title: Identifying super-enhancer-derived signatures with prognostic value through selective inhibitors (Microarray gene expression data)

city: Guangzhou

first: Jiajun

last: Zhang

address: #58，Zhongshan 2nd Road

institute: the First Affiliated Hospital of Sun Yat-Sen University

summary:
CDK12 and CDK13 promote transcription elongation within the gene body and regulate the processivity of RNAPII. THZ531 inhibits the enzymatic activity of CDK12 and 13 through covalent binding.
Gene expression profiling was performed to investigate the THZ531-induced transcription effect, and search the subset of sensitive genes in osteosarcoma cell lines, U2-OS and SJSA-1.

overall_design: Total RNA was extracted from U2-OS or SJSA-1 cells treated with DMSO (control), 50, 200, and 800 nM THZ531 for 6 hours, respectively, using TRIzol reagent.An Affymetrix GeneChip® PrimeView™ Human Gene Expression Array was used for the microarray analysis. The hybridization data were analyzed using Affymetrix GeneChip Command Console Software.

first: Guanyu

last: Huang

first: Xuelin

first: Yu

last: Xu

first: Shuo

last: Chen

first: Qinghua

last: Cao

first: Weihai

last: Liu

first: Yiwei

last: Fu

first: Qiang

last: Jia

first: Jingnan

last: Shen

first: Junqiang

last: Yin


title: Adipokine chemerin impairs the receptive and metabolic functions of endometrial epithelial cells revealed by transcriptomic analysis

status: Public on Jan 31 2024

city: Shenzhen

first: Ming

last: yu

address: 1068 Xueyuan Avenue, Shenzhen University Town

country: China

institute: Chinese Academy of Sciences

type: Expression profiling by high throughput sequencing

summary: Endometrium, the lining of the uterus, changes dynamically in response to fluctuations in ovarian hormones. The proper endocrine environment regulates endometrial functions: menstruation and supporting pregnancy. Obesity is closely related to endometrial dysfunction, which seriously affects women's health and fertility, but the pathological mechanism is unknown. Chemerin is an adipokine involved in multiple biological events such as immunity and metabolism by acting on its functional receptors. This study aimed to characterize the effects of chemerin on human endometrial epithelial cells by RNA-Seq.

overall_design: We used RNA-Seq (RNA-sequencing) to compare transcriptome levels in 12Z cells without or treated with recombinant human (rh)-chemerin. Six samples were included: NC-1, NC-2, NC-3, rhChemerin-1, rhChemerin-2, and rhChemerin-3.

last: Yu

first: Yichun

last: Wang

first: Jian

middle: V


title: PFA ependymoma primary and recurring tumors show differences in cellularity, DNA methylation and relevant copy number variations.

city: Hamburg

first: Swenja

last: Gödicke

address: Martinistrasse 52

country: Germany

institute: Research Institute Children‘s Cancer Center Hamburg

summary: Posterior fossa type A (PF-EPN-A, PFA) ependymoma are aggressive tumors that mainly affect children and have a poor prognosis. Histopathology shows significant intratumoral heterogeneity, ranging from loose tissue to often sharply demarcated, extremely cell dense tumor areas. To determine molecular differences in morphologically different areas and to understand their clinical significance, we analyzed 113 PF-EPN-A samples, including 40 corresponding relapse samples. Relapsing tumors displayed a higher proportion of cell dense areas (p=0.036), a change in PF-EPN-A methylation subtypes (13/32 patients), and novel chromosome 1q gains and 6q losses (12/32 cases) compared to corresponding primary tumors.

overall_design: Six pairs of posterior fossa type A ependymoma (PF-EPN-A) primary tumors and their respective first relapse were analysed, one sample per primary and relapse each.  In the original study, the six cases were analysed together with additional primary relapse pairs from the CNS tumor reference cohort established by Capper et al. in 2018 [PMID: 29539639, GEO accession GSE109381] and Wenger et al. 2022 [PMID: 35842717, GEO accession GSE247880].

first: Ulrich

last: Schüller


title: High and low cell density areas in posterior fossa ependymoma type A have a distinct transcriptome

summary: Posterior fossa type A (PF-EPN-A, PFA) ependymoma are aggressive tumors that mainly affect children and have a poor prognosis. Histopathology shows significant intratumoral heterogeneity, ranging from loose tissue to often sharply demarcated, extremely cell dense tumor areas. Spatial transcriptomics of six cases allow for a comparison of the transcriptome of high and low cell density areas.

overall_design: Spatial transcriptomic analysis of six PFA ependymomas with clearly demarcated high and low cell density regions using the NanoString GeoMx Digital Spatial Profiler. Three regions of interest (ROI) per cell density category were analysed for each case.


title: CIC-DUX4 chromatin profiling reveals new epigenetic dependencies and actionable therpaeutic targets in CIC-rearranged sarcomas [ChIP-seq]

city: Lausanne

first: Nicolo

last: Riggi

state: VD

address: Bugnon 25

department: Département de Pathologie Expérimentale

country: Switzerland

institute: CHUV

type: Genome binding/occupancy profiling by high throughput sequencing

summary: CIC-DUX4-rearranged sarcoma (CDS) is a rare and aggressive soft tissue tumor that occurs most frequently in young adults. The key oncogenic driver of this disease is the expression of the CIC-DUX4 fusion protein as a result of chromosomal rearrangements. CIC-DUX4 displays chromatin binding properties, and is therefore believed to function as an aberrant transcription factor. However, the chromatin remodeling events induced by CIC-DUX4 are not well understood, limiting our ability to identify new mechanism-based therapeutic strategies for these patients. Here we generated a genome wide profile of CIC-DUX4 DNA occupancy and associated chromatin states in human CDS cell models and primary tumors. Combining chromatin profiling, proximity ligation assays, as well as genetic and pharmacological perturbations, we show that CIC-DUX4 operates as a potent transcriptional activator at its binding sites.  This property is in contrast with the repressive function of the wild type CIC protein, and is mainly mediated through the direct interaction of CIC-DUX4 with the acetyltransferase p300. In keeping with this, we show p300 to be essential for CDS tumor cell proliferation, and its pharmacological inhibition to significantly impact tumor growth in vitro andin vivo. Taken together, our study elucidates the mechanisms underpinning CIC-DUX4-mediated transcriptional regulation and suggests a potential therapeutic approach for the clinical management of CDS patients.

overall_design:
Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for histone variants H3K27ac, H3K4me3, H3K4me1, for DUX4 transcription factor and p300 Co-factor in CDS1, CDS2 cell lines and in CIC2, CIC3 and CIC4 primary tumors

***************************************************************
The raw fastq data for the 12 Hs primary tumor samples have been deposited at https://zenodo.org/records/10141898
***************************************************************

first: Arnaud

last: Bakaric

first: Viviane

last: Praz

first: Sanalkumar

last: Rajendran


title: Transcriptional Consequences of Trisomy 21 on Neural Induction

city: Madison

first: Anita

last: Bhattacharyya

state: Wisconsin

address: 1500 Highland Ave

department: Waisman Center

country: USA

institute: University of Wisconsin - Madison

summary: Down syndrome, caused by trisomy 21, is a complex developmental disorder associated with intellectual disability and reduced growth of multiple organs. Structural pathologies are present at birth, reflecting embryonic origins. A fundamental unanswered question is how an extra copy of human chromosome 21 contributes to organ-specific pathologies that characterize individuals with Down syndrome. Relevant to the hallmark intellectual disability in Down syndrome, how does trisomy 21 affect neural development? We tested the hypothesis that trisomy 21 exerts effects on human neural development as early as neural induction. Bulk RNA sequencing was performed on isogenic trisomy 21 and euploid human induced pluripotent stem cells (iPSCs) at successive stages of neural induction: embryoid bodies at Day 6, early neuroectoderm at Day 10, and differentiated neuroectoderm at Day 17. Gene expression analysis revealed over 1,300 differentially expressed genes in trisomy 21 cells along the differentiation pathway compared to euploid controls. Less than 5% of the gene expression changes included upregulated chromosome 21 encoded genes at every timepoint. Genes involved in specific growth factor signaling pathways (Wnt and Notch), metabolism (including interferon response and oxidative stress), and extracellular matrix were altered in trisomy 21 cells. Further analysis revealed heterochronic expression of genes. This comprehensive analysis reveals that trisomy 21 impacts discrete developmental pathways at the earliest stages of neural development. Further, the results suggest that metabolic dysfunction arises early in embryogenesis in trisomy 21 and may thus affect development and function more broadly.

overall_design: Stranded bulk RNAseq was performed on three replicates of  isogenic (Trisomy21 or control)  iPSC-derived embryoid bodies at day6, three replicates of early neuroectoderm at day 10, and  three replicates of  differentiated neuroectoderm at day 17.

first: Jose

middle: L

last: Martinez

first: Jennifer

middle: G

last: Piciw

first: Madeline

last: Crockett

first: Isabella

middle: A

last: Sorci

first: Nikunj

last: Makwana

first: Carissa

last: Sirois

first: Yathindar

last: Giffin-Rao


title: Genome-wide binding profile of Halo-tagged cohesin

status: Public on Feb 01 2024

city: Berkeley

first: Robert

last: Tjian

state: CA

address: University of California, Berkeley 450 Li Ka Shing #3370

department: MCB

institute: UC Berkeley

summary: We determined the genome-wide binding profile of CTCF and cohesin subunits Smc1a and Smc3 in wild type mouse ES cells and compared them to a double FLAG-Halo-mCTCF/mRad21-SNAPf-V5 knock-in mES line, generated by CRISPR/Cas9-mediated genome editing to perform imaging experiments.

overall_design: ChIP-Seq of CTCF, Smc1a and Smc3 cohesin subunits in wild type mouse ES cells (WT) and in mouse ES cells homozygous for FLAG-Halo-CTCF and Rad21-SNAPf-V5 (C59 clone). ChIP-Seq libraries were prepared using normal serum IgGs as a control, and including total inputs as reference datasets.

first: Anders

last: Sejr Hansen

first: Claudia

last: Cattoglio

first: Xavier

last: Darzacq


title: Single-cell landscape of the cellular microenvironment in three different colonic polyp subtypes in children

city: Beijing

first: Yongjie

last: Liu

address: No. 1 West Beichen Road, Chaoyang District

institute: Institute of Genetics and Developmental Biology

summary: scRNA-seq was applied to map the cellular landscape of colonic polyps from pediatric patients with SJP, JPS or PJS and aged-matched colonic tissues to help dissect polyp heterogeneity among different polyp subtypes and identify the underlying cellular and molecular events that may control disease outcome

overall_design:
we performed scRNA-seq of dissociated fresh polyp tissues from 18 patients who underwent colonoscopy or radical surgeries and 2 normal colon tissues

***************************************************************
Submitter states that raw dada files were not provided due to ethical restrictions.
***************************************************************

first: Youcai

last: Deng

first: Yafei


title: Clinically relevant molecular hallmarks of PFA ependymomas display intratumoral heterogeneity and correlate with tumor morphology.

first: Swenja

last: Gödicke

type:
Methylation profiling by array
Other

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

overall_design: Refer to individual Series


title: Transcriptomic profile of multiple sclerosis patients treated with fingolimod

city: Madrid

first: Alicia

last: Sanchez

address: Joaquín Rodrigo, 2 Majadahonda

country: Spain

institute: Instituto de Investigación Sanitaria Puerta de Hierro-Segovia de Arana

summary: Fingolimod is an immunomodulatory sphingosine-1-phosphate (S1P) analogue approved for the treatment of relapsing-remitting multiple sclerosis (RRMS). The identification of biomarkers of clinical response to fingolimod is a major necessity in MS to identify optimal responders and avoid the risk of disease progression in non-responders. With this aim, we used RNA-sequencing to study the transcriptomic changes induced by fingolimod in peripheral blood mononuclear cells of MS-treated patients and their association with clinical response. Samples were obtained from 10 RRMS patients (5 responders and 5 non-responders) at baseline and at 12 months of fingolimod therapy. Fingolimod exerted a vast impact at the transcriptional level, identifying 7155 differentially expressed genes (DEGs) compared to baseline that affected the regulation of numerous signalling pathways and cellular processes. These DEGs were predominantly immune-related, including genes associated with S1P metabolism, cytokines, lymphocyte trafficking, master transcription factors of lymphocyte functions and the NF-kB pathway. Responder and non-responder patients exhibited a differential transcriptomic regulation during fingolimod treatment, with responders presenting a higher number of DEGs (6405) compared to non-responders (2653). These transcriptomic differences offer the potential of being exploited as biomarkers of clinical response to fingolimod.

overall_design: We extracted peripheral blood mononuclear cells from 10 multiple sclerosis patients immediately before starting treatment with fingolimod (basal) and at 12 months (12m) of therapy with fingolimod. Patients were classified according to their clinical response to fingolimod into responders or non-responders using the NEDA-3 status at 2 years of fingolimod therapy.

last: Sánchez-Sanz

first: Antonio

last: García-Merino

middle: J

last: Sánchez-López

first: Rafael

last: Muñoz-Viana


title: CIC-DUX4 chromatin profiling reveals new epigenetic dependencies and actionable therpaeutic targets in CIC-rearranged sarcomas [RNA-seq]

first: Nicolo

last: Riggi

overall_design:
To investigate the function of CIC-DUX4 fusion protein in CDS cells we knocked down CIC-DUX4 by two shRNAs in CDS1 cell line and performed RNA-seq
To assess the effect of p300 inhibition in CDS cells, CDS2 cells were treated either with a control or with a p300 degrader and RNA-seq data from those two conditions was used for comparison

first: Arnaud

last: Bakaric

first: Viviane

last: Praz

first: Sanalkumar

last: Rajendran

first: Luisa

last: Cironi


title: CIC-DUX4 chromatin profiling reveals new epigenetic dependencies and actionable therpaeutic targets in CIC-rearranged sarcomas


title: Effect of R22W mutation in TFRC gene on gene expression in PBMCs

city: Adelaide

first: Nick

last: Warnock

state: South Australia

address: UniSA Bradley Building, North Terrace

department: Centre for Cancer Biology

country: Australia

institute: SA Pathology

summary: TFRC, also known as CD71, regulates the uptake of transferrin-bound iron into cells through receptor-mediated endocytosis. In a patient with a combined immunodeficiency, we identified a homozygous missense mutation in TFRC gene leading to R22W amino acid change in the cytoplasmic tail of the receptor. This mutation impairs the endocytosis of TFRC, which results in profound aberrations in the immune system.

overall_design: To investigate the impact of R22W mutation in TFRC, we performed RNA-sequencing on PBMCs from the patient as well as 3 age-matched healthy controls.

first: Nicholas

middle: I

first: Damon

last: Tumes

first: Gokhan

last: Cildir

first: Baran

last: Erman


title: Single nucleus RNA sequencing reveals heterogeneity among multiple white adipose tissue depots

city: Changsha

first: Limin

last: Xie

state: Hunan

address: No.139，Renmin Road Central Changsha, Hunan, China

institute: The second xiangya hospital of central south university

summary: Regardless of its anatomical site, adipose tissue shares a common energy-storage role but exhibits distinctive properties.   Exploring the cellular and molecular heterogeneity of white adipose tissue (WAT) is crucial for comprehending its function and properties.   In this study, we employed Single nucleus RNA sequencing (snRNA-seq) to test five representative depots including inguinal, epididymal, mesenteric, perirenal, and pericardial adipose tissues in mice under physiological conditions.   By analyzing the contents of main cell categories and gene profiles of various depots, we identified their distinctive physiological properties.

overall_design: To construct the atlas of cell types in different adipose tissue depots, we performed snRNAseq of epididymal white adipose tissue (EWAT), subcutaneous white adipose tissue (SWAT), mesenteric white adipose tissue (MWAT), perirenal white adipose tissue (NWAT) and peri-heart white adipose tissue (HWAT) pooled from mice fed chow diet for analysis.

first: Tuo

first: Wanyu

last: Hu

first: Haowei

last: Zhang


title: Maternal Western Diet Programs Cardiometabolic Dysfunction and Hypothalamic Inflammation via Epigenetic Mechanisms Predominantly in the Male Offspring [Methyl-seq]

city: New Orleans

first: Mona

last: Elgazzaz

state: LA

address: 533 Bolivar Street

department: Cardiovascular Center

institute: LSUHSC

type: Methylation profiling by high throughput sequencing

summary: Maternal exposure during pregnancy is a strong determinant of offspring health outcomes. Such exposures induce changes in the offspring epigenome resulting in gene expression and functional changes. In this study, we investigated the effect of maternal Western hypercaloric diet (HCD) programming during the perinatal period and its effect on neuronal plasticity and cardiometabolic health in adult offspring. C57BL/6J dams were fed HCD for 1 month prior to mating with regular diet (RD) sires and kept on the same diet throughout pregnancy and lactation. At weaning, offspring were maintained on either HCD or RD for 3 months duration. Maternal programming resulted in male-specific hypertension and hyperglycemia, with both males and females showing increased sympathetic tone to the vasculature. Surprisingly, programmed male offspring fed on HCD exhibited lower glucose levels, less insulin resistance, and leptin levels compared to non-programmed HCD-fed male mice. Hypothalamic genes involved in glial and astrocytic differentiation were differentially methylated in programmed male offspring. Genes involved in inflammation and type 2 diabetes were targeted by differentially expressed miRNA in programmed male offspring. Methyl-seq data were supported by our findings of astrogliosis and microgliosis as well as increased microglial activation in programmed males in the paraventricular nucleus (PVN). Aligned with programming-induced protective effect in HCD male mice, we observed lower protein levels of hypothalamic TGFβ2, NF-κB2, NF-κBp65, Ser-pIRS1, and GLP1R compared to non-programmed HCD-fed male mice. In conclusion, our study shows that maternal HCD programs neuronal plasticity in the offspring and results in male-specific hypertension and hyperglycemia. On the other hand, we observed a compensatory role of programming potentially by priming metabolic pathways to handle excess nutrients in a more efficient way.

overall_design: These are methyl-seq data driven from the hypothalamus of programmed mice with perinatal hypercaloric diet and non-programmed mice with either postnatal HCD or regular diet. First part of the name refers to maternal diet and the second part refers to offspring diet.


title: Acute gastrointestinal permeability after traumatic brain injury in mice precedes a bloom in Akkermansia muciniphila supported by intestinal hypoxia

city: Cincinnati

first: Anthony

middle: Joseph

last: DeSana

state: Ohio

address: 231 Albert Sabin Way

department: Neurosurgery

institute: University of Cincinnati

summary: Traumatic brain injury (TBI) initiates not only complex neurovascular and glial changes within the brain but also pathophysiological responses that extend beyond the central nervous system. The peripheral response to TBI has become an intensive area of research, as these systemic perturbations can induce dysfunction in multiple organ systems. As there are no approved therapeutics for TBI, it is imperative that we investigate the peripheral response to TBI to identify targets for future intervention. Of particular interest is the gastrointestinal (GI) system. Even in the absence of polytrauma, brain-injured individuals are at increased risk of suffering from GI-related morbidity and mortality. Symptoms such as intestinal dysmotility, inflammation, ulceration, and fecal incontinence can drastically diminish quality of life. The GI tract is inhabited by trillions of microbes that have been implicated as modulators of many neurological disorders. Clinical and preclinical studies implicate gut dysbiosis, a pathological imbalance in the normally symbiotic microbiota, as both a consequence of TBI as well as a contributing factor to brain damage. However, our understanding of this interplay is still limited. While relatively little is known about the effects of TBI on the structure and function of the GI tract, prior studies report that experimental TBI induces intestinal barrier dysfunction and morphological changes. To confirm these findings in the current model of TBI, male C57BL/6J mice underwent a sham control or a controlled cortical impact (CCI) procedure to induce a contusive brain injury, and intestinal permeability was assessed at 4 h, 8 h, 1 d, and 3 d post-injury. An acute, transient increase in permeability was observed at 4 h after CCI. Histological analyses of the ileum and colon at multiple time points from 4 h to 4 wks revealed no overt morphological changes, suggesting that CCI induced a short-lived physiologic dysfunction without major structural alterations to the GI tract. As the microbiome is a modulator of GI physiology, we performed 16s gene sequencing on fecal samples collected prior to and over the first month after CCI or sham injury. Microbial community diversity was assessed using common metrics of alpha and beta diversity. Alpha diversity was lower in the CCI injury group and beta diversity differed among groups, although these effects were not observed in all metrics. Subsequent differential abundance analysis revealed that the phylum Verrucamicrobiota was increased in CCI mice at 1, 2, and 3 d post-injury when compared to sham mice. Subsequent qPCR identified the Verrucamicrobiota species as Akkermansia Muciniphila, an obligate anaerobe that resides in and helps regulate the intestinal mucus layer and barrier. To determine whether TBI promotes changes to the GI tract favorable for the proliferation of A. muciniphila, mucus-producing goblet cells and the level of GI hypoxia were evaluated. Goblet cell density in the medial colon was significantly increased at 1 d, while colon hypoxia was significantly increased at 3 d. Taken together, these studies show that CCI induces transient intestinal barrier dysfunction followed by increased goblet cell density and hypoxia in the colon with a concomitant increase in A. muciniphila that may suggest a compensatory response to systemic stress after TBI.

overall_design:
To investigate the effect of traumatic brain injury (TBI) on the gut microbiome we utilized a controlled cortical impact (CCI) model of TBI in male C57bl/6j mice with the control group being considered a sham mouse. Sham mice received all parts of the CCI procedure except for the impact to exposed dura (nSHAM = 6, nCCI =7).To establish a timecourse of microbiome changes, fecal samples were collected prior to injury (00d below) and at 1 day (01d), 2 days (02d), 3 days (03d), 1 week (07d), 2 weeks (14d), and 4 weeks (28d) after sham or CCI procedure. Fecal samples were flash frozen and stored at -80C until DNA extraction (QIAamp PowerFecal Pro DNA kit)
Sequencing of the 16s rRNA gene was conducted by the University of Kentucky Genomics Core using the Illumina MiSeq platform. Sequencing libraries were prepared as per Illumina documentation for the V3-V4 region using the suggested primers (Fwd: 5' TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGCCTACGGGNGGCWGCAG; Rev: 5' GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGGACTACHVGGGTA TCTAATCC), quantified, and normalized prior to sequencing
Resultant paired end reads were joined, processed, and analyzed within R using dada2 and phyloseq (based on the workflow published by Callahan, Sankaran, Fukuyama, McMurdie and Holmes; 2017) to obtain an OTU table, Taxonomy table (SILVA 138), and phylogenetic tree within a phyloseq object. Two samples were excluded for low sequencing depth: the 03d and 14d samples from Sham4.  Diversity metrics were then generated for various alpha and beta diverisity metrics. Due to large variation in read depth, sequences were rarefied for alpha diversity metrics only.
To assess differential abundance, we chose to compare injury groups at matched timepoints. ANCOM-BC was run to generate differential abundance comparisons between sham and CCI mice at each timepoint for the phylum, class, order, and family level (results are found in supplementary file).

first: Steven

last: Estus

first: Terrence

last: Barrett

first: Kathryn

middle: E

last: Saatman


title: Clinically relevant molecular hallmarks of PFA ependymomas display intratumoral heterogeneity and correlate with tumor morphology

first: Swenja

last: Gödicke

summary: Posterior fossa type A (PF-EPN-A, PFA) ependymoma are aggressive tumors that mainly affect children and have a poor prognosis. Histopathology shows significant intratumoral heterogeneity, ranging from loose tissue to often sharply demarcated, extremely cell dense tumor areas. To determine molecular differences between these morphologically different areas and to understand their clinical significance, we analyzed 113 PF-EPN-A samples, including 40 corresponding relapse samples. Inter alia, DNA methylation profiles were analysed for high and low cell density regions seperately in 21 cases.  Tumor areas with low and high cell density showed diverging DNA methylation profiles regarding their similarity to distinct previously discovered PF-EPN-A subtypes in 9/21 cases. Prognostically relevant chromosomal changes at 1q and 6q showed spatial heterogeneity within single tumors.

overall_design: Of 21 heterogenous PFA ependymoma, DNA methylation profiles from high and low cell density areas as well as overall DNA methylation profiles from routine diagnostics were obtained and analysed.

first: Ulrich

last: Schüller


title: Down-regulation of N4-acetylcytidine modification in myeloid cells attenuates immunotherapy and exacerbates hepatocellular carcinoma progression

city: Hang Zhou

last: Xu

address: Huansha Roud

institute: Zhejiang University

summary: To resolve the patterns of TILs in HCC, we performed scRNA-seq on the TILs isolated from the three groups (P: control group, T: immunotherapy group, TR: immunotherapy plus REM group; n=2 per group) at two time points (1 w and 2 w)

overall_design: Comparative gene expression profiling analysis of single-cell RNA-seq data for  the TILs isolated from tumor of mice hepatocellular carcinoma orthotopic transplantation model.


title: Maternal Western Diet Programs Cardiometabolic Dysfunction and Hypothalamic Inflammation via Epigenetic Mechanisms Predominantly in the Male Offspring

type: Non-coding RNA profiling by high throughput sequencing


title: Role of FGF23 and DMP1 in osteoblastogenesis

city: Chicago

first: Valentin

last: David

state: Illinois

address: 320 E Superior Street

department: Medicine

institute: Northwestern University


title: Role of FGF23 and DMP1 in osteoblastogenesis in cultured BMSCs at single cell level

summary: Primary bone marrow cells from murine long bones were cultured in osteoblastic medium for 21 days. scRNAseq and differential expression analyzes were used to highlight the importance of FGF23 and DMP1 in osteoblastogenesis

overall_design: mRNA profiles of differentiated Bone marrow stromal cells (BMSCs) from wild-type (WT) mice,  mice with an osteocyte-specific deletion of Fgf23,  harboring a floxed first exon of the Fgf23 gene and expressing a transgene containing a Cre recombinase sequence downstream of the Dmp1 promoter (Fgf23cKO), Dmp1 global knockout mice (Dmp1KO) and compound  Dmp1KO/Fgf23cKO mice.

first: Aline

last: Martin

first: Jane

last: Thomas


title: Effect of Sirt6 knockout on gene expression in P7 neural stem cells

first: Yufei

last: Wei

address: 5 Dong Dan San Tiao

institute: Peking Union Medical College

summary: As a member of class III histone deacetylases, Sirt6 has various functions including regulation of genomic stability, DNA repair, cancer, metabolism and ageing.Deficiency of Sirt6 is lethal and causes brain development redardation. We generated Emx1-cre induced Sirt6 conditional knockout mice model and found that Sirt6 deficiency promoted self-renew of neural precursor cells (NPCs) and inhibited differentiation. This result promotes understanding of the role of Sirt6 in brain development and NPCs’ fate determination and provides clues to explain the generality and difference between species.

overall_design: To investigate the influence of Sirt6 on neural stem cells, we isolated neural progenitor cells from WT and Sirt6 cKO P7 mice and cultured in DMEM/F12 proliferation medium.For neurosphere RNA-seq, RNA was isolated from the 7th day culturing NPCs according to the manufacturer’s instructions. RNA-seq was performed by Annoroad, China. Data analysis was performed by Active Motif and Novogene.

first: Xinhuan

last: Wang

first: Wei

last: Liu


title: Single cell transcriptomic representation of social dominance in prefrontal cortex and the influence of preweaning maternal and postweaning social environment

city: New York

first: Miklos

last: Toth

state: NY

address: 1300 York Ave

institute: Weill Cornell Medicine

summary: Social dominance encompasses winning dyadic contests and gaining priority access to resources and reproduction. Disposition to dominance is influenced by environmental factors, particularly during early postnatal life and adolescence. A disinhibitory mPFC microcircuit has been implicated in the expression of dominance in the “tube test” paradigm of social competition in mice, but the neuronal and transcriptional plasticity associated with the environment induced increase in social dominance is not known. We previously reported that male pups raised by physically active (as opposed to sedentary) dams exhibit dominance and increased reproductive fitness, and here we show that social isolation from weaning also increases dominance. By using these preweaning and postweaning environmental models, we tested if dominance is associated with transcriptional plasticity and a specific transcriptional profile in one or more cell types in the mPFC. Given that the mPFC is composed of several cell types, we used single cell transcriptomics to characterize the influence of the preweaning maternal and postweaning social environment on cell-type specific gene expression. The preweaning maternal effect, but not postweaning social isolation, caused gene expression changes in a wide range of cell types including pyramidal neurons, various interneurons, and astrocytes. However, both the maternal effect and social isolation induced the coordinated downregulation of synaptic channel, receptor, and adhesion genes in parvalbumin positive (PV) interneurons. This suggests an impaired PV interneuron-mediated inhibition of pyramidal cells in animals predisposed to dominance, a notion consistent with dominant behavior being driven by the disinhibition of mPFC pyramidal neurons.

overall_design: PL of mPFC was dissected at P21 from C57BL/6 mice. Cohort 1 has 2 groups (GH Run, GH Sed). Cohort 2 has 4 groups (GH Run, GH Sed, SI Run, SI Sed)

first: Katherine

last: Lopez

first: Madelyn

last: Baker


title: CK1α suppresses autoimmunity by restraining the cGAS-STING signaling

city: Shanghai

first: Haiyang

last: Hu

address: 320 Yueyang Road

institute: PICB

summary: Stimulator of interferon genes (STING), the central hub protein of the cGAS-STING signaling, is essential for type I IFN production of innate immunity. However, prolonged or excessive activation of STING is highly related to autoimmune diseases, most of which exhibit the hallmark of elevated expression of type I interferons and IFN-stimulated genes (ISGs). Thus, the activity of STING must be stringently controlled to maintain immune homeostasis. Here, we reported that CK1α, a protein serine/threonine kinase, was essential to prevent the over-activation of STING-mediated type I IFN signaling through autophagic degradation of STING. Mechanistically, CK1α interacted with STING upon the cGAS-STING pathway activation and promoted STING autophagic degradation by enhancing the phosphorylation of p62 at serine 349, which was critical for p62 mediated STING autophagic degradation. Consistently, SSTC3, a selective CK1α agonist, significantly attenuated the response of the cGAS-STING signaling by promoting STING autophagic degradation. Importantly, pharmaceutical activation of CK1α using SSTC3 markedly repressed the systemic autoinflammatory responses in the Trex1-/- mouse autoimmune disease model and effectively suppressed the production of IFNs and ISGs in the PBMCs of SLE patients. Taken together, our study reveals a novel regulatory role of CK1α in the autophagic degradation of STING to maintain immune homeostasis. Manipulating CK1α through SSTC3 might be a potential therapeutic strategy for alleviating STING-mediated aberrant type I IFNs in autoimmune diseases.

overall_design: Total RNA was isolated and sequenced by deep sequencing using Illumina HiSeq 2500

first: Mingyu

last: Pan

first: Jing

last: Sun

first: Chen


title: Obesity and sex hormones interact to promote CSF hyperdynamics in an obese rodent model of idiopathic intracranial hypertension

city: Copenhagen

first: Søren

middle: Norge

last: Andreassen

state: Region Hovedstaden

address: Blegdamsvej 3

department: Department of Neuroscience

country: Denmark

institute: University of Copenhagen

summary: Idiopathic intracranial hypertension (IIH) is a syndrome exhibiting elevated intracranial pressure (ICP), visual disturbances, and severe headache. IIH primarily affects young obese women, though it can occur in individuals of any age, BMI, and sex. IIH is characterized by systemic metabolic dysregulation with a profile of increased androgen hormones. However, the contributions of obesity/hormonal perturbations to cerebrospinal fluid (CSF) dynamics remains unresolved. We employed obese female Zucker rats and adjuvant testosterone to reveal IIH causal drivers. ICP and CSF dynamics were determined with in vivo experimentation and magnetic resonance imaging, testosterone levels assessed with mass spectrometry, and choroid plexus function revealed with transcriptomics. Obese rats had undisturbed CSF testosterone levels and no changes in ICP or CSF dynamics. Chronic adjuvant testosterone treatment of obese rats elevated the CSF secretion rate, although with no effect on the ICP, due to the elevated CSF drainage capacity of these rats. Obesity in itself therefore does not suffice to recapitulate the IIH symptoms, but modulation of CSF dynamics comes about with adjuvant testosterone treatment, mimicking the androgen excess observed in female IIH patients. Obesity-induced androgen dysregulation may thus play a crucial role in the disease mechanism of IIH.

overall_design: Differential expression analysis of female lean and obese Zucker rats, treated with vehicle (VEH) or testosterone (TT)

middle: N

first: Jonathan

middle: H

last: Wardman

first: Mette

last: Jensen

first: Nanna

last: MacAulay


title: Genome-wide survey by ChIP-seq reveals CREB1 regulation of lncRNAs in gastric cancer.

city: Jinan

first: Peng

last: Gao

address: Wen Hua Xi Road 44

institute: Shandong University

summary: cAMP responsive element binding protein 1 (CREB1) is a transcription factor belonging to the basic leucine zipper (bZIP) family. Previous studies on the transcriptional regulatory targets of CREB1 have focused on protein-coding genes. The non-coding targets regulated by CREB1 in gastric cancer remain to be further studied. Herein, the genome-wide mapping of CREB1 binding in gastric cancer cell AGS was determined by chromatin immunoprecipitation sequencing.

overall_design: AGS cell lysates were sonicated and immunoprecipitated with anti-CREB1 antibody (Cell Signaling, MA, USA, Cat# 9197, rabbit monoclonal). ChIP-sequencing analysis was performed on two samples: AGS-IP and AGS-Input.

first: Ya-Wen


title: Targeted proteomics analysis of Cutaneous Lupus Erythematosus patient interstitial skin fluid and plasma

city: North Grafton

first: Jillian

middle: M

last: Richmond

state: Massachusetts

address: 200 Westboro Road

department: Comparative Pathobiology

institute: Tufts Cummings School of Veterinary Medicine


title: Targeted proteomics analysis of Cutaneous Lupus Erythematosus patient interstitial skin fluid and plasma (Inflammation panel data)

summary: We performed a targeted proteomics analysis of Cutaneous Lupus Erythematosus (CLE) patient blister biopsies and plasma using Olink Proteomics panels to validate the blister biopsy technique using previously identified biomarkers, to confirm protein-level expression of biomarkers previously identified at the RNA level, and to identify new biomarkers of disease.

overall_design: Protein biomarkers in lesional and nonlesional interstitial skin fluid and blood plasma from 4 CLE patients and 3 healthy controls were measured using the Olink Proteomics Target 96 Inflammation panel v.3022.

first: Mehdi

last: Rashighi


title: Targeted proteomics analysis of Cutaneous Lupus Erythematosus patient interstitial skin fluid and plasma (Neuro Exploratory panel data)

overall_design: Protein biomarkers in lesional and nonlesional interstitial skin fluid and blood plasma from 4 CLE patients and 3 healthy controls were measured using the Olink Proteomics Target 96 Neuro Exploratory panel v.3911.


title: Hypoxia-driven deSUMOylation of EXOSC10 promotes adaptive changes in the transcriptome profile

status: Public on Jan 30 2024

city: Göttingen

last: Bohnsack

address: Humboldtallee 23

institute: University Medical Centre Göttingen

summary:
Reduced oxygen availability (hypoxia) triggers adaptive cellular responses via hypoxia-inducible factor (HIF)-dependent transcriptional activation. Adaptation to hypoxia also involves transcription-independent processes like post-translational modifications, however these mechanisms are poorly characterized. Investigating the involvement of protein SUMOylation in response to hypoxia, we discovered that hypoxia strongly decreases the SUMOylation of Exosome subunit 10 (EXOSC10), the catalytic subunit of the RNA exosome, in a HIF-independent manner. EXOSC10 is a multifunctional exoribonuclease enriched in the nucleolus that mediates the processing and degradation of various RNA species. We demonstrate that the Ubiquitin-specific protease 36 (USP36) SUMOylates EXOSC10 and we reveal SUMO1/sentrin-specific peptidase 3 (SENP3) as the enzyme mediating deSUMOylation of EXOSC10. Under hypoxia, EXOSC10 dissociates from USP36 and translocates from the nucleolus to the nucleoplasm concomitant with its deSUMOylation.
Loss of EXOSC10 SUMOylation does not detectably affect rRNA maturation but affects the mRNA transcriptome by modulating the expression levels of hypoxia-related genes. Our data suggest that dynamic modulation of EXOSC10 SUMOylation and localization under hypoxia regulates the RNA degradation machinery to facilitate cellular adaptation to low oxygen conditions.

overall_design: RNA-seq analysis was performed for HeLa cells grown in normoxia and hypoxia. RNA-seq was also performed on HeLa cells deleted of endogenous EXOSC10 and expressing Flag-tagged wild-type EXOSC10 or EXOSC10 K583R.

first: Chrysa

last: Filippopoulou

first: Chairini

middle: C

last: Thome

first: Sofia

last: Perdikari

first: Evgenia

last: Ntini

first: George

last: Simos

first: Georgia

last: Chachami


title: METTL16, eIF3a and eIF3b binding transcripts in HepG2 liver cancer cells [RIP-seq]

city: Duarte

first: Rui

last: Su

address: 1500 E Duarte Rd

institute: City of Hope

summary:
To investigate the specific binding transcripts of METTL16, eIF3a and eIF3b in liver cancer cells, we established HepG2 cell lines following METTL16, eIF3a and eIF3b overexpression.
We then performed RNA Immunoprecipitation (RIP) in HepG2 cells, and both the input and immunoprecipitated RNA were used for sequencing.

overall_design: Comparative binding transcripts of METTL16, eIF3a and eIF3b in HepG2 cells.

first: Meilin

last: Xue

first: Lei

last: Dong

first: Yangchan

last: Li

first: Hao

last: Chen

first: Jianjun


title: Effect of depletion of METTL16 on gene expression of Huh7 liver cancer cells [RNA-seq]

summary:
To investigate the mechanism of METTL16 in the regulation of tranlation and HCC development, we established Huh7 cell lines following METTL16 knockout (KO) by CRISPER-Cas9 system.
We then performed gene expression profiling analysis using data obtained from RNA-seq of Huh7 cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Huh7 cells and its KO derivatives (sgNS verse sgMETTL16).


title: Farm Animal Exposure, Respiratory Illnesses, and Nasal Cell Gene Expression

status: Public on Jan 29 2024

city: Madison

first: James

last: Gern

state: WI

address: K4/918 CSC, 600 Highland Ave

department: Pediatrics

institute: University of Wisconsin-Madison

summary: Background: Farm exposures in early life reduce the risks for childhood allergic diseases and asthma. There is less information about how farm exposures relate to respiratory illnesses and mucosal immune development.  Objective: We hypothesized that children raised in farm environments have a lower incidence of viral illnesses over the first two years of life than non-farm children. We also analyzed between farm exposures or respiratory illnesses were related to patterns of nasal cell gene expression.  Methods: The Wisconsin Infant Study Cohort (WISC) birth cohort enrolled farm and non-farm pregnant women from central Wisconsin. Parents reported prenatal farm and other environmental exposures. Illness frequency and severity were assessed using illness diaries and periodic surveys. Nasopharyngeal cell gene expression at age two years was compared to farm exposure and respiratory illness history.  Results: There was a higher rate of respiratory illnesses in the non-farm vs. farm group (rate ratio 0.82 [0.69,0.97], p=0.020), but no significant differences in wheezing illnesses. There was a stepwise reduction in rates of respiratory illnesses in children exposed at least weekly to 0, 1, or ≥2 animals (p=0.006). In analyzing nasal cell gene expression, farm exposures and preceding respiratory illnesses were positively related to gene signatures for mononuclear cells and innate and antimicrobial responses.   Conclusions: Children exposed to farms and farm animals had lower rates of respiratory illnesses over the first two years of life. Both farm exposures and preceding respiratory illnesses were associated with increased innate immune responses, suggesting that these exposures stimulate mucosal immune responses to reduce subsequent illness frequency.

overall_design: Assessment of nasopharyngeal gene expression in two-year-old children in a prospective birth cohort study to identify gene patterns associated with exposure to farm environment and respiratory illness frequency.

first: Joshua

last: Brownell

first: Kristine

last: Lee

first: Deborah

last: Chasman

first: Ronald

last: Gangnon

first: Casper

last: Bendixsen

first: Katherine

last: Barnes

last: Grindle

first: Tressa

last: Pappas

first: Yury

last: Bochkov

first: Amy

last: Dresen

first: Christine

last: Hou

first: David

middle: B

last: Haslam

last: Seroogy

first: Irene

last: Ong


title: Extracellular Vesicle and Particle miRNAs in Human Milk

city: Lebanon

first: Caitlin

last: Howe

state: NH

address: 1 Medical Center Dr

department: Epidemiology

institute: Geisel School of Medicine at Dartmouth

summary: EVP miRNAs levels were measured in the supernatant fraction of 54 human milk samples collected approximately 6 weeks postpartum from individuals in New Hampshire using the NanoString nCounter Human v3 miRNA expression panel

overall_design: 54 human milk samples


title: A disrupted FOXP3 transcriptional signature underpins regulatory T cells insufficiency in early pregnancy failure

status: Public on Jan 28 2024

first: Sarah

last: Robertson

address: 4 North Terrace

department: Discipline of Obstetrics and Gynaecology

institute: The University of Adelaide

summary: Regulatory T (Treg) cell defects are implicated in disorders of embryo implantation and placental development, but the origins of Treg cell dysfunction are unknown. Here, we comprehensively analyzed the phenotypes and transcriptional profile of peripheral blood Treg cells in individuals with early pregnancy failure (EPF). Compared to fertile subjects, EPF subjects had 32% fewer total Treg cells and 54% fewer CD45RA+CCR7+ naïve Treg cells amongst CD4+ T cells, accompanied by lower Treg:Th1 and Treg:Th17 ratios. An altered phenotype with reduced transcription factor FOXP3 and suppressive marker CTLA4 was also evident. RNAseq demonstrated an aberrant gene expression profile, with upregulation of pro-inflammatory genes including CSF2, IL4, IL17A, IL21, and IFNG, in EPF Treg cells. In silico analysis revealed 25% of the Treg cell dysregulated genes are targets of FOXP3 control. We conclude that Treg cell defects in EPF can arise due to loss of lineage fidelity associated with impaired FOXP3 regulation.

overall_design: Transcriptional profiling of peripheral blood Treg cells in individuals with early pregnancy failure (EPF) compared to fertile subjects.

first: Lachlan

last: Moldenhauer

first: Kerrie

last: Foyle

first: Jasmine

last: Wilson

first: Ying

middle: Y

last: Wong

last: Sharkey

first: Ella

middle: S

last: Green

first: Simon

last: Barry

first: M

last: Hull


title: Clinical and Biomarker Results from A Phase II Trial of Combined Cabozantinib and Durvalumab in Patients with Chemotherapy-refractory Colorectal Cancer (CRC): CAMILLA CRC Cohort

status: Public on Jan 27 2024

city: Pittsburgh

first: Ayah

middle: N.

last: Al-Bzour

state: Pennsylvania

address: Pittsburgh

department: Department of Medicine, Division of Hematology & Oncology

institute: University of Pittsburgh Medical Center (UPMC)

summary: CAMILLA is a basket trial (NCT03539822) evaluating cabozantinib plus the ICI durvalumab in chemorefractory gastrointestinal cancer. Herein, are the phase II colorectal cohort results. 29 patients were evaluable. 100% had confirmed pMMR/MSS tumors. Primary endpoint was met with ORR of 27.6% (95% CI 12.7-47.2%). Secondary endpoints of 4-month PFS rate was 44.83% (95% CI 26.5-64.3%); and median OS was 9.1 months (95% CI 5.8-20.2). Grade≥3 TRAE occurred in 39%. In post-hoc analysis of patients with RAS wild type tumors, ORR was 50% and median PFS and OS were 6.3 and 21.5 months respectively. Exploratory spatial transcriptomic profiling of pretreatment tumors showed upregulation of VEGF and MET signaling, increased extracellular matrix activity and pre-existing anti-tumor immune responses coexisting with immune suppressive features like T cell migration barriers in responders versus non-responders. Cabozantinib plus durvalumab demonstrated anti-tumor activity, manageable toxicity, and have led to the activation of the phase III STELLAR-303 trial.

overall_design: single-center, open-label, phase I/II multi-cohort trial evaluating cabozantinib plus durvalumab in patients with advanced, treatment-refractory, gastrointestinal malignancies (NCT03539822). The paper is reportig the phase II colorectal cancer cohort molecular and clinical results

first: Anwaar

last: Saeed

first: Robin

last: Park

first: Harsh

last: Pathak

first: Junqiang

last: Dai

first: Milind

last: Phadnis

first: Raed

last: Al-Rajabi

first: Anup

last: Kasi

first: Joaquina

last: Baranda

first: Weijing

last: Sun

first: Stephen

last: Williamson

first: Yu-Chiao

last: Chiu

first: Hatice

last: Osmanbeyoglu

first: Rashna

last: Madan

first: Hassan

last: Abushukair

first: Kelly

last: Mulvaney

first: Andrew

last: Godwin

first: Azhar


title: Targeting MYC induces lipid droplet accumulation by upregulation of HILPDA in clear cell renal cell carcinoma

city: Solna

first: Irene

last: Stevens

address: Tomtebodavägen 23A (Gamma5)

department: Department of Microbiology, Tumor and Cell Biology

country: Sweden

institute: Karolinska Institutet

summary: Metabolic reprogramming is critical during clear cell renal cell carcinoma (ccRCC) tumorigenesis, manifested by accumulation of lipid droplets (LDs), organelles that have emerged as new hallmarks of cancer. Yet, regulation of their biogenesis is still poorly understood. Here, we demonstrate that MYC inhibition in ccRCC cells lacking the von Hippel Lindau (VHL) gene leads to increased triglyceride content potentiating LD formation in a glutamine-dependent manner. Notably, LD accumulation is prevented, and tumor burden reduced in vivo upon concurrent inhibition of MYC signaling and glutamine metabolism. Furthermore, we identified the hypoxia inducible lipid droplet associated protein (HILPDA) as the key driver for induction of MYC-driven LD accumulation and demonstrated that conversely, proliferation, LD formation, and tumor growth are impaired upon its downregulation. Finally, analysis of ccRCC tissue as well as healthy renal control samples, postulated HILPDA as a specific ccRCC biomarker. Together, these discoveries provide an attractive approach for development of new therapeutic interventions for the treatment of this type of renal cancer.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for clear cell renal cell carcinoma cell line RCC4 with loss of VHL gene (RCC4 VHL-) and the same cell line wirh VHL reintroduction (RCC4 VHL+)  These two cell lines were treated with either control (DMSO) or MYC inhibitor JQ1.

first: Lourdes

last: Sainero-Alcolado

first: Elisa

last: Garde-Lapido

first: Marteinn

middle: T

last: Snaebjörnsson

first: Sarah

last: Schoch

first: María Victoria

last: Ruiz-Pérez

first: Christine

last: Dyrager

first: Vicent

last: Pelechano

first: Håkan

last: Axelson

first: Almut

last: Schulze

first: Marie

last: Arsenian-Henriksson


title: MiR-204-5p may Regulate Oxidative Stress in Myopia and Myopia-Related Retinopathy

status: Public on Jan 26 2024

city: Hangzhou

first: hao

last: lei

state: Zhejiang province

address: No. 866, Yuhangtang Road, Xihu District, Hangzhou City, Zhejiang Province

department: biology

institute: zhejiang university

summary: Introduction: The mechanisms underlying myopia and myopia-related retinopathy remain not fully understood. We proposed to examine the function and underlying mechanisms of miR-204-5p in myopia development. Methods: The miR-204-5p expression level was assessed in the vitreous humor (VH) of a cohort consisting of 11 patients with high myopia (HM) and 16 control patients undergoing retinal surgery. The functional implications of miR-204-5p in ARPE-19 cells were assessed, encompassing cell aggressiveness. Thioredoxin-interacting protein (TXNIP) was found as a possible target of miR-204-5p through mRNA sequencing, and its interaction with miR-204-5p was confirmed employing luciferase assay and western blotting. Furthermore, the miR-204-5p function in regulating oxidative stress was examined by measuring reactive oxygen species (ROS) accumulation. Results: miR-204-5p was found to be significantly reduced in the VH of HM patients. Overexpression of miR-204-5p suppressed cell proliferation, migration, invasion, and apoptosis in ARPE-19 cells. The bioinformatics analysis demonstrated that miR-204-5p can modulate the genes associated with pathways relevant to myopia, including glycosaminoglycan (GAG) degradation, lysosome, and TGF−beta signaling pathway. The direct targeting of miR-204-5p on TXNIP has been confirmed through validation, and its downregulation mediated the miR-204-5p impacts on ARPE-19 cells. Moreover, miR-204-5p overexpression significantly reduced ROS accumulation by targeting TXNIP. Conclusion: Our findings revealed the possible contribution of the miR-204-5p/TXNIP axis in myopia development by regulating oxidative stress, which may provide new targets and novel therapeutic strategies to combat this prevalent and debilitating condition.

overall_design:
To investigate the possible target of miR-204-5p, we established ARPE-19 cell lines transfected with miR-204-5p or miR-NC.
we then performed gene expression profiling analysis using data obtained from RNA-seq of miR-204-5p transfected ARPE-19 cells and miR-NC transfected ARPE-19 cells(containing 3 biological replications each group)
comparative gene expression profiling analysis of RNA-seq data for miR-204-5p transfected ARPE-19 cells and miR-NC transfected ARPE-19 cells


title: In situ single-cell profiling sheds light on IFI27 localisation during SARS-CoV-2 infection

city: brisbane

first: Arutha

last: Kulasinghe

address: 37 kent st

institute: University of Queensland

summary: The utilization of single-cell resolved spatial transcriptomics to delineate immune responses during SARS-CoV-2 infection was able to identify  macrophages to have elevated expression of IFI27 in areas of infection.

overall_design: CosMxTM technology [CosMxTM Human Universal Cell Characterization RNA Panel (1000-plex) + 20 custom genes; Nanostring, USA] was applied to rapid autopsy lung tissues from 18 patients infected with SARS-CoV-2 patients who died from respiratory failure (ARDS), with SARS-CoV-2 infection confirmed by RTqPCR of nasopharyngeal swabs. 2 tissue microarrays were constructed from 30 tissue block cores, with up to 2 cores per patient, resulting 112 fields of view (FoVs) across 60 cores. The following cell surface markers were used for morphology visualization: B2M/CD298, PanCK, CD45, CD3 antibodies and DAPI.

first: Chin

middle: W

last: Tan


title: Life without stress protection – consequences of abrogating the heat shock response in S. cerevisiae

city: Garching

first: Johannes

last: Buchner

state: Bavaria

address: Ernst-Otto-Fischer Strasse 8

department: Center for Protein Assemblies and Department of Chemistry

institute: Technische Universität München

summary: The response to proteotoxic stresses such as heat shock is an ancient and ubiquitous transcriptional program allowing organisms to maintain protein homeostasis under changing environmental conditions. We depleted or deleted the three stress-specific transcription factors, Hsf1, Msn2 and Msn4, in S. cerevisiae and determined the effects on the transcriptome and proteome. Msn2/4 are responsible for a broad transcriptional reprogramming which includes i. a. the response to oxidative stress as well as biosynthesis of the protective sugar trehalose and glycolysis enzymes. Hsf1 activates the synthesis of molecular chaperones. In the absence of stress protection, thermal stress results in massive protein aggregation including many essential proteins. As a last resort to sustain life this triggers the transcriptomic induction of sporulation likely via the cell wall integrity signaling pathway.

overall_design: The dataset contains 20 different samples measured  in triplicates (60 sequencing data sets): 4 strains at (25°C, 37°C HS after 10min and 30 min, 42°C HS after 10 Min and 30 min) = 4 strains x 5 conditions x 3 Replicates = 60 samples.

first: Moritz

last: Mühlhofer

first: Felix

last: Offensperger

last: Reschke

first: Georg

last: Wallmann

first: Gergely

last: Csaba

first: Evi

last: Berchtold

first: Helmut

last: Blum

first: Martin

last: Haslbeck

first: Ralf

last: Zimmer


title: Transcriptomic and epigenetic dissection of spinal ependymomas (SP-EPN) identifies clinically relevant subtypes enriched for tumors with and without NF2 mutation [RNA-seq]

city: Hamburg

first: Karoline

last: Hack

address: Martinistraße 52

department: Children's Cancer Center Hamburg

institute: University Medical Center Hamburg-Eppendorf

summary: Background: Ependymomas encompass multiple, clinically relevant tumor types based on localization and molecular profiles. Although tumors of the methylation class “spinal ependymoma” (SP-EPN) represent the most common intramedullary neoplasms in children and adults, their developmental origin is ill-defined, molecular data are scarce, and the potential heterogeneity within SP-EPN remains unexplored. The only known recurrent genetic events in SP-EPN are loss of chromosome 22q and NF2 mutations, but neither types and frequency of these alterations nor their clinical meaning have been described in a large, epigenetically defined series. Methods: We mapped SP-EPN transcriptomes (n=76) to developmental atlases of the developing and adult spinal cord to uncover potential developmental origins of these tumors. In addition, transcriptomic, epigenetic (n=234), genetic (n=140), and clinical analyses (n=115) were integrated for a detailed overview on this entity. Results: Integration of transcriptomic ependymoma data with single-cell atlases of the spinal cord identified mature adult ependymal cells to display highest similarities to SP-EPN. Unsupervised hierarchical clustering of tumor data together with integrated analysis of methylation profiles identified two molecular SP-EPN subtypes. Subtype 1 predominantly contained NF2 wild type sequences with regular NF2 expression but revealed more extensive copy number alterations. Subtype 2 harbored previously known germline or sporadic NF2 mutations and was NF2-deficient in most cases, more often showed multilocular disease, and demonstrated a significantly reduced progression-free survival. Conclusion: Based on integrated molecular profiling of a large tumor series we identify two distinct SP-EPN subtypes with important implications for genetic counseling, patient surveillance, and drug development priorities.

overall_design: To investigate the intertumoral heterogeneity of  the  methylation  class  “spinal ependymoma” (SP-EPN) bulk RNA sequencing was performed of 76 SP-EPN from formalin-fixed paraffin-embedded (FFPE) tissues.

first: Sina

last: Neyazi

first: Erika

last: Yamazawa

first: Tanaka

last: Shota

first: Ulrich

last: Schüller


title: Excessive heavy metals enrichment disturbs the liver function through gut microbe in great Himalayan leaf-nosed bat (Hipposideros armiger)

city: Changchun

first: Yutao

last: Li

address: Jingyue Street

institute: Northeast Normal University

summary: Heavy metals residue in the natural ecosystem had become one global environmental problem that was eager to solve. Due to the non-biodegradability, organism could deposit excessive heavy metals elements into tissues. Existing literature proposed that prolonged heavy metals enrichment had comprehensive toxicity to multi-organs of vertebrates. However, little research focus on the molecular mechanism for the hepatotoxicity of heavy metal enrichment to Chiroptera. In the present study, ten Hipposideros armiger individuals from Yingde City (YD, relatively pollution-free) and Chunwan City (CW, excessive heavy metals emission) were dissected while environment samples were also obtained. To corroborate the toxicity mechanism of heavy metals to bats liver, multi-omics, pathology and molecular biology methods were performed. Our results showed that more Cd and Pb elements were significantly enriched in bats liver and food sources in the CW group. In addition, prolonged heavy metals accumulation disturbed the hepatic transcription profiling associated with solute carriers family, ribosome pathway, ATP usage and heat shock proteins. Excessive heavy metals enrichment also altered the relative abundance of typical gut microbe taxa to inhibit the tight-junction protein expression. We also found that the levels of superoxide dismutase, glutathione peroxidase and glutathione were decreased while ROS density and malondialdehyde content were elevated after excessive heavy metals enrichment. Besides, hepatic fat accumulation and inflammation injury were also observed under the excessive heavy metals enrichment while the metabolism biomarkers contents were decreased. Therefore, prolonged heavy metals enrichment would induce a series of hepatotoxicity by disturbing the microbes-gut-liver axis and hepatic transcription modes, which could decrease the overall metabolism level in bats. Our study provided protection strategy for biodiversity conservation and raised public attention to environment pollution.

overall_design: Two caves located in the Guangdong Province were selected in the present experiment. One is located in Yingde City (YD) ,  the other is located in Chunwan City (CW).Hipposideros armiger were caught using mist-nets at midnight.Only five male adult individuals in each cave were euthanized by inhaling ethyl ether and removed the liver tissue quickly.


title: Transcriptomic and epigenetic dissection of spinal ependymomas (SP-EPN) identifies clinically relevant subtypes enriched for tumors with and without NF2 mutation [WES]

overall_design: Examination of the genomic landscape of the methylation class “spinal ependymoma” (SP-EPN) by whole exome sequencing of 29 SP-EPN from formalin-fixed paraffin-embedded (FFPE) tissues.


title: Parental pericentromeric methylation status drives methylome remodeling and heterosis in Arabidopsis hybrids [smallRNAseq]

city: Freising

first: Frank

last: Johannes

address: Emil-Ramann str. 4

department: Department of Molecular Life Sciences

institute: Technical University of Munich

summary: A large number of epiHybrids families were generated by crossing a male sterile maternal plant of the Columbia accession (msCol) to different paternal ddm1-2 derived epiRILs (Johannes et al., 2009)

overall_design: We performed smallRNAseq analysis for 36 epiHybrids, their corresponding 36 paternal parents (epiRILs) and the msCol maternal plants.

first: Ioanna

last: Kakoulidou

first: Thomas

last: Altmann

first: Rhonda

last: Meyer


title: Parental pericentromeric methylation status drives methylome remodeling and heterosis in Arabidopsis hybrids [WGBS_epiRILs]

summary:
WGBS of 169 ddm1-derived epiRILs
169 ddm1-derived epigenetic recombinant inbred lines (epiRILs) were obtained from the Versailles Arabidopsis Stock center of INRA (http://publiclines.versailles.inra.fr/) and they were propagated in a fully automatic phenotyping facility for small plants at the Leibniz Institute of Plant Genetics and Crop Plant Research (IPK). Whole Genome Bisulphite Sequencing was performed at the Beijing Genome Institute.

overall_design:
We performed Whole Genome Bisilphute Sequencing to 169 epiHybrids, 160 epiRILs and the 2 msCol plants that used for the crosses
Raw data have been analyzed again (GSE171414)


title: Parental pericentromeric methylation status drives methylome remodeling and heterosis in Arabidopsis hybrids [WGBS_epiHybrids]

summary:
WGBS of 169 ddm1-derived epiHybrids and their corresponding maternal msCol lines
A large number of epiHybrids families (169 epiHybrids) were generated by crossing a male sterile maternal plant of the Columbia accession (msCol) to different paternal ddm1-2 derived epiRILs (Johannes et al., 2009)

overall_design: We performed Whole Genome Bisilphute Sequencing to 169 epiHybrids, 160 epiRILs and the 2 msCol plants that used for the crosses


title: Parental pericentromeric methylation status drives methylome remodeling and heterosis in Arabidopsis hybrids [WGS]

summary: WGreS of 2 male sterile Columbia lines (msCol)

overall_design: A large number of epiHybrids families (169 epiHybrids)were generated by crossing a male sterile maternal plant of the Columbia accession (msCol) to different paternal ddm1-2 derived epiRILs (Johannes et al., 2009)


title: Uncovering the potential molecular mechanism of liraglutide to alleviate the effects of high glucose on myoblasts based on high-throughput transcriptome sequencing technique

status: Public on Jan 25 2024

city: Qinhuangdao

first: Dongmei

last: Fan

address: 258 Wenhua Road, Haigang District

institute: The first hospital of QinHuangdao

summary: Myoblasts play an important role in muscle growth and repair, but the high glucose environment severely affects the function of myoblasts. The purpose of this study is to explore the potential molecular mechanism of liraglutide in alleviating the effects of high glucose environments on myoblasts.High-throughput transcriptome sequencing technique was used to sequence C2C12 myoblast from different treated groups.

overall_design: The sequencing samples in this study included C2C12 cell control group (NC group), C2C12 cell high glucose (25 mmol/L) treated group (H group) and C2C12 cell high glucose (25 mmol/L) + liraglutide (200 nmol/L) treated group (H+L group). RNA sequencing was performed to obtain the differentially expressed mRNAs (DEmRNAs).

first: Yunjie

last: Zhang

first: Lanyu

last: Lu

first: Fuzai

last: Yin

first: Bowei

last: Liu


title: Hyperactive mTORC1 in Lung Mesenchyme Induces Endothelial Cell Dysfunction and Pulmonary Vascular Remodeling

city: Philadelphia

first: Apoorva

last: Babu

state: PA

address: SCTR, 3400 Civic Center Blvd

department: Cardiovascular Institute

institute: University of Pennsylvania

summary: Lymphangioleiomyomatosis (LAM) is a progressive cystic lung disease caused by tuberous sclerosis complex 1/2 (TSC1/2) gene mutations resulting in activation of the mechanistic target of rapamycin complex 1 (mTORC1). A subset of LAM patients develops pulmonary vascular remodeling and pulmonary hypertension. To model LAM disease, we utilized an mTORC1 gain-of-function mouse model with a Tsc2 knock-out (Tsc2KO) specific to lung mesenchyme (Tbx4LME-CreTsc2fl/fl), similar to the mesenchyme specific genetic alterations seen in human disease. As early as 8 weeks of age, ECs from Tbx4LME-CreTsc2fl/fl mice exhibited marked transcriptomic changes despite absence of morphological changes to the distal lung microvasculature. In contrast, 1 year old Tbx4LME-CreTsc2fl/fl mice spontaneously developed pulmonary vascular remodeling with increased medial thickness. We subsequently performed single cell RNA-sequencing of 1 year old mouse lung and identified paracrine ligands originating from Tsc2KO mesenchyme impacting arterial endothelial cells.  These cells contained transcriptionally altered genes including those in pathways associated with blood vessel remodeling, highlighting the pathogenic importance of the mesenchymal-endothelial cell axis.

overall_design: Whole murine lung single cells suspension in one year Tbx4Tsc2 WT and KO; samples were CD45 depleted with 10% spiked back into CD45- fractions and then loaded on 10x genomic platform for single cell RNA sequencing

first: Susan

last: Lin

first: Vera

last: Krymskaya


title: Dynamic changes of macrophage polarization during Salmonella infection in zebrafish

city: Montpellier

first: Mai-Eva

last: Nguyen-chi

address: Pl. Eugène Bataillon

country: France

institute: CNRS

summary:
To investigate the polarization status of macrophages during salmonella persistent infection we established a model of Salmonella enterica serovar Thyphimurium infection in the zebrafish larva in which salmonella survive long term inside the host. In this model, during initial stages of the infection, macrophages are recruited to the infection site and express tnfa. By contrast, in the late stages of the infection, macrophages form clusters at the infection site and do not express tnfa.
The objective is to characterize the transcriptional profile of macrophages in early stage of infection (4 hours post-infection) and late stage of infection (4 days post-infection).

overall_design: Comparative gene expression profiling analysis of RNA-seq data for macrophages from Salmonella infected larvae at 4 hours post-infection (4 replicates) and 4 days post-infection (4 replicates). Controls are macrophages from non-infected larvae at 4 hours post-infection (4 replicates) and 4 days post-infection (3 replicates).

first: Jade

last: Leiba

first: Christina

last: Begon-Pescia

first: Mai

last: Nguyen-Chi


title: Multi-omic profiling of Müller cells in diabetic retinopathy identifies the glucocorticoid receptor as a master regulator of the gliotic response

city: Munich

first: Antje

last: Grosche

address: Grosshaderner Str. 9

institute: Ludwig-Maximilian University Munich

summary: Diabetic retinopathy (DR), the leading cause of blindness in working-age adults, is thought to be primarily a microvascular complication of diabetes. Müller cells, the major macroglia of the retina, are important for maintaining a healthy and functional retina and play a critical role in several pathological events during DR disease progression as they are a central element of the retinal neurovascular unit. Here, we aim to improve our understanding of Müller cell-specific signaling pathways that are altered during disease progression in order to develop novel gene therapy strategies targeting Müller cells in DR. To achieve this, we used a multi-omics approach on purified Müller cells from 6-month-old control and diabetic db/db mice, including (i) RNA-seq followed by oPOSSUM-3 transcription factor (TF) binding site cluster analysis, (ii) glial chromatin landscape analysis by ATAC-seq, and (iii) Müller cell proteomics by MS/MS mass spectrometry. This led to the identification of the glucocorticoid receptor (GR, gene ID: Nr3c1) as the most promising candidate. Its transcripts and protein were most highly expressed in Müller cells and significantly reduced in cells from diabetic mice, its target gene cluster was downregulated in Müller cells from diabetic animals, and importantly, it was identified as a potential master regulator not only by oPOSSUM analysis based on differentially expressed mRNA in Müller cells, but also validated by the ATAC-seq approach. Next, we investigated the effect of GR modulation in an in vitro cortisol-stimulated retinal explant model. Cortisol not only increased GR phosphorylation levels, but also induced changes in the expression of known downstream GR target genes. Finally, we evaluated whether AAV-mediated GR overexpression in Müller cells improves retinal functionality and found moderate functional improvements in electroretinogram recordings. Although synthetic and topical glucocorticoids are widely used in ophthalmology with undeniable beneficial effects, our study provides valuable new insights into the role of GR signaling and glial alterations in the diabetic retina and thus supports the therapeutic concept of locally enhancing the GR signaling axis. However, our finding of reduced GR levels in Müller cells of the diabetic retina suggests that therapeutic approaches should aim at increasing the expression of the receptor rather than adding more ligands. This may result in optimized local efficacy with fewer systemic unwarranted side effects.

overall_design: Retina from eyes of diabetic db/db mice and non-diabetic controls  were isolated and digested to produce a cell suspension. For each genotype a set of 12 and 24 week old mice was used. From the suspension we isolated CD31 positive endothelial cells, CD11b positive microglia and CD29 positive Müller cells using a sequential magnetic bead activated cell sorting approach. These three cell fraction and the flowthrough fraction were used to isolate RNA and prepare the RNAseq libraries.

first: Pfaller

last: Anna M

first: Kaplan

last: Lew

first: Carido

last: Madalena

first: Grassmann

last: Felix

first: Diaz-Lezama

last: Nundehui

first: Ghaseminejad

last: Farhad

first: Hoffelner

last: Patricia

first: Wunderlich

last: Kirsten

first: Glänzer

last: Sarah

first: Klöting

last: Nora

first: Pannicke

last: Thomas

first: Weber

last: Bernhard HF

first: Koch

last: Susanne

first: Bonev

last: Boyan

first: Hauck

last: Steafanie M

first: Grosche

last: Antje


title: Gene expression data from CD8+ T cell subsets

status: Public on Jan 24 2024

city: Tartu

first: Lehte

last: Turk

address: Ravila 19

country: Estonia

institute: University of Tartu

summary:
As humans age, their memory T cell compartment expands due to the lifelong exposure to antigens. This expansion is characterized by the presence of terminally differentiated CD8+ T cells (Temra), which possess NK cell-like phenotype and are associated with chronic inflammatory conditions. Temra cells are predominantly driven by the sporadic reactivation of cytomegalovirus (CMV), yet their epigenomic patterns and cellular heterogeneity remain understudied.
To address this gap, we correlated their gene expression profiles with chromatin openness and conducted single-cell transcriptome analysis, comparing them to other CD8+ subsets and CMV-responses.

overall_design: PBMCs were stimulated before cell sorting with CMV pp65 peptide pool (PepTivator) for 16-24h in CO2 enriched thermostat at 37C. CD8+ T cell subsets from 28 different individuals (>65 y old) were sorted with MA900 Multi-Application Cell Sorter (Sony Biotechnology) and collected at 4C into collections tubes containing TRIzol reagent. 96 samples were subjected to microarray analysis of which 91 had a good quality. We analysed altogether 4 CD8+ T cell subsets of which 12 were CMV-reactive T cells, 24 naive T cells, 27 memory T cells and 28 Temra cells.

last: Türk

first: Liina

last: Tserel

first: Pärt

last: Peterson


title: Parental pericentromeric methylation status drives methylome remodeling and heterosis in Arabidopsis hybrids [Transcriptome]

first: Frank

last: Johannes

overall_design: We performed transcriptome analysis for 36 epiHybrids, their corresponding 36 paternal parents (epiRILs) and the msCol maternal plants.

first: Ioanna

last: Kakoulidou

first: Thomas

last: Altmann

first: Rhonda

last: Meyer


title: Immune Restoring (IR) CAR-T Cells Display Superior Antitumor Activity and Reverse Immunosuppressive TME in a Humanized ccRCC Orthotopic Mouse Model

city: Boston

first: JAE WON

last: CHO

state: MA

address: 60 Fenwood Road

department: Neurology

institute: Brigham and Women's Hospital

summary: Here we report a humanized clear cell renal cell carcinoma (ccRCC) orthotopic NSG-SGM3  mouse model (hccRCC-NSG-SGM3) with reconstituted human lymphocytes derived from fetal CD34+ hematopoietic stem cells (HSCs) bearing human ccRCC skrc-59 cells under the kidney capsule. Human leukocyte antigen (HLA) matched CD34+ HSCs were used for the humanization to reduce T cell alloreactivity against skrc-59 human ccRCC cells.  Tumors were collected and sorted for CD45+ tumor infiltrated leukocytes (TILs) to profile the tumor microenvironment (TME) in hccRCC-NSG-SGM3. By comparing to patient data from prospective clinical trials of the anti-PD-1 monoclonal antibody (mAb) nivolumab in advanced ccRCC, the results demonstrated that the CD45+ TILs from hccRCC-NSG-SGM3 reconstitutes most CD45+ cell types, including NK cells, dendritic cells, exhausted CD8 T cells, regulatory T cells (Tregs), that are observed in advanced ccRCC patient TME. Furthermore, Anti-carbonic anhydrase IX (CAIX) G36 immune restoring (IR) chimeric antigen receptor (CAR) T cells secreting PD-L1 targeted immune checkpoint inhibitor (ICI) mAb (G36-PDL1) exhibited superior tumor control compared to G36 CAR-T cells with anti-SARS mAb (G36-SARS) and anti-BCMA A716 CAR-T cells with anti-PD-L1 mAb (A716-PDL1). In addition, G36-PDL1 CAR-T cells restored active anti-tumor immunity at tumor site uncovered by 10X genomics single cell RNA sequencing (scRNA-seq) and single cell T cell receptor sequencing (scTCR-seq).

overall_design: CD45+ immune cells from tumor sample in humanized mouse model

first: Yufei

last: Wang

first: Jae-Won

last: Cho

first: Gabriella

last: Kastrunes

first: Alicia

last: Buck

first: Cecile

last: Razimbaud

first: Aedin

last: Culhane

first: Jiusong

last: Sun

first: David

last: Braun

first: Toni

last: Choueiri

first: Catherine

last: Wu

first: Kristen

last: Jones

first: Quang-De

last: Nguyen

first: Zhu

last: Zhu

first: Kevin

last: Wei

first: Sabina

last: Signoretti

first: Nicholas

last: Hayden

first: Madison

middle: L

last: O'Donnell

first: Ying

last: Huang

first: Martin

last: Hemberg

first: Gordon

last: Freeman

first: Wayne

last: Marasco


title: Endothelial cells adopt a pro-reparative immune responsive signature during cardiac injury

status: Public on Jan 23 2024

city: Houston

first: Jong

last: Kim

state: TX

address: One Baylor Plaza

institute: Baylor College of Medicine

summary: Modulation of the heart's immune microenvironment is crucial for recovery after ischemic events such as myocardial infarction (MI). Endothelial cells (ECs) can have immune regulatory functions; however, interactions between ECs and the immune environment in the heart after MI remain poorly understood. We identified an EC-specific IFN responsive and immune regulatory gene signature in adult and pediatric heart failure (HF) tissues. Single-cell transcriptomic analysis of murine hearts subjected to MI uncovered an EC population (IFN-ECs) with immunologic gene signatures similar to those in human HF. IFN-ECs were enriched in regenerative-stage mouse hearts and expressed genes encoding immune responsive transcription factors (Irf7,Batf2, andStat1). Single-cell chromatin accessibility studies revealed an enrichment of these TF motifs at IFN-EC signature genes. Expression of immune regulatory ligand genes by IFN-ECs suggests bidirectional signaling between IFN-ECs and macrophages in regenerative-stage hearts. Our data suggest that ECs may adopt immune regulatory signatures after cardiac injury to accompany the reparative response. The presence of these signatures in human HF and murine MI models suggests a potential role for EC-mediated immune regulation in responding to stress induced by acute injury in MI and chronic adverse remodeling in HF.

overall_design: Mouse were subjected to MI at P1 or P8, Whole hearts or cd31 enriched cells were collected 3 days after MI for each time point. Each sample were used to analysis ATAC at the single cell level. Mouse were subjected to MI at P1 or P8, Whole hearts or cd31 enriched cells were collected 3 days after MI for each time point. Each sample were used to analysis RNA at the single cell level.

first: Hali

last: Long

first: Jeffrey

middle: D

last: Steimle

first: Francisco

last: Grisanti Canozo

first: Xiao

last: Li

first: Minjun

last: Park

first: M

last: Samee

first: James

middle: F

last: Martin


title: Analysis of murine tail lymphedema tissue between TNTSham and TNTProx1 groups

city: Indianapolis

first: Aladdin

last: Hassanein

state: IN

address: 545 Barnhill Dr, Suite 232

department: Surgery

institute: Indiana University

summary: Murine tail lymphedema tissue were obtained from TNTSham and TNTProx1 group. Total RNA was extracted and cDNA library was prepared.

overall_design: Transcriptome profile of murine tail lymphedema tissues

first: Ganesh

last: Mohan

first: Imran

last: Khan

first: Mithun

last: Sinha


title: Dissecting the sequence and structural determinants guiding m6A deposition and evolution via inter- and intra-species hybrids

city: Rehovot

first: Ran

last: Shachar

address: 234 Herzl St.

department: Department of Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

summary: N6-methyladenosine (m6A) is the most abundant mRNA modification, primarily implicated in controlling mRNA stability. The distribution of m6A varies considerably between and within species, and genetic variants associated with differences in m6A levels between humans have been associated with disease. Yet, the determinants governing m6A variability are poorly understood: It is unclear whether it is driven by changes in genetic sequences (‘cis’) or cellular environments (‘trans’) and what its underlying mechanisms are. Here we dissect these determinants via interspecies hybrids in yeast and mammalian systems, allowing us to interrogate methylation at two distinguishable alleles in a shared environment. We find that m6A evolution is driven primarily in ‘cis’, and identify two mechanisms driving m6A changes: (1) Sequence variations leading to formation/disruption of m6A consensus motifs, and (2) Changes in local mRNA secondary structure, whereby RNA structuredness inhibits m6A formation. We demonstrate that secondary structure is causal, and that gain and loss of structure - even when driven by mutations distant from the modified position - are sufficient to abolish and acquire methylation, respectively. Using intra-species hybrids, massively parallel reporter assays and reanalyzing m6A-QTLs among 60 human individuals, we reveal the combined role of sequence and structure in shaping variability in m6A levels also across individuals from the same species. Finally, we demonstrate that differences in m6A levels between homologous genes lead to allele-specific changes in gene expression. Our findings thus define the determinants governing m6A evolution and diversity and characterize the consequences thereof on gene expression regulation.

sample_organism: Saccharomyces cerevisiae x Saccharomyces paradoxus

overall_design: We performed m6A-seq2 RNA sequencing of polyA-selected mRNA from multiple samples. For yeast, we sequenced Saccharomyces cerevisiae and Saccharomyces paradoxus yeast strains along with their F1 hybrid (IME4 KO and IME 4 WT), with 3 replicates for each strain (total 18 samples). For mammalian cells, we sequenced 3T3 mice cell line, BJ human cell line, JC001 cell line, JC002 cell line, and JC003 cell line, with 2 replicates for each (total 10 replicates). Additionally, we sequenced mouse embryonic stem cells originating from mating the two mouse strains house mouse and castaneous, 2 replicates.

first: Schraga

last: Schwartz


title: Leveraging chromatin state transitions for regulatory networks identification in heart regeneration

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: The limited regenerative capacity of the human heart is responsible for the high morbidity and mortality world-wide. In contrast, zebrafish possess a robust regenerative capacity. Here, we have characterized the chromatin state transitions during zebrafish heart regeneration and interrogated how gene expression patterns are orchestrated. We found a massive gain of repressive chromatin marks one day after myocardial injury, followed by a large-scale acquisition of active chromatin characteristics on day 4 and a switch to a repressive state on day 14. The correlative analysis predicted known and less well-characterized transcription factors and transcription factor ensembles involved in these transitions and classified them into activators or repressors of specific gene expression programs. Detailed analysis revealed that rapid transcriptional responses involved in extracellular matrix reorganization and TOR signaling involve the engagement of super-enhancers, while H3K4me3 breadth highly correlates with transcriptional activity and the dynamic transcriptional changes at genes involved in proteolysis, cell cycle activity, and cell differentiation. Finally, we detected significant evolutionary conservation between the regulatory regions that drive zebrafish and neonatal mouse regeneration, suggesting that reactivation of transcriptional and epigenetic networks converging on these conserved elements might unlock the regenerative potential of adult human hearts

overall_design: Cryoinjury was performed in adlt zebrafish heart and crosslinked chromatin was used to perform ChIP-seq at different time points

first: Julio

last: Cordero

first: Adel

last: Elsherbiny


title: Parental pericentromeric methylation status drives methylome remodeling and heterosis in Arabidopsis hybrids

first: Frank

last: Johannes

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

overall_design: Refer to individual Series


title: Inflammatory neuropathy driven by a pathologically expanded, clonal lineage of IL-21 producing CD4+ T cells [TCR-seq]

city: Los Angeles

first: Maureen

middle: A

last: Su

state: CA

address: 615 Charles E. Young Dr. S

department: Microbiology, Immunology, and Molecular Genetics

institute: UCLA David Geffen School of Medicine

summary: CIDP (chronic inflammatory demyelinating polyneuropathy) is a debilitating immune-mediated neuropathy characterized by progressive weakness and sensory loss. Peripheral nerves from affected patients and mouse models show infiltrating CD4+ T cells, and CD4+ T cells from affected mice are sufficient to transfer neuropathy to immunodeficient recipients, suggesting an important role for CD4+ T cells in disease pathogenesis. Yet, key properties of pathogenic CD4+ T cells remain incompletely understood. Here, we report that IL-21 expression is highly expressed and a unique feature of terminally-differentiated effector CD4+ T cells within peripheral nerves of neuropathic mice. IL-21-expressing CD4+ T cells are comprised of two transcriptionally distinct, clonally expanded populations, which express genes associated with Tfh and Tph subsets.  Remarkably, TCR clonotypes were shared between these two IL-21-expressing populations, suggesting lineage differentiation from a common progenitor. Finally, we demonstrate that IL-21 signaling is required for pathogenic T cell infiltration into peripheral nerves through upregulation of CXCR6, a chemokine receptor that promotes CD4+ T cell localization in peripheral nerves. Together, these findings highlight IL-21 signaling, Tfh and Tph differentiation, and CXCR6-mediated cellular localization as key pathogenic pathways and potential therapeutic targets in inflammatory neuropathies.

overall_design: This dataset contains single cell TCR-seq data from sciatic nerve-infiltrating CD45+ cells isolated from 4 neuropathic NOD.AireGW/+ mice

first: Maryamsadat

last: Seyedsadr

first: Madison

last: Bang

first: Ethan

last: McCarthy

first: Shirley

last: Zhang

first: Ho-Chung

last: Chen

first: Mahnia

last: Mohebbi

first: Melissa

middle: G

last: Lechner

first: Jason

middle: K

last: Whitmire


title: Inflammatory neuropathy driven by a pathologically expanded, clonal lineage of IL-21 producing CD4+ T cells [scRNA-seq]

overall_design: This dataset contains single cell RNA-seq data from sciatic nerve-infiltrating CD45+ cells isolated from 4 neuropathic NOD.AireGW/+ mice


title: Time-dependent Effects of BRAF-V600E on Cell Cycling, Metabolism, and Function in Engineered Myocardium

city: Durham

first: Nenad

last: Bursac

state: NC

address: 101 Science Dr. Rm. 1169

department: Biomedical Engineering

institute: Duke University

summary: Candidate cardiomyocyte (CM) mitogens such as those affecting ERK signaling pathway represent potential targets for functional heart regeneration. We explored whether activating ERK via a constitutively active mutant of BRAF, BRAF-V600E (caBRAF), can induce pro-proliferative effects in neonatal rat engineered cardiac tissues (ECTs). Sustained CM-specific caBRAF expression induced chronic ERK activation, significant tissue growth, deficit in sarcomeres and contractile function, and tissue stiffening, all of which persisted for at least 4 weeks of culture. CaBRAF-expressing CMs in ECTs exhibited broad transcriptomic changes, shift to glycolytic metabolism, loss of connexin-43, and a pro-migratory phenotype. Transient, doxycycline-controlled caBRAF expression revealed that the induction of CM cycling is rapid, precedes functional decline, and the effects are reversible only with a short-lived ERK activation. Together, direct activation of the BRAF kinase is sufficient to modulate CM cycling and functional phenotype, offering mechanistic insights into roles of ERK signaling in the context of cardiac development and regeneration.

overall_design: Bulk RNA-sequencing from engineered cardiac tissues comparing tissues transduced with a control lentivirus (mCherry only) to tissues transduced with a lentivirus expressing BRAF-V600E-2A-mCherry, both viruses were driven by the muscle-specific MHCK7 promoter. Each sequencing sample is the bulk sequencing data from 6-8 tissues pooled from one cell batch such that each treatment group and time point (we assessed at 1wk and 2wk in vitro) is comprised of three biological replicates.

first: Nicholas

last: Strash

first: Sophia

last: DeLuca

first: Geovanni

last: Janer Carattini

first: Yifan

first: Tianyu

last: Wu

first: Abbigail

last: Helfer

first: Jacob

last: Scherba

first: Isabella

last: Wang

first: Mehul

last: Jain

first: Ramona

last: Naseri


title: Cytotoxic CD8+ Temra cells show loss of chromatin accessibility at genes associated with T cell activation

first: Pärt

last: Peterson

address: Ravila 19-A1038

department: Department of Biomedicine

institute: Institute of Biomedicine and Translational Medicine

summary:
As humans age
their memory T cell compartment expands due to lifelong exposure to antigens. This expansion is characterized by the presence of terminally differentiated CD8+ T cells (Temra)
which possess an NK cell-like phenotype and are associated with chronic inflammatory conditions. Temra cells are predominantly driven by sporadic cytomegalovirus reactivation (CMV)
yet their cellular heterogeneity remains understudied. To address this gap
we measured their gene expression profiles and conducted single-cell transcriptome analysis. We show that CD8+ Temra cells are highly heterogeneous and describe subsets specific to old age and CMV infection.

overall_design:
scRNA-Seq
---------------------
Authors allude to patient privacy issues by stating the following:
We've performed scRNA-seq sequencing of human-derived samples. The donors were profiled for CMV infection status as we studied CMV-specific CD8 Temra cells. We consider the possible genotype-phenotype link to be sensitive enough to warrant omission of raw FASTQ files.

first: Liina

last: Tserel

first: Igor

last: Filippov


title: Single cell analysis revealed that two distinct, unique CD4+ T cell subsets were increased in the small intestinal intraepithelial lymphocytes of aged mice

status: Public on Jan 22 2024

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

country: Japan

institute: Toray Industries,Inc.

summary: Recent advances in research suggest that aging has a controllable chronic inflammatory disease aspect. Aging systemic T cells, which secrete pro-inflammatory factors, affect surrounding somatic cells, and accelerate the aging process through chronic inflammation, have attracted attention as potential therapeutic targets in aging. On the other hand, there are few reports on the aging of the intestinal immune system, which differs from the systemic immune system in many ways. In the current study, we investigated the age-related changes in the intestinal immune system, particularly in T cells. The most significant changes were observed in the CD4+ T cells in the small intestinal IEL, with a marked increase in the proportion of this fraction in old mice and reduced expression of the co-stimulatory molecules CD27 and CD28, which are characteristic of aging systemic T cells. The proliferative capacity of aging IEL CD4+ T cells was significantly more reduced than that of aging systemic T cells. Comprehensive transcriptome analysis showed that the expression of inflammatory cytokines such as TNF was not upregulated, whereas Cd8α, NK receptors, and Grazymes were upregulated in aging IEL CD4+ T cells. Functional analysis showed that aging IEL T cells had a higher cytotoxic function against intestinal tumor organoids in vitro than young IEL T cells. scRNAseq revealed that splenic T cells show a transition from naïve to memory T cells, whereas intestinal T cells show the emergence of a CD8αα+CD4+ T cell fraction in aged mice, which is rarely seen in young cells. Further analysis of the aging IEL CD4+ T cells showed that two unique subsets are increased, which are distinct from the systemic CD4+ T cells. Subset 1 has a pro-inflammatory component, with expression of IFNγ and upregulation of NFkB signaling pathways. Subset 2 does not express IFNγ, but upregulates inhibitory molecules and nIEL markers. Expression of granzymes and CD8α was common to both. These two fractions were in opposite positions in the clustering by UMAP and indeed had different TCR repertoires.  They may be involved in the suppression of intestinal aging and longevity through anti-tumor immunity, elimination of senescent cells and stressed cells in the aging environment. This finding could be a breakthrough in aging research.

overall_design: T cells were harvested from the small intestinal epithelium or spleen of 4-6 mice per group and used for gene expression analysis by microarray.

first: Yuki

last: Yonemoto

first: Yasuhiro

last: Nemoto

first: Ryo

last: Morikawa

first: Nana

last: Shibayama

first: Shigeru

last: Oshima

first: Takashi

last: Nagaishi

first: Tomohiro

last: Mizutani

first: Go

last: Ito

first: Satoru

last: Fujii

first: Ryuichi

last: Okamoto


title: DNMT3B PWWP mutations cause hypermethylation of heterochromatin (WGBS)

city: Edinburgh

first: Duncan

last: Sproul

state: Mid Lothian

address: Crewe Road South

department: MRC Human Genetics Unit

country: United Kingdom

institute: University of Edinburgh

summary: The correct establishment of DNA methylation patterns is vital for mammalian development and is achieved by the de novo DNA methyltransferases DNMT3A and DNMT3B. DNMT3B localises to H3K36me3 at actively transcribing gene bodies through its PWWP domain. It also functions at heterochromatin through an unknown recruitment mechanism. Here we find that knockout of DNMT3B causes losses of methylation predominantly at H3K9me3-marked heterochromatin and that DNMT3B PWWP domain mutations or deletion result in striking increases of methylation in H3K9me3-marked heterochromatin. Removal of the N-terminal region of DNMT3B affects its ability to methylate H3K9me3-marked regions. This region of DNMT3B directly interacts with HP1-alpha and facilitates the bridging of DNMT3B with H3K9me3-marked nucleosomes in vitro. Our results suggest that DNMT3B is recruited to H3K9me3 marked heterochromatin in a PWWP-independent manner that is facilitated by the protein's N-terminus through an interaction with a key heterochromatin protein. More generally, we suggest that DNMT3B plays a role in DNA methylation homeostasis at heterochromatin, a process which is disrupted in cancer, aging and Immunodeficiency, Centromeric Instability and Facial Anomalies (ICF) syndrome.

overall_design: This series contains WGBS from human cancer cell lines. HCT116 cells and derivatives lacking DNMT3B or expressing mutant DNMT3B were grown before genomic DNA was extracted and DNA methylation levels analysed by Whole Genome Bisuflite sequencing (WGBS).


title: DNMT3B PWWP mutations cause hypermethylation of heterochromatin (RNA-seq)

overall_design: This series contains RNA-seq from human cancer cell lines. HCT116 cells and derivatives lacking DNMT3B or expressing mutant DNMT3B were grown before RNA was extracted and transcript levels analysed by RNA-seq.