title: Effect of Lactobacillus.salivarius HHuMin-U on gene expression of VK2/E6E7 juman vaginal cell lines.

city: Seoul

first: Juwon

last: Choi

address: 50 Yonsei-ro, Seodaemun-gu

institute: Yonsei University

summary: Vulvovaginal candidiasis (VVC) is a common mucosal infection caused by Candida albicans, characterized by inflammation and disruption of epithelial immunity. Probiotic therapy has emerged as a promising approach for managing VVC by modulating host immune responses and enhancing mucosal defenses. In this study, we investigated the therapeutic potential of Lactobacillus salivarius HHuMin-U (HMU) against VVC using in vitro and in vivo models. HMU treatment enhanced the expression of antimicrobial peptides (AMPs) such as DEFB1 and S100A8 and modulated cytokine production (e.g., IL-6, IL-8) in vaginal epithelial cells. Furthermore, RNA sequencing of HMU-treated VK2/E6E7 cells revealed significant transcriptional changes, including upregulation of epithelial barrier function and immune-enhancing pathways. Gene Set Enrichment Analysis (GSEA) identified the NF-κB pathway as a critical regulator of HMU-induced immunity. In vivo, HMU administration significantly reduced fungal burden, mitigated tissue inflammation, and improved epithelial integrity in a murine model of VVC. The sequencing data presented in this report provide a comprehensive transcriptomic landscape of HMU-treated vaginal epithelial cells and offer insights into its underlying mechanisms. These findings support the therapeutic potential of HMU as a probiotic agent for VVC management.

overall_design: To investigate the effects of Lactobacillus salivarius HHuMin-U (HMU) on vaginal epithelial cells, VK2/E6E7 cells were seeded and divided into two groups. Control: PBS-treated; HMU: HMU-treated at a concentration of 1×10^8 CFU/mL. Cells were treated with PBS or HMU for 6 hours before total RNA was extracted using the RNeasy Mini Kit (Qiagen, Hilden, Germany). Three biological replicates were prepared for each group.

first: Sanguine

last: Byun

first: Jay-Young

last: Jo


title: Paternal histone H2A variant incorporation and function before and after fertilization in C. elegans [RNA-seq]

status: Public on Feb 01 2025

city: San Francsisco

first: Diana

last: Chu

state: CA

address: 1600 Holloway Ave

department: Biology

country: USA

institute: San Francisco State University

type: Expression profiling by high throughput sequencing

summary: During spermatogenesis, chromatin repackaging transforms germ cells into sperm and transmits paternal epigenetic information to embryos. We have found distinct functions in these processes for two C. elegans H2A variants, HTAS-1, a sperm-specific paralog, and HTZ-1, a conserved H2A.Z homolog. HTAS-1 activates and represses gene expression less than two-fold, indicating HTAS-1 does not globally silence genes. In contrast, during spermatogenesis HTZ-1 regulates different germline genes compared to HTAS-1. During oogenesis, HTZ-1 strongly represses sperm gene expression over six-fold and activates oocyte and sex-independent genes, revealing tissue-specific modes of HTZ-1 regulation. ChIP-seq analysis of sperm chromatin shows HTZ-1 is present in 75% of HTAS-1 targets. HTZ-1 is incorporated at promoters of targets not occupied by HTAS-1 but is depleted in promoters of genes also occupied by HTAS-1. Instead HTAS-1 and HTZ-1 incorporate within gene bodies of shared targets. Post- fertilization, paternally-contributed HTAS-1 regulates the expression of a large number of genes in mixed-staged embryos. Correspondingly, loss of HTAS-1 causes decreased fertility and delayed development. Our studies indicate H2A variants have distinct incorporation mechanisms during sperm formation and tissue-specific functions in gene expression and fertility.

overall_design: We performed short-read RNA-sequencing on HTZ-1 and HTAS-1 knockouts and wildtype controls. For HTAS-1, we examined knockouts vs wildtype expression in male gonads and mixed embryos. For HTZ-1, we compared expression between wildtypes and knockouts in male and hermaphrodite germlines.

first: Swadha

last: Singh

first: Keiko

last: Hokeness

first: Tomoko

last: Tabuchi

first: Jesus

last: Hinojosa Paiz

first: Eric

last: Tang

first: Emma

last: Harms


title: Paternal histone H2A variant incorporation and function before and after fertilization in C. elegans [ChIP-seq]

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for histone variants HTZ-1 and HTAS-1 was performed in C. elegans sperm.

first: Susan

last: Strome


title: identify the secreted gene in Casp8-silenced mouse hepatocyte cell line

city: New York

first: Xiaobo

last: Wang

state: NY

address: 630 W 168tth street

department: Medicine

institute: Columbia University

summary: Hepatocyte caspase-8 is elevated in MASH and promotes fibrosis independently of apoptosis changes. To investigate how hepatocyte caspase-8 might drive liver fibrosis progression in MASH, we focused on activated hepatic stellate cells (HSCs), which are the primary source of collagen-producing myofibroblasts and central players in MASH fibrosis. To assess a potential link between hepatocyte caspase-8 and HSC activation, we used an ex vivo model where primary murine HSCs were cultured with conditioned media from siCasp8-treated or control primary hepatocytes. Supporting our hypothesis, HSC activation markers were reduced in HSCs exposed to conditioned media from Casp8-silenced AML12 hepatocytes compared to controls. To pinpoint caspase-8-dependent secretory proteins that could activate HSCs, we conducted RNAseq on these cells, identifying secretory genes reduced in Casp8-silenced AML12 hepatocytes.

overall_design: Scrambled control siRNA and Casp8 siRNAs were transfected into AML12 cells using Lipofectamine RNAiMAX (Life Technologies) at a final concentration of 40 nM siRNA in 24-well plates, following the manufacturer’s instructions. After 48 hours, the cells were collected for RNA sequencing. Gene expression profiling was performed using RNA-seq data from four biological replicates. Comparative analysis of gene expression focused on differences between scrambled (scr) control and siCasp8-treated AML12 hepatocyte cells.

first: Ira

last: Tabas


title: Gene expression profile at single cell level of OVA+ cells elicited by LTA1/OVA vaccine at different time points and CD4+T cells from naïve spleen as control

city: New Orleans

first: Jay

last: Kolls

state: LA

address: 1430 Tulane Ave

institute: Tulane University

summary: Our previous work showed that vaccine elicited Klebsiella pneumoniae specific CD4+ tissue resident memory (TRM) cells in the lung provide serotype independent immunity against K. pneumoniae for up to 6 months.  However, vaccine efficacy wanes in proportion to lung CD4+ TRM cell number.  To study what controls TRM maintenance, apart from antigen, we developed an LTA/1Ovalbumin (OVA) model and tetramer pulldown method to enrich OVA+ lung CD4+ TRM cells over time. We applied single-cell RNA-sequencing (scRNA-seq) of these cells, collected on days 30, 90 and 184 after prime immunization with OVA and our prior Th17 adjuvant, E. coli heat labile toxin A1 (LTA1). As control, we used splenic CD4+ T cells from naive mice

overall_design: OVA+ cells from different time points were enriched by OVA-tetramer pulldown and analyzed by scRNAseq.

first: Kejing

last: Song

first: Haoran

last: Yang

middle: K


title: RNA m1A methyltransferase TRMT61A induces MAPK/ERK signaling and is a therapeutic target in colorectal cancer [MeRIP-Seq]

city: hong kong

first: xiaoting

last: zhang

address: Rm 708, 7/F., Li Ka Shing Medical Science Building , Prince of Wales Hospital, Shatin, N.T., Hong Kong

department: Faculty of Medicine

country: China

institute: The Chinese University of Hong Kong

summary: The role of N1-methyladenosine (m1A) in cancer remains poorly understood. Here we investigate the functional importance of RNA m1A methyltransferase TRMT61A in colorectal cancer (CRC) and assess its potential as a therapeutic target. Our findings demonstrate consistent elevation of TRMT61A expression and RNA m1A levels in primary CRC tissues, which correlate significantly with poor patient survival. Through CRISPR/Cas9 screenings, TRMT61A is the most essential gene among m1A regulators. We further elucidate that TRMT61A facilitates CRC tumorigenesis and progression by enhancing the stability of mRNA of crucial targets, including ONECUT2, thereby activating the MAPK/ERK signaling pathway in an m1A-dependent manner. Of note, we show promising anti-CRC effects by inhibiting TRMT61A using nanoparticleencapsulated siTRMT61A or our identified small molecule compound, PGG. Collectively, our study uncovers the essential role of TRMT61A-m1A in CRC by activating the ONECUT2-MAPK/ERK pathway. Targeting TRMT61A holds promise as a therapeutic approach for treating CRC.

overall_design: To identify the functional downstream effectors of TRMT61A, we performed meRIP-seq in HCT116 cells with or without TRMT61A knockout


title: RNA m1A methyltransferase TRMT61A induces MAPK/ERK signaling and is a therapeutic target in colorectal cancer [Ribo-Seq]


title: Casz1 is required for both inner hair cell fate stabilization and outer hair cell survival

city: Beijing

first: Zhiyong

last: Liu

address: 7 Science Park Road ZGC Life Science Park

institute: National Institute of Biological Sciences, Beijing

summary: Cochlear inner hair cells (IHCs) and outer hair cells (OHCs) require different transcription factors for their cell fate stabilization and survival, suggesting separate mechanisms are involved. Here, we found that the transcription factor Casz1 was crucial for early IHC fate consolidation and for OHC survival during mouse development. Loss of Casz1 resulted in transdifferentiation of IHCs into OHCs, without affecting OHC production. However, long-term OHC survival was compromised in Casz1 mutant mice. In addition,  the transcription factor Gata3 was downregulated in Casz1-deleted IHCs and overexpressing Gata3 partially rescued IHC properties, OHC numbers, and hearing in Casz1-deleted mice. Thus, Casz1 plays critical roles in early IHC fate stabilization and OHC survival and could potentially provide a lead for therapies aimed at regenerating both IHCs and OHCs.

overall_design: P10_WT OHCs were manually picked using the genetic mouse model, Slc26a5FlpO/+; Rosa26FSF-H2BEGFP/+. The P10_Casz1 CKO OHCs were manually picked using the genetic mouse model, Atoh1Cre/+; Casz1flox/flox; Slc26a5FlpO/+; Rosa26FSF-H2BEGFP/+. Both WT and Casz1 CKO OHCs were labelled with nuclear GFP.

first: Yuwei

last: Sun

first: Minhui

last: Ren

first: Yu

last: Zhang

first: Shuting

last: Li

first: Zhengnan

last: Luo

first: Suhong

first: Shunji

last: He

first: Guangqin

first: Di

first: Suzanne

middle: L

last: Mansour

first: Lei


title: RNA m1A methyltransferase TRMT61A induces MAPK/ERK signaling and is a therapeutic target in colorectal cancer II

overall_design: To identify the functional downstream effectors of TRMT61A, we performed RNA-seq in HCT116 cells with or without TRMT61A knockout

first: XIAOTING

last: ZHANG

last: QIN

first: FENFEN

last: JI


title: Single cell ATAC sequencing in Skeletal cells

first: Matthew

last: Greenblatt

address: 1161 York Ave APT 1a

department: Pathology and Laboratory Medicine

institute: WEILL CORNELL MEDICAL COLLEGE

summary: To determine lineage and differentiation relationship among skeletal cells in native environment, we performed tracking of  clonal and sub-clonal mitochondrial mutations across population. Specifically, we utilized PolGD257A/D257A mice with a mitochondrial DNA “mutator” phenotype that provide a rich substrate of somatic mutations to facilitate clonal lineage tracing among skeletal cells. Here, CD24+CD29+SSCs, CD29+COPs, CD24+CAPs, CD24-CD29-cells, THY+ osteolineage cells, CD200-CD105+ adipolineage cells and CD45+ hematopoietic cells were isolated from the femurs of 3-month-old PolGD257A/D257A mice, co-labelled with both FACS  and CITE-seq antibodies, and were subjected to a modified single cell ATAC-seq method  for single cell sequencing of mtDNA variants. Our data establish that CD24+CD29+SSCs share a clonal lineage with adipolineage and osteolineage cells, providing the first evidence of clonal multipotency in skeletal cells and thus, establishes the direct  in vivo evidence for our model of skeletal cell differentiation.

overall_design: Here, CD24+CD29+SSCs, CD29+COPs, CD24+CAPs, CD24-CD29-cells, THY+ osteolineage cells, CD200-CD105+ adipolineage cells and CD45+ hematopoietic cells were isolated from the femurs of 3-month old PolGD257A/D257A mouse femurs co-labelled with both FACS  and CITE-seq antibodies, and were subjected to a modified single cell ATAC-seq method  for single cell sequencing of mtDNA variants.

first: Shawon

last: Debnath

first: Tuo

first: Tamara

last: Prieto Fernandez

first: Srafaraz

last: Lalani


title: RNA m1A methyltransferase TRMT61A induces MAPK/ERK signaling and is a therapeutic target in colorectal cancer I

first: xiaoting


title: Islet single-cell transcriptomic profiling during obesity-induced beta cell expansion

city: Houston

first: Aaron

middle: R

last: Cox

state: TX

address: 1825 Pressler St

department: Institute of Molecular Medicine

institute: University of Texas Health Science Center at Houston

summary: Transcriptional mechanisms of beta cell proliferation are incompletely understood. We used single-cell transcriptomics to identify gene networks and signaling pathways central to beta cell proliferation

overall_design: Islets were isolated from control (wild-type; Lepr-lp/lp) and Lepr KO (Ubc-CreERT2;Lepr-lp/lp) mice on day 9 after the start of tamoxifen treatment, which was used to induce Cre-recombination at the Lepr leading to hyperphagia, weight gain, and beta cell mass expansion.

first: Peter

middle: M

last: Masschelin

first: Scott

middle: A

last: Ochsner

first: Sean

last: Hartig

first: Niel

middle: J

last: McKenna


title: RNA-seq Analysis of OCI-AML3 Cells Treated with Different Compounds

city: Jena

first: Faezeh

last: Ghazvini Zadegan

address: Hans-Knoll-Strase 2

department: Department of Hematology/Oncology, Clinic of Internal Medicine II

country: Germany

institute: Institute of Molecular Cell Biology, Center for Molecular Biomedicine Jena (CMB)

summary: Acute myeloid leukemia (AML) remains a challenging hematologic malignancy, necessitating the exploration of novel treatment strategies. In this study, we investigated the effects of all-trans retinoic acid (ATRA), AM80, and their combination treatments with GSK-LSD1 and MB3 on gene expression in OCI-AML3 cells.

overall_design: This study evaluates the effects of ATRA, AM80, and combination treatments with GSK-LSD1 and MB3 on OCI-AML3 cells, compared to untreated cells.


title: Transcriptome analyses reveal key features of mouse seminal vesicle during aging

city: Guangzhou

first: Yun

last: Xie

state: China

address: No. 58 Zhongshan 2nd Road, Yuexiu District, 0080, China.

institute: sun yat-sen university

summary: Despite the dramatic changes in morphology occurring in the seminal vesicles during aging, the transcriptomic characteristics are poorly understood. Thus, we performed a bulk RNA sequencing on seminal vesicle samples from 3-month-old, 13-month-old, and 21-month-old mice to elucidate transcriptomic changes in this study. Comparing 3-month-old mice with the 21-month-old, inflammatory and immune response were identified as the most significantly biological process in upregulated differentially expressed genes (DEGs). Meanwhile, “chemokine signaling pathway” was identified as a key pathway. Indeed, a series of DEGs were enriched in “chemokine signaling pathway”, including Ccl6, Ccl8, Ccl9, Ccr2, Ccr5 and Ccr7. Hub genes such as Ptprc, Adgre1, H2-Ab1 and Ctss were obtained through Protein-Protein interaction network analysis among the continuously up-regulated differentially expressed genes in mouse seminal vesicles at three different ages. These analyses revealed an increased status of immune and inflammatory response in the aged seminal vesicles. In addition, multiple aging-associated DEGs were identified, including Vcam1, Apoe and Cdkn1a. To our knowledge, this study is the first to investigate the general transcriptome landscape of the seminal vesicles in a murine model of natural aging, which may provide novel insights involved in aging-related seminal vesicle dysfunction.

overall_design: seminal vesicle RNA-seq in 3, 13, 21-mo


title: CXCL14 suppresses the progression of colon cancer by regulating tumor epithelial-mesenchymal transition and tumor microenvironment [MC38-CXCL14]

city: Shanghai

first: Jingjing

last: Li

address: 800 Dongchuan Rd.

department: School of Pharmacy

institute: Shanghai Jiao Tong University

summary: Background：The widespread silencing of CXCL14 in advanced colon cancer underscores the association between CXCL14 and the development of colon cancer. Some studies have demonstrated in vitro that CXCL14 can inhibit the growth and metastasis of colon cancer cell, and it has also been studied in other disease models for its regulation of immune cell infiltration. Aims: The aim of this study is to clarify the transcriptional regulation of colon cancer cells mediated by CXCL14 and its regulatory role in the tumor microenvironment. Method：We analyzed the expression characteristics of CXCL14 in clinical databases of colon cancer. CXCL14 overexpression cell lines were established to study its functions on gene transcriptional regulation and cell physiology. Through subcutaneous tumor models, we investigated the effects of CXCL14 on the immune microenvironment. Result：Firstly, the clinical data revealed that CXCL14 is silenced during cancer progression, and negatively associated with EMT and cell proliferation markers, and positively associated with the abundance of T cells and NK cells in colon tissue. Secondly, RNA-seq reveals that CXCL14 overexpression is negatively associated with cell EMT, and inhibits tumor migration and invasion. Western blot (WB) assay confirmed that CXCL14 inhibits the Erk/MAPK and Akt signaling pathways. Finally, subcutaneous tumor models demonstrate that CXCL14 overexpression inhibited tumor growth, increased the infiltration of tumor-associated T cells and DC cells, activated the anti-tumor immune response, antigen processing and presentation, and T helper differentiation in the tumor microenvironment. Conclusion：CXCL14 becomes silenced in late-stage colon cancer samples. In vivo and in vitro experiments demonstrate that CXCL14 inhibits tumor EMT, proliferation, and metastasis through autocrine signaling. It also enhances the infiltration of T and NK lymphocytes through paracrine signaling and inhibits the proliferation of subcutaneous tumors.

overall_design: we utilized the TetOn expression system to establish a tetracycline-inducible expression vector, TetOn-CXCL14, for CXCL14 overexpression (figure S2). Subsequently, MC38 cell line that was stably transfected the plasmid was screened, named MC38-TetOn-CXCL14. We utilized doxycycline (DOX) to induce MC38-TetOn-CXCL14 cells to express CXCL14 for 3 days. Cells were collected before and after induction for RNA sequencing analysis (Geneplus, Beijing, China). Each sample had two biological replicates: DOX+ cells and DOX- cells.

first: Yinjie

last: Zhang


title: Ziziphora clinopodioides Lam. Attenuates AS through Modulation of Lipid Metabolism and Oxidative Stress Pathways: Evidence from Multi-Omics Analyses

city: Urumqi

first: Binghong

last: Liu

address: No. 567, Shangde North Road, Shuimogou District, Urumqi, Xinjiang Uygur Autonomous Region

department: College of TCM Xinjiang Medical University

institute: Xinjiang Medical University

summary: This study investigated the therapeutic effects of Ziziphora clinopodioides Lam. (ZCL) on atherosclerosis (AS) through transcriptomic and metabolomic analyses. Using ApoE-/- mice model and CoCl2-induced THP-1 macrophage hypoxia model, the study found that ZCL reduced blood lipid levels, alleviated hypoxia-induced cellular damage via PI3K/Akt/HIF-1 pathway, and regulated fatty acid metabolism and calcium-related pathways. The findings support ZCL as a potential natural therapeutic agent for AS management.

overall_design: A total of 120 mice (20 C57BL/6J and 100 ApoE-/- mice) were used. ApoE-/- mice were fed high-fat diet and randomly assigned to 5 groups (n=20 each): Model group, Atorvastatin group (5 mg/kg/day), Low-Dose group (1.28 g/kg/day ZCL), Medium-Dose group (2.56 g/kg/day ZCL), and High-Dose group (5.12 g/kg/day ZCL). Treatment lasted 15 weeks. RNA-seq analysis was performed on aortic tissue samples.

first: Hongbing

first: Jianxin

first: Yanshun

last: Wang

first: Xuehua

last: Yan

first: Dongqing

last: An


title: Neutralizing the IL-7Ra limits injury in ANCA-associated glomerulonephritis

city: Melbourne

first: Maliha

last: Alikhan

state: VIC

address: Level 5, Block E, Monash Medical Centre, 246 Clayton Road, Clayton

department: Department of Medicine

country: Australia

institute: Monash University

summary: Increased T cell IL-7Rα (CD127) signaling is associated with poor prognosis in ANCA-associated vasculitis patients, whereas genes linked to T cell exhaustion such as PD-1 correlate with fewer relapses and better patient outcomes. This study characterised intrarenal CD127 and PD-1 expressing CD4+ and CD8+ T cells in mice with anti-MPO glomerulonephritis by RNA sequencing and examined the functional role of IL-7Rα in experimental glomerulonephritis mediated by anti-MPO T cell autoimmunity. There were 3,738 and 2,726 genes differentially expressed between intrarenal CD127-PD-1+ and CD127+PD-1- CD8+ and CD4+ T cells, respectively, with a substantial overlap of differentially expressed genes between CD8+ and CD4+ T cells. Both CD127-PD-1+ CD8+ and CD4+ T cells were enriched for previously described T cell exhaustion signatures that predict prognosis in autoimmune disease. As effector memory T cells drive inflammation, we blocked CD127 after the induction of anti-MPO autoimmunity. Compared with control IgG, anti-IL-7Rα antibodies limited histological injury, reduced albuminuria and reduced numbers of glomerular and interstitial leukocytes, with reduced intrarenal chemokine and pro-inflammatory cytokine expression. Intrarenal effector memory and exhausted CD4+ and CD8+ T cells are present in experimental anti-MPO glomerulonephritis. Neutralising effector memory T cells via the IL-7Rα after the induction of autoimmunity limits intrarenal inflammation and disease. IL-7Rα may be a therapeutic target in ANCA-associated vasculitis.

overall_design: Mice were immunised with recombinant mouse MPO and then low-dose sheep anti-mouse basement membrane (BM) globulin was administered to trigger glomerulonephritis. Twenty-one days later, kidneys were isolated and the following cells were flow sorted: CD4+CD127+PD-1-, CD4+CD127-PD-1+, CD8+CD127+PD-1- and CD8+CD127-PD-1+. Pooled cells from three mice were used for the sorting and there were three experiments per group except for sample CD4+CD127-PD-1+ because it failed quality control. We then performed gene expression profiling to investigate the the differentially expressed genes between the four populations.

first: Kazuya

last: Kishimoto

first: Limy

last: Wong

first: Peemapat

last: Prakongtham

first: Alana

last: Audin

first: Kim

last: O'Sullivan

first: Juli

last: Jaw

first: A

last: Kitching


title: Targeting redox-sensitive MBD2-NuRD condensate for  tumor therapy

city: shanghai

first: heyang

last: wei

address: 131 Dongan Road, Xuhui District

institute: Fudan University

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

overall_design: Refer to individual Series


title: Functional Dynamics of Dendritic Cells in Response to Cutibacterium acnes Strains Associated with Healthy and Acne-prone Skin

city: Los Angeles

first: Giorgia

last: Del Vecchio

address: 610 Charles E Young Dr S, Room 5146

institute: University of California Los Angeles

summary: The pathogenesis of acne vulgaris is multifactorial and is influenced by the presence of Cutibacterium acnes. This study investigated how different strains of C. acnes, associated with either healthy skin (CH) or acne-prone skin (CA), selectively modulate the function of three dendritic cell (DC) subtypes: Langerhans cell-derived (LCDC), monocyte-derived (moDCs), and myeloid (mDCs). Our findings revealed that all DC subtypes secreted varying levels of TGF-β, IL-1β, IL-6, IL-12p70, and IL-23 in response to C. acnes stimulation. Notably, moDCs exhibited the highest cytokine secretion in response to CA-ribotypes, indicating their potent immune responsiveness. Conversely, LCDCs were the least responsive, regardless of the ribotypes. Principal component (PCA) and gene ontology (GO) analysis of bulk RNA sequencing data of DCs exposed to C. acnes identified extensive transcriptional changes, particularly in immune response pathways. moDCs showed the most pronounced transcriptional changes, aligning with their high cytokine secretion levels. Additionally, we identified specific genes upregulated by CA-ribotypes, with notable differences among the DC types, highlighting the unique contributions of each DC subtype to the skin's immune defense mechanisms against C. acnes. Overall, our study underscores the complexity of DC responses in the skin's immune environment and provides valuable insights into their roles in acne.

overall_design: LCDC moDC and mDC cells have been stimulated with selected C. acne strains for 24 hours. The total RNA has been extracted to perform bulk RNA-sequencing and define the immune signatures unique to each DC cell type.

first: NamPhuong

middle: N

last: Nguyen

first: Kelsey

last: Ouyang

first: Matteo

last: Pellegrini

first: George

middle: W

last: Agak


title: Tie2 activation relieves lymphedema by improving lymphatic endothelial integrity [Mouse RNA-seq]

city: Daegu

first: Bo-Yoon

last: Park

address: 170 Hyeonchung-ro

country: South Korea

institute: Yeungnam University

summary: The aim of this study was to evaluate genetic differences between lymphedema, lymph node transfer and lymph node transfer with ABTAA treatment mouse model using NGS-derived transcriptase profiling (RNA-seq) and quantitative reverse transcriptase chain reaction (qRT-PCR) methods in mouse fat tissue.

overall_design: mRNA expression profile by Illumina platform in lymphedema, lymph node transfer and lymph node transfer with ABTAA treatment mouse model

first: Il-Kug

last: Kim


title: Transcriptomics insight into the metabolism of the toxic producing Microcystis aeruginosa PCC 7806

city: Paris

first: Rachel

last: Legendre

address: 28, rue du docteur Roux

department: Research and Resource Center for Scientific Informatics

country: France

institute: Institut Pasteur

summary: Microcystis is a genus of unicellular cyanobacteria capable of growing massively in freshwater ecosystems around the world and producing various toxins such as microcystins. We studied using an RNA-Seq approach the transcriptomes of three axenic strains of Microcystis, comprising the modele strain PCC 7806, selected because of their genetic potential for natural products. We assessed the expression of biosynthetic gene clusters during a 24-hour day/night cycle.

overall_design: The strain PCC 7806 was cultured axenically in triplicate in 1.5 L of BG11 medium under a night and day rythm. The sampling was perfomed at 8 time points, (i) at 7 am, 60 min before the transition from dark to light (t1_N); (ii) 9 am, 60 min after the transition from dark to light (t2_D); (iii) 12 am (t3-D); (iv) 4 pm (t4_D); (v) 8 pm, 1 h before the transition from light to dark (t5_D); (vi) 10 pm, 60 min after the transition from light to dark (t6_N); (vii) 2 am, i.e. the middle of the night (t7_N), and (viii) in the end of the night period (t8_N, 24-h after the first sampling point).

first: Pancrace

last: Claire

first: Varet

last: Hugo

first: Sismeiro

last: Odile

first: Dillies

last: Marie-Agnès

first: Legendre

last: Rachel

first: Coppee

last: Jean-Yves

first: Humbert

last: Jean-François

first: Gugger

last: Muriel


title: CXCL14 suppresses the progression of colon cancer by regulating tumor epithelial-mesenchymal transition and tumor microenvironment [Tumor]

first: Jingjing

last: Li

overall_design: To investigate the role of CXCL14 in the tumor microenvironment, we used MC38 transgenic cells that can inducibly express CXCL14 through DOX induction. Subcutaneous injection of these cells led to the formation of subcutaneous tumors. By inducing CXCL14 expression with DOX, we obtained tumors with overexpressed CXCL14. We performed experiments using C57 mice, which were divided into control and DOX-induced groups, with four animals per group. When the tumors reached 300mm^3, they were harvested. RNA-seq was used to obtain transcriptome data from tumor tissues that were either uninduced or induced with DOX, and differential expression genes were identified. Through gene enrichment analysis, we investigated the impact of CXCL14 on the tumor microenvironment.

first: Yinjie

last: Zhang


title: METTL3-m6A methylation inhibits Type II Alveolar Epithelial Cells proliferation and viability by promoting Pten mRNA stability and translation efficiency in the acute lung injury

first: Qiuyun

last: Wang

state: Shanghai

address: 197 Ruijin Er Road, Shanghai

institute: Ruijin Hospital

type:
Expression profiling by array
Other

summary: In this dataset, we include the m6A methylated RNA data obtained from normal AECII  (NC group) and AECII transfected with shMettl3 (T group).

overall_design:
We generated the following comparisons using Fold-change (FC) ≥ 2 or ≤ 0.5, and p < 0.05 were used to identify the differentially m6A methylated RNAs.The total RNAs were immunoprecipitated with anti-N6-methyadenosine (m6A) antibody. The modified RNAs were eluted from the immunoprecipitated magnetic beads as the “IP”. The unmodified RNAs were recovered from the supernatant as “Sup”.  Two channel arrays were used for these samples but the data were analyzed as single-channel so that each sample  represents either IP or supernatent and the sample table includes the normalized signal values.
Pleaes note that each raw data file contains both IP and SUP raw data and is linked to the corresponding IP sample records.

first: Jie

last: Shen

first: Shiyuan

last: Luo

first: Zhize

last: Yuan

first: Qiang

first: Qianzi

last: Yang

first: Yan

first: Lei

last: Zhuang


title: Pulmonary microvascular endothelial cells support alveolar epithelial growth via bone morphogenetic protein 6 secretion

city: Groningen

first: Reinoud

last: Gosens

address: Antonius Deusinglaan 1

department: Molecular Pharmacology

country: Netherlands

institute: University of Groningen

summary: Chronic obstructive pulmonary disease (COPD) is characterized by progressive airflow limitation and emphysema development, associated with enhanced tissue destruction and defective repair. Supporting cells in the alveolar niche play a crucial role in guiding the activation of alveolar epithelial progenitor cells during repair. Despite their close anatomical proximity, understanding of the supportive role of the pulmonary microvascular endothelium in adult alveolar epithelial repair remains limited. We hypothesized that angiocrine factors secreted by pulmonary endothelial cells support alveolar epithelial cell growth. Here, we report that human pulmonary microvasculature endothelial cells (HPMECs) support murine and human alveolar organoid formation through paracrine signaling via the secretion of extracellular vesicles and soluble factors. Transcriptomic and proteomic analysis pinpointed HPMEC-derived bone morphogenetic protein 6 (BMP6) as a critical factor for alveolar organoid formation. BMP6 deficiency was associated with reduced Wnt signaling and augmented oxidative stress signaling in murine lung tissue. Furthermore, BMP6 promoted alveolar epithelial cell growth, whereas function-blocking antibodies targeting BMP6 inhibited the beneficial effect of endothelial cells on murine alveolar organoid formation. Taken together, our findings highlight BMP6 as a key regulator of adult epithelial repair and suggest its potential as a therapeutic target for lung repair, particularly in individuals with COPD.

overall_design: Wild-type and BMP6 KO mice were exposed to either air or cigarette smoke for 4 weeks or 24 weeks. Lungs were collected afterwards and processed for mRNA isolation and RNA sequencing.

first: Luke

last: van der Koog

first: Xinhui

last: Wu

first: Dyan

last: Nugraha

first: Ken

last: Bracke

first: Fien

last: Verhamme


title: methylGrapher: Genome-Graph-Based Processing of DNA Methylation Data from Whole Genome Bisulfite Sequencing

city: Saint Louis

first: Ting

state: Missouri

address: 4515 McKinley Avenue

institute: WUSTL

type: Methylation profiling by high throughput sequencing

summary: Genome graphs, including the recently released draft human pangenome graph, can represent the breadth of genetic diversity and thus transcend the limits of traditional linear reference genomes.  However, there are no genome-graph-compatible tools for analyzing whole genome bisulfite sequencing (WGBS) data. To close this gap, we introduce methylGrapher, a tool tailored for accurate DNA methylation analysis by mapping WGBS data to a genome graph. Notably, methylGrapher can reconstruct methylation patterns along haplotype paths precisely and efficiently. To demonstrate the utility of methylGrapher, we analyzed the WGBS data derived from five individuals whose genomes were included in the first Human Pangenome draft as well as WGBS data from ENCODE (EN-TEx). Along with standard performance benchmarking, we show that methylGrapher fully recapitulates DNA methylation patterns defined by classic linear genome analysis approaches. Importantly, methylGrapher captures a substantial number of CpG sites that are missed by linear methods, and improves overall genome coverage while reducing alignment reference bias. Thus, methylGrapher is a first step towards unlocking the full potential of Human Pangenome graphs in genomic DNA methylation analysis.

overall_design: To validate the method, we conducted DNA methylation profiling using WGBS on individuals within the 1000 Genomes Project.

first: Wenjin

first: Juan

middle: F

last: Macias-Velasco

first: Xioayu

last: Zhuo

first: Chad

last: Tomlinson

first: Edwards

last: Belter

first: Daofeng


title: Transcriptional profiling of lungs from SARS-CoV-2-infected K18-hACE2 mice

city: Galveston

first: Shailendra

last: Chauhan

state: Texas

address: UTMB Health - Galveston Campus 301 University Boulevard

department: Pathology

institute: UTMB

summary: To explore the effects of SARS-CoV-2 proteins on expression of host genes in lung of infected mice, 4 groups of K18-hACE2 mice (4 mice per group) were mock-infected or infected cells with SARS-CoV-2 WT or its NPS1, or NSP15 mutants respectively.The mice were euthanized at  4 days post-infection to collect the lungs to isolate RNA for RNA sequencing.

overall_design:
4 groups of K18-hACE2 mice (4 mice per group) were mock-infected or infected cells with SARS-CoV-2 WT or its NPS1, or NSP15 mutants respectively.The mice were euthanized at  4 days post-infection to collect the lungs to isolate RNA for RNA sequencing.
L, R, N and RR were used to label the 4 different mice for each group. They are the animal IDs in the same cage.

first: Alexander

last: Bukreyev

first: Fuchun

last: Zhou


title: Intestinal Cyp24a1 regulates vitamin D locally independent of systemic regulation by renal Cyp24a1 in mice

city: Durham

first: Hiroki

last: Kitai

state: NC

address: 2 Genome Ct. Rm 2017

department: Medicine, Division of Nephrology

institute: Duke University

summary: Vitamin D is a central regulator of mineral homeostasis, but its cell-type-specific effects are poorly understood. Here, we tested the effects of acute calcitriol injection on gene expressions in mouse kidneys and intestine (jejunum) using single-cell RNA sequencing.

overall_design: To evaluate the difference in gene expressions between control mice and vitamin D-treated mice in each cell type, we performed single-cell transcriptomic analyses with 10x Chromium 3' v3.1 using dissociated total kidney cells and intestinal cells (duodenum, 1:1 for villus and crypt-derived cells).

first: Michaela

last: Fuchs

last: Grabner

first: Melody

last: Shi

first: Susan

last: Murray

first: Emily

last: Burke

first: Nejla

last: Latic

first: Venkat

last: Thiriveedi

first: Jatin

last: Roper

first: Koki

last: Abe

first: Tomokazu

last: Souma

first: Myles

last: Wolf


title: FXR isoforms drive differentiation and differentially inhibit proliferation in colorectal cancer

city: Utrecht

first: Saskia

middle: van

last: Mil

address: Universiteitsweg 100

department: Center for Molecular Medicine

institute: UMC Utrecht

summary: The Farnesoid X Receptor (FXR) is a bile acid-activated transcription factor which is downregulated in colorectal cancer (CRC), and has been coined as a tumor suppressor in CRC based on mouse studies.  FXR is expressed as multiple isoforms of which α3 and α4 are predominantly expressed in the colon. These isoforms differ in a 12-bp region in the DNA binding domain, which is included in α3 and excluded in α4, due to alternative splicing. The 12bp exclusion results in additional alternative DNA binding and transcriptional profiles in the liver. To investigate the mechanistic and isoform-dependent underpinnings of the tumor suppressive action of FXR, we used human colon organoids in which mutations in four known CRC-driver genes; AKPS, KRAS, p53 and SMAD4 (AKPS), are engineered. We first confirmed that FXR expression is nearly absent already in early-stage CRC organoids, and show that this is due to constitutive Wnt signaling activation. Strikingly, lentiviral overexpression of FXRα4, not FXRα3, reduced proliferation in AKPS organoids in a ligand-independent manner. Transcriptomics indicated that FXRα4 selectively reduced EGFR signaling. Upon ligand addition, both FXRα3 and α4 AKPS organoids changed morphology and started budding, indicative of epithelial differentiation. Gene set enrichment analyses revealed that enterocyte, Paneth and goblet cell progenitor expression patterns were significantly enriched. In addition, electron microscopy showed the appearance of microvilli and increased nuclear circularity, indicative of differentiation towards columnar epithelium, in ligand-stimulated FXRα3 and FXRα4 AKPS organoids.  In conclusion, next to a ligand-dependent and isoform-independent effect on differentiation, we describe for the first time that FXR has isoform-dependent tumor-suppressive effects via inhibition of EGFR signaling.

overall_design: To identify the effect of FXRa3 and FXRa4 overexpression and activation in an organoid model for colorectal cancer. FXRa3 and FXRa4 were overexpressed using lentiviral constructs and activated using obeticholic acid for 3 days. RNA was isolated and sequenced.

first: Judith

middle: C

last: de Jong

first: Monique

middle: D

last: Appelman

last: van Mil


title: RIPK4 driven by TP53 mutations promotes resistance to PANoptosis and metastasis of CRC by phosphorylation of MTHFD1 [RIPK4_sh_seq]

first: Long

last: Yu

state: --- Select One ---

address: dongfengdonglu

institute: Sun Yat-sen University Cancer Center

summary: In this study, we found that RIPK4 protein driven by TP53 mutation is highly expressed in CRC, which can promote the phosphorylation level of MTHFD1 (Methylenetetrahydrofolate Dehydrogenase, Cyclohydrolase And Formyltetrahydrofolate Synthetase 1), a key enzyme of carbon metabolism, promote the generation of NADPH in CRC cells, and reduce the level of ROS, thus promoting PANoptosis resistance and distant metastasis of CRC cells. We explain the novel mechanism of metastasis induced by the TP53 mutation in terms of post-translational modification and clarify the biological role of the RIPK4 protein in CRC, which can be used as a new target for the treatment of metastatic CRC.

overall_design: Compare the mRNA changes in LoVo cells after 72 hours of RIPK4 gene interference.

first: Zhenlin

last: Hou


title: RIPK4 driven by TP53 mutations promotes resistance to PANoptosis and metastasis of CRC by phosphorylation of MTHFD1


title: Expression data of small and large intestinal epitheliall cells from Nfat5fl/fl  and Nfat5IEC-KO mice

city: Seoul

first: Bong-Ki

last: Hong

address: 222 Banpo-daero, Seocho-gu

department: School of Medicine

institute: Catholic University of Korea

summary:
Gene expression profile data of small and large intestinal epitheliall cells from Nfat5fl/fl  and Nfat5IEC-KO mice
We used microarrays to detail the global programme of gene expression of small and large intestinal epitheliall cells from Nfat5fl/fl  and Nfat5IEC-KO mice and identified differential genes.

overall_design: Small and lage intestinal cells were isolated for RNA extraction and hybridization on the Affymetrix GeneChip Mouse Gene 2.0 ST array. We sought to obtain up- or down-regulated gene expression of small and large intestinal epithelial cells from Nfat5fl/fl  and Nfat5IEC-KO mice. To that end, we hand-selected most down-regulated genes of small and large intestinal epitheliall cells from Nfat5fl/fl  and Nfat5IEC-KO mice

first: Wan-Uk

last: Kim

first: Se-Hyeon

last: Park


title: Effect of CDK12-IN-3 on uterine serous carcinoma cell line

city: Beijing

first: xuewu

last: you

address: 11 Xizhimen South Street, Xicheng District

institute: peking university peoples' hospital

summary: Bulk RNA sequencing was performed to detect transcriptome changes in SPEC-2 cells after CDK12-IN-3(50nM) treatment.

overall_design: SPEC-2 cells in the experimental group were treated with CDK12-IN-3(50nM) for 72 hours compared with SPEC-2 cells in the blank control group. Each group of cells had 3 replicates. We then performed gene expression profiling on the mrna-seg data from six cell samples.

first: xuerun

last: liu

first: jianliu

last: wang


title: The CGG triplet repeat binding protein 1 counteracts DNA secondary structure formation to prevent transcription-replication stress

city: Munich

first: Stephan

last: Hamperl

state: Bayern

address: Feodor-Lynen-Strasse 21

department: Institute of Epigenetics and Stem Cells

institute: Helmholtz-Zentrum Munich

summary: CGGBP1 has been implicated in transcription regulation. We tried to investigate the molecular mechanism of how transcription is regulated by depletion of CGGBP1 protein.

overall_design: siRNA for CGGBP1 or its control was transfected into U-2OS Tet-ON cells and cultured for 72h followed by SLAM-Seq analysis.

first: Henning

last: Ummethum

first: Florian

last: Erhard


title: Zalfermin and semaglutide have beneficial effects liver histology and fibrotic gene in a murine model of NASH

city: Oxford

first: Maria

last: Dermit

state: Oxfordshire

country: United Kingdom

institute: Novo nordisk research centre oxford

summary: The potential clinical benefits of FGF21 analogues for the treatment of NASH has evolved significantly within the last years. However, despite clinical meaningful effect on NASH resolution and fibrosis the body weight loss in humans have been less impressive. Thus, a combination of an FGF21 analogue with a GLP-1 receptor agonist may add additional benefit to the treatment of NASH due to complimentary mode of action compared to stand alone therapies

overall_design: RNA-sequencing data. CHOW diet: Vehicle n=8; AMLN diet: Vehicle  n=8, AMLN diet:  Zalfermin low dose (n=8), high dose  (n=8); Semaglutide low dose (n=8, one sample highlighted excluded during quality control)   high dose (n=8). Combination Zalfermin high and Semaglutide high (n=8).

first: Jenny

last: Norlin

first: Nikos

last: Sidiropoulos

first: Matthew

middle: P

last: Gillum

first: Elisabeth

last: Galsgaard

first: Markus

last: Latta

first: Birgitte

last: Andersen


title: Transcriptome analysis of atad3-null zebrafish embryos elucidates possible disease mechanisms

city: Jerusalem

first: Inbar

last: Plaschkes

address: The Hebrew University of Jerusalem - Ein Kerem

department: The Faculty of Medicine - Ein Kerem

country: Israel

institute: HUJI

summary: ATAD3A is a nuclear gene encoding the ATAD3A protein which has diverse roles in the mitochondria, affecting various cellular processes ranging from mitochondrial dynamics and mtDNA maintenance to metabolism pathways and mitochondrial interactions with other organelles. Pathogenic variants in this gene cause neurological diseases in humans with recognizable genotype-phenotype correlations. Using CRISPR/Cas9 genome editing, we generated a knockout (KO) model for the ortholog gene atad3 in zebrafish., in order to further characterize the gene and its role in health and disease. We examined the phenotype, mitochondrial content and mitochondrial activity of the mutant embryos, and compared the transcriptome of wild-type and mutant embryos at 3 days post-fertilization (dpf) via RNAseq. Results were validated by quantitative real-time PCR at 3dpf and 5dpf. Atad3-null zebrafish embryos demonstrated microcephaly, small eyes, pericardial edema and thinning of the musculature, closely correlating with the human disease. Mitochondrial content and activity were reduced. Transcriptome analysis revealed an expected decline in most mitochondrial pathways in the mutant embryos. In addition, we witnessed a global upregulation of cytosolic tRNA synthetases, presumably secondary to mitochondrial stress and possibly endoplasmic reticulum (ER)-stress. Differential expression of select genes was confirmed in fibroblasts from an affected individual. Zebrafish atad3-null embryos can be used as a reliable model of human ATAD3A-associated disorders, as the pathways and processes differentially expressed in this model are similar to the ones in humans. Moreover, our study confirms mitochondrial dysfunction as the primary underlying pathogenic mechanism in ATATD3A-associated disorders.

overall_design: Using CRISPR/cas9 gene editing technology, we created a zebrafish line heterozygous for atad3 deletion. Embryos of two heterozygous fish were collected at 3 days post fertilization (dpf), when phenotype begins to be apparent, for DNA and RNA extraction. DNA was used for genotyping and RNA was pooled according to genotype. Transcriptome compares siblings, wild-type and atad3-null embryos.

first: Shlomit

last: Ezer

first: Shira

last: Yanovsky-Dagan

first: Nathan

last: Ronin

first: Shahar

last: Rotem-Bamberger

first: Orli

last: Halstuk

first: Hadar

last: Benyamini

first: Ann

last: Saada-Reisch

first: Adi

last: Inbal

first: Tamar

last: Harel


title: Heritable non-genetic phenotypes are enriched for stress responses as a form of bet hedging

city: Newark

first: Mark

last: Blenner

state: Delaware

department: Department of Chemical and Biomolecular Engineering

institute: University of Delaware

summary: To produce humanized therapeutics, Chinese hamster ovary (CHO) cells have become the preferred host organism. During manufacturing batches, these cells encounter critical levels of environmental stressors such as ammonia, lactate, and osmolality accumulation that can significantly reduce cell health and productivity. It is therefore crucial that stress adaptation and resistance be factored into cell line development (CLD) considerations. An alternative to screening stress sensitivity during CLD, where the scaled-down micro-environment makes it difficult, is selecting for or engineering cell lines with a stress resistant phenotype. In this study, we employee population-based transcriptomic analysis and differential gene expression analysis on stress-induced CHO cells to identify biomarkers for engineering stress resistance. These biomarkers are identified as genes displaying heritable properties while being differentially expressed in the presence of manufacturing relevant stress levels. Using this workflow, 199 genes displayed transcriptional variability characteristic of a bistable system that formed six network communities of co-fluctuating genes. These communities were enriched in genes related to response to stimuli, regulation of apoptotic processes, and regulation of gene expression or metabolic pathways. Significant overlap with differentially expressed genes in stress-induced production fed-batch flasks reinforce the relevancy of these heritable genes states for stress adaptation. Assessing the overlap and the biological function, six genes were identified as promising biomarkers for engineering a stress-resistant phenotype. Cell line engineering methods may be employed in the future to bias clonal populations for higher stress tolerance and adaptability to manufacturing stress, therefore increasing cell health and productivity in at-scale bioreactors.

overall_design:
Population-based transcriptomic analysis, known as MemorySeq, in which single-cell derived mini-pools (40 samples) of CHOZN® GS -/- ZFN Clone 23 gene expression is measured in an attempt to correlate highly variable genes with those displaying heritable patterns. Samples compared to bulk RNA-Seq as a noise control to monitor innate biological variability. Collection of genes demonstrating heritable expression patterns compared to differentially expressed genes from day 5 of stress-induced production fed-batch flasks to identify heritable genes critical to stress recognition and adaptation
Please note that only R1 raw data fastq file is provided for the 'MemorySeq_Sample26_Single-Cell-26' sample (as R2 file is corrupted).

first: Grissom

last: Spencer

first: Dixon

last: Zachary

first: Singh

last: Abhyudai

first: Blenner

last: Mark


title: PILRA regulates microglial neuroinflammation and lipid metabolism as a candidate therapeutic target for Alzheimer’s disease

city: South San Francisco

first: David

last: Tatarakis

email: tatarakis@dnli.com, genomics@dnli.com

state: California

address: 161 Oyster Point Blvd

department: Discovery Genomics

institute: Denali Therapeutics

summary: This study seeks to test how PILRA KO affects human microglial response to AD pathology in vivo using a xenotransplant mouse model of AD and single-cell RNA-sequencing.

overall_design: WT and PILRA KO iPSC-derived HSCs were transplanted into immune-deficient mice in a WT or 5XFAD AD model background and allowed to mature into microglia for 6 months. Cells were harvested and FACS sorted then single-cell libraries were built and sequenced.

first: Tanya

last: Weerakkody

first: Kathryn

last: Monroe

first: Mathew

last: Blurton-Jones


title: Tie2 activation relieves lymphedema by improving lymphatic endothelial integrity [Human RNA-seq]

first: Bo-Yoon

last: Park

summary: The aim of this study was to evaluate genetic differences between lymphedema patient and normal using NGS-derived transcriptase profiling (RNA-seq) and quantitative reverse transcriptase chain reaction (qRT-PCR) methods in human fat tissue.

overall_design: mRNA expression profile by Illumina platform in patient and normal fat tissue

first: Il-Kug

last: Kim


title: Genome-wide characterization of fragile and resistant nucleosomes in response to cold stress in maize [RNA-seq]

city: Nanjing

first: huang

middle: ran

last: ran

address: weigang 1

institute: Nanjing Agricultural College

summary: Distinct nucleosome architectures decode key regulatory information related to various cellular processes. However, how fragile (Fra-Nus) and resistant (Res-Nus) nucleosomes, with sensitivity and resistance to MNase cleavage, respectively, are reprogrammed and their potential biological implications under cold treatment is completely uncharacterized in plants. To this end, we conducted MNase-seq with light, medium and heavy MNase digestion in combination with multi-omics data (RNA-seq, ChIP-seq, MH-seq and resequencing data) between COLD and CK.

overall_design: MNase-seq with light, medium and heavy MNase-seq between COLD and CK. Chip-seq of H3K27me3, H3k4me3, H3k9ac between COLD and CK.  RNA-seq between COLD and CK. MH-seq between COLD and CK.

first: Wenli

last: Zhang

first: Ranran

last: Huang

first: Yining

last: Shi


title: Resolution of SARS-CoV-2 infection in human lung tissues is driven by CD163+ inflammatory monocytes (RNA-Seq)

first: Jacquelyn

last: Turcinovic

address: Galveston National Laboratory, 301 University Blvd.

department: Microbiology and Immunology

institute: University of Texas Medical Branch

summary: The lung-resident immune mechanisms driving resolution of SARS-CoV-2 infection in humans remain elusive due to limitations associated with human studies. Using mice co-engrafted with a human immune system and fetal lung xenograft (fLX), we mapped the immunological events defining resolution of SARS-CoV-2 infection in human lung tissues. Viral particles and RNA are rapidly cleared from fLX following a peak of viral replication. Clearance is associated with the emergence of a short-lived inflammatory monocyte (iMO) and a macrophage-like T-cell subset enriched in viral RNA. iMO exhibit an exclusive antiviral response, and the upregulation of monocyte chemoattractive signals by infected fLX underscores a link between circulating CD4+ monocyte recruitment and iMO differentiation. Consistently, mice systemically depleted for human CD4+ cells but not for CD3+ T-cells fail to robustly clear infection and display signatures of chronic infection. Our findings uncover iMO differentiation as a critical hallmark of successful resolution of SARS-CoV-2 infection in human lung tissues, and open avenues to understand the drivers of persistently active SARS-CoV-2 infection.

overall_design: Bulk RNA-seq from fetal lung xenografts in BLT-L mice infected with SARS-CoV-2. Samples taken 2 and 12 days postinfection (dpi) were compared to naïve.

first: Devin

last: Kenney


title: Genome-wide characterization of fragile and resistant nucleosomes in response to cold stress in maize

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

overall_design: Refer to individual Series


title: The DNA methylation profiles of 20 healthy controls

city: Rochester

first: Tao

last: Ma

state: MN

address: 200 1st ST SW

institute: Mayo Clinic

type: Methylation profiling by genome tiling array

summary: Genome wide DNA methylation profiling of 20 healthy individuals. The Illumina Infinium MethylationEPIC array v1 (850K) was used to obtain DNA methylation profiles across approximately 865,000 CpGs in Peripheral blood mononuclear cells.

overall_design: Bisulphite converted DNA from the 20 samples were hybridised to the Illumina Infinium MethylationEPIC array

first: Mrinal

middle: S

last: Patnaik

first: Jenna

last: Fernandez

first: Moritz

last: Binder

first: Liguo

last: Wang


title: Resolution of SARS-CoV-2 infection in human lung tissues is driven by CD163+ inflammatory monocytes (scRNA-Seq)

overall_design: Single-cell RNA-seq from fetal lung xenografts in BLT-L mice infected with SARS-CoV-2. Samples taken 2 and 12 days postinfection (dpi) were compared to naïve.

first: Christelle

last: Harly


title: Genome-wide characterization of fragile and resistant nucleosomes in response to cold stress in maize [ChIP-seq]

overall_design: MNase-seq with light, medium and heavy MNase-seq between COLD and CK.Chip-seq of H3K27me3, H3k4me3, H3k9ac between COLD and CK. RNA-seq between COLD and CK. MH-seq between COLD and CK


title: Casz1 is required for both inner hair cell fate stabilization and outer hair cell survival

first: Zhiyong

last: Liu

address: 7 Science Park Road ZGC Life Science Park

institute: National Institute of Biological Sciences, Beijing

summary: Cochlear inner hair cells (IHCs) and outer hair cells (OHCs) require different transcription factors for their cell fate stabilization and survival, suggesting separate mechanisms are involved. Here, we found that the transcription factor Casz1 was crucial for early IHC fate consolidation and for OHC survival during mouse development. Loss of Casz1 resulted in transdifferentiation of IHCs into OHCs, without affecting OHC production. However, long-term OHC survival was compromised in Casz1 mutant mice. In addition,  the transcription factor Gata3 was downregulated in Casz1-deleted IHCs and overexpressing Gata3 partially rescued IHC properties, OHC numbers, and hearing in Casz1-deleted mice. Thus, Casz1 plays critical roles in early IHC fate stabilization and OHC survival and could potentially provide a lead for therapies aimed at regenerating both IHCs and OHCs.

overall_design: Casz1 -/- IHCs were manually picked using the genetic mouse model: Atoh1Cre/+; Casz1flox/flox; Rosa26-CAG-Loxp-stop-Loxp-3xGFP(Ai47)/Rosa26-CAG-Frt-stop-Frt-tdTomato; Fgf8-Flpo/+. In this model, Casz1 -/- IHCs can be simultaneously labelled with GFP and Tdtomato. In total, 73 GFP+/Tdtomato+ Casz1-/- IHCs at P14 (P14_Casz1-/- IHCs in brief) were manually picked under the fluorescent microscope. The de-novo picked 73 Casz1-/- IHCs at P14 along with the 55 wild type IHCs at P14 in our previous study (GSE199369), were pooled together for further smart-seq based single-cell transcriptomic assay.

first: Yuwei

last: Sun

first: Minhui

last: Ren

first: Yu

first: Shuting

last: Li

first: Zhengnan

last: Luo

first: Suhong

first: Shunji

last: He

first: Guangqin

first: Di

first: Suzanne

last: Mansour

first: Lei

last: Song


title: RIPK4 driven by TP53 mutations promotes resistance to PANoptosis and metastasis of CRC by phosphorylation of MTHFD1 [Anokis_seq]

city: Guangzhou

first: Long

last: Yu

overall_design: Compare the mRNA changes in SW620 and LoVo cells under adherent and suspension conditions for 72 hours.

first: Zhenlin

last: Hou


title: RNA-sequencing of alpha beta hydrolase domain 6 (ABHD6) wild type (WT) versus knockout (KO) Huh7 hepatoma cells with or without palmitic acid treatment.

city: Cleveland

first: Ernest

last: Chan

state: OH

address: 10900 Euclid Ave, Robbins E211

department: PQHS

institute: CWRU

summary: Primary liver cancer accounts for approximately 700,000 deaths worldwide annually ranking third in cancer-related mortality, with hepatocellular carcinoma (HCC) comprising the great majority of these tumors. Recently there has been an emphasis on the role of metabolic syndrome in the development of cirrhosis and HCC, as non-alcoholic fatty liver disease (NAFLD) is currently a leading cause of HCC in the United States. We previously identified the lipid hydrolase alpha/beta hydrolase domain 6 (ABHD6) as a key mediator of the development of metabolic syndrome and intimately involved in cell signaling, making it a prime target for investigation in NAFLD-related HCC. ABHD6 displays higher expression within HCC tumor cores when compared to adjacent non-tumor tissue in human subjects. Using an in vivo antisense oligonucleotide (ASO)-driven knockdown approach, we have shown the inhibition of ABHD6 prevents the development and progression of HCC in an obesity/NAFLD-driven mouse model. Additionally, a xenograft model of using the human Huh7 cell line displayed reduced tumor engraftment and growth with ABHD6 genetic deletion and small molecule inhibition. ABHD6 knockout cells demonstrated increased levels of bis(monoacylglycerol)phosphates (BMPs), lipids relevant to high fat diet-induced lysosomal dysfunction, and knockout cells also demonstrated altered autophagy and lysosomal activity using in vitro model of saturated fatty acid-induced lipotoxicity. These studies reveal novel lipid signaling mechanisms by which NAFLD progresses towards HCC and provide support for ABHD6 as a potential therapeutic target in HCC.

overall_design: RNA from HUH7 WT and ABHD6 KO cells was harvested before (i.e. in basal media) and after 24 and 48 hours of palmitic acid treatment.

first: Danny

last: Orabi

first: E

first: J

last: Brown


title: Tppp3 acts as a new therapeutic gene for optic nerve regeneration

city: Pittsburgh

first: Kun-Che

last: Chang

state: PA

address: 1622 Locust St

department: Department of Ophthalmology

institute: University of Pittsburgh School of Medicine

summary: In this study, we investigated the role of Tppp3 overexpression on axon regeneration and RGC survival in a mouse optic nerve crush model. We observed that Tppp3 overexpression upregulates expression levels of axon regeneration-induced genes and cellular pathways, such as BMP4 and neuroinflammation, thereby resulting in improved RGC survival and axon regeneration.

overall_design: We performed RNA-seq on injured retina samples treated with Tppp3 AAV2 overexpression vector or control AAV2 vector 2 days after optic nerve crush. We wanted to to identify the regulatory mechanism that contributes to the axon regeneration and RGC survival after Tppp3 overexpression.

first: Mishal

last: Rao


title: Effect and mechanism of signal peptide and maltose on recombinant type III collagen production in Pichia pastoris

city: Xi’an

first: yin

middle: xing

last: wang

address: beilin

institute: northwest

summary: In order to investigate the specific mechanism of maltose on the production of recombinant type III collagen by Komagataella phaffii GS115, Two groups were set up, control group C using BMMY medium and experimental group M using BMMY + 1% maltose.

overall_design: At 48h, we subjected the RNA-seq data from groups M and C to gene expression profiling.

first: Xingyin

last: Wang

first: Pan

first: Weina

first: Chenhui

last: Zhu

first: Daidi

last: Fan


title: Effects of m6A modification on turnover of newly synthesized mRNAs at the transcriptome level.

city: Houston

first: Ann-Bin

last: Shyu

address: 6431 Fannin Street, Rm 6.200

institute: The University of Texas Health Science Center at Houston

summary: We developed a method to deconvolute decays of m6A mRNAs and their unmethylated isoforms from newly synthesized total RNAs across the transcriptome to study the effects of m6A modification on decays of not only the m6A-modified RNA pool but also the unmehnylated isoform pool.

overall_design: M6A-RIP-seq was combined with time-course experiments using BrU-mediated metabolic labeling approach to monitor how decays of newly synthesized m6A mRNA and unmethylated isoform mRNA pools may be different at the transcriptome level. Thirty-six RNA samples were generated from two biological repeats.

first: Chyi-Ying

last: Chen


title: Transcriptome-based mapping of m6A sites in newly synthesized mRNA population in U2OS cells.

summary: The goal was to see whether and how mRNA stability is linked to m6A peak position in newly synthesized mRNA population.

overall_design: U2OS cells were metabolically labeled with bromouridine (BrU). Total cytoplasmic mRNA was extracted from labeled U2OS cells followed by BrU-RNA immunoprecipitation (BrU-RIP) to purify BrU-labeled mRNAs that represent a pool of newly synthesized mRNA. Four RNA samples were collected and fragmented to an average size of about 100nt, which was followed by m6A-RNA IP of m6A site-bearing RNA fragments.


title: Genome-Wide Profiling and Differential Expression of mRNA and microRNA in Vitrified–Warmed Mouse Blastocyst

city: Taichung

first: Chi-Ying

last: Lee

address: No.30-6, Sec. 1, Changping Rd., Beitun Dist., Taichung 406, Taiwan

country: Taiwan

institute: Taiwan IVF center, Lee's women's hospital

summary: Blastocyst vitrification has significantly changed the embryo transfer method.Vitrification of human blastocysts may result in higher implantation success rates and heavier birth weightsin subsequent frozen embryo transfer cycles. This study investigated the effects of vitrification onthe transcriptome profiles and implantationof mouse blastocysts. First, a fold-change cutoff of±2 was used to distinguish differentially expressed genes. Transcriptomic analysis indicatedthat differentially expressed genes of vitrified–warmed blastocysts were mainly related to cell development, proliferation, projection,motility,and calcium-binding protein and MAPK-related signaling pathways.Second, we performed reverse transcriptase-quantitative polymerase chain reaction to verify the gene expression in the next-generation sequencing results, including increased genes such as GPR132, CDK6, FOS, and NFAT2and decreased genes such as DKK3 and MAPK10. Finally, blastocysts may communicate with the maternal uterine via microRNA to regulate gene expression in the embryo and endometrium. Prediction of microRNA candidateswas performed using the results of next-generation sequencing transcriptomicanalysis and validatedthroughmicroRNA assay. A total of 12 validated blastocyte microRNAs may affect uterine epithelial cell adhesion, trophectoderm development, invasive capacity, or immune responses to increase pregnancy success rates. In conclusion, vitrification alters the transcriptome of mouse blastocysts, resulting in small changes in gene expression and an increased implantation success rate.

overall_design: Embryos from B6CBF1 mice were cultured in human tubal fluidfor 3days. Embryo transfer was performed 2.5 days following mating. Six vitrified–warmed blastocysts were transferred to the right uterine horn in the same recipient. The same number of fresh blastocystswere transferred to the left uterine horn of pseudopregnant recipients. The mice were euthanized4days after embryo transfer.

first: Han-Ni

last: Tsai

first: En-Hui

last: Cheng

first: Tsung-Hsien

first: Pin-Yao

last: Lin

first: Chun-I

first: Maw-Sheng


title: Genome-wide characterization of fragile and resistant nucleosomes in response to cold stress in maize [MNase-seq]

first: huang

last: ran

overall_design: MNase-seq with light, medium and heavy MNase-seq between COLD and CK. Chip-seq of H3K27me3, H3k4me3, H3k9ac between COLD and CK. RNA-seq between COLD and CK. MH-seq between COLD and CK.

first: Wenli

last: Zhang

first: Ranran

last: Huang

first: Yining

last: Shi


title: Effects of m6A modification and YTHDF2 knockdown on global mRNA turnover

summary: We developed a method to deconvolute decays of m6A mRNAs and their unmethylated isoforms from total RNAs across the transcriptome and combined this method with the knockdown of m6A reader protein to study the effect on global mRNA turnover.

overall_design: M6A-RIP-seq approach was combined with time-course experiments to monitor total RNA, m6A mRNA and unmethylated isoform mRNA decays across the transcriptome upon DF2 knockdown by two different DF2 siRNAs. Knockdown with a control siRNA was used as a negative control.  A total of fifty-four RNA samples was generated.


title: RNA Sequencing Facilitates Quantitative Analysis of rat pancreas islet beta cell Transcriptomes in uric acid treat

city: guangzhou

first: li

last: xueyan

address: NO.74 2nd Zhongshan Road

institute: Sun Yat-Sen University

summary: The effect of uric acid on islet function remains to be confirmed,We applied GSIS, immunofluorescence staining, WB, and flow cytometry to observe the protective effects of uric acid on beta cell apoptosis and insulin deficiency.To further explore the molecular mechanisms involved in this,we found UA could directly suppressed GSIS in both INS-1E cells and primary isolated islets in a dose- and time-dependent manner. RNAseq suggested that CHOP/NLRP3 is critical in the UA-induced beta cell dysfunction. These data suggest that UA might be an independent risk factor for beta cell function which induced beta cell dysfunction via OAT2/chop/ NLRP3 pathway. which provided new insight into the diabetogenic effect of UA.

overall_design: Examination of the transcriptome of INS-1E cell lines in the presence of uric acid with three replicates.

first: Xueyan

last: Li


title: Expression profiles of microRNAs in fetus and lamb muscle tissue.

first: Zhen

institute: Nanjing Agricultural University

type: Non-coding RNA profiling by high throughput sequencing

summary: We report the application of single-molecule-based sequencing technology for high-throughput profiling of miRNAs in goat muscle tissue.We identified 1120 miRNAs in fetus and lamb muscle tissue; 895 were known miRNAs and 313 were novel miRNAs. According to analysis, 192 miRNAs were up-regulated in fetus samples compared to lamb samples, while 121 miRNAs were down-regulated.To confirmed stage-specific differences in the abundance of certain miRNAs, we focused on the most up-regulated miRNA and found to be predominantly expressed in lamb muscle tissue, suggesting a potential role in muscle development.It has become a molecular marker for breeding programs of mutton production.

overall_design: MicroRNA profiles in the longissimus muscle of fetus (75 day of pregnancy) and lamb (1 day of age)

first: Yixuan


title: RNA-Sequece Analysis of si-YBX1and SI-NC IN 231 CELLS

city: Jiaxing

first: Huadong

last: Ni

address: zhonghuan nan road 1882

institute: Department of Anesthesiology and Pain Research Center, The Affiliated Hospital of Jiaxing University

summary: RNA-seq was used to analyze the differential expression of mRNAs between si-YBX1 and si-NC231 cells.

overall_design: YBX1was knocked down by transfection with YBX1 Smart Silencer in 231cells. After 48h, we obtained the samples.

first: Hai-ting

last: Liu

first: Sen

first: Xiang-yu

last: Guo

first: Guo-hao


title: Transcriptome-wide mapping of m6A sites with or without YTHDF2 (DF2) knock-down in U2OS cells.

first: Ann-Bin

summary: The goal was to see whether and how mRNA stability is linked to m6A peak position in mRNA. The RNA-seq data set in this submission represents a technical RNA-seq repeat of samples 1, 3, 5, 6, 7, and 8 described in a previous GEO submission (GSE181079).

overall_design: Total cytoplasmic mRNA was extracted from U2OS cells with or without DF2 knockd-down. Six RNA samples were collected and fragmented to an average size of about 100nt, which was followed by m6A-RNA IP of m6A site-bearing RNA fragments.

first: Chyi-Ying


title: Genome-wide characterization of fragile and resistant nucleosomes in response to cold stress in maize [MH-seq]

overall_design: MNase-seq with light, medium and heavy MNase-seq between COLD and CK. Chip-seq of H3K27me3, H3k4me3, H3k9ac between COLD and CK. RNA-seq between COLD and CK.MH-seq between COLD and CK.


title: Loss of Spindly sensitizes EML4-ALK v3 lung cancer cells to HSP90 inhibitors

city: London

first: Chi

address: 15 Cotswold Road

department: Division of Cancer Therapeutics

institute: The Institute of Cancer Research

summary: Heat Shock Protein 90 inhibitors (HSP90i) have shown encouraging activity in EML4-ALK+ non-small cell lung cancer (NSCLC) patients but clinical responses have been heterogeneous. It has been suggested that distinct EML4-ALK variants may have a differential impact on the response to HSP90 inhibition. Here, we show that NSCLC cells harboring the most common EML4-ALK variant 1 (v1) or variant 3 (v3) are similarly sensitive to HSP90i. To discover new genetic alterations that could be involved in stratifying sensitivity, we performed a genome-wide CRISPR/Cas9 knockout screen and found that loss of Spindly increases the sensitivity of EML4-ALK v3, but not v1, NSCLC cells to low concentrations of HSP90i from three distinct chemical families. Upon loss of Spindly, prolonged exposure to low concentrations of HSP90i impairs chromosome congression and cellular fitness. Collectively, our data suggest that mutations leading to loss of Spindly in EML4-ALK v3 NSCLC patients may increase sensitivity to low doses of HSP90i.

overall_design: H2228 cells stably expressing lentiviral Cas9 were transduced with non-targeting sgRNA, or sgRNA targeting SPLD1 gene. Control or SPLD1-knockout cells were then treated with DMSO or tanespimycin (17-AAG), and effects of sgRNA-guided gene knockout and/or tanespimycin treatment were investigated using RNAseq.

first: Marco

last: Licciardello

first: Ahn

middle: T

last: Le

first: Robert

last: Doebele

first: Paul

last: Clarke

last: Workman


title: Non-self induced AIG2A and AIG2B genes repress two chemical defense pathways to modulate plant immunity

city: Ithaca

first: Zhixue

last: Wang

address: 236 Tower Rd

institute: Cornell University

summary: we performed whole genome transcriptome (RNA-seq) analysis to understand how AIG2 genes influence plant immunity.

overall_design: Examination of whole genome transriptome (RNA-seq) in Col-0, aig2abc, pad4, aig2abcpad4. Two-week-old plants growing under constant light at 22C were used for RNA extraction.

first: Jian

last: Hua


title: m6A modification governs the stability of both methylated and unmethylated mRNA isoforms across the transcriptome

last: Shyu

overall_design: Refer to individual Series


summary: The goal was to see whether and how mRNA stability is linked to m6A peak position in mRNA.

overall_design: Total cytoplasmic mRNA was extracted from U2OS cells with or without DF2 knockd-down. Eight RNA samples were collected and fragmented to an average size of about 100nt, which was followed by  m6A-RNA IP of m6A site-bearing RNA fragments.

last: Chen


title: Primary cilia, transition zone protein B9d1 is required for proper cell growth and ribosome biogenesis during meiotic prophase in males

city: Stanford

first: Kazuteru

last: Hasegawa

address: Lorry Lokey Stem Cell Research Building (SIM1), G2165 265 Campus Drive

institute: Stanford University

summary: To investigate how primary cilia or ciliary signaling pathway(s) influence gene expression profile during meiotic prophase in male flies, we used RNA-seq from testes of B9d1 Knock-down, Tektin-C Knock-down, Klp59D Knock down, wild-type and sa-/- mutant.

overall_design: Each sequencing assay included spermatocyte-enriched samples and wild-type samples, with 2 replicates for each condition

first: Hosu

last: Sin

first: Dan

last: Lu

first: Margaret

last: Fuller


title: Next-Generation Sequencing Facilitates Quantitative Analysis of Control and FTO Inhibitor-treated Uterine Leiomyosarcoma Cell Transcriptome

city: Chicago

first: Qiwei

last: Yang

state: IL

address: 5821 S Drexel Ave

department: Obstetrics and Gynecology

institute: The University of Chicago

summary: We report that FTO inhibition alters multiple biological pathways in uterine leiomyosarcoma cells

overall_design: Examine the transcriptome alteration in uterine leiomyosarcoma cells with or without FTO inhibitor

first: Ayman

last: Al-Hendy


title: Bulk ATAC sequencing on different skeletal cell subsets isolated from PolG D257A/D257A mouse femurs

city: New York

first: Matthew

last: Greenblatt

state: NY

address: 1161 York Ave APT 1a

department: Pathology and Laboratory Medicine

institute: WEILL CORNELL MEDICAL COLLEGE

summary: To determine lineage and differentiation relationships among skeletal cell types in their native environment, we utilized PolGD257A/D257A mice with a mitochondrial DNA “mutator” phenotype for tracking clonal and sub-clonal mitochondrial mutations across skeletal populations .

overall_design: Perform FACS isolation of different skeletal cell subsets from 3 month old PolG D257A/D257A mouse femurs

first: Shawon

last: Debnath

first: Tuo

last: Zhang

first: Sarfaraz

last: Lalani

first: Jason

last: Mc Cormick


title: Bulk RNA sequencing on CD24+CD29+SSCs isolated from femurs of mice exposed to Low fat diet and High fat diet for 4 weeks

summary: To understand how High fat diet and Low fat diet exposure alters gene expression profile in CD24+CD29+SSC present in the bone.

overall_design: Perform FACS isolation of CD24+CD29+SSCs from mouse femurs after 4 weeks of diet exposure and subjecting them to RNA sequencing


title: The effect of fusiogenicity on transcription profile: Transcription profiles of hyper-fusiogenic and hypo-fusiogenic mutants were tested on HEK293T cells via transfection at 17 h

city: ITHACA

first: Hector

last: Aguilar-Carreno

state: New York

address: T8016A Veterinary Research Tower

summary: To delineate cellular processes involved in NiV FG combination and mutants with different fusiogenecity, we have employed whole genome microarray expression profiling as a discovery platform to identify the upregulated and downregulated genes. Total RNA was collected from transfected cells and untransfected controls. Cy3 labeled cRNA is used for hybridization platform Agilent Human 4 x 44K gene expression array.

overall_design: FG and mutants transfections were performed at 17h. These transfected cells were compared to untransfected HEK293T cells. Five replicates were performed for each condition.

last: Aguilar

first: Joshua

last: Adkins


title: NiV infection transcriptomics profile on HEK29T cells

summary: To delineate cellular processes involved in NiV infection, we have employed whole genome microarray expression profiling as a discovery platform to identify the upregulated and downregulated genes. Total RNA was collected from infected cells and uninfected controls. Cy3 labeled cRNA is used for hybridization platform Agilent Human 4 x 44K gene expression array.

overall_design: Time-course based infections were performed at moi 1. 4h, 8h, 12h, 16h infections were compared to uninfected HEK293T cell transcriptomics. Five replicates were performed for each condition, and labeled as A through E.


title: Transcriptomics profile of NiV genes F, G, M and combinations on HEK293T cells using transfection at 44 h

summary: To delineate cellular processes involved in NiV F, G, M, and combinations, we have employed whole genome microarray expression profiling as a discovery platform to identify the upregulated and downregulated genes. Total RNA was collected from transfected cells and untransfected controls. Cy3 labeled cRNA is used for hybridization platform Agilent Human 4 x 44K gene expression array.


title: Interactive relationships between potential miRNAs and target mRNAs in deep venous thrombosis identified by RNA sequencing

city: shijiazhuang

first: qingxian

last: wang

address: No.139 Ziqiang Road, Qiaoxi District

department: Department of Orthopedic Trauma

institute: Orthopedic Research Institution of Hebei Province

summary: Background: Deep venous thrombosis is one of the most common peripheral vascular diseases that lead to major morbidity and mortality. We aimed to identify potential differentially expressed miRNAs and target mRNAs, which were helpful in understanding the potential molecule mechanism of deep venous thrombosis.

overall_design: Serum samples from 3 female patients with calf intermuscular vein thrombosis and 3 female patients with fracture group (as controls) were collected for miRNA bank sequencing, and the expression profiles of differential miRNA were analyzed


title: Compartmentalization and persistence of dominant (regulatory) T cell clones indicates antigen skewing in juvenile idiopathic arthritis

city: Utrecht

first: Aridaman

last: Pandit

address: Heidelberglaan 100

institute: University Medical Center Utrecht

summary: We performed T cell receptor (TCR) sequencing to study immune cell composition and (hyper-)expansion of circulating and joint-derived Tregs and non-Tregs in Juvenile Idiopathic Arthritis (JIA, N=9). We studied different joints affected at the same time, as well as over the course of relapsing remitting disease.

overall_design: Examination of circulating and joint derived (regulatory) T cell receptors from JIA patents

first: Femke

last: van Wijk

first: Gerdien

last: Mijnheer

first: Nila

middle: H

last: Servaas

first: Jing

middle: Y

last: Leong

first: Arjan

last: Boltjes

first: Eric

last: Spierings

first: Phyllis

first: Liyun

last: Lai

first: Alessandra

last: Petrelli

first: Sebastiaan

last: Vastert

first: Rob

last: de Boer

first: Salvatore

last: Albani


title: The effect of fusiogenicity on transcription profile: Transcription profiles of hyper-fusiogenic and hypo-fusiogenic mutants were tested on HEK293T cells via transfection at 21 h

overall_design: FG and mutants transfections were performed at 21h. These transfected cells were compared to untransfected HEK293T cells. Five replicates were performed for each condition.


title: Consideration of genetic and sex effects in mice enhances consilience with human addiction studies

city: Bar Harbor

first: Michael

middle: C.

last: Saul

state: ME

address: 600 Main St

institute: The Jackson Laboratory

summary: Concerns about translation of findings across species and external validity of rodent models are often based on results from narrow investigations of populations with limited diversity. Sources of individual variation – including genetics and sex – are not often directly encompassed in model organism studies. Explicit inclusion of individual differences in rodent research has the potential to reveal conserved phenotypes and molecular systems relevant to human addiction. As with most complex diseases, risk for cocaine use disorder is subject to considerable inter-individual variation. We surveyed cocaine-related behavioral traits in both males and females of eight inbred mouse strains whose genomes collectively capture 90% of the genetic diversity of the mouse species. Across these strains, individual differences explained a substantial proportion of variance in cocaine-responsive or cocaine response-predictive behavioral and physiological phenotypes. The inclusion of wild-derived mouse strains often extended the phenotypic ranges of these behaviors beyond the range observed in conventional domestic laboratory mouse strains. Striatum transcriptional responses to cocaine were also highly dependent upon strain and sex differences, with most cocaine-responsive genes being differentially expressed in a manner moderated by strain, sex, or their combination. We compared the strain- and sex-mediated transcriptional responses to cocaine in mice to transcriptomic analysis of people with cocaine use disorder, finding that mouse similarity to humans was highly dependent upon mouse genetic background and sex. Specifically, male WSB/EiJ mice and female NOD/ShiLtJ mice exhibited the greatest extent of neural transcriptional consilience with humans with cocaine use disorder. Model organism diversity thus represents a crucial source of biological information that can substantially improve external validity of research into addiction risk mechanisms.

overall_design: This RNAseq dataset includes 128 mice from 8 inbred strains (129S1/SvImJ, A/J, C57BL/6J, NOD/ShiLtJ, NZO/HlLtJ, CAST/EiJ, PWK/PhJ, and WSB/EiJ), two sexes (sex_chrY: M, F), and who received repeated injections of either cocaine (injection: cocaine, sham). Choroid plexus contamination was identified in some samples  (choroid_plexus). Total RNA libraries were prepared using ribosomal depletion and sequenced to a median depth of 132M reads.

first: Jared

middle: R

last: Bagley

first: Lauren

last: Bailey

first: Udita

last: Datta

first: Price

middle: E

last: Dickson

first: Rainy

last: Dodd

first: Leona

last: Gagnon

first: Violet

last: Kimble

last: Leonardo

first: Sam-Moon

last: Kim

first: Ashley

last: Olson

first: Tyler

last: Roy

first: Sarah

last: Schoenrock

first: Troy

last: Wilcox

first: J

last: Jentsch

first: Ryan

last: Logan

first: Colleen

last: McClung

first: Vivek

last: Philip

first: Laura

middle: G

last: Reinholdt

first: Stacey

last: Sukoff Rizzo

first: Lisa

last: Tarantino

first: Elissa

last: Chesler


title: The effects of fenofibrate and fish oil on gene expression in peripheral blood mononuclear cells, muscle, and adipose tissue from overweight and obese individuals

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

institute: Wageningen University

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


title: The effects of fenofibrate and fish oil on gene expression in peripheral blood mononuclear cells, muscle, and adipose tissue from overweight and obese individuals [PBMC]

summary: The molecular effects of the non-selective dietary PPARalpha agonists n-3 LCPUFAs were compared side-by-side with those of the selective synthetic PPARalpha agonist fenofibrate on whole-genome gene expression in peripheral blood mononuclear cells (PBMCs), white adipose tissue (WAT), and muscle in overweight and obese subjects. Eleven overweight and obese subjects participated in a randomized, double-blind, placebo-controlled intervention trial and received in random order 3.7 g/d n-3 fatty acids (providing 1.7 g/d EPA and 1.2 g/d DHA), 200 mg fenofibrate or placebo treatment for 6 weeks separated by a wash-out period of at least 2-weeks. Fenofibrate changed 5 of the analysed 64 PPARalpha target genes in PBMC, 4 in muscle, and 2 in WAT, whereas fish oil changed 2 genes in WAT only. Both treatments changed 17 out of 25 similar pathways in PBMCs, related to xenobiotic metabolism, biosynthesis of steroids, lipid metabolism, transcription, proteasome function, Th1 immunity, propanoate metabolism and nucleotide metabolism. The majority (18 out of 25) of downregulated pathways in WAT were similarly changed in PBMCs after fish oil and related to lipid metabolism and amino acid metabolism. Fenofibrate and fish oil hardly affected pathways in muscle. In PBMCs, fenofibrate and fish oil only regulated 9 similar genes in metabolic syndrome-related pathways, which were IL25, TICAM1, PRDX2, PTGS1, AGK, FDPS, LDLR, TNNI3, LMAN1 and PTGS1. Overall, 6-weeks treatment with n-3 LCPUFAs and fenofibrate hardly affected PPARalpha target genes in overweight and obese subjects. Pathway analyses suggested that gene expression profiles in PBMCs can provide information about regulated metabolic processes by fish oil and fenofibrate in WAT, but not muscle. Expression of the individual genes, however, hardly overlapped between the tissues.

overall_design:
Eleven subjects with a BMI of at least 27 kg/m2 particpated in a randomized, double-blind, placebo-controlled, crossover study, and were exposed fish oil, fenofibrate and placebo. After exposure, gene expression was determined in peripheral blood mononuclear cells, white adipose tissue and muscle tissue by microarrays.
PBMC data presented here.

first: Marjolijn

last: Bragt

first: Mark

middle: V

last: Boekschoten

first: Michael

last: Müller

first: Ronald

last: Mensink


title: NiV genes F, G, and FG combination transfection transcriptomics profile on HEK293T cells

first: Hector

last: Aguilar-Carreno

summary: To delineate cellular processes involved in NiV F, G, and FG combination, we have employed whole genome microarray expression profiling as a discovery platform to identify the upregulated and downregulated genes. Total RNA was collected from transfected cells and untransfected controls. Cy3 labeled cRNA is used for hybridization platform Agilent Human 4 x 44K gene expression array.

overall_design: Time-course based transfections were performed at 6h, 12h, and 29h post-transfection time-points. These transfected cells were compared to untransfected HEK293T cells. Five replicates were performed for each condition.

last: Aguilar

first: Joshua

middle: N

last: Adkins


title: The effects of fenofibrate and fish oil on gene expression in peripheral blood mononuclear cells, muscle, and adipose tissue from overweight and obese individuals [muscle]

overall_design:
Eleven subjects with a BMI of at least 27 kg/m2 particpated in a randomized, double-blind, placebo-controlled, crossover study, and were exposed fish oil, fenofibrate and placebo. After exposure, gene expression was determined in peripheral blood mononuclear cells, white adipose tissue and muscle tissue by microarrays.
Muscle data presented here.


title: HeV genes F, G, and FG combination transfection transcriptomics profile on HEK29T cells

summary: To delineate cellular processes involved in HeV F, G, and FG combination, we have employed whole genome microarray expression profiling as a discovery platform to identify the upregulated and downregulated genes. Total RNA was collected from transfected cells and untransfected controls. Cy3 labeled cRNA is used for hybridization platform Agilent Human 4 x 44K gene expression array.

overall_design: Time-course based transfections were performed at 6h, 12h, and 21h post-transfection time-points. These transfected cells were compared to untransfected HEK293T cells. Five replicates were performed for each condition.


title: The effects of fenofibrate and fish oil on gene expression in peripheral blood mononuclear cells, muscle, and adipose tissue from overweight and obese individuals [WAT]

overall_design:
Eleven subjects with a BMI of at least 27 kg/m2 particpated in a randomized, double-blind, placebo-controlled, crossover study, and were exposed fish oil, fenofibrate and placebo. After exposure, gene expression was determined in peripheral blood mononuclear cells, white adipose tissue and muscle tissue by microarrays.
WAT data presented here.


title: Differential effects of m6A modification and YTHDF2 knockdown on global mRNA turnover

first: Ann-Bin

last: Shyu

summary: We developed a method to deconvolute decays of m6A mRNAs and their unmethylated isoforms from total RNAs across the transcriptome and combined it with the knockdown of m6A reader protein to study it's effect on global mRNA turnover.

overall_design: M6A-RIP-seq approach was combined with time-course experiments to monitor m6A mRNA and unmethylated isoform mRNA decays across the transcriptome upon DF2 knockdown. Knockdown with a negtaive control siRNA was used as a control. Fifty-four samples of total cytoplasmic RNA were generated.

first: Chyi-Ying

middle: A

last: Chen


title: Organ-specific function of PPARa

summary:
The peroxisome proliferator-activated receptor alpha (PPARα) is a fatty acid-activated transcription factor that governs a variety of biological processes. Little is known about the role of PPARα in the small intestine. Since this organ is frequently exposed to high levels of PPARα ligands via the diet, we set out to characterize the function of PPARα in small intestine using functional genomics experiments and bioinformatics tools. PPARα was expressed at high levels in both human and murine small intestine. Detailed analyses showed that PPARα was expressed highest in villus cells of proximal jejunum. Microarray analyses of total tissue samples revealed, that in addition to genes involved in fatty acid and triacylglycerol metabolism, transcription factors and enzymes connected to sterol and bile acid metabolism, including FXR and SREBP1, were specifically induced. In contrast, genes involved in cell cycle and differentiation, apoptosis, and host defense were repressed by PPARα activation. Additional analyses showed that intestinal PPARα dependent gene regulation occurred in villus cells. Functional implications of array results were corroborated by morphometric data. The repression of genes involved in proliferation and apoptosis was accompanied by a 22% increase in villus height, and a 34% increase in villus area of wild-type animals treated with WY14643. This is the first report providing a comprehensive overview of processes under control of PPARα in the small intestine. We show that PPARα is an important transcriptional regulator in small intestine, which may be of importance for the development of novel foods and therapies for obesity and inflammatory bowel diseases.
Keywords: Identification of organ specifc target genes

overall_design:
Pure bred wild-type (129S1/SvImJ) and PPARα-null (129S4/SvJae) mice were treated with the synthetic PPARα ligand WY14,643 (0.1% w/w) for 5 days. Small intestine and liver were removed and total RNA was isolated.
In total 4 experimental groups were present: wild type mice fed the control diet (AIN93M), wild type mice fed the control diet supplemented with 0.1% w/w WY14,643 for 5 days, PPARα knockout mice fed the control diet, PPARα knockout mice fed the control diet supplemented with 0.1% w/wWY14,643 for 5 days.
RNA of 4 biological replicates was hybridized to Affymetrix 430 2.0 arrays.
Five microgram total RNA was labelled according to the ENZO-protocol, fragmented and hybridized according to Affymetrix's protocols.

first: Meike

last: Bunger

first: Philip

middle: J

last: de Groot

first: Sander

last: Kersten

last: Muller


title: Mannose reduces fructose metabolism and reverses MASH in human liver slices and murine models in vivo

status: Public on Jan 31 2025

city: NEW YORK

first: Charles

last: DeRossi

address: 1 Gustave L. Levy Place, Box, Annenberg 14-12

department: Pediatrics

institute: Icahn School of Medicine at Mount Sinai

summary: Background & Aims: Fibrosis drives liver-related mortality in metabolic dysfunction-associated steatohepatitis (MASH), yet we have limited medical therapies to target MASH-fibrosis progression. Here we report that mannose, a simple sugar, attenuates MASH steatosis and fibrosis in two robust murine models and human liver slices.  Methods: The well-validated FAT-MASH murine model for liver steatosis and fibrosis was employed. Mannose was supplied in the drinking water at the start (“Prevention” group) or at week 6 of the 12-week MASH regimen (“Therapy” group). The in vivo anti-fibrotic effects of mannose supplementation were tested in a second model of carbon tetrachloride (CCl4)-induced liver fibrosis. A quantitative and automated digital pathology approach was used to comprehensively assess steatosis and fibrosis phenotypes.  Mannose was also tested in vitro in human and primary mouse hepatocytes conditioned with free fatty acids alone or with fructose, and Human Precision Cut Liver Slices (hPCLS) from patients with end-stage MASH cirrhosis.  Results: Oral mannose supplementation improved liver fibrosis in vivo in both FAT-MASH and CCl4 mouse models, as well as in hPCLS MASH samples. Mannose also reduced liver steatosis in FAT-MASH mice, and in human and mouse hepatocytes in vitro. Ketohexokinase (KHK), the main enzyme in fructolysis, was decreased with mannose in whole mouse liver, cultured hepatocytes, and hPCLS. Removal of fructose or overexpression of KHK each abrogated the anti-steatotic effects of mannose.  Conclusions: This study identifies mannose as a novel therapeutic candidate for MASH that mitigates steatosis by dampening hepatocyte KHK expression and exerts independent anti-fibrotic effects in two mouse models and human liver tissue slices.

overall_design: RNA-seq profiling of total mouse liver RNA from mice raised for 12 weeks (starting age 8 weeks old, end 20 weeks) on normal chow diet, or high fat/sugar/cholesterol diet with weekly low dose carbon tetrachloride IP injection (FAT-MASH regimen). Treatment groups were without mannose, 5% mannose, or 20% mannose in drinking water (ad libitum) for 12 weeks (Prevention groups), or mannose commencing at 6-weeks on diet (Therapy groups).

first: John

last: Hong

first: Jaime

last: Chu


title: Modeling sex differences in humans using isogenic induced pluripotent stem cells (RRBS)

city: Jerusalem

first: Ithai

last: Waldhorn

address: Kiryat Hadassah

department: Goldyne Savad Institute of Gene Therapy

institute: Hebrew University

summary: We developed a cellular model to study sex differences in humans. Using somatic cells from a mosaic Kleinefelter patient, we generated isogenic human induced pluripotent stem cell lines with different sex chromosome complements – 47,XXY / 46,XX / 46,XY and 45,X0.

overall_design: Reduced representation bisulfite sequencing (RRBS) of six isogenic hiPSC cell lines - XX1, XX2, XX3, XY1, XY2, XY3

first: Benjamin

last: Reubinoff


title: Endoplasmic reticulum proteins impact penetrance in a pink1-mutant Drosophila model

city: Lübeck

first: Hauke

last: Busch

state: Schleswig-Holstein

address: Ratzeburger Allee 160

department: Lübeck Institute of Experimental Dermatology

institute: University of Lübeck

summary: Parkinson’s disease (PD) is a neurodegenerative disorder with a high variability of age at onset, disease severity, and progression. This suggests that other factors, including genetic, environ-mental, or biological factors, are at play in PD. Loss of PINK1 causes a recessive form of PD and is typically fully penetrant; however, it features a wide range in disease onset, further supporting the existence of protective factors, endogenous or exogenous, to play a role. Loss of Pink1 in Drosophila melanogaster results in locomotion deficits, also observed in PINK1-related PD in humans. In flies, Pink1 deficiency induces defects in the ability to fly; none-theless, around ten percent of the mutant flies are still capable of flying, indicating that advanta-geous factors affecting penetrance also exist in flies. Here, we aimed to identify the mechanisms underlying this reduced penetrance in Pink1-deficient flies. We performed genetic screening in pink1-mutant flies to identify RNA expression alterations affecting the flying ability. The most important biological processes involved were transcription-al and translational activities, endoplasmic reticulum (ER) regulation, and flagellated movement and microtubule organization. We validated 2 ER-related proteins, zonda, and windbeutel, to positively affect the flying ability of Pink1-deficient flies. Thus, our data suggest that these pro-cesses are involved in the reduced penetrance and that influencing them may be beneficial for Pink1 deficiency.

overall_design: w pink1B9 null mutants and controls (w pink1RV) were kindly provided by Jeehye Park and Jongkyeong Chung (Korea Advanced Institute of Science and Technology). y[1] w[*]; M{RFP[3xP3.PB] w[+mC]=UAS-KDELR-RFP}ZH-22A (UASKdelR) were generously shared by the Katanaev laboratory (Department of Pharmacology and Toxicology, University of Lausanne) . Two independent lines of Zda (w1118; PBac{IT.GAL4}zda0818-G4 (Zda1) and y1 w67c23; P{EPgy2}zdaEY08359 (Zda2)), and daughterless Gal4 (DaGal4) were purchased from the Bloomington Stock Center (Indianapolis, United States of America). M[UAS-Torsin.ORF.3xHA.GW]ZH-86Fb (UASTor-sin) and M[UAS-Wbl.ORF.3xHA.GW] (UASWbl) were purchased from the FlyORF stock center (Zurich, Switzerland). One-day-old male flies were collected and tested for their flying ability. Flies were placed in an empty vial that was gently tapped. Flies able or unable to fly were scored one and zero, respectively. For the sequencing analyses, the offspring of each parent pair that was able to fly (group 4) was separately collected from those that were not able to fly (group 3). RNA sequencing was performed on four different groups. Group 1 are control flies (pink1RV), group 2 are pink1B9-mutant flies of which none of the offspring was able to fly, groups 3 and 4 are pink1B9-mutant flies that are offspring from the same parent, but in group 3, none of the flies were able to fly, while in group 4 all the flies were able to fly.

first: Fabian

last: Ott

first: Melissa

last: Voss

first: Christine

last: Klein