title: Sp140L Is a Herpesvirus Restriction Factor [Day8_WT_vs_LPKO_BulkRNAseq]

overall_design: Bulk RNAseq of B cells 8 days post-infection with LPKO virus or WT virus


title: Sp140L Is a Herpesvirus Restriction Factor [Day5_LPKO_vs_SP100_SP140L_KO_BulkRNAseq]

status: Public on Nov 20 2024

city: Durham

first: Jana

last: Cable

state: NC

address: 213 Research Dr.

department: Molecular Genetics and Microbiology

country: USA

institute: Duke University

type: Expression profiling by high throughput sequencing

summary: Herpesviruses, including the oncogenic Epstein-Barr Virus (EBV), must bypass host DNA sensing mechanisms to drive infection and pathogenesis. The first viral latency protein expressed, EBNA-LP, is essential for the transformation of naïve B cells, yet its role in evading host defenses remains unclear. Using single-cell RNA sequencing of EBNA-LP-Knockout (LPKO)-infected B cells, we reveal an antiviral response landscape implicating the ‘speckled proteins’ as key restriction factors countered by EBNA-LP. Specifically, loss of SP100 or the primate-specific SP140L reverses the restriction of LPKO, suppresses a subset of canonically interferon-stimulated genes, and restores viral gene transcription and cellular proliferation. Notably, we also identify Sp140L as a restriction target of the herpesvirus saimiri ORF3 protein, implying a role in immunity to other DNA viruses. This study reveals Sp140L as a restriction factor that we propose links sensing and transcriptional suppression of viral DNA to an IFN-independent innate immune response, likely relevant to all nuclear DNA viruses.

overall_design: Bulk RNAseq of B cells 5 days post-infection with LPKO virus and CD46 alone or CD46 and Sp100 or Sp140L knocked out, or WT with CD46 knocked out.

last: M Cable

first: Wiyada

last: Wongwiwat

first: Jenna

last: C Grabowski

first: Robert

last: E White

first: Micah

last: A Luftig


title: Identify the interplay between N6-methyladenine and gene regulation under hypoxia by randomized empirical model (6mA)

status: Public on Nov 21 2024

city: Taoyuang

first: Kou-Juey

last: Wu

state: Taiwan

address: No.15, Wenhua 1st Road, Gueishan Dist

department: Cancer Genome Research Center

country: Taiwan

institute: Chang Gung Memorial Hospital at Linkou

summary: This dataset encompasses comprehensive analyses of the epigenetic mark N6-methyladenine (6mA) in human cell lines, focusing on its role under hypoxic conditions and its association with cancer progression. Addressing the challenge of 6mA's low abundance in mammals, we have innovated the 6mA-ChIP-exo-5.1 method. This technique enhances the sensitivity and accuracy of 6mA detection, employing exonuclease-dependent antibody-based approaches combined with whole genome amplification (WGA) to minimize potential noise and false positives.

overall_design: FaDu, a head and neck cancer cell line, was purchased from Bioresource Collection and Research Center (BCRC, Hsinchu, Taiwan). The cell line was cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% FBS, 1 mM sodium pyruvate, and 1× Antibiotic-Antimycotic (Gibco), under the conditions of 5% CO2 at 37°C. The mycoplasma absence was tested by Mycoplasma PCR Detection Kit (abm) before the experiments. Knockdown of METTL4 was achieved using a previously established method with lenti-virus infection. For hypoxic conditions, cells were incubated in an environment of 1% O2, 5% CO2, and 94% N2 at 37°C for 18 hours.

first: Kai-Wen

last: Hsu

first: Joseph

middle: C

last: Lai


title: A temporal cortex cell atlas highlights gene expression dynamics during human brain maturation [snRNA-seq]

city: Cape Town

first: Dorit

last: Hockman

address: Anzio Road

department: Department of Human Biology

country: South Africa

institute: University of Cape Town

summary: The human brain undergoes protracted post-natal maturation, guided by dynamic changes in gene expression. Most studies exploring these processes have used bulk tissue analyses, which mask cell type-specific gene expression dynamics. Here, using single nucleus (sn)RNA-seq on temporal lobe tissue, including samples of African ancestry, we build a joint paediatric and adult atlas of 75 cell subtypes, which we verify with spatial transcriptomics. We explore the differences between paediatric and adult cell subtypes, revealing the genes and pathways that change during brain maturation. Our results highlight excitatory neuron subtypes, including the LTK and FREM subtypes, that show elevated expression of genes associated with cognition and synaptic plasticity in paediatric tissue. The resources we present here improve our understanding of the brain during its development and contribute to global efforts to build an inclusive brain cell map.

overall_design: Donated ante-mortem temporal coretx tissue samples from paediatric and adult patients were analysed using the 10x Genomics snRNA-seq protocol


title: Multi-omics approaches reveal that Diffuse Midline Gliomas are susceptible to replication stress therapy and cholesterol biosynthesis inhibition [RNA-seq]

city: Stanford

first: Anastasia

last: Hains

email: hainsa@uchicago.edu, hains@stanford.edu

state: CA

address: 269 Campus Drive

institute: Stanford University

summary: The fatal Diffuse Midline Gliomas (DMG) are characterized by an undruggable H3K27M mutation in H3.1 or H3.3. K27M impairs normal development by stalling of differentiation. As replication timing influences gene expression, cell fate, and cellular response to therapeutics, we undertook a multi-omics approach (Repli-seq, cell cycle RNA-seq, single cell RNA-seq) in DMG cells (H3.1K27M and H3.3K27M subgroups) and tumors in comparison to normal brain to gain an appreciation for targetable pathways in DMG. DMG cells presented differential replication timing in each subgroup, which, in turn, correlated with significant differential gene expression including the cholesterol biosynthesis pathway. Consistent with these findings, DMG tumors presented high replication stress and cholesterol biosynthesis pathway signatures. Moreover, DMG cells were specifically vulnerable to an inhibitor of the cholesterol pathway and to a replication stress therapy, singly and in combination. In conclusion, this combinatorial genomics approach revealed insights into therapeutic opportunities for this incurable disease.

overall_design: To investigate the impact of the K27M mutations over cell cycle on gene expression in DMG, we performed RNA-seq on populations of cells in four cell cycle phases: G1, early S (ES), late S (LS), and G2

first: A

middle: E

first: J

middle: G

last: Marques

first: K

last: Chetal

first: C

middle: A

last: Biagi

last: Gonzalez-Sandoval

first: R

last: Pillai

last: Gatto

middle: I

last: Sadreyev

first: M

last: Filbin

last: Van Rechem


title: Human introns contain conserved tissue-specific cryptic poison exons

city: Moscow

first: Dmitri

middle: D

last: Pervouchine

address: Bolshoy Bul'var, 30, str 1

department: Skoltech Center for Molecular and Cellular Biology

country: Russia

institute: Skolkovo Institute of Science and Technology

summary: Eukaryotic cells express a large number of transcripts from a single gene due to alternative splicing. Despite hundreds of thousands of splice isoforms being annotated in databases, it has been reported that the current exon catalogs remain incomplete. At the same time, introns of human protein-coding genes contain a large number of evolutionarily conserved elements with unknown function. Here, we explore the possibility that some of them represent cryptic exons that are expressed in rare conditions. We identified a group of cryptic exons that are similar to the annotated exons in terms of evolutionary conservation and RNA-seq read coverage in the GTEx dataset. Most of them were poison, i.e. generated an NMD isoform upon inclusion, and many showed signs of tissue-specific and cancer-specific expression and regulation. We performed RNA-seq in A549 cell line treated with cycloheximide to inactivate NMD, and confirmed using qPCR that seven of eight exons tested are, indeed, expressed. This study shows that introns of human protein-coding genes contain cryptic poison exons, which reside in conserved intronic regions and remain not fully annotated due to insufficient representation in RNA-seq libraries.

overall_design: To investigate whether novel poison exons are indeed targeted by NMD, we performed RNA-seq in A549 cell line treated with cycloheximide to inactivate NMD. We then compared the inclusion level of novel and annotated cassette exons in cycloheximide-treated and untreated cells.

first: Sergey

last: Margasyuk

first: Antonina

last: Kuznetsova

first: Lev

last: Zavileyskiy

first: Maria

last: Vlasenok

first: Dmitry

last: Skvortsov


title: Vascular dysfunction is the primary cause of symptom onset in a mouse  model of oxaliplatin-induced peripheral neuropathy: comparison of gene expression in blood vessels from mouse brain and sciatic nerves [BHE-BHN_A2017]

city: PARIS

first: Stephane

last: Le Crom

address: 46 rue Ulm

department: Genomic Core Facility

country: France

institute: IBENS

summary: Oxaliplatin-induced peripheral neuropathy (OIPN) is an adverse side effect of this chemotherapy used for gastrointestinal cancers. The continuous pain experienced by OIPN patients often result in the reduction or discontinuation of chemotherapy, thereby affecting patient survival. Several pathogenic mechanisms involving sensory neurons were shown to participate in the occurrence of OIPN symptoms. However, the dysfunction of the blood-nerve barrier as a source of nerve alteration had not been thoroughly explored. To characterise the vascular contribution to OIPN symptoms, we undertook two comparative transcriptomic analyses from mouse purified brain and sciatic nerve blood vessels (BVs), and nerve BVs after oxaliplatin or control administration. The dataset provided here show raw data obtained when gene expression regulation was assessed by transcriptomic analyses where we compared purified blood vessels (endothelial cells and mural cells incl. smooth muscle cells and pericytes) from mouse brain and sciatic nerve.

overall_design:
Comparison of gene expression in blood vessels from brain and sciatic nerves of mice
The mouse strain for both experiments (GSE255096 and GSE255097) was C57BL/6.

first: Sonia

last: Taïb

first: Juliette

last: Durand

first: Anne-Cécile

last: Boulais

first: Vianney

last: Dehais

first: Sabrina

last: Martin

first: Martine

last: Cohen-Salmon

first: Corinne

last: Blugeon

first: Laurent

last: Jourdren

first: Jamilé

last: Hazan

first: Isabelle

last: Brunet


title: A temporal cortex cell atlas highlights gene expression dynamics during human brain maturation [Spatial Transcriptomics]

first: Dorit

last: Hockman

overall_design: Donated ante-mortem temporal coretx tissue samples from paediatric and adult patients were analysed using the 10x Genomics Visium spatial transcriptomics protocol


title: Cryoablation of primary breast cancer tumors induces a systemic abscopal effect altering TIME (Tumor-Immune Micro-Environment) in distant tumors.

status: Public on Nov 19 2024

city: Lubbock

first: Flavia

last: Sardela de Miranda

state: TX

address: 3601 4th Street

department: Surgery

institute: TTUHSC

summary: Despite recent advances, triple-negative breast cancer (TNBC) patients remain at high risk for recurrence and metastasis, which creates the need for innovative therapeutic approaches to improve patient outcomes. Cryoablation is a promising, less invasive alternative to surgical resection, capable of inducing tumor necrosis via freeze/thaw cycles. Necrotic cell death results in increased inflammatory signals and release of preserved tumor antigens, which have the potential to boost the local and systemic anti-tumor immune response. Thus, compared to surgery, cryoablation enhances the activation of T cells leading to an improved abscopal effect, defined as the occurrence of a systemic response after local treatment. We previously showed with a bilateral-tumor mouse model of TNBC that cryoablation of the primary tumor leads to increased infiltration of distant tumors by tumor infiltrating lymphocytes (TILs) and decreased rates of recurrence and metastasis. However, the early drivers of the cryoablation-generated abscopal effect are still unknown and knowledge of the mechanism could provide insight into improving the anti-tumor immune response through pharmacologic immune modulation in addition to cryoablation. Here we show that cryoablation of mouse mammary carcinomas results in smaller distant tumors that harbor increased frequencies of anti-tumor cells [such as natural killer (NK) cells], accompanied by a systemic increase in the frequency of migratory conventional type 1 dendritic cells (cDC1; CD103+ XCR1+), compared to resection. The changes in cell frequencies are mirrored by the immune gene signature of the distant tumors, with cryoablation inducing genes involved with NK cell activation and leukocyte-mediated toxicity, including IL11ra1 and Pfr1. These results better define the early mechanisms through which cryoablation improves tumor elimination, which is mediated by enhanced frequencies of anti-tumoral cells such as NK and cDC1s at the distant tumor and in the spleen of mice treated with cryoablation, respectively.

overall_design: To investigate the expression of genes involved with the pro- and anti-tumoral activity at distant tumors from cryoablation and resection, in a mouse model of triple-negative breast cancer using 4T1-12B cells bilaterally trasplanted in the mammary fat-pad of BALB/c mice.

first: Rakhshanda

middle: L

last: Rahman

first: Dalia

last: Matinez-Marin

first: Michael

middle: W

last: Melkus

first: Rachel

last: Babcock


title: Regulation of antimicrobial peptides in Hermetia illucens in response to fungal exposure

city: Jerusalem, Kiryat Shemona

first: Neta

last: Herman

address: Kiryat Shemona

department: Gentics, Nutrition

country: Israel

institute: Hebrew University Of Jerusalem, Migal

summary: The black soldier fly (Hermetia illucens) is important in antimicrobial peptides (AMP) research due to its exposure to diverse microbial environments. However, the impact of different fungal exposures on AMP abundance in H. illucens has not been thoroughly explored. Our study focused on basal conditions and interactions with three fungi: the non-pathogenic Candida tropicalis (isolated from larval gut), Saccharomyces cerevisiae, and the pathogenic Beauveria bassiana. Using RNA-seq and LC-MS/MS, we found that under standard conditions, the majority of AMPs belonged to the Lysozyme, Cecropin, and Defensin classes, with Defensins exhibiting the highest quantification levels. Exposure to any of the fungi upregulated AMP gene expression, indicating immune activation. Notably, exposure to C. tropicalis and B. bassiana led to notable downregulation of AMPs in H. illucens larvae compared to S. cerevisiae, suggesting these fungi may suppress or modulate the host immune response to aid their survival and colonization. The immune response of H. illucens larvae revealed that S. cerevisiae and B. bassiana trigger similar AMP pathways, whereas C. tropicalis elicits a distinct response with upregulation of Defensins and Cecropins. Lysozymes, known for their antibacterial and antifungal activity, were upregulated in response to S. cerevisiae and B. bassiana, but downregulated with C. tropicalis, potentially facilitating fungal survival in the larvae’s gut. This suggests that C. tropicalis adapts to reduce immune pressure, while B. bassiana may suppress AMPs to persist. Understanding these mechanisms opens possibilities for leveraging AMPs in combating C. tropicalis, which is implicated in human diseases.

overall_design: To study how pathogenic and non-pathogenic fungi affect the mRNA expression levels of AMP genes in H. illucens, we raised H. illucens larvae on a standard diet supplemented with different fungi: B. bassiana, S. cerevisiae, C. tropicalis, and a control group (no fungi added). Four days after the fungal treatment we extracted RNA from the fat bodies and performed RNA-seq analysis.We conducted differential expression analysis for the different treatments relative to the control using all expressed genes and then focused specifically on AMP-expressed genes in subsequent analyses.

first: Herman

last: Neta

first: Vitenberg

last: Tzach

first: Hayouka

last: Zvi

first: Opatovsky

last: Itai


title: Transcriptome Analysis of Porcine Immune Cells Stimulated by Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) and Caesalpinia sappan Extract

status: Public on Nov 18 2024

city: Chiang Mai

first: patipan

last: hnokaew

state: Mueang Chiang Mai

address: 239 Huay Kaew Rd, Tambon Su Thep, Mueang Chiang Mai District, Chiang Mai 50200, Thailand

department: Office of Research Administration

country: Thailand

institute: Chiang Mai University

summary: The current level of knowledge on transcriptome responses triggered by Caesalpinia sappan (CS) extract in porcine peripheral blood mononuclear cells (PBMCs) after porcine reproductive and respiratory syndrome virus (PRRSV) infection is limited. Therefore, in the present study, we aimed to detect significant genes and pathways involved in CS extract supplementation responsiveness of PBMCs after PRRSV infection. RNA sequencing was conducted on PBMCs, which were isolated from six weaned piglets. The resultant transcriptional responses were examined by mRNA sequencing. Differential expression analysis identified 263 and 274 differentially expressed genes (DEGs) between the PRRSV and CTRL groups, and the PRRSV+CS and CTRL groups, respectively. Among these, ZNF646 and KAT5 emerged as the most promising candidate genes, potentially influencing the interaction between PRRSV-infected PBMCs and CS extract supplementation through the regulation of gene networks and cellular homeostasis during stress. Two pathways were detected to be associated with CS extract supplementation responsiveness: the cellular response to stress pathway and the NF-kB signaling pathway. Consequently, our study reveals a novel mechanism underlying cellular stress response and the NF-κB signaling pathway in PRRSV-infected PBMCs, and identifies a potential application of CS extract for activating the NF-κB signaling pathway. In conclusion, by supplementing CS extract in PBMC cells infected with PRRSV, we found that CS extract modulates PRRSV infection by inducing cellular stress, which is regulated by the NF-κB signaling pathway. This induced stress creates an adverse environment for PRRSV survival. This study contributes to a deeper understanding of the therapeutic targets and pathogenesis of PRRSV infection. Importantly, our results demonstrate that CS extract has the potential to be a candidate for modulating PRRSV infection.

first: Chaiwat

last: Arjin

first: Phongsakorn

last: Chuammitri

first: Korawan

last: Sringarm

first: Patipan

last: Hnokaew


title: The master male sex determinant Gdf6Y of the turquoise killifish arose through allelic neofunctionalization

city: Jena

first: Philipp

last: Koch

address: Beutenbergstraße 11

department: Core Facility Life Science Computing

country: Germany

institute: Leibniz Institute on Aging - Fritz Lipmann Institute

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: RNA-Seq analysis of pubertal mammary epithelial cells reveals novel n-3 polyunsaturated fatty acid transcriptomic changes in the fat-1 mouse model

status: Public on Nov 17 2024

city: Guelph

first: Connor

last: Buchanan

state: Ontario

address: 50 Stone Road East

department: Human Health and Nutritional Sciences

country: Canada

institute: University of Guelph

summary: Background/Objectives: Early exposure of nutrients during pubertal mammary gland development may reduce the risk of developing breast cancer later in life. Anticancer, n-3 polyunsaturated fatty acids (n-3 PUFA) are shown to modulate pubertal mammary gland development, however, the mechanisms of action remains unclear. Prior work focuses on effects at the whole tissue level, and little is known at the cellular level, such as mammary epithelial cells (MEC), which are implicated in cancer development. Methods: This pilot study examined the effects of lifelong n-3 PUFA exposure on the transcriptome by RNA-Seq in isolated MEC of pubertal (6–8-week-old) female fat-1 transgenic mice capable of de novo n-3 PUFA synthesis. edgeR and DESeq2 were used separately for the differential expression analysis of RNA sequencing data followed by Benjamini-Hochberg procedure for multiple testing correction. Results: Nine genes were found concordant and significantly different (p ≤ 0.05) by both DESeq2 and edgeR methods. These genes were associated with multiple pathways, suggesting that n-3 PUFA stimulates estrogen-related signalling (Mllt10, Galr3, Nrip1) and a glycolytic profile (Soga1, Pdpr, Uso1) while offering protective effects for immune and DNA damage responses (Glpd1, Garre1, Rpa1) in MEC during puberty. Conclusions: This pilot study highlights the utility of RNA-Seq to better understand mechanistic effects of specific nutrients such as n-3 PUFA in a cell-specific manner. Thus, further studies are warranted to investigate cell-specific mechanisms by which n-3 PUFA influences pubertal mammary gland development and breast cancer risk later in life.

overall_design:
To investigate the transcriptomic effects of lifelong n-3 polyunsaturated fatty acid exposure in isolated mammary epithelial cells from female transgenic fat-1 mice compared to lifelong n-6 polyunsaturated fatty acid exposed wildtype (WT)  during puberty using bulk RNA-Seq.
To reduce cofounding effects from dietary feeding, all mice maintained on their parental diet of 10% fat (w/w) from safflower oil that contains 70% of the essential n-6 PUFA linoleic acid, which transgenic fat-1 mice will endogenously utilize to synthesize individual n-3 PUFA in all tissues, including in the mammary gland.

first: Rahbika

last: Ashraf

first: Lyn

last: Hillyer

first: Wangshu

last: Tu

first: Jing

last: Kang

first: Sanjeena

last: Subedi

first: David

last: Ma


title: Widespread termination of mammalian RNA polymerase II at T-rich DNA sequences (RNA-Seq)

status: Public on Nov 28 2024

city: Exeter

first: Steven

last: West

state: Devon

address: Stocker Rd

department: Living Systems Institute

country: United Kingdom

institute: University of Exeter

summary: The best-studied mechanism of eukaryotic RNA polymerase II (RNAPII) transcriptional termination is at protein-coding genes and involves endonucleolytic cleavage of the nascent RNA at the polyadenylation site. The RNAPII-associated cleavage product is then degraded 5'→3’ by XRN2 to elicit termination. In contrast, prokaryotic RNAP and eukaryotic RNAPIII often terminate directly over T-tracts in the non-template DNA strand. Here, we demonstrate a similar capability for mammalian RNAPII. This mechanism terminates snRNA transcription, which we unexpectedly show to be Integrator-independent. It is more generally employed where RNAPII elongation competence is low, especially in promoter-proximal regions and downstream of some protein-coding genes. In contrast, RNAPII within gene bodies does not terminate at T-tracts. Finally, XRN2-dependent, and T-tract termination are usually independent: the former acts following polyadenylation site cleavage, whereas the latter is employed where XRN2 cannot be engaged. Overall, we propose that RNAP’s retain the potential to terminate over T-rich sequences throughout evolution

overall_design: Comparative meta and gene expression analysis of nuclear RNA sequencing (RNA-Seq) for EXOSC3-dTAG, XRN2-dTAG and parental HCT116 degron cell lines (with or without KD)

first: Lee

last: Davidson

first: Jérôme

middle: O

last: Rouvière

first: Rui

last: Sousa-Luís

first: Taka

last: Nojima

first: Nicholas

last: Proudfoot

first: Torben

last: Heick Jensen

first: Steve


title: Single cell gene expression profiling of bone marrow derived DN thymocytes from wild-type or Bcl11b timing enhancer deletion (ΔTE) mice.

city: Seattle

first: Hao Yuan

last: Kueh

state: WA

address: 3720 15th Ave NE

institute: University of Washington

summary: Removing the Bcl11b timing enhancer delays Bcl11b activation and results in decreased T cell output and increased ILC production in the thymus. We used single cell RNA sequencing (scRNA-seq) to analyze the transcriptional programs that are altered and lead to increased ILC generation in Bcl11b ΔTE mice.

overall_design: Bone marrow-derived DN1 (CD44+CD25-), DN2a (CD44+CD25+Bcl11b-), and DN2b (CD44+CD25+Bcl11b+) progenitors were FACS-purified from WT or ΔTE mice and re-cultured on OP9-DL1 stromal cells for four days before harvesting them for scRNA-seq.

first: Nicholas A

last: Pease


title: Transcriptome analysis revealed that ischemic postprocessing improved the expression of inflammatory genes in lung ischemia-reperfusion injury

city: Wenzhou

first: Liangen

last: Lin

state: Zhejiang

address: No. 299 Guan Road, Louqiao Street, Ouhai District

country: China

institute: wenzhou people's hospital

summary: The actual mechanism of lung protection by I-post-C is unknown. The objective of this study was to explore the protective mechanism and potential molecular regulatory network of I-post-C on lung tissue.

overall_design: Transcriptome analysis was conducted on rat lung tissues from sham, ischemia-reperfusion (IR), and I-post-C groups using mRNA-Seq.

first: Congcong

last: Sun

first: Yuanwen

last: Ye

first: Peng

last: Zhu

first: Linglong

last: Chen


title: TF ChIP-seq Drosophila melanogaster (supplemental)

status: Public on Nov 16 2024

first: Louis

last: Gevirtzman

department: Genome Science

type: Genome binding/occupancy profiling by high throughput sequencing

summary: A catalog of transcription factor (TF) binding sites in the genome is critical for deciphering regulatory relationships.  Here we present the culmination of the efforts of the modENCODE (Model Organism ENCyclopedia Of DNA Elements) and modERN (model organism Encyclopedia of Regulatory Networks) consortia to systematically assay TF binding events in vivo in two major model organisms, Drosophila melanogaster (fly) and Caenorhabditis elegans (worm).  These datasets comprise 605 TFs identifying 3.6M sites in the fly and 356 TFs identifying 0.9 M sites in the worm, and represent the majority of the regulatory space in each genome. We demonstrate that TFs associate with chromatin in clusters termed “metapeaks”, that larger metapeaks have characteristics of high occupancy target (HOT) regions, and that the importance of consensus sequence motifs bound by TFs depends on metapeak size and complexity.  Combining ChIP-seq data with single cell RNA-seq data in a machine learning model identifies particular TFs with a prominent role in promoting target gene expression in specific cell types, even differentiating between parent-daughter cells during embryogenesis.  These data are a rich resource for the community that should fuel and guide future investigations into TF function.  To facilitate data accessibility and utility, all strains expressing GFP-tagged TFs are available at the stock centers for each organism.  The chromatin immunoprecipitation sequencing data are available through the ENCODE Data Coordinating Center, GEO, and through a direct interface (http://epic.gs.washington.edu/modERN/) that provides rapid access to processed data sets and summary analyses, as well as widgets to probe the cell type-specific TF-target relationships.

overall_design: Peak calling of sequence files using ENCODE TF/Histone ChIP-Seq pipeline version 1.3.6 https://github.com/ENCODE-DCC/chip-seq-pipeline2

first: Michelle

last: Kudron

first: Alec

last: Victorsen

first: Bridget

last: Lear

first: Jiahao

last: Gao

first: Jinrui

last: Xu

first: Swapna

last: Samanta

first: Emily

last: Frink

first: Adri

last: Tran-Pearson

first: Chau

last: Huynh

first: Dionne

last: Vafeados

first: Ann

last: Hammonds

first: William

last: Fisher

first: Martha

last: Wall

first: Greg

last: Wesseling

first: Vanessa

last: Hernandez

first: Zhichun

first: Mary

last: Kasparian

first: Kevin

last: White

first: Ravi

last: Allada

first: Mark

last: Gerstein

first: LaDeana

last: Hillier

first: Susan

last: Celniker

first: Valerie

last: Reinke

first: Robert

middle: H

last: Waterston


title: CREBH Regulates Mitochondrial Unfolded Protein Response to Maintain Energy Homeostasis

status: Public on Nov 15 2024

city: Detroit

first: Kezhong

last: Zhang

state: MI

address: 540 E Canfield street

department: CMMG

institute: Wayne State University

summary: The Mitochondrial Unfolded Protein Response (UPRmt), a mitochondria-originated stress response to altered mitochondrial proteostasis, plays important roles in various pathophysiological processes. In this study, we revealed that the endoplasmic reticulum (ER)-tethered stress sensor CREBH regulates UPRmt to maintain mitochondrial homeostasis and function in the liver. CREBH is enriched in and required for hepatic Mitochondria-Associated Membrane (MAM) expansion induced by energy demands. Under a fasting challenge or during the circadian cycle, CREBH is activated to promote expression of the genes encoding the key enzymes, chaperones, and regulators of UPRmt in the liver. Activated CREBH, cooperating with peroxisome proliferator-activated receptor α (PPARα), activates expression of Activating Transcription Factor (ATF) 5 and ATF4, two major UPRmt transcriptional regulators, independent of the ER-originated UPR (UPRER) pathways. Hepatic CREBH deficiency leads to accumulation of mitochondrial unfolded proteins, decreased mitochondrial membrane potential, and elevated cellular redox state. Dysregulation of mitochondrial function caused by CREBH deficiency coincides with increased hepatic mitochondrial oxidative phosphorylation (OXPHOS) but decreased glycolysis. CREBH knockout mice display defects in fatty acid oxidation and increased reliance on carbohydrate oxidation for energy production. In summary, our studies uncover that hepatic UPRmt is activated through CREBH under physiological challenges, highlighting a molecular link between ER and mitochondria in maintaining mitochondrial proteostasis and energy homeostasis under stress conditions.

overall_design: To understand the mechanistic basis by which CREBH regulates energy metabolism, we performed RNA-sequencing (RNA-seq) analysis with three of each liver tissues of CREBH-KO and WT control mice under the energy demand triggered by fasting. We then did gene expression profiling analysis between CREBH-KO and WT using data obtained from RNA-seq

first: Hyunbae

last: Kim

first: Qi

last: Chen

first: Donghong

last: Ju


title: Gene expression profile of Purkinje cells in Kcnd3 F227del mice

city: Taipei

first: Ting-Fen

last: Tasi

address: No. 155, Sec. 2, Li-Nong Street, Peitou

department: Department of Life Sciences and Institute of Genome Sciences

institute: National Yang Ming Chiao Tung University

summary: Spinocerebellar ataxia type 22 (SCA22) caused by KCND3 mutations is an autosomal dominant disorder. We establish a mouse model carrying the Kcnd3 F227del mutation to study the molecular pathogenesis. Four findings are pinpointed. Firstly, the heterozygous mice exhibit an early onset of defects in motor coordination and balance, which mirror the SCA22 patients. The degeneration and a minor loss of Purkinje cells together with the concurrent presence of neuroinflammation, as well as the previous finding on electrophysiological changes, may all contribute to the development of the SCA22 ataxia phenotype in mice carrying the Kcnd3 F227del mutant protein. Secondly, the mutant protein is retained by the endoplasmic reticulum and Golgi leading to activation of the unfolded protein response and a severe trafficking defect that affects its membrane destination. Intriguingly, profound damage to Golgi is the earliest manifestation. Thirdly, transcriptomic analysis revealed that the Kcnd3 F227del mutation down-regulates a panel of genes involved in the functioning of synapse and neurogenesis which are tightly linked to the functioning of Purkinje cells. Finally, no ataxia phenotypes are detectable in knockout mice carrying a loss-of-function Kcnd3 mutation. Thus, the Kcnd3 F227del is a dominant-negative mutation. Additionally, this mouse model can serve as a pre-clinical model for exploring therapeutic strategies to treat patients.

overall_design: To gain a better understanding of how the Kcnd3 F227del mutation causes its phenotypic defects, we employed microdissection laser capture to isolate cerebellar tissues enriched with Purkinje cells from mice at 1.5 months old  and perform RNA-sequencing. analysis.

first: Hao-Chih

last: Hung

first: Jia-Han

last: Lin

first: Yuan-Chi

last: Teng

first: Cheng-Heng

last: Kao

first: Pei-Yu

last: Wang

first: Bing-Wen

last: Soong

last: Tsai


title: Multi-omics approaches reveal that Diffuse Midline Gliomas are susceptible to replication stress therapy and cholesterol biosynthesis inhibition [Repli-seq]

first: Anastasia

last: Hains

overall_design: To investigate replication timing in DIPG cell lines we performed Repli-seq on four subphases (S1, S2, S3, and S4) of S phase

first: A

first: J

last: Marques

first: K

last: Chetal

first: C

last: Biagi

last: Gonzalez-Sandoval

first: R

last: Pillai

last: Gatto

last: Sadreyev

first: M

last: Filbin

last: Van Rechem


title: Perinuclear assembly of vimentin intermediate filaments induces cancer cell nuclear dysmorphia

first: Ke-Wei

last: PAN

address: No. 155, Sec. 2, Linong St. Beitou Dist., Taipei City 112304, Taiwan

summary: Nuclear dysmorphia, characterized by crumpled or lobulated polymorphic nuclear shapes, has been used as an index for the malignant grades of certain cancers. The expression of vimentin, a type III intermediate filament protein, is a hallmark of the epithelial-to-mesenchymal transition. However, it remains unclear whether vimentin is involved in cancer cell nuclear dysmorphia. In this study, we found that vimentin intermediate filaments (VIFs) frequently accumulated at the concave of dysmorphic nucleus in breast cancer MDA-MB-231 cells. Depletion of vimentin apparently restored the nuclear shape of the cells, which was devastated by re-expression of vimentin, but not its assembly-defective Y117D mutant. Depletion of plectin, a cytoskeletal linker, partially prevented the perinuclear accumulation of VIFs and concomitantly restored the nuclear shape of the cells. In addition, depletion of vimentin in lung cancer A549 cells largely prevented nuclear dysmorphia during the epithelial-to-mesenchymal transition induced by transforming growth factor-β. Moreover, we found that VIF-mediated nuclear dysmorphia led to defects in DNA repair. Together, our results unveil a novel role of VIFs in cancer cell nuclear dysmorphia, which is associated with genome instability.

overall_design: To investigate vimentin-induced nuclear dysmorphia in the regulation of DNA repair, we established MDA-MB-231 VIM-/- cells by Crispar-Cas9 approach.

first: Hong-Chen

last: Chen


title: ChIP-seq Drosophila melanogaster and Caenorhabditis elegans

first: Louis

last: Gevirtzman

sample_organism:
Caenorhabditis elegans
Drosophila melanogaster


title: Knockdown of Ketohexokinase Versus Inhibition of Its Kinase Activity Exert Divergent Effects on Fructose Metabolism

status: Public on Nov 14 2024

city: Boston

first: Jonathan

middle: M

last: Dreyfuss

state: MA

address: 1 Joslin Pl

department: Bioinformatics & Biostatistics Core

institute: Joslin Diabetes Center

summary: Excessive fructose intake is a risk factor for the development of obesity and its complications. Targeting ketohexokinase (KHK), the first enzyme of fructose metabolism, has been investigated for the management of MASLD. We compared the effects of systemic, small molecule inhibitor of KHK enzymatic activity to hepatocyte-specific, GalNAc-siRNA mediated knockdown of KHK in mice on a HFD. We measured KHK enzymatic activity, extensively quantified glycogen accumulation, performed RNAseq analysis, and enumerated hepatic metabolites using mass spectrometry. Both KHK siRNA and KHK inhibitor led to an improvement in liver steatosis, however, via substantially different mechanisms. KHK knockdown decreased the de novo lipogenesis pathway, whereas the inhibitor increased the fatty acid oxidation pathway. Moreover, KHK knockdown completely prevented hepatic fructolysis and improved glucose tolerance. Conversely, the KHK inhibitor only partially reduced fructolysis, but it also targeted triokinase, mediating the third step of fructolysis. This leads to the accumulation of fructose-1 phosphate, resulting in glycogen accumulation, hepatomegaly, and impaired glucose tolerance. Overexpression of wild-type, but not kinase-dead KHK in cultured hepatocytes increased hepatocyte injury and glycogen accumulation when treated with fructose. The differences between KHK inhibition and knockdown are, in part, explained by the kinase-dependent and independent effects of KHK on hepatic metabolism.

overall_design: We had mice on normal diet or HFD. A subgroup of mice on HFD was treated with KHK inhibitor twice daily for 4 weeks, starting at 6 to 10 weeks on the diets or with KHK siRNA injected subcutaneously every two weeks starting from 6 to 10 weeks on the diet. The four groups of mice were sacrificed after 10 weeks. RNAseq was performed for RNA isolated from the liver.

first: Samir

last: Softic


title: RSK1 is an exploitable dependency in myeloid malignancies [CUT&Tag]

city: St. Louis

first: Tim

last: Kong

state: MO

address: CSRB 8838

institute: Washington University School of Medicine

overall_design: THP-1 cells were treated with DMSO or 5 µM PMD-026 for 24h. CUT&Tag was performed using H3K27ac antibodies or IgG control.

first: Stephen

middle: T

last: Oh


title: RSK1 is an exploitable dependency in myeloid malignancies [scRNA-seq]

overall_design: scRNA-seq was performed on non-lymphoid PBMCs from patient 551599 at PV and MF disease stages.


title: RSK1 is an exploitable dependency in myeloid malignancies [ATAC-seq]

overall_design: THP-1 cells were treated with DMSO or 5 µM PMD-026 for 24h. ATAC-seq was performed.


title: Dual targeting of processive transcription for Myc-driven circuitry in medulloblastoma

city: Denver

first: Pluto

last: Bio

state: CO

address: 3575 Ringsby Ct Suite 414

institute: Pluto Bio


title: RSK1 is an exploitable dependency in myeloid malignancies [RNA-seq]

overall_design:
HEL cells were treated in duplicate with DMSO control or 10 µM PMD-026 for 24 hours.

MV4-11 cells were treated in duplicate with DMSO control, 500 nM PMD-026, or 50 nM quizartinib for 24 hours.

Three unique primary patient CD14+ monocytes were treated with DMSO control or 5 µM PMD-026 for 6 hours.


title: Full-length direct RNA sequencing uncovers stress-granule dependent RNA decay upon cellular stress

city: Baltimore

first: Emmanouil

last: Maragkakis

state: MD

address: 251 Bayview Blvd, 10B133 Baltimore

department: Laboratory of Genetics and Genomics (LGG)

institute: National Institute on aging

summary:
To investigate the role of oxidative stress on RNA dynamics, we treatd HeLa cell lines with 500 µM of arsenite.
We then explored the role of XRN1, CHX and ISRIB on mRNA shrotening using the data obtained from dRNA seq

overall_design: We performed the comparative transcript length difference analysis between control and arsenite treated cells in the presence of XRN1, CHX, and ISRIB

first: Showkat

last: Dar

first: Sulochan

last: Malla

first: Vlastimil

last: Martinek

first: Matthew

middle: J

last: Payea

first: Christopher

last: Lee

first: Jessica

last: Martin

first: Aditya

last: Khandeshi

first: Jennifer

last: Martindale

first: Cedric

last: Belair

first: Manolis


title: Comprehensive gene expression analysis using iPS cells derived from patients with sleep bruxism [snRNA-seq]

status: Public on Nov 13 2024

city: Ota-ku

first: Taro

last: Sato

state: Tokyo

address: 2-1-1 Kitasenzoku

department: Prosthodontics

country: Japan

institute: Showa University School of Dentistry

summary: Sleep bruxism (SB) is a disorder in which patients repeatedly make involuntary jaw movements during sleep. In this study, we performed single nucleus RNA sequencing (CTRL:SB = 1:1) using iPS cell-derived neurons established from SB patients to investigate gene expression of each neural subtype specific to SB patients.

overall_design:
To investigate gene expression of each neural subtype specific to SB patients, we established human iPSCs(hiPS) from three SB patients (SB1, SB2, and SB3) diagnosed with SB using clinical diagnostic criteria and also had the risk allele (C) of HTR2A SNP rs6313 and three unaffected controls (CTRL1, CTRL2, and CTRL3) without the risk allele.  Neurons were induced to differentiate from each sample.
We then performed gene expression profiling analysis using data obtained from single nucleus RNA-seq (snRNA-seq) of two different samples.
Comparative gene expression profiling analysis of snRNA-seq data of neurons from patients with SB (SB2) and controls (CTRL2).

first: Akihiro

last: Yamaguchi

first: Wado

last: Akamatsu

first: Kazuyoshi

last: Baba


title: TF ChIP-seq Caenorhabditis elegans (supplemental)

first: Louis

last: Gevirtzman

first: Michelle

last: Kudron

first: Alec

last: Victorsen

first: Bridget

last: Lear

first: Jiahao

last: Gao

first: Jinrui

last: Xu

first: Swapna

last: Samanta

first: Emily

last: Frink

first: Adri

last: Tran-Pearson

first: Chau

last: Huynh

first: Dionne

last: Vafeados

first: Ann

last: Hammonds

first: William

last: Fisher

first: Martha

last: Wall

first: Greg

last: Wesseling

first: Vanessa

last: Hernandez

first: Zhichun

last: Lin

first: Mary

last: Kasparian

first: Kevin

last: White

first: Ravi

last: Allada

first: Mark

last: Gerstein

first: LaDeana

last: Hillier

first: Susan

last: Celniker

first: Valerie

last: Reinke

first: Robert

last: Waterston


title: Towards melanoma in situ vaccination with multiple ultra-narrow X-ray beams

city: Bern

first: Nadia

last: Mercader

address: Baltzerstrasse 2

country: Switzerland

institute: University of Bern

summary: Despite the recent progress, current treatment modalities are not able to eradicate cancer. We show that Microbeam Radiotherapy (MRT), an innovative type of Spatially Fractionated Radiotherapy, can control murine melanoma by activating the host’s own immune system. The beneficial effects are very pronounced in comparison to uniform radiotherapy, traditionally employed in the clinic. Our results displayed that MRT increased antigen presentation, activating Cytotoxic T Lymphocytes (CTLs) which are essential to MRT’s treatment efficacy in melanoma. Depletion of CTLs abrogated treatment response. Multiplex nucleic acid hybridization technology revealed key features of lymphocyte populations such as proliferation, differentiation, and ligand-receptor interactions. In addition, CTLs were shown to be essential for locoregional metastatic control and systemic abscopal effects confirmed by activation of antigen presenting cells and CTL trafficking in the tumour-draining lymph nodes. MRT induces a robust antitumour immune response, matching the characteristics of in situ vaccination, that could be exploited to treat a variety of treatment-resistant malignancies.

overall_design: We analysed 24 melanomas from 5 different treatment groups: 5 unirradiated controls collected 12 days post-tumour implantation (n=4), 2 and 7 days postMRT (n=5/group), 2 and 7 days post-uniform RT (n=5/group). Melanomas were snap frozen in isopentane and kept at –80 °C degrees immediately after being harvested.

first: Verdiana

last: Trappetti

first: Cristian

last: Fernandez-Palomo

first: Prateek

last: Arora

first: Marine

last: Potez

first: Nahoko

last: Shintani

first: Valentin

last: Djonov


title: Gene expression dysregulation in whole blood of patients with C. difficile infection

status: Public on Nov 24 2024

city: Liverpool

first: Maria

last: Tsakiroglou

address: Block A, Waterhouse Building, 1-5 Brownlow Street,

department: Department of Pharmacology and Therapeutics

institute: University of Liverpool

summary: Background: Clostridioides difficile (C. difficile) is a global threat and has significant implications for individuals and health care systems. Little is known about host molecular mechanisms and transcriptional changes in peripheral immune cells. This is the first gene expression study in whole blood of patients with C. difficile infection.  Methods: We took blood and stool samples from patients with toxigenic C. difficile infection (CDI), non-toxigenic C. difficile infection (GDH), inflammatory bowel disease (IBD), diarrhoea from other causes (DC) and healthy controls (HC). We performed transcriptome-wide RNA profiling on peripheral blood to identify diarrhoea common and CDI unique gene sets.  Results: Diarrhoea groups upregulated innate immune responses with neutrophils at the epicentre. The common signature associated with diarrhoea was non-specific and shared by various other inflammatory conditions. CDI had a unique 45-gene set reflecting downregulation of humoral and T cell memory functions. Dysregulation of immunometabolic genes was also abundant and linked to immune cell fate during differentiation.  Conclusions: Whole transcriptome analysis of white cells in blood from patients with toxigenic C. difficile infection showed that there is an impairment of adaptive immunity and immunometabolism.

overall_design: 278 whole blood samples were assayed, with some participants in the CDI group also measured ~2 weeks post-baseline. In total there are 78 samples from the CDI group at baseline, plus 27 at the 2-week time point; 45 samples from the diarrhoea from other causes (DC) group; 37 samples from the non-toxigenic C. difficile infection (GDH) group; 40 from the inflammatory bowel disease (IBD) group and 51 from the healthy control (HC) group.

first: Anthony

last: Evans

first: Alejandra

last: Carracedo

first: Margaret

last: Little

first: Rachael

last: Hornby

first: Paul

last: Roberts

first: Eunice

last: Zhang

first: Fabio

last: Miyajima

first: Munir

last: Pirmohamed


title: Fibrillarin homologs are required for divergent cell lineage development by translational regulation in planarian homeostasis and regeneration

city: 杭州市

first: li

last: yucong

state: 浙江省

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生

overall_design: Refer to individual Series


title: Fibrillarin homologs are required for divergent cell lineage development by translational regulation in planarian homeostasis and regeneration [Ribo-seq]

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生

summary: Translational regulation in adult regenerative tissue remains unclear. Planarians, renowned for remarkable cell turnover and tissue regeneration capabilities, are regenerative flatworms that provide an ideal model to address the gap in knowledge between translational control and cell turnover during adult tissue homeostasis and regeneration. Fibrillarin (FBL) is an RNA 2-O’-methyltransferase crucial for rRNA processing, playing a pivotal role in translational regulation. We explored this in planarian Schmidtea mediterranea and identified two FBL homologs: Smed-fbl-1 (fbl-1) and Smed-fbl-2 (fbl-2) are essential for homeostasis and regeneration, but have distinct roles. fbl-1 is enriched in neoblasts and essential for multiple progenitor cell differentiation. Conversely, fbl-2 is expressed in egr5+ epidermal progenitors, crucial for late-stage epidermal lineage specification. Knockdown (KD) of fbl-1 and fbl-2 resulted in different 2-O’-methylation patterns, suggesting their influence on specific mRNA translation during regeneration. Riboseq analysis revealed that fbl-1 KD reduced the translation of genes associated with alternative splicing, cell cycle, and DNA replication, while fbl-2 KD reduced the translation of genes related to protein stability. Interestingly, fbl-2+ cells spatially correlated with wnt-1+ cells, hinting at fbl-2’s role in its localization. Our study indicated that duplicate fbl genes may have a compensatory role in the development of specific cell lineages. This finding underscores the significance of rRNA modification in translation regulation during the maintenance and regeneration of adult tissues.

overall_design: To investigate translational and transcriptional regulation upon fbl KD, we established an approach to capture the translated mRNA  in planarian. 3 biological repeats of each experimental group (egfp, egfp 2x, fbl-1, and fbl-2).

first: Jiajia

last: Chen

first: Yan

last: Wang

first: Jiaqi

last: Yang

first: Hongwej

first: Zhi

last: Xie

first: Kai

last: Lei


title: Fibrillarin homologs are required for divergent cell lineage development by translational regulation in planarian homeostasis and regeneration [RiboMeth-Seq]

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生

overall_design: To investigate 2-O'-methylation in 18S and 28S rRNA upon fbl KD, we established an approach to capture the methylated sites in planarian. 3 biological repeats of each experimental group (egfp, egfp 2x, fbl-1, and fbl-2 2x).

first: Yucong

last: Li

first: Hui


title: Intrinsically Disordered Regions Steer the Function Coordination of the Traveling Chromatin Modifier During Pol II Elongation

city: Shanghai

first: Bing

address: South Chongqing Road 280

department: Department of Biochemistry and Molecular Cell Biology

institute: Shanghai Jiao Tong University School of medicine

sample_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae


title: Intrinsically Disordered Regions Steer the Function Coordination of the Traveling Chromatin Modifier During Pol II Elongation (RNA-Seq)

summary: The Rpd3S histone deacetylase complex suppresses cryptic initiation and maintains genomic integrity by deacetylating transcribed nucleosomes subsequent to RNA Pol II passage. Recent cryo-EM structure analysis of Rpd3S emphasized the significance of two asymmetrical Rco1/Eaf3 dimers in nucleosome binding. However, the mechanism by which Rpd3S interacts with nucleosomal substrates while traveling with elongating Pol II remains elusive. In this study, we elucidate the crucial role of the Rco1 N-terminal Intrinsically Disordered Region (IDR) in regulating Pol II association. Mutations within the K/R cluster of Rco1 IDR significantly impede Rpd3S binding to CTD, while leaving the overall complex integrity and nucleosome recognition unaffected. Moreover, we identify the Rco1-PHD1 and Eaf3-CHD domains as the minimal module responsible for specific interaction with Ser5-phosphorylated CTD. The Rco1 IDR functions by relieving autoinhibition from its C-terminal regions, enabling the binding of PHD-CHD to CTD. Additionally, we uncover an evolutionarily conserved mechanism governing the distinct roles of the asymmetrical Rco1/Eaf3 dimers, which coordinate nucleosome engagement and Pol II binding. These findings offer valuable new perspectives on the functional dynamics of mobile epigenetic modifying complexes that accompany processive machinery.

overall_design: Gene expression profiling analysis of cph1, cph2, or set2 deletion strains using RNA-seq to evaluate transcriptome changes in S. pombe

first: Yixuan

last: Pan

first: Meiyang

last: Liu

first: Qi


title: mRNA bisulfite sequencing of pluripotent stem cells and the derived cardiomyocytes

city: Tainan City

first: Po-Hsien

middle: Joseph

last: Huang

address: 1 University Rd.

department: Biochemistry and Molecular Biology

institute: National Cheng Kung University

summary: The regulation of RNA 5-methylcytosine (m5C) modification during the differentiation process of hPSC to the derived cardiomyocytes remains unclear, and the RNA m5C have been shown to enhance innate immune response and associated with tumor progression. The purpose of this study was to provide the RNA m5Cs profiles in human pluripotent stem cells and its derived cardiomyocytes by bsRNA-seq, which provides the positions and methylation levels for future studies.

overall_design: Three sources of pluripotent stem cells and the derived cardiomyocytes were prepared for transcriptome-wide identification of 5-methylcytosine modifications by bsRNA-seq.

first: Szu-Ying

first: Yi-Hsien

last: Fang

first: Chen-Yu

first: Jou-Hsien

last: Wu

first: Yan-Shen

last: Shan

first: Yen-Wen


title: Bulk RNA-seq of MDA-MB-361 perturbation validation

city: Dallas

first: Yihan

state: Texas

address: 5323 Harry Hines Blvd.

institute: UT Southwestern

summary: This series contains the bulk RNA-seq validation experiments of NFYC promoter perturbation and enhancer chr13:32639465-32639967 (hg38 coordinates) perturbation in MDA-MB-361 cells.

overall_design: Bulk RNA-seq of two perturbations (NFYC promoter and chr13:32639465-32639967 enhancer)

first: Gary

last: Hon


title: Comprehensive gene expression analysis using iPS cells derived from patients with sleep bruxism

first: Taro

last: Sato

summary: Sleep bruxism (SB) is a disorder in which patients repeatedly make involuntary jaw movements during sleep. In this study, we performed bulk RNA sequencing (CTRL:SB = 3:3) using iPS cell-derived neurons established from SB patients to investigate gene expression patterns specific to SB patients.

overall_design:
To investigate gene expression patterns specific to SB patients, we established human iPSCs(hiPS) from three SB patients (SB1, SB2, and SB3) diagnosed with SB using clinical diagnostic criteria and also had the risk allele (C) of HTR2A SNP rs6313 and three unaffected controls (CTRL1, CTRL2, and CTRL3) without the risk allele.  Neurons were induced to differentiate from each sample.
We then performed gene expression profiling analysis using data obtained from bulk RNA-seq of six different samples.
Comparative gene expression profiling analysis of bulk RNA-seq data of neurons from patients with SB (SB1, SB2, and SB3) and controls (CTRL1, CTRL2, and CTRL3).

first: Akihiro

last: Yamaguchi

first: Wado

last: Akamatsu

first: Kazuyoshi

last: Baba


title: Single-cell CRISPRi screens of breast cancer associated enhancers

summary: This series contains the single-cell CRISPRi screens of MDA-MB-361 cells and MDA-MB-231 cells targeting 3512 enhancers associated breast cancer GWAS variants and somatic mutations.

overall_design: Two screens were performed in two different cell lines. For MDA-MB-361 cells, 8 lanes of 10x Chromium Next GEM Single-cell 3' HT reactions were performed. Each lane of reaction contain single-cell transcriptome, sgRNA enrichment and CellPlex libraries. For MDA-MB-231 cells, 16 lanes of 10x Chromium Next GEM Single-cell 3' reactions were perform.


title: RSK1 is an exploitable dependency in myeloid malignancies.

first: Tim

last: Kong

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


title: flt1 inactivation promotes zebrafish cardiac regeneration by enhancing endothelial activity and limiting the fibrotic response

status: Public on Nov 12 2024

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

summary: VEGFA administration has been explored as a pro-angiogenic therapy for cardiovascular diseases including heart failure for several years; however, many challenges remain.  Here we investigate a different approach to augmenting VEGFA bioavailability, one that achieves more physiological VEGFA concentrations by deleting VEGFR1/FLT1, a VEGFA decoy receptor.  We find that, following cryoinjury, zebrafish flt1 mutant hearts display enhanced coronary revascularization and endocardial expansion, increased cardiomyocyte dedifferentiation and proliferation, and decreased scarring.  Suppressing Vegfa signaling in flt1 mutants abrogates the beneficial effects of flt1 deletion.  Transcriptomic analyses of cryoinjured flt1 mutant hearts revealed enhanced endothelial MAPK/ERK signaling and downregulation of the transcription factor gene egr3.  Using genetic tools, we observe egr3 upregulation in the regenerating endocardium and find that Egr3 promotes myofibroblast differentiation.  These data suggest that with enhanced VEGFA bioavailability, the cardiac endothelium limits myofibroblast differentiation via egr3 downregulation, thereby providing a more permissive microenvironment for cardiomyocyte replenishment after injury.

overall_design: Comparative gene expression analysis between cryoinjured wild-type zebrafish ventricles and flt1 mutant ventricles at 96 hours post-cryoinjury.

first: Zhen-Yu

last: Wang

first: Armaan

last: Mehra

first: Qian-Chen

first: Agatha

last: Ribeiro da Silva

first: Thomas

last: Juan

first: Mario

last: Looso

first: Jan

last: Detleffsen

first: Didier

middle: Y

last: Stainier

first: Rubén

last: Marín-Juez


title: PRDX1-TLR4-p65 axis inhibits RANKL-mediated osteoclast differentiation

city: Cheongju

first: Kyunghwan

last: Kim

address: Rm #202a, Bldg. S1-5, 1 chungdae-ro

country: South Korea

institute: Chungbuk National University

summary: Peroxiredoxin 1 (PRDX1), traditionally known as an intracellular antioxidant enzyme, has emerged as a regulator of inflammatory responses via Toll-like receptor 4 (TLR4) signaling. Despite this, the mechanistic details of the PRDX1-TLR4 axis and its impact on osteoclast differentiation remain elusive. Here, we show that PRDX1 suppresses RANKL-induced osteoclast differentiation. Utilizing pharmacological inhibitors, we reveal that PRDX1 inhibits osteoclastogenesis through both TLR4/TRIF and TLR4/MyD88 pathways. Transcriptome analysis revealed PRDX1-mediated alterations in gene expression, particularly upregulating serum amyloid A3 (SAA3) and aconitate decarboxylase 1 (ACOD1), known inhibitors of osteoclast differentiation. Mechanistically, PRDX1-TLR4 signaling activates p65, promoting SAA3 and ACOD1 expression while inhibiting NFATc1, a master regulator of osteoclastogenesis. Remarkably, PRDX1 redirects p65 binding from NFATc1 to SAA3/ACOD1 promoters, thereby suppressing osteoclast formation. Structural analysis showed that monomeric variants of PRDX1 with enhanced TLR4 binding exhibit potent inhibition of osteoclast differentiation. Our findings elucidate the inhibitory role of PRDX1-TLR4 axis in osteoclastogenesis, providing insights into therapeutic strategies for bone-related disorders.

overall_design: To explore the impact of PRDX1 on osteoclast differentiation, bone marrow macrophages (BMMs) were exposed to RANKL (100ng/ml) for 48 hours, with or without the presence of PRDX1.


title: Open chromatin landscapes of breast cancer cell lines

first: Yihan

summary: Chromatin openness is a good indicator of non-coding regulatory elements. Here, we generated ATAC-seq of 8 breast cancer cell lines covering different breast cancer subtypes as an overview of the open chromatin landscapes.

overall_design: ATAC-seq of 8 different breast cancer cell lines.

first: Gary


title: IL-2 and TGF-b1 promote regulatory activity in NK cells following Hematopoietic Stem Cell Transplantation

city: Toronto

first: Sarah

last: Crome

state: ON

address: 101 College Street

institute: University Health Network

summary: Natural Killer(NK) cell activity is influenced by cytokines and microenvironment factors, resulting in remarkably diverse functions ranging from contributing to inflammatory responses to instead inhibiting T cell and B cell activity, thereby serving as rheostats of adaptive immunity. Using scRNAseq, we identified a TGFb1highCD56brightNK cell population associated with protection from acute Graft-versus-Host Disease. We further define a role for the combination of IL-2 and TGF-b in promoting NK cells to acquire a regulatory phenotype. ‘Induced’ regulatory NK cells produce high amounts of TGF-b1, inhibited T cells, could promote naïve T cells differentiation into regulatory T cells, and exhibited a unique transcriptional program that includes expression of IKZF2(HELIOS) and ZNF683(HOBIT). This phenotype was not stable, and induced regulatory NK cells lost the ability to secrete TGF-b1 upon exposure to different cytokines. These findings define protective CD56brightNK cells in Hematopoietic Stem Cell Transplant, and support IL-2 and TGF-b1 promote regulatory NK cells.

overall_design:
PBMCs were isolated from HSCT recipients with or without GVHD and analyzed using scRNA sequencing. Cells expressing markers of natural killer cells were taken for comparisons between patients with and without GVHD.

***************************************************************
Raw files not provided due to patient privacy concerns
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first: Jessica

last: Mathews

first: Kyle

last: Reid

middle: Q


title: Collagen signaling and matrix stiffness regulate multipotencyin glandular epithelial stem cells in mice [microarray]

city: Bruxelles

first: Yura

last: Song

address: 808, route de Lennik

country: Belgium

institute: Université Libre de Bruxelles

summary: To understand the molecular mechanisms regulating multipotency after transplantation of mammary gland basal cells

overall_design: 4 samples

first: Cédric

last: Blanpain

first: Alexandra

last: Van Keymeulen


title: Collagen signaling and matrix stiffness regulate multipotency in glandular epithelial stem cells in mice

first: Alessia

last: Centonze

first: Chen

last: Jiang


title: Collagen signaling and matrix stiffness regulate multipotencyin glandular epithelial stem cells in mice [bulk RNA-Seq]

summary: Glandular epithelia, including mammary gland (MG) and prostate, are composed of luminal and basal cells. During embryonic development, glandular epithelia arise from multipotent stem cells (SCs) giving rise to basal and luminal cells. However, these multipotent SCs are replaced after birth by unipotent basal and unipotent luminal SCs. Different conditions, such as basal cell transplantation, luminal cell ablation, and oncogene expression, can reinduce multipotency in adult basal SC (BaSCs) of different glandular epithelia. The mechanisms regulating the reactivation of multipotency in BaSCs are incompletely understood. Here, we compared the transcriptional signature of BaSCs from MG and prostate in different conditions associated with multipotency in adult mice and uncovered that Collagen I expression was commonly upregulated across the different conditions associated with multipotency. Using MG and prostate organoids, we demonstrated that increasing collagen concentration or stiffness of the extracellular matrix (ECM) promote BaSC multipotency. Single cell RNA-seq of MG organoids in the presence of high concentration of Collagen I or in a stiffer ECM activate a hybrid bipotent state and uncovered a gene signature and signaling pathways associated with bipotent BaSCs. Finally, we demonstrated the importance of 1integrin/FAK/AP-1 axis in the regulation of BaSC multipotency in response to Col1 signaling and ECM stiffness. Altogether our study uncovers the key role of Collagen signaling and ECM stiffness in the regulation of multipotency in glandular epithelia.

overall_design: Ventral lobe of 20 mice at P10-P12 were collected and separated by tips and ducts by chopping. CD45+, CD31+ and CD140a+ cells were excluded (Lin+) before analysis of the epithelial basal (EpCamhigh/CD49fhigh) and luminal (EpCamhigh/CD49flow) cells and those cells were analysed by classical RNAseq.

first: Elisavet

last: Tika


title: p48Cre;LSL-KrasG12D Mouse Acinar and PanIN LCM RNA-Seq

status: Public on Nov 11 2024

city: Jacksonville

first: Peter

last: Storz

state: FL

address: 4500 San Pablo Rd

department: Department of Cancer Biology

institute: Mayo Clinic

summary: The goal of this study is to identify changes in gene expression between acinar and low-grade PanIN lesions in p48Cre;LSL-KrasG12D mice.

overall_design: Using laser capture microdissection (LCM), acinar cells and low-grade (LG) panIN were isolated from p48Cre;LSL-KrasG12D (KC) mice.

first: Ligia

last: Bastea

first: Alicia

last: Fleming Martinez


title: Identify the interplay between N6-methyladenine and gene regulation under hypoxia by randomized empirical model (ChIP-seq)

city: Taoyuang

first: Kou-Juey

last: Wu

state: Taiwan

address: No.15, Wenhua 1st Road, Gueishan Dist

department: Cancer Genome Research Center

institute: Chang Gung Memorial Hospital at Linkou

summary: In this study, we employed ChIP-seq for histone modifications related to gene activation, such as H3K4me1, H3K4me3, and H3K27Ac, to investigate the role of N6-methyladenine (6mA) in chromatin accessibility under hypoxic conditions.

overall_design: FaDu, a head and neck cancer cell line, was purchased from Bioresource Collection and Research Center (BCRC, Hsinchu, Taiwan). The cell line was cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% FBS, 1 mM sodium pyruvate, and 1× Antibiotic-Antimycotic (Gibco), under the conditions of 5% CO2 at 37°C. The mycoplasma absence was tested by Mycoplasma PCR Detection Kit (abm) before the experiments. Knockdown of METTL4 was achieved using a previously established method with lenti-virus infection. For hypoxic conditions, cells were incubated in an environment of 1% O2, 5% CO2, and 94% N2 at 37°C for 18 hours.

first: Kai-Wen

last: Hsu

first: Joseph

last: Lai


title: Intratumoral administration of lipid nanoparticles carrying mRNA encoding for IL-21, IL-7, and 4-1BBL induces anti-tumor immunity in preclinical tumor models.

city: Brussels

first: Daliya

last: Kancheva

address: Laarbeeklaan 103, Building E

institute: Vrije Universiteit Brussel - VIB

summary: Local delivery of mRNA-based immunotherapy offers a promising avenue for personalized medicine as it enables the production of specific immunomodulatory proteins that can stimulate the immune system to recognize and eliminate cancer cells, showcasing encouraging results in preclinical tumor models while minimizing systemic side effects. Nonetheless, efficient mRNA delivery is challenging due to its rapid degradation by ribonucleases and limited cellular uptake. Here, we developed and employed ionizable lipid nanoparticles (LNPs) to intratumorally deliver an mRNA mixture encoding the cytokines IL-21 and IL-7 and the immunostimulatory molecule 4-1BB ligand (Triplet LNP). The Triplet LNP led to a profound increase in the frequency of tumor-infiltrating granzyme B+ CD8+ T cells and their capacity to secrete IFN-γ, leading to tumor eradication in a CD8+ T cell-dependent manner. Ultimately, the Triplet LNP showed superior therapeutic efficacy to anti-PD1 against the orthotopic triple-negative breast carcinoma model E0771, highlighting the therapeutic potential of the Triplet LNP in multiple murine tumor models.

overall_design: CD45+ cells sorted from subcutaneous MC38 tumors and tumor-draining lymph nodes of mice treated with triplet LNP, control LNP (ntrIL21) or PBS (pooled from 5 mice per sample)

first: Ahmed

last: Hamouda

last: Filtjens

first: Elisabeth

last: Brabants

first: Ayla

last: Debraekeleer

first: Jan

last: Brughmans

first: Lotte

last: Jacobs

first: Pauline

last: Bardet

first: Ismaël

last: Varela

first: Marian

last: Crabbé

first: Emile

last: Clappaert

first: Lize

last: Allonsius

first: Eva

last: Hadadi

first: Stefaan

last: De Koker

first: Bruno

last: De Geest

first: Sofie

last: Deschoemaeker

first: Florence

last: Lambolez

first: Damya

last: Laoui


title: A Penta-Component Mpox mRNA Vaccine Induced Protective Immunity in Naive and Simian Immunodeficiency Virus Infected Nonhuman Primates

city: Beijing

first: Rui-Ting

last: Li

state: Beijing

address: No.20 Dongda Street, Fengtai District

department: State Key Laboratory of Pathogen and Biosecurity

institute: Beijing Institute of Microbiology and Epidemiology

summary: The transcriptome profiles of tissues from sham or AR- MPXV immunized macaques after MPXV infection.

overall_design: The transcriptome profiles of skin/spleen tissues from sham or AR- MPXV immunized macaques after MPXV infection.

first: Qing

last: Ye

first: Rong-Rong

last: Zhang


title: A high-quality chromosome-level genome assembly of the traditional Chinese medicinal herb Zanthoxylum nitidum

status: Public on Nov 10 2024

city: NanNing

first: Jianping

last: Jiang

state: Guangxi

address: No. 189, Changgang Road, Xingning District, Nanning, Guangxi

institute: Guangxi Botanical Garden of Medicinal Plants, Naning, China

summary: Transcriptomic data from seven different tissues of Z. nitidum were collected to unveil the functional patterns of the BBE family in the biosynthesis of benzophenanthridine alkaloids

overall_design: The samples in this study were collected from 3-years-old individual plants grown at an artificial planting base in Nanning City, Guangxi Province (109°11′E, 22°31′N). The plant was identified by Prof. Yudeng Peng (Guangxi Botanical Garden of Medicinal Plants, China). This study utilized tissue materials from fresh leaves, fruits, roots, and stems for genomic and transcriptomic investigations, with three independent biological replicates collected for each sample type. The root tissues were categorized based on their size into large roots (≥ 3 cm in diameter), medium roots ( ≥ 2 cm and < 3cm in diameter), and small roots (≥1 and <2 cm in diameter). The stems were classified based on their size into old stems (≥3 cm in diameter) and tender stems (≥1 and <3 cm in diameter).

first: Yanxia

last: Zhu

first: Qingsong

last: Dong

first: Yude

last: Peng


title: Concomitant loss of TET2 and TET3 results in T cell expansion and genomic instability

city: Chapel Hill

first: Ageliki

middle: Tsagaratou

last: Tsagaratou

state: NC

address: 8001-B Burnett-Womack Bldg.

department: Department of Genetics

institute: University of North Carolina at Chapel Hill

summary: TET proteins are tumor suppressors that through their catalytic activity oxidize 5-methylcytosine to 5-hydroxymethylcytosine, to promote DNA demethylation and to regulate gene expression. Notably, TET2 is the second most frequently mutated gene in hematological malignancies, including T cell lymphomas. However, murine models with deletion of TET2 do not exhibit T cell expansion, presumably due to redundancy with other members of the TET family of proteins. In order to gain insight on the TET mediated molecular events that safeguard T cells from aberrant proliferation we performed serial adoptive transfers of murine CD4 T cells that lack concomitantly TET2 and TET3 to fully immunocompetent congenic mice. Our data reveal a progressive acquisition of malignant traits upon loss of TET2 and TET3 that is characterized by loss of genomic integrity, acquisition of aneuploidy and upregulation of the protooncogene Myc.

overall_design: In this report, we aim to decipher the impact of TET proteins in controlling in vivo proliferation of peripheral T cells. We employ adoptive transfer of Tet2/3 DKO T cells and we discover that Tet2/3 DKO CD4 cells exhibit upregulation of cell cycle genes upon serial transplantation. This altered gene expression program endows Tet2/3 DKO CD4 cells with increased proliferative capacity and acquisition of malignant traits, such as oligoclonal expansion and chromosomal copy number (CCN) variations, resulting in aggressive lymphoproliferative disorders. In addition, we demonstrate that as the TET deficient cells acquire a hyperproliferative profile they can expand remarkably fast, within 10 days, in recipient mice. During this rapid expansion of transplanted Tet2/3 DKO T cells, by employing an unbiased, single cell transcriptomic approach, we reveal that while the immune environment of the host mice becomes rapidly activated, it fails to annihilate the expansion of the donor T cells.

first: Siyao

last: Liu


title: Collagen signaling and matrix stiffness regulate multipotency in glandular epithelial stem cells in mice [scRNA-Seq]

first: Yura

last: Song

overall_design: The mammary gland organoid from fat pads of 8-to-9-week-old virgin mice without lymph nodes were cultured under different stiffness and analysed using scRNA-seq.

first: Cédric

last: Blanpain

first: Alessia

last: Centonze

first: Chen


title: RNA-seq in fetal mice brain following c-Flip knockdown

city: Guang Dong

first: Ting

last: Xie

state: Guang Dong

address: No.66,Gongchang Road,Guangming District,Shenzhen,Guangdong 518107,P.R.China

institute: SUN YAT-SEN UNIVERSITY

summary: We characterized the comprehensive set of differentially expressed genes resulting from the knockdown of c-Flip in the E13.5 fetal head and  identified the transcriptional profile of ZIKV-induced DEGs in the context of c-Flip deficiency

overall_design: Female wild type mice aged 8 to 10 weeks and male c-Flip+/- mice aged 10 to 12 weeks were set up for timed-matings and at embryonic days (E5.5) pregnant mice were inoculated with 2 mg of anti-IFNAR antibody (MAR1-5A3, Leinco Technologies). At E6.5, mice were infected intraperitoneally (i.p.) with 200ul of 1*10^6 plaque forming unit (PFU), and the mock-infected mice were injected with 200ul PBS as control. Mice in each group were observed daily for the signs of disease and death for 7 days post infection (dpi). They were sacrificed at E13.5 (dpi), and the fetal brains were collected for viral load study and transcriptome analysis.


title: Revealing the Immune Response of Sitona callosus to Beauveria bassiana Infection through Integrative Analyses of Transcriptomics and Metabolomics

city: Yinchuan

address: No. 489, Helan Mountain West Road, Xixia District, Yinchuan City, Ningxia

institute: NingXia University

summary: The legume pest Sitona callosus poses a significant threat to alfalfa growth. Due to its unique life cycle, Beauveria bassiana has emerged as an effective fungus for controlling S. callosus . We conducted a comprehensive analysis of the transcriptome and metabolome of S. callosus infected by B. bassiana. Differential expression of antifungal genes, including heat shock genes, cytochrome P450 (CYP450) genes, cathepsin proteases, and C-type lectin were identified in S. callosus. Pathway analysis revealed associations between immune genes and metabolites involved in autophagy-animal, glucagon signaling pathway, and glycerophospholipid metabolism. These findings provide valuable insights for enhancing the control efficacy of Beauveria bassiana on Sitona callosus.

overall_design: In order to determine the immune response of Sitona callosus infected by Beauveria bassiana. Transcriptomic tests were performed on Sitona callosus after infection with Beauversiana bassiana and the uninfected one.

first: Xinpu

last: Wang


title: Tissue-resident memory CD8 T Cell Diversity is Spatiotemporally Imprinted

city: Seattle

first: Maximilian

last: Heeg

state: WA

address: 615 Westlake Ave N

institute: Allen Institute for Immunology

summary: Tissue-resident memory CD8 T cells (TRM) provide protection from infection at barrier sites. In the small intestine, TRM cells are found in at least two distinct subpopulations: one with higher expression of effector molecules and another with greater memory potential. However, the origins of this diversity remain unknown. We proposed that distinct tissue niches drive TRM phenotypic heterogeneity. To test this, we leveraged spatial transcriptomics of human samples, a murine model of acute systemic viral infection, and a newly established strategy for pooled optically-encoded gene perturbations to profile the location, interaction, and transcriptome of pathogen-specific TRM differentiation at single-transcript resolution. We developed computational approaches to capture cellular locations along three anatomical axes of the small intestine and to visualize the spatiotemporal distribution of cell types and gene expression. Our study reveals that the intestinal architecture’s regionalized signaling supports two distinct TRM cell states: differentiated TRM and progenitor-like TRM cells, located in the upper versus lower villus, respectively. This diversity is mediated by distinct ligand-receptor activities, cytokine gradients, and specialized cellular contacts. Blocking TGFb or Cxcl9/10-sensing by antigen-specific CD8 T cells revealed a model consistent with anatomically delineated early fate specification. Ultimately, our framework for the study of tissue immune networks has revealed that T cell location and functional state are fundamentally intertwined.

platform_organism:
Homo sapiens
Mus musculus
synthetic construct

overall_design:
Spatial transcriptomics (Xenium) of mouse small intestine at day 6, 8, 30 and 90 after infection with LCMV and adoptive transfer of P14 CD8 T cells.
Spatial transcriptomics (Xenium) of uninfected mouse small intestine.
Spatial transcriptomics (Xenium) of mouse small intestine at day 7 after infection with LCMV and adoptive transfer of perturbed P14 CD8 T cells.
Spatial transcriptomics (MERSCOPE) of mouse small intestine at day 8 after infection with LCMV and adoptive transfer of Tgfbr2 KO or WT P14 T cells.
Spatial transcriptomics (Xenium) of human ileum biopsies.

first: Miguel

last: Reina-Campos

first: Alexander

last: Monell

first: Ananda

last: Goldrath


title: Efficient derivation of functional astrocytes from human induced pluripotent stem cells (hiPSCs)

status: Public on Nov 08 2024

city: Brno

first: Martina

last: Zapletalová

address: Kamenice 5

department: Department of Biochemistry

country: Czech Republic

institute: Masaryk University

summary: Astrocytes are specialized glial cell types of the central nervous system (CNS) with remarkably high abundance, morphological and functional diversity. Astrocytes maintain neural metabolic support, synapse regulation, blood-brain barrier integrity and immunological homeostasis through intricate interactions with other cells, including neurons, microglia, pericytes and lymphocytes. Due to their extensive intercellular crosstalks, astrocytes are also implicated in the pathogenesis of CNS disorders, such as ALS (amyotrophic lateral sclerosis), Parkinson’s disease and Alzheimer’s disease. Despite the critical importance of astrocytes in neurodegeneration and neuroinflammation are recognized, the lack of suitable in vitro systems limits their availability for modeling human brain pathologies. Here, we report the time-efficient, reproducible generation of astrocytes from human induced pluripotent stem cells (hiPSCs). Our hiPSC-derived astrocytes expressed characteristic classical markers of mature astrocytes, such as GFAP, S100b, ALDH1L1 and AQP4. Furthermore, hiPSC-derived astrocytes displayed spontaneous calcium transients and responded to inflammatory stimuli by the secretion of type A1 and type A2 astrocyte-related cytokines.

overall_design:
Two control human iPSC lines (BIOT.009 and BIOT.021) were used in this study, derived from healthy female donors and characterized earlier. Neural progenitor cells (NPC) were generated from the iPSCs by dual inhibition of the SMAD signalling pathway using LDN193189 and SB431542 [18, 19], then subsequently used for astrocyte differentiation.
The hiPSC-derived neural progenitor cells (NPCs) were propagated for at least 10 days in a completed neural maintenance medium. Cells were passaged with Accutase upon reaching confluence, and they were plated into poly-ornithine-laminin (POL)-coated plates with a seeding density of 50.000-150.000 cells/cm2. NPCs were seeded into matrigel-coated plates on day 14. To initiate the generation of astroglial progenitor cells (APCs), the culture medium was changed to medium into astrocyte growth medium the next day. The medium was changed every other day until the 21st day of differentiation. At the 21st day of astrocyte induction, APCs were seeded into matrigel-coated plates in an astrocyte induction medium with a density of 25.000-50.000 cells/cm2. The next day the medium was switched to astrocyte maturation medium, which was changed every other day until day 42.
Total RNA from cellular pellet samples was isolated using TRI Reagent (Merck, USA) with RapidOutput DNA removal kit (ThermoFisher Scientific, USA). The quantity and quality of RNA extracts were analyzed by using a Qubit 4 fluorometer (ThermoFisher Scientific, USA) and Fragment Analyzer (Agilent, USA). Complementary DNA (cDNA) libraries were synthesized using the NEBNext® Poly(A) mRNA Magnetic Isolation Module and NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (NEB, UK). RNA sequencing was performed on the Illumina NovaSeq 6000 platform with the NovaSeq S4 300 kit generating 150 bp pair-end reads (Illumina, USA). The sequencing quality of each read was assessed by FastQC, erroneous reads were filtered out using Trimmed Galore.  Trimmed sequence reads were mapped to the human genome sequence hg38 by using the R package module Rbowtie2 and Rsamtooks. Differentially expressed genes (DEGs) with |log2 fold change| > 1 and q < 0.01 (FDR-adjusted P-values) were selected in DeSeq2.

first: Balazs

last: Szeky

first: Veronika

last: Juráková

first: Eliska

last: Fousková

first: Anita

last: Feher

first: Melinda

last: Zana

first: Vivien

last: Réka Karl

first: János

last: Farkas

first: Maria

last: Bodi-Jakus

first: Radek

last: Kučera

first: Jan

last: Lochman

first: Andras

last: Dinnyes


title: Selectively targeting the AdipoR2-CaM-CaMKII-NOS3 axis by SCM-198 as a rapid-acting therapy for advanced acute liver failure

status: Public on Nov 09 2024

city: Shanghai

first: Gufa

last: Lin

address: 1239 Siping road Tongji university

department: Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, School of Life Sciences and Technology, Tongji University

institute: Tongji University

summary: In acute liver failure (ALF), liver regeneration deficiency is frequently observed, which is the leading cause of ALF and has a high mortality rate. If not treated promptly, ALF may lead to the need for a liver transplant due to limited treatment options. Here, we report the discovery of a 4-guanidino-n-butyl syringate (Leonurine), which has a hepatoprotective effect and can promote regeneration in mouse liver and human embryonic stem cell-induced liver organoids after acute liver injury (ALI). Leonurine demonstrated excellent safety and pharmacokinetics in vivo and was able to significantly reduce mortality in mice after administration of a lethal 24-hour dose of thioacetamide (TAA) or acetaminophen (APAP), which is fully protective compared to treatment with N-acetyl cysteine (NAC) loss of protection. We have synthesized a Leonurine biotinylation probe and have identified adiponectin receptor 2 (AdipoR2), a progesterone and adiponectin receptor family member, as a selective binding partner of Leonurine with a dissociation constant at micromolar levels. Depleting nitric oxide (NO) levels in hepatocytes is the leading cause of liver regeneration deficiency following ALI. The reduction of AdipoR2-Calmodulin (CaM)-endothelial nitric oxide synthase (NOS3) complex activity decreased NO production in hepatocytes, a significant contributor to the ALF phenotype induced by liver regeneration deficiency. Leonurine can form a guanidine-arginine pairing with the AdipoR2 arginine 335 (R335) site to enhance the activity level of AdipoR2 and increase the NO content in hepatocytes, promoting liver regeneration, and quickly antagonize ALF. The oxygen atom of AdipoR2 tyrosine 274 (Y274) interacts with the oxygen atom of Leonurine through hydrogen bonds, significantly enhancing the hydrophobicity of AdipoR2 arginine 275 (R275) residue, thereby activating its surface activity, reducing the molecular switch stability of R275 and aspartate 117 (D117) configurations, which increased the hydrophilic effect, thus regulating Ca2+ inflow but not significantly affecting the AMP level of hepatocytes and finally increasing CaM activity to upregulate the activity of the AdipoR2-CaM-eNOS complex, resulting in increased NO production. In vitro, the knockdown of AdipoR2 or the introduction of a mutant that does not bind to Leonurine blunts the effect of Leonurine's up-regulation of AdipoR2-CaM-eNOS complex activity. In vivo, the knock-out of AdipoR2 or NOS3 eliminated liver protection and regeneration, which Leonurine mediates. The evidence suggests that Leonurine possesses therapeutic benefits for patients without significant adverse effects. Our findings indicate that Leonurine possesses the potential to provide a rapid-acting treatment for the exercise of therapeutic benefits in ALF.

overall_design: To investigate the role of Leonurine binding to AdipoR2 receptor in the treatment of hepatic pharmacologic injury, we injected wild-type and Adipor2 knock-out mice with APAP, followed by injection of Leonurine and saline for the treatment. Mouse liver RNA samples were collected for sequencing. We then performed gene expression analysis by RNA-seq of four groups (APAP-WT-Leo, APAP-WT-Saline, APAP-Adipor2KO-Leo, APAP-Adipor2KO-Saline) to obtain differentially expressed genes for investigate the mechanism of Leonurine action in the treatment of drug-induced liver injury through Adipor2.

first: Rui

last: Wang

first: Youwei

last: Chen

first: JIazhen

last: Han

first: Huikang

last: Ye

first: Huiran

last: Yang

first: Qianyan

last: Li

first: Yizhen

last: He

first: Boyu

last: Ma

first: Junjie

last: Zhang

first: Yanli

last: Ge

first: Zhe

first: Bo

last: Sun

first: Huahua

last: Liu

first: Liming

last: Cheng

first: Zhirong


title: Transcriptomics analysis of sciatic nerves with conditional deletion of Nedd4 in the Schwann cell (SC) lineage during development.

city: Zurich

first: Jorge

middle: A.

last: Pereira

address: Otto-Stern-Weg 7

department: Dep. of Biology

institute: ETH Zurich

summary: RNA sequencing was performed to evaluate the transcriptome of sciatic nerves extracted from mice with conditional deletion of Nedd4 in the SC-lineage during development.

overall_design: The dataset was generated with sciatic nerves extracted from mice at 5 days of age (P5). The genotypes analyzed include 4 independent control animals  ( Nedd4tm3.1Bros flox/flox) and 4 independent conditional Nedd4 knockout animals in the SC-lineage  (Tg(Mpz-cre)26Mes +/- :  Nedd4tm3.1Bros flox/flox), abbreviated as mpzNedd4cKO.

first: Cristina

last: Fimiani

first: Ueli

last: Suter


title: ID1 and ID3 functions in the modulation of the tumor immune microenvironment in Adult Patients with B-Cell Acute Lymphoblastic Leukemia

city: New Orleans

first: Jovanny

last: Zabaleta

state: LA

address: 1700 Tulane Ave

department: Interdisciplinary Oncology

institute: LSUHSC

summary: The diagnosis of B-Cell acute lymphoblastic leukemia (B-ALL) in adults often carries a poor prognosis. ID1 and ID3 genes have been identified as predictors of poor response in Colombian adult B-ALL patients, playing roles in cancer development. In different cancer models, these genes have been associated with immune regulator populations within the tumor immune microenvironment (TIME). B-ALL development alters the immune cell composition and the bone marrow (BM) tumor microenvironment, affecting disease progression and response to therapy. This study analyzes gene expression levels of ID1 and ID3 in relation to TIME and immune evasion. This exploratory study analyzed BM samples from 10 B-ALL adult patients diagnosed at the National Cancer Institute of Colombia. First, RT-qPCR was used to assess ID1 and ID3 expression in BM tumor cells. Flow cytometry characterized immune populations in the TIME. RNA-seq evaluated immune genes associated with B-ALL immune response, while xCell and cytosig analyzed TIME cell profiles and cytokines. Pathway analysis, gene ontology, and differential gene expression (DEGs) were examined, with functional enrichment analysis performed using KEGG ontology. Patients were divided into two groups based on ID1 and ID3 expression, namely basal and overexpression. A total of 94 differentially expressed genes were identified between these groups, with top overexpressed genes associated with neutrophil pathways. Gene set enrichment analysis revealed increased expression of genes associated with neutrophil degranulation, immune response-related neutrophil activation, and neutrophil-mediated immunity. These findings correlated with xCell data. Overexpression group showed significant differences in neutrophils (p=0.0008), monocytes (<0.0001) and CD4+ naive T cells (p=0.0240) compared to basal group patients. Microenvironment and immune scores were also significantly different (p=0.0016 and p=0.0017, respectively), consistent with the flow cytometry results. Elevated cytokine levels associated with neutrophil activation supported these findings. Validation was performed using the TARGET and MILE B-ALL cohorts. Our results show important differences between the expression level of ID1 and ID3 in cancer cells and the populations of TIME, suggesting a role in evading the immune response of ID1 and ID3 in B-ALL, mainly related to neutrophil pathways.

overall_design: We use RT-qPCR to evaluate the expression levels of ID1 and ID3 in BM tumor cells. Immune populations within the tumor immune microenvironment (TIME) were characterized through flow cytometry. RNA sequencing (RNA-seq) was employed to investigate immune-related genes associated with the B-ALL immune response. Additionally, the xCell and cytosig tools were utilized to analyze the cellular profiles and cytokine patterns within the TIME. The study also included pathway analysis, gene ontology, and differential gene expression (DEG) analysis, with functional enrichment carried out using KEGG ontology. Based on the expression levels of ID1 and ID3, patients were categorized into basal and overexpression groups.

first: Nathaly

last: Poveda-Garavito

first: Carlos

last: Orozco

first: Yulieth

last: Torres-Llanos

first: Nataly

last: Cruz-Rodriguez

first: Sandra

last: Quijano

first: Alba

last: Combita


title: Concomitant loss of TET2 and TET3 results in T cell expansion and genomic instability [WGS]

status: Public on Nov 07 2024

city: New York

first: Tarmo

last: Äijö

address: 162 5th Avenue

department: Center for Computational Biology

institute: Flatiron Institute

type: Genome variation profiling by high throughput sequencing

summary: TET proteins are tumor suppressors that through their catalytic activity oxidize 5-methylcytosine to 5-hydroxymethylcytosine, to promote DNA demethylation and to regulate gene expression. Notably, TET2 is one of the most frequently mutated genes in hematological malignancies, including T cell lymphomas. However, murine models with deletion of TET2 do not exhibit T cell expansion, presumably due to redundancy with other members of the TET family of proteins. In order to gain insight on the TET mediated molecular events that safeguard T cells from aberrant proliferation we performed serial adoptive transfers of murine CD4 T cells that lack concomitantly TET2 and TET3 to fully immunocompetent congenic mice. Our data reveal a progressive acquisition of malignant traits upon loss of TET2 and TET3 that is characterized by loss of genomic integrity, acquisition of aneuploidy and upregulation of the protooncogene Myc.

overall_design: To test whether loss of TET2 and TET3 could endow Tet2/3 DKO CD4 cells with hyperproliferative capacity, we performed serial transplantations of sorted, highly pure Tet2/3 DKO CD4 cells in congenic CD45.1+ recipients, that have not received any irradiation. After 16 weeks, we witnessed that the transferred CD45.2+ Tet2/3 DKO cells have evaded the immune surveillance of the recipients and have expanded. At this point, we isolated CD45.2+ cells by FACS sorting  and re-transplanted them in new CD45.1+ immunocompetent recipients. The second transplantation resulted in significant acceleration of the expansion of the transplanted cells which became apparent within 2-4 weeks. To assess chromosomal copy number we performed whole genome sequencing. Genomic DNA was isolated from sorted wild type CD4 cells, or sorted expanded CD45.2+ Tet2/3 DKO cells after one or two serial transplantations in congenic CD45.1+ recipient mice.

first: Ageliki

last: Tsagaratou


title: cis- and trans-regulatory contributions to a hierarchy of factors influencing gene expression variation

city: Middletown

first: Joseph

last: Coolon

state: CT

address: 52 Lawn Avenue

department: Biology

institute: Wesleyan University

summary: Gene expression variation results from numerous sources including genetic, environmental, life stage, and even the environment experienced by previous generations. While the importance of each has been demonstrated in diverse organisms, their relative contributions remain understudied because few investigations have simultaneously determined each within a single experiment. Here we quantified genome-wide gene expression traits in Drosophila, quantified the contribution of multiple different sources of trait variation and determined the molecular mechanisms underlying observed variation. Our results show that there is a clear hierarchy in our data with genome and developmental stage contributing on average considerably more than current and finally previous generation environmental effects. We also determined the role of cis and trans-regulatory changes across different sources of trait variation, highlighting their importance in adaptation and environmental responses and showing unexpectedly that transgenerational effects herein were predominantly associated with changes in trans-regulation.

sample_organism: Drosophila simulans x Drosophila sechellia

overall_design: Differential gene expression analysis of D. sechellia and D. simulans, and D. sechellia x D. simulan hybrid larval and adult flies exposed to standard media and food supplemented with octanoic acid in both the current generation and previous generation  using RNA-sequencing.

first: Siddhant

last: Kalra

first: Stephen

last: Lanno

first: Guadalupe

last: Sanchez


title: Mitochondrial Dynamics Govern Whole-body Regeneration Through Stem Cell Pluripotency and Mitonuclear Balance [RNAi scRNA-seq]

city: 杭州市

first: li

last: yucong

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生

summary: To further identity the relationship between neoblast pluripotency and mitochondrial dynamics in cell lineage commitment,single-cell RNA sequencing was used to further analyze the compositions of mito low cells. To further identify the relationship between all different tissues cells and mito chondrial dynamics, snRNA-seq was used to further analyisis.

overall_design: Isolation by flow cytometry to get the mito low cells in RNAi planarians. Isolation by flow cytometry to get the mito low cells in RNAi planarians.Isolating the cell nuclei in RNAi planarians.

first: Xue

last: Pan

first: Yun

last: Zhao

first: Yucong

last: Li

first: Kai

last: Lei


title: Mitochondrial Dynamics Govern Whole-body Regeneration Through Stem Cell Pluripotency and Mitonuclear Balance [scRNA-seq]

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生

summary: To further identity the relationship between neoblast pluripotency and mitochondrial dynamics in cell lineage commitment,single-cell RNA sequencing was used to further analyze the compositions of mito low and mito high cells

overall_design: Isolation by flow cytometry to get the mito low and mito high cells in wild type planarians


title: Mitochondrial Dynamics Govern Whole-body Regeneration Through Stem Cell Pluripotency and Mitonuclear Balance

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生

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

overall_design: Refer to individual Series


title: Mitochondrial Dynamics Govern Whole-body Regeneration Through Stem Cell Pluripotency and Mitonuclear Balance [bulk RNA-seq]

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生

summary: To investigate the mechanism of mitochondrial morphology in neoblast pluripotenc and whole body regeneration,the Bulk RNA-seq and single cell RNA-seq data were needed.

overall_design: Bulk RNA-sequencing and single-cell RNA sequencing on experimental cells and planarians


title: Zebrafish are resilient to the loss of major diacylglycerol acyltransferase enzymes

city: Baltimore

first: Steven

last: Farber

address: 3400 N Charles St

institute: Johns Hopkins University

summary: In zebrafish, maternally deposited yolk is the source of nutrients for embryogenesis prior to digestive system maturation.  Yolk nutrients are processed and secreted to the growing organism by an extra-embryonic tissue, the yolk syncytial layer (YSL).  Export of lipid from the YSL occurs through the production of triacylglycerol-rich lipoproteins.  Here we report that mutations in the triacylglycerol synthesis enzyme, diacylglycerol acyltransferase-2 (Dgat2), cause yolk sac opacity due to aberrant accumulation of cytoplasmic lipid droplets in the YSL.  Though triacylglycerol synthesis continues, it is not properly coupled to lipoprotein production as dgat2 mutants produce fewer, smaller, ApoB-containing lipoproteins.  Unlike DGAT2-null mice, which are lipopenic and die soon after birth, zebrafish dgat2 mutants are viable, fertile and exhibit normal mass and adiposity.  Residual Dgat activity cannot be explained by the activity of other known Dgat isoenzymes, as dgat1a;dgat1b;dgat2 triple mutants continue to produce YSL lipid droplets and remain viable as adults.  Further, the newly identified diacylglycerol acyltransferase, Tmem68, is also not responsible for the residual triacylglycerol synthesis activity.  Unlike overexpression of Dgat1a and Dgat1b, monoacylglycerol acyltransferase-3 (Mogat3b) overexpression does not rescue yolk opacity, suggesting it does not possess Dgat activity in the YSL.  However, mogat3b;dgat2 double mutants exhibit increased yolk opacity and often have structural alterations of the yolk extension.  Quadruple mogat3b;dgat1a;dgat1b;dgat2 mutants either have severely reduced viability and stunted growth, or do not survive past 3 days post fertilization, depending on the dgat2 mutant allele present.  Our study highlights the remarkable ability of vertebrates to synthesize triacylglycerol through multiple biosynthetic pathways.

overall_design: We performed differential RNA-seq analysis between zebrafish dgat2sa13945 mutants and wild-type siblings.  Analyses were focused on the mid-sections of embryos (yolk syncytial layer and dorsal musculature) at 3 days post fertilization.  Each sample consisted of pools of 6 mutant or 6 WT fish.  Three samples per genotype were obtained, each from a different clutch of fish.

first: Meredith

last: Wilson