title: Comparative analysis of syngeneic mouse models of high-grade serous ovarian cancer

city: Ottawa

first: David

last: Cook

state: ON

address: 501 Smyth Rd

department: Cancer Therapeutics Program

institute: Ottawa Hospital Research Institute

summary: Ovarian cancers exhibit high rates of recurrence and poor treatment response. Preclinical models that recapitulate human disease are critical to develop new therapeutic approaches. Syngeneic mouse models allow for the generation of tumours comprising the full repertoire of non-malignant cell types but have expanded in number, varying in cell type of origin, method for transformation, and ultimately, the properties of the tumours they produce. Here we have performed a comparative analysis of high-grade serous ovarian cancer models based on transcriptomic profiling of 22 cell line models, and intrabursal and intraperitoneal tumours from 12. Among cell lines, we identify distinct signalling activity, such as elevated inflammatory signalling in STOSE and OVE16 models, and MAPK/ERK signalling in ID8 and OVE4 models; metabolic differences, such as reduced glycolysis-associated expression in several engineered ID8 subclones; and relevant functional properties, including differences in EMT activation, PD-L1 and MHC class I expression, and predicted chemosensitivity. Among tumour samples, we observe increased variability and stromal content among intrabursal tumours. Finally, we predict differences in the microenvironment of ID8 models engineered with clinically relevant mutations. We anticipate that this work will serve as a valuable resource, providing new insight to help select models for specific experimental objectives.

overall_design: RNA-seq of syngeneic models of high grade serous ovarian cancer, including 22 cell line models, and intrabursal and intraperitoneal tumours from 12

first: Cook

last: David

first: Vanderhyden

last: Barbara


title: Effect of efferent duct ligatation on the transcriptome of the first 3 proximal segments of the murine epididymis

status: Public on Sep 11 2023

city: Washington

first: Danielle

last: Sosnicki

state: DC

address: 3001 Connecticut Ave NW

country: USA

institute: Smithsonian's National Zoo and Conservation Biology Institute

type: Expression profiling by high throughput sequencing

summary: To examine the effect of efferent duct ligation (EDL) on the gene expression of epididymal segments 1-3, we performed EDL procedures on WT mice and harvested the epididymides 3-weeks after surgery and sequenced the transcriptome of individual segments 1, 2, and 3 of ligated epididymides and control (non-ligated) epididymides

overall_design: Comparative gene expression profiling analysis of RNA-seq data from segments 1, 2 and 3 of ligated epididymides (L1, L2, L3) after efferent duct ligations (EDL) and segments 1-3 of control (non-ligated) epididymides (C1, C2, C3). Two batches of sequencing runs were performed (3017 and 3097) each containing one of each sample (L1, L2, L3, C1, C2, C3)

middle: M

first: Roy

last: Cohen

first: Atsushi

last: Asano

first: Jacquelyn

middle: L

last: Nelson

first: Chinatsu

last: Mukai

first: Pierre

last: Comizzoli

first: Alexander

middle: J

last: Travis


title: ZNF683 marks a CD8+ T cell population associated with anti-tumor immunity following anti-PD-1 therapy for Richter syndrome [RNA-Seq]

city: Copenhagen

first: William

middle: Winston

last: Agace

address: Blegdamsvej 3B

department: Skin Immunology Research Center

country: Denmark

institute: Copenhagen University

summary: Unlike many other hematologic malignancies, Richter syndrome (RS), an aggressive B cell lymphoma originating from indolent chronic lymphocytic leukemia, is responsive to PD-1 blockade. To discover the determinants of response, we analyzed single-cell transcriptome data generated from 17 bone marrow samples longitudinally collected from 6 RS patients. Response was associated with intermediate exhausted CD8 effector/effector memory T cells marked by high expression of the transcription factor ZNF683, determined to be evolving from stem-like memory cells and divergent from terminally exhausted cells. This signature overlapped with that of tumor-infiltrating populations from PD-1 responsive solid tumors. ZNF683 was found to directly target key T cell genes (TCF7, LMO2, CD69) and impact pathways of T cell cytotoxicity and activation. Analysis of pre-treatment peripheral blood from 10 independent RS PD-1 treated patients, as well as solid tumor PD-1 treated patients, supported an association of ZNF683high T cells with response.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Jurkat cells with or without ZNF683 expression

first: Erin

last: Parry

first: Stephanie

last: Deng

first: Camilla

middle: K

last: Lemvigh

first: Catherine

last: Wu


title: Knockout of MXRA8 in MDA-MB-231 cells

city: Guelph

first: Roger

last: Moorehead

address: 50 Stone Rd E

department: Biomedical Sciences

country: Canada

institute: University of Guelph

summary: Matrix remodeling associated protein 8 or MXRA8 is a transmembrane protein that can binds arthritogenic alpha viruses like the Chikunggunya virus and provide viral entry into cells. MXRA8 can also interact with integrin β3 and thus possibly regulate cell-cell interactions and binding to the extracellular matrix. While MXRA8 has been associated with reduced survival in patients with colorectal and renal clear cell cancers, the role of MXRA8 in breast cancer remains unexplored. Our previous work exploring genes that mediate the anti-tumor effects of the miR-200c/141 cluster in breast cancer identified MXRA8 as a potential suppressor of breast cancer growth and metastasis. In the current study, MXRA8 was knocked out in the human triple negative breast cancer cell line, MDA-MB-231. Loss of MXRA8 reduce cell proliferation in vitro but had no effect on apoptosis or migration in cultured cells. However, loss of MXRA8 significantly delayed tumor development and reduced metastatic dissemination to the lungs in a xenograft model. RNA sequencing identified three genes, ADMATS1, TIE1, and BMP2 whose expression were significantly reduced in MXRA8 knockout tumors compared to control tumors. MXRA8 staining of a human breast cancer tissue array revealed higher levels of MXRA8 in primary tumors and metastases of aggressive tumor subtypes (TNBC and HER2+) compared to less aggressive, ER+ breast cancers.  Our findings demonstrate for the first time that MXRA8 regulates the progression of human TNBC possibly through influencing the interaction of tumor cells with their microenvironment.

overall_design: MXRA8 was knocked out in MDA-MB-231 cells using Crispr-Cas. RNA sequencing was performed on two different knockout clones and a control clone  grown in two dimensional culture and following injection into the mammary glands of NCG mice.


title: Morphine Re-arranges Chromatin Spatial Architecture of Primate Cortical Neuron

status: Public on Sep 12 2023

city: Helsinki

first: Liang

last: Wang

address: Viikinkaari 5

country: Finland

institute: University of Helsinki

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

overall_design: Refer to individual Series


title: Morphine Re-arranges Chromatin Spatial Architecture of Primate Cortical Neuron [HiC]

summary: Purpose:The goals of this study are to investigate the 3D chromatin architecture of cortical neurons in rhesus monkeys treated with morphine for 90 days using digestion-ligation-only high-throughput chromosome conformation capture technology  combined with  transcriptome profiling (RNA-seq).

overall_design: Investigate the alteration of chromatin architecture after chronic morphine administration in rhesus monkey

first: Xiaobo

last: Cen


title: eIF3d controls the persistent integrated stress response

city: Boston

first: Amy

middle: Si-Ying

last: Lee

state: MA

address: 450 Brookline Ave SM520

department: Cancer Immunology and Virology

institute: DFCI

summary: All cells respond to intrinsic and extrinsic stresses by reducing global protein synthesis and activating select gene programs necessary for survival. Here, we show the fundamental integrated stress response (ISR) is driven by the non-canonical cap-binding protein eIF3d which acts as a master effector to control core stress response orchestrators, the translation factor eIF2ɑ and the transcription factor ATF4. We find that during persistent stress, eIF3d activates translation of the protein kinase GCN2, inducing eIF2ɑ phosphorylation and inhibiting global protein synthesis. In parallel, eIF3d upregulates the m6A demethylase enzyme ALKBH5 to drive 5′ UTR-specific demethylation of stress response genes, including ATF4. Ultimately, this cascade converges on ATF4 expression by increasing mRNA engagement of translation machinery and enhancing ribosome bypass of upstream open reading frames. Our results reveal that eIF3d acts as a critical life-or-death decision point during adaptation to chronic stress and uncover a synergistic signaling mechanism in which translational cascades dynamically complement transcriptional amplification to control essential cellular processes.

overall_design:
We performed RNA-Seq or m6A-eCLIP analysis of HEK293T expressing WT or phosphomimetic eIF3d during chronic ER stress. We also performed eIF3d-Subunit-Seq analysis of HEK293T during chronic ER stress.
Grant:  National Institutes of Health (1R35GM142527).

middle: S

first: Shaoni

last: Mukhopadhyay

first: Maria

middle: E

last: Amodeo


title: Distinct early transcriptional regulations by turgor and osmotic potential changes in the root of Arabidopsis

city: Montpellier

first: Sandrine

last: Ruffel

address: 2 Place Viala

department: Montpellier University

country: France

institute: INRA

summary: In a context of climate change, deciphering signaling pathways leading to plant adaptation to drought, water availability, and salt tolerance is a crucial question. A common crossing point of these plant stresses is their impact on plant water potential, a composite physico-chemical variable reflecting the availability of water for the plant biological and biochemical processes such as growth or stomatal aperture. The water potential of plant cells is mainly driven by their turgor pressure and osmotic potential. Here we investigated the effect of a variety of osmotic treatments in the root of Arabidopsis plants grown in hydroponics. Measurement of the cortical cells turgor pressure with a cell pressure probe allowed to control the intensity of the treatments and, in particular, preserve the cortex from plasmolysis. Transcriptome analyses at early time point (15min) showed specific and quantitative transcriptomic responses for both osmotic and turgor pressures in the root. Our results highlight how water-related biophysical parameters can shape the transcriptome and provide putative candidates to explore further the early perception of water stress in plants.

overall_design: Col-0 wild-type plants were grown in a standard hydroponic solution. One part of the plants was transferred to the same hydroponic solution as a control for the osmotic pressure. The other part of the plants was transferred to the same hydroponic solution supplemented with various concentrations of various solutes : Sodium chloride at 25, 50, 75 or 100mM or Sorbitol at 50, 100 or 150mM or Polyethylene glycol 8000 at 75, 100, 125 or 150mM or Ethylene glycol at 50, 100, 150 or 200mM. Root collection was done 15 minutes after application of the osmotic treatments.

first: Yann

last: Boursiac

first: Gabriel

last: Krouk


title: Morphine Re-arranges Chromatin Spatial Architecture of Primate Cortical Neuron [RNA-seq]

summary: Purpose: The goals of this study are to investigate the 3D chromatin architecture of cortical neurons in rhesus monkeys treated with morphine for 90 days using digestion-ligation-only high-throughput chromosome conformation capture technology  combined with  transcriptome profiling (RNA-seq).


title: Genome-wide CRISPR-Cas9 screen reveals selective vulnerability of ARID1A deficiency   Hepatocellular Carcinoma

city: Beiing

first: TAO

last: XING

state: Beiing

address: Beiing

country: China

institute: Peking University Cancer Hospital

summary: To uncover therapeutic strategies for ARID1A deficient HCC, we performed genome-scale CRISPR–Cas9 based synthetic lethality screens using ARID1A deficiency HCC cellular model

overall_design: Briefy, Cas9 stably expressed cells (~5000-fold library coverage in each group) were infected withThe Toronto human knockout pooled (TKOv3) lentiviral library at a low MOI (0.2~0.3) and selected for 3 days with 2~5 ug/ml puromycin. A part of these transfected cells was harvested at baseline (T0), the rest of cells allowed to grow for three weeks and collected(T21).

first: Tao

last: Xing


title: Calorie Restriction Outperforms Bariatric Surgery in Reversing Obesity-Driven Tumor Progression in a Mouse Model of Triple Negative Breast Cancer

city: chapel hill

first: michael

middle: francis

last: coleman

state: North Carolina

address: 235 dauer drive

institute: UNC

type: Methylation profiling by high throughput sequencing


title: NCOA5 haploinsufficiency in myeloid cells sufficiently causes non-alcoholic steatohepatitis and hepatocellular carcinoma

city: East Lansing

first: Hua

last: Xiao

state: Michigan

address: 567 WILSON RD, RM 2201

department: Physiology

institute: Michigan State University

summary: Molecular and cellular mechanisms causing the onset and progression of non-alcoholic fatty liver disease (NAFLD), non-alcoholic steatohepatitis (NASH), and HCC remain poorly understood.  Here we show that myeloid-cell-specific heterozygous deletion of Ncoa5 (Ncoa5ΔM/+) sufficiently causes the development of NAFLD/NASH and HCC in male mice. The platelet factor 4 (PF4) overexpressed by Ncoa5ΔM/+ intrahepatic macrophages is identified as a potent mediator to trigger lipid accumulation in hepatocytes by inducing expression of genes promoting lipogenesis.  Enrichment score of the gene expression signature derived from Ncoa5ΔM/+ hepatic macrophages correlated with unfavorable clinical parameters of NAFLD patients. Moreover, in HCC patients, the high PF4 expression correlated with poor overall survival and increased infiltrations of M2 macrophages, exhausted CD8 T cells, and MDSCs in HCCs. Our results reveal a novel macrophage-underlying mechanism for the onset of NAFLD and NASH-related HCC and suggest that NCOA5-PF4 axis is a potential target for therapeutic inhibition of NAFLD/NASH progression.

overall_design: mRNA profiles of liver F4/80+ non-parenchymal cells from 6.5-month-old male mice with myeloid-lineage-cell-specific Ncoa5 heterozygous deletion and loxp control male mice. 4 mice in each group.

first: Yueqi

last: Zhang

first: Yue

last: Luo


title: Effects of linoleic acid metabolite on liver gene expression in a diet-induced NAFLD/NASH model.

city: Shizuoka

first: Tetsuya

last: Hosooka

state: Shizuoka

address: 52-1 Yada

country: Japan

institute: University of shizuoka

summary:
To investigate the alterlation of  liver gene expression  by linoleic acid (LA) metabolite HYA  (10-hydroxy-cis-12-octadecenoic acid) in a diet-induced NAFLD/NASH model,
we evaluated liver of male C57BL/6J mice fed a nomal diet (ND), a high fat diet (HFD, Control(CT)), HFD supplemented with 1% HYA (HYA), or HFD supplemented with 1% LA (LA) for 26 weeks from 5-week-old.
We then performed gene expression profiling analysis using data obtained from RNA-seq of these 4 groups.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for liver of 4 groups[ND, Control, HYA, LA].

first: Yukiko

last: Imi

first: Nanaho

last: Kasahara


title: A subpopulation of lipogenic brown adipocytes drives thermogenic memory [Spatial Transcriptomics]

city: Philadelphia

first: Patrick

last: Lundgren

state: PA

address: 302 Johnson Pavilion, 3610 Hamilton Walk

institute: University of Pennsylvania

summary: Spatial transcriptomics of brown adipose tissue from thermoneutrality (TN) and from mouse that had undergone transient acute cold exposure 4 days previously (1cyc)

overall_design: Brown adipose tissue was collected from mouse at thermoneutrality and mouse that had undergone transient acute cold exposure 4 days previously. Sample preparation, sectioning, staining, imaging, library preparation, and sequencing was performed following the Visium protocol (10X Genomics).

first: Christoph

last: Thaiss


title: ZNF683 marks a CD8+ T cell population associated with anti-tumor immunity following anti-PD-1 therapy for Richter syndrome [CUT&RUN]

first: William

last: Agace

summary:
Unlike many other hematologic malignancies, Richter syndrome (RS), an aggressive B cell lymphoma originating from indolent chronic lymphocytic leukemia, is responsive to PD-1 blockade. To discover the determinants of response, we analyzed single-cell transcriptome data generated from 17 bone marrow samples longitudinally collected from 6 RS patients. Response was associated with intermediate exhausted CD8 effector/effector memory T cells marked by high expression of the transcription factor ZNF683, determined to be evolving from stem-like memory cells and divergent from terminally exhausted cells. This signature overlapped with that of tumor-infiltrating populations from PD-1 responsive solid tumors. ZNF683 was found to directly target key T cell genes (TCF7, LMO2, CD69) and impact pathways of T cell cytotoxicity and activation. Analysis of pre-treatment peripheral blood from 10 independent RS PD-1 treated patients, as well as solid tumor PD-1 treated patients, supported an association of ZNF683high T cells with response.
CUT&RUN sequencing for histone modifications H3K4me3, IgG isotype (control) and ZNF683 (Hobit) on/off

overall_design: Erin,M,Parry

first: Stephanie

last: Deng

first: Camilla

last: Lemvigh

first: Catherine

last: Wu


title: The bone transcription factor Osterix controls extracellular matrix and node of Ranvier related gene expression in oligodendrocytes [RNA-seq]

city: Chicago

first: Benayahu

last: Elbaz

state: Illinois

address: 303 E. Chicago Ave. Ward 7-641. Chicago, IL 60611

department: Neurology

institute: Northwestern University

summary: Oligodendrocytes are the primary producers of many extracellular matrix (ECM) related proteins found in the central nervous system (CNS), thereby, these cells play a critical role in the determination of brain stiffness, node of Ranvier formation, perinodal ECM deposition and perineuronal net formation. The transcription factors that control ECM related gene expression in oligodendrocytes remain unknown. Here, we found that the transcription factor Osterix (also known as Sp7) binds in proximity to genes important for CNS ECM and node of Ranvier formation and mediates their expression. Oligodendrocyte specific ablation of Sp7 changes ECM composition and brain stiffness, and results in aberrant node of Ranvier formation. Sp7 is known to control osteoblast maturation and bone formation. Our comparative analyses suggests that Sp7 plays a conserved biological role in oligodendrocytes and in bone forming cells, where it mediates brain and bone tissue stiffness by controlling the expression of ECM components.

overall_design: To explore the role of Sp7 ablation on gene expression, total RNA-seq data from primary cultured oligodendrocytes derived from the brains of WT and Sp7-ablated mice was compared.

first: Maia

last: Vardy

first: Haley

last: Tokars

first: Yulia

last: Dzhashiashvili

first: Alaa

last: Darwish

first: Sara

last: Isaac

first: Amir

last: Eden

first: Brian

last: Popko


title: Mechanisms of endothelial injury and transplant-associated thrombotic microangiopathy in tandem autologous hematopoietic stem cell transplant for neuroblastoma

city: Cincinnati

first: Stella

last: Davies

state: OH

address: 3333 Burnet Ave

department: Cancer & Blood Disease Institute

institute: Cincinnati Children's Hospital

summary: Our data indicate that endothelial injury is increased in auto-stem cell transplant patients receiving the specific conditioning regimen carboplatin, etoposide and melphalan and is associated with clinical TA-TMA.  Moreover, our data identify specific pathways that can be targeted to treat or prevent TA-TMA.

overall_design: RNAseq was performed on glomerular endothelial cells cultured with serum from neuroblastoma patients who developed TA-TMA (n=5), timepoint-matched serum from neuroblastoma patients who did not develop TA-TMA (n=4) and complete media alone (no human serum, n=1).

first: Anthony

last: Sabulski

first: Sheyar

last: Abdullah

first: Nathan

last: Luebbering

first: Benjamin

last: Aunins

first: Sonata

last: Jodele


title: The bone transcription factor Osterix controls extracellular matrix and node of Ranvier related gene expression in oligodendrocytes [ChIP-seq]

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: Genome binding profile of SP7 was studied by  Chip-seq performed on primary cultured oligodendrocye derived from the brain of WT and Sp7-ablated mice.


title: A subpopulation of lipogenic brown adipocytes drives thermogenic memory

first: Patrick

last: Lundgren


title: Interferon-induced IL-10 drives systemic T-cell dysfunction during chronic liver injury

city: Bonn

first: Susanne

last: Schmidt

address: Venusberg-Campus 1

department: Institute of Clin. Chemistry and Clin. Pharmacology

country: Germany

institute: University Hospital Bonn

summary: Patients with chronic liver disease (CLD), including cirrhosis, are at increased risk of intractable viral infections and are hyporesponsive to vaccination. Hallmarks of CLD and cirrhosis include microbial translocation and elevated levels of type I interferon (IFN-I). We aimed to investigate the relevance of microbiota-induced IFN-I in the impaired adaptive immune responses observed in CLD. We combined bile duct ligation (BDL) and carbon tetrachloride (CCl4) models of liver injury with vaccination or lymphocytic choriomeningitis virus infection in transgenic mice lacking IFN-I in myeloid cells (LysM-Cre IFNARflox/flox), IFNAR-induced IL-10 (MX1-Cre IL10flox/flox) or IL-10R in T cells (CD4-DN IL-10R). Key pathways were blocked in vivo with specific antibodies (anti-IFNAR and anti-IL10R). We assessed T-cell responses and antibody titers after HBV and SARS-CoV-2 vaccinations in patients with CLD and healthy individuals in a proof-of-concept clinical study. We demonstrate that BDL- and CCL4-induced prolonged liver injury leads to impaired T-cell responses to vaccination and viral infection in mice, subsequently leading to persistent infection. We observed a similarly defective T-cell response to vaccination in patients with cirrhosis. Innate sensing of translocated gut microbiota induced IFN-I signaling in hepatic myeloid cells that triggered excessive IL-10 production upon viral infection. IL-10R signaling in antigen-specific T cells rendered them dysfunctional. Antibiotic treatment and inhibition of IFNAR or IL-10Ra restored antiviral immunity without detectable immune pathology in mice. Notably, IL-10Ra blockade restored the functional phenotype of T cells from vaccinated patients with cirrhosis. Innate sensing of translocated microbiota induces IFN-/IL-10 expression, which drives the loss of systemic T-cell immunity during prolonged liver injury.

overall_design: mRNA sequencing of T cells isolated from liver of mice with BDL (n=4) and sham control mice (n=4)

first: Philipp

last: Hackstein

first: Jasper

last: Spizer

first: Lisa

last: Assmus

first: Helena

last: Horvatic

middle: V

first: Percy

last: Knolle

first: Zeinab


title: The bone transcription factor Osterix controls extracellular matrix and node of Ranvier related gene expression in oligodendrocytes [ATAC-seq]

first: Benayahu

last: Elbaz

overall_design: Genome-wide chromatin accessibility was studied by ATAC-seq on primary cultured oligodendrocyte lineage cells, derived from the brain of WT and Sp7-ablated mice.

first: Maia

last: Vardy

first: Haley

last: Tokars

first: Yulia

last: Dzhashiashvili

first: Alaa

last: Darwish

first: Sara


title: Genome-wide DNA-binding analysis for Stat92E in Drosophila testis by DamID

status: Public on Sep 10 2023

city: Beijing

first: Ruiyan

last: Kong

address: 105 Xi San Huan Bei Lu, Haidian District, Beijing

institute: Capital Normal University

summary: Purpose: Genome-wide DNA-binding analysis for Stat92E in Drosophila testis cyst cells by DNA adenine methyltransferase identification(DamID).Methods: DNA adenine methyltransferase identification (DamID) on Stat92E driven by c587Gal4ts;hopTum-l

overall_design: Dam(Control) or Stat92E-Dam transgenes were expressed in testis cyst cells by c587Gal4ts;hopTum-l.The testis with 2 day at 29℃ was used for DamID-seq, followed by deep sequencing analysis.

first: Zhouhua

last: Li


title: PML modulates epigenetic composition of chromatin to regulate expression of pro-metastatic genes in triple-negative breast cancer [ATAC-seq]

city: Milan

first: Rosa

last: Bernardi

address: via Olgettina 60

country: Italy

institute: San Raffaele Scientific Institute

summary: The promyelocytic leukemia (PML) protein organizes nuclear aggregates known as PML nuclear bodies (PML-NBs), where many transcription factors and transcriptional regulators converge to be regulated. Specific associations of PML and PML-NBs with chromatin are described in different cell types, further implicating PML in transcriptional regulation. However, a complete understanding of the functional consequences of PML association to DNA in a cellular context where it regulates relevant phenotypes is still lacking.We examined the role of PML in chromatin association and transcription in triple-negative breast cancer (TNBC), a pathological condition where PML exerts important oncogenic functions. We find that PML associates discontinuously with large heterochromatic PML-associated domains (PADs) that contain gene-rich euchromatic sub-domains locally depleted of PML. PML promotes heterochromatic organization in PADs and expression of pro-metastatic genes embedded in these sub-domains. Importantly, this occurs outside PML-NBs, suggesting that nucleoplasmic PML exerts a cell type-relevant function of transcriptional regulation. PML also plays an indirect regulatory function in TBNC cells by promoting the expression of pro-metastatic genes outside PADs.Our findings demonstrate that PML is an important transcriptional regulator of metastasis and pro-oncogenic metagenes in TNBC cells, via distinct molecular activities that include indirect transcriptional regulation and direct epigenetic organization of heterochromatin domains that embed regions of localized transcriptional activity.

overall_design: ATAC-sequencing in control and PML silenced MDA-MB-231 cells.

first: Cristina

last: Fracassi

first: Martina

last: Ugge

first: Mohamed

last: Abdelhalim

first: Ettore

last: Zapparoli

first: Dejan

last: Lazarevic

first: J

last: Morelli Marco

first: Philippe

last: Collas


title: A subpopulation of lipogenic brown adipocytes drives thermogenic memory [snRNAseq]

first: Patrick

last: Lundgren

summary: Sustained responses to transient stimuli are important for animals to survive and reproduce in their environment. However, the mechanisms that underlie altered responses to temporary shifts in abiotic factors, such as temperature, remain poorly understood. Here, we find that transient cold exposure leads to sustained transcriptional and metabolic adaptations in brown adipose tissue, which are critical for an improved thermogenic response to secondary cold encounter. Primary thermogenic challenge triggers the delayed induction of a lipid biosynthesis program even after cessation of the original stimulus, which protects from subsequent exposures. By combining single-nucleus RNA sequencing, spatial transcriptomics, and immunofluorescence imaging, we discover that this lipogenic response is carried out by a distinct subpopulation of brown adipocytes that is localized along the perimeter of classical Ucp1high brown adipocytes. The protective effect of the lipogenic program is associated with the production of acyl carnitines, and supplementation of acyl carnitines recapitulates improved secondary cold responses even in the absence of lipogenesis. Overall, our data highlight the importance of heterogenous brown adipocyte populations for “thermogenic memory” in the setting of repeated cold exposure, which may have implications for therapeutic efforts leveraging short-term thermogenesis to counteract the hypercaloric state of obesity.

overall_design: Brown adipose tissue was collected from 5 mice at thermoneutrality and 5 mice that had undergone transient acute cold exposure 4 days previously. Nuclei isolation was then performed as previously described. Nuclei from the 5 mice for each condition were pooled. Sorted nuclei were then immediately encapsulated into droplets, libraries prepared using the 10X Genomics platform and sequencing was performed on NextSeq 550 instrument using 150-cycle kit. BCL files were demultiplexed, aligned to mouse mm10 genome, filtered, and UMI counted using CellRanger (10X Genomics).

first: Christoph

last: Thaiss


title: Staphylococcal Nuclease and Tudor Domain Containing protein SND1 interacts with ERG and plays a critical role in prostate cancer in vivo

city: Seattle

first: Ilsa

last: Coleman

state: WA

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Center

summary: SND1 and its partner MTDH promote cancer and therapeutic resistance; however, the mechanisms responsible for their function and potential cooperation with other oncogenes are not completely understood. We report here that oncoprotein ERG binds to the SND1/MTDH protein complex via the Tudor domain of SND1. ERG is an ETS-domain transcriptional factor, which is recombined and overexpressed in approximately half of human prostate cancers. siRNA-mediated knockdowns and CRISPR-Cas9-mediated knockout of SND1 in human prostate epithelium cell lines revealed a critical role of SND1 in proliferation of ERG-overexpressing prostate epithelial cells. Transcriptional analysis of ERG-positive human prostate cancer cells demonstrated significant overlap between genes regulated by ERG and SND1. Mechanistically, we found that ERG promoted nuclear localization of SND1/MTDH. Significantly, forced nuclear localization of SND1 by addition of exogenous nuclear localization sequences (NLS) prominently increased its growth promoting function irrespective of the status of ERG expression. To determine if SND1 is necessary for prostate cancer tumorigenesis in vivo, we generated mice with prostate-epithelium-specific deletion of Snd1. We found that inactivation of Snd1 did not impact normal prostate gland homeostasis. However, prostate epithelium-specific deletion of Snd1 in autochthonous mouse model of prostate cancer (PB-Cre/ERG/PTENflox/flox mice) showed greatly reduced invasive cancer growth and tumor burden.  Moreover, gene expression analysis revealed a significant overlap between in vivo prostate transcriptional signatures of ERG and Snd1. We conclude that SND1 plays a critical role in prostate tumorigenesis and targeting SND1 may represent a potential therapeutic target in prostate cancer.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: RNA sequencing of VCaP cell  line and mouse prostate samples using Illumina TruSeq Stranded mRNA Library prep and sequenced on Illumina NovaSeq 6000.

first: Sheng-You

last: Liao

first: Dmytro

last: Rudoy

first: Luan

middle: T

last: Phan

first: Olga

last: Klezovitch

first: Julian

last: Kwan

first: Michael

middle: C

last: Haffner

first: Dapei

first: Peter

last: Nelson

first: Andrew

last: Emili

first: Valeri

last: Vasioukhin


title: Inhibitory effect of VNLG-152R on breast cancer cells MDA-MB-231

status: Public on Sep 08 2023

city: Baltimore

first: Carrie

last: McCracken

state: MD

address: 670 W. Baltimore St

department: Institute for Genome Sciences

institute: Institute of Genome

summary: In previous studies, our research demonstrated that VNLG-152R exhibits inhibitory effects on Triple Negative Breast Cancer (TNBC) cells both in vitro and in vivo. The TNBC cell line MDA-MB-231 cells were treated with VNLG-152R. A total of 337 genes were differentially expressed when MDA-MB-231 cells were treated with 10 μM VNLG-152R for 24h; 259 genes were upregulated and 78 downregulated. Through proteome analyses, we discovered that VNLG-152R upregulates the expression of E3 ligase Synoviolin 1 (SYVN1), also called 3-hydroxy-3-methylglutaryl reductase degradation (HRD1) in TNBC cells. Moreover, we provide genetic and pharmacological evidence to demonstrate that SYVN1 mediates the ubiquitination and subsequent proteasomal degradation of MNK1/2, the only known kinases responsible for phosphorylating eIF4E. Phosphorylation of eIF4E being a rate-limiting step in the formation of the eIF4F translation initiation complex, the degradation of MNK1/2 by VNLG-152R and its analogs impedes dysregulated translation in TNBC cells, resulting in the inhibition of tumor growth. Importantly, our findings were validated in vivo using TNBC xenograft models derived from MDA-MB-231, MDA-MB-468, and MDA-MB-453 cell lines, representing different racial origins and genetic backgrounds. These xenograft models, which encompass TNBCs with varying androgen receptor (AR) expression levels, were effectively inhibited by oral administration of VNLG-152R and its deuterated analogs in NRG mice.

overall_design: Vehicle Control-DMSO in trplicates and VNLG-152R 10 µM, in triplicates; treatment duration-24 hours.

first: Retheesh

last: Thankan

first: Elizabeth

last: Thomas

first: Puranik

last: Purushottamachar

first: Vincent

last: Njar


title: Increased biohydrogen production by deletion of uncharacterized DNA-binding protein discovered in hyperthermophilic archaeon Thermococcus onnurineus NA1

city: Busan

first: LEE

middle: SEONG

last: HYUK

address: Haeyang-ro

department: Department of Marine Biotechnology

country: South Korea

institute: Korea Institute of Ocean Science and Technology

summary: In ordet to understand in vivo role of uncharacterized DNA-binding protein (TON_1525) in T. onnurineus NA1, TON_1525 gene deletion mutant was constructed. Also transcriptome analysis was perfomed between wild type and mutant strains to measure changed expression profile of genes by deletion of TON_1525 gene under CO supplemented medium.

overall_design: Expreesion profile of genes in wild type and 1525 deletion mutant strains under CO-supplemented condition was measured.

first: Seong

middle: H

last: Lee

first: Hyun

first: Sung

middle: G

last: Kang


title: Lung tumor-infiltrating Treg have divergent transcriptional profiles and function linked to checkpoint blockade response [mouse]

first: Kellie

middle: N

last: Smith

address: 1650 Orleans Street

institute: Johns Hopkins University

summary: Regulatory T cells (Treg) are conventionally viewed to suppress endogenous and therapy-induced anti-tumor immunity; however, their role in modulating responses to immune checkpoint blockade (ICB) is unclear. In this study, we integrated single-cell RNAseq/TCRseq of >73,000 tumor-infiltrating Treg (TIL-Treg) from anti-PD-1-treated and treatment naive non-small cell lung cancers (NSCLC) with single cell analysis of tumor-associated antigen (TAA)-specific Treg derived from a murine tumor model. We identified 10 subsets of human TIL-Treg, most of which have high concordance with murine TIL-Treg subsets. Notably, only one subset selectively expresses high levels of OX40 and GITR, whose engangement by cognate ligand mediated proliferative programs and NF-kB activation, as well as multiple genes involved in Treg suppression, including LAG3. Functionally, the OX40hiGITRhi subset is the most highly suppressive ex vivo and its higher representation among total TIL-Treg correlated with resistance to PD-1 blockade. Surprisingly, in the murine tumor model, we found that virtually all TIL-Treg expressing T cell receptors that are specific for TAA fully develop a distinct Th1-like signature over a two-week period after entry into the tumor, down-regulating FoxP3 and up-regulating expression of TBX21 (Tbet), IFN and certain pro-inflammatory granzymes. Transfer learning of a gene score from the murine TAA-specific Th1-like Treg subset to the human single-cell dataset revealed a highly analogous subcluster that was enriched in anti-PD-1 responding tumors. These findings demonstrate that TIL-Treg partition into multiple distinct transcriptionally-defined subsets with potentially opposing effects on ICB-induced anti-tumor immunity and suggest that TAA-specific TIL-Treg may positively contribute to anti-tumor responses.

overall_design: Libraries were prepared accordingn to 10X Genomics protocols for 5' barcoded GEX, feature barcode, and V(D)J TCR (Version 1)

first: Arbor

last: Dykema

first: Jiajia

last: Zhang


title: Metabolic crosstalk between skeletal muscle cells and liver through IRF4-FSTL1 in nonalcoholic steatohepatitis

city: Shanghai

first: Kong

last: Xingxing

address: Songhu Road 2005

department: School of Life Sciences

institute: Fudan University

summary: Inter-organ crosstalk has gained more and more attention recently. However, the mechanisms under this remain incompletely understood. Here, we revealed an endocrine pathway regulated by skeletal muscle IRF4 that manipulates liver pathology. We studied that skeletal muscle specifically deleted IRF4 (F4MKO) mice showed ameliorated liver steatosis, inflammation and fibrosis, without changes in body weight on NASH diet. Proteomics analysis of serum suggested that follistatin-like protein 1 (FSTL1), as a myokine, might linked the communication between skeletal muscle and liver. Dual luciferase assays showed that IRF4 can transcriptionally regulated FSTL1 and reconstitution of FSTL1 expression in skeletal muscle of F4MKO mice, using adeno-associated virus, was sufficient to restore the liver pathology. Furthermore, we performed co-culture experiments to verify different receptors contribute to FSTL1’s function in different cell types of liver. Finally, we found serum FSTL1 level was positively correlated with NASH progression in human, whereas the mRNA level of Fstl1 and its receptors were downregulated in liver biopsy from NASH patients. These data reveal a signaling pathway from skeletal muscle to liver via IRF4-FSTL1-receptors in the pathogenesis of NASH and implicate useful targets for the management of NASH.

overall_design: Three liver tissue samples of each group for RNA sequencing were collected. Total RNA was isolated using the Trizol method according to manufacturer’s instructions. RNA quality was measured using the Agilent 2100 Bioanalyzer (RNA 6000 Nano Kit; Agilent Technologies, Santa Clara, CA, USA). cDNA libraries for each sample were constructed as reported previously  Libraries were sequenced on BGIseq500 platform (BGI-Shenzhen, China), using 150 bp paired-end reads aimed at 30 million reads per sample.The raw sequencing data was filtered with trim-galore (v0.6.7) by removing reads containing sequencing adapter and reads with low-quality base. The clean reads were mapped to the reference genome (mm10) using Hisat2 (2.2.1). Quantification of gene expression was calculated using FeatureCounts (v2.0.1), converted to transcripts per million (TPM) using the R software. We conducted a differential gene expression analysis comparing F4MKO versus control and overexpression of FSTL1 in F4MKO (F4MKO+FSTL1) versus F4MKO. Subsequently, differential expression analysis between groups was conducted using the DESeq2(1.3.40) with adjust P value < 0.05 and |FC|>1.5. We used the obtained log2FC to perform a gene-set enrichment analysis to detect pathways and biological processes enriched with profiling genes.


title: Tumor-adjacent lung transcriptome as a predictor of recurrence in early-stage lung adenocarcinoma [bulk RNA-seq]

city: New York

first: Aristotelis

last: Tsirigos

address: 435 E 30th St

institute: NYU School of Medicine

summary: Bulk RNA-seq analysis of matched tumor/normal samples

first: Igor

last: Dolgalev

first: Aris

first: Nina

last: Murrell


title: Stromal netrin-1 coordinates renal arteriogenesis and mural cell differentiation

city: Dallas

first: Thomas

last: Carroll

address: 6000 Harry Hines Blvd.

institute: UT Southwestern

summary: The kidney vasculature has a complex architecture that is essential for renal function. The molecular mechanisms that direct development of kidney blood vessels are poorly characterized. We identified a regionally-restricted, stroma-derived signaling molecule, netrin-1 (Ntn1), as a regulator of renal vascular patterning. Stromal progenitor (SP)-specific ablation of netrin-1 (Ntn1SPKO) resulted in smaller kidneys with fewer glomeruli, as well as profound defects of the renal artery and transient blood flow disruption. Notably, Ntn1 ablation resulted in loss of arterial vascular smooth muscle cell (vSMC) coverage and in ectopic SMC deposition at the kidney surface. This was accompanied by dramatic reduction of arterial tree branching that perdured postnatally. Transcriptomic analysis of Ntn1SPKO kidneys revealed dysregulation of vSMC differentiation, including downregulation of Klf4 which we find expressed in a subset of SPs. Stromal Klf4 deletion similarly resulted in decreased smooth muscle coverage and arterial branching, however without the disruption of renal artery patterning and perfusion seen in Ntn1SPKO. These data suggest a stromal Ntn1-Klf4 axis that regulates stromal differentiation, and reinforce stromal-derived smooth muscle as a key regulator of renal blood vessel formation.

overall_design: 6 samples; 3 replicates for Foxd1GC+ controls and Foxd1GC+; Ntn1flox/flox mutants

first: Peter

last: Luo

first: Ondine

last: Cleaver


title: 3D genome organization coordinates key regulators of lineage specification in mammary epithelial cells [T8_Omni-C]

city: Parkville

first: Gordon

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

summary: In order to understand gene regulation of epithelial cells in the mouse mammary gland, we have generated a comprehensive epigenetic atlas from freshly sorted myoepithelial (basal), luminal progenitor (LP) and mature luminal (ML) from adult mice (9 week-old) encompassing gene expression profiling, histone and polymerase II CUT&Tag sequencing, chromatin accessibility via ATAC-seq and chromatin interactions. We further studied the basal compartment by sorting to additional cell type population: Tspan8+ (quiescent basal, QBa) and Tspan8- (active basal, ABa) cells.

overall_design: We then performed Omni-CTM, a DNase-based HiC protocol which measures the interaction frequency of all loci in the genome on mouse epithelial mammary gland cell types in the basal compartment: sorted Tspan8+ (quiescent basal, QBa, Lin-/CD29hi/CD24+/Tspan8+) and Tspan8- (active basal, ABa, Lin-/CD29hi/CD24+/Tspan8-) cellular populations from adult mice in triplicate.

first: Hannah

middle: D

last: Coughlan

first: Michael

last: Milevskiy


title: 3D genome organization coordinates key regulators of lineage specification in mammary epithelial cells [T8_CUT&Tag]

overall_design: We then performed CUT&Tag on mouse epithelial mammary gland cell types in the basal compartment: sorted Tspan8+ (quiescent basal, QBa, Lin-/CD29hi/CD24+/Tspan8+) and Tspan8- (active basal, ABa, Lin-/CD29hi/CD24+/Tspan8-) with antibodies for: H3K27me3, H3K4me1, H3K4me3, H3K36me3, H2AK119ub, H3K9ac, H3K9me2, H3K9me3, H3K27ac, PolII and IgG.


title: Microenvironmental network of clonal CXCL13+CD4+ T cells and regulatory T cells in pemphigus chronic blisters

city: Seoul

first: Taehee

last: Kim

address: 211 Eonjuro, Gangnam-gu

department: Department of Dermatology and Cutaneous Biology Research Institute

institute: Gangnam Severance Hospital, Yonsei University College of Medicine

summary: Pemphigus, a rare autoimmune bullous disease mediated by anti-desmoglein autoantibodies, can be controlled with systemic medication like rituximab and high-dose systemic corticosteroids combined with immunosuppressants. However, some patients continue to experience chronically recurrent blisters in a specific area, requiring long-term maintenance systemic therapy. We demonstrate the presence of skin tertiary lymphoid structures (TLSs) with desmoglein-specific B cells in chronic blisters from pemphigus patients. In the skin TLSs, CD4+ T cells predominantly produced CXCL13. These clonally expanded CXCL13+CD4+ T cells exhibited features of activated Th1-like cells and downregulated genes associated with T-cell receptor-mediated signaling. Regulatory T cells (Tregs) are in direct contact with CXCL13+CD4+ memory T cells and increased CXCL13 production of CD4+ T cells through IL-2 consumption and TGF-β stimulation. Lastly, Intralesional corticosteroid injection improved chronic blisters and reduce skin TLSs in patients with pemphigus.  This study concludes that skin TLSs are associated with the persistence of chronically recurrent blisters in pemphigus patients, and the microenvironmental network involving CXCL13+CD4+ T cells and Tregs within these structures plays an important role in CXCL13 production.

overall_design: Skin with chronic blisters was obtained from patients with pemphigus. Immunologic properties of the skin were analyzed by single-cell RNA and TCR sequencing.

first: Dawoon

last: Han

first: A

middle: Y

first: Ji

last: Choi

first: Mi

last: Cho

first: Ahreum

last: Song

first: Changhyeon

first: Joon

last: Shim

first: Honesty

first: Hillary

middle: B

last: D'Angio

first: Ryan

last: Preska

first: Aaron

last: Mayer

first: Miri

first: Eun-Ji

first: Tae-Gyun

first: Eui-Cheol

last: Shin

first: Kyemyung

last: Park

first: Do-Young

first: Soo-Chan

first: Jong


title: Pharmacologic Activation of a Compensatory Integrated Stress Response Kinase Promotes Adaptive Mitochondrial Remodeling in Perk-deficient Cells

status: Public on Sep 09 2023

city: La Jolla

first: R.

middle: Luke

last: Wiseman

address: 10550 N Torrey Pines Rd

department: Dept. of Molecular Medicine

institute: The Scripps Research Institute

summary: mRNA sequencing of WT or PERK-/- MEFs treated with the ISR activating compounds BtdCPU, Halofuginone, and Thapsigargin.

overall_design: Mouse embryonic fibroblasts

first: Valerie

last: Perea

first: Kelsey

middle: R

last: Baron

first: Vivian

last: Dolina

first: Giovanni

last: Aviles

first: Jessica

last: Rosarda

first: Martin

last: Kampmann

first: R

middle: L


title: Identify and characterize the polyploidization process of primary human proximal tubular cells (hPTC) [scRNA-seq]

city: Firenze

first: Roberto

last: Semeraro

address: Viale Pieraccini, 6

department: Medicina Sperimentale e Clinica

institute: Università degli studi di Firenze

summary: We generated single-cell RNA sequencing (scRNAseq) datasets of primary cultures of  human proximal tubular cells stimulated with TGF-β1 or vehicle. Following TGF-β1 stimulation, hPTC expressed TGF-β1 and its downstream targets. Moreover, TGF-β1-treated hPTC were characterized by a differential expression of pro-fibrotic genes, which we had recently showed to be characteristic of polyploid hPTC and were enriched with hypertrophy, indicative of cell polyploidization.

overall_design: Analyze the role of  TGF-β1 in promoting polyploidization in primary human proximal tubular cells (hPTC)

first: Letizia

last: De Chiara

first: Elena

last: Lazzeri

first: Paola

last: Romagnani


title: Comprehensive analysis of the gene expression profile of the male and female BTBR mice with diabetic nephrology

city: Ya'an

first: Jianning

last: Chen

state: Sichuan

address: 46, Xinkang Road

institute: Sichuan Agricultural University

summary:
To explore genes and pathways that were differently regulated in the progression of diabetic nephrology in different gender mice, we performed  RNA-seq of kidney from BTBRob/ob (diabetic nephrology) mice   and wild type (WT) mice.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 2 different gender groups.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for male BTRTob/ob mice, male WT mcie, female BTRTob/ob mice and female WT mice .

first: Ying

last: Wang


title: 3D genome organization coordinates key regulators of lineage specification in mammary epithelial cells [MEC_Omni-C]

first: Gordon

middle: K

last: Smyth

overall_design: We then performed Omni-CTM, a DNase-based HiC protocol which measures the interaction frequency of all loci in the genome in duplicate of each of the sorted cellular populations from adult mice: myoepithelial (basal, Lin-/CD29hi/CD24+), luminal progenitor (LP, Lin-/CD29low/CD24+/CD61hi) and mature luminal (ML, Lin-/CD29low/CD24+/CD61low).

first: Hannah

last: Coughlan

first: Michael

last: Milevskiy


title: 3D genome organization coordinates key regulators of lineage specification in mammary epithelial cells [T8_ATAC]

overall_design: We then performed ATAC-seq on mouse epithelial mammary gland cell types in the basal compartment: sorted Tspan8+ (quiescent basal, Qba, Lin-/CD29hi/CD24+/Tspan8+) and Tspan8- (active basal, ABa, Lin-/CD29hi/CD24+/Tspan8+) cellular populations from adult mice in duplicate.


title: 3D genome organization coordinates key regulators of lineage specification in mammary epithelial cells [MEC_ATAC]

overall_design: We then performed ATAC-seq sorted on myoepithelial (basal, Lin-/CD29hi/CD24+), luminal progenitor (LP, Lin-/CD29low/CD24+/CD61hi) and mature luminal (ML, Lin-/CD29low/CD24+/CD61low) cellular populations from adult mice in triplicate.


title: TDP-43 pathology in Drosophila induces glial-cell type specific toxicity that can be ameliorated by knock-down of SF2/SRSF1

first: Oliver

last: Tam

state: New York

department: Institute for Systems Genetics

institute: NYU Grossman School of Medicine

summary: Accumulation of cytoplasmic inclusions of TAR-DNA binding protein 43 (TDP-43) is seen in both neurons and glia in a range of neurodegenerative disorders, including amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD) and Alzheimer’s disease (AD). Disease progression involves non-cell autonomous interactions among multiple cell types, including neurons, microglia and astrocytes. We investigated the effects in Drosophila of inducible, glial cell type-specific TDP-43 overexpression, a model that causes TDP-43 protein pathology including loss of nuclear TDP-43 and accumulation of cytoplasmic inclusions. We report that TDP-43 pathology in Drosophila is sufficient to cause progressive loss of each of the 5 glial sub-types. But the effects on organismal survival were most pronounced when TDP-43 pathology was induced in the perineural glia (PNG) or astrocytes. In the case of PNG, this effect is not attributable to loss of the glial population, because ablation of these glia by expression of pro-apoptotic reaper expression has relatively little impact on survival. To uncover underlying mechanisms, we used cell-type-specific nuclear RNA sequencing to characterize the transcriptional changes induced by pathological TDP-43 expression. We identified numerous glial cell-type specific transcriptional changes. Notably, SF2/SRSF1 levels were found to be decreased in both PNG and in astrocytes. We found that further knockdown of SF2/SRSF1 in either PNG or astrocytes lessens the detrimental effects of TDP-43 pathology on lifespan, but extends survival of the glial cells. Thus TDP-43 pathology in astrocytes or PNG causes systemic effects that shorten lifespan and SF2/SRSF1 knockdown rescues the loss of these glia, and also reduces their systemic toxicity to the organism.

overall_design: We sought to distinguish the contribution of TDP-43 proteinopathy in each glial cell type to the animal’s survival. Using celltype specific Gal4 lines (methods) and the temperature sensitive Gal80 (Gal-80ts) approach, we induced post development over-expression of TDP-43 in each of the 5 individual glial cell types.This temperature switch expression system allowed us to avoid effects on development from over-expressing TDP-43 during glial specification, and also permitted us to determine the timecourse of lethality after induction on the first day of adult life

first: Sarah

last: Krupp

first: Isabel

last: Hubbard

first: Molly

last: Gale Hammell

first: Josh

last: Dubnau


title: Inflammation in the tumor-adjacent lung as a predictor of clinical outcome in lung adenocarcinoma

first: Aristotelis

last: Tsirigos

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

overall_design: Refer to individual Series


title: Drosha-dependent microRNAs modulate FUS-mediated neurodegeneration in vivo

city: Pittsburgh

first: Dhivyaa

last: Rajasundaram

address: 4401 Penn Avenue

department: Pediatrics

institute: University of Pittsburgh

type: Non-coding RNA profiling by high throughput sequencing

summary: Mutations in Fused in Sarcoma (FUS) gene cause the familial and progressive form of amyotrophic lateral sclerosis (ALS). FUS is a nuclear RNA-binding protein involved in RNA processing and the biogenesis of a specific set of microRNAs. Here we report that Drosha and two previously uncharacterized Drosha-dependent miRNAs are strong modulators of FUS expression and prevent the cytoplasmic segregation of insoluble mutant FUS in vivo. We demonstrate that depletion of Drosha mitigates FUS-mediated degeneration, survival, and motor defects in Drosophila. Mutant FUS strongly interacts with Drosha and causes its cytoplasmic mis-localization into the insoluble FUS inclusions. Reduction in Drosha levels increases the solubility of mutant FUS. Interestingly, we found two Drosha dependent microRNAs, miR-378i and miR-6832-5p, which differentially regulate the expression, solubility, and cytoplasmic aggregation of mutant FUS in iPSC neurons and mammalian cells. More importantly, we report different modes of action of these miRNAs against mutant FUS. Whereas miR-378i may regulate mutant FUS inclusions by preventing G3BP-mediated stress granule formation, miR-6832-5p may affect FUS expression via other proteins or pathways. Overall, our research reveals a possible association between ALS-linked FUS mutations and the Drosha-dependent miRNA regulatory circuit, as well as a useful perspective on potential ALS treatment via microRNAs.

overall_design:
Small RNA profiling to identify the key Drosha-dependent miRNAs that are critical for FUS function and turnover independent of 3ʹUTR
Small RNAs were isolated from Drosha knockout (DKO) and HEK293T cells transfected with wild-type and FUS-R521C cDNA constructs, and miRNA transcriptome was profiled and mapped to the human reference genome and other snRNA databases

first: Sukhleen

last: Kour

first: Tyler

last: Fortuna

first: Udai

last: Pandey


title: 3D genome organization coordinates key regulators of lineage specification in mammary epithelial cells [MEC_CUT&Tag]

overall_design: We then performed CUT&Tag in duplicate for each of the sorted cellular populations from adult mice: myoepithelial (basal, Lin-/CD29hi/CD24+), luminal progenitor (LP, Lin-/CD29low/CD24+/CD61hi) and mature luminal (ML, Lin-/CD29low/CD24+/CD61low) with antibodies for: H3K27me3, H3K4me1, H3K4me3, H3K36me3, H2AK119ub, H3K9ac, H3K9me2, H3K9me3, H3K27ac, PolII and IgG.


title: Non-canonical BIM-regulated energy metabolism determines drug-induced liver necrosis.

city: Konstanz

first: Rebekka

last: Lambrecht

address: Universitaetsstrasse 10

institute: University of Konstanz

summary: Paracetamol (acetaminophen, APAP) overdose severely damages mitochondria and triggers several apoptotic processes in hepatocytes, but the final outcome is fulminant necrotic cell death, resulting in acute liver failure and mortality. Here, we studied this switch of cell death modes and demonstrate a non-canonical role of the apoptosis-regulating BCL-2 homolog BIM/Bcl2l11 in promoting necrosis by regulating cellular bioenergetics. BIM deficiency enhanced total ATP production and shifted the bioenergetic profile towards glycolysis, resulting in persistent protection from APAP-induced liver injury. Modulation of glucose levels and deletion of mitofusins confirmed that severe APAP toxicity occurs only in cells dependent on oxidative phosphorylation. Glycolytic hepatocytes maintained elevated ATP levels and reduced ROS, which enabled lysosomal recycling of damaged mitochondria by mitophagy. The present study highlights how metabolism and bioenergetics affect drug-induced liver toxicity, and identifies BIM as important regulator of glycolysis, mitochondrial respiration, and oxidative stress signaling.

overall_design: We performed RNA sequencing of murine livers of overnight fasted mice and fed mice.

first: Samara

last: Naim

first: Thomas

last: Kaufmann

last: Brunner


title: Cutaneous arsenical exposure induces distinct metabolic transcriptional alterations of kidney cells

status: Public on Sep 07 2023

city: Birmingham

first: Kyle

middle: Hartley

last: Moore

state: Alabama

department: Division of Nephrology

institute: University of Alabama at Birmingham

summary: Arsenicals are deadly chemical warfare agents which primarily cause death through systemic capillary fluid leakage and hypovolemic shock. Arsenicals are also known to cause acute kidney injury, a condition that contributes to arsenical-associated death due to the necessity of the kidney in maintaining whole-body fluid homeostasis. Because of the global health risk that arsenicals pose, a nuanced understanding of how arsenical exposure can lead to kidney injury is needed. Our study utilized a non-targeted transcriptional approach to evaluate the effects of cutaneous exposure to phenylarsine oxide, a common arsenical, in a murine model. Here, we demonstrate an upregulation of metabolic pathways such as fatty acid oxidation and PPAR-𝛼 signaling within proximal tubule epithelial cells and endothelial cells in the kidney. We also reveal highly upregulated single genes related to metabolism and metabolic switching within these same cell types which may serve as future therapeutic targets. The ability of arsenicals to inhibit enzymes such as pyruvate dehydrogenase have been previously described in vitro. This along with our own data lead us to conclude that arsenical-induced acute kidney injury may be due to a metabolic impairment in proximal tubule and endothelial cells, and that appropriately ameliorating these metabolic effects may lead to the development of life-saving therapies.

overall_design: C57/BL6J mice were administered phenylarsine oxide topically or ethanol as a vehicle control and kidneys were harvested six and twenty-four hours later for single nuclei RNA sequencing.

first: Laurence

middle: M

last: Boitet

first: Darshan

last: Shimoga

first: Amie

last: Traylor

first: Stephanie

last: Esman

first: Elise

last: Erman

first: Ritesh

last: Srivastava

first: Jasim

last: Khan

first: Mohammad

last: Athar

first: Anupam

last: Agarwal

first: James

middle: F

last: George


title: Targeting TCA cycle through Cuproptosis confers Synthetic Lethality to ARID1A Deficiency Hepatocellular Carcinoma [Cut&Run]

city: Beiing

first: TAO

last: XING

address: Beiing

institute: Peking University Cancer Hospital

summary: To further explore the mechanisms of  glucose metabolic reprogramming in ARID1A deficiency HCC, we conducted multi-omics profilings in ARID1A deficient and wild type Hep3B cells.

overall_design: Cleavage under targets and Release using nuclease (Cut-and-Run) for ARID1A or HIF-1α cells in Hep3B cells

first: Tao

last: Xing


title: 3D genome organization coordinates key regulators of lineage specification in mammary epithelial cells [RNASeq_T8]

first: Yunshun

last: Chen

state: VIC

address: 1G Royal Parade

department: ACRF Cancer Biology and Stem Cells

summary:
In order to understand gene regulation of epithelial cells in the mouse mammary gland, we have generated a comprehensive epigenetic atlas from freshly sorted myoepithelial (basal), luminal progenitor (LP) and mature luminal (ML) from adult mice (9 week-old) encompassing gene expression profiling, histone and polymerase II CUT&Tag sequencing, chromatin accessibility via ATAC-seq and chromatin interactions. We further studied the basal compartment by sorting to additional cell type population: Tspan8+ (quiescent basal, QBa) and Tspan8- (active basal, ABa) cells.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 2 different cell types Tspan8+ and Tspan8- cells.

overall_design: RNA-seq profiles of mouse epithelial mammary gland cell types in the basal compartment: sorted Tspan8+ (quiescent basal, Qba, Lin-/CD29hi/CD24+/Tspan8+) and Tspan8- (active basal, ABa, Lin-/CD29hi/CD24+/Tspan8-) cellular populations from adult mice in triplicate.

first: Gordon

last: Smyth

first: Hannah

last: Coughlan

first: Michael

last: Milevskiy


title: Aptamer-Based Proteomics Measuring Preoperative Cerebrospinal Fluid Protein Alterations Associated with Postoperative Delirium

city: Boston

first: Simon

last: Dillon

state: Massachusetts

address: 99 Brookline Ave, Research North Bldg, Room 107

department: IMBIO

institute: BIDMC RESEARCH

summary: Delirium is a common postoperative complication among older patients with many adverse outcomes.  Due to lack of validated biomarkers, prediction and monitoring of delirium by biological testing is not currently feasible.  Circulating proteins in cerebrospinal fluid (CSF) may reflect biological processes causing delirium.  Our goal was to discover and investigate candidate protein biomarkers in preoperative CSF that were associated with development of postoperative delirium in older surgical patients.  We employed a nested case–control study design coupled with high multiplex affinity proteomics analysis to measure 1305 proteins in preoperative CSF.  Twenty-four matched delirium cases and non-delirium controls were selected from the Healthier Postoperative Recovery (HiPOR) cohort and the associations between preoperative protein levels and postoperative delirium were assessed using t-test statistics with further analysis by systems biology to elucidate delirium pathophysiology.  Proteomics analysis identified 32 proteins in preoperative CSF that significantly associate with delirium (t-test p<0.05).  Due to the limited sample size these proteins did not remain significant by multiple hypothesis testing using the Benjamini-Hochberg correction and q-value method.  Three algorithms were applied to separate delirium cases from non-delirium controls.  Hierarchical clustering classified 40/48 case-control samples correctly, principal components analysis separated 43/48.  The receiver operating characteristic curve yielded an area under the curve [95% confidence interval] of 0.91 [0.80-0.97].  Systems biology analysis identified several key pathways associated with risk of delirium: inflammation, immune cell migration, apoptosis, angiogenesis, synaptic depression and neuronal cell death.  Proteomics analysis of preoperative CSF identifies 32 proteins that might discriminate individuals who subsequently develop postoperative delirium from matched control samples.  These proteins are potential candidate biomarkers for delirium and may play a role in its pathophysiology.

overall_design: CSF samples were run on the SomaScan Assay Cells & Tissue Kit, 1.3k (SomaLogic #900-00009), which measures the expression of 1305 human proteins using single-stranded modified Slow Off-rate Modified DNA Aptamers (SOMAmers) [3].  20 ul of CSF from each patient sample were run at a 15% dilution in 1X serum diluent.  Three provided kit controls and one no-protein buffer control were analyzed in parallel with the CSF samples.  Median normalization and calibration of the SomaScan data were performed according to standard quality control (QC) protocols at SomaLogic [4].  All 48 HiPOR samples, plus all controls, passed the QC criteria.

first: Towia

middle: A

last: Libermann


title: Pulmonary ILC2s differentially depend on epithelial cell- and lymphatic endothelial cell-IL-7 in acute and chronic airway inflammations

city: Kyoto

first: Koichi

last: Ikuta

state: Kyoto

address: 53 Shogoin-Kawaharamacho, Sakyo-ku

department: Department of Virus Research

institute: Institute for Frontier Life and Medical Sciences, Kyoto University

summary: This study reveals the role of IL-7 produced by pulmonary stromal cells for the maintenance and activation of group 2 innate lymphoid cells (ILC2s) in the lung.

overall_design: Transcriptional profiling of lung ILC2s from IL-7-flox/flox (control) and SPC-Cre; IL-7-flox/flox mice

first: Daichi

last: Takami


title: RNA sequencing of livers of adult MAPL KO and control mice.

city: Montreal

first: Aurèle

last: Besse-Patin

address: 3801 University Street

institute: McGill University

summary: Mitochondrial and peroxisomal anchored protein ligase (MAPL) is a dual ubiquitin and small ubiquitin-like modifier (SUMO) ligase with context-dependent roles in mitochondrial quality control, cell death and inflammation in cultured cell lines. Here, we show that physiological MAPL function in organismal context converges on metabolic control, as knockout mice are viable, but lean, highly insulin sensitive, and protected from high fat-diet induced obesity. MAPL loss leads to liver-specific activation of the integrated stress response, inducing secretion of starvation hormone FGF21, known to drive the reduction of white fat stores and promote insulin sensitivity. During aging, MAPL knockout mice developed fully penetrant spontaneous hepatocellular carcinoma, which is pathologically distinct from NASH/NAFLD-linked liver cancers. Mechanistically, proximity interaction analysis revealed the peroxisomal bile acid transporter ABCD3 (PMP70) as a primary MAPL interacting partner, SUMOylated in a MAPL-dependent manner. MAPL knockout leads to increased bile acid production coupled with defective regulatory feedback in liver in vivo and in isolated primary hepatocytes, suggesting cell-autonomous function. Together, our findings establish MAPL function as a central regulator of bile acid synthesis whose loss led to the profound disruption of bile acid feedback mechanisms. The unique metabolic consequences of MAPL loss in liver, along with evidence of tumor suppression through the regulation of cell survival pathways, lead ultimately to a new animal model of spontaneous hepatocellular carcinoma.

overall_design: For differential expression analysis, transcriptomes of MAPL KO mice were comared to corresponding control mice. Comparisons were made separately for females and males.

first: Olesia

last: Ignatenko

first: Vanessa

last: Goyon

first: Heidi

last: McBride


title: Effect of CCK-8s injection (20 ug/kg BW i.p.) on mRNA translational activity in hypothalamic oxytocin neurons of mice fed standard chow or high-fat/high-sugar diet (RiboTag;TRAP)

city: Neuherberg

first: Dominik

last: Lutter

address: Ingolstädter Landstraße 1

department: Institute for Diabetes and Obesity

institute: Helmholtz Zentrum München

summary: Oxytocin-expressing paraventricular hypothalamic neurons (PVN^OT neurons) integrate afferent signals from the gut including cholecystokinin (CCK) to adjust whole-body energy homeostasis. However, the molecular underpinnings by which PVN^OT neurons orchestrate gut-to-brain feeding control remain unclear. Here, we show that mice undergoing selective ablation of PVNOT neurons fail to reduce food intake in response to CCK and develop hyperphagic obesity on chow diet. Notably, exposing wildtype mice to a high-fat/high-sugar (HFHS) diet recapitulates this insensitivity towards CCK, which is linked to diet-induced transcriptional and electrophysiological aberrations specifically in PVNOT neurons. Restoring OT pathways in DIO mice via chemogenetics or polypharmacology sufficiently re-establishes CCK?s anorexigenic effects. Lastly, by single-cell profiling, we identify a specialized PVN^OT neuronal subpopulation with increased ?-opioid signaling under HFHS diet, which restrains their CCK-evoked activation. In sum, we here document a novel (patho)mechanism by which PVN^OT signaling uncouples a gut-brain satiation pathway under obesogenic conditions.

overall_design:
We treated male Oxt-ires-Cre;RiboTag mice with either vehicle or CCK, collected hypothalami 2h post injection, pooled 2-3 tissues per sample, and affinity purified conditionally HA-tagged ribosomes (incl translating mRNA) specifically from oxytocin neurons.
We then performed gene expression profiling analysis using data obtained from RNA-seq of immunoprecipitates versus inputs (n=4 per group) from standard chow diet fed mice and inputs only from high-fat/high-sugar diet fed mice (n=4 per group)
Comparative gene expression profiling analysis of RNA-seq data for TRAP (translating ribosome affinity pufification) between vehicle and CCK-treated mice across immunopreciptates per diet.
HTSeq quantification of transcript expression

first: Tim

last: Gruber

first: Franziska

last: Lechner

first: Cahuê

last: De Bernardis Murat

first: Raian

last: Eduardo Contreras

first: Eva

last: Sanchez-Quant

first: Viktorian

last: Miok

first: Ophelia

last: Le Tuc

first: Ismael

last: Gonzales-Garcia

first: Elena

last: Garcia-Clave

first: Ferdinand

last: Althammer

first: Quirin

last: Krabichler

first: Lisa

last: DeCamp

first: Russell

last: Jones

first: Rhiannan

last: Hope Williams

first: Paul

last: Pfluger

first: Timo

last: Müller

first: Steve

last: C Woods

first: Celia

last: P Martinez-Jimenez

first: Matthias

last: Tschöp

first: Valery

last: Grinevich

first: Cristina

last: García-Cáceres


title: 3D genome organization coordinates key regulators of lineage specification in mammary epithelial cells [RNASeq_MEC]

first: Yunshun

last: Chen

summary:
In order to understand gene regulation of epithelial cells in the mouse mammary gland, we have generated a comprehensive epigenetic atlas from freshly sorted myoepithelial (basal), luminal progenitor (LP) and mature luminal (ML) from adult mice (9 week-old) encompassing gene expression profiling, histone and polymerase II CUT&Tag sequencing, chromatin accessibility via ATAC-seq and chromatin interactions. We further studied the basal compartment by sorting to additional cell type population: Tspan8+ (quiescent basal, QBa) and Tspan8- (active basal, ABa) cells.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 3 different cell types.

overall_design: RNA-seq profiles of mouse epithelial mammary gland cell types, sorted myoepithelial (basal, Lin-/CD29hi/CD24+), luminal progenitor (LP, Lin-/CD29low/CD24+/CD61hi) and mature luminal (ML, Lin-/CD29low/CD24+/CD61low) cellular populations from adult mice in triplicate.

first: Gordon

last: Smyth

first: Hannah

last: Coughlan

first: Michael

last: Milevskiy


title: 3D genome organization coordinates key regulators of lineage specification in mammary epithelial cells


title: Tumor-adjacent lung transcriptome as a predictor of recurrence in early-stage lung adenocarcinoma [snRNA-seq]

first: Aristotelis

last: Tsirigos

summary: Single nuclei RNA analysis of adjacent normal tissue to predict recurrence in lung cancer patients

overall_design: 10x Genomics-based single nuclei RNA seq

first: Nina

last: Murrell

first: Aris


title: ADAR1 suppression in human astrocytes

city: Fort Collins

first: Cali

middle: Madison

last: McEntee

state: CO

address: 910 Moby Dr

department: Health and Exercise Science

institute: Colorado State University

summary: ADAR1 regulates the accumulation of endeognouse double-stranded RNA (dsRNA), a pro-inflammatory/innate immune activator. The purpose of this study was to measure the effects of ADAR1 suppression in human astrocytes and determine RNAs regulated by ADAR1. Primary human astrocytes were culture and transfected with a scramble or ADAR1 siRNA. RNA was isolated from these cells for total RNA-seq to analyze changes in gene/repetitive element expression and RNA editing.

overall_design: Total RNA-seq on scramble siRNA and ADAR1 siRNA transfected primary human astrocytes

first: Alyssa

last: Cavalier

first: Thomas

middle: J

last: LaRocca


title: Nos1ap constitutive null mice embryonic day 13.5 heart transcriptome

city: Houston

first: Ashish

last: Kapoor

state: TX

address: 1825 Pressler St. Rm SRB 530C

institute: University of Texas Health Science Center at Houston

summary: To assess the impact of Nos1ap loss on heart transcriptome during development, RNA-seq was performed in heart tissue from wildtype (males; n=5) and Nos1ap null homozygous (males; n=5) embryonic day 13.5 (e13.5) mice, and assessed for differential gene expression. At a false discovery rate of 1% and an absolute log2-fold change over 1, only two genes (Mt2 and Gm7694) were differentially expressed. These findings indicate that constitutive loss of Nos1ap has no major widespread impact on transcriptome in e13.5 hearts.

overall_design: poly-A RNA-seq in embryonic day 13.5 mouse heart from five wildtype males and five Nos1ap constitutive null males.

first: Dallas

last: Auer

first: Aravinda

last: Chakravarti


title: Hypoxia-induced translational profiles of murine fetal liver derived macrophages (FLDM)

city: New Haven

first: Timur

middle: O

last: Yarovinsky

state: CT

address: 300 George Street, 7th floor Cardiology Bender lab

department: Yale Cardiovascular Research Center

institute: Yale University

summary: We report changes in total and translated poly(A) RNA in mouse fetal liver derived macrophages after exposure to hypoxia. We employed translating ribosome affinity purification (TRAP) to isolate polysomal RNA from mouse fetal liver derived macrophages after exposure to hypoxia.

overall_design: Total and translated poly(A) RNA samples were isolated from day E14.5 FLDM isolated from 3 conditional HuR-knockout (Csf1r-iCre.HuRfl/fl) and 2 control mice (Csf1r-iCre.HuR+/+) expressing ribosomal protein L10a fused to EGFP. FLDM were differentiated in vitro and exposed to normoxia or hypoxia (1% O2) conditions for 18 h.

first: Nicholas

middle: S

last: Wilcox

first: Jeffrey

last: Bender


title: Upregulated c-JUN  induces aberrant transposable element mobilization, cGAS-STING activation and cell death in Alzheimer's disease

city: London

first: Marco

last: Trizzino

state: UK

address: Imperial College Road

department: Life Sciences

country: United Kingdom

institute: Imperial College London

summary: In this study we leveraged several lines of AD patient derived induced Pluripotent Stem Cells (iPSCs) and differentiated them into hippocampal neuronal progenitors, hippocampal CA3 neurons and cerebral organoids.  Our goals were to i) investigate the transcriptional networks altered in the AD lines at the different developmental stages (progenitors, neurons, organoids), ii) link the altered gene regulatory networks to aberrant AP-1 activity, and iii) to profile TEs aberrantly active in the AD lines, with the goal of identifying a mechanism for TE derepression and to unveil the consequences that this process has on neuronal physiology.  With these experiments, we demonstrate that many of the genes differentially expressed between the AD lines the healthy controls are c-JUN targets.  Further, we find that most of the aberrantly de-repressed TEs harbor the AP-1 binding motif, and that aberrant TE mobilization leads to cytoplasmic accumulation of RNA-DNA hybrids, observed both in the progenitors and in the organoids. Importantly this phenomenon elicits cGAS-STING activation and ultimately cell-death.  Notably, by using a c-JUN peptide that inhibits c-JUN phosphorylation, we demonstrate that c-JUN inhibition in the AD lines is sufficient to rescue the expression of many differentially expressed genes, and to significantly reduce aberrant TE mobilization, cytoplasmic RNA-DNA accumulation, cGAS-STING activation and cell death.

overall_design: Using patient-derived iPSCs to study transposons role in Alzheimer's disease

first: Chiara

last: Scopa

first: Samantha

last: Barnada

first: Maria

middle: E

last: Ciccardi

first: Davide

last: Trotti


title: Hypoxia-induced translational profiles of murine bone marrow derived macrophages (BMDM)

summary: We report changes in total and translated poly(A) RNA in mouse bone marrow derived macrophages after exposure to hypoxia.   We employed translating ribosome affinity purification (TRAP) to isolate polysomal RNA from mouse bone marrow derived macrophages after exposure to hypoxia

overall_design: Total and translated poly(A) RNA samples were isolated from BMDM isolated from 3 conditional HuR-knockout (Csf1r-iCre.HuRfl/fl) and 3 control mice (Csf1r-iCre.HuR+/fl) expressing ribosomal protein L10a fused to EGFP. BMDM were differentiated in vitro and exposed to normoxia or hypoxia (1% O2) conditions for 18 h.


title: Data-driven transcriptomics analysis identifies PCSK9 as a novel potential liver rejuvenation agent

city: Gothenburg

first: Muhammad

last: Arif

state: Västra Götaland

address: Blå Straket 5/WLAB

department: Department of Molecular and Clinical Medicine

country: Sweden

institute: University of Gothenburg

summary: Aging is an inevitable process in life that leads to numerous systemic effects on the human body. Here, we investigated systematically the effect of aging on the liver using a rat model of aging using data-driven approaches. We performed systems biology approaches to analyze genome-wide transcriptomics data from liver samples obtained from 3- and 19 months old rats. We observed significant alterations in multiple biological processes, including (1) disruption of mitochondrial functions and protein synthesis, and (2) activation of immune and inflammation pathways and lipid metabolism. We validated our results in two independent aging datasets. Finally, we demonstrated the power of the co-expression network to identify novel driver genes for liver aging and confirmed our findings in human aging subjects. Overall, we identified and validated a liver-specific gene, PCSK9, as a potential therapeutic target for attenuating the aging effect on the liver.

overall_design: We generated transcriptomics data from liver tissue from a total of 12 F344 rats, with 6 rats from each young (3 months) and aged (19 months) group

first: Csaba

last: Matyas

first: Partha

last: Mukhopadhyay

first: Burhan

last: Yokus

first: Eszter

last: Trojnar

first: Janos

last: Palosczi

first: Bruno

last: Paes-Leme

first: Suxian

last: Zhao

first: Falk

middle: W

last: Lohoff

first: Haskó

last: György

first: Pal

last: Pacher


title: Regional Gene Expression in the Retina, Optic Nerve Head, and Optic Nerve of Mice with Optic Nerve Crush and Experimental Glaucoma

status: Public on Sep 06 2023

city: Baltimore

first: Casey

last: Keuthan

address: 400 N Broadway, Smith Bldg, Rm 3001-N

institute: Johns Hopkins University

summary: A major risk factor for glaucomatous optic neuropathy is the level of intraocular pressure (IOP), which can lead to retinal ganglion cell axon injury and cell death. The optic nerve has a rostral unmyelinated portion at the optic nerve head followed by a caudal myelinated region. The unmyelinated region is differentially susceptible to IOP-induced damage in rodent models and in human glaucoma. While several studies have analyzed gene expression changes in the mouse optic nerve following optic nerve injury, few were designed to consider the regional gene expression differences that exist between these distinct areas. We performed bulk RNA-sequencing on the retina and on separately micro-dissected unmyelinated and myelinated optic nerve regions from naïve C57BL/6 mice, mice after optic nerve crush, and mice with microbead-induced experimental glaucoma (total = 36). Gene expression patterns in the naïve unmyelinated optic nerve showed significant enrichment of the Wnt, Hippo, PI3K-Akt, and transforming growth factor β pathways, as well as extracellular matrix–receptor and cell membrane signaling pathways, compared to the myelinated optic nerve and retina. Gene expression changes induced by both injuries were more extensive in the myelinated optic nerve than the unmyelinated region, and greater after nerve crush than glaucoma. Changes present three and fourteen days after injury largely subsided by six weeks. Gene markers of reactive astrocytes did not consistently differ between injury states. Overall, the transcriptomic phenotype of the mouse unmyelinated optic nerve was significantly different from immediately adjacent tissues, likely dominated by expression in astrocytes, whose junctional complexes are inherently important in responding to IOP elevation.

overall_design:
To characterize the region-specific transcriptome of mouse eyes in a naïve state and following optic nerve (ON) crush and experimental ocular hypertension injury models.
Tissue from mouse retinas and separately micro-dissected unmyelinated ON (UON) and myelinated ON (MON) were collected (n=4 replicate samples per experimental group, sexes pooled for n=2 RNA-seq libraries).
We then performed gene expression profiling analysis using data obtained from bulk RNA-seq of retina, UON, and MON tissue regions from naïve C57BL/6 mice (control, 0D), at two time points following ON crush (three days, 3D; two weeks, 2W), and at three time points following microbead-induced experimental glaucoma (three days, 3D; two weeks, 2W; six weeks, 6W).
Gene expression profiling analysis of RNA-seq data comparing tissue regions (retina, UON, and MON) and treatments/time points (naïve, crush, and glaucoma).

first: Julie

last: Schaub

first: Meihan

last: Wei

first: Weixiang

last: Fang

first: Sarah

last: Quillen

first: Elizabeth

last: Kimball

first: Thomas

middle: V

last: Johnson

first: Hongkai

last: Ji

first: Donald

last: Zack

first: Harry

last: Quigley


title: Unannotated microprotein EMBOW switches WDR5 between epigenetic and mitotic roles during cell cycle

city: west Haven

middle: A.

last: Slavoff

address: 600 west campus drive

department: Chemistry

institute: Yale university

summary: The highly conserved WD40-repeat protein WDR5 is part of multiple functional complexes both inside and outside the nucleus, interacting with the MLL/SET1 histone methyltransferases that catalyze histone H3 lysine 4 (H3K4) di- and tri-methylation (me2,3), and KIF2A, a member of the Kinesin-13 family of microtubule depolymerase. It is currently unclear whether, and how, the distribution of WDR5 between complexes is regulated. Here, we show that an unannotated microprotein dually encoded in the human SCRIB gene regulates the association of WDR5 with epigenetic and KIF2A complexes. We propose to name this alt-protein EMBOW, or microprotein that is the epigenetic to mitotic binder of WDR5. Loss of EMBOW decreases WDR5 interaction with KIF2A, displaces WDR5 from the spindle pole during G2/M phase, and shortens the spindle length, hence prolonging G2/M phase and delaying cell proliferation. On the other hand, loss of EMBOW increases WDR5 interaction with epigenetic complexes, including KMT2A/MLL1, and promotes WDR5 association with chromatin and binding to the target genes, hence increasing H3K4me3 levels of target genes. Together, these results implicate EMBOW as a regulator of WDR5 that switches it between epigenetic and mitotic regulatory roles during cell cycle, explaining how mammalian cells can temporally control the multifunctionality of WDR5.

overall_design: Examination of WDR5 binding and histone modification H3K4me3 in wild-type and EMBOW knock-out HEK 293T cells

first: Yanran

last: Chen

first: Xiongwen

last: Cao

first: Haomiao

last: Su


title: Activation Induced Deaminase defines a mature Burkitt-like lymphoma in the mouse

city: Madrid

first: Carmen

middle: Gómez-Escolar

last: Arias

state: Madrid

address: Calle Melchor Fernández Almagro 3

country: Spain

institute: CNIC

summary: Germinal centers (GCs) are the sites of secondary antibody diversification and underlie the mechanism of action of many vaccination strategies. Activation-induced deaminase (AID) triggers secondary antibody diversification through the introduction of somatic changes in immunoglobulin genes which lead to the generation of antibodies of higher affinity and more specialized effector functions. However, AID can also target other genomic regions, giving rise to mutations and chromosome translocations with oncogenic potential. Many human lymphomas originate from mature B cells that have undergone the GC reaction, such as the diffuse large B cell lymphoma, the follicular lymphoma and Burkitt lymphoma, and carry chromosome translocations. Mature B cell lymphomagenesis has been modeled in the mouse by the genetic introduction of chromosome translocations. Here, we present the first in-depth characterization of one such model, λ-MYC mice. We found that young pre-tumor stage mice had a prominent block in early B cell differentiation that resulted in the generation of very aggressive tumors lacking surface B cell receptor (BCR) expression, indicating that a large fraction of tumors in λ-MYC mice arise from B cell precursors rather than from mature B cells. Further, we assessed the contribution of AID to B cell lymphomagenesis in λ-MYC mice by using a genetic tracer of AID expression. Only a fraction of tumors contained GC-experienced cells defined by AID expression. AID-expressing tumors associated with longer survival and resembled mature Burkitt lymphomas. Thus, AID expression defines Burkitt lymphomagenesis in λ-MYC mice.

overall_design: Lymphoma cells were isolated by FACS from two independent λ-MYC mice based on Tom+ protein (AID historical expression). The four samples (B220+ IgM+ Tom+/-) were subjected to bulk RNA-sequencing for differential expression analysis.

last: Gómez-Escolar

first: Ester

last: Marina-Zárate

first: Almudena

last: Ramiro


title: PICKLE RELATED 2 is a neofunctionalised gene duplicate under positive Darwinian selection with antagonistic effects to the ancestral PICKLE gene on the seed transcriptome

city: Galway

first: Charles

last: Spillane

state: Galway

address: University Road

country: Ireland

institute: Plant and Agribioscience Centre

summary: The evolution and diversification of proteins capable of remodelling domains has been critical for transcriptional reprogramming during cell fate determination in multicellular eukaryotes. Chromatin remodelling proteins of the CHD3 family have been shown to have important and antagonistic impacts on seed development in the model plant, Arabidopsis thaliana, yet the basis of this functional divergence remains unknown. In this study, we demonstrate that genes encoding the CHD3 proteins PICKLE (PKL) and PICKLE-RELATED 2 (PKR2) originated from a duplication event during the diversification of crown Brassicaceae, and that these homologues have undergone distinct evolutionary trajectories since this duplication, with PKR2 fast-evolving under positive selection, while PKL is evolving under purifying selection. We find that the rapid evolution of PKR2 under positive selection reduces the encoded protein’s intrinsic disorder, possibly suggesting a tertiary structure configuration which differs from that of PKL. Our whole genome transcriptome analysis of gene expression in seeds of pkr2 and pkl mutants reveals that they act antagonistically on the expression of specific sets of genes, providing a basis for their differing roles in seed development. Our results provide insights on gene duplication and neofunctionalization can lead to differing and antagonistic selective pressures on transcriptomes during plant reproduction, as well as on the evolutionary diversification of the CHD3 family within seed plants.

overall_design: To investigate the relative evolution and changing roles of the chromatin remodelers PKR2 and PKL, we analyzed the transcriptome of developing seeds (3 DAP) from simple mutants pkl-1 and pkr2-2 as well as from the double mutant pkl-10;pkr2-2. All transcriptomic data was compared to the Wild-type Col-0.

first: Gilles

last: Dupouy

first: Ronan

last: Cashell

first: Galina

last: Brychkova

first: Reetu

last: Tuteja

first: Peter

middle: C

last: McKeown


title: Gene Expression data of MTA1-deficient human cord blood-derived HSCs

city: Lund

first: Kristijonas

last: Zemaitis

address: BMC A12

institute: Lund University

summary: Human CB HSC enriched cells were transduced with shRNAs targeting MTA1 to identify changes in global transcription programme and understand the mechanisms behind MTA1 knock down induced phenotype.

overall_design: CD34+CD38-CD90+CD45RA- cells sorted from human cord blood were lentivirally transduced with either shRNAs targeting MTA1 or control shRNA. In order to focus on immediate changes, the GFP+ cells were sorted 60 h after transduction for global gene expression profiling.

first: Agatheeswaran

last: Subramaniam

first: Jonas

last: Larsson


title: (RNA-seq) Spic regulates one-carbon metabolism and histone methylation in ground-state pluripotency

city: Belfast

first: Yaser

last: Atlasi

address: Lisburn Road

department: patrick G Johnston Centre for Cancer research

institute: Queen's University Belfast

summary: Understanding mechanisms of epigenetic regulation in embryonic stem cells (ESCs) is of fundamental importance for stem cell and developmental biology. Here we identify Spic, a member of the ETS family of transcription factors, as a specific marker of ground state pluripotency. We show that Spic is rapidly induced in ESCs cultured with GSK3-, MEK-inhibitors and LIF (2iL), and in response to MEK/ERK inhibition. ChIP-seq analysis demonstrated that Spic binds to enhancer elements that are associated with pluripotency genes. Interaction proteomics and genomic profiling confirmed that SPIC interacts with NANOG and stabilizes its binding to chromatin in 2iL-ESCs. Additional gain of function and loss of function experiments revealed that Spic controls genes involved in one carbon (1C) metabolism, Bhmt, Bhmt2, and Dmgdh, and the flux of SAM-to-SAH in 2iL-ESCs. By maintaining low levels of SAM, Spic controls the level of H3K4me3 and H3R17me2 histone methylation in ground state ESCs. Our data highlight the role of uncharacterized axillary transcription factors that link cellular metabolism to epigenetic regulation in ground state pluripotency.

overall_design: RNA-seq Spic-KO, -OE, and -WT mouse ESCs

first: Fatemeh

last: Mirzadeh Azad

first: Eduard

last: Struys

first: Victoria

last: Wingert

first: Luciana

last: Hannibal

first: Ken

last: Mills

first: Joop

last: Jansen

first: Daniel

last: Longley

first: Hendrik

last: Stunnenberg


title: Spic regulates one-carbon metabolism and histone methylation in ground-state pluripotency

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

overall_design: Refer to individual Series


title: (ATAC-seq_and_ChIP-seq) Spic regulates one-carbon metabolism and histone methylation in ground-state pluripotency

overall_design: ATAC-seq and ChIP-seq  of SPIC and NANOG  in Spic-KO, -OE, and -WT mouse ESCs

middle: H

middle: G


title: DPP9 Stabilizes NRF2 to Suppress Ferroptosis and Induce Sorafenib Resistance in Clear Cell Renal Cell Carcinoma

city: Shanghai

first: Xuanzhi

last: Zhang

state: Shanghai

address: Dong'an Road NO.130

institute: Fudan University

summary: we performed the RNA-sequencing to compare the transcriptome of DPP9 KO 786-O cells and negative control 786-O cells.

overall_design: DPP9 was knocked out in 786O cell line, and the transcriptional changes of genes after knocked out were explored by RNA sequencing.


title: Altered T cell infiltration and enrichment of leukocyte regulating pathways within aged skeletal muscle are associated impaired muscle function following influenza infection

status: Public on Sep 05 2023

city: Farmington

first: Laura

last: Haynes

address: 263 Farmington Avenue

department: Center on Aging

institute: UCONN Health

summary: Older adults have diminished immune responses that increase susceptibility to infectious diseases, such as influenza (flu). In older adults, flu infection can lead to hospitalization, catastrophic disability, and mortality. We previously demonstrated severe and prolonged muscle degradation and atrophy in aged mice during flu infection. Here, we utilized an unbiased transcriptomic analysis to elucidate mechanisms of flu-induced muscular declines in a mouse model. Our results showed age-related gene expression differences including downregulation of genes associated with muscle regeneration and organization and upregulation of genes associated with pro-inflammatory cytokines and migratory immune pathways in aged mice when compared to young. Pathway analysis revealed significant enrichment of leukocyte migration and T cell activation pathways in the aged muscle during infection. Intramuscular CD4 T cells increased in both young and aged mice during infection, while intramuscular CD8 T cells increased exclusively in aged muscle. CD4 T cells in young muscle were regulatory T cells (Treg), while those in aged were T follicular helper (Tfh) and Th2 cells. Correspondingly, IL-33, an important cytokine for Treg accumulation within tissue, increased only in young flu-infected muscle. Conversely, CXCL10 (IP-10) increased only in aged muscle suggesting a continued recruitment of CD8 T cells into the aged muscle during flu infection. Overall, our findings elucidate a link between flu-induced disability and dysregulated intracellular T cell recruitment into flu-injured muscle with aging. Furthermore, we uncovered potential pathways involved that can be targeted to develop preventative and therapeutic interventions to avert disability and maintain independence following infection.

overall_design: We utilized an unbiased transcriptomic approach to determine global gene expression changes within the skeletal muscle throughout the course of fu infection via RNA sequencing. Young (n=10/time point) and aged (n=9–10/time point) C57BL/6 mice were intranasally infected with 500 EID50 of PR8 infuenza and analyzed at various DPI. The gastrocnemius muscle was harvested at various days post infection (DPI) and RNA was isolated

first: Spencer

middle: R

last: Keilich

first: Andreia

middle: N

last: Cadar

first: Darcy

middle: T

last: Ahern

first: Blake

middle: L

last: Torrance

first: Erica

last: Lorenzo

first: Dominique

last: Martin

first: Jenna

last: Bartley


title: Mastication stimuli regulate the heart beat rate through the rhythmic regulation by hypothalamic-autonomic system in the weaning stage rat

city: bunkyo

first: yoshikazu

last: saito

state: tokyo

institute: university of tokyo

summary:
Using DNA microarray analysis, vasopressin, cocaine-amphetamine regulated transcript prepropeptide, corticotropin releasing hormone, and thyrotropin releasing hormone, all of which are involved in the sympathetic activation of heart rate, were found to be down-regulated in the chow diet group.
Our results provided the molecular and physiological bases for understanding the autonomic nervous regulation of cardiovascular function by the mastication stimuli.

overall_design: Three-week-old male Wistar rats were administered powdered (P-gloup) or solid (C-gloup) feed and water ad libitum for eight days, and the mRNA expression in the hypothalamus was compared between the two groups.

first: Seonmi

last: Lee

first: Ryota

last: Tochinai

first: Akihito

last: Yasuoka

first: Toshitada

last: Nagai

first: Yoshikazu

last: Saito

first: Masayoshi

last: Kuwahara

first: Keiko

last: Abe

first: Tomiko

last: Asakura


title: A truncated HIV Tat demonstrates potent and specific latency reversal activity

city: Beerse

first: Filmon

last: Eyassu

address: Turnhoutseweg 30

country: Belgium

institute: Janssen Pharmaceutica

summary:
The barrier to HIV-1 functional cure is caused by a small pool of latently infected resting CD4 T-cells that persist under antiretroviral therapy. Notably this latent reservoir of infected cells will produce replication-competent infectious virus once prolonged suppressive HAART is withdrawn. The reactivation of HIV-1 gene expression in T-cells harboring latent provirus in HIV-1 patients under HAART will likely result in depletion of this latent reservoir due to cytopathic effects and immune clearance. Many studies have investigated small molecules that reactivate HIV-1 gene expression but to date no latency reversal agent (LRA) has been identified to be specific, non-toxic, and effective in primary T-cells isolated from HIV-1 infected individuals undergoing long-term HAART. Stochastic fluctuations in HIV-1 tat gene expression have been attributed to be essential in the viral progression to latency.
We hypothesized that exposing Tat to latently infected CD4 T-cells will result in potent latency reversal. Our results indicate the capacity of an engineered Tat to reactivate HIV-1 in latently infected cells from patients to a similar degree as the protein kinase C agonist PMA (Phorbol 12-Myristate 13-Acetate) while showing no T-cell activation nor any significant transcriptome perturbation in primary CD4 T-cells.

overall_design: 4 donors CD4 cells, treatment with either, T66, PHA1 or PBS; comparison made for each treatment

first: Ellen

last: Van Gulck

first: Marion

last: Pardons

first: Erik

last: Nijs

first: Nick

last: verheyen

first: Koen

last: Dockx

first: Christel

last: Van den Eynde

first: Jerel

last: Vega

first: Eric

last: Florence

first: Brigitte

last: Autran

first: Nancy

last: Archin

first: David

last: Margolis

first: Kristine

last: Katlama

first: Chiraz

last: Hamimi

first: Ilse

last: Van den Wyngaert

first: Linos

last: Van de Kerckhove

first: Daniel

last: Boden