title: Generation and Integrated Analysis of Advanced Patient- derived Orthoxenograft Models (PDOX) for the Rational Assessment of Targeted Therapies in Endometrial Cancer

city: L'Hospitalet de Llobregat

first: David

last: Llobet

state: Barcelona

address: Gran Via de L'Hospitalet 199-203

department: Gynecologic cancer

country: Spain

institute: Bellvitge Biomedical Research Institute (IDIBELL)

summary: Clinical management of endometrial cancer (EC) is handicapped by the limited availability of second line treatments and bona fide molecular biomarkers to predict recurrence. These limitations have hampered the treatment of these patients, whose survival rates have not improved over the last four decades. The advent of coordinated studies such as the TCGA_UCEC have partially solved this issue, but the lack of proper experimental systems still represents a bottleneck that precludes translational studies from successful clinical testing in EC patients. Within this context, we present the first study reporting the generation of a collection of endometrioid EC patient-derived orthoxenograft (PDOX) mouse models that we believe can overcome these experimental constraints and pave the way towards state-of-the-art precision medicine in EC. We have characterized our collection of primary tumors and derived PDOXs through an integrative approach based on transcriptomics, mutational profiles and morphological analysis; and demonstrate that EC tumors engrafted in the mouse uterus retain the main molecular and morphological features from analogous tumor donors. Finally, we have harnessed the molecular properties of these tumors to assess the therapeutic potential of trastuzumab, a HER2 inhibitor with growing interest in EC, using patient-derived organotypic multicellular tumor spheroids and in vivo experiments.

overall_design: A collection of patient-derived orthoxenografts (PDOXs) from 15 endometrioid endometrial cancer patients were generated and a gene expression profiling analysis using data obtained from RNA-seq was conducted.

first: Xavier

last: MATIAS-GUIU

first: Alberto

last: VILLANUEVA

last: LLOBET-NAVAS


title: Transcriptome changes after NEN treament in neuroblastoma cell

status: Public on Oct 26 2022

city: palo alto

first: Jiangbin

last: ye

state: California

address: 269 Campus Drive CCSR-South 1245

country: USA

institute: Stanford university

type: Expression profiling by high throughput sequencing

summary: To study the gene expression changes after niclosamide ethanolamine (NEN) treament in neuroblastoma cell, we treated SK-N-BE(2) with 1µM NEN for 24hours. The RNA were extracted from the cells and submitted for RNA sequencing.

overall_design: Proper number of cells were plate in 10cm dish before  treatment by DMSO or 1µM NEN for 24h.  Each group contain 3 biological replicates.

last: Ye

first: Haowen

last: Jiang


title: Correlation analysis between gut microbiota characteristics and melasma

status: Public on Oct 25 2022

city: Dalian

first: Cong

last: Liu

address: 222 Zhongshan Road

country: China

institute: First Affiliated Hospital of Dalian Medical University

summary: To compare the similarities and differences in species diversity of the gut microbiota between the patients with melasma and healthy subjects. The feces were collected for 16S rRNA sequencing analysis of the gut microbiota.

overall_design: 16S rRNA  sequencing analysis for fecal samples of the patients with melasma and healthy subjects (control group)

first: Dan

last: He

first: Anye

last: Yu

first: Yaru

last: Deng

first: Li

last: Wang

first: Zhiqi

last: Song


title: MEX3A mediates p53 degradation to suppress ferroptosis and facilitate ovarian cancer tumorigenesis

city: Taipei

first: Wendy

middle: W

last: Hwang-Verslues

state: Not in USA

address: No. 128, Sec. 2, Academia Road, Nangang District, Genomics Research Center, Academia Sinica

country: Taiwan

institute: Academia Sinica

summary: Epithelial ovarian cancer (OC) is a highly heterogeneous and malignant female cancer with an overall low survival rate. p53 mutation is a predominant genetic factor thought to be responsible for poor clinical outcome. Despite the fact that ovarian clear cell carcinoma (OCCC) shows more severe prognosis, drug resistance, metastasis and recurrence compared to other OC subtypes, mutations in p53 are much less frequent. The underlying mechanisms crucial for tumorigenesis and malignancy of OC harboring wild-type (WT) p53 remain poorly understood. We found that upregulation of MEX3A, which is a dual-function protein containing a RING finger domain and an RNA binding domain, was correlated with poor survival in OC. MEX3A overexpression enhanced tumorigenic activity in RMG-1 and OVISE OCCC cell lines. In contrast, depletion of MEX3A in PA-1 ovarian teratocarcinoma cells and TOV21G OCCC cells reduced cell survival and proliferative ability in cell-based assays, as well as inhibited tumor growth and prolonged survival in orthotopic xenograft models. MEX3A depletion did not alter p53 mRNA level but did increase the protein stability of WT p53. MEX3A-mediated p53 protein degradation was crucial to prevent ferroptosis and enhance tumorigenesis as p53 knockdown reversed the effects of MEX3A depletion. Together, our observations identified MEX3A as an important oncogenic factor promoting tumorigenesis in OC cells harboring WT p53.

overall_design: A total of six samples were analyzed: PA-1 and TOV21G cells without (sh-Ctrl) or with MEX3A-depletion (sh-MEX3A#1 or sh-MEX3A#2). For each cell line, the expression profiles of each MEX3A depleted clone, sh-MEX3A#1 or sh-MEX3A#2, were compared to the sh-Ctrl.


title: Intracellular Galectin-3 Is a Sensor of Lipopolysaccharide that Promotes Glycolysis through Activating mTORC1

city: Beijing

first: Xing

last: Chen

address: Capital Medical University

institute: Capital Medical University

summary: Galectin-3 is a carbohydrate binding protein implicated in cell-cell interaction and cell growth. Interestingly, recent studies suggest that galectin-3 is involved in cell metabolism and linked to diabetes and cancer. How galectin-3 might act as a diabetogenic and tumorogenic factor remains to be investigated. Here we report that intracellular galectin-3 is physically associated with Rag GTPases and Ragulator of the mTORC1 signaling machinery on lysosomes. We show that galectin-3 senses lipopolysaccharide (LPS) to facilitate the interaction of Rag GTPases and Ragulator, leading to activation of Rag GTPases thus lysosomal loading of mTOR and activation of mTORC1. Integrative genomics and transcriptomics analyses reveal that the LPS/galectin-3-Rag GTPases/Ragulator-mTORC1 axis regulates a cohort of genes including GLUT1 (glucose transporter member 1) that functions in glucose uptake and glycolysis and HK2 (hexokinase 2) and PKM2 (pyruvate kinase M2) that catalyze the first and last step of glycolysis, respectively. Indeed, galectin-3 deficiency severely compromises LPS-promoted glycolysis. Importantly, in diabetes patients, the expression of HK2 was significantly reduced, and in hepatocellular carcinoma (HCC), thyroid cancer, and prostate cancer, galectin-3 is highly expressed, and its level of expression is positively correlated with that of HK2 and PKM2 and negatively correlated with the prognosis of HCC patients. Our study unravels that galectin-3 is a sensor of LPS, an important modulator of the mTORC1 signaling, and a critical regulator of glucose metabolism, adding to the understanding of diabetogenesis and tumorigenesis.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HEK-293T cells treated with siCon and siGal3 or Control and Torin1. HEK-293T cells were treated with or without siGal3 or Torin 1 for 24 hours, and total RNAs were extracted for cDNA synthesis, library construction and sequencing.

first: Yongfeng

last: Shang


title: Myeloid-specific SHP-2 ablation alters the fate commitment of myeloid cells and induces anti-tumor immunity

city: Boston

first: Vassiliki

middle: A.

last: Boussiotis

state: MA

address: 330 Brookline Ave

institute: Beth Israel Medical Center

summary: We generated mice with conditional targeting of the Ptpn11 gene (encoding for Shp-2) in T cells (Shp-2fl/flLckCre) or myeloid cells (Shp-2fl/flLysMCre). Although no difference in tumor growth was observed between Shp-2fl/flLckCre and control mice and both groups were similarly benefitted by PD-1 blockade, Shp-2fl/flLysMCre mice had significantly diminished tumor growth that was not further decreased by anti-PD-1 treatment. As revealed by RNA-seq, myeloid-specific Shp-2 ablation was paralleled by expansion of activated myeloid cells and macrophages with molecular signatures of enhanced neutrophil and macrophage differentiation, phagocytosis, antigen-presenting function, TLR and type I IFN signaling, chemokine production, and expression of immunostimulatory molecules, which promoted T cell recruitment and activation.

overall_design: Control Shp-2fl/fl and Shp-2fl/flLysMCre mice were inplanted with M17 tumors and 15 days later GR-1+ MDSC were collected from the spleen, and CD11b+F4/80+ TAMs were collected from the tumor site. RNA was extracted and differential gene expression was examined by RNAsequencing. Two replicates of RNA samples isolated from GR1+ MDSC per experimental group were analyzed. Three replicates of RNA samples isolated from TAMs per experimental group were analyzed.

middle: A

first: Anthos

last: Christofides

first: Ioannis

middle: S

last: Vlachos

first: Xanthi-Lida

last: Katopodi


title: Myeloid-specific ablation of Pdcd1 alters fate comittment of tumor-associated macrophages and induces anti-tumor immunity

summary: We generated mice with conditional targeting of the Pdcd1 gene (encoding for PD-1) in myeloid cells (Pdcd1-2fl/flLysMCre). Pdcd1-2fl/flLysMCre mice had significantly diminished tumor growth. As revealed by RNA-seq, myeloid-specific Pdcd1 ablation was paralleled by generation of myeloid cells with monocytic dominance, and activated macrophages with molecular signatures of enhanced myeloid cell differentiation, macrophage activation, phagocytosis, TLR and NF-kB signaling, chemokine and cytokine production, and expression of immunostimulatory molecules.

overall_design: Control Pdcd1fl/fl and Pdcd1fl/flLysMCre mice were inplanted with M17 tumors and 15 days later CD11b+F4/80+ TAMs were collected from the tumor site. RNA was extracted and differential gene expression was examined by RNAsequencing. Three replicates of RNA samples isolated from TAMs per experimental group were analyzed.


title: TNFα and IFNγ cooperate for efficient pro- to anti-inflammatory transition of macrophages during muscle regeneration (RNA-Seq)

city: Vancouver

first: Fabio

last: Rossi

state: BC

address: 2222 Health Sciences Mall

department: School of Biomedical Engineering

country: Canada

institute: University of British Columbia

summary: IFNγ is traditionally known as a pro-inflammatory cytokine with diverse roles in antimicrobial and antitumor immunity. Yet, findings regarding its sources and functions during the regeneration process following a sterile injury are conflicting. Here, we show that natural killer (NK) cells are the main source of IFNγ in regenerating muscle. Beyond this cell population, IFNγ production is limited to a small population of T cells. We further show that NK cells do not play a major role in muscle regeneration following an acute injury or in dystrophic mice. Surprisingly, the absence of IFNγ per se also has no effect on muscle regeneration following an acute injury. However, the role of IFNγ is partially unmasked when TNFα is also neutralized, suggesting a compensatory mechanism. Using transgenic mice, we showed that conditional inhibition of IFNGR1 signaling in muscle stem cells or fibro-adipogenic progenitors does not play a major role in muscle regeneration. In contrast to common belief, we found that IFNγ is not present in the early inflammatory phase of the regeneration process, but rather peaks when macrophages are acquiring an anti-inflammatory phenotype. Our further transcriptomic analysis suggests that IFNγ cooperates with TNFα to regulate the transition of macrophages from pro- to anti-inflammatory. The absence of the cooperative effect of these cytokines on macrophages, however, does not result in significant regeneration impairment likely due to the presence of other compensatory mechanisms. Our findings support the arising view of IFNγ as a pleiotropic inflammatory regulator rather than an inducer of the inflammatory response.

overall_design: Dissection of the role of IFNγ in muscle regeneration and fibrosis

first: Farshad

last: Babaeijandaghi

first: Lin

last: Tung

first: Tara

last: Stach


title: Single-cell ATAC-Seq and RNa-seq of human and mouse basal cell carcinoma (BCC)

city: Stanford

first: Anthony

last: Oro

state: CA

address: 269 Campus Drvie

department: Dermatology

institute: Stanford University

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: A skeletal-muscle senescence blueprint defines an aged-like inflamed niche that inhibits regeneration over lifetime [ATAC-seq]

city: Barcelona

first: Eusebio

last: Perdiguero

address: Dr. Aiguader 88

department: Department of Medicine and Life Sciences

institute: UPF

summary: A new sorting protocol was used to identify and isolate different senescent cell types from damaged muscles of young and geriatric mice. Analysis revealed conservation of two universal senescence hallmarks (inflammation and fibrosis) across cell type, regeneration time, and aging, while cell identity traits were preserved. Senescent cells create an “aged-like” inflamed niche, mirroring inflammation-associated with aging (inflammaging), that arrests stem cell proliferation and regeneration.

overall_design: Muscles were mechanically disaggregated and incubated in Dulbecco's Modified Eagle's medium (DMEM) containing liberase (Roche) and dispase at 37°C with agitation for 1-2 hours. When required, SPiDER-b-gal reagent (Dojindo) was added during the second hour. The supernatant was then filtered and cells were incubated in lysis buffer (BD Pharm Lyse) for 10 min on ice, resuspended in PBS with 2.5% fetal bovine serum (FBS), and counted. BV711-conjugated anti- CD45 (BD), APC-Cy7-conjugated anti F4/80 (Biolegend), PE- conjugated anti-a7-integrin (Ablab), APC-conjugated anti-CD31 (eBioscience) and PE-Cy7-conjugated anti-Sca-1 (Biolegend) antibodies were used to isolate MCs (CD45+ and F4/80+), SCs (a7-integrin+, CD45+, F4/80+ and CD31+) and FAPs (Sca-1+, MCs CD45+, F4/80+, a7-integrin+ and CD31+). PE-Cy7-conjugated anti-CD45 antibody (Biolegend) was used to isolate CD45 positive and negative populations. SPiDER-b-gal (SPiDER) was employed to isolate senescent cells (SPiDER+) from non-senescent cells (SPiDER–) of each cell type. Isolated cells were subjected to ATAC-seq. Pools of 3 animals were used for each sample.

first: Victoria

last: Moiseeva

first: Lai

last: Yiwei

first: Juan

last: An

first: Oleg

last: Deryagin

first: Giacomo

last: Volpe

first: Miguel

last: Esteban

first: Yasuyuki

last: Ohkawa

first: Pura

last: Munoz-Canoves


title: Single-cell RNA-Seq (scRNA-Seq) of mouse basal cell carcinoma (BCC)

summary: We used scRNA-Seq to examine BCC tumor heterogeneity.

overall_design: Three mouse BCC tumors were processed for scRNA-Seq. For the Sample 1/mBCC, the tumor was simply dissociated and processed for scRNA-Seq. For Sample 2/mBCC_DMSO and Sample 3/mBCC_VISMO, tumors were treated with drug of vehical (see treatment protocol).

first: Daniel

last: Haensel

first: Sadhana

last: Gaddam


title: Human Th17 cells engage gasdermin E pores to release IL-1a upon NLRP3 inflammasome activation [Array]

status: Public on Oct 24 2022

city: Jena

first: Alberto

last: Garcia Lopez

state: Thuringia

address: Adolf-Reichwein-Straße 23

department: Microbiome Dynamics

country: Germany

institute: Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute

summary: Adaptive immune responses are tailored to the invading microbial antigen and tissue microenvironment, resulting in diverse context-specific inflammatory signatures. There is emerging evidence that innate immune responses coopt adaptive properties such as memory. Whether T cells harness innate immune signaling pathways to diversify their repertoire of effector functions remains unknown. Here, we found that human T cells expressed gasdermin E (GSDME), a membrane pore-forming molecule that has recently been shown to execute pyroptotic cell death and thus to serve as a potential cancer checkpoint. In T cells, GSDME expression was, in contrast, associated with durable viability and was repurposed for the tunneled release of the innate danger signal IL-1a. This property was restricted to a subset of human Th17 cells with antigen specificity for C. albicans and was regulated by a T-cell-intrinsic NLRP3 inflammasome and its engagement of a proteolytic cascade of successive caspase-8, caspase-3 and GSDME cleavage following T-cell receptor stimulation and calcium-licensed calpain maturation of the pro-IL1a form. This equipped human Th17 cells with a so far overlooked effector function that contributes to the clearance of C. albicans. Our results propose GSDME pore formation in T cells as a mechanism of unconventional cytokine release through harnessing of innate signaling platforms in response to adaptive stimuli. This finding diversifies the functional repertoire and mechanistic equipment of T cells and thus suggests new therapeutic strategies for targeting the proinflammatory identity of human Th17 cells in anti-fungal host defense.

overall_design: Th17 cells expressing or supressing IL1B (3 biological for each condition, 6 samples in total)

first: Ying-Yin

last: Chao

first: Alisa

last: Puhach

first: David

last: Frieser

first: Mahima

last: Arunkumar

first: Laurens

last: Lehner

first: Thomas

last: Seeholzer

first: Albert

last: Garcia-Lopez

first: Marlot

last: van der Wal

first: Silvia

last: Fibi-Smetana

first: Axel

last: Dietschmann

last: Sommermann

first: Leila

last: Taher

first: Mark

last: Gresnigt

first: Femke

last: van Wijk

first: Gianni

last: Panagiotou

last: Krappmann

first: Olaf

last: Groß

first: Christina

middle: E

last: Zielinski


title: Chronic Prenatal Delta-9-tetrahydrocannabinol Exposure Adversely Impacts Placental Function and Development in a Rhesus Macaque Model

city: Beaverton

first: Lyndsey

middle: Elizabeth

last: Shorey-Kendrick

state: Oregon

address: 505 NW 185th Ave

institute: Oregon Health and Science University

summary:
To investigate the impact of THC exposure on placenta RNA/gene expression
Edibles were administered prior to the animal’s daily chow to ensure consumption on an empty stomach and to confirm complete ingestion. Animals were slowly titrated up to 2.5mg/7kg/day of THC using published weight-based medical cannabis acclimation recommendations approximately 4 months prior to undergoing time-mated breeding. Each THC-exposed pregnant animal (n=5) continued to consume a daily edible of 2.5mg/7kg/day throughout pregnancy.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for rhesus macaque placentas exposed to THC prenatally (n=5 animals per group)

first: Jamie

last: Lo


title: Sexually Dimorphic Increases in Bone Mass Following Tissue-specific Overexpression of Runx1 in Osteoclast Precursors

city: Atlanta

first: Mohd

middle: Nazir

last: Khan

state: GA

address: 21 Ortho Lane

department: Orthopaedics

institute: Emory University

summary: We investigated the skeletal effects of conditional overexpression of Runx1 in preosteoclasts by crossing novel Runx1 gain-of-function mice (Rosa26-LSL-Runx1) with LysM-Cre transgenic mice.

overall_design: The global expression profile duirng osteclast differentiation at day 3 and 5 was compared between Rosa26-Runx1tg/+ cells (control mice) and LysM-Cre;Rosa26-Runx1tg/+ cells (Runx1 gain-of-function) to determine the effects of Runx1 upregulation on osteoclast formation

first: M

last: Díaz-Hernández

first: C

last: Kinter

first: S

middle: R

last: Watson

first: G

last: Mella-Velazquez

first: J

last: Kaiser

last: Liu

first: N

middle: M

middle: L

last: Roberts

last: Lorenzo

first: Drissi

last: Hicham


title: Human Th17 cells engage gasdermin E pores to release IL-1a upon NLRP3 inflammasome activation [RNA-seq]

first: Alberto

last: Garcia Lopez

overall_design: Resting T-cell clones categorized as IL-1a+ (> 30% IL-1a expression, n = 4) and IL-1a– (0% IL-1a expression, n = 3) were restimulated with phorbol-12-myristat-13-acetat (PMA) and ionomycin (both from Sigma–Aldrich) for 3 h.

first: Ying-Yin

last: Chao

first: Alisa

last: Puhach

first: David

last: Frieser

first: Mahima

last: Arunkumar

first: Laurens

last: Lehner

first: Thomas

last: Seeholzer

first: Albert

last: Garcia-Lopez

first: Marlot

last: van der Wal

first: Silvia

last: Fibi-Smetana

first: Axel

last: Dietschmann

last: Sommermann

last: Taher

last: Gresnigt

last: van Wijk

first: Daniel


title: TNFα and IFNγ cooperate for efficient pro- to anti-inflammatory transition of macrophages during muscle regeneration (scRNA-Seq)

first: Fabio

last: Rossi

first: Farshad

last: Babaeijandaghi

first: Lin

last: Tung

first: Tara

last: Stach


title: Remarkable Lung Heterogeneity at Single-Cell Resolution and the Role of Sex as a Biological Variable in Neonatal Hyperoxic Lung Injury

city: Philadelphia

first: Abiud

last: Cantu

state: Pennsylvania

address: 3615 Civic Center Blvd

department: Neonatology

institute: Children's Hospital of Philadelphia

summary: The goal of the project was to delineate sex-specific differences in the neonatal lung exposed to postnatal hyperoxia to model the pathophysiologic mechanisms in the human disease; bronchopulmonary dysplasia (BPD).

overall_design: C57BL6J neonatal mice were exposed to room air or hyperoxia from PND1-5 to 95% FiO2 or mainatined in room air. Mice were euthanized at PND7. Single cell suspension were prepared for each of the four groups: male room air, female room air, male hyperoxia and female hyperoxia at the PND7 time point.  Each sample was comprised of pooled lung tissue from three mice.

first: Manuel

first: Xiaoyu

last: Dong

first: Connor

last: Leek

first: Xiao

last: Wang

first: Eniko

last: Sajti

first: Krithika

last: Lingappan


title: DNA dioxygenases Tet2/3 control epithelial differentiation [ATAC-seq]

city: BOSTON

first: Guodong

last: Chen

address: 609 Albany Street, ROOM 414

institute: Boston University

summary:
Execution of lineage-specific differentiation programs requires tight coordination between many regulators including Ten-eleven translocation (TET) family enzymes catalyzing 5-methylcytosine oxidation in DNA. Here, by using Keratin 14-Cre-driven ablation of Tet genes in skin epithelial cells, we demonstrate that ablation of Tet2/Tet3 result in marked alterations of hair shape and length followed by hair loss. We show that through DNA demethylation, Tet2/Tet3 control chromatin accessibility, Dlx3 binding and promoter activity of the Krt25 and Krt28 genes regulating hair shape, as well as regulate interactions between the Krt28 gene promoter and distal enhancer. Moreover, Tet2/Tet3 also control three-dimensional chromatin topology in Keratin type I/II gene loci via DNA methylation-independent mechanisms. These data demonstrate the essential roles for Tet2/3 in establishment of lineage-specific gene expression program and control of Dlx3/Krt25/Krt28 axis in hair follicle epithelial cells and implicate modulation of DNA methylation as a novel approach for hair growth control.
We performed ATAC-seq from sorted hair matrix keratinocytes of wild type and TetDKO (Krt14-Cre, Tet2 flox/flox, Tet3 flox/flox) mice at P4.5 which are treated or untreated with 5-aza.

overall_design: ATAC-seq kit (active motif, #81286) is purchased from active motif company. As the manual described, 100K sorted cells are suspended in 100 μl ice-cold ATAC Lysis Buffer for nuclei extraction, and nuclei are incubated in 50 μl of Tagmentation Master Mix for DNA tagmentation. After purification, the DNA is amplified with NEBNext® High-Fidelity 2x PCR Master Mix (NEB, #M0541) as well as unique i5 and i7 index primers for 10 cycles to prepare DNA library. Paired-end sequencing is performed in the Illumina Nextseq500 Midoutput PE75 system (2 x 75 bp).

first: Iqra

last: Fatima

first: Qin

last: Xu

first: Michael

middle: Y

last: Fessing

first: Andrei

middle: N

last: Mardaryev

first: Andrey

last: Sharov

first: Elena

last: Rozhkova

first: Guoliang

first: Vladimir

last: Botchkarev


title: Krüppel-like factor 4 regulates the cytolytic effector function of exhausted CD8 T-cells [ATAC-Seq]

city: Seoul

first: Jinwoo

last: Nah

address: 1, Gwanak-ro, Gwanak-gu, Seoul

department: Life science

country: South Korea

institute: Seoul National University

summary:
Since exhausted CD8 T-cells are known to have a strong epigenetic imprint, which is a major obstacle for reinvigoration, we investigated whether the induced Klf4 expression could change the epigenetic status of the exhausted CD8 T-cells.
For this, we performed ATAC-sequencing and compared chromatin landscapes between naïve, in vitro generated effector, exhausted (GFP-induced), and reinvigorated (KLF4-induced) CD8 T-cells.

overall_design: ATAC-sequencing for naïve, in vitro generated effector, exhausted (pRetroX-GFP/Dox+), and reinvigorated (pRetroX-Klf4/Dox+) CD8 T-cells.

first: Rho

last: Seong


title: Human Th17 cells engage gasdermin E pores to release IL-1alpha upon NLRP3 inflammasome activation

city: Graz

first: Silvia

last: Fibi-Smetana

state: Styria

address: Stremayrgasse 16

department: Biomedical Informatics

country: Austria

institute: Graz University of Technology

summary: Adaptive immune responses are tailored to the invading microbial antigen and tissue microenvironment, resulting in diverse context-specific inflammatory signatures. There is emerging evidence that innate immune responses coopt adaptive properties such as memory. Whether T cells harness innate immune signaling pathways to diversify their repertoire of effector functions remains unknown. Here, we found that human T cells expressed gasdermin E (GSDME), a membrane pore-forming molecule that has recently been shown to execute pyroptotic cell death and thus to serve as a potential cancer checkpoint. In T cells, GSDME expression was, in contrast, associated with durable viability and was repurposed for the tunneled release of the innate danger signal IL-1. This property was restricted to a subset of human Th17 cells with antigen specificity for C. albicans and was regulated by a T-cell-intrinsic NLRP3 inflammasome and its engagement of a proteolytic cascade of successive caspase-8, caspase-3 and GSDME cleavage following T-cell receptor stimulation and calcium-licensed calpain maturation of the pro-IL1 form. This equipped human Th17 cells with a so far overlooked effector function that contributes to the clearance of C. albicans. Our results propose GSDME pore formation in T cells as a mechanism of unconventional cytokine release through harnessing of innate signaling platforms in response to adaptive stimuli. This finding diversifies the functional repertoire and mechanistic equipment of T cells and thus suggests new therapeutic strategies for targeting the proinflammatory identity of human Th17 cells in anti-fungal host defense.

overall_design: Gene expression patterns in Th17 cells with and without gasdermin E knock-out.

first: Ying-Yin

last: Chao

first: Alisa

last: Puhach

first: David

last: Frieser

first: Mahima

last: Arunkumar

first: Laurens

last: Lehner

first: Thomas

last: Seeholzer

first: Albert

last: Garcia-Lopez

first: Marlot

last: van der Wal

first: Axel

last: Dietschmann

last: Sommermann

first: Leila

last: Taher

first: Mark

last: Gresnigt

first: Femke

last: van Wijk

first: Gianni

last: Panagiotou

first: Daniel

last: Krappmann

first: Olaf

last: Groß

first: Christina

last: Zielinski


title: TP53-related signature for predicting prognosis and tumor microenvironment characteristics in bladder cancer: a multi-omics study  1  microenvironment characteristic

city: Nanning

first: Zhenxing

last: Wang

state: Guangxi

address: Zhongshan Street

department: Center for Genomic and Personalized Medicine

institute: Guangxi Medicla University

summary: Background: The tumor suppressor gene TP53 is frequently mutated or inactivated in bladder cancer (BLCA), which is implicated in the pathogenesis of tumor. However, the cellular mechanisms of TP53 mutations are complicated, yet well-defined, but their clinical prognostic value in the management of BLCA remains controversial. This study aimed to explore the role of TP53 mutation in regulating the tumor microenvironment (TME), elucidate the effects of TP53 activity on BLCA prognosis and immunotherapy response.  Methods: A TP53-related signature based on TP53-induced and TP53-repressed genes was used to construct a TP53 activity-related score and classifier. The abundance of different immune cell types was determined using CIBERSORT to estimate immune cell infiltration. Moreover, the heterogeneity of the tumor immune microenvironment between the high and low TP53 score groups was further evaluated using single-cell mass cytometry (CyTOF) and imaging mass cytometry (IMC). Moreover, pathway enrichment analysis was performed to explore the differential biological functions between tumor epithelial cells with high and low TP53 activity scores. Finally, the receptor–ligand interactions between immune cells and tumor epithelial cells harboring distinct TP53 activity were analyzed by single-cell RNA-sequencing.  Results: The TP53 activity-related gene signature differentiated well between TP53 functional retention and inactivation in BLCA. BLCA patients with low TP53 scores had worse survival prognosis, more TP53 mutations, higher grade, and stronger lymph node metastasis than those with high TP53 scores. Additionally, CyTOF and IMC analyses revealed that BLCA patients with low TP53 scores exhibited a potent immunosuppressive TME. Consistently, single-cell sequencing results showed that tumor epithelial cells with low TP53 scores were significantly associated with high cell proliferation and stemness abilities and strongly interacted with immunosuppressive receptor–ligand pairs.  Conclusions: Patients with BLCA with low TP53 scores have a worse prognosis and a more immunosuppressive TME. This TP53 activity-related signature can serve as a potential prognostic signature for predicting the immune response, which may facilitate the development of new strategies for immunotherapy in BLCA.  Keywords: bladder cancer, TP53, immunosuppression, tumor microenvironment

overall_design: RNA-seq of bladder cancer

first: Yuting

last: Tao

first: Xia

last: Li

first: Yushan

last: Zhang

first: Qiuyan

first: Xi


title: Krüppel-like factor 4 regulates the cytolytic effector function of exhausted CD8 T-cells

first: Jinwoo

last: Nah


title: Krüppel-like factor 4 regulates the cytolytic effector function of exhausted CD8 T-cells [RNA-Seq]

summary:
To identify the role of KLF4 on exhausted CD8 T-cells, we retrovirally transduced Klf4 into OT-I CD8 T-cells on day1 of in vitro exhaustion model and repeatedly treated OVA peptide to induce exhaustion.
Then we analyzed the gene expression profiles of these transduced cells by RNA-sequencing.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for CD8 T-cells transduced with MigRI and Klf4

first: Rho

last: Seong


title: A skeletal-muscle senescence blueprint defines an aged-like inflamed niche that inhibits regeneration over lifetime

first: Eusebio

last: Perdiguero


title: Effect of Rad6 backside beta-turn mutations on gene expression

city: Salt Lake City

first: Mahesh

middle: B

last: Chandrasekharan

state: UT

address: 2000 Circle of Hope Room 4343

department: Radiation Oncology

institute: University of Utah SOM

summary: Rad6 E2 ubiquitin-conjugating enzyme and Bre1 E3 ubiquitin ligase catalyze histone H2B Lysine-123 monoubiquitination (H2Bub1), which stabilizes nucleosomes and regulates the trans-histone H3K4 and K79 methylation during gene transcription and other nuclear processes. The interaction interfaces within the Rad6-Bre1-containing H2B ubiquitin-conjugating complex have remained unknown. By solving the crystal structure of Rad6 along with a non-RING domain N-terminal region of Bre1, we report a beta-turn in Rad6's so-called backside region away from catalytic pocket as a binding site for a homodimer of Bre1 E3 ligase. Using quantitative ChIP-seq or ChIP-Rx, we further demonstrate that Rad6's backside beta-turn residues also govern the chromatin binding dynamics and transcriptional regulatory functions of the Rad6-Bre1 complex.

overall_design: Gene expression changes were generated from six different yeast strains representing wild type control, rad6 null and bre1 null mutants, and beta-turn mutants: rad6-P43L, rad6-P47T and rad6-E49K. Three independent biological samples were grown for each strain, total RNA was isolated, and libraries were prepared, sequenced, and analyzed separately.

first: Prakash

middle: K

last: Shukla

first: Jesse

last: Bissell

first: Timothy

middle: J

last: Parnell


title: Hepatic nonvesicular cholesterol transport is critical for systemic lipid homeostasis

city: Los Angeles

first: Peter

last: Tontonoz

address: 675 Charles E. Young Drive South, MRL 6619

department: Pathology and Laboratory Medicine

institute: UCLA

summary: In cell models, changes in the “accessible” pool of plasma membrane (PM) cholesterol are linked with the regulation of ER sterol synthesis and metabolism by the Aster family of nonvesicular transporters. However, the relevance of such nonvesicular transport mechanisms for lipid homeostasis in vivo has not been defined. Here we reveal two physiological contexts that generate accessible PM cholesterol and engage the Aster pathway in liver: fasting and reverse cholesterol transport (RCT). During fasting, adipose tissue–derived fatty acids activate hepatocyte sphingomyelinase to liberate sequestered PM cholesterol. Aster-dependent cholesterol transport during fasting facilitates cholesteryl ester (CE) formation, cholesterol movement into bile, and VLDL production. During RCT, HDL delivers excess cholesterol to the hepatocyte PM through SR-BI. Loss of hepatic Asters impairs cholesterol movement into feces, raises plasma cholesterol levels, and causes cholesterol accumulation in peripheral tissues. These results reveal fundamental mechanisms by which Aster cholesterol flux contributes to hepatic and systemic lipid homeostasis.

overall_design: RNA-seq was performed on liver from male C57BL/6J mice fasted for 4 hours or 16 hours (n = 3, 3). Total RNA was extracted using TRIzol and the RNeasy Mini Kit with on-column DNase I digestion (Qiagen). Library preparation and sequencing was done at GENEWIZ. Adapter and quality trimming of raw FASTQ files was performed using Trimmomatic. FastQC was used to analyze FASTQ files before and after trimming. Trimmed FASTQ files were aligned to GRCm38/mm10 using STAR. HTSeq-count was used to extract gene counts and differential gene expression analysis was performed using DESeq2.

first: Xu

last: Xiao

first: Kevin

last: Qian


title: RNA-seq of anterior and posterior amygdala of two mouse strains

city: Münster

first: Marisol

last: Herrera-Rivero

state: NRW

address: Albert-Schweitzer-Campus 1

institute: University of Münster

summary: 19 female mice of the C57BL/6J and B6D2F1N strains were housed in either standard (control) or enriched (including access to playgrounds) conditions. The animals were trained to perform a cognitive judgement bias test. Upon completion of training, the animals underwent the test paradigm and were sacrificed. Anterior and posterior portions of the amygdala were finally dissected for RNA-sequencing.

overall_design: RNA-seq

first: Lena

last: Bohn

first: Anika

last: Witten

first: Kay

last: Jüngling

first: Hans-Christian

last: Pape

first: Sylvia

last: Kaiser

first: S

middle: H

last: Richter

first: Monika

last: Stoll

first: Norbert

last: Sachser


title: Identification of GP33-specific CD8 T cell clones responding to chronic infection with LCMV-Clone13

status: Public on Oct 23 2022

city: Chicago

first: Weiguo

last: Cui

state: IL

address: 303 E Chicago Ave

department: Pathology

institute: Northwestern University

summary: T cells specific for a certain antigen are a heterogeneous population characterized by cells expressing different T Cell Receptors (TCRs). As the TCR determines the avidity of a T cell clone for its cognate antigen, this feature has also a significant impact on the fate of such clone during antigenic challenge. In the context of chronic viral infection, T cells specific for the chronic virus differentiate into exhausted cells with limited functionality. We find that, in the process of exhaustion following infection with LCMV-Clone13, certain clones of CD8 T cells specific for the LCMV immunodominant epitope GP33 are enriched compared to others.

overall_design: 3 C57BL/6 mice were infected with LCMV-Clone13 and eutnaized 27 days after infection. Spleens were collected and splenocytes pooled together before proceding to staining with GP33-loaded tetramers to ientify GP33-specific CD8 T cells. These cells were then sorted by FACS and then used for scRNAseq of their TCRs.

first: Nikhil

last: Joshi

first: Martina

last: Damo

first: Moujtaba

last: Kasmani


title: Synapse to nuclear information transmission by presenilin1-cleavage of PTPRT is undermined in Alzheimer’s disease

city: Edison

first: Jiali

last: Li

state: middlesex

address: 65 James ST

department: Neuroscience Intitute

institute: HMH JFK Medical Center

summary: PTPRT (receptor-type tyrosine-protein phosphatase T), as a brain-specific type 1 transmembrane protein, plays important function in neurodevelopment and synapse formation. Here, we report that the downregulated levels of Ptprt mRNA and protein is found in both human AD and APP/PS1 mouse brains. We further identified that PTPRT intracellular domain (ICD), which was released by ADAM10- and g-secretase-dependent cleavage of PTPRT, efficiently translocated to the nucleus via a conserved nuclear localization signal. RNA sequencing reveals that expression of the PICD alone can profoundly alter the expression of genes associated with synapse function and dephosphorylation, phosphatase and cell adhesion. Inhibition of nuclear-localization of PICD via the mutation of its nuclear localization signal (NLS) leads to accumulation of phosphorylated signal transducer and activator of transcription 3 (p-STAT3), which is a substrate of PTPRT and eventually resulted in neuronal cell death. AVV1-PICD in vitro and in vivo robustly decreases the levels of phosph-STAT3(Y705) in APP/PS1 neurons, attenuates Ab pathology, and improves synaptic function and behavioral deficits in APP/PS1 mice. Our findings define a novel role of decreased PTPRT and its nuclear ICD fragment in the events promote AD pathogenesis.

overall_design: There are two groups, aav1-gfp-expressing n2a cells and aav1-PICD-expressing n2a cells . For each group, total RNAs were prepared using PureLink micro-to-midi total RNA purification system (Invitrogen). Libraries were prepared from RNA of three 3 biologically independent experiments. Sequence-libraries of each sample were equimolarly pooled and sequenced at the core facility of Kunming Institute of Zoology.

first: Lianwe


title: Quantifying propagation of DNA methylation and hydroxymethylation with iDEMS

city: Copenhagen

first: Anja

last: Groth

address: Blegdamsvej 3B

country: Denmark

institute: CPR

summary: DNA methylation is a critical epigenetic mark in mammalian cells. Many aspects of DNA methylation maintenance have been characterized, however the exact kinetics of post-replicative methylation maintenance remain a subject of debate. Here we develop isolation of DNA by EdU-labelling for Mass Spectrometry (iDEMS), a highly sensitive, quantitative mass spectrometry-based method for measuring DNA modifications on metabolically labelled DNA. iDEMS reveals an unexpectedly hemi-methylated landscape on nascent DNA. Combining iDEMS with metabolic labelling reveals that methylation maintenance is outpaced by cell division in mouse embryonic stem cells. Our approach shows hydroxymethylation is perpetually asymmetric between sister strands in favor of the parental, template strand. iDEMS can be coupled with immunoprecipitation of chromatin proteins, revealing features of DNA methylation-histone modification crosstalk and suggesting a model for interplay between methylation and nucleosome assembly. iDEMS therefore elucidates long-standing questions about DNA modification propagation and provides an important orthogonal technology to understanding this process in dynamic cellular contexts.

overall_design: iDEMS time series from dsDNA and stranded samples, ChIP-iDEMS, and EM-seq in mouse embryonic stem cells and/or mouse embryonic fibroblast cells.

first: Kathleen

last: Stewart-Morgan

first: Cristina

last: Requena

first: Valentin

last: Flury

first: Qian

last: Du

first: Zoe

last: Heckhausen

first: Petra

last: Hajkova


title: ETV6 Deficiency and Microsatellite Enhancers Drive Transcriptional Dysregulation in B-Lymphoblastic Leukemia: RNA-Seq

city: Ann Arbor

first: Russell

middle: James Hubbard

last: Ryan

state: MI

address: 4306 Rogel Cancer Center, 1500 E Medical Center Dr.

institute: University of Michigan Medical School

summary: Distal enhancers play critical roles in sustaining oncogenic gene expression programs. We obtained ATAC-Seq data and ChIP-Seq data using antibodies against the H3K27ac histone mark, transcription factors ERG and ETV6, and input chromatin from B-ALL cell lines and comparator B-cell cancer cell lines, including B-ALL with biallelic ETV6 inactivation, ETV6-RUNX1, and intact ETV6. We identify aberrant enhancer-like activation of GGAA tandem repeats as a characteristic feature of B-cell acute lymphoblastic leukemia (B-ALL) with genetic defects of the ETV6 transcriptional repressor, including ETV6-RUNX1+ and ETV6-null B-ALL. We show that GGAA repeat enhancers are direct activators of previously identified ETV6-RUNX1+ B-ALL “signature” genes, including likely oncogenic drivers. When restored to ETV6-deficient B-ALL cells, ETV6 directly binds to GGAA repeat enhancers, represses their acetylation, downregulates adjacent genes, and inhibits B-ALL growth. In ETV6-deficient B-ALL cells, we find that the ETS transcription factor ERG directly binds to GGAA microsatellite enhancers and is required for sustained activation of many repeat enhancer-activated genes. Together, our findings reveal a novel epigenetic gatekeeper function of the ETV6 tumor suppressor gene and establish microsatellite enhancers as a key mechanism underlying the unique gene expression program of ETV6-RUNX1+ B-ALL.

overall_design: RNA-Seq was used to perform differential gene expression analysis on Reh B-ALL cells with inducible expression of ETV6 transgenes or control.

first: Rohan

last: Kodgule

first: Joshua

last: Goldman


title: Effect of Rad6 backside beta-turn mutations

first: Mahesh

last: Chandrasekharan

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

overall_design: Refer to individual Series


title: MUC16 is a critical molecule for the pancreatic tumor microenvironment and metastasis in PDAC

status: Public on Oct 22 2022

city: Omaha

first: Surinder

last: Batra

address: 42 and Emile

institute: UNMC

summary: Investigate the cooperative action of MUC16 with other defined oncogenic mutations in the metastasis of PC using Muc16–/– mice

overall_design: We colleted the pancreas tissues from KPC and KPC Muc16-/- mice at 25 weeks followed by whole transcriptome analysis using RNA sequencing.

first: Moorthy

middle: P

last: Ponnusamy

first: Imayavaramban

last: Lakshmanan

first: Saravanakumar

last: Marimuthu


title: Effect of Rad6 backside beta-turn mutations on the chromatin occupancy of the histone H2B ubiquitin-conjugating complex subunits

summary: Rad6 E2 ubiquitin-conjugating enzyme and Bre1 E3 ubiquitin ligase catalyze histone H2B Lysine-123 monoubiquitination (H2Bub1), which stabilizes nucleosomes and regulates the trans-histone H3K4 and K79 methylation during gene transcription and other nuclear processes. The interaction interfaces within the Rad6-Bre1-containing H2B ubiquitin-conjugating complex has remained unknown. By solving the crystal structure of Rad6 along with a non-RING domain N-terminal region of Bre1, we report a beta-turn in Rad6's so-called backside region away from catalytic pocket as a binding site for a homodimer of Bre1 E3 ligase. Using quantitative ChIP-seq or ChIP-Rx, we further demonstrate that Rad6's backside beta-turn residues also govern the chromatin binding dynamics of the Rad6-Bre1 complex.

overall_design: Genome-wide occupancy maps were generated from yeast strains representing 3V5-epitope-tagged wild type Rad6 or the backside beta-turn mutants: rad6-P43L, rad6-P47T and rad6-E49K. A bre1 null strain was also used as a negative or background control. Two independent biological samples were grown for each S. cerevisiae strain. S. cerevisiae cells were mixed with spike-in or reference endogenous genome C. glabrata cells expressing cgRad6 with C-terminal protein AG tag at 2:1 ratio before chromatin preparation by sonication. Chromatin immunoprecipitation was performed using V5 or custom Bre1 antibodies, libraries were prepared from ChIP and input DNA, sequenced, and analyzed separately.

first: Prakash

last: Shukla

first: Jesse

last: Bissell

first: Timothy

last: Parnell


title: Effect of water stress, high light, heat stress and their factorail stress combinations on transcriptome of Carrizo citrange and Cleopatra mandarin

city: Vila-real

first: Damián

last: Balfagón Sanmartín

state: Castellón

address: C/Polo Bernabé, Nº40, piso 3 puerta 7

institute: Universitat Jaume I

summary: To investigate transcriptomic response of two citrus rootstocks with different ability to tolerate abiotic stresses

overall_design: Comparative gene expression profiling analysis of RNA-seq data of plants subjected to each stress condition and its control

last: Balfagón

first: Aurelio

last: Gómez Cadenas


title: Paired scRNA-seq and scTCR-seq of GP33-specific CD8 T cells in chronic LCMV infection

first: Weiguo

last: Cui

summary: Chronic viral infection results in CD8 T cell exhaustion. Here, we use paired single-cell RNA sequencing (scRNA-seq) and single-cell T cell receptor sequencing (scTCR-seq) to investigate CD8 T cell phenotypic and clonal heterogeneity in multiple mice during the late stage of LCMV Clone 13 infection.

overall_design: Mice were infected with 2 million PFU LCMV Clone 13. On day 33 (Mouse 1, M1), 33 (M2), and 35 (M3), mice were euthanized and spleens were harvested. GP33-specific CD8 T cells were FACS sorted and the 10x Genomics pipeline was used to perform single-cell RNA and TCR library construction. Libraries were sequenced on an Illumina NextSeq 500 platform.

first: Moujtaba

last: Kasmani


title: Peripheral B cells from patients with HCV-associated B cell lymphoma exhibit an anergic-like transcriptional profile and evidence of clonal expansion

city: Bethesda

first: Amanda

last: Henning

state: MD

address: 9000 Rockville Pike

institute: National Institutes of Health

summary: Chronic HCV infection remains a global health concern due to its involvement in hepatic and extrahepatic diseases, including B cell non-Hodgkin’s lymphoma (BNHL). Clinical and epidemiological evidence support a causal role for HCV in BNHL development, although mechanistic insight is lacking. We performed RNA-sequencing on peripheral B cells from patients with HCV, BNHL, and HCV-associated BNHL to identify unique and shared transcriptional profiles associated with transformation. In patients with HCV-associated BNHL, we observed enrichment of an anergic gene signature and evidence of clonal expansion that was correlated with expression of epigenetic regulatory genes. Our data support a role for viral-mediated clonal expansion of anergic-like B cells in HCV-associated BNHL development, and suggest epigenetic dysregulation as a potential mechanism driving expansion. We propose epigenetic mechanisms may be involved in both HCV-associated lymphoma and regulation of B cell anergy, representing an attractive target for clinical interventions.

overall_design: mRNA profiling of peripheral B cells isolated from patients with chronic HCV infection (n=9), B cell non-Hodgkin's lymphoma (n=6), HCV-associated B cell non-Hodgkin's lymphoma (n=6), and healthy donors (n=6)

first: Valeria

last: De Giorgi


title: MeRIP-seq

city: Shanghai

first: Jinhong

last: Tang

address: Yishan road 600,Xuhui district,Shanghai

institute: Shanghai Jiao Tong University Affiliated Sixth People’s Hospital

type: Methylation profiling by high throughput sequencing

summary: As the most prevalent chemical modifications on eukaryotic mRNAs, N6-methyladenosine (m6A) methylation was reported to participate in the regulation of various metabolic diseases. In order to investigate the roles of m6A methylation in non-alcoholic fatty liver disease (NAFLD). The high-throughput sequencing was performed to identify the m6A methylation patterns in HFD mice.

overall_design: MeRIP-seq for 6 samples.

first: Long

last: Wang

first: Jinghui

last: Guo

first: Xiangyun

last: Zhao

first: Wei

last: Wei

first: Weiwei

last: Liu

first: Huining

last: Fan


title: ETV6 Deficiency and Microsatellite Enhancers Drive Transcriptional Dysregulation in B-Lymphoblastic Leukemia: ATAC-Seq data

first: Russell

last: Ryan

overall_design: ATAC-Seq peaks from B-cell cancer cell lines were merged into a consensus set of peaks for differential analysis of NFR-associated histone acetylation. Differential chromatin accessibility signal was also compared between cell lines at loci of interest.

first: Rohan

last: Kodgule

first: Joshua

last: Goldman


title: The multifaceted role of GCM1 during trophoblast differentiation in the human placenta

city: London

first: Stephen

last: Renaud

state: Ontario

address: 1151 Richmond Street

department: Anatomy and Cell Biology

institute: University of Western Ontario

summary: Human trophoblast stem cells were infected with lentivirus to knockdown the transcription factor GCM1. RNA-seq was then utilized to determine global transcriptomic changes between control and GCM1-deficient human trophoblasts either cultured as cytotrophoblasts or induced to form extravillous trophoblasts. This study provides insight into the molecular mechanisms regulating extavillous trophoblast development.

overall_design: Transcriptomic profile of control and GCM1-deficient trophoblast stem cells.

first: Mariyan

last: Jeyarajah


title: Patient-specific and Gene-corrected Induced Pluripotent Stem Cell-derived Endothelial Cells Elucidate Single-cell Phenotype of Pulmonary Veno-occlusive Disease

status: Public on Oct 21 2022

city: Beijing

first: Baihui

last: Ma

address: 167 Beilishi Road

institute: Fuwai Hospital

summary: PVOD is a rare form of pulmonary hypertension characterized by the preferential remodeling of the pulmonary venules. Hereditary PVOD is caused by biallelic variants of the EIF2AK4 gene. Three PVOD patients who carried the compound heterozygous variants of EIF2AK4 and two healthy controls were recruited and iPSCs were generated from human peripheral blood mononuclear cells (PBMCs). The EIF2AK4 c.2965C>T variant (PVOD#1), c.3460A>T variant (PVOD#2) and c.4832_4833insAAAG variant (PVOD#3) were corrected by CRISPR/Cas9 in PVOD-iPSCs to generate isogenic controls and gene-corrected-iPSCs (GC-iPSCs). PVOD-iPSC-ECs exhibited a decrease in GCN2 protein and mRNA expression, when compared to control and GC-ECs. PVOD-ECs exhibited an abnormal endothelial cell phenotype featured by excessive proliferation and angiogenesis. The abnormal phenotype of PVOD-ECs was normalized by AKT inhibitors AZD5363 and MK2206. These findings help elucidate the underlying molecular mechanism of PVOD in humans, and identify promising therapeutic drugs for treating the disease

overall_design: Comparative gene expression profiling analysis of RNA-seq data for PVOD-endothelial cells and GC-PVOD-endothelial cells.

first: Tianjiao

last: Li

first: Wenke

first: Hang

last: Yang

first: QIxian

last: Zeng

first: Zihang

last: Pan

first: Kai

first: Qianlong

last: Chen

first: Changming

last: Xiong

first: Zhou

last: Zhou


title: Baseline gene expression profiling determines long-term benefit to programmed cell death protein 1 axis blockade

city: New Haven

first: Ioannis

last: Vathiotis

address: 310 Cedar St

institute: Yale

summary: Treatment with immune checkpoint inhibitors has altered the course of malignant melanoma, with approximately half of the patients with advanced disease surviving for more than 5 years after diagnosis. Currently, there are no biomarker methods for predicting outcome from immunotherapy. Here, we obtained transcriptomic information from a total of 105 baseline tumor samples comprising two cohorts of patients with advanced melanoma treated with programed cell death protein 1 (PD-1)-based immunotherapies. Gene expression profiles were correlated with progression-free survival (PFS) within consecutive clinical benefit intervals (i.e., 6, 12, 18, and 24 months). Elastic net binomial regression models with cross validation were utilized to compare the predictive value of distinct genes across time. Lasso regression was used to generate a signature predicting long-term benefit (LTB), defined as patients who remain alive and free of disease progression at 24 months post treatment initiation. We show that baseline gene expression profiles were consistently able to predict long-term immunotherapy outcomes with high accuracy. The predictive value of different genes fluctuated across consecutive clinical benefit intervals, with a distinct set of genes defining benefit at 24 months compared to earlier outcomes. A 12-gene signature was able to predict LTB following anti-PD-1 therapy with an area under the curve (AUC) equal to 0.92 and 0.74 in the training and validation set, respectively. Evaluation of LTB, via a unique signature may complement objective response classification and characterize the logistics of sustained antitumor immune responses.

overall_design: Retrospective analysis of 105 pretreatment samples

first: David

last: Rimm


title: Krüppel-like factor 4 regulates the cytolytic effector function of exhausted CD8 T-cells [SMART-Seq]

city: Seoul

first: Jinwoo

last: Nah

address: 1, Gwanak-ro, Gwanak-gu, Seoul

institute: Seoul National University

summary:
To identify the role of KLF4 on exhausted CD8 T-cells in vivo, we adoptively transferred PmelI CD8 T-cells transduced with MigRI/Klf4 into MC38-gp100 tumor-bearing Rag2 KO mice on day7.
We then isolated tumor-infiltrating PmelI CD8 T-cells on day15 and their gene expression profiles were analyzed by SMART-seq.
Also,  to investigate the effect of KLF4 deficiency, we isolated PD1+ CD8+ TILs from MC38 tumor-bearing control and Klf4 cKO mice on day14, and SMART-seq was performed.

overall_design: Comparative gene expression profiling analysis of SMART-seq data for PmelI CD8 T-cells transduced with MigRI/Klf4 and PD1+ CD8+ TILs from contol/Klf4 cKO mice.

first: Rho

last: Seong


title: ETV6 Deficiency and Microsatellite Enhancers Drive Transcriptional Dysregulation in B-Lymphoblastic Leukemia: ChIP-Seq data

first: Russell

last: Ryan

overall_design: ChIP-Seq datasets were aligned to hg38. De novo peak calling was performed on TF ChIP-Seq datasets. Both TF and H3K27ac ChIP-Seq datasets were used to compare normalized signal across cell lines and experimental conditions for loci of interest.

first: Rohan

first: Joshua


title: An autocrine signaling circuit in hepatic stellate cells underlies advanced fibrosis in non-alcoholic steatohepatitis

city: South San Francisco

first: Ian

last: Driver

state: California

address: 486 Cabot Road

department: Bioinformatics

institute: Gordian Biotechnology

summary: Advanced hepatic fibrosis, driven by the activation of hepatic stellate cells (HSCs), affects millions world-wide and is the strongest predictor of mortality in non-alcoholic steatohepatitis (NASH), yet there are no approved anti-fibrotic therapies. To identify novel anti-fibrotic drug targets, we integrated progressive transcriptomic and morphological responses that accompany HSC activation in advanced disease using single nuclear RNA sequencing and tissue clearing in a robust, murine NASH model. In advanced fibrosis, an autocrine HSC signaling circuit emerges that is comprised of 68 receptor-ligand interactions conserved between murine and human NASH. These predicted interactions are supported by the parallel appearance of markedly increased direct stellate cell-cell contacts in murine NASH. As proof of principle, pharmacological inhibition of one such autocrine interaction, NTRK3-NTF3, inhibits human HSC activation in culture and reverses advanced murine NASH-fibrosis in vivo. We have uncovered a novel repertoire of previously uncharacterized anti-fibrotic drug targets underlying advanced fibrosis in vivo. The findings suggest a novel therapeutic paradigm in which stage-specific therapies could yield enhanced anti-fibrotic efficacy in patients with advanced fibrosis.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Total nuclei were extracted from snap frozen liver tissue of patients or mice and analyzed using single nuclei RNA-seq

first: Scott

last: Friedman


title: A metabolic associated fatty liver disease risk variant in MBOAT7 regulates toll like receptor induced outcomes [ATAC-seq]

city: Westmead

first: Brian

last: Gloss

state: NSW

address: 176 Hawkesbury Rd

department: Scientific Platforms

country: Australia

institute: Westmead Institute of Medical Research

summary: The breakdown of toll-like receptor (TLR) tolerance results in tissue damage. Here we provide evidence that membrane bound O-acyltransferase domain containing 7 (MBOAT7) is a crucial negative regulator of TLR signaling. MBOAT7 deficiency in macrophages as observed in patients with metabolic (dysfunction) associated fatty liver disease (MAFLD) and in COVID-19, alters membrane phospholipid composition. We demonstrate that this is associated with a redistribution of arachidonic acid toward proinflammatory eicosanoids, induction of endoplasmic reticulum stress, mitochondrial dysfunction, and remodelling of the accessible inflammatory-related chromatin landscape culminating in macrophage inflammatory responses to TLRs. Activation of MBOAT7 reverses these effects. These outcomes are further modulated by the MBOAT7 rs8736 (T) MAFLD risk variant. Our findings suggest that MBOAT7 can be exploited as a therapeutic target for diseases associated with dysregulation of the TLR signaling cascade.

overall_design: ATAC-seq

first: Jawaher

last: Alharthi

first: Mohammed

last: Eslam


title: A metabolic associated fatty liver disease risk variant in MBOAT7 regulates toll like receptor induced outcomes [Cut&Tag]

overall_design: Cut & Tag


title: Effect of hydrazine on gene expression of FE1 cells

city: North Chicago

first: Rita

last: Ciurlionis

address: 1 North Waukegan Road

institute: Abbvie

summary: RNASeq gene expression analysis was performed on total RNA extracted from FE1 cells treated with 0, 1, 4, 6 and 10mM hydrazine for 4hr or 4hr plus 20hr washout


title: Gene expression analysis of hematopoietic niche cells in the zebrafish kidney

city: Kanazawa

first: Isao

last: Kobayashi

state: Ishikawa

address: Kakumamachi

country: Japan

institute: Kanazawa University

summary: The zebrafish is an excellent model for the study of hematopoiesis. The use of fluorescently labeled transgenic lines allows us to isolate various hematopoietic cell types. Moreover, transplantation and cell culture assays enable to test the ability for hematopoietic repopulation and differentiation in isolated hematopoietic cells. The zebrafish counterpart of the mammalian bone marrow is the kidney, termed the "kidney marrow", providing an attractive tool for studying hematopoietic niches. Here, we isolated two candidate niche cell populations from the zebrafish kidney, pericytes and sinusoidal endothelial cells. Sinusoidal endothelial cells have been shown to endocytose acetylated low-density lipoprotein (Ac-LDL), whereas pericytes can be labeled by pdgfrb expression. Therefore, pericytes and sinusoidal endothelial cells were isolated by using pdfgrb:GFP and kdrl:Cerulean injected with Alexa Fluor 488-conjugated Ac-LDL, respectively. In addition, we also utilized a cell line generated from the zebrafish kidney, zebrafish kidney stromal (ZKS), which have been shown to support proliferation of various hematopoietic precursors (Stachula et al., 2009). In this study, we performed RNA-seq analysis using these three fractions to investigate the gene expression profile of each niche cell fraction. Three distinct conditions of gata2a:GFP+ runx1:mCherry+ (DP) hematopoietic stem/progenitor cells were also analyzed: uncultured gata2a+ runx1+ cells (DP_uncul), gata2a+ runx1+ cells co-cultured with ZKS cells (DP_cocul), and gata2a+ runx1+ cells co-cultured with ZKS cells in the presence of both IWR-1-endo and Thpo (DP_IW+Th).

overall_design: mRNA profiles of isolated ZKS cells, pericytes, sinusoids, and gata2a+ runx1+ (DP) in the zebrafish kidney were generated by Quartz-seq using Illumina NextSeq500.

first: Koki

last: Kimura

first: Mao

last: Kondo


title: A metabolic associated fatty liver disease risk variant in MBOAT7 regulates toll like receptor induced outcomes [RNA-seq]

overall_design: RNA-seq


title: Profound phenotypic and epigenetic heterogeneity of the HIV-1 infected CD4+ T cell reservoir

city: Philadelphia

first: Vincent

last: Wu

state: PA

address: 402 Johnson Pavilion

department: Microbiology

institute: University of Pennsylvania

summary: Understanding the complexity of the long-lived HIV reservoir during antiretroviral therapy (ART) remains a major impediment for HIV cure research. To address this, we developed single-cell viral ASAPseq to precisely define the unperturbed peripheral blood HIV-infected memory CD4+ T cell reservoir from antiretroviral treated people living with HIV (ART-PLWH) via the presence of integrated accessible proviral DNA in concert with epigenetic and cell surface protein profiling. We identified profound reservoir heterogeneity within and between ART-PLWH, characterized by novel and known surface markers within total and individual memory CD4+ T cell subsets. We further uncovered novel epigenetic profiles and transcription factor motifs enriched in HIV-infected cells that suggest infected cells with accessible provirus, irrespective of reservoir distribution, are poised for reactivation during ART treatment. Together, our findings reveal the extensive inter- and intrapersonal cellular heterogeneity of the HIV reservoir, and establish an initial multiomic atlas to develop targeted reservoir elimination strategies.

overall_design:
1 ASAPseq run from in vitro infection. 2 ASAPseq runs from chronic infection. 5 ASAPseq runs from ART-treated infection.

The file GSE199727_tsaCatalog.txt contains the antibody IDs for all ADT analyzed in this study.

first: Michael

last: Betts


title: Cooperative ETS Transcription Factors Enforce Adult Endothelial Cell Fate and Cardiovascular Homeostasis [scRNA-Seq]

status: Public on Oct 20 2022

city: New

first: Sean

last: Houghton

state: NY

address: 1300 York Ave

institute: Weill Cornell Medicine

summary: Single cell RNAseq of control (Ctl) and ERG and FLI1 transduced human MSCs

overall_design: Human cultured MSCs transduced with either control or ERG and FLI1 vectors were harvested, sorted for live cells, and processed for single cell RNAseq analysis.

first: Tomer

last: Itkin

first: Shahin

last: Rafii


title: Loss of autism-candidate CHD8 perturbs neural crest development and intestinal homeostatic balance [scRNA-seq]

city: Illkirch

first: Christelle

last: Golzio

state: Alsace

address: 1 rue Laurent Fries

country: France

institute: IGBMC

summary: Individuals with mutations in CHD8 present with gastrointestinal complaints, yet the underlying mechanisms are understudied. Here, utilizing a stable constitutive chd8 mutant zebrafish model, we found that the loss of chd8 leads to reduced number of vagal neural crest cells (NCCs), enteric neural and glial progenitors, emigrating from the neural tube and that their early migration capability was altered. At later stages, although the intestinal colonization by the NCCs was complete, we found decreased numbers of both serotonin-producing enterochromaffin cells and NCC-derived serotonergic neurons, suggesting an intestinal hyposerotonemia in absence of chd8. Further, transcriptomic analyses revealed altered expression of key receptors and enzymes in serotonin and acetylcholine signaling pathways. Tissue examination of chd8 mutants revealed thinner intestinal epithelium accompanied by accumulation of neutrophils and decreased numbers of goblet cells and eosinophils. Last, single-cell sequencing of whole intestines showed a global disruption of the immune balance with perturbed expression of inflammatory interleukins and changes in immune cell clusters. Our findings propose a causal developmental link between chd8, NCC development, intestinal homeostasis, and autism-associated gastrointestinal complaints.

overall_design: 2 samples were analyzed: 1 chd8+/+ (wild-type) and 1 chd8sa19827/sa19827 (homogous mutants). Each sample is comprised of dissociated cells from the mid and posterior intestine of 3 adult zebrafish.

first: Gaëlle

last: Hayot

first: Mathieu

last: Massonot

first: Céline

last: Keime

first: Elodie

last: Faure


title: Circular RNAs impinge on non-cell-autonomous mechanisms to regulate tumorigenesis. [RNA-seq]

city: Houston

first: Jlenia

last: Guarnerio

state: TX

address: 6767 Bertner Ave

department: Genetics

institute: MD Anderson Cancer Center

summary: We report transcriptomic changes in mouse soft-tissue sarcoma cells upon knock-down of the endogenous circRNA, circCsnk1g3. We find that circCsnk1g3 knockdown results in upregulation of signaling pathways related to both production of and response to type-I and type-II interferons

overall_design: Transcriptomic profiling of soft-tissue sarcoma cells—control or knocked down for circCsnk1g3.

first: Guarnerio

last: Jlenia

first: Ko

last: Emily


title: Circular RNAs impinge on non-cell-autonomous mechanisms to regulate tumorigenesis. [scRNA-Seq]

summary: The functional contribution of many circular RNAs (circRNAs) to cancer is poorly understood. Here, we report that knockdown in sarcoma cells of the endogenous circRNA, circCsnk1g3, modulates changes in immune cell proportions and expression profiles in the tumor lung microenvironment.

overall_design:
Single-cell transcriptomic profiling subcutaneous mouse sarcomas, with or without expression of circCsnk1g3. Soft-tissue sarcoma cells were generated as transformed mouse mesenchymal stem cells (p53-/-Ccne1+) which formed subcutaneous tumors when transplanted in mice,. To examine the effect of tumor circRNA expression on the microenvironment, tumor cells were additionally transduced with an shRNA to knock down circCsnk1g3, or with a nontargeting shRNA (shSCR). Tumors were transplanted into mice seeded on polyurethane scaffolds. Tumors were harvested, digested, and enriched for CD45+ immune cells. Immune cells from each mouse were individually hashtagged with sequenceable oligos, and then pooled and captured with the 10X Chromium 3' Single-Cell workflow.

Each sample represents pooled immune-enriched cells isolated from two groups of mouse tumors (n=4 mice per group):
Mouse sarcoma (p53-/-Ccne1+) bearing a non-targeting control shRNA (shSCR).
Mouse sarcoma (p53-/-Ccne1+) bearing an shRNA to knock down circCsnk1g3 expression (shcircCsnk1g3).

first: Emily

last: Ko


title: Discovery and Pharmacological Characterization of JNJ-64619178, a Novel Small-Molecule Inhibitor of PRMT5 with Potent Antitumor Activity

status: Public on Oct 19 2022

city: Charlestown

first: Timothy

last: Graubert

state: Massachusetts

address: 149, 13th Street, Navy Yard

department: Cancer Center

institute: Massachusetts General Hospital

summary: The goal of this study is to evaluate the pharmocological novel inhibitor of PRMT5 namely JNJ-64619178 on clones derived from K562 cell lines which have been CRISPR engineered to carry mutations frequently observed in hematologic cancers on splicing factor SF3B1.

overall_design:
SF3B1 specific guide RNAs which harbored specific mutations were used to target the nucleotides that code for Lysine at amino acid positions 700 (K700) to be converted to Glutamic acid(E) so as to obtain K700E alleles in K562 cell lines .
Subsequently, RNA-sequencing was carried out from individual clones.

first: Sumit

last: Rai

first: Vineet

last: Sharma


title: ETV6 Deficiency Unlocks ERG-Dependent Microsatellite Enhancers to Drive Aberrant Gene Activation in B-Lymphoblastic Leukemia

city: Ann Arbor

first: Russell

last: Ryan

address: 4306 Rogel Cancer Center, 1500 E Medical Center Dr.

institute: University of Michigan Medical School

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

overall_design: Refer to individual Series


title: Single-cell transcriptomic profiling reveals a metabolic aspect of non-apoptosis in inherited retinal degeneration

city: Kunming

first: kangwei

last: Jiao

state: Yunnan

address: 176 Qingnian

department: Ophthalmology

institute: Yunnan University

summary: The aim of this study was to provide deeper insight into the complex network of molec-ular and cellular changes that underlie inherited retinal degeneration by systematically mapping the transcriptional changes that occur in the degenerating mouse retina.

overall_design: Rd1 and C3H wild type mice at different time points of P11(n = 3; Retina n = 6), P13 (n = 3; Retina n = 6) and P17 (n = 3; Retina n=6) were sacrificed regardless of gender for single cell RNA-sequencing (scRNA-seq) to profile the impact of rd1 mutation during mouse retina development.

first: Yiyi

last: Chen

first: Jie

last: Yan

first: Lan

last: Wang

first: Shirley

last: Yu

first: Yujie

last: Dong

first: Kangwei

first: François

last: Paquet-Durand


title: Circular RNAs impinge on non-cell-autonomous mechanisms to regulate tumorigenesis.


title: BosR: a novel biofilm-specific regulator in Pseudomonas aeruginosa

city: Burnaby

first: Travis

last: Blimkie

state: British Columbia

address: 8888 University Drive

department: MBB

institute: Simon Fraser University

summary: Biofilms are the most common cause of bacterial infections in humans and notoriously hard to treat due to their ability to withstand antibiotics and host immune defenses. To overcome the current lack of effective antibiofilm therapies and guide future design, the identification of novel gene targets is crucial. In this regard, transcriptional regulators have been proposed as promising targets for antimicrobial drug design, since they simultaneously affect multiple genes, typically lack human orthologs, and can be inactivated by small molecules that prevent dimerization. Therefore, a Transposon insertion sequencing approach was employed to systematically identify regulatory genes phenotypically affecting biofilm growth in Pseudomonas aeruginosa PA14. A screen of a pool of 300,000 transposon insertion mutants identified 349 genes involved in biofilm growth on hydroxy apatite, including 47 regulators. Detection of 19 regulatory genes participating in well-established biofilm pathways validated the results. An additional 28 novel prospective biofilm regulators suggested the requirement of multiple one-component transcriptional regulators. Defect phenotypes were confirmed for five one-component transcriptional regulators PA14_43720, PA14_56430, PA14_36180, arsR and merD as well as the protein kinase yeaG, which have not been implicated in biofilm growth before. Promisingly, the transcriptional regulator PA14_43720 displayed a conserved role in biofilm growth since its ortholog in P. aeruginosa strain PAO1 was also required for biofilm growth. Overall, our results highlighted that the gene network driving biofilm growth is complex and involves regulators beyond the primarily studied groups of two-component systems and cyclic diguanylate signaling proteins.

overall_design: TnSeq experiments on PA14 grown under different conditions, namely planktonic and biofilm, for 96 hours. Additionally, the TnSeq pool was characterized at T0 as a reference condition. Each condition included three biological replicates.

first: Melanie

last: Dostert

first: Corrie

last: Belanger

first: Lucas

last: Pedraz

first: Morgan

last: Alford

first: Reza

middle: F

last: Falsafi

first: Bhavjinder

last: Dhillon

first: Cara

last: Haney

first: Amy

last: Lee

first: Robert

last: Hancock


title: Multiomic analysis reveals conservation of cancer associated fibroblast phenotypes across species and tissue of origin [scRNA-seq]

city: Stanford

first: Michael

last: Januszyk

state: CA

address: 257 Campus Dr

institute: Stanford University

summary: Cancer associated fibroblasts (CAFs) are integral to the solid tumor microenvironment. Once thought to be a relatively uniform population of matrix-producing cells, the arrival of single cell RNA sequencing has revealed diverse CAF phenotypes. Here, we further probe CAF heterogeneity with a comprehensive multiome approach. Using paired, same-cell chromatin accessibility and transcriptome analysis, we provide an integrated analysis of CAF subpopulations over a complex spatial transcriptomic and proteomic landscape to identify three superclusters – steady state-like (SSL), mechanoresponsive (MR) and immunomodulatory (IM) CAFs. These superclusters are recapitulated across multiple tissue types and species. Selective disruption of underlying mechanical force or immune checkpoint inhibition therapy results in shifts in CAF subpopulation distributions and impacts tumor growth. As such, the balance among CAF superclusters may have considerable translational implications. Collectively, this research expands our understanding of CAF biology, identifying regulatory pathways in CAF differentiation and elucidating novel therapeutic targets in a species- and tumor-agnostic manner.

overall_design: scRNA-seq of unsorted cells from tumor samples from mouse breast, human breast, and human pancreas cancer using the 10X genomics platform

first: Deshka

last: Foster

first: Daniel

last: Delitto


title: Multi-modal single-cell and whole-genome sequencing of minute, frozen specimens to propel clinical applications [slideseq]

city: New York

first: Johannes

middle: C

last: Melms

state: New York

address: 650 W 168th Street

department: Medicine

institute: Columbia University

summary: We provide 5' and/or 3' single cell and single nuclei RNA sequencing data for matched comparisons of profiling from fresh (single cells) and frozen (single nuclei) samples of a non small cell lung cancer sample, a cutaneous melanoma sample , and a primary uveal melanoma sample. We also provide matched samples processed with published dissociation protocols (*TST and *CST) for two samples as comparison. Next, we profiled three sequential biopsies (one pre-treatment and two on-treatment) from the KEYNOTE-001 trial by 5' single-nuclei RNA sequencing from frozen specimens. For these three datapoints we provide matched SlideSeq V2 spatial transcriptomic data. Finally, we provide 5' single nuclei RNA-sequencing data for 7 liver-metastatic uveal melanoma samples profiled at pre, on, and post treatment timepoints with MEK-inhibitor selumetinib. For all samples profiled with 5' capture we also provide TCR receptor information. This study provides a framework for the application of single nuclei RNA-sequencing on clinical grade specimens, and demonstrates the feasibility of this approach to dissect the biology of archival specimens or rare diseases.

overall_design:
Single-cell/nuclei RNA sequencing of 21,094 cells from 5 cutaneous melanoma brain metastasis samples. Single-cell/nuclei RNA sequencing of 21,977 cells from 3 uveal melanoma primary samples. Single-cell/nuclei RNA sequencing of 33,418 cells from 6 non-small-cell lung cancer brain metastasis samples. Single-nuclei RNA sequencing of 3,735 cells of matched melanoma and non-small-cell lung cancer samples processed by alternative protocols (*TST and *CST). Single-nuclei RNA sequencing of 35,238 cells from 3 cutaneous melanoma metastasis samples, 1 before treatment with anti-PD1 therapy, 2 during treatment. Matched spatial transcriptomics of 3 cutaneous melanoma metastasis samples profiled by SlideSeq V2. Single-nuclei RNA sequencing of 169,015 cells from 20 uveal melanoma liver metastasis samples, 7 before treatment with selumetinib, 7 during treatment, and 6 post-treatment.
Submitter states:"This submission does not contain raw data files as the fastq files contain protected patient information. Fastq files will be deposited to dbGaP.”

first: Benjamin

last: Izar

first: Yiping

last: Wang

first: Elham

last: Azizi

first: Joy

last: Fan


title: Single-cell profiling identifies ACE+ granuloma macrophages as a non-permissive niche for intracellular bacteria during persistent Salmonella infection

first: Yuan

last: Xue

address: 318 Campus Drive

summary: Macrophages mediate key antimicrobial responses against intracellular bacterial pathogens, such as Salmonella enterica. Yet, they can also act as a permissive niche for these pathogens to persist in infected tissues within granulomas, which are immunological structures comprised of macrophages and other immune cells. We apply single-cell transcriptomics to investigate macrophage functional diversity during persistent Salmonella enterica serovar Typhimurium (STm) infection in mice. We identify determinants of macrophage heterogeneity in infected spleens and describe populations of distinct phenotypes, functional programming, and spatial localization. Using a STm mutant with impaired ability to polarize macrophage phenotypes, we find that angiotensin converting enzyme (ACE) defines a granuloma macrophage population that is non-permissive for intracellular bacteria and their abundance anticorrelates with tissue bacterial burden. Disruption of pathogen control by neutralizing TNF is linked to preferential depletion of ACE+ macrophages in infected tissues. Thus ACE+ macrophages have limited capacity to serve as cellular niche for intracellular bacteria to establish persistent infection.

overall_design: 10X genomics 3' V3.1 scRNA-seq of FACS-sorted immune cells isolated from the spleens of Salmonella typhimurium SL1344-infected 129X1/SvJ mice.

first: Xue

last: Yuan

first: Pham

last: Trung


title: Transcriptional Profiling of Enterococcus faecalis During Surface Penetration

first: Diana

middle: K.

last: Morales

department: Obstetrics and Gynecology

summary: To investigate the transcriptional changes that Enterococcus faecalis undergoes during agar surface-penetration, which promote cell envelope remodeling and tolerance to stress.

overall_design: Comparative gene expression analysis of RNA-seq data for agar-penetrating versus non-penetrating E. faecalis cells.

first: Yusibeska

last: Ramos


title: CircPRKAA1 activates a Ku80/Ku70/SREBP1 axis driving de novo fatty acid synthesis in cancer cells

city: Hefei

first: Qidong

last: Li

state: Anhui

address: 443 Huangshan Road, Shushan district

institute: Lianxin Liu Lab

summary: Many metabolism-related genes undergo alternative splicing to generate circular RNAs although their functions remain poorly understood. Here we report that circPRKAA1, a circRNA derived from the α1 subunit of AMPK, fulfils a fundamental role in maintaining lipid homeostasis. CircPRKAA1 expression facilitates fatty acid synthesis and promotes lipid storage through two coordinated functions. First, circPRKAA1 promotes a tetrameric complex between the Ku80/Ku70 heterodimer and the mature form of sterol regulatory element-binding protein-1 (mSREBP1) to enhance the stability of mSREBP1. Secondly, circPRKAA1 selectively binds to the promoters of the ACC1, ACLY, SCD1 and FASN genes to recruit mSREBP1, upregulating their transcription and increasing fatty acid synthesis to promote cancer growth. Moreover, circPRKAA1 biogenesis is negatively regulated by AMPK activity with lower AMPK activation in hepatocellular carcinoma tissues frequently associated with elevated circPRKAA1 expression. Together, this work identifies circPRKAA1 as an integral element of AMPK-regulated reprogramming of lipid metabolism in cancer cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HepG2 cells with circPRKAA1 Knockdown

first: Hanhui

last: Yao

first: Yichun

first: Lianxin

last: Liu


title: Multi-modal single-cell and whole-genome sequencing of minute, frozen specimens to propel clinical applications [scRNA and snRNA]


title: Autonomous rhythmic activity in glioma networks drives brain tumor growth

city: Heidelberg

first: Frank

last: Winkler

address: Im Neuenheimer Feld 400

department: Neurology Clinic and National Center for Tumor Diseases

institute: University Hospital Heidelberg, Heidelberg

summary:
Glioblastoma cell networks harbor a plastic population of highly active glioblastoma cells that display rhythmic Ca2+ oscillations and are particularly connected to others. Targeting the autonomous rhythmic activity of periodic tumor cells by pharmacological interference with the potassium channel KCa3.1 strongly compromised global network communication. This led to a marked reduction of tumor cell viability within the entire network, reduced tumor growth in mice, and prolonged animal survival. The dependency of glioblastoma networks on periodic Ca2+ activity generates a vulnerability that can be exploited for the development of novel therapies, with KCa3.1 inhibiting drugs as one example.
To investigate the molecular mechanism of KCa3.1 blockade, we exposed glioblastoma cells to Senicapoc, a selective inhinitor of the KCa3.1 channel, and performed gene expression profiling analysis using data obtained from RNA-Seq.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for S24 cells and its Senicapoc treated derivates.

first: David

last: Hausmann

first: Dirk

last: Hoffmann

first: Varun

last: Venkataramani

first: Erik

last: Jung

first: Sandra

last: Horschitz

first: Svenja

last: Tetzlaff

first: Ammar

last: Jabali

first: Ling

last: Hai

first: Tobias

last: Kessler

middle: D

last: Azorin

first: Sophie

last: Weil

first: Alexandros

last: Kourtesakis

first: Philipp

last: Sievers

first: Antje

last: Habel

first: Michael

middle: O

last: Breckwoldt

first: Matthia

middle: A

last: Karreman

first: Miriam

last: Ratliff

first: Julia

last: Messmer

first: Yvonne

last: Yang

first: Ekin

last: Reyhan

first: Susann

last: Wendler

first: Cathrin

last: Löb

first: Chanté

last: Mayer

first: Katherine

last: Figarella

first: Matthias

last: Osswald

first: Gergely

last: Solecki

first: Felix

last: Sahm

first: Olga

last: Garaschuk

first: Thomas

last: Kuner

last: Koch

last: Schlesner

first: Wolfgang

last: Wick


title: Therapy-induced senescence in a human melanoma cancer cell line

city: Barcelona

first: Camille

last: Stephan Otto Attolini

state: Select a State or Province

address: Baldiri Reixac 10

department: Biostatistics and bioinformatics Unit

institute: IRB Barcelona

summary: RNA-sequencing of control and senescent (7 day palbociclib) human melanoma SK-MEL-103 cells.

overall_design: Senescence was induced in the human melanoma cell like SK-MEL-103 using the CDK4/6 inhibitor drug palbociclib (PD-0332991) for 7 days. RNA was harvested on day 7 of treatment, while cells were still exposed to palbociclib.

last: Stephan-Otto Attolini

first: Marta

last: Kovatcheva

first: Nacho

last: Pons


title: ENAP1 regulates plant response to the droguht stress

city: Austin

first: Hong

last: Qiao

address: 2506 speedway, NMS5.324

department: Department of Molecular Biosciences

institute: The University of Texas at Austin

summary: We measured the transcriptome changes in 10-day-old seedlings exposed to Mock and 25% PEG8000 treatment to investigate the differentially regulated genes by ENAP1/2 in response to dehydration

overall_design: Col-0 and enap1-1enap2 were grown in half- strength MS media for 10 days in the 16/8 light period and transferred on filter paper saturated with media solution (Mock) or media containing 25% PEG8000 (Dehydration) for 4h. The whole seedlings were sampled for RNA extraction and RNA-seq libraries.

first: Bo

last: Zhao

first: Zhengyao

last: Shao


title: Transcriptional  changes following SARS-CoV-2 infection of primary astrocytes

city: San Francisco

first: Warner

middle: C.

last: Greene

address: 1650 Owens St

institute: Gladstone institute ,UCSF

summary: We used bulk RNA seq to invistigate how SARS-CoV-2 changes host profile in astrocytes. SARS-CoV-2 infection of astrocytes induces type I interferon and inflammatory response.

overall_design: Primary human astrocytes isolated from human cortex were mock infected or SARS-CoV-2 infected at MOI=1 or MOI=5.


title: HMGNs Regulate White Adipocyte Browning By Stabilizing Cell Identity [RNA-Seq]

city: Bethesda

first: Michael

last: Bustin

address: Building 37, Room 3122

department: NCI

institute: NIH

summary: We report mRNA seq during time course of white preadipocyte browning from WT and HMGN1 and HMGN2 double knockout (DKO) mice . Moreover, we support our finding that loss of HMGN promotes white adipocyte browning with RNA seq of WT and DKO MEFs transdifferentiation into brown-like adipocytes.

overall_design: mRNA sequencing was performed on white preadipocytes (Day 0), differentiating  preadipocytes (day 3 and day 6) and brown-like adipocytes (day 9) from WT and HMGN1 and HMGN2 double knockout (DKO) mice with three replicates in each group.

first: Ravikanth

last: Nanduri

first: Takashi

last: Furusawa

first: Alexei

last: Lobanov

first: Bing

last: He

first: Carol

last: Xie

first: Kimia

last: Dadkhah

last: Kelly

first: Oksana

last: Gavrilova

first: Frank

last: Gonzalez


title: HMGNs Regulate White Adipocyte Browning By Stabilizing Cell Identity [ChIP-Seq]

summary: We report H3K27ac ChIP seq during time course of white preadipocyte browning from WT and HMGN1 and HMGN2 double knockout (DKO) mice .

overall_design: H3K27ac ChIP sequencing was performed on white preadipocytes (Day 0), differentiating  preadipocytes (day 3 and day 6) and brown-like adipocytes (day 9) from WT and HMGN1 and HMGN2 double knockout (DKO) mice with three replicates in each group.


title: HMGNs Regulate White Adipocyte Browning By Stabilizing Cell Identity


title: HMGNs Regulate White Adipocyte Browning By Stabilizing Cell Identity [scRNA-Seq]

summary: We report single-cell RNA seq (scRNA seq) at day 0 and day 6  of white preadipocyte browning from WT and HMGN1 and HMGN2 double knockout (DKO) mice. This supports our finding that loss of HMGN promotes white adipocyte browning with RNA seq of WT and DKO MEFs transdifferentiation into brown-like adipocytes.

overall_design: Single-cell RNA sequencing was performed on white preadipocytes (Day 0), differentiating  preadipocytes  (day 6) from WT and HMGN1 and HMGN2 double knockout (DKO) mice with two replicates in each group.


title: Transcriptomic analysis of hybrid embryos in polyploid wheat

city: Wuhan

first: Qiang

last: Li

state: Saskatchewan

address: #1 Shizishan Street

institute: Huazhong Agricultural University

summary: To investigate genome-wide maternal and paternal contributions to polyploid grain development, we produced and analyzed transcriptomes from zygote to mature stage embryos as well as two endosperm stages derived from reciprocal crosses between tetraploid and hexaploid wheats.

sample_organism:
Triticum aestivum
Triticum turgidum

platform_organism:
Triticum aestivum
Triticum turgidum

overall_design: Total RNA were extracted from the embryo and endosperm from the F1 progeny of 4 combinations of reciprocal crosses in wheat species .

first: Daoquan

last: Xiang


title: Human engineered skeletal muscle of hypaxial origin from pluripotent stem cells with advanced function and regenerative capacity

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

summary: Human pluripotent stem cell derived muscle models show great potential for translational research. Here, we describe novel developmentally inspired methods for the derivation of skeletal muscle cells and their utility in three-dimensional skeletal muscle organoid formation as well as skeletal muscle tissue engineering. Three-dimensional organoid and tissue engineered models exhibit organotypic maturation and function and regenerative responses, recapitulating canonical properties of bona fide skeletal muscle in vivo. Key steps include the directed differentiation of human pluripotent stem cells to embryonic muscle progenitors of hypaxial origin followed by primary and secondary fetal myogenesis with development of a satellite cell pool and evidence for innervation in vitro. Regenerative competency was demonstrated in a cardiotoxin injury model with evidence for satellite cell activation as underlying mechanism.

overall_design: Total RNA transcriptome of skeletal muscle differentiation of human pluripotent stem cells obtained at day 0, 1, 4, 8, 13, 22, 29, 60 of 2D differentiation and day 60 3D engineered skeletal muscle (ESM).

first: Mina

last: Shahriyari

first: Orr

last: Shomroni

first: Malte

last: Tiburcy


title: Host metabolic reprogramming during immune activation promotes intracellular bacterial survival (2DG)

city: Rehovot

first: Roi

last: Avraham

address: Herzl St 234

country: Israel

institute: Weizmann Institute of Science

summary: Intracellular pathogens, such as Salmonella enterica serovar Typhimurium (S.Tm), are able to sense and respond to a changing host cell environment. Macrophages exposed to microbial products undergo metabolic changes that are increasingly understood to drive a productive inflammatory response. However, the role of macrophage metabolic reprogramming in bacterial adaptation to the intracellular environment has not been explored. Here we show that changes in host metabolic state serve as a signal detected byS.Tm. Using metabolic profiling and dual RNA-seq, we show that succinate accumulates in infected macrophages and is sensed by intracellular S.Tm to promote induction of virulence genes. Succinate uptake by the bacterium drives induction of pmrAB-dependent genes and SPI-2 virulence-associated regulon. S.Tm lacking the DcuB transporter for succinate uptake display impaired intracellular survival. Our work demonstrates that accumulation of metabolic intermediates, necessary for macrophage activation, promote intracellular survival of pathogens, opening a new realm of metabolic host-pathogen crosstalk.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium

overall_design: 4 bacterial culture samples of Salmonella enterica serovar Typhimurium (WT or manZ bacteria, with or without 2-DG) in triplicates

first: Gili

last: Rosenberg

first: Dror

last: Yehezkel

first: Noa

last: Nissani

first: Shelly

last: Hen-Avivi

first: Shirley

last: Brenner

first: Maxim

last: Itkin

first: Sergey

last: Malitsky

last: Bossel Ben-Moshe


title: RNA sequencing of patient derived xenograft sample AML-346, AML-356, AML-388 and AML-661 using prime-seq

status: Public on Oct 18 2022

city: Munich

first: Irmela

last: Jeremias

address: Feodor-Lynenstr. 21

department: Research Unit Apoptosis in Hematopoietic Stem Cells

institute: Helmholtz Zentrum München, German Center for Environmental Health (HMGU), Munich, Germany

summary: We generate CRISPR/Cas9 patient derived xenograft (PDX) models of acute myeloid leukemia. Mimicking anti-cancer therapy in patients, PDX cells with gene knockouts were re-transplanted into mice. In fluorochromes guided, competitive in vivo trials, a subset of PDX models showed a clear growth disadvantage upon knockout, indicating essential functions for WT1 and DNMT3A.

overall_design:
A mixture of WT1 KOs, DNMT3A KOs and control PDX cells were isolated out of the murine bone marrow after the mice reached advanced leukemia stage and sorted for single population.The mRNA expression pattern was analyzed.
----------------------------
Authors state "Due to German law, we are not allowed to publish raw sequencing data."

first: Maryam

last: Ghalandary

first: Yuqiao

last: Gao

first: Vindi

last: Jurinovic

first: Ehsan

last: Bahrami


title: HMGNs Regulate White Adipocyte Browning By Stabilizing Cell Identity [ATAC-Seq]

first: Michael

last: Bustin

state: MD

summary: We report ATAC seq of white preadipocytes from iWAT of WT and HMGN1 and HMGN2 double knockout (DKO) mice .

overall_design: We used ATAC seq of white preadipocytes (in triplicates) to elucidate the role of HMGN in adipocyte browning

first: Ravikanth

last: Nanduri

first: Takashi

last: Furusawa

first: Alexei

last: Lobanov

first: Bing

last: He

first: Carol

last: Xie

first: Kimia

last: Dadkhah

last: Kelly

first: Oksana

last: Gavrilova

first: Frank

last: Gonzalez


title: Host metabolic reprogramming during immune activation promotes intracellular bacterial survival (glycerol or succinate)

first: Roi

last: Avraham

platform_organism: Salmonella enterica subsp. enterica serovar Typhimurium

overall_design: 2 bacterial culture samples of Salmonella enterica serovar Typhimurium (grown in glycerol or succinate medium) in triplicates

first: Gili

last: Rosenberg

first: Dror

last: Yehezkel

first: Noa

last: Nissani

first: Shelly

last: Hen-Avivi

first: Shirley

last: Brenner

last: Itkin

last: Malitsky


title: Host metabolic reprogramming during immune activation promotes intracellular bacterial survival (host and bacteria)

overall_design: DualSeq data. 18 Mus musculus samples (control, manZ, and WT bacteria, with or without 2-DG at 0.5h, 6h and 24h post-infection) in triplicates. 12 Salmonella enterica serovar Typhimurium samples (manZ and WT bacteria, with or without 2-DG at 0.5h, 6h and 24h posut-infection) in triplicates.

first: Maxim

first: Sergey

last: Bossel Ben-Moshe


title: Host succinate is a signal for activation of Salmonella virulence during intracellular infection

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

overall_design: Refer to individual Series


title: The Effect of Steroid and ERa agonism on Th2 cells

city: LONDON

first: Lisa

last: Cameron

state: ON

address: 1151 Richmond street, Dental Sciences Building Room 4035

department: Pathology and Laboratory Medicine

institute: WESTERN UNIVERSITY

summary: Allergic asthma is a T helper 2 (Th2) cell-associated inflammatory disease, driven by cytokines such as IL-4, IL-5, and IL-13. Th2 cells express the G-protein-coupled receptor CRTh2, a receptor for prostaglandin D2 (PGD2) that influences Th2 function and survival. Inhaled glucocorticosteroids are the primary treatment of allergic asthma and improve asthma symptoms by inhibiting Th2 cytokine production. Women are more likely than men to have severe asthma and to have symptoms requiring a hospital visit. These findings lead us to consider a mechanism by which female sex hormones could influence Th2 cell response to glucocorticosteroid. Using whole-mRNA sequencing, we examined gene expression in primary Th2 cells following exposure to glucocorticosteroids (0.1µM) in the presence or absence of an estrogen mimic, PPT (10µM).

overall_design: Gene expression in a primary Th2 cell line following treatment with Dexamethasone, PPT or both. Three replicates per condition, four conditions including control (Ethanol vehicle). 12 samples total.

first: Lauren

last: Solomon


title: A divergent and complementary transcriptional response in poxvirus-infected and bystander inflammatory monocytes is partly dictated by interferon.

city: Huntingdon Valley

first: Carolina

last: Rezende Melo da Silva

state: Pennsylvania

address: 2527 Morgan run

department: Microbiology and Immunology

institute: Thomas Jefferson University


title: Multi-modal single-cell and whole-genome sequencing of minute, frozen specimens to propel clinical applications

first: Johannes

last: Melms


title: RNA transcriptomics using cervical exfoliative cytology samples in 9 patients with HPV related disease

city: Daegu

first: Yeseul

last: Choi

address: Chilgokjungang-daero 136 gil

institute: KNU

summary: Cervical cancer is the fourth most common type of cancer is women worldwide,and it is a major cause of cancer-related deaths in developing countries. Despite the marked reduction oberved in the rates of this disease as a result of screening programs, it is necessary to develop robust biomarkers that can detect the neoplastic early in HPV-related cervical leisons. We performed comparative mRNA seqeuncing from exfoliative cervical cytology from nine Korean women on the Illumina NovaSeq6000 platforms. The pathological tissues mathced to the corresponding cytological samples were simulanously confirmed and were considered to be endpoint diagnosis. The pathological dianoses consisted of three cases of chronic cervicitis, 2 high-grade squamous intraepithelial leisons(HSILs), 2squamous cell carcinomas in situ(CIS); and 2 invasive quamous cell carcinomas (SQCCs), respectively. Using bioinformatics analyses, differentially expressed genes (DEGs; absolute fold change >1; p<0.05) were applied for Gene Ontology (GO), Gene Set EnrichmentAnalysis (GSEA), and protein-protein interaction (PPI) networks.

overall_design: We performed comparative mRNA seqeuncing from exfoliative cervical cytology from nine Korean women on the Illumina NovaSeq6000 platforms. The pathological tissues mathced to the corresponding cytological samples were simulanously confirmed and were considered to be endpoint diagnosis. The pathological diagnoses consisted of three cases of chronic cervicitis, 2 high-grade squamous intraepithelial leisons (HSILs), 2 squamous cell carcinomas in situ (CIS); and 2 invasive quamous cell carcinomas (SQCCs), respectively.

first: Nora

last: Park

first: Gun

last: Chong

first: Hyung

middle: S

last: Han