title: Combined effects of genetic background and diet on mouse metabolism and gene expression

status: Public on Mar 04 2024

city: Charlottesville

first: Mete

last: Civelek

state: VA

address: Center for Public Health Genomics, PO Box 800717

institute: University of Virginia

summary: In humans, dietary patterns impact weight and metabolism differentially across individuals. To uncover genetic determinants for differential dietary effects, we subjected four genetically diverse mouse strains to humanized diets (American, Mediterranean, vegetarian, and vegan) with similar macronutrient composition, and performed body weight, metabolic parameter, and RNA-seq analysis. We observed pronounced diet- and strain-dependent effects on weight, and triglyceride and insulin levels. Differences in fat mass, adipose tissue and skeletal muscle glucose uptake, and gene expression changes in most tissues were strain-dependent. In visceral adipose tissue ~400 genes responded to diet in a strain-dependent manner, many of them in metabolite transport and lipid metabolism pathways and several previously identified to modify diet effects in humans. Thus, genetic background profoundly impacts metabolism, and dietary patterns modify effects. This study paves the way for future mechanistic investigations into strain-diet interactions in mice and translation to precision nutrition in humans.

overall_design: We obtained four strains of 12 week old male mice (A/J, DBA/2J, C57BL/6J, SJL) and fed them mouse versions of four populat human diets (American, Mediterranean, vegetarian, vegan) for 6 weeks. Using two mice of each strain and diet combination at 18 weeks of age, we harvested metabolic tissues (liver, quadriceps muscle, brown adipose (BAT), subcutaneous adipose (SAT), and visceral adipose (VAT)) and isolated mature RNA species.We sequenced them using the NovaSeq6000 S4 (150bp PE) with the TruSeq Stranded mRNA Library Prep Kit. We obtained >  50M total reads per sample, >25M read1 and read2. Processed data QC using fastQC, adapters removed with trimGalore, alignment to GRCm39 using hisat2 with relaxed mismatch penality for non-C57BL/6J mice. Reads quantified using ht-seq with fractional alignment.

first: Jordan

middle: N

last: Reed

first: Faten

last: Hasan

first: Abhishek

last: Karkar

first: Dhanush

last: Banka

first: Jameson

last: Hinkle

first: Preeti

last: Shastri

first: Navya

last: Srivastava

first: Stephen

last: Sherping

first: Sarah

middle: E

last: Newkirk

first: Heather

last: Ferris

first: Bijoy

last: Kundu

first: Sibylle

last: Kranz

first: Susanna

last: Keller


title: Anti-viral defense by an ADP-ribosyltransferase that targets mRNA to block translation (RIP-Seq in vivo)

status: Public on Mar 09 2024

city: Cambridge

first: Christopher

middle: Ross

last: Doering

state: MA

address: 31 Ames St

department: Biology

country: USA

institute: MIT

summary: Host-pathogen conflicts are crucibles of molecular innovation. Selection for immunity to pathogens has driven the evolution of sophisticated immunity mechanisms throughout biology, including in bacteria that must evade their viral predators known as bacteriophages. Here, we characterize a toxin-antitoxin-chaperone system, CmdTAC, in Escherichia coli that provides robust defense against infection by T4 phage. During infection, newly synthesized capsid protein triggers dissociation of the chaperone CmdC from the CmdTAC complex, leading to destabilization and degradation of the antitoxin CmdA, with consequent liberation of the toxin CmdT, an ADP-ribosyltransferase. Strikingly, CmdT does not target a protein, DNA, or structured RNA, the known targets of other ADP-ribosyltransferases. Instead, CmdT modifies the N6 position of adenine in GA dinucleotides within single-stranded RNAs to robustly block mRNA translation and viral replication. Our work reveals both a new mechanism of anti-phage defense and a new class of ADP-ribosyltransferases that targets mRNA.

sample_organism:
Escherichia coli
Escherichia phage T4

platform_organism:
Escherichia coli
Escherichia phage T4

overall_design: The goal of this experiment is to identify ADP-ribosylated RNAs by IP enrichment from RNA harvested from cells infected with T4 +/- CmdTAC phage defense system. The CmdT toxin of the CmdTAC system is an ADP-ribosyltransferase that targets RNA

middle: R

last: Vassallo

first: Michael

last: Laub


title: Human macrophages THP-1: Infected with three different strains of Brucella melitensis

status: Public on Mar 07 2024

city: Mexico City

first: Cloé

last: Queijeiro-Barroso

state: Mexico City

address: Av Universidad 3000

department: FMVZ/Microbiología

country: Mexico

institute: Universidad Nacional Autónoma de México

summary: Transcriptional profile compairing  infected human macrophages at 2 and 4 h p.i.  with virulent strain Brucella melitensis BM16M vs wildtype BM133 , BM16M vs mutant LVM31, BM133 vs 16M.

overall_design: Three-strains experiment, BM16M infected macrophages vs BM133 infected macrophages 2 h p.i. BM16M infected macrophages vs LVM31 infected macrophages 2 h p.i. BM133 infected macrophages vs LVM31 infected macrophages 2 h p.i. BM16M infected macrophages vs BM133 infected macrophages 4 h p.i. BM16M infected macrophages vs LVM31 infected macrophages 4 h p.i. BM133 infected macrophages vs LVM31 infected macrophages 4 h p.i.  One microarray per experiment. Three biological replicates per experiment.

first: Cloe

first: Antonio

last: Verdugo-Rodríguez


title: Single Cell Transcriptomic Profiling of MYBPC3-associated Hypertrophic Cardiomyopathy Across Species Reveals Conserva-tion of Biological Process but Not Gene Expression

status: Public on Mar 06 2024

city: Boston

first: Samia

last: Ali

state: Massachusetts

address: 800 Washington Street

department: Molecular Cardiology Research Institute

institute: Tufts Medical Center

type: Expression profiling by high throughput sequencing

summary: Single RNA sequencing analysis of myosin binding protein C3 (mybpc-3) associated Hypertrophic Cardiomyopathy to identify single cell gene expression changes across common pathological mechanisms and species-specific distinctions in human, feline, and murine heart tissues.

sample_organism:
Homo sapiens
Felis catus
Mus musculus

platform_organism:
Homo sapiens
Felis catus
Mus musculus

overall_design: Interventricular septal (IVS) myectomy heart tissue was obtained from human patients and felines with left ventricular outflow tract obstruction (LVOT) and organ donors or control [as in the case for felines]. Whole heart from a knock-in mouse model with a truncated form of myosin binding protein C3 and Wild Type were sampled using snRNA-seq.

first: Gayani

last: Perera

middle: T

last: Chin


title: Anti-viral defense by an ADP-ribosyltransferase that targets mRNA to block translation

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

overall_design: Refer to individual Series


title: Transcriptomic and V(D)J profiling at the single cell level of plasmablasts from lymph nodes of mice immunized with bMOG protein

city: Quebec

first: Luc

last: Vallières

state: Quebec

address: 2705 Laurier Boulevard

department: Neuroscience

country: Canada

institute: University Hospital Center of Quebec – Laval University

summary: Autoantibodies contribute to many autoimmune diseases, yet there is no therapy to neutralize them selectively. A popular mouse model, experimental autoimmune encephalomyelitis (EAE), could serve to develop such a therapy, provided we can better understand the nature and importance of the autoantibodies involved. In this study, we analyzed autoantibody-secreting extrafollicular plasmablasts in mice with EAE induced by immunization with a mutated myelin oligodendrocyte glycoprotein (MOG) antigen called bMOG. These CD138+ cells were enriched from lymph nodes at day 8 post-immunization and analyzed by single-cell RNA sequencing using 10× Genomics technologies. Here we provide the raw and processed data obtained from the gene expression (GEX) and VDJ cDNA libraries.

overall_design: Single-cell suspensions were prepared from inguinal lymph nodes of mice at day 8 post-immunization with bMOG. CD138+ cells were enriched using the EasySep Mouse CD138 Positive Selection Kit (Stemcell Technologies). Cells were processed with the Chromium Single Cell Chip A and Chromium Controller (10× Genomics) with the goal of analyzing ~6,000 cells per mouse. RNA samples were pooled for reverse transcription and amplification to generate gene expression and V(D)J libraries using the Single Cell 5’ Library Kit and Single Cell V(D)J Enrichment Kit (10× Genomics). Libraries were pooled and sequenced using both Illumina Hiseq 2500 PE100 technology (low pass) at the University Hospital Center of Quebec and Illumina NovaSeq 6000 S4 PE150 technology (high pass) at Genome Quebec. Sequencing results from both technologies were combined for bioinformatics analyses.

first: Catherine

last: Bélanger

first: Juan

middle: M

last: Dominguez

first: Jacques

last: Corbeil


title: Remodelling of the immune landscape by IFNγ counteracts IFNγ-dependent tumour escape in mouse tumour models

city: Oxford

first: Audrey

last: Gerard

address: Roosevelt Dr.

country: United Kingdom

institute: The Kennedy Institute of Rheumatology

summary: IFNγ-dependent remodelling of the myeloid immune landscape underlies control of IFNγ-insensitive tumors

overall_design: C57Bl6 WT mice were engrafted with the melanoma cell line B16 expressing OVA. CD45+ T cells were isolated by Fluorescence-activated cell sorting (FACS) from the tumor after 12 days and subjected to scRNA sequencing

last: Gérard

first: Vivian

last: Lau


title: Anti-viral defense by an ADP-ribosyltransferase that targets mRNA to block translation (RNA-Seq)

overall_design: The goal of this experiment is to look globally at the changes in T4 transcription +/- cmdTAC expression. RNA was harvest from T4 infected cells +/- cmdTAC at 15 and 30 minutes post-infection. Harvested RNA was rRNA depleted and made into a cDNA library for sequencing on an Illumina NextSeq 5000 machine. We then calculated the transcripts per million (TPM) values for all coding sequences in the T4 genome at both timepoints post-infection and compared the TPM values between +cmdTAC and -cmdTAC samples, looking at changes in the TPM ratio between timepoints and for T4 genes of different peak expression times.


title: Anti-viral defense by an ADP-ribosyltransferase that targets mRNA to block translation (RIP-Seq in vitro)

overall_design: The goal of this experiment is to identify transcripts modified by the ADP-ribosyltransferase CmdT with an in vitro approach. CmdT was incubated with RNA extracted from E. coli infected with the bacteriophage T4 and supplied biotinylated NAD+ and then a streptavidin pulldown was performed on the RNA to identify modified transcripts.


title: Regulatory principles of human mitochondrial gene expression revealed by kinetic analysis of the RNA life cycle.

status: Public on Mar 20 2024

first: Mary

last: Couvillion

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School


title: Circulating senescent myeloid cells drive blood brain barrier breakdown and neurodegeneration

status: Public on Mar 01 2024

city: New York

first: MATTHEW

middle: Dae-Young

last: PARK

state: NY

address: 50 East 98th Street, 6A-1

institute: Icahn School of Medicine at Mount Sinai

summary: Neurodegenerative diseases (ND) are characterized by a progressive loss of neuronal function. Mechanisms of ND pathogenesis are incompletely understood hampering the development of effective therapies.  Langerhans cell histiocytosis (LCH) is an inflammatory neoplastic disorder caused by hematopoietic progenitors expressing MAPK activating mutations that differentiate into senescent dendritic cells that drive formation of lesions.  Some patients with systemic LCH subsequently develop progressive and incurable neurodegeneration (LCH-ND). Here, we show that LCH-ND is caused by hematopoietic cells that are clonal with systemic LCH lesion histiocytes. Strikingly, we discovered that circulating BRAFV600E+ myeloid cells cause the breakdown of the blood-brain barrier (BBB), enabling migration of into the brain where they differentiate into senescent, inflammatory macrophages that accumulate in the brainstem and cerebellum.  Blocking MAPK activity and senescence programs synergistically reduced parenchymal infiltration, neuroinflammation and neurologic damage in preclinical LCH-ND.  MAPK activation in circulating myeloid cells represents a novel and targetable mechanism of ND.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for sorted myeloid cells from BRAFV600E WT and mutant mice.

first: Matthew

middle: D

last: Park

first: C

last: Wilk


title: TEAD2 mediates the ground-state pluripotency by chromatin looping

status: Public on Mar 03 2024

city: guangzhou

first: xiaotao

last: dong

address: 190 Kai Yuan Avenue

country: China

institute: Chinese Academy of Sciences

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Mouse embryonic stem cells (mESCs) cultured in 2i (MEK and GSK3 kinase inhibitor)/LIF and serum/LIF that we called 2i-ESCs and serum-ESCs represent ground and confused pluripotent states, respectively. However, the transcription factors that regulate ground pluripotency through chromatin-associated characteristics are not yet fully understood. By mapping chromatin accessibility and transcription factor regulatory networks during the interconversion of 2i-ESCs and serum-ESCs, we have identified TEAD2 as highly enriched in 2i-specific peaks. While Tead2 knockout did not affect the pluripotency or differentiation ability of either 2i-ESCs or serum-ESCs, it did prevent the establishment of the 2i-specific state and the exit from the serum-specific state. TEAD2 binds to active regions in 2i-specific genes and activates their expression by regulating enhancer-promoter (EP) interactions during serum-to-2i transition. Remarkably, TEAD2-mediated EP interactions were independent of chromatin architecture proteins YY1 and CTCF, but instead appear to be facilitated by TEAD2 homodimer formation.

overall_design:
Dynamic gene expression and chromatin accessibility profiling of  interconversion of serum-ESCs and 2i-ESCs. Examination of TEAD2, H3K27ac, YY1, SMC1 binding sites in 2i-ESCs or cells on day 6 of serum-to2i transition.  Examination of chromatin interactions in cells on day 6 of serum-to2i transition with or without Tead2-knockout.

Tead2-knockout SL-ESC lines and 2iL-ESCs with mutated TEAD2 motifs at B4galt6 promoter were generated by using CRISPR/Cas9. Cells from the sixth day of SL-to-2iL transition after Tead2-knockout, as well as mutated 2iL-ESCs, were collected and 4C-seq analysis was performed.

Tead2-FLAG-AviTag knock-in 2iL- and SL-ESC lines were genetically generated by using the CRISPR/Cas9 system. Cells were then collected for Biotin ChIP-seq. Tead2-knockout SL-ESC lines were also generated by using CRISPR/Cas9. Wild-type and Tead2-knockout  cells were collected from the sixth day of SL-to-2iL transition and H3K27ac and H3K4me1 CUT&Tag experiments were performed. 2iL-ESC lines with mutation of TEAD2 motifs in the B4galt6 promoter region were generated by using CRISPR/Cas9, and wild-type and mutated 2iL-ESCs were then collected for H3K27ac CUT&Tag experiments.

Tead2-knockout SL-ESC lines were generated by using the CRISPR/Cas9 system. Wild-type and Tead2-knockout cells were collected from the  day 0 and day 21 of SL-to-2iL transition and BL-HiC analysis was performed.

Tead2-knockout SL-ESC lines were generated by using the CRISPR/Cas9 system. Cells from the  day 15 and 21 of SL-to-2iL transition after Tead2 knockout were collected and RNA-seq was performed. During the SL-to-2iL transition, siRNA targeting Tead4 gene and negative control were transfected, and siNC and siTead4 cells from the day 0 and 6 of transition were collected and RNA-seq was performed.

first: Hongjie

last: Yao

first: Rong

last: Guo

first: Xiaotao

last: Dong


title: Molecular, Cellular, and Developmental Organization of the Mouse Vomeronasal organ at Single Cell Resolution

status: Public on Feb 29 2024

city: Kansas City

first: C.

middle: Ron

last: Yu

state: MO

department: Yu Lab

institute: Stowers Institute For Medical Research

summary: We have generated single cell transcriptomic atlases of vomeronasal organs (VNO) from juvenile and adult mice. Combined with spatial molecular imaging, we uncover a distinct, previously unidentified class of cells that express the vomeronasal receptors and a population of canonical olfactory sensory neurons in the VNO. High resolution trajectory and cluster analyses reveal the lineage relationship, spatial distribution of cell types, and a putative cascade of molecular events that specify the V1r, V2r, and OR lineages from a common stem cell population. The expression of vomeronasal and olfactory receptors follow power law distributions, but there are high variabilities in average expression levels between individual receptor and cell types. Substantial co-expression is found between receptors across clades, from different classes, and between olfactory and vomeronasal receptors, with nearly half from pairs located on the same chromosome. Interestingly, the expression of V2r, but not V1r, genes is associated with various transcription factors, suggesting distinct mechanisms of receptor choice associated with the two cell types. We identify association between transcription factors, surface axon guidance molecules, and individual VRs, thereby uncovering a molecular code that guides the specification of the vomeronasal circuitry. Our study provides a wealth of data on the development and organization of the accessory olfactory system at both cellular and molecular levels to enable a deeper understanding of vomeronasal system function.

overall_design: Mice VNOs were dissected in cold oxygenated ACSF following Ma et al, 2011. Dissected epitheliums were dissociated in papain solution (20mg/mL papain and 3mg/mL L-cysteine in HBSS) with RNase-free DNase I (10unit) at 37°C for 15-20 minutes. 0.01% BSA in PBS was added to the digestion solution before filtering with 70µm and 30µm filters (pluriSelect). Dissociated cells were washed twice in 0.01% BSA with final volume 1mL, followed by Draq5 (25µM) and DAPI (0.5µg/mL) staining 5min on ice. Draq5+/DAPI- cells (live/nucleated cells) were sorted on BD Influx cytometer (BD Bioscience) with 100µm nozzle. Dissociated sorted cells were assessed for concentration and viability via Luna-FL cell counter (Logos Biosystems). Cells deemed to be at least 90% viable were loaded on a Chromium Single Cell Controller (10x Genomics), based on live cell concentration.

first: Max

last: Hills Jr

first: Limei

last: Ma

first: Ai

last: Fang

first: Thelma

last: Chiremba

first: Seth

last: Malloy

first: Allison

last: Scott

first: Anoja

last: Perera


title: MaizeCODE reveals bi-directionally expressed enhancers that harbor molecular signatures of maize domestication [TIL11 RNA]

status: Public on Feb 23 2024

city: Cold Spring Harbor

first: Jonathan

last: Cahn

address: 1 Bungtown Rd

institute: CSHL

type: Non-coding RNA profiling by high throughput sequencing

summary: Modern maize was domesticated from Teosinte parviglumis, with subsequent introgressions from Teosinte mexicana, yielding increased kernel row number, loss of the hard fruit case and dissociation from the cob upon maturity, as well as fewer tillers. Molecular approaches have identified several transcription factors involved in the development of these traits, yet revealed that a complex regulatory network is at play. MaizeCODE deploys ENCODE strategies to catalog regulatory regions in the maize genome, generating histone modification and transcription factor ChIP-seq in parallel with transcriptomics datasets in 5 tissues of 3 inbred lines which span the phenotypic diversity of maize, as well as the teosinte inbred TIL11. Integrated analysis of these datasets resulted in the identification of a comprehensive set of regulatory regions in each inbred, and notably of distal enhancers which were differentiated from gene bodies by their lack of H3K4me1. Many of these distal enhancers expressed noncoding enhancer RNAs bi-directionally, reminiscent of “super enhancers” in animal genomes. We show that pollen grains are the most differentiated tissue at the transcriptomic level, and share features with endosperm that may be related to McClintock’s chromosome breakagefusion-bridge cycle. Conversely, ears have the least conservation between maize and teosinte, both in gene expression and within regulatory regions, reflecting conspicuous morphological differences selected during domestication. The identification of molecular signatures of domestication in transcriptional regulatory regions provides a framework for directed breeding strategies in maize.

overall_design: Whole transcriptome sequencing (RNA-seq) was performed on multiple tissues and multiple inbred lines of zea mays

first: Melissa

last: Kramer

first: Jorg

last: Denkow

first: Xu

last: Xiaosa

first: Michael

last: Regulski

first: Robert

last: Martienssen

first: Thomas

last: Gingeras


title: MaizeCODE reveals bi-directionally expressed enhancers that harbor molecular signatures of maize domestication [W22 RNA]


title: Single cell transcriptomics of vomeronasal neuroepithelium reveals a differential endoplasmic reticulum environment amongst neuronal subtypes

status: Public on Feb 28 2024

city: Hyderabad

first: Adish

last: Dani

state: Telangana

address: 36/P, Gopanpally

country: India

institute: Tata Institute of Fundamental Research, Hyderabad

summary: Specialized chemosensory signals elicit innate social behaviors in individuals of several vertebrate species, a process that is thought to be mediated via the accessory olfactory system (AOS). The AOS comprising the peripheral sensory vomeronasal organ (VNO) has evolved elaborate molecular and cellular mechanisms to detect chemo signals. To gain insight into the cell types, developmental gene expression patterns and functional differences amongst neurons, we performed single cell transcriptomics of the mouse vomeronasal sensory epithelium. Our analysis reveals diverse cell types with gene expression patterns specific to each. Pseudo-time developmental analysis indicates that neurons originating from common progenitors diverge in their gene expression during maturation with transient and persistent transcription factor expression at critical branch points. Comparative analysis across two of the major neuronal subtypes that express divergent GPCR families and the G-protein subunits Gnai2 or Gnao1, reveals significantly higher expression of endoplasmic reticulum (ER) associated genes within Gnao1 neurons. We also specific combinatorial expression pattern of V2R and H2-Mv genes in Gnao1 neurons. These gene expression patterns, along with differential localization of ER chaperones and structural proteins indicate fundamental differences in ER function associated with neuronal differentiation.

overall_design: Vomeronasal organ from male and female C57BL/6J animals was dissected and processed separately. The neuroepithelium was separated and single cell dissociation was performed. The dissociated suspension was used for single cell RNA sequencing on 10X genomics platform

first: GVS

last: Devakinandan


title: Age-associated chromatin re-organization in progenitor B cells

city: Bethesda

first: Yaqiang

last: Cao

state: Maryland

address: 9000 Rockville Pike

department: System Biology Center

institute: NHLBI

type: Genome variation profiling by high throughput sequencing

summary: Three-dimensional (3D) organization of the genome is essential for precise patterns of gene expression required for biological processes, however its role in physiological aging is not known.Here we show that large scale chromatin re-organization distinguishes bone marrow progenitor (pro-) B cells of old mice from that of young mice.These changes result in increased interactions at the compartment level and reduced interactions within topologically associated domains (TADs).One genomic region that transitions from compartment A to B with age contains the gene encoding Ebf1, a key regulator of normal B cell development.Genetically reducing Ebf1 recapitulates some features of old pro-B cells.TADs that are most reduced with age also harbor genes important for function and development of pro-B cells, including the immunoglobulin heavy chain (IgH) gene locus.Weaker intra-TAD interactions at IgH correlate with reduced utilization of distally located variable gene segments in VDJ recombination.Our observations implicate 3D chromatin re-organization as a major driver of pro-B cell phenotypes that impair B lymphopoiesis with age.

overall_design: Hi-C, capture Hi-C, ChIP-seq, HiChIP and RNA-seq were used to study the changes of chromatin structures in progenitor B cells during aging.

first: Fei

first: Hansen

last: Du

first: Fatima

middle: Z

last: Braikia

first: Noah

last: Ollikainen

first: Le

last: Zong

first: Marc

last: Bayer

first: Xiang

last: Qiu

first: Bongsoo

last: Park

first: Roshni

last: Roy

first: Satabdi

last: Nandi

first: Dimitra

last: Sanrantopoulou

first: Aisha

middle: H

last: Bianchi

first: Isabel

last: Beerman

first: Keji

last: Zhao

first: Rudolf

last: Grosschedl

first: Ranjan

last: Sen


title: MaizeCODE reveals bi-directionally expressed enhancers that harbor molecular signatures of maize domestication [NC350 RNA]

first: Jonathan

last: Cahn

first: Melissa

last: Kramer

first: Jorg

last: Denkow

first: Xu

last: Xiaosa

first: Michael

last: Regulski

first: Robert

last: Martienssen

first: Thomas

last: Gingeras


title: MaizeCODE reveals bi-directionally expressed enhancers that harbor molecular signatures of maize domestication

sample_organism:
Zea mays
Zea mays subsp. parviglumis

platform_organism:
Zea mays
Zea mays subsp. parviglumis


title: MaizeCODE reveals bi-directionally expressed enhancers that harbor molecular signatures of maize domestication [ChIP-seq]

overall_design: Chromatin Immunoprecipitation sequencing (ChIP-seq) of H3K27ac, H3K4me1 and H3K4me3 was performed on multiple tissues and multiple inbred lines of zea mays.ChIP-seq of transcription factors GT1 and TU1A were done in B73 ears.


title: Mitochondrial genome variation affects humoral and cell-mediated innate immune responses and infection outcomes

city: Edinburgh

first: Pedro

last: Vale

state: Edinburgh

address: Ashworth Labs, Charlotte Auerbach Road

department: School of Biological Sciences

institute: University of Edinburgh

summary: The role of mitochondria in both adaptive and innate immune responses is increasingly recognized, but the role of natural mitochondrial DNA (mtDNA) variation as an immunomodulatory factor has received less attention. One reason for this is the difficulty of separating the effect of mtDNA from that of the nuclear genome. By utilizing the fruit fly Drosophila melanogaster, a powerful model system, we created cytoplasmic hybrids, aka. cybrid lines, where unique mtDNAs (mitotypes) were introgressed into a controlled isogenic nuclear background. We harnessed a panel of cybrid lines to study the effect of mtDNA variation on humoral and cell-mediated innate immune responses. Mitotypes exhibited heterogeneity in infection outcomes upon bacterial, viral and parasitoid infections. One mitotype of note, mtKSA2  appeared to be more immunocompetent when compared to other mitotypes. We performed transcriptomic profiling of uninfected flies and flies infected with bacteria or a virus and compared them to a different mitotype in the same nuclear background to find the mechanistic basis of the immunocompetence. We found that mtKSA2 caused an upregulation of TCA and OXPHOS related genes and a downregulation of a multiple genes encoding for antimicrobial peptides in uninfected flies. Upon infection, mtKSA2 flies produced unique transcriptomes that were separated by infection type and duration. When we examined immune cells (hemocytes) in mtKSA2 larvae, we noted an increase in hemocyte numbers. These hemocytes were activated in the absence of infection,  increased their production of  ROS, and showed evidence of increased encapsulation efficiency upon parasitoid wasp infection. Overall, our results show that mtDNA variation acts as an immunomodulatory factor in both humoral and cell-mediated innate immunity and that specific mitotypes provide enhanced protection against infections.

overall_design: 1-4 days old, mated females and males were infected with Staphylococcus aureus (PIG1) or  Providencia rettgeri (DSM4542) by pricking the flies with a tungsten needle dipped in bacterial solution (OD600=0.1). Samples were collected 8 and 20 hours after infecting the flies. Systemic infection with DCV was introduced to 2-5 days old, mated females and males by pricking as described with the bacterial infections. DCV inoculum of 10^8 viral particles was used. Samples were collected 3 days after the infection with DCV. As controls, uninfected flies of similar age were collected.

first: Tiina

middle: S

last: Salminen

first: Laura

last: Vesala

first: Yuliya

last: Basikhina

first: Megan

last: Kutzer

first: Tea

last: Tuomela

first: Tilman

last: Tietz

first: Ryan

last: Lucas

first: Katy

last: Monteith

first: Arun

last: Prakash

middle: F


title: Polygenic Risk for Alcohol Use Disorder Affects Cellular Responses to Ethanol Exposure in a Human Microglial Cell Model I

status: Public on Feb 19 2024

city: Piscataway

first: Ronald

middle: P.

last: Hart

state: NJ

address: 604 Allison Rd Rm B430

department: Cell Biology & Neuroscience

institute: Rutgers University

summary: Polygenic risk scores (PRS) assess genetic susceptibility to Alcohol Use Disorder (AUD), yet their molecular implications remain underexplored. Neuroimmune interactions, particularly in microglia, are recognized as significant contributors to AUD pathophysiology. We investigated the interplay between AUD PRS and ethanol in human microglia derived from iPSCs from individuals with high-or low-PRS (HPRS or LPRS) of AUD. Ethanol exposure induced elevated CD68 expression and morphological changes in microglia, with differential responses between HPRS and LPRS microglial cells. Transcriptomic analysis revealed expression differences in MHCII complex and phagocytosis-related genes following ethanol exposure; HPRS microglial cells displayed enhanced phagocytosis and increased CLEC7Aexpression, unlike LPRS microglial cells. Synapse numbers in co-cultures of induced neurons with microglia after alcohol exposure were lower in HRPS co-cultures, suggesting possible excess synapse pruning. This study provides insights into the intricate relationship between AUD PRS, ethanol, and microglial function, potentially influencing neuronal functions in developing AUD.

overall_design: Cultures of microglial cells, differentiated from multiple iPSC lines prepared from subjects with AUD and high polygenic risk (HPRS) and unaffected with low polygenic risk (LPRS) were treated with 75 mM ethanol or untreated.  Total cellular RNA was prepared and compared for effects of ethanol treatment or ethanol interaction with AUD-polygenic risk.

first: Xindi

last: Li

first: Jiayi

last: Liu

first: Anat

last: Kreimer

middle: P

first: Zhiping

last: Pang


title: MaizeCODE reveals bi-directionally expressed enhancers that harbor molecular signatures of maize domestication [B73 RNA]

first: Jonathan

last: Cahn

first: Melissa

last: Kramer

first: Jorg

last: Denkow

first: Xu

last: Xiaosa

first: Michael

last: Regulski

first: Robert

last: Martienssen


title: ARID1A governs silencing of sex-linked transcription during male meiosis in the mouse.

city: Chapel hill

first: Terry

last: Magnuson

state: NC

address: 120 Mason Farm Road, Genetics Medicine Bldg.,

institute: University of North Carolina at Chapel Hill


title: ARID1A governs silencing of sex-linked transcription during male meiosis in the mouse [CUT&RUN]

summary: We present evidence implicating the BAF (BRG1/BRM Associated Factor) chromatin remodeler in meiotic sex chromosome inactivation (MSCI). By immunofluorescence (IF), the putative BAF DNA binding subunit, ARID1A (AT-rich Interaction Domain 1a), appeared enriched on the male sex chromosomes during diplonema of meiosis I. The germ cell-specific depletion of ARID1A resulted in a pachynema arrest and failure to repress sex-linked genes indicating a defective MSCI. Consistent with this defect, mutant sex chromosomes displayed an abnormal presence of elongating RNA polymerase II coupled with an overall increase in chromatin accessibility detectable by ATAC-seq. By investigating potential mechanisms underlying these anomalies, we identified a role for ARID1A in promoting the preferential enrichment of the histone variant, H3.3, on the sex chromosomes, a known hallmark of MSCI. Without ARID1A, the sex chromosomes appeared depleted of H3.3 at levels resembling autosomes. Higher resolution analyses by CUT&RUN revealed dramatic shifts in sex-linked H3.3 associations from discrete intergenic sites and broader gene-body domains to promoters in response to the loss of ARID1A. Several sex-linked sites displayed ectopic H3.3 occupancy that does not co-localize with DMC1 (DNA Meiotic Recombinase 1). This observation suggests a requirement for ARID1A in DMC1 localization to the asynapsed sex chromatids. We conclude that ARID1A-directed H3.3 localization influences sex chromosome gene regulation and DNA repair during meiosis I.

overall_design: ARID1A and H3.3 genomic localizations in pachytene spermatocytes were determined by CUT&RUN (Cleavage Under Targets and Release Using Nuclease). CUT&RUN assays were performed on cryopreserved Arid1aWT and Arid1acKO pachytene spermatocytes (500,000 cells/genotype) obtained by Sta-Put. For ARID1A, CUT&RUN was performed in triplicates per genotype with two different antibodies. H3.3 CUT&RUN was performed in duplicates on Arid1aWT and triplicates on Arid1acKO samples.

first: Debashish

middle: U

last: Menon

first: Noel

last: Murcia


title: Regionalized cell and gene signatures govern oesophageal epithelial homeostasis.

status: Public on Feb 22 2024

city: Stockholm

last: Hagemann-Jensen

address: Solnavägen 9

department: Department of Cell and Molecular Biology

country: Sweden

institute: Karolinska Institutet

summary: Regionalized disease prevalence is a common feature of the gastrointestinal tract. Herein, we employed regionally resolved Smart-seq3 single-cell sequencing, generating a comprehensive cell atlas of the adult oesophagus. Characterizing the oesophageal axis, we unveil non-uniform distribution of epithelial basal cells, fibroblasts and immune cells. In addition, we reveal a position-dependent, but cell subpopulation-independent, transcriptional signature, collectively generating a regionalized landscape.  Combining in vivo models with organoid co-cultures, we demonstrate that proximal and distal basal progenitor cell states are functionally distinct. We find that proximal fibroblasts are more permissive for organoid growth compared to distal fibroblasts and that the immune cell profile is regionalized in two dimensions, where proximal-distal and epithelial-stromal gradients impact epithelial maintenance. Finally, we predict and verify how WNT-, BMP-, IGF- and NRG-signalling are differentially engaged along the oesophageal axis. We establish a cellular and transcriptional framework for understanding oesophageal regionalization, providing a functional basis for epithelial disease susceptibility.

overall_design: Oeosphageal epithelial and stromal cells were separately isolated based on Fluorescence-activating cell sorting (FACS). In addition, anti-CD45-PE/Cy7 staining was performed to specifically enrich for immune cells. Subsequently, cells were analyzed using scRNA-seq.

first: David

last: Grommisch

first: Maria

last: Genander


title: RNA-seq of DEN induced tumor in liver in SIX1 S225Kfl/fl and Alb-Cre;SIX1 S225Kfl/fl liver specific knockin mice

status: Public on Feb 07 2024

city: Beijing

first: Ling

address: 20th Dong Street, Fengtai District

institute: Beijing Institute of Biotechnology

summary: To investigate the SIX1 S225K-regulated gene compared SIX1 in DEN induced tumor in the liver specific knockin mice

overall_design: To induce liver tumorigenesis, SIX1 S225Kfl/fl group and Alb-Cre;SIX1 S225Kfl/fl group liver specific knockin mice were injected intraperitoneally at 2 weeks of age with 25 mg/kg DEN for 28 weeks.


title: ARID1A governs silencing of sex-linked transcription during male meiosis in the mouse [RNA-seq]

overall_design: RNA-seq was performed to determine the influence of ARID1A on meiotic transcription during pachynema.RNA-seq was performed in quadruplicate on RNA obtained from frozen pellets of Arid1aWT and Arid1acKO pachytene spermatocytes purified by Sta-Put gravity sedimentation.


title: ARID1A governs silencing of sex-linked transcription during male meiosis in the mouse [ATAC-seq]

overall_design: Changes in chromatin accessibility in response to the loss of ARID1A was determined by ATAC-seq. Cryopreserved aliquots of Arid1aWT and Arid1acKO pachytene spermatocytes purified by Sta-Put were processed in quadruplicate (100,000 cells/replicate) for ATAC-seq.


title: Global decay of regulatory chromatin architecture promotes rebalancing of gene expression during colorectal cancer development [RNA-seq II]

status: Public on Feb 11 2024

city: Palo ALto

first: Yizhou

last: Zhu

state: CA

address: 3165 Porter Dr, Rm 2260

institute: Stanford University

summary: Although the 3D genome architecture is essential for long-range gene regulation, the significance of physical chromatin interactions is challenged by recent findings of mutual insensitiveness between contact propensity and gene expression. Here we report hundred basepair-resolution profiling of chromatin conformation in 33 colon tissues tracing the formation and malignant transformation of colorectal polyps. We identified progressive genome-wide decays of chromatin structures such as interaction stripes and loops on all types of cis-regulatory elements, particularly promoters, independent to the alterations of DNA methylation and chromatin accessibility. Instead of linearly correlated with degree of structural decays, transcription levels shifted toward correction of their quantitative mismatching with corresponding promoter contact propensity. These observations suggest increasing sensitivity of transcription to regulatory architecture integrity along with its loss during early cancer development, a mechanism which may provide novel insights to the misregulations of cancer driving genes.

overall_design: mRNA-seq was performed on three colon organoids (1 unaffected mucosa, 2 adenomatous polyps), HT29, HCT116, and primary human colon epithelial cell lines. Differential gene expression analyses were performed for each sample with our without 24 hours of 500 JQ1 treatment. Each sample and condition includes two biological replicates.

last: Snyder


title: Transcriptomic signature of white adipose tissue from wild type and Acod1-deficient mice in response to high fat diet

status: Public on Feb 05 2024

city: Milan

first: Tanja

last: Eberhart

address: Via Olgettina

country: Italy

institute: IRCCS San Raffaele Scientific Institute

summary: Aconitate decarboxylase 1 (ACOD1) is the enzyme synthesizing itaconate, an immuno-regulatory metabolite tuning host-pathogen interactions. Such functions are achieved by affecting metabolic pathways regulating inflammation and microbe survival. However, at the whole-body level, metabolic roles of itaconate remain largely unresolved. By using multiomics-integrated approaches, here we show that ACOD1 responds to high-fat diet consumption in mice by promoting gut microbiota alterations supporting metabolic disease. Genetic disruption of itaconate biosynthesis protects mice against obesity, alterations in glucose homeostasis and liver metabolic dysfunctions by decreasing meta-inflammatory responses to dietary lipid overload. Mechanistically, fecal metagenomics and microbiota transplantation experiments demonstrate such effects are dependent on an amelioration of the intestinal ecosystem composition, skewed by high-fat diet feeding towards obesogenic phenotype. In particular, unbiased fecal microbiota profiling and axenic culture experiments point towards a primary role for itaconate in inhibiting growth of Bacteroidaceae and Bacteroides, family and genus of Bacteroidetes phylum, the major gut microbial taxon associated with metabolic health. Specularly to the effects imposed by Acod1 deficiency on fecal microbiota, oral itaconate consumption enhances diet-induced gut dysbiosis and associated obesogenic responses in mice. Unveiling an unrecognized role of itaconate, either endogenously produced or exogenously administered, in supporting microbiota alterations underlying diet-induced obesity in mice, our study points ACOD1 as a target against inflammatory consequences of overnutrition.

overall_design: Gene expression profiling was performed using data obtained from RNA-seq derived from inguinal (iWAT) and epididymal (eWAT) white adipose tissues from wild type mice receiving normal chow diet and high fat diet (HFD) (60% kalories from fat) and Acod1-/- mice receiving HFD.

first: Simone

last: Cardaci


title: H3K9me3 and H4K29me3 CUT&Tag of therapy-induced senescent and diapause-like cancer cells

status: Public on Feb 01 2024

city: Great Abington

first: Laia

last: Richart Gines

state: Cambridgeshire

address: Granta Park

institute: Altos Labs

summary: Analysis of the H3K9me3 and H4K20me3 differential localization over the genome of cancer cells in three conditions: proliferating cells, doxorubicin-treated cells (senescent) and INK128-treated cells (diapause-like). Two cell lines were used to perform the experiment: human melanoma SK-mel-147 cells and human NSCLC A549 cells.

overall_design:
Senescence was induced by treating SK-Mel-147 and A549 cells with doxorubicin (100nM). The diapause-like state was induced by treating SK-Mel-147 and A549 with INK128 (100 or 200nM). Cells were collected 7 days after the beginning of the treatment and the CUT&Tag protocol was performed.

[UPDATE] Nov-20-2024: Cell line SK-Mel-103 was corrected to SK-Mel-147.

first: Valentina

last: Ramponi

last: Gines

first: Marta

last: Kovatcheva

first: Camille

last: Attolini

first: Alice

last: E Lord

first: Gabriella

last: Ficz

first: Manuel

last: Serrano


title: RNA-seq analysis of Schwann cell knockout of ATP citrate lyase (ACLY)

city: Madison

first: John

last: Svaren

state: WI

address: 1500 Highland Ave.

department: Comparative Biosciences

institute: University of Wisconsin

summary: Formation of myelin by Schwann cells is tightly coupled to nervous system development and is important for neuronal function and long-term maintenance. Perturbation of myelin causes a number of specific disorders that are among the most prevalent diseases affecting the nervous system. Schwann cells synthesize myelin lipids de novo rather than relying on uptake of circulating lipids, and the metabolic sources of myelin formation and maintenance in vivo remain unresolved. One of these questions is how a central metabolite in myelin formation, Acetyl CoA, is generated in myelinating cells. Acetyl CoA-generating pathways are induced at the level of gene expression to support high demands for lipid synthesis and acetylation reactions. However, recent studies have shown that glucose-derived Acetyl CoA itself is not required for myelination, and the requirements of mitochondrially-derived Acetyl CoA has never been tested for myelination in vivo. Several older labeling studies have demonstrated the possibility that cytosolic Acetyl CoA-generating pathways from acetate/ketone bodies satisfy the high demands for lipid synthesis and histone acetylation, and we have employed knockout mice to test the required pathways. Intriguingly, metabolic pathways play different role during the postnatal synthesis of myelin lipids in the postnatal period compared to myelin maintenance postweaning.

overall_design: RNA-seq analysis of sciatic nerve of control and Acly knockout in Schwann cells

first: Schneider

last: Andrew

first: Svaren

last: John


title: A genome wide CRISPR/Cas9 screening to identifiy potential embryonic diapause and diapause-like cancer cell survival genes

city: Barcelona

last: Stephan Otto Attolini

state: Select a State or Province

address: Baldiri Reixac 10

department: Biostatistics and bioinformatics Unit

country: Spain

institute: IRB Barcelona

summary: Diapause-like cancer cells represent a fuel for tumor relapse and strategies that leads to their elimination could be helpful in the context of minimal residual disease and tumor relapse. Here, through a genome-wide CRISPR/Cas9 screen performed in mouse embryonic stem cells undergoing diapause, we identify different genes potentially involved in the survival of diapause-like cancer cells. Further validation experiments in cancer cell lines led to the identification of the pathway NRF2-KEAP1, the 1C metabolism and the DNA methyltransferase DNMT1 as pathways involved in the survival of diapause-like cancer cells.

overall_design: Mouse embryonic stem cells (mESC) were induced to diapause via INK128 treatment (100nM). 5 days after the diapause induction, Cas9 was activated in diapause cells by the addition of doxycycline to the media for 3 days. Doxycyline was also adminstered to proliferating mESC. Screen was conducted in biological triplicate.

last: Stephan-Otto Attolini


title: Pig Taste Cell-Derived Organoids Synthesize Insulin

status: Public on Jan 31 2024

city: Baltimore

first: Supriyo

last: De

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

summary: Previously we showed that taste receptor cells in situ in taste buds synthesize insulin. Here we describe a model of pig taste organoid culture in which we have promoted insulin expression by induction of quiescence. The cellular heterogeneity of the lingual epithelium is maintained in the organoids, and stem cell type and organoid architecture can be controlled through changes in media composition and/or use of static versus dynamic culture. Pig taste organoids were maintained long term and organoids cultured in low sheer stress dynamic exhibited an architecture and expression profile akin to the native tissue. Porcine taste organoids also contained insulin, and the insulin critical transcription factors MAFA and PAX4. These results provide a pig model of taste organoid culture that can be used universally and bring us closer to the use of the taste tissue as a new renewable source of beta cells

overall_design: In order to compare and contrast the gene expression profiles of porcine foliate organoids against the porcine foliate native tissue, total RNA was extracted from porcine foliate native tissue and the complementary organoid culture in Passage 1. This total RNA was then subjjected to RNA-Seq and differential gene expression analysis. Furthermore, to compare and contrast the gene expression profiles of porcine foliate organoids grown in LPM against porcine foliate organoids grown in LPM (day 0 to day 10) and then transfered to CQ (day 10 to day 16/17), total RNA was extracted (using Qiagen RNEasy MiniKit) from comparable organoid cultures grown only LPM, and cultures that were finished off with CQ. This total RNA was then subjected to RNA-Seq and differential gene expression analysis.

first: Hasitha

last: Premathilake

first: Qin

last: Yao

first: Nandita

last: Vegesna

first: Jennifer

last: O'connell

first: Josphine

last: Egan

first: Maire

last: Doyle


title: ASCL1 Drives Tolerance to Osimertinib in EGFR Mutant Lung Cancer in Permissive Cellular Contexts

status: Public on Feb 06 2024

city: New Haven

first: Bomiao

last: Hu

state: CT

address: 310 Cedar Street

institute: Yale University

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

overall_design: Refer to individual Series


title: CRISPR screening identifies synergy between BET and mTOR inhibitors in cholangiocarcinoma through impaired serine glycine one carbon metabolism [RNA-seq]

city: Houston

first: yan

last: zhu

state: TX

address: 1515 Holcombe Blvd.

institute: MD Anderson

summary: Patients with cholangiocarcinoma have poor clinical outcomes due to late diagnoses, poor prognoses, and limited treatment strategies. To identify novel drug combinations for this disease, we have conducted a genome-wide CRISPR screen anchored on the bromodomain and extraterminal domain (BET) PROTAC degrader ARV-825, from which we identified anti-cancer synergy when combined with genetic ablation of members of the mTOR pathway. This combination effect was validated using multiple pharmacological BET and mTOR inhibitors, accompanied by increased levels of apoptosis and cell cycle arrest. In a xenograft model, combined BET degradation and mTOR inhibition induced tumor regression. Mechanistically, the two inhibitor classes converged on H3K27ac-marked epigenetic suppression of the serine glycine one carbon (SGOC) metabolism pathway, including the key regulators PHGDH and PSAT1. Knockdown of PSAT1 was sufficient to replicate synergy with single agent inhibition of either BET or mTOR. Our results tied together epigenetic regulation, metabolism, and apoptosis induction as key therapeutic targets for further exploration in this underserved disease.

overall_design: Compare RNA from each group (vehicle, BETp, mTORi, and BETp + mTORi) of CCA cell lines (SNU1079 and SSP25) with 48h of drug treatment

first: Yan

last: Zhu

first: Jason

last: Roszik

first: Traver

last: Hart

first: Lawrence

last: Kwong


title: CRISPR screening identifies synergy between BET and mTOR inhibitors in cholangiocarcinoma through impaired serine glycine one carbon metabolism [CHIP-seq]

overall_design: Compare H3K27ac from each group (vehicle, BETp, mTORi, and BETp + mTORi) of SNU1079 with 48h of drug treatment


title: Maintenance of hematopoietic stem cells by tyrosine-unphosphorylated STAT5 and JAK inhibition

city: Shanghai

first: Xiaonan

last: Wang

address: 227 Chongqing South Road

department: School of Public Health

institute: Shanghai Jiao Tong University School of Medicine

summary: Adult hematopoietic stem cells (HSCs) are responsible for the lifelong production of blood and immune cells and must respond to extracellular cues including cytokines. The JAK/STAT pathway is a highly conserved pathway, activated by many cytokines, in which tyrosine-phosphorylated STATs (pSTATs) function as transcription factors. STAT5 is a pivotal downstream mediator of several cytokines known to regulate hematopoiesis but its function in the HSC compartment remains poorly understood. Here we show that STAT5-deficient HSCs exhibited an unusual phenotype - reduced multi-lineage repopulation and self-renewal combined with reduced cell cycle entry and increased differentiation. This reflected not only loss of a canonical pSTAT5 transcriptional program but also loss of distinct functions mediated by tyrosine-unphosphorylated STAT5 (uSTAT5). Consistent with this concept expression of an unphosphorylatable STAT5B mutant constrained HSC differentiation, promoted HSC maintenance and upregulated transcriptional programs associated with quiescence and stemness.  Moreover, treatment with a JAK1/2 inhibitor (ruxolitinib) increased the uSTAT5:pSTAT5 ratio, constrained HSC differentiation and proliferation and promoted HSC maintenance, thus phenocopying uSTAT5B overexpression. Our results therefore reveal a previously unrecognized interplay between pSTAT5 and uSTAT5 in the control of HSC function. In addition the demonstration that JAK inhibition promotes HSC maintenance has implications for gene therapy using HSCs and may contribute to the failure of JAK inhibitors to eradicate myeloproliferative neoplasms.

overall_design: To evaluate the long-term functional capacity of uSTAT5B overexpressing HSCs, WT CD45.2 ESLAM HSCs were sorted and transduced with lentivirus containing STAT5B-YF, STAT5B-WT and EV in SCF and IL-11 cultures. Five days after infection, cells were sorted for viability (DAPI-, Thermo Fisher) and green fluorescent protein (GFP) expression and processed according to the manufacturer’s protocol for 10x Chromium (10x Genomics, Pleasanton, CA) experiments .

first: Matthew

middle: J

last: Williams

first: Hugo

last: Bastos

first: Michelle

last: Wantoch

first: Hyun

last: Park

first: Gabriela

last: Grondys-Kotarba

first: Dean

middle: C

last: Pask

first: Tina

middle: L

last: Hamilton

first: Nicola

middle: K

last: Wilson

first: Sarah

last: Kinston

first: Ryan

last: Asby

first: Rachel

last: Sneade

first: George

last: Vassiliou

first: Elisa

last: Laurenti

first: Juan

last: Li

first: Berthold

last: Göttgens

first: Anthony

last: Green


title: Integration of Transcriptomic and Metabolomic Analysis Reveals Possible Molecular Mechanisms of Leaf Growth and Development in Disanthus cercidifolius var. longipes

status: Public on Jan 29 2024

city: Changsha

first: Guolong

last: Wu

state: Hunan

address: South of Shaoshan Road No.498

institute: Central South University Forestry and Technology

summary: Disanthus cercidifolius var. longipes is an important but rare tree species used in plant studies due to its highly ornamental leaves. However, its sciophilous nature and low photosynthetic efficiency make it difficult to cultivate on a large scale. In this study, we collected leaves of D. cercidifolius var. longipes at three developmental stages to assess its photosynthetic capacity and photoprotection mechanisms. Primary metabolites were quantified and separate and joint analyses of the transcriptome and metabolome were carried out. Our results revealed significant changes in the contents of flavonoids, free amino acids, and other substances during development. Metabolome and transcriptome analyses showed that the photosynthesis-related pathways changed rapidly, increasing at first and then decreasing. Under low photosynthetic capacity, flavonoids and anthocyanins were synthesized to achieve photoprotection, with synthesis of these compounds and other pathway-related genes and metabolites showing a significant increase. Total flavonoids also followed this trend. Our findings provide insights into the shade-loving plant's photoprotection mechanisms and nutrient synthesis strategy, which involve quick nutrient production over a short period. This study could aid in developing D. cercidifolius var. longipes into a street or foliage tree through selective breeding.

overall_design: To assess its photosynthetic capacity and photoprotection mechanisms, the leaves of D. cercidifolius var. longipes at three developmental stages were collected, and their primary metabolites were quantified. Separate and joint analyses of the transcriptome and metabolome were carried out.


title: 5-Hydroxymethylcytosine Profiling of Cell-Free DNA Identifies Bivalent Genes That Are Prognostic of Survival in High-Risk Neuroblastoma

city: Chicago

first: Mark

last: Applebaum

state: IL

address: 900 E 57th St

department: Pediatrics, Section of Hematology/Oncology

institute: University of Chicago

summary:
Purpose: Neuroblastoma is the most common extracranial solid tumor in childhood. We previously showed that circulating cell-free DNA (cfDNA) and tumor biopsy derived 5-hydroxymethylcytosime (5-hmC) profiles identified patients with neuroblastoma who experienced subsequent relapse. Here, we hypothesized that 5-hmC modifications selectively enriched in cfDNA compared with tumor biopsy samples would identify epigenetic changes associated with aggressive tumor behavior and identify novel biomarkers of outcome in patients with high- risk neuroblastoma.

Methods: 5-hmC profiles from cfDNA (n = 64) and tumor biopsies (n = 48) were compared. Two neuroblastoma cell lines underwent chromatin immunopre- cipitation followed by sequencing (ChIP-Seq) for H3K27me3, H3K4me3, and H3K27ac; kethoxal-associated single-stranded DNA sequencing; hmC-Seal for 5-hmC; and RNA-sequencing (RNA-Seq). Genes enriched for both H3K27me3 and H3K4me3 in the included cell lines were defined as bivalent. Using bivalent genes defined in vitro, a bivalent signature was established in three publicly available cohorts of patients with neuroblastoma through gene set variation analysis. Differences between tumors with high or low bivalent signatures were assessed by the Kaplan-Meier method and Cox proportional hazards models.

Results: In cfDNA compared with tumor biopsy derived 5-hmC profiles, we found in- creased 5-hmC deposition on Polycomb Repressive Complex 2 target genes, a finding previously described in the context of bivalent genes. We identified 313 genes that bore bivalent chromatin marks, were enriched for mediators of neuronal differentiation, and were transcriptionally repressed across a panel of heterogeneous neuroblastoma cell lines. In three distinct clinical cohorts, low bivalent signature was significantly and independently associated with worse clinical outcome in patients with high-risk neuroblastoma.

Conclusion: Low expression of bivalent genes is a biomarker of worse outcome in patients with high-risk neuroblastoma.

overall_design: This SuperSeries is composed of the SubSeries listed below; refer to individual Series


title: Integrative single-cell multi-omics of CD19-CARpos and CARneg T cells suggest drivers of immunotherapy response in B-ALL

status: Public on Jan 27 2024

first: Mercedes

last: Guerrero Murillo

state: Barcelona

address: Ctra de Can Ruti, Camí de les Escoles, s/n,

institute: Institut de Recerca contra la Leucèmia Josep Carreras

summary: Despite initial high-rates of complete response, <50% of B-cell acute lymphoblastic leukemia (B-ALL) patients treated with CD19-directed chimeric antigen receptor (CAR)-T cells maintain durable remissions. We integrated clonal kinetics and genetic heterogeneity with single-cell-TCR sequencing and single-cell-RNA sequencing, respectively, to explore the cellular dynamics response of both non-transduced (CARneg) and transduced (CARpos) T-cells. CARneg and CARpos T-cells were longitudinally interrogated in the manufactured infusion product (IP) and in peripheral blood at the time of CAR-T cell expansion peak following infusion in five adult B-ALL patients treated with CD19CAR-T products.

overall_design: scRNAseq and scTCRseq data of 5 patients treated with CD19CAR-T products. For each patient there is sequenced data with transducted (CARpos) and non-transducted data (CARneg) from the infusion product and the peak of expansion (in vivo).

last: Guerrero-Murillo

first: Pablo

last: Menendez

first: Clara

last: Bueno


title: One-carbon metabolites control cellular identity [Bulk RNA-seq_myoblast]

status: Public on Jan 24 2024

city: La Jolla

first: LEI

last: SHI

address: 10010 N Torrey Pines  Rd, GEL-B

institute: Salk Institute for Biological Studies

summary: Metabolomic analyses reveal the specific array of metabolites present in a cell type or tissue at any given time. Multiple lines of evidence indicate that metabolites provide a readout of ongoing cellular functions, and changes in the metabolome correlate with specific biological processes1–4 as seen, for instance, during cellular differentiation. These changes are potentially associated with the regulation of signaling pathways and gene expression networks that are critical to alter cellular identity5–7. However, it is less clear whether specific metabolites or metabolic pathways can drive changes in cellular identity. To identify metabolites engaged with cell state transitions, we performed metabolomic analyses at the earliest stages of cellular differentiation and uncovered metabolites transiently upregulated just as the first transcriptional changes emerged. Specifically, we observed a wave of one-carbon metabolism conserved between three different multipotent stem cell types. Treatment of fully differentiated cells with these metabolites caused the loss of mature identity and transition toward progenitor-like states, thus demonstrating that the metabolome plays a causative role in initiating and modulating cell fate. Our studies reveal a metabolic intervention that can reprogram cellular phenotypes and could potentially be applied in regenerative medicine applications

overall_design: bulk RNA sequencing myoblast c2c12 at differentiation time points including 0hour, 3hours, 6hours, 9hours and 12hours.

first: Reyna

last: Hernandez-Benitez

first: Lei

last: Shi

last: Izpisua Belmonte


title: One-carbon metabolites control cellular identity [Bulk RNA-seq]

overall_design: bulk RNA sequencing of four primary  cell lines including neural stem cells(NSCs), Glioblastoma(GB),astrocytes and MIM-treated astrocytes.


title: Transcriptomic analysis of Tdap-IPV whole blood immune responses II

status: Public on Jan 22 2024

city: Nijmegen

first: Dimitri

last: Diavatopoulos

address: Geert Grooteplein Zuid 10

country: Netherlands

institute: Radboud University Medical Center

summary: Control of pertussis depends on primary vaccination of infants in combination with booster vaccination of children, adults, and recently also pregnant women. Tetanus-diptheria-acellular pertussis (Tdap) booster vaccines are frequently given in many countries and can be formulated with inactivated poliovirus (Tdap-IPV). Although Tdap-IPV provides clinical protection, both pertussis antibody levels and clinical protection decay shortly after vaccination. This highlights the need for a better understanding of the mechanisms of immunogenicity of aP-containing combination vaccines, which may explain the longevity of the antibody response to vaccination. In order to identify immune signatures that are induced by Tdap-IPV vaccination and which can be associated with humoral responses, we analyzed changes in gene expression.

overall_design: RNA sequencing analysis was performed on whole blood collected at baseline (Day 0) and one day (Day 1) post-vaccination from children (11-13 years old, n = 13, Oxford cohort) who received a dose of Tdap-IPV.

first: J

last: Gillard

first: D

middle: A

first: M

last: Babiceanu

first: B

last: Schanen

last: Huynen

first: P

middle: B

last: Venkatasubramanian

first: A

last: Kettring


title: Intervention with metabolites emulating endogenous cell transitions accelerates muscle regeneration in young and aged mice

status: Public on Jan 23 2024

summary: Tissue regeneration following an injury requires dynamic cell-state transitions that allow for establishing the cell identities required for the restoration of tissue homeostasis and function. Here, we present a biochemical intervention that induces an intermediate cell state mirroring a transition identified during normal differentiation of myoblasts and other multipotent and pluripotent cells to mature cells. When applied in somatic differentiated cells, the intervention, composed of one-carbon metabolites, reduces some dedifferentiation markers without losing the lineage identity, thus inducing limited reprogramming into a more flexible cell state. Moreover, the intervention enabled accelerated repair after muscle injury in young and aged mice. Overall, our study uncovers a conserved biochemical transitional phase that enhances cellular plasticity in vivo and hints at potential and scalable biochemical interventions of use in regenerative medicine and rejuvenation interventions that may be more tractable than genetic ones.


title: Transcriptomic analysis whole blood single innate immune cells for analysis of of Tdap-IPV immune responses

summary: Control of pertussis depends on primary vaccination of infants in combination with booster vaccination of children, adults, and recently also pregnant women. Tetanus-diptheria-acellular pertussis (Tdap) booster vaccines are frequently given in many countries and can be formulated with inactivated poliovirus (Tdap-IPV). Although Tdap-IPV provides clinical protection, pertussis antibody levels decay shortly after vaccination. This highlights the need for a better understanding of the mechanisms of immunogenicity of aP-containing combination vaccines, which may explain the longevity of the antibody response to vaccination. In order to identify immune signatures that are induced by Tdap-IPV vaccination and which may be associated with humoral responses, we analyzed changes in gene expression.

overall_design: Single cell RNA sequencing analysis was performed on innate immune cells isolated from red blood cell-lysed fresh whole blood collected at baseline (Day 0) and one day (Day 1) post-vaccination from children (11-15 years old, n = 7, Netherlands cohort) who received a dose of Tdap-IPV. CD14+ CD16± monocytes, CD14- CD16+ monocytes, myeloid dendritic cells, plasmacytoid dendritic cells, natural killer cells, and neutrophils were single-cell sorted with flow cytometry into 384-well plates for library preparation and sequencing. Samples were processed in two batches.

last: Brazda

first: H

middle: G

last: Stunnenberg


title: Transcriptomic analysis of Tdap-IPV whole blood immune responses

overall_design: RNA sequencing analysis was performed on whole blood collected at baseline (Day 0) and one day (Day 1) post-vaccination from children (11-15 years old, n = 14) who received a dose of Tdap-IPV. These samples are from the Netherlands cohort.


title: ASCL1 Drives Tolerance to Osimertinib in EGFR Mutant Lung Cancer in Permissive Cellular Contexts [PDX RNA-seq]

first: Bomiao

last: Hu

summary: The majority of EGFR mutant lung adenocarcinomas respond well to EGFR tyrosine kinase inhibitors (TKIs). However, most of these responses are partial with drug tolerant residual disease remaining even at the time of maximal response. This residual disease ultimately leads to relapses which eventually develop in most patients. To investigate the cellular and molecular properties of residual tumor cells in vivo, we leveraged patient-derived models of EGFR mutant lung cancer. Subcutaneous EGFR mutant PDXs were treated with the 3rd generation TKI osimertinib until maximal tumor regression. Residual tissue inevitably harbored tumor cells that were transcriptionally, but not mutationally, distinct from bulk pre-treatment tumor. Using single cell transcriptional profiling we found evidence of cells matching the profiles of drug-tolerant cells present in the pre-treatment tumor. In one of the PDXs analyzed, osimertinib treatment caused dramatic transcriptomic changes that featured upregulation of the neuroendocrine lineage transcription factor ASCL1. Mechanistically, we found that ASCL1 confers drug tolerance by initiating an epithelial-to-mesenchymal gene expression program in permissive cellular contexts. Our study reveals fundamental insights into the biology of drug tolerance, the plasticity of cells through TKI treatment and explains why specific phenotypes are only observed in certain tumors.

overall_design: To profile the gene expression in drug tolerant residual disease, multiple EGFR mutant lung cancer PDXs were treated with osimertinib until drug tolerance emerges and untreated and residual tumor samples were collected for RNA-seq.

first: Fernando

last: de Miguel

first: Zongzhi

last: Liu

first: Mary

last: Melnick

first: Anna

last: Estape

last: Wurtz

first: Andrew

last: Xiao

first: Don

middle: X

last: Nguyen

first: Katerina

last: Politi


title: Impact of Nucleosomal DNA Sequences on SWR Remodeler Activity and Histone H2A.Z Targeting

status: Public on Jan 13 2024

city: Stony Brook

first: Ed

last: Luk

address: 100 Nicolls Rd, Life Sciences Building

department: Biochemistry and Cell Biology

institute: Stony Brook University

summary: The variant histone H2A.Z is deposited into nucleosomes immediately downstream of promoters, where it plays a critical role in transcription. The site-specific deposition of H2A.Z is catalyzed by the SWR complex, a conserved chromatin remodeler with affinity for promoter-proximal nucleosome-depleted regions (NDRs) and histone acetylation. By comparing the genomic distribution of H2A.Z in wild-type and SWR-deficient cells, we found that SWR is also responsible for depositing H2A.Z at thousands of non-canonical sites not directly linked to NDRs or histone acetylation. To understand the targeting mechanism of H2A.Z, we presented SWR to a library of canonical nucleosomes isolated from yeast and analyzed the preferred substrates. Our results revealed that SWR preferentially deposited H2A.Z into a subset of endogenous H2A.Z sites, which are overrepresented by polyadenine tracks on the top strands of the DNA duplex at the nucleosomal entry-exit sites. Insertion of polyadenine sequences into recombinant nucleosomes near the outgoing H2A-H2B dimer enhanced SWR’s affinity for the nucleosomal substrate and increased its H2A.Z insertion activity. These findings suggest that the genome encodes sequence-based information that facilitates remodeler-mediated targeting of H2A.Z.

overall_design: To determine the genomic locations of SWR-dependent H2A.Z nucleosomes, we compared the ChIP-seq profiles of H2A.Z in WT and swc2∆ cells. Experimentally, bulk chromatin was isolated from spheroplasted cells followed by fragmentation into mainly mono-nucleosomes by limited micrococcal nuclease (MNase) digestion. The nucleosomes were subjected to immunoprecipitation with anti-FLAG agarose targeting the 2xFLAG epitope tag on the C-terminus of H2A.Z. The immunoprecipitated DNA fragments were sequenced using the Illumina platform and mapped to the yeast genome (version R64-1-1). This experimental design applies to samples: GSM8008562, GSM8008561, GSM8008560, and GSM8008559. LP001.bw, LP004.bw, LP007.bw, and LP010.bw are the processed input DNA associated with the ChIP-seq samples GSM8008562, GSM8008561, GSM8008560, and GSM8008559, respectively. LP002.bw, LP005.bw, LP008.bw, and LP011.bw are the processed flow-through DNA associated with the ChIP-seq samples GSM8008562, GSM8008561, GSM8008560, and GSM8008559, respectively. LP157.bw, LP159.bw, LP161.bw, and LP163.bw are MNase-seq data for the indicated cell lines.  The experimental design for LP157.bw, LP159.bw, LP161.bw, and LP163.bw are the same as indicated above, except that the nucleosomes were not subjected to immunoprecipitation.

first: Converso

last: Cynthia

first: Pierrakeas

last: Leonidas

first: Luk

last: Ed


title: Single-cell transcriptomes of CD8+ T cells from patients with HR-MDS and AML

status: Public on Jan 12 2024

city: Alexandroupolis

first: Athanasios

last: Tasis

address: University Hospital of Alexandroupolis

country: Greece

institute: Democritus University of Thrace

summary: Treatment with hypomethylating agents (HMA), and specifically azacitidine (AZA), is the standard of care for patients with higher-risk myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML) that are not eligible to receive intensive chemotherapy. Despite research efforts, it is not possible to predict response to treatment with HMA. In this study, we aimed to identify immune cell signatures in the bone marrow (BM) associated with treatment outcomes. By employing mass cytometry, we performed an in-depth immunophenotypic analysis in BM samples deriving from patients with myeloid neoplasms prior to treatment initiation. We identified an increased pre-treatment frequency of a CD8+ T cell subset, characterized as CD57+CXCR3+CCR7-CD45RA+, in patients with MDS and AML who did not respond to treatment with AZA, compared to responders. Furthermore, a baseline frequency of more than 29% of CD57+CXCR3+CD8+ T cells was correlated with poor overall survival. We further engaged scRNA-seq to assess the transcriptional profile of BM CD8+ T cells from treatment-naïve patients with MDS and AML, to identify molecular signatures in CD8+ T subpopulations associated with favorable outcomes. Response to treatment was positively associated with enrichment of IFN-mediated pathways coupled with enhanced cytotoxic signature, whereas enrichment of the TGF-β signaling pathway was observed in cell clusters from non-responders. Together, this study identified a specific CD57+CXCR3+ CD8+ T cell population with predictive value in patients with MDS and AML treated with AZA, and characterized molecular signatures in CD8+ T cells linked to cytokine signaling that were associated with treatment outcomes.

overall_design:
Bone marrow mononuclear cells were stained with antibodies targeting surface antigens, subsequently incubated with Cell Multiplexing Oligos (3' CellPlex Kit Set A, 10x Genomics) and CD8+ T cells were isolated by FACS. Sorted cells from samples were combined by three and subjected to scRNAseq analysis using the Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (Dual Index) (10X Genomics).
Please note that the 'Supplementary_file_scRNAseq_GEO_Tasis_et_al.xlsx' contains further information regarding the patient samples, e.g. age, group, Cell Multiplexing Oligo used etc.

first: Maria

last: Grigoriou

first: Nikos

middle: E

last: Papaioannou

first: Ioannis

last: Mitroulis


title: Early antiviral responses in monocytes and dendritic cells are associated with persistent humoral immunity to pertussis following Tdap-IPV vaccination

status: Public on Jan 21 2024

first: Dimitri

last: Diavatopoulos


title: Transcriptomic analysis of therapy-induced senescent and diapause-like cancer cells

first: Camille

last: Stephan Otto Attolini

summary: RNA-sequencing of proliferating, doxorubicin-induced senescent, palbociclib (CDK4/6i)-induced senescent and INK128-induced diapause-like human melanoma SK-MEL-147 cells and human NSCLC A549

overall_design: Senescence was induced by treating SK-MEL-147 and A549 cells with doxorubicin and palbociclib. The diapause-like state was induced by treating SK-Mel-103 and A549 with INK128. Cells were collected 7 days after the beginning of the treatment and RNA was extracted.

last: Attolini

first: Manuel

last: Serrano

first: Valentina

last: Ramponi

first: Nacho

last: Pons


title: RNA Sequencing Analysis of Human Ovarian Cancer Cell Line OVCAR5 Treated with Stearic Acid, Oleic Acid, and CAY10566

status: Public on Jan 01 2024

city: Kyoto

first: Jumpei

last: Ogura

state: Kyoto

address: 54 Shogoin Kawaharacho, Sakyo-ku

department: Department of Gynecology and Obstetrics

country: Japan

institute: Kyoto University Graduate School of Medicine

summary: This study investigates the anti-proliferative effects of long chain fatty acids on cancer cells, focusing on the specific impacts of oleate and stearate. We explored how these fatty acids, prevalent in biological systems, influence cellular processes. Our analysis revealed that the top 10 significantly upregulated Gene Ontology (GO) categories in OVCAR5 cells treated with 50 µM stearate (compared to control cells) are enriched in pathways related to the unfolded protein response (UPR) and endoplasmic reticulum (ER) stress.

overall_design: Our experimental design involved the treatment of OVCAR5 cells with various compounds for 24 hours. The treatments included: (i) DMSO (control), (ii) 1 µM CAY10566, (iii) 50 µM stearate with DMSO, (iv) 50 µM stearate with 1 µM CAY10566, (v) 50 µM oleate with DMSO, and (vi) 50 µM oleate with 1 µM CAY10566. After treatment, total RNA was extracted from each sample for RNA sequencing.

first: Koji

last: Yamanoi

first: Shiro

last: Takamatsu


title: Transcription Factor Condensates Mediate Clustering of MET Regulon and Enhancement in Gene Expression

status: Public on Jan 08 2024

city: University Park

first: James

last: Lee

state: PA

address: 406 South Frear Building

department: Biochemistry and Molecular Biology

institute: Pennsylvania State University

type: Methylation profiling by high throughput sequencing

overall_design: Refer to individual Series


title: Genomic differences in fibroblasts, iPSC, iMSC and mesenchymal stem cells in mice

status: Public on Dec 31 2023

city: Kunming

first: Weizhou

last: Wang

state: Yunnan

address: Chunrong West Road

institute: Kunming Medical University

summary: Mouse fibroblasts can be reprogrammed into iPSC by Yamanaka factor. iPSC can be derived into iMSC under certain induction conditions. iMSC and MSC have similar cellular properties. However, the genomic differences of these cell types are not clear. RNA-seq sequencing was used to clarify the possible genetic differences.

overall_design: Mouse fibroblasts were reprogrammed into iPSC. iPSC were induced to differentiate into iMSC under certain induction conditions. Mouse fibroblasts, iPSC, iMSC and BMSC were collected and total RNA was extracted. RNA-seq sequencing was used to compare the genetic differences.

first: Wei

first: Yang

first: Fei

last: He

first: Yong

last: Chen

first: Zhi

last: Tang


title: single-nuclear level mRNA and ATAC multiome sequencing of enriched retinal ganglion cells from postnatal day 42 mouse

status: Public on Dec 26 2023

first: Ying

last: Xin

state: MD

address: 400 N Broadway (Smith Building)

institute: Johns Hopkins University

summary: The dataset deposited here provides single-nuclear level transcriptome (RNA-seq) and epigenome (ATAC-seq) of vGlut2-based purified retinal ganglion cells (RGCs), from P42 adult mouse eyes, which can be compared with other datasets conducted on developmental mouse RGCs or aging mouse RGCs

overall_design: Retinas from the vGlut2-Cre;LSL-Sun1GFP mice aged postnatal 42 days were dissociated to expose cell nuclei. GFP+ nuclei of RGCs were enriched with anti-GFP MACS. Final concentration of 4000~5000 nuclei/uL loading onto the 10X Genomics multiome platform.

first: C

last: Qian

first: Y

last: Qi

first: H

first: B

last: Dong

first: D

last: Zack

first: S

last: Blackshaw

last: Hattar

first: FQ

last: Zhou

first: J


title: MiRNA Profiling of Colonic Epithelial Cell Populations by Next Generation Sequencing

city: Kaunas

first: Rūta

last: Inčiūraitė

address: Mickeviciaus st. 9

country: Lithuania

institute: Lithuanian University of Health Sciences

summary: Ulcerative Colitis is an autoimmune inflammatory bowel disease that causes chronic inflammation in the colon and the rectum. Althoung extensively researched, the underlying molecular mechanisms of Ulcerative Colitis remain elusive. Especially, there is a lack of understanding about regulatory non-coding miRNA expression during Ulcerative Colitis in a cell type-specific context. Therefore, we performed high-throughput miRNA profiling of Fluorescence Activated Cell Sorting (FACS)-enriched CD66a+ and CD44+ colonic epithelial cell populations from colon tissue biopsies of 16 patients with active Ulcerative Colitis, 15 patients with quiescent Ulcerative Colitis and 17 Symptomatic Control individuals.

overall_design: MiRNA profiling in Fluorescence Activated Cell Sorting (FACS)-enriched CD66a+ and CD44+ colonic epithelial cell populations of patients with active Ulcerative Colitis, quiescent Ulcerative Colitis and Symptomatic Control individuals

first: Jurgita

last: Skieceviciene

first: Simonas

last: Juzenas

first: Ruta

last: Inciuraite


title: single-nucleus RNA-seq of enriched retinal ganglion cells (RGCs) with RGC-specific overexpression of hOprm1 under optic nerve crush injury condition

summary: Through a comparative analysis of RGC subclasses exhibiting varying levels of resilience to cell death, based on cell-cell interaction analysis, we identified the Mu-opioid receptor, encoded by the Oprm1 gene, as a novel neuroprotective factor for pan-RGCs. Functionally and with the sequencing dataset deposited here, we validated Oprm1 as a neuroprotective factor for RGCs, by demonstrating that overexpression of Oprm1 in RGCs not only led to a markedly increased survival rate of RGCs following several different types of retinal injuries, but also significantly improved visually-guided perception behaviors.

overall_design: Retinas from the vGlut2-Cre;LSL-Sun1GFP mice under 5-day ONC or 5-day ONC with hOprm1 overexpression were dissociated to expose cell nuclei. GFP+ nuclei of RGCs were enriched with anti-GFP MACS. Final concentration of 4000~5000 nuclei/uL loading onto the 10X Genomics Single-Nuclei 3’ HT platform.


title: One-carbon metabolites control cellular identity [scRNA-seq]

first: LEI

last: SHI

overall_design: Single cell RNA sequencing of three primary  cell lines including neural stem cells(NSCs),astrocytes and MIM-treated astrocytes.

first: Reyna

last: Hernandez-Benitez

first: Lei

last: Shi

first: Juan

last: Izpisua Belmonte


title: MiRNA Profiling of Colon Tissue by Next Generation Sequencing

summary: Ulcerative Colitis is an autoimmune inflammatory bowel disease that causes chronic inflammation in the colon and the rectum. Althoung extensively researched, the underlying molecular mechanisms of Ulcerative Colitis remain elusive. Especially, there is a lack of understanding about regulatory non-coding miRNA expression during Ulcerative Colitis. Therefore, we performed high-throughput miRNA profiling of  colon tissue biopsies from XX patients with active Ulcerative Colitis, XX patients with quiescent Ulcerative Colitis and XX Symptomatic Control individuals.

overall_design: MiRNA profiling in colon tissue of patients with active Ulcerative Colitis, quiescent Ulcerative Colitis and Symptomatic Control individuals


title: Epigenetic aging of seminal fluid is associated with inflammation

status: Public on Dec 22 2023

city: Los Angeles

first: Matteo

last: Pellegrini

address: 610 Charles E. Young Drive South

department: Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

summary: Male infertility has been a primary cause of global infertility, affecting 8-12% of couples worldwide. Previous studies have shown that semen quality decreases with advanced aging with an increased presence of inflammatory cells. In this study, we examined the DNA methylation of seminal fluid to understand how the methylome changes with age and infertility. We also compare the age associated changes in semen to those observed in buccal swabs in order to characterize differences in epigenetic aging across diverse tissues. We found that infertility associated changes in the DNA methylation of semen are driven by changes in cell composition, while those associated with aging are linked to inflammatory genes. Many age associated sites are demethylated with advanced aging and are associated with the activation of inflammatory pathways. By contrast, we do not observe age associated changes in inflammatory genes in buccal swab methylomes, which instead are characterized by changes to bivalent promoters. Our study suggests that DNA methylation could serve as a biomarker for male infertility assessment in addition to the standard semen analysis.

overall_design: To examine the changes in DNA methylation of seminal fluids along with age and to compare across tissues, we collected semen and buccal samples from 83 individuals. We then performed targeted bisulfite sequencing on the samples. Finally, we analyzed the DNA methylation data for all individuals.

first: Junxi

last: Feng


title: Genome-wide nucleosome-resolution map of promoter-centered interactions in human cells corroborates the enhancer-promoter looping model

status: Public on Dec 24 2023

city: Moscow

first: Arkadiy

last: Golov

address: Vavilova, 34/5

country: Russia

institute: Institute of Gene Biology, RAS

summary: The enhancer-promoter looping model, in which enhancers activate their target genes via physical contact, has been the dominant hypothesis in the field for decades. However, a systematic testing of this hypothesis has not been conducted, primarily due to the absence of suitable experimental techniques. In this study, we present a new MNase-based proximity ligation method called MChIP-C, allowing for the measurement of protein-mediated chromatin interactions at single-nucleosome resolution on a genome-wide scale. By applying MChIP-C to study H3K4me3 promoter-centered interactions in K562 cells, we found that it had greatly improved resolution and sensitivity compared to restriction endonuclease-based C-methods. This allowed us to identify EP300 histone acetyltransferase and the SWI/SNF remodelling complex as potential candidates for establishing and/or maintaining enhancer-promoter interactions. Finally, leveraging data from published CRISPRi screens, we found that most functionally-verified enhancers do physically interact with their cognate promoters, supporting the enhancer-promoter looping model.

overall_design: Crosslinked K562 cells were subjected to MNase digestion, proximity ligation, chromatin immunoprecipitation with H3K4me3 antibodies (Active motif, 39016) and deep sequencing, the whole procedure was dubbed MChIP-C. MChIP-C was performed in 4 biological replicates. Conventional H3K4me3 (Active motif, 39016) ChIP-seq was performed in one replicate.

first: Alexey

last: Gavrilov

first: Noam

last: Kaplan

first: Sergey

middle: V

last: Razin


title: Epithelial zonation along the mammalian small intestine defines five discrete metabolic domains [Mouse_scRNA-seq II]

status: Public on Dec 21 2023

city: San Francisco

first: Rachel

middle: Klapper

last: Zwick

address: 513 Parnassus Ave.

institute: University of California, San Francisco

summary: Longitudinal zonation of epithelial cells across the mammalian small intestine defines five domains of nutrient absorption.

overall_design: Sorted epithelial cells and intestinal progenitor cells (intestinal stem cells and transit amplifying cells) were collected from 30 equal segments across the full length of 2 murine small intestines, barcoded using MULTIseq technology, pooled, and sequenced.

first: Dario

last: Boffelli

first: Ophir

middle: D

last: Klein


title: Epithelial zonation along the mammalian small intestine defines five discrete metabolic domains [Human_scRNA-seq II]

overall_design: Sorted epithelial cells and intestinal progenitor cells were collected from 30 equal segments across the full length of the human small intestine, barcoded using MULTIseq technology, pooled, and sequenced.


title: Statistical inference with a manifold-constrained RNA velocity model uncovers cell cycle speed modulations

status: Public on Dec 18 2023

city: Lausanne

first: Gioele

last: La Manno

state: Vaud

address: Station 19

department: BMI

country: Switzerland

institute: EPFL

summary: Across a range of biological processes, cells undergo coordinated changes in gene expression, resulting in transcriptome dynamics that unfold within a low-dimensional manifold. Single-cell RNA-sequencing (scRNA-seq) only measures temporal snapshots of gene expression, yet information on the underlying low-dimensional dynamics can be extracted using RNA velocity, which models unspliced and spliced RNA abundances to estimate the rate of change of gene expression. Available RNA velocity algorithms can be fragile and rely on heuristics that lack statistical control. Moreover, the estimated vector field is not dynamically consistent with the traversed gene expression manifold. Here, we develop a generative model of RNA velocity and a Bayesian inference approach that solves these problems. Our model couples velocity field and manifold estimation in a reformulated, unified framework, so as to coherently identify the parameters of an autonomous dynamical system. Focusing on the cell cycle, we implemented VeloCycle to study gene regulation dynamics on one-dimensional periodic manifolds and validated using live-imaging its ability to infer actual cell cycle periods. We benchmarked RNA velocity inference with sensitivity analyses and demonstrated one- and multiple-sample testing. We also conducted Markov chain Monte Carlo inference on the model, uncovering key relationships between gene-specific kinetics and our gene-independent velocity estimate. Finally, we applied VeloCycle to in vivo samples and in vitro genome-wide Perturb-seq, revealing regionally defined proliferation modes in neural progenitors and the effect of gene knockdowns on cell cycle speed. Ultimately, VeloCycle expands the scRNA-seq analysis toolkit with a modular and statistically rigorous RNA velocity inference framework.

overall_design: The raw data files here correspond to the new scRNA-seq datasets generated for this study. These include three scRNA-seq samples for RPE1 cells (two with FUCCI-RPE cells and one with a regular RPE1 cell line). For all other corresponding processed data files and notebooks related to this study, please see the corresponding GitHub and Zenodo pages.

first: Alex

middle: R

last: Lederer

first: Maxine

last: Leonardi

first: Lorenzo

last: Talamanca

first: Antonio

last: Herrera

first: Colas

last: Droin

first: Irina

last: Khven

first: Hugo

last: Carvalho

first: Alessandro

last: Valente

first: Albert

last: Dominguez Mantes

first: Pau

last: Mulet Arabi

first: Luca

last: Pinello

first: Felix

last: Naef


title: Serum Protein Risk Stratification Score for Diagnostic Evaluation of Metabolic Dysfunction-Associated Steatohepatitis (MASH)

city: Boston

first: Simon

middle: T

last: Dillon

state: Massachusetts

address: 99 Brookline Ave, Research North Bldg, Room 107

department: IMBIO

institute: BIDMC RESEARCH

summary: Reliable non-invasive tools to diagnose at risk metabolic dysfunction-associated steatohepatitis (MASH) are urgently needed to improve management. We developed a risk stratification score incorporating proteomics-derived serum markers with clinical variables to identify high risk MASH patients (NAFLD Activity Score (NAS) >4 and fibrosis score >2). In this three-phase proteomic study of biopsy-proven metabolic dysfunction-associated steatotic fatty liver disease (MASLD), we first developed a multi-protein predictor for discriminating NAS>4 based on SOMAscan proteomics quantifying 1,305 serum proteins from 57 US patients. Four key predictor proteins were verified by ELISA in the expanded US cohort (N=168), and enhanced by adding clinical variables to create the 9-feature MASH Dx Score which predicted MASH and also high risk MASH (F2+).  The MASH Dx Score was validated in two independent, external cohorts from Germany (N=139) and Brazil (N=177).  The discovery phase identified a 6-protein classifier that achieved an AUC of 0.93 for identifying MASH. Significant elevation of four proteins (THBS2, GDF15, SELE, IGFBP7) was verified by ELISA in the expanded discovery and independently in the two external cohorts. MASH Dx Score incorporated these proteins with established MASH risk factors (age, BMI, ALT, diabetes, hypertension) to achieve good discrimination between MASH and MASLD without MASH (AUC:0.87- discovery; 0.83- pooled external validation cohorts), with similar performance when evaluating high risk MASH F2-4 (vs. MASH F0-1 and MASLD without MASH).  The MASH Dx Score offers the first reliable non-invasive approach combining novel, biologically plausible ELISA-based fibrosis markers and clinical parameters to detect high risk MASH in patient cohorts from the US, Brasil and Europe.

overall_design: Serum samples (57), five pooled serum controls, and one buffer control were analyzed using the SOMAscan Assay Kit for human serum 1.3k, measuring expression of 1,305 proteins according to the manufacturer’s standard protocol (SomaLogic; Boulder, CO). Data quality control, normalization, and calibration were done according to the manufacturer’s protocol.

first: Towia

last: Libermann


title: Differential gene expression among HEK293T WT, LRPPRC-KO, LRPPRC-KO + WT, and LRPPRC-KO + Leigh Syndrome French Canadian type LRPPRC

first: Mary

last: Couvillion

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

summary: To investigate the role of LRPPRC and mutant LRPPRC on the stability of the mitochondrially encoded mRNA transcripts.

overall_design: Samples include two replicates each of mitochondrial ribosome profiling in LRPPRC KO + LSFC point mutant, along with matched RNA-seq prepared as described in Ingolia et al, 2012. The remaining 8 RNA-seq samples, also two replicates each, were prepared by novogen using their lncRNA library preparation service.

first: Antoni

last: Barrientos

first: Flavia

last: Fontanesi

first: J

last: Moran

first: Stirling

last: Churchman

first: Iliana

last: Soto


title: Break-induced replication underlies formation of inverted triplications and generates unexpected diversity in haplotype structures

city: Houston

first: Christopher

last: Grochowski

state: Texas

address: 1 Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

summary: The duplication-triplication/inverted-duplication (DUP-TRP/INV-DUP) structure is a type of complex genomic rearrangement (CGR). Although it has been identified as an important mutation signature of pathogenicity for genomic disorders and cancer genomes, its architecture remains unresolved. Here we studied the genomic architecture of DUP-TRP/INV-DUP by investigating the DNA of 24 patients identified by array comparative genomic hybridization (aCGH) on whom we found evidence for the existence of 4 out of 4 predicted structural variant (SV) haplotypes. Using a combination of short-read genome sequencing (GS), long-read GS, optical genome mapping and StrandSeq the haplotype structure was resolved in 18 samples. The point of template switching in 4 samples was shown to be a segment of ~2.2-5.5 kb of 100% nucleotide similarity. These data provide experimental evidence supporting the hypothesis that inverted LCRs act as a recombinant substrate. This type of CGR can result in multiple conformers which contributes to generate diverse SV haplotypes in susceptible loci.

overall_design: The goal of this experiment was to determine the precise genomic architecture of patients harboring a duplication-triplication/inverted-duplication complex genomic rearrangement.

middle: M

first: Claudia


title: Identification of Hedgehog signaling responsive genes in A. sagrei and M. musculus via transcriptional profiling

status: Public on Dec 15 2023

city: Athens

first: Douglas

last: Menke

state: Georgia

address: 500 DW Brooks drive

institute: University of Georgia

summary: The brown anole lizard, Anolis sagrei, is an emerging squamate model for developmental and functional genetic studies.  To develop additional tools and resources for mechanistic studies of signaling pathways and cellular processes in A. sagrei, we established an in vitro system.  Using this approach, we studied Hedgehog (Hh) signaling, one of the key developmental signaling pathways, which has evolved across the metazoa.  We investigated Hh pathway-induced transcriptional changes in two evolutionarily distinct tetrapods: A. sagrei, and M. musculus, to identify the species-specific and evolutionarily shared responses. We report that ~45 % of genes induced as a response to Hh pathway activation in A. sagrei, are shared with M. musculus. To further increase the versatility of A. sagrei as a squamate model system for gene editing and genomic studies, we established and characterized a new immortalized A. sagrei embryonic fibroblast cell line ASEC-1. We performed whole-genome sequencing analysis to annotate the set of polymorphisms within this cell line. We conclude that transcriptome characterization of the ASEC-1 cell line would permit further investigations dissecting the complex biological and evolutionary aspects of Hh signaling.

sample_organism:
Mus musculus
Anolis sagrei

platform_organism:
Mus musculus
Anolis sagrei

overall_design: The Hedgehog pathway was activated by treating 48 hr serum-starved cells with optimum concentration of a pharmacological compound, Smoothened agonist (SAG). Total RNA was collected after SAG exposure.  SAG-induced transcriptome from primary embryonic fibroblasts was generated by deep sequencing using 5 biological replicates and from the ASEC-1 cell line by deep sequencing using 4 replicates.

first: Sukhada

middle: P

last: Samudra

first: Sungdae

last: Park

first: Tryggvi

last: McDonald

first: Jonathan

last: Eggenschwiler


title: A novel oncomicropeptide encoded by DSP-AS1 exhibits proneoplastic properties in lung adenocarcinoma by facilitating YTHDF1-induced translation initiation through mediation of mRNA circularization

status: Public on Dec 04 2023

city: Shanghai

first: zhenchuan

last: liu

address: No. 389, Xincun Road

department: Department of Thoracic Surgery

institute: Shanghai Tongji Hospital Affiliated with Tongji University

summary: Functional micropeptides can hide inside RNA previously annotated as non-coding, their roles in the tumorigenesis of lung cancer remain largely unknown. Here, combining Ribo-seq, mass spectrometry and bioinformatics, we characterize a 46 amino-acid length oncogenic micropeptide encoded by lncRNA DSP-AS1, that we named Desmoplakin Associated MicroPeptide (DAMP), in lung adenocarcinoma (LUAD). DAMP is aberrantly overexpressed in LUAD and confers an unfavorable prognosis, its pro-neoplastic properties with respect to augmented proliferation, survival and invasiveness were validated in vitro and in vivo. DAMP colocalizes with translation machinery and induces translational reprogramming both by elevating global protein synthesis and by selectively upregulating the translation of mRNA group encoding oncogenic factors in LUAD. Mechanistically, DAMP simultaneously binds cap-binding subunit eIF4G and YTHDF1, a m6A reader that could fuel translation initiation by recruiting eIF3 to methylated mRNA. The above interactions lead to the formation of a “closed loop” between YTHDF1 and eIF4G bridged by DAMP, which makes YTHDF1 to be spatially in proximity with translation initiation complex and successfully loading of ribosomal 40S subunit onto target mRNAs. Targeting DAMP exhibited significant anti-cancer effects in vitro and in vivo. Our findings not only unravel the oncogenic role of a previously unrecognized micropeptide through orchestrating mRNA translation but also provide a strong rationale in the design of anti-cancer therapy targeting translation machinery in LUAD.

overall_design:
To identify lncRNAs with coding potential, we performed ribo-seq and paired mRNA seq in LUAD cell line H1975.
To further clarify the mRNA regulated by novel peptide DAMP and investigate their translation dynamics, LUAD cell line H1975 with or without DAMP knockout were subjected to ribo-seq. Coupled mRNA-seq was carried out to control for the difference in ribosome-protected fragments due to differences in mRNA abundances resulting from altered RNA transcription.

first: Zhenchuan

last: Liu

first: Tingting

last: Wang

first: Shaorui

last: Gu

first: Yongxin

last: Zhou