title: Transcriptional Regulation of Protein Synthesis by Mediator Kinase Represents a Therapeutic Vulnerability in MYC-driven Medulloblastoma

city: Aurora

first: Dong

last: Wang

state: CO

institute: University of Colorado, Anschutz Campus

summary: MYC-driven medulloblastoma (MB) is a highly aggressive cancer type with poor prognosis and limited treatment options. Through CRISPR-Cas9 screening of MB cell lines, we identified the Mediator-associated kinase CDK8 as a critical regulator of MYC-driven MB. Loss of CDK8 substantially reduces MYC expression, induces pronounced transcriptional changes, suppresses monosome assembly, and decreases ribosome biogenesis and protein synthesis, consequently inhibiting MB growth. Mechanistically, CDK8 regulates the occupancy of RNA polymerase II at specific chromatin loci, facilitating an epigenetic alteration that promotes the transcriptional regulation of ribosomal genes. Targeting CDK8 effectively diminishes the stem-like neoplastic cells characterized by hyperactive ribosome biogenesis. Furthermore, we demonstrated that the combined inhibition of CDK8 and mTOR synergizes to optimize therapeutic outcomes in vivo and in vivo. Overall, our findings establish a connection between CDK8-mediated transcriptional regulation and mRNA translation, suggesting a promising new therapeutic approach that targets the protein synthesis for MYC-driven MB.

overall_design: To study the role of CDK8 in MYC-driven medullolbastoma, we performed RNA-Seq and cut&run of MB cells after genetic knockdown or pharmacological inhibition of CDK8

first: Rajeev

last: Vibhakar


title: Latent Epigenetic Programs in Müller Glia Contribute to Stress, Injury, and Disease Response in the Retina

status: Public on Dec 01 2024

city: Memphis

first: Michael

middle: A

last: Dyer

state: Tennessee

address: 262 Danny Thomas

department: DNB

country: USA

institute: St. Jude Children's Research Hospital

type: Expression profiling by high throughput sequencing

summary: Previous studies have demonstrated the dynamic changes in chromatin structure during retinal development that correlate with changes in gene expression. However, a major limitation of those prior studies was the lack of cellular resolution. Here, we integrate single-cell (sc) RNA-seq and scATAC-seq with bulk retinal data sets to identify cell type–specific changes in the chromatin structure during development. Although most genes’ promoter activity is strongly correlated with chromatin accessibility, we discovered several hundred genes that were transcriptionally silent but had accessible chromatin at their promoters. Most of those silent/accessible gene promoters were in the Müller glial cells. The Müller cells are radial glia of the retina and perform a variety of essential functions to maintain retinal homeostasis and respond to stress, injury, or disease. The silent/accessible genes in Müller glia are enriched in pathways related to inflammation, angiogenesis, and other types of cell-cell signaling and were rapidly activated when we tested 15 different physiologically relevant conditions to mimic retinal stress, injury, or disease in human and murine retinae. We refer to these as “pliancy genes” because they allow the Müller glia to rapidly change their gene expression and cellular state in response to different types of retinal insults. The Müller glial cell pliancy program is established during development, and we demonstrate that pliancy genes are necessary and sufficient for regulating inflammation in the murine retina in vivo. In zebrafish, Müller glia can de-differentiate and form retinal progenitor cells that replace lost neurons. The pro-inflammatory pliancy gene cascade is not activated in zebrafish Müller glia following injury, and we propose a model in which species-specific pliancy programs underly the differential response to retinal damage in species that can regenerate retinal neurons (zebrafish) versus those that cannot (humans and mice).

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Retina were dissected from the eye cup in Retinal Explant Media (REM). 1.5mm punches were taken from each eye using a biopsy punch and placed on a Nuclepore 1.0uM membrane floating on 2mL of REM (+/- stress) in a 12-well dish. 50uL of REM was removed from the dish and placed on the retinal punches. The retinal punches were incubated for 24 hours (37C, 5% CO2) for culture control retina. After culture, retinal punches were dissociated in Trizol and RNA was extracted and submitted for RNAseq.

first: Jackie

last: Norrie


title: Mechanosensitive Piezo1 is crucial for periosteal stem cell-mediated fracture healing

status: Public on Dec 19 2024

city: Shijiazhuang

first: Siming

last: Jia

address: 河北省石家庄市河北医科大学第三医院

country: China

institute: 河北医科大学

overall_design: At 10 days (n = 5) and 20 (n = 5) days post fracture (dpf), the callus was isolated from each mouse

first: Weijian

last: Liu

first: Wei

last: Chen

first: Yingze

last: Zhang


title: The histone chaperone Spt6 controls chromatin structure through its conserved N-terminal domain [MNase-Seq]

status: Public on Nov 25 2024

city: Boston

first: James

middle: L

last: Warner

state: MA

address: 77 Avenue Louis Pasteur, Room 358

department: Genetics

institute: Harvard Medical School

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The disassembly and reassembly of nucleosomes by histone chaperones is an essential activity during eukaryotic transcription elongation. This highly conserved process maintains chromatin integrity by transiently removing nucleosomes as barriers and then restoring them in the wake of transcription. While transcription elongation requires multiple histone chaperones, there is little understanding of how most of them function and why so many are required. Here, we show that the histone chaperone Spt6 acts through its acidic, intrinsically disordered N-terminal domain (NTD) to bind histones and control chromatin structure. The Spt6 NTD is essential for viability and its histone binding activity is conserved between yeast and humans. The essential nature of the Spt6 NTD can be bypassed by changes in another histone chaperone, FACT, revealing a close functional connection between the two. Our results have led to a mechanistic model for dynamic cooperation between multiple histone chaperones during transcription elongation.

overall_design: Micrococcal nuclease sequencing (MNase-seq) analysis to determine whether the Spt6 NTD is required for normal chromatin structure. Since the Spt6Δ2-238 protein does not support viability in Saccharomyces cerevisiae, we used a strain in which the genome-encoded Spt6 could be rapidly depleted using an auxin-inducible degron while expressing either no (empty vector), wild-type (Spt6), or mutant (Spt6Δ2-238) versions of Spt6 from a plasmid. We then performed MNase digestion on cells grown in non-depleted (DMSO) and depleted (IAA) conditions. Experiments were performed in biological triplicate (rep1, rep2, and rep3).

first: Vanda

last: Lux

first: Vaclav

last: Veverka

first: Fred

last: Winston


title: The histone chaperone Spt6 controls chromatin structure through its conserved N-terminal domain [ChIP-seq]

overall_design: Chromatin immunoprecipitation sequencing (ChIP-seq) analysis to determine whether the Spt6 NTD contributes to chromatin binding. Since the Spt62-238 protein does not support viability in Saccharomyces cerevisiae, we used a strain in which the genome-encoded Spt6 could be rapidly depleted using an auxin-inducible degron while expressing either wild-type (Spt6) or mutant (Spt6Δ2-238) versions of Spt6 from a plasmid. We could distinguish the two versions of Spt6 as genome-encoded allele was tagged with a V5 epitope tag and the plasmid-encoded allele was tagged with a Flag epitope tag. We then performed ChIP to determine levels of V5, FLAG, and Rpb1 association with chromatin in non-depleted (DMSO) and depleted (IAA) conditions. Experiments were performed in biological triplicate (here, rep2, rep3, and rep4). Replicate 1 was not analyzed due to poor sonication of chromatin.


title: Effect of deletion of UTX expression in NY8.3 progenitor CD8+ T cells

city: Los Angeles

first: Ho Chung

state: CA

address: 609 Charles E Young Dr E

department: MIMG

institute: University of California, Los Angeles

summary: Type 1 diabetes (T1D) is a chronic autoimmune disease resulting from the destruction of insulin-producing beta cells. This persistence is due to the continual replenishment of short-live effector CD8+ T cells (autoimmune mediators, Tmed) in the pancreatic lymph nodes (pLNs) by a long-lived reservoir of stem-like memory CD8+ T cells (autoimmune progenitors, Tprog). We are investigating an epigenetic regulator UTX playing the role in Tprog to Tmed conversion. The NOD mice with T cell-specific UTX deficiency (UTXTCD mice) were protected from T1D. In addition, the deletion of UTX in CD8+ T cells resulted in the accumulation of Tprog and loss of Tmed populations in pLNs. The function of UTX is to demethylate the histone mark, H3K27 tri-methylation, leading to the open chromatin accessibility for gene expression. ATAC-seq and RNA-seq of antigen specific Tprog cells revealed a role of UTX in closing chromatin at progenitor gene loci while enforcing accessibility at effector gene loci. Taken together, these findings point to the potential of targeting UTX-mediated conversion of Tprog into Tmed for interrupting the T1D autoimmune response.

overall_design: To investigate the gene expression and chromatin accessibility regulated by UTX, we sorted the Ly108+CXCR6- CD8+ T cells harvested from pancreatic lymph node of NOD.NY8.3 (NY8.3) mice and T cell specific deletion UTX deficient NY8.3 mice (UTXTCD.NY8.3). We then perform gene expression profiling using RNA-seq and ATAC-seq. There are 3 samples for each group (NY8.3 and UTXTCD.NY8.3)

first: Shirley

first: Lisa

last: Kohn

first: Hsing Hui

first: David

last: Sailer

first: Ethan

last: McCarthy

first: Maryam

last: Seyedsadr

first: Zikang

last: Zhou

first: Xihui

last: Yin

first: Nicole

last: Wilkinson

first: Melissa

last: Lechner

first: Willy

last: Hugo

first: Maureen

last: Su


title: Two pathogenic germline truncating variants of BRCA2 confer different haploinsufficiency phenotypes

status: Public on Nov 21 2024

city: Paris

first: Elodie

last: Girard

address: 11-13 rue Pierre et Marie Curie

country: France

institute: Institut Curie

summary: Inactivating germline monoallelic mutations in the tumor suppressor BRCA2 predispose to breast and ovarian cancer. BRCA2 is essential in DNA repair via homologous recombination (HR). Tumorigenesis in this setting is thought to require the inactivation of the second allele; however, this event is not always observed suggesting haploinsufficiency. We investigated this question recreating two BRCA2 pathogenic truncating variants in heterozygosis in breast epithelial cells. One prompted sensitivity to PARP inhibitors (PARPi) and reduced HR capacity unlike the other. The other resulted in transcriptomic and epigenetic changes including histone H4 acetylation levels and NF-kB activation that we link to PCAF acetyl transferase. These changes impacted on cell migration and proliferation in 2D and 3D, processes that were also deregulated in tumors. Our work demonstrates that distinct truncating variants of BRCA2 are not phenotypically equivalent. It also identifies PCAF as shaping BRCA2-related gene expression. These findings may have implications in cancer prevention.

overall_design: RNA-seq experiments of 9 samples extracted from the MCF10A cell lines: 3 WT controls, 6 with a pathogenic BRCA2 truncating alteration- 3 with a c.999del5 (del5) and 3 with a c.5946delT  (delT).

first: Anna

last: Minello

first: Aura

last: Carreira


title: Integrated multiomic analysis identifies TRIP13 as a mediator of alveolar  epithelial type II cell dysfunction in idiopathic pulmonary fibrosis

status: Public on Nov 18 2024

city: Glendale

first: Crystal

last: Marconett

address: 1856 Kirkby Rd

department: Translational Genomics

institute: Keck School of Medicine

summary: Idiopathic pulmonary fibrosis (IPF) is a lethal progressive lung disease urgently needing new therapies. Current treatments only delay disease progression, leaving lung transplant as the sole remaining option. Recent studies support a model whereby IPF arises because alveolar epithelial type II (AT2) cells, which normally mediate distal lung regeneration, acquire airway and/or mesenchymal characteristics, preventing proper repair. Mechanisms driving this abnormal differentiation remain unclear. We performed integrated transcriptomic and epigenomic analysis of purified AT2 cells which revealed genome-wide alterations in IPF lungs. The most prominent epigenetic alteration was activation of an enhancer in thyroid receptor interactor 13 (TRIP13), coinciding with TRIP13 upregulation. TRIP13 is broadly implicated in epithelial-mesenchymal plasticity and transforming growth factor-beta signaling. In cultured human AT2 cells and lung slices, small molecule TRIP inhibitor DCZ0415 prevented acquisition of the mesenchymal gene signature characteristic of IPF, suggesting TRIP13 inhibition as a potential therapeutic approach to fibrotic disease.

overall_design: AT2 cells purified from primary human normal and IPF samples underwent bulk RNAseq and bulk ATACseq profiling and data integration to determine the extent and effect of epigenomic remodeling on AT2 biology in IPF. Bulk ATACseq was also performed on primary proximal lung basal cells.

first: Laurence

last: St. Pierre

first: Asres

last: Berhan

first: Eun

last: Sung

first: Juan

middle: R

last: Alvarez

first: Hongjun

last: Wang

first: Yanbin

last: Ji

first: Yixin

last: Liu

first: Haoze

last: Yu

first: Angela

last: Meier

first: Kamyar

last: Afshar

first: Eugene

middle: M

last: Golts

first: Grace

middle: Y

last: Lin

first: Alessandra

last: Castaldi

first: Ben

last: Calvert

first: Amy

last: Ryan

first: Beiyun

first: Ite

last: Offringa

middle: N

first: Zea

last: Borok


title: Functional Genomics of Human Skeletal Development and the Patterning of Height Heritability [RNA-Seq]

status: Public on Nov 15 2024

city: Stanford

first: Daniel

last: Richard

address: 290 Jane Stanford Way

institute: Stanford University

summary: High-resolution profiling of epigenetic/transcriptomic behaviours of chondrocytes during skeletal development suggest the importance of generalized growth to adult height patterning

overall_design: Epigenetic and transcriptomic profiling of in-vivo chondrocyte populations

first: Pushpanathan

last: Muthuirulan

first: Mariel

last: Young

first: Terence

middle: D

last: Capellini


title: Functional Genomics of Human Skeletal Development and the Patterning of Height Heritability

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

overall_design: Refer to individual Series


title: Botrytis cinerea genes activated in infection process

status: Public on Nov 01 2024

city: Beijing

first: Daoxin

last: Xie

address: School of Life Sciences, Room 407, Renhuan Building, Tsinghua University

institute: Tsinghua University

summary: To screen Botrytis genes activated in infection process, we performed gene expression profiling analysis using data obtained from RNA-seq of Botrytis cinerea cultured in vitro or infecting Arabidopsis leaves.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Botrytis cinerea cultured in vitro or with infection on Arabidopsis leaves.

first: Jiaojiao

last: Wang

first: Dewei

last: Wu


title: Functional Genomics of Human Skeletal Development and the Patterning of Height Heritability [ATAC-Seq]


title: Deciphering the Transcriptomic Landscape of Type 2 Diabetes: Insights from Bulk RNA Sequencing and Single-Cell Analysis [RNA-seq]

status: Public on Oct 30 2024

city: Saint-Petersburg

first: Aleksandr

last: Tkachenko

address: Mendeleyevskaya line, 3

country: Russia

institute: D. O. Ott Research Institute of Obstetrics and Gynecology

summary: Type 2 diabetes (T2D) is a chronic metabolic disorder characterized by insulin resistance and relative insulin deficiency. It is a significant public health concern worldwide, with an estimated prevalence of over 422 million individuals affected globally. This number is projected to rise, making diabetes one of the leading causes of morbidity and mortality. It is associated with numerous severe microvascular and macrovascular complications, including retinopathy, nephropathy, cardiovascular diseases, and neuropathy, which substantially impact patients' quality of life and healthcare systems. The global prevalence of T2D necessitates a deeper understanding of its underlying mechanisms to develop more effective prevention and treatment strategies. Recent advancements in transcriptomics and single-cell technologies have revolutionized our ability to investigate the cellular and molecular landscapes of T2DM. Transcriptomic analysis provides insights into gene expression patterns in T2D, revealing pathways involved in insulin signaling, metabolic regulation, and inflammation. The importance of inflammation driven by immune cells in the pathogenesis of T2D has been repeatedly demonstrated. This makes research focused on the analysis of gene expression in whole blood cells especially relevant. Transcriptomic markers of T2D have been investigated in studies utilizing expression arrays and RNA-seq. While expression arrays allow for the analysis of a gene set limited by the design of microarrays, RNA-seq allows investigating the entire transcriptome. A study focused on the analysis of transcriptomic markers of T2D in whole blood using RNA-seq demonstrated differential expression of genes associated with inflammation, insulin resistance, and mitochondrial dysfunction. However, the heterogeneity of immune cell populations poses significant challenges in understanding the disease's complexity. Single-cell RNA sequencing (scRNA-seq) enables researchers to dissect this cellular diversity, allowing for the identification of distinct cell types and their specific contributions to T2DM progression. By integrating transcriptomic data with single-cell analyses, we can elucidate the dynamic interactions between various cell types and their roles in T2DM. In this study, we aimed to analyze transcriptomic markers of T2D in whole blood cells and conduct single-cell sequencing on isolated PBMCs from T2D patients and healthy controls in order to advance our understanding of the processes involved in the pathogenesis of T2D and to highlight the significance of transcriptomic and single-cell research in T2D studies.

overall_design: To investigate transcriptomic changes in patients with type 2 diabetes we compared single cell RNA sequencing and bulk RNA sequencing data from affected individuals with data from healthy controls

first: Alexander

first: Ziravard

last: Tonyan

first: Yulia

last: Nasykhova

first: Yuri

last: Barbitoff

first: Iaroslav

last: Renev

first: Maria

last: Danilova

first: Anastasiia

last: Mikhailova

first: Olga

middle: B

last: Glavnova

first: Sergey

middle: V

last: Chepanov

last: Selkov

first: Nikita

last: Golovkin

first: Margarita

middle: E

last: Vlasova

first: Andrey

middle: S

last: Glotov


title: A nucleoside signal generated by a fungal endophyte regulates host cell death and promotes root colonization

status: Public on Nov 17 2024

city: Cologne

first: Gregor

last: Langen

address: Zuelpicher Str. 47b

department: Institute for Plant Sciences

country: Germany

institute: University of Cologne

summary: Regulated host cell death is part of a plant defense strategy against pathogens but it is also involved in accommodating certain beneficial root microbes. We have identified extracellular metabolites and intracellular metabolic signals that contribute to beneficial root fungal endophyte colonization, and uncovered a conserved cell death mechanism likely co-opted for establishing plant-endophyte symbiosis.

overall_design: The response of 12-day-old  Arabidopsis thaliana Col-0 seedlings was analysed 3 and 12 hours after treatment with 500 µM dAdo in 2.5 mM MES buffer pH 5.6 or MES buffer alone. Gene expression was analysed using RNAseq, pseudoaligned to the TAIR10 transcriptome.

first: Nick

last: Dunken

first: Heidi

last: Widmer

first: Gerd

middle: U

last: Balcke

first: Henryk

last: Straube

first: Nyasha

last: Charura

first: Pia

last: Saake

first: Concetta

last: De Quattro

first: Hanna

last: Rövenich

first: Stephan

last: Wawra

first: Mamoona

last: Khan

first: Claus-Peter

last: Witte

first: Armin

last: Djamei

first: Matias

last: Zurbriggen

first: Jonas

last: Schön

first: Alain

last: Tissier

first: Alga

last: Zuccaro


title: Involvement of Wnt/β-catenin Signaling Pathway in Curdione-Induced Reproductive Toxicity Revealed by Multiomics Profiling in HTR-8/SVneo Cells

status: Public on Nov 14 2024

city: Fuzhou

first: Jiaxin

last: Wen

address: No.1 Xuefu North Road, Fuzhou, Fujian, China

institute: Fujian Medical University

summary: This study aims to explore the mechanism of curdione-induced toxicity damage in HTR-8/SVneo cells through the epigenetics, proteomics, and metabolomics, and experimental verification.

overall_design: Curdione exposure induces ROS accumulation, mitochondrial dysfunction, DNA damage and disruption of tight junctions in HTR-8/SVneo cells.

first: Qibin

last: Wu

first: Mengting

last: Chen

first: Yifan

last: Lin

first: Jian

last: Zhang


title: Land plant-specific H3K27 methyltransferases ATXR5 and ATXR6 control plant development and stress responses [Rice RNA-seq]

status: Public on Nov 07 2024

first: Xiaoyi

last: Li

address: west beichen

department: Chinese Academy of Sciences

institute: Institute of Genetics and Developmental Biology

summary: The colonization of land by plants relies on numerous evolutionary innovations crucial for terrestrial adaptation. These include advances in sexual reproduction and the ability to properly respond to various environmental stresses, which involve precise control of their regulatory genes. A notable genetic innovation in land plants is the emergence of histone lysine methyltransferases ATXR5/6, which specifically catalyse the repressive histone H3 lysine 27 monomethylation (H3K27me1). However, the evolutionary reason for land plants to develop these enzymes remains unclear. In this study, we investigate the importance of ATXR5/6 by generating strong atxr5;axtr6 double mutants in Arabidopsis. Our results show that ATXR5/6 are essential for plant reproductive development and play a critical role in supporting normal plant growth by repressing the transcription of stress responsive genes. In addition, ATXR5/6 are necessary for maintaining H3K27 trimethylation (H3K27me3), likely by providing H3K27me1 as a substrate for further methylation. We also demonstrate that the function of ATXR5/6 in regulating reproductive development and responsive genes is conserved in the monocot rice. We propose that land plants may have evolved ATXR5/6 to assist in the transcriptional regulation necessary for terrestrial adaptation

overall_design: To test the function of ATXR5/6 in other plants, we generated the null osatxr5;osatxr6 mutant in rice and found that OsATXR5/6 are also essential for plant reproduction

first: Danhua

last: Jiang

first: Jie

last: Pan


title: BACH2 Controls Seeding and Establishment of Long-Lived HIV-1 Reservoir in CD4+ T cells

city: Saint Louis

first: Hongbo

last: Gao

state: MO

address: 425 S Euclid Ave

institute: Washington university in St. Louis

summary: Despite antiretroviral therapy, HIV mainly persists in memory CD4+ T cells in people living with HIV. Most long-lived viral reservoir cells are infected near the time of therapy initiation. A better understanding of the early events in reservoir seeding presents opportunities for preventing latent reservoir formation. Here, we demonstrated that CD4+ T cells expressing CCR5, permissive to HIV-1 infection, are effector or terminally differentiated cells. BACH2 is expressed by a small subset of CCR5+ cells and reverses their terminal differentiation. BACH2-mediated memory differentiation is impeded due to heightened inflammation before treatment initiation. Mice with a BACH2 knockout human immune system has a reduced frequency of HIV-1 reservoir cells and do not experience virus rebound after treatment discontinuation. Our study reveals that BACH2 is essential to the seeding of long-lived HIV-1 reservoir and demonstrates the potential of targeting BACH2 at the time of treatment initiation to eliminate HIV-1 reservoirs in T cells.

overall_design: Human primary CD4+ T cells were purified by negative selection with MojoSort™ Human CD4 T Cell Isolation Kit (Biolegend). Purified CD4+ T cells (106 cells/mL) were cultured in RPMI 1640 medium supplemented with 10% FCS, penicillin (100 unit/mL) and streptomycin (100 µg/mL). To generate activated cells, CD4+ T cells were stimulated with plate-bound anti-CD3 and anti-CD28 antibodies at 1μg/mL (BioLegend) for 3 days in the presence of 20 ng/mL IL-2. Stimulated CD4+ T cells were cultured with 20 ng/mL IL-2 for 6 days. CCR5+ and CCR5- CD4+ T cells were sorted followed by bulk RNA-Seq experiments.

first: Yuhao

first: Kolin

last: Clark

first: Liang

last: Shan


title: CIRCULATING SERUM MICRO-RNA AS NON-INVASIVE DIAGNOSTIC BIOMARKERS OF ENDOMETRIOSIS

city: Brescia

first: Stefano

last: Calza

state: Brescia

address: Viale Europa 11

department: DMMT

country: Italy

institute: University of Brescia

summary: Total RNA was extracted from 400 ul of serum with the miRNeasy Serum/Plasma advanced Kit (Qiagen)  and quantified using the Qubit microRNA assay kit (Thermo Fisher Scientific). cDNA templates were prepared using the TaqMan Advanced miRNA cDNA Synthesis Kit (Thermo Fisher Scientific), starting from 10 ng of RNA.  RT-qPCR carried out on a QuantStudio 12K Flex (Applied Biosystems) using the TaqMan OpenArray miRNA panel.

overall_design: This study was conducted on serum samples collected prior to surgery from 67 patients with endometriosis and 60 control women with benign gynecological conditions not linked to endometriosis, as confirmed by histological examination.

first: Antonella

last: Ravaggi


title: Single-cell RNA sequencing defines the interplay between tumor cells, virus and microenvironment in nasopharyngeal carcinoma

first: ruoyan

address: Yiheyuan street

institute: Peking University

summary:
Purpose: While viruses play critival roles in many human malignancies, the influence of virus infection on the tumor microenviroment(TME) and how this impacts disease progression are poorly characterized.
Methods:  we applied both Smart-seq2  and 10X Genomics chemistry to ~104000 cells from 19 EBV+ NPC patients and 7 nonmalignant nasopharyngeal biopsies.
Results:
1. We have defined the complex interplay between tumor cells, virus infection, and the TME at single-cell resolution. 2. An epithelial-immune dual feature of malignant cells was discovered and associated with poor prognosis. 3. Stromal and immune cells in the TME were remodeled by tumor cells and virus infection. 4. EBV gene expression was found to correlate with complement factor expression in malignant cells, which, in turn, mediated T cell modulation and recruitment. 5. We subtyped NPC patients into 5 groups with different prognoses according to their respective TME compositions.
Conclusion: Our results provide new insights into the multicellular ecosystem of NPC and offer important clinical implications.

overall_design: NPC single-cell mRNA profiles of primary and lymph node metatstesis were generated through Smart-seq2 and 10X genomic chemistry ,using Illumina Hiseq-X ten.

first: Shanzhao

last: Jin

first: Ruoyan


title: Differentially expressed genes between WT and AtC3H3 OX, and WT and AtC3H26 OX

city: Busan

first: Yong-Hwan

last: Moon

address: Busandaehak-ro 63Beon-gil 2, Geumjeong-gu

department: Molecular Biology

country: South Korea

institute: Pusan National University

summary: Salinity is a pressing issue causing widespread crop loss, prompting plants to adapt through changes in gene expression. This study investigated the role of the non-tandem CCCH zinc finger protein gene AtC3H3 in Arabidopsis in response to salt stress. AtC3H3, a gene from the non-TZF gene family and known for its RNA-binding and ribonuclease activity, was found to be upregulated under osmotic stresses such as high salt and drought. When overexpressed in Arabidopsis, AtC3H3 led to increased tolerance to salt stress, not drought stress. qRT-PCR analysis showed that the expression of both well-known ABA-dependent salt stress-responsive genes, such as RAB18, RD29B, and RD22, and representative ABA-independent salt stress-responsive genes, such as DREB2A and DREB2B, was significantly higher in AtC3H3 OXs than WT under NaCl treatment, indicating its involvement in both ABA-dependent and ABA-independent signaling pathways. mRNA-Seq analysis using NaCl-treated WT and AtC3H3 OXs revealed no potential target mRNAs of the RNase function of AtC3H3, suggesting that the potential targets of AtC3H3 might be non-coding RNAs, not mRNAs.  The study conclusively demonstrates that AtC3H3 plays a crucial role in salt stress tolerance by influencing the expression of salt stress-responsive genes. These findings have opened a new avenue for understanding plant stress mechanisms and suggest potential strategies for enhancing crop resilience to salinity.

overall_design: Differential gene expression between WT and AtC3H3 OX, as well as between WT and AtC3H26 OX, was examined under both no treatment and NaCl treatment conditions at 10 days after germination under SD conditions (8-hour-light and 16-hour-dark cycle) on a whole-genome level.

first: Hye-Yeon

last: Seok

first: Sun-Young

last: Lee


title: Land plant-specific H3K27 methyltransferases ATXR5 and ATXR6 control plant development and stress responses [Arabidopsis RNA-seq]

overall_design: To explore potential reasons for the additional developmental abnormalities in atxr5;atxr5;atxr6hyp;atxr6c-1 compared to atxr5;atxr6hyp


title: Effects of RG2833 (HDAC1/3 Inhibitor) on the gene expression of Female TgF344 Alzheimer’s disease Rat model.

status: Public on Oct 27 2024

city: New York

first: Kelechi

last: Ndukwe

state: NY

address: 695 Park Ave, New York, NY 10065

department: Biology

institute: Hunter College City University of New York Graduate Center

summary: We investigated the long-term therapeutic effects of oral administration of a brain-penetrant HDAC1/3 inhibitor RG2833 in a Fisher transgenic 344-AD (TgF344-AD) rats model of AD. We treated for 6 months, starting at 5 months of age administering the drug in rodent chow at ~30mg/kg of body weight. After treatment we performed experiements to show the effects of drug treatment on spatial memory deficits. We show significantly improved hippocampal-dependent spatial memory performance in TgF344-AD female.

overall_design:
To investigate the effect of RG2833 on hippocampal gene expression, we have 5 (chow treated rats) TgF344 and 5 (RG2833 chow treated) rats.
At 11 months of age, the rats were anaesthetized intraperitoneally with ketamine (100 mg/kg) and xylazine (10 mg/kg) and transcardially perfused with cold RNAse-free 1× PBS. Left hippocampi were removed and snap frozen for RNAseq analysis.
Left hemisphere of the hippocampus. F1 – F5 (untreated transgenic rats), FRG1 – FRG5 (transgenic AD rats treated with the drug RG2833).
Female Rats started RG2833 treatment at 5-months of age and were treated for 6 months untli they were 11 months old. ). For this experiment, the gene expression for the drug treated transgenic rats will be compared to that of the untreated transgenic group (FRG/F)

first: Osama

last: Chaudry

first: Lei

last: Xie

first: Patricia

last: Rockwell

first: Maria

last: Figueiredo-Pereira

first: Peter

last: Serrano


title: Effects of RG2833 (HDAC1/3 Inhibitor) on the gene expression of Male TgF344 Alzheimer’s disease Rat model.

summary: We investigated the long-term therapeutic effects of oral administration of a brain-penetrant HDAC1/3 inhibitor RG2833 in a Fisher transgenic 344-AD (TgF344-AD) rat model of AD. We treated for 6 months, starting at 5 months of age administering the drug in rodent chow at ~30mg/kg of body weight. After treatment we performed experiments to show the effects of drug treatment on spatial memory deficits and gene expression.

overall_design:
To show the effects of RG2833-treatment on gene expression levels, Hippocampi of 5 drug-treated and 5 untreated transgenic rats of male rats were analysed for gene expression by RNAseq
At 11 months of age, the rats were anaesthetized intraperitoneally with ketamine (100 mg/kg) and xylazine (10 mg/kg) and transcardially perfused with cold RNAse-free 1× PBS. Left hippocampi were removed and snap frozen for RNAseq analysis.
Left hemisphere of the hippocampus. M1 – M5 (untreated transgenic rats), MRG1 – MRG5 (transgenic AD rats treated with the drug RG2833).
Male Rats started ibudilast tretment at 5-months of age and were treated for 6 months untli they were 11 months old. ). For this experiment, the gene expression for the drug treated transgenic rats will be compared to that of the untreated transgenic group (MRG/M)


title: A novel anti-epileptogenesis strategy of temporal lobe epilepsy based on nitric oxide donor

status: Public on Oct 21 2024

city: Nanjing

first: fan

last: meng

address: Longmian Avenue 101

institute: Nanjing Medical University

summary: The molecular mechanism underlying the role of hippocampal hilar interneuron degeneration in temporal lobe epilepsy (TLE) remains unclear. Especially, very few studies have focused on the role of neuronal nitric oxide synthase (nNOS, encoded by Nos1) containing hilar interneurons in TLE. In the present study, Nos1 conditional knockout mice were constructed, and we found that selective deletion of Nos1 in hilar interneurons rather than dentate granular cells (DGCs) triggered epileptogenesis. The level of nNOS was downregulated in patients and mice with TLE. Nos1 deletion led to excessive epilepsy-like excitatory input circuit formation and hyperexcitation of DGCs. Replenishment of hilar nNOS protein blocked epileptogenic development and memory impairment in pilocarpine-induced TLE mice. Moreover, chronic treatment with DETA/NONOate, a slowly released exogenous nitric oxide (NO) donor, prevented aberrant neural circuits of DGCs and the consequent epileptogenesis without acute antiseizure effects. Therefore, we concluded that NO donor therapy may be a novel anti-epileptogenesis strategy, different from existing antiseizure medications (ASMs), for curing TLE.

overall_design: Young adult male mice (6-8 weeks old) were subcutaneously injected with pilocarpine to induce status epilepticus and PBS for control. Multiple dentate gyri were taken out (pilocarpine = 14 , PBS = 9 ) and pooled to create a composite sample for single-nuclei RNA sequencing after 10 weeks post-status when animals were in the chronic epileptic phase.


title: IRF2BP2 affects T-ALL cell proliferation by cooperating with master transcription factors [Cut&Tag]

status: Public on Oct 26 2024

city: Suzhou

first: Zimu

last: Zhang

state: Jiangsu

address: Zhongnan Street

institute: Children’s Hospital of Soochow University

summary: Knocking down IRF2BP2 led to decreased T-cell acute lymphoblastic leukemia (T-ALL) cell survival and growth both in vitro and in vivo. To explore IRF2BP2-dependent gene regulation, RNA-seq analysis was conducted and the differently expressed genes were revealed in the IRF2BP2-knockdown J.gamma1 cells in comparison to control group. Cleavage Under Targets and Tagmentation (CUT&Tag) showed the co-localization of IRF2BP2 with several master transcription factors on chromatin in J.gamma1 cells.

overall_design: CUT&Tag using antibody against IRF2BP2, RUNX1, ERG, ELF1 and ETS1 in J.gamma1 cells.

first: Juanjuan

last: Yu

first: Shaoyan

last: Hu

first: Jian

last: Pan


title: Effects of RG2833 (HDAC1/3 Inhibitor) on the gene expression of Male and Female TgF344 Alzheimer’s disease Rat model.


title: Predicting modulaters of TE-driven chromatin 3D structure

city: Shenzhen

first: Andrew

middle: P

last: Hutchins

address: 1088 Xueyuan Rd

department: Bioinformatics

institute: Southern University of Science and Technology


title: Identification of Notch ligand useage by splenic B cells using Dll1 and Dll4 Notch ligand blockade.

status: Public on Oct 18 2024

city: Philadelphia

first: Brian

middle: Thomas

last: Gaudette

state: PA

address: 3620 Hamilton Walk, Pathology and Laboratory Medicine

department: Pathology and Lab Medicine

institute: University of Pennsylvania

summary: Marginal zone (MZ) B cells leverage Notch2 signals to attain rapid differentiation responses and positional cues with in the spenic environment.To determine the likely molecular source of Notch2 signals we sought to block the Notch ligands delta-like ligand 1 (Dll1) and delta-like ligand 4 (Dll4) in wildtype mice using in-vivo treatment with monoclonal blocking antibodies. Splenic populations of MZ B cells and follicular B cells were sort purified after 12, 24 and 48 hours of blockade and analyzed by RNA-seq.

overall_design: C57BL/6 (10-12 weeks of age) were treated with anti-Dll1, anti-Dll4  blocking antibodies or isotype control antibodies for 12-48 hours prior to sacrifice. Marginal zone B cells (CD19+, CD93-, CD1d+, CD23-) and follicular B cells (CD19+, CD93-, CD1d-, CD23+) were purified by FACS sorting and RNA-sequencing library generation.

first: Anneka

last: Allman

middle: T

first: David

first: Ivan

last: Maillard


title: Marginal zone B cells receive robust Notch2 signals within the B cell follicle in the absense of S1pr1 signaling.

summary: Marginal zone (MZ) B cells have innate-like response characteristics due to a unique ability receive and integrate Notch2 signals in the spleen. There is evidence showing MZ B cells receive these signals both in the marginal sinus and the B cell follicle. The relative strength and conservation of these Notch signals is not yet clear. Therefore, we generated mice in which S1pr1 is deleted in mature B cells. These mice have MZ B cells by phenotype but these cells are retained in the follicle and unable to transit to the marginal zone. In this experiment we examined the impact of Notch2 signaling in these cells and cre expressing control animals using in vivo anti-Notch2 antibody blockade followed by RNA-sequencing.

overall_design: S1pr1-floxed mice were mated to Mb1cre mice to conditionally delete S1pr1 in B cells. S1pr1 conditional knockout (S1pr1FL/FL.Mb1Cre/+ mice and S1pr1+/+.Mb1Cre/+  control animals were treated with anti-Notch2 blocking antibodies or isotype control antibodies for 48 or 96 hours prior to sacrifice. Marginal zone B cells (CD19+, CD93-, CD1d+, CD23-) and follicular B cells (CD19+, CD93-, CD1d-, CD23+) were purified by FACS sorting and RNA-sequencing library generation.


title: Splenic fibroblasts control marginal zone B-cell movement and function via two distinct Notch2-dependent regulatory programs

overall_design: Refer to individual Series


title: Identification of Myc-dependent and -independent Notch2 signatures in marginal zone B cells.

summary: Marginal zone (MZ) B cells leverage Notch2 signals to attain rapid differentiation responses and positional cues with in the spenic environment. While it is known that a major player in Notch2 signaling in MZ B cells is the proto-oncogene Myc, it is not clear to what extent MZ B cells use Notch2 signals in Myc-independent manner. In this study we conditinally and inducibly deleted Myc in mature B cells and then used in vivo delivery of anti-Notch2 antibodies to separated Myc-dependent and -independent Notch2 signaling in MZ B cells.

overall_design: Myc-floxed mice were mated to hCD20Tam-Cre mice to conditionally and inducibly delete Myc in B cells following tamoxifen treatment. Myc conditional knockout (MycFL/FL.hCD20Tam-Cre mice and Myc+/+.hCD20Tam-Cre  control animals were fed tamoxifen in their diet for 4 weeks and then treated with anti-Notch2 blocking antibodies or isotype control antibodies for 24 hours prior to sacrifice. Marginal zone B cells (CD19+, CD93-, CD1d+, CD23-) and follicular B cells (CD19+, CD93-, CD1d-, CD23+) were purified by FACS sorting and RNA-sequencing library generation.


title: Spatially defined multicellular functional units in colorectal cancer revealed from single cell and spatial transcriptomics - scRNAseq v2

city: Cambridge

first: Simon

last: Mages

address: 415 Main St.

institute: Broad Institute

summary: While advances in single cell genomics have helped to chart the cellular components of tumor ecosystems, it has been more challenging to characterize their specific spatial organization and functional interactions. Here, we combine single cell RNA-seq, spatial transcriptomics by Slide-seq, and in situ multiplex RNA analysis, to create a detailed spatial map of healthy and dysplastic colon cellular ecosystems and their association with disease progression. We profiled inducible genetic CRC mouse models that recapitulate key features of human CRC, assigned cell types and epithelial expression programs to spatial tissue locations in tumors, and computationally used them to identify the regional features spanning different cells in the same spatial niche. We find that tumors were organized in cellular neighborhoods, each with a distinct composition of cell subtypes, expression programs, and local cellular interactions. Comparing to scRNA-seq and Slide-seq data from human CRC, we find that both cell composition and layout features were conserved between the species, with mouse neighborhoods correlating with malignancy and clinical outcome in human patient tumors, highlighting the relevance of our findings to human disease. Our work offers a comprehensive framework that is applicable across various tissues, tumors, and disease conditions, with tools for the extrapolation of findings from experimental mouse models to human diseases.

overall_design: Single-cell suspensions from healthy colon or dysplastic lesions were processed to generate single cell suspensions. All cell suspensions were counted to achieve a uniform concentration of 7,000 cells per microliter for capture by 10x Chromium controller following the manufacturer protocol for the v2 3’ kit (10X Genomics, Pleasanton, CA).

first: Inbal

last: Avraham-Davidi

first: Leah

last: Caplan

first: Danielle

last: Dionne

first: Toni

last: Delorey


title: Land plant-specific H3K27 methyltransferases ATXR5 and ATXR6 control plant development and stress responses [H3K27me3 ChIP-seq]

first: Xiaoyi

last: Li

overall_design: The deposition of H3K27me1 by ATXR5/6 is considered replication coupled. Similarly, the maintenance of another repressive histone mark, H3K27me3, is also closely linked with DNA replication. It has been proposed that H3K27me1 deposition might facilitate the restoration of H3K27me3 after DNA replication. To assess the requirement of ATXR5/6 in H3K27me3 maintenance, we performed ChIP-seq to examine H3K27me3 profiles in WT and atxr5;atxr5;atxr6hyp;atxr6c-1

first: Danhua

last: Jiang

first: Jie


title: Transcriptional response of the cacao pathogen Moniliophthora perniciosa to a strobilurin fungicide

city: Piracicaba

first: Paulo

last: Teixeira

state: SP

address: Av. Pádua Dias, 11

country: Brazil

institute: University of São Paulo (ESALQ/USP)

summary: Witches' broom disease (WBD) is a major constraint for cacao production in the Americas. The severe socioeconomic impact of WBD encouraged the evaluation of different control strategies, including the use of strobilurin fungicides. These molecules inhibit mitochondrial respiration, thus impairing ATP generation and leading to oxidative stress. These chemicals, however, have proven ineffective against the WBD pathogen Moniliophthora perniciosa. Here, we demonstrate that M. perniciosa tolerates high concentrations of strobilurins under in vitro conditions and highlight a set of molecular alterations that correlate with strobilurin tolerance in this fungus. Short-term exposure of M. perniciosa to the commercial strobilurin azoxystrobin led to the up-regulation of genes encoding enzymes of the glyoxylate cycle, gluconeogenesis, and fatty acid and amino acid catabolism, indicating that the fungal metabolism is remodeled to compensate for reduced ATP production. Furthermore, cell division, ribosome biogenesis, and sterol metabolism were repressed, which agrees with the impaired mycelial growth on azoxystrobin. Genes associated with cellular detoxification and response to oxidative stress (e.g., cytochrome P450s, membrane transporters and glutathione s-transferases) were strongly induced by the drug and represent potential strategies used by the pathogen to mitigate the toxic effects of the fungicide. Remarkably, exposure of M. perniciosa to azoxystrobin resulted in the spontaneous generation of a mutant with increased resistance to strobilurin. Comparative genomics and transcriptomics revealed alterations that may explain the resistance phenotype, including a large deletion in a putative transcriptional regulator and significant changes in the mutant transcriptome. Overall, this work provides important advances towards a comprehensive understanding of the molecular basis of strobilurin resistance in a tropical fungal pathogen. This is a fundamental step to efficiently employ these fungicides in agriculture and to prevent the emergence of strobilurin resistance.

overall_design: We evaluated the early effects of azoxystrobin on the M. perniciosa transcriptome through a time-course experiment spanning the first eight hours of exposure to the fungicide. Three biological replicates of each M. perniciosa isolate (FA553 and its derivatives FDS01 and FDS02) were cultivated separately in MYEA medium for 28 days. Fungal mycelia were then transferred to liquid cultures and incubated at 28oC under 150 rpm agitation. After seven days, two grams of wet mycelium were transferred to 20 mL of Malt light liquid medium, either without fungicide (control condition) or supplemented with 50 mg/L azoxystrobin (treated condition). Samples were harvested for RNA extraction at five time points: 0 minutes (i.e., immediately after fungal inoculation into the culture media), 30 minutes, 2 hours, 4 hours, and 8 hours.

first: Paula

last: Prado

first: Daniela

last: Thomazella


title: IRF2BP2 affects T-ALL cell proliferation by cooperating with master transcription factors

first: Zimu

last: Zhang

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


title: Spatially defined multicellular functional units in colorectal cancer revealed from single cell and spatial transcriptomics - scRNAseq v3 with cell multiplexing

overall_design: Single-cell suspensions from healthy colon or dysplastic lesions were processed to generate single cell suspensions. All cell suspensions were counted to achieve a uniform concentration of 7,000 cells per microliter  before pooling for capture  by 10x Chromium controller following the manufacturer protocol for the v3 3’ kit (10X Genomics, Pleasanton, CA). antibody_index_XXX.csv gives the mapping from HTOs to samples


title: Spatially defined multicellular functional units in colorectal cancer revealed from single cell and spatial transcriptomics - scRNAseq v2 with cell multiplexing

overall_design: Single-cell suspensions from healthy colon or dysplastic lesions were processed to generate single cell suspensions. All cell suspensions were counted to achieve a uniform concentration of 7,000 cells per microliter  before pooling for capture  by 10x Chromium controller following the manufacturer protocol for the v2 3’ kit (10X Genomics, Pleasanton, CA). antibody_index_XXX.csv gives the mapping from HTOs to samples


title: Centralized control of dynamic gene regulatory circuits governs human T cell rest and activation [CRISPR_Screens]

status: Public on Oct 15 2024

city: San Francisco

first: Alexander

last: Marson

address: 1650 Owens St

institute: UCSF Gladstone Institutes

summary: The ability of individual cells to maintain a distinct identity and respond to transient environmental signals requires tightly controlled regulation of gene networks. However, how discrete sets of gene regulators coordinate circuits that respond to extracellular cues remains poorly defined. The need for context-dependent regulation is prominent in human CD4+ T cells, where distinct cell lineages must respond to diverse signals to orchestrate effective adaptive immune responses and maintain homeostasis. Here, we performed CRISPR screens in multiple primary human CD4+ T cell contexts to identify regulators that control expression of IL2RA, which is a canonical marker of T cell activation in pro-inflammatory effector T cells (Teffs) and constitutively expressed in anti-inflammatory regulatory T cells (Tregs) where it is required for fitness. Strikingly, the majority of identified regulators are required in discrete cell type and stimulation timepoints, and a subset even had opposite functional effects in different conditions. Using single-cell transcriptomics after pooled perturbation of context-specific screen hits, we characterized specific factors as regulators of overall rest or activation and constructed state-specific regulatory networks. Upstream of these networks, MED12 – a component of the Mediator complex – serves as a dynamic orchestrator of regulators across conditions, governing both cell type- and stimulation-specific gene expression. MED12 interacts with the histone modifying complex COMPASS, affecting chromatin state and expression of genes encoding key context- and lineage-specific regulators; including rest maintenance factor KLF2 and activation promoting genes. We demonstrated that CRISPR ablation of MED12 blunted this cell state transition and protected T cells from activation-induced cell death. Overall, this work leverages CRISPR screens performed across primary cell conditions to identify context-specific regulators and dynamic gene circuits required to establish resting and activated T cell states.

overall_design: Pooled CRISPR KO screens for IL2RA. Screens were performed using a library targeting trans regulators and immune genes in CD4+ T cell subsets.

first: Maya

last: Arce

first: Jennifer

last: Umhoefer

first: Nadia

last: Arang

first: Sivakanthan

last: Kasinathan

first: Jacob

middle: W

last: Freimer

first: Zachary

last: Steinhart

first: Haolin

last: Shen

first: Minh

last: Pham

first: Mineto

last: Ota

first: Anika

last: Wadhera

first: Dmytro

last: Dorovskyi

first: Yuan

last: Zhou

first: Dajani

last: Rama

first: Yan

last: Chen

first: Qi

last: Liu

last: Shy

first: Ansuman

last: Satpathy

first: Julia

last: Carnevale

first: Nevan

middle: J

last: Krogan

first: Jonathan

middle: K

last: Pritchard


title: TAZ-mediated enhancement of adipogenesis in goat adipose mesenchymal stem cells induced by TNF-α

status: Public on Oct 17 2024

city: Hohhot

first: Dongjun

state: Inner Mongolia

address: 235 Daxue west road  Saihan District

institute: Inner Mongolia University

summary: Obesity is a clinical condition characterised by a chronic, low-grade inflammatory state. Adipose-derived mesenchymal stem cells (ADSCs) have a multidirectional differentiation potential to adipocytes. However, the relationship between adipogenesis and inflammation is not yet fully understood.TAZ (WW domain containing transcription regulator 1) can act as a molecular rheostat to fine-tune the osteoblast and adipocyte differentiation balance. In this study, we investigated the role of TAZ in the adipogenesis of Arbas cashmere goat ADSCs (gADSCs). We observed elevated TAZ expression levels during the adipogenesis of gADSCs. Overexpression and knockdown of TAZ were performed in stably transfected gADSCs cell lines, and RNA-seq analysis revealed that TAZ was associated with adipogenesis. TAZ overexpression promoted adipose differentiation of gADSCs, while TAZ knockdown had the opposite effect. In addition, TAZ overexpression and knockdown altered the expression of YAP1 (Yes1 associated transcriptional regulator) and TAZ in the nucleus. TAZ regulated the mRNA expression level and secretion level of tumor necrosis factor (TNF)-α, promoting adipose differentiation of gADSCs. Notably, TNF-α counteracted the inhibitory effect of sh-TAZ on the adipose differentiation of gADSCs. Collectively, these findings suggest that TAZ regulates adipogenesis in gADSCs by modulating TNF-α, which is of particular significance in several metabolic disorders where the amount or function of adipose tissue is altered.

overall_design: To investigate the effect of TAZ on adipogenesis of gADSCs, we constructed gADSCs cell lines OE-TAZ. RNA-seq was performed with OE-TAZ and Control cells. Based on the RNA-seq data, an expression profile was generated.


title: Centralized control of dynamic gene regulatory circuits governs human T cell rest and activation [Perturb-CITE-seq]

first: Alexander

last: Marson

overall_design: Perturb-CITE-seq performed with 2 donors including resting and stimulated CD4+ Tregs and Teffs

first: Maya

last: Arce

first: Jennifer

last: Umhoefer

first: Nadia

last: Arang

first: Sivakanthan

last: Kasinathan

first: Minh T.N

first: Yan Yi

first: Brian


title: Whole-genome bisulfite sequencing in the whole blood of three dog breeds

city: Fujimino

first: Miyuki

last: Nakamura

state: Saitama

country: Japan

institute: KDDI research Inc

type: Methylation profiling by high throughput sequencing

summary: DNA methylation patterns reflect the status of individual tissues, such as cell composition, age, and the local environment in mammals.  This experiment addressed the DNA methylation landscape in the dog genome across three breeds: Shiba, Dachshund (Miniature), and Poodle (Toy).  A comprehensive profile of whole-genome DNA methylation from the whole blood of three dog breeds was generated using whole-genome bisulfite sequencing.

overall_design: Whole-genome bisulfite sequencing was performed with whole blood obtained from nineteen individual dogs across three breeds: Shiba, Dachshund (Miniature), and Poodle (Toy).


title: Centralized control of dynamic gene regulatory circuits governs human T cell rest and activation [ChIPseq_MED12_RNAPol_CXXC1]

overall_design: ChIPseq experiment comparing changes in Teff after MED12 KO compared to AAVS1 KO control samples. Each assay was performed for resting and stimulated Teffs from two human donors.

first: Jacob

last: Freimer

first: Zachary

last: Steinhart

first: Haolin

last: Shen

first: Minh

last: Pham

first: Mineto

last: Ota

first: Anika

last: Wadhera

first: Dmytro

first: Yuan

first: Dajani


title: Spatially defined multicellular functional units in colorectal cancer revealed from single cell and spatial transcriptomics - Slide-Seq

first: Simon

last: Mages

overall_design: Mouse colons were flashed with cold PBS and a segment that includes the lesion and surrounding tissue (or a respective healthy segment from normal mice) was dissected. Samples were then mounted in cold OCT, flash frozen on dry ice covered with ETOH until and long-term stored in -80℃. 10microm sections were cut and the Slide-seq V2 protocol was used as previously described. Four and six arrays were collected from normal colons and premalignant lesions respectively. The muscularis was fit onto the array of both healthy and dysplastic lesions to allow appropriate orientation.

first: Inbal

last: Avraham-Davidi

first: Leah

last: Caplan

first: Evan

last: Murray


title: Centralized control of dynamic gene regulatory circuits governs human T cell rest and activation [Bulk_RNA]

first: Alexander

overall_design: Bulk RNAseq performed on resting and stimulated CD4+ Tregs and Teffs following arrayed CRISPR KO of Mediator complex subunits.

first: Maya

first: Jennifer

first: Nadia

first: Sivakanthan

last: Dorovskyi

last: Zhou

last: Rama

first: Yan

last: Chen

first: Qi

last: Liu

last: Shy

first: Ansuman

last: Satpathy

first: Julia

last: Carnevale

first: Nevan

last: Krogan

first: Jonathan

last: Pritchard


title: RNA sequencing of distinct histologic regions of primary human hepatoblastomas by Smart-3SEQ

status: Public on Oct 13 2024

city: Cincinnati

first: Peng

middle: Vijaykumar

last: Wu

state: OH

address: 3333 Burnet Ave., MLC7013

institute: Cincinnati Children's Hospital Medical Center

summary: To characterize histology-based transcriptional heterogeneity of human hepatoblastoma, Smart-3SEQ was used to perform RNA sequencing of distinct histologic regions isolated by laser capture microdissection from formalin-fixed paraffin-embedded primary human hepatoblastoma specimens.

overall_design: RNA sequencing was performed on 74 distinct histologic regions isolated by laser capture microdissection from 17 FFPE primary human hepatoblastoma specimens

first: Chunfang

last: Zhu

first: Sujay

last: Vennam

first: Robert

last: West

first: Roel

last: Nusse


title: Centralized control of dynamic gene regulatory circuits governs human T cell rest and activation [MED12_KO_CUTnRUN_H3K4]

last: Marson

overall_design: CUT&RUN experiment comparing changes in Teff after MED12 KO compared to AAVS1 KO control samples or kinase inhibitor treatment (SEL120-24A) compared to H2O control treatment. Each assay was performed for resting and stimulated Teffs from three human donors.

last: Arce

last: Umhoefer

last: Arang

last: Kasinathan

first: Jacob

last: Freimer

first: Zachary

last: Steinhart

first: Haolin

last: Shen

first: Minh

last: Pham

first: Mineto

last: Ota

first: Anika

last: Wadhera

first: Dmytro

first: Yuan

first: Dajani

first: Brian

middle: R


title: Centralized control of dynamic gene regulatory circuits governs human T cell rest and activation [H3K27ac_CUTnRUN]

first: Alexander

summary: The ability of individual cells to maintain a distinct identity and respond to transient environmental signals requires tightly controlled regulation of gene networks. However, how discrete sets of nuclear regulators coordinate dynamic circuits that respond to extracellular cues remains poorly defined. This is prominent in CD4+ T cells, where cells must respond to diverse immunogenic signals to orchestrate effective adaptive immune responses and maintain immune homeostasis. Here, we performed CRISPR screens in multiple primary human CD4+ T cell contexts to identify nuclear regulators that control expression of IL2RA, a canonical marker of T cell activation that is differentially regulated between pro-inflammatory effector T cells and anti-inflammatory regulatory T cells. Strikingly, we discovered that the majority of identified regulators function within discrete cell type and stimulation timepoints, and a subset even had opposite effects across conditions. Using single-cell transcriptomics and surface proteomics after pooled perturbation of context specific screen hits, we characterized many factors as regulators of overall rest or activation and constructed state-specific regulatory networks. KLF2, MYB, and SOCS3 were distinguished as interconnected repressors of activation in resting T cells while GATA3 and MYC are required for proper stimulation response. Upstream of these circuits, MED12 – a component of the Mediator complex – serves as a dynamic orchestrator of trans regulators across conditions, governing both cell type and stimulation specific gene expression. Chromatin analysis revealed how MED12 coordinates key regulators as T cells transition to and from rest and activation. We demonstrated that CRISPR ablation of MED12 blunted this transition and protected T cells from activation-induced cell death.

overall_design: H3K27ac CUT&RUN for CRISPR KO primary human CD4+ Teffs and CD4+ Tregs. Samples include both resting and stimulated Teffs and Tregs.  AAVS1 KOs samples serve as wild-type controls for the dataset.

first: Maya

middle: M

first: Jennifer

last: Dorovskyi

first: Yan

last: Chen

first: Qi

last: Liu

last: Shy

first: Julia

last: Carnevale

last: Pritchard


title: Spatially defined multicellular functional units in colorectal cancer revealed from single cell and spatial transcriptomics

first: Simon

last: Mages

overall_design: Refer to individual Series


title: Centralized control of dynamic gene regulatory circuits governs human T cell rest and activation

status: Public on Oct 14 2024

last: Marson


title: Transcriptome RNA Sequencing Data Set of Differential Gene Expression in Salmonella enterica serovar Typhimurium 14028S within Acanthamoeba castellanii, and under Oxidative and Starvation Stress Conditions

status: Public on Oct 10 2024

city: Orenburg

last: Balkin

address: 11 Pionerskaya st.

institute: Institute for Cellular and Intracellular Symbiosis

summary: Here we present high-resolution transcriptomic data on Salmonella gene expression under optimal, starvation and hydrogen peroxide conditions, and after 8 and 15 hours of co-culture with A. Castellanii.

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

overall_design: To assess changes in global Salmonella gene expression during long-term infection of amoebae, we performed RNA sequencing of total Salmonella RNA within A. castellanii at late stages of infection (8 h and 15 h) and also compared three free-living cultures grown under different conditions, including rich medium (LB), poor medium (PAS), and exposure to hydrogen peroxide.

first: Yuri

last: Gogolev


title: PDGF-BB overexpression in p53 null oligodendrocyte progenitors increases H3K27me3 and induces transcriptional changes which favor proliferation

status: Public on Oct 08 2024

first: Patrizia

last: Casaccia

address: 85 St Nicholas Terrace

department: Neuroscience

institute: ASRC-CUNY

summary: Proneural gliomas are aggressive brain tumors characterized by enrichment of oligodendrocyte progenitor cell (OPC) transcripts and genetic alterations. In this study we sought to identify transcriptional and epigenetic differences between OPCs with Trp53 deletion and PDGF-BB overexpression (BB-p53n), which form aggressive gliomas when transplanted in mouse brains, and those carrying only p53 deletion (p53n), which do not. We used unbiased histone proteomics and RNA-seq analysis on these two OPC populations and detected higher levels of H3K27me3 in BB-p53n compared to p53n OPCs. The BB-p53n OPC were characterized by higher levels of transcripts related to proliferation and lower levels of those related to differentiation. Pharmacological inhibition of histone H3K27 trimethylation in BB-p53n OPC reduced cell cycle transcripts and increased the expression of differentiation markers. These data suggest that PDGF-BB overexpression in p53 null OPC results in histone post-translational modifications and consequent transcriptional changes favoring proliferation while halting differentiation, thereby promoting the early stages of transformation.

overall_design: To investigate the effects of PDGF-BB expression in p53 null primary OPCs. Separately to investigate the effects of EZH2 inhibition on p53 null PDGF-BB expressing primary OPCs

first: Huang

last: Dennis

first: Mela

last: Angeliki

first: Canoll

last: Peter

first: Casaccia

last: Patrizia


title: Single cell RNA-sequence reveals the transcriptional dynamics of tumor immune micrenvironment by LDHA inhibition in cancer cells

status: Public on Oct 09 2024

city: Fukuoka

first: Chikanori

last: Tsutsumi

address: 3-1-1 Maidashi, Higashi-ku

department: Department of Surgery and Oncology, Graduate School of Medical Sciences

institute: Kyushu University

summary: In this study, we investigeted the impact of LDHA inhibition in cancer cell on the tumor immune microenvironment (TIME) of orthotopic syngeneic PDAC tumors. Our results indicate that the TME with high-glucose and low-lactate can promote the antigen-presenting function of DCs and enhance the activity of CD8+ T cells.

overall_design: 1 sample integrated from 5 orthotopic syngeneic PDAC tumors transplanted KPC shNC. 1 sample integrated from 5 orthotopic syngeneic PDAC tumors transplanted KPC shLDHA.

first: Bo

last: Zhang

first: Kenoki

last: Ohuchida


title: RNA Infrastructure Profiling Illuminates Transcriptome Structure in Crowded Spaces

status: Public on Oct 12 2024

city: Stanford

first: Lu

last: Xiao

state: California

address: 369 N-S Axis, Stauffer I, 109

institute: Stanford University

summary: The cellular function of RNA is intimately linked to its structure. The 3D structure of RNA is intricate and compact, and is often complexed with other macromolecules for regulatory interaction. These interactions frequently lead to occluded environments that block structure probing by current reagents. Our RNA infrastructure profiling method (RISP) quantitatively compares standard acylation probes to new small-sized probes, and reveals ca. 80% more structural data for intracellular RNAs underlying protein contacts. Comparative analysis also reveals information about close contacts in ribonucleoprotein complexes such as small nuclear RNAs in the spliceosome. In addition, RISP analysis with small agent AcIm reveals pronounced signals for m6A methylation sites of RNAs in their native cellular setting, even in crowded environments.

overall_design: The sequencing experiments were performed in two biological replicates. Comparative analysis of deep sequencing data using our RBRP popeline with certain adjustment identifies structure information in crowded space.

first: Eric

last: Kool


title: The grass–microbiome-rumen axis in grazing sheep farming intervened by supplementary feeding

city: Beijing

first: hua

middle: xiu

last: ma

address: NO.2 Yuanmingyuan weat road

institute: China Agriclutural university

summary: This study identifies key microbiome and epithelial cell subtypes involved in grass digestion and VFA metabolism in the rumen. By integrating multi-omic data, we reveal novel links between microbial activity, epithelial cell function, and grassland foraging, providing critical insights into mechanisms underlying grass prevalence and their implications for optimizing ruminant health and productivity. This research enhances our understanding of the grass-microbiome- rumen axis and its role in sustainable grazing systems.

overall_design: we selected six lambs using scRNAseg,  tissues were collected from the ven_x0002_tral sac region of the rumen.


title: N-Palmitoylglycine activates transient receptor potential channel 5 and increases the risk of Brugada syndrome

status: Public on Oct 05 2024

first: Hongxuan

last: Xu

address: No.8 Xishiku Street

department: Cardiology

institute: Peking university first hospital

summary: Brugada syndrome (BrS) is an arrhythmic disorder associated with an increased risk of sudden cardiac death; however, current treatment options are limited due to their side effects and variable efficacy. In this study, we employed Mendelian randomization analysis utilizing proteomic, transcriptomic, and metabolomic data to identify potential therapeutic targets for BrS. Our findings indicate that N-palmitoylglycine (PalGly) is linked to an increased risk of BrS and interacts with BrS-associated proteins, demonstrating moderate binding affinities for proteins such as DCC, CR1, CTSB, NAAA, DEFB1, EPHA1, IGF1/IGFBP3/ALS, and LTA. Although PalGly does not interact with Nav1.5, it enhances calcium sparks in ventricular cardiomyocytes. We determined that the calcium-modulating effect of PalGly is mediated by its binding to and activation of the transient receptor potential channel 5 (TRPC5) channel. Furthermore, PalGly was found to shorten the QT interval and action potential duration in Langendorff-perfused rabbit hearts and ventricular cardiomyocytes. Transcriptomic and lipidomic analyses of PalGly-treated neonatal rat cardiomyocytes revealed significant modulation of immune pathways, akin to the effects observed with TRPC5 agonists. Collectively, our study underscores the involvement of PalGly and TRPC5 in the pathophysiology of BrS.

overall_design: To investigate the cardiac effect of N-palmitoylglycine, we extracted neonatal rat cardiomyocytes and stimulated these cells with 1 μM N-palmitoylglycine 24h hours.

first: Bingxun

last: Li

first: Lin

last: Wu


title: Analysis of gene expression in Mel Z cells grown on plastic (MP).

city: Moscow

first: Nickolai

last: Tchurikov

address: 32, Vavilova str.

department: Department of Epigenetic Mechanisms of Gene Expression Regulation

institute: Engelhardt Institute of Molecular Biology

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

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

middle: A

last: Kravatsky

first: Amalia

last: Vartanian


title: Comprehensive transcriptome characterization deciphers mechanisms underpinning the positive selection of B cells in germinal centers.

status: Public on Oct 04 2024

first: Louise

last: Matheson

address: Babraham Research Campus

department: Laboratory of Lymphocyte Signalling and Development

country: United Kingdom

institute: The Babraham Institute


title: Environmental dose of Bisphenol S exposure to brown adipose tissue accelerates aging

status: Public on Sep 20 2024

city: Chengdu

first: Man

last: Zhu

state: Sichuan

address: No. 4, Section 2, Jianshe North Road, Chenghua District, Chengdu City, Sichuan, China

department: School of Medicine

institute: University of Electronic Science and Technology of China

summary: Bisphenol S (BPS), a common industrial chemical, is increasingly recognized for its potential to disrupt physiological functions even at environmental doses. In this study, we investigated the effects of BPS exposure on lifespan and health span using Caenorhabditis elegans and mouse models. We found that BPS accumulates in brown adipose tissue (BAT), inducing BAT aging by triggering mitochondrial dysfunction, chronic inflammation, altered intercellular communication, cellular senescence, deregulated nutrient-sensing pathways, impaired macroautophagy, and loss of proteostasis. These changes accelerated aging in multiple organs, including the heart, liver, kidneys, lungs, and skeletal muscle. Notably, BAT transplantation experiments revealed that BAT from BPS-exposed mice induced accelerated aging in non-exposed mice, while BAT from non-exposed mice mitigated aging in BPS-exposed mice. In summary, this study is the first to demonstrate that environmental doses of BPS promote systemic aging by disrupting BAT energy metabolism.

overall_design: Transcriptome sequencing was conducted on total RNA extracted from BAT tissues of mice (veh group: n=8; BPS group: n=7), using the NovaSeq 6000 platform (Illumina) at the Beijing Genomic Institution (BGI, China).

first: Xue

last: Wen


title: Molecular Profiling Reveals Immunosuppressive Tumor Immune Microenvironment in Primary versus Paired Asynchronous Metastatic Clear Cell Renal Cell Carcinoma

status: Public on Sep 27 2024

city: Ann Arbor

first: Simpa

last: Salami

state: MI

address: 1500 E Medical Center Dr

department: Urology

institute: University of Michigan

summary: Clear cell renal cell carcinoma (ccRCC) is a highly immune infiltrated cancer, but how the tumor immune microenvironment (TIME) evolves during disease progression is unknown. Insights into heterogeneity within primary ccRCC raise questions about potential heterogeneity between primary and paired metastatic tumors. This information may improve understanding of immune evasion leading to metastatic disease and response to immunotherapy. In this study, we characterize and compare the TIME of primary ccRCC with paired asynchronous metastases. We demonstrate higher infiltration of immunosuppressive cells in the TIME of primary ccRCC compared with metastatic sites. Further studies are necessary to determine the prognostic and therapeutic significance of these findings. Understanding the heterogeneity of the tumor immune microenvironment in RCC, both intratumorally and between metastatic sites, has important clinical implications for selecting appropriate therapies and developing predictive biomarkers. Future research should focus on elucidating the impact of these findings on immunotherapeutic responses and patient outcomes in ccRCC.

overall_design: Analysis of ccRCC patients who developed recurrence post radical nephrectomy and had both primary and metastatic tissue available. Whole-transcriptome sequencing was performed on formalin-fixed paraffin-embedded (FFPE) specimens using the illumina platform. Differential expression gene (DEG) analysis was performed using R package edgeR. Gene set enrichment analyses (GSEA) to identify hallmark pathway enrichment was performed using R package fgsea. TIME deconvolution was quantified using CIBEROSRT, an in silico flow cytometry tool.

first: Brittney

middle: H

last: Cotta

first: Srinivas

last: Nallandhighal

first: Zayne

last: Knuth

first: Nathan

last: Graham

first: Yuping

first: Rui

last: Wang

first: Amy

last: Kasputis

first: Xuhong

last: Cao

first: Aaron

last: Udager

first: Saravana

last: Dhanasekaran

first: Ganesh

last: Palapattu

first: Rohit

last: Mehra

first: Marcin

last: Cieslik

first: Todd

last: Morgan


title: Responses of grapevine cells to physiological doses of ethanol, among which induced resistance to heat stress

city: Castanet-Tolosan

first: Alice

last: DIOT

state: Occitanie

address: 24 Chem. de Borde Rouge

institute: LRSV

summary: Grapevine is a plant of agronomic interest, which is able to cope with several stresses: heat, drought, and hypoxia, among others. A recent study showed very low oxygen levels inside grape berries, linked to ethanol content. Other studies have established the link between ethanol and tolerance to various stresses: heat stress, drought, and high salinity. The causes of such tolerance induced by ethanol are not well understood. In our study, three-week-old Gamay calli were characterised for their endogenous O2 levels (78 ± 43 µM at 2.1 mm inside the callus) and endogenous ethanol concentration (406 ± 2 µM). Subsequently, a transcriptomic study of these cells was conducted, at 6 and 24 hours post-treatment with 1 mM ethanol. After 6 hours post-treatment, ethanol addition led to 386 Differentially Expressed Genes (DEGs) compared to the controls. Analyses of the gene classes modulated by ethanol showed that many genes involved in heat response were up-regulated, notably the small Heat Shock Proteins (sHSP). Next, we showed that grape cells primed with ethanol experienced less pigment leakage due to heat stress compared to the controls. This result was further supported by a similar observation in Arabidopsis seedlings, for which heat stress-induced electrolyte leakage was reduced by ethanol priming. his study confirms previous observations regarding the beneficial role of ethanol priming in protecting plants against heat stress and provides a comprehensive set of RNA-seq data to further decipher the mechanisms involved in such adaptation. The small heat shock proteins seem involved in this chemical priming response.

overall_design:
To identify the molecular pathways differentially regulated by a physiological dose of ethanol in Vitis vinifera (cv. Gamay Fréaux var. Teinturier) cell cultures, we carried out a genome-wide transcriptomic analysis by RNA-seq.
RNA was extracted from grapevine calli treated with 100 µL of either a 1 mM ethanol solution or a control solution. Prior to treatment, the grapevine cell cultures were grown for three weeks under controlled conditions, with a 16-hour day/8-hour night photoperiod, temperatures of 25°C during the day and 20°C at night, and a light intensity of 150 μmol/m²/s. Samples were collected at either 6 or 24 hours after the control or ethanol treatment.

last: Diot

first: Guillaume

last: Madignier

first: Ellie

last: Maza

first: Anis

last: Djari

first: DiValentin

last: Olivia

first: Chen

last: Yi

first: Blanchet

last: Simon

first: Christian

last: Chervin


title: Transcriptomic profiling of antibiotic-resistant Salmonella Heidelberg in the presence of commensal Escherichia coli of poultry origin

status: Public on Sep 17 2024

city: Gainesville

first: Yasir Razzaq

last: khan

state: Florida

address: 2015 SW 16th Ave

department: Large Animals Clinical Sciences

institute: university of Florida

summary: The non-typhoidal Salmonella enterica serotype Heidelberg is a major foodborne pathogen primarily transmitted to humans through contaminated poultry products. Current control measures emphasize novel approaches to mitigate Salmonella Heidelberg colonization in poultry and the contamination of poultry products, thereby reducing its transmission to humans. This study highlight that commensal E. coli 47-1826 can potentially be used to control of S. Heidelberg 18-9079 in poultry

sample_organism: Salmonella enterica subsp. enterica serovar Heidelberg

overall_design: To investigate the differential gene expression in S. Heidelberg 18-9079,  we  co-cultured the S. Heidelberg 18-9079 with E. coli 47-1826 in anaerobic environment

first: Yasir

last: Khan

first: Lekshmi

last: Edison

first: Thomas

last: Denagamage

first: Subhashinie

last: Kariyawasam


title: Immunomodulatory effects of microbiota-derived propionate in systemic lupus erythematosus

status: Public on Sep 30 2024

city: League city

first: Hui

last: Wang

state: Texas

address: 301 University Blvd.

institute: UTMB

summary: We performed RNAseq on total RNA extracted from kidney tissues from MRL-lpr micetreated with propionate and controls.We then performed differential expression analysis, meta-analysis, and gene set enrichment anaylsis using data obtained by RNA-seq of control and PA-treated mice.

overall_design: Mice were treated with PA for 6 weeks and kidney tissues were used for RNAseq.

first: Wang

last: Hui

first: M

last: Firoze Khan


title: Transcriptome expression profile from lungs of mice infected with H7N9 between control and TFF2 treatment groups

status: Public on Sep 18 2024

city: Shanghai

first: Wei

middle: hui

last: Fu

address: No. 2901 Callang Road,Jinshan District

institute: Shanghai Public Health Clinical Center

summary: To further validate the protective mechanism of TFF2 in influenza infection, we used whole genome microarray expression profiling as a discovery platform to screen and identify differentially expressed genes in host immune response. The results indicate that TFF2 downregulates the expression of NF kB signaling pathway related genes and inflammatory cytokine genes.

overall_design: 6-8 week-old female C57/BL6 mice were given TFF2 protein via aerosol inhalation 2 hours before infection, and then infected with H7N9 virus. TFF2 protein was administered again 1 and 3 days after infection. On the 1st, 3rd, and 7th day after infection, mouse lung tissues were collected and RNA was extracted. After mixing total RNA of three mice in each group, transcriptome microarray analysis was performed.

first: Weihui


title: Divergent aging of nulliparous and parous mammary glands reveals IL33+ hybrid epithelial cells

status: Public on Sep 12 2024

city: Santa Cruz

first: Paloma

last: Medina

address: 1156 High St.

institute: University of California Santa Cruz

summary: Aging increases breast cancer risk while an early first pregnancy reduces a woman’s life-long risk. While several studies have explored the effect of either aging or pregnancy on mammary stem/progenitor cells, the combined effect of both remains unclear. Here, we interrogate the functional and transcriptomic changes at single-cell resolution in the mammary gland of aged nulliparous and parous mice to discover that pregnancy normalizes age-related imbalances in lineage composition, while also inducing a differentiated cell state. Importantly, we uncover a minority population of Il33-expressing epithelial cells that express both luminal and basal markers (i.e. hybrid), which accumulate in aged nulliparous mice but are significantly reduced in aged parous mice. Functionally, IL33 treatment of mammary epithelial cells from young mice phenocopies aged nulliparous epithelial cells, induces proliferation and promotes formation of organoids with Trp53 knockdown. Collectively, our study demonstrates that pregnancy blocks the age-associated imbalances in lineage integrity in the basal layer, including a decrease in Il33+ hybrid cells, that could potentially contribute to pregnancy-induced breast cancer protection.

overall_design: We performed scRNA-seq from mammary glands of 18m NP and 18m P mice using 10x chromium scRNA-seq (n=3 mice/group) as per manufacture’s protocol using the 5’ Gene expression workflow (1 GEM per condition, 3 mice pooled in equal proportions per condition) Libraries were sequenced on the Illumina NovoSeq 6000 Platform by Medgenome, Inc. Reads were mapped to the mouse genome (mm10). Additionally, we integrated an 18m NP data set from Tabula Muris Senis. For quality control, we used Scanpy’s ‘scanpy.pp.calculate_qc_metrics’, ‘scanpy.pp.filter_genes’, and scanpy.pp.filter_cells. We applied filters to eliminate (1) genes that are detected in less than 3 cells, (2) cells that have less than 200 genes, (3) cells with gene counts < 600 or > 8,000, (4) cells with total counts of UMIs per cell < 2,000 or > 12,000, and (5) cells with mitochondrial gene ratio > 1.5%. The mitochondrial gene ratio was defined as the percentage of UMIs mapped to mitochondrial genes compared to non-mitochondrial genes within each cell; cells with a high ratio are indicative of non-viable or apoptotic cells. Doublets were identified using Scrublet, these cells were then filtered out. After filtering, the datasets were concatenated, the UMI counts for each cell were then normalized using a target sum of 1e4, and then log transformed using ‘scanpy.pp.log1p’, which computes X=log(X+1), where log denotes the natural logarithm.

first: Andrew

last: Olander

first: Veronica

last: Haro Acosta

first: Sara

last: Kaushik

first: Matijis

last: Dijkgraaf

first: Shaheen

last: Sikandar


title: Single cell RNA sequencing of primary human hepatoblastoma tumoroids

first: Peng

last: Wu

summary: Single cell RNA sequencing was used to characterize transcriptional heterogeneity of primary patient-derived hepatoblastoma tumoroids.

overall_design: Single cell RNA sequencing was performed on ten primary human hepatoblastoma tumoroids at early passage (P1-P2) using the 10x Genomics 3' platform.

middle: V

first: Roel

last: Nusse

first: Maurizio

last: Morri

first: Norma

last: Neff


title: Discovery of chromosomal inversions in the mosquito Aedes aegypti

status: Public on Sep 06 2024

city: Blacksburg

first: Maria

last: Sharakhova

state: VIRGINIA

address: 360 West Campus Drive

department: Entomology

institute: Virginia polytechnic institute and state university

summary: Chromosomal inversions play a fundamental role in evolution and have been shown to be responsible for the epidemiologically important traits in malaria mosquitoes. However, they have never been characterized in the major vector of arboviruses Aedes aegypti because of the poor structure of its polytene chromosomes. In this study, we applied a Hi-C proximity ligation approach to identify chromosomal inversions in 23 recently collected strains of Ae. aegypti from its worldwide distribution, two old laboratory colonies, and Ae. mascarensis.

sample_organism:
Aedes aegypti
Aedes mascarensis

platform_organism:
Aedes aegypti
Aedes mascarensis

overall_design: To invetigate chromosomal inversions in Ae. aegypti, we applied Hi-C to identify chromosomal inversions in 25 strains of Ae. aegypti from its world-wide distribution and Ae. mascarensis


title: Differential contribution of P73+ Cajal-Retzius cells and Reelin to cortical morphogenesis

status: Public on Sep 04 2024

city: paris

first: Frederic

last: Causeret

address: 24 bd de montparnasse

department: Imagine Institute

institute: Inserm

summary: Cajal-Retzius cells (CRs) are a peculiar neuronal type within the developing mammalian cerebral cortex. One of their best documented feature is the robust secretion of Reln, a glycoprotein essential for the establishment of cortical layers through the control of radial migration of glutamatergic neurons. Although CRs and Reln are tightly associated, a direct assessment of their relative contribution to cortical morphogenesis is still lacking. Here we took advantage of the Gmnc-/- mouse model, in which CRs are initially produced but abnormally specified and undergo early apoptosis leading to a severe depletion, to investigate the consequences of CRs loss on neocortical lamination and hippocampal morphogenesis. We then compared to the phenotype of CRs-specific conditional Reln deletion in order to evaluate the relative contribution of CRs and Reln. We found that neocortical lamination defects upon CRs depletion are relatively modest, and partially recapitulated by Reln loss. By contrast, hippocampal morphogenesis was far more affected by CRs depletion than Reln loss. In addition, we found the lateral cortex especially sensitive to CRs depletion, but not Reln loss. These data support a model whereby CRs-derived Reln and Reln-independent signals differentially contribute to the morphogenesis of distinct regions of the developing cortex.

overall_design: The forebrain of four Gmnc-/- P0 animals originating from two distinct litters and four wild-type littermates were collected. The region encompassing the lateral and dorsal cortex as well as the hippocampus was dissected on both hemispheres and samples were pooled according to their genotype. Cells were dissociated and two Next GEM Single Cell 3’ v3.1 libraries were produced (one per genotype).

first: Vicente

last: Elorriaga

first: Frédéric


title: RNA-Seq of Primary HSCs of Wild-type and Cyp1b1 Knockout Mice with Thioacetamide Treatment

city: Pittsburgh

first: Wen

last: Xie

state: Pennsylvania

address: 335 Sutherland Dr

department: Center for Pharmacogenetics and Department of Pharmaceutical Sciences

institute: University of Pittsburgh

summary: The goal of this study was to compare transcriptomes of mouse primary HSCs isolated from wild-type or Cyp1b1 knockout mice with PBS or thioacetamide (TAA) treatment.

overall_design: RNA-Seq analysis of primary HSCs isolated from wild-type or Cyp1b1 knockout mice treated with 3 doses of PBS or TAA for every 3 days.

first: Hung-Chun

last: Tung

first: Sihan

last: Li


title: Compartment-specific transcriptome of motor neurons reveals impaired extracellular matrix signaling and activated cell cycle kinases in FUS-ALS

status: Public on Sep 10 2024

city: Rostock

first: Andreas

last: Hermann

state: Mecklenburg-Western Pomerania

address: Gehlsheimer Str.20

department: Neurology

institute: University Medical Center Rostock

summary: Mutations in the gene fused-in-sarcoma (FUS) have been implicated in the motor neuron disease Amyotrophic lateral sclerosis (ALS). However, it is poorly understood how these gene mutations lead to selective motor neuron (MN) degeneration and if there are common pathomechanisms across disease etiology. To address the biological impact of the FUS-P525L mutation on the transcriptome of neurons, we applied RNA-sequencing (RNA-seq) method, using microfluidic chambers, to generate axonal as well as soma compartment specific profiles from isogenic induced pluripotent stem cells (iPSCs)-derived motor neurons. We demonstrate high purity of axonal and soma fractions, and further show that the axonal transcriptome is very specific from somas with fewer number of transcripts. Notably, functional enrichment analysis revealed a unique and distinct transcriptional landscape in both axonal and soma compartments including specific transcript types, most of which were required for RNA metabolism and DNA damage/cell cycle related processes, that were likely altered by FUS mutation. Among altered transcripts, we identified robust upregulation of polo-like kinase 1 (PLK1), a master regulator of cell cycle-related events, in FUS-P525L mutant MNs and confirmed that inhibition of PLK1 increases late apoptotic or necrosis-induced neuronal cell death in mutant neurons compared to healthy controls. Taken together, our findings provide insights into compartment-specific transcriptomics in FUS-ALS neuronal model and we propose that PLK1 activation is a consequence of MN-specific upregulation, possibly contributing to the DNA-damage response and other associated pathways including cell cycle and cytoskeleton machinery.

overall_design: Patient-derived isogenic spinal motoneurons (MNs) expressing either normal (FUS WT) or mutant P525L FUS-eGFP (FUS P525L) were matured for 14 DIV using microfluidic chambers, where somas (n=6)  and axons (n=6) were harvested and total RNA was isolated for RNA-sequencing. The main cell model used in this study were neurons derived from FUS-WT-EGFP and FUS-P525L-EGFP that were generated as a part of previous study (Naumann, Pal et al. 2018). Briefly, fibroblasts carrying R521C FUS mutation obtained from a 58-year-old female were reprogrammed into iPSC using cDNA of OCT4, SOX2, KLF4 and cMYC delivered via retroviral vectors. Next, CRISPR/Cas9 genome editing was used to i) correct the R521C mutation into WT FUS and to tag it with EGFP to generate the FUS WT EGFP line or ii) replace the R521C mutation into P525L FUS mutation and to tag it with EGFP to generate FUS P525L EGFP line. Differentiation of hiPSC into spinal motor neurons (MNs) was carried out based on the protocol from Reinhardt et al. 2013. RNA-sequencing was performed on 2 cell lines (isogenic control and FUSP525L) resulting in the following 4 groups:control somas (n=3), control axons (n=3), FUSP525L somas (n=3) and FUSP525L axons (n=3). A total of 12 samples were analyzed here.

first: Vitaly

last: Zimyanin

first: Banaja

last: Dash

last: Petzold

first: Mathias

last: Lesche


title: Type 2 Diabetes Specific Spatial Differential Gene Expression in Pancreas Visium Data

status: Public on Aug 31 2024

city: Bethesda

first: Neelam

last: Sinha

state: Maryland

address: 4998, BATTERY LN, APT 206

department: NHGRI

institute: NIH

summary: Understanding the spatial distribution of gene expression in the pancreas could provide new insights into its function and islet biology. Visium spatial gene expression is a powerful tool for quantifying gene expression of cells within their spatial context. We describe the generation and analysis of spatial transcriptomics data from six pancreas samples from healthy donors. Our analysis revealed high expression of INS within islets. However, we also identified a bleed of highly abundant islet genes (e.g., INS, GCG) into surrounding tissue areas. Through computational analyses, we successfully corrected for this bleed. We then identify genes which are spatially differentially expressed in the Type 2 Diabetes samples.  We provide these data for researchers to study the organization of the pancreas and islets.

overall_design:
human pancreatic tissue flash frozen with isopentane; tissue sections prepared and processed with the 10X Genomics Visium Spatial Gene Expression Reagent kit
>>>Raw data were deposited in dbGaP under phs001188.v3.p1 due to patient privacy concerns.<<<<

first: Lori

middle: L

last: Bonnycastle

first: Mike

last: Erdos

first: Caleb

last: Grenko

first: Zoe

last: Weiss

first: Cassie

last: Robertson

first: Narisu

last: Narisu

first: Leland

last: Taylor

first: Francis

last: Collins


title: Gene expression profile at single cell level of brain metastasis-associated astrocytes

status: Public on Aug 30 2024

city: Madrid

first: Manuel

last: Valiente

address: Melchor Fernández Almagro, 3

country: Spain

institute: CNIO

summary: We used single cell RNA sequencing (scRNA-seq) to analyze the heterogeneity of astrocytes in brain metastasis

overall_design:
Astrocytes from naive brains and brains from intracranially injected mice with B16/f10-BrM cell line were enriched in the samples using anti-ACSA2 microbeads and analyzed using scRNAseq.

UPDATE: [Jan-29-2026] The title of GSM7119480 was changed from 'Pool of 3 naive brains' to 'Pool of 3 B16/F10-BrM brains', and the title of GSM7119481 was changed from 'Pool of 3 B16/F10-BrM brains' to 'Pool of 3 naive brains'. The raw and processed data associated with the Sample records have not changed.

first: Neibla

last: Priego

first: Carolina

last: Hernández-Oliver


title: Notch signaling suppresses neuroendocrine differentiation and alters the tumor immune microenvironment in advanced prostate cancer

status: Public on Aug 28 2024

city: Boston

first: Sheng-Yu

last: Ku

state: MA

address: 44 Binney St, Dana Building, DA1422, MA 02215

department: Medical Oncology

institute: Dana Farber Cancer Institute

summary: Neuroendocrine prostate cancer (NEPC) is an aggressive, androgen-independent variant of prostate cancer (PCa) that most commonly develops in patients as a mechanism of therapeutic resistance. The underlying mechanisms driving PCa lineage plasticity and trans-differentiation to a neuroendocrine lineage are not fully understood. Here, we identify Notch signaling as a key suppressor of neuroendocrine differentiation in PCa. Restoration of Notch signaling in NEPC models results in phenotypic conversion towards a non-neuroendocrine state with expression of prostate luminal cell markers and immunologic changes including up-regulation of MHC Class I and II and type I interferon signaling that correlate with changes in the tumor immune microenvironment. Overall, these data provide new insights into how Notch signaling influences PCa lineage plasticity and points to new therapeutic avenues to modulate it.

overall_design:
To investigate the role of ASCL1 in neuroendocrine prostate cancer, we knocked out ASCL1 using CRISPR-Cas9 in NEPC organoids, WCM154, and inoculated organoids in vivo to investigate the tumor phenotype.
We performed RNA-seq on control (sgGFP) and ASCL1 knockout (sgASCL1) tumors from three independent mice per condition. Differential expresesion analysis was then performed to illuminate gene expression.

first: Kei

last: Muzino

first: Himisha

last: Beltran


title: MYC and p53 cooperate through VEGF signaling to repress cytotoxic T cell and immunotherapy responses in prostate cancer

status: Public on Aug 26 2024

city: New York

first: Yu-Jui

last: Ho

state: New York

address: 417 E 68th St

department: Cancer Biology & Genetics Program

institute: Memorial Sloan Kettering Cancer Center

summary: To study the genetic factors that influence the immune landscape of castration-resistant prostate cancer (CRPC), we utilized a flexible, electroporation-based system to introduce genetic alterations relevant to human disease directly into the prostate glands of mice. These electroporation-based genetically engineered mouse models (EPO-GEMM) recapitulate features of traditional models, and allow us to investigate distinct genetic subtypes of prostate cancer within an intact tumor-immune microenvironment. We observed differences between genetic subtypes of CRPC, with MYC-driven subtypes exhibiting a "cold" immune landscape compared to others. Interestingly, we found that the compound loss of different tumor suppressors such as Pten or p53 with MYC further impacts the inflammatory profile of prostate cancer, with MYC and p53  (MP) alterations cooperating to drive VEGF expression and immune suppression. VEGF signaling blockade resulted in re-activation of cytotoxic T cell anti-tumor immunity and restored sensitivity to immunotherapy in MP CRPC. Thus, by leveraging the power of EPO-GEMMs to generate distinct subtypes of CRPC, our studies reveal a functional role for VEGF signaling in driving prostate cancer immune evasion and validate the VEGF pathway as an actionable therapeutic target in MYC and p53 altered prostate cancer.

overall_design: For RNA-seq analysis of the transcriptional profiles of PtPRb EPO-GEMM prostate tumors, total RNA was extracted from bulk tissue using the RNeasy Mini Kit (Qiagen). Purified polyA mRNA was subsequently fragmented, and first and second strand cDNA synthesis performed using standard Illumina mRNA TruSeq library preparation protocols. Double stranded cDNA was subsequently processed for TruSeq dual-index Illumina library generation.

first: Katherine

middle: C

last: Murphy

first: Kelly

middle: D

last: DeMarco

first: Lin

last: Zhou

first: Yvette

last: Lopez

first: Yu-jui

first: Junhui

last: Li

first: Shi

last: Bai

first: Karl

last: Simin

first: Lihua

last: Zhu

first: Arthur

last: Mercurio

first: Marcus

last: Ruscetti