title: Transcriptome shifts triggered by vitamin A and SCD genotype interaction in Duroc pigs

status: Public on Sep 12 2021

city: Lleida

first: Roger

last: Ros-Freixedes

address: Av Rovira Roure, 191

institute: Universitat de Lleida

summary: Background  The composition of intramuscular fat depends on genetic and environmental factors, including the diet. In pigs, we identified a haplotype of three SNP mutations in the steaoryl-coA desaturase (SCD) gene promoter associated with higher content of monounsaturated fatty acids in intramuscular fat. The second of these three SNPs (rs80912566, C>T) affected a putative retinol response element in the SCD promoter. The effect of dietary vitamin A restriction over intramuscular fat content is controversial in pigs as it seems to depend on the genetic line and the duration of the restriction. This study aims to investigate changes in the muscle transcriptome in SCD rs80912566_TT and CC pigs fed with and without vitamin A supplement during the fattening period.  Results  Vitamin A did not affect carcass fattening traits and fatty acid composition in muscle, but we observed an interaction between vitamin A and SCD genotype on the desaturation of muscle fatty acids. The diet without vitamin A supplement tended to enlarge the compositional differences between genotypes. The interaction between diet and genotype was also evident at the transcriptome level, the highest number of differentially expressed genes were detected between SCD rs80912566_TT pigs fed with the two diets.    Conclusions  Restricting dietary vitamin A during the fattening period did not improve intramuscular fat content despite relevant changes in muscle gene expression, both in coding and non-coding genes. Despite this, there was a significant interaction between the SCD genotype and the dietary vitamin A, which affected the quality of the meat through a change in the saturation index of intramuscular fat and activated general pathways of retinol response in a SCD genotype-dependant manner.

overall_design: Total of 40 pig muscle samples in 4 comparison groups:  9 samples with SCD-TT genotype and high vitamin A in diet; 8 samples with SCD-TT genotype and low vitamin A in diet; 13 samples with SCD-CC genotype and high vitamin A in diet; and 10 samples with SCD-CC genotype and low vitamin A in diet

first: N

last: Pena

first: J

last: Estany

first: R

last: González-Prendes

first: E

last: Sole


title: CROP-seq of hiPSC-derived astrocytes (scRNA-Seq)

status: Public on Aug 24 2021

city: San Francisco

first: Kun

last: Leng

state: Calfironia

address: 675 Nelson Rising Lane, 3rd Floor

department: Institute for Neurodegenerative Diseases

country: USA

institute: University of California San Francisco

type: Expression profiling by high throughput sequencing

summary: In response to central nervous system injury or disease, astrocytes become reactive, adopting context-dependent states with altered functions. Certain inflammatory insults induce reactive astrocyte states that lose homeostatic functions and gain neurotoxicity, and likely contribute to neuroinflammatory and neurodegenerative diseases. However, the cellular pathways controlling these states are not fully understood. Here, we combined single-cell transcriptomics with CRISPRi screening in human iPSC-derived astrocytes to systematically interrogate inflammatory reactivity. We found that autocrine-paracrine IL-6 and interferon signaling downstream of canonical NF-kB activation drove two distinct inflammatory reactive states dependent on STAT3 and IRF1, respectively. Furthermore, these states corresponded with those observed in other experimental contexts, including in vivo, and their markers were upregulated in the human brain in Alzheimer's disease and ischemic-hypoxic encephalopathy. These results and the platform we established have the potential to guide the development of therapeutics to selectively modulate different aspects of inflammatory astrocyte reactivity.

overall_design: hiPSC-derived astrocytes (iAstrocytes) with stable integration of CRISPRi machinery were transduced with a lentiviral sgRNA library in the CROP-seq vector (Datlinger et al, PMID: 28099430) to knockdown a set of genes hypothesized to control inflammatory reactivity. iAstrocytes were then treated with vehilce (Veh) or IL1a+TNF+C1q (ITC) to induce inflammatory reactivity, and then processed for single-cell RNA-sequencing using 10x v3. The sgRNA identities of each cell was recovered by targeted PCR enrichment of poly-adenylated transcripts containing the sgRNA sequence from the 10x cDNA (see Datlinger et al). This dataset includes both the 10x RNA libraries as well as the CROP-seq PCR enrichment libraries.

first: Martin

last: Kampmann


title: CROP-seq of hiPSC-derived astrocytes (bulk RNA-Seq)

overall_design: hiPSC-derived astrocytes generated using different protocols, hiPSC-derived neurons, and hiPSC-derived neural progenitor cells were treated with vehicle vs. IL1a+TNF+C1q for 24h


title: A Stk4 -Foxp3-P65 Transcriptional Complex Promotes Treg Cell Activation and Homeostasis

status: Public on Sep 01 2021

city: Boston

first: KLaus

last: Schmitz-Abe

state: MA

address: 300 Longwood Avenue

department: Asthma, Allergy and Immunology

institute: Children's Hospital Boston

type: Genome variation profiling by high throughput sequencing

summary: The molecular programs involved in regulatory T (Treg) cell activation and homeostasis remain incompletely understood. Here we show that T cell receptor (TCR) signaling in Treg cells induces the nuclear translocation of Stk4, leading to the formation of a Stk4/NF-b p65/Foxp3 complex that regulates Foxp3 and p65-dependent transcriptional programs. The formation of this complex was stabilized by Stk4-dependent phosphorylation of Foxp3 serine 418. Stk4 deficiency in Treg cells, either alone or in synergy with that of its homologue Stk3, precipitated a fatal autoimmune lymphoproliferative disease characterized by decreased Treg cell p65 expression and nuclear translocation, impaired NF-b p65/Foxp3 complex formation and defective Treg cell activation. In an adoptive immunotherapy model, over-expression of p65 or the phosphomimetic Foxp3S418E in Stk3/4-deficient Treg cells ameliorated their immune regulatory defects. Our studies identify Stk3/4 as an essential TCR-responsive regulator of p65-Foxp3-dependent transcription that promotes Treg cell-mediated immune tolerance.

overall_design: There are two groups: the Foxp3YFPCre Treg group vs. Foxp3YFPCre/+Stk3∆/∆Stk4∆/∆ Treg group. The mice around 4-5 weeks were sacked and the CD4+YFP+ splenic cells were isolated for analysis.

first: Ye

last: Cui

first: Klaus

first: Talal

middle: A

last: Chatila


title: High-throughput sequencing of splenic B cells to evaluate the tumor transcriptome in Eµ-MTCP1 vs Eµ-TCL1 vs wildtype mouse models

city: Columbus

first: Janek

middle: S

last: Walker

state: Ohio

address: 410 W 12th Ave

department: Division of Hematology, Department of Internal Medicine

institute: The Ohio State University

summary:
Purpose: Karyotype screening in patients with chronic lymphocytic leukemia (CLL) has identified a rare chromosome translocation, t(X;14)(q28;q32), placing the mature T cell proliferation 1 (MTCP1) gene under transcriptional control of the immunoglobulin (IGH) locus. To establish the role of MTCP1 as a driving gene in CLL, we generated a novel mouse model (Eµ-MTCP1) which recapitulates overexpression of MTCP1 in murine immature and mature B cells. Eµ-MTCP1 mice developed a CLL-like disease found in the blood, spleen, lymph nodes, and other tissues.  As the MTCP1 protein shares significant homology with the TCL1A oncoprotein, and the Eµ-TCL1 mouse model is widely used as an preclinical tool in CLL due to the development of a CLL-like disease in the blood, spleen, and other tissues, we aimed to evaluate the transcriptome between the CLL-like disease of Eµ-MTCP1 and Eµ-TCL1 mice.
Methods: Transgenic Eµ-MTCP1 mice were generated on a C57BL/6NTac background at The Ohio State University Comprehensive Cancer Center’s Transgenic Mouse Facility via pronuclear injection of linear constructs derived from a plasmid vector encoding murine VH promoter-IgH-Eμ enhancer elements followed by human cDNA encoding the p13 kDa MTCP1 protein. Eµ-MTCP1 and Eµ-TCL1 mice were aged and monitored for development of CLL-like disease my monthly flow cytometry assessment of the blood. Upon reaching significant accumulation in the blood (>60%), mice were randomly chosen for euthanization and cell populations were isolated from the spleen according to previously described protocols. From this suspension, B cells were isolated using EasySepTM mouse pan B cell isolation kit (STEMCELL Technologies; Cat #19844). Cell pellets were captured and washed in PBS on ice prior to resuspension in TRIzol reagent and stored at -80°. Total RNA was isolated from TRIzol suspensions using a chloroform/ethanol extraction method and quantified via Qubit RNA HS Assay kit (Invitrogen). The Clontech SMARTer v4 kit (Takara Bio USA, Inc.) was used for global preamplification. Illumina sequencing libraries were derived from the resultant cDNA using the Illumina Nextera XT DNA Library Prep Kit following manufacturer’s instructions. RNA-sequencing libraries were prepared with the Illumina Tru-Seq stranded kit and sequenced on a Hiseq 4000 targeting 40x10E6 fragments per sample. Transcript-level abundances were estimated using Salmon with the genocode mouse release 23, imported using tximport, with normalization and differential expression computed with DESeq2. Data processing was performed according to the CLEAR workflow, which identifies reliably quantifiable transcripts in low-input RNA-seq for differentially expressed gene (DEG) transcripts using gene coverage profiles. MiXCR (v3.0.5) was used with default parameters except the rnaseq alignment was replaced with kaligner2 to identify preprocessed reads containing CDR3 regions from B-cell heavy, kappa, and lambda chains, generating a list of unique CDR3 sequences associated with their relative abundances and specific V(D)J gene usage. MiXCR then generates a list of unique CDR3 sequences associated with their relative abundances and specific V(D)J gene usage. To verify expression of the human MTCP1 and TCL1 transgene (hMTCP1 & hTCL1) in mice, transcript level abundances were estimated using Salmon with a modified gencode mouse reference that contained sequences from human MTCP1 and human TCL1 genes extracted from the grch38 human reference.
Results & Conclusion: Across splenic B cells isolated from both Eµ-MTCP1 and Eµ-TCL1 mice there was prominent usage of distinct heavy chain BCR gene loci in each mouse analyzed. In contrast, wildtype mice exhibited high degree of variability in heavy chain V gene usage without dominant emergence of any gene, indicative of a heterogeneous mixture of splenic B cells. Similar patterns suggesting clonal leukemic populations were observed by kappa and lamba light chain usage. The complexity and aggressive nature of human CLL is often stratified by IGHV mutation status of the malignant B cell population. The most abundant tumorigenic clones isolated from spleens of Eµ-MTCP1 and Eµ-TCL1 mice both exhibited low mutational burden in IGHV, well below the threshold for classification as “mutated." The low mutational burden in this region is consistent with the aggressive, IGHV-unmutated, subtype of human CLL. Moreover, we aimed to determine the overall transcriptional profile of these monoclonal tumor cells and to establish relation to that of the CLL-like cells in Eµ-TCL1 mice. Principal component analysis of the global transcription profile revealed distinct clustering of Eµ-MTCP1 and Eµ-TCL1 tumor cell transcriptomes along PC2, with significant segregation from wildtype littermates across PC1. Analysis of the overall gene expression pattern between Eµ-MTCP1 and Eµ-TCL1  transgenic strains revealed a significant overlap in genes most variable from B cells of wildtype animals. A considerable degree of overlap in gene expression was noted when directly comparing Eµ-MTCP1 and Eµ-TCL1 expression profiles, with a total of only 92 of 27,054 analyzed genes having significant variation (p<0.001) from one transgenic model to the other.

overall_design: Three Eµ-MTCP1 and three Eµ-TCL1 age-matched mice having reached significant disease burden were randomly selected for RNA-sequencing. Three wildtype mice (littermates confirmed by PCR to not contain the hMTCP1 transgene) were used as control.

first: Zachary

last: Hing

first: James

last: Cronin

first: Katie

last: Williams

first: Jordan

middle: N

last: Skinner

first: Casey

middle: B

last: Cempre

first: Charles

middle: T

last: Gregory

first: Larry

middle: P

last: Beaver

first: Brandi

middle: R

first: John

middle: C

last: Byrd

last: Blachly

first: Rosa

last: Lapalombella


title: Human prostate cancer bone metastases have an actionable immunosuppressive microenvironment

status: Public on Aug 29 2021

first: Shenglin

last: Mei

address: 10 Shattuck Street

institute: Harvard medical school (DMBI)

summary: We collected unique sets of tissue fractions from each patient: solid metastatic tissue (Tumor fraction), liquid bone marrow at the site of the metastasis (Involved), as well as liquid bone marrow from a vertebral body distant from the tumor site (Distal). This allowed for a comparison within the same individual, controlling for inter-individual variation. Bone marrow samples from patients undergoing hip replacement surgery (Benign) served as a non-malignant comparator group. The transcriptional composition of all samples was assessed using single-cell RNA-seq (scRNA-seq).

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
Bone marrow were disaggregated and profiled by 10X Genomics Single cell 3 gene expression V2.

**The records have been updated with raw data for samples GSM4274678-GSM4274709 on May 12, 2022.

first: NINIB

last: Baryawno


title: An RNA signature for tuberculosis risk in pregnant women: a prospective cohort study from Pune, India

city: Salvador

first: Artur

middle: Trancoso Lopo

last: Queiroz

address: Rua Waldemar Falcão, 121

country: Brazil

institute: Instituto Gonçalo Moniz

summary: Background: Pregnant and postpartum women are at high risk of developing active tuberculosis (TB), but transcriptional TB studies have excluded pregnant women. We identified differentially expressed genes (DEGs) in pregnant women who did and did not progress to active TB. Methods: We followed a cohort of pregnant Indian women with TB infection for one year postpartum, collecting blood at study entry, 6 weeks postpartum and active TB diagnosis. A prospective signature of risk was identified by comparing whole blood RNA sequencing data from women who developed active TB postpartum (cases) with those who remained healthy (controls). Results: We identified 9 cases and matched them to 18 controls by HIV status and gestational age. A gene set of risk was identified: Expression of KCNIP4 > 2.2 log CPM and S1PR4 < 7.3 log CPM indicated a high probability of developing active TB postpartum. SF3B4 (>4.3 log CPM) and PGAM1 (>6.6 log CPM) correctly classified postpartum cases and controls. Both pairs displayed high accuracy (AUC >0.9) and were unique from 36 published TB signatures.Conclusions: We identified two genes that prospectively differentiated pregnant women who developed active TB postpartum from those who did not. If validated, this signature could be useful in targeted TB prevention programs.

overall_design: gene expression analysis in TB/HIV infected women

first: J

last: Mathad

first: A

first: R

last: Bhosale

first: M

last: Alexander

first: S

first: V

last: Kulkarni

first: B

last: Andrade

last: Gupta


title: Epithelial TGFβ activation engages growth-factor signalling to circumvent cell death and drive intestinal tumorigenesis with aggressive features.

status: Public on Aug 13 2021

city: Glasgow

first: Dustin

last: Flanagan

state: Glasgow

address: Garscube Estate, Switchback Road, , Bearsden

country: United Kingdom

institute: Cancer Research UK Beatson Institute

summary: The pro-tumourigenic role of epithelial TGFβ in colorectal cancer (CRC) has been controversial. Here we identify a cohort of aggressive ‘bad acting’ early-stage (T1) disseminating tumours characterised by high cell-intrinsic TGFβ signalling emanating from the epithelium, not stroma. To address its functional significance, we activated TGFβ signalling in the murine intestinal epithelium either alone or in concert with the common tumour suppressive and oncogenic mutations found in CRC, namely Apc and Kras. Consistent with previous studies, we found that activation of TGFβ rapidly induced apoptosis in Apc-mutant intestine and completely killed Apc-mutant organoids. However, in the presence of both Apc and Kras mutation, activation of TGFβ within the epithelium rampantly accelerates tumourigenesis. Importantly the transcriptional signatures derived from these mice overlapped with the “bad acting” T1 human tumours and this signalling could also predict recurrence in stage II CRC. Mechanistically, the activation of intrinsic TGFβ induced the expression of a growth-factor signalling module containing EGFR that synergised with Apc and Kras to drive marked activation of MAPK signalling. Importantly, inhibition of MEK and/or EGFR suppressed the acceleration conferred by TGFβ even in Kras-mutant cells, which are refractory to MEK/EGFR inhibition in the absence of epithelial TGFβ. Together, we identify both a determinant of early dissemination and a potential vulnerability for tumours with these born-to-be-bad traits.

overall_design: RNA sequencing analysis of genetically engineered mouse models in the presence/absence of drug treatment

middle: J

first: Raheleh

last: Amirkhah

first: Kathryn

last: Gilroy

first: Owen

last: Sansom


title: CROP-seq of hiPSC-derived astrocytes

first: Kun

last: Leng

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

overall_design: Refer to individual Series


title: YTHDF1-regulated oncogenic translation program offers a therapeutic target for acute myeloid leukemia

status: Public on Sep 28 2021

city: Zhanjiang

first: Yun-Guang

last: Hong

state: Guangdong

address: #236 Yuanzhu Road, Chikan District, Zhanjiang

department: Zhanjiang Institute of Clinical Medicine

country: China

institute: Zhanjiang Central Hospital, Guangdong Medical University

summary: N6-methyladenosine (m6A), the most abundant modification in mRNAs, has been defined as a crucial modulator in the progression of acute myeloid leukemia (AML), while the detailed mechanism remains elusive. Here we report that YTHDF1, an m6A reader protein, is overexpressed in human AML samples with enrichment in leukemia stem cells (LSCs). Whereas YTHDF1 is dispensable for normal hematopoiesis in mice, depletion of YTHDF1 attenuates self-renewal and proliferation of patient-derived LSCs, and impedes leukemia establishment in immunodeficient mice. Mechanistically, YTHDF1 promotes the translation of diverse m6A-modified oncogene mRNAs particularly cyclin E2. We applied a structure-based virtual screening of FDA-approved drugs and identified tegaserod as a potential YTHDF1 inhibitor. Tegaserod blocks the direct binding of YTHDF1 with m6A-modified mRNAs and inhibits YTHDF1-regulated mRNA translation. Moreover, tegaserod inhibits leukemogenesis in vitro and in mice, phenocopying the loss of YTHDF1. Together, our study defines YTHDF1 as an integral regulator of AML progression at the translational level and identifies tegaserod as a potential therapeutic agent for AML by targeting YTHDF1.

overall_design: Investigating the role of YTHDF1 in AML

first: Zhigang

last: Yang

first: Yan

last: Chen

first: Tian

last: Liu

first: Yuyuan

last: Zheng

first: Guo-Cai

last: Wu

first: Yinhui

first: Juan

last: Xia

first: Ruiting

last: Wen

first: Wenxin

first: Yi

last: Zhao

first: Jin

first: Xiangwei

last: Gao

first: Zhanghui


title: RNAseq analysis of the herbicide propyzamide on a pre-clinical model of IBD

status: Public on Aug 04 2021

first: Zhaorong

last: Li

address: 60 Fenwood Road

institute: Dana Farber Cancer Institute

summary: Propyzamide induces inflammation on colon from TNBS-treated mice

overall_design: Examination of propyzamide effect on TNBS- induced colitis

first: Liliana

last: Sanmarco

first: Chun

last: Chao

first: Francisco

last: Quintana


title: Nuclear fractionation reveals chromatin-enriched RNA binding proteins and transcriptional regulatory activity of QKI5 during monocytic differentiation

status: Public on Sep 09 2021

city: Beijing

first: Yue

last: Huo

state: Beijing

address: Dongcheng District, Dongdan 3 Tiao 5 Hao

department: State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences

institute: Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College

type: Genome binding/occupancy profiling by high throughput sequencing

summary:
Background: Cellular RNA binding proteins (RBPs) have multiple roles in post-transcriptional control, and some are shown to bind DNA. However, the global localization and the general chromatin-binding ability of RBPs are not well-characterized and remain undefined in hematopoietic cells.
Results: We first provide a full view of RBPs' distribution pattern in the nucleus and screen for chromatin-enriched RBPs (Che-RBPs) in different human cells. Subsequently, by generating ChIP-seq, CLIP-seq and RNA-seq datasets and conducting combined analysis, the transcriptional regulatory potential of certain hematopoietic Che-RBPs are predicted. From this analysis, quaking (QKI5) emerges as a potential transcriptional activator during monocytic differentiation. QKI5 is over-represented in gene promoter regions, independent of RNA or transcription factors. Furthermore, DNA-bound QKI5 activates the transcription of several critical monocytic differentiation-associated genes, including CXCL2, IL16 and PTPN6. Finally, we show that the differentiation promoting activity of QKI5 is largely dependent on CXCL2, irrespective of its RNA binding capacity.
Conclusions: Our study indicates that Che-RBPs are versatile factors that orchestrate gene expression in different cellular contexts, and identifies QKI5, a classic RBP regulating RNA processing, as a novel transcriptional activator during monocytic differentiation.

overall_design: ChIP-seq, RIP-seq, and RNA-seq

last: Ren

first: Weiqian

first: Xiaoshuang

last: Wang

first: Jia

last: Yu

first: Fang


title: seCLIP of C. elegans EIF-3.G in the cholinergic motor neurons

status: Public on Aug 18 2021

city: La Jolla

first: Stephen

middle: M

last: Blazie

state: CA

address: 9500 Gilman Drive

institute: UC San Diego

summary: Protein translation is tightly regulated at the initiation phase, which entails exceedingly complex interactions among multiple EIF initiation factors to bring the ribosome to the mRNA and scan the 5’ leader sequence for the start codon. EIF-3 contains multiple subunits with essential and emerging regulatory activities throughout the translation initiation pathway.  However, it remains poorly understood how individual components of the EIF3 complex contribute to the selective regulation of translation in multicellular organisms. Here, through studies of a missense mutation in C. elegans EIF-3.G, an RNA-binding subunit of EIF3, we have dissected mechanisms of how regulation of protein translation initiation modulates neuronal excitation.  EIF-3.G(C130Y) alters a conserved Zinc Finger and behaves as a gain-of-function.  We show that while EIF-3.G(C130Y) permits essential aspects of translation initiation, this variant functionally involves its RNA binding activity in regulating protein synthesis. We mapped EIF-3.G binding sites in the C. elegans cholinergic motor neuron transcriptome and identified a significant representation of mRNAs containing long and GC-rich 5' UTRs and in mRNAs exhibiting activity-dependent transcript level changes. Our results suggest that modulation of the scanning process of translation initiation by EIF3 contributes homeostatic regulation to synaptic activity changes.

overall_design: Two replicate experiments were performed in strains containing 3xFLAG-tagged EIF-3.G(+), EIF-3.G(C130Y), or EIF-3.G(∆RRM). A single replicate seCLIP experiment was performed with a negative control without a transgene in a wild type C. elegans background (N2). EIF-3.G(+) and EIF-3.G(∆RRM) transgenes were in the background of acr-2(n2420) and EIF-3.G(C130Y) transgene was in the background of eif-3.G(C130Y); acr-2(n2420).

first: Seika

last: Takayanagi-Kiya

first: Katherine

last: McCulloch

first: Yishi

last: Jin


title: Yap/Taz inhibit goblet cell fate to maintain lung epithelial homeostasis (RNA-seq)

status: Public on Aug 19 2021

city: BOSTON

first: Boting

last: Ning

state: Massachusetts

address: 72 E Concord St

institute: BOSTON UNIVERSITY

summary: Proper lung function relies on precisely balanced numbers of specialized epithelial cell types that work together and are maintained in homeostasis. In this study we have described essential roles for the transcriptional regulators YAP and TAZ, which are key effectors of Hippo pathway signaling, in maintaining lung epithelial homeostasis. Phenotypes associated with Yap/Taz deletion include alveolar defects and a striking development of goblet cell metaplasia throughout the airways. Knockdown of YAP and TAZ in HBECs similarly drives mucin expression. The TEAD family of transcription factors are well characterized partners of the YAP/TAZ transcriptional effectors, and we have found that knockdown of TEAD1-4 similarly drives elevated mucin expression. In order to further understand the role of the TEAD transcription factors in human lung epithelial cell fate, we conducted TEAD Chromatin Immunopreciptitation (ChIP)-Sequencing.

overall_design: HBECs were cultured in PneumaCult-Ex Plus and transfected with a pool of 3 unique controls or dual Yap/Taz targeting siRNAs. All experiments were performed in triplicate and cells were collected 48 hours after transfection. Total RNA was extracted using the RNeasy Mini Kit (Qiagen).  Libraries were prepared using the Illumina TruSeq RNA Sample Preparation Kit v2. The libraries from individual samples were pooled in groups of 15 for cluster generation on the Illumina cBot using Illumina TruSeq Single-Read Cluster Kit and then sequenced on an Illumina NextSeq 500 instrument.

first: Andrew

last: Tilston-Lunel

first: Xaralabos

last: Varelas


title: scRNA sequencing time series of human iPSC-derived hematopoietic progenitors (with or without Notch activation from day 0-2) developing into T cells from day 12 to day 42 compared with freshly isolated human thymocytes.

first: Carlos

last: Villacorta-Martin

address: 670 Albany St

institute: Center for Regenerative Medicine at Boston University

summary: scRNA sequencing time course covering 5 time points from progenitors to maturing T cells

overall_design: We undertook scRNA sequencing of day 12 progenitors with and without Notch activation from day 0-2, day 13 (one day of co-culture), day 16 (early events toward the T/NK lineage), day 20 (large populations of T/NK progenitors seen by flow at this time point), and day 42 (maturing T cells).  N=2 for each time point from separate differentiations.  1 sample of freshly isolated post natal human thymocytes was used as a primary cell control.  All samples were FACS sorted for live, CD45+ cells before single cell capture using InDrops technique at HMS.

first: Dar

last: Heinze

first: Gustavo

last: Mostoslavsky


title: Yap/Taz inhibit goblet cell fate to maintain lung epithelial homeostasis


title: Transient JAK/STAT pathway inhibition prevents natural occurring B-ALL development in genetically predisposed Pax5+/- mice

status: Public on Jul 02 2021

city: Salamanca

first: Isidro

last: Sánchez García

address: Campus Miguel de Unamuno

department: Centro de inv. del Cáncer (CIC).

country: Spain

institute: Inst. de Inv. Biomédica de Salamanca (IBSAL). H. U. de Salamanca. Inst. de Biología Molecular y Celular del Cáncer (IBMCC).

summary:
We used microarrays to investigate gene expression changes in bone marrow B220+ cells from Pax5+/- and wild-type mice after ruxolitinib treatment during 2 weeks.
Preventing development of B cell acute lymphoblastic leukemia (B-ALL), a disease with devastating effects in children, is a longstanding and unsolved challenge in medicine. In humans and mice, germline alterations in the Pax5 gene can lead to B-ALL. Preclinical studies have shown that this malignant transformation only occurs under an immune stress through the accumulation of secondary mutations in the JAK/STAT pathway. Here we describe that transient oral administration of ruxolitinib, a drug targeting the JAK/STAT pathway, can mitigate the risk of B-ALL in Pax5+/- mice. Although exposure to infection strongly potentiates leukemogenesis, the development of B-ALL was significantly impeded by transient in vivo treatment of Pax5+/- mice with ruxolitinib early in life (p-value=0.0332). These findings provided the first in vivo evidence for an effective preventive strategy for B-ALL development in genetically predisposed mice.

overall_design: Bone marrow B220+ cells of 4 Pax5+/- and 5 WT mice treated with ruxolitinib compared with bone marrow B220+ cells of 4 Pax5+/- and 5 WT untreated mice.

first: Ana

last: Casado-García

first: Marta

last: Isidro-Hernández

first: Ninad

last: Oak

first: Andrea

last: Mayado

first: Christine

last: Mann-Ran

first: Javier

last: Raboso-Gallego

first: Silvia

last: Alemán-Artega

first: Alexandra

last: Buhles

first: Dario

last: Sterker

first: Oscar

last: Blanco

first: Alberto

last: Orfao

first: Diego

last: Alonso-López

last: De Las Rivas

first: Susana

last: Riesco

first: Pablo

last: Prieto-Matos

last: García Criado

first: María

last: García Cenador

first: Thomas

last: Radimerski

first: Manuel

last: Ramírez-Orellana

first: César

last: Cobaleda

first: Jun

last: Yang

first: Carolina

last: Vicente-Dueñas

first: Andreas

last: Weiss

first: Kim

middle: E

last: Nichols

last: Sánchez-García


title: ATAC-seq of human tonsillar B-cell populations

status: Public on Aug 03 2021

city: New York

first: Ashley

middle: Stephen

last: Doane

state: NY

address: 1300 York Ave

institute: Weill Cornell Medicine

summary: ATAC-seq in sorted GC centroblasts (GCB: CD20+CD44-CD10+CXCR4+), GC centrocytes (CC: CD20+CD44-CD10+CXCR4-), naïve B cells (NB: CD20+CD44+CD10-IgD+), memory B cells (MB: CD20+CD44+CD10-CD38-CD27+), and plasma cells (PC: CD20+CD44+CD10-CD38+CD27+)


title: Dual RNASeq reveals NTHi-macrophage transcriptomic changes during intracellular persistence

status: Public on Aug 23 2021

city: Southampton

first: Jodie

last: Ackland

state: Hampshire

address: Mail Point 810, Level F, South Block Southampton General Hospital, Tremona Road

department: Clinical and Experimental Sciences, Faculty of Medicine

institute: University of Southampton

summary: Nontypeable Haemophilus influenzae (NTHi) is a pathobiont which chronically colonises the airway of individuals with chronic respiratory disease. It is unclear how NTHi persists in the airway, however accumulating evidence suggests that NTHi can invade and persist within macrophages. To better understand the mechanisms of NTHi persistence within macrophages, this work developed an in vitro model of NTHi intracellular persistence using human monocyte-derived macrophages (MDM). Dual RNA Sequencing was used to assess MDM and NTHi transcriptomic regulation occurring simultaneously during NTHi persistence. This work demonstrates that NTHi can invade and persist within human macrophages. Macrophages activate innate immune responses, whereas NTHi persistence was facilitated by transcriptomic adaptations in bacterial metabolic, stress response and ribosome pathways. This research provides transcriptomic insights into NTHi-macrophage interactions, enhances our understanding of how NTHi can utilise host immune cells to chronically colonise the airway and identifies potential bacterial gene pathways that may be attractive therapeutic targets

sample_organism:
Haemophilus influenzae
Homo sapiens

platform_organism:
Haemophilus influenzae
Homo sapiens

overall_design: Monocyte derived macrophages (MDM) were infected with NTHi ST14 at MOI 100, or left uninfected (controls) for 6 h, washed with gentamicin for 90 min and incubated in antibiotic free infection media until 24 h. RNA from five biological repeats was harvested at 7.5 h (following 90 min gentamicin wash, indicated as the 6h timepoint) and at 24 h using Trizol and total RNA was extracted using miRNeasy kit. Samples were supplied to Novogene (Hong Kong) for sequencing. Briefly, ribosomal RNA (rRNA) was removed from all samples using Illumina® Ribo-Zero Plus rRNA Depletion Kit. Libraries were generated using the NEBNext®Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA). Sequencing was performed using NovaSeq 6000 Illumina platform and 150-base pair (bp) paired end reads were generated using a sequencing depth of 90 million reads.

middle: I

last: Heinson

first: David

middle: W

last: Cleary

first: Myron

last: Christodoulides

first: Tom

last: Wilkinson

first: Karl

last: Staples


title: Targeting Histone K4 Trimethylation for Treatment of Cognitive and Synaptic Deficits of Mouse Models of Alzheimer's Disease

status: Public on Jul 14 2021

city: Buffalo

first: Zhen

last: Yan

address: 955 Main St

institute: SUNY Buffalo


title: BioVacSafe (Biomarkers for enhanced vaccine immunosafety) Influenza challenge

status: Public on Jul 01 2021

city: Berlin

first: January

last: Weiner

address: Charitéplatz 1

department: CUBI

country: Germany

institute: Berlin Institute of Health, Charité Medical University of Berlin

summary: Transciptional responses in T cells in blood and BAL from healthy adult volunteers infected with influenza

overall_design: Healthy volunteers were inoculated intranasally with influenza. For each individual samples were colected from BAL and blood at 3 timepoints (day: 0, 7 and 28). Samples were targeted fro CD4 and CD8. Finaly, for each donor infected and uninfected samples were considered.

first: Hans-Joachim

last: Mollenkopf

first: Christopher

last: Chiu

first: Suzanna

last: Paterson


title: Targeting Histone K4 Trimethylation for Treatment of Cognitive and Synaptic Deficits of Mouse Models of Alzheimer's Disease (ChIP-seq)

summary: We performed chromatin immunoprecipitation sequencing (ChIPseq) to profile genome-wide occupancy of H3K4me3 in PFC from WT mice and P301S Tau mice

overall_design: Examination of the transcriptional changes of target genes related to the alteration of H3K4me3 of two 6 mo. old  PS19(P301S), and two 6 mo. old control (C57BL/6 x C3H)  mice from PFC tissue were compared.

first: Jamal

last: Williams

first: Qing

last: Cao


title: Transcriptome of DLD-1 co-cultured with or without Fusobacterium nucleatum

status: Public on Jun 24 2021

city: Chengdu

first: Xin

last: Zheng

state: Sichuan

address: No. 14, Section 3, Renmin South Road

institute: Sichuan University

summary: To determine the glycolysis promoting effect of F. nucleatum and its underlying mechanisms, we performed RNA-seq to compare the gene expression profiles of DLD-1 cultured with or without F. nucleatum.

overall_design: Examination of DLD-1 co-cultured with F. nucleatum versus DLD-1 cultured alone (treat with PBS). Each group has 3 biological replicates.

first: Rui

last: Liu

first: Chenchen

last: Zhou

first: Haopeng

last: Yu

first: Wanyi

last: Luo

first: Jianhui

last: Zhu

first: Jiaxin

first: Xian

last: Peng

first: Quan

last: Yuan

first: Canhua

last: Huang

first: Xuedong


title: Microarray Expression Profiling of Punicalagin, Myricetin and Quercetin Treated Leukemia Cell Line (THP-1)

status: Public on Jun 30 2021

city: Jeddah

first: Sajjad

last: Karim

state: Makka

address: Sulemania, CEGMR-80216

department: Center of Excellence in Genomic Medicine Research

country: Saudi Arabia

institute: King Abdulaziz University

summary:
THP-1 monocyte were differentiated to macrophage using PMA for 24 hrs, then (THP-1) macrophage were treated with DMSO, Punicalagin, Myricetin or Quercetin for 24 hrs.
Transcriptional expression profiling was performed with Affymetrix GeneChips. Target preparation, hybridization, washing and staining, and probe array scanning were done to process array.

overall_design: Three different passages of THP-1 monocyte were used 6, 7, and 8. THP-1 moncyte were differentiated to macrophage using PMA for 24 hrs. THP-1 macrophage were treated with DMSO, Punicalagin, Myricetin or Quercetin for 24 hrs.

first: Etimad

last: Huwait

first: Salma

middle: Y

last: Saddeek

first: Sanaa

last: Almowallad

first: Rehab

middle: F

last: Al-Masabi

first: Nofe

last: Alganmi


title: BRD9-containing non-canonical BAF chromatin remodeling complex acts as a barrier to somatic cell reprogramming

status: Public on Jun 15 2021

city: Istanbul

first: Ayse Derya

last: Cavga

address: Rumelifeneri Yolu, Sariyer

country: Turkey

institute: Koc University


title: Host response to RhCMV/SIV immunization through subcutaneous and oral route

status: Public on Jun 28 2021

city: Minneapolis

first: Michael

last: Gale

state: Minnesota

address: 689 23rd Ave SE

department: Microbiology and Immunology

institute: University of Minnesota

summary: Strain 68-1–derived Rhesus Cytomegalovirus (RhCMV) vectors expressing simian immunodeficiency virus (SIV) proteins (RhCMV/SIV) are able to elicit and maintain cellular immune responses that stringently control and subsequently clear a mucosal challenge with highly pathogenic SIV in 50-60% of vaccinated rhesus monkeys (RMs). Here, we utilize whole blood transcriptomic profiling to identify host responses correlated to RhCMV/SIV efficacy.

overall_design: Longitudinal mRNA profiling of whole blood from rhesus macaques during immunization with RhCMV/SIV.


title: High-throughput RNA-sequencing transcriptome analysis of ABC-DLBCL revealed new targets genes

status: Public on Aug 05 2021

city: Madrid

first: Juana

last: Serrano Lopez

address: Avda Reyes Catolicos 2

institute: IIS-FJD

summary: Purpose: we searched for new potential druggable therapeutic targets through the description of high or low abundance transcripts that might be critical for ABC DLBCL cells.

overall_design: The bulk of DLBCL were categorized in Cell-Of-Origen (COO) by Nanostring platform prior to deep transcriptome analysis by RNA sequencing (RNA-seq). After comparing GCB and ABC transcriptomes, a set of 79 genes were found differentially expressed (DE). By performing Gene Set Enrichment Analysis (GSEA), two main pathways were enriched and were related to metabolism and immune pathways.

last: Serrano-Lopez

first: Joaquin

last: Garcia


title: BRD9-containing non-canonical BAF chromatin remodeling complex acts as a barrier to somatic cell reprogramming (ATAC-Seq)

summary: Epigenetic reprogramming requires extensive remodeling of chromatin landscapes to silence gene expression programs which sustain cell identity. ATP-dependent chromatin-remodeling complexes are important regulators of chromatin structure and gene expression; however, the role of Bromodomain containing protein 9 (BRD9) and the associated ncBAF (non-canonical BRG1-associated factors) complex in somatic cell reprogramming remains unknown. Here, we show that inhibition and acute degradation of BRD9 increases the efficiency by which induced pluripotent stem cells (iPSCs) can be generated from human fibroblasts. Genetic suppression of BRD9 as well as ncBAF complex subunit GLTSCR1, but not the closely related BRD7, phenocopied this effect. CRISRP/Cas9-mediated knockout of BRD9 demonstrated that  it is dispensable for establishment and maintenance of human pluripotency. Mechanistically, BRD9 inhibition facilitates reprogramming by downregulating somatic cell type-specific genes and decreasing chromatin accessibility at somatic enhancers. Collectively, these results establish BRD9 as an important safeguarding factor for somatic cell identity whose inhibition lowers barriers to reprogramming.

overall_design: Examination of transposase accessible chromatin in fibroblast cells upon BRD9 inhibition or OSKM expression. Three biological replicates from each treatment were prepared. Fibroblast cells were treated with I-BRD9, dBRD9 or DMSO (control) for 5 days and cells were reprogrammed for 6 days with DMSO treatment.

first: Kenan

last: Sevinç

first: Tamer

last: Onder


title: scRNAseq and TCRseq of hepatic and splenic CD8T cells from normal diet fed (ND), HFHC diet fed (HFHC), and resolution induced (RES) mice.

status: Public on Jun 11 2021

city: Shinjuku-ku

first: Yohei

last: Mikami

state: Tokyo

address: Shinanomachi 35

country: Japan

institute: Keio University School of Medicine

summary: To explore key features associated with the resolution process in liver fibrosis, we here applied a unique murine model, in which mice were fed HFHC diet for   24 weeks, and then continued with the HFHC diet (HFHC) or switched to a normal diet (RES) for 5 weeks. We noted that both the frequency and number of intrahepatic CD8+ T cells remained significantly high in RES mice compared to normal diet-fed mice (ND). To reveal the transcriptome profiling-based subtypes of  CD8+T cells present during the liver fibosis resolution, we performed scRNA-seq analysis. Total of 25851 cells were  clustered into 17 clusters based on the gene signatures. We revealed CD69+CD103-CD8+ Trm cell enrichment in fibrosis resolution livers. scTCR-seq analysis further revealed the clonal enrichment mainly in the Cd44+Sell-S1pr1- liver Trm fractions. In addition, TCR clonotypes enriched in liver CD8+ Trm cells of RES mice were expanded compared to those in liver CD8+ T cells of ND mice, and rarely detected in spleen CD8+ T cells.

overall_design: mRNA and TCR repatoire profiles of liver CD8T cells derived from 35weeks old WT, HFHC, or RES mice.

first: Yuzo

last: Koda

first: Yuya

last: Hagihara

first: Takanori

last: Kanai

first: Nobuhiro

last: Nakamoto


title: Long non-coding RNA landscape of patients biopsies from advanced Triple Negative Breast Cancer

status: Public on Jun 04 2021

city: Tlalpan

first: Claudia

last: Rangel Escareño

state: CDMX

address: Periferico Sur

department: Departamento de Genómica Computacional

country: Mexico

institute: Instituto Nacional de Medicina Genómica

summary:
The response to specific treatments relies on precise biomarkers, thereby avoiding undesirable toxicities and diminishing the cost. Due to the lack of treatment options in triple-negative breast cancer, it is crucial to search biomarkers with reasonable specificity and sensibility to recognize clusters of patients who could benefit from the cutting-edge oncologist treatments available nowadays.
Microarrays were used to detail the global gene expression program to stratified TNBC patients according to TNBCtype software developed by Vanderbilt University and then identified lncRNAs expressed differentially through the TNBC subtypes.

overall_design: FFPE samples were selected from advanced TNBC patients according to clinical criteria for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain a homogeneous population of patients at stages III and IV to increase the temporal resolution of expression profiles. To that end, we selected patients according to the clinical criteria attended in the National Cancer Institute of Mexico from 2007 to 2010 as described in the paper. Advanced TNBC FFPE samples were selected according to clinical criteria for RNA extracction and hybridization on Affymetrix microarrays. We sought to obtain homogeneous population of patients at stage III and IV in order to increase the temporal resolution of expression profiles. To that end we selected patients  according to clinical criteria described in the paper.

first: Raúl

last: Espinosa

last: Escareño

first: Rubén

last: Bautista

first: Everardo

middle: G

last: Millán

first: Alette

middle: O

last: Gómez


title: Transcriptome expression analysis of IL-12 influenced mouse podocyte

status: Public on Jun 02 2021

city: Jinhua

first: Weiqiang

last: Lin

state: Zhejiang

address: Shangcheng street N1

institute: The Fourth Affiliated Hospital, Institute of Translational Medicine, Zhejiang University School of Medicine

summary: To explore the effect of IL-12 treatment on podocyte function and related signalling pathways. After 6 hours treatment of podocytes with the screened differential cytokine IL-12, which was found to affect cell migration ability and cytoskeleton, RNA-seq sequencing was performed on control and IL-12-treated podocytes respectively to look for differentially expressed genes and signalling pathways and to search for potential mechanisms of MCD recurrence.

overall_design: Transcriptome expression analysis of IL-12 treatment and control podocyte.


title: Ethoxysanguinarine, Baicalin, Gastrodin and Valsartan treatment lower Angiotensin-II-induced blood pressure

status: Public on May 14 2021

city: Fuzhou

first: Jun

last: Peng

state: Fujian

address: 1 Qiuyang Road, Minhou Shangjie

department: Academy of Integrative Medicine

institute: Fujian University of Traditional Chinese Medicine

summary: The goals of this study is to identify the differential expressed genes in abdominal aorta of C57BL/6 mice with or without Angiotensin II (AngII) treatment, and compare the differential expressed genes in the abdominal aorta of Ang II infused C57BL/6 mice after Ethoxysanguinarine (ETH), Baicalin (BAI), Gastrodin (GAS) or valsartan (VAL) treatment. Briefly, the mice (n=30) were randomly divided into 6 groups: control, AngII, AngII + ETH, AngII + BAI, AngII + GAS and AngII + VAL groups (n=5 for each group). Mice in Control and AngII groups were infused with saline and 500 ng/kg/min of AngII respectively, and orally administrated with saline; the mice in AngII + ETH, AngII + BAI and AngII + GAS groups were infused with AngII (500 ng/kg/min) and orally administrated with 5 mg/kg /day of ETH, BAI or GAS daily for total 4 weeks. The mice in AngII + VAL group were infused with AngII (500 ng/kg/min) and orally administrated with 10.4mg/kg /day of VAL. Then the abdominal aortas were used to identify differentially expressed genes among different groups.

overall_design: RNA sequencing was performed to compare differential expressed genes in abdominal aorta of C57BL/6 mice in following 6 groups: control, AngII, AngII + ETH, AngII + BAI, AngII + GAS and AngII + VAL groups (n=5 for each group).

first: Aling

last: Shen

first: Huixin

last: Liu

first: Ying

last: Cheng

first: Meizhu

last: Wu

first: Xiuli

last: Zhang

first: Nanhui

last: Xu


title: A single N6-methyladenosine site in lncRNA HOTAIR regulates its function in breast cancer cells

status: Public on May 15 2021

city: Mobile

first: Justin

last: Roberts

state: AL

address: 5851 USA Drive North, MSB 3370

department: Pharmacology

institute: University of South Alabama

summary: N6-methyladenosine (m6A) modification of RNA plays important roles in normal and cancer biology, but knowledge of its function on long noncoding RNAs (lncRNAs) remains limited. Here, we investigate whether m6A regulates the function of the human HOTAIR lncRNA, which contributes to multiple pro-tumor phenotypes in triple-negative breast cancer (TNBC) cells. We identify 14 individual m6A sites within HOTAIR, with a single site (A783) consistently methylated. Mutation of A783 impairs cellular proliferation and invasion in HOTAIR-overexpressing TNBC cells. m6A at A783 regulates HOTAIR’s ability to localize to chromatin and induce gene expression changes. A783 mutant HOTAIR reverses wild-type effects beyond baseline, demonstrating a potential antimorphic behavior. HOTAIR interacts with nuclear m6A reader YTHDC1 and YTHDC1-HOTAIR interactions are required for chromatin localization and gene repression. Our work demonstrates how modification of one base in a lncRNA can elicit a distinct gene regulation mechanism and drive disease-associated phenotypic changes.

overall_design:
MeCLIP: M6A identification in 2 cell lines (MDA-MB-231 pB-HOTAIRA783U (3 replicates) and MDA-MB-231 pB-AntiLuciferase (1 replicate)) using modified eCLIP-based library preparation and custom analysis pipeline.
RNAseq: PolyA-selected high-throughput RNA sequencing for 3 cell lines, 3 replicates each (MDA-MB-231 with pB-HOTAIRWT, pB-HOTAIRA783U, and pB-AntiLuciferase).

first: Allison

last: Porman

first: Aaron

last: Johnson


title: Translatome analysis of Mycobacterium tuberculosis

city: New Delhi

first: G Aneeshkumar

last: Arimbasseri

state: Delhi

address: Aruna Asaf Ali Marg

department: Molecular Genetics Laboratory

country: India

institute: National Institute of Immunology

summary: We present the data obtained from high-resolution ribosome profiling analysis of Mycobacterium tuberculosis grown under standard conditions (log phase) and cells subjected to oxidative stress (50 µM cumene hydroperoxide) and pH stress (pH 4.5). Our data shows pervasive ribosome pausing in the M. tb translatome. A large number of genes show very high pause immediately downstream to the translation start site. Moreover, serines and alanines in the E site of the ribosome exhibit highest pause scores.

overall_design: Ribosome profiling analysis of M. tb grown to log phase, subjected to oxidative stress (50µM cumene hydroperoxide) and pH stress (pH 4.5).

first: Gopalakrishnan

middle: A

first: Smitha

last: Soman

first: Somdeb

last: Chattopadhyay


title: BRD9-containing non-canonical BAF chromatin remodeling complex acts as a barrier to somatic cell reprogramming (RNA-Seq)

first: Ayse Derya

last: Cavga

overall_design: Examination of BRD9 inhibition's effect on gene expression profile of fibroblast cells. Three biological replicates from each condition were prepared. Fibroblast cells were treated with BI-7273, I-BRD9, dBRD9 or DMSO (control) for 5 days or fibroblast cells were transduced with lentiviral contructs to express Cas9 and gRNA targeting BRD9 or non-targeting gRNA (control). An iPSC clone was also used to understand gene expression profile of pluripotent stem cells.

first: Kenan

last: Sevinç

first: Tamer

last: Onder


title: Direct RNA ONT sequencing of pine roots under ammonium nutrition

status: Public on May 22 2021

city: Malaga

first: Cesar

last: Lobato-Fernandez

state: Malaga

address: Bulevar Louis Pasteur 21

department: Biochemistry and Biomolecular Biology

institute: University of Malaga

summary: Epitranscriptomics modifications constitute a gene expression checkpoint in all living organism including plants. Considering the relevance of nitrogen nutrition and metabolism for the correct plant growth and development, it can be hypothesized that epitranscriptome changes must regulate every biological process in plants including nitrogen nutrition. In the present work, the epritranscriptomics changes in maritime pine roots caused by ammonium nutrition have been monitored through direct RNA sequencing using Oxford Nanopore Technology. The main transcriptome responses to ammonium nutrition affected to transcripts involved in nitrogen and carbon metabolisms, defense response, hormone synthesis and signaling, and translation. Additionally to a global detection of epitranscriptomics marks, the m6A deposition and its dynamics have been identified, which seems to be important regulators of translation when compared with the proteomic profiles of the same samples. In this sense, the obtained results suggest that protein translation is finely regulated through the epitranscriptomics marks maybe through changes in mRNA polyA length, transcript amount and ribosome protein composition. The multiomics results in the present study suggest that the epitranscriptome must modulate the responses to development and environmental changes, including ammonium nutrition, through buffering, filtering and focusing the final products of the gene expression.

overall_design: Ammonium nutrition was studied at short times (24 hours) in roots from one month-old seedlings of maritime pine. Control seedlings were irrigated with 80 mL of water (C) and the experimental seedlings with 80 mL of 3 mM NH4Cl. Root samples were collected at 24 hours post-irrigation and immediately frozen in liquid N. This experiment was carried out three independent times. The polyA-RNA was isolated and sequenced using Direct-RNA sequencing kit (SQK-RNA001) for MInION (Oxford Nanopore Technologies). Reads were employed for gene expression analyses and epitranscriptomics studies.

first: Francisco

last: Ortigosa

first: César

last: Lobato-Fernández

first: Juan

last: Pérez-Claros

last: Cantón

first: Concepción

last: Ávila

last: Cánovas

first: Rafael

last: Cañas


title: Multi-resolution deconvolution of spatial transcriptomics data reveals continuous patterns of inflammation

status: Public on May 05 2021

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

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

overall_design: Refer to individual Series


title: RTF1 and SPT6 stimulate transcription elongation by two distinct mechanisms

status: Public on Jun 21 2021

city: Göttingen

first: Kristina

last: Žumer

address: Am Faßberg 11

department: Department of Molecular Biology

institute: Max Planck Institute for Multidisciplinary Sciences

summary: We have previously shown that the RNA polymerase II (Pol II)-DSIF complex associates with the PAF1 complex (PAF), RTF1 and SPT6 to form an activated elongation complex in vitro. Here we investigate the mechanisms that these factors use to stimulate Pol II elongation in vivo. We combine rapid factor depletion from human cells with genome-wide analyses of changes in RNA synthesis and occupancy with engaged Pol II. Whereas depletion of PAF subunits has little effect on transcription in vivo, depletion of RTF1 or SPT6 strongly compromises RNA synthesis, albeit in fundamentally different ways. RTF1 depletion decreases Pol II velocity, whereas SPT6 depletion impairs Pol II progression through nucleosomes. These results show that distinct transcription elongation factors stimulate Pol II velocity and Pol II progression through chromatin in vivo. Our results also provide evidence for two distinct barriers to elongation at the beginning of genes, the promoter-proximal pause site and the +1 nucleosome.

overall_design: Samples for each condition were collected in biological duplicates. Cells were treated with dTAG7 for 1 or 4 hours, the corresponding control cells were treated for the same duration with vehicle only (DMSO) at the same vol/vol dilution.

last: Zumer

first: Kerstin

last: Maier

first: Lucas

last: Farnung

first: Martin

last: Jaeger

first: Petra

last: Rus

first: Georg

last: Winter

first: Patrick

last: Cramer


title: Multi-resolution deconvolution of spatial transcriptomics data reveals continuous patterns of inflammation (Spatial scRNA-Seq)

summary: The function of mammalian cells is largely influenced by their tissue microenvironment and by inter- celllular interactions. Advances in spatial transcriptomics open the way for studying these important determinants of cellular function, by enabling a transcriptome wide evaluation of gene expression in-situ. A critical limitation of the current technologies, however, is that their resolution is limited to regions (spots) of sizes well beyond that of a single cell, thus providing measurements for cell-aggregates which may mask critical interactions between neighboring cells of different types. While joint analysis with single cell RNA-sequencing (scRNA-seq) can be leveraged to alleviate this problem, current analyzes are limited to a discrete view of cell type proportion inside every spot. This limitation becomes critical in the common case where, even within a cell type, there is a continuum of  cell states, which can not be clearly demarcated and may reflect important differences in the cells’ function and interaction with their surrounding. To address this, we developed Deconvolution of Spatial Transcriptomics profiles using Variational Inference (DestVI), a probabilistic method for multi- resolution analysis for spatial transcriptomics, which explicitly models continuous variation within cell types. Using simulations, we demonstrate that DestVI is capable of providing higher resolution compared to the existing methods, and that it is also the first method to enable an estimate of gene expression by every cell type inside every spot. We then introduce an automated pipeline for analysis of a tissue, as well as comparison between tissues. We apply DestVI and this pipeline to study the response of lymph nodes to a pathogen and to explore the spatial organization of a mouse tumor model. In both cases, we demonstrate that DestVI can provide a reliable view of the organization of these tissues, and that it is capable of identifying important cell-type specific changes in gene expression - between different tissue regions or between conditions. DestVI is available as an open-source software in the scvi-tools codebase (https://scvi-tools.org).

overall_design: Lymph nodes from mice treated with mycobacterium or PBS or MCA205 tumor were used. Auricular LNs and the MCA205 tumor were prepared according to Visium spatial protocols of tissue preparation guide (10x genomics). Firstly, freshly obtained tissue samples were snap frozen in liquid nitrogen, then embedded in chilled Optimal Cutting Temperature compound (OCT; Tissue-Tek) and frozen on dry ice, then stored at -80°C in a sealed container for later use. For Visium samples preparation, OCT-embedded tissue blocks were cut to 10 µm thick using a LEICA CM1950 machine and mounted on the Visium spatial gene expression slide.

first: Romain

last: Lopez

first: Hadas

last: Keren-Shaul

first: Baoguo

last: Li

first: Pierre

last: Boyeau

first: Michael

last: Jordan

first: Merav

last: Kedmi

first: David

last: Pilzer

first: Allon

last: Wagner

first: Yoseph

last: Addad

first: Nir

last: Yosef


title: Multi-resolution deconvolution of spatial transcriptomics data reveals continuous patterns of inflammation (scMARS-Seq)

first: Ido

last: Amit

overall_design: MCA205 fibrosarcoma tumor were injected into mice. After 14 days, to prepare tumor infiltrating leukocytes single cell suspensions, the tumors underwent mechanical (gentle-MACSTM C tube, Miltenyi Biotec Inc., San Diego, CA) and enzymatic digestion (0.1mg/ml DNase type I (Roche), and 1mg/ml Collagenase IV (Worthington) in RPMI-1640) for 10 minutes at 37°C and repeat one more time. Cells then filtered through 100 µm cell strainer, washed with an ice cold sorting buffer, centrifuged (5 min, 4°C, 350 g), and stained with fluorophores conjugated anti-mouse CD45 antibodies on ice 30 minutes avoid light.  After staining, cells were washed and resuspended in a cold washing buffer (0.5% BSA and 2 mM EDTA in PBS), filtered through a 70 µm cell strainer. Before sorting, cells were stained with propidium iodide to exclude dead/dying cells. Cell sorting was performed using a BD FACSAria Fusion flow cytometer (BD Biosciences), gating for CD45+ cells after exclusion of dead cells and doublets.


title: Multi-resolution deconvolution of spatial transcriptomics data reveals continuous patterns of inflammation (scRNA-Seq)

overall_design: Lymph nodes from mice treated with mycobacterium or PBS were digested in IMDM containing 100 µg/mL Liberase TL and 100 µg/mL DNase I (both from Roche, Germany) for 20 minutes at 37°C. Last 5 minutes of incubation, EDTA was added at a final concentration of 10 mM. Cells were collected, filtered through a 70mm cell strainer, washed with PBS + 0.04% BSA for a final concentration of 1000 cells/µL. before loading into the 10x genomics chromium instrument.


title: Botulinum toxin A enhances the rates of embryo implantation via elevation of endometrial angiogenesis

city: SEONGNAM-SI

first: YOUN JUNG

last: KANG

address: 335 PANGYO-RO

department: MEDICINE

country: South Korea

institute: CHA University

summary: Intrauterine BoTA treatment has a beneficial effect on vascular reconstruction of functional endometrium prior to embryo implantation by increasing endometrial blood flow near the uterine cavity suggesting BoTA treatment as a potential therapeutic strategy for patients who are suffering from repeated implantation failure with the problems with endometrial receptivity.

overall_design: As a non-invasive treatment strategy, BoTA was infused into one side of mouse uterine horns and saline was infused into the other side of horns for the control (N=28). Assessment of BoTA impact on the endometrium at day3 and day8.

first: Youn-Jung

last: Kang

first: Hwa

middle: S

last: Koo

first: Min-Ji

last: Yoon

first: Chang-Jin

last: Lee

first: Seon-Hwa

last: Hong

first: Hwijae

last: Cha

first: Jungho

last: Ahn


title: The Bromodomain and extraterminal (BET) inhibitor attenuates inflammatory response and cell migration in human microglia

status: Public on Apr 28 2021

city: Ansan

first: Young Gyu

last: Chai

state: Gyeonggi-do

address: 55 Hanyangdaehak-ro

department: Molecualr & Life Science

institute: Hanyang Univ.

summary: We investigated the mechanisms underlying the anti-inflammatory and anti-migratory function and genes targeted by JQ1 in lipopolysaccharide (LPS)-activated human microglia HMC3 cells using RNA sequencing.  The BET inhibitor JQ1 attenuates the LPS-induced inflammatory and migratory response. In addition, LPS-induced IRF1 was inhibited by JQ1, and IRF1 suppressed microglial migration by regulating inflammation and migration genes.

overall_design: The gene expression profile was performed with control HMC3 (Con), JQ1-treated HMC3 (JQ1), LPS-treated HMC3 (LPS), LPS+JQ1-treated HMC3 (LPS+JQ1). Samples were generated by deep sequencing, in triplicate, using Illumina 2500.

first: Young


title: Infection of rat epithelial cells with a Salmonella typhimurium strain expressing Rck, PagN and the T3SS1 system (14028Sur) and two Salmonella typhimurium strains invalidated for entry factors (i.e. D(rck, pagN) and DinvASur)

status: Public on May 02 2021

city: Jouy-en-Josas

first: Marco

last: Moroldo

address: Domaine de Vilvert

department: Animal Genetics

country: France

institute: INRA

summary: The aim of this work was to study the cellular gene expression profiles associated with the entry mechanism of Salmonella typhimurium. Whatever the bacterial strain used for infection, the expression of numerous genes associated with the extracellular matrix was modified.

overall_design: Six biological replicates for non-infected cells, six for the cells infected with the DinvASur and the 14028Sur strains and five biological replicates for the cells infected with the D(rck, pagN) strain.

first: Anne

last: Chaussé

first: Sylvie

last: Roche

first: Philippe

last: Velge


title: Genomic environments scale the activities of diverse core promoters

status: Public on May 01 2021

city: St. Louis

first: Barak

last: Cohen

state: MO

address: 4515 McKinley Ave

department: Department of Genetics

institute: Washington University in St. Louis

summary: One model for how cells integrate cis-regulatory information is that housekeeping and developmental core promoters respond specifically to certain types of enhancers or chromatin features at different chromosomal locations. We tested this model using a genome-integrated massively parallel reporter assay (MPRA) to measure the activity of hundreds of diverse core promoters at four genomic locations While genomic locations had large effects on expression, the relative strengths of core promoters were preserved across locations regardless of promoter class, suggesting that their intrinsic activities are scaled at different genomic locations. We further show that core promoter scaling is a genome-wide phenomenon by testing six core promoters at thousands of locations across the genome. While the rank order of core promoters is preserved, the scaling of expression across the genome is non-linear and depends on the genomic location and the strength of the core promoter, but not on its class, suggesting that housekeeping and developmental promoters do not make different interactions with the surrounding genomic environment. Instead, our results support a modular genome in which genomic environments containing different enhancers and chromatin features scale the activities of core promoters in an independent, but non-linear manner.

sample_organism:
Homo sapiens
Escherichia coli DH5[alpha]

overall_design:
patchMPRA: A library of 676 core promoters was integrated into 4 different genomic locations in K562 cells. DNA and RNA was harvested from the cell lines and the barcodes of the library were amplified and sequenced.
Episomal MPRA: Library of core promoters was transiently transfected into K562 cells and RNA was harvested after 24 hours. The barcodes of the RNA and plasmid library were amplified and sequenced.
TRIP: Six promoters were randomly barcoded and integrated into the K562 genome with piggyBac transposase. DNA and RNA was harvested from the cell lines and the barcodes were amplified and sequenced.

first: Clarice

middle: K


title: Spatial transcriptome profiling by MERFISH reveals fetal liver hematopoietic stem cell niche architecture.

status: Public on Apr 16 2021

city: Zhengzhou

first: Yanfang

last: Lu

state: Henan

address: Weiwu road 7th

institute: Zhengzhou University


title: Spatial transcriptome profiling by MERFISH reveals fetal liver hematopoietic stem cell niche architecture [scRNA-seq]

summary: The hematopoietic stem cell (HSC) niche has been extensively studied in bone marrow, yet a more systematic investigation into the microenvironment regulation of hematopoiesis in fetal liver is necessary. Here we investigate the spatial organization and transcriptional profile of individual cells in both wild type and Tet2-/- fetal livers, by multiplexed error robust fluorescence in situ hybridization (MERFISH). We find that specific pairs of fetal liver cell types are preferentially positioned next to each other. Ligand-receptor singling molecule pairs such as Kitl and Kit are enriched in neighboring cell types. The majority of HSCs are directly in contact with endothelial cells (ECs) in both wild type and Tet2-/- fetal livers. Loss of Tet2 increases the number of HSCs, and upregulates Wnt and Notch signaling genes in the HSC niche. Two subtypes of ECs – arterial ECs and sinusoidal ECs – and other cell types contribute distinct signaling molecules to the HSC niche. Collectively, this study provides a comprehensive picture and bioinformatic foundation for HSC spatial regulation in fetal liver.

overall_design: Here we performed single-cell RNA sequencing of E14.5 whole fetal liver cells and E14.5 fetal liver HSCs by 10x Genomics platform. For whole fetal liver single cell RNA sequencing, fetal liver tissues were isolated from E14.5 C57BL/6 pregnant mice and digested by dissociation enzyme (Accutase) for 10 min at room temperature. Red blood cells were removed using 1×RBC lysis buffer at 4 °C. Then, cells were passed through a 40 μm strainer and re-suspended in cold DPBS with 0.04% (wt/vol) BSA. For sorted HSC single cell RNA sequencing, fetal liver tissues were isolated from E14.5 C57BL/6 pregnant mice and in cold 1×PBS dissociated into single cell suspension by pipetting up and down through 15 mL pipette. Red blood cells were removed using 1×RBC lysis buffer at room temperature for 5 min. Cells were incubated for 5 minutes at room temperature and mixed constantly by inverting the tube. After that, cells were centrifuged for 5 minutes then the supernatant was carefully removed without disturbing the pellet cells. Cells were resuspended in cold 1×PBS with 0.5% BSA, passed through a 40 μm strainer. To sorting HSCs, we added Biotin Lineage depletion cocktail (anti-Mac1, anti-CD3ε, anti-B220, anti-Gr-1, anti-CD11b and anti-Ter119) and streptavidin Particles Plus-DM befor sorting. Lineage positive cells were depleted by transferring cells to a magnetic stand. Enriched lineage negative cells were further stained with antibodies (LSK CD150+CD34-CD48-Flt3-). Then HSCs were sorted with FACS AriaII (BD Biosciences). Finally, we took 8,000 cells for 10x library preparation using Chromium Single Cell 3′ Reagent Kits (v2) for each sample according to the manufacturer’s description.

first: Miao

last: Liu

first: Jennifer

last: Yang

first: Sherman

last: Weissman

first: Xinghua

last: Pan

first: Samuel

last: Katz

first: Siyuan

last: Wang


title: Spatial transcriptome profiling by MERFISH reveals fetal liver hematopoietic stem cell niche architecture [bulk RNA-seq]

overall_design: E14.5 pregnant female C57BL/6 WT mice were used for fetal liver preparation. Total RNA was extracted from E14.5 fetal liver using RNeasy Mini Kit. mRNA was isolated using the Dynabeads mRNA Purification Kit. The cDNA libraries were produced with a NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® and NEBNext® Multiplex Oligos for Illumina® according to the manufacturer’s description. Paired-end reads were aligned to the mouse genome (Gencode vM14) with Tophat and transcripts were assembled with Cufflinks.


title: Multiple causal variants underlie genetic associations in humans

status: Public on May 24 2021

city: Stanford

first: Stephen

middle: B

last: Montgomery

state: Califonia

address: 300 Pasteur Drive, Edwards Building R248A

institute: Stanford University

summary: We applied a massively parallel reporter assay (MPRA) in lymphoblastoid cells to functionally evaluate 49,256 allelic pairs, representing 30,893 genetic variants in high, local linkage disequilibrium for 744 independent cis-expression quantitative trait loci (eQTLs) assessed for colocalization across 114 traits.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: We performed three independent transfections of our MPRA library into GM12878 cells by electroporation and recovered RNA after 24 hours. We quantified barcode counts in the cDNA samples as well as the plasmid pool by single-end Illumina sequencing. Barcodes mapping to the same oligo in the oligo pool were summed to generate raw oligo counts and aggregated across replicates.

first: Nathan

last: Abell

first: Marianne

last: DeGorter

first: Michael

last: Gloudemans

first: Emily

last: Greenwald

first: Kevin

last: Smith

first: Zihuai

last: He


title: Gene expression analysis of Nrg1 stimulated zebrafish hearts  [mRNA]

status: Public on Apr 14 2021

city: Madison

first: jianhong

last: ou

state: WI

address: 330 N Orchard Street

institute: Morgridge institute for research

summary: We report high-throughput profiling of gene expression from whole zebrafish ventricles. We profile mRNA in uninjured ventricles and those undergoing 7 days of cardiomyocyte hyperplasia after genetic stimulation of Nrg1. This study provides a framework for understanding transcriptional changes during adult models of regeneration.

overall_design: Examination of gene expression in cardiomyocytes under different states of proliferation.

first: M

last: Pronobis

first: S

last: Zheng

middle: P

last: Singh

first: J

last: Goldman

first: K

middle: D

last: Poss


title: Cytolines as models to study the impact of different cytoplasms on gene expression under heat stress conditions

status: Public on Apr 09 2021

city: Cluj-Napoca

first: Simona

last: Visan

state: Cluj

address: 34-36 Republicii

department: Functional Genomics, Proteomics and Experimental Pathology

country: Romania

institute: The Oncology Institute “Prof Dr. Ion Chiricuta”,

summary: Using maize cytolines (same nucleus but different cytoplasms), our research adds a new facet to the paradigm explaining gene expression changes in response to heat stress in an effort to maintain the homeostasis, linking the response to the genetic divergence of the nuclear and organellar genomes.

overall_design: One-color microarray study was performed to measure differences in gene expression of three samples under normal conditions and when exposed to heat stress. Four biological replicates for each condition were used.

first: Ioana

middle: V

last: Ardelean

first: Loredana

last: Balacescu

first: Oana

last: Sicora

first: Ovidiu

first: Lia

last: Mladin

first: Voichita

last: Has

first: Mihai

last: Miclaus


title: Next generation sequencing analysis of transcripts expressed in mouse epidermis

status: Public on Apr 13 2021

city: Yokohama-shi

first: Jafar

last: Sharif

state: Kanagawa-ken

address: 1-7-22 Suehiuro-cho, Tsurumi-ku

department: IMS

institute: RIKEN

summary: RNAseq analysis was performed to analyze the genes expressed in whole epidermis and upper layer epidermis (SG1 and SG2 cells) isolated from adult mouse ear.

overall_design: Whole epidermis of mouse ear was isolated by dispase treatment. Upper layer epidermis (containing SG1 and SG2 cells) was isolated by exofoliative toxin A treatment.

first: Takeshi

last: Matsui


title: Single-Cell Omics Reveals Dyssynchrony of the Innate and Adaptive Immune System in Progressive COVID-19

status: Public on Apr 05 2021

city: New Haven

first: Steven

last: Kleinstein

state: Ct

address: 300 George St.

department: Pathology

institute: Yale University


title: Single-Cell Omics Reveals Dyssynchrony of the Innate and Adaptive Immune System in Progressive COVID-19 [CITE-seq]

summary: A dysregulated immune response against the SARS-CoV-2 virus plays a critical role in severe COVID-19. However, the molecular and cellular mechanisms by which the virus causes lethal immunopathology are poorly understood. Here, we utilize multi-omics single-cell analysis to probe dynamic immune responses in patients with stable or progressive manifestations of COVID-19, and assess the effects of tocilizumab, an anti-IL-6 receptor monoclonal antibody. Coordinated profiling of gene expression and cell lineage protein markers reveals a prominent type-1 interferon response across all immune cells, especially in progressive patients. An anti-inflammatory signature in monocytes and a pre-exhaustion phenotype in activated T cells are hallmarks of progressive disease. Single-cell T and B cell receptor repertoire analysis reveal a skewed clonal distribution of CD8 T cells and a primary B cell response with possible contribution from memory B cells. Our in-depth immune profiling reveals dyssynchrony of the innate and adaptive immune interaction in progressive COVID-19, which may contribute to delayed virus clearance and has implications for therapeutic intervention.

overall_design: 18 PBMC samples from 10 patients at various time points were studied. Age and sex matched healthy subjects (n=13) whose samples were collected before the COVID-19 pandemic were used as controls. Single-cell RNA sequencing (scRNA-seq) was performed, as well as surface protein libraries (CITE-seq), T cell receptor (TCR) libraries and B cell receptor (BCR) libraries. Detailed sample metadata are included in the tar archive with the processed data. The processed data for the control samples exist solely within the Seurat Rds file. There are no additional metadata or processed data files for the control samples, as there are for the COVID-19 samples.

first: Avraham

last: Unterman

first: Tomokazu

last: Sumida

first: David

last: Hafler

first: Naftali

last: Kaminski

first: Charles

last: Dela Cruz


title: The Autism-Associated Protein CHD8 Is Required for Cerebellar Development and Motor Function

city: Kanazawa

first: Atsuki

last: Kawamura

state: Ishikawa

address: 13-1 Takaramachi

department: Department of Histology and Cell Biology

institute: Graduate School of Medical Sciences, Kanazawa University

summary: Mutations in the gene encoding the chromatin remodeler CHD8 are a highly penetrant risk factor for autism spectrum disorder (ASD). Although cerebellar abnormalities have been involved in ASD pathogenesis, the underlying mechanisms of CHD8 in the regulation of cerebellar function has remained unknown, however. Here we show that the cerebellar granule neurons–specific deletion of Chd8 manifests reduced proliferation and differentiation of granule neuron progenitors, leading to cerebellar hypoplasia and motor coordination defects in mice. CHD8 was found to regulate the expression of neuronal genes and to be required for maturation of cerebellar granule neurons. Furthermore, we found that CHD8 is preferentially bound to promoter regions and is necessary for modulation of local chromatin accessibilities at promoter regions of active gene. Our results thus uncover a critical role for CHD8 in cerebellar development and have important implications for understanding the cerebellar contributions to ASD pathogenesis.

overall_design: RNA-seq (quadruplicate) and ChIP-seq (duplicate) analysis in granule neuron progenitors (GNPs) isolated from the cerebellum of mice at P7

last: Kawmaura

first: Keiichi

last: Nakayama


title: Single-Cell Omics Reveals Dyssynchrony of the Innate and Adaptive Immune System in Progressive COVID-19 [single-cell RNA-seq]

overall_design: 18 PBMC samples from 10 patients at various time points were studied. Age and sex matched healthy subjects (n=13) whose samples were collected before the COVID-19 pandemic were used as controls. Single-cell RNA sequencing (scRNA-seq) was performed, as well as surface protein libraries (CITE-seq), T cell receptor (TCR) libraries and B cell receptor (BCR) libraries. The processed data for the control samples exist solely within the Seurat Rds file. There are no additional metadata or processed data files for the control samples, as there are for the COVID-19 samples.


title: Defining the regulons of Pseudomonas aeruginosa transcriptional regulators

status: Public on Apr 12 2021

city: Warszawa

first: Adam

last: Kawałek

address: Pawinskiego 5A

department: Department of Microbial Biochemistry

country: Poland

institute: Institute of Biochemistry and Biophysics, PAS

overall_design: Refer to individual Series


title: Bacteria Induce Skin Regeneration via IL-1  Signaling

status: Public on Apr 01 2021

city: Baltimore

first: Luis

last: Garza

state: Maryland

address: 1551 Orleans Street

department: Dermatology

institute: Johns Hopkins University


title: JAK inhibitors dampen activation of interferon-stimulated transcription of ACE2 isoforms in human airway epithelial cells

status: Public on Apr 23 2021

city: Bethesda

first: Hye Kyung

last: Lee

state: MD

address: 8 CENTER DR RM 107

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

institute: National Institutes of Health (NIH)

summary: SARS-CoV-2 infection of human airway epithelium activates genetic programs leading to progressive hyperinflammation in COVID-19 patients. Here, we report on transcriptomes activated in primary airway cells by interferons and their suppression by Janus kinase (JAK) inhibitors. Deciphering the regulation of the angiotensin-converting enzyme 2 (ACE2), the receptor for SARS-CoV-2, is paramount for understanding the cell tropism of SARS-CoV-2 infection. ChIP-seq for activating histone marks and Pol II loading identified candidate enhancer elements controlling the ACE2 locus, including the intronic dACE2 promoter. Employing RNA-seq, we demonstrate that interferons activate expression of dACE2 and, to a lesser extent, the genuine ACE2 gene. Interferon-induced gene expression was mitigated by the JAK inhibitors baricitinib and ruxolitinib, used therapeutically in COVID-19 patients. Through integrating RNA-seq and ChIP-seq data we provide an in-depth understanding of genetic programs activated by interferons, and our study highlights JAK inhibitors as suitable tools to suppress these in bronchial cells.

overall_design: ChIP-seq and RNA-seq was used to chracterizae chromatin strucutres and gene expression profiles in cytokine stimulation.


title: Expression data from Staphylococcus aureus and Phosphate buffered saline (PBS) treated mouse wound bed

summary: Environmental factors that enhance regeneration are largely unknown. We hypothesized that skin bacteria modulate regeneration. Here, we assessed low, medium, and high levels of bacterial burden in Wound Induced Hair follicle Neogenesis (WIHN), a rare adult organogenesis model. WIHN levels and stem cell markers indeed correlated with bacterial counts, being lowest in germ free (GF), intermediate in conventional specific pathogen free (SPF), and highest even in mice infected with pathogenic Staphylococcus aureus. We identified IL-1β and keratinocyte-dependent IL-1R-MyD88 signaling as necessary and sufficient for bacteria to promote regeneration. Finally, in a small clinical trial, we found that a topical broad-spectrum antibiotic slowed skin wound healing. These results counter conventional notions that infection inhibits regeneration and the need for full sterility of small wounds.

overall_design: 21-day-old, 8 to 12 -gram male and female mice in their first telogen phase were selected. Mice were anesthetized with vaporizing anesthesia (Baxter, Isoflurane), shaved, and denuded of 1.44 cm² full thickness skin using sterile procedures. PBS and 1e7 /100ul  S. aureus were injected under the scab on wound day3.

first: Gaofeng

last: Wang


title: Expression data from germ free (GF) and specific pathogen free (SPF) mouse wound bed

overall_design: 21-day-old, 8 to 12 -gram male and female Germ free (GF) and specific pathogen free (SPF)  mice in their first telogen phase were selected. Mice were anesthetized with vaporizing anesthesia (Baxter, Isoflurane), shaved, and denuded of 1.44 cm² full thickness skin using sterile procedures. Samples were collected from the mice scar on wound day 12.


title: Ribosome profiling analysis of Neuro2a cells with Ebp1 knockdown

status: Public on Mar 23 2021

city: Berlin

first: Matthew

middle: Lee

last: Kraushar

state: Berlin

address: Ihnestrasse 63-73

department: Department of Computational Molecular Biology

institute: Max Planck Institute for Molecular Genetics

summary: We perform Ribosome Profiling (Riboseq) analysis of mouse Neuro2a neuronal cultures in Ebp1-siRNA knockdown vs. scrambled-siRNA control conditions in biological triplicate to assess the translation-specific function of Ebp1

overall_design: Each biological triplicate analyzed for both ribosome-protected mRNA fragments after RNAse digestion (Riboseq), and total steady-state mRNA (RNASeq), followed by high-throughput sequencing.

middle: L


title: Vaseline and Neosporin treated human popliteal fossae (PF) skin wound bed

overall_design: 4-mm punch biopsies, microbiome swabs, and clinical photographs of bilateral popliteal fossae (PF). were obtained from participants under the above IRB protocol. Participants were asked to avoid washing 24 hours prior to sample collection and to use scent-free, non-antibacterial soap for the duration of the study. Samples were collected at two visits spanning an average of 15 days, including at a baseline visit prior to intervention (Day 0) and at a follow-up visit following secondary intention to obtain post-treatment samples (Day 15). A total of 12 skin biopsies were obtained from 3 individuals at identical anatomical sites across 2 time points. For tissue collection, 1% lidocaine with epinephrine was administered, and 4mm full-thickness punch biopsies were obtained from the center PF. For the left PF, the wound was washed with Hibiclens (Molnlycke, 57516), and Neosporin was applied (Johnson & Johnson); for the right PF, Vaseline (Unilever) was applied. Both sites were occluded with bandages, and participants were asked to rebandage left and right PF daily with Neosporin and Vaseline, respectively, until wound closure to evaluate the changes in gene expressions.


title: Transcriptome profile of the anterior pituitary gland in pigs during maternal recognition of pregnancy

status: Public on Mar 11 2021

city: Olsztyn

first: Agata

last: Zmijewska

address: Oczapowski 1a

department: Demartment of Animal Anatomy and Physiology

institute: Univeristy of Warmia and Mazury

summary: The knowledge regarding the reproductive-status-related changes occurring within the transcriptome of the porcine pituitary is limited. This study aimed to compare pituitary gland gene expression profiles of pigs during the maternal recognition of pregnancy period (days 12-13 of pregnancy) with pigs during the respective days of the estrous cycle using a microarray approach. Analysis indicated 482 differentially expressed genes (DEGs) with a FC ≥ 1.5 (p < 0.05) in the pituitary of pregnant vs. estrous-cyclic pigs. Among them, 68 were up-regulated and 414 were down-regulated. The evaluated DEGs were annotated to 39 gene ontology (GO) biological processes terms, 13 GO cellular components terms, and 10 GO molecular function terms. Among the evaluated DEGs were selected genes coding for proteins potentially involved in the regulation of early pregnancy in pigs and used for gene interaction analysis and validation of microarray results. Analysis of the relationships among DEGs during maternal recognition of pregnancy showed that some of them are connected with, i.e., TGFβ signaling pathway, follicle-stimulating hormone, prolactin, and growth hormone synthesis or activity, adipocytokines responsivity, angiogenesis, immune response, prostaglandin synthesis and inter-pituitary cell to cell interactions. The findings expand the knowledge regarding the molecular mechanisms appearing in the pituitary in pigs during the maternal recognition period of pregnancy.

overall_design: We analized anterior pituitary glands obtained from 8 indyviduals (n=8). Pituitaries were collected from mature gilts on days 12-13 of early pregnancy (n = 4) and the estrous cycle (n = 4).

first: Wioleta

last: Czelejewska

first: Ewa

middle: M

last: Drzewiecka

first: Anita

last: Franczak


title: Protein synthesis in the developing neocortex at near-atomic resolution reveals Ebp1-mediated neuronal proteostasis at the 60S tunnel exit

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


title: Ebp1-selective ribosome profiling analysis of Neuro2a cells with Ebp1-immuno-precipitation

summary: We perform Selective Ribosome Profiling (SeRP) analysis of mouse Neuro2a neuronal cultures with Ebp1-immuno-precipitation in biological duplicate to assess the translation-specific function of Ebp1

overall_design: Each biological replicate analyzed for ribosome-protected mRNA fragments after RNAse digestion in both Ebp-ribosome immuno-precipitation conditions, and the total input ribosome pool, followed by by high-throughput sequencing.


title: Transcriptome analyses of variegated leaf development in ornamental kale

status: Public on Mar 27 2021

city: Shenyang City

first: jie

last: ren

address: Dongling Road NO.120

institute: Shenyang Agricultural University

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of leaf color at different development stages. The goals of this study are to compare chlorophyll metabolism and chloroplast organization transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis

Methods: leaf mRNA profiles of 12 RNA sequencing libraries (S1, S2, S3_S, and S3_C) were generated by deep sequencing, in triplicate, using an Illumina HiSeq 4000 system. After removing reads of low quality, those that remained were mapped to the reference genome (ftp://ftp.ensemblgenomes.org/pub/release-38/plants/genbank/brassica_oleracea/) using the HISAT package, allowing for a maximum of two mismatches and multiple alignments per read (up to 20 by default). qRT–PCR validation was performed using SYBR Green assays

Results: Using an optimized data analysis workflow, we mapped about 571.74 million sequence reads per sample to the the reference genome (ftp://ftp.ensemblgenomes.org/pub/release-38/plants/genbank/brassica_oleracea/) and identified 1028, 4323, 428, and 1033 DEGs were detected in pairwise comparison (S2 vs. S1, S3_S vs. S2, S3_S vs. S2, and S3_S vs. S3_C, respectively). The DEGs were associated with ‘photosynthesis’, ‘carbon fixation in photosynthetic organisms’, ‘porphyrin and chlorophyll metabolism’ and other pathways in the Kyoto Encyclopedia of Genes and Genomes database; DEGs related to chloroplast organization were identified in the Gene Ontology analysis. The DEGs identified by RNA sequencing were confirmed by qRT-PCR analysis, indicating that the data were reliable. These findings provide information that can be useful for investigating the molecular basis for leaf variegation in ornamental kale and other plants.

Conclusions: The results presented here reveal changes in the transcriptome profile of a variegated leaf kale. DEGs related to chlorophyll metabolism and chloroplast organization were detected. These results demonstrate that leaf color at different stages of development is influenced by chloroplast and pigment metabolism, providing a foundation for investigating the molecular basis for leaf variegation in ornamental kale and other plants.

first: Hui

last: Feng

first: Jie

last: Ren


title: Global circadian transcript profile of mouse anterior hypothalamus entrained by inverted feeding

city: Chongqing

first: Min-Dian

last: Li

address: 30 Gaotanyan Main Street

department: Cardiology

institute: Southwest Hospital, Third Military Medical University (Army Medical University)

summary: Circadian clocks in peripheral organs are entrained by feeding. Eating in the right time is crucial to maintain metabolic health, whereas eating in the wrong time increases the susceptibility to metabolic diseases. It is unknown how change of mealtime impacts circadian transcriptomes in peripheral organs and brain, such as liver, heart, kidney and visceral adipose tissue. Here, we presented global circadian transcript profile of mouse tissues (i.e. kidney, anterior hypothalamus) entrained by inverted feeding to compile an atlas for mechanistic insights into how feed-fast cycle regulates circadian biology.

overall_design: RNA-seq of transcriptome in mouse anterior hypothalamus collected from daytime-restricted feeding (DRF) or nighttime-restricted feeding (NRF, reference), totaling 56 samples


title: Single cell RNA sequencing of large and small airway surface epithelium in newborn cystic fibrosis (CF) and non-CF pigs

status: Public on Mar 16 2021

city: Iowa City

first: Alejandro

middle: A.

last: Pezzulo

state: Iowa

address: 6316 Pappajohn Biomedical Discovery Building

department: Department of Internal Medicine

institute: Universty of Iowa

summary: The goal of this study was to compare cell composition and gene expression patterns for different cell types in large and small airways of CFTR+/+ (non-CF) and CFTR-/- (CF) pigs.

overall_design: Tissue samples from trachea and small airways (< 2 mm) were collected from newborn pigs, prepared for single cell sequencing via 10X Genomics Chromium controller, and sequenced on Illumina HiSeq4000

first: Andrew

last: Thurman

first: Wenjie

last: Yu

first: Joseph

last: Zabner

first: Michael

middle: J

last: Welsh


title: Distinct cardiac transcriptomic clustering in titin and lamin a/c-associated dilated cardiomyopathy patients

status: Public on Mar 09 2021

city: Maastricht

first: Kasper

last: Derks

state: Limburg

address: P. Debyelaan 25

department: Clinical Genetics

country: Netherlands

institute: Maastricht University Medical Center

summary: RNA profiles strongly differ in TTNtv and LMNA-mutated DCM patients, despite clinical similarities as other pathogenic variant carriers such as RBM20 and MYH7, suggesting a specific genetic effect on the cardiac transcriptome in addition to the effect of the clinical component.

overall_design: Comparing RNA-seq profiles of genetic DCM patients

first: Job

last: Verdonschot

middle: W


title: Characterization of the pathogenic effects of Entamoeba gingivalis infection of gingival cells by transcriptome analysis and electron microscopy

status: Public on Feb 21 2021

first: January

last: Weiner

address: Charitéplatz 1

department: CUBI

institute: Berlin Institute of Health, Charité Medical University of Berlin

summary: The protozoan Entamoeba gingivalis colonizes the healthy oral mucosa with a prevalence of 15%. Colonization can be asymptomatic and it is considered that it is not pathogenic. However, it is able to invade lacerated oral mucosa where it ingests fragments of live cells, suggesting pathogenous potential. Here, we characterized the transcriptomes of gingival cells after infection with Entamoeba gingivalis using RNA Sequencing and observed pathogen interaction with the epithelial monolayer barrier by scanning electron microscopy. In epithelial and fibroblast cells, strongest differential expression showed gene set ‘chemokines and inflammatory molecules in myeloid cells’ (AUC=0.9, effect size 5.15, adj. P=3.1x10e-19) and “Cell cycle and growth arrest” (AUC=0.91 (effect size=4.56, adj. P=4.8x10e-9), respectively. The most upregulated genes in epithelial cells were TNF (fold change 430) and IL8 (fold change 359) and in fibroblasts ZN331 (fold change 18). We showed that Entamoeba gingivalis killed live epithelial cells by trogocytosis demonstrating strong pathogenic potential.

overall_design: Single-end RNA-Seq of primary human fibroblasts or primary human endothelial cells stimulated with Entamoeba gingivalis

first: Xin

last: Bao

first: Oliver

last: Meckes

first: Henrik

last: Dommisch

first: Arne

last: Soenke Schaefer


title: RNA-Seq analysis of total mouse neocortex during development

first: Matthew

last: Kraushar

summary: We report the quantification of steady-state mRNA coding for ribosomal proteins, translation-associated proteins, and Ebp1 (Pa2g4) in mouse total neocortex brain lysates at embryonic days 12.5, 14, 15.5, 17 and postnatal day 0

overall_design: Examination of gene expression in biological duplicate samples of mouse neocortex lysates


title: TPX2 Amplification-Driven Aberrant Mitosis in Long-Term Cultured Human Embryonic Stem Cells

status: Public on Feb 26 2021

city: Busan

first: Haeseung

last: Lee

address: 63 Beon-gil 2, Busandaehag-ro, Geumjeong-gu

department: College of Pharmacy

institute: Pusan National University

summary:
Although human embryonic stem cells (hESCs) are equipped with highly effective machinery for the maintenance of genome integrity, the frequency of genetic aberrations during long-term in vitro hESC culture has been a serious issue that raises concerns over their safety in future clinical applications.
By passaging hESCs over a broad range of timepoints, we found that mitotic aberrations, such as the delay of mitosis, multipolar centrosomes, and chromosome mis-segregation, were increased in the late-passaged hESCs (LP-hESCs) in parallel with polyploidy compared to early-passaged hESCs (EP-hESCs).
Through high-resolution genome-wide approaches and by following transcriptome analysis, we found that LP-hESCs with a minimal amplicon in chromosome 20q11.21 highly expressed TPX2 (targeting protein for Xklp2), a key protein for governing spindle assembly and cancer malignancy.
Consistent with these findings, the inducible expression of TPX2 in EP-hESCs reproduced aberrant mitotic events, such as the delay of mitotic progression, spindle stability, misaligned chromosomes, and polyploidy. This data suggests that the amplification and increased transcription of the TPX2 gene at 20q11.21 could contribute to an increase in aberrant mitosis due to altered spindle dynamics.

overall_design: Gene expression profiles of four hESC lines (P1-P4) in duplicate.

first: Hyuk-Jin

last: Cha


title: Global circadian transcript profile of mouse peripheral tissues and brain entrained by inverted feeding


title: FRCs promote Treg function in acute graft-versus-host disease (aGvHD)

status: Public on Mar 03 2021

city: Würzburg

first: Haroon

last: Shaikh

state: Bayern

address: Zinklesweg 10

department: Department of Internal Medicine II

institute: University Hospital Würzburg

summary: Knockout of MHC class II on Ccl19 expressing fibroblastic reticular cells results in the hyper-activation of allogenic CD4+ T cells in the effoctor phase of aGvHD, due to the dyregulation of regulatory T cells (Tregs).

overall_design: CD4+ CD90.1+ T cells mRNA profiles of allo-HCT (FVB to B6 model) at day +30 in B6.H2-Ab1fl and MHCIIΔCcl19 mice

first: Zeinab

last: Mokhtariasl

first: Jörn

last: Pezoldt


title: Interleukin-17 governs hypoxic adaptation of injured epithelium [CITE-seq & single-cell RNA-seq]

status: Public on Feb 18 2021

city: New York

first: Shruti

last: Naik

state: NY

address: 435 East 30th Street

country: USA

institute: NYU Langone Health

summary: To define the composition of “first responder” lymphocytes that may engage in crosstalk with injured epithelium we profiled the lymphoytes from unwounded health skin and skin from different time points after wounding with CITE-seq and single-cell RNA-sequencing.

overall_design: Lymphocytes (CD45.2+ CD90.2+ TCR Vγ3 - )from unwounded skin, 3, and 5 days post wounding were sorted based on surface marker staining. Cells were prelabeled with surface epitope marking oligo-tagged antibodies and sample specific oligo-tagged Totalseq-A antibodies (Biolegend, see table 1). Hashed samples were pooled for scRNA-seq with 10X Chromium 3' v3 platform. RUN1 and RUN2 represent technical replicates.

first: Piotr

last: Konieczny

first: Xing

last: Yue

first: Ikjot

last: Sidhu


title: Interleukin-17 governs hypoxic adaptation of injured epithelium [bulk RNA-seq]

summary: RORgt deficency impaired wound re-epithelialization. We adopted low-input RNA-seq of purified wound epithelium to explore the underlying epithelial cell functional difference between wild type and RORgt deficient mice during wound healing.

overall_design: Migrating  and nonmigrating wound edge epithelial cells were sorted based on their different surface markers,  gene expression were compared  between wild type and Rorgt deficient mice with low-input RNA seq.