title: Gene expression data after treated with TCI04 in MDA-MB-231 cells

city: Tianjin

first: Ping

last: Zhou

state: Tianjin

address: No1 Huanhuxi Load

institute: Tianjin Medical University Cancer Institute and Hospotal

summary:
TCI04 inhibits cell invasion and synergistically enhanced Paclitaxel activity in MDA-MB-231 cells.
We used microarrays to detail the global programme of gene expression in MDA-MB-231 cells after treated with TCI04 and identified distinct classes of up- or down-regulated genes during this process.

overall_design: MDA-MB-231 cells were selected for RNA extraction and hybridization on Affymetrix microarrays. 50 μM of TCI04 was used for treating MDA-MB-231 cells and PBS was used as controls.

first: Peng

last: Chen


title: Persistent epigenome anomalies in induced pluripotent stem cells from late-onset sporadic Alzheimer’s disease cases

status: Public on Jul 30 2024

city: Montreal

first: Gilbert

last: Bernier

state: Quebec

address: 5690 rosemont boulevard

country: Canada

institute: HMR

type: Expression profiling by high throughput sequencing

type: Methylation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Effect of low-intensity pulsed ultrasound modulates disease progression in the SOD1G93A mouse model of amyotrophic lateral sclerosis

city: Shanghai

first: zihao

last: Liu

address: Yishan Road 600

country: China

institute: Shanghai jiaotong university

summary: The LIPUS treatment in the oxidation-reduction process and inflammatory response of SODG93A mouse.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for SODG93A mouse with and without LIPUS treatment.

first: Xiaojie

last: Zhang

first: Yuanyi

last: Zheng


title: Persistent epigenome anomalies in induced pluripotent stem cells from late-onset sporadic Alzheimer’s disease cases [scRNA-seq]

summary: Reprogramming of adult somatic cells into induced pluripotent stem cells (iPSCs) resets the aging clock and is thought to erase other epigenomic marks. Here we show that iPSCs from late-onset sporadic Alzheimer’s disease (AD) cases retain epigenomic anomalies that supersede developmental defects, genomic instability, and neurodegeneration. When compared to iPSCs from elderly controls, AD iPSCs display reduced BMI1 and KDM5A expression, a more relax heterochromatin, and an altered DNA methylome. AD neuroepithelial cells show lesser efficient neural induction and forebrain specification, together with perturbed WNT signaling. They also present a unique genomic instability phenotype characterized by replication stress and DNA damage at the nuclear envelope-associated heterochromatin. BMI1 knockdown in control neuroepithelial cells phenocopied the AD-related pathologies. Long-term AD neuronal cultures show a dedifferentiation and loss-of-cell identity phenotype resembling epigenome erosion. BMI1 overexpression in AD neurons mitigates amyloid accumulation, tau pathology, heterochromatin fragmentation and G4 DNA induction. These findings implicate persistent epigenomic anomalies or uncharacterized genetic alterations working in trans on the epigenome in AD iPSCs, which could have broader implications in our understanding of the disease origin and pathophysiological mechanisms.

overall_design: neurones differentiated from CTL and AD iPSC were sequenced in order to study the composition of the culture.


title: Persistent epigenome anomalies in induced pluripotent stem cells from late-onset sporadic Alzheimer’s disease cases [RNA-seq]

overall_design: CTL and AD samples were compared at multiple timepoint from iPSC to fully differentiated neurons


title: RNA-binding protein A1CF modulates plasma triglyceride levels  through posttranscriptional regulation of stress-induced VLDL secretion

status: Public on Jul 31 2024

city: La Jolla

first: Gene

last: Yeo

state: CA

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

country: USA

institute: UCSD

summary: A recent human exome-chip study on plasma lipids identified a missense mutation in the 3 A1CF (APOBEC1 complementation factor) gene that associates with elevated TG levels, but how A1CF, 4 an RNA binding protein, influences plasma TG is unknown.

first: Jennie

last: Lin

first: Donna

middle: M

last: Conlon

first: Xiao

last: Wang

first: Eric

middle: V

last: Nostrand

first: YoSon

last: Park

first: Alanna

last: Strong

first: Behram

last: Rdmanesh

first: Sekar

last: Kathiresan

first: Yoseph

last: Barash

first: Daniel

middle: J

last: Rader

first: Kiran

last: Musunuru


title: Brain regional and cell type-specific chromatin changes among sporadic, GBA1 variant, and APOE E4 Parkinson’s Disease

city: Stanford

first: Eloise

last: Berson

address: 291 Campus Drive

institute: Stanford University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Parkinson’s disease (PD) involves myriad genetic, behavioral, and environmental factors that make the identification of effective therapeutic targets challenging. We leverage a novel, validated AI approach to identify cell type- and brain region-specific epigenomic features in 6 brain regions from 35 individuals with varying genetic risk for PD as well as clinical and pathological controls (CTRL, n=15). We observed that astrocytes of substantia nigra (SUNI) are the major regional and cellular site of differentially accessible regions (DARs) between sporadic PD (SPOR_PD+, n=15) and GBA1 mutation-carriers with PD (GBA1_PD+, n=16); Seven of these SUNI DARs not only fully separated SPOR_PD+ from GBA1_PD+ cases but could also fully separate LRRK2 mutation carriers with PD from these other two forms of PD (n=3). Molecular estimation of PD progression, which correlated with the progression of neuropathologic stage, reveals that chromatin differences between SPOR_PD+ and GBA1_PD+ increase along the predicted disease progression, with broad cell type significant differences in epigenomic profiles at predicted later stages of the disease. Having APOE 4 (n=14 cases) was shown to affect various cell types mainly in the superior and middle temporal gyrus and substantial nigra. Using a multicellular co-accessibility network analysis, we identify neuron-specific epigenomic modules that correlate with the presence of at least one APOE 4 and the increase of PD pathological and clinical phenotypes. Our results suggest that APOE 4 could contribute to PD pathogenesis through chromatin change in neural cells related to synaptic and neuronal projection processes. This study expands our understanding of genetic risk effects in Parkinson's disease and provides a blueprint framework for investigating the cellular basis of genetic risk effects in disease.

overall_design: Bulk ATAC-seq

first: M

middle: R

last: Corces


first: Jian

middle: ming

last: Yang

address: No22.Qixiangtai Rd.,Heping Dist,Tianjin P.R. China

institute: Tianjin Medical University

summary: PIM1 is constitutively active and involved in various cellular processes, including cell survival, proliferation, and differentiation by phosphorylating a wide range of substrates. We investigated whether PIM1 is involved in the pathogenesis of ulcerative colitis (UC).We performed RNA sequencing analysis in Caco2 cells infected with vector or PIM1 to study the molecular mechanisms through which PIM1 regulates goblet cell numbers.

overall_design: Gene expression profiles of Caco2 cells infected with vector or PIM1 were generated by deep sequencing, using an illumina Novaseq™ 6000.To identify DEGs (differential expression genes) between two different samples, the expression level of each transcript was calculated according to the FPKM method.

first: Quan

first: Jianming

first: Yawen

last: Xiao


title: RNA sequencing analysis of IECs from WT and PIM1+/- mice

summary: PIM1 is constitutively active and involved in various cellular processes, including cell survival, proliferation, and differentiation by phosphorylating a wide range of substrates. We investigated whether PIM1 is involved in the pathogenesis of ulcerative colitis (UC).We performed RNA sequencing analysis in intestinal epithelial cells (IECs) from PIM1-deficient mice and WT mice to study the molecular mechanisms through which PIM1 regulates goblet cell numbers.

overall_design: Gene expression profiles of IECs from WT and PIM1+/- mice were generated by deep sequencing, using Illumina NovaSeq 6000.To identify DEGs (differential expression genes) between two different samples, the expression level of each transcript was calculated according to the transcripts per million reads (TPM)method. RSEM was used to quantify gene abundances.


title: Cell culture differentiation and proliferation conditions influence the in vitro regeneration of the human airway epithelium

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

summary: The human airway mucociliary epithelium can be recapitulatedin vitro using primary cells cultured in an Air-Liquid Interface (ALI), a reliable surrogate to perform pathophysiological studies. As tremendous variations exist between media used for ALI-cultured human airway epithelial cells, our study aimed to evaluate at a single-cell level the impact of several media (e.g. BEGMTM, PneumaCultTM, “Half&Half” and “Clancy”) on cell type distribution. Our work revealed the impact of these media on cell composition, gene expression profile, cell signaling or epithelial shape. We also established that proliferation in PneumaCultTM-Ex Plus favored secretory cells fate, showing the key influence of proliferation media on late differentiation epithelial characteristics. Altogether, our data offer a comprehensive repertoire for evaluating the effects of culture conditions on airway epithelial differentiation and will help to choose the most relevant medium according to the phenomenon to be investigated such as cilia or mucus biology or viral infection. We detail useful parameters that should be explored to document airway epithelial cell fate and shaping.

overall_design:
The study here generated single-cell dataset of human airways after in vitro regeneration at the Air-Liquid Interface. Samples from 2 donors were used for the establishment of Human Bronchial Epithelial Cell cultures (HBECs) and were analyzed during proliferation, at the onset of differentiation (ALI0) and after full differentiation (ALI28), in 4 distinct culture media. Single-cell RNAseq was performed with 10x v2 using hashtag antibodies for multiplexing, and sequenced on a NextSeq 500. Samples from 3 additional donors were used for the establishment of Human Nasal Epithelial Cell cultures (HNECs) and were analyzed during proliferation in three distinct culture media. Single-cell RNAseq was performed with 10x v2 without multiplexing, and sequenced on a NextSeq 2000. Raw data has been submitted to EGA web portal under accession number EGAS00001007572 (https://ega-archive.org/studies/EGAS00001007572).
Note from submitter: we uploaded the raw data at the European Genome-Phenome Archive (EGA) as required by our consortium policy (Human Cell Atlas) under accession number : EGAS00001007572.

first: Elisa

last: Redman

first: Morgane

last: Fierville

first: Amélie

last: Cavard

first: Marie-Jeanne

last: Arguel

first: Sandra

last: Ruiz Garcia

first: Cédric

last: Girard

first: Pascal

last: Barbry

first: Brice

last: Marcet

first: Laure-Emmanuelle

last: Zaragosi


title: Spatially resolving the tumour microenvironment of head and neck cancer to discover novel predictive biomarkers of immunotherapy response

city: brisbane

first: Arutha

last: Kulasinghe

address: 37 kent st

country: Australia

institute: University of Queensland

summary: DSP RNA profling using the whole transcriptome atlas kit was performed on a cohort of head and neck cancer tumour samples from patients who received immunotherapy.

overall_design:
Differential expression and geneset analysis was performed on the tumour and stroma regions of a tumour microarray to identify differences between responders (5 cores, n=2) and non-responders (8 cores, n=4).

***************************************************************
Submitter declares that FASTQ raw data files are not available.
***************************************************************

first: Naomi

last: Berrell


title: Merkel cell polyomavirus pan-T antigen knockdown reduces cancer cell stemness and promotes neural differentiation independent of RB1

city: Heidelberg

first: Jürgen

last: Becker

address: Im Neuenheimer Feld 280

country: Germany

institute: Deutsches Krebsforschungszentrum

summary: Merkel cell carcinoma (MCC) is a highly aggressive skin cancer associated with integration of Merkel cell polyomavirus (MCPyV). MCPyV-encoded T-antigens (TAs) are pivotal for sustaining MCC’s oncogenic phenotype, i.e., repression of TAs results in reactivation of the RB pathway and subsequent cell cycle arrest. However, the MCC cell line LoKe, characterized by a homozygous loss of the RB1 gene, exhibits uninterrupted cell cycle progression after shRNA-mediated TA repression. This unique feature allows an in-depth analysis of the effects of TAs beyond inhibition of the RB pathway, revealing the decrease in expression of stem cell-related genes upon panTA-knockdown. Analysis of gene regulatory networks identified members of the E2F family (E2F1, E2F8, TFDP1) as key transcriptional regulators that maintain stem cell properties in TA-expressing MCC cells. Furthermore, minichromosome maintenance (MCM) genes, which encodes DNA-binding license proteins essential for stem cell maintenance, were suppressed upon panTA-knockdown. The decline in stemness occurred simultaneously with neural differentiation, marked by the increased expression of neurogenesis-related genes such as neurexins, BTG2, and MYT1L. This upregulation can be attributed to heightened activity of PBX1 and BPTF, crucial regulators of neurogenesis pathways. The observations in LoKe were confirmed in an additional MCPyV-positive MCC cell line in which RB1 was silenced prior to panTA-knockdown. Moreover, spatially resolved transcriptomics demonstrated reduced TA expression in situ in a part of a MCC tumor characterized by neural differentiation. In summary, TAs are critical for maintaining stemness of MCC cells and suppressing neural differentiation, irrespective of their impact on the RB-signaling pathway.

overall_design:
We employed LTA-independent MCC cell line LoKe to perform dox-inducible pan-TA knockdown, followed by single-cell RNA sequencing of the knockdown cells with uninduced control cells.
LoKe cells were cultured in RPMI medium supplemented with non-essential amino acid and 10% fetal bovine serum. Construction of lentiviral vectors allowing Doxycyclin (Dox) inducible short-hairpin RNA (shRNA) was performed.
Primer sequences designed to target the nucleotides 391–419 (accession number: EU375803) present in all TA mRNAs was cloned into FH1tUTG vector resulting in TA.shRNA.tet allowing Dox-inducible shRNA and constitutive GFP (green fluorescence protein) expression.


title: A developing HPA axis permits neonatal immune sensitivity to common allergens [scRNA-Seq]

city: New York

first: Dr. Shruti

last: Naik

state: NY

address: 1425 Madison Ave

department: Immunology and Immunotherapy

institute: Icahn School of Medicine at Mount Sinai

summary: Atopic and allergic diseases predominantly manifest in early life, a period of profound growth and maturation. Yet, there is a dearth of information on the impact of developmental parameters on the neonatal immune reaction to allergens. Here we demonstrate that common allergens including house dust mite (HDM) elicited potent type 17 inflammatory responses from neonatal but not adult mice. HDM-induced inflammation was abolished in Rorgt-, gd T cell-, or epithelial IL-17RC- deficient animals and surprisingly did not require nociceptors or lymph node engagement. Instead, neonatal CD301b+ type 2 conventional dendritic cells (cDC2s) abundantly engulfed allergen and locally activated gd T cells in the skin. Despite uptaking equivalent antigen to neonates, adult cDC2s did not promiscuously activate in the skin. Mechanistically, this discrepancy was not attributable to cell-intrinsic differences arising from the distinct developmental origins of neonatal and adult cDC2s. Instead, neonatal cDC2 hyperactivation could be traced to a lower systemic glucocorticoid level, a consequence of an immature hypothalamic-pituitary-adrenal (HPA) axis in early life, and could be reversed by cortisol administration at the time of allergen challenge. These findings bring to fore the influence of organismal developmental factors in shaping immune sensitivity to allergens in early life.

overall_design: To dissect the baseline composition of  antigen presenting cell populations  we isolated immune cells from neonate and adult dorsal skin and performed single cell RNA sequencing. To characterize the activation of dendritic cells in house dust mite (HDM) treated neonate skin, we performed single cell RNA sequencing with neonate skin cells isolated 9 hours after PBS and HDM inoculation.

first: Yue

last: Xing

first: Ikjot

last: Sidhu

first: Aleksandr

last: Prystupa

first: Shruti


first: Jian

last: Yang

summary: PIM1 is constitutively active and involved in various cellular processes, including cell survival, proliferation, and differentiation by phosphorylating a wide range of substrates. We investigated whether PIM1 is involved in the pathogenesis of ulcerative colitis (UC).We performed ChIP-seq analysis for HDAC2 to study the molecular mechanisms through which PIM1 regulates goblet cell numbers.

overall_design: ChIP-seq analysis for HDAC2 in Caco2 cells infected with vector or PIM1.The ChIP and input DNA fragments were processed for end repair and A-tailing using the NEBNext End Repair/dA-Tailing Module (E7442, NEB)

first: Quan

last: Wang

first: Jianming

first: Yawen

last: Xiao


title: Genome-wide studies identify genes directly regulated by PML_RARα fusion protein and co-activator BRD4 [ChIP-Seq]

first: Peng

last: Jin

address: Ruijin Rd. II

department: Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics

institute: Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

summary: Acute promyelocytic leukemia (APL) is characterized by a specific t(15;17) chromosome translocation that generates the promyelocytic leukemia/retinoic acid receptor-α (PML_RARα) fusion gene. However, the global association between PML_RARα and transcriptional co-regulators, and the rules of their association in governing the key processes during the leukemogenesis remain unclear. Here, we performed the genome-wide binding profiling of BRD4 in NB4, an APL patient-derived cell line. Moreover, we also performed ChIP-seq of PML_RARα and BRD4 upon genetic or pharmacological pertubation of PML_RARα or BRD4 to determine how they target regulatory elements.

overall_design: Genome-wide binding profiling of PML_RARa and BRD4 in NB4 cells as well as PML_RARa in K562 cells using ChIP-seq.

first: Kankan

first: Yi

last: Zhang


title: Zfp697 is an RNA-binding protein that regulates skeletal muscle inflammation and remodeling (Zfp697 transduced primary mouse myotubes RNA-Seq)

city: Solna

first: Igor

last: Cervenka

address: Solnavägen 9

department: Physiology and Pharmacology

country: Sweden

institute: Karolinska Institutet

summary: Muscle atrophy is a morbidity and mortality risk factor that happens with disuse, chronic disease, and ageing. Recovery from atrophy involves changes in protein synthesis and different cell types such as muscle fibers, and satellite and immune cells. Here we show that the previously uncharacterized gene and protein Zfp697 is a damage-induced regulator of muscle regeneration. Zfp697/ZNF697 expression is transiently elevated during recovery from muscle atrophy or injury in mice and humans. Sustained Zfp697 expression in mouse muscle leads to a gene expression signature of chemokine secretion, immune cell recruitment, and extracellular matrix remodeling. Myofiber-specific Zfp697 ablation hinders the inflammatory and regenerative response to muscle injury, compromising functional recovery. We uncover Zfp697 as an essential mediator of the interferon gamma response in muscle cells that functions primarily as an ncRNA-binding protein, most notably the pro-regenerative miR-206. This work identifies Zfp697 as an integrator of cell-cell communication necessary for tissue regeneration.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from differentiated primary mouse myotubes infected with adenovirus endoding either Zfp697 gene or GFP as a control. Experiment contains three replicates for each condition

first: Jorge

middle: C

last: Correia

first: Paulo

last: Jannig

first: Maya

middle: L

last: Gosztyla

first: Serge

last: Ducommun

first: Stine

last: Præstholm

first: Kyle

last: Dumont

first: Liu

last: Zhengye

first: Qishan

last: Liang

first: Daniel

last: Edsgärd

first: Olof

last: Emanuelsson

first: Paul

last: Gregorevic

first: Tomas

last: Venckunas

first: Marius

last: Brazaitis

first: Sigitas

last: Kamandulis

first: Johanna

middle: T

last: Lanner

first: Gene

middle: W

last: Yeo

last: Ruas


title: Control of cholesterol-induced adipocyte inflammation by the Nfe2l1-Atf3 pathway

city: Munich

first: Carolin

last: Jethwa

address: Max-Lebsche-Platz 30

department: Institute for Cardiovascular Prevention

institute: Ludwig-Maximilians-University

summary: While adipocytes are critical pillars of energy metabolism, their dysfunction is linked to adipose tissue (AT) inflammation, insulin resistance, and ectopic lipotoxicity in cardiometabolic diseases. However, he mechanisms causing adipocyte inflammation and insulin resistance remain unclear. Here, we show that excess cholesterol induces adipocyte dysfunction, which is suppressed by the transcription factor Nfe2l1 (nuclear factor erythroid derived-2, like-1). Nfe2l1 is required to sustain proteasome function in adipocytes and proteotoxic stress induces adipocyte inflammation via the activation of Atf3. In humans, the Nfe2l1-proteasome pathway is inversely correlated to body mass index (BMI) in an adipose-depot specific manner. In mice, loss of adipocyte Nfe2l1 caused AT inflammation with a pronounced infiltration of macrophages and T cells. Mice lacking adipocyte Nfe2l1 displayed severe adipocyte dysfunction during diet-induced obesity (DIO), characterized by lower adipokine levels, steatosis, glucose intolerance and insulin resistance. Nfe2l1ΔAT mice on an Apoe-deficient (Apoe-/-) background fed a cholesterol-rich Western Diet (WD), developed a lipoatrophy-like syndrome, dyslipidemia, and enhanced atherosclerosis. Our results reveal an important role for proteasome-mediated proteostasis in adipocytes and indicate that Nfe2l1 is linked to metabolic health in humans and preclinical mouse models. Promoting proteostasis in adipocytes may thus alleviate inflammation in obesity, potentially averting adverse cardiometabolic outcomes.

overall_design: To investigate the impact of Nfe2l1 and Atf3 on cholesterol homeostasis, we generated primary white adipocytes from murine subcutaneous adipose tissue in which we silenced Nfe2l1, Atf3 and both of them with siRNAs. To induce cholesterol loading of the adipocytes, we treated them with 400 µM cholesterol conjugated to methyl-β-cyclodextrin for 6 h. We sequenced four replicates for each condition.

first: Alexander

last: Bartelt


title: Zfp697 is an RNA-binding protein that regulates skeletal muscle inflammation and remodeling (Zfp697 transduced primary mouse myotubes ChIP-Seq)

first: Igor

last: Cervenka

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for Flag and normal mouse IgG as a control in differentiated mouse myotubes transduced with Flag-Zfp697 adenovirus. Experiment was performed in triplicates.

first: Jorge

last: Correia

first: Paulo

last: Jannig

last: Gosztyla


title: Profile of gene expression in murine tubular cells MCTs treated with the cytokine TWEAK

status: Public on Jul 29 2024

city: Madrid

first: Ana Belen

last: Sanz

address: Avda. Reyes Catolicos 2

country: Spain

institute: IIS-Fundacion Jimenez Diaz

summary:
Treatment of acute kidney injury (AKI) is suboptimal. TWEAK is known to mediate cell death and inflammation in AKI. Transcriptomic analysis of murine tubular cells will allow us to identify novel mediators and therapeutic targets of this pathology.
TWEAK is an inflammatory cytokine which is upregulated in AKI. Transcriptomic analysis of TWEAK-stimulated cultured murine tubular epithelial cells identified downregulation of peroxisome proliferator activated  receptor-g coactivador-1a (PGC-1a) and its target  genes (mitochondrial proteins Ndufs1, Sdha, and Tfam) as a shared feature.

overall_design: MCT tubular cells were exposed to 100 ng/ml TWEAK for 6 h or vehicle (n = 3 independent experiments)

first: Ana

middle: B

first: Alberto

last: Ortiz

first: Adrian

last: Ramos

first: Maria

middle: D

last: Sanchez-Niño


title: Extracellular matrix sulfation in the tumor microenvironment stimulates cancer stemness and invasiveness

city: Istanbul

first: Nurcan

last: Tuncbag

state: Istanbul

address: Koc University, College Of Eng Sna Z28

country: Turkey

institute: Koc University

summary: Tumor extracellular matrices (ECM) exhibit aberrant changes in composition and mechanics compared to normal tissues. Proteoglycans (PG) are vital regulators of cellular signaling in the ECM with ability to modulate receptor tyrosine kinase (RTK) activation via their sulfated glycosaminoglycan (sGAG) side chains. However, their role on tumor cell behavior is controversial. Here, we demonstrate that PGs are heavily expressed in lung adenocarcinoma patients in correlation with invasive phenotype and poor prognosis. We developed an engineered human lung tumor model which recapitulate the increase of sGAGs in tumors in an organotypic matrix with independent control of stiffness, viscoelasticity, ligand density and porosity. Our model reveals that increased sulfation stimulates extensive proliferation, epithelial-mesenchymal transition and stemness in cancer cells. We identified the FAK-PI3K-Akt signaling axis as a mediator of sulfation-induced molecular changes in cells upon activation of a distinct set of RTKs within tumor-mimetic hydrogels. We employed an integrative omics and network modeling approach to uncover the transcriptomic landscape of tumor cells in response to sulfation which demonstrated resemblance to PG-rich patient tumors.

overall_design: RNA sequencing was performed to compare the overall mRNA expression levels of A549 cells grown in AlgLung and S-AlgLung hydrogels with three replicates for each condition.

first: Ece

last: Ozturk

first: Alican

last: Kusoglu

first: Deniz

last: Örnek

first: Aslı

last: Dansık


title: RNA sequencing for wild type and shENO1 U937cells.

city: Dalian

first: Jinsong

last: Yan

address: 9 west section, Lvshun south road, Dalian, Liaoning Province, China

department: Institute of Cancer Stem Cell

institute: Dalian Medical University

summary: We systematically evaluated the expression pattern and function of ENO1 in AML. Knockdown ENO1 significantly inhibited ERK pathway phosphorylation, ERK pathway inhibitors significantly inhibited proliferation, clonal formation, migration and invasion of AML cells in vitro, blocked cell cycle and promoted apoptosis of AML cells, and activators of ERK pathway could reverse the effects of knockdown ENO1 on AML cells. The results showed that knockdown ENO1 inhibited the proliferation and invasion of AML cells in mice by inhibiting the activation of ERK pathway, and induced a significant increase in the overall survival rate of mice. Overall, this study aims to explore the role of ENO1 in the development and progression of AML and its potential mechanism, in order to provide a potential target for the treatment of AML.

overall_design: Exploring the effect for knowdown ENO1 in AML cell line U937


title: Natural and non-natural cytokine receptors generate diverse cell states to enhance T cell therapy

first: Yang

last: Zhao

address: Beckman B169B, 279 Campus Drive

department: MCP

summary: Cytokines augment T cell function, but the nature of the optimal signals are not well defined. We deployed orthogonal cytokine-receptors to diversify the JAK/STAT signaling profiles elicited by orthogonal IL-2. We designed chimeric receptors consisting of the orthogonal IL-2 receptor extracellular domain (ECD) fused to intracellular domains (ICDs) from receptors for other common gamma chain cytokines as well as ICDs from interferon receptor, IL-10 receptor and homodimeric receptor families not expressed on T cells. Such non-natural pairings with the common gamma chain expand the JAK/STAT signaling space in T cells. Natural and non-natural orthogonal chimeric receptors led to distinct T cell fates in tumors, including naturally occurring states (Tc2 differentiation driven by orthogonal chimeric IL4R) and synthetic states (myeloid-like T cells driven by orthogonal chimeric granulocyte colony stimulating factor receptor). The orthogonal chimeric IL22R (o22R) potently activated STAT-1, -3, -4, and -5, imparting T cells with stem-like and effector properties. The pronounced anti-tumor functionality mediated by o22R and oGCSFR was linked to remodeling of the exhaustion-associated epigenome. Our study broadens the cytokine receptor repertoire, providing novel solutions to overcome barriers for using engineered T cells to treat cancer.

overall_design: NSG mice were inoculated s.c. with A375 cells (1 × 106) and received i.v. adoptive cell transfer of 3 × 106 NY-ESO-1 TCR-T cells (WT NY-ESO-1 TCR-T cells, or ho22R, or hoGCSFR expressing NY-ESO-1 TCR-T cells) on day 10 post-tumor inoculation followed by i.p. administration of MSA-hoIL-2 (2.5 × 104 unit  × 3 doses, 2.5 × 104 unit  × 3 doses) or PBS control every other day until day 20. On day 21, mice were sacrificed, tumors were minced and dissociated using a human tumor dissociation kit (Miltenyi Biotec) and a gentleMACS Octo Dissociator (Miltenyi Biotec). Tumor-infiltrating lymphocytes (TILs) were first enriched by density gradient centrifugation against Percoll (GE healthcare), and then stained with surface markers and DAPI (Sigma-Aldrich). CD3+ EGFR+ or CD3+ EGFR+YFP+ T cells were sorted using an Aria II sorter (BD Biosciences) at the Stanford Share FACS Facility for ATAC sequencing.

first: Masato

last: Ogishi

first: Chirs

last: Garcia


title: Capture of germ-line competent stem cells between rosette-stage and formative pluripotent states [CUT&Tag]

city: Hefei

first: shoudong

last: ye

address: No 111, Jiu Long Road

department: Cell Biology

institute: Anhui University

summary: The establishment of stem cells with varying pluripotency potentials is crucial for understanding the developmental progression of pre- and post-implantation embryos. Despite the advancement through the proposal of the formative pluripotent state, the model of pluripotent development remains incomplete. Here, we derived a novel type of pluripotent stem cells from mouse embryonic stem cells and sustained them in vitro through the application of MEK inhibitor PD0325901, Tankyrase inhibitor IWR1, and adenylate cyclase activator Forskolin. These cells exhibit distinct transcriptome and epigenetic profiles, resembling the epiblasts of E5.0-E5.5, and reside between rosette-like stem cells and formative stem cells. We refer to them as rfISCs (Intermediate stem cells between RSCs and FSCs). rfISCs can differentiate into germ cells in vitro and form blastocyst chimeras in vivo. Additionally, the formation of rfISCs is governed by distinct signaling pathways and transcription factors. Specifically, IWR1-mediated inhibition of Wnt signaling enhances Tcf7l1-mediated Otx2 expression, essential for rfISCs generation yet prone to inducing neural differentiation, whereas Forskolin induces Id1 transcription, suppressing neural lineage gene expression via the PKA pathway. Hence, co-overexpression of Id1 and Otx2 is sufficient to sustain rfISCs stability. The emergence of rfISCs aids in comprehending early embryo development.

overall_design: CUT&Tag sequencing for genomic enrichment of H3K27me3 and H3K4me3 in rfISCs


title: Gene expression level in Aedes aegypti midgut four days post blood fed or Zika virus infection in single cell level

city: New Haven

first: Tse-Yu

last: Chen

state: CT

address: 300 Cedar St.

institute: Yale University

summary: Mosquito midgut is the first tissue encounter the virus. We apply single cell RNA sequencing to investigate the gene difference in cell level between blood fed and Zika virus infected midgut.

overall_design: We collected 50 Aedes aegypti female midgut from blood fed and from Zika virus contained blood at 4 days post infection. Single cell was isolated from the midgut tissue and proceed to scRNAseq with both oligo dT and Zika virus RT primer. Result was analyze the transcript difference between different cell type under virus infection.

first: Hamidah

last: Raduwan

first: Alejandro

last: Marín López

first: Yingjun

last: Cui

first: Erol

last: Fikrig


title: The MUC5B IPF risk variant promotes a distal airway secretory phenotype and loss of alveolar markers

city: Aurora

first: Ivana

last: Yang

state: CO

address: 1635 Aurora Ct

institute: University of Colorado

summary: The dominant risk factor for the development of idiopathic pulmonary fibrosis (IPF) is a common variant in the promoter region of the airway mucin MUC5B, variant rs35705950. The MUC5B promoter variant enhances MUC5B expression in the terminal respiratory bronchiole, where it is normally absent. We pursued a spatial gene expression approach to understand how the MUC5B variant influences IPF in age-matched unaffected and IPF lung tissue specimens.

overall_design:
We used the Nanostring Digital Spatial Profiler platform to analyze transcriptional profiles from 310 separate lung regions from 75 age-matched donors who were either unaffected (21) or had IPF (54). Formalin-fixed, paraffin-embedded tissues were obtained from the Lung Tissue Research Consortum or from patients undergoing lung transplant at the University of Colorado (Colorado Multi-Institutional Review Board protocol #15-1147). Acquired regions fell into one of five categories: Airway, alveolus, transition zones characterized by fibroblastic foci, dense fibrosis, or honeycomb cysts guided by our pathologist (C.D.C.). Specimens were genotyped for the IPF risk variant in the promoter for the MUC5B gene, rs35705950 G;T, with 7 control specimens and 31 IPF specimens containing at least one copy of the variant allele.

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Due to this being human subjects data, we are not including raw data files.
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first: Jonathan

middle: S

last: Kurche

last: Cardwell

first: Carlyne

last: Cool

first: Rachel

middle: Z

last: Blumhagen

first: Evgenia

last: Dobrinskikh

first: David

last: Heinz

first: Jeremy

middle: A

last: Herrera

last: Schwartz


title: TG6050, an oncolytic vaccinia virus encoding interleukin-12 and anti-CTLA-4 antibody induces tumor regression through profound tumor microenvironment remodeling and strong antitumor adaptive immune response [scRNA-seq]

city: Illkirch-Graffenstaden

first: Jules

last: Deforges

address: Boulevard Gonthier d'Andernach

institute: Transgene SA

summary: By their selective infection or replication into tumors, oncolytic viruses trigger profound modifications of tumor immune microenvironment with a massive infiltration and activation of T cells. This tumor warming up can be further amplified by the local delivery of powerful immunomodulatory molecules encoded into virus’ genome. Those properties are particularly of interest for tumor poorly infiltrated or infiltrated with anergic T cells to reverse patient’s unresponsiveness to immune checkpoint inhibitors (ICI).   TG6050 is a new oncolytic vaccinia virus encoding single-chain human Interleukin-12 (hIL-12) and full length anti-cytotoxic T-lymphocyte-associated antigen-4 (@CTLA-4) monoclonal antibody. Replication, oncolysis, selectivity, transgenes expression and functionality of TG6050 were characterized in vitro. Virus and IL-12 pharmacokinetics, antitumoral activities (alone or combined with ICI), and mechanism of action (MOA) were investigated in “hot” (highly infiltrated) and “cold” (poorly infiltrated) syngeneic murine tumor models. MOA was deciphered by monitoring both systemic and tumor immune responses, and tumor transcriptome analyses. Finally, TG6050 safety after repeated intravenous administrations was evaluated in cynomolgus monkeys and special attention was paid to the level of circulating IL-12 potentially associated with toxic effects.  In vitro or in vivo replication of TG6050 in tumor cells allows local expression of functional IL-12 and @CTLA-4. The expression of transgenes, together with the virus replication, translated into an antitumoral activity in both “cold and “hot” tumor murine models that was further amplified by combination with ICI. Analysis of tumor microenvironment (TME) after TG6050 treatment showed an increase of interferon gamma, CD8+ T cells, M1/M2 macrophages ratio and a drastic decrease of regulatory T cells. Those local modifications were observed together with an enhanced systemic and specific antitumor adaptive immune response. In toxicology studies, the virus did not produce any observable adverse effects in cynomolgus monkeys.    Conclusions: TG6050 allows the delivery of functional IL-12 and @CTLA-4 into tumor resulting in an excellent antitumor activity along with a shift towards an inflamed TME, and a boost of the systemic antitumor T-cells. Toxicological studies in macaques demonstrated the safety of TG6050. Together these results paved the way for clinical evaluation of TG6050 in metastatic non-small cell lung cancer (NCT05788926).

overall_design: CT26 tumours treated with the vaccinia virus mTG6050 expressing anti-CTLA-4 and IL-12 (COPTG19859), or untreated

first: Fadi

last: Azar

first: Jean-Baptiste

last: Marchand

first: Eric

last: Quéméneur


title: Persistent epigenome anomalies in induced pluripotent stem cells from late-onset sporadic Alzheimer’s disease cases [BiSulfite-seq]

city: Montreal

first: Gilbert

last: Bernier

address: 5690 rosemont boulevard

institute: HMR

summary: Reprogramming of adult somatic cells into induced pluripotent stem cells (iPSCs) resets the aging clock and is thought to erase other epigenomic marks. Here we show that iPSCs from late-onset sporadic Alzheimer’s disease (AD) cases retain epigenomic anomalies that supersede developmental defects, genomic instability, and neurodegeneration. When compared to iPSCs from elderly controls, AD iPSCs display reduced BMI1 and KDM5A expression, a more relax heterochromatin, and an altered DNA methylome. AD neuroepithelial cells show lesser efficient neural induction and forebrain specification, together with perturbed WNT signaling. They also present a unique genomic instability phenotype characterized by replication stress and DNA damage at the nuclear envelope-associated heterochromatin. BMI1 knockdown in control neuroepithelial cells phenocopied the AD-related pathologies. Long-term AD neuronal cultures show a dedifferentiation and loss-of-cell identity phenotype resembling epigenome erosion. BMI1 overexpression in AD neurons mitigates amyloid accumulation, tau pathology, heterochromatin fragmentation and G4 DNA induction. These findings implicate persistent epigenomic anomalies or uncharacterized genetic alterations working in trans on the epigenome in AD iPSCs, which could have broader implications in our understanding of the disease origin and pathophysiological mechanisms.

overall_design: iPSC cell lines from AD and CTL where sequenced in order to study the different methyation profile of these two conditions in iPSC


title: Harmonized cross-species cell atlases of trigeminal and dorsal root ganglia

city: Boston

first: Shamsuddin

last: Bhuiyan

state: MA

address: 60 Fenwood Road

institute: Brigham and Women's Hospital

summary: Peripheral sensory neurons in the dorsal root ganglion (DRG) and trigeminal ganglion (TG) are specialized to detect and transduce diverse environmental stimuli including touch, temperature, and pain to the central nervous system. Recent advances in single-cell RNA-sequencing (scRNA-seq) have provided new insights into the diversity of sensory ganglia cell types in rodents, non-human primates, and humans, but it remains difficult to compare transcriptomically defined cell types across studies and species. Here, we built cross-species harmonized atlases of DRG and TG cell types that describe 18 neuronal and 11 non-neuronal cell types across 6 species and 31 studies. We then demonstrate the utility of this harmonized reference atlas by using it to annotate newly profiled DRG nuclei/cells from both human and the highly regenerative axolotl. We observe that the transcriptomic profiles of sensory neuron subtypes are broadly similar across vertebrates, but the expression of functionally important neuropeptides and channels can vary notably. The new resources and data presented here can guide future studies in comparative transcriptomics, simplify cell type nomenclature differences across studies, and help prioritize targets for future analgesic development.

overall_design: Beta-III tubulin:GAP43-EGFP transgenic axolotls (125) 7-8cm in length (snout to tail) were anesthetized in 0.1% tricaine. For DRG dissociation at single-cell level, 10X Genomics “Dissociation of Mouse Embryonic Neural Tissue for Single Cell RNA Sequencing” protocol was adapted to axolotl tissue. DRGs of brachial plexus nerves located at C3, C4 and C5 were collected from both left and right sides and combined (total of 6 DRGs) in a single tube containing chilled 0.7X HBSS buffer and kept on ice. For dissociation, 400ul papain (Worthington Biochemical, Cat: #LK003178) dissolved in 0.7X PBS was pre-warmed in 37˚C water bath for 10 minutes to activate the enzyme. HBSS was removed and activated papain was added onto DRGs. The DRG in papain was placed in 37˚C water bath for 20 minutes. After the incubation, DRGs were settled in the bottom of the tube by a brief spin at 200g for 1min and papain was removed. 500ul DRG media consisting of Neurobasal Plus Medium at 60% (v/v), (Thermo Scientific, cat: A3582901), 50X B-27 Plus Supplement stock at 1X (Thermo Scientific, cat: A3582801), 100X insulin-transferrin-selenium stock at 1% (v/v), (Peprotech, cat: 41400045), 250μg/mL amphotericin B stock at 1% (v/v), (Sigma-Aldrich, cat: A2942), gentamicin at 50mg/ml (Sigma-Aldrich, cat:  G1264), 50ug/ml recombinant human β-NGF stock at 1:1000, (Peprotech, cat: 450-01) mixed in Ringer’s solution (115mM NaCl, 2.5mM KCl, 2mM CaCl2, 10mM HEPES pH7.4, 0.5 mM EDTA dissolved in water and ph adjusted to 7.4 with NaOH) was added. DRGs were triturated in media using 1000 μl pipette. Trituration was performed slowly and gently until most of the tissue was dissociated. After dissociation, sample was centrifuged at 200g for 3min. The supernatant was removed, and the pellet was resuspended in 100 μl of0.7XPBS+%0.04 BSA. Cell count and single-cell sequencing were performed by Harvard University Bauer Sequencing core. Luna-FL Dual Fluorescence Cell Counter was used to assess number of viable cells. Cell count was repeated 4 times and averaged to determine the final cell count, viability, and cell size. Total of 405 cells/μl with 100% cell viability were present in the final cell suspension in first sample and 486 cells/μl with 97% viability in the second set. scRNA-seq libraries were prepared with the Chromium™ Single Cell 3′ NextGEM, Library and Gel Bead Kit v3.1.

first: Mengyi

last: Xu

first: Parth

last: Bhatia

first: William

last: Renthal


title: GSDMD-mediated metabolic crosstalk licenses a pro-regenerative niche for tissue repair

city: Hangzhou

first: Di

last: Wang

address: Yuhangtang Road.866

institute: Zhejiang University

summary: The establishment of an early pro-regenerative niche is crucial for tissue regeneration. Gasdermin D (GSDMD)-dependent pyroptosis accounts for the release of inflammatory cytokines upon various insults. However, little is known about its role in tissue regeneration followed by homeostatic maintenance. Here, we show that macrophage GSDMD deficiency delayed tissue recovery, with little impact on the local inflammatory milieu or the lytic pyroptosis process. Metabolite secretome profiling of hyperactivated macrophages unveiled the non-canonical metabolite-secreting function of GSDMD. And we further identified 11,12-epoxyeicosatrienoic acid (11,12-EET) as a bioactive pro-healing oxylipin, secreted from hyperactive macrophages in a GSDMD-dependent manner. Indeed, accumulation of 11,12-EET by direct supplementation or deletion of its hydrolytic enzyme Ephx2 accelerated muscle regeneration. We further demonstrated that the Ephx2 level accumulated within aged muscle, which led to a decreased intramuscular 11,12-EET level. And consecutive 11,12-EET treatment rejuvenated aged muscle. Mechanistically, 11,12-EET amplifies fibroblast growth factor/FGF receptor (FGF-FGFR) signaling by modulating FGF liquid-liquid phase separation, hence boosting the activation and proliferation of muscle stem cells (MuSCs). These data depict a GSDMD-guided metabolite crosstalk between macrophages and MuSCs that governs the repair process, which offers new therapeutic insights for the regeneration of injured or aged tissues.

overall_design: TA muscle tissue was collected from mice with the indicated treatment or genotype. After washing with ice-cold PBS, the tissue was minced into 2-3 mm pieces and washed twice with ice-cold PBS. Digestion was performed with digestion buffer [0.5 mg/mL Collagenase I (Sigma), 0.5 mg/mL Collagenase V (Sigma), and 0.5 mg/mL Dispase (Worthington)] at 37℃ with 100 rpm for 10 min, and stopped with an equal volume of ice-cold PBS containing 10% FBS. Cell suspensions were passed through a 70-30 µm filter twice, counted with a cell counter (Countstar), and centrifuged at 400 g for 6 min at 12℃. Cells were resuspended with RPMI 1640 (Gibco) on ice. The remaining muscle tissue was digested with 6 ml 0.25% Trypsin-EDTA at 37℃ with 100 rpm for 10 min, and stopped with an equal volume of ice-cold PBS containing 10% FBS, followed by 2 PBS washes and passage through 70-30 µm filters. The two cell portions were collected and red blood cells were removed using 4 ml Red Blood Cell Lysis Solution. Then the suspension was resuspended in 1× PBS (0.04% BSA) and centrifuged twice at 300 g for 3 min at 4℃. The cell pellet was resuspended in 50 μL of 1× PBS (0.04% BSA). The overall cell viability was confirmed by trypan blue exclusion, which was required to be >85%, single cell suspensions were counted using a cell counter, and the final concentration was adjusted to 700-1200 cells/μL. The single-cell suspensions were loaded to 10x Chromium to capture 8,000-10,000 single cells according to the manufacturer’s instructions with the 10X Genomics Chromium Single-Cell 3’ kit (V3).

first: Sheng

last: Chen

first: Zhexu

last: Chi


title: Tissue-resident memory T cells overcome tolerance to renal autoantigen and orchestrate immune-mediated nephritis

city: Freiburg

first: Frederic

last: Arnold

address: Hugstetterstr. 55

department: Internal Medicine IV

institute: University of Freiburg Medical Center

summary: Differential transcriptome analysis of activated splenic CD8 T cells revealed a hybrid phenotype in the context of renal autoantigen crosspresentation, combining hallmarks of activation and T cell dysfunction.

overall_design: OT-1 cells were isolated (FACS sorting) from spleens and lymph nodes  of 2 wildtype and 2 NOH mice 7 days after adoptive transfer and activating LM-OVA infection and analyzed using scRNA-seq (10x platform).

first: Sagar

last: Sagar

first: Yakup

last: Tanriver


title: Impact of EET on muscle stem cell

summary: Cardiotoxin (CTX)-induced acute muscle injury is a paradigmatic self-limiting sterile injury model for exploring the tissue regeneration process, which consists of a series of tightly-regulated events, including an initial inflammatory response the activation of muscle stem cells (MuSCs, also termed satellite cells) during the early stage after injury, as well as later inflammation resolution along with MuSC proliferation and differentiation. This study set out to determine the potential impact of lipid 11,12-EET on murine MuSCs function.

overall_design: Primary MuSCs were isolated and cultured with/without 11,12-EET for 2 days. Total RNA was isolated and purified using TRIzol reagent (Invitrogen) and used for bulkRNA sequencing.


title: BET protein-dependent E2F pathway confers bell-shaped type resistance to tankyrase inhibitors in APC-mutated colorectal cancer

city: Tokyo

first: Shun

last: Morino

address: 3-8-31, Ariake, Koto-ku

country: Japan

institute: JFCR

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

overall_design: Refer to individual Series


title: BET protein-dependent E2F pathway confers bell-shaped type resistance to tankyrase inhibitors in APC-mutated colorectal cancer [RNA-seq]

summary: In colorectal cancer (CRC), WNT/β-catenin signaling is aberrantly activated mainly by loss-of-function mutations in adenomatous polyposis coli (APC) and is involved in tumor progression. Tankyrase inhibitors, which suppress WNT/β-catenin signaling, are under pre-clinical and clinical trials, while their resistance mechanisms remain unclear. In this study, we established tankyrase inhibitor-resistant CRC cells, JC73-RK100, from APC-mutated patient-derived CRC cells. JC73-RK100 cells and several CRC cells were sensitive to tankyrase inhibitors at low concentrations but were resistant at high concentrations (i.e., bell-shaped dose response: BSDR). Mechanistically, tankyrase inhibitors at high concentrations promoted BRD3/4-dependent E2F target gene transcription and over-activated cell cycle progression in the BSDR cells. BET inhibitors canceled the bell-shaped dose response to tankyrase inhibitors. Taken together, these observations suggest that combination of tankyrase and BET inhibitors would be a useful therapeutic approach to overcome a subset of resistance to tankyrase inhibitors.

overall_design: Examination of RNA-sequencing in (1) colorectal cancer PDC JC73 and JC73-RK100 cells treated with or without tankyrase inhibitor RK-582, and (2) JC73-RK100 cells treated with RK-582 with or without BET inhibitor I-BET-762.

first: Tetsuo

last: Mashima

first: Hiroyuki

last: Seimiya


title: Injection of vancomycin effect on the kidney in mouse

city: 福岡市

first: Yuya

last: Yoshida

state: 福岡県

address: 東区馬出3-1-1 九州大学薬学部棟本館3F 薬剤学教室, 薬物動態学分野

institute: Kyushu-university

summary: Although vancomycin, which is frequently used to treat drug-resistant bacterial infections, induces acute kidney injury (AKI) with high frequency, the only effective treatment is discontinuation of the drug, so analysis of effective avoidance methods is urgently needed.  In this study, the expression of mRNA in the kidney prepared from1/2 nephrectomized mice which injected vancomycyn was investigated.

overall_design: Differential gene expression between saline and vancomycin-injected mouse was measured on the kidney

first: Naoya

last: Matsunaga

first: Kaori

last: Yasuda

first: Atsushi

last: Doi


title: Negative supercoil senses temperature to modulate meiotic crossovers and chromosomes

city: Jinan

first: liangran

last: zhang

state: Shandong

address: Jingshi Street

department: State Key Laboratory of Microbial Technology

institute: Shandong University

summary: Crossover recombination is a hallmark of meiosis, which holds the paternal and maternal chromosomes (homologs) together for their faithful separation, meanwhile, it promotes genetic diversity of progenies. The pattern of crossover is mainly controlled by the architecture of meiotic chromosomes. Environmental factors, especially temperature, also play an important role in modulating crossovers. However, it is unclear how temperature affects crossovers. Here, we examined the distributions of budding yeast axis components (Red1, Hop1, and Rec8) and the CO-associated Zip3 foci in detail in different temperatures, and found that both increased and decreased temperatures result in shorter meiotic chromosome axes and more crossovers. Further investigations showed that altered temperature coordinately enhanced the hyperabundant accumulation of Hop1 and Red1 on chromosomes and the number of Zip3 foci. Most importantly, temperature-induced alterations in axis distribution and Zip3 foci depend on the changes in DNA negative supercoil. These findings suggest that yeast meiosis senses temperature changes by increasing the level of negative supercoil to increase crossovers and modulate chromosome organization. These findings provide a novel view in understanding the effect and mechanism of temperature on meiosis recombination and chromosome organization, and thus also have an important implication in evolution and breeding.

overall_design: ChIP-seq analysis of binding of Red1, Hop1, Rec8, Zip3 and TMP(marker of negative supercoils) in S. cerevisiae during meiosis.

first: Yingjin

last: Tan

first: Taicong

first: Liangran

last: Zhang

first: Shunxin


title: Transcriptomic analysis of Salmonella Typhimurium exposed to sub-lethal sonophotocatalytic disinfection

city: Bhubaneswar

first: Suraj

middle: Kumar

last: Tripathy

state: Odisha

address: Campus 11

department: Biotechnology

country: India

institute: KIIT-DU

summary: We report the transcriptomic changes in Salmonella Typhimurium exposed to sub-lethal sonophotocatalytic disinfection. The current data suggests that more than 120 genes are significantly expressed during the process. The genes associated with the flagellar assembly were found to be significantly up-regulated during the disinfection, which may have impacts on the phenotypic attributes of the bacteria.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

overall_design: Examination of Salmonella Typhimurium treated with sonophotocatalysis and it comparison with untreated bacteria

first: A

middle: P

last: Habeeb Rahman

first: Amrita

last: Mishra

first: Cecilia

last: Stalsby Lundborg

last: Kumar Tripathy


title: Genome-wide studies identify genes regulated by co-activator BRD4 in APL cells [RNA-seq]

city: Shanghai

first: Peng

last: Jin

address: Ruijin Rd. II

institute: Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

summary: Acute promyelocytic leukemia (APL) is characterized by a specific t(15;17) chromosome translocation that generates the promyelocytic leukemia/retinoic acid receptor-α (PML/RARα) fusion gene. However, the mechanism underlying PML/RARα mediated transcriptional dysregulation remain unclear. Here, we performed the transcription profiling of BRD4 in NB4, an APL patient-derived cell line.

overall_design: Expression profiling of NB4 cells before and after BRD4 inhibition using RNA-seq.

first: Kankan

last: Wang

first: Yi


title: Targeting novel m6A reader KHSRP impairs pancreatic ductal adenocarcinoma progression via attenuating FAK signaling

city: Guangzhou

first: Zhou

last: yifan

state: 周一帆

address: 74 Zhongshan Second Road

institute: Sun Yat-sen University Cancer Center

summary: We report KH-type splicing regulatory protein (KHSRP) as a novel m6A reader with oncogenic functions in pancreatic ductal adenocarcinoma (PDAC). KHSRP recognizes and stabilizes its target mRNAs (e.g., MET, ITGAV and ITGB1) in an m6A-dependent manner, therefore activating downstream FAK signaling and promoting PDAC progression. Targeting KHSRP shows promising anti-tumoral effects in vitro and in vivo, indicating that KHSRP may serve as a therapeutic target for PDAC.

overall_design: We performed m6A individual-nucleotide resolution cross-linking and immunoprecipitation sequencing (miCLIP-seq) and photoactivatable-ribonucleoside-enhanced crosslinking and immunoprecipitation sequencing (PAR-CLIP-seq) for KHSRP to investigate whether KHSRP possesses the characteristics of m6A-binding protein. To explore the underlying mechanism of KHSRP-mediated tumor progression, we conducted RNA sequencing (RNA-seq). We further performed mRNA stability analysis to examine the effect of KHSRP on mRNA lifetime.

first: Jialiang

first: Zilan

last: Xu


title: Small RNA next generation sequencing of miRNAs in MCF7 cells derived mammosphere treated with withaferin A

city: Bathinda

first: Shashank

last: Kumar

state: Punjab

address: VPO Guddha

department: Biochemistry

institute: CENTRAL UNIVERSITY OF PUNJAB

type: Non-coding RNA profiling by high throughput sequencing

summary: In this study, we reporte the altered miRNAs expression in the human breast cancer cell line (MCF7) derived mammosphere in response to withaferin A IC50 concentrations (2 µM)..

overall_design: Withaferin A is a major pharmacological active constituent of Withania somnifera (Solanaceae). In this study we were aimed to identify the diffentially expressed known/novel miRNAs using next generation sequencing (NGS) in withaferin A treated MCF7 derived mammosphere.  For this, MCF7 cells were initially treated with withaferin A with 2 µM concentration (experimental groups) and without treated MCF7 cells (the control group) were allowed to form spheres and incubated at 37 ºC under a 95% humid environment in an incubator having 5% CO2 for five days. Three samples were assigned for each group.


title: Gene expression analysis of NCI-H727 cells transfected with siRNA against PROX1

status: Public on Jul 28 2024

city: Toyoake

first: Kouhei

last: Sakurai

address: 1-98 Dengakugakubo, Kutsukake-cho

department: Department of Joint Research Laboratory of Clinical Medicine, School of Medicine

institute: Fujita Health University

summary:
This study aimed to reveal downstream genes of PROX1 in a carcinoid-derived cell line NCI-H727.
We performed gene expression microarray after PROX1 knockdown in NCI-H727 cells.

overall_design: NCI-H727 cells were transfected with si-negative control (si-NC) or siRNA against PROX1 (si-PROX1), and gene expression microarray was performed.

first: K


title: Calycosin inhibited MIF-mediated inflammatory chemotaxis of macrophages to ameliorate ischemia reperfusion-induced acute kidney injury

city: Luzhou

first: Honglian

state: Sichuan

address: No. 182, Chunhui Road, Longmatan District

department: Research Center for Integrative Medicine

institute: the Affiliated Traditional Medicine Hospital of Southwest Medical University

summary: Acute kidney disease caused by ischemia-reperfusion (IRI-AKI) is characterized by ectopic inflammation and tubular injury, in which macrophage infiltration and inflammatory activation play a critical pathogenic role. Calycosin is an active flavone from the root of Astragalus membranaceus and shows anti-inflammatory effects in various diseases. In this study, we investigated the renoprotective role of calycosin against IRI-AKI and the underlying mechanism. Our results showed that calycosin treatment reduced the levels of serum creatinine and urea nitrogen along with attenuated tubular necrosis and cast formation in IRI-AKI mice. Calycosin significantly suppressed the activation of NF-κB signaling and the expression of inflammatory mediators IL-1β and TNF-α in IRI-AKI kidneys. In vitro, calycosin inhibited LPS-induced inflammatory activation in RAW 264.7 cells. Interestingly, RNA-seq revealed that calycosin remarkably down-regulated chemotaxis-related pathways in RAW 264.7 cells. Among the differentially expressed genes, Ccl2/MCP-1, a critical chemokine mediating macrophage inflammatory chemotaxis, was down-regulated in both LPS-stimulated RAW 264.7 cells and IRI-AKI kidneys. Consistently, calycosin treatment attenuated macrophage infiltration in the IRI-AKI kidneys. Importantly, in combination with target prediction, molecular docking, and surface plasmon resonance, we showed that calycosin can directly bind to macrophage migration inhibitory factor (MIF). Functionally, calycosin abrogated MIF-stimulated NF-κB signaling activation and Ccl2 expression and MIF-mediated chemotaxis in RAW 264.7 cells without influencing its expression. Collectively, calycosin protects from IRI-AKI by suppressing MIF-mediated macrophage inflammatory chemotaxis. Calycosin could be a promising candidate medicine for clinical treatment of IRI-AKI.

overall_design: To study the anti-inflammatory effect of calycosin in macrophage, the RAW 264.7 cells were pretreated with 100 ug/mL of calycosin for 24 hours followed by stimulation with 300 ng/mL LPS for 6 hours. RNA was collected for RNA-seq. Transcriptome difference was analyzed in vehicle-treated cells, cells treated with LPS, and cells treated calycosin and LPS.

first: Li

first: Ze

last: Peng


title: Transcriptome changes in C57BL/6 mice after a high-fat diet

city: Zhengzhou

first: yu

last: dongsheng

state: He Nan

address: The First Affiliated Hospital of Zhengzhou University

summary: Background and aims: Trichosanthis Pericarpium injection (TPI) produces a significant effect on regulating lipid metabolism and antioxidation, whose effects on non-alcoholic fatty liver disease (NAFLD) still remain unclear. In this study, we delved into the pharmacological functions of TPI on NAFLD and its underlying mechanisms. Methods: NAFLD mice model was induced by administering a high-fat diet (HFD) for 12 weeks, followed by intraperitoneal injection of TPI for 4 weeks. Concurrently, to explore the potential mechanisms, we utilized AML12 cells exposed to oleic acid (OA) as an in vitro model. Non target metabolomics and transcriptomics were used to explore the mechanism by which TPI improves lipid metabolism in mouse liver. Results: Our findings indicate that TPI significantly improved metabolic abnormalities and hepatic fat deposition in HFD mice. TPI treatment also yielded analogous results in AML12 cells treated with OA. Metabolomic analysis revealed alterations in metabolites in NAFLD mice, with ABC transporters exhibiting the most prominent changes. Further screening of gene changes related to this pathway showed a significant increase in ABCC5 expression in the NAFLD mice, while TPI treatment effectively reduced the expression level of ABCC5. Transcriptomic analysis demonstrated a marked increase in the expression of the transcription factor KLF6 in the NAFLD group, which positively correlated with ABCC5 expression. Further luciferase reporter gene experiments confirmed that KLF6 can directly regulate the expression of ABCC5, thereby affecting lipid metabolism and participating in the development of NAFLD. Notably, TPI treatment was able to reverse this process. Conclusions: In conclusion, TPI improves NAFLD by alleviating hepatic lipid metabolism dysregulation through the KLF6/ABCC5 pathway.

overall_design: C57BL/6 mice in chow group were fed with a standard laboratory rodent chow diet (Chow) (Xietong Organism, Nanjing, China), and the other three groups were fed with a high fat diet (HFD, 60% fat, 20% carbohydrate, 20% protein; Research Diets, New Brunswick, USA) for 12 weeks as previously described.

first: Dongsheng

last: Yu


title: The effects and underlying mechanisms of mutated hepatitis B virus preS gene on the development of hepatocellular carcinoma

first: Shiliang

last: Cai

address: 800 Xiangyin Road

institute: Second Military Medical University

summary: The groups with the highest tumor incidences, M1, M2and preS2 deletion, were involved. WT and Vector mice served as the control group. In total, 15 tissues of Sleeping Beauty mice models were involved in microarray analysis, including 3 liver tissues from the empty vector group,3 liver tissues from the WT group, 3 tumor tissues from the M1 group, 3 tumor tissues from the M2 group,and 3 tumor tissues from the preS2 deletion group. The samples were randomly selected from each group.

overall_design: PreS fragments (WT/M1/M2/preS2 deletion) or Vector were delivered into Fah deficient mice with Sleeping Beauty transposon system at 8-10 weeks of age . After 150 days, the mice were anesthetized with carbon dioxide and sacrificed. All the RNA from their liver or tumor are extracted for gene expression chips.

first: Rui

last: Pu

first: Wenbin

last: Liu

first: Zixiong

last: Li


title: Profile of gene expression in experimental acute kidney injury

city: Madrid

first: Ana Belen

last: Sanz

address: Avda. Reyes Catolicos 2

institute: IIS-Fundacion Jimenez Diaz

summary:
Treatment for acute kidney injury (AKI) is suboptimal. A better understanding of its pathogenesis may lead to new therapeutic approaches. Kidney transcriptomics analyses of murine folic acid-induced AKI (FA-AKI) will allow us to identify new mediators and therapeutic targets of this pathology.
Folic acid nephropathy is a classical model of AKI characterized by acute renal failure, tubular cell death, interstitial leukocyte infiltration and subsequent tubular regeneration that has been reported in humans.

overall_design: C57BL/6 female mice received a single intraperitoneal injection of folic acid (Sigma-Aldrich, Merck Darmstadt, Germany) 250 mg/kg in 0.3 mol/L sodium bicarbonate or vehicle (n=3 per group). Mice were euthanized at 24h

first: Ana

first: Alberto

last: Ortiz

first: Adrian

last: Ramos

first: Maria

last: Sanchez-Niño


title: Developmental defects in ectodermal appendages caused by missense mutation in edaradd gene in the nfr mangrove killifish, Kryptolebias marmoratus

city: Exeter

first: Paul

middle: Andrew

last: O'Neill

state: --- Select a state ---

address: Stocker Road

country: United Kingdom

institute: University of Exeter

summary: The mangrove killifish, Kryptolebias marmoratus, can reproduce with self-fertilisation, offering a unique and useful genetic tool for generation of genetic mutants and quick identification of mutated genes. From an ENU-mutated mangrove killifish line R228, we have isolated a novel mutant line, no-fin-ray/nfr in which homozygous mutant of adult fish fin ray development is largely reduced. Besides the reduction of the fin, the nfr mutant also exhibited other phenotype associated with ectodermal cell lineages including loss of scales, deformation in the gill structure such as decreasing the number of gill filaments, the reduction in the number of jaw teeth, pharyngeal teeth and gill rakers. Illumina RNAseq with 3 embryos each from mutants, siblings and the parental WT strain Hon9 (only 9 embryos as total) identified a mutation in the edaradd in a highly conserved C-terminal death domain. Edaradd is known as a cytoplasmic accessory protein for the Ectodysplasin A (EDA) signalling pathway. To confirm the crucial role of edaradd during fin development, CRISPR RNAs were designed to knock out the gene in another killifish species, Arabian killifish. Indeed, Arabian killifish edaradd crispants showed a potent reduction of the fin development with 100% frequency. Furthermore, EDA crispants also showed identical phenotypes to that of edaradd crispants, confirming the fin defect in the mutants/crispants is caused by the signalling pathway of the EDA in the killifish species.   These data demonstrate a powerful genetic approach using isogenic self-fertilising mangrove killifish as a tool for identifying mutants and their mutation, and revealed the crucial role of edaradd for the first time in the fish fin development and other ectoderm derived epithelial tissues.

overall_design: RNAseq was conducted using embryos from no-fin-ray mutants, siblings, and wild type mangrove killifish. Mutated genes in the no-fin-ray mutant were identified.

first: Hussein

last: Saud

first: Brian

last: RIng

first: Tetsuhiro

last: Kudoh


title: The Clinical Significance of CRNDE Gene Methylation, Polymorphisms, and CRNDEP Micropeptide Expression in Ovarian Tumors

status: Public on Jul 27 2024

city: Warsaw

first: Lukasz

middle: Michal

last: Szafron

address: Roentgena 5

country: Poland

institute: The Maria Sklodowska-Curie National Research Institute of Oncology

summary: Abstract: CRNDE is an oncogene expressed as a long non-coding RNA. However, our team previously reported that the CRNDE gene also encodes a micropeptide, CRNDEP. The amino acid sequence of CRNDEP has recently been revealed by other researchers, too. This study aimed to investigate genetic alterations within the CRNDEP-coding region of the CRNDE gene, methylation profiling of this gene, and CRNDEP expression analysis. All investigations were performed on clinical material from patients with ovarian tumors of diverse aggressiveness. We found that CRNDEP levels were significantly elevated in highly aggressive tumors compared to benign neoplasms. Consistently, a high level of this micropeptide was a negative, independent, prognostic, and predictive factor in high-grade ovarian cancer (hgOvCa) patients. The cancer-promoting role of CRNDE(P), shown in our recent study, was also supported by genetic and epigenetic results obtained herein, revealing no CRNDEP-disrupting mutations in any clinical sample. Moreover, in borderline ovarian tumors (BOTS), but not in ovarian cancers, the presence of a single nucleotide polymorphism in CRNDE, rs115515594, significantly increased the risk of recurrence. Consistently, in BOTS only, the same genetic variant was highly overrepresented compared to healthy individuals. We also discovered that hypomethylation of CRNDE is associated with increased aggressiveness of ovarian tumors. Accordingly, hypomethylation of this gene’s promoter/first exon correlated with hgOvCa resistance to chemotherapy, but only in specimens with accumulation of the TP53 tumor suppressor protein. Taken together, these results contribute to a better understanding of the role of CRNDE(P) in tumorigenesis and potentially may lead to improvements in screening, diagnosis, and treatment of ovarian neoplasms.

overall_design: In this project, methylomes of 153 serous ovarian tumors have been analyzed using the Infinium MethylationEPIC v1.0 BeadChip microarrays (Illumina). The cohort consisted of 16 formalin-fixed paraffin-embedded (FFPE) borderline ovarian tumors without the BRAF V600E mutation (BOT), 16 FFPE BOT with the BRAF V600E mutation (BOT.V600E), 11 snap-frozen BOT, 5 snap-frozen BOT.V600E, 3 FFPE low-grade ovarian cancers (lgOvCa), 6 snap-frozen lgOvCa, 4 FFPE high-grade ovarian cancers (OvCa), and 92 snap-frozen OvCa.

first: Laura

first: Roksana

last: Iwanicka-Nowicka

first: Agnieszka

last: Podgorska

first: Arkadiusz

middle: M

last: Bonna

first: Piotr

last: Sobiczewski

first: Jolanta

last: Kupryjanczyk


title: Single-cell transcriptomics reveals distinct molecular alterations of human renal cell carcinoma-derived endothelial cells that are stable in ex vivo primary culture

city: Seattle

first: Yuexin

last: Xu

state: WA

address: 1100 Fairview Ave N, D4-100, Fred Hutchinson Cancer Research Center

institute: Fred Hutchinson Cancer Research Institute


title: Single-cell transcriptomics reveals distinct molecular alterations of human renal cell carcinoma-derived endothelial cells that are stable in ex vivo primary culture [RNA-Seq]

summary: Even though tumor endothelial cells are a key component of the tumor microenvironment and represent the main interface between tumor cells and the host’s circulation and immune system, their phenotypes and functional properties are relatively poorly understood. To address this deficit, we purified tumor and matched normal endothelial cells from highly vascularized kidney cancer specimens and performed single cell RNA-seq to characterize endothelial cell gene expression patterns and heterogeneity. We found that tumor endothelial cells from multiple donors shared a common phenotype with increased expression of pathways related to extracellular matrix regulation, cell-cell communication and insulin growth factor signaling. We also found that while normal endothelial cells from kidney and liver were divergent, most tumor endothelial cells from kidney and liver cancer shared common gene expression signatures suggesting a congruence of tumor endothelial cell phenotypes. Using RNA-seq, we determined that many of the differentially regulated genes between tumor and normal endothelial cells were maintained in primary culture, which in turn permitted study of their functional phenotypes in vitro. Cultured tumor endothelial cells were resistant to apoptosis after trophic factor removal and displayed increased adhesiveness for CD+ CD25+ T regulatory cells. Our studies delineate the unique functional and immunophenotypic properties of kidney cancer tumor endothelial cells, which will serve as the basis to develop new therapies.

overall_design: Three pairs of TEC and NEC cultures at passage three as well as the corresponding primary normal kidney and RCC tumor tissues were trypsinized to single-cell suspension. The primary endothelial cells were enriched by sorting on DAPI-CD31+CD144+ population.


title: Parvalbumin expression does not account for discrete electrophysiological profiles of glutamatergic ventral pallidal subpopulations.

city: Saint Louis

first: Meaghan

last: Creed

state: MO

address: 4370 Duncan Ave

department: Anesthesiology

institute: Washington University

summary: The ventral pallidum (VP) has emerged as a critical node in the mesolimbic reward system. Modulating the VP can impact the subjective valuation of rewards, reward motivation, and reward seeking under conflict, making it an attractive target for clinical neuromodulation therapies that manage substance use disorders. To understand how to rationally modulate the VP, we need a better understanding of the electrophysiological properties of VP neurons and the molecular and biophysical determinants of these properties. Here, we used patch-clamp electrophysiology to characterize the intrinsic properties of glutamatergic VP (VPGlu) neurons and observed two distinct electrophysiological profiles: VPGlu neurons that undergo depolarization block in response to progressively increasing current injection amplitudes and those that were resistant to depolarization block. To explore the mechanisms that could contribute to these distinct profiles, we used targeted ribosome affinity purification to identify ion channel subunits and regulatory proteins by isolating actively transcribed mRNA selectively from VPGlu neurons. We then used this transcriptomic information to implement a Markov Chain Monte Carlo method to parameterize a large population of biophysically distinct multicompartment models of VPGlu neurons conforming to either subpopulation. Based on prior literature suggesting parvalbumin (PV) is expressed in a subset of VPGlu neurons, and that PV expression governs the firing properties of those neurons, we tested the hypothesis that PV expression accounted for differences in subgroups, by increasing the maximal firing frequency and conferring resistance to depolarization block. In contrast, our model determined that PV expression at physiological levels had no effect on maximum firing rate. However, supraphysiological expression levels of PV appeared to induce a depolarization block in previously depolarization block-resistant neuron models, suggesting that other intracellular calcium-binding proteins could play a role in determining the firing phenotype of VPGlu neurons. We corroborated this result with single-cell patch-clamp RT-PCR, which confirmed that PV expression did not distinguish the two electrophysiologically distinct subpopulations. Together, these findings establish that VPGlu neurons are composed of biophysically distinct subpopulations that have not been appreciated in prior studies interrogating the function of this population. With the advent of novel tools for cell-type specific pharmacology and targeted neurostimulation, this understanding will be critical for developing strategies to rationally modulate VPGlu cells to treat disorders characterized by maladaptive reward seeking.

overall_design: We used translating ribosome affinity purification (TRAP) to isolate RNA bound to ribosomes in glutamatergic neurons in the ventral pallidum and performed bulk RNA sequencing and differential gene expression analysis to compare this TRAP fraction to the input fraction.

first: Lisa

last: Fang

first: Robert

last: Graham


title: Single-cell transcriptomics reveals distinct molecular alterations of human renal cell carcinoma-derived endothelial cells that are stable in ex vivo primary culture [scRNA-seq]

overall_design: We performed scRNA-seq on TECs and NECs isolated by flow cytometry from 4 different donor nephrectomies. The RCC tumor type was confirmed as clear cell renal cell carcinoma (ccRCC) for all 4 patients on the final pathology report and confirmed by SA. The 4 donors were batched into two separate scRNA-seq libraries. In order to determine the purity of the isolated cell populations, primary TECs/NECs, we spiked in HUVECs and an aliquot of the entire tumor/normal adjacent tissue (NAT) single cell suspension


title: Expression profiles of long noncoding RNAs and mRNAs in primary porcine macrophages (PAMs) Infected with African swine fever virus

city: hangzhou

first: Hu

last: boli

state: zhejiang

address: Yuhangtang Road No.866

institute: Zijingang Campus of Zhejiang University

summary: Long noncoding RNAs (lncRNAs) participate in regulating many biological processes. However, their roles in African swine fever virus(ASFV) pathogenicity are largely unknown. Here, we analyzed the expression profile of lncRNAs and mRNAs in the ASFV-infected  or uninfected PAMs by high-throughput sequencing

overall_design: Expression profiles of long noncoding RNAs and mRNAs in PAMs infected by ASFV were generated by deep sequencing, in triplicate, using Illumina NovaSeq 6000.

first: Tianqi

last: Yu

first: Z

last: Zhang

first: Y

last: Chen

first: B

last: Hu

first: J

last: Gu

last: Zhou


title: Chromatin accessibility in mouse Epiblast stem cells induced with Mixl1

city: WESTMEAD

first: PIERRE

last: OSTEIL

state: NSW

address: 214 Hawkesbury Road

department: Embryology

institute: CMRI

summary: We performed ATAC-seq in a epiblast stem cell model of mouse gastrulation to determine the effect of Mixl1 knockout and induction on chromatin accessibility.

overall_design: ATAC-seq of Mixl1-knockout and Mixl1-inducible mouse Epiblast stem cells after 2 d of serum differentiation

first: Pierre

last: Osteil

first: Nazmus

last: Salehin

first: Patrick

last: Tam


title: Multi-omics datasets for finer-scale dissection of chromatin architecture alterations in radiation induced malignant transformation of bronchial epithelial cells [Micro-C]

status: Public on Jul 26 2024

city: Beijing

first: Yi

address: No. 28 Fuxing Rd， Haidian district，Beijing

institute: Chinese PLA General Hospital

summary: we generated CUT&Tag, ATAC-seq, RNA-seq, high-resolution Hi-C and Micro-C datasets for finer-scale dissection of chromatin architecture alterations in radiation induced malignant transformation of bronchial epithelial cells.

overall_design: Micro-C profiles of normal control human bronchial epithelial cells, TP63 overexpressed human bronchial epithelial cells and radiation induced lung cancer cells

last: pingkun

first: L

last: qiaowei


title: Multi-omics datasets for finer-scale dissection of chromatin architecture alterations in radiation induced malignant transformation of bronchial epithelial cells [STAG2 CUT&Tag]

overall_design: STAG2 CUT&Tag profiles of normal control human bronchial epithelial cells, TP63 overexpressed human bronchial epithelial cells and radiation induced lung cancer cells


title: Multi-omics datasets for finer-scale dissection of chromatin architecture alterations in radiation induced malignant transformation of bronchial epithelial cells [TP63 CUT&Tag]

overall_design: TP63 CUT&Tag profiles of normal control human bronchial epithelial cells, TP63 overexpressed human bronchial epithelial cells and radiation induced lung cancer cells


title: Multi-omics datasets for finer-scale dissection of chromatin architecture alterations in radiation induced malignant transformation of bronchial epithelial cells [CTCF CUT&Tag]

overall_design: CTCF CUT&Tag profiles of normal control human bronchial epithelial cells, TP63 overexpressed human bronchial epithelial cells and radiation induced lung cancer cells


title: A Self-Complementary AAV Proviral Plasmid System to Reduce Aberrant Cross-Packaging and ITR Promoter Activity in AAV Vector Preparations (Long-read)

city: Columbus

first: Scott

last: Harper

state: Ohio

address: Center for Gene Therapy, 575 Children’s Crossroads Room WC3740

institute: The Research Institute at Nationwide Children's Hospital

summary: Adeno-associated viral vectors (AAV) are a leading delivery system for gene therapy in animal models and humans.  With several FDA-approved AAV gene therapies on the market, issues related to vector manufacturing have become increasingly important. In this study, we focused on potentially toxic DNA contaminants that can arise from AAV proviral plasmids, the raw materials required for manufacturing recombinant AAV in eukaryotic cells.  Typical AAV proviral plasmids are circular DNAs containing a therapeutic gene cassette flanked by natural AAV inverted terminal repeat (ITR) sequences, and a plasmid backbone carrying prokaryotic sequences required for plasmid replication and selection in bacteria. While the majority of AAV particles package the intended therapeutic payload, some capsids instead package the bacterial sequences located on the proviral plasmid backbone.  Since ITR sequences also have promoter activity, potentially toxic bacterial open reading frames can be produced in vivo, thereby representing a safety risk.  In this study, we describe a new AAV proviral plasmid for vector manufacturing that (1) significantly decreases cross-packaged bacterial sequences; (2) increases correctly packaged AAV payloads; and (3) blunts ITR-driven transcription of cross-packaged material to avoid expressing potentially toxic bacterial sequences.  This system may help improve the safety of AAV vector products.

overall_design: Constructs 1 and 5 were packaged into AAV9. Genomic DNA was extracted by Azenta Life Sciences and then sequenced on the PacBio Ile platform.

first: Noah

middle: K

last: Taylor

first: Matthew

middle: J

last: Guggenbiller

first: Pranali

last: Mistry

first: Oliver

last: King

middle: Q


title: Effect of chronic type I IFN exposure on the transcriptional, metabolic profiles of human monocyte-derived macrophages

city: Dublin

first: Gina

middle: R

last: Leisching

address: St James's Hospital

department: Clinical Medicine

country: Ireland

institute: Trinity College Dublin

summary: The impact of chronic exposure to type I interferons (IFN)α2a,2b, and β, on macrophage metabolism, intimately linked to macrophage function, is not well understood. This study assesses the nuanced host responses induced by type I IFN cytokines, offering insights for potential therapeutic approaches in diseases associated with these cytokines. Employing a combination of transcriptional profiling and real-time functional analysis, we delineated the temporal evolution of metabolic reprogramming in response to chronic interferon exposure. Our results reveal distinct transcriptional metabolic profiles between macrophages chronically exposed to IFNα and IFNβ. IFNβ significantly diminishes the oxygen consumption rate and glycolytic proton extrusion rate in macrophages. Conversely, IFNα2b decreased parameters of mitochondrial fitness and induced a shift towards glutamine oxidation. Assessing the ability of macrophages to induce glycolysis in response to antigenic stimuli (LPS and iH37Rv), we found that chronic exposure to all IFN subtypes limited glycolytic induction. This study addresses a critical oversight in the literature, where individual roles of IFN subtypes are frequently amalgamated and lack distinction. These findings not only provide novel insights into the divergent effects of interferon α2a,α2b, and β on macrophage metabolism but also highlight their potential implications for developing targeted therapeutic strategies.

overall_design: Peripheral blood mononuclear cells (PBMC) were isolated from the buffy coats of healthy donors by density-gradient centrifugation over Lymphoprep (StemCell Technologies). Cells were washed, resuspended at 2.5x106 PBMC/ml in RPMI (Gibco) supplemented with 10% AB human serum (Sigma90 Aldrich), and plated onto non-treated tissue culture plates (Costar). Cells were maintained in humidified incubators for 7 days at 37°C and 5% CO2. Human IFNβ (IF014, Merck, KGaA, Darmstadt), IFNα2a (11100-1, PBL assay science, NJ, USA), and IFN IFNα2b (11105-1, PBL assay science, NJ, USA) were added at a concentration of 1000U/ml for 5 day before analysis. On day 5 of chronic type I IFN exposure, RNA from each treatment group was extracted using the RNeasy® Plus Mini Kit (Qiagen, Limburg, Netherlands). The NanoString nCounter Human Metabolic Pathways Panel (Cat # XT-CSO-HMP1-12, N = 6 per IFN subtype; transcripts of 768 metabolic genes) was used to generate gene expression data.

first: Anjali

last: Yennemadi

first: Karl

last: Gogan

first: Joseph

last: Keane


title: Features of chronic urticaria after COVID-19 mRNA vaccine, a real-life cohort study

city: Lausanne

first: Yannick

last: Muller

state: Vaud

address: Rue du Bugnon 46

department: Center for Human Immunology and Vaccinology

country: Switzerland

institute: Lausanne University Hospital (CHUV)

summary: New onsets of chronic urticaria (CU) have been reported after repeated immunizations, mainly with the Moderna mRNA-1273 vaccine (Spikevax). This study aims to evaluate patients with CU after COVID-19 mRNA vaccination. The contribution of SARS-Cov2 infection, atopy and IgE against the vaccine was analyzed. We monitored the features of patients who developed CU after vaccination in the Canton of Vaud through two surveys conducted in 2022 and 2023. Fifty individuals with CU underwent blood tests, and their results were compared with individuals without a history of urticaria (N=135). The presence of anti-vaccine IgE was detected with basophil activation tests (BAT). We assessed anti-SARS-Cov2 humoral response, and the presence of IgEs against common respiratory allergens (Phadiatop) as a surrogate for atopy. Post-vaccination CU occurred after a median interval of 10 days and significantly more after the Spikevax booster, affecting middle-aged individuals (median 41, 66% females). In 2023, CU was still active in 53% of the cases. Inducible forms of CU, primarily dermographism, were reported in 54% (2022) and 61% (2023) of the cases. BAT positivity was not specific to CU, anti-nucleocapsid positivity, or atopy but was significantly associated with higher anti-spike neutralizing activities and younger age. Four CU patients tolerated an additional dose of mRNA vaccine with no disease exacerbation/recurrence. The spikevax booster induced anti-vaccine IgE independently of CU, the latter being not directly associated with COVID-19 infection nor atopy. The tolerance to a new booster in 4/4 patients suggests that the Spikevax vaccine indirectly triggered CU in predisposed individuals.

overall_design: Blood samples were collected from patients with chronic urticaria and healthy controls in PAXgene Blood RNA tubes. RNA-seq libraries were generated from the blood samples and used to perform differential gene expression analysis and pathway enrichment analyses.

first: Johan

last: Schwab

first: Gustavo

last: Ruiz Buendía

first: Natacha

last: Madelon

first: Arnaud

last: Didierlaurent


title: Synthetic RIG-I agonist-mediated cancer immunotherapy synergizes with MAP-Kinase inhibition against BRAF mutated melanoma

city: Bonn

first: Thais

middle: Marina

last: Schlee-Guimarães

address: Venusberg-Campus 1

department: Institute of Clinical Chemistry and Clinical Pharmacology

institute: University Hospital, University of Bonn

summary: The implementations of targeted molecular therapies and immunotherapy in melanoma vastly improved the therapeutic outcome in patients with limited efficacy of surgical intervention. Nevertheless, a large fraction of melanoma patients still remains refractory or acquires resistance to these new forms of treatment, illustrating a need for improvement. Here we report that the clinically relevant combination of MAP kinase inhibitors Dabrafenib and Trametinib synergizes with RIG-I agonist-induced immunotherapy to kill BRAF-mutated human and mouse melanoma cells. Kinase inhibition did not compromise the agonist-induced innate immune response of the RIG-I pathway in host immune cells. In a melanoma transplantation mouse model, the triple therapy outperformed the individual therapies. Our study suggests that targeted activation of RIG-I with its synthetic ligand 3pRNA could vastly improve tumor control in a substantial fraction of melanoma patients receiving MAP kinase inhibitors.

overall_design: A375 cells were treated for 24 hours with DMSO, Dabrafenib, Trametinib or the combination of both. Additionally, each condition was left unstimulated, transfected with CA21 control RNA or the activating RIG-I ligand 3pRNA. Total RNA was isolated and subjected to poly-A based library preparation.

first: Christian

last: Grützner

last: Schlee-Guimaraes

first: Marius

last: Jentsch

first: Jonathan

last: Schmid-Burgk

first: Marcel

last: Renn

first: Rayk

last: Behrendt

first: Gunther

last: Hartmann


title: Modeling Neutrophil Heterogeneity Contribution to Burn Healing in Larval Zebrafish

city: Madison

first: Huy

last: Dinh

state: WI

address: 1111 Highland Avenue

institute: University of Wisconsin-Madison

summary: Neutrophils accumulate early in burn wounds, and their activation is associated with more severe burns. Understanding their functionality would facilitate the development of a more targeted therapeutic strategy for healing. However, we still lack a view of the cellular and functional heterogeneity in neutrophils involved in thermal injuries. Here, we establish the use of larval zebrafish for understanding neutrophil responses in burn. Zebrafish model allows for linking neutrophil states and their functions in real time through genetic modifications and live imaging. We performed single-cell transcriptional (scRNA-Seq) mapping of myeloid cells during a 3-day time course in burn and unwounded conditions. We identified transcriptionally distinct states in myeloid cells that form a consistent population structure across time points and conditions. By comparing burn and unwounded conditions, we found subtype-specific enrichment of biological processes and differential usage of gene regulatory networks. Pseudotime and RNA velocity analyses predict distinct branched trajectories for neutrophils, with one branch resembling the process of human neutrophil maturation. The other branch is not transcriptionally conserved with humans and is highly associated with leukocyte migration functionality, suggesting its engagement at the wound site. Transcriptional network analysis identified RAR/RXR family transcription factors as potential upstream factors driving this trajectory divergence in neutrophils. Furthermore, we characterized the transcriptional dynamics of cell-cell interactions in both conditions by time. Among burn-induced signaling pathways, we found il6-il6r signaling as a time-point-specific macrophage-neutrophil interaction, suggesting the importance of timing in innate immune response in burn. Finally, to test the translational value of our fish model, we examined zebrafish neutrophil state signatures in human burn patient samples. We found homolog expression of immature neutrophils positively correlates with the degree of total body surface area (TBSA) in patients. Flow cytometry confirmed the presence of neutrophils carrying these signatures in patient's blood. Our findings demonstrate the potential of using zebrafish as a model to identify early innate immune response signatures that could inform a timely treatment of burn in humans. This work builds the molecular foundation and a comparative single-cell genomic framework to guide future identification of actionable pathways to burn wound healing in patients.

overall_design: At 6/24/48 hour-post-burn (hpb), burned and unwounded larvae at matching developmental stages (3/4/5 day-post-fertilization (dpf)) were transferred to 35 mm dish containing calcium-free PBS for 15 min and then anesthetized with tricaine methanesulfonate (MS222, 200 mg/L). A total of 150 fish were used for each time point by condition. Each dish of fish was digested with 2 mL digestion solution (0.25% trypsin, 1mM EDTA in PBS) at 28.5˚C for 90 min with gentle pipetting every 10 min. Digestion was stopped by adding 200 mL digestion stop solution (1mM CaCl2, 100% FBS). Dissociated cells were filtered with 40 mm cell strainers and centrifuged for 3 min at 3,000 rpm at 4 ̊C. Cell pellets were resuspended in PBS with 10% FBS plus DAPI (1mg/mL). Fluorescence activated cell sorting (FACS) was performed at University of Wisconsin Carbone Cancer Center Flow Lab using BD FACSAria. Targeted cells passed gating for cells versus debris, singles versus doublets, live versus dead and were high in either 488 nm/561 nm channel. Both dendra+ (488 nm channel) and mCherry+ (561 nm channel) cells were sorted into PBS with 10% FBS. Post sorting, cells were directly used for library construction in a Chromium controller at the Gene Expression Center of the University of Wisconsin-Madison Biotechnology Center (RRID: SCR_017757). Samples were processed with Chromium Single Cell Gene Expression Solution 3’ v2 (10X Genomics).

first: Yiran

last: Hou

first: Parth

last: Khatri

first: Julie

last: Rindy

first: Anna

last: Huttenlocher


title: Gene expression analysis of human sickle cell disease (SCD) and healthy donor (HD) CD34+ hematopoietic stem/progenitor cells (HSPCs) treated with CRISPR/Cas9 targeting the HBG promoters or untreated samples

city: Padova

first: Oriana

last: Romano

address: Via U. Bassi 58/B

department: Molecular Medicine

country: Italy

institute: University of Padova

summary: We have investigated gene expression changes occurring in samples electroporated with Cas9 ribonucleoprotein (RNP) complexes targeting the -196 or the -197 nucleotide upstream of the HBG promoters or the unrelated AAVS1 locus

overall_design: We performed RNA-seq analysis in SCD and HD CD34+ HSPCs (3 donors) that were preactivated for 2 days, then electroporated with Cas9 RNP containing guide RNA targeting the -196 or the -197 nucleotide upstream of the HBG promoters or the unrelated AAVS1 locus, and then cultured for 2 additional days. Control untreated cells were also cultured for a total of 4 days.

first: Giacomo

last: Frati

first: Annarita

last: Miccio

first: Megane

last: Brusson


title: Cohesin trajectories shape the epigenetic and transcriptional landscape of clustered Protocadherin genes for single neuron identities

city: SAN FRANCISCO

first: Lea

last: Kiefer

state: CA

address: 1651 4th Street, Weill Neurosci RM 471A

institute: UCSF

summary: Cellular individuality is often achieved by stochastic expression of single genes within tandemly-arrayed gene families. This principle is epitomized by the stochastic choice of clustered Protocadherin (Pcdh) genes which generates the extraordinary cell-surface diversity required for neural circuit assembly during development. However, the molecular mechanisms by which this diversity arises are not fully understood. Here, we show that stochastic Pcdh gene choice requires “escape” from silent heterochromatin by a distal transcriptional enhancer. These enhancer/promoter encounters, that lead to promoter derepression, are catalyzed by cohesin, whose processivity, density and stalling at boundaries define the probability of choice of Pcdh genes by determining the probability of enhancer/promoter contacts in mouse olfactory sensory and cortical neurons. We propose that coupling between an epigenetic switch and the modularity of cohesin trajectories allows for different Pcdh profiles to arise across neuronal cell-types, underlying the diversities of their morphologies and functions in the nervous system. More broadly these principles add a layer of regulatory finesse for the generation of transcription diversity from genes arranged in clusters.

overall_design: Examination of  single-cell and bulk RNA, CTCF/Cohesin localization on chromatin, genome folding and DNA methylation levels within the clustered Protocadherin locus  in olfactory sensory neurons and cortical neurons from mice carrying genetic mutations.

first: Simon

last: Gaudin

first: Sandy

last: Rajkumar

first: Gabrielle Isabelle

middle: F

last: Servito

first: Jennifer

last: Langen

first: Michael

middle: H

last: Mui

first: Shayra

last: Nawsheen

first: Daniele

last: Canzio


title: Single-cell profiling reveals altered immune landscape and impaired NK cell function in gastric cancer liver metastasis

city: Jinan

first: Detian

last: Yuan

address: Wenhuaxi 44

institute: Shandong University

summary: Gastric cancer (GC) is a substantial global health concern, and the development of liver metastasis (LM) in GC represents a critical stage linked to unfavorable patient prognoses. In this study, we employed single-cell RNA sequencing (scRNA-seq) to investigate the immune landscape of GC liver metastasis, revealing several immuno-suppressive components within the tumor immune microenvironment (TIM).

overall_design: We employed scRNA-seq to comprehensively analyze the immune landscape in gastric cancer liver metastasis. We collected tissues from three liver metastases (LM) of gastric cancer, along with matched primary GC samples. Additionally, we included three liver samples from healthy donors (HL) for comparison.

first: Xiaolong

last: Tang

first: Hui

last: Qu