title: IL-33 controls IL-22-dependent antibacterial defense by modulating the microbiota.

city: Berlin

first: Bastian

last: Opitz

address: Augustenburgerplatz 1

department: Department of Infectious Diseases, Respiratory Medicine and Critical Care

institute: Charité – Universitätsmedizin Berlin

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

overall_design: Refer to individual Series


title: IL-33 controls IL-22-dependent antibacterial defense by modulating the microbiota [scRNA-seq]

status: Public on Mar 19 2024

country: Germany

type: Expression profiling by high throughput sequencing

summary: IL-22 plays a critical role in defending against mucosal infections, but how IL-22 production is regulated is incompletely understood. Here, we show that mice lacking IL-33 or its receptor ST2 (IL-1RL1) were more resistant to Streptococcus pneumoniae lung infection than wild-type animals, and that single nucleotide polymorphisms in IL33 and IL1RL1 were associated with pneumococcal pneumonia in humans. The effect of IL-33 on S. pneumoniae infection was mediated by negative regulation of IL-22 production by innate lymphoid cells (ILCs), but independent of ILC2s as well as IL-4 and IL-13 signaling. Moreover, IL-33´s influence on antibacterial defense was dependent on housing conditions of the mice, and mediated by the modulatory effect of IL-33 on the intestinal microbiota. Collectively, we reveal that IL-33 controls IL-22-dependent antibacterial defense by modulating the microbiota. Our study thus provides insight into the bidirectional crosstalk between the innate immune system and the microbiota and how it shapes susceptibility to bacterial infection.

overall_design: Infection of mice with S.pn., lung digestion to single cells, sorting for CD90+ CD127+ ILCs with a quarter of the lung and spiked back into whole lung digest. 10x protocol scRNAseq. 60hpi animals abx treatment from 30hpi on.

first: Ivo

last: Röwekamp


title: IL-33 controls IL-22-dependent antibacterial defense by modulating the microbiota [bulk RNA-seq]

summary: IL-22 plays a critical role in defending against mucosal infections, but how IL-22 production is regulated is incompletely understood. Here, we show that mice lacking IL-33 or its receptor ST2 (IL-1RL1) were more resistant to Streptococcus pneumoniae lung infection than wild-type animals, and that single nucleotide polymorphisms in IL33 and IL1RL1 were associated with pneumococcal pneumonia in humans. The effect of IL-33 on S. pneumoniae infection was mediated by negative regulation of IL-22 production by innate lymphoid cells (ILCs), but independent of ILC2s as well as IL-4 and IL-13 signaling. Moreover, IL-33´s influence on antibacterial defense was dependent on the housing conditions of the mice, and mediated by IL-33´s modulatory effect on the intestinal microbiota. Collectively, we reveal that IL-33 controls IL-22-dependent antibacterial defense by modulating the microbiota. Our study thus provides insight into the bidirectional crosstalk between the innate immune system and the microbiota and how it shapes susceptibility to bacterial infection.

overall_design: Infection with S.pneumoniae, single cell digestion of lungs, sort for CD127+ ST2+ CD90+ ILC2s, bulkseq of 7 samples


title: Extreme structural heterogeneity rewires glioblastoma chromosomes to sustain patient-specific transcriptional programs [RNA-Seq]

city: Göttingen

first: Argyris

last: Papantonis

state: Goettingen

address: Robert-Koch-Str. 40

department: Institute of Pathology

institute: University Medical Center Göttingen

summary: Glioblastoma multiforme encompasses a range of brain malignancies marked by phenotypic and transcriptional heterogeneity, which is thought to render these tumors aggressive, resistant to therapy, and inevitably recurrent. However, little is known about how the spatial organization of glioblastoma genomes underlies this heterogeneity and its effects. We compiled a cohort of 28 patient-derived glioblastoma stem-like lines (GSCs) known to reflect the properties of their tumor-of-origin; six of these came from primary-relapse tumor pairs in the same patient. We generated and analyzed kbp-resolution whole-genome chromosome conformation capture (Hi-C) data from all GSCs to systematically map >3,100 structural variants (SVs) and >6,300 neoloops. By combining Hi-C, histone modification, and gene expression data with 3D chromatin folding simulations, we explain how the pervasive, uneven, and idiosyncratic occurrence of neoloops sustains tumor-specific transcriptional programs via the formation of new enhancer-promoter contacts. We also exemplify how neoloops, albeit scarcely recurring, can help us infer potential patient-specific vulnerabilities. Thus, our data serve as a resource for dissecting glioblastoma biology and heterogeneity, as well as for informing therapeutic approaches.

overall_design:
Hi-C and RNA-seq are applied to 28 low passage IDH-wild type GSC samples, including pairs of GSCs from primary and recurrent tumors from 3 patients. Cut&tag for H3K27me3 and CTCF are applied to 10 samples and 5 samples, respectively.
NOTE FROM SUBMITTER: >>The raw data files have not been included due to privacy concerns<<

first: Ting

last: Xie

first: Adi

last: Danieli-Mackay

first: Mariachiara

last: Buccarelli

first: Q

last: Giorgio D’Alessandris

first: Ioanna

last: Papadionysiou

first: Nadine

last: Übelmesser

first: Liverana

last: Lauretti

first: Lucia

last: Ricci-Vitiani


title: ARID1B regulates BCL11B-mediated non-canonical Activin signaling to maintain mesenchymal stem cell homeostasis in the mouse incisor.

status: Public on Mar 20 2024

city: Los Angeles

first: Mingyi

last: Zhang

state: CA

address: 2250 Alcazar Street, CSA103, HSC

department: Center for Craniofacial Molecular Biology

country: USA

institute: University of Southern California

type: Genome binding/occupancy profiling by high throughput sequencing


title: Extreme structural heterogeneity rewires glioblastoma chromosomes to sustain patient-specific transcriptional programs [Hi-C]


title: IL-33 controls IL-22-dependent antibacterial defense by modulating the microbiota [shotgun sequencing]

overall_design:
Shotgun sequencing of 65 stool samples of infected mice from different vivaria
Sample_list.xlsx is necessary for the R script to reproduce the analysis
Please note that raw data is unavailable as fastq files have been deleted.


title: The zebrafish heart harbors a thermogenic beige fat depot analog of human epicardial adipose tissue

first: Suphansa

last: Sawamiphak

address: Robert-Rössle-Str. 10

institute: Max-Delbrück-Centrum für Molekulare Medizin

summary: The main goal of this study was to examine the presence and specific transcriptomic profile of epicardial adipose tissue (eAT) in zebrafish.  We assessed how cold treatment affects the epicardial adipose tissue. Additional we provided some key differences between human, mouse and zebrafish epicardial adipose tissue.

sample_organism:
Danio rerio
Mus musculus

platform_organism:
Danio rerio
Mus musculus

overall_design: We compared the transcriptomes of zebrafish eAT (epicardial adipose tissue) and vAT (visceral adipose tissue) using RNA sequencing (RNA-Seq) from adult female zebrafish. Adult zebrafish  were acclimated from 27°C (control temperature) to 18°C by gradual reduction of tank water at the rate of 1 °C/h with an external water chiller. Cold-acclimated fish were maintained at 18±1°C for 24h, while control fish were maintained at 27±1°C. Hearts were isolated to harvest eAT for RNA sequencing

first: Paul-Andres

last: Morocho-Jaramillo

first: Ilan

last: Kotlar-Goldaper

first: Bhakti-Irene

last: Zakarauskas-Seth

first: Bettina

last: Purfürst

first: Alessandro

last: Filosa


title: Chromosome pairing, stress response, and the interwoven layers of 3D chromatin organization

city: Omaha

first: Jordan

last: Rowley

state: NE

address: 42nd and Emile street

department: Genetics Cell Biology and Anatomy

institute: University of Nebraska Medical Center


title: Transcriptome analysis of Katnal2 knock-out mutant and wild-type mice

city: Daejeon

first: Eunjoon

last: Kim

address: Kuseong-dong

department: Center for Synaptic Brain Dysfunctions/Department of Biological Sciences

country: South Korea

institute: IBS/KAIST

summary: Autism spectrum disorders (ASD) frequently accompany macrocephaly, which could involve hydrocephalic enlargement of brain ventricles. Katnal2 is a microtubule-related protein strongly implicated in ASD. However, it remains unclear whether Katnal2 knockout (KO) in mice leads to microtubule-related cellular deficits and ASD-related phenotypes. We found here that Katnal2-KO mice display social communication deficits, including excessive courtship ultrasonic vocalizations and decreased mating success. Katnal2-KO brains show age-dependent ventricular enlargements and motile ciliary deficits in ependymal cells lining ventricular walls. Katnal2-KO hippocampal neurons, surrounded by lateral ventricles, show limited blood volumes and flow and age-dependent synaptic functional deficits involving synaptic gene downregulation and ASD-like transcriptomic changes. Early postnatal Katnal2 re-expression prevents the ventricular and behavioral phenotypes in Katnal2-KO adults. These results suggest that Katnal2 critically regulates ependymal ciliary function, ventricular volume, CSF circulation, synaptic function, and social communication and that ependymal ciliopathies could underlie ASD-related macrocephaly, ventriculomegaly, and hydrocephalus

overall_design: Whole brain transcriptome analysis of Katnal2 knock-out mutant and wild-type mice age of 3 and 10 weeks

first: Ryeonghwa

last: Kang

first: Kyungdeok

first: Hyojin


title: Hi-C data from Drosophila melanogaster cell line Kc167 in different osmostress conditions.

summary: Chromatin is organized into a 3D interwoven tapestry of multi-layer architectural features important for controlling gene expression. How distinct layers influence each other and quickly they quickly they respond to cellular environment is unclear. Using Hi-C in Drosophila melanogaster, we measure how 3D chromatin organization responds to cellular hyperosmotic stress. In combination with the hd-pairing method, we demonstrate that chromosome unpairing represents a fast an reversible response to hyperosmotic stress. We identify a novel function of the Z4 protein as an anti-pairer, which we demonstrate is necessary for changes to chromatin organization during hyperosmotic stress. Finally, we demonstrate how changes to pairing impacts the other interwoven layers of 3D chromatin organization.

overall_design: Hi-C samples from LacZ Isotonic, LacZ osmostress, LacZ Recovery, Z4KD Isotonic, Z4KD osmostress and Z4KD recovery groups, 2 replicates from each study group. First set of ChIP-seq data is from LacZ Isotonic immunoprecipitated with CAP-H2 antibody, LacZ Osmostress with CAP-H2 and Z4 antibodies, and Z4KD Isotonic with CAP-H2 antibody. Each group has 2 replicates. Second set of ChIP-seq data is from LacZ Osmostress and Z4KD immunoprecipitated with RNAPII antibody. Each group has 2 replicates. ATAC-seq data is from LacZ Isotonic and Z4KD Isotonic groups, each has 2 replicates.

first: Marta

last: Puerto

first: Mamta

last: Shukla

first: Paula

last: Bujosa

first: Juan

last: Perez-Roldan

first: Srividya

last: Tamirisa

first: Francesc

last: Posas

first: Fernando

last: Azorin

first: M

middle: J


title: Threonine Phosphorylation of STAT1 Restricts Interferon Signaling and Promotes Innate Inflammatory Responses

status: Public on Mar 18 2024

city: Kanagawa

first: Kazuki

last: Okuyama

address: 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama

department: IMS

country: Japan

institute: RIKEN Yokohama

summary: Since its discovery over three decades ago, signal transducer and activator of transcription 1 (STAT1) has been extensively studied as a central mediator for interferons (IFNs) signaling and antiviral defense. Here, using genetic and biochemical assays, we unveil Thr748 as a conserved IFN-independent phosphorylation switch in Stat1, which restricts IFN signaling and promotes innate inflammatory responses following the recognition of the bacterial-derived toxin lipopolysaccharide (LPS). Genetically-engineered mice expressing phospho-deficient threonine748–to-alanine (T748A) mutant Stat1 are resistant to LPS–induced lethality. Of note, T748A mice exhibited undisturbed IFN signaling, as well as total expression of Stat1. Further, the T748A point-mutation of Stat1 recapitulates the safeguard effect of the genetic ablation of Stat1 following LPS-induced lethality, indicating that the Thr748 phosphorylation contributes inflammatory functionalities of Stat1. Mechanistically, LPS-induced Toll-like receptor 4 endocytosis activates a cell-intrinsic IκB kinase (IKK)–mediated Thr748 phosphorylation of Stat1, which promotes macrophages inflammatory response while restricting the IFN and anti-inflammatory responses. Depletion of macrophages restores the sensitivity of the T748A mice to LPS-induced lethality. Together, our study indicates a phosphorylation-dependent functional dichotomy of Stat1 in innate immune responses: IFN phospho-tyrosine dependent, and inflammatory phospho-threonine dependent. Better understanding of the Thr748 phosphorylation of Stat1 may uncover novel pharmacologically targetable molecules and offer better treatment modalities for sepsis, a disease that claims millions of lives annually.

overall_design: To investigate the effect of the Thr748 phosphorylation of Stat1 on macrophages function following LPS stimulation, we performed RNA-seq analysis of bone marrow derived macrophages (BMDMs) and peritoneal cavity macrophages (PCMs) from wildtype (Wt) and Stat1T78A mutant littermates. Two biological replicates of 2× 105 of BMDMs or 1× 106 of PCMs with or without LPS treatment were lysed in 0.5 ml of TRIzol Reagent (Thermo Fisher). RNA-seq analysis was performed by Genome Information Research Center (GIRC, Osaka University). In brief, total RNA was extracted and preparation of cDNA libraries was performed using a TruSeq stranded mRNA sample prep kit (Illumina, catalog no. 20020594) according to the manufacturer’s instructions. Sequencing was performed on an Illumina HiSeq 2500 platform in the 75-base single-end mode. Illumina Casava1.8.2 software was used for basecalling. Sequenced reads were mapped to the mouse reference genome sequences (mm10) using TopHat version 2.0.13 in combination with Bowtie2 version 2.2.3 and SAMtools version 0.1.19. The fragments per kilobase of exons per million mapped fragments (FPKM) was calculated using Cuffnorm version 2.2.1. RNA-seq read files were processed and analyzed on Galaxy platform (https://usegalaxy.org/). Qualities of reads were evaluated by fastQC (v0.73), and reads were mapped onto GRCm38/mm10 genome using HISAT2 (v2.2.1) with default setting after the trimming of adaptor sequences. Count files were generated by use of featureCounts (v2.0.3), and differentially expressed genes were investigated using DESeq2 (v2.11.40.7).

first: Tadamitsu

last: Kishimoto

first: Hozaifa

last: Metwally


title: Chromosomal instability can favor macrophage-mediated immune response and induce a broad, vaccination-like anti-tumor IgG response [RNA-Seq]

city: Philadelphia

first: Dennis

last: Discher

state: PA

address: 129 Towne Building

institute: University of Pennsylvania

summary: Chromosomal instability (CIN), a state in which cells undergo mitotic aberrations that generate chromosome copy number variations, generates aneuploidy and is thought to drive cancer evolution. Although associated with poor prognosis and reduced immune response, CIN generates aneuploidy-induced stresses that could be exploited for immunotherapies. Macrophages, particularly, have been understudied in the CIN context. Here, through MPS1 inhibition-induced CIN in poorly immunogenic B16F10 mouse melanoma, we find that CIN- afflicted cancer cells skew macrophages towards an anti-cancer phenotype while also pushing them away from a pro-cancer one. We confirm these findings via RNA-sequencing, protein expression, and short-term tumor studies. These results further translate to in vivo efficacy in suppressing tumor growth: Mice can survive challenges of CIN-afflicted tumors. Long-term survival, however, is dependent on CD47 expression and IgG opsonization. Mice bearing CIN- afflicted tumors with wild-type CD47 levels see prolonged survival compared to their chromosomally stable counterparts, but all succumb. Mice bearing CIN-afflicted CD47 knockout tumors, however, show 28% long-term survival. When CD47 knockout was further paired with IgG opsonization, survival rate increased to 97%. Successful rejection and clearance of CIN- afflicted tumors induced de novo anti-cancer IgG antibodies that were multi-epitope and functionally promoted macrophage-mediated phagocytosis. These de novo IgG antibodies could also suppress in vitro tumoroid and in vivo tumor growth in a CD47 knockout context. These results highlight an unexpected therapeutic benefit from CIN when paired with maximal macrophage anti-cancer activity: an anti-cancer vaccination-like antibody response that can lead to durable cures and further potentiate cell-mediated acquired immunity.

overall_design: Mice were subcutaneously injected with B16F10 cells previously treated with MPS1i (reversine) or DMSO vehicle control. Five or ten days after tumor inoculation, mice were euthanized, and tumors were excised and disaggregated for bulk RNA-sequencing.

first: Steven

middle: H

last: Phan

first: Brandon

last: Hayes

first: Mai

last: Wang

middle: E


title: Chromosomal instability can favor macrophage-mediated immune response and induce a broad, vaccination-like anti-tumor IgG response [scRNA-Seq]

overall_design: One whole volume of conditioned media from B16F10 cells treated with either MPS1i or DMSO was added to BMDMs with fresh media. 24 h after treatment, BMDMs were processed for single-cell RNA-sequencing.


title: An Irf2-expressing oncolytic virus changes the susceptibility of tumor to antitumor T cells and promotes promotes tumor clearance

city: Pittsburgh

first: Saumendra

middle: N

last: Sarkar

state: Pennsylvania

address: UPMC Hillman Cancer Center, 5117 Centre Avenue

department: UPMC Hillman Cancer Center

institute: University of Pittsburgh

summary: According to our previous studies, IRF1-deficient (IRF1-KO) tumor cells showed significantly reduced tumor growth when injected in several syngeneic mouse models including the B16-F10 melanoma, indicating that tumor cells require IRF1 for sustained tumor progression. Depletion of CD8+ T cells or NK cells could restore tumor growth of IRF1-KO cells. In addition, we found that loss of IRF1 in tumor cells could decrease the IFNγ-induced expression of PD-L1. To examine if IRF1 can be a target for cancer immunotherapy, we attempted to comprehensively identify genes that are specifically regulated by IRF1 in tumor cells that contribute to the tumor progression and the suppression of immune surveillance. Our RNA-seq data suggest that IRF1 regulates not only the expression of immune inhibitory ligands, but also the production of class I MHC molecules.

overall_design: B16-F10 WT and IRF1-KO cells were intradermally injected into C57BL/6 mice. Tumors were harvested at day 12 post injection, and subjected to dissocation into single cell suspension. Tumor cells were negatively selected by anti-CD45 and anti-CD31, and positively selected by anti-CD105. The purified tumor cells were subjected to RNA-seq analysis.

first: Lulu

last: Shao


title: ATAC-seq data from Drosophila melanogaster cell line Kc167 in different osmostress conditions

first: Jordan

last: Rowley

overall_design: ATAC-seq data is from LacZ Isotonic and Z4KD Isotonic groups, each has 2 replicates.

first: Marta


title: Effect of estrogen on transcriptomic profile in iWAT of old aged mice

city: Chicago

first: Jooman

last: Park

state: IL

address: 909 S Wolcott Ave COMRB 1120

department: Dept. of Physiology and Biophysics

institute: University of Illinois at Chicago

summary: Beige adipocyes are compromised with aging even upon cold exposure. Besides, estrogen levels, which have metabolic benefit ,are also decreased with aging. However, the relationship between beige adipocyte and estrogen in aging  remains poorly understood. In this study, the potential role of estrogen in iWAT of old aged mice was investigated. To elucidate functional outcomes, we performed RNA-sequencing analysis using vehicle treated group and estrogen treated group upon cold exposure

overall_design: To investigate the role of estrogen function in beige adipocytes in iWAT in old aged mice, we performed gene expression analysis using data obtained from RNA-sequencing. comparative gene expression profiling between vehicle treated group and estrogen treated group.

first: Yuwei

last: Jiang


title: Gene expression of lymphoma tissues from FBW7 KO mice

city: Shanghai

first: Zhaohua

last: Cai

state: Shanghai

address: 241 West Huaihai Road

country: China

institute: Shanghai Chest Hospital: Shanghai Jiao Tong University Affiliated Chest Hospital

summary:
During maturation of hematopoietic stem/progenitor cells (HSPCs) to fully   differentiated mature B lymphocytes, developing lymphocytes may undergo malignant transformation and produce B-cell lymphomas. Emerging evidence shows that through the endothelial-hematopoietic transition, specialized endothelial cells called the hemogenic endothelium can differentiate into HSPCs. However, the contribution of genetic defects in hemogenic endothelial cells to B-cell lymphomagenesis has not yet been investigated.
/

overall_design: Gene expression data was obtained using an Affymetrix GeneChip Mouse   Gene 2.0 ST Array and mRNAs isolated from mesenteric lymph nodes (mLNs) from lymphoma-bearing Fbw7ΔEC mice and normal mLNs from WT mice (n = 3 biological replicates per group).

first: Ming-hui

last: Zou


title: Ordered and disordered regions of the Origin Recognition Complex direct differential in vivo binding at distinct motif sequences.

city: Somerville

first: Michal

last: Chappleboim

state: MA

address: 73A Bartlett

department: Systems Biology

institute: Harvard Medical School

type: Methylation profiling by high throughput sequencing

summary: The Origin Recognition Complex (ORC) seeds replication-fork formation by binding to DNA replication origins, which in budding yeast contain a 17bp DNA motif. High resolution structure of the ORC-DNA complex revealed two base-interacting elements: a disordered basic patch (Orc1-BP4) and an insertion helix (Orc4-IH). To define the ORC elements guiding its DNA binding in vivo, we mapped genomic locations of 38 designed ORC mutants, revealing that different ORC elements guide binding at different sites. At silencing-associated sites lacking the motif, ORC binding and activity were fully explained by a BAH domain. Within replication origins, we reveal two dominating motif variants showing differential binding modes and symmetry: a non-repetitive motif whose binding requires Orc1-BP4 and Orc4-IH, and a repetitive one where another basic patch, Orc1-BP3, can replace Orc4-IH. Disordered basic patches are therefore key for ORC-motif binding in vivo, and we discuss how these conserved, minor-groove interacting elements can guide specific ORC-DNA recognition.

overall_design: Genome-wide binding of the wild-type and over 40 mutations of the Origin Replication Complex in budding yeast.

first: Segev

last: Naveh-Tassa

first: Miri

last: Carmi

first: Yaakov

last: Levy

first: Naama

last: Barkai


title: Species-specific responses during Seoul orthohantavirus infection in human and rat lung microvascular endothelial cells

city: Rotterdam

first: Barry

last: Rockx

address: Wytemaweg 80

department: Viroscience

country: Netherlands

institute: Erasmus MC

summary: Orthohantaviruses are viruses generally carried by rodents in which they do not cause overt disease. Seoul orthohantavirus (SEOV) predominantly exists as a persistent infection in the omnipresent reservoir host, the Norway rat, Rattus norvegicus. Upon respiratory transmission via aerosolized infectious rodent excreta to humans, SEOV causes an acute disease named hemorrhagic fever with renal syndrome (HFRS). Lack of disease in rats is attributed to downregulation of pro-inflammatory and upregulation of regulatory host responses. As lung microvascular endothelial cells (LMECs) represent a primary target of infection in both human and rats, infections in these cells provide a unique opportunity to study the central role of LMECs in the dichotomy between pathogenicity in both species. In this study, host responses to SEOV infection in primary human and rat LMECs were directly compared on a transcriptional level. As infection of rat LMECs was more efficient than human LMECs, most anti-viral defense responses were also observed earlier in rat LMECs. Most prominently SEOV-induced processes in both species included responses to cytokine stimulus, negative regulation of innate immune responses, responses to type I and II interferons, regulation of pattern recognition receptor signaling and MHC-I signaling. However, over time, in the  rat LMECs, responses shifted from an anti-viral towards a more immunotolerant state displayed by a PD-L1, B2M-, JAK2-focused interaction network aiding in negative regulation of cytotoxic CD8-positive T cell activation. This suggests a novel mechanism demonstrating how species-specific orthohantavirus-induced endothelium and T cell cross-talk might be crucial for development of acute disease in humans and persistence in rodents.

sample_organism:
Homo sapiens
Rattus norvegicus

platform_organism:
Homo sapiens
Rattus norvegicus

overall_design: To investigate the host response of both the reservoir rodent host, Rattus norvegicus and human to Seoul orthohantavirus, we infected primary lung microvascular endothelial cells of both species in triplicate and performed bulk RNA-Sequencing at two time points. We then compared differential gene expressions and performed pathway enrichment analyses between virus- and mock-infected samples

first: Danny

last: Noack

first: Mirjam

last: van den Hout - van Vroonhoven

first: Carmen

last: Embregts

first: Wilfred

last: . van IJcken

first: Marion

middle: G

last: .  Koopmans


title: ChIP-seq and data from Drosophila melanogaster cell line Kc167 in different osmostress conditions.

first: Jordan

overall_design: First set of ChIP-seq data is from LacZ Isotonic immunoprecipitated with CAP-H2 antibody, LacZ Osmostress with CAP-H2 and Z4 antibodies, and Z4KD Isotonic with CAP-H2 antibody. Each group has 2 replicates. Second set of ChIP-seq data is from LacZ Osmostress and Z4KD immunoprecipitated with RNAPII antibody. Each group has 2 replicates.

last: Puerto

first: Mamta

last: Shukla

first: Paula

last: Bujosa

first: Juan

last: Perez-Roldan

first: Srividya

last: Tamirisa

first: Francesc

last: Posas

first: Fernando

last: Azorin

first: M


title: Gene expression of wild-type C57BL/6 mouse lungs infected with C2-202 human metapneumovirus (HMPV)

first: John

last: Williams

address: 4401 Penn Avenue

department: Pediatrics

institute: University of Pittsburgh School of Medicine

summary: Human metapneumovirus (HMPV) is a primary causative agent of acute lower respiratory tract infections.  We used single cell RNA-sequencing (scRNA-seq) to assess lung immune profiles in a mouse model of HMPV infection.

overall_design: Mice were either infected with C2-202 HMPV (5E5 total PFU) or mock-infected with cell lysate (resuspended in PBS to total 100-uL volume and delivered intratracheally). Cells were collected from lungs of mice euthanized day 1 post-infection, processed to single cell suspensions, and analyzed using scRNA-seq.

first: Jorna

last: Sojati

first: Kong

last: Chen


title: Targeting PI3Kgamma dependency in leukemia treatment [ATAC-seq]

city: Boston

first: Qingyu

last: Luo

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

summary: Phosphoinositide 3-kinase gamma (PI3Kγ) is implicated as a target to repolarize tumor-associated macrophages and promote anti-tumor immune responses in solid cancers. However, cancer cell-intrinsic roles of PI3Kγ are unclear. Here, by integrating unbiased genome-wide CRISPR interference screening with functional analyses across acute leukemias, we define a selective dependency on the PI3Kγ complex in a high-risk subset that includes myeloid, lymphoid, and dendritic lineages. This dependency is characterized by innate inflammatory signaling and elevation of PIK3R5, which encodes a regulatory subunit of PI3Kγ that we find stabilizes the active enzymatic complex when overexpressed. Mechanistically, we identify PAK1 as a noncanonical substrate of PI3Kγ that mediates this cell-intrinsic dependency independently of AKT. PI3Kγ inhibition dephosphorylates PAK1, activates a transcriptional network of NFκB-related tumor suppressor genes, and impairs mitochondrial oxidative phosphorylation. We find that treatment with the selective PI3Kγ inhibitor eganelisib is effective in leukemias with activated PIK3R5, either at baseline or by exogenous inflammatory stimulation. Notably, the combination of eganelisib and cytarabine prolongs survival over either agent alone, even in patient-derived leukemia xenografts with low baseline PIK3R5 expression, as residual leukemia cells after cytarabine treatment have elevated G protein-coupled purinergic receptor activity and PAK1 phosphorylation. Taken together, our study reveals acute leukemia dependency on a noncanonical PI3Kγ signaling pathway amenable to near-term evaluation in patients using inhibitors already in clinical development.

overall_design: Assay for transposase-accessible chromatin with sequencing (ATAC-seq) in leukemia PDX samples showing high or low PIK3R5 expression.

first: Andrew

middle: A

last: Lane


title: Targeting PI3Kgamma dependency in leukemia treatment [cytarabine persistence]

overall_design: To investigate the differentially expressed genes between cytarabine-persistent leukemia cells and untreated cells.


title: Targeting PI3Kgamma dependency in leukemia treatment

overall_design: Refer to individual Series


title: Targeting PI3Kgamma dependency in leukemia treatment [PI3Kgamma inhibition]

overall_design: To investigate the transcriptome changes after PI3Kgamma inhibition, we either treated CAL-1 cells with the PI3Kgamma inhibitor eganelisib or depleted PIK3R5 by CRISPRi.


title: Extreme structural heterogeneity rewires glioblastoma chromosomes to sustain patient-specific transcriptional programs [CUT&TAG]

first: Argyris

last: Papantonis

overall_design:
Hi-C and RNA-seq are applied to 28 low passage IDH-wild type GSC samples, including pairs of GSCs from primary and recurrent tumors from 3 patients. Cut&tag for H3K27me3 and CTCF are applied to 10 samples and 5 samples, respectively.
>>NOTE FROM SUBMITTER: The raw data files have not been included due to privacy concerns<<

first: Ting

last: Xie

first: Adi

last: Danieli-Mackay

first: Mariachiara

last: Buccarelli

first: Q

last: Giorgio D’Alessandris

first: Ioanna

last: Papadionysiou

first: Nadine

last: Übelmesser

first: Liverana

last: Lauretti

first: Lucia

last: Ricci-Vitiani


title: Herpesvirus remodel organization and function of mitochondria as infection proceeds

city: Kuopio

first: Henri

last: Niskanen

department: A.I. Virtanen Institute

country: Finland

institute: University of Eastern Finland

summary: During the infection, viruses target mitochondria to promote viral replication. Infection-induced stress during the progression of infection leads to the regulation of antiviral defenses and mitochondrial metabolism which are opposed by counteractions of viral factors. The precise structural and functional changes that underlie how mitochondria react to the infection remain largely unclear. Our multimodal integration of advanced imaging, genomics, and metabolomics draws a comprehensive picture of time-dependent changes in mitochondria as HSV-1 infection proceeds from early to late infection.

overall_design: Vero cells were infected with HSV1 and samples for GRO-Seq were collected 4 or 8 hours post infection.

first: Salla

last: Mattola

first: Minna

last: Kaikkonen

first: Elina

last: Mäntylä

first: Maija

last: Vihinen-Ranta


title: Neoantigen-targeted DC vaccine generates durable T cell responses exhibiting the full spectrum of differentiation states in NSCLC patients

city: Ghent

first: Laurenz

last: De Cock

address: Corneel Heymanslaan 10

department: Department of Diagnostic Sciences

country: Belgium

institute: Ghent University

summary: Background. Dendritic cell (DC)-based neoantigen vaccination holds potential as a safe and effective adjuvant therapy for patients with early-stage, resectable NSCLC. DCs have the unique ability to elicit robust antitumoral T-cell responses, while neoantigens are ideal targets to elicit high-affinity T cell responses with excellent tumor specificity. Here, we present the results of a phase I clinical trial in which a novel DC vaccine targeting neoantigens was evaluated in six patients with early stage, resected NSCLC. Methods. Autologous monocyte-derived DCs loaded with neoantigens (Neo-mDCs) were manufactured according to a 4-day protocol. Neo-mDCs were injected intravenously following an intrapatient dose escalation scheme. Primary endpoint of the trial was safety. Secondary endpoints were feasibility, immunogenicity, and relapse-free survival. Results. Vaccine manufacturing was feasible in 6 of 10 patients. Toxicity was limited to grade 1-2 adverse events. Systemic T cell responses were observed in 5 out of 6 vaccinated patients and were dominated by CD8+ T cells, which could be detected ex vivo at high frequencies >1.5 years after the last dose. Furthermore, single cell analysis indicated that the CD8+ T cell responsive population was polyclonal and exhibited the near entire spectrum of T cell differentiation states, including a naïve-like state associated with long lasting memory, but excluding exhausted cell states. Three of six vaccinated patients experienced disease relapse.Conclusion. Neo-mDC vaccination is safe, feasible and induces polyclonal populations of neoantigen-specific T-cell responses containing long lasting memory and effector cells in early-stage NSCLC patients, suggesting clinical potential.

overall_design: We aimed to study the differentiation states and clonal expansion of neoantigen-vaccine responding T cells over the course of vaccination and during oncological follow-up. Therefore, we performed a single cell RNA sequencing experiment on the BD Rhapsody system. First, we isolated all CD8+ T cells from a baseline blood sample from two patients, 08 and 11. This to get an overview of all possible differentiation states of CD8+ T cells. Subsequently, we isolated neoantigen-vaccine responding CD8+ T cells from both patients at serial time points during treatment and 3 weeks and 6 months post-treatment through a pHLA tetramer staining. On these cells we performed single cell RNA and TCR sequencing. In this second sequencing experiment we also included two neoantigen responsive T cell lines, one from each patient, to use as a control for the single cell TCR sequencing.

first: Joline

last: Ingels

first: Niels

last: Vandamme

first: Bart

last: Vandekerckhove


title: Next Generation Sequencing Analysis of human hepatocellular cercinoma cells HLF single cultured and  HLF co-cultured with CD4+ T cells isolated from healthy donors

city: Osaka

first: Hanh

middle: Vinh

last: Ngo

state: Osaka

address: 1-4-3 Asahimachi, Abeno-ku

department: Department of Hepatology

institute: Osaka Metropolitan University

summary: In this study, we investigated the role of CD40 in liver cancer progression. We elucidated the complex interplay between CD40 presenting in cancer cells with their ligand in T cells, and its interaction driven the dowstream signalings of cancer cell proliferation and apoptosis pathways.

overall_design:
To investigate the change of liver cancer cell line - HLF before and after exposed to healthy donors 'CD4+ T cells
We performed gene expression profiling analysis using data obtained from RNA-seq of 2 groups, in which HLF single cultrure served as control group and HLF-T cells co-culture sereved as treatment group

first: Kawada

last: Norifumi

first: Thuy

middle: T

last: Le

middle: V


title: Absence of chromosome axis proteins recruitment prevents meiotic recombination chromosome-wide in the budding yeast Lachancea kluyveri (CC-Seq)

city: Marseille

first: Sylvain

middle: Quentin

last: Legrand

address: 27 Bd Lei Roure

country: France

institute: CNRS

summary: Here we studied the budding yeast Lachancea kluyveri, a cousin of the model Saccharomyces cerevisiae, in order to try to understand the mechanism responsible for the absence of meiotic recombination on its almost entire sex chromosome (Brion et al. 2017). We performed meiotic DSB mapping using CC-seq (Gittens 2019). Briefly, we observed a distribution of meiotic DSBs mainly in gene promoters as in S. cerevisiae and a depletion within Lakl0C-left (the 1 Mb long domain on the sex chromosome with no meiotic recombination). Also, we noted a poor conservation of DSB hotspots strength between L. kluyveri and S. cerevisiae.

overall_design: This data set contains maps of Spo11-linked DNA breaks in the L. kluyveri dsae2 genome generated by CC-seq of meiotic CBS 10367 cells. Cells were treated 6 hours after sporulation induction.

first: Asma

last: Saifudeen

first: Hélène

last: Bordelet

first: Julien

last: Vernerey

first: Arnaud

last: Guille

first: Amaury

last: Bignaut

first: Agnès

last: Thierry

first: Laurent

last: Acquaviva

first: Maxime

last: Gaudin

first: Aurore

last: Sanchez

first: Dominic

last: Johnson

first: Anne

last: Friedrich

first: Joseph

last: Schacherer

first: Matthew

last: Neale

first: Valérie

last: Borde

first: Romain

last: Koszul

first: Bertrand

last: Llorente


title: Inhibition of HDAC activity directly reprograms murine embryonic stem cells to trophoblast stem cells

city: Guangzhou

first: Man

last: Zhang

state: Guangdong

address: No.9, XingDaoHuanBei Road, Guangzhou International Bio-island, Haizhu District

department: Department of Basic Research

institute: Guangzhou Laboratory

summary: Embryonic stem cells (ESCs) can differentiate into all cell types of each of the embryonic germ layers. ESCs can also generate totipotent 2C-like cells and trophectodermal cells. However, these latter transitions occur at low frequency due to epigenetic barriers, the nature of which are not fully understood. Here, we show that mouse ESCs treated with sodium butyrate, an HDAC inhibitor, have a greatly increased 2C-like cell population and can transdifferentiate into trophoblast stem cells (TSCs). Interestingly, this ESC to TSC transition is a direct reprogramming event that does not require transition through a 2C-like state. Mechanistically, butyrate inhibits Class I histone deacetylases activities in LSD1-HDAC1/2 corepressor complex, increasing acetylation levels in the regulatory regions of 2C and TSC specific genes. Importantly, butyrate treated cells acquire the capacity to generate blastocyst-like structures that can develop beyond the implantation stage in vitro and induce decidualization in vivo. These results uncover how epigenetic changes can expand the potency of ESCs.

overall_design: Mouse ESCs (Day -2) were treated with 0.5 mM NaB for 2 days in ESC medium and followed by culturing in TSC medium for 2 days (Day 2).

first: M

first: B

last: Huang

first: X

last: Peng

last: Zhai

first: J

last: Hu


title: Bulk-RNA seq for Macrophages sorted from mouse lungs post influenza infection

first: Gan

last: Zhao

state: PA Pennsylvania

address: 384E Old Vet Quad 3800 spruce street

summary:
To investigate whether SPARCL1 affects lung macrophage polarization in vivo
RNA sequencing (RNA-seq) of isolated lung macrophages (CD45+Ly6G-CD64+F4/80+) on day 20 post-influenza infection was used to further examine the consequences of EC overexpression of Sparcl1.

overall_design: FACS-sorted lung macrophages (CD45+/Ly6G-/CD64+/F4/80+) from ECSparcl1-OE and WT mice on D20 post influenza infection were used for sequencing.

first: Andrew

last: Vaughan


title: A kinetic dichotomy between mitochondrial and nuclear gene expression processes

city: Sherbrooke

first: Karine

last: Choquet

state: Québec

address: 3201 rue Jean-Mignault

department: Biochemistry and Functional Genomics

country: Canada

institute: Université de Sherbrooke

summary: Oxidative phosphorylation (OXPHOS) complexes, encoded by both mitochondrial and nuclear DNA, are essential producers of cellular ATP, but how nuclear and mitochondrial gene expression steps are coordinated to achieve balanced OXPHOS subunit biogenesis remains unresolved. Here, we present a parallel quantitative analysis of the human nuclear and mitochondrial messenger RNA (mt-mRNA) life cycles, including transcript production, processing, ribosome association, and degradation. The kinetic rates of nearly every stage of gene expression differed starkly across compartments. Compared to nuclear mRNAs, mt-mRNAs were produced 1100-fold higher, degraded 7-fold faster, and accumulated to 160-fold higher levels. Quantitative modeling and depletion of mitochondrial factors, LRPPRC and FASTKD5, identified critical points of mitochondrial regulatory control, revealing that the mitonuclear expression disparities intrinsically arise from the highly polycistronic nature of human mitochondrial pre-mRNA. We propose that resolving these differences requires a 100-fold slower mitochondrial translation rate, illuminating the mitoribosome as a nexus of mitonuclear co-regulation.

overall_design: Direct RNA nanopore sequencing for analysis of mitochondrial transcriptome

first: Erik

last: McShane

first: Mary

last: Couvillion

first: Robert

last: Ietswaart

first: Gyan

last: Prakash

first: Brendan

middle: M

last: Smalec

first: Iliana

last: Soto

first: Autum

middle: R

last: Baxter-Koenigs

first: L

middle: S

last: Churchman


title: Extreme structural heterogeneity rewires glioblastoma chromosomes to sustain patient-specific transcriptional programs

city: Göttingen

first: Argyris

last: Papantonis

address: Robert-Koch-Str. 40

institute: University Medical Center Göttingen

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

first: Ting

last: Xie


title: Pyrrole-based inhibitors of RND-type efflux pumps reverse antibiotic resistance and display antivirulence potential

city: Chandigarh

first: Nisha

last: Mahey

state: Chandigarh

address: Sector 39A

department: BERPDC

country: India

institute: CSIR-Institute of Microbial Technology

summary: Efflux pumps of the resistance-nodulation-division (RND) superfamily, particularly the AcrAB-TolC and MexAB-OprM, besides mediating intrinsic and acquired resistance, also intervene in bacterial pathogenicity. Inhibitors of such pumps could restore activities of antibiotics and curb bacterial virulence. Here, we identify pyrrole-based compounds that boost antibiotic activity in Escherichia coli and Pseudomonas aeruginosa by inhibiting their archetype RND transporters. The discovered efflux pump inhibitors (EPIs) inhibit the efflux of fluorescent probes, attenuate persister formation, and diminish resistant mutant development. Molecular docking and biophysical studies revealed that the EPIs bind to AcrB. EPIs also possess an anti-pathogenic potential and attenuate P. aeruginosa virulence in vivo. The excellent efficacy of the EPI-antibiotic combination was evidenced in animal lung infection and sepsis protection models. These findings indicate that EPIs discovered herein with no off-target effects and negligible toxicity are potential antibiotic adjuvants to address life-threatening bacterial infections.

overall_design: Comparative analysis of the the transcriptional profile of P. aeruginosa PAO1 in the presence and absence of sub-inhibitory concentration of Ar5 and PAβN

first: Rushikesh

last: Tambat

first: Ritu

last: Kalia

first: Rajnita

last: Ingavale

first: Nishtha

last: Chandal

first: Srajan

last: Kapoor

first: Dipesh

middle: K

last: Verma

first: Krishan

last: Thakur

first: Sanjay

last: Jachak

first: Hemraj

last: Nandanwar

first: Akriti

last: Kodesia


title: Transcriptional reprogramming by SPI1 (PU.1) modulates Alzheimer’s disease phenotypes in mouse models

city: Indianapolis

first: Luke

middle: Child

last: Dabin

state: Indiana

department: Medical and Molecular Genetics

institute: Indiana University

summary: SPI1 (PU.1) was recently reported as a genetic risk factor of Alzheimer’s disease (AD) in large-scale genome-wide association studies (GWAS). However, it is unknown whether PU.1 should be downregulated or increased to have therapeutic benefits. This is a critical question that must be answered before initiating any drug discovery project. To investigate the effect of modulating PU.1 level on AD pathology, we performed biochemical, histological, transcriptomic, and proteomic analyses using PU.1-knockdown and overexpression mouse models. PU.1-knockdown markedly increased amyloid-b (Ab) levels, amyloid plaque deposition, and gliosis. Conversely, PU.1-overexpression significantly decreased Ab levels, amyloid plaque deposition, gliosis, and dystrophic neurites. Furthermore, we identified several biological pathways, such as immune response pathways and complement system, regulated by the altered PU.1 expression through the analyses of proteomics as well as bulk and single-cell transcriptomics data. Our data provide crucial in vivo data to guide future therapeutic strategies for AD.

overall_design: Data contains single-cell RNA-sequencing data from two female 5XFAD;PU.1 wildtype and two female 5XFAD;PU.1 transgenic mice

first: Byungwook

last: Kim

middle: C

first: Mason

middle: D

last: Tate

first: Hande

last: Karahan

first: Ahmad

last: Sharify

first: Huan

last: Sun

first: Md

last: Al-Amin

first: Stéphanie

last: Philtjens

first: Daniel

last: Smith

first: Dom

last: Acri

first: Younghye

last: Moon

first: Mathias

last: Jucker

first: Junmin

last: Peng

first: Jungsu


title: Sex-Specific Developmental Gene Expression Atlas Unveils Dimorphic Gene Networks in C. elegans

status: Public on Mar 17 2024

city: Rehovot

first: Rizwanul

last: Haque

state: Israel

address: Herzl St 234, Rehovot

department: Brain Sciences

country: Israel

institute: Weizmann Institute of Science

summary: Sex-specific traits and behaviors are facilitated by the acquisition of unique properties in the nervous system of each sex during development and continues in adulthood. However, the genetic events responsible for introducing these sex-specific features remain poorly understood. In this study, we created a comprehensive gene expression atlas for both sexes of the nematode Caenorhabditis elegans across development. By comparing the transcriptome of pure populations of hermaphrodites and males from early larval stages to adulthood, we discovered numerous differentially expressed genes, including neuronal gene families like transcription factors, neuropeptides, and GPCRs. We identified INS-39, an insulin-like peptide, as a prominent male-biased gene expressed specifically in ciliated sensory neurons. We show that INS-39 serves as an early-stage male marker, facilitating the effective isolation of males in high-throughput experiments. Analysis of ins-39 knock out animals revealed pleiotropic sex-specific roles in temperature sensation, survival in cold temperatures, resilience against high hydrogen peroxide levels, and dauer entry, while also playing a shared, dimorphic role in early life stress. This study offers a comparative sexual and developmental gene expression database for C. elegans, which will facilitate research into the genetic regulation of the sexual development of other organisms. Furthermore, it highlights conserved candidate genes that may underlie the sexually-dimorphic manifestation of different human diseases

overall_design:
Whole animal RNA-seq profiles from five developmental stages (L1, L2, L3, L4 and YA) from nematode N2 wild-type and dpy-28(y1);him-8(e1489) strain of Caenorhabditis elegans grown at 25oC. N2 wild-type strain of Caenorhabditis elegans were all hermaphrodite while dpy-28(y1);him-8(e1489) strain of Caenorhabditis elegans were >98% males. (each group has four biological repeats). Totaling 40 samples (10 groups with four biological repeats).
To compare the transcriptome of pure populations of hermaphrodites and males from early larval stages to adulthood (L1, L2, L3, L4 and YA) in both sexes (hermaphrodites and males) of nematode Caenorhabditis elegans.

first: Sonu-Peedikayil

last: Kurien

first: Hagar

last: Setty

first: Yehuda

last: Salzberg

first: Gil

last: Stelzer

first: Einav

last: Litvak

first: Hila

last: Gingold

first: Oded

last: Rechavi

first: Meital

last: Oren-Suissa


title: Absence of chromosome axis proteins recruitment prevents meiotic recombination chromosome-wide in the budding yeast Lachancea kluyveri (Hi-C)

city: PARIS

first: Helene

last: Bordelet

address: 25-28 Rue du Dr Roux

institute: Institut Pasteur

overall_design: Hi-C experiments were performed using the CBS 10367 isolate. Equal samples were harvested from the four flasks at 0, 2, 3, 4, 5, 6, 7 and 8 hours post meiosis induction.

first: Sylvain

last: Legrand

first: Asma

last: Saifudeen

first: Hélène

first: Julien

last: Vernerey

first: Arnaud

last: Guille

first: Amaury

last: Bignaut

first: Agnès

last: Thierry

first: Laurent

last: Acquaviva

first: Maxime

last: Gaudin

first: Aurore

last: Sanchez

first: Dominic

last: Johnson

first: Anne

last: Friedrich

first: Joseph

last: Schacherer

first: Matthew

last: Neale

first: Valérie

last: Borde

first: Romain

last: Koszul

first: Bertrand

last: Llorente


title: Macrophages suppress cardiac reprogramming of  fibroblasts in vivo via IFN-mediated intercellular self-stimulating circuit

status: Public on Mar 15 2024

city: beijing,China

first: Hao

last: Wang

address: No. 5, Yiheyuan Road, Haidian District, Beijing

institute: Peking University


title: The catabolism of ethylene glycol by Rhodococcus jostii RHA1 and its dependence on mycofactocin

city: Vancouver

first: Raphael

last: Roccor

email: r.roccor@gmail.com, leltis@mail.ubc.ca

state: BC

address: 2350 Health Sciences Mall

department: Microbiology & Immunology

institute: The University of British Columbia

summary: Ethylene glycol (EG) is a widely used industrial chemical with manifold applications and is also generated in the degradation of plastics such as PET. Rhodococcus jostii RHA1 (RHA1), a potential biocatalytic chassis, grows on EG. Transcriptomic analyses revealed four clusters of genes potentially involved in EG catabolism: the mad locus, predicted to encode mycofactocin-dependent alcohol degradation, including the catabolism of EG to glycolate; two GCL clusters, predicted to encode glycolate and glyoxylate catabolism; and the mft genes, predicted to specify mycofactocin biosynthesis. Bioinformatic analyses further revealed that the mad and mft genes are widely distributed in mycolic acid-producing bacteria such as RHA1. Neither ΔmadA nor ΔmftC RHA1 mutant strains grew on EG but grew on acetate. In resting cell assays, the ΔmadA mutant depleted glycolaldehyde but not EG from culture media. These results indicate that madA encodes a mycofactocin-dependent alcohol dehydrogenase that initiates EG catabolism. In contrast to some mycobacterial strains, the mad genes did not appear to enable RHA1 to grow on methanol as sole substrate. Finally, a strain of RHA1 adapted to grow ~3× faster on EG contained an overexpressed gene, aldA2, predicted to encode an aldehyde dehydrogenase. When incubated with EG, this strain accumulated lower concentrations of glycolaldehyde than RHA1. Moreover, ecotopically expressed aldA2 increased RHA1’s tolerance for EG further suggesting that glycolaldehyde accumulation limits growth of RHA1 on EG. Overall, this study provides insights into the bacterial catabolism of small alcohols and aldehydes and facilitates the engineering of Rhodococcus for the upgrading of plastic waste streams.

overall_design: RHA1 was grown on 30 mM acetate, EG, or glycolate in M9 Goodies medium to mid-log phase. An adapted strain of RHA1, RHA1-EG derived by adaptive laboratory evolution of sequential growth on increasing EG concentrations from 30 mM to 180 mM EG, was grown on 30 mM EG.

first: Jie

last: Liu

first: Lindsay

last: Eltis


title: Macrophages suppress cardiac reprogramming of  fibroblasts in vivo via IFN-mediated intercellular self-stimulating circuit (CUT&Tag)

summary: Direct conversion of cardiac fibroblasts (CFs) to cardiomyocytes (CMs) in vivo to regenerate heart tissue is an attractive approach. After myocardial infarction (MI), heart repair proceeds with an inflammation stage initiated by monocytes infiltration of the infarct zone establishing an immune microenvironment. However, whether and how the MI microenvironment influences the reprogramming of CFs remains unclear. Here, we found that in comparison with cardiac fibroblasts (CFs) cultured in vitro, CFs that transplanted into infarct region of MI mouse models resisted to cardiac reprogramming. RNA-seq analysis revealed upregulation of interferon (IFN) response genes in transplanted CFs, and subsequent inhibition of the IFN receptors increased reprogramming efficiency in vivo. Macrophage-secreted IFN-β was identified as the dominant upstream signaling factor after MI. CFs treated with macrophage-conditioned medium containing IFN-β displayed reduced reprogramming efficiency, while macrophage depletion or blocking the IFN signaling pathway after MI increased reprogramming efficiency in vivo. Co-IP, BiFC and Cut-tag assays showed that phosphorylated STAT1 downstream of IFN signaling in CFs could interact with the reprogramming factor GATA4 and inhibit the GATA4 chromatin occupancy in cardiac genes. Furthermore, upregulation of IFN-IFNAR-pSTAT1 signaling could stimulate CFs secretion of CCL2/7/12 chemokines, subsequently recruiting IFN-β-secreting macrophages. Together, these immune cells further activate STAT1 phosphorylation, enhancing CCL2/7/12 secretion and immune cell recruitment, ultimately forming a self-reinforcing positive feedback loop between CFs and macrophages via IFN-IFNAR-pSTAT1 that inhibits cardiac reprogramming in vivo. Cumulatively, our findings uncover an intercellular self-stimulating inflammatory circuit as a microenvironmental molecular barrier of in situ cardiac reprogramming that needs to be overcome for regenerative medicine applications.

overall_design: To  validate the hypothesis by which p-STAT1 interacts with GATA4, hindering the GATA4 capacity in binding and transcription in myocardial-related genes, we performed the chromatin occupancy profiling of GATA4 in MICFs using CUT&Tag (cleavage under targets and tagmentation) followed by next-generation sequencing in 1 week after treatment with MG(HA)T+DMSO+shNT (referred to as “Control”), MG(HA)T+ p-STAT1-inhibitors+shNT (referred to as “STAT-i”), or MG(HA)T+DMSO+shIfnar2 (referred to as “shIfnar2”).

first: Junbo

last: Yang

first: Yihong

last: Cai

first: Yang

last: Zhao


title: Macrophages suppress cardiac reprogramming of  fibroblasts in vivo via IFN-mediated intercellular self-stimulating circuit (RNA-Seq)

overall_design: In order to investigate the in vivo suppressors of CFs reprogramming, we established a transplantation system that enables comparison of the same cells expressing a combination of reprogramming factors between in vivo and in vitro conditions, to preclude potential differences in gene delivery efficiency. Briefly, we digested in vitro cultured MICFs (cardiac fibroblasts isolated from adult mice with myocardial infarction) infected with lentiviruses tetracycline-inducible expressing MGT (polycistronic construct including Mef2c, Gata4 and Tbx5), Myo+S (separates virus driving expression of Myocd and Sall4) (Zhao et al., 2021), and eGFP, respectively, and transplanted them into hearts of mice with surgically induced MI (MI hearts hereafter). A portion of these infected MICFs were retained for concurrent in vitro culture with the addition of doxycycline (Dox). On days 7 and days 14 after transplantation and Dox administration, we used FACS to isolate eGFP+ transplanted MICFs from the hearts of MI mice and compare them with FACS-isolated eGFP+ MICFs with sustained in vitro culture


title: Cold stress induces rapid gene-specific changes in the levels of H3K4me3 and H3K27me3 in Arabidopsis thaliana

city: Berlin

first: Lea

middle: Andree Charlotte

last: Faivre

state: Berlin

address: Königin Luise Str. 12-16

department: Biologie, Chemistry, Pharmacy

institute: Freie Universitaet Berlin

summary: When exposed to low temperatures, plants undergo a drastic reprogramming of their transcriptome in order to adapt to their new environmental conditions, which primes them for potential freezing temperatures. While the involvement of transcription factors in this process, termed cold acclimation, has been deeply investigated, the potential contribution of chromatin regulation remains unelucidated. A large proportion of cold-inducible genes carries the repressive mark histone 3 lysine 27 trimethylation (H3K27me3), which has been hypothesized as maintaining them in a silenced state in the absence of stress, but which would need to be removed or counteracted upon stress perception. However, the fate of H3K27me3 during cold exposure was so far only explored in a locus specific manner. In this study, we offer an epigenome profiling of H3K27me3 and its antagonist active mark histone 3 lysine 4 trimethylation (H3K4me3) during short-term cold exposure. Both chromatin marks undergo rapid redistribution upon cold exposure, however, the gene sets undergoing H3K4me3 or H3K27me3 differential methylation are distinct, refuting the simplistic idea that gene activation relies on a switch from an H3K27me3 repressed chromatin to an active form enriched in H3K4me3. Coupling the ChIP-seq experiments with transcriptome profiling reveals that differential histone methylation correlates with changes in expression. Interestingly, only a subset of cold-regulated genes lose H3K27me3 during their induction, indicating that H3K27me3 is not an obstacle to transcriptional activation. In the H3K27me3 methyltransferase curly leaf (clf) mutant, many cold regulated genes display reduced H3K27me3 levels but their transcriptional activity is not altered prior or during a cold exposure, suggesting that H3K27me3 may serve a more intricate role in the cold response than simply repressing the cold-inducible genes in naïve conditions.

overall_design: Arabidopsis thaliana plants were grown for 21 days in short days before being placed at 4°C for 3h or 3 days.  RNAseq was performed on three biological replicates for each condition.

first: Léa

first: Nathalie-Francesca

last: Kinscher

first: Ana

middle: B

last: Kuhlmann

first: Xiaocai

last: Xu

first: Jose

last: Muino

first: Kerstin

last: Kaufmann

first: Daniel

last: Schubert


title: Senescence defines a distinct subset of myofibroblasts that orchestrates immunosuppression in pancreatic cancer

city: St. Louis

first: David

last: DeNardo

email: johnbaer@wustl.edu, ddenardo@wustl.edu

state: Missouri

address: 660 S Euclid Ave.

department: Internal Medicine

institute: Washington University in St. Louis

summary: Therapeutic resistance in PDAC is largely attributed to a unique tumor microenvironment embedded with an abundance of cancer associated fibroblasts (CAFs). Distinct CAF populations were recently identified, but the phenotypic drivers and specific impact of CAF heterogeneity remain unclear. In this study, we identify a subpopulation of senescent myofibroblastic CAFs (SenCAFs) in mouse and human PDAC. These SenCAFs are a subset of myofibroblastic CAFs that localize near tumors ducts, have distinct phenotypes and accumulate with PDAC progression. To assess the impact of endogenous SenCAFs in PDAC, we employed a LSL-KRASG12D;p53flox;p48-CRE;INK-ATTAC (KPPC-IA) mouse model of spontaneous PDAC with inducible senescent cell depletion. Senescence depletion with the KPPC-IA model or with the senolytic drug ABT263/Navitoclax, delayed tumor progression, reduced fibrosis, and relieved immune suppression in macrophages and T lymphocytes. Collectively, our findings demonstrate that SenCAFs promote PDAC progression and immune cell dysfunction.

overall_design: Examination of the tumor microenvironment with depletion of senescent fibroblasts in PDAC

first: Jad

last: Belle

first: John

last: Baer


title: Reduced cardiac antioxidant defenses mediate increased susceptibility to workload-induced myocardial injury in males with genetic cardiomyopathy.

city: Minneapolis

first: DeWayne

last: Townsend

state: Minnesota

address: 2231 6th Street SE

department: Integrative Biology and Physiology

institute: University of Minnesota

summary: Ongoing cardiomyocyte injury is a major mechanism in the progression of heart failure, particularly in dystrophic hearts. Due to the poor regenerative capacity of the adult heart, cardiomyocyte death results in the permanent loss of functional myocardium. Understanding the factors contributing to myocyte injury is essential for the development of effective heart failure therapies. As a model of persistent cardiac injury, we examined mice lacking β-sarcoglycan (β-SG), a key component of the dystrophin glycoprotein complex (DGC). The loss of the sarcoglycan complex markedly compromises sarcolemmal integrity in this β-SG-/- model. Our studies aim to characterize the mechanisms underlying dramatic sex differences in susceptibility to cardiac injury in β-SG-/- mice. Male β-SG-/- hearts display significantly greater myocardial injury and death following isoproterenol-induced cardiac stress than female β-SG-/- hearts. This protection of females was independent of ovarian hormones. Male β-SG-/- hearts displayed increased susceptibility to exogenous oxidative stress and were significantly protected by angiotensin II type 1 receptor (AT1R) antagonism. Increasing general antioxidative defenses or increasing the levels of S-nitrosylation both provided protection to the hearts of β-SG-/- male mice. Here we demonstrate that increased susceptibility to oxidative damage leads to an AT1R-mediated amplification of workload-induced myocardial injury in male β-SG-/- mice. Improving oxidative defenses, specifically by increasing S-nitrosylation, provided protection to the male β-SG-/- heart from workload-induced injury. These studies describe a unique susceptibility of the male heart to injury and may contribute to the sex differences in other forms of cardiac injury.

overall_design: 3-4 biological replicates were analyzed for each of 4 conditions (2 genotypes; two sexes per genotype)

first: Katharine

last: Sharpe

first: Kaleb

last: Fischer


title: Cold stress induces rapid gene-specific changes in the levels of H3K4me3 and H3K27me3 in Arabidopsis thaliana [ChIP-Seq]

overall_design: Arabidopsis thaliana plants were grown for 21 days in short days before being placed at 4°C for 3h or 3 days. In order to follow the histone methylation dynamic upon cold stress, chromatin extraction was performed for H3K4me3 and H3K27me3, for two biological replicates.


overall_design: Refer to individual Series


title: T cell dysfunction in ARDS based on miRNA and mRNA integration analysis (RNA-Seq)

city: Suita

first: Daisuke

last: Motooka

address: 3-1, Yamadaoka

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

summary: Acute respiratory distress syndrome (ARDS) is a respiratory failure in critically ill patients, and the molecular mechanisms underlying its pathogenesis and severity are poorly understood. We evaluated mRNA and miRNA in patients with ARDS and elucidated the pathogenesis of ARDS, following mRNA and miRNA integration analysis. Thirty-four ARDS patients were compared with 15 healthy donors. 1233 mRNAs and 6 miRNAs were upregulated and 1580 mRNAs and 13 miRNAs were downregulated in ARDS patients compared healthy donors. In both mRNA and miRNA-targeted mRNA, the canonical pathway analysis showed that PD-1 and PD-L1 cancer immunotherapy pathway was most activated and Th2 pathway was most suppressed. miR-149-3p and several miRNAs were identified as upstream regulators. Integrated analysis of mRNAs and miRNAs showed that T cells were dysfunctional in ARDS patients.

overall_design: The peripheral blood of the patient with ARDS was collected within 24 hours of admission. Sequencing of mRNA and miRNA was performed using whole blood from ARDS patients and healthy donors.

first: Yumi

last: Mitsyama

first: Hisatake

last: Matsumoto

last: Okuzaki


title: T cell dysfunction in ARDS based on miRNA and mRNA integration analysis

type: Non-coding RNA profiling by high throughput sequencing


title: T cell dysfunction in ARDS based on miRNA and mRNA integration analysis (miRNA-Seq)


title: Unleashing natural IL-18 activity using an anti-IL-18BP blocker antibody induces potent immune stimulation and anti-tumor effects

city: Holon

first: Roy

last: Granit

address: 26 Harokmim St. Bldg D

institute: Compugen LTD

summary: Recombinant cytokines have limited anti-cancer efficacy mostly due to narrow therapeutic window and systemic adverse effects. IL-18 is an inflammasome induced proinflammatory cytokine that enhances T and NK cell activity and stimulates IFNg production. The activity of IL-18 is naturally blocked by a high affinity endogenous binding protein (IL-18BP). IL-18BP is induced in the tumor microenvironment (TME) in response to IFNg upregulation in a negative feedback mechanism. In this study we found that IL-18 is upregulated in the TME compared to the periphery across multiple human tumors and most of it is bound to IL-18BP. Bound IL-18 levels were largely above the amount required for T cell activation in vitro, implying that releasing IL-18 in the TME could lead to potent T cell immune activation. To restore the activity of endogenous IL-18 we generated COM503, a high affinity anti-IL-18BP antibody (Ab), that blocks the IL-18BP:IL-18 interaction and displaces pre-complexed IL-18 to enhance T cell and NK cell activation. In vivo, administration of a surrogate anti-IL-18BP Ab, either alone or in combination with anti-PD-L1 Ab, resulted in significant tumor growth inhibition and increased survival across multiple mouse tumor models. Moreover, anti-IL-18BP Ab induced pronounced TME-localized immune modulation including an increase in polyfunctional non-exhausted T and NK cell numbers and activation. In contrast, no increase in inflammatory cytokines and lymphocyte numbers or activation state was observed in serum and spleen. Taken together, blocking IL-18BP using an Ab is a promising novel approach to harness cytokine biology for the treatment of cancer.

overall_design: E0771 tumor cells were inoculated in C57Bl/6 mice. At tumor volume of 250mm^3, mice were randomized (n=6 per group) and either treated with anti-IL-18BP Ab or isotype control (15mg/kg) twice a week for total of 3 treatments. Tumors were harvested 24 hours after the 3rd treatment and enzymatically dissociated to generate cell suspension, following CD45 enrichment cells were profiled using 10x Chromium X.

first: Assaf

last: Menachem

first: Eran

last: Ophir

middle: Z

first: Sandra

last: Vols

first: Masha

last: Frenkel

first: Keren

last: Cohen

first: Zoya

last: Alteber

first: Sergey

last: Nemzer


title: Identification of mitochondrial RNAs [1]

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

summary: Mitochondria were isolated from heart tissue and the remaining tissue fraction was collected to identify RNA enriched in mitochondria.

overall_design: Mitochondria were isolated from heart tissue, processed by lysis and differential centifugation to collect RNA enriched in the respective compartments.

first: M

last: Weiss

first: T

last: Boettger

first: S

last: Guenther


title: Identification of mitochondrial RNAs [II]

summary: Mitochondria were isolated from skeletal muscle and the remaining tissue fraction was collected to identify RNA enriched in mitochondria.

overall_design: Mitochondria were isolated from skeletal muscle, processed by lysis and differential centifugation to collect RNA enriched in the respective compartments.


title: Identification of mitochondrial RNAs in brown adipose tissue

summary: Mitochondria were isolated from brown adipose tissue and the remaining tissue fraction was collected to identify RNA enriched in mitochondria.

overall_design: Mitochondria were isolated from brown adipose tissue, processed by lysis and differential centifugation to collect RNA enriched in the respective compartments.


title: Differential expression analysis of Aspergillus niger genes in mRMA level between in seed medium and fermentation media for L-malic acid production

city: NanJing

first: Chi

last: Zhang

state: Jiangsu

address: 1 WenYuan Road

department: School of Food Science and Pharmaceutical Engineering

institute: Nanjing Normal  University

summary: Generally, A. niger undergoes two steps consisting of seed stage and fermentation stage to synthesize malic acid. However, it remains unknown which metabolic pathways, regulators, and key genes respond to the transition from seed medium to fermentation medium. In this study, we obtained the total mRMA of a high L-malate-yielding strain A. niger RG0095 at seed stage and fermentation stage, respectively, and performed a global differential expression analysis.

overall_design: To investigate the mRNA expression changes of RG0095 genes between seed culture and fermentation culture, the fresh RG0095 spores were cultured in seed medium for 20 h and then the resulting mycelium were transferred into fermentation medium for  72 h. The gene expression profiling analysis using data obtained from RNA-seq of one strain at 2 time points. Comparative gene expression profiling analysis of RNA-seq data for RG0095 stain in two culture state at 2 time points.

first: Tingting

first: Qing

last: Xu


title: Deficiency of ADAR2 ameliorates metabolic-associated fatty liver disease via AMPK signaling pathways in obese mice

status: Public on Mar 14 2024

city: Tainan

first: Siao Muk

last: Cheng

address: No. 367, Sheng-Li Rd., North District

country: Taiwan

institute: National Institutes of Cancer Research

summary: Non-alcoholic fatty liver disease (NAFLD) is a chronic disease caused by hepatic steatosis. Adenosine deaminases acting on RNA (ADARs) catalyze adenosine to inosine RNA editing. However, the functional role of ADAR2 in NAFLD is unclear.  ADAR2+/+/GluR-BR/R mice (wild type, WT) and ADAR2−/−/GluR-BR/R mice (ADAR2 KO) mice were fed with standard chow or high-fat diet (HFD) for 12 weeks. ADAR2 KO mice exhibited protection against HFD–induced glucose intolerance, insulin resistance, and dyslipidemia. Moreover, ADAR2 KO mice displayed reduced liver lipid droplets in concert with decreased hepatic TG content, improved hepatic insulin signaling, better pyruvate tolerance, and increased glycogen synthesis. Mechanistically, ADAR2 KO effectively mitigated excessive lipid production via AMPK/Sirt1 pathway. ADAR2 KO inhibited hepatic gluconeogenesis via the AMPK/CREB pathway and promoted glycogen synthesis by activating the AMPK/GSK3β pathway. These results provided novel evidence that ADAR2 KO protected against NAFLD progression through activation of AMPK signaling pathways.

overall_design: ADAR2+/+/GluR-BR/R mice (wild type, WT) and ADAR2−/−/GluR-BR/R mice (ADAR2 KO) mice were fed with standard chow (CHOW) or high-fat diet (HFD) at the age of 5 week for 12 weeks. Mouse liver were isolated for RNA extract. Samples type: mouse liver samples; Replicates: duplicate; Groups:HFD_WT, HFD_KO

first: Mei-Lang

last: Kung

first: Yun-Han

last: Wang

first: Kai-Pi

first: Yu-Lin

last: Li

first: Yi-Tsen

last: Hsiao

first: Bertrand

last: Tan

first: Yun-Wen

last: Chen


title: Activation of Bivalent Gene POU4F1 Promotes and Maintains Basal-like Breast Cancer

city: Guangzhou

first: jiahui

last: zhang

address: 107 Yanjiang West Road

institute: Sun Yat-sen Memorial Hospital, Sun Yat-sen University

summary: Basal-like breast cancer (BLBC) is the most aggressive molecular subtype of breast cancer with worse prognosis and fewer treatment options. The underlying mechanisms upon BLBC transcriptional dysregulation and its upstream transcription factors (TFs) remain unclear. Here, among the hyperactive candidate TFs of BLBC identified by bioinformatic analysis, POU4F1 is uniquely upregulated in BLBC and is associated with poor prognosis. POU4F1 is necessary for the tumor growth and malignant phenotypes of BLBC through regulating G1/S transition by direct binding at the promoter of CDK2 and CCND1. More importantly, POU4F1 maintains BLBC identity by repressing ERα expression through CDK2-mediated EZH2 phosphorylation and subsequent H3K27me3 modification in ESR1 promoter. Knocking out POU4F1 in BLBC cells reactivates functional ERa expression, rendering BLBC sensitive to tamoxifen treatment. In-depth epigenetic analysis reveals that the subtype-specific re-configuration and activation of the bivalent chromatin in the POU4F1 promoter contributes to its unique expression in BLBC, which is maintained by DNA demethylase TET1. Together, these results reveal a subtype-specific epigenetically activated TF with critical role in promoting and maintaining BLBC, suggesting that POU4F1 is a potential therapeutic target for BLBC.

overall_design: The basal-like breast cancer lines HS578T and BT549 were transfected with two independent siRNA targeting POU4F1 or control siRNA for 36 h.

first: Jiahui

first: Nanyan

last: Miao

first: Liyan

last: Lao


title: Human Brain Small Extracellular Vesicles Contain Selectively-Packaged, Full-Length mRNA [bulk Iso-Seq]

city: La Jolla

first: Jerold

last: Chun

state: CA

address: 1090 N. Torrey Pines Rd

institute: Sanford Burnham Prebys Medical Discovery Institute

summary: Brain cells release and take up small extracellular vesicles (sEVs) containing bioactive nucleic acids. sEV exchange is hypothesized to contribute to stereotyped spread of neuropathological changes in the diseased brain. We assessed mRNA from sEVs of non-diseased (ND) and Alzheimer’s disease (AD) human postmortem brains, using short- and long-read sequencing. sEV transcriptomes were distinct from bulk tissue, showing enrichment for multiple genes including mRNAs encoding ribosomal proteins and L1Hs transposable elements. AD versus ND sEVs showed enrichment of inflammation-related and depletion of synaptic signaling mRNAs. sEV mRNA from cultured murine primary neurons, astrocytes, or microglia showed similarities with human brain sEVs and revealed cell-type specific packaging. Nearly 80% of human brain sEV transcripts sequenced using long-read sequencing were full-length. Motif analyses of sEV-enriched full-length isoforms revealed RNA-binding proteins that may be associated with sEV loading. Collectively, we show that mRNA in brain sEVs is selectively-packaged and altered by disease state.

overall_design: sEVs were prepared from neuron, astrocyte, and microglia mouse primary cultures in order to examine cell type-specific packaging of sEV mRNA using long-read sequencing (PacBio)

first: Linnea

last: Ransom

first: Christine

last: Liu

first: Emily

last: Dunsmore

first: Carter

last: Palmer

first: Juliet

last: Nicodemus

first: Nyssa

last: Williams


title: Changes in chromatin accessibility in intratumoral CD8+ T cell subsets between young and aged TME

city: Boston

first: Alex Chang-Yu

address: 149 13th Street, 7th floor, Room 7103

department: Krantz Family Center for Cancer Research

institute: Massachusetts General Hospital

summary: Here, we present genome-wide comparisons of chromatin accessibility from endogenous CD8+ T cells and transferred OT-1 CD8+ T cells in young vs. aged B16-OVA tumors using ATAC-seq. This ATAC-seq dataset includes three different intratumoral CD8+ T cell subsets, such as TProg: Slamf6+Tim-3-, TTerm: Slamf6-Tim-3+, and TTAD: Slamf6-Tim-3-, as well as naive CD8+ T cells from spleens.

overall_design: Live tumor-infiltrating CD8+ T cells or OT-1 CD8+ T cells from tumors on day 15 after tumor inoculation were sorted and pooled into 2 or 3 independent biological replicates, which ranged from 5,000 to 50,000 cells per genotype/subset combination (TProg: Slamf6+Tim-3-, TTerm: Slamf6-Tim-3+, and TTAD: Slamf6-Tim-3-). Pelleted cells were incubated in 5–50 μl of reaction mix containing 2×TD, Tn5 enzyme, 2% digitonin in nuclease-free water at 37 °C for 30 min with agitation at 1000 RPM. MinElute Reaction Cleanup kit (Qiagen) was used for DNA purification. Following PCR, bead cleanup was done using AMPure XP beads (Beckman Coulter/Agencourt), library quality was verified using Tapestation analysis, and library quantification was confirmed by KAPA Library Quantification Kit Illumina® Platforms (Roche). Sequencing was performed on NextSeq500 or NextSeq 1000 sequencer using paired-end 50 bp reads.

first: Alex

first: Sneha

last: Jaiswal

first: Daniela

last: Martinez

first: Debattama

last: Sen


title: Modeling kidney development, disease, and plasticity with clonal expandable nephron progenitor cells and nephron organoids

city: Los Angeles

first: Kari

middle: Ann

last: Koppitch

address: 1425 San Pablo Street, BCC 312

department: Stem Cell

institute: USC

summary: Nephron progenitor cells (NPCs) self-renew and differentiate into nephrons, the functional units of the kidney. Here we report manipulation of p38 and YAP activity creates a synthetic niche that allows the long-term clonal expansion of primary mouse and human NPCs, and induced NPCs (iNPCs) from human pluripotent stem cells. Cultured iNPCs resemble closely primary human NPCs, generating nephron organoids with abundant distal convoluted tubule cells, which are not observed in published kidney organoids. The synthetic niche reprograms differentiated nephron cells into NPC state, recapitulating the plasticity of developing nephron in vivo. Scalability and ease of genome-editing in the cultured NPCs allow for genome-wide CRISPR screening, identi-fying novel genes associated with kidney development and disease. A rapid, efficient, and scala-ble organoid model for polycystic kidney disease was derived directly from genome-edited NPCs, and validated in drug screen. These technological platforms have broad applications to kidney development, disease, plasticity, and regeneration.

overall_design: Cell populations profiling analysis of expanded iNPC-derived nephron organoids collected at Day 21 time point through 10x Genomics Multiome (scRNA/scATAC-seq) assays

first: Biao

last: Huang

first: Zipeng

last: Zeng

first: Hui

last: Li

first: Zexu

first: Xi

first: Jinjin

last: Guo

first: Chennan

last: Zhang

first: Megan

middle: E

last: Schreiber

first: Andrew

middle: P

last: McMahon

first: Zhongwei


title: Transcriptional differences between intratumoral CD8+ T cells in young and aged tumors at single cell resolution

last: Chen

summary: Single-cell RNA sequencing of  intratumoral CD8+ T cells (and CD45+ cells)  from young and aged mice

overall_design: Live tumor-infiltrating CD8+ T cells (or OT-1 CD8+ T cells) and/or intratumoral CD45+ cells were sorted from tumors on day 15 after tumor inoculation by BD FACSSymphony S6 Sorter (BD). Sorted cells were pooled into groups (five biological replicates per group) with independent mice being labeled with TotalSeq-B Hashtags (Biolegend). Cells were counted and loaded onto the Chromium Controller (10X Genomics) for a target recovery of 10,000 single cells per run. Samples were then processed using the 10X Single Cell 3’v3.1 kit per the manufacturer’s protocol. Sequencing was done on an Illumina NovaSeq S2 or NextSeq 1000/2000 sequencer using 100-cycle kits with paired-end reads.


title: Cell of origin epigenetic priming determines susceptibility to Tet2 oncogenic mutation [bulk ATAC-seq]

city: Cambridge

first: Fabiana

last: Duarte

state: Massachusetts

address: 7 Divinity Avenue

department: HSCRB

institute: Harvard University

summary: Hematopoietic stem cell mutations can result in clonal hematopoiesis (CHIP) but the clinical outcomes are heterogeneous. The nature of the founder mutation and secondary mutations likely drive emergent neoplastic disease. We investigated how the cell state where the TET2 mutation occurs affects susceptibility to that commonly occurring CH mutation. Here, we provide evidence that risk is written in the epigenome of the cell of origin. By characterizing cell states that underlie myeloid differentiation and linking this information to an inducible system to assess myeloid progenitor clones, we provide evidence that epigenetic markers of the cell where Tet2 mutation occurs stratifies clonal behaviors. Specifically, Sox4 fosters a global cell state of high sensitization towards Tet2 KO. Using GMP and primary HSC models, we show that Sox4 promotes cell dedifferentiation, alters cell metabolism and increases the in vivo clonal output of mutant cells. Our results validate the hypothesis that epigenetic features can predispose specific clones for dominance and explain why an identical mutation can result in different outcomes.

overall_design: Hematopoietic clones conditionally immortalized from primary myeloid progenitors using HoxB8 retrovirus fused to Estrogen Receptor domain (Hoxb8-ER) were profiled by bulk ATAC-seq. 28 individual clones were generated from a Tet2 fl/fl mouse and each of them was divided into cohorts for induction of Tet2 KO or control. Each clone pair is derived from an individual GMP cell. 24 clone pairs were generated in the presence of SCF, which primes them towards granulocytic fate, and 4 of them were derived in the presence of GM-CSF which arrests them at a more mature stage and directs them towards a monocyte-macrophage fate.

first: Giulia

last: Schiroli

first: Vinay

last: Kartha


title: CUT&Tag of oxygen-induced retinopathy mouse retina

first: Emil

last: Kriukov

address: 20 Staniford St

institute: Schepens Eye Research Institute

summary: c-Fos and c-Jun form activator protein 1 (AP-1) transcription factors that regulate gene expression by binding to specific motifs on the genome. To investigate c-Fos regulating genes in OIR rod photoreceptor cells, we performed CUT&Tag subjecting normoxia P14 and OIR P14 retina using c-Fos, H3K27ac (enhancer maker), H3K4me3 (active promoter maker), and H3K27me3 ( gene repression maker) antibodies.

overall_design: CUT&Tag DNA-sequencing (CUT&Tag) for transcription factor c-Fos, and Control IgG as well as Histone modification H3K4me3, H3K27me3, and H3K27ac.

first: Ye

last: Sun

first: Satoshi

last: Kaneko

first: Tianxi

last: Wang

first: Petr

last: Baranov


title: Cell of origin epigenetic priming determines susceptibility to Tet2 oncogenic mutation [scRNA-seq]

overall_design: Bone marrow hematopoietic progenitor cells from inducible Tet2 mutant mice or matched controls were profiled using the Chromium Single Cell Reagent Kit v3.1. Our dataset included populations spanning from HSC to mature myeloid effector cells (Lin- progenitors, CD11b+ cells), and sorted GMPs (Lin- cKit+ Sca1- CD34+ CD16/32+).


title: Cell of origin epigenetic priming determines susceptibility to Tet2 oncogenic mutation

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


title: Human Brain Small Extracellular Vesicles Contain Selectively-Packaged, Full-Length mRNA

first: Jerold

last: Chun

summary: Brain cells release and take up small extracellular vesicles (sEVs) containing bioactive nucleic acids. sEV exchange is hypothesized to contribute to stereotyped spread of neuropathological changes in the diseased brain. We assessed mRNA from sEVs of non-diseased (ND) and Alzheimer’s disease (AD) human postmortem brain, using short- and long-read sequencing. sEV transcriptomes were distinct from bulk tissue, showing enrichment for multiple genes including mRNAs encoding ribosomal proteins and L1Hs transposable elements. AD versus ND sEVs showed enrichment of inflammation-related and depletion of synaptic signaling mRNAs. sEV mRNA from cultured murine primary neurons, astrocytes, or microglia showed similarities with human brain sEVs and revealed cell-type specific packaging. Nearly 80% of human brain sEV transcripts sequenced using long-read sequencing were full-length. Motif analyses of sEV-enriched full-length isoforms revealed RNA-binding proteins that may be associated with sEV loading. Collectively, we show that mRNA in brain sEVs is selectively-packaged and altered by disease state.

overall_design: sEVs were prepared from neuron, astrocyte, and microglia mouse primary cultures in order to examine cell type-specific packaging of sEV mRNA

first: Linnea

last: Ransom

first: Christine

last: Liu

first: Emily

last: Dunsmore

first: Carter

last: Palmer

first: Juliet

last: Nicodemus

first: Nyssa

last: Williams


title: Cell context is the third axis of synergy for ATR inhibition and cisplatin in Ewing sarcoma

status: Public on Mar 13 2024

city: Philadelphia

first: Rebecca

last: Kaufman

address: 3400 Civic Center Blvd

department: Center for Childhood Cancer Research

institute: Children's Hospital of Philadelphia

summary: Purpose: The importance of cellular context to the synergy of DNA Damage Response (DDR) targeted agents is important for tumors with mutations in DDR pathways, but less well-established for tumors driven by oncogenic transcription factors. In this study, we exploit the widespread transcriptional dysregulation of the EWS-FLI1 transcription factor to identify an effective DDR targeted combination therapy for Ewing Sarcoma (ES).  Experimental Design: We used matrix drug screening to evaluate synergy between a DNA-PK inhibitor (M9831) or an ATR inhibitor (berzosertib) and chemotherapy. The combination of berzosertib and cisplatin was selected for broad synergy, mechanistically evaluated for ES selectivity, and optimized for in vivo schedule.  Results: Berzosertib combined with cisplatin demonstrates profound synergy in multiple ES cell lines at clinically achievable concentrations. The synergy is due to loss of expression of the ATR downstream target CHEK1, loss of cell cycle checkpoints, and mitotic catastrophe. Consistent with the goals of the project, EWS-FLI1 drives the expression of CHEK1 and five other ATR pathway members. The loss of expression is not due to transcriptional repression and instead caused by degradation coupled with suppression of protein translation. The profound synergy is realized in vivo with a novel optimized schedule of this combination in subsets of ES models leading to durable complete responses in 50% of animals bearing two different ES xenografts.     Conclusions: These data exploit EWS-FLI1 driven alterations in cell context to broaden the therapeutic window of berzosertib and cisplatin to establish a promising combination therapy and a novel in vivo schedule.

overall_design: CUT&Tag for EWS-FLI binding with siEWS-FLI and siNEG

first: Seneca

last: Kinn-Gurzo

first: Patrick

middle: J

last: Grohar


title: Inflammation durably imprints memory CD4+ T cells

city: New York

first: Sophie

middle: L

last: Gray-Gaillard

state: New York

address: 429 E. 29th Street, room 314

institute: NYU School of Medicine

summary: Memory CD4 T cells are critical to human immunity, yet it is unclear if viral inflammation during memory formation has long-term consequences. Here, we compared transcriptional and epigenetic landscapes of Spike (S)-specific memory CD4 T cells in 24 individuals whose first exposure to S was via SARS-CoV-2 infection or mRNA vaccination. Nearly two years after memory formation, S-specific CD4 T cells established by infection remained enriched for transcripts related to cytotoxicity and for interferon-stimulated genes, likely due to a chromatin accessibility landscape altered by inflammation. Moreover, S-specific CD4 T cells primed by infection had reduced proliferative capacity in vitro relative to vaccine-primed cells. Furthermore, the transcriptional state of S-specific memory CD4 T cells was minimally altered by booster immunization and/or breakthrough infection. Thus, these data demonstrate the durable imprint of inflammation on CD4 T cell memory which affected function and may have consequences for long-term immunity.

overall_design: Using multimodal single-cell RNA sequencing, we compared Spike-specific CD4+ memory T cells in 22 individuals around the time of the participants’d SARS-CoV-2 mRNA vaccination, with stratification by whether the participants’t exposure to Spike was via virus or mRNA vaccine. We compared chromatin accessibility and gene expression in Spike-specific CD4+ memory T cells in 12 individuals six months after either SARS-CoV-2 infection or mRNA vaccination using TEA-seq.

first: Sabrina

last: Solis

first: Han

last: Chen

first: Clarice

last: Monteiro

first: Grace

last: Ciabattoni

first: Marie

middle: I

last: Samanovic

first: Amber

last: Cornelius

first: Tijaana

first: Emilie

last: Geesey

first: Miguel

last: Rodriguez

first: Mila

last: Ortigoza

first: Ellie

middle: N

last: Ivanova

first: Sergei

last: Koralov

first: Mark

last: Mulligan

first: Ramin

last: Herati


title: Effect of group III phospholipase A2 deletion in antigen-induced asthma modeled lung

city: Tokyo

first: Yoshitaka

last: Taketomi

address: 7-3-1 Hongo, Bunkyo-ku,

department: CDBIM, Graduate School of Medicine,

institute: The University of Tokyo

summary:
Asthma is a chronic inflammatory disease of the airways characterized by recurrent episodes of airway obstruction, hyperresponsiveness, remodeling, and eosinophilia. Phospholipase A2s (PLA2s), which release fatty acids and lysophospholipids from membrane phospholipids, have been implicated in exacerbating asthma by generating pro-asthmatic lipid mediators, but an understanding of the association between individual PLA2 subtypes and asthma is still incomplete. Here, we show that group III secreted PLA2 (sPLA2-III) plays an ameliorating, rather than aggravating, role in asthma pathology. In both mouse and human lungs, sPLA2-III was expressed in bronchial epithelial cells and decreased during the asthmatic response. In an ovalbumin (OVA)-induced asthma model, Pla2g3-/- mice exhibited enhanced airway hyperresponsiveness, eosinophilia, OVA-specific IgE production, and type 2 cytokine expression as compared to Pla2g3+/+ mice. Lipidomics analysis showed that the pulmonary levels of several lysophospholipids, including lysophosphatidylcholine, lysophosphatidylethanolamine, and lysophosphatidic acid (LPA), were decreased in OVA-challenged Pla2g3-/- mice relative to Pla2g3+/+ mice. LPA receptor 2 agonists suppressed thymic stromal lymphopoietin expression in bronchial epithelial cells and reversed airway hyperresponsiveness and eosinophilia in Pla2g3-/- mice, suggesting that sPLA2-III negatively regulates allergen-induced asthma at least by producing LPA. Thus, the activation of the sPLA2-III-LPA pathway may be a new therapeutic target for allergic asthma.
Microarray gene profiling of the OVA-challenged lung revealed that the genes related to cytokines and inflammatory response were highly changed in Pla2g3-/- mice relative to Pla2g3+/+ mice

overall_design: Model, antigen (OVA)-induced asthma. Mice were sensitized with intraperitoneal injections of ovalbumin (10 µg) plus 1.3 mg of aluminum hydroxide (alum adjuvant) on days 0 and 14. On days 26, 27, and 28, the mice were challenged with 1% OVA aeroallergen for 30 min per day.; Tissues, whole lung; Groups, Pla2g3 knockout (–/–) and wild-type (+/+); Condiotion, 48 h after final antigen challenge versus control; RNA, total RNA samples pooled from four samples.

first: Asako

last: Hamu-Tanoue

first: Yasumasa

last: Nishito

first: Hiromasa

last: Inoue

first: Makoto

last: Murakami


title: ATRX guards against aberrant differentiation in mesenchymal progenitor cells [RNA-seq]

first: Douglas

last: Barrows

state: NY

address: 1230 York Ave

institute: Rockefeller University

summary: Alterations in the tumor suppressor ATRX are recurrently observed in several cancer types including sarcomas, which are mesenchymal neoplasms. ATRX has multiple epigenetic functions including heterochromatin formation and maintenance and regulation of transcription through modulation of chromatin accessibility. Here, we show in murine mesenchymal progenitor cells (MPCs) that Atrx deficiency aberrantly activated mesenchymal differentiation programs. This includes adipogenic pathways where ATRX loss induced expression of adipogenic transcription factors (Pparγ and Cebpα) and enhanced adipogenic differentiation in response to differentiation stimuli. These changes are linked to loss of heterochromatin near mesenchymal lineage genes together with increased chromatin accessibility and gains of active chromatin marks at putative enhancer elements and promoters.  Finally, we observed depletion of H3K9me3 at transposable elements, which are derepressed including near mesenchymal genes where they could serve as regulatory elements.  Our results demonstrate ATRX functions to buffer against differentiation in mesenchymal progenitor cells, which has implications for understanding ATRX loss of function in sarcomas.

overall_design: We determined genes that changes in expression with the expression of ATRX deficiency in undifferentiated pleomorphic sarcoma cell line, using RNA-seq followed by gene expression analyses.

first: Yan

last: Fang

first: Yakshi

last: Dabas

first: Sam

last: Singer

first: Thomas

last: Carroll

first: William

last: Tap

first: Benjamin

middle: A

last: Nacev


title: Cell of origin epigenetic priming determines susceptibility to Tet2 oncogenic mutation [scATAC-seq]

first: Fabiana

last: Duarte

overall_design: Bone marrow hematopoietic progenitor cells from inducible Tet2 mutant mice or matched controls were profiled using the BioRad SureCell single-cell ATAC-seq platform. Our dataset included populations spanning from HSC to mature myeloid effector cells (Lin- progenitors, CD11b+ cells), and sorted GMPs (Lin- cKit+ Sca1- CD34+ CD16/32+).

first: Giulia

last: Schiroli

first: Vinay

last: Kartha


title: Changes in miRNA expression in offspring hypothalamus after exposure to maternal obesity

first: Laura

last: Dearden

address: Addenbrookes Hospital

department: Institute of metabolic science

country: United Kingdom

institute: University of Cambridge

summary: The purpose of this study was to identify miRNA that are differentially regulated in the arcuate nucleus of the hypothaamus (ARC) and paraventricular nucleus of the hypothalamus (PVH) after perinatal exposure to maternal obesity.

overall_design: c57bl6J mouse model of maternal obesity. This sequencing data is from the male offpsring of lean or obese dams when offspring were 8 weeks of age. All aninals were culled in fed state. Arcuate nucleus and paraventricular nucleus was laser captured from cryostectioned brains for RNA extraction.

first: Isadora

last: Furigo

first: Lucas

last: Pantaleao

first: Susan

last: Ozanne


title: ATRX guards against aberrant differentiation in mesenchymal progenitor cells [CUT&RUN]

overall_design: Characterization of the genome-wide incoporation of histone posttranslational modifications in undifferentiated pleomorphic sarcoma cell line


title: ORAI1 inhibition as an efficient preclinical therapy for tubular aggregate myopathy and Stormorken syndrome

city: Illkirch-Graffenstaden

first: Jocelyn

last: Laporte

address: 1 rue Laurent Fries

institute: IGBMC

summary: Tubular aggregate myopathy (TAM) and Stormorken syndrome (STRMK) are clinically overlapping disorders characterized by childhood-onset muscle weakness and a variable occurrence of multi-systemic signs including short stature, thrombocytopenia, and hyposplenism. TAM/STRMK is caused by gain-of-function mutations in the Ca2+ sensor STIM1 or the Ca2+ channel ORAI1, both regulating Ca2+ homeostasis through the ubiquitous SOCE (store-operated Ca2+ entry) mechanism. Functional experiments in cells have demonstrated that the TAM/STRMK mutations induce SOCE overactivation, resulting in excessive influx of extracellular Ca2+. There is currently no treatment for TAM/STRMK, but SOCE is amenable to manipulation. Here we crossed Stim1R304W/+ mice harboring the most common TAM/STRMK mutation with Orai1R93W/+ mice carrying an ORAI1 mutation partially obstructing Ca2+ influx. Compared with Stim1R304W/+ littermates, Stim1R304W/+Orai1R93W/+ offspring showed a normalization of bone architecture, spleen histology, and muscle morphology, an increase of thrombocytes, and improved muscle contraction and relaxation kinetics. Accordingly, comparative RNA- sequencing detected more than 1200 dysregulated genes in Stim1R304W/+ mice and revealed a major restoration of gene expression in Stim1R304W/+Orai1R93W/+ mice. Altogether, we provide physiological, morphological, functional, and molecular data highlighting the therapeutic potential of ORAI1 inhibition to rescue the multi-systemic TAM/STRMK signs, and we identified myostatin as a suitable biomarker for TAM/STRMK in human and mouse.

overall_design: We performed RNA-seq on WT, Stim1R304W/+ (Stim1KI),Orai1+/- (Orai1KO), Orai1R93W/+ (Orai1KI), Stim1R304W/+Orai1R93W/+ (Stim1KIOrai1KI), and Stim1R304W/+Orai1+/-(Stim1KIOrai1KO) tibialis anterior muscle samples


title: ATRX guards against aberrant differentiation in mesenchymal progenitor cells (ATAC-Seq)

overall_design: We determined the chromatin accessibilities in genome-wide scale in mesenchymal protenitor cells with ATRX WT or loss of ATRX.