title: Dynaimic changes in glomerular cells in the development of diabetes

city: Shanghai

first: Yi

last: Shi

address: Fenglin 180

institute: FUDAN University, China

summary:
To investigate dynamic changes in glomerular cells, including podocyte, mesangial cells and glomerular endothelial cells,  in the development of diabetic nephropathy
We then performed gene expression profiling analysis using data obtained from RNA-seq of glomerular  cells of control(m/m), diabetic (db-/- 6-week-old) and diabetic nephropathy (db-/- 10-week-old with  albuminuria) mice

overall_design: Comparative gene expression profiling analysis of RNA-seq data for isolated glomerulare cells

first: Tingting

last: Li

first: Kaiyuan

last: Shen

first: Baixue

last: Yu

first: Jiawei

first: Mei

last: Meng

first: Wenjie

last: Liu

first: Qunye

last: Tang

first: Tongyu

last: Zhu

first: Xin

first: Susan

last: Leung


title: Single-cell transcriptional profiles in glomeruli from type 2 db-/- mice

status: Public on Oct 27 2023

country: China

type: Expression profiling by high throughput sequencing

summary: Diabetic nephropathy is a chronic complication of diabetes, presenting albuminuria at an early stage and leading to renal failure. Kidney is a complicated organ, which is responsible for body fluids control, acid-base balance, and removal of toxins. To better understand the progress of diabetic nephropathy, mice renal cortex of control mice, six-week db-/- (increased serum glucose without pathological changes in kidneys), and ten-week db-/- (with pathological changes in kidneys) were collected for single-cell sequencing analyses. A subgroup of glomerular endothelial cells with pro-angiogenetic features was identified in diabetic kidneys.

overall_design: Mice renal cortex of control mice (n=2), six-week (n=2) and ten-week db-/- (n=2) were collected for single-cell sequencing analyses (10xGenomics platform).

last: Wang

middle: W


title: Aged intestinal stem cells propagate cell-intrinsic sources of inflammaging in mice [Capture-C]

status: Public on Oct 26 2023

city: Heidelberg

first: Erica

last: Valentini

address: Im Neuenheimer Feld 580

country: Germany

institute: DKFZ

summary: Low-grade chronic inflammation is considered a hallmark of ageing and associated with impaired tissue function and development of disease. However, how cell-intrinsic and -extrinsic factors interact to establish this phenotype, termed inflammaging, remains poorly understood. We addressed this question in the mouse intestinal epithelium, using organoid cultures to dissect stem cell-intrinsic and -extrinsic sources of increased inflammatory signaling upon ageing. At the single-cell level, we found that inflammaging establishes differently in cells along the crypt-villus axis, including intestinal stem cells (ISCs). Importantly, the inflammaging phenotype was stably propagated by aged ISCs in organoid cultures and associated with increased chromatin accessibility of inflammation-associated loci in vivo and ex vivo, indicating a cell-intrinsic memory of inflammation. Mechanistically, we show that expression of inflammaging genes is dependent on STAT1 signaling. Together, our data reveal that inflammaging in the intestine is promoted by a cell-intrinsic mechanism, stably propagated by ISCs and associated with a disbalance in immune homeostasis.

overall_design: Combinatorial approach of bulk and single-cell RNA-Seq on epithelial cells from the proximal small intestine of 3 young (2-3 months of age) and 3 aged (20-22 months fo age) mice; cells were freshly isolated by tissue digest and following FACS-based cell sorting. Complementary bulk RNA-Seq & ATAC-Seq was performed from small intestinal organoids derived from young (2-3 months of age) and aged (20-22 months fo age) mice. (Bulk RNA-Seq: n=6 per age, ATAC-Seq: n=3 per age)

first: Maja

middle: C

last: Funk

first: Jan

middle: G

last: Gleixner

first: Florian

last: Heigwer

first: Dominik

last: Vonficht

first: Zeynep

last: Aydin

first: Elena

last: Tonin

first: Stefania

last: Del Prete

first: Sylvia

last: Mahara

first: Yannick

last: Throm

first: Jenny

last: Hetzer

first: Danijela

last: Heide

first: Oliver

last: Stegle

first: Duncan

middle: T

last: Odom

first: Angelika

last: Feldmann

first: Simon

last: Haas

first: Mathias

last: Heikenwalder

first: Michael

last: Boutros


title: Aged intestinal stem cells propagate cell-intrinsic sources of inflammaging in mice [ATAC_invivo]

first: Erica

last: Valentini

type: Genome binding/occupancy profiling by high throughput sequencing

first: Maja

last: Funk


title: Disruption of SUV39H1-mediated H3K9 methylation sustains CAR T cell function

city: New York

first: Michel

last: Sadelain

address: 1275 York Avenue, Box 182

country: USA

institute: Memorial Sloan Kettering Cancer Cener

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

overall_design: Refer to individual Series


title: S-adenosylmethionine treatment affects histone methylation in prostate cancer cells

first: Thomas

last: Schmidt

address: Grabengasse 1

institute: Heidelberg University

summary: S-adenosylmethionine represents a potent inhibitor of cancer cell proliferation, migration and invasion in vitro. The reason remains unclear. Here, we examined if treatment with exogenous SAM is capable of causing alterations in the methylation of the histone markers H3K4me3 and H3K27me3, which are both known to be important in the initiation and progression of prostate cancer.

overall_design:
PC-3 cells were treated with 200µmol SAM, a concentration known to cause anticancerogenic effects. The treatment was stopped after 120h. Three treated samples and controls (as well as input samples) were used to perform ChIP with antibodies against H3K4me3 and H3K27me3. Subsequently massive parallel sequencing was performed for all samples and controls.
Exogenous treatment with SAM affects Histone methylation in prostate cancer cells.

first: Arthur

last: Mathes

first: Alexander

last: Neumann

first: Merve

middle: B

last: Duman

first: Gergana

last: Dobreva


title: Microarray data of ICR lenses

city: Fukui

first: Masaru

last: Takashima

address: 3-9-1 Bunkyo

country: Japan

institute: University of Fukui


title: Microarray data of ICR lenses at each week of age

summary: Analysis of gene expression changes during cataract progression.

overall_design:
A total of 7 samples were analyzed: samples with no cataracts (2weeks,4weeks), samples with cortical opacity (8weeks,10weeks), samples with posterior subcapsular opacity (12weeks) samples with nuclear opacity (14weeks,18weeks).
Differences in expression profiles due to cataract progression were identified.

first: Kei

last: Taniguchi

first: Masaya

last: Nagaya

first: Shunki

last: Yamamura

first: Yoshihiro

last: Takamura

last: Inatani

last: Oki


title: SCR106 splicing factor modulates abiotic stress responses by maintaining the RNA splicing in rice

city: Jeddah

first: Haroon

last: Butt

state: Makkah

address: King Abdullah University of Science and Technology (KAUST) Thuwal, 23955-6900

department: BESE

country: Saudi Arabia

institute: KAUST

summary: We investigated the function of the plant-specific SR protein SC106 in pre-mRNA splicing regulation and abiotic stress responses in rice. The loss-of-function mutant, SC106, showed increased sensitivity to salt. We performed genome-wide analyses of gene expression and splicing in seedlings subjected to salt stress and identified multiple splice isoforms from stress-responsive genes dependent on SC106.

overall_design: 7-day-old seedlings of sc106 mutant, and WT germinated on 125mM NaCl and mock conditions. . The RNA-seq libraries were constructed using TruSeq mRNA stranded kit following the standard protocol and sequenced on the Nova-seq platform to generate high-quality paired-end reads.

first: Abdulrahman

last: Alhabsi

first: Ikram

last: Blilou

first: Magdy

middle: M

last: Mahfouz


title: Engineering irradiated tumor-derivedmicroparticles as personalized vaccines toenhance antitumor immunity

city: Wuhan

first: Yu

last: Tian

address: NO.156,Wujiadun,Jianghan District

institute: Cancer center,Union hospital, Tongji medical colloge,Huazhong university of science and technology

summary: The inadequate activation of antigen-presenting cells, the entanglement of T cells, and the highly immunosuppressive conditions in the tumor microenvironment (TME) are important factors that limit the effect of cancer vaccines. Studies have shown that individualized and broad antigens can fully activate anti-tumor immunity and inhibiting the function of TGF-β can facilitate T cell migration to tumor sites. Based on our previous study, we introduced a new vaccine strategy by engineering irradiated tumor cell-derived microparticles (RT-MPs), which have both individualized and broad antigens, to induce broad antitumor effects and cause immunogenic death. Encouraged by the proinflammatory effects of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein and the high affinity between TGF-βR2 and TGF-β, we developed RT-MPs with the SARS-CoV-2 spike protein and TGF-βR2. We found that this spike protein and high TGF-βR2 expression induces the innate immune response and ameliorates the immunosuppressive TME, thereby promoting T cell activation and infiltration, and ultimately inhibiting tumor growth. In addition, when combined with anti-programmed death 1 (anti-PD-1) the engineered RT-MPs were able to generate an immune memory response and eliminate subcutaneous tumors. Our study provides a novel strategy for producing an effective personalized anti-tumor vaccine for clinical application.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Bone marrow derived dentritic cells and RT-MP treated Bone marrow derived dentritic cells.

first: Yajie

last: Sun

first: Shuhui

last: Wu

first: Ai

last: Huang


title: The murine meninges acquire lymphoid tissue properties and harbour autoreactive B cells during chronic Trypanosoma brucei infection

city: Manchester

first: Juan

middle: Fernando

last: Quintana

address: 2.18c CTF, Grafton Street

department: Lydia Becker Institute of Immunology and Inflammation

country: United Kingdom

institute: University of Manchester

summary: The meningeal space is an important structure in the brain borders, which provides immunosurveillance for the central nervous system, but the impact of infections on the meningeal immune landscape is far from being fully understood. Trypanosoma brucei, the causative agents of Human African Trypanosomiasis or sleeping sickness, accumulates in the meningeal spaces, inducing severe meningitis and resulting in death if left untreated. Thus, sleeping sickness represents an attractive model to study immunological dynamics in the meninges during infection. Here, combining single cell transcriptomics and mass cytometry by time of flight (CyTOF), coupled with in vivo interventions, we found that chronic T. brucei infection triggers the development of ectopic lymphoid aggregates (ELAs) in the murine meninges during chronic infection. These infection-induced ectopic structures are defined by the presence of ER-TR7+ fibroblastic reticular cells (FRCs) and follicular dendritic cells (FDCs) that initiate a signalling cascade driving local T cell activation towards a T follicular helper (TFH)-like phenotype, as well as B cell class switching. Furthermore, the meningeal-resident plasma cells display activity typically associated with germinal centre reactions and are able to produce antibodies able to recognise mouse brain antigens, which correlates with cortical (and white matter) demyelination. Lastly, we found that systemic lymphotoxin (LT) signalling blockade led to a significant depletion of meningeal FDCs and autoreactive B cells, indicating that LTsignalling is critical to induce and maintain local responses in the meninges. Taken together, we provide evidence that the meningeal immune response results in the acquisition of lymphoid tissue-like properties during chronic T. brucei infection. These findings have broader implications for understanding the mechanisms underlying the formation ELAs during chronic inflammation resulting in autoimmunity, as observed in other demyelinating neurodegenerative disorders such as multiple sclerosis.

overall_design: Single cell suspensions from naïve and T. brucei infected meningeal preparations were analysed by single cell transcriptomics (10X Genomics)

middle: F

first: Matthew

last: Sinton

first: Lalit

middle: K

last: Dubey

first: Praveena

last: Chandrasegaran

first: John

last: Ogunsola

first: Moumen

last: Al Samman

first: Neil

middle: A

last: Mabbott

first: Annette

last: MacLeod


title: Chromatin state transitions in the Drosophila intestinal lineage reveal principles of cell type specification [DamID]

city: Gif-sur-Yvette

first: Katarzyna

last: Siudeja

address: 1, Avenue de la Terrasse

country: France

institute: Institute for Integrative Biology of the Cell (I2BC), INSERM U1280, CEA, CNRS, Université Paris-Saclay

summary:
To investigate the chromatin state into an adult stem cell lineage, we generate cell-type specific chromatin state maps in the adult Drosophila intestine and identify principal chromatin state transitions during lineage determination.
we profiled the binding sites of five chromatin-associated proteins from which the previously described five major types of chromatin.

overall_design: Comparative chromatin accessibility (ATAC-seq) as well as gene expression (RNA-seq) in Drosophila ISC/EB in control and H1 RNAi conditions

first: M

last: Josserand

first: N

last: Rubanova

first: L

last: Gervais

first: A

middle: J

last: Bardin


title: Aged intestinal stem cells propagate cell-intrinsic sources of inflammaging in mice [single-cell RNA-seq]

first: Erica

last: Valentini

summary: During ageing, cell-intrinsic and extrinsic factors lead to the decline of tissue function and organismal health. Disentangling these factors is important for developing effective strategies to prolong organismal healthspan. Here, we addressed this question in the mouse intestinal epithelium, which forms a dynamic interface with its microenvironment and receives extrinsic signals affecting its homeostasis and tissue ageing. We systematically compared transcriptional profiles of young and aged epithelial cells in vivo and ex vivo in cultured intestinal organoids. We found that all cell types of the aged epithelium exhibit an inflammation phenotype, which is marked by MHC class II upregulation and most pronounced in enterocytes. This was accompanied by elevated levels of the immune tolerance markers PD-1 and PD-L1 in the aged tissue microenvironment, indicating dysregulation of immunological homeostasis. Intestinal organoids from aged mice still showed an inflammation signature after weeks in culture, which was concurrent with increased chromatin accessibility of inflammation-associated loci. Our results reveal a cell-intrinsic, persistent inflammation phenotype in aged epithelial cells, which might contribute to systemic inflammation observed during ageing.

overall_design: Combinatorial approach of bulk and single-cell RNA-Seq of epithelial cells from the proximal small intestine of 3 young (2-3 months of age) and 3 aged (20-22 months of age) mice; cells were freshly isolated by tissue digest and following FACS-based cell sorting. Complementary bulk RNA-Seq & ATAC-Seq was performed from small intestinal organoids derived from young (2-3 months of age) and aged (20-22 months fo age) mice. (Bulk RNA-Seq: n=6 per age, ATAC-Seq: n=3 per age)

first: Maja

last: Funk

first: Jan

last: Gleixner

first: Florian

last: Heigwer

first: Zeynep

last: Aydin

first: Elena

last: Tonin

first: Jenny

last: Hetzer

first: Danijela

last: Heide

first: Oliver

last: Stegle

first: Mathias

last: Heikenwälder

first: Michael

last: Boutros


title: Aged intestinal stem cells propagate cell-intrinsic sources of inflammaging in mice [ATAC-Seq]

last: Heikenwalder


title: Aged intestinal stem cells propagate cell-intrinsic sources of inflammaging in mice [in vivo bulk RNA-Seq]

first: Dominik

last: Vonficht

first: Stefania

last: Del Prete

first: Sylvia

last: Mahara

first: Yannick

last: Throm

first: Duncan

last: Odom

first: Angelika

last: Feldmann

first: Simon

last: Haas


title: Self-organizing Single-Rosette Brain Organoids (SOSRS) from Human Pluripotent Stem Cells

city: Ann Arbor

first: Qianyi

last: Ma

state: MI

address: 1141 E Catherine St

department: Human Genetics

institute: University of Michigan

summary: We report single-cell RNA-sequencing data characterizing the cell types and variability in self-organizing single rosette forebrain organoids differentiated for 1mo, 3mo, and 5mo with 4, 6, and 3 SOSRS used, respectively. The data shows increasing cellular diversity over differentiation time with a high degree of similarity in the cell diversity between SOSRS differentiated to the same timepoint.

overall_design: scRNA-sequencing for brain organoids at 1, 3, and 5 months with 4, 6, and 3 SOSRS used to compare cell types and variailbility. Cells from each organoid were labelled with an antibody-based cell hashing technique to allow multi-sample pooled analyses to reduce batch effects.

first: Andrew

last: Tidball

first: Jun

last: Li

first: Jack

last: Parent


title: Microarray data from 4-, 8-, and 10-week-old ICR lenses

first: Masaru

last: Takashima

summary: Analysis of gene expression changes during cortical cataract progression in ICR.

overall_design:
A total of 12 samples were analyzed: three ICR lenses samples without cataracts (4weeks), each three ICR lens samples with cortical opacity (8weeks, 10weeks), and SD rat lens samples without cataracts (4weeks, 8weeks, 10weeks),
Genes whose expression fluctuated from 4 to 8 or 10 weeks of age in the ICR were extracted. In addition, genes whose expression fluctuated from 4 to 8 or 10 weeks of age in SD rats to exclude genes whose expression fluctuated as the ICR grew and genes common to fluctuating genes in the ICR were excluded from the refinement.

first: Kei

last: Taniguchi

first: Masaya

last: Nagaya

first: Shunki

last: Yamamura

first: Yoshihiro

last: Takamura

last: Inatani

last: Oki


title: Aged intestinal stem cells propagate cell-intrinsic sources of inflammaging in mice [ex vivo bulk RNA-Seq]

first: Erica

last: Valentini

first: Maja

last: Funk

first: Jan

last: Gleixner

first: Florian

last: Heigwer

first: Zeynep

last: Aydin

first: Elena

last: Tonin

first: Jenny

last: Hetzer

first: Danijela

last: Heide

first: Oliver

last: Stegle

first: Mathias

last: Heikenwalder

first: Michael

last: Boutros


title: A gene regulatory network critical for axillary bud dormancy directly controlled by Arabidopsis BRANCHED1

city: Wageningen

first: Sam

middle: Wijnand

last: van Es

address: Droevendaalsesteeg

department: Plant Developmental Systems

country: Netherlands

institute: Wageningen University and Research

summary:
The control of branch outgrowth is critical for plant fitness, stress resilience and crop yield. The Arabidopsis thaliana transcription factor BRANCHED1 (BRC1) plays a pivotal role in this process: it integrates signals that control shoot branching to inhibit axillary bud growth. Despite the remarkable activity of BRC1 as a potent growth inhibitor, the mechanisms by which it promotes and maintains bud dormancy are still largely unknown.
Here we combine ChIP-seq, transcriptomic and systems biology approaches to characterize the BRC1-regulated gene network. We identify a group of BRC1 direct target genes encoding transcription factors (BTFs) that orchestrate, together with BRC1, an intricate transcriptional network enriched in ABA signalling components. The BRC1 network is enriched in feed-forward loops and feed-back loops, robust against noise and mutation, reversible in response to stimuli, and stable once established. This knowledge which will prove fundamental to adapt plant architecture and crop production to an ever-changing climate.

overall_design: Induction experiment of BRC1 using an estradiol induction system. RNA-seq was performed on tissue from the inducible line (GFP-BRC1ind) and the brc1-2 k.o as control. A ChIP-seq was performed on the inducible line with Input as control. Ten day old seedlings were treated with 5ml of 10uM estradiol on plate. Tissue was harvested after 5 hours.

first: Aitor

last: Munoz-Gasca

first: Fransisco

last: Romero-Campero

first: Eduardo

last: Gonzalez-Grandio

first: Pedro

last: de los Reyes

first: Carlos

last: Tarancón

first: Aalt-Jan

middle: D

last: van Dijk

first: Wilma

last: van Esse

first: Gerco

last: Angenent

first: Richard

last: Immink

first: Pilar

last: Cubas


title: Spliceosome malfunction causes neurodevelopmental disorders with overlapping features (fly)

status: Public on Oct 25 2023

city: Philadelphia

first: Dong

last: Li

state: PA

address: 3615 Civic Center BLVD

institute: Children's Hospital of Philadelphia

summary: Pre-mRNA splicing is a highly coordinated process. While its dysregulation has been linked to neurological deficits, our understanding of the underlying molecular and cellular mechanisms remains limited. We implicated pathogenic variants in U2AF2 and PRPF19, encoding spliceosome subunits in neurodevelopmental disorders (NDDs), by identifying 46 unrelated individuals with 23 de novo U2AF2 missense variants (including seven recurrent variants in 30 individuals) and six individuals with de novo PRPF19 variants. Eight U2AF2 variants dysregulated splicing of a model substrate. Neuritogenesis was reduced in human neurons differentiated from human pluripotent stem cells carrying two U2AF2 hyper-recurrent variants. Neural loss of function of the Drosophila orthologs, U2af50 and Prp19, led to lethality, abnormal mushroom body (MB) patterning, and social deficits, differentially rescued by wild- type and mutant U2AF2 or PRPF19. Transcriptome profiling revealed splicing substrates or effectors (including Rbfox1, a third splicing factor), which rescued MB defects in U2af50 deficient flies. Upon re-analysis of negative clinical exomes followed by data sharing, we further identified six NDD patients carrying RBFOX1 missense variants which, by in vitro testing, showed loss of function. Our study implicates three splicing factors as NDD causative genes and establishes a genetic network with hierarchy underlying human brain development and function.

overall_design: fly brain tissues harvested at the 3rd instar larval stage from WT controls and elav-Gal4 driving knockdown flies for U2af50 and Prp19


title: Spliceosome malfunction causes neurodevelopmental disorders with overlapping features (human)

overall_design: we performed transcriptomic profiling of the hPSC isogenic model with 24 samples (10 colonies of Arg149Trp, 4 colonies of Arg150Cys, and 10 WT colonies)


title: Aged intestinal stem cells propagate cell-intrinsic sources of inflammaging in mice

first: Erica

last: Valentini


title: Ikaros is a principal regulator of Aire+ mTEC homeostasis, thymic mimetic cell diversity, and central tolerance [Tuft cell RNA-seq]

city: San Francisco

first: Jun Hyung

last: Sin

state: CA

address: 513 Parnassus Ave S-1076

department: Pediatrics

institute: University of California, San Francisco

summary: The zinc-finger transcription factor Ikaros (Ikzf1) modulates key gene expression programs important for hematopoietic development, and coding mutations in IKZF1 are found in patients with immunodeficiency, leukemia, and autoimmunity.  While Ikaros has a well-established function in hematopoiesis, its role in other cell types is less well defined.  Here, we uncover new functions for Ikaros in thymic epithelial lineage development and show that Ikzf1 expression in medullary thymic epithelial cells (mTECs) is required for both Autoimmune Regulator positive (Aire+) mTEC development and tissue-specific antigen (TSA) gene expression.  Accordingly, TEC-specific deletion of Ikzf1 in mice results in a profound decrease in Aire+ mTECs, a global loss of TSA gene expression, and the development of autoimmunity.  Moreover, Ikaros shapes thymic mimetic cell diversity and its deletion results in a dramatic expansion of thymic tuft cells and muscle-like mTECs and a loss of other Aire-dependent mimetic populations.  Single-cell analysis reveals Ikaros modulates core transcriptional programs in TECs that correlate with the observed cellular changes.  Our findings highlight a previously undescribed role for Ikaros in regulating epithelial lineage development and function, and suggest that failed thymic central tolerance could contribute to the autoimmunity seen in humans with IKZF1 mutations.

overall_design: To investigate the differential gene expression of thymic tuft cells between Foxn1-Cre(-) Ikzf1fl/fl mice and Foxn1-Cre(+) Ikzf1fl/fl mice. We generated conditional Foxn1 conditional KO mice and FACS sorted L1CAM+ tuft cells and performed DE analysis on the two mice genotypes.

first: Juliana

last: Sucharov Costa

middle: R

last: Waterfield


title: Ikaros is a principal regulator of Aire+ mTEC homeostasis, thymic mimetic cell diversity, and central tolerance [Pou2f3 RNA-seq]

overall_design: We have found that deletion of Ikaros in mTECs results in changes in mTEC cellular heterogeneity with an expansion of tuft cells and loss of Aire+ mTECs that are deficient in both Ikzf1 and Pou2f3 to determine the effect of Ikaros on gene expression in the absence of Tuft cells


title: Cohesin and CTCF do not assemble TADs in Xenopus sperm and male pronuclei

city: Vienna

first: Roman

last: Stocsits

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP - Research Institute of Molecular Pathology

summary: Paternal genomes are compacted during spermiogenesis and de-compacted following fertilization. These processes are fundamental for inheritance but incompletely understood. We analyzed these processes in the frog Xenopus laevis, whose sperm can be assembled into functional pronuclei in egg extracts in vitro. In such extracts, cohesin extrudes DNA into loops, but in vivo cohesin only assembles topologically-associating domains (TADs) at the mid-blastula transition (MBT). Why cohesin assembles TADs only at this stage is unknown. We first analyzed genome architecture in frog sperm and compared it to human and mouse. Our results indicate that sperm genome organization is conserved between frogs and humans and occurs without formation of TADs. TADs can be detected in mouse sperm samples, as reported, but these structures might originate from somatic chromatin contaminations. We therefore discuss the possibility that the absence of TADs might be a general feature of vertebrate sperm. To analyze sperm genome remodeling upon fertilization, we reconstituted male pronuclei in Xenopus egg extracts. In pronuclei, chromatin compartmentalization increases but cohesin does not accumulate at CTCF sites and assemble TADs. However, if pronuclei are formed in the presence of exogenous CTCF, CTCF binds to its consensus sites, cohesin accumulates at these and forms short-range chromatin loops, which are preferentially anchored at CTCF’s N-terminus. These results indicate that TADs are only assembled at MBT because before this stage CTCF sites are not occupied and cohesin only forms short-range chromatin loops.

sample_organism:
Xenopus laevis
Homo sapiens
Mus musculus

overall_design: Hi-C in human, mouse and Xenopus laevis sperm, pronuclei generated by incubating de-membranated Xenopus laevis sperm in Xenopus egg extract and Xenopus laevis XL177 cells.

first: Gregor

last: Jessberger

first: Csilla

last: Várnai

first: Wen

last: Tang

first: Georg

last: Stary

first: Jan

last: Peters


platform_organism:
Xenopus laevis
Homo sapiens
Mus musculus


title: Chromatin state transitions in the Drosophila intestinal lineage reveal principles of cell type specification

first: Katarzyna

last: Siudeja


title: Chromatin state transitions in the Drosophila intestinal lineage reveal principles of cell type specification [ATAC-seq]

first: M

last: Josserand

first: N

last: Rubanova

first: L

last: Gervais

first: A

last: Bardin


sample_organism:
Xenopus laevis
Mus musculus

platform_organism:
Xenopus laevis
Mus musculus

overall_design: Chromatin immunoprecipitation DNA sequencing (ChIP-Seq) with antibodies against Smc3 and CTCF in pronuclei generated by incubating de-membranated Xenopus laevis sperm in Xenopus egg extract and Xenopus laevis XL177 cells.


title: A CYBDOM protein impacts iron homeostasis and primary root growth under phosphate deficiency in Arabidopsis

city: LAUSANNE

first: JOAQUIN

last: CLUA

address: BIOPHORE

department: DBMV

country: Switzerland

institute: UNIL

summary: Phosphate is an essential macronutrient required for plant growth and development. However, it is present at suboptimal levels in many terrestrial ecosystems. To ameliorate this limitation, plants have evolved developmental and physiological mechanisms known as phosphate starvation responses (PSR). One of the main PSR in Arabidopsis thaliana is a deep restructuration of the root system architecture, which includes a reduction in primary root growth resulting in a shallower root system better adapted to explore the nutrient-rich topsoil. Intense research over the last years has shown that this developmental change is dependent on the accumulation and redistribution of iron (Fe) at the root tip, which in turn, participates in Fenton reactions and generates reactive oxygen species that affect meristem function and cell elongation. We have recently identified and characterized a cytochrome-containing protein in A. thaliana, named CRR, which is involved in the primary root growth response to phosphate starvation. Our results showed that CRR is an ascorbate-dependent ferric-reductase whose expression levels modulates iron distribution pattern in the root, affecting meristem function and cell elongation. Moreover, this activity also has shown to be critical for iron toxicity tolerance since CRR determines the transport rate of iron from root to shoot.

overall_design: Arabidopsis thaliana seedlings Col-0 or a CRR mutant line (crr), were grown on plus (+Pi; control condition) or minus (-Pi) phosphate conditions for 7 days and root tissue was used for the transcriptomic analysis

first: Joaquin

last: Clua

first: Jonatan

last: Montpetit

first: Yves

last: Poirier


title: Transcription profile of infiltrating monocytes derived from 3D liver cancer cell line spheroids

city: Bangkok

first: Tanapat

last: Palaga

address: Payathai Road, Pathumwan

department: Microbiology

country: Thailand

institute: Chulalongkorn University

summary: To study the molecular mechanism of tumor associated macrophages (TAMs), the RNA of infiltrating monocytes derived from in vitro liver cancer spheroid model were performed. The results indicated that the cholesterol metabolism-related genes enriched in the infiltrating monocytes, which presented the M2-like TAM phenotypes.

overall_design: In this study, the infiltrating monocytes isolated from 3D liver cancer cell lines consisted of infiltrating monocytes in HepG2 spheroids and the infiltrating monococytes in PLC/PRF/5 spheroids. The freshly isolated monocytes from PBMCs were control. The gene expressions were performed on NanoString nCounter Human Myeloid Innate Immunity Panel.

first: Pornlapat

last: Keawvilai

first: Patipark

last: Kueanjind

first: Jeerameth

last: Klomsing


title: CircRNA expression profiling for human normal artery and  atherosclerotic artery

city: Guangzhou

first: Yu

last: Zhou

state: Guangdong

address: No 58, Zhongshan 2nd street

department: Division of Vascular Surgery

institute: The First Affiliated Hospital, Sun Yat-sen University

summary: Atherosclerosis is a chronic process that leads to ischemic heart disease, strokes, and peripheral vascular disease. While circRNA are implicated in a variety of diseases, their role in atherosclerosis is not well understood. This study aims to investigate how dysregulated circRNA contribute to atherosclerosis.

overall_design: The differentially expressed circRNA between 3 normal arteries and 3 atherosclerotic arteries were examined using Arraystar Human circRNA Array V2system.

first: Shenming

last: Wang

first: Zuojun

last: Hu


title: New Chromatin Run-On Reaction Enables Global Mapping of Active RNA Polymerase Locations in an Enrichment-free Manner

city: Hangzhou

first: Jianzhao

last: Liu

address: 866 Yuhangtang Rd, Hangzhou, Zhejiang Province, P.R. China

institute: Zhejiang University

summary: The status of cellular RNA polymerases’ locations mirrors global transcriptional activity. A number of methods have been developed to map the distribution of RNA polymerase II (RNPII) genomewide, most of which took advantages of im-munoprecipitations of RNPII complexes or nucleotide analog-labeled nascent RNAs followed by high-throughput sequenc-ing. Given the tedious procedures involved in enrichment and sequencing library construction experiments, development of a simple method that conquers these issues is highly beneficial to the field. Here we report a mutation-based and enrich-ment-free Global chromatin Run-On sequencing (mGRO-seq) technique to map strand-specific RNPII locations ge-nomewide at near base resolution. An ATP analog, named N6-allyladenosine triphosphate (a6ATP), was designed and incor-porated into nascent RNAs at RNPII-located positions during a chromatin run-on assay. The chromatin RNAs were purified and subjected to a mild iodination reaction, which quantitatively transformed a6A into 1,N6-cyclized adenosine (cyc-A). During reverse transcription of RNA to complementary DNA (cDNA), base misincorporation at opposite site of cyc-A oc-curred and mutation reads were generated in the cDNA high-throughput sequencing. Bioinformatics analysis identified the genomewide RNPII location distributions from the characteristic A-mutated sites. mGRO-seq yields both the profile of RNPII sites and the chromatin RNA abundance from one experiment. To sum up, our work demonstrated a new simple and cost-effective method for mapping RNA polymerase locations genomewide, which holds great promise for single-cell char-acterization of RNPII distributions.

overall_design: Identification of RNA polymerase active sites in HeLa cell line using mGRO-seq method.

first: Minsong

last: Gao

first: Yini

last: Li


title: Microbial-ligand independent regulation of lymphpoiesis by NOD1

city: Bethesda

first: Stephen

last: Brooks

state: MD

address: 50 SOUTH DR, RM 1140

department: Biodata Mining and Discovery Section

institute: NIAMS/NIH

summary: Aberrant differentiation of progenitor cells in the hematopoietic system is known to severely impact host immune responsiveness. Here we demonstrate that NOD1, a cytosolic innate sensor of bacterial peptidoglycan, also functions in murine hematopoietic cells as a major regulator of both the generation and differentiation of lymphoid progenitors as well as peripheral T lymphocyte homeostasis. We further show that NOD1 mediates these functions by facilitating STAT5 signaling downstream of hematopoietic cytokines. In steady-state, loss of NOD1 resulted in a modest but significant decrease in numbers of mature T, B and NK cells. During systemic protozoan infection, this defect was markedly enhanced leading to host mortality. Lack of functional NOD1 also impaired T-cell-dependent anti-tumor immunity while preventing colitis. These findings reveal that in addition to its classical role as a bacterial ligand receptor, NOD1 plays an important function in regulating adaptive immunity through interaction with a major host cytokine signaling pathway.

overall_design: Total CD4+ T lymphocytes were purified from the spleen and lymph nodes of WT, NOD1-/- or DCARD NOD1 mice with CD4 Micro beads (Miltenyi Biotec, 130-117-043) and AutoMACS (Milteny Biotec). To isolate lineageneg population, total bone marrow cells were treated with a cocktail of biotin-labelled anti-CD3, CD4, CD8, NK1.1, CD11b, CD11c, CD19, B220, Ly6G and TER-119 Ab, followed by incubation with anti-biotin macro beads (Miltenyi Biotec, #130-090-485) and separation on AutoMACS. RNA was extracted from approximately 1 million MACS-purified CD4+ T cells or Lineageneg BM cells with TRIzol (ThermoFisher Scientific, #15596026). An RNA-seq library was then prepared using 200 ng of total RNA and a TruSeq SR RNA sample prep kit (Illumina, #FC-122-1001) according to the manufacturer’s protocol. Libraries were sequenced for 50 cycles (single read) with a HiSeq 2000 (Illumina). Raw sequencing data were processed with CASAVA 1.8.2 software to convert and demultiplex BCL to FastQ.

first: Chiaki

last: Iwamura

first: Hidetaka

last: Ohnuki

first: Francis

last: Flomerfelt

first: Lixin

last: Zhang

first: Alexie

last: Carletti

first: Hidefumi

last: Wakashin

first: Yohei

last: Mikami

first: Yuka

last: Kanno

first: Ronald

middle: E

last: Gress

first: Giovanna

last: Tosato

first: Toshinori

last: Nakayama

first: John

last: O'Shea

first: Alan

last: Sher

first: Dragana

last: Jankovic


title: Chromatin state transitions in the Drosophila intestinal lineage reveal principles of cell type specification [RNA-seq]

first: Katarzyna

last: Siudeja

first: M

last: Josserand

first: N

last: Rubanova

first: L

last: Gervais

first: A

last: Bardin


title: Immunization with the adenovirus-induced T cell response and apoptosis – prophylactic vaccine design against SARS-CoV-2

status: Public on Oct 24 2023

city: Warsaw

first: Monika

middle: Maria

last: Staniszewska

address: Poleczki 19

department: CEZAMAT

country: Poland

institute: Warsaw University of Technology

summary: New universal prophylactic vaccine platforms are needed to prevent or reduce the impact of future respiratory viral infections. While the attribute of T memory cells is particularly attractive in the context of vaccine design for viral infection, the efficiency of T and B memory cell-mediated protection generated under the adenoviral vector was tested. We studied the mechanism using the platform/ immunological factor combination (AdV1+rRBD): adenovirus AdV1 (adjuvant) armed with inducible co-stimulator ICOS and CD40 ligand in combination with recombinant spike protein rRBD (antigen) to promote the differentiation of memory T and B cells. Additionally, adenovirus AdV2 (adjuvant) without ICOS and CD40 ligand in combination with rRBD was tested. Investigating ex vivo T cell responses to the platform-specific stimuli, we found higher frequencies of CD8+ than CD4+ platform-specific T cells vs mock. The cytometric analysis showed that T cells confer protection against SARS-CoV-2 via elevated T cell subsets: CD8+TEMRA (57.6% ± SD 3.3 vs mock 39.6% ± SD 4.83) and CD4+TNAÏVE (59.6% ± SD 0.4 vs mock 50.8% ± SD 1.9). We found that CD8+TEM, CD8+TSCM, and CD8+TCM are antigen-experienced subpopulations generated via the platform after 7 days. When stimulated with the immunological factors, B cells changed from the production of IgM and IgD to isotype IgG. The CD40 gene was significantly expressed (RT-qPCR) in VERO E6 after stimulation with the platform. RNA-seq profiling identified Th1, Th2, and Th17 cell differentiation gene expression patterns that effectively protect against different pathogens. RNA-seq analysis determined signaling pathways that control immunological mechanisms by which the platform induces protective immunity: MAPK cascade, adipocytokine, cAMP, TNF, and Toll-like receptor (TLR) signaling pathway. The formulation (AdV1+rRBD) increased the production of IL-6, IL-8, and TNF vs the mock (P<0.0001). The whole-genome sequencing of VERO E6 showed differences in the expression of apoptosis gene stimulated with the platforms vs mock. Moreover, apoptotic hallmarks were identified and quantified using flow cytometry. We proved that immunogenic factors compromised plasma membrane integrity (RNA-seq). To sum up, the proposed adenoviral platform generated innate and adaptive immunity for the complex and robust regulatory system to prevent SARS-CoV-2 infections.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for VERO E6 ATCC cells and its infected derivatives by AdV1 IC100 (AdV-D24-ICOSL-CD40L-100 VP/mL), AdV2 IC100 (AdV-D24-WT 100 VP/mL), Pseudo-SARS-CoV-2 IC100 (Pseudovirus SARS-CoV-2 100 VP/mL), AdV1+pseudo-SARS-CoV-2 IC100 (AdV-D24-ICOSL-CD40L + Pseudovirus SARS-CoV-2 100 VP/mL), AdV2+pseudo-SARS-CoV-2 IC100 (AdV-D24-WT + Pseudovirus SARS-CoV-2 100 VP/mL).

first: Joanna

last: Baran

first: Łukasz

last: Kuryk

first: Teresa

last: Szczepińska

first: Michał

last: Łaźniewski

first: Mariangela

last: Garofalo

first: Anna

last: Mazurkiewicz-Pisarek

first: Diana

last: Mikiewicz

first: Alina

last: Mazurkiewicz

first: Maciej

last: Trzaskowski

first: Magdalena

last: Wieczorek

last: Pancer

first: Ewelina

last: Hallmann

first: Lidia

last: Brydak

first: Dariusz

last: Plewczynski

first: Tomasz

last: Ciach

first: Jolanta

last: Mierzejewska


title: Transcriptomic Profiling of Early Synucleinopathy in Rats Induced with Preformed Fibrils

city: Grand Rapids

first: Joseph

last: Patterson

address: 400 Monroe NW

institute: Michigan State University

summary: Examination of early phases of synucleinopathy when inclusions are present, but long before neurodegeneration occurs, is critical to both understanding disease progression and the development of disease modifying therapies. The rat alpha-synuclein (α-syn) preformed fibril (PFF) model induces synchronized synucleinopathy that recapitulates the pathological features of Parkinson’s disease (PD) and can be used to study synucleinopathy progression. In this model, phosphorylated α-syn (pSyn) inclusion-containing neurons and reactive microglia (major histocompatibility complex-II immunoreactive) peak in the substantia nigra pars compacta (SNpc) months before appreciable neurodegeneration. However, it remains unclear which specific genes are driving these phenotypic changes. To identify transcriptional changes associated with early synucleinopathy, we used laser capture microdissection of the SNpc paired with RNA sequencing (RNASeq). Precision collection of the SNpc allowed for the assessment of differential transcript expression in the nigral dopamine neurons and proximal glia. Transcripts upregulated in early synucleinopathy were mainly associated with an immune response, whereas transcripts downregulated were associated with neurotransmission and the dopamine pathway. A subset of 29 transcripts associated with neurotransmission/vesicular release and the dopamine pathway were verified in a separate cohort of males and females to confirm reproducibility. Within this subset, fluorescent in situ hybridization (FISH) was used to localize decreases in the Syt1 and Slc6a3 transcripts to pSyn inclusion-containing neurons. Identification of transcriptional changes in early synucleinopathy provides insight into the molecular mechanisms driving neurodegeneration.

overall_design: Male and female hTH-EGFP rats (Taconic #12141; NTac:SD-Tg (TH-EGFP) 24Xen) received intrastriatal injections of alpha-synuclein preformed fibrils. Rats were 3 mo at surgery and 5 mo at tissue collection. Laser capture microdissection was used to isolate the substantia nigra pars compacta, and RNASeq used to examine transcript expression.

last: Kochmanski

first: Caryl

last: Sortwell


title: The DNA repair enzyme, Aprataxin, plays a role in innate immune signaling

city: Newcastle upon Tyne

first: Rebekah-Louise

last: Scanlan

address: Westgate Rd

institute: Newcastle University

summary: Ataxia with oculomotor apraxia type 1 (AOA1) is a progressive neurodegenerative disorder characterized by a gradual loss of coordination of hand movements, speech, and eye movements. AOA1 is caused by inactivation mutation in the APTX gene.APTX resolves abortive DNA ligation intermediates. APTX deficiency may lead to the accumulation of 5'-AMP termini, especially in the mitochondrial genome. The consequences of APTX deficiency includes impaired mitochondrial function, increased DNA single-strand breaks, elevated reactive oxygen species production, and altered mitochondrial morphology. All of these processes can cause misplacement of nuclear and mitochondrial DNA, which can activate innate immune sensors to elicit an inflammatory response.This study explores the impact of APTX knockout in microglial cells, the immune cells of the brain. RNA-seq analysis revealed significant differences in the transcriptomes of wild-type and APTX knockout cells, especially in response to viral infections and innate immune pathways. Specifically, genes and proteins involved in the cGAS-STING and RIG-1/MAVS pathways were downregulated in APTX knockout cells, which suggests an impaired immune response to cytosolic DNA and RNA.The clinical relevance of these findings was supported by analyzing publicly available RNA-seq data from AOA1 patient cell lines. Comparisons between APTX-deficient patient cells and healthy control cells also revealed altered immune responses and dysregulated DNA-and RNA-sensing pathways in the patient cells.Overall, this study highlights the critical role of APTX in regulating innate immunity, particularly in DNA-and RNA-sensing pathways. Our findings contribute to a better 2 This is a provisional file, not the final typeset article understanding of the underlying molecular mechanisms of AOA1 pathology and highlights potential therapeutic targets for this disease.

overall_design: To investigate the function of APTX in DNA- and RNA-sensing pathways in microglial HMC3 cells. To achieve this we generated CRISPR-Cas9-mediated APTX KO HMC3 cells. Cells were either unstimulated (NS) or dsDNA stimulated (IS).

first: Helena

last: Madsen

first: Louise

last: Pease

first: Mansour

last: Akbari

first: Lene

last: Rasmussen

first: Daryl

middle: P

last: Shanley

first: Vilhelm

last: Bohr


title: Ikaros is a principal regulator of Aire+ mTEC homeostasis, thymic mimetic cell diversity, and central tolerance (scRNA seq)

first: Jun Hyung

last: Sin

overall_design: EPCAM+Ly51- medullary thymic epithial cells were sorted and collected for scRNA-sequencing to further investigate the differences in gene expression between conditionally deleted Ikaros mice and control mice

first: Juliana

last: Sucharov Costa

first: Michael

last: Waterfield


title: Single Cell Analysis of Gene expression profile as single cell level of chronic diabetic foot ulcers and chronic non-diabetic foot ulcer Foot Wounds

city: New Haven

first: Valerie

last: Horsley

address: 260 Whitney

institute: Yale University

summary: We investigate the changes between diabetic and non-diabetic wound healing process in chronic foot ulcer.

overall_design: Single cells were enzymatically released from tissues, live cells isolated by MACS beads,  and cells were submited for scRNA-seq libraries preparation

first: Quan

last: Phan

first: Teresa

last: Schaefer-Sandoval

first: Diane

last: King


title: Ikaros is a principal regulator of Aire+ mTEC homeostasis, thymic mimetic cell diversity, and central tolerance [Ikaros scATAC-seq]

overall_design: scATACseq on sorted EPCAM+ mTECs from conditionally deleted Ikzf1 mice


title: Substrate stiffness modulates cardiac fibroblast activation, senescence and proinflammatory secretory phenotype

city: Aurora

first: Timothy

last: McKinsey

state: CO

department: Medicine

institute: University of Colorado Anschutz Medical Campus

summary: In vitro cultures of primary cardiac fibroblasts (CFs), the major extracellular matrix (ECM)-producing cells of the heart, are used to determine molecular mechanisms of cardiac fibrosis.  However, the supraphysiologic stiffness of tissue culture polystyrene (TCPS) automatically triggers the conversion of CFs into an activated myofibroblast-like state, and serial passage of the cells results in the induction of replicative senescence.  These dramatic phenotypic switches confound interpretation of experimental data obtained with cultured CFs. In an attempt to circumvent TCPS-induced activation and senescence of CFs, we utilized poly (ethylene glycol) (PEG) hydrogels as cell culture platforms with low and high stiffness formulations to mimic healthy and fibrotic cardiac ECM, respectively.  As hypothesized, low hydrogel stiffness converted activated CFs into a quiescent state with reduced abundance of a-smooth muscle actin (a-SMA)-containing stress fibers.  Unexpectedly, lower substrate stiffness concomitantly augmented CF senescence, marked by elevated senescence-associated b-galactosidase (SA-b-Gal) activity and increased expression of p16 and p21, which are cyclin-dependent kinase (CDK) inhibitors and markers of senescence. Using dynamically stiffening hydrogels with phototunable crosslinking capabilities, we demonstrate that substrate-induced CF senescence is partially reversible. RNA-sequencing analysis revealed widespread transcriptional reprogramming of CFs cultured on low stiffness hydrogels, with a dramatic reduction in the expression of profibrotic genes encoding ECM proteins, and an attendant increase in expression of NF-kB-responsive inflammatory genes that typify the senescence-associated secretory phenotype (SASP).  Our findings further demonstrate that alterations in matrix stiffness profoundly impact CF cell state transitions, and suggest mechanisms by which CFs change phenotype in vivo depending on the stiffness of the myocardial microenvironment to which they are exposed.

overall_design: Transcriptomic profiling by RNA sequencing was performed using RNA from cultured primary adult rat ventricular fibroblasts cultured on tissue culture polystyrene or two-dimensional soft poly(ethylene glycol) norbornene hydrogel at passage 3 and passage 6.

first: Marina

last: Felisbino

first: Marcello

last: Rubino

first: Joshua

last: Travers

first: Katherine

last: Schuetze

first: Madeleine

last: Lemieux

first: Kristi

middle: S

last: Anseth

first: Brian

last: Aguado


title: Chromatin profiling following SWI/SNF inhibition in neuroblastoma cells [ChIP-seq]

city: Houston

first: H. Courtney

last: Hodges

state: TX

address: 1 Baylor Plaza, BCM 229

department: Department of Molecular & Cellular Biology

institute: Baylor College of Medicine

summary: To assess the genome-wide effects of SWI/SNF activity in MYCN-amplified neuroblastoma cells, we performed ChIP-seq in IMR-32 cells treated with either DMSO or the SWI/SNF inhibitor BRM014. Pronounced loss of chromatin occupancy was observed for members of the neuroblastoma core regulatory circuitry within 1 hour.

overall_design: ChIP-seq in neuroblastoma cells

first: Katerina

last: Cermakova

first: H

middle: C


title: Regulation of DNA accessibility across the cell cycle by SWI/SNF complexes [ATAC-seq]

summary: To identify dynamic changes in DNA accessibility with cell-cycle phase resolution following SWI/SNF inactivation, we compared the ATAC-seq signals in IMR32 cells treated with the small-molecule catalytic inhibitor of SWI/SNF BRM014 or DMSO, which were sorted by their cell cycle stage using a FUCCI live-cell fluorescent indicator. Analysis of these locations revealed that SWI/SNF-dependent sites are regulated in cyclic patterns throughout the cell cycle.

overall_design: ATAC-seq in IMR32 cells


title: NAC61 regulates late and post-ripening associated processes in grape comprising a NAC60-NAC dependent regulatory network

city: Paterna

first: José Tomás

last: Matus

state: Valencia

address: Carrer del Catedràtic Agustín Escardino Benlloch

country: Spain

institute: Institute for Integrative Systems Biology

summary: NACs (NAM/ATAF/CUC) proteins are plant-specific transcription factors with key roles in plant development and stress responses. Here, Vitis vinifera NAC61 was selected for its functional characterization as one of the key candidates of the grape post-harvest withering process. VviNAC61 is particularly expressed at veraison and post-veraison berry stages and also shows a high expression in lignified tissues such as roots, tendrils, seeds and rachis. In leaves, VviNAC61 achieves its highest expression at senescence stage. In line with this observation, a NAC family multispecies phylogenetic tree revealed that VviNAC61 clusters with VviNAC33 and AtANAC046, both involved in regulating senescence processes. VviNAC61 was transiently overexpressed in N. benthamiana leaves, showing wilting/water-soaking symptoms correlated to low stomatal conductance, high leaf temperature, increased loss of the membrane integrity and accumulation of hydrogen peroxide and water. Transcriptomic analysis of cultivar ‘Thompson Seedless’ leaves transiently overexpressing VviNAC61 and the search of TF-bound genes by DAP-seq was allowed us to narrow down a list of VviNAC61-regulated genes. The ‘secondary metabolism’, ‘transcription factor regulation’ and ‘oxidative stress’ functional categories were found to be the most enriched among the candidate target genes. More in detail, several genes encoding for the phenylpropanoid pathway-related enzymes, several MYBs and NAC genes (including VviNAC61), were bound in their promoter region by this TF and were among the upregulated genes. Direct regulation of the stilbene synthase regulator VviMYB14, the abiotic stress-related gene DHN1b, the Botrytis cinerea susceptibility gene VviWRKY52 and the VviNAC61 self-regulation were validated through dual luciferase assays. Lastly, the upstream regulation mechanism of VviNAC61 was further investigated demonstrating that VviNAC61 is controlled by and interacts with VviNAC60, a proposed master regulator of grapevine organ maturation.

overall_design: Identification of binding sites for NAC61 transcription factor in Vitis vinifera by direct sequencing of affinity purified genomic DNA fragments.

first: José

first: Sara

last: Zenoni

first: Chiara

last: Foresti

first: Luis

last: Orduña


title: Divergent molecular networks program functionally distinct CD8+ skin-resident memory T cells

city: Parkville

first: Jan

last: Schroeder

state: Victoria

address: Peter Doherty Institute Melbourne

department: DMI

country: Australia

institute: University of Melbourne

summary: scRNA CITE-seq with paired TCR from mouse CD8+ T cells in skin and spleen after Staphylococcus epidermidis association

overall_design:
Polyclonal CD8+ T cells were sort-purified from skin (CD44hiCD69+CD103+) or spleen (CD44hi) of bone marrow chimeras reconstituted with WT (B6 or CD4-cre), Hobit KO or cMaf CD4-cre cKO cells 14-18d after Staphylococcus epidermidis association. Sort-purified cells were barcoded with hashtag oligos and pooled for sequencing. Libraries were prepared using 10x Genomics kits. Naïve transgenic CD8+ gBT-I cells (CD44lo) were also sorted from the spleen and included as a control.
the citeseq_reference file contains the HTO sequences for the demultiplexing.

first: Simone

middle: L

last: Park

first: Laura

last: Mackay


title: KDM6A/UTX promotes spermatogenic gene expression across generations but is dispensable for male fertility

first: Bluma

last: Lesch

state: CT

address: 333 Cedar Street

department: Genetics

summary: Paternal chromatin undergoes extensive structural and epigenetic changes during mammalian spermatogenesis, producing sperm with an epigenome optimized for the transition to embryogenesis. Lysine demethylase 6a (KDM6A, also called UTX) promotes gene activation in part via demethylation of H3K27me3, a developmentally important repressive modification abundant throughout the epigenome of spermatogenic cells and sperm. We previously  demonstrated increased cancer risk in genetically wild type mice derived from a paternal germ line lacking Kdm6a (Kdm6a cKO), indicating a role for KDM6A in regulating heritable epigenetic states. However, the regulatory function of KDM6A during spermatogenesis is not known. Here, we show that Kdm6a is transiently expressed in spermatogenesis, with RNA and protein expression largely limited to late spermatogonia and early meiotic prophase. Kdm6a cKO males do not have defects in fertility or the overall progression of spermatogenesis. However, hundreds of genes are deregulated upon loss of Kdm6a in spermatogenic cells, with a strong bias towards downregulation coinciding with the time when Kdm6a is expressed. Misregulated genes encode factors involved in chromatin organization and regulation of repetitive elements, and a subset of these genes was persistently deregulated in the male germ line across two generations of offspring of Kdm6a cKO males. Genome-wide epigenetic profiling revealed broadening of H3K27me3 peaks in differentiating spermatogonia of Kdm6a cKO mice, suggesting that KDM6A demarcates H3K27me3 domains in the male germ line. Our findings highlight KDM6A as a transcriptional activator in the mammalian male germ line that is dispensable for spermatogenesis but important for safeguarding gene regulatory state intergenerationally.

overall_design: bulk RNA-seq, single cell RNA-seq, ATAC-seq, and CUT&Tag for H3K27me3 in control and Kdm6a knockout spermatogenic cells and testis

first: Benjamin

middle: W

last: Walters

first: Shannon

last: Rainsford


title: An Epigenetic Memory of Inflammation Induces Context-Dependent Lineage Plasticity in the Pancreas with Divergent Phenotypic Outcomes [bulk ATAC-seq]

city: New York

first: Rohit

last: Chandwani

state: NY

address: 413 East 69th St, BRB 1360G

department: Surgery

institute: Weill Cornell Medicine

summary: Inflammation is essential to the disruption of tissue homeostasis, and, in the pancreas, can destabilize the identity of terminally differentiated acinar cells. Herein we employ lineage-traced mouse models to delineate the chromatin dynamics that accompany the cycle of metaplasia and regeneration following pancreatitis, and unveil the presence of an epigenetic memory of inflammation in the pancreatic acinar cell compartment. We observe that despite histologic resolution of pancreatitis, acinar cells fail to return to their molecular baseline after several months, representing an incomplete cell fate decision. In vivo, this epigenetic memory controls lineage plasticity, with diminished metaplasia in response to a second inflammatory insult but increased tumorigenesis with an oncogenic Kras mutation. We demonstrate that both persistent chromatin and transcriptional changes constituting memory are recalled with oncogenic stress. Together, our findings define the dynamics and recall of an epigenetic memory of inflammation that impacts cell fate decisions in a context-dependent manner.

overall_design: Characterization of bulk chromatin accessibility via ATAC-seq of lineage-traced acinar and acinar-derived cells treated with caerulein (or saline as control) following 2 days, 3 weeks, 6 weeks, 12 weeks, or 18 weeks of recovery.

first: David

last: Falvo


title: An Epigenetic Memory of Inflammation Induces Context-Dependent Lineage Plasticity in the Pancreas with Divergent Phenotypic Outcomes [Acute Pancreatitis scRNA-seq]

overall_design: Characterization of single-cell gene expression via scRNA-seq of pancreatic cells following treatment with either saline or caerulein and either 2 days (S2D and C2D) or 6 weeks of recovery (S6W and C6W)


title: Genome-wide profiling of SMARCA4 in neuroblastoma cells [ChIP-seq]

summary: To reveal the genome-wide targets of SWI/SNF complexes in neuroblastoma cells, we performed ChIP-seq of SMARCA4 (BRG1) in IMR-32, KELLY, and SK-N-DZ cells. We used these libraries to examine chromatin occupancy profiling. Analysis of locations reveal that SMARCA4 targets directly regulate sites regulated by the neuroblastoma core regulatory circuitry.


title: An Epigenetic Memory of Inflammation Induces Context-Dependent Lineage Plasticity in the Pancreas with Divergent Phenotypic Outcomes [memory + KrasG12D scRNA-seq]

overall_design: Characterization of single-cell gene expression via scRNA-seq of pancreatic cells following treatment with either saline or caerulein and 12 weeks of recovery before (mtS and mtC) or 2 days after mutant Kras activation (mktS and mktC)


title: DNA accessibility sites requiring SMARCA4 activity in neuroblastoma cells [ATAC-seq]

summary: To reveal the genome-wide targets of SWI/SNF complexes in neuroblastoma cells, we performed ATAC-seq in IMR-32 cells with or without SMARCA4 inactivation. To identify changes in DNA accessibility following SMARCA4 inactivation, we used either the small-molecule catalytic inhibitor BRM014, auxin-induced degradation of IMR-32 cells engineered with SMARCA4 tagged to the minimal auxin-induced degron (SMARCA4-mAID), or the corresponding vehicle controls. Analysis of these locations reveal that SMARCA4-dependent sites are located at enhancers used by the neuroblastoma core regulatory circuitry.

overall_design: ATAC-seq in neuroblastoma cells


title: Unbiased discovery of natural sequence variants that influence fungal virulence

status: Public on Oct 23 2023

city: St Louis

first: Michael

last: Brent

state: Missouri

address: 4515 McKinley Ave

institute: Washington University

summary: Isolates of Cryptococcus neoformans, a fungal pathogen that kills almost 200,000 people worldwide each year, differ at a few thousand up to almost a million DNA sequence positions compared to a 19-megabase reference genome. We used bulked segregant analysis and association analysis, genetic methods that require no prior knowledge of sequence function, to address the key question of which naturally occurring variants influence fungal virulence. We identified a region containing such variants, prioritized them, and engineered strains to test our findings in a mouse model of infection. At one locus we identified a 4-nt variant in the PDE2 gene, which severely truncates its phosphodiesterase product and significantly alters virulence. Our studies demonstrate a powerful and unbiased strategy for identifying key genomic regions in the absence of prior information, suggest revisions to our assumptions about cAMP levels and about common laboratory strains, and provide significant sequence and strain resources to the community.

overall_design: Comparative expression between KN99a and C8 strains of Cryptococcus neoformans before and after culture ifor 24 hours in RPMI + 10% mouse serum (37°C, 5% CO2).

first: Daniel

last: Agustinho

first: Holly

last: Brown

first: Guohua

last: Chen

first: Tamara

last: Doering


title: SMARCA4-dependent regulation of chromatin and transcription in neuroblastoma

first: H. Courtney

last: Hodges

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

overall_design: Refer to individual Series


title: Spliceosome malfunction causes neurodevelopmental disorders with overlapping features

city: Philadelphia

first: Dong

last: Li

address: 3615 Civic Center BLVD

institute: Children's Hospital of Philadelphia

summary: Pre-mRNA splicing is a highly coordinated process. While its dysregulation has been linked to neurological deficits, our understanding of the underlying molecular and cellular mechanisms remains limited. We implicated pathogenic variants in U2AF2 and PRPF19, encoding spliceosome subunits in neurodevelopmental disorders (NDDs), by identifying 46 unrelated individuals with 23 de novo U2AF2 missense variants (including 7 recurrent variants in 30 individuals) and 6 individuals with de novo PRPF19 variants. Eight U2AF2 variants dysregulated splicing of a model substrate. Neuritogenesis was reduced in human neurons differentiated from human pluripotent stem cells carrying two U2AF2 hyper-recurrent variants. Neural loss of function (LoF) of the Drosophila orthologs U2af50 and Prp19 led to lethality, abnormal mushroom body (MB) patterning, and social deficits, which were differentially rescued by wild-type and mutant U2AF2 or PRPF19. Transcriptome profiling revealed splicing substrates or effectors (including Rbfox1, a third splicing factor), which rescued MB defects in U2af50-deficient flies. Upon reanalysis of negative clinical exomes followed by data sharing, we further identified 6 patients with NDD who carried RBFOX1 missense variants which, by in vitro testing, showed LoF. Our study implicates 3 splicing factors as NDD-causative genes and establishes a genetic network with hierarchy underlying human brain development and function.

sample_organism:
Drosophila melanogaster
Homo sapiens

platform_organism:
Drosophila melanogaster
Homo sapiens


title: Competition for H2A.Z underlies the developmental impacts of repetitive element de-repression

city: Rochester

first: Fanju

last: Meng

address: 601 Elmwood Avenue

department: Biomedical Genetics

institute: University of Rochester Medical Center

type: Methylation profiling by high throughput sequencing

summary: The histone variant H2A.Z is central to early embryonic development, determining transcriptional competency through chromatin regulation of gene promoters and enhancers. In addition to genic loci, we find that H2A.Z resides at a subset of evolutionarily young repetitive elements, including DNA transposons, LINEs, and LTRs, during early zebrafish development. Moreover, increases in H2A.Z occur when repetitive elements become transcriptionally active. Acquisition of H2A.Z corresponds with a reduction in the repressive histone modification H3K9me3, and a moderate increase in chromatin accessibility. Notably however, de-repression of repetitive elements also leads to a significant reduction in H2A.Z over non-repetitive genic loci. Genic loss of H2A.Z is accompanied by transcriptional silencing at adjacent coding sequences, but remarkably, these impacts are mitigated by augmentation of total H2A.Z protein, via transgenic over-expression. Our study reveals that levels of H2A.Z protein determine embryonic sensitivity to de-repression of repetitive elements, that repetitive elements can function as a nuclear sink for epigenetic factors, and that competition for H2A.Z greatly influences overall transcriptional output during development. These findings uncover general mechanisms in which counteractive biological processes underlie phenotypic outcomes.

overall_design: Genome wide DNA methylation profiling by anchor-based bisulfite sequencing after Dacitabine treatment in developing zebrafish embryos

last: Delatte


title: Transfer RNA pools in human cells are controlled by selective gene expression [tRNA-Seq]

city: Planegg

first: Danny

last: Nedialkova

state: Bayern

address: Am Klopferspitz 18

institute: Max Planck Institute for Biochemistry

type: Non-coding RNA profiling by high throughput sequencing

summary: Transfer RNAs are required for translating genetic information into protein sequence. The human genome contains hundreds of tRNA genes, many of which in multiple copies. How their expression is regulated to control functional tRNA levels is unknown. Here, we combined quantitative tRNA profiling and ChIP-Seq to measure tRNA expression upon differentiation of human induced pluripotent stem cells (hiPSC) into neuronal and cardiac cells. We find that tRNA transcript pools vary substantially, while the abundance of tRNAs with distinct anticodons, which governs decoding rates, is more stable among cell types. Mechanistically, RNA Polymerase III (Pol III) samples a wide range of tRNA genes in hiPSC and becomes constrained to a housekeeping subset upon differentiation. This is mediated by diminished mTOR signaling, which activates the Pol III repressor MAF1. Our data rationalize how tRNA anticodon pools are buffered in different cellular contexts and reveal that mTOR activity drives selective tRNA expression.

overall_design: Human induce pluoripotent stem cells (hiPSC), and derived neural progenitors (NPC), mature neurons, and cardiomyocytes (CM) were cultured. Subsequent chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for RNA Polymerase III subunit RPC1, TFIIIB subunit BRF1, histone modifications H3K4me3 and K3K27me3, ATAC-Seq, RNA-Seq, ribosome profiling followed by sequencing (Ribo-Seq) and tRNA-Seq datasets were generated to investigate the regulation of tRNA genes upon differentiation of hiPSCs.

first: Lexi

last: Gao

first: Andrew

last: Behrens

first: Geraldine

last: Rodschinka

first: Sergio

last: Forcelloni

first: Sascha

last: Wani

first: Katrin

last: Strasser


title: Transfer RNA pools in human cells are controlled by selective gene expression [Ribo-seq]


title: Transfer RNA pools in human cells are controlled by selective gene expression [ChIP-seq]


title: Transfer RNA pools in human cells are controlled by selective gene expression [ATAC-seq]


title: Topoisomerase 1 facilitates nucleosome reassembly at stress genes during recovery [RNA-seq]

city: Barcelona

first: Montserrat

last: Vega

state: Barcelona

address: C/ Dr. Aiguader 88, lab 383

department: MELIS

institute: Universitat Pompeu Fabra

summary: Investigate the role of topoisomerase 1 in the response to oxidative stress

overall_design: Gene expression profiling using RNA-seq obtained from a wild-type and a top1 deleted strain under untreated conditions and after 30 minutes of 1mM peroxide treatment

first: Rodrigo

last: Fraile

first: Kevin

last: de Castro Cogle

last: Castillo

first: Roger

last: Anglada

first: Ferran

last: Casals

first: José

last: Ayté

first: Ernesto

last: Lowy-Gallego

first: Elena

last: Hidalgo


title: Competition for H2A.Z underlies the developmental impacts of repetitive element de-repression [CUT&Tag]

last: Meng

overall_design: H2A.Z, H3K9me3 genomic profiling and gene expression in DMSO, 5AzadC and TDCIPP treated zebrafish embryos at 6hpf and 12hpf were generated by next-generation sequencing.


title: An epigenetic memory of inflammation controls context-dependent lineage plasticity in the pancreas [bulk RNA-seq]

first: Rohit

last: Chandwani

overall_design: Characterization of bulk gene expression via RNA-seq of lineage-traced acinar and acinar-derived cells from either KrasG12D or KrasWT mice treated with caerulein (or saline as control) following 2 days, 3 weeks, or 12 weeks of recovery, with or without delayed activation of TdTomato +/- KrasG12D expression via tamoxifen administratio, as indicated

first: David

last: Falvo


first: Fanju

overall_design: H2A.Z genomic profiling and gene expression in DMSO, 5AzadC and TDCIPP treated zebrafish embryos at 6hpf and 12hpf were generated by next-generation sequencing.


title: Transcriptional effects of SMARCA4 inhibition on neuroblastoma cells [4sU RNA-seq]

first: H. Courtney

last: Hodges

summary: To reveal fast-acting transcriptional effects of SWI/SNF inhibition in neuroblastoma cells, we performed 4sU metabolic labeling followed by RNA-seq in IMR-32, KELLY, and SK-N-DZ cells and compared the effects of BRM014 with DMSO vehicle control. We also compared these effects to auxin-induced degradation of SMARCA4 in engineered cells with the minimal auxin-induced degron (SMARCA4-mAID). Analysis of transcripts reveal that SMARCA4 inhibition leads to suppression of transcripts involved in the G1 checkpoint.

overall_design: RNA-seq in neuroblastoma cells

first: Katerina

last: Cermakova

first: H


title: An Epigenetic Memory of Inflammation Induces Context-Dependent Lineage Plasticity in the Pancreas with Divergent Phenotypic Outcomes


title: A subset of pro-inflammatory spiny mice macrophages promotes a regenerative phenotype in mouse fibroblasts

city: Cincinnati

first: Mike

last: Adam

state: Ohio

address: 240 Albert Sabin Way

department: CBDI

institute: Cincinnati Children's Hospital Research Foundation

summary: Macrophages play an essential role in tissue regeneration. However, the ability to dissect the role of macrophages in regeneration from their role in wound healing with scar has been hampered by a lack of comparative systems. In this study, we use a mammalian model of tissue regeneration and scar formation to contrast the role of macrophages in both wound healing paradigms. The African Spiny mouse (A. cahirinus) can regenerate tissue of the external ear pinnae after 4mm biopsy punch. The common lab mouse (M. musculus) forms a scar after the same injury. We test the potential of bone marrow derived macrophages from both species to activate local ear fibroblasts and find macrophages from A. cahirinus are able to induce a matrix turnover phenotype in fibroblasts from both species. We identify growth factors and cytokines specific to macrophages derived from A. cahirinus, and using single cell RNAseq and screening with these factors, we identify populations of macrophages unique to a regenerating injury compared to scar forming injury. Finally we test how macrophage populations change over time in a regenerating injury and how they differ from each stage in a scar forming system

sample_organism:
Acomys cahirinus
Mus musculus

platform_organism:
Acomys cahirinus
Mus musculus

overall_design: Injured Mus and Acomys ear tissues were analyzed using 10X single-cell rna-seq

first: Steve

last: Potter

first: Ashley

last: Seifert


title: Experimental and Bioinformatic upgrade for genome-wide mapping of nucleosomes in Trypanosoma cruzi

city: Buenos Aires

first: Josefina

last: Ocampo

address: Vuelta de Obligado 2490

country: Argentina

institute: INGEBI-CONICET

summary: We adapted the widely used digestion of chromatin with micrococcal nuclease (MNase) followed by deep sequencing to the parasite Trypanosoma cruzi, which presents numerous singularities. In this work, we use the hybrid CL Brener strain  carrying two set of chromosomes from two substantially different parental strains. The hybrid strain CL Brener is composed of the Esmeraldo-like and non Esmeraldo-like haplotypes. Additionally, part of the genome was not assembled into any of the haplotypes. Sometimes the community working in the field uses just one haplotype as reference genome for simplicity. In this work, we emphasize the importance of using its whole genome as a reference. Moreover, we extended our analysis to a clonal strain, Sylvio-X10.

overall_design: We mapped nucleosomes genome wide from exponentially growing epimastigotes of the Cl Brener and Sylvio-X10 strains. An exhaustive and thorough computational workflow was developed for data analysis, highlighting the relevance of using its whole genome as a reference instead of the commonly used Esmeraldo-like haplotype. Moreover, the performance of two aligners, Bowtie2 and HISAT2 was tested to find the most appropriate tool to map any genomic read to reference genomes bearing this complexity.

first: María

last: Beati

first: Milena

last: Massimino Stepñicka

first: Salomé

last: Vilchez Larrea

first: Guillermo

last: Alonso


title: Effect of erythritol on gene expression of Staphylococcus coagulans

status: Public on Oct 22 2023

city: Fuchu-shi

first: Saki

last: Onishi-Sakamoto

state: Tokyo

address: 3-8-1 Harumi-cho

institute: Tokyo University of Agriculture and Technology

summary: We performed a transcriptome analysis of Staphylococcus coagulans with and without 5% (w/w) erythritol exposure to validate the mechanism of growth inhibition.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Staphylococcus coagulans with and without 5% (w/w) erythritol exposure

first: Tadashi

last: Fujii

first: Takumi

last: Tochio

first: Koji

last: Nishifuji


title: Symmetry breaking of tissue mechanics in wound induced hair follicle regeneration [scRNA-seq]

city: Los Angeles

first: Hans I-Chen

last: Harn

address: 2011 Zonal Ave. HMR304

institute: University of Southern California

summary: Tissue regeneration is a process that recapitulates the molecular and mechanical aspects of development and evolution. We use the wound-induced hair neogenesis (WIHN) model to investigate the mechanical and molecular responses of the laboratory (Mus) and African spiny (Acomys) mice. Laboratory and spiny mice showed an opposite trend of spatiotemporal morphogenetic field for WIHN during wound healing, and wound stiffness gradient across the whole wound bed predicated pattern of hair formation. Using bulk and single-cell RNA-seq analysis and K14-Cre-Twist1 transgenic mice, we identified the central role of the Twist1 pathway as the mediator of epidermal-dermal interaction and the emergence of periodic hair primordia. Lastly, we generated a Turing model with an underlying measure of stiffness to support a two-scale tissue mechanic model to explain the setup of a morphogenetic field from a wound bed (mm scale) or periodically arranged hair primordia from a morphogenetic field (μm scale). Delineating the common and distinct chemo-mechanical events during regenerative wound healing between laboratory and African spiny mice reveal its evo-devo advantages, which provide new perspectives for regenerative medicine.

overall_design: Single-cell mRNA sequencing for back skin from naïve mice using Drop-Seq

first: Hans

middle: I


title: Kruppel-like factor 2+ CD4 T cells avert microbiota induced intestinal inflammation [Fluidgm]

first: Sing Sing

last: Way

address: 3333 Burnet Avenue, MLC 7017

institute: Cincinnati Children's

summary: Commensal immune tolerance requires cells that actively sense and suppress inflammation.  To understand how commensal tolerance works, mice colonized with recombinant Candida albicans expressing model MHC II peptide 2W1S were used to track CD4 cells with surrogate commensal specificity by tetramer staining and enrichement. Interestingly, half of the commensal CD4 cell lack expression of established T helper lineage defining transcription markers after intranuclear staining and flow cytometry. To more comprehensively investigate commensal cells, FACS sorted commensal CD4 cells with commensal specificity were analysed individually using single cell RNA sequencing.

overall_design: 2W1S-specific CD4 cells from secondary lymphoid organ among mice colonized with recombinant Candida albicans expressing 2W1S model antigen were FACS pruifed, and subjected to single cell RNA sequecing using the Fluidigm platform.

first: Tony

last: Jiang

first: Ty

last: Troutman

first: Tzu-Yu

last: Shao

first: Sing


title: Kruppel-like factor 2+ CD4 T cells avert microbiota induced intestinal inflammation


title: C5aR2 regulates STING-mediated interferon beta production in human macrophages

city: Cardiff

first: Van Dien

last: Nguyen

address: Heath Park

department: School of Medicine

institute: Cardiff University

summary: The complement system mediates diverse regulatory effects across the immune system. C5aR2, an enigmatic receptor for anaphylatoxin C5a, has been shown to modulate PRR-dependent pro-inflammatory cytokine secretion in human macrophages. However, the specific downstream targets and underlying molecular mechanisms are less defined. In this study, CRISPR-Cas9 was used to generate macrophage models lacking C5aR2, which were used to probe the role of C5aR2 in the context of PRR stimulation. cGAS and STING-induced IFN-β secretion was significantly increased in C5aR2 KO THP-1 cells and C5aR2-edited primary human monocyte-derived macrophages, and expression of STING and IRF3 was increased in C5aR2 KO cell lines, implicating C5aR2 as a regulator of the IFN-β response to cGAS-STING pathway activation. Transcriptomic analysis by RNAseq revealed that nucleic acid sensing and antiviral signalling pathways were significantly up-regulated in C5aR2 KO THP-1 cell lines. These results suggest that C5aR2 is a negative regulator of nucleic acid sensing in macrophages, with potential relevance for viral infection and anti-tumour immunity.

overall_design: PMA-differentiated THP-1 cells (WT, C5aR1 KO or C5aR2 KO) in 75 cm2 flasks were stimulated with culture medium containing 5 µg/mL cAIM(PS)2 Difluor (Rp/Sp), 50 ng/mL C5a or vehicle for 6 hours. Supernatants were harvested for IFN-β ELISA to confirm response to stimulation as a quality control, cells were washed twice with PBS then harvested using TrypLE Express Enzyme. Cells were centrifuged at 300 x g for 5 minutes, the supernatant was removed and the cells were snap-frozen on dry ice. RNASeq was performed by GENEWIZ, comprising total RNA isolation, library preparation with poly(A) selection and 150 bp paired-end sequencing using an HiSeq 2500 (Illumina)

first: Lee

last: Booty

first: You

last: Zhou

first: Van


title: Topoisomerase 1 facilitates nucleosome reassembly at stress genes during recovery.

first: Montserrat

last: Vega


title: Targeting Neutrophil Elastase in murine breast cancer tumors

status: Public on Oct 21 2023

first: Khandan

last: Keyomarsi

state: Texas

address: 1515 Holcombe Blvd

department: Experimental Radiation Onc

institute: University of Texas - MD Anderson Cancer Center

summary:
To investigate the function of neutrophil elastase in breast cancer metastasis, as a function of time
We then performed gene expression profiling analysis using data obtained from PyMT tumors (N=5 each) that are either WT or knockout for Neutrophil Elastase i.e. NEKO.

overall_design: 5 PyMT tumors each were collected from WT and NEKO mice at 12-14 weeks of age, which is endpoint for these mice and the stage when metastasis has already occurred.

first: Keyomarsi

last: Khandan

first: Lulla

last: Amriti


title: IL-10-expressing CAR T cells resist dysfunction and mediate durable clearance of solid tumors and metastases

status: Public on Oct 20 2023

city: Stanford

first: Yang

last: Zhao

address: Beckman B169B, 279 Campus Drive

department: MCP

institute: Stanford University

summary: We used single-cell sequencing to compare gene expression and cell subset distribution of conventional CAR-T cells and IL-10-expressing CAR-T cells in the spleen and tumors.

overall_design: In a murine tumor model, we sorted HER2 CAR-T cells and IL-10 HER2 CAR-T cells in tumors and spleens at day 18 post-tumor inoculation. The groups were as follows: G1 - HER2 CAR-T cells in tumors, G2 - IL-10 expressing HER2 CAR-T cells in tumors, and G3 - IL-10 expressing HER2 CAR-T cells in the spleen.

first: Li

last: Tang


title: Interactome between ASFV and host immune pathway proteins

city: Wuhan

first: Yingying

last: Lei

state: China

address: NO. 1 shizishan Street, Hongshan District

institute: Huazhong Agricultural University

summary: To systematically delineate the Protein–Protein Interaction (PPI) network between ASFV and host immune pathway proteins, and ASFV-ASFV PPI, we used the recombination-based library vs library high-throughput yeast two-hybrid (RLL-Y2H) screening system.

overall_design: We used RLLNP (https://github.com/thxie/RLLNP) to obtain the protein interaction information

first: Jinxia

last: Dai

first: Gang

last: Cao

first: Qijun

last: Wu

first: Ya

last: Zuo


title: Transfer RNA pools in human cells are controlled by selective gene expression [RNA-seq]

first: Danny

last: Nedialkova

first: Lexi

last: Gao

first: Andrew

last: Behrens

first: Geraldine

last: Rodschinka

first: Sergio

last: Forcelloni

first: Sascha

last: Wani

first: Katrin

last: Strasser


title: Competition for H2A.Z underlies the developmental impacts of repetitive element de-repression

first: Fanju

last: Meng

overall_design: Refer to individual Series


title: Kruppel-like factor 2+ CD4 T cells avert microbiota induced intestinal inflammation [RNA-seq]

first: Sing Sing

last: Way

department: Pediatrics

summary: Commensal immune tolerance requires cells that actively sense and suppress inflammation. Here we show this is in large part mediated by CD4 cells that express the transcriptional regulator KLF2. Suppression by KLF2+ CD4 cells requires cell-intrinsic TCR stimulation. To investigate how KLF2 CD4 cells perform this role, gene expression by purified KLF2+ compared with KLF2-negative CD4 cells were evaluated with TCR stimulation in vitro and control non-stimulated cells.

overall_design: Splenocytes were harvested from KLF2(GFP) FOXP3(RFP) dual reporter mice, and sort purification for FOXP3-negative KLF2+ CD44hi compared with FOXP3-negative KLF2-negative  CD44hi cells. Sort purified cells were stimulated with anti-CD3 (2.5 micrograms/mL) plus anti-CD28 antibody (1.25 micrograms/mL ) compared with no stimulation controls for 48 hours prior to RNA harvest.

first: David

last: Haslam

first: Ty

last: Troutman

first: Tzu-Yu

last: Shao

first: Sing


title: The ncBAF complex regulates transcription in AML through H3K27ac sensing by BRD9 (CUT&Run)

city: Pittsburgh

last: Klein

state: PA

address: 4249 Fifth Ave

department: Biological Sciences

institute: University of Pittsburgh

summary: The non-canonical BAF complex (ncBAF) subunit BRD9 is essential for acute myeloid leukemia (AML) cell viability but has an unclear role in leukemogenesis. Because BRD9 is required for ncBAF complex assembly through its DUF3512 domain, precise bromodomain inhibition is necessary to parse the role of BRD9 as a transcriptional regulator from that of a scaffolding protein. To understand the specific role of BRD9 bromodomain function in regulating AML, we selected a panel of five AML cell lines with distinct driver mutations, disease classifications, and genomic aberrations and subjected them to short-term BRD9 bromodomain inhibition. We characterized the bromodomain-dependent growth of these cell lines, identifying a dependency in AML cell lines but not HEK293T cells. To define a mechanism through which BRD9 maintains AML cell survival, we examined nascent transcription, chromatin accessibility, and ncBAF complex binding genome-wide after bromodomain inhibition. We identified extensive regulation of transcription by BRD9 bromodomain activity, including repression of myeloid maturation factors and tumor suppressor genes, while standard AML chemotherapy targets (Bcl2, Btk, Kit) were repressed by inhibition of the BRD9 bromodomain. BRD9 bromodomain activity maintained accessible chromatin at both gene promoters and gene-distal putative enhancer regions, in a manner that qualitatively correlated with enrichment of BRD9 binding. Furthermore, we identified reduced chromatin accessibility at GATA, ETS, and AP-1 motifs and increased chromatin accessibility at SNAIL-, HIC-, and TP53-recognized motifs after BRD9 inhibition. We interpret these data as signifying a role for BRD9 in regulating the differentiation block that is common to all AML subtypes through modulation of accessibility at hematopoietic transcription factor binding sites.

overall_design: Genomic profiling (CUT&RUN) samples, treated for 6 hours with either the BRD9 bromodomain inhibitor I-BRD9 or vehicle control (DMSO). Five different AML cell lines are profiled in duplicate (Kasumi-1, KG-1, ML-1, MV-4-11, and U937).

first: Santana

middle: M

last: Lardo

first: Sarah

last: Hainer


title: Stem cell technology provides novel tools to understand the impact of human variation on malaria

city: Kilifi

first: Abdirahman

last: Abdi

state: Not US or Canada

address: Mombasa-Malindi Road

department: Bioscience

country: Kenya

institute: KEMRI-Wellcome Trust Research Programme

summary: Plasmodium falciparum parasites have a complex life cycle, but the most clinically relevant stage of the disease is the invasion of erythrocytes and the proliferation of the parasite in the blood. The influence of human genetic traits on malaria has been known for a long time, however understanding the role of the proteins involved is hampered by the anuclear nature of erythrocytes that makes them inaccessible to genetic tools. Here we overcome this limitation with a differentiation protocol to derive erythroid cells in vitro from a diversity of human stem cells and an adaptation of flow cytometry to detect hemozoin. We combine this strategy with genome editing to show that deletion of basigin ablates invasion while deletion of ATP2B4 has a minor effect and that erythroid cells from reprogrammed patient-derived HbBart αthalassemia samples poorly support infection. This approach offers vast potential for understanding the impact human polymorphisms on malaria.

overall_design: Three replicates per differentiation stage

first: Alena

last: Pance

first: Bee

last: Ng

first: Kioko

last: Mwikali

first: Manousos

last: Koutsourakis

first: Chukuma

last: Agu

first: Foad

last: Rouhani

first: Ruddy

last: Montandon

first: Frances

last: Law

first: Hannes

last: Ponstingl

first: Julian

last: Rayner


title: ZNF524 directly binds telomeres and supports their integrity via TRF2/RAP1

city: Singapore

first: Dennis

last: Kappei

address: 14 Medical Drive, #11-01 (Bench 11), Centre for Translational Medicine

department: Cancer Science Institute of Singapore

country: Singapore

institute: National University of Singapore

summary: Telomeres are nucleoprotein structures at the ends of linear chromosomes. In humans, they consist of TTAGGG repeats, which are bound by dedicated proteins such as the shelterin complex. This complex blocks unwanted DNA damage repair at telomeres, e.g. by suppressing non-homologous end joining (NHEJ) through its subunit TRF2. We here describe ZNF524, a zinc finger protein that directly binds telomeric repeats with nanomolar affinity and reveal the base-specific sequence recognition by co-crystallization with telomeric DNA. ZNF524 localizes to telomeres in vivo, as shown among other approaches by ChIP-seq analysis, and specifically maintains the presence of the TRF2/RAP1 subcomplex at telomeres without affecting the other shelterin members. Loss of ZNF524 concomitantly results in an increase in DNA damage signaling and recombination events. Overall, ZNF524 is a direct telomere-binding protein involved in the maintenance of telomere integrity.

overall_design: U2OS stable cell lines carrying ZNF524 WT-GFP ZNF524 ZF2 mutant-GFP or NLS-GFP were generated by lentiviral transduction followed by antibiotic selection and FACS sorting using the doxycycline-inducible pLIX_403 plasmid (Addgene #41395). Cells were seeded in medium supplemented with 300 ng/mL doxycycline 48h prior to the experiment to induce expression. GFP-Trap magnetic agarose beads (Chromotek) were used in these ChIP-seq reactions that were carried out in triplicates.

first: D

first: F

last: Butter

first: H

last: Braun

first: V

last: Khanchandani

first: A

last: Hillairet


title: Topoisomerase 1 facilitates nucleosome reassembly at stress genes during recovery [Mnase-seq]

first: Montserrat

last: Vega

overall_design: Nucleosome profiling using MNAse-seq obtained from a wild-type and a top1 deleted strain under untreated conditions and after 2, 5 and 15 minutes of 1mM peroxide treatment

first: Rodrigo

last: Fraile

first: Kevin

last: de Castro Cogle

first: David

last: Castillo

first: Roger

last: Anglada

first: Ferran

last: Casals

first: José

last: Ayté

first: Ernesto

last: Lowy-Gallego

first: Elena

last: Hidalgo


title: The ncBAF complex regulates transcription in AML through H3K27ac sensing by BRD9 (TT-Seq)

last: Klein

overall_design: Nascent RNA-seq (TT-seq) samples, treated for 6 hours with either the BRD9 bromodomain inhibitor  I-BRD9 or vehicle control (DMSO). Five different AML cell lines are profiled in duplicate (Kasumi-1, KG-1, ML-1, MV-4-11, and U937).

first: Santana

last: Lardo

first: Sarah

last: Hainer


title: The ncBAF complex regulates transcription in AML through H3K27ac sensing by BRD9 (ATAC-Seq)

summary: The non-canonical BAF complex (ncBAF) subunit BRD9 is essential for acute myeloid leukemia (AML) cell viability but has an unclear role in leukemogenesis. Because BRD9 is required for ncBAF complex assembly through its DUF3512 domain, precise bromodomain inhibition is necessary to parse the role of BRD9 as a transcriptional regulator from that of a scaffolding protein. To understand the specific role of BRD9 bromodomain function in regulating AML, we selected a panel of five AML cell lines with distinct driver mutations, disease classifications, and genomic aberrations and subjected them to short-term BRD9 bromodomain inhibition. We characterized the bromodomain-dependent growth of these cell lines, identifying a dependency in AML cell lines but not HEK293T cells. To define a mechanism through which BRD9 maintains AML cell survival, we examined nascent transcription, chromatin accessibility, and ncBAF complex binding genome-wide after bromodomain inhibition. We identified extensive regulation of transcription by BRD9 bromodomain activity, including ATACseq_Repression of myeloid maturation factors and tumor suppressor genes, while standard AML chemotherapy targets (Bcl2, Btk, Kit) were ATACseq_Repressed by inhibition of the BRD9 bromodomain. BRD9 bromodomain activity maintained accessible chromatin at both gene promoters and gene-distal putative enhancer regions, in a manner that qualitatively correlated with enrichment of BRD9 binding. Furthermore, we identified reduced chromatin accessibility at GATA, ETS, and AP-1 motifs and increased chromatin accessibility at SNAIL-, HIC-, and TP53-recognized motifs after BRD9 inhibition. We interpret these data as signifying a role for BRD9 in regulating the differentiation block that is common to all AML subtypes through modulation of accessibility at hematopoietic transcription factor binding sites.

overall_design: ATAC-seq samples, treated for 6 hours with either the BRD9 bromodomain inhibitor  I-BRD9 or vehicle control (DMSO). Five different AML cell lines are profiled in duplicate (Kasumi-1, KG-1, ML-1, MV-4-11, and U937).


title: Transcriptomic approach reveals splicing dysregulation in spinocerebellar ataxia type 1

city: New Haven

first: Evrett

middle: Nathanial

last: Thompson

address: 333 Cedar Street

department: Cell Biology

institute: Yale School of Medicine

summary: Spinocerebellar ataxia type 1 (SCA1) is caused by a polyglutamine expansion in the ATXN1 gene leading to an expanded polyglutamine tract in the ATAXIN-1 protein. Ataxin-1 is broadly expressed throughout the brain and is known to be involved in regulating gene expression; however, it is not yet determined if mutant ataxin-1 regulates alternative splicing events. Utilizing SCA1 mouse models, we performed bulk RNA sequencing and looked for misregulated alternative splicing (mAS) events in SCA1 mouse cerebella. We found that mutant ataxin-1 causes mAS events to occur in the SCA1 mouse cerebella. Furthermore, we showed that abnormal splicing events predominantly occur in cell types that express mutant ataxin-1. Less than 25% of the mAS events were also differentially expressed genes (DEGs) and therefore their transcriptional dysregulation was previously unknown in the context of SCA1. We show through gene ontology analysis that mAS events reveal new biological pathways: mAS events showed changes in structural morphogenesis whereas DEGs showed changes in ion channel and transmembrane transport. We also report that mutant ataxin-1 causes dysregulation of expression of other ataxia-causing genes, providing evidence for molecular basis of clinical similarity among otherwise heterogeneous inherited cerebellar ataxias. We also identified the potential mechanism by which mutant ATXN1 causes mAS through its interaction with RBFOX1.

overall_design: Comparative transcriptomic analysis of RNA-seq data for mouse cerebella extracted from WT FVB/NJ and Atxn1-82Q transgenic FVB/NJ mice. Samples were collected from 5-, 12-, 20-, and 52-week old mice with four biological replicates collected from 5-week old and three biological replicates collected from 12-, 20-, and 52-week old mice.

first: Victor

last: Olmos

middle: N

first: Neha

last: Gogia

first: Kimberly

last: Luttik

first: Vaishnavi

last: Veeranki

first: Luhan

last: Ni

first: Serena

last: Sim

first: Kelly

last: Chen

first: Janghoo

last: Lim


title: Aiolos modulates IL-15 responsiveness of intestinal intraepithelial lymphocytes [CUT&RUN]

city: St. Louis

first: Marco

last: Colonna

address: 425 S. Euclid

department: Pathology and Immunology

institute: Washington University in St. Louis

summary: Intestinal intraepithelial lymphocytes (IEL) are capable of rapid innate-like responses to microenvironmental cues. While poised to activation, IEL effector functions must be stringently controlled. Aiolos is an Ikaros zinc finger (IKZF) family member encoded by Ikzf3 that promotes histone deacetylation. Here, we found that Aiolos is a crucial regulator of IEL activation. Ikzf3–/– CD8αα+ IEL expressed high levels of innate NK receptors, cytotoxic enzymes, cytokines and chemokines. Single cell RNAseq of IEL revealed that Ikzf3 deficiency mostly amplified the effector machinery of a CD8αα+ IEL subset characterized by high expression CD122, the receptor for IL-15. Furthermore, Ikzf3 deficiency increased IEL responsiveness to IL-15. Aiolos binding sites were close to  those for STAT5 and RUNX transcription factors that promote IL-15 signaling and cytolytic programs, respectively; lack of Ikzf3 increased accessibility and histone acetylation of these chromatin regions. Ikzf3 deficiency increased susceptibility to colitis, demonstrating the functional relevance of Aiolos-mediated regulation of IEL effector functions.

overall_design: gd IEL and DN IEL from Aiolos-deficient and control mice were used for CUT&RUN-seq for Aiolos.

first: Kentaro

last: Yomogida


title: Aiolos modulates IL-15 responsiveness of intestinal intraepithelial lymphocytes

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


title: Aiolos modulates IL-15 responsiveness of intestinal intraepithelial lymphocytes [RNA-seq]

overall_design: gd IEL and DN IEL from Aiolos-deficient and control mice were used.