title: An adult-stage transcriptional program for survival of serotonergic connectivity

status: Public on Mar 24 2022

city: Cleveland

first: Evan

last: Deneris

state: Ohio

address: 2210 Circle Dr., Robbins E640

department: Neurosciences

institute: Case Western Reserve University

summary:
Neurons must function for decades of life but how these non-dividing cells are
preserved is poorly understood. Using mouse serotonin (5-HT) neurons as a model, we discovered a novel adult-stage transcriptional program specialized to ensure the preservation of serotonergic connectivity. We uncover a switch in Lmx1b and Pet1 transcription factor function from controlling embryonic axonal growth to sustaining a transcriptomic signature of serotonergic connectivity comprising functionally diverse synaptic and axonal genes. Adult-stage deficiency of Lmx1b and Pet1 caused slowly progressive degeneration of 5-HT synapses and axons, increased susceptibility of 5-HT axons to neurotoxic injury, and abnormal stress responses. Axon degeneration occurred in a die back pattern and was accompanied by accumulation of alpha-synuclein and APP in spheroids and mitochondrial fragmentation without cell body loss. Our findings suggest neuronal connectivity is transcriptionally protected by maintenance of connectivity transcriptomes; progressive decay of such transcriptomes may contribute to age-related diseases of brain circuitry.

overall_design: 5-HT neuron RNA-seq profiles of control (iCON), Pet1CKO, Lmx1bCKO, and Pet1/Lmx1b DKO at 10 days and 1 month post-tamoxifen were generated by deep sequencing, in triplicate, using Illumina HiSeq 550. The sequence reads that passed quality filters were mapped to the UCSC mm10 mouse genome using Hisat2.

first: Meagan

last: Kitt

first: Nobuko

last: Tabuchi

first: William

last: Spencer

first: Xinrui

last: Zhang

first: Heath

last: Robinson

first: Lin

last: Mei


title: Single cell analysis reveals mechanisms of heterogeneity and plasticity of leukemia initiating cells [CITEseq]

city: Boston

first: Edroaldo

last: Lummertz da Rocha

state: MA

address: 1 Blackfan Circle

department: Hematology/Oncology

country: USA

institute: Boston Children's Hospital

type: Expression profiling by high throughput sequencing

summary: Leukemia initiating cells (LICs) self-renew indefinitely to fuel leukemic growth and spark disease relapse.  Previously thought to be primitive and rare, the LIC state may actually be heterogeneous and dynamic, allowing LICs to evade therapy.  Here, we use single cell transcriptomics to dissect the ontogeny of MLL-rearranged B-lymphoblastic leukemia (MLL-r B-ALL).  Although we identify primitive, rare LICs, we also find more phenotypically differentiated LICs that possess the capability to replenish the full cellular diversity of MLL-r B-ALL.  We find that activation of MYC-driven oxidative phosphorylation drives this process of cell state conversion, defining a new mechanism of LIC plasticity.

overall_design:
This study was initially designed to define LICs in MLL-r B-ALL, relying on xenotransplantation with LDA and terminal leukemia incidence by day 150 post-transplant as endpoints.  This endpoint was chosen based on the approximately 100-day latency of bulk transplanted leukemia cells at a dose of 10,000 cells per transplant.  We hypothesized that transplantation of LIC-enriched populations would shift latency earlier and transplantation of LIC-depleted would shift the latency further.  Leukemia populations were isolated and xenotransplanted with investigators monitoring recipient mouse health blinded to the cell source.  At the onset of morbidity, mice were euthanized to harvest tissues and bone marrow.  At the completion of the experiment, the experimental conditions were unblinded, and LIC frequency calculated by LDA analysis, or survival analyzed by log-rank test, where indicated.  For quantification of flow cytometry or expression data, the statistical tests used are indicated.  Student’s t-tests were used and analysis was unpaired, except where otherwise indicated.
The raw data will be available at dbGaP.
dbGap number: 42161
The study is called 'Study of leukemia stem cells in B-ALL' registered to Robert Rowe.

first: R

middle: G

last: Rowe


title: CRISPR screens for host factors critical for infection by SARS-CoV-2 variants of concern

status: Public on Mar 27 2022

city: Rehovot

first: Noam

last: Stern-Ginossar

address: 234 herzel

department: Molecular Genetics

country: Israel

institute: Weizmann Institute

summary: The global spread of SARS-CoV-2 lead to the most challenging pandemic in this century, posing major economic and health challenges worldwide. Revealing host genes essential for infection by multiple variants of SARS-CoV-2 can provide insights into the virus pathogenesis, and facilitates the development of novel broad-spectrum host-directed therapeutics. Here, employing genome-scale CRISPR screens, we provide a comprehensive data-set of cellular factors that are exploited by WT-SARS-CoV-2 as well as two additional recently emerged variants of concerns (VOCs), Alpha and Beta. These screens identified known and novel host factors critical for SARS-CoV-2 infection, including various components belonging to the Clathrin-dependent transport pathway, ubiquitination and Heparan sulfate biogenesis. In addition, the host phosphatidylglycerol biosynthesis processes appeared to have major anti-viral functions. Comparative analysis of the different VOCs revealed the host factors KREMEN2 and SETDB1 as potential unique candidates required only to the Alpha variant, providing a possible explanation for the increased infectivity of this variant. Furthermore, the analysis identified GATA6, a zinc finger transcription factor, as an essential pro-viral gene for all variants inspected. We revealed that GATA6 directly regulates ACE2 transcription and accordingly, is critical for SARS-CoV-2 cell entry. Analysis of clinical samples collected from SARS-CoV-2 infected individuals showed an elevated level of GATA6, indicating the important role GATA6 may be playing in COVID-19 pathogenesis. Finally, pharmacological inhibition of GATA6 resulted in down-modulation of ACE2 and consequently to inhibition of the viral infectivity. Overall, we show GATA6 represents a target for the development of anti-SARS-CoV-2 therapeutic strategies and reaffirm the value of the CRISPR loss-of-function screens in providing a list of potential new targets for therapeutic interventions.

sample_organism: Severe acute respiratory syndrome coronavirus 2

overall_design: Genome-wide CRISPR screen (GeCKO library) in Calu3 cells infected with different SARS-CoV-2 strains (WT, alpha and beta) or left uninfected.

first: Ma'ayan

last: Israeli

first: Yaara

last: Finkel

first: Nir

last: Paran

first: Yfat

last: Yahalom-Rone

first: Theodor

last: Chitlaru

first: Ofir

first: Inbar

last: Cohen-Gihon

first: Adi

last: Beth-Din

first: Tomer

last: Israely

first: Moshe

last: Aftalion

first: Reut

last: Falach

first: Uri

last: Elia

first: Ital

last: Nemet

first: Limor

last: Kliker

first: Michal

last: Mandelboim

first: Ofer

last: Cohen

last: Bercovich-Kinori


title: Nutrient sensing mediated by O-GlcNAcylation regulates gene expression through epigenetic mechanisms during embryonic neurogenesis

status: Public on Mar 26 2022

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

summary: We show that pharmacological upregulation of O-GlcNAc levels during hESCs-neuronal differentiation leads to upregulation of key neurogenic TF gene which in turn is associated with increased H3K4me3 levels, reduction in H3K27me3 levels and increase in Pol IISer5 phosphorylation. Our results demonstrate O-GlcNAc mediated sensitivity of chromatin to nutrient status, and indicate how metabolic dysregulations could affect stem cell fate decisions through epigenetic gene regulatory mechanisms

overall_design: RNA-seq in four stages of hESC neural differentiation on samples treated with TMG and solvent control

first: Suraiya

middle: A

last: Ansari

first: Shama

last: Parween


title: Close related Drug-Resistance Beijing isolates of Mycobacterium tuberculosis reveal a different transcriptomic signature in a murine disease progression model.

city: Bogota

first: Juan

middle: Manuel

last: Anzola

state: Bogota

country: Colombia

institute: CorpoGen

summary: Mycobacterium tuberculosis (MTB) Beijing genotype is associated with high virulence and drug resistance worldwide. In Colombia, the Beijing genotype circulates since 1997 predominantly on the pacific coast, being the Beijing-Like SIT-190 more prevalent. This genotype conforms to a drug-resistant cluster and shows a fatal outcome in patients. To better understand virulence determinants, we performed a transcriptomic analysis with a Beijing-Like SIT-190 isolate (BL-323), and Beijing-Classic SIT-1 isolate (BC-391) in progressive tuberculosis (TB) murine model. RNA was extracted from mice lungs on days 3, 14, 28, and 60. On average, 0.6% of the total reads mapped against MTB genomes and of those, 90% against coding genes. The strains were independently associated as determined by hierarchical cluster and multidimensional scaling analysis. Gene ontology showed that in strain BL-323 enriched functions were related to host immune response and hypoxia, while proteolysis and protein folding were enriched in the BC-391 strain. Altogether, our results suggested a differential transcriptional program when evaluating these two closely related strains. The data presented here could potentially impact the control of this emerging, highly virulent and drug resistance genotype.

overall_design: We used Balb/c Mice infected with two close related Mycobacterium tuberculosis Beijing Strains. Afther the infection kinetics we obtained the whole trancriptome of the M. tuberculosis at early, middle and late infection stage to se the whole expression profile of the bacteria in the animal experimental model directrly from lungs

first: María

middle: I

last: Cerezo-Cortés

last: Rodríguez

middle: M

first: Dulce

last: Mata-Espinosa

first: Estela

last: Bini

first: Brenda

middle: N

last: Marquina Castillo

first: Jorge

last: Barrios-Payan

first: Fernanda

last: Cornejo-Granados

first: Adrian

last: Ochoa-Leyva

first: Patricia

last: Del Portillo

first: Martha

last: Murcia

first: Rogelio

last: Hernández-Pando

first: Lucia

last: Zatarain-Barrón


title: Single cell analysis reveals mechanisms of heterogeneity and plasticity of leukemia initiating cells

first: Edroaldo

last: Lummertz da Rocha

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Single cell analysis reveals mechanisms of heterogeneity and plasticity of leukemia initiating cells [Seq-Well]

summary: Leukemia initiating cells (LICs) self-renew indefinitely to fuel leukemic growth and spark disease relapse. Previously thought to be primitive and rare, the LIC state may actually be heterogeneous and dynamic, allowing LICs to evade therapy. Here, we use single cell transcriptomics to dissect the ontogeny of MLL-rearranged B-lymphoblastic leukemia (MLL-r B-ALL). Although we identify primitive, rare LICs, we also find more phenotypically differentiated LICs that possess the capability to replenish the full cellular diversity of MLL-r B-ALL. We find that activation of MYC-driven oxidative phosphorylation drives this process of cell state conversion, defining a new mechanism of LIC plasticity.

overall_design:
This study was initially designed to define LICs in MLL-r B-ALL, relying on xenotransplantation with LDA and terminal leukemia incidence by day 150 post-transplant as endpoints. This endpoint was chosen based on the approximately 100-day latency of bulk transplanted leukemia cells at a dose of 10,000 cells per transplant. We hypothesized that transplantation of LIC-enriched populations would shift latency earlier and transplantation of LIC-depleted would shift the latency further. Leukemia populations were isolated and xenotransplanted with investigators monitoring recipient mouse health blinded to the cell source. At the onset of morbidity, mice were euthanized to harvest tissues and bone marrow. At the completion of the experiment, the experimental conditions were unblinded, and LIC frequency calculated by LDA analysis, or survival analyzed by log-rank test, where indicated. For quantification of flow cytometry or expression data, the statistical tests used are indicated. Student’s t-tests were used and analysis was unpaired, except where otherwise indicated.
The raw data will be available at dbGaP:
dbGap number: 42161
The study is called 'Study of leukemia stem cells in B-ALL' registered to Robert Rowe.

first: R

last: Rowe


title: Single cell analysis reveals mechanisms of heterogeneity and plasticity of leukemia initiating cells [ChIP-Seq]

overall_design:
This study was initially designed to define LICs in MLL-r B-ALL, relying on xenotransplantation with LDA and terminal leukemia incidence by day 150 post-transplant as endpoints.  This endpoint was chosen based on the approximately 100-day latency of bulk transplanted leukemia cells at a dose of 10,000 cells per transplant.  We hypothesized that transplantation of LIC-enriched populations would shift latency earlier and transplantation of LIC-depleted would shift the latency further.  Leukemia populations were isolated and xenotransplanted with investigators monitoring recipient mouse health blinded to the cell source.  At the onset of morbidity, mice were euthanized to harvest tissues and bone marrow.  At the completion of the experiment, the experimental conditions were unblinded, and LIC frequency calculated by LDA analysis, or survival analyzed by log-rank test, where indicated.  For quantification of flow cytometry or expression data, the statistical tests used are indicated.  Student’s t-tests were used and analysis was unpaired, except where otherwise indicated.
The raw data will be available at dbGaP:
dbGap number: 42161
The study is called 'Study of leukemia stem cells in B-ALL' registered to Robert Rowe.


title: Single cell analysis reveals mechanisms of heterogeneity and plasticity of leukemia initiating cells [inDrop]


title: Single cell analysis reveals mechanisms of heterogeneity and plasticity of leukemia initiating cells [bulk RNA-seq]

overall_design:
This study was initially designed to define LICs in MLL-r B-ALL, relying on xenotransplantation with LDA and terminal leukemia incidence by day 150 post-transplant as endpoints. This endpoint was chosen based on the approximately 100-day latency of bulk transplanted leukemia cells at a dose of 10,000 cells per transplant. We hypothesized that transplantation of LIC-enriched populations would shift latency earlier and transplantation of LIC-depleted would shift the latency further. Leukemia populations were isolated and xenotransplanted with investigators monitoring recipient mouse health blinded to the cell source. At the onset of morbidity, mice were euthanized to harvest tissues and bone marrow. At the completion of the experiment, the experimental conditions were unblinded, and LIC frequency calculated by LDA analysis, or survival analyzed by log-rank test, where indicated. For quantification of flow cytometry or expression data, the statistical tests used are indicated. Student’s t-tests were used and analysis was unpaired, except where otherwise indicated.

The raw data will be available at dbGaP:
dbGap number: 42161
The study is called 'Study of leukemia stem cells in B-ALL' registered to Robert Rowe.


title: Transcriptome differences analysis between Yersinia pestis 201 wild strain and fyuA mutant strain

status: Public on Mar 22 2022

city: Bei Jing

first: chen

last: yulu

address: changbai road 155

country: China

institute: Chinese Center for Disease Control and Prevention

summary:
Purpose: In previous studies, we found that the fyuA gene plays an important role in the virulence and pathogenicity of Yersinia pestis strain 201. In order to globally observe which functions of the fyuA gene also affect Y. pestis, we performed RNA-seq on the Y. pestis wild strain 201-WT and mutant strains △fyuA and △fyuAGCAdel, hoping to find their differences at the transcription level, so that better elucidate the effect of fyuA gene on Y. pestis gene transcription.
Methods: Total RNA was extracted using the PureLink™ RNA Mini Kit, and then used for creating a cDNA library and deep sequencing. According to the values of Fragments Per Kilobase of Transcript per Million Mapped Reads (FPKM), the ratio of transcript levels between WT and ΔfyuAGCAdel groups was used as the logarithm to the base 2 (twofold change). The differential values of at least a 2-fold were applied to analyze the differential expression of genes according to the Y. pestis 91001 genome annotation. The transcriptome data were verified by qPCR.
Results: We found that compared with 201-WT, genes related to siderophore synthesis such as ybtS, ybtX, ybtQ, irp2, irp1, ybtU, ybtT and ybtE were significantly down-regulated at either 26 ℃ or 37 ℃. At 37 ℃, the genes related to type Ⅲ secretion system were significantly up-regulated.

overall_design: Y. pestis WT strain 201 and fyuA mutants at 26 ℃ or 37 ℃ in TMH.

first: Yulu

last: Chen

first: Kai

last: Song

first: Yajun


title: MYC drives aggressive prostate cancer by disrupting transcriptional pause release at androgen receptor targets at androgen receptor targets

status: Public on Mar 28 2022

first: Xintao

last: Qiu

address: 440 brookline ave

institute: Dana Faber Cancer Institute


title: Differential and divergent activity of Insulin-like Growth Factor Binding Protein 6 (IGFBP6) in  platinum-sensitive versus platinum-resistant high-grade serous ovarian carcinoma cell lines.

status: Public on Mar 23 2022

city: Foggia

first: Annamaria

last: Piscazzi

address: Viale Pinto 1

country: Italy

institute: Università di Foggia

summary: IGFBP6 is a secreted protein with a controversial role in human malignancies, being downregulated  in the majority of human cancers, but upregulated in selected tumors. Ovarian carcinoma (OC) is a human malignancy characterized by IGFBP6 downregulation, even though the significance of its low expression during ovarian carcinogenesis is still poorly understood. IGFBP6 expression levels and the activation of its signaling pathway were evaluated in two matched OC cell lines derived from a high-grade serous ovarian cancer before and after platinum resistance (PEA1 and PEA2 cells,respectively). A whole genome gene expression analysis was comparatively performed in both cell lines upon IGFBP6 stimulation by Illumina technology. IGFBP6 gene expression in human OCs data were obtained from public datasets. Gene expression data from public datasets confirmed the downregulation of IGFBP6 from normal ovarian tissues to primary and metastatic OCs. The comparative analysis of platinum-sensitive (PEA1) and platinum-resistant (PEA2) cell lines showed quantitative and                                                  qualitative differences in the activation of IGFBP6 signaling. Indeed, IGFBP6 enhanced ERK1/2 phosphorylation only in PEA1 cells and induced a more evident and significant gene expression reprogramming in PEA1 compared to PEA2 cells. Furthermore, the analysis of  selected genes modulated by IGFBP6 (i.e., FOS, JUN, TNF, IL6, IL8, and EGR1) showed an inverse regulation in PEA1 versus PEA2 cells, as well as selected hallmarks and IL-6 signaling were ositively regulated in PEA1, while inhibited in PEA2 cells.These data suggest that loss of IGFBP6 signaling may play a role in ovarian cancer progression, being likely associated to the development of platinum resistance.

overall_design: Sample PEA1 ctrl  PEA1 IGFBP6(1ug/ml 2h) PEA2 ctrl  PEA2 IGFBP6(1ug/ml 2h) TRIPLICATE

first: Giovanni

last: Calice

first: Valentina

last: Condelli

first: Fabiana

last: Crispo


title: Transcriptome analysis of AoPEX1 and AoPEX6 in nematode-trapping fungus Arthrobotrys oligospora

status: Public on Mar 19 2022

city: Kunming

first: Qianqian

last: Liu

state: Yunnan Province

address: No. 2, Cuihu North Road, Wuhua District, Kunming

department: School of Life Sciences

institute: Yunnan University

summary: Transcriptomic analysis revealed that differentially expressed genes in the absence of AoPEX1 and AoPEX6 were involved in cell cycle, ribosome, proteasome.

overall_design: Examination of differential genes in WT, ΔAopex1 and ΔAopex6 mutant strains and prediction of multiple cytological processes that may affect trap formation in Arthrobotrys oligospora.

first: Dongni

last: Li

first: Kexin

last: Jiang

first: Jinkui

last: Yang


title: Single-cell RNA-sequencing of proximal colon epithelial cells from Gpr35 knock-out mice

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel

summary: We performed a single-cell transcriptome analysis of proximal colon epithelial cells from 4 Gpr35 KO and 4 WT female littermates mice at a steady state.

overall_design: Crypts were dissociated to single-cell suspensions sorted for CD326+, CD45- and CD31- cells, and the eight samples were loaded onto the wells of a single 10X Genomics Chromium controller.

first: Hassan

last: Melhem

first: Jan

last: Niess

first: Julien

last: Roux


title: Expression data from wild-type, ccr4∆, and ccr4∆ pbp1∆ yeast cells.

status: Public on Mar 18 2022

city: Tsukuba

first: Kenji

last: Irie

state: JAPAN

address: 1-1-1 Tennoudai

department: Medicine

country: Japan

institute: University of Tsukuba

summary: Wild type, ccr4∆, ccr4∆ pbp1∆ cells were grown in YPD medium from log phase to stationary phase. Total RNAs ere extracted and subjected to microarray analysis.

first: Yasuyuki

last: Suda


title: RNA Polymerase II Pausing Factor NELF in CD8+ T Cells Promotes Anti-Tumor Immunity

city: Washington

first: Rong

state: DC

address: 2300 I Street

department: Biochemistry and Molecular Medicine

institute: The George Washington University

summary: The master transcriptional regulator T cell factor 1 (TCF1) is required for the anti-tumor functions of memory and stem-like CD8+ T cells. However, how TCF1 partners with other transcription factors to orchestrate the gene activation program critical for anti-tumor immunity remains poorly understood. Here we show that negative elongation factor B (NELFB), an RNA polymerase II pausing factor, cooperates with TCF1 in T cell responses to cancer. Genetic ablation of mouse Nelfb in mature T lymphocytes severely impaired anti-tumor immunity responding to both primary tumor challenge and tumor antigen-mediated vaccination. NELFB depletion resulted in more exhausted, and reduced memory, T cell populations, whereas its ectopic expression boosted host anti-tumor immunity and efficacy of chimeric antigen receptor (CAR) T-cell immunotherapy. Mechanistically, NELFB is physically associated with TCF1 and recruited preferentially to TCF1-enriched transcriptional enhancers and promoters in CD8+ T cells. Nelfb ablation significantly restricted chromatin accessibility to these TCF1-associated loci. Thus, NELFB is a previously unrecognized functional partner of TCF1 that potentiates the chromatin openness of TCF1-targeting regulatory elements. Our findings also suggest that augmenting NELFB expression in CD8+ T cells may improve therapeutic outcomes of anti-cancer CAR-T immunotherapies.

overall_design: CD8+ T cells were isolated from WT/KO mice spleen for scRNA-seq, ATAC-seq, Pol II ChIP-seq, bulk RNA-seq. WT CD8+ T cells from WT mice spleen were used for NELFB ChIP-seq.

first: Bogang

last: Wu

first: Xiaowen

last: Zhang

first: Huai-Chin

last: Chiang


title: Genetic and transcriptomic characteristics of RhlR-dependent quorum sensing in cystic fibrosis isolates of Pseudomonas aeruginosa: isolate E167

city: Seattle

first: Kyle

middle: Lowe

last: Asfahl

state: Washington

address: 1705 NE Pacific St

department: Microbiology

institute: University of Washington

summary: In people with the genetic disease cystic fibrosis (CF), bacterial infections involving the opportunistic pathogen Pseudomonas aeruginosa are a significant cause of morbidity and mortality. P. aeruginosa uses a cell-cell signaling mechanism called quorum sensing (QS) to regulate many virulence functions. One type of QS consists of acyl-homoserine lactone (AHL) signals produced by LuxI-type signal synthases, which bind a cognate LuxR-type transcription factor. In laboratory strains and conditions, P. aeruginosa employs two AHL synthase/receptor pairs arranged in a hierarchy, with the LasI/R system controlling the RhlI/R system and many downstream virulence factors. However, P. aeruginosa isolates with inactivating mutations in lasR are frequently isolated from chronic CF infections. We and others have shown that these isolates frequently use RhlR as the primary QS regulator. RhlR is rarely mutated in CF and environmental settings. We were interested if there were reproducible genetic characteristics of these isolates and if there was a central group of genes regulated by RhlR in all isolates. We examined five isolates and found signatures of adaptation common to CF isolates. Here, we analyzed CF clinial isolate E167. In this strain, RhlR positively regulates 78 genes, including those coding for known virulence factors. These results suggest a key group of QS-regulated factors important for pathogenesis of chronic infection, and position RhlR as a target for anti-QS therapeutics. Our work underscores the need to sample a diversity of isolates to understanding QS beyond what has been described in laboratory strains.

overall_design: Examination of a rhlR-deletion mutant of a cystic fibrosis isolate of Pseudomonas aeruginosa vs. the isogenic parent strain

middle: L

first: Nicole

middle: E

last: Smalley

first: Alexandria

middle: P

last: Chang

first: Ajai

last: Dandekar


title: Genetic and transcriptomic characteristics of RhlR-dependent quorum sensing in cystic fibrosis isolates of Pseudomonas aeruginosa: isolate E113

summary: In people with the genetic disease cystic fibrosis (CF), bacterial infections involving the opportunistic pathogen Pseudomonas aeruginosa are a significant cause of morbidity and mortality. P. aeruginosa uses a cell-cell signaling mechanism called quorum sensing (QS) to regulate many virulence functions. One type of QS consists of acyl-homoserine lactone (AHL) signals produced by LuxI-type signal synthases, which bind a cognate LuxR-type transcription factor. In laboratory strains and conditions, P. aeruginosa employs two AHL synthase/receptor pairs arranged in a hierarchy, with the LasI/R system controlling the RhlI/R system and many downstream virulence factors. However, P. aeruginosa isolates with inactivating mutations in lasR are frequently isolated from chronic CF infections. We and others have shown that these isolates frequently use RhlR as the primary QS regulator. RhlR is rarely mutated in CF and environmental settings. We were interested if there were reproducible genetic characteristics of these isolates and if there was a central group of genes regulated by RhlR in all isolates. We examined five isolates and found signatures of adaptation common to CF isolates. Here, we analyzed CF clinial isolate E113. In this strain, RhlR positively regulates 186 genes, including those coding for known virulence factors. These results suggest a key group of QS-regulated factors important for pathogenesis of chronic infection, and position RhlR as a target for anti-QS therapeutics. Our work underscores the need to sample a diversity of isolates to understanding QS beyond what has been described in laboratory strains.


title: Genetic and transcriptomic characteristics of RhlR-dependent quorum sensing in cystic fibrosis isolates of Pseudomonas aeruginosa: isolate E125

summary: In people with the genetic disease cystic fibrosis (CF), bacterial infections involving the opportunistic pathogen Pseudomonas aeruginosa are a significant cause of morbidity and mortality. P. aeruginosa uses a cell-cell signaling mechanism called quorum sensing (QS) to regulate many virulence functions. One type of QS consists of acyl-homoserine lactone (AHL) signals produced by LuxI-type signal synthases, which bind a cognate LuxR-type transcription factor. In laboratory strains and conditions, P. aeruginosa employs two AHL synthase/receptor pairs arranged in a hierarchy, with the LasI/R system controlling the RhlI/R system and many downstream virulence factors. However, P. aeruginosa isolates with inactivating mutations in lasR are frequently isolated from chronic CF infections. We and others have shown that these isolates frequently use RhlR as the primary QS regulator. RhlR is rarely mutated in CF and environmental settings. We were interested if there were reproducible genetic characteristics of these isolates and if there was a central group of genes regulated by RhlR in all isolates. We examined five isolates and found signatures of adaptation common to CF isolates. Here, we analyzed CF clinial isolate E125. In this strain, RhlR positively regulates 28 genes, including those coding for known virulence factors. These results suggest a key group of QS-regulated factors important for pathogenesis of chronic infection, and position RhlR as a target for anti-QS therapeutics. Our work underscores the need to sample a diversity of isolates to understanding QS beyond what has been described in laboratory strains.


title: Genetic and transcriptomic characteristics of RhlR-dependent quorum sensing in cystic fibrosis isolates of Pseudomonas aeruginosa: isolate E131

summary: In people with the genetic disease cystic fibrosis (CF), bacterial infections involving the opportunistic pathogen Pseudomonas aeruginosa are a significant cause of morbidity and mortality. P. aeruginosa uses a cell-cell signaling mechanism called quorum sensing (QS) to regulate many virulence functions. One type of QS consists of acyl-homoserine lactone (AHL) signals produced by LuxI-type signal synthases, which bind a cognate LuxR-type transcription factor. In laboratory strains and conditions, P. aeruginosa employs two AHL synthase/receptor pairs arranged in a hierarchy, with the LasI/R system controlling the RhlI/R system and many downstream virulence factors. However, P. aeruginosa isolates with inactivating mutations in lasR are frequently isolated from chronic CF infections. We and others have shown that these isolates frequently use RhlR as the primary QS regulator. RhlR is rarely mutated in CF and environmental settings. We were interested if there were reproducible genetic characteristics of these isolates and if there was a central group of genes regulated by RhlR in all isolates. We examined five isolates and found signatures of adaptation common to CF isolates. Here, we analyzed CF clinial isolate E131. In this strain, RhlR positively regulates 105 genes, including those coding for known virulence factors. These results suggest a key group of QS-regulated factors important for pathogenesis of chronic infection, and position RhlR as a target for anti-QS therapeutics. Our work underscores the need to sample a diversity of isolates to understanding QS beyond what has been described in laboratory strains.


title: Genetic and transcriptomic characteristics of RhlR-dependent quorum sensing in cystic fibrosis isolates of Pseudomonas aeruginosa: isolate E104

summary: In people with the genetic disease cystic fibrosis (CF), bacterial infections involving the opportunistic pathogen Pseudomonas aeruginosa are a significant cause of morbidity and mortality. P. aeruginosa uses a cell-cell signaling mechanism called quorum sensing (QS) to regulate many virulence functions. One type of QS consists of acyl-homoserine lactone (AHL) signals produced by LuxI-type signal synthases, which bind a cognate LuxR-type transcription factor. In laboratory strains and conditions, P. aeruginosa employs two AHL synthase/receptor pairs arranged in a hierarchy, with the LasI/R system controlling the RhlI/R system and many downstream virulence factors. However, P. aeruginosa isolates with inactivating mutations in lasR are frequently isolated from chronic CF infections. We and others have shown that these isolates frequently use RhlR as the primary QS regulator. RhlR is rarely mutated in CF and environmental settings. We were interested if there were reproducible genetic characteristics of these isolates and if there was a central group of genes regulated by RhlR in all isolates. We examined five isolates and found signatures of adaptation common to CF isolates. Here, we analyzed CF clinial isolate E104. In this strain, RhlR positively regulates 48 genes, including those coding for known virulence factors. These results suggest a key group of QS-regulated factors important for pathogenesis of chronic infection, and position RhlR as a target for anti-QS therapeutics. Our work underscores the need to sample a diversity of isolates to understanding QS beyond what has been described in laboratory strains.


title: Chromatin profiles classify castration-resistant prostate cancers suggesting therapeutic targets

city: New York

first: Yu

last: Chen

state: NY

address: 1275 York Ave, Box 20

department: Human Oncology and Pathogenesis Program

institute: Memorial Sloan Kettering Cancer Center


title: Whole transcriptome analysis of human kidney cells after exposure to cigarette smoke extract.

status: Public on Mar 16 2022

city: Taipei

first: Yung-Li

last: Wang

address: 250 Wu-Hsing Street

country: Taiwan

institute: Graduate Institute of Clinical Medicine, Taipei Medical University

summary: Cigarette smoke (CS) is one of risk factor to chronic obstructive pulmonary disease that is the major causes of death in the world. Furthermore, CS is an independent risk factor for chronic kidney disease (CKD) in the general adult population. The goal of this project was to identified the mechanisms of renal damage that might be associated with exposure to CS extract (CSE) in human kidney proximal tubular epithelial cell line (HK-2 cells) cells.

overall_design: RNA sequencing of human kidney proximal tubular epithelial cell line (HK-2 cells) after 24 hours exposure to 0.6% CSE.

first: Yu-Jhe

last: Chiu

first: Wen-Chih

last: Liu

first: Hui-Wen


title: Effect of monoacylglycerol lipase inhibition on intestinal permeability of rats with severe acute pancreatitis

city: Wuhan

first: Dong

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

summary: Endocannabinoid 2-arachidonoylglycerol (2-AG) is an anti-nociceptive lipid that is inactivated through cellular uptake and subsequent catabolism by monoacylglycerol lipase (MAGL).  In this study, we investigated the effects of MAGL inhibition on intestinal permeability and explored the possible mechanism.  A rat model of severe acute pancreatitis (SAP) was established.  Rats were divided into three groups according to treatment.  We analyzed intestinal permeability to fluorescein isothiocyanate-dextran and the levels of inflammatory factors interleukin-6 (IL-6) and tumor necrosis factor-α (TNF-α) and 2-AG.  Hematoxylin and eosin staining was used to assess histological tissue changes.  In vivo intestinal permeability was evaluated by transmission electron microscopy.  We obtained ileum tissues, extracted total RNA, and applied RNA-sequencing.  Sequencing data were analyzed by bioinformatics.  Inflammatory factor levels were higher, while 2-AG levels were lower in the SAP group compared with the control group.  Administration of JZL184 to rats with SAP increased the levels of 2-AG and lowered the levels of IL-6 and TNF-α.  Notably, intestinal permeability was improved by JZL184 as demonstrated by fluorescein isothiocyanate-dextran measurement, hematoxylin and eosin staining, and transmission electron microscopy.  RNA-sequencing showed significant transcriptional differences in SAP and JZL184 groups compared with the control group.  KEGG analysis showed that the up- or downregulated genes in multiple comparison groups were enriched in two pathways, focal adhesion and PI3K-Akt signaling pathways.  Differential alternative splicing (AS) genes, such as Myo9b, Lsp1, and Git2, have major functions in intestinal diseases.  A total of 132 RNA-binding proteins (RBPs) were screened by crossing the identified abnormally expressed genes with the reported RBP genes.  Among them, Hnrnpdl coexpressed the most AS events as the main RBP.  MAGL inhibition improved intestinal mucosal barrier injury in SAP rats and induced a large number of differentially expressed genes and alternative splicing events.  Hnrnpdl might play an important role in improving intestinal mucosal barrier injury by affecting alternative splicing events.

overall_design: SD rats were randomly divided into the following three groups 24 hours after the surgery: Control group, SAP group and SAP treated with JZL184 group.

first: Jing

first: Hongwei

last: Xu

first: Tianjie

first: Changqin


title: RNA-seq data analysis of CD123 loss samples

status: Public on Mar 14 2022

city: Houston

first: Yuan

last: Qi

state: TX

address: 1400 Pressler St

department: Bioinformatics & Computational Biology

institute: University of Texas M.D. Anderson Cancer Center

summary: Molecular analysis of CD123 loss following UCART123 treatment.

overall_design: The RNA were extracted from CD123- cells or CD123+ cells from UCART123 treated mice in PDX-3 experiment. In the PDX study, mice treated with UCART123 experienced CD123-negative relapse. Unexpectedly, we identified not a single, but three diverse mechanisms of CD123 loss amongst mice that relapsed with CD123- disease: genomic loss of CD123 DNA; a truncated transcript containing only exons 2-9; and predominant alternative splicing (skipping from exon 2 to exon 5) which is reminiscent of CD19 epitope loss in B-cell acute lymphoblastic leukemia36. The most plausible explanation is the selection of a small pre-existing population of clones lacking CD123, that were enriched upon the selective pressure of UCART123 therapy.

first: T

last: Cai

first: M

last: Konopleva


title: Rescuing voluntary motor behavior in a Parkinson´s disease model by aCRISPR mediated reprogramming of striatal astrocytes into induced GABAergic neurons

status: Public on Mar 15 2022

city: Neuherberg

first: Wolfgang

last: Wurst

address: Ingolstaedter Landstrasse 1

department: Institute of Developmental Genetics

country: Germany

institute: Helmholtz Zentrum München

summary: Cell replacement strategies of affected cells have been performed in clinical studies of Parkinson´s disease with variable outcome. Conversion of endogenous glial cells into functional neurons might represent a more reliable alternative, thus here we developed a knock-in mouse line carrying a dual dCas9 transactivator system (dCAM), which allowed the conditional activation of the endogenous genes Ascl1, Lmx1a, and Nr4a2 in striatal astrocytes in vivo by delivering sgRNAs specific for their endogenous loci. In order to move this successful approach toward translation, we established an AAV based activator system carrying intein-split-dCas9-VP64, SAM (AAV-dCAS) activators, and the specific sgRNAs targeting transcription factor combinations. Both systems, the dCAM and the AAV-dCAS approach were successful in reprogramming of striatal astrocytes into GABAergic neurons, which functionally integrate into striatal circuits as evidenced by the alleviation of specific motor behaviors in a 6-OHDA Parkinson’s disease model. Thus, the AAV-dCAS approach may enable clinical therapies for Parkinson´s disease by reprogramming striatal astrocytes.

overall_design: Examination of cell composition and astrocyte to neuron reprogramming in murine striatal tissue.

first: J

last: Giehrl-Schwab

first: F

last: Giesert

first: B

last: Rauser

last: Lao

first: S

last: Lefort

first: I

last: Ibarra

first: C

last: Koupourtidou

middle: D

last: Luecken

last: Truong

last: Fischer-Sternjak

last: Ninkovic

last: Hölter

first: D

last: Vogt Weisenhorn

last: Theis

last: Götz

first: W


title: Intestinal epithelial Kruppel-like factor 5 (KLF5) protects against Th17-mediated immune response in a murine model of colitis

city: Stony Brook

first: Jason

last: Shieh

address: 101 Nicolls Rd.

institute: Stony Brook University

summary: We have developed a murine model with intestinal epithelial specific inducible knockout of KLF5 where we have identified a Th17-mediated immune response. Bulk RNA-sequencing data showed an increase in transcript number of inflammatory markers, such as Il17a and Il22. Furthermore, when we performed GSEA analysis, we observed increased correlation to activated Th17 response responses, and network analysis of pathways indicated a positive correlation with an overall immune response in the intestinal tissue. Along with increased immune response, we performed 16s rRNA sequencing and observed changes in abundance of the microbiota. While we did not observed changes within the alpha diversity, possibly due to the acute response of our current timeline, we found changes that clustered our Klf5 knockdown out from our controls.

sample_organism:
Mus musculus
feces metagenome

platform_organism:
Mus musculus
feces metagenome

overall_design: Performed Bulk RNA sequencing and 16s rRNA sequencing on Corn-oil treated and Tamoxifen treated Villin-CreERT2;KLF5(fl/fl) mice.

first: Timothy

middle: H

last: Chu

first: Yang

last: Liu

first: Julie

last: Kim

first: Ainara

middle: R

last: De Sabando

first: Soma

middle: S

last: Kobayashi

first: Sui

middle: Y

last: Zee

first: Brian

last: Sheridan

first: Agnieszka

middle: B

last: Bialkowska

first: Vincent

middle: W

last: Yang


title: Muscle fiber type-dependence effect of exercise on genomic networks in aged mice models

city: Seoul

first: Summin

last: Lee

state: Gwanak-gu

address: 1, gwanak-ro

country: South Korea

institute: Seoul National university

summary: the intervention period was 4 weeks, and treadmill exercises were conducted for all exercise groups. Two sessions per day were administered. A minimum of a one-hour break was allocated between sessions. the 9-week-old C57BL/6 young male mice and 84-week-old mice were purchased from Central Lab. The groups were divided into young control (YC), young exercise (YE), old control (OC), and old exercise (OE) groups. Each group comprised three mice and all mice were subjected to RNA sequencing analysis.

overall_design: Examination of gene expression profiles of young control (YC), young exercise (YE), old control (OC), old exercise (OE) in each soleus and gastrocnemius.

first: Sunmin

first: Hyo

last: Moon

first: Min

middle: c

first: Woori

last: Bae

first: Koung

middle: j

last: Yoon


title: Lupus susceptibility loci predispose mice to clonal lymphocytic responses and myeloid expansion

city: Boston

first: Elliot

last: Akama-Garren

address: 200 Longwood Ave

institute: Harvard Medical School

summary: Lupus susceptibility results from the combined effects of numerous genetic loci, but the contribution of these loci to disease pathogenesis has been difficult to study due to the large cellular heterogeneity of the autoimmune immune response.  We performed single cell RNA, B cell receptor (BCR), and T cell receptor (TCR) sequencing of splenocytes from mice with multiple polymorphic lupus susceptibility loci.  We not only observed lymphocyte and myeloid expansion, but also characterized changes in subset frequencies and gene expression, such as decreased CD8 and marginal zone B cells and increased Fcrl5 and Cd5l expressing macrophages.  Clonotypic analyses revealed expansion of B and CD4 clones, and TCR repertoires from lupus prone mice were distinguishable by algorithmic specificity prediction and unsupervised machine learning classification.  Myeloid differential gene expression, metabolism, and altered ligand-receptor interaction were associated with decreased antigen presentation.  This dataset provides novel mechanistic insight into the pathophysiology of a spontaneous model of lupus, highlighting potential therapeutic targets for autoantibody mediated disease.

overall_design: scRNA-seq, scBCR-seq, and scTCR-seq was performed on 4 mice (2 controls and 2 autoimmune mice)

first: Michael

middle: C

last: Carroll


title: ChIP-seq of ZEB1 in MCF7-V breast carcinoma cell line transduced with a doxycyline-inducible construct to express ZEB1

city: Geneva

first: Didier

last: Picard

address: Sciences III

institute: University of Geneva

summary: The epithelial to mesenchymal transition (EMT) is implicated in the metastatic spread of breast cancer cells. EMT transcription factors (TF) regulate different stages of EMT states. In breast cancers, estrogen receptor α (ERα) maintains the epithelial characteristics of breast tumors and is indispensable for efficient endocrine therapy. In this study we investigate whether and how ZEB1, an EMT-TF affects ERα signaling at early stages of EMT and metastasis.

overall_design: We did ZEB1 ChIP-seq of cells stably expressing a doxycyline-inducible construct to express ZEB1 in presence of doxycycline. To induce ZEB1 in stable cell line we used 2 µg/ml doxycyline (DOX).

first: Nastaran

last: Ghahhari


title: High-resolution translatome analysis reveals cortical cell programs during early soybean nodulation

status: Public on Mar 21 2022

city: Columbia

first: Gary

last: Stacey

state: Missouri

address: 271E Christopher S. Bond Life Sciences Center

institute: University of Missouri at Columbia

summary: The TRAP-seq process is dependent on the expression of a cell layer-specific His-FLAG-tagged ribosomal protein L18 (HF-GmRPL 18), which allows for the immunoprecipitation of ribosomes with their corresponding mRNA to produce tissue-specific translatomes (Zanetti et al., 2005; Castro‐Guerrero et al., 2016).To capture events occurring in the cortex during the early stages of infection and initial cortical cell divisions, we inoculated plants and performed a time-course collection of root samples at 72- and 96-hour post inoculation (hpi) followed by TRAP-seq. Immunoblot analysis indicated that an adequate amount of protein was present for immunoprecipitation. To study rhizobial-induced transcriptional changes in the cortex during early nodule development, we identified a soybean promoter (Glyma.18g53890, Figure 1B) expressed exclusively in the cortex cells using LCM (Kerk et al., 2003; Casson et al., 2008) followed by transcriptional analysis. The cortex-specific promoter was used to drive the expression of GmRPL18 in soybean hairy roots. To capture events occurring in the cortex during the early stages of infection and initial cortical cell divisions, we inoculated plants and performed a time-course collection of root samples at 72- and 96-hour post inoculation (hpi) followed by TRAP-seq. Immunoblot analysis indicated that an adequate amount of protein was present for immunoprecipitation (Figure 1C). Taken together, time-course cortex-specific TRAP-seq was established for studying of early nodule development in soybean.

overall_design: Examination of 2 different time point (72hpi and 96hpi) samples with or without B.Japonicum treatment using translating ribosome affinity purification (TRAP) followed by RNA sequencing technology

first: Jaehyo

last: Song

first: Michelle

middle: Z

last: Tadra-Sfeir

first: Bruna

last: Montes-Luz

first: Yaya

last: Cui

first: Lingtao

last: Su

first: Dong

last: Xu


title: Transcriptome analysis in treated MCF7-V breast carcinoma cell line stably expressing a doxycyline-inducible construct to express ZEB1.

summary: The epithelial to mesenchymal transition (EMT) is implicated in the metastatic spread of breast cancer cells. EMT transcription factors (TF) regulate different stages of EMT states. In breast cancers, estrogen receptor α (ERα) maintains the epithelial characteristics of breast tumors and is indispensable for efficient endocrine therapy. In this study we investigate whether and how ZEB1, an EMT-TF affects ERα signaling at early stages of EMT and metastasis. In MCF7-V cells, we used RNA-seq to study the impact of ZEB1 on the ERα transcriptome in breast cancer cells induced with DMSO, 17-beta estradiol (E2), and forskolin + 3-isobutyl-1-methylxanthine (IBMX) (FI).

overall_design: We did RNA-seq in wild type MCF7-V breast cancer cells and in cells with a doxycyline-inducible construct to express ZEB1 in presence of dxycycline. We induced ERα activation by DMSO, 17-beta estradiol (E2), and Forskolin + 3-isobutyl-1-methylxanthine (IBMX) (FI). To induce ZEB1 in stably expressing doxycyline-inducible constrcut to express ZEB1, we used 2 µg/ml doxycyline (DOX). nDOX stands no doxycycline.

middle: M


title: ChIP-seq of estrogen receptor α in wild type MCF7-V and in MCF7-V breast carcinoma cell line transduced with a doxycyline-inducible construct to express ZEB1.

summary: The epithelial to mesenchymal transition (EMT) is implicated in the metastatic spread of breast cancer cells. EMT transcription factors (TF) regulate different stages of EMT states. In breast cancers, estrogen receptor α (ERα) maintains the epithelial characteristics of breast tumors and is indispensable for efficient endocrine therapy. In this study we investigate whether and how ZEB1, an EMT-TF affects ERα signaling at early stages of EMT and metastasis. We did ERα ChIP-seq in wild type MCF7-V cells for comparative studies. We also did ERα ChIP-seq in cells stably expressing a doxycycline-inducible construct to express ZEB1. This was to determine the impact of ZEB1 on the ERα cistrome in MCF7-V breast cancer cells induced with DMSO, 17-beta estradiol (E2), and forskolin + 3-isobutyl-1-methylxanthine (IBMX) (FI).

overall_design: We did ChIP-seq in wild type MCF7-V breast cancer cells and in cells stably expressing a doxycyline-inducible construct to express ZEB1 in presence of dxycycline. To induce ZEB1 in stable cell line we used 2 µg/ml doxycyline (DOX).


title: Zebrafish tumors driven by overexpression of human IRF4

city: Singapore

first: Tze King

last: Tan

address: 14 Medical Drive

department: Cancer Science Institute

country: Singapore

institute: National University of Singapore

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

overall_design: Refer to individual Series


title: Transcriptomic analysis of RNA-sequencing data from nontransgenic and transgenic tau SPAM mice

city: Gainesville

first: Benoit

last: Giasson

state: FL

address: 1275 Center Drive, BMS J427

institute: University of Florida

summary: We performed RNA-sequencing of nontransgenic and transgenic By line of tau SPAM mice (expressing the S320F/P301S aggregating mutations) at different ages of 2, 4, and 6 months. All of the samples were obtained from brain cortex.

overall_design: Comparison of differentially expressed genes between nontransgenic mice and transgenic tau SPAM mice at different ages of 2, 4, and 6 months. Differential expression analysis was focused on aged tau SPAM mice and nontransgenic mice of 6 months.

first: Giasson

last: Benoit

first: Xia

last: Yuxing


title: Genome-wide investigation of Pasteurella multocida identifies the stringent response as a negative regulator of hyaluronic acid capsule production

city: Clayton

first: Thomas

last: Smallman

state: Victoria

address: 19 Innovation walk

country: Australia

institute: Monash University

summary: Pasteurella multocida is a Gram-negative capsulated bacterium responsible for a range of diseases that cause severe morbidity and mortality in livestock animals. The hyaluronic acid (HA) capsule produced by P. multocida serogroup A strains is a critical virulence factor. In this study, we utilised transposon-directed insertion site sequencing (TraDIS) to identify genes essential for in vitro growth of P. multocida, and combined TraDIS with discontinuous density gradients (TraDISort) to identify genes required for HA capsule production and regulation in this pathogen. Analysis of mutants with a high cell density phenotype, indicative of the loss of extracellular capsule, led to the identification of 69 genes important for capsule production. These genes included all previously characterized genes in the capsule biosynthesis locus, and fis and hfq that encode known positive regulators of P. multocida capsule. Many of the other capsule-associated genes identified in this study were involved in regulation or activation of the stringent response, including spoT and relA that encode proteins that regulate the concentration of guanosine alarmones. Disruption of the autoregulatory domains in the C-terminal half of SpoT using insertional mutagenesis resulted in reduced expression of capsule biosynthesis genes and an acapsular phenotype. Overall, these findings have greatly increased the understanding of hyaluronic acid capsule production and regulation in P. multocida.

overall_design: Transposon-directed insertion site sequencing of P. multocida strain VP161 Himar1 mutant library after growth in rich media, and following isolation of acapsular mutants using Percoll gradients

first: Galain

last: Williams

first: Marina

last: Harper

first: John

last: Boyce


title: H3K27ac ChIP-seq analysis for zebrafish normal thymus and tumors driven by overexpression of human IRF4

summary: H3K27ac ChIP-seq analysis was performed using zebrafish normal thymus and primary tumors to analyze potential regulatory elements activated by IRF4 overexpression.

overall_design: A transgenic zebrafish line expressing human IRF4 and mCherry genes under zebrafish lck promoter and a control line expressing mCherry gene only under zebrafish lck promoter were established. Normal thymus from control line and tumor cells from IRF4-transgenic line were sorted and crosslinked with formaldehyde for 10 min. DNA was enriched by chromatin-immunoprecipitation (ChIP) and analyzed by BGISEQ-500. A sample of whole cell lysate (WCL) was sequenced and used as the background to determine enrichment. ChIP was performed using an antibody against H3K27ac antibody (Abcam, ab4729).

first: Stella

last: Amanda

first: Tze

middle: K

first: Jolynn

last: Ong

first: Madelaine

last: Theardy

first: Takaomi

last: Sanda


title: RNA-seq analysis for IRF4-driven zebrafish tumors after JQ1 treatment

summary: RNA-seq analysis was performed using tumor cells driven by IRF4 to analyze gene expression changes after JQ1 treatment

overall_design: The human IRF4 gene and mCherry fluorescent marker gene were transduced under the zebrafish lck promoter in zebrafish.  After the development of lymphoma phenotype, animals were treated with JQ1 or control DMSO for 1 or 3 days.  Tumor cells were harvested and sorted by flow cytometry based on mCherry fluorescence expression.  Total RNAs were harvested from each sample and then applied for RNA-seq analysis.


title: Single cell RNA-seq analysis for normal lymphocytes and IRF4-driven zebrafish tumors

summary: Single cell RNA-seq analysis was carried out for 1 normal sample from a control zebrafish line (lck-mCherry) and 5 non-tumor and 14 tumor samples from the IRF4 transgenic line (lck-IRF4).  Tumor cells were harvested from the animals with or without heterozygous p53 mutation at different time points of tumor development.

overall_design: Human IRF4 gene was overexpressed together with mCherry under the zebrafish lck promoter.  Samples were harvested from control or IRF4-transgenic zebrafish (lck-IRF4) with or without heterozygous p53 mutation. mCherry positive cells sorted by flow cytometry.  Normal cells was prepared from a control zebrafish which overexpresses only mCherry.  Single cell RNA-seq analysis was performed by 10X Genomics using 3' Chromium Single Cell Technique.


title: Study of  ebola virus VP35 protein on gene expression in HepG2 cells

city: beijing

first: Lin

last: Zhu

address: Taiping 27 road

institute: Academy of military medical sciences AMS PLA

summary:
The overall effect of VP35 on host gene expression were investigated by the differentially expressed genes (DEG) analysis in cells transfected with or without Flag-VP35
Gene expression in HepG2 cells transfected with VP35 or vector was analyzed with a gene expression microarray

overall_design: HepG2 cells were transfected with the plasmids Flag-VP35 or Flag, and each group has  three independent replicates. Forty-eight hours later, total RNA from six samples was extracted using the RNeasy mini kit (QIAgen, USA) according to the manufacturer’s protocol. After first-strand cDNA synthesis with Poly-dT primer and second-strand cDNA synthesis, the cDNA was subjected to Gene Expression Microarray analysis following the manufacturer’s protocol. The chips were scanned with a GeneChip Scanner G2565CA (Agilent).


title: RNA-seq profiles on hESC-derived macrophage

city: Chicago

first: Joyce

middle: huanhuan

last: Chen

state: IL

address: 5801 S Ellis Ave, Chicago

department: Pritzker School of Molecular Engineering

institute: Uchicago

summary: We hypothesize that the different types of macrophages have distinct responses to SARS-CoV-2 infection. To test this hypothesis, we characterized cellular responses to SARS-CoV-2 at 24h- or 48h-post SARS-CoV-2 infection in M0, M1 or M2 macrophages derived from human pluripotent stem cells using high-throughput RNA sequence and other assays

overall_design: RNA profiles on 3 types of hESC-derived macrophages with or without SARS-CoV-2 infection

first: Huanhuan

middle: J

first: Fuyu

last: Duan

first: Kui

last: Zhang


title: Modulation of the Drosophila Transcriptome by Developmental Exposure to Alcohol

city: Greenwood

first: Vijay

last: Shankar

state: South Carolina

address: 115 Milford Pines Drive

institute: Clemson University

summary: Prenatal exposure to ethanol can cause fetal alcohol spectrum disorder (FASD), a prevalent and preventable pediatric disorder. Identifying genetic risk alleles for FASD is impossible in human populations, but the Drosophila genetic model can provide insights.  We analyzed changes in genome-wide gene expression in 96 wild-derived inbred fly lines after exposure to alcohol during development. We found extensive sexual dimorphism in the effect of alcohol on gene expression along with effects on adult locomotor activity and sleep. Genetic networks associated with changes in gene expression include both protein-coding and non-coding transcripts, including a female-specific module of small nucleolar RNAs that regulate pseudouridylation of ribosomal RNA. These data support a regulatory role for non-coding elements in response to developmental alcohol exposure.

overall_design: We selected 96 lines of the Drosophila melanogaster Genetic Reference Panel (DGRP) across the range of phenotypic variation of effects of alcohol exposure on viability and developmental time (Dataset S1) and reared them on cornmeal-molasses-agar medium supplemented with10% (v/v) ethanol at 25°C, 60-75% relative humidity and a 12-hr light-dark cycle at equal larval densities. We collected two replicates of mated 3-5-day old flies (25 females and 30 males per line) for a total of 384 samples. These samples were sequenced using Illumina HiSeq and combined with previous RNASeq data on the same fly lines from Everett et al 2020 (10.1101/gr.257592.119) for a treatment vs baseline comparison.

first: Tatiana

middle: V

last: Morozova

first: Rebecca

middle: A

last: MacPherson

first: Trudy

middle: F

last: Mackay

first: Robert

last: Anholt


title: Impact of the EMT inducer ZEB1 on ER   cistrome and transcriptome in breast cancer cells

first: Didier

last: Picard


title: Viral mimicry of Interleukin-17A by SARS-COV-2 ORF8

status: Public on Mar 11 2022

city: Cleveland

first: Xin

last: Wu

email: xinwu628@gmail.com, wux2@ccf.org

state: OH

address: 9500 Euclid Ave., NE2-251

department: Cancer Biology

institute: Cleveland Clinic Lerner Research Institute

summary: SARS-CoV-2 infection triggers cytokine-mediated inflammation, leading to a myriad of clinical presentations in COVID19. The SARS-CoV-2 ORF8 is a secreted and rapidly evolving glycoprotein. Patients infected with SARS-CoV-2 ORF8-deleted variants are associated with mild disease outcomes, but the molecular mechanism this behind is unknown. Here, we report that SARS-CoV-2 ORF8 is a viral cytokine that is similar but distinct from interleukin 17A (IL-17A) as it induces stronger and broader human IL-17 receptor (hIL-17R) signaling than IL-17A. ORF8 primarily targeted blood monocytes and induced the heterodimerization of hIL-17RA and hIL-17RC, triggering robust inflammatory response. Transcriptome analysis revealed that besides its activation of the hIL-17R pathway, ORF8 upregulated gene expressions for fibrosis signaling and coagulation dysregulation. A naturally occurring ORF8 L84S variant that highly associated with mild COVID-19 showed reduced hIL-17RA binding and attenuated inflammatory responses. This study discovers SARS-CoV-2 ORF8 as a viral mimicry of IL-17 cytokine to contribute COVID-19 severe inflammation.

overall_design: After treatment with mock, ORF8, or hIL-17A, human monocytes were isolated from whole blood of male and female donors. Total RNA was isolated with RNeasy Micro Kit (74004) from QIAGEN, and the RNA-seq library was prepared using the KAPA mRNA HyperPrep Kit (KR1352), according to manufacturers’ instructions. Sequence reads were obtained using Illumina NovaSeq 6000 as well as the Illumina MiSeq systems with the help of Genomics Core in the Cleveland Clinic Foundation.

first: Jae

middle: U

last: Jung


title: RNA Sequencing of Cardiac in STZ-induced Rat model Uncovers Potential Target of Diabetic cardiomyopathy

status: Public on Mar 13 2022

city: Guangzhou

first: Yangbo

last: Xi

address: Huangpu avenue

institute: Jinan University

summary: Diabetic cardiomyopathy (DCM) is one of the major causes of heart failure in diabetic patients, but its pathogenesis remains unclear. Long non-coding RNAs (lncRNAs) are involved in the development of various cardiovascular diseases, but is little known in DCM. We build diabetic cardiomyopathy (DCM) rat model and investigated the genome-wide expression profiling of cardiac lncRNAs and mRNAs in rat model with and without DCM by RNA sequencing, to uncovers potential path mechanisms target of DCM.

overall_design: Sprague Dawley (SD) rats (8 weeks old, male) injection with a single dose of 50 mg/kg streptozocin (STZ) to build the DCM rat model. Total RNA was isolated from left ventricular tissue of SD rats at 96 days after STZ injection (Control sample, n=5 and Model sample, n=5). The RNA-sequencing were performed on the Illumina sequencing platform (HiSeqTM 2500). Further bioinformatics analysis included co-expression, ceRNA network and functional enrichment analysis of deregulated lncRNAs and mRNAs were performed.

first: Dongping

first: Jianmin

last: Xiao

first: Zhihui

last: Dong


title: Single cell analysis of MCF7-V breast carcinoma cell line stably expressing a doxycyline-inducible construct to express ZEB1 in presence of dxycycline.

summary: The epithelial to mesenchymal transition (EMT) is implicated in the metastatic spread of breast cancer cells. EMT transcription factors (TF) regulate different stages of EMT states. In breast cancers, estrogen receptor α (ERα) maintains the epithelial characteristics of breast tumors and is indispensable for efficient endocrine therapy. In this study we investigate whether and how ZEB1, an EMT-TF affects ERα signaling at early stages of EMT and metastasis. In MCF7-V cells, we performed scRNA-seq to evaluate if ZEB1 modulates cellular heterogeneity at early EMT states in breast cancer cells.

overall_design: Cells express ZEB1 in presence of 2 µg/ml doxycycline. FACS-sorted Epcam_high and EpCAM_low cell populations from MCF7-V-ZEB1 cells were subjected to scRNA-seq. 6000 cells were used for each cell population.

first: Nastaran

last: Ghahhari


title: Comparative multi-tissue profiling reveals extensive tissue-specificity in transcriptome reprogramming

status: Public on Mar 10 2022

city: Genève

first: Noushin

last: Hadadi

address: 1 rue Michel-Servet

department: Physiology and Cellular Metabolism

summary: Comparative multi-tissue RNA sequencing using a panel of organs including spleen, bone marrow, spinal cord, Quadriceps, brain, hypothalamus, ileum, liver, subcutaneous-, visceral- and brown adipose tissues

overall_design: mRNA profiles of 11 tissues of WT male 8 weeks old C57BL/6J mice

first: Martina

last: Spiljar


title: Innovative mouse models for the tumor suppressor activity of Protocadherin-10 isoforms

status: Public on Mar 12 2022

city: Zwijnaarde

first: Liesbet

last: Martens

address: Technologiepark 927

department: VIB Inflammation Research Center

country: Belgium

institute: VIB-University of Ghent

summary: Background: Nonclustered mouse protocadherin genes (Pcdh) encode proteins with a typical single ectodomain and a cytoplasmic domain with conserved motifs completely different from those of classic cadherins. Alternative splice isoforms differ in the size of these cytoplasmic domains. In view of the compelling evidence for gene silencing of protocadherins in human tumors, we started investigations on Pcdh functions in mouse cancer models. Methods: For Pcdh10, we generated two mouse lines: one with floxed exon 1, leading to complete Pcdh10 ablation upon Cre action, and one with floxed exons 2 and 3, leading to ablation of only the long isoforms of Pcdh10. In a mouse medulloblastoma model, we used GFAP-Cre action to locally ablate Pcdh10 in combination with Trp53 and Rb1 ablation. From auricular tumors, that also arose, we obtained tumor-derived cell lines, which were analyzed for malignancy in vitro and in vivo. By lentiviral transduction, we re-expressed Pcdh10 cDNAs. RNA-Seq analyses were performed on these cell families. Results: Surprisingly, not only medulloblastomas were generated in our model but also tumors of tagged auricles (pinnae). For both tumor types, ablation of either all or only long isoforms of Pcdh10 aggravated the disease. We argued that the perichondrial stem cell compartment is at the origin of the pinnal tumors. Immunohistochemical analysis of these tumors revealed different subtypes. We obtained several pinnal-tumor derived (PTD) cell lines and analyzed these for anchorage-independent growth, invasion into collagen matrices, tumorigenicity in athymic mice. Re-expression of either the short or a long isoform of Pcdh10 in two PTD lines counteracted malignancy in all assays. RNA-Seq analyses of these two PTD lines and their respective Pcdh10-rescued cell lines allowed to identify many interesting differentially expressed genes, which were largely different in the two cell families. Conclusions: A new mouse model was generated allowing for the first time to examine the remarkable tumor suppression activity of protocadherin-10 in vivo. Despite lacking several conserved motifs, the short isoform of Pcdh10 was fully active as tumor suppressor. Our model contributes to scrutinizing the complex molecular mechanisms of tumor initiation and progression upon PCDH10 silencing in many human cancers.

overall_design: 21 samples: 3 replicates of tumor-derived, protocadherin-10 (Pcdh10) ablated cell line PTD25; 3 replicates of PTD25 rescued with long isoform 4 of Pcdh10; 4 replicates of PTD25 rescued with short isoform 1 of Pcdh10; 3 replicates of tumor-derived, Pcdh10 ablated cell line PTD7; 3 replicates of PTD7 rescued with long isoform 4 of Pcdh10; 4 replicates of PTD7 rescued with short isoform 1 of Pcdh10.

first: Irene

last: Kleinberger

first: Ellen

last: Sanders

first: Katrien

last: Staes

first: Marleen

last: Van Troys

first: Shinji

last: Hirano

first: Tino

last: Hochepied

first: Kelly

last: Lemeire

first: Christophe

last: Ampe

first: Frans

last: van Roy


title: Microglial NF-κB drives tau spreading and toxicity in a mouse model of tauopathy

city: New York

first: Li

last: Gan

address: 413 East 69th Street, 9th Floor BB904

department: Helen and Robert Appel Alzheimer’s Disease Research Institute

institute: Weill Cornell Medicine


title: Comparison of Transcription Profiles of M. smegmatis overexpressing wild type and phopshorylation defective PknK

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

summary: We have shown that elevated levels of wild-type M. tuberculosis PknK (PknK Mtb), but not phosphorylation-defective PknKMtb, in Mycobacterium smegmatis cause significant retardation of growth rate and altered colony morphology (Malhotra et al., 2012).  LIX79  (WT PknK) and LIX80 (PknK K55M mutant) M. smegmatis strains will be grown in LB and induced with 0.2% acetamide for the induction of wild type or phosphorylation defective pknK gene. RNA and Protein will be isolated from cultures pelleted at times—24 h (24h) and 96 h (96 h) post induction. M. smegmatis strain LIX70 containing the empty vector will be induced at the same time-points and used as a control in hybridization. Two independent replicate experiments will be done.

overall_design: Two color Experiment,Organism: Mycobacterium smegmatis, Agilent Genotypic Technology designed Custom Mycobacterium smegmatis Whole Genome 8x15k GE Microarray (AMADID-43029)

first: Vandana

last: Malhotra


title: scRNA profiles on hESC-derived lung cells and lung-macrophage co-cultured cells

first: Joyce

last: Chen

summary: We established a co-culture model using cells derived from hPSC and studied the transcriptomes on the lung cells and  the co-cultures using scRNA-seq.

overall_design: scRNA profiles on hESC-derived lung cells and the co-cultures with M1 or M2 macrophages, respectively.

first: Huanhuan

first: Fuyu

last: Duan


title: Integrating transcription factor abundance with chromatin accessibility in human erythroid lineage commitment

city: Stanford

first: Amy

state: CA

address: 279 Campus Drive West

institute: Stanford University

summary: We present InTAC-seq, a method for simultaneous quantification of genome-wide open chromatin and intracellular protein abundance in fixed cells. Using InTAC we directly observe variation in chromatin accessibility and transcription factor motif occupancy driven by differences in transcription factor protein abundance.   By purifying bone marrow progenitor cells based on GATA1 protein expression, we establish its role in both functional and epigenetic restriction of erythroid cell identity in human hematopoiesis.

overall_design: ATAC-seq profiling of K562 cells, GM12878 cells, and primary human bone marrow progenitor cells

first: Reema

last: Baskar


title: RNA-seq analysis for zebrafish tumors driven by overexpression of human IRF4

first: Tze King

last: Tan

summary: RNA-seq analysis was performed using zebrafish primary tumors and control thymus to analyze gene expression changes after IRF4 overexpression.

overall_design: Human IRF4 gene was overexpressed under the zebrafish lck promoter.  Tumor cells were harvested from IRF4-transgenic zebrafish (lck-IRF4) with or without heterozygous p53 mutation.   Normal thymus cells were also harvested from control zebrafish (lck-mCherry).

first: Stella

last: Amanda

first: Tze

first: Takaomi

last: Sanda


title: Transcriptional regulation of cellular mechanosignaling by PREP1 (PKNOX1)

city: Milan

first: Francesco

last: Blasi

address: Via Adamello 16

institute: IFOM

summary: Mechanosignaling, initiated by the extracellular physical forces and propagated through the intracellular cytoskeletal network, triggers signaling cascades leading to processes such as embryogenesis, tissue maintenance and disease development. While signal transduction by transcription factors occurs downstream of cellular mechanosensing, nothing is known about the cell intrinsic mechanisms that can regulate mechanosignaling.  Here we show that transcription factor PREP1 (PKNOX1) regulates the expression of LINC complex proteins and mechanotransduction of YAP-TAZ. PREP1 depletion upsets the nuclear membrane protein stoichiometry rendering nuclei soft. However, reduced nuclear tension is not conveyed to the cytoplasm, since these cells display fortified actomyosin network with bigger focal adhesion complexes resulting in greater traction forces at the substratum. Intriguingly, YAP-TAZ remains localized to the cytoplasm irrespective of the substrate rigidity indicating disrupted mechanotransduction. Our data demonstrate a hitherto unknown transcriptional mechanism which regulate mechanosignaling upstream of YAP-TAZ transduction.

overall_design: Chip-seq analysis of Prep1 (pknox1) binding profiles in human cardiac mesenchymal stromal cells

first: Divya

last: Purushothaman

first: Laura

last: Bianchi

first: Dmitry

last: Penkov

first: Alessandro

last: Poli

first: Qingsen

last: Li

first: Fabrizio

last: Pennacchio

first: Francesca

last: Pramotton

first: Elena

last: Sommariva

first: Jelena

last: Vermezovic

first: Marco

last: Foiani

first: Nils

last: Gauthier

first: Paolo

last: Maiuri


title: Regulated interaction of ID2 with the anaphase-promoting complex links progression through mitosis with reactivation of cell-type-specific transcription

first: Anna

last: Lasorella

state: New York

address: 1130 St Nicholas Ave

department: Irving Cancer Research Center

institute: Columbia University

summary: Tissue-specific transcriptional activity is silenced in mitotic cells but it remains unclear whether the mitotic regulatory machinery interacts with tissue-specific transcriptional programs. We show that such cross-talk involves the controlled interaction between core subunits of the anaphase-promoting complex (APC) and the ID2 substrate. The N-terminal region of ID2 bound to core APC subunits, which formed an ID2-compatible pocket that optimally oriented ID2 in the APC-CDH1 complex. Phosphorylation of serine-5 by CDK1 prevented the association of ID2 with core APC, impaired ubiquitylation and stabilized ID2 protein at the mitosis-G1 transition leading to inhibition of basic Helix-Loop-Helix (bHLH)-mediated transcription. The serine-5 phosphomimetic mutant of ID2 that inefficiently bound core APC remained stable during mitosis, delayed exit from mitosis and reloading of bHLH transcription factors on chromatin. It also locked cells into a “mitotic stem cell” transcriptional state resembling the pluripotent program of embryonic stem cells. The substrates of APC-CDH1 SKP2 and Cyclin B1 share with ID2 the phosphorylation-dependent, D-box-independent interaction with core APC. These results reveal a new layer of control of the mechanism by which substrates are recognized by APC.

overall_design: RNA-Seq profiling of 27 samples (3 cell conditions: ID2 S5D, ID2 WT, EV; 3 time points: 0 h, 8 h, 10 h; 3 replicates each).

first: Antonio

last: Lavarone

first: Luciano

last: Garofano


title: MUC1 triggers lineage plasticity of Her2 positive mammary tumor

city: shanghai

first: Zhi

last: Pang

address: 180 fenglin road

department: Liver Cancer Institute,

institute: Zhongshan Hospital,Fudan University

summary: The aberrant overexpression of mucin 1 (MUC1) and human epidermal growth factor receptor 2 (HER2) are often observed in breast cancer. However, the role of concomitant of MUC1/HERR2 in the development of breast cancer has not been fully illustrated. Following analysis public microarray datasets that revealed a correlation of double positive of MUC1 and HER2 to a worse clinical outcome, we generated a mouse model overexpressing both Her2 and MUC1 cytoplasmic domain (MUC1-CD) to investigate their interaction in mammary carcinogenesis. Coexpression of Her2 and MUC1-CD confers growth advantage and promotes the development of spontaneous mammary tumors. Genomic analysis uncovers that enforced expression of MUC1-CD and Her2 induces mammary tumor lineage plasticity which is supported by gene reprogramming and mammary stem cell enrichment. With gain- and loss-of function strategies, we show that coexpression of Her2 and MUC1-CD was associated with down-regulation of TCA cycle genes in tumors. Importantly, the reduction of TCA cycle genes induced by MUC1-CD is is significantly connected to the poor prognosis in HER2+ breast cancer patients. In addition, MUC1 augments Her2 signaling pathway by inducing Her2/Egfr dimerization. These findings collectively demonstrate the vital role of MUC1-CD/Her2 collaboration in shaping mammary tumor landscape and highlight the prognostic and therapeutic implication of MUC1 in patients with Her2+ breast cancer.

overall_design: Two replicates for MUC1WT/Her2+ and four for MUC1CD+/Her2+. Each pair included one tumor tissue and one normal adjacent tissue.

first: Lei

last: Huang


title: Identification and Characterization of a Novel Long Noncoding RNA that Regulates Osteogenesis in Diet-Induced Obesity Mice

city: Boston

first: Zhekai

last: Hu

address: 1 Kneeland St

institute: TUFTS UNIVERSITY

summary:
Non-insulin-dependent diabetes mellitus adversely alters bone cell functions, causing decreased bone quality. Emerging evidence suggests that long noncoding RNAs (lncRNAs) participate in a vast repertoire of biological processes and play essential roles in gene expression and posttranscriptional processes.  LncRNAs are also implicated in the pathogenesis of many human diseases. To investigate the functional link the specific lncRNA and elucidate the molecular mechanisms, we assessed the structure of the bones from diet-induced obese (DIO) mice and wild type (WT) mice screened mRNAs and lncRNAs, and functionally identified a specific lncRNA.
18-week old male DIO mice (12-week high fat diet) and 18-week old male WT mice  were used for microarray assay and comparison of the gene characteristics

overall_design: Jake, Chen

first: Qisheng

last: Tu

first: Kevin

middle: Zhekai

last: HU

first: Jake

last: Chen


title: Achieving Stable X-chromosome Inactivation in Human Embryonic Stem Cells

city: Ann Arbor

first: Sundeep

last: Kalantry

state: Michigan

address: 1241 E Catherine Street

department: Human Genetics

institute: University of Michigan

summary: X-inactivation is a paradigm of epigenetic transcriptional regulation.  Human embryonic stem cells (hESCs) that harbor an inactivated X-chromosome often undergo erosion of X-inactivation upon prolonged culture.  Here, we investigate the sources of X-inactivation instability by deriving new primed pluripotent hESC lines.  We find that the composition of culture media dramatically influenced the expression of XIST lncRNA, a key regulator of X-inactivation.  hESCs cultured in a defined medium stably maintained XIST RNA coating, whereas hESCs cultured in the widely-used mTeSR1 medium lost XIST RNA expression.  We pinpointed lithium chloride in mTeSR1 as a cause of XIST RNA loss.  The addition of LiCl or inhibitors of glycogen synthase kinase 3 (GSK-3) proteins, which are inhibited by lithium, to the defined hESC culture medium impeded XIST expression. Together, these data may reconcile the observed variations in X-inactivation in hESCs and inform the culture of pluripotent stem cells for disease modeling and regenerative medicine.

overall_design: Eight samples weree analyzed by RNA-Seq. Six are female hESC line UM90-14. Two samples are human foreskin fibroblast feeders. Two samples were collected at passage 6 and six samples were collected at passage 28.

first: Marissa

last: Cloutier

first: Surinder

last: Kumar

first: Emily

last: Buttigieg

first: Laura

last: Keller

first: Brandon

last: Lee

first: Aaron

last: Williams

first: Sandra

last: Mojica-Perez

first: Indri

last: Erliandri

first: Andre

last: Monteiro Da Rocha

first: Kenneth

last: Cadigan

first: Gary

middle: D

last: Smith


title: Mitochondrial electron transport chain is necessary for NLRP3 inflammasome activation

status: Public on Mar 09 2022

first: Navdeep

middle: S

last: Chandel

address: 303 E Superior St, SQ5

department: Pulmonary and Critical Care

institute: Northwestern University

summary: The NLRP3 inflammasome is linked to sterile and pathogen-dependent inflammation, and its dysregulation underlies many chronic diseases. Mitochondria have been implicated as regulators of NLRP3 inflammasome through multiple mechanisms including generation of mitochondrial ROS. Here we report that mitochondrial electron transport chain (ETC) complexes I, II, III and V inhibitors all prevent NLRP3 inflammasome activation. Ectopic expression of Saccharomyces cerevisiae NADH dehydrogenase (NDI1) or Ciona intestinalis alternative oxidase (AOX), which can respectively complement the functional loss of mitochondrial complex I or III, without generation of ROS, rescued NLRP3 inflammasome activation in the absence of endogenous mitochondrial complex I or complex III function. Metabolomics revealed phosphocreatine (PCr), which can sustain ATP levels, as a common metabolite that is diminished by mitochondrial ETC inhibitors. PCr depletion decreased ATP levels and NLRP3 inflammasome activation. Thus, mitochondrial ETC sustains NLRP3 inflammasome activation through PCr-dependent generation of ATP but a ROS independent mechanism.

overall_design: Bulk RNAseq of mouse bone marrow derived macrophages treated with or without LPS and Piericidin A from VAV-Cre WT or NDI1 mice(n = 40, 5/group)

first: Leah

last: Billingham


title: Transcriptome (RNA-Seq) of HEK293T and HEK293TΔALKBH5ΔFTO cells

city: Pushchino

first: Ivan

last: Kulakovskiy

address: Institutskaya 4

country: Russia

institute: Institute of Protein Research

summary: We present RNA-Seq data obtained from HEK293T cells and HEK293T cells with ALKBH5 and FTO demethylases double knockout (HEK293TΔALKBH5ΔFTO), showing m6A-dependent transcriptome alterations.

overall_design: The RNA-Seq libraries were constructed from cytoplasmic RNA w/o polyA-selection. Three independent biological replicates were made for HEK293T and double knockout cells.

first: Egor

last: Smolin

first: Andrey

last: Buyan

first: Dmitry

middle: N

last: Lyabin

first: Irina

last: Eliseeva


title: A multi-level investigation of the genetic relationship between endometriosis and ovarian cancer histotypes

status: Public on Mar 07 2022

city: Los Angeles

first: Kate

last: Lawrenson

address: 8700 Beverly Blvd.

institute: Cedars-Sinai Medical Center

summary: Endometriosis is associated with increased risk of epithelial ovarian cancers (EOCs). Using data from large endometriosis and EOC genome-wide association meta-analyses we estimate the genetic correlation and evaluate the causal relationship between genetic liability to endometriosis and EOC histotypes, and identify shared susceptibility loci. We estimate a significant genetic correlation (rg) between endometriosis and clear cell (rg=0.71), endometrioid (rg=0.48) and high-grade serous (rg=0.19) ovarian cancer, associations supported by Mendelian randomization analyses. Bivariate meta-analysis identify 28 loci associated with both endometriosis and EOC, including 19 with evidence for a shared underlying association signal. Differences in the shared risk suggest different underlying pathways may contribute to the relationship between endometriosis and the different histotypes. Functional annotation using transcriptomic and epigenomic profiles of relevant tissues/cells highlights several target genes. This comprehensive analysis reveals profound genetic overlap between endometriosis and EOC histotypes with valuable genomic targets for understanding the biological mechanisms linking the diseases.

overall_design: H3K27ac ChIP-seq of two endometriosis tissues and two stroma tissues; ATAC-seq of five Fallopian tube samples (from three different tissues), one clear cell and ten high-grade serous ovarian cancers.

first: Sally

last: Mortlock

first: Rosario

middle: I

last: Corona

first: Pik

last: Kho

first: Paul

last: Pharoah

first: Ji

middle: H

last: Seo

first: Matthew

middle: L

last: Freedman

first: Simon

last: Gayther

middle: T

last: Siedhoff

first: Peter

last: Rogers

first: Ronald

last: Leuchter

first: Christine

last: Walsh

first: Ilana

last: Cass

first: Beth

middle: Y

last: Karlan

first: B

last: Rimel

first: Grant

middle: W

last: Montgomery

first: Siddhartha

middle: P

last: Kar


title: Transcriptome changes associated with boron applications in pear fruit

status: Public on Mar 08 2022

city: 扬州

first: 东贺

last: 刘

address: wenhuilu

department: Yuanzhi College

institute: yzau

summary: To uncover the mechanisms underlying pear fruit response to boron application, a comprehensive transcriptome analysis was performed. Boron application significantly induced expression of sorbitol metabolism and sucrose metabolism genes.Boron application also increased the expression of starch degradation, fatty acid synthesis, IAA  degradation, GA synthesis and inhibit the expression of ethylene synthesis gene.

overall_design: mRNA sequencing of pear fruit  with boron application

first: Xiao

last: Liu

first: Chunlei

last: Wang

first: Donghe


title: Next Generation Sequencing of SARS-CoV-2 infected lung epithelial cells derived from iPSC

first: Rajarshi

last: Pal

address: CCAMP, NCBS

institute: Eyestem research

summary: We present evidence on how a lung epithelial cell culture system based on human induced pluripotent stem cells (hiPSC) could emerge as a relevant and sensitive platform for modelling SARS-CoV-2 infection. In order to develop a human model system, we differentiated hiPSC into lung epithelial lineage (airway and alveolar cells) through a three-step protocol. De novo generated cells were authenticated by spatiotemporal expression of stage specific markers including SOX2, FOXJ1 and CC10 in proximal cells and SOX9, FOXP2, SFTPC, MUC5AC, and CC10 in distal cells. Further we showed upregulation of ACE2 and TMPRSS2, the two proteins responsible for SARS-CoV-2 binding and invasion into the host lung in our iPSC-derived proximal and distal lung epithelial cells. In order to find out whether our in-house created lung cell culture system was permissive to SARS-CoV-2 infection, two viral doses representing two multiplicities of infections (MOIs) was tested. Plaque assay, RT-PCR, and ICC results demonstrated that the virus was able to enter and replicate inside these cells in a reproducible manner. Further, transcriptomics (RNA seq) data uncovered a robust epithelial cell-specific response to virus infection including perturbation of metabolic processes, disruption in alveolar and airway maturation program, in addition to the well-known upregulation of antiviral defense and immune responses.

overall_design: We generated lung epithelial cells from induced pluripotent stem cells and infected them with SARS-CoV-2 virus at different MOI and different time points. RNA was isolated and sequenced from the control uninfected and SARS-CoV-2 infected cells. We tried to understand the CoVID-19 disease pathology, inflammatory profile, lung structural and functional patterns post infection.


title: Microglial NF-κB drives tau spreading and toxicity in a mouse model of tauopathy [bulk RNA-Seq]

first: Li

last: Gan

summary: Activation of microglia is a prominent pathological feature in tauopathies, including Alzheimer’s disease. How microglia activation contributes to tau toxicity  remains largely unknown. Here we show that nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) signaling, activated by tau, drives microglial-mediated tau propagation and toxicity. Constitutive activation of microglial NF-κB exacerbated, while inactivation diminished, tau seeding and spreading in young PS19 mice. Inhibition of NF-B activation enhanced the retention while reduced the release of internalized pathogenic tau fibrils from primary microglia and rescued microglial autophagy deficits. Remarkably, inhibition of microglial NF-κB in aged PS19 mice rescued tau-mediated learning and memory deficits, restored overall transcriptomic changes while increasing neuronal tau inclusions. Single cell RNA-seq revealed that tau-associated disease states in microglia were diminished by NF-B inactivation and further transformed by constitutive NF-B activation. Our study establishes a central role for microglial NF-B signaling in mediating tau spreading and toxicity in tauopathy.

overall_design: bulk RNAseq of primary microglia treated with vehicle or tau fibrils; adult microglia isolated from 11-month-old male non-transgenic control mice and PS19 mice; primary microglia with endogenous IKKβ expression or IKKβCA overexpression and primary microglia with wildtype IKKβ expression or deletion of IKKβ; cortical tissues from Ikbkb+/+, Ikbkb-/-, IkbkbWT, IkbkbCA, Ikbkb+/+;P301S+ and Ikbkb-/-;P301S+ male mice

first: Chao

last: Fan

first: Rabia

middle: R

last: Khawaja

first: Bangyan

first: Lihong

last: Zhan

first: Lay

last: Kodama

first: Marcus

last: Chin

first: Yaqiao

last: Li

first: David

last: Le

first: Yungui

last: Zhou

first: Carlo

last: Condello

first: Lea

last: Grinberg

first: William

last: Seeley

first: Bruce

last: Miller

first: Sue-Ann

last: Mok

first: Jason

middle: E

last: Gestwicki

first: Ana

last: Cuervo

first: Wenjie

last: Luo


title: A T-cell resilience model associated with response to immunotherapy in multiple tumor types

status: Public on Mar 05 2022

city: Bethesda

first: Peng

last: Jiang

state: Maryland

address: 41 Center Drive

department: Center for Cancer Research

institute: National Cancer Institute

summary: Despite breakthroughs in cancer immunotherapy, most tumor-reactive T cells cannot persist in solid tumors due to an immunosuppressive environment. We developed Tres (Tumor-resilient T cell, https://resilience.ccr.cancer.gov), a computational model and web server that utilizes single-cell transcriptomic data to identify signatures of T cells that are resilient to immunosuppressive signals, such as TGFβ, TRAIL, and PGE2. Analyzing T-cell transcriptomic data from 72 pretreatment and 84 pre-manufacture patient samples, Tres reliably predicts the clinical effectiveness of immune checkpoint blockade or adoptive cell transfer in melanoma, lung, and B-cell malignancies. Further, Tres identified FIBP, whose functions are largely unknown without previous links to T cells, as the top negative marker of tumor-resilient T cells across many cancers. FIBP knockouts in murine and human CD8+ T cells significantly enhanced T-cell mediated cancer-killing in invitro co-cultures. Further, Fibp knockout in murine T cells potentiated the in-vivo efficacy of adoptive cell transfer by limiting cholesterol metabolism, which otherwise inhibits effector T-cell function. These results demonstrate Tres’s utility in identifying clinical biomarkers of T-cell effectiveness and potential therapeutic targets for immunotherapies in solid tumors.

overall_design: Examination of Fibp and Rosa26 (control) knockouts in Pmel1 TCR T cells. Each knockout condition has three samples from three independent CRISPR guide RNAs. One parental sample is also included.

first: Yu

last: Zhang


title: Enhanced anti-cancer effects of conditioned medium from hypoxic human adult dermal fibroblasts on cervical cancer cells [dataset 2]

status: Public on Mar 04 2022

city: Seoul

first: Kyu-Hyun

last: Han

address: 81 Irwon-ro, Gangnam-gu

department: Division of Vascular Surgery

institute: Samsung Medical Center, Sungkyunkwan University School of Medicine

summary: Hypoxia regulates fibroblast function by changing intracellular signaling and secretion factors, which influences the states of nearby cells. In this work, we investigated the effects of conditioned medium (CM) from human adult dermal fibroblasts (HDFs) cultured in normoxic and hypoxic conditions on cervical cancer (HeLa) cells. The HeLa cells showed decreased cell viability, in-creased apoptosis, and cell cycle arrest in response to CM from hypoxic-cultured HDFs (H-CM) compared with CM from normoxic-cultured HDFs (N-CM). Among the proteins up-regulated (> 2-fold) in H-CM compared with N-CM, LTBR decreased the viability of HeLa cells. Among the intracellular proteins down-regulated (> 2-fold) in HeLa cells treated with H-CM compared with N-CM, the most enriched biological process GO term and KEGG pathway were protein deubiq-uitination and hsa05166:HTLV-I infection, respectively. In the protein–protein interaction net-work of intracellular proteins with altered expression (> 2-fold), 1 up-regulated (TNF) and 8 down-regulated (ESR1, MCL1, TBP, CD19, LCK, PCNA, CHEK1, and POLA1) hub proteins were defined. Among the down-regulated hub proteins, the most enriched biological process GO term and KEGG pathway were leading strand elongation and hsa05166:HTLV-I infection, respectively. This study reveals that H-CM had enhanced anti-cancer effects on cervical cancer cells compared with N-CM, and it induced intracellular signaling patterns related to those enhanced anti-cancer effects.

overall_design: Human adult dermal fibroblasts (HDFs) were cultured in 21% O2 as the normoxic condition and 1% O2 as the hypoxic condition. Conditioned medium from normoxic HDFs (N-CM) and hypoxic HDFs (H-CM) were harvested, and treated to HeLa cells for 24 hours. Up- and down-regulated intracellular proteins (> 2-fold) in HeLa cells treated with H-CM compared with N-CM were analyzed using Fullmoon Signaling explorer array.

first: Ae-Kyeong

last: Kim

first: Dong-ik


title: Enhanced anti-cancer effects of conditioned medium from hypoxic human adult dermal fibroblasts on cervical cancer cells [dataset 1]

overall_design: Human adult dermal fibroblasts (HDFs) were cultured in 21% O2 as the normoxic condition and 1% O2 as the hypoxic condition. Conditioned medium from normoxic HDFs (N-CM) and hypoxic HDFs (H-CM) were harvested, and up- and down-regulated proteins (> 2-fold) in H-CM compared with N-CM were investigated using RayBiotech Human L1000 Array.


title: Enhanced anti-cancer effects of conditioned medium from hypoxic human adult dermal fibroblasts on cervical cancer cells

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

overall_design: Refer to individual Series


title: Identification of genes involved in germline regeneration in adult undifferentiated spermatogonia following a low dose busulfan treatment

city: CLAYTON

first: Robin

middle: Mark

last: Hobbs

state: VIC

address: 27-31 Wright Street

department: Centre for Reproductive Health

institute: Hudson Institute of Medical Research

summary: Mammalian spermatogenesis and male fertility are sustained by a small population of spermatogonial stem cells (SSCs) in the testis. In particular, germ cells are highly sensitive to chemotherapies and radiation, placing male cancer patients at a higher risks of treatment-induced infertility. While SSCs surive the treatment may restore the germline and ferility, it remains unknown how SSCs mediate the regenerative responses to re-establish the germline. In this study, we used a mouse model of chemotherapy-induced germline damage and recovery to identify differentially expressed genes in homeostatic (from untreated control mice) versus regenerative SSCs (busulfan-treated mice) and potential effectors driving the initiation of regeneration.

overall_design: Undifferentiated spermatogonia were isolated by flow sorting from 4 adult untreated control and 4 busulfan treated mice at day 10.

middle: M

first: Hue

last: La

first: Jinyue

last: Liao

first: Julien

last: Legrand

first: Fernando

middle: J

last: Rossello

first: Ai-Leen

last: Chan

first: Antonella

last: Papa

first: TinLap

last: Lee


title: Transcriptome profiles of Streptomyces coelicolor A3(2) wild type treated with kanamycin and iron

first: Joon-Sun

last: Choi

state: Not US or Canada

address: Seoul National University

institute: Seoul National University

summary: We determine genes that responsible for iron induced resistance to kanamycin in Streptomyces coelicolor. Iron acts as a inducing agent for resistance to bactericidal antibiotics with concentration dependent manner. Identification of iron-dependent differentially expressed genes in wild-type by RNA-seq identified more than 100 genes. This series encompasses the RNA-seq data of our study.

overall_design: Transcriptome profiles from combination of kanamycin/iron-treated or non-treated wild-type were obtained using Illumina NovaSeq. RNA samples were prepared in biologically independent duplicates.

first: Yeong-Jae

last: Seok

first: Jung-Hye

last: Roe


title: SIFT-seq: VDJ and scRNA-seq of T cells targeting public neoantigens

status: Public on Mar 03 2022

first: Friederike

last: Dündar

address: 1300 York Ave

department: Physiology & Biophysics

institute: Weill Cornell Medicine

summary: We developed a modular, high-throughput discovery platform to simultaneously test whether Mut PIK3Ca is immunogenic and to retrieve paired a/b TCR gene sequences that confer specificity to this NeoAg. This method, termed Stimulation Induced Functional TCR sequencing (SIFT-seq), combines single-cell (sc) TCR V(D)J and transcriptome sequencing. Here, microwell cultures of in vitro stimulated T cells with confirmed neoantigen-specific recognition are selected for SIFT-seq. Matched aliquots of selected wells are acutely stimulated with autologous antigen-presenting cells presenting WT or Mut PI3Ka and the transcriptomic profile of individual clonotypes is assessed to identify neoantigen-specific T cells and retrieve their TCR gene sequences.

overall_design:
Naïve CD8+ T cells from healthy donor samples were stimulated in vitro with mutated PIK3CA. Following a qPCR screen to identify mutation-specific upregulation of inflammatory transcript, positive wells were selcted for SIFT-seq. Matched aliquots were restimulated acutely with antigen-presenting wells expressing WT or mutated PIK3CA and subject to single-cell RNA-seq and V(D)J immunoprofiling using the 10x genomics platform. All clonotypes associated with a mutation-specific activation signature were identified and their TCR gene sequences were retrieved. Candidate TCR gene sequences were retrovirally transferred to open-repertoire T cell to confirm mutation-specific recognition.
Note from submitter: The FASTQ files are not supplied because the data was generated from human patients/donors (patient privacy).

first: Smita

last: Chandran

first: Christopher

middle: A

last: Klebanoff