title: Behavioral, Neurotransmitter and Transcriptomic Analyses in male and female Fmr1 Knockout Mice

status: Public on Aug 26 2024

city: Tallahassee

first: Cynthia

last: Vied

state: Florida

address: 1115 W. Call St

department: Translational Science Laboratory

institute: Florida State University

summary: Fragile X Syndrome is an inherited X-linked disorder associated with intellectual disabilities that begin in childhood and last a lifetime. The symptoms overlap with autism spectrum disorder, and the syndrome predominantly affects males. Consequently, FXS research tends to favor analysis of social behaviors in males, leaving a gap in our understanding of other behavioral traits, especially in females. Here we used a mouse model of FXS to analyze developmental, behavioral, neurochemical, and transcriptomic profiles in males and females. Our behavioral assays demonstrated locomotor hyperactivity, motor impulsivity, increased “approach” behavior in an approach-avoidance assay, and deficits in nest building behavior. Analysis of brain neurotransmitter content revealed deficits in striatal GABA, glutamate, and serotonin content. RNA sequencing of the ventral striatum unveiled expression changes associated with neurotransmission as well as motivation and substance use pathways. Sex differences were identified in nest building behavior, striatal neurotransmitter content, and ventral striatal gene expression. In summary, our study identified sex differences in specific behavioral, neurotransmitter, and gene expression phenotypes and gene set enrichment analysis identified significant enrichment of pathways associated with motivation and drug reward.

overall_design: Ventral striatum mRNA from adult C57BL6( https://www.jax.org/strain/000664) and Fmr1 KO (https://www.jax.org/strain/003025) male and female mice were analyzed by RNA sequencing using an Illumina NovaSeq 6000

first: Deirdre

last: McCarthy

first: Mia

middle: X

last: Trupiano

first: Angeli

middle: J

last: Canekeratne

first: Yuan

last: Wang

first: Christopher

last: Schatschneider

first: Pradeep

last: Bhide


title: Severe induction of aberrant DNA methylation by nodular gastritis in adults

status: Public on Aug 27 2024

city: Shinagawa-ku

first: Hideyuki

last: Takeshima

state: Tokyo

department: Institute for Advanced Life Sciences

country: Japan

institute: Hoshi University

type: Methylation profiling by genome tiling array

summary:
Background: Nodular gastritis (NG) is characterized by marked antral lymphoid follicle formation, and is a strong risk factor for diffuse-type gastric cancer in adults. However, it is unknown whether aberrant DNA methylation, which is induced by atrophic gastritis (AG) and is a risk for gastric cancer, is induced by NG. Here, we analyzed methylation induction by NG.

Methods: Gastric mucosal samples were obtained from non-cancerous antral tissues of 16 NG and 20 AG patients with gastric cancer and 5 NG and 6 AG patients without, all age- and gender-matched. Genome-wide methylation analysis and expression analysis were conducted by a BeadChip array and RNA-sequencing, respectively.

Results: Clustering analysis of non-cancerous antral tissues of NG and AG patients with gastric cancer was conducted using methylation levels of 585 promoter CpG islands (CGIs) of methylation-resistant genes, and a large fraction of NG samples formed a cluster with strong methylation induction. Promoter CGIs of CDH1 and DAPK1 tumor-suppressor genes were more methylated in NG than in AG. Notably, methylation levels of these genes were also higher in the antrum of NG patients without cancer. Genes related to lymphoid follicle formation, such as CXCL13/CXCR5 and CXCL12/CXCR4, had higher expression in NG, and genes involved in DNA demethylation TET2 and IDH1, had only half the expression in NG.

Conclusions: Severe aberrant methylation, involving multiple tumor-suppressor genes, was induced in the gastric antrum and body of patients with NG, in accordance with their high gastric cancer risk.

overall_design:
Genome-wide DNA methylation analysis was conducted by an Infinium HumanMethylationEPIC BeadChip array of FFPE samples.

***Please note that the records have been updated with IDAT files on Oct 8, 2024.

first: Akiko

last: Sasaki

first: Satoshi

last: Yamashita

first: Toshikazu

last: Ushijima


title: Characterization of the effect of deleting the Gata6 gene in E (embryonic day) 11.5 OFT (outflow tract).

city: Madrid

first: Jose Luis

last: de la Pompa

state: MADRID

address: Melchor Fernández Almagro 3

country: Spain

institute: Centro Nacional de Investigaciones Cardiovasculares (CNIC)

type: Expression profiling by high throughput sequencing

summary: To investigate the role of Gata6 in OFT development, we generated a Gata6 heterozygous mice, harvested OFT at E11.5, and determined gene expression profiles, using bulk RNA-seq.

overall_design: Gene expression profiling with RNA-seq was performed in three pools of four pairs of E11.5 OFT per genotype: control (WT) and Gata6STOP/+ (MUT).

first: Rebeca

last: Piñeiro-Sabarís

first: Donal

last: MacGrogan

first: José Luis


title: Robust differentiation of human pluripotent stem cells into mural progenitor cells via transient activation of NKX3.1

city: Boston

first: Yonglin

last: Zhu

state: MA

address: 300 Longwood Ave

department: Cardiac Surgery

country: USA

institute: Boston Children's Hospital

summary: Mural cells are central to vascular integrity and function. In this study, we demonstrate the innovative use of the transcription factor NKX3.1 to guide the differentiation of human induced pluripotent stem cells into mural progenitor cells (iMPCs). By transiently activating NKX3.1 in mesodermal intermediates, we developed a method that diverges from traditional growth factor-based differentiation techniques. This approach efficiently generates a robust iMPC population capable of maturing into diverse functional mural cell subtypes, including smooth muscle cells and pericytes. These iMPCs exhibit key mural cell functionalities such as contractility, deposition of extracellular matrix, and the ability to support endothelial cell-mediated vascular network formation in vivo.

overall_design: Using bulk RNA sequencing, we compared gene expression profiles of induced mural progenitor cells (iMPC_NKX3.1, #13-15) derived from hiPSCs (#7-9) with primary vascular smooth muscle cells (hpVSMC, #10-12) and mesenchymal cells (hbMSC, #4-6, control group). Additionally, we contrasted iMPCs with induced smooth muscle cells (iSMCs, #16-18) generated via a different growth factor-driven protocol to study their differentiation into mature smooth muscle cells or pericytes. To assess differentiation, we conducted a 7-day co-culture of iMPCs with endothelial cells (coECiMPC, #1-3). Employing scRNA sequencing, we investigated iPSC differentiation into iMPCs and explored mural cell heterogeneity due to EC interaction. Our study sampled crucial stages: day 0 (iPSCs, #22), day 2 (MePCs after mesodermal differentiation, #20), day 4 (iMPCs post-NKX3.1 activation, #21), and day 11 post 7-day iMPC-EC co-culture (#19).

first: Juan

last: Melero-Martin

first: Umji

last: Lee

first: Yadong

last: Zhang


title: Single-cell analysis identifies distinct macrophage phenotypes associated with pro-disease and pro-resolving functions in the endometriotic niche

city: Coventry

first: Erin

last: Greaves

address: Gibbet Hill Campus

department: Division of Biomedical Sciences

country: United Kingdom

institute: University of Warwick

summary: Endometriosis negatively impacts the health-related quality of life of 190 million women worldwide. Novel advances in non-hormonal treatments for this debilitating condition are desperately needed. Macrophages play a vital role in the pathophysiology of endometriosis and represent a promising therapeutic target. In the current study, we revealed the full transcriptomic complexity of endometriosis-associated macrophage subpopulations using single-cell analyses in a preclinical mouse model of experimental endometriosis. We have identified two key lesion-resident populations that resemble i) tumour-associated macrophages (characterized by expression of Folr2, Mrc1, Gas6 and Ccl8+) that promoted expression of Col1a1 and Tgfb1 in human endometrial stromal cells and increased angiogenic meshes in human umbilical vein endothelial cells, and ii) scar-associated macrophages (Mmp12, Cd9, Spp1, Trem2+) that exhibited a phenotype associated with fibrosis and matrix remodelling. We also described a population of pro-resolving large peritoneal macrophages (LpM) that align with a lipid-associated macrophage phenotype (Apoe, Saa3, Pid1) concomitant with altered lipid metabolism and cholesterol efflux. Gain of function experiments using an Apoe mimetic resulted in decreased lesion size and fibrosis, and modification of peritoneal macrophage populations in the preclinical model. Using cross-species analysis of mouse and human single-cell datasets, we determined the concordance of peritoneal and lesion-resident macrophage subpopulations, identifying key similarities and differences in transcriptomic phenotypes. Ultimately, we envisage that these findings will inform the design and use of specific macrophage-targeted therapies and open new avenues for the treatment of endometriosis.

overall_design: We used a menses mouse model of endometriosis. From donor endometrium (+4-6 hours P4 withdrawal; n=5 mice), endometriosis lesions (lesions from n=10 mice) and peritoneal lavage from Sham (n=5) and Endometriosis mice (n=5), 200,000 CD45+ cells were FACS sorted into 1ml PBS + 2% FBS using a FACS Fusion. Cells were barcoded using a 10X Genomics Chromium ControllerTM using established pipelines. Libraries were sequenced by Edinburgh Genomics using a NovaSeq 6000 sequencing system (Illumina®, San Diego, USA)

first: Yasmin

last: Henlon

first: Kavita

last: Panir

first: Iona

last: McIntrye

first: Chloe

last: Hogg

first: Priya

last: Dhami

first: Antonia

middle: O

last: Cuff

first: Anna

last: Senior

first: Niky

last: Moolchandani-Adwani

first: Elise

middle: T

last: Courtois

first: Andrew

middle: W

last: Horne

first: Matthew

last: Rosser

first: Sascha

last: Ott


title: Epigenetic reader ZMYND11 noncanonical function restricts HNRNPA1-mediated stress granule formation and oncogenic activity

city: shanghai

first: cheng

last: Lian

address: dongan road 131

country: China

institute: Fudan university

summary: To investigate the function of ZMYND11 in  prostate cancer, we knockdown ZMYND11 in 22Rv1 cells and do RNA-seq.

overall_design: We then performed gene expression profilling analysis using data obtained from RNA-seq of 22Rv1 cells.

first: Gong-Hong

last: Wei

first: Cheng

first: Chunyi

first: Zixian

last: Wang


title: Molecular and functional landscape of malignant serous effusions for precision oncology

city: Zurich

first: Berend

last: Snijder

address: Otto-Stern-Weg 3

department: D-BIOL

country: Switzerland

institute: ETH Zurich

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

overall_design: Refer to individual Series


title: Molecular and functional landscape of malignant serous effusions for precision oncology [MSE_drug_treated]

summary: Personalized treatment for patients with advanced solid tumors critically depends on the deep characterization of tumor cells. These patients frequently develop malignant serous effusions (MSE). The value of MSE-based tumor cell characterization for guiding precision oncology is, however, currently unclear. Here, we present a comprehensive characterization of a pan-cancer cohort of 150 MSE samples at the cellular, molecular, and functional level. Our integrative analysis reveals dynamic cellular heterogeneity in MSE, and uncovers links between tumor driver mutations and ex vivo growth patterns. Strong concordance between genomic and transcriptional profiles of MSE and their corresponding solid tumors validates their use as a model system for solid tumor biology. We link baseline gene expression patterns to global ex vivo drug sensitivity, and demonstrate that drug-induced transcriptional changes in MSE are highly indicative of compound mode of action. Two case studies exemplify the utility of our approach in investigating acquired resistance to targeted therapy and identifying treatment options for relapsed solid tumors. In summary, our study provides a functional multi-omics view on a pan-cancer MSE cohort and underlines the utility of MSE-based precision oncology.

overall_design: Transcriptomes of bulk MSE samples after ex vivo drug treatment were analyzed by high-throughut 3'-digital gene expression profiling using a modified DRUG-seq protocol (Original protocol: Ye et al,  2018, PMID: PMC9207813).

first: Rebekka

last: Wegmann

first: Lorenz

last: Bankel

first: Christian

last: Britschgi


title: H3K4me2 distinguishes a distinct class of enhancers during the maternal-to-zygotic transition

city: Pittsburgh

first: Miler

last: Lee

state: PA

address: 4249 Fifth Ave

department: Biological Sciences

institute: University of Pittsburgh

type: Genome binding/occupancy profiling by high throughput sequencing

summary: After egg fertilization, an initially silent embryonic genome is transcriptionally activated during the maternal-to-zygotic transition. In zebrafish, maternal vertebrate pluripotency factors Nanog, Pou5f3 (OCT4 homolog), and Sox19b (SOX2 homolog) (NPS) play essential roles in orchestrating embryonic genome activation, acting as “pioneers” that open condensed chromatin and mediate acquisition of activating histone modifications. However, some embryonic gene transcription still occurs in the absence of these factors, suggesting the existence of other mechanisms regulating genome activation. To identify chromatin signatures of these unknown pathways, we profiled the histone modification landscape of zebrafish embryos using CUT&RUN. Our regulatory map revealed two subclasses of enhancers distinguished by presence or absence of H3K4me2. Enhancers lacking H3K4me2 tend to require NPS factors for de novo activation, while enhancers bearing H3K4me2 are epigenetically bookmarked by DNA hypomethylation to recapitulate gamete activity in the embryo, independent of NPS pioneering. Thus, parallel enhancer activation pathways combine to induce transcriptional reprogramming to pluripotency in the early embryo.

overall_design: Histone modification CUT&RUN was performed on zebrafish 1K-cell to shield stage embryos

middle: D

last: Hurton


title: Molecular and functional landscape of malignant serous effusions for precision oncology [MSE_baseline]

overall_design: Baseline transcriptomes of bulk MSE samples were analyzed by high-throughut 3'-digital gene expression profiling using a modified DRUG-seq protocol (Original protocol: Ye et al, 2018, PMID: PMC9207813).


title: Recruitment of the m6A/Am demethylase FTO to target RNAs by the telomeric zinc finger protein ZBTB48 [RNA-seq]

city: Toronto

first: Ulrich

last: Braunschweig

state: Ontario

address: 160 College Street

department: Donnelly Centre

country: Canada

institute: University of Toronto

summary: Fat mass and obesity-associated protein (FTO) can remove both the N6-methyladenosine (m6A) and N6, 2′-O-dimethyladenosine (m6Am) methylation marks that function in multiple aspects of posttranscriptional regulation. Here, we demonstrate that Zbtb48, a C2H2-zinc finger protein that functions in telomere maintenance, associates with FTO and binds both mRNA and the telomere-associated regulatory RNA TERRA to regulate the functional interactions of FTO with target transcripts. Specifically, depletion of Zbtb48 affects targeting of FTO to sites of m6A/m6Am modification, changes cellular m6A/m6Am levels and, consequently, alters decay rates of target RNAs. Zbtb48 ablation also accelerates growth of HCT-116 colorectal cancer cells and modulates FTO-dependent regulation of Metastasis-associated protein 1 (MTA1) transcripts by controlling the binding to MTA1 mRNA of the m6A reader IGF2BP2. Our findings thus uncover a previously unknown mechanism of posttranscriptional regulation in which Zbtb48 co-ordinates RNA-binding of the m6A/m6Am demethylase FTO to control expression of its target RNAs.

overall_design: RNA-seq of HEK293 cells upon knockdown of ZBTB48 or control non-targeting knockdown, each in duplicate.

first: Syed

last: Nabeel-Shah

first: Shuye

last: Pu

first: Giovanni

middle: L

last: Burke

first: Nujhat

last: Ahmed

first: Hyunmin

first: Shaghayegh

last: Farhangmehr

first: Mingkun

last: Wu

first: Hua

last: Tang

first: Gouqing

last: Zhong

first: Edyta

last: Marcon

first: Zhaolei

last: Zhang

first: Benjamin

last: Blencowe

first: Jack

middle: F

last: Greenblatt


title: Recruitment of the m6A/Am demethylase FTO to target RNAs by the telomeric zinc finger protein ZBTB48 [iCLIP-seq]

overall_design: iCLIP-seq data of ZBTB48 and FTO (with no treatment, overexpression of ZBTB48, or GFP control) and  in HEK293 cells, including FTO upon overexpression of ZBTB48; iCLIP of m6A upon overexpression of FTO, ZBTB48, or GFP control; each with 2-4 replicates and size-matched input sample.


title: Recruitment of the m6A/Am demethylase FTO to target RNAs by the telomeric zinc finger protein ZBTB48 [ChIP-seq]

overall_design: ChIP-Seq of ZBTB48 in HEK293 cells and input, each in duplicate


title: Endothelial derived, secreted long non-coding RNAs Gadlor1 and Gadlor2 aggravate cardiac remodeling

city: Mannheim

first: Joerg

last: Heineke

address: Ludolf-Krehlstr. 7-11 Tridomus B

department: Cardiovascular Physiology

country: Germany

institute: Medical Faculty of Mannheim Heidelberg University

summary:
Background: Pathological cardiac overload triggers maladaptive myocardial remodeling that predisposes to the development of heart failure. The contribution of long non-coding RNAs (lncRNAs) to intercellular signaling during cardiac remodeling is largely unknown.
Methods: We analyzed the expression of Gadlor 1 and Gadlor2 lncRNAs in mouse hearts, mouse cardiac cells, extracellular vesicles (EVs), human failing hearts as well as patient serum. Gadlor knock-out (KO) mice were generated and analyzed. The effect of Gadlor knock-out and Gadlor overexpression during cardiac pressure overload induced by transverse aortic constriction (TAC) was analyzed by echocardiography, histological analyses and RNA sequencing in isolated cardiac cells. Gadlor1/2 interaction partners were identified by RNA antisense purification coupled with mass-spectrometry (RAP-MS).
Results: In the heart, the related lncRNAs Gadlor1 and 2 are mainly expressed in endothelial cells and to a lesser extent in fibroblasts. Gadlor1/2 are upregulated in failing mouse hearts as well as in the myocardium and in serum of heart failure patients. Interestingly, Gadlor1 and 2 are secreted from endothelial cells within EVs, which are taken up by cardiomyocytes. Gadlor-KO mice exerted reduced cardiomyocyte hypertrophy, diminished myocardial fibrosis and improved cardiac function, but paradoxically suffered from sudden death during prolonged overload. Gadlor overexpression, in turn, triggered hypertrophy, fibrosis and cardiac dysfunction. Mechanistically, Gadlor1 and Gadlor2 inhibit angiogenic gene expression in endothelial cells, while promoting the expression of pro-fibrotic genes in cardiac fibroblasts. In cardiomyocytes, Gadlor1/2 upregulate mitochondrial genes, but downregulate angiogenesis genes, while interacting with the transcriptional regulator Glyr1 and the calcium/calmodulin-dependent protein kinase type II (CaMKII), entailing cardiomyocyte hypertrophy and perturbed cardiomyocyte calcium dynamics.
Conclusions: We describe that Gadlor1 and 2, two related, novel lncRNAs, are upregulated in cardiac pathological overload and are secreted from endothelial cells within EVs. Gadlor1/2 induce cardiac dysfunction, cardiomyocyte hypertrophy and myocardial fibrosis by exerting heterocellular effects on cardiac cellular gene-expression and by affecting calcium dynamics in cardiomyocytes, which take up the Gadlor1/2 by EV mediated transfer from endothelial cells. Targeted inhibition of Gadlor lncRNAs in endothelial cells or fibroblasts might serve as therapeutic strategy in the future.

overall_design: Cardiac EC, FB and CM lysates from WT and Gadlor-KO mice after 2 weeks of pressure overload by transverse aortic constriction (TAC)

first: Merve

last: Keles


title: NanoStrong miRNA from DU145 CF and HF cells

status: Public on Aug 24 2024

city: LA

first: Paul

middle: C

last: Boutros

address: UCLA

department: Human Genetics

institute: UCLA

summary:
NanoString duplicate runs were created for CF- and HF-resistant cells, and for matched parental duplicate samples corresponding to each radioresistant cell type.
Prostate cancer is the second most common cause of cancer death in men, and radiotherapy is a standard curative therapy for localized disease. Unfortunately, aggressive radioresistant relapses can arise, and the molecular underpinnings of radioresistance are unknown. Modern clinical radiotherapy is evolving to deliver higher doses of radiation in fewer fractions (hypofractionation). We therefore analyzed genomic, transcriptomic and proteomic data to characterize the determinants of prostate cancer radioresistance in cells treated with both conventionally fractionated and hypofractionated radiotherapy. Independent of fractionation schedule, resistance to radiotherapy involved massive genomic instability and abrogation of DNA mismatch repair. Specific prostate cancer driver genes were modulated at the RNA and protein levels, with distinct protein subcellular responses to radiotherapy. Conventional fractionation led to a far more aggressive biomolecular response than hypofractionation. Testing pre-clinical candidates identified in cell lines, we revealed POLQ as a radiosensitizer. POLQ-modulated radioresistance in model systems and was predictive of it in large patient cohorts. Pharmacologic and genetic inhibition of POLQ re-sensitized radioresistant cells, creating signatures seen in primary patient cohorts. The molecular response to radiation is highly multi-modal, and sheds light on prostate cancer lethality.

overall_design: We analyzed miRNA data to characterize the determinants of prostate cancer radioresistance in cells treated with both conventionally fractionated and hypofractionated radiotherapy.

first: Stanley

middle: K

last: Liu


title: METTL3 Confers Oxaliplatin Resistance Through the Activation of G6PD-enhanced Pentose Phosphate Pathway in Hepatocellular Carcinoma

status: Public on Aug 23 2024

city: Guangzhou

first: Yongrui

last: Lv

state: Guangdong

address: 651 Dongfengdong Road

institute: Sun Yat-sen University Cancer Center

summary: Oxaliplatin-based therapeutics is a widely used treatment approach for hepatocellular carcinoma (HCC) patients; however, drug resistance poses a significant clinical challenge. Epigenetic modifications have been implicated in the development of drug resistance. In our study, employing siRNA library screening, we identified that silencing the m6A writer METTL3 significantly enhanced the sensitivity to oxaliplatin in both in vivo and in vitro HCC models. Further investigations through combined RNA-seq and non-targeted metabolomics analysis revealed that silencing METTL3 impeded the pentose phosphate pathway (PPP), leading to a reduction in NADPH and nucleotide precursors. This disruption induced DNA damage, decreased DNA synthesis, and ultimately resulted in cell cycle arrest. Mechanistically, METTL3 was found to modify E3 ligase TRIM21 near the 3'UTR with N6-methyladenosine, leading to reduced RNA stability upon recognition by YTHDF2. TRIM21, in turn, facilitated the degradation of the rate-limiting enzyme of PPP, G6PD, through the ubiquitination-proteasome pathway. Importantly, high expression of METTL3 was significantly associated with adverse prognosis and oxaliplatin resistance in HCC patients. Notably, treatment with the specific METTL3 inhibitor, STM2457, significantly improved the efficacy of oxaliplatin. These findings underscore the critical role of the METTL3/TRIM21/G6PD axis in driving oxaliplatin resistance and present a promising strategy to overcome chemoresistance in HCC.

overall_design: To investigate the effect of METTL3 on HCC cells, the total RNA of Huh7 stable cell-lines transfected with shNC or shMETTL3 lentivirus were subjected to RNA-seq.

first: Xiaohan

last: Jin

first: Fengjie

last: Bie

first: Dan

last: Xie

first: Muyan

last: Cai


title: Recruitment of the m6A/Am demethylase FTO to target RNAs by the telomeric zinc finger protein ZBTB48

first: Ulrich

last: Braunschweig


title: Astrocyte-Derived Clusterin Disrupts Glial Physiology to Obstruct Remyelination in Mouse Models of Demyelinating Diseases

city: guangzhou

first: Chen

last: Chen

address: tianhe

department: Department of Neurosurgery

institute: Lingnan hospital, branch of the Third Affiliated Hospital of Sun Yat-sen University

summary: Multiple sclerosis (MS) is a debilitating demyelinating disease characterized by remyelination failure attributed to inadequate oligodendrocyte precursor cells (OPCs) differentiation and aberrant astrogliosis. A comprehensive cell atlas reanalysis of clinical specimens brings to light heightened clusterin (CLU) expression in a specific astrocyte subtype links to active lesions in MS patients. Our investigation reveals elevated astrocytic CLU levels in both active lesions of patient tissues and female murine MS models. CLU administration stimulates primary astrocyte proliferation while concurrently impedes astrocyte-mediated clearance of myelin debris. Intriguingly, CLU overload directly impedes OPCs differentiation and induces OPCs and OLs apoptosis. Mechanistically, CLU suppresses PI3K-AKT signaling in primary OPCs via very low-density lipoprotein receptor. Pharmacological activation of AKT rescues the damage inflicted by excess CLU on OPCs and ameliorates demyelination in the corpus callosum. Furthermore, conditional knockout of CLU emerges as a promising intervention, showcasing improved remyelination processes and reduced severity in murine MS models.

overall_design: Part 1, to study the differentially expressed genes in primary astrocytes after CLU treatment for 24 hours (library name: AST-CLU-1; AST-CLU-2; AST-CLU-3; AST-CTRL-1; AST-CTRL-2; AST-CTRL-3); Part 2, to study the differentially expressed genes in NPC-induced OPCs after CLU treatment for 24 hours (library name: OPC-24h-CLU-1; OPC-24h-CLU-2; OPC-24h-CLU-3; OPC-24h-CTRL-1; OPC-24h-CTRL-2; OPC-24h-CTRL-3); Part 3, to study differentially expressed genes in NPC-induced OPCs after CLU treatment for 3 hours (library name: OPC-3h-CLU-1; OPC-3h-CLU-2; OPC-3h-CLU-3; OPC-3h-CTRL-1; OPC-3h-CTRL-2; OPC-3h-CTRL-3).

first: Wei

last: Qiu

first: Xiaodong

first: Feng

last: Qin


title: Characterization of RNAs captured through a new engineered protein-mediated affinity purification

city: Chengdu

first: Zhihong

last: Xue

state: Sichuan

address: No. 20, 3rd section, South Renmin Road

institute: Sichuan University

summary: We generated a new recombinant protein HARD (High-affinity RNA-binding Domain) with non-sequence-specific high-affinity on RNAs and developed the immobilized-HARD protein-mediated RNA affinity purification approach (HARD-AP).We showed that HARD-AP successfully captured all RNA biotypes.

overall_design: We incubated the HARD beads (chemically conjugate the HARD protein onto agarose resin) with the total RNA of HEK293 cells and then purified RNAs left on beads after stringently washing.We performed Ribo-Zero RNA sequencing (RNA-seq) of the HARD beads-bound RNAs and input RNAs to test the nature of the captured RNAs.


title: CLIP-seq of Csrp1 in mouse embryoid bodies of day 9

summary: V6.5 mESCs over-expressing V5-tagged Csrp1 and wild-type mESCs were differentiated into embryoid bodies (EBs) and collected at day 9 for CLIP-seq.

overall_design: Two biologically independent replicates were prepared for V5-tagged Csrp1 and wild-type CLIP-seq. The two wild-type CLIP-seq samples were used as the negative control.


title: Quantitative analysis of the transcriptome of C. elegans

status: Public on Aug 22 2024

city: Shanghai

first: Hongru

last: Lin

state: Shanghai

address: Siping road 1239

department: life and science technology

institute: Tongji university

summary: We investigated the transcriptomic changes associated with hlh 30 gene overexpression and knockout in Aβ nematode CL4176

overall_design: We overexpressed and knocked out hlh 30 gene in Aβ nematode CL4176, and performed transcriptome sequencing on the first day of adult stage

first: Hongbing

last: Wang

last: Zhang


title: RNA-seq analysis of wild-type and csrp1KO mESCs and embryoid bodies of day 9

summary: mESCs were in vitro differentiated into embryoid bodies under suspension cultured condition and was collected at day 9 of differentiation. Polyadenylated mRNAs of mESCs and EBs were isolated and used to build the sequencing library.

overall_design: Generation of csrp1KO mESC cell line: we generated csrp1KO through CRSPR/Cas9-mediated genome editing and confirmed the loss of Csrp1 protein through Western blot. Three biologically independent replicates were included for each sample.


title: Anchored Kaolin Scales on Cotton: Towards Rapid and Safe Hemostasis

city: hefei

first: Guangzhen

address: jinzhai road 96

department: Chemistry

institute: University of Science and Technology of China

summary: we fabricate a bioinspired hemostatic dressing (AKOC) with robust interfacial integration of kaolin and cotton through a potentially scalable self-assembly strategy for efficient and safe hemostasis.

overall_design: Repaired tissues from liver trauma were collected on days 14 to evaluate the degree of chronic inflammatory caused by different hemostatic dressings (Quik-clot treated liver as control, AKOC treated liver as sample).

first: Yao

first: Shuhong

last: Yu


title: RNA-seq analysis of wild-type and csrp1KO mESCs and embryoid bodies of day 9, and CLIP-seq of Csrp1 in mouse embryoid bodies of day 9


title: MBNL splicing factors regulate the microtranscriptome of skeletal muscles (mouse, skeletal muscle, developmental panel)

city: Poznan

first: Agnieszka

last: Mykowska

address: Uniwersytetu Poznanskiego 6

country: Poland

institute: Adam Mickiewicz University

type: Non-coding RNA profiling by high throughput sequencing

summary: Muscleblind-like proteins (MBNLs) regulate various RNA-processing steps, including alternative splicing, polyadenylation, RNA stability, and mRNA intracellular localization. In myotonic dystrophy type 1 (DM1), the most common muscular dystrophy in adults, MBNLs are sequestered on toxic RNA containing expanded CUG repeats, which leads to disruption of MBNL-regulated processes and disease features of DM1. Herein, we showed the significance of MBNLs in the regulation of microtranscriptome dynamics during postnatal development of skeletal muscles and in microRNA (miRNA) misregulation observed in mouse models and patients with DM1. We identified multiple miRNAs sensitive to insufficiency of MBNL proteins and revealed that many of them were postnatally regulated, which was correlated with increases in the activity of these proteins during this process. In adult Mbnl1-knockout mice, miRNA expression exhibited an adult-to-newborn shift. We identified two mechanisms through which MBNLs influence miRNA levels. First, MBNL loss induces transcriptional changes in miRNA precursors. Second, MBNLs affect miRNA biogenesis by regulating the alternative splicing of miRNA primary transcripts. We propose that the expression of miR-23b, miR-27b and miR-24-1, produced from the same cluster, depends on the MBNL-sensitive inclusion of alternative exons containing miRNA sequences. Our findings suggest that MBNL sequestration in DM1 is partially responsible for altered miRNA activity. This study provides new insights into the biological roles and functions of MBNL proteins as regulators of miRNA expression in skeletal muscles.

overall_design: MicroRNA (miRNA) sequencing from skeletal muscles (quadriceps) of WT postnatal day 1 (n=3), postnatal day 5 (n=3), postnatal day 14 (n=3) and postnatal day 90 (n=3) mice

last: Piasecka

first: Michal

last: Sekrecki

first: Arkadiusz

last: Kajdasz

last: Szczesniak

first: Lukasz

last: Sznajder

first: Krzysztof

last: Sobczak


title: Investigation of Chimeric Transcripts Derived from LINE-1 and Alu Retrotransposons in Cerebellar Tissues of Individuals with Autism Spectrum Disorder (ASD)

city: Bangkok

first: Tewarit

last: Sarachana

address: 154 Rama 1 Rd. Wangmai Pathumwan

country: Thailand

institute: Chulalongkorn University

summary: LINE-1 and Alu retrotransposons are components of the human genome and have been implicated in many human diseases. These elements can influence human transcriptome plasticity in various mechanisms. Chimeric transcripts derived from LINE-1 and Alu can also impact the human transcriptome, such as exonization and post-transcriptional modification. However, its specific role in ASD neuropathology remains unclear, particularly in the cerebellum tissues. We performed RNA-sequencing of post-mortem cerebellum tissues from ASD and unaffected individuals for transposable elements profiling and chimeric transcript identification. The majority of free transcripts of transposable elements were not changed in the cerebellum tissues of ASD compared with unaffected individuals. Nevertheless, we observed that chimeric transcripts derived from LINE-1 and Alu were embedded in the transcripts of differentially expressed genes in the cerebellum of ASD, and these genes were related to developments and abnormalities of the cerebellum.  In addition, the expression levels of these genes were correlated with the significantly decreased thickness of the molecular layer in the cerebellum of ASD. We also found that global methylation and expression of LINE-1 and Alu elements were not changed in ASD, but observed in the ASD sub-phenotypes. Our findings showed associations between transposable elements and cerebellar abnormalities in ASD, particularly in distinct phenotypic subgroups. Further investigations using appropriate models are warranted to elucidate the structural and functional implications of LINE-1 and Alu elements in ASD neuropathology.

overall_design: Post-mortem cerebellum tissues from ASD and unaffected individuals were originally obtained from the Harvard Brain Tissue Resource Center. The snap-frozen post-mortem brain tissues used in this study consist of 13 samples from cerebellum tissues of ASD (n=8) and unaffected controls (n=5). The snap-frozen post-mortem brain tissues were used for RNA isolations before molecular analysis. Total RNA was sent to BGI Hong Kong for RNA-sequencing analysis using the MGI DNBSEQ technology platform. Briefly, total RNA was used to prepare stranded mRNA library construction by mRNA enrichment and was then sequenced by the DNBSEQ-G400 (150 bp paired-end).

first: Thanit

last: Saeliw

first: Songphon

last: Kanlayaprasit

first: Surangrat

last: Thongkorn

first: Kwanjira

last: Songsritaya

first: Bumpenporn

last: Sanannam

first: Depicha

last: Jindatip

first: Valerie

last: Hu


title: MBNL splicing factors regulate the microtranscriptome of skeletal muscles (human, skeleta muscle, DM1 and non-DM)

overall_design: MicroRNA (miRNA) sequencing from skeletal muscles of DM1 (n=3) and non-DM (n=2) individuals


title: MBNL splicing factors regulate the microtranscriptome of skeletal muscles (mouse, skeletal muscle, Mbnl-KO panel)

overall_design: MicroRNA (miRNA) sequencing from skeletal muscles of WT (n=3), Mbnl1KO (n=3) and Mbnl2KO (n=3) mice


title: MBNL splicing factors regulate the microtranscriptome of skeletal muscles

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: USP50 suppresses alternative RecQ helicase use and deleterious DNA2 activity during replication

status: Public on Aug 21 2024

city: Birmingham

first: Joanna

middle: Ruth

last: Morris

state: West Midlands

address: IBR West 2nd floor, Medical School, Vincent Drive, WX 2.45, Egdbaston

institute: University of Birmingham

summary: Mammalian DNA replication relies on various DNA helicases and nuclease activities to ensure accurate genetic duplication, but how different helicase and nuclease activities are properly directed remains unclear. Here, we identify the ubiquitin-specific protease, USP50, as a chromatin-associated protein required to promote ongoing replication, fork restart, telomere maintenance, cellular survival following hydroxyurea or pyridostatin treatment, and suppression of DNA breaks near GC-rich sequences. We find that USP50 supports proper WRN: FEN1 localisation at or near stalled replication forks. Nascent DNA in cells lacking USP50 shows increased association of the DNA2 nuclease and RECQL4 and RECQL5 helicases and replication defects in cells lacking USP50, or FEN1 are driven by these proteins. Consequently, suppression of DNA2 or RECQL4/5 improves USP50-depleted cell resistance to agents inducing replicative stress and restores telomere stability. These data define an unexpected regulatory protein that promotes the balance of helicase and nuclease use at ongoing and stalled replication forks..

overall_design: INDUCE-Seq and Illumina sequencing on DNA samples from Hela cells treated for three days with either control siRNA or USP50 siRNA

first: Hannah

last: Mackay

first: Helen

middle: R

last: Stone

first: George

middle: E

last: Ronson

first: Katherine

last: Ellis

first: Alexander

last: Lanz

first: Yara

last: Aghabi

first: Alexandra

last: Walker

first: Katarzyna

last: Starowicz

last: Garvin

first: Patrick

last: van Eijk

first: Stefan

middle: A

last: Koestler

first: Elizabeth

last: Anthony

first: Ann Liza

last: Piberger

first: Anoop

middle: S

last: Chauhan

first: Poppy

last: Conway-Thomas

first: Alina

middle: V

last: Vaitsiankova

first: Sobana

last: Vijayendran

first: James

last: Beesley

first: Eva

last: Petermann

first: Eric

last: Brown

first: Ruth

middle: M

last: Densham

first: Simon

middle: H

last: Reed

first: Felix

last: Dobbs

first: Marco

last: Saponaro


title: Deficiency of Tlr7 and Irf7 increases the severity of COVID-19 through the reduced interferon production [scRNA-seq]

status: Public on Aug 20 2024

city: New Orleans

first: Jay

last: Kolls

state: LA

address: 1430 Tulane Ave

department: Medicine

institute: Tulane University

summary: Toll-like receptor 7 (Tlr7) deficiency-accelerated severe COVID-19 is associated with reduced production of interferons (IFNs). However, the underlying mechanisms remain elusive. Here, we demonstrate that the deficiency of Tlr7 and Irf7 globally and/or in immune cells in mice increases the severity of COVID-19 via impaired IFN activation in both immune and/or non-immune cells, leading to increased lung viral loads. These effects are associated with reduced IFN alpha and gamma production. The deficiency of Tlr7 in the infected mice tends to cause the reduced production and nuclear translocation of Interferon regulatory factor 7 (IRF7), indicative of reduced IRF7 activation. Despite higher amounts of lung viral antigen, Tlr7 or Irf7 deficiency resulted in substantially reduced production of antibodies against SARS-CoV-2, thereby delaying the viral clearance. These results highlight the importance of the activation of TLR7 and IRF7, leading to IFN production on the development of innate and adaptive immunity against COVID-19.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Irf7 KO mice at 2DPI and non infected B6 mice.

first: Chenxiao

last: Wang

first: Mst

middle: s

last: Khatun

first: Calder

last: Ellsworth

first: Zheng

last: Chen

first: Mohammad

last: Islamuddin

first: Ana

last: Karina

first: Nisperuza

last: Vidal

last: Alam

first: Shumei

last: Liu

first: Nicholas

middle: J

last: Maness

first: Robert

last: Blair

first: Xuebin

last: Qin


title: Single-cell analysis of oral mucosa immune cells in mouse models of periodontal disease

first: Ulka

last: Sachdev-Ost

address: 300 Halket Street Suite 5414

institute: University of Pittsburgh School of Medicine

summary: Periodontal health, disease, and reoslution are characterized by a diverse cellular immune response in the oral mucosa. We used scRNAseq to robustly characterize the imme cell repertoire and asosciated changes across changes of conditions of health and disease.

overall_design: Immune cells were isolated from the maxillary oral mucosa of mice via FACS according to the presence or absence of CD45 cell surface marker and analyzed via scRNAseq

first: Paul

last: Cantalupo

first: Vishal

last: Soman

first: Uma

last: Chandran

first: Daniel

last: Clark


title: Efficient Circularization of Protein-Encoding RNAs via a Novel Cis-Splicing System

city: Suzhou

first: shaojun

last: Qi

address: B8, Lane 21, Dong Yan Li Rd, Suzhou Industry Park,Suzhou ,Jiang Su, China

department: Department of mRNA Sciences

institute: Suzhou Abogen Biosciences Co., Ltd.

summary: Circular RNAs (circRNAs) have emerged as a promising alternative to linear mRNA, owing to their unique properties and potential therapeutic applications, driving the development of novel approaches for their production. This study introduces a cis-splicing system that efficiently produces circRNAs by incorporating a ribozyme core at one end of the precursor, thereby eliminating the need for additional spacer elements between the ribozyme and the gene of interest (GOI). In this cis-splicing system, sequences resembling homologous arms at both ends of the precursor are crucial for forming the P9.0 duplex, which in turn facilitates effective self-splicing and circularization. We demonstrate that the precise recognition of the second transesterification site depends more on the structural characteristics of P9.0 adjacent to the ωG position than on the nucleotide composition of the P9.0-ωG itself. Further optimization of structural elements, like P10 and P1-ex, significantly improves circularization efficiency. The circRNAs generated through the cissplicing system exhibit prolonged protein expression and minimal activation of the innate immune response. This study provides a comprehensive exploration of circRNA generation via a novel strategy and offers valuable insights into the structural engineering of RNA, paving the way for future advancements in circRNA-based applications.

overall_design: To assess the sequence integrity at the splicing sites following the two-step transesterification reactions of various precursors, we conducted RNA-Seq analysis on the circularized products. The differences among the precursors primarily stem from the designs of the recognition elements (Recognizers) at both ends, including Δspacers-ωG, Loop-ωG, Arm-Loop-ωG, Arm-ωG, and ωC. In the in vitro transcription reactions (IVT), the products resulting from the cotranscriptional circularization of all precursors were individually subjected to RNA-Seq analysis.

first: Shaojun

first: Huiming

last: Wang

first: Guopeng

first: Qianshan

first: Peng

last: Gao

first: Bo

last: Ying


title: Transcriptome analysis reveals miRNA expression profiles in hypothalamus tissues during the sexual development of Jining grey goats

city: Tai'an

first: Qing

last: Li

address: Tai’an, Shandong Province, P.R. China

institute: College of Animal Science and Veterinary Medicine

summary: In order to reveal the changes of microRNA spectrum in hypothalamus tissues of goats from birth to sexual maturity, smallRNA sequencing was performed on hypothalamus tissues of Jining grey goats at 4 developmental stages after birth. Twenty libraries from 4 different developmental stages (5 goats per stage) were successfully constructed and the corresponding miRNA expression profiles were obtained.

overall_design: To investigate the dynamics of hypothalamic microRNA expression profiles at four developmental stages after birth, we performed smallRNA sequencing using hypothalamic tissue from goats at four developmental stages with five biological replicates per developmental stage. Under the same breeding environment and management conditions, all goats have free access to food and water.

first: Tianle

last: Chao

first: Jianmin


title: The RNA binding protein HNRNPA2B1 regulates RNA abundance and motor protein activity in neurites

city: Aurora

first: Matthew

last: Taliaferro

state: CO

department: Biochemistry and Molecular Genetics

institute: University of Colorado Anschutz Medical Campus

summary: RNA molecules are localized to subcellular regions through interactions between localization-regulatory cis-elements and trans-acting RNA binding proteins (RBPs). However, the identities of RNAs whose localization is regulated by a specific RBP as well as the impacts of that RNA localization on cell function have generally remained unknown. Here, we demonstrate that the RBP HNRNPA2B1 acts to keep specific RNAs out of neuronal projections. Using subcellular fractionation, high-throughput sequencing, and single molecule RNA FISH, we find that hundreds of RNAs demonstrate markedly increased abundance in neurites in HNRNPA2B1 knockout cells. These RNAs often encode motor proteins and are enriched for known HNRNPA2B1 binding sites and motifs in their 3′ UTRs. The speed and processivity of microtubule-based transport is impaired in these cells, specifically in their neurites. HNRNPA2B1 point mutations that increase its cytoplasmic abundance relative to wildtype lead to stronger suppression of both RNA mislocalization and transport defects than seen with wildtype HNRNPA2B1. We further find that the subcellular localizations of HNRNPA2B1 target RNAs are sensitive to perturbations of RNA decay machinery, suggesting that it is HNRNPA2B1’s known role in regulating RNA stability that may explain these observations. These findings establish HNRNPA2B1 as a negative regulator of neurite RNA abundance and link the subcellular activities of motor proteins with the subcellular abundance of the RNAs that encode them.

overall_design: We profiled subcellular transcriptomes of neuronal cells with and without HNRNPA2B1.

first: Taliaferro

last: Matthew


title: Inducible keratinocyte-specific Mettl3-deficient mice develop spontaneous skin lesions

first: Lian

last: Cui

state: China

address: 1278 Baode Road

institute: Shanghai Skin Disease Hospital

summary: We conducted RNA sequencing analysis on skin tissues obtained from spontaneous inflammatory skin lesions in keratinocyte-specific Mettl3 knockout (K14CreERT2;Mettl3fl/fl) mice and their controls (Mettl3fl/fl). In brief, we observed spontaneous skin inflammation in the tail of K14CreERT2;Mettl3fl/fl mice 2-3 weeks following tamoxifen injection. The objective of this study was to investigate the impact and underlying mechanism of Mettl3 in epidermal keratinocytes regarding skin inflammation

overall_design: First, mice were injected with tamoxifen for five consecutive days to induce knockdown of mettl3 in epidermal keratinocytes. four weeks after the injection, skin samples were collected from the spontaneously inflamed areas of the tails of K14CreERT2;Mettl3fl/fl mice as well as from the normal tails of control mice (Mettl3fl/fl) and processed by liquid nitrogen milling, followed by RNA isolation.

first: Yuling

last: Shi

first: Chunyuan

last: Guo


title: N6-methyladenosine (m6A) modification in HEK (primary human epidermal keratinocytes)

type: Methylation profiling by high throughput sequencing

summary: We conducted an analysis of N6-methyladenosine (m6A) modifications in HEK (primary human epidermal keratinocytes). The primary aim of this investigation was to establish a molecular framework elucidating the role of m6A modifications in modulating the functional of keratinocytes.

overall_design: MeRIP-seq profiling of HEK (primary human epidermal keratinocytes) was isolated, with each experimental group consisting of two replicates.

first: You

last: Wu

first: Bingjie

first: Yawei


title: ZIC2 and ZIC3 promote SWI/SNF recruitment to safeguard progression towards human primed pluripotency

city: Montreal

first: William

middle: A.

last: Pastor

state: Quebec

address: 3655 Promenade Sir-William-Osler

department: Biochemistry

institute: McGill University

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

first: Ishtiaque

last: Hossain


title: N6-methyladenosine (m6A) modification in patients with psoriasis or atopic dermatitis [MeRIPseq_Human]

summary: We analyzed m6A modifications in skin lesions of patients with psoriasis or atopic dermatitis (AD). The results of this study will help to gain insight into the molecular basis of m6A modification in inflammatory skin diseases such as psoriasis or atopic dermatitis.

overall_design: Skin tissues were collected from 4 patients with psoriasis or 4 patients with atopic dermatitis (AD) and 4 healthy controls. RNA was then extracted for MeRIP-seq analysis.


title: CircPOLA2 sensitizes NSCLC cells to ferroptosis and suppresses tumorigenesis via the Merlin-YAP signaling pathway

city: Nanchang

first: Kaiying

last: Xu

state: Jiangxi

address: No. 17, Yongwai zheng Street

department: Department of Thoracic Surgery

institute: The First Affiliated Hospital of Nanchang University

summary: Circular RNAs (circRNAs) have been implicated in the tumorigenesis of non-small cell lung cancer (NSCLC). Ferroptosis is considered a mechanism to suppress tumorigenesis. Herein, we identified a novel downregulated circRNA, circPOLA2 (hsa_circ_0004291), in NSCLC tissues and found that it was correlated with advanced clinical stage in patients. Nuclear-cytoplasmic fractionation assays and FISH assays confirmed that circPOLA2 was predominantly localized in the cytoplasm. Overexpression of circPOLA2 promoted lipid peroxidation and ferroptosis in NSCLC cells, thereby inhibiting cell proliferation and migration, while knockdown of circPOLA2 exerted the opposite effects. Mechanistically, circPOLA2 interacted with Merlin, a critical regulator of the Hippo pathway, and restricted Merlin phosphorylation at S518, leading to the activation of the Hippo pathway. In addition, circPOLA2 enhanced ferroptosis in NSCLC cells by activating the Hippo pathway. Together, circPOLA2 sensitizes cells to ferroptosis and suppresses tumorigenesis in NSCLC by facilitating Merlin-mediated activation of the Hippo signaling pathway.

overall_design: To screen for circRNAs that contribute to the progression of NSCLC progression, 4 pairs of NSCLC (adenocarcinoma) and adjacent normal lung tissues were used for RNA-Seq analysis.

first: Feng

last: Yang

first: Jian

last: Tang


title: N6-methyladenosine (m6A) modification in HaCaT cells (immortalized human keratinocyte cell line) treated with STM2457 in the presence or absence of M5 (inflammatory factor cocktail) stimulation [MeRIPseq_KC]

summary: We conducted an analysis of N6-methyladenosine (m6A) modifications in HaCaT cells, an immortalized human keratinocyte cell line, following treatment with METTL3 inhibitor, STM2457, under conditions of either M5 (inflammatory factor cocktail) stimulation or its absence. The primary aim of this investigation was to establish a molecular framework elucidating the role of m6A modifications in modulating the functional dynamics of keratinocytes within an inflammatory milieu.

overall_design: HaCaT cells were subjected to a 24-hour treatment regimen with the METTL3 inhibitor STM2457, succeeded by a subsequent 24-hour exposure to either M5 or phosphate-buffered saline (PBS). Each experimental group comprised two replicates.


title: Mettl3 deficiency in epidermal keratinocytes exacerbates psoriasis-like inflammation [MeRIPseq_mice]

summary: We analyzed epidermal samples from keratinocyte-specific knockout Mettl3 (K14CreERT2;Mettl3fl/fl) mice and their controls (Mettl3fl/fl) in imiquimod-induced psoriasis-like skin lesions. Briefly, we established an imiquimod-induced psoriasis model in K14CreERT2;Mettl3fl/fl mice and their controls after tamoxifen injection, and epidermal samples were separated and collected from the skin lesions of the mice after 3 or 6 days of modeling (n=3 per group). The aim of this study was to investigate the mechanism by which Mettl3-mediated epidermal m6A methylation affects skin inflammation.

overall_design: At 7 weeks of age, 62.5 mg of IMQ Cream (5%) is applied topically to the shaved backs of mice daily for 3 or 6 days. Dorsal skin samples were excised from adult mice and treated with 3 mg/ml dispase II for 16 hours at 4 °C, and then the epidermis was separated from the dermis under a microscope.


title: The Role of the miR-30a-5p/BCL2L11 Pathway in Rosmarinic Acid-induced Apoptosis in MDA-MB-231 induced Breast Cancer Stem-like Cells

status: Public on Aug 19 2024

city: Fuzhou

first: Wei

address: 福州市闽侯荆溪关口366号

institute: Fujian medical university

summary:
Background: Rosmarinic acid (RA), a natural phenolic acid, exhibits promising anti-cancer properties. The abnormal expression of microRNA (miRNA) regulates the gene expression and plays a role as an oncogenic or tumor suppressor in TNBC. However, the biological role of RA in miR-30a-5p on BCL2L11 during MDA-MB-231 induced breast cancer stem-like cells (BCSCs) progression and its regulatory mechanism have not been elucidated.
Objective: To investigate whether RA inhibited the silencing effect of miR-30a-5p on the BCL2L11 gene and promoted apoptosis in BCSCs.
Materials and Methods: We assessed the migration, colony formation, proliferation, cell cycle, and apoptosis of BCSCs after RA treatment using the wound-healing assay, colony formation assay, CCK-8 assay, and flow cytometry, respectively. The expression of mRNA and protein levels of BCL-2, Bax, BCL2L11, and P53 genes in BCSCs after RA treatment was obtained by real-time polymerase chain reaction and Western blot. Differential miRNA expression in BCSCs was analyzed by high-throughput sequencing. Targetscan was utilized to predict the targets of miR-30a-5p. The dual luciferase reporter system was used for validation of the miR-30a-5p target.
Results: Wound-healing assay, colony formation assay, CCK-8 assay, and cell cycle assay results showed that RA inhibited migration, colony formation and viability of BCSCs, and cell cycle arrest in the G0-G1 phase. At the highest dose of RA, we noticed cell atrophy, while the arrest rate at 100 μg/mL RA surpassed that at 200 μg/mL RA. Apoptotic cells appeared early (Membrane Associated Protein V FITC+, PI-) or late (Membrane Associated Protein V FITC+, PI+) upon administration of 200 μg/mL RA, Using high-throughput sequencing to compare the differences in miRNA expression, we detected down-regulation of miR-30a-5p expression, and the results of dual luciferase reporter gene analysis indicated that BCL2L11 was a direct target of miR-30a-5p.
Conclusion: RA inhibited the silencing effect of miR-30a-5p on the BCL2L11 gene and enhanced apoptosis in BCSCs.
Keywords
Apoptosis; miR-30a-5p; BCSCs; Rosmarinic acid; Triple-negative breast cancer

first: Yuefen

last: Zhang

first: Xiaomin

last: Huang

first: Dan

first: Qi

last: Lin

first: Hailin

last: Zhuang

first: Hong


title: Genomic and Transcriptomic Analysis of Ninein Alternative Splicing Between C57BL/6J and DBA/2J Mice

city: Richmond

first: Michael

last: Miles

state: VA

department: Pharmacology and Toxicology

institute: Virginia Commonwealth Univ.

summary: Ethanol’s anxiolytic actions contribute to increased consumption and the development of Alcohol Use Disorder (AUD).  Our laboratory previously identified genetic loci contributing to the anxiolytic-like properties of ethanol in BXD recombinant inbred mice, derived from C57BL/6J (B6) and DBA/2J (D2) progenitor strains. That work identified Ninein (Nin) as a candidate gene underlying ethanol’s acute anxiolytic-like properties in BXD mice. Nin has a complex exonic content with known alternative splicing events that alter cellular distribution of the NIN protein. We hypothesize that strain-specific differences in Nin alternative splicing contribute to changes in Nin gene expression and B6/D2 strain differences in ethanol anxiolysis. Using quantitative reverse-transcriptase PCR to target Nin alternative splicing, we identified isoform-specific exon expression differences between B6 and D2 mice in prefrontal cortex, nucleus accumbens and amygdala. We extended this analysis using deep RNA sequencing in B6 and D2 nucleus accumbens samples and that Nin expression was significantly higher in D2 mice. Furthermore, exon utilization and alternative splicing analyses identified 8 differentially utilized exons and significant exon-skipping events between the strains, including 3 novel splicing events in the 3’ end of the Nin gene that were specific to the D2 strain. Our studies provide the first in-depth analysis of Nin alternative splicing in brain and identify a potential genetic mechanism altering Nin expression between B6 and D2 mice, thus contributing to differences in the anxiolytic-like properties of ethanol between these strains. This work contributes to our understanding of genetic differences modulating ethanol actions on anxiety that may contribute to the risk for alcohol use disorder.

overall_design: Ethanol Naive male C57BL/6J and DBA/2J mice were used to explore basal strain differences in Ninein Alternative Splicing. NAc tissue was harvested and gene expression assessed by Illumina NextSeq2000 RNAseq.

first: Emma

last: Gnatowski

first: Jessica

last: Jurmain

first: Mikhail

last: Dozmorov

first: Jennifer

middle: T

last: Wolstenholme


title: Differential compatibilities between rhizobium strains and cultivated and wild  soybeans revealed by anatomical and RNA-seq analyses.

city: Knoxville

first: Tarek

last: Hewezi

address: 2621 Morgan Circle

institute: University of Tennessee, Knoxvile

summary: Various species of rhizobium establish compatible symbiotic relationships with soybean (Glycine max) leading to the formation of nitrogen-fixing nodules in roots. The formation of functional nodules is mediated through complex developmental and transcriptional reprogramming that involves the activity of thousands of plant genes. However, host transcriptome responses that determine the outcome of the symbiotic interactions leading to the formation of functional or non-functional nodules remain unexplored. In this study, we investigated differential compatibilities between rhizobium strains (Bradyrhizobium diazoefficiens USDA 110Bradyrhizobium sp. strain LVM 105) and cultivated and wild soybeans. The nodulation assays revealed that both USDA 110 and LVM 105 strains effectively nodulate G. soja but only USDA 110 can form symbiotic relationships with Williams 82. RNA-seq data revealed that USDA 110 and LVM 105 induce distinct transcriptome programming in functional mature nodules formed on G. soja roots where genes involved in nucleosome assembly, DNA replication, regulation of cell cycle, and defense responses play key roles. Transcriptome comparison also suggested that activation of genes associated with cell wall biogenesis and organization and defense responses together with downregulation of genes involved in the biosynthesis of isoprenoids and antioxidant stress are associated with the formation of non-functional nodules on Williams 82 roots. Moreover, our analysis implies that increased activity of genes involved in oxygen binding, amino acid transport, and nitrate transport differentiates between fully-developed nodules in cultivated versus wild soybeans.

sample_organism:
Glycine max
Glycine soja

platform_organism:
Glycine max
Glycine soja

overall_design: In this study, we investigated transcriptome reprogramming in 25-day-old nodules induced by USDA 110 and LVM 105 in William 82 and G. soja(3 replicates per treatment) using RNA-seq and determined the biological processes and molecular functions controlling soybean response to nodulation by USDA 110 and LVM 105.

first: Hari

last: Krishnan

first: Sobhan

last: Bahrami Zadegan


title: Transcriptomic profile of ischemic and non-ischemic skeletal muscle tissue from peripheral artery disease patients

city: Sydney

first: Mary

last: Kavurma

state: New South Whales

address: 7 Eliza Street, Newtown

country: Australia

institute: Heart Research Insitute

summary: Peripheral artery disease (PAD) can cause limb pain and ulcers that won't heal. It is a leading cause of amputation, yet the moleculer mechanims that drive disease are poorly understood. To gain insights into mechanims of PAD at the transcriptome level, we performed sc-RNA-seq on non-ischemic and ischemic tissue from a male PAD patient who had undergone a below knee amputation.

overall_design: Skeletal muscle tissue was collected from the lower limb of a male patient with PAD who had undergone below knee limb amputation. Ischemic tissue was collected from the flexor hallucis longus and non-ischemic was collected from the tibialis anterior, close to the amputation site.

first: Elaina

last: Kelland

first: Joseph

last: Powell

first: Sian

middle: P

last: Cartland


title: Signature Analysis of High-Throughput Transcriptomics Screening Data for Mechanistic Inference and Chemical Grouping

city: RTP

first: Logan

last: Everett

state: North Carolina

address: 109 T.W. Alexander Dr

department: Office of Research and Development

institute: U.S. Environmental Protection Agency

summary: High-throughput transcriptomics (HTTr) uses gene expression profiling to characterize the biological activity of chemicals in in vitro cell-based test systems. As an extension of a previous study testing 44 chemicals, HTTr was used to screen an additional 1751 unique chemicals from the EPA’s ToxCast collection in MCF7 cells using eight concentrations and an exposure duration of 6 hours. We hypothesized that concentration-response modeling of signature scores could be used to identify putative molecular targets and cluster chemicals with similar bioactivity. Clustering and enrichment analyses were conducted based on signature catalog annotations and ToxPrint chemotypes to facilitate molecular target prediction and grouping of chemicals with similar bioactivity profiles. Enrichment analysis based on signature catalog annotation identified known mechanisms-of-action (MeOAs) associated with well-studied chemicals and generated putative MeOAs for other active chemicals. Chemicals with predicted MeOAs included those targeting estrogen receptor (ER), glucocorticoid receptor (GR), retinoic acid receptor (RAR), the NRF2/KEAP/ARE pathway, AP-1 activation and others. Using reference chemicals for ER modulation, the study demonstrated that HTTr in MCF7 cells was able to stratify chemicals in terms of agonist potency, distinguish ER agonists from antagonists, and cluster chemicals with similar activities as predicted by the ToxCast ER Pathway model. Uniform manifold approximation and projection (UMAP) embedding of signature-level results identified novel ER modulators with no ToxCast ER Pathway model predictions. Finally, UMAP combined with ToxPrint chemotype enrichment was used to explore the biological activity of structurally-related chemicals. The study demonstrates that HTTr can be used to inform chemical risk assessment by determining in vitro points-of-departure, predicting chemicals’ molecular mechanism(s)-of-action (MeOA) and grouping chemicals with similar bioactivity profiles.

overall_design: In a previous study, we established experimental and computational workflows for HTTr screening in a human cell model (Harrill et al., 2021). The TempO-Seq human whole transcriptome assay (Yeakley et al., 2017) was used to identify biological pathway altering concentrations (BPACs) and characterize the biological activity of test chemicals. The present study applies those methods to a much larger chemical space. Here, we screened 1751 unique chemicals from the ToxCast chemical collection in MCF7 cells using HTTr and the same experimental conditions as described previously (Harrill et al., 2021).

first: Joshua

last: Harrill

first: Derik

last: Haggard

first: Laura

last: Word

middle: L

last: Bundy

first: Bryant

last: Chambers

first: Felix

last: Harris

first: Clinton

last: Willis

first: Russell

last: Thomas

first: Imran

last: Shah

first: Richard

last: Judson


title: Metabolic pathways for lignin-related aromatic compounds elucidated in a Xanthomonas phytopathogen

city: Campinas

first: Joaquim

last: Martins Junior

state: SP

address: Rua Giuseppe Maximo Scolfaro 10000

department: Brazilian Biorenewables National Laboratory LNBR

country: Brazil

institute: Brazilian Center for Research in Energy and Materials CNPEM

summary: Convergent microbial biocatalysis has emerged as a promising approach for the conversion of lignin side-streams into value-added chemicals in recent decades. However, the current knowledge of metabolic pathways directing the bioconversion of lignin-related aromatics is still limited to a few microbial species and unavailable for some of these compounds. Thus, the aim of this study was to identify the genes involved in the bioconversion of aromatic compounds in Xanthomonas citri subsp. citri 306 (X. citri 306), a bacterium belonging to a compelling yet untapped genus for studies on lignin-related aromatics metabolism. For this purpose, we used an integrative approach including genome data mining, RNA-seq, enzymology and gene knockout studies. The RNA-seq analysis revealed a total of 278 to 1464 differentially expressed genes (DEGs) in the aromatic-containing conditions compared to the control XVM2m-glucose, evidencing the importance of these compounds in modulating various physiological processes of X. citri 306 beyond the pathways related to their metabolism. Moreover, this work revealed the operon molRKAB, which plays a role in the first catabolic steps of the three main monolignols (p-coumaryl, coniferyl and sinapyl alcohols), besides showing all the enzymatic steps funneling them up to the tricarboxylic acid cycle. Additionally, the study uncovered aryl aldehyde reductases and efflux strategies that likely function to protect the pathogen from aromatics toxicity. Together, these findings enhance the current understanding of Xanthomonas metabolism and transcriptional responses to lignin-related aromatic compounds, shedding light on the diverse metabolic pathways available to enable the engineering of microbial chassis dedicated to lignin valorization.

overall_design: To investigate the transcriptional profile of X. citri 306 in response to lignin-related compounds, samples of cells grown on XVM2m minimal medium supplemented with six lignin-related aromatic compounds, three complex mixtures of lignin-derived compounds, and glucose (reference) were collected in four biological replicates. Total RNA was extracted and used to generate RNA-Seq libraries. Differential expression analysis was carried out by pairwise comparisons between X. citri 306 grown in XVM2m supplemented with lignin-related aromatics and XVM2m(G) containing glucose (reference medium).

first: Damaris

middle: B

last: Martim

first: Douglas

last: Paixão

last: Junior

first: Gabriela

middle: F

last: Persinoti

first: Priscila

middle: O

last: Giuseppe


title: RNA-seq: Stress increases sperm respiration and motility in mice and men

first: Nickole

last: Moon

address: 12700 East 19th Avenue, RC2, Rm 9480

institute: University of Colorado

summary: Cumulative stress and adverse experiences precipitate changes in overall health, disrupting homeostasis and increasing disease. Stress is a known driver of allostatic changes, allowing for cellular adaptation in the face of environmental challenges. However, the molecular mechanisms regulating allostasis and long-term changes in intra- and intercellular signaling important for health are not clear. In males, chronic stress produces lasting changes in epididymal epithelial cell (EEC) intercellular signaling and extracellular vesicle (EV) composition important for sperm maturation. Here we used this system to assess the mechanisms regulating allostasis and the role of EVs to impact downstream target cell physiology and function. We found that prior corticosterone treatment decreased EEC energy requirements and altered mitochondrial ultrastructure, with changes in the cellular set point involving the mitochondrial complex I. CUT&RUN sequencing and gene co-expression network analysis separately identified significant epigenetic and transcriptomic reprogramming important for mitochondrial function. We found this new EEC allostatic state regulated EV intercellular communication with sperm, where EVs isolated from stress EECs increased sperm mitochondrial respiration, ultimately increasing sperm motility. These data support a signaling pathway by which a new cellular allostatic setpoint can be communicated to other cells, affecting their function.

overall_design: Immortalized mouse distal caput epididymal epithelial (DC2) cells at monolayer confluency, the media was replaced, and cells were either treated with 1:1000 vehicle (ethanol; resulting in 0.1% ethanol) or 1:1000 corticosterone in ethanol (Cayman Chemical, 16063; 1.4mM, resulting in 500 ng/ml of corticosterone). The media was replaced 72 hours (day 3) and 144 h (day 6) following the treatment. Cells were collected at media changes prior to treatment, immediately following treatment on day 3, after 3 days of recovery on day 6, or after 6 days of recovery on day 9. For cell collection, cells were trypsinized in 0.25% trypsin-EDTA (Gibco), centrifuged at 500xg for 3 min, and frozen at -80°C until further analysis.

first: Christopher

last: Morgan

first: Tracy

last: Bale


title: CUT&RUN-seq: Stress increases sperm respiration and motility in mice and men


title: Stress increases sperm respiration and motility in mice and men

overall_design: Refer to individual Series


title: miR-449a may prevent neurodegeneration in Alzheimer's Disease by repressing the  cell cycle machinery in neurons

city: Delhi

first: Chen

last: Chongtham

state: Delhi

address: Aruna Asaf Ali Road

country: India

institute: National Institute of Immunology

summary: Aberrant activation of cell cycle of terminally-differentiated neurons results in their apoptosis and is known to contribute to neuronal loss in various neurodegenerative disorders like Alzheimer's Disease. However, the mechanisms that regulate Cell Cycle Related Neuronal Apoptosis (CRNA) are poorly understood.  miRNA being one of the key components in gene regulation, the study was focused to identify the deregulated miRNA in neurodegeneration. Therefore, we utilized small RNA sequencing technology to compare the miRNA profile in cortical neurons from wild type and transgenic mouse model for AD (TgAD). In our quest to understand the regulation of the cell cycle related genes by miRNA, we identified the miRNA that are deregulated in neurons from TgAD mice. miRNA sequencing data revealed several deregulated miRNA that are known or were predicted to target cell cycle related genes.

overall_design: Comparison of the miRNA profile in WT and Transgenic mouse model of Alzheimer's disease.

first: Monika

last: Chauhan

first: Soumya

last: Kusumakshi

first: G

last: Arimbasseri

first: Pushkar

last: Sharma


title: Immunocompatible Elastomer with increased resistance to the foreign body response

status: Public on Aug 17 2024

city: Hangzhou

first: Xianchi

last: Zhou

address: Yuhangtang road

institute: Zhejiang University

summary: Polymeric elastomers are extensively employed to fabricate implants intended for prolonged implantation. However, implantation of the elastomers can induce strong immune rejection reaction known as foreign body response (FBR), resulting in the rejection of foreign implants and thereby diminishing their in vivo efficacy. Herein, we present a group of immunocompatible elastomers, termed easy-to-synthesize vinyl-based anti-FBR dense elastomers (EVADE), synthesized via a straightforward and scalable method. In contrast to the pronounced immune reaction triggered by the commonly used implantable elastomers, EVADE materials effectively suppress the inflammation and long-term capsule formation in subcutaneous models of rodents and non-human primates for at least one year and two months, respectively. Implantation of EVADE materials significantly reduces the expression of inflammation-related proteins S100A8/A9 in adjacent tissues compared to polydimethylsiloxane (PDMS). We also show that inhibition or knockout of S100A8/A9 leads to substantial attenuation of fibrosis in mice, suggesting a target for fibrosis inhibition. Continuous subcutaneous insulin infusion (CSII) catheters constructed from EVADE elastomers demonstrate significantly improved longevity and performance compared to commercial catheters. The EVADE materials reported here may enhance and extend function in various medical devices by resisting local immune responses to implanted biomaterials.

overall_design: For procedures in mice, the EVADE materials (H50, H70, and H90) and PDMS sheets were cut into discs with a biophysical punch (4 mm in diameter). Elastomers samples were sterilized with 75% ethanol, washed with normal saline, and implanted subcutaneously in C57BL/6 female mice. The implantation procedure was as follows. In brief, mice were anesthetized with 3% isoflurane in oxygen, shaved, and disinfected the skin with iodine. An 8 mm longitudinal incision was made on the dorsal surface using surgical scissors to access the subcutaneous space. Then subcutaneous pockets about 0.5 cm away from the incision were created with blunt forceps to implant the elastomer discs. After implantation, the incisions were closed using 5-0 taper-tipped PGA absorbable sutures. Mice were monitored until recovery from anesthesia and raised for 1 day, 2 weeks, 4 weeks, 3 months, 6 months, or longer, respectively. The mice grew normally without discomfort after the implantation, and no body weight loss was observed during the entire experiment.


title: Identification of novel embryonic differentiation stage by combined cell tracking and high dimensional protein imaging

city: Basel

first: Markus

last: Auler

address: Schanzenstrasse 44

department: Department of Biosystems Science and Engineering ETH

institute: ETH Zürich

summary: Pluripotent mouse embryonic stem cells (ESCs) can differentiate to all germ layers and serve as an in vitro model of embryonic development. To better understand the differentiation paths traversed by ESCs committing to different lineages, we tracked individual differentiating ESCs by timelapse imaging followed by multiplexed high-dimensional Imaging Mass Cytometry (IMC) protein quantification. This links continuous live single-cell molecular NANOG and cellular dynamics quantification over 5-6 generations to protein expression of 37 different molecular regulators in the same single cells at the observation endpoints. Using this unique data set including kinship history and live lineage marker detection, we show that NANOG downregulation occurs generations prior to, but is not sufficient for neuroectoderm lineage commitment. Unexpectedly, we could identify a novel developmental cell type co-expressing both the canonical Sox1 neuroectoderm and FoxA2 endoderm markers in vitro and confirm the presence of such a population in the post-implantation embryo as well. RNASeq revealed cells co-expressing SOX1 and FOXA2 to have a unique cells state characterised by expression of both endoderm as well as neuroectoderm genes with lineage potential towards both germ layers.

overall_design: To better characterize the Sox1 and FoxA2 co-expressing cells (markers of neuroectoderm and endoderm respectively) discovered from proteomincs experiments as well as the lineage portential of their progeny, we generated a double reporter mouse embryonic stem cells line Sox1-EGFP/FoxA2mCherry. These cells underwent Retinoic Acid (RA) differentiation for 2-,4- or 6 days, were FACS sorted based on reporter expression into populations of interest and underwent bulk RNASeq. In addition, Sox1-FoxA2+, Sox1+FoxA2- and Sox1+FoxA2+ cells were isolated by FACS sorting after 2 days of RA diffentiation, replated and allowed to grow for an additional 2- or 4- days in RA medium prior to RNA extraction. These samples are marked with 'Progeny' in the sample name

first: Geethika

last: Arekatla

first: Timm

last: Schroeder


title: Improving blood vessel function in peripheral artery disease: endothelial-derived TRAIL generates stable microvessels in ischemia via TRAIL-R2

first: Mary

last: Kavurma

summary: Ischemia reduction in peripheral artery disease (PAD) through angiogenesis requires endothelial cell (EC) and pericyte interactions to form stable microvascular networks, but processes mediating this are disrupted in PAD. Patients with cardiovascular disease have suppressed levels of tumour necrosis factor-related apoptosis-inducing ligand (TRAIL). The contribution of endothelial cell (EC)-derived TRAIL to generating stable blood vessel networks and the impact of its receptors in PAD is unknown.We used scRNA-seq to identify molecular determinants that are altered in ischemic tissues of EC-specifc TRAIL KO mice vs littremate control mice, specifically looking at EC-pericyte interactions.

overall_design: Gastrocnemius muscle were collected from corneol and ishemic limbs, digested, crupreserved, and then subjected to scRNA-seq for analysis

first: Elaina

last: Kelland

first: Sian

last: Cartland

first: Malathi

middle: I

last: Dona

first: Alex

last: Pinto


title: Enhancer-promoter hubs organize transcriptional networks promoting oncogenesis and drug resistance

status: Public on Aug 16 2024

city: Philadelphia

first: Robert

middle: Babak

last: Faryabi

state: Pennsylvania

address: Room 553 BRB II/III, 421 Curie Boulevard

department: Pathology

institute: University of Pennsylvania


title: Enhancer-promoter hubs organize transcriptional networks promoting oncogenesis and drug resistance (RNA-Seq)

summary: Recent advances in high-resolution mapping of spatial interactions among regulatory elements support the existence of complex topological assemblies of enhancers and promoters known as enhancer-promoter hubs or cliques. Yet, organization principles of these multi-interacting enhancer-promoter hubs and their potential role in regulating gene expression in cancer remains unclear. Here, we systematically identified enhancer-promoter hubs in breast cancer, lymphoma, and leukemia. We found that highly interacting enhancer-promoter hubs form at key oncogenes and lineage-associated transcription factors potentially promoting oncogenesis of these diverse cancer types. Genomic and optical mapping of interactions among enhancer and promoter elements further showed that topological alterations in hubs coincide with transcriptional changes underlying acquired resistance to targeted therapy in T cell leukemia and B cell lymphoma. Together, our findings suggest that enhancer-promoter hubs are dynamic and heterogeneous topological assemblies with the potential to control gene expression circuits promoting oncogenesis and drug resistance.

overall_design: Strand-specific RNA-seq was performed in triplicates in parental and ibrutinib-resistant REC-1 cells.

first: Jelena

last: Petrovic

first: Yeqiao


title: Assessing a single-cell multi-omic analytic platform to characterize ex vivo-engineered T cell therapy products

city: South San Francisco

first: Dayue

last: Chen

state: California

address: 1 DNA Way

institute: Genentech

summary: Genetically engineered CD8+ T cells are being explored for the treatment of various cancers. Analytical characterization represents a major challenge in the development of genetically engineered cell therapies, especially assessing the potential off-target editing and product heterogeneity. As conventional sequencing techniques only provide information at the bulk level, they are unable to detect off-target CRISPR translocation or editing events occurring in minor cell subpopulations. Here we report the analytical development of a single-cell multi-omic DNA and Protein assay to characterize genetically engineered cell products for safety and genotoxicity assessment. We were able to quantify on-target edits, off-target events, and potential translocations at the targeting loci with per-cell granularity, providing important characterization data of the final cell product.  Conclusion: Single cell multi-omics approach provides the resolution required to understand the composition of cellular products and identify critical quality attributes (CQAs).

overall_design: Single-cell, amplicon-based DNA and protein sequencing were performed on edited T cells from four different donors (edited CGT products) upon simultaneous knocking out of the three loci: TRAC, TRBC1 and TRBC2.

first: Maryam

last: Moshref

first: Jerry

last: Lo

first: Andrew

last: McKay

first: Julien

last: Camperi

first: Joseph

last: Schroer

first: Norikiyo

last: Ueno

first: Shu

last: Wang

first: Saurabh

last: Gulati

first: Somayeh

last: Tarighat

first: Steffen

last: Durinck

first: Ho-Young

last: Lee


title: Enhancer-promoter hubs organize transcriptional networks promoting oncogenesis and drug resistance (ATAC-Seq)

overall_design: ATAC-seq was performed to assess chroamtin accessibility in DMSO-treated parental and ibrutinib-resistant REC-1 cells in triplicates.

last: Zhou


title: Enhancer-promoter hubs organize transcriptional networks promoting oncogenesis and drug resistance (ChIP-Seq)

overall_design: ChIP-seq was performed to access H3K27ac in DMSO-treated parental and ibrutinib-resistant REC-1 cells in duplicates.


title: Gene expression signature in ablated IL-38 PyMT tumors dependent on 𝛾𝛿 T cells

city: Frankfurt

first: Andreas

last: Weigert

address: Theodor-Sern-Kai 7

institute: Goethe-University

summary: We studied the impact of IL-38 neutralization on tumor immune control in PyMT mammary carcinoma mouse model via γδ T cells. To that end, whole transcriptome profile of PyMT tumors upon in vivo IL-38 neutralization and γδ-TCR blockage were generate via next generation mRNA sequencing on a NextSeq 2000 sequencer.

overall_design: Total RNA was isolated from polyoma middle T oncogene (PyMT)-induced tumors from WT mice treated in vivo with either anti-IL-38 antibodies (n=6) or IgG isotype control (n=5). For the γδ-TCR blockage, WT mice were treated in vivo with IgG isotype control (n=4) and IL-38 KO treated with either anti-γδ-TCR antibodies (n=4) or IgG isotype control (n=4).

first: Priscila

last: da Silva


title: Inducible mucosa-like differentiation of head and neck cancer cells drives the epigenetically determined loss of cell malignancy

status: Public on Aug 15 2024

city: Bielefeld

first: Ingo

last: Todt

address: Morgenbreede 1

department: Ear, nose and throat medicine

institute: University of Bielefeld

summary: Human papillomavirus-negative head and neck squamous cell carcinoma (HNSCC) is a highly malignant disease with high death rates that have remained substantially unaltered for decades. Therefore, new treatment approaches are urgently needed. Human papillomavirus-negative tumors harbor areas of terminally differentiated tissue that are characterized by cornification. Dissecting this intrinsic ability of HNSCC cells to irreversibly differentiate into non-malignant cells may have striking tumor-targeting potential.

overall_design: Primary head and neck squamous cell carcinoma cell cultures were established in a serum-free medium to investigate the differentiation potential of HNSCC. The cells were differentiated with a serum medium and cultured for 8 days until full differentiation was achieved. Both cultures under the control condition (PNEU) and the differentiation condition (CFM) have been analyzed using ATAC-seq.

first: Sarah

last: Gendreizig

first: Felix

last: Oppel


title: Rnf20 levels modulate the VEGF-Notch signaling circuits during sprouting angiogenesis

status: Public on Aug 18 2024

city: Mannheim

first: Gergana

last: Dobreva

state: Baden Württemberg

address: Ludolf-Krehl-Str. 7-11

department: Cardiovascular Genomics and Epigenomics

institute: Medical Faculty Mannheim/University of Heidelberg

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

first: Julio

middle: D

last: Cordero Henriquez

first: Nalan

last: Tetik-Elsherbiny


title: Mettl1-dependent m7G tRNA modification is essential for maintaining fertility and proper spermatogenesis in Drosophila melanogaster

city: Wako city

first: Shintaro

last: Iwasaki

address: 2-1, Hirosawa

department: CPR

institute: RIKEN

summary: N7-methylguanosine (m7G) in variable loop region of tRNA stabilizes target tRNA expression, which is catalyzed by METTL1/WDR4 heterodimer. Here, we unveil essential functions of Mettl1 in Drosophila fertility. Mettl1-knockout (Mettl1-KO) decreases elongated spermatid and mature sperm, which is fully rescued by Mettl1-transgene expression, but not catalytic dead Mettl1-transgene, demonstrating that Mettl1-dependent m7G is required for spermatogenesis. Mettl1-KO shows loss of m7G modification on subset of tRNAs and decreased level of tRNA expression. Strikingly, overexpression of translational elongation factor EF1α that can compete with rapid tRNA decay (RTD) pathway in S. cerevisiae, significantly counteract the sterility in Mettl1-KO male, supporting a critical role of m7G tRNA modification in spermatogenesis. Ribo-seq analysis shows that Mettl1-KO elevates ribosome collisions at codons decoded by reduced tRNAs and significantly reduces translation of genes involved in elongated spermatid formation and sperm stability.  These findings reveal a developmental role for m7G tRNA modifications and suggest that m7G modification-dependent tRNA stability differs among tissues.

overall_design: Ribosome profiling and RNA-Seq of testis of fly

first: Shunya

last: Kaneko

first: Keita

last: Miyoshi

first: Kotaro

last: Tomuro

first: Makoto

last: Terauchi

first: Ryoya

last: Tanaka

last: Kondo

first: Naoki

last: Tani

first: Kei-Ichiro

last: Ishiguro

first: Atsushi

last: Toyoda

first: Azusa

last: Kamikouchi

first: Hideki

last: Noguchi

first: Kuniaki

last: Saito


title: Control of epigenomic landscape and development of fetal male germ cells through L-serine metabolism

city: Sendai

first: Yohei

last: Hayashi

state: Miyagi

address: 4-1 Seiryo-machi, Aobaku

department: Institute of Development, Aging and Cancer

institute: Tohoku University

summary: Sex-specific metabolic characteristics emerge in the mouse germline after reaching the genital ridges around embryonic day 10.5, coinciding with the initiation of sexual differentiation. However, the impact of such metabolic characteristics on the development of male and female germ cells remains unclear. In this study, we observed the specific upregulation in male fetal germ cells of D-3-phosphoglycerate dehydrogenase (PHGDH), the primary enzyme in the serine-glycine–one-carbon (SGOC) metabolic pathway. A concurrent increase was observed in a downstream metabolite, S-adenosylmethionine (SAM), a crucial substrate for protein and nucleic acid methylation. Inhibiting PHGDH in fetal testes resulted in reduced SAM levels in germ cells, accompanied by increases in the number of germ cells and the undifferentiated spermatogonia ratio. Furthermore, PHGDH inhibition led to a decrease in the methylation of histone H3 and DNA, resulting in aberrations in gene expression profiles. In summary, our findings underscore the significant role of certain metabolic mechanisms in the development of male germ cells.

overall_design: To ivestigate the role of serine metabolic pathways in male germ cell differentiation, we  prepared male germ cells sorted from cultured fetal testes with the addition of DMSO (control) or CBR-5884 (a inhibitor of serine metabolism). We then performed RNA-seq analysis of 2 different conditions with 2 biological replicates.


title: Gene expression profile at single cell level of human nasal primary airway cells from DNAH5 subjects

city: St Louis

first: Amjad

last: Horani

address: 660S Euclid Ave

institute: Washington University

summary: DNAH5 is an cilia dynein motor . We used single cell RNA sequencing (scRNA-seq) to analyze the changes in cells types and gene expression profile of subjects with variants in DNAH5  compared to healthy individuals

overall_design: Nasal cells were isolated and diffrentiated using Air-liquid phase conditions, and analyzed using scRNAseq.


title: Enhancer-promoter hubs organize transcriptional networks promoting oncogenesis and drug resistance (HiC)

first: Robert

last: Faryabi

overall_design: Hi-C was performed to assess genome folding in DMSO-treated parental and ibrutinib-resistant REC-1 cells.

first: Jelena

last: Petrovic

first: Yeqiao

last: Zhou


title: Mapping origins of variation in neural trajectories of human pluripotent stem cells [RNA-seq BRNiPSC246]

city: Baltimore

first: Carlo

last: Colantuoni

state: MD

address: 733 N Broadway

department: Neurology

institute: Johns Hopkins Univ. School of Medicine

summary: Variability between human pluripotent stem cell (hPSC) lines remains a challenge and opportunity in biomedicine.  We identify differences in the spontaneous self-organization of individual hPSC lines during self-renewal that lie along a fundamental axis of in vivo development.  Distinct stable and dynamic transcriptional elements were revealed by decomposition of RNA-seq data in pluripotency and early lineage emergence.  Stable differences within pluripotency predicted regional bias in the dynamics of neural differentiation that were also observed in large collections of hPSC lines.  Using replicate human induced PSC (hiPSC) lines and paired adult tissue, we demonstrate that cells from individual humans expressed unique transcriptional signatures that were maintained throughout life.  In addition, replicate hiPSC lines from one donor showed divergent expression phenotypes driven by distinct chromatin states.  These stable transcriptional states are under both genetic and epigenetic control and predict bias in subsequent forebrain and hindbrain neural trajectories. These results define mechanisms controlling transcription in pluripotency to first establish human neural diversity.

overall_design: Of the 3 series in this super series, this covers RNAseq of 2 replicate hiPSC lines from each of 3 new donors (2053, 2063, 2075) at 2, 4, and 6 days of self-renewal and early lineage differentiation (used in Figure 5).

first: S

middle: K

last: Kim

first: A

last: Jaishankar

first: G

last: Stein-O’Brien

first: K

last: Ogawa

first: N

last: Micali

first: Y

last: Wang

first: T

last: Hyde

first: J

middle: E

last: Kleinman

last: Voss

first: E

last: Fertig

last: Shin

last: Cross

last: Brandon

first: D

middle: R

last: Weinberger

middle: G

last: Chenoweth

last: Hoeppner

last: Seo

last: Sestan

first: C

first: R

last: McKay


title: Mapping origins of variation in neural trajectories of human pluripotent stem cells [SOX21 KO RNA-seq]

last: Colantuoni

overall_design: Of the 3 series in this super series, this covers RNAseq of WT and SOX21 KO lines derived from hESC line SA01 in self-renewal and early lineage differentiation (used in Figure 3).

last: Kim

last: Jaishankar

last: Stein-O’Brien

middle: M

middle: H


title: Mapping origins of variation in neural trajectories of human pluripotent stem cells [RNA-seq]

overall_design: Of the 3 series in this super series, this covers RNAseq data from the 3 hESC lines (SA01, UC06, H9)and 3 hiPSC lines (i07, i13, i04) at 2, 4, and 6 days of self-renewal and early lineage differentiation (used in Figures 1 & 2).

last: Ogawa

last: Micali

last: Wang

last: Hyde

middle: J


title: 3D chromatin architecture of drug-tolerant cancer cells at single-cell resolution (scDNA-seq dataset)

status: Public on Aug 14 2024

city: San Antonio

first: Yufan

last: Zhou

state: TX

address: 7703 Floyd Curl Dr

institute: UT health Science Center at San Antonio

summary: Anticancer drug therapy generally elicits the drug tolerance after long-term treatment. Recent studies suggested that 3D chromatin structures of cancer cells were intimately linked to drug resistance. However, 3D chromatin structures in drug-tolerant cancer cells at single-cell resolution haven’t been elucidated. Here we performed single-cell Hi-C (scHi-C) analysis to examine the 3D chromatin structures in three stages of breast cancer cells. Then Single-cell RNA-seq data were integrated with scHi-C data. scDNA-seq data were also been generated.

overall_design: To fully understand the 3D chromatin structures of drug-tolerant cancer cells at single-cell resolution, we designed scHi-C approach for analyzing a breast cancer cell model system, MCF7, MCF7M1 and MCF7TR cells. A total of 293 cells (89 MCF7 cells, 91 MCF7M1 cells, 113 MCF7TR cells) were used for scHi-C profiling and 22,425 cells (6,172 MCF7 cells, 10,156 MCF7M1 cells, 6,097 MCF7TR cells) were used for single-cell RNA-seq (scRNA-seq) profiling . Total of 105 cells (33 of MCF7 cells, 33 of MCF7M1 and 39 of MCFTR cells) were used for single-cell DNA-seq (scDNA-seq) profiling This is the dataset stored for scDNA-seq data.


title: 3D chromatin architecture of drug-tolerant cancer cells at single-cell resolution (scRNA-seq dataset)

summary: Anticancer drug therapy generally elicits the drug tolerance after long-term treatment. Recent studies suggested that 3D chromatin structures of cancer cells were intimately linked to drug resistance. However, 3D chromatin structures in drug-tolerant cancer cells at single-cell resolution haven’t been elucidated. Here we performed single-cell Hi-C (scHi-C) analysis to examine the 3D chromatin structures in three stages of breast cancer cells. Then Single-cell RNA-seq data were integrated with scHi-C data.

overall_design: To fully understand the 3D chromatin structures of drug-tolerant cancer cells at single-cell resolution, we designed scHi-C approach for analyzing a breast cancer cell model system, MCF7, MCF7M1 and MCF7TR cells. A total of 293 cells (89 MCF7 cells, 91 MCF7M1 cells, 113 MCF7TR cells) were used for scHi-C profiling and 22,425 cells (6,172 MCF7 cells, 10,156 MCF7M1 cells, 6,097 MCF7TR cells) were used for single-cell RNA-seq (scRNA-seq) profiling . This is the dataset stored for scRNA-seq data.

first: Victor

last: Jin


title: Mesenchymal Osr1+ cells regulate embryonic lymphatic vessel formation

city: Berlin

first: Pedro

last: Vallecillo García

state: Berlin

address: Augustenburger Platz 1

department: Hematology and Oncology

institute: Charité Berlin

summary: The lymphatic system is formed during embryonic development by the commitment of specialized lymphatic endothelial cells (LECs) and their subsequent assembly in primary lymphatic vessels. While lymphatic cells are in continuous contact with mesenchymal cells during development and in adult tissues, the role of mesenchymal cells in lymphatic vasculature development remains poorly characterized. Here, we show that a subpopulation of mesenchymal cells expressing the transcription factor Osr1 are in close association with migrating LECs and established lymphatic vessels in mice. Lineage tracing experiments revealed that Osr1+ cells precede LEC arrival during lymphatic vasculature assembly in the back of the embryo. Using Osr1-deficient embryos and functional in vitro assays, we show that Osr1 acts in a non-cell autonomous manner controlling proliferation and early migration of LECs to peripheral tissues. Thereby, mesenchymal Osr1+ cells control in a bimodal manner the production of extracellular matrix scaffold components and signal ligands critical for lymphatic vessel formation.

overall_design: To assess LEC defects in E13.5 Osr1-deficient embryos, we first isolated E13.5 LECs (PDPN+ PECAM1+) cells via fluorescence activated cell sorting (FACS).  Next, we performed transcriptome analysis of E13.5 LECs from Osr1controls and Osr1GCE/GCE embryos.

last: Vallecillo-García

first: Mickael

last: Orgeur

first: Bernd

last: Timmermann

first: Sigmar

last: Stricker


title: Mapping origins of variation in neural trajectories of human pluripotent stem cells

first: Carlo

overall_design: Refer to individual Series


title: Effects of azithromycin on blood inflammatory gene expression and cytokine production in sarcoidosis

city: Cottingham

first: Simon

last: Hart

state: East Yorkshire

address: Castle Hill Hospital

department: Respiratory Research Group

institute: Hull York Medical School/ University of Hull

summary: The effects of azithromycin on whole blood gene expression using the nCounter XT human autoimmune profiling panel was assessed in 8 sarcoidosis patients before and after 1 month of azithromycin treatment.

overall_design: Blood samples (1ml) from patients with pulmonary sarcoidosis at baseline (visit 1) and after 1 month's treatment with azithromycin 250mg daily (visit 2) were drawn into tubes (TruCulture®, Myriad-RBM) containing 100 ng/ml LPS or null control (no stimulant). After stimulation for 24h at 37°C, samples were separated into supernatants (aliquoted and stored at -70°C for later cytokine analysis) and cell pellets (mixed with 3ml RNAlater® (Ambion) and stored at -70°C).


title: 3D chromatin architecture of drug-tolerant cancer cells at single-cell resolution