title: Time-course RNA sequencing of SCLC response to combination chemotherapy

city: Los Angeles

first: David

last: Shia

address: 630 Charles E Young Dr S

institute: UCLA

overall_design: Comparative gene expression profiling over drug response time course

first: Brigitte

last: Gomperts


title: A role for gene expression and mRNA stability in nutritional compensation of the circadian clock

status: Public on Dec 16 2022

city: Hanover

first: Christina

middle: M

last: Kelliher

state: NH

address: 7400 Hinman

department: Molecular & Systems Biology

country: USA

institute: Geisel School of Medicine at Dartmouth

type: Expression profiling by high throughput sequencing

summary:
To identify the role of the cleavage and polyadenylation CFIm complex (NCU02152 and NCU09014) in the circadian clock, mRNA 3' End Sequencing was performed on a knockout mutant and compared to control samples.
Hundreds of polyadenylation sites are affected by loss of CFIm complex activity in Neurospora crassa.

overall_design: 3' End Sequencing was performed on biological duplicate samples from 25C, constant light cultures grown for 72 hours to identify poly(A) tail locations.

first: Elizabeth-Lauren

last: Stevenson

first: Jennifer

middle: J

last: Loros

first: Jay

middle: C

last: Dunlap


title: An NPAS4:NuA4 complex couples synaptic activity to DNA repair [sBLISS-seq]

city: BOSTON

first: ELIZABETH

last: POLLINA

state: MA

address: 220 LONGWOOD AVENUE, GOLDENSON 405

department: Neurobiology

institute: HARVARD MEDICAL SCHOOL

summary: Neuronal activity is critical for adaptive circuit remodeling but poses an inherent risk to the stability of the genome across the long lifespan of post-mitotic neurons. Whether neurons have acquired specialized genome protection mechanisms that enable them to withstand decades of potentially damaging stimuli during periods of heightened activity is not known. Here we identify the first example of a neuronal-specific DNA repair mechanism via a new form of the NuA4/TIP60 chromatin modifier that assembles in activated neurons around the inducible, neuronal-specific transcription factor NPAS4. We purify this complex directly from the brain and demonstrate its function in eliciting activity-dependent changes to neuronal transcriptomes and neuronal circuitry. NPAS4:NuA4 binds at fragile regulatory regions that undergo neuronal activity-induced DNA double-strand breaks and recruits additional DNA repair machinery to stimulate the repair of these sites. Gene regulatory elements bound by the NPAS4:NuA4 complex are partially protected from age-dependent accumulation of somatic mutations. Impaired NPAS4:NuA4 signaling leads to a cascade of cellular defects including dysregulated transcriptional responses to activity, loss of control over neuronal inhibition, and genome instability, culminating in reduced longevity at the organismal level. In addition, mutations in several components of the NuA4 complex are reported to lead to neurodevelopmental disorders and autism. Together, these findings identify a neuronal-specific complex that couples neuronal activity directly to genome preservation and whose disruption may contribute to developmental disorders, neurodegeneration and aging.

overall_design: To map DNA breaks across a timecourse of stimulation, sBLISS-seq was performed in the hippocampus of 4 week old WT mice. Nuclei were collected at 0, 2, or 10 hours post low dose KA stimulation. Experiments were performed with 8 - 10 replicates per timepoint. To assess the role of NPAS4 in DNA DSB accumulation, Npas4fl/fl or Tip60fl/fl mice were infected with AAVs expressing wither Cre-mCherry or DelCre-GFP.  DelCre is a nuclease-deficient Cre that cannot excise and so mice are wild-type for the gene of interest.  Nuclei were collected at 0, 2, or 10 hours post KA stimulation.  Experiments were performed in at least triplicate.  Samples collected from WT mice injected with AAVs expressing wither Cre-mCherry or DelCre-GFP serve as a control for Cre toxicity.

first: Elizabeth

middle: A

last: Pollina

first: Daniel

last: Gilliam

first: Michael

middle: E

last: Greenberg


title: An NPAS4:NuA4 complex couples synaptic activity to DNA repair [ATAC-Seq]

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: Excitatory pyramidal neurons were isolated from the hippocampi of B6;129-Gt(ROSA)26Sor<tm5(CAG-Sun1/sfGFP)Nat>/J (Jackson labs Stock 021039) X B6.Cg-Tg(Camk2a-cre)T29-1Stl/J (Jackson labs Stock 005329) using the INTACT method.  Mice were stimulated with glutamate agonist kainic acid and collected at either 0 or 2 hours post stimulation.  Experiments were performed in triplicate.


title: Neuronal and astrocytic contributions to Huntington’s disease dissected following mutant Huntingtin (mHTT) lowering

status: Public on Dec 15 2022

first: Riki

last: Kawaguchi

state: CA

address: 760 Westwood Plaza, Room 37-420

department: Department of Psychiatry and Neurology Department of Psychiatry

institute: University of California, Los Angeles

summary: We used cell-specific zinc finger protein (ZFP) transcriptional repressors to lower mHTT and experimentally evaluated the consequences of neuronal and astrocytic mHTT lowering on HD pathophysiology using cell-type specific RNA-seq

overall_design: The mHTT load was lowered in astrocytes and evaluated astrocytic and neuronal RNA-seq, in neurons and evaluated neuronal and astrocytic RNA-seq, in astrocytes brain-wide using PHP.eB AAVs, and in neurons using instrastriatal AAVs. Bulk-tissue (INPUT) and neuron-specific RNA-seq were performed in the striatum. A-Delta and N-Delta are control ZFP viruses. A-ZFP and N-ZFP are functional mHTT repressor viruses.

first: Mohitkumar

middle: R

last: Gangwani

first: Baljit

middle: S

last: Khakh


title: An NPAS4:NuA4 complex couples synaptic activity to DNA repair [ChIP-Seq]

overall_design: Excitatory pyramidal neurons were isolated from the hippocampi of B6;129-Gt(ROSA)26Sor<tm5(CAG-Sun1/sfGFP)Nat>/J (Jackson labs Stock 021039) X B6.Cg-Tg(Camk2a-cre)T29-1Stl/J (Jackson labs Stock 005329) using the INTACT method.  Mice were stimulated with glutamate agonist kainic acid and collected at either 0 or 2 hours post stimulation. 3 replicates of γH2AX ChIP were performed at each timepoint and input controls are included. NPAS4 ChIP was performed on whole hippocampal tissue samples without INTACT.


title: Identifying NFIB target genes in mammalian cells

city: Houston

first: Yue

last: Lu

state: TX

address: 1881 East Road

department: Epigenetics & Molecular Carcinogenesis

institute: The University of Texas MD Anderson Cancer Center

summary: NFIB is a transcription factor that can both positively and negatively regulate gene transcription. We have identified NFIB as an arginine methylation substrate of CARM1. To elucidate how CARM1 could regulate NFIB target genes by methylating NFIB, we performed this ChIP-seq to firstly identify NFIB direct binding gengs.

overall_design: Three independent antibodies were used in the ChIP-seq analysis for the global distribution of NFIB in HeLa cells. Two NFIB antibodies from Abcam and Bethyl were used for regular HeLa cells, while GFP antibody was used for HeLa cells with stable GFP-NFIB overexpression. Two technical replicates of DNA libraries each antibody and the corresponding total input libraries were prepared. The H3R17me2a antibody was used for the global distribution of CARM1 substrates in HeLa cells.

first: Guozhen

last: Gao

first: Kevin

last: Lin

first: Mark

middle: T

last: Bedford


title: Stress promotes RNA G-quadruplex folding in human cells

city: New Haven

first: Junjie

last: Guo

state: CT

address: 295 Congress Ave, BCMM 154B

institute: Yale University School of Medicine

summary: Guanine (G)-rich nucleic acids can fold into G-quadruplex (G4) structures under permissive conditions. Although many RNAs contain sequences that fold into RNA G4s (rG4s) in vitro, their folding and functions in vivo are not well understood. Here, we showed that the folding of putative rG4s in human cells into rG4 structures was dynamically induced by stress. By using high-throughput dimethylsulfate probing, we identified hundreds of endogenous stress-induced rG4s. Our results demonstrated that stress-induced rG4s were enriched in mRNA 3′-untranslated regions and enhanced mRNA stability. Furthermore, stress-induced rG4 folding was readily reversible upon stress removal. In summary, our study revealed the dynamic regulation of rG4 folding in living human cells and suggests suggested that widespread rG4 motifs may have a global regulatory impact on mRNA stability and cellular stress response.

overall_design: G4-DMS-seq was performed to (1)  identify endogenous G4 regions in the polyA+ transcriptome of U2OS cells and (2) measure their in vivo folding states under either physiological or starvation conditions.

middle: U


title: An NPAS4:NuA4 complex couples synaptic activity to DNA repair [SiMSen-Seq (amplicon)]

overall_design: Neuronal DNA  was isolated from the hippocampus of WT mice at young (3 month), middle (12 month), or old (23-27 month) ages. 3-4 samples were collected per age group.


title: An NPAS4:NuA4 complex couples synaptic activity to DNA repair

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

overall_design: Refer to individual Series


title: Cellular senescence in malignant cells promotes tumorigenesis in mouse and patient glioblastoma [p16]

city: Paris

first: Isabelle

last: Leroux

address: 47 Boulevard de l'Hôpital

country: France

institute: Paris Brain Institute

summary: The goal of this study is to identify the senescent cells expressing high level of p16Ink4a (p16Ink4a Hi) in GBMs and characterize their action on the tumor microenvironment at an early timepoint. We introduced the p16-3MR transgene in the GBM mouse model to selectively delete p16Ink4a Hi senescent cells upon ganciclovir (GCV) injection. We compared p16-3MR+GCV  to  WT+GCV control GBMs that were harvested 7 days after the last GCV injection.

overall_design: Bulk RNAseq of five p16-3MR + GCV vs four WT + GCV mouse GBMs at early timepoint (7 days after the last treatment shot)

last: Le Roux

first: Rana

last: Salam

first: Alexa

last: Saliou

first: Justine

last: Guégan

first: Mathilde

last: Bertrand


title: Cellular senescence in malignant cells promotes tumorigenesis in mouse and patient glioblastoma [mir-NRF2]

summary: The goal of this transcriptomic analysis is to decipher whether NRF2 pathway plays a role in the induction of pro-tumoral senescence in glioblastoma (GBM).

overall_design: Bulk RNAseq of three miR-ctl vs three miR-NRF2 mouse GBMs at endpoints


title: Cellular senescence in malignant cells promotes tumorigenesis in mouse and patient glioblastoma [10X scRNA-seq]

summary: The goal of this study is to identify the senescent cells expressing high level of p16Ink4a (p16Ink4a Hi) in GBMs, at an early timepoint. We introduced the p16-3MR transgene in the GBM mouse model to selectively delete p16Ink4a Hi senescent cells upon ganciclovir (GCV) injection. We compared two p16-3MR+GCV  to two WT+GCV control GBMs that were harvested 7 days after the last GCV injection. p16Ink4a Hi senescent cells were a subset of malignant cells, mostly grouped in the astrocyte cluster and to a lesser extend in the NP-like cluster. We also found that p16Ink4a Hi senescent cells deletion modifies the cell state of malignant cells and modulates the tumor microenvironment. This study allowed us to define a GBM senescence signature.

overall_design: scRNAseq of two WT+GCV vs two p16-3MR+GCV mouse GBMs at early timepoint


title: Astrocyte-neuron contributions to Huntington’s disease dissected with ZFPs

summary: We performed cell-type specific RNAseq in astrocytes and neurons in the presence or absence of ZFP transcriptional repressors in the striatum of R6/2 mouse model of HD.

overall_design: Mutant huntingtin was reduced in a cell-specific manner either in astrocytes or neurons using zinc-finger protein (ZFP) transcriptional repressors. Cell-type specific RNA-seq using RiboTag approach was carried out in astrocytes and neurons in combination with mHTT reduction with ZFPs.


title: Cellular senescence in malignant cells promotes tumorigenesis in mouse and patient glioblastoma [bulk RNA-seq]

summary:
GBM mouse model: The goal of this study is to compare the transcriptomic landscape at the endpoint of GBMs upon senescent cells deletion. We introduced the p16-3MR transgene in the GBM mouse model to selectively delete senescent cells expressing high level of p16Ink4a (p16Ink4a Hi) upon ganciclovir (GCV) injection. We compared p16-3MR+GCV GBMs to two control conditions, either WT+GCV or p16-3MR+GCV. We showed a slight decreased of p16Ink4a transcripts in p16-3MR+GCV compared to WT+GCV GBMs and GSEA demonstrated significant down-regulation of senescence pathways in p16-3MR+GCV GBMs compared to control GBMs.
GBM-derived organoids: We used a mouse GBM-derived organoids model to further explore the function of Nrf2, that we identified as one potential trigger of the pro-tumoral action of p16Ink4a Hi malignant cells. We compared GBM-derived organoids treated with the senolytic ABT263 (Navitoclax; inhibitor of the anti-apoptotic proteins Blcl2 and BCL-xL) or vehicle (vhc) after 14 days in culture. We validated ABT263 efficacy via the significant downregulation of the expression of p16Ink4a, p15Ink4b and p21Cip1 senescent markers. We further identified upon senolytic treatment, downregulated genes encoding for SASP. Importantly, GSEA revealed a significant downregulation of Nrf2 pathway upon senolytic treatment.

overall_design:
GBM mouse model: Bulk RNAseq on WT+GCV, p16-3MR+vhc and p16-3MR+GCV mouse GBMs at end timepoints.
GBM-derived organoids: Bulk RNAseq on GBM-derived organoids treated with ABT263 (2µM) or vhc.


title: Cellular senescence in malignant cells promotes tumorigenesis in mouse and patient glioblastoma [RNA-seq]

summary: We performed a scRNAseq analysis conducted at the endpoint of our GBM mouse model. We compared differentially expressed up-regulated genes in p16Ink4a positive vs p16Ink4a negative malignant cells. The goal was to compare this dataset with two other transcriptomic datasets, to explore the upstream regulator(s) of senescence in malignant cells. We found that Nuclear Factor Erythroid 2 Like 2 (Nfe2l2) signaling pathway was enriched in the 3 data sets.

overall_design: ddSeq of a p16-3MR mouse GBM at end timepoints


title: Kaposi’s sarcoma-associated herpesvirus induces specialized ribosomes to efficiently translate viral lytic mRNAs

status: Public on Dec 14 2022

city: Leeds

first: James

last: Murphy

state: West Yorkshire

address: Claredon Way

department: Faculty of Biological Sciences

country: United Kingdom

institute: University of Leeds

summary: Historically, ribosomes have been viewed as unchanged homogeneous macromolecular machines with no intrinsic regulatory capacity for mRNA translation. However, an emerging concept is that heterogeneity of ribosomal composition exists, which can exert a regulatory function or specificity in translational control. This is supported by recent discoveries identifying compositionally distinct ‘specialized ribosomes’ that actively regulate mRNA translation. Viruses lack their own translational machinery and impose a high translational demand on the host cell during replication. Whilst viruses have evolved a variety of mechanisms to overcome this, we hypothesize that some viruses manipulate the host cell to produce specialized ribosomes to preferentially translate viral transcripts. Quantitative proteomic analysis has identified changes in the stoichiometry and composition of precursor ribosomal complexes during the switch from latent to lytic KSHV replication. Intriguingly, we demonstrate the enhanced association of ribosomal biogenesis factors BUD23 and NOC4L, and a previously uncharacterized KSHV lytic protein, ORF11, with small ribosomal subunit precursor complexes during lytic KSHV infection. Notably, BUD23 depletion resulted in significantly reduced viral gene expression and progression through the lytic cascade, culminating in a dramatic reduction of infectious virion production. Importantly, ribosome profiling demonstrated that BUD23 is essential for the reduced association of ribosomes with KSHV uORFs in late lytic genes, required for the efficient translation of the main open reading frame. Together our results provide new mechanistic insight into KSHV-mediated manipulation of cellular ribosome composition inducing a population of specialized ribosomes to facilitate efficient translation of viral mRNAs.

sample_organism:
Homo sapiens
Human gammaherpesvirus 8

platform_organism:
Homo sapiens
Human gammaherpesvirus 8

overall_design:
TREx BCBL1-Rta cells, a primary effusion lymphoma B cell line latently infected with Kaposi's sarcoma-associated herpesvirus (KSHV) and modified to contain doxycycline inducible myc-RTA. Samples were collected from two TREx BCBL1-Rta cell lines where lytic replication of KSHV had been induced by doxycycline for 36 hours and each cell line stably expressed either a scrambled control shRNA or a shRNA targeting BUD23. From each cell line a polyA RNA reference sample was collected and a ribosome footprint sample. Two biological replicates were completed for this experiment.
The final manuscript discusses KSHV data.

first: Elton

last: Vasconcelos

first: Julie

middle: L

last: Aspden

first: Adrian

last: Whitehouse


title: Single cell RNA sequencing analysis of mouse cochlear supporting cell transcriptomes with activated ERBB2 receptor, a candidate mediator of hearing restoration mechanisms

status: Public on Dec 13 2022

city: Rochester

first: Cameron

last: Baker

state: NY

address: 601 Elmwood Ave

institute: University of Rochester

summary: One potential approach to restore hearing is to enforce regeneration of hair cells (HCs) through induction of cellular signaling pathways in supporting cells (SCs) that promote dedifferentiation and proliferation.  We previously showed that the constitutive activation of ERBB2 signaling in cochlear SCs indirectly promoted SC differentiation to HCs, both in vivo and in vitro.  In the current study, we aimed at identifying mechanisms and molecular pathways activated in SCs with constitutive ERBB2 signaling.  To this end, we used single cell RNA sequencing (scRNA-seq) to characterize the transcriptomes of individual neonatal mouse cochlear SCs that were induced to express ERBB2.  We found that induction of ERBB2 in vivo resulted in generation of a new distinct cluster of cells with unique transcriptome.  This population has de novo expression of two members of the small integrin-binding ligand n-linked glycoproteins (SIBLING) family and their regulators.  We confirm expression of the SIBLING Secreted phosphoprotein 1 (SPP1) as one of the most up-regulated genes in response to ERBB2 activation.  SPP1 mediates signaling through the CD44 receptor, promoting survival, proliferation, and differentiation of osteoblast lineage cells.  Histological analyses of cochlear samples collected from young adult mice confirmed that induction of ERBB2 after noise exposure resulted in up-regulation of both SPP1 and its receptor CD44, and the formation of mitotic sensory stem-like cell aggregates in the organ of Corti.  Our results suggest that ectopic activation of ERBB2-signaling in young adult mice secondarily promotes SPP1/CD44 signaling, possibly altering the microenvironment of the organ of Corti.

overall_design: The scRNA-seq analysis of supporting cells with activated ERBB2 signaling was performed using mouse line harboring an inducible “Tet-On” mutant ErbB2 transgene encoding a constitutively active ERBB2 protein (CA-ERBB2), which does not require ligand binding or heterodimerization with other ERBB partners for active signaling.  To limit induction of CA-ERBB2 activation to cochlear supporting cells, CA-ERBB2 mouse line was crossed with mouse line harboring an inducible DNA Cre recombinase under control of the supporting cell gene promoter Fgfr3. Double heterozygotic mice harboring both an inducible “Tet-On” CA-ErbB2 and an Fgfr3-iCre transgene were bred to homozygous line harboring a “floxed” TA transcription factor, with an IRES-GFP to use as a lineage marker (“ROSA-rtTA-GFP”).  The  pups with CA-ErbB2 and Fgfr3-iCre genes (denoted here as “CA-ERBB2”) were used for analysis of transcriptome of supporting cells with activated ERBB2.  Pups harboring Fgfr3-iCre were used as “Control”.  Activation of iCRE was performed by two injections of tamoxifen at P0 and P1, which resulted in activation of GFP expression to label supporting cells.  Induction of CA-ERBB2 expression was performed at P2 by doxycycline injection.  The organs of Corti were dissected from P3 pups, and GFP+ supporting cells were purified by fluorescence-activated cell sorting (FACS).  RNA cDNA libraries were prepared and sequenced from about 300 GFP+ single cells per genotype collected in three independent FACS experiments.

first: Dorota

last: Piekna-Przybylska

first: Daxiang

first: Jingyuan

last: Zhang

first: John

last: Ashton

first: Patricia

last: White


title: An NPAS4:NuA4 complex couples synaptic activity to DNA repair [CUT&RUN]

first: ELIZABETH

last: POLLINA

overall_design: CUT&RUN was performed in the hippocampal tissue isolated from wild-type mice for members of the NPAS4:NuA4 complex.  For most factors, experiments were performed in at least duplicate (exception EP400 Bethyl laboratories). CUT&RUN experiments performed with rabbit IgG serve as controls for non-specific antibody binding.  In the case of NPAS4 CUT&RUN, controls for binding specificity include experiments performed with NPAS4 antibody in Npas4 KO mice and unstimulated tissue, where little to no NPAS4 is expressed.  CUT&RUN in unstimulated tissue, where little to no FOS is expressed, serves as a control for specificity of FOS binding. In addition, CUT&RUN was performed in the hippocampus of Npas4fl/fl mice infected with AAVs expressing wither Cre-mCherry or DelCre-GFP.  DelCre is a nuclease-deficient Cre that cannot excise and so mice are wild-type for the gene of interest.

first: Elizabeth

last: Pollina

first: Daniel

last: Gilliam

first: Michael

last: Greenberg


title: Transcriptome and Small RNA analysis of C.elegans from Parental P0 to F3 generations under hypoxic stress in both WT and hrde-1 mutant

city: Boston

first: Eric

last: Greer

address: 320 Longwood Avenue

department: Newborn Medicine/Department of Pediatrics

institute: Boston Children's Hospital/Harvard Medical School

type: Non-coding RNA profiling by high throughput sequencing


title: Association of Environmental Exposure to Chromium with Differential DNA Methylation: An Epigenome-Wide Study

city: Beijing

first: Jingtao

last: Wu

address: Dong Dan San Tiao Wu Hao

country: China

institute: Chinese Academy of Medical Sciences

type: Methylation profiling by genome tiling array

summary:
To identified the differential methylation of genes and regions to elucidate the mechanisms of toxicity related to environmental chromium exposure.
Fasting whole blood samples were collected by clinicians in ethylenediaminetetraacetic acid (EDTA) anticoagulant tubes, and stored them at −80 °C. A DNeasy Blood and Tissue Kit (Qiagen) was used to isolate DNA from whole blood. The purity and concentration of DNA were estimated using Nanodrop 2000 (ThermoScietific). Approximately 500 ng of genomic DNA from each sample was used for sodium bisulfite conversion with the EZ DNA methylation Gold Kit (Zymo Research, USA) in accordance with the manufacturer’s standard protocol. Genome-wide DNA methylation was performed using the Illumina Infinium HumanMethylation850K (EPIC) BeadChip (Illumina Inc, USA) in accordance with the manufacturer’s instructions.

overall_design: To reveal epigenome-wide DNA methylation patterns in response to Cr exposure, a cross-sectional study was conducted in Taihe district, Jinzhou City, Liaoning Province of northeast China, which experienced severe Cr pollution in the 1960s. Because of the large-scale production of ferroalloys, large amounts of wastewater, ore residue, and gas containing Cr(VI) were discharged into the environment surrounding Taihe district. Although the local government has taken restorative measures, the local environment experienced severe Cr(VI) pollution, and relatively high levels of Cr remain. Participants are included in the present study, who have lived in local areas for more than 40 years without occupational Cr exposure and the history of cancers. Finally, the Cr exposure group comprised 10 individuals from Cr-exposed regions along a contaminated river less than 10 km from the ferroalloy factory, and the unexposed group comprised 10 individuals from unexposed regions at least 50 km from that factory. Both groups had similar lifestyles, cultural backgrounds, and socioeconomic status. All participants signed informed consent forms.

first: Meiduo

last: Zhao

first: Qun

last: Xu


title: Characterization of human stem cell derived Somitoid model

first: Yannis

last: Djeffal

state: Massachusetts

address: 60 Fenwood road

department: Pathology/Genetics

institute: Brigham and Women’s Hospital/Harvard Medical School

summary: To model human somitogenesis in vitro, we developped a 3D model called Somitoid. We performed RNA sequencing on cells from different time points to characterize the transcriptional profiles.

overall_design: Samples are either all cells from different time points of differentiation (48h, 66h, 120h), or FACS-enriched cell portions based on differential MESP2 and UNCX gene expression levels; Three replicas for each sample.

first: Yuchuan

last: Miao

first: Kongju

last: Zhu

first: Olivier

last: Pourquie


title: Small RNAseq analysis of C.elegans from Parental P0 to F3 generations under hypoxic stress in both WT and hrde-1 mutant [small RNA-seq]

summary: The goal of small RNA-seq is to identify the differentially expressed small RNAs (microRNA, 22G RNA, piRNA, snoRNA) in the wild-type (WT) and hrde-1 mutant of  C.elegans at the normoxia reared and hypoxia treatment conditions at P0 generation, and those small RNAs maintained dysregulation in F1, F2 and F3 generation.

overall_design: Total RNA from WT and hrde-1 under normoxia or hypoxia treatment worms from P0 to F3 generations were extacted, and 32 small RNA libraries were built using the Nextflex Small RNA-seq Kit v3 (NOVA-5132-06), in duplicate for each condition, using single-end 85 bp on Illumina Illumina Nextseq 500 platform

first: Simon

middle: Y

last: Wang


title: The H2A.Z.1/PWWP2A/NuRD-associated protein HMG20A controls early head and heart developmental transcription programs [ATAC-seq]

status: Public on Dec 12 2022

city: Giessen

first: Marek

last: Bartkuhn

state: Hessen

address: Aulweg 132

department: Biomedical Informatics and Systems Medicine

country: Germany

institute: Justus-Liebig-University Giessen

summary: Specialized chromatin-binding proteins are required for DNA-based processes during development. We recently established PWWP2A as direct histone variant H2A.Z interactor involved in mitosis and cranial-facial development. Here, we identify the H2A.Z/PWWP2A-associated HMG20A protein as part of several chromatin-modifying complexes including NuRD, and to localize to genomic regulatory regions. Hmg20a depletion causes severe head and heart developmental defects in Xenopus laevis due to neural crest cell (NCC) and cardiomyocyte (CM) differentiation malfunctions. Such defects are pheno-copied in HMG20A-depleted mESCs, which show inefficient differentiation into NCCs and CMs. Accordingly, loss of HMG20A caused striking deregulation of transcription programs involved in epithelial-mesenchymal transition (EMT) and cardiac differentiation, thereby shedding light on HMG20A-specific developmental defects. Collectively, our findings implicate HMG20A as part of the H2A.Z/PWWP2A/NuRD-axis and as a key modulator during NCC and cardiomyocyte differentiation by guiding intricate developmental transcription programs.

overall_design: influence on chromatin accesibility of HMG20A depletion in primed mouse embyonic stem cells

first: A

last: Herchenröther

first: T

last: Friedrich

first: J

last: Lan

first: M

first: S

middle: B

last: Hake


title: Transcriptome analysis in C.elegans from Parental P0 to F3 generations under hypoxic stress in both WT and hrde-1 mutant [RNA-seq]

summary: The goal of RNA-seq is to identify the differentially expressed genes in the wild-type (WT) and hrde-1 mutant of  C.elegans at the normoxia reared and hypoxia treatment conditions at P0 generation, and those maintained dysregulated genes in F1, F2 and F3 generation.  Two biological replicates were assigned for each group and in total 32 groups were prepared for RNA-seq libraries with 500 ng mRNA as starting materials using NEXTflex Illumina qRNA-Seq Library Prep Kit (Bioo Scientific). We mapped about 20 - 30 million reads per sample to C.elegans (WS235) with RSEM pipline. Differential analysis were conducted using EdgeR. The significant genes were conducted by computing NB exact genewise tests with corrected p < 0.05.

overall_design: Messenger RNA from WT and hrde-1 under normoxia or hypoxia treatment worms from P0 to F3 generations were extacted, and cDNA libraries were generated for deep sequencing, in duplicate, using paired-end 150bp on Illumina Hiseq4000 platform


title: The H2A.Z.1/PWWP2A/NuRD-associated protein HMG20A controls early head and heart developmental transcription programs [RNA_CM_AH]

overall_design: Genomic localisation and influence on transcriptome of HMG20A in Hela Kyoto and in vitro mouse cardiac differentiation

first: Andreas

first: Tobias

first: Jie

first: Sandra


title: The H2A.Z.1/PWWP2A/NuRD-associated protein HMG20A controls early head and heart developmental transcription programs [HeLa_RNA_AH]


title: The H2A.Z.1/PWWP2A/NuRD-associated protein HMG20A controls early head and heart developmental transcription programs [CNR_CM_AH]


title: The H2A.Z.1/PWWP2A/NuRD-associated protein HMG20A controls early head and heart developmental transcription programs [HeLa_ChIP_AH]


title: Barrier-to-autointegration Factor 1 (BAF) Promotes Gammaherpesvirus Reactivation from Latency

city: Chapel Hill

first: Blossom

last: Damania

state: NC

address: 450 West Drive

department: Microbiology and Immunology

institute: University of North Carolina at Chapel Hill

summary: Gammaherpesviruses, including Kaposi’s sarcoma-associated herpesvirus (KSHV) and Epstein-Barr virus (EBV), are DNA viruses that are globally associated with human cancers and establish lifelong latency in the human population. Detection of gammaherpesviral infection by the cGAS-STING innate immune DNA-sensing pathway is critical for suppressing viral reactivation from latency, a process that promotes viral pathogenesis and transmission. We report that Barrier-to-autointegration factor 1 (BAF)-mediated suppression of the cGAS-STING signaling pathway is necessary for reactivation of KSHV and EBV. We demonstrate a novel role for BAF in destabilizing cGAS expression and show that BAF expression in latently infected, reactivating, or uninfected cells leads to suppression of type I interferon-mediated antiviral responses and inhibition of viral replication. Furthermore, BAF overexpression resulted in decreased cGAS expression at the protein level.  These results establish BAF as a key regulator of the lifecycle of gammaherpesviruses and a potential target for treating viral infections and malignancies.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for iSLK.219 cells treated with non-targeting control (NTC) siRNA or BANF1-targeting (BAF) siRNA. Cells in each  siRNA treatment group was harvested before and after 48 hours of doxycycline treatment to reactivate KSHV lytic gene expression. Duplicate biological replicates were collected for each  condition/timepoint combination.

first: Grant

last: Broussard

first: Guoxin

last: Ni

first: Zhigang

last: Zhang

first: Qian

last: Li

first: Patricio

last: Cano

first: Dirk

middle: P

last: Dittmer


title: Expression data from liver of Recombinant human IgG1 treated high-fat-diet-induced ApoE-/- mice

city: Guangzhou

first: sujun

last: xiao

state: Guangdong

address: No.1023,South Shatai Road, Baiyun District

institute: Southern Medical University

summary: On the basis of the clear role of Recombinant human IgG1 in the reduction of  liver triglyceride (TG) level elevated by high-fat-diet,  the potential effector genes of Recombinant human IgG1 are screened by means of transcriptional techniques.

overall_design: 9 male ApoE-/- mice were randomly divided into 3 groups including control group (N), high-fat-diet group (PBS) and high-fat-diet with Recombinant human IgG1 treatment group (Ab). Briefly, four-weeks-old male ApoE-/- mice were fed a high fat diet( about 4700kcal/kg, 17% of calories from protein, 43% of calories from carbohydrate, 41% of calories from fat ) for 20 weeks and were subsequently transferred to chow food for 1 week, then the mice were treated with intraperitoneal injections of PBS or 3 mg of either Recombinant human IgG1 at age of 25 weeks. After two additional injections at 26 and 27 weeks of age, mice were sacrificed at 29 weeks of age for following analysis. According to the results of liver Oil Red O staining and  TG detection, 3 liver samples of each group were detected by trancriptional techniques.

first: Sujun

last: Xiao

first: Ming

last: Zhao


title: ARID1A loss in pancreas leads to islet developmental defect and metabolic disturbance  ,Islet cell ChIP-Seq HDAC6 arid1a

status: Public on Dec 11 2022

city: Tainan

first: Tzu-Lei

last: Kuo

state: Taiwan

address: No. 367, Sheng Li Road

department: Institute of Cancer Research

country: Taiwan

institute: Taiwan NHRI

summary: ARID1A is a tumor suppressor gene mutated in 7-10% of pancreatic cancer patients. However, its function in pancreas development and endocrine regulation is unclear. We generated mice that lack Arid1a expression in the pancreas. Our results showed that deletion of the Arid1a gene in mice caused a reduction in islet numbers and insulin production, both of which are associated with diabetes mellitus (DM) phenotype.we performed chromatin immunoprecipitation-sequencing analysis (ChIP-seq) to study genome-wide HDAC6 occupancy in the control and Arid1a-depleted islet cells.

overall_design: We generate mice that lack Arid1a expression in the pancreas. Islets from the control and PCAL/L mice were isolated and analysis with ChIP-seq.

first: Kuang-Hung

last: Cheng

first: Li-Tzong

last: Chen

first: Wen-Chun

last: Hung


title: Tbx2 and Tbx3 regulate cell fate progression of the otic vesicle for inner ear development

city: Bronx

first: Hansoo

last: Song

state: New York

address: 1301 Morris Park Ave

department: Genetics

institute: Albert Einstein College of Medicine

summary: The morphogenesis of the otic vesicle (OV) to form inner ear organs serves as an excellent model system to understand cell fate acquisition on a single cell level. Tbx2 and Tbx3 (Tbx2/3) encode closely related T-box transcription factors that are expressed widely in the mammalian otic vesicle (OV). Inactivation of both genes in the Pax2-Cre lineage (Tbx2/3cKO) results in failed morphogenesis of the OV into inner ear organs. To understand the basis of these defects, single cell RNA-sequencing (scRNA-seq) was performed on the OV lineage using Pax2-Cre, in controls versus Tbx2/3cKO embryos, at stage E10.5. We identified a multipotent population termed otic progenitors that are localized to the anterior ventrolateral region of the OV in controls and are marked by expression of Fgf18, Sox3, and Cxcl12. The otic progenitor population was increased three-fold in Tbx2/3cKO embryos, concomitant with dysregulation of genes in these cells as well as reduced progression to more differentiated states of prosensory and nonsensory cells. An ectopic neural population of cells was detected in the posterior OV of Tbx2/3cKO embryos due to increased expression of Neurog1 and NeuroD1 but with reduced maturation. As all three cell fates were affected in Tbx2/3cKO embryos, we suggest that Tbx2/3 promotes progression of multipotent otic progenitors to more differentiated cell types in the OV.

overall_design: Single Cell RNA-sequencing from micro dissected tissue around the otic vesicle and cochleovestibular ganglion of Pax2-Cre;Rosa26-GFPf/+ and Pax2-Cre;Tbx2f/f;Tbx3f/f;Rosa26-GFPf/+ embryos at E10.5

first: Bernice

last: Morrow


title: A comprehensive characterisation of fetal and mature retinal cell identity to assess the fidelity of retinal organoids

status: Public on Dec 10 2022

city: Sydney

first: Hani

middle: Jieun

last: Kim

address: The University of Sydney

country: Australia

institute: The University of Sydney

summary: Retinal organoids derived from pluripotent stem cells have been widely used to model development and disease of the human eye. Yet there is a lack of studies that have systematically evaluated the fidelity of the organoids to their in vivo counterpart. This is particularly relevant for evaluating the efficacy of therapeutic applications and culture protocol performance. To this end, we performed an extensive meta-atlas characterisation of cellular identities of the human eye, covering a wide range of developmental stages. The resulting map uncovered previously unknown biomarkers of major retinal cell types and those associated with cell-type specific maturation. Using these retinal identities from fetal and adult tissue as the map, we systematically assessed the fidelity of the retinal organoids to mimic the human eye, enabling us to comprehensively benchmark the current protocols for retinal organoid generation.

overall_design: Single-cell RNA sequencing of 3-month-old retinal organoids

first: Michelle

last: O’Hara-Wright

first: Daniel

first: To

middle: H

last: Loi

first: Robyn

last: Jamieson

first: Anai

last: Gonzalez-Cordero

first: Pengyi

last: Yang


title: Oncolytic ORFV induces antitumor immunity

status: Public on Dec 09 2022

city: Changchun

first: Jiyu

last: Guan

state: Jilin

address: 5333 Xi'an Road

institute: Jilin University

summary: To study the oncolytic effect of ORFV on tumors, we performed ORFV treatment (i.t.) in B16 engrafted tumors, changes of gene transcripts were detected

overall_design: ORFV and Vehicle treated tumors were isolated and analyzed by RNA sequencing

first: Wenqi

last: He

first: Jing

last: Lin

first: Shihui

last: Sun


title: Discovery and Functional Analysis of Secondary Hair Follicle miRNAs during Annual Cashmere Growth

city: Shenyang

first: Wang

middle: Ming

address: 120 Dongling Road

institute: shenyang agricultural university

summary: Secondary hair follicles (SHF) produce the thermoregulatory cashmere in goat. MiRNAs were reported playing indispensable roles in hair follicle formation and growth. However, most studies examining miRNAs related to cashmere have been performed on goat skin. It still remains obscure that which miRNAs are highly expressed in SHFs or how miRNAs affect the cashmere growth. In the present study, we isolated the SHFs under dissecting microscope and analyzed the miRNA signatures during annual cashmere growth. Small RNA sequencing followed by genome-wide expression analysis reveals that early anagen is a crucial phase for miRNA regulation on the cashmere growth, which was uncovered by two predominant groups of miRNAs. Although they exhibit opposite expression patterns, both groups demonstrated sharp changes of expression when transit from early anagen to mid-anagen. In addition, we identified 96 miRNA signatures that differentially expressed between different phases among 376 miRNAs. Functional analysis of the predicted target genes for highly expressed or differentially expressed miRNAs indicated that these miRNAs were involved in signal pathways associated with SHF development, regeneration and regression. Furthermore, miR-143-3p is preferentially expressed in SHFs and Itga6 was identified as one of targets. The dual-luciferase and in situ hybridization assay demonstrated that miR-143-3p directly repressed the expression of Itga6, suggesting a possible novel role for miR-143-3p in the cashmere growth.

overall_design: Genome-wide discovery and molecular characterization of secondary hair follicle miRNAs in cashmere goat across six-time points each with two biological replicates (male and female), representing phases of anagen (May and Sep), catagen (Nov and Dec) and telogen (Feb and Mar).

first: Hui-Ling

last: Xue

first: Ming-Lin

last: Wang

first: Han

last: Dai

first: Sheng-Da

last: Sheng

first: Yan-Lei

last: Liu


title: The H2A.Z.1/PWWP2A/NuRD-associated protein HMG20A controls early head and heart developmental transcription programs

first: Marek

last: Bartkuhn

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: The CXXC5-CRL4B-NuRD Repressor Complex Promotes Breast Carcinogenesis by Regulating the TSC1/mTOR pathway

first: Zhaohan

last: Zhang

address: 10 You’anmen Outer West 1st Street

department: Biochemistry and Molecular Biology

institute: Capital Medical University

summary: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for CXXC5,CUL4B as well as MTA1 in MCF-7 cells.The pathophysiological function of the CXXC family-member CXXC5 remains to be explored. Here we report that CXXC5 is physically associated with the CRL4B complex and the NuRD complex. Genome-wide investigation of transcriptional targets revealed that the CXXC5/CRL4B/NuRD complex represses a panel of genes including TSC1 that are critically involved in cell growth and the regulation of the mTOR pathway, leading to activation of PD-L1. Intriguingly, CXXC5 expression was increased after stimulation with vitamin B2, whereas vitamin D treatment was accompanied by decreased expression of CXXC5. We demonstrated that the CXXC5-CRL4B-NuRD complex promotes cancer cell proliferation. Elevation of CXXC5, CUL4B, and MTA1 expression during cancer progression corresponded to diminished TSC1 expression, and high levels of CXXC5, CUL4B, and MTA1 strongly correlated with higher histological grades and poor prognosis. We further identified that CXXC5 is bimodally regulated by different kinds of vitamins. Our study revealed that CXXC5-mediated TSC1 suppression activates the mTOR pathway, reduces autophagic cell death, induces PD-L1-mediated immune suppression and results in tumor development, providing a possible mechanistic insight into the pathophysiological function of CXXC5.

overall_design: Breast cancer cell line MCF-7 with different antibodies.

first: Lin

last: Shan

first: Wenjuan

first: Minghui

last: Zhao

first: Geyu

last: Ze


title: Cellular senescence in malignant cells promotes tumorigenesis in mouse and patient glioblastoma.

first: Isabelle

last: Leroux


title: The mediating roles of the oral microbiome in saliva and subgingival sites between e-cigarette smoking and gingival inflammation

city: Baltimore

first: Bongsoo

last: Park

state: Maryland

address: 251 Bayview Blvd

department: Translational Gerontology Branch

institute: National Institute on Aging

summary: In this paper, we first report that EC smoking significantly increases the odds of gingival inflammation. Then, we seek to identify and explain the mechanism that underlies the relationship between EC smoking and gingival inflammation via the oral microbiome. We performed mediation analyses to assess if EC smoking affects the oral microbiome, which in turn affects gingival inflammation. For this, we collected saliva and subgingival samples from EC users and non-users and profiled their microbial compositions via 16S rRNA amplicon sequencing. We then performed α-diversity, β-diversity, and taxonomic differential analyses to survey the disparity in microbial composition between EC users and non-users. We found significant increases in α-diversity in EC users and disparities in β-diversity between EC users and non-users.

overall_design: 16S rRNA amplicon sequencing (EC users and Non-users).

first: Hyunwook

last: Koh

first: Michael

last: Patatanian

first: Shyam

last: Biswal


title: A genome-wide relay of signalling-responsive enhancers drives hematopoietic specification (Enhancer Reporter Sequencing)

city: Birmingham

first: Peter

last: Keane

address: Vincent Drive

department: Institute for Cancer and Genomic Sciences

institute: University of Birmingham

summary: Developmental control of gene expression critically depends on distal cis-regulatory elements including enhancers which interact with promoters to activate gene expression. Multiple genome-wide studies have mapped chromatin and genomic features of such elements. However, the enhancer definition is operational, and no global experiments have been conducted to date that identify their cell type and cell stage-specific transcription stimulatory activity in a chromatin context. Here, we describe a high-throughput method that identifies thousands of cis-elements capable of stimulating transcriptional activity from a minimal promoter using the blood progenitor differentiation from embryonic stem cells as model. We show that hematopoietic specification and blood cell-specific gene expression are controlled by the concerted action of thousands of differentiation stage-specific sets of cis-elements which respond to cytokine signals terminating at signalling responsive transcription factors. Our work presents a major advance in our understanding of developmental gene expression control in the hematopoietic system and beyond.

overall_design: Targeted DNA sequencing of fragment libraries cloned into an enhancer reporter cassette in the HPRT locus of HM-1 ES cells and their differentiated progeny. Populations of cells were sorted for Venus-YFP reporter activity into negative, low, medium and high.

first: Bejamin

last: Edginton-White

first: Alexander

last: Maytum

first: Sophie

middle: G

last: Kellaway

first: Debbie

middle: K

last: Goode

first: Inti

last: Pagnuco

first: Salam

last: Assi

first: Luke

last: Ames

first: Mary

last: Clarke

middle: N

last: Cockerill

first: Berthold

last: Göttgens

first: Jean-Baptiste

last: Cazier

first: Constanze

last: Bonifer


title: mRNA aging shapes the Cap2 methylome in mammalian mRNA

city: New York

first: Vladimir

last: Despic

address: 1300 York Ave

department: Pharmacology

institute: Weill Cornell Medicine

summary: The mRNA cap structure is a major site of dynamic mRNA methylation.  mRNA caps exist in either the Cap1 or Cap2 form, depending on the presence of 2’-O-methylation on the first, or both the first and second transcribed nucleotide, respectively.  However, the identity of Cap2-containing mRNAs and the function of Cap2 are unclear.  Here we describe CLAM-Cap-Seq, a method for transcriptome-wide mapping and quantification of Cap2.  We find that unlike other epitranscriptomic modifications, Cap2 can occur on all mRNAs.  Cap2 is formed through a slow continuous conversion of mRNAs from Cap1 to Cap2 as mRNAs age in the cytosol.  As a result, Cap2 is enriched on long-lived mRNAs.  We find that large increases in the abundance of Cap1 leads to activation of RIG-I, especially in conditions where RIG-I expression is increased.  The methylation of Cap1 to Cap2 markedly reduces the ability of RNAs to bind and activate RIG-I.  We find that the slow Cap2 methylation rate allows Cap2 to accumulate on host mRNAs yet ensures that low Cap2 levels occur on newly expressed viral RNAs.  Overall, these results reveal an immunostimulatory role for Cap1, and that Cap2 functions to reduce activation of the innate immune response.

sample_organism:
Caenorhabditis elegans
Drosophila melanogaster
Danio rerio
Homo sapiens
Mus musculus

overall_design: We developed next-generation sequencing methods for quantification of Cap2 methylation in bulk mRNA (CapTag-seq), as well as in individual mRNAs in a transcriptome-wide manner (CLAM-Cap-seq). Furthermore, we developed tools for measuring translation and stability of transcript-start nucleotide (TSN) mRNA isoforms by combining polysome profiling and actinomycin D treatment with TSS-seq (transcription start site-sequencing).

first: Samie

last: Jaffrey


title: A genome-wide relay of signalling-responsive enhancers drives hematopoietic specification (ATAC-seq)

overall_design: ATAC-Seq chromatin profiling from ES cells differentating to hematopoetic progenitor cells in a system using serum and a serum free system, allowing study of changes in cytokine signalling.


title: A genome-wide relay of signalling responsive enhancers drives hematopoietic specification [ATAC-seq]


title: A genome-wide relay of signalling-responsive enhancers drives hematopoietic specification (Single cell RNA-Seq)

overall_design: Chromium 10x Genomics - Single cell RNA-Seq of ES cells differentating to hematopoetic progenitor cells. Cultered in media containing VEGF or without VEGF


title: Identification and N6-Methyladenosine Modification of the different genes in the peri-infarct cortex of PT mice response to circSCMH1 using MeRIP-seq.

status: Public on Dec 08 2022

city: Nanjing

first: bin

last: li

address: No.87 of Dingjiaqiao

institute: Southeast University

summary: Whole MeRIP-sequencing analysis was performed and analyzed by Lc. Aksomics Co. Ltd. (Shanghai, China). The peri-infarct cortex from sham mice, PT mice with EV-Vector, and PT mice with EV-circSCMH1 was collected in TRIzol. Total RNAs were qualified by agarose gel electrophoresis and quantified using Nanodrop. mRNA was isolated and then fragmented to 100-nucleotide-long fragments. m6A methylated mRNAs were enriched with anti-N6-methyadenosine(m6A) antibody. We use commercial kit for RNA-seq library prepa ration of m6A mRNA and input samples. Completed libraries were qualified and then sequenced on Hiseq 4000 platform.

overall_design: Examination of N6-Methyladenosine Modification by Over-expressed circSCMH1 in the peri-infarct cortex of PT mice by MeRIP-seq.

first: Bin

last: Li

first: Honghong

last: Yao


title: A genome-wide relay of signalling-responsive enhancers drives hematopoietic specification

first: Peter

last: Keane


title: Quercetin Prevents Intestinal Stem Cell Aging via Scavenging ROS and Inhibiting Insulin Signaling in Drosophila

status: Public on Dec 06 2022

city: Chengdu

first: Yan

last: La

address: 37 Guoxue Lane, Wuhou District, Chengdu City, Sichuan Province

institute: Sichuan University

summary: Adult stem cells undergo functional degeneration during aging. Quercetin exhibits many beneficial effects against aging and aging-related diseases. Using Drosophila as a model, we explore the efficacy of quercetin against adult stem cell aging and provide effective and feasible therapeutic solutions for preventing the aging-related functional decline of stem cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Drosophila intestine with and without quercetin supplementation

first: La

last: Yan

first: Juanyu

last: Zhou


title: Single cell RNA sequencing and lineage tracing confirm mesenchyme to epithelial transformation (MET) contributes to repair of the endometrium at menstruation

status: Public on Dec 07 2022

city: Edinburgh

first: Philippa

middle: TK

last: Saunders

address: 47 Little France Crescent

department: College of Medicine and Veterinary Medicine

institute: The University of Edinburgh

summary: We profile the transcriptomes of over 20,000 mouse single cells, yielding molecular definitions for mesenchymal and epithelial cell types present in the mouse uterus during post-menstrual tissue repair. We identify a novel population of fibroblasts that express genetic markers associated with both mesenchymal and epithelial phenotypes in the repairing mouse uterus. Further trajectory analysis indictates a differentiation trajectory between mesenchymal and epithelial cells indicative of a putative mesenchymal-to-epithelial transition (MET) event occuring during post-menstrual tissue repair. Our work provides a platform to further understand the roles of these cell populations in uterine physiology and disease and for comparisons between wound healing events in the endometrium and other adult tissue which are prone to fibrosis.

overall_design: 10X Genomics Single cell 3' gene expression V3

first: Phoebe

middle: M

last: Kirkwood

first: Douglas

last: Gibson

first: Isaac

middle: W

last: Shaw

first: Ross

last: Dobie

first: Olympia

last: Kelepouri

first: Neil

middle: C

last: Henderson


title: Acclimation of Nodularia spumigena CCY9914 to inorganic phosphate limitation

city: Rostock-Warnemünde

first: Christiane

last: Hassenrück

address: Seestraße 15

department: Biological Oceanography

institute: Leibniz Institute for Baltic Sea Research Warnemünde (IOW)

summary: Nodularia spumigena is a toxic, filamentous cyanobacterium capable to fix atmospheric N2, which is often dominating cyanobacterial bloom events in the Baltic Sea and other brackish water systems worldwide. Phosphate (P) limitation has been considered as one environmental parameter that is somehow promoting the establishment of cyanobacterial mass developments. In the present study, we analyzed the response of the N. spumigena strain CCY9914 towards strong P limitation in an experimental approach. Filaments of N. spumigena were incubated under P-replete and P-deplete conditions for 21 days. Samples for RNA-seq were collected after 7 and 14 days. Growth of the strain was diminished under P-deplete conditions, however, filaments contained more polyphosphate under P-deplete compared to P-replete conditions. High polyphosphate contents were also detected within heterocysts. After 7 days, approximately 100 genes were upregulated in P-deplete filaments, among them was a high proportion of genes encoding proteins related to P-homeostasis such as transport systems for different P species. Many of these genes became also up-regulated after 14 days compared to 7 days in filaments grown under P-replete conditions, which was consistent with the almost complete consumption of dissolved P in these cultures after 14 days. In addition to genes directly related to P starvation, for example genes encoding proteins for bioactive compound synthesis, gas vesicle formation, or sugar catabolism were stimulated under the P-deplete conditions. Collectively, our data permitted to describe an experimentally validated P-stimulon in N. spumigena CCY9914 and provide evidence that severe P limitation could indeed support bloom formation by this filamentous strain.

overall_design: Filaments of N. spumigena were incubated under P-replete and P-deplete conditions for 21 days. Three independent biological replicates were set-up for each phosphate treatment and sampling day. Samples were sacrificed for analyses at day 0, 7, 14, and 21 of the experiment. Samples for RNA-seq were collected after 7 and 14 days.

first: Mariano

last: Santoro

first: Matthias

last: Labrenz

first: Martin

last: Hagemann


title: Molecular states during acute COVID-19 reveal distinct etiologies of long-term sequelae

first: Ryan

middle: Conrad

last: Thompson

address: 1 Gustave L. Levy Place

department: Charles Bronfman Institute for Personalized Medicine

institute: Icahn School of Medicine at Mount Sinai

summary: Post-acute sequelae of SARS-CoV-2 infection are debilitating, clinically heterogeneous, and of unknown molecular etiology. A transcriptome-wide investigation was performed in acutely infected patients followed clinically into the post-acute period. Distinct gene-expression signatures of post-acute sequelae were already present in whole-blood during acute infection, with innate and adaptive immune cells implicated in different symptoms. Two clusters of sequelae exhibited divergent plasma-cell associated gene-expression patterns. In one cluster, sequelae associated with higher expression of immunoglobulin-related genes in an anti-spike antibody titer-dependent manner. In the other, sequelae associated independently of these titers with lower expression of immunoglobulin-related genes, indicating lower non-specific antibody production in subjects with these sequelae. This relationship between lower total immunoglobulins and sequelae was validated in an external cohort. Altogether, multiple etiologies of post-acute sequelae were already detectable during SARS-CoV-2 infection, directly linking these sequelae with the acute host response to the virus and providing early insights into their development.

overall_design:
Bulk RNA-seq of whole blood sampled longitudinally from hospitalized COVID-19 cases during acute infection as well as from healthy and hospitalized controls. See https://www.synapse.org/#!Synapse:syn35874390/ for full clinical data, RNA-seq QC data, and other data and metadata.
--------------------------
The Mount Sinai COVID-19 Biobank Team

first: Nicole

last: Simons

first: Lillian

last: Wilkins

first: Esther

last: Cheng

first: Diane

last: Del Valle

first: Gabriel

middle: E

last: Hoffman

first: Carlo

last: Cervia

first: Brian

last: Fennessy

first: Konstantinos

last: Mouskas

first: Nancy

middle: J

last: Francoeur

first: Jessica

middle: S

last: Johnson

first: Lauren

last: Lepow

last: Le Berichel

first: Christie

last: Chang

first: Aviva

last: Beckmann

first: Ying-chih

last: Wang

first: Kai

last: Nie

first: Nicholas

last: Zaki

first: Kevin

last: Tuballes

first: Vanessa

last: Barcessat

first: Mario

middle: A

last: Cedillo

first: Dan

last: Yuan

first: Laura

last: Huckins

first: Panagiotis

last: Roussos

first: Thomas

last: Marron

first: Benjamin

last: Glicksberg

first: Girish

last: Nadkarni

first: James

middle: R

last: Heath

first: Edgar

last: Gonzalez-Kozlova

first: Onur

last: Boyman

first: Seunghee

last: Kim-Schulze

first: Robert

last: Sebra

first: Miriam

last: Merad

first: Sacha

last: Gnjatic

first: Eric

last: Schadt

first: Alexander

last: Charney

first: Noam

middle: D


title: Transcriptional profiling of Pseudomonas aeruginosa WT and Pho mutant colony biofilms in response to ethanol and Candida albicans

city: Farmington

first: Mark

last: Adams

address: 10 Discovery Drive

institute: The Jackson Laboratory

summary: Pseudomonas aeruginosa is an opportunistic pathogen frequently isolated from co-infections with Candida albicans and other ethanol-producing organisms. We found that ethanol, including that produced by C. albicans, stimulates the PhoB regulon in P. aeruginosa. We identify a subset of PhoB-regulated genes as differentially expressed in response to ethanol which are slightly different than the set of genes with increased expression in a genetically induced low phosphate response via pstB mutation.

overall_design: Genome-wide transcriptional profiles of Pseduomonas aerguinosa after growth for 24 hours in colony biofilms on minimal media with or without 1 % ethanol or in co-culture with ethanol-producing (adh1∆/ADH1) or non-ethanol-producing (adh1∆/∆) Candida albicans.

first: Georgia

last: Doing

first: Deborah

last: Hogan


title: Skin regeneration is enabled in the absence of fibroblast inflammatory priming

city: Calgary

first: Jeff

last: Biernaskie

state: Alberta

address: 3330 Hospital Drive NW

department: Comparative Biology and Experimental Medicine

country: Canada

institute: University of Calgary

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

Project abstract: In adult mammals, skin wound healing has evolved to favor rapid repair through the formation of fibrotic scar.  These dermal scars are dysfunctional and may lead to chronic disfigurement and disability, yet the biologic mechanisms that drive fibrosis and prevent tissue regeneration remain unknown. Here, we report that reindeer (Rangifer tarandus) antler velvet exhibits regenerative wound healing, whereas identical full-thickness injury in dorsal back skin of the same animal forms fibrotic scar. This regenerative capacity is retained even following ectopic transplantation of velvet to a scar-forming site, demonstrating that this latent regenerative capacity is innate to velvet cells and independent of local factors derived from the growing antler. Single cell RNA-sequencing of uninjured skin revealed a marked divergence in resting fibroblast transcriptional states and immunomodulatory function. Uninjured velvet fibroblast shared a striking resemblance with human fetal fibroblasts whereas uninjured back skin fibroblasts exhibited an overrepresentation of pro-inflammatory genes resembling adult human fibroblasts.  Identical skin injury resulted in site-specific fibroblast polarization; back fibroblasts exacerbated the inflammatory response, whereas velvet fibroblasts adopted an immunosuppressive state and reverted back to a regeneration-competent ground state. Consequently, velvet wounds exhibited an accelerated adoption of anti-inflammatory immune states and an expedited resolution of immune response. This study demonstrates reindeer as a novel comparative mammalian model to study both adult skin regeneration (velvet) and scar formation (back skin) within the same animal. Our study underscores the importance of fibroblast heterogeneity in shaping local immune cell functions that ultimately polarize wound healing outcomes. Purposeful, acute modulation of fibroblast-mediated immune signaling represents an important therapeutic avenue to mitigate scar and improve wound healing.


title: Early life provision of 12-HETE by neutrophils imprints self-renewing capacity on alveolar macrophages

status: Public on Dec 05 2022

city: Chicago

first: Luis

middle: B

last: Barreiro

address: 900 E 57th Street

institute: University of Chicago

summary: The goal of this study is to determine the role of the 12/15-lipoxygenase pathway in the development and maintenance of alveolar macrophages.

overall_design: For scRNA-Seq, CD45+ cells were isolated from the lungs of PND1 WT and Alox15-/- mice (n=1 mouse per group) using Stemcell EasySep mouse CD45 kit. For ATAC-Seq, alveolar macrophages were isolated from adult (6-8 weeks, broncho-alveolar lavages) or neonates (PND3, cell sorted from whole lungs) WT or Alox15-/- animals (n=3 mice per group).

first: Erwan

last: Pernet

first: Sarah

last: Sun

first: Nicole

last: Sarden

first: Saideep

last: Gona

first: Angela

last: Nguyen

first: Nargis

last: Khan

first: Martin

last: Mawhinney

first: Kim

last: Tran

first: Julia

last: Chronopoulos

first: Dnyandeo

last: Amberkar

first: Mina

last: Sadeghi

first: Alexandre

last: Grant

first: Shradha

last: Wali

first: Renaud

last: Prevel

first: Jun

last: Ding

last: Martin

first: Ajitha

last: Thanabalasuriar

first: Bryan

last: Yipp

first: Maziar

last: Divangahi


title: Distinct Transcriptomic and Metabolomic Profiles Characterize NSAID-Induced Urticaria/Angioedema Patients Undergoing Aspirin Desensitization

city: Singapore

first: Nicholas

last: Ang

address: 8a Biomedical Grove, Singapore 138648

country: Singapore

institute: Singapore Immunology Network (SIgN)

summary:
Background:
There is limited data on the mechanisms of aspirin desensitization in patients with nonsteroidal anti-inflammatory drug (NSAID)-induced urticaria/angioedema (NIUA).
Objectives:
To characterize the transcriptomic and metabolomic profiles of NIUA patients undergoing aspirin desensitization.
Methods:
Peripheral blood mononuclear cells (PBMCs) and plasma were separated from the blood of NIUA patients undergoing aspirin desensitization for coronary artery disease and NSAID-tolerant controls.  RNA was isolated from PBMCs and subjected to mRNA- and lncRNA-seq.  Plasma samples were analyzed using LC-MS/MS for metabolite shifts using a semi-targeted metabolomics panel.
Results:
Eleven patients with NIUA and 10 healthy controls were recruited.  The mRNA gene profiles of pre- versus post-desensitization and healthy control versus post-desensitization did not differ significantly.  However, we identified 739 mRNAs and 888 lncRNAs as differentially expressed from pre-aspirin desensitization patients and controls.  A 12-mRNA gene signature was trained using a machine learning algorithm to distinguish between controls, post-dose and pre-dose samples.  Ingenuity Pathway Analysis identified 5 canonical pathways that were significantly enriched in pre-aspirin desensitization samples.  Interleukin (IL)-22 was the most upregulated pathway.  To investigate the potential regulatory roles of the differentially expressed lncRNA on the mRNAs, 9 lncRNAs and 12 mRNAs showed significantly correlated expression patterns in the IL-22 pathway.  To validate the transcriptomics data, IL-22 was measured in the plasma samples of the subjects using ELISA.  IL-22 was significantly higher in pre-aspirin desensitization patients compared to controls.  In parallel, metabolomic analysis revealed stark differences in plasma profiles of pre-aspirin desensitization patients and healthy controls. In particular, 2-hydroxybenzoic acid (salicylic acid) was significantly lower in pre-aspirin desensitization patients compared to healthy controls.
Conclusion:
This is the first study to combine both transcriptomic and metabolomic approaches in patients with NIUA, which contributes to a deeper understanding about the pathogenesis of NIUA and may potentially pave the way towards a molecular diagnosis of NSAID hypersensitivity.

overall_design: 10 NIUA patients and 10 NSAID-tolerant controls were recruited for the transcriptomics study.  Blood from NIUA patients were collected at basal state, immediately before the start of aspirin desensitization (pre-dose samples).  Patients underwent a rapid aspirin desensitization protocol, as described in the supplemental information.  Blood was collected again after the end of the procedure (1 h after the last dose, post-dose samples).

first: Sen

middle: H

last: Tay


title: Timing and cell specificity of senescence drives postnatal lung development and injury

city: Providence

first: Nathalie

last: Oulhen

state: RI

address: 185 meeting street

institute: Brown university

summary: Senescence causes age-related diseases and stress-related injury. Paradoxically, it is also essential for organismal development. Whether senescence contributes to lung development or injury in early life remains unclear. This work defines the ontogeny of lung senescence and provides an optimal therapeutic window for mitigating neonatal hyperoxic lung injury by clearing senescence.

overall_design: Newborn C57BL/6J (<12 h old) along with their mothers were exposed to room air or hyperoxia (>95% O2) for 3 days in an A-chamber. The dams were switched between exposed litters and room air control litters every 24 h in 3 days exposed animals to avoid maternal injury. For time points beyond pnd3, the pups were allowed to recover in room air until postnatal da 7 (pnd7). All animal experiments were reviewed and approved by the Institutional Animal Care and Use Committee of Brown University. At pnd7, lung from hyperoxia-exposed mice was dissociated into single cell, and suspensions from three mouse lungs were pooled. The FACS was utilized to sort C12FDG positive cells from the lung suspensions. Single cell encapsulation was performed using the Chromium Single Cell Chip G kit on the 10× Genomics Chromium Controller, and single cell cDNA was sequenced by Genewiz on the Illumina Hiseq (2×150 bp paired-end runs). We also revisited and mined our published scRNA-seq dataset from hyperoxia- or air-exposed mice at pnd7 as controls (PMID: 34417156). Computational analysis on expression of genes involved in senescence and SASP (senescence-associated secretory phenotype) was analyzed using the R package Seurat v 3.2.1.

first: Hongwei

last: Yao

first: Abigail

middle: L

last: Peterson

first: Salu

last: Rizal

first: Alejandro

last: Scaffa

first: Joselynn

last: Wallace

first: Katy

last: Hegarty

first: Hajime

last: Maeda

first: Jill

last: Kreiling

first: Guilherme

last: Barbosa

first: Jason

last: Chang

first: Kelsey

last: Huntington

first: Monique

last: De Paepe

first: Phyllis

last: Dennery


title: Flt3- and Tie2-Cre tracing identifies regeneration in sepsis from multipotent progenitors but not hematopoietic stem cells

first: Xi

last: Wang

address: Longmian Avenue 101, Jiangning District

institute: Nanjing Medical University

summary: Increased hematopoietic stem cell (HSC) proliferation in response to infections might reflect enhanced HSC contributions for rapid replenishment of blood and immune cell compartments. However, there is no direct evidence in vivo for enhanced HSC differentiation to natural challenges. Here we studied by non-invasive fate mapping HSC differentiation for a comprehensive set of hematopoietic challenges, including irradiation, polymicrobial sepsis, bleeding, antibody-mediated ablation of granulocytes or B lymphocytes (akin to Rituximab in humans), and genetic lymphocyte deficiency. HSC sensed systemic infection, upregulated transcription factors promoting stem cell self-renewal (Foxp1, Atf4), stem cell maintenance (cMyc and nMyc), transcription in stressed cells (Hsf1) and suppression of apoptosis (E2f4), and enhanced their proliferation. However, none of these acute or chronic hematopoietic stressors enhanced HSC output in situ, suggesting HSC protection and maintenance rather than heightened differentiation. This disconnect may prioritize the long-term integrity of HSC over short-term enhanced productivity in response to hematopoietic perturbations.

overall_design: HSC, ST-HSC, MPP, and CMP were purified by cell sorting from male C57BL/6 (RosaYFP) mice one day (#29 and #31), or three days (#40) after infection, or uninfected mice (#24, #25 and #42). For the “day 1” experiment, two biological replicates for each group (infected and uninfected) were sorted. Single cells were captured using the Chromium System according to the Chromium Single Cell 3’ Reagent Kit protocols (10x Genomics).

first: Ann-Kathrin

last: Fanti

first: Katrin

last: Busch

first: Alessandro

last: Greco

first: Thomas

last: Höfer

first: Hans-Reimer

last: Rodewald


title: Genome wide mapping of DBP6-HTP binding sites in yeast by CRAC

city: PARIS

first: Simon

last: Lebaron

address: 4 avenue de l'observatoire

institute: Université Paris Descartes

summary: We report the application of the Cross-Linking and cDNA (CRAC) technique to identify binding sites of DBP6, ribosome assembly factors, on RNAs in vivo. Once sequenced, RNAs associated have been aligned to the yeast genomes and enrichment of specific RNAs has been studied in more details. Specifically apparition of Mutation/deletion in the reads are of interesdt since they mostly corresponds to prceise site of cross-link between bait protein and target RNA. Here DBP6-HTP is mostly bound to snoRNAs (SNR30, SNR10, SNR42, SRN3,SRN190 and SNR13) and 25S rRNA around the same binding sites of the identifed snoRNAs.

overall_design: We compare sequences enrichement of RNAs associated to Nap1_HTP or to a mock (un-tagged) control after protein/RNA cross-link in vivo.

first: Odile

last: Humbert

first: Anthony

last: Henras

first: Ali

last: Khreiss


title: Transcriptional response of M. tuberculosis (Mtb) STPKs

status: Public on Dec 03 2022

city: Seattle

first: Christoph

last: Grundner

state: WA

address: 307 Westlake Ave N

department: CGIDR

institute: Seattle Children's Research Institute

summary: To understand the transcriptional response of M. tuberculosis (Mtb) STPKs, we performed transcriptomics on WT and STPK mutants grown to stationary phase.

overall_design: Bacteria were harvested at early stationary phase.  RNA was isolated and gene expresion quantified by sequencing.

first: Andrew

last: Frando


title: Endogenous expression of the R-RAS2 GTPase carrying the Q72L hotspot mutation is relevant for the tumorigenic phenotype of cancer cells

city: Salamanca

first: L. Francisco

last: Lorenzo-Martín

state: Castilla y León

address: Campus Miguel de Unamuno

country: Spain

institute: University of Salamanca (USAL) – Centro de Investigación del Cáncer (CIC)

summary:
The R-RAS2 GTPase has been considered quite similar to classical RAS proteins at the regulatory, signaling, and functional level. The interest in this GTPase has been reinvigorated upon the recent discovery that a long-tail hotspot RRAS2 mutation found in human tumors (Gln72 to Leu) can act as a potent oncogenic driver.
Here, we report that the Q72L mutation and other gain-of-function mutations of RRAS2 play roles in tumor initiation and maintenance. Such roles are unlikely to be redundant to those normally executed by classical RAS proteins.

overall_design: Control and R-RAS2Q72L-knockout A2780 cells

first: Laura

last: Clavaín

first: Isabel

last: Fernández-Pisonero

first: Nieves

last: Movilla

first: L

middle: F

first: Blanca

last: Nieto

first: Antonio

last: Abad

first: Rósula

last: García-Navas

first: Clara

last: Llorente-González

first: Manuel

last: Sánchez-Martín

first: Miguel

last: Vicente-Manzanares

first: José

last: García-Aznar

first: Eugenio

last: Santos

first: Balbino

last: Alarcón

first: Mercedes

last: Dosil

first: Xosé

last: Bustelo


title: Humanized V(D)J-rearranging and TdT-expressing Mouse Vaccine Models with Physiological HIV-1 Broadly Neutralizing Antibody Precursors

status: Public on Dec 01 2022

city: Boston

first: Frederick

last: Alt

state: MA

address: 1 Blackfan Circle

department: Program in Cellular and Molecular Medicine

institute: Boston Children's Hospital

summary: Antibody heavy chain (HC) and light chain (LC) variable region exons are assembled by V(D)J recombination. V(D)J junctional regions encode complementarity-determining-region 3 (CDR3), an antigen-contact region immensely diversified through non-templated nucleotide additions ("N-regions") by terminal deoxynucleotidyl transferase (TdT).  HIV-1 vaccine strategies seek to elicit human HIV-1 broadly neutralizing antibodies (bnAbs), such as the potent CD4-binding site VRC01-class bnAbs.  Mice with primary B cells that express receptors (BCRs) representing bnAb precursors are used as vaccination models. VRC01-class bnAbs uniformly use human HC VH1-2 and commonly use human LCs Vk3-20 or Vk1-33 associated with an exceptionally short 5-amino-acid (5-aa) CDR3.  Prior VRC01-class models had non-physiological precursor levels and/or limited precursor diversity.  Here, we describe VRC01-class rearranging mice that generate more physiological primary VRC01-class BCR repertoires via rearrangement of VH1-2, as well as Vk1-33 and/or Vk3-20 in association with diverse CDR3s.  Human-like TdT expression in mouse precursor B cells increased LC CDR3 length and diversity and also promoted generation of shorter LC CDR3s via N-region suppression of dominant microhomology-mediated Vk-to-Jk joins.  Priming immunization with eOD-GT8 60mer, which strongly engages VRC01 precursors, induced robust VRC01-class germinal center (GC) B cell responses. Vk3-20-based responses were enhanced by N-region addition, which generates Vk3-20-to-Jk junctional sequence combinations that encode VRC01-class 5-aa CDR3s with a critical E residue. VRC01-class-rearranging models should facilitate further evaluation of VRC01-class prime and boost immunogens.  These new VRC01-class mouse models establish a prototype for generation of vaccine-testing mouse models for other HIV-1 bnAb lineages that employ different HC or LC Vs.

overall_design: HTGTS-rep-seq and HTGTS-SHM-seq

first: Sai

last: Luo

first: Changbin

last: Jing

first: Adam

middle: Y

last: Ye

first: Sven

last: Kratochvil

first: Cristopher

last: Cottrell

first: Ja-hyun

last: Koo

first: Aimee

last: Williams

first: Lucas

last: Vieira Francisco

first: Himanshu

last: Batra

first: Edward

last: Lamperti

first: Yuxiang

last: Zhang

first: Alessandro

last: Barbieri

first: John

middle: P

last: Manis

first: Barton

last: Haynes

first: William

last: Schief

first: Facundo

last: Batista

first: Ming

last: Tian


title: Transcritome analysis of HeLa cells under ER or metabolic stress

status: Public on Dec 02 2022

city: Hefei

first: Xiaolin

last: Wang

address: Huangshan Road

institute: USTC

summary: To investigate functional ncRNAs in response to cellular stresses, we performed high-throughput RNA sequencing (RNA-seq) of HeLa cells under ER or metabolic stresses.

overall_design: We performed ribosomal RNA (rRNA) depleted RNA sequencing (RNA-seq) of human HeLa cells treated with thapsigargin (TG, inducing ER stress) or glucose deprivation (GD, inducing metabolic oxidative stress).

first: Xiuzhi

last: Li

first: Jingxin


title: Transcription of HBV cccDNA is synchronized at single-cell level and orchestrated by expression of HBx

city: Beijing

first: Zhiyi

last: Jing

address: 7 Science Park Road ZGC Life Science Park

institute: NIBS

summary: Chronic infection of Hepatitis B virus (HBV) remains a public health problem worldwide. HBV infection relies on the persistence of covalently closed circular DNA (cccDNA) in the nucleus and actively cccDNA transcription. To understand HBV cccDNA transcription regulation at single cell level, we isolated primary human hepatocytes from liver humanized FRG mice infected by one or more (two or three) HBV genotypes, and we quantified transcripts of HBV structural genes in single cells. HBV transcripts were ascribed to the transcription of individual HBV genes by 5’ end sequencing thus avoiding the ambiguity caused by the overlap of viral genome coding at the 3’ ends. Transcripts from different cccDNA in single cells were separated according to the single-nucleotide polymorphism (SNP) among different HBV genotypes. We found that the transcription of HBV follows “all-or-none” pattern in single cells: either all of the individual cccDNA molecules actively transcribe simultaneously, or, none of them generates transcripts of the structural genes. In vitro cell infection assays with recombinant HBV are consistent with the sequencing results of ex vivo samples from natural HBV infection, and also confirm that such a pattern is apparently controlled by the expression of HBx protein. These results strongly support a synchronized transcription model of HBV cccDNA molecules in single hepatocytes, and provide new insight helpful for developing HBV cure strategy.

overall_design:
02 humanized liver samples treated with HBV for 150days, 18 humanized liver samples treated with HBV for 180days, 492 humanized liver samples treated with Genotype A and D HBV for 77 days, 907 humanized liver samples treated with Genotype A,C and D HBV for 119 days, HBV X Minus PHH sample treated with HBV for 7days were collected for single cell RNA sequencing by 10X Genomics)
18 humanized liver samples treated with HBV for 180days, 993 humanized liver samples treated with HBV for 193days were collected for DNA sequencing

first: Bo

last: Peng

first: Wenhui

first: Bin


title: High-throughput sequencing analyses of transcript changes in growth plates upon dexamethasone treatment

city: Shanghai

first: Yuan

last: Xiao

address: No.197, Rui Jin Er Road

department: Department of Pediatrics

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

summary: Glucocorticoid-induced growth retardation (GIGR) is a common adverse effect of glucocorticoid treatment in pediatric patients. Accumulating evidence indicates that non-coding RNAs (ncRNAs) are involved in the pathogenesis of GIGR, but the roles of specific ncRNAs in growth remain largely unknown. In this study, we established an in vivo GIGR rat model by 7- or 14- day dexamethasone (Dex) treatment and performed high-throughput RNA sequencing to identify mRNAs, lncRNAs, circRNAs, and miRNAs differentially expressed in GIGR rats relative to control rats in the growth plates.High-throughput RNA sequencing identified 1718 mRNAs, 896 lncRNAs, 60 circRNAs, and 72 miRNAs with differing expression levels at 7d group. At 14d group, 1515 mRNAs, 880 lncRNAs, 46 circRNAs, and 55 miRNAs with differential expression were identified. Eight mRNAs were validated by RT-qPCR, with expression level differences consistent with RNA sequencing data. Function enrichment analyses indicate that the PI3K-Akt signaling pathway, NF-kappa B signaling pathway, and TGF-beta signaling pathway participated in the development of the GIGR. Then, ceRNA networks were constructed to investigate the potential molecular mechanisms of ncRNAs. These results provide new insights for exploring the molecular mechanisms underlying GIGR.

overall_design: mRNA, lncRNA,circRNA and miRNA profiles of growth plate chondrocytes from GIGR rats and control rats

first: Mingyue

last: Yin


title: Distinct roles for human mtIF2 and mtIF3 in non-canonical mitochondrial translation.

city: Stockholm

first: Shreekara

last: Gopalakrishna

state: Solna

address: Solnavägen 9

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

summary: The synthesis of mitochondrial OXPHOS complexes is central to cellular metabolism, yet many molecular details of mitochondrial translation remain elusive. It is commonly held view that translation initiation in human mitochondria proceeded in a manner similar to bacterial systems, with the mitoribosomal small subunit bound to the initiation factors, mtIF2 and mtIF3, along with initiator tRNA and an mRNA. However, unlike in bacteria, most human mitochondrial mRNAs lack 5′ leader sequences that can mediate small subunit binding, raising the question of how leaderless mRNAs are recognized by mitoribosomes. By using novel in vitro mitochondrial translation initiation assays, alongside biochemical and genetic characterization of cellular knockouts of mitochondrial translation factors, we describe unique features of translation initiation in human mitochondria. We show that in vitro, leaderless mRNA transcripts can be loaded directly onto assembled 55S mitoribosomes, but not onto the mitoribosomal small subunit (28S). In addition, we demonstrate that while mtIF2 is indispensable for mitochondrial translation, mtIF3 activity is not required for translation of leaderless mitochondrial transcripts but is essential for translation of ATP6 in the case of the bicistronic ATP8/ATP6 transcript. Our results confirm important evolutionary divergences of the mitochondrial translation system, and further our understanding of a process central to eukaryotic metabolism.

overall_design: Mitochondrial Ribosome profiling RNASeq data of Mitochondrial ribosomal profling from mtIF3 knock-out HEK cells versus wildtype

first: Cristina

last: Remes

first: Anas

last: Khawaja

first: Sarah

last: Pearce

first: Adam

last: Dinan

first: Miriam

last: Cipullo

first: Vasileios

last: Kyriakidis

first: Jingdian

first: Xaquin

last: Dopico

first: Olessya

last: Yukhnovets

first: Ilian

last: Atanassov

first: Andrew

last: Firth

first: Barry

last: Cooperman

first: Joanna

last: Rorbach


title: Compound heterozygous mutations in the noncoding RNU4ATAC gene affect the homeostasis and function of the Integrator complex

city: Villeurbanne

first: Audric

last: Cologne

address: 43 Bd du 11 Novembre 1918

institute: CNRS

summary: Various genetic diseases associated with microcephaly and developmental defects are due to pathogenic variants in the U4atac snRNA, a component of the minor spliceosome essential for the removal of U12-type introns from eukaryotic messenger RNAs. While it has been shown that a few RNU4ATAC mutations result in impaired binding of essential protein components, the molecular defects of the vast majority are still unknown. Here, we used cells derived from two RNU4ATAC compound heterozygous (g.108_126del;g.111G>A) twin patients with MOPD1 phenotypes to analyze the molecular consequences of the mutations on snRNPs formation and splicing. We show that the U4atac108_126del mutant is unstable and that the 111G>A mutation located in the apical 3’ stem-loop of U4atac induces defects in 3’-end maturation giving rise to decreased levels of mature U4atacG111A snRNA as well as of minor di- and tri-snRNPs. We also found that the mutant cells have alterations in splicing of minor introns and contain lower levels of INTS7 and INTS10 proteins. Altogether, our results demonstrate that the compound heterozygous g.108_126del;g.111G>A U4atac mutations lead to defects in 3’-end processing of U4atac transcripts and affect the homeostasis and function of the Integrator complex.

overall_design: RNA-seq on mRNA from 1 control and 2 MOPD1 patients (2 replicates of each)

first: Remy

last: Bordonne

first: Vicent

last: Lacroix

first: Sylvie

last: Mazoyer

first: Patrick

last: Edery


title: CD4 + T-cell help explains clinical benefit of specific intra-tumoral dendritic cell states in human cancer

city: Leiden

first: Yanling

last: Xiao

country: Netherlands

institute: LUMC

summary: Classical type 1 dendritic cells (cDC1) have a low abundance in the tumor microenvironment (TME), but positively correlate with patient survival. We hypothesized that the ability of cDC1 to relay CD4+ T-cell help for the cytotoxic T lymphocyte (CTL) response explains their clinical benefit. In vitro, contact with activated CD4+ T-cells enabled human cDC1, but no other DC types, to induce a CTL response to cell-associated tumor antigens. Single cell transcriptomics revealed that CD4+ T-cell help uniquely optimized cDC1 and no other DC types in many functions that support antigen cross-presentation and T-cell priming. We robustly identified “helped” cDC1 in a multitude of human cancer types by the overlap in their transcriptomic signature with that of recently defined, positively prognostic tumor-infiltrating DC states. As predicted from the functional effects of CD4+ T-cell help, the transcriptomic signature of “helped” cDC1 correlated with tumor infiltration by CTL and Thelper(h)-1 cells, overall survival and response to PD-1-targeting immunotherapy. These findings reveal a critical role of CD4+ T-cell help delivery via cDC1 to CTL in the TME

overall_design: PBMCs from 3 healthy donors were stained with the appropriate antibodies and within the live CD3-CD19-HLA-DR+ population, pDC (CD11c-CD14-CD303+), cDC1 (CD11c+CD14-CD141+), cDC2 (CD11c+CD14-CD1c+), and moDC (CD11c+CD14+CD1c+CD206+) were sorted, RNA was isolated, cDNA was generated and sequenced.

first: Xin

last: Lei

first: Jannie

last: Borst


title: Uncharged tRNAGln as an indicator of intracellular amino acid level upregulates UBC expression to maintain its charging level I

status: Public on Nov 30 2022

city: Ibaraki

first: Tomonori

last: Kimura

state: Osaka

address: 7-6-8 Saito-Asagi

department: Center for Rare Disease Research

country: Japan

institute: National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN)

summary: We profiled the cellular tRNA charging landscape using next-generation sequencing and identified a subset of tRNA that sense nutrients. The charging levels of tRNAGln were exclusively and significantly decreased in response to amino acid starvation.

overall_design: 3 biological replicates of tRNA from primary lung or dermal fibroblasts under amino acid starvation or amino acid rich condition are analyzed

first: Yusuke

last: Tsukamoto

first: Yumi

last: Nakamura

first: Makoto

last: Hirata

first: Daisuke

last: Okuzaki

first: Ryuichi

last: Sakate


title: Variable phenotypes and penetrance between and within different zebrafish transition zone mutants

city: Birmingham

first: John

last: Parant

state: AL

address: 1670 University Blvd

institute: University of Alabama at Birmingham

summary: Meckel Syndrome, Nephronophthisis, Joubert Syndrome, and Bardet-Biedl Syndrome have mutations in proteins that localize to the ciliary transition zone (TZ). The phenotypically distinct syndromes suggest these TZ proteins have differing functions. However, mutations in a single TZ gene can result in multiple syndromes suggesting the phenotype is influenced by modifier genes. We performed a comprehensive analysis of ten zebrafish TZ mutants including mks1, tmem216, tmem67, rpgrip1l, cc2d2a, b9d2, cep290, tctn1, nphp1, and nphp4, as well as mutants in ift88 and ift172. Our data indicate variations in phenotypes exists between different TZ mutants, supporting different tissue specific functions of these TZ genes. Further we observed phenotypic variations within progeny of a single TZ mutant, reminiscent of multiple disease syndromes being associated with mutations in one gene. In some mutants the dynamics of the phenotype became complex with transitory phenotypes that are corrected over time. We have also demonstrated that multiple-guide derived CRISPR/Cas9 F0 “Crispant” embryos recapitulate zygotic null phenotypes, and rapidly identified ciliary phenotypes in 11 cilia-associated gene candidates (ankfn1, ccdc65, cfap57, fhad1, nme7, pacrg, saxo2, c1orf194, ttc26, zmynd12, and cfap52).

overall_design: The homozygous mutant (including ift172, ift88, b9d2, mks1, cc2d2a, tmem216, cep290, tmem67) embryos were obtained from multiple pairs of heterozygous mutant crosses. The rpgrip1l-/- embryos were obtained from multiple pairs of homozygous crosses. The wild-type embryos were obtained from multiple pairs of AB-strain wild-type crosses (the zebrafish strain used for generating all cilia-related mutants). To obtain embryos from same developmental stage for each allele, 20-min timed mating were performed. For 5 days post fertilization (dpf) analysis, RNA was harvested from, ift172, ift88, b9d2, tmem216, cep290, tmem67 mutant embryos (~30-35 mutant embryos/sample) sorted at 2 dpf based on the curled-down tail (CDT) phenotype. b9d2 and mks1 mutant embryos were identified by genotyping DNA extracted from the 5-dpf embryo tail. For 2 dpf analysis, RNA was harvested from rpgrip1l-/- embryos (~30-35 embryos/sample) that were sorted into two groups based on the CDT and normal-looking (normal) phenotype. RNA samples were prepared with Qiagen RNeasy Plus Mini Kit. RNA library was prepared with Illumina RNA with PolyA selection package and sequenced with Illumina HiSeq 2x150bp, single index.


title: Uncharged tRNAGln as an indicator of intracellular amino acid level upregulates UBC expression to maintain its charging level

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

overall_design: Refer to individual Series


title: Innate type 2 immunity controls hair follicle commensalism by Demodex mites [IL-4, IL-13]

status: Public on Nov 29 2022

city: San Francisco

first: Roberto

last: Ricardo-Gonzalez

state: CA

address: 513 Parnassus Ave, HSE-1001

institute: University of California San Francisco

summary: Demodex mites are obligate commensal parasites of hair follicles (HF) in mammals.  Normally asymptomatic, inflammatory outgrowth of mites can accompany malnutrition, immune dysfunction and aging, but mechanisms restricting Demodex outgrowth and pathogenesis are not defined. Here, we show that control over mite HF colonization of mice requires ILC2s, IL-13, and its receptor IL-4Ra, but not IL-4 or the adaptive immune system.  Epithelial HF-associated ILC2s elaborate IL-13 that attenuates HF and epithelial cell proliferation at anagen onset; in their absence, Demodex colonization leads to increased epithelial proliferation and replacement of gene programs for repair by aberrant inflammatory programs leading to loss of barrier function and premature HF exhaustion over time.  Humans with rhinophymatous acne rosacea, a nasal inflammatory condition associated with a high burden of Demodex, had increased HF inflammatory cells with decreased type 2 cytokines, consistent with the inverse relationship seen in mice. Our studies uncover a critical role for skin ILC2s and IL-13, which comprise an immune checkpoint necessary to sustain cutaneous integrity and restrict pathologic infestation by colonizing HF mites.

overall_design: 2-month-old female WT B6 mice were injected I.P. with 3ug of IL-4 or IL-13 on days -5, -3, and -1 before harvest and analyses. These samples were processed concurrently with WT B6 uninfected controls or WT B6 exposed to Demodex mite for 1 month (GSE197982).

first: Andrew

last: Schroeder

first: Richard

last: Locksley


title: Uncharged tRNAGln as an indicator of intracellular amino acid level upregulates UBC expression to maintain its charging level V

overall_design: 5 biological replicates of RNA from TIG-1 cells under amino acid starvation or amino acid rich condition are analyzed


title: Uncharged tRNAGln as an indicator of intracellular amino acid level upregulates UBC expression to maintain its charging level IV

overall_design: 4 biological replicates of RNA from TIG-1 cells under amino acid starvation or amino acid rich condition are analyzed


title: Uncharged tRNAGln as an indicator of intracellular amino acid level upregulates UBC expression to maintain its charging level VI

overall_design: 5 biological replicates of tRNA from young or old TIG-1 cells under amino acid starvation or amino acid rich condition are analyzed


title: Microglia renewal in old mice enhances the cellular fitness to cope with stroke

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

institute: CIBEREHD

summary: Microglial cells of the aged brain manifest signs of dysfunction that could contribute to the worst neurological outcome of stroke in the elderly. Treatment with colony-stimulating factor 1 receptor antagonists enables microglia depletion that is followed by microglia repopulation after interruption of the treatment, without any known harm to the mice. We used this strategy aiming to rejuvenate microglia function and ameliorate stroke outcome in aged mice.  Cerebral ischemia/reperfusion induced strong innate immune responses in microglia highlighted by prominent type-I interferon signalling, together with cellular metabolic perturbances and lipid droplet biogenesis. Old age increased innate immune responses in microglia, which also showed more lipid droplets than microglia of young mice. Microglia renewal in old mice prevented the exaggerated type I interferon response observed in microglia after stroke, reduced the lipid droplet content, and improved the neurological outcome of stroke. This study shows that microglia renewal in old mice rejuvenates some features of old microglia and improves stroke outcome.

overall_design: Transcriptomic analysis from Brain microglia in young (Y)  (n=7) and old (O) (n=5). Induction for microglia repopulation were done in young (Y-re) (n=3) and old mices (n=8).

first: A

last: Planas

first: M

last: Arbaizar

first: J

last: Pedragosa

first: C

last: Casal


title: STING governs RCC growth through mitochondrial regulation of VDAC2

city: Chapel Hill

first: Austin

last: Hepperla

address: 7018B Mary Ellen Jones Building

institute: University of North Carolina at Chapel Hill

summary: STING is an innate immune sensor for immune surveillance of viral or bacterial infection and maintenance of an immune-friendly microenvironment to unfavored tumorigenesis. Whether and how STING exerts any innate immunity independent function remains elusive. Here, we report that STING expression is increased in RCC patients and STING governs RCC growth through non-canonical innate immune signaling by maintaining mitochondrial ROS and calcium homeostasis. Mechanistically, we identify mitochondrial calcium transporter VDAC2 as a new STING binding partner and downstream effector, through suppression of which STING controls proper mitochondrial ROS/calcium levels. We also find palmitoylation of STING-C88/C91 residues is critical to mediate STING interaction with VDAC2 and inhibiting STING palmitoyl-transferases ZDHHCs by 2-BP significantly impedes RCC cell growth. Together, our studies reveal an innate immunity-independent function of STING in regulating RCC mitochondrial function and growth. We hope our study provides a rationale to apply palmitoylation inhibitors to treating RCC.

overall_design: RNA-seq in ccRCC cell line A498 with two STING knockdowns (sh29 and sh45) versus knockdown control (shCtrl)

first: Zhichuan

last: Zhu

first: Xin

last: Zhou

first: Hongwei

last: Du

first: Erica

last: Cloer

first: Jiaming

last: Zhang

first: Liu

last: Mei

first: Ying

last: Wang

first: Xianming

last: Tan

first: Yang

first: Jeremy

last: Simon

first: Huanghe

last: Yang

first: Jean

middle: G

last: Cook

first: Michael

last: Major

first: Ganpietro

last: Dotti

first: Pengda

last: Liu


title: Comparison of microglia of old vs. young ischemic male mice

first: Juanjo

last: Lozano

summary: We subjected old (21-22 month) and young (3-4 month) male C57BL/6  mice to 45 min transient oclusion of the middle cerebral artery and obtained the brain four days later. We obtained bodipy+ microglia from the ischemic brain tissue by FACS.

overall_design: Transcriptomic analysis from  microglia of old (n=3)  vs. Young (n=4) male mice.

first: A

middle: M

last: Planas

first: M

last: Arbaizar

last: Gallizioli

first: J

last: Pedragosa

last: JLozano


title: Uncharged tRNAGln as an indicator of intracellular amino acid level upregulates UBC expression to maintain its charging level III

first: Tomonori

last: Kimura

first: Yusuke

last: Tsukamoto

first: Yumi

last: Nakamura

first: Makoto

last: Hirata

first: Daisuke

last: Okuzaki

first: Ryuichi

last: Sakate


title: The N6-methyladenosine RNA landscape in aged mouse hippocampus

status: Public on Nov 28 2022

city: Brisbane

first: He

last: Huang

state: QUEENSLAND

address: THE UNIVERSITY OF QUEENSLAND, ST LUCIA

institute: The University of Queensland


title: Uncharged tRNAGln as an indicator of intracellular amino acid level upregulates UBC expression to maintain its charging level II

overall_design: 4 biological replicates of tRNA from TIG-1 cells under amino acid starvation or amino acid rich condition are analyzed