title: Transcriptomic analysis of tumor self-seeded cells, primary tumor cells, and circulating tumor cells in liver cancer

status: Public on Jun 24 2024

city: Woolloongabba

first: Haotian

last: Yang

address: 37 Kent Street

department: Frazer Institute

institute: The University of Queensland

summary: Recent studies have indicated a multi-directional seeding of circulating tumor cells (CTCs). Apart from seeding to distant tissues (cancer metastases), CTCs can also reinfiltrate and colonize already established tumors. This process of “tumor self-seeding” provides new insights into the dynamics of tumor progression, and has been indicated to promote tumor growth, angiogenesis, and invasion. Thus, therapeutic targeting of tumor self-seeded cells (TSCs) may provide effective strategies for preventing tumor progression. However, TSCs have not been well identified and characterized due to unsuitable animal models. Therefore, this study aims to develop a novel animal model to recapitulate the process of tumor self-seeding and characterize the transcriptional and functional profiles of TSCs in liver cancer. Using our tumor self-seeding model, TSCs, primary tumor cells (PCs), and CTCs were identified and isolated by fluorescence-activated cell sorting (FACS). RNA sequencing of the purified cells identified TSCs as a subpopulation of PCs. Further analyses showed that TSCs were enriched with gene sets of cancer metastasis and invasiveness, suggesting TSCs may provide novel cell targets with diagnostic, prognostic, or therapeutic potential.

overall_design: RNA profile of TSCs, PCs, and CTCs isolated from the tumor self-seeding model.

first: Xiaowen

last: Liang


title: Cancer-associated fibroblasts (CAFs) gene signatures predict outcomes in breast and prostate tumor patients

status: Public on Jun 21 2024

city: Rende

first: Rosamaria

last: Lappano

state: Cs

address: via P. Bucci

country: Italy

institute: University of Calabria

type: Expression profiling by high throughput sequencing

summary: Over the last two decades, tumor-derived RNA expression signatures have been developed for the two most commonly diagnosed tumors worldwide, namely prostate and breast tumors, in order to improve both outcome prediction and treatment decision-making. In this context, molecular signatures gained by main components of the tumor microenvironment, such as cancer-associated fibroblasts (CAFs), have been explored as prognostic and therapeutic tools. Nevertheless, a deeper understanding of the significance of CAFs-related gene signatures in breast and prostate cancers still remains to be disclosed. RNA sequencing technology (RNA-seq) was employed to profile and compare the transcriptome of CAFs isolated from patients affected by breast and prostate tumors. The differentially expressed genes (DEGs) characterizing breast and prostate CAFs were intersected with data from public datasets derived from bulk RNA-seq profiles of breast and prostate tumor patients. Pathway enrichment analyses allowed us to appreciate the biological significance of the DEGs. K-means clustering was applied to construct CAFs-related gene signatures specific for breast and prostate cancer and to stratify independent cohorts of patients into high and low gene expression clusters. Kaplan-Meier survival curves and log-rank tests were employed to predict differences in the outcome parameters of the clusters of patients. Decision-tree analysis was used to validate the clustering results and boosting calculations were then employed to improve the results obtained by the decision-tree algorithm. Data obtained in breast CAFs allowed us to assess a signature that includes 8 genes (ITGA11, THBS1, FN1, EMP1, ITGA2, FYN, SPP1, and EMP2) belonging to pro-metastatic signaling routes, such as the focal adhesion pathway. Survival analyses indicated that the cluster of breast cancer patients showing a high expression of the aforementioned genes displays worse clinical outcomes. Next, we identified a prostate CAFs-related signature that includes 11 genes (IL13RA2, GDF7, IL33, CXCL1, TNFRSF19, CXCL6, LIFR, CXCL5, IL7, TSLP, and TNFSF15) associated with immune responses. A low expression of these genes was predictive of poor survival rates in prostate cancer patients. The results obtained were significantly validated through a two-step approach, based on unsupervised (clustering) and supervised (classification) learning techniques, showing a high prediction accuracy (≥ 90%) in independent RNA-seq cohorts. We identified a huge heterogeneity in the transcriptional profile of CAFs derived from breast and prostate tumors. Of note, the two novel CAFs-related gene signatures might be considered as reliable prognostic indicators and valuable biomarkers for a better management of breast and prostate cancer patients.

overall_design: Identification of CAFs-related gene signatures for breast and prostate cancer patients by integrating RNA-seq data from both primary  CAFs and cancer patients datasets.


title: Function of ARID1A during osteoclastogenesis

status: Public on Jun 23 2024

city: Shanghai

first: Jiahui

last: Du

address: Zhizaoju Road 639

country: China

institute: Shanghai Jiao Tong University

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Systematic Study on the Three-Dimensional Genome of Escherichia Coli and Its Thermal Adaptation Mechanism (RNA-Seq)

city: wuhan

first: Xuting

last: Wang

state: hubei

address: hongshan

institute: HuaZhong Agriculture University

summary: Total RNA was extracted and sequenced from Escherichia coli cultured to log phase and stable phase at 37 ° C and 45 ° C, respectively. The transcriptome data of Escherichia coli under four different growth conditions were obtained.

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: The transcripome data of Escherichia coli cultured at 45℃ and 37℃ to log phase and stable phase were extracted and cross-compared

first: Binguang

last: Ma


title: Systematic investigation of mitochondrial transfer between cancer cells and T cells at single-cell resolution

city: Philadelphia

first: Bo

last: Li

state: PA

address: 3501 Civic Center Blvd

department: Department of Pathology and Laboratory Medicine

country: USA

institute: The Children’s Hospital of Philadelphia, University of Pennsylvania

summary: Mitochondrion (MT) as the energy-producing organelle participates in most metabolic activities of mammalian cells. Unidirectional mitochondrial transfer from T cells to cancer cells was recently observed “metabolically empowering” cancer cells while “depleting immune cells”, providing new insights into Tumor-T cell interaction and immune evasion. Here, we leveraged the increasingly adopted single-cell RNA-seq technology and introduced MERCI, a statistical deconvolution method for tracing and quantifying the process of mitochondrial trafficking between cancer and T cells. MERCI was benchmarked using data generated from a coculture system of MT-labeled cancer and T cells to accurately predict the recipient cells and their mitochondrial compositions. We independently demonstrated the cellular MT transfer signals and validated the MERCI performance by additionally generating a gold-standard mtscATAC-seq dataset. Application of MERCI to single cell human cancer samples identified a novel MT transfer phenotype and its signature genes involved in cytoskeleton remodeling, energy production and TNFα signaling pathways. Application of MERCI to ovarian cancer spatial transcriptomes revealed the prevalence of MT transfer in the tumor tissue of high T cell infiltration, which is elevated in the endothelium-rich regions. Finally, MT transfer is associated with high cell cycle activity and poor clinical outcome in our pan-cancer analysis through MERCI. In summary, MERCI enabled systematic investigation of a novel aspect of Tumor-T cell interaction and revealed MT-transfer related genes and pathways that may lead to new therapeutic opportunities.

overall_design: The KP lung cancer cells were provided initially by Dr. Esra Akbay. The KP-mito-DsRed stable cell line was generated in the lab with pDsRed2-Mito vector transfection using PEI MAX® with long-term selection using G418 following manufacture’s protocol. All cancer cell lines were grown in 5% FBS supplemented RPMI 1640. Cell lines were routinely tested using a mycoplasma contamination and cultured under 5% CO2 at 37 ֯C. Splenocytes were isolated by harvesting the spleen from 6-8 weeks old mice following red blood cell lysis with ACK buffer. CD8+ T cells were isolated by immunomagnetic negative selection using EasySepTM mouse CD8+ T cell isolation kit. Isolated T cells were then stained with MitoTrackerTM green FM at 100 nM concentration at 37°C for 30 min following the manufacturer’s instruction. MitoTrackerTM green FM at indicated concentration would not stain all T cell mitochondria positive, to avoid non-mitochondrial labeling. Stained CD8+ T cells were then washed with medium, centrifuged down, and then resuspended to remove access dye in the medium. Isolated CD8+ T cells were maintained in 10% heat deactivated FBS supplemented RPMI 1640. In the control experiment, KP-mito-DsRed cancer cells were labeled with MitoTrackerTM red CMXRos using the same procedure. scRNA-seq was performed by the 10x Genomics single-cell 5′ V(D)J library platform. Single-cell suspension of negative controls and sorted cells were counted manually under a microscope stained with trypan blue. The concentration of single-cell suspensions was adjusted to 900-1000 live cell/μl. Cells were loaded at 10,000 cells/chip position. Single-cell libraries were generated with Chromium Single Cell V(D)J Reagent Kit (10x Genomics, PN-10000006, PN-10000009) following per manufacturer’s instruction. Purified libraries were analyzed by Illumina NovaSeq with 150-bp paired-end reads at a targeted median read depth of 100,000 reads per cell. Mitochondrial single-cell assay for transposase-accessible chromatin with sequencing (mtscATAC-seq) technique was performed strictly following the revised 10x scATAC-seq protocol developed by Lareau et al. Briefly, after washing, the sorted cells were fixed in 1% formaldehyde in PBS for 10 min at RT, quenched with glycine solution to a final concentration of 0.125 M before washing cells twice in PBS via centrifugation at 400 g, 5 min, 4°C. Cells were subsequently treated with lysis buffer (10mM Tris-HCL pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1% NP40, 1% BSA) for 3 min for CD8+ T cells and 5 min for KP cells on ice, followed by adding 1 ml of chilled wash buffer and inversion (10mM Tris-HCL pH 7.4, 10mM NaCl, 3mM MgCl2, 1% BSA) before centrifugation at 500 g, 5 min, 4°C. The supernatant was discarded, and cells were diluted in 1x Diluted Nuclei buffer (10x Genomics) before counting using Trypan Blue and a Countess II FL Automated Cell Counter (Invitrogen). mtscATAC-seq libraries were generated using the 10x Chromium Controller and the Chromium Next GEM Single Cell ATAC Kit v2 (PN-1000406) according to the manufacturer’s instructions (CG000496 Rev-B), and sequencing was run on Illumina NovaSeq 6000 (Novogene) using paired-end sequencing of 150-bp read length, aiming to allocate 35,000 paired-end reads per cell in a mtscATAC-seq library.

first: Zhang

last: Hongyi

first: Yu

last: Xuein

first: Ye

last: Jianfeng

last: Anli

first: Li

last: Bo


title: Detecting small cell transformation in patients with advanced EGFR mutant lung adenocarcinoma through epigenomic cfDNA profiling

status: Public on Jun 20 2024

city: Boston

first: Jacob

middle: Eli

last: Berchuck

state: MA

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

type: Methylation profiling by high throughput sequencing

summary: Histologic transformation to small cell lung cancer (SCLC) is an increasingly common resistance mechanism to EGFR tyrosine kinase inhibitors in EGFR mutant lung adenocarcinoma (LUAD) that is underdiagnosed in clinical practice due to the requirement for tissue biopsy. Early and accurate detection of transformed (t)SCLC has important prognostic and therapeutic implications. To address this unmet need, we first comprehensively profiled the epigenomes of metastatic lung tumors finding widespread epigenomic reprogramming during histologic transformation from LUAD to SCLC. We then utilized a novel approach for epigenomic profiling of cell-free DNA, which discriminated patients with EGFR mutant tSCLC from patients with EGFR mutant LUAD with greater than 90% accuracy. This first demonstration of the ability to accurately, and non-invasively, detect small cell transformation in patients with EGFR mutant LUAD through epigenomic cfDNA profiling is a critical step towards a new paradigm of diagnostic and therapeutic precision for patients with advanced lung cancer.

overall_design: To characterize the epigenomic landscape of transformed (t)SCLC relative to LUAD and de novo SCLC, we performed chromatin immunoprecipitation sequencing (ChIP-seq) to profile the histone modifications H3K27ac, H3K4me3, and H3K27me3, methylated DNA immunoprecipitation sequencing (MeDIP-seq), and assay for transposase-accessible chromatin sequencing (ATAC-seq) on 26 lung cancer patient-derived xenograft (PDX) tumors. These PDXs comprised 13 lung adenocarcinoma, 4 transformed SCLC, and 9 de novo SCLC tumors.

first: Talal

last: El Zarif

first: Catherine

middle: B

last: Meador

first: Xintao

last: Qiu

first: Aaron

middle: N

last: Hata

first: Matthew

middle: L

last: Freedman

middle: E


title: Time course of ethylene and ACC response in ETR1 receptor mutants in roots

city: Richmond

first: Wright Center for Clinical and Translational Research

last: Bioinformatics Core

state: VA

address: 203 E Cary St

institute: Virginia Commonwealth University

summary: ETR1 receptor mutants etr1-3 (loss-of-function) and etr1-7 (gain-of-function) were treated with either ethylene or its biosynthetic precursor, ACC (1-aminocyclopropane-1-carboxylate) for 0, 1, 4, and 24 hours.

overall_design: WT (Col-0), etr1-3, and etr1-7 seeds were germinated on MS media (with mesh) and grown for 5 days. Then, seedlings were transferred to new MS media. For ACC treatment, new plates contained 0.75uM ACC. For ethylene treatment, seedlings were transferred to control plates and placed into chambers where they were treated with 0.3ppm ethylene. After indicated times (0hr, 1hr, 4hr, 24hr), roots were cut from seedlings and frozen on liquid nitrogen before RNA extraction.

first: Gloria

last: Muday

first: Alexandria

last: Harkey

first: Joëlle

last: Mühlemann

first: Amy

last: Olex

first: Maleana

last: Khoury


title: RNA-seq and CUT&RUN of erythroblasts upon perturbation of gamma-hemoglobin repressors

status: Public on Jun 19 2024

city: Basel

first: Alejandro

last: Reyes

address: Fabrikstrasse 22

department: Data Sciences

country: Switzerland

institute: Novartis Institutes For BioMedical Research

summary: Through high throughput compound screening, we've identified compounds that induce the expression of fetal hemoglobin. This study contains RNA-seq and CUT&RUN data of a novel target, WIZ.

overall_design: The experiments contain erythroblast data at different differentiation times, where WIZ was perturbed either through a low molecular weight inhibitor that degrades it or by CRISPR-mediated knockdown.


title: Chromatin conformation and histone modification profiling across human kidney anatomic regions

city: New Haven

first: Haikuo

last: Li

state: CT

address: 55 Prospect St

institute: Washington University in St. Louis

first: Benjamin

middle: D

last: Humphreys


title: Liver-specific Mettl14 deletion induces nuclear heterotypia and dysregulates RNA export machinery

status: Public on Jun 18 2024

city: Princeton

last: Lin

state: NJ

address: Washington Road

department: Molecular Biology

institute: Princeton University

summary: Modification of RNAs with N6-methadenosine (m6A) has gained attention in recent years as a general mechanism of gene regulation. In the liver, m6A and its associated machinery has been studied as a potential biomarker of disease and cancer, with impacts on metabolism, cell cycle regulation, and pro-cancer state signaling. In vivo studies have begun to explore the effects of m6A in the liver, but differences in outcome of deletion of m6A writers Mettl3 and Mettl14 have not been thoroughly described or explained. Similarly, in vivo studies of the effects of m6A readers such as Ythdf1 and Ythdf2 have not been extended to characterize impacts of dysregulation of these reader proteins in the liver. To understand Mettl14 function, as well as Ythdf1 and Ythdf2, we developed mouse models and found a Mettl14 deletion specific phenotype of progressive liver injury characterized by nuclear heterotypia, with studies highlighting changes in mRNA splicing, processing and export leading to increases in mRNA surveillance and recycling.

overall_design: Comparative gene expression profiling (RNA-seq) of livers from Mettl14[fl/fl] or Mettl14[fl/fl]/Alb-Cre mice.

first: Keith

middle: A

last: Berggren

first: Saloni

last: Sinha

first: Michael

middle: P

last: Schwoerer

first: Stephanie

last: Maya

first: Thomas

middle: R

last: Cafiero

first: Yongzhen

last: Liu

first: Hans

last: Gertje

first: Saori

last: Suzuki

first: Andrew

last: Berneshawi

first: Sebastian

last: Carver

first: Brigitte

last: Heller

first: Daniel

last: Beard

first: Danyang

last: Wang

first: John

middle: M

last: Cullen

first: Ralph

last: Kleiner

first: Nicholas

last: Crossland

first: Robert

last: Schwartz

first: Alexander

last: Ploss


title: H3K9 methylation regulates heterochromatin silencing through incoherent feedforward loops

status: Public on Jun 27 2024

city: Bunkyo, Tokyo

first: Soichi

last: Inagaki

department: Department of Biological Sciences

country: Japan

institute: Graduate School of Science, The University of Tokyo

summary: Histone H3 lysine-9 methylation (H3K9me) is a hallmark of the condensed and transcriptionally silent heterochromatin. It remains unclear how H3K9me controls transcription silencing and how cells delimit H3K9me domains to avoid silencing essential genes. Here, using Arabidopsis genetic systems that induce H3K9me2 in genes and transposons de novo, we show that H3K9me2 accumulation paradoxically also causes the deposition of the euchromatic mark H3K36me3 by a SET domain methyltransferase, ASHH3. ASHH3-induced H3K36me3 confers anti-silencing by preventing the demethylation of H3K4me1 by LDL2, which mediates transcriptional silencing downstream of H3K9me2. These results demonstrate that H3K9me2 not only facilitates but orchestrates silencing by actuating antagonistic silencing and anti-silencing pathways, providing insights into the molecular basis underlying proper partitioning of chromatin domains and the creation of metastable epigenetic variation.

overall_design: 2-week-old Arabidopsis plants grown on MS plates are used for mRNA-seq, ChIP-seq and Enzymatic DNA methylation (EM)-seq.


title: Unraveling epithelial cell heterogeneity in adamantinomatous craniopharyngioma using single-cell and spatially resolved analysis

status: Public on Jun 26 2024

city: Nanchang

first: Tao

last: Hong

state: Jiangxi province

address: 17 Yong Wai Zheng Street

institute: the First Affiliated Hospital of Nanchang University

summary: Adamantinomatous craniopharyngioma (ACP) is an intractable and histologically complex epithelial neoplasm with variable pathognomonic features, while its cellular composition, particularly the epithelial component, is poorly characterized. Herein, a single-nucleus transcriptome atlas specific to ACP was constructed by performing a single-nucleus RNA sequencing (snRNA-seq) survey of 55967 nuclei in 6 ACP samples from 3 patients. We revealed 6 epithelial subtypes with diverse molecular functions in ACP by integrating snRNA-seq, spatial transcriptomic (ST) and immunostaining data. Additionally, we investigated the potential regulatory mechanism of ACP calcification by performing a trajectory analysis and transcription factor regulon analysis. Finally, we characterized the molecular characteristics of neurons and discovered potential epithelial cell–neuron crosstalk in ACP tissues. Overall, this large-scale single-nucleus atlas combined with ST provides, for the first time, unprecedented insights into epithelial cell heterogeneity within ACP and can serve as a resource for further investigation of tumor dynamics.

overall_design:
6 frozen ACP samples from 3 patients (two samples from each patient) were underwent single-nucleus RNA sequencingand and 4 APC sections  from 3 paitents were underwent spatial transcriptomics.

***Please note that all processed data files have been updated on July 7 2024***

first: Jie

last: Wu

first: Shaoyang

last: Li

first: Chenxing

last: Yang


title: Gene expression profile at single cell level of three adult, non-diabetic, human islets

status: Public on Jun 15 2024

city: Edmonton

first: Patrick

last: MacDonald

state: AB

address: 6-040 Li Ka Shing Centre

country: Canada

institute: University of Alberta

summary: This data set contains 41,432 islet cells from three adult non-diabetic human islet donors (two female, one male) sequenced using 10X Genomics Chromium.

overall_design: Pancreases were retrieved from three adult, non-diabetic, human donors and islets were isolated. After culture, islets were dissociated into single cells and sent for scRNA-seq analysis.

first: Cara

last: Ellis

first: MD

last: Amin


title: Interleukin-17 directly stimulates tumor infiltrating Tregs to prevent cancer development [scRNA-seq]

status: Public on Jun 14 2024

city: Farmington

first: Kepeng

address: 263 Farmington Ave

department: Immunology

institute: UConn Health

summary: Interleukin-17 (IL-17) family cytokines promote protective inflammation for pathogen resistance, but also facilitate autoimmunity and tumor development. A direct signal of IL-17 to regulatory T cells (Tregs) has not been reported and may help explain these dichotomous responses. Here we show in mice that IL-17 Receptor A (IL-17RA) is expressed in Tregs that reside in mouse mesenteric lymph nodes and colon tumors, as well as in patients with colorectal cancer (CRC). Ablation of IL-17RA, specifically in Tregs, resulted in increased Th17 cells, and exacerbated tumor development. Mechanistically, tumor-infiltrating Tregs exhibit a unique gene signature that is linked to their activation, maturation, and suppression function, and this signature is in part supported by the direct signaling of IL-17 to Tregs. To study pathways of Treg programming, we found that loss of IL-17RA in tumor Tregs resulted in reduced RNA splicing, and downregulation of several RNA binding proteins that are known to regulate alternative splicing and promote Treg function. Taken together, we report a direct role of IL-17 in promoting Treg maturation and function in CRC.

overall_design: Bone marrow cells from Foxp3-YFP-Cre+/Il17raF/F (KO) and Foxp3-YFP-Cre+/Il17raF/+ (WT control) mice were adoptively transferred into 6-8-week-old Cdx2-Cre+/ApcF/+ mice. Bone marrow recipient mice were then sacrificed at 5 months of age, and their mesenteric lymph nodes (MLN) and tumors were disected.

first: William

middle: C

last: Theune

first: Ju

last: Chen


title: Epigenetic and transcriptional consequences in the endosperm of chemically induced transposon mobilization in Arabidopsis

city: Uppsala

first: Juan

last: Santos-González

state: Uppsala

address: Almas Allé 5

department: Department of Plant Biology and Forest Genetics

country: Sweden

institute: SLU

summary: Genomic imprinting, an epigenetic phenomenon leading to parent-of-origin-specific gene expression, has independently e v olv ed in the en- dosperm of flo w ering plants and the placenta of mammals—tissues crucial f or nurturing embry os. While transposable elements (TEs) frequently colocalize with imprinted genes and are implicated in imprinting establishment, direct in v estigations of the impact of de no v o TE transposition on genomic imprinting remain scarce. In this study, we explored the effects of chemically induced transposition of the Copia element ONSEN on genomic imprinting in Arabidopsis thaliana . Through the combination of chemical TE mobilization and doubled haploid induction, we gener- ated a line with 40 new ONSEN copies. Our findings reveal a preferential targeting of maternally expressed genes (MEGs) for transposition, aligning with the colocalization of H2A.Z and H3K27me3 in MEGs—both previously identified as promoters of ONSEN insertions. Additionally, we demonstrate that chemically-induced DNA hypomethylation induces global transcriptional deregulation in the endosperm, leading to the breakdo wn of MEG imprinting. T his study pro vides insights into the consequences of chemically induced TE remobilization in the endosperm, re v ealing that chemically-induced epigenome changes can ha v e long-term consequences on imprinted gene expression.

overall_design: RNAseq, WGBS and CUT&Tag datasets were obtained from INTACT purified endosperm nuclei from Col × Ler (L) reciprocal crosses at 4 days after pollination (DAP).  WGBS and CUT&Tag were generated in duplicates using the INTACT line (referred as C) or TEmob (T3, referred as Cm) genetic background in recirpocal crosses with Ler (L). RNAseq libraries were generated in triplicates from TEmob (Cm) x Ler (L) reciprocal crosses.

first: Gerardo

last: del Toro de León

first: Joram

last: van Boven

first: Wen-Biao

last: Jiao

first: Haorang

last: Peng

first: Korbinian

last: Schneeberger

first: Claudia

last: Köhler


title: Soluble Glycoprotein VI Predicts Abdominal Aortic Aneurysm Growth Rate and is a Novel Therapeutic Target

status: Public on Jun 22 2024

city: Cincinnati

first: Tyler

last: Benson

state: OH

address: CVC 3976 231 Albert Sabin Way

institute: University of Cincinnati

summary: A common feature in patients with abdominal aortic aneurysms (AAA) is the formation of a nonocclusive intraluminal thrombus (ILT) in regions of aortic dilation. Platelets are known to maintain hemostasis and propagate thrombosis through several redundant activation mechanisms, yet the role of platelet activation in the pathogenesis of AAA associated ILT is still poorly understood. Thus, we sought to investigate how platelet activation impacts the pathogenesis of AAA. Using RNA-sequencing, we identify that the platelet-associated transcripts are significantly enriched in the ILT compared to the adjacent aneurysm wall and healthy control aortas.  We found that the platelet specific receptor glycoprotein VI (GPVI) is among the top enriched genes in AAA ILT and is increased on the platelet surface of AAA patients. Examination of a specific indicator of platelet activity, soluble GPVI (sGPVI), in two independent AAA patient cohorts is highly predictive of a AAA diagnosis and associates more strongly with aneurysm growth rate when compared to D-dimer in humans. Finally, intervention with the anti-GPVI antibody (JAQ1) in mice with established aneurysms blunted the progression of AAA in two independent mouse models. In conclusion, we show that levels of sGPVI in humans can predict a diagnosis of AAA and AAA growth rate, which may be critical in the identification of high-risk patients. We also identify GPVI as a novel platelet-specific AAA therapeutic target, with minimal risk of adverse bleeding complications, where none currently exist.

overall_design: Human AAA tissue was obtained from four patients (4 males) aged 65 ± 7.7 years (mean ± SD; range 45 to 71 years) undergoing open aneurysm repair (between 2015 and 2018) at the University of Rochester Medical Center in Rochester, NY under an approved University of Rochester Cardiovascular Tissue Bank Internal Review Board Application (RSRB 00036669).  The patient criteria for open surgical repair were defined as AAA diameter exceeding 55 mm for males, AAA diameters between 50 and 55 mm for females, rapidly expanding aortic diameters (≥ 5 mm in 6 months with a minimum diameter of 40 mm), or symptoms attributable to AAA and AAA rupture.  Mural thrombi (easily separated from the aortic wall) were collected during surgery, along with residual aortic wall fragments, and were immediately flash frozen until RNA extraction.  Control tissue was procured from the infrarenal aortas of 5 males aged 58 ± 6.6 years (mean ± SD; range 42 to 65 years) cause of death deemed non-aortic causes.  Tissues were collected within 24 hours of death and flash frozen for analysis. To identify what genes were enriched within the ILT as a part of the overall AAA, comparisons between the transcriptome of thrombi and surroding aortic tissue was performed.

middle: W

first: Albert

last: Owens III


title: Non-Canonical BAF and mSWI/SNF Regulates POU2F3 and are Selective Targetable Dependencies for POU2F3-Positive Small Cell Lung Cancer

first: Cigall

last: Kadoch

state: Massachusetts

address: 440 Brookline Ave

department: Pediatric Oncology

institute: Dana Farber Cancer Institute

summary: ~12% of SCLCs are marked by the lineage transcription factor POU2F3, which is essential in all POU2F3-positive SCLCs. Thus, approaches to directly or indirectly inhibit POU2F3 could lead to new therapeutic strategies for POU2F3-positive SCLCs. Here we use a positive selection screening strategy where endogenous POU2F3 is fused to the suicide gene DCK*. Cells that express endogenous POU2F3-DCK* are killed in the presence of the nucleoside analog BVdU and only cells that downregulate the POU2F3-DCK* fusion survive. Genome-wide CRISPR/Cas9 resistance screens with BVdU in POU2F3-DCK* cells uncovered that inactivation of SMARCD1 or BRD9, both components of the non-canonical BAF (ncBAF) complex, markedly downregulate endogenous POU2F3. We find that all POU2F3-positive SCLC cell lines relative to ASCL1-positive and NEUROD1-positive cell lines, are exquisitely sensitive to mSWI/SNF complex inhibition using SMARCA2/4 inhibitors; while pure non-neuroendocrine POU2F3-positive SCLC cell lines are highly sensitive to ncBAF complex inhibition using highly selective BRD9 degraders. Mechanistically, BRD9 binds and regulates POU2F3 target genes including POU2F3 itself. BRD9 degraders or SMARCA2/4 inhibitors robustly decrease accessibility of POU2F3 target genes effectively shutting off POU2F3 function. Moreover, BRD9 degraders or SMARCA2/4 inhibitors decrease tumor growth and increase survival of mice bearing non-neuroendocrine POU2F3 xenografts. This works shows that mSWI/SNF and ncBAF tightly regulate POU2F3 expression and activity and nominate mSWI/SNF or ncBAF inhibition as druggable therapeutic strategies to selectively target POU2F3-positive SCLCs.

overall_design:
To investigate the relationship between POU2F3 and mSWI/SNF activity in POU2F3+ small cell lung cancer (SCLC), we assess the gene expression and chromatin accessibility effects across 4 POU2F3+ SCLC lines treated with FHD286, which is a selective SMARCA2/4 inhibitor. We performed RNA-seq and ATAC-seq on NCIH211, CORL311, NCIH526, and NCIH1048 treated with either DMSO or 100nM FHD286 for 72 hours.

To understand how non-neuroendocrine POU2F3+ SCLC are sensitive to ncBAF activity, we assessed the gene expression and chromatin accessibility effects on NCIH211 and NCIH1048 treated with either DMSO or FHD609, which is a specific bromodomain-targeting PROTAC for BRD9. We performed RNA-seq and ATAC-seq on NCIH211 and NCIH1048 treated with either DMSO or 100nM FHD609 for 72 hours.

We assessed how POU2F3 binding is affected by SMARCA2/4 inhibition or BRD9 degradation. We performed POU2F3, RPB1, H3K27ac, and BRD9 ChIP-seq in NCIH1048 treated with DMSO or FHD286. We also performed POU2F3 and H3K27ac ChIP-seq in NICH1048 treated with FHD609.

first: Kevin

last: So

first: Alexander

last: Ying


title: Interleukin-17 directly stimulates tumor infiltrating Tregs to prevent cancer development [bulk RNA-seq]

last: Wang


title: snRNA-seq of human cutaneous neurofibromas before and after selumetinib treatment implicates role of altered Schwann cell states, inter-cellular signaling, and extracellular matrix in treatment response

city: Birmingham

first: Deeann

last: Wallis

state: Al

address: 720 20th St S

department: Genetics

institute: University of Alabama at Birmingham

summary: Neurofibromatosis Type I is caused by loss of function variants in the NF1 gene.  Most patients with NF1 develop skin lesions called cutaneous neurofibromas (cNFs). Currently the only approved therapeutic for NF1 is selumetinib, mitogen -activated protein kinase inhibitor.  The purpose of this study is to analyze the transcriptome of cNF tumors before and after selumetinib treatment to both understand tumor composition and response.  We obtained biopsy sets of tumors both pre- and post- selumetinib treatment from the same individuals and were able to collect sets from four separate individuals. We sequenced a total of 5,844 nuclei and identified 30,442 genes in the untreated group and sequenced 5,701 nuclei and identified 30,127 genes in the selumetinib treated group. We identified populations of Schwann cells, fibroblasts, pericytes, myeloid cells, melanocytes, keratinocytes, and two populations of endothelial cells and calculated their frequencies in both groups. While we anticipated that cell proportions might change with treatment, we did not identify any one cell population that changed significantly, likely due to an inherent level of variability between tumors.  We also evaluated differential gene expression based on drug treatment in each cell type. Ingenuity pathway analysis (IPA) was also used to identify pathways that differ after treatment.  As anticipated, we identified a significant decrease in ERK/MAPK signaling in cells including Schwann cells but most specifically in myeloid cells.  Interestingly, there is a significant decrease in opioid signaling in myeloid and endothelial cells; this downward trend is also observed in Schwann cells and fibroblasts.  Cell communication was assessed by RNA velocity, Scriabin, and CellChat.  Together they indicate that Schwann cells and fibroblasts have dramatically altered cell states defined by specific gene signatures following treatment (RNA velocity).  There are dramatic changes in receptor-ligand pairs following treatment (Scriabin), and robust intercellular signaling between virtually all cell types associated with extracellular matrix (ECM) pathways (Collagen, Laminin, Fibronectin, and Nectin) is downregulated after treatment. These gene signatures and interaction pathways suggest they might be a key determinate for response.

overall_design:
Transcriptomic evaluation of frozen matched patient pre- and post- selumetinib treated cNFs using snRNA-seq to evaluate the response to selumetinib treatment.
ADT antibodies details:
ADT: barcode sequence: hashtagged sample
TotalSeq-B0451 Nuclear Pore Complex Proteins: TTCCTGCCATTACTA: 1v1, 5v1, 2v1
TotalSeq-B0452 Nuclear Pore Complex Proteins: CCGTACCTCATTGTT: 15v1, 13v1, 1vc3, 2v7
TotalSeq-B0453 Nuclear Pore Complex Proteins: GGTAGATGTCCTCAG: 15v4, 13v4, 6v1
TotalSeq-B0457 Nuclear Pore Complex Proteins: CTTATCACCGCTCAA: 5v4, 6v3

first: Christian

middle: X

last: Fay

first: Cameron

last: Church

first: Emil

last: Kriukov

first: Petr

last: Baranov

first: David

last: Crossman


title: Leveraging Integrated RNA Sequencing to Decipher Adrenomedullin’s Protective Mechanisms in Experimental Bronchopulmonary Dysplasia

status: Public on Jun 17 2024

city: Houston

first: Amrit

last: Koirala

state: TX

address: 1 Baylor Plaza

institute: Baylor College of Medicine

summary: Bronchopulmonary dysplasia (BPD) is a chronic lung disease commonly affecting premature infants, with limited therapeutic options and increased long-term consequences. Adrenomedullin (Adm), a proangiogenic peptide hormone, has been found to protect rodents against experimental BPD. This study aims to elucidate the molecular and cellular mechanisms through which Adm influences BPD pathogenesis using a lipopolysaccharide (LPS)-induced model of experimental BPD in mice. Bulk RNA sequencing of Adm-sufficient (wild-type or Adm+/+) and Adm-haplodeficient (Adm+/-) mice lungs, integrated with single-cell RNA sequencing data, revealed distinct gene expression patterns and cell type alterations associated with Adm deficiency and LPS exposure. Notably, computational integration with cell atlas data revealed that Adm-haplodeficient mouse lungs exhibited gene expression signatures characteristic of increased inflammation, natural killer (NK) cell frequency and decreased endothelial cell and type II pneumocyte frequency. Furthermore, in silico human BPD patient data analysis supported our cell type frequency finding, highlighting elevated NK cells in BPD infants. These results underscore the protective role of Adm in experimental BPD and emphasize that it is a potential therapeutic target for BPD infants with an inflammatory phenotype.

overall_design: This dataset consists of bulk RNA-seq data generated from 12 whole lung tissues ofAdm-haplodeficient(Adm+/-) and WT (Adm+/+) mice in response to LPS (lipopolysaccharide) treatment or control PBS in triplicates.

first: Binoy

last: Shivanna

first: Lukas

last: Simon

first: Cristian

last: Coarfa


title: Remodeling of anti-tumor immunity with antibodies targeting a p53 mutant

first: Dafei

last: Chai

state: Texas

address: Alkek Building One Baylor Plaza

summary: p53 is the most mutated gene in cancer, yet there are no effective drugs targeting p53 mutants. Here, we report the development of monoclonal antibodies targeting a p53 hotspot mutation E285K (E285K-mAbs). These mAbs recognize the mutant E285K epitope without cross-reactivity against wild-type p53. They are delivered by lipid nanoparticles (LNPs) that encapsulate DNA plasmids.  The LNP-pE285K-mAbs in the IgG1 formats exhibit a robust anti-tumor effect, facilitating the infiltration of immune cells, including CD8+ T cells, B cells, and NK cells. Single-cell sequencing reveals that the therapeutic effects of IgG1 are associated with reduced immune inhibitory signaling, increased MHC signaling from B cells to CD8+ T cells, and enriched anti-tumor T cell and B cell receptor profiles. The E285K-mAbs can also be made in the dimeric IgA (dIgA) format. The anti-tumor activity of IgA is dependent on PIGR, whereas that of IgG1 is dependent on TRIM21. These findings indicate that targeting specific mutant epitopes through DNA-encoded and LNP-delivered mAbs represents a novel approach for precision medicine against p53 mutants in PIGR- or TRIM21-positive cancers.

overall_design: CD45+ cells were isolated from tumors in both the experimental group (LNP-pE285K-mAb) and the control group (LNP-Ctrl). We employed single-cell RNA sequencing (scRNA-seq) to investigate the differences in tumor-infiltrating immune cells within the tumors.

first: Junhao


title: Estrogen-induced chromatin looping changes identify a subset of functional regulatory elements

status: Public on Jun 12 2024

city: Salt Lake City

first: Jason

last: Gertz

state: UT

address: 2000 circle of hope drive

department: Oncological Sciences

institute: University of Utah

summary: Transcriptional enhancers can regulate individual or multiple genes through long-range three-dimensional (3D) genome interactions, and these interactions are commonly altered in cancer. Yet, the functional relationship between changes in 3D interactions associated with regulatory regions and differential gene expression appears context-dependent. In this study, we used HiChiP to capture changes in 3D genome interactions between active regulatory regions of endometrial cancer cells in response to estrogen treatment and uncovered significant differential long-range interactions that are strongly enriched for estrogen receptor  (ER) bound sites (ERBS). The ERBS anchoring differential loops with either a gene’s promoter or distal regions were correlated with larger transcriptional responses to estrogen compared to ERBS not involved in differential interactions. To functionally test this observation, CRISPR-based Enhancer-i was used to deactivate specific ERBS, which revealed a wide range of effects on the transcriptional response to estrogen. However, these effects are only subtly and not significantly stronger for ERBS in differential loops. In addition, we observed an enrichment of 3D interactions between the promoters of estrogen up-regulated genes and found that looped promoters can work together cooperatively. Overall, our work suggests that changes in 3D genome structure upon estrogen treatment identify some functionally important regulatory regions; however, these changes aren’t required for a transcriptional response to E2 in endometrial cancer cells.

overall_design: Endometrial cancer cell lines treated with estrogen or vehicle control and profiled using H3K27ac Hi-ChIP

first: Hosiana

last: Abewe

first: Jeffery

last: Vahrenkamp


title: Systematic Study on the Three-Dimensional Genome of Escherichia Coli and Its Thermal Adaptation Mechanism (3C-Seq)

first: Xuting

address: hongshan

institute: HuaZhong Agriculture University

summary: Chromosome conformation capture and sequencing experiments were carried out at 37℃ and 45℃ for E. coli in logarithmic phase and stable phase, respectively. Three-dimensional DNA interaction data of E. coli under four different growth conditions and control group were obtained

platform_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: The 3D genomic data of Escherichia coli cultured at 45℃ and 37℃ to log phase and stable phase were extracted and cross-compared

first: Binguang

last: Ma


title: Sample multiplexing for retinal single-cell RNA-sequencing

first: Justin

address: 1 Baylor Plaza, Baylor College of Medicine

department: ophthalmology

summary: Single cell RNA sequencing (ScRNA-seq) often requires sample pooling, but sample variance is rarely addressed. We perform scRNA-seq on retinal ganglion cells with retina-multiplexing to assess the whether this enables comparisons between retinas of an experiment.

overall_design: Retinal ganglion cells (RGCs) of Vglut2-Tdtomato-Ai9 mice were  enriched and isolated by negative-rod immunopanning using an anti-CD73 antibody and Fluorescence-Activated Cell Sorting (FACS) selecting for positivity of a Thy1-APC antibody and Tdtomato expression. Cholesterol-modified-oligos were used during RGC isolation for multiplexing. Samples were prepared and  sequenced with the use of the 10x Genomics 3' chromium platform.

first: Ting

middle: K

last: Chu

first: Maria

last: Polo-Prieto

first: Yong

last: Park

first: Yumei

last: Li

first: Rui

last: Chen

first: Graeme

last: Mardon

first: Benjamin

last: Frankfort

first: Nicholas

last: Tran


title: Mammalian SWI/SNF complex activity regulates POU2F3 and constitutes a targetable dependency in small cell lung cancer

first: Leslie

last: Duplaquet

address: 360 Longwood Ave

institute: DFCI

summary: Small cell lung cancers (SCLC) are comprised of heterogeneous subtypes marked by lineage-specific transcription factors, including ASCL1, NEUROD1, and POU2F3. POU2F3-positive SCLC, ~12% of all cases, are uniquely dependent on POU2F3 itself; as such, approaches to attenuate POU2F3 expression may represent new therapeutic opportunities for this subtype. Here using genome-scale CRISPR/Cas9-based screens reporting on POU2F3 expression in SCLC cell lines, we define mSWI/SNF complexes, including non-canonical BAF complexes (ncBAF), as top regulators of POU2F3 and dependencies specific to the POU2F3-positive subtype. Notably, clinical-grade pharmacologic mSWI/SNF complex inhibition attenuates proliferation of all POU2F3-positive SCLCs, while disruption of ncBAF via BRD9 degradation is uniquely effective in pure non-neuroendocrine POU2F3-SCLCs. mSWI/SNF complexes maintain accessibility over gene loci central to POU2F3-mediated gene regulatory networks. Finally, chemical targeting of SMARCA4/2 mSWI/SNF ATPases and BRD9 decrease POU2F3-SCLC tumor growth and increase survival in vivo. Taken together, these results define mSWI/SNF-mediated global governance of the POU2F3 oncogenic program and suggest mSWI/SNF inhibition as a therapeutic strategy in SCLC.

overall_design: Comparative gene expression profiling analysis of RNA-seq data in 4 POU2F3-expressing human small cell lung cancer (SCLC) cell lines treated with a BRD9 degrader (WA-68-VQ71), a SMARCA2/4 inhibitor (BRM014) or DMSO

first: Matthew

middle: G

last: Oser


title: Affinity maturation broadens influenza vaccine-induced antibody responses in humans

status: Public on Jun 13 2024

first: Steven

last: Kleinstein

state: Ct

address: 300 George St.

department: Pathology

institute: Yale University

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

relation:
SuperSeries of: GSE211865
SuperSeries of: GSE211869

overall_design: Refer to individual Series


title: Expression of the transcription factor HIF-1α in NKp46+ innate lymphoid cells limits inflammation and fibrosis upon chronic colitis

city: Zurich

first: Zheng

last: Fan

address: Winterthurerstrasse 190

department: Anatomy Institute

institute: University of Zurich

summary: Innate lymphoid cells (ILCs) are critically involved in intestinal adaptation to microenvironmental challenges (Colonna, 2018; Guendel et al., 2020) and the gut mucosa is characterized by low oxygen. Adaptation to low oxygen is mediated by Hypoxia-inducible transcription factors (HIFs) the HIF-1α subunit shapes the ILC phenotype upon acute experimental colitis and contributes to intestinal damage. However, the impact of HIF signaling in NKp46+ ILC in the context of repetitive mucosal damage and chronic inflammation, as it typically occurs during inflammatory bowel disease, is unknown. In a model of chronic colitis, mice lacking the HIF-1α isoform in NKp46+ ILCs show a decrease in NKp46+ ILC1s but a concomitant rise in neutrophils as well as Ly6C high macrophages. Single-nuclei RNA sequencing suggests enhanced interaction of mesenchymal cells with other cell compartments in the colon of HIF-1α KO mice and a loss of mucus-producing enterocytes as well as intestinal stem cells. This was, furthermore, associated with increased BMP-integrin signaling, expansion of profibrotic fibroblasts subsets and intestinal fibrosis. In summary this suggests that HIF-1 α mediated ILC1 activation, although detrimental upon acute colitis, protects against excessive inflammation and fibrosis during chronic intestinal damage.

overall_design: In order to assess the impact of HIF1α-deficiency in NKp46+ cells on the gut microenvironment beyond the immune cell compartment at the whole tissue level and at single-cell resolution, we performed single nuclei RNA sequencing on frozen colon tissue from WT and HIF1α KO mice after chronic DSS exposure.

first: Eric

last: Nelius

first: Christian

last: Stockmann


title: Examining Transcriptomic Alterations in Rat Models of Intracerebral Hemorrhage and Severe Intracerebral Hemorrhage

status: Public on Jun 11 2024

city: Hualien

first: Mohammed Thangameeran

last: Shaik Ismail

state: Hualien

address: No. 701, Section 3, Zhongyang Rd

department: Institute of Medical Science

country: Taiwan

institute: Tzu Chi University

summary: Intracerebral hemorrhage (ICH) is a life-threatening condition associated with significant morbidity and mortality. Understanding the molecular mechanisms underlying ICH and its severe form is crucial for developing effective therapeutic strategies. This study investigates transcriptomic alterations in rodent models of ICH and severe intracerebral hemorrhage to shed light on the genetic pathways involved in hemorrhagic brain injury. We performed principal component analysis, revealing distinct principal component segments of normal rats compared to intracerebral hemorrhage and severe intracerebral hemorrhage rats. We further employed heatmaps and volcano plots to identify differentially expressed genes and utilized bar plots and KEGG pathway analysis to elucidate the different molecular pathways involved. Using comprehensive RNA sequencing and bioinformatics analyses, we identified a multitude of differentially expressed genes in both the ICH and severe ICH models. Our results revealed 5679 common genes among the normal, intracerebral hemorrhage, and severe intracerebral hemorrhage groups in the upregulated genes group, and 1196 common genes in the downregulated genes. A volcano plot comparing the groups further highlighted common genes, including PDPN, TIMP1, SERPINE1, TUBB6, and CD44. These findings underscore the complex interplay of genes involved in inflammation, oxidative stress, and neuronal damage. Furthermore, pathway enrichment analysis uncovered key signaling pathways, including the TNF signaling pathway, protein processing in the endoplasmic reticulum, MAPK signaling pathway, and Fc gamma R-mediated phagocytosis, implicated in the pathogenesis of ICH.

overall_design: RNA sequencing was utilized to examine transcriptomic changes in rat models of ICH and severe ICH. Differential expression analysis, coupled with functional and pathway enrichment analyses, provided insights into the underlying molecular mechanisms of ICH.

first: Shaik

middle: I

last: Thangameeran

first: Hock-Kean

last: Liew

first: Sheng-Tzung

last: Tsai

first: Cheng-Yoong

last: Pang


title: BACH1 suppresses cellular senescence, obesity, and short lifespan by ferroptotic FGF21 secretion

city: Sendai

first: Hironari

last: Nishizawa

address: 2-1 Seiryo-machi, Aoba-ku

department: Department of Biochemistry

institute: Tohoku University Graduate School of Medicine

summary: Ferroptosis is a form of regulated cell death characterized by iron-dependent lipid peroxidation. While ferroptosis has been identified as a mechanism for suppressing cancer, its overall physiological significance remains poorly understood. Recent studies have revealed that labile iron and lipid peroxides are released from ferroptotic cells, leading to the propagation of ferroptosis through lipid peroxidation. However, other specific effects of secreted factors derived from ferroptotic cells remain unclear. We constructed a model cell system capable of inducing ferroptosis by re-expressing the transcription factor BACH1, a potent inducer of ferroptosis, in immortalized mouse embryonic fibroblasts (iMEFs). We investigated the impact of the secreted factors from ferroptotic cells with the iMEFs. As a result, we observed that the administration of supernatant media from ferroptotic iMEFs activated proliferation of hepatoma cells and suppressed cellular senescence-like features. This suggested that ferroptotic MEFs secrete anti-senescent substances. Transcriptome analysis of ferroptotic MEFs revealed an increase in the secretion of longevity factor FGF21 in a BACH1-dependent manner. Furthermore, the anti-senescent effects of the supernatant media from these ferroptotic cells were canceled by the knockout of Fgf21. Totally, it is suggested that BACH1 promotes ferroptosis in fibroblasts and contributes to the suppression of cellular senescence in neighboring cells by inducing FGF21 secretion from fibroblasts. It was also discovered that BACH1 not only activates indirectly the transcription of FGF21 by enhancing ferroptotic stress but also increases FGF21 protein level by suppressing the selective autophagic degradation of FGF21 through the transcriptional repression for Sqstm1 and Lamp2a. This represents a dual mechanism of FGF21 upregulation mediated by BACH1, suggesting that BACH1 is a potent inducer of FGF21 expression. It was also found that the BACH1-ferroptosis-FGF21 axis can suppress obesity of mice under high fat diet or short lifespan of progeria mice, closely associated phenotypes with aging. The inhibition of these aging-related phenotypes is considered to be a novel physiological significance of ferroptosis, and BACH1 is considered to function as a longevity gene by promoting ferroptotsis and subsequent FGF21 expression.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Hepa1 cells and Bach1-knockout pMEFs cultured in control or ferroptotic cells-derived medium.

first: Mitsuyo

last: Matsumoto

first: Kazuhiko

last: Igarashi


title: Inhibition of histone acetyltransferase attenuates 3D chromatin-mediated insulin signaling in pancreatic cancer (Hi-C dataset)

status: Public on Jun 10 2024

city: San Antonio

first: Yufan

last: Zhou

address: 7703 Floyd Curl Dr

institute: UT health Science Center at San Antonio

summary: Inhibition of histone acetyltransferase has been widely used to be effectively treat cancers in many studies. However, it’s not clear how the downstream signaling responds to the inhibitor in pancreatic cancer. Here we performed Hi-C experiments to canonical and patient-derived pancreatic cancer cells with the treatment of small molecule inhibitor ICG-001 which has dual function to block both WNT signaling and histone acetyltransferase. This is in situ Hi-C dataset.

overall_design: Pancreatic cancer cell line PANC1, and newly established cell lines from patient-derived tumor xenograft (PATX) program PATC53 were treated with ICG-001 at the concentration of 10 µM for 48 hours. Then in situ Hi-C experiments were performed for these cells.

first: Victor

last: Jin


title: Gene expression profiles of the liver and skeletal muscle in germ-cell-removed animals

city: Osaka

first: Kota

last: Abe

address: 3-1 Yamadaoka, Suita

institute: RIMD, Osaka univ

summary: The function of germ cells in somatic growth and aging is demonstrated in invertebrate models but remains unclear in vertebrates. Here, we demonstrate sex-dependent somatic regulation by germ cells in the short-lived vertebrate model Nothobranchius furzeri. In females, germ-cell-removal shortened lifespan, decreased estrogen, and increased insulin-like growth factor 1 (IGF-1) signaling. In contrast, germ-cell-removal in males improved their health state with increased vitamin D signaling. Body size increased in both sexes, but it was caused by different signaling pathways, i.e., IGF-1 and vitamin D in females and males, respectively. Thus, vertebrate germ cells regulate somatic growth and aging through different endocrine system pathways, depending on the sex, which may underlie the sexual difference in the reproductive strategies.

overall_design: The liver and skeletal muscle from N. furzeri injected with control morpholino antisense oligo (MO) or MO targeting dnd were sampled at young (1.5 months) and old (three months) age for males and females. Total RNAs were extracted and analyzed by BRB-seq.

first: Tohru

last: Ishitani

first: Kaori

last: Tanaka

first: Yasuyuki

last: Okawa


title: Single-cell transcriptomic and targeted genomic profiling reveal CRTAM and PLCB1 as novel hub genes for anti-TNFα therapy response in Crohn's disease

city: Maribor

first: Mario

middle: Smode

last: Gorenjak

address: Taborska ulica 8

country: Slovenia

institute: Faculty of Medicine, University of Maribor

summary: The lack of reliable biomarkers of response to anti-TNFα biologicals hinders personalized therapy for Crohn’s disease (CD) patients. The motivation behind our study is to shift the paradigm of anti-TNFα biomarker discovery towards specific immune cell sub-populations using single-cell RNA-sequencing.

overall_design: The single-cell RNA sequencing was performed on PBMCs samples from CD patients either naïve to biological therapy, in remission while on adalimumab, or while on ustekinumab but previously non-responsive to adalimumab. Sieves for stringent downstream gene selection consisted of gene ontology and independent cohort genomic profiling. Replication and meta-analyses were performed using publicly available raw RNA sequencing files of sorted immune cells, and association analysis summary. Machine learning, mendelian randomization and oligogenic risk score methods were deployed to validate DEGs highly relevant to anti-TNFα therapy response.

first: Boris

last: Gole

first: Larisa

last: Goričan

first: Uršula

last: Prosenc Zmrzljak

first: Uroš

last: Potočnik


title: Spatial Chromosome Organization and Adaptation of Escherichia coli under Heat Stress

city: Wuhan

first: binguang

last: ma

address: No.1,Shizishan Street, Hongshan

institute: Huazhong Agricultural University


title: Construction of a ceRNA network and screening of potential biomarkers and molecular targets in male smokers with chronic obstructive pulmonary disease

status: Public on Jun 09 2024

city: Kunming

first: xiqian

last: xing

state: Yunnan

address: No. 176, Qingnian Road

department: Department of Respiratory Medicine

institute: The Affiliated Hospital of Yunnan University, The Second People's Hospital of Yunnan Province

type: Non-coding RNA profiling by high throughput sequencing

summary: Background. Circular RNAs (circRNAs) play an important role in the occurrence and development of diseases. However, the role of circRNAs in male smokers with chronic obstructive pulmonary disease (COPD) remains unclear.  Methods. Stable COPD patients and healthy controls were recruited. Peripheral blood mononuclear cells (PBMCs) were extracted. After high-throughput RNA sequencing (RNA-Seq) of PBMCs, a bioinformatics method was used to analyse differentially expressed (DE) circRNAs (DEcircRNAs) and mRNAs (DEmRNAs).  Results. Total of 114 DEcircRNAs and 58 DEmRNAs were identified. Functional enrichment analysis showed that processes related to COPD include the regulation of interleukin (IL)-18, IL-5 and the NLRP3 inflammasome; differentiation of T helper type 1 (Th1), Th2, and Th17 cells, and the AMPK, Wnt, JAK-STAT, and PI3K-Akt signalling pathways. In the protein–protein interaction (PPI) network, the core genes were MYO16, MYL4, SCN4A, NRCAM, HMCN1, MYOM2, and IQSEC3. Small-molecule prediction results revealed potential drugs for the COPD treatment. Additionally, the circRNA-miRNA-mRNA competitive endogenous RNA (ceRNA) regulatory network was constructed.  Conclusion. This study identified a set of dysregulated circRNAs and mRNAs and revealed potentially important genes, pathways, new small-molecule drugs and ceRNA regulatory networks in male smokers with COPD. These circRNAs might be prospective biomarkers or potential molecular targets of the ceRNA mechanism for COPD.

first: Xiqian

last: Xing

first: Jiao

last: Yang

first: Shuanglan

last: Xu

first: Jie

last: Liu

first: Ting

first: Jihua

last: Zhang

first: Zeqin

last: Fan

first: Yunchun

first: Jorina

last: Basnet

first: Liqiong

first: Xiao

last: Li


title: Ehmt2 Inactivation in Pancreatic Epithelial Cells Shapes the Transcriptional Landscape and Inflammation Response of the Whole Pancreas [RNA-seq]

status: Public on Jun 06 2024

city: Milwaukee

first: Gwen

last: Lomberk

state: Wisconsin

address: 8701 W Watertown Plank Rd, Milwaukee, WI 53226

institute: Medical College of Wisconsin

summary: The Euchromatic Histone Methyl Transferase Protein 2 (EHMT2), also known as G9a, deposits transcriptionally repressive chromatin marks that play pivotal roles in the maturation and homeostasis of multiple organs.Recently, we have shown that Ehmt2 inactivation in the mouse pancreas alters growth and immune gene expression networks, antagonizing Kras-mediated pancreatic cancer initiation and promotion. Here, we elucidate the essential role of Ehmt2 in maintaining a transcriptional landscape that protects organs from inflammation. Comparative RNA-seq studies between normal postnatal and young adult pancreatic tissue from Ehmt2 conditional knockout animals (Ehmt2 fl/fl ) targeted to the exocrine pancreatic epithelial cells (Pdx1-Cre and P48 Cre/+ ), reveal alterations in gene expression networks in the whole organ related to injury-inflammationrepair, suggesting an increased predisposition to damage. Thus, we induced an inflammation repair response in the Ehmt2 fl/fl pancreas and used a data science-based approach to integrate RNA-seq-derived pathways and networks, deconvolution digital cytology, and spatial transcriptomics. We also analyzed the tissue response to damage at the morphological, biochemical, and molecular pathology levels. The Ehmt2 fl/fl pancreas displays an enhanced injury-inflammation-repair response, offering insights into fundamental molecular and cellular mechanisms involved in this process. More importantly, these data show that conditional Ehmt2 inactivation in exocrine cells reprograms the local environment to recruit mesenchymal and immunological cells needed to mount an increased inflammatory response. Mechanistically, this response is an enhanced injury-inflammationrepair reaction with a small contribution of specific Ehmt2-regulated transcripts. Thus, this new knowledge extends the mechanisms underlying the role of the Ehmt2- mediated pathway in suppressing pancreatic cancer initiation and modulating inflammatory pancreatic diseases.

overall_design: Pancreatic mRNA profiles of 22 mice with backgrounds of PDX1/P48 wild type (WT) and EHMT2 knockout (KO) mice treated with or without caerulein. Replicates vary from 2-4 samples per condition

first: Raul

last: Urrutia

first: Gareth

last: Pollin

first: Angela

last: Mathison


title: Single-cell transcriptomic reveals heterogeneous feature of myeloid-derived suppressor cells in newborns

city: Tianjin

first: Meng

last: Yao

address: 22 Qixiangtai Road

institute: Tianjin Medical University

summary: In order to gain deep insights into the molecular characteristics and heterogeneity of MDSCs in human newborns, low-density CD11b+HLA-DR-/low immature myeloid cells from the peripheral blood of term infants, preterm infants, and adults control were subjected to single-cell RNA sequencing (scRNA-seq).

overall_design: Peripheral blood samples were collected from full-term,  preterm and adult controls. Single-cell suspensions of peripheral blood mononuclear cells (PBMCs) were obtained by centrifuging human blood samples on a Ficoll gradient. The strategy for MDSCs was CD11b+HLA-DR-/lo. Live immature myeloid cell in RPMI1640 supplemented with 20% FBS were sorted in a BD FACSAria III cell sorter (BD Biosciences).


title: Ehmt2 Inactivation in Pancreatic Epithelial Cells Shapes the Transcriptional Landscape and Inflammation Response of the Whole Pancreas [Spatial transcriptomics]

summary: The Euchromatic Histone Methyl Transferase Protein 2 (EHMT2), also known as G9a, deposits transcriptionally repressive chromatin marks that play pivotal roles in the maturation and homeostasis of multiple organs.Recently, we have shown that Ehmt2 inactivation in the mouse pancreas alters growth and immune gene expression networks, antagonizing Kras-mediated pancreatic cancer initiation and promotion. Here, we elucidate the essential role of Ehmt2 in maintaining a transcriptional landscape that protects organs from inflammation. Comparative RNA-seq studies between normal postnatal and young adult pancreatic tissue from Ehmt2 conditional knockout animals (Ehmt2 fl/fl ) targeted to the exocrine pancreatic epithelial cells (Pdx1-Cre and P48 Cre/+ ), reveal alterations in gene expression networks in the whole organ related to injury-inflammationrepair, suggesting an increased predisposition to damage. Thus, we induced an inflammation repair response in the Ehmt2 fl/fl pancreas and used a data science-based approach to integrate RNA-seq-derived pathways and networks, deconvolution digital cytology, and spatial transcriptomics. We also analyzed the tissue response to damage at the morphological, biochemical, and molecular pathology levels. The Ehmt2 fl/fl pancreas displays an enhanced injury-inflammation-repair response, offering insights into fundamental molecular and cellular mechanisms involved in this process. More importantly, these data show that conditional Ehmt2 inactivation in exocrine cells reprograms the local environment to recruit mesenchymal and immunological cells needed to mount an increased inflammatory response. Mechanistically, this response is an enhanced injury-inflammationrepair reaction with a small contribution of specific Ehmt2-regulated transcripts. Thus, this new knowledge extends the mechanisms underlying the role of the Ehmt2-mediated pathway in suppressing pancreatic cancer initiation and modulating inflammatory pancreatic diseases.

overall_design: Spatial transcriptomics profiles of wild type (WT) and EHMT2 knockout (KO) mice treated with or without caerulein to induce acute pancreatitis


title: A combination treatment based on drug repurposing demonstrates mutation-agnostic efficacy in pre-clinical retinopathy models [scRNA-seq: Rd10]

city: Warsaw

first: Marcin

last: Tabaka

address: Kasprzaka 44/52

country: Poland

institute: International Centre for Translational Eye Research

summary: To determine the gene expression changes in the retina of 2-month-old Rd10 mice reared in darkness throughout their lifespan, we collected retina samples from Rd10 and WT (C57BL/6J mice) mice, generated single-cell suspensions, and performed scRNA-Seq (10X Genomics). One group of Rd10 mice was treated for 1 month via dietary administration of tamsulosin, metoprolol and bromocriptine drug cocktail.

overall_design: Vehicle- and TMB-treated Rd10 mice: One retina from four female Rd10 mice were pooled to prepare single-cell suspensions at a final concentration of 1,000 cells/µl. WT mice: One retina from two female and two male C57BL/6J mice were pooled to prepare single-cell suspensions at a final concentration of 1,000 cells/µl. For each group, freshly dissociated cells (~16,500) were loaded into a 10x Genomics Chromium Single Cell system using v3 chemistry following the manufacturer's instructions.

first: Henri

last: Leinonen

first: Elliot

middle: H

last: Choi


title: Prediction of broadly neutralizing antibodies [BD Rhapsody]

status: Public on Jun 04 2024

city: Epalinges

first: Mathilde

last: Foglierini-Perez

address: Chemin de Boveresses 155

institute: CHUV

summary: We generated the humoral immune repertoire of circulating memory B cells from healthy and HIV infected immune donors. These repertoires were used to predict specific HIV antibodies directed against gp120/gp41.

overall_design: Peripheral blood mononuclear cells (PBMC) were isolated from a pool of HIV infected donors. Single-cell BCR repertoire sequencing of CD19+ cells was performed using  BD Rhapsody Single-Cell Analysis System from BD Biosciences.

first: Pauline

last: Nortier

last: Foglierini

first: Philippe

last: Jacquet

first: Rachel

last: Schelling

first: Mathieu

last: Perreau

first: Laurent

last: Perez

first: Rahel

last: Winiger

first: Sijy

last: O'Dell

first: Davide

last: Demurtas

first: Maxmillian

last: Mpina

first: Omar

last: Lweno

first: Yannick

last: Muller

first: Constantinos

last: Petrovas

first: Claudia

last: Daubenberger

first: Nicole

last: Doria-Rose

first: Raphael

last: Gottardo


title: Inhibition of histone acetyltransferase attenuates 3D chromatin-mediated insulin signaling in pancreatic cancer (RNAseq dataset)

first: Yufan

last: Zhou

summary: Inhibition of histone acetyltransferase has been widely used to be effectively treat cancers in many studies. However, it’s not clear how the downstream signaling responds to the inhibitor in pancreatic cancer. Here we performed Hi-C experiments and RNA-seq to canonical and patient-derived pancreatic cancer cells with the treatment of small molecule inhibitor ICG-001 which has dual function to block both WNT signaling and histone acetyltransferase. This is RNA-seq dataset.

overall_design: Four kinds of cell lines including the pancreatic cancer cell line PANC1, and two newly established cell lines from patient-derived tumor xenograft (PATX) program PATC53 and PATC50, and human pancreatic epithelial cell line HPNE  were treated with ICG-001 at the concentration of 10 µM for 48 hours. Then RNA-seq experiments were performed for these cells.

first: Victor

last: Jin


title: Prediction of broadly neutralizing antibodies [10X]

first: Mathilde

last: Foglierini-Perez

overall_design: Peripheral blood mononuclear cells (PBMC) were isolated from one healthy donor (D1) ,  1 HIV infected donor (D2) and 2 pools of  HIV infected donor (G3 and G4). Single-cell BCR repertoire sequencing of CD19+ cells, for each donor/pool, was performed using  Single Cell V(D)J Reagent Kit v2 from 10X Genomics.

first: Pauline

last: Nortier

last: Foglierini


title: Construction of multilayered small intestine-like tissue by reproducing interstitial flow

city: Kyoto

first: Kazuo

last: Takayama

state: Kyoto

address: Shogoin Kawaharacho 53, Sakyo-ku

department: Center for iPS Cell Research and Application

institute: Kyoto University

summary: Recent advances have made modeling human small intestines in vitro possible, but it remains a challenge to recapitulate fully their structural and functional characteristics. We suspected interstitial flow within the intestine, powered by circulating blood plasma during embryonic organogenesis, to be a vital factor. We aimed to construct an in vivo-like multilayered small intestinal tissue by incorporating interstitial flow into the system and, in turn, developed the micro-small intestine systems by differentiating definitive endoderm and mesoderm cells from human pluripotent stem cells simultaneously on a microfluidic device capable of replicating interstitial flow. This approach enhanced cell maturation and led to the development of a three-dimensional small intestine-like tissue with villi-like epithelium and an aligned mesenchymal layer. Our micro-small intestine system not only overcomes the limitations of conventional intestine models but also offers a unique opportunity to gain insights into the detailed mechanisms underlying intestinal tissue development.

overall_design: Human micro-small intestine systems were dissociated by trypsin treatment and analyzed using scRNA-seq.


title: Lung injury-induced endothelial cell states persist in aging-associated non-resolving fibrosis

city: Boston

first: Single Cell

last: Sequencing Core

address: 72 E. Concord St

institute: BU Single Cell Sequencing Core

summary: The capacity of lung tissue to heal without scarring deteriorates with aging. The pulmonary vasculature has emerged as a central regulator of lung repair, and aging-associated endothelial cell dysfunction has been associated with defective lung response to injury and sustained fibrosis. To shed light into aging-associated cellular and transcriptional responses of lung endothelial cells during lung fibrogenesis, we carried out a single cell RNA-seq analysis of bleomycin-treated young (2 months) and aged (72 months) lungs during the early phase of fibrosis resolution (30 days post bleomycin). This analysis revealed that lung injury was associated with the appearance of distinct populations of endothelial cells that exhibit “activated” transcriptional states, originating from virtually all vascular beds. Activated endothelial cells deriving from venous and capillary beds were the most represented in aged compared to young lungs. Longitudinal single-cell analysis together with lineage tracing revealed that activated endothelial cells appeared transiently during the peak of collagen production in young lungs and disappeared during the resolution phase. Conversely, activated endothelial cell states persisted in aged lungs around fibrotic areas, indicating a failure of the aged vascular tissue to return to quiescence. We provide evidence that an axis between YAP and TrkB signaling acts as a node that directs injury-induced capillary endothelial cell activation in vivo and lung capillary morphogenesis ex vivo. Together, these data provide insights into the aging-related dynamics of lung endothelial cells in response to injury.

overall_design: Male young (2 months old) and aged (18 months old) C57BL/6J mice were administered with Bleomycin (1 U/kg) intratracheally. Thirty days after bleomycin challenge, whole lungs were isolated and digested using a mixture of collagenase and dispase to create a single-cell suspension used for single-cell sequencing.

first: Giovanni

last: Ligresti

first: Xaralabos

last: Varelas

first: Ahmed

last: Raslan


title: Effects of mcFA on epigentic changes in A375 melanoma.  [ChIP-seq]

status: Public on Jun 01 2024

city: New York

first: Ting-Hsiang

last: Huang

state: New York

institute: Memorial Sloan Ketteting Cancer Center

summary: To study the epigenome profile of melanoma cells upon mcFAs administration, we stimulated A375 cells using octanoate for 48-hrs followed by H3K27ac ChIP-seq analysis with 2 biological replicates.

overall_design: Differential gene expression profiling to identify upregulated targets and gene signatures through GSEA analysis.

first: Richard

last: Koche


title: mRNA profiling in dss1(I) and dss1(V) mutant lines of Arabidopsis thaliana under oxidative stress (hydrogen peroxide)

status: Public on Jun 03 2024

city: Belgarde

first: Ivana

last: Nikolic

address: Vojvode Stepe 444a

country: Serbia

institute: Institute of Molecular Genetics and Genetic Engineering (IMGGE), University of Belgrade

summary: The Arabidopsis genome contains two highly homologous DSS1 genes, AtDSS1(I) and AtDSS1(V). This study was designed to identify the functional differences between AtDSS1s, focusing on their potential roles in oxidative stress. We generated single dss1(I) and dss1(V) mutant lines of both Arabidopsis DSS1 genes using CRISPR/Cas9 technology. The sensitivity of homozygous mutant lines with large indels (dss1(I)del25 and dss1(V)ins18) were analyzed to oxidative stress. Plant seedlings were exposed to oxidative stress induced by 10 mM hydrogen peroxide. Transcriptome analysis revealed that the absence of either of DSS1 genes caused alterations in the expression of different genes under stress conditions.

overall_design: In order to carry out RNA sequencing of three different biological samples (wild-type, dss1(I), and dss1(V) (mutants under oxidative stress), 400 ng of the isolated RNA per sample were sent to Novogene Bioinformatics Technology Co. Ltd (Cambridge CB4 0FW, United Kingdom) at room temperature stabilized by DNA/RNA shield buffer (Zymo Research, Irvine, USA). RNA material of each sample was collected from three biologically independent experiments.

first: Gordana

last: Timotijevic


title: RNA sequencing analysis of HG/PA treated podocytes.

city: Wenzhou

first: guang

last: liang

state: Wenzhou

address: Wenzhou medical university of  higher education park  chashan town

department: School of Pharmaceutical Sciences

institute: Wenzhou Medical University

summary: Recent studies have shown the crucial role of podocyte injury in the development of diabetic nephropathy. Ubiquitination/deubiquitination is a post-translational modification of proteins, which is widely involved in the occurrence and development of diseases. The purpose of this study was to investigate the role of OTUD5, a deubiquitination enzyme, in podocyte injury and reveal its regulatory mechanism in the pathogenesis of diabetic nephropathy. RNA-seq analysis indicated a significantly increased expression of OTUD5 in HG/PA-stimulated podocytes.

overall_design: we performed RNA sequencing analysis on the podocytes (MPC5) of three control grous and three HG/PA treament grous.

first: Ying

last: Zhao

first: Shijie

last: Fan

first: Hong

last: Zhu

first: Guang

last: Liang


title: Rbpms2 promotes female fate upstream of the nutrient sensing Gator2 complex component, Mios

first: Florence

last: Marlow

address: Madison Ave

department: CDRB

institute: Icahn  School of Medicine Mount Sinai

summary: Reproductive success relies on proper establishment and maintenance of biological sex. In many animals, including mammals, the primary gonad is initially ovary in character. We previously showed the RNA binding protein (RNAbp), Rbpms2, is required for ovary fate in zebrafish. Here, we identified Rbpms2 targets in oocytes(Rbpms2-bound oocyte RNAs; rboRNAs). We identify Rbpms2 as a translational regulator ofrboRNAs, which include testis factors and ribosome biogenesis factors. Further, genetic analyses indicate that Rbpms2 promotes nucleolar amplification via the mTorc1 signaling pathway, specifically through the mTorc1-activating Gap activity towards Rags 2 (Gator2) component, Missing oocyte (Mios). Cumulatively, our findings indicate that early gonocytes are in a dual poised, bipotential state in which Rbpms2 acts as a binary fate-switch. Specifically, Rbpms2 represses testis factors and promotes oocyte factors to promote oocyte progression through an essential Gator2-mediated checkpoint, thereby integrating regulation of sexual differentiation factors and nutritional availability pathways in zebrafish oogenesis.

overall_design:
To determine the RNA targets of Rbpms2, we generated wildtype female zebrafish expressing Rbpms2-mApple or mApple alone fusion proteins exclusively in the germline. Immunoprecipitation was performed in 2 adult female ovaries per transgene. Crosslinked and uncrosslinked samples for Rbpms2-mApple expressing fish and crosslined and uncrosslinked samples for mApple expressing fish were sequenced. RNAs found in the Rbpms2-mApple crosslinked and the mApple crosslinked and uncrosslinked datasets that were also present in the Rbpms2-mApple uncrosslinked dataset were excluded. RNAs present only in the uncrosslinked datasets were counted as RNA targets of Rbpms2.
To characterize the transcriptional differences of rbpms2 mutants vs wildtype fish prior to sex determination (21 days post fertilization), we performed bulk RNA sequencing on n=3 21 dpf wildtype and n=3 rbpms2 mutant fish. DESeq was then performed for Differential Gene Expression Analysis.

first: Miranda

last: Wilson

first: Shannon

last: Romano

first: Nitya

last: Khatri

first: Devora

last: Aharon

first: Yulong

last: Liu

first: Odelya

last: Kaufman

first: Bruce

last: Draper


title: Effect of mcFAs on transcription reprogramming in melanoma cells

first: Ting-Hsiang

last: Huang

summary: To study the transcriptomics profile of melanoma cells upon mcFAs administration, we stimulated A375 cells using octanoate for 48-hrs followed by RNA-seq analysis with 2 biological replicates.


title: Real-time quantitative PCR analysis of mouse peritoneal macrophages

status: Public on May 31 2024

city: Manhasset

first: Atsushi

last: Murao

address: 350 Community Dr

institute: The Feinstein Institutes for Medical Research

summary:
Background: The disruption of the circadian clock is associated with inflammatory and immunological disorders. BMAL2, a critical circadian protein, forms a dimer with CLOCK, activating transcription. Extracellular cold-inducible RNA-binding protein (eCIRP), released during sepsis, can induce macrophage endotoxin tolerance. We hypothesized that eCIRP modulates BMAL2 expression and promotes macrophage endotoxin tolerance through triggering receptor expressed on myeloid cells-1 (TREM-1).
Methods: C57BL/6 wild-type (WT) male mice were subjected to sepsis by cecal ligation and puncture (CLP). Serum was collected 20 hours post-CLP to assess eCIRP levels. Peritoneal macrophages (PerM) and immortalized bone marrow-derived macrophages (iBMDMs) were seeded into plates and treated with recombinant mouse (rm) CIRP (eCIRP) at various doses. Induction of BMAL2 activation in iBMDM was performed by transfection of BMAL2 CRISPR activation plasmid. Circadian gene expression profiles in eCIRP-treated macrophages were determined by PCR array and confirmed by qPCR. Cytokine levels in the culture supernatants were assessed by ELISA. The interaction of BMAL2 in the PD-L1 promoter was determined by computational modeling and confirmed by the BIAcore assay.
Results: PCR array screening of circadian clock genes in peritoneal macrophages treated with eCIRP revealed the elevated expression of BMAL2, CRY1, and PER2. eCIRP serum levels were increased in septic mice. In eCIRP-treated macrophages, TREM-1 deficiency prevented the upregulation of these circadian genes. Macrophages pre-treated with eCIRP exhibited reduced TNFá and IL-6 release upon LPS challenge, indicating macrophage endotoxin tolerance. In addition, eCIRP increased the expression of PD-L1, IL-10, and STAT3, markers of immune tolerance. Interestingly, TREM-1 deficiency reversed eCIRP-induced macrophage endotoxin tolerance. In macrophages, inducible BMAL2 expression correlated with increased PD-L1 expression. In septic human patients, blood monocytes exhibited increased expression of BMAL2 and PD-L1 in comparison to healthy subjects. Computational modeling and BIAcore assay identified a putative binding region of BMAL2 in the PD-L1 promoter, suggesting BMAL2 positively regulates PD-L1 expression in macrophages.
Conclusion: eCIRP upregulates BMAL2 expression via TREM-1, leading to macrophage endotoxin tolerance in sepsis. Targeting eCIRP to maintain circadian rhythm may correct endotoxin tolerance and enhance host resistance to bacterial infection.

overall_design:
Peritoneal macrophages (PerM) were isolated from WT C57BL/6 male mice and TREM-1-/- (triggering receptor expressed on myeloid cells-1) male mice.  After cultured overnight, these cells were treated with PBS or rmCIRP (recombinant mouse cold-inducible RNA-binding protein) at concentration 1 μg/ml for 24 h.  We used Qiagen mouse circadian rhythms RT2 Profiler PCR Array panel to evaluate the gene expression.
qPCR gene expression profiling. Equal amount total RNA from each sample was used for gene expression analysis.

first: Mian

last: Zhou


title: Simulated microgravity recapitulates early molecular events and sex differences of knee osteoarthritis

status: Public on May 30 2024

city: Edmonton

first: Zhiyao

last: Ma

state: Alberta

institute: University of Alberta

summary: This study aims to establish an osteoarthritis (OA)-like phenotype in human meniscus models under SMG conditions and assess whether sex-dependent expression patterns indicative of knee OA (KOA) are present under short-term SMG. Cell cultures were maintained on human matrix coated surface to maintain original phenotype.

overall_design: Primary fibrochondrocytes obtained from six donors (three male and three female) without KOA were cultured on human matrix coated surface and used to engineer human meniscus constructs. The constructs were cultured under normal gravity and simulated microgravity for seven days, and samples were collected on days 0, 1, 3, and 7. The expression levels of selected markers and whole transcriptome profile were assessed using RT-qPCR and RNA sequencing.

first: David

last: Li

first: Michelle

last: Lan

first: Adam

last: Bulenyi

first: Margaret

last: Vyhlidal

first: Melanie

last: Kunze

first: Adetola

last: Adesida


title: A DGCR8/FLII-dominated on-off switch for immediate-early genes governs embryo implantation in mouse and human

city: Beijing

first: Xuehui

last: Lv

address: No.5 Yiheyuan Road, Haidian district, Beijing, 100871, China

institute: Peking University

summary: As an essential checkpoint for successful pregnancy, mammalian embryo implantation initiates fetal-maternal communication. However, the underlying transcriptional regulation governing such a fast transition is still unknown. Here, we identify a DGCR8/FLII-dominated on-off switch for immediate-early genes (IEGs) governing pluripotency transition and morphogenesis of epiblasts upon embryo implantation. In mouse naïve embryonic stem cells (mESCs), we find the Microprocessor component DGCR8, but not DROSHA, can recognize mRNA stem-loop structures and further interact with and occupy transcriptional activator FLII to directly suppress transcription of non-miRNA target genes. Interestingly, when mESCs exit from naïve pluripotency, ERK signaling is quickly activated to induce FLII phosphorylation and disrupt DGCR8/FLII interaction. Phosphorylated FLII then binds to AP1, a typical IEG, to mediate the transcriptional activation of cell migration-related genes to establish poised pluripotency. Re-occupation of FLII by DGCR8 drives poised ESCs into formative pluripotency. Disruption of the DGCR8/FLII-mediated transcriptional activation inhibits the naïve-poised-formative ESC transition and the corresponding embryonic morphogenesis during implanting period, which is conserved in mouse and human.

overall_design: For naïve hESC differentiation, 5×105 trypsinized single naïve cells were seeded on a MEF feeder layer in human ESC medium  [DMEM/F12, 15% FBS, 5% KnockOut Serum Replacement, 2 mM L-glutamine, 1% NEAA, 0.1 mM β-mercaptoethanol and 8 ng/ml FGF2] supplemented with 10 µM Y-27632. ESCs were collected at different time points (0 h, 36 h, 77 h and 113 h) for single-cell RNA-seq.

last: Lyu


title: Lung injury-induced endothelial cell states persist in aging-associated non-resolving fibrosis II

first: Single Cell

last: Sequencing Core

overall_design: Lineage-tracing experiments were conducted in Aplnr-Cre-ER(T):Rosa26-mdtTomato/mGFP reporter mice. Both male and female mice at 2 months of age were utilized for this study. To permanently label capillary endothelial cells (ECs), mice were administered tamoxifen (5 injections of 75 mg tamoxifen/kg body weight, daily). Following labeling, mice were subjected to lung injury induced by intratracheal administration of bleomycin (1 U/kg). For the experimental groups, lung tissues were collected at various time points: uninjured sham mice (n=3), and mice harvested at 14 days (n=2) and 35 days (n=2) after bleomycin challenge. Lung tissues were dissociated into a single-cell suspension for further analysis

first: Giovanni

last: Ligresti

first: Xaralabos

last: Varelas

first: Ahmed

last: Raslan


title: Tracking-seq reveals the heterogeneity of off-target effects in CRISPR/Cas9-mediated genome editing

first: Xun

address: Haidian District

department: School of Medicine

institute: Tsinghua University

summary: The continued development of novel genome editors calls for a universal method to analyze their off-target effects. Here we describe a versatile method, called Tracking-seq, for in situ identification of off-target effects that is broadly applicable to common genome-editing tools, including Cas9, base editors and prime editors. Through tracking replication protein A (RPA)-bound single-stranded DNA followed by strand-specific library construction, Tracking-seq requires a low cell input and is suitable for in vitro, ex vivo and in vivo genome editing, providing a sensitive and practical genome-wide approach for off-target detection in various scenarios. We show, using the same guide RNA, that Tracking-seq detects heterogeneity in off-target effects between different editor modalities and between different cell types, underscoring the necessity of direct measurement in the original system.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Tracking-seq (Tracking RPA-bound ssDNA by sequencing) for various genome-editing tools and cell types to detect off-target effects.


title: Gene expression of pdgfrb+ cells in the intact and injured spinal cord.

status: Public on Jun 07 2024

first: Xianming

last: Wu

state: Chaoyang District

address: Unit 2, No.1 West Beichen Road

institute: Institute of Genetics and Developmental Biology, Chinese Academy of Sciences

summary: Spinal cord injury (SCI) leads to fibrotic scar formation at the lesion site, which finally affects axon regeneration and motor functional recovery. Myofibroblasts have been regarded as the main cell types that filled in the fibrotic scar, however, the cell source of myofibroblasts in transection and crush SCI model remain to be elusive. Here we used lineage tracing or single cell transcription sequencing to investigate the cell origin of fibrotic scar. We found fibrotic scars were filled from PDGFRβ+ daughter cells in spinal cord in crush SCI or transection SCI. The parenchyma perivascular-derived and meninges-derived PDGFRβ+ fibroblasts, but not PDGFRβ+ pericytes, proliferated and contributed to fibrotic cells in the lesion core. The percentage of meninges-derived fibroblasts specifically was higher than parenchyma perivascular-derived fibroblasts in transection model, which might contribute to the more fibrotic scar in transection model than crush model. These findings may provide theoretical support for the treatment of spinal cord injury.

overall_design: Pdgfrb+ cells were isolated from Pdgfrb-CreER::R26-TdT mice by Fluorescence-activated cell sorting (FACS) depending on tdtomato signal.

first: Xiaoyu

last: Xue

first: Jianwu

last: Dai


title: Prediction of broadly neutralizing antibodies

first: Mathilde

last: Foglierini-Perez

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

overall_design: Refer to individual Series

first: Pauline

last: Nortier

last: Foglierini

first: Philippe

last: Jacquet

first: Rachel

last: Schelling

first: Matthieu

last: Perreau

first: Rahel

last: Winiger

first: Sijy

last: O'Dell

first: Davide

last: Demurtas

first: Maxmillian

last: Mpina

first: Omar

last: Lweno

first: Yannick

last: Muller

first: Constantinos

last: Petrovas

first: Claudia

last: Daubenberger

first: Nicole

last: Doria-Rose

first: Raphael

last: Gottardo

first: Laurent

last: Perez


title: Effect of VDR knockdown on the gene expression of K562 cells after 10h

city: Jinan City

first: Yan

last: Xu

address: No. 44 Wenhua West Road

institute: Shandong University

summary: To investigate the effect of VDR in the regulation of K562 cells. We then performed gene expression profiling analysis using data obtained from RNA-seq of 2 different cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for K562 cells from shNC and shVDR.

first: Baobing

last: Zhao


title: Standardized generation of human iPSC-derived hematopoietic organoids and macrophages utilizing a benchtop bioreactor platform under fully defined conditions

status: Public on May 29 2024

city: Hannover

first: Svenja

last: Gaedcke

address: Carl-Neuberg-Str. 1

country: Germany

institute: Hannover Medical School

summary: There is a significant demand for intermediate-scale bioreactors in academic and industrial institutions to produce cells for various applications in drug screening and/or cell therapy. However, the application of these bioreactors in cultivating hiPSC-derived immune cells and other blood cells is noticeably lacking. To address this gap, we have developed a xeno-free and chemically defined intermediate-scale bioreactor platform, which allows for the generation of standardized human iPSC-derived hematopoietic organoids and subsequent continuous production of macrophages (iPSC-Mac).

overall_design: Human iPSC-Mac derived from three different iPSC lines were harvested as described in the study. Viable cells were purified by fluorescence activated cell sorting (FACS) on basis of scatter properties and exclusion of 4′,6-diamidino-2-phenylindole (DAPI) positive events, which has been added immediately before sorting (0.1 µg/ml final concentration).


title: Prediction of broadly neutralizing antibodies [Singleron]

first: Mathilde

last: Foglierini-Perez

summary: We generated the humoral immune repertoire of circulating memory B cells from healthy and HIV infected immune donors. These repertoires were used to predict specific HIV antibodies directed against gp120/gp41.

overall_design: Peripheral blood mononuclear cells (PBMC) were isolated from a pool of HIV infected donors. Single-cell BCR repertoire sequencing of CD19+ cells was performed using  sCircle® Single Cell Full Length Immunoreceptor Library Kit from Singleron technology.

first: Pauline

last: Nortier

last: Foglierini

first: Philippe

last: Jacquet

first: Mathieu


title: Validation of sgRNAs against acaa2 and tlr4 in zebrafish.

first: Ting-Hsiang

last: Huang

summary: To study the knockout efficiency of Acaa2 and TLR4 in vivo.

overall_design: To identify CRISPR variants on Acaa2 and TLR4 genetic locus.

first: Huang

last: Ting-Hsiang

first: Ma

last: YiLun


title: ZBP1-mediated apoptosis and inflammation exacerbate steatotic liver ischemia/reperfusion injury

first: Jinyang

last: Gu

address: 1277 Jiefang avenue

institute: Union hospital, Tongji medical college, Huazhong university of science and technology

summary: Abstract Background & Aims: In liver transplantation, steatotic donor livers are rapidly increasing but are more susceptible to ischemia-reperfusion (I/R) injury. This study aimed to investigate the underlying mechanisms and identify therapeutic targets.     Methods: Cell death markers were determined in donor livers and animal models. Casp8f/f;Alb-Cre, Ripk1D138N/D138N, Tnf-/-, Ripk3-/-, Trif-/-, Zbp1-/- mice were fed high fat diet or choline-deficient high fat diet to induce steatotic livers and were then subjected to I/R injury to investigate the mechanisms of cell death and inflammation. Primary mouse or human hepatocytes were isolated and subjected to hypoxia-reoxygenation challenge to further elucidate the regulation mechanisms.     Results: Apoptosis- and inflammation-induced injury was exacerbated in I/R process of steatotic livers, with inflammation-induced injury playing a more predominant role. In both normal and steatotic livers, caspase-8 ablation mitigated I/R injury by reducing apoptosis but not inflammation while RIPK1 kinase inhibition more effectively protected against I/R injury by alleviating both apoptosis and inflammation. Z-DNA binding protein 1 (ZBP1) but not TNF-α deficiency inhibited RIPK1 activation and protected against I/R injury in steatotic livers but not normal livers. In steatotic livers, overmuch palmitic acid triggered ZBP1 transcription through activating JNK pathway. During liver transplantation, excessive reactive oxygen species were generated during I/R injury and triggered ZBP1 oligomerization, which led to the kinase activation of RIPK1 and the subsequent aggravation of apoptosis- and inflammation-induced injury.    Conclusions: ZBP1-mediated apoptosis and inflammation exacerbate steatotic liver I/R injury, which could be leveraged to protect steatotic donor livers in transplantation.

overall_design: The RNA-seq data includes the following two sections. 1) Zbp1+/+ and Zbp1-/- mice were fed high fat diet for 4 months and subjected to 1 h ischemia/6 h reperfusion operation. The livers were harvested and RNA were extracted for RNA-seq. 2) Wildtype mice were injected AAV8 to overexpress Zbp1 in the livers (Vector was the nagative control). 1 month later, 10 mg/kg Nec-1s was injected peritoneally to the mice. After 1 h, the mice were subjected to 1 h ischemia/6 h reperfusion operation. The livers were harvested and RNA was extracted for RNA-seq.

first: Ran

last: Liu


title: Effects of mcFA on epigentic changes in A375 melanoma [ATAC-seq]

summary: To study the epigenome profile of melanoma cells upon mcFAs administration, we stimulated A375 cells using octanoate for 48-hrs followed by ATAC-seq analysis with 2 biological replicates.

first: Richard

last: Koche


title: Construction of multilayered small intestine-like tissue by reproducing interstitial flow

first: Kazuo

last: Takayama

summary: Recent advances have made modeling human small intestines in vitro possible, but it remains a challenge to recapitulate fully their structural and functional characteristics. We suspected interstitial flow within the intestine, powered by circulating blood plasma during embryonic organogenesis, to be a vital factor. We aimed to construct an in vivo-like multilayered small intestinal tissue by incorporating interstitial flow into the system and, in turn, developed the micro-small intestine systems by differentiating definitive endoderm and mesoderm cells from human pluripotent stem cells simultaneously on a microfluidic device capable of replicating interstitial flow. This approach enhanced cell maturation and led to the development of a three-dimensional small intestine-like tissue with villi-like epithelium and an aligned mesenchymal layer. Our micro-small intestine system not only overcomes the limitations of conventional intestine models but also offers a unique opportunity to gain insights into the detailed mechanisms underlying intestinal tissue development.

overall_design: The micro-small intestine systems were mechanically recovered from the microfluidic devices, and then total RNA was collected and RNA-seq was performed.


title: The transcriptional response of Trichomonas vaginalis to Trichomonas-derived extracellular vehicles

status: Public on May 28 2024

city: Los Angeles

first: Joshua

middle: Andrew

last: Kochanowsky

state: California

address: 619 Charles E Young Dr E

department: Microbiology, Immunology and Molecular Genetics

institute: University of California Los Angeles

summary: Trichomonas vaginalis, a common sexually transmitted parasite that colonizes the human urogenital tract, secretes extracellular vesicles (TvEVs) that are taken up by human cells and are speculated to be taken up by parasites as well. While the crosstalk between TvEVs and human cells has led to insight into host:parasite interactions, the role of TvEVs in infection have largely been one-sided, with little known about the effect of TvEV uptake by T. vaginalis. Approximately 11% of infections are found to be co-infections of multiple T. vaginalis strains. Clinical isolates often differ in their adherence to and cytolysis of host cells, underscoring the importance of understanding the effects of TvEV uptake within the parasite population. To address this question our lab observed the effects of EV uptake by T. vaginalis on parasite gene expression. Using RNA-seq, we showed that TvEVs upregulate expression of predicted parasite membrane proteins and identified a novel adherence factor, heteropolysaccharide binding protein (HPB2).

overall_design: Six biological replicates were analyzed for each of 2 conditions (Mock, TvEV)

first: Patricia

middle: J

last: Johnson