title: Smc3 acetylation, Pds5 and Scc2 control the translocase activity that establishes cohesin dependent chromatin loops

city: Toulouse

first: christophe

last: chapard

address: 118 route de Narbonne

department: CBI - MCD

institute: CNRS

summary: Cohesin is a DNA translocase instrumental in the folding of the genome into chromatin loops, with functional consequences on DNA-related processes. Chromatin loop length and organization likely depend on cohesin processivity, translocation rate, and stability on DNA. Here we investigate and provide a comprehensive overview of the roles of various cohesin regulators in tuning chromatin loop expansion. We demonstrate that Scc2, which stimulates cohesin ATPase activity, is also essential for cohesin translocation, driving loop expansion in vivo. Smc3 acetylation during S-phase counteracts this activity through the stabilization of Pds5, which finely tunes the size and stability of loops in G2.

overall_design: Examination of cohesin subunit occupancy on genome in the presence of non acetylable Smc3-RR and analysis of 3D chromosome configuration using HiC methods and yeast mutants

first: Nathalie

last: Bastié

first: Christophe

last: Chapard

first: Frederic

last: Beckouët

first: Romain

last: Koszul


title: The effects and underlying mechanisms of mutated hepatitis B virus X gene on the development of hepatocellular carcinoma

status: Public on Mar 02 2022

city: Shanghai

first: Xi

last: Chen

address: 8th Panshan Road

country: China

institute: Second Military Medical University

summary: The groups with the highest tumor incidences, M3-HBx and Ct-HBx, were involved. WT-HBx and empty vector mice served as the control group. In total, 12 tissues of Sleeping Beauty mice models were involved in microarray analysis, including 3 liver tissues from the empty vector group,3 liver tissues from the WT-HBx group, 3 tumor tissues from the M3-HBx group, and 3 tumor tissues from the Ct-HBx group. The samples were randomly selected from each group.

overall_design: HBx fragments (WT/M3/Ct) or empty vector were delivered into Fah deficient mice with Sleeping Beauty transposon system at 8-10 weeks of age . After 150 days, the mice were anesthetized with carbon dioxide and sacrificed. All the RNA from their liver or tumor are extracted for gene expression chips.

first: Wenbin

last: Liu

first: Xinyu

last: Zhou


title: Targeting E-prostanoid 3 receptor ameliorates liver fibrosis through enhancing adhesion and cytotoxicity of NK cells toward HSCs

status: Public on Feb 19 2022

city: Tianjin

first: Yujun

last: Shen

address: 22 Qixiangtai Road, Heping District

institute: Tianjin Medical University

type: Expression profiling by high throughput sequencing

summary: Natural killer (NK) cells exhibit anti-fibrotic properties in liver fibrosis (LF) by suppressing activated hepatic stellate cell (HSC) populations. Prostaglandin (PG) E2 plays a dual role in innate and adaptive immunity. E-prostanoid 3 receptor (EP3) was markedly downregulated in NK cells from liver fibrosis mice and patients with liver cirrhosis. NK cell-specific deletion of EP3 aggravated hepatic fibrogenesis in mouse models of LF. For an in-depth analysis of the molecular alterations mediated by EP3 in NK cells, single-cell RNA sequencing (scRNA-seq) was performed using CD27+CD11b+ NK cells. GO, KEGG, GSEA revealed that the adhesion signaling pathway was downregulated in EP3-deficient NK cells. This phenotype was confirmed by qRT-PCR and function experiments. Thus, EP3 is required for adhesion and cytotoxicity of NK cells toward HSCs and may serve as a therapeutic target for the management of LF.

overall_design: Flow sorted splenic CD27+CD11b+ NK cells from two mice from each group (EP3F/F and NKp46CreEP3F/F) were pooled for droplet-based single-cell RNA-seq (10x Genomics platform).

first: Xixi

last: Tao


title: Pharmacodynamics of malignant mesothelioma MSTO-211H dn-TEAD2 xenograft recurrence.

status: Public on Feb 17 2022

city: Vitry-sur-Seine

first: Emmanuel

last: Spanakis

address: 1 Imp. des Ateliers

department: Oncology

country: France

institute: Sanofi

summary: We investigate the dependence of human malignant pleural mesothelioma on a functional YAP1-TEAD transcription factor complex to maintain fully established tumors in vivo. We show that, in a dysfunctional Hippo genetic background, expression of a doxycycline-dependent dominant negative TEAD2 temporarily modulates YAP1/TEAD-dependent gene expression and inhibits growth of established tumor xenografts. Recovery of tumor growth is associated with TEAD-dependent transcription comparable to untreated tumors, therefore, re-activation of TEAD transcription complexes.

overall_design: Human malignant mesothelioma MSTO-211H cells transfected with a doxycycline-dependent dominant negative-TEAD2 (dn-TEAD2) construct were inoculated subcutaneously in mice and allowed to grow to about 300 mm3 under glucose supplementation. At time 0, the mice were split into groups receiving doxycycline or not. After a short but significant inhibition of xenograft growth by doxycycline, the tumors in treated animals regained growth rates comparable to untreated controls. We followed transcription at the end of the experiment when all untreated, and fully, or partially treated xenografts grew at similar rates.

first: Loreley

last: Calvet

first: Odette

last: Dos-Santos

first: Sandrine

last: Valence

first: Véronique

last: Jean-Baptiste

first: Jean-Christophe

last: Le Bail

first: Armelle

last: Buzy

first: Pascal

last: Paul

last: Henry

first: Jack

last: Pollard

first: Sukhvinder

last: Sidhu

first: Jürgen

last: Moll

first: Laurent

last: Debussche

first: Iris

last: Valtingojer


title: Human malignant mesothelioma NCI-H226 cells treated with TEAD inhibitor K-975 in SCID mice.

summary: We investigate the dependence of human malignant mesothelioma on functional TEAD transcription factors to maintain fully established tumors in vivo. We show that TEAD inhibitor K-975 stops tumor growth in vivo, eventually causing tumor regression, by downregulating TEAD activity and altering, thus, TEAD-dependent transcription in a dysfunctional Hippo genetic background. Our data  validate the concept of inhibiting an activated YAP1/TEAD complex for the treatment of malignant pleural mesothelioma patients.

overall_design: Five replicate mice per treatment group were inoculated subcutaneously with NCI-H226 cells and treated with three different doses of K-975, or with the vehicle. Tumors were removed at four different time-intervals after treatment.  Two untreated groups served as controls. Whole transcriptomes were evaluated by RNA-seq. One vehicle sample dropped out.

first: Christophe


title: Differences in RNA polymerase II complexes and their interactions with surrounding chromatin on human and cytomegalovirus genomes [ChIP-seq]

city: Iowa City

first: David

last: Price

state: IA

address: 500 Newton Road, 260 EMRB

department: Biochemistry

country: USA

institute: University of Iowa

type: Genome binding/occupancy profiling by high throughput sequencing

summary: To investigate the chromatin structure surrounding human RNA polymerase II (Pol II) transcription on host and viral genomes, chromatin immunoprecipitation (ChIP) was performed following digestion of HCMV infected primary human foreskin fibroblasts (HFFs) with DNA Fragmentation Factor (DFF). DFF is a human endonuclease responsible for cleaving between nucleosomes during apoptosis. We found that utilizing DFF as the front end for ChIP-Seq in place of sonication or Micrococcal nuclease (MNase) offered new insights into the connections between active transcription and the local chromatin on the host and that these connections were completely absent on the HCMV genome.

overall_design: Nuclei from multiple different cell types that were either infected with HCMV strains TB40e or Towne or uninfected were rapidly isolated following no treatment, treatment with P-TEFb inhibitor flavopiridol, or treatment with XPB inhibitor triptolide. Resulting nuclei were then digested with DNA fragmentation Factor (DFF), an endonuclease with reduced intra-nucleosomal cutting as compared to Micrococcal nuclease (MNase), to generate primarily mono-nucleosomes. After release of chromatin from the nucleus following light sonication, transcription complex factors and histone modifications were then immunoprecipitated from the released chromatin.

first: Benjamin

middle: M

last: Spector

first: Mrutyunjaya

last: Parida

first: Chris

middle: B

last: Ball

first: Ming

last: Li

middle: H


title: Conditional expression of a dominant negative-TEAD2 construct modulates YAP1/TEAD-dependent transcription and arrests growth of human malignant mesothelioma MSTO-211H [TEAD2-dn] xenografts.

first: Emmanuel

last: Spanakis

summary: We investigate the dependence of human malignant pleural mesothelioma on a functional YAP1-TEAD transcription factor complex to maintain fully established tumors in vivo. We show that, in a dysfunctional Hippo genetic background, expression of a dominant negative TEAD2 modulates YAP1/TEAD-dependent gene expression and inhibits growth of established tumor xenografts. Our data demonstrate that, in the context of a mutated Hippo pathway, TEAD2 activity is essential to maintain the growth of mesothelioma tumors in vivo, thus validating the concept of inhibiting the activated YAP1/TEAD complex for the treatment of malignant pleural mesothelioma patients.

overall_design: Human malignant mesothelioma MSTO-211H cells transfected with a doxycycline-dependent dominant negative-TEAD2 (dn-TEAD2) construct were inoculated subcutaneously in mice and allowed to grow to about 300 mm3 under glucose supplementation. At time 0, the mice were split into groups receiving doxycycline or not. The effects of doxycycline (dn-TEAD2 expression) on tumor size and gene expression (transcriptome) were evaluated times 0, 24, 96, or 216 hours of treatment.

first: Loreley

last: Calvet

first: Odette

last: Dos-Santos


title: Conditional expression of sh-YAP1 modulates YAP1/TEAD-dependent transcription and causes regression of established human malignant mesothelioma MSTO-211H [sh-YAP1] xenografts.

summary: We investigate the dependence of human malignant pleural mesothelioma on a functional YAP1-TEAD transcription factor complex to maintain fully established tumors in vivo. We show that, in a dysfunctional Hippo genetic background, downregulation of YAP1 by shRNA results in modulation of YAP1/TEAD-dependent gene expression and regression of established tumor xenografts. Our data demonstrate that, in the context of a mutated Hippo pathway, YAP1 activity is essential to maintain the growth of mesothelioma cells in vivo, thus validating the concept of inhibiting the activated YAP1/TEAD complex for the treatment of malignant pleural mesothelioma patients.

overall_design: Malignant pleural mesothelioma MSTO-211H cells transfected with a doxycycline-dependent sh-YAP1 construct were inoculated subcutaneously in mice and allowed to grow to about 300 mm3 under glucose supplementation. At time 0, the mice were split into groups receiving doxycycline or not. The effects of doxycycline supplementation (sh-YAP1 expression) on tumor size and gene expression (transcriptome) were evaluated at times 0 (before treatment), 24, 96, or 216 hours of treatment.

first: Sandrine

last: Valence

first: Véronique

last: Jean-Baptiste

first: Jean-Christophe

last: Le Bail


title: Short-Term Adaptations in Skeletal Muscle Mitochondrial Oxidative Capacity and Metabolic pathways to Breaking Up Sedentary Behaviors with Short-Frequent Bouts of Physical Activity Compared to a Matched Daily Single-Continuous Bout in Obese Adults

status: Public on Feb 16 2022

city: Oklahoma City

first: Michael

middle: C.

last: Rudolph

state: OK

address: 975 NE 10th St. BRC North rm 364

department: Biochemistry and Physiology

institute: OUHSC

summary: We compared the short-term (4-day) adaptations in skeletal muscle mitochondrial function and gene expression between short-frequent bouts of physical activity and time matched single-continuous physical activity.

overall_design: Inactive adults (N = 19, Age: 32.2 ± 6.4 years, BMI: 30.3 ± 3.0 kg/m2) completed three interventions, SED: sedentary control, MICRO: 5-min brisk walking each hour for 9hr/d, ONE: daily 45-min continuous brisk walking bout. Fasted skeletal muscle biopsies were collected the morning of day 5.

first: Nathan

middle: P

last: De Jong

middle: C


title: Expression data from mouse lung epithelial cells during E. coli pneumonia in the presence or absence of LIF neutralization (6 h)

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

state: MA

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

summary:
Leukemia inhibitory factor (LIF) is a cytoprotective cytokine that reduces lung injury during pneumonia. The purpose of this study was to determine the influence of LIF on pneumonia-induced gene changes in lung epithelium.
Mice received intratracheal instillations of vehicle (PBS) or Escherichia coli (10^6 CFU). Control IgG or anti-LIF specific IgG was included in the instillate. 6 hours after the challenge, lung epithelial cells (EpCAM+/CD45-) were sorted from enzymatic lung digests and used for RNA isolation and microarray analysis.

overall_design: RNA from 3 separate groups of mice (3 mice per group) was analyzed: 1) 6h Vehicle/control IgG-treated; 2) 6h E. coli/control IgG-treated; and 3) 6h E. coli/anti-LIF-specific IgG.

first: Elim

first: Katrina

last: Traber

first: Lee

last: Quinton


title: Expression data from mouse lung epithelial cells during E. coli pneumonia in the presence or absence of LIF neutralization (24 h)

summary:
Leukemia inhibitory factor (LIF) is a cytoprotective cytokine that reduces lung injury during pneumonia. The purpose of this study was to determine the influence of LIF on pneumonia-induced gene changes in lung epithelium.
Mice received intratracheal instillations of vehicle (PBS) or Escherichia coli (10^6 CFU). Control IgG or anti-LIF specific IgG was included in the instillate. 24 hours after the challenge, lung epithelial cells (EpCAM+/CD45-) were sorted from enzymatic lung digests and used for RNA isolation and microarray analysis.

overall_design: RNA from 3 separate groups of mice (3 mice per group) was analyzed: 1) 24h Vehicle/control IgG-treated; 2) 24h E. coli/control IgG-treated; and 3) 24h E. coli/anti-LIF-specific IgG.


title: Identification of highly cross-reactive mimotopes for a public T cell response in murine melanoma

status: Public on Feb 15 2022

city: CAMBRIDGE

first: Duncan

middle: Matthew

last: Morgan

address: 500 Main St

department: Koch Institute

institute: MIT

summary: While immune checkpoint blockade results in durable responses for some patients, many others have not experienced such benefits. These treatments rely upon reinvigorating specific T cell-antigen interactions. However, it is often not known what antigens are being recognized by T cells, or how to potently induce antigen-specific responses in a broadly applicable manner. Here, we characterized the CD8+ T cell response to a murine model of melanoma following combination immunotherapy to determine the basis of tumor recognition. Sequencing of tumor-infiltrating T cells revealed a repertoire of highly homologous TCR sequences that were particularly expanded in treated mice and which recognized an antigen from murine leukemia virus, an endogenous retrovirus. While vaccination against this peptide failed to raise a protective T cell response in vivo, engineered antigen mimotopes induced a significant expansion of CD8+ T cells cross-reactive to the original antigen. Vaccination with mimotopes resulted in killing of antigen-loaded cells in vivo yet failed to delay tumor growth in a prophylactic vaccine paradigm. Together, this work demonstrates the identification of a dominant tumor-associated antigen and mimotopes that are highly cross-reactive to the endogenous antigen across multiple individuals.

overall_design: Analysis of tumor-infiltrating cells from mice bearing B16F10 tumors.

first: Beth

middle: E

last: Grace

first: Coralie

last: Backlund

first: Byong

last: Kang

first: Nishant

middle: K

last: Singh

first: Brooke

middle: D

last: Huisman

first: C

middle: G

last: Rappazzo

first: Kelly

last: Mohnihan

first: Laura

last: Maiorino

first: Connor

middle: S

last: Dobson

first: Taeyoon

last: Kyung

first: Khloe

last: Gordon

first: Patrick

middle: V

last: Holec

first: Overbeck

last: Mbah

first: Daniel

last: Garafola

first: Shengwei

last: Wu

first: J

last: Love

first: K

last: Wittrup

first: Darrell

middle: J

last: Irvine

last: Birnbaum


title: Identification of a retinoic acid-dependent definitive hematopoietic progenitor from human pluripotent stem cells [scRNA-seq]

status: Public on Feb 14 2022

city: New York

first: Stephanie

last: Luff

state: NY

address: 1425 Madison Ave

department: Cell, Developmental, & Regenerative Biology

institute: Icahn School of Medicine at Mount Sinai

summary: The generation of the hematopoietic stem cells (HSCs) from human pluripotent stem cells (hPSCs) is a major goal for regenerative medicine. HSCs derive from hemogenic endothelium (HE) in a retinoic acid (RA)-dependent manner1. While a WNT-dependent (WNTd) patterning of nascent mesoderm specifies clonally multipotent definitive HE from hPSCs2,3, this HE is functionally unresponsive to RA4. Here we show that WNTd mesoderm, prior to HE specification, is comprised of two distinct KDR+CD34negT+ populations. In a TGFb-independent manner, CXCR4negCYP26A1+ mesoderm is specified, which gives rise to HOXA+ multilineage definitive HE, in an RA-independent manner. In contrast, CXCR4+ALDH1A2+ mesoderm is specified in a TGFb-dependent manner, and gives rise to multilineage definitive HE in a stage-specific, RA-dependent manner. Further, this NOTCH-dependent HE harbored HOXA expression resembling fetal HE. This model of human hematopoietic development defines the mesodermal origins of multiple waves of hematopoiesis, and that RA-dependent hematopoietic development occurs prior to HE development.

overall_design: Whole day 3 embroid bodies (EBs) from WNTi (IWP2 + ACTIVIN A) and WNTd (CHIR99021 + SB43152) were harvest and processed using the 10X platform.

middle: A

first: John

last: Creamer

first: Sara

last: Valsoni

first: Carissa

last: Dege

first: Rebecca

last: Scarfo

first: Analisa

last: Dacunto

first: Ivan

last: Merelli

first: Samantha

last: Morris

first: Andrea

last: Ditadi

first: Christopher

last: Sturgeon


title: Identification of a retinoic acid-dependent definitive hematopoietic progenitor from human pluripotent stem cells

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

overall_design: Refer to individual Series


title: A velvet transcription factor specifically activates mating through a novel surface protein in the human fungal pathogen Cryptococcus deneoformans

status: Public on Feb 10 2022

city: beijing

first: lei

last: chen

address: NO.1 Beichen West  Road, Chaoyang District, Beijing 100101, China

institute: the institute of microbiology chinese academy of sciences

summary: Sexual reproduction facilitates infection by the production of both a lineage advantage and infectious sexual spores in the ubiquitous human fungal pathogen Cryptococcus deneoformans. However, the regulatory determinants specific for initiating mating remain poorly understood. Here, we identified a velvet family regulator, Cva1, that strongly promotes sexual reproduction in C. deneoformans. This regulation was determined to be specific, based on a comprehensive phenotypic analysis of cva1 under 25 distinct in vitro and in vivo growth conditions. We further revealed that Cva1 plays a critical role in the initiation of early mating events, especially sexual cell-cell fusion, but is not important for the late sexual development stages or meiosis. Thus, Cva1 specifically contributes to mating activation. Importantly, a novel mating-responsive surface protein, Cfs1, serves as the key target of Cva1 during mating, since its absence nearly blocks cell-cell fusion in C. deneoformans and its sister species C. neoformans. Together, our findings provide insight into how C. deneoformans ensures regulatory specificity of mating.

overall_design: 4 samples contain wildtype and cva1Δ at one time point with 2 repeats

first: Huimin

last: Liu

first: Xiaoxia

last: Yao

first: Weixin

last: Ke

first: Hao

last: Ding

first: Guang-Jun

last: He


title: FAM111A is dispensable for electrolyte homeostasis in mice

status: Public on Feb 13 2022

city: Nijmegen

first: Jeroen

last: de Baaij

address: Geert Grooteplein 26-28

department: Physiology

country: Netherlands

institute: Radboudumc

summary: Autosomal dominant mutations in FAM111A are causative for Kenny-Caffey syndrome type 2. Patients with Kenny-Caffey syndrome suffer from severe growth retardation, skeletal dysplasia, hypoparathyroidism, hypocalcaemia, hyperphosphataemia and hypomagnesaemia. While recent studies have reported FAM111A to function in antiviral response and DNA replication, its role in regulating electrolyte homeostasis remains unknown. In this study, we assessed the role of FAM111A in the regulation of serum electrolyte balance using a Fam111a knockout (Fam111a-/-) mouse model. Fam111a-/- mice displayed a normal weight and serum parathyroid hormone (PTH) concentration and exhibited unaltered magnesium, calcium and phosphate levels in serum and 24-hour urine. Expression of calciotropic (including Cabp28k, Trpv5, Klotho and Cyp24a1), magnesiotropic (including Trpm6, Trpm7, Cnnm2 and Cnnm4) and phosphotropic (Slc20a1, Slc20a2, Slc34a1 and Slc34a3) genes in the kidneys, duodenum and colon were not affected by Fam111a depletion. Only Slc34a2 expression was significantly upregulated in the duodenum, but not in the colon. Analysis of femurs showed unaffected bone morphology and density in Fam111a-/- mice. Kidney and parathyroid histology were also normal in Fam111a-/- mice. In conclusion, our study is the first to characterise the function of FAM111A in vivo and we report that FAM111A is not essential for growth or electrolyte homeostasis in mice.

overall_design: Four randomly selected samples from Fam111a+/+ and three samples from Fam111a-/- mice were sent for RNA sequencing. Quality control and RNAseq were performed by BaseClear B.V. (Leiden, The Netherlands).

first: Barnabas

last: Ilenwabor

first: Heidi

last: Schigt

first: Andreas

last: Kompatscher

first: Caro

last: Bos

first: Bram

last: van der Eerden

first: Joost

last: Hoenderop


title: Time-lapse RNA-seq analysis to study transcriptional regulation by early signals in De Novo Root Regeneration in Arabidopsis

first: Lin

last: XU

address: 300 Fenglin Road

department: Chinese Academy of Sciences

institute: Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences

summary: Detached Arabidopsis leaves can regenerate adventitious roots, providing a platform to study de novo root regeneration (DNRR). We performed time-lapse RNA-seq within 12 h to reveal transcriptional changes in response to early signals in DNRR.

overall_design: Arabidopsis seeds (Col-0 and the coi1-2 mutant) were germinated and grown on 1/2 MS medium with 1% sucrose at 22°C under a 16-h light/8-h dark photoperiod for 12 d. The first pair of rosette leaves from 12-d-old seedlings were cut at the junction of the blade and petiole, and the detached blades were cultured on sucrose-free B5 medium at 22°C under 24-h light conditions. The entire tissues of leaf explants at time 0 (t0), 10 min, 30 min, 1 h, 2 h, 4 h, 8 h and 12 h after detachment were harvested and frozen in liquid nitrogen for RNA extration. Library construction and deep sequencing were carried out using the Illumina HiSeq 3000 platform following the manufacturer's instructions by Genergy Biotechnology (Shanghai, China).

last: Xu

first: Wu

first: Yuyun

last: Zhang


title: Time-lapse RNA-seq analysis to study the gene networks in cell fate transition in de novo root regeneration from detached Arabidospis leaves

summary: Detached Arabidopsis leaves can regenerate adventitious roots, providing a platform to study de novo root regeneration (DNRR). We performed time-lapse RNA-seq within 5 d revealed activation of gene networks in cell fate transition.

overall_design: We used the adventitious rooting assay from detached Arabidopsis leaves in this study. We performed time-lapse RNA-seq analysis of the wounded region of leaf explants at t0, 6 h, 12 h, 1 d, 2 d, 3 d, 4 d, and 5 d after detachment to study the gene networks in cell fate transition.


title: Spatially Annotated Single Cell Sequencing for Unraveling Intratumor Heterogeneity

city: Rotterdam

first: Miao-Ping

last: Chien

address: Wytemaweg 80

department: Molecular Genetics

institute: Erasmus University Medical Center

summary: Intratumor heterogeneity is a major obstacle to effective cancer treatment. Current  methods to study intratumor heterogeneity using single-cell RNA sequencing (scRNAseq)  lack information on the spatial organization of cells. While state-of-the art spatial  transcriptomics methods capture the spatial distribution, they either lack single cell  resolution or have relatively low transcript counts. Here, we introduce spatially  annotated single cell sequencing, based on the previously developed functional single  cell sequencing (FUNseq) technique, to spatially profile tumor cells with deep scRNA-seq  and single cell resolution. Using our approach, we profiled cells located at different  distances from the center of a 2D epithelial cell mass. By profiling the cell patch in  concentric bands of varying width, we showed that cells at the outermost edge of the  patch responded strongest to their local microenvironment, behaved most invasively, and  activated the process of epithelial-to-mesenchymal transition (EMT) to migrate to lowconfluence  areas. We inferred cell-cell communication networks and demonstrated that  cells in the outermost ~10 cell wide band, which we termed the invasive edge, induced  similar phenotypic plasticity in neighboring regions. Applying FUNseq to spatially annotate  and profile tumor cells enables deep characterization of tumor subpopulations, thereby  unraveling the mechanistic basis for intratumor heterogeneity.

overall_design: scRNA-seq was performed in various regions at different distances from the center of a 2D epithelial tumor model using functional single-cell sequencing. Gene expression profiles in the center and at the edge of the tumor were analyzed to quantify the level of EMT in MCF10A cells. Two separate experimental setups were used: we either profiled the tumor model in concentric rings of equal width (i.e. center, middle and outer; approx. ~1000 um wide bands) or we profiled the invasive edge of the tumor model at a higher resolution (i.e. comparing the center with the outermost edge; ~10 cell wide band). Cells in the different regions are phototagged using photoactivatable Janelia Fluor 549 and photoactivatable Janelia Fluor 646 dyes, after which cells are sorted based on fluoresence and subjected to scRNA-seq. For each setup, 2 biological replicates are present.

first: Myrthe

last: Smit

first: Kate

last: Feller

first: Li

last: You

first: Jelle

last: Storteboom

first: Yasin

last: Begce

first: Cecile

last: Beerens

first: Miao Ping


title: Single-Cell RNA-seq analysis of cell lineages in De Novo Root Regeneration

summary: Detached Arabidopsis leaves can regenerate adventitious roots, providing a platform to study de novo root regeneration (DNRR). We performed single-cell RNA-seq analysis and revealed that regeneration primarily originated from vascular stem-cell organizer within procambium, followed by step-by-step changes of transcriptome in cell fate transition, including gradually erasing the vascular stem-cell organizer identity and recruiting the root development program.

overall_design: We used the adventitious rooting assay from detached Arabidopsis leaves in this study. Single-cell RNA-seq was performed using the wounded region of detached leaves cultured on B5 medium for 4 d .

last: Liu


title: The impact of species-wide gene expression variation on Caenorhabditis elegans complex traits

city: Evanston

first: Gaotian

address: 2205 Tech Drive

department: Department of Molecular Biosciences

institute: Northwestern University

summary: Transcriptomic analysis on 207 genetically distinct C. elegans wild strains

overall_design: We used genome-wide association mappings to investigate the genetic basis underlying gene expression variation and revealed complex genetic architectures.

first: Nicole

last: Roberto

first: Daehan

last: Lee

first: Steffen

middle: R

last: Hahnel

first: Erik

last: Andersen


title: The spliceosome component Usp39 controls B cell development by regulating immunoglobulin gene rearrangement

status: Public on Feb 08 2022

city: Shenzhen

first: Guixin

last: Ruan

state: Guangdong

address: 1088 Xueyuan Avenue

department: Biology

institute: Southern University of Science and Technology

summary: The spliceosome is a large ribonucleoprotein complex responsible for pre-mRNA splicing and genome stability maintenance. Disruption of the spliceosome activity may lead to developmental disorders and tumorigenesis.  However, the physiological role that the spliceosome plays in B cell development and function is still poorly defined. Here, we demonstrate that ubiquitin-specific peptidase 39 (Usp39), a spliceosome component of the U4/U6.U5 tri-snRNP complex, is essential for B cell development. Ablation of Usp39 in B cell lineage blocks pre-pro-B to pro-B cell transition in the bone marrow, leading to a profound reduction of mature B cells in the periphery. We show that Usp39 specifically regulates immunoglobulin gene rearrangement in a spliceosome-dependent manner, which involves modulating chromatin interactions at the Igh locus. Moreover, our results indicate that Usp39-deletion reduces the pre-malignant B cells in Eμ-Myc transgenic mice and significantly improves their survival.

overall_design: RNA-Seq of pre-pro-B cells in Usp39 fl/fl and Usp39 fl/fl mb1-cre mice; RNA-Seq of small pre-B cells in Usp39 fl/fl and Usp39 fl/fl cd19-cre mice; Hi-C-Seq of pre-pro-B cells in Usp39 fl/fl and Usp39 fl/fl mb1-cre mice

first: Gui-xin

first: Xijun

last: Ou

first: Rui


title: Transcriptomic changes upon NaCl treatment dependent on GA biosynthesis and signaling.

city: Uppsala

first: Frauke

last: Augstein

address: Almas Allé 5

department: IOB

country: Sweden

institute: Uppsala University

summary: Distinct transcriptome changes upon salt exposure are dependent on DELLA and GA-signaling. We performed RNA-sequencing on mock and NaCl- treated Arabidopsis plants to investigate the role of GA-levels and signaling, in particular DELLAs, on gene expression changes upon salt exposure

overall_design: Transcriptomic changes in 1cm roots of 5 day old Arabidopsis plants upon treatment with 140mM NaCl/ mock for 1h or 8h. Genotypes used in this experiment: Ler (wt), gai-t6 rga-t2 rgl1-1 rgl2-1 rgl3-4 (della quintuple mutant), ga4, gai

first: Annelie

last: Carlsbecker


title: A synergistic interaction between HDAC- and PARP inhibitors in childhood tumors with chromothripsis

city: Heidelberg

first: Aurélie

last: Ernst

address: Im Neuenheimer Feld 580

country: Germany

institute: DKFZ Heidelberg

type: Methylation profiling by genome tiling array

summary:
Expression data of medulloblastoma patient derived xenograft spheroids upon BGB 290 and romidepsin treatment alone and in combination:
Romidepsin and BGB 290 shows synergistic growth inhibition in medulloblastoma patient derived xenograft spheroid models in vitro and in vivo.

Chromothripsis is a form of genomic instability characterized by the occurrence of tens to hundreds of clustered DNA double-strand breaks in a one-off catastrophic event. Rearrangements associated with chromothripsis are detectable in numerous tumor entities and linked with poor prognosis in some of these, such as Sonic Hedgehog medulloblastoma, neuroblastoma and osteosarcoma. Hence, there is a need for therapeutic strategies eliminating tumor cells with chromothripsis. Defects in DNA double-strand break repair, and in particular homologous recombination repair, have been linked with chromothripsis. Targeting DNA repair deficiencies by synthetic lethality approaches, we performed a synergy screen using drug libraries (n = 375 compounds, 15 models) combined with either a PARP inhibitor or cisplatin. This revealed a synergistic interaction between the HDAC inhibitor romidepsin and PARP inhibition. Functional assays, transcriptome analyses, and in vivo validation in patient-derived xenograft mouse models confirmed the efficacy of the combinatorial treatment.

overall_design:
We used microarrays to detail the differential gene expression upon BGB 290 and romidepsin treatment either alone and in combination to determine the underlying cause of synergistic interaction between the two anticancer drugs.
Cells from 3 Sonic Hedgehog medulloblastoma patient derived xenograft spheroid models (LFS_MB_P, primary tumor, LFS_MB_1R, first relapse and RCMB18) were treated with either vehicle control, BGB 290 (IC20), romidepsin (IC20) or BGB 290 (IC20) with romidepsin (IC20) for 24 hours. Pictures were taken using a bright-field microscope to determine the effect of the treatment on the spheroid growth. RNA was then isolated and expression data were generated using Affymetrix Clariom S arrays.

Copy number states from EPIC and 450K methylation arrays were assessed by the Bioconductor package conumee.
11 samples were profiled on IlluminaHumanMethylation850k arrays

first: Umar

last: Khalid

first: Murat

last: Iskar

first: John

last: Wong

first: Marc

last: Zapatka


title: Transcriptomic analysis of the duckling liver mRNA methylome following infection by the virulent and attenuated Hepatitis A virus type 1 strains

city: wuhan

first: dong

last: chen

state: Hubei

address: GaoXin 2nd Road

institute: ablife

type: Methylation profiling by high throughput sequencing

summary: Duck hepatitis A virus (DHAV) modulates host physiology and gene expression. The RNA modiﬁcation N6-methyladenosine (m6A) modulates mRNA fate and thus affects many biological processes in mammals. Neither modifications on mRNAs have been reported in avian species. Here, we used immunoblot analysis and LC-MS/MS to show the presence of m6A modification in ducking liver, and a decreased m6A modification by virulent DHAV-1 (CH) strain when compared to the attenuated vaccine DHAV-1 (CK). The m6A-seq analysis of the duckling liver at four post-infection time points revealed predominant distribution at CDS region, and a virus-induced time-dependent increase to decrease change in the peak signals. In particular, we only found ACU consensus sequence in the motif enriched by the duckling m6A peaks, which is a part of the classic mammalian m6A motif GGACU. Notably, the most enriched motif in the duckling m6A peaks was GAAGAAG. Strikingly, combination analysis of the difference in the levels of gene expression and m6A modification in duckling livers infected by CK- and CH-strains showed a strong correlation between these two molecular mechanisms. GO analysis showed that genes showing coupled change in m6A modification and gene expression level in responding to the DHAV-1 virulence were enriched in pathways including defense response to virus and immune response. Overall, this work reveals a sophisticated m6A modification profile in duckling liver, which is sensitive to DHAV-1 infection and involved in distinguishing and responding to the virulence

overall_design: we use m6A-seq technology to profile the transcriptome-wide mRNA modifications of duckling liver infected by virulent DHAV-1 CH (CH) and attenuated vaccine DHAV-1 CH60 (CK) infection

first: Weili

last: Quan

first: Minshu

last: Wang


title: Sex Differences in Heart Mitochondria: Relationship to Diastolic Dysfunction

status: Public on Jan 31 2022

city: Los Angeles

first: Calvin

last: Pan

address: 675 Charles Young Dr South

institute: UCLA

summary: As part of genetic studies of heart failure in mice, we observed that heart mitochondrial DNA levels and function tend to be reduced in females as compared to males. We also observed that expression of genes encoding mitochondrial proteins were higher in males than females in human cohorts. Heart failure with preserved ejection fraction (HFpEF) exhibits a sex bias, being more common in women than men, and we hypothesized that mitochondrial sex differences might underlie this bias.  We tested this in a panel of genetically diverse inbred strains of mice, termed the Hybrid Mouse Diversity Panel (HMDP). Indeed, we found that mitochondrial gene  expression was highly correlated with diastolic function, a key trait in HFpEF.  Consistent with this, studies of a “two-hit” mouse model of HFpEF confirmed that mitochondrial function differed between sexes and was strongly associated with a number of HFpEF traits. By integrating data from human heart failure and the mouse HMDP cohort, we identified the mitochondrial protein Acsl6 as a genetic determinant of diastolic function. We validated its role in HFpEF using adenoviral over-expression in the heart. We conclude that sex differences in mitochondrial function underlie, in  part, the sex bias in diastolic function.

overall_design: C57BL/6J mice were placed on either a control diet (chow) or a high-fat diet supplemented with L-NAME.  Heart tissue was isolated from the resulting 8 pairs of male mice and 7 pairs of female mice and RNA extracted from these hearts were sequenced.  Differential expression was performed on the resulting counts.

first: A

last: Lusis

first: Y

last: Cao


title: Programme of Self-Reactivity for Innate-Like T Cell-Mediated Cancer Immunosurveillance

status: Public on Feb 04 2022

first: Christina

last: Leslie

address: 1275 York Ave

institute: Memorial Sloan Kettering Cancer Center

summary: The concept of cancer immunosurveillance ascribes a role of cellular immunity in eliminating transformed cells with cytotoxic CD8+ T cells being a primary mediator. Cancer cells can express neoantigens to prime conventional CD8+ T cells which nonetheless transition to a dysfunctional state of exhaustion characterized by high expression of the immune checkpoint co-inhibitory receptor PD-1. Despite the clinical success of anti-PD-1 to revive cancer immunity, many patients do not respond to checkpoint blockade therapies. Of note, recent studies have revealed an incredible heterogeneity among tumor-infiltrating CD8+ T cells with the PD-1+ population being only a fraction, and yet, beside the PD-1+ subset, the identity of other populations of CD8+ T cells remains largely unknown. Here, in an unbiased survey of CD8+ T cells present in murine and human malignancies, we rediscovered a population of FCER1G+ innate-like T cells that we have previously shown to possess high cytotoxic potential and are resistant to exhaustion, hereon termed ‘killer innate-like T cells’, or ILTCks. While tumor-infiltrating CD8+PD-1+ T cells were oligoclonal, ILTCks were polyclonal with broad reactivity to unmutated tumor-associated antigens. ILTCks were not differentiated from conventional CD8+ T cells, but arose from ILTCk-committed progenitors following early encounter with cognate antigens during thymocyte development. Committed ILTCk thymic progenitors were continuously generated throughout life, and replenished the ILTCk compartment during tumor progression. Notably, expansion and effector differentiation of intratumoral ILTCks depended on high expression of IL-15 in cancer cells, and inducible activation of IL-15 signaling in adoptively transferred ILTCk progenitors suppressed tumor growth. Thus, antigen receptor self-reactivity and unconventional ontogeny distinguish ILTCks from CD8+PD-1+ T cells as a new class of tumor-elicited immune response. Strategies targeting ILTCks may enhance and complement current conventional CD8+ T cell-based cancer immunotherapies, in particular against tumors with low mutation burden or refractory to checkpoint blockade modalities.

overall_design: Single-cell and bulk RNA-seq data corresponding to Chou,Zhang et al 2022.  Single cell RNA-seq datasets include data from two cancer types- murine breast cancer (1 dataset in main figure, and 1 in extended), and two biological replicates of murine prostate cancer (TRAMP mice), for analysis in the extended figure.  These datasets were generated to discover the abILTCk population.  Bulk RNA-seq datasets correspond to thymic conventional CD8 single positive (SP) progenitors (2 biological replicates) and ILTCk progenitors (2 biological replicates) with analysis included in the extended figure, as well as murine NK1.1+/- abILTCk (2 biological replicates each) cells and PD1+ conventional T cells (2 biological replicates).

first: Chirag

last: Krishna

first: Ming

middle: O

last: Li

first: Chun

last: Chou

first: Xian

last: Zhang


title: RNA-sequencing of brain microvascular endothelial cell dysfunction in an isogenic juvenile iPSC model of Huntington’s disease

status: Public on Feb 01 2022

city: BALTIMORE

first: Peter

last: Searson

state: MD

address: 3400 North Charles Street

institute: Johns Hopkins University

summary: Huntington's disease (HD) is associated with dysfunction of the blood-brain barrier, including brain microvasscular endothelial cells (BMECs). We report changes in gene expression of induced pluripotent stem cells (iPSCs) and iPSC-derived brain microvascular endothelial cell-like cells (iBMECs) derived from an isogenic pair of iPSCs with either 180 (HD-corrected) or 18 (HD180) CAG repeats in the HTT gene.

overall_design: 8 total samples collected; n =2 samples of iPSCs and iBMECs from HD180 and HD-corrected isogenic iPSCs

first: Raleigh

middle: M

last: Linville


title: Single-cell Sequencing of Microglia following Repopulation Reveals Distinct Clusters and Transcriptomic Signatures in the 3xTg Alzheimer's Disease Model

city: Rochester

first: O'Banion

last: Kerry

state: United States of America

address: 601 Elmwood Ave

institute: University of Rochester

summary: In this study, we aimed to deplete the aging microglia and investigate the impact of the newly-born microglia in Alzheimer's pathology using the 3xTg mouse model. Specifically, >24 mo male 3xTg mice were given chow containing 1200mg/kg PLX5622 (AIN-76A-D1001i, Research Diests, NJ, USA) for 2 weeks to deplete their microglia. Control diet with the same base formula were given to control group and to experimental groups during a 4-week repopulation phase immediately following PLX treatment. At the end of the repopulation, we pooled sorted, viable microglia (CD45int CD11b) from 3-5 mice/group and ran single-cell RNAseq analysis to determine the similarities and differences between the aged and repopulated cells in the context of Alzheimer's Disease. We also included non-transgenic controls as a separate group.

overall_design: Microglia (CD45int CD11b+) pooled from 3-5 mice/group were sorted from isolated hippocampi and processed for single-cell RNAseq.

first: Berke

last: Karaahmet

first: Monique

last: Mendes

first: Laura

last: Owlett

first: Joshua

last: Boyer

first: Lee

last: Trojanczyk

last: Olschowka

first: Ania

last: Majewska

first: Kerry

last: O’Banion


title: Histone Acetylation Regulator Gcn5 Mediates Drug Resistance and Virulence of Candida glabrata

status: Public on Jan 28 2022

city: Nutley

first: Liang

last: Chen

state: NJ

address: 340 Kingsland Street

institute: Hackensack-Meridian Health Center for Discovery and Innovation

summary: This study explored the transcriptional change of Candida glabrata cells due to GCN5 deletion. We also compared the transcriptional responses to fluconazole and micafungin in WT and gcndelta cells relative to respective no drug controls.

overall_design: Overnight culture of WT and gcn5Δ was inoculated in liquid YPD at an initial OD600 of 0.2 and grown at 37°C with shaking to OD600 of 0.6. Cells were then treated with fluconazole (8μg/ml) or micafungin (15ng/ml) for 2 hours. Untreated WT and gcn5Δ cells were grown in parallel. Cells were harvested at the end of 2h treatment and subjected to RNA extraction with two biological replicates for each strain/treatment group.

first: Yanan

last: Zhao

first: Shuying

last: Yu


title: Modulation of the tumor promoting functions of cancer associated fibroblasts by phosphodiesterase type 5 inhibition increases the efficacy of chemotherapy in human preclinical models of esophageal adenocarcinoma

status: Public on Jan 29 2022

city: Nottingham

first: Nigel

last: Mongan

address: University Park

department: Biodiscovery Institute

country: United Kingdom

institute: University of Nottingham

summary: The chemotherapy resistance of esophageal adenocarcinomas (EAC) is underpinned by cancer cell extrinsic mechanisms of the tumor microenvironment (TME). We demonstrate that by targeting the tumor-promoting functions of the predominant TME cell type, cancer associated fibroblasts (CAF) with phosphodiesterase type 5 inhibitors (PDE5i) we can enhance the efficacy of standard-of-care chemotherapy. These findings demonstrate that CAF drive chemotherapy resistance in EAC and can be targeted by repurposing PDE5i, a safe and well tolerated class of drug administered to millions of patients world-wide to treat erectile dysfunction.

overall_design: RNA sequencing was used to compare the transcriptomes of esophageal cancer specimens, and esophageal cancer specimen derived cells established and expanded on fibroblast feeder layer cells and subsequently grown in 3D-tumour growth assays with and without mesenchymal stem cells (as described in detailed in PMID:27736801).

first: Benjamin

last: Sharpe

first: Annette

last: Hayden

first: Antigoni

last: Manousopoulou

first: Andrew

last: Cowie

first: Robert

last: Walker

first: Jack

last: Harrington

first: Fereshteh

last: Izadi

first: Stella

last: Breininger

first: Jane

last: Gibson

first: Oliver

last: Pickering

first: Eleanor

last: Jaynes

first: Ewan

last: Kyle

first: John

last: Saunders

first: Simon

middle: L

last: Parsons

first: Alison

last: Ritchie

first: Philip

last: Clarke

first: Pamela

last: Collier

first: David

last: Bates

first: Kiren

last: Yacqub-Usman

first: Spiros

last: Garbis

first: Zoë

last: Walters

first: Matthew

last: Rose-Zerilli

first: Anna

last: Grabowska

first: Timothy

last: Underwood


title: N6-Methyladenosine Methylomic Landscape of Ureteral Deficiency in Reflux Uropathy and Obstructive Uropathy

city: Shanghai

first: qi

last: qi

address: 399 wanyuan road

department: Children’s Hospital

institute: Fudan university

summary:
Congenital anomalies of the kidneys and urinary tracts (CAKUT) represent the most frequent cause for chronic kidney failure in children.
In this dataset, we include the m6A methylated RNA data obtained from children patients with obstructive megaureter (M group) and primary vesicoureteral reflux (V group) . These data are used to obtain a total of 228 mRNAs differ btween these two diseases.

overall_design: Six samples were analyzed with 33700 probes. We generated the following comparisons using Fold-change (FC) ≥ 1.5 or ≤ 0.7, and p < 0.05 were used to identify the differentially m6A methylated RNAs. Two channel arrays were used for these samples but the data were analyzed as single-channel so that each sample  (GSM) represents either IP or supernatent and the sample table includes the normalized signal values.

first: Hua

last: SHI

first: Tianchao

last: XIANG

first: Jiayan

last: FENG

first: Xue

last: YANG

first: Yaqi

last: LI

first: Ye

last: FANG

first: Linan

last: XU

first: Qi

last: QI

first: Jian

last: SHEN

first: Liangfeng

last: TANG

first: Yubo

last: SUN

first: Qian

first: Xiang

last: WANG

first: Hong

first: Jia

last: RAO


title: Monocular Visual Deprivation in Macaca Fascicularis: A mRNA Sequencing Profile of LGN Tissues.

city: GuangZhou

first: Zhongshu

last: Tang

address: 54 South Xianlie Road

institute: Sun Yat-sen University

summary: We sutured the left eyelid of one-month-old Macaca Fascicularis. Three months later, their LGN tissues were captured and mRNA sequencing was carried out to study the effect of monocular deprivation on gene expression in Macaca Fascicularis.

overall_design: mRNA profiles of Macaca Fascicularis with monocular visual deprivation and non-treatment

first: Jianhua

last: Yan

first: Wei

last: Chen

first: Dongyue

last: Lin


title: Transcriptome and translatome of ribosomal protein-deficient human cells

status: Public on Jan 27 2022

city: Guangzhou

first: Yizhao

last: Luan

address: Xianlie South Rd. 54, Yuexiu Dist

department: Zhongshan Ophthalmic Center

institute: Sun Yat-sen university

summary: Human ribosomes are made of around 80 ribosomal proteins (RPs) and four ribosomal RNAs. To explore gene expression regulation by RPs at the transcriptional and translational levels, parallel RNA-seq and Ribo-seq were conducted in A549 cells after knockdown of individual RP.

overall_design: 75 human RPs were knocked-down by specific siRNAs one-by-one in A549 cells, and the RP-deficient cells were subjected to parallel RNA-seq and Ribo-seq. Gene expression in RP-deficient cells was compared with that in the control cells treated by non-targeting siRNAs. In total, we prepared 105 Ribo-seq libraries, with 105 paired RNA-seq libraries, for 78 human RPs as well as 8 control samples, where biological replicates were performed for 16 RPs and for 3 control samples.

first: Jiaqi

last: Yang

first: Zhi

last: Xie


title: Next Generation Sequencing Facilitates Quantitative Analysis of transcriptomes in Multiple Myeloma (MM) cell lines treated with DMSO and Indirubin-3’-monoxime (I3MO)

status: Public on Jan 26 2022

city: Tianjin,China

first: Mu

last: Hao

address: 288 Nanjing Road, Heping District, Tianjin

institute: State Key Laboratory of Experimental Hematology, Chinese Academy of Medical Sciences & Peking Union Medical College

summary: To determine what signaling pathways are affected by I3MO in MM cells, 5 MM cell lines including ANBL6, ANBL6 BR, ARP1, RPMI-8226, and U266, were cultured with DMSO or 5/10µM I3MO for 48 h. Total RNAs of 2 x 10^6  cells for each sample were extracted using the RNeasy Mini Kit (Qiagen). The RNA yield was determined by Nanodrop technology (Thermo Fisher Scientific), and quality was verified on the Agilent 2100 bioanalyzer (Agilent Technologies). cDNA libraries were prepared for sequencing using standard Illumina protocols, followed by sequencing on the NextSeq500 Sequencing System (Illumina). We used gene expression profiling data to determine differential expression of genes in MM cells in culture with DMSO or I3MO.

overall_design: Examination of gene-profiling data in MM cells repsonse to control or I3MO treatment.

first: Zhen

last: Yu

first: Xiaojing

last: Wei

first: Lanting

last: Liu

first: Teng

last: Fang

first: Hao

last: Sun


title: Prior BNT162b vaccination enhances interferon-JAK-STAT regulated antiviral programs in hospitalized COVID-19 patients infected with the SARS-CoV-2 Beta variant

status: Public on Jan 25 2022

city: Bethesda

first: Hye Kyung

last: Lee

address: 8 CENTER DR RM 107

department: National Institute of Diabetes and Digestive and Kidney (NIDDK)

institute: National Institutes of Health (NIH)

summary: SARS-CoV-2 infection activates interferon-controlled signaling pathways and elicits a wide spectrum of immune responses and clinical manifestations in human patients. Here, we investigate the impact of prior vaccination on the innate immune response of hospitalized COVID-19 patients infected with the SARS-CoV-2 Beta variant through RNA sequencing of Peripheral Blood Mononuclear Cells. Four patients had received the first dose of BNT162b about 11 days prior to the onset of COVID-19 symptoms and five patients were unvaccinated. Patients had received dexamethasone treatment. Immune transcriptomes were obtained at days 7-13, 20-32 and 42-60 after first symptomology. RNA-seq revealed an enhanced JAK-STAT-mediated immune transcriptome response at day 10 in vaccinated patients as compared to unvaccinated ones. This increase had subsided by day 35. Expression of the genes encoding the antiviral protein oligoadenylate synthetase (OAS) 1, which is inversely correlated with disease severity, and other key antiviral proteins was increased in the vaccinated group. We also investigated the immune transcriptome in naïve individuals receiving their first dose of BNT162b and identified a gene signature shared with the vaccinated COVID-19 patients. Our study demonstrates that RNA-seq can be used to monitor molecular immune responses elicited by the BNT162b vaccine, both in naïve individuals and in COVID-19 patients, and it provides a biomarker-based approach to systems vaccinology.

overall_design: RNA-seq were performed with peripheral blood mononuclear cells (PBMCs) of COVID-19 patients infected by SARS-CoV-2 Beta varient (Beta) and SARS-CoV-2 naïve vaccinated individuals.

first: Hye

first: Ludwig

last: Knabl


title: Effect of leptin deficiency in Bmal1 knockout mice across different tissues

city: Lausanne

first: Benjamin

last: Weger

state: VD

address: Station 15

department: SV

institute: EPFL

summary: Obesity and liver diseases are associated with the disruption of the circadian clock that orchestrates mammalian physiology to optimize nutrient metabolism and storage. We show here that the activity of the circadian clock regulator BMAL1 is perturbed during liver fibrosis in humans. To understand the impact of BMAL1 perturbation in obesity and liver diseases, we assessed the impact of a high fat diet or leptin deficiency on Bmal1 knockout mice. While Bmal1 knockout mice were prone to obesity, they were protected against insulin resistance, hepatic steatosis, inflammation, and fibrosis. In addition to direct transcriptional regulation of metabolic programs by BMAL1, we show that adaptation disruption of the growth hormone and sex hormone pathways plays a critical role in this protection. Similar endocrine perturbations correlate with the development of liver fibrosis in humans, but were absent in hepatocyte specific Bmal1 knockout mice. This suggestsing that systemic endocrine perturbation associated with circadian disruptionthe disruption of BMAL1 activity is critical for the pathogenesis of metabolic and liver diseases.

overall_design: RNA-Seq from mRNA of mouse liver, sceletal muscle and epididymal white adipose tissue in mice with different genotypes including ob/ob Bmal1 WT, ob/ob Bmal1 KO, wt/wt Bmal1 WT and wt/wt Bmal1 KO.

first: Céline

last: Jouffe

first: Eva

last: Martin

first: Cédric

last: Gobet

first: Aline

last: Charpagne

first: Delphine

last: Morin-Rivron

first: Mojgan

last: Masoodi

first: N

middle: H

last: Uhlenhaut

first: Frédéric

last: Gachon


title: Prognostic value of SPODD1 in esophageal squamous cell carcinoma: a comprehensive study based on bioinformatics and validation

status: Public on Jan 23 2022

city: fuzhou

first: yangfan

last: zhang

address: Fujian Normal University Qishan Campus, College Town, Fuzhou, Fujian Province

institute: FJNU

summary: The expression of SPOCD1 was up-regulated in ESCC tissues compared to those in normal tissues. In the high SPOCD1 expression group, we found apparent mutations in TP53, TTN, and MUC 16 genes, which were 92%, 36%, and 18%, respectively. GO and KEGG enrichment analysis of SPOCD1 and its co-expressed genes demonstrated that it may serve as an ESCC oncogene by regulating the genes expression in the essential functions and pathways of tumorigenesis, such as glycosaminoglycan binding, Cytokine-cytokine receptor interaction, and Ras signaling pathway. Besides, the immune cell infiltration results revealed that SPOCD1 expression was positively correlated with Macrophages M0 and Mast cells activated cells, and negatively correlated with plasma cells and T cells follicular helper cell infiltration. Finally, ESCC patients with high expression of SPOCD1 indicated poor overall survival. The qRT-PCR demonstrated that the SPOCD1 expression in ESCC tissues was significantly higher than adjacent tissues (P < 0.001).

overall_design: We performed RNA-seq on 6 ESCC tumor and 6 adjacent normal tissue samples obtained from 6 individuals using Illumina HiSeq 2500.

first: Zhizhong

last: Lin

first: Lin

last: Chen

first: Tingting

last: Wu

first: Yiping

last: Zhang

first: Xinyi

last: Huang

first: Yuanmei

first: Junqiang

first: Yuanji

last: Xu


title: Diurnal profiling of mouse liver of hepatocyte specific BMAL1 KO mice (Bmal1 HepKO)

first: Benjamin

summary: Obesity and liver diseases are associated with the disruption of the circadian clock that orchestrates mammalian physiology to optimize nutrient metabolism and storage. We show here that the activity of the circadian clock regulator BMAL1 is perturbed during liver fibrosis in humans. To understand the impact of BMAL1 perturbation in obesity and liver diseases, we assessed the impact of a high fat diet or leptin deficiency on Bmal1 knockout mice. While Bmal1 knockout mice were prone to obesity, they were protected against insulin resistance, hepatic steatosis, inflammation, and fibrosis. In addition to direct transcriptional regulation of metabolic programs by BMAL1, we show that adaptation of the growth hormone and sex hormone pathways plays a critical role in this protection. Similar endocrine perturbations correlate with the development of liver fibrosis in humans, suggesting that endocrine perturbation associated with circadian disruption is critical for the pathogenesis of metabolic and liver diseases.

overall_design: RNA-Seq from mouse liver mRNA of Alb::Cre_+/0 Bmal1_loxP/loxP (Bmal1 HepKO) and Alb::Cre_0/0 Bmal1_loxP/loxP (Bmal1 HepWT) genotypes

first: Céline

first: Meltem


title: Disruption of the circadian clock component BMAL1 elicits an endocrine adaption impacting on insulin sensitivity and liver disease.

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

overall_design: Refer to individual Series


title: small-RNA sequencing of sEV isolated from plasma of astronauts

status: Public on Jan 12 2022

city: Yerevan

first: Arsen

last: Arakelyan

state: Yerevan

address: 7 Hasratyan St.

department: Bioinformatics

country: Armenia

institute: Institute of Molecular Biology NAS RA

type: Non-coding RNA profiling by high throughput sequencing

summary: We sought to determine whether the spaceflight environment can induce alterations in small extracellular vesicles (sEV) smallRNA content and their utility as biomarkers. Using small RNA sequencing (sRNAseq), we evaluated the impact of the spaceflight environment on sEV miRNA content in peripheral blood (PB) plasma of 14 astronauts, who flew STS missions between 1998-2001. Samples were collected at three-time points:10 days before the launch (L-10), the day of return (R-0), and three days post-landing (R+3).

overall_design: Comparison of small RNA expression from blood sEVs at 3 time points.

first: David

last: Goukassian

first: Sankar

last: Addya

first: Mattew

last: Coleman

first: Venkata

middle: N

last: Garikipati

first: Paul

last: Mills


title: A miR-125 / Sirtuin-7 pathway drives pro-calcific potential of myeloid cells in diabetic vascular disease

status: Public on Jan 15 2022

city: Padova

first: Giulio

last: Ceolotto

address: Via Orus 2B

department: Medicine

country: Italy

institute: University of Padova

summary:
Aims/hypothesis. Ectopic calcification is a typical feature of diabetic vascular disease and resembles an accelerated aging phenotype. We previously found an excess of myeloid calcifying cells (MCCs) in diabetic patients. We herein examined molecular and cellular pathways linking atherosclerotic calcification with calcification by myeloid cells in the diabetic milieu.
Methods. We first examined the associations among coronary calcification, MCC levels, and mononuclear cell gene expression in a cross-sectional study of 87 type 2 diabetic patients undergoing elective coronary angiography. Then, we undertook in vitro studies on mesenchymal stem cells (MSCs) and on the THP-1 myeloid cells line to verify the causal relationships of the observed associations.
Results. Coronary calcification was associated with 2.8-times higher MCC levels (p=0.037) and 50% elevated expression of the osteogenic gene RUNX2 in mononuclear cells, whereas expression of Sirtuin-7 (SIRT7) was inversely correlated with calcification. In standard differentiation assays of MSCs, SIRT7 knockdown activated the osteogenic program and worsened calcification, especially in the presence of high (20 mM) glucose. In the monocytic cell line THP-1, SIRT7 downregulation drove a pro-calcific phenotype, whereas SIRT7 overexpression prevented high-glucose induced calcification. Through the JAK/STAT pathway, high glucose induced miR-125b-5p, which in turn targeted SIRT7 in myeloid cells and was directly associated with coronary calcification.
Conclusions/interpretation. We describe a new pathway elicited by high glucose trough the JAK/STAT cascade, involving regulation of SIRT7 by mir-125b-5p driving calcification by myeloid cells. This pathway is associated with coronary calcification in diabetic patients and may be a target to tackle diabetic vascular disease.

overall_design: mRNA profile on osteo-THP-1 cultured in high (20mM) glucose and normal (5 mM) glucose


title: A High-Resolution Route Map Reveals Distinct Stages of Chondrocyte Dedifferentiation

status: Public on Jan 20 2022

city: Hangzhou

first: Yishan

address: #866 Yuhangtang Road

institute: Zhejiang University


title: A High-Resolution Route Map Reveals Distinct Stages of Chondrocyte Dedifferentiation (RNA-Seq)

summary:
Objectives: Articular cartilage damage has become a universal health burden. Despite the recent progresses in cell-based cartilage regeneration, chondrocyte dedifferentiation has compromised the clinical outcomes, which is frequently seen in chondrocyte expansion and osteoarthritis, involving functional phenotype loss. However, its concept remains elusive with unknown intermediate process and mechanisms. Here we demonstrated a time-lapse atlas of chondrocyte dedifferentiation, to provide molecular details and informative biomarkers for clinical chondrocyte evaluation.
Methods:  Single-cell RNA sequencing (scRNA-seq) was employed to dissect the chondrocyte dedifferentiation and identify distinct cellular subpopulations. To validate the findings, live-cell metabolic assay, high-resolution imaging and ¡°assay for transposase-accessible chromatin with high throughput sequencing¡± (ATAC-seq) were conducted. Using a chemical inhibitor BTB06584 affecting on mitochondrial F1F0ATPase, we revealed the recovery potential of early and late dedifferentiated chondrocytes.
Results:Our findings shape a biphasic model consist of early and late dedifferentiation stages. Early dedifferentiated chondrocytes uniquely obtained a transient glycolytic phenotype with an activation of metabolic and anti-oxidant genes; late dedifferentiated chondrocytes exhibited ultrastructural changes including mitochondrion damages and stress-associated chromatin remodeling. Using a chemical inhibitor BTB06584, we revealed that early and late dedifferentiated chondrocytes possessed distinguished recovery potential from functional phenotype loss. BTB06584 treatment ameliorated early phenotype loss through inhibiting MAPK pathway. Notably, this two-stage transition was validated in human chondrocyte culture. An image-based approach was established for clinical utilization, to efficiently predict chondrocytes plasticity with stage-specific biomarkers.
Conclusion: Thus this study lays a foundation for future clinical chondrocyte quality regulation and provides insights for deeper understanding of chondrocyte dedifferentiation.

overall_design: We employed scRNA-seq of serial-passaged murine chondrocytes (P0, 2, 4 and 8) to reconstruct a time-lapse atlas of chondrocyte dedifferentiation.

first: Yeke

last: Yu


title: Systems medicine dissection of chromosome 1q amplification reveals a novel PBX1-FOXM1 axis for targeted therapy in multiple myeloma

status: Public on Jan 16 2022

city: London

first: Nikolaos

last: Trasanidis

address: Hammersmith Campus, Commonwealth Building, 4th Floor,, Du Cane Road, Imperial College London

department: Department of Immunology and Inflammation,

institute: Imperial College London

summary: Here we report the use of high-throughput sequencing technologies (RNA-seq, ChIP-seq) to identify the molecular programme of PBX1 and FOXM1 in multiple myeloma cells (MM1S, U266 cell lines). We performed Chromatin Immunoprecipitation followed by sequencing (ChIP-seq) against PBX1 in MM1S and U266 cells (n=2). In addition, we identifed the transcriptome of PBX1-depleted and FOXM1-depleted myeloma cells 3 days after transduction with shRNA-expressing lentiviral vectors.  Molecular characterization revealed PBX1 as a novel epigenetic regulator of myeloma cell survival and proliferation. PBX1 directly and unilaterally controls the FOXM1 transcriptional programme and, together,they regulate the high-risk transcriptional signature of chr1q-amplified cells. Pharmacological inhibition of the unified PBX1-FOXM1 axis with thiostrepton showed selectivity against chr1q-amplified MM. Altogether, these data reveal PBX1-FOXM1 axis as a novel therapeutic avenue against chr1q-amplified MM.

overall_design: Identification of the transcriptional and epigenomic programmes of PBX1 and FOXM1 in MM1S and U266 multiple myeloma cells using ChIP-seq and RNA-seq.

first: Anastasios

last: Karadimitris


title: methyl-Seq of Pediatric ARDS Nasal and Bronchial Brushings

status: Public on Jan 06 2022

city: Cincinnati

first: Brian

middle: Michael

last: Varisco

state: OH

address: 3333 Burnet Avenue, MLC 7006

department: Critical Care Medicine

institute: Cincinnati Children's Hospital Medical Center

summary: The objective of this study was to identify differences in the nasal methylome of patients with Pediatric ARDS (PARDS) compared to controls and to observe how this might change over time. We found two different methylomic patterns.  Subgroup 1 was comprised of entirely of PARDS subjects, and Subgroup 2 contained both control and PARDS subject.  Subgroup 1was characterized by hypomethylation of genes related to cell adhesion and hypermethylation of cell metabolism-related genes. Over time, the methylation pattern of PARDS subjects changed, but the pattern of control subjects was stable. Five concurrent bronchial and nasal specimens were obtained showing very few differences in methylation between these two collection sites.

overall_design: Comparison of PARDS and Control methylation

first: James

last: Williams


title: Tfap2b specifies an embryonic melanocyte stem cell population that retains adult multi-fate potential

status: Public on Jan 11 2022

city: Edinburgh

first: E. Elizabeth

last: Patton

address: Institute of Genetics and Cancer, Crewe Road South

institute: MRC Human Genetics Unit, University of Edinburgh

summary: Melanocytes, our pigment producing cells, originate from neural crest-derived progenitors during embryogenesis and from multiple stem cell niches in adult tissues. Although pigmentation traits are known risk-factors for melanoma, we lack lineage markers with which to identify melanocyte stem cell populations and study their function. Here, by combining live-imaging, scRNA-seq and chemical-genetics in zebrafish, we identify the transcription factor Tfap2b as a functional marker for the melanocyte stem cell (MSC) population that resides at the dorsal root ganglia site. Tfap2b is required for only a few late-stage embryonic melanocytes, and instead is essential for MSC-dependent melanocyte regeneration. Our lineage-tracing data reveal that tfap2b-expressing MSCs have multi-fate potential, and are the cell-of-origin for a discrete number of embryonic melanocytes, large patches of adult melanocytes, and two other pigment cell types; iridophores and xanthophores. Hence, Tfap2b confers MSC identity, and thereby distinguishes MSCs from other neural crest and pigment cell lineages.

overall_design: scRNA-seq (10x Genomics) of mitfa:GFP and crestin:mCherry cells sorted from either untreated or ErbBi-treated 24hpf old embryos. 1 replicate per treatment

first: Alessandro

last: Brombin

first: Tamir

last: Chandra

first: E


title: Adipocyte-Specific Ablation Of PU.1 Promotes Energy Expenditure and Ameliorates Metabolic Syndrome In Aging Mice

city: Houston

first: Scott

middle: Andrew

last: Ochsner

state: TX

address: One Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

summary: Here, we investigated the role of adipocyte PU.1 in the development of age-associated metabolic syndrome. We generated mice with adipocyte specific PU.1 knockout, assessed metabolic changes in young and aged PU.1fl/fl (control) and AdipoqCre PU.1fl/fl(aPU.1KO) mice, including body weight, body composition, energy expenditure and glucose homeostasis. We also performed transcriptional analyses using RNA-Sequencing of adipocytes from these mice.

overall_design: Sequencing was performed on adipocyte samples from PU.1 fl/fl (control) and PU.1 fl/fl-AdipoqCre (PU.1 knockout) mice, with 3 replicates in each group.

first: Keyun

last: Chen

first: Alejandra

last: De Angulo

first: Xin

last: Guo

first: Aditya

last: More

first: Eduardo

last: Lopez

last: Saul

first: Weijun

last: Pang

first: Yuxiang

last: Sun

first: Neil

last: McKenna

first: Qiang

last: Tong


title: Heart profiling in HMDP (high-fat/high-sucrose diet)

city: Los Angeles

first: Calvin

last: Pan

address: 675 Charles Young Dr South

institute: UCLA

summary: Identify genes in the heart whose expression is under genetic regulation in the Hybrid Mouse Diversity Panel (HMDP). The HMDP comprises classical inbred and recombinant inbred wild type mice. The TPM values of genes were used for genome wide association. These data are used to identify candidate genes at loci associated with cardiovascular traits.

overall_design: GWAS for gene expression in heart in inbred strains fed chow diet for 8 weeks followed by high-fat/high-sucrose diet for 8 weeks

first: Aldons

last: Lusis

first: Yang

last: Cao


title: Precise Transcript Reconstruction with End-Guided Assembly

status: Public on Jan 08 2022

city: Wageningen

first: Michael

last: Nodine

state: Gelderland

address: Radix West

department: Plant Sciences

institute: Wageningen University & Research

summary: Accurate annotation of transcript isoforms is crucial to understand gene functions, but automated methods for reconstructing full-length transcripts from RNA sequencing (RNA-seq) data remain imprecise. We developed Bookend, a software package for transcript assembly that incorporates data from different RNA-seq techniques, with a focus on identifying and utilizing RNA 5′ and 3′ ends. Through end-guided assembly with Bookend we demonstrate that correct modeling of transcript start and end sites is essential for precise transcript assembly. Furthermore, we discovered that utilization of end-labeled reads present in full-length single-cell RNA-seq (scRNA-seq) datasets dramatically improves the precision of transcript assembly in single cells. Finally, we show that hybrid assembly across short-read, long-read, and end-capture RNA-seq datasets from Arabidopsis, as well as meta-assembly of RNA-seq from single mouse embryonic stem cells (mESCs) can produce end-to-end transcript annotations of comparable quality to reference annotations in these model organisms.

overall_design: Two PacBio Iso-seq libraries were generated each using 10 µg of total RNA from Arabidopsis inflorescences containing unopened floral buds. Total RNA was extracted with TRIzol following the method described in (Schon et al. 2018. Genome Research)  to yield two biological replicates with an RNA integrity number (RIN) of 9.0 and 9.2, respectively. SMRTbell libraries were constructed by the Vienna BioCenter Core Facilities (VBCF) and sequenced on a Sequel SMRT Cell 1M.

last: Schon


title: The difference between diarrhea piglets and normal piglets

status: Public on Jan 03 2022

city: Changsha

first: Yiwen

last: He

address: num.36 Lu shan road, Yuelu district, Changsha, China

institute: Hunan normal university

summary: Sixty crossbred piglets (Duroc*Landrace*Yorkshire) weaned at the age of 21 days were maintained for one week and had free access to feed and water. During this week, all the piglets were scored for the severity of diarrhea.   Diarrhea index was scored as follows: 1= hard feces; 2= no scours, feces of normal consistency; 3= mild scours, soft, partially formed feces; 4= moderate scours, loose, semi-liquid feces; 5= watery feces; as previously did   Those piglets with a score of 4 or 5 for three continuous days were designated as diarrhea piglets, while those piglets with a score of 1 or 2 for three continuous days were designated as normal piglets..

first: Xihong

last: Zhou


title: A purine metabolic checkpoint that prevents autoimmunity and autoinflammation (Dendritic cell RNA Seq dataset)

status: Public on Jan 04 2022

city: Cambridge

first: Gavin

last: Sewell

state: Cambridgeshire

address: Puddicombe Way

department: Jeffrey Cheah Biomedical Centre, University of Cambridge

institute: Cambridge Institute of Therapeutic Immunology and Infectious Disease

summary: Mutations resulting in loss of FAMIN (C13orf31) cause systemic juvenile idiopathic arthritis and very early onset inflammatory bowel disease, while a common I254V substitution increases susceptibility to leprosy and Crohn’s disease. In this study, we compare mRNA transcriptional profiles of bone marrow-derived dendritic cells (DCs) from mice genetically engineered to express Faminp.254I (non-risk), Faminp.254V (risk variant) and Faminp.284R (mutant) at their endogenous loci. We also compare BMDCs from mice lacking FAMIN expression -/- (knockout, KO) with FAMIN+/+ (wild type, WT) mice.

overall_design: BMDCs were cultured from Faminp.254I (n=5), Faminp.254V (n=6) and Faminp.284R (n=5) mice, and from mFAMIN+/+ (n=4) with mFAMIN-/- (n=4) mice, cDC1 subsets isolated and stimulated with LPS, and transcriptional profiles compared.

middle: W

first: Arthur

last: Kaser


title: Single-nucleus RNA sequencing analysis of normal-appearing brains from RRMS and SPMS patients

city: La Jolla

first: Yasuyuki

last: Kihara

state: California

address: 10901 N Torrey Pines Rd

institute: Sanford Burnham Prebys Medical Discovery Institute

summary: snRNA-seq reveals that normal-appearing brain regions from RRMS and SPMS patients have divergent cell type-specific gene expression profiles, with clinical ramifications for approved sphingosine 1-phosphate (S1P) receptor modulators.

overall_design: Post-mortem prefrontal cortices (BA10) from donors who suffered from RRMS or SPMS were cryo-sectioned at 300 µm and were processed for nuclei isolation. Single-nucleus capture (target capture of 5,000 nuclei per sample) and library preparation was conducted using Chromium Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3 (10x Genomics) and Chromium Single Cell B Chip Kit (10X Genomics) according to the manufacturer's instruction. Single-nucleus libraries were sequenced on the Illumina NovaSeq 6000 machine at GENEWIZ, Inc. Raw FASTQ files were input into the cellranger count pipeline (Cell Ranger V3.0.2, 10x Genomics) to align reads to the GRCh38 human genome.

first: Kihara

last: Yasuyuki

first: Zhu

last: Yunjiao


title: Integrated Genomic Analysis of Genes encoding ATP-Dependent Chromatin Remodelers Identifies CHD7 as a Potential Target for Colorectal Cancer Therapy

status: Public on Jan 01 2022

city: Tianjin

first: Chenghao

last: Xuan

address: 22 Qixiangtai Road

institute: Tianjin Medical University

summary: To decipher how CHD7 knockdown affects the growth of colorectal cancer cells, we undertook an unbiased genomic approach to define the transcriptional program controlled by CHD7 in RKO cells.

overall_design: Examination of gene expression changes in CHD7 knockdown and control RKO cells.

first: Xingyan

last: Zhang


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Ahi1-/- mouse embryonic fibroblasts cells Transcriptomes

city: Suzhou

first: Hongguang

address: Renai load 199

institute: Soochow University

summary: We report the application of RNA sequencing technology for high-throughput profiling of gene expression in mammalian cells. By  sequencing from mouse embryonic fibroblasts RNA, we generated genome-wide gene expression maps of mouse embryonic fibroblasts cells. We found a significant difference of relatived gene in Ahi1+/+and Ahi1-/- cells in the basal state. These findings help to understand more functions and roles of the Ahi1 gene.

overall_design: Mouse embryonic fibroblasts cell mRNA profiles of  wild type (WT) and Ahi1-/- mice

first: Zheng

last: Hui

first: Xun

last: Xingshun

first: Zhang

last: Hongguang

first: Wang

last: Bin


title: Single-cell RNA sequencing atlas from a bivalve larva enhances classical cell lineage studies

status: Public on Jan 02 2022

city: Vienna

first: David

middle: Andrés

last: Salamanca-Díaz

address: Djerassiplatz 1

country: Austria

institute: University of Vienna

summary: Here, we report on the gene expression profile of individual cells of the trochophore larva of the invasive freshwater bivalve Dreissena rostriformis as inferred from single cell RNA sequencing. We generated transcriptomes of 632 individual cells and identified seven transcriptionally distinct cell populations. Developmental trajectory analyses identify cell populations that, for example, share an ectodermal origin such as the nervous system, the shell field, and the prototroch. To annotate these cell populations, we examined ontology terms from the gene sets that characterize each individual cluster. These were compared to gene expression data previously reported from other lophotrochozoans. Genes expected to be specific to certain tissues, such as Hox1 (in the shell field), Caveolin (in prototrochal cells), or FoxJ (in other cillia-bearing cells) provide evidence that the recovered cell populations contribute to various distinct tissues and organs known from morphological studies. This dataset provides the first molecular atlas of gene expression underlying bivalve organogenesis and generates an important framework for future comparative studies into cell and tissue type development in Mollusca and Metazoa as a whole.

overall_design: Whole organism single-cell RNAseq datasets using the 10X genomics platform on D. rostriformis trochophore larval stages 13-15 hours post fertilization

first: D

first: S

last: Schulreich

first: A

last: Cole

last: Wanninger


title: RNA transcriptomics of healthy and PI-IBS colonic biopsies

status: Public on Dec 31 2021

city: Rochester

first: Asha

last: Nair

address: 200 1ST ST SW

institute: Mayo Clinic

summary: A subset of post-infection irritable bowel syndrome (PI-IBS) patients have elevated, or high fecal proteolytic activity (PA). Fecal PA has been shown to correlate with increased symptom severity as well as lower quality of life scores, increased fecal output and increased intestinal permeability. To address the underlying mechanisms of barrier disruption as a consequence of high fecal PA, colonic biopsies were collected from healthy individuals PI-IBS patients (n=11). Individuals diagnosed with PI-IBS were further divided in to 2 subgroups, high PA and low PA as defined by the PA in matched fecal samples. RNA was extracted from the biopsies for bulk RNA sequencing to understand transcriptional differences between healthy and high PA PI-IBS patients as well as high PA and Low PA PI-IBS patients.

overall_design: Colonic biopsies were collected from healthy individuals (5) and PI-IBS patients (n=11). Healthy individuals provide a baseline transcriptomic profile of a normal colon and therefore used as a basis for understanding changes at the transcriptomic level in high PA PI-IBS patients. Additionally, low PA PI-IBS patients were included to understand transcriptional differences between high and low PA within the disease state.

first: Adam

last: Edwinson

first: Lu

last: Yang

first: Stephanie

last: Peters

first: Nikita

last: Hanning

first: Patricio

last: Jeraldo

first: Pratik

last: Jagtap

first: Joshua

middle: B

last: Simpson

first: Tzu-Yi

first: Praveen

last: Kumar

first: Subina

last: Mehta

first: Margaret

last: Breen-Lyles

first: Lakshmikanth

last: Chikkamenahalli

first: Rondell

middle: P

last: Graham

first: Benedicte

last: De Winter

first: Robin

last: Patel

first: Surendra

last: Dasari

first: Purna

last: Kashyap

first: Timothy

last: Griffin

first: Jun

last: Chen

first: Gianrico

last: Farrugia

first: Matthew

last: Redinbo

first: Madhusudan

last: Grover


title: Pulmonary interstitial macrophages are required to mediate the pro-tumorigenic effects of IL-9

city: Indianapolis

first: Mark

last: Kaplan

state: IN

address: 635 Barnhill Dr. MS 420

department: Microbiology and Immunology

institute: Indiana University

summary: We demonstrate that deficiency of IL-9 signaling inhibits lung tumor growth in multiple models. In defining the IL-9-responsive cells in the lung tumor models, we found IL-9 regulates lung heterogeneity by inhibiting alveolar macrophage and promoting the expansion of both CD11c+ and CD11c- interstitial macrophage populations. Interstitial macrophages are a critical IL-9-responsive population that is required to promote lung tumor growth. Mechanistically, the IL-9/macrophage axis requires arginase1 (Arg1) to mediate tumor growth. Adoptive transfer of Arg1+ but not Arg1- lung macrophages to Il9r-/- mice dramatically increases the tumor growth. In parallel, the elevated expression of IL-9R and Arg1 in human tumor associated macrophages is correlated with poor prognosis among lung cancer patients. Moreover, targeting IL-9 signaling in lung macrophages limited lung tumor growth.

overall_design: Exam the gene expression of interstitial macrophages in tumor bearing WT and Il9r knock-out mice

first: Yongyao

last: Fu

first: Hongyu

last: Gao


title: RNA sequencing of L4-L6 mouse Dorsal Root Ganglia 3 days post sciatic nerve crush and naive following 10 days of Indole-3-propionic acid treatment

city: Miami

first: Matt

middle: C

last: Danzi

state: FL

address: 1095 NW 14th Terrace, Lois Pope LIFE Center 4-26

institute: University of Miami

summary:
Purpose: compare the response of DRG neurons to indole-3-propionic acid treatment before and after sciatic nerve injury
Results: we found that IPA induced transcription changes before and after injury inside the DRG tissue. In particular expression of immune system related genes

overall_design: Method: RNAseq from sciatic mouse L4-L6 DRG tissue after the following treatment: a) 10 days of 20 mg/kg indole-3-propionic acid (IPA in PBS) or vehicle (PBS) daily gavage b) 10 days of 20 mg/kg/ IPA (in PBS) or vehicle (PBS) daily gavage followed by sciatic nerve crush injury and 3 additional days of IPA treatment. Pool of sciatic DRGs from 2 mice were used for each RNAseq sample.DRG were collected in RNase later reagent, and crushed with RNase free micropestle for RNA extraction. Biological triplicates of each condition were generated.

first: Elisabeth

last: Serger

first: Simone

last: Di Giovanni


title: Transcriptomic insight into viviparous growth in water lily

city: Urumqi

first: Zhang

middle: Qing

last: hua

state: Xinjiang

address: Liudao Bay Street

institute: The Second Affiliated Hospital of Xinjiang Medical University

summary: Here We revealed the complex mechanism of viviparity in water lily. The transcriptomic signatures identified in this pathway are important basis for future breeding and research of viviparity in water lily and other plant species.

sample_organism:
Nymphaea colorata
Nymphaea micrantha

platform_organism:
Nymphaea colorata
Nymphaea micrantha

overall_design: The plants of two Nymphaea species N. micrantha (X) and N. colorata (L)

first: Qun

last: Su

first: Hong-Yan

last: Wang

first: Min

last: Tian

first: Xian-Min

last: Li

first: Chun-Niu

first: Zhan-Wen

last: Huang

first: Zhao-Yang

last: Bu

first: Jia-shi

last: Lu


title: IL-36 and IL-17A Cooperatively Induce a Psoriasis-like Gene Expression Response in Human Keratinocytes

city: New York

first: James

last: Krueger

address: 1230 York Avenue

department: Center for Clinical and Translational Science

institute: The Rockefeller University

summary: In this study we tested interactions between IL-36 and IL-17A in human keratinocytes. 24 hours of IL-36 stimulation in keratinocytes promoted IL-36, IL-17C, and characteristic psoriasis-related molecule expressions in normal human epidermal keratinocytes in dose-dependent manners as measured by mRNA and protein quantification.

overall_design: 12 cultured samples of  human keratinocytes stimulated with IL-36 and IL-17 family cytokines, as single cytokines and also as a combination were evaluated by gene expression profiling with Affymetrix U133 2.0Plus arrays

middle: G

first: Shunsuke

last: Miura

first: Sandra

last: Garcet


title: Polarizing Cytokines and Staphylococcus aureus Cooperatively Induce Atopic Dermatitis-Like Transcriptomes

summary: Background: Atopic dermatitis (AD) is a common inflammatory skin disease with a TH2 immune polarity and is often colonized with Staphylococcus aureus. Despite recent advances in understanding Staphylococcus species infection and the impact of polar TH cytokines on the skin, the interactions between these factors in AD pathology are poorly understood.  Methods: AD-related key immune biomarkers were measured by quantitative real-time PCR in human keratinocytes exposed heat-killed S. epidermidis or S. aureus with/without polar T-cell derived cytokines such as IFN-γ (TH1), IL-4/IL-13 (TH2), and IL-22 (TH22). Further analysis was performed by RNA-sequencing to define broader responses in both Staphylococcus species and polar cytokines. The similarity of gene expression patterns in AD skin lesions and stimulated keratinocytes was evaluated by gene-set variation analysis (GSVA).  Results: Gene expression analysis exhibited distinct immune responses in keratinocytes depending on individual bacterial or polar cytokine exposure. Besides, numerous genes were synergistically upregulated by the combination exposure of bacteria and polar TH cytokines. Moreover, GSVA revealed that combined exposure of S. aureus and IL-4 + IL-13 exhibited significantly higher correlations with a genomic signature of AD skin lesions than their single exposure or combinations of other polar TH cytokines.  Conclusions: Our findings provide novel insights into AD-related transcriptional activation and illustrate a potentially novel pathogenic function of S. aureus and IL-4/IL-13 interactions in AD.

overall_design: human keratinocyte mRNA profiles exposed heat-killed Staphylococcus epidermidis or Staphylococcus aureus with/without polarizing T-cell derived cytokines: IFN-γ, IL-4, IL-13, and IL-22.

first: Kazuhiko

last: Yamamura

first: Mika


title: Mapping developmental paths of monkey primordial germ-like cell differentiation from pluripotent stem cells by single cell RNA sequencing analysis

city: Kunming

first: Jian

last: Liu

address: Zhiyuan Road,Chenggong

institute: Institute of Primate Translational Medicine, KUST

summary:
The induction of the primordial germ-like cells (PGCLCs) from primate pluripotent stem cells (PSCs)provides a powerful system to study the cellular and molecular mechanism underlying germline specification, which are difficult to study in vivo. However a comprehensive single cell RNA sequencing(scRNA-seq) analysis of the developmental trajectory of PGCLCs differentiation that also dissects the required niche has not been achieved.
Here, we applied the embryoid body (EB) differentiation system to induce PGCLCs specification from male and female monkey naïve-state PSCs and then performed high throughput scRNA-seq analysis of approximately 40000 of naïve cells and cells within EBs.
We found that EBs provided a niche for PGCLCs differentiation by secreting growth factors critical for PGCLCs specification, such as BPM2, BMP4 and WNT3. Moreover, the developmental trajectory of PGCLCs was reconstituted and gene expression dynamics were revealed. Our study outlines the roadmap of PGCLCs specification from PSCs and provides insights that will improve the differentiation efficiency of PGCLCs from PSCs.

sample_organism:
Macaca fascicularis
Macaca mulatta

platform_organism:
Macaca fascicularis
Macaca mulatta

overall_design: Six samples (female and male 4i-state cells, and day 2 and day 4 EBs)

first: Tao

last: Tan


title: scRNA-seq reveals tumor microenvironment remodeling induced by local intervention-based immunotherapy

status: Public on Dec 29 2021

city: Norman

first: KAILI

last: LIU

state: Oklahoma

address: 173 Felgar St

institute: The University of Oklahoma

summary: Laser immunotherapy (LIT) combines local photothermal therapy (PTT), to disrupt tumor homeostasis and release tumor antigens, and an intratumorally administered immunostimulant, N-dihydrogalactochitosan (GC), to induce antitumor immune responses. We performed single-cell RNA sequencing on tumor-infiltrating leukocytes of MMTV-PyMT mouse mammary tumors to determine LIT-induced myeloid and lymphoid compartment remodeling.  Analysis of 49,380 single cell transcriptomes from different treatment groups revealed proinflammatory IFNa, IFNg, and TNFa cytokine signaling pathways were enriched in both lymphoid and myeloid cells isolated from LIT-treated tumors. Interestingly, the CD4+ and CD8+ T cells in LIT and GC treated tumors resided in an activated state while immune cells in untreated and PTT-treated tumors remained in a neutral/resting state. Additionally, monocytes recruited into the LIT-treated tumors were driven towards proinflammatory M1-like macrophage phenotypes or monocyte-derived dendritic cells. Our results reveal that LIT prompts immunological remodeling of the tumor microenvironment by initiating broad proinflammatory responses to drive antitumor immunity.

overall_design: transcriptional profiling of CTRL, PTT, GC, LIT treated CD45+ tumor infiltrating cells performed by single-cell RNA sequencing

first: Ashley

last: Hoover

first: Kaili

first: Christa

middle: I

last: DeVette

first: Jason

last: Krawic

first: Connor

last: West

first: Delaney

last: Medcalf

first: Alana

last: Welm

first: Xiao-Hong

last: Sun

first: William

last: Hildebrand

first: Wei

last: Chen


title: Phosphorylation of Ribosomal Protein S6 differentially affects mRNA translation based on ORF length

status: Public on Dec 22 2021

city: Heidelberg

first: Jonathan

last: Bohlen

address: Im Neuenheimer Feld 581

institute: DKFZ

summary: Phosphorylation of Ribosomal Protein S6 (RPS6) was the first post-translational modification of the ribosome to be identified and is a commonly-used readout for mTORC1 activity. Although the cellular and organismal functions of RPS6 phosphorylation are known, its molecular consequences on translation are less well understood. Here we use selective ribosome footprinting to analyze the location of ribosomes containing phosphorylated RPS6 on endogenous mRNAs in cells. We find that RPS6 becomes progressively dephosphorylated on ribosomes as they translate an mRNA. As a consequence, average RPS6 phosphorylation is higher on mRNAs with short coding sequences (CDSs) compared to mRNAs with long CDSs. Loss of RPS6 phosphorylation causes a correspondingly larger drop in translation efficiency of mRNAs with short CDSs than long CDSs. Interestingly, mRNAs with 5’ TOP motifs are translated well also in the absence of RPS6 phosphorylation despite short CDS lengths, suggesting they are translated via a different mode. In sum this provides a dynamic view of RPS6 phosphorylation on ribosomes as they translate mRNAs and the functional consequence on translation.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: We develop modification selective ribosome footprinting to determine the rate of RPS6 phosphorylation of translating ribosomes across the translatome. This allows us to gain mechanistic understanding of the role of RPS6 phosphorylation in ribosome function.

first: Aurelio

last: Teleman

first: Mykola

last: Roiuk


title: Identification of AIA_H related genes and BHGZD therapeutic effect related genes. [array]

status: Public on Dec 03 2021

city: Beijing

first: Weijie

last: LI

address: Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, No. 16, Nanxiaojie, Dongzhimennei, Beijing 100700, China

summary: To obtain AIA_H related genes [the significant differentially expressed genes (DEGs) of AIA_H model group vs. Normal control group] and BHGZD therapeutic effect related genes [DEGs of BHGZD treatment group vs. AIA_H model group], the microarray analysis was carried out.

overall_design: 9 rat samples were randomly divided into three groups (3 per group): (1) Normal control group (Con); (2) AIA-H model  group (AIA_H); (3) BHGZD treatment group (AIA_H_BHGZD).

last: Li


title: Environmental dependent heterosis and transgressive gene expression in reciprocal hybrids between the channel catfish Ictalurus punctatus and the blue catfish Ictalurus furcatus

status: Public on Jan 05 2022

city: Auburn University

first: Xu

last: Wang

state: AL

address: 273 CASIC Building, Auburn Research Park, 559 Devall Dr

department: Pathobiology, College of Veterinary Medicine

institute: Auburn University

summary: The hybrid between female channel catfish (Ictalurus punctatus) and male blue catfish (Ictalurus furcatus) is superior in feed conversion, disease resistance, carcass yield, and harvestability compared to both parental species. However, heterosis and heterobeltiosis only occur in pond culture, and channel catfish grow much faster than the other genetic types in small culture units. This environment-dependent heterosis is intriguing, but the underlying genetic mechanisms are not well understood. In this study, phenotypic characterization and transcriptomic analyses were performed in the channel catfish, blue catfish, and their reciprocal F1s reared in tanks. The results showed that the channel catfish is superior in growth-related morphometrics, presumably due to significantly lower innate immune function, as investigated by reduced lysozyme activity and alternative complement activity. RNA-seq analysis revealed that genes involved in fatty acid metabolism/transport are significantly upregulated in channel catfish compared to blue catfish and hybrids, which also contributes to the growth phenotype. Interestingly, hybrids have a 40-80% elevation in blood glucose than the parental species, which can be explained by a phenomenon called transgressive expression (overexpression/underexpression in F1s than the parental species). A total of 1,140 transgressive genes were identified in F1 hybrids, indicating that 8.5% of the transcriptome displayed transgressive expression. Transgressive genes upregulated in F1s are enriched for glycan degradation function, directly related to the increase in blood glucose level. This study is the first to explore molecular mechanisms of environment-dependent hetero-sis/heterobeltiosis in a vertebrate species and sheds light on the regulation and evolution of heterosis vs. hybrid incompatibility.

sample_organism: Ictalurus punctatus x Ictalurus furcatus

overall_design: Profile of transcriptome-wide gene expression levels in the liver in the channel catfish, the blue catfish, and their reciprocal F1 hybrids.


title: Gene expression profile upon CASP4 knockdown in oncogene-induced senescence

status: Public on Dec 11 2021

city: Santander

first: Juan Carlos

last: Acosta

state: Cantabria

address: C. Albert Einstein, 22

department: Institute of Biology and Biotechnology of Cantabria (IBBTEC)

country: Spain

institute: Consejo Superior de Investigaciones Cientificas (CSIC)

summary: In the present study, we analyze the effect of knocking down CASP4 in IMR90 ER:RAS primary lung cells five and eight days after the addition of  4-Hydroxytamoxifen by analyzing the transcriptome using Ampliseq RNA sequencing. We observed that caspase-4 targeting dampens the mRNA expression induction of critical senescence-associated secretory phenotype factors while increasing the transcription of  E2F target genes and genes related to the G2/M checkpoint.

overall_design: IMR90 ER:STOP or ER:RAS cells were transfected with non-targeting pool (NTP) siRNAs or a pool of 4 different sequences targeting caspase-4 (CASP4). Total mRNA was extracted and expression profiles were analyzed.

first: Irene

last: Fernández-Duran

first: Juan


status: Public on Nov 30 2021

city: Saskatoon

first: Brian

last: Eames

state: Saskatchewan

address: 107 Wiggins Road

department: Anatomy and Cell Biology

country: Canada

institute: University of Saskatchewan

summary: LCM-RNA-Seq data obtained from chick HH36 chondrocytes and osteoblasts at different stages of differentiation -immature chondrocytes and mature (hypertrophic) chondrocytes- isolated from the head (ceratobranchial) and limb (humerus).

overall_design: Chondrocyte and osteoblast mRNA profiles of wild type chick

first: B

middle: F

first: Patsy

last: Gomez-Picos


title: Integrated Analysis of Genes Encoding ATP-Dependent Chromatin Remodelers Identifies CHD7 as a Potential Target for Colorectal Cancer Therapy

city: tianjin

first: zhenyu

last: shi

state: 天津

address: West Huan-Hu Rd, Ti Yuan Bei, Hexi District  Tianjin, 300060, P.R.China

institute: Tianjin Medical University Cancer Institute and Hospital

summary: We experimentally demonstrated that CHD7 promotes the growth of colorectal cancer cells in vitro and in vivo. Mechanistically, RNA-seq and ATAC-seq approaches together with ChIP assays indicated that CHD7 can bind to the promoters of target genes to maintain chromatin accessibility and facilitate transcription. We found that CHD7 knockdown downregulates AK4 expression and activates AMPK phosphorylation, thereby promoting the phosphorylation and stability of p53 and leading to the inhibition of the colorectal cancer growth. Our genomic analyses of ATPCRs across large-scale cancer specimens identified potential therapeutic targets and our experimental studies revealed a novel CHD7-AK4-AMPK-p53 axis that plays an oncogenic role in colorectal cancer.

overall_design: Examination of chromatin accessibility changes in CHD7 knockdown and control RKO cells.

first: Xingyan

last: Zhang