title: DDX18 coordinates nucleolus phase separation and chromatin organization to control the pluripotency of human embryonic stem cells [DDX18_iCLIP-seq]

first: XIANLE

last: SHI

state: NY

address: 168 street

institute: CUMC

summary: Pluripotent stem cells are unique in their large nucleus and manifestly open chromatin structure with hypertranscriptional activities. How the nucleolus, the largest membraneless and phase-separated subnuclear organelle, maintains its structural integrity in pluripotency maintenance remains incompletely understood. By studying nucleolus-specific DEAD-box RNA helicase-18 (DDX18) in human embryonic stem cells, we discover mechanisms controlling nucleolus phase separation and chromatin organization.

overall_design: RNA-seq (s) were designed to reveal DDX18 function in human ESC idetity maintenance. iCLIP-seq (s) as well as ChIP-seq were designed to reveal DDX18 binding RNA and DNA.

first: Xianle

last: Shi

first: Jianlong

last: Wang

first: Jihong

last: Yang

first: Xin

last: Huang


title: DDX18 coordinates nucleolus phase separation and chromatin organization to control the pluripotency of human embryonic stem cells [DDX18_CHIP-seq]

status: Public on Nov 07 2024

city: New York

country: USA

type: Genome binding/occupancy profiling by high throughput sequencing


title: Blockade of PF4-induced Th1-Treg polarization enhances anti-tumor immunity

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

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

type: Expression profiling by high throughput sequencing

summary: The tumor microenvironment (TME) contains various immune-suppressive cells such as regulatory T cells (Tregs) and M2-like tumor associated macrophages (TAMs) that express the enzyme arginase I (Arg1). T helper 1-polarized Treg (Th1-Treg) is a Treg subset that markedly accumulate in tumor tissues, suppressing anti-tumor immunity. However, little is known about the mechanism behind the abundant presence of Th1-Tregs in TME. Here we show that Arg1-expressing TAMs (Arg1+ TAMs) play critical roles for the high Th1-Treg ratio in TME. Selective depletion of Arg1+ TAMs using the VeDTR system inhibited tumor growth and concurrently reduced the Th1-Treg ratio in TME. Notably, Arg1+ TAMs secreted platelet factor 4 (PF4) that polarized Tregs to Th1-Tregs in a CXCR3-dependent manner. Both genetic PF4 inactivation and PF4 neutralization hindered Th1-Treg accumulation in TME, consequently suppressing tumor growth. Collectively, our study highlights the importance of M2-like TAM-produced PF4 for high Th1-Treg levels in TME to suppress anti-tumor immunity, and demonstrates PF4 neutralization as a potential cancer immunotherapeutic strategy by intervening the M2-like TAM/Th1-Treg axis.

overall_design: MC38 or B16F10 cells were subcutaneously transplanted into Cx3cr1-Cre/VeDTR(ΔFRT) mice. CD45(+)YFP(+) cells were isolated from the tumor and spleen of the same tumor-bearing mice, and single-cell RNA sequencing was performed. GSM7987093 and GSM7987094 are data from MC38-inoculated mice, while GSM8499134 and GSM8499135 are data from B16F10-inoculated mice.

first: Ayumi

last: Kuratani

last: Okuzaki

first: Masahiro

last: Yamamoto


title: Intermittent fasting triggers interorgan communication to suppress hair follicle regeneration

city: Hangzhou

first: Bing

last: Zhang

state: Zhejiang

address: No. 600 Dunyu Road, Sundun Town, Xihu District

department: School of Life Sciences

country: China

institute: Westlake University

summary: Intermittent fasting has gained increasing popularity globally for its potential benefits for improving health and managing weight, but how it impacts the homeostasis and regeneration of peripheral tissues remains elusive. Here we report that in mice, commonly used intermittent fasting regimens negatively affect hair regeneration by selectively inducing apoptosis in activated hair follicle stem cells (HFSCs). Through manipulating animals' daily feeding schedules and caloric intake, we have found that the impaired hair regeneration is primarily caused by the extended fasting periods within these regimens, rather than a reduction in total caloric intake or alterations in circadian rhythm. As the fasting period lengthens, the severity of the defects worsens. Mechanistically, extended periods of fasting activate the hypothalamic-pituitary-adrenal axis, prompting the release of lipolytic hormones from the adrenal glands into circulation. This triggers rapid lipolysis in dermal adipocytes, elevating levels of free fatty acids within the skin. Consequently, fatty acid oxidation is activated in HFSCs, causing increased cellular oxidative stress and apoptosis. Surgical removal of adrenal glands, genetic inhibition of fatty acid oxidation in HFSCs, or enhancement of HFSCs’ antioxidant capability genetically or pharmaceutically prevents fasting-induced stem cell death. Our study reveals a detrimental effect of intermittent fasting on somatic stem cells and peripheral tissue regeneration, and identifies a close crosstalk between an ancient neuroendocrine mechanism and a critical niche component that functions as a “brake” to halt tissue regeneration when the supply of nutrients becomes unstable.

overall_design:
Cell type: FACS purified hair follicle stem cells (HFSCs) and epidermal stem cells (EpiSCs) from mouse skin; 3 conditions: Ad libitum, Fasting for 24 hours, and Fasting for 48 hours; 2 replicates for EpiSCs, and 3 replicates for HFSCs each condition.
Cell type: FACS purified hair follicle stem cells (HFSCs) from mouse skin; 2 conditions: 6 months of Ad libitum and 6 months of Alternative day fasting (sampled at the day after fasting); 2 replicates for HFSCs each condition.
Cell type: FACS purified hair follicle stem cells (HFSCs) from mouse skin; 2 replicates for HFSCs at 2nd telogen.

first: Han

last: Chen

first: Chao

last: Liu

first: Shiyao

last: Cui

first: Jingyu

last: Peng

first: Xiaoling

last: Yu


title: Multi-omics approach reveals genes and pathways affected in Miller-Dieker Syndrome

city: Notre Dame

first: Jessica

middle: A

last: Brown

state: IN

address: 251 Nieuwland Science Hall

department: Chemistry and Biochemistry

institute: University of Notre Dame

summary: Miller-Dieker Syndrome (MDS) is a rare neurogenetic condition resulting from a heterozygous deletion of 26 genes in the MDS locus on human chromosome 17. Often MDS patients die in utero but of those who are born, only ~10% reach ten years old. Current treatments for MDS are based on the individual’s symptoms, which aim to prevent complications and control seizures. A detailed understanding of the pathogenesis of MDS through gene expression studies would be useful in developing precise medical approaches toward MDS. To better understand MDS at the molecular level, we performed RNA sequencing on RNA and mass spectrometry on total protein isolated from BJ (non-MDS) cells and GM06097 (MDS) cells, which were derived from a healthy and an MDS patient, respectively. Differentially expressed genes (DEGs) at the RNA and protein levels involved genes associated with phenotypic features reported in MDS patients (CACNG4, ADD2, NEAS, SHANK2), signaling pathways (WNT, GABBR2, CAMK2B, TRAM-1), and nervous system development (CAMK2B, BEX1, AHNAK). Phenotypic assays validated enhanced calcium signaling, cell migration defects and downregulated protein translation in MDS. Interestingly, methyltransferase-like protein 16 (METTL16), a protein encoded in the MDS locus, displayed a significant role in cell migration and protein translation defects in MDS cells. Although DNA and RNA modifying enzymes were among the DEGs and the intracellular SAM/SAH ratio was 8-fold lower in MDS cells, global nucleoside modifications remained unchanged. Thus, this study identified specific genes and pathways responsible for the gene expression changes, which could lead to better therapeutics for MDS patients.

overall_design: To invesitigate the RNA level expression changes in Miller-Dieker Syndrome (MDS), RNA-seq apporach was utilized on the total RNA extracted from BJ (control) and GM06097 cells (MDS patient-derived cells). Illumina HiSeq 2000 sequencing (paired-end) was performed on the total RNA extracted from these 2 cell types with 4 biological replicates each.

first: Gowthami

last: Mahendran

first: Kurtis

last: Breger

first: Philip

middle: J

last: McCown

first: Jacob

middle: P

last: Hulewicz


title: Targeting CD206+ macrophages disrupts the establishment of a key anti-tumor immune axis [scRNA-seq]

status: Public on Nov 08 2024

city: San Francisco

first: Bushra

last: Samad

state: CA

address: 505 Parnassus Ave

institute: USCF Immunoprofiler

summary: CD206 is a common marker of a putative immunosuppressive ‘M2’ state in tumor-associated macrophages (TAMs). We made a novel conditional CD206 (Mrc1) knock-in mouse to specifically visualize and/or deplete CD206+ TAMs. Early depletion of CD206+ macrophages and monocytes (Mono/Macs) led to the indirect loss of conventional type I dendritic cells (cDC1), CD8 T cells and NK cells in tumors. CD206+ TAMs robustly expressed CXCL9, contrasting with stress-responsive Spp1-expressing TAMs and immature monocytes, which became prominent with early depletion. CD206+ TAMs differentially attracted activated CD8 T cells, and the NK and CD8 T cells in CD206-depleted tumors were deficient in Cxcr3, and cDC1-supportive Xcl1 and Flt3l expression. Disrupting this key anti-tumor axis decreased tumor control by antigen-specific T cells in mice. In human cancers, a CD206Replete, but not a CD206Depleted Mono/Mac gene signature correlated robustly with CD8 T cell, cDC1 and NK signatures, and associated with better survival. These findings negate the unqualified classification of CD206+ ‘M2-like’ macrophages as immunosuppressive.

overall_design: CD2dsRedOT-I CD8 T cells were adoptively transferred into Csf1rCre; Mrc1-LSL-Venus-DTR mice bearing B78chOVA tumors. 12d after T cell injection with or without early depletion by DTx administration every 2-3 days, tumors were isolated, sliced and prepared for spatial barcoding. Three zones - outer, mid, inner were barcoded by the localization of Venus, dsRed and SHG signals and spatial transcriptomics performed by ZipSeq using a anti-CD45 anchor. Samples listed here include the DTx treated group only while the untreated control group samples are included in an earlier GEO submission id # GSE201074

first: Arja

last: Ray

first: Kenneth

last: Hu


title: Blockade of PF4-induced Th1-Treg polarization enhances anti-tumor immunity (Bulk RNA-Seq)

first: Daisuke

last: Motooka

summary: The tumor microenvironment (TME) contains various immune-suppressive cells such as T helper 1-polarized regulatory T cells (Th1-Tregs). However, little is known about the mechanism behind the abundant presence of Th1-Tregs in TME. In this work, we demonstrate that selective depletion of arginase I (Arg1)-expressing tumor associated macrophages (Arg1+ TAMs) inhibits tumor growth and concurrently reduces the Th1-Treg ratio in TME. Notably, Arg1+ TAMs secrete platelet factor 4 (PF4) that reinforces interferon-γ (IFN-γ)-induced Treg polarization into Th1-Tregs in a manner dependent on CXCR3 and the IFN-γ receptor. Both genetic PF4 inactivation and PF4 neutralization hinder Th1-Treg accumulation in TME, consequently suppressing tumor growth. Collectively, our study highlights the importance of Arg1+ TAM-produced PF4 for high Th1-Treg levels in TME to suppress anti-tumor immunity, and demonstrates PF4 neutralization as a potential cancer immunotherapeutic strategy.

overall_design: Bulk RNA-seq analysis of gene expression profiles in intra-tumoral RFP(+) or RFP(-) CD45+, Ly6C(-), Ly6G(-), NK1.1(-), B220(-), CD90.2(-), MHCII(+), F4/80(+), CD11b(+) cells (TAMs) from B16F10- or MC38-bearing Arg1-RFP mice (n = 3).

last: Kuratani


title: Expression data from human trisomy 21 and euploid fibroblasts, iPSCs, and neural progenitor cells

status: Public on Nov 06 2024

city: Bethesda

first: Laura

middle: L

last: Baxter

state: MD

address: 35A Convent Drive

department: NHGRI

institute: NIH

summary:
Trisomy of human chromosome 21 (T21) gives rise to Down syndrome, the most frequent life-born autosomal aneuploidy. To enable in vitro analyses of the cellular and moelcular mechanisms leading to the neurological alterations associated with T21, we created and characterized a panel of genomically diverse T21 and euploid induced pluripotent stem cells (iPSCs) from fibroblasts obtained from the Coriell Institute for Biomedical Research, and we then differentiated these iPSCs into neural progenitor cells (NPCs).
Microarray transcriptomic analyses were performed on this panel of fibroblasts, iPSCs, and NPCs, identifying genes and pathways that were altered in T21 lines relative to euploid as well as genes and pathways in NPCs that showed inter-individual variability.

overall_design: This study used cell lines obtained from racially diverse individuals with trisomy for human chromosome 21 along with age-and sex-matched euploid control cell lines. One RNA sample was collected per line. Fibroblast, iPSC, and NPC cDNA samples were hybridized to Affymetrix Clariom S HT arrays (902970, Thermofisher Scientific).


title: Single-cell and spatial transcriptomics identify COL6A3 as a prognostic biomarker in undifferentiated pleomorphic sarcoma [scRNA-Seq]

city: Dallas

first: Jason

middle: C

last: Klein

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

summary: Undifferentiated pleomorphic sarcoma (UPS) and related tumors are the most common type of soft tissue sarcoma. However, this spectrum of tumors has different etiologies with varying rates of metastasis and survival. Two dermal-based neoplasms in this class of pleomorphic sarcomas, atypical fibroxanthoma (AFX) and pleomorphic dermal sarcoma (PDS), are challenging to differentiate at initial biopsy but vary significantly in prognosis. We performed single-cell transcriptomics on five AFX and PDS biopsy specimens as well as both single-cell and spatial transcriptomics on one PDS excision specimen to better characterize these tumors. The top differential genes between AFX and PDS were predictive of overall survival in 17 other cancers included in the Human Protein Atlas. Of these genes, COL6A3 and BGN predicted overall survival and metastasis-free survival in independent cohorts of 46 and 38 UPS tumors, respectively. COL6A3 was most predictive of overall survival in UPS patients and outperformed an established sarcoma prognostic gene panel at predicting metastasis in UPS.

overall_design: scRNAseq was performed with 10X Chromium Single Cell Gene Expression Flex. FFPE blocks for each sample were prepared per protocol CG000632 Rev C. Library preparation was conducted per protocol CG000691 Rev A. One million cells per sample were used for probe hybridization. 12,000 cells were loaded per sample. Libraries were sequenced on a Novaseq X 25B flowcell with PE 151bp reads and NextSeq2K, P3 with 28 and 90bp reads.

last: C Klein

first: Lei

last: Wang

first: Douglas

last: Strand

first: Chewlan

last: Lastufka

first: Gregory

last: Hosler

first: Gary

last: Hon


title: METTL14-mediated m6A differentially orchestrates brown and white adipose tissue transcriptomes to regulate systemic metabolism

city: Chicago

first: Cheng-Wei

last: Ju

state: Illinois

address: 929 East 57th Street, GCIS, Room E313

institute: The University of Chicago

type: Methylation profiling by high throughput sequencing

summary: Human brown and white adipocytes (hBAT and hWAT) display markedly distinct m6A landscapes; besides, in insulin-resistant humans and mice, methyltransferase like 14 (METTL14) expression differs significantly between BAT and WAT in the context of its correlation with insulin sensitivity. We therefore employed independent BAT- and WAT-specific METTL14 knockout models to unveil the cell-type specificity of m6A mRNA methylation. Mettl14 knockout via Ucp1-cre or Adipoq-cre drivers in BAT and WAT, respectively, yields divergent metabolic outcomes in mouse.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
Mettl14fl/fl mice on a C57BL/6N background (De Jesus et al. 2019) were crossed with Ucp1cre strain (stock no.024670, the Jackson Laboratory) or Adipoqcre strain (stock no.028020, the Jackson Laboratory)  mice, which do not harbor the nicotinamide nucleotide transhydrogenase (Nnt) mutation, to generate the knockouts.
For studies on diet-induced obesity and long-term insulin resistance, M14fl/fl,M14fl/fl-Ucp1cre, and M14fl/fl-Adipoqcre mice were fed either 10% fat LFD or a conventional 60% fat HFD for 14 weeks, starting at 6 weeks of age. To examine tissue-specific insulin sensitivity, mice were fasted for 16 hours.

first: Ling

last: Xiao

first: Rohit

middle: N

last: Kulkarni

first: Chuan

last: He


title: The maternal X chromosome impairs cognition and accelerates brain aging through epigenetic modulation in female mice II

first: Dena

last: Dubal

state: California

address: 675 Nelson Rising Lane, Rm 292

department: Department of Neurology

institute: University of California San Francisco

summary: To compare gene expression between old C57BL6 female mice treated with either control lentivirus or CRISPRa+ lentivirus, we used a flurorescence-based cell sorting to collect neurons expressing GFP (from the sgRNA) from the hippocampus of the mice from each group.Then we performed gene expression analysis using data obtained from RNA-seq of the old neurons in the hippocampus of both groups.

overall_design: Comparative gene expression profiling analysis for old C57BL6 mice treated with either control lentivirus or CRISPRa+ lentivirus. Each experimental group has 4 biological replicates

first: Samira

last: Abdulai-Saiku


title: Ongoing replication stress tolerance and clonal T cell responses distinguish liver and lung recurrence and outcomes in pancreatic cancer

city: Portland

first: Rosalie

last: Sears

state: OR

address: 2730 SW Moody Ave, CL4RS

department: Molecular and Medical Genetics

institute: Oregon Health & Science University

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

overall_design: Refer to individual Series


title: Role of Mac1 in gene regulation under copper limiting conditions in Fusarium oxysporum [ChIP-seq]

city: Córdoba

first: Antonio

last: Di Pietro

state: Córdoba

address: Campus Rabanales, Edificio Gregor Mendel, 1

department: Genetics

country: Spain

institute: Universidad de Cordoba

summary: The transcription factor Mac1 is a key regulator of copper homeostasis and controls the transcriptional response to copper-limiting conditions in fungi. Expression analyses performed in the soil-borne plant pathogen Fusarium oxysporum revealed that almost all copper starvation-induced genes are downregulated in the absence of the regulator Mac1. The aim of this ChIP-seq analysis is to elucidate which of these genes are direct targets of Mac1.

overall_design: Identification of Mac1-DNA interactions under copper limiting conditions and presence of copper in Fusarium oxysporum f. sp. lycopersici 4287 by ChIP-seq analysis. A mac1Stag mutant, expressing a version of Mac1 protein with the oligopeptide S-tag fused to the C-terminus, was constructed for the analysis. The S-tag was used as the epitope for the antibody α-S-tag (SAB2702227, Sigma-Aldrich®). Wt samples were used as negative control in the immunoprecipitacion assay. Three biological replicates of mac1Stag mutant were used.

first: Rafael

last: Palos-Fernández

first: María

middle: V

last: Aguilar-Pontes

first: Gema

last: Puebla-Planas

first: Harald

last: Berger

first: Lena

last: Studt-Reinhold

first: Joseph

last: Strauss

first: Manuel

middle: S

last: López-Berges


title: DDX18 coordinates nucleolus phase separation and chromatin organization to control the pluripotency of human embryonic stem cells [RNA-seq]

first: XIANLE

last: SHI

overall_design: RNA-seq (s) were designed to reveal DDX18 function in human ESC identity maintenance. iCLIP-seq (s) as well as ChIP-seq were designed to reveal DDX18 binding RNA and DNA.

first: Xianle

last: Shi

first: Jianlong

last: Wang

first: Jihong

last: Yang

first: Xin

last: Huang


title: DDX18 coordinates nucleolus phase separation and chromatin organization to control the pluripotency of human embryonic stem cells.


title: Reprogramming of cells during embryonic transfating: overcoming a reprogramming block

city: DURHAM

first: Alejandro

last: Berrio

state: NC

address: 124 Science Dr

department: Biology

institute: Duke University

summary: “Regulative development” demonstrated by many animal embryos, is the ability to replace missing cells or parts. The underlying molecular mechanism(s) of that ability is not well understood.   If sea urchin micromeres (skeletogenic cell progenitors) are removed at the 16-cell stage, early endoderm initiates a sequential switch in cell fates, called “transfating”. Without micromeres, other mesoderm cells also are initially absent, as their specification depends on signaling from micromeres. Most mesoderm cells later return by transfating, but pigment cells do not. ScRNA-seq, tracked over time, reveals the reprogramming sequence of those replacements.  Beginning with an early endoderm specification state, cells progress through endomesoderm, then mesoderm, and finally distinct skeletogenic and mesodermal specification states emerge, but pigment cells do not. Rescue of pigment cells was found to be a consequence of signal timing: if Delta is expressed prior to Nodal, pigment cells return.  Thus, transfating operates through a sequence of switches in gene regulatory states, and reprogramming fails if endogenous negative signals occur prior to positive signals in the replacement sequence.

overall_design: 7 scRNA-seq samples capturing 7 time points over 18 hours of micromereless sea urchin development

first: Esther

last: Miranda

first: Abdull

last: Massri

first: Anton

last: Afanassiev

first: Geoffrey

last: Schiebinger

first: Gregory

last: Wray

first: David

middle: R

last: McClay


title: Decoupling the Biochemical and Mechanical Effects of Muscle Exercise on Motor Neurons with 2.5D Actuating Matrices [240614Ram_RNA-seq]

city: Cambridge

first: Vincent

last: Butty

state: MA

address: 77 Massachusetts Avenue Bldg 68-317A

department: Biology / Koch Institute / Bioengineering / CEHS

institute: Massachusetts Institute of Technology

summary: We wanted to query the differences and similarities between our wild-type C2C12 cell line and our optogenetic ChR2 C2C12 myoblasts on the same day of differentiation. After 6 days on muscle differentiation medium, we extracted the RNA and sequenced it for 6 wells each.

overall_design:
Transcriptomic comparison of wild-type C2C12 and ChR2-optogenetic C2C12
The O1-O6 samples were six wells of optogenetic C2C12 myoblast that were differentiated in high glucose medium with IGF and aminocaproic acid for six days prior to RNA extraction. Samples WT1-WT6 are the control samples which underwent the same culture conditions but using a WT line.

first: Bu

last: Angel

first: Raman

last: Ritu


title: Survivin promotes stem cell competence for skin cancer initiation [scRNA-seq]

city: Bruxelles

first: Yura

last: Song

address: 808, route de Lennik

country: Belgium

institute: Université Libre de Bruxelles

summary: Stem cells (SCs) and not progenitors (Ps) act as cells of origin of Basal Cell Carcinoma (BCC). The mechanisms promoting BCC formation in SCs or restricting tumour development in Ps are currently unknown. In this study, we transcriptionally profiled SCs and Ps and found that Survivin, a pleiotropic factor that promotes cell division and inhibits apoptosis was preferentially expressed in SCs.  Using genetic gain and loss of function mouse models, we showed that Survivin deletion in oncogene-expressing SCs prevents BCC formation. Survivin overexpression renders Ps competent to BCC formation by promoting cell survival and division while preventing apoptosis and differentiation. We identified SGK1, as a key downstream factor of Survivin, and its inhibition prevents BCC formation. This study uncovers the role and mechanisms by which Survivin regulates the competence of SCs to initiate BCC formation promoting the survival of oncogene-expressing SCs and self-renewing division while restricting differentiation and apoptosis.

overall_design: To investigate the role of Survivin in Basal Cell Carcinoma formation we FACS-isolated a) SmoM2-YFP-expressin cells  cells from the Involucrin-CREER/Rosa-SmoM2 mice and b) cells expressing SmoM2-YFP and Survivin-mCharry in cells from Involucrin-CREER/Rosa-SmoM2/Krt14rtTA/Survivin GOF mice. We  performed single cell RNA seq in the FACS-isolated cells.

first: Rahul

last: Sarate

first: Cédric

last: Blanpain

first: Adriana

last: Sánchez-Danés


title: An inner membrane complex protein IMC1g in Plasmodium berghei plays an essential role in asexual erythrocytic proliferation and transmission

city: Shenyang

first: Xiaotong

last: Zhu

state: Liaoning

address: No. 77 Puhe Road Shenyang North NEW AREA

department: Department of Immunology

institute: China Medical University

summary: The inner membrane complex (IMC), a double-membrane organelle underneath the plasma membrane in apicomplexan parasites, plays a significant role in motility and invasion and confers shape to the cell. We characterized the function of PbIMC1g, a component of the IMC1 family member in Plasmodium berghei. PbIMC1g is recruited to the IMC in late schizonts, activated gametocytes, and ookinetes. Pairwise yeast two-hybrid assays demonstrate that PbIMC1g interacts with IMC1c, a component of the PHIL1 complex, and the core sub-repeat motif ‘EKI(V)V(I)EVP’ in PbIMC1g is essential for this interaction. Localization of PbIMC1g to the IMC was dependent on its IMCp domain, while its C-terminus and palmitoylation sites were required for the full efficiency of proper IMC targeting. PbIMC1g is required for asexual stage development, and its conditional knockdown resulted in a defect in schizogony. Additionally, PbIMC1g was also important for male gametogenesis and ookinete development. As an IMC component that assists in anchoring the glideosome to the subpellicular network, PbIMC1g was also involved in ookinete motility and mosquito midgut invasion. IMC1g from the human parasite P. Plasmodium vivax could functionally replace PbIMC1g in P. berghei, confirming the evolutionary conservation of IMC1g proteins in Plasmodium spp. Together, this work reveals an essential role of IMC1g in the parasite life cycle and suggests that IMC1 family members likely contribute to parasite gliding and invasion.

overall_design: About 108 purified activated gametocytes from PbIMC1gcKD [+]/[-] TMP parasites were lysed in 10 × volumes of TRIzol (Thermofisher) and used for total RNA extraction. The experiment was repeated at three-week intervals to obtain samples as biological duplicates. Sample preparations were performed as described]. Briefly, mRNA was enriched using poly-T oligo-attached magnetic beads. Reverse transcription was performed with SuperScript II (Invitrogen) using random primers. The reaction was then treated with RNaseH to remove the RNA template and cleaned using DNA Clean and Concentrator Kit (Zymo Research). The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced using the Illumina platform. RNA-seq raw data were initially filtered by fastq to obtain high-quality, clean data. Adapter trimming was performed using cutadapt version 1.13 (http://cutadapt.readthedocs.io/en/stable/guide.html). Processed reads were aligned to the P. berghei ANA genome (assembly PlasmoDB-67) with Hisat2 v2.0.4 [108] and deduplicated according to UMI using UMI-tools (v1.0.0) [109]. Reads counts were obtained with HTSeq v0.9.1. Differential expression analysis of genes between the PbIMC1gcKD parasites cultured in both [+] and [-] TMP conditions were determined using the DESeq R package (1.18.0). The p-values were adjusted using the Benjamini-Hochberg procedure, which controls the false discovery rate (FDR). Genes with an adjusted P value <0.05 found by DESeq were assigned as differentially expressed. GO enrichment analysis was implemented using the GOseq R package.

first: Yinjie

last: Liu

first: Shitong

last: Cheng

first: Gang

last: He

first: Duo

last: Wang

first: Sicong

first: Lumeng

last: Chen

first: Dawei

first: Liying

first: Yonghui

last: Feng

first: Liwang

last: Cui

first: Yaming

last: Cao


title: Effect of mRNA vaccine on Epigenetic and Transcriptomic Profiles of Kupffer Cells (CUT&RUN)

city: Bangkok

first: Tanapat

last: Palaga

address: Payathai Road, Pathumwan

department: Microbiology

country: Thailand

institute: Chulalongkorn University

summary: Analysis of genome wide distribution of an active histone mark, trimethylated lysine 4 on histone H3 protein subunit (H3K4me3) showed that an mRNA/LNP immunization resulted in increased H3K4me3 in the regulatory regions of various genes, the expression of some of which were upregulated. In addition, H3k4me3 may indicate that the chromatins of some genes are in the “poised” state where it will influence the expression upon next stimuli.

overall_design: mRNA/LNP was administered via intramuscular route (10 µg per mouse). ChIP seq was performed in genomic DNA isolated from F4/80+ liver resident macrophages from livers of mice immunized with OVA mRNA/LNP or PBS control.

first: Chitsuda

last: Pongma

first: Atsadang

last: Boonmee

first: Salisa

last: Benjaskulluecha

first: Pornlapat

last: Keawvilai

first: Benjawan

last: Saechue


title: The Transcription factor FgSfp1 orchestrates mycotoxin deoxynivalenol biosynthesis in Fusarium graminearum

city: Shanghai

first: Shuting

last: Sun

address: yueyang road 320

institute: Shanghai Institute of Nutrition and Health,CAS

summary: Fusarium graminearum (F. graminearum) and its derivative mycotoxin deoxynivalenol (DON) are highly concerned with food security, safety and sustainability worldwide. The molecular mechanism regulates DON biosynthesis in F. graminearum remains enigmatic, despite several transcription factors (TFs) have been revealed containing regulatory functions. Here, we first characterized a zinc finger-contained TF, FgSfp1. Interestingly, contrast to the previous knowledge, all TRI-cluster genes were abnormally upregulated in ∆FgSfp1 while Tri proteins abundance rationally decreased, resulting in a 95.4% reduction of DON yield simultaneously. Further evidence determined FgSfp1 acted as a nutrient-sensing factor coordinates genetic expression efficiency through interference of ribosomal biogenesis process. Specifically, FgSfp1-depletion leads to ribosome biogenesis assembly factor (RiBi) expression attenuation along with DON precursor acetyl-CoA synthase reduction since FgSfp1 actively interacts with RNA 2’-O-methylation enzyme FgNop1 revealed by Bi-FC and subsequently influences mRNA translation capacity. In conclusion, we elucidated that the FgSfp1 orchestrates DON biosynthesis via participating RNA posttranscriptional modification for ribosomal RNA maturation, offering new insights into the DON biosynthesis regulation. Ultimately, this novel TF might be a key regulator for DON contamination control in the whole food chain.

overall_design: Three replicates for each sample.

first: Aibo

last: Wu


title: Adaptive Biotechnologies TCRbeta sequencing of 174 primary and 42 metastatic pancreatic ductal adenocarcinoma tumor samples from FFPE curls and 215 matched blood plus 73 additional blood samples

first: Rosalie

last: Sears

summary: Patients with metastatic pancreatic ductal adenocarcinoma (PDAC) survive longer if disease spreads to the lung but not the liver. We generated overlapping, multi-omic datasets to identify molecular and cellular features that distinguish patients whose disease develops liver metastasis (liver cohort) from those whose disease develops lung metastasis without liver metastases (lung cohort). Lung cohort patients survived longer than liver cohort patients, despite sharing the same tumor subtype. We developed a pORG gene set enriched in liver cohort versus lung cohort primary tumors. We identified ongoing replication stress (RS) response pathways in high pORG/liver cohort tumors, while low pORG/lung cohort tumors had greater densities of lymphocytes and shared T cell clonal responses. Our study demonstrates that liver-avid PDAC is associated with tolerance to ongoing RS, limited tumor immunity, and less favorable outcomes; whereas low RS, lung-avid/liver-averse tumors are associated with active tumor immunity that may account for favorable outcomes.

overall_design:
From a de-identified dataset of 1,873 patients diagnosed with and/or treated for PDAC at our institution between 2004 and 2020, we identified 422 patients for which we had specimens with sequencing data (N=374) and/or specific evidence of disease metastasis site(s) from the OHSU Cancer Registry and disease-relevant computed tomography (CT) scans to allow for cohort classification. Patients whose primary tumor was located at the Ampulla of Vater but classified as pancreatobiliary subtype were included (N=9). The Adaptive Biotechnologies human TCRB sequencing service was used to sequence both primary and metastatic tumors (25mm thick FFPE curls) and matched blood (frozen leukocytes). Blood specimens were categorized as associated with primary disease or metastatic disease based on the following criteria: The blood specimen was considered primary-associated if it was collected before or on the day of primary tumor resection, metastasis-associated if it was collected after a recurrence, or uncharacterized if it was collected after resection and before recurrence. For patients not treated by resection, the blood was considered primary-associated if it was collected 180 days before the latest date the patient was confirmed metastasis free on imaging. The blood was considered metastasis-associated if it was collected after the patient had metastasis confirmed on imaging or was collected within 30 days before metastasis was detected on imaging.

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*** Adaptive Biotechnologies does not release raw data ***
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first: Brett

last: Sheppard

first: Jonathan

last: Brody

first: Jason

middle: M

last: Link

first: Dove

last: Keith

first: Carl

last: Pelz


title: Effect of mRNA vaccine on Epigenetic and Transcriptomic Profiles of Kupffer Cells (RNA-Seq)

summary: The result show that an mRNA/LNP vaccine induced significant numbers of differentially expressed genes (DEG). The analysis identified 123 DEGs between control PBS and mRNA/LNP vaccinated groups where 23 genes and 100 genes were upregulated and downregulated, respectively, in the mRNA/LNP group. To understand the biological changes from the transcriptomic data, gene set enrichment analysis (GSEA) was performed using the whole transcriptome data set. GSEA identified the biological pathways associated with interferon gamma response and protein secretion as the top two ‘Hallmark’ gene sets enriched in OVA mRNA/LNP group, compared to PBS group.

overall_design: The mRNA encoding a model antigen ovalbumin (OVA) were prepared by in vitro translation  and the mRNA was formulated with LNP for mRNA delivery. mRNA/LNP was administered via intramuscular route (10 µg per mouse). RNA-seq was performed in total RNA isolated from F4/80+ liver resident macrophages from livers of mice immunized with OVA mRNA/LNP or PBS control.


title: Decoupling the Biochemical and Mechanical Effects of Muscle Exercise on Motor Neurons with 2.5D Actuating Matrices

first: Vincent

last: Butty


title: Physiological and transcriptomic characterization of cold acclimation in endodormant grapevine under different temperature regimes

city: Geneva

first: Hongrui

last: Wang

address: 630 W. North Street

department: School of Integrative Plant Science, Horticulture section

institute: Cornell University

summary: Changes in temperature during the dormant season, such as the unusual cold or warmth linked to climate change, can affect cold acclimation and endanger the viability of the grape and wine industry. To tackle this problem, we carried out two experiments in a controlled environment to examine the effects of various temperature conditions on the process of cold acclimation in grapevine buds during endodormancy, using transcriptomic monitoring through 3'RNA-seq.

overall_design: In Experiment 1, grapevine buds in endodormancy were exposed to controlled temperatures of 22 °C, 11 °C, 7 °C, 4 °C, and 2 °C, and samples were collected at regular intervals of 7, 13, 20, 26, 34, 41, 55, and 69 days after treatment from growth chambers. Experiment 2 was conducted simultaneously with Experiment 1 but divided into two phases: phase I and phase II. In phase I, cuttings taken from the same sample used in Experiment 1 were exposed to constant temperatures of 11°C, 7 °C, and 2 °C in separate growth chambers, starting from 0 days after collection and ending at 26 days after collection. In phase II, which started at day 26 and ended at day 69 after collection, single node cuttings from the 11 °C, 7 °C, and 2 °C treatments were transferred to another growth chamber and subjected to a temperature fluctuation treatment with a mean temperature of 7 °C and a daily variation of ±5 °C (maximum of 12 °C and minimum of 2 °C).

first: Al

last: Kovaleski

last: Londo


title: Survivin promotes stem cell competence for skin cancer initiation [RNA-seq]

first: Yura

last: Song

overall_design: To investigate the role of Survivin in Basal Cell Carcinoma formation we isolated SmoM2-YFP-expressing cells from the Krt14-CREER/Rosa-SmoM2, Involucrin-CREER/Rosa-SmoM2, Krt14-CREER/Rosa-SmoM2/ SurvivinLOF and  Involucrin-CREER/Rosa-SmoM2/Krt14rtTA/SurvivinGOF mice and performed bulk RNA seq.

first: Rahul

last: Sarate

first: Cédric

last: Blanpain

first: Adriana

last: Sánchez-Danés


title: Gene expression analysis of WT vs Wdr47 deficient primary neurons

city: Illkirch

first: Juliette

last: GODIN

address: 1 rue LAurent Fries

country: France

institute: IGBMC

summary: Corpus callosum (CC) is the largest interhemispheric connection that is largely formed by the axons of layer 2/3 callosal projection neurons (CPNs) through a series of tightly regulated cellular events.Defects in any of those steps may prevent the proper development of the corpus callosum resulting in a spectrum of disorders collectively referred to as corpus callosum dysgenesis (CCD). Here, we report 5 patients carrying bi-allelic variants in WDR47 presenting CCD together with microcephaly. Using a combination of in vitro and in vivo mouse models and complementation assays, we show that independently from its previously identified functions in neuronal migration and neurite extension, Wdr47 is required for survival of callosal neurons by contributing to the maintenance of mitochondrial and microtubule homeostasis. We further provide evidence that severity of the CCD phenotype is determined by the degree of the loss of function caused by the variants. Taken together, we identify WDR47 as a novel causative gene for corpus callosum abnormalities.

overall_design: To investigate how Wdr47 promotes neuronal survival, we established primary neuronal cultures from WT or Wdr47 deficient neurons. We then performed gene expression analysis at DIV6, 2 days before induction of neuronal death, using data obtained from RNA-seq of 4 samples per genotype coming from 3 independent cultures.

first: Efil

last: Bayam

first: Binnaz

last: Yalcin

last: Godin


title: Pseudohypoxia Due to PHD2 Deficiency Induces Endothelial Resistance to Apoptosis and Inflammation Independent of HIF2 alpha via AKT Activation and AIP1 Loss

first: Gabriela

last: Ferreyra

address: 9000 Rockville Pike - Building 10 room 4D03

department: CCMD

institute: Clinical Center

summary:
PHD2 silencing activated AKT and ERK, inhibited JNK, and decreased AIP1, inhibiting apoptosis and proliferation and activating STAT. Like PHD2, AIP1 silencing affected the same kinase pathways and produced a similar dysfunctional endothelial cell phenotype, which was at least partially reversible with AKT inhibition. Transcriptomic profiling of human lung microvascular endothelial cells revealed that silencing PHD2 or AIP1 both induced an IFN/STAT-biased inflammatory signature with repression of E2F and MYC target genes. These in vitro results mirrored findings in lung vascular endothelial cells and tissues from PAH patients as well as rodent models of PAH.
PHD2 deficiency in human lung vascular endothelial cells induced an apoptosis-resistant, inflammatory, and hypo-proliferative phenotype. AKT activation and AIP1 loss, but not HIF signaling, drove these phenotypic aberrations.

overall_design: Microarray analysis was conducted on samples from five independent experiments using LMVECs from the same donor at the same passage number to minimize variability. Cells were transfected with either scrambled pool non-targeting control siRNA, specific PHD2 (siPHD2, 15 nM), AIP1 (siAIP1, 15 nM), or both (siBoth) siRNA for 48 hours, and total RNA was then extracted using RNeasy miniprep kits (Qiagen).

first: Shuibang

first: Cumhur

middle: Y

last: Demirkale

first: Keytam

last: Awad

first: Li-Yuan

last: Chen

last: Elinoff

first: Robert

last: Danner


title: Epigenetics CRISPRi screen in mouse neuronal progenitor cells (NPCs)

city: duarte

first: LU

last: YANG

address: 1500 duarte rd

institute: city of hope

summary: This dataset examined the epigenetic gene effect on mouse NPCs with Upf2 gene knockout (KO). The sgRNA sequencing results form the epigenetics CRISPRi screen sample are reported.

overall_design: CRISPR sgRNA sequencing: dCas9-Krab-expressing NPCs were harvested from the Upf2(f/f) mice, and transduced with a lentiviral CRISPRi library targeting mouse epigenetics genes (Total 3630 sgRNAs). The integrated sgRNA were amplified from each sample using DCF01 5’-CTTGTGGAAAGGACGAAACACCG-3’ and DCR03 5’- CCTAGGAACAGCGGTTTAAAAAAGC-3’ for high-throughput sequencing (SE75, NextSeq550).

first: Sika

last: Zhang

first: Chun-Wei

first: Lu

last: Yang


title: DAP-seq reveals FvSEP3 directly targets downstream genes relevant to strawberry fruit ripening

status: Public on Nov 05 2024

city: Beijing

first: Tang

last: RenkunTang

state: (optional)

address: Xiangshan, Haidian District

institute: Institute of Botany, Chinese Academy of Sciences

summary: To better understand FvSEP3-mediated transcriptional regulation of fruit ripening, we performed DNA affinity purification sequencing (DAP-seq) to uncover FvSEP3 directly binding sites at the genome level. For DAP-seq analysis, the recombinant FvSEP3 fusion protein was used to purify the sheared genomic DNA of strawberry fruits. Two independent biological replicates of DAP-seq and DNA 'input' negative control libraries were prepared and submitted for deep sequencing.

overall_design: Genomic DNA enrichment profiles in strawberry fruit of 30 DPA wild-type were generated by DAP-seq.Two independent biological replicates and DNA 'input' negative control libraries were prepared and submitted for deep sequencing.

first: Guozheng

last: Qin

first: Renkun

last: Tang


title: Genomic and Histologic Analysis of Uterine Leiomyosarcoma from Leiomyoma with Bizarre Nuclei

first: Christopher

last: Felicelli

address: 303 East Chicago Avenue

department: Pathology

institute: Northwestern University Feinberg School of Medicine

summary: Leiomyoma with bizarre nuclei (LM-BN) is a rare variant of leiomyoma with a benign clinical course. In contrast, leiomyosarcoma (LMS) is a high-grade, malignant neoplasm characterized by high recurrence rates and poor survival. While LM-BN and LMS show distinct morphologies, they share similar immunoprofile and molecular alterations, with both considered “DNA unstable”. Rare cases of LM-BN associated with LMS have been reported, however the histogenesis and molecular relationship between these two tumors remains unclear. In this study, we assessed 11 cases of LMS arising in conjunction with LM-BN and further analyzed the clinical, histologic, and molecular characteristics of these lesions. Tumor slides were examined by histology and immunohistochemistry to confirm the presence of both LMS and LM-BN components. LM-BN and LMS had similar p16 and p53 IHC patterns, but LMS had a higher Ki-67 index and lower ER/PR expression. Digital image analysis based on nuclear and cytologic features revealed spatial relationships between LMS and LM-BN. Genomic copy number alteration (CNA) demonstrated the same clonal origin of LMS from existing LM-BN through conserved copy number alterations. LMS harbored higher CNAs and frequent loss of the TP53, Rb, PTEN, and/or CDKN2A genomic region than LM-BN, indicative of tumor progression. Spatial transcriptome analysis defined uniquely expressed gene signatures in a geographical distribution, demonstrating molecular evidence of regional cell specific differences of LM-BN and LMS. Mutation analysis of large oncogenic panel revealed many shared functional gene alterations in both LM-BN and LMS, but more highly enriched in LMS. Our findings for the first time suggest that a subset of LMS arise from an existing LM-BN.

overall_design: Four cases with the best distributions of both LMS and LM-BN back-to-back within 6x6mm regions were selected for spatial transcriptomic RNA-seq. To confirm the RNA quality of each FFPE tissue block, 1-2 curls (10um thickness each) were used for RNA extraction using Qiagen RNeasy FFPE kit (Qiagen 73504) according to manufactures’ protocol. Extracted RNA was examined by Agilent Bioanalyzer RNA pico chip to confirm the DV200 >30%. Simultaneously, the tissue morphology was examined on H&E-stained slide to identify the presence of both LMS and LM-BN components.

first: Felicelli

last: Christopher

first: Wei

last: Jian-Jun

first: Schipma

last: Matthew


title: Classification of pediatric soft and bone sarcomas using DNA methylation-based profiling

city: Campinas

first: Felipe

last: Silva

address: R. Márcia Mendes, 506

country: Brazil

institute: Boldrini

summary: Pediatric sarcomas present heterogeneous morphology, genetics and clinical behavior posing a challenge for an accurate diagnosis. DNA methylation is an epigenetic modification that coordinates chromatin structure and regulates gene expression, determining cell type and function. DNA methylation-based tumor profiling classifier for sarcomas (known as sarcoma classifier) from the German Cancer Research Center (Deutsches Krebsforschungszentrum) was applied to 122 pediatric sarcomas referred to a reference pediatric oncology hospital. The classifiers reported 88.5% of agreement between histopathological and molecular classification confirming the initial diagnosis of all osteosarcomas and Ewing sarcomas. Transcriptome raw data quality was verified with FASTQC. We used STAR-fusion to identify and annotate fusion transcripts based on discordant read alignments with default configurations. ChimeraViz was used to plot fusion-genes.

overall_design: RNA was extracted with RNeasy Kit (QIAGEN, Hilden, Germany; cat. ID: 74106) and quantified with High Sensitivity Qubit™ RNA Assay Kits (Invitrogen™, Waltham, MA, USA; cat. ID: Q32855). Transcriptome assay was performed using Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus (Illumina, San Diego, CA, USA) and sequenced on the NextSeq550 or NOVAseqX (Illumina Inc, San Diego, CA, USA). Paired-end runs were sequenced in 74 cycles per read (2 X 74), with an average of 41.5 million reads per sample.

first: Mariana

last: Maschietto


title: N6-methyladenosine RNA methylomes in diploid strawberry fruit of wild-type and Fvalkbh10b mutant at 27 DPA

summary: To decipher the mechanisms by which FvALKBH10B regulates fruit ripening, we performed m6A sequencing (m6A-seq) using mRNA from fruits of wild type and Fvalkbh10b mutant. The libraries for sequencing were prepared with 3 replicates, in which the mRNA samples were independently prepared. FvALKBH10B mutation leads to a delay in fruit ripening and causes global m6A hypermethylation of 1859 genes.

overall_design: mRNA m6A methylation profiles in diploid strawberry fruits of 27 DPA wild-type and Fvalkbh10b mutant were generated with three independent biological replicates, using the Illumina NovaseqTM 6000.


title: ROS-induced cytosolic release of mitochondrial PGAM5 accelerates colorectal cancer progression via MST3-mediated YAP activation

city: Beijing City

first: Shiyang Wang

middle: Shiyang

last: Wang

state: Beijing City

address: 2 West Yuanmingyuan Road, Haidian District, Beijing, China

institute: China Agricultural University

summary: Aberrant mtROS release in response to mitochondrial stress are considered to be a major novel feature of neoplastic transformation. However, the molecular mechanisms by which mtROS contribute to CRC development have not been fully elucidated. In this study, we showed that upon sensing the mtROS signal, the mitochondrially localized phosphatase PGAM5 undergoes cleavage in the mitochondrial transmembrane domain, and then the Cleaved PGAM5 is released into the cytoplasm. Subsequently, Cleaved PGAM5 binds to the kinase MST3 in the cytoplasm to promote MST3 dephosphorylation, resulting in a decrease in MST3 activity. Importantly, MST3 inactivation failed to regulate YAP phosphorylation, leading to YAP translocation into the nucleus, consequently promoting CRC proliferation and metastasis. Collectively, our findings identified the PGAM5-MST3-YAP axis as an important molecular mechanism through which mtROS promotes CRC development.

overall_design: To investigate the regulatory role of MST3 in colon cancer, we overexpressed MST3 in colon cancer cell line HCT116.

first: Shiyang


title: The maternal X chromosome impairs cognition and accelerates brain aging through epigenetic modulation in female mice

city: San Francisco

first: Dena

last: Dubal

address: 675 Nelson Rising Lane, Rm 292

institute: University of California San Francisco

summary:
To compare gene expression between the materal X (Xm) and paternal X (Xp), we used a flurorescence-based cell sorting to separate the maternal X from the paternal X. Then we performed gene expression analysis using data obtained from RNA-seq of young Xm and Xp cells

To compare gene expression between the materal X (Xm) and paternal X (Xp) in neurons from both young and old mice, we used a flurorescence-based cell sorting to separate the maternal X from the paternal X. Then we performed gene expression analysis using data obtained from RNA-seq of young and old Xm and Xp neurons.

overall_design:
Comparative gene expression profiling analysis for young Xm and Xp cells. Each experimental group has 5 biological replicates

Comparative gene expression profiling analysis for young and old Xm and Xp cells. Each experimental group has 5 biological replicates

first: Samira

last: Abdulai-Saiku


title: The role of HNRNPU and the nuclear matrix in human pluripotent stem cells [RIP-Seq]

city: Shenzhen

first: Andrew

last: Hutchins

address: 1088 Xueyuan Rd

department: Bioinformatics

institute: Southern University of Science and Technology

summary: During early embryogenesis the fertilized zygote proceeds through an intricate developmental program, accompanyed by DNA and chromatin remodelling. However, the mechanisms governing this reconfiguring are poorly understood. Parts of the embryogenesis developmental program can be captured in vitro in the form of two types of human pluripotent stem cells (hPSC): naïve and primed hPSCs. Naïve hPSCs resemble the inner cell mass of the blastocyst, whilst primed hPSCs resemble the post-implantation embryo. The nucleus is made of DNA wrapped around chromatin, and the nuclear matrix, a proteinaceous gel that provides  structure. Here, we show that disruptions in the nuclear matrix caused primed hPSCs to spontaneously convert to the naïve, earlier embryonic state.

overall_design: RIP-seq was performed on hPSCs (H1 line) or 293T cells using an antibody against HNRNPU, or anb IgG control antibody. Input RNA was also sequenced.

first: Gang

last: Ma

first: Xiuling

last: Fu


title: Gene expression changes upon CD63 knockdown in esophageal squamous cell carcinoma cell lines

city: Chiba-Shi

first: Yasunori

last: Matsumoto

state: Chiba

address: 1-8-1 Inohana, Chuo-Ku

department: Frontier Surgery

institute: Chiba University

summary:
The purpose of this analysis is to analyze the changes in gene expression that occur in cancer cells when CD63 is knocked down in esophageal squamous cell carcinoma (ESCC) cell lines.
We performed a comprehensive analysis of mRNA in CD63 knockdown human ESCC cell lines (TE2, TE15) using microarrays.

overall_design: Two human ESCC cell lines (TE2 and TE15) were transfected with siRNA (OriGene CD63 siRNA, cat No. SR300689A) using lipofectamine, total RNA was extracted 48 hours later and analyzed using SurePrint G3 Human GE microarray v.3.0 (Agilent).


title: The role of HNRNPU and the nuclear matrix in human pluripotent stem cells [Hi-C]

overall_design: Hi-C was performed in hPSCs (H1 line) in cells transfected with an shRNA targetting Luciferase (LUC) as a control, or against (HNRNPU)


title: The role of HNRNPU and the nuclear matrix in human pluripotent stem cells [MAR-Seq]

overall_design: MAR-seq was performed in hPSC H1 cells to idnetify scaffold attachment sites.


title: A DNA methylation database of human and mouse hematological malignancy cell lines

city: Badalona

first: Manel

last: Esteller

state: Barcelona

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

department: Cancer and Leukemia Epigenetics and Biology Program (PEBCL)

institute: Josep Carreras Leukaemia Research Institute (IJC)

summary: Human cancer cell lines constitute useful models to model the primary disease and many relevant findings in tumor biology have been originated from them since the first immortalized cell line (HeLa) was obtained. The easy experimental intervention, the purity of the transformed cells and their versatility to undergo high-throughput screenings represent advantageous features of the established cancer cell lines. Herein, we have obtained the DNA methylation profiles of 210 cell lines derived from hematological malignancies utilizing comprehensive DNA methylation microarrays that interrogate more than 850,000 and 285,000 CpG sites from human and mouse genomes, respectively.

overall_design: Bisulphite converted DNA from 210 hematological cell lines, 180 from human and 30 from mouse were hybridized to the Illumina Infinium HumanMethylationEPIC version 1.0 microarray and Infinium Mouse Methylation BeadChip, respectively.

first: Aleix

last: Noguera-Castells

first: Carlos

last: Garcia-Prieto

first: Gerardo

last: Ferrer

first: Veroncia

last: Davalos

first: Fernando

last: Setien

first: Eulàlia

last: Genescà

first: Jordi

last: Ribera

first: Josep Maria


title: The role of HNRNPU and the nuclear matrix in human pluripotent stem cells [scRNA-Seq]

overall_design: Single cell RNA-seq was performed in hPSCs (H1 line) in cells transfected with shRNAs targetting Luciferase (LUC) as a control, or against HNRNPU


title: Sub-compartment specific small non-coding RNA expression deregulation and altered nucleoli in mesial temporal lobe epilepsy

city: Utrecht

first: Ronald

middle: Jeroen

last: Pasterkamp

state: Utrecht

address: Universiteitsweg 100

department: Translational Neuroscience

country: Netherlands

institute: University Medical Center Utrecht

summary: Large scale changes in coding and non-coding RNA expression is a common feature of the resected hippocampal tissue from pharmacoresistant mesial temporal lobe epilepsy (mTLE) patients. However, there is very less insight on the expression and localization changes of the key regulatory RNAs at a sub-compartment level contributing to pathological mechanisms in mTLE. In the present study we set out to understand the global sub-compartment specific changes in miRNA expression and localization and the alterations in the nucleus that possibly drive these changes and the consequences towards mTLE pathogenesis. We compared the nuclear and cytoplasmic distribution of miRNAs by small RNA-seq in subcellular fractionations of hippocampal tissue from mTLE patients and controls. Several miRNAs were found to be specifically enriched in the nucleus of hippocampal cells from patients compared to the controls, where miR-92b-3p (a miRNA-enriched in neurons) was the most de-regulated nuclear miRNA. By performing miR-92b co-immunoprecipitation (co-IP) assay on N2A nuclei and RNA-seq we identified enrichment of mTLE relevant pathways involving mitochondrial and ribosomal processes.

overall_design: To understand the nuclear targets of miR-92b, we performed pulldown assays for biotin-tagged miR-92b in nuclear and whole cell compartments from mouse neuroblastoma N2A cells. Biotin immunoprecipitation was performed after overexpression of miR-92b or a Scramble mimic tagged with biotin. Cellular fractionations were performed and RNA collected from nuclear and whole cell fractions was subjected to total RNA sequencing.

first: Vamshidhar

last: Vangoor

first: Giuliano

last: Giuliani

first: Marina

last: de Wit

first: Morten

middle: T

last: Venø

first: Jørgen

last: Kjems

first: R


title: The role of HNRNPU and the nuclear matrix in human pluripotent stem cells

first: Andrew

last: Hutchins

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

overall_design: Refer to individual Series


title: ROS-induced cytosolic release of PGAM5 accelerates cancer progression via MST3-YAP axis

first: Shiyang Wang

last: Wang

overall_design: To investigate the function of MST3 in CRC regulation, we generated MST3 intestinal epithelial knockout mice and treated them with AOM&DSS.We then performed gene expression profiling using mRNA-seq data from the intestinal epithelium of littermate mice.

first: Shiyang


title: Compartment-specific small RNA sequencing profile of Hippocampal and Cortical cells from Mesial Temporal Lobe Epilepsy tissue

type: Non-coding RNA profiling by high throughput sequencing

summary: Mesial temporal lobe epilepsy (mTLE) is a chronic neurological disease characterized by recurrent seizures. The pathogenic mechanisms underlying TLE involve defects in post-transcriptional regulation of gene expression. Previously we have shown the differences in cell compartment specific differential expression of coding transcripts in mTLE hippocampal and cortical samples compared to post-mortem controls (Vangoor et al., MedRxiv. 2021). On the same set of patient samples containing subcellular RNA from resected hippocampal (HC) and neo-cortical (Cx) tissue from mTLE no hippocampal sclerosis (non-HS) and mTLE HS International League Against Epilepsy (ILAE) Type 1 or mTLE+HS patients and postmortem control tissue, we applied small RNA sequencing (smRNA-seq). SmRNA-seq was analyzed for investigating the expression profiles of small non-coding RNA species as microRNAs and transferRNA fragments in human mTLE and control hippocampal tissue.

overall_design: In our recent study we established a protocol to isolate pure nuclear and cytoplasmic fractions from human tissue (Vangoor et al., MedRxiv. 2021). Small RNA sequencing (smRNA-seq) was performed on the same set of samples using illumina platform on five HC mTLE non-HS and five HC postmortem controls. Similarly, neo-cortical (Cx) tissue samples from six mTLE non-HS and six mTLE+HS samples and six Cx postmortem controls. From the data obtained, small non-coding RNA differential expression analysis was performed to identify mTLE specific changes among subcellular compartments.

last: Giulani

first: Noora

last: Puhakka

first: Peter

last: van Eijsden

middle: H

last: Gosselar

last: van Rijen

first: Pierre

last: de Graan


title: GPR124 Protects against Podocyte Senescence and Injury in Diabetic Kidney Disease

city: Jinan

first: Yujia

last: Li

address: 44#, Wenhua Xi Road

institute: Shandong University

summary: Cellular senescence is associated with the progression of diabetic kidney disease (DKD), and accelerated podocyte senescence promotes the pathogenesis of renal damage. We found that GPR124 was reduced in cultured human podocytes treated with high glucose (HG).To further clarify the role of GPR124 in podocytes, we overexpressed GPR124 via plasmid-harboring adenovirus infection.  By RNA sequencing analysis of podocytes with different treatment, we observed  GPR124 overexpression significantly affected several kinds of cell adhesion.

overall_design: Pairwise comparison of gene expression in 4 different groups of podocytes (3 samples per group) was performed by RNA sequencing, including NC control, NC HG, OE control and OE HG.

first: Xiaojie


title: RIF1 acts as a gatekeeper of B cell identity during late differentiation

city: Berlin

first: Michela

last: Di Virgilio

address: Robert-Rössle-Str. 10

country: Germany

institute: Max Delbrück Center for Molecular Medicine

summary: RIF1 is a multifunctional protein that promotes immunoglobulin (Ig) isotype diversification. Whether RIF1 plays additional roles in adaptive immunity is unknown. In this study, we observed an upregulation of RIF1 expression following mature B cell activation, while its deficiency led to a deregulated expression profile enriched in genes typically expressed in B cell progenitors and plasma cells (PC). RIF1 ablation resulted in increased plasmablast formation ex vivo and enhanced terminal differentiation into PC upon immunization. Therefore, RIF1 serves as a cell identity gatekeeper during late B cell differentiation, providing an additional layer of control in the establishment of humoral immunity.

overall_design: To elucidate the role of RIF1 in B-cell development and plasma blast differentiation, we extracted spleenocytes from CD19 Cre/+ mice and Rif1 F/F CD19 Cre/+ mice. Following isolation, these cells were stimulated with a cytokine-LPS cocktail, and subsequently harvested at 48, 72, and 96-hour intervals post-activation. To gain an in-depth understanding and to make a comprehensive comparison of the gene expression profiles, the samples were subjected to analysis via next-generation sequencing.


title: Evolutionary fingerprint in rodent PD1 confers weakened activity and enhanced tumor immunity compared to human PD1

city: La Jolla

first: Takeya

last: Masubuchi

address: 9500 Gilman Dr.

institute: University of California San Diego

summary: Mechanistic understanding of the immune checkpoint receptor PD1 is largely based on mouse models, but human and mouse PD1 orthologs exhibit only 59.6% identity in amino acid sequences, raising the question of potential cross-species functional differences. Based on our biochemical evidence that human PD1 is more inhibitory than mouse PD1, we addressed the functional consequence of PD1 humanization in a mouse melanoma model with adoptively transferred T cells.  Using CITE-seq (cellular indexing of transcriptomes and epitopes by sequencing), we found that humanization of PD1 intracellular domain (ICD) in CD8 T cells decreases the numbers, effector functions, and differentiation of intratumoral T cells. Specifically, PD1 humanization reduced the number of effector-like exhausted T cell subset while increasing the precursor-exhausted T cell subset, the latter of which is known to respond to anti-PD(L)1 therapy.

overall_design: Adoptively transferred P14 TCR-transgenic CD8 T cells expressing either wild-type or ICD-humanized mouse PD1 were isolated from the B16.gp33 tumor in each mice, hash-tagged with ssDNA-conjugated anti-MHCI total-seq antibodies, and then analyzed using CITE-seq.

first: Lin

last: Chen

first: Nimi

last: Marcel

first: George

last: Wen

first: Christine

last: Caron

first: Jibin

last: Zhang

first: Yunlong

last: Zhao

first: Gerald

last: Morris

first: Xu

first: Stephen

last: Hedrick

first: Li-Fan

last: Lu

first: Chuan

last: Wu

first: Zhengting

last: Zou

first: Jack

middle: D

last: Bui

first: Enfu

last: Hui


title: PTBP1 Lactylation Promotes Glioma Stem Cell Maintenance through PFKFB4-Driven Glycolysis

first: Tao

last: Xin

state: Shandong

address: 16766 Jingshi Road

department: Department of Neurosurgery

institute: The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital

summary: Longstanding evidence implicates glioma stem cells (GSCs) as the major driver for glioma propagation and recurrence. GSCs have a distinctive metabolic landscape characterized by elevated glycolysis. Lactate accumulation resulting from enhanced glycolytic activity can drive lysine lactylation to regulate protein functions, suggesting that elucidating the lactylation landscape in GSCs could provide insights into glioma biology. Herein, we demonstrated that global lactylation was significantly elevated in GSCs compared to differentiated glioma cells (DGCs). PTBP1, a central regulator of RNA processing, was hyperlactylated in GSCs, and SIRT1 induced PTBP1 delactylation. PTBP1-K436 lactylation supported glioma progression and GSC maintenance. Mechanistically, K436 lactylation inhibited PTBP1 proteasomal degradation by attenuating the interaction with TRIM21. Moreover, PTBP1 lactylation enhanced its RNA-binding capacity and facilitated PFKFB4 mRNA stabilization, which further increased glycolysis. Together, these findings uncovered a lactylation-mediated mechanism in GSCs driven by metabolic reprogramming that induces aberrant epigenetic modifications to further stimulate glycolysis, resulting in a vicious cycle to exacerbate tumorigenesis.

overall_design: Gene expression profiles were obtained from PTBP1-knockdown BT67 glioma stem cell line samples (n=6) using high throughput sequencing.

first: Zijian

last: Zhou


title: The role of HNRNPU and the nuclear matrix in human pluripotent stem cells [CUT&Tag]

first: Andrew

last: Hutchins

overall_design: CUT&Tag was performed on hPSCs (H1 lines) transfected with shRNAs targetting either luciferase (shLUC) as a control, or HNRNPU (shHNRNPU), or in untransfected cells. Antibodies used in the CUT&Tag were raised against H3K4me1,  H3K27ac or HNRNPU.

first: Gang

last: Ma

first: Xiuling

last: Fu


title: Cardiomyocytes and stromal cells cross-talk influences the pathogenesis of arrhythmogenic cardiomyopathy: a multi-level analysis uncovers DLK1-NOTCH pathway role in fibro-adipose remodeling

city: Milan

first: Mattia

last: Chiesa

address: Via Parea 4

department: Bioinformatics and Artificial Intelligence facility

country: Italy

institute: Centro Cardiologico Monzino IRCCS

summary: Different cell types individually contribute to set the Arrhythmogenic Cardiomyopathy (ACM) phenotype with either functional abnormalities (cardiomyocytes; CM) or fibro-fatty substitution (cardiac mesenchymal stromal cells; cMSC). The relative contribution of the CM and cMSC derangements to determine disease evolution and electrical instability is still poorly understood. Here we showed that a patient-specific multicellular cardiac system, which models the functional interaction between CM and cMSC, provides insight into the relative contribution of different cell types to ACM phenotypes.

overall_design: Cell cultures (CM and cMSC) were lysed in RL lysis buffer (Norgen Biotek corp.). RNA was isolated from cells by using a Total RNA Purification kit (Norgen Biotek corp.). The quantification of the isolated RNA was determined by Qubit™ 4 Fluorometer (Invitrogen), and a quality check was performed. The RNA samples that passed the quality check were then sent to Eurofins Ltd Genomic Service for sequencing.RNA libraries were prepared for transcriptome sequencing using standard Illumina protocols in frame of the INVIEW Transcriptome Discover protocol. For library preparation, mRNA was fragmented, and random hexamer-primed cDNA synthesis was performed. Paired-end read sequencing (2 x 150 bp) was performed on the Illumina HiSeq 4000. Reads were aligned on human genome reference (GRCh38/hg38 version 104 ) by BWA software (v0.7.1)  and mapped reads were used to quantify the gene expression, exploiting FeatureCounts (v2.0.0) .

first: Angela

last: Maione

first: Ilaria

last: Massaiu

first: Paolo

last: Poggio

first: Elena

last: Sommariva


title: The role of HNRNPU and the nuclear matrix in human pluripotent stem cells [ATAC]

overall_design: ATAC-seq was performed on hPSCs (H1 lines) transfected with shRNAs targetting either luciferase (shLUC) as a control, or HNRNPU (shHNRNPU)


title: The role of HNRNPU and the nuclear matrix in human pluripotent stem cells [RNA-Seq]

overall_design: RNA-seq was performed in hPSCs (H1 line) in cells transfected with shRNAs targetting Luciferase (LUC) as a control or shRNAs targetting HNRNPU or MATR3


title: Systematic reconstruction of molecular pathway signatures using scalable single-cell perturbation screens

status: Public on Nov 04 2024

city: New York

first: Rahul

last: Satija

state: NY

address: 101 6th Ave

institute: New York Genome Center

summary: Recent advancements in functional genomics have provided an unprecedented ability to measure diverse molecular modalities, but learning causal regulatory relationships from observational data remains challenging. Here, we leverage pooled genetic screens and single cell sequencing (i.e. Perturb-seq) to systematically identify the targets of signaling regulators in diverse biological contexts. We demonstrate how Perturb-seq is compatible with recent and commercially available advances in combinatorial indexing and next-generation sequencing, and perform more than 1,500 perturbations split across six cell lines and five biological signaling contexts. We introduce an improved computational framework (Mixscale) to address cellular variation in perturbation efficiency, alongside optimized statistical methods to learn differentially expressed gene lists and conserved molecular signatures. Finally, we demonstrate how our Perturb-seq derived gene lists can be used to precisely infer changes in signaling pathway activation for in-vivo and in-situ samples. Our work enhances our understanding of signaling regulators and their targets, and lays a computational framework towards the data-driven inference of an ‘atlas’ of perturbation signatures.

overall_design: We performed Perturb-seq experiments in six different cancer cell lines from different tissues of origin: A549 (lung), MCF7 (breast), HT29 (colon), HAP1 (bone marrow), BxPC3 (pancreas), and K562 (bone marrow). To facilitate multiplexed gene knockdown screens, we modified each of these lines to express a CRISPR interference (CRISPRi) dCas9-KRAB-MeCP2 cassette. We exposed each cell line to five distinct stimuli representing well-established pathway regulators: interferon-beta (IFNB), interferon-gamma (IFNG), transforming growth factor beta (TGFB), tumor necrosis factor-alpha (TNFA), and insulin (INS). For each pathway, we selected 44 to 61 genes based on a literature review of known regulators. For each gene, we selected three independent single guide RNAs (sgRNA) from the Dolcetto genome-wide CRISPRi library, as well as 14 non-targeting (NT) controls. For each pathway, we separately infected all six cell lines with the pathway-specific sgRNA library, and then stimulated infected cells with the corresponding cytokine for 24 hours to activate signaling.

first: Longda

last: Jiang

first: Carol

last: Dalgarno

first: Efthymia

last: Papalexi

first: Isabella

last: Mascio

first: Hans-Hermann

last: Wessels

first: Huiyoung

last: Yun

first: Nika

last: Iremadze

first: Gila

last: Lithwick-Yanai

first: Doron

last: Lipson


title: Analysis of population heterogeneity in CHO cells by genome-wide DNA methylation analysis and by multi-modal single-cell sequencing [WGBS]

city: Heidelberg

first: Elias

last: Böhl

address: Im Neuenheimer Feld 580

department: Divison of Epigenetics

institute: German Cancer Research Center (DKFZ)

summary: CHO cells are major hosts for the industrial production of therapeutic proteins and their production stability is of considerable economic significance. It is widely known that CHO cells can rapidly acquire genetic alterations, which affects their genetic homogeneity over time. However, the role of non-genetic mechanisms, including epigenetic mechanisms such as DNA methylation, remains poorly understood. We have now used whole-genome bisulfite sequencing to establish single-base methylation maps of eight independent CHO cell lines. Our results identify CpG islands and low-methylated regions as conserved elements with dynamic DNA methylation. Interestingly, methylation patterns were found to cluster clearly along the three main branches of CHO evolution, with no directional changes over short culture periods. Furthermore, multi-ome single-cell sequencing of 9,833 nuclei from three independent cultures revealed dynamic subpopulation structures characterized by robust expression differences in pathways related to protein production. Our findings thus provide novel insights into the epigenetic heterogeneity of CHO cells and support the development of epigenetic biomarkers that trace the emergence of subpopulations in CHO cultures.

overall_design: For the analysis of epigenetic heterogeneity and variability in CHO cells, a comparative whole-genome bisulfite sequencing (WGBS) of eight independent CHO cell lines was performed.

first: Günter

last: Raddatz

first: Frank

last: Lyko


title: Analysis of population heterogeneity in CHO cells by genome-wide DNA methylation analysis and by multi-modal single-cell sequencing [time series]

overall_design: To analyze dynamic methylation changes in the CHO genome, we used whole-genome bisulfite sequencing (WGBS) of three independent fed-batch bioreactor cultures of a CHO K1-derived clone expressing a therapeutic antibody (Nivolumab biosimilar). Each culture was sampled at seven different timepoints over a period of two weeks


title: Elevated microRNA-187 causes cardiac endothelial dysplasia to promote congenital heart disease through inhibition of NIPBL [ATAC-Seq]

status: Public on Nov 03 2024

city: shanghai

first: tan

last: zizheng

address: songhu road

institute: Fudan university

summary: Dysplasia of cardiac endothelial cells significantly contributes to congenital heart disease (CHD), the most common congenital disability. The regulatory role of miRNAs in this process remains elusive. This study identified elevated miR-187 expression in embryonic heart endothelial cells from CHD fetuses. Using a conditional knock-in model, we showed that increased miR-187 levels in embryonic endothelial cells induce CHD in homozygous fetal mice, closely mirroring human CHD. Mechanistically, miR-187 targets NIPBL, which is responsible for recruiting the cohesin complex and facilitating chromatin accessibility between enhancers and promoters. Consequently, the endothelial cell-specific upregulation of miR-187 inhibited NIPBL, leading to reduced chromatin accessibility and impaired gene expression, which hindered endothelial cell development and ultimately caused heart septal defects and reduced heart size both in vitro and in vivo. Importantly, exogenous miR-187 expression in human cardiac organoids mimicked developmental defects in the cardiac endothelial cells, reversible by NIPBL replenishment. Our findings establish the miR-187/NIPBL axis as a potent regulator that inhibits cardiac endothelial cell development by attenuating the transcription of numerous endothelial genes, with our mouse and human cardiac organoid models effectively replicating severe defects from minor perturbations.

overall_design: To investigate the regulation of chromatin openness in endothelial cells by miR-187/NIPBL axis, we overexpressed miR-NC, miR-187, and miR-187/NIPBL in endothelial cells induced by human embryonic stem cell differentiation.Then ATAC seq analysis was conducted to compare differences in chromatin openness.

first: Chao

last: Li

first: Zizheng

last: Tan

first: Hongdou

first: Xiaoying

last: Yao

first: Chuyue

last: Peng

first: Yue

last: Qi

first: Bo

last: Wu

first: Tongjin

last: Zhao

first: Chentao

first: Jianfeng

last: Shen

first: Hongyan

last: Wang


title: A Blood-based Transcriptomic Signature Stratifies Severe Crohn's disease and Defines Potentially Targetable Therapeutic Pathways

city: Los Angeles

first: Rivkah

last: Gonsky

address: 8700 Beverly Blvd. Davis Building, Room D4062

department: Gastroenterology/IBIRI

institute: Cedars-Sinai

summary: Surgical resection in severe Crohn's disease is a common consequence of therapeutic failure. We identified 2 severe CD subtypes: one similar to non-IBD subjects, the other exhibited a mucosal-like gene signature, altered T-cell subsets, severity features and decreased pro-inflammatory expression post-surgery. These findings may identify targets for CD subtype-specific therapeutic and biomarker development.

overall_design: CD3+ T-cells were purified from paired blood and mucosa from 100 CD and 17 non-inflammatory bowel disease (IBD) subjects requiring surgery. Longitudinal samples (n=49) were collected 4-13 months postoperatively. Expression profiles were generated by RNA-Seq. Transcriptional Risk Scores (TRS), T-cell subset deconvolution, gene pathway and kinase analyses were performed.

first: Evan

last: Adams

first: Alka

last: Potdar

first: Gregory

last: Botwin

first: Eva

last: Biener-Ramanujan

first: Dermot

middle: B

last: McGovern

first: Jonathan

middle: G

last: Braun

first: Phillip

last: Fleshner

first: Stephan

last: Targan


title: Elevated microRNA-187 causes cardiac endothelial dysplasia to promote congenital heart disease through inhibition of NIPBL [ATAC-seq Heart]

first: tan

last: zizheng

overall_design: To investigate the effect of increased miR-187 expression on chromatin openness in mouse heart, we performed ATAC seq sequencing on the heart tissues of WT mice in P0 phase and miR-187 overexpressing mice.

first: Chao

last: Li

first: Zizheng

last: Tan

first: Hongdou

first: Xiaoying


title: Elevated microRNA-187 causes cardiac endothelial dysplasia to promote congenital heart disease through inhibition of NIPBL [CUT&Tag]

overall_design: To investigate the transcriptional regulation of miR-187/NIPBL axis on endothelial cells, we overexpressed miR-NC and miR-187 in endothelial cells induced by human embryonic stem cell differentiation (hESC-ECs). we performed CUT&Tag-seq experiments of NIPBL compared to that of H3K27Ac as controls for the active promoter and enhancer regions in hESC-ECs.

last: Yao

first: Chuyue

last: Peng

first: Yue

last: Qi

first: Bo

first: Tongjin

first: Chentao


title: Analysis of population heterogeneity in CHO cells by genome-wide DNA methylation analysis and by multi-modal single-cell sequencing

first: Elias

last: Böhl

overall_design: Refer to individual Series


title: Elevated microRNA-187 causes cardiac endothelial dysplasia to promote congenital heart disease through inhibition of NIPBL

overall_design: In order to investigate the regulation of miR-187 on the transcriptome of endothelial cell, we overexpressed miR-187 and control miR-NC in EA.hy 926 cells. Then transcriptome sequencing and data analysis were performed to compare the differential expression of different genes.

last: Wu

last: Zhao

first: Jianfeng

last: Shen

first: Hongyan

last: Wang


title: Analysis of population heterogeneity in CHO cells by genome-wide DNA methylation analysis and by multi-modal single-cell sequencing [multiome]

overall_design: Nuclei of Humira-Antibody producing Humira431 CHO (A*Star BTI) cells were isolated and processed according to the protocol of the 10X Single Cell Multiome ATAC + Gene Expression kit.

first: Günter

last: Raddatz

first: Frank

last: Lyko


title: Single cell sequencing and retrograde barcode tracing reveal human DA neuron identities based on projection patterns in stem cell-derived grafts

city: Lund

first: Petter

last: Storm

state: Select...

address: Sölvegatan 19, BMC A11

country: Sweden

institute: Lund University

summary: Groundbreaking research in the last decade has definitively established human pluripotent stem cells (hPSCs) as a powerful source for the unlimited generation of dopamine (DA) neurons used in cell-based therapy in Parkinson’s disease (PD). However, DA neurons constitute a heterogeneous group of cells with different molecular identities and, consequently, different functions and innervation targets. Moreover, the inaccessibility of the human brain has so far hindered our understanding of the highly complex human DA system and, therefore, the design of DA neuron subtype-specific differentiation protocols for more effective cell replacement therapies. Currently, DA neurons – located in human ventral midbrain – can only be reliably distinguished based on their projection patterns. Here, we used hPSCs to derive and then transplant DA neurons into a rat model of PD. After one year of transplantation, we performed single nucleus RNA sequencing (snRNAseq) of ~80,000 human nuclei to transcriptionally define cell type composition and obtained a comprehensive map of DA neuron molecular identities. Exploiting the fact that transplanted DA neurons innervated and integrated within the host circuitry, we then combined snRNAseq with axonal retrograde AAV barcoding to trace the projection patterns of molecularly distinct human DA neuron subtypes in the grafts. We thus defined human DA neuron transcriptional profiles based on their target-specific outgrowth in the host brain. The resulting datasets provide an unprecedented resource both for elucidating the molecular basis of human DA neuron diversity as well as for developing more targeted cell-based therapies, with major implications for outcomes of PD patients.

overall_design:
Single-nuclei RNA-seq of stem cell derived midbrain grafts
NOTE FROM SUBMITTER: Due to privacy concerns we are unable to submit raw data and has hence only uploaded count matrices.

first: Malin

last: Parmar

first: Alessandro

last: Fiorenzano


title: Transcription factor TCF1 binds Rorgt and orchestrates a regulatory network that determines homeostatic Th17 cell state [RNA-seq]

city: Boston

first: The Gene Lay Institute of

last: Immunology and Inflammation

address: 60 Fenwood Road,

institute: Brigham and Women's Hospital

summary: CD4+ T helper 17 (Th17) cells encompass a spectrum of cell states including homeostatic cells that maintain physiological functions such as barrier integrity and pathogenic cells that drive autoimmune tissue inflammation. Identifying the regulators that determine these cell states will provide means to control tissue inflammation without compromising the physiological functions of Th17 cells. Here, we identified TCF1 as the key regulator that determines Th17 cell state. IL-23, a cytokine critical for inducing pathogenic Th17 cells, decreased TCF1 expression. Consistent with this observation, conditional deletion of Tcf7/TCF1 in mature myelin-specific T cells conferred pathogenicity to homeostatic Th17 cells independent of IL-23. Conversely, sustained TCF1 expression impaired acquisition of pathogenicity. Integration of transcriptional and chromatin accessibility data showed that TCF1 maintained homeostatic state through a regulatory network involving ETS family transcription factors, EGR1, and FOXO1 and by binding to and interfering with RORt activity. Our findings provide mechanistic insight into how the homeostatic and pathogenic Th17 cell states are determined and into the association of genetic variants in TCF7 with susceptibility to autoimmunity.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for 2D2 Th17cells between 2D2 dlck-Cre+Tcf7 fl/fl IL17aGFP+ and 2D2 dlck-Cre- Tcf7fl/fl IL17aGFP+  in mouse

first: Davide

last: Mangani

first: Ayshwarya

last: Subramanian

first: Linglin

last: Huang

first: Yufan

first: Thais

last: Moreira

first: Dandan

last: Yang

first: S

last: Krovi

first: Hanning

last: Cheng

first: Alexandra

last: Schnell

first: Karen

middle: O

last: Dixon

first: Vasundhara

last: Singh

first: Raymond

middle: A

last: Sobel

first: Howard

last: Weiner

first: Vijay

middle: K

last: Kuchroo

first: Ana

last: Anderson


title: Transcription factor TCF1 binds Rorgt and orchestrates a regulatory network that determines homeostatic Th17 cell state [ATAC-seq]

overall_design: ATAC-seq for 2D2 Th17cells between 2D2 dlck-Cre+Tcf7 fl/fl IL17aGFP+ and 2D2 dlck-Cre- Tcf7fl/fl IL17aGFP+  in mouse

last: Wu

middle: L

middle: C


title: Single-Cell RNA Sequencing Analysis of PRRSV Infection

status: Public on Nov 02 2024

city: Anseong-si

first: Jun-Mo

last: Kim

address: 4726 Seodong-daero, Daedeok-myeon

country: South Korea

institute: Chung-Ang University

summary: To analyze gene expression profiles at the single-cell level in pigs infected with PRRSV (Porcine Reproductive and Respiratory Syndrome Virus), aiming to understand the dynamic changes in gene expression, immune responses, and cellular interactions during PRRSV infection, and identify potential targets for intervention or prevention

overall_design: Bronchoalveolar lavage fluid (BALF) cells were isolated from pigs infected with PRRS virus at different time points and scRNA-seq was performed


title: Transposon and mRNA are distinguished by piRNA’s pairing and piRNA’s expression levels in Ovarian Somatic Cell.

city: Tokyo

first: Masaru

last: Ariura

address: Shinanomachi, Shinjuku-ku

institute: Keio university

summary: Piwi-interacting RNAs (piRNAs) are the main repressors of transposable elements (TEs) in animal germlines. In Drosophila, Piwi-piRNA complexes associate with nascent TE transcripts to drive heterochromatin formation and TE repression. However, previous studies have shown that Piwi also associates with large amounts of mRNAs, raising the question of how Piwi discriminates between mRNAs and TEs. To answer this question, we performed a comprehensive analysis of Piwi-associated RNAs, compositionally and functionally, to decipher the targeting rules of Piwi-piRNA complexes. While Piwi initially identifies its targets through the seed sequence, it requires pairing well beyond the seed, nearly a perfect match, to elicit a repressive response. In addition to the complementarity of piRNAs to their targets, their abundance must reach a certain threshold to be functional. Together, these findings explain large differences in target repression of Piwi-associated RNAs and reveals how Piwi efficiently distinguishes TEs from mRNAs despite associating with both.

overall_design: ChIP-seq for H3K9me3 and H3K4me3 in pMT- Ovarian Somatic Cell (OSC), Piwi CLASH in WT OSC, CAGE in EGFP KD and Piwi KD OSC, Iso-seq in EGFP KD and Piwi KD OSC, Pacbio Genome sequensing in OSC, scRNA-seq in OSC

first: M

first: H

last: Siomi

first: Y

middle: W

last: Iwasaki

last: Ishizu


title: Xenium Spatial Transcriptomics with human breast cell typing panel in human treatment naïve primary PDAC

city: Philadelphia

first: Carson

last: Poltorack

state: PA

address: 421 Curie Blvd, Rm 445

institute: University of Pennsylvania Perelman School of Medicine

summary: In this study we provide evidence that cancer associated fibroblasts in mouse and human PDAC models are proficient in the synthesis of monounsaturated fatty acids and may feed these MUFAs to cancer cells, enabling their evasion of SFA-associated lipotoxicity in the tumor microenvironment. The desaturation of SFAs to MUFAs by SCD is an oxygen-dependent process and cancer cells experience hypoxia in the PDAC TME. Therefore, we hypothesized that CAFs would be spatially positioned more near to blood vessels and have greater access to molecular oxygen with which to perform SFA desaturation. We therefore profiled the spatial distribution of cells in 8 treatment-naive human PDAC cases to determine whether CAFs indeed have greater access to vasculature than cancer cells.

overall_design: We analyzed 8 independent tumors using a predesigned 280-gene probeset with the Xenium (in situ hybridization-based) spatial transcriptomics platform commercialized by 10x Genomics. We selected the human breast cell typing panel because it was the predesigned panel with the largest number of genes expected to be expressed in human PDAC.


title: 3D hydrogel culture system for generation of fibrosis-associated macrophages

city: South San Francisco

first: Jason

middle: Anthony

last: Vander Heiden

state: CA

address: 1 DNA Way

department: Biological Research AI Development

institute: Genentech

summary: We identified a subpopulation of macrophages that are specifically enriched in interstitial lung disease. To better understand the functional relevance of this population with regards to disease pathogenesis by manipulating them in vitro, we attempted to induce this state in cell culture by prepurposing a published 3D hydrogel culture system originally designed to generate hematopoietic progenitor cells from PBMCs.

overall_design: Whole blood from three healthy donors was collected. PBMCs were extracted and put into the 3D hydrogel culture system described by Xu et al. (doi:10.1007/s13238-021-00900-4), cultured for 8 days, and then extracted from the hydrogel for scRNA-seq. Donors were pooled for scRNA-seq to be later computational separated by genetic demultiplexing.

first: Daryle

middle: J

last: DePianto

first: Tobias

last: Heigl

first: Omar

last: Salem

first: Shannon

last: Turley

last: Rock

first: Graham

last: Heimberg


title: Transcription factor TCF1 binds Rorgt and orchestrates a regulatory network that determines homeostatic Th17 cell state

first: The Gene Lay Institute of

last: Immunology and Inflammation

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


title: Elevated microRNA-187 causes cardiac endothelial dysplasia to promote congenital heart disease through inhibition of NIPBL [Endothelial cell RNA-seq]

first: tan

last: zizheng

overall_design: In order to investigate the regulation of miR-187/NIPBL axis on the transcriptome of endothelial cell development, we overexpressed miR-187 alone and co overexpressed miR-187, NIPBL, and control miR-NC in endothelial cells induced by human embryonic stem cell differentiation. Then transcriptome sequencing and data analysis were performed to compare the differential expression of different genes.

first: Chao

last: Li

first: Zizheng

last: Tan

first: Hongdou

first: Xiaoying

last: Yao

first: Chuyue

last: Peng

first: Yue

last: Qi

first: Bo

first: Tongjin

last: Zhao

first: Chentao

first: Jianfeng

last: Shen

first: Hongyan

last: Wang


title: Expression profiling of whole kidney marrow cells derived from wild type and rad21 heterozygous mutant adult zebrafish [bulkRNA-seq]

city: Dunedin

first: Jisha

last: Antony

state: Otago

address: 58 Hanover Street

country: New Zealand

institute: University of Otago

summary: Bulk RNA sequencing analyses of whole kidney marrow tissue isolated from wild type and rad21 heterozygous mutant adult zebrafish.

overall_design: RNA sequencing was carried out on whole kidney marrow tissue isolated from adult zebrafish that were wild type or carry germline heterozygous mutation in the rad21 gene. The zebrafish rad21 allele used in this study was rad21nz171, which contains a nonsense mutation in exon 8 of the zebrafish rad21a gene converting a glycine to a stop codon. The wild type zebrafish utilized were the wild type siblings obtained from in cross of rad21 heterozygous mutant zebrafish. RNA sequencing was carried out in triplicates and each replicate consisted of whole kidney marrow pooled from three adult zebrafish.

first: Gregory

last: Gimenez

first: Julia

last: Horsfield


title: Combined blockade of CXCR4 and PD1 enhances intratumoral dendritic cell activation and immune responses against hepatocellular carcinoma

first: Pin-Ji

last: Lei

state: Massachusetts

address: 100 Blossom Street

department: Department of Radiation Oncology

institute: Massachusetts General Hospital

summary: Immune checkpoint inhibitors (ICIs) have revolutionized the treatment of unresectable hepatocellular carcinoma (HCC), but their impressive efficacy is seen in a fraction of patients. One key mechanism of immunotherapy resistance is the paucity of dendritic cells (DCs) in liver malignancies. Here, we tested the combined blockade of programmed death receptor 1 (PD1) and CXCR4, a receptor for CXCL12, a pleiotropic factor that mediates immunosuppression in tumors. Using orthotopic grafted and autochthonous HCC models with underlying liver damage, we evaluated treatment feasibility and efficacy.

overall_design: To establish an orthotopic HCC mouse model with liver damage, RIL-175 cells were implanted in male C57Bl/6 mice, after five weeks of CCl4 treatment (20% (vol/vol) in olive oil, 150-µl gavage, three times per week). When the largest tumors reached ~5mm in diameter (after 12-16 weeks), mice were randomly assigned to a treatment group. Tumor growth was monitored by high-frequency ultrasound imaging. Tumors were collected from mice treated with control IgG, anti-PD1 antibody alone, anti-CXCR4 antibody alone, and anti-PD1 antibody in combination with anti-CXCR4 antibody. Total RNA was extracted from the freshly isolated tumor tissues using Qiagen kits. The RNA quality examination and sequencing library construction were conducted at the Molecular Biology Core Facilities of the Dana Farber Cancer Institute (Boston, USA).

first: Satoru

last: Morita

first: Dan

last: Duda


title: Expression profiling of whole kidney marrow cells derived from wild type and rad21 heterozygous mutant adult zebrafish [scRNA-seq]

summary: Single cell transcriptome analyses of whole kidney marrow cells isolated from wild type and rad21 heterozygous mutant adult zebrafish.

overall_design: Single Cell RNA sequencing on whole kidney marrow cells isolated from adult zebrafish that were wild type or carry germline heterozygous mutation in the rad21 gene. The zebrafish rad21 allele used in this study was rad21nz171, which contains a nonsense mutation in exon 8 of the zebrafish rad21a gene converting a glycine to a stop codon. The wild type zebrafish utilized were the wild type siblings obtained from in cross of rad21 heterozygous mutant zebrafish. Single cell RNA sequencing was carried out in duplicates and each replicate consisted of cells dissociated from a pool of 2-4 adult whole kidney marrow.


title: Cytotoxic and Molecular Effects of Soil Extracts from the Agbogbloshie Electronic-Waste Site on Fish and Human Cell Lines.

status: Public on Nov 01 2024

city: Sainte-Anne-de-Bellevue

first: Niladri

last: Basu

state: Quebec

address: 21,1111 Lakeshore Blvd, Apt #2

country: Canada

institute: McGill University

summary: Effect-based methods (EBM) are of growing interest in environmental monitoring programs. Few EBM have incorporated transcriptomics even though these provide a wealth of biological information and can be modeled to yield transcriptomic points of departure (tPODs). The study objectives were to: A) characterize cytotoxic effects of soil extracts on the rainbow trout RTgill-W1 and the human Caco-2 cell lines; B) measure gene expression changes and calculate tPODs; and C) compare in vitro responses to available measures of plastic-related compounds and metals. Extracts were prepared from 35 soil samples collected at the Agbogbloshie E-waste site (Accra, Ghana). Cells were exposed to six soil concentrations (0.3 to 9.4 mg dry weight of extract (eQsed)/ml). Many samples caused cytotoxicity with RTgill cells being more sensitive than Caco-2 cells. Eleven samples were analyzed for transcriptomics in both cell lines, with responses measured in all samples (52 to 5925 differentially expressed genes) even in the absence of cytotoxicity. In RTgill cells there was concordance between cytotoxic measures in tPOD values (spearman = 0.85). Though trends between in vitro measures and contaminant data were observed, more work is needed in this area before definitive conclusions are drawn. Nonetheless, this study helps support ongoing efforts in establishing alternative testing strategies (e.g., alternative to animal methods; toxicogenomics) for the assessment of complex environmental samples.

sample_organism:
Oncorhynchus mykiss
Homo sapiens

platform_organism:
Oncorhynchus mykiss
Homo sapiens

overall_design: Caco-2 and RTgill-W1 cell lines were exposed to extracts prepared from soil samples collected at various e-waste sites, at various concentrations. Endpoints examined were cytotoxicity and transcriptomics

first: Krittika

last: Mittal

first: Ke

last: Xu

first: Jingyun

last: Zheng

first: Stephane

last: Bayen

first: Julius

last: Fobil


title: ZNF350 gene polymorphisms promote the response to Peg-IFNα therapy through JAK-STAT signaling pathway in patients with chronic hepatitis B

city: fuzhou

first: Jianhui

last: Guo

address: 20 Chazhong Road

institute: First Affiliated Hospital of Fujian Medical University

summary: The varying individual responses to Peg-IFNα in patients with CHB pose significant hurdles in treatment optimization, and the underlying mechanisms remain unclear. We aimed to identify genetic polymorphisms influencing the efficacy of Peg-IFNα in patients with HBeAg-positive CHB，with the goal to predict Peg-IFNα response before treatment.

overall_design:
We enrolled124 HBeAg-positive CHB patients treated with Peg-IFNα, and conducted assessment of immunological markers and mRNA expression of pivotal genes, establishing correlations with SNPs, functional genes of SNPs, and efficacy of Peg-IFNα treatment.
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Authors state "we don't have iDAT" files.

first: Shaoying

first: Tianbin

last: Chen

first: Yongbin

last: Zeng

first: Ya

last: Fu

first: Qishui

last: Ou