title: ZFP281-BRCA2 prevents R-loop accumulation during DNA replication

city: Nanjing

first: Xiaoxu

last: Liu

state: Jiangsu

address: 2 Sipailou

department: Institute of Life Sciences

institute: Southeast University

summary: R-loops are prevalent in mammalian genomes and involved in many fundamental cellular processes. Depletion of BRCA2 leads to aberrant R-loop accumulation, contributing to genome instability. Here, we show that ZFP281 cooperates with BRCA2 in preventing R-loop accumulation to facilitate DNA replication in embryonic stem cells. Mechanistically, we demonstrate that ZFP281 can interact with BRCA2, and that BRCA2 is enriched at G/C-rich promoters and requires both ZFP281 and PRC2 for its proper recruitment to the bivalent chromatin at the genome-wide scale. Furthermore, depletion of ZFP281 or BRCA2 leads to accumulation of R-loops over the bivalent regions, and compromises activation of the developmental genes by retinoic acid during stem cell differentiation. In summary, our results reveal that ZFP281 recruits BRCA2 to the bivalent chromatin regions to ensure proper progression of DNA replication through preventing persistent R-loops.

overall_design: ChIP-seq of BRCA2 in EED WT and KO ES cells. ChIP-seq of BRCA2 in mES cells after ZFP281 shRNA and non-targeting shRNA. ChIP-seq of BRCA2 in ZFP281 WT and KO ES cells.

first: Chengqi

last: Lin


title: Gene expression profiling of NUAK kinase overexpression in Drosophila larval muscle development

status: Public on May 30 2022

city: Manhattan

first: Erika

middle: R

last: Geisbrecht

state: KS

address: 141 Chalmers Hall, Chalmers Hall

department: Biochemistry and Molecular Biophysics

country: USA

institute: Kansas State University

type: Expression profiling by high throughput sequencing

summary: Signal transduction pathways mediated by kinases control diverse biological outputs at the level of cells and tissues to regulate a diverse array of biological and developmental events. To gain insight into how muscle expression of the evolutionarily conserved NUAK kinase regulates the transcriptional landscape during Drosophila melanogaster development, we performed high-throughput sequencing of RNA from either whole larvae or dissected muscle fillets at the end of larval development. Raw data was generated using the Illumina HiSeq platform. After trimming and mapping to the Drosophila reference genome, differential gene expression and GO enrichment analysis were completed.

overall_design:
Comparative gene expression profiling analysis of RNA-seq data for mef2>lacZ control or NUAK (mef2>NUAK 548 or mef2>NUAK 550) overexpression samples.
grant information: RO1 AR060788
Mechanisms Underlying Muscle Development and Maintenance in Drosophila, NIH/NIAMS

first: David

last: Brooks


title: Calcium/calmodulin-dependent protein kinase IV promotes imiquimod-induced psoriatic inflammation via macrophages and keratinocytes in mice

status: Public on May 28 2022

city: Ningbo

first: Liang

last: Yong

state: Zhejiang

address: No. 59, Liuting Street

country: China

institute: The First Affiliated Hospital of Ningbo University

summary: CaMK4 has an important function in autoimmune diseases, and the contribution of CaMK4 in psoriasis remains obscure. Here, we show that CaMK4 expression is significantly increased in psoriatic lesional skin from psoriasis patients compared to healthy human skin as well as inflamed skin from an imiquimod (IMQ)-induced mouse model of psoriasis compared to healthy mouse skin. Camk4-deficient (Camk4−/−) mice treated with IMQ exhibit reduced severity of psoriasis compared to wild-type (WT) mice. There are more macrophages and fewer IL-17A+γδ TCR+ cells in the skin of IMQ-treated Camk4−/− mice compared to IMQ-treated WT mice. CaMK4 inhibits IL-10 production by macrophages, thus allowing excessive psoriatic inflammation. Deletion of Camk4 in macrophages alleviates IMQ-induced psoriatic inflammation in mice. In keratinocytes, CaMK4 inhibits apoptosis as well as promotes cell proliferation and the expression of pro-inflammatory genes such as S100A8 and CAMP. Taken together, these data indicate that CaMK4 regulates IMQ-induced psoriasis by sustaining inflammation and provides a potential target for psoriasis treatment.

overall_design: Comparison of transcription profile between the whole skin of IMQ-treated WT (Camk4+/+) and KO (Camk4−/−) mice.


title: Hematopoietic differentiation of human iPSC is hardly affected by knockouts in DNMT3A exons despite loss of de novo DNA methylation

status: Public on May 31 2022

city: Aachen

first: Wolfgang

last: Wagner

address: Pauwelsstrasse 20

department: Helmholtz Institute for Biomedical Engineering

country: Germany

institute: RWTH Aachen University

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

overall_design: Refer to individual Series


title: A complex epigenome-splicing crosstalk governs epithelial to mesenchymal transition in metastasis and brain development

city: Odense M

first: Vijay

last: Tiwari

state: Denmark

address: Campusvej 55

department: Institut for Molekylær Medicin (IMM)

country: Denmark

institute: Queen’s University Belfast

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Epithelial to Mesenchymal Transition (EMT) renders epithelial cells migratory properties. While epigenetic and splicing changes have been implicated in EMT, the mechanisms governing their crosstalk remain poorly understood. Here, we discovered a C2H2 zinc finger protein, ZNF827, is strongly induced during various contexts of EMT including in brain development and breast cancer metastasis and is required for the molecular and phenotypic changes underlying EMT in these processes. Mechanistically, ZNF827 mediated these responses by orchestrating a large-scale remodeling of the splicing landscape by recruiting HDAC1 for epigenetic modulation of distinct genomic loci, thereby slowing RNA Pol II progression and altering the splicing of genes encoding key EMT regulators in cis. Our findings reveal an unprecedented complexity of crosstalk between epigenetic landscape and splicing programme in governing EMT and identify ZNF827 as a master regulator coupling these processes during EMT in brain development and breast cancer metastasis.

overall_design: RNA-seq ChIP-seq, CUT&TAG and fastGRO analysis of HMLE cells following ZNF827 depletion during TGFbeta-induced EMT

first: Sanjeeb

last: Sahu

first: Eneritz

last: Agirre

first: Mohammed

last: Inayatullah

first: Reini

last: Luco

first: Juan

last: Belmonte


title: Response of M. guilliermondii to macrophage phagocytosis

status: Public on May 25 2022

city: Houston

first: Michael

last: Lorenz

state: TX

address: 6431 Fannin

institute: UTHealth Houston

summary: Pathogenic Candida fungi are a leading cause of opportunistic, hospital-associated bloodstream infections with high mortality rates, typically in immunocompromised patients. Several species, including C. albicans, the most prevalent cause of infection, belong to the monophyletic CUG clade of yeasts. Much is known about the interaction of C. albicans with innate immune cells, which are crucial for controlling infection. Phagocytosis of C. albicans elicits transcriptional induction of several pathways involved in catabolism of non-glucose carbon sources that are important for virulence, termed alternative carbon metabolism. However, the response of other CUG clade species has not been characterized. In a separate dataset, we profiled transcriptional responses to primary murine bone marrow derived macrophages in six Candida species. Here we additionally profiled the response of M. guilliermondii, a yeast that is known as a cause of disseminated candidiasis as well as cutaneous infections. We find that similar to other CUG-clade Candida species, it mounts a robust alternative carbon metabolism response to phagocytosis.

sample_organism:
Mus musculus
Meyerozyma guilliermondii ATCC 6260

overall_design: The transcriptional response of M. guilliermondii to phagocytosis was analysed by incubating M. guilliermondii fungi in mammalian medium in the presence or absence of primary macrophages for 1 hour, followed by RNA extraction and sequencing. This experiment was performed in triplicate.


title: Single-Cell Analysis Reveals the Range of Transcriptional States of Circulating Human Neutrophils

status: Public on May 24 2022

city: Bethesda

first: Stephen

state: MD

address: 50 SOUTH DR, RM 1140

department: Biodata Mining and Discovery Section

institute: NIAMS/NIH

summary: Neutrophils are the most abundant leukocytesin human peripheral blood and are essential components of the innate immune system. Until recently, neutrophils were thought to be homogeneous and transcriptionally inactive, but both concepts are being challenged by a growing body of data. To date, neutrophils have been characterized based on discrete parameters like cell-surface markers, buoyancy, maturity, or tissue localization.Single-cell RNA sequencing (scRNA-seq) has been an important addition to the set of analytical tools, as itoffers an unbiased view of cells along a continuum of transcriptional states, including those that fall between theoretically more stable endpoints. However, the use of scRNA-seqto characterize transcriptional variation in neutrophils has proven technically difficult, explaining in part the paucity of published single-cell data on neutrophils compared to other celltypes. We report a modified analysis pipeline that substantially increases the detection of human neutrophils in scRNA-seq. We applied this pipeline to the study of > 185,000 human neutrophils. Our findings indicate that circulating human neutrophils are transcriptionally heterogeneous cells, which can be classified based on their transcriptional state into one of four clusters that are highly reproducible among healthy human subjects. We demonstrate that neutrophils shiftfrom relatively immature (Nh0) cells, through a transitional phenotype (Nh1), into one of two endpoints defined by either relative transcriptional inactivity (Nh2) or high expression oftype I interferon-induciblegenes (Nh3).Transitions among states are characterized by the expression of specific transcription factors. By simultaneouslymeasuring surface proteinand intracellular transcriptabundance at the single-cell level, we show that these four transcriptional subsets are independent of the canonical surface proteins that are commonly used to define and characterize human neutrophils.These findings provide a new view of human neutrophil heterogeneity, along a continuum of transcriptional states, with potential implications for the characterization of neutrophils in health and disease.

overall_design: Single cell neutrophil analysis in human healthy peripheral blood

first: Gustaf

last: Wigerblad

first: Qilin

last: Cao

first: Faiza

last: Naz

first: Manasi

last: Gadkari

first: Kan

last: Jiang

first: Sarthak

last: Gupta

first: Liam

last: O'Neill

first: Stefania

last: Dell'Orso

first: Mariana

last: Kaplan

first: Luis

last: Franco


title: Interpreting gene co-regulation and metabolic profiling in the unique starch metabolism of Arabidopsis dpe2/phs1 mutant reveals insights into control mechanism of the starch granule number

status: Public on May 23 2022

city: Potsdam-Golm

first: Joerg

last: Fettke

state: Brandenburg

address: Karl-Liebknechtstr. 24/25, Building 20

institute: University of Potsdam

summary:
An Arabidopsis double mutant lacking both the cytosolic Disproportionating enzyme 2 (DPE2) and the plastidial Glucan phosphorylase (PHS1) revealed a unique starch metabolism. Dpe2/phs1 was reported to have a dwarf growth phenotype, an uneven starch distribution in the rosettes, and a strongly reduced starch granule number per chloroplast when grown under diurnal rhythm. Here we analyzed dpe2/phs1 in more detail and found that it showed three distinct growth periods. In young plants the starch granule number was similar to Col-0, then the starch granule number decreased massively down to one or no granule per chloroplast followed by an increase of the granule number. Thus, in dpe2/phs1 the control over the starch granule number is impaired and it is not defective in starch granule initiation. The data also show that the granule number is not fixed and is regulated over the entire plant growth. Further, also the chloroplasts revealed alterations during these three periods with a partially strong aberrant morphology in the middle phase. Interestingly, the unique metabolism perpetuated if starch degradation is further impaired by additionally lack of Isoamylase 3 and Starch excess 4. Transcriptomic studies and metabolic profiling of dpe2/phs1 revealed a gene co-regulation of most starch metabolism related genes and a clear metabolic separation. Further most senescence-induced genes were found to up-regulated more than 2-fold in the starch-less mature leave. Thus, dpe2/phs1 is a unique source to understand especially the starch granule number regulation in detail.
We performed gene expression profiling analysis using data obtained from RNA-seq of 3 stages from both Col-0 and dpe2/phs1.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for 3 stages, designated as the Prior Period; young and mature leaves of the Retard Period; and the Recovery Period from both Col-0 and dpe2/phs1.

first: Xiaoping

last: Li


title: RNA-seq data from PBMC of M.tb-infected and M.tb-uninfected infants in MVA85A clinical trial

city: Oxford

first: Shuailin

address: Old Road Campus Research Building

country: United Kingdom

institute: University of Oxford

summary: Frozen PBMC from infants 7 days before randomization (PBMC from two infant were 28 days after randomization) were stimulated in RPMI with 10% Feotal calf serum (FCS) at 5 million/ml with 1 million CFU/ml BCG (SII) or left unstimulated in a total volumn of 200ul/well in 96-well plates. Cells were incubated  for 12 hours (37C, 5% CO2). Plates were centrifuged and 200ul supernatant was removed without disrupting the pellet and transferred into clean U-bottom plates. The plates were centrifuged again, the supernatant were flicked-out  and the cells were resuspended in 200ul RLT buffer with beta-mercaptoethanol (10ul/ml). The samples were mixed with the buffer to lyse the cells and the plates were sealed and stored at -20C. At the time of RNA-extraction, plates were thawed at 37% for 10 mins. RNA extraction was performed using the Qiagen RNeasy kit following manufacturer's instructions (including optional DNase digestion) and RNA was eluted twice, 30 ul per elution. RNA was quantified by nanodrop and samples were stored at -80C.

overall_design: Frozen PBMC from M.tb-infected and M.tb-uninfected infants 7 days before randomization (except that PBMC from 2 M.tb-infected infant were 28 days after randomization) were stimulated with eitehr BCG or media for 12 hours, RNA were then extracted.

first: Iman

last: Satti

first: Rachel

last: Wittenberg


title: Temperature-dependent small RNA expression depends on wild genetic backgrounds of Caenorhabditis briggsae

status: Public on May 22 2022

city: Toronto

first: Daniel

last: Fusca

state: ON

address: 25 Willcocks Street

department: Department of Ecology and Evolutionary Biology

country: Canada

institute: University of Toronto

type: Non-coding RNA profiling by high throughput sequencing

summary: Geographically distinct populations can adapt to the temperature conditions of their local environment, leading to temperature-dependent fitness differences between populations. Consistent with local adaptation, phylogeographically distinct Caenorhabditis briggsae nematodes show distinct fitness responses to temperature. The genetic mechanisms underlying local adaptation, however, remain unresolved. To investigate the potential role of small noncoding RNAs in genotype-specific responses to temperature, we quantified small RNA expression using high-throughput sequencing of C. briggsae nematodes from tropical and temperate strain genotypes reared under three temperature conditions (14˚, 20˚, 30˚C). Strains representing both tropical and temperate regions showed significantly lower expression of PIWI-interacting RNAs (piRNAs) at high temperatures, primarily mapping to a large ~7 Mb long piRNA cluster on chromosome IV. We also documented decreased expression of 22G-RNAs antisense to protein-coding genes and other genomic features at high rearing temperatures for the thermally-intolerant temperate strain genotype, but not for the tropical strain genotype. Reduced 22G-RNA expression was widespread along chromosomes and among feature types, indicative of a genome-wide response. Targets of the EGO-1/CSR-1 22G-RNA pathway were most strongly impacted compared to other 22G-RNA pathways, implicating the CSR-1 Argonaute and its RNA-dependent RNA polymerase EGO-1 in the genotype-dependent modulation of C. briggsae 22G-RNAs under chronic thermal stress. Our work suggests that gene regulation via small RNAs may be an important contributor to the evolution of local adaptations.

overall_design:
Small RNA sequencing from 2 strains of Caenorhabditis briggsae (AF16 and HK104), each reared in 3 different temperature conditions (14ºC, 20ºC, 30ºC) with 3 biological replicates per genotype-temperature combination.

Note: The processed data files were updated on Sep 30, 2022.

middle: D

first: Eesha

last: Sharma

middle: G

last: Weiss

first: Julie

middle: M

last: Claycomb

first: Asher

last: Cutter


title: Transcription factor paralogs orchestrate alternative gene regulatory networks by context-dependent cooperation with multiple cofactors

city: New York

first: Siqian

last: Feng

state: New York

address: 625 W. 130th Street

institute: Columbia University

summary: In eukaryotes, members of large transcription factor families often exhibit similar DNA binding properties in vitro, yet initiate paralog-specific gene regulatory networks in vivo. The serially homologous first (T1) and third (T3) thoracic legs of Drosophila, which result from alternative gene regulatory networks specified by the Hox proteins Scr and Ubx, respectively, offer a unique opportunity to address this paradox in vivo. Genome-wide analyses using epitope-tagged alleles of both Hox loci in the T1 and T3 leg imaginal discs, which are the precursors to the adult appendages and ventral body regions, show that ~8% of Hox binding is paralog-specific. Binding specificity is mediated by interactions with distinct cofactors in different domains: the known Hox cofactor Exd acts in the proximal domain and is necessary for Scr to bind ~70% of its paralog-specific targets, while in the distal leg domain, we identified the homeodomain protein Distal-less (Dll) as a novel Hox cofactor that enhances Scr binding to a different subset of genomic loci. Reporter genes confirm the in vivo roles of Scr+Dll and suggest that ~1/3 of paralog-specific Hox binding in enhancers is functional. Together, these findings provide a genome-wide view of how Hox paralogs, and perhaps paralogs of other transcription factor families, orchestrate alternative downstream gene networks and suggest the importance of multiple, context-specific cofactors.

sample_organism:
Drosophila melanogaster
synthetic construct

overall_design: RNA-seq (3 biological replicates) was used to characterize the transcriptomes of T1, T2 and T3 leg discs. ATAC-seq (2 biological replicates) was used to profile chromatin accessibility in T1, T2 and T3 leg discs. The 3xFLAG tag was inserted into the endogenous Hox genes Scr and Ubx. A 3xFLAG-Scr(YPWM*) allele, which encodes a mutant 3xFLAG-Scr protein unable to interact with the Hox cofactor Exd, was also generated. ChIP-seq (2 biological replicates) against various 3xFLAG-tagged Hox proteins was performed, and the wild type animals, which lacks the 3xFLAG tag, was used as negative control. ChIP-seq was also performed against the homeodomain TF Dll. Gel-free Selex-seq was used to characterize the binding preferences of selected TF monomers and heterodimers.

first: Ryan

middle: E

last: Loker

first: Richard

middle: S

last: Mann


title: Evidence that conserved essential genes are enriched for pro-longevity factors

status: Public on May 20 2022

city: Richmond

first: Alaattin

last: Kaya

state: VA

address: 1000 West Carry St, Room 126

department: Biology

institute: Virginia Commonwealth University

summary: At the cellular level, many aspects of aging are conserved across species. This has been demonstrated by numerous studies in simple model organisms like Saccharomyces cerevisiae, Caenorhabdits elegans, and Drosophila melanogaster. Because most genetic screens examine loss of function mutations or decreased expression of genes through reverse genetics, essential genes have often been overlooked as potential modulators of the aging process. By taking the approach of increasing the expression level of a subset of conserved essential genes, we found that 21% of these genes resulted in increased replicative lifespan in S. cerevisiae. This is greater than the ~3.5% of genes found to affect lifespan upon deletion, suggesting that activation of essential genes may have a relatively disproportionate effect on increasing lifespan. The results of our experiments demonstrate that essential gene overexpression is a rich, relatively unexplored means of increasing eukaryotic lifespan.

overall_design: Examination of gene expression changes for selected long-lived yeast strains along with WT control.


title: Detect-seq on transfected HEK293T cells [Targeted deep sequencing data]

status: Public on Jun 01 2022

city: Beijing

first: Hua-nan

last: Zhao

state: Beijing

address: 5 Yiheyuan Road Haidian District

department: School of Life Sciences

institute: Peking University

summary: We used a new technology, named Detect-seq, to perform genome sequencing on transfected HEK293T cells to see DdCBEs' off-target mutations. Besides, targeted-amplicon sequencing and ATAC-seq data were applied to validate the results of Detect-seq.

overall_design: We applied DdCBEs to generate on-target editings on mt-DNA to see DdCBEs' editing performance and evaluate their effects on the whole mitochondrial genome. This is the Targeted deep sequencing(Target-seq) part. Target-seq was performed as previously reported. Primers containing the paired Illumina adaptor sequences in the overhangs were designed based on regions flanking the targeting sites (Supplementary table 2). A 10-nt barcode was also added into each primer pairs to reduce the detection limit from 10-1 to 10-5[nm in press]. 10-100 ng of genomic DNA was used for the first round of PCR amplification using NEBNext® Q5U® Hot Start HiFi PCR Master Mix (NEB, M0543L) for approximately 10 cycles. The PCR products were purified with 1× Agencourt AMPure XP beads and eluted in nuclease-free water. The second round of amplification was performed on the purified DNA samples with different index primers for about 15 cycles. The PCR products were purified with 0.8× Agencourt AMPure XP beads and eluted in nuclease-free water. The libraries were quantified using Qubit dsDNA HS Assay kit (Invitrogen) and Qubit 2.0 Fluorometer (INVITROGEN), and then pooled together for high-throughput sequencing by Illumina HiSeq X Ten.

first: Zhixin

last: Lei

first: Haowei

last: Meng

first: Lulu

last: Liu

first: Huanan


title: Unravelling the chromatin landscape and enhancer logic mediating spatiotemporal patterning of early cardiovascular progenitors [RNA-seq]

status: Public on May 18 2022

city: Brussels

first: Cedric

last: Blanpain

state: anderlecht

address: Route de Lennik 808, Bat C, C6-126

country: Belgium

institute: Université Libre de Bruxelles (ULB)

summary: The mammalian heart arises from various populations of Mesp1-expressing cardiovascular progenitors (CPs) that are specified during the early stages of gastrulation. Mesp1 acts as a master regulator of CP specification and differentiation. However, how Mesp1 regulates the chromatin landscape of nascent mesodermal cells to define the temporal and spatial patterning of the distinct populations of CP remains unknown. Here, by combining ChIP-seq, RNA-seq and ATAC-seq during mouse pluripotent stem cell differentiation, we defined the temporal remodelling of the chromatin landscape mediated by Mesp1. We identified different enhancers that are temporally regulated to erase the pluripotent state and specify the pools of CPs that mediate heart development.  We found that Mesp1 acts as a pioneer transcription factor (TF) and identified Zic TFs as essential cofactors that regulate Mesp1 pioneer activity at key mesodermal enhancers, thereby regulating the chromatin remodelling and gene expression associated with the specification of the different populations of CPs in vivo. Our study identifies the dynamics of the chromatin landscape and enhancer remodelling associated with temporal patterning of early mesodermal cells into the distinct populations of CPs that mediate heart development.

overall_design: Replicated RNA-seq samples of differentiating mouse pluripotent stem cells with (dox) and without (no dox) induction of Mesp1, in 2i, or on day 4 sorted based on Flk1/Pdgfra expression

first: Xionghui

last: Lin

first: Benjamin

last: Swedlund

first: Emilie

last: Calonne

first: Francois

last: Fuks

first: Cédric


title: Unravelling the chromatin landscape and enhancer logic mediating spatiotemporal patterning of early cardiovascular progenitors


title: Single cell analysis of the aging hypothalamus

city: Providence

first: Kaitlyn

last: Hajdarovic

state: RI

address: 69 Brown St

department: Neuroscience

institute: Brown University

summary: Alterations in metabolism, sleep patterns, body composition, and hormone status are all key features of aging. The hypothalamus is a well-conserved brain region that controls these homeostatic and survival-related behaviors. Despite the importance of this brain region in healthy aging, little is known about the intrinsic features of hypothalamic aging. Here, we utilize single nuclei RNA-sequencing to assess the transcriptomes of 40,064 hypothalamic nuclei from young and aged female mice. We identify cell type-specific signatures of aging in neurons, astrocytes, and microglia, as well as among the diverse collection of neuronal subtypes in this region. We uncover key changes in cell types critical for metabolic regulation and body composition, as well as in an area of the hypothalamus linked to cognition. In addition, our analysis reveals female-specific changes in sex chromosome regulation in the aging brain. This study identifies critical cell-specific features of the aging hypothalamus in mammals.

overall_design: 4 young and 4 aged biological replicates of female whole hypothalamus

middle: H

first: Doudou

last: Yu

first: Lexi-Amber

last: Hassell

first: Shane

last: Evans

first: Sarah

last: Packer

first: Nicola

last: Neretti

first: Ashley

last: Webb


title: Unravelling the chromatin landscape and enhancer logic mediating spatiotemporal patterning of early cardiovascular progenitors [ChIP-seq]

overall_design: ChIP-seq samples targeting 3HA-tagged Mesp1, 3-HA tagged Zic3 and H3K27Ac


title: Single-cell RNA-sequencing combined with TCR-sequencing of GP66+ splenic CD4+ T cells on day 10 post LCMV Cl13 infection

status: Public on May 10 2022

city: Chicago

first: Weiguo

last: Cui

state: IL

address: 303 E Chicago Ave

department: Pathology

institute: Northwestern University

summary: Here, we applied scRNA and TCR-seq approaches to determine the heterogeneity and clonal landscape of GP66+CD4+ T cells during LCMV clone 13 infection

overall_design: GP66-specific CD4+ T cells were FACS-sorted from two indiviual LCMV Cl13-infected C57BL/6 mice on day 10 p.i. Samples were loaded on the Chromium Controller (10x Genomics). Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 5′ v2 Reagent Kit (10x Genomics) according to manufacturer’s protocol.

first: Ryan

last: Zander

first: Achia

last: Khatun


title: mRNA-seq of zebrafish treated with sex hormone 17β-estradiol and aromatase inhibitor exemestane during sex development

status: Public on May 11 2022

city: Wuhan

first: Zhen-Xia

last: Chen

state: Hubei

address: No.1 Shizishan Street

department: College of Life Science and Technology

institute: Huazhong Agricultural University

summary: To identify key genes in the early sex development of zebrafish, we generated zebrafish (AB strain) feminized by sex hormone 17β-estradiol (E2, CAS: 50-28-2, 100 ng/L) and masculinized by aromatase inhibitor exemestane (EM, CAS: 107868-30-4, 10 μg/L), and detected their transcriptomes by RNA-seq.

overall_design: PolyA+ RNA-seq were performed on 56 samples of four exposure treatments and five exposure periods, with 2-3 replicates at each exposure treatment and period. Each sample contained 25 zebrafish. The exposure treatments included (1) DMSO (100 μg/L), (2) EM + DMSO, (3) E2 +DMSO, and (4) EM+ E2 + DMSO.

first: Yi-Xuan

last: Tu

first: Lu

first: Zhuang

last: Yang

first: Run-Ze

last: Li


title: Integrative epigenomic and transcriptomic analysis reveals the requirement of JUNB for hematopoietic fate induction

first: Jie

address: Qing Hua Yuan

department: Basic Medical Sciences, School of Medicine

institute: Tsinghua University

summary:
To advance our understanding of the dynamics of the gene regulation during each step of in vitro HSPC, we surveyed global gene expression, chromatin accessibility (ATAC-seq), chromatin immunoprecipitation sequencing (ChIP-seq) for active H3K4me3 and repressive H3K27me3 histone mark, from hPSCs and purified intermediates across HSPC differentiation.
Methods: ATAC-seq, bulk RNA-seq, scRNA-seq, ChIP-seq, scATAC-seq, Cut & Tag

overall_design: Bulk RNA-seq, ATAC-seq, H3K4me3 and H3K27me3 ChIP-seq were performed with hPSCs and hPSC derived VMEs, EPCs and HPCs . Besides, we performed scATAC-seq and scRNA-seq to investigate the transcriptomic signature of HEC generated in in vitro system.

first: Xia


title: Neurons burdened by DNA double strand breaks incite microglia activation through antiviral-like signaling in neurodegeneration.

city: Cambridge

first: Li-Huei

last: Tsai

state: Massachusetts

department: Picower Institute for Learning and Memory

institute: MIT

summary: DNA double strand breaks (DSBs) are linked to neurodegeneration and senescence. However, it is not clear how DSB-bearing neurons influence neuroinflammation associated with neurodegeneration. Here, we characterize DSB-bearing neurons from the CK-p25 mouse model of neurodegeneration using single-nucleus, bulk, and spatial transcriptomic techniques. DSB-bearing neurons enter a late-stage DNA damage response marked by NFκB-activated senescent and antiviral immune pathways. In humans, Alzheimer’s disease pathology is significantly associated with immune activation in excitatory neurons. Spatial transcriptomics reveal that regions of CK-p25 brain tissue dense with DSB-bearing neurons harbor signatures of inflammatory microglia, which is ameliorated by NFκB knock-down in neurons. Inhibition of NFκB in DSB-bearing neurons also reduces microglia activation in organotypic mouse brain slice culture. In conclusion, DSBs activate immune pathways in neurons, which in turn adopt a senescence-associated secretory phenotype to elicit microglia activation. These findings highlight a novel role for neurons in the mechanism of disease-associated neuroinflammation.

overall_design: We used the CK-p25 mouse model of neurodegeneration to study the role of DSB-bearing neurons in neurodegeneration. Two male CK-p25 mice and two male CK mice were used for bulk RNA-sequencing. Stage 1, Stage 2, Baseline neurons, and Glia (so termed by NeuN and gH2AX imunoreactivity) were sorted from each mouse using FANS, then sequenced. For single-nucleus RNA-seq, Stage 1, Stage 2, Baseline neurons, and Glia were sorted and sequenced from three CK-p25 animals and three CK control littermates 1-week and 2-weeks after p25 induction. A total of 1,357 single nucleus libraries were prepared using SMARTseq2 chemistry. Three biological replicates each were used for bulk RNA-seq of etoposide-treated primary neurons (50um, 6hours), and dmso-control primary neurons. Three biological replicates each were used for bulk RNA-seq of FAN-sorted microglia nuclei from CK-p25 p65kd, CK-p25 Scramble, and CK Control PBS mice. Microglia nuclei were sorted based on PU.1 immunoreactivity.

first: Gwyneth

last: Welch

first: Qiao

last: Su

first: Andreas

last: Pfenning

first: Carles

middle: A

last: Boix

first: Manolis

last: Kellis

first: Eloi

last: Schmauch


title: RNA-seq analysis of peripheral nerve in Mpz D61N model of CMT1B

status: Public on May 01 2022

city: Madison

first: John

last: Svaren

state: WI

address: 1500 Highland Ave.

department: Comparative Biosciences

institute: University of Wisconsin

summary: The goal of the experiment was to assess gene expression  in sciatic nerve of Mpz D61N model of CMT1B compared to wild type littermate.

overall_design: For each condition, three independent biological replicates were prepared, each of which are pooled from 3 mice.

first: Shuang

last: Liu

first: Phu

last: Duong

first: Francesca

last: Veneri

first: Maurizio

last: D'Antonio


title: Unravelling the chromatin landscape and enhancer logic mediating spatiotemporal patterning of early cardiovascular progenitors [ATAC-seq]

first: Cedric

last: Blanpain

overall_design: assay for transposase-accessible chromatin using sequencing (ATAC-seq) on differentiating mouse pluripotent stem cells where the expression of Mesp1 is doxycycline-inducible

first: Xionghui

last: Lin

first: Benjamin

last: Swedlund

first: Emilie

last: Calonne

first: Francois

last: Fuks

first: Cédric


title: Transcriptomic and epigenetic disruptions in excitatory neurons in Dnmt3a conditional knockout mouse

city: La Jolla

first: Joseph

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

type: Methylation profiling by high throughput sequencing

summary: We created a mouse line in which deletion of exon 19 of Dnmt3a is driven by the Neurod6 promoter (also known as Nex-Cre line). In this conditional knockout (cKO), Dnmt3a is functionally ablated in excitatory neurons in the neocortex and hippocampus starting in mid/late gestation (~E13-15). With an affinity purification approach to isolate tagged nuclei in mice (similar to INTACT; [Deal R.B. and Henikoff S. A simple method for gene expression and chromatin profiling of individual cell types within a tissue. Dev. Cell 18,1030-1040. (2010)]), we characterized the genome-wide patterns of transcription, DNA methylation, and histone modifications in excitatory pyramidal neurons of the frontal cortex from the Dnmt3a cKO and control mice. Our data provide a detailed assessment of the molecular basis of the accompanying changes of neurophysiological and behavioral phenotypes in the cKO mice, and suggest a complex interaction between DNA methylation and Polycomb-mediated repression in the epigenetic regulation in developing brain cells.

overall_design: RNA-seq, MethylC-seq and ChIP-seq for histone modifications using INTACT-purified nuclei of excitatory pyramidal neurons from the mouse frontal cortex

first: Junhao

last: Li

first: Antonio

last: Pinto-Duarte

first: Mark

last: Zander

first: Chi-Yu

last: Lai

first: Julia

last: Osteen

first: Linjing

last: Fang

first: Chongyuan

last: Luo

first: Jacinta

last: Lucero

first: Rosa

last: Gomez-Castanon

first: Joe

last: Nery

first: Isai

last: Silva-Garcia

first: Yan

last: Pang

first: Susan

middle: B

last: Powell

first: Eran

last: Mukamel

first: M

last: Behrens


title: ORAI1 is required for T cell mediated allergic airway inflammation but not antiviral immunity in the lung

first: Stefan

last: Feske

state: NY

address: 550 First Avenue

institute: New York University School of Medicine

summary: This study investigates the role of store-operated calcium entry (SOCE) in T cell-mediated immune responses to pulmonary influenza A virus (IAV) infection and allergic airway inflammation after immunization by house dust mite (HDM) allergens. We conducted a comparative gene expression analysis of antigen-specific CD4+ T cells from wildtype (WT) and Orai1fl/fl Cd4Cre mice that were adoptively transferred to TCRalpha knockout mice followed by sensitization / challenge with HDM or infection with influenza A virus (IAV) strain x31. Donor CD4+ T cells were isolated from the lungs of host mice at days 9 (IAV) and 14 (HDM), RNA was isolated and processed for bulk RNA sequencing.

overall_design: Comparative transcriptome analysis of wildtype (WT) and ORAI1-deficient CD4+ T cells isolated from the lungs of mice after influenza A virus (IAV) infection or house dust mice (HDM, asthma) challenge

first: Sascha

last: Kahlfuss

first: Dimitrius

last: Raphael


title: Single cell analysis of endometriosis reveals a coordinated transcriptional program driving immunotolerance and angiogenesis across eutopic and ectopic tissues

status: Public on May 05 2022

city: Farmington

first: William

middle: F

last: Flynn

state: CT

address: 10 Discovery Drive

institute: The Jackson Laboratory

summary: Endometriosis is characterized by growth of endometrial-like tissue outside of the uterus affecting many women during their reproductive age, causing years of pelvic pain and potential infertility. Its pathophysiology remains largely unknown, limiting early diagnosis and treatment. We characterized peritoneal and ovarian lesions at single-cell transcriptome resolution and compared to matched eutopic endometrium, control endometrium, and organoids derived from these tissues, generating data on over 122,000 cells across 14 individuals. We spatially localized many of the cell types using imaging mass cytometry. We identify a perivascular mural cell unique to the peritoneal lesions with dual roles in angiogenesis promotion and immune cell trafficking. We define an immunotolerant peritoneal niche, fundamental differences in eutopic endometrium and between lesions microenvironments, and an unreported progenitor-like epithelial cell subpopulation. Altogether, this study provides a holistic view of the endometriosis microenvironment representing a comprehensive cell atlas of the disease in hormonally treated patients, essential information for advancing therapeutics and diagnostics.

overall_design: Biopsies were collected from a total of 27 patients, 19 with confirmed endometriosis and 8 patients control. Biopsies were subjected to single cell experiments, bulk sequencing and cell hashing on patient-derived organoid. Single cells experiement were conducted on 31 biopsies consisting of  3 control and  9 eutopic endometrium, 8 ectopic peritoneal, 6 ectopic peritoneal adjacent, 4 ectopic ovary of endometriosis patient. A total of 24 biopsies were subjected to bulk sequencing, consist of 5 control and 7 eutopic endometrium, 6 ectopic peritoneal, 6 ectopic ovary of endometriosis patient. Single-cell cell hashing experiment were conducted on patient-derived organoid from 2 control and 4 eutopic endometrium, 4 ectopic peritoneum, 1 ectopic peritoneal adjacent of endometriosis patient. All single cell experiments were performed on 10x Genomics platform.

first: Yuliana

last: Tan

first: Paul

last: Robson

first: Danielle

last: Luciano

first: Elise

middle: T

last: Courtois


title: G1/S restriction point controls phasic gene expression during early mouse development and differentiation of ESCs

status: Public on May 02 2022

city: San Francisco

first: Robert

last: Blelloch

address: 35 Medical Center Way, RMB, Pod B, 912E, UCSF

institute: UCSF

summary: Pluripotent embryonic stem cells have a unique cell cycle structure with a suppressed G1/S restriction point and little differential expression across the cell cycle phases. Here, we evaluate the link between G1/S restriction point activation, phasic gene expression, and cellular differentiation. Expression analysis reveals a gain in phasic gene expression across lineages between embryonic days E7.5 and E9.5. Genetic manipulation of the G1/S restriction point regulators miR-302 and P27 respectively accelerates or delays the onset of phasic gene expression in mouse embryos. Relief of miR-302-mediated p21 or p27 suppression expedites embryonic stem cell differentiation, while a constitutive Cyclin E mutant blocks it. Together, these findings uncover a causal relationship between emergence of the G1/S restriction point with a gain in phasic gene expression and cellular differentiation.

overall_design:
mRNA and miRNA expression profiling between cell cycle phases in bulk and single cell E7.5, E8.5 and E9.5 mouse embryos. Wild-type embryos are profiled in all cases, miR-302 knockout and p27 knockout embryos are profiled in a subset of the experiments. mRNA expression profiles of cell cycle phase sorted 3T3, embryonic stem cell (ESC) and differentiating ESCs (wt and Ccne1 mutant) are also included.
Comparative gene expression profiling analysis of RNA-seq data for cell cycle phase sorted 3T3, ESC  and differentiated (wild type and mutant) cells.
This work was also funded by a CIHR Fellowship awarded to Brian DeVeale.

first: Brian

last: DeVeale


title: Direct cell-to-cell transfer in stressed tumor microenvironment aggravates tumorigenic or metastatic potential in pancreatic cancer

city: Seoul

first: Giyong

last: Jang

address: Daehakro

country: South Korea

institute: Seoul national university, college of medicine

summary: Pancreatic cancer exhibits a characteristic tumor microenvironment (TME) due to enhanced fibrosis and hypoxia and is particularly resistant to conventional chemotherapy. However, the molecular mechanisms underlying TME-associated treatment resistance in pancreatic cancer are not fully understood. Here, we developed an in vitro TME mimic system comprising pancreatic cancer cells, fibroblasts and immune cells, and a stress condition, including hypoxia and gemcitabine. Cells with high viability under stress showed evidence of increased direct cell-to-cell transfer of biomolecules. The resulting derivative cells (CD44high/SLC16A1high) were similar to cancer stem cell-like-cells (CSCs) with enhanced anchorage-independent growth or invasiveness and acquired metabolic reprogramming. Furthermore, CD24 was a determinant for transition between the tumorsphere formation or invasive properties. Pancreatic cancer patients with CD44low/SLC16A1low expression exhibited better prognoses compared to other groups. Our results suggest that crosstalk via direct cell-to-cell transfer of cellular components foster chemotherapy-induced tumor evolution and that targeting of CD44 and MCT1(encoded by SLC16A1) may be useful strategy to prevent recurrence of gemcitabine-exposed pancreatic cancers.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for pancreatic cancer cells

first: Jaeik

last: Oh

first: Sung-Yup

last: Cho

first: Charles

last: Lee


title: GATA-3 is a proto-oncogene in T-cell lymphoproliferative neoplasms.

status: Public on Apr 30 2022

city: Ann Arbor

first: Chenguang

last: Wang

state: Michigan

address: 1500E Medical Center Dr, Room 4411

department: Department of Internal Medicine

institute: University of Michigan

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

overall_design: Refer to individual Series


title: Gene transfer agents promote survival and DNA repair during stationary phase for Caulobacter crescentus (ChIP-Seq)

first: Kevin

last: Gozzi

state: MA

address: 31 Ames St

institute: Massachusetts Institute of Techonology

summary: Gene transfer agents (GTAs) are prophage-like entities found in many bacterial genomes that cannot propagate themselves and instead package ~5-15 kbp fragments of the host genome that can be subsequently transferred to related recipient cells. Although suggested to facilitate horizontal gene transfer in the wild, no clear physiological role for GTAs has been elucidated. Here, we demonstrate that the a-proteobacterium Caulobacter crescentus produces bona fide GTAs. The production of Caulobacter GTAs is tightly regulated by a novel transcription factor, RogA, that represses gafYZ, which are direct activators of GTA gene transcription. Cells lacking rogA or expressing gafYZ produce GTAs harboring an ~8.3 kbp fragment of the genome that can, after cell lysis, promote transfer of DNA into recipient cells. Notably, we find that GTAs promote the survival of Caulobacter in stationary phase and following DNA damage by providing recipient cells a template for homologous recombination-based repair. This function may be broadly conserved in other GTA-producing organisms and explain the prevalence of this unusual horizontal gene transfer mechanism.

overall_design: Chromatin-immunoprecipitation with deep sequencing experiments (ChIP-seq) were performed on stationary-phase Caulobacter crescentus (see the supplementary Materials and Methods for the exact treatment that were applied to each strain).

first: Ngat

last: Tran

first: Joshua

middle: W

last: Modell

first: Tung

middle: K

last: Le

first: Michael

last: Laub


title: YAP induces an oncogenic transcriptional program through TET1-mediated epigenetic remodeling in liver growth and tumorigenesis

status: Public on May 09 2022

city: Dallas

first: Duojia

last: Pan

state: Texas

address: 6001 Forest Park

department: Physiology

institute: UT Southwestern Medical Center

summary: Epigenetic remodeling is essential for oncogene-induced cellular transformation and malignancy. In contrast to histone posttranslational modification, how oncogenic signaling remodels DNA methylation remains poorly understood. The oncoprotein YAP, a coactivator of the TEAD transcription factors mediating Hippo signaling, is widely activated in human cancer. Here we identify the 5-methylcytosine dioxygenase TET1 as a direct YAP target and a master regulator that coordinates the genome-wide epigenetic and transcriptional reprogramming of YAP target genes in the liver. YAP activation induces the expression of TET1, which physically interacts with TEAD to cause regional DNA demethylation, histone H3K27 acetylation and chromatin opening in YAP target genes to facilitate transcriptional activation. Loss of TET1 not only reverses YAP-induced epigenetic and transcriptional changes but also suppresses YAP-induced hepatomegaly and tumorigenesis. These findings exemplify how oncogenic signaling regulates site specificity of DNA demethylation to promote tumorigenesis and implicate TET1 as a potential target for modulating YAP signaling in physiology and diseases.

overall_design:
liver mRNA profiles of doxycycline treated control, YAP transgenic, Tet1 KO YAP transgenic mice and decitabine treated Tet1 KO YAP transgenic mice

methylated DNA were collected with Methylminer kits. TEAD and TET1 associated DNA fragment were collected with specific antibody as described

first: Bo-Kuan

last: Wu

first: Szu Chieh

last: Mei


title: Gene transfer agents promote survival and DNA repair during stationary phase for Caulobacter crescentus (SMRTbell)

overall_design: PacBio long-read sequencing was performed on GTA-packaged DNA from sationary-phase Caulobacter crescentus samples expressing gafYZ from an inducible promoter.


title: Gene transfer agents promote survival and DNA repair during stationary phase for Caulobacter crescentus (RNA-Seq)

overall_design: RNA-seq was performed on stationary-phase Caulobacter crescentus samples, including WT NA1000 cells or cells with a deletion in rogA, as well as cells expressing gafYZ (or an empty vector) in inducing and non-inducing conditions.


title: Peripheral Blood Monocyte Abundance Predicts Outcomes in Breast Cancer Patients

status: Public on Apr 26 2022

city: Nashville

first: Margaret

middle: L

last: Axelrod

state: TN

address: 2200 Pierce Ave, 777 PRB

department: Medicine

institute: Vanderbilt University

summary: Biomarkers of response are needed in breast cancer to stratify patients to appropriate therapies and avoid unnecessary toxicity. Peripheral blood gene expression and cell type abundance were used to identify biomarkers of response and recurrence in neoadjuvant chemotherapy treated breast cancer patients. Higher peripheral blood monocyte abundance after neoadjuvant chemotherapy was associated with improved prognosis in multiple independent cohorts of breast cancer patients.

overall_design: We used RNA sequencing on whole blood of breast cancer patients, prior to surgery, and looked for differences in gene expression by surgical outcome

first: Justin

last: Balko


title: Comparative parallel meta-analysis of cells undergoing reprogramming to pluripotency and trophectoderm states

status: Public on Apr 28 2022

city: Jerusalem

first: Tommy

last: Kaplan

address: Givat Ram Campus

department: School of Computer Science and Engineering

country: Israel

institute: Hebrew University

type: Genome variation profiling by high throughput sequencing

summary: During early embryogenesis, totipotent cells undergo asymmetric cell divisions, resulting in two compartments in the early embryo: the inner cell mass (ICM) that gives rise to pluripotency cells and an outer layer of trophectoderm (TE). It is only at the 32-64- cell stage when a clear segregation between the two cell types can be observed.  This proposes a ‘T’-like model where cells of each stage (2-16-cell stage) of the early embryo undergo a relatively similar changes in their transcriptome and epigenome before specification. Here, we sought to understand whether cells acquiring pluripotency or trophectoderm state, by reprogramming factors (OSKM vs GETM), share similar processes between themselves such as those of the early embryo.  To that end, we conducted a comparative parallel meta-analysis on cells undergoing reprogramming to induced pluripotent stem cells (iPSCs) and induced trophoblast stem cells (iTSCs) and examined their transcriptome (i.e. Bulk RNA-seq and SC-RNA-seq), methylome (i.e. RRBS), chromatin accessibility and activity (i.e. ATAC-seq and Chip-seq for H3K4me2 and H3K27ac) and genomic stability (CNVs) along the process. Our analysis revealed that, in contrast to cells of the pre-segregation embryo that mostly resemble each other in each stage, cells undergoing reprogramming to pluripotency and TSC states, exhibit unique and specific trajectories from the beginning of the process till the end, suggesting a ‘V’-like behavior. Although similar processes such as somatic identity loss, proliferation, MET and metabolic shift occur in the two models, each of the processes mostly uses different sets of genes and regulatory elements to induce its own fate. We characterized each trajectory in details and illuminated key aspects that are either shared or distinguished between the two states. Using these analyses, we identified previously unknown markers for faithful reprogramming process and key factors that drastically inhibit both reprogramming processes. We show that this comparative parallel meta-analysis is a powerful tool to understand nuclear reprogramming and cellular plasticity at large.

first: Mohammad

last: Jaber

first: Ahmed

last: Radwan

first: Netanel

last: Loyfer

first: Mufeed

last: Abdeen

first: Shulamit

last: Sebban

first: Thorsten

last: Kolb

first: Marc

last: Zapatka

first: Kirill

last: Makedonski

first: Aurelie

last: Ernst

first: Yosef

last: Buganim


title: m6A and YTHDF proteins control the subcellular localization of select neuronal mRNAs [RIP- and RNA-seq]

city: D

first: Kate

last: Meyer

state: NC

address: 307 Research Drive Box 3711

department: Biochemistry

institute: Duke University School of Medicine

summary: The transport of mRNAs to distal subcellular compartments is an important component of spatial gene expression control in neurons. However, the mechanisms that control mRNA localization in neurons are not completely understood. Here, we identify the abundant base modification, m6A, as a novel regulator of this process. Transcriptome-wide analysis following genetic loss of m6A reveals hundreds of transcripts that exhibit altered subcellular localization in hippocampal neurons. Additionally, using a reporter system, we show that mutation of specific m6A sites in select neuronal transcripts diminishes their localization to neurites. Single molecule fluorescent in situ hybridization experiments further confirm our findings and identify the m6A reader proteins YTHDF2 and YTHDF3 as mediators of this effect. Our findings reveal a novel function for m6A in controlling mRNA localization in neurons and enable a better understanding of the mechanisms through which m6A influences gene expression in the brain.

overall_design: YTHDF1, YTHDF2 or YTHDF3 RIP-seq on primary hippocampal neurons cultured for 14 days in culture.

first: Mathieu

middle: N

last: Flamand


title: The effect of ATR inhibition on the replication timing program

city: Pittsburgh

first: Hatice

middle: Ulku

last: Osmanbeyoglu

state: Pennsylvania

address: 5607 Baum Blvd

department: Biomedical Informatics

institute: University of Pittsburgh

summary: as a part of the project looking into the role of ATR in regulating replication initiation and to investigate the rapid replication of CD8+ T cells, we report the replication timing analysis of murine CD8+ T cells and fibroblasts treated with ATR kinase inhibitor AZD6738

overall_design: CD8+ T cells and fibroblasts were treated with DMSO or 5uM AZD6738 for total of 1 h and labeled ongoing replication with 10uM BrdU for the last 30 min. of treatment.

first: Norie

last: Sugitani

first: Moiseeva

last: Tatiana

first: Christopher

middle: J

last: Bakkenist

first: Palmer

last: Drake

middle: U


title: Characterizing human pluripotent stem cell derived kidney organoids by single-cell RNA sequencing of whole organoids and bulk RNA sequencing of organoid-derived podocytes for comparison with immortalized podocytes and in vivo podocytes

status: Public on Apr 25 2022

city: Nijmegen

first: Martijn

last: Broek

address: Geert Grooteplein 24, route 846

department: Molecular Biology

country: Netherlands

institute: Radboud university - RIMLS Science

summary: We performed single-cell sequencing to characterize the cell types that are present in human induced pluripotent stem cell derived (iPS) kidney organoids and their transcriptional profile. Furthermore, using bulk RNA sequencing we compared the transcriptional profile of kidney organoid derived podocytes from a wildtype iPS line, an iPS line with 2 mutations in podocin (NPHS2) which causes clinical manifestation of nephrotic syndrome and an iPS line with one of these mutations repaired which causes no clinical symptoms. For reference and comparison we took along human in vivo glomeruli and a human conditionally immortalized podocyte cell line.

overall_design:
For single-cell RNA sequencing, we used one organoid sample (no replicates). For bulk RNA sequencing, we included three samples per condition (N=3, except for wildtype 2 were we had an n=2) of the following conditions: Mutant, repaired, wildtype, wildtype2, glomerulus, ciPOD.

**RAW DATA not provided due to patient privacy concerns**

first: Jitske

last: Jansen

first: Bartholomeus

last: van den Berge

last: van den Broek

first: Michiel

last: Schreuder

first: Bart

last: Smeets


title: m6A and YTHDF proteins control the subcellular localization of select neuronal mRNAs [RNA-seq and DART-seq]

summary: The transport of mRNAs to distal subcellular compartments is an important component of spatial gene expression control in neurons. However, the mechanisms that control mRNA localization in neurons are not completely understood. Here, we identify the abundant base modification, m6A, as a regulator of mRNA localization in neurons. Transcriptome-wide analysis of mRNA localization in neurons following genetic loss of m6A reveals hundreds of transcripts that exhibit altered subcellular localization. Additionally, using a reporter system, we show that mutation of specific m6A sites in select neuronal transcripts diminishes their localization to neurites. Single molecule fluorescent in situ hybridization experiments further confirm our findings and identify the m6A reader proteins YTHDF2 and YTHDF3 as mediators of this effect. Our findings reveal a novel function for m6A in controlling mRNA localization in neurons and enable a better understanding of the mechanisms through which m6A influences gene expression in the brain.

overall_design: RNA abundance measurement and m6A sites profiling in the soma and neurite compartments of wildtype and Mettl3-/- hippocampal neurons. Primary neurons were grown on microporous membrane and treated with KCl for 2 hours. Total RNA was extracted from the top (soma) and bottom (neurite) of the membrane and used for RNA-seq or in vitro DART-seq library preparation in duplicates. For DART-seq, Mettl3-/- samples are used as control for identification of m6A sites in WT samples.

middle: D


title: m6A and YTHDF proteins control the subcellular localization of select neuronal mRNAs


title: The chromatin dynamics of the TFAP2A/ MITF genetic interation in melanocyte development.

city: Iowa City

first: Colin

last: Kenny

state: Iowa

address: 51 Newton Road 100 Bowen Science Building Iowa

department: Anatomy and Cell Biology

institute: University of Iowa

summary: In developing melanocytes and in melanoma cells, multiple paralogs of the Activating-enhancer-binding Protein 2 family of transcription factors (TFAP2) contribute to expression of genes encoding pigmentation regulators, but their interaction with Microphthalmia transcription factor (MITF), a master regulator of these cells, is unclear. Supporting the model that Tfap2 facilitates MITF's ability to activate expression of pigmentation genes, single-cell seq analysis of zebrafish embryos revealed that pigmentation genes are only expressed in the subset of mitfa-expressing cells that also express Tfap2 paralogs. To test this model in SK-MEL-28 melanoma cells we deleted the two TFAP2 paralogs with highest expression, TFAP2A and TFAP2C, creating TFAP2 knockout (TFAP2-KO) cells. We then assessed gene expression, chromatin accessibility, binding of TFAP2A and of MITF, and the chromatin marks H3K27Ac and H3K27Me3 which are characteristic of active enhancers and silenced chromatin, respectively. Integrated analyses of these datasets indicate TFAP2 paralogs directly activate enhancers near genes enriched for roles in pigmentation and proliferation, and directly repress enhancers near genes enriched for roles in cell adhesion. Consistently, compared to WT cells, TFAP2-KO cells proliferate less and adhere to one another more. TFAP2 paralogs and MITF co-operatively activate a subset of enhancers, with the latter necessary for MITF binding and chromatin accessibility. By contrast, TFAP2 paralogs and MITF do not appear to co-operatively inhibit enhancers. These studies reveal a mechanism by which TFAP2 profoundly influences the set of genes activated by MITF, and thereby the phenotype of pigment cells and melanoma cells.

overall_design: TFAP2A and MITF binding sites were identified by Cleavage Under Targets and Release Using Nuclease (CUT&RUN), TFAP2 regulated enhancers and promoters were identifed by ATAC-Seq, and TFAP2 regulated genes were identied by RNA-Seq.

first: Robert

last: Cornell


title: Cell fate roadmap with pre-implantation lineage signatures during primed-to-naive transition process

city: Shanghai

first: Bi

last: Yan

address: Siping Road 1239

institute: Tongji university

summary: We describe the global cell roadmap during primed-to-naive transition process in single-cell level by performing integrated scRNA-seq analysis between primed, day 6, day 8, day 10, day14 and naïve (10× genomics)scRNA-seq libraries generated in this study.

overall_design: Analyzing transcriptional profiles in single-cell level during primed-to-naive transition process.

first: Yan

last: Bi

first: Zhifen

last: Tu

first: Yixuan

last: Wang


title: Tissue-resident memory CD8+ T cells possess unique transcriptional, epigenetic and functional adaptations to different tissue environments [TRMinTissues scRNA-seq]

status: Public on Apr 18 2022

first: John

middle: Tyler

last: Crowl

state: California

address: 5107 Natural Sciences Building 0377, 9500 Gilman Drive

institute: University of California - San Diego

summary: CD8+ memory T cells are critical components of protective immunity to intracellular pathogens and tumors. While many memory CD8+ T cells recirculate throughout the body, others remain lodged in tissues and guard common sites of pathogen entry. Contributions of the specific tissue environment to tissue-resident memory T cell (Trm) differentiation and homeostasis have been implicated but are not well understood. Here, we define the diversity of gene expression and genome accessibility by mouse CD8+ Trm populations in distinct organs and identify molecules critical for Trm generated in response to acute viral infection. We find that CD8+ TRM across different tissues possess both shared and tissue-specific transcriptional and epigenetic signatures. Notably, Trm in the intestine and salivary gland express TGFb-induced genes and are maintained by ongoing TGFb signaling while those in the fat, kidney, and liver are not.  By constructing transcriptional-regulatory networks for each Trm population, we identify the repressor Hic1 as a critical regulator of Trm differentiation, particularly for Trm of the small intestine. This study provides a framework for understanding how Trm adapt to distinct tissue environments and identifies tissue-specific transcriptional regulators that mediate these adaptations, informing strategies to enhance protective memory responses at the sites most vulnerable to infection.

overall_design: Single-cell RNA-sequencing of P14 CD8+ T cells (specific for LCMV-Armstrong) isolated from the Spleen, Blood, IEL, Kidney, Salivary Gland, and Liver 32 days after intial infection.

first: Maximillian

last: Heeg

first: Amir

last: Ferry

first: J

last: Milner

first: Kyla

last: Omilusik

first: Clara

last: Toma

first: Zhaoren

last: He

last: Chang

first: Ananda

last: Goldrath


title: Tissue-resident memory CD8+ T cells possess unique transcriptional, epigenetic and functional adaptations to different tissue environments [Hic10E RNA-seq]

overall_design: RNA-sequencing of P14 CD8+ T cells (specific for LCMV-Armstrong) transduced with either an empty or Hic1 overexpression vector and isolated from the Spleen 7 days after intial infection.


title: Live-seq for live cell transcriptome profiling

city: Lausanne

first: Wanze

last: Chen

address: SV IBI-SV UPDELA, Station 19

country: Switzerland

institute: EPFL

summary: Single-cell RNA-seq (scRNA-seq) has greatly advanced the characterization of cellular heterogeneity in physiological and pathological conditions. However, since cells are lysed and can thus only be profiled once, it is currently impossible to perform downstream functional assays on the same cells and to obtain a direct scRNA-seq-based read-out of transcriptional dynamics. Here, we present Live-seq, a novel single cell transcriptomic biopsy approach based on fluidic force microscopy that differs from other scRNA-seq methods because the cells can be kept alive for further analysis. We demonstrate that live-seq allows the identification of both cell types and states. In addition, when coupled to an inverted optical microscope, it uniquely enables linking single cell transcriptomes to downstream functional properties through real-time imaging.

overall_design: There are 1012 samples in total, with 296 Live-seq samples, 564 scRNA-seq samples and 162 scRNA-seq samples those were previously subjected to Live-seq extraction (scRNA_post_Liveseq). All this information is included in the "extract protocol" column of the metadata sheet. Both the Live-seq and scRNA-seq samples contains four different cell types/treatments, which include ASPC, IBA cell, RAW264.7 cell with and without LPS treatment (40 ng/ul). Note that Raw264.7_G9 is a Raw264.7 subline expressing mCherry under the control of Tnf promoter and EGFP-Rela fusion protein. For scRNA_post_Liveseq, the cells were harvest 0h, 1 hour or 4 hours post Live-seq extraction. This information is included in the “source name” and “treatment protocol” column of the metadata sheet. The title of each sample is named by this manner: "extraction protocol"."source name". "treatment protocol"."characteristics: Batch"."(a unique sample number)". For a few Live-seq samples, double extraction on the same cells were applied. A unique ID was generated in the “characteristics: double_extraction_pairs” column for the same cells, while “double_extraction_order” indicates the first or the second extraction.

first: Orane

last: Guillaume-Gentil


title: Tissue-resident memory CD8+ T cells possess unique transcriptional, epigenetic and functional adaptations to different tissue environments.


title: Double RNA-seq analysis of Calmodulin indirect knockout in Toxoplasma gondii TATI strain

status: Public on Apr 14 2022

city: Wuhan

first: Yanqin

last: Zhou

state: Hubei province

address: No.1, Shizishan Street, Hongshan District

institute: Huazhong agricultural university

summary: Toxoplasma gondii is an apicomplexan parasite infecting human and animals, causing huge health concerns and economic losses. Calcium ion, a critical second messenger in cells, can regulate related vital activities, particularly in parasite invasion and escape processes. Calmodulin (CaM) is a short, highly conserved Ca2+ binding protein found in all eukaryotic cells, including apicomplexan parasites. After binding to Ca2+, CaM can be activated to interact with a variety of proteins (such as enzymes). Since direct destruction of CaM is impossible, few studies have been conducted on the function of CaM in T. gondii. We generated the CaM indirect knockout strain (iCaM) using a tetracycline-off system with CaM promoter sequence in T. gondii TATI strain, and compared the transcriptomes of tachyzoites with and without Calmodulin.

overall_design: The human foreskin fibroblast cells (HFF) were inoculated by iCaM strain with or without Anhydrotetracycline hydrochloride (ATc) for about 40 h. Freshly parasites were harvested by mechanically disrupting host cells. Total RNA was extracted for RNAseq. Clean data were obtained by removing low-quality reads and some reads containing adapters from raw data. The clean data were aligned to the Toxoplasma gondii TgGT1 genome (ToxoDB-43) using HISAT2 v2.0.5. Differential expression analysis was performed using DESeq2 R package (1.16.1) with a default parameter.

first: Yongle

last: Song

first: Longjiao

last: Li

first: Xinyu

last: Mo


title: Tubulointerstitial RNAseq counts from adults in the Neptune Cohort

status: Public on Apr 15 2022

first: Sean

last: Eddy

state: MI

address: 1150 West Medical Center Drive

summary: Tubulointerstitial Transcriptome in the Neptune Cohort

overall_design:
Tubulointerstitial Transcriptome
-----------------------------------------
Raw data (fastq) files are available upon approved ancillary study request from the NEPTUNE consortium (please see https://www.neptune-study.org/ancillary-studies; email contact: NEPTUNE-STUDY@umich.edu)

first: Felix

last: Eichinger

first: Laura

last: Mariani

first: Raji

last: Menon

first: Brad

last: Godfrey

first: Matthias

last: Kretzler


title: Single-cell targeted DNA methylation analysis of human B cells

status: Public on Apr 11 2022

city: Barcelona

first: Lars

last: Velten

address: C. Dr. Aiguader 88, P05

department: Bioinformatics and Genomics

country: Spain

institute: CRG

summary: This dataset demonstrates scTAM-seq, a method for profiling the methylation state of up to 600 CpGs in 10,000 cells with dropout rates of <7%. Besides CpG methylation, scTAM-seq also profiles the expression of select surface proteins in the same cells. We provide for each sample separate protein and methylation fastq and csv files. Here, scTAM-seq was applied to B cells from human peripheral blood and bone marrow.

overall_design: scTAM-seq combines single-cell PCR in droplets (Mission Bio Tapestri platform) with the digestion of genomic DNA using the methylation-sensitive restriction enzyme HhaI. This enzyme selectively cuts unmethylated GCGC recognition sites, while leaving methylated sites intact. Hence, upon digestion of  genomic DNA in barcoded single-cell droplets, amplicons containing targeted CpGs can only be amplified from methylated recognition sites. scTAM-seq can cover 600 CpGs in up to 10,000 cells, and can be combined with single-cell readouts of surface protein expression as well as somatic mutations. For this pilot study, we designed a panel of 592 amplicons, of which 424 contained CpGs showing dynamic DNAm during B-cell differentiation, i.e., CpGs differentially methylated between hematopoietic stem cells (HSCs), pre-B-cells, immature B-cells, naive B-cells and memory B-cells. The remaining amplicons serve as controls and include amplicons without HhaI recognition sites, as well as amplicons covering CpGs that are constitutively methylated or unmethylated in B-cells. We applied scTAM-seq to B-cells from bone marrow and blood while additionally profiling the expression of 46 cell-surface proteins by staining cells with oligonucleotide-tagged antibodies. For both samples, we generated data from two experimental conditions, one digested by HhaI and one undigested control. We obtained data for 5,340-9,583 cells passing quality filters.

first: Agostina

last: Bianchi

first: Michael

last: Scherer

first: Roser

last: Zaurin

first: Renee

last: Beekman


title: Single-cell RNA-seq uncovers the pathological alterations of pancreatic islets in type 2 diabetes mice

status: Public on Apr 09 2022

city: Beijing

first: Kai

last: Chen

address: 8th Xishiku Street

department: General Surgery

institute: Peking University First Hospital

summary: Pancreatic islet beta cell heterogeneity has been identified, which plays a pivotal role in the pathological alterations of pancreatic islets in type 2 diabetes (T2D) mice. However, pathological alterations of beta cells in type 2 diabetes (T2D) mice remain to be investigated. We isolated pancreatic islets from the control and T2D mice and conducted scRNA-seq analysis using the 10x Genomics platform. Pathological alterations of beta cells in T2D were also explored.

overall_design: The Lepr knockout mouse model was used. The islets were isolated from three control (BKS_WT; m/m) and three type 2 diabetes (BKS_DB; db/db) mice at ages of 9 weeks. The isolated islets were cultured overnight and enzymatically digested to generate single-cell suspensions for scRNA-seq.


title: Genetic profiling of breast cancer stem cell spheres exposed to immune surveillence

status: Public on Apr 06 2022

city: Cleveland

first: Kuan-Hui

middle: Ethan

state: MS

address: 1003 W Sunflower Rd

institute: Delta State University

summary: mouse 4T1 breast cancer stem cell spheres were co-culutred with in vivo tumor antigen primed splenocytes, with in vivo tumor antigen primed splenocytes plus ex vivo reinforced activation via anti-CD3/CD28 beads or without co-culturing with splenocytes. Stem cell spheres were then collected and sunjected for gene expression analyses using RNA sequencing.

overall_design: RNA expression profiles in mouse 4T1 breast cancer stem cell spheres

first: KuanHui

first: Yiling


title: Gene expression of ZNF335, RNPC3, CLP1 and LIN52 inducible knockouts in HeLa cells

status: Public on Apr 01 2022

city: Cambridge

first: Jimmy

last: Ly

address: 455 main street

department: Biology

institute: Whitehead Institute

summary: From our pooled optical screen, we identified an unexpected role for ZNF335, a transcription factor, in spindle bipolarity. We also found that RNPC3, CLP1 or LIN52 are regulators of gene expression on various levels, displayed an unexpected, specific kinetochore defect. Here we generated individual doxycycline-inducible Cas9 cell lines expressing lentiviral-integrated sgRNAs targeting ZNF335, LIN52, CLP1, and RNPC3 to evaluate differential roles in gene expression regulation.

overall_design:
Here we generated individual doxycycline-inducible Cas9 cell lines expressing lentiviral-integrated sgRNAs targeting ZNF335, LIN52, CLP1, and RNPC3 to evaluate differential roles in gene expression regulaion.
Biological replicates were defined as replicate doxycycline inductions of Cas9 expression. A negative control sgRNA sequence was used that targets a single locus. N=2 biological replicates were performed for each gene target.

first: Luke

last: Funk

first: Kuan-Chung

last: Su

first: David

last: Feldman

first: Avtar

last: Singh

first: Brittania

last: Moodie

first: Paul

middle: C

last: Blainey

first: Iain

middle: M

last: Cheeseman


title: Sex disparities in influenza: a multiscale network analysis (Female ferrets)

city: New York

first: Christian

last: Forst

address: One Gustave L. Levy Place

department: Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

summary: This study utilized a network-based approach to characterize the blood transcriptome collected over the course of infection with influenza A virus from female and male ferrets to dissect sex-biased gene expression shaped by genetically determined differences. It provides molecular insights into genetically driven sex differences in transcriptional regulation of immune responses.

overall_design: Whole blood transcriptome profiles from 36 male ferrets were measured at days 1, 3, 5, 8, and 14 post infection. Plaque assays from nasal swabs were performed to determine the viral burden. The relative weight of each animal was determined at corresponding time points, with weight = 1 pre-infection.


title: Sex disparities in influenza: a multiscale network analysis (Male ferrets)

overall_design: Whole blood transcriptome profiles from 36 male ferrets were measured at days 1, 3, 5, and 8 post infection. Plaque assays were performed to determine the viral burden from nasal swabs. The relative weight of each animal was determined at corresponding time points.


title: Sex disparities in influenza: a multiscale network analysis

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

overall_design: Refer to individual Series


title: Brg1 plays an essential role for intestinal tumor stem cells to maintain intestinal tumors in mice and human colorectal cancer cells

status: Public on Mar 31 2022

city: Kyoto

first: Takaaki

last: Yoshikawa

address: 54 Shogoin-Kawahara-cho

department: Gastroenterology and Hepatology

country: Japan

institute: Kyoto University Graduate School of Medicine

summary:
Brg1, a core subunit of the SWI/SNF chromatin remodeling complex, is essential for intestinal stem cells in mice. Therefore, we investigated the role of BRG1 in human colorectal cancer cells.
We found that BRG1 was essential for maintainance of stem cell properties of human colorectal cancer cells.

overall_design: We suppressed BRG1 expression of human colorectal cancer cells and extracted total RNA from control groups and siBRG1 groups.

first: Akihisa

last: Fukuda


title: Molecular and Cellular Mechanisms for Differential Effects of Chronic Social Isolation Stress in Males and Females

status: Public on Mar 22 2022

city: Buffalo

first: Fengwei

last: Yang

address: 955 Main St

institute: University at Buffalo

summary: Chronic social isolation stress during adolescence induces susceptibility for neuropsychiatric disorders. Here we show that 5-week post-weaning isolation stress induces sex-specific behavioral abnormalities and neuronal activity changes in the prefrontal cortex (PFC), basal lateral amygdala (BLA), and ventral tegmental area (VTA). Chemogenetic manipulation, optogenetic recording, and in vivo calcium imaging identify that the PFC to BLA pathway is causally linked to heightened aggression in stressed males, and the PFC to VTA pathway is causally linked to social withdrawal in stressed females. Isolation stress induces genome-wide transcriptional alterations in a region-specific manner. Particularly, the upregulated genes in BLA of stressed males are under the control of activated transcription factor CREB, and CREB inhibition in BLA normalizes gene expression and reverses aggressive behaviors. On the other hand, neuropeptide Hcrt (Hypocretin/Orexin) is among the top-ranking downregulated genes in VTA of stressed females, and Orexin-A treatment rescues social withdrawal. These results have revealed molecular mechanisms and potential therapeutic targets for stress-related mental illness.

overall_design: Male control BLA (3 replicates) vs male stress BLA (3 replicates), female control VTA (3 replicates) vs female stress VTA (3 replicates)

first: Zi-Jun

last: Wang

first: Treefa

last: Shwani

first: Junting

last: Liu

first: Ping

last: Zhong

first: Freddy

last: Zhang

first: Arnd

last: Pralle

first: Zhen

last: Yan


title: Expression data from WT and ISG15 KO HaCaT cells stimulated with interferon-a and treated with combination treatment of Ruxolitinib, TGFb and Doxycycline

status: Public on Mar 17 2022

city: Hannover

first: Frank

last: Pessler

state: Niedersachsen

address: Feodor Lynen Str. 7

institute: Twincore

summary: Analysis of gene expression in WT and ISG15 KO HaCaT cells, stimulated with IFNa and treated with ruxolitinib (RUX), transforming growth factor beta (TGFb) and doxycycline (DOXY) to investigate the effects of treatments on transcriptional response in the cells.

overall_design: WT and ISG15 KO HaCaT cells were stimulated with interferon-a for 8 hours. Cells were then treated with ruxolitinib (RUX), transforming growth factor beta (TGFb) and doxycycline (DOXY) for 16 hours. RNA was extracted, and subjected to transcriptome profiling array  Clariom™ S Assay, human.

first: Robert

last: Geffers


title: Uncovering the mesendoderm gene regulatory network through multi-omic data integration

status: Public on Mar 30 2022

city: Irvine

first: Kitt

middle: D.

last: Paraiso

address: 4410 Nat Sci II, University of California, Irvine

department: Department of Developmental and Cell Biology

institute: University of California, Irvine

summary: We report the ChIP-seq analysis of multiple Xenopus transcription factors binding. Also, we report loss-of-function transcriptomic analysis of Tcf7l1 by RNA-seq at different developmental stages. These newly generated datasets are analyzed using self-organizing maps, along with previously published Xenopus genomic data.

overall_design: ChIP-seq was performed using antibodies against Xenopus tropicalis transcription factors (Mix1, Sia1, Smad1, Sox7, Vegt and Ventx2) where embryos were processed at different stages of early development. RNA-seq datasets were generated from uninjected embryos and Tcf7l1 morpholino injected embryos. These multi-omic datasets, along with literature curated ChIP-seq, RNA-seq and ATAC-seq datasets, were analyzed using Self-Organizing Maps to elucidate the gene regulatory network principles of early mesendoderm development.


title: Gene expression of C28/I2 cells with SDF-1 and natural products treatment

status: Public on Mar 09 2022

city: Shenzhen

first: Yan

last: WANG

address: 1068 Xueyuan Ave

institute: Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences

summary: SDF-1 has been reported to trigger ADAMTS4,5 overexpression through activating CXCR4 signaling in chondrocytes. Here we described the transcriptional changes of SDF-1-treatment as well as natural products CXCR4 antagonists treatment.

overall_design: Transcriptional profiling was employed to test whether natural product CXCR4 antagonists can inhibit SDF-1-induced intracellular signaling in C28/I2 cells.

first: Qian

last: Xie

first: Jianhui

last: Liang


title: Tissue-resident memory CD8+ T cells possess unique transcriptional, epigenetic and functional adaptations to different tissue environments [TRMinTissues RNA-seq]

city: La Jolla

first: John

last: Crowl

overall_design: RNA-sequencing of P14 CD8+ T cells (specific for LCMV-Armstrong) isolated from the Spleen, Blood, IEL, Kidney, Salivary Gland, and Liver 32 days after intial infection.

first: Maximillian

last: Heeg

first: Amir

last: Ferry

first: J

last: Milner

first: Kyla

last: Omilusik

first: Clara

last: Toma

first: Zhaoren

last: He

last: Chang

first: Ananda

last: Goldrath


title: NHR-49 controls a HIF-1 independent hypoxia adaptation pathway in Caenorhabditis elegans

status: Public on Mar 16 2022

city: Vancouver

first: Stefan

last: Taubert

state: BC

address: 950 W 28th Ave, CMMT Room 2024

department: Medical Genetics

institute: UBC

summary: The response to insufficient oxygen, termed hypoxia, is orchestrated by the conserved master regulator Hypoxia-Inducible Factor-1 (HIF-1), which is hyperactive in many cancers. Here, we describe a HIF-1 independent hypoxia response pathway controlled by Caenorhabditis elegans Nuclear Hormone Receptor NHR-49, an orthologue of mammalian lipid metabolism regulator Peroxisome Proliferator-Activated Receptor alpha (PPARα). nhr-49 is required for worm survival in hypoxia and is synthetically lethal with hif-1 in this context, demonstrating independent activity. RNA-seq data show that nhr-49 regulates a set of hif-1 independent hypoxia responsive genes, including autophagy genes that promote hypoxia survival. We further identified the Nuclear Hormone Receptor nhr-67 as a negative regulator and the Homeodomain-interacting Protein Kinase hpk-1 as a positive regulator in the NHR-49 pathway. Together, our experiments describe an essential hypoxia response pathway controlled by nhr-49 that includes new upstream and downstream components and is as important as hif-1 dependent hypoxia adaptation.

overall_design: Three genotypes were analyzed (wild-type N2, nhr-49(nr2041), and hif-1(ia4)) of L4 Caenorhabditis elegens followng 3 hour exposure to eitehr 21% oxygen or 0.5% oxygen. Each condition was repeated 3 times, for a total of 18 samples.

first: Kelsie

middle: R

last: Doering

first: Xuanjin

last: Cheng

first: Luke

last: Milburn

first: Dana

last: Miller


title: Multi-omics analyses of changes in the tumor microenvironment of pancreatic adenocarcinoma following neoadjuvant treatment with anti-PD-1 antibody

status: Public on Mar 07 2022

city: Baltimore

first: Elana

middle: Judith

last: Fertig

state: MD

address: 670 W. Baltimore Street, 3rd floor

department: Institute for Genome Sciences

institute: University of Maryland, Baltimore

summary: Successful pancreatic ductal adenocarcinoma (PDAC) immunotherapy necessitates optimization and maintenance of activated effector T cells (Teffs). We prospectively collected and applied multi-omics analysis to paired, pre- and post-treatment PDAC specimens collected in a platform neoadjuvant study of GVAX vaccine +/- nivolumab (anti-PD-1) to uncover sensitivity and resistance mechanisms. We show that GVAX-induced tertiary lymphoid aggregates become immune-regulatory sites in response to GVAX+nivolumab. Higher densities of tumor-associated neutrophils (TANs) following GVAX+nivolumab portend poorer overall survival (OS). Increased T cells expressing CD137 associated with cytotoxic Teff signatures and correlated with increased OS. Bulk and single-cell RNA-sequencing found that nivolumab alters CD4+ T cell chemotaxis signaling in association with CD11b+ neutrophil degranulation, and CD8+ T cell expression of CD137 required for optimal T cell activation. These findings provide new insights into PD-1-regulated immune pathways in PDAC that should inform more effective therapeutic combinations that include TAN regulators and T cell activators.

overall_design:
Examination of patients participating in the studied clinical trial (NCT02451982). Read counts used in Cancer Cell available as GSE197613_NewGeneCounts.txt.gz and used for the normalization in JEM as GSE197613_JEM_counts_combined_TIIC-RNA-seq.txt.gz and GSE197613_JEM_gene_logtpm_filtered_TMM_qn_normalized_nivo_select_TIIC-RNA-seq.txt.gz.

**RAW data will be submitted to dbGAP**

first: Lei

last: Zheng

first: Elizabeth

last: Jaffee

first: Keyu

last: Li

first: Joseph

last: Tandurella


title: Phototoxic effects of nonlinear optical microscopy on cell cycle, oxidative states, and gene expression

status: Public on Mar 06 2022

city: Berkeley

first: Xinyi

last: Zhang

state: CA

address: 327 Stanley Hall

institute: UC Berkeley

summary: Nonlinear optical imaging modalities, such as stimulated Raman scattering (SRS) microscopy, use pulsed-laser excitation with high peak intensity that can perturb the native state of cells. In this study, we used bulk RNA sequencing, quantitative measurement of cell proliferation, and fluorescent measurement of the generation of reactive oxygen species (ROS) to assess phototoxic effects of near-IR pulsed laser radiation, at different time scales, for laser excitation settings relevant to SRS imaging. We define a range of laser excitation settings for which there was no significant change in mouse Neuro2A cells after laser exposure. This study provides guidance for imaging parameters that minimize photo-induced perturbations in SRS microscopy to ensure accurate interpretation of experiments with time-lapse imaging or with paired measurements of imaging and sequencing on the same cells.

overall_design: Bulk RNA-sequencing of mouse neuroblastoma (N2A) cells with and without laser irradiation. Three replicates were sequenced for each condition.

first: Gabriel

last: Dorlhiac

first: Markita

middle: P

last: Landry

first: Aaron

last: Streets


title: Tissue-resident memory CD8+ T cells possess unique transcriptional, epigenetic and functional adaptations to different tissue environments [ATAC-seq]

first: John

last: Crowl

address: 5107 Natural Sciences Building 0377, 9500 Gilman Drive

summary: CD8+ memory T cells are critical components of protective immunity to intracellular pathogens and tumors. While many memory CD8+ T cells recirculate throughout the body, others remain lodged in tissues and guard common sites of pathogen entry. Contributions of the specific tissue environment to tissue-resident memory T cell (Trm) differentiation and homeostasis have been implicated but are not well understood. Here, we define the diversity of gene expression and genome accessibility by mouse CD8+ Trm populations in distinct organs and identify molecules critical for Trm generated in response to acute viral infection. We find that CD8+ TRM across different tissues possess both shared and tissue-specific transcriptional and epigenetic signatures. Notably, Trm in the intestine and salivary gland express TGFb-induced genes and are maintained by ongoing TGFb signaling while those in the fat, kidney, and liver are not.  By constructing transcriptional-regulatory networks for each Trm population, we identify the repressor Hic1 as a critical regulator of Trm differentiation, particularly for Trm of the small intestine. This study provides a framework for understanding how Trm adapt to distinct tissue environments and identifies tissue-specific transcriptional regulators that mediate these adaptations, informing strategies to enhance protective memory responses at the sites most vulnerable to infection.

overall_design: ATAC-sequencing of P14 CD8+ T cells (specific for LCMV-Armstrong) isolated from the Spleen, Blood, IEL, Kidney, Salivary Gland, and Liver 32 days after intial infection.

middle: T

first: Maximillian

last: Heeg

first: Amir

last: Ferry

first: J

last: Milner

first: Kyla

last: Omilusik

first: Clara

last: Toma

last: He


title: The Drosophila BEAF Insulator Protein Interacts with the Polybromo Subunit of the PBAP Chromatin Remodeling Complex [Mnase-seq]

status: Public on Mar 05 2022

city: Baton Rouge

first: Craig

last: Hart

state: Louisiana

address: Life Science Building, LSU

department: Biological Sciences

institute: Louisiana State University

summary:
We examine the effect of this interaction on gene expression and chromatin structure using precision run-on sequencing (PRO-seq) and micrococcal nuclease sequencing (MNase-seq) after RNAi-mediated knockdown in cultured S2 cells.
We examine the effect of the interaction between BEAF and polybromo on gene expression and chromatin structure using precision run-on sequencing (PRO-seq) and micrococcal nuclease sequencing (MNase-seq) after RNAi-mediated knockdown in cultured S2 cells.

overall_design: Two biological replicates were sampled for each RNAi treatment, LacZ, BEAF, and polybromo. Nuclei were isolated and used for library preparation.

last: McKowen

first: Satya

middle: V

last: Avva

first: Mukesh

last: Maharjan

first: Fabiana

last: Duarte

first: Jacob

last: Tome

first: Jamie

last: Wood

first: Sunday

last: Negedu

first: Yunkai

last: Dong

last: Lis


title: The global transcriptomic profile in the manganese-stressed wild type, DglnA and DmntPDglnA E. coli strains

city: Chandigarh

first: Dipak

last: Dutta

email: dutta@imtech.res.in, ddutta25@gmail.com

state: Chandigarh

address: Sector 39-A

department: Molecular Biochemistry

country: India

institute: CSIR IMTECH

summary: We have grown the E. coli strains in the presence or absence of 1mM MnCl2 to observe if GlnA has some role in mitigating maganese stress. We identified the pathways that are altered under manganese stress. From the analyses, we noticed that nitrogen metabolism genes, glutamate glutamine cycle enzymes coding genes, pH homeostasis genes play crucial roles in mitigating manganese stress. GlnA plays central role in such manganes-shock managnement.

overall_design: Organism : Escherichia coli , Agilent custom E.coli Gene Expression  8x15k Array (AMADID: 068043) designed by Genotypic Technology Private

first: Arunima

last: Kalita

first: Amit

last: Arora


title: The Drosophila BEAF Insulator Protein Interacts with the Polybromo Subunit of the PBAP Chromatin Remodeling Complex


title: The Drosophila BEAF Insulator Protein Interacts with the Polybromo Subunit of the PBAP Chromatin Remodeling Complex [PRO-seq]

middle: K

first: John


title: A trade-off for maintenance of multidrug-resistance IncHI2 plasmids in Salmonella Typhimurium through co-evolution

status: Public on Mar 02 2022

city: Guangzhou

first: Jinfei

last: Zhang

state: Guangdong

address: 483 Wushan Road

institute: SCAU

summary: Plasmid maintenance costs to bacterial hosts is closely linked to the mechanisms that underlie plasmid fitness and how these costs are resolved. Herein, we performed multiple (63) serial passage to explore the compensatory mechanisms of co-evolution of multidrug-resistant IncHI2 plasmid pJXP9 and S. Typhimurium strain ATCC 14028 with or without antibiotic selection. pJXP9 could be maintained at for hundreds of generations even without drug exposure. Decreased lag times and higher competitive advantages were observed in end-point evolved strains bearing pJXP9 compared to ancestral strains. Genomic and transcriptomic analyses revealed that the fitness costs of pJXP9 in ATCC 14028 were derived from not only specific plasmid genes, particularly the multidrug-resistant region and conjugation transfer region I, but also the conflicts resulting from chromosomal gene interactions. Correspondingly, plasmid-borne deletions of these regions could compensate the fitness cost due to the presence of the plasmid. Furthermore, mutations and mRNA alterations in chromosomal genes involved in physiological functions were also adaptative. These functions included decreased flagellar motility, oxidative stress resistance and fumaric acid synthesis, and increased Cu resistance. Our findings suggest that plasmid maintenance through plasmid-bacteria co-evolution is a trade-off between increasing plasmid vertical transmission and impairing its horizontal transmission and bacterial physiological phenotypes.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium

overall_design: RNA was extracted from clones cultured in LB broth after 4 h mating in the absence of antibiotics.Bacterial cells were collected by 8000×g centrifugation for 10 min. The library was constructed using an Illumina TruSeq RNA sample Prep Kit v2and sequenced by the Illumina Hiseq-2000. The reads that passed the Illumina quality filter were kept for sequence analysis.

first: Liangxing

last: Fang

first: Manxia

last: Chang

first: Ming

last: Cheng


title: Tissue-resident memory CD8+ T cells possess unique transcriptional, epigenetic and functional adaptations to different tissue environments [CAPvsColl RNA-seq]

status: Public on Apr 18 2022

last: Crowl

institute: University of California - San Diego

first: Maximillian

last: Heeg

first: Amir

last: Ferry

first: J

last: Milner

first: Kyla

last: Omilusik

first: Clara

last: Toma

first: Zhaoren

last: He

first: Ananda

middle: W

last: Goldrath


title: Gene expression analysis of human salivary gland and organoid at single cell resolution

status: Public on May 05 2022

city: Seoul

first: Jae-Yol

last: Lim

address: 50-1, Yonsei-ro, Seodaemun-gu

department: Department of Otorhinolaryngology

institute: Yonsei University College of Medicine

summary: Salivary glands that produce and secret saliva, which is essential for lubrication, digestion, immunity, and oral homeostasis, consist of diverse cells. Maintenance of diverse salivary gland cells in organoids remains problematic. Here, we established human salivary gland organoids, which is composed of multiple cellular subsets, from 3 major salivary glands, including parotid gland (PG), submandibular gland (SMG), and sublingual gland (SLG). Human salivary gland organoids expressed gland-specific genes and proteins of acinar, myoepithelial, and duct cells. Organoids were maintained in growth media (named GEM) and further underwent differentiation in differentiation media (named DAM). Our study will provide an experimental platform for the exploration of mechanisms involvled in tissue regeneration, development, or several salivary gland diseases.

overall_design: Single cell RNA sequencing of human salivary gland tissues and organoids. Comparative analysis of single cell RNA-seq for human SMG organoids cultured for 1 month and 3 months.

first: Donghyun

last: Kim

first: Kwon

middle: Y

last: Tak

first: Jong-Eun

last: Park


title: Patient-derived parathyroid organoids as tracer and drug-screening application model

status: Public on Feb 28 2022

city: Groningen

first: Rob

last: Coppes

address: Ant. Deusinglaan 1

department: Biomedical Sciences of Cells and Systems

institute: University Medical Center Groningen

summary: Parathyroid diseases are characterized by dysregulation of calcium homeostasis and alterations in parathyroid hormone (PTH) excretion. The understanding of parathyroid hyperplastic growth and the development of tracers for imaging and treatment could benefit from in vitro models. Therefore, we aim to establish stem cell-derived three-dimensional organoids representing human parathyroid tissue in vitro. Patient-derived hyperplastic parathyroid tissue was dispersed and parathyroid organoids (PTO) were cultured, characterized by immunofluorescence, and RNA-sequencing was performed. Functional PTO testing was performed by calcium-response measurements, drug screening, PET (11C-methionine) and SPECT-tracer (99mTc-sestamibi) validation. PTO in vitro self-renewal potential was assessed to show the presence of putative stem cells. RNA-sequencing confirms that PTO phenocopy hyperplastic parathyroid tissue. Exposure to increasing calcium concentrations and to PTH-lowering drugs, resulted in a significantly reduced PTH excretion. Next to this, the PTO showed specific binding of 11C-methionine to the targeted receptor. Additionally, when organoids were incubated with 99mTc-sestamibi, we observed a higher uptake in PTOs from patients with a positive scan compared to patients with a negative scan. In conclusion, we present a patient-derived PTO culture, that recapitulates the originating tissue on gene and protein expression and functionality. We demonstrate the potential of PTOs for physiology studies and therapeutic target and tracer discovery.

overall_design: Examination of (dis)similarities between hyperplastic parathyroid gland tissue, PTOs and dPTOs.

first: Schelto

last: Kruijff


title: Integration analysis reveal De Novo Angioimmunoblastic T Cell Lymphoma with Virus Responsive CD8+ T cell Features

status: Public on Feb 25 2022

city: Singapore

first: jinmiao

last: chen

address: 8A Biomedical Grove, #04-06 Immunos

country: Singapore

institute: Singapore Immunology Network

summary: AITL usually consists of a small population of malignant T cells extensively infiltrated by multiple lineages of other immune cells. It is challenging to characterize the tumour cells with traditional histopathology or next-generation sequencing technique using bulk tumour. However, the recent advances in single-cell sequencing technologies have enabled scientists to dissect cellular heterogeneity and gain new insights into cell origins and tumorigenesis of various hematologic malignancy5-8. In this study, we holistically analysis a typical case of AITL tumour using single-cell profiling, including CITE-Seq and immune repertoire sequencing on the same cell. The integration analysis revealed that the neoplastic cells are more similar to CD8+ cytotoxic T cells instead of Tfh cells. Moreover, we further confirmed that GAPDH-activated NFκB pathway was the key driver pathway on tumorigenesis.

overall_design: An 80-year-old male of Chinese was diagnosed as AITL according to the WHO Classification of Tumours of Haematopoietic and Lymphoid Tissues (2016). The fresh tissue specimen (AITL3823) was obtained from cervical lymph node.

first: Huang

last: Dachuan

first: Li

last: Mengwei

first: Chen

last: Jinmiao

first: Ong

last: Kiat