title: Identification of putative encoding smORF genes in drosophila imaginal discs

city: Berlin

first: Benedikt

last: Obermayer

address: Chariteplatz 1

department: Core Unit Bioinformatics

institute: Berlin Institute of Health

summary: We aim to identify the genes that encode for putatives smORF peptides in imaginal leg disc at larval and pupal stages

overall_design: RNA sequencing of imaginal leg discs at wandering larval stage 3 (wL3) and 2 hours after pupal formation (2h APF)

first: Damien

last: Markus

first: Aurore

last: Pelletier

first: Muriel

last: Boube

first: Fillip

last: Port

first: Michael

last: Boutros

first: François

last: Payre

first: Jennifer

last: Zanet


title: Joint single-cell transcriptomics and epigenomics analysis reveal key regulators of CAR T cell stemness and antitumor immunity

status: Public on Oct 09 2023

city: Dallas

first: Chen

last: Yao

state: Texas

address: 5901 FOREST PARK RD, NS6 218

country: USA

institute: UT Southwestern Medical Center

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

summary: In this study, we revealed the molecular network governing the differentiation of CAR T cells into transcriptionally and epigenetically distinct subsets. Using two mouse cancer models with different sensitivities to CAR T-cell therapy, we showed that CD8+ CAR T cells transitioned from the stem-like to effector-like subset in B-cell ALL but developed into exhausted T cells in the solid tumor. By simultaneously profiling transcriptomic and epigenomic analyses in single cells, we demonstrated that lineage-defining TFs were often controlled by exceptionally high numbers of cis-regulatory elements and regulated distinct chromatin states foreshadowing transcriptional changes during T cell differentiation. Different CAR T-cell subsets were governed by distinct gene regulatory networks with TFs as hubs. We showed that FOXP1 was a hub TF in the stem-like network and promoted the antitumor response and stemness of CAR T cells while limiting their transition to the effector-like subset. In contrast, KLF2, a hub TF in the effector-like network, controlled the lineage choice between effector-like and exhausted subsets by driving the effector program and suppressing the exhaustion program.

overall_design: CAR T cells isolated from spleen, bone marrow or tumor were sorted for scRNA-Seq or multiome anallysis.

first: Tuoqi

last: Wu

first: Ziang

last: Zhu

first: Guohua

last: Lou


title: The cell-nonautonomous function of ID1 supports AML progression from the microenvironment via ANGPLT7

status: Public on Oct 04 2023

city: Shanghai

first: Jiaying

last: Zhang

state: Shanghai

address: 320 Yue Yang Road

department: CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health

country: China

institute: Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences

summary: Bone marrow microenvironment (BMM) can maintain and regulate HSC and LSC via secreted components or direct interaction. Increasing evidence indicates that dissecting and targeting BMM-driven mechanisms of LSC might provide key adjuvant therapies to eradicate leukemia. ID1, a key transcriptional regulator in LSC previously identified by us, controls cytokine/chemokine production in the BMM, but the role of ID1 in AML-BMM remains obscure. Here, we report that ID1 is highly expressed in AML-BMM, especially in bone marrow mesenchymal stem cell (BMSC), and deletion of Id1 in BMM resulted in impaired AML progression in AML mouse model. Mechanistically, we found that Id1 deficiency markedly reduced the protein level of SP1 in mesenchymal cells co-cultured with AML cells. Through Id1-interactome analysis, we discovered Id1 interacts with Rnf4, the ubiquitin E3 ligase, and led to decreased Sp1 degradation. Disrupting ID1-RNF4 interaction by truncates in mesenchymal cells significantly decreased SP1 protein level and retarded the AML cell proliferation. We identified the target of Sp1, Angptl7, was the primary differentially expression protein factor in Id1-/- bone marrow supernatant fluid (BMSF) to regulate AML progression in mice. Taken together, our study highlights the critical role of ID1 in AML-BMM and assists development of diagnostic/therapeutic strategies for AML.

overall_design: To evaluate the non-cell-autonomous function of Id1 on LICs in vivo, we employed an AML1-ETO9a(AE9a)/MLL-AF9 driven AML mouse transplantation model. After 6 weeks transplantation, Id1+/+ and Id1-/- mouse BMSC were harvested and cultured in a-MEM supplemented with 10% FBS. After the adherent MSCs are seen under the microscope, the total RNA is extracted. RNA-seq library prepared and sequenced by novogene, Beijing, China.

first: Ming-Yue

last: Fei

first: Yong

last: Wang

first: Bin-He

last: Chang

first: Lan


title: A genetically engineered mouse model of NUT carcinoma

city: Boston

first: Chris

last: French

state: MA

address: 77 avenue louis Pasteur, NRB 652

department: Pathology

institute: Brigham and Women's Hospital

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: COX17 acetylation via MOF-KANSL complex promotes mitochondrial integrity and function

city: Freiburg

first: Asifa

last: Akhtar

address: Stuebeweg 51

department: Chromatin Regulation

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

summary: Reversible acetylation of mitochondrial proteins is a regulatory mechanism central to adaptive metabolic responses. Yet, how such functionally relevant protein acetylation is achieved remains unexplored. Here, we reveal an unprecedented role of the MYST family lysine acetyltransferase MOF in energy metabolism via mitochondrial protein acetylation. Loss of MOF-KANSL complex members led to mitochondrial defects including fragmentation, reduced cristae density and impaired mitochondrial electron transport chain (mtETC) complex IV (CIV) integrity in primary mouse embryonic fibroblasts. We demonstrate COX17, a CIV assembly factor, as a bona fide acetylation target of MOF. Loss of COX17 or expression of its non-acetylatable mutant phenocopied the mitochondrial defects observed upon MOF depletion. The acetylation-mimetic COX17 rescues these defects and maintains CIV activity even in the absence of MOF, suggesting an activatory role of mtETC protein acetylation. Fibroblasts from MOF syndrome patients with intellectual disability also revealed respiratory defects that could be restored by alternative oxidase, acetylation-mimetic COX17 or mitochondrially targeted MOF. Overall, our findings highlight the critical role of MOF-KANSL complex in mitochondrial physiology and provide new insights into MOF syndrome.

overall_design: We generated total RNA-Seq profiles of primary MEFs grown in glucose or galactose medium to investigate the impact of MOF depletion on expression of MitoCarta genes. Furthermore, we analyzed the effect of heterozygous point mutations in MOF on its function as an epigenetic regulator in primary HDFs.

first: Sukanya

last: Guhathakurta

first: Niyazi

middle: U

last: Erdogdu


title: The Tbx20-TLE Interaction is Essential for the Maintenance of the Second Heart Field

status: Public on Oct 03 2023

city: Chapel Hill

first: Whitney

last: Edwards

state: NC

address: 133 North Medical Drive

department: Biology

institute: University of North Carolina Chapel Hill

summary: T-box transcription factor 20 (Tbx20) plays a multifaceted role in cardiac morphogenesis and controls a broad gene regulatory network. However, the mechanism by which Tbx20 activates and represses target genes in a tissue-specific and temporal manner remains unclear. Studies show that Tbx20 directly interacts with the Transducin-like Enhancer of Split (TLE) family of proteins to mediate transcriptional repression. However, a function for the Tbx20-TLE transcriptional repression complex during heart development has yet to be established. We created a mouse model with a two-amino acid substitution in the Tbx20 EH1 domain, thereby disrupting the Tbx20-TLE interaction. Disruption of this interaction impaired critical morphogenic events, including cardiac looping and chamber formation. Transcriptional profiling of Tbx20EH1Mut hearts and analysis of putative direct targets revealed misexpression of the retinoic acid pathway and cardiac progenitor genes. Further, we show that altered cardiac progenitor development and function contribute to the severe cardiac defects in our model. Our studies indicate that TLE-mediated repression is a primary mechanism by which Tbx20 controls gene expression.

overall_design: To investigate the role of the Tbx20/TLE repressive complex in heart development, we generated a mouse model with a two amino acid substitution in the Tbx20 engrailed homology domain (Tbx20EH1Mut). We then performed RNA-seq analysis on wild-type and Tbx20EH1Mut hearts at embryonic day 9.5.

first: Frank

last: Conlon


title: Chromosome-specific maturation of the epigenome in the Drosophila male germline

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

summary: Spermatogenesis in the Drosophila male germline proceeds through a unique transcriptional program controlled both by germline-specific transcription factors and by testis-specific versions of core transcriptional machinery. This program includes the activation of genes on the heterochromatic Y chromosome, and reduced transcription from the X chromosome, but how expression from these sex chromosomes is regulated has not been defined. To resolve this, we profiled active chromatin features in the testes from wildtype and meiotic arrest mutants and integrate this with single-cell gene expression data from the Fly Cell Atlas. These data assign the timing of promoter activation for genes with germline-enriched expression throughout spermatogenesis, and general alterations of promoter regulation in germline cells. By profiling both active RNA polymerase II and histone modifications in isolated spermatocytes, we detail widespread patterns associated with regulation of the sex chromosomes. Our results demonstrate that the X chromosome is not enriched for silencing histone modifications, implying that sex chromosome inactivation does not occur in Drosophila. Instead, a lack of dosage compensation in spermatocytes accounts for the reduced expression from this chromosome. Finally, profiling uncovers dramatic ubiquitinylation of histone H2A and lysine-16 acetylation of histone H4 across the Y chromosome in spermatocytes that may contribute to the activation of this heterochromatic chromosome.

overall_design: We used Cleavage under targets and Tagmentation (Cut-and-Tag), a chromatin profiling strategy in which antibody-targeted controlled integration of DNA sequencing adapters produces libraries for paired-end DNA sequencing.

first: James

last: Anderson

first: Steven

first: Kami

last: Ahmad


title: An essential role for miR-15/16 in Treg suppression and restriction of proliferation

city: San Francisco

first: K. Mark

last: Ansel

state: CA

address: 513 Parnassus Ave. UCSF Box 0414

department: Microbiology & Immunology

institute: UCSF

summary: The miR-15/16 family is a highly expressed group of tumor suppressor miRNAs that target a large network of genes in T cells to restrict their cell cycle, memory formation and survival. Upon T cell activation, miR-15/16 are downregulated, allowing rapid expansion of differentiated effector T cells to mediate a sustained immune response. Here, using conditional deletion of miR-15/16 in immunosuppressive regulatory T cells (Tregs) that express FOXP3, we identify new functions of the miR-15/16 family in T cell immunity. miR-15/16 are indispensable to maintain peripheral tolerance by securing efficient suppression by a limited number of Tregs. miR-15/16-deficiency alters Treg expression of critical functional proteins including FOXP3, IL2Rα/CD25, CTLA4, PD-1 and IL7Rα/CD127, and results in accumulation of functionally impaired FOXP3loCD25loCD127hi Tregs. Excessive proliferation in the absence of miR-15/16 inhibition of cell cycle programs shifts Treg diversity and produces an effector Treg phenotype characterized by low expression of TCF1, CD25 and CD62L, and high expression of CD44. These Tregs fail to control immune activation of CD4+ effector T cells, leading to spontaneous multi-organ inflammation and increased allergic airway inflammation in a mouse model of asthma. Together, our results demonstrate that miR-15/16 expression in Tregs is essential to maintain immune tolerance.

overall_design: Live CD4+FOXP3+ Tregs (bulk cKO, bulk WT and WT CD25hi and CD25lo bin) were isolated from murine spleen and lymph nodes by FACS. cKO Tregs refer to miR-15/16 deficient Tregs. Samples are biological replicates of 2-5 mice per group.

first: Kristina

last: Johansson

first: K

middle: M


title: Integrative analysis reveals a conserved role for the amyloid precursor protein in proteostasis during aging

city: Frederick

first: Anthony

last: Cicalo

state: MD

address: 8400 Research Plaza

department: Neurology

institute: NMRC BDRD

summary: Aβ peptides derived from the amyloid precursor protein (APP) have been strongly implicated in the pathogenesis of Alzheimer’s disease. However, the normal function of APP and the importance of that role in neurodegenerative disease is less clear. We recovered the Drosophila ortholog of APP, Appl, in an unbiased forward genetic screen for neurodegeneration mutants. We performed comprehensive single cell transcriptional and proteomic studies of Appl mutant flies to investigate Appl function in the aging brain.

overall_design: Control and  Appl deleted fly brains were dissociated, cells were isolated and analyzed using scRNAseq.

first: Vanitha

last: Nithianandam

first: Mel

middle: B

last: Feany


title: Spatial extracellular vesicle microRNA profiles in ID8-T6 cells bearing mice

city: Nagoya

first: Kosuke

last: Yoshida

state: Aichi

address: 65 Tsuruma-cho

country: Japan

institute: Nagoya University

type: Non-coding RNA profiling by high throughput sequencing

summary: We newly invented the EV sheet, which is a unique nanofiber paper to capture extracellular vesicles from around 10 uL of bio-fluids. In this study, we investigated miRNA profiles of ID8-T6 cells bearing mice.

overall_design: We attached the EV sheet to the moistened organs to collect a tiny amount of ascites. Total RNA was extracted from the EV sheet, and small RNA libraries were prepared. Finally, a single-end sequence was performed. Similarly, tissue miRNA profiles were obtained.

first: Akira

last: Yokoi

first: Takao

last: Yasui

first: Masami

last: Kitagawa


title: A genetically engineered mouse model of NUT carcinoma (CUT&RUN)

first: Chris

last: French

summary: We created a genetically engineered mouse model (GEMM) of NC that forms a Brd4-NUTM1 fusion gene upon tamoxifen-induction of Sox2-driven Cre. Two GEMM-derived cell lines were developed whose transcriptomic and epigenetic landscapes, characterized by RNAseq and CUT&RUN, show striking overlap with those of primary GEMM tumors. GEMM primary tumor and cell lines form very large H3K27ac-enriched super-enhancers that are unique to hNC, termed megadomains, that are invariably associated with key hNC-defining transcriptional oncogenic targets, Myc and Trp63.

overall_design:
Compartive epigenomic profiling analysis of cultured 311E and 317E GEMM-derived cell lines in duplicate, one fresh GEMM tumor sample, and two fresh normal gastric mucosa samples from SOX2-/-BRD4-NUTM1+/- control mice. The 311E cultured cells sampled for this study were treated with DMSO control, ABBV-075 (9nM), or taz (1uM).

Compartive epigenomic profiling analysis of cultured 311E GEMM-derived cell lines in duplicate. The 311E cultured cells sampled for this study were treated with DMSO control and ABBV-075 (9nM) for 96hrs.

first: R

middle: T

last: Durall

first: Julianna

last: Huang


title: Carbon dioxide regulates cholesterol levels through SREBP2

status: Public on Oct 06 2023

city: REHOVOT

first: NITYANAND

last: BOLSHETTE

address: HRZL STREET

department: Biomolecular sciences

country: Israel

institute: Weizmann Institute of sciences

summary: In mammals, O2 and CO2 levels are tightly regulated and are altered under various pathological conditions. While the molecular mechanisms that participate in O2 sensing are well characterized, little is known regarding the signaling pathways that participate in CO2 signaling and adaptation. Here, we show that CO2 levels control a distinct cellular transcriptional response that differs from mere pH changes. Unexpectedly, we discovered that CO2 regulates the expression of cholesterogenic genes in a SREBP2-dependent manner and modulates cellular cholesterol accumulation. Molecular dissection of the underlying mechanism suggests that CO2 triggers SREBP2 activation through changes in endoplasmic reticulum membrane cholesterol levels. Collectively, we propose that SREBP2 participates in CO2 signaling and that cellular cholesterol levels can be modulated by CO2 through SREBP2

overall_design: RNA-sequencing on mouse embryonic fibroblasts, treated with either low CO2  or NaOH for 0 h, 2 h and 4h.

first: Nityanand

last: Bolshette

first: Saar

last: Ezagouri

first: Marina

last: Golik

first: Gad

last: Asher


title: Differenatiation of mRNA expression  in METTL3-depleted macrophages

first: Xiao

last: Han

state: Select state...

address: 399 Wanyuan Rd, Minhang, Shanghai, China

institute: Children’s Hospital of Fudan University

summary: N6-methyladenosine (m6A), the most prevalent internal messenger RNA modification, plays critical roles in diverse biological processes. To characterize the potential involvement of METTL3 in macrophage function, transcriptome sequencing (RNA-seq) was performed in human THP1-derived macrophages with METTL3 depletion. We identified 266 genes that were differentially expressed in METTL3-depleted macrophages (≥ 1.5-fold change, P < 0.05), among which 44% (118 genes) were downregulated and 56% (148 genes) were upregulated. Notably, M2 macrophages activation-associated genes were robustly enhanced in METTL3-depleted macrophages. This study highlights the critical roles of m6A on regulation macrophages homeostasis.

overall_design: The mRNA profiles of  WT and METTL3-depleted macrophages under IL-4 stimulation. Three  independent experiments were performed at each treatment.

first: Wenfeng

last: Xiao


title: Prevalence of chromosomal alterations in first-trimester spontaneous pregnancy loss

status: Public on Oct 05 2023

city: Maastricht

first: Rick

last: Essers

state: Limburg

address: P. Debyelaan 25

department: Clinical Genetics

country: Netherlands

institute: Maastricht University Medical Centre (MUMC+)

type: Methylation profiling by genome tiling array

summary: Pregnancy loss is often caused by chromosomal abnormalities of the conceptus. The prevalence of these abnormalities and the allocation of (ab)normal cells in embryonic and placental lineages during intrauterine development remain elusive. We analyzed 1,745 spontaneous pregnancy losses and found that roughly half (50.4%) of the products of conception (POC) were karyotypically abnormal, with maternal and paternal age independently contributing to the increased genomic aberration rate in pregnancy loss. We applied genome haplarithmisis to a subset of 94 pregnancy losses with normal parental and POC karyotypes. Genotyping of parental DNA as well as POC extraembryonic mesoderm and chorionic villi DNA, representing embryonic and trophoblastic tissues, enabled characterization of the genomic landscape of both lineages. Of these pregnancy losses, 35.1% had chromosomal aberrations not previously detected by karyotyping, increasing the rate of aberrations of pregnancy losses to 67.8% by extrapolation. In contrast to viable pregnancies where mosaic chromosomal abnormalities are often restricted to chorionic villi, such as confined placental mosaicism, we found a higher degree of mosaic chromosomal imbalances in extraembryonic mesoderm rather than chorionic villi in pregnancy losses. Our results stress the importance of scrutinizing the full allelic architecture of genomic abnormalities in pregnancy loss to improve clinical management and basic research of this devastating condition.


title: S-SCAM is essential for synapse formation

status: Public on Oct 02 2023

city: Bordeaux

first: Julio

middle: Santos

last: Viotti

address: 146 Rue Léo Saignat

country: France

institute: Institute for Interdisciplinary Neuroscience (IINS)

summary: Synapse formation is critical for the wiring of neural circuits in the developing brain. The synaptic scaffolding protein S-SCAM/MAGI-2 has important roles in the assembly of signaling complexes at postsynaptic densities. However, the role of S-SCAM in establishing the entire synapse is not known. Here, we report significant effects of RNAi-induced S-SCAM knockdown on the number of synapses in early stages of network development in vitro. In vivo knockdown during the first three postnatal weeks reduced the number of dendritic spines in the rat brain neocortex. Knockdown of S-SCAM in cultured hippocampal neurons severely reduced the clustering of both pre- and postsynaptic components. This included synaptic vesicle proteins, pre- and postsynaptic scaffolding proteins, and cell adhesion molecules, suggesting that entire synapses fail to form. Correspondingly, functional and morphological characteristics of developing neurons were affected by reducing S-SCAM protein levels: neurons displayed severely impaired synaptic transmission and reduced dendritic arborization. A next generation sequencing approach showed normal expression of housekeeping genes, but changes of expression levels in 39 synaptic signaling molecules in cultured neurons. These results indicate that S-SCAM mediates the recruitment of all key classes of synaptic molecules during synapse assembly and is critical for the development of neural circuits in the developing brain.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for hippocampal neuronal cultures from rats (Rattus norvergicus) in wild-type condition and knock-down of S-SCAM.

first: Nina

last: Wittenmayer

first: Andonia

last: Petkova-Tuffy

first: Max

last: Borgmeyer

first: Chungku

last: Lee

first: Jürgen

last: Becker

first: Andreas

last: Böning

first: Sebastian

last: Kügler

first: JeongSeop

last: Rhee

middle: S

first: Thomas

last: Dresbach


title: Statistical learning quantifies transposable element-mediated cis-regulation

city: Lausanne

first: Julien

last: Duc

state: VAUD

address: Station 19 CH-1015 Lausanne

department: School of Life Science

country: Switzerland

institute: EPFL

summary: KLF4 and ZNF611 ChIP-seq when overexpressed in primed or in naive respectively

overall_design: ChIP-seq and ATAC-seq in Naive Human embryonic stem cells

first: Cyril

last: Pulver

last: Pontis


title: RNA sequence (RNA-seq) profiling of SynIX strain

city: New York

first: Jitong

last: Cai

state: NY

address: 435 E 30th street

department: NYU Langone Health

institute: NYU Langone Health

summary: We describe the complete synthesis, assembly, debugging and characterization of a synthetic 404,963 bp yeast chromosome, synIX. Combined chromosome construction methods were used to synthesize the left arm of synIX (synIXL) and retrofit previously described synIXR. During synIX strain characterization, we identified and resolved a bug related to EST3, a gene involved in telomerase function, producing a synIX strain with near wild-type fitness. To facilitate future synthetic chromosome consolidation and increase flexibility of chromosome transfer between distinct strains we combined chromoduction, a method to transfer a whole chromosome between two strains, with conditional centromere destabilization to substitute a chromosome of interest for its native counterpart. We found that both synIX transfer via chromoduction and wild-type IX destabilization were efficient methods. We observed that wild-type II tended to co-transfer with synIX and was co-destabilized with wild-type IX, suggesting a potential gene dosage compensation relationship between these two chromosomes.

overall_design: To assess the effects of synthetic genome design on gene expression levels, we performed  mRNA sequencing of SynIX strain yLHM1601 against wildtype strain BY4741 at 30C and 37C.

first: Laura

middle: H

last: McCulloch

first: Jef

middle: D

last: Boeke


title: Gene expression in macrophages from mice fed in Western diet

city: Barcelona

first: Antonio

last: Postigo

state: BARCELONA

address: Casanova 143. Cellex 1B

country: Spain

institute: IDIBAPS/ICREA

summary: The objective is identify new mechanism implicated in the response of macrophage to high-fat diet.

overall_design: Macrophages were isolated from the aorta of mice fed in western diet. The experiment was conduced in triplicate.

first: MC

last: Martinez-Campanario

first: Anna

last: Esteve-Codina


title: RNA-seq of Myeloproliferative neoplasms primary CD34+ HSPCs and cell lines after tamoxifen treatment

city: Cambridge

first: Irina

last: Mohorianu

address: Puddicombe Way

department: Wellcome-MRC Cambridge Stem Cell Institute

country: United Kingdom

institute: University of Cambridge


title: RNAseq of JAK2V617F-positive MPN cell lines after 4-Hydroxytamoxifen treatment

summary: Gene expression profile in HEL/UKE-1 cells after 4-hour 4-Hydroxytamoxifen treatment

overall_design: For RNA-Seq of JAK2V617F-mutated human cells lines, three cells lines (HEL cells, UKE-1 with and without Horse Serum, UKE-1+/-HS respectively) were treated with 10 μM tamoxifen or vehicle for 4 h and RNA was extracted from tamoxifen-treated cells by Trizol  and cleaned-up with RNeasy Mini Columns . RNA-Seq libraries were prepared from total RNA using poly(A) enrichment of the mRNA and sequenced by HiSeq 4000.

first: Zijian

last: Fang

first: Giuditta

middle: C

last: Fattori

last: McKerrell

first: Rebecca

last: Boucher

first: Aimee

last: Jackson

first: Rachel

last: Fletcher

first: Jose-Ezequiel

last: Martin

first: Sonia

last: Fox

first: James

last: Roberts

last: Glover

first: Erica

last: Harris

first: Luigi

last: Grassi

first: Alba

last: Rodriguez-Meira

first: Adam

middle: J

last: Mead

first: Steven

last: Knapper

first: Joanne

last: Ewing

first: Nauman

last: Butt

first: Manish

last: Jain

last: Francis

first: Fiona

last: Clark

first: Jason

last: Coppell

first: Mary

middle: F

last: McMullin

first: Frances

last: Wadelin

first: Srinivasan

last: Narayanan

first: Dragana

last: Milojkovic

first: Mark

middle: W

last: Drummond

first: Mallika

last: Sekhar

first: Maike

last: Paramor

first: E

last: Baxter

middle: L

last: Godfrey

first: Claire

middle: N

last: Harrison

first: Simón

last: Méndez-Ferrer


title: Human serous cavity macrophages and dendritic cells possess counterparts in the mouse with a distinct distribution between species

status: Public on Oct 17 2023

city: St Louis

first: Jichang

last: Han

state: MO

address: 4905 Children's PI

institute: Washington University in St Louis

summary: In mouse peritoneal and other serous cavities, the transcription factor Gata6 drives the identity of the major cavity resident population of macrophages, with a smaller subset of cavity-resident macrophages dependent on the transcription factor Irf4. Here we showed that GATA6+ macrophages in the human peritoneum were rare, regardless of age. Instead, more human peritoneal macrophages aligned with mouse CD206+ LYVE1+ cavity macrophages that represent a differentiation stage just preceding expression of Gata6. Low abundance of CD206+ macrophages was retained in C57BL/6J mice fed a high-fat diet or in wild-captured mice, suggesting that differences between serous cavity-resident macrophages in humans and mice were not environmental. Irf4-dependent mouse serous cavity macrophages aligned closely with human CD1c+CD14+CD64+ peritoneal cells that, in turn, resembled human peritoneal CD1c+CD14-CD64- cDC2. Thus, major populations of serous cavity-resident mononuclear phagocytes in humans and mice shared common features but the proportions of different macrophage differentiation stages greatly differ between the two species and DC2-like cells were especially prominent in humans.

overall_design:
Peritoneal wash was collected at the beginning of the procedure before it was affected by the surgical process. Patients recruited including those receiving laparoscopic surgeries including Roux-en-Y gastric bypass (RYGB) surgery, sleeve gastrectomy, gastrostomy tube placement, cholecystectomy, or inguinal hernia repair without any other clinical indication of peritoneal pathological conditions. Live CD45+ immune cells were sorted for sequencing
>>>Raw data are being deposited in dbGaP due to patient privacy concerns<<<

first: Alexandre

last: Gallerand

first: Emma

last: Erlich

first: Beth

middle: A

last: Helmink

first: Shaina

middle: R

last: Eckhouse

first: Francesca

last: Dimou

first: Baddr

last: Shakhsheer

first: Hannah

last: Phelps

first: Rachel

last: Mintz

first: Daniel

last: Lee

first: Emily

last: Onufer

last: Zhang

first: Gwendalyn

last: Randolph


title: Spatial extracellular vesicle microRNA profiles in ovarian cancer

first: Kosuke

last: Yoshida

summary: We newly invented the EV sheet, which is a unique nanofiber paper to capture extracellular vesicles from around 10 uL of bio-fluids. In this study, we investigated miRNA profiles of tumor-surface ascites, serum, and urine using the EV sheet.

overall_design: We attached the EV sheet to the moistened organs to collect a tiny amount of ascites. Moreover, the EV sheet was soaked in a tiny amount of ascites, serum, and urine. Then, total RNA was extracted from the EV sheet, and small RNA libraries were prepared. Finally, a single-end sequence was performed. Similarly, tissue miRNA profiles were obtained.

first: Akira

last: Yokoi

first: Takao

last: Yasui

first: Masami

last: Kitagawa


title: Depletion of tet2 results in age-dependent changes in DNA methylation and gene expression in a zebrafish model of myelodysplastic syndrome

status: Public on Oct 01 2023

city: Charlottesville

first: Francine

last: Garrett-Bakelman

state: Virginia

address: 1340 Jefferson Park Avenue , Pinn hall 6054

department: Department of Biochemistry and Molecular Genetics

institute: University of Virginia

type: Methylation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Glucocorticoid Receptor Action in Breast Cancer

city: Utrecht

first: Stefan

last: Prekovic

address: Universiteitsweg 100

department: CMM

institute: UMC Utrecht


title: Bulk RNAseq of  primary CD34+ HSPCs in Myeloproliferative neoplasms patients receiving tamoxifen

first: Irina

last: Mohorianu

summary: TAMARIN study is a Phase II, multicenter, single arm A’herns design clinical trial assessing tamoxifen’s safety and activity in reducing molecular markers of disease burden in MPN.The primary outcome (≥50% allele burden reduction at 24 weeks) was met by 3/37 patients; 5/37 additional patients showed ≥25% reductions. CD34+ HSPCs were collected from responders and non-respondersin the baseline line and 24W after tamoxifen treatment. RNAseq was performed to investigate the molecular signature about tamoxifen sensitivity and pharmacological mechanism of tamoxifen in MPN patients.

overall_design: Eligibility criteria included MPN patients aged ≥60 years, with eligible women being post-menopausal (defined as amenorrhoeic for at least 12 consecutive months following cessation of all exogenous hormonal treatments); confirmed diagnosis of JAK2-V617F, CALR 5bp insertion (exon 9), or CALR 52bp deletion (exon 9) positive ET, PV or MF (primary or secondary) for ≥ 6 months. Tamoxifen was provided at the common dose used in ER+ breast cancer (20 mg oral daily, progressively escalated to 40 mg daily upon good tolerance and when there was no hematological response or mutant allele burden reduction at 12w). All patients received trial treatment for 24 weeks. Treatment continuation was encouraged but not mandated after 24w for patients who did not experience persistent side effects greater than grade 1 or thrombotic events of any grade and that fulfilled one or more of the following criteria at 24 weeks: ≥25% reduction in allele burden compared to baseline; improvement of haematological response compared to baseline without changes in cytoreductive therapy dose according to 2009 ELN criteria for ET/PV patients and to IWG-MRT response criteria for MF patients; a decrease in requirement for cytoreduction without deterioration of haematological response compared to baseline according to 2009 ELN criteria for ET/PV patients and to IWG-MRT response criteria for MF patients. Their response was reassessed after 36 and 48 weeks of treatment as applicable.

first: Zijian

last: Fang

first: Giuditta

last: Fattori

first: Thomas

last: McKerrell

first: Rebecca

last: Boucher

first: Aimee

last: Jackson

last: Fletcher

first: Jose-Ezequiel

last: Martin

first: Sonia

last: Fox

first: James

last: Roberts

last: Glover

first: Erica

last: Harris

first: Luigi

last: Grassi

first: Alba

last: Rodriguez-Meira

first: Adam

last: Mead

first: Steven

last: Knapper

first: Joanne

last: Ewing

first: Nauman

last: Butt

first: Manish

last: Jain

first: Sebastian

last: Francis

first: Fiona

last: Clark

first: Jason

last: Coppell

first: Mary

last: McMullin

first: Frances

last: Wadelin

first: Srinivasan

last: Narayanan

first: Dragana

last: Milojkovic

first: Mark

last: Drummond

first: Mallika

last: Sekhar

first: Maike

last: Paramor

first: E

last: Baxter

first: Anna

last: Godfrey

first: Claire

last: Harrison

first: Simón

last: Méndez-Ferrer


title: Depletion of tet2 results in age-dependent changes in DNA methylation and gene expression in a zebrafish model of myelodysplastic syndrome [DNAmethylation]

first: Francine

last: Garrett-Bakelman

summary: Myelodysplastic Syndrome (MDS) is a heterogenous group of clonal hematopoietic disorders characterized by ineffective hematopoiesis, cytopenias and dysplasia. The gene encoding Ten-ele¬ven translocation 2 (TET2), a dioxygenase enzyme that catalyzes the conversion of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine, is a recurrently mutated tumor suppressor gene in MDS and other myeloid malignancies. Previously, we reported a stable zebrafish line with a loss-of-function mutation in the tet2 gene.  The tet2m/m mutant zebrafish developed a pre-MDS state with kidney marrow dysplasia but normal circulating blood counts by 11 months of age and accompanying anemia signifying the onset of MDS by 24 months of age. In the current study, we collected progenitor cells from the kidney marrows of the adult tet2m/m and tet2wt/wt fish at 4 and 15 months of age and performed enhanced reduced representation of bisulphite sequencing (ERRBS) and bulk RNA-seq to measure changes in DNA methylation and gene expression of HSPCs. A global increase in DNA methylation of gene promoter regions and CpG islands was observed in tet2m/m HSPCs at 4 months of age when compared to the wildtype. Further, hypermethylated genes were significantly enriched for targets of SUZ12 and MTF2 - involved in polycomb repressive complex 2 (PRC2). However, between 4 and 15 months of age, however, we observed a paradoxical global decrease in DNA methylation in tet2m/m HSPCs. Gene expression analysis identified upregulation of genes associated mTORC1 signaling and interferon gamma and alpha response in tet2m/m HSPCs at 4 months of age when compared to the wildtype. Downregulated genes in HSPCs of tet2 mutant fish at 4 months of age were enriched for cell cycle regulation, heme metabolism, and IL2/STAT5 signaling, possibly related to increased self-renewal and clonal advantage in HSPCs with tet2 loss of function. Finally, there was an overall inverse correlation between overall increased promoter methylation and gene expression.

overall_design: To understand the effect of tet2 loss on the genomic CpG methylation patterns  and gene expression patterns to identify potential molecular mechanisms that associate with clonal expansion of the progenitor cells and disease progression to myelodysplastic syndrome

first: Yaseswini

last: Neelamraju

first: Evisa

last: Gjini

first: Sagar

last: Chhangawala

first: Shuning

last: He

first: Ashley

last: Nguyen

first: Chang-Bin

last: Jing

first: Caroline

last: Sheridan

first: Yariv

last: Houvras

first: Ari

last: Melnick

first: Thomas

last: Look

last: Garret-Bakelman


title: Transcriptome analysis of Bacillus cereus strain INRA C3 in response to iron depletion and lactoferrin, accomplished by RNA sequencing

city: Hannover

first: Nadja

last: Jessberger

address: Bischofsholer Damm 15

department: Institute for Food Quality and Food Safety

institute: University of Veterinary Medicine Hannover, Foundation

summary: The iron-binding glycoprotein lactoferrin exhibits anti-bacterial activity. To investigate the overall response of Bacillus cereus to lactoferrin, total transcriptome analyses were performed. Growth conditions were mMOD minimal medium, minimal medium plus 10 mg/ml lactoferrin, as well as minimal medium without iron source for comparison. Differential regulation of genes involved in iron acquisition as well as genes encoding enterotoxins and further virulence factors was of special interest.

overall_design: For subsequent RNA sequencing, strain INRA C3 was grown for two hours in mMOD minimal medium, mMOD-Fe (without iron source) and mMOD supplemetned with 10 mg/ml lactoferrin. Two biological replicates were prepared per growth condition.

first: Clara-Sophie

last: Jugert

first: Andrea

last: Didier


title: Evolution of neuronal cell classes and types in the vertebrate retina [Tree_Shrew]

first: Joshua

middle: William

last: Hahn

address: 3747 W Stevens Wy NE

department: Department of Neurobiology & Biophysics

institute: University of Washington

summary: The basic plan of the retina is conserved across vertebrates, yet species differ profoundly in their visual needs (Baden et al., 2020). One might expect that retinal cell types evolved to accommodate these varied needs, but this has not been systematically studied. Here, we generated and integrated single-cell transcriptomic atlases of the retina from 17 species: humans, two non-human primates, four rodents, three ungulates, opossum, ferret, tree shrew, a teleost fish, a bird, a reptile and a lamprey. Molecular conservation of the six retinal cell classes (photoreceptors, horizontal cells, bipolar cells, amacrine cells, retinal ganglion cells [RGCs] and Müller glia) is striking, with transcriptomic differences across species correlated with evolutionary distance. Major subclasses are also conserved, whereas variation among types within classes or subclasses is more pronounced. However, an integrative analysis revealed that numerous types are shared across species based on conserved gene expression programs that likely trace back to the common ancestor of jawed vertebrates. The degree of variation among types increases from the outer retina (photoreceptors) to the inner retina (RGCs), suggesting that evolution acts preferentially to shape the retinal output. Finally, we identified mammalian orthologs of midget RGCs, which comprise >80% of RGCs in the human retina, subserve high-acuity vision, and were believed to be primate-specific (Berson, 2008); in contrast, the mouse orthologs comprise <2% of mouse RGCs. Projections both primate and mouse orthologous types are overrepresented in the thalamus, which supplies the primary visual cortex. We suggest that midget RGCs are not primate innovations, but descendants of evolutionarily ancient types that decreased in size and increased in number as primates evolved, thereby facilitating high visual acuity and increased cortical processing of visual information.

overall_design: Single nucleus RNA-seq was performed on nuclei isolated from frozen retina. Fluorescence-activated cell sorting was used to collect DAPI-positive nuclei. For some collections, DAPI+ nculei were further seprated using NEUN/RBFOX3 and/or CHX10/VSX2 expression as an strategy to enrich for RGCs and/or bipolar cells, respectively (PLease note that he enrichment strategy was not effective for some species/samples). Approximately 8000 nuclei were recovered from each sample, and each nucleus was sequenced to a depth of ~40000 reads.

first: Aboozar

last: Monavarfeshani

first: Mu

last: Qiao

first: Allison

last: Kao

first: Yvonne

last: Kölsch

first: Ayush

last: Kumar

last: Rasys

first: Rose

last: Richardson

first: Herwig

last: Baier

first: Robert

last: Lucas

first: Wei

last: Li

first: Markus

last: Meister

last: Trachtenberg

first: Wenjun

last: Yan

first: Yi-Rong

last: Peng

last: Sanes

first: Karthik

last: Shekhar


title: Evolution of neuronal cell classes and types in the vertebrate retina [Squirrel]

last: Hahn

first: Ashley


title: Glucocorticoid Receptor Action in Breast Cancer [ChIP-Seq]

first: Stefan

last: Prekovic

summary: Various omics datastreams related to  mechanisms underlying glucocorticoid receptor action in breast cancer cells - we performed mRNA sequencing and ER/GR-ChIP sequencing.

overall_design: MCF-7 cells, treated with Dexamethasone, Fulvestrant, or left untreated.

first: Wilbert

last: Zwart


title: Glucocorticoid Receptor Action in Breast Cancer [RNA-Seq]


title: A genetically engineered mouse model (GEMM) of NUT carcinoma (RNA-Seq)

city: Boston

first: Chris

last: French

address: 77 avenue louis Pasteur, NRB 652

institute: Brigham and Women's Hospital

summary: NUT carcinoma (NC) is a highly aggressive subtype of squamous carcinoma driven by the BRD4-NUT fusion oncoprotein. Closely resembling human NC (hNC), GEMM tumors (mNC) are poorly differentiated squamous carcinomas that express high levels of MYC and metastasize to organs (liver, lung) and regional lymph nodes. Two GEMM-derived cell lines were developed whose transcriptomic and epigenetic landscapes, characterized by RNAseq and CUT&RUN, show striking overlap with those of primary GEMM tumors. As in hNC, BRD4-NUT functions to block differentiation and maintain growth of mNC, as evidenced by BRD4-NUT knockdown and treatment of mNC cell lines with BET bromodomain inhibitors (BETi). Mechanistically, GEMM primary tumor and cell lines form very large H3K27ac-enriched super-enhancers that are unique to hNC, termed megadomains, that are invariably associated with key hNC-defining transcriptional oncogenic targets, Myc and Trp63.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for treated 311E and untreated 317E cell lines cultured in triplicate, two fresh GEMM tumors from which the two cell lines were derived, three fresh esophageal mucosa samples from SOX2-/-BRD4-NUTM1+/- control mice, and one primary human patient tumor sample from pleural fluid. 311E cell line cells were treated with ABBV-075 (9nM), tazemetostat (taz, 1uM), taz + ABBV=075, or with DMSO for 96h.

first: R

last: Durall

first: Yeying

last: Huang


title: MVA.scIL12 treatment in a mouse model of peritoneal carcinomatosis (PCa)

city: Pamplona

first: Jose

last: Gonzalez

state: Navarra

address: C/PIO XII s/n

institute: FIMA

summary: RNA-seq analysis of MC38 cell line omental metastases treated intraperitoneally or intravenously with MVA expressing scIL-12 (rMVA-scIL12)

overall_design:
Comparative gene expression profiling analysis of RNA-seq data from in vivo treated tumors. Tumor bearing omenta were excised 24h after intraperitoneal or intravenous injections with rMVA.empty (MVA-BN) or rMVA.scIL12.
(contributor)  UNIDAD DE GENOMICA (Unidad NGS), CIMA- Universidad de Navarra

first: Ángela

last: Bella

first: Fernando

last: Aranda

first: Pedro

last: Berraondo

first: José

last: González-Gomariz

first: Nordic

last: Bavarian


title: Development of a novel guinea pig model producing transgenerational endothelial transcriptional changes driven by maternal food restriction and a second metabolic insult of high-fat diet.

city: PORTLAND

first: Hillary

last: Le

state: OR

address: 3303 S Bond Ave

institute: Oregon Health & Science University

summary: Developmental programming of chronic adverse cardiovascular health outcomes has been studied both using numerous human populations and an array of animal models. However, the mechanisms that produce transgenerational effects have been difficult to study due to a lack of developmentally relevant models. As such, how increased disease risk is carried to the second generation has been poorly studied. We hypothesized that the endothelium which mediates many acute and chronic vascular inflammatory responses is a key player in these effects, and epidemiological studies implicate transgenerational nutritional effects on endothelial health. To study the mutigenerational effects of maternal undernutrition on offspring endothelial health, we developed a model of transgenerational nutritional stress in guinea pigs, a translationally relevant precocial species with a relatively short lifespan. First- and second- generation offspring were subjected to a high fat diet in adolescence to exacerbate negative cardiovascular health. To assess transcriptional changes, we performed bulk RNA-sequencing in carotid artery endothelial cells, with groups stratified as prenatal control or food restricted, and postnatal control or high fat diet. We detected statistically significant gene alterations for each dietary permutation, some of which were unique to treatments and other transcriptional signatures shared by multiple or all conditions. These findings highlight a core group of genes altered by high fat diet that is shared by all cohorts and a divergence of transgenerational effects between the prenatal ad libitum and dietary restriction groups. This study establishes the groundwork for this model to be used to better understand the interplay of prenatal stress and genetic reprogramming.

overall_design: Two adult male (550-600g) and 8 nulliparous female (400-450g) Hartley Guinea Pigs were purchased from Charles River Laboratories and housed in individual cages. All animals were weighed three times per week. Purchased animals were fed a standard, control chow (LabDiets 5025, 13% energy from fat, 27% from protein, 60% from carbohydrate) ad libitum for 3 weeks to acclimate and weight and food intake were recorded daily. Following this acclimatization period, half of the female guinea pigs received 70% of the average (per kg body weight) daily ad libitum diet (PR; Prenatal Food Restriction) for 3 weeks; the remainder of the females (PC; Prenatal Ad libitum Control), and all males received 100% of the average (per kg body weight) daily ad libitum diet. Male and female guinea pigs were mated overnight, and mating confirmed by the presence of a vaginal plug. Control guinea pigs remained on their designated diet for the duration of gestation (~70 days) and throughout lactation (~28d days). Food-restricted dams remained on 70% of ad libitum diet until 34dGA (days gestational age, ~mid gestation), after which they were placed on 90% of ad libitum diet until the end of lactation; this increase in feed is to prevent weight loss during the latter half of pregnancy.Offspring were born spontaneously and litter size was culled to 3 pups per dam. Offspring were housed with their mother until weaning at 28 days. Pup selection for culling was pseudo-random in order to maintain equal numbers of male and female offspring in each study group, and to maintain equal mean pup weights between culled and unculled groups. After weaning, all offspring were fed a control diet until at least 8 weeks of age. A subset of female F1 offspring were used as breeders to produce F2 offspring, and remained on an ad libitum control chow diet for the remainder of the study, including during pregnancy. F1 breeders were mated with newly-purchased unrelated adult male Hartley Guinea Pigs purchased from Charles River Laboratories, as described above. At 8 weeks of age, half of remaining non-breeding F1 offspring were fed ad libitum control chow (PC-C or PR-C) while other half were placed on an ad libitum high-fat chow (PC-H or PR-H) for 12 weeks; food intake was monitored daily, and animals were weighed 3 times per week. The high fat chow was based on the standard lab chow LabDiet 5025, supplemented with 0.25% cholesterol, 15% fat from pork fat, and 2.5% fructose (38% energy from fat, 20% from protein, 42% from carbohydrate). Offspring diets were pseudo-randomly assigned to avoid siblings receiving the same treatment. Offspring were born spontaneously and treated as described above for the non-breeding F1 offspring. At 8 weeks of age, offspring received either ad libitum control chow (PC-C-C or PR-C-C) or ad libitum high-fat chow (PC-C-H or PR-C-H). At 20 weeks of age, 3 animals each from PC-C, PC-H, PR-C, PR-H, PC-C-C, PC-C-H, PR-C-C, PR-C-H were euthanized with intravenous overdose of commercial barbituate (Somnasol, 390mg/ml pentobarbital sodium). A carotid artery was rapidly cannulated in situ. The vessel was flushed with 1X PBS (Gibco) to remove blood, followed by 100uL of TRIzol Reagent (Invitrogen) to collect endothelial cell contents. RNA was isolated using RNeasy Micro kit (Qiagen) and quality was assessed using Agilent 2100 Bioanalyzer with RNA 6000 Pico chip by the OHSU Gene Profiling Shared Resource. All samples had an RNA Integrity Number (RIN) score of above 5.0. Samples were stored at -80C until sequencing. Short-read sequencing assays were performed by the OHSU Massively Parallel Sequencing Shared Resource. Raw data was checked for quality using FastQC, trimmed using Trimmomatic, aligned using STAR, and analyzed for differential gene expression using DESeq2 in R.

first: Matthew

last: Hagen

first: Samantha

last: Louey

first: Hagai

last: Tavori

first: Kent

last: Thornburg

first: George

last: Giraud

first: Monica

last: Hinds

first: Anthony

middle: P

last: Barnes


title: Condensin positioning at telomeres by shelterin proteins drives sister-telomere disjunction in anaphase

city: Lyon

first: Pascal

last: BERNARD

address: 46 allée d'Italie

department: LBMC

institute: CNRS

summary: The localization of condensin along chromosomes is crucial for their accurate segregation in anaphase. Condensin is enriched at telomeres but how and for what purpose had remained elusive. Here we show that fission yeast condensin accumulates at telomere repeats through the balancing acts of Taz1, a core component of the shelterin complex that ensures telomeric functions, and Mit1, a nucleosome-remodeler associated with shelterin. We further show that condensin takes part in sister-telomere separation in anaphase, and that this event can be uncoupled from the prior separation of chromosomes arms, implying a telomere-specific separation mechanism. Consistent with a cis-acting process, increasing or decreasing condensin occupancy specifically at telomeres modifies accordingly the efficiency of their separation in anaphase. Genetic evidence suggests that condensin promotes sister-telomere separation by counteracting cohesin. Thus, our results reveal a shelterin-based mechanism that enriches condensin at telomeres to drive in cis their separation during mitosis.

overall_design: Condensin localisation and chromatin loop formation in fission yeast cells arrested in metaphase. (1) samples for calibrated ChIP-seq of fission yeast Cnd2-GFP in WT, cut14-208, cut3-477 or mit1D mutant cells arrested in metaphase, with 2 technical and biological replicates. (2) samples for Hi-C-seq in WT or cut14-208  fission yeast cells arrested in metaphase, with 2 technical and biological replicates.

first: Léonard

last: Colin

first: Esther

last: Toselli

last: Bernard

first: Laurent

last: Modolo

first: Nicolas

last: Chanard

first: Stephane

last: Schaak

first: Olivier

last: Cuvier


title: Evolution of neuronal cell classes and types in the vertebrate retina [Lizard]

city: Seattle

first: Joshua

last: Hahn

first: Aboozar

last: Monavarfeshani

first: Mu

last: Qiao

first: Allison

last: Kao

first: Yvonne

last: Kölsch

first: Ayush

last: Kumar

first: Ashley

middle: M

last: Rasys

first: Rose

last: Richardson

first: Herwig

last: Baier

first: Robert

last: Lucas

first: Wei

last: Li

first: Markus

last: Meister

last: Trachtenberg

first: Wenjun

last: Yan

first: Yi-Rong

last: Peng

last: Sanes

first: Karthik

last: Shekhar


title: Prevalence of chromosomal alterations in first-trimester spontaneous pregnancy loss

first: Rick

last: Essers

summary:
Extensive genome analysis of pregnancy loss products by genome haplarithmisis.
Pregnancy loss (PL) is the primary pregnancy complication, mostly caused by chromosomal abnormalities of the conceptus. However, the nature and prevalence of these abnormalities and the allocation of (ab)normal cells in embryonic and placental compartments during intrauterine development remains elusive. We analyzed 1,745 spontaneous PLs and found that ~50% were karyotypically normal. We applied genome haplarithmisis to 91 PL families with normal karyotypes, following whole-genome genotypes of the parents as well as of the extraembryonic mesoderm (EM) and chorionic villi (CV), representing embryonic and placental cells, of the product of conception (POC), which allowed characterizing genomic landscape of both lineages. 36.4% of these PLs have chromosomal aberrations not previously detected by karyotyping. In contrast to viable pregnancies where mosaic chromosomal abnormalities are often restricted to the CV, we find that in spontaneous abortions, the situation is reversed with a higher degree of mosaic chromosomal imbalances in EM rather than CV.

overall_design:
From 1987 to 2021, A total of 1745 spontaneous PLs were analyzed using karyotyping. 866 (49.6%) were classified as normal and 879 (50.4%) as abnormal. The karyotypes of fetal tissue was determined by conventional metaphase analysis (n=1745) or additional testing by comparative genomic hybridization (CGH) and fluorescence in situ hybridization (FISH), as described previously37,38. All the samples with abnormal karyotype were excluded for downstream haplarithmisis. Of the karyotypically normal cases, 111 families were randomly selected for SNP haplotyping, given that fetal (EM and CV) and parental blood samples were available without previously identified genetic predisposition was in any of the couples. Twenty families have been excluded due to the DNA of one or more family members being of insufficient quality causing low SNP call rates or due to one or both parents not being the biological parent, making proper haplotyping analysis impossible . Ninety-one families have been successfully analyzed by haplarithmisis. Of those, forty-two were categorized as SPL (loss of one pregnancy) and forty-nine as RPL (loss of two or more consecutive pregnancies).
The data is provided in quartest structure,including  Father, Mother, chrionic villi (CV) sample  and extra-embryonic mesoderm (EM).
Please note that each processed data file was generated from multiple samples as inidcated in the corresponding sample description.

first: Igor

last: Lebedev

first: Ants

last: Kurg

first: Elizaveta

last: Fonova

first: Servi

last: Stevens

first: Rebekka

last: Koeck

first: Ulrike

last: von Rango

first: Lloyd

last: Brandts

first: Spyridon

last: Deligiannis

first: Tatyana

middle: V

last: Nikitina

first: Elena

last: Sazhenova

first: Ekatarina

last: Tolmacheva

first: Anna

last: Kashevarova

first: Dmitry

last: Fedotov

first: Viktoria

last: Demeneva

first: Gleb

last: Drozdov

first: Salwan

last: Al-Nasiry

first: Merryn

last: Macville

first: Arthur

last: van den Wijngaard

first: Jos

last: Dreesen

first: Aimee

last: Paulussen

first: Alexander

last: Hoschen

first: Han

middle: G

last: Brunner

first: Andres

last: Salumets

first: Masoud

middle: Z

last: Esteki


title: Depletion of tet2 results in age-dependent changes in DNA methylation and gene expression in a zebrafish model of myelodysplastic syndrome [RNAseq]

first: Francine

last: Garrett-Bakelman

overall_design: To understand the effect of tet2 loss on the CpG methylation state of the genome and gene expression patterns to identify potential molecular mechanisms that associate with clonal expansion of the progenitor cells and disease progression in myelodysplastic syndrome

first: Yaseswini

last: Neelamraju

first: Evisa

last: Gjini

first: Sagar

last: Chhangawala

first: Shuning

last: He

first: Ashley

middle: T

last: Nguyen

first: Chang-Bin

last: Jing

first: Caroline

last: Sheridan

first: Yariv

last: Houvras

first: Ari

last: Melnick

first: Thomas

last: Look

last: Garret-Bakelman


title: Evolution of neuronal cell classes and types in the vertebrate retina [cow]

first: Joshua

last: Hahn

first: Aboozar

last: Monavarfeshani

first: Mu

last: Qiao

first: Allison

last: Kao

first: Yvonne

last: Kölsch

first: Ayush

last: Kumar

last: Rasys

first: Rose

last: Richardson

first: Herwig

last: Baier

first: Robert

last: Lucas

first: Wei

last: Li

first: Markus

last: Meister

last: Trachtenberg

first: Wenjun

last: Yan

first: Yi-Rong

last: Peng

last: Sanes

first: Karthik

last: Shekhar


title: Evolution of neuronal cell classes and types in the vertebrate retina [ferret]

last: Hahn

overall_design: Single cell RNA-seq was performed on cells isolated from fresh retina. Fluorescence-activated cell sorting was used to collect Calcein blue(CB)-positive live cells. For some collections, CB+ cells were further seprated using CD90/THY1 and/or CD73 expression as an strategy to enrich for RGCs and/or to deplete phototreceptors, respectively (Please note that he enrichment strategy was not effective for some species/samples). Approximately 8000 cells were recovered from each sample, and each cell was sequenced to a depth of ~40000 reads.

first: Ashley


title: Evolution of neuronal cell classes and types in the vertebrate retina [Zebrafish]

last: Monavarfeshani


title: Evolution of neuronal cell classes and types in the vertebrate retina [Pig]

last: Qiao


title: Evolution of neuronal cell classes and types in the vertebrate retina [Sheep]

last: Kao


title: Evolution of neuronal cell classes and types in the vertebrate retina [Peromyscus]

last: Kölsch


title: Evolution of neuronal cell classes and types in the vertebrate retina [Marmoset]

last: Kumar


title: Evolution of neuronal cell classes and types in the vertebrate retina [Opossum]

last: Rasys


title: Stromal STAT5-mediated trophic activity regulates hematopoietic multipotent progenitor niche factors

city: Atlanta

first: Peng

last: Qiu

state: GA

address: 950 Atlantic Dr. NW

institute: Georgia Institute of Technology

summary: Signal transducer and activator of transcription 5 (STAT5a and STAT5b) are intrinsically critical for normal hematopoiesis but are also expressed in stromal cells. However, hematopoiesis-supporting stromal function has not been reported. Here, STAT5ab knockout (KO) was generated with a variety of bone marrow hematopoietic and stromal Cre transgenic mouse strains.  Pan-hematopoietic deletion with Vav1-Cre was the positive control for loss of multipotent hematopoietic function but surprisingly dysregulated niche factor mRNA expression and deleted STAT5ab in CD45neg cells. Single cell transcriptome analysis of mouse bone marrow from wild-type or Vav1-Cre KO mice showed major changes in hematopoietic stem cell myeloid commitment genes and upregulated protein translation genes throughout myeloid-primed clusters.

overall_design: Bone marrow cells were harvested from the femurs and tibias of 4 Vav1-Cre/+ or Vav1-Cre/+/STAT5abflox/flox mice (8-12 weeks). The cells were lineage depleted using a mouse lineage cell depletion kit (Miltenyi Biotech, Auburn, CA) and stained with FITC-labeled lineage antibodies (Gr-1, Mac-1, B220, Ter119, CD3, CD4, CD8a), anti-c-Kit-APC, anti-Sca-1-PE-Cy7 (Thermo Fisher Scientific, Norcross, GA), and dead cells were excluded by staining with propidium iodide dye. KLS cells were sorted (sorting purity ~6% with 605 CD45neg cells among 10008 total sorted KLS cells) using BD FACSAria III Cell Sorter. For sorting bone marrow stromal cells, cells were isolated as described(79). Briefly, mouse bones (tibia and femur) were isolated and cleaned from 6-8 weeks old mice, then were crushed and cut into tiny pieces with sterile scissors, incubated them in 20 ml of preheated DMEM plus 0.2% (wt/vol; 40 mg) collagenase at 110 rpm at 37°C for 1 hour ). The cell suspension was filtered through a 70-μm cell strainer and bone fragment was further crushed and washed to liberate cells out of the bone into solution. CD45+ cells were depleted with mouse CD45 microbeads from Miltenyi Biotech( Auburn, CA) and stained with anti-Ter119-PE  (BD Biosciences, San Jose, CA), anti-CD45-FITC, Anti-CD71-Alexa 700, Anti-Sca-1-PE-Cy7 and Anti-CD140a-APC (Thermo Fisher Scientific, Norcross, GA). CD45negTer119neg/lowCD71negSca-1+CD140a+ MSCs were sorted using BD FACSAria III Cell Sorter. Sorted cells were immediately processed for single cells RNA sequencing.

first: Kevin

last: Bunting

first: Zhengqi

last: Wang


title: Evolution of neuronal cell classes and types in the vertebrate retina [human]

first: Joshua

first: Aboozar

last: Richardson

last: Baier

last: Lucas

last: Li


title: Single-cell Architecture and Functional Requirement of Alternative Splicing during Hematopoietic Stem Cell Emergence [RNA-Seq]

city: Beijing

first: Jia

last: Yu

address: Dong Dan San Tiao 5, Dongcheng District

institute: Peking Union Medical College

summary: Hematopoietic stem cells (HSCs) are well known to generate from a rare hemogenic population of embryonic endothelial cells through a dynamic fate transition, accompanied by widespread changes in gene regulatory networks. Nevertheless, RNA splicing, a striking feature in shaping transcriptome and enabling the generation of vast transcripts and diverse proteins, has never been illustrated in this transient endothelial to HSC conversion. Here, we constructed an isoform-based transcriptome landscape during HSC development at single-cell resolution, which enables the identification of hemogenic signature isoforms, as well as stage-specific splicing events. Combining with functional screening, we showed that the inclusion of such hemogenic-specific exons was essential for hemogenic function in vitro. Moreover, their gradual appearance along with HSC specification from endothelial cells was orchestrated by the splicing regulator Srsf2. Therefore, early Srsf2 deficiency from endothelia cells dramatically impaired the HSC generation, which was accompanied by changes in the splicing pattern of several master hematopoietic regulators. These results redefine our understanding of the dynamic transcriptome diversity and demonstrate that the elaborate control of splicing governs cell fate in HSC formation.

overall_design: Single-cell full-length RNA-sequencing of EC-associated cell populations.

first: Fang

first: Puwen

last: Tan

first: Pengcheng

last: Zhang

first: Yue

last: Ren

first: Jie

last: Zhou

first: Dong

first: Bin

last: Liu

first: Yu

last: Lan


title: Resource of single cell gene expression profiles in a planarian Dugesia japonica

status: Public on Sep 30 2023

city: Sagamihara

first: Makoto

last: Kashima

state: Kanagawa

address: 5-1-16, Fuchinobe

institute: Aoyama Gakuinn University


title: Distinct transcriptional profiles in the different phenotypes of neurofibroma from the same neurofibromatosis 1 subject

city: Suita

first: Wei-Ning

state: Osaka

address: 2-2 Yamadaoka

department: Dermatology

institute: Osaka University

summary:
Background: Neurofibromatosis 1 (NF1) is one of the most common hereditary neurocutaneous disorders. Among clinical phenotypes of NF1, cutaneous neurofibroma (cNF) and plexiform neurofibroma (pNF) display distinct clinical manifestations and pNF should be carefully followed up due to its potential for malignant transformation. However, the detailed distinct features of pNF compared to the other phenotypes in NF1 remains unclear.
Objective: To elucidate whether transcriptional features are altered between cNF and pNF within the same patient.
Methods: Single-cell RNA-sequencing was performed on the isolated cNF and pNF cells from the same patient. Immunohistochemical analysis was conducted on 6 cNF and 5 pNF specimens from different subjects.
Results: cNF and pNF have different microenvironment and distinct transcriptional profiles. Schwann cells with robust metabolic capacity and fibroblasts with cancer-associated fibroblast-like phenotype are enriched in pNF, while CD8 T cells with tissue residency markers are endowed in cNF. The density of CD8 T cells is histologically augmented in cNF.
Conclusion: cNF and pNF, the different NF phenotypes in NF1, are transcriptionally distinct in terms of various involved cell types including immune cells.

overall_design: Neurofibromas were isolated by FACS and analyzed using scRNA-seq.

first: Hanako

last: Koguchi-Yoshioka

first: Keisuke

last: Nimura

first: Rei

last: Watanabe

first: Manabu

last: Fujimoto

first: Mari

last: Wataya-Kaneda


title: Sex-limited experimental evolution drives transcriptomic divergence in a hermaphrodite

status: Public on Sep 29 2023

city: Lund

first: Jessica

middle: K.

last: Abbott

state: Skåne

address: Sölvegatan 37

country: Sweden

institute: Lund University

summary: The evolution of gonochorism from hermaphroditism is linked with the formation of sex chromosomes, as well as the evolution of sex-biased and sex-specific gene expression to allow both sexes to reach their fitness optimum. There is evidence that sexual selection drives the evolution of male-biased gene expression in particular. However, previous research in this area in animals comes from either theoretical models or comparative studies of already old sex chromosomes. We therefore investigated changes in gene expression under three different selection regimes for the simultaneous hermaphrodite Macrostomum lignano subjected to sex-limited experimental evolution (i.e., selection for fitness via eggs, via sperm, or a control regime allowing both). After 21 and 22 generations of selection for male-specific or female-specific fitness, we characterized changes in whole-organism gene expression. We found that female-selected lines had changed the most in their gene expression. Although annotation for this species is limited, GO-term and KEGG pathway analysis suggests that metabolic changes (e.g., biosynthesis of amino acids and carbon metabolism) are an important adaptive component. As predicted, we found that expression of genes previously identified as testis-biased candidates tended to be downregulated in the female-selected lines. We did not find any significant expression differences for previously identified candidates of other sex-specific organs, but this may simply reflect that few transcripts have been characterized in this way. In conclusion, our experiment suggests that changes in testis-biased gene expression are important in the early evolution of sex chromosomes and gonochorism.

overall_design: We carried out sex-limited experimental evolution in a hermaphrodite using a GFP marker as a proxy for sex. F lines were selected for female fitness (fecundity), M lines were selected for male fitness (fertilization success), and in the C lines half of the marked individuals were selected for female fitness and the other half for male fitness. There were 4 replicate lines within each selection treatment (i.e. F1, F2, F3, F4, M1, M2, M3, M4, C1, C2, C3, C4). RNAseq data was obtained from two pooled samples of 40 individuals each from all selection lines (one sample in generation 21 and the other in generation 22). We also seequenced 3 samples of the ancestral GFP stock. 3 samples were excluded prior to sequencing due to low amounts of RNA (C1gen22, F1gen21, and M3gen22), for a total of 24 samples.

first: Aivars

last: Cirulis

first: Anna

middle: K

last: Nordén

first: Allison

last: Churcher

first: Steven

last: Ramm

first: Kira

middle: S

last: Zadesenets


title: Molecular profiling of bone marrow stromal cells from healthy donors and patients with chronic myeloid leukemia

city: Huddinge

first: HONG

last: QIAN

state: Stockholms Lan

address: Neo, HERM, Floor 7, Hälsovägen 7,

department: Department of Medicine

institute: Karolinska Institute

summary: Evidence indicates that chronic myeoid leukemia (CML) stem cells (LSC) persistence is due to bone marrow (BM) niche protection. However, little is known about the underlying molecular mechanisms. We here characterized CML patient BM cellular niches including endothelial cells, mesenchymal stem cells and mature stromal cells that were freshly isolated by fluorescence-activated cell sorting.

overall_design: Examination of mRNA profiles in bone marrow endothelial cells, mesenchymal stem cells and mature stromal cells sorted from healthy and patients with chronic myeloid leukemia

first: Hong

last: Qian

first: Monika

last: Dolinska

first: Huan

last: Cai

first: Xidan

last: Li

first: Mikael

last: Sigvardsson


title: Genome-wide maps of chromatin state changes in bone marrow derived macrophages (BMDMs) isolated from Baf60a KO or WT mice

city: Ann Arbor

first: Yang

last: Zhao

address: 2800 Plymouth Rd

institute: University of Michigan

summary: Bone marrow cells from Baf60a KO or WT mice were differentiated into BMDMs and treated with or without oxLDL for 48h.

overall_design: Quantification of BRG1 binding peak in Baf60a KO and WT BMDMs using ChIPseq.

first: Jifeng

last: Zhang

first: Eugene

last: Chen


title: Transcriptome analysis of bone marrow derived macrophages (BMDMs) isolated from C57 mice

summary: Bone marrow cells from Baf60a KO or WT  mice were differentiated into BMDMs, followed by RNA extraction and sequencing at the University of Michigan AGC.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for WT and Baf60a KO BMDMs.


title: Molecular mechanisms of increased survival of Vibrio cholerae flrA mutant in amoeba

city: Sydney

first: M. Mozammel

last: Hoque

state: NSW

address: 15 Broadway, Ultimo

department: Australian Institute for Microbiology & Infection (AIMI)

country: Australia

institute: University of Technology Sydney

summary: Mutation in flagellar transcriptional regulatory gene (flrA) result in increased V. cholerae growth and intracellular survival in the amoeba host Acanthamoeba castellanii. To identify molecular mechanisms behind the increased survival and growth of the flrA mutant transcriptomics assay was done.

overall_design: To compare transcriptomes of the flrA mutant during amoeba predation RNA-seq and transcriptomics analysis was performed. The V. cholerae A1552 wt strain and its isogenic flrA mutant were used to infect A. castellanii at 100 MOI.

first: Diane

last: McDougald


title: Molecular profiling of CML CD34+CD38- cells 6h and 24h post stimulation with conditioned media (CM) derived from either CXCL14 overexpressed NIH3 (NIH3-CXCL14) cells or control cells.

summary: We here by prospectively characterizing BM stormal cells from healthy donors and patients with chornic myeloid leukemia (CML) have found that CXCL14 is dysregulated in CML patient bone marrow niche. Further, CXCL14 promotes TKI therapy response to CML LSCs in vitro and in vivo. To further determine the molecular mechanisms of CXCL14 action, we performed RNA sequencing of CML CD34+CD38- cells 6-24h post stimulation with conditioned media (CM) derived from either NIH3-CTRL or NIH3-CXCL14 cells.

first: Arne

last: Östman


title: Differenatiation of mRNA expression in PTX3-depleted macrophages

city: Shanghai

first: Xiao

last: Han

address: 399 Wanyuan Rd, Minhang, Shanghai, China

institute: Children’s Hospital of Fudan University

summary: PTX3, as the long member of the pentraxin family, is produced mainly by dendritic cells, macrophages, and endothelial cells in response to inflammation. Growing amount of studies suggest that PTX3 can exert potential contradictory roles in inflammation regulation, antimicrobial resistance, and disease pathogenesis, depending on the tissue context, cellular source, and levels of production. To characterize the potential involvement of PTX3 in macrophage function, transcriptome sequencing (RNA-seq) was performed in human THP1-derived macrophages with PTX3 depletion. Notably,genes enrichment in PI3K/AKT signaling , JAK/STAT signaling and autophagy pathway were observed in PTX3 deficiency macrophages. This study highlights the critical roles of PTX3 on regulation macrophages homeostasis.

overall_design: The mRNA profiles of  WT and PTX3-depleted macrophages under IL-4 stimulation. Three  independent experiments were performed at each treatment.

first: Wenfeng

last: Xiao


title: Transcriptome analysis of bone marrow derived macrophages (BMDMs) isolated from atherosclerotic C57 mice

summary: Bone marrow cells from atherosclerotic Baf60a KO or WT mice were differentiated into BMDMs, followed by RNA extraction and sequencing at the University of Michigan AGC.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for atherosclerotic WT and Baf60a KO BMDMs.


title: Loss of MEF2A induces replicative stress responses that trigger IFN production

city: Columbus

first: Adriana

last: Forero

state: Ohio

address: 460 W 12th Ave

institute: The Ohio State University

summary: Interferons (IFN) are induced by sensing of self and non-self RNA or DNA by pathogen recognition receptors. In particular, the aberrant accumulation of cytosolic nucleic acids or the accumulation of DNA lesions has the potential to activate the STING pathway to induce IFNs. While aberrant self-DNA sensing can cause autoimmunity, negative regulators keep these under check. Here we report that MEF2A is a novel negative regulator of inflammation which suppresses the induction of IFNs at homeostasis. We show that MEF2A deficiency results in the spontaneous induction of type I IFN and robust downstream ISG expression in a STING-dependent and cGAS-independent manner.  We demonstrate that the IFN response elicited by MEF2A depletion could protect cells from cardiotropic virus infections. We found that the loss of MEF2A triggered the replicative stress response to promote a DDX41/STING-dependent induction type I IFN response. The replicative stress response is dependent on ATR kinase activity, as inhibition of ATR abrogated STING activation and type I IFN production. Thus, our study connects MEF2A with protection from maladaptive type I IFN responses due to replicative stress response across various cell types as well as links the DDX41-dependent activation of STING to the replicative stress response.

overall_design:
Mock and MEF2Ai  RNA  samples from AC16 cardiomyocytes

Gene expression following siRNA depletion of MEF2A in WT and DDX41 defficient cells

first: Julian

last: Smith

first: Jack

last: Dowling

first: Matthew

middle: I

last: McFadden

first: Andrew

last: Karp

first: Johannes

last: Schwerk

first: Ram

last: Savan


title: A framework to validate fluorescently labeled DNA-binding proteins for single-molecule experiments

city: Bloomington

first: Xindan

last: Wang

state: IN

address: 1001 E 3rd St

department: Biology

institute: Indiana University at Bloomington

summary: Due to the enhanced labeling capability of maleimide-based fluorescent probes, lysine-cysteine-lysine (KCK) tags are frequently added to proteins for visualization. In this study, we employed in vitro single-molecule DNA flow-stretching assay as a sensitive way to assess the impact of the KCK-tag on the property of DNA-binding proteins. Using Bacillus subtilis ParB as an example, we show that, although no noticeable changes were detected by in vivo fluorescence imaging and chromatin immunoprecipitation (ChIP) assays, the KCK-tag substantially altered ParB’s DNA compaction rates, its response to nucleotide binding and to the presence of the specific sequence (parS) on the DNA. While it is typically assumed that short peptide tags minimally perturb protein function, our results urge researchers to carefully validate the use of tags for protein labeling. Our comprehensive analysis can be expanded and used as a guide to assess the impacts of other tags on DNA-binding proteins in single-molecule assays.

overall_design: ChIP-seq experiments were performed on wild type and mutant cells of Bacillus subtilis PY79 growing in rich media.

first: X


title: Sequencing of Physically Interacting Cells in Human Kidney Allograft Rejection Reveals Insights into Immune Cell Interactions

city: st louis

first: andrew

last: malone

address: 4525 laclede ave

institute: Washington University

summary: We sequenced the transriptomes of 31203 cells from 11 human kidney transplant biopsies. We used the CITE-seq approach to generate these single cell multiomics data. We then used a computational pipeline called PIC-seq to deconvolute the transcriptional signatures of each contributing cell in a PIC by comparing PIC gene expression to a theoretical PIC.

overall_design: There are 11 biopsy samples included in this study with diagnoses of ABMR, TCMR, mixed rejection and non-rejection diagnosis.

middle: F

last: Malone


title: Lymph node myeloid cells

city: Kumamoto

first: Yoshihiro

last: Komohara

address: Honjo 1‐1‐1, Chuouku

department: Department of Cell Pathology

institute: Graduate School of Medical Sciences, Kumamoto University

summary: C57BL/6J mice were treated with natural compounds (naringenin and naringin). CD11b-postive myeloid cells were sorted from lymph nodes, and RNA was isolated from sorted cells.

overall_design: Following C57BL/6J mice were administrated oraly by each compounds (200mg/kg) for 5 days, inguinal lymph nodes were resected. Single cell suspension was performed and then myeloid cells were sorted.


title: USF1 modulates transcription and cellular functions by regulating multiple transcription factors in Huh7 cells.

status: Public on Sep 28 2023

city: Zhengzhou

first: Yan-li

last: Zeng

state: Henan

address: No.7 of Weiwu Road

department: Department of Infectious Diseases

institute: Henan Provincial People’s Hospital

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

overall_design: Refer to individual Series


title: BACH1  regulates angiogenesis related gene expression

city: Nanjing

first: Zhiqiang

last: Huang

state: Jiangsu

address: Hankou 22

department: Medical School

institute: Nanjing University

summary: Study the function of BACH1 in lung tumor angiogenesis

overall_design: Use the CUT&TAG to uncover the regulation mechanism of BACH1 induced angiogenesis  at molecular level  in 3D lung tumor cells.

first: Ting

first: Ning

last: Liang

first: Martin

last: Bergo


title: Primary cilia control Oligodendrocyte Precursor Cell proliferation in white matter injury via Hedgehog-independent CREB signaling.

city: San Francisco

first: Stephen

last: Fancy

state: CA

address: 675 Nelson Rising Lane

institute: University of California, San Francisco

summary: Remyelination after white matter injury (WMI) often fails in diseases such as multiple sclerosis due to improper recruitment and repopulation of oligodendrocyte precursor cells (OPCs) in lesions. How OPCs elicit specific intracellular programs in response to a chemically and mechanically diverse environment to properly regenerate myelin remains unclear. OPCs construct primary cilia, specialized signaling compartments that transduce Hh and GPCR signals. We investigated the role of primary cilia in the OPC response to WMI. Removing cilia from OPCs genetically via deletion of Ift88 results in OPCs failing to repopulate WMI lesions due to reduced proliferation. Interestingly, loss of cilia does not affect Hh signaling in OPCs or their responsiveness to Hh signals, but instead leads to dysfunctional cAMP-dependent CREB-mediated transcription. As inhibition of CREB activity in OPCs reduces proliferation, we propose that a GPCR/cAMP/CREB signaling axis initiated at OPC cilia orchestrates OPC proliferation during development and in response to WMI.

overall_design: To investigate the function of cilia in oligodendrocyte precursor cells, RNA-sequencing was performed on OPCs isolated from the cortices of 4-6 mice for each sample at P11. OPCs were isolated from mice in which cilia were conditionally deleted using Ift88 floxed allele (Ift88 cKO). Mice containing one wildtype copy of Ift88 were used as controls. A total of 3 Ift88 cKO and 3 control samples were used for this study.

first: Kimberly

last: Hoi


title: The methylome of buccal epithelial cells is influenced by age, sex, and physiological properties

city: Los Angeles

first: Matteo

last: Pellegrini

address: 405 Hilgard Avenue

institute: UCLA

summary: Epigenetic modifications, particularly DNA methylation, have emerged as regulators of gene expression and are implicated in various biological processes and disease states. Understanding the factors influencing the epigenome is essential for unravelling its complexity. In this study, we aimed to identify how the methylome of buccal epithelial cells, a non-invasive and easily accessible tissue, is associated with demographic and health-related variables commonly used in clinical settings, such as age, sex, blood immune composition, hemoglobin levels, and others. We developed a model to assess the association of multiple factors with the human methylome and identify the genomic loci significantly impacted by each trait. We demonstrated that DNA methylation variation is accurately modeled by several factors. We confirmed the well-known impact of age and sex and unveiled novel clinical factors associated with DNA methylation, such as blood neutrophils, hemoglobin, red cell distribution width, high-density lipoprotein cholesterol, and urea. Genomic regions significantly associated with these traits were enriched in relevant transcription factors, drugs and diseases. Among our findings, we showed that neutrophil-impacted loci were involved in neutrophil functionality and maturation. Similarly, hemoglobin-influenced sites were associated with several diseases, including aplastic anemia, and the genomic loci affected by urea were related to congenital anomalies of the kidney and urinary tract. Our findings contribute to a better understanding of the human methylome plasticity and provide insights into novel factors shaping DNA methylation patterns, highlighting their potential clinical implications as biomarkers and the importance of considering these physiological traits in future medical epigenomic investigations.

overall_design: We collected buccal swabs from a cohort of 178 individuals. Genomic DNA was extracted from buccal cells and DNA methylation was measured using targeted bisulfite sequencing.


title: MicroRNA and protein cargos of human limbal epithelial cell-derived exosomes and their regulatory roles in limbal stromal cells of diabetic and non-diabetic cornea

city: West Hollywood

first: AGCT

last: Core

address: 8687 Melrose Ave, PDC B230

department: BMS

institute: Cedars Sinai Medical Center

summary: Epithelial and stromal/mesenchymal limbal stem cells contribute to corneal homeostasis and cell renewal. Extracellular vesicles (EVs), including exosomes (Exos), can be paracrine mediators of intercellular communication. Previously, we described cargos and regulatory roles of limbal stromal cell (LSC)-derived Exos in non-diabetic (N) and diabetic (DM) limbal epithelial cells (LEC). Presently, we quantify the miRNA and proteome profiles of human LEC-derived Exos and their regulatory roles in N- and DM-LSC. We revealed some miRNA and protein differences in DM vs. N-LEC-derived Exos' cargos including proteins involved in Exo biogenesis and packaging that may affect Exo production and ultimately cellular crosstalk and corneal function. Treatment by N-Exos, but not by DM-Exos enhanced wound healing in cultured N-LSC and increased proliferation rate in N and DM LSCs vs. corresponding untreated (control) cells. N-Exos treated LSC reduced keratocyte markers ALDH3A1 and lumican, and increased MSC markers CD73, CD90 and CD105 vs. control LSC. These being opposite to the changes quantified in wounded LSCs. Overall, N-LEC Exos have a more pronounced effect on LSC wound healing, proliferation, and stem cell marker expression than DM-LEC Exos. This suggests that regulatory miRNA and protein cargo differences in DM- vs. N-LEC-derived Exos could contribute to the disease state.

overall_design: 3 DM and 3 N samples

first: Nagendra

last: Verma

first: Drirh

last: Khare

first: Adam

last: Poe

first: Cynthia

last: Amador

first: Sean

last: Ghiam

last: Fealy

first: Shaghaiegh

last: Ebrahimi

first: Odelia

last: Shadrokh

first: Xue

middle: Y

last: Song

first: Chintda

last: Santiskulvong

first: Mitra

last: Mastali

first: Sarah

last: Parker

first: Aleksandr

last: Stotland

first: Jennifer

last: Van Eyk

first: Alexander

last: Ljubimov

first: Mehrnoosh

last: Saghizadeh


title: Genome-wide maps of chromatin accessibility changes in bone marrow derived macrophages (BMDMs) isolated from Baf60a KO or WT mice

first: Yang

last: Zhao

overall_design: Quantification of chromatin accessibility and transcription factor footprints in Baf60a KO and WT BMDMs using ATACseq.

first: Jifeng

last: Zhang

first: Eugene

last: Chen


title: Disrupting cellular memory to overcome drug resistance

city: Philadelphia

first: Sydney

middle: M.

last: Shaffer

state: PA

address: 421 Curie Blvd

department: Department of Pathology

institute: University of Pennsylvania

summary: Plasticity enables cells to change their gene expression state in the absence of a genetic change. At the single-cell level, these gene expression states can persist for different lengths of time which is a quantitative measurement referred to as gene expression memory. Because plasticity is not encoded by genetic changes, these cell states can be reversible, and therefore, are amenable to modulation by disrupting gene expression memory. However, we currently do not have robust methods to find the regulators of memory or to track state switching in plastic cell populations. Here, we developed a lineage tracing-based technique to quantify gene expression memory and to identify single cells as they undergo cell state transitions. Applied to human melanoma cells, we quantified long-lived fluctuations in gene expression that underlie resistance to targeted therapy. Further, we identified the PI3K and TGF-β pathways as modulators of these state dynamics. Applying the gene expression signatures derived from this technique, we find that these expression states are generalizable to in vivo models and present in scRNA-seq from patient tumors. Leveraging the PI3K and TGF-β pathways as dials on memory between plastic states, we propose a "pretreatment" model in which we first use a PI3K inhibitor to modulate the expression states of the cell population and then apply targeted therapy. This plasticity informed dosing scheme ultimately yields fewer resistant colonies than targeted therapy alone. Taken together, we describe a technique to find modulators of gene expression memory and then apply this knowledge to alter plastic cell states and their connected cell fates.

overall_design: Melanoma cells were growth in tissue culture and some were barcoded, sorted using FACS, and/or have undergone different treatments depending on the experiment (more details below and in the manuscript). We then perfomed single-cell RNA sequencing using 10X Genomics, or ATAC sequencing.

first: Guillaume

last: Harmange

first: Raul

last: R Hueros

first: Dylan

last: Schaff


title: Combined gene expression and chromatin accessibility analysis of the mouse MOE.

city: New York

first: Ariel

last: Pourmorady

state: NY

address: 3227 Broadway

department: Neurobiology and Behavior

institute: Columbia University

summary: We used combined snRNA/snATAC seq to analyze olfactory sensory neuron accessibility patterns over development.

overall_design: Cells of the mouse MOE were dissociated and nuclei were extracted to perform combined snRNA/snATAC library generation via the 10x Genomics protocol.

first: Stavros

last: Lomvardas


title: Chromatin Conformation Capture in gg8tTAtetOP2 Olfactory Sensory Neurons

summary: We performed HiC, Liquid HiC, and H3K27ac HiChIP in gg8tTA; tetOP2 OSNs sorted from the mouse main olfactory epithelium (MOE).

overall_design: All samples are GFP+ cells from gg8tTA>tetOP2iGFP mouse MOE and were processed for HiC, Liquid Hi-C, or H3K27ac HiChIP.


title: Olfactory receptor mRNAs act as selfish non-coding RNAs that enforce transcriptional singularity


title: STAT4 promotes Bhlhe40 induction to drive protective IFN-g from natural killer cells during viral infection [IL18R1KO RNA-seq]

first: Hyunu

last: Kim

address: 417 E 68th St

department: Immunology

institute: Memorial Sloan Kettering Cancer Center

summary: NK cells represent a cellular component of the mammalian innate immune system, and mount rapid responses against viral infection, including the secretion of the potent anti-viral effector cytokine IFN-g. Following mouse cytomegalovirus (MCMV) infection, Bhlhe40 was the most highly induced transcription factor in NK cells among the basic helix-loop-helix family. Bhlhe40 upregulation in NK cells depended upon IL-12 and IL-18 signals, with the promoter of Bhlhe40 enriched for STAT4 and the permissive histone H3K4me3, and STAT4-deficient NK cells showing an impairment of Bhlhe40 induction and diminished H3K4me3. Transcriptomic and protein analysis of Bhlhe40-deficient NK cells revealed a defect in IFN-g production during MCMV infection, resulting in diminished protective immunity following viral challenge. Finally, we provide evidence that Bhlhe40 directly promotes IFN-g by binding throughout the Ifng loci in activated NK cells. Thus, our study reveals how STAT4-mediated control of Bhlhe40 drives protective IFN-g secretion by NK cells during viral infection.

overall_design:
To investigate the transcriptional changes of NK cells during early MCMV infection with and without intact IL18R1, we performed RNA-seq using NK cells from WT and IL18R1-/-(KO) mice.
RNA-seq was performed on FACS sorted Ly49H+ NK cells at d0 and d2 in vivo MCMV infection, where WT and IL18R1KO NK cells are paired per replicate for given infection time point (for example, D0 WT rep3 is paired with D0 KO rep3, but not D2 WT rep 3).

first: Sam

last: Sheppard

first: Colleen

last: Lau

first: Joseph

middle: C

last: Sun


title: Plasma Multi-omics Nucleic Acid Landscape of Gastrointestinal Cancer [long RNA PBMC]

city: Beijing

first: Zhi

middle: John

last: Lu

address: Shuangqing Road

department: School of Life Sciences

institute: Tsinghua University

summary: We sequenced 8 colorectal cancer patients' PBMC samples, and 6 healthy donors' PBMC samples. These individuals' plasma RNA have been profiled.

overall_design: RNA-seq of homo sapiens: colorectal cancer patient's PBMCs; Provided by Peking University First Affiliated Hospital.

first: Shaozhen

last: Xing

first: Siqi

last: Wang

first: Yuhuan

last: Tao


title: Olfactory receptor mRNAs act as selfish non-coding RNAs that enforce transcriptional singularity (OR Switching Experiment)

summary:
To investigate roles for olfactory receptor coding sequence mRNA in trans olfactory receptor gene silencing, and OR-gene enhancer recruitment.
Olfactory receptor (OR) choice provides an extreme example of allelic competition for transcriptional dominance, as every olfactory neuron stably transcribes one out of more than ~2,000 OR alleles1,2. OR gene choice is mediated by a multi-chromosomal enhancer hub that activates transcription at a single OR3,4, followed by ORtranslation dependent feedback that stabilizes this choice5,6. However, with more than one OR enhancer hub in each nucleus7, the mechanism by which only one OR allele is chosen for transcription remains enigmatic. Here, using single cell genomics, we show that only one of the OR enhancer hubs formed in each neuron retains euchromatic features and sustains transcriptional competence. Further, we provide evidence that OR transcription recruits enhancers and reinforces enhancer hub activity locally, while OR RNA inhibits transcription in competing hubs over distance, promoting OR protein-independent transition to singularity. While OR RNA synthesis is sufficient to break the symmetry between equipotent enhancer hubs, OR translation stabilizes transcription at the prevailing hub, revealing dual non-coding and coding mechanisms implemented by OR RNAs for transcriptional prevalence. We propose that coding mRNAs can function as “selfish” non-coding RNAs that influence nuclear architecture, enhance their own transcription, and inhibit their competitors, with generalizable implications in probabilistic cell fate decisions.

overall_design: We devised an experimental strategy to test the effects on OR switching on open chromatin (ATAC), OR expression (RNA), and enhancer hub engagement (HiC). Using mor28-i-Cre; tdTom fl/+, OMP-tTA; tetO-P2 mice we were able to FACsort GFP+, tdT+, and GFP+/tdT+ cells to examine the nature by which the expression of one OR can be used to silence another.


title: Pevonedistat sensitizes cancer cells to oncolytic VSVd51 virotherapy

city: Ottawa

first: Boaz

last: Wong

state: Ontario

address: 501 Smyth Road

country: Canada

institute: Ottawa Hospital Research Institute

summary: To investigate the ability for pevonedistat to sensitize renal 786-0 carcinoma cells to VSVd51 oncolyic virotherapy, we treated cells with monotherapies or combination and sequencinced the transcriptome for antiviral interferon impact

overall_design: RNA was extracted after 24 hours of infection with VSVd51 from each condition and subject to sequencing.

first: Kristy

last: Ng

first: Jean-Simon

last: Diallo


title: Plasma Multi-omics Nucleic Acid Landscape of Gastrointestinal Cancer [Tissue RNA-seq]

summary: We sequenced 30 tissue samples from 15 colorectal cancer patients, including tumor and tumor-adjacent normal tissue (> 2cm from the primary tumor). These patients' plasma has been profiled.

overall_design: RNA-seq of homo sapiens: colorectal cancer patient's plasma; Provided by Peking University First Affiliated Hospital; Constructed by NEBNext Ultra™ II RNA Library Prep Kit for Illumina; Purpose: To explore the relationship between plasma and tumor-microenvironment.


title: Single Cell nuclear architecture of olfactory sensory neurons expressing a known OR

summary: To study OR gene/enhancer 3D relationships in single cells we performed DipC in OSNs expressing a known OR

overall_design: Dip-C a form of single-cell HiC was performed on sorted olfactory sensory neurons from the mouse olfactory epithelium.


title: USF1 modulates transcription and cellular functions by regulating multiple transcription factors in Huh7 cells [ChIP-seq]

first: Yan-li

last: Zeng

summary: Liver cancer, including hepatocellular carcinoma (HCC), is a malignant tumor type with high metastasis and mortality rate in worldwide. Upstream transcription factor 1 (USF1) is a canonical transcription factor (TF) and associated with the pathogenesis of several cancers, while its biological functions and molecular targets in HCC are not clear. In this study, we overexpressed USF1 in Huh7 cells and used whole transcriptome profile sequencing (RNA-seq) and chromatin immunoprecipitation sequencing (ChIP-seq) methods to systematically investigate the downstream targets of USF1. Following polymerase chain reaction (PCR) was used to validate the downstream targets. Based on the results, we found USF1 significantly regulated 350 differentially expressed genes (DEGs). Up DEGs were mainly protein coding genes, and enriched in immune and inflammation response pathways; while down DEGs were mainly lncRNAs, indicating the regulatory feature of USF1. We also detected USF1 directly bound to the promoter region of 2492 genes, which may deeply participate in the viral progression and cell proliferation pathways. By integrating these two datasets, we detected 16 overlapped genes, including down lncRNA-NEAT1 and up TF-ETV5. Down lncRNA-NEAT1 showed reverse expression pattern and prognosis result to USF1 in liver cancer patients, while up TF-ETV5 showed consistent result to USF1. Promoter region motif analysis indicated that ETV5 had more binding motifs and genes than USF1 itself for USF1-regulated DEGs, indicating that USF1 may indirectly modulate gene expression by regulating ETV5 expression in Huh7 cells. Finally, we validated the direct interaction between USF1 and the promoter of ETV5 using ChIP-qPCR. In summary, our results demonstrated that USF1 binds to the promoter region of thousands of genes, and affects large part of DEGs by indirectly manner. The downstream genes, including lncRNA-NEAT1 and TF-ETV5, may also tightly participate in the regulated network by USF1 and have potential functions in the progression of HCC. The USF1 and its downstream targets could be used as potential targets for HCC therapy in future.

overall_design: In order to explore the biological function and molecular mechanism of Upstream transcription factor 1 (USF1) in hepatocellular carcinoma(HCC),in this study, we overexpressed USF1 in Huh7 cells and used whole transcriptome profile sequencing (RNA-seq) and chromatin immunoprecipitation sequencing (ChIP-seq) methods to systematically investigate the downstream targets of USF1.

first: Fei

last: Gao

first: Can

last: Zhang

first: Pei-pei

last: Ren

first: Li

last: Ma

first: Xin

first: Ru-zheng

first: Yi

last: Kang


title: Plasma Multi-omics Nucleic Acid Landscape of Gastrointestinal Cancer [miRNA-seq]

summary: We sequenced cell-free nucleaic acid (cfNA) for 2 major cancer types (44 samples of colorectal cancer and 36 samples of stomach cancer) and 81 samples of healthy individuals collected in China. Cancer related signaling pathway  were identified. Cancer detection and specific classification were achieved through combining both cfRNA and cfDNA reads.

overall_design: small RNA-seq of Homo sapiens: patient's plasma from colorectal and stomach cancer and healthy control; Provided by Peking University First Affiliated Hospital.

first: Pengfei

last: Bao