title: Targeting of the CD161 Inhibitory Receptor Enhances Bone Marrow-Resident Memory CD8+ T Cell-mediated Immunity Against Multiple Myeloma [Mice RNA-seq]

overall_design: The 5TGM1 MM model was established by intravenously injecting luciferase-expressing 5TGM1 cells (1×10⁶ cells in 200 μL PBS) into C57BL/KaLwRij mice. On week 5 post-tumor injection, mice exhibiting increased bioluminescence signals were randomized into two treatment cohorts: an isotype control antibody group and an anti-NK1.1 monoclonal antibody (mAb) group.Antibodies were administered via intraperitoneal injection (5 mg/kg) twice per week. On day 14 post-antibody administration, BM single-cell suspensions were collected, and CD8a+ T cells were isolated using the CD8a+ T Cell Isolation Kit , total RNA was extracted using the RNA rapid extraction kit for RNA sequencing.


title: Targeting of the CD161 Inhibitory Receptor Enhances Bone Marrow-Resident Memory CD8+ T Cell-mediated Immunity Against Multiple Myeloma [CART scRNA-seq]

status: Public on Dec 04 2025

city: Changsha

first: Liwen

last: Wang

state: Hunan

address: 138 Tongzipo road

department: Department of Hematology

country: China

institute: Third Xiangya Hospital, Central South University

type: Expression profiling by high throughput sequencing

summary: Immune checkpoint inhibitors (ICIs) have transformed the treatment of many solid tumors. Still, their effectiveness in multiple myeloma (MM) remains underwhelming, highlighting the need to explore alternative approaches beyond conventional ICIs. Here, we identify CD161 as a novel inhibitory receptor on bone marrow resident memory CD8+ T cells (BM CD8+ TRMs), known for their sustained presence and vital role in local immune surveillance in MM BM tumor microenvironment. The CD161-CLEC2D axis, where CD161 interacts with CLEC2D on MM cells, mediates immune suppression and TRMs dysfunction. Blocking CD161 enhances TRMs function, including tissue residency, proliferation, and antitumor activity. Combining CD161 blockade with CAR-T therapy significantly alleviates CAR-T exhaustion, improving its therapeutic efficacy. Additionally, a similar CD161-driven exhaustion program is observed in other hematologic malignancies. These findings suggest that targeting the CD161-CLEC2D axis could offer a promising strategy to enhance MM treatment outcomes and CAR-T efficacy.

overall_design: We collected BM and PB samples from one relapsed/refractory multiple myeloma (RRMM) patients on the 35th day post-BCMA CAR-T infusion. PBMCs and BMNCs were isolated using density gradient centrifugation with Ficoll. CAR-T cells were sorted based on CD3 and BCMA CAR expression via flow cytometry and subjected to single-cell sequencing

first: Linzhi

last: Xie

first: Yi

last: Zhou

first: Xin

last: Li


title: CRISPR/Cas9-mediated deletion of MADD induces cell cycle arrest and apoptosis in anaplastic thyroid cancer cells

city: Chicago

first: Jason

middle: M

last: Wood

state: IL

address: 900 S Ashland Ave rm 1057

department: Research Informatics Core

country: USA

institute: University of Illinois at Chicago

summary: Anaplastic thyroid cancer (ATC) is an aggressive malignancy with a poor prognosis and limited treatment options. Previous studies have shown that selective downregulation of the MADD (MAP32 kinase-activating death domain-containing protein) gene isoform increases ATC cell susceptibility to TRAIL-induced apoptosis. However, the existence of multiple MADD gene isoforms raised the possibility of functional compensation. This study aimed to definitively evaluate the role of MADD in ATC by employing CRISPR-Cas9 to delete the entire MADD gene. CRISPR-Cas9-mediated MADD knockout, performed in three ATC cell lines (8505C, C643, and HTH7) with distinct mutational backgrounds, significantly impaired ATC cell function in vitro, as indicated by reduced viability, increased apoptosis, decreased migration, and G0/G1 cell cycle arrest. RNA-seq analysis revealed alterations in genes related to cell survival, proliferation, and metastasis. In the orthotopic ATC mouse model, MADD deletion dramatically suppressed tumor growth, reduced lung metastases, and prolonged survival. Our findings demonstrate that MADD plays a crucial role in ATC cell survival, proliferation, and metastasis. The consistent effects observed across multiple cell lines and in vivo models suggest that MADD may represent a promising therapeutic target for this aggressive malignancy.

overall_design: RNA-seq profiling of 8505C, C643, and HtH7 cell lines and their derivatives based on CRISPR-Cas9 knockdown of the MADD gene.

first: Velavan

last: Bakthavachalam

first: Mark

middle: A

last: Sanborn

first: Manikannan

last: Mathayan

first: Satyajeet

last: Salunkhe

last: Maienschein-Cline

first: Suman

last: Setty

first: Basirudeen

last: Kabeer

first: Jalees

last: Rehman

first: Bellur

middle: S

last: Prabhakar


title: Immune profiling of the lung in Influenza-Associated Pulmonary Aspergillosis using CITE-seq

city: Zwijnaarde

first: VIB

last: Single Cell Core

address: Technologiepark-Zwijnaarde 71

department: VIB Single cell core

country: Belgium

institute: VIB

summary: Influenza-associated pulmonary aspergillosis (IAPA) is a severe fungal superinfection affecting critically ill influenza patients. Current treatments target pathogens but do not address the dysregulated host immune responses that drive morbidity. Host-directed immunotherapies could overcome this treatment gap. In this study, we used CITE-seq to compare transcriptional and surface antibody expression in immune cell populations within the lung tissue of mice with IAPA, influenza infection, Aspergillus infection, and healthy controls. This dataset provides comprehensive immune profiling, offering insights into the immune landscape of the lung during IAPA compared to single infections and healthy controls, which could aid in the development of targeted immunomodulatory therapies. These findings are part of a broader investigation, as detailed in the study "Anakinra restores the immunological misfiring that drives influenza-associated pulmonary aspergillosis." Here, we identified IL-1 inflammation, extensive neutrophil activation, and NET release as key features of IAPA pathogenesis. This inflammation led to an immunological imbalance that impaired neutrophil function, creating a permissive environment for Aspergillus. Blocking the IL-1 receptor with anakinra reduced inflammation, restored neutrophil function, and protected influenza-infected mice from invasive pulmonary aspergillosis and death. These results underscore the critical role of IL-1 inflammation in IAPA and suggest that anakinra could be a promising immunomodulatory therapy for IAPA patients.

overall_design: To further refine the different immune cell populations in the lung, we performed CITE-seq on CD45+ sorted lung cells from Healthy control (HC) (n=3), Aspergillus (n=3), influenza (n=4) and IAPA (n=4) mice on day 7

first: Laura

last: Seldeslachts

first: Sirima

last: Kraisin

first: Intan M.W.

last: Dewi

first: Simon

last: Feys

first: Frederik

last: Staels

first: Marina

last: Gkountzinopoulou

first: Cato

last: Jacobs

first: Birger

last: Tielemans

first: Eliane

last: Vanhoffelen

first: Agustin

last: Reséndiz-Sharpe

first: Lander

last: De Herdt

first: Oswin

last: Kwan

first: Niels

last: Vandamme

first: Jana

last: Roels

first: Julika

last: Neumann

first: Teresa

last: Prezzemolo

first: Bert

last: Malengier-Devlies

first: Mathias

last: Stroobants

first: Agostinho

last: Carvalho

first: Patrick

last: Matthys

first: Lieve

last: Naesens

first: Katrien

last: Lagrou

first: Mona

last: Khan

first: Peter

last: Mombaerts

first: Georgios

last: Chamilos

first: Erik

last: Verbeken

first: Kimberly

last: Martinod

first: Frank L.

last: van de Veerdonk

first: Joost

last: Wauters

first: Greetje

last: Vande Velde

first: Stephanie

last: Humblet-Baron


title: N'-(1-phenylethylidene)-benzohydrazide cytotoxicity is LSD1 independent and linked to Fe-S cluster disruption in Ewing sarcoma

city: Columbus

first: John

middle: William

last: Sherman

state: Ohio

address: 575 Childrens Crossroads

department: Center for Childhood Cancer

institute: Nationwide Children's Hospital

summary: The purpose of the study was to investigate the overlap in cytotoxic and gene regulatory activity between reversible LSD1 inhibitor SP-2509 (HCI-2509) and Compounds 15, 19, and 20 which share structural similariy with SP-2509 but lack LSD1 inhibitory activity. Additionally we compared these compounds to RNAi of EWS::FLI1 (iEF) or Luciferase control (iLuc), as has been done with SP-2509, as well as with OG-L002, an irreversible LSD1 inhibitor with minimal cytotoxic activity.

overall_design:
RNA-seq of wildtype A673 cells treated with vehicle (DMSO), Compounds 15, 19 or 20, or irreversible LSD1 inhibitor OG-L002 (2uM) for 48 hrs. Data was combined with samples from 2 additional datasets. That data is from GSE94502 (iEF and iLuc samples) and GSE98787 (A673_DMSO and A673_HCI_2509 samples). Data exclusively from this GEO submission is located in the geo_counts.csv file, while the complete count matrix used for analysis is located in the counts.csv supplementary file.

***************************************************************
The table below lists GEO accessions reused/reanalyzed for this study.
***************************************************************

middle: W

first: Emily

last: Theisen


title: Endothelial clock regulates retinal angiogenesis and ganglion cell function

city: Cleveland

first: Sujata

last: Rao

state: OH

address: 2022 E 105th St i building

institute: Cole eye, Cleveland Clinic foundation

summary: Angiogenesis, the formation of new blood vessels from existing ones, is essential for physiological and pathological processes such as wound healing, organ development, and tumor growth. It is a tightly regulated process influenced by both intrinsic and extrinsic factors. Emerging evidence shows a link between biological clocks that regulate physiological rhythms and angiogenesis through the modulation of angiogenic factors like vascular growth factors (Vegfa). Thus, the clock system can directly modulate the timing and efficiency of angiogenic processes. This study aimed to investigate the role of key circadian clock genes, Bmal1 and Per2, in retinal angiogenesis. Endothelial cell specific deletion of these genes significantly impairs vessel growth though distinct phenotypic differences emerge between the two knockout models as angiogenesis progresses. RNA-sequencing (RNA-seq) analysis of retinal endothelial cells reveals that circadian clocks predominantly influence the expression of genes involved in cell proliferation. Notably, vascular endothelial cell (VEC) proliferation is diurnally regulated, which is disrupted in the Bmal1 knockout animals leading to a reduction in the numbers of the Brn3a positive retinal ganglion cells (RGCs).  These alterations are further associated with compromised retinal circuitry and function.  Thus, this study uncovers critical roles for Bmal1 and Per2 in regulating retinal angiogenesis, emphasizing the importance of circadian control of cell proliferation in vascular development and retinal function.

overall_design: RNA-seq was performed on retinal endothelial cells sorted from Bmal1 mutant and tdTomato control postnatal (P) 7.5 mice using FACS. Cells were selected based on tdTomato and GFP expression driven by Pdgf-icreER, allowing for the comparison of transcriptomic changes between mutants and controls

first: Vijay

middle: k

last: Jidigam

first: Josh

last: Gallop

first: Brianna

last: Shimandle

first: Rebecca

middle: D

last: Fuller

first: Madison

middle: B

last: Kirby

first: Minzhong

last: Yu

first: Richard

last: Lang

last: rao


title: Quantitative Modeling of the Short-Term Response to Nitrogen Availability that Coordinates Early Events in Lateral Root Initiation

city: Berkeley

first: Allison

last: Gaudinier

state: CA

address: 54 Mulford Hall, Blackman Lab, University of California, Berkeley

institute: UC Berkeley

summary: To find novel factors in early root system architecture responses to nitrate conditions, we performed Arabidopsis thaliana root transcriptome profiling of a short-term time course in limiting and sufficient nitrate conditions.

overall_design: Col-0 seeds were surface sterilized and plated on mesh on 1mM KNO3 media and stratified for 2 days at 4°C . Plates were then placed vertically and grown in 22°C in 16 hour days/8 hour nights. 7 day old plants were transferred either to new 1mM or 10mM KNO3 plants at two hours post-dawn in the growth chamber. Per biological replicate, two plates per time point were transferred then combined. Root tissue was then harvested and flash frozen in liquid N2 at 0 min (mesh was picked up and placed down on the same plate to account for mechanical responses to transfer), 15 min, 45 min, 90 min, and 180 min.

first: Lisa

last: Van den Broeck

first: Miguel

last: Moreno-Risueño

first: Joel

last: Rodriguez-Medina

first: Rosangela

last: Sozzani

first: Siobhan

last: Brady


title: Constitutive androstane receptor in macrophages regulates Toll-like receptor 4-mediated innate immune responses during endotoxemic liver injury

city: Guangzhou

first: Renjie

last: Cao

address: No. 132, East Tianhe Road

department: School of Pharmaceutical Sciences

institute: Sun-yat sen university

summary: Macrophage proinflammatory hyperactivation drives the pathogenesis of acute liver injury, a common complication of severe sepsis. The nuclear receptor constitutive androstane receptor (CAR) modulates xenobiotic and endobiotic metabolism, but its role in endotoxin-induced liver injury remains unclear. Our study aims to reveal the regulatory effect of CAR on macrophages under LPS stimulation and uncover the underlying mechanism. Here, we report that CAR is highly expressed in human and murine macrophages. Dexamethasone and CITCO, human CAR agonists, triggered CAR nuclear translocation, attenuating inflammation in primary hMDMs from healthy donors. CAR agonists markedly attenuated endotoxin-induced liver damage in mice, alleviating hepatocyte death and hepatic inflammation. Macrophage-hepatocyte coculture confirmed that CAR inhibited inflammation through macrophage crosstalk. CAR-mediated hepatoprotection and anti-inflammatory effects were absent in AAV8-F4/80-Car-treated mice, confirming the essential role of CAR in macrophages. Mechanistically, CAR interacts with Tlr4 and influences its mRNA stability, and the suppressive effects of CAR on TLR4 were proven in Tlr4-KO mice. Furthermore, CAR activation reduced LPS-induced inflammation in BMDMs, Raw264.7 cells, and THP-1 cells, and Car or Tlr4 knockdown abolished CAR-mediated immunosuppression. Overall, macrophage CAR activation attenuated endotoxin-induced liver injury and hepatic inflammation through the TLR4 signaling pathway, providing insights for treating inflammatory liver diseases.

overall_design: RNA-seq profilling of the livers of Wild type C57BL/6 mice that accepted LPS/GaIn challenges,with vehicle or TCP pretreatment.

first: Tingting

last: Zhao

first: Ying

last: Wang


title: Effects of aging on the gut tube of the short-lived Turquoise killifish: Reduced intestinal stem cell activity associated by altered gene expression that is reversed by intermittent fasting

city: Vienna

first: Christian

last: Schoefer

address: Schwarzspanierstraße 17

department: Center for Anatomy and Cell Biology

country: Austria

institute: Medical University of Vienna

summary: The process of aging is associated with a decline in cellular, tissue, and organ function, which give rise to a range of health issues. Mounting evidence indicates that dietary restriction counters age-dependent effects and increases and enhances health and longevity in whole organisms, while less is known of aging and nutrition on individual organs of an organism. Here, we studied the responsible organ for nutrient uptake, the intestinal tube, along the lifetime of an organism. A longitudinal study was conducted on the morphology and gene expression of the gut tubes of the very short-lived aging model system African turquois killifish (Nothobranchius furzeri). The aim was to investigate the age and nutrition-related effects on gut tissue preservation at stages corresponding to human newborn, adolescence, adult and old age. The intestinal mucosa is characterized by folds and intervening interfold regions, in which the intestinal stem cells were localized. The stem cells were found to occur in clusters and that the cycling time of stem cells extends at old age. Concomitantly, we found a reduction in intestinal length and volume with age. Age-dependent gene expression revealed significant alterations in the expression of peripheral circadian clock genes and marker genes of stem cell niches. Notably, the majority of these genes retained their adult gene expression levels at old age after dietary restriction. Thus, our results demonstrate that the decline of structural intestinal tissue homeostasis is caused by a declining activity of stem cells, and that these effects are counteracted by dietary restriction

overall_design: Gene expression profiling by RNA-seq of whole intestine at week 10, at week 20 and at week 20 with dietary restriction.

first: Michael

last: Kothmayer

first: Sylvia

last: Laffer

first: Phillip

last: Widmayer

first: Elmar

middle: E

last: Ebner

first: Fehima

last: Ugarak

first: David

last: Martin

first: Stefan

middle: H

last: Geyer

first: Kareem

last: Elsayad

first: Wolfgang

middle: J

last: Weninger

first: Sabine

last: Lagger

first: Klara

last: Weipoltshammer

first: Oliver

last: Pusch

last: Schöfer


title: A non-coding RNA risk pathway in schizophrenia in which miR-137 induces the lncRNA GOMAFU through a pathological transcription network

city: Atlanta

first: Bing

last: Yao

address: 615 Michael Street

department: Department of Human Genetics

institute: Emory University

summary: MicroRNAs (miRNAs) and long non-coding RNAs (lncRNAs) regulate broad gene networks through distinct mechanisms, which govern normal brain development and function but are dysregulated in schizophrenia (SCZ). However, how disease-risk miRNAs and lncRNAs co-operate to form pathogenic pathways that contribute to the complex etiology of SCZ remains poorly understood. In this study, we identified a novel miRNA-lncRNA risk pathway for SCZ in which the well-recognized SCZ-risk factor miR-137 enhances expression of the SCZ-risk lncRNA GOMAFU in human neuron development. We found vigorous upregulation of GOMAFU during the development of multiple types of human neurons in vivo and in culture . Interestingly, histone acetylation down-regulates GOMAFU in iPSC-derived human neurons, likely through inducing transcription repressors of GOMAFU, represented by the miR-137-traget E2F6.  Indeed, we observed co-regulation of MIR137HG with GOMAFU during normal human neuron development and in SCZ brains and further demonstrated that miR-137 is necessary and sufficient for enhancing GOMAFU expression. Moreover, we identified transcriptomic changes induced by miR-137 in a human neuronal progenitor cell line and discovered that miR-137 integrates the functional co-operation of histone acetylation and transcription factors to  drive GOMAFU expression. Strikingly, a significant number of miR-137-regulated transcription factors are predicted to bind the GOMAFU promoter and affected in SCZ brains, which form a highly interactive molecular network. Together, these studies unveil the miR-137-GOMAFU non-coding RNA pathway in human neurons connected by SCZ-affected transcription factors, providing a new mode of functional integration between non-coding and coding risk genes of SCZ that form a pathological network.

overall_design: RNA-seq profiling of hsa-miR-137 mimic treated and wildtype BE(2)-M17 cells.

first: Peng

last: Teng

last: Zhou

first: Yangping

last: Li

first: Li

last: Ku

first: Feng

first: Zhexing

last: Wen

first: Yue

last: Feng


title: Liver molecular networks associated with drinking behavior in nonhuman primates [Array]

city: Winston-Salem

first: Jeannie

last: Chan

state: NC

address: Medical Center Boulevard

department: Internal Medicine

institute: Wake Forest School of Medicine

type: Methylation profiling by genome tiling array

summary: To test the hypothesis that molecular changes in the induction phase when rhesus macaques consume the same escalating doses of alcohol in a 3-month period are predictive of drinking behavior as light drinkers (LD) or very heavy drinkers (VHD) when they have free access to alcohol.   The sirtuin signaling pathway and a molecular network regulated by the estrogen receptor were enriched with differentially expressed genes and proteins in liver biopsy samples of VHD vs. LD  when animals were alcohol naïve.  After consuming the same amount of alcohol for 3 months by LD and VHD, the sirtuin signaling pathway and MYC regulatory network were most significantly enriched with differentially expressed genes and proteins in both groups in response to alcohol. However, majority of the differentially abundant genes and proteins in this pathway and network differed between LD and VHD. Moreover, the epigenetic mechanisms regulating the response to alcohol are primarily through microRNAs in LD and primarily through DNA methylation in VHD.

overall_design: Rhesus monkeys (~4.6 years old, males) were used for the study. Before and after the induction phase, liver biopsies were performed. During the induction phase, monkeys consumed the same amount of alcohol. After the induction phase, monkeys had free access to alcohol for 12 months, and they were classifiied as LD or VHD based on daily alcohol consumption. Liver samples from three LD that consumed 1.5 g ethanol/kg/day and three VHD that consumed 4.0 g ethanol/kg/day at the end of the free access period were used for mRNA and microRNA (miRNA) sequencing.  Gene and protein expression in VHD livers was compared to that in LD livers before the induction phase. Also, gene and protein expression after induction was compared to that before induction to determine the molecular response to alcohol in LD and VHD livers. Differential DNA methylation sites associated with differentially expressed genes were also analyzed.

first: Laura

last: Cox

first: James

last: Daunais

first: Timothy

last: Howard

first: Ge

first: Sobha

last: Puppala

first: Betsy

last: Ferguson

first: Kathleen

last: Grant

first: Michael

last: Olivier


title: CD8αα+ intraepithelial lymphocytes recruited from peripheral CD4+ and CD8+ T cells represent functionally distinct lineages [TCR-seq]

city: Singapore

first: Lukasz

last: Wojciech

address: 5 Science Drive 2 Blk MD4

country: Singapore

institute: Nus

summary: The TCRαβ CD8αα+ intraepithelial lymphocytes (IELs) play a significant role in primary immune defence in the small intestine. The canonical model of their development distinguishes TCRαβ IELs into induced and natural (TCRαβ CD8αα+) types, each influenced by distinct developmental pathways and antigen encounters. It is believed that natural CD8αα+ IELs differentiate solely from triple positive (TP) CD4+CD8αβ+CD8αα+ thymic progenitors that recognized self MHC-peptide complexes with high affinity but avoided deletion during selection. Our investigation reveals that, in addition to this central commitment, the CD8αα+ IELs undergo in situ enrichment through recruitment from peripheral CD4+ and CD8αβ+ T cell populations. We found that the functional makeup of individual clones within the CD8αα+ IEL subset is dictated by their origin. We demonstrate that expression of Bmp7 or Ly49 (Ly49C, F, H, and I) serve as markers indicating the CD8αα+ IELs’ peripheral provenance: CD8αβ+ and CD4+ T lymphocytes, respectively.

overall_design: To generate Next-Generation Sequencing (NGS) libraries encompassing the entire T cell receptor (TCR) repertoire, total RNA was extracted from sorted TCRβ CD8αα+ Ly49+, TCRβ+ CD8αα+ Bmp7+, TCRβ+ CD8αα+ DN IEL and peripheral CD4+ and CD8+ T cells. The reverse transcriptase reaction employing template-switching primers with the sequence TAAGAGACAGCAACTACTACTGCrGrGrGr (where r ,indicates ribonucleotide). Two rounds of amplification for the TCR cDNAs were conducted using Q5® High-Fidelity DNA Polymerase (NEB, Massachusetts, USA) following the manufacturer's instructions. The primers used in the first PCR round: For-TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGCAACTACTACTGC Rev-GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGGGTACACAGCAGGTTCTGG

first: Nicholas

middle: R

last: Gascoigne


title: RNA-seq of Drosophila aging stage 14 follicles

first: Jun Wei

last: Pek

address: 1 Research Link National University of Singapore

institute: Temasek Life Sciences Laboratory

summary: We report the identification of mRNA and circular RNA in Drosophila stage 14 follicles during aging.

overall_design: RNA was obtained from stage 14 follicles and subjected to deep sequencing.


title: Comparative gene expression profiling analysis of hippocampus and liver RNA-seq data for young (3-month-old) and aged (22-month-old) WT mice in both control and ethanol feeding conditions.

city: Kansas City

first: Hongmin

last: Ni

state: KS

address: 3901 Rainbow Blvd, MS-1018

institute: The University of Kansas Medical Center

summary: Alcohol consumption is believed to affect Alzheimer's disease (AD) risk, but the contributing mechanisms are not well understood. A potential mediator of the proposed alcohol-AD connection is autophagy, a degradation pathway that maintains organelle and protein homeostasis. The purpose of this study is to explore whether chronic alcohol consumption worsens the age-related decline in lysosomal biogenesis in the brain and exacerbates cognitive decline associated with aging. To explore the effect of alcohol on brain autophagy, we exposed young (3-month old) and aged (23-month old) mice to chronic plus binge alcohol-feeding paradigms and the mouse brain and liver RNA were extracted followed by RNA sequencing analysis.

overall_design: The mice were subjected to the Gao-Binge alcohol model. RNA sequensing analysis was performed using the hippocampus and liver tissues. Gene expression profiling analysis was conducted using data obtained from RNA-seq of 4 different groups.

first: Wen-Xing

last: Ding

first: Hong-Min

first: Wanqing

last: Liu


title: Tissue-specific RNA-seq of Atsdr4l-5 dig2 mutant seeds

city: Vancouver

first: Liang

last: Song

state: British Columbia

address: 2231-6270 University Boulevard

department: Botany

country: Canada

institute: University of British Columbia

summary: Arabidopsis thaliana SEED DORMANCY 4-LIKE (AtSDR4L) and its paralog Dynamic Influencer of Gene Expression 2 (DIG2) act as transcriptional co-repressors to promote seed-to-seedling phase transition. Their regulatory roles at the temporal and tissue-specific scales remain elusive. Here, we show that mutant phenotypes of Atsdr4l dig2 are alleviated by abscisic acid (ABA) antagonists and gibberellin (GA). Dissected mutant embryos exhibit stunted growth, reduced cell expansion and differentiation. The double mutant results in many similar changes in gene expression in the seed coat and the embryo, with a subset of the genes differentially expressed tissue-specifically. Transcriptomes of Atsdr4l-5 dig2 seed compartments form a distinct cluster from those of the mutant seedlings of Atsdr4l and Polycomb Repressive Complex-related genes, suggesting developmental stage-specific role of these regulators.Together, these results demonstrated that AtSDR4L and DIG2 work in concert to launch the growth potential in embryo and alleviate the constraints in seed coat to prepare seeds for germination.

overall_design: Embryo and seed coat were isolated from mature seeds of Atsdr4l-5 dig2 mutant and Col-0 wildtype with three biological replicates each. Total RNA was extracted and mRNA was enriched by polyA selection for RNA-seq profiling of the differentially expressed genes between the mutant and the wildtype in both tissues .

first: Bailan

last: Lu

first: Dongeun

last: Go


title: Non-apoptotic caspase-8 is critical for orchestrating exaggerated inflammation during severe SARS-CoV-2 infection

city: Melbourne

first: Dylan

last: Sheerin

state: VIC

address: 1G Royal Parade

country: Australia

institute: WEHI

summary: Inflammation and cytokine release are hallmarks of severe COVID-19. While pro-grammed cell death is known to drive inflammation, its role in SARS-CoV-2 patho-genesis remains unclear. Using gene-targeted murine COVID-19 models with tran-scriptomic and proteomic analyses, we found that caspase-8 is critical for cytokine release and inflammation. Loss of caspase-8 reduced disease severity and viral loads in mice, and interestingly, this occurred independently of its apoptotic func-tion. Instead, reduction in SARS-CoV-2 pathology was linked to decreased IL-1β levels and inflammation. Loss of pyroptosis and necroptosis mediators, in gene-targeted animals, provided no additional benefits in mitigating disease outcomes beyond that conferred by loss of caspase-8. Transcriptional profiling of caspase-8 knockout animals confirmed that improved outcomes were due to reduced pro-inflammatory responses, rather than changes in cell death signaling. Elevated ex-pression of caspase-8 and FLIP in infected lungs, alongside caspase-8 mediated cleavage of the NF-kB signaling suppressor N4BP1, suggests a role of this signal-ing axis in overt inflammation. Collectively, these findings highlight non-apoptotic caspase-8 as a driver of severe COVID-19 through modulation of inflammation, not through the induction of apoptosis.

overall_design: Comparative gene expression profiling analysis of murine lung bulk RNA-seq data. Contrasts were made between wild-type (C57BL/6) mice and knockouts of pyroptosis and necroptosis effector (C1/11/12/R3), as well as pyroptosis, necroptosis and apoptosis deficient mice (C1/11/12/8/R3) infected with the SARS-CoV-2 P21 virus (Bader et al, PNAS, 2023).

first: Stefanie

last: Bader

first: Marcel

last: Doerflinger


title: Effect of RNase E mutations on whole transcriptome expression profile of E. coli soft-agar plate culture

city: Taipei

first: Sue

last: Lin-Chao

address: 128 Academia Road, Section 2, Nankang,

department: Institute of Molecular Biology

country: Taiwan

institute: Academia Sinica

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

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: Refer to individual Series


title: The impact of RNase E C-terminal truncation mutant compared with wildtype RNase E on whole transcriptome expression profile of E. coli soft-agar plate culture

summary: RNase E is involved in the post-transcriptional gene regulation of a broad spectrom of RNA species involving in different biological processes. Frequently RNase E cooperates with other protein components to form a RNA degradosome to regulate gene expression. Here, we aim to study the impact of RNA degradosome formation on E. coli  gene expression by comparing the whole transcriptiome isolate from wildtype Rne strain and Rne C-terminal truncated strain that deleting the RNA degradosome binding domain. We choose to study the bacterial growth conditions in soft-agar culture because it is a condition more silimar to that in the gut of warm-blooded organism compared to merely liquid culture condition.Here we found different groups of transcript that was affected by Rne C-termianl truncation mutant. Altogether, our data give insight into the complex regulation of RNase E/RNA degradosome in transcripts involved in different biological processes of soft-agar growing system.

platform_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: To understand the impact of RNase E on gene expression, we compared wildtype strain MG1655 with RNase E C-terminal deletion strain Rned500. RNA samples were isolated from bacterial culture grown on 0.35% soft-agar LB plate after 24 h incubation.

first: Wei-Syuan

last: Wang

first: Shu-Yung

last: Tung

first: Chen-Hsin

last: Yu


title: fMyBP-C is a vital regulator in young and aged fast skeletal muscle homeostasis

city: Tucson

first: Sakthivel

last: Sadayappan

state: AZ

address: 1656 E Mabel Street, Medical Research Building, Rm 315, Cellular and Molecular Medicine

department: Cellular and Molecular Medicine

institute: University of Arizona College of Medicine

summary: Skeletal Myosin binding protein-C (MyBP-C) paralogs, slow (sMyBP-C) and fast (fMyBP-C) interacts with myosin and actin filaments within sarcomeres, modulating the force development during contraction. These display differential expression in muscle fibres, with fMyBP-C higher in fast twitch fibres. However, our knowledge about the changes in the fMyBP-C expression in diseased conditions and its role in skeletal muscle aging is lacking. In this study we use mice model lacking fMyBP-C  to understand its significance in skeletal muscle physiology. Skeletal muscle samples from wild type and Mybpc2 knockout (C2-/-)old male mice (22 months) were used to define the role of fMyBP-C in aging. Western immunoblotting was employed to analyze the expression of fMyBP-C and sMyBP-C, and phosphorylation status of sMyBP-C. The impact of C2-/- and aging on the fiber type, size, and number as well as general muscle structure was assessed by immunohistochemistry and electron microscopy. The functional effect of C2-/- and aging was measured in terms of in vivo  and ex vivo muscle force generation. Lastly, RNA sequencing was performed to identify the molecular pathways dysregulated in the C2-/- mediated muscle dysfunction in young and old mice. The aged male C2-/- mice compared to their wildtype counterparts, display significant deficits in muscle strength and endurance, accompanied by changes in muscle fiber size and molecular signaling pathways critical for muscle homeostasis.Thus, fMyBP-C is an important regulator of muscle function and homeostasis in the young and aged fast-twitch muscle fibers. The absence of fMyBP-C aggravates the effect of aging on muscle structure and function. fMyBP-C has the potential to be a therapeutic target to modulate muscle wasting caused by aging and disease.

overall_design: Mybpc2 KO mouse model (C2-/-)  was generated by the targeted replacement of Mybpc2 exon 2 to 22 with a Neo cassette flanked by two LoxP sites. The Tibialis anterior muscle dissected from 22 months old male Wildtype and C2-/- (n=4 in each group). RNA extracted from TA muscles are subjected to RNA Sequencing to determine the altered molecular signatures.

first: Akhil

last: Baby

first: Kalyani

last: Ananthamohan

first: Taejeong


title: KLK1 prevents colorectal inflammation-cancer transformation via B1R-mediated ECM pathway

city: Nanjing

first: yang

last: sun

state: Jiangsu

address: Nanjing University Academy of Sciences, No. 163 Xianlin Avenue, Qixia District, Nanjing City, Jiangsu Province

department: Life Sciences

institute: Nanjing University

summary: This study comprehensively describes the etiology, diagnosis and treatment of ulcerative colitis (UC). First, the history, characteristics and increasing incidence of UC worldwide are introduced. The diagnostic criteria of UC are summarized, emphasizing the importance of comprehensive clinical symptoms, endoscopy, histopathology and other methods. In terms of treatment, corresponding treatment strategies for UC patients of different severity in clinical practice are described. In addition, the development of new treatment methods, such as cytokine therapy and intestinal microbiota transplantation, are also discussed. The role of the kallikrein-kinin system (KKS) in UC and its potential therapeutic significance are further analyzed. The possibility of KKL1 in the treatment of UC is explored. KLK1 is a tissue kallikrein that is currently being studied as a drug for the treatment of acute cerebral infarction. KLK1 may have the potential to treat UC by relaxing blood vessels and improving microcirculation. Experiments have found that the expression of intestinal tissue kallikrein is reduced in the acute enteritis model, while KLK1 can play a therapeutic role in this model and lead to the restoration of endogenous intestinal tissue kallikrein expression. KLK1 has potential application prospects as a drug for the treatment of acute enteritis, but it also has limitations in clinical applications and requires further in-depth research and improvement.

overall_design: RNA-seq profiling of wildtype NCM460 cells and their knockdown cells (siKLK1)

first: Lisha

last: Zhou

first: Meijing

first: Shunji

first: Yang

last: Sun


title: Multiclonal competition reveals impaired cell fitness of GATA2 deficient cells [ATAC-seq]

city: L'Hospitalet de Llobregat

first: Alessandra

last: Giorgetti

state: Barcelona

address: Avinguda de la Granvia de l’Hospitalet, 199

department: PCMRC

country: Spain

institute: IDIBELL

type: Genome binding/occupancy profiling by high throughput sequencing

summary: GATA2 deficiency has been identified as a common hereditary cause of myelodysplastic syndromes (MDS) and acute myeloid leukemia in children. Penetrance and expressivity within affected families is often variable, suggesting that cooperating factors are required to trigger the disease. Somatic mutations in MDS driver genes (SETBP1, ASXL1) have been identified GATA2-MDS. The molecular mechanism that triggers the leukemic progression in GATA2 carriers remains unknown. Particularly, these questions remain unanswered: 1) whether GATA2 germline mutation itself is sufficient to trigger MDS/AML 2) whether SETBP1 and ASXL1 mutations induce the malignant transformation. Addressing these questions has been difficult due to the lack of faithful human disease models. Here I studied in vitro/in vivo engineered cord blood CD34+ cells carrying  GATA2 mutation alone or in combination with SETBP1/ASXL1 mutations in NSG mice to evaluate the engraftment capacity and the clonal evolution. Specifically, CRISPR/Cas9/rAAV6 was used to introduce the R398W mutation in CD34+ cells alone (GATA2) or in combination with SETBP1 and ASXL1 mutations (Multiplex). Primary and secondary transplantation showed similar multilineage constitution in all the conditions. Interestingly, genetic studies indicated that the predominant expanded clones in the multiplex condition carried SETBP1+ASXL1 mutations, while clones with only GATA2 mutation were lost. To study the impact of the mutations at transcriptomic level, scRNAseq is underway. In vitro data confirmed that cells carrying the GATA2 R398W mutation have an impaired clonogenic capacity and proliferation, recapitulating MDS patient phenotype. In summary, we developed a human model of clonal competition by CRISPR/Cas9 targeting CD34+ cells. Our findings strongly suggest that GATA2 R398W mutation is not sufficient to increase cell fitness, suggesting that co-operating of genetic, epigenetic, niche and stressor factors are necessary to trigger the disease.

overall_design: CRISPR/Cas9 combined with rAAV6 was employed to knock in the GATA2-R398W-EGFP mutation in human CD34+ cells. Both GATA2-R398W-EGFP and control cells were cultured for ten days before being processed for ATAC-seq analysis

first: Damia

last: Romero-Moya


title: Multiclonal competition reveals impaired cell fitness of GATA2 deficient cells [RNA-seq]

overall_design: CRISPR/Cas9 combined with rAAV6 was employed to knock in the GATA2-R398W-EGFP mutation in human CD34+ cells. Both GATA2-R398W-EGFP and control cells were cultured for ten days before being processed for RNA extraction


title: Transcriptome of bone marrow  cells from mice with osteoporosis induced bu hindlimb unloading

city: Xi'an

first: Chen

last: Zhang

address: Xinsi road

department: Department of hematology

institute: Tangdu Hospital

summary: In order to investigate whether the bone marrow environment of OP-HU mice could lead to the expansion of HSCs and myeloid-biased hematopoiesis, bulk RNA-seq of was performed with whole bone marrow cells of mice after hindlimb unloading

overall_design: Three replicates of bone marrow cells from the femurs of mice with or without osteoporosis induced by hindlimb unloading

first: Li

last: Liu

first: Weiwei

last: Qin


title: Exploring the Transformative Effects of Calorie Restriction on the Lacrimal Gland in Adult Mice

city: La Jolla

first: Helen

last: Makarenkova

address: 10550 N Torrey Pines Rd, MB-218

department: Molecular Medicine

institute: The Scripps Research Institute

summary: Dry eye disease affects millions worldwide and can result from age-related lacrimal gland (LG) dysfunction, which correlates with a decline in LG secretory cell function and chronic inflammation. This study investigates the potential of calorie restriction (CR) to maintain LG and ocular surface health. Female C57BL/6J mice were subjected to 40% CR for 4 months (start age 6/7 until 10/11M) and compared to mice receiving food ad libitum (AL). LGs bulk RNA sequencing was performed, and fastq files were uploaded on ROSALIND® for processing. Differentially Expressed Genes (DEGs) were analyzed in Metascape to identify the biological pathways significantly modified by CR, and findings were validated.  RNA sequencing of LGs subjected to CR compared to ad libitum revealed 589 significant DEGs, with 259 downregulated and 330 upregulatedPathways enriched in upregulated DEGs suggested increase in secretory functions and lipid metabolism, while pathways enriched in downregulated DEGs are related to immune cell activation, the adaptive immune system, extracellular matrix remodeling, and metalloproteinases. These changes were validated by individual qPCR. CR also decreased the age-related dry eye phenotype compared to the ad libitum group. Our results suggest that CR can maintain the health of the LG and ocular surface by reducing inflammation and supporting the LG's secretory function.

overall_design: To assess whether CR can slow down inflammation in the LG of adult mice, 6/7M mice were assigned to either an AL or a 40% CR for four months. At 10/11M of age, the mice were euthanized. To determine the genes affected by CR in the LG, we compared the transcriptomes of mice subjected to CR (n = 4) with those fed an AL diet (n = 4) using bulk RNA sequencing of LGs.

first: Olivier

last: Mauduit

first: Prashant

last: Kumar

first: Kaitlin

middle: K

last: Scholand

first: Laura

last: Schaefer

first: Anmar

last: Abu-Romman

first: Vanessa

last: Delcroix

first: Zhiyuan

first: Aude

middle: I

last: Sindikubwabo

first: Ron

last: Korstanje

middle: P

first: Cintia

last: de Paiva


title: Genome-wide profiling by Next Generation Sequencing reveals protective effects of dietary EPA+DHA on chemotherapy-induced muscle toxicity in a clinically relevant model of colorectal cancer

city: Edmonton

first: Sambasivarao

last: Damaraju

state: Alberta

address: 11560 University Avenue

department: Laboratory Medicine and Pathology

institute: University of Alberta

summary: Introduction: Tumor induced skeletal muscle loss is well recognized in the cancer domain. Chemotherapy-induced loss of skeletal muscle mass (muscle atrophy) is also a challenging side effect of cancer treatment. Retaining muscle mass is key to tolerance to chemotherapy and outcomes, hence interventions to preserve muscle mass warrant investigations. We aimed to investigate the protective effects of dietary fish oil (EPA+DHA) on chemotherapy-induced muscle atrophy through a comprehensive  mRNA expression analysis of gastrocnemius muscle using Next Generation RNA Sequencing (NGS) to delineate the underlying molecular mechanisms of muscle homeostasis. Methods: Female Fischer 344 rats were fed either a control diet for the entire study or switched to a diet containing fish oil (2.0 g /100 g of diet) at the start of chemotherapy. All rats received tumor implantation and tumor was allowed to grow for 2weeks. The various groups included tumor-bearing rats on a control diet (TUMOR) euthanized prior to chemotherapy administration, tumor-bearing rats that received two cycles of chemotherapy (irinotecan + 5-fluorouracil; FOLFIRI) while on a control diet (CONTROL) or fish oil diet (FO). After two cycles of FOLFIRI, RNA was extracted from gastrocnemius muscle and subjected to NGS. Differential Expression of Genes (DEG) was performed using DEseq2, with a fold-change cut-off ≥ 1.5 and p-value < 0.05. Ingenuity Pathways Analysis (IPA) was used for functional annotation of DEGs, canonical pathways, and upstream regulators. Results: Transcriptomic analysis revealed distinct alterations in skeletal muscle gene expression profiles in response to chemotherapy and fish oil supplementation. In the comparison between CONTROL and TUMOR groups, 272 genes exhibited differential expression (DE), with 55.15% upregulated and 44.85% downregulated. Conversely, in the comparison between the FO and CONTROL groups, 274 genes showed DE, with 72.99% upregulated and 27.01% downregulated. Biological functional analysis reveals that Chemotherapy led to the alteration of genes involved in the proliferation of muscle cells (p<10-7), connective tissue disorder (p<10-6),  apoptosis (p<10-3),  and neurodevelopmental disorders (p<10-3). The provision of FO exclusively altered immune-related functions, as seen by the downregulation of several genes in the leukocyte extravasation pathway (-log p-value 5.92, z-score -2.83). Moreover, upstream analysis predicted the inhibition of key transcription factors involved in myogenic regeneration by chemotherapy treatment in rats on a control diet, while cytokines that drive inflammation were predicted to be inhibited by FO.  Conclusion: Chemotherapy negatively impacts processes involved in muscle homeostasis, including muscle cell proliferation and regeneration. Furthermore, the provision of fish oil primarily influenced inflammation pathways by the down-regulation of genes involved in the leukocyte extravasation pathway. Our findings provide novel insights into the molecular mechanisms underlying chemotherapy-induced muscle toxicity and the potential therapeutic benefits of dietary fish oil supplementation in mitigating muscle atrophy.

overall_design: RNA sequencing was performed from muscle of rats bearing tumor, treated with chemotherapy with control diet or fish oil diet.

first: Bhumi

last: Bhatt

first: Vera

last: Mazurak


title: Targeting Polycomb for treatment of KMT2A-rearranged AML using AML-iPSCs as a model system

city: Huddinge

first: Anna

last: Palau

address: Hälsovägen 9

country: Sweden

institute: Karolinska Institutet


title: Transcriptional analysis on ischemia-reperfusion injury of mouse normal or steatotic livers

city: Wuhan

first: Jinyang

last: Gu

address: 1277 Jiefang avenue

institute: Union hospital, Tongji medical college, Huazhong university of science and technology

summary: More and more steatotic livers undergo resection or transplantation but they exhibit higher susceptibility to ischemia-reperfusion injury (IRI), which results in increased perioperative complication morbidity and mortality. To investigate the underlying mechanisms, we conducted RNA-seq with liver samples derived from mice that were fed either high-fat-diet (HFD) or normal diet (ND) and experienced either IRI or sham operation.

overall_design: Mice were fed either HFD or ND for 4 months. After liver steatosis model was constructed, the mice were subjected to either IRI or sham operation. For IRI, the left and middle branch of hepatic pedicle was ligated; after 1 h ischemia, the ligation was removed and liver reperfusion was confirmed visually; after 6 h reperfusion, the mice were anesthetized and liver samples were collected. For sham operation, the branch of hepatic pedicle was not ligated and the other procedures were the same as IRI. Thus, the experiment involves four groups: ND-Sham (NS), ND-IRI (NI), HFD-Sham (HS), HFD-IRI (HI).

first: Ran


city: Wuhan City

first: Zhuojin

last: Wu

address: 1095 Jiefang Avenue

institute: Tongji Hospital affiliated to Tongji Medical College of Huazhong University of Science & Technology

summary: In this study, we utilized snRNA-seq combined with a mouse model of intracerebral hemorrhage to explore the gene expression heterogeneity of brain cells at different stages post-ICH, aiming to construct a single-nucleus transcriptomic atlas for ICH and further elucidate its pathogenesis to identify potential therapeutic targets.

overall_design: snRNA-seq analysis of perihematomal tissues at different stages in an ICH mouse model, including sham,ICH-6h, ICH-24h, ICH-72h, one sample for each group

first: Zhouping

last: Tang

first: Chao

last: Pan

first: Danyang

last: Chen


title: TET1 suppresses thyroid function by remodeling histone modifications in PAX8 promoter to down-regulate its expression

city: hangzhou

first: Hui

last: Dang

state: zhejiang

address: 866 Yuhangtang Road, Xihu District

institute: Zhejiang University

summary: Ten Eleven Translocation 1 (TET1) is a 5-methylcytosine dioxygenase, and its mediated DNA demethylation has been implicated in human diseases. However, its role in regulating thyroid function remains totally unknown. Here, we first generated thyroid-specific Tet1 knockout  mouse model (Thy-Tet1-/-) and their control mice (Thy-Tet1+/+).

overall_design: treatment three mice (Thy-Tet1-/-) and  control three mice (Thy-Tet1+/+).

first: Peng

last: Hou

first: Meiju

last: Ji


title: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) analysis of ZNF148 in chondrocytes

city: Nanchang

first: Jinghong

last: Yuan

state: Jiangxi

address: No.1 Minde Road

institute: The Secondly Affiliated Hospital of Nanchang University

summary: Chromatin Immunoprecipitation (ChIP) was performed by fixing chondrocytes with formaldehyde, lysing them, and fragmenting chromatin via sonication. Specific antibodies of ZNF148 (Santa Cruz, sc-398148X, 200碌g/0.1ml) were used to immunoprecipitate protein-DNA complexes, followed by washing, reverse crosslinking and DNA purification for subsequent RT-qPCR or ChIP-seq analysis

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) analysis targeting ZNF148 in chondrocytes

first: Yameng

last: Wang

first: Jingyu

last: Jia

first: Xijuan

last: Liu


title: High fat diet and entotoxemia promoted esophagogastric junction tumor through inflammation associated carcinogenesis

city: Sendai

first: Kaname

last: Uno

address: 1-1 Seiryo Aoba-ku

department: Gastroenterology

country: Japan

institute: Tohoku University

summary:
High fat diet and entotoxemia induced inlammation associated carcinogenesis at the esophagogastric junction tumor through inflammation associated
The promotion of the carcinogenesis may be related to gut dysbiosis related to high fat diet.

overall_design: We utilized the macroarray analysis of the carcinogenesis in Gan mice between the control group mice and the HFD+entodoxema group

first: Keisuke

last: Kusano


title: Gene expression signature of ex vivo expanded TILs for 14 day

city: Seongnam-si

first: Daun

last: Jung

state: Gyeonggi-do

address: Bundang-gu, 삼평동 689

department: Department of Pathology

country: South Korea

institute: CHA Bundang Medical Center

summary: We performed RNA sequencing to employ an unbiased approach to identify the altered gene expression enhancing the function of ex vivo expanded TILs cells for 14 days, and transcriptionally compared TIL cultured W/O anti-GITR (WIO group) and TIL cultured with anti-GITR (WIOG group)

overall_design: mRNA profiles of sorted CD8+ T cells in day14 WIO TILs and day 14 WIOG TILs

first: Hee Jung

last: An


first: Tianhao

last: Zou

address: 1277 Jiefang Avenue

institute: Huazhong University of Science and Technology

summary: Hexokinase is a key enzyme in the glycolytic pathway, but its role in RIPK1-mediated apoptosis is not clear. We therefore treated MEFs with sicontrol as well as siHK2 and performed RNA-seq

overall_design: Transfection of MEFs was treated with negative control siRNA or siHk2.Thus, the experiment involves two groups: siControl, siHk2

first: Jinyang


title: Mutations of schizophrenia risk gene SETD1A dysregulate synaptic function in human neurons

city: New Brunswick

first: Zhiping

last: Pang

state: New Jersey

address: 89 French Street Floor 3, Room 3233

department: Child Health Institute of New Jersey

institute: Rutgers University

summary: Schizophrenia (SCZ) is a complex neuropsychiatric disorder associated with both common risk variants of small effect sizes and rare risk variants of high penetrance. Rare protein truncating variants (PTVs) in SETD1A (SET Domain Containing 1A) show a strong association with SCZ; however, it remains largely unclear how rare PTVs in SETD1A contribute to the pathophysiology of SCZ. To understand the impact of SETD1A rare PTVs in human neurons, we CRISPR/Cas9-engineered five isogenic pairs of human induced pluripotent stem cells (iPSCs), with a recurrent heterozygous patient-specific PTV mutation c.4582-2delAG in two donor lines and a heterozygous frameshift mutation c.4596_4597insG (p. Leu1533fs) in three donor lines. These two mutations are predicted to cause a premature stop codon in exon 16 of SETD1A, leading to the loss of the conserved SET domain that is critical for its histone methyltransferase activity. We found that these presumably loss-of-function (LoF) mutations caused the SETD1A mRNAs to be degraded by nonsense-mediated decay (NMD), accompanied by a reduction of full-length SETD1A protein level in iPSCs.  We then characterized the morphological, electrophysiological, and transcriptomic impacts of the SETD1A+/- LoF mutations in iPSC-derived human excitatory neurons induced by NGN2. We found that the SETD1A+/- exon-16 LoF mutations altered dendrite complexity, dysregulated synaptic transmission, and synaptic plasticity, likely by dysregulating genes involved in synaptic function. These results provide mechanistic insights into how SETD1A+/- exon-16 patient-specific LoF mutations affect neuron phenotypes that may be relevant to the pathophysiology of SCZ.

overall_design: Ngn2-iNs culture are generated from human iPSCs and whole RNA was extracted from ~ 6-week-old neuronal culture. For patient-specific c.4582-2delAG (del) mutation, we had 2 isogenic pairs coming from 2 different genetic backgrounds CD07 and C11C with 3 technical replicates for each pair; for heterozygous frameshift mutation c.4596_4597insG (p. Leu1533fs), we had 3 isognic pairs coming from 3 different genetic backgrounds (CD07, CD15 and CD19) with 2-3 biological replicates for each pair.

first: Xiao

last: Su

first: Jiayi

first: Tiffany

last: Le

first: Anat

last: Kreimer


title: Exploring the role of cyclin D1 in the pathogenesis of multiple myeloma beyond cell-cycle regulation

city: Salamanca

first: Ignacio

last: Cardona-Benavides

address: Campus Miguel Unamuno

department: Hematology

institute: Centro de Investigación del Cáncer

summary:
Background: Several studies have demonstrated that cyclins D could be a unifying event in multiple myeloma (MM), despite its great genomic heterogeneity. Cyclins D are primarily known for their role in cell proliferation, yet MM is not typically considered a proliferative disease. This paradox led us to hypothesize that cyclins D might have additional roles in the pathogenesis of MM beyond cell-cycle regulation.  Methods: Basal levels of cyclins D were quantified by RT-qPCR and capillary electrophoresis nanoimmunoassay (CNIA) in nine MM cell lines. CCND1 and CCND2 were ectopically overexpressed in the MM cells lacking them. Changes were analyzed by transcriptome arrays and multidimensional flow cytometry. We validated some of the findings observed in vitro in newly diagnosed MM patients.
Results: Cyclin D proteins were predominantly localized in the cytoplasm, where their expression was mutually exclusive. Ectopic overexpression of cyclin D1 or D2 did not affect cell proliferation in most cell lines. Transcriptome analysis revealed that cyclin D1 overexpression influenced the adhesion pathway, significantly upregulating genes such as ZO-1 and FLNA. In addition, cells with ectopic cyclin D1 overexpression had an altered actin cytoskeleton with reduced attachment to certain matrices. Immunophenotypic changes, such as an increase in CD56-negative cells were also observed after cyclin D1 overexpression. This finding was validated in a set of 49 MM patients, where 73% of those with high levels of cyclin D1 expression had CD56-negative cells, while only 11% with low levels were CD56-negative (p<0.001). Consistent with these observations, patients with high cyclin D1 levels had significantly more circulating tumor cells (CTCs) than those not expressing cyclins D (p<0.001).  Conclusions: Our study revealed previously undescribed functions of cyclin D1 in the pathogenesis of MM, associated particularly with cell adhesion and morphology, independent of their canonical function in cell-cycle control. These findings were supported by the association between cyclin D1 overexpression and increased levels of CTCs. Both findings suggest roles for cyclin D1 in determining cell metastatic capacity, and thereby in MM dissemination and extramedullary disease.

overall_design: Two cell lines, KMS28-BM and KMS28-PE, were utilized to evaluate three experimental groups: control, CCND1 overexpression, and CCND2 overexpression. Biological triplicates were conducted for each condition.

first: Cardona-Benavides

last: Ignacio J.

first: Cristobal-Vargas

last: Sara

first: De Ramón

last: Cristina

first: Rojas

last: Elizabeta A.

first: Misiewicz-Krzeminska

last: Irena

first: Isidro

last: Isabel

first: Pérez

last: José Juan

first: Paiva

last: Bruno

first: Puig

last: Noemi

first: Mateos

last: María-Victoria

first: Corchete

last: Luis A.

first: Cuadrado

last: Myriam

first: Gutiérrez

last: Norma C.


title: Effect of M. elsdenii on gene expression of bone marrow derived dendritic cells

city: Shanghai

first: Xinxin

last: Hou

address: 1200 Cailun Road

institute: Shanghai University of Traditional Chinese Medicine

summary: Bacteria-driven mechanism underlying inflammation-related colon pathologies remains undetermined. We identified that Megasphaera elsdenii (M. elsdenii), was highly abundant in inflammatory bowel diseases (IBD) and colorectal cancer (CRC) cohorts. To understand the possible mechanism by which M. elsdenii affects DC function, we sequenced BMDC RNAs with and without M. elsdenii treatment.. A subset of genes involved in immune activation, inflammation and antigen presentation, including Il1b, Ifng, Il23, Il12, Cd40, Icos, Cd80, H2-M2 and H2-K2, were increased by M. elsdenii, whereas genes related to immunosuppression (Arg1, Mrc1, Cd163) were downregulated. Enrichment analysis of the KEGG pathway and GO term showed that the Toll-like receptor (TLR) signaling pathway and NF-κB signaling pathway in BMDCs were notably upregulated by M. elsdenii. We further performed western blot, receptor inhibitors and shRNA assays, and showed  that M. elsdenii promotes DC maturation and activation through TLR4 ligation, leading to the activation of NF-κB and IRF4 and subsequent induction of pro-inflammatory cytokines and co-stimulatory molecules.

overall_design: To explore the mechanism of M. elsdenii on the activation of DCs, we isolated bone marrow-derived dendritic cells (BMDC) and treated with M. elsdenii or PBS on day 6 for another 24 hours and then harvested for RNA-seq. We used biological triplicates.


title: Multi-omics Sequencing reveals Epigenetic Regulation in Actinic Keratosis and Cutaneous Squamous Cell Carcinoma [ATAC-seq]

city: Kunming

first: Li

last: He

state: Yunnan

address: No. 295 Xichang Road

institute: First Affiliated Hospital of Kunming Medical University

summary: Cutaneous squamous cell carcinoma (cSCC) is an important type of skin cancer. It is difficult to diagnose and treat, which seriously endanger people’s the physical and mental health. Actinic keratosis (AK) induced by ultraviolet radiation is the precancerous lesion of cSCC. The mechanism of occurrence and development of cSCC is still unclear, and the research on epigenetics is even less. In this project, we intend to study the mechanism of cSCC, especially the transformation from normal skin to AK, cSCC and the metastasis in late stage of cSCC, using multi-omics sequencing technology with experimental methods. Through the integrated analysis of multi-omics information such as DNA methylation, RNA methylation, chromatin accessibility and transcriptome, we obtained the epigenetic map of different stages of cSCC and identified the potential key epigenetic driving factors for cSCC. This project provided an important scientific basis for the clinical treatment and drug development of cSCC, as well as method reference for the study of other cancers.

overall_design: Collected samples comprised 5 AK, 5 cSCC, and 10 normal skin samples with epidermal and dermal layers, followed by parallel RNA m6A-seq, 850K DNA methylation array, and ATAC-seq analyses

first: Yazhou

last: Sun

first: DanDan

last: Zou

first: Xinjie

last: Li

first: Jiaying

last: Liu

first: Ke

first: Xianxin

last: Lai

first: Yutong

first: Tianshun

last: Gao

first: Xin


title: Multi-omics Sequencing reveals Epigenetic Regulation in Actinic Keratosis and Cutaneous Squamous Cell Carcinoma [850K DNA methylation array]


title: Targeting Polycomb for treatment of KMT2A-rearranged AML using AML-iPSCs as a model system [CAGEseq]

first: Anna

last: Palau

summary: Pediatric and infant Acute myeloid leukemia (AML) often harbor chromosomal translocations involving the KMT2A gene, encoding theKMT2A lysine methyltransferase, and produce in-frame fusions of KMT2A to other chromatin-regulatory proteins. The KMT2A chromosomal rearrangements (KMT2A-r) are associated with bad prognosis, resistance to chemotherapy and high rates of relapse. Therefore, new therapeutic options are needed for this AML subtype. Here, we aim to identify epigenetic regulators involved in the development of KMT2A-r AML that can be exploited towards new treatments. Mutant and isogenic wild type iPSC lines generated from a KMT2A-r patient were differentiated into hematopoietic progenitor cells to investigate differences in gene expression and transcriptional regulation. KMT2A-r cells exhibited an aberrant gene expression signature with delayed or continuously repressed gene expression. The repressed genes display bivalent histone marks and become repressed by the Polycomb repressive complex (PRC). Targeted inhibition of the PRC2 member EZH2 restores the repressed signature to normal expression levels. Our results suggest that inhibition of PRC2 could be complement to treatment of KMT2A-r AML.

overall_design: control- and AML-iPSCs were differentiated into hematopoietic stem progenitor cells (HSPC) and collected for CAGEseq at day 0 (iPSC), day 8, day 10 and day 12 of HSPC differentiation.

first: Jonas

last: Thier

first: Andrew

last: Tae-Jun Kwon

first: David

last: Cabrerizo Granados

first: Bogumił

last: Kaczkowski

first: Erik

last: Arner

first: Vanessa

last: Lundin

first: Andreas

last: Lennartsson


title: Targeting Polycomb for treatment of KMT2A-rearranged AML using AML-iPSCs as a model system [RNAseq]

overall_design: control- and AML-iPSCs were differentiated into hematopoietic stem progenitor cells (HSPC) and treated with DMSO as vehicle (1:2000), UNC1999 (2 uM), or UNC1999 (2 uM) + 5-Azacytidine (1 uM).


title: Screening and Modeling of LUAD-Associated Predictive and Prognostic Genes Based on Multi-Omics Data

city: Beijing

first: Zhi

middle: John

last: Lu

address: Shuangqing Road

department: School of Life Sciences

institute: Tsinghua University

summary: LUAD is widespread worldwide with onset mainly in the low-grade stage due to early screen. However, the ambiguity surrounding small-sized nodules often leads to hesitation in deciding between surgery and surveillance. Liquid biopsy which leverages the cell-free RNA (cfRNA) shows excellent classification performance among disease groups in addition to the non-invasive feature. This research utilizes liquid biopsy to construct an effective screening system to aid with the further differentiation of benign diseases from lung cancers.

overall_design: Peripheral whole blood samples were collected from individuals before therapy or surgery using EDTA-coated vacutainer tubes. Plasma was separated within 2 hr after collection by centrifuge at 1,900 g for 10 min at 4 ℃. All plasma samples were aliquoted and stored at -80°C. CfRNAs were extracted using QIAzol Lysis Reagent (QIAGEN, Beijing, China), and DNA contamination was removed by Recombinant DNase I (RNase-free) (TAKARA, Beijing, China). End repair and polyadenylation were performed using E. coli Poly(A) Polymerase (NEB, Beijing, China), and T4 Polynucleotide Kinase (NEB, Beijing, China). Reverse transcription and libraries were prepared according to DETECTOR-seq protocol with minor modifications by replacing original TSO with uracil-containing TSO and extra digestion with Uracil-DNA Glycosylase (NEB, Beijing, China) after reverse transcription. Library quantification was performed by Qubit dsDNA HS Kit. Library fragment size and quality were checked using Agilent 2100 Bioanalyzer. Libraries were sequenced on MGI Tech DNBSEQ-T7 with PE150.

first: Kairui

last: Hu

first: Qing

last: Zhan

first: Jinghui

last: Wang


title: CDH11 contributes to bladder cancer progression via regulation of mitochondrial energy metabolism.

city: Toon

first: Osuke

last: Arai

state: Japan

address: Ehime

department: Urology

institute: Ehime Univercity

summary: Patients with advanced bladder cancer (BC) have a poor prognosis and limited treatment options. Therefore, we searched for potential new therapeutic targets using existing big data. First, we collected gene expression datasets of BC cell lines from the Gene Expression Omnibus (GEO) and extracted genes that were highly expressed in advanced BC cell lines. We also extracted genes highly expressed in advanced BC patients from The Cancer Genome Atlas (TCGA). We performed an integrated analysis of these genes to identify genes involved in BC progression, combined with Kaplan-Meier analysis, and identified CDH11 as an involved gene in bladder cancer progression. CDH11 knockdown (KD) cells were established using shRNA against UM-UC-3, an advanced BC cell line. While CDH11 KD did not alter cell proliferation, invasion nor migration in vitro, CDH11 KD significantly suppressed tumor growth in in vivo subcutaneous xenograft mice model. RNA-seq revealed that CDH11 KD cells decreased the expression of genes related to mitochondrial metabolism, and in fact, a flux analyzer revealed decreased mitochondrial activity in the KD cell line. Furthermore, the experiments using CDH11 inhibitor also showed a decrease in mitochondrial activity in vitro, and inhibition of tumor growth in vivo as well as knockdown experiments. These results suggest that CDH11 is involved in BC progression and is a potential therapeutic target.

sample_organism:
Homo sapiens
Mus

platform_organism:
Homo sapiens
Mus

overall_design: To investigate the role of CDH11 in bladder cancer (UM-UC-3), CDH11 was knocked down using shRNA.

first: Yuta

last: Yanagihara

first: Ryuta

last: Watanabe

first: Noriyoshi

last: Miura

first: Tadahiko

last: Kikugawa

first: Takashi

last: Saika

first: Yuuki

last: Imai


title: Modification of Titanium-based implant materials by Zn-doped calcium phosphate coatings improves corrosion resistance, biomineralization, antibacterial efficacy and immunocompatibility

city: Mannheim

first: Guanhao

last: Li

state: Baden-Württemberg

address: Ludolf-Krehl Strasse 13-17

department: Institute of Transfusion Medicine and Immunology

country: Germany

institute: Medical Faculty Mannheim, Heidelberg University

summary: Implant-induced chronic inflammation and aseptic implant failure represent serious clinical challenges in orthopedics, dentistry, and reconstructive surgery. Our study aimed to develop an implant material that minimizes acute and chronic inflammation while providing long-term integration properties. We systematically investigated the innate immune responses modulated by the addition of Zn to CaP coatings, using whole transcriptome profiling through RNA sequencing (RNA-Seq).

overall_design: The coatings were produced on Ti64 alloy (ELI grade) substrates by the microarc oxidation method (MAO). The treatment was performed in aqueous electrolytes containing C10H12CaN2Na2O8, (NH4)3PO4, KH2PO4 and C4H6O4Zn as a Zn component. The electrolyte was agitated by a magnetic stirrer. The coatings were produced by applying a unipolar waveform with a constant peak current density of 5 A dm−2, 50% duty cycle, and 1 kHz frequency. The duty cycle is defined as the ratio of the anodic on-time per cycle to the total time of the cycle. The electrical parameters were chosen in such a way that layer thicknesses between 10 and 20 µm were achieved. Ti64_CaP_Zn25, Ti64_CaP_Zn50, Ti64_CaP_Zn75, and Ti64_CaP_Zn100 were prepared by adding zinc acetate as a zinc carrier in the doping solutions to CaP, with concentrations of 25 g/L, 50 g/L, 75 g/L, and 100 g/L, respectively. Buffy coats obtained from German Red Cross Blood Service Baden-Württemberg – Hessen were diluted at a ratio of 1:1 with Ca2 +- and Mg2 +-free phosphate-buffer saline (PBS) (Biochrom, Berlin, Germany). CD14+ monocytes were isolated by 2 sequential gradient centrifugations followed by the soring with CD14 Microbeads (Miltenyi Biotech, Bergisch Gladbach, Germany). Monocytes were cultivated for 6 days on the cell culture plastic or sample disks at a concentration of 2×106 cells/mL in macrophage serum-free medium X-Vivo 10 (Lonza) supplemented with 5 ng/mL M-CSF (Peprotech, Hamburg, Germany) and cytokines as follows: For M0, no cytokines were added; for M1, 100 ng/mL of IFNγ (Peprotech, Hamburg, Germany) was added; and for M2, 10 ng/mL of IL-4 was added. Cells were harvested for RNA isolation and RNA-seq.

first: Julia

last: Kzhyshkowska

first: Jürgen

last: Schmidt

first: Quan

last: Liu


title: Human Placental Extract Enhances Neonatal Epithelial Reparative Capacity in Porcine Models

city: Chapel Hill

first: Matthew

last: Niederhuber

address: 250 Bell Tower Dr.

institute: UNC-Chapel Hill

summary: The devastation caused by necrotizing enterocolitis (NEC) has only continued to claim the lives of infants despite advances in neonatal medicine. To address the acute, and often severe, intestinal epithelial damage caused by NEC, therapeutics are needed that directly target epithelial recovery and cellular regeneration processes. Amniotic fluid and its derivatives have shown therapeutic benefit for NEC though these elements remain difficult to obtain. We therefore investigated the capacity of a decellularized human placental extract (HPE) comparable to amniotic fluid for its ability to prevent against and enhance recovery from NEC using in vitro and in vivo models. Healing responses of hypoxia or scratch-wound injured primary neonatal porcine ileal epithelial cells following HPE application were analyzed. In vivo, NEC was induced in neonatal piglets through a combination of preterm delivery and formula feeding.  Treated piglets received enteral HPE while control were nil per os prior to formula initiation. In vitro, HPE treatment accelerated scratch closure and increased proliferating cell number, without enhanced tight junction recovery following hypoxia. In vivo, HPE treatment increased weight gain, decreased macroscopic and histological damage, and increased ileal crypt epithelial cell proliferation. Transcriptomic analysis of monolayer cultures treated with HPE was undertaken after observation of similar effects in both in vitro and in vivo platforms. Increases in shared gene pathways associated with epithelial wound healing, proliferation, and migration were identified including members of the Wnt family.  In sum, these findings suggest that HPE can enhance the reparative capacity of neonatal epithelium in the context of NEC.

overall_design: 2-3 replicates each of neonatal porcine ileal monolayers from 6 independent animals with and without Human Placental Extract (HPE) treatment

first: McKinney-Aguirre

last: Caroline

first: Stewart

last: Amy

first: Freund

last: John

first: Singh

last: Abhishek

first: Hojnacki

last: Jenna

first: Tomblyn

last: Seth

first: Berger

last: Michael

first: Washburn

last: Scott

first: Gonzalez

last: Liara


title: A vagal sensory-to-sympathetic axis restrains anti-tumor immunity

city: Philadelphia

first: Chengcheng

last: Jin

state: PA

address: BRB II/III, Room 732-734, 421 Curie Blvd

department: Department of Cancer Biology

institute: University of Pennsylvania

summary: Body-brain communication has emerged as a key regulator of tissue homeostasis. Solid tumours are innervated by different branches of the peripheral nervous system, and increased tumour innervation is associated with poor cancer outcomes. However, it remains unexplored how the brain senses and responds to tumours in peripheral organs, and how tumour-brain communication influences cancer immunity. Here, we identify a previously unrecognized tumour-brain axis that promotes oncogenesis by establishing an immune-suppressive tumour microenvironment (TME). Combining genetically engineered mouse models with neural tracing, calcium imaging and single-cell transcriptomics, we demonstrate that lung adenocarcinoma induces increased innervation, activation and transcriptional alterations in vagal sensory neurons (VSNs), a major interoceptive system connecting visceral organs to the brain. Mechanistically, Npy2r+ vagal sensory nerves transmit signals from lung tumours to brainstem nuclei, driving elevated sympathetic efferent activity in the TME. This, in turn, suppresses anti-tumour immunity via β2-adrenergic signaling in alveolar macrophages. Disruption of this sensory-to-sympathetic pathway through genetic, pharmacological or chemogenetic approaches significantly inhibited lung tumour growth by enhancing immune responses against cancer. Collectively, these results reveal a bidirectional tumour-brain communication involving vagal sensory input and sympathetic output that cooperatively regulate anti-cancer immunity; targeting this tumour-brain circuit may provide new treatments for visceral organ cancers.

overall_design: To understand how lung tumors influence the transcriptome of vagal sensory neurons (VSNs), we performed single cell RNA-sequencing analysis of VSNs isolated from healthy or tumor-bearing mice

first: Haohan

last: Wei

first: Chuyue

last: Yu

first: Rui

last: Chang


title: Changes in 3D genome organization of hepatocellular carcinoma (HCC) cells induced by lipid overload

first: Liang

last: Li

state: Shanghai

address: 225 Changhai Road

institute: Eastern Hepatobiliary Surgery Hospital

summary: We analyzed the 3D genome organization via the High-throughput/resolution chromosome conformation capture (Hi-C) data generated from lipid overload-induced HCC cells.

overall_design: HepG2 cell lines were treated with 1% BSA (fatty acid-free) DMEM cell culture medium containing 120 μM palmitic acid (PA) and 240 μM oleic acid (OA) (for PA+OA group) or v/v 1/1000 DMSO (for mock group) for 48 hrs. The 3D genome organization via the High-throughput/resolution chromosome conformation capture (Hi-C) data generated from PA+OA or Mock-induced HCC cells were then analyzed.

first: Hongyang

last: Wang

first: Jingbo

last: Fu

first: Yanping


title: Study on peripheral blood methylation and transcriptome in patients with Graves' disease and Graves' ophthalmopathy

city: Xi'an

first: YuFeng

last: Liu

state: ShanXi

address: The First Affiliated Hospital of Xi'an Jiao Tong University

summary: By studying the differences in transcriptional and methylation levels between the GO (Graves' ophthalmopathy) patient group and the GH (Graves' hyperthyroidism) patient group, we aim to explore the pathogenic mechanisms of GO in patients with GH, and provide intervention guidance for the prevention of GO.

overall_design: 1. moderately to severely active GO; 2. CAS score >=3; 3. the grade of NOSPECS >= 4; 4. the duration of GO is less than 3 months; 5. the age in the range of [18, 92]. 1. newly diagnosed (duration < 2 months); 2. the age in the range of [18, 95].


title: Lipid overload-induced DNA double stands breaks foci in HCC genome

summary: Lipotoxicity-induced hepatic DNA damage responses (DDRs) contribute to malignant progression of MASH-related HCC, but the underlying mechanism is unclear. Using DSB marker phosphorylation of the Ser139 residue of the histone variant H2AX (γH2AX) antiby-mediated CUT&Tag-seq, a global increase of DSBs induced by PA+OA was observed.

overall_design: Using DSB marker phosphorylation of the Ser139 residue of the histone variant H2AX (γH2AX) antibody-mediated CUT&Tag-seq to reveal a global of DSBs foci in  lipid overload-induced or mock-induced HepG2 cells


title: Nanomaterial specific cell pertubation patterns during lung inflammation in a single cell resolution

city: Munich

first: Lianyong

last: Han

state: Bavaria

address: Ingolstädter Landstraße 1

institute: Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH)

summary: The cellular mode of actions of inhaled nanomaterials are poorly understood, though shape and biopersistence of nanomaterials long-since raise concerns in respiratory toxicology. Here we longitudinally analyzed cellular perturbations to three carbonaceous nanomaterials of different shape and toxicity upon pulmonary delivery to mice at single cell resolution. Focusing on the course of lung inflammation, our research aims to reveal highly nanomaterial-specific contributions of cell niches.

overall_design: Four 10-12 week old, female C57BL/6 mice were anesthetized with midazolam/ medetomidine/fentanyl (MMF) and instilled intratracheally with 50 μl of either carbon nanoparticle (CNP; 20 μg),  multi walled carbon nanotube (MWCNT; 15 μg) or double walled carbon nanotube (DWCNT; 50 μg), 0.1 μg LPS or sham (0.5 mg/mL lung surfactant in water) per mouse. Whole lung tissue was harvested from 4 mice per group after 12h, 6d or 28d for live single cell and tissue analyses (Drop Seq).

first: Carola

last: Voss

first: Meshal

last: Ansari

first: Tobias

last: Stoeger


title: Lipid overload-induced R Loops formed by m6A-modified circTACC3

summary: To further elucidate the pathological characteristics of circTACC3-R loops in the HCC genome, circR loops were enriched by DRIP from lipid overload-induced HCC cells. Based on this premise, we devised an oligonucleotide probe specifically targeting the BSJ region of circTACC3, and used a ChIRP assay to selectively enrich the circR loops formed by endogenous circTACC3, named “DRIP-ChIRP”, by which specific enrichment of circTACC3 was detected within global circR loops and circTACC3-R loops

overall_design: circR loops were enriched by DRIP from (S9.6 Antibody) lipid overload-induced HepG2 cells. Based on this premise, we devised an oligonucleotide probe specifically targeting the BSJ region of circTACC3, and used a ChIRP assay to selectively enrich the circR loops formed by endogenous circTACC, by which specific enrichment of circTACC3 was detected within global circR loops and circTACC3-R loops


title: The effect of chronic intermittent hypoxia (CIH) on amyloid pathology in 5XFAD mice

city: Madison

first: Jyoti

last: Watters

state: WI

address: 2015 Linden Dr

department: Comparative Biosciences

institute: University of Wisconsin

summary: We analyzed gene expression from 10-month old WT and 5XFAD mice exposed to chronic intermittent hypoxia (CIH) or normoxia beginning at 4 months of age.

overall_design: 10 month old (female) or 8-month old (male) WT (C57Bl6) or 5XFAD mice that had been exposed to chronic intermittent hypoxia (6.5% O2) or normoxia (21%)  in 90 second intervals for 8 hours during their sleep cycle beginning at 4 months of age. Microglia were immunomagnetically isolated from the cerebrum of mice and total RNA was isolated for sequencing.

first: Kaitlyn

last: Marino

first: Andrea

middle: C

last: Ewald

first: Jaidynne

middle: N

last: Lash

first: Erin

last: McCann

first: Shibani

last: Ram

first: Phinea

middle: Z

last: Romero

first: Tao

first: Abigail

middle: L

last: Radcliff

first: Tracy

last: Baker

first: Tyler

last: Ulland


title: SWI/SNF complex ATPase activity supports normal syncytiotrophoblast differentiation and shields from EVT differentiation [ATAC-seq]

city: Vienna

first: Andreas

last: Lackner

address: Schwarzspanierstrasse 17

department: Center for Anatomy and Cell Biology

institute: Medical University of Vienna

summary: Syncytiotrophoblast (ST) differentiation is essential for proper formation of the placenta. Using human trophoblast stem cells as a model system, we dissect the role of SWI/SNF ATPase function during this process. We compare gene expression, chromatin accessibility, SWI/SNF occupancy and histone modifications of non-treated control cells with cell treated with BRM014, selective inhibitor of BRM and BRG1 ATPase function, induced to differentiate into ST-like cells by forskolin treatment. Gene expression was monitored at 0h, 12h, 24h and 72h of differentiation and epigenomic assays were carried out in self-renewing conditions (0h) and 24h of ST differentiation.

overall_design: 3’ RNAseq, ChIPseq and ATACseq data of normal and SWI/SNF inhibited Trophoblast stem cells at 24h into ST differentiation by Forskolin treatment

first: Henrieta

last: Papuchova

first: Paulina

last: Latos


title: SWI/SNF complex ATPase activity supports normal syncytiotrophoblast differentiation and shields from EVT differentiation [RNA-seq]


title: SWI/SNF complex ATPase activity supports normal syncytiotrophoblast differentiation and shields from EVT differentiation [ChIP-seq]


title: AE9a leukemia cells located in endosteal region exhibit a transcriptional signature enriched in hypoxia and high Ddit4 expression

city: Tianjin

first: Yishuang

last: Li

address: 288 Nanjing Road, Tianjin 300020, P. R. China

institute: State Key Laboratory of Experimental Hematology

summary: Like normal HSCs, LSCs appear to reside in endosteal BM niche and utilize hypoxic niche for their stemness maintenance. To determine the molecular mechanism that regulating the stemness of LSCs, we performed RNA-seq analyses on leukemia cells isolated from collagenase treated bone (endosteal BM, EBM) and from conventional flushed BM (central BM, CBM) of AE9a leukemia mice.

overall_design: Transcriptome sequencing of leukemia cells isolated from collagenase treated bone (endosteal BM,EBM) and from conventional flushed BM (central BM,CBM) of AE9a leukemia mice.

first: Jianxiang

last: Wang

first: Qing

last: Rao


title: Ddit4 deficiency leads to a defect in AE9a induced leukemia development

summary: Our research indicated knock out of DDIT4 markedly suppresses leukemia initiation potential, leukemia maintenance and self-renewal of AE9a leukemia cells in vivo. To better understand the molecular mechanisms underlying the role of DDIT4 in self-renewal of LSC and leukemia initiation, we performed global gene expression profiling by RNA sequencing on AE9a-Ddit4+/+ and AE9a-Ddit4-/- leukemia cells.

overall_design: Transcriptome sequencing of leukemia cells from AE9a-Ddit4+/+ and AE9a-Ddit4-/- mice.


title: Landscape of the m6A modification and expression of circRNAs in MASH-related hepatocellular carcinoma

first: Liang

summary: N6-methyladenosine (m6A) RNA methylation is the most abundant form of RNA modification in eukaryotes, and it affects various aspects of posttranscriptional regulation of circRNA functions. This study aims to elucidate the landscape of the m6A modification and expression of circRNAs in metabolic dysfunction-associated steatohepatitis (MASH)-related hepatocellular carcinoma (HCC) at the level of the epitranscriptomics and identify new potential therapeutic targets.

overall_design: Five human MASH-related HCC tumor tissues and paired adjacent tissues were examined utilizing the m6A-circRNA epitranscriptomics microarray. The relative expression, relative m6A modification rate, and absolute m6A modification quantity of the circRNAs were compared between these two groups.

first: Jingbo

last: Fu

first: Yanping

last: Wei

first: Hongyang


title: Multi-omics Sequencing reveals Epigenetic Regulation in Actinic Keratosis and Cutaneous Squamous Cell Carcinoma [m6A-seq]

first: Li

last: He

summary: Cutaneous squamous cell carcinoma (cSCC) is an important type of skin cancer. It is difficult to diagnose and treat, which seriously endanger people’s the physical and mental health. Actinic keratosis (AK) induced by ultraviolet radiation is the precancerous lesion of cSCC. The mechanism of occurrence and development of cSCC is still unclear, and the research on epigenetics is even less. In this project, we intend to study the mechanism of cSCC, especially the transformation from normal skin to AK, cSCC and the metastasis in late stage of cSCC, using multi-omics sequencing technology with experimental methods. Through the integrated analysis of multi-omics information such as DNA methylation, RNA methylation, chromatin accessibility and transcriptome, we obtained the epigenetic map of different stages of cSCC and identified the potential key epigenetic driving factors for cSCC. This project provided an important scientific basis for the clinical treatment and drug development of cSCC, as well as method reference for the study of other cancers.

overall_design: Collected samples comprised 5 AK, 5 cSCC, and 10 normal skin samples with epidermal and dermal layers, followed by parallel RNA m6A-seq, 850K DNA methylation array, and ATAC-seq analyses

first: Yazhou

last: Sun

first: DanDan

last: Zou

first: Xinjie

first: Jiaying

last: Liu

first: Ke

first: Xianxin

last: Lai

first: Yutong

first: Tianshun

last: Gao

first: Xin


title: Effect of depletion of PNPLA1 in gene expression during keratinocyte differentiation on reconstructed human epidermis

city: Toulouse

first: Nathalie

last: JONCA

state: France

address: CHU Purpan

country: France

institute: INSERM UMR1291 - CNRS UMR 5051 - Université Toulouse III

summary: Congenital ichthyoses are rare and disabling genodermatoses caused by mutations in genes involved in the epidermal barrier. More than 60 genes are known to be involved. However, 5-10% of the genetic variants identified in those genes are rarely or not described and their pathogenicity not yet demonstrated. They are therefore classified as Variants of Uncertain Significance (VUS) that leave number of patients undiagnosed, precluding prognosis, counselling and treatment.  We report here, an experimental strategy to reclassify VUS identified in congenital ichthyosis-causing genes tested for PNPLA1 variants. PNPLA is a transacylase essential for the skin barrier formation. It catalyzes the biosynthesis of acylceramides (AcylCer) in the stratum granulosum by esterification of ω-hydroxy ceramides with linoleic acid. We successfully characterized three PNPLA1 VUS identified in three patients with congenital ichthyosis, opening the possibility to extend the approach to other ichthyosis-causing genes.

overall_design: We generated immortalized keratinocyte cell lines (N/TERT-2G) CrisprCas9-knockout (KO) for the ichthyosis-causing gene PNPLA1. Three PNPLA1 VUS were ectopically expressed in the corresponding KO cell line by lentiviral transduction and the resulting cells were used to produce reconstructed human epidermis (RHE). To further characterized the KO PNPLA1 icthyosis model, we performed gene expression profiling analysis using data obtained by RNAseq of WT reconstructed epidermis vs 3 PNPLA1 KO clones

first: Nuria

last: Pell

first: Severine

last: Courrech

last: Garnier

first: Anne-Alicia

last: Gonzalez

first: Emeline

last: Lhuillier


title: Single-cell transcriptomics revealed molecular vulnerability in a human midbrain-like organoid model of Parkinson's Disease [MERFISH]

city: Singapore

first: Matas

last: Vitkauskas

address: 60 Biopolis St.

department: Genome Institute of Singapore

institute: A*star research entities

summary: The human midbrain-like organoid (hMLO) is a key model system for investigating pathological features of Parkinson’s disease (PD), yet how its molecular landscape relates to cellular vulnerability in PD remains unclear. We performed an in-depth single-cell characterization of our previously established hMLO model up to 150 days in vitro. Our hMLOs exhibited various physiological cell types and broad topographical patterning that resemble that of human fetal midbrain. We further identified four distinct dopamine-producing neuron (DaN) subtypes whose molecular profiles span a key transcriptomic axis in the selective vulnerability of DaNs in PD. Deletion of PARK7, a highly penetrant PD-causing gene, from hMLOs induced cell type-dependent molecular perturbations in mitochondrial activity and synapse biology, and recapitulated PD pathophysiology including α-synuclein aggregation, Lewy Body-like inclusions and DaN degeneration with extended culture. This study highlights the utility of our hMLO model in manifesting pathological features and cell type-specific vulnerability, enabling mechanistic studies into PD pathophysiology.

overall_design: 10 wild-type hMLO samples that are day 60, 11 DJ-1 KO hMLO samples that are day 60

first: Jessica

last: Xie

first: Yang

last: Lin

first: Ng

last: Hui

first: Liu

last: Jinyue


title: Single-cell transcriptomics revealed molecular vulnerability in a human midbrain-like organoid model of Parkinson's Disease [scRNA-Seq]

overall_design: We characterized our previously established human pluripotent stem cell-derived three-dimensional organoid model of the human midbrain (hMLO) with single-cell and spatial resolution. We also investigated the effect of a PD-causing mutation, namely loss-of-function of the DJ-1 protein, with batch-matched WT and isogenic DJ-1 KO hESC-derived hMLOs. These scRNAseq experiments were performed across the period of day 65-153.


title: Single-cell transcriptomics revealed molecular vulnerability in a human midbrain-like organoid model of Parkinson's Disease [RNA-Seq]

overall_design: To understand the efffects of the PD-causing mutation loss of function of DJ-1 in our previously established human pluripotent stem cell-derived 3D midbrain organoid model, we used CRISPR/Cas9 genome editing to generate an isogenic knockout line and performed bulk RNA sequencing of day 60 hMLOs.

first: NgLast na

first: Jinyue


title: APC coordinates GSK3 phosphorylation of SETD8 to suppress colorectal cancer [RNA-seq]

city: Boston

first: Zvi

last: Cramer

state: MA

address: 30 Caldwell St

summary: Colorectal cancer (CRC) is the second-leading cause of cancer-related deaths with increasing incidence globally. Mutations in the tumor suppressor APC initiate CRC at least in part by preventing the GSK3 kinase from phosphorylating β-CATENIN, leading to its constitutive stabilization and transactivation of mitogenic target genes. While the importance of β-CATENIN phosphorylation by GSK3 is well-established, APC regulation of GSK3 activity upon other targets with potential oncogenic relevance are not understood. Here, we identify the H4K20 methyltransferase SETD8 as target of GSK3 phosphorylation requiring functional APC in the intestinal epithelium. We found that phosphorylation by GSK3 restrains the oncogenic activity of SETD8, with loss of phosphorylation sensitizing mice to oncogenic insults. Mechanistically, phosphorylation alters the role of SETD8 in transcriptional regulation, most notably by preventing it from activating oncogenic YAP signaling and an oncogenic fetal-like transcriptional program. These results underscore the importance of SETD8 in CRC and represent a novel β-CATENIN -independent oncogenic consequence of APC loss.

overall_design: To determine the transcriptional effects of SETD8 T140 phosphorylation in colorectal cancer, we overexpressed human WT or T140D SETD8 in murine colorectal tumoroids and then delivered sgRNAs targetting endogenous murine Setd8 via lentivirus. RNA was collected 4 days after lentiviral infection

first: Christopher

last: Lengner

first: Mario

middle: A

last: Blanco


title: Effect of endothelial YAP/TAZ on neuroinflammation and outcome after ischemic stroke in mice

city: Berlin

first: January

last: Weiner

address: Charitéplatz 1

department: CUBI

institute: Berlin Institute of Health, Charité Medical University of Berlin

summary: In the acute phase of ischemic stroke, endothelial cell (EC) dysfunction leads to breakdown of the blood-brain barrier with increased vascular permeability, vascular inflammation, and transendothelial migration of leukocytes. ECs are also critical for long-term regenerative processes, such as post-stroke angiogenesis, enabling the transition from brain injury to repair. Yes-associated protein 1 (YAP) and WW domain-containing transcriptional regulator 1 (TAZ) are co-transcriptional regulators of EC proliferation and apoptosis. Several studies showed that YAP/TAZ is essential for developmental angiogenesis. However, the role of YAP/TAZ in adult angiogenesis and particularly in experimental stroke is unknown. Here, we subjected mice with an inducible EC-specific deletion of YAP and TAZ (YT-iKO) to 30-min middle cerebral artery occlusion (MCAo) followed by reperfusion to investigate the effects of endothelial YAP/TAZ on acute and long-term outcome after ischemic stroke.  First, we examined mRNA expression of genes related to YAP/TAZ signaling in ischemic brain tissue, such as Id1, Smad6, Ankrd and Ccn2. We found a transient induction with highest expression levels acutely after stroke. Surprisingly, endothelial YAP/TAZ deficiency resulted in reduced lesion volumes 28 days after MCAo, whereas acute lesion size 3 days after stroke did not differ. Moreover, Yap/Taz iEC-KO animals showed no gross differences in vessels morphology 28 days after stroke, and no effect was detected on blood vessel density and EC density. We therefore speculated whether angiogenesis-independent effects of YAP/TAZ might also be associated with improved long-term outcome after stroke.  To better understand the underlying mechanisms, we performed RNA sequencing of ECs isolated from ischemic brain tissue of YT-iKO compared with CTRL animals 72h post stroke. Here, we identified differently expressed gene sets involved in inflammatory responses. Therefore, we studied the non-endothelial tissue environment of the brain. We found, that EC YAP/TAZ deletion led to increased expression of anti-inflammatory genes accompanied by increased infiltration of myeloid cells, suggesting a protective phenotype. Besides, acute microglia proliferation was reduced in Y/T-iKO animals. Overall, our results provide new insights into the role of endothelial YAP/TAZ in neuroinflammation after cerebral ischemia. YAP/TAZ may therefore be a potential therapeutic target for the treatment of ischemic stroke.

overall_design: YT-iKO (Pdgfb-iCreERT2+/-:Yapfl/fl:Wwtr1fl/fl ) and CTRL (Pdgfb-iCreERT2+/+:Yapfl/fl:Wwtr1fl/fl) mice received 30 min MCAo or sham surgery. CD31+ brain endothelial cells (bEC) from YT-iKO and CTRL animals were isolated 72 hours after surgery by FACsort (DAPI-, CD45-, CD31+). RNA-seq analysis of bEC from YT-iKO and CTRL animals for sham and MCAo groups were performed in quadruple replicates.

first: Ria

last: Göttert


title: Unveiling Ageing-Associated and Caloric Restriction-Associated Changes in miRNA Expression in Rat Skeletal Muscle and the Mechanisms Mediating their Effects on Muscle Cell Function

city: Liverpool

first: Gulam

last: Altab

address: 6 West Derby Street

country: United Kingdom

institute: University of Liverpool

type: Non-coding RNA profiling by high throughput sequencing

summary:
The mechanisms underlying skeletal muscle ageing, whilst poorly understood, are thought to involve dysregulated micro (mi)RNA expression. Using young and aged rat skeletal muscle tissue, we applied high-throughput RNA sequencing to comprehensively study alterations in miRNA expression occurring with age, as well as the impact of caloric restriction (CR) on these changes. Furthermore, the function of the proteins targeted by these age- and CR-associated miRNAs was ascertained.
Numerous known and novel age-associated miRNAs were identified of which CR normalised 45.5% to youthful levels. Our results suggested miRNAs upregulated with age to downregulated proteins involved in muscle tissue development and metabolism, as well as longevity pathways, such as AMPK and autophagy. Furthermore, our results found miRNAs downregulated with age to upregulate pro-inflammatory proteins, particularly those involved in innate immunity and the complement and coagulation cascades. Interestingly, CR was particularly effective at normalising miRNAs upregulated with age, rescuing their associated protein coding genes but was less effective at rescuing anti-inflammatory miRNAs downregulated with age.
Lastly, the effects of a specific miRNA, miR-96-5p, identified by our analysis to be upregulated with age, were studied in culture C2C12 myoblasts.  We demonstrated miR-96-5p to decrease cell viability and markers of mitochondrial biogenesis, myogenic differentiation and autophagy. Overall, our results provide useful information regarding how miRNA expression changes in skeletal muscle, as well as the consequences of these changes and how they are ameliorated by CR.

overall_design: Using rat tissue, using rna-sequencing we aimed to identify the key changes in miRNA expression observed in muscle ageing of rats between young (6 months), old (28 months) and old CR (28 months). In addition, we endeavoured to assess to what extent these changes could be reversed using CR.

first: Gulum

first: Brian

last: Merry

first: Charles

middle: W

last: Beckett

first: Priyanka

last: Raina

first: Ana

last: Soriano-Arroquia

first: Bruce

last: Zhang

first: Aphrodite

last: Vasilak

first: Katarzyna

last: Goljanek-Whysall

first: Joao

last: De Magalhaes