title: High-throughput sequencing of oxidative stress for Human gastric cancer cell lines treatment with Bioactive polypeptide chelating selenium  (ACBP-S-Se)

city: Huhehaote

first: Xiulan

last: Su

address: Jinshan street

institute: Inner Mongolia Medical University

summary: The functional gene analyses revealed 911 upregulated genes and 1122 downregulated genes after ACBP-S-Se treatment in MKN-45 cells. From the functional enrichment analyses of oxidative stress-related genes, a total of 75 genes with significant differences were selected . From the gene interaction mapping, CDKN1A, CCNB1, TXN and MAP3K5 were extracted due to the roles of most genes with which they associate and to the significantly enriched pathways, which can be used as downstream molecules.according to the interaction of genes related to oxidative stress and lncRNAs, networks of oxidative stress genes and lncRNA interactions (lncRNA FPKM>5) were constructed via lncRNA trans and cis analysis (TRANS_ENERGY<-50). The results showed that the network contained 55 genes related to oxidative stress and 37 lncRNAs.The selected lncRNAs included MSTRG.13268.2, ENST00000508832, ENST00000580180, ENST00000454068, ENST00000607476,ENST00000504539, ENST00000326677, ENST00000448718, ENST00000531126 and MSTRG.5031.1.the expression of oxidative stress-related genes (the 4 selected genes) in The Cancer Genome Atlas (TCGA) and the expression of CDKN1A was increased after treatment with ACBP-S-Se, but the expression of this gene was lower in tumor samples than in paracancerous samples. The expression of the other three genes was decreased after treatment with ACBP-S-Se but was lower in tumor samples than in paracancerous samples.

overall_design: Examination of oxidative stress by ACBP-S-Se in MKN-45 cells.


title: Effects of Nr6a1 overexpression in neural progenitors at the chromatin level [ATAC-seq]

status: Public on Apr 22 2024

city: London

first: M Joaquina

last: Delas

address: 1 Midland Road

department: Briscoe Lab

country: United Kingdom

institute: The Francis Crick Institute

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The vertebrate neural tube generates a large diversity of molecularly and functionally distinct neurons and glia from a small progenitor pool. While the role of spatial patterning in organising cell fate specification has been extensively studied, temporal patterning, which controls the timing of cell type generation, is equally important. Here we define a global temporal programme in the spinal cord. This governs cell fate choices by regulating chromatin accessibility in neural progenitors. Perturbation of this cis-regulatory programme affects sequential transitions in spinal cord progenitors and the identity of progeny. The temporal programme operates in parallel to spatial patterning, ensuring the timely availability of regulatory elements for spatial determinants to direct cell-type specific gene expression. These findings identify a chronotopic spatiotemporal integration strategy in which a global temporal chromatin programme determines the output of a spatial gene regulatory network resulting in the temporally and spatially ordered allocation of cell type identity.

overall_design: ATACseq of mouse neural progenitor at day 9 in the differentiation protocol overexpressing either control or Nr6a1.

first: M

middle: J

first: James

last: Briscoe

first: Isabel

last: Zhang


title: Effects at the transcriptomic level after knockout of Eed, Ezh2, Brd8 or Nr6a1 in spinal cord neural progenitor differentiation [bulkRNAseq]

type: Expression profiling by high throughput sequencing

overall_design: Transfection-based KO was induced at day 0 of differentiation. The indicated timepoints were collected and analyzed for each KO.


title: Effect of mutating MpGLR on gene expression after wounding 1

city: Madrid

first: Enrique

last: Rojo

state: Madrid

address: Darwin 3

department: Plant Molecular Genetics

country: Spain

institute: CSIC

summary: To establish the role of the Glutamate Receptor-like gene in Marchantia polymorpha, MpGLR , in wound-induced gene expression changes, we compared the transcriptomes of plants that are wild type for MpGLR to the transcriptomes of Mpglr-9, a deletion mutant in MpGLR, analyzing samples from intact plants and from wounded plants, both from damaged tissues and from systemic undamaged tissues of wounded plants.

overall_design: To investigate the function of MpGLR in wound-induced gene expression changes, we generated the CRISPR-cas deletion mutant Mpglr-9. We then performed gene expression profiling analysis using data obtained from RNA-seq of intact plants and of wounded plants, both from damaged tissues and from systemic undamaged tissues of those wounded plants. Samples were collected 4 hours after wounding the plants, at which time  samples from intact plants were also collected. Plants were wounded by crushing two thallus lobes with serrated forceps (wounded tissues) while the adjacent undamaged lobes were collected as distal non-damaged tissues (systemic tissues). Three independent biological replicates of each sample were sequenced. Every independent biological replicate contained tissues from 9 plants.


title: The UFM1 System Alleviated Fatty Acid Oxidation and Chondrocyte Senescence via the UFMylation of CAVIN1

city: Hangzhou

first: Panyang

last: Shen

address: Qingchun road

department: Medical College

country: China

institute: Zhejiang University

summary: Osteoarthritis (OA) is a widespread age-related joint disease caused by the gradual loss of chondrocyte function along with age. Here, we found that UFMylation modification was lower-leveled in senescent cartilage, mediated chondrocyte senescence and OA phenotypes through targeting CAVIN1, which acted as a stimulator in chondrocyte senescence, mainly through promoting CPT1 expression and activating fatty acid β-oxidation (FAO). Physiologically, FAO was at a very low level in chondrocytes, while the anomalous activation of FAO accelerated chondrocyte senescence. UFMylation of CAVIN1 promoted its binding with TRIP12, leading to ubiquitination degradation. Therefore, UFMylation played a pivotal role in post-translationally modification of CAVIN1. Polymeric micellar nanoparticles (NPs) conjugated with UFM1 improved the stability of UFM1 recombinant protein (UFM1-rp), and extended the retention time of UFM1-rp in the mouse joint cavity. The administration of UFM1 into mouse joints using an advanced NP delivery system is effective in attenuating age-related pathogenesis. Therefore, we uncovered a previously unknown mechanism, UFM1-CAVIN1-CPT1 axis, in the protection of OA progression and constructed a new drug for OA treatment, and have provided important preliminary evidence toward the translation of our findings into clinical usage.

overall_design: Cartilage was obtained from 3 knee replacement patients, and the extracted chondrocytes were divided into two groups, one as a control group and the other as a CAVIN1 knockout group, with 3 biological replicates per group.

first: Shuying

first: Jianjun

last: Ma

first: Xing

last: Zhao


title: Effect of mutating MpGLR on gene expression after wounding II

summary: To establish the role of the Glutamate Receptor-like gene in Marchantia polymorpha, MpGLR , in wound-induced gene expression changes, we compared the transcriptomes of plants that are wild type for MpGLR to the transcriptomes of Mpglr-7, a deletion mutant in MpGLR, analyzing samples from intact plants and from wounded plants, both from damaged tissues and from systemic undamaged tissues of wounded plants.

overall_design: To investigate the function of MpGLR in wound-induced gene expression changes, we generated the CRISPR-cas deletion mutant Mpglr-7. We then performed gene expression profiling analysis using data obtained from RNA-seq of intact plants and of wounded plants, both from damaged tissues and from systemic undamaged tissues of those wounded plants. Samples were collected 2 hours after wounding the plants, at which time  samples from intact plants were also collected. Plants were wounded by crushing two thallus lobes with serrated forceps (wounded tissues) while the adjacent undamaged lobes were collected as distal non-damaged tissues (systemic tissues). Three independent biological replicates of each sample were sequenced. Every independent biological replicate contained tissues from 8 plants.


title: Analysis of local and systemic wound response in Marchantia polymorpha

summary: Transcriptional profiling of Marchantia polymorpha Takaragaike-1 wild-type genotype, in samples from intact plants (NW, non-wounded) and from wounded plants, both in locally damaged tissue (W, wounded) and in systemic non-wounded tissues of the damaged plants (SD, systemic tissues of damaged plants)

overall_design: Three-condition experiment, intact plants (NW), locally damaged tissue (W) and systemic non-wounded tissues of the damaged plants (SD).  Biological replicates: 2


title: The effect of EZH2 knockdown on gene expression in KDM6A-deficient KYSE180 cells following exposure to ionizing radiation [RNA-seq]

city: 蚌埠市

first: 嘉昊

last: 管

state: 安徽省

address: 安徽省蚌埠市龙子湖区凤阳东路536号4幢1单元1002

institute: 安徽医科大学第一附属医院

summary: To elucidate the mechanism by which EZH2 regulates the radiosensitivity of KDM6A-deficient ESCC cells, we established KYSE180-shEZH2 and control KYSE180-shluc cells.  48 hours after exposure to 6Gy IR, we performed gene expression profiling analysis using RNA-seq data from KYSE180-shEZH2 and control KYSE180-shluc.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for KYSE180-shEZH2 and and control KYSE180-shluc cell lines.

first: Guizhen

last: Pan

first: Yeye

last: Xia

first: Mengyu

last: Hao

first: Jiahao

last: Guan

first: Zhuting

last: Tong


title: Effect of IQGAP3 silencing on HaCaT keratinocytes under normal conditions or inflammatory cytokine stimulation

city: Moscow

first: Alena

middle: D

last: Zolotarenko

address: Gubkina street 3

country: Russia

institute: Vavilov Institute of General Genetics Russian Academy of Sciences

summary: Scaffold protein IQGAP3 mediates assembly of multiprotein complexes, orchestrating intracellular signaling pathways. Earlier we have found it to be overexpressed in lesional psoriatic skin. IQGAP3 is involved in cell proliferation and chemokine signaling that are key processes in psoriasis, so we decided to investigate the molecular basis of its role in psoriatic phenotype of keratinocytes. Transcriptome profiling of HaCaT keratinocytes allowed us to identify a wide range of psoriasis-associated pathways to be altered in IQGAP3-knockdown cells. NFkB signaling, EGFR signaling, p38/MAPK and ERK1/ERK2 activation, lipid metabolism and cytokine production as well as the response to the inflammatory cytokine stimulation were altered in the knockdown cells. Real-time analysis of cell growth revealed the alterations of proliferation and wound healing. The balance between proliferation and apoptosis of skin cells was altered, as well as the skin barrier functions and the production of IL-6 and IFNg. However, the diversity of the pathway alterations in the knockdown cells led us to the conclusion that IQGAP3 may not be the best target for the therapeutic inhibition to normalize the phenotype of keratinocytes in psoriasis.

overall_design: To investigate IQGAP3 roles in signal transduction and development of psoriatic phenotype of keratinocytes, we have knocked it down using shRNA and stimulated HaCaT_sh and HaCaT_ctrl lines with inflammatory cytokines  (IL17, TNFa, IFNg)

first: Sergey

last: Bruskin


title: Lats1/2 depletion in male sertoli cells

city: Saint-Hyacinthe

first: Nour

last: Abou Nader

state: Québec

address: 3200 rue sicotte

department: Biomédecine vétérinaire

country: Canada

institute: Université de Montréal

summary:
In order to understand the role of Hippo pathway in mice testes, we inactivated lats1/2 in a transgenic mouse model using the cre recombinase system in Sertoli cells.
RNAseq analysis on whole e15.5 testes were performed on male mice

overall_design: RNAseq gene expression profile for  WT (Lats1flox/flox;Lats2flox/flox) and KO mice adrenal glands (Lats1flox/flox;Lats2flox/flox;Amh-cre) (n=3/group)

first: Alexandre

last: Boyer


title: METTL3-mediated chromatin contacts promote phase separation during senescence [Mettl3-HiChIP-seq]

city: Houston

first: Yuan

last: Qi

state: TX

address: 1400 Pressler St

department: Bioinformatics & Computational Biology

country: USA

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

summary: Cellular senescence is a stable state of growth arrest that emerges as a response to stress. The methyltransferase complex (MTC) has been shown to facilitate the expression of the senescence-associated secretion phenotype (SASP) factors via genome-wide redistribution. However, whether and how MTC impacts on the three-dimensional (3D) chromatin organization and its functional implications during senescence remain largely unknown. Here we show that the MTC complex coordinates its enzymatic activity-dependent and -independent functions to enforce cellular senescence. Specifically, METTL3-mediated chromatin loops induce Hexokinase 2 (HK2) expression during senescence. The elevated HK2 expression subsequently promotes liquid-liquid phase separation (LLPS), manifesting as stress granules. These phase-separated stress granules act as reservoirs to sequester cell-cycle related mRNAs harboring polymethylated m6A sites, impeding their efficient translation. Overall, we uncover a mechanism by which senescent cells utilize phase-separated stress granules, facilitated by MTC-mediated HK2 activation, to sequester cell-cycle related mRNAs in governing senescence-associated stable growth arrest.

overall_design: METTL3 HiChIP-seq to monitor three-dimensional (3D) chromatin organization in control and senescent IMR90 cells.

first: Chen

last: Wang

first: Hideki

last: Tanizawa

first: Rugang

last: Zhong


title: A shared temporal program for ventral spinal cord progenitors [CaTS-RNA]

first: M Joaquina

last: Delas

overall_design: Mouse ES cell differentiation to spinal cord progenitors was sampled every two days from day 5 to day 11. Specific progenitors (p0-p1, p2 and pMN) were isolated and their chromatin accessibility or transcirption examined.

first: M

first: James

last: Briscoe

first: Isabel

last: Zhang


title: METTL3-mediated chromatin contacts promote phase separation during senescence [KAS-seq]

overall_design: KAS-seq to monitor transcriptional activation in control and senescent IMR90 cells with vector, METTL3, or METTL14 knockdown.


title: METTL3-mediated chromatin contacts promote phase separation during senescence [H3K27Ac-HiChIP-seq]

overall_design: H3K27Ac HiChIP-seq to monitor enhancer- and promoter-centered interactions in control and senescent IMR90 cells with vector, METTL3, or METTL14 knockdown.

first: Lu


title: Exploring the effects of DPP inhibition on the tumor immune landscape using RNAseq

city: Baltimore

first: Elana

middle: Judith

last: Fertig

state: MD

address: 670 W. Baltimore Street, 3rd floor

department: Institute for Genome Sciences

institute: University of Maryland, Baltimore

summary:
We examined the effects of an oral small molecule DPP inhibitor (BXCL701) on PDAC tumor
growth and tumor immune landscape using mT3-2D and Pan02 subcutaneous syngeneic murine models in C57BL/6 mice

overall_design: Exploration of the effects of DPP inhibition on the tumor immune landscape at different time points using RNAseq in C57BL/6 mice

first: Melanie

middle: L

last: Loth


title: To investigate the effects of NRF2 inhibitors (pyrimethamine and mitoxantrone) on gene expression in a human esophageal squamous cell carcinoma cell line (KYSE70)

city: Camden

first: Xiaoxin

middle: Luke

last: Chen

state: NJ

address: 403 Haddon Ave

institute: Coriell Institute for Medical Research

summary: To study the effects of NRF2 inhibitors (pyrimethamine or mitoxantrone) on human esophageal squamous cell carcinoma cells.

overall_design: 10 µM pyrimethamine or 20 nM mitoxantrone vs. control for 72 h.

first: Chorlada

last: Paiboonrungruang

first: Zhaohui

last: Xiong


title: Comparing  the transcriptomic responses of  Caenorhabditis elegans exposed to cadmium  from L1 to  L3 versus L1 to L4 stage

first: Stephen

last: Sturzenbaum

address: 150 Stamford Street

department: Analytical, Environmental and Forensic Sciences

institute: King's College London

summary: Cadmium is a naturally occurring heavy metal, and it is widely used in industry. Due to its persistent toxic effect, cadmium is classified as a category one human carcinogen. Its toxicity has been extensively studied in different organisms, including the nematode Caenorhabditis elegans. To investigate the transcriptomic responses following  cadmium during early life exposure, C. elegans larval were exposed either from L1 to L3 stage or L1 to L4 stage to 20 µM cadmium chloride. RNAseq was applied to identified the changes of the transcriptome and the pathways which are specific to each stage. Overall, the result revealed that the highest responsive genes in both exposure scenario were linked to oxidative stress, lipid metabolism and ion binding. Additionally, some of these genes are well characterized and linked to specific functions, but some have no known function, however these uncharacterized genes are differentially expressed in both stages as a result of cadmium toxicity.Numerous transcripts were identified in one stage but not at the other. Furthermore, a general trend was observed where a larger number of genes  were differentially expressed at L3 stage compared to L4, which suggest stage specific sensitivity   in response to cadmium exposure.

overall_design: The global transcriptome was compared in wild type (N2) nematodes which were cultured in the presence or absence of 20 μM of Cadmuim chloride for 27 and 47 hours from L1 stage to L3 stage or L1 to L4 stage.

first: Norah

last: Almutairi

first: Volker

last: Arlt


title: Combined transcriptome and miRNA-based analysis of the molecular mechanism of collection preference in Italian honey bees

city: Jinzhong

first: Lina

last: Guo

state: Shanxi

address: No.1, Mingxian South Road, Taigu District

institute: Shanxi Agricultural University

summary: A combined transcriptomic and miRNA-based analysis of the molecular mechanism of collection preference in Italian honey bees was conducted, mainly selecting the long-range sensor tentacles and the proximal sensor mouthparts.

overall_design: We then performed gene expression profiling using data obtained from RNA-seq of the tentacles and beaks of Italian honeybees from three experimental groups.


title: Endometrial gene expression differences in women with coronavirus disease 2019

city: Valencia

first: Patricia

last: Sebastian-Leon

state: Valencia

address: EDIFICIO BIOPOLO - LA FE, Avenida Fernando Abril Martorell, 106 - Torre A, Planta 1ª

department: Genomics and Systems Reproductive Medicine

institute: IVI-RMA Foundation

summary: Objective: To study the potential effect of COVID-19 on the endometrium of affected symptomatic women.  Design: Preliminary study of the endometrial transcriptomes in women with COVID-19 through RNA sequencing.  Setting: Hospital and university laboratories.  Subjects: Women with COVID-19 lacking SARS-CoV-2 infection in endometrial tissue.  Intervention/Exposure: Endometrial biopsy collection.   Main outcomes measures: Endometrial gene expression and functional analysis of patients with COVID-19 versus uninfected individuals.   Results: COVID-19 systemic disease alters endometrial gene expression in 75% of women, with patients exhibiting a preponderance of 163 up-regulated (e.g., UTS2, IFI6, IFIH1, BNIP3) and 72 down-regulated genes (e.g., CPZ, CDH3, IRF4) (FDR<0.05). A total of 161 dysregulated functions (36 up-regulated and 125 down-regulated) were typically enriched in COVID-19 endometria, including upregulation in pathways involved in response to virus and cytokine inflammation, highlighting upregulation of a COVID-19 response pathway.   Conclusion: COVID-19 affects endometrial gene expression despite the absence of SARS-CoV-2 particles in endometrial tissues.

overall_design: A total of 24 endometrial samples were collected for this study. Fourteen biopsies (COVID-19 group) came from COVID-19 patients hospitalized at Hospital Universitari i Politècnic La Fe (Valencia, Spain) (14); these patients had a positive result (cycle threshold, CT < 37) for SARS-CoV-2 infection indicated by real-time polymerase chain reaction (RT-PCR) of nasopharyngeal swabs. The other ten endometria (control group) were derived from patients with benign gynecological disorders not related to endometrium (negative result in a COVID-19 RT-PCR diagnostic test of nasopharyngeal swabs) of the same hospital. Then, samples with a good RNA quality (DV200 > 30%) were analyzed through RNA-seq to detect gene expression changes with an untargeted approach between both groups (COVID-19 and control). Finally, sequencing raw data were preprocessed, normalized, and functionally interpreted using bioinformatics procedures for reporting which genes and functions are altered in the endometrium due to the disease.

first: Lucía

last: de Miguel-Gómez

last: Sebastián-León

first: Mónica

last: Romeu

first: Nuria

last: Pellicer

first: Amparo

last: Faus

first: Antonio

last: Díaz-Gimeno

first: Irene

last: Cervelló


title: Foxp1 suppresses cortical angiogenesis and attenuates HIF-1alpha signaling to promote neural progenitor cell maintenance.

city: New York

first: Caroline

last: Pearson

state: NY

address: 1300 York Avenue

department: Brain and Mind Research Institute

institute: Weill Cornell Medicine

summary: To investigate the function of Foxp1 in the regulation of radial glial differentiation, we established Foxp1flox/flox;Emx1Cre mouse line in which Foxp1 is removed in cortical radial glia. We then performed gene expression profiling analysis using data obtained from bulk RNA-seq of 4 Cre negative controls and 2 mutants at E12.5.

overall_design: Comparative gene expression profiling analysis of bulk RNA-seq data for RNA extracted from Control and Foxp1cKO lateral cortex at E12.5.

first: Bennett

last: Novitch

first: Jessie

middle: E

last: Buth


title: Distribution of Small RNAs Along Transposable Elements in Vitis vinifera During Somatic Embryogenesis

city: Bari

first: Vitantonio

last: Pantaleo

address: Via Amendola 165/a

country: Italy

institute: Institute for Sustainable Plant Protection

summary: In the present study we have generated a parallel analysis of the 5' RNA ends  (PARE) referred to polyadenylated RNAs in somatic embryos from in vitro culture of immature anthers of Vitis vinifera. PARE analysis include also a shortRNA analysis of same material. We have submitted the sRNAseq to mirPROOF and miRCAT (srna_workbench software at http://srna-workbench.cmp.uea.ac.uk) in order to recognize known and putative novel miRNAs, respectively that could be present in somatic embryos. In addition, aRNAs and PARE libraries were integrated in order to identify those 5' RNA ends that could be explained by sRNAs (i.e. identify transcripts that could be cleaved by sRNAs). We have used publicly available annotations and we gained a deep insight into the gene families and the transcriptional regulation mediated by miRNAs in V. vinifera somatic embryos. Gene expression is finely regulated to specific paralogues in gene families such as the NADPH-dependent diflavin oxidoreductase, Phosphoserine aminotransferase, Ethylene-responsive transcription factors,  glutathione S-transferase par C, just to name a few. We have indeed characterized at least 4,000 mRNA targets. Size fractionated small RNA from total RNA extracts of somatic Embryos  cv. "Brachetto" were ligated to adapters, purified again and reverse transcribed. After PCR amplification the sample was subjected to Illumina high throughput pyrosequencing. The kit used is TrueSeq Small RNA kit, Illumina. Please see www.illumina.com for details of the sequencing technology. PARE libraries were generated starting from Poly(A) fraction. The protocol used have been previously described in German et al., 2009, Nature protocols. Please see www.illumina.com for details of the sequencing technology.

overall_design: Identification of regulatory non-coding RNAs in plant somatic embryos

first: Gambino

last: Giorgio

first: Szittya

last: Gyorgy

first: Pantaleo

last: Vitantonio


title: Imprinting of the neonatal gut epithelium by flagellated commensal bacteria

status: Public on Apr 21 2024

city: Aachen

first: Hieu

middle: Trong

last: Nguyen

address: Pauwelstrasse 30

department: Institut für Molekulare Medizin

country: Germany

institute: RWTH Aachen University Hospital

summary: Aim: Microbial colonization of the intestine in newborns is a critical event that regulates host physiology with lifelong consequences. However, there is a need to identify microbial molecules and mechanisms that play a role in this process. We aimed to elucidate the effects of flagellin, an important immunomodulatory component involved in bacterial motility, on intestinal epithelial functions. Methods: Germfree mice were colonized with synthetic bacterial communities, including a flagellated mouse gut isolate of Escherichia coli or a ΔfliC mutant thereof that lacks flagella. The offspring of these mice were studied at 7 days of age by single-cell RNA sequencing of epithelial cells isolated from the small intestine. Results: Enterococcus faecalis was the most dominant species in the small intestine of newborn mice. Blautia pseudococcoides was detected at low relative abundances. Colonization by either E. coli strain reduced the relative abundance of E. faecalis to 10% on average, and E. coli became the dominant member, with no substantial differences between mice colonized with the wildtype or mutant strain. The distribution of cell types within the small intestinal epithelium was skewed toward specialized cells (goblet, enteroendocrine, stem cells) at the expense of enterocytes in mice colonized with flagellated bacteria. These mice were characterized by higher expression of genes involved in cell-cell interactions (Npl, Epcam) and responses to infection (Ctsl) in enterocytes and enhanced translation (ribosomal proteins) in stem cells. In contrast, genes involved in lipid homeostasis (transport and metabolism; Apoc 2/4, Dgat2, Fabp 1/2, Mttp) in all cell types and inflammatory and androgen-related pathways in specialized cell types were less expressed in epithelial cells exposed to wildtype E. coli. Conclusion: These findings suggest that early life exposure to flagellated commensal bacteria influences cellular processes underlying tissue metabolism and remodeling in the small intestine.

overall_design: To investigate the effect of flagellin on intestinal epithelial functions, germfree mice were colonized with OMM9, OMM9+flagellated E. coli and OMM9+ E. coli mutant thereof that lacks flagella. The offspring of these mice were studied at 7 days of age by single-cell RNA sequencing of epithelial cells isolated from the small intestine.

first: Atscharah

last: Panyot

last: Trong Nguyen

first: Thomas

last: Clavel

first: Mathias

last: Hornef


title: Time-resolved function of cell polarity kinases PRKCZ and PRKCI in CNS myelination [snrna_oligo]

city: New Haven

first: Rieke-Marie

last: Hackbarth

state: CT

address: 300 Cedar St

department: Immunobiology

institute: Yale

summary: The atypical Protein Kinase C (aPKC) is a critical component of the PAR polarity complex, as well as of cell polarity in general. There are two paralogs of aPKC in the mammalian genome. Their expression pattern and functional role in oligodendrocyte lineage differentiation and development remains heretofore uncharacterized. Here we show that both paralogs of aPKC – PRKCI, the primary transcript of Prkci and PKMz, an alternate transcript of Prkcz – are expressed during oligodendrocyte differentiation, yet are functionally non-redundant. Asymmetric cell division and early specification of the oligodendrocyte fate stage required both paralogs. By contrast, the stage of oligodendrocyte maturation involving membrane polarization and myelination of axons continued to require PKMz, but no longer needed PRKCI. Taken together, our results indicate to a two-stage role of aPKCs and cell polarity in oligodendrocyte differentiation and development.

overall_design: To understand the effects of aPKC paralogs in OL lineage development, we performed single nucleus (sn)RNA-seq of  cerebral cortices from Control and Prkci f/f and Prkcz f/f mice crossed with Ng2-cre+ or Plp1-creERT+ at various time  points, using the 10X Genomics platform (3-4 biological replicates for each genotype) and injected some of them  with 4-OH Tamoxfien followed by cuprizone-mediated demyelination.

first: Maria

last: Mercau

first: Xinran

last: Liu

first: Haowei

last: Wang

first: Le

last: Zhang

first: Malay

middle: K

last: Basu

first: Carla

middle: V

last: Rothlin

first: Sourav

last: Ghosh


title: Interactions of strigolactone and karrikin signaling pathways on the levels of other phytohormones in rosette leaves of Arabidopsis

city: Changchun

first: Liangliang

last: Li

address: 4888 Shengbei Street, Kuancheng District

department: Northeast Institute of Geography and Agroecology

institute: Chinese Academy of Sciences

summary: To understand the combined role of SL and KAR signaling pathways in regulating levels and metabolism of other plant hormones, we performed the compare transcriptome profiling d14 kai2 and WT plants. Aligent´s whole Arabidopsis Gene Expression Microarray (G2519F-021169, V4, 4x44K) was used.

overall_design: Two-week-old WT and d14 kai2 mutant plants were transferred from GM plates to soil and grown for 10 additional day. The rosette leaves of this 24-d-old seedlings were harvested and frozen in liquid nitrogen immediately. Total RNA was prepared and used for the microarray hybridization. Three biological repeats were used for each plant for transcriptome analysis using the Arabidopsis Oligo 44K DNA microarray (Version 4.0, Agilent Technology).

first: Chenbo

last: Zhu

first: Kun

last: Xu

first: Yasuko

last: Watanabe

first: Maho

last: Tanaka

first: Motoaki

last: Seki

first: Keiichi

last: Mochida

first: Mikiko

last: Kojima

first: Hitoshi

last: Sakakibara

first: Kien

middle: H

first: Ha

last: Chu

first: Hengxia

last: Yin

first: Lam-Son

middle: P

last: Tran

first: Xiaojian

first: Weiqiang


title: Swd2/Cps35 determines H3K4 tri-methylation via interactions with Set1 and Rad6_Chromatin occupancy of Set1 in several strains

city: Chuncheon

first: Junsoo

last: Oh

country: South Korea

institute: Kangwon National University

summary: Histone H3K4 tri-methylation (H3K4me3) catalyzed by Set1/COMPASS, is a prominent epigenetic mark found in promoter-proximal regions of actively transcribed genes. H3K4me3 relies on prior monoubiquitination at the histone H2B (H2Bub) by Rad6 and Bre1. Swd2/Cps35, a Set1/COMPASS component, has been proposed as a key player in facilitating H2Bub-dependent H3K4me3. However, a more comprehensive investigation regarding the relationship among Rad6, Swd2 and Set1 is required to further understand the mechanisms and functions of the H3K4 methylation. We investigated the genome-wide occupancy patterns of Rad6, Swd2 and Set1 under various genetic conditions, aiming to clarify the roles of Set1 and Rad6 for occupancy of Swd2. Swd2 peaks appear on both 5’region and 3’region of genes, which are overlapped with its tightly bound two complexes, Set1 and CPF (Cleavage and Polyadenylation Factor), respectively. In the absence of Rad6/H2Bub, Set1 predominantly localized to the 5ʹ region of genes, while Swd2 lost all the chromatin binding. However, in the absence of Set1, Swd2 occupancy near the 5’region was impared and rather increased in the 3’ region. This study highlights that catalytic activity of Rad6 is essential for all the ways of Swd2’s binding to the transcribed genes and Set1 redistributes the Swd2 to 5’region for accomplishments of H3K4me3 in the genome-wide level.

overall_design:
Sample number (1) ~ (16): We performed a-Set1 ChIPseq with WT(1~2), Δset1(3~4), Δrad6(5~6), Δbre1(7~8), Sen1overexpressed WT(9~10), Sen1overexpressed Δswd2(11~12), 551WT(13~14), and 551Δbre1(15~16) strains. Experiments were performed in duplicates, and a-Set1 ChIPseq with Δset1 strain(3~4) was performed to reveal the background signal of the experiment.
Please note that each processed data file was generated from both replicates and is linked to the corresponding rep1 sample records.

first: Jung-Shin

last: Lee

first: Shinae

last: Park

first: Jueun

last: Kim

first: Eun-Jin

first: Yong-Joon

last: Cho


title: Time-resolved function of cell polarity kinases PRKCZ and PRKCI in CNS myelination [bulk_oligo]

first: Rieke-Marie

last: Hackbarth

overall_design: To understand the effects of aPKC paralogs in OL lineage development, we performed bulk RNA sequencing of cerebral cortices from Control and Prkci f/f and Prkcz f/f mice crossed with Ng2-cre+ at P30. (3-4 biological replicates for each genotype)

first: Maria

last: Mercau

first: Xinran

last: Liu

first: Haowei

last: Wang

first: Le

last: Zhang

first: Malay

last: Basu

first: Carla

last: Rothlin

first: Sourav

last: Ghosh


title: Swd2/Cps35 determines H3K4 tri-methylation via interactions with Set1 and Rad6_H3K4me3 ChIPseq in WT and several strains

summary: Histone H3K4 tri-methylation (H3K4me3) catalyzed by Set1/COMPASS, is a prominent epigenetic mark found in promoter-proximal regions of actively transcribed genes. H3K4me3 relies on prior monoubiquitination at the histone H2B (H2Bub) by Rad6 and Bre1. Swd2/Cps35, a Set1/COMPASS component, has been proposed as a key player in facilitating H2Bub-dependent H3K4me3. However, a more comprehensive investigation regarding the relationship among Rad6, Swd2 and Set1 is required to further understand the mechanisms and functions of the H3K4 methylation. We investigated the genome-wide occupancy patterns of Rad6, Swd2 and Set1 under various genetic conditions, aiming to clarify the roles of Set1 and Rad6 for occupancy of Swd2. Swd2 peaks appear on both 5’region and 3’region of genes, which are overlapped with its tightly bound two complexes, Set1 and CPF (Cleavage and Polyadenylation Factor), respectively. In the absence of Rad6/H2Bub, Set1 predominantly localized to the  5ʹ region of genes, while Swd2 lost all the chromatin binding. However, in the absence of Set1, Swd2 occupancy near the 5’region was impared and rather increased in the 3’ region. This study highlights that catalytic activity of Rad6 is essential for all the ways of Swd2’s binding to the transcribed genes and Set1 redistributes the Swd2 to 5’region for accomplishments of H3K4me3 in the genome-wide level.

overall_design:
Chromatin immunoprecipitation DNA sequencing (ChIP-seq) for histone modifications H3K4me3 in WT and several strains in Saccharomyces cerevisiae.
Please note that processed data file generated from both replicates is linked to the corresponding *rep1 sample records.


title: Postoperative risk of IDH mutant glioma-associated seizures and their potential management with IDH mutant inhibitors

city: Chicago

first: Lucas

last: Santana-Santos

state: IL

address: 710 N. Fairbanks Court, Olson 2-459

department: Pathology

institute: Northwestern University

summary: To investigate the peri-tumoral effect of IDHmut vs IDHwt glioma, we engrafted IDHmut or IDHwt mouse glioma intracranially in C57BL/6 mice.

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of peri-tumoral tissue at day 12 post-engraftment

first: Michael

last: Drumm

first: Craig

last: Horbinski


title: MiRNA sequencing revealed differentially expressed miRNAs in MHCC97H Hepatoma Cancers Cells exosomes Co-cultured with Xanthatin

city: Nantong

first: YU

last: WU

address: Nantong, 226001, PR China;

institute: Nantong Hospital of Traditional Chinese Medicine

type: Non-coding RNA profiling by high throughput sequencing

summary: Xanthatin is a natural sesquiterpene lactone isolated in the 1960s from Xanthium strumarium L., which has significant antitumor activity in a variety of cell lines implicated in cancers. High-throughput sequencing was performed on the exosomal miRNAs, and a set of miRNAs differentially expressed in Xanthatin-treated MHCC97H cells were obtained.

overall_design: Include 6 samples, 3 are exosomes of MHCC97H cell,another 3 are exosomes of MHCC97H cell co-incubated with Xanthatin.

first: Yu

last: Wu

first: Jie

first: Zhengying

last: Hua

first: Nong

last: Zhou


title: RIP sequencing in PANC-1 cells to map the YBX1-binding mRNA  of PANC-1 cells treated with CAF-derived Evs

status: Public on Apr 20 2024

city: Guangzhou

first: Chonghui

last: Hu

address: NA Zhongshan 2nd Road, Guangzhou

institute: Guangdong Provincial People’s Hospital

summary: Perineural invasion (PNI) is a unique biological feature of pancreatic cancer and is a key cause of pancreatic cancer metastasis, recurrence and poor postoperative survival, but its mechanism is largely unclarified. Clinical sample analysis and endoscopic ultrasonographic elasticity scoring indicated that cancer-associated fibroblasts (CAFs) are closely related to the occurrence of PNI. Furthermore, CAF-derived extracellular vesicles played an extremely important role in PNI in a dorsal root ganglion (DRG) coculture model and sciatic nerve model. Next, we demonstrated that CAFs promoted PNI via extracellular vesicle transmission of PNI-associated transcript (PIAT). To explored the potential mRNA interacted with YBX1, we we performed YBX1 RNA immunoprecipitation–sequencing (RIP-seq).

overall_design: PANC-1 cells were pretreated with CAFs-derived Evs and collected for YBX1 RIP-seq. Briefly, target antibodies were immobilized on protein A/G magnetic beads for 30 min at room temperature. Then cell lysate was added into the mixture and incubated overnight at 4 °C. Finally, the precipitated RNAs were purified for deep sequencing.

first: Shangyou

last: Zheng

first: Rufu

last: Chen


title: lncRNA profile of CAFs isolated from Pancreatic cancer

summary: Perineural invasion (PNI) is a unique biological feature of pancreatic cancer and is a key cause of pancreatic cancer metastasis, recurrence and poor postoperative survival, but its mechanism is largely unclarified. Clinical sample analysis and endoscopic ultrasonographic elasticity scoring indicated that cancer-associated fibroblasts (CAFs) are closely related to the occurrence of PNI. Furthermore, CAF-derived extracellular vesicles played an extremely important role in PNI in a dorsal root ganglion (DRG) coculture model and sciatic nerve model. To explore the lncRNA packaged in CAFs EVs, we conducted the lncRNA profile of CAFs isolated from pancreatic cancer

overall_design: CAFs were isolated from pancreatic cancer and collected for lncRNA-seq.


title: Expression data from SNU-449 cells transfected with USP48

city: Nanning

first: Bo

last: Tang

address: No. 6 Shuangyong Road

institute: The First Affiliated Hospital of Guangxi Medical University

summary:
Deubiquitinating enzymes (DUBs) are divided into seven subgroups based on sequence and structure and perform the roles of mediating the deubiquitination of substrate proteins, regulating protein function, and participating in various cellular life activities. Among them, the ubiquitin-specific protease family (USP) is the DUB subtype with the most members and structural diversity discovered so far. USP48 is a member of the USP family of ubiquitin-specific proteases and has been found to promote glioblastoma by deubiquitinating the Gli1 transcription factor and to promote the progression of non-small-cell lung cancer through inhibition of the Wnt/β-catenin signaling pathway.
We used microarrays to detail changes in gene expression regulated by USP48 overexpression in HCC cells.

overall_design: Alterations in gene expression were noted in SNU-449 cells that underwent stable transfection with USP48 overexpression, in comparison to SNU-449 cells transfected with a control empty vector.


title: mRNA profile of PANC-1 treated with CAF-derived Evs

summary: Perineural invasion (PNI) is a unique biological feature of pancreatic cancer and is a key cause of pancreatic cancer metastasis, recurrence and poor postoperative survival, but its mechanism is largely unclarified. Clinical sample analysis and endoscopic ultrasonographic elasticity scoring indicated that cancer-associated fibroblasts (CAFs) are closely related to the occurrence of PNI. Furthermore, CAF-derived extracellular vesicles played an extremely important role in PNI in a dorsal root ganglion (DRG) coculture model and sciatic nerve model. Next, we demonstrated that CAFs promoted PNI via extracellular vesicle transmission of PNI-associated transcript (PIAT). To determine how CAF EVs exert its function, we performed mRNA sequencing on PANC-1 treated with CAFs-derived EVs

overall_design: PANC-1 cells were pretreated with CAFs-derived Evs and collected for mRNA-seq.


title: Swd2/Cps35 determines H3K4 tri-methylation via interactions with Set1 and Rad6_Chromatin occupancy of Rad6 and Swd2 in several strains.

first: Junsoo

last: Oh

overall_design: Sample number (1) ~ (5): We performed a-HA ChIPseq with strains expressing Swd2-3HA at its chromosomal locus in wildtype or ∆rad6 background to identify the chromatin occupancy of Swd2-3HA by the presence or absence of Rad6. Experiments were performed in duplicates, and we performed a-HA ChIPseq with a yeast strain without any epitope tag ((5)Notag) to reveal the background signal of the experiment. Sample number (6) ~ (12): We performed a-Myc ChIPseq with strains expressing Rad6-9Myc at its chromosomal locus in wildtype to identify the chromatin occupancy of Rad6-9Myc. Also, we performed a-Myc ChIPseq with yeast strains expressing Swd2-3HA and Rad6-9Myc (or Rad6-C88A-9Myc) at its chromosomal loci to identify the change of the chromatin occupancy of Rad6-9Myc by the catalytic activity of Rad6. Experiments were performed in duplicates, and we performed a-Myc ChIPseq with a yeast strain without any epitope tag ((12)Notag) to reveal the background signal of the experiment. Sample number (13) ~ (21): We performed a-HA ChIPseq with yeast strains expressing Swd2-3HA and Rad6-9Myc (or Rad6-C88A-9Myc) at its chromosomal loci to identify the change of the chromatin occupancy of Swd2-3HA by the catalytic activity of Rad6. Also, we performed a-HA ChIPseq with strains expressing Swd2-6HA at its chromosomal locus in wildtype or ∆set1 background to identify the change of chromatin occupancy of Swd2-6HA by the presence or absence of Set1. Experiments were performed in duplicates, and we performed a-HA ChIPseq with a yeast strain without any epitope tag ((21)Notag) to reveal the background signal of the experiment.

first: Jung-Shin

last: Lee

first: Shinae

last: Park

first: Jueun

last: Kim

first: Eun-Jin

first: Yong-Joon

last: Cho


title: RNA sequencing of bacterial samples under salt stress [CL3]

city: Noida

first: Rajnish

middle: Prakash

last: Singh

address: A 10, A Block, Block A, Industrial Area, Sector 62, Noida

country: India

institute: Jaypee Institute of Information Technology

summary: This study aimed to investigate the survival of an environmental isolate under salt stress and to identify the various genes involved in stress protection following RNA sequencing analysis. The obtained results provide new targets that will allow understanding the in-depth mechanisms involved in the adaptation of bacteria to salt stress.

overall_design: The RNA sequencing of bacterial samples was performed with (8% salt stress) and without salt stress.

first: R


title: RNA sequencing of bacterial samples under salt stress [CL2]


title: Gene expression profiling by adenoviral CYB5R3 overexpression in non-small cell lung cancer (NSCLC) cell line, NCI-H1299

city: Daejeon

first: Misun

last: Won

address: 125 Kwahag-ro, Yuseong-gu

department: Personalized Genomic Medicine Research Center

institute: Korea Research Institute of Bioscience and Biotechnology

summary: To investigate the tumor suppressor roleof CYB5R3 in lung cancer, we infected with adenoviral empty vector (EV) or CYB5R3 in NCI-H1299 cells.

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of 3 different cells. Comparative gene expression profiling analysis of RNA-seq data for NCI-H1299 cells (PBS, adenoviral EV, adenoviral CYB5R3).

first: Joo-Young

last: Im


title: RNA sequencing of bacterial samples


title: Expression data from breast cancer cell line 4T1

city: Nanjing

first: Xinyue

last: Gu

address: Chunhua Street

institute: China pharmaceutical university

summary:
MiR-9 plays an irreplaceable role in regulating the progression of breast cancer. In order to study the role of miR-9 in promoting MDSC recruitment in the tumor microenvironment, we need to explore the genetic process of miR-9 regulation.
We used microarrays to detail the global program of miR-9 down-regulated gene expression and identified different categories of regulated genes in this process.

overall_design: A breast cancer cell line with stable knockdown of miR-9 was constructed by lentivirus infection for RNA extraction and Affymetrix microarray hybridization. The experimental group and the control group were repeated 3 times.


title: Enfortumab Vedotin Induces Immunogenic Cell Death and Shows Enhanced Preclinical Antitumor Activity When Combined With a PD-1 Inhibitor

status: Public on Apr 19 2024

city: Bothell

first: John

last: Gosink

email: john@gosink.org, john.gosink@pfizer.com

state: WA

department: Computational Biology

institute: Pfizer

summary: Enfortumab vedotin is a Nectin-4-directed antibody–drug conjugate designed to deliver the microtubule-disrupting agent monomethyl auristatin E (MMAE) in tumor cells. Using preclinical models of urothelial cancer (UC), we expand the understanding of the multifaceted mechanism of action for enfortumab vedotin that includes direct cytotoxicity on Nectin-4–positive tumor cells, indirect bystander effect on neighboring Nectin-4–negative tumor cells, and MMAE-mediated induction of immunogenic cell death (ICD) and associated increase in activated immune cells in the tumor microenvironment. Importantly, vaccination with enfortumab vedotin-treated tumor cells drives antitumor immunity and provides protection against rechallenge in mice. MMAE-mediated ICD induction modulates the tumor microenvironment in a complementary manner to immune checkpoint inhibition. Accordingly, enfortumab vedotin plus PD-1 inhibitor shows enhanced antitumor activity in vivo. These preclinical results demonstrate the underlying mechanisms consistent with the significantly improved clinical outcomes observed for enfortumab vedotin plus pembrolizumab relative to chemotherapy in the first-line treatment of la/mUC.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: T24-hNectin-4 cells were cultured as described and resuspended in 50% Matrigel before subcutaneous injection of 5×106 T24-hNectin-4 xenograft tumor cells (0.1 mL volume) in the flanks of athymic nude female mice (Envigo, BALB/cAnNHsd). Tumor pieces were passaged via trocar needle two times to establish consistent engraftment. On Day 15 post implantation, tumor volumes reached ~200 mm3 (calculated using 0.5 × [length] × [width]2), and the mice were treated with a single intraperitoneal (IP) dose of 3 mg/kg enfortumab vedotin. As a control, mice were treated with 3 mg/kg IgG-MMAE. Tumors were harvested 5 days after treatment and processed for RNA-seq (Illumina HiSeq platform),

first: Devra

last: Olson

first: Patrick

last: Younan

first: Bernard

middle: A

last: Liu

first: Gabriele

last: Blahnik-Fagan

first: Katie

last: Snead

first: Elena

last: Tenn

first: Kelly

last: Hensley

first: Disha

last: Saheytya

first: Albina

last: Nestrerova

first: Margo

last: Zaval

first: Anthony

last: Cao

first: Christine

last: O'Day

first: Ryan

last: Heiser

first: Timothy

middle: S

last: Lewis

first: Shyra

last: Gardai

first: Taisuke

last: Nakazawa

first: Masashi

last: Shimazaki

first: Christopher

last: Carosina

first: Sharsti

last: Sandall


title: A Novel Approach to Generate Enzyme-free Single Cell Suspensions from archived Tissues for miRNA Sequencing

city: Saarbrücken

first: Annika

last: Engel

state: Saarland

address: Campus E2 1

department: Center for Bioinformatics

institute: Saarland University

summary: Obtaining high-quality omics data at the single-cell level from archived human tissue samples is crucial for gaining insights into cellular heterogeneity and pushing the field of personalized medicine forward. In this technical brief we present a comprehensive methodological framework for the efficient enzyme-free preparation of tissue-derived single cell suspensions and their conversion into single-cell miRNA sequencing libraries. The resulting data from this study have the potential to deepen our understanding of miRNA expression at the single-cell level and its relevance in the context of the examined tissues. The workflow encompasses tissue collection, RNALater immersion, storage, thawing, TissueGrinder-mediated dissociation, miRNA lysis, library preparation, sequencing, and data analysis. Quality control measures ensure reliable miRNA data, with specific attention to sample quality. The UMAP analysis reveals tissue-specific cell clustering, while miRNA diversity reflects tissue variations. The presented workflow effectively processes preserved tissues, extending opportunities for retrospective analyses and biobank utilization.

overall_design: Single-cell miRNA sequencing method for archived human tissues

first: Stefan

last: Scheuermann

first: Sarah

last: Hücker

first: Nicole

last: Ludwig

first: Philipp

last: Lebhardt

first: Jens

last: Langejürgen

last: Kirsch


title: m5C MeRIP sequencing in PANC-1 cells to map the m5C methylome of PANC-1 cells treated with CAF-derived Evs

first: Chonghui

last: Hu

type: Methylation profiling by high throughput sequencing

summary: EV-packaged PIAT mediates EGR1, NTRK1 and SMAD7 mRNA stability in a YBX1-dependent manner. To explore whether YBX1 enhances EGR1, NTRK1 and SMAD7 mRNA stability in an m5C-dependent manner, we conducted m5C-seq in PANC-1 cells to map the m5C methylome of PANC-1 cells treated with CAF-derived EVs.

overall_design: PANC-1 cells were pretreated with CAFs-derived Evs and collected for m5C MeRIP-seq. Briefly, m5C RNA immunoprecipitation was performed with the GenSeqTM m5C RNA IP Kit (GenSeq Inc., China) by following the manufacturer’s instructions. Both the input samples without immunoprecipitation and the m5C IP samples were used for RNA-seq library geneMouseion with NEBNext® Ultra II Directional RNA Library Prep Kit (New England Biolabs, Inc., USA). The library quality was evaluated with BioAnalyzer 2100 system (Agilent Technologies, Inc., USA). Library sequencing was performed on an illumina Novaseq 6000 instrument with 150bp paired-end reads.

first: Shangyou

last: Zheng

first: Yu

last: Zhou

first: Rufu

last: Chen


title: Interaction with Myeloma Suppresses Ciliogenesis and osteogenesis of Bone Marrow Stromal Cells

city: Tianjin

first: Zhiqiang

last: Liu

address: 22 Qixiangtai Rd

department: Pathophysiology

institute: Tianjin Medical University

summary: Impaired bone marrow stromal cells (BMSCs) within the bone niche of multiple myeloma (MM) patients are implicated in the development of myeloma bone disease (MBD) and disease progression. However, the specific mechanisms are not yet fully understood.

overall_design: Examination of differentially expressed genes in human BMSCs cocultured with myeloma cells.

first: Ying

last: Xie

first: Zhaoyun


title: HDGFR2 regulates osteogenic differentiation by balancing histone crotonoylation and acetylation modifications [RNA-Seq]

summary: Epigenetics regulates the expression of osteogenic genes and mediates the osteogenic differentiation of MSCs. It was found that hepatoma-derived growth factor (HDGFR2) is a histone methylated reader protein, which can recognize histone methylation modification and play an important "switch" role in gene transcriptional regulation. It is unclear whether HDGFR2 is involved in bone formation studies. Our study aims to investigate the effect of HDGFR2 on osteogenic differentiation and provide evidence for BMSCs as seed cells for tissue regeneration. We found that compared with the wild-type (WT) mice, the bone mass of the femur and the root furcation bone in HDGFR2-KO mice was significantly elevated to attenuate age-related bone loss. Compared with the BMSCs in WT mice, the cloning and osteogenic differentiation of BMSCs in HDGFR2-KO mice were significantly accelerated, and vice versa when HDGFR2 was overexpressed. GO analysis suggested that differential genes were mainly involved in osteoblast differentiation, ossification, collagen fiber tissue and mineralization. The bone defect repair ability of HDGFR2-KO mice was significantly enhanced compared to the control group. Moreover, the depletion of HDGFR2 suppressed periodontal bone loss. The HDGFR2 interacts with the active regulator of SIRT1 (AROS) and sirtuin family deacetylases to form a chromatin remodeling complex, and AROS regulated osteogenesis through combining with HDFGR2. The decreased ratio of H3K18 crotonylation to acetylation improved the transcription of osteogenic genes in HDGFR2 knockout BMSCs. Taken together, these data demonstrated that the knockdown of HDGFR2 could promote osteogenic differentiation and bone repair, providing a new theoretical basis for bone tissue regeneration.

overall_design: To examine transcriptome profiles in the BMSCs from the WT and HDGFR2-KO mice.

first: Meilin

first: Yixuan

last: Wang


title: HDGFR2 regulates osteogenic differentiation by balancing histone crotonoylation and acetylation modifications [Cut & Tag]

summary: Epigenetics regulates the expression of osteogenic genes and mediates the osteogenic differentiation of MSCs. It was found that hepatoma-derived growth factor (HDGFR2) is a histone methylated reader protein, which can recognize histone methylation modification and play an important "switch" role in gene transcriptional regulation. It is unclear whether HDGFR2 is involved in bone formation studies. Our study aims to investigate the effect of HDGFR2 on osteogenic differentiation and provide evidence for BMSCs as seed cells for tissue regeneration.

overall_design: Examination of histone modification in WT and HDGFR2 knockoout BMSCs


title: GFPT2 knockdown effects on the tumor immune microenvironment though scRNA-seq

first: Jiawen

last: Cui

state: Jiangsu

address: TongJiaXiang #24

institute: China Pharmaceutical University

summary: Through comprehensive genetic and pharmacological analyses across various models, we have identified glutamine fructose-6-phosphate transaminase 2 (GFPT2) as a key facilitator of immune evasion in EGFR-mutated NSCLC. GFPT2 escalates the expression and glycosylation of PD-L1, PVR and CD276, bolstering their interactions with CD8+T cells, and amplifies CD73 glycosylation, thereby intensifying adenosine-mediated CD8+T cells suppression. These actions collectively reduce tumor cell vulnerability to CD8+T cell-mediated death. Moreover, GFPT2 regulates EGFR glycosylation, which consequentially modulates the EGFR-dependent secretion of CXCL10 and VEGF, thus impeding CD8+T cell infiltration within tumors.

overall_design: We performed the scRNA-seq analysis of 2 lung tumor tissues based on the 10X Genomics platform to investigate tumor immune microenvironment and cell-cell communication, using the shRNA to knock down GFPT2.

first: Luyao

last: Ao

first: Wenjing

last: Jia

first: Qixing

last: Gong


title: Kidney single cell sequencing results from 10-day unilateral ureteral obstruction mice

city: Fuzhou

first: Zhimin

address: Chazhong Road NO.20

institute: the First Affiliated Hospital, Fujian Medical University, Fuzhou

summary: Renal fibrosis is a common consequence of various progressive nephropathies, including obstructive nephropathy, and ultimately leads to kidney failure. Infiltration of inflammatory cells is a prominent feature of renal injury after draining blockages from the kidney, and correlates closely with the development of renal fibrosis. However, the underlying molecular mechanism behind the promotion of renal fibrosis by inflammatory cells remains unclear. Herein, we showed that unilateral ureteral obstruction (UUO) induced Gasdermin D (GSDMD) activation in neutrophils, abundant neutrophil extracellular traps (NETs) formation and macrophage-to-myofibroblast transition (MMT) characterized by α-smooth muscle actin (α-SMA) expression in macrophages. Gsdmd deletion significantly reduced infiltration of inflammatory cells in the kidneys and inhibited NETs formation, MMT and thereby renal fibrosis. Chimera studies confirmed that Gsdmd deletion in bone marrow-derived cells, instead of renal parenchymal cells, provided protection against renal fibrosis. Further, specific deletion of Gsdmd in neutrophils instead of macrophages protected the kidney from undergoing fibrosis after UUO. Single-cell RNA sequencing identified robust crosstalk between neutrophils and macrophages. In vitro, GSDMD-dependent NETs triggered p65 translocation to the nucleus, which boosted the production of inflammatory cytokines and α-SMA expression in macrophages by activating TGF-β1/Smad pathway. In addition, we demonstrated that caspase-11, that could cleave GSDMD, was required for NETs formation and renal fibrosis after UUO. Collectively, our findings demonstrate that caspase-11/GSDMD-dependent NETs promote renal fibrosis by facilitating inflammation and MMT, therefore highlighting the role and mechanisms of NETs in renal fibrosis.

overall_design: Harvested cells at the required densities were combined with gel beads  containing the barcoded information along with a mixture of cells and  enzymes. Oil surfactant droplets in a microfluidic double-cross system were used for encapsulation to generate Gel Beads-In-Emulsions (GEMs). GEMs were passed through a reservoir and collected while the gel beads were lysed to release the barcode sequence. The cDNA fragment was then reverse transcribed before the sample was labeled. The gel beads and the oil droplets are ruptured and PCR amplification was performed using the generated cDNA as a template. The products of all GEMs were mixed and a standard sequencing library is constructed. The cDNA was first enzymatically digested into fragments of about 200300 base pairs (bp), together with the library building process of traditional secondgeneration sequencing such as sequencing junction and primers. Finally, the DNA library was generated by PCR amplification

first: Yanfang

last: Xu


title: A Repressive Type of TEAD4 Condensation and Engineering a Glue Peptide Therapy Against Cancer [Cut&Tag]

city: shanghai

first: yang

last: tang

address: Yueyang Road 320

institute: Shanghai Institute of Biochemistry and Cell Biology

summary: Transcriptional factors (TFs) act as central determinants to coordinate cell death and survival by differentially modulating gene expression. Here, we systematically identified many TFs including TEAD4 forming condensates in stressed cells. In sharp contrast to YAP-induced transcription-activating condensation of TEAD4, we found co-factors such as VGLL4 and RFXANK could alternatively induce repressive condensation of TEAD4 to trigger cell death. Illustrated by VGLL4, we mechanistically revealed that the heterotypic interactions between TEAD4 with VGLL4 favors its oligomerization and assembly of large condensates to manifest a nonclassical inhibitory function of this transcription factor, i.e., causing DNA/chromatin to be aggregated and entangled, which eventually impede gene expression. Based on these findings, we engineered a linker peptide (GLUP) to selectively “glue” TEAD4 molecules together, therefore forcefully driving its repressive condensation against YAP-induced activation. This glue peptide displayed a strong antitumor effect via inhibition of TEAD4-related gene transcription. Collectively, this work revealed a new type of phase separation, i.e., repressive condensation of TFs, and revealed how cofactor-induced differential condensation orchestrate opposite functions of a given TF, and further developed a new class of antitumor strategy by artificially inducing repressive condensation.

overall_design: Cut&Tag assay for TEAD4 antibody in HGC-27 cells treated with or without GLUP peptide

first: Yang

last: Tang

first: Liwei

last: An

first: Hui

last: Zhang


title: A Repressive Type of TEAD4 Condensation and Engineering a Glue Peptide Therapy Against Cancer [RNA-Seq_TEAD4KO]

overall_design: To investigate the function of GLUP peptide in cancer, we perform RNA-Seq anlysis to find the altered pathway in this GLUP-treated group. To test the specificity of GLUP peptide, we also perform RNA-Seq anlysis  in WT and TEAD4 knockout cell with or without GLUP treatment.


title: AML1-ETO and CCND2 overexpression¬ cooperate to drive acute myeloid leukemia initiation and progression

first: junli

last: mou

address: Nanjing Road 288

institute: Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College

summary: Increasing numbers of clinical cohorts have detected CCND2 mutations in acute myeloid leukemia (AML), especially in the subtype of AML with t(8;21) translocation. As known, this AML subtype is characterized by the formation of AML1-ETO fusion gene. However, AML1-ETO fusion gene alone is not sufficient to drive leukemia development, additional mutations are required for leukemogenesis. Here, we aim to investigate whether mutated CCND2 can cooperate with AML1-ETO fusion gene to drive leukemia initiation and progression.  In our previous study, the conditional AML1-ETO knock-in mouse model (AML1/ETO mouse), which represented a pre-leukemia stage as myeloproliferative neoplasm phenotype, was established. To confirm whether the AML1-ETO and CCND2 mutation can cooperate to drive leukemia, the mice transduction and transplantation model harboring both AML1-ETO and CCND2 gene (both wildtype and mutant) were established. Upon the assessment of the phenotype, biological features and survival of the mice, only the mice overexpressing the AML1-ETO and CCND2 simultaneously were eventually progressed to leukemia. Besides, compared to mice overexpressing AML-ETO gene alone, mTOR and cell cycle-related pathways were significantly enriched in mice harboring both AML1-ETO and CCND2. And the selective mTOR inhibitor, Everolimus, can reduce the leukemia burden and prolong the survival of this group of mice. In conclusion, we confirmed that introduction of the CCND2 gene into the AML/ETO pre-leukemia mice can trigger the development of leukemia. We also confirmed that CCND2 overexpression resulted in the upregulation of the mTOR pathway and inhibiting the pathway may be a therapeutic agent for this subtype of leukemia.

overall_design: In our previous study, the conditional AML1-ETO knock-in mouse model (AML1/ETO mouse), which represented a pre-leukemia stage as myeloproliferative neoplasm (MPN) phenotype), was established (data unpublished), and the AML1-ETO fusion gene was fused with an mCherry tag. The coding sequences of wild type (CCND2wt) and mutated type (CCND2mut, Thr280Ala) were cloned into the retroviral vector MSCV-IRES-EGFP respectively. Then the corresponding viruses were generated and used to infect the AML1/ETO mouse  fetal liver cells, which were harvested from the embryos  at day 12.5 (E=12.5). 1×105 mCherry+ GFP+ cells were injected into lethally irradiated C57BL/6 mice through tail vein with supportive cells. All the mice were divided into three groups and, which was named with Vector (MSCV-IRES-EGFP, Vec hereinafter), CCND2wt (MSCV-IRES-CCND2wt-EGFP), CCND2mut (MSCV-IRES-CCND2mut-EGFP), respectively. The survival curve and biological characteristics of the three groups of mice were then monitored.

first: Junli

last: Mou

first: Qianqian

last: Huang

first: Xiaoyu

first: Wenbing

first: Yu

first: Yihan

last: Mei

first: Runxia

last: Gu

first: Yingxi

first: Kejing

first: Haiyan

last: Xing

first: Qing

last: Rao

first: Min

first: Shaowei

last: Qiu

first: Jianxiang


title: The estrogen and androgen responses in the immortalized human prostate cancer cell line VCaP

city: Québec

first: Étienne

last: Audet-Walsh

address: 2705, boulevard Laurier

institute: CRCHU de Québec

summary: The aim of the study was to identify the genes regulated by the estrogen receptor alpha (ERa) in a human prostate cancer cell line (VCaP), with and without the co-activation of the oncogene AR (androgen receptor).

overall_design: Twelve VCaP cell line samples have been treated with either Ethanol (control), 17β-Estradiol, R1881 (metribolone, a synthetic androgen), or both Estradiol and R1881. Each condition has been done in triplicates and sequenced using Illumina NovaSeq 6000.

first: Camille

last: Lafront

first: Lucas

last: Germain


title: An exosomal circRNA signature in the diagnosis and prognostification of cholangiocarcinoma: circRNA microarray analysis for 10 human bile samples

city: Chengdu

first: Ningyuan

last: Wen

address: No.37 GuoXueXiang, Wuhou district, Chengdu, China

institute: West China Hospital, Sichuan University

type:
Expression profiling by array
Non-coding RNA profiling by array

summary: We have completed the Arraystar Human circRNA Array V2 analysis of 10 bile exosome samples (5 cholangiocarcinoma-induced biliary obstruction vs. 5 benign biliary obstruction). Total RNA from each sample was quantified using the NanoDrop ND-1000. The sample preparation and microarray hybridization were performed based on the Arraystar’s standard protocols. Briefly, total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs. Then, the enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar). The labeled cRNAs were hybridized onto the Arraystar Human circRNA Array V2 (8x15K, Arraystar). After having washed the slides, the arrays were scanned by the Agilent Scanner G2505C.      Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the R software limma package. Differentially expressed circRNAs with statistical significance between two groups were identified through Volcano Plot filtering. Differentially expressed circRNAs between two samples were identified through Fold Change filtering. Hierarchical Clustering was performed to show the distinguishable circRNAs expression pattern among samples.

overall_design:
Exosomal circRNA from 10 human bile samples (5 cholangiocarcinoma vs. 5 bile duct stones) were analysed using circRNA microarry.
contributor: KangChen Services

first: Dingzhong

last: Peng

first: Jiong

last: Lu

first: Bei

last: Li


title: A Repressive Type of TEAD4 Condensation and Engineering a Glue Peptide Therapy Against Cancer [RNA-Seq399]

first: yang

last: tang

overall_design: To investigate the function of GLUP peptide in cancer, we perform RNA-Seq anlysis to find the altered pathway in this GLUP-treated group.

first: Yang

last: Tang

first: Liwei

last: An

first: Hui


title: The reprogrammation of the estrogen and androgen responses in murine prostate cancer

summary: The first aim of the study was to identify the genes regulated by the estrogen receptor alpha (ERa) in the normal mouse prostate, with and without the co-activation of the androgen receptor. The second objective was to decipher the changes in the estrogen and androgen responses in a tumoral context from prostate cancer-developping mice.

overall_design: Sixteen normal prostate and 14 prostate cancer from mice have been collected, and treated with either Vehicle (control), 17β-Estradiol, Testosterone or a combination of both 17β-Estradiol and Testosterone. There were at least three replicates per condition, and samples were sequenced using Illumina NovaSeq 6000.


title: Epigenetic age oscillates during the day (Neu 54 yr old)

city: Vilnius

first: Karolis

last: Koncevičius

address: Saulėtekio al. 7

department: Institute of Biotechnology, Life Sciences Center

country: Lithuania

institute: Vilnius University

summary: Since their introduction, epigenetic clocks have been extensively used in aging and human disease research. In this study, we reveal an intriguing pattern: epigenetic age predictions display a 24-hour periodicity. These paradoxical age oscillations can be attributed to variations in blood cell type composition and epigenomes, both of which demonstrate circadian rhythmicity. This discovery emphasizes the significance of factoring-in the time of day to obtain accurate estimates of epigenetic age.

overall_design: Peripheral blood samples were collected continuously every 3 hours for 24 hours from a 54 year old caucasian male. Collection started at circadian time 9 (CT9), corresponding to 9AM local time. Methylation profile obtained using Illumina Infinium EPIC Human Methylation Beadchip. The microarray experiment was performed in technical triplicates. Sample Neu54yo_ZT21_replicate2 was removed as outlier during the analysis and is not included in the processed data.

first: Akhil

last: Nair

first: Aušrinė

last: Šveikauskaitė

first: Agnė

last: Šeštokaitė

first: Auksė

last: Kazlauskaitė

first: Audrius

last: Dulskas

first: Artūras

last: Petronis


title: Epigenetic age oscillates during the day

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

overall_design: Refer to individual Series


title: Tumor immune dysfunction and exclusion subtypes in bladder cancer and pan-cancer: a novel molecular subtyping strategy and immunotherapeutic prediction model

city: Xuhui District

first: Kun

last: Zheng

state: Shanghai

address: No. 600, Yishan Road, Xuhui District, Shanghai

department: Department of Urology

institute: Shanghai 6th Peoples Hospital Affiliated to Shanghai Jiao Tong University

summary: Molecular subtyping is expected to enable bladder cancer (BC) precise treatment. However, reliable subtyping strategies for clinical application remains defective and controversial. Given the significance of tumor immune dysfunction and exclusion (TIDE) in tumor immune escape and immunotherapy, we aimed to develop a novel TIDE-based subtyping method to facilitate personalized management. Transcriptome data of BC was used to evaluate the heterogeneity and the status of TIDE patterns. We identified 69 TIDE biomarker genes and classified BC samples into three subtypes using consensus clustering. Subtype I showed the lowest TIDE status and malignancy with the best prognosis and highest sensitivity to immune checkpoint blockade (ICB) treatment, which was enriched of metabolic related signaling pathways. Subtype III represented the highest TIDE status and malignancy with the poorest prognosis and resistance to ICB treatment, resulting from its inhibitory immune microenvironment and T cell terminal exhaustion. Subtype II was in a transitional state with intermediate TIDE level, malignancy, and prognosis. We further confirmed the existence and characteristics of our novel TIDE subtypes using real-world BC samples. This subtyping method was proved to be more efficient than previous known methods in identifying non-responders to immunotherapy. We also propose that combining our TIDE subtypes with known biomarkers can potentially improve the sensitivity and specificity of these biomarkers. Moreover, besides guiding ICB treatment, this classification approach can assist in selecting the frontline or recommended drugs. Finally, we confirmed that the TIDE subtypes are conserved across the pan-tumors. In conclusion, our novel TIDE-based subtyping method can serve as a powerful clinical tool for BC and pan-cancer patients, and potentially guiding personalized therapy decisions for selecting potential beneficiaries and excluding resistant patients of ICB therapy.

overall_design: After obtaining patient consent and approval from the institutional research ethics committee, we collected 31 surgical resection samples of bladder tumors from 20 patients who hospitalized in the Department of Urology, Shanghai Sixth People's Hospital. For all resected tumor samples, we invited pathology experts to review the samples for accurate pathological diagnosis of the patients. All tumor samples were collected within 5 minutes after excision and immediately placed in liquid nitrogen for preservation. Subsequently, they were operated for bulk RNA sequencing (LY dataset) to validate the TIDE subtypes. RNA quality was measured with Bioanalyzer 2100 system and RNA Nano 6000 Assay Kit. mRNA was purified from total RNA with magnetic beads with poly-T oligos. mRNA was fragmented with divalent cations and high temperature. First and second strand cDNA were made with random primers, M-MuLV Reverse Transcriptase (RNase H-), DNA Polymerase I and RNase H. cDNA ends were polished and adenylated. Adaptor with hairpin loop structure was ligated to cDNA. cDNA fragments of about 370~420 bp were selected with AMPure XP system. PCR was done with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. PCR products were cleaned with AMPure XP system and library quality was checked with Agilent Bioanalyzer 2100 system. Index-coded samples were clustered with cBot Cluster Generation System and TruSeq PE Cluster Kit v3-cBot-HS (Illumia). Libraries were sequenced on Illumina Novaseq platform and 150 bp paired-end reads were obtained. Raw data of fastq format were processed with fastp software. Reads with adapter, ploy-N and low quality were removed. Clean data were obtained and Q20, Q30 and GC content were calculated. Reference genome and gene model annotation files were downloaded from genome website. Reference genome index was built with Hisat2 v2.0.5. Clean reads were aligned to reference genome with Hisat2 v2.0.5. Gene model annotation file was used by Hisat2 to make splice junctions database and get better mapping result. Mapped reads were assembled in reference-based way with StringTie (v1.3.3b). StringTie used new network flow algorithm and optional de novo assembly step to make and quantify full-length transcripts for each gene locus. Reads numbers for each gene were counted with featureCounts v1.5.0-p3. FPKM of each gene was calculated based on gene length and reads count.

first: Youlong

last: Hai

first: Hongqi

last: Chen

first: Yukun

last: Zhang

first: Xiaoyong

last: Hu

first: Kai

last: Ni


title: Epigenetic age oscillates during the day (WBC-Neu 52 yr old)

overall_design: Peripheral blood samples were collected continuously every 3 hours for 72 hours from a 52 year old caucasian male. Collection started at circadian time 13 (CT13), corresponding to 1PM local time with one missing time point at CT52. Methylation profile obtained using Illumina Infinium 450K Human Methylation Beadchip. The microarray experiment was performed in technical duplicates. Sample WBCminusNeu_ZT82 and it's technical replicate were removed as outliers during the analysis and are not included in the processed data.


title: Circuit-wide gene network analysis reveals sex-specific roles for phosphodiesterase enzymes in cocaine addiction

city: New York

first: Aarthi

last: Ramakrishnan

state: New York

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

summary: Cocaine use disorder is a significant public health issue without an effective pharmacological treatment. Successful treatments are hindered in part by an incomplete understanding of the molecular mechanisms in the brain that underly long-lasting maladaptive plasticity and addiction-like behaviors. In this study, we leverage a large RNA-sequencing dataset to generate gene co-expression networks across 6 interconnected regions of the brain’s reward circuitry from mice that underwent saline or cocaine self-administration, followed by a 24-hour or 30-day withdrawal period and a saline or cocaine challenge. We identify phosphodiesterase 1b (Pde1b), a Ca2+/calmodulin-dependent enzyme that catalyzes the hydrolysis of cAMP and cGMP, as one of the top hub genes within a nucleus accumbens (NAc) gene module that was bioinformatically associated with addiction-like behavior. Within Drd1- and Drd2-expressing medium spiny neurons (D1 and D2 MSNs) in the NAc, we found that chronic cocaine selectively upregulates Pde1b expression in D2 MSNs. Using a virus-mediated overexpression approach, we demonstrate that Pde1b in the NAc influences cocaine self-administration behavior, locomotor responses, electrophysiological properties of MSNs, and cocaine-induced transcriptomic adaptations in a cell-type- and sex-dependent manner. Together, we identify novel gene modules across the brain’s reward circuitry associated with addiction-like behavior and explore the role of Pde1b in regulating the molecular, cellular, and behavioral response to cocaine.

overall_design: we overexpressed Pde1b in NAc neurons, injected WT male or female mice with saline or cocaine (20 mg/kg) for 10 days, and performed RNA-seq

first: Collin

last: Teague

first: Xianxiao

last: Zhou

first: Bin

first: Eric

last: Nestler


title: A role of DDR2 and substrate stiffness on cancer cell transcriptome and proliferation

first: Cong

last: Xiao

state: MA

address: Hess 9th floor,1470 Madison AVE

institute: Icahn School of Medicine-Mt Sinai

summary: Extracellular matrix (ECM) regulates carcinogenesis. As a major ECM component, collagen interacts with integrin and a non-typical receptor discoidin domain receptor tyrosine kinase 2 (DDR2), but how DDR2 regulates cancer progression is poorly understood. Apart from its signaling function, ECM provides a mechanical environment for cancer, but the impact of biomechanics on cancer remains enigmatic. Here, we performed RNA-seq of a human neuroblastoma cell line SH-SY5Y. We found that DDR2 knockdown, but not increasing substrate stiffness, upregulated pro-proliferative genes and down-regulated axonogenesis genes. Surprisingly, despite no transcriptome changes, increasing of stiffness attenuates SH-SY5Y cell proliferation, an effect also observed after DDR2 knockdown. Our results indicate that two ECM effectors, DDR2 and biomechanics, could control cancer cell proliferation through different mechanisms.

overall_design: To investigate how DDR2 regulates cancer progresion, we did DDR2 knock down in SH-SY5Y cell line, then followed by RNA-seq.

first: Theadora

last: Vessella

first: Steven

last: Xiang

first: Qi

last: Wen


title: Epigenetic age oscillates during the day (Neu 30 yr old)

first: Karolis

last: Koncevičius

overall_design: Peripheral blood samples were collected continuously every 3 hours for 24 hours from a 30 year old caucasian male. Collection started at circadian time 8 (CT8), corresponding to 8AM local time. Methylation profile obtained using Illumina Infinium EPIC Human Methylation Beadchip. The microarray experiment was performed in technical triplicates. Sample Neu30yo_ZT20_replicate1 was removed as outlier prior to normalization and is not included in the processed data.

first: Akhil

last: Nair

first: Aušrinė

last: Šveikauskaitė

first: Agnė

last: Šeštokaitė

first: Auksė

last: Kazlauskaitė

first: Audrius


title: A Repressive Type of TEAD4 Condensation and Engineering a Glue Peptide Therapy Against Cancer [ChIP-Seq 1]

first: yang

last: tang

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for H3K27ac，H3K27me3  in GLUP peptide treated HGC-27 cells.

first: Yang

last: Tang

first: Liwei

last: An

first: Hui


title: Single nuclei chromatin accessibility and transcriptomic map of breast tissues of women of diverse genetic ancestry [scRNA-seq]

city: Indianapolis

first: Harikrishna

last: Nakshatri

state: IN

address: 980 W. Walnut St. R3C218C

department: General Surgery

institute: Indiana University School of Medicine

summary: Single nuclei analysis is allowing robust classification of cell types in an organ that helps to establish relationships between cell-type specific gene expression and chromatin accessibility status of gene regulatory regions. Using breast tissues of 92 healthy donors of various genetic ancestry, we have developed a comprehensive chromatin accessibility and gene expression atlas of human breast tissues. Integrated analysis revealed 10 distinct cell types in the healthy breast, which included three major epithelial cell subtypes (luminal-hormone sensing, luminal adaptive secretory precursor, and basal-myoepithelial cells), two endothelial subtypes, two adipocyte subtypes, fibroblasts, T-cells, and macrophages. By integrating gene expression signatures derived from epithelial cell subtypes with spatial transcriptomics, we identify specific gene expression differences between lobular and ductal epithelial cells and age-associated changes in epithelial cell gene expression patterns and signaling networks. Among various cell types, luminal adaptive secretory cells and fibroblasts showed genetic ancestry dependent variability as a subpopulation of luminal adaptive secretory cells with alveolar progenitor (AP)  cell state were enriched in Indigenous American (IA) ancestry and fibroblast populations were distinct in African ancestry. ESR1 expression pattern was distinctly different in tissues from IA compared to the rest, with a high level of ESR1 expression extending to AP cells and crosstalk between growth factors and Estrogen Receptor signaling is evident in these AP cells. In general, cell subtype-specific gene expression did not correlate with chromatin accessibility differences, suggesting that transcriptional regulation independent of chromatin accessibility governs cell type-specific gene expression in the breast.

overall_design: Breast tissues from healthy women who donated breast tissues for research purpose were used in this study. Tissue collection protocol is described in Star Protocols 3:101047. AAF-African American women. Samples listed as nulliparous or parous are from White women. Each set contained breast tissues of five women. Therefore, age, BMI and preganacy status varied. Samples from parous and nulliparous were from under the age 50.

first: Poornima

last: Bhat-Nakshatri

first: Duojiao

last: Chen

first: Aditi

last: Khatpe

first: Guanglong

last: Jiang

first: Patrick

middle: C

last: McGuire

first: Cihat

last: Erdogan

first: Hongyu

last: Gao

first: Yunlong

last: Liu

first: Felicia

last: New

first: Rana

last: German

first: Anna

middle: M

last: Storniolo


title: Single nuclei chromatin accessibility and transcriptomic map of breast tissues of women of diverse genetic ancestry [GeoMx]

overall_design:
FFPE sections from donors with two time tissue donations were selected for the study. Each slide contained two 5 micrometer sections from FFPE blocks. Each slide represented one donor with 2 barcodes representing 2-time donations. Each donor had three repeats (3 slides per donor). The sections were cut with Leica DB80 LS blades (Leica #14035843488) on a rotary microtome instrument (Leica RM2125 RTS) and placed on the center of a Superfrost Plus Microscope slide (Fisher scientific #1255015). Tissue sections were placed in the center of the slide and be no larger than 35.3 mm x 14.1 mm.  Regions of interest (ROIs) were selected after staining the slides with pan-keratin, alpha-SMA and FABP4 antibodies. All ROIs passed a sequencing quality control assessment. Next, negative control probes were used to estimate background and downstream gene detection and to remove outliers. The limit of quantification (LOQ) of each ROI was calculated using the geometric mean and geometric standard deviation of the negative control probes to identify genes detected above background in the experiment. All ROIs passed LOQ-based filtering with more than 1% of genes detected.
Breast tissues from healthy donors donated 10 years apart; first number in the title column correspond to first donation and the second correspond to donation from the same donor 10 years later.


title: A Repressive Type of TEAD4 Condensation and Engineering a Glue Peptide Therapy Against Cancer [RNA-Seq]

last: Zhang


title: Single nuclei chromatin accessibility and transcriptomic map of breast tissues of women of diverse genetic ancestry [10X single-cell multiome]

overall_design: Breast tissue samples used in this study are healthy donors who donated breast tissues for research purpose. Breast tissue collection procedure and sample process are described in Star Protocols 3:101047. Breast tissues from BRCA1 and BRCA2 mutation carriers are from prophylactic mastectomy or tumor adjacent normal. Breast tissues from five donors were pooled together for the analysis. There fore age, bmi and pregnanacy information varied from set to set.


title: A Repressive Type of TEAD4 Condensation and Engineering a Glue Peptide Therapy Against Cancer


title: Activin A and CCR2 regulate the function of macrophages in testicular fibrosis caused by experimental autoimmune orchitis

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

summary: Treatment of bone marrow-derived macrophages with activin A in vitro increased the expression of Ccr2, Fn1, Cxcr4, and Mmp2 and these effects were abolished by follistatin.

overall_design: In order to investigate whether activin A contributes to inflammatory and fibrotic responses by regulating macrophages, mouse BMDMs were stimulated with activin A in vitro. FST288 was used as an antagonist of activin A.

first: Monika

last: Fijak

first: Wei

last: Peng

last: Guenther


title: Single nuclei chromatin accessibility and transcriptomic map of breast tissues of women of diverse genetic ancestry

last: Nakshatri


title: Effect of depletion of TRIP12 on gene expression in adult murine pancreatic acinar cells and murine pancreatic cancer cell lines

city: Toulouse

first: Marlène

last: DUfresne

address: 2 Avenue Hubert Curien

country: France

institute: Inserm

summary: To investigate the role of the E3 ubiquitin ligase Thyroid Receptor Interacting Protein 12 (TRIP12) in pancreatic acinar cell identity and pancreatic carcinogenesis, we used genetically engineered mouse models of pancreas-selective Trip12 deletion, mutant Kras (G12D) and mutant P53 (R172H). We performed gene expression analysis using RNA-seq data from adult acinar cells. We established cell lines from murine pancreatic tumors.

overall_design: Comparative gene expression analysis of RNA-seq data from three TRIP12 knockout and three TRIP12 expressing pancreatic acinar cells. Comparative gene expression analysis of RNA-Seq  data from three cell lines established from two Trip12 expressing KPC pancreatic murine tumors, from two Trip12 knockout KPC tumors and from two Trip12 heterozygous KPC tumors.

last: Dufresne

first: Manon

last: Brunet

first: Jérôme

last: Torrisani

first: Claire

last: Vargas

first: Guillaume

last: Labrousse


title: A Repressive Type of TEAD4 Condensation and Engineering a Glue Peptide Therapy Against Cancer [ChIP-Seq 2]

first: yang

last: tang

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for TEAD4 in GLUP peptide treated HGC-27 cells.

first: Yang

last: Tang

first: Liwei

last: An

first: Hui


title: Tight Junction Claudins-associated vascular heterogeneity determines organotypic metastasis

city: Houston

first: Kalluri

last: Lab

state: Texas

address: 1901 East Rd

institute: UT MD Anderson Cancer Center

summary:
To identify the underlying mechanisms associated with lung and kidney fibrosis inducing lung metastasis, we evaluated global transcriptomic changes in healthy lung, fibrotic lung fibrosis, and lung from mice with kidney fibrosis.
Results provide information on the vascular remodeling of the lungs with organ fibrosis. Lung fibrosis is induced with intratracheal bleomycin administration. Kidney fibrosis is induced by unilateral ureter obstruction (UUO).

overall_design: Total RNA isolated from healthy kidney, healthy lung, fibrotic kidney, fibrotic lung, and lung from mice with kidney fibrosis

first: Valerie

last: LeBleu

first: Toru

last: Miyake


title: OTUB2 silencing promotes ovarian cancer via mitochondrial metabolic reprogramming and can be synthetically targeted by CA9 inhibition

city: Beijing

first: Yabing Nan

last: Yabing Nan

address: 17 Panjiayuan Nanli, Chaoyang Diistrict

institute: Cancer Hospital Chinese Academy of Medical Sciences

summary:
These findings delineate the mechanism of OTUB2 epigenetic silencing in ovarian cancer, demonstrate the critical roles of OTUB2/SNX29P2 in inhibiting glycolysis and eliciting cuproptosis in cancer cells and suggest that CA9 inhibitor treatment is a promising therapeutic option for OTUB2-silenced tumors.
To investigate the downstream pathway regulated by OTUB2/SNX29P2, we performed RNA sequencing (RNA-seq) in ES-2 cells expressing EV, OTUB2 or SNX29P2.

overall_design: RNA-seq of ES-2 cells expressing EV, OTUB2 or SNX29P2

first: Yabing

first: Xiaowei

last: Wu

first: Qingyu

last: Luo

first: Wan

last: Chang


title: Ablation of placental REST deregulates fetal brain metabolism and impacts gene expression of the offspring brain at the postnatal and adult stages

city: Columbia

first: SUSANTA

last: BEHURA

state: MO

address: 920 East Campus Dr

institute: University of Missouri

summary: In this study, the transcriptional repressor REST (Repressor Element 1 Silencing Transcription factor) was ablated in the mouse placenta to investigate molecular and cellular impacts on the offspring brain at different life stages. Ablation of placental REST deregulated several brain metabolites, including glucose and lactate that fuel brain energy, vitamin C (ascorbic acid) that functions in the epigenetic programming of the brain during postnatal development, and glutamate and creatine that help the brain to respond to stress conditions during adult life. Bulk RNA-seq analysis showed that a lack of placental REST persistently altered multiple transport genes, including those related to oxygen transportation in the offspring brain. While metabolic genes were impacted in the postnatal brain, different stress response genes were activated in the adult brain. DNA methylation was also impacted in the adult brain due to the loss of placental REST, but in a sex-biased manner. Single-nuclei RNA-seq analysis showed that specific cell types of the brain, particularly those of the choroid plexus and ependyma, which play critical roles in producing cerebrospinal fluid and maintaining metabolic homeostasis, were significantly impacted due to the loss of placental REST. These cells showed significant differential expression of genes associated with the metabotropic (G coupled protein) and ionotropic (ligand-gated ion channel) glutamate receptors, suggesting an impact of ablation of placental REST on the glutamatergic signaling of the offspring brain. The study expands our understanding of placental influences on the offspring brain.

overall_design: RNA-seq was performed with embryonic brain at day 15 (E15), postnatal brain day 7 (P7) and adult brain at week 8 (W8)  from control and knockout mice (three each time point).

first: Maliha

last: Islam

first: Ananya

last: Samal

first: Daniel

last: Davis

first: Susanta

last: Behura


title: Adiposity alters protective mechanisms of progesterone through dysregulation of endometrial metallothionein expression

city: Chicago

first: Julie

last: Kim

address: 303 E. Superior St

department: Obstetrics and Gynecology

institute: Northwestern University

summary: In this study, we sought to understand the effects of excess adipose on the benign endometrium. We used a physiologic in vitro coculture system consisting of multicellular organoids of the benign human endometrium and adipose spheroids in the presence of estradiol, progesterone, and testosterone to mimic the menstrual cycle. Gene expression analysis of endometrial organoids under high adiposity conditions revealed downregulation of genes normally expressed in secretory endometrium, suggestive of an altered progesterone response. Genes associated with ion homeostasis and detoxification of reactive oxygen species were also downregulated, including the metallothionein (MT) family of genes. We demonstrated that MT gene expression in endometrial organoids was regulated by progesterone specifically in the epithelial cells, and that progesterone receptor is recruited to the promoters of MT genes in endometrial epithelial cells. We illustrated the impact of MT dysregulation by silencing MT genes in endometrial epithelial cells, resulting in increased DNA damage. Our results reveal that exposing the endometrium to high adiposity can compromise the protective effects of progesterone, dysregulate MT genes in the endometrial epithelium, and leave the endometrium vulnerable to ROS-induced DNA damage.

overall_design: Endometrial organoids (multicellular) from 4 patients were cultured with adipose spheroids in an in vitro coculture system  in the presence of estradiol, progesterone, and testosterone to mimic the menstrual cycle.

first: Alina

last: Murphy

first: Huma

last: Asif

first: Ji-Yong


title: Ablation of placental REST deregulates fetal brain metabolism and impacts gene expression of the offspring brain at the postnatal and adult stages (snRNA-seq)

summary: The Repressor Element-1 Silencing Transcription (REST) factor is a transcriptional repressor.  The aim of this study is to characterize role of REST in placental influences on offspring brain. REST was ablated in mouse placenta by mating mouse carrying floxed (FL) alleles of REST with mouse that expresses Cre recombinase under the control of the promoter of placenta-specific gene Gcm1 (glial cells missing 1). To investigate placental influence on gene expression of adult offspring brain cells, single-nuclei RNA-seq was performed. Data analysis showed that ablation of placental REST significantly impacted specific pathways in choroid plexus and ependymal cells of the offspring brain.

overall_design: snRNA-seq was performed with  adult brain at week 8 (W8)  from control and knockout mice.


title: Roles of LTBP1 in the gastric cancer cells

city: Yangsan

first: Sae-Ock

last: Oh

state: Gyeongsangnam-do

department: Anatomy

institute: Pusan National University School of Medicine

summary: We report the effect of LTBP1 on the RNA expression profiling in MKN28 gastric cancer cells

overall_design: RNA expression was compared between control (scrambled) and LTBP1-knockdowned cells. The stable cell lines expressing shLTBP1 or shSCR plamid were established


title: Fusobacterium nucleatum Induces PD-L1 Expression by Tumor-Associated Macrophages and Inhibits Anti-Tumor Immunity in Colorectal Cancer.

first: Xie

last: qin

address: Minchi first road, pujiang town, minhang district, Shanghai

institute: LC sciences

summary: Fusobacterium nucleatum (Fn) infection has been linked to the initiation and development of colorectal cancer (CRC). However, the underlying mechanisms remains unexplored.   Tissues from Fn-infected mice were first collected for single-cell RNA sequencing. we investigated the correlation between Fn infection and accumulations of tumor associated macrophages (TAMs) in tissues from human CRC or AOM/DSS treated mice. The impact of Fn on biological function of TAMs were interrogated. We deciphered the mechanisms for interaction between Fn and TAMs in CRC. We explored the impact of Fn infection on immune-checkpoint blockade (ICB) treatment in a multicohort study.The analysis of single-cell RNA sequencing revealed an enrichment of TAMs in Fn positive tissues. A significant correlation between Fn DNA level and TAMs was observed. Functionally, Fn could recruit TAMs in CRC tissues and promote their biological functions by enhancing PD-L1 expression and thus suppressing CD8+ T cells. Mechanistically, Fn infection led to increased secreted IL-6 via TLR4/MyD88/NF-κB pathways, and the activated IL-6/STAT3 pathway enhanced PD-L1 expression in TAMs. By using several mice models, we found IL-6 inhibition, loss of MyD88 or anti-PD-L1 treatment could significantly inhibit tumorigenesis. Clinically, Fn positive patients tended to be more sensitive to ICB treatment, with a better prognosis than Fn-negative patients.

overall_design: We constructed a mouse CRC model with AOM/DSS intervention. After Fusobacterium nucleatum (Fn) or PBS (control) intervention, we extracted colorectal tumor tissues in both group for single cell sequencing (n = 3 in control(PBS) group and n = 3 in Fn group)

first: Yz

last: Yang

first: Yl

last: Ma


title: Loss of retinoic acid signaling drives immune escape in IDH mutant gliomas

city: Pittsburgh

first: Nduka

last: Amankulor

state: PA

address: 200 Lothrop Street

department: Neurological Surgery

institute: University of Pittsburgh

summary: Gliomas are immunologically cold tumors that can be broken into several categories based on either RNA expression profiles or methylation profiles, with isocitrate dehydrogenase (IDH) mutations defining a major segregration between types. IDH mutant gliomas often exhibit defects in the retinoic acid pathway. We treated mice harboring IDH mutant gliomas with all-trans retinoic acid, and found that this treatment cause reductions in tumor growth and a swith in immune profiles in the tumor microenvironment.

overall_design: Neurospheres (50,000 cells) were injected into the striatium of 6 week old mice. Mice were treated with either 10 mg/kg ATRA or control intra-peritoneally every other day until they were sacrificed based on signs of CNS pathology. 5-prime based single-cell RNAseq was then performed on manually dissected and digested tumors.

first: Anthony

middle: R

last: Cillo

first: Aparna

last: Rao

first: Xiaoran

last: Zhang

first: Tullia

last: Bruno

first: Dario

last: Vignali