title: Glutamine deficiency drives transforming growth factor-β signaling activation that gives rise to myofibroblastic carcinoma-associated fibroblasts

city: Tokyo

first: Yoshihiro

last: Mezawa

institute: Juntendo University

summary: Tumor-promoting carcinoma-associated fibroblasts (CAFs), abundant in the mammary tumor microenvironment (TME), maintain transforming growth factor-β (TGF-β)-Smad2/3 signaling activation and the myofibroblastic state, the hallmark of activated fibroblasts. How myofibroblastic CAFs (myCAFs) arise in the TME and which epigenetic and metabolic alterations underlie activated fibroblastic phenotypes remain, however, poorly understood. We herein show global histone deacetylation in myCAFs present in tumors to be significantly associated with poorer outcomes in breast cancer patients. As the TME is subject to glutamine (Gln) deficiency, human mammary fibroblasts (HMFs) were cultured in Gln-starved medium. Global histone deacetylation and TGF-β-Smad2/3 signaling activation are induced in these cells, largely mediated by class I histone deacetylase (HDAC) activity. Additionally, mechanistic/mammalian target of rapamycin complex 1 (mTORC1) signaling is attenuated in Gln-starved HMFs, and mTORC1 inhibition in Gln-supplemented HMFs with rapamycin treatment boosts TGF-β-Smad2/3 signaling activation. These data indicate that mTORC1 suppression mediates TGF-β-Smad2/3 signaling activation in Gln-starved HMFs. Global histone deacetylation, class I HDAC activation, and mTORC1 suppression are also observed in cultured human breast CAFs. Class I HDAC inhibition or mTORC1 activation by high-dose Gln supplementation significantly attenuates TGF-β-Smad2/3 signaling and the myofibroblastic state in these cells. These data indicate class I HDAC activation and mTORC1 suppression to be required for maintenance of myCAF traits. Taken together, these findings indicate that Gln starvation triggers TGF-β signaling activation in HMFs through class I HDAC activity and mTORC1 suppression, presumably inducing myCAF conversion.

overall_design: ChIP-seq using anti-H3K27ac antibody for exp-CAF2 cells treated with DMSO, TSA or SB431542


status: Public on Nov 03 2023

country: Japan

overall_design: Microarray data of exp-CAF2 cells treated with DMSO, TSA or SB431542


title: Molecular mechanisms associated with cis-platin intrinsic resistance in early drug-tolerant persister cells of lung adenocarcinoma cell lines

city: Ciudad de Mexico

first: Rodolfo

middle: Luis

last: Chavez-Dominguez

state: Ciudad de Mexico

address: Calz. de Tlalpan 4502

country: Mexico

institute: Instituto Nacional de Enfermedades Respiratorias

type: Expression profiling by high throughput sequencing

summary: To investigate the mechanism associated with cis-platin intrinsic resistance, we established a model of early drug-tolerant persister cells by exposing lung adenocarcinoma cell lines to the drug for 24 h. Then, we analyzed the transcriptome using RNA-seq from 4 different lung adenocarcinoma cell lines.

overall_design: Differential expression analysis of RNA-seq data for cis-platin persister cells and untreated controls.

first: Mario

last: Perez-Medina

first: Maribel

last: Soto-Nava

first: Santiago

last: Avila-Rios

first: Alfonso

last: Mendez-Tenorio

first: Miriam

last: Galicia-Velasco

first: Dolores

last: Aguilar-Cazares

first: Jose

middle: S

last: Lopez-Gonzalez


title: Effect of ATGL knockdown by siRNA in human umbilical vein endothelial cells

city: Philadelphia

first: Yifan

last: Yang

state: PA

address: 3400 Spruce Str

country: USA

institute: University of Pennsylvania

summary:
To investigate the role of ATGL in endothelial cell function, we knockdown ATGL with siRNA and compared with siCTL.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 3 different samples each condition.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HUVECs under siCTL vs siATGL condition

first: Yang

last: Yifan

first: Kim

last: Boa

first: Arany

last: Zolt


title: Expression data from Lund Human Mesencephalic cells (LUHMES) exposed to acute and persistent oxidative DNA damage

status: Public on Nov 04 2023

city: Sheffield

first: Irina

last: Vazquez Villasenor

address: 385a Glossop Road

department: Neuroscience

country: United Kingdom

institute: Sheffield Institute for Translational Neuroscience, The University of Sheffield

summary:
Oxidative DNA damage in neurons activates a DNA damage response (DDR) to promote repair. Under a chronic oxidative environment these processes may be altered and promote accumulation of unrepaired DNA damage and continued activation of a DDR, leading to apoptosis or senescence activation. Accumulation of oxidative DNA damage are features of brain ageing and neurodegeneration but the effects of persistent DNA damage in neurons are not well characterised.
We developed a model of persistent oxidative DNA damage in human neurons in vitro (LUHMES) by exposing them to a sub-lethal concentration of hydrogen peroxide (H2O2) following a "single stress" and “double stress” protocols. We characterised the neuronal transcriptome under these circumstances using microarray analysis.

overall_design: Single-stressed post-mitotic LUHMES in culture were exposed to 50 μM H2O2. Double-stressed post-mitotic LUHMES were exposed to a second 50 μM H2O2 stress 6 hours after the first one. Control LUHMES were exposed to vehicle (distilled water). LUHMES under the three different conditions were kept in culture for a further 96 hours and harvested at this time-point for total RNA isolation and microarray analysis.

last: Vazquez-Villasenor

first: Claire

middle: J

last: Garwood

first: Paul

middle: R

last: Heath

first: Julie

middle: E

last: Simpson

first: Heather

last: Mortiboys

first: Stephen

middle: B

last: Wharton


title: Next Generation Sequencing of Cells Derived from Directed Differentiation of Wild Type and E2A Knockout Human ESCs into Cardiomyocytes

city: Shanghai

first: xiuya

last: li

address: Dongan Road 130

country: China

institute: Fudan University

summary: This study aimed  to compare mRNA profiles of cells derived from directed differentiation of wild type and E2A knockout human ESCs  into cardiomyocytes. Using an optimized data analysis workflow, we  identified 34,800 transcripts in  WT and E2A -/-  cardiac mesoderm cells (day3), early cardiomyocytes (day7) and later cardiomyocytes (day15). The transcripts showed 1889 differential expression genes (1099 upregulated and 790 downregulated) between the WT and E2A -/- cells, with a fold change ≥2.0 and p value <0.05.  Hierarchical clustering of differentially expressed genes  discovered that these genes may contribute to related phenotypes of E2A knockout cardiomyocytes.

overall_design: mRNA profiles of wild type and E2A knockout cells from day3, day7 and day15 during human ESCs (H7)-cardiomyocytes directed differentiation were generated by deep sequencing, using Illumina HiSeqX10.

first: Xiuya

last: Li

first: Fei

last: Gao

first: Xiaochen

last: Wang


title: A Novel Role for A20-Regulated CNS Endothelial ICOSL in Immune Cell Adhesion and Autoimmune Neuroinflammation

city: Mainz

first: Federico

last: Marini

address: Obere Zahlbacher Strasse 69

department: Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI)

country: Germany

institute: University Medical Center - Mainz

summary: A20 is a ubiquitin-modifying protein that negatively regulates canonical NF-κB signaling and mutations in A20/TNFAIP3 have been associated with a variety of autoimmune diseases, including multiple sclerosis (MS). We found that deletion of A20 in central nervous system (CNS) endothelial cells (BEC) enhances experimental autoimmune encephalomyelitis (EAE), a mouse model of MS. These mice showed increased numbers of CNS-infiltrating immune cells during neuroinflammation and in the steady state. While the integrity of the barrier was not impaired, we observed a strong activation of the endothelium in A20ΔBEC mice, with dramatically increased levels of the adhesion molecules ICAM-1 and VCAM-1. We furthermore discovered ICOSL as novel adhesion molecule expressed by A20-deficient BECs. Silencing of ICOSL in BECs ameliorated the severity of an active EAE disease in wildtype mice and significantly delayed the onset of symptom development. Furthermore, blocking of ICOSL on primary CNS-derived endothelial cells impaired the adhesion of different T cell populations to the monolayer. Taken together, we here report a novel function of A20-regulated ICOSL expressed on CNS endothelial cells during inflammation. We propose that BEC-ICOSL contributes to the firm adhesion of T cells to the barrier, promoting T cell transmigration into the CNS and eventually driving autoimmune neuroinflammation.

overall_design: CNS-endothelial knockout of A20 versus wildtype-like control and wildype-like EAE control

first: Lisa

last: Johann

first: Ari

last: Waisman


title: Anti-adipogenesis effect of indole-3-acrylic acid on human preadipocytes and HFD- induced zebrafish

status: Public on Nov 02 2023

first: Ling

last: Zhang

address: 1111 XianXia Road

institute: Tongren Hospital, Shanghai Jiao Tong University School of Medicine

summary: Obesity, defined as excessive or abnormal body fat accumulation, which could significantly increase the risk of cardiovascular disease, type 2 diabetes mellitus (T2DM) diseases and seriously affect people's quality of life. More than 2 billion people are overweight, and the incidence of obesity is increasing rapidly worldwide, it has become a widely concerned public health issue in the world. Diverse evidence show that active metabolites are involved in the pathophysiological processes of obesity. However, whether the downstream catabolite of tryptophan, 3-indole acrylic acid (IA), is involved in obesity remains unclear. Here, we found that the content of IA in peripheral blood serum of overweight people was significantly lower than that of normal people. In addition, supplementation with IA in zebrafish larvae induced by a high fat diet (HFD) dramatically reduced HFD induced lipid accumulation. IA had no effect on proliferation and apoptosis of preadipocytes, but significantly inhibited adipogenesis of preadipocytes by down-regulate CEBPα and PPARγ. RNA-Seq and functional analysis revealed that IA regulated the adipogenesis of preadipocytes through stimulate the phosphorylation of STAT1. Taken together, IA has been identified as a potent metabolite for the prevention or treatment of obesity.

overall_design: We performed gene expressiong profilling analysis using data obtained from RNA-seq of human visceral preadipocytes with or without reagent

first: Jianfang

first: Xirong

last: Guo


title: The impact of aging on beta-cell functionality and structural integrity under metabolic stress conditions in diabetes-prone and diabetes-resistant mice [ob].

city: Nuthetal

first: Richard

last: Kehm

address: Arthur-Scheunert-Allee 114-116

department: Molecular Toxicology

institute: German Institute of Human Nutrition Potsdam-Rehbruecke

summary: Young and aged, diabetes-prone (NZO/HIBomDife) as well as diabetes-resistant (B6.V-Lep ob/ob) mice exhibited different islet functions and phenotypes in response to a carbohydrate-rich diet (CRD) subsequent to a high-fat, carbohydrate-free diet (HFD). To unravel the molecular basis underlying these alterations, a microarray-based transcriptome analysis of isolated pancreatic islets before and after 2 days of CRD feeding was performed. A high number of differentially expressed genes associated with redox homeostasis, in particular Thioredoxin-interacting protein (Txnip), as well as genes involved in cell cycle entry and cell proliferation, such as cyclins, cyclin-dependent kinases and Mki67 were identified and associated with these changes. In addition, aged NZO/HIBomDife and age-matched, B6.V-Lep ob/ob mice revealed a high overlap of regulated genes, also linked to cell cycle progression under the same dietary regimen.

overall_design: Metabolic-stressed induced gene expression in murine pancreatic islets was determined at week 18 (young) and 39 (aged) of HFD feeding as well as 2 days after an additional CRD intervention (n = 5 mice per group).

first: Annika

last: Höhn

first: Tilman

last: Grune


title: Defining the Relationship Between Cellular and Extracellular Vesicle (EV) Content in Breast Cancer via an Integrative Multi-Omic Analysis

city: St Lucia

first: Rebecca

last: Lane

state: QLD

address: Cnr College and Cooper Rds

department: Australian Institute for Bioengineering and Nanotechnology (AIBN)

country: Australia

institute: The University of Queensland

summary:
Much recent work has been dedicated to exploring the utility of extracellular vesicles (EVs) as circulating cancer biomarkers. This is driven by the understanding that the molecular cargo of EVs reflects their originating cell, meaning EVs may enable non-invasive tumour surveillance. Few attempts have been made, however, to empirically validate this assumption on the -omic level and define the relationship between the molecular phenotype of cells and EVs.
To this end, we present an integrative multi-omic analysis of a panel of breast cancer cell lines and corresponding EVs. Transcriptomic analysis of the cells was first used to confirm that expression of disease-related transcripts remained stable following transition to a low serum EV production medium. Proteomic analysis of the EVs indicated that neither the ER nor PR protein could be directly detected in EVs, but cellular expression of ER could be indirectly inferred from the EV proteome.
Transcriptomic analyses generally suggested a direct positive correlation between transcript levels in cells and EVs. Integrative analysis suggested that the EV proteome and transcriptome captured select hallmarks of aberrant pathway activity in the originating cells, supporting the potential use of EVs to non-invasively monitor molecular evolution in breast cancers.

overall_design: Sequencing of total RNA isolated from breast cancer cell-derived extracellular vesicles (EVs)

first: Darren

last: Korbie

first: Ahmed

last: Mohamed

first: Kum

middle: K

last: Khanna

first: Michelle

middle: M

last: Hill

first: Matt

last: Trau


title: scRNAseq of skeletal tissue during zebrafish craniofacial development

city: Boston

first: Shannon

last: Fisher

state: MA

address: 700 Albany Street

institute: Boston University

summary: We used scRNAseq to characterize differentiation of cell populations during zebrafish craniofacial development. We focused critical stages during suture formation, and compared wildtype fish to mutants lacking the transcription factor sp7, that display striking abnormalities in skull and suture formation.

overall_design: Dissociated cells were isolated from heads of wildtype and sp7 mutant zebrafish at  ~5.8 mm SL (2 weeks post-fertilization) and ~7 mm SL (3wpf). To enrich for skeletal tissues, brain and eyes were removed before dissociation. To aid in dissection and transcript analysis, fish carried two transgenes, -117BMPER: egfp and sp7: mcherry. Cells were analyzed by scRNAseq.

first: Xuan

middle: A

last: He

first: Alexandra

last: Scalici


title: Breaking through NGF-TrkA immunosuppression in melanoma sensitizes immunotherapy for durable memory T cell protection [TCR-seq]

city: Durham

first: Liuyang

last: Wang

state: NC

address: 213 Research Drive

institute: Duke University

summary: Melanomas are generated from melanocytes, the neural crest derivatives sharing a neuroectodermal origin with the nervous system. In investigating whether immune privilege of the nervous system might be exploited by melanoma, we found that nerve growth factor (NGF) exerts both melanoma cell-intrinsic and -extrinsic immunosuppression. In melanoma cells, autocrine NGF engages TrkA receptor to desensitize IFN-gammasignaling, leading to T and NK cell exclusion. In effector T cells, which upregulate surface TrkA expression upon T cell receptor (TCR) activation, paracrine NGF dampens TCR signaling and effector function. Targeting NGF genetically or pharmacologically with larotrectinib sensitizes melanoma responsiveness to immune checkpoint blockade (ICB) therapy for tumor eradication and induces durable protection by eliciting robust memory of low-affinity T cells. Together, these findings uncover a comprehensive mechanism through which the NGF-TrkA axis suppresses anti-tumor T cell immunity, thus providing a novel mode of action to repurpose larotrectinib for immune sensitization. Moreover, by enlisting low-affinity tumor-specific T cells, anti-NGF reduces acquired resistance to ICB therapy and prevents melanoma recurrence.

overall_design: This data contains 4 TCR-seq datasets. 1. For B16OVA experiment, B16OVA cells were subcutaneously injected into C57BL/6J mice. Total RNA was extracted from melanoma tissues day 11 and analyzed by RNA-seq. 2. For YUMM experiment, YUMM1.7 cells were subcutaneously injected into C57BL/6J mice. Total RNA was extracted from melanoma tissues day 12 and analyzed by RNA-seq. 3. For dLN_KO experiment, C57BL/6J mice were subcutaneously injected with 50,000 Ctrl or NGF sgRNA B16-OVA cells. All mice in the Ctrl sgRNA group were sacrificed when tumor growth limits were exceeded. Tumor-free mice in the NGF sgRNA group were rechallenged with B16-OVA cells on day 78. 9 days later, OVA-tetramer+ CD8+ T cells were sorted from tumor draining lymph nodes and submitted for TCRb-seq. 4. For dLN_NT_aPD-1 and dLN_KO_aPD-1 experiment, C57BL/6J mice were subcutaneously injected with 50,000 Ctrl or NGF sgRNA B16-OVA cells. 250 ug/mouse anti-PD-1 antibody was given twice. Tumor-free mice in both groups were rechallenged with B16-OVA cells on day 78. 9 days later, OVA-tetramer+ CD8+ T cells were sorted from tumor draining lymph nodes and submitted for TCRb-seq. 5. For OVAtetramer_high and  OVAtetramer_low experiment, C57BL/6 mice were vaccinated i.v. with 0.1 LD50 of attenuated recombinant Listeria-OVA strain. OVA-tetramer-high and –low CD8 T cells were FACS-sorted from spleen on day 7 after a single vaccination, and then submitted for TCRb-seq.

first: Tao

last: Yin

first: Poorva

last: Mudgal

first: Qi-Jing

last: Li

first: Xiao-Fan


title: Runx3 restoration regresses K-Ras–activated mouse lung cancers and inhibits recurrence

city: Cheongju

first: Jung-Won

last: Lee

address: 1, Chungdae-ro

department: Department of Biochemistry, School of Medicine

country: South Korea

institute: Institute for Tumor Research

summary: Comparision of the gene expression profiles of the RUNX3 Knock out and RUNX3 restored cells.

overall_design: we obtained immortalized cell lines from KPRL/F-TAM(-) lung cancers (KPR-). Treatment of KPR- cell lines with 4-hydroxytamoxifen (4-OHT) restored Runx3, generating KPRrestored cell lines. We confirmed that Runx3 was restored at 8 h after 4-OHT treatment. To identify genes regulated by Runx3 in the K-Ras–activated lung cancer cells, we performed mRNA sequencing (RNA-seq) in KPR- cells and KPRrestored cells.

first: You-Soub

first: Ja-Yeol

first: Suk-Chul

last: Bae


title: The STEMRI trial: magnetic resonance spectroscopy imaging can define tumor areas enriched in glioblastoma-stem-like cells

city: Toulouse

first: Anthony

last: Lemarie

address: 2 Av. Hubert Curien

country: France

institute: INSERM

summary: Despite maximally-safe resection of the MRI-defined contrast-enhanced (CE) central tumor area and chemo-radiotherapy, most glioblastoma patients relapse within one year in peritumor FLAIR regions. Spectroscopic MRI (MRSI) can discriminate metabolic tumor areas with higher recurrence potential as CNI+ regions (Choline/N-acetyl-aspartate Index>2) can predict relapse sites. As relapses are mainly imputed to glioblastoma stem-like cells (GSC), CNI+ areas might be GSC-enriched. We conducted a prospective trial in 16 GBM patients subjected to preoperative MRSI/MRI and surgery/chemo-radiotherapy to investigate GSC content in CNI+ versus CNI- biopsies from CE/FLAIR. Biopsy characterization by RNAseq revealed that FLAIR/CNI+ areas were enriched in stem-related gene signature, but also in pathways related to DNA repair, adhesion/migration and mitochondrial bioenergetics.

overall_design: 51 biopsy samples obtained from 16 patients in 4 different tumor regions defined by MRI/MRSI ((1) FLAIR/CNI-; (2) FLAIR/CNI+; (3) CE/CNI-; (4)CE/CNI+). No technical replicates and no reference samples

last: Lemarié

first: Elizabeth

last: Cohen-Jonathan Moyal

first: Juan

middle: P

last: Cerapio Arroyo

first: Caroline

last: Delmas

first: Vincent

last: Lubrano


title: Effect of radiation exposure on gene expression in neurospheres

city: Cincinnati

first: Nathan

last: Salomonis

state: OH

address: 3333 Burnet Avenue

department: Biomedical Informatics

institute: Cincinnati Children's Hospital

summary: To investigate the radiotoxicity on Neural Progenitor Cells (NPC) in neuropsheres exposed to x-ray radiation

overall_design: We performed gene expression profiling analysis using bulk RNA-seq of neurospheres irradiated with three different radiation intensities (0 and 1Gy) 3 days after seeding.

first: Bedika

last: Pathak

first: Taylor

last: Lange

first: Kristin

last: Lampe

first: Ella

last: Hollander

first: Marina

last: Oria

first: Kendal

last: Murphy

first: Mathieu

last: Sertorio

first: Marc


title: Effect of HSF1 overexpression in  non-tumorigenic human breast epithelial MCF10A cell line

city: Bergen

first: Tomasz

last: Stokowy

address: Nygardsgaten 5

department: IT Division

country: Norway

institute: University of Bergen

summary: To elucidate the mechanism of the epithelial-mesenchymal transition observed in MCF10A cell with HSF1 overexpression, we performed RNA-seq analyses. They revealed that cadherin signaling pathway (P00012) was the most enriched in the set of genes down-regulated in these cells. In addition to CDH1 and CDH2, 19 genes encoding protocadherins also showed reduced expression. Among the genes most severely affected in cells with HSF1 overexpression were many genes encoding cell adhesion or cytoskeleton-organizing proteins (e.g. GJA5, NID2, TUBA1A, MFAP5, TAGLN were inhibited, TTC25, CADM3, IQGAP2, SDK2, CEACAM6, FAT2 were upregulated).

overall_design: To investigate the action of HSF1 in MCF10A cells, we established cells with stable HSF1 overexpression using lentiviruses. We then performed gene expression profilling using data from RNA-seq.

first: Natalia

last: Vydra

first: Patryk

last: Janus

first: Wiesława

last: Widłak


title: Cardiac pericytes contribute to myofibroblast expansion and vascular maturation following myocardial infarction

city: Bronx

first: Silvia

middle: C

last: Hernandez

state: New York

address: 1300 Morris Park Avenue

department: Medicine-Cardiology

institute: Albert Einstein College of Medicine

summary: Pericytes have been implicated in regulation of inflammatory, reparative, fibrogenic and angiogenic responses in several different organs and pathologic conditions. Although the adult mammalian heart contains abundant pericytes, their fate and involvement in myocardial disease remains unknown. We used NG2Dsred;PDGFRaEGFP pericyte-fibroblast dual reporter mice and inducible NG2CreER mice to study the fate and phenotypic modulation of pericytes in a model of myocardial infarction. The transcriptomic profile of pericyte-derived fibroblasts was studied using PCR arrays. The transcriptomic profile of NG2 lineage cells (pericytes) was studied in control and infarcted hearts using single cell RNA-sequencing analysis. The role of TGF-b signaling in regulation of pericyte phenotype in vivo was investigated using pericyte-specific Tgfbr2 knockout mice. In vitro, the effects of TGF-b were studied in cultured human placental pericytes.In normal mouse hearts, NG2 and PDGFRa identified distinct non-overlapping populations of pericytes and fibroblasts respectively. Following myocardial infarction, a population of cells expressing both pericyte and fibroblast markers emerged. These cells expressed large amounts of extracellular matrix (ECM) genes. Lineage tracing demonstrated that in the infarcted region, a subpopulation of pericytes underwent fibroblast conversion. Single cell RNA-seq experiments demonstrated expansion and diversification of pericyte-derived cells in the infarct, associated with emergence of subpopulations exhibiting accentuated matrix gene synthesis. In vitro studies and the profile of pericyte-derived fibroblasts identified TGF-b as a potentially causative mediator in fibrogenic activation of infarct pericytes. However, pericyte-specific Tgfbr2 disruption had no significant effects on myofibroblast infiltration and collagen deposition in the infarct. Pericyte-specific TGF-b signaling was involved in vascular maturation, mediating formation of a mural cell coat investing infarct neovessels. These reparative effects of infarct pericytes protected the infarcted heart from dilative remodeling.

overall_design: Cardiac pericytes of inducible NG2creER:R26tdTomato mice (NG2 lineage tracing mice) were isolated by Fluorescece-activated cell sortin (FACS) based on the presence of Tomato signal after exclusion of CD31+ and CD45+ cells. Previous to cell isolation mice were treated with tamoxifen and surgery was preformed for the infarct groups (n=3). Seven days after surgery, hearts were harvested for control (n=2, 2 mice per n) and infarcted (n=3, 2 mice for n1 and n2 and 1 mice for n3) mice. Samples were anilyzed using scRNAseq.

first: Linda

last: Alex

first: Izabela

last: Tuleta

first: Anis

last: Hanna

first: Harikrishnan

last: Venugopal

first: Maider

last: Astorkia

first: Claudio

last: Humeres

first: Akihiko

last: Kubota

first: Kai

last: Su

first: Deyou

last: Zheng

first: Nikolaos

middle: G

last: Frangogiannis


title: Fine root gene expression of Norway spruce cuttings

city: Helsinki

first: Sannakajsa

middle: Velmala

last: LUKE

address: Latokartanonkaari 9

country: Finland

institute: Natural resources Institute Finland Luke

summary: We investigated root associated fungi in young Norway spruce (Picea abies) cuttings rooted from slow- and fast-growing trees showing variable growth rate in long-term field experiments and compared their roots’ gene expression patterns five and 18 months after adventitious root initiation. Gene expression patterns of adventitious roots could not be systematically linked with the growth phenotype at the initiation of root formation, and thus fundamental differences in the receptiveness of fungal symbionts could not be assumed.

platform_organism:
Picea glauca
Picea sitchensis

overall_design: 8 spruce genotypes and two sampling timepoints

first: Leena

last: Hamberg

first: Jarno

last: Vanhatalo

last: Velmala

first: Andy

middle: F

last: Taylor

first: John

last: MacKay

first: Sebástien

last: Caron

first: Fred

last: Asiegbu

first: Risto

last: Sievänen

first: Pasi

last: Raumonen

first: Tuija

last: Hytönen

first: Taina

last: Pennanen


title: The impact of HPV16 and HPV18 E6/E7 oncogenes on gene expression in non-tumorigenic keratinocytes (HaCaT cells)

city: Guadalajara

first: Adriana

middle: Del Carmen

last: Aguilar Lemarroy

state: Jalisco

address: Sierra Mojada 800, Independencia Oriente, 44340 Guadalajara, Jal.

department: División de Inmunología

institute: Centro de Investigación Biomédica de Occidente

summary:
This analysis aimed to identify differentially expressed genes in non-tumorigenic keratinocytes transduced with E6/E7 oncogenes of HPV16 or 18. The working cell models were named HaCaT E6/E7 HPV16, HaCaT E6/E7 HPV18, and HaCaT pLVX (empty lentiviral vector) as controls. mRNA sequencing was performed on the Illumina NovaSeq 6000 platform by Novogene Bioinformatics Technology Co., Ltd, Beijing, China, with two independent replicate sequences for each cell model.
Methodology: The bioinformatics pipeline analysis was executed as described below: Rstudio (v2023.06.1+524) and Galaxy (https://www.usegalaxy.orgaccessed on 15 August 2023) open-source platforms were used to analyze the Illumina raw data. The Quality Check was performed through the FastQC tool (v0.12.1); afterward, all the reads were processed by the Rsubread package (v2.14.2); at that point, the reads were trimmed and aligned to the Human Genome Reference (GRCh38.p14 v43). The resulting output was the BAM files, of which the number of reads was counted by the featureCounts tool (v2.0.3); at the final step, the Differential Expression Analysis was settled by DESeq2 tool (v2.11.40.8). The differential gene expression measurements were normalized by DESeq2´s median of ratios (median of ratio of gene counts relative to geometric mean per gene) method. All chemokine genes with an adjusted p-value (adj p) ≤ 0.05 and fold change (Log2FC) > 1 .5 or < -1.5 were selected as differentially expressed genes (DEGs). Some genes from the resulting outputs were validated through qPCR.
Conclusions: Our study found 3296 differentially expressed genes in HaCaT E6/E7 HPV16 and 1943 in HaCaT E6/E7 HPV18. These results suggest that E6/E7 oncogenes from HPV16 and 18 can broadly modify transcriptomic expression.

overall_design: Total RNA extraction was achieved on transduced keratinocytes infected with lentiviral particles that bear the E6/E7 genes of HPV16 or 18; this process was addressed in duplicate. The keratinocytes transduced with the empty pLVX vector were used as calibrator in the comparison of each of the cell models. After that, the two replicates were compared as a single end of each model vs. the control for the development of the differential expression analysis.

first: Leonardo

last: Fernandez-Avila

first: Aribert

last: Castro-Amaya

first: Luis

last: Jave-Suarez

last: Aguilar-Lemarroy


title: Cervical Cancer derived cell lines: Gene Expression Profile

summary:
This analysis aimed to identify differentially expressed genes in Cervical Cancer derived cell lines. The working cell lines were SiHa, HeLa and C33A. The non-tumorigenic HaCaT cell line was included as control. mRNA sequencing was performed on the Illumina NovaSeq 6000 platform by Novogene Bioinformatics Technology Co., Ltd, Beijing, China, with two independent replicate sequences for each cell model.
Methodology: The execution of the bioinformatics pipeline analysis was carried out according to the following description: Rstudio (v2023.06.1+524) and Galaxy (https://www.usegalaxy.orgaccessed on 15 August 2023) open-source platforms were used to analyze the Illumina raw data. The Quality Check was conducted through the FastQC tool (v0.12.1). Afterward, all the reads were processed by the Rsubread package (v2.14.2); at that point, the reads were trimmed and aligned to the Human Genome Reference (GRCh38.p14 v43). The obtained output was: the BAM files, of which the number of reads was counted by the featureCounts tool (v2.0.3); at the final step, the Differential Expression Analysis was settled by the DESeq2 tool (v2.11.40.8). The differential gene expression measurements were normalized by DESeq2's median of ratios (median of ratio of gene counts relative to geometric mean per gene) method. All chemokine genes with an adjusted p-value (adj p) minus or equal to 0.05 and fold change (Log2FC) up to 2 or less than minus 2 were selected as differentially expressed genes (DEGs). Some genes from the resulting outputs were validated through qPCR.
Conclusions: Our study found 5850 differentially expressed genes for SiHa cell lines, 6698 for HeLa, and 6707 for C33a.

overall_design: Cervical cancer-derived cell lines underwent total RNA extraction. (SiHa, HeLa, and C33A); this process was addressed in duplicate, except for C33A with a single replicate. HaCaT cell line was used as calibrator for comparing each group. After that, the replicates were compared as a single end of each cell line vs. the control for the development of the differential expressionanalysis.

first: Andrea

last: Molina-Pineda


title: Cell-autonomous effects of APOE4 in restricting microglial response in brain homeostasis and Alzheimer’s disease

city: Jacksonville

first: Yingxue

last: Ren

state: FL

address: 4500 San Pablo Rd S

institute: Mayo Clinic

summary: Cells in the cortex of mice expressing apoE3 or apoE4 in the microglia were isolated and subjected to the single-cell RNA seq to investigate the effects of microglia/CNS-associated macrophages (CAMs) apoE on the brain transcriptomic profiles. Our data revealed that microglia/CAM-expressed apoE3 promotes antigen presentation and immune patnways, whereas apoE4 down-regulates complement and promotes stress-related responses.

overall_design: Amyloid model mice with or without expressing apoE3 or apoE4 in microglia/CAMs (total 24 mice) were analyzed.  N=6/group (3 male and female mice per group). The four groups are Ctrl (C) vs. Tamoxifen (T)-induced apoE3 or apoE4.

first: Chia-Chen

last: Liu

last: Wang

first: Yuka

last: Martens

first: Zonghua

last: Li


title: Prim-O-glucosylcimifugin ameliorates aging-impaired endogenous tendon regeneration capacity via rejuvenating senescent tendon stem/progenitor cells

city: Beijing

first: Yan

state: Beijing

address: No. 22 South Street, Zhongguan Street

department: Peking University School and Hospital of Stomatology

institute: Peking university

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

overall_design: Refer to individual Series


title: Prim-O-glucosylcimifugin ameliorates aging-impaired endogenous tendon regeneration capacity via rejuvenating senescent tendon stem/progenitor cells [DMSO-treated and POG-treated Passage 12 TSPCs]

summary:
Adult tendon stem/progenitor cells (TSPCs) are essential for tendon maintenance, regeneration, and repair, yet they become susceptible to senescence with age, impairing the self-healing capacity of tendons. In this study, we employ a recently developed deep-learning-based efficacy prediction system to screen potential stemness-promoting and senescence-inhibiting drugs from natural products using the transcriptional signatures of stemness. The top-ranked candidate prim-O-glucosylcimifugin (POG), a saposhnikovia root extract, could ameliorate TPSC- senescent phenotypes caused by long-term passage and natural aging in rats and humans, as well as restore self-renewal and proliferation capacities, and tenogenic potential of aged TSPCs. In vivo, the systematic administration of POG or the local delivery of POG nanoparticles functionally rescues endogenous tendon regeneration and repair capacity in aged rats to levels similar to normal animals. Mechanistically, POG protects TSPCs against functional impairment during both passage-induced and natural aging by simultaneously suppressing nuclear factor-κB and downregulating mTOR signaling with induction of autophagy. Together, the strategy by pharmacological intervention with deep learning-predicted compound POG could rejuvenate aged TSPCs and improve the regenerative capacity of aged tendons.
We performed mRNA microarray analyses of  DMSO-treated and POG-treated Passage 12 TSPCs and identified meaningful genes in down-regulated and up-regulated group

overall_design: DMSO-treated and POG-treated Passage 12 TSPCs were harvested.Then total RNA was extracted using Trizol reagen, and following labeling, fragmented cDNA was hybridized for 16 h at 45 oC on GeneChip Affymetrix Rat Transcriptome Array 1.0 (Affymetrix))

first: Yu


title: Lamin A upregulation reorganizes the genome during rod photoreceptor degeneration

city: Ottawa

first: José Alex

last: Lourenço Fernandes

state: ON

address: 501 Smyth Rd

country: Canada

institute: Ottawa Hospital Research Institute

summary: Neurodegenerative diseases are accompanied by dynamic changes in gene expression, including the upregulation of hallmark stress-responsive genes. While the transcriptional pathways that impart adaptive and maladaptive gene expression signatures have been the focus of intense study, the role of higher order nuclear organization in this process is less clear. Here, we examine the role of the nuclear lamina in genome organization during the degeneration of rod photoreceptors. Two proteins had previously been shown to be necessary and sufficient to tether heterochromatin at the nuclear envelope. The lamin B receptor (Lbr) is expressed during development, but downregulates upon rod differentiation. A second tether is the intermediate filament lamin A (LA), which is not normally expressed in murine rods. Here, we show that in the rd1 model of retinitis pigmentosa, LA ectopically upregulates in rod photoreceptors at the onset of degeneration. LA upregulation correlated with increased heterochromatin tethering at the nuclear periphery in rd1 rods, suggesting that LA reorganizes the nucleus. To determine how heterochromatin tethering affects the genome, we used in vivo electroporation to misexpress LA or Lbr in mature rods in the absence of degeneration, resulting in the restoration of conventional nuclear architecture. Using scRNA-seq, we show that reorganizing the nucleus via LA/Lbr misexpression has relatively minor effects on rod gene expression. Next, using ATAC-seq, we show that LA and Lbr both lead to marked increases in genome accessibility. Novel ATAC-seq peaks tended to be associated with stress-responsive genes. Together, our data reveal that heterochromatin tethers have a global effect on genome accessibility, and suggest that heterochromatin tethering primes the photoreceptor genome to respond to stress.

overall_design: After flow cytometric sorting, cells were barcoded with ‘anchor’ and ‘co-anchor’ lipid-modified oligonucleotides generously provided by the Zev Gartner lab. Barcode oligonucleotides were purchased from Integrated DNA Technologies as follows. Barcode 1: F: 5′- CCTTGGCACCCGAGAATTCCAGGAGAAGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA-3′; Barcode 2: F: 5′- CCTTGGCACCCGAGAATTCCACCACAATGAGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA-3′; Barcode 3: F: 5′- CCTTGGCACCCGAGAATTCCATGAGACCTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA-3′;  Each replicate was incubated with barcode oligonucleotides for 10 minutes. Cells were pelleted and washed 3 times with PBS. Replicates were pooled and processed in a single 10X Genomics Chromium run.

first: Ivana

last: Herrera

first: Khatereh

last: Shir-Mohammadi

first: Jasmine

last: Levesque

first: Pierre

last: Mattar


title: Prim-O-glucosylcimifugin ameliorates aging-impaired endogenous tendon regeneration capacity via rejuvenating senescent tendon stem/progenitor cells [DMSO-treated and POG-treated TSPCs]

summary:
Adult tendon stem/progenitor cells (TSPCs) are essential for tendon maintenance, regeneration, and repair, yet they become susceptible to senescence with age, impairing the self-healing capacity of tendons. In this study, we employ a recently developed deep-learning-based efficacy prediction system to screen potential stemness-promoting and senescence-inhibiting drugs from natural products using the transcriptional signatures of stemness. The top-ranked candidate prim-O-glucosylcimifugin (POG), a saposhnikovia root extract, could ameliorate TPSC- senescent phenotypes caused by long-term passage and natural aging in rats and humans, as well as restore self-renewal and proliferation capacities, and tenogenic potential of aged TSPCs. In vivo, the systematic administration of POG or the local delivery of POG nanoparticles functionally rescues endogenous tendon regeneration and repair capacity in aged rats to levels similar to normal animals. Mechanistically, POG protects TSPCs against functional impairment during both passage-induced and natural aging by simultaneously suppressing nuclear factor-κB and downregulating mTOR signaling with induction of autophagy. Together, the strategy by pharmacological intervention with deep learning-predicted compound POG could rejuvenate aged TSPCs and improve the regenerative capacity of aged tendons.
We performed mRNA microarray analyses of DMSO-treated and POG-treated TSPCs  from 18-month-old rats and identified meaningful genes in down-regulated and up-regulated group

overall_design: DMSO-treated and POG-treated TSPCs from 18-month-old rats were harvested.Then total RNA was extracted using Trizol reagen, and following labeling, fragmented cDNA was hybridized for 16 h at 45 oC on GeneChip Affymetrix Rat Transcriptome Array 1.0 (Affymetrix))


title: The TMEM106B T186S coding variant increases neurite arborization and synaptic density in primary hippocampal neurons

city: Houston

first: Caleb

last: Wood

state: TX

address: 1 Baylor Plaza

institute: Baylor College of Medicine

summary: The lysosomal protein TMEM106B was identified as a risk modifier of multiple dementias including frontotemporal dementia and Alzheimer's disease.  The gene comes in two major haplotypes, one associated with disease risk, and by comparison, the other with protection.  Only one coding polymorphism distinguishes the alleles, a threonine-to-serine substitution at residue 185 (186 in mouse).  Transcriptional studies suggest synaptic, neuronal, and cognitive preservation in subjects with the protective haplotype, while in vitro studies revealed dramatic effects of TMEM106B deletion on neuronal development.  Despite this background, the field has not yet resolved whether coding variant is biologically meaningful, and if so, whether it has any specific effect on neuronal phenotypes.  Here we studied how loss of TMEM106B or expression of the lone coding variant affected transcriptional signatures in the mature brain and neuronal structure during development in primary neurons. We show that homozygous expression of the TMEM106B T186S variant in knock-in mice increased cortical expression of genes associated with excitatory synaptic function and axon outgrowth, and promoted neurite branching, dendritic spine density, and synaptic density in primary hippocampal neurons.  In contrast, constitutive TMEM106B deletion affected transcriptional signatures of myelination without altering neuronal development in vitro.  Our findings show that the T186S variant is functionally relevant and may contribute to disease resilience during neurodevelopment.

overall_design: 4 groups of animals were included in this study. Animals were either homozygous for the knocked-in TMEM106B T186S allele, had TMEM106B deleted, or their respective wild-type littermates. Each TMEM106B manipulation was only compared to its wildtype littermate controls.

first: Quynh

last: Nguyen

first: Peter

last: Kim

first: Joanna

middle: L

last: Jankowsky


title: HIRA-mediated loading of histone variant H3.3 controls androgen-induced transcription by regulation of AR/BRD4 complex assembly at enhancers [Dex RNA-seq]

city: Gainesville

first: Alberto

last: Riva

address: 2033 Mowry Rd

department: ICBR

institute: University of Florida

summary: To study the function of histone variant H3.3 pathway in prostate cancer (PCa) we knocked out androgen receptor (AR) and H3.3 chaperones HIRA and DAXX in R1-AD1 FLAG-HA-H3F3A cell line. We analyzed the effect of Dexamethasone treatment on the transcriptome in these four cell lines.

overall_design: RNA-seq data for R1-AD1 FLAG-HA-H3F3A (WT androgen receptor) prostate cancer cells and its derivatives (AR KO, HIRA KO, DAXX KO);

first: Viacheslav

last: Morozov

first: Alexander

last: Ishov


title: Short C-terminal Musashi-1 proteins regulate pluripotency states in embryonic stem cells

status: Public on Nov 05 2023

city: Shanghai

first: Gufa

last: Lin

address: 1239 Siping road Tongji university

department: Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, School of Life Sciences and Technology, Tongji University

institute: Tongji University

summary: To understand the function of MSI1 in pluripotent stem cells, RNA-seq assays were performed on mouse embryonic stem cells R1, MSI1 knockout cell line R1-C5, human embryonic stem cells H9, RRM knockout cell line H9-C8, MSI1 full-length overexpression cell line H9-MSI1OE, MSI1C variant overexpression cell line H9-MSI1 (138-362) OE , H9-MSI1(272-362)OE. RNA bound by MSI1 in R1 and H9, and MSI1C variants MSI1 (138-362), MSI1(272-362) were detected using RIP-seq.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: RNA-seq for mESC cell line R1 (R1-WT and MSI1-KO cell line R1-C5 ), hESC cell line H9 (H9-WT, MSI1 RRM KO cell line H9-C8, MSI1 overexpression cell H9-MSI1FL and MSI1-C variant  overexpression cell H9-MSI1V138 and H9-MSI1V272). RIP-seq for MSI1 binding RNA in R1 and H9 by using anti-MSI1 antibody for RIP. RIP-seq for MSI1-C variants binding RNA in H9 by using anti-Flag antibody for RIP.

first: Youwei

last: Chen


title: Breaking through NGF-TrkA immunosuppression in melanoma sensitizes immunotherapy for durable memory T cell protection [RNA-Seq 1]

first: Liuyang

last: Wang

summary: Melanomas are generated from melanocytes, the neural crest derivatives sharing a neuroectodermal origin with the nervous system. In investigating whether immune privilege of the nervous system might be exploited by melanoma, we found that nerve growth factor (NGF) exerts both melanoma cell-intrinsic and -extrinsic immunosuppression. In melanoma cells, autocrine NGF engages TrkA receptor to desensitize IFN-gamma signaling, leading to T and NK cell exclusion. In effector T cells, which upregulate surface TrkA expression upon T cell receptor (TCR) activation, paracrine NGF dampens TCR signaling and effector function. Targeting NGF genetically or pharmacologically with larotrectinib sensitizes melanoma responsiveness to immune checkpoint blockade (ICB) therapy for tumor eradication and induces durable protection by eliciting robust memory of low-affinity T cells. Together, these findings uncover a comprehensive mechanism through which the NGF-TrkA axis suppresses anti-tumor T cell immunity, thus providing a novel mode of action to repurpose larotrectinib for immune sensitization. Moreover, by enlisting low-affinity tumor-specific T cells, anti-NGF reduces acquired resistance to ICB therapy and prevents melanoma recurrence.

overall_design: 1,000,000 B16F10 cells were subcutaneously injected into C57BL/6J mice. Total RNA was extracted from melanoma tissues on day 15 and analyzed by RNA-seq. There were two grops: Control sgRNA group (C1-4) and NGF sgRNA group(Nko1-4); each had 4 biological replicates.

first: Tao

last: Yin

first: Poorva

last: Mudgal

first: Qi-Jing

first: Xiao-Fan


title: Mucosal and systemic physiological changes underscore the welfare risks of environmental hydrogen sulphide in post-smolt Atlantic salmon (Salmo salar)

city: ÅS

first: Gerrit

last: Timmerhaus

address: Osloveien 1

institute: Nofima AS

summary: Transcriptomics ananlysis of olfactory organs of Atlantic salmon. Controls/untreated (C) fish were compared to fish that were exposed to low (L) or high (H) concentrations of hydrogen sulphide.

overall_design: 36 custom Agilent microarrys were used. 6 fish per treatment and time point. Two time points: two and four weeks. Three treatments: controls, low and high H2S exposure.

first: Carlo

last: Lazado


title: Breaking through NGF-TrkA immunosuppression in melanoma sensitizes immunotherapy for durable memory T cell protection [scRNA-Seq]

summary: Melanomas are generated from melanocytes, the neural crest derivatives sharing a neuroectodermal origin with the nervous system. In investigating whether immune privilege of the nervous system might be exploited by melanoma, we found that nerve growth factor (NGF) exerts both melanoma cell-intrinsic and -extrinsic immunosuppression. In melanoma cells, autocrine NGF engages TrkA receptor to desensitize IFN-gammasignaling, leading to T and NK cell exclusion. In effector T cells, which upregulate surface TrkA expression upon T cell receptor (TCR) activation, paracrine NGF dampens TCR signaling and effector function. Targeting NGF genetically or pharmacologically with larotrectinib sensitizes melanoma responsiveness to immune checkpoint blockade (ICB) therapy for tumor eradication and induces durable protection by eliciting robust memory of low-affinity T cells. Together, these findings uncover a comprehensive mechanism through which the NGF-TrkA axis suppresses anti-tumor T cell immunity, thus providing a novel mode of action to repurpose larotrectinib for immune sensitization. Moreover, by enlisting low-affinity tumor-specific T cells, anti-NGF reduces acquired resistance to ICB therapy and prevents melanoma recurrence.

overall_design: B16 cells with Ctrl or NGF sgRNA were injected into C57BL/6J mice. Melanoma tissues were harvested on day 10 and CD45+ cells from melanoma tissues were sorted by FACS for single cell RNA-seq. FACS sorting purity was around 85%.

last: Li


title: HIRA-mediated loading of histone variant H3.3 controls androgen-induced transcription by regulation of AR/BRD4 complex assembly at enhancers [RNA-Seq]

summary: To study the function of histone variant H3.3 pathway in androgen receptor-driven transcription in prostate cancer (PCa) we knocked out androgen receptor (AR) and H3.3 chaperones HIRA and DAXX in R1-AD1 (wild type AR) and R1-D567 (deltaLBD AR) cell lines. Integrative analysis with RNA-seq, ChIP-seq and ATAC-seq revealed that HIRA KO deregulates androgen-induced gene expression in PCa by reducing H3.3 incorporation, diminishing H3.3S31Ph and H3K27Ac, thus modifying recruitment of BRD4 and altering AR binding within enhancers of target genes.

overall_design: RNA-seq data for R1-AD1 FLAG-HA-H3F3A (WT androgen receptor) and R1-D567 FLAG-HA-H3F3A (deltaLBD androgen receptor) prostate cancer cells and its derivatives (AR KO, HIRA KO, DAXX KO, HIRA shRNA)


title: HIRA-mediated loading of histone variant H3.3 controls androgen-induced transcription by regulation of AR/BRD4 complex assembly at enhancers

type: Genome binding/occupancy profiling by high throughput sequencing


title: Breaking through NGF-TrkA immunosuppression in melanoma sensitizes immunotherapy for durable memory T cell protection [RNA-Seq 2]

overall_design: CD8+ T cells were isolated by MACS from 6-8 week old C57BL/6 mice, and activated by plate-bound anti-CD3/28 antibodies. 72 hr later, activated CD8+ T cells were further treated by 200 ng/ml recombinant murine NGF for another 24 hr. Cells were then collected for bulk RNA-seq. There were two groups, including control (C1-3) and NGF-treatment group (mNGF1-3); each was triplicated.


title: Breaking through NGF-TrkA immunosuppression in melanoma sensitizes immunotherapy for durable memory T cell protection


title: HIRA-mediated loading of histone variant H3.3 controls androgen-induced transcription by regulation of AR/BRD4 complex assembly at enhancers [ATAC-Seq]

overall_design: ATAC-seq data for R1-AD1 FLAG-HA-H3F3A (WT androgen receptor) prostate cancer cells and its derivatives (AR KO, HIRA KO, DAXX KO)

last: Morozv


title: Small airway cell cultures from IPF and post-COVID lung fibrosis patients illustrate disease signatures and differential responses to TGF-β1 treatment (Bulk RNA sequencing)

city: GRAND RAPIDS

first: Xiaopeng

state: MI

address: 400 Monroe Ave NW

department: Pediatrics & Human Development

institute: Michigan State University

summary: In USA, approximately 50,000 people are diagnosed with idiopathic pulmonary fibrosis (IPF) annually; and almost 40,000 of them die. IPF is a condition in which an injury to the lung leads to accumulation of scar tissue. This fibrotic tissue impairs the lungs’ ability to absorb necessary amount of oxygen. The exact etiology of IPF is unknown, but recent evidence suggests that the distal small airways (those having a diameter of less than 2mm) play a role in the early pathogenesis of IPF. Pathologic features of IPF include increased collagen deposition, the collapse of distal small airways, and the buildup of fibroblast/myofibroblast cells. Many of these features are also observed in the lungs of patients following COVID-19 infection. IPF patients who suffer from infection by COVID-19 have poor clinical outcomes and may require a lung transplant due to a significant increase in fibrotic tissue following the illness. This study aimed to investigate possible mechanisms that contribute to worsening lung fibrosis in IPF patients after being diagnosed with COVID-19. Small airway cell cultures derived from IPF and post-COVID-19 IPF patient transplant tissues along with normal lungs were submitted for RNA-sequencing and subsequent differential gene expression analysis. It has been observed that TGFB pathway is activated upon lung injury or illness, signalling profibrotic cascade. Thus, while culturing small airways ,fraction of cells were treated with TGFB.

overall_design: Transcriptomic profile of small airways from IPF, post-COVID19 fibrosis and normal lungs with or without TGFB treatment (3 disease states  X  2 treatments  X 3 biological replicates = 18 samples )

first: Katie

last: Uhl

first: Shreya

last: Paithankar

first: Dmitry

last: Leshchiner

first: Tara

last: Jager

first: Mohamed

last: Abdelgied

first: Kaylie

last: Tripp

first: Angela

last: Peraino

first: Maximiliano

middle: T

last: Kakazu

first: Cameron

last: Lawson

first: Dave

last: Chesla

first: Jeremy

last: Prokop

first: Bin

first: Refa

last: Girgis


title: Transcriptional dysregulation impairs efficacy of neural stem cell activation during aging [ATAC-seq]

city: Shantou

first: Chengyang

middle: Peter

last: Huang

address: 22 Xinling Street

institute: Shantou University Medical College

summary: To examine whether chromatin accessibility is associated with transcription of age-dependent genes in NSC aging, we profiled the chromatin accessibility at the promoters and enhancers of age-dependent genes using the assay for transposase-accessible chromatin with sequencing (ATAC-seq).

overall_design: Primary NSCs were isolated from the subventricular zone of the lateral ventricles (SVZ) in the brains of young and aged mice, respectively. The NSCs were maintained in the initial proliferation medium and used in ATAC-Seq analysis.

first: Meiyang


title: Transcriptional dysregulation impairs efficacy of neural stem cell activation during aging [ChIP-seq]

summary: To get insight into the histone modification in the transcriptional dysregulation of NSC aging, we profiled the principal regulatory histone marks at the promoters and enhancers of age-dependent genes using ChIP-sequencing.

overall_design: Primary NSCs were isolated from the subventricular zone of the lateral ventricles (SVZ) in the brains of young and aged mice, respectively. The NSCs were maintained in the initial proliferation medium and used in ChIP-sequencing analysis.


title: Transcriptional dysregulation impairs efficacy of neural stem cell activation during aging [RNA-seq]

summary: To identify age-dependent genes of NSCs, we applied bulk RNA sequencing to profile the transcriptomic changes between the young and aged NSCs that were isolated from the brain SVZ.

overall_design: Primary NSCs were isolated from the subventricular zone of the lateral ventricles (SVZ) in the brains of the young and aged mice, respectively. The isolated NSCs were maintained in the initial proliferation medium and used in total RNA extraction and bulk RNAseq library generation.


title: Transcriptional dysregulation impairs efficacy of neural stem cell activation during aging.

summary: To study the role of  MLL complex in transcriptional dysregulation of NSC aging, we performed ChIP-seq of MLL complex subunits (Kmt2d, Rbbp5, and Wdr5) and Cbx3 in young and aged NSCs to analyze their binding activity at promoters of age-dependent genes.


title: Transcriptional and epigenetic dysregulation impairs generation of proliferative neural stem and progenitor cells during brain aging

summary: Here we show that the aging of neural stem and progenitor cells (NSPCs) in the mouse brain is characterized by a decrease in the generation efficacy of proliferative NSPCs, rather than the changes in lineage specificity of NSPCs. We reveal that the downregulation of age-dependent genes in NSPCs drives cell aging by decreasing the population of actively proliferating NSPCs, while increasing the expression of quiescence markers. We find that epigenetic deregulation of MLL complex at promoters leads to transcriptional inactivation of age-dependent genes, highlighting the importance of the dynamic interaction between histone modifiers and gene regulatory elements in regulating transcriptional program of aging cells. Our study sheds light on the key intrinsic mechanisms driving stem cell aging through epigenetic regulators and identifies potential rejuvenation targets that could restore the function of aging stem cells.

overall_design: Single-cell RNA-seq, bulk RNA-seq, ChIP-seq, and ATAC-seq were conducted to investigate the transcriptional and epigenetic mechanisms underlying the aging of neural stem and progenitor cells. ChIP-seq was carried out on both young and aged cells to profile key histone marks, including H3K4me3, H3K27me3, and H3K27ac, as well as the MLL complex.


title: Transcriptomic profiling of senescent human stromal cells upon medicinal intervention with rutin

first: Yu

last: Sun

address: 320 Yueyang Rd, Life Sciences Building A #1508

department: Shanghai Institute of Nutrition and Health

institute: Chinese Academy of Sciences

summary: Aging and age-related pathologies can be delayed by specifically targeting the senescence-associated secretory phenotype (SASP), a hallmark feature of senescent cells. Achieving the goal using natural or synthetic agents would have a tremendous impact on the quality of lifespan and burden of age-related chronic diseases. We report the potential of rutin, a bioactive phytochemical component derived from natural plants specifically ginkgo boliva, in targeting senescent cells via suppression of the SASP. This study demonstrates the efficacy of rutin as medicinal agent in controlling the influence of senescent human stromal cells and provides a strong rationale for its future use in aging intervention and geriatric medicine.

overall_design: Examination of in vitro efficacy of rutin, a polyphenolic compound in treating human senescent stromal cells (PSC27 line). Ginkgo biloba products are widely consumed herbal supplements that contain ingredients with anti-oxidant potentials. However, the active agents in ginkgo biloba extracts (GBE) remain unclear, and its major ingredients such as rutin has not been extensively investigated in cellular senescence. This assay was performed beyond previous studies reporting the effects of GBE in anti-diabetic, anti-cataract therapy, anti-inflammation and anti-tumor therapies.

first: Hanxin

last: Liu


title: Factors contributing to Chimeric Antigen Receptor T-cell Therapy efficacy in pediatric oncology patients

city: La Jolla

last: Li

state: California

address: 9500 Gilman Dr

department: Pediatrics

institute: University of California, San Diego

summary:
Immune cell populations are composed of multiple cell types and their functions are tightly connected through their interactions. Cancer immunotherapy enhances the immune system’s ability to recognize and fight cancer and diminish cancer’s ability to evade the immune system. In Chimeric Antigen Receptor T-cell (CAR-T) therapy, T-cells are engineered to eliminate cancer cells by targeting cell surface markers. Problems with CAR-T therapy include relapse due to loss of persistence of CAR-T cells and loss of CD19 expression on leukemia cells. The mechanisms of CAR-T failure need to be elucidated and exploring these mechanisms will identify potential treatment options and improve outcomes.
Utilizing single-cell RNA seq (scRNA-seq), we investigated the interactions between CAR-T cells and the immune cells in pediatric ALL patients who’ve received CAR-T therapy. We analyzed the lymphocyte composition and gene expression profile at different time-points of ALL patients through CAR-T cell therapy. We have compared this data in responders with relapse patients after CAR-T infusion. Focusing on significantly altered immune cell populations and their gene markers, we  employ in vitro and in vivo models to validate their function.

overall_design: PBMC or BMMC from the patients' blood or bone marrow were isloated by EasySep™ Direct Human PBMC Isolation Kit following the manufacturer’s instructions. Then they were used for single-cell RNA-Seq library generation by 10X Genomics Chromium Single Cell 3' Reagent kit (V2/V3).  The library were sequenced  by HiSeq 4000/Novaseq at the IGM Genomics core, UCSD.

first: Tariq

last: Rana

first: Zhouting

last: Zhu


title: RGCC-mediated PLK1 activity drives breast cancer lung metastasis by phosphorylating AMPKα2 to activate oxidative phosphorylation and fatty acid oxidation

status: Public on Nov 01 2023

city: Chongqing

first: Shaojie

last: Cheng

state: -- None selected --

address: No.1, Yi-Xue-Yuan Road, Yu-Zhong District

institute: Chongqing Medical University

summary:
Background: More than 90% mortality of triple negative breast cancer (TNBC) patients are attributed to cancer metastasis with organotropism. Lung is the frequent site of TNBC metastasis. However, the precise mechanism of lung-specific metastasis of TNBC, particularly the driving factors, is not well understood.
Methods: RNA sequencing was performed to identify patterns of gene expression associated with lung metastatic behavior using 4T1-LM3, 231-LM3 and their parental cells (4T1-P, 231-P). Expressions of RGCC, encoding the completion 32 protein response protein, were detected in TNBC cells and tissues by qRT-PCR, western blotting and IHC. Kinase activity assay were performed to evaluated PLK1 kinase activity and the amount of phosphorylated AMP-activated protein kinase α2 (AMPKα2). RGCC-mediated metabolism was determined by UHPLC system. Oxidative phosphorylation was evaluated by JC-1 staining and oxygen consumption rate (OCR) assay. Fatty acid oxidation assay, NADPH and ROS was applied to measure the status of RGCC-mediated fatty acid oxidation. The chemical sensitivity of cells was evaluated by CCK8 assay.
Results: RGCC is aberrantly upregulated in pulmonary metastatic cells. High level of RGCC is significantly related with lung metastasis rather than other organ metastases. RGCC can effectively promote the kinase activity of PLK1, and activated PLK1 phosphorylates AMPKα2 to facilitate TNBC lung metastasis. Mechanistically, Survival and colonization of TNBC cells in the lungs by upregulating oxidative phosphorylation of mitochondria to obtain more energy and promoting fatty acid oxidation to produce abundant NADPH and sustains redox homeostasis, thus prevents excessive accumulation of potentially detrimental ROS in metastatic tumor cells, ultimately establishing metastases. Importantly, targeting RGCC in combination with paclitaxel/carboplatin effectively suppresses pulmonary metastases of TNBC in a mouse model.
Conclusions: The enhanced RGCC is closely associated with lung-specific metastasis of TNBC. RGCC leads to activation of AMPKα2 and downstream signaling through RGCC-driven PLK1 activity to facilitate TNBC lung metastasis, which may determine a potential value of RGCC-driven OXPHOS and fatty acid oxidation as an important therapeutic target.

overall_design: Methods: The total RNA was extracted from 4T1-LM3, MDA-MB-231/LM3 and their corresponding parental cells using TRIzol reagent (Invitrogen). Subsequently, RNA was purified through rRNA depletion and then subjected to cDNA synthesis and RNA amplification. Next, RNA sequencing was carried out by Shengyin Biotech (Shanghai, China), and differential gene expression (DEG) analysis was performed using the DESeq2 package.

first: Xueying

last: Wan

first: Manran


title: Transcriptional dysregulation impairs efficacy of neural stem cell activation during aging [scRNA-seq]

summary: To gain insight of the decreasing activation efficacy in the aging NSCs, we performed single-cell transcriptomics analysis using the Chromium Single Cell 3’ platform (10x Genomics).

overall_design: Primary NSCs were isolated from the subventricular zone of the lateral ventricles (SVZ) in the brains of the young and aged mice, repectively. The isolated cells were used in scRNAseq analysis.


title: Alveolar differentiation drives resistance to KRAS inhibition in lung adenocarcinoma

city: New York

first: ZHUXUAN

last: LI

state: NY

address: 417 E 68th St

department: Cancer Biology and Genetics

institute: Memorial Sloan Kettering Cancer Center

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

overall_design: Refer to individual Series


title: Alveolar differentiation drives resistance to KRAS inhibition in lung adenocarcinoma [scRNA-seq]

summary: Lung adenocarcinoma (LUAD), commonly driven by KRAS mutations, is responsible for 7% of all cancer mortality. The first allele-specific KRAS inhibitors were recently approved in LUAD, but clinical benefit is limited by intrinsic and acquired resistance. LUAD predominantly arises from alveolar type 2 (AT2) cells, which function as facultative alveolar stem cells by self-renewing and replacing alveolar type 1 (AT1) cells. Using genetically engineered mouse models, patient-derived xenografts, and patient samples we found inhibition of KRAS promotes transition to a quiescent AT1-like cancer cell state in LUAD tumors. Similarly, suppressing Kras induced AT1 differentiation of wild-type AT2 cells upon lung injury. The AT1-like LUAD cells exhibited high growth and differentiation potential upon treatment cessation, whereas ablation of the AT1-like cells robustly improved treatment response to KRAS inhibitors. Our results uncover an unexpected role for KRAS in promoting intra-tumoral heterogeneity and suggest targeting alveolar differentiation may augment KRAS-targeted therapies in LUAD.

overall_design: Normal lung alveolar type 2 cells and tumor cells of KP tumors were isolated from KP mouse model using flurescence-activated cell soring and analyzed by scRNAseq or bulk RNAseq.

first: Zhuxuan

first: Xueqian

last: Zhuang

first: Chunhao

last: Pan

first: Simon

last: Joost

first: Stefan

last: Torborg

first: Tuomas

last: Tammela


title: Expression Landscape of RNA-binding proteins (RBPs) during adipogenesis and diet-induced obesity

city: Riyadh

first: Sameer

last: Mohammad

address: Ali Al Arini, Ar Rimayah, P.O. Box 3660, Mail code 1515

country: Saudi Arabia

institute: KAIMRC, KSAU-HS

summary: Impact of adipogenic differentiation on the global gene expression  in murine cell line 3T3-L1

overall_design: Gene expression patterns between the undifferentiated (Day 0) and differentiated (Day 7) 3T3-L1 cells using high-throughput RNA sequencing

first: Ghida

last: Dairi

first: Abdulrahman

last: Alswaji

first: Mamoon

last: Rashid


title: Ileum single cells expression in mice lacking Pgc1α in the intestine in response to western diet feeding.

city: Toulouse

first: Hervé

last: Guillou

address: 180 Chemin de Tournefeuille

department: ToxAlim

institute: INRAE

summary: To generate iPGC1α-/- mice, PGC1αfl/fl mice were intercrossed with Vil1-Cre mice to obatin Vil1-CreTg/-PGC1αfl/- mice. These mice were then backcrossed with PGC1αfl/fl mice to restore homozygosity for the iPGC1α floxed allele. Male Vil1-CreTg/-PGC1αfl/fl mice were bred to PGC1αfl/fl to produce the mice used in the study.  PGC1αfl/fl (iPGC1afl/fl) littermates were used as controls.

overall_design: Eight-weeks old mice were treated for 8 weeks weeks with 42% Kcal/fat diet enriched with saturated fats (0.2% total cholesterol, milk fat) (Teklad, TD.180342). Chow diet was used as control. Mice were randomly assigned to treatment groups for in vivo studies. All mice were sacrificed randomly fasted at ZT 3. For ileum section, the isolation of single cells was performed by a modification of Weiser method.

first: Elena

last: Piccinin

first: Claire

last: Naylies

first: Anne-Marie

last: Loustau

first: Yannick

last: Lippi

first: Nicolas

last: Loiseau

first: Antonio

last: Moschetta


title: Coordinated Regulation of Myonuclear DNA Methylation, mRNA, and miRNA Levels Associates with the Metabolic Response to Rapid Synergist Ablation-Induced Skeletal Muscle Hypertrophy in Female Mice

city: Lexington

first: Ahmed

last: Ismaeel

state: Kentucky

address: 900 S Limestone St

department: Physiology

institute: University of Kentucky

type: Non-coding RNA profiling by high throughput sequencing

summary: We investigatedmyonucleus-specific microRNA transcriptomes following an acute hypertrophic stimulus in mouse plantaris.

overall_design: We performed myounclear small RNA-sequencing during 72 hours of plantaris muscle mechanical overload in the mouse to molecularly define the early phase of skeletal muscle fiber hypertrophy. The analysis of myonucleus-specific mature microRNAs and other small RNA species complements previously published methylation and transcriptional information.

first: A

first: Y

last: Wen

first: K

last: Murach

first: F

last: von Walden


title: Pathophysiology of androgen-associated endothelial cell dysfunction in phenotype A polycystic ovarian syndrome revealed by iPSCs modeling

city: Taipei

first: Chia-Lang

last: Hsu

address: No. 7, Zhongshan S. Rd.

department: Department of Medical Research

country: Taiwan

institute: National Taiwan University Hospital

summary: Abundant evidence suggests that women with polycystic ovary syndrome (PCOS) have increased metabolic aberrations and cardiovascular risks and present with signs of endothelial cell (EC) dysfunction. However, whether and how androgen is involved in the pathogenesis of EC dysfunction in PCOS remains unclear. Induced pluripotent stem cells (iPSCs) were established in two PCOS patients and two control participants and further differentiated into ECs via monoculture under chemically defined conditions. Both PCOS patients were phenotype A (present with oligomenorrhea, hyperandrogenism, and polycystic ovarian morphology) and were diagnosed with metabolic syndrome. Single-cell transcriptomic analysis of the iPSC-derived ECs revealed functional differences involving the cell cycle process, vascular endothelial growth factor (VEGF) signaling and apoptosis between the PCOS and control groups. Decreased expression of cell proliferation and cell cycle related genes were noted in the PCOS iPSC-derived ECs. Dihydrotestosterone (DHT) treatment significantly enhanced cell proliferation and angiogenic function in the control iPSC-derived ECs. In contrast, significantly deteriorated cell proliferation accompanied with diminished expression of androgen receptor/cyclin-dependent kinase 1/VEGF signaling pathway was shown in the PCOS iPSC-derived ECs after DHT treatment, alongside with impaired angiogenesis demonstrated by the tube formation and wound healing assay. In conclusion, disease-specific iPSCs were successfully established in phenotype A PCOS patients with metabolic syndrome and served as an effective platform for disease modeling in this specific subgroup. Both intrinsic and androgen-induced cellular proliferation and angiogenesis were significantly impaired in the PCOS iPSC-derived ECs, providing new pathogenic evidence for androgen-mediated EC dysfunction and possibly further cardiovascular consequences.

overall_design: single-cell RNA-seq

first: C

last: Wu

first: H

middle: N

last: Ho


title: Interferon Regulatory Factor 6 Determines Epithelial Cell Development and Immunity 2

city: Portland

first: Timothy

middle: J

last: Nice

state: OR

address: 3181 SW Sam Jackson Park Rd

department: Molecular Microbiology and Immunology

institute: Oregon Health & Science University

summary: Intestinal epithelial cells (IECs) form a primary barrier against microbial invasion. Prior studies of enteric pathogens have indicated that IEC defense mechanisms are distinct from those of other cell types. For example, antiviral defense of IECs depends on type III interferon whereas most cell types depend on type I IFN. Interferon regulatory factors (IRFs) are a family of transcription factors with well-described roles in stimulation of IFN cytokines, but IRF6 is unique in its preferential expression by epithelial lineages. IRF6 has primarily been studied in epidermal development, but has relatively unknown roles in the intestinal epithelium. Here, we found that Irf6 KO regulated IFN-stimulated antiviral immunity of IECs but had no effect on macrophages. RNseq analysis of Irf6 KO cells showed significant differences in the IFN-stimulated gene expression program that correlated with the magnitude of antiviral gene stimulation. We also found significant baseline phenotypic and transcriptional changes in Irf6 KO IECs, with reduced rate of growth and preturbation of growth and differentiation pathway genes. Knockout of Irf6 in primary IEC organoids also resulted in slower growth and smaller size. Transcriptional analysis of Irf6 KO organoids indicated reduced expression of genes in the epithelial differentiation pathwya, including Wnt and Notch pathway genes, as well as increased expression of a subset of IFN-stimulated genes. These data indicate a previously unappreciated role of Irf6 in shaping the IEC transcriptome, including baseline epithelial development genes and IFN-stimulated genes.

overall_design: Mouse IEC organoid lines (derived from Mx1-GFP mice, Uccellini et al., 2012; doi: 10.1016/j.celrep.2018.11.030) were transduced with lentivirus encoding Cas9 and gRNA against Irf6 or non-targeting control, and monoclonal isolates were sequence-confirmed for disruption of the Irf6 locus. Treatments were added to cultured cells, and single cells were isolated twenty-four hours after treatments. Samples were collected in experimental triplicate.

first: Austin

last: Wright


title: Alveolar differentiation drives resistance to KRAS inhibition in lung adenocarcinoma [RNA-seq]

first: ZHUXUAN

last: LI

first: Zhuxuan

last: Li

first: Xueqian

last: Zhuang

first: Chunhao

last: Pan

first: Simon

last: Joost

first: Stefan

last: Torborg

first: Tuomas

last: Tammela


title: Hypothalamic tanycytes as mediators of maternally programmed seasonal plasticity

city: Tromsoe

first: Shona

last: Wood

address: Hansine Hansens veg 18

institute: UiT

summary: Environments with seasonal fluctuations requires inhabitants to anticipate their metabolic demands to survive. Drastic changes in food availability and temperature impose pressing challenges, especially during the first weeks of life. Offspring born early and late in the breeding season require different metabolic strategies. The mother’s melatonin levels ensures this in utero, acting as an internal mirror of day length. The melatonin levels programs the offspring to either grow fast and reproduce quickly (early born), or grow slow and delay maturation until next spring (late born). Thyroid hormone availability is altered by the melatonin signal and drives these differing metabolic strategies. Tanycytes located in the ependymal zone of the 3rd ventricle of the hypothalamus are at the crux of this change in thyroid hormone availability. Current literature provide ample evidence that these cells serve as a gatekeeper of metabolic feedback circuits, and photoperiodic history cues. Despite recent advances, our mechanistic understanding of how tanycytes regulate metabolic trajectories remains elusive. Here we used a well-established maternal photoperiodic programming paradigm to decipher the mechanism tanycytes utilise to dictate the offspring metabolic trajectory. The paradigm only rely on variable gestational light exposure to alter metabolic phenotype. Laser capture microdissection of ependymal zone enabled us to perform RNAseq on tanycyte enriched samples.

overall_design: Siberian hamsters were gestated either on long photoperiod (LP, 16 hours of light per 24 hours) or short photoperiod (SP, 8 hours of light per 24 hour) and were maintained on those photoperiods until weaning (P21). At weaning (P21), a subgroup of the animals from both LP and SP were assigned to the same intermediate photoperiod (LPIP, SPIP, 14 hours of light per 24 hours). Animals were sampled for laser capture microdissection (LCMD) at P50.

middle: H

first: David

last: Hazlerigg

first: Vebjørn

last: Melum


title: RNA-Seq of BRQ-treated and control B16F10 cells

city: xi'an

first: Wei

last: Gaofei

state: Shaanxi

address: beilin

institute: Northwestern Polytechnical University

summary: B16F10 cells treated with DMSO or BRQ were collected and then the total RNA was isolated. After removal of the remaining genomic DNA, mRNA was purified from total RNA using polyT and then fragmented with 10× RNA fragmentation buffer and the RNA-seq library was constructed using Hieff NGS Ultima Dual-mode mRNA Library Prep Kit and was sequenced.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for BRQ treated group and control group. Each group was replicated for three times.

first: Ruizhuo

last: Lin

first: Gaofei

last: Wei


title: Gene expression in lung tissue, blood and spleen of mice with severe acute pancreatitis

city: Beijing

first: Yiqiu

last: Peng

state: China

address: No.17 Qihelou Road, Dongcheng District

institute: Beijing Obstetrics and Gynecology Hospital, Capital Medical University

summary: Severe acute pancreatitis (SAP) is a critical disease, often complicated with multiple organ dysfunction, which seriously endangeres the life safety of patients. Previous studies have shown that cGAS-STING signaling pathway is significantly activated in mice with severe acute pancreatitis. In this study, we studied the gene expression in different tissues of normal mice and SAP mice to understand the differentially expressed genes and find the downstream genes of cGAS-STING signaling pathway.

overall_design: The specific process involved dividing the C57BL/6 mice into two groups: control (CON) and severe pancreatitis (SAP). The SAP group was given intraperitoneal injections of caerulein 100 µg/kg every hour after fasting for 12 h, a total of seven times. 10 mg/kg LPS was given immediately after the seventh intraperitoneal CAE injection. The CON group was assigned intraperitoneal injections of the same amount with normal saline Lung, blood and spleen were collected after 24 h of modeling.


title: PDGFRβ signaling cooperates with β-catenin to modulate c-Abl and biologic behavior of desmoid-type fibromatosis [ChIP-seq]

first: Bic

last: MSKCC

address: 1275 York Ave.

institute: Memorial SLoan-Kettering Cancer Center

summary: Purpose: This study sought to identify signaling pathways that modulate β-catenin function in desmoid cells, affecting natural history and sorafenib response. Experimental Design: In vitro experiments utilized primary desmoid cell lines to examine interaction of β-catenin signaling with other pathways. Relevance of in vitro results was assessed in surgical specimens and Alliance trial A091105 correlative biopsies.  Results: CTNNB1 knockdown inhibited hypoxia-regulated gene expression in vitro and reduced levels of HIF1α. Expression of hypoxia-associated genes clustered desmoids separately from normal mesenchymal tissue. ChIP-seq identified ABL1 as a β-catenin transcriptional target that modulated HIF1α protein expression and desmoid cell proliferation. Abrogation of either CTNNB1 or HIF1 inhibited the ability of desmoid cells to induce VEGFR2 phosphorylation and tube formation in endothelial cell co-cultures. Sorafenib inhibited this activity directly but also reduced HIF1α protein expression and c-Abl activity while inhibiting PDGFRβ signaling in desmoid cells. Conversely, c-Abl activity and desmoid cell proliferation were positively regulated by activation of PDGF signaling. Reduction in PDGFRβ and c-Abl phosphorylation was commonly observed in samples from patients after treatment with sorafenib; baseline samples in patients with greater drug response tended to have higher baseline PDGFRβ/c-Abl pathway activation.  Conclusions: The β-catenin transcriptional target ABL1 is necessary for proliferation and maintenance of HIF1α protein expression in desmoid cells. Regulation of c-Abl activity by PDGF signaling and targeted therapies modulates desmoid cell proliferation, thereby suggesting a reason for variable biologic behavior between tumors, a mechanism for sorafenib activity in desmoids, and markers predictive of outcome in patients.

first: Julian

last: Rozenberg

first: Jia

last: Hu

first: Aimee

last: Crago


title: the change of mRNA expression in SKOV3 cells after treated with placental extracellular vesicles

city: Auckland

first: Xinyi

last: Sun

address: 85 Park Road, Grafton

country: New Zealand

institute: the university of auckland

summary: There is a cross-link between the placenta and cancer development, as the placenta is grown as a highly invasive tumour-like organ. However, placental development is strictly controlled. Although the underlying mechanism of this control is largely unknown, it is now well-recognised that extracellular vesicles (EVs) released from the placenta play an important role in controlling placenta proliferation and invasion, as placental EVs have shown their effect on regulating maternal adaptation. Better understanding the tumour-like mechanism of the placenta could help to develop a therapeutic potential in cancers.

overall_design: treat SKOV3 ovarian cancer cells with placental extracellular vesicles, to investigate the change in the expression level of mRNA in SKOV3 cells

first: Qi

last: Chen

first: Min

last: Zhao

first: Yunhui

last: Tang


title: Effect of vitamin D supplementation on muscle transcriptome in pigs, estimated by 3`quant mRNA-seq

city: Balice

first: Anna

middle: Dominika

last: Steg

address: Krakowska 1

department: Department of Animal Molecular Biology

country: Poland

institute: National Research Institute of Animal Production

summary: We report the anaysis of the effect of the supplementation of pigs feed with high doses of vitamin D on the muscle transcriptome. We observed significant changes in the expression of only one gene - IFNGR2.

overall_design: Animals were kept in individual straw-bedded pens with free access to water. At the 85th day of life, pigs were randomly assigned to one of 3 groups so that animaln fron one litter were divided among alll three groups. Pigs were fed with isoprotein and isoenergetic feeds differing only in the amount of vitamin D (0, 5000, 10000 IU/kg of feed). Experiment was continued for 90 days.

first: Maria

last: Oczkowicz


title: HELZ promotes R loop resolution to facilitate DNA double-strand break repair by homologous recombination

city: Atlanta

first: Bing

last: Yao

address: 615 Michael Street

department: Department of Human Genetics

institute: Emory University

summary: Successful R-loop homeostasis consists of its timely biogenesis and removal throughout the genome to regulate diverse cellular processes. Yet, they are considered hazardous source to our genome when their turnover goes awry. Here, we report HELZ, a novel player in R-loop homeostasis and DNA repair pathway. HELZ mediates resistance to several DNA damaging agents, and localizes to DSBs and its depletion increases R-loops fostering genomic instability. Loss of HELZ results in impaired homologous recombination (HR) due to R-loops accumulation, with an increase in classical-non-homologous end joining (c-NHEJ), suggesting a role for HELZ in regulating DSB repair pathway choice. Rad51 retention at DSBs is governed by HELZ mediated R-loop accumulation. Mechanistically, our data show that HELZ complexes with BRCA1 and facilitates its recruitment to DSBs in an R-loop dependent manner. Collectively, our data support a model in which HELZ recruits BRCA1 and facilitates R loop resolution at DSBs to promote HR and therefore maintains genome stability.

overall_design: R-loop profiles of HELZ knockdown U2OS cells

first: Ramona

last: Haji-Seyed-Javadi

first: Yingzi

last: Hou

middle: S

last: Yu


title: RNA polymerase II dynamics and mRNA stability feedback scale mRNA amounts with cell size

city: Stanford

first: Georgi

middle: Kolev

last: Marinov

address: 279 Campus Drive West, Beckman Center, B-257A/259

department: Genetics

institute: STANFORD UNIVERSITY

summary: A fundamental feature of cellular growth is that total protein and RNA amounts increase with cell size to keep concentrations approximately constant. A key component to this is that global transcription rates increase in larger cells. Here, we identify RNAPII as the limiting factor scaling mRNA transcription with cell size in budding yeast, as transcription is highly sensitive to the dosage of RNAPII but not to other components of the transcriptional machinery. Our experiments support a dynamic equilibrium model where global RNAPII transcription at a given size is set by the mass-action recruitment kinetics of unengaged nucleoplasmic RNAPII to the genome. However, this only drives a sub-linear increase in transcription with size, which is then partially compensated for by a decrease in mRNA decay rates as cells enlarge. Thus, limiting RNAPII and feedback on mRNA stability work in concert to scale mRNA amounts with cell size.

sample_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae
Nakaseomyces glabratus

overall_design: ChIP-seq and RNA-seq experiments using S. cerevisiae with a spike-in of S. pombe or C. glabrata cells for spike-in normalisation.

first: Matthew

last: Swaffer

middle: K

first: Huan

last: Zheng

first: Lucas

last: Fuentes Valenzuela

first: Crystal

middle: Y

last: Tsui

first: Andrew

middle: W

last: Jones

first: Jessica

last: Greenwood

first: Anshul

last: Kundaje

first: William

last: Greenleaf

first: Rodrigo

last: Reyes-Lamothe

first: Jan

last: Skotheim


title: Serrate modulates N6-Methyladenosine (m6A) RNA modification in Arabidopsis

city: Lincoln

first: Chi

last: Zhang

state: NE

address: 1901 Vine Street

institute: University of Nebraska - Lincoln

type: Methylation profiling by high throughput sequencing

summary: N6-methyladenosine (m6A) is the most common prevalent internal modifications found in many of the eukaryotic mRNA and plays an important role in RNA metabolism including pre-mRNA processing, mRNA stability, RNA splicing, RNA export and nuclear retention. Serrate is a component of the Dicer complex, plays as a key factor in RNA metabolism. We here reported SERRATE acts as a key regulator of mRNA m6A modification in Arabidopsis. Loss function of SE results in significant global m6A level reduction in the se-1 mutant comparing to the Col-0. SE positively regulates the transcription of MTA and MTB. In addition, SE physically interacts and functionally works with the m6A writer complex MTA and MTB which affects the binding of m6A methylase to mRNA. Taking together, our data provides a molecular framework that SE modulates m6A mRNA modification in Arabidopsis.

overall_design: To investigate the function of SERRATE regulation of the N6-Methyladenosine modification in Arabidopsis, we perferred the comparative m6A profiling analysis for se-1 mutant and Col-0 wildtype.

first: Lu

last: Gan

first: Shengjun

last: Li

first: Bin


title: Aging-associated Decline in Vascular Smooth Muscle Cell Mechanosensation is Mediated by Piezo1 Channel II

city: Brooklyn

first: Ngoc

last: Luu

address: 6 Metrotech Center

institute: New York University

summary: Aging of the vasculature is associated with detrimental changes in vascular smooth muscle cell (VSMC) mechanosensitivity to extrinsic forces in their surrounding microenvironment. However, how chronological aging alters VSMCs’ ability to sense and adapt to mechanical perturbations remains unexplored. Here, we show defective VSMC mechanosensation in aging measured with ultrasound tweezers-based micromechanical system, force instantaneous frequency spectrum and transcriptome analyses.  The mechanobiological study reveals thataged VSMCs adapt a relatively inert solid-like state with altered actin cytoskeletal integrity, resulting in an impairment in their mechanosensitivity and dynamic mechanoresponse to mechanical perturbations. The aging-associated decline in mechanosensation behaviors is mediated by hyperactivity of Piezo1-dependent calcium signaling. Inhibition of Piezo1 alleviates vascular aging and partially restores the loss in dynamic contractile properties in aged cells. Altogether, our study reveals the novel signaling pathway underlying aging-associated aberrant mechanosensation in VSMC and identifies Piezo1 as a potential therapeutic mechanobiological target to alleviate vascular aging.

overall_design: Single-cell RNA-sequencing libraries of four groups of vascular smooth muscle cells extracted from C57BL/6 mice  young (12 weeks) and old (58-78 weeks) cultured in four different treatments. Young + Angiotensin II and Old + siPiezo1 are the experimental groups, while Young and Old are the control groups.

first: Weiqiang

last: Chen


title: Insertional mutations on RsFLC2 compromises vernalization response of radish (Raphanus sativus L.)

city: Anseong-si,

first: Sang Woo

last: Lee

address: 4726 Seodong-daero, Daedeok-myeon

department: Plant Science and Technology

institute: CHUNG-ANG UNIVERSITY

summary: In this study, scientific efforts to grasp molecular details underlying vernalization-triggered floral transition were undertaken in radish (Raphanus sativus L.). We performed a comparative transcriptomic analysis between normal flowering ‘Jinjudaepyung’ and very late flowering inbred line, ‘Simu’.

overall_design: Three different vernalization treatment (NV (Non-vernalization), Vernalization (V40), After-veranlization (AV)) to Raphanus sativus L. whole plants: Non-vernalization; 4weeks old (green house condition); Vernalization; 10weeks old (green house condition); After-veranlization;12weeks old

first: Dong-Hwan

last: Kim


title: Transcriptome-wide m6A methylation of Wuhua yellow-feathered chicken ovary revealed potential molecular mechanisms underlying the low egg performance

city: Meizhou

first: Congjun

last: Jia

address: xueyuan road

institute: Guangdong Meizhou Vocational and Technical College

summary: RNA N6-melthyladenosine has been suggested to play important roles in various biological processes. Chicken ovary development is a process controlled by complex gene regulations. In this study, transcriptome-wide m6A methylation of the Wuhua yellow-feathered chicken ovaries before and after sexual maturation was profiled to identify potential molecular mechanisms underlying chicken ovary development. The results showed that m6A levels of mRNAs changed dramatically during sexual maturity. A total of 1476 differential m6A peaks were found between these two stages with 662 significantly up-regulated methylation peaks and 814 down-regulated methylation peaks after sexual maturation. A positive correlation was found between the m6A peaks and gene expression levels. Functional enrichment analysis indicated that apoptosis related pathways might be the key molecular regulatory pathway underlying the poor reproductive performance of Wuhua yellow-feathered chicken. The fine expressional regulation of genes related to follicles development and follicle atresia controlled by m6A during the maturity results in the poor reproductive performance in the Wuhua yellow-feathered chicken. However, the regulatory mechanisms are still unclear, thus more further studies are required. The pathways and corresponding candidate genes found here may be useful for molecular design breeding for improving egg production performance in Chinese local chicken breed, and it will also benefit for the genetic resource protection of valuable avian species.

overall_design: Detection of m6A in Wuhua yellow-feathered chicken before and after sexual maturity

first: Jia

last: Congjun

first: Zhang

last: Mengling


title: Nascent elongating transcript sequencing (NET-seq) show different pause registers with apyrase treatment during library preparation

city: Madison

first: Robert

last: Landick

state: Wisconsin

address: 1550 Linden drive

department: Department of Biochemistry

institute: University of Wisconsin–Madison

summary: Transcriptional pausing aids gene regulation by cellular RNA polymerases (RNAPs). In many bacteria, a surface-exposed domain inserted into the catalytic trigger loop (TL) of RNAP, called SI3 in Escherichia coli, modulates pausing and is essential for growth. Here we describe a viable E. coli strain lacking SI3 enabled by a suppressor TL substitution (β'Ala941→Thr; ∆SI3*). ∆SI3* increased transcription rate in vitro relative to ∆SI3, possibly explaining its viability, but retained both positive and negative effects of ∆SI3 on pausing. ∆SI3* inhibited pauses stabilized by nascent RNA structures (pause hairpins; PHs) but enhanced other pauses. Using NET-seq, we found that ∆SI3*-enhanced pauses resemble the consensus elemental pause sequence whereas sequences at ∆SI3*-suppressed pauses, which exhibited greater association with PHs, were more divergent. ∆SI3*-suppressed pauses also were associated with apparent pausing one nt upstream from the consensus sequence, often generating tandem pause sites. These '–2 pauses' were stimulated by pyrophosphate in vitro and by addition of apyrase to degrade residual NTPs during NET-seq sample processing. We propose that some pauses are readily reversible by pyrophosphorolysis or single-nucleotide cleavage. Our results document multiple ways that SI3 modulates pausing in vivo and may explain discrepancies in consensus pause sequences in some NET-seq studies.

sample_organism:
Escherichia coli
Bacillus subtilis

platform_organism:
Escherichia coli
Bacillus subtilis

overall_design: Examination of nascent transcripts in WT E. coli with apyrase treatment to remove free rNTPs after cell homogenization. A B. subtilis strain is used as spike-in control for quantitative analysis.

first: Yu

last: Bao


title: PDGFRβ signaling cooperates with β-catenin to modulate c-Abl and biologic behavior of desmoid-type fibromatosis [RNA-seq II]

city: New York

first: Bic

last: MSKCC

summary: The mechanisms underlying oncogenesis in desmoid-type fibromatosis are poorly understood.  This project sought to understand how β-catenin may function to promote desmoid formation and how external signaling by PDGFRβ modulates this activity.  To examine this question, RNA-seq was performed on CTNNB1 knock-downs.  Gene set enrichment analysis suggested that the oncogene controlled HIF1 and angiogenesis pathways; expression of related genes accurately differentiated desmoids analyzed by U133A array from normal mesenchymal tissues.  We identified c-ABL as a direct transcriptional target of β-catenin that promoted HIF1α expression in desmoid cells.  We also noted that c-ABL activity was enhanced by PDGFRβ.  PDGFRβ enhanced desmoid cell proliferation and c-ABL was necessary for desmoid proliferation.  To identify potential markers of PDGFRβ/c-ABL activity in vivo, we assessed RNA-seq of desmoid cells treated with PDGF-BB.  ERG1 transcription was highly upregulate and IHC of ERG1 was subsequently used to assess outcomes in desmoid patients with biopsies available for testing.

overall_design:
1. Primary desmoid cell line DES9525 were treated with shRNA directed against CTNNB1, selected with antibiotic and RNA-seq analyzed on both CTNNB1 knock-downs and scramble controls
2. Primary desmoid cell line DES9525 was treated with PDGF-BB (20ng/ml) for 24 hours and RNA-seq performed on both treated and untreated cells

last: Hu

first: Aimee

middle: M

last: Crago


title: PDGFRβ signaling cooperates with β-catenin to modulate c-Abl and biologic behavior of desmoid-type fibromatosis [RNA-seq I]


title: Single Cell Transcriptomics identifies a WNT7A-FZD5 Signaling Axis that maintains Fallopian Tube Stem Cells in Patient-derived Organoids [bulk RNA-seq]

city: Oxford

first: Ahmed

middle: Ashour

last: Ahmed

state: Oxfordshire

address: John Radcliffe Hospital, Headley way

department: Weatherall Institute of Molecular Medicine

institute: University of Oxford

summary: Despite its significance to reproduction, fertility, sexually transmitted infections and various pathologies, the fallopian tube (FT) is relatively understudied. Strong evidence points to the FT as the tissue-of-origin of high grade serous ovarian cancer (HGSOC), the most fatal gynaecological malignancy. HGSOC precursor lesions arise specifically in the distal FT (fimbria) which is reported to be enriched in stem-like cells. Investigation of the role of FT stem cells in health and disease has been hampered by a lack of characterization of FT stem cells and lack of models that recapitulate stem cell renewal and differentiation in vitro. Using optimized organoid culture conditions to address these limitations, we found that FT stem cell renewal is highly dependent on WNT/β-catenin signaling and engineered endogenous WNT/β-catenin signaling reporter organoids to biomark, isolate and characterize putative FT stem cells. Using functional approaches as well as bulk and single cell transcriptomic analyses, we show that an endogenous hormonally-regulated WNT7A-FZD5 signaling axis is critical for self-renewal of human FT stem cells, and that WNT/β-catenin pathway-activated cells form a distinct transcriptomic cluster of FT cells enriched in ECM remodelling and integrin signaling pathways. In addition, we find that the WNT7A-FZD5 signaling axis is dispensable for mouse oviduct regeneration. Overall, we provide a deep characterization of FT stem cells and their molecular requirements for self-renewal, paving the way for mechanistic work investigating the role of stem cells in FT health and disease.

overall_design: Bulk RNA-seq of patient-derived Fallopian tube Wnt/β-catenin signalling reporter organoids

first: Abdulkhaliq

last: Alsaadi

first: Mara

last: Artibani


title: PDGFRβ signaling cooperates with β-catenin to modulate c-Abl and biologic behavior of desmoid-type fibromatosis

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

overall_design: Refer to individual Series