title: Transcriptomic analysis of pals-25(icb98gf) mutants in C. elegans

status: Public on Sep 02 2022

city: London

first: Michalis

last: Barkoulas

address: SAF Building, South Kensington

institute: Imperial College London

summary: We used RNA-seq to identify gene expression changes in C. elegans pals-25(icb98gf) mutants

overall_design: Comparative gene expression of pals-25(icb98) to wild-type animals at the L4 life stage

first: Manish

last: Grover


title: Epigenome analysis of placental tissue sample from pregnant women with Sickle Cell Disease (SCD) and pregnant women without SCD.

status: Public on Sep 03 2022

city: Campinas

first: Pedro

last: Cruz

address: Av Candido Rondon 400

country: Brazil

institute: UNICAMP

type: Methylation profiling by genome tiling array

summary: Pregnancy in Sickle Cell Disease (SCD) women is associated to increased risk of clinical and obstetrical complications. Placentas from SCD pregnancies can present increased abnormal findings, which may lead to placental insufficiency, favoring adverse perinatal outcome. These placental abnormalities are well known and reported, however little is known about the molecular mechanisms, such as epigenetics. Thus, our aim was to evaluate the DNA methylation profile in placentas from women with SCD (HbSS and HbSC genotypes), compared to uncomplicated controls (HbAA). We included in this study 11 pregnant women with HbSS, 11 with HbSC and 21 with HbAA genotypes. Illumina Methylation EPIC BeadChip was used to assess the whole placental DNA methylation. Pyrosequencing was used for array data validation and qRT-PCR was applied for gene expression analysis. Our results showed high frequency of hypermethylated CpGs sites in HbSS and HbSC groups with 73.5% and 76.2% respectively, when compared with the control group. Differentially methylated regions (DMRs) also showed an increased hypermethylation status for the HbSS (89%) and HbSC (86%) groups, when compared with the control group methylation data. DMRs were selected for methylation validation (4 DMRs-HbSS and 3 DMRs the HbSC groups) and after analyses three were validated in the HbSS group, and none in the HbSC group. The gene expression analysis showed differential expression for the PTGFR (-2.97-fold) and GPR56 (3.0-fold) genes in the HbSS group, and for the SPOCK1 (-2.40-fold) and ADCY4 (1.80-fold) genes in the HbSC group. Taken together, these data strongly suggest that SCD (HbSS and HbSC genotypes) can alter placental DNA methylation and lead to gene expression changes. These changes possibly contribute to abnormal placental development and could impact in the clinical course, especially for the fetus, possibly leading to increased risk of abortion, fetal growth restriction (FGR), stillbirth, small for gestational age newborns and prematurity.

overall_design: Bisulphite converted DNA from the 23 samples were hybridised to the Illumina Infinium MethylationEPIC Assay.

first: Gislene

middle: P

last: Gil

first: Mônica

middle: B

last: Melo


title: ADAM17-mediated EGFR ligand shedding  directs macrophage-promoted cancer cell  invasion

city: Copenhagen

first: Marie

last: Kveiborg

state: non-US Resident

address: Ole Maaløes Vej 5

country: Denmark

institute: University of Copenhagen

type: Expression profiling by high throughput sequencing

summary: Macrophages in the tumor microenvironment have a substantial impact on tumor progression. Depending on the signaling environment in the tumor, macrophages can either support or constrain tumor progression. It is therefore of therapeutic interest to identify the tumor-derived factors that control macrophage education. With this aim, we correlated the expression of A Disintegrin and Metalloproteinase (ADAM) proteases, which are key mediators of cell-cell signaling, to the expression of protumorigenic macrophage markers in human cancer cohorts. We identified ADAM17, a sheddase upregulated in many cancer types, as a protein of interest. Depletion of ADAM17 in cancer cell lines reduced the expression of several protumorigenic markers in neighboring macrophages in vitro as well as in mouse models. Moreover, ADAM17–/– educated macrophages demonstrated a reduced ability to induce cancer cell invasion. Using mass spectrometry–based proteomics and ELISA, we identified HB-EGF and AREG, shed by ADAM17 in the cancer cells, as the implicated molecular mediators of macrophage education. Additionally, RNA-Seq and ELISA experiments revealed that ADAM17-dependent HB-EGF ligand release induced the expression and secretion of CXCL chemokines in macrophages, which in turn stimulated cancer cell invasion. In conclusion, we provide evidence that ADAM17 mediates a paracrine EGFR-ligand-chemokine feedback loop, whereby cancer cells hijack macrophages to promote tumor progression.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for bone marrow derived macrophages co-cultured with 4T1 wt or 4T1 ADAM17 knock-out cells for 48h; Seq was performed by BGI

first: Sebastian

last: Gnosa


title: Cell type profiling in salamanders identifies innovations in vertebrate forebrain evolution[st46]

city: New York

first: Maria

middle: ANTONIETTA

last: Tosches

address: 1212 Amsterdam Ave

country: USA

institute: Columbia University

summary: The evolution of advanced cognition in vertebrates is associated with the expansion of specialized areas in the forebrain (the six-layered neocortex in mammals and the dorsal ventricular ridge in birds and reptiles). Both areas exhibit complementary higher order brain functions, but it remains debated whether they developed convergently, or descended from a brain region already present in the last common ancestor of amniotes. To reconcile these views, we investigated the development, molecular identity, and connectivity of telencephalic neuron types in the Spanish newt, Pleurodeles waltl. These reveal that major neuron classes are conserved in tetrapods. Additionally, a glutamatergic neuron type in the ventral pallium displays key characteristics similar to the reptilian dorsal ventricular ridge (aDVR) and the mammalian piriform cortex (PC), suggesting that brain areas for advanced cognition evolved independently in mammals and reptiles and birds.

overall_design: scRNAseq of Pleurodeles Waltl telencephalon

middle: A

first: Jamie

last: Woych

first: Alonso

middle: O

last: Gurrola

first: Astrid

last: Deryckere

first: Eliza

last: Jaeger

first: Eli

last: Gumnit


title: Cell type profiling in salamanders identifies innovations in vertebrate forebrain evolution

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

overall_design: Refer to individual Series


title: Cell type profiling in salamanders identifies innovations in vertebrate forebrain evolution [st50]

last: Ortega Gurrola


title: Cell type profiling in salamanders identifies innovations in vertebrate forebrain evolution[st41]


title: Cell type profiling in salamanders identifies innovations in vertebrate forebrain evolution [st36]


title: Cell type profiling in salamanders identifies innovations in vertebrate forebrain evolution III


title: Cell type profiling in salamanders identifies innovations in vertebrate forebrain evolution II


title: Cell type profiling in salamanders identifies innovations in vertebrate forebrain evolution IV


title: Resistance to targeted therapies in the brain tumor microenvironment is not drive by genetic mutations

city: West Haven

first: Francesc

last: Lopez

state: CT

department: Department of Genetics

institute: Yale University

summary: The brain is a major sanctuary site for metastatic lung cancer cells that evade systemic therapies. We performed pharmacological, biological, and molecular studies to identify the functional link between drug resistance and central nervous system (CNS) relapse in late-stage EGFR mutant non-small cell lung cancer, which frequently progresses in the brain even when treated with the brain penetrant EGFR inhibitor osimertinib. Despite widespread osimertinib distribution in vivo, the brain microvascular tumor microenvironment (TME) is associated with the persistence of malignant cell sub-populations which are poised to further proliferate in the brain as osimertinib-resistant lesions over time. Cellular and molecular features of this poised state are commonly regulated through RhoA signaling, which potentiates the outgrowth of disseminated tumor cells on osimertinib treatment, preferentially in response to extracellular laminin and in the brain. Thus, we identify pre-existing and adaptive features of metastatic and drug resistant cancer cells, which are enhanced by RhoA and the brain TME during the evolution of osimertinib resistant disease.

overall_design: Whole-exome sequencing performed on C2 and R2 cells growing in culture and  R2 cells growing in the brain at resistance

first: Sally

middle: J

last: Adua

last: Lopez-Giraldez

first: Don

middle: X

last: Nguyen


title: The brain tumor microenvironment primes metastatic cells for resistance to targeted therapies

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Species specific RNA-seq performed in control (C2) and resistant (R2) human cell populations growing in mouse brain when treated with vehicle or osimertinib. There are 6 in vivo sample groups each with 3-4 reps. The same control and resistant cell populations growing in culture and treated with vehicle or osimertinib were also sent for sequencing (3 reps each).

first: Zongzhi

last: Liu


title: Cell type profiling in salamanders identifies innovations in vertebrate forebrain evolution I


title: Cell type profiling in salamanders identifies innovations in vertebrate forebrain evolution [E4]


title: Transcriptome and chromatin accessibility analyses of UHRF1 KO osteosarcoma cell lines

city: Irvine

first: Claudia

last: Benavente

state: CA

address: 839 Medical Sciences Ct, Sprague Hall 108

institute: University of California, Irvine

type: Genome binding/occupancy profiling by high throughput sequencing


title: Transcriptome analysis of UHRF1 KO osteosarcoma cell lines

summary: We used UHRF1 knockout cell lines and matched controls in human osteosarcoma cell lines to investigate the role of UHRF1 in tumorigenesis. UHRF1 loss drastically decreased cell proliferation and decreased migration, invasion, and metastasis.

overall_design: mRNA profiles from non-targeting CRISPR sgRNA and UHRF1-targeting CRISPR sgRNA osteosarcoma cell lines were generated by deep sequencing using Illumina HiSeq 4000.

first: Jie

last: Wu


title: Chromatin accessibility analysis of UHRF1 KO osteosarcoma cell lines

overall_design: ATAC-seq profiles from non-targeting CRISPR sgRNA and UHRF1-targeting CRISPR sgRNA osteosarcoma cell lines were generated by deep sequencing using Illumina HiSeq 4000.


title: Genome-wide maps of chromatin state in human primary CAR-T cells

city: Stanford

first: Julia

last: Belk

state: California

address: 450 Serra Mall

institute: Stanford University


title: Multidimensional analysis and therapeutic development using patient iPSC-derived disease models of Wolfram syndrome

status: Public on Sep 01 2022

city: Saint Louis

first: Fumihiko

last: Urano

state: Missouri

address: 660 South Euclid Ave

institute: Washington University School of Medicine

summary: Wolfram syndrome is a rare genetic disorder largely caused by pathogenic variants in the WFS1 gene and manifested by diabetes mellitus, optic nerve atrophy, and progressive neurodegeneration. Recent genetic and clinical findings have revealed Wolfram syndrome as a spectrum disorder. Therefore, a genotype-phenotype correlation analysis is needed for diagnosis and therapeutic development. Here, we focus on the WFS1 c.1672C>T, p.R558C variant which is highly prevalent in the Ashkenazi-Jewish population. Clinical investigation indicates that subjects carrying the homozygous WFS1 c.1672C>T, p.R558C variant show mild forms of Wolfram syndrome phenotypes. Expression of WFS1 p.R558C is more stable compared to the other known recessive pathogenic variants associated with Wolfram syndrome. Human induced pluripotent stem cell (iPSC)-derived islets (SC-islets) homozygous for WFS1 c.1672C>T variant recapitulate genotype-related Wolfram syndrome phenotypes. Enhancing residual WFS1 function by a combination treatment of chemical chaperones mitigates detrimental effects caused by the WFS1 c.1672C>T, p.R558C variant and increases insulin secretion in SC-islets. Thus, the WFS1 c.1672C>T, p.R558C variant causes a mild form of Wolfram syndrome phenotypes, which can be remitted with a combination treatment of chemical chaperones. We demonstrate that our patient iPSC-derived disease model provides a valuable platform for further genotype-phenotype analysis and therapeutic development for Wolfram syndrome.

overall_design: Single cell RNAseq of SC-islets derived from Wolfram syndrome iPSCs

first: Rie

last: Kitamura

first: Kristina

middle: G

last: Maxwell

first: Jeffrey

middle: R

last: Millman


title: Resistance to targeted therapies in the brain tumor microenvironment occurs through selection of cells with distinct transcriptomic profiles

overall_design: scRNA-sequencing performed on PC9, PC9-BrM4, C2, and R2 cells growing in culture


title: T Cell Reinvigoration upon ACK1/TNK2 inhibition Overcomes Immune Resistance

city: St Louis

first: Tiandao

last: Li

state: MO

address: 4444 Forest Park Ave

institute: Washington University

summary: Solid tumors are highly refractory to immune checkpoint blockade (ICB) therapies due to the functional impairment of the effector T cells and its trafficking back to the tumor. The T cell activation is negatively regulated by C-terminal Src kinase (CSK), however, the exact mechanism of CSK’s T cell-restraining activity remains unknown. Here, we show that the primeval oncogenic tyrosine kinase, ACK1 dampens T-cell response by augmenting CSK activity through a novel Tyr18-phosphorylation. Ack1/Tnk2-knockout mice exhibited a loss of CSK Tyr18-phosphorylation and activation of CD8+ and CD4+ T cells, compromising ICB-resistant tumor growth. Further, ICB-treated Castration-resistant prostate cancer (CRPC) patients revitalized ACK1/pY18-CSK signaling, revealing it to be the critical molecular mechanism for ICB insensitivity. Consistently, ICB-resistant tumor growth was suppressed upon treatment with a new class of ACK1 small-molecule inhibitor, (R)-9b. Interestingly, (R)-9b caused increase in leukocyte attractant, CXCL10 in cancer cells, thus navigating newly activated T cells to the tumors, creating a `self-sabotaging loop’. Overall, harnessing unique dichotomous mode of ACK1 that controls immune response of the T cells, and cytokine levels in tumor microenvironment, provides an unprecedented opportunity to sensitize immune-resistance.

overall_design: C4-2B cancer cells were treated overnight with 1µM (R)-9b (overnight) and RNA was prepared from these cells.

first: Nupam

last: Mahajan


title: A double negative thymocyte specific enhancer augments Notch1 signaling to direct early T cell progenitor expansion,  lineage restriction and b-selection.

city: Charlestown

first: Katia

last: Georgopoulos

state: MA

address: 13th street

department: CBRC

institute: Harvard Medical School

summary: T-cell differentiation requires Notch1 signaling. Here we show that an enhancer upstream of Notch1 active in double-negative (DN) thymocytes is responsible for raising Notch1 signaling intra-thymically.  This enhancer is required to expand multipotent progenitors intra-thymically while delaying early differentiation until lineage restrictions are established. Early thymic progenitors lacking the enhancer show accelerated differentiation through the DN stages and increased frequency of B-, ILC-, and NK-cell differentiation. Transcription regulators for T-cell lineage restriction and commitment are expressed normally, but ILC- and NK-cell gene expression persists after T-lineage commitment and TCR V-DJ recombination, Cd3 expression and -selection are impaired. This Notch1 enhancer is inactive in double-positive (DP) thymocytes. Its aberrant reactivation at this stage in Ikaros mutants is required for leukemogenesis. Thus, the DN-specific Notch1 enhancer harnesses the regulatory architecture of DN and DP thymocytes to achieve carefully orchestrated changes in Notch1 signaling required for early lineage restrictions and normal T-cell differentiation.

overall_design: 34 bulk RNAseq, 4 single-cell RNAseq

first: Mariko

last: Kashiwagi


title: Single-cell RNA sequencing of Ddr2 slie/slie and littermate control

city: Dallas

first: Alec

last: Bancroft

state: Texas

address: 6000 Harry Hines Blvd

department: Surgery

institute: University of Texas Southwestern Medical Center

summary: Single-cell RNA sequencing was performed on injured and uninjured hindlimb tissue of Ddr2 slie/slie mice and littermate controls following 30% total body surface area burn and Achilles’ tenotomy injury to determine the role of DDR2 in heterotopic ossification and aberrant differentiation during wound healing.

overall_design: Ddr2 slie/slie mice (n=2) and littermate controls (n=2) were placed under isoflurane anesthesia and provided subcutaneous buprenorphine analgesic prior to 30% total body surface area burn and concurrent left Achilles’ tenotomy. Tissue from the left injury site, which includes the Achilles’ tendon, from the tendon-muscular junction at the gastrocnemius muscle and calcaneal enthesis, and surrounding tissue posterior to the tibia, was dissected one week following injury. Right limb tissue was also harvested to serve as the contralateral limb control. Injured left limb tissue within each group was combined for processing, as were right limbs for each group. Tissue was digested and processed into a single-cell suspension for sequencing. Four samples were submitted for single-cell RNA sequencing including Ddr2 slie/slie injured tissue, Ddr2 slie/slie uninjured tissue, littermate control injured tissue, and littermate control uninjured tissue.

first: Chase

last: Pagani

middle: C

first: Spencer

last: Barnes

first: Benjamin

last: Levi


title: The oncometabolite D-2HG alters T cell metabolism to impair CD8+ T cell function

city: boston

first: Giulia

last: Notarangelo

state: Massachusetts

address: 45 shattuck street

summary: The tumor-derived oncometabolite D-2HG impairs CD8+ T cell function through a novel metabolic target

overall_design: We performed RNA-seq profiling on CD8+ T cells activated for 6 hours in the presence of D-2HG, L-2HG or left untreated (N=3).

first: Kiran

last: Kurmi

first: Christophe

last: Benoist

first: Marcia

last: Haigis


title: PI3K/AKT signaling allows for MAPK/ERK pathway independency mediating dedifferentiation-driven treatment resistance in melanoma

city: Freiburg

first: Patrick

last: Metzger

address: Breisacher Str. 153

department: Institute for Medical Bioinformatics and Systems Medicine

country: Germany

institute: University Hospital Freiburg

summary: Current therapeutic management of advanced melanoma patients largely depends on their BRAF mutation status. However, the vast heterogeneity of the tumors hampers the success of therapies targeting the MAPK/ERK pathway alone. Dissecting this heterogeneity will contribute to identifying key players in the oncogenic progression to tailor more effective therapies. We performed a comprehensive molecular and phenotypic characterization of a panel of patient-derived BRAFV600E-positive melanoma cell lines. Transcriptional profiling was used to identify groups of coregulated genes whose expression relates to an increased migratory potential and a higher resistance. A decrease in sensitivity to MAPK/ERK pathway inhibition with vemurafenib or trametinib corresponded with an increasing quiescence and migratory properties of the cells. This was accompanied by the loss of transcriptional signatures of melanocytic differentiation, and the gain of stem cell features that conferred highly-resistant/mesenchymal-like cells with increased xenobiotic efflux capacity. Nevertheless, targeting of the implicated ABC transporters did not improve the response to vemurafenib, indicating that incomplete BRAF inhibition due to reduced drug uptake is not a main driver of resistance. Rather, indifference to MAPK/ERK pathway inhibition arose from the activation of compensatory signaling cascades. The PI3K/AKT pathway in particular showed a higher activity in mesenchymal-like cells, conferring a lower dependency on MAPK/ERK signaling and supporting stem-like properties that could be reverted by dual PI3K/mTOR inhibition with dactolisib. In case of MAPK/ERK independency, therapeutic focus may be shifted to the PI3K/AKT pathway to overcome late-stage resistance in melanoma tumors that have acquired a mesenchymal phenotype.

overall_design: 4 different patient-derived melanoma cell lines with 3 replicates each were characterized. All carry the BRAF V600E mutation

first: Eyleen

last: Corrales

first: Ella

last: Levit-Zerdoun

first: Ralf

last: Mertes

first: Ariane

last: Lehmann

first: Julia

last: Münch

first: Steffen

last: Lemke

first: Silke

last: Kowar

first: Melanie

last: Börries


title: Neuropilin-2 Promotes the Development of Neuroendocrine Prostate Cancer

city: Spokane

first: Boyang

last: Wu

state: Washington

address: 412 E. Spokane Falls Blvd

institute: Washington State University

summary: The overall goal of this study was to compare gene expression profiles in control and NRP2-knockdown prostate cancer cells.

overall_design: Stable silencing of NRP2 in enzalutamide-resistant human prostate cancer cell lines, C4-2B ENZR, was established using shRNA-expressing lentiviral infection followed by antibiotic selection. Two samples were analyzed by RNA-Seq.


title: Triplexes are Dynamic DNA Secondary Structures Formed in vivo and Linked to Genome Instability [END-seq]

city: Shanghai

first: Wei

state: Shanghai

address: 320 yueyang road

department: Center for Excellence in Molecular Cell Science

country: China

summary: Numerous indirect, genetic approaches in various experimental systems have implicated dynamic alternative non-B DNA structures in human physiology and disease. Nevertheless, direct detection of dynamic DNA structures in vivo remains a challenge. To address this problem, we developed a new methods to visualize ssDNA containing alternative DNA structures. We described an uncharted landscape of dynamic alternative DNA structures formed by DNA cruciform and DNA triplexes (H-DNA) that contribute to genome instability.

overall_design: We used a combinatorial approach of END-seq, S1-END-seq and P1-END-seq to detect alternative DNA structures in vivo in human cells

first: Gabriel

last: Matos-Rodrigues

first: Niek

last: van Wietmarschen

first: Veenu

last: Tripathi

first: Natasha

last: Koussa

first: Raphael

last: Pavani

first: Elsa

last: Callen

first: William

last: Nathan

first: Frida

last: Belinky

first: Ashraf

last: Mohammed

first: Marek

last: Napierala

first: Karen

last: Usdin

first: Aseem

middle: Z

last: Ansari

first: Sergei

middle: M

last: Mirkin

first: André

last: Nussenzweig


title: Triplexes are Dynamic DNA Secondary Structures Formed in vivo and Linked to Genome Instability [pacBio WGS]

institute: Center for Excellence in Molecular Cell Science

overall_design: Whole genome sequencing in APH pulsed cells to check mutagenesis at H-DNA repeats under replication stress.


title: Triplexes are Dynamic DNA Secondary Structures Formed in vivo and Linked to Genome Instability


title: Constitutive bone marrow adipocytes suppress local bone formation and support hematopoietic stem and progenitor cells

city: Ann Arbor

first: Ziru

last: Li

state: MI

address: 2800 Plymouth Rd.

department: Molecular & Integrative Department

institute: University of Michigan

summary:
Methods: Whole distal tibial bones were collected from male control or BMAd-DTA mice at 24 weeks of age.
Results: Using an optimized data analysis workflow, we mapped over 20 million sequence reads per sample to the mouse genome (UCSC mm10) and identified 22,600 transcripts in the whole distal tibial bones of control or BMAd-DTA mice using STAR with default parameters. We identified 841 genes that were significantly changed in BMAd-DTA mice; of these, 432 genes were up-regulated. Pathway analysis revealed that this gene set is enriched in ossification, extracellular matrix organization, and osteoblast differentiation pathways.
Conclusion: The increased bone mass in BMAd-DTA mice appears to be secondary to enhanced bone formation, suggesting a local effect caused by depletion of BMAd.

overall_design: Gene profiling of whole distal tibial bones from control or BMAd-DTA mice fed an ad libitum diet for 24 weeks.

first: Hui

last: Yu

first: Ormond

last: MacDougald


title: Trigeminal neurons control immune-bone cell interactions and metabolism in apical periodontitis

city: San Antonio

first: Katherine

middle: Vivian

last: Lillis

state: TX

address: 7703 Floyd Curl Dr

department: Endodontics

institute: UNIVERSITY OF TEXAS HLTH SCI CTR SAN ANTONIO

summary: Apical periodontitis (AP) is an inflammatory disease occurring following tooth infection with distinct osteolytic activity. Despite increasing evidence that sensory neurons participate in regulation of non-neuronal cells, their role in the development of AP is largely unknown. We hypothesized that Nav1.8+ nociceptors regulate bone metabolism changes in response to AP. Methods: A selective ablation of nociceptive neurons in Nav1.8Cre/ DTALox mouse line was used to evaluate the development and progression of AP using murine model of infection-induced AP. Micro-computed tomography examination was applied to quantify osteolytic lesions following induction of AP. Additionally, RT-PCR, RNAscope, and immunohistochemical (IHC) analysis were used to investigate the expression of immune cells, osteoblasts, and osteoclasts. Co-culture of trigeminal ganglia (TG) neurons from DTALox (control) and Nav1.8Cre/ DTALox mice with either IDG-SW3 or MC3T3-E1 osteoblast precursor cell lines or RAW264.7 murine macrophages were used to assess osteoblast and osteoclast function, by RNA sequencing, mineralization, and osteoclastic assays. Results: Ablation of Nav1.8+ nociceptors had earlier progression of AP with larger osteolytic lesions compared to the controls. IHC and RNAscope analysis demonstrated greater number of macrophages, T-cells, osteoclast and osteoblast precursors as well as an increased RANKL:OPG ratio at earlier time points among Nav1.8Cre/ DTALox mice. There was an increased expression of IL-1a and IL-6 within lesions of nociceptor-ablated mice. Further, co-culture experiments demonstrated that TG neurons promoted osteoblast mineralization and inhibited osteoclastic function. Conclusion: The findings suggest that TG Nav1.8+ neurons contribute to modulation of the AP development by delaying the influx of immune cells, promoting osteoblastic differentiation, and decreasing osteoclastic activities. This newly uncovered mechanism could become a therapeutic strategy for the treatment of AP and minimize the persistence of osteolytic lesions in refractory cases.

overall_design: Trigeminal ganglia (TG) were harvested from Nav1.8Cre/ DTALox and Nav1.8Cre control mice, and cells were isolated via enzymatic digestion process, as previously described (Austah et al. 2019; Patwardhan et al. 2005). Single cell suspensions at the concentration of (~5x104 cells/insert) were seeded on 24-well plate polyethylene cell culture inserts (1μm-pore sizes) (Millipore-Sigma) precoated with 50μg/ml laminin (Sigma, MO) in growth medium containing Alpha Modified Eagle's Medium (αMEM) (Life Technologies, Carlsbad, CA), 10% heat-inactivated fetal bovine serum (HI-FBS) (Life Technologies, Carlsbad, CA), and 1X Glutamine-Penicillin- Streptomycin (Invitrogen, CA). TG cells were allowed to attach for 24 hours in 5% CO2 and 37ºC in the presence of 10μM cytosine β-D- arabinofuranoside (Ara-C) (Sigma) to halt the non- neuronal cell proliferation, producing a neuron-enriched culture (Henriquez et al. 2013; Nicole et al. 2001). The control TG preparations are called TG-cre, and nociceptor-ablated cultures are called TG-DTA, where Nav1.8+, or sensory neuron specific (SNS), cells are ablated. The inserts containing either TG-cre or TG-DTA neuronal-enriched primary cultures were transferred to 24-well plates containing IDG-SW3 osteoblast precursor cells for osteoblast co-cultures.

middle: V

first: Stephen

middle: E

last: Harris

first: Anibal

last: Diogenes


title: Function-selective targeting of the extracellular signal-regulated kinase (ERK1/2) mitigates multiple pathophysiological features of allergen-induced asthma in mice

city: Philadelphia

first: Deepak

last: Deshpande

state: PA

address: 1020 Locust Street

department: Center for Translational Medicine

institute: Thomas Jefferson University

summary:
Purpose: To test the in vivo effectiveness of a novel function-selective inhibitor of ERK1/2 in a murine model of house dust mite (HDM)-induced allergic asthma.
Methods: Mice challenged with HDM for 3 weeks were treated with SF-3-030 or vehicle and asthma phenotype was assessed by histology and lung function measurements. Total RNA from lung samples were subjected to RNAseq analysis to determine the molecular signature perturbed by SF-3-030 treatment in mice.
Results: RNA-seq analysis revealed modulation (up- or down-regulation) of expression of a number of genes by HDM challenge. SF-3-030 treatment significantly modulated the expression of genes involved in HDM-induced airway inflammation, cell proliferation, and extracellular matrix production.
Conclusion: Function-selective inhibitor of ERK1/2 SF-3-030 mitigates multiple features of asthma in a murine model by modulating expression of genes involved in the regulation of key pathological functions in airway cells.

overall_design: BALB/c mice were treated with HDM every day for 5 days/week for 3 weeks. A group of mice was treated with vehicle or 10 mg/kg SF-3-030 intranasally 30 min prior to the HDM challenge. Lung functions and histology were assessed after 3 weeks. Lung tissues harvested from mice were used for total RNA extraction and subjected to RNA-seq analysis. Differential gene expression and pathway analysis were performed. Asthma phenotype data in mice were also generated by histology, biochemical analysis, and lung mechanics studies.

first: Sushrut

middle: D

last: Shah

first: Ajay

last: Nayak

first: Pawan

last: Sharma

first: Dominic

last: Villalba

first: Sankar

last: Addya

first: Weiliang

last: Huang

first: Paul

last: Shapiro

first: Maureen

last: Kane


title: Polymer-coated gold nanoparticles target Age-Associated B cells in vivo

city: Geneva

first: Viola

last: Puddinu

address: CMU-Rue Michel-Servet 1

country: Switzerland

institute: University of Geneva

summary: Engineered gold nanoparticles (GNPs) have become a useful tool in various therapeutic and diagnostic applications. Uncertainty remains regarding possible impacts of GNPs to the immune system. In this regard, we investigated the interactions of polymer-coated GNPs with B cells and their functions in mice as they constitute a crucial part of the immune system and represent a potential target for systemically administered GNPs. Surprisingly, we observed that polymer-coated GNPs mainly interact with the recently identified subpopulation of B lymphocytes named Age-associated B cells (ABCs). Importantly, we also showed that GNPs did not affect the percentages of other B cell populations in different organs. Furthermore, GNPs did not activate B cell innate-like immune responses in any of the tested conditions, nor did they impair adaptive B cell responses in immunized mice. Together, these data provide an important contribution to otherwise limited knowledge about GNP interference with B cell immune function, and demonstrate that GNPs represent a safe tool to target ABCs in vivo for various potential applications.

overall_design: gene expression analysis of GNP-positive and negative B cell subpopulations

first: Sandra

last: Hočevar

first: Laetitia

last: Haeni

first: Alke

last: Petri-Fink

first: Julia

last: Wagner

first: Montserrat

last: Alvarez

first: Martin

last: James

first: David

last: Clift

first: Carole

last: Bourquin


title: Mutation of histone H3 serine 28 to alanine influences H3K27me3-mediated gene silencing in Arabidopsis thaliana

city: Gatersleben, Stadt Seeland, Germany

first: Hua

last: Jiang

address: Corrensstraße 3

institute: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben

summary: Histone modifications are essential for chromatin activity and play an important role in many biological processes. Trimethylation of histone H3K27 (H3K27me3) is a repressive modification established by Polycomb repressive complex 2 (PRC2). Although the presence of the histone H3 serine 28 phosphorylation (H3S28ph) modification at adjacent amino acid residues has both positive and negative effects on Polycomb silencing in mammals, little is known about the effect of H3S28ph on H3K27me3-mediated gene silencing in plants. In this study, we show that mutating H3S28A in Arabidopsis causes a dominant-negative effect that leads to an early-flowering phenotype by promoting the expression of flowering-promoting genes independently of abnormal cell division. While H3S28ph levels decreased due to the H3S28A mutation, H3K27me3 levels at the same loci did not increase. Moreover, we observed decreased H3K27me3 levels at some known PRC2 target genes in H3.3S28A transgenic lines, rather than the expected enhanced H3K27me3-mediated silencing. In line with the reduced H3K27me3 levels, the expression of the PRC2 catalytic subunits CLF and SWN decreased. Taken together, these data demonstrate that H3.3S28 is required for PRC2-dependent H3K27me3-mediated silencing in Arabidopsis, suggesting that H3S28 has a non-canonical function in H3K27me3-mediated gene silencing.

overall_design: We compared the transcriptomes and genome profiles of H3S28ph and H3K27me3 for Col, H3.1, H3.3, H3.1S28A, and H3.3S28A.

first: Linhao

last: Xu

first: Jinping

last: Cheng


title: Menopausal Transition: Prospective Study of Estrogen Status, Circulating MicroRNAs, and Biomarkers of Bone Metabolism

city: Prague

first: Jiri

last: Baloun

address: Na Slupi 450/4

department: Department of experimental rheumatology

country: Czech Republic

institute: Institute of Rheumatology

summary: We carried out Massive Parallel Sequencing (MPS) to reveal circulating miRNA profiles of 44 patients before and after oophorectomy, as well as in oophorectomized women on estrogen therapy. The sequencing platform identified 1305 miRNA species, out of which 439 miRNAs were present with the base mean, computed by DESeq2, more than 10. We identified 17 miRNAs, which were different in sera with sufficient and low estrogen levels.

overall_design: miRNA profiling of 44 sera from women before and after oophorectomy, as well as in oophorectomized.

first: Jan

last: Stepan


title: PPM1D suppresses p53-dependent transactivation and cell death by inhibiting the HRI-eIF2alpha-ATF4 pathway.

city: Aurora

first: Joaquin

last: Espinosa

state: CO

department: Pharmacology, Linda Crnic Institute for Down Syndrome

institute: University of Colorado Anschutz Medical Campus

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

overall_design: Refer to individual Series


title: PRC2-indepdendent actions of H3.3K27M in embryonic stem cell differentiation

city: Jerusalem

first: Lea

last: Cohen

address: Edmond J. Safra Campus

country: Israel

institute: HUJI

summary: The histone H3 variant, H3.3, is localized at specific regions in the genome, especially promoters and active enhancers, and has been shown to play important roles in development. A lysine to methionine substitution in position 27 (H3.3K27M) is a main cause of Diffuse Intrinsic Pontine Glioma, a lethal type of pediatric cancer. H3.3K27M has a dominant-negative effect by inhibiting the Polycomb Repressor Complex 2 (PRC2) activity. Here, we studied the immediate, genome-wide, consequences of the H3.3K27M mutation independent of PRC2 activity. We developed Doxycycline (Dox)-inducible mouse embryonic stem cells (ESCs) carrying a single copy of WT-H3.3, H3.3K27M and H3.3K27L, all fused to HA. We performed RNA-Seq and ChIP-Seq at different timepoints following Dox in undifferentiated and differentiated ESCs. We find increased binding of H3.3 around transcription start sites in cells expressing both H3.3K27M and H3.3K27L compared with WT, but not in cells treated with PRC2 inhibitors. Differentiated cells carrying either H3.3K27M or H3.3K27L retain expression of ESC-active genes, in expense of expression of genes related to neuronal differentiation. Taken together, our data suggest that a modifiable H3.3K27 is required for proper histone incorporation and cellular maturation, independent of PRC2 activity.

overall_design: We generated Doxycycline (Dox)-inducible KH2 FLIP-in mouse ESCs expressing a single copy of WT, K27M or K27L SNAP-HA-H3.3. We performed RNA-seq and ChIP-seq using HA-specific antibodies, H3K27me3-specific antibodies, and H3K27ac-specific antibodies at 4,8,24,72 hrs following Dox addition. We also differentiated our ESCs using retinoic acid and performed RNA-seq and ChIP-seq using HA-specific antibodies at 24 and 72 hrs following Dox.

first: Binyamin

last: Kaffe

first: Eden

last: Deri

first: Chen

last: Leibson

first: Malka

middle: N

last: Rafinia

first: Eran

last: Meshorer


title: RNA sequencing data of 2102EP, VM-CUB-1, Caki-1 and DU-145 cells treated with epigenetic agent LAK31 and DMSO as solvent control

city: Düsseldorf

first: Daniel

last: Nettersheim

state: NRW

address: Moorenstr. 5

department: Dep. of Urology

institute: Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University

summary: RNA sequencing data of cell lines of urological malignancies treated with the epigenetic agent LAK31 or DMSO as solvent control.

overall_design: Single end 3' RNA sequencing of  cell lines (2102EP, VM-CUB-1, Caki-1,DU-145) treated with epigenetic agent LAK31. DMSO was used as solvent control. Cells were treated with the epi-drug for 16 h.


title: PPM1D suppresses p53-dependent transactivation and cell death by inhibiting the HRI-eIF2alpha-ATF4 pathway [ChIP-seq]

summary: The p53 transcription factor is a master regulator of cellular stress responses restrained by repressors such as MDM2 and the phosphatase PPM1D. Activation of p53 with pharmacological inhibitors of its repressors is being tested in clinical trials for cancer therapy, but efficacy has been limited by poor induction of tumor cell death. We demonstrate that dual inhibition of MDM2 and PPM1D induces cell death in multiple cancer cell types via amplification of the p53 transcriptional program through the eIF2alpha -ATF4 pathway. PPM1D inhibition induces phosphorylation of eIF2alpha, ATF4 accumulation, and ATF4-dependent enhancement of p53-dependent transactivation upon MDM2 inhibition. Dual inhibition of p53 repressors depletes heme and induces HRI-dependent eIF2alpha phosphorylation. Pharmacological induction of eIF2alpha phosphorylation synergizes with MDM2 inhibition to induce cell death and halt tumor growth in mice. These results demonstrate that PPM1D inhibits both the p53 network and the integrated stress response controlled by eIF2alpha, with clear therapeutic implications.

overall_design: Effects of MDM2 and PPM1D inhibition on p53 occupancy in TPC1 and K1 cell lines.

first: Zdenek

last: Andrysik


title: RNAseq of brain and muscle from Nadk2 and Pla2g6 mutant mice at early and late phenotypic time points

city: Bar Harbor

first: Robert

last: Burgess

state: ME

address: 600 Main St

institute: The Jackson Laboratory

summary: RNA sequencing for differential gene expression analysis was performed from brain and muscle of Nadk2 mutant mice and littermate controls at 5 and 11 weeks of age, and in Pla2g6 mutant mice and littermate controls at 6 and 13 weeks of age, representing early stage and late stage phenotypic time points.

overall_design: Comparison of gene expression between mutant and wild type littermate mice for two different mutations in two different tissues at early and late time points

middle: W


title: Genetic roles of Hnf4 family transcription factors in zebrafish development and microbial response

city: Durham

first: John

middle: F

last: Rawls

state: NC

address: 213 Research Drive

institute: Duke University School of Medicine

summary: The goal of this study was to better understand the roles of Hnf4 fmaily transcription factors in zebrafish development and intestinal function. We used RNA-sequencing to compare gene expression changes in digestive tracts dissected from 6dpf larval zebrafish. Our first experiment compared samples from wild type and hnf4g-/- zebrafish which were either raised germ free or with a conventional microbiota starting at 3dpf. The second experiment compared samples from wild type, hnf4g-/-, and hnf4a-/-;hnf4g-/-  zebrafish conventionally raised from 0dpf with a microbiota. Each sample consists of RNA extracted from 10-15 pooled gastrointestinal tracts, and 4 biological replicates per treatment group were sequenced.

overall_design: mRNA profiles of gastrointestinal tracts dissected from 6dpf larval zebrafish from two experiments were analyzed and compared: 1) WTCV, WTGF, hnf4g-/-CV, hnf4g-/-GF 2) WTCR, hnf4g-/-CR, hnf4a-/-;hnf4g-/-CR

first: Jennifer

middle: K

last: Heppert

first: Colin

last: Lickwar


title: Genome-wide profiling of the expression of exosomal circRNAs in patients with hepatic alveolar echinococcosis

city: Erzurum

first: Selçuk

last: Özdemir

address: Atatürk University Faculty of Veterinary Medicine

country: Turkey

institute: Atatürk University

summary: Hepatic echinococcosis (HE) caused by Echinococcus spp. transmitted from carnivores is known as a severe zoonotic disease that formed into hepatic cystic echinococcosis (HCE) and hepatic alveolar echinococcosis (HAE). It continues to be a serious public health issue around the world. HAE is uncommon infection which is characterized by poor prognosis but it is the most life-threatening compare to HCE. Many cases of HAE are recognized at forward stages because clinical symptoms may remain silent in about 10 years of incubation period. Several pathological cases could be observed including septicemia, abscess, recurrent cholangitis, and portal hypertensive gastrointestinal bleeding in untreated people. It is provided that correlated factors includes CD44, Soluble ST2 (sST2), Plasma IL-23, IL-27, and IL-5 for metastasis and prognosis for patients with HAE were identified. However, data on metastatic and prognostic marker are still so poor. Recent studies have revealed that circRNAs are enriched and stable in exosomes. Exosomal circRNAs may be localized in platelet-derived extracellular vesicles, hepatic cells, and pancreatic cancer cells. Studies have suggested that it is possible that cells may transfer circRNAs by excreting them in exosomes. Whereas there are a lot of studies on cancer and other human diseases related exosomal circRNA, no studies on hepatic alveolar echinococcosis-related exosomal circRNAs in humans. Current study provides that exosomal circular RNAs from healthy humans and humans with hepatic alveolar echinococcal disease were detected and characterized using the RNA sequencing.

overall_design: Examination of exosomal circRNA in the patients with hepatic alveolar echinococcosis.

first: Gürkan

last: Öztürk


title: ATAC sequencing data of 2102EP, VM-CUB-1, Caki-1 and DU-145 cells treated with epigenetic agent LAK31 (2102EP additionally: Romidepsin, Quisinostat and MZ-1) and DMSO as solvent control

summary: ATAC sequencing data of cell lines of urological malignancies treated with epigenetic agents LAK31, Romidepsin, Quisinostat and MZ-1.

overall_design: ATAC sequencing of cell lines (2102EP, VM-CUB-1, Caki-1, DU-145) treated with epigenetic agent LAK31 (2102EP additionally: Romidepsin, Quisinostat and MZ-1). DMSO was used as solvent control. Cells were treated with the epi-drug for 16 h.


title: Global miRNA Expression of Bone Marrow Mesenchymal Stem/Stromal Cells in Fanconi Anemia Patients Before Transplantation and Unpaired Bone Marrow Donors

city: Ankara

first: Ayşen

last: Özcan

address: Sihhiye

department: Department of Stem Cell Sciences

institute: Hacettepe University

summary:
Fanconi anemia (FA) is a rare genetic disorder characterized by genomic instability, developmental defects and bone marrow failure. Homeostasis of hematopoietic stem cells (HSCs) in the bone marrow partly relies on their direct or indirect interactions with the mesenchymal stem/stromal cells (MSCs). miRNAs can play a critical role during these interactions. There is no study available so far addressing the miRNA profile of bone marrow (BM-) MSCs in the FA disease state.
Non-coding RNA expression profiling was performed in BM-MSCs obtained from Donors, as well as FA patients before bone marrow transplantation (preBMT) using GeneChip miRNA 2.0 array. Quality Control (QC) was performed via Normalized Unscaled Standard Errors (NUSE) and Relative Log Expression (RLE) before further analysis.

overall_design: Non-coding RNA expression profiling was performed using total RNAs including small RNAs isolated from passage three BM-MSCs, which are obtained from Donors (n=5 after QC; designated as HUSCS-D) preBMT FA patients (n=4 after QC; designated as HUSCS-FA).

first: M

last: Keles

first: A

last: Keskus

first: I

last: Cagnan

first: O

last: Konu

last: Gunel-Ozcan


title: A double negative thymocyte specific enhancer augments Notch1 signaling to direct early T cell progenitor expansion,  lineage restriction and -selection.

city: Charlestown

first: Katia

last: Georgopoulos

address: 13th street

institute: Harvard Medical School

summary: T cell differentiation requires Notch1 signaling. Here we show that an enhancer upstream of Notch1 active in double-negative (DN) mouse thymocytes is responsible for raising Notch1 signaling intra-thymically.  This enhancer is required to expand multipotent progenitors intra-thymically while delaying early differentiation until lineage restrictions are established. Early thymic progenitors lacking the enhancer show accelerated differentiation through the DN stages and increased frequency of B-, ILC-, and NK-cell differentiation. Transcription regulators for T cell lineage restriction and commitment are expressed normally, but ILC- and NK-cell gene expression persists after T cell lineage commitment and TCRb V-DJ recombination, Cd3 expression and b-selection are impaired. This Notch1 enhancer is inactive in double-positive (DP) thymocytes. Its aberrant reactivation at this stage in Ikaros mutants is required for leukemogenesis. Thus, the DN-specific Notch1 enhancer harnesses the regulatory architecture of DN and DP thymocytes to achieve carefully orchestrated changes in Notch1 signaling required for early lineage restrictions and normal T cell differentiation.

overall_design: 3 ChIP-seq samples

first: Mariko

last: Kashiwagi


title: Global miRNA Expression of Bone Marrow Mesenchymal Stem/Stromal Cells in Fanconi Anemia Patients Before and After Bone Marrow Transplantation, and their Allogeneic Bone Marrow Donors

summary:
Fanconi anemia (FA) is a rare genetic disorder characterized by genomic instability, developmental defects and bone marrow failure. Homeostasis of hematopoietic stem cells (HSCs) in the bone marrow partly relies on their direct or indirect interactions with the mesenchymal stem/stromal cells (MSCs). miRNAs can play a critical role during these interactions. There is no study available so far addressing the miRNA profile of bone marrow (BM-) MSCs in FA disease state.
Non-coding RNA expression profiling was performed in BM-MSCs obtained from Donors (siblings of FA patients) as well as FA patients before (preBMT) and after bone marrow transplant (postBMT) using GeneChip miRNA 2.0 Array. Quality Control (QC) was performed via Normalized Unscaled Standard Errors (NUSE) and Relative Log Expression (RLE) before further analysis.

overall_design: Non-coding RNA expression profiling was performed using total RNAs including small RNAs isolated from passage 3 BM-MSCs, which are obtained from Donors (n=3 after QC; designated as HUSCS-D), preBMT FA patients (n=3 after QC; designated as HUSCS-FA) and postBMT FA patients (n=3 after QC; designated as HUSCS-FAxx-T).


title: EGR1 CHIP and RNA sequencing following EGR1 knockdown in CD34+ human hematopoeitic stem and progenitor cells

city: Chicago

first: Angela

last: Stoddart

state: IL

address: 900 E. 57th Street, Lab 5220A

department: Pathology

institute: University of Chicago

summary: Therapy-related myeloid neoplasms (t-MN) share many similarities with AML de novo in the elderly.  One common factor is that they arise in the setting of chronic inflammation, likely due to advanced age or chemotherapy-induced senescence. Here, we examined the impact of haploinsufficient loss of the del(5q) tumor suppressor gene, EGR1, commonly deleted in high-risk MNs.  In mice, under the exogenous inflammatory stress of either serial transplant or successive doses of the alkylating agent ENU, Egr1-haploinsufficient hematopoietic stem cells (HSCs) exhibit a clonal advantage. Complete loss of EGR1 function is incompatible with transformation; mutations of EGR1 are rare and are not observed in the remaining allele in del(5q) patients and complete knockout of Egr1 in mice leads to HSC exhaustion. Using chromatin immunoprecipitation sequencing (ChIP-seq), we identify EGR1 binding sites in human CD34+ cord blood-derived stem and progenitor cells (HSPCs) and show that EGR1 binds genes critical for stem cell differentiation, inflammatory signaling, and the DNA damage response. Notably, in the chromosome 5 sequences frequently deleted in patients, there is a significant enrichment of innate and inflammatory genes, which may confer a fitness advantage in an inflammatory environment.  Short hairpin RNA (shRNA) mediated silencing of EGR1 biases HSPCs towards a self-renewal transcriptional signature. In the absence of EGR1, cells upregulate MYC-driven proliferative signals, downregulate CDKN1A (p21), disrupt the DNA damage response, and downregulate inflammation - adaptations anticipated to confer a relative fitness advantage for stem cells especially in an environment of chronic inflammation.

overall_design: RNA sequencing following EGR1 knockdown in CD34+ human hematopoeitic stem and progenitor cells (HSPC) isolated from cord blood. EGR1 CHIP-seq from  CD34+ HSPCs.

first: Megan

last: McNerney

first: Michelle

last: Le Beau


title: Patient-derived micro-organospheres (MOS) enable clinical precision oncology

first: Xiling

last: Shen

address: 101 Science Dr., CIEMAS

department: Biomedical Engineering

institute: Duke University

summary: Patient-derived xenografts (PDX) and organoids (PDO) have been shown to model clinical response to cancer therapy. However, it remains challenging to use these models to guide timely clinical decisions for cancer patients. Here we used droplet emulsion microfluidics with temperature control and dead-volume minimization to rapidly generate thousands of Micro- Organospheres (MOS) from low-volume patient tissues, which serve as an ideal patient-derived model for clinical precision oncology. A clinical study of newly diagnosed metastatic colorectal cancer (CRC) patients using a MOS-based precision oncology pipeline reliably predicted patient treatment outcome within 14 days, a timeline suitable for guiding treatment decisions in clinic. Furthermore, MOS capture original stromal cells and allow T cell penetration, providing a clinical assay for testing immuno-oncology (IO) therapies such as PD-1 blockade, bispecific antibodies, and T cell therapies on patient tumors.

overall_design: Using high-throughput sequencing technology (single cell sequencing and whole exon sequencing) to validate micro organospheres can keep the immune microenvironment and also keep genetic mutation status from patient derived tumor tissues.

first: Ding

last: Shengli

first: Dohlman

last: Anders

first: Nick

last: Giroux


title: Genome wide transcriptional change by  GPR155/LYCHOS  loss

city: Berkeley

first: Roberto

last: Zoncu

address: Li Ka Shing Center, 1951 Oxford Street, Rm330F

department: Molecular Cell Biology

institute: University of California Berkeley

summary: Cholesterol, a key building block for cellular membranes and a precursor for steroid hormones, was recently identified as a major nutrient input that activates the master growth regulator, mammalian Target of Rapamycin Complex 1 (mTORC1) kinase. Here we identify a novel lysosomal tranmembrane protein , which we name LYsosomal CHOlesterol Signaling (LYCHOS, previously annotated as GPR155/DEPDC3), as an essential factor that enables cholesterol-dependent activation of mTORC1. RNAseq analysis of LYCHOS-depleted cells showed a pronounced dowregulation of  metabolic genes involved in glycolysis, pentose phosphate pathway and lipid biosynthesis.

overall_design: HEK293T cells  were infected with lentivirus <shLuc+ FLAG METAP2>, <shLYCHOS + FLAG METAP2> and <shLYCHOS + LYCHOS WT FLAG>  and  RNA was extracted 5 days post-infection and analyzed by RNA-sequencing

first: Hijai

last: Shin


title: Global miRNA Expression of Bone Marrow Mesenchymal Stem/Stromal Cells in Fanconi Anemia Patients Before Transplantation and their Allogeneic Bone Marrow Donors

last: Özcan

summary:
Fanconi anemia (FA) is a rare genetic disorder characterized by genomic instability, developmental defects and bone marrow failure. Homeostasis of hematopoietic stem cells (HSCs) in the bone marrow partly relies on their direct or indirect interactions with the mesenchymal stem/stromal cells (MSCs). miRNAs can play a critical role during these interactions. There is no study available so far addressing the miRNA profile of bone marrow (BM-) MSCs in the FA disease state.
Non-coding RNA expression profiling was performed in BM-MSCs obtained from Donors (siblings of FA patients), as well as FA patients before bone marrow transplantation (preBMT) using GeneChip miRNA 2.0 Array. Quality Control (QC) was performed via Normalized Unscaled Standard Errors (NUSE) and Relative Log Expression (RLE) before further analysis.

overall_design: Non-coding RNA expression profiling was performed using total RNAs including small RNAs isolated from passage 3 BM-MSCs, which are obtained from Donors (n=6 after QC; designated as HUSCS-D) and FA patients (n=6 after QC; designated as HUSCS-FA).


title: Human Somitoids Generated by Reprogramming Pax8+ Urine Cells [GEO-Seq]

city: Hangzhou

first: Xingnan

last: Huang

address: No.18 Shilongshan Road

institute: Westlake University

summary: To illustrate the transcriptional features of UiSomitoid

overall_design:
Sequencing the intervally collected 55 sections in a whole UiSomitoid at day9.
Building library and sequencing UiSomitoid at Day2, Day4, Day6 and Day9.


title: RNA-Seq of baboon kidney cortex biopsies [high sodium diet]

city: Winston Salem

first: Laura

middle: A

last: Cox

address: 1 Medical Center Blvd

department: Internal Medicine

institute: Wake Forest School of Medicine

summary: Blood pressure and the kidney cortex transcriptome response to sodium diet challenge in female nonhuman primates

overall_design: Female baboons consumed a low sodium diet for 6 weeks followed by a high sodium diet for 6 weeks. Blood collections, continuous blood pressure collection by wireless telemetry, and ultrasound guided kidney biopsies were collected at the end of each diet. This study utilizes weighted gene coexpression network analysis to investigate underlying gene networks underlying blood pressure response to sodium in the female primate kidney cortex transcriptome. Establishing genetic networks involved in blood pressure response to sodium in baboon kidneys is essential for translating understanding of it’s role to human physiology and disease impacting women and for development of precision medicine.

first: Angelica

last: Riojas

first: Kimberly

last: Spradling-Reeves


title: Human Somitoids Generated by Reprogramming Pax8+ Urine Cells [scRNA-seq]

summary: To illustrate the transcriptional features of UiPSM and  UiPSM reprogramming

overall_design: Sequencing the collected the cell samples in the reprogramming proocess including Day0,Day3,day6,day9


title: ISL1 is an essential determinant of structural and functional tonotopic representation of sound

city: Vestec

first: Šárka

last: Benešová

address: Prumyslova 595

department: Institute of Biotechnology

institute: Czech Academy of Science

summary: A cardinal feature of the auditory pathway is frequency selectivity represented in the form of a tonotopic map from the cochlea to the cortex. The molecular determinants of the auditory frequency map are unknown. Here, we discovered that the transcription factor ISL1 regulates features of auditory neurons, including the formation of the spiral ganglion neuron (SGN) and peripheral and central processes that shape the tonotopic representation of the auditory map. We selectively knocked out Isl1 in auditory neurons using Neurod1Cre strategies. In the absence of Isl1, SGNs migrate into the central cochlea and beyond. The cochlear wiring is profoundly reduced and disrupted. The central axons of Isl1 mutants lose their topographic projections and segregation at the cochlear nucleus. Transcriptome analysis of SGNs shows that Isl1 regulates neurogenesis, axonogenesis, migration, and the functional properties of neurons. Surprisingly, notable auditory processing features are preserved despite the significant hearing impairment, revealing central auditory pathway resilience and plasticity in mutant mice. Mutant mice demonstrate altered acoustic startle reflex, prepulse inhibition, characteristics of compensatory neural hyperactivity centrally. Our findings show that the Isl1 is one of the obligatory factors required to sculpt auditory structural and functional tonotopic maps. Still, upon Isl1 deletion, the ensuing compensatory plasticity of the auditory pathway does not suffice to overcome developmental changes at the peripheral sensory organ.

overall_design: 12 samples are analyzed (biological replicates of 6 control and 6 mutant samples) each containing 100 FACS-sorted tdTomato+ neurons.

first: Iva

last: Filova

first: Kateryna

last: Pysanenko

first: Mitra

last: Tavakoli

first: Simona

last: Vochyanova

first: Martina

last: Dvorakova

first: Romana

last: Bohuslavova

first: Ondrej

last: Smolik

first: Sarka

last: Benesova

first: Lukas

last: Valihrach

first: Ebenezer

last: Yamoah

first: Josef

last: Syka

first: Bernd

last: Fritzsch

first: Gabriela

last: Pavlinkova


title: Wildfire Smoke-Induced Transcriptomic Changes in the Mouse Lung and Heart

city: Chapel Hill

first: Julia

last: Rager

address: 135 Dauer Drive, CB 7431

institute: UNC

summary: These analyses set out to evaluate transcriptomic responses in the mouse lung and heart in response to simulated wildland fire exposure conditions. These exposure conditions were based on smoke condensate consisting of particulate matter and semivolative organic compounds resulting from the burning of five biomass fuels; namely eucalyptus, pine, pine needles, peat, and red oak. These biomasses were evaluated under two burn conditions: flaming and smoldering.

overall_design: Biological responses resulting from these exposures have been previously evaluated using an in vivo model (CD-1 mice) and an Ames mutagenicity assay (Kim et al. 2018, PMID: 29373863). For the in vivo evaluation, female mice were exposed to biomass smoke condensate samples using 50 uL saline containing 2 mg/mL PM administered to the lungs by oropharyngeal aspiration. Samples were collected at 4 and 24 h post-exposure. Mouse lung toxicity response data included alterations in immune cell populations, including neutrophil and macrophage counts, as well as protein markers of inflammation and tissue damage. The in vivo toxicity responses associated with each biomass burn condition were evaluated on the basis of equal mass as well as emission factors derived from the amount of biomass fuel consumed. Here, we expanded upon this important study by integrating toxicity responses, including newly generated transcriptional signatures, with chemical profiles to further characterize systems-level toxicity associated with wildfire smoke and provide much-needed understanding towards which components of wildfire smoke are the most harmful.


title: Single-cell transcriptomic profiles of hPSC-derived cardiac cells of various lineages and stages

city: Toronto

first: Gordon

last: Keller

state: Ontario

address: 101 College Street

department: McEwen stem cell institute

country: Canada

institute: University of Toronto

summary: Using the hPSC system, we modelled multi-lineage (FHF, aSHF and pSHF) human embryonic cardiogenesis from mesoderm specification to cardiomyocyte differentiation and described these processes using single-cell RNA sequencing.

overall_design: hPSC-derived cardiac mesoderm (day 3), late mesoderm (day 4), progenitor (day 6) and cardiomyocyte (day 20)

first: Donghe

last: Yang


title: Single Cell RNA sequencing of blood leukocytes from IL1rn-deficient mice

city: Boston

first: Pui

last: Lee

address: 60 Fenwood Rd.

institute: Brigham and Womens Hospital

summary: We performed single cell RNA sequencing on peripheral blood leukocytes from BALB/c mice and IL1rn-deficient mice treated with vehicle or rapamycin

overall_design: Peripheral blood cells collected from 8 week old mice (n = 4 per group).  Cells from the same group were pooled and labeled with hashtag antibodies. After flow cytometry sorting for live cells, cells were loaded for single cell RNA sequencing.

first: Zhengping

last: Huang

first: Peter

last: Nigrovic


title: Wildfire Smoke-Induced MicroRNA Changes in Mouse Plasma Extracellular Vesicles

type: Non-coding RNA profiling by high throughput sequencing

summary: These analyses set out to evaluate changes in microRNA signatures in the mouse plasma in response to simulated wildland fire exposure conditions. These exposure conditions were based on smoke condensate consisting of particulate matter and semivolative organic compounds resulting from the burning of two biomass fuels; namely , peat and red oak. These biomasses were evaluated under two burn conditions: flaming and smoldering. Saline exposures were also carried out as negative controls.

overall_design: Biological responses resulting from these exposures have been previously evaluated using an in vivo model (CD-1 mice) and an Ames mutagenicity assay (Kim et al. 2018, PMID: 29373863). For the in vivo evaluation, female mice were exposed to biomass smoke condensate samples using 50 uL saline containing 2 mg/mL PM administered to the lungs by oropharyngeal aspiration. Samples were collected at 4- and 24 h post-exposure. Mouse lung toxicity response data included alterations in immune cell populations, including neutrophil and macrophage counts, as well as protein markers of inflammation and tissue damage. The in vivo toxicity responses associated with each biomass burn condition were evaluated on the basis of equal mass as well as emission factors derived from the amount of biomass fuel consumed. Here, we expanded upon this important study by integrating toxicity responses, including newly generated microRNA signatures from extracellular vesicles isolated from select plasma samples.

first: Kyle

last: Roell


title: Transcriptome analysis of Streptococcus suis upon exposure to sub-lethal concentrations of LL-37

city: Wageningen

last: van Baarlen

address: De Elst 1

department: Animal Sciences

country: Netherlands

institute: Wageningen University

summary: Streptococcus suis is a major pig pathogen as well as an emerging zoonotic pathogen. We studied the generic and adaptive resistance response of S. suis upon exposure to sub-lethal concentrations of the human cathelicidin LL-37. We aimed to search for inducible mechanisms of resistance to AMPs as well as induction of virulence gene expression upon exposure to AMPs, in order to gain insights into host-derived factors that might mediate S. suis pathogenesis.

overall_design:
In this experiment, S. suis bacteria were grown into mid-exponential growth phase in THB, transferred to PBS supplemented with 5% THB and exposed to three different conditions (no peptide, 0.1 µM LL-37, or 0.25 µM LL-37) and RNA was extracted at two timepoints (after 10 or 30 min exposure).

These data are included in Chapter 3 of the Ph.D. thesis of Rogier Gaiser (https://edepot.wur.nl/387767).

first: Gaiser

last: Rogier

first: Michiel

last: Wels


title: TaSRO1 interacts with and suppresses TaSIP1 to fine tune mitochondrial retrograde signaling and enhance salinity stress tolerance

city: Qingdao

first: Mei

last: Wang

state: Shandong

address: Binhai road 72

institute: Shandong University

summary: The goal of this study is to compare the differential genes between wild type and TaSIP1 overexpression transgenic wheat plants. We used wild-type (WT) and three independent TaSIP1-∆C overexpressing (∆COE) wheat lines to perform RNA sequencing. As a result, TaSIP overexpression lead to  transcriptomic reprogramming. Most of the mitochondrial dysfunction stimulon (MDS) genes, including AtAOX1a, were upregulated substantially by the overexpression of TaSIP1-∆C.

overall_design: Quantitative analysis of wild type and TaSIP1 overexpression transgenic wheat transcriptomes.

first: Guangmin

last: Xia


title: Microarray analysis in vessels from control rats (Wistar-Kyoto rats) and disease model rats (Hypertensive rats)

status: Public on Aug 31 2022

city: Imabari

first: Masashi

last: Mukohda

state: Ehime

address: 1-3 Ikoinooka, Imabari

country: Japan

institute: Okayama University of Science

summary: Gene profiling in vessels

overall_design: Vessels were isolated from four male control rats and four male disease model rats.

first: Fumiyo

last: Saito


title: Determination of the VanS regulon in Clostridioides difficile

first: Boris

last: Belitsky

address: 136 Harrison Ave

department: Molecular Biology and Microbiology

institute: Tufts University School of Medicine

summary: We isolated suppressors of a ∆ddl mutant strain with constitutively active allelles of the vanS gene. VanS is a histidine kinase of a two-component system that regulates expression of the vanG operon. Transcriptomes of wild-type and ∆ddl vanS (R334L) strains were compared.

overall_design: Comparative RNAtag-Seq of wild-type and ∆ddl vanS (R334L) cells


title: The Granulocyte Progenitor Stage is a Key Target of IRF8-Mediated Regulation of Myeloid-Derived Suppressor Cell Production

city: Buffalo

first: Jianmin

state: NY

address: Elm and Carlton Streets

department: Bioinformatics and Biostatistics

institute: Roswell Park Comprehensive Cancer Center

summary: Alterations in myelopoiesis are common across various tumor types, resulting in immature populations termed myeloid-derived suppressor cells (MDSCs). MDSC burden correlates with poorer clinical outcomes, credited to their ability to suppress antitumor immunity. MDSCs consist of two major subsets, monocytic and polymorphonuclear (PMN). Intriguingly, the latter subset predominates in many patients and tumor models, though the mechanisms favoring PMN-MDSC responses remain poorly understood. Ordinarily, lineage-restricted transcription factors regulate myelopoiesis that collectively dictate cell fate. One integral player is interferon regulatory factor-8 (IRF8), which promotes monocyte/dendritic cell differentiation while limiting granulocyte development. We recently showed that IRF8 inversely controls MDSC burden in tumor models, particularly the PMN-MDSC subset. However, where IRF8 acts in the pathway of myeloid differentiation to influence PMN-MDSC production has remained unknown. Here, we showed that: 1) tumor growth was strongly associated with a selective expansion of newly defined IRF8lo granulocytic progenitors (GPs); 2) tumor-derived GPs had an increased ability to form PMN-MDSCs; 3) tumor-derived GPs shared gene expression patterns with IRF8-/- GPs, suggesting that IRF8 loss underlies GP expansion; and 4) enforced IRF8 overexpression in vivo selectively constrained tumor-induced GP expansion. These findings support the hypothesis that PMN-MDSCs result from selective expansion of IRF8lo GPs, and that strategies targeting IRF8 expression may limit their load to improve immunotherapy efficacy.

overall_design: 2 mouse samples

first: Colleen

last: Netherby

first: Michelle

last: Messmer

first: Lauren

last: Burkard-Mandel

first: Austin

last: Miller

first: Eduardo

last: Cortes

first: Michael

last: Nemeth

first: Scott

last: Abrams


title: Human cardiac pericytes are susceptible to SARS-CoV-2 infection

city: St. Louis

first: Stacey

middle: Lynn

last: Rentschler

state: Missouri

address: 660 S Euclid Ave

department: Medicine

institute: Washington University in St. Louis

summary: Coronavirus disease 2019 (COVID-19) is associated with serious cardiovascular complications, including myocarditis, thrombosis, and dysregulated hemodynamic responses. The mechanism(s) underlying these disease manifestations are incompletely understood. Given a critical role for pericytes in supporting endothelial cell health and maintaining vascular integrity, we hypothesized that infection of pericytes could explain some of the cardiovascular complications of COVID-19. Here, we present evidence of SARS-CoV-2 infection in cardiac pericytes in patients with COVID-19 myocarditis. We show that cardiac pericytes are permissive to SARS-CoV-2 infection in organotypic slice and primary cell cultures. SARS-CoV-2 enters cardiac pericytes through an ACE2 and endosomal-dependent mechanism. Consequences of cardiac pericyte infection include upregulation of inflammatory chemokine and cytokine expression, type I interferon signaling, mediators of endothelial constriction, and cell death. Collectively, these data demonstrate that human cardiac pericytes are susceptible to SARS-CoV-2 infection and suggest a possible role for pericyte infection in the pathogenesis of COVID-19.

overall_design: RNA sequencing of pericytes 4 days post-inoculation. Cardiac pericytes from 3 donors were inoculated with SARS-CoV-2 mNeonGreen at an multiplicity of infection (MOI) of 1  (5 technical replicates/donor) or mock (3 technical replicates/donor).

first: Brittany

last: Brumback

first: Oleksandr

last: Dmytrenko

middle: L

first: Kory

last: Lavine


title: DNA Methyltransferase regulates nitric oxide homeostasis and virulence in a chronically adapted Pseudomonas aeruginosa strain

city: Shenzhen

first: Yang

last: Liu

state: Guangdong

address: Liuxian

institute: Sustech Hospital

summary: Pseudomonas aeruginosa is an opportunistic pathogen which causes acute and chronic infections that are difficult to treat. Comparative genomic analysis has showed a great genome diversity among P. aeruginosa clinical strains and revealed important regulatory traits during chronic adaptation. While current investigation of epigenetics of P. aeruginosa is still lacking, understanding the epigenetic regulation may provide biomarkers for diagnosis and reveal important regulatory mechanisms. The present study focused on characterization of DNA methyltransferases (MTases) in a chronically adapted P. aeruginosa clinical strain TBCF10839. Single-molecule real-time sequencing (SMRT-seq) was used to characterize the methylome of TBCF. RCCANNNNNNNTGAR and TRGANNNNNNTGC were identified as target motifs of DNA MTases, M.PaeTBCFI and M.PaeTBCFII, respectively. LC-MS/MS analysis of DNA methylation was employed to verify the MTase activities. Transcriptomic analysis showed that ΔM.PaeTBCFII knockout mutant significantly downregulated nitric oxide reductase (NOR) regulating and coding gene expression such as nosR and norB, which contain methylated motifs in their promoters or coding regions. These predicted target motifs in nosR and norB were not methylated in the ΔM.PaeTBCFII knockout mutant. ΔM.PaeTBCFII exhibited reduced intercellular survival capacity in NO-producing RAW 264.7 macrophages and attenuated virulence in Galleria mellonella infection model. While the complemented strain recovered these defective phenotypes. Further phylogenetic analysis demonstrated that homologs of M.PaeTBCFII is frequently exists in P. aeruginosa sp as well as other bacteria species. Our work therefore provided new insights on the relationship between DNA methylation, NO detoxification, and bacterial virulence, laying a foundation for further exploring the molecular mechanism of DNA methyltransferase in regulating the pathogenicity of P. aeruginosa.

overall_design: P. aeruginosa TBCF were grown in Luria-Bertani (LB) liquid media at 37°C with constant shaking at 220 rpm with aeration. The in-frame deletion mutagenesis of methyltransferase ap or/and cp was performed through two-step allelic exchange. P. aeruginosa TBCF and mutants were cultured to mid log phase. Total RNA extraction and purification was performed for 3 biological replicates of each strain using RNeasy Mini Kit (QIAGEN) and RNase-Free DNase Set (QIAGEN) according to the manufacturer’s protocol. 1μg of total RNA was used for the construction of sequencing libraries. RNA sequencing was performed on Illumina NovaSeq 6000 sequencing platform generating 150 bp paired-end reads. Raw reads of the samples were preprocessed and analyzed using RSEM v1.3.1 with unique mapping setting (--bowtie-m), using P. aeruginosa TBCF genome as reference.

first: Shuhong

last: Han

first: Jihong


title: Screening and analysis of differentially expressed circRNAs and miRNAs in chronic diabetic extremity wounds [miRNA-Seq]

status: Public on Aug 30 2022

city: Nanchang

first: Dewu

address: 17 Yongwai Street

institute: Institute of Burn Injury, The First Affiliated Hospital of Nanchang University

summary: To investigate the expression of circRNAs, miRNAs, and related co-expression and competitive endogenous RNA (ceRNA) in diabetic chronic refractory wounds

overall_design: Six abnormally expressed circRNAs and miRNAs were detected by reverse transcription qPCR to verify the results of RNA sequencing. The dysregulated genes were enriched and analyzed by gene ontology and the Kyoto Encyclopedia of genes and genomes was used to clarify their main functions. ceRNA network were constructed

first: Xiaoliang

last: Li


title: PROX1 transcription factor is a master transcriptional regulator and essential for the stemness and growth of rhabdomyosarcoma

city: Helsinki

first: Riikka

last: Kivelä

address: Haartmaninkatu 8

country: Finland

institute: University of Helsinki and Wihuri Research Institute

summary: Rhabdomyosarcoma (RMS) is an aggressive pediatric cancer in need of novel therapies. Here we show that the PROX1 transcription factor, which is essential for myoblast differentiation, is highly expressed in RMS tumors. We demonstrate that PROX1 regulates RMS cell proliferation, stemness and rhabdosphere formation in vitro and RMS tumor formation in mouse xenograft models. By using proximity labeling and mass spectrometry, we found that PROX1 interacts with the NuRD and CoREST (HDAC) complexes. PROX1 depletion reprogrammed the RMS transcriptome to resemble benign mesenchymal stem cells and repressed previously identified RMS effector transcripts, placing it upstream of these genes. Our studies reveal a major role of PROX1-HDAC interaction in RMS and give insights for novel therapeutic targets.

overall_design: RNA sequencing (RNA-seq) analysis of four biological replicates of PROX1 silenced (75% deletion) and control RD cells.

first: Nebeyu

middle: Y

last: Gizaw


title: Screening and analysis of differentially expressed circRNAs and miRNAs in chronic diabetic extremity wounds [array]

overall_design: Six abnormally expressed circRNAs and miRNAs were detected by reverse transcription qPCR to verify the results of RNA sequencing. The dysregulated genes were enriched and analyzed by gene ontology and the Kyoto Encyclopedia of genes and genomes was used to clarify their main functions. ceRNA network were constructed.


title: RNA-seq reveals potential gene biomarkers in Pimephales promelas for exposure to treated wastewater effluent

city: Milwaukee

first: Rebecca

last: Klaper

state: WI

address: 600 E Greenfield Avenue

institute: University of Wisconsin - Milwaukee

summary: We investigated the impacts of wastewater effluent exposure on gene expression in adult fathead minnows, a freshwater fish commonly used as an ecotoxicological model.

overall_design: Examination of upstream and downstream effluent exposure on gene transcription

first: Peter

middle: G

last: Schumann

first: Emma

middle: B

last: Meade

first: Hui

last: Zhi

first: Gregory

middle: H

last: LeFevre

first: Dana

last: Kolpin

first: Shannon

last: Meppelink

first: Luke

last: Iwanowicz

first: Rachael

last: Lane

first: Angela

last: Schmoldt

first: Olaf

last: Mueller


title: Screening and analysis of differentially expressed circRNAs and miRNAs in chronic diabetic extremity wounds

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

overall_design: Refer to individual Series


title: Relieving Dyrk1a repression of MKL1 corrects developmental defects in infantile megakaryocytes

city: Charlottesville

first: Fujun

last: Qin

state: VA

address: 345 Crispell Dr.

institute: University of Virginia

summary: Adult and fetal megakaryocytes are morphologically different. These differences contribute to neonatal thrombocytopenia in premature neonates and in neonates after infection and also contribute to poor megakaryocytes engrafment after umbilical cord blood transplant. We found that Dyrk1a kinase inhibition shift the fetal megakaryocytes phenotype toward adult phenotype. This effect is mediated by MKL1 the master regulator of megakaryocytes morphogenesis. To identify  deferences between adult and fetal megakaryocytes we performed RNA seq of adult derived megakaryocytes and fetal derived megakaryocytes treated and untreated with Dyrk inhibitors. Through this approach we identified cohorts of genes co-regulated in adult megakaryocytes and fetal megakaryoctes treated with the dyrk inhibitors. More importantly, we found that the dyrk inhibition in fetal megakaryocytes leads to upregulation of a significant number of MKL1 target genes.

overall_design:
CB-DMSO vs CB-EHT 1610
CB-DMSO vs CB-Harmine
CB-DMSO vs PB-DMSO

first: Kamaleldin

last: Elagib

first: Sandeep

last: Singh

first: Xinrui

last: Shi

first: Adam

last: Goldfarb


title: RNA sequencing of the regulatory network of ginsenoside biosynthesis under Ro stress in the hairy roots of Panax ginseng

status: Public on Aug 27 2022

city: Zhengzhou

first: yanyong

last: cao

state: henan

address: No. 116, Huayuan Road

institute: Henan Academy of Agricultural Sciences

summary: Panax ginseng C.A. Meyer is a precious Chinese herbal medicine belonging to the Araliaceae family. Because ginseng is extremely taboo, it seriously restricts the sustainable development of the ginseng industry. The allelopathic effect of triterpenoid saponins is one of the important incentives for continuous cropping disorders. However, there are few studies on the mechanism of allelopathic autotoxicity of triterpenoid ginsenosides. Therefore, this study took ginseng hairy roots as the research object, exogenously added ginsenoside Ro to regulate the growth of hairy roots, and measured the changes in its physiological and saponin content. It was found that ginseng hairy roots grew significantly under Ro-0.5 mg/L stress. Inhibition, the specificity of root tip cell injury was obvious, promoted the accumulation of endogenous hormones IAA and SA, and inhibited the accumulation of ABA and JA. The accumulation of ginsenosides was significantly inhibited (except Rg3) under Ro-0.5 mg/L stress. The mRNA analysis of the Ro-0.5 mg/L group and CK group showed that the differentially expressed genes were mostly concentrated in the hormone signal transduction pathway. The genes ARF7 and EFM were up-regulated, and XTH23 and ZOX1 were down-regulated, which can be used as important candidates for hormone-responsive continuous cropping disorders. Gene. 74 differentially expressed miRNAs were identified based on miRNA sequencing, of which 22 were up-regulated and 52 were down-regulated. The target genes of ptc-miR156k_L+1, mtr-miR156b-5p, gma-miR156a_R+1, and mtr-miR156e were all TRINITY_DN14567_c0_g4, TRINITY_DN14567_c0_g4 is a gene in the plant hormone signal transduction pathway, and the four miRNAs are all negatively correlated with mRNA, indicating that ptc-miR156k_L+1, mtr-miR156b-5p, gma-miR156a_R+1, and mtr-miR156e are very likely involved in ginseng Response to continuous cropping disorders and regulation of ginsenoside synthesis. Our findings will provide a useful platform for unraveling the continuous cropping barrier of ginseng and new insights into the genetic engineering of plant stress responses.

overall_design:
From the perspective of plant physiology, ecology, and molecular biology, this study took the hairy roots of ginseng with relatively controllable experimental conditions as the research object, added ginsenoside Ro exogenously to simulate the phenomenon of continuous cropping obstacles, and dynamically detected the morphological changes. The damage degree of tip cells was measured, the contents of ginsenosides and endogenous hormones in hairy roots were measured, the response law of ginsenoside biosynthesis to ginsenoside Ro stress was explored, and the response law of ginsenoside-induced allelopathic damage to ginseng endogenous substances accumulation was revealed. Combined with mRNA and miRNA sequencing technologies, comprehensively analyze the toxic mechanism of ginseng's allelopathic interference at the transcriptional and post-transcriptional levels after ginsenoside Ro allelopathic stress.
Only the transcriptome sequencing results are used in this study.

first: Xiangru

last: Meng

first: Tao

last: Zhanga

first: Changbao

last: Chen


title: Co-administration of MDR1 and BCRP or EGFR/PI3K inhibitors overcomes lenvatinib resistance in hepatocellular carcinoma

status: Public on Aug 26 2022

city: Beijing

first: Juan

last: Liu

state: China

address: No 168, Litang Road

institute: Beijing Tsinghua Changgung Hosptial

summary:
To investigate the mechanism of lenvatinib resistance, we established the lenvatinib resistant Huh7 (Huh7 LR) cells by continuous exposuring to lenvatinib (1–20 μM) for approximately 10 months.
We then performed gene expression profiling analysis using data obtained from RNA-seq of Huh7 parental (Huh7 P) cells and the lenvatinib resistant Huh7 (Huh7 LR) cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Huh7 parental (Huh7 P) cells and the lenvatinib resistant Huh7 (Huh7 LR) cells.

last: LIU

first: Dawei

last: SUN


title: Transcriptome profiling of Microbacterium resistens MZT7 reveals mechanisms of 17β-estradiol response and biotransformation

status: Public on Aug 24 2022

city: Changchun

first: Peng

last: Hao

address: Xincheng Street

institute: Jilin Agricultural University School of Veterinary Medicine

summary: 17β-estradiol (E2) pollution has attracted much attention, and the existence of E2 poses certain risks to the environment and human health. However, the mechanism of microbial degradation of E2 remains unclear. In this study, the location of E2-degrading enzymes was investigated, and transcriptome analysis of Microbacterium resistens MZT7 (M. resistens MZT7) exposed to E2. The degradation of E2 by M. resistens MZT7 was via the biological action of E2-induced intracellular enzymes. With the RNA sequencing, we found 1,109 differentially expressed genes (DEGs). Among, 773 genes were up-regulated and 336 genes were down-regulated. The results of the RNA sequencing indicated the DEGs were related to transport, metabolism, and stress response. Genes for transport, transmembrane transport, oxidoreductase activity, ATPase activity, transporter activity and quorum sensing were up-regulated. Genes for tricarboxylic acid cycle, ribosome, oxidative phosphorylation and carbon metabolism were down-regulated. These findings provide some new insights into the molecular mechanism of biotransformation of E2 by M. resistens MZT7.

overall_design: In this study, we first localized the E2 degrading enzyme. Then we investigated the transcriptional differences between E2-treated and non-E2-treated strain MZT7 by RNA-seq technology to reveal the degradation mechanism and its response to E2 at the transcriptional level.

first: Zongshuo

last: Lv

first: Sicheng

last: Wu

first: Yunhang

last: Gao


title: Meiotic DNA breaks activate a streamlined response that largely avoids protein level changes

status: Public on Aug 29 2022

city: New York

first: Andreas

last: Hochwagen

address: 1009 Silver Center 100 Washington Square East

institute: New York University

summary: Meiotic cells introduce a large number of programmed DNA breaks into their genome to stimulate meiotic recombination and ensure controlled chromosome inheritance and fertility. To understand cells respond to these breaks we compared the proteome, phosphoproteome, and transcriptome of meiotic cells that can make breaks to the cells that cannot form breaks.

overall_design: RNA-Seq analysis of spo11-YF and SPO11 samples from three independent timecourses

first: Funda

last: Kar

first: Christine

last: Vogel


title: Effect of PUS1 knockdown on gene expression in  MDA-MB-231 breast cancer cells

city: NanJing

first: Zheng

last: Fang

state: Jiang Su

address: Guangzhou Road

department: Department of General Surgery, the First Affiliated Hospital

institute: Nanjing Medical University

summary:
To  identify the downstream target genes  of PUS1 on breast cancer cells, we established MDA-MB-231 cell lines in which PUS1 has been knocked down by shRNA.
We then performed gene expression profiling analysis using data obtained from RNA-seq of  PUS1 knockdownMDA-MB-231 cells as well as negative control shRNA group

overall_design: Compare negative control shRNA and PUS1 knockdown MDA-MB-231 cancer cells using RNA-seq.

first: Zhen

last: Zhu


title: Induced pluripotent stem cell-derived cells model brain microvascular endothelial cell glucose metabolism

status: Public on Aug 22 2022

city: College Park

first: Alisa

last: Morss Clyne

state: MD

address: 8278 Paint Branch Dr.

institute: University of Maryland

summary: To investigate the validity of using iPSC-derived brain microvascular endothelial-like cells (BMEC) as a model of human BMEC metabolism, we ran RNA-sequencing on iPSC-derived BMEC and compared gene expression of glycolytic and TCA enzymes to publically avaliable primary BMEC datasets.

overall_design: RNA-sequencing data for iPSC-derived BMEC cultured in DMEM supplemented with B27.

first: Callie

last: Weber

first: Bilal

last: Moiz

first: Sophia

last: Zic

first: Viviana

last: Alpizar Vargas

first: Andrew

last: Li


title: Gene expression profile magnetic beads sorted CD8+ T cells from naïve splenocytes and OVA257-264 peptide activated splenocytes from WT and Susd2-/-  OT-I mice

status: Public on Aug 28 2022

city: Columbus

first: Cankun

last: Wang

state: OH

address: 281 W Lane Ave, Columbus, OH 43210

institute: The Ohio State University Wexner Medical Center

summary: CD8+ T cells are phenotypically heterogeneous with varying degrees of functional change. We used Bulk RNA sequencing ( Bulk RNA-seq) to analyze the differences betwteen WT and Susd2-/- OT-I mice.

overall_design: CD8+ T cells were isolated by the EasySep Mouse CD8+ T Cell Isolation Kit (STEMCELL Technologies) from total splenocytes of either WT or Susd2-/- OT-I mice left untreated or stimulated with OVA257-264 for 3 days. There are 2 samples in WT and 2 samples in Susd2-/- at Day0, and  2 samples  WT and 2 samples in Susd2-/- at Day3.

first: Bao

last: Zhao

first: Haitao

last: Wen


title: Perturbation of O-GlcNAcylation homeostasis in Drosophila early embryos influences neurodevelopment by tuning facultative heterochromatin formation

status: Public on Aug 21 2022

city: Changsha

first: Yaowen

last: Zhang

address: Xiangya hospital, Xiangya Road

institute: Central South University

summary: Protein O-GlcNAcylation is a monosaccharide posttranslational modification maintained by two evolutionarily conserved enzymes, O-GlcNAc transferase (OGT) and O-GlcNAcase (OGA). Mutations in human OGT have recently been associated with neurodevelopmental disorders, and yet whether and how the disturbed O-GlcNAcylation homeostasis impact the development of nervous system is not fully understood. Here, we generate transgenic Drosophila lines that conditionally express Clostridium perfringens OGA (CpOGA) to perturbate the homeostasis of protein O-GlcNAcylation. We reveal that lowering O-GlcNAcylation level, even just during early embryogenesis, can affect olfactory learning ability in adulthood. Mechanistically, decline of protein O-GlcNAcylation accompanies with emergence of facultative heterochromatin. The forced downregulation of global O-GlcNAcylation by exogenous CpOGA activity promotes nuclear foci formation of Polycomb-group protein Polyhomeotic (Ph) and accumulation of K27 trimethylation of histone H3 (H3K27me3), leading to enhanced facultative heterochromatin formation, which in turn interferes zygotic expression of several neurodevelopmental genes, particularly short of gastrulation (sog), a component of an evolutionarily conserved signaling system required for specification of neuroectoderm. Our findings highlight the importance of early embryonic O-GlcNAcylation homeostasis for the formation of a fully functional nervous system, casting new light on the etiology of OGT-associated intellectual disability.

overall_design: 6 ChIP samples and 2 unenriched input control from the same crosslinked chromatin pool. PolyA RNA profiles of embryos with injecting CpOGA_WT and Cp_OGA_DM.

first: Y

first: X

last: Lei

first: D

last: van Aalten

first: K

last: Yuan


title: Role of Thy-1 in cutaneous fibrosis

city: Rochester

first: Marc

last: Nuzzo

address: 601 Elmwood Ave Box 695

department: AIR

institute: University of Rochester

summary: Thy-1 (CD90) is a multifactorial protein which is highly expressed in fibroblasts but whose role in fibrosis is not clear.  We performed bulk RNA-sequencing in the cutaneous bleomycin model to assess the transcriptomic effects of Thy-1 deficiency

overall_design: Assessment of gene expression in wildtype and Thy-1 knockout mice treated with bleomycin or PBS for 21 days

first: Roberta

last: Marangoni

first: Benjamin

last: Korman


title: Danlu Tongdu Tablets: Safety evaluation and mechanism of hepatotoxicity in Sprague-Dawley rats

status: Public on Aug 25 2022

first: Zhang

middle: Hai

last: Jing

address: A4, East Yinghua Street

department: Institute of chinese material medica

institute: China academy of chinese medical sciences

summary: Based on the acute and chronic toxicity study, we further focused on the impact of Danlu Tongdu (DLTD) on the liver. At the end of 26 weeks of administration, 4 male rats were selected from the control group and the high-dose group respectively for transcriptome analysis. The selection criteria were random selection from the control group, the four rats selected from the high-dose. group showed pathological changes in the liver.

overall_design: Rats were randomized into 2 groups. Rats in the control group (4 rats)  were treated with ultrapure water; rats in the high-dose group (4 rats)  were treated with 6.67 g/kg Danlu Tongdu.

first: Haijing

first: Yifei

last: Yang

first: Ting

last: Liu


title: Comparative analysis of piRNA sequences, targets and functions in Caenorhabditis nematodes

status: Public on Aug 23 2022

first: Wen

last: Tang

state: Ohio

address: 1060 Carmack Rd

department: Department of Biological Chemistry and Pharmacology

institute: The Ohio State University

summary: Piwi proteins and Piwi-interacting RNAs (piRNAs) are best known for their roles in suppressing transposons and promoting fertility. Yet piRNA biogenesis and its mechanisms of action differ widely between distantly related species. To better understand the evolution of piRNAs, we characterized the piRNA pathway in C. briggsae, a sibling species of the model organism C. elegans. Our analyses define 25,883 piRNA producing-loci in C. briggsae. piRNA sequences in C. briggsae are extremely divergent from their counterparts in C. elegans, yet both species adopt similar genomic organization and transcription program that drive piRNA expression. By examining production of Piwi-dependent secondary small RNAs, we identified a set of protein-coding genes that are evolutionarily conserved piRNA targets. In contrast to C. elegans, small RNAs mapped to ribosomal RNAs or histone transcripts are not hyper-accumulated in C. briggsae. Instead, we found that fewer introns in transcripts are associated with hyper-accumulation of small RNAs. Together our work highlights evolutionary conservation and divergence of the nematode piRNA pathway and provides insights into its role in endogenous gene regulation.

sample_organism:
Caenorhabditis briggsae
Caenorhabditis elegans

overall_design: Small RNA high-throughput sequencing was done using RNA from adult wild type and prg-1 mutant animals in C. elegans and C. briggsae. C. briggsae PRG-1 IP was preformed using adult animals. Differential gene expression analysis, and other analyses, was done to identify C. briggsae piRNA loci, as well as smRNA abundance changes between wild type and prg-1 mutants.

last: Pastore

first: Hannah

last: Hertz


title: Effects of manganese and its concomitant administration with isoniazid on macrophages infected with Mycobacterium tuberculosis

city: Bengbu

first: Qian

last: Kaiqiang

state: --- Select One ---

address: China

department: School of Life Sciences

institute: Bengbu Medical College

summary: In order to study the effect of manganese on the immunity of macrophages, we established a model of infection with Mycobacterium tuberculosis and treated it with manganese and isoniazid for 12 hours

overall_design: We divided into 5 samples from manganese treatment alone and treatment with isoniazid, each with three biological replicates, to explore the effect on macrophages

first: Kaiqiang

last: Qian

first: Jun

last: Xi


title: clampFISH 2.0 enables rapid, scalable amplified RNA detection in situ

city: Philadelphia

first: Arjun

last: Raj

state: PA

address: 415 Curie Blvd

department: Bioengineering

institute: University of Pennsylvania

summary: We developed an amplified single-molecule RNA FISH method called clampFISH 2.0. To validate its performance, we used clampFISH 2.0 on two cell lines, WM989 A6-G3 cells and WM989 A6-G3 cells grown in vemurafenib, and across 10 genes, compared clampFISH 2.0 spot counts to the FPKM values from bulk RNA sequencing.

overall_design: Resistant colonies were isolated from a plate of WM989 A6-G3 cells which were treated with 1µM vemurafenib. Bulk RNA sequencing was performed as described in Goyal et al. 2021 (https://doi.org/10.1101/2021.12.08.471833) for each resistant colony as well as drug-naive WM989 A6-G3 cells. For this analysis, a single resistant colony was included for comparison to the drug-naive WM989 A6-G3 cells. Briefly, we conducted standard bulk paired-end (37:8:8:38) RNA sequencing using RNeasy Micro (Qiagen, 74004) for RNA extraction, NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB E7490L), NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB, E7770L), NEBNext Multiplex Oligos for Illumina (Dual Index Primers Set 1) oligos (NEB, E7600S), and an Illumina NextSeq 550 75 cycle high-output kit (Illumina, 20024906), as previously described (Mellis et al. 2021; Shaffer et al. 2017). Prior to extraction and library preparation, the samples were randomized to avoid any experimental and human biases. We aligned RNA-seq reads to the human genome (hg19) with STAR v2.5.2a and counted uniquely mapping reads with HTSeq v0.6.1 (Dobin et al. 2013; Mellis et al. 2021; Shaffer et al. 2017) and outputs count matrix. The counts matrix was used to obtain tpm and other normalized values for each gene using scripts provided at: https://github.com/arjunrajlaboratory/RajLabSeqTools/tree/master/LocalComputerScripts

first: Yogesh

last: Goyal

first: Ian

last: Dardani


title: Effect of AKTIP depletion in breast cancer cells

status: Public on Aug 19 2022

city: Pokfulam

first: Lydia

last: Cheung

address: 21 Sassoon Road

department: School of Biomedical Sciences

country: Hong Kong

institute: University of Hong Kong

summary: Copy number loss of AKTIP gene is frequently observed in breast cancer particularly luminal breast cancer. To determine the alterations in transcriptome upon AKTIP loss in luminal breast cancer cell line MCF7 and triple negative breast cancer cell line SKBR3, RNAseq of cells transfected with AKTIP siRNA was performed.

overall_design: Transient transfection of AKTIP siRNA for 72 hours in two cell lines, mock transfected cells as control. Two biological replicates per condition.


title: Allele-specific differential regulation of monoallelically expressed autosomal genes in the cardiac lineage [CUT&Tag]

city: Cold Spring Harbor

first: Gayan

middle: Indhu

last: Balasooriya

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

summary: We reported the allele-specific single cell RNA sequencing in highly morphogenic (C57Bl6J-maternal x CASTEiJ-paternal) male F1 mouse embryonic stem cells (mESC) and in vitro mESC derived six cardiac lineage cell types. We demonstrated distinctive gene regulation based on the parental origin of the alleles. We showed that deterministic and stochastic monoalleleic gene classes are distinctive in regulation and are involved in unique processes. In this study we highlighted the importance of parental origin-specific gene expression in development, homeostasis and disease.

overall_design: Examination of allele-specific histone signatures in F1 mESCs.

middle: I

first: David

last: Spector