title: Differential tumor immune microenvironment coupled with tumor progression or tumor eradication in HPV-antigen expressing squamous cell carcinoma (SCC) models.

city: Pittsburgh

first: Jing

middle: Hong

last: Wang

state: PA

address: 5117 Centre Ave, Suite 2.35

department: Department of Medicine

institute: University of Pittsburgh

summary: Human papilloma virus (HPV) is an etiological factor of head and neck squamous cell carcinoma (HNSCC).  To investigate the role of HPV antigen in anti-tumor immunity, we established mouse models by expressing HPV16 E6 and E7 in a SCC tumor cell line.  We obtained two HPV antigen-expressing clones (C-225 and C-100) transplantable into C57BL/6 recipients.  We found that C-225 elicited complete eradication in C57BL/6 mice (eradicated), whereas C-100 grew progressively (growing).  We examined immune tumor microenvironment (TME) using flow cytometry and found that eradicated or growing tumors exhibited differential immune profiles that may influence the outcome of anti-tumor immunity.  Surprisingly, the percentage of CD8 and CD4 tumor-infiltrating lymphocytes (TILs) was much higher in growing (C-100) than eradicated (C-225) tumor. However, the TILs upregulated PD-1 and LAG-3 more potently and exhibited impaired effector functions in growing tumor compared to their counterparts in eradicated tumor.  C-225 TME is highly enriched with myeloid cells, especially polymorphonuclear (PMN) myeloid-derived suppressor cells (MDSC), whereas the percentage of M-MDSC and tumor-associated macrophages (TAMs) was much higher in C-100 TME, especially M2-TAMs (CD206+). The complete eradication of C-225 depended on CD8 T cells and elicited anti-tumor memory responses upon secondary tumor challenge. We employed DNA sequencing to identify differences in the T cell receptor of peripheral blood lymphocytes pre- and post-secondary tumor challenge. Lastly, C-225 and C-100 tumor lines harbored different somatic mutations.  Overall, we uncovered differential immune TME that may underlie the divergent outcomes of anti-tumor immunity by establishing two SCC tumor lines, both of which express HPV16 E6 and E7 antigens. Our experimental models may provide a platform for pinpointing tumor-intrinsic versus host-intrinsic differences in orchestrating an immunosuppressive TME in HNSCCs and for identifying new targets that render tumor cells vulnerable to immune attack.

overall_design:
PBMCs were isolated from peripheral blood samples collected from C-225 tumor-bearing mice (n=7) on day 102 (pre-PBMC) and day 116 (post-PBMC) after the first tumor inoculation. Each mouse has 2 samples sequenced including pre- and post-PBMC. In total, 14 samples were sequenced for 7 tumor-bearing mice.  RBC was lysed as described above, and genomic DNA was purified and used for TCRb sequencing with ImmunoSEQ platform by Adaptive Biotechnologies.  ImmunoSEQ Analyzer was employed to retrieve, process, and track the TCRb sequencing data. The data was further analyzed using R version 4.3.0 as described previously (24). Clonal proportion and clonotype tracking were analyzed with Immunarch (1.0.0) in R version 4.2.0.
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Authors state "Adaptive Biotechnology does not release raw data and provides only processed data files to the customers."

first: Arpitha

last: Shivarudrappa


title: Genome-wide and Cell-type Selective Profiling of In Vivo Small Noncoding RNA:Target RNA Interactions by Chimeric RNA Sequencing

status: Public on Jul 11 2024

city: Baltimore

first: Mollie

last: Meffert

address: 725 N. Wolfe St.

country: USA

institute: Johns Hopkins University School of Medicine

summary: Small noncoding RNAs (sncRNAs) can regulate biological processes by impacting posttranscriptional gene expression through repressing the levels and translation of targeted transcripts. Despite clear biological importance of sncRNAs, developed approaches to unambiguously define sncRNA:target RNA interactions in a genome-wide manner remain challenging and have not been widely adopted. We present CIMERA-seq, a robust strategy that incorporates covalent ligation of sncRNAs to their target RNAs within the RNA-induced silencing complex (RISC) and direct detection of the in vivo interactions by sequencing the resulting chimeric RNAs. Modifications are incorporated that increase the capacity for processing low abundance samples and which permit cell-type selective profiling of sncRNA:target RNA interactions, as demonstrated in mouse brain cortex. CIMERA-seq represents a cohesive and optimized method for unambiguously characterizing the in vivo network of sncRNA:target RNA interactions in numerous biological contexts and even subcellular fractions. Genome wide and cell-type selective CIMERA-seq enhances researchers’ ability to study the role of sncRNAs in mediating post-transcriptional gene regulation in diverse model systems and tissue types.

overall_design: sex and age matched C57BL/6 mice forebrain; genome-wide and cell-type selective miRNA:target RNA seq from Ago-CLIP, IgG for negative control.

middle: K

first: Xinbei

last: Li

first: William

middle: T

last: Mills IV

first: Daniel

middle: S

last: Jin


title: Identifying the role of FOXM1 in human primary renal tubular epithelials using bulk RNA-seq and Cut&Run to understand its role in acute kidney injury and repair

status: Public on Jul 10 2024

city: St. Louis

first: Monica

last: Chang-Panesso

state: MO

address: 600 S. Euclid Ave CB 8126

department: Medicine / Nephrology

institute: Washington University in St. Louis

type: Genome binding/occupancy profiling by high throughput sequencing

type: Expression profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Effect of human child or adult digestion reproduced in a dynamic in vitro gastrointestinal model on Cryptosporidium parvum transcriptome

city: NOUZILLY

first: Julie

last: TOTTEY

address: INRAE  Val de Loire UMR ISP 1282

country: France

institute: INRAE

summary: The impact of digestive physicochemical parameters on Cryptosporidium parvum transcriptome was analysed in a human and age-dependent context using a dynamic in vitro gastrointestinal model. The sophisticated TIM-1 in vitro model was used for a comparative analysis of C. parvum gene expression under the digestive conditions encountered in young children (from 6 months to 2 years) or in adults following the simulated ingestion of a glass of water contaminated with C. parvum oocysts. The C. parvum gene expression profile was analysed by RNA-sequencing in the inoculum, as well as the gastric and ileal effluents collected from the TIM-1 system. Results showed that time and compartment of digestion lead to the strongest modification of parasite transcriptome. Accordingly, the highest number of differentially expressed genes was observed in parasite samples collected in child or adult ileal effluents between 120 and 180 min of digestion, where invasive stages (sporozoites) are predominant.

overall_design: Five samples, three replicates per sample. Oocyst inoculum sample (1); Gastric effluents collected from the TIM-1 between 0 and 20 min of child (2) or adult (3) digestion; Ileal effluents collected from the TIM-1 between 120 and 180 min of child (4) or adult (5) digestion.

last: Tottey

first: Sonia

last: Lacroix-Lamandé


title: Spectrotemporal profiling of ultrasonic vocalizations during neonatal opioid withdrawal reveals a kappa opioid receptor component in female mice

status: Public on Jul 09 2024

city: Boston

first: Camron

middle: D

last: Bryant

state: MA

address: 140 The Fenway

department: Department of Pharmaceutical Sciences - Center for Drug Discovery

institute: Northeastern University

summary: Opioid use during pregnancy can lead to negative infant health outcomes, including neonatal opioid withdrawal syndrome (NOWS). NOWS comprises gastrointestinal, autonomic nervous system, and neurological dysfunction that manifest during spontaneous withdrawal. Current treatments involve non-pharmacological and pharmacological interventions, however, there is no one standardized approach, in part because of variability in NOWS severity. To effectively model NOWS traits in mice, we used a third trimester-approximate opioid exposure paradigm, where neonatal inbred FVB/NJ and outbred Carworth Farms White (CFW) pups were injected twice-daily with morphine (10-15 mg/kg, s.c.) or saline (0.9%, 20 ul/g, s.c.) from postnatal day (P) one to P14. We observed reduced body weight gain, hypothermia, thermal hyperalgesia, and increased ultrasonic vocalizations (USVs). Neonatal USVs are emitted exclusively in isolation to communicate distress and thus serve as a model behavior for affective states. On P14, we observed altered USV syllable profiles during spontaneous morphine withdrawal, including an increase in Complex 3 syllables in FVB/NJ females (but not males) and in CFW mice of both sexes. Brainstem transcriptomics revealed an upregulation of the kappa opioid receptor (Oprk1), whose activation has previously been shown to contribute to withdrawal-induced dysphoria. Treatment with the kappa opioid receptor (KOR) antagonist, nor-BNI (30 mg/kg, s.c.), significantly reduced USV emission in FVB/NJ females, but not FVB/NJ males during spontaneous morphine withdrawal. Furthermore, treatment with the KOR agonist, U50,488h (0.625 mg/kg, s.c.), was sufficient to increase USV emission on P10 (both sexes) and on P14 (females only) in FVB/NJ mice. Together, these results indicate a female-specific recruitment of the dynorphin/KOR system in neonatal opioid withdrawal symptom severity.

overall_design: To determine the effects of twice-daily morphine exposure on neonatal transcriptome, we collected brainstem tissue during spontaneous withdrawal on P16.

first: Kelly

last: Wingfield

first: Teodora

last: Misic

first: Kaahini

last: Jain

first: Carly

last: McDermott

first: Kayla

last: Richardson

first: Mia

middle: B

last: Rubman

first: Jacob

middle: A

last: Beierle

first: Sophia

last: Miracle

first: Emma

middle: J

last: Sandago

first: Britahny

middle: M

last: Baskin

first: Kristyn

middle: N

last: Borrelli

first: Emily

last: Yao

first: Elisha

last: Wachman


title: Autism-associated CHD8 controls reactive gliosis and neuroinflammation via remodeling chromatin in astrocytes [Microglia RNA-seq]

city: Montréal

first: Platon

last: Megagiannis

state: QC

address: 3801 Rue University

department: Neurology and Neurosurgery

country: Canada

institute: McGill University

summary: Reactive changes of glial cells during neuroinflammation impact brain disorders and disease progression. Elucidating the mechanisms that control reactive gliosis may help understand brain pathophysiology and improve outcomes. Here, we report that adult ablation of the ASD-associated CHD8 in astrocytes attenuates reactive gliosis via remodeling chromatin accessibility, changing gene expression. Conditional Chd8 deletion in astrocytes, but not microglia, suppresses reactive gliosis by impeding astrocyte proliferation and morphological elaboration. Astrocyte Chd8 ablation alleviates lipopolysaccharide-induced neuroinflammation and septic-associated hypothermia in mice. Astrocytic CHD8 plays an important role in neuroinflammation by altering the chromatin landscape, regulating metabolic and lipid-associated pathways, and astrocyte-microglia crosstalk. Moreover, we show that reactive gliosis can be directly mitigated in vivo using an AAV-mediated Chd8 gene editing strategy. These findings uncover a role of ASD-associated CHD8 in the adult brain, which may warrant future exploration of targeting epigenetic pathways in reactive gliosis and neuroinflammation in injury and neurological diseases.

overall_design: Bulk tissue RNA seq from cortex samples of mice with astrocyte specific Chd8 cKO after LPS or Saline injections, compared to controls. This designed was chosen to probe for transcriptional changes after Chd8 cKO in astrocytes at the baseline and during neuroinflammation

first: Yuan

last: Mei

first: Tony

last: Kwan

first: Trey

last: Ideker

first: Yang

last: Zhou


title: KRYPTONITE shapes TAD-like boundaries through the control of H3K9ac [ChIP-Seq]

city: Paris

first: Jing

last: An

address: 630 Rue Noetzlin

institute: Universite Paris Saclay

summary: Employing high-throughput sequencing and advanced microscopy techniques, we explored twenty-six histone modifications and Pol II distribution landscape in tomato (Solanum lycopersicum). Our findings revealed a comprehensive epigenetic landscape, uncovering distinct chromatin states associated with heterochromatin formation and gene silencing, allowing for the classification of genomic regions.

overall_design:
Comparative analysis of ChIP-seq data for tomato M82 wild type and Kyp mutant

**Please note that the sample records have been updated on Oct 9, 2024****

first: Rim

last: Chaouche

first: Qingyi

last: Wang

first: Ying

last: Huang

first: Moussa

last: Benhamed

first: David

last: Latrasse


title: Gene expression profile at single-cell level of cardiac cells derived from adult heart following injury

city: Rehovot

first: Jacob

middle: Kobi

last: Elkahal

address: Herzl St 234

department: Molecular cell biology

country: Israel

institute: Weizmann Institute od Science

summary: Myocardial injury may ultimately lead to adverse ventricular remodeling and development of heart failure (HF), which is a major cause of morbidity and mortality worldwide. Given the slow pace and substantial costs of developing new therapeutics, drug repurposing is an attractive alternative. Studies of many organs, including the heart, highlight the importance of the immune system in modulating injury and repair outcomes. Glatiramer-acetate (GA) is an immunomodulatory drug prescribed for patients with multiple sclerosis. Here we report that short-term GA treatment improves cardiac function and reduces scar area in a mouse model of acute myocardial infarction and a rat model of ischemic HF. We provide mechanistic evidence indicating that in addition to its immunomodulatory functions, GA exerts beneficial pleiotropic effects, including cardiomyocyte protection and enhanced angiogenesis. Overall, these findings highlight the potential repurposing of GA as a future therapy for a myriad of heart diseases.

overall_design: Given the dynamic nature of immune cell activation in the first week following MI,  we wanted to gain deeper insights on the effects of GA on the inflammatory response following acute MI. Therefore, we performed single-cell RNA-sequencing (scRNA-seq) on CD45+-enriched cardiac cells and we have chosen to focus on 1 and 4 dpi.

first: Gal

last: Aviel

first: Kfir

last: Baruch Umansky

first: Hanna

last: Bueno-Levy

first: Zachary

last: Petrover

first: Yulia

last: Kotlovski

first: Daria

last: Lendengolts

last: Kain

first: Tali

last: Shalit

first: Lingling

last: Zhang

first: Shoval

last: Miyara

first: Matthias

middle: P

last: Kramer

first: Yifat

last: Merbl

first: Stav

last: Kozlovski

first: Ronen

last: Alon

first: Rina

last: Aharoni

first: Ruth

last: Arnon

last: Mishaly

first: Uriel

last: Katz

first: Dean

last: Nachman

first: Rabea

last: Asleh

first: Offer

last: Amir

first: Eldad

last: Tzahor

first: Rachel

last: Sarig


title: Effects of over-expression of PLEK2 on gene expression in 22RV1 cells

city: Chicago

first: Xu

last: Han

state: IL

address: 303 E Chicago Avenue

department: Pathology

institute: Northwestern University

summary: We previously found that loss of Plek2 decreased Akt activity and reverted disease phenotypes in hematopoietic system specific Pten knockout mice. Pten knockout mice also show prostate cancer phenotype. Using a well known Pten prostate-specific knockout mouse model, we found that loss of Plek2 also reverted tumorigenesis of prostate cancer via decreasing Akt pathway activity. Furthermore, we found that PLEK2 over-expression increased AKT pathway activity and promoted proliferation in 22RV1 cells which is a kind of prostate cancer cell line. To explore additional pathway which PLEK2 may involve in prostate cancer, we performed RNA sequencing in PLEK2 over-expressed  and control 22RV1 cells.

overall_design: To explore additional pathway PLEK2 involving in prostate cancer, we performed PLEK2 over-expression (OV) in 22RV1 cells. Total RNAs were extracted from PLEK2 OV and control groups, followed by RNA sequencing, in triplicate, using Hiseq4000 1x 50bp platform.

first: Peng

last: Ji


title: Different doses of androgens induce the expression of distinct gene expression programs [ChIP-Seq]

city: Durham

first: Xiaodi

last: Qin

address: 2424 Erwin Road

institute: Duke Cancer Institute

summary: Most prostate cancers express the androgen receptor (AR), and tumor growth and progression are facilitated by exceptionally low levels of systemic or intratumorally produced androgens. Paradoxically, high dose androgens have also shown considerable efficacy in the treatment of patients with late-stage metastatic PCa. In probing the mechanisms that enable cells to recognize and respond to different levels of the same hormone, it was determined that low levels of androgens, functioning through an AR monomer, facilitates a non-genomic activation of the mTOR signaling pathway to drive proliferation. Conversely, high dose androgens facilitate the formation of AR dimers to suppress c-MYC expression, inhibit proliferation and drive a transcriptional program associated with a differentiated phenotype. These findings highlight the inherent liabilities in current approaches used to inhibit AR action in PCa and are instructive as to strategies that can be used to develop new therapeutics for this disease and other androgenopathies.

overall_design: To identify AR directly regulated enhancers responsible for the non-linear proliferative responses to androgens, we performed an unbiased genome wide ChIP-sequencing study in both VCaP and LNCaP cells. VCaP and LNCaP cells where treated with either vehicle, or increasing concentrations of low-dose 0.01, 0.03, 0.06, 0.1 nM R1881) or High-Dose (10nM R1881) androgens for 24 hrs.

first: Rachid

last: Safi

first: Paige

last: Watkinson

first: Marissa

last: Lee

first: Adam

last: Blattler

first: Celia

last: Fontanillo

first: Kouros

last: Owzar

first: John

last: Norris

first: Donald

last: McDonnell


title: Different doses of androgens induce the expression of distinct gene expression programs (RNA-Seq)

overall_design: To explore the molecular mechanisms underlying the biphasic response to androgens, we performed RNA-seq in both LNCaP and VCaP cells following treatment with vehicle, increasing concentrations of low-dose 0.01, 0.03, 0.06, 0.1 nM R1881) or High-Dose (10nM R1881) androgens for 24 hrs.


title: Enhancing tumor response to adoptive T cell therapy by targeting PHD2/3 in CD8 T cells

city: Brussels

first: Jingjing

last: Zhu

address: Avenue Hippocrate 74

country: Belgium

institute: de Duve Institute/Ludwig Institute for Cancer Research

summary: In our study, we utilized cutting-edge CrisPR-Cas9 technology to evaluate the effects of deleting prolyl hydroxylase domain-containing enzymes (PHD) 2 and 3, which stabilizes HIF-1 signaling, in CD8 T cells that have already undergone differentiation and activation, mirroring the conditions encountered in clinical settings. Our study revealed a significant boost in T-cell activation and effector functions after PHD2/3 deletion, and conclusively established its dependence on HIF-1. This improvement in CD8 T cell performance translated into a remarkable enhancement in the response to adoptive T cell therapy, across various tumor models, even including those reported to be extremely resistant to immunotherapeutic interventions. Furthermore, our data provide compelling evidence that the increased effector functions observed in PHD-deficient (KO) CD8 T cells are intricately linked to an increased glycolytic flux. These findings hold significant promise for advancing CD8 T -cell based therapies and overcoming the immune suppression barriers within challenging tumor microenvironments.

overall_design: To decipher the impact of HIF-1 signaling on the function of CD8 T cells, we generated activated murin TCRP1A CD8 T lymphocytes in which HIF-1a or PHD2/3 have been knock-out by Crispr-Cas9 nucleofection technology. We then performed RNA-seq analysis on HIF-1a KO, PHD2/3 KO and WT (control) CD8 T cells which have been incubated in norrmoxia or hypoxia for 48 hours. Samples were analysed in biological triplicates.

first: Tereza

last: Dvorakova

first: Veronica

last: Finisguerra

first: Matteo

last: Formenti

first: Axelle

last: Loriot

first: Boudhan

last: Loubna

first: Benoit

last: Van den Eynde


title: Base-resolution m5C profiling across the mammalian transcriptome by bisulfite-free enzyme-assisted chemical labeling approach

city: Hangzhou

first: Xiaoyu

last: Li

state: Zhejiang

address: 866 Yuhangtang Road

department: SCHOOL OF BASIC MEDICAL SCIENCES

country: China

institute: Zhejiang University

type: Methylation profiling by high throughput sequencing

summary: 5-methylcytosine (m5C) is a prevalent RNA modification crucial for gene expression regulation. However, accurate and sensitive m5C sites identification remains challenging due to severe RNA degradation and reduced sequence complexity during bisulfite sequencing (BS-seq). Here, we report m5C-TAC-seq, a bisulfite-free approach combining TET-assisted m5C-to-f5C oxidation with selective chemical labeling, therefore enabling direct base-resolution m5C detection through pre-enrichment and C-to-T transitions at m5C sites. With m5C-TAC-seq, we comprehensively profiled the m5C methylomes in human and mouse cells, identifying a substantially larger number of confident m5C sites. Through perturbing potential m5C methyltransferases, we deciphered the responsible enzymes for most m5C sites, including the characterization of NSUN5's involvement in mRNA m5C deposition. Additionally, we characterized m5C dynamics during mESC differentiation. Notably, the mild reaction conditions and preservation of nucleotide composition in m5C-TAC-seq allow the m5C detection in chromatin-associated RNAs. The accurate and robust m5C-TAC-seq will advance research into m5C methylation functional investigation.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: To achieve a bisulfite-free, base-resolution m5C detection strategy, we combined TET-assisted m5C-to-f5C oxidation with selective chemical labeling. This approach enables direct base-resolution m5C detection through pre-enrichment and C-to-T transitions at m5C sites.

first: Liang

last: Lu

first: Yuenan

last: Zhou

first: Xiaoting

last: Zhang


title: Different doses of androgens induce the expression of distinct gene expression programs (ATAC-Seq)

first: Xiaodi

last: Qin

overall_design: To identify molecular events responsible for the non-linear proliferative responses to androgens, we performed an unbiased genome-wide survey of changes in chromatin accessibility with the goal of identifying potential cis-acting elements enriched in LD versus HD treated PCa cells. To this end, we performed an assay for transposase-accessible chromatin using sequencing (ATAC-seq) in both VCaP and LNCaP cells following treatment with vehicle, increasing concentrations of low-dose 0.01, 0.03, 0.06, 0.1 nM R1881) or High-Dose (10nM R1881) androgens for 24 hrs.

first: Rachid

last: Safi

first: Paige

last: Watkinson

first: Marissa

last: Lee


title: Different doses of androgens induce the expression of distinct gene expression programs


title: KIT-expressing cells in the mouse fetal liver

city: Kumamoto

first: Saori

last: Morino-Koga

state: Kumamoto

address: 2-2-1 Honjo, Chuo-ku

department: Institute of Molecular Embryology and Genetics

country: Japan

institute: Kumamoto University

summary: Various blood lineages, including lymphoid cells and myeloid cells, are produced from hematopoietic stem cells (HSCs) in the bone marrow. However, HSCs aren’t developed in the bone marrow during mouse embryogenesis. The first HSCs are found in the aorta-gonad-mesonephros region, the yolk sac, and the fetal liver, although the number is very few at embryonic day (E) 11. Most HSCs are observed in the fetal liver at E12. To understand the specific genes of nascent HSCs, we performed single-cell RNA-seq analysis of KIT-expressing cells sorted from the fetal liver at E12. We identified the nascent HSC population and found some feature genes in those cells. Therefore, our data will help us understand the nascent HSCs.

overall_design: Single-cell RNA-seq analysis of KIT-expressing cells sorted from the mouse fetal liver at E12

first: Tomomasa

last: Yokomizo

first: Toshio

last: Suda

first: Minetaro

last: Ogawa


title: Baf155 establishes chromatin priming to promote hematopoietic regeneration and function [bulk ATAC]

city: Saint Louis

first: Changxu

last: Fan

state: Missouri

address: 4515 McKinley Avenue, Room 5213

department: Genetics

summary: Chromatin priming promotes cell type-specific gene expression, lineage differentiation, and development. The mechanism of chromatin priming has not been well understood. Mouse hematopoietic stem and progenitor cells (HSPCs) lacking the Baf155 subunit of the BAF (BRG1/BRM associated factor) chromatin-remodeler produced a significantly reduced number of mature blood cells, leading to a failure of hematopoietic regeneration upon transplantation and 5-FU injury. Baf155 deficient HSPCs, while showing impaired mature blood cell production, generated a higher frequency of myeloid cells with fewer B and CD8+ T cells at homeostasis, supporting a more immune-suppressive tumor microenvironment and enhanced tumor growth. Single-nuclei multi-omic analysis revealed that Baf155 deficient HSPCs failed to establish accessible chromatin and levels of lineage-specific transcripts were considerably lower. Regions that showed a substantial loss in chromatin accessibility were enriched for enhancers and binding motifs for hematopoietic lineage-specific transcription factors. Our study provides a fundamental mechanistic understanding of the role of Baf155 in establishing chromatin priming with functional consequences in regeneration or tumor immunity.

overall_design: Bulk ATAC assay was performed on WT and Baf155 KO KSL and GMP cells. No 5-FU treatment.

first: Jun

last: Wu

first: Xiaoyun

last: Xing

first: Ting

last: Wang

first: Kyunghee

last: Choi


title: Global 13C tracing and metabolic flux analysis of intact human liver tissue ex vivo

status: Public on Jul 08 2024

city: Solna

first: Roland

last: Nilsson

address: Akademiska Stråket 1

department: Dept. of Medicine, Solna

country: Sweden

institute: Karolinska Institutet

summary: Liver metabolism is central to human physiology and influences the pathogenesis of common metabolic diseases. Yet, our understanding of human liver metabolism remains incomplete, with much of current knowledge based on animal or cell culture models that do not fully recapitulate human physiology. Here, we performed in-depth measurement of metabolism in intact human liver tissue ex vivo using global 13C tracing, non-targeted mass spectrometry and model-based metabolic flux analysis. Cultured liver tissue exhibited normal anatomical structure and retained canonical liver functions such as glucose production, albumin and VLDL synthesis at near-physiological rates. Isotope tracing with a highly 13C-labeled medium generated 13C enrichment in hundreds of compounds, allowing qualitative assessment of a wide  range of metabolic pathways within a single experiment. This confirmed well-known features of liver metabolism, but also revealed unexpected metabolic activities such as de novo creatine synthesis and branched-chain amino acid transamination, where human liver appears to differ from rodent models. Metabolic flux analysis identified glycogenolysis as the main source of glucose production, which could be suppressed by pharmacological inhibition of glycogen phosphorylase. Glucose production ex vivo also correlated with donor plasma glucose, suggesting that cultured liver tissue retains individual metabolic phenotypes. Moreover, liver tissue responded to postprandial levels of nutrients and insulin by suppressing glucose production and increasing nutrient uptake. Isotope tracing ex vivo allows measuring human liver metabolism with great depth and resolution in an experimentally tractable system.

overall_design:
Transcriptome analysis of fresh human liver tissue and liver tissue slices cultured for 24 hours in different media.

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Submitter states that missing raw data are being made available for controlled access in EGA.
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first: Nina

last: Grankvist


title: Baf155 establishes chromatin priming to promote hematopoietic regeneration and function [single cell multiome - ATAC + GEX]

overall_design: single cell multiome ATAC + GEX assays were performed on WT and Baf155 KO HSPCs, 9 or 11 days after 5FU injury.


title: Synthetic lethal CRISPR screen identifies a cancer cell-intrinsic role of PD-L1 in regulation of vulnerability to ferroptosis [CUT&Tag]

city: Hubei

first: Yang-Ying-Fan

last: Feng

address: Luonan stress

institute: wuhan university

summary: Despite the remarkable success of programmed death 1/PD-L1 inhibition in tumor therapy, only a minority of patients benefits from it. Previous studies suggest the anti-PD-1 treatment failure may attribute to the intrinsic functions of PD-L1 in cancer cells. Here, we established a genome-wide CRISPR synthetic lethality screen to systematic explore the PD-L1 intrinsic function in head and neck squamous cell carcinoma (HNSCC) cells. Ferroptosis related genes were identified to be essential for PD-L1 deficient cell viability. Genetic and pharmacological induction of ferroptosis accelerated cell death in PD-L1 knockout cells. PD-L1 knockout cells were also highly susceptible to immunogenic ferroptosis in vitro and in vivo. Mechanistically, nuclear PD-L1 transcriptionally activated SOD2 expression to maintain redox homeostasis. Importantly, the lower ROS and ferroptosis were observed in HNSCC patients with the higher expression of PD-L1. In summary, our study illustrates that PD-L1 confers ferroptosis resistance by activating SOD2-meidated redox homeostasis in HNSCC cells, indicating an enhanced therapeutic effect can be achieved by targeting the intrinsic PD-L1 function during immunotherapy.

overall_design: CUT&Tag followed by sequencing assays were perfromed in HSC3 PD-L1 KO cells with overexpression of Flag-tagged PD-L1.

first: Yicun

last: Li

first: Yangyingfan

first: Wei

first: Hongyu

last: Yang

first: Gang

last: Chen


title: Synthetic lethal CRISPR screen identifies a cancer cell-intrinsic role of PD-L1 in regulation of vulnerability to ferroptosis [CRISPR screening]

overall_design: We employed a genome-wide CRISPR knock-out screen for synthetic lethal interactions of programmed death-ligand 1 (PD-L1) in the human head and neck squamous cell carcinoma (HNSCC) cell line CAL27. There are 2 samples done in duplicate in PD-L1 knockout and its control.

last: Zhang


title: ATAC-seq analysis of histone variant H2BE in neuronal chromatin

status: Public on Jul 17 2024

city: Philadelphia

first: Emily

last: Feierman

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

overall_design: WT and H2BE-KO primary cortical neurons were isolated from E16.5 mice, infected with H2B, WT H2BE, H2BE-I39V, or GFP control, and culture for 12 days for ATAC-sequencing (n=3-8 biological replicates per group).


title: TnSeq study evaluating the impact of Atg5 and Atg7 on survivial of Mycobacterium tuberculosis transposon mutants in IFN-gamma-activated murine bone marrow-derived macrophages

first: Jennifer

last: Philips

address: 660 South Euclid Avenue

summary: Mycobacterium tuberculosis impairs host lysosomal trafficking pathways. Xenophagy and LC3-associated phagocytosis (LAP) are lysosomal trafficking pathways that normally clear intracellular microbes. The xenophagy and LAP pathways depend upon ATG5 and ATG7, which result in the lipidation of LC3-I to LC3-II.  How Mtb undermines these innate immune defenses of the host in not well understood. We used a transposon sequencing (Tn-seq) screen to identify bacterial factors that are required for the bacilli to resist ATG5 and ATG7-dependent processes. We found that that mutants defective in production of PDIM are attenuated in murine macrophages, and they are able to survive in macrophages lacking ATG5 or ATG7.

overall_design: To identified Mtb factors which are required to resist xenophagy and/or LAP, we infected IFN-g-activated BMDMs that were WT (Atg5fl/fl Cre- and Atg7fl/fl Cre-) or Atg-deficient (Atg5fl/fl LysM-Cre+ and Atg7fl/fl LysM-Cre+) with a pool of saturated Himar1 transposon (Tn) mutants. After 5 days of infection, colony forming units (CFU) were collected for isolation of genomic DNA from surviving bacilli, subject to library preparation, sequenced by Illumina HiSeq, and analyzed using TRANSIT.

first: Sandeep

last: Upadhyay

first: Andrew

last: Olive

first: Christopher

last: Sassetti


title: Identification of resistance mechanisms to small-molecule inhibition of YAP/TEAD-regulated transcription [RNA-seq]

city: Melbourne

first: Kieran

last: Harvey

state: VIC

address: 305 Grattan St

country: Australia

institute: Peter MacCallum Cancer Centre

summary: The Hippo tumour suppressor pathway controls transcription by regulating nuclear abundance of YAP and TAZ, which activate transcription with the TEAD1-TEAD4 DNA-binding proteins. Recently, several small-molecule inhibitors of YAP and TEADs have been reported, with some now entering clinical trials for different cancers. Here, we investigated the cellular response to TEAD palmitoylation inhibitors, using genomic and genetic strategies. Genome-wide CRISPR/Cas9 screens revealed that mutations in genes from the Hippo, MAPK and JAK-STAT signaling pathways all modulate the cellular response to TEAD inhibition. Inhibition of TEAD palmitoylation strongly reduced YAP/TEAD target expression, whilst only mildly impacting YAP/TEAD genome binding. Additionally, expression of MAPK pathway genes was induced upon inhibition of TEAD palmitoylation, which coincided with YAP/TEAD redistribution to AP-1 transcription factor binding sites. Consistent with this, combined inhibition of TEAD and the MAPK protein MEK, synergistically blocked proliferation of several mesothelioma and lung cancer cell lines and more potently reduced the growth of patient-derived lung cancers in vivo. Collectively, we reveal mechanisms by which cells can overcome small-molecule inhibition of TEAD palmitoylation and potential strategies to enhance the anti-tumor activity of emerging Hippo pathway targeted therapies.

overall_design: RNA-seq data of mesothelioma cells under DMSO or VT107 treatment conditions

first: Aishwarya

last: Kulkarni

first: Varshini

last: Mohan

first: Tracy

last: Tang

first: Leonard

last: Post

first: Murray

last: Manning

first: Niko

last: Thio

first: Benjamin

last: Parker

first: Joseph

last: Rosenluh

first: Yih-Chih

last: Chan

first: Mark

last: Dawson

last: Vissers


title: scRNA-seq + TCR-seq of mouse polyclonal CD4+ T cells during blood-stage malaria infection.

city: Melbourne VIC 3004, AU

first: Cameron

middle: Gerard

last: Williams

address: 792 Elizabeth Street

department: Department of Microbiology and Immunology

institute: University of Melbourne

summary: Blood-stage malaria infection induces differentiation of several effector CD4 + T subsets including Tfh and Th1 cells. The cues and microarchitectural niches required in secondary lymphoid organs for their formation were previously uncharacterised. Here we used scRNA-seq to profile CD4+ T cell transcriptomes upon malaria infection as a reference dataset for deconvolution of spatial transcriptomic data.

overall_design: Mice were infected with Plasmodium chabaudi chabaudi AS (PcAS)-parasitised Red Blood Cells (pRBCs). CD4+ T cells were recovered at Day 7 post-infection to undergo processing and generate scRNA-seq dataset.

first: Hyun

last: Lee

first: Marcela

middle: L

last: Moreira

middle: G

first: Shihan

last: Li


title: Spatial transcriptomics of mouse spleens during steady state and malaria infection. [d0_d7_slideseqV2]

summary: Blood-stage malaria infection induces differentiation of several effector CD4 + T subsets including Tfh and Th1 cells. The cues and microarchitectural niches required in secondary lymphoid organs for their formation were previously uncharacterised. Here we used spatial transcriptomics to characterise the microarchitecture of mouse spleen before and during malaria infection, and mapping the spatial and molecular requirements of Tfh/Th1 differentiation.

overall_design: Mice were infected with Plasmodium chabaudi chabaudi AS (PcAS) parasitised RBCs (pRBCs) or a saline control. At Day 7, whole spleens were recovered and fresh frozen to generate Slide-seqV2 datasets.

first: Evan

last: Murray

first: Jessica

last: Engel

first: Megan

last: Soon

first: Irving

last: Barrera


title: scRNA-seq mouse splenocytes prior to and during blood-stage malaria infection.

summary: Blood-stage malaria infection induces differentiation of several effector CD4 + T subsets including Tfh and Th1 cells. The cues and microarchitectural niches required in secondary lymphoid organs for their formation were previously uncharacterised. Here we used scRNA-seq to profile splenocyte transcriptomes at steady state or upon malaria infection as a reference dataset for deconvolution of spatial transcriptomic data.

overall_design: Mice were infected with Plasmodium chabaudi chabaudi AS (PcAS)-parasitised Red Blood Cells (pRBCs) or a saline control. Splenocytes were recovered at Day 7 post-infection to undergo processing and generate scRNA-seq dataset.


title: mouse and malaria infection

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

overall_design: Refer to individual Series


title: Pateamine A mediates RNA sequence-selective translation repression by anchoring eIF4A and DDX3 to GNG motifs

city: Wako

first: Shintaro

last: Iwasaki

address: 2-1 Hirosawa

department: Cluster for Pioneering Research

institute: RIKEN

summary: Small molecule compounds that inducespark the mRNA-selective translation repression, are attracting interesthave arisen due to their potential for expansion ofin druggable space expansion. However, only limited examples have been reported to datewere found. Here we showed that pateamine A (PatA) represses translation in an mRNA-selective manner by clamping eIF4A, a DEAD-box RNA-binding protein, on GNG motifs. Through systematic comparison of multiple eIF4A inhibitors by ribosome profiling, we found that PatA has a unique mRNA selectivity in translation repression. Unbiased Bind-n-Seq revealed that PatA provides a sequence preference toward GNG motifs to eIF4A in an ATP-independent manner. This unusual RNA binding sterically hindered scanning by 40S ribosomes. In silico simulation, quantum chemical calculation, and subsequent development of an inactive PatA derivative concluded that the charge of the secondary amine on the trienyl arm determines G selectivity. Moreover, we found that DDX3, another DEAD-box protein, was an alternative target of PatA, phenocopying the effect on eIF4A. Our results provide an example of sequence-selective anchor of RNA-binding proteins and mRNA-selective inhibition of protein synthesis by a small molecule compound.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: The translational impact of the compounds including Hipp, San, or DMDA-PatA was examined through ribosome profiling. RNA pulldown-Seq was conducted to explore the interaction between mRNAs and eIF4A1 in the presence of DMDA-PatA. RNA Bind-n-Seq was performed to elucidate the sequence preferences of RNA binding proteins in the presence of DMDA-PatA, iPr-DMDA-PatA, or RocA.

first: Hironori

last: Saito

first: Yuma

last: Handa

first: Mingming

last: Chen

first: Tilman

last: Schneider-Poetsch

first: Yuichi

last: Shichino

first: Mari

last: Takahashi

first: Daniel

last: Romo

first: Minoru

last: Yoshida

first: Alois

last: Fürstner

first: Takuhiro

last: Ito

first: Kaori

last: Fukuzawa


title: Baf155 controls hematopoietic differentiation and regeneration through chromatin priming

first: Changxu

last: Fan

institute: Washington University in St. Louis


title: Wheat-RegNet: An encyclopedia of common wheat hierarchical regulatory network

city: shanghai

first: yijing

last: zhang

address: 2005 Songhu Road

department: Biochemistry

institute: Fudan University

summary: Common wheat is one of the most widely cultivated staple crops worldwide. Elucidating the gene regulatory network will provide essential information for mechanism studies and targeted manipulation of gene activity for breeding. However, detecting cis-regulatory elements and transcription factor (TF) bindings in the extremely large intergenic regions of the wheat genome is challenging. Linking cis-regulatory elements and TF binding to target genes is even more difficult given that enhancers can function irrespective of the strand and distance from target genes. Combining genome-wide TF binding profiles, epigenomic patterns, and transcriptome analysis is a compelling approach to detect the hierarchical regulatory network. We generated and collected 189 TF binding profiles, 90 epigenomic datasets, and 2,356 transcriptomic datasets in common wheat, which were further integrated using machine learning approach to infer direct target genes and the hierarchical regulatory network. We developed a web-based platform, Wheat-RegNet, that provides four major functions: (i) to identify regulatory elements regulating input gene(s), and to infer the tissue and environmental response specificity; (ii) to identify the TFs responsible for regulating input gene(s) or locus/loci; (iii) to construct the hierarchical regulatory network regulating input gene(s); and (iv) to browse hundreds of TF binding, epigenomic, and transcriptomic profiles of an input region or gene(s). Well-organized results and multiple tools for interactive visualization are available through a user-friendly web interface, making Wheat-RegNet a highly useful resource for exploring gene regulatory information for hypothesis-driven studies and for targeted manipulation for breeding research in common wheat. Wheat-RegNet is freely available at http://bioinfo.sibs.ac.cn/Wheat-RegNet

overall_design: DNase-seq for mixed 100 different varieties of wheat leaves collected at the two-leaf stage.

first: Tengfei

last: Wang

first: Xiaotong

last: Lv

first: Shilong

last: Tian

first: Fei

last: Zhao

first: Hao

last: Li

first: Wenli

last: Zhang

first: Yijing


title: Insulin receptor deletion in kidney intercalated cells suppresses collecting duct immune defenses

city: Columbus

first: John

middle: David

last: Spencer

state: OH

address: 700 Children's Drive

institute: Nationwide Children's Hospital

summary: Urinary tract infection (UTI) significantly impacts people with diabetes mellitus. Insulin resistance, the primary abnormality leading to Type 2 diabetes, is defined by inefficient insulin receptor signaling. In the kidney, insulin receptor deletion in intercalated cells increases UTI susceptibility. Here, we use RNA sequencing to profile the transcriptomes of enriched intercalated cell and neighboring principal cell populations from mice with intercalated cell-specific insulin receptor deletion and compare expression profiles to wild-type mice. We also establish unique intercalated cell and principal cell cultures to assess the functional impact of insulin receptor deletion. Transcriptomic analysis and culture models demonstrate intercalated cells with insulin receptor deletion are more susceptible to uropathogenic Escherichia coli infection and have suppressed integrated stress responses. They also show the integrated stress response is necessary to activate NFkB-mediated immune responses. When NFkB is silenced, intercalated cells do not activate innate immune responses, including the production of antimicrobial peptides, which increases infection susceptibility.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for FACS enriched intercalated cells and principal cells from IR floxed control mice and Atp6v1b1-Cre/IRKO mice.

first: Laura

last: Schwartz


title: Identification of resistance mechanisms to small-molecule inhibition of YAP/TEAD-regulated transcription

status: Public on Jul 07 2024

first: Kieran

last: Harvey


title: Full-length single-cell BCR sequencing paired with RNA sequencing reveals convergent responses to vaccination

city: Cambridge

first: Darrell

middle: J.

last: Irvine

address: 77 Massachusetts Ave

institute: Massachusetts Institute of Technology

summary: Single-cell RNA sequencing can resolve transcriptional features from individual cells, but techniques capable of resolving the variable regions of B cell receptors (BCRs) – defining features that confer antigen specificity to B cells – remain limited, especially from widely-used 3`-barcoded libraries. Here, we report a method that can recover paired, full-length variable region sequences of BCRs from 3`-barcoded single-cell whole transcriptome libraries.  We applied this method to produce accurate, full-length BCR sequences from cDNA of human PBMC generated following the 10x Genomics 3`GEX protocol.

overall_design: B cells of interest were isolated from PBMC using immunomagnetic selection and analyzed with the 10x Genomics 3` GEX platform for single-cell RNA sequencing.

first: Yiming

first: Duncan

last: Morgan

first: J

middle: C

last: Love


title: Cell surface-targeted immunocytokines program systemic anti-tumor immunity

summary: Systemically-administered cytokines are potent immunotherapy agents but exhibit severe dose-limiting toxicities. To overcome this challenge, cytokines have been engineered for intratumoral retention following local delivery. However, despite inducing regression of treated lesions, tumor-localized cytokines often elicit only modest abscopal effects at distal untreated tumors. Here we report a localized cytokine therapy that safely elicits potent systemic anti-tumor immunity by engineered targeting of the ubiquitous leukocyte receptor CD45. CD45-targeted immunocytokines (αCD45-Cyt) exhibit significantly diminished internalization rates relative to their wild-type counterparts; this prolonged surface retention sustains downstream pSTAT induction and enables both cis and trans signaling between lymphocytes. Intratumoral αCD45-Cyt administration led to decoration of leukocytes in the tumor and tumor-draining lymph node (TDLN) without systemic exposure. Therapeutically, a single dose of αCD45-IL12 followed by a single dose of αCD45-IL15 eradicated both treated tumors and untreated distal lesions in multiple syngeneic mouse tumor models. Mechanistically, prolonged exposure to αCD45-Cyt in the tumor and TDLN reprogrammed CD8+ T cells in the TDLN to exhibit an anti-viral transcriptional signature and expanded tumor-specific effector T cells in both the tumor and TDLN. CD45 anchoring represents a broad platform for protein retention by host immune cells for use in immunotherapy.

overall_design: To understand how localized αCD45-Cyt treatment elicited such potent systemic immunity against B16F10 tumor, we performed gene expression profiling analysis on live CD3+CD8+CD44+p15E+ cells using data obtained from RNA-seq of 3 experimental groups and 5 mice from each experimental group, with a total number of 15 mice. Mice from the control group were injected with PBS. Mice from the second and third group were injected with IgG-Cyt and aCD45-Cyt therapies, respectively. Each sample represents cells from an individual mouse from this study.

first: Luciano

last: Santollani

last: Maiorino

first: Joseph

last: Palmeri

first: Jordan

last: Stinson

first: Lauren

last: Duhamel

first: Kashif

last: Qureshi

first: Jack

last: Suggs

first: Owen

last: Porth

first: William

last: Pinney III

first: Riyam

last: Al Msari

first: Dane

last: Wittrup


title: In utero exposure of delta-9-tetrahydrocannabinol (THC) affects vascular transcriptome in rhesus macaques

city: PORTLAND

first: Hillary

last: Le

state: OR

address: 3303 S Bond Ave

institute: Oregon Health & Science University

summary: Cannabis is commonly used in pregnancy for symptoms of nausea and pain, especially in the first trimester. Cannabis remains a federally illicit drug in the United States, but local legalization trends have resulted in increased availability and a decreased perception of harm. Unfortunately, limited scientifically rigorous information exists to inform decisions on use. Delta-9-tetrahydrocannabinol (THC, the main psychoactive component of cannabis) can cross the placenta and bind to cannabinoid receptor 1 (CB1) on the fetus. Because CB1 receptors are expressed in cardiomyocytes and endothelial cells, this suggests that THC exposure may impact fetal cardiovascular development. To understand this impact, our group used an established rhesus macaque model of chronic edible THC use during pregnancy. Animals were slowly titrated to a heavy THC dose (2.5mg/7kg/day) for 4 months preconception. Dams continued this daily THC dose throughout pregnancy with c-section delivery near term. Our model showed a decreased heart-to-body weight ratio from THC exposure. We examined the underlying changes in this selective fetal growth restriction of the cardiovascular system through tissue, protein, and gene expression analyses. H istological analysis of coronal sections of the heart and cross sections of the aorta showed no changes in collagen expression or maturity. Western blot analysis of collagen III expression showed no changes in left or right ventricle. Elastin expression was also unchanged in the aorta. To assess transcriptional changes, we performed bulk RNA-sequencing of vascular cells in the fetal aorta, umbilical vein, and umbilical artery, which revealed differentially expressed genes involved in metabolism and inflammation.  These results suggest potential cardiovascular harm from in utero THC exposure by altering endothelial metabolism and inflammation.

overall_design: Indoor-housed female rhesus macaques (n = 10) were maintained on a standard chow diet (TestDiet). Animals were given a daily cookie containing THC made with research-grade THC obtained directly from the National Institute of Drug Abuse (NIDA). Animals were slowly titrated up to 2.5 mg/7 kg/day of THC approximately four months prior to conception. Animals (n=5) continued daily THC edible throughout pregnancy until cesarean section delivery at gestational day 155. Fetal necropsy was performed and heart and umbilical cord tissues were processed as described in detail below. Aorta and umbilical cord vessels were harvested and sectioned for multiple use processing. Three centimeters of each vessel, in duplicate, was cannulated and flushed with 1X PBS (Gibco) to remove blood followed by 100uL of TRIzol Reagent (Invitrogen) to lyse luminal cells and collect RNA. The effluent was immediately frozen on dry ice and stored at -70oC.

first: Le

last: Hillary

first: Shorey-Kendrick

last: Lyndsey

first: Hinds

last: Monica

first: McCarty

last: Owen

first: Lo

last: Jamie

first: Anderson

last: Deirdre


title: Galectin 3-binding protein (Lgals3bp) depletion attenuates hepatic fibrosis by reducing transforming growth factor-β1 (TGF-β1) availability and inhibits hepatocarcinogenesis [ATAC-seq]

status: Public on Jul 06 2024

city: Hwasun-gun

first: Dae-Hwan

last: Kim

state: Jeollanam-do

address: 264, Seoyang-ro, Hwasun-eup

department: Hematology and Oncology

country: South Korea

institute: Chonnam National University Medical School and Hwasun Hospital

summary: Background: Increased Galectin 3-binding protein (Lgals3bp) serum levels have been used to assess hepatic fibrosis stages and the severity of hepatocellular carcinoma (HCC). Considering the crucial role of transforming growth factor-β1 (TGF-β1) in the emergence of these diseases, the present study tested the hypothesis that Lgals3bp regulates the TGF-β1 signaling pathway.  Methods: The expression levels of Lgals3bp and TGF-β1 were analyzed in patients with non-alcoholic steatohepatitis (NASH) and HCC. Multiple omics techniques, such as RNA-sequencing, transposase-accessible chromatin-sequencing assay, and liquid chromatography-tandem mass spectrometry proteomics, were used to identify the regulatory mechanisms for the Lgals3bp-TGF-β1 axis. Moreover, the effects of altered TGF-β1 signaling in chronic inflammatory conditions were investigated in conditional Lgals3bp-knockin and Lgals3bp-knockout mice.  Results: In patients with NASH and HCC, the levels of Lgals3bp and TGF-β1 exhibited positive correlations. Stimulation of Lgals3bp by the inflammatory cytokine interferon α in HCC cells or ectopic overexpression of Lgals3bp in hepatocytes promoted the expression levels of TGFB1. Aggravated fibrosis was observed in the livers of hepatocyte-specific Lgals3bp knock-in mice, with increased TGF-β1 levels. Lgals3bp directly bound to and assembled integrin αV, an integral mediator required for releasing active TGF-β1 from extracellular latent complex with the rearranged F-actin cytoskeleton. The released TGF-β1 activated JunB transcription factor, which in turn promoted the TGF-β1 positive feedback loop. Lgals3bp deletion in the hepatocytes downregulated TGF-β1 signaling and CCl4 induced fibrosis. Finally, Lgals3bp depletion hindered hepatocarcinogenesis by limiting the availability of fibrogenic TGF-β1. Conclusion: Lgals3bp plays a crucial role in hepatic fibrosis and carcinogenesis by controlling the TGF-β1 signaling pathway, making it a promising therapeutic target in TGF-β1-related diseases.

overall_design: To investigate the chromatin-accessibility changes in Hepa-1c1c7 cells induced by Lgals3bp, the 16h serum-starved cells were treated with vehicle or 5ug/mL of recombinant Lgals3bp for 6h, and the transposed DNA fragments were prepared in triplicate after tagmentation.

first: Ik-Joo

last: Chung


title: Glioblastoma induces the recruitment and differentiation of hybrid neutrophils from skull bone marrow

city: San Francisco

first: Manish

last: Aghi

state: CA

address: 505 Parnassus Avenue, #M774A

institute: UCSF

summary: Tumor-associated neutrophils (TANs) are an under-characterized population in glioblastoma. We use scRNA-seq to explore phenotypic diversity among these cells.

overall_design: Peripheral blood neutrophils (PBNs) and TANs were isolated from GBM patients via FACS. Cells were stained with fluorophore-conjugated anti-human CD45 (HI30), CD16 (3G8), and CD66b (6/40c), and live CD45+CD66b+CD16hi neutrophils were sorted on a 4-laser 6-channel Sony SH800 cell sorter using ‘normal purity’ settings.

first: Meeki

last: Lad

first: Angad

last: Beniwal

first: Saket

last: Jain

first: Poojan

last: Shukla

first: Venina

last: Kalistratova

first: Jangham

last: Jung

first: Sumedh

last: Shah

first: Garima

last: Yagnik

first: Atul

last: Saha

first: Ankita

last: Sati

first: Husam

last: Babikir

first: Alan

last: Nguyen

first: Sabraj

last: Gill

first: Jennifer

last: Rios

first: Jacob

last: Young

first: Austin

last: Lui

first: Diana

last: Salha

first: Aaron

last: Diaz

middle: K


title: SW1783_Discovery and utilization study of the dominant pharmacological action organ of Aconitum carmichaeli Debeaux using multiple bioinformatic analyses

status: Public on Jul 05 2024

city: Daejeon

first: Musun

last: Park

address: 1672 Yuseong-daero, Yuseong-gu

institute: Korean Institute of Oriental Medicine

summary: This study aimed to identify the modes of action (MOA) of Aconitum carmichaeli Debeaux water extract (ACDW) in SW1783 cell line.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for ACDW (500 ug/mL, 100 ug/mL, and 20 ug/mL, respectively) and vehicle control (2% DMSO).


title: Galectin 3-binding protein (Lgals3bp) depletion attenuates hepatic fibrosis by reducing transforming growth factor-β1 (TGF-β1) availability and inhibits hepatocarcinogenesis [PH RNA-seq]

first: Dae-Hwan

last: Kim

overall_design: To investigate the transcriptome changes in wild type or Lgals3bp knock-out mouse primary hepatocytes by induced by interferon alpha, cells were treated with recombinant interferon alpha for 6h, and total RNA was prepared in triplicate.

first: Ik-Joo

last: Chung


title: HT29_Discovery and utilization study of the dominant pharmacological action organ of Aconitum carmichaeli Debeaux using multiple bioinformatic analyses

summary: This study aimed to identify the modes of action (MOA) of Aconitum carmichaeli Debeaux water extract (ACDW) in HT29 cell line.


title: Galectin 3-binding protein (Lgals3bp) depletion attenuates hepatic fibrosis by reducing transforming growth factor-β1 (TGF-β1) availability and inhibits hepatocarcinogenesis [RNA-seq]

overall_design: To investigate the transcriptome changes in Hepa-1c1c7 cells induced by Lgals3bp, the 16h serum-starved cells were treated with vehicle or 5ug/mL of recombinant Lgals3bp for 6h subsequently, and total RNA was prepared in triplicate.


title: CRISPRi Screen for Investigating the RORC RNA Switch Mechanisms in Jurkat Cells

first: Hani

last: Goodarzi

department: Biochemistry and Biophysics

summary: RNA structural switches are key regulators of gene expression in bacteria, yet their characterization in Metazoa remains limited. Here we present SwitchSeeker, a comprehensive computational and experimental approach for systematic identification of functional RNA structural switches. We applied SwitchSeeker to the human transcriptome and identified 245 putative RNA switches. To validate our approach, we characterized a previously unknown RNA switch in the 3’UTR of the RORC transcript. In vivo DMS-MaPseq, coupled with cryogenic electron microscopy, confirmed its existence as two alternative structural conformations. Furthermore, we used genome-scale CRISPR screens to identify trans factors that regulate gene expression through this RNA structural switch. We found that nonsense-mediated mRNA decay acts on this element in a conformation-specific manner. SwitchSeeker provides an unbiased, experimentally-driven method for discovering RNA structural switches that shape the eukaryotic gene expression landscape.

overall_design: To investigate how the RORC RNA switch influences gene expression at the molecular level, we performed genome-wide CRISPRi screens in Jurkat T cells using two eGFP reporter constructs: one with the native RORC switch and another with the 77-GA mutation that favors conformation 1.

first: Matvei

last: Khoroshkin

first: Aidan

last: Winters


title: Massively parallel reporter assay for identification of RNA switches

overall_design: To measure the effect of candidate RNA switches on gene expression, we used the Massively Parallel Reporter Assay. We cloned a library of candidate RNA switch sequences into a dual eGFP-mCherry fluorescent reporter vector, directly downstream of the eGFP ORF. We used eGFP fluorescence to measure the effect of candidate RNA switches on gene expression, and we used mCherry fluorescence as an endogenous control. We transduced HEK293 cells with this synthetic library, used flow-cytometry to sort cells by eGFP/mCherry expression ratio, and sequenced the genomic DNA and RNA from the resulting eight pools of cells

first: Albertas

last: Navickas


title: DMS-MaPseq of RORC reporters and endogeneous RORC locus [reporter mutants]

overall_design: To understand the dynamics of RORC RNA switch under differrent contexts, the effects of different mutations on RORC switch was tested in 293T cells expressing different versions of RORC mutants.

first: Shaopu

last: Zhou

first: Jackson

last: Goudreau


title: Itaconate uptake via SLC13A3 improves hepatic antibacterial innate immunity

city: Beijing

first: Chao

last: Chen

address: Datun

department: CAS Key Laboratory of Infection and Immunity

institute: Institute of Biophysics, Chinese Academy of Sciences

summary: Itaconate is an immunoregulatory metabolite produced by the mitochondrial enzyme immune-responsive gene 1 (IRG1) in inflammatory macrophages. We recently identified an important mechanism by which itaconate is released from inflammatory macrophages. However, it remains unknown whether extracellular itaconate is taken up by non-myeloid cells to exert immunoregulatory functions. Here, we used a custom-designed CRISPR screen to identify the dicarboxylate transporter solute carrier family 13 member 3 (SLC13A3) as an itaconate importer and to characterize the role of SLC13A3 in itaconate-improved hepatic antibacterial innate immunity. Functionally, liver-specific deletion of Slc13a3 impairs hepatic antibacterial innate immunity in vivo and in vitro. Mechanistically, itaconate uptake via SLC13A3 induces transcription factor EB (TFEB)-dependent lysosomal biogenesis and subsequently improves antibacterial innate immunity in murine hepatocytes. These findings identify SLC13A3 as a key itaconate importer in murine hepatocytes and will aid in the development of potent itaconate-based antibacterial therapeutics.

overall_design: As the human membrane transporter CRISPRi library (customized by Corus Biotechnology Inc., Nanjing in China) contains 7441 sgRNAs targeting 1241 membrane transporter genes, cBioITA-expressing 293T cells were infected with the lentivirus library at an MOI of 0.3 to obtain an average of 400-fold coverage of the library. At 48 hours post-infection, the cells were selected with 2 µg ml-1 of puromycin for 5 days. Infected cells expressing the gRNA library treated with 3 mM itaconate for 1 hour, and then sorted into a cBioITAbottom population (the lowest 25% of cells) and a cBioITAtop population (the highest 25% of cells) according to the cBioITA fluorescence intensity. The sorted cells (approximate 3 × 10^6 cells/population) were collected for genomic DNA (gDNA) extraction using a Blood & Cells Culture DNA Maxi kit (Qiagen), followed by PCR amplification of DNA fragments containing gRNA sequences using a Phanta Super-Fidelity DNA Polymerase kit (Vazyme). The PCR amplicons were sequenced by the Genewiz Bioinformatics Institute (Suzhou, China).

first: Xinjian

last: Li


title: DMS-MaPseq of RORC reporters and endogeneous RORC locus [reporter cell lines]

overall_design: To understand the dynamics of RORC RNA switch under differrent contexts, we established 5 RORC reporter cell lines (ZR-75-1 (breast), MCF-7 (breast), HepG2 (liver), LNCaP  (prostate), LS174T (colon)) and performed targeted DMS-MaPseq of the RNA switch locus.


title: DMS-MaPseq of RORC reporters and endogeneous RORC locus

overall_design: To understand the dynamics of RORC RNA switch under differrent contexts, we profiled endogeneous RORC locus across 5 cell lines (ZR-75-1 (breast), MCF-7 (breast), HepG2 (liver), LNCaP  (prostate), LS174T (colon)).


title: Comparative transcriptomic profiling of overexpression of PsrA in Pseudomonas aeruginosa PAO1

city: Hsinchu

first: Li-Ching

last: Kok

address: 101, Section 2, Kuang-Fu Road

department: Institute of Molecular Medicine

country: Taiwan

institute: National Tsing Hua University

summary: PsrA, a transcription factor belonging to the TetR family, is known to participate in the regulation of fatty acid metabolism, type III secretion system, and quinolone signaling in Pseudomonas aeruginosa. Using a psrA overexpression strain, this study conducted a transcriptomic analysis to examine the role of PsrA in P. aeruginosa PAO1.

overall_design: We cloned psrA in the multicopy plasmid pMMB66EH and then introduced the recombinant plasmid into P. aeruginosa PAO1. The psrA overexpressing strain, named PAO1 [pMMBpsrA], was examined and compared with the parental strain PAO1 carried the empty vector pMMB66EH, named PAO1[pMMB66EH].

first: Hwan-You

last: Chang

first: Yu-Hsuan

last: Liao

first: Yi-Ling

last: Lo


title: Loss of 3-O-sulfotransferase enzymes, Hs3st3a1 and Hs3st3b1, reduces kidney and glomerular size and disrupts glomerular architecture

city: Bethesda

first: Vaishali

last: Patel

state: Maryland

address: 9000 Rockville Pike

department: NIDCR

institute: National Institutes of Health

summary: Heparan sulfate (HS) is an important component of the kidney anionic filtration barrier, the glomerular basement membrane (GBM). HS chains attached to proteoglycan protein cores are modified by sulfotransferases in a highly ordered series of biosynthetic steps resulting in immense structural diversity due to negatively charged sulfate modifications. 3-O-sulfation is the least abundant modification generated by a family of seven isoforms but creates the most highly sulfated HS domains. We analyzed the kidney phenotypes in the Hs3st3a1, Hs3st3b1 and Hs3st6 -knockout (KO) mice, the isoforms enriched in kidney podocytes. Individual KO mice show no overt kidney phenotype, although Hs3st3b1 kidneys were smaller than wildtype (WT). Furthermore, Hs3st3a1-/-; Hs3st3b1-/- double knockout (DKO) kidneys were smaller but also had a reduction in glomerular size relative to wildtype (WT). Mass spectrometry analysis of kidney HS showed reduced 3-O-sulfation in Hs3st3a1-/- and Hs3st3b1-/-, but not in Hs3st6-/- kidneys. Glomerular HS showed reduced HS staining and reduced ligand-and-carbohydrate engagement (LACE) assay, a tool that detects changes in binding of growth factor receptor-ligand complexes to HS. Interestingly, DKO mice have increased levels of blood urea nitrogen, although no differences were detected in urinary levels of albumin, creatinine and nephrin. Finally, transmission electron microscopy showed irregular and thickened GBM and podocyte foot process effacement in the DKO compared to WT. Together, our data suggest that loss of 3-O-HS domains disrupts the kidney glomerular architecture without affecting the glomerular filtration barrier and overall kidney function.

overall_design:
Vaishali N. Patel
contributor: NIDCD/NIDCR Genomics and Computational Biology Core

first: James

middle: R

last: Ball

first: Sophie

middle: H

last: Choi

first: Ethan

last: Lane

first: Zhangjie

last: Wang

first: Marit

last: Aure

first: Carlos

middle: U

last: Villapudua

first: Changyu

last: Zheng

first: Christopher

last: Bleck

first: Heba

last: Mohammed

first: Zulfeqhar

last: Syed

first: Jian

last: Liu

first: Matthew

last: Hoffman


title: RNA-Seq data of mouse retina, retinal pigment epithelium and cones

first: Hong

state: MD

department: NIDDK

institute: NIH

summary: The differentiation of cone photoreceptors, which mediate daylight vision and color vision, depends critically upon thyroid hormone.However, the route of access of blood-borne thyroid hormone to cones is undefined because cones reside behind the blood-retina barrier. This study uses genetic manipulation of a membrane transporter for thyroid hormone (Mct8) in mouse models to show a role for the retinal pigment epithelium (RPE), which forms the outer blood-retina barrier, in the control of cone differentiation.The results suggest a paracrine-like mechanism promotes thyroid hormone-mediated cone differentiation. The findings suggest that in addition to the transport of essential solutes and support of photoreceptor homeostasis, the RPE controls  hormonal signaling required for cone differentiation.

overall_design: RNA-seq analysis was performed on purified RPE cells, bulk retinal tissue, and also on isolated single cones from mouse genetic  models. To distinguish between M-dominant and S-dominant cone types, samples were taken from superior and inferior areas of the retina, respectively. RPE samples were taken from superior and inferior areas of the eye to investigate the possibility of spatial distinctions in the transcriptome of RPE cells. An Mct8-knockout allele (Mct8-) was used to determine the total requirement for Mct8. The retinal transcriptome of a hypothyroid strain, Tshr-/-, was also analyzed.  The role of the RPE was established by RPE-specific conditional deletion of a floxed Mct8 allele using an RPE-specific Cre driver transgene (Best1cre). As an X-linked gene, for females, the Mct8 flox allele was combined with a germline Mct8 null allele (Mct8 fl/null).  The results of the study suggest that Mct8 thyroid hormone transporter in the RPE promotes differentiation of cones in the retina.

first: Ye

first: Lily

last: Ng

first: Heike

last: Heuer

first: Douglas

last: Forrest


title: Short-term cold exposure induces persistent epigenomic memory in brown fat [GRO-Seq]

first: Mohit

middle: K.

last: Midha

summary: Deficiency of the epigenome modulator histone deacetylase 3 (HDAC3) in brown adipose tissue (BAT) impairs the ability of mice to survive in near-freezing temperatures. Here, we report that short-term exposure to mild cold temperature (STEMCT: 15°C for 24 hours) averted lethal hypothermia of mice lacking HDAC3 in BAT (HDAC3 BAT KO) exposed to 4°C. STEMCT restored the induction of the thermogenic coactivator PGC-1a along with UCP1 at 22°C, which is greatly impaired in HDAC3-deficient BAT, and deletion of either UCP1 or PGC-1a prevented the protective effect of STEMCT. Remarkably, the protection of HDAC3 BAT KO mice from cold intolerance following STEMCT lasted for up to 7 days. Transcriptional activator C/EBPb was induced by short-term cold exposure in mouse and human BAT and, uniquely, remained high for 7 days following STEMCT. Furthermore, analysis of C/EBPb activity revealed increased binding following STEMCT at genes, including the enhancers/promotors of UCP1 and PGC-1a. These results reveal the existence of a cold-adaptive epigenomic memory mediated by C/EBPb that is persistent and HDAC3-independent.

overall_design: To evaluate if the effect of cold exposure is observed at enhancer regions in control and HDAC3-deficent mice.

first: Shin-ichi

last: Inoue

first: Mitchell

last: Lazar


title: Short-term cold exposure induces persistent epigenomic memory in brown fat [RNA-Seq]

overall_design: To evaluate if the effect of cold exposure is observed in the long term in control and HDAC3-deficent mice.

middle: A


title: Short-term cold exposure induces persistent epigenomic memory in brown fat [ATAC-Seq]


title: A streamlined method to generate endothelial cells from human pluripotent stem cells via transient doxycycline-inducible ETV2 activation

city: Boston

first: Allen Chilun

last: Luo

state: Massachusetts

address: 300 Longwood Ave

department: Cardiac Surgery

institute: Boston Children's Hospital

summary: The development of reliable methods for producing functional endothelial cells (ECs) is crucial for progress in vascular biology and regenerative medicine. In this study, we present a streamlined and efficient methodology for the differentiation of human induced pluripotent stem cells (iPSCs) into induced ECs (iECs) that maintain the ability to undergo vasculogenesis in vitro and in vivo using a doxycycline-inducible system for the transient expression of the ETV2 transcription factor. This approach mitigates the limitations of direct transfection methods, such as mRNA-mediated differentiation, by simplifying the protocol and enhancing reproducibility across different stem cell lines. We detail the generation of iPSCs engineered for doxycycline-induced ETV2 expression and their subsequent differentiation into iECs, achieving over 90% efficiency within four days. Through both in vitro and in vivo assays, the functionality and phenotypic stability of the derived iECs were rigorously validated. Notably, these cells exhibit key endothelial markers and capabilities, including the formation of vascular networks in a microphysiological platform in vitro and in a subcutaneous mouse model. Furthermore, our results reveal a close transcriptional and proteomic alignment between the iECs generated via our method and primary ECs, confirming the biological relevance of the differentiated cells. The high efficiency and effectiveness of our induction methodology pave the way for broader application and accessibility of iPSC-derived ECs in scientific research, offering a valuable tool for investigating endothelial biology and for the development of EC-based therapies.

overall_design: We analyzed three biological replicates for iPSCs (hiPS-BJ273), ECFCs, modRNA-ETV2 iECs (S1ETV2), and Dox-ETV2 iECs (2D-iEC).

first: Yonglin

last: Zhu

first: Juan

last: Melero-Martin


title: Short-term cold exposure induces persistent epigenomic memory in brown fat [ChIP-Seq

institute: University of Pennsylvania

overall_design: Chromatin immunoprecipitation DNA sequencing for HDAC3, ERRalpha and C/EBPbeta  in interscapular BAT of mice.


title: Dor regulates alpha-KG metabolic pathways in mature oligodendrocytes to enhance myelination and reverse age-related remyelination decline [RNA-seq II]

city: Chengdu

first: XueLian

last: He

state: Sichuan

address: Renmin Road

institute: Sichuan University

summary: Impairment of oligodendrocyte (OL) myelinogenic potential, rather than inability of oligodendrocyte precursors to differentiate, is implicated in remyelination failure in demyelinating diseases such as multiple sclerosis. However, the mechanisms underlying myelinogenesis and age-related decline in remyelination remain elusive. Here, we identify a mature-OL-active transcriptional regulator Dor as a critical mediator of CNS myelination and remyelination. Genomic occupancy and transcriptomic analyses revealed that Dor interacts with Sox10 and targets the enhancers of myelinogenesis-regulatory genes including a newly identified OL-enriched nuclear factor Prr18 required for OL maturation. Metabolomic profiling showed that Dor is critical for alpha-ketoglutarate (alpha-KG) production and lipid biosynthesis. Supplementation with alpha-KG enhanced lipid biosynthesis and restored OL maturation defects in Dor-mutant mice while reversing the age-associated decline in remyelination efficiency and memory deficits in aging mice. Thus, our findings connect the OL-active Dor regulatory activity to alpha-KG-mediated lipid metabolism in mature OLs to thereby facilitate myelin production and remyelination.

overall_design: O4+ OLs isolated from cortices of control and Dor iKO mice treated with TAM from P5 to P9

first: Xuelian

first: Guojiao

last: Huang

first: Zhidan

last: Li

first: Xuezhao


title: Gene expression profile at single cell level of mitfa:GFP labelled zebrafish cells at 24hpf

city: Delhi

first: Vivek

middle: T

last: Natarajan

state: Delhi

address: Mathura Road

country: India

institute: CSIR-IGIB

summary: Melanocytes of the skin have traditionally been viewed as a homogeneous population, however, recent findings suggest the existence of distinct cell states within the melanocyte population. To investigate this further, we employed the zebrafish as a valuable model system for studying melanocyte biology. The zebrafish offers advantages such as its transparent nature and the availability of transgenic lines that allow specific labeling of melanocytes. In our study, we utilized a transgenic zebrafish line, Tg(mifa:GFP), that expresses green fluorescent protein (GFP) under the control of a melanocyte-specific promoter, mitfa, labelling only those cells in which mitfa promoter is active. We then performed single-cell RNA sequencing (scRNA-seq) analysis to explore the diversity of mitfa:GFP-positive cells.

overall_design: Tg(mitfa:GFP) zebrafish embryos were raised till 24 hours post fertilization (hpf) and then the cells were isolated. The cells expressing mitfa:GFP were then sorted into low and high GFP population using a flow cytometer

first: Ayush

last: Aggarwal

first: Babita

last: Sharma


title: Epithelial aPKC deficiency leads to stem cell loss preceding metaplasia in colorectal cancer initiation [RNA-Seq]

city: New York

first: Jorge

last: Moscat

state: NY

address: 1188 York Avenue

department: Pathology and Laboratory Medicine

institute: WEILL CORNELL MEDICINE

summary: The early mechanisms of spontaneous tumor initiation that precede the accumulation of cancer mutations are largely unknown. We show that reduced aPKC levels correlate with stem cell loss and the induction of revival and metaplastic programs in serrated- and conventional-initiated pre-neoplastic lesions, which is perpetuated in colorectal cancers (CRC). Acute inactivation of PKCl/i in vivo and in organoids is sufficient to stimulate JNK in non-transformed intestinal epithelial cells (IECs), which promotes cell death and the rapid loss of the intestinal stem cells (ISC), including LGR5+ cells. This is followed by the accumulation of revival stem cells (RSC) at the bottom of the crypt and fetal metaplastic cells (FMC) at the top, creating two spatiotemporally distinct cell populations that depend on JNK-induced AP-1 and YAP. These cell lineage changes are maintained during cancer initiation and progression and determine the aggressive phenotype of human CRC irrespective of their serrated or conventional origin

overall_design: Colonic organoids isolated  from Prkcif/fPrkczf/f;Villin-CreERT2 Veh- or 4-OH-Tamoxifen were treated for 3 days and profiled to RNA sequencing

first: Hiroto

last: Kinoshita

first: Anxo

last: Martinez-Ordoñez

first: Tania

last: Cid-Diaz

first: Qixiu

last: Han

first: Angeles

last: Duran

first: Yu

last: Muta

first: Yuki

last: Nakanishi

first: Hiroaki

last: Kasashima

first: Masakazu

last: Yashiro

first: Kiyoshi

last: Maeda

first: Ana

last: Albaladejo-Gonzalez

first: Daniel

last: Torres-Moreno

first: José

last: García-Solano

first: Pablo

last: Conesa-Zamora

first: Maria

last: Diaz-Meco


title: The unique catalytic properties of PSAT1 mediate metabolic adaptation to glutamine blockade

city: COLD SPRING HARBOR

first: Yijian

last: Qiu

address: 1 BUNGTOWN RD

department: Cancer center

institute: COLD SPRING HARBOR LABS

summary: Cultured cancer cells frequently rely on the consumption of glutamine and its subsequent hydrolysis to glutamate by the mitochondrial enzyme glutaminase (GLS). However, this metabolic addiction can be lost in the tumor microenvironment (TME), rendering GLS inhibitors ineffective in the clinic. Here, we show that seemingly glutamine-addicted breast cancer cells ultimately adapt to chronic glutamine starvation, or targeted GLS inhibition, via the AMPK-mediated upregulation of the serine synthesis pathway (SSP). In this context, the key product of the SSP is not serine itself, but a-ketoglutarate (a-KG). Mechanistically, we find that the phylogenetically distinct transaminase phosphoserine aminotransferase 1 (PSAT1) has a unique capacity for sustained a-KG production when glutamate is severely depleted. Breast cancer cells with intrinsic or acquired resistance to glutamine starvation or GLS inhibition are highly dependent on SSP-supplied a-KG. Accordingly, pharmacological disruption of the SSP prevents adaptation to glutamine blockade, yielding a potent drug synergism that abolishes breast tumor growth in vivo. These findings highlight how metabolic redundancy can be context dependent, with the catalytic properties of different metabolic enzymes that act on the same substrate determining which pathways can support tumor growth in a particular nutrient environment. This in turn has practical consequences for therapies targeting cancer metabolism.

overall_design: To obtain unbiased insights into the mechanisms underlying breast cancer cell adaptation to chronic glutamine withdrawal, we used RNA-seq analysis to compare parental MDA-MB-231 cells with their glutamine-independent derivatives (MDA-MB-231GlnIND cells).


title: Dor regulates alpha-KG metabolic pathways in mature oligodendrocytes to enhance myelination and reverse age-related remyelination decline [RNA-seq]

first: XueLian

last: He

overall_design: Gene expression comparison betwwen controls and Dor mutants of the optic nerves.

first: Xuelian

first: Guojiao

last: Huang

first: Zhidan

last: Li

first: Xuezhao

last: Liu


title: Dor regulates alpha-KG metabolic pathways in mature oligodendrocytes to enhance myelination and reverse age-related remyelination decline [CUT&Tag]

overall_design: Using CUT&Tag to inverstigate genomic occupancy of Dor for OPC, iOL(D1) and mOL(D3).


title: CyCoNP lncRNA establishes cis and trans RNA-RNA interactions to supervise neuron physiology (RNA-seq).

city: Rome

first: Irene

last: Bozzoni

address: Piazzale Aldo Moro 5

department: Biology and Biotechnologies "Charles Darwin"

country: Italy

institute: Sapienza University of Rome

summary: The combination of morphogenetic and transcription factors together with the sinergic aid of noncoding RNAs and their cognate RNA binding proteins (RBP) contribute to shape MN identity. Here, we extend the noncoding perspective of human MN, by detailing the molecular and biological activity of CyCoNP (as Cytoplasmic Coordinator of Neural Progenitors) a highly expressed and MN-enriched human lncRNA. Through RNA purification and loss of function experiments followed by RNA-sequencing, we found that CyCoNP sustains a specific neuron differentiation program, required for the physiology of both neuroblastoma cells and hiPSC-derived MN, mainly by establishing RNA-RNA interactions with the mRNA of NCAM1, a key player in neurogenesis involved in many steps of Central Nervous System development. Specifically, we were able to dissect a dual RNA-mediated mechanism according to which CyCoNP can bind to and sequester, in a stoichiometry-permissive manner, a microRNA that targets pro-neuronal genes included NCAM1 on which the lncRNA play an additional local “in cis” regulation by a direct RNA-RNA interaction. These data highlight novel circuitries involved in the control of human neuron physiology and point out as RNA molecules and the complex relationships they can establish may represent the building blocks of sophisticated cellular mechanisms.

overall_design: RNA Sequencing of 1.5 days differentiated SK-N-BE cells treated with si-SCR or si-CyCoNP

first: Fabio

last: Desideri

first: Alessandro

last: Grazzi

first: Adriano

last: Setti


title: CyCoNP lncRNA establishes cis and trans RNA-RNA interactions to supervise neuron physiology (CyCoNP RNA Pulldown).

overall_design: RNA Sequencing of CyCoNP endogenous RNA pull-down compared to LacZ control pull-down


title: Thymosin α1 reverses oncolytic adenovirus-induced M2 polarization of macrophages to improve antitumor immunity and therapeutic efficacy

status: Public on Jul 04 2024

city: Nanjing

first: kua

last: liu

state: Jiangsu

address: 22 Hankou Road

institute: Nanjing University

summary: Although oncolytic adenoviruses have been widely studied for their direct oncolytic activity and immunomodulatory role in cancer immunotherapy, the immunosuppressive feedback loop induced by oncolytic adenoviruses remains poorly studied. Here, we showed that type V adenovirus (ADV) induces the polarization of tumor-associated macrophages (TAMs) to the M2 phenotype and increases the infiltration of regulatory T cells (Tregs) in the tumor microenvironment (TME). By selectively compensating for these deficiencies, Tα1 reprogrammed “M2-like” TAMs toward an antitumoral phenotype, thereby reprogramming the TME into a state more beneficial for antitumor immunity. Moreover, ADVTα1 was constructed by harnessing the merits of all the components for the aforementioned combinatorial therapy. Both in vitro and in vivo data showed that both exogenously supplied and adenovirus-produced Tα1 orchestrate TAM reprogramming and enhance the antitumor efficacy of ADV via CD8+ T cells, showing promising prospects for clinical translation. Our findings provide inspiration for improving oncolytic adenovirus combination therapy and designing new oncolytic engineered adenoviruses.

overall_design: To understand the mechanism of regulation of macrophages by ADV infection and additional Ta1 peptide,we performed RNA sequencing (RNA-seq) on 4T1 cells treated with PBS, ADV or ADV combined with Ta1 for 48 hours.Next, these 4T1 cells were cocultured with macrophages at ratio of 10:1 for 18 hours. We then performed gene expression profling analysis using data obtained fo RNA-seq of macropahges treated with different interventions.

first: Kua

first: Lingkai

last: Kong


title: Gene expression profile at single cell level of cultured normal human epidermal melanocytes (NHEMs) [NHEM_FSK_scRNA]

first: Vivek

last: Natarajan

summary: NHEMs are considered as a homogeneous population in the human epidermis. We used single cell RNA sequencing (scRNA-seq) to analyze the diversity of NHEMs in culture.

overall_design: NHEMs were cultured in Medium 254 (M254) and treated with 20µM forskolin (fsk) either every day or every alternate day for 7 days

first: Aggarwal

last: Ayush

first: Natarajan

last: Vivek T


title: Conserved transcriptional regulation by BRN1 and BRN2 in neocortical progenitors drives mammalian neural specification and neocortical expansion

city: Baltimore

first: Soraia

last: Barao

address: 725 N Wolfe St PCTB 1015

department: Neuroscience

institute: JHU

summary:
To investigate BRN1/2 function in neocortical development, we knockout BRN1/2 in the dorsal telencephalon (BRN1/2 cKO)
We then performed gene expression profiling analysis using data obtained from scRNA-seq of 13 different mice at E12.5 and E14.5

overall_design: Comparative gene expression profiling analysis of RNA-seq data for BRN1/2 cKO and control littermates at E12.5 and E14.5

first: Yijun

last: Xu

first: Jose

last: Llongueras

first: Rachel

last: Vistein

first: Loyal

last: Goff

first: Kristina

last: Nielsen

first: Byoung-Il

last: Bae

first: Richard

middle: S

last: Smith

first: Christopher

last: Walsh

first: Genevieve

last: Stein-O'Brien

first: Ulrich

last: Mueller


title: Guidelines for performing Ribosome Profling in Plants Including Structural Analysis of rRNA fragments

city: Potsdam

first: Reimo

last: Zoschke

address: Am Mühlenberg 1

country: Germany

institute: Max Planck Institute of Molecular Plant Physiology

summary: Here, we compile valuable insights gathered over years of generating Ribo-seq datasets from different plant species and experimental setups. We tested the effects of variable ribonuclease treatments for the generation of ribosome protected fragments (RPFs). We tested rRNA depletion strategies designed specifically for Arabidopsis and Tobacco. We also compare ligation-free to ligation-based library preparation strategies for generating Ribo-seq libraries.

sample_organism:
Arabidopsis thaliana
Nicotiana tabacum

platform_organism:
Arabidopsis thaliana
Nicotiana tabacum

overall_design: RPFs were generated following different nuclease treatments, followed by the preparation of Ribo-seq libraries.

first: Michael

last: Ting


title: Differential programs of melanocyte cell states

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

sample_organism:
Danio rerio
Homo sapiens
Mus musculus

platform_organism:
Danio rerio
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Gene expression and chromatin accessibility profile at single cell level of B16 cells [B16_D0_3_5_scMulti]

summary: B16 F10 is a depigmented mouse melanoma cell line which is considered as a homogeneous cell population. These cells when cultured at a very low density of 100 cells/cm2 starts to pigment progressively. We used single nucleus RNA+ATAC sequencing (scMultiomics) to analyze the transciptional diversity and to investigate the epigenetic basis of this diversity of day 0, 3 and 5 B16 cells cultured at low density.

overall_design: B16 F10 cells were cultured at a very low density of 100 cells/cm2 for 3 or 5 days. Cells cultured at high density and used to setup low density cultures were taken as day 0 sample.


title: GV-971 prevents severe acute pancreatitis by remodeling the microbiota-metabolic-immune axis

city: Guangdong Guangzhou, China

first: chen

last: xi

address: 1 Xinzao Road, Xinzao Town, Panyu District, Guangzhou City, Guangdong Province,

institute: Guangzhou medical university

summary: Despite recent advances, severe acute pancreatitis (SAP) remains an extremely lethal inflammation with limited treatment options. Here, we provide compelling evidence of GV-971 (sodium oligomannate), an anti-Alzheimer's medication, as being a protective agent in various mouse SAP models. Microbiome sequencing, along with fecal microbiota transplantation and mass cytometry technology, unveiled that GV-971 reshapes the gut microbiota, increasing Faecalibacterium populations and modulating both peripheral and intestinal immune systems. A metabolomics analysis of cecal contents from GV-971–treated SAP mice further identified short-chain fatty acids, including propionate and butyrate, as key metabolites in inhibiting macrophage M1 polarization and subsequent lethal inflammation by blocking the MAPK pathway. These findings suggest GV-971 as a promising therapeutic for SAP by targeting the microbiota metabolic immune axis.

overall_design: For metabolite treatment, prior to experimentation, sodium propionate, and sodium butyrate were pre-incubated with RAW264.7 cells for 24 hours. Subsequently, the corresponding metabolites were administered in combination with 1 μg/mL LPS for 6 hours. Following this treatment, RAW 264.7 cells were collected for RNA-Sequencing to study the impact of propionate and butyrate on transcriptome.

first: Xi

last: Chen

first: Jinbao

last: Liu

first: Xin

first: Daolin

last: Tang


title: H3K27ac ChIP sequencing of low and high pigment B16 cells [B16_D5_LP_HP_ChIPSeq]

first: Vivek

last: Natarajan

summary: In one of our earlier studies, we have shown that, through a pH-mediated feed-forward loop, H3K27ac selectively activates pigmentation genes and accentuates melanocyte differentiation at the population level. Here we used the B16 progressive pigmentaiton model that harbours multiple melanocyte states in the same culture. We sorted the low and high pigment cells at day 5 and investigated the differences in H3K27ac mark between the low and high pigment melanocyte sub-populations.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for histone modification H3K27ac in low and high pigment B16 cells sorted from the same culture.

first: Aggarwal

last: Ayush

first: Natarajan

last: Vivek T


title: Transcriptome Analysis of the Effects of High Temperature on Zygotic Genome Activation in Porcine Embryos

city: Cheongju

first: Chenglin

last: Zhan

state: Chungcheong-buk do

address: Chungdae-ro 1, Seowon-Gu

department: department of animal science

institute: chungbuk national university

summary: Damage to the development of porcine gametes and embryos caused by high temperatures (HT) is one of the main reasons for the decline in the economic benefits of the livestock industry. Zygotic genome activation (ZGA) marks the beginning of gene expression programs in mammalian pre-implantation embryos. In pigs, ZGA occurs at the 4-cell (4C) stage, indicating that correct gene expression at this stage plays an important regulatory role in embryonic development. However, the effect of the HT environment on early porcine embryonic development and the RNA expression profile of ZGA remain unclear. In this study, we compared the RNA transcription patterns of porcine 4C embryos under normal and HT conditions using RNA-seq and identified 326 differentially expressed genes (DEGs). These changes were mainly related to DNA polymerase activity, DNA replication, and nucleotidyltransferase activity. In addition, entries for reverse transcription and endonuclease activity were enriched, indicating that ZGA interfered under HT conditions. Further comparison of the experimental results with the porcine ZGA gene revealed 39 ZGA genes among the DEGs. KEGG and GSEA analysis showed that the oxidative phosphorylation pathway was significantly enriched and signaling pathways related to energy metabolism were significantly downregulated. We also found that NDUFA6 and CDKN1A were located at the center of the protein-protein interaction network diagram of the DEGs. In summary, HT conditions affect mitochondrial function and oxidative phosphorylation levels, and lead to changes in the expression pattern of ZGA in early porcine embryos, with its hub genes NDUFA6 and CDKN1A.

overall_design: To explore the effect of high temperature on zygotic genome activation of porcine embryos, the embryos were cultured at 41.5 ℃. Embryos were collected at the 4-cell stage for sequencing.

first: Ming-Hong

last: Sun

first: Cheng-Lin

first: Xiao-Han

last: Li

first: Song-Hee

last: Lee

first: Xiang-Shun

last: Cui


title: Zeb1-mediated control of PUFA-phospholipids in EMT/plasticity-associated cancer cell ferroptosis

city: Erlangen

first: Yussuf

last: Hajjaj

address: Glueckstr. 6

institute: FAU

summary: Therapy resistance and metastasis, the most fatal steps in cancer, are often triggered by a (partial) activation of the epithelial-mesenchymal-transition (EMT)-program. A mesenchymal phenotype predisposes to ferroptosis, a cell death pathway exerted by an iron and oxygen-radical mediated peroxidation of phospholipids containing polyunsaturated fatty acids (PUFAs). We here describe that various forms of EMT-activation, including TGFB-stimulation, increase ferroptosis-susceptibility in cancer cells, which depends on the EMT-transcription factor Zeb1. Among other effects, we demonstrate that Zeb1 increases the ratio of phospholipids containing pro-ferroptotic PUFAs over cyto-protective monounsaturated fatty acids (MUFAs) and modulates the expression of underlying crucial lipogenic enzymes (and ACSL4). Pharmacological inhibition of selected lipogenic enzymes (SCD and FADS2) allows the manipulation of ferroptosis-sensitivity in a Zeb1-dependent manner. Our data are of potential translational relevance and suggest a combination of ferroptosis-activators and SCD-inhibitors for the treatment of aggressive cancers expressing Zeb1, which might also be a useful predictive marker for such a combination therapy

overall_design: ChIP-seq for H3K27ac histone modification in MDA-MB-231 cell lines control and ZEB1 knockdown

first: Simone

last: Brabletz

first: Thomas


title: Microglia contribute to polyG-dependent neurodegeneration in neuronal intranuclear inclusion disease

city: Shanghai

first: Yangye

last: Lian

address: Xuhui No.180, Fenglin Road

institute: Zhongshan Hospital affiliated to Fudan University

summary: Neuronal intranuclear inclusion disease (NIID) is a neurodegenerative disease caused by GGC repeat expansion of NOTCH2NLC. Despite the identification of uN2CpolyG, a toxic polyglycine (polyG) protein, the pathogenic mechanisms of NIID remain unclear. Herein, we investigated the role of polyG by expressing wild-type NOTCH2NLC, expanded NOTCH2NLC with 100 GGC repeats (translating or not translating into uN2CpolyG), or mutated NOTCH2NLC that encodes a pure polyG without GGC-repeat RNA and C-terminal stretch (uN2CpolyG-dCT) in mice. Both uN2CpolyG and uN2CpolyG-dCT induced the formation of inclusions composed by filamentous materials and caused neurodegenerative phenotypes in mice, including impaired motor and cognitive performance, shortened lifespan, and pathological lesions such as white matter lesions, microgliosis, and astrogliosis. By contrast, the sole expression of GGC-repeat RNA was non-pathogenic. Combining with bulk and single-nuclei RNA-seq, we determined the common molecular signatures associated with expressing uN2CpolyG and uN2CpolyG-dCT in the brain, especially the up-regulation of inflammation and microglia markers whereas down-regulation of immediate early genes and splicing factors. Importantly, microglia-mediated inflammation was visualized in NIID patients by positron emission tomography, which correlated with white matter atrophy levels. Moreover, microglia ablation ameliorated neurodegeneration in uN2CpolyG-expressing mice but did not alter polyG inclusions. Together, these results demonstrate that polyG is critical for the pathogenesis of NIID, and microglia contribute to polyG-induced neurodegeneration.

overall_design: To analyze molecular characteristics of different cell populations, we performed single nuclei RNA-seq (snRNA-seq) on cerebral cortices of ATG-GGC11 (n=2)  and ATG-GGC100 (n=3) mice groups.

first: Shaoping

last: Zhong


title: Microglia contribute to polyG-dependent neurodegeneration in neuronal intranuclear inclusion disease II

overall_design: To explore the transcriptomic alterations induced by polyG proteins, we performed bulk RNA-seq on cerebral cortices of AAV-injected mice.