title: Mesenchymal stem cells overexpressing neuropeptide S promote the recovery of rats with spinal cord injury by activating the PI3K/AKT/GSK3β signaling pathway

city: Wuxi

first: 文慧

last: 杨

state: 江苏 Jiangsu

address: 1800 Lihu Avenue

institute: 江南大学 Jiangnan University

summary: Overexpressing EMSCs can significantly improve the therapeutic effect of spinal cord injury in rats, which provides strong support for the feasibility of the use of gene modification of mesenchymal stem cells in clinical applications.

overall_design: Total RNA was extracted from EMSCs and NPS-EMSC by TRIzol Reagent, in duplicate3.

first: wenhui

last: yang

first: yilu

last: li

first: yushi

last: tang


title: Small molecule treatment alleviates photoreceptor cilia defects in LCA5-deficient human retinal organoids

status: Public on Feb 19 2025

city: London

first: Michael

last: Cheetham

address: 11-43 Bath St

department: Institute of Ophthalmology

country: United Kingdom

institute: University College London

type: Expression profiling by high throughput sequencing

summary: Bialleleic pathogenic variants in LCA5 cause one of the most severe forms of Leber congenital amaurosis, an early-onset retinal disease that results in severe visual impairment. Here, we report the use of gene editing to generate isogenic LCA5 knock-out (LCA5 KO) induced pluripotent stem cells (iPSC) and their differentiation to retinal organoids. The molecular and cellular phenotype of the LCA5 KO retinal organoids was studied in detail and compared to isogenic controls as well as patient-derived retinal organoids.  The absence of LCA5 was confirmed in retinal organoids by immunohistochemistry and western blotting. There were no major changes in retinal organoid differentiation or ciliation, however, the localisation of CEP290 and IFT88 was significantly altered in LCA5 KO and patient photoreceptor cilia with extension along the axoneme. The LCA5-deficient organoids also had shorter outer segments and rhodopsin was mislocalised to the outer nuclear layer. We also identified transcriptomic and proteomic changes associated with the loss of LCA5. Importantly, treatment with the small molecules eupatilin, fasudil or a combination of both drugs improved rhodopsin traffic to the outer segment and reduced mislocalisation of rhodopsin in the outer nuclear layer. The treatments also effectively reduced  CEP290 and IFT88 accumulation along the cilia. The improvements in cilia-associated protein localisation and traffic were accompanied by significant changes in the transcriptome towards control gene expression levels in many of the differentially expressed genes. In summary, iPSC-derived retinal organoids are a powerful model for investigating the molecular and cellular changes associated with loss of LCA5 function and highlight the therapeutic potential of small molecules to treat retinal ciliopathies.

overall_design: Comparison of LCA5-knockout organoids treated with either eupatilin or fasudil against untreated knockout control organoids.

first: Dimitra

last: Athanasiou

first: Tess

last: Afanasyeva

first: Niuzheng

last: Chai

first: Kalliopi

last: Ziaka

first: Katarina

last: Jovanovic

first: Rosellina

last: Guarascio

first: Karsten

last: Boldt

first: Julio

last: Corral-Serrano

first: Naheed

last: Kanuga

first: Ronald

last: Roepman

first: Rob

last: Collin


title: Single-cell RNA sequencing of breast cancer cells from fresh fixed (FF) and formalin-fixed paraffin-embedded (FFPE) tissue identified multi-ciliary cells

city: Madrid

first: Silvia

last: Gonzalez-Martinez

address: M-607, Km. 9, 100, Fuencarral-El Pardo

department: Pathological Anatomy

country: Spain

institute: Ramon y Cajal University Hospital

summary: This study evaluates the feasibility of using formalin-fixed paraffin-embedded (FFPE) and fixed fresh (FF) breast carcinoma samples for single-cell RNA sequencing (scRNAseq), highlighting the potential of archival FFPE tissues in clinical research and retrospective studies.

overall_design: Four breast carcinoma samples from two patients (2 fresh and 2 FFPE) were processed and sequenced using single-cell RNA sequencing (scRNAseq) to assess the suitability of FFPE and fixed fresh (FF) samples for scRNAseq.

last: González Martínez

first: José

last: Palacios


title: The RNA M5C Methyltransferase NSUN2 Promotes Progression of Hepatocellular Carcinoma by Enhancing PKM2-Mediated Glycolysis

city: Shanghai

first: Qin

last: Qi

address: South Wanping road 650

country: China

institute: Shanghai University of traditional chinese medicine

summary: mRNA m5C-RIP-Seq for five paired hepatocellular carcinoma and adjacent noncancerous liver tissues

overall_design: mRNA m5C-RIP-seq was performed in  five paired HCC and ANL tissues to elucidate the transcriptomic m5C profile of HCC


title: CircRNA-mediated ceRNA regulatory networks: transcriptomic insights into obesity type 2 diabetes progression and treatment strategies.

city: beijing

first: Guangjian

last: Jiang

address: Beijing University of Traditional Chinese Medicine, No. 11 North Third Ring East Road, Beijing City

institute: Beijing University of Chinese Medicine, Beijing

summary: To investigate the pathogenesis of diabetes and identify novel biomarkers, we analyzed circRNA and mRNA expression profiles in serum samples from obese diabetic patients (O-T2DM) using high-throughput RNA sequencing. Our results showed that 442 differentially expressed circRNAs (343 up-regulated and 99 down-regulated) and 2756 differentially expressed mRNAs (277 up-regulated and 2479 down-regulated) were significantly differentially expressed in the O-T2DM group compared with the Control group. The biological function of DEmRNAs was subsequently investigated using WGCNA and enrichment assays. Pathway analysis revealed that the differentially expressed mRNAs were enriched in T cell receptor, cellular senescence, NK cell-mediated cytotoxicity, IL-17, lipids and atherosclerosis, actin cytoskeleton, etc. The circRNA-miRNA-mRNA regulatory network constructed by combining theoretical prediction and clinical experimental data revealed the potential regulatory effects of hsa_circ_0060614 and hsa-mir-4668- 3p on MT2A gene. Expression levels of these three genes were verified in plasma samples from the O-T2DM group and the Control group using qRT-PCR. Our results provide a wealth of transcriptome data for further studies of obesity type 2 diabetes. The ceRNA regulatory network we obtained may have guiding significance for the diagnosis and treatment of O-T2DM.

overall_design:
We analyzed circRNA and mRNA expression profiles in serum samples from obese diabetic patients (O-T2DM) using high-throughput RNA sequencing.

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Due to patient privacy, we cannot provide raw data.
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first: Xian-Jie

last: Zhen

first: Yue-Lin

last: Zhang

first: Nan-Nan

last: Liu

first: Jin-Fang

last: Dou

first: Tao

last: Wu

first: Chu-Yue

first: Jing

first: Guang-Jian


title: MCF-7 cordycepin polysome profiling

city: Nottingham

first: Keith

last: Spriggs

state: Notts

address: University Park

department: Pharmacy

institute: University of Nottingham

summary: 3’deoxyadenosine, also known as cordycepin, has been widely researched as a potential treatment for cancer, yielding promising results in tissue culture as well as in pre-clinical models. A wide variety of mechanisms of action have been proposed, with little agreement between different studies. Here, we confirm that cordycepin triphosphate is likely to be the active metabolite of cordycepin. Data from single and high throughput experiments showed that cordycepin represses growth factor induced gene expression. Bioinformatic analysis, quantitative PCR and western blotting confirmed that cordycepin blocks the PI3K/AKT/mTOR and/or MEK/ERK pathways in 6 cell lines. Effects of cordycepin on translation through mTOR pathway repression were detectable within 30 minutes, indicating a rapid process. Our data show that cordycepin has a broadly similar mechanism of action in all cell lines studied and indicate that its therapeutic target is a cordycepin triphosphate sensitive molecule that is required for growth factor signal transduction.

overall_design: MCF-7 cells were treated with DMSO or 50 μM cordycepin for 30 minutes (four replicates for each condition), RNA was separated into subpolysomal and polysomal fractions on a sucrose gradient, purified, labelled with cy5 and cy3 using a dye swap in duplicate, and microarray analysis performed.

first: Cornelia

middle: H

last: de Moor

first: Jialiang

last: Lin

first: Steven

last: Lawrence


title: A systems pharmacology study of cordycepin demonstrates it blocks growth factor signal transduction

overall_design: Wildtype and AMPKα doulble knockout cells were serum starved 24 hours prior to treatment with DMSO or 25 uM cordycepin (in DMSO) for 20 minutes before stimulation with EGF (15 nM) for 30 minutes


title: MCF-7 cordycepin treatment (Agilent mouse 60K microarray)

overall_design: MCF-7 cells were treated with DMSO or 50 μM cordycepin for 2 hours in independent triplicate, total RNA was isolated and microarray analysis performed.

first: Asma

last: Khurshid

middle: A


title: MCF-7 serum withdrawal (Agilent mouse 60K microarray)

overall_design: MCF-7 cells were incubated for four hours in serum free medium (serum withdrawal) or kept in the medium in which they were seeded (control), total RNA was isolated and microarray analysis performed.

first: Richa

last: Singhania

first: Graeme

middle: J

last: Thorn


title: A systems pharmacology study of cordycepin demonstrates it blocks growth factor signal transduction [MDA-MD-231]

overall_design: MDA-MB-231 Fluc cells were treated with 50 μM cordycepin or DMSO for 2 hours. RNA was isolated and RNAseq performed in duplicate.


title: Pathway-based network medicine identifies novel natural products for Alzheimer's disease

city: Beijing

first: Yumei

last: Liang

address: Changchun Street 45

department: Xuanwu hospital

institute: Capital Medical University

summary: Natural products exhibit potential as candidates for developing multi-target agents for Alzheimer's disease treatment. The aim of this study is to utilize network-based medicine to identify novel natural products for Alzheimer's disease, and investigate their efficacy and mechanisms of action. In this study, we identified (-)-Vestitol and Salviolone as new potential natural products for treating Alzheimer's disease via an Alzheimer's disease-related pathway-gene network. Both natural products improved the cognition of APP/PS1 transgenic mice, reduced Aβ deposition, and lowered soluble toxic Aβ levels in the brain. Notably, a synergistic effect was observed when the two natural products were combined. Transcriptomic analysis and qRT-PCR experiments revealed that the synergistic mechanism of (-)-Vestitol and Salviolone combination is associated with the regulation of a broader range of AD-related pathways and genes, particularly the neuroactive ligand-receptor interaction pathway and calcium signaling pathway.

overall_design: To investigate the mechanism of the synergistic effect of the combination of (-)-Vestitol and Salviolone, APP/PS1 transgenic mice were randomly assigned to each of five groups (n = 8 per group), and eight C57BL/6J mice were assigned as wild type group. These groups were intraperitoneally administered with vehicle, (-)-Vestitol, Salviolone, (-)-Vestitol and Salviolone, and Donepezil. The brain cortex of wild type group, control group, (-)-Vestitol group, Salviolone group, and combination group (n = 5 per group, randomly selected) were used to perform RNA-seq for analyzing gene expression differences of control group compared to wild type group, and treatment groups compared to control group.

first: Jianping

last: Jia

first: Siqi

last: Xie


title: Pre-clinical efficacy of CDK7 inhibitor-based combinations against myeloproliferative neoplasms (MPN) transformed to AML

city: Houston

first: Xiaoping

last: Su

state: Texas

address: 7300 Brompton St, Apt 5633

country: USA

institute: MD Anderson Cancer Center

summary: Rising blast-percentage or secondary (s) AML transformation (sAML) in MPNs leads to JAK inhibitor (JAKi) therapy-resistance and poor survival. Here, we demonstrate that the CDK7 inhibitor (CDK7i) SY-5609 treatment depletes phenotypically-characterized post-MPN-sAML stem/progenitor cells. In the cultured post-MPN sAML SET2 and HEL as well as patient-derived (PD) post-MPN-sAML cells, SY-5609 treatment inhibited growth and induced lethality, while sparing normal cells. RNA-Seq analysis following SY-5609 treatment demonstrated reduced mRNA expressions of MYC, MYB, CDK4/6, PIM1, and CCND1, but increased mRNA levels of CDKN1A and BCL2L1. Mass spectrometry of SY-5609-treated MPN-sAML cells also demonstrated reduced c-Myc, c-Myb, PIM1, and CDK4/6 but increased p21, caspase 9 and BAD protein levels. CRISPR-mediated CDK7 depletion also reduced viability of HEL cells. CyTOF analysis of SY-5609-treated PD, post-MPN-sAML stem/progenitor cells showed reduced c-Myc, CDK6 and PU.1, but increased protein levels of CD11b, p21 and cleaved Caspase 3. Co-treatment with SY-5609 and ruxolitinib was synergistically lethal in HEL, SET2 and PD post-MPN-sAML cells.  A CRISPR screen in SET2 and HEL cells revealed BRD4, CBP and p300 as co-dependencies with SY-5609 treatment. Accordingly, co-treatment with SY-5609 and the BETi OTX015 or pelabresib or with the CBP/p300 inhibitor GNE-049 was synergistically lethal in MPN-sAML cells (including those exhibiting TP53 loss). Finally, in the HEL-Luc/GFP xenograft model, compared to each agent alone, co-treatment with SY-5609 and OTX015 reduced post-MPN-sAML burden and improved survival without inducing host toxicity. These findings demonstrate promising preclinical activity of the CDK7i-based combinations with BETi or HATi against advanced-MPNs, including post-MPN-sAML.

overall_design: Paired end RNA Seq of HEL92.1.7 and patient derived JAK2-V617F-expressing post-MPN sAML cells treated with SY-1365 or SY-5609  for 16 hours.

first: Warren

last: Fiskus

first: Kapil

last: Bhalla


title: Role of the FOXM1/CMA/ER stress axis in regulating the progression of nonalcoholic steatohepatitis

city: Xi'an

first: Shuoyi

last: Ma

address: No. 127, Changle West Road, Xincheng District

institute: Xijing Hospital of Digestive Diseases, Fourth Military Medical University

summary: Background and aim: The molecular mechanisms underlying the progression of nonalcoholic fatty liver (NAFL) to nonalcoholic steatohepatitis (NASH) remain unclear; however, the role of autophagy in these mechanisms has attracted extensive attention. This study aimed to investigate the role of chaperone-mediated autophagy (CMA) in NAFL-to-NASH progression and elucidate the underlying mechanisms. Methods: Hepatic CMA activity was analyzed in patients with NASH and mouse models of NASH. LAMP2A was knocked down or overexpressed to assess the effects of hepatocyte-specific CMA on NAFL-to-NASH progression. Mice were fed a high-fat diet or a methionine–choline-deficient diet to induce NAFL or NASH. Palmitic acid was used to mimic lipotoxicity-induced hepatocyte damage in vitro. The promoter activity of FOXM1 was evaluated via chromatin immunoprecipitation and dual-luciferase reporter assay. Results: Hepatic CMA activity was substantially low in patients and mice with NASH. Knockdown of LAMP2A resulted in hepatocyte-specific CMA deficiency, which promoted hepatic inflammation and fibrosis in mice with NASH. In addition, CMA deficiency exacerbated endoplasmic reticulum (ER) stress and hepatocyte damage in vivo and in vitro. Mechanistically, CMA deficiency in hepatocytes increased cholesterol accumulation by blocking the degradation of HMGCR, a rate-limiting enzyme of cholesterol synthesis, and the accumulated cholesterol subsequently induced ER stress and hepatocyte damage. Restoration of hepatocyte-specific CMA activity effectively ameliorated diet-induced NASH and ER stress in vivo and in vitro. FOXM1 negatively regulated the transcription of LAMP2A by directly binding to its promoter. Upregulation of FOXM1 impaired CMA and enhanced ER stress, which in turn increased FOXM1 expression, resulting in a vicious circle and promoting the development of NASH. Conclusions: This study highlights the role of the FOXM1/CMA/ER stress axis in NAFL-to-NASH progression and proposes novel therapeutic targets for NASH.

overall_design: To explore the transcriptional regulation of LAMP2A in NASH, transcriptomic analysis was performed in liver tissues from mice fed MCD for 4 weeks and those from mice fed a normal diet.

first: Jingbo

last: Wang


title: Two unrelated distal genes activated by a shared enhancer benefit from localizing inside the same small topological domain (4C).

city: Utrecht

first: Peter

last: Krijger

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

summary: Enhancers are tissue-specific regulatory DNA elements that can activate transcription of genes over distance. Their target genes most often locate in the same topologically associating domain (TAD). TADs are structural entities within chromosomes in which cohesin DNA loop extrusion supports intra-domain DNA contacts and CTCF-bound boundaries serve to halt and concentrate paralogous genes. Enhancers shared by multiple unrelated genes may be more common than those acting on paralogous gene clusters, but are underexplored. Here, we analyzed the interplay between an enhancer and two distal, functionally unrelated, genes residing at opposite domain boundaries. The enhancer stimulated boundary and gene-gene contacts and required cohesin as well as two intact domain boundaries to support gene activation. The two genes preferentially transcribed when spatially together, but did not rely on each other’s transcription, nor showed gene competition. Placing them and the enhancer in smaller domains caused their upregulation. Domain boundaries, therefore, can support long-range enhancer-promoter communication inside domains. Boundary proximity thereby matters as the distal enhancer functions more effectively inside smaller domains. We propose that smaller domains have more concentrated cohesin loop extrusion activity to facilitate enhancer action over distance.

overall_design: 4C-seq data with viewpoints located in the MYEOV-CCND1 locus of WT, enhancer deleted, MYEOV deleted, CCND1 deleted and CTCF2 deleted K562 cells.

first: Yike

last: Huang

first: Marjon

middle: M

last: Verstegen

first: Sjoerd

middle: D

last: Tjalsma

middle: L

first: Kavvya

last: Gupta

first: Minhee

last: Park

first: Alistair

last: Boettiger

first: Wouter

last: de Laat


title: Two unrelated distal genes activated by a shared enhancer benefit from localizing inside the same small topological domain (HiC).

overall_design: Capture Hi-C data with probes capturing the MYEOV-CCND1 locus of WT, enhancer deleted, MYEOV deleted, CCND1 deleted and CTCF2 deleted K562 cells.


title: Time courses analysis of the effect of latrunculin B-treatment on gene expression in in vitro differentiated pancreatic progenitor cells.

city: København N

first: Adam Kappel

last: Rump

address: Blegdamsvej 3

department: DanStem

country: Denmark

institute: University of Copenhagen

summary: The organization of the actin cytoskeleton is known to influence the endocrine versus ductal fate choice during pancreas development via YAP. However, the intermediate mechanism between changes to actin polymerization and changes in YAP activity during pancreas development has not been identified. Pharmacological inhibition of actin polymerization has also been shown to be a stronger inducer of endocrine fate choice than pharmacological inhibition of YAP activity, indicating that actin depolymerization may induce endocrine fate choice via additional pathways. To identify these mechanisms, we performed bulk RNA-sequencing of in vitro differentiated ESC-derived pancreatic progenitor cells treated with latrunculin B for 3, 6, 12, or 24 hours. This sequencing dataset revealed multiple promising candidates for actin depolymerization-induced YAP inactivators and YAP-independent endocrine induction, which have been validated by additional methods.

overall_design: To investigate the intermediate effects between actin depolymerization and endocrine specification, ESC-derived pancreatic progenitor cell were treated with the actin depolymerization agent latrunculin B for 3, 6, 12 or 24 hours. These samples were compared to samples harvested before treatment and samples harvested after 24 hours of DMSO treatment. Duplicates of 24hr untreated and 12hr LatB treated and triplicates of other samples were sequenced.

first: Adam

first: Anant

last: Mamidi

first: Henrik

last: Semb


title: Gene expression analysis in C28/I2 cells: Comparison of OENC, DPP4 Overexpression, and DPP4 Overexpression with 4,5-Dicaffeoylquinic Acid Treatment Using RNA-Seq

city: chengdu

first: li

last: xinyu

address: renmin south road

institute: westchina hospital

summary: To examine the effects of DPP4 overexpression and its modulation by 4,5-Dicaffeoylquinic acid on  chondrocytes, we established C28/I2 cell lines with DPP4 overexpression (DPP4OE), control empty vector (OENC), and DPP4OE treated with 4,5-Dicaffeoylquinic acid. Gene expression profiling analysis was performed using RNA sequencing (RNA-seq) with biological replicates to investigate the global transcriptomic changes associated with these conditions.

overall_design: To investigate the effects of DPP4 overexpression and its modulation by 4,5-Dicaffeoylquinic acid in C28/I2 chondrocytes, we established cell lines with DPP4 overexpression (DPP4OE), control empty vector (OENC), and DPP4OE treated with 4,5-Dicaffeoylquinic acid. Each condition was performed with three biological replicates. We then performed gene expression profiling analysis using RNA sequencing (RNA-seq) to obtain comprehensive transcriptomic data. This experimental design aims to elucidate the molecular changes associated with DPP4 overexpression and the impact of 4,5-Dicaffeoylquinic acid treatment in chondrocytes.

first: Zeyu

first: Xinyu

last: Li

first: Zhao

last: Zhang


title: CircPRMT5, a potential salivary biomarker, facilitates the progression of head and neck squamous cell carcinoma via the IGF2BP3-SERPINE1 pathway

city: Guangzhou, Guangdong

first: Siqi

last: Jiang

address: No.56 Lingyuanxi Road

institute: Sun Yat-sen University

summary: Background: Circular RNAs (circRNAs) represent a newly identified class of non-coding RNAs that can be secreted into body fluids via exosomes and subsequently detected. While the function of circPRMT5 has been partially elucidated in certain tumor types, its role and underlying mechanisms in head and neck squamous cell carcinoma (HNSCC) remain inadequately understood. Furthermore, the diagnostic potential of circPRMT5 in saliva necessitates additional investigation.Methods: The expression of circPRMT5 was quantified using qRT-PCR. The biological function of circPRMT5 in HNSCC progression was confirmed both in vitro and in vivo. RNA sequencing (RNA-Seq) was used to find downstream targets for circPRMT5-IGF2BP3. IGF2BP3 and SERPINE1 expression levels were assessed using qRT-PCR, Western blotting, and immunohistochemistry. Additionally, the localization and interaction of circPRMT5, IGF2BP3 protein, and SERPINE1 in HNSCC were evaluated using RNA-FISH, immunofluorescence (IF), and RNA immunoprecipitation (RIP) assays. Ultimately, saliva exosomes were collected, identified and assessed using Western Blot, electron microscopy, particle size analysis and qRT-PCR.Results: Findings revealed that circPRMT5 was upregulated in HNSCC and promoted its proliferation and metastasis in vitro and in vivo. Mechanistically, circPRMT5 stabilized IGF2BP3 protein, which in turn stabilized SERPINE1 mRNA. Notably, the proliferative, invasive, and migratory effects of circPRMT5 in HNSCC were contingent upon the involvement of IGF2BP3 and SERPINE1. Furthermore, circPRMT5 levels were significantly elevated in the saliva of HNSCC patients, and positively correlated with increased lymph node metastasis and advanced T stage. These findings underscored the high diagnostic and predictive potential of circPRMT5 in HNSCC.Conclusions: CircPRMT5 plays a crucial role in promoting HNSCC proliferation and metastasis via the IGF2BP3-SERPINE1 pathway. It serves as a noninvasive diagnostic biomarker, indicating its potential as a valuable diagnostic and therapeutic target for HNSCC patients.

overall_design: To cooperative funtion circPRMT5/IGF2BP3 complex in the regulation of head and neck squamous cell carcinoma differentiation, we established scc15 sh2(has been circPRMT5 knocked down by shRNA) and scc15 si1(has been IGF2BP3 knocked down by siRNA).We then performed gene expression profiling analysis using data obtained from RNA-seq of one cell with two different treatment. Comparative gene expression profiling analysis of RNA-seq data for SCC15 cell and its KD derivatives

first: Zhaona

last: Fan


title: Delphinapterus leucas skin transcriptome sequencing and assembly, and comparison between two Canadian populations

city: Burnaby

first: Antoine

middle: Etienne

last: Simond

state: BC

address: 8888 university drive

department: Biological Sciences

country: Canada

institute: Simon Fraser University

summary: The St. Lawrence Estuary (SLE) beluga (Delphinapterus leucas) population in Canada is endangered, and endocrine disrupting contaminants such as polychlorinated biphenyls (PCBs), polybrominated diphenyl ethers (PBDEs), and other halogenated flame retardants (HFRs) have been identified as a threat to the recovery of this population. While targeted approaches such as quantitative reverse transcription PCR (RT-qPCR) have been widely used to assess the impacts of contaminants on marine mammals, including SLE beluga, few studies have employed transcriptomics. Here, we (1) evaluate the skin transcriptome profiles of adult male SLE beluga and adult males from a Arctic population less exposed to contaminants (Eastern Beaufort Sea; EBS) used as a reference to identify gene transcripts and biological pathways associated with blubber concentrations of organic contaminants (i.e., PCBs, PBDEs and other HFRs), and (2) assess correlations between several gene transcripts previously identified as biomarkers of organic contaminants in marine mammals and organohalogen concentrations in both populations and estimate threshold values in beluga skin for potential biological effects. Results will provide new and valuable knowledge that identify biological pathways associated with organic contaminant exposure in beluga, which may serve as predictors for higher-level health effects in at-risk populations such as SLE beluga.

overall_design:
Total RNA was extracted using TRIzol from the skin of adult male beluga from two populations being exposed to different and contrasting levels of organohalogenated contaminants (i.e., PCBs, PBDEs, and other flame retardants). We then performed a differential gene expression analysis using data obtained from RNA-sequencing. We also identified genes that were directly related to the contaminants of interest.
Please note that the "traits.csv" contains traits data of each samples, i.e., contaminant data (ng/g lw), population, sampling date, RNA quality (RIN number).

middle: E

first: Véronique

last: Lesage

first: Jonathan

last: Verreault

first: Lisa

last: Loseto

first: Magali

last: Houde

first: Ashley

last: Elliott

first: Marie

last: Noël

first: Tanya

last: Brown


title: Effect of Overexpression of DPP4 on Gene Expression in C28/I2 Chondrocyte Cells

city: Chengdu

first: zhang

last: zhao

address: Guoxue Lane, Wuhou District

institute: Sichuan University

summary: We report here the overexpression of DPP4 in C28/I2 chondrocyte cells to investigate the changes induced by elevated levels of this gene. DPP4 is known as a marker of cellular senescence, yet its regulatory mechanisms remain unclear. In this study, we utilized the C28/I2 cell line to overexpress DPP4 and analyzed the resultant effects on gene expression and cellular behavior. Our findings reveal that DPP4 overexpression influences several pathways associated with chondrocyte function and senescence. Specifically, we observed alterations in pathways related to extracellular matrix organization, inflammatory response, and cellular aging. These results suggest that DPP4 plays a significant role in the modulation of chondrocyte senescence and may provide new insights into the mechanisms of cellular aging. Taken together, our data provide a molecular framework for understanding how DPP4 overexpression impacts chondrocyte physiology and offers potential targets for therapeutic intervention in age-related cartilage diseases.

overall_design: To investigate the effects of DPP4 overexpression in chondrocyte cells, we established C28/I2 cell lines using plasmid vectors to overexpress DPP4 (DPP4OE) and corresponding control cells with empty vectors (OENC). The samples included in this submission consist of three biological replicates for each condition: three DPP4OE samples and three OENC samples. The experimental conditions and variables under investigation include the differential gene expression profiles between DPP4 overexpressing cells and control cells. Gene expression profiling was performed using RNA sequencing to analyze the transcriptomic changes induced by DPP4 overexpression. This design allows for a comparative analysis to identify the impact of DPP4 overexpression on chondrocyte function and cellular senescence markers.

last: Huang

last: Lin


title: LFch potential as therapeutic for multiple myeloma

city: Chuncheon

first: Young-Saeng

last: Jang

state: gangwondo

address: Biomedical science B-213

country: South Korea

institute: Kangwon National University

summary: Lactoferrin-derived peptide chimera, LF chimera (LFch) is a synthetic peptide that mimics the functional unit of lactoferrin with antibacterial activity. Since antimicrobial peptides (AMPs) are known to be promising candidates for cancer treatment, in this study, we explored the potential of LFch for the treatment of multiple myeloma (MM), a malignant clonal plasma cell disease of the bone marrow. LFch effectively inhibited MM1S, MM1R, and RPMI8226 multiple myeloma cell growth and induced the early and late phase of apoptosis whereas did not a normal PBMCs. Furthermore, LFch modulated the relative gene expression of survival, apoptosis, and mitochondrial dysfunction at the transcriptional levels.

overall_design: Gene profiling of LFch-treated multiple myeloma cell line by RNA-seq

first: Shima

middle: B

last: Dehkohneh

first: Donghwan

last: Ahn

first: Sun

middle: S

last: Choi

first: Seung

middle: G

last: Kang


title: Single-nucleus and spatial transcriptomics of human ovary: Molecular insights into signaling pathways underlying primary ovarian insufficiency in classic galactosemia [Spatial transcriptomics]

city: Bethesda

first: Raghuveer

last: Kavarthapu

state: MD

address: 10 Center Dr, Bldg 10, Room 1E3340

department: NICHD

institute: National Institutes of Health (NIH)

summary: Classic galactosemia (CG) is a rare inborn error of galactose metabolism caused by mutations in GALT gene. Primary ovarian insufficiency (POI) is a later complication that affects 80% of women with CG due to significant decline in ovarian follicle reserve. The definite mechanisms underlying the early onset of POI in CG patients is not fully understood. We utilized spatial transcriptomics from 10x Visium to generate spatial landscape of human ovaries from pre-pubertal girls with CG to investigate dynamic gene expression profiles in the ovarian follicles and stromal cells.

overall_design: CG and control ovarian FFPE sections were processed for Visium spatial transcriptomic protocol (10x Genomics).

first: Hong

last: Lou

first: Thang

last: Pham

first: Han

last: Do

first: Taylor

last: Badger

first: Jacqueline

middle: C

last: Yano

first: Ramya

last: Balasubramanian

first: Maria

last: De La Luz Sierra

first: Veronica

last: Gomez-Lobo


title: APOE genotype or brain amyloid alters the plasma proteome in elderly subjects without dementia

city: New York

first: Joseph

last: Castellano

state: NY

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

summary: Recent work has bolstered the possibility that peripheral changes may be relevant to Alzheimer’s disease pathogenesis in the brain. While age-associated blood-borne proteins have been targeted to restore function to the aged brain, it remains unclear whether other dysfunctional systemic states can be exploited for similar benefits. Here we investigate whether APOE allelic variation or presence of brain amyloid are associated with plasma proteomic changes and the molecular processes associated with these changes. Using the SOMAscan assay, we measured 1,305 plasma proteins from 53 homozygous, APOE3 and APOE4 subjects without dementia. We investigated the relationship of either the APOE-ε4 allele or amyloid positivity with plasma proteome changes by linear mixed effects modeling and ontology-based pathway and module trait correlation analyses. APOE4 is associated with plasma protein differences linked to atherosclerosis, tyrosine kinase activity, cholesterol transport, extracellular matrix, and synaptogenesis pathways. Independent of APOE4, we found that subjects likely harboring brain amyloid exhibit plasma proteome signatures associated with AD-linked pathways, including neurovascular dysfunction. Our results indicate that APOE4 status or presence of brain amyloid are associated with plasma proteomic shifts prior to the onset of symptoms, suggesting that systemic pathways in certain risk contexts may be plausible targets for disease modification.

overall_design: Plasma proteomics from elderly, homozygous APOE3 and APOE4 human subjects

first: S

last: Philippi

first: J


title: Gene expression profile at single cell level of cells from whole lung to assess MAGE-A4 expressing tumor alterations in tumor microenvironment

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

summary: Melanoma Antigen-A4 (MAGE-A4) is a common cancer testis antigen expressed in human non-small cell lung cancer; however, whether and how it contributes to cancer initiation and progression has remained less clear. We engineered mice to express human MAGE-A4 specifically in Club cells of the bronchial epithelium, with or without loss of Pten in the same cells, to investigate the role of MAGE-A4 in tumor initiation and development. We used single cell transcriptomics and flow cytometry to evaluate the immune and other cells in the lung/lung tumor microenvironment that were altered in response to this cancer testis antigen. We found that endothelial cells in MAGE-A4 expression models upregulate CXCL12, which likely contributes to the increased plasma cell recruitment to the lungs infiltrating MAGE-A4-expressing lung tumors in both mouse and human. Single cells were isolated from whole lung of mice at 5 months of age when tumor had developed in MAG4/Pt lungs and were analyzed using scRNA-seq.

overall_design: Single cells were isolated from whole-lung from 4 genotypes of mice: CCSPWT MAGE-A4LSL Ptf/f (Cre-MAG4/Pt (wild-type)), CCSPiCre Ptf/f (Pt), CCSPiCre MAGE-A4LSL (MAG4), CCSPiCre MAGE-A4LSL Ptf/f (MAG4/Pt) and analyzed using scRNA-seq.

first: Farrah

last: Kheradmand

first: Xiang

last: Zhang

first: Yichao

last: Shen

first: Dominique

last: Armstrong


title: Metabolic characterization of two white-rot fungi in diverse cultivation environments reveals biotechnologically relevant biosynthetic pathways

city: Golden

first: Davinia

last: Salvachua

state: CO

address: 15013 Denver West Parkway

institute: National Renewable Energy Laboratory

summary: White-rot fungi stand out as highly efficient organisms for the mineralization of biopolymers, such as lignin and polysaccharides, into CO2 and H2O. Despite their significant potential for biotechnological applications, the intracellular metabolism of WRF remains largely overlooked. Building on recent findings regarding the utilization of lignin-related aromatic compounds as carbon sources by WRF, our objective was to gain further insights into these catabolic processes. For this purpose, two WRF, Trametes versicolor and Gelatoporia subvermispora were cultivated in different environments – agitation and static incubation modes and variations in the level of antioxidants – during the conversion of a lignin-related aromatic compound and cellobiose. To comprehensively assess their metabolic responses, we employed transcriptomics, proteomics, lipidomics, metabolomics, and microscopy analyses. The results underscore that both incubation mode and the presence of antioxidants impact sugars and aromatic catabolism, as well as lipid composition of the fungal mycelia. In addition, these analyses reveal biosynthetic pathways for the production of extracellular fatty acids and phenylpropanoids by these WRF, both products with relevance in biotechnological applications. Overall, we demonstrate that cultivation conditions play a crucial role in shaping bioprocesses that involve WRF and provide additional insights into carbon flux in nature.

sample_organism:
Trametes versicolor
Gelatoporia subvermispora

overall_design: Gelatoporia subvermispora and Trametes versicolor were cultured for 10 and 6 days, respectively, then treated with 4-hydroxybenzoate in the presence or absence of antioxidents, with or without agitation.

first: Lummy

last: Monteiro

first: Carlos

last: del Cerro

first: Teeratas

last: Kijpornyongpan

first: Allison

last: Yaguchi

first: Anna

last: Bennett

first: Bryon

last: Dohohoe

first: Kelsey

last: Ramirez

first: Hugh

last: Mitchell

first: Samuel

middle: O

last: Purvine

first: Lye

last: Markillie

first: Meagan

last: Burnet

first: Kent

last: Bloodsworth

first: Benjamin

last: Bowen

first: Thomas

last: Harwood

first: Katherine

last: Louie

first: Trent

last: Northen


title: Gene expression profile at single cell level of cultuted bovine mammosphere-derived epithelial cells (MDECs)

city: Ithaca

first: Gerlinde

middle: R.

last: Van de Walle

address: 235 Hungerford Hill Rd

department: Baker Institute for Animal Health

institute: Cornell University

summary: Bovine mammosphere-derived epithelial cells are a population with reported stem cell-like properties. We assessed these cells using scRNA-seq for markers of pluripotency and other features associated with the effects of their conditioned medium (CM).

overall_design: Parenchymal tissue of a non-lactating cow (B. taurus) was isolated by means of a biopsy and was dissociated into single cells. MDECs were isolated using previously established protocols.  Upon isolation of colonies and formation of a monolayer, the cells were analyzed using scRNA-seq. Protocol described in "Ledet, M.M., Vasquez, A.K., Rauner, G. et al. The secretome from bovine mammosphere-derived cells (MDC) promotes angiogenesis, epithelial cell migration, and contains factors associated with defense and immunity. Sci Rep 8, 5378 (2018). https://doi.org/10.1038/s41598-018-23770-z"

first: Nikola

last: Danev

first: Rebecca

last: Harman

middle: R


title: Cullin-5 controls the number of megakaryocyte-committed stem cells to prevent excess megakaryopoiesis and thrombocytosis

city: Parkville

first: Carolyn

last: de Graaf

state: VIC

address: 1G Royal Parade

country: Australia

institute: WEHI

summary: Cullin-5 (Cul5) coordinates assembly of cullin-RING-E3 ubiquitin (Ub) ligase (CRL) complexes that include Suppressor of Cytokine Signaling (SOCS)-box-containing proteins. The SOCS-box proteins function to recruit specific substrates to the complex for ubiquitination and degradation. In hematopoiesis, SOCS-box proteins are best known for regulating the actions of cytokines that utilize the JAK-STAT signaling pathway. However, the roles of most SOCS-box proteins have not been studied in physiological contexts and any actions for Cul5/SOCS complexes in signaling by several hematopoietic cytokines, including thrombopoietin (TPO) and interleukin-3 (IL-3), remain unknown. To define additional potential roles for Cul5/SOCS complexes, we generated mice lacking Cul5 in hematopoiesis; the absence of Cul5 is predicted to impair the SOCS-box-dependent actions of all proteins that contain this motif. Here, we show that Cul5-deficient mice develop excess megakaryopoiesis and thrombocytosis revealing a novel mechanism of negative regulation of megakaryocyte-committed stem cells, a distinct population within the hematopoietic stem cell pool that have been shown to rapidly, perhaps directly, generate megakaryocytes, and which are produced in excess in the absence of Cul5. Cul5-deficient megakaryopoiesis is distinctive in being at least in part independent of TPO/Mpl and involves signaling via the beta-common and/or beta-IL-3 receptors, with evidence of deregulated responses to IL-3. This process is independent of the interferon-alpha/beta receptor (IFNARI), previously implicated in inflammation-induced activation of megakaryocyte-committed stem cells, which may suggest distinct regulation of these cells at steady state and under stress.

overall_design: LSK cells (Linegage negative, Kit + , Sca1 + bone marrow cells) FACS sorted from wild type and Cul5-/- mice were loaded onto a Chromium Controller (10X Genomics). Single cell 3' v2 transcriptome libraries were obtained following manufacturer's instructions. Samples were pooled and sequenced on NextSeq (Illumina) (75bp kit, paired end, where 98bp were sequenced for genomic read).

first: Maria

last: Kauppi

first: Kira

last: Behrens

first: AnneMarie

last: Welch

first: Warren

last: Alexander


title: Transcriptome analysis in the colon of mice with constitutive active STAT6 expression in intestinal epithelial cells

city: Erlangen

first: David

last: Voehringer

address: Wasserturmstrasse 3-5

department: Department of Infection Biology

country: Germany

institute: University Clinic Erlangen

summary: We investigated which genes in colon tissue are differentially expressed due to constitutive active STAT6 signaling in intestinal epithelial cells (VillinCre_STAT6vt). Therefore, we performed RNA sequencing of colon tissue from naive VillinCre_STAT6vt mice and littermate controls (STAT6vt).

overall_design: We isolated RNA from colon tissue of naive VillinCre_STAT6vt (Cre+) and STAT6vt (Cre-) mice and performed bulk RNA sequencing.

first: Stefanie

last: Westermann

first: Daniel

last: Radtke


title: Transgenerational inheritance of diabetes susceptibility in male offspring with maternal hyperandrogenism [WGBS]

city: Jinan

first: Shourui

last: Hu

address: wenhuaxi road 44

institute: Shandong University

type: Methylation profiling by high throughput sequencing

summary: Maternal hyperandrogenism is closely related to metabolic disorders, yet its transgenerational effects on male descendants remain unclear. Here we demonstrate that hyperandrogenism in women predisposes their sons to islet β-cell dysfunction. Male offspring mice with prenatal androgen exposure exhibited hyperglycemia and glucose intolerance due to compromised insulin secretion. Notably, these metabolic disturbances were transmitted across three generations, and exacerbated by aging and a high-fat diet. Altered DNA methylations in F1 sperm and F2 islet contribute to suppressed β-cell functional genes. We identified shared differentially methylated signatures in F1 sperm, type 2 diabetes patients, and sons with maternal hyperandrogenism. Furthermore, caloric restriction and metformin treatments in F1 males corrected hyperglycemic defects and prevented their transmission to offspring. Our findings highlight the transgenerational inheritance of hyperglycemia and β-cell dysfunction in male offspring from maternal hyperandrogenism via DNA methylation changes, providing methylation biomarkers and therapeutic strategies to safeguard future generations’ metabolic health.

overall_design: To investigate the effect of prenatal androgen exposure on offspring metabolism, we sequenced sperm from first-generation male mice


title: Two unrelated distal genes activated by a shared enhancer benefit from localizing inside the same small topological domain

first: Peter

last: Krijger

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

overall_design: Refer to individual Series


title: Transgenerational inheritance of diabetes susceptibility in male offspring with maternal hyperandrogenism [RNA-Seq]

overall_design: To investigate the effect of prenatal androgen exposure on offspring metabolism, we sequenced pancreatic islets from second-generation male mice


title: Seryl-tRNA synthetase inhibits Wnt signaling and breast cancer progression and metastasis

city: La Jolla

first: Justin

last: Wang

state: CA

address: 10550 N Torrey Pines Rd

institute: The Scripps Research Institute

summary: Tumors require ample protein synthesis to grow, and aminoacyl-tRNA synthetases, as critical translation factors, are expected to support cancer progression. Unexpectedly, overexpression of seryl-tRNA synthetase (SerRS) suppresses primary tumor growth of breast cancer. However, the effects of SerRS on metastasis have not been studied. We observe a decrease in SerRS expression in breast cancer patient metastases compared to matched primary tumors, suggesting an inhibitory role of SerRS in metastasis. Through mouse metastasis models using breast cancer cell lines overexpressing SerRS, we show that SerRS impedes both primary tumor growth and establishment of metastases. By inducing SerRS overexpression after primary tumor implantation, we demonstrate the potential of SerRS as an anticancer therapeutic. Through tumor RNA-Seq, we identify Wnt signaling among the top SerRS-regulated pathways. Using cell-based studies, we confirm SerRS suppresses Wnt signaling and metastatic processes in breast cancer cells. To our knowledge, this is the first study to show a translation factor can act as both a tumor and metastasis suppressor.

overall_design: Primary breast tumors of BALB/c mice orthotopically injected with 4T1-tet-on-Luciferase stable mouse breast cancer cell lines (expressing tet-on vector control, mSerRS wild-type, mSerRS AA mutant)

first: Lei

last: Jiang


title: RNA-seq in human Molm13 cells with CRISPR knockout of COX4I1

city: duarte

first: LU

last: YANG

address: 1500 duarte rd

institute: city of hope

summary: This dataset examined the effect of COX4I1 knockout in the gene expression profiling (RNA-seq) of human Molm13 cells.

overall_design: Cas9-expressing human Molm13 cells were transduced with sgCtrl and sgCOX4I1. RNAseq: The total RNA was extracted using the RNeasy Mini Kit (74104, QIAGEN) and submitted for RNA-seq at Novogene (PE150, NovoSeq6000).

first: Chun-Wei

last: Chen

first: Lu

last: Yang

first: Leisi

last: Zhang


title: Involvement of Icaritin in the Regulation of Osteocyte Exosomal MicroRNAs

city: Suzhou

first: Yujiang

last: Liu

address: Yangsu Road No.18

institute: Suzhou TCM Hospital Affiliated to Nanjing University of Chinese Medicine

type: Non-coding RNA profiling by high throughput sequencing

summary: In this study, we isolated exosomes from ICA-treated osteocytes and sequenced small RNAs from them and controls with the aim of exploring the regulatory role of ICA on osteocyte exosomal miRNAs, which in turn can contribute to the understanding of the potential molecular mechanisms involved in bone repair by ICA.

overall_design: To explore the effects of ICA on the regulation of osteocyte exosomal miRNAs and to promote the understanding of the potential molecular mechanisms involved in bone repair by ICA，MLO-Y4 medium was collected after treatment with PBS (CON), 0.1 μM ICA(LICA) or 10 μM ICA(HICA) for 24h. Exosomes were isolated and purified according to standard methods, and identified by transmission electron microscopy, nanoparticle tracking analysis and protein blotting. Exosomal miRNAs were analysed by small RNA sequencing.

first: Kaijia

first: Xianda

first: Xiaofeng

last: Shen


title: Mechanism for local attenuation of DNA replication at double-strand breaks

first: Christophe

last: Redon

address: 37 Convent Drive

institute: NIH

type: Genome binding/occupancy profiling by high throughput sequencing

summary: DNA double-strand breaks (DSBs) destroy the continuity of our genome with consequences for malignant transformation. Massive DNA damage can elicit a cellular checkpoint response that prevents cell proliferation. However, how highly aggressive cancer cells, which can tolerate widespread DNA damage, respond to DSBs alongside continuous chromosome duplication is unknown. Here we show that DSBs induce a local, hitherto unreported genome maintenance mechanism that inhibits replication initiation in DSB-containing topologically associating domains (TADs) without affecting DNA synthesis at other genomic locations. This process is facilitated by Mediators of Replication and DSBs (MRDs). In normal and cancer cells, MRDs include the TIMELESS-TIPIN complex and the WEE1 kinase, which actively dislodges the TIMELESS-TIPIN complex from replication origins adjacent to DSBs and prevents initiation of DNA synthesis at DSB-containing TADs. Dysregulation of MRDs, or disruption of 3D chromatin architecture by dissolving TADs, results in inadvertent replication in damaged chromatin and increased DNA damage in cancer cells. We propose that the intact MRD cascade precedes DSB repair to prevent genomic instability, which is otherwise observed when replication is forced, or when genome architecture is challenged, in the presence of DSBs. These observations reveal a previously undiscovered vulnerability in the DNA replication machinery that may be exploited to therapeutically target cancer cells.

overall_design: BrdU seq, ChIP seq, Nascent strand seq

first: Robin

last: Sebastian

first: Eric

last: Sun

first: Michael

last: Fedkenheuer

first: Haiqing

last: Fu

first: SeolKyoung

last: Jung

first: Bhushan

last: Thakur

first: Gianluca

last: Pegoraro

first: Andy

last: Tran

first: Lorinc

last: Pongor

first: Jacob

last: Gross

first: Sara

last: Mosavarpour

first: Nana

last: Kusi

first: Anagh

last: Ray

first: Anjali

last: Dhall

first: Rafael

last: Casellas

first: Mirit

middle: I

last: Aladjem


title: Single-nucleus and spatial transcriptomics of human ovary: Molecular insights into signaling pathways underlying primary ovarian insufficiency in classic galactosemia

first: Raghuveer

last: Kavarthapu

summary: Classic galactosemia (CG) is a rare inborn error of galactose metabolism caused by mutations in GALT gene. Primary ovarian insufficiency (POI) is a later complication that affects 80% of women with CG due to significant decline in ovarian follicle reserve. The definite mechanisms underlying the early onset of POI in CG patients is not fully understood. We utilized single-nucleus RNA sequencing (snRNA-seq) to generate a single-nucleus transcriptomic atlas of human ovaries from pre-pubertal girls with CG to investigate dynamic gene expression profiles in ovarian follicles and stromal cells. Our snRNA-seq analysis revealed activation of several key genes involved in endoplasmic reticulum-stress and oxidative stress pathways which can promote apoptosis and autophagy of follicles. PTEN/PI3K/AKT signaling pathway crucial for primordial follicle activation and survival was dysregulated as evident by upregulated PTEN transcripts, marked reduction in phospho-AKT and increased CASP9 immunostaining intensity in the ovarian follicles of CG group.

overall_design: Nuclei were isolated from flash-frozen ovarian tissues from five classic galactosemia and four control patients using a 10X genomics chromium nuclei isolation kit. Nuclei suspension samples were loaded onto chromium microfluidic chip used to generate single-cell gel bead emulsions using the 10x Genomics Chromium controller. Later cDNA amplification was performed, and libraries were prepared as per the manufacturer’s protocol. Libraries were pooled and sequenced on S2 flow cell (paired-end 100 bp) using an Illumina NovaSeq 6000 platform.

first: Hong

last: Lou

first: Thang

last: Pham

first: Han

last: Do

first: Taylor

last: Badger

first: Jacqueline

last: Yano

first: Ramya

last: Balasubramanian

first: Maria

last: De La Luz Sierra

first: Veronica

last: Gomez-Lobo


title: Expression data from  ALDH2 knockdown in head and neck cancer cells.

city: Kaohsiung

first: Yi-Fang

last: Yang

address: No. 386, Dajhong 1st Rd., Zuoying Dist., Kaohsiung City 813414, Taiwan.

department: Medical Education and Research

country: Taiwan

institute: Kaohsiung Veterans General Hospital

summary:
We demonstrate that ALDH2 knockdown increased multiple canonical pathways and transcriptions factors
We used microarrays to analyze the potential mechanism by which ALDH2 regulates gene expression.

overall_design: TW2.6 cell line knockdown ALDH2 for RNA extraction and hybridization on Aaffymetrix-calvin-array.

first: Yu-Hsuan

last: Lin


title: 41BB agonist targeted to fibroblast activation protein α synergizes with radiotherapy in murine breast tumor

city: Pamplona

first: Eneko

last: Garate

address: Avenida de Pío XII, 55

institute: CIMA

summary: Background: Ionizing radiation (IR) is a double-edge sword for immunotherapy as it may cause both immunosuppressive and immunostimulatory effects. The interactions of IR with the tumor microenvironment (TME) is a key factor for this balance. Fibroblast activation protein (FAP) is expressed on the surface of CAFs in many cancer types and its presence is associated with poor immune response to immune checkpoint blockade in patients. We hypothesize that IR increases FAP expression in CAFs, therefore the combination of IR with targeted immunomodulators such as an agonistic FAP-4-1BBL bispecific antibody fusion protein could enhance the immune-mediated antitumoral effect of these treatments given in combination. Methods: Murine transplantable TS/A tumor cells line was used to investigate increases in FAP expression in tumors after irradiation by IHQ and RT-PCR. We treated bilateral tumor-bearing mice in which only one of the lesions was locally irradiated (2 × 6 Gy) given alone or in combination with a systemic administration of the FAP-4-1BBL bispecific construct. Tumor sizes were followed over time and in the cellular composition microenvironment (TME) was assessed by immunochemistry and multiplex tissue immunofluorescence. Selective depletions of immune cell populations were used to delineate the immune system requirements for efficacy. Antibody of interest was labeled and tracked its distribution by CT. Colorectal carcinoma samples were also validated. Results: Irradiation of TS/A+CAF tumors showed clear increases of FAP expression levels after local irradiation. The suboptimal radiotherapy regimen in combination with FAP targeted 4-1BBL worked to attain primary tumor control as well as partial abscopal effect. Immune landscape analysis showed an effector and proinflammatory phenotype with an increased infiltration of immune cells. The antitumoral mechanism relied on CD8+ T cells, IFN-I, IFN-γ and CD137 expression. Biodistribution studies of bispecific antibody performed indicated enhanced tumor targeting after tumor irradiation. Human sample results confirmed enhanced immune infiltration and FAP expression after radiotherapy treatment. Conclusion: Our data provides a proof- of- concept and mechanistic insights pertaining the therapeutic efficacy of bispecific FAP-41BBL combined with local radiotherapy.

overall_design: As our treatment was the combination of radiotherapy with muFAP-4-1BBL, we had 4 experimental groups to consider: vechile, radiotherapy, muFAP-4-1BBL and RT+muFAP-41BBL. We performed RNAseq of tumor in each condition to see differences in gene expression.

first: Irantzu

last: Serrano

first: Leticia

last: Fernández

first: María

last: Rodríguez


title: Cannabidiol restores hematopoietic stem cell stemness in mouse through Atf2-Lrp6 axis after acute irradiation

city: Beijing

first: Zhijie

last: Bai

state: 北京Beijing

address: Taiping Road, Haidian District

institute: beijing institute of radiation

summary: Single-cell RNA sequencing analysis demonstrated that the expression levels of genes associated with stemness along with Wnt and BMP signaling pathways were restored by cannabidiol treatment through the upregulation of Atf2, a transcription factor possessing multifunctional properties.

overall_design: BMNCs from wildtype mice, mice treated with 6.0 Gy gamma-irradiation with or without CBD treatment were FACS-sorted and remixed for sc-RNA-seq


title: Loss of STIM1/2 in salivary glands disrupts ANO1 function but does not induce Sjögren’s syndrome.

city: Abu dhabi

first: Youssef

last: Idaghdour

state: Abu dhabi

address: Saadiyat Marina District

department: Biology

country: United Arab Emirates

institute: NYUAD

summary: Primary Sjogren’s syndrome (pSS) is an autoimmune disease characterized by xerostomia (dry mouth), lymphocytic infiltration into salivary glands and the presence of SSA and SSB autoantibodies. Xerostomia is caused by hypofunction of the salivary glands and has been considered a driver in pSS development. Saliva production is regulated by sympathetic input into the gland initiating intracellular Ca2+ signals that activate the store operated Ca2+ entry (SOCE) pathway eliciting sustained Ca2+ influx. SOCE is mediated by the STIM1 and STIM2 proteins and the ORAI1 Ca2+ channel. However, there are no studies on the effects of lack of STIM1/2 function in salivary acini in animal models or its impact on pSS. Here we report that male and female mice lacking Stim1 and Stim2 (Stim1/2K14Cre) in salivary glands hyposalivate upon pilocarpine stimulation and showed reduced intracellular Ca2+ levels via SOCE in parotid acini. Bulk RNASeq of the parotid glands of Stim1/2K14Cre showed a decrease in Stim1/2 genes but not in other Ca2+ associated genes mediating saliva fluid secretion, yet SOCE was functionally required for the activation of the Ca2+ activated chloride channel ANO1. Ageing Stim1/2K14Cre mice showed no evidence of lymphocytic infiltration in the glands or elevated levels of SSA or SSB autoantibodies in the serum which may be linked to the downregulation of the toll-like receptor 8 (Tlr8) in Stim1/2K14Cre mice. This is supported by an increase in TLR8 gene expression in a salivary gland cell line following SOCE stimulation. Moreover, salivary gland biopsies of pSS patients showed increased STIM1 and TLR8 expression. These results implicate SOCE as an important activator of ANO1 and saliva fluid secretion in salivary glands but loss of SOCE does not result in pSS. Importantly, our data suggest a link between SOCE and TLR8 signaling which may have implications in inflammatory responses in salivary glands.

overall_design: A tissue-specific knockout mouse model was generated using the Cre-LoxP system. The Stim1 and Stim2 genes were selectively deleted, particularly in keratin-14 (K14)-expressing salivary gland epithelial cells.

first: Ga-Yeon

last: Son

first: Anna

last: Zou

first: Manikandan

last: Vinu

first: Saruul

last: Zorgit

first: Amanda

last: Wahl

first: Kai

middle: T

last: Huang

first: Fang

last: Zhou

first: David

last: Yule

first: Stefan

last: Feske

first: Rodrigo

last: Lacruz


title: Epigenetic Disruptions in the Offspring Hypothalamus in Response to Maternal Infection

city: Urbana

first: Sandra

last: Rodriguez Zas

state: IL

address: 1207 W. Gregory Dr.

institute: University of Illinois

summary: Female and male 21 days of age  pigs were studied. Half of the pigs were prenatally exposed to immune activation from virally-infected gilts, and half were not exposed.

overall_design: Hypothalamus DNA samples were obtained at 21 days of age and were subjected to Reduced Representation Bisulfite (RRBS) sequencing.


title: HPV-related oropharyngeal head and neck cancer (gene-expression)

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

country: Italy

institute: IRCSS Istituto Nazionale Tumori

summary: HPV-positive squamous oropharyngeal carcinomas (OPCs) have a more positive prognosis compared to HPV-negative OPCs. Nevertheless, the prognosis of some of these tumors is dismal, and currently there are no established prognostic biomarkers in clinical practice. Our study is aimed at evaluating the performances of gene expression signatures that have been previously reported.

overall_design: A cohort of 18 HPV positive OPC patients was retrieved in our institute. Formalin-fixed, paraffin-embedded (FFPE) samples of the primary tumor were collected, and tumor areas were manually macrodissected, excluding non-tumor/necrotic areas. After total RNA extraction, quantification, and quality checks, gene-expression was obtained by DASL microarrays (Illumina). The following demographic and clinical data were collected: i) age; ii) sex; iii) site (OPC); iv) TNM8= AJCC/UICC staging system 8th edition; v) OS_status (1=dead; =alive); vi) OS_time (months)


title: SYISL affects fetal mice muscle fiber number by regulating maternal intestinal microbiota and their metabolites

city: wuhan

first: wei

last: jiang

address: No.1, Shizishan Street, Hongshan District, Wuhan, China

institute: Huazhong Agricultural University

summary: The formation of embryonic muscle fibers during the prenatal period determines the number of muscle fibers after birth. Our previous studies showed that SYISL gene knockout (KO) mice significantly increased the number of total muscle fibers, but the underlying mechanism remains unclear. In this study, we found that the development of embryonic muscle fibers was significantly influenced by the interaction between host SYISL genotype and maternal gut microbiota. SYISL KO alters the composition of the female mice maternal gut microbiota, significantly increases the relative abundance of Prevotella (P<0.05). Fecal microbiota transplantation (FMT) experiments indicated that fecal suspension from KO female mice significantly increased the number of offspring muscle fibers.  Our study provides the new evidence for the interaction between maternal single gene and gut microbiota on the embryonic muscle development of the offspring.

overall_design: In order to investigate the regulatory role of SYISL during embryonic muscle development, samples of wild-type (WT) and SYISL knockout (KO) 18.5-day embryonic mouse leg muscles were collected, and RNA-seq analysis was conducted.

first: Hao

last: Zuo

first: Wei

last: Jiang

first: Rong

last: Zheng

first: Bo


title: Tranilast inhibits hepatic lipid response in nonalcoholic steatohepatitis by deacetylating LKB1

city: Hefei

first: Weiwei

last: Qin

address: Huangshan road

institute: University of Science and Technology of China

summary: Nonalcoholic fatty liver disease (NAFLD), a progressive hepatic disease with ectopic fat accumulation, can evolve toward nonalcoholic steatohepatitis (NASH). To date, there is still no approved drug therapy, which remains a major unmet need. Previous study has indicated that tranilast ameliorates hepatic fibrosis and stellate cells activation in dietary rat model of NASH. However, the precise mechanism of tranilast in anti-NASH remains unclear.

overall_design: we performed a RNA sequencing analysis of liver from high-fat and high-cholesterol(HFHC)compared to HFHC and tranilast subjects

first: Sihui

last: Luo


title: Transcriptomic Analysis of Long Non-coding RNAs and mRNAs in a Mouse Model of Venous Thrombosis

first: Zhenguo

last: Zhai

address: No.2 East yinghua road

department: Department of Pulmonary and Critical Care Medicine

institute: China-japan Friendship Hospital

summary: Recent advancements have identified numerous long non-coding RNAs (lncRNAs) involved in various biological processes and diseases. However, the roles of lncRNAs in venous thromboembolism (VTE) remain largely unexplored. This study aims to elucidate the expression profiles of lncRNAs and mRNAs in a well-established animal model of VTE. Acute thrombosis was induced by surgical ligation of the inferior vena cava (IVC) within 24 hours. The thrombus burden in venous vessels was evaluated using hematoxylin and eosin staining and Masson's trichrome staining. The IVC and associated thrombus were harvested 24 hours post-ligation, and the extracted RNA was subjected to RNA sequencing (RNA-seq) analysis. This study offers a comprehensive overview of the expression profiles of lncRNAs and mRNAs in a murine model of venous thrombosis, providing novel insights into the roles of RNAs in VTE.

first: Risheng

last: Hao

first: Haobo

last: Li

first: Chen

last: Wang


title: Evaluation of the effect of maternal immune activation and weaning on hypothalamus of 22 day old pigs

summary: Female and male pigs were studied. Half of the pigs were exposed to immune activation from virally-infected mothers, and half were not exposed. At 21 days of age half the pigs were weaned and the remainder remained with the sow.

overall_design: RNA samples were obtained at 22 days of age. Hypothalamus RNA samples were subjected to paired-end RNA sequencing

last: Zas


title: ANGPTL3 regulates the peroxisomal translocation of SmarcAL1 in response to cell growth states

city: Boston

first: Yu-Xin

last: Xu

state: United States

address: 185 Cambridge Street Simches Research Building, CPZN 5.500

department: Center for Genomic Medicine

institute: Massachusetts General Hospital

summary: Angiopoietin-like 3 (ANGPTL3) is a key regulator of lipoprotein metabolism, known for its potent inhibition on intravascular lipoprotein and endothelial lipase activities. Recent studies have shed light on the cellular functions of ANGPTL3. However, the precise mechanism underlying its regulation of cellular lipid metabolism remains elusive. We recently reported that ANGPTL3 interacts with the chromatin regulator SMARCAL1, which plays a pivotal role in maintaining cellular lipid homeostasis. Here, through a combination of in vitro and in vivo functional analyses, we provide evidence that ANGPTL3 indeed influences cellular lipid metabolism. Increased expression of Angptl3 prompted the formation of lipid droplets (LDs) in response to slow growth conditions. Notably, under the conditions, Angptl3 accumulated within cytoplasmic peroxisomes, where it interacts with SmarcAL1, which translocated from nucleus as observed previously. This translocation induced changes in gene expression favoring triglyceride (TG) accumulation. Indeed, ANGPTL3 gene knockout (KO) in human cells increased the expression of key lipid genes, which could be linked to elevated nuclear localization of SMARCAL1, whereas the expression of these genes decreased in SMARCAL1 KO cells. Consistent with these findings, the injection of Angptl3 protein to mice led to hepatic fat accumulation derived from circulating blood, a phenotype likely indicative of its long-term effect on blood TG, linked to SmarcAL1 activities. Thus, our results suggest that the Angptl3-SmarcAL1 pathway may confer the capacity for TG storage in cells in response to varying growth states, which may have broad implications for this pathway in regulating energy storage and trafficking.

overall_design: Human hepatoma Huh7 cell lines with ANGPTL3 KO or WT ANGPTL3 were generated using CRISPR genome editing system. Total RNA from those cell lines were used for RNA-seq assays to detect the gene expression difference between the cells with ANGPTL3 KO and the control cells with WT ANGPTL3.


overall_design: Rat hepatoma McA cell lines were transfected with Fc or Fc-Angptl3 expression constrcuts and stable cell lines with Fc or Fc-Angptl3 expression were selected. Total RNA from those cell lines were used for microarray assays to detect the gene expression difference between the two stable cell lines under the normal growth condition.


title: Aberrant NUP98 condensates activate leukemogenic genes via discrete genomic engagement

city: Houston

first: Isaac

last: Hilton

address: 6500 Main St

department: Bioengineering

institute: Rice University

summary: NUP98 FG repeats trigger hematopoietic malignancies when aberrantly fused to various DNA/chromatin binding domains. However, how these heterogeneous NUP98 fusions drive oncogenesis remains unclear. Here we fuse different NUP98 FG repeat compositions to dCas9 and establish that NUP98 FG repeats are sufficient to activate human genes via cooperative activity at human endogenous promoters. Further, we find that NUP98-FG repeats spontaneously undergo liquid-liquid phase separation and co-condensate with other transcriptional coactivators in human cells, which we show is indispensable for transcriptional activation. We also define a threshold of NUP98 FG repeat numbers required for biomolecular condensation and gene activation that is consistent with NUP98 FG repeat lengths observed across clinical cohorts. Using ChIP-seq and live cell imaging, we further demonstrate that although NUP98 FG repeats can robustly shuttle into cell nuclei, engagement with the human genome is directed solely through fusion partner. Interestingly, two frequent oncogenic fusions, NUP98-HOXA9 and NUP98-KDM5A exhibit discrete genomic engagement landscapes and gene-regulatory modes in that NUP98-HOXA9 initiates strong transcription via intragenic super enhancer-like binding and increased intrachromosomal contacts, while NUP98-KDM5A activates genes via strict localization to promoters. Additionally, in primary human HSCs, NUP98-HOXA9 and NUP98-KDM5A globally dysregulate transcription in a largely non-overlapping manner. Nevertheless, both oncogenic fusion proteins directly drive the inappropriate activation of core leukemia-associated oncogenes, which occurs coincident with the downregulation of genes associated with HSC lineage commitment. Altogether, our studies point toward a conserved core set of potential therapeutic targets driving NUP98-associated cancers and clarify the transcriptional and oncogenic role of aberrant NUP98 condensates.

overall_design: To investigate the binding profile and oncogenic transcriptional regulatory role of NUP98 fusions in human cells, we perfomed ChIP-seq and RNA-seq analysis of several NUP98 fusions in HEK293T and human HSCs, respectively.

first: Jing

first: Mario

last: Escobar

first: Alex

last: Ma


title: Transgenerational inheritance of diabetes susceptibility in male offspring with maternal hyperandrogenism

first: Shourui

last: Hu

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

overall_design: Refer to individual Series


title: Single-cell multiomics study of cell-type-specific neuron activation unravels context-dependent gene regulation of brain disorders [030]

status: Public on Feb 18 2025

city: Evanston

first: Jubao

last: Duan

address: 1001 University Place

department: Center for Psychiatric Genetics

institute: NorthShore University HealthSystem

summary: Genome-wide association studies (GWAS) have identified many risk genes for neuropsychiatric disorders (NPD) such as schizophrenia (SCZ). However, functional interpretation of these GWAS findings remains challenging; a major hurdle is that polygenic risk may manifest its effect conditionally upon neural activation, i.e., context-dependent. Human induced pluripotent stem cell (hiPSC)-derived neurons are a tractable cellular model for ascertaining context-dependent polygenic effects, e.g., neural activation that may mimic the physiological effects of environmental stimuli. Here, we modelled neural activation by depolarisation using high potassium chloride (KCl) in co-cultured excitatory/inhibitory neurons of 100 hiPSC lines (28 from SCZ donors), followed by assaying single-cell multiomes (scRNA/ATAC-seq) of over 700,000 nuclei from neurons at 0 hr (unstimulated), 1 hr (early response), and 6 hr (later response) of high KCI exposure. We linked genes with open chromatin peaks for each main neural subtype (GABAergic inhibitory, NEFM+ or NEFM-excitatory neurons) and confirmed a significant correlation between peak accessibility and target gene expression. Compared to static genes/peaks, dynamic ones, specifically those activity-upregulated, were more enriched for NPD GWAS risk, with the most robust enrichment for SCZ. Based on the dynamic gene expression pattern across the three time points, we found NPD risk genes tend to be continuously upregulated (i.e., with up-up dynamics). We further analysed context-specific SCZ-associated differentially expressed genes (DEGs) using MAST for single neurons of 28 SCZ cases and 72 controls. We found that 3-5%, 4-6%, and 15-23% of genes were SCZ-associated DEGs in NEFM+ excitatory, NEFM- excitatory, and GABAergic neurons, respectively, most of which were cell activity-specific. Notably, we found that SCZ-associated DEGs in high-activity neurons were more enriched for synapse-related GO terms and NPD risk genes. Interestingly, upstream regulatory sequences of the stimulation-specific SCZ-associated DEGs were enriched for binding sites of TCF4, which is a strong GWAS risk gene and was considered the master regulator of other SCZ-related genes. Moreover, the upregulated genes in SCZ cases in the stimulated (only at 6hr) NEFM+ excitatory neurons showed strong enrichment for GO terms related to cholesterol synthesis. Single-neuron DEG analysis for 28 SCZ cases and 28 matched controls gave similar results. Our study suggests that many NPD genes may only elicit disease-relevant effects upon neuronal activation, providing novel insights into how polygenic risk factors interact with environmental stimuli for NPD.

overall_design: Raw FASTQ files complies 10x Genomics multiome scARC (scRNA-seq + scATAC-seq) standard. Library generated using cultured glutamatergic and GABAergic neurons derived from iPS cells with Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Kit. The output folders, including all matrices files, of Cell Ranger 2.0.2 were packaged and compressed sample-wise in according to their BioSample and SRA metadata

first: Siwei

last: Zhang


title: Single-cell multiomics study of cell-type-specific neuron activation unravels context-dependent gene regulation of brain disorders [029]


overall_design: Rat hepatoma McA cell lines were transfected with Fc or Fc-Angptl3 expression constrcuts and stable cell lines with Fc or Fc-Angptl3 expression were selected. Total RNA from those cell lines were used for microarray assays to detect the gene expression difference between the two stable cell lines under low growth condition.


title: Transcriptome and proteome correlation during APETALA1-mediated activation of flower development in Arabidopsis

city: Bellaterra

first: Jose Luis

last: Riechmann

state: Barcelona

address: Campus UAB - Edifici CRAG

institute: Center for Research in Agricultural Genomics

summary: We characterized genome expression at proteome level and correlated it with unbiased transcript expression data to obtain a dynamic view of early Arabidopsis flower development.

overall_design: Time-course experiment conducted using the pAPETALA1(AP1):AP1-GR ap1 cal floral induction system, that consisted of five subsequent days after the dexamethasone-induced activation of floral initiation. The experimental design included four complete biological replicates, for a total of six samples. Each experimental sample was used for both transcript profiling (RNA-seq) and shotgun proteomics (nLC-ESI-MS/MS).

first: Raquel

last: Álvarez-Urdiola

first: Martí

last: Bernardo-Faura

first: Víctor

last: M González Miguel

first: José

last: Matus


title: Differential expression profiles analysis of miRNA in granulomatous lobular mastitis

city: changsha

first: ling

last: jie

state: hunan

address: xue shi

institute: Hunan university of Chinese medicine

summary: Purpose:analysing the differential expression of miRNAs in tissue between GLM patients and healthy controls, provide a comprehensive differential expression profile of miRNAs, screen out possible biomarkers, and elucidate post-transcriptional regulation from the whole level.Methods: The expression profile of miRNAs was measured here by high-throughput sequencing in tissue of GLM patients and healthy controls. Significantly differentially expressed miRNAs were screened by threshold setting and cluster analysis, and their target genes were analysed by gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes(KEGG) enrichment.Results: a total of 31,077 miRNAs were predicted by high-throughput sequencing.Under the condition of threshold ∣log2 fold change (log2FC)|>2.5, qvalue<0.001, 13 miRNAs that were expected to be GLM biomarkers were sreened out. The expression of 13 miRNAs in the GLM group were higher than in the control group, as follows: hsa-miR-106a-5p, hsa-miR-155-5p, hsa-miR-20b-5p, hsa-miR-223-5p, hsa-miR-3916, hsa-miR-4433a-3p, hsa-miR-4433b-5p, hsa-miR-451a, hsa-miR-4659a-3p, hsa-miR-4802-3p, hsa-miR-5571-3p, hsa-miR-624-5p, and hsa-miR-942-3p. Cell and biological process were the most significantly enriched GO term and KEGG pathway.Conclusions: This is the first report detailing genome-wide miRNA profiling of GLM, and the possible targets and pathways of GLM were analysed from bioinformatic analysis. This study finds that 13 significantly differential expressed miRNAs may have important theoretical significance and potential application value and need subsequent large-sample clinical trials for further validation.

overall_design: 10 patients diagnosed with granulomatous lobular mastitis and 10 healthy volunteers

first: Jie

last: Ling

first: Xianmin

last: Xie

first: Weifang

last: Huang

first: Jun

last: Luo

first: Yue

first: Hongqiao

last: Fan

first: Lifang

last: Liu


title: Single-cell multiomics study of cell-type-specific neuron activation unravels context-dependent gene regulation of brain disorders [024]


title: Host-microbiome response to hyperbaric oxygen treatment in ulcerative colitis

first: Gene

last: Yeo

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

summary: Pre- and post-hyperbaric oxygen sequencing of mucosal biopsies of ulcerative colitis patients to understand host response to hyperoxia

overall_design: In this post-hoc analysis of a phase 2A sham-controlled double-blind randomized trial, we aimed to understand the hyperbaric oxygen therapy specific mucosal effects in ulcerative colitis patients hospitalized for moderate-severe flares. Pre- and post-intervention mucosal biopsies were obtained through lower endoscopy at study day 10 among ulcerative colitis patients receiving hyperbaric oxygen therapy (2.4 atmospheres, 100% oxygen, 90 minute sessions) and compared against patients receiving sham hyperbaric air (1.34 atmospheres, room air, 90 minutes). In total we included, 5 hyperbaric treated and 8 sham treated patients. bulk-RNA sequencing was performed with replicates and compared between groups.

first: Robert

middle: H

last: Mills

first: Marvic

last: Carrillo-Terrazas

first: Yash

last: Mittal

first: Brian

last: Yee

first: Christella

last: Widjaja

first: Fernando

last: Vargas

first: Kevin

last: Nguyen

first: Kelly

last: Weldon

first: Julia

last: Gauglitz

first: Gail

last: Ackerrmann

first: Gregory

last: Humphrey

first: Lindsay

last: DeRight-Goldasich

first: Tara

last: Schwartz

first: Austin

last: Swafford

first: Corey

last: Siegel

first: Pradipta

last: Ghosh

first: Pieter

last: Dorrestein

first: Rob

last: Knight

first: David

last: Gonzalez

middle: W

first: John

last: Chang

first: Parambir

last: Dulai


title: The Chromatin Remodeler Chromodomain Helicase DNA Binding Protein 2 Promotes Colorectal Cancer Progression

city: New York

first: Maria

middle: Victoria

last: Revuelta

state: New York

address: 1300 York Avenue

department: Medicine

institute: Weill Cornell Medicine

summary: Integrative analysis of colorectal cancer (CRC) whole genomes and matched transcriptomes revealed that somatic promoter mutations are associated with increased Chromodomain helicase DNA-binding protein 2 (CHD2) levels. In both primary and metastatic CRC patients, elevated CHD2 levels are associated with worse prognosis and overall survival. We find that CHD2 increases promoter-transcription start site-chromatin accessibility and transcriptional upregulation of multiple oncogenes. In vitro, elevated CHD2 promoted CRC cell proliferation, migration and growth. In orthotopic xenografts, CHD2 promoted higher tumor burden and abdominal metastases, most prominently to the liver. FTD/TPI is an FDA approved chemotherapy for advanced chemo-refractory CRC. In orthotopic CRC models, FTD/TPI was highly effective in reducing metastases and prolonging survival for CHD2 high expressing CRCs. Thus, high CHD2 expression may be a potential CRC chemopredictive biomarker for FTD/TPI. Overall, these results provide new insights into the role of non-coding mutations and CHD2 levels to promote CRC growth and metastasis.

overall_design: Examination of CHD2 high, basal and low expressing HT29 cells

first: Mavee

last: Witherspoon

first: Tawny

last: Cuykendall

first: Eric

last: Liu

middle: V

first: Ergang

last: Wang

first: Olivier

last: Elemento

first: Xiling

last: Chen

first: Ekta

last: Khurana

first: Steven

last: Lipkin


title: RNA-sequencing of gastric tissues derived from five inflamed-type and five desert-type tumors

city: Fuzhou

first: Guangtan

last: Lin

state: Fujian

address: No. 29 Xinquan Road

department: Department of Gastric Surgery

institute: Fujian Medical University Union Hospital

summary: Transforming gastric tumors from immunosuppressive to immunostimulatory is a potential approach to enhance immune checkpoint blockade  response. Here, we developed a chromosomal instability subtype gastric cancer mouse model with an immunoactive tumor microenvironment (TME) and a stem cell-originated mouse-derived allograft model with an immunosuppressed TME to investigate mechanisms regulating the tumor immunophenotype and uncover therapeutic strategies to remodel the TME.

overall_design: We collected gastric tissues derived from five inflamed-type and five desert-type tumors and then applied for RNA-sequencing.

first: Longlong

last: Cao


title: Temporal constraints on enhancer usage and enhancer-promoter connectivity shape the regulation of limb gene transcription [CUT&Run]

city: Geneva

first: Guillaume

last: Andrey

address: Rue Michel-Servet 1

department: Department of Genetic Medicine and Development

country: Switzerland

institute: University of Geneva

summary: The repertoire of enhancers orchestrating gene expression during embryonic development shapes the forms and functions of organs. Within regulatory landscapes, enhancers control their target genes through spatially distinct or overlapping activities. However, the temporal specificity of enhancers repertoires—how their activities change over time to dynamically influence gene expression—is less well characterized. In this study, we introduce the regulatory trajectory framework to monitor how enhancer landscapes govern gene transcription in vivo across extensive developmental periods. This paradigm conceptually involves transcriptional initiation, marking the beginning of gene expression, followed by its maintenance over time, and ultimately decommissioning, leading to gene repression. To track and sort cells undergoing these distinct phases, we devised a transgenic recorder approach at the Shox2 model locus. Through this method, we discovered that cells maintaining Shox2 transcription in early and late limb development relies on distinct, temporally restricted enhancer repertoires. We demonstrate that eliminating early- or late-acting enhancers only transiently affects Shox2 expression indicating that these enhancer repertoires function independently. Additionally, we found that changes in the locus' 3D topology associate with enhancer activities and that a rapid loss of enhancer-promoter contacts occurs during decommissioning. Finally, we show that the decommissioning of the Shox2 locus can be actively driven by Hoxd13, a gene which expression is known to antagonize Shox2. Overall, our work uncovers the dependency of developmental genes on enhancers with temporally restricted activities to generate complex expression patterns over time and shed light on the dynamics of enhancer-promoter interactions.

overall_design: We devised a dual-reporter system to monitor Shox2 regulatory trajectories and sort cells undergoing these distinct phases. First, we inserted in mouse embryonic stem cells (mESCs), 1kb upstream of the Shox2 transcriptional start site, a regulatory sensor cassette constituted by a minimal β-globin promoter, a mCherry reporter gene followed by a destabilized PEST sequence, a P2A self-cleavage sequence and a CRE recombinase gene. These cells cells were then retargeted to integrate, at the Rosa26 locus, a cassette with a splice acceptor followed by a floxed 3x SV40pA STOP signal and the EYFP gene open reading frame. We studied the transcriptional identity of these cells by scRNA-seq. We the profile the identity of sorted cells by RNA-seq and their regulatory profile by CHiC and ChIP-seq

first: Raquel

last: Rouco


title: scRNA-sequencing of gastric tissues derived from three inflamed-type and three desert-type tumors

overall_design: We collected gastric tissues derived from three inflamed-type and three desert-type tumors and then applied for scRNA-sequencing.


title: Reduced TBX5 dosage causes human atrial disease by undermining developmental gene regulation of atrial cardiomyocyte identity [scRNA-seq]

city: San Francisco

first: Benoit

last: Bruneau

address: 1650 Owens St

institute: Gladstone Institutes

summary: In a TBX5-linked human cellular model of atrial disease, we examined the gene networks controlled by TBX5 during human atrial differentiation using single-cell RNA and ATAC sequencing.

overall_design: Wildtype, TBX5 heterozygous and homozygous mutant iPSCs were differentiated to atrial cardiomyocytes. At day 20 or day 45 of differentiation, cells were harvested for single-cell RNA sequencing and analyzed using Seurat. Two replicates per genotype per timepoint were harvested.

first: Kavitha

last: Rao

first: Irfan

last: Kathiriya


title: Distinct endothelial pathomechanisms drive arterio-venous malformation in Alk1 or Smad4 loss-of-function conditions

city: Berlin

first: Andranik

last: Ivanov

address: Chariteplatz 1

department: Core Unit Bioinformatics

institute: Berlin Institute of Health

summary: Hereditary hemorrhagic telangiectasia (HHT) is an inherited autosomal dominant disorder associated with mutations in the bone morphogenetic protein (BMP) pathway. Inherited heterozygous loss of function mutations and acquired loss of heterozygosity  in either Alk1, Eng, or Smad4 lead to the development of arteriovenous malformations (AVMs), which trigger local vessel instability, hypoxia and vessel leakage or rupture. Current models assume common cellular pathomechanisms culminating in altered endothelial cell (EC) shape regulation, directional migration and proliferation control as a consequence of deficient BMP pathway signaling in ECs under the influence of blood-flow mediated shear stress. Here we report that loss of Alk1 or Smad4 surprisingly triggers very distinct endothelial phenotypes, signaling dynamics and transcriptional changes in ECs, both in vitro and in vivo.  EC behavior in both in vivo and  mosaic flow cultures  illustrate that cells deficient in Smad4 effectively migrate against the direction of fluid shear, from veins to arteries, whereas cells lacking Alk1 fail to polarize and migrate against flow. Our data suggest that AVMs triggered by Smad4 mutations occur through hyperpruning of capillaries, thus precipitating flow in a single shunt, whereas AVMs caused by Alk1 mutation grow by cell accumulations close to the vein, as well as the persistence of a hyperdense plexus that drives nidus formation. We propose that the cellular pathomechanisms leading to AVM formation are not the same if the upstream BMP receptor Alk1, or the downstream common transcription factor Smad4 are mutated, raising the prospect for urgently needed, mechanism-based, therapeutic avenues that need to be tailored to correcting the specific pathomechanism.

overall_design: In order to understand the how SMAD4 and Alk1 loss of function affects the transcriptome of endothelial cells exposed to laminar shear stress, we combined siRNA knockdown and flow exposure over time. Human umbilical venous endothelial cells (HUVECs) which were treated with following siRNAs: siCTRL, siSMAD4, siAlk1, and exposed to 4 or 16 hours of laminar fluid shear stress. Static controls were also collected for each condition. In addition, wildtype HUVECs were also used as a reference control, as well as a double knockdown of siAlk1+siSMAD4 (siDouble) as an additional control. In total, there are 5 treatment groups - WT, siCTRL, siSMAD4, siAlk1, siDouble; and 3 flow groups - static, 4h, 16h. Samples were collected from 3 independent experiments.

first: Olya

last: Oppenheim

first: Eireen

last: Bartels-Klein

first: Holger

last: Gerhardt

first: Dieter

last: Beule

first: Tatiana

last: Borodina


title: Spatial confinement induces reciprocating migration of epidermal keratinocytes and forms triphasic epithelia

city: Sapporo

first: Takuma

last: Nohara

state: Hokkaido

department: Dermatology

country: Japan

institute: Hokkaido University

summary: Epithelial cells undergo epithelial-mesenchymal transition (EMT) during migration and regain their epithelial phenotype in the post-migration phase (mesenchymal-epithelial transition; MET). Keratinocytes (KCs), skin epithelial cells, placed on a microporous membrane migrated through 3.0 µm or larger micropores.  Live imaging of immortalized HaCaT KCs which stably express green fluorescent protein (GFP)-labelled LifeAct (LifeAct-HaCaTs) revealed that KCs moved in a reciprocating manner with actin-rich filopodia-like structures of KCs extending into and out of the 3.0 µm micropores. HaCaT KCs cultured on 3.0 µm pored-membranes upregurated the genes associated with tissue development and cell differenciation compared with on 0.4 µm-pored membranes. These results demonstrate that KCs migrate through confined spaces in a reciprocating manner, which might help form triphasic epithelia, recapitulating wound healing processes.

overall_design: LifeAct-HaCaTs were seeded on 0.4 µm- or 3.0 µm-pored PET membranes at the concentration of 5.0 x10^5 /ml and cultured for 48 hours. Cells above the membrane were then collected by a scraper. RNA was extracted using the RNeasy Mini kit (Qiagen, Hilden, Germany).

first: Ken

last: Natsuga


title: tsRNA-49-73-Glu-CTC: A Promising Serum Biomarker in NSCLC

city: Qingdao

first: chenyu

last: li

address: No. 308 Ningxia Road, Qingdao City

institute: Qingdao University

summary: Objective Lung cancer has the highest incidence and mortality rates globally, with the majority of cases classified as non-small cell lung cancer (NSCLC). Due to the absence of specific tumor biomarkers, most lung cancer cases are diagnosed at an advanced stage. Therefore, the identification of novel molecular biomarkers with high sensitivity and specificity for early diagnosis is deemed crucial for enhancing the treatment of NSCLC. Transfer RNA-derived small RNA (tsRNA) is closely associated with malignant tumors and holds promise as a potential biomarker for tumor diagnosis. This study aimed to investigate whether serum tsRNA could serve as a biomarker for NSCLC. Methods Differentially expressed tsRNAs were identified through high-throughput sequencing of serum samples obtained from patients with NSCLC and healthy individuals. Additional serum samples were collected for validation using Reverse Transcription Quantitative Polymerase Chain Reaction (RT-qPCR). The diagnostic performance of these tsRNAs was assessed through Receiver Operating Characteristic (ROC) Curve Analysis. Furthermore, preliminary functional exploration was undertaken through cell experiments. Results tsRNA-49-73-Glu-CTC is highly expressed in the serum of patients with NSCLC and demonstrates superior diagnostic value compared to commonly used tumor markers in clinical practice, such as Carcinoembryonic Antigen (CEA), Neuron-Specific Enolase (NSE), and Cytokeratin 19 Fragment (CYFRA). A combined diagnostic approach enhances the accuracy of NSCLC detection. Additionally, tsRNA-49-73-Glu-CTC is highly expressed in A549 cells, and transfection with a tsRNA-49-73-Glu-CTC inhibitor significantly reduces both proliferation and migration capabilities. Conclusions tsRNA-49-73-Glu-CTC has the potential to serve as a novel molecular diagnostic biomarker for NSCLC and plays a significant role in the biological processes associated with NSCLC proliferation and migration.

overall_design: To analyze the differential expression of tsRNA between non-small cell lung cancer patients and healthy individuals, we collected serum samples from three untreated NSCLC patients and three healthy individuals undergoing routine physical examinations for high-throughput sequencing.

first: Chenyu

last: Li

first: Shenjie

last: Zhong

first: Juan

last: Chen

first: Xiaofeng

last: Mu


title: Dux cluster duplication ensures full activation of totipotent genes

city: Kunming

first: meiqi

last: Lin

address: Kunming, Yunnan province

institute: LPBR

summary: Zygotic genome activation (ZGA) confers to the mouse two-cell (2C)embryo a unique transcriptional profile characterized by transient up-regulation of many totipotency-related genes and MERVL retrotransposons. Intriguingly, those genes are duplicated and clustered in the genome during evolution, including Dux cluster, Obox and Zscan4 family members in mice. However, the contribution and biological significance of the totipotency-related gene duplication events in early embryo development remain poorly understood. Here, we focus on Dux cluster, the master regulator of ZGA that is necessary and sufficient for the induction of 2C-like cells (2CLCs) and activation of totipotency-related genes in mouse embryonic stem cells (mESCs). By reducing Dux gene copies from 31 to 0 or 1 through CRISPR-Cas9 technology, we generate Dux-KO and Dux (n=1)mESC lines, respectively. We uncover that the totipotency-related gene transcriptional profile is awakened to a much lesser extent in Dux (n=1) mESCs compared to wild-type (WT) mESCs following global DNA demethylation reprogramming or induction of DNA damage, mimicking the intrinsic events in preimplantation development. Together, Dux cluster duplication is critically required for the full activation of ZGA transcripts.

overall_design: To investigate the effects of Dux cluster duplication on the activation of two-cell specific transcripts during zygotic genome activation (ZGA), we generated Dux-KO and Dux (n=1) mESCs by CRISPR-Cas9 technology. We performed gene expression profiling analysis using data obtained from RNA-seq of WT, Dux-KO and Dux (n=1) mESCs. To determine whether Dux cluster duplication is critical for efficient and full activation of ZGA transcripts during early embryo development associated with the global DNA demethylation process, we treated WT, Dux-KO and Dux (n=1) mESCs with DNMT1 protein degrader GSK3484862 to mimic the DNA demethylation reprogramming events. Comparative gene expression profiling analyses of RNA-seq data from WT, Dux-KO and Dux (n=1) mESCs treated with DMSO and 2 uM GSK-3484862 for 3 days were conducted.

first: Jiameng

last: Dan

first: Meiqi

first: Zeling

last: Du

first: Yirang

last: Zhang


title: Aging-linked deterioration of RNA metabolism destabilizes the stress response of neurons [RNASeq, RiboSeq]

city: Tucson

first: Kevin

last: Rhine

state: AZ

address: 1703 E Mabel St

department: Pharmacology & Toxicology

institute: University of Arizona

summary: Aging is one of the most prominent risk factors for neurodegeneration, yet the molecular mechanisms underlying the deterioration of old neurons are mostly unknown. To efficiently study neurodegeneration in the context of aging, we transdifferentiated primary human fibroblasts from aged healthy donors directly into neurons, which retained their aging markers. Here we show that aged neurons are broadly depleted of RNA-binding proteins, especially spliceosome components. Intriguingly, splicing proteins – like the dementia and ALS-associated protein TDP-43 – mislocalize to the cytoplasm in aged neurons, which leads to widespread alternative splicing. Cytoplasmic spliceosome components typically are recruited to stress granules, but aged neurons suffer from chronic stress that prevents this sequestration. We link chronic stress to the malfunctioning ubiquitylation machinery, poor HSP90α chaperone activity, and the failure to respond to new stress events. Together our data demonstrates that aging-linked deterioration of RNA biology is a key driver of poor resiliency in aged neurons.

overall_design: Riboseq of isogenic transdifferentiated and iPSC-derived neurons; bulk RNA was isolated from untreated cells whereas RNA for ribosomal footprinting (to calculate translation efficiency) was derived from cells treated with cycloheximide, which locks RNA on ribosomes

first: Rachel

first: Hema

last: Kopalle

first: Xuezhen

last: Ge

first: Elle

last: Epstein

first: Orel

last: Mizrahi

first: Assael

middle: A

last: Madrigal

first: Hsuan-Lin

last: Her

first: Trent

last: Gomberg

first: Anita

last: Hermann

first: Joshua

last: Schwartz

first: Amanda

middle: J

last: Daniels

first: Uri

last: Manor

first: John

last: Ravits

first: Robert

last: Signer

first: Eric

last: Bennett

first: Gene

last: Yeo


title: Aging-linked deterioration of RNA metabolism destabilizes the stress response of neurons [RNA-seq]

first: Kevin

overall_design: NGS RNA-seq of isogenic transdifferentiated and iPSC-derived neurons before, immediately after, and 24 h after acute stress treatment with 0.5 mM sodium arsenite; deep sequencing was also performed for pre-stress conditions

last: Li

middle: L


title: Single-Cell RNA Sequencing Identifies Molecular Biomarkers Predicting Late Progression to CDK4/6 Inhibition in Patients with HR+/HER2- Metastatic Breast Cancer

first: Khandan

last: Keyomarsi

state: Texas

address: 1515 Holcombe Blvd

department: Experimental Radiation Onc

institute: University of Texas - MD Anderson Cancer Center

overall_design: Refer to individual Series