title: TDP-43 stable deficiency leads to transcriptional dysregulation and transposable elements activation via global  R-loops and 5hmC landscape alteration [ATAC-Seq]

city: Atlanta

first: Bing

last: Yao

institute: Emory University

summary: TAR DNA-binding protein 43 (TDP-43) is an RNA/DNA-binding protein involved in many aspects of RNA metabolism, but its molecular roles in regulating gene and tTransposable eElements (TEs) transcription transcription is not extensively explored. TDP-43 loss-of-function via due to progressive cytoplasmic aggregations serves as a pathological hallmark and potential causality for several neurodegenerative diseases. While rRecent evidence suggest TDP-43 acute knockdown of TDP-43 affects the formation of R-loops formation, a nuclear DNA:RNA hybrid structures implicated in transcription regulation, . However, how its stable and chronic functional perturbation of TDP-43, which more closely resembles age-related neurodegeneration, impact global transcriptome via R-loop dysregulation remains unclear. Here we show demonstrate that stable and prolonged TDP-43 loss-of-function results in slowed impaired cell proliferation and impaired DNA damage response. At the molecular level, TDP-43 stable knockdown impacts key gene expression through concomitantly altering intragenic R-loops dynamics and its crosstalk with and thea DNA covalent modification 5-hydroxymethylcytosine (5hmC) in cis, as well as long- range R-loops-mediated enhancer-promoter interactions in trans. Furthermore, we find TDP-43 stable knockdown induces massive disease-related TEstransposable elements (TEs) activation via influencing R-loop and 5hmC homeostasis in many of these loci. Our results highlight previous underdeveloped transcriptional roles of TDP-43 via R-loops regulation in coding genes, distal regulatory elements and TEs, and suggest that TDP-43 proteinopathies transcriptionally contributes to the etiology of neurodegenerative disorders.

overall_design: TDP-43 knockdown by shRNA, ATAC-seq

first: Yingzi

last: Hou

first: Yangping

last: Li


title: TFAP2 paralogs regulate midfacial development in part through a conserved ALX genetic pathway [RNA-Seq]

status: Public on Jan 01 2024

city: Iowa City

first: Eric

last: Van Otterloo

state: Iowa

address: 801 Newton Rd

country: USA

institute: University of Iowa

type: Expression profiling by high throughput sequencing

summary: Cranial neural crest development is governed by positional gene regulatory networks (GRNs). Fine-tuning of the GRN components underly facial shape variation, yet how those in the midface are connected and activated remain poorly understood. Here, we show that concerted inactivation of Tfap2a and Tfap2b in the murine neural crest, even during the late migratory phase, results in a midfacial cleft and skeletal abnormalities. Bulk and single-cell RNA-seq profiling reveal that loss of both Tfap2 members dysregulates numerous midface GRN components involved in midface morphogenesis, patterning, and differentiation. Notably, Alx1/3/4 (Alx) transcript levels are reduced, while ChIP-seq analyses suggest TFAP2 directly and positively regulates Alx gene expression. TFAP2 and ALX co-expression in midfacial neural crest cells of both mouse and zebrafish further implies conservation of this regulatory axis across vertebrates. Consistent with this notion in zebrafish, tfap2a mutants present abnormal alx3 expression patterns, Tfap2a binds alx loci, and tfap2a-alx3 genetic interactions are observed. Together, these data demonstrate TFAP2 paralogs regulate vertebrate midfacial development by activating expression of ALX transcription factors.

overall_design: To investigate the role of TFAP2 (Tfap2a and Tfap2b) in midface neural crest cell development, we isolated E10.5 frontonasal and maxillary prominence tissue from 3 Tfap2a;Tfap2b;Wnt1CRE mutants, and 3 sibling matched controls, and conducted bulk RNA sequencing of the cDNA generated.

first: Timothy

last: Nguyen


title: TFAP2 paralogs regulate midfacial development in part through a conserved ALX genetic pathway [ChIP-seq]

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: To investigate the regions of TFAP2 binding, genome wide, E11.5 wild-type craniofacial prominences (including the frontonasal, maxillary, and mandibular prominence) were harvested and subjected to chromatin immunoprecipitation using  a TFAP2 antibody (which recognizes TFAP2A, TFAP2B, and TFAP2C). Immunoprecipitated samples along with 'input' were sequenced.


title: TFAP2 paralogs regulate midfacial development in part through a conserved ALX genetic pathway

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

overall_design: Refer to individual Series


title: PAF1c links S-phase progression to immune evasion and MYC function in pancreatic carcinoma [ChIP-seq/CUT&RUN]

city: Wuerzburg

first: Martin

last: Eilers

address: Am Hubland

department: Chair for Biochemistry and Molecular Biology

country: Germany

institute: University of Wuerzburg

summary: In pancreatic ductal adenocarcinoma (PDAC), endogenous MYC is required for S-phase progression and escape from immune surveillance. Here we show that MYC in PDAC cells is needed for the recruitment of the PAF1c transcription elongation complex to RNA polymerase and that depletion of CTR9, a PAF1c subunit, enables long-term survival of PDAC-bearing mice. PAF1c is largely dispensable for normal proliferation and regulation of MYC target genes. Instead, PAF1c limits DNA damage associated with S-phase progression by being essential for the expression of long genes involved in replication and DNA repair. Surprisingly, the survival benefit conferred by CTR9 depletion is not due to DNA damage, but to T-cell activation and restoration of immune surveillance. This is because CTR9 depletion releases RNA polymerase and elongation factors from the body of long genes and promotes the transcription of short genes, including MHC class I genes. The data argue that functionally distinct gene sets compete for elongation factors and directly link MYC-driven S-phase progression to tumor immune evasion.

overall_design: Chromatin binding of RNAPII, SPT6, SPT5, CTR9 and MYC upon CTR9 depletion

first: Abdallah

last: Gaballa

first: Peter

last: Gallant

first: Carsten

middle: P

last: Ade


title: The RORɣ/SREBP2 pathway is a master regulator of cholesterol metabolism and serves as potential therapeutic target in t(4;11) leukemia

city: Saarbrücken

first: Julia

middle: Maria

last: Schulze-Hentrich

address: Campus, Building A2.4

department: Genetics and Epigenetics

institute: Saarland University

summary: Dysregulated cholesterol homeostasis promotes tumorigenesis and progression. Therefore, metabolic reprogramming constitutes a new hallmark of cancer. However, until today, only few therapeutic approaches exist to target this pathway due to the often-observed negative feedback induced by agents like statins leading to controversially increased cholesterol synthesis upon inhibition. Sterol regulatory element-binding proteins (SREBPs) are key transcription factors regulating the synthesis of cholesterol and fatty acids. Since SREBP2 is difficult to target, we performed pharmacological inhibition of retinoic acid receptor (RAR)-related orphan receptor gamma (RORγ), which acts upstream of SREBP2 and serves as master regulator of the cholesterol metabolism. This resulted in an inactivated cholesterol-related gene program with significant downregulation of cholesterol biosynthesis. Strikingly, these effects were more pronounced than the effects of fatostatin, a direct SREBP2 inhibitor. Upon RORγ inhibition, RNA sequencing showed strongly increased cholesterol efflux genes leading to leukemic cell death and cell cycle changes in a dose- and time-dependent manner. Combinatorial treatment of t(4;11) cells with the RORγ inhibitor showed additive effects with cytarabine and even strong anti-leukemia synergism with atorvastatin by circumventing the statin-induced feedback. Our results suggest a novel therapeutic strategy to inhibit tumor-specific cholesterol metabolism for the treatment of t(4;11) leukemia.

overall_design: human cord blood-derived CD34+ cells were modified using CRISPR/Cas9 to carry an endogenous t(4;11) translocation. RNA sequencing was performed using TruSeq mRNA Stranded Sequencing (Illumina) from three donors in technical duplicates, comparing XY018-treated and untreated cells.

first: Estelle

last: Erkner

first: Thomas

last: Hentrich

first: Corina

last: Schneidawind


title: The Helicobacter pylori Methylome is Acid-Responsive due to Regulation by the Two-Component System ArsRS and the Type I DNA Methyltransferase HsdM1 (HP0463)

city: Williamsburg

first: Mark

last: Forsyth

state: Virginia

address: 540 Landrum Dr

department: Biology

institute: William & Mary

summary: Helicobacter pylori colonizes the gastric epithelium and is the leading cause of gastric adenocarcinoma. There is increasing evidence that DNA methylation regulates gene expression in addition to its role in genome protection. In this study, we characterize the impact of acidity, the Two-Component System (TCS) ArsRS, Autoinducer-2, and the Type I m6A DNA methyltransferase HsdM1 (HP0463) on the Helicobacter pylori methylome. Transcription of hsdM1 increases at least 4-fold in the absence of the sensory histidine kinase ArsS, the major acid sensing protein of H. pylori. HsdM1 exists in the phase-variable operon hsdR1-hsdM1. Phase-locking hsdR1 (HP0464), the restriction endonuclease gene, has significant impacts on the transcription of hsdM1. To determine the impacts of methyltransferase transcription patterns on the methylome, we conducted methylome sequencing on samples that had undergone prolonged acid-exposure experiment. We found differentially methylated motifs between pH 7 and pH 5 growth conditions, and that deletions of arsS and hsdM1 interfere with the epigenetic acid response. Deletion of arsS leads to altered hsdM1 expression and alters the activity of multiple methyltransferases in both conditions indicating that the ArsRS TCS, in addition to its role in acid acclimation via direct effects on regulon member transcription, may also indirectly impact gene expression via regulation of the methylome. We characterized the target motif of HsdM1 (HP0463) to be (H)HTCAVN6TGY. HsdM1 may hierarchically regulate the Type II m5C DNA methyltransferase HP1121. This complex regulation of DNA methyltransferases, and thus differential methylation patterns, may have implications for the decades-long persistent infection by H. pylori.

overall_design: Three Helicobacter pylori 26695 mutant strains were used for our experiments: a metranidazole-resistant control strain (ΔrdxA, referenced as 1' or control mutant), a strain with a deletion of the hsdM1 gene (ΔrdxA-ΔhsdM1, referenced as ΔhsdM1), and a strain with a deletion of the arsS gene (ΔrdxA-ΔarsS, referenced as ΔarsS). Each strain underwent a 72 hour growth in either pH 5 or pH 7 SFBB-cholesterol-vancomycin broth culture conditions, following a subculture procedure every 24 hours. Genomic DNA was extracted using the Bio-Rad gDNA extraction kit. Sequencing was performed via the PacBio Sequel Machine using Single Molecule, Real-Time (SMRT) sequencing. Azenta Life Sciences performed SMRT-seq and data analysis with the SMRT Analysis software through PacBio.

first: Elise

middle: H

last: Zimmerman

first: Erin

middle: L

last: Ramsey

first: Katherine

middle: E

last: Hunter

first: Sarah

middle: M

last: Villadelgado

first: Celeste

last: Phillips


title: PAF1c links S-phase progression to immune evasion and MYC function in pancreatic carcinoma [4sU-seq]

overall_design: 4sU sequencing upon the expression of shRNA targeting either luciferase control or Ctr9


title: TDP-43 stable deficiency leads to transcriptional dysregulation and transposable elements activation via global  R-loops and 5hmC landscape alteration [5hmC-Seal-seq]

status: Public on Jan 03 2024

first: Bing

last: Yao

address: 615 Michael Street

department: Department of Human Genetics

type: Methylation profiling by high throughput sequencing

overall_design: TDP-43 knockdown by shRNA, 5hmC-Seal-seq

first: Yingzi

last: Hou

first: Yangping

last: Li


title: PAF1c links S-phase progression to immune evasion and MYC function in pancreatic carcinoma [BLISS]

first: Martin

last: Eilers

summary: In pancreatic ductal adenocarcinoma (PDAC), MYC is required for S-phase progression and escape from immune surveillance. Here we show that recruitment of the PAF1c transcription elongation complex to RNA polymerase depends on MYC and that depletion of CTR9, a PAF1c subunit, enables long-term survival of PDAC-bearing mice. PAF1c is largely dispensable for unperturbed proliferation and regulation of MYC target genes. Instead, PAF1c limits DNA damage associated with transcription-replication conflicts by being essential for expression of long DNA repair genes. Surprisingly, the survival benefit conferred by CTR9 depletion is not due to DNA damage, but to restoration of immune surveillance. This occurs because CTR9 depletion releases RNA polymerase and the histone chaperone SPT6 from the body of long genes, promoting transcription of short genes that include MHC class-I genes. The data show that functionally distinct gene sets compete for elongation factors and directly link MYC-driven S-phase progression to tumor immune evasion.

overall_design: Sequencing of double-strand breaks in cells exposed to AZD6738 with or without MYC depletion


title: PAF1c links S-phase progression to immune evasion and MYC function in pancreatic carcinoma


title: PAF1c links S-phase progression to immune evasion and MYC function in pancreatic carcinoma [RNA-seq]

overall_design: RNA sequencing upon CTR9, CDC73 or MYC depletion.

first: Abdallah

last: Gaballa


title: PAF1c links S-phase progression to immune evasion and MYC function in pancreatic carcinoma [CUTnRun and ChIP]

overall_design: Chromatin binding of RNAPII, SPT6, SPT5, CTR9 and MYC upon CTR9 depletion and of MYC upon MYC depletion

first: Peter

last: Gallant


title: scRNA gene expression of breast tumors with mutant p53 or mutant p53 deleted [scRNA-seq]

city: Houston

first: Yuan

last: Qi

state: TX

address: 1400 Pressler St

department: Bioinformatics & Computational Biology

institute: University of Texas M.D. Anderson Cancer Center

summary: We conducted gene expression analysis from total tumor treated with AAV-Control or AAV-mut-p53 deleted in an acute setting.

overall_design: scRNA sequencing analysis was conducted in AAV-Control (N=2) or AAV-mut-p53 deleted (N=5).

first: Denada

last: Dibra

first: Guillermina

last: Lozano


title: Transcriptomic alteration of SOD1-G93A mutation and leptin deficiency in the adipose tissue

status: Public on Dec 31 2023

city: Madrid

first: Silvia

last: Corrochano

address: Calle del Prof Martín Lagos

department: Neurología

country: Spain

institute: Instituto de Investigación Sanitaria del Hospital Clínico San Carlos

summary: Amyotrophic lateral sclerosis (ALS) is a multifactorial and complex fatal degenerative disorder. Both patients and animal models have significant dysregulation in metabolism that can be associated with body weight loss and hypermetabolism. A higher body mass index appears to have protective effects on the disease, but the role of adipose tissue is still not well understood. In this work we have proposed the following objectives: a) determine the effects that the SOD1G93A mutation has on adipose tissue b) study how an increase in body mass through a genetic deficiency in leptin impacts in the adipose tissue of mice SOD1G93A.

overall_design: To investigate the effects of SOD1G93A mutation and leptin deficiency on the adipose tissue , the iWAT depots of WT,  Lepob/+, SOD1G93A, SOD1G93A-Lepob/+  female mice, was dissected at 90 days of age, and the RNA was isolated to perform the bulk RNA-sequencing study (n=4 per group).

first: Luis

middle: C

last: Fernández-Beltrán

first: Zeinab

last: Ali

first: Juan

last: Godoy-Corchuelo

first: Irene

last: Garcia-Toledo


title: Antifungal activity of the repurposed drug disulfiram against Cryptococcus neoformans.

city: Nanjing

first: Min

last: Peng

state: Jiangsu

address: No. 305 Zhongshan East Road, Xuanwu District, Nanjing, Jiangsu Province, China 210002

country: China

institute: Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, China

summary: Fungal infections have become a clinical challenge due to the emergence of drug-resistance of invasive fungi and a rapid increase of novel pathogens. The development of drug resistance has further restricted the use of antifungal agents. Therefore, there is anurgentneedto searchforalternativetreatmentoptions for Cryptococcus neoformans (C. neoformans). Disulfiram (DSF) has a high human safety profile and promising applications as an antiviral, antifungal, antiparasitic, and anticancer agent. In contrast, the effect of DSF on Cryptococcus has yet to be thoroughly researched. This study investigated the antifungal effect and mechanism of DSF againstC. neoformansto provide a new theoretical foundation for treating Cryptococcal infections. In vitro studies demonstrated that DSF inhibitedCryptococcusat minimum inhibitory concentrations (MICs) ranging from 1.0 to 8.0 μg/mL. Combined antifungal effects were also observed with 5-fluorocytosine, amphotericin B, terbinafine, or ketoconazole. In vivo, DSF exerted asignificantprotectiveeffectforGalleria mellonella infected with C. neoformans.Mechanistic investigations showed that DSF dose-dependently inhibited the melanin, urease, acetaldehyde dehydrogenase, capsule, and biofilm formation or viability ofC. neoformans.Further study indicated DSF affectedC. neoformansby interfering with multiple biological pathways, including replication, metabolism, membrane transport, and biological enzyme activity. Potentially essential targets of these pathways included acetaldehyde dehydrogenase, catalase, ATP-binding cassette transporter (ABC transporter) AFR2, and iron-sulfur cluster transporter ATM1. These findings contribute to the understanding of mechanisms inC. neoformans, and provide new insights for the application of DSF.

overall_design: To investigate further mechanisms of DSF against C. neoformans, we analyzed the regulation of the expression at the transcriptional level. A1-A3 (parallel replicates) were H99 control groups, and B1-B3 were H99 treated with 4 μg/mL of disulfiram through sequencing of the RNA-seq.

first: Chen

last: Zhang

first: Yuan-yuan

last: Duan

first: Hai-bo

last: Liu

first: Xin-yuan

first: Qian

last: Wei

first: Qi-ying

last: Chen

first: Hong

last: Sang

first: Qing-tao

last: Kong


title: N4-acetylcytidine modifies primary microRNAs for processing in cancer cells

city: Shanghai

first: Jianxiu

last: Yu

address: Room 202, Building 7, 280 South Chongqing Road

department: Department of Biochemistry and Molecular Cell Biology

institute: Shanghai Jiao Tong University school of medicine

type: Non-coding RNA profiling by high throughput sequencing

summary: N4 acetylcytidine (ac4C) modification mainly occurs on tRNA, rRNA, and mRNA, playing an important role in the expression of genetic information. However, it is still unclear whether microRNAs have undergone ac4C modification and their potential physiological and pathological functions. In this study, we identified that NAT10/THUMPD1 acetylates primary microRNAs (pri-miRNAs) with ac4C modification. Knockdown of NAT10 suppresses and augments the expression levels of mature miRNAs and pri-miRNAs, respectively. Molecular mechanism studies found that pri-miRNA ac4C promotes the processing of pri-miRNA into precursor miRNA (pre-miRNA) by enhancing the interaction of pri-miRNA and DGCR8, thereby increasing the biogenesis of mature miRNA. Knockdown of NAT10 attenuates the oncogenic characters of lung cancer cells by regulating miRNA production in cancers. Moreover, NAT10 is highly expressed in various clinical cancers and negatively correlated with poor prognosis. Thus, our results reveal that NAT10 plays a crucial role in cancer initiation and progression by modulating pri-miRNA ac4C to affect miRNA production, which would provide an attractive therapeutic strategy for cancers.

overall_design: mRNA and LncRNA assocatied with ac4C profiles, mRNA and LncRNA assocatied with NAT10 profiles, mRNA and miRNA expression profiles in A549-shNAT10 stable cell lines.

first: Hailong


title: Effect of RGRN-305 on MC903-induced skin inflammation in mice

city: Aarhus

first: Hakim

last: Ben Abdallah

state: Denmark

address: Palle Juul-Jensens Boulevard 45

department: Dermatology and Venerology

country: Denmark

institute: Aarhus University Hospital

summary: The aim was to demonstrate that RGRN-305 suppresses MC903-induced atopic dermatitis like-alterations in gene expression.

overall_design: Mice were challenged with MC903 or vehicle on right ears of mice followed by treatment with RGRN-305 or dexamethasone daily for 9 days. Ear biopsies were collected at the end of the experiment (day 9) and RNA sequenced (gene expression analysis). Number of mice in treatment groups: vehicle = 6,  MC903 =8, MC903+RGRN-305 = 8, MC903+Dexamethasone = 4.

middle: B

last: Abdallah


title: DNA methylome, R-loop and clinical exome profiling of patients with sporadic Amyotrophic Lateral Sclerosis

city: Debrecen

first: Lorant

last: Szekvolgyi

address: Egyetem ter 1.

department: Department of Pharmacy

country: Hungary

institute: University of Debrecen


title: DNA methylome, R-loop and clinical exome profile of patients with sporadic Amyotrophic Lateral Sclerosis (RRBS)

summary: Amyotrophic Lateral Sclerosis (ALS) is a fatal neurodegenerative disorder characterised by the death of motor neurons, the aetiology of which is essentially unknown. Here, we present an integrative epigenomic study in blood samples from seven clinically characterised sporadic ALS patients to elucidate molecular factors associated with the disease. We used clinical exome sequencing (CES) to study DNA variants, DNA-RNA hybrid immunoprecipitation sequencing (DRIP-seq) to assess R-loop distribution, and reduced representation bisulfite sequencing (RRBS) to examine DNA methylation changes. The above datasets were combined to create a comprehensive repository of genetic and epigenetic changes associated with the ALS cases studied. Our data descriptor is expected to guide further mechanistic studies on ALS to discover underlying genetic causes and develop new epigenetic therapies to combat this life-threatening disease.

overall_design: To investigate the changes of DNA methylation in relation to ALS, we performed RRBS (reduced representation bisulfite sequencing) experiment on blood samples from 6 patients diagnosed with ALS (that had no other disease) and from 6 healthy individuals (control).

first: Orsolya

last: Feró

first: Dóra

last: Varga

first: Éva

last: Nagy

first: Zsolt

last: Karányi

last: Sipos

first: József

last: Engelhardt

first: Nóra

last: Török

first: István

last: Balogh

first: Borbála

last: Vető

last: Likó

first: Ábel

last: Fóthi

first: Zoltán

last: Szabó

first: Gábor

last: Halmos

first: László

last: Vécsei

first: Tamás

last: Arányi

first: Lóránt

last: Székvölgyi


title: DNA methylome, R-loop and clinical exome profile of patients with sporadic Amyotrophic Lateral Sclerosis (CES)

last: Szekvolgyi

overall_design: To investigate the DNA variants in relation to ALS, we performed CES (clinical exome sequencing) experiment on blood samples from 7 patients diagnosed with ALS (that had no other disease).


title: DNA methylome, R-loop and clinical exome profile of patients with sporadic Amyotrophic Lateral Sclerosis (DRIP)

overall_design: To investigate the R-loop profile in relation to ALS, we performed DRIP-seq experiment on blood samples from 7 patients diagnosed with ALS (that had no other disease).

last: Feró


title: Reconstructed Human Skin with Hypodermis Shows Essential Role of Adipose Tissue in Skin Metabolism

city: Amsterdam

first: Jonas

last: Jäger

address: De Boelelaan 1108

country: Netherlands

institute: Amsterdam UMC

summary: Characterize reconstructed human skin (RhS) models metabolically and investigate the role of adipose tissue in skin metabolism.

overall_design: RNA-sequencing to compare expression profiles of RhS and adipose-RhS, epidermis and dermis separately with four biological replicates.

first: Irit

last: Vahav

first: Maria

last: Thon

first: Taco

last: Waaijman

first: Bas

last: Spanhaak

first: Michael

last: de Kok

first: Ranjit

middle: K

last: Bhogal

first: Susan

last: Gibbs

first: Jasper

middle: J

last: Koning


title: Expression profiling in R/M HNSCC treated with immunotherapy

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

country: Italy

institute: IRCSS Istituto Nazionale Tumori

overall_design: Refer to individual Series


title: Expression profiling in R/M HNSCC treated with immunotherapy (testing set)

summary: In recurrent/metastatic (RM) head and neck squamous cell cancer (HNSCC) not amenable to salvage surgery or radiation, the overall survival remains unsatisfactory, and the patients often experience a huge burden of symptoms requiring treatments that could achieve objective response on the disease itself. Recently, treatment with immune checkpoint inhibitors (ICI) has shown survival benefit in randomized clinical trials both in the setting of platinum pre-treated patients and in patients at their first line of treatment, with the expression of PDL1 on the tumor. Despite the introduction of ICI, only a small subset of RM HNSCC patients achieves long-term survivorship. We aim at identifying predictors of outcome and evaluating a gene expression signature (Cl6-immunereactive) in patients treated with ICI therapy. Our data highlight the presence of biological underlying differences able to predict outcome following treatment with ICI for platinum-refractory RM-HNSCC.

overall_design: For testing purposes, an independent cohort was collected and R/M HNSCC patients treated with immune checkpoint inhibitor as single agent were retrospectively evaluated and enrolled if they had an overall survival less than 6 months (short-term survivors, STS) or longer than 18 months (long-term survivors, LTS) since beginning of the therapy.


title: RNA-seq analysis revealed that crizotinib-induced cardiomyocyte death,  and cardiac dysfunctionapoptosis is related to autophagosome-lysosome fusion  and mitochondrial injury

city: Hang Zhou

first: Zhifei

last: Xu

address: 866 Yuhangtang Road

institute: Zhejiang University

summary: Crizotinib, a widely used dual ALK/MET/ROS1  inhibitor, have been seriously limited due to cardiac adverse effects. Here, we found that crizotinib caused left ventricular dysfunction, structural damage and pathological remodeling in mice and induced cardiomyocyte apoptosis and mitochondrial injury. Here, we demonstrated that crizotinib lead to aberrant accumulation of MET protein by interrupting autophagosome-lysosome fusion and knockdown of MET expression or re-activating autophagy flux rescued the cardiomyocytes death and mitochondrial injury caused by crizotinib. We identified that inhibition of the phosphorylation of AMPKSer485/491 reduced the transcriptional level of genes required for autophagosome-lysosome fusion by inhibiting the nuclear localization of FoxO1. Recovering the phosphorylation of AMPKSer485/491 by AAV-mediated overexpression of the AMPK (T485D) or metformin treatment rescued the cardiotoxicity caused by crizotinib.

overall_design: 3 Control Samples and 3 Crizo-treated Samples

first: Peihua

last: LUO

first: Qiaojun

last: He


title: Expression profiling in R/M HNSCC treated with immunotherapy (training set)

overall_design: This was a translational research on a single-arm, open-label, multicenter, phase IIIb clinical trial (NIVACTOR) in patients with Recurrent or Metastatic (RM) platinum-refractoy HNSCC treated with nivolumab (EudraCT Number: 2017-000562-30). The NIVACTOR study enrolled 127 R/M HNSCC patients to fulfill both clinical and translational endpoints.  Whole transcriptome RNA profiling was feasible on 80 FFPE tissue specimens. There are no significant differences between the whole cohort and the subset used for the gene-expression profiling in terms of their gender, age, PS, smoking, primary tumor site, stage, site of metastatis, PDL1 status (TPS or CPS).


title: Integrative high-throughput enhancer surveying and functional verifying divulges YY2 condensed regulatory axis conferring risk for osteoporosis

status: Public on Dec 29 2023

city: Xi'an

first: Xiao-Feng

last: Chen

state: Shaanxi

address: No.28 Xianning West Road

department: School of Life Sciences and Technology

institute: Xi'an Jiaotong University

type: Genome variation profiling by high throughput sequencing

summary: The precise roles of chromatin organizations at osteoporosis risk loci remains largely elusive. Here we combined chromatin interaction conformation (Hi-C) profiling and self-transcribing active regulatory region sequencing (STARR-seq) to qualify enhancer activities of prioritized osteoporosis-associated SNPs. We identified 319 SNPs with biased allelic enhancer activity effect (baaSNPs) which linked to hundreds of candidate target genes through chromatin interactions across 146 loci. Functional characterizations revealed active epigenetic enrichment for baaSNPs, and prevailing osteoporosis-relevant regulatory roles for their chromatin interacted genes. Further motif enrichment and network mapping prioritized several putative key transcription factors (TFs) controlling osteoporosis binding to baaSNPs. Specifically, we selected on top ranked TF and deciphered that an intronic baaSNP (rs11202530) could allele-preferentially bind to YY2 to augment PAPSS2 expression through chromatin interactions and promote osteoblast differentiation. Our results underlined roles of TF-mediated enhancer-promoter contacts for osteoporosis, which may help better understand the intricate molecular regulatory mechanisms underlying osteoporosis-risk loci.

overall_design: We prioritized 5,642 candidate osteoporosis-associated SNPs interacted with nearby genes promoters through combing GWAS fine-mapping and Hi-C profiling for high-throughput biased enhancer qualification by STARR-seq.  A 120-bp genomic sequence centered on each SNP was extracted, with identical adapter sequence added on the 5′ and 3′ region. Oligonucleotides for 150-bp length SNPs on both reference and alternative alleles were synthesized in a CustomArray. Firstly, STARR-seq plasmid library was constructed using hSTARR-seq_ORI vector and amplified oligonucleotides. Secondly, The plasmid library was transfected into human osteoblast-like cell line U2OS for 24h. Finally, the plasmid library and RNA extracted after transfection were used to construct input and output sequencing libraries respectively. The library preparations were sequenced on an Illumina Novaseq 6000 platform (PE150) and paired-end reads were generated. Three biological replicates were performed for input or output library.

first: Chen

last: Xiao-Feng

first: Duan

last: Yuan-Yuan

first: Jia

last: Ying-Ying

first: Dong

last: Qian-Hua

first: Shi

last: Wei

first: Zhang

last: Yan

last: Shan-Shan

first: Li

last: Meng

first: Liu

last: Zhongbo

last: Fei

first: Huang

last: Xiao-Ting

first: Hao

last: Ruo-Han

first: Zhu

last: Dong-Li

first: Jing

last: Rui-Hua

first: Guo

first: Yang

last: Tie-Lin


title: Human amnion epithelial cell therapy reduces hypertension-induced vascular stiffening and cognitive impairment

status: Public on Dec 30 2023

city: Bundoora

first: Quynh Nhu

last: Dinh

state: VIC

address: Kingsbury Drive & Plenty Rd

country: Australia

institute: La Trobe University

summary: We investigated the effect of amnion epithelial cells on hypertension-induced transcriptomic changes in the brain

overall_design: N=6 per group. 4 treatment groups

first: Quynh

middle: N

first: T

last: De Silva


title: Etrolizumab-s fails to control E-Cadherin-dependent co-stimulation of highly stimulated cytotoxic T cells associated with Crohn’s disease

status: Public on Dec 28 2023

city: Erlangen

first: Mark

last: Dedden

state: Bayern

address: Schwabachanlage 12

department: Department of Medicine 1

institute: Universitätsklinikum Erlangen

summary: To interrogate the potential of αEβ7 integrin as a target in Crohn’s disease (CD), we single cell RNA-sequenced T cells from a patient with CD and a non-IBD control

overall_design: We sorted integrin α4-expressing memory T cells from the peripheral blood of a control donor and patient with CD and submitted these cells to single cell RNA-sequencing

first: Maximilian

last: Wiendl

first: Sebastian

last: Zundler


title: Loss of B cell Tolerance is TCR Dependent [IgG2a CTD array]

city: Boston

first: Elliot

last: Akama-Garren

state: MA

address: 200 Longwood Ave

institute: Harvard Medical School

summary:
We used protein arrays to measure IgG2a autoantibodies associated with Connective Tissue Diseases (CTDs) from retrogenic chimeras
Sera was isolated from irradiated Icos-/-;CD45.1 mice reconstituted with 564Igi;Icos-/- bone marrow mixed with Icos-/-;CD45.1 bone marrow and WT bone marrow (BMchim.564) or retrogenic HSCs expressing TCR-A (BMchim.564-Icos.RAG-TCRA), TCR-B (BMchim.564-Icos.RAG-TCRB), or TCR-C (BMchim.564-Icos.RAG-TCRC). 564Igi (564homo) and 564Igi;Icos-/- (564homo.Icos) sera were included as controls.

overall_design: Protein arrays were constructed by coupling antigens to carboxylated magnetic beads. Arrays consisting of conjugated beads were then used to probe patient serum or plasma samples, healthy control samples, and autoimmune prototype samples. Samples were run in duplicate. A Luminex FLEXMAP 3D® system was used to quantitatively measure autoantibody reactivity in each sample in units of mean flourescent intensity (MFI).

first: Xihui

last: Yin

first: Tyler

last: Prestwood

first: Paul

last: Utz

first: Michael

last: Carroll


title: Loss of B cell Tolerance is TCR Dependent [IgG2c CTD array]

summary:
We used protein arrays to measure IgG2c autoantibodies associated with Connective Tissue Diseases (CTDs) from retrogenic chimeras
Sera was isolated from irradiated Icos-/-;CD45.1 mice reconstituted with 564Igi;Icos-/- bone marrow mixed with Icos-/-;CD45.1 bone marrow and WT bone marrow (BMchim.564) or retrogenic HSCs expressing TCR-A (BMchim.564-Icos.RAG-TCRA), TCR-B (BMchim.564-Icos.RAG-TCRB), or TCR-C (BMchim.564-Icos.RAG-TCRC). 564Igi (564homo) and 564Igi;Icos-/- (564homo.Icos) sera were included as controls.


title: Loss of B cell Tolerance is TCR Dependent [IgG CTD array]

summary:
We used protein arrays to measure IgG autoantibodies associated with Connective Tissue Diseases (CTDs) from retrogenic chimeras
Sera was isolated from irradiated Icos-/-;CD45.1 mice reconstituted with 564Igi;Icos-/- bone marrow mixed with Icos-/-;CD45.1 bone marrow and WT bone marrow (BMchim.564) or retrogenic HSCs expressing TCR-A (BMchim.564-Icos.RAG-TCRA), TCR-B (BMchim.564-Icos.RAG-TCRB), or TCR-C (BMchim.564-Icos.RAG-TCRC). 564Igi (564homo) and 564Igi;Icos-/- (564homo.Icos) sera were included as controls.


title: Molecular effects of cardiac contractility modulation in patients with heart failure of ischemic aetiology uncovered by transcriptome analysis

city: Saint-Petersburg

first: Margarita

last: Sorokina

address: Akkuratova 2

country: Russia

institute: Almazov National Medical Research Centre

summary: In this study we investigated the fundamental aspects of rhythm disturbance in patients with chronic heart failure who underwent the implantation of support device Optimizer (OPT). We evaluated the changes in molecular pathways as well as in clinical indicators after the devise implantation

overall_design: Libraries were prepared with TruSeq Stranded mRNA kit, samples were RNA-sequenced on Illumina NextSeq 2000, read length 51 bp.

first: Anna

middle: A

last: Kostareva

first: Ksenia

middle: S

last: Sukhareva


title: Loss of B cell Tolerance is TCR Dependent

type:
Other
Protein profiling by protein array

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


title: Investigation of Campylobacter concisus gastric epithelial pathogenicity

status: Public on Dec 27 2023

city: Sydney

first: Li

last: Zhang

state: NSW

address: Botany Street

department: School of Biotechnology and Biomolecular Sciences

institute: University of New South Wales

summary: The gastric epithelial gene responses to Campylobacter concisus infection were investigated by comparative differential expression analysis

overall_design: Comparative gene expression profiling analysis of RNA-seq data for AGS cells with and without Campylobacter concisus treatment was performed


title: YY1-dependent transcriptional regulation manifests at the morula stage

status: Public on Dec 26 2023

city: Kofu

first: Mizuki

last: Sakamoto

country: Japan

institute: University of Yamanashi

summary: YY1 plays multifaceted roles in various cell types. We recently reported that YY1 regulates nucleosome organization in early mouse embryos (Sakamoto et al. Genes Dev 2023). However, despite the impaired nucleosome organization in the absence of YY1, the transcriptome was minimally affected in eight-cell embryos. We then hypothesized that YY1 might prepare a chromatin environment to regulate gene expression at later stages. To test this possibility, we performed a transcriptome analysis at the morula stage. We found that a substantial number of genes are aberrantly expressed in the absence of YY1. Furthermore, our analysis revealed that YY1 is required for the transcription of retrotransposons in early embryos.

overall_design: Total RNA-seq was performed using mouse early embryos.

first: Takashi

last: Ishiuchi


title: Integrative Genomic Analyses Reveal Putative Cell Type-specific Targets of theDrosophilaEts Transcription Factor Pointed

first: Komal Kumar

last: Bollepogu Raja

address: One Baylor plaza

department: Pathology and Immunology

institute: baylor college of medicine

summary: The Ets domain transcription factors direct diverse biological processes throughout all metazoans and are implicated in development as well as in tumor initiation, progression and metastasis. The Drosophila Ets transcription factor Pointed (Pnt) is the downstream effector of the Epidermal growth factor receptor (Egfr) pathway and is required for cell cycle progression, specification, and differentiation of most cell types in the larval eye disc.  Despite its critical role in development, very few targets of Pnt have been reported previously. Here, we employed an integrated approach by combining genome-wide single cell and bulk data to identify putative cell type-specific Pnt targets. First, we used chromatin immunoprecipitation with high-throughput sequencing (ChIP-seq) to determine the genome-wide occupancy of Pnt in late larval eye discs. We identified enriched regions that mapped to an average of 6,941 genes, the vast majority of which are novel putative Pnt targets. Next, we integrated ChIP-seq data with two other larval eye single cell genomics datasets (scRNA-seq and snATAC-seq) to reveal 157 putative cell type-specific Pnt targets that may help mediate unique cell type responses upon Egfr-induced differentiation. Finally, our integrated data also predicts cell type-specific functional enhancers that were not reported previously. Together, our study provides a greatly expanded list of putative cell type-specific Pnt targets in the eye and is a resource for future studies that will

overall_design: ChIP-seq for pointed transcription factor in Drosophila larval eye disc

first: Komal

last: Raja

first: Kelvin

last: Yeung

first: Yoon-Kyung

last: Shim

first: Graeme

last: Mardon


title: Sequencing Reveals miRNAs Enriched in the Developing Mouse Enteric Nervous System

city: Philadelphia

first: Robert

middle: O

last: Heuckeroth

state: PA

address: 3615 Civic Center Blvd Rm 1115

institute: Children's Hospital of Philadelphia Research Institute


title: Sequencing Reveals miRNAs Enriched in the Developing Mouse Enteric Nervous System [miRNA]

summary: The enteric nervous system (ENS) is an essential network of neurons and glia in the bowel wall. Defects in ENS development can result in Hirschsprung disease (HSCR), a life-threatening condition characterized by severe constipation, abdominal distention, bilious vomiting, and failure to thrive. A growing body of literature connects HSCR to alterations in miRNA expression, but there are limited data on the normal miRNA landscape in the developing ENS. We sequenced small RNAs (smRNA-seq) and messenger RNAs (mRNA-seq) in ENS precursors of mid-gestation Ednrb-EGFP mice and compared them to aggregated RNA from all other cells in the developing bowel. Our smRNA-seq results identified 73 miRNAs that were significantly enriched and highly expressed in the developing ENS, with miR-9, miR-27b, miR-124, miR-137, and miR-488 as our top 5 miRNAs that are conserved in humans. However, contrary to prior reports, our follow-up analyses of miR-137 showed that loss of Mir137 in Nestin-cre, Wnt1-cre, Sox10-cre, or Baf53b-cre lineage cells had no effect on mouse survival or ENS development. Our data provide important context for future studies of miRNA in HSCR and other ENS diseases and highlight open questions about facility-specific factors in development.

overall_design: We isolated E13.5 EDNRB-EGFP bowel, sorted GFP-positive enteric neural crest–derived cells (ENCDCs) from GFP-negative non-ENCDCs, then sequenced all small RNAs from both populations. The processed data file contains CPM counts after alignment by STAR and normalization by PORT.

first: Christopher

last: Pai

first: Rajarshi

last: Sengupta


title: Sequencing Reveals miRNAs Enriched in the Developing Mouse Enteric Nervous System [mRNA]


title: Dual RNA Seq of Salmonella-positive and Salmonella-negative small intestinal epithelial cells using the neonatal infection model

city: Aachen

first: Matthias

middle: W

last: Hornef

address: Pauwellstr 30

department: Medical Microbiology

institute: Uniklinik Aachen

summary: The intestinal epithelium is the first line of defence against invasive enteric pathogens. Removal of infected cells by exfoliation prevents mucosal translocation and systemic infection in the adult host, but is less commonly observed in the neonatal small intestine. Instead, here we describe non-professional efferocytosis of Salmonella-infected enterocytes by neighbouring intestinal epithelial cells in the neonatal intestine. Intestinal epithelial stem cell organoid co-cultures of neonatal and adult cell monolayers with damaged enterocytes replicated this observation, confirmed the age-dependent ability of intestinal epithelial cells for efferocytosis and identified the critical involvement of the 'eat-me' signals and adaptors phosphatidylserine and C1q as well as the 'eat-me' receptors integrin-v (CD51) and CD36 in cellular uptake. Consistent with this, massive epithelial cell membrane protrusions and CD36 accumulation at the contact site with apoptotic cells were observed in the infected neonatal host in vivo. Efferocytosis of infected small intestinal enterocytes by neighbouring epithelial cells may represent a previously unrecognised mechanism of neonatal antimicrobial host defense to maintain barrier integrity.

overall_design: C57BL/6 mice will be infected on day 1 after birth with 100 CFU S. Tm. carrying a FPV-mCherry plasmid (pmCherry, kindly provided by Leigh Knodler, NIH, Hamilton, USA). Enterocytes will be isolated from total small intestinal tissues using a previously established EDTA-based protocol at d4p.i. (Lotz et al., 2006). Alexa Fluor® conjugated EpCam and CD45 antibodies in combination with flow cytometric (FACS) sorting will be used to further enrich enterocytes and remove immune cells. EpCam+ CD45- enterocytes (Ep+) will then be pooled from several animals of an infected litter and individually gated and sorted according to their intracellular Salmonella status (Ep+Sal+ = pmCherry+ or Ep+Sal- = pmCherry-). In parallel, EpCam+ CD45- enterocytes (Ep+) will be sorted from non-infected age-matched (5 day old) neonates using a similar protocol and allow defining the gate for Salmonella negative enterocytes. RNA will be isolated from the four independent FACS sorting experiments using the QIAGEN RNeasy Micro or RNeasy Midi Kit for Ep+Sal+ population or Ep+Sal- population and Ep+ population from non-infected neonates, respectively. cDNA libraries were generated according to published protocol (Westermann et al., 2016) and gene expression analysis was performed using DESeq2 as described in Westermann et al. paper (Westermann et al., 2016)

first: Kaiyi

last: Ballmaier

first: Alexander

last: Westermann

first: Konrad

last: Förstner

first: Mathias


status: Public on Dec 25 2023

city: Grand Rapids

first: Ian

last: Beddows

state: MI

address: 333 Bostwick

institute: Van Andel Institute

summary: NF1 deficiency drives metabolic reprogramming in ER+ breast cancer. This reprogramming is characterized by oxidative ATP constraints, glutamine TCA influx, and lipid pool expansion, and these metabolic changes introduce novel metabolic-to-targeted inhibitor synergies.

overall_design: 6 samples derived from the human MCF7 cell line. Cells were grown in DMEM no phenol red + 10% charcoal-stripped FBS + penicillin streptomycin for 3 days and then treated with 10nM beta-estradiol (E2) for 24hr. The samples are divided into 2 genotypes, each with 3 samples. The genotypes are empty vector control (NF1-EV) and NF1 mutant (NF1-45)

first: Carrie

last: Graveel

first: Elizabeth

last: Tovar

first: Matt

last: Steensma


title: Endometrial DNA methylation signatures of cattle fertility

city: Bonn

first: Dessie Salilew

last: Wondim

address: Endenicher Allee 15

institute: University of Bonn

summary: This study was done to identify endometrial DNA methylation marks that can be associated with pregnancy outcomes in postpartum cows at the time of breeding.  Results showed that postpartum cows that could become pregnant could be distinguishable based on their endometrial DNA methylation patterns at the time of breeding.

overall_design: Twelve days post-calving, cows were offered either a control diet or supplemented daily with rumen-protected methionine (RPM) and cows exhibiting heat 50-64 days postpartum were artificially inseminated. Endometrial cytobrush samples were collected 4-8 hours after insemination and  classified based on the pregnancy out comes as those derived from cows that resulted in pregnancy or resulted in no pregnancy and subject to reduced representative bisulfate sequencing for DNA methylation analysis

first: Dessie

last: Salilew-Wondim

first: Ernst

last: Tholen

first: Eva

last: Held-Hoelker

first: Karl

last: Shellander

first: Carina

last: Blaschka

first: Marc

last: Drillich

first: Michael

last: Iwersen

first: David

last: Suess

first: Samuel

last: Gebremedhn

first: Dawit

last: Tesfaye

first: Claudia

last: Parys

first: Ariane

last: Helmbrecht

first: Jessie

last: Guyader

first: Dennis

last: Miskel

first: Nares

last: Trakooljul

first: Klaus

last: Wimmer

last: Hoelker


title: γδ T cell antigen receptor polyspecificity enables T cell responses to a broad range of immune challenges

city: Stanford

first: Yueh-hsiu

last: Chien

state: CA

address: Stanford University

department: Microbiology and Immunology

institute: Stanford University

summary: γδ T cells are essential for immune defense and modulating physiological processes. While they have the potential to recognize large numbers of antigens through somatic gene rearrangement, the antigens which trigger most γδ T cell response remain unidentified, and the role of antigen recognition in γδ T cell function is contentious. Here, we show that some γδ T cell receptors (TCRs) exhibit polyspecificity, recognizing multiple ligands of diverse molecular nature. These ligands include haptens, metabolites, neurotransmitters, posttranslational modifications, as well as peptides and proteins of microbial and host origin. Polyspecific γδ T cells are enriched among activated cells in naive mice and the responding population in infection. They express diverse TCR sequences, have different functional potentials, and include the innate-like γδ T cells, such as the major IL-17 responders in various pathological/physiological conditions. We demonstrate that encountering their antigenic microbiome metabolite maintains their homeostasis and functional response, indicating that their ability to recognize multiple ligands is essential for their function. Human γδ T cells with similar polyspecificity also respond to various immune challenges. This study demonstrates that polyspecificity is a prevalent feature of γδ T cell antigen recognition, which enables rapid and robust T cell responses to a wide range of challenges, highlighting a unique function of γδ T cells.

overall_design: To better understand the functional potential of poly-specific γδ T cells, Cy3+HA+ γδ T cells were sorted from the spleen of naïve mice and subjected to single-cell RNA-seq analysis by Smart-seq2.

first: Jing

last: Guo


title: Compartmentalization and synergy of osteoblasts drive bone formation in the regenerating fin

status: Public on Dec 22 2023

city: Dresden

first: Fabian

last: Rost

address: Pfotenhauerstraße 108

institute: MPI-CBG

summary: This study investigated the cell composition and lineage relationships of FACS (fluorescence activated cell sorting)-enriched epidermal, bone forming (osteoblast) and (non-osteoblast) blastemal fin regenerate cells by single cell (sc) RNA sequencing. The repetitive cell harvesting in four-week intervals revealed a constant gene regulation over four successive regeneration rounds in the early outgrowth stage. In addition, the sc RNA dataset uncovered a potential lineage relationship between distal blastema cells and osteoblasts during fin regeneration. These findings, together with the identification of novel fin regenerate markers, advance our understanding of complex tissue regeneration in zebrafish.

overall_design: To study potentially underrepresented cell populations during zebrafish fin regeneration, we harvested single cells and FACS-enriched for siam+, shha+, osterix+, RUNX2+ cells via respective mCherry and GFP reporter fluorophores. We performed gene expression analysis using data obtained from RNA seq of enriched cells from 4 successive regeneration stages at 3 dpa.

first: Nicole

last: Cudak

first: Alejandra

last: López-Delgado

first: Thomas

last: Kurth

first: Mathias

last: Lesche

first: Susanne

last: Reinhardt

first: Andreas

last: Dahl

first: Steffen

last: Rulands

first: Franziska

last: Knopf


title: Spliceosomal helicases DDX41/SACY-1 and PRP22/MOG-5 both contribute to proofreading against proximal 3’ splice site usage

city: Santa Cruz

first: Alan

last: Zahler

address: 1156 High St.

department: MCD Biology

institute: UC Santa Cruz

summary: Alleles of C. elegans genes mog-5 and sacy-1 were found to increase usage of proximal 3' splice sites

overall_design: Alternate splicing analysis of sacy-1(tn1385) vs N2(wildtype) and mog-5(az192) vs N2

first: Sol

last: Katzman

first: Kenneth

last: Osterhoudt


title: iPSC-derived models of PACS1 syndrome reveal transcriptional and functional deficits in neuron activity

city: Portland

first: Lauren

last: Rylaarsdam

state: OR

address: 3181 S.W. Sam Jackson Park Road

department: Molecular & Medical Genetics

institute: Oregon Health & Science University

summary: PACS1 syndrome is a neurodevelopmental disorder characterized by intellectual disability and distinct craniofacial abnormalities resulting from a de novo p.R203W variant in phosphofurin acidic cluster sorting protein 1 (PACS1). PACS1 is known to play roles in the endosomal pathway and nucleus, but how the p.R203W variant affects developing neurons is not fully understood. In this study we differentiated stem cells towards 2D and 3D neuronal models to investigate the impact of the PACS1 syndrome-causing variant on neurodevelopment. While few deleterious effects were detected in PACS1(+/R203W) neural precursors, mature PACS1(+/R203W) glutamatergic neurons in cortical organoids exhibited impaired expression of genes involved in synaptic signaling processes. The single-cell RNA sequencing data from dorsal cortical organoids after 40 and 88 days of differentiation can be found here. Subsequent characterization of neural activity using calcium imaging and multielectrode arrays revealed the p.R203W PACS1 variant leads to a prolonged neuronal network burst duration mediated by an increased inter-spike interval. These findings demonstrate the impact of the PACS1 p.R203W variant on developing human neural tissue and uncover putative electrophysiological underpinnings of disease.

overall_design: Five day 40 (1 Control 1, 1 Control 3, 1 CRISPR R203W, 1 Affected 1, and 2 combined Affected 2) and four day 88 (2 Control 2, 1 CRISPR R203W, and 1 Affected 1) cortical organoids across four independent differentiations were cultured and processed for single-cell RNA sequencing analysis.

first: Jennifer

last: Rakotomamonjy

first: Eleanor

last: Pope

first: Alicia

last: Guemez-Gamboa


title: Multigenerational paternal high-fat diet gradually exacerbates environmental stress-induced testicular dysregulated expression of mRNAs in offspring

city: Hefei

first: Yong-Wei

last: Xiong

state: Anhui

address: Hefei 230032, China

institute: Anhui Medical University

summary: To investigate the mechanism by which paternal exposure to high-fat diet (HFD) exacerbates environmental stress-impaired testicular germ cell development in offspring, testicular RNA sequencing was performed in H+Cd (the offspring were treated with Cd after paternal exposure to one-generational HFD) and  H+H+Cd (the offspring were treated with Cd after paternal exposure to bi-generational HFD) groups. Compared with HFD1D group and HFD2D group, 229 mRNAs were upregulated and 268 mRNAs were downregulated, screened for a 1.2-fold change and adjusted with P < 0.05.  GO analysis revealed that downregulated mRNAs were related to multiple biological processes, including the "retinol metabolic process," the "reproductive process," and the "spermatogenesis".

overall_design: F0 generation male mice were fed NC or HFD from 5 weeks to 15 weeks old, and then mated with NC-fed female mice to breed F1 generation. Similarly, partial F1 generation male mice continued to be fed HFD for 10 weeks, and mated with normal female to breed F2 generation. Male mice of F1 and F2 generations were exposed to CdCl2 for 10 weeks, and named  H+Cd or H+H+Cd group respectively. Total RNA of mouse testes was extracted, and quality inspections were performed. The sequencing library was constructed with 2.0 μg total RNA from each sample.

first: Hua

last: Wang

first: Yongwei


title: Effect of high-fat diet exposure on mouse sperm RNA m6A modified expression profile

summary: To further investigate the effect of high-fat diet on m6A modified expression profiles of mouse sperm RNA, we used whole-genome microarray expression profiles as a discovery platform to identify differential m6A modified genes under high-fat diet exposure. Male mice were fed normal chow (C) or 60% high-fat diet (HFD) from 5 weeks to 15 weeks old, and then sperm were obtained for Arraystar m6A-mRNA&lncRNA Epitranscriptomic Microarray. Results showed that hyper-methylated mRNAs were involved in multiple biological processes, including the "reproductive process," "gamete generation," and "spermatogenesis".

overall_design: Male mice were fed normal chow (C) or 60% high-fat diet (HFD) from 5 weeks to 15 weeks old, and then sperm were obtained.  Three replicated experiments were performed using different donors for each experiment.


title: Gene expression profile at single cell level of neuroblastoma tumors and their tumor microenvironment

city: Amsterdam

first: Sander

middle: Roeland

last: van Hooff

address: Meibergdreef 9

department: Center for Experimental and Molecular Medicine (CEMM),

institute: AUMC

summary: Neuroblastoma (NBL) tumors are considered heterogeneous tumors. So far, little detailed information available on their immune environment. We used single cell RNA sequencing (scRNA-seq) to analyze the tumor microenvironment of neuroblastoma.

overall_design:
Fresh neuroblastoma tumor samples (n=10 before treatments, n=14 after induction chemotherapy) were enzymatically digested and single-cell FACS sorted into plates for scRNA-seq.
NOTE FROM SUBMITTER: raw data can not be included due to patient privacy concerns

first: J

last: Wienke

last: Molenaar

first: K

last: Keller

first: W

last: Kholosy


title: Tracing back primed resistance in cancer via sister cells

city: Helsinki

first: Shuyu

last: Zheng

state: Uusimaa

address: Biomedicum 1U, Haartmaninkatu 8

department: Faculty of Medicine

country: Finland

institute: University of Helsinki

summary: Exploring non-genetic evolution of cell states during cancer treatments has become attainable by recent advances in lineage-tracing methods. However, transcriptional changes that drive cells into resistant fates may be subtle, necessitating high resolution analysis. We developed ReSisTrace that uses shared transcriptomic features of synchronized sister cells to predict the states that prime treatment resistance. We applied ReSisTrace in ovarian cancer cells to dissect primed resistance against olaparib, carboplatin or natural killer (NK) cells, and  discovered a novel connection between DNA repair deficiency and susceptibility to NK cells. Furthermore, we identified small molecules driving cells to sensitive states prior to treatment. In summary, ReSisTrace resolves pre-existing transcriptional features of treatment vulnerability, facilitating both molecular patient stratification for personalized treatments and discovery of synergistic pre-sensitizing therapies.

overall_design: We developed ReSisTrace to reveal the cell states that are primed to treatment resistance. We allowed uniquely labeled, synchronized cells to divide once, after which half of the cells (pre-treatment samples) were analyzed by scRNA-seq, while the other half underwent the treatment. Surviving cells were allowed to recover, and then analyzed by scRNA-seq to identify resistant lineages and their expression profiles (post-treatment samples). We applied ReSisTrace in HGSOC cell line Kuramochi to address primed resistance against carboplatin chemotherapy, the PARP inhibitor olaparib, and anti-tumor immunity represented by natural killer (NK) cells. We also included a non-treatment control that mimicked the splitting, re-plating, and growth conditions of the drug treatment experiments. All the assays are performed in two replicates.

first: Jun

last: Dai

first: Jing

last: Tang

first: Anna

last: Vähärautio


title: ZNF143 deletion alters enhancer/promoter looping and CTCF/cohesin geometry

status: Public on Dec 21 2023

city: Shanghai

first: Mo

last: Zhang

address: 800 Dongchuan Road

institute: Shanghai Jiaotong University

overall_design: Refer to individual Series


title: ZNF143 deletion alters enhancer/promoter looping and CTCF/cohesin geometry (ChIP-Seq)

summary: The transcription factor ZNF143 contains seven tandem zinc fingers and is involved in 3D genome construction; however, the mechanism by which ZNF143 functions in chromatin looping remains unclear. Here, we show that ZNF143 directionally recognizes diverse genomic sites and is required for chromatin looping between these sites. In addition, ZNF143 is located between CTCF and cohesin at numerous CTCF sites and ZNF143 removal narrows the space between CTCF and cohesin. Moreover, genetic deletion of ZNF143, in conjunction with acute CTCF depletion, revealed that ZNF143 and CTCF collaborate to regulate higher-order genome organization. Thus, ZNF143 is recruited by CTCF to the CTCF sites to regulate TAD formation and genome compartmentalization whereas directional recognition of DNA motifs directly by ZNF143 itself regulates promoter activity via chromatin looping.

overall_design: Chromatin Immunoprecipitation DNA-sequencing (ChIP-seq) for histone modification H3K27me3 in HEC-1-B cells.

first: Qiang

last: Wu


title: Heat stress during male meiosis impairs cytoskeletal organization, spindle assembly and tapetum degeneration in wheat

city: Martonvásár

first: Attila

last: Fábián

address: Brunszvik 2

institute: Centre for Agricultural Research

summary: We demonstrate here that heat stress severely alters the cytoskeletal configuration, cell structure, and global gene expression in male meiocytes and the tapetum layer, in a genotype-dependent manner. ‘Ellvis’, a heat-tolerant winter wheat cultivar, showed high fertility and only scarce structural aberrations upon exposure to high temperature. In addition, heat shock genes and genes involved in the alleviation of reactive oxygen species were significantly upregulated in ‘Ellvis’ and the expression of meiosis-specific and important developmental genes showed high stability in this cultivar. In the heat-sensitive Mv 17-09, however, genes participating in cytoskeletal fiber nucleation, the spindle assembly checkpoint (SAC) genes, and tapetum-specific developmental regulators were all downregulated. These alterations may be related to the decreased cytoskeleton content, frequent micronuclei formation, and the erroneous persistence of the tapetum layer observed in the sensitive genotype.

overall_design: Control and heat stressed (35 ⁰C for 24h at the time of meiosis) anthers of Mv 17-09 and Ellvis cultivars were subjected to RNA seq to reveal the transcriptional background of heat susceptibility of meiosis.


title: Temporally resolved single-cell transcriptomics defines immune dysfunction trajectories in glioblastoma

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

summary: Immune cells sense their environment and adapt their state. Deciphering cellular trajectories unfolding over time is fundamental for understanding biology. Empirical in vivo genomic technologies measuring both cell state and time are lacking. Here, we present Zman-seq, a single-cell technology tracking transcriptomic dynamics across time by introducing fluorescent time stamps into immune cells. We applied Zman-seq to resolve immune cell state-transitions of the dysfunctional tumor immune microenvironment (TME) of glioblastoma (GBM). By measuring the exposure time of infiltrating immune cells in the TME, Zman-seq defines the cellular and molecular trajectories underlying immune incompetence in GBM. Within 24 hours, cytotoxic NK cells transitioned to a dysfunctional program  regulated by Tgfb1, while monocytes differentiated into immunosuppressive macrophages in 36-48 hours. Anti-TREM2 antagonistic antibody reshaped the TME by redirecting monocytes to pro-inflammatory macrophages. Zman-seq is a broadly applicable technology enabling empirical measurements of differentiation trajectories guiding the development of more efficacious immunotherapies.

overall_design: Wt B6 mice were injected or not injected with GL261 cells into the right striatum. Some mice did not receive tumor. Some tumor bearing mice were treated with anti-TREM2 antibody or isotype control at days 2 and 7, some did not receive treatment. Mice were injected with fluorescent antibodies on days 11-12. On day 13 brains were extracted and single cell suspension enriched for CD45 cells were prepared. For some untreated mice blood, spleen, colon and lung tissue was also processed and CD45+ cells extracted. This was followed by single cell FACS index sorting into 384-well plates. Single cell RNAseq libraries were prepared with the MARSseq protocol and sequenced with Illumina Novaseq.

first: Daniel

last: Kirschenbaum

first: Ken

last: Xie

first: Florian

last: Ingelfinger

first: Yonatan

last: Katzenelenbogen

first: Kathleen

last: Abadie

first: Thomas

last: Look

first: Fadi

last: Sheban

first: Truong

last: Phan

first: Baoguo

last: Li

first: Pascale

last: Zwicky

last: Yofe

first: Eyal

last: David

first: Kfir

last: Mazuz

first: Jinchao

last: Hou

first: Yun

last: Chen

first: Hila

last: Shaim

first: Soeren

last: Becker

first: Marco

last: Colonna

first: Nir

last: Yosef

first: Katayoun

last: Rezvani

first: Fabian

last: Theis

first: Tobias

last: Weiss

first: Assaf

last: Weiner


title: Casein kinase 2 complex: a central regulator of multiple pathobiological signaling pathways in Cryptococcus neoformans

city: Seoul

first: Yong-Sun

last: Bahn

address: 50, Yonsei-ro, Seodaemun-gu, Seoul, Republic of Korea

department: Department of Biotechnology

country: South Korea

institute: Yonsei university

summary: Casein kinase 2 (CK2) is a potential therapeutic target for several human diseases due to its crucial roles in growth, differentiation, and metabolic homeostasis. This study delves into the role of the CK2 complex in Cryptococcus neoformans, a key fungal pathogen causing meningitis. In C. neoformans, the CK2 complex is made up of a main catalytic subunit (Cka1) and two regulatory subunits (Ckb1 and Ckb2). The primary role of Cka1 is as a protein kinase, while Ckb1/2 assist in various cellular functions. Triple mutants without all three subunits exhibited more pronounced defects than mutants lacking only Cka1, hinting at potential independent functions of Ckb1/2. In animal studies, mutants without these subunits showed a sharp decline in virulence. Moreover, CK2 disruption affected many effector proteins and disrupted key signaling pathways crucial for the pathogenicity of C. neoformans. Overall, the findings highlight the importance of the CK2 complex in fungal biology and its potential as a target for new antifungal treatments.

overall_design: The wild-type, cka1∆, and ckb1∆ ckb2∆ cka1∆ strains were first cultured overnight at 30°C and then transferred to fresh YPD medium until they reached an OD600 of 0.8. Cells were collected, flash-frozen, and lyophilized. Total RNA was extracted using Easy-BLUE (17061, iNtRON, South Korea) and further purified with an RNeasy minikit (74106, Qiagen, Germany). This process was repeated for three independent cultures of each strain. Using 1 g of total RNA, cDNA libraries were prepared with the TruSeq mRNA library kit (Illumina, USA) and sequenced on an Illumina platform.  Post-sequencing, reads were processed to remove adaptor and low-quality sequences using Cutadpat v2.4 with Python 3.7.4 with adapter sequence (64). The reads were processed as previously described (65) and aligned to the C. neoformans H99 reference genome using Hisat2 v2.2.1 and the Hisat and Bowtie2 algorithm. Annotation data were obtained from the NCBI FTP server. The “-p 30” and “—dta -1” options, along with other default settings, were used to run Hisat2. Aligned reads were converted and sorted using Samtools v0.1.19 with default parameters except for the “-Sb -@ 8” option for converting and the “-@ 20 –m 2000000000” option for sorting (66). The “-p 12” option was used by Stringtie v1.3.6 to perform transcript assembly and abundance estimation. Transcript abundance was quantified using FPKM (Fragments Per Kilobase of Exon per Million Fragments Mapped) values (66). Data matrices were generated and analyzed using the R package “isoformswitchanalyzerR”. Quality control was assessed through DEBrowser (67). The analysis of differentially expressed genes (DEGs) was conducted with DESeq2 v1.24 (68, 69), and results were visualized using the Enhanced Volcano package in R v4.1.0 (70), with a cutoff of more than two-fold changes and a P-value of less than 0.05.

first: Yeseul

last: Choi

first: Seong-Ryong

last: Yu

first: Ann-Yae

first: Sangkyu

last: Lee

first: Ran

last: Seo

first: Han-Seung

first: Jong-Seung


title: Current androgen deprivation induces androgen receptor-independent prostate cancer via HGF and Wnt activation to foster nuclear export and ribosome biogenesis [scRNA-Seq]

city: Duarte

first: Zijie

last: Sun

address: 1500 E. Duarte Rd.

department: Cancer Biology

institute: City of Hope

summary: To inhibit the re-activation of AR-promoted tumor growth via residual androgens, more potent AR antagonists and inhibitors for androgen synthesis have been developed in the decades. While these second-generation antagonists/inhibitors showed some effectiveness clinically, they also induced more diverse CRPC phenotypes. Specifically, a subpopulation of AR- and neuroendocrine (NE)-null PC cells, DNPC, occurs frequently in CRPC patients treated with abiraterone and enzalutamide, increasing metastatic CRPC incidences and the mortality of PCa. Understanding the mechanisms for DNPC will directly improve clinical outcomes.

overall_design: Two sequencing datasets were analyzed containing prostatic adenocarcinoma and carcinoma tissues

first: admin

last: admin


title: ZNF143 deletion alters enhancer/promoter looping and CTCF/cohesin geometry (RNA-Seq)

first: Mo

last: Zhang

overall_design: We generated CTCF-AID cells by merging the AID tag with the CTCF gene in TiR1-expressing HEC-1-B cells.. We performed RNA sequencing on the cells to investigate changes in gene that treated with auxin for 0h or 24h.

first: Qiang

last: Wu


title: Current androgen deprivation induces androgen receptor-independent prostate cancer via HGF and Wnt activation to foster nuclear export and ribosome biogenesis [RNA-seq]

summary: To inhibit the re-activation of AR-promoted tumor growth via residual androgens, more potent AR antagonists and inhibitors for androgen synthesis have been developed in the decades. While these second-generation antagonists/inhibitors showed some effectiveness clinically, they also induced more diverse castration-resistant prostate cancer (CRPC) phenotypes. Specifically, a subpopulation of AR- and neuroendocrine (NE)-null PC cells, DNPC, occurs frequently in CRPC patients treated with abiraterone and enzalutamide, increasing metastatic CRPC incidences and the mortality of prostate adenocarcinoma (PCa). Understanding the mechanisms for DNPC will directly improve clinical outcomes.

overall_design: Two or Three replicates were included in each group.


title: Single-cell insights into immune dysregulation in rheumatoid arthritis flare versus drug-free remission

city: Newcastle upon Tyne

first: Kenneth

middle: Frank

last: Baker

address: Framlington Place

department: Translational and Clinical Research Institute

country: United Kingdom

institute: Newcastle University

summary: Immune-mediated inflammatory diseases (IMIDs) are typically characterised by relapsing and remitting flares of inflammation. However, the unpredictability of disease flares impedes their study. Addressing this critical knowledge gap, we used the experimental medicine approach of immunomodulatory drug withdrawal in rheumatoid arthritis (RA) remission to synchronise flare processes, allowing characterisation with unprecedented detail. We used single cell RNA sequencing to analyse the diversity and comparative longitudinal changes in paired circulating lymphocyte samples from 12 patients with RA in remission prior to drug cessation (on-drug remission) and after drug cessation (either off drug flare, or drug-free remission) as part of the Biomarkers of Remission in Rheumatoid Arthritis (BioRRA) Study.

overall_design: CD3+CD4+CD45RO+PD1hi T cells, CD3+CD8+CD45RO+PD1hi T cells, and CD3-CD19+ B cells were isolated from peripheral blood mononuclear cells from patients with RA before and after csDMARD cessation, and analysed by scRNAseq using the BD Rhapsody platform

middle: F


title: Androgen deprivation induces double-null prostate cancer via aberrant activation of nuclear export and ribosomal biogenesis by HGF and Wnt axes

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


city: Beijing

first: Donglai

last: Wang

address: #5 Dong Dan San Tiao

institute: Chinese Academy of Medical Sciences & Peking Union Medical College

summary:
To determined ZBTB11 and SET regulates genes in NCI-H1299, we esteblished NCI-H1299 cell lines in which ZBTB11 and SET has been knocked down by si-RNA.
We then conducted differential expressed genes analysis using data generated form RNA-seq of H1299 cell lines at the condition of two genes knocked down.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for NCI-H1299 cells and its KD derivatives

first: Wenbin

last: Xu


title: Effect of Ifnar1 Knockdown in a mouse model of Cerebral Interferonopathy

city: Carlsbad

first: Christine

last: Hong

address: 2855 Gazelle Ct

department: Neurology

institute: Ionis Pharmaceuticals

summary: To investigate effect of antisense oligonucleotides targeting the murine IFNa receptor (Ifnar1 ASOs) in a transgenic mouse model of cerebral interferonopathy (GIFN), mice were injected intracerebroventricularly with Ifnar1 ASOs.  We performed DGE-Seq on brain cortex samples to determine the impact of ASOs on the transcriptome. Treatment of GIFN mice with Ifnar1 ASOs resulted in a significant decrease in Interferon gene expression and dampened the hyperinflammatory transcriptomic landscape in the brains of GIFN mice.

overall_design: Comparative gene expression profiling analysis of transcriptome sequencing data for cortex samples from wildtype and transgenic mice treated with Ifnar1 ASOs or Vehicle.

first: Fredrik

last: Kamme

first: Barney

last: Viengkhou

first: Markus

last: Hofer


title: AR interacts with GATA3 to induce a luminal epithelial phenotype in breast cancer through regulation of lineage-restricted genes [ER-positive_PDX_GATA3_ChIP-seq]

city: ADELAIDE UNIVERSITY

first: Geraldine

last: Laven-Law

state: South Australia

address: Adelaide Health & Med Sci Bldg, Corner George St & North Terrace

institute: The University of Adelaide

summary: GATA3 transcription factor is considered critical for luminal development and differentiation in normal and malignant mammary epithelial cells (MECs). The androgen receptor (AR) has also been associated with luminal gene expression profiles in breast cancer, independent of the estrogen receptor (ER), and has been shown to promote a basal to luminal phenotype transition in mouse MECs. To date, the potential interaction of GATA3 and AR in transcriptional regulation of lineage driver genes in breast cancer has never been investigated. Our unbiased proteomic analysis identified GATA3 as a novel AR interacting protein in a variety of breast cancer cell types regardless of ER expression. We showed that AR and GATA3 interact in the cytoplasm and nucleus of normal and malignant breast epithelia, an interaction increased by androgen treatment. Androgen stimulation of breast cancer cells also induced nuclear translocation of AR and GATA3 and resulted in enrichment of co-localized AR and GATA3 chromatin binding events. Using ER+ and/or ER- breast cancer cell lines and ER+ patient-derived xenograft (PDX) models of breast cancer, we identified a conserved subset of AR agonist-induced AR and GATA3 co-occupied cis-regulatory elements across all models. Knockdown experiments indicated that GATA3 acts as an AR co-regulator to upregulate transcription of known luminal-lineage genes (e.g. EHF, AQP3, and KDM4B) and downregulate basal-lineage genes (e.g. SMAD3 and ELK3). Also, we showed an induction in the chromatin accessibility at those subsets of common AR-GATA3 cis-regulatory elements, which drive the luminal lineage identity in breast cancer upon androgen stimulation. Collectively, AR-GATA3 interaction and function provide a mechanism underpinning epithelial breast cancer cells that are classified as having a luminal mature transcriptome independent of ER status, through regulating the expression of lineage-restricted markers.

overall_design: GATA3 ChIP-seq on two estrogen receptor-positive and endocrine-resistant patient-derived xenograft (PDX) breast cancer tumor models (GAR15-13 and HCI-005) treated short-term with either a vehicle or AR agonist (GAR15-13; Enobosarm, HCI-005; DHT).

first: L

last: Hosseinzadeh

first: G

first: S

last: Pederson

first: A

last: Dwyer

first: W

middle: D

last: Tilley

first: T

last: Hickey


title: AR interacts with GATA3 to induce a luminal epithelial phenotype in breast cancer through regulation of lineage-restricted genes [ER-negative_cell_line_ChIP-seq]

overall_design: AR, GATA3, and H3K27ac ChIP-seq on two estrogen receptor-negative breast cancer cell lines (MDA-MB-453 and MFM-223) under serum-deplete conditions, after 4 h vehicle or DHT treatment.

first: Z

last: Kikhtyak


title: AR interacts with GATA3 to induce a luminal epithelial phenotype in breast cancer through regulation of lineage-restricted genes [ER-positive_cell_line_GATA3_ChIP-seq]

overall_design: GATA3 ChIP-seq on two estrogen receptor-positive breast cancer cell lines (T-47D and ZR-75-1) under serum-deplete conditions, after 4 h vehicle, E2, DHT, or combination E2+DHT treatment.


title: ZBTB11 binding genes in NCI-H1299

summary: ZBTB11 binding genes in NCI-H1299

overall_design: To determined ZBTB11 binding genes in NCI-H1299, we use ZBTB11 and IgG (as negative control) antibody to performed ChIP-seq assay.

first: Han

last: Yao


title: AR interacts with GATA3 to induce a luminal epithelial phenotype in breast cancer through regulation of lineage-restricted genes [ER-negative cell line RNA-seq]

overall_design: RNA-seq on two estrogen receptor-negative breast cancer cell lines (MDA-MB-453 and MFM-223) after 6 hours with either a vehicle or 10 nM DHT


title: AR interacts with GATA3 to induce a luminal epithelial phenotype in breast cancer through regulation of lineage-restricted genes


title: Mapping the anti-cancer activity of α-connexin carboxyl-terminal (aCT1) peptide in resistant HER2+ breast cancer

status: Public on Dec 20 2023

city: Indianapolis

first: Elizabeth

last: Yeh

state: Indiana

address: 635 Barnhill Drive, Medical Science Building A418

department: Pharmacology and Toxicology

institute: Indiana University School of Medicine

summary: This study aims to examine the mechanisms for the anti-cancer effects of a therapeutic peptide agent targeted to connexin 43 (Cx43) called alpha-connexin carboxyl-terminal peptide (aCT1). Findings from this study identify the effect of aCT1 on breast cancer signaling using a resistant HER2+ breast cancer cell line.

overall_design: Total of 6 samples: aCT1 (n=3) and control (n=3). Control is the control/reference sample.

first: Adrian

last: Oblak

first: Kim


title: Aberrant upregulation of RUNX3 activates developmental genes to drive metastasis in gastric cancer (HiChIP)

city: Chiba

first: Masaki

last: Fukuyo

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

department: Department of Molecular Oncology

institute: Chiba University

summary: Gastric cancer metastasis is a major cause of mortality worldwide. Inhibition of RUNX3 in gastric cancer cell lines reduced migration, invasion, and anchorage independent growth in vitro. Following splenic inoculation, CRISPR-mediated RUNX3-knockout HGC-27 cells show suppression of xenograft growth and liver metastasis. We interrogated the potential of RUNX3 as a metastasis driver in gastric cancer by profiling its target genes. Transcriptomic analysis revealed strong involvement of RUNX3 in the regulation of multiple developmental pathways, consistent with the notion that RUNX family genes are master regulators of development. RUNX3 promoted “cell migration” and “extracellular matrix” programs, which are necessary for metastasis. Of note, we found pro-metastatic genes WNT5A, CD44 and VIM among the top differentially expressed genes in RUNX3-knockout versus control cells. Chromatin immunoprecipitation sequencing and HiChIP analyses revealed that RUNX3 bound to the enhancers and promoters of these genes, suggesting that they are under direct transcriptional control by RUNX3. We show that RUNX3 promoted metastasis in part through its upregulation of WNT5A to promote migration, invasion, and anchorage-independent growth in various malignancies. Our study therefore reveals the RUNX3-WNT5A axis as a key targetable mechanism for gastric cancer metastasis.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for active histone modification H3K27ac, H3K4me3, and H3K4me1 as well as the transcription factor RUNX3 in wildtype or RUNX3 knock-out HGC27 cells

first: Kazuto

last: Suda

first: Yoshiaki

last: Ito

first: Atsushi

last: Okabe

first: Bahityar

last: Rahmutulla

last: Kaneda


title: miRNA expression profiling of hTERT-immortalized renal proximal tubule epithelial (RPTEC/TERT1) cell treated with mesenchymal stem cell-conditioned miedium (BMSC-CM) on polyacrylamide (PAA) gel platform

city: Asan-si

first: Dayeon

last: Kang

address: 22, Soonchunhyang-ro, Sinchang-myeon

institute: Soon Chun Hyang University

summary: Chronic kidney disease (CKD) is a progressive condition characterized by sustained alterations in kidney structure and function. Long-term kidney fibrosis is marked by glomerulosclerosis, vascular sclerosis, and tubulointerstitial fibrosis. Therefore we investigated the therapeutic potential of BMSC-CM on RPTEC/TERT1 in a fibrotic environment. Using PAA gel platforms, we mimicked the stiffness typical of chronic kidney disease patients' kidneys.

overall_design: We performed miRNA expression profiling of RPTEC/TERT1 cells under both soft and stiff conditions. Subsequently, the cells were treated with BMSC-CM, and miRNA expression profiling was conducted using the NanoString platform with three samples for each condition.

first: Yunji

last: Kim

first: Nayoung

last: Suh


title: Aberrant upregulation of RUNX3 activates developmental genes to drive metastasis in gastric cancer.

overall_design: Refer to individual Series


title: Disruption of DNA methylation-mediated cranial neural crest proliferation and differentiation causes orofacial clefts in mice

city: Nutley

first: Andy

last: Madrid

state: NJ

address: 111 Ideation Way

institute: Hackensack Meridian Health

summary: Orofacial clefts of the lip and palate are widely recognized to result from complex gene–environment interactions, but inadequate understanding of environmental risk factors has stymied development of prevention strategies. We interrogated the role of DNA methylation, an environmentally malleable epigenetic mechanism, in orofacial development. Expression of the key DNA methyltransferase enzyme DNMT1 was detected throughout palate morphogenesis in the epithelium and underlying cranial neural crest cell (cNCC) mesenchyme, a highly proliferative multipotent stem cell population that forms orofacial connective tissue. Genetic and pharmacologic manipulations of DNMT activity were then applied to define the tissue- and timing-dependent requirement of DNA methylation in orofacial development. cNCC-specific Dnmt1 inactivation targeting initial palate outgrowth resulted in OFCs, while later targeting during palatal shelf elevation and elongation did not. Conditional Dnmt1 deletion reduced cNCC proliferation and subsequent differentiation trajectory, resulting in attenuated outgrowth of the palatal shelves and altered development of cNCC-derived skeletal elements. Finally, we found that the cellular mechanisms of cleft pathogenesis observed in vivo can be recapitulated by pharmacologically reducing DNA methylation in multipotent cNCCs cultured in vitro. These findings demonstrate that DNA methylation is a crucial epigenetic regulator of cNCC biology, define a critical period of development in which its disruption directly causes OFCs, and provide opportunities to identify environmental influences that contribute to OFC risk.

overall_design: RNA sequencing was used to compare transcriptomic differences in DNMT1 conditional knockout animals, WT animals, animals treated with AzadC or vehicle control, using three (pooled) animals as treatment group biological replicates.


title: AR interacts with GATA3 to induce a luminal epithelial phenotype in breast cancer through regulation of lineage-restricted genes [ER-positive cell line RNA-seq]

first: Geraldine

last: Laven-Law

overall_design: RNA-seq on two estrogen receptor-positive breast cancer cell lines (T-47D and ZR-75-1) cultured in steroid-deplete conditions after 6 hours with either a vehicle or 10 nM DHT

first: L

last: Hosseinzadeh

first: G

first: S

last: Pederson

first: A

last: Dwyer


title: Aberrant upregulation of RUNX3 activates developmental genes to drive metastasis in gastric cancer (ChIP-seq)


title: Aberrant upregulation of RUNX3 activates developmental genes to drive metastasis in gastric cancer (RNA-seq)


title: Gene expression profile of murine thymic B cells in the presence or absence of CD40 signaling

city: Munich

first: Thomas

last: Korn

email: thomas.korn@tum.de, c.sie@tum.de

address: Ismaninger Str. 22

department: Experimental Neuroimmunology

institute: Technical University of Munich

summary: The thymus contains some B cells that are located at the corticomedullary junction. We found that these thymic B cells express and present the water channel protein AQP4 and are necessary and sufficient to mediate the negative selection of AQP4-reactive thymocytes. In order to express and present AQP4, thymic B cells need to be licensed through a CD40 signal. Here, we tested the significance of CD40 signaling in thymic B cells for the expression and presentation of distinct autoantigens (besides AQP4) to orchestrate thymocyte selection for these autoantigens.

overall_design: 2000 B cells per sample were sorted from the thymus of naive, untreated wild type (WT, C57BL/6, Charles River) or CD40KO (JAX strain 002927) mice aged 6-8 weeks (5 mice per genotype) and then subjected to bulk RNAseq. After the initial run, the same libraries were sequenced again to increase overall sequencing depth.

first: Ali

last: Afzali

first: Lucy

last: Nirschl

first: Rupert

last: Öllinger

first: Andreas

last: Muschaweckh

first: Irene

last: Bonafonte Pardàs

first: Christopher

last: Sie


title: Leukaemia Exposure Alters the Transcriptional Profile and Function of BCR-ABL Negative Macrophages in the Bone Marrow Niche

city: Glasgow

first: Vignir

last: Helgason

address: Wolfson Wohl Cancer Research Centre, Garscube Estate, Glasgow, Bearsden

institute: The University of Glasgow

summary: Macrophages are fundamental cells of the innate immune system that support normal haematopoiesis, fight infection and play roles in both anti-cancer immunity and tumour progression. However, the function of macrophages in myeloid leukaemias remains largely unknown due to difficulties in isolating non-transformed cells from those derived from the malignant clone. Here we use a state-of-the-art chimeric mouse model of chronic myeloid leukaemia (CML) to study the impact of the dysregulated bone marrow (BM) microenvironment on bystander macrophages. Utilising both single cell RNA sequencing (scRNA-seq) of Philadelphia chromosome (Ph) negative macrophages and secretory proteomics of murine c-Kit+ stem/progenitor cells we have uncovered that macrophages exposed to a CML environment are altered transcriptionally and have reduced phagocytic function. Comparison of CML exposed macrophages to control counterparts by scRNA-seq has demonstrated significant heterogeneity in bone marrow (BM) macrophages, with the CML niche driving two unique subpopulations of immature and anti-inflammatory macrophages. Furthermore, we have identified that CML exposed macrophages can be separated from their normal counterparts via differential expression of surface markers CD36 and TGFBI, thereby providing us with a novel strategy to isolate Ph- macrophages in a CML BM niche. Finally, we have demonstrated that the dysregulated CML protein secretome is partially responsible for the in vivo alterations of macrophages, uncovering aberrant production of the immune modulatory protein lactotransferrin (LTF), and showing exposure to CML secreted factors suppresses phagocytosis, mitochondrial respiration, and inflammatory gene expression in BM macrophages.

overall_design: Bone marrow macrophages from four C57/Bl6 mice (2 control and 2 CML) were isolated by Fluorescence-activated cell sorting (FACS) according to staining with monoclonal antibodies to mouse CD45.1, CD45.2, CD11b, F4/80.

first: Amy

last: Dawson

first: Joana

last: Bittencourt-Silvestre

first: Ya-Ching

last: Hsieh

first: Isabel

last: van Loon

first: Giovanny

middle: R

last: Blanco

first: Angela

last: Ianniciello

first: Puneet

last: Agarwal

first: Hassan

last: Almasoudi

first: Laura

last: McCluskey

first: Lisa

last: Hopcroft

first: Mary

middle: T

last: Scott

first: Pablo

last: Baquero

first: Karen

last: Dunn

first: David

last: Vetrie

first: Seth

last: Coffelt

first: Ravi

last: Bhatia

first: Helen

last: Wheadon

first: Sara

last: Zanivan

first: Kristina

last: Kirschner


title: Single-cell multi-omics decodes regulatory programs during development of mouse secondary palate II

status: Public on Dec 19 2023

city: HOUSTON

first: Zhongming

last: Zhao

state: Texas

address: 7000 Fannin St

department: School of Biomedical Informatics

institute: UTHealth

summary: Perturbations in gene regulation during palatogenesis can lead to cleft palate, which is among the most common congenital birth defects. However, currently there is no comprehensive multiomics map of the developing secondary palate. Here, we perform single-cell multiome sequencing and profile chromatin accessibility and gene expression simultaneously within the same cells (n = 36,154) isolated from mouse secondary palate across embryonic days (E) 12.5, E13.5, E14.0, and E14.5. We construct five trajectories representing continuous differentiation of cranial neural crest-derived multipotent cells into distinct lineages. By linking open chromatin signals to gene expression changes, we characterize the underlying lineage-determining transcription factors. In silico perturbation analysis identifies transcription factors SHOX2 and MEOX2 as important regulators of the development of the anterior and posterior palate, respectively. In conclusion, our study chart epigenetic and transcriptional dynamics in palatogenesis, serving as a valuable resource for further cleft palate research.

overall_design: The anterior (n=2) and posterior (n=2) 1/3 palatal shelves of E14.0 C57BL/6J mice were microdissected, isolated, and then subjected to ChIP-seq with either SHOX2 antibody (JK-6E) (sc-81955, Santa Cruz), MEOX2 Antibody (A-8) (Sc-376748, Santa Cruz), or normal rabbit IgG (2729, Cell Signaling Technology) as a negative control. The ChIP assays were performed according to the manufacture’s instruction using SimpleChIP® Enzymatic Chromatin IP Kit (Magnetic Beads) (9003, CST). Two independent ChIPs were conducted for library generation for each group.

first: Fangfang

last: Yan

first: Akiko

last: Suzuki

first: Chihiro

last: Iwaya

first: Guangsheng

last: Pei

first: Xian

last: Chen

first: Hiroki

last: Yoshioka

first: Meifang

last: Yu

first: Lukas

last: Simon

first: Junichi

last: Iwata


title: Effect of Parenteral Trace Element Supplementation on RNA-sequencing Profile of Peripheral Blood in Peripartum Dairy Cows

city: La Plata

first: Guillermo

last: Giovambattista

state: Buenos Aires

address: Calle 60 y 118 S/N

department: Facultad de Ciencias Veterinarias

country: Argentina

institute: CONICET-UNLP

summary: The transition period is the most critical stage in the lactation cycle of dairy cattle. During this period, cows are subjected to high levels of oxidative stress. One way of managing this stress is through mineral supplementation with antioxidant micronutrients. The aim of this study was to evaluate the gene expression of transition dairy cows supplemented with the antioxidant trace elements copper (Cu), zinc (Zn), manganese (Mn) and selenium (Se). The study was carried out in a commercial Holstein dairy farm located in General Belgrano, province of Buenos Aires, Argentina. Cows (n=200) were randomly assigned to either a supplemented or a control group. Blood samples were obtained seven days after calving and used to determine superoxide dismutase and glutathione peroxidase activity, antioxidant capacity and thiobarbituric acid reactive substances. Additionally, RNA-sequencing analysis was performed. The oxidative stress index differed significantly between groups, despite only two differentially expressed genes which codify for second messengers (adjusted p value < 0.05). This would suggest that trace mineral supplementation of transition dairy cows would not induce changes in gene expression profiles in pathways associated with oxidative stress and immune function, since their expression is already high in response to the high oxidative stress levels and the dietary changes associated with this period. Nevertheless, considering the role of these minerals as cofactors, a higher availability in the supplemented group would increase antioxidant enzyme activity.

overall_design: Transcriptomic profile of peripheral blood in Holstein cows in the transition period that had been supplemented and control animals

first: Francisco

last: Calcaterra

first: Maria

middle: E

last: Fernandez

first: Leonidas

middle: H

last: Olivera

first: Loza

last: Guzman

first: Sebastian

last: Picco


title: EP300 facilitates human trophoblast stem cell differentiation.

city: Amsterdam

first: Remco

last: Keijser

address: Meibergdreef 9

department: Reproductive Biology Laboratory

institute: Amsterdam UMC

summary: Early placenta development involves cytotrophoblast differentiation into extravillous trophoblast (EVT) and syncytiotrophoblast (STB). Defective trophoblast development and function may result in severe pregnancy complications, including fetal growth restriction and pre-eclampsia. The incidence of these complications is increased in pregnancies of fetuses affected by Rubinstein–Taybi syndrome, a developmental disorder predominantly caused by heterozygous mutations in CREB-binding protein (CREBBP) or E1A-binding protein p300 (EP300). Although the acetyltransferases CREBBP and EP300 are paralogs with many overlapping functions, the increased incidence of pregnancy complications is specific for EP300 mutations. We hypothesized that these complications have their origin in early placentation and that EP300 is involved in that process. Therefore, we investigated the role of EP300 and CREBBP in trophoblast differentiation, using human trophoblast stem cells (TSCs) and trophoblast organoids. We found that pharmacological CREBBP/EP300 inhibition blocks differentiation of TSCs into both EVT and STB lineages, and results in an expansion of TSC-like cells under differentiation-inducing conditions. Specific targeting by RNA interference or CRISPR/Cas9-mediated mutagenesis demonstrated that knockdown of EP300 but not CREBBP, inhibits trophoblast differentiation, consistent with the complications seen in Rubinstein–Taybi syndrome pregnancies. By transcriptome sequencing, we identified transforming growth factor alpha (TGFA, encoding TGF-α) as being strongly upregulated upon EP300 knockdown. Moreover, supplementing differentiation medium with TGF-α, which is a ligand for the epidermal growth factor receptor (EGFR), likewise affected trophoblast differentiation and resulted in increased TSC-like cell proliferation. These findings suggest that EP300 facilitates trophoblast differentiation by interfering with at least EGFR signaling, pointing towards a crucial role for EP300 in early human placentation.

overall_design: TSCs were transfected with EP300 siRNA, CREBBP siRNA, or nontargeting siRNA as a control, and EVT differentiation was induced the following day. Given the relatively short-term effect of transfected siRNA, we harvested the siRNA-transfected cells at day 4 of EVT differentiation. We performed bulk RNA sequencing on the siRNA-transfected cells to get more insight into genes and pathways regulated by EP300 and CREBBP during EVT differentiation.

first: A

last: van Voorden

first: Geertruda

last: Veenboer

first: Solange

last: Lopes Cardozoa

first: Dina

last: Diek

first: Jennifer

last: Vlaardingerbroek

first: Marie

last: van Dijk

first: Carrie

last: Ris-Stalpers

first: Ans

middle: M

last: van Pelt

first: Gijs

last: Afink


title: Zinc finger DNA-binding conditioned site-specific recombination

city: Dresden

first: Maciej

last: Paszkowski-Rogacz

address: Tatzberg 47/49

department: UCC / Medical Faculty and University Hospital Carl Gustav Carus

institute: Technische Universität Dresden

summary: Programmable nucleases and designer-recombinases are prominent genome editing tools that hold great potential for the treatment of human genetic disorders. However, both of these tools alone are not optimal for clinical applications. We present an approach that combines the ease of targeting of programmable nucleases with editing safety and accuracy of site-specific recombinases. We find that insertional fusions of zinc-finger DNA-binding domains (ZFDs) into the coding sequence of designer-recombinases generate conditional enzymes that are inactive, unless the ZFD binds its target site placed in the vicinity of the recombinase binding site. This induced-fit activity is transferable to a recombinase with relaxed specificity, representing the prototype of a new class of genome editing enzymes that opens exciting perspectives for flexible, seamless, and precise genome surgery.

overall_design: ChIP-Seq based examination of D7ZF recombinase-zinc finger fusion binding sites in a human cell line.

first: Liliya

last: Mukhametzyanova

first: Paszkowski-Rogacz

last: Maciej

first: Frank

last: Buchholz