Berlin

first: Nikolaus

last: Rajewsky

address: Hannoversche Str. 28

department: BIMSB

institute: Max Delbrück Center for Molecular Medicine

summary: To investigate interactions of Cdr1as and miR-7 in mouse neuron, we cultured primary mouse cell in which each target gene has been knocked out from C57BL/6N mouse and overexpression of pri-miR-7a

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of primary mouse cortical neurons from 4 different conditions

first: Seungjoon

last: Kim

first: Cledi

last: Cerda Jara

first: Gwendolin

last: Thomas


title: Clostridioides difficile Toxin B subverts germinal center formation and antibody recall responses by stimulating a drug-treatable CXCR4-dependent mechanism

status: Public on Apr 25 2024

city: Oklahoma City

first: Kaylee

last: Norman

state: OK

address: 940 Statond L Young Blvd

department: Microbiology and Immunology

institute: University of Oklahoma Health Sciences Center

summary: Recurrent Clostridioides difficile infection (CDI) results in significant morbidity and mortality. We previously established that CDI in mice did not protect against reinfection and was associated with poor pathogen-specific B cell memory (Bmem), recapitulating our observations with human Bmem. Herein, we demonstrate that the secreted toxin TcdB2 is responsible for subversion of Bmem responses. TcdB2 from an endemic C. difficile strain delayed IgG class switch following vaccination, attenuated IgG recall to a vaccine booster, and prevented germinal center formation. The mechanism of TcdB2 action included increased B cell CXCR4 expression and responsiveness to its ligand CXCL12, accounting for altered cell migration and a failure of germinal center-dependent Bmem. These results were reproduced in a C. difficile infection model and an FDA-approved CXCR4-blocking drug rescued germinal center formation. We therefore provide mechanistic insights into C. difficile-associated pathogenesis and illuminate a target for clinical intervention to limit recurrent disease.

overall_design: Female mice (n=4 per group) were given 200 µl PBS vehicle control, 10 ng D270N, or 10 ng TcdB2 in PBS by the s.c. route. Seven days post treatment, RNA was purified from aLNs and iLNs. Gene expression was quantified using the Nanostring™ nCounter SPRINT profiler platform.

first: Mark

last: Lang


title: TNF-NFkB-p53 axis restricts in vivo survival of hPSC-derived dopamine neuron

first: Hyein

last: Cho


title: Plasmacytoid dendritic cells regulate megakaryocyte and platelet homeostasis in steady state and disease

city: Munich

first: Anne

last: Dueck

state: Bavaria

address: Biedersteiner Str.29

department: Institute of Pharmacology and Toxicology

institute: TUM

summary: The hematopoietic system gives rise to a heterogeneous population of terminally differentiated cells that reside in the bone marrow (BM) to fulfill their roles in immunity, blood clotting and tissue oxygenation. Hematopoietic stem and progenitor cells are at the apex of a hierarchically organized maturation cascade constantly replenishing the pool of differentiated cells to maintain blood cell homeostasis. The bone marrow microenvironment is functionally compartmentalized by heterogeneous niche cells that provide physical and soluble signals to spatio-temporally organize hematopoiesis. Megakaryocytes (MKs) are niche cells of hematopoietic origin that support hematopoietic stem cell (HSCs) homeostasis and generate circulating platelets. Platelet production involves the release of MK fragments while their cell body is entirely consumed in a process termed thrombopoiesis. Consequently, replenishment of fragmented MKs from MK progenitors (termed megakaryopoiesis) is required to ensure sufficient platelet production, but also to maintain MK homeostasis within the HSC niche. Here, we used intravital imaging of the megakaryocytic lineage to identify the spatio-temporal patterns of megakaryopoiesis during steady state and thrombocytopenia. We show that MK consumption during thrombopoiesis is compensated by immediate and local proliferation of MK progenitors. MK homeostasis is controlled by plasmacytoid dendritic cells (pDCs) that scan the BM and secrete Interferon alpha (INFa) upon detection of exhausted megakaryocytes to trigger megakaryopoiesis. We identified local pDC-derived INFa release as a physiological inflammatory stimulus of the bone marrow niche that synchronizes megakaryopoiesis and thrombopoiesis to maintain homeostasis of MKs and platelets in steady state and under stress. Viral infection with SARS-CoV-2 can manipulate pDC-driven MK proliferation leading to inappropriate megakaryopoiesis, which has been associated with thrombotic complications during COVID-19.

overall_design: RNA-Sequencing of murine megakaryocyte progenitors after depletion of platelets and plasmacytoid dendritic cells.

first: Florian

last: Gaertner

first: Hellen

last: Ishikawa-Ankerhold

first: Susanne

last: Stutte

first: Michael

last: Lorenz

first: Steffen

last: Massberg


title: DOT1L controls NK cell activation and lineage integrity [ChIP-seq]

city: Esch-sur-Alzette

first: Sebastian

last: Scheer

address: 29, rue Henri Koch

department: Infection and Immunity

country: Luxembourg

institute: Luxembourg Institute of Health

summary: Epigenetic modifiers are promising targets to improve therapies in patients with cancer. Targeting the methyltransferase DOT1L with small molecule inhibitors has shown promising effects on the control of cancerous cells. However, these small molecules are given systemically and may have a profound impact on non-cancerous cells, such as the cells of the immune system. In the innate immune system, natural killer (NK) cells are a critical subset of cells with important roles in controlling transformed cells and tumour inflammation. Previous studies have shown that NK cells can convert into ILC1-like cells in a TGFβ-rich tumour microenvironment (TME). Additionally, cancer patients with acute myeloid leukemia (AML) or chronic lymphocytic leukemia (CLL) have increased frequencies of ILC1 cells in peripheral blood mononuclear cells (PBMCs), which show reduced production of proinflammatory cytokines and decreased granzyme B production. In this study, we identify DOT1L as a critical regulator of NK cell activation and lineage integrity. We generated NKp46-conditional DOT1L knockout mice (DOT1L.Ncr1) and observed increased frequencies of ILC1-like cells (CD49b+ CD49a+, CD62L-) and reduced frequencies of NK cells (CD49b+ CD49a-, CD62L+) in these mice. While the absence of DOT1L increases the sensitivity to TGFβ, the increased expression of CD49a is highly intrinsic and only partially dependent on TGFβ signalling. Functionally, the increased presence of ILC1-like cells in the tumour microenvironment of DOT1L.Ncr1 mice leads to decreased tumour control. Our assessment of the transcriptional program reveals alternative uses of transcription factors, such as the AP-1 family or SMAD2/3, to maintain NK cell activation and lineage integrity. Our findings provide evidence for a previously unknown role of DOT1L in NK cell biology, and demonstrate the importance of maintaining NK cell lineage integrity for effective tumour control. These findings have significant implications for the development of improved therapies for cancer or other NK cell-lineage dependent malignancies.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for histone variants H3K79me2 in NK cells.


title: single-cell RNA-seq of cardiac tissue from offsprings of dams with different fibre intake levels

status: Public on Apr 24 2024

first: Francine

middle: Coelho

last: Marques

address: 25 Rainforest Walk

department: School of Biological Sciences

summary: We proposed that the maternal intake of fibre could influence the epigenetic conditions in the womb, consequently altering the cardiac characteristics of the offspring. Additionally, we speculated that maternal fibre intake might lead to significant changes in cardiac gene expression in the offspring by promoting the production of short-chain fatty acids (SCFAs). To examine the impact of maternal high fibre intake on the cellular composition of the heart, we conducted single-cell RNA sequencing (scRNA-seq) analysis on cardiac tissue from 6-week-old offspring who had not been subjected to any external challenges.

overall_design: Female mice were allowed to feed ad libitum for the duration of pregnancy and lactation. We used diets high in resistant starches, a prebiotic type of fibre (referred to as "high-fibre", SF11-025) or low in resistant starches ("low-fibre", SF09-028) both obtained from Specialty Feeds. Once offspring reached 3-weeks of age (weaning age), all animals were placed on a standard chow from Specialty Feeds. Food was replenished twice a week for the duration of the intervention. Following euthanasia of offspring mice at 6 week, cardiac puncture was performed to remove blood.

first: Malathi

middle: I

last: Dona

first: Hamdi

last: Jama


title: Perinatal opioid exposure and outcomes of exposed offspring in early adolescence

first: Adrian

last: Flores

address: 4355 Davenport Street, 14

institute: UNMC

summary: The opioid epidemic has received considerable attention, but the impact on perinatal opioid-exposed (POE) offspring remains underexplored. This study addresses the emerging public health challenge of understanding and treating POE children. We examine two scenarios using preclinical models: offspring exposed to oxycodone (OXY) in utero (IUO) and postnatally (PNO). We hypothesized exposure to OXY during pregnancy primes offspring for neurodevelopmental deficits and severity of deficits is dependent on timing of exposure. Notable findings include reduced head size and brain weight in offspring. Molecular analyses revealed significantly lower levels of inflammasome-specific genes in the prefrontal cortex (PFC). Gene Set Enrichment Analysis (GSEA) and Ingenuity Pathway Analysis (IPA) highlighted the enrichment of genes associated with mitochondrial and synapse dysfunction in POE offspring. Western blot analysis validated IPA predictions of mitochondrial dysfunction in PFC-derived synaptosomes. Behavioral studies identified significant social deficits in POE offspring. This study presents the first comparative analysis of PNO- and IUO-offspring during early adolescence finding PNO-offspring have considerably greater deficits. The striking difference in deficit severity in PNO-offspring suggests that exposure to opioids in late pregnancy pose the greatest risk for offspring well-being.

overall_design: To investigate the impacts of pre-natal versus post-natal oxycodone exposure on offspring wellbeing in early adolescence. Two dams were used per treatment condition (2 animals were used per dam): 4 control , 4 PNO, 4 IUO. RNA was isolated from the prefrontal cortex and these samples were sequenced.

first: Nghi

last: Nguyen

first: Samarth

last: Sanketh

first: Murali

last: Devanaboyina

first: Pranavi

last: Athota

first: Sankarasubramanian

last: Jagadesan

first: Chittibabu

middle: B

last: Guda

first: Sowmya

last: Yelamanchili

first: Gurudutt

last: Pendyala


title: Mutant IDH1 inhibition activates tumor immunity via endogenous reverse transcriptase and dsDNA sensing

city: Dallas

first: Samuel

last: McBrayer

state: Texas

address: 6000 Harry Hines Blvd

department: Children's Research Institute

institute: UT Southwestern Medical Center

summary: Isocitrate Dehydrogenase 1 (IDH1) is the most commonly mutated metabolic gene across human cancers. Mutant IDH1 (mIDH1) generates the oncometabolite (R)-2-hydroxyglutarate, disrupting enzymes involved in epigenetics and other processes. A hallmark of IDH1-mutant solid tumors is T cell exclusion, whereas mIDH1 inhibition in preclinical models restores anti-tumor immunity. Here, we define a cell-autonomous mechanism of mIDH1-driven immune evasion. IDH1-mutant solid tumors show striking, selective hypermethylation and silencing of the cytoplasmic dsDNA sensor, CGAS, compromising innate immune signaling. mIDH1 inhibition restores DNA demethylation, derepressing CGAS and transposable element (TE) subclasses. dsDNA produced by TE-reverse transcriptase activates cGAS, triggering viral mimicry and stimulating anti-tumor immunity. Thus, we demonstrate that mIDH1 epigenetically suppresses innate immunity and link endogenous reverse transcriptase activity to the mechanism of action of an FDA-approved oncology drug.

overall_design: To investigate Cgas expression in IDH1 WT and IDH1 mutant gliomas, we established glioma stem-like cell lines from our genetically engineered mouse models, and performed mRNA-seq

first: Yi

last: Xiao

first: Diana

last: Shi


title: Expression profile analysis of long non-coding RNAs in condyloma acuminatum in a Chinese female population by RNA-sequencing and bioinformatics [clip-seq]

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

country: China

institute: ABLife, Inc.

summary: This study aimed to explore the differential lncRNAs in CA and their probable function on CA development.We used RNA-sequencing to assess the genome-wide expression levels of lncRNAs in CA and paired adjacent normal tissues. We further validated the candidate lncRNAs in larger-size of CA specimen using RT-qPCR. Furthermore, the functional enrichment analysis for these candidate lncRNAs and differential mRNAs were analyzed using GO terms, KEGG and STRING database. The coexpressed mRNAs for the candidate lncRNAs, calculated by Pearson?s correlation coefficient, were also analyzed using GO analysis.A total of 657 lncRNAs and 1486 mRNAs were found to dysregulated in CA compared to adjacent mucosal tissues. The microarray data of candidate lncRNAs, including HOXC13-AS, HOTAIR, PICSAR, FGF14-AS1, ADGRD1-AS1, TMEM108-AS1, TUSC7 and FGF10-AS1, were validated with a larger-size of specimen using RT-qPCR. The functional GO term and pathways analysis of DEGs are associated with the pathogenesis and development of CA, including cell proliferation and development, cellular adhesion, immune defense, cell migration and chemotaxis, angiogenesis, and maintaining skin hemostasis.LncRNAs that were differentially expressed between CA and normal tissues may be helpful to explore effective recurrence risk markers and potential intervention targets for CA.

overall_design: MeRIP-sequencing analysis of m6A modification versus input in condyloma acuminatum

first: Xiaoyan

last: Liu


title: Comparison of Tape-Stripping Platforms as Non-Invasive Solutions for Skin Biomarker Discovery

city: San Diego

first: Erica

last: Montano

state: CA

address: 12340 El Camino Real

institute: DermTech

summary: Use of tape stripping for the collection of stratum corneum is a versatile and reliable procedure for the evaluation of the human skin health, including assessments of the skin barrier function, microbial content, and disease biomarkers. The tape stripping procedure is widely referenced; however, the number and type of tapes required for sample collection vary considerably, and the lack of standardized sampling, processing and normalization protocols complicate data comparison and interpretation. We have compared the performances of two commonly used non-invasive skin sampling platforms by collecting skin tissue from 34 healthy volunteers and applying standardization throughout the workflow, from sampling to data analysis. Our results showed significant differences in the amounts of tissue collected per tape, erythema levels, RNA and protein yields. RNA extracts from both platforms were suitable for sequencing; comparable input and quality of reads were produced for both test groups, however significant differences were found in the percentage of uniquely mapped reads and detected genes. This data highlights processing optimization as an important step in maximizing the efficiency of biomolecule extraction from tape strips and further presents a tape stripping method suitable for fast, efficient, and non-invasive epidermal tissue collection applicable to skin biomarker discovery.

overall_design: To compare two non-invasive skin sampling platforms for collecting stratum corneum  and assessing peformance of each platform we sampled the foreheads of healthy volunteers via tape stripping. Samples underwent extraction and RNA extracts were used for sequencing.  Variables evaluated include the quality and mapping efficiency of reads and the number of detected genes.

middle: N

first: Ailyn

last: Tapia

first: Michael

last: Howell

first: Jelena

last: Ostojić


title: ER-associated degradation adapter Sel1L is required for CD8+ T cell function and memory formation following acute viral infection

city: Ann Arbor

first: Luis

middle: O

last: Correa-Medero

state: MI

address: 109 Zina Pitcher Place

institute: University of Michigan

summary: The maintenance and persistence of antigen-specific CD8+ T cells underlies the efficacy of vaccines and immunotherapies. Pathways that contribute to the loss of CD8+ T cells are not completely understood. Uncovering the pathways underlying the limited persistence of CD8+ T cells would be of significant benefit for developing novel strategies of promoting T cell persistence and identifying patients whose T cells could function best for treatment. Here, we demonstrate the experience of endoplasmic reticulum (ER) stress in differentiating murine CD8+ T cells in vitro and in vivo. ER-associated degradation (ERAD) adapter Sel1L was found to be selectively induced in activated CD8+ T cells. Loss of Sel1L limited CD8+ T cell function and memory formation following acute viral infection. Mechanistically, Sel1L is required for optimal T cell oxidative metabolism and mitochondrial fusion. Finally, we demonstrate that human CD8+ T cells experience ER stress after activation and that ER stress is negatively associated with improved T cell functionality in bispecific antibody therapy and chimeric antigen receptor T cell therapy. Together these results demonstrated that ER stress and ERAD are important and novel regulators of T cell function and persistence.

overall_design: WT and Sel1LcKO P14 were sorted from LCMV-Armstrong infected host at D8 post infection and RNA-seq was conducted

first: Shannon

middle: A

last: Carty


title: Expression profile analysis of long non-coding RNAs in condyloma acuminatum in a Chinese female population by RNA-sequencing and bioinformatics

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

overall_design: Refer to individual Series


title: Expression profile analysis of long non-coding RNAs in condyloma acuminatum in a Chinese female population by RNA-sequencing and bioinformatics [RNA-seq]

overall_design: RNA-seq of condyloma acuminatum or adjcent mucocal tissues


title: Targeting CEBPA to restore cellular identity and tissue homeostasis in pulmonary fibrosis.

city: Austin

first: Qi

last: Tan

state: MN

address: 801 16th Ave NE

department: The Hormel Institute

institute: Univesity of Minnesota

summary: scRNA-seq of lung cells from Cebpa floxed control mice and Cebpa SftpcCre KO mice

overall_design: These cells were isolated from the lung of Cebpa floxed control mice and Cebpa SftpcCre KO mice  using liberase-DNase I Solution treatment and FACS sorting for live cells

first: Jack

last: Wellmerling

first: Daniel

middle: J

last: Tschumperlin


title: DrugMap: A quantitative pan-cancer analysis of cysteine ligandability

city: Charlestown

first: Mariko

middle: Sidi

last: Takahashi

state: Massachusetts

address: 149 13th Street, Charlestown Navy Yard

department: Cancer Center

institute: MGH


title: DrugMap: A quantitative pan-cancer analysis of cysteine ligandability (RNA-Seq)

summary: SOX10 is a lineage-restricted transcription factor important for melanoma proliferation and survival. Our data demonstrate that SOX10 genetic depletion by CRISPR/Cas9 significantly impaired melanoma proliferation. We chose 7 different melanoma, all of which exhibited growth dependency on SOX10 with different levels. To define the SOX10 transcriptional signature shared with different SOX10-dependent melanoma, we performed bulk RNA-seq on 7 melanoma transfected with siSOX10 or siControl. Each melanoma cell line was plated and transfected with each siRNA to deplete SOX10 protein expression. After 72 hrs, cells were lysed with Buffer TCL(QIAGEN) supplemented with 2-ME and stored at -80C until use. Libraries from each cell line were made with the modified Smart-seq2 protocol. Each replicate was uniquely barcoded and all the samples were pooled for sequencing. (2) We developed a chemical probe (SH-0029) that covalently engages SOX10. To examine the effect of SH-0029 on SOX10 target genes, SOX10-dependent SKMEL5 melanoma were plated and treated with SH-0029, SH-0105 (a control probe), or DMSO(vehicle) for 48h. Total RNA was extracted with NucleoSpin RNA extraction kit (MACHEREY-NAGEL) and mRNA was subsequently purified with poly dT-attached magnetic beads. We found that downregulated genes induced by SH-0029 treatment strongly overlapped with those by SOX10 genetic depletion, suggesting that SOX10 covalent ligand controls SOX10 transcriptional network.

overall_design: Expression profiling by high throughput sequencing


title: Stem-like T cells are associated with the pathogenesis of ulcerative colitis in humans [bulkRNAseq_MouseLPL]

first: Pandurangan

last: Vijayanand

address: 9420 Athena Circle

department: Vaccine Discovery

institute: La Jolla Institute for Immunology

summary: To understand the role of T cells in the pathogenesis of ulcerative colitis (UC), we analyzed colonic T cells isolated from UC patients and controls.  We identified colonic CD4+ and CD8+ T lymphocyte subsets with gene expression profiles resembling stem-like progenitors, previously reported in animal models of diabetes and other contexts. Stem-like T cells were increased in inflamed areas compared to non-inflamed regions from the same patients.  Furthermore, TCR sequence analysis indicated stem-like T cells were clonally related to pro-inflammatory T cells, suggesting their involvement in sustaining effectors that drive inflammation. Using an adoptive transfer colitis model, we demonstrated that CD4+ T cells deficient in BCL-6, a transcription factor promoting T cell stemness, had decreased colon T cells, reduced TH17 cells, and diminished pathogenicity. Our results establish a strong association between stem-like T cell populations and UC pathogenesis, highlighting the potential of targeting this population to improve clinical outcomes.

overall_design: Splenic naïve CD4+ T cell from TcfGFP mice were isolated and transferred into Rag1 KO recipent mice to induce colitis. Then GFP+ and GFP- CD4+ T cells from the Rag1 KO mouse colon lamina propria were isolated for bulk RNA seq.

first: Yingcong

last: Li

first: Ciro

last: Ramírez-Suástegui

first: Richard

last: Harris

first: Francisco

middle: E

last: Castañeda-Castro

last: Giles

first: Jiani

last: Chai

first: Gregory

last: Seumois

first: Tilman

last: Sanchez-Elsner

first: Fraser

last: Cummings

first: Mitchell

last: Kronenberg


title: Stem-like T cells are associated with the pathogenesis of ulcerative colitis in humans. [scRNAseq_MouseLPL]

overall_design: In the adoptive T cell transfer model of colitis, 1 x 105 splenic wildtype naïve CD4+CD45RBhighCD25- T cells and 5 x 105 splenic TCRb+CD8b+CD4- T cells from Bcl6fl/flCd8aCre mice or Bcl6fl/fl mice were transferred into Rag1 KO mice. 6-10 weeks later, CD8+ T cells were isolated form mouse colon lamina propria for single cell RNA seq analysis.


title: DrugMap: A quantitative pan-cancer analysis of cysteine ligandability (ChIP-Seq)

summary: SOX10 plays important roles in development of neural crest lineages and melanocyte lineages. SOX10 binding sites on chromatin have been characterized in glial lineages, but fewer focused on melanoma. To examine chromatin occupancy of SOX10 and chromatin landscape in melanoma, we performed ChIP-seq analysis of SOX10 and H3K27ac in SOX10-dependent melanoma SKMEL5. We confirmed SOX10 binding in genes previously reported as direct targets of SOX10, including ERBB3 and IL16. Importantly, SOX10 chemical probe (SH-0029) treatment abrogated the expression of these genes, suggesting that pharmacological perturbation of SOX10 modifies SOX10 transcriptional network and downregulates SOX10 target genes.

overall_design: Genome binding/occupancy profiling by high throughput sequencing


title: Multiscale topology classifies and quantifies cell types in subcellular spatial transcriptomics

city: Oxford

first: Rui

last: Qi

state: Oxford

address: Old Road Campus

country: United Kingdom

institute: University of Oxford

summary: Spatial transcriptomics has the potential to transform our understanding of RNA expression in tissues. Classical array-based  technologies produce multiple-cell-scale measurements requiring deconvolution to recover single cell information. However, rapid advances in subcellular measurement of RNA expression at whole-transcriptome depth necessitate a fundamentally different approach. To integrate single-cell RNA-seq data with nanoscale spatial transcriptomics, we present a topological method for automatic cell type identification (TopACT). Unlike popular decomposition approaches to multicellular resolution data, TopACT is able to pinpoint the spatial locations of individual sparsely dispersed cells without prior knowledge of cell boundaries. In extant mouse brain data, TopACT locates previously undetectable macrophages. Pairing TopACT with multiparameter persistent homology landscapes predicts immune cells forming a peripheral ring structure within kidney glomeruli in a murine model of lupus nephritis, which we experimentally validate with multiplex imaging. The proposed topological data analysis unifies multiple biological scales, from subcellular gene expression to multicellular tissue organization.

overall_design: Topological data analysis of spatial transcriptomics datasets for cell type identification.

first: Katherine

last: Benjamin

first: Aneesha

last: Bhandari

first: Jessica

middle: D

last: Kepple

first: Zhouchun

last: Shang

first: Yanan

last: Xing

first: Yanru

last: An

first: Nannan

last: Zhang

first: Yong

last: Hou

first: Tanya

middle: L

last: Crockford

first: Oliver

last: MacCallion

first: Fadi

last: Issa

first: Joanna

last: Hester

first: Ulrike

last: Tillmann

first: Heather

last: Harrington

middle: R

last: Bull


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

city: Paris

first: Claire

last: Rougeulle

address: 35 rue Helene Brion

department: Epigenetics and Cell Fate

institute: Université Paris Cité, CNRS

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

overall_design: RNA-seq on 3 independent clones of XIST CRISPRi naïve hESCs treated with doxycyclin. Untreated clones were used as controls. Also RNA-seq on 3 replicates of 1 XIST KO clone and WT. RNA-seq on 3 independent clones of XACT KO (naïve) and WT (primed). RNA-seq after siRNA knockdown of SPEN protein using two different mixes of siRNAs.

first: Charbel

last: Alfeghaly


title: GABA does not regulate stomatal CO2 signalling in Arabidopsis

city: Glen Osmond

first: Bo

last: Xu

address: Plant Research Centre

institute: University of Adelaide

summary: The DEG indicated that the genomic deletion in gad2-1 led to significant down-regulation of MPK12 and BPS2

overall_design: To investigate the Differential Gene Expression (DEG) in the leaves of Arabidopsis wildtype Col-0, gad2 and gad1/2/4/5 mutants with or without ABA treatments.

first: Marcus

last: Dittrich

first: Tobias

last: Müller


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

overall_design: RAP-seq for XIST in naïve and primed hESCs. 2 independent replicates per condition were used.


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

overall_design: MeD-seq on 3 independent replicates of naïve hESCs


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


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

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


title: Conserved role of hnRNPL in alternative splicing of epigenetic modifiers enables B cell activation

city: Montréal

first: Javier

middle: M

last: Di Noia

state: QC

address: 110 Pine Avenue West

country: Canada

institute: Institut de recherches cliniques de Montréal (IRCM)

summary: The multifunctional RNA-binding protein hnRNPL has been implicated in antibody class switching but its broader function in B cells is unknown. Here, we show that hnRNPL is essential for B cell activation, and thereby germinal center and antibody responses. Upon activation, hnRNPL-deficient B cells show proliferation defects and increased apoptosis. The comparative analysis of RNA-seq data from B cells and another 8 hnRNPL-depleted cell types reveals a common function in the Myc and E2F transcriptional programs required for proliferation, likely borne out of a large alternative splicing change affecting multiple transcription regulators. Notably, while individual gene expression changes were cell type specific, several alternative splicing events affecting histone modifiers like SIRT1, KDM6A, and NSD2, were conserved across cell types, which could contribute to gene expression changes upon hnRNPL loss. SIRT1 reduction due to alternative splicing, and other transcriptional changes suggested mitochondrial defects in hnRNPL-deficient B cells. We confirmed dysfunctional mitochondria and ROS overproduction, which could explain the B cell activation defect. Thus, hnRNPL is essential for the resting to activated B cell transition by regulating transcriptional programs, most likely by splicing regulation affecting several histone modifiers.

overall_design:
To investigate gene expression and splicing changes upon hnRNPL depletion in activated B cells, CD21-cre mice were crossed with hnRNPL F/F mice.
We then perform paired-end RNA-seq of hnRNPL F/F CD21-cre and CD21-cre (control) splenic B cells, stimulated with LPS+IL4 for 24h.
Differential gene expression for WT vs hnRNPL-deficient activated B cells. Normalized counts, log2 fold changes and DESeq2 padj values are in the supplementary file "norm_counts.txt".

first: Poorani

last: Subramani

first: Jennifer

last: Fraszczak

first: Anne

last: Helness

last: Estall

first: Tarik

last: Möröy


title: Aberrant RNA polymerase Initiation and Processivity on the Genome of a Herpes Simplex Virus 1 Mutant Lacking ICP27

city: Ithaca

first: Joel

last: Baines

address: 235 Hungerfordhill Rd

institute: Cornell University

summary: Within the first 15 minutes of infection, herpes simplex virus 1 (HSV-1) immediate early proteins repurpose cellular RNA polymerase (Pol II) for viral transcription. An important role of the viral infected cell protein 27 (ICP27) is to facilitate viral pre-mRNA processing and export of viral mRNA to the cytoplasm. Here, we use precision nuclear run-on followed by deep sequencing (PRO-seq) to characterize transcription of a viral ICP27 null mutant. At 1.5 and 3 hours post infection (hpi) we observed Increased total levels of Pol II on the mutant viral genome and accumulation of Pol II downstream of poly A sites indicating increased levels of initiation and processivity.  By 6 hpi Pol II accumulation on specific mutant viral genes was higher than wt virus either at or upstream of poly A signals, depending on the gene. The PRO-seq profile of the ICP27 mutant on late genes at 6 hpi was similar but not identical to that caused by treatment with flavopiridol, a known inhibitor of RNA processivity. This pattern was different from PRO-seq profiles of other α gene mutants, and upon inhibition of viral DNA replication with PAA. Together, these results indicate that ICP27 contributes to the repression of aberrant viral transcription at 1.5 and 3 hpi by inhibiting initiation and decreasing RNA processivity.  However, ICP27 is needed to enhance processivity on most late genes by 6 hpi in a mechanism distinguishable from its role in viral DNA replication.

sample_organism:
Drosophila melanogaster
Homo sapiens
Human alphaherpesvirus 1

overall_design: To investigate how HSV-1 ICP27 cooperatively functions to alter RNA polymerase processivity during lytic infection before the onset of viral DNA replication

last: Birkenheuer


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

overall_design: To investigate the chromatin accessibility in naïve hESCs, we performed ATAC-seq on 3 independent naïve hESCs replicates.


title: Loss of Kmt2c or Kmt2d drives brain metastasis via KDM6A-dependent upregulation of MMP3

city: Boston

first: Kornelia

last: Polyak

state: MA

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute


title: Loss of Kmt2c or Kmt2d drives brain metastasis via KDM6A-dependent upregulation of MMP3 [RNA-seq]

summary: Histone lysine methyltransferases KMT2C and KMT2D are among the most commonly mutated genes in the highly metastatic TNBC subtype of breast cancer. However, it is not known if mutations of either of these genes similarly effect epigenomic and transcriptomic landscape or if a specific downstream target might influence metastases. Here, we generated heterogenous Kmt2c or Kmt2d KO murine TNBC cell lines side-by-side and performed in vivo metastases assay in syngeneic immunocompetent mice. Deficiency for either Kmt2c or Kmt2d, both, induced brain metastases from formerly non-metastatic cells. scRNAseq showed activation of pro-inflammatory pathways but conversely also increase of immune checkpoint blocking genes. Interestingly, histone mass spectrometry revealed changes of H3K27 but not the main substrate H3K4. However, ChIPseq for both, H3K4 and H3K27 modifications showed significant changes compared to wildtype cells. Strikingly, genome occupancy of H3K27me3 was reduced while H3K27 demethylase KDM6A was enriched on genomes of KO cells. Integration with gene expression data revealed significant correlations with histone and KDM6A ChIPseq, identifying them as a main driver of Kmt2c or Kmt2d KO-specific gene regulation. Although our datasets revealed more unique than shared signatures, we found Mmp3 being a common target upon Kmt2c or Kmt2d KO. Indeed, downregulation of Mmp3 reversed induction of Kmt2c and Kmt2d KO-dependent brain metastases. Finally, we found that Kdm6a knockdown reduces Mmp3 levels, again, leading to reduction of brain metastases of Kmt2c or Kmt2d KO cells.

overall_design: We generated either Kmt2c or Kmt2d KO derivatives of the 168FARN an 67NR cell line using CRISPR/Cas9

first: Marco

last: Seehawer

first: Li

last: Zheqi

first: Jun

last: Nishida

first: Pierre

last: Foidart

first: Andrew

last: Reiter

first: Ernesto

last: Rojas

first: Marie-Anne

last: Goyette

first: Paloma

last: Cejas

first: Seth

last: Goldman

first: Karen

last: Adelman

first: Henry

last: Long

first: Malvina

last: Papanastasiou


title: Stem-like T cells are associated with the pathogenesis of ulcerative colitis in humans [scRNAseq_Mouse]

first: Pandurangan

last: Vijayanand

summary: To understand the role of T cells in the pathogenesis of ulcerative colitis (UC), we analyzed colonic T cells isolated from UC patients and controls. We identified colonic CD4+ and CD8+ 32 T lymphocyte subsets with gene expression profiles resembling stem-like progenitors, previously reported in animal models of diabetes and other contexts. Stem-like T cells were increased in inflamed areas compared to non-inflamed regions from the same patients. Furthermore, TCR sequence analysis indicated stem-like T cells were clonally related to pro-inflammatory T cells, suggesting their involvement in sustaining effectors that drive inflammation. Using an adoptive transfer colitis model, we demonstrated that CD4+ 38 T cells deficient in BCL-6, a transcription factor promoting T cell stemness, had decreased colon T cells, reduced TH17 cells, and diminished pathogenicity. Our results establish a strong association between stem-like T cell populations and UC pathogenesis, highlighting the potential of targeting this population to improve clinical outcomes.

overall_design: Colonic CD4 T cells were isolated from adoptive T cell transfer model of colitis using mice. Rag-/- mice received naïve or CD4+, CD45RBhigh, CD25- T cells (WT) and BCL-6 deficient CD4+ T cells (KO).

first: Yingcong

last: Li

first: Ciro

last: Ramírez-Suástegui

first: Richard

last: Harris

first: Francisco

last: Castañeda-Castro

first: Daniel

last: Giles

first: Jiani

last: Chai

first: Gregory

last: Seumois

first: Tilman

last: Sanchez-Elsner

first: Fraser

last: Cummings

first: Mitchell

last: Kronenberg


title: Stem-like T cells are associated with the pathogenesis of ulcerative colitis in humans [scRNAseq_Human]

overall_design: Colonic T cells were isolated from healthy donors, inflamed and non-inflamed tissue from patientes with ulcerative colitis, and non-inflamed tissue from remission donors.


title: Stem-like T cells are associated with the pathogenesis of ulcerative colitis in humans

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: In vitro reconstitution of epigenetic reprogramming in the human germ line [10X]

city: Kyoto

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

country: Japan

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: Transcriptome 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: iPSC-derived healthy human astrocytes selectively load miRNAs   targeting neuronal genes into extracellular vesicles

city: Toronto

first: Lina

last: Antounians

state: Ontario

address: 686 Bay St

institute: The Hospital for Sick Children

type: Non-coding RNA profiling by high throughput sequencing

summary: We performed RNA-seq on human iPSC derived astrocytes and iPSC derived astrocyte derived extracellular vesicles.

overall_design: RNA-seq of PGPC14WT astrocyte differentiations, primary human commercial astrocytes, and astrocyte derived extracellular vesicles.

first: Sara

last: Gordillo-Sampedro


title: Loss of Kmt2c or Kmt2d drives brain metastasis via KDM6A-dependent upregulation of MMP3 [scRNA-seq]

first: Kornelia

last: Polyak

first: Marco

last: Seehawer

first: Li

last: Zheqi

first: Jun

last: Nishida

first: Pierre

last: Foidart

first: Andrew

last: Reiter

first: Ernesto

last: Rojas

first: Marie-Anne

last: Goyette

first: Paloma

last: Cejas

first: Seth

last: Goldman

first: Karen

last: Adelman

first: Henry

last: Long

first: Malvina

last: Papanastasiou


title: In vitro reconstitution of epigenetic reprogramming in the human germ line

first: Yukihiro

last: Yabuta


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

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: G6PD and ACSL3 are synthetic lethal partners of NF2 in Schwann cells

city: Heidelberg

first: Aurelio

last: Teleman

address: Im Neuenheimer Feld 580

institute: German Cancer Research Center (DKFZ)


title: Multiscale topology classifies and quantifies cell types in subcellular spatial transcriptomics [human snRNA-seq]

status: Public on Apr 23 2024

first: Rui

last: Qi

overall_design:
Topological data analysis of spatial transcriptomics datasets for cell type identification.
human snRNA-Seq

first: Katherine

last: Benjamin

first: Aneesha

last: Bhandari

first: Jessica

last: Kepple

first: Zhouchun

last: Shang

first: Yanan

last: Xing

first: Yanru

last: An

first: Nannan

last: Zhang

first: Yong

last: Hou

first: Tanya

last: Crockford

first: Oliver

last: MacCallion

first: Fadi

last: Issa

first: Joanna

last: Hester

first: Ulrike

last: Tillmann

first: Heather

last: Harrington

last: Bull


title: XIST dampens X chromosome activity in a SPEN-dependent manner during early human development [CUT&RUN]

first: Claire

last: Rougeulle

overall_design: CUT&RUN for active (H3K4me3, H3K27ac) and repressive (H3K27me3, H2AK119Ub, and H3K9me3) histone modifications in naïve and primed hESCs. For naïve hESCs, 3 independent clones of XIST CRISPRi doxycycline treated cells and 2 replicates of 1 XIST KO clone were used.

first: Charbel

last: Alfeghaly


first: Aurelio

last: Teleman

summary: Neurofibromatosis Type II is a genetic condition caused by loss of the NF2 gene, resulting in activation of the YAP/TAZ pathway and recurrent growth of benign tumors from Schwann cells, the glia of the peripheral nervous system. Unfortunately, no pharmacological therapy is currently available for NFII. Here, we undertake a genome-wide CRISPR/cas9 screen to search for synthetic-lethal genes that, when inhibited, cause death of NF2 mutant cells but not NF2 wildtype cells. We thereby identify ACSL3 and G6PD as two synthetic-lethal partners for NF2. We find that NF2 mutant Schwann cells are vulnerable to G6PD inhibition because they have low levels of ME1. G6PD and ME1 redundantly generate cytosolic NADPH needed by cells to fight oxidative stress. Lack of either one of the two is compatible with cell viability, but down-regulation of both leads to Schwann cell death. Since genetic deficiency for G6PD is tolerated in the human population, this raises the possibility that G6PD could be a pharmacological target for NFII.

overall_design: RNA-Seq Schwann Cells, NF2-WT, Schwann Cells, NF2-KO, Schwann Cells, NF2-WT + Cas9, Schwann Cells, NF2-KO + Cas9

first: Kyrkou

last: Athena

first: Teleman

last: Aurelio


title: Premature aging  in growth-plate and periosteum resident skeletal stem cells is responsible for bone loss

city: Shanghai

first: Dandan

last: Cao

address: 1239 Siping Road, Yangpu District

institute: Tongji University

summary: Skeleton system has shown high cell heterogeneousity. Different subpopulation of skeleton stem cells or mesenchymal stem cells have been identified by using varied protein markers. However, the decline of which cell types are responsible for age-related bone loss and what characteristic changes of these cells during aging remain to be determined. In the current study, we constructed a conditional premature aging model by deletion of Zmpste24 (Z24) in different cell types. We found that Prx1Cre; Z24fl/fl mice displayed bone loss while OsxCre; Z24fl/fl mice did not, indicating the populations of Prx1Cre +Osxcre- cells are responsible for age-related bone loss. Using single-cell RNA sequencing, we found two populations exit in Prx1Cre; Ai9+ mice but not in OsxCre; Ai9+ mice. Most strikingly, these two populations were declined in Prx1Cre;Z24fl/fl mice, compared to Prx1Cre;Z24fl/+ mice. The two populations, one is Prx1Cre;CD73+ resident in growth plate, called gpSSCs, responsible for trabecular bone loss. Another is Prx1Cre; Sca1+ resident in periosteum, called pSSCs, responsible cortical bone decrease. More importantly, the naturally aged mice also showed the decrease of these two cell types. By integration of chromatin and transcriptional profiling, we found that these two cell populations displayed increased p53 mediated DNA damage and decreased extracellular matrix (ECM) constituents, supporting the degeneration of two populations during aging. Finally, we found that AgrcCreER Z24fl/fl mice displayed the decrease of trabecular bone, but not cortical bone, consistent with  AgrcCreER could only label trabecular bone, but not cortical bone. Overall, our study identified two skeleton stem cells, gpSSCs and pSSCs, which are responsible for the age-related bone loss in trabecular bone and cortical bone, respectively.

overall_design: To isolate periosteal cells, femurs and tibias were placed in ice-cold PBS after the overlying skin and muscle were carefully removed. The periosteum was scratched using scalpel and forceps gentelly and then incubated with prewarmed digestion solution (2 mg/ml Collagenase (sigma,c6885);2mg/ml Dispase2 (Roche); 200 ug/ml DNase1;10mg/ml Kolliphor P 188 (sigma,15759); 1x HBSS without Mg2+ & Ca2+)at 37°C for 30 minutes. The dissociated periosteal cells were washed twice by centrifugation at 600g for 5 min with ice-cold PBS, 2% FBS. To isolate growth plate cells, dissected growth plates were minced using a scalpel and incubated with 0.15% collagenase(sigma,c6885) at 37°C for 90 minutes on a shaking incubator. Cells were pelleted and resuspended in ice-cold PBS, 2% FBS.The cells were stained with eFluor 450 anti-CD31 (eBioscience,48-0311-80), PerCP/Cy5.5 anti-CD45 (BioLegend, 103132), APC/Cy7 anti-mouse Ter-119 (BioLegend, 116223), BV421 anti mouse CD73 (Biolegend, 127217) or Parcific blue anti Sca1 (BioLegend, 108120) for 30 min. Then cells were measured by BC Cytoflex X after twice of wash by centrifugation at 600g for 5 min with ice-cold PBS, 2% FBS. The data were then analyzed with the CytExpert software.

first: Weiguo

last: Zou

first: Rui

last: Yue

first: Ruici

last: Yang


title: Transcriptome analysis of RNA-sequencing data for 2-D08-treated SK-LMS-1 cells

city: Hwasun-eup

first: Hosouk

last: Joung

state: Jeollanam-do

address: 264, Seoyang-ro

country: South Korea

institute: Chonnam National  University

summary: 2ʹ,3ʹ,4ʹ-trihydroxyflavone (2-D08) is a synthetic flavone that mechanistically has been identified as a specific inhibitor of protein SUMOylation. Recent studies have demonstrated that 2-D08 has various biological functions, including anticancer. We aimed to obtain additional insights into the effects of 2-D08 and conducted transcriptome analyses using RNA-sequencing (RNA-seq) in SK-LMS-1 leiomyosarcoma cells.

overall_design: We performed RNA-seq on two SK-LMS-1 cells treated with 2-D08 (50μM) for 48 hours and two untreated SK-LMS-1 cells.

first: Hyunju

last: Liu


title: Multiscale topology classifies and quantifies cell types in subcellular spatial transcriptomics [Xenium]

last: Qi

overall_design:
Topological data analysis of spatial transcriptomics datasets for cell type identification.
Xenium In Situ Spatial Gene Expression Profiling of Diseased Renal Tissue

first: Katherine

last: Benjamin

first: Aneesha

last: Bhandari

first: Jessica

last: Kepple

first: Zhouchun

last: Shang

first: Yanan

last: Xing

first: Yanru

last: An

first: Nannan

last: Zhang

first: Yong

last: Hou

first: Tanya

last: Crockford

last: MacCallion


title: The different impact of drug-resistant Leishmania on the transcription programs activated in neutrophils.

city: Lausanne

first: Sandra

last: Calderon

address: Génopode Building

department: Center for Integrative Genomics

country: Switzerland

institute: University of Lausanne

summary: Drug resistance threatens the effective control of infections, including parasitic diseases such as leishmaniases. Neutrophils are essential players in antimicrobial control, but their role in drug-resistant infections is poorly understood. Here, we evaluated human neutrophil response to clinical parasite strains having distinct natural drug susceptibility. We found that Leishmania antimony drug resistance significantly altered the expression of neutrophil genes, some of them transcribed by specific neutrophil subsets. Infection with drug-resistant parasites increased the expression of detoxification pathways and reduced the production of cytokines. Among these, the chemokine CCL3 was predominantly impacted, which resulted in an impaired ability of neutrophils to attract myeloid cells. Moreover, decreased myeloid recruitment when CCL3 levels are reduced was confirmed by blocking CCL3 in a mouse model. Collectively, these findings reveal that the interplay between naturally drug-resistant parasites and neutrophils modulates the infected skin immune microenvironment, revealing a key role of neutrophils in drug resistance.

overall_design: To evaluate the response of human neutrophils to parasite strains having distinct drug susceptibility, we first isolated neutrophils from the peripheral blood of three healthy donors (dA, dB, dC). We infected neutrophils ex vivo with either drug-resistant parasites (R) or drug-susceptible parasites (S), or left the cells uninfected (UN). Neutrophils were harvested for RNA-sequencing after 6h of culture. Differential gene expression analysis was performed between infected conditions vs uninfected, as well as between cells exposed to drug-resistant parasites vs drug-susceptible parasites.

first: Míriam

last: Díaz-Varela

first: Andrea

last: Sánchez-Hidalgo

last: Calderon-Copete

first: Virginie

last: Tacchini

first: Tobias

last: Shipley

first: LadyGiovanna

last: Ramírez

first: Julien

last: Marquis

first: OlgaLucía

last: Fernández

first: Nancy

last: Gore Saravia

first: Fabienne

last: Tacchini-Cottier


title: AtSDR4L and DIG1 interact with VAL2 to promote seed-to-seedling transition

city: VANCOUVER

first: Liang

last: Song

state: British Columbia

address: 2231-6270 UNIVERSITY BLVD

department: Botany

institute: University of British Columbia

summary: During the embryonic-to-vegetative transition in plants, many genes that were active in seeds become transcriptionally turned off. Recently, we reported a new transcriptional corepressor of the embryonic program, SEED DORMANCY 4-LIKE (AtSDR4L). Multiple lines of evidence suggest that AtSDR4L plays an essential role in regulating the transition from seed to seedling, possibly by collaborating with components of Polycomb Repressive Complexes (PRCs) and PRC-associated proteins VIVIPAROUS1/ABI3-LIKE (VAL) proteins. Through yeast-two-hybrid (Y2H) assays and genome-wide binding analysis, we demonstrated that AtSDR4L and DIG1 physically interact with VAL2 but not with VAL1. The interactions depend on the C-terminal halves of AtSDR4L and DIG1, and the N-terminal half of VAL2. AtSDR4L binds to target loci in germinating seeds, preceding reduced accumulation of H3K27me3 Atsdr4l seedlings at a few loci important for seed development. These findings suggest AtSDR4L, and potentially DIG1, facilitate the recruitment of PRC2 through VAL2 to inactivate seed development genes, thus promoting the seed-to-seedling transition.

overall_design: Chromatin immunoprecipitation DNA-seq (ChIP-seq) was performed to map the histone modification H3K27me3 in 1 and 3-day-old seedlings of Arabidopsis wilde-type and Atsdr4l mutants. Additionally, ChIP-seq was conducted to investigate AtSDR4L binding in germinating seeds treated with 5 uM ABA.

first: Milad

last: Alizadeh

first: Bailan

last: Lu


title: Multiscale topology classifies and quantifies cell types in subcellular spatial transcriptomics [stereo-seq]

first: Rui

last: Qi

overall_design:
Topological data analysis of spatial transcriptomics datasets for cell type identification.
stereo-seq

first: Katherine

last: Benjamin

first: Aneesha

last: Bhandari

first: Jessica

last: Kepple

first: Zhouchun

last: Shang

first: Yanan

last: Xing

first: Yanru

last: An

last: Zhang

last: Hou

first: Oliver

first: Fadi

last: Issa

first: Joanna

last: Hester

first: Ulrike

last: Tillmann

first: Heather

last: Harrington

last: Bull


title: Loss of Kmt2c or Kmt2d drives brain metastasis via KDM6A-dependent upregulation of MMP3 [ChIP-seq]

first: Kornelia

last: Polyak

department: Medical Oncology

first: Marco

last: Seehawer

first: Li

last: Zheqi

first: Jun

last: Nishida

first: Pierre

last: Foidart

first: Andrew

last: Reiter

first: Ernesto

last: Rojas

first: Marie-Anne

last: Goyette

first: Paloma

last: Cejas

first: Seth

last: Goldman

first: Karen

last: Adelman

first: Henry

last: Long

first: Malvina

last: Papanastasiou


title: Reduction of ZFX levels decreases histone H4 acetylation and increases Pol2 pausing at target promoters [GRO-seq]

city: Los Angeles

first: Peggy

last: Farnham

address: 1450 Biggy St, NRT6514

department: Biochemistry and Molecular Medicine

institute: University of Southern California

summary: The ZFX transcriptional activator binds to CpG island promoters, with a major peak at ~200-250bp downstream from transcription start sites. Because ZFX binds within the transcribed region, we investigated whether it regulates transcriptional elongation. We used GRO-seq to show that loss or reduction of ZFX increased the pause ratio at ZFX-regulated promoters. To further investigate the mechanisms by which ZFX regulates transcription, we determined regions of the protein needed for transactivation and for recruitment to the chromatin. Interestingly, although ZFX has 13 grouped zinc fingers, deletion of the first 11 fingers produces a protein that can still bind to chromatin and activate transcription. We next used TurboID-MS to detect ZFX-interacting proteins, identifying ZNF593, proteins that interact with the N-terminal transactivation domain (e.g. histone modifying proteins), and proteins that interact with ZFX when it is bound to the chromatin (e.g. TAFs and other histone modifying proteins). Our studies support a model in which ZFX enhances elongation at target promoters by recruiting H4 acetylation complexes and reducing pausing.

overall_design: To profile the effects of ZFX on Pol2 pausing in human cell lines. siRNA knockdowns with siZFX and a control siRNA oligo were performed in LN-229 cells with 2 biological replicates. 293T cells and 293T cells with ZFX and ZNF711 knockouts (DKO) were also performed with 2 biological replicates.

first: Emily

last: Hsu

first: Katherine

last: Hutchison

first: Yao

last: Liu

first: Charles

last: Nicolet

first: Shannon

last: Schreiner

first: Nathan

last: Zemke


title: LABS: linear amplification-based bisulfite sequencing for ultrasensitive cancer detection from cell-free DNA

city: Chicago

first: Xiaolong

last: Cui

state: IL

address: 680 N Lake Shore Drive

department: Department of Preventive Medicine

institute: Northwestern University

summary: Methylation-based liquid biopsies show promise in detecting cancer from circulating cell-free DNA, but current limitations impede clinical application. Most assays necessitate substantial DNA inputs, posing challenges. Underrepresented tumor DNA fragments may go undetected during exponential amplification steps of traditional sequencing methods. Here we report LABS (Linear Amplification based Bisulfite Sequencing), enabling linear amplification of bisulfite-treated DNA fragments in a genome-wide, unbiased fashion, detecting cancer abnormalities with sub-nanogram inputs. Applying LABS to 100 patient samples revealed cancer-specific patterns, copy number alterations, and enhanced cancer detection accuracy by identifying tissue-of-origin and immune cell composition.

overall_design: For method validation, we compared our LABS method with two commonly used commercial methods: EpiGnome and MethylC-seq. For clinical usage, we collected cfDNA samples from 50 CRC, 16 PDAC, and 34 control patients.

first: Ji

last: Nie

first: Krissana

last: Kowitwanich

first: Alana

last: Beadell

first: Diana

last: West-Szymanski

first: Wei

last: Zhang

first: Mengjie

last: Chen

first: Chuan

last: He


title: Reduction of ZFX levels decreases histone H4 acetylation and increases Pol2 pausing at target promoters [ChIP-Seq]

overall_design: ChIP-seq


title: Reduction of ZFX levels decreases histone H4 acetylation and increases Pol2 pausing at target promoters

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


title: Reduction of ZFX levels decreases histone H4 acetylation and increases Pol2 pausing at target promoters [RNA-Seq]

overall_design: To profile the effects of ZFX on gene expression in human cell lines. siRNA knockdowns with siZFX and/or siZNF593 and a control siRNA oligo were performed in LN-229 cells with 3 biological replicates. 293T cells with ZFX and ZNF711 knockouts (DKO) were transfected with mutant ZFX constructs or the empty vector control pCMV6-Entry with 3 biological replicates.


title: Single-cell RNA sequencing (scRNA-seq) of all IL-23R+ cell types in the small intestine of healthy  mice

city: New York

first: Jordan

last: Zhou

state: NY

address: 413 E 69th St

institute: Weill Cornell Medical College

summary: Single cell RNA-sequencing on all IL-23 receptor expressing cells in the intestine, revealing a dominance of lymphocytes including T cells and group 3 innate lymphoid cells (ILC3s).

overall_design: For scRNA-seq, IL-23R+ immune cells were sorted from small intestine of IL-23R-eGFP KI (JAX 035863) mice and stimulated with  recombinant mouse IL-23 for 2 hours.

first: Anees

last: Ahmed

first: Gregory

last: Sonnenberg


title: Effect of Terpenes from Poria Cocos: Verification of Therapeutic Modes of Action for Alzheimer’s Disease using Molecular Docking, Drug-induced Transcriptomes and Diffusion Network

city: Daejeon

first: Musun

last: Park

address: 1672 Yuseong-daero, Yuseong-gu

institute: Korean Institute of Oriental Medicine

summary: This study aimed to identify the modes of action (MOA) of Poria Cocos water extract (PCW) in HT29 cell line.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for PCW (500 ug/mL, 100 ug/mL, and 20 ug/mL, respectively), positive control (wortmannin 10uM and LY294002 10uM, respectively), and vehicle control (2% DMSO).


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

first: Yukihiro

last: Yabuta

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: Linker histone H1 regulates homeostasis of heterochromatin associated cRNAs [ChIP-Seq 3]

city: Barcelona

first: Oscar

last: Reina Garcia

state: Barcelona

address: C/Baldiri Reixac 10

department: Biostatistics and Bioinformatics

institute: IRB Barcelona

summary: Chromosomal RNAs (cRNAs) are a poorly understood fraction of cellular RNAs that co-purify with chromatin. Here we show that, in Drosophila, cRNAs constitute a heterogeneous group of RNA species that cover ~28% of the genome. Intriguingly, we found that cRNAs are highly enriched in heterochromatic transcripts. Our results show that heterochromatic cRNAs interact with the hnRNP A/B proteins hrp36 and hrp48 to assemble into RNP particles. We also show that depletion of linker histone dH1, a major component of chromatin, impairs assembly of hrp36 and hrp48 onto heterochromatic cRNAs. Concomitantly, impaired cRNAs assembly induces the accumulation of heterochromatic cRNAs and the formation of unscheduled RNA::DNA hybrids (R-loops). Linker histones H1 are known to regulate chromatin structure and compaction and, indeed, we show that dH1 depletion perturbs chromatin organization, reducing nucleosome occupancy and specifically increasing accessibility and 3D interactions within heterochromatin. These perturbations facilitate annealing of cRNAs to the DNA template, enhancing R-loops formation and cRNAs retention at heterochromatin. Altogether, these results unveil the unexpected contribution of linker histones to RNPs assembly and homeostasis of cRNAs.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for RNA PolII in knockdown of H1 on S2 cells.

first: Paula

last: Bujosa

last: Reina

first: Adrià

last: Caballé

first: Jordi

last: Bernués

first: Fernando

last: Azorín


title: Effect of Terpenes from Poria Cocos: Verification of Therapeutic Modes of Action for Alzheimer’s Disease using Molecular Docking, Drug-induced Transcriptomes and Diffusion Network [SW1783]

first: Musun

last: Park

summary: This study aimed to identify the modes of action (MOA) of Poria Cocos water extract (PCW) in SW1783 cell line.


title: Linker histone H1 regulates homeostasis of heterochromatin associated cRNAs [ChIP-seq 2]

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for hrp36 and hrp48 in knockdown of H1 on S2 cells.


title: Machine learning identifies activation of RUNX/AP-1 as drivers of mesenchymal and fibrotic regulatory programs in gastric cancer

status: Public on Apr 22 2024

city: Baltimore

first: Michael

last: Beer

state: MD

address: 733 N. Broadway

department: Biomedical Engineering and Genetic Medicine

institute: Johns Hopkins University

summary: We performed ATAC-seq in a set of 25 gastric cancer cell lines to detect differential activation of regulatory programs.

overall_design: ATAC-seq chromatin accessibility profiling of 25 gastric cancer cell lines.

first: Shamaine

middle: W

last: Ho

first: Patrick

last: Tan