title: Divergent metabolic programs control two populations of MAIT cells that protect the lung

status: Public on Mar 29 2023

first: Thomas

last: Riffelmacher

address: Athena Circle drive

institute: La Jolla Institute for Immunology

summary: Although mucosal associated invariant T (MAIT) cells provide rapid, innate-like responses, they are not pre-set and memory-like responses have been described for MAIT cells following infections. The importance of metabolism for controlling these responses, however, is unknown. Following pulmonary immunization with a Salmonella vaccine strain, mouse MAIT cells expanded as separate CD127-Klrg1+ and CD127+Klrg1- antigen-adapted populations that differed for their transcriptome, function and localization in lung tissue. These populations remained altered from steady-state for months as stable, separate MAIT cell lineages with enhanced effector programs and divergent metabolism. CD127+ MAIT cells engaged in an energetic, mitochondrial metabolic program, which was critical for their maintenance and IL-17A synthesis. This program was supported by high fatty acid uptake and mitochondrial oxidation and relied on highly polarized mitochondria and autophagy. After vaccination, CD127+ MAIT cells protected mice against Streptococcus pneumoniae infection. In contrast, Klrg1+ MAIT cells had dormant, but ready-to-respond mitochondria and depended instead on Hif1a-driven glycolysis. They responded vigorously to cytokines and participated in protection from influenza virus. These metabolic dependencies may enable tuning of memory-like MAIT cell responses for vaccinations and immunotherapies.

overall_design: RNAseq of mouse MAIT cells sorted by Tetramer, TCR and dump exclusion

first: Simon

last: Brunel

first: Vianka

last: Castellan

first: Shilpi

last: Chandra


title: Young and old breast skin, and fibroblast cell line RNA seq data

status: Public on Mar 30 2023

city: Boston

first: Tomonori

last: Oka

state: MA

department: CBRC

country: USA

institute: Massachusetts general hospital

type: Expression profiling by high throughput sequencing

summary: Young and old breast skin, normal fibroblast cell line, senescent fibroblast cell line RNA seq data

overall_design: We collected young (less than 27-year old) and old normal breast skin samples (over 58-year old) from surgery and investigated which gene is changed in old skin compared to young skin. We also bought a commercially available fibroblast cell line and passaged it for 27 times. We investigated gene expression in senescent induced (27 times passaged) fibroblasts compared to non-senescent induced (4 times passaged) firboblasts.

first: Tatsuya

last: Hasegawa

first: Shadmehr

last: Demehri


title: The UHRF1 protein is a key regulator of retrotransposable elements and innate immune response to viral RNA in human cells

status: Public on Mar 31 2023

city: Coleraine

first: Colum

middle: Patrick

last: Walsh

state: County Londonderry

address: Cromore Road

department: Life and Health Sciences

country: United Kingdom

institute: Ulster University

type:
Methylation profiling by array
Expression profiling by array

summary: While epigenetic mechanisms such as DNA methylation and histone modification are known to be important for gene suppression, relatively little is still understood about the interplay between these systems. The UHRF1 protein can interact with both DNA methylation and repressive chromatin marks, but its primary function in humans has been unclear. To determine what that was, we first established stable UHRF1 knockdowns in normal, immortalized human fibroblasts. Although these showed a loss of DNA methylation across the whole genome, transcriptional changes were dominated by the activation of genes involved in innate immune signaling, consistent with the presence of viral RNA from retrotransposable elements (REs). We confirmed using mechanistic approaches that 1) REs were demethylated and transcriptionally activated, producing double-stranded RNA; 2) this triggered activation of interferons and interferon-stimulated genes and 3) the pathway was conserved across other adult cell types. Restoring UHRF1 in either transient or stable knockdown systems could abrogate RE reactivation and the interferon response. Notably, UHRF1 itself could also re-impose RE suppression in the absence of DNA methylation, but not if the protein contained point mutations affecting histone 3 with trimethylated lysine 9 (H3K9me3) binding. Our results therefore show for the first time that UHRF1 can act as a key regulator of retrotransposon silencing even in the absence of DNA methylation.

overall_design: Stable knockdowns of Ubiquitin Like With PHD And Ring Finger Domains 1 UHRF1 were generated in hTERT-immortalised adult fibroblasts using shRNA. WThTERT-1604 cells were used in triplicate as a control. Genome wide methylation and transcriptional levels were assayed using the Illumina 450k BeadChip and subsequently analysed using bioinformatic approaches. Genes targets of relevant interest identified through bioinformatic mining were validated using wet lab approaches.

first: Rachelle

last: Irwin

first: Catherine

last: Scullion

first: Sara-Jayne

last: Thursby

first: Meiling

last: Sun

first: Avinash

last: Thakur

first: Rothbart

last: Scott

first: Guoliang

last: Xu

middle: P


title: Induction of a torpor-like hypothermic and hypometabolic state in rodents by ultrasound

city: st louis

first: Hong

last: Chen

state: MO

address: 4511 Forest Park Ave

institute: Washington University in st louis

summary: Torpor is an energy-conserving state in which animals dramatically decrease their metabolic rate and body temperature to survive harsh environmental conditions. Here, we report the noninvasive, precise, and safe induction of a torpor-like hypothermic and hypometabolic state in rodents by remote transcranial ultrasound stimulation at the hypothalamus preoptic area (POA). We achieve a long-lasting (> 24 hours) torpor-like state in mice via closed-loop feedback control of ultrasound stimulation with automated detection of body temperature. Ultrasound-induced hypothermia and hypometabolism (UIH) is triggered by activation of POA neurons, involves the dorsomedial hypothalamus as a downstream brain region and subsequent inhibition of thermogenic brown adipose tissue. Single-nucleus RNA-sequencing of POA neurons reveals TRPM2 as an ultrasound-sensitive ion channel, the knockdown of which suppresses UIH. We also demonstrate that UIH is feasible in a non-torpid animal, the rat. Our findings establish UIH as a promising technology for the noninvasive and safe induction of a torpor-like state. To investigate the mechanism of ultrasound-induced neuronal activation, we applied ultrasound stimulation in hypothalamic preoptic area region and performed single-nuclei RNA sequencing in the ultrasound stimulated neurons (US+) and neurons without ultrasound stimulation (US-). In our sn-RNAseq analysis, we examined the association between the expression of neuronal activation markers (or IEGs) and ion channels, as well as neuron types.

overall_design: The hypothalamic preoptic area from ultrasound-stimulated (US+) and sham (CON, US-) groups, involving 4 mice per group.  Brain tissues were dissected approximately 1 hour after ultrasound stimulation.

first: Yaoheng

last: Yang


title: Gene expression changes in HEK293 cells following PEG10 overexpression.

city: Boulder

first: Alexandra

last: Whiteley

state: CO

address: 596 UCB

institute: University of Colorado, Boulder

summary: The goal of this study was to determine transcriptional changes in HEK293 cells upon overexpression of various forms of Paternally Expressed Gene 10, or PEG10. Cells were transfected either with control, or with PEG10 gag, gag-pol, or isolated NC fragment constructs and RNA isolated for RNA-Seq analysis.

overall_design: Three independent passages of HEK293 cells were transfected with PEG10-expressing constructs (gag-pol, gag, NC) or control (LifeAct).

first: Holly

middle: H

last: Black

first: William

last: Campodonico

middle: M


title: CUT-TAG for NB4 cell line with either no treatment or LDB1 overexpression

city: Suzhou

first: Fang

last: Fang

state: Jiangsu

address: 92 Zhongnan street

country: China

institute: Children’s Hospital of Soochow University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to explore CUT-TAG results for LDB1 in NB4 cell line.

overall_design: 1 NB4 sample with no treatment and 1 NB4 sample with LDB1 overexpression

first: Pan

last: Jian

first: Lu

last: Lihui


title: Olfactory and neuropeptide inputs to appetite neurons in the arcuate nucleus

status: Public on Mar 27 2023

city: Seattle

first: Linda

last: Buck

state: Washington

address: 1100 fairview ave North

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Centre

summary: We report RNA sequencing of single Agrp neurons isolated from the arcuate nucleus of the hypothalamus. Analyses of Agrp neuron transcriptomes reveals differential expression of receptors for multiple neuromodulators. Neuroanatomical mapping of known ligands of the receptors define subsets of neurons directly upstream of AgRP neurons in specific brain areas.

overall_design: Isolation of fluorescently labelled individuals cells disociated from the mouse arcuate nuclues. Cells were visualized and isolated using a micropipette under a microscope, followed by cell lysis, RT, and cDNA synthesis.


title: Integrating lipid metabolism, pheromone production and perception by Fruitless and Hepatocyte Nuclear Factor 4

status: Public on Mar 25 2023

city: New Orleans

first: Jie

state: Louisiana

address: 1700 Tulane Ave

department: School of Medicine, Department of Biochemistry

institute: Tulane University

summary: Our study found that the non-sex specific Fru isoform (FruCOM) is necessary for pheromone biosynthesis in hepatocyte-like oenocytes for sexual attraction. Loss of FruCOM in oenocytes resulted in adults with reduced levels of the cuticular hydrocarbons (CHCs), including sex pheromones, and show altered sexual attraction and reduced cuticular hydrophobicity. To further determine the downstream related mechanism, we performed bulk RNAseq analysis on the oenocyte of Drosophila melanogaster.

overall_design:
Adult oenocytes were carefully dissected in 1 x PBS before RNA extraction. Total RNAs were extracted from 7-day-old adult oenocytes using the Zymo RNA preparation kit. Two replicates were collected for each genotype. NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Ultra II RNA Library Prep Kit for Illumina were used for library preparation. The libraries were sequenced using an Illumina HiSeq 2500 system, obtaining 40 million reads for each sample. As a result, multiple metabolic pathways and the CHC biosynthetic pathway regulated by Fru were revealed.
https://zenodo.org/record/7752914


title: Single Nucleus RNA Sequencing of Human Kidney Allografts with Cellular Rejection

status: Public on Mar 28 2023

first: Jamil

middle: R

last: Azzi

address: 221 Longwood ave

department: Transplantation Research Center

institute: Brigham and Women's Hospital

summary: Kidney transplant recipients are currently treated with nonspecific immunosuppressants that cause severe systemic side effects. Current immunosuppressants were developed based on their effect on T-cell activation rather than the underlying mechanisms driving alloimmune responses. Thus, understanding the role of the intragraft microenvironment will help us identify more directed therapies with lower side effects. To understand the role of the alloimmune response and the intragraft microenvironment in cellular rejection progression, we conducted a Single nucleus RNA sequencing (snRNA-seq) on one human non-rejecting kidney allograft sample, one borderline sample, and T-cell mediated rejection (TCMR) sample (Banff IIa). We studied the differential gene expression and enriched pathways in different conditions, in addition to ligand-receptor (LR) interactions.Pathway analysis of T-cells in borderline sample showed enrichment for allograft rejection pathway, suggesting that the borderline sample reflects an early rejection. Hence, this allows for studying the early stages of cellular rejection. Moreover, we showed that focal adhesion (FA), IFNg pathways, and endomucin (EMCN) were significantly upregulated in endothelial cell clusters (ECs) of borderline compared to ECs TCMR. Furthermore, we found that pericytes in TCMR seem to favor endothelial permeability compared to borderline. Similarly, T-cells interaction with ECs in borderline differs from TCMR by involving DAMPS-TLRs interactions. Our data revealed novel roles of T-cells, ECs, and pericytes in cellular rejection progression, providing new clues on the pathophysiology of allograft rejection.

overall_design: We used frozen human kidney allograft biopsies from three different patients diagnosed with non-rejection, borderline rejection, and T-cell mediated rejection based on Banff criteria. Non-rejection sample was used as a control. We isolated single nuclei and performed single nuclei RNA sequencing.

first: Ahmad

last: Halawi

first: Abdullah

last: ElKurdi

first: Katherine

last: Vernon

first: Anna

last: Greka

first: Pierre

last: Khoueiry


title: Gene expression profiling of granuloma T cells in M. tuberculosis infected rhesus macaques reveals a critical role for CD30

status: Public on Mar 24 2023

city: Bethesda

first: Timothy

middle: G

last: Myers

state: MD

address: 50 South Drive, Room 5509

department: Research Technologies Branch

institute: National Institute of Allergy and Infectious Diseases

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

sample_organism:
Macaca mulatta
Mus musculus

platform_organism:
Macaca mulatta
Mus musculus

overall_design: Refer to individual Series


title: Gene expression profiling of granuloma T cells in M. tuberculosis infected rhesus macaques reveals a critical role for CD30 [Mus musculus]

summary: Control of Mycobacterium tuberculosis infection requires generation of T cells that migrate to granulomas, complex immune structures surrounding sites of bacterial replication. Here we compared the gene expression profiles of T cells in pulmonary granulomas, bronchoalveolar lavage and blood of Mtb-infected rhesus macaques to identify granuloma-enriched T cell genes. TNFRSF8/CD30 was among the top genes that was upregulated in both CD4 and CD8 granuloma T cells and independent of bacterial loads. Transcriptomic profiling of lung T cells from Mtb-infected mixed bone marrow chimeric mice showed that CD30 directly promotes CD4 T cell differentiation and effector molecule expression. Moreover, in mice CD30 expression on CD4 T cells is required for survival of Mtb infection. These results show the CD30 co-stimulatory axis is highly upregulated on granuloma T cells and is critical for the generation of protective T cell responses against Mtb infection.

overall_design: RNA-seq of mouse CD4  T-cells. Balanced 2-factor design (WT/KO; MTb Activated/ Naïve), N=4 mice per group

first: Taylor

middle: W

last: Foreman

first: Daniel

middle: L

last: Barber


title: Analysis of p65 genomic location changes with IL-17 blockade

city: Barcelona

first: Oscar

last: Reina Garcia

state: Barcelona

address: C/Baldiri Reixac 10

department: Biostatistics and Bioinformatics

country: Spain

institute: IRB Barcelona

summary: We characterize the effect that IL-17 blockade has on p65 genomic location in epidermal aged cells

overall_design: p65 ChIP-seq of adult, aged epidermal cells upon treatment with IL-17 neutralizing antibodies or a control IgG

first: Paloma

last: Solá

first: Elisabetta

last: Mereu

first: Júlia

last: Bonjoch

first: Marta

last: Casado

last: Reina

first: Manel

last: Esteller

first: Holger

last: Heyn

first: Guiomar

last: Solanas

first: Salvador

last: Aznar Benitah


title: Trancriptomics effect of IL-17 blockade on aged murine epidermal cells

summary: We characterize the anti-inflammatory effect that IL-17 blockade has on epidermal aged cells

overall_design: total RNA-seq of aged epidermal cells upon treatment with IL-17 neutralizing antibodies or a control IgG


title: Trancriptomics effect of IL-17 blockade on aged murine epidermal cells [young vs old]

overall_design: total RNA-seq of young and aged epidermal cells upon treatment with control IgG

first: Solá

last: Paloma

first: Mereu

last: Elisabetta


title: Gene expression profiling of granuloma T cells in M. tuberculosis infected rhesus macaques reveals a critical role for CD30 [Macaca mulatta]

status: Public on Mar 22 2023

overall_design: RNA-seq of CD4 and CD8 T-cells isolated from pulmonary granulomas from 4 non-human primates infected with Mycobacterium tuberculosis strain Erdman


title: Temporal Genomics Mechanisms Underlying Disease and Aging [RNA-Seq]

status: Public on Mar 21 2023

city: University Park

first: Idan

last: Shalev

state: PA

address: 219 Biobehavioral Health Building, Penn State University

institute: Penn State University

summary: Given the salient role of early-life adversity (ELA) and the resulting biological embedding in disease risk, there is a critical need to understand the mechanisms operating at multiple levels of analysis in order to promote effective clinical treatments and intervention efforts for survivors. An example for such an effort could be to utilize models of dynamic cellular markers as individual-level factors to account for variation in intervention response and clinical outcomes. Results of this study will lead to new knowledge about specific gene expression pathways in response to stress, and whether the response is moderated by previous exposure to early adversity, shorter telomere length (a marker of cellular aging) and self-report mental-health measures. Thus, the long-term effects of this study will advance our understanding on stress-related transcriptomic changes that play a downstream role in disease susceptibility and accelerated aging, with the goal of targeting specific pathways and genes for potential intervention studies and pharmacological treatments to reverse the effects of exposure to early adversity. For example, considering high failure rates for depression treatments, and in order to tailor individual interventions, identifying objective changes in stress-induced gene expression may help to predict intervention efficacy in clinical and non-clinical settings, as seen, for example, in breast and leukemia cancers. Thus, findings will have a range of impacts for basic science, intervention studies and clinical practice that will influence treatments to match the specific cellular processes operating within an individual.

overall_design: Testing was carried out in Penn State's Clinical Research Center (CRC). The CRC has rooms for conducting the Trier Social Stress Test (TSST) stress-task and for no-stress control condition. Participants made two visits to the CRC, one week apart, on the same day of the weekday. Sessions were scheduled from 11:00 am to 4:15 pm and four blood samples were collected at 11:30am, 12:45pm, 1:45pm and 4:15pm. We used a randomized counter-balanced order for the two sessions (i.e., TSST and control conditions where TSST started at 12:00pm) with group membership blind to the subjects and lab personnel. In the no-stress control condition, participants were instructed to sit in a room, read magazines, and to refrain from any stressful activities (e.g., cell-phone use was restricted). In total, eight samples were collected from each participant across both sessions. For full details of study protocol, please see Shalev et al., 2020, PLoS One; doi: 10.1371/journal.pone.0221310. PMCID: PMC7122782

first: Abner

middle: T

last: Apsley


title: Transcriptomic profiling of Tg(fabp10a:hUHRF1-EGFP)high zebrafish livers and control siblings at 5 dpf

city: Abu Dhabi

first: Kirsten

last: Sadler Edepli

state: Abu Dhabi

department: Biology

country: United Arab Emirates

institute: New York University Abu Dhabi

summary: Overexpression of high levels of human UHRF1 tagged with EGFP (hUHRF1-EGFP)high in zebrafish hepatocytes induces cellular senescence by 5 days post fertilization (dpf) and hepatocellular carcinoma by 15-20 dpf. The goal of this study is to compare the transcriptome profile of zebrafish livers with (hUHRF1-EGFP)high overexpression compared to WT siblings. RNAseq was performed on RNA extracted from pools of microdissected liveres by using RiboZero libary prep to capture all transcripts, including transposable elements, that are expressed in the livers.

overall_design: Tg(fabp10a:hUHRF1-EGFO)high+/- were incrossed and the resulting larvae were raised and the liver from 20-30 larvae was manually dissected from 5 independent clutches at 120 hpf. Livers with UHRF1 overexpression were selected based on EGFP fluorescence and non-transgenic siblings with no fluorescence were collected as controls. Livers were manually dissected under the stereomicroscope and put directly in Trizol for total RNA  extraction. RNA was DNAseI treated, depleted for ribosomal RNA by using  Ribo-Zero Gold treatment and used for Illumina  Truseq RNA sample prep kit, version 2.

first: Elena

last: Magnani

middle: C

last: Sadler


title: Global effects of pharmacologic inhibition of OSBP in human umbilical vein endothelial cells

status: Public on Mar 20 2023

city: Helsinki

first: Juuso

last: Taskinen

address: Tukholmankatu 8

country: Finland

institute: Minerva Foundation Institue for Medical Research

summary: We investigate how the pharmaceutical inhibtion of OSBP with SWG or OSW1 affected the macromolecule profile of human umbilical vein endothelial cells by transcriptomic and lipidomic profiling

overall_design: Comparative gene expression profiling analysis of RNA-seq data for SWG or DMSO treated HUVECs

first: Vesa

last: Olkkonen

first: Hanna

last: Ruhanen

first: Reijo

last: Käkelä

first: Silke

last: Matyisk


title: Human CCR6+ Th cells show both an extended stable gradient of Th17 activity and imprinted plasticity [Spsingh-10x-TCR-plus-transcriptome-kit]

first: Timothy

last: Myers

summary: Th17 cells have been investigated in mice primarily for their contributions to autoimmune diseases. However, the pathways of differentiation of Th17 and related Th cells (type 17 cells)  and the structure of the type 17 memory population in humans are not well understood; such understanding is critical for manipulating these cells in vivo. By exploiting differences in levels of surface CCR6, we found that human type 17 memory cells, including individual T cell clonotypes, form an elongated continuum of type 17 character along which cells can be driven by increasing RORt. This continuum includes cells preserved within the memory pool with potentials that reflect the early preferential activation of multiple over single lineages. The CCR6+ cells’ phenotypes and epigenomes are stable across cell divisions under homeostatic-like conditions. Nonetheless, activation in polarizing and non-polarizing conditions can yield additional functionalities, revealing, respectively, both environmentally induced and imprinted mechanisms that contribute differentially across the continuum to yield the unusual plasticity ascribed to type 17 cells.

overall_design: Single cell (10x) combination whole-transcriptome and TCR V(D)J specific10x libraries (10x) were generated from the same single cells. Cell populations were FACS-sorted T-cell subsets defined by graded CCR6 expression (CCR6neg, CCR6low, CCR6int, CCR6high). Independently from two different human donors.

first: Satya

last: Singh

first: Joshua

last: Farber


title: Human CCR6+ Th cells show both an extended stable gradient of Th17 activity and imprinted plasticity [Spsingh-10xTCR-CMV]

overall_design: Single cell TCR V-d-J sequencing of 4 T-cell subsets with graded levels of CCR6. Independent replicates from two donors. This experiment utilizes an enrichment of an anti-CMV sub-population of T-cells ,which decreases the TCR diversity such that shared clonotypes can be detected and tracked across the CCR6 subsets.


title: Temporal Genomics Mechanisms Underlying Disease and Aging


title: Temporal Genomics Mechanisms Underlying Disease and Aging [DNA Methylation]

summary: Given the salient role of early-life adversity and the resulting biological embedding in disease risk, there is a critical need to understand the mechanisms operating at multiple levels of analysis in order to promote effective clinical treatments and intervention efforts for survivors. An example for such an effort could be to utilize models of dynamic cellular markers as individual-level factors to account for variation in intervention response and clinical outcomes. Results of this study will lead to new knowledge about specific gene expression pathways in response to stress, and whether the response is moderated by previous exposure to early adversity, shorter telomere length (a marker of cellular aging) and self-report mental-health measures. Thus, the long-term effects of this study will advance our understanding on stress-related transcriptomic changes that play a downstream role in disease susceptibility and accelerated aging, with the goal of targeting specific pathways and genes for potential intervention studies and pharmacological treatments to reverse the effects of exposure to early adversity. For example, considering high failure rates for depression treatments, and in order to tailor individual interventions, identifying objective changes in stress-induced gene expression may help to predict intervention efficacy in clinical and non-clinical settings, as seen, for example, in breast and leukemia cancers. Thus, findings will have a range of impacts for basic science, intervention studies and clinical practice that will influence treatments to match the specific cellular processes operating within an individual.


title: Effect of the lysphosphatidylcholine analogue edelfosine on gene expression in Saccharomyces cerevisiae

status: Public on Mar 19 2023

city: Calgary

first: Vanina

last: Zaremberg

state: Alberta

address: 2500 University Dr NW

department: Biological Sciences

country: Canada

institute: University of Calgary

summary: To investigate the impact of a lysolipid burden in the nuclear envelope on the regulation of gene expression, particularly in tethered nuclear domains, we treated cells with edelfosine.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for S. cerevisiae cells treated with edelfosine for 60 minutes.

first: Maria

last: Sosa Ponce

first: Jennifer

middle: A

last: Cobb


title: Coordinated stimulation of axon regenerative and neurodegenerative transcriptional programs by Atf4 following optic nerve injury

city: San Francisco

first: Trent

last: Watkins

email: trentw@bcm.edu, trent.watkins@ucsf.edu

state: CA

address: 675 Nelson Rising Lane, Rm 214A

department: Neurology

institute: University of California at San Francisco

summary: To understand the contributions of the Integrated Stress Response (ISR) to the axon regenerative and neurodegenerative transcriptional programs activated by axon injury in the CNS, we evaluated by RNA-seq the retinal transcriptomes of conditional knockout mouse lines for components of the ISR three days after optic nerve crush injury. Prior to injury, intravitreal injection of AAV2-mTagBFP2-ires-Cre under the control of the human synapsin-1 promoter facilitated neuron-specific knockout of Eif2ak3, the gene that encodes the ER stress-responsive kinase Perk; Atf4, the gene that encodes the ISR mediator Activating transcription factor-4; or Ddit3, the gene that encodes another transcription factor that can mediate the ISR, C/ebp homologous protein, or CHOP. We compared the expression profiles of these transgenic retinas after injury to retinas from wildtype mice with and without injury to identify transcripts whose regulation by axon injury is dependent on ISR signaling.

overall_design: Comparative gene expression analysis of whole mouse retina 3 days post-optic nerve crush (3 dpc) across three transgenic lines (ATF4 cKO, PERK cKO, and CHOP cKO, n=4-5 per genotype) compared to similarly treated wildtype retinas (n=5), with uninjured wildtype (n=4) serving as an additional control.

first: Preethi

last: Somasundaram

first: Melissa

last: Rudy

first: Nicholas

last: Tran


title: A hyper-quiescent chromatin state is a barrier to productive regeneration during aging. [DNA-Seq]

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

summary: Epigenetic alterations are one of the key hallmarks of aging. Emerging evidence in model organisms, senescent cell cultures and limitedly, murine, and human tissue samples suggest local effects impacting genes and regulatory elements. However, how chromatin changes broadly affect euchromatin-heterochromatin balance, three-dimensional chromatin conformation, histone composition and global transcriptome has not been addressed. Furthermore, the cause and impact of these alterations on tissue function and age-related loss of regeneration is not well-understood. Here, using murine liver as a model for regeneration and an integrated multi-omics approach, we find that aged cells assume a severely repressed hyper-quiescent chromatin state characterized by a condensed chromatin, broad heterochromatinization driven by H3K27me3, global suppression of the transcriptome and inability of the chromatin to self-interact over long distances. Interestingly, concomitant targeted chromatin opening occurs over developmental gene promoters leading to loss of cell identity. We extend our findings to other quiescent tissues including human liver biopsies. Our findings reveal that global chromatin alterations promote a cellular state that is refractory to injury sensing and repair. Local chromatin changes compromise cellular identity. Together, this study provides possible explanations for age-related loss of regeneration and tissue function at the chromatin level.

overall_design: DNA-seq of chromatin eluted at different salt concentrations. n= 2 replicates per group.

last: Yang

first: Payel

last: Sen


title: Oxygen Toxicity Causes Cyclic Damage by Destabilizing Specific Fe-S Cluster-Containing Protein Complexes

status: Public on Mar 18 2023

first: Xuewen

last: Chen

address: 1650 Owens Street

institute: Gladstone Institutes

summary: Oxygen is toxic across all three domains of life. Yet, the underlying molecular mechanisms remain largely unknown. Here, we systematically investigate the major cellular pathways affected by excess molecular oxygen. We find that hyperoxia destabilizes a specific subset of Fe-S cluster (ISC)-containing proteins, resulting in impaired diphthamide synthesis, purine metabolism, nucleotide excision repair, and electron transport chain (ETC) function. Our findings translate to primary human lung cells and a mouse model of pulmonary oxygen toxicity. We demonstrate that the ETC is the most vulnerable to damage, resulting in decreased mitochondrial oxygen consumption. This leads to further tissue hyperoxia and cyclic damage of the additional ISC-containing pathways. In support of this model, primary ETC dysfunction in the Ndufs4 KO mouse model causes lung tissue hyperoxia and dramatically increases sensitivity to hyperoxia-mediated ISC damage. This work has important implications for hyperoxia pathologies, including bronchopulmonary dysplasia, ischemia-reperfusion injury, aging, and mitochondrial disorders.

overall_design: The genome-wide CRISPR screen was performed in K562 cells exposed to 50% oxygen (hyperoxia) or 21% oxygen (normoxia) to identify pathways contributing to hyperoxia toxicity in cells.

first: Alan

last: Baik

first: Augustinus

last: Haribowo

first: Isha

last: Jain


title: Gene expression data from murine lung cells of C57BL6JJcl and Mayumi-Emphysema mouse

status: Public on Mar 26 2023

city: Izumo

first: Ryosuke

last: Tanino

address: 89-1 Enya

department: Department of Internal Medicine

country: Japan

institute: Shimane University

summary: Mayumi-Emphysema (ME) mouse is an inbred strain originally from C57BL/6JJcl (B6) by serial intercrossing more than 20 times. ME mouse can be maintained by regular accommodation and are viable and fertile. However, ME mouse spontaneously develops hereditary emphysema with aging. ME mouse shows partial emphysema at young and panlobular-like emphysema at adult. To find features in emphysematous lung cells of young ME mice, we compared gene expression from lung specimens of control B6 and ME mice at 8-week age.

overall_design: To compare gene expression between B6 and ME mice, we mixed total RNA by 6-biological replicate from lung cells of B6 or ME mice at 8-week old.

first: Yukari

last: Tsubata

first: Takamasa

last: Hotta

first: Tamio

last: Okimoto

first: Yoshihiro

last: Amano

first: Mayumi

last: Takechi

first: Tetsuya

last: Tanaka

first: Tomomi

last: Akita

first: Mamiko

last: Nagase

first: Chikamasa

last: Yamashita

first: Koichiro

last: Wada

first: Takeshi

last: Isobe


title: Human CCR6+ Th cells show both an extended stable gradient of Th17 activity and imprinted plasticity

status: Public on Mar 17 2023

first: Timothy

last: Myers

type: Methylation profiling by genome tiling array

sample_organism:
Homo sapiens
unidentified


title: miRNA expression in male mice in the basolateral amygdala following restraint stress

city: Bristol

first: Valentina

last: Mosienko

address: University Walk

institute: University of Bristol

summary:
Analysis of miRNA expression in amygdalae of male C57BL/6J mice following a 6-hour of restraint stress in comparison to control, stress-naïve animals.
In this study, we identified overxepression of miR-483-5p in the amygdala of male mice following stress.

overall_design: Amygdalae from wild-type control (n=12) and restraint stressed mice (n=12) were isolated. RNA pulled from three mice was hybridized to one replicate giving a total n number of 4 for  samples per group.

first: Robert

last: Pawlak

first: Mariusz

last: Mucha

first: Nathan

last: Skene


title: Human CCR6+ Th cells show both an extended stable gradient of Th17 activity and imprinted plasticity [humanmethylation450]

overall_design: HumanMethylation450 assay of 4 human donors, CD4+CD45RO- and CD4+CD45RO+ T-cells sorted into  CCR6neg, CCR6low, CCR6int and CCR6high subsets

first: Satya

last: Singh

first: Joshua

last: Farber


title: A hyper-quiescent chromatin state is a barrier to productive regeneration during aging.

first: Supriyo

last: De

type: Methylation profiling by high throughput sequencing

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Cdk5i peptide treatment in aged Tau P301S mice

city: Cambridge

first: Ravikiran

last: Raju

address: 15A Maple Ave

department: Picower Institute

institute: MIT

summary: To investigate the effects of Cdk5i peptide treatment on gene expression in cortical neurons that isolated from aged Tau P301S mice

overall_design: We began delivery of either Cdk5i or scrambled peptides every other day by IP injection (20 mg/kg body weight) to a group of Tau P301S mice aged 7 to 9 months old. We isolated NeuN+ nuclei from cortical tissue of 7- to 9-month-old animals for downstream RNA-seq analysis.

first: Ping-Chieh

last: Pao

first: Li-Huei

last: Tsai


title: IFN-g and Androgens Synergistically Disrupt Mitochondrial Function in Murine Myocytes

status: Public on Mar 15 2023

first: Thomas

middle: Joshua

last: Meyer

address: 41 Center Drive, Building 41, Room B620

department: National Cancer Institute

institute: National Institutes of Health

summary: We report here, aberrant cardiovascular activity in vivo in an autoimmune mouse model with persistent low-level expression of IFN-g (designated ARE mice) linked with androgen exposure, results in a mitochondrial and metabolic deficiency.

overall_design: 4 WT and 4 ARE-/- male mice hearts are examined via bulk RNAseqencing

first: John

last: Fenimore

first: Danielle

last: Springer

first: Julio

last: Valencia

first: Maria

middle: E

last: Romero

first: Elijah

middle: F

last: Edmondson

first: Sudhirkumar

last: Yanpallewar

first: Thea

last: Spindel

first: Elizabeth

last: Engle

middle: J

first: Michael

last: Sanford

first: Dan

last: McVicar

first: Howard

last: Young


title: FACT maintains pluripotency factor expression through gene-distal regulation in embryonic stem cells [ATAC-Seq]

city: Pittsburgh

first: David

middle: Charles

last: Klein

address: 4249 Fifth Ave

institute: University of Pittsburgh

summary: The mammalian FACT complex is a highly conserved histone chaperone with essential roles in transcription elongation, histone deposition, and maintenance of stem cell state. FACT is essential for viability in pluripotent cells and cancer cells, but otherwise dispensable for most mammalian cell types. FACT deletion or inhibition can block reprogramming of fibroblasts to induced pluripotent stem cells, yet the molecular mechanisms through which FACT regulates cell fate decisions remain unclear. To determine the mechanism by which FACT regulates stem cell identity, we used the auxin-inducible degron systems to deplete murine embryonic stem cells of FACT subunit SPT16 and subjected depleted cells to genome-wide factor localization, nascent transcription analyses, and genome-wide nucleosome profiling. Inducible depletion of SPT16 reveals a critical role in regulating targets of the master regulators of pluripotency: OCT4, KLF4, MYC, NANOG, and SOX2. Depletion of SPT16 leads to increased nucleosome occupancy at genomic loci occupied by these transcription factors, as well as gene-distal regulatory sites defined by DNaseI hypersensitivity. This heightened occupancy suggests a mechanism of nucleosome filling, wherein the sites typically maintained in an accessible state by FACT are occluded through loss of FACT-regulated nucleosome spacing. 20% of transcription arising from gene-distal regions bound by these factors is directly dependent on FACT, and putative gene targets of these non-coding RNAs are highly enriched for pluripotency in pathway analyses. Upon FACT depletion, transcription of Pou5f1 (OCT4), Sox2, and Nanog are downregulated, suggesting that FACT not only co-regulates expression of the encoded proteins’ targets, but also the pluripotency factors themselves. We find that FACT maintains cellular pluripotency through a complex regulatory network of both coding and non-coding transcription.

overall_design:
ATAC-seq
8 ATAC-seq libraries, with two replicates per condition in two independently-targeted cell lines (SPT16-V5-AID C-terminal tag). Control samples were treated with EtOH, while experimental samples were treated with IAA.

first: Santana

last: Lardo

first: Sarah

last: Hainer


title: Importance of Atg5, Atg16L1 and Atg7 in mouse bone marrow-derived macrophages infected for 48h with M. tuberculosis Erdman

status: Public on Mar 06 2023

city: Berkeley

first: Guillaume

last: Golovkine

address: 1951 Oxford Street

institute: UC Berkeley

summary: To identify cellular pathways altered in autophagy-deficient macrophages during M. tuberculosis infection, we performed 3' Tag-RNA-seq on RNA harvested from Atg5fl/fl LysMcre+/+, Atg16L1fl/fl LysMcre+/+ and Atg7fl/fl LysMcre+/+ mouse bone marrow derived macrophages, and their respective LysMwt/wt control cells, both after 48 hours of infection with M. tuberculosis Erdman and or in mock-infection controls.

overall_design:
RNA was harvested from Atg5fl/fl, Atg16L1fl/fl, Atg7fl/fl, Atg5fl/fl LysMcre+/-, Atg16L1fl/fl LysMcre+/-, Atg7fl/fl LysMcre+/-,  Atg5fl/fl LysMcre+/+, Atg16L1fl/fl LysMcre+/+ and Atg7fl/fl LysMcre+/+ bone-marrow derived macrophages either infected for 48 hours with M. tuberculosis Erdman or mock-infected. Samples were analyzed from 3 independent biological replicates.
contributor: UC Davis Genome Center DNA Technologies and Expression Analysis Core

first: Nicholas

last: Garelis

first: Jeffery

middle: S

last: Cox


title: FACT maintains pluripotency factor expression through gene-distal regulation in embryonic stem cells

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


title: Human CCR6+ Th cells show both an extended stable gradient of Th17 activity and imprinted plasticity [methylationEPIC]

first: Timothy

last: Myers

overall_design: MethylationEpic assay of 2 human donors, CD4+CD45RO- and CD4+CD45RO+ T-cells sorted into  CCR6neg, CCR6low, CCR6int and CCR6high subsets

first: Satya

last: Singh

first: Joshua

last: Farber


title: RSV-induced Cytoskeletal Inflammation

status: Public on Mar 10 2023

city: Grand Forks

first: Danielle

last: Perley

state: North Dakota

address: 1301 N Columbia Rd

institute: University of North Dakota Genomics Core

summary: We studied RSV infection in an appropriate in vitro model of respiratory epithelium, a pseudostratified and fully differentiated mucociliary epithelium of normal human bronchial epithelial (NHBE) cells. RSV infection increased actin cytoskeleton without compromising adherent-, tight-, and tricellular-junctions as well as ciliary functions and epithelial tissue barrier integrity. This increased cytoskeleton depends on actin polymerization and the induction of proinflammatory cytokines and chemokines. Thus, we observed a novel signature “increased cytoskeleton” termed “cytoskeletal inflammation” in RSV-infected respiratory epithelium that presumably lacks classical antigen presenting cells, such as resident dendritic cells and macrophages. Our results suggest that RSV-induced cytoskeletal inflammation is a noncanonical earliest host response to the pathogen and contributes to airway inflammation.

overall_design: A four-week pseudostartified highly differentiated respiratory epithelium establsihed by 3D air-liquid inteerface culturing of priamry normal human bronchial epithelial (NHBE) cells. The respiratory epithelium was infected with RSV expressing green fluorescing protein (RSV-GFP) at a multiplicity of infection of 4 (MOI=4) for six days. Total RNA was extracted with DNAse-treatment from the mock-infected and RSV-GFP infected respiratory epithelium for whole genome trasncriptome analysis by RNAseq.

first: Masfique

last: Mehedi


title: FACT maintains pluripotency factor expression through gene-distal regulation in embryonic stem cells [MNase-seq]

overall_design: MNase-seq


title: Intrathecal delivery of AAV-NDNF ameliorates disease progression of ALS mice

status: Public on Mar 05 2023

city: shanghai

first: cheng

last: wei

address: haike road 230

institute: shanghaitech

summary:
Amyotrophic lateral sclerosis (ALS) is a uniformly lethal neurodegenerative disease characterized by progressive deterioration of motor neurons, neuromuscular denervation, leading to severe paralysis and breathe failure.  Adeno-associated virus (AAV)-mediated delivery of trophic factors is being considered as a potential disease-modifying therapeutic avenue. Here we show a marked effect of AAV-mediated over-expression of Neuron-derived neurotrophic factor (NDNF) on SOD1G93A ALS model mice.
We performed gene expression profiling analysis using data obtained from RNA-seq of SOD1G93A mice injected with AAV-GFP or AAV-NDNF at postnatal days 74.

overall_design: AAV-GFP or AAV-NDNF were intrathecally administrated into SOD1G93A mice at P74 and samples of the spinal cord ventral part were subjected to bulk RNA-sequence analysis at P104.

first: Cheng

last: Wei

first: Huang

last: Jing

first: Zhen-Ge

last: Luo


title: Context-dependent DNA methylation signatures in animal livestock [SGBS_MarbledCrayfish]

status: Public on Mar 02 2023

city: Heidelberg

first: Geetha

last: Venkatesh

address: Im Neuenheimer Feld 580

country: Germany

institute: DKFZ

summary: DNA methylation is an important epigenetic modification that is widely conserved across animal genomes. It is widely accepted that DNA methylation patterns can change in a context-dependent manner, including in response to changing environmental parameters. However, this phenomenon has not been analyzed in animal livestock yet, where it holds major potential for biomarker development. Building on the previous identification of population-specific DNA methylation in clonal marbled crayfish, we have now generated numerous base-resolution methylomes to analyze location-specific DNA methylation patterns. We also describe the time-dependent conversion of epigenetic signatures upon transfer from one environment to another. We further demonstrate production system-specific methylation signatures in shrimp, river-specific signatures in salmon and farm-specific signatures in chicken. Together, our findings provide a detailed resource for epigenetic variation in animal livestock and suggest the possibility for origin tracing of animal products by epigenetic fingerprinting.

overall_design: Overall 15 abdominal muscle samples from marbled crayfish were analyzed. The samples were collected at different time-points namely 0, 1, 4, 13 months.

first: F

last: Lyko

first: G

last: Raddatz


title: Context-dependent DNA methylation signatures in animal livestock [WGBS_Lvannamei]

overall_design: Overall 21 abdominal muscle samples from shrimp were analyzed. The samples were collected from four different locations.


title: FACT maintains pluripotency factor expression through gene-distal regulation in embryonic stem cells [TT-seq]

first: David

last: Klein

overall_design: TT-seq

first: Santana

last: Lardo


title: Context-dependent DNA methylation signatures in animal livestock [WGBS_MarbledCrayfish]

overall_design: Overall 25 abdominal muscle samples from marbled crayfish were analyzed. The samples were collected from 11 different locations.


title: FACT maintains pluripotency factor expression through gene-distal regulation in embryonic stem cells [CUT&RUN]

overall_design: CUT&RUN

first: Sarah

last: Hainer


title: Effect of inhibition of Setdb1 on gene expression in AML12 cells

city: Guangzhou

first: Zhigang

last: Wang

state: GuangDong

address: 195 Dongfeng West Road, Yuexiu District, Guangzhou City, Guangdong Province

department: KingMed School of Laboratory Medicine

institute: Guangzhou Medical University

summary: To investigate the mRNA expression regulated by Setdb1, we established  AML12 knockdown cell model by infecting Setdb1 siRNA for 72 hours

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of 2 different cell groups (siNC vs siSetdb1, 3 samples per group).

first: Yi

last: Zhang

first: Yanhui

last: Li


title: A single-cell proteomic and transcriptomic assay identifies genes related to polyfunctionality of CAR-T cells targeting GPC1 in pancreatic cancer

status: Public on Mar 04 2023

city: Bethesda

first: Mitchell

last: Ho

address: 37 Convent Dr, Bldg 37 Rm 5002

department: Laboratory of Molecular Biology

institute: National Cancer Institute

summary: To understand the molecular determinants of CAR-T cell polyfunctionality, we simultaneously measured the protein and RNA expression levels of 23 single CD8+ D4-IgG4H-CD28TM CAR T cells targeting GPC1 stimulated with T3M4 pancreatic cancer cells. We identified two CAR-T clusters, low polyfunctionality and high polyfunctionality subsets, in a 2D t-SNE plot. Moreover, our single-cell mRNA expression profiling revealed 23 genes that displayed statistically significant, concordant differences between the two cell subsets.

overall_design: D4-IgG4H-CD28TM CAR-T cells targeting GPC1 were stimulated with T3M4 pancreatic cancer cells,  then grouped into high-polyfunctionality and low-polyfunctionality subsets based on the cytokine secretion profile. Then scRNA-seq was used to analyze upregulated genes in each subset.

first: Dana

last: Ashworth

first: Weiming

last: Ni

first: Jing

last: Zhou

last: Coit

first: Tenzin

last: Lhakhang

first: Jeff

last: Sabina


title: Human CCR6+ Th cells show both an extended stable gradient of Th17 activity and imprinted plasticity [BeadChipHumanWG-6]

first: Timothy

last: Myers

address: 50 South Drive, Room 5509

institute: National Institute of Allergy and Infectious Diseases

summary: Th17 cells have been investigated in mice primarily for their contributions to autoimmune diseases. However, the pathways of differentiation of Th17 and related Th cells (type 17 cells)  and the structure of the type 17 memory population in humans are not well understood; such understanding is critical for manipulating these cells in vivo. By exploiting differences in levels of surface CCR6, we found that human type 17 memory cells, including individual T cell clonotypes, form an elongated continuum of type 17 character along which cells can be driven by increasing RORt. This continuum includes cells preserved within the memory pool with potentials that reflect the early preferential activation of multiple over single lineages. The CCR6+ cells’ phenotypes and epigenomes are stable across cell divisions under homeostatic-like conditions. Nonetheless, activation in polarizing and non-polarizing conditions can yield additional functionalities, revealing, respectively, both environmentally induced and imprinted mechanisms that contribute differentially across the continuum to yield the unusual plasticity ascribed to type 17 cells.

overall_design: Illumina BeadChip RNA expression assay of 9 human donors, CD4+CD45RO- and CD4+CD45RO+ T-cells sorted into  CCR6neg, CCR6low, CCR6int and CCR6high subsets, with or without PMA stimulation

first: Satya

last: Singh

first: Joshua

last: Farber


title: A genome-wide screen reveals new regulators of the 2-cell-like cell state

city: Paris

first: Pierre-Antoine

last: Defossez

address: 35 rue Hélène Brion

country: France

institute: Epigenetics and Cell Fate Unit

summary: In mammals, only the zygote and blastomeres of the early embryo are totipotent. This totipotency is mirrored in vitro by mouse '2-cell-like cells' (2CLCs), which appear at low frequency in cultures of embryonic stem cells (ESCs). Because totipotency is not completely understood, we carried out a genome-wide CRISPR knockout screen in mouse ESCs, searching for mutants that reactivate the expression of Dazl, a gene expressed in 2CLCs. Here we report the identification of four mutants that reactivate Dazl and a broader 2-cell-like signature: the E3 ubiquitin ligase adaptor SPOP, the Zinc-Finger transcription factor ZBTB14, MCM3AP, a component of the RNA processing complex TREX-2, and the lysine demethylase KDM5C. All four factors function upstream of DPPA2 and DUX, but not via p53. In addition, SPOP binds DPPA2, and KDM5C interacts with ncPRC1.6 and inhibits 2CLC gene expression in a catalytic-independent manner. These results extend our knowledge of totipotency, a key phase of organismal life.

overall_design: Whole genome bisulfite sequencing and RNA sequencing have been performed on mouse embryonic stem cells grown  in serum or 2i conditions. ChIP sequencing and CUT&RUN sequencing have been performed on mouse ES cells grown in serum conditions

first: Nikhil

last: Gupta

first: Lounis

last: Yakhou

first: Julien

last: Albert

first: Anaelle

last: Azogui

first: Laure

last: Ferry

first: Olivier

last: Kirsh

first: Fumihito

last: Miura

last: Battault

first: Kosuke

last: Yamaguchi

first: Marthe

last: Laisné

first: Cécilia

last: Domrane

first: Frédéric

last: Bonhomme

first: Arpita

last: Sarkar

first: Marine

last: Delagrange

first: Bertrand

last: Ducos

first: Gael

last: Cristofari

first: Takashi

last: Ito

first: Maxim

middle: V

last: Greenberg


title: The landscape of circular RNAs in neuroblastoma II

status: Public on Feb 28 2023

city: Leipzig

first: Jörg

last: Fallmann

address: Härtelstraße 16ß18

institute: Leipzig University

summary: Circular RNAs (circRNAs), a noncoding RNA class originating from alternative splicing, are highly abundant in neural tissues and were shown to regulate gene expression e.g. by interacting with microRNAs and RNA-binding proteins. Neuroblastoma is an embryonal neoplasia, which arises from undifferentiated neural crest cells. Here, we aimed to explore, whether circRNAs influence the pathogenesis of high-risk neuroblastoma. We performed whole-transcriptome sequencing of 104 primary neuroblastoma samples of all risk-groups and identified 5,203 unique circRNAs involving 2,302 genes. Candidate circRNA expression did not correlate with host gene expression, indicating independent regulatory mechanisms. circRNAs were significantly downregulated in the MYCN-amplified high-risk tumors. These findings were independently reproduced in a tetracycline-inducible MYCN-overexpression system based on a non MYCN-amplified neuroblastoma cell line, suggesting that MYCN drives this global circRNA repression. We identified the RNA helicase DHX9 as a mediator of this global suppressive effect of MYCN on circRNAs. Comparing our RNA sequencing data with other cancers and controls revealed a circRNA subset specifically upregulated in neuroblastoma that included a circRNA derived from the ARID1A tumor suppressor gene. Specific circARID1A knockdown resulted in reduced proliferation, cell numbers and viability, prompted apoptosis and induced a differentiated phenotype. Neither knockdown, nor overexpression of circARID1A influenced ARID1A mRNA and protein levels significantly. To dissect the potential mode of function, we performed a pulldown assay with subsequent mass spectrometry. We identified the RNA-binding protein KHSRP as an interaction partner that participates in the mechanism of action of circARID1A. In summary, this study highlights an important role of circRNAs in neuroblastoma biology and may establish this RNA class as a future therapeutic target and biomarker.

overall_design: Long-read sequencing of 6 neuroblastoma cell lines after digestion of ribosomal and linear RNA to enrich for circRNAs.

first: Steffen

last: Fuchs

first: Joerg

first: Stephan

last: Bernhart

first: Johannes

last: Schulte


title: The landscape of circular RNAs in neuroblastoma I

overall_design: Induction of MYCN expression in the neuroblastoma cell line SK-N-SH for 5d


title: Context-dependent DNA methylation signatures in animal livestock [RRBS_chicken]

first: Geetha

last: Venkatesh

overall_design: Overall 36 samples from chicken were analyzed. These 36 samples were collected from six different locations namely USA, Australia, Germany, Finland, Iran and Thailand.

first: F

last: Lyko

first: G

last: Raddatz


title: FACT maintains pluripotency factor expression through gene-distal regulation in embryonic stem cells [TT-Seq]

first: David

last: Klein

overall_design:
TT-seq
8 TT-seq libraries, with two replicates per condition in two independently-targeted cell lines (SPT16-V5-AID C-terminal tag). Control samples were treated with EtOH, while experimental samples were treated with IAA.

first: Santana

last: Lardo

first: Sarah

last: Hainer


title: AR dimerization surface mutants and wt in PC3 cells

status: Public on Mar 01 2023

city: Hospitalet de Llobregat

first: Alvaro

last: Aytes

address: Granvia 199

department: ProCURE

institute: IDIBELL

summary: Mutations of the androgen receptor (AR) associated with prostate cancer and androgen insensitivity syndrome may profoundly influence its structure, protein interaction network and binding to chromatin, resulting in altered transcription signatures and drug responses. Current structural information fails to explain the effect of pathological mutations on AR structure-function relationship. Here we have thoroughly studied the effects of selected mutations that span the complete dimer interface of AR ligand-binding domain (AR-LBD) using X-ray crystallography in combination with in vitro, in silico, and cell-based assays. We show that these variants alter AR-dependent transcription and responses to anti-androgens by inducing a previously undescribed allosteric switch in the AR-LBD that increases exposure of residue Arg761 and ultimately leads to its enhanced methylation. We also corroborate the relevance of residues Arg761 and Tyr764 for AR dimerization and function. Together, our results reveal allosteric coupling of AR dimerization and post-translational modifications as a disease mechanism with implications for precision medicine.

overall_design: Prostate Cancer PC3 cells were infected with lentiviral particles to express wild type or dimerization surface mutants of the Androgen Receptor.

first: Eva

last: Estebanez-Perpiña

first: Pablo

last: Fuentes-Prior

first: Andrea

last: Alegre-Marti

first: Alba

last: Jimenez-Panizo

first: Adrian

last: Martinez-Tebar


title: Altered expression of SELF-PRUNING disrupts meristem homeostasis and facilitates delivery of signals to the meristem

city: Denton

first: Roisin

last: McGarry

state: TX

address: 1511 West Sycamore

department: Dept. of Biological Sciences, BioDiscovery Institute

institute: University of North Texas

summary: Meristem maintenance, achieved through the highly conserved CLAVATA-WUSCHEL (CLV-WUS) regulatory circuit, is fundamental in balancing stem cell proliferation with cellular differentiation. Disruptions to meristem homeostasis can alter meristem size, leading to enlarged organs. Cotton, the world’s most important fiber crop, shows inherent variation in fruit size. Leveraging meristem regulation could benefit cotton agriculture and increase yields of high-quality fibers. Using virus-based gene manipulation in cotton, we altered expression of genes functioning in the CLV-WUS circuit to perturb meristem regulation and increase fruit size.  Targeted alteration of individual components of the CLV-WUS circuit only modestly fasciated flowers and fruits. Unexpectedly, controlled expression of meristem regulator SELF-PRUNING (SP) dramatically increased the impacts of altered CLV-WUS expression on flower and fruit fasciation. Meristem transcriptomics show SP and genes of the CLV-WUS circuit are expressed independently from each other, suggesting these gene products are not acting in the same path. Virus-induced silencing of GhSP facilitated delivery of other signals to the meristem to dramatically alter organ specification. SELF-PRUNING has a role in cotton meristem homeostasis, and changes in GhSP expression increased access of virus-based signals to the meristem.

overall_design: Comparative gene expression profiling of meristems isolated from cotton (Gossypium hirsutum) Coker 312 plants infected with viruses targeting genes of the CLAVATA-WUSCHEL meristem maintenance circuit.

first: Brian

last: Ayre

first: Harmanpreet

last: Kaur

first: Yen-Tung

last: Lin

first: Guadalupe

last: Lopez Puc

first: Leor

last: Eshed Williams

first: Esther

last: van der Knaap


title: Context-dependent DNA methylation signatures in animal livestock

first: Geetha

last: Venkatesh

sample_organism:
Penaeus vannamei
Gallus gallus
Procambarus virginalis

overall_design: Refer to individual Series


title: The landscape of circular RNAs in neuroblastoma

first: Jörg

last: Fallmann


title: Differential expression of Dusp1 and immediate early response genes in hippocampus of rats, subjected to forced swimming test

status: Public on Feb 27 2023

city: Moscow

first: Ivan

middle: Nikolaevitch

last: Vlasov

address: Akademika Kurchatova square, 2

country: Russia

institute: National Research Center «Kurchatov Institute»

summary: This submission contains a result of a  study of transcriptional profiles in the brains of rats that were exposed to the FST.  RNA-seq is performed on hyppocampus tissues of rats 20 minutes and 24 hours after FST.

overall_design: Examination of transcriptome, derived from rats 20 minutes and 24 hours after forced swimming test

first: Elena

last: Filatova

first: Petr

last: Slominskiy

first: Maria

last: Shadrina


title: Integrative physiological, transcriptome, and metabolomic unveil the chilling responses of two melon genotypes

status: Public on Feb 25 2023

first: shi

last: yao

address: jinqi road

department: Horticultural Research Institute

institute: Shanghai Academy of Agricultural Sciences

summary: The physiological indicators, transcriptome, and metabolome of two melon varieties with contrasting chilling tolerance (‘162’, chilling-tolerant; ‘13-5A’ ,chilling-sensitive) were analyzed under chilling stress.

overall_design: Two melon varieties with contrasting chilling tolerance (‘162’, chilling-tolerant; ‘13-5A’ ,chilling-sensitive) were analyzed under 4℃ chilling stress at 0h and 12h.

first: Qiannan

last: Diao

first: Yongping

last: Zhang


title: RNA Sequencing Facilitates Quantitative Analysis of lncSync-null and wild-type mouse heart cardiomyocytes

city: Beijing

first: Jie

state: Beijing

address: Tsinghua University

department: Basic Medical Sciences, School of Medicine

institute: Tsinghua University

summary: Purpose: The goals of this study are to compare miRNAs enriched in lncSync-null mouse heart cardiomyoctes to discover mechanism of lncSync in mamalian development.

overall_design: e13.5 and adult heart cardiomyoctes from lncSync-null and wildtype

first: Rujin

last: Huang


title: Genome-wide H3K27me3 and H3K4me3 analyses in Arabidopsis

first: li

last: peng

institute: PSC


title: Transcriptomic profile of germinal center B cells from conditional GC-specific (Cg1-Cre) Crebbp-HET, Kmt2d-HET, and compound Crebbp-HET/Kmt2d-HET mice, with littermate controls

city: New York

first: Laura

last: Pasqualucci

state: NY

address: 1130 St Nicholas Avenue

department: Institute for Cancer Genetics

institute: Columbia University

summary: Inactivating mutations of the KMT2D methyltransferase and the CREBBP acetyltransferase are among the most common genetic alterations in B-cell lymphoma and co-occur in 40-60% of follicular lymphoma (FL) and diffuse large B cell lymphoma (DLBCL) cases, suggesting they may be co-selected. Here we show that combined germinal center (GC)-specific haploinsufficiency of Crebbp and Kmt2d synergize in vivo to promote the expansion of abnormal GCs, a common pre-neoplastic event. These enzymes form a biochemical complex on selected enhancers/super-enhancers that are critical for the delivery of signals in the GC light-zone and are only corrupted upon dual Crebbp/Kmt2d loss, both in mouse GC B cells and in human DLBCLs. Moreover, we find that CREBBP directly acetylates KMT2D in GC-derived B cells. Accordingly, inactivation of CREBBP by FL/DLBCL-associated truncating and/or missense mutations abrogates its ability to catalyze KMT2D acetylation. Importantly, genetic and pharmacologic loss of CREBBP and the consequent decrease in KMT2D acetylation leads to reduced levels of H3K4me1, supporting a role for acetylation in modulating KMT2D activity. These data identify a direct biochemical and functional interaction between CREBBP and KMT2D, with implications for their role as tumor suppressors in FL/DLBCL and for the development of combinatorial therapies targeting enhancer defects induced by their loss.

overall_design: Conditional Crebbp fl/+Cg1Cre, Kmt2d fl/+Cg1Cre, Crebbp fl/+Kmt2d fl/+Cg1Cre and  wild type mice were immunized with sheep red blood cells at day 0 and day 5, and sacrificed 7 days after the second immunization. Germinal center B cells (B220+CD95+PNA+) were sorted from splenic B cells. Total RNA was extracted from single cell suspensions, assessed for quality on a Bioanalyzer, and used for library construction and next generation sequencing on an Illumina NovaSeq 6000 instrument

first: Antony

last: Baden Holmes


title: Genome-wide H3K27me3 analysis in Arabidopsis

summary: To explore the bivalent histone modifications in the Arabidopsis genome, we examined genome-wide histone 3 lysine-27 trimethylation (H3K27me3) and histone 3 lysine-4 trimethylation (H3K4me3) in 5-day-old seedlings (Col-0) by ChIP-seq. We found that more than 1300 genes loci contain both H3K27me3 and H3K4me3.

overall_design: Nuclei were extracted from 5-day-old WT (Col-0) seedlings as previously described (Louwers et al., 2009), followed by chromatin immunoprecipitation with Magna ChIP A/G kit (Millipore). DNA libraries were constructed using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB), and subsequently were sequenced on X Ten (Illumina). Three biologically independent samples have been analyzed.

first: Yang

last: Ou

first: Yuehui

last: He


title: Sequencing Facilitates Quantitative Analysis of lncSync-null and wild-type mouse heart cardiomyocytes

type: Non-coding RNA profiling by high throughput sequencing


title: microRNA Sequencing Facilitates Quantitative Analysis of lncSync-null and wild-type mouse heart cardiomyocytes


title: Genome-wide H3K4me3 analysis in Arabidopsis


title: A novel splicing variant of DJ-1 specific to Parkinson’s disease induces mitochondrial dysfunction

status: Public on Feb 26 2023

city: Daejeon

first: Inkyung

last: Jung

address: KAIST, 291 Daehak-ro, Yuseong-gu

country: South Korea

institute: KAIST

summary: We characterize differentially spliced genes in postmortem human substantia nigra samples derived from various disease conditions, and discover a novel Parkinson's disease-associated splice variant, DJ-1 lacking exon 6.

overall_design: Total RNA sequencing was performed on postmortem human substantia nigra tissues from 1 Parkinson's disease, 6 Alzheimer's disease, and 5 Lewy body cases

first: N

last: Cho

first: J

last: Joo

first: S

last: Cha

first: I

first: K

last: Kim


title: Pluripotency-Independent Induction of Human Trophoblast Stem Cells from Fibroblasts [RNA-Seq]

status: Public on Feb 21 2023

city: Jerusalem

first: Yosef

last: Buganim

address: Hadassah Medical School

department: Department of Developmental Biology and Cancer Research

country: Israel

institute: The Hebrew University

summary: Transcription profile analysis revealed similarity/dissimilarity between human blastocyst derived trophoblast stem cells (hbdTSCss), human induced trophoblast stem cells (hiTSCs), human foreskin fibroblasts (HFFs) and pluripotent stem cells (hESCs, hiPSCs)

overall_design: HFFs reprogrammed into hiTSC lines by transient ectopic expression of GATA3, OCT4, KLF4, MYC (GOKM) were subjected to RNA-seq, along with samples of HFFs, hbdTSCss, hESCs and hiPSCs

first: Moriyah

last: Naama

first: Ahmed

last: Radwan

first: Valery

last: Zayat

first: Shulamit

last: Sebban


title: Meis1 establishes the pre-hemogenic endothelial state prior to Runx1 expression II

status: Public on Feb 22 2023

city: Vancouver

first: Aly

last: Karsan

state: British Columbia

institute: Canada's Michael Smith Genome Sciences Centre

summary: Hematopoietic stem and progenitor cells (HSPCs) originate from an endothelial-to-hematopoietic transition (EHT) during embryogenesis. Characterization of early hemogenic endothelial (HE) cells is required to understand what drives hemogenic specification and to accurately define cells capable of undergoing EHT. Using Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq), we defined the early subpopulation of pre-HE cells based on both surface markers and transcriptomes. We identified the transcription factor Meis1 as an essential regulator of hemogenic cell specification in the embryo prior to Runx1 expression. Meis1 is expressed at the earliest stages of EHT and distinguishes pre-HE cells primed towards the hemogenic trajectory from the arterial endothelial cells that continue towards a vascular fate. Endothelial-specific deletion of Meis1 impaired the formation of functional Runx1-expressing HE which significantly impeded the emergence of pre-HSPC via EHT. Our findings implicate Meis1 in a critical fate-determining step for establishing EHT potential in endothelial cells.

overall_design: Primary aortic endothelial cells were transduced to overexpressed Meis1 or a control vector, each done in triplicates.

first: Patrick

last: Coulombe

first: Amanda

last: Fentiman

first: Jeremy

middle: D

last: Parker

first: Derek

last: Tam

first: Eric

last: Yung

first: R

middle: K

last: Humphries


title: Human T follicular helper cells seed the germinal center-resident regulatory pool

status: Public on Feb 23 2023

city: Philadelphia

first: James

last: Garifallou

state: Pennsylvania

address: 3615 Civic Center Boulevard, ARC1014

department: Neonatology

institute: Children's Hospital of Philadelphia

summary: FOXP3+ T follicular regulatory cells (Tfrs) control germinal center (GC) responses by steering antibody formation away from self-reactivity and toward microbe/vaccine recognition. As originally described, murine Tfr cells descend exclusively from thymically-derived, self-antigen recognizing, T regulatory cells (Tregs), but newer animal models suggest vaccine-recognizing T follicular helper (Tfh) cells can assume regulatory roles as GCs mature. To test the hypothesis that the human Tfr pool is heterogenous in function and provenance, we used paired TCRVA and TCRVB sequencing to distinguish tonsillar Tfr cells clonally related to the natural Tregs (nTfr) from those induced from Tfh cells (iTfr). Through in silico predictions and in vitro tonsillar organoid lineage tracking, we identified a Tfh to iTfr developmental trajectory that passed through a distinct CD25hiBLIMP1+FOXP3- transitional stage. The genes and proteins that iTfr and nTfr cells express differentially were utilized as handles to precisely pinpoint the in situ locations of cells from each subset via multi-plex microscopy and to establish divergent functional adaptations. In total, we characterize human iTfr cells as a GC-resident CD38+ Tfr subset that descend from Tfh lineage cells to gain suppressive qualities while retaining their capacity for GC B-cell help.

overall_design: 8 single-cell RNAseq libraries with paired gene expression and V(D)J data were analyzed, 1 library also included CITE-Seq (ADT) data.

first: Michael

last: Gonzalez

first: Carole

last: Le Coz

first: Neil

last: Romberg


title: Expression of neutrophilic genes in patients diagnosed with Kawasaki disease and healthy controls

status: Public on Feb 20 2023

city: Suzhou

first: Yunjia

last: Tang

address: No 92, Zhongnan Street

institute: Children's Hospital of Soochow University

summary: Kawasaki disease (KD) is considered the main contributor to acquired heart diseases in developed countries. However, the precise pathogenesis of KD remains unclear. Neutrophils played roles in KD. This study aimed to select hub genes in neutrophils in acute KD. mRNA microarray of neutrophils from four acute KD patients and three healthy controls was performed to screen differentially expressed mRNAs (DE-mRNAs). DE-mRNAs were analyzed and predicted by Gene Ontology (GO), Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathways, and protein-protein interaction networks. Real time-PCR was finally conducted to confirm the reliability and validity of the expression level of DE-mRNAs from blood samples of healthy controls and KD patients in both acute and convalescent stage.

overall_design: Venous blood (2 ml) was collected from the KD patients (n=4) and healthy controls (n=3) in EDTA-containing tubes and neutrophils were isolated within two hours using EasySep direct human neutrophil isolation kit. The total RNA was extracted using Total RNA Isolation Reagent.

first: Haitao

last: Lv


title: Pluripotency-Independent Induction of Human Trophoblast Stem Cells from Fibroblasts [ChIP-Seq]

first: Yosef

last: Buganim

summary: ChIP-seq analysis revealed similarity/dissimilarity in deposition of H3K4me2 histone mark between human blastocyst derived trophoblast stem cells (hbdTSCs), human foreskin fibroblasts (HFFs) and pluripotent stem cells (hESCs) compared with HFFs which underwent 3 days of ectopic expression of GATA3, OCT4, KLF4, MYC (GOKM) or OCT4, SOX2, KLF4 and MYC (OSKM).

overall_design: HFFs which underwent 3 days of ectopic expression of GOKM or OSKM utilizing a tetO system were subjected to ChIP-seq with anti-H3K4me2 antibody, along with samples of untreated HFFs, hbdTSCs and hESCs.

first: Moriyah

last: Naama


title: Pluripotency-Independent Induction of Human Trophoblast Stem Cells from Fibroblasts [ATAC-Seq]

summary: ATAC-seq analysis revealed similarity/dissimilarity in chromatin accessibility between human blastocyst derived trophoblast stem cells (hbdTSCs), human foreskin fibroblasts (HFFs) and pluripotent stem cells (hESCs) compared with HFFs which underwent 3 days of ectopic expression of GATA3, OCT4, KLF4, MYC (GOKM) or OCT4, SOX2, KLF4 and MYC (OSKM).

overall_design: HFFs which underwent 3 days of ectopic expression of GOKM or OSKM utilizing a tetO system were subjected to ATAC-seq, along with samples of untreated HFFs, hbdTSCs and hESCs.

first: Ahmed

last: Radwan

first: Valery

last: Zayat


title: Hepatic gene expression profiles during fed–fasted–refed state in mice [mRNA-seq]

status: Public on Feb 24 2023

first: NANA

last: JI

address: Dongan road 130

institute: Fudan university

summary: Regulation of nutrient status during fasting and refeeding plays an important role in  maintaining metabolic homeostasis in the liver. Thus, we investigated the impact of the  physiological fed–fasted–refed cycle on hepatic gene expression in nutrient-sensitive  mice. We performed transcriptomic analysis of liver samples in fed, fasted and refed  groups of mice. Through mRNA-sequencing (RNA-Seq) and miRNA-Seq, we  compared fasted and fed states (fasted versus fed cohort) as well as refed and fasted  states (refed versus fasted cohort) to detect dynamic alterations of hepatic mRNA–  miRNA expression during the fed–fasted–refed cycle

overall_design: The animal procedures were approved by the Animal Experiment Ethics Committees  of Shanghai Jiao Tong University School of Medicine. Wild-type male C57BL/6J mice  aged 8 weeks were purchased from Shanghai Laboratory Animal Company (SLAC,  Shanghai, China). All mice were housed at 21±1°C with a humidity of 55±10% and 12-  h light/12-h dark cycle in a specific-pathogen-free facility. After 2 weeks of  acclimatization, mice were divided into three groups. The fasted group was fed a regular  diet with subsequent fasting for 24 h. The refed group underwent 24 h fasting and was  refed a fixed-calorie meal for 2 h. Mice were anesthetized with sodium pentobarbital  (Nembutal, 80 mg/kg, i.p.) and killed during the fasted and refed states. Liver tissues  were harvested and snap-frozen in liquid nitrogen for further analysis.  RNA-Seq

first: Yan

last: Lu

first: Min

last: Zhang

first: Nana

last: Ji

first: Liping

last: Xiang

first: Bing

last: Zhou


title: Chemotherapy-mediated changes in the immune cell landscape of murine triple negative breast cancer.

city: Dallas

first: Siyuan

address: 6001 Forest Park Rd

department: Department of Pathology

institute: UT Southwestern Medical Center

summary: We performed CITE-seq (10x Genomics-based) to profile and compare the transcriptomes and cell surface expression of immune epitopes in the primary breast tumors of transgenic mice (C3-1-TAg)  with or without MCT chemotherapy. We sequenced a total of six different tumor samples. We created an antibody pool consisting of 35 different antibodies and stained each sample individually with this antibody pool. Then, we stained each sample with it's own unique hashing antibody so that we could subsequently pool the samples for loading onto the 10x Chromium and later prepare one library consisting of all sight samples and finally separate each sample in silico by it's unique hashing antibody. The samples are as follows: (1) HTO1: tumor of PBS treated C3-1-TAg mouse; (2) HTO2: tumor of PBS treated C3-1-TAg mouse;  (3) HTO3: tumor of PBS treated C3-1-TAg mouse;  (4) HTO4: tumor of MCT treated C3-1-TAg mouse;  (5) HTO5: tumor of MCT treated C3-1-TAg mouse; (6) HTO6: tumor of MCT treated C3-1-TAg mouse. The following sample comparisons were made: HTO1, HTO2, and HTO3 versus HTO4, HTO5, and HTO6.

overall_design: Breast tumors were isolated from C3-1-TAg mice treated with either MCT or PBS for 4 weeks. These mice were started on treatment when the tumors were around 5 mm* 5 mm in size. Tumors were dissociated using collagenase enzyme and the single cells were enriched with CD45+ immune cells using MACS magnetic beads (Miltenyi). We created an antibody pool consisting of 35 different antibodies and stained each sample individually with this antibody pool. Then, we stained each sample with it's own unique hashing antibody so that we could subsequently pool the samples for loading onto the 10x Chromium and later prepare one library consisting of all eight samples and finally separate each sample in silico by it's unique hashing antibody.

first: Bhavana

last: Palakurthi


title: Identification of the key epigenetic determinants of chondrocyte aging in humans

city: Los Angeles

first: Denis

last: Evseenko

address: 1450 Biggy St

department: Orthopaedic Surgery

institute: University of Southern  California

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


title: A Multipronged Unbiased Strategy Guides the Development of an anti-EGFR/EPHA2 Bispecific Antibody for Combination Cancer Therapy

city: Saskatoon

first: Franco

last: Vizeacoumar

state: Saskatchewan

address: 4D40 Health Sciences Building, 107 Wiggins Road

department: Oncology

institute: University of Saskatchewan

summary:
Purpose: Accumulating analyses of pro-oncogenic molecular mechanisms triggered a rapid development of targeted cancer therapies. Although many of these treatments produce impressive initial responses, eventual resistance onset is practically unavoidable. One of the main approaches for preventing this refractory condition relies on the implementation of combination therapies. This includes dual-specificity reagents that affect both of their targets with a high level of selectivity. Unfortunately, selection of target combinations for these treatments is often confounded by limitations in our understanding of tumor biology. Here, we describe and validate a multipronged unbiased strategy for predicting optimal co-targets for bispecific therapeutics.
Experimental design: Our strategy integrates ex-vivo genome-wide loss of function screening, BioID interactome profiling and gene expression analysis of patient data to identify the best fit co-targets. Final validation of selected target combinations is done in tumorsphere cultures and xenograft models.
Results: Integration of our experimental approaches unambiguously pointed towards EGFR and EPHA2 tyrosine kinase receptors as molecules of choice for co-targeting in multiple tumor types. Following this lead, we generated a human bispecific anti-EGFR/EPHA2 antibody that, as predicted, very effectively suppresses tumor growth, compared to its prototype anti-EGFR therapeutic antibody, cetuximab.
Conclusion: Our work not only presents a new bispecific antibody with a high potential for being developed into clinically-relevant biologics, but more importantly, successfully validates a novel unbiased strategy for selecting biologically optimal target combinations. This is of a significant translational relevance, as such multifaceted unbiased approaches are likely to augment the development of effective combination therapies for cancer treatment.

overall_design: Samples were collected at different time points after treating cells with IgG or anti-EphA2 and probes were prepared to hybridize to microarray chips to identify anti-EphA2 resistant genes.

first: Amr

last: El Zawily

first: Frederick

first: Behzad

middle: M

last: Toosi

first: Nocolas

last: Bisson

first: Tajib

last: Mirzabekov

first: Andrew

last: Freywald


title: Celf1 and Postnatal Lens Microarray

status: Public on Feb 18 2023

city: Newark

first: Salil

middle: Anil

last: Lachke

state: Delaware

address: 351 Wolf Hall, University of Delaware

department: Biological Sciences

institute: University of Delaware

summary: Celf1 germline or conditional deletion mouse mutants exhibit fully penetrant lens defects including cataract. To gain insight into gene expression changes underlying these lens defects, microarray comparison was performed for lenses obtained from control and Celf1 conditional deletion mutant mice.

overall_design: Microarray comparison of lenses from mixed background (C57BL/6J, FVB) control (Celf1lacZKI/+)and mutant (Celf1cKO) mice was performed

first: Archana

last: Siddam


title: Transcriptome analysis of four maize lines to detect the different responses to chilling stress and reveal the survival mechanisms in maize

status: Public on Feb 19 2023

city: Ithaca

first: yuan

last: jiang

address: 306 Tower Rd

institute: cornell university

summary: Purpose: The goal of this analysis is that to reveal the different expression pattern in chilling-tolerant and chilling susceptible lines under chilling stress.Chilling is a major stress to plants of subtropical and tropical origins including maize. To reveal molecular mechanisms underlying chilling tolerance and chilling survival, we investigated maize transcriptome responses to chilling stress in differentiated leaves and roots as well as in crowns with meristem activity for survival. Chilling stress on maize shoots and roots is found to each contribute to seedling lethality in maize. Comparison of maize lines with different chilling tolerance capacity reveals that chilling survival in maize is highly associated with upregulation in leaves and crowns of abscisic acid response pathway, transcriptional regulators and metal ion transporters as well as downregulation of heat response in crowns. Comparison of chilling treatment on whole and part of the plants reveals that response to distal-chilling is very distinct from, and sometimes opposite to, response to local- or whole-plant chilling in both leaves and roots, suggesting a communication between shoots and roots in environmental perception. In sum, this study details chilling responses in leaves, roots and crowns and reveals potential chilling survival mechanism in maize, which lays ground for further understanding survival and tolerance mechanisms under low but non-freezing temperatures in tropical and subtropical plants.

overall_design: Examination of 4 different maize lines, and normal temperature for control group, while 4 treatment for experiment group.

first: Chunmei

last: Xue

first: Yuan

last: Jiang

first: Jian

last: Hua


title: Hepatic gene expression profiles during fed–fasted–refed state in mice

city: shanghai

first: NANA

last: JI

overall_design: Refer to individual Series


title: Hepatic gene expression profiles during fed–fasted–refed state in mice [miRNA-seq]

first: Yan

last: Lu

first: Min

last: Zhang

first: Nana

last: Ji

first: Liping

last: Xiang

first: Bing


title: microRNAs expression Profiles in plasma from spinal  tuberculosis patients and healthy volunteers

city: Xi’an

first: Zili

last: Wang

address: NO.737, Xitai Road, High-tech Zone

department: Spine Surgery

institute: Xi’an International Medical Center Hospital Affiliated to Northwest University

summary: The differential expression of plasma miRNAs was analyzed in spinal tuberculosis patients and healthy volunteers using the Exiqon miRNA PCR array platform.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: The plasma samples from 8 healthy volunteers and  12 spinal tuberculosis patients were analyzed.

first: wang

last: zili


title: Appropriate local pH value boosting the efficacy of fibroblast growth factor to promote wound repair

city: Whenzhou

first: Ruyi

last: Fan

address: Yongzhong

institute: Wenzhou Institute, University of Chinese Academy of Sciences

summary: To explore whether the application of FGF with different isoelectric points in wounds with different pH values, GelMA hydrogels with different pH values were prepared to maintain the wounds microenvironment with the same pH values, in which aFGF and bFGF were loaded as well.interferes with the healing process to different degrees,

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of 21 mice in 7 groups.

first: Qiao

last: Pan

first: Rui

last: Chen

first: Jiayi

last: Yuan


title: Alleviating classB vitamin requirement for fast growth of Saccharomyces cerevisiae in oxic conditions

city: Delft

first: Marcel

last: van den Broek

address: Van der Maasweg 9

country: Netherlands

institute: Delft University of Technology

summary: Saccharomyces cerevisiae is bradytroph for class B vitamins, it means that yeast cells exhibit slower growth in the absence of an external source of these metabolites. Alleviating these nutritional requirements for optimal growth performance would represent a valuable phenotypic characteristic for industrial strains since this would result in cheaper processes that would also be less susceptible to contaminations. In the present study, suboptimal growth of S. cerevisiae in absence of either pantothenic acid, para-aminobenzoic acid (pABA), pyridoxine, inositol and biotin were corrected by single or double gene overexpression of ScFMS1, ScABZ1/ScABZ2, ScSNZ1/ScSNO1, ScINO1 and the Cyberlindnera fabianii BIO1, respectively. Several strategies were attempted to improve growth of S. cerevisiae CEN.PK113-7D in absence of thiamine, revealing that overexpression of ScTHI4 and ScTHI4/ScTHI5 improved growth up to 83% of the maximum specific growth rate of the reference CEN.PK113-7D in vitamins containing medium.  By combining overexpression of solely seven S. cerevisiae genes and the heterologous CfBIO1, the strain IMX2816 was fast-growing at a maximum specific growth rate of 0.33 ± 0.01 h-1 in medium devoid of all vitamins. Secondly, this strain exhibited physiological performances in oxic glucose-limited chemostat cultures at a dilution rate of 0.1 h-1 in absence of vitamins similar to that of the reference strain CEN.PK113-7D grown in fully supplemented medium. These physiological similarities were further emphasized by the limited differences observed in comparative transcriptome analysis from the chemostat culture grown cells that were essentially affecting genes of the class B vitamins biosynthetic pathways. This work paves the way towards construction of the first fast growing vitamin-independent S. cerevisiae strain.

overall_design: The goals of this study were to investigate whether simple strategies can be found to eliminate single vitamin requirements and if the found solutions could be combined yielding a vitamin-independent S. cerevisiae strain. Next, the engineered strain was characterized for growth performance in batch and chemostat cultures and compared to a parental strain requiring vitamin supplementation for optimal growth. Finally, transcriptome data of the engineered strain grown in absence of vitamins was analyzed and compared to its isogenic reference grown in presence of vitamins.

first: Jean-Marc

last: Daran

first: Anna

last: Wronska

first: Thomas

last: Perli

first: Anja

last: Ehrmann


title: Pluripotency-Independent Induction of Human Trophoblast Stem Cells from Fibroblasts [RRBS]

first: Yosef

last: Buganim

summary: RRBS analysis revealed similarity/dissimilarity between human blastocyst derived trophoblast stem cells (hbdTSCs), human induced trophoblast stem cells (hiTSCs), human foreskin fibroblasts (HFFs) and pluripotent stem cells (hESCs, hiPSCs)

overall_design: HFFs reprogrammed into hiTSC lines by transient ectopic expression of GATA3, OCT4, KLF4, MYC (GOKM) were subjected to RRBS-protocol to assess differentially methylated regions, along with samples of HFFs, hbdTSCs, hESCs and hiPSCs

first: Moriyah

last: Naama

first: Ahmed

last: Radwan

first: Valery

last: Zayat

first: Shulamit

last: Sebban


title: Village In a Dish: A Model System for Population-scale hiPSC Studies

status: Public on Feb 14 2023

city: Darlinghurst

first: Drew

last: Neavin

state: New South Wales

address: 384 Victoria St

department: Cellular Science

country: Australia

institute: Garvan Institute of Medical Research


title: Village In a Dish: A Model System for Population-scale hiPSC Studies [scRNA-Seq]

summary: The mechanisms by which DNA alleles contribute to disease risk, drug response, and other human phenotypes are highly context-specific, varying across cell types and under different conditions. Human induced pluripotent stem cells (hiPSCs) are uniquely suited to study these context-dependent effects, but to do so requires cell lines from hundreds or thousands of individuals. Village cultures, where multiple hiPSC lines are cultured and differentiated in a single dish, provide an elegant solution for scaling hiPSC experiments to the necessary sample sizes required for population-scale studies. Here, we show the utility of village models, demonstrating how cells can be assigned back to a donor line using single-cell sequencing and addressing whether line-specific signalling alters the transcriptional profiles of companion lines in a village. We generated single-cell RNA sequence data from hiPSC lines cultured independently (uni-culture) and in villages at three independent sites. Using a mixed linear model framework, we estimate that the proportion of transcriptional variation across cells is predominantly due to donor effects, with minimal evidence of variation due to culturing in a village system. We demonstrate that the genetic, epigenetic or hiPSC line-specific effects explain a large percentage of gene expression variation for many genes, not the village status. This is reiterated by replication of previously identified genetic effects. Finally, we demonstrate consistency in the landscape of cell states between uni- and village-culture systems. We demonstrate that village methods can effectively detect hiPSC line-specific effects, including sensitive dynamics of cell states.

overall_design: Eight samples that have three samples multiplexed with antibody hash tags that each contained three multiplexed iPSCs. These were each captured with 10x Genomics.

middle: R

first: Angela

last: Steinmann

first: Nona

last: Farbehi

first: Han

last: Chiu

first: Maciej

last: Daniszewski

first: Himanshi

last: Arora

first: Yasmin

last: Bermudez

first: Cátia

last: Moutinho

first: Chia-Ling

last: Chan

first: Monique

last: Bax

first: Mubarika

last: Tyebally

first: Vikkitharan

last: Gnanasambandapillai

first: Chuan

last: Lam

first: Uyen

last: Nguyen

first: Damián

last: Hernández

first: Grace

last: Lidgerwood

first: Bob

last: Graham

first: Alex

middle: W

last: Hewitt

first: Alice

last: Pébay

first: Nathan

last: Palpant

first: Joseph

last: Powell


title: Pluripotency-Independent Induction of Human Trophoblast Stem Cells from Fibroblasts

first: Yosef

last: Buganim


title: NAT10 mediated ac4C tRNA modification promotes EGFR mRNA translation and gefitinib resistance in cancers

status: Public on Feb 16 2023

city: Guangzhou

first: Wei

last: Wei

state: -- None selected --

address: 越秀区中山二路

institute: 中山大学附属第一医院

summary: The diverse RNA modifications play essential functions in gene expression regulation. Aberrant RNA modifications are frequently associated with cancers, while the underlying mechanisms and clinical significance remain poorly understood. Here we revealed that the ac4C RNA acetyltransferase NAT10 is significantly upregulated in esophageal cancers (ESCA) and associated with poor ESCA prognosis. In addition, using cancer cell lines, xenograft tumor models, Nat10 conditional knockin and conditional knockout mice, in vivo ESCA tumorigenesis model and chemical inhibition approaches, we uncovered the critical physiological functions of NAT10 in promoting esophageal cancer tumorigenesis and progression in vitro and in vivo. Mechanistically, NAT10 depletion reduced the abundance of ac4C-modified tRNAs and significantly decreased the translation efficiencies of mRNAs enriched for ac4C-modified-tRNA decoded codons. We further identified EGFR as a key downstream target that facilitates NAT10’s oncogenic functions in promoting esophageal cancer progression. In terms of clinical significance, we demonstrated that NAT10 promotes esophageal cancer resistance to EGFR inhibitor gefitinib, and combination of NAT10 depletion and gefitinib treatment synergistically inhibits esophageal cancer progression in vitro and in vivo. Our data uncovered novel molecular mechanisms underlying esophageal cancer progression at the layer of mRNA translation control and provided molecular insights for development of effective cancer therapeutic strategies.

overall_design:
RNA-seq was used to study the differenially expressed genes upon NAT10 knockout or ctrl cells.
ac4C-rip-seq was used to study the differenially expressed tRNA upon NAT10 knockout or ctrl cells.

first: Shuibin

last: Lin


title: EGR1 overexpression in HeLa cells [EGR1oe_RNAseq]

status: Public on Feb 12 2023

city: Pozzuoli

first: Francesco

last: Panariello

state: Napoli

address: Via Campi Flegrei 34

country: Italy

institute: TIGEM

summary: Transcriptional regulation of gene expression plays a fundamental role in coordinating molecular and metabolic responses to stress conditions. The stress-responsive Transcription Factor EB (TFEB), the master controller of lysosomal biogenesis and autophagy, is regulated at the post-translational level by the nutrient-sensitive kinase complex TORC1. However, little is known about the transcriptional regulation of TFEB in physiological and pathological conditions. Here, we show that during starvation, the immediate-early gene EGR1 binds to the TFEB promoter and positively regulates TFEB expression. EGR1 depletion dampened TFEB-mediated transcriptional response to starvation and significantly inhibited cell proliferation in cellular and 3D spheroid models of Birt-Hogg-Dube' (BHD) syndrome, a TFEB-driven inherited cancer condition. Consistently, the MEK1/2 inhibitor Trametinib, known to inhibit EGR1 expression, suppressed the proliferation of BHD patient-derived cancer cells, suggesting that pharmacological inhibition of the EGR1-TFEB axis may represent a therapeutic strategy to counteract constitutive TFEB activation in cancer-associated conditions.

overall_design: RNA-seq of HeLa cells transduced with CTRL and EGR1-overexpressing plasmids

first: Marcella

last: Cesana


title: Extensive sex differences in depression-linked variants functionally assayed in mouse brain

status: Public on Feb 10 2023

city: St. Louis

last: Dougherty

state: MO

address: 660 S Euclid Ave, Campus Box 8232

department: Genetics

institute: Washington University in St. Louis

sample_organism:
Mus musculus
Adeno-associated virus 9

platform_organism:
Mus musculus
Adeno-associated virus 9

overall_design:
Refer to individual Series

Additional grant information: 571009 - Joseph Dougherty - Simons Foundation


title: Gene expression alterations in the postmortem hippocampus from older patients with bipolar disorder – a hypothesis generating study

city: Sao Paulo

first: Camila

last: Nascimento

state: Sao Paulo

address: Rua Dr. Ovídio Pires de Campos, 785

department: Psychiatry

country: Brazil

institute: University of Sao Paulo

summary: Gene expression of samples from the postmortem hippocampus of older bipolar disorder subjects and controls. Gene expression data was generated using the SurePrint G3 Human Gene Expression v3 microarray. Rank feature selection was performed to identify a subset of features that can optimally differentiate BD and controls.

overall_design: Case control - Gene expression profile of postmortem hippocampus samples from older bipolar disorder (BD) subjects and controls were compared in order to identify genes of interest for the BD pathophysiology

first: Helena

last: Kim

first: Paula

last: Nunes

first: Renata

middle: P

last: Leite

first: Katia

last: De Oliveira

first: André

last: Barbosa

first: Fernanda

middle: B

last: Bertonha

first: Carlos

last: Filho

first: Wilson

last: Jacob-Filho

first: Ricardo

last: Nitrini

last: Pasqualucci

first: Lea

middle: T

last: Grinberg

first: Claudia

last: Suemoto

last: Brentani

first: Beny

last: Lafer


title: IDENTIFICATION AND FUNCTIONAL DEMONSTRATION OF A FETAL-SPECIFIC AXIS THAT POTENTLY SUPPRESSES MLL-FUSION DRIVEN MURINE AML

status: Public on Feb 08 2023

city: Lund

first: Phuong

last: Cao Thi Ngoc

address: BMC, B1222b, Klinikgatan 26

country: Sweden

institute: Lund University

summary: MLL-rearrangements (MLL-r) are recurrent genetic events in acute myeloid leukemia (AML) and frequently associate with poor prognosis. In infants, MLL-r have been suggested to be sufficient to drive transformation. However, despite the prenatal origin of MLL-r, the incidence of congenital leukemia is very low with transformation usually occurring postnatally. The influence of prenatal signals on leukemogenesis, such as those mediated by the fetal-specific RNA binding protein LIN28B, remains controversial. Here, using a dual-transgenic mouse model that co-express MLL-ENL and LIN28B, we investigated the impact of LIN28B on AML. We show that LIN28B impedes the progression of MLL-r AML through a compromised leukemia initiating cell activity and a suppression of MYB signaling. Mechanistically, rather than involving the well-studied Lin28B-let7 miR axis, we found that LIN28B directly bound MYBBP1A mRNA, a co-repressor of MYB, and that positively correlated with MYBBP1A protein levels. Overexpression of MYBBP1A in MLL-ENL driven leukemogenesis largely phenocopied the tumor suppressor effects of LIN28B. Thereby, our work proposes that the developmentally-restricted expression of LIN28B during fetal development provides a protection against MYB-dependent AML.

overall_design: iCLIP seq was performed on GMLPs from L28BME to map the genome-wide LIN28B-RNA associations. FLAG antibody was used to immunoprecipitate LIN28B-RNA complexes. ME cells were used as a control for non-specific binding.

first: Mohamed

last: Eldeeb

first: Ouyang

last: Yuan

first: Nicola

last: Guzzi

first: Anna

last: Konturek-Ciesla

first: Trine

middle: A

last: Kristiansen

first: Sowndarya

last: Muthukumar

first: Jeffrey

last: Magee

first: Cristian

last: Bellodi

first: Joan

first: David

last: Bryder