title: Synthetic IDE inhibitors sensitize and reverse acquired resistance of multiple myeloma cells to proteasome inhibitors

city: BRONX

first: Fabien

last: Delahaye

address: 1300 Morris Park Avenue

department: Genetics

institute: AECOM

summary: The use of proteasome inhibitors (PIs) is the backbone of multiple myeloma (MM) treatment. However, almost all MM patients who initially respond to PIs eventually develop resistance to these drugs. The discovery of a pharmacological intervention that increase the potency of PIs in order to reduce their dose and/or restore the sensitivity of MM cells to PIs is an important avenue in MM research. Insulin Degrading Enzyme (IDE) is a druggable protease known to modulate proteasome. We show here that, in two independent cohorts, a high expression of IDE in cells from MM patients is associated with shorter overall survival. Likewise, we designed specific, cell permeable, IDE inihibitors and showed that full pharmacological engagement of IDE is associated with enhanced sensitivity to PIs of MM cell lines, as well as of primary patient MM cells. Furthermore, treatment of PI-resistant MM cells with the inhibitor overcomes their resistance to PI. Finally we designed an improved IDE inhibitor suitable for in vivo pharmacology. This inhibitor which develops multiple interactions with IDE at the catalytic site and display good pharmacocinetic properties, boosts the anti-myeloma potency of bortezomib in a syngenic mouse model of MM. In vitro, it appears that IDE inhibition reduces the residual proteasome activty in PI-treated cells and increases the apoptotic potency of carfilzomib through induction of an Integrated Stress Response associated with strongly reduced IGF1 and IGF1R expressions. The pharmacological profile of this new combination appears highly desirable for the treatment of MM.

overall_design: Total RNA of HeLa cells treated with DMSO, 20nM carfilzomib (CFZ), 15µM of compound 1a (CPD 1a) or the combination of these two compounds for 8h or 24h was extracted using the NucleoSpin® RNA extraction (Macherey-Nagel, Hoerdt, France). Total RNA of HeLa cells at the time of treatment (0h) was also extracted. The experiment was repeated 4 times.

first: Laetitia

last: Lesire


title: In vitro and transcriptomic variation in Neisseria musculi morphotypes correlate with colonization variability and persistence in vivo

status: Public on Sep 15 2024

city: Athens

first: Nathan

middle: John

last: Weyand

state: OH

address: 7 Depot Street

department: Biological Sciences

country: USA

institute: Ohio University

type: Expression profiling by high throughput sequencing

summary: Asymptomatic colonization of the upper respiratory tract is a common trait of the two exclusive human pathogens, Neisseria gonorrhoeae and Neisseria meningitidis. In vivo models of pathogenic neisserial infections are heterologous systems that permit short-term persistence but do not fully recapitulate infections in humans. Studying Neisseria musculi (Nmus), an oral commensal, in laboratory mice allows investigation of Neisseria-host interactions that avoids host restriction barriers. Nmus produces smooth and rough morphotypes on solid media. We compared the in vitro phenotypes, biofilm transcriptomes, and in vivo colonization patterns and burdens of the Nmus morphotypes. We observed that the two morphotypes differ in biofilm formation, aggregation, pilin production, and transformation frequency in vitro. These phenotypes strongly correlated with differential expression of a set of genes in the Nmus biofilms including those that encoded factors for bacterial attachment. In vivo, the smooth morphotype stably colonized the oral cavities of all inoculated A/J and C57BL/6J mice at higher burdens compared to the rough. Following nasal inoculations, we detected transient Nmus nasal colonization. The smooth morphotype was able to reach higher burdens more quickly in the nasal cavity and on oral swabs following dissemination to the oral cavity. Gut colonization burdens fluctuated over time. Interestingly, both morphotypes colonized the oral cavities of A/Js at higher magnitudes than in C57BL/6Js. Collectively, our results demonstrate that colonization by Nmus can be affected by various factors including Nmus morphotypes, inoculation routes, anatomical niches, and host backgrounds. The Nmus-mouse model can use variable morphotype-host combinations to study the dynamics of neisserial asymptomatic colonization and persistence in multiple extragenital niches.

overall_design:
Six data sets in total. Three replicates of biofilms formed by the two N. musculi morphotypes.

Two separate analyses were performed. One analysis was done using two replicates for each condition (GSM5582130 and GSM5582131 [smooth] and GSM5582134 and GSM5582135 [rough]) and one analysis was done using all three replicates per condition. Samples include the normalized data for the two replicate analysis and the three replicate analysis. The DESeq output files for each analysis are available on foot of this record.

first: Eliza

last: Thapa

first: Leah

last: Lauderback

first: Cassandra

last: Simmons

first: Donald

middle: L

last: Holzschu

first: Adonis

last: D’Mello

first: Mancheong

last: Ma

first: Magdelene

last: So

first: Hervé

last: Tettelin

middle: J


title: Effect of mutant GNAS expression in the doxycycline-inducible Kras;Gnas mouse model of IPMN using scRNA-seq

city: New York

first: Anirban

last: Maitra

state: NY

address: Smilow 910, 522 1st Ave

department: Perlmutter Cancer Center

institute: New York University Grossman School of Medicine

summary: We investigated the effect of GNAS(R201C) expression in the Kras;Gnas model of pancreatic intraductal papillary mucinous neoplasms where transgenic mutant GNAS is doxycycline inducible (LGKC; p48(Cre), Kras(LSL-G12D), Rosa26(LSL-rtTA)), Tg(TetO-GNAS(R201C)) using scRNA-seq of dissociated pancreatic tissues.

overall_design: Four Kras;Gnas mice were fed with doxycycline or normal lab feed for 10 weeks starting at 8 weeks of age (2 mice per group). Pancreata were dissociated and subjected to scRNA-seq.

first: Yuki

last: Makino

first: Kimal

last: Rajapakshe

first: Fredrik

last: Thege


title: A soft stromal niche promotes hematopoietic stem cell maintenance and rejuvenation

city: Shanghai

first: Dandan

last: Cao

address: 1239 Siping Road, Yangpu District

country: China

institute: Tongji University

summary: Bulk RNA-seq data of 2D- vs. 3D-cultured human bone marrow stromal cells.

overall_design: RNA-seq libraries from 3 biological replicates of 2D- and 3D-cultured human BMSCs were subjected to paired-end sequencing by HiSeq XTen systems (Illumina, 150 bp reads).

first: Rui

last: Yue

first: Liting

last: Xu

first: Xiaoying

last: Zhang

first: Yanhua


title: Glucocorticoids induce a maladaptive epithelial stress response to aggravate acute kidney injury [ATAC]

status: Public on Sep 14 2024

city: Bad Nauheim

first: Carsten

last: Kuenne

address: Ludwigstrasse 43

department: Bioinformatics

country: Germany

institute: Max Planck Institute for Heart and Lung Research

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Acute kidney injury (AKI) is a frequent and challenging clinical condition associated with high morbidity and mortality. In AKI, renal tubular epithelial cells (TECs) are a primary site of damage, and recovery from AKI depends on TEC plasticity. However, the molecular mechanisms underlying adaptation and maladaptation of TECs in AKI remain largely unclear. Here, our analyses of mouse kidney tubuloids showed that TEC injury resulted in activation of the glucocortiocoid receptor by endogenous glucocorticoids, which aggravated tubular damage. The detrimental effect of endogenous glucocorticoids on injured TECs was exacerbated by the administration of the widely clinically used synthetic glucocorticoid, dexamethasone, as indicated by experiments in mouse kidney tubuloids. Mechanistically, studies in mouse tubuloids demonstrated that glucocorticoid receptor signaling in injured TECs orchestrated a maladaptive transcriptional program to hinder DNA repair and to amplify injury-induced DNA double-strand break formation, as well as to dampen mTOR activity and mitochondrial bioenergetics. This study identifies glucocortiocoid receptor activation as a mechanism of epithelial maladaptation, which is functionally important for acute kidney injury.

overall_design: The renal cortices of 4 wildtype mice were dissected, and tubuloids were grown in matrigel. Tubuloids were treated without or with myoglobin (to induce tubular injury). After 12 hours of treatment, tubuloids were subjected to ATAC-seq.

first: Thomas

last: Worzfeld

first: Stefan

last: Günther


title: Glucocorticoids induce a maladaptive epithelial stress response to aggravate acute kidney injury

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

overall_design: Refer to individual Series


title: Development and IND-enabling studies of a novel Cas9 genome-edited autologous CD34+ cell therapy to induce fetal hemoglobin for sickle cell disease

city: Memphis

first: Shengdar

last: Tsai

state: TN

address: 262 Danny Thomas Pl

department: Department of Hematology

institute: St Jude Children's Research Hospital

summary: To determine the genome-wide spectrum and persistence of genomic rearrangements, we applied UniDirectional Targeted Sequencing (UDiTaS) in edited normal donor CD34+ HSPCs. At day 5 and 14 post-electroporation, no reproducible translocations or structural genomic re-arrangements were identified.

overall_design:
UDiTaS assay to detect genomic translocations in edited CD34+ HSPCs at day 5 and day 14 in three normal donors (pre-GMP engineering runs, n=3)
g34_bcl11a samples are treated with two gRNAs and pre-GMP samples are treated with 1 gRNA.

first: Varun

last: Katta

first: Yichao

last: Li


title: Glucocorticoids induce a maladaptive epithelial stress response to aggravate acute kidney injury [RNA]

overall_design: The renal cortices of 4 wildtype mice were dissected, and tubuloids were grown in matrigel. Tubuloids were treated without or with myoglobin (inducing tubular injury) and dexamethasone (100 nM). After 12 hours of treatment, tubuloids were subjected to RNA-seq.


title: Cancer-relevant alternative RNA splicing events driven by the PRMT5-E2F1 axis in high risk neuroblastoma

city: St. Petersburg

first: Alexander

last: Kanapin

address: 7/9 University Emb.

department: Institute for Translational Biomedicine

country: Russia

institute: St Petersburg Universoty

summary: Neuroblastoma (NB) is a devastating childhood cancer that remains clinically unmet. There is an urgency to develop new approaches to treat the disease. Protein arginine methyltransferase (PRMT5) is over-expressed in a wide variety of cancers and has been implicated with a key oncogenic role, achieved in part through its control of the master transcription regulator E2F1. Here, we have investigated the relevance of the interplay between PRMT5 and E2F1 in neuroblastoma and found that elevated expression occurs in poor prognosis high-risk disease. Cell lines derived from NB that recapitulate high PRMT5 and E2F1 expression exhibit increased levels of alternative RNA splicing compared to their low expression cell counterparts.  Cancer-relevant exon-skipping events in apoptotic genes were apparent in high expressing NB cells which resulted in protein isoforms with decreased apoptotic activity. Pharmacological inhibition of PRMT5 or inactivation of E2F1 activity reduced exon skipping and reinstated normal apoptotic activity. Our findings show that a cancer relevant alternative splicing programme desensitises high risk NB to apoptosis. The critical role ascribed to PRMT5 and E2F1 in attaining the alterative RNA splicing programme equally identifies PRMT5 as a potential therapeutic target for neuroblastoma disease.

overall_design: To investigate the impact of NMYC, E2F1, and PRMT5 on gene expression in neuroblastoma, we performed RNA-seq and downstream gene expression analysis in CHP134 cells (high expressors of NMYC, E2F1 and PRMT5) and GIMEN cells (low expressors of NMYC, E2F1 and PRMT5) treated with either DMSO or a PRMT5 inhibitor (T1-44).  Regulation of alternative splicing was also examined using the rMATS data package.  Subsequent to this, we generated a CHP134 cell line that had the E2F1 gene knocked out by CRISPR (Cr), and performed another RNA-seq and gene expression analysis on wild-type cells, or E2F1 Cr cells treated with DMSO or T1-44

first: Laurel

middle: T

last: Bate-Eya

first: Simon

middle: M

last: Carr

first: Gulsah

last: Albayrak

first: Amit

last: Shretha

first: Anastasia

last: Samsonova

first: Nicholas

middle: B

last: La Thangue


title: Influence of nano-enzyme on gene expression during oxidative stress of human mesenchymal stem cells

city: Chengdu

first: Mingru

last: Bai

address: Renmin Road No.14

institute: Sichuan University

summary: Stem cells are severely weakened by elevated reactive oxygen species (ROS) in the inflammatory bone defect microenvironment. It is therefore of critical importance to modulate the level of extracellular ROS for the reversal of stem cell unfavorable environment. Here, we present an electron-donable heterojunction with Ru-Cu pair sites (Ru-Cu/EDHJ) for catalytic reactive oxygen species (ROS) scavenging. We here report the changes of transcription factors human mesenchymal stem cells (hMSCs) with/without treatment with Ru-Cu/EDHJ under the oxidative stress condition.

overall_design: To investigate the function of Ru-Cu/EDHJ  in stem cell protection in high level of ROS microenvironment. We then performed gene expression profiling analysis using data obtained from RNA-seg of hMSCs in 4 conditions (Ctrl, H2O2, CeO2+H2O2, Ru-Cu/EDHJ+H2O2).


title: Induction of a distinct macrophage population and protection from lung injury and fibrosis by Notch2 blockade

city: South San Francisco

first: Sandra

last: Melo

address: 1 DNA Way

institute: Genentech, Inc.

summary: Macrophages are pleiotropic and diverse cells that populate all tissues of the body. Besides tissue-specific resident macrophages such as alveolar macrophages, Kupffer cells and microglia, multiple organs harbor at least two subtypes of other resident macrophages at steady state. During certain circumstances, like tissue insult, additional subtypes of macrophages are recruited to the tissue from the monocyte pool. Recently, a recruited macrophage population marked by expression of Spp1, Cd9, Gpnmb, Fabp5, and Trem2 has been described in several models of organ injury and cancer, and linked to fibrosis in mice and humans. Here, we show that Notch2 blockade given systemically or locally led to an increase in this putative pro-fibrotic macrophage in the lung. Single cell RNA sequencing suggested that the newly arising population derived from monocytes when Notch2 blockade was systemic or derived from alveolar macrophages when Notch2 blockade was local. Unexpectedly, using a bleomycin and COVID19 model of lung injury and fibrosis, we found that the expansion of these macrophages before lung injury ameliorated rather than promoted fibrosis. This suggests that these damage-associated macrophages are not drivers of fibrosis in the lung.

overall_design: Interstitial macrophages (IM), alveolar macrophages (AM), monocytes (mono), were sorted from lungs of ctrl mice or mice treated with anti-Notch2-antibody.

first: Mayra

last: Cruz Tleugabulova

middle: P

first: Aaron

last: Wong

first: Alex

last: Arlantico

first: Meizi

last: Liu

first: Joshua

last: Webster

first: Cary

last: Austin

first: Julia

last: Lau

first: Marco

last: De Simone

first: Ben

last: Korin

first: Shimrit

last: Avraham

first: Jessica

last: Lund

first: Surinder

last: Jeet

last: Reiss

first: Hannah

last: Bender

first: Spyridon

last: Darmanis

first: Zora

last: Modrusan

first: Hans

last: Brightbill

first: Steffen

last: Durinck

first: Michael

middle: S

last: Diamond

first: Andrey

last: Shaw

first: Maximilian

last: Nitschke


title: The functional study of DEK in 786-O cells [ChIP]

city: Shenzhen

first: Wei

last: Chen

state: Guangdong

address: No. 1088 Xueyuan Avenue, Nanshan District

department: School of Life Sciences

institute: Southern University of Science and Technology

summary: To study the function of DEK, we carried out multi-omic analysis to investigate the transcriptome and epigenome alterations upon DEK knockout, as well as the genome-wide DNA binding of DEK in 786-O cells.

overall_design: DEK ChIP-seq in 786-O cells

first: Huanhuan

last: Cui

first: Mengran

last: Wang

first: Rui


title: The functional study of DEK in 786-O cells


title: The functional study of DEK in 786-O cells [ATAC]

overall_design: ATAC-seq in 786-O cells


title: RNA sequencing of HDFs(Human dermal fibroblasts) with or without Sal-B and UVB treatment

first: Sun

middle: Jia

last: Ming

address: No. 639, Zhi Zao Ju Road,

department: Department of Plastic & Reconstructive Surgery

institute: Shanghai Ninth People’s Hospital

summary: Skin aging is a complex biological process that is influenced by multiple factors, including environmental and genetic factors. Ultraviolet (UV) irradiation can cause short-term sun damage, such as erythema and edema, as well as chronic damage, which accelerates skin aging and produces skin wrinkles and skin laxity. Salvianolic acid B (Sal-B) is the most abundant and bioactive water-soluble extractant from the well-known herbal medicine--Salvia Miltiorrhiza in Chinese traditional medicine. Many studies have found that Sal-B exerts powerful antioxidant and anti-inflammatory effects. Therefore, we speculate that salvianolic acid B may have potential therapeutic value in the aspect of anti-photoaging.

overall_design: Examination of HDFs sequencing comparing the UVB+Sal-B addition(100μmol/L) group[UVB-Sal-B], UVB group[UVB] and control group[Ctrl]

first: Jiaming

last: Sun

first: Li

last: Yu


title: The functional study of DEK in 786-O cells [RNA]

overall_design: RNA-seq in 786-O cells


title: Comparable levels of innate immune responses between low DIPs and high DIPs LAIV inoculations in the mouse upper respiratory tract revealed by scRNA-seq

status: Public on Sep 13 2024

city: Changchun

first: Weiheng

last: Su

state: Jilin

address: No. 2699, Qianjin Street

institute: Jilin University

summary: To investigate the extent of replication and strength of innate immune responses of low DIPs and high DIPs H3N2 LAIVs in mouse turbinate tissues, the 48-hpi transcriptomes were analyzed using scRNA-seq.

overall_design: Female 6–8-week-old BALB/c mice were intranasally immunized with of low DIPs LAIV, high DIPs LAIV or placebo. The turbinate and adjacent mucosal tissues were isolated at 48 hpi for scRNA-seq.

first: Min

last: Wu

first: Peihan

first: Fei


title: RNA-seq analysis of gene expression profile in Setd2 WT and KO germinal center B cells and Phf19  WT and KO germinal center B cells

city: Nanjing

first: Yuchao

last: Jing

state: Jiangsu

address: 101 Longmian Ave Jiangning District

department: Immunology

institute: Nanjing Medical University

summary: The goals of this study are to compare gene expression profiles of Setd2 WT and KO germinal center B cells and reveal the underlying mechanisms by which Setd2 regulates germinal center B cell responses. Further  our study aims to compare gene expression profiles of Phf19 WT and KO germinal center B cells reveal the underlying mechanisms by which Phf19 regulates germinal center B cells responses. Finally, we combine the two profiles and investigate the relation shape betweeen Setd2 dependent regulation and Phf19 dependent regulation.

overall_design: The germinal center B cell specific Setd2-deficient mice and WT control mice were immunized and 10e6 germinal center B cells were FACS sorted for RNA extraction, and the germinal center B cell specific Phf19-deficient mice and WT control mice were immunized and 10e6 germinal center B cells were FACS sorted for RNA extraction.  Library were then generated with illumina protocol and subject to NGS and bioinformatic analysis.

first: Xiaoming

first: Yang

last: Zhang

first: Yuliang


title: The Regulation of MicroRNA-21 by Interleukin-6 and its Role in the Development of Fibrosis in Endometriotic Lesions

city: Grand Rapids

first: Gregory

last: Burns

state: MI

address: 400 Monroe Ave NW

department: Obstetrics, Gynecology and Reproductive Biology

institute: Michigan State University

type: Non-coding RNA profiling by high throughput sequencing

summary: Endometriosis is one of the most common causes of chronic pelvic pain and infertility that affects 10% of women of reproductive age. It is currently defined as the presence of endometrial epithelial and stromal cells at ectopic sites; however, advances in endometriosis research have some authors believing that endometriosis should be re-defined as “a fibrotic condition in which endometrial stroma and epithelium can be identified”. microRNAs (miRNAs) are regulatory molecules that potentially play a role in endometriotic lesion development. There is evidence that suggests that miRNAs, including microRNA-21 (miR-21), participate in fibrotic processes in different organs, including the heart, kidney, liver and lungs. The objective of this study was to understand the role of miR-21 and the mechanisms that can contribute to the development of fibrosis by determining how IL-6 regulates miR-21 expression and how this miRNA regulates the transforming growth factor beta (TGF-β) signaling pathway to promote fibrosis. We investigated the expression of miR-21 in the baboon and mouse model of endometriosis and its correlation with fibrosis. We demonstrated that inflammation and fibrosis are present at a very early stage of endometriosis and that the inflammatory environment in the peritoneal cavity, which includes interleukin 6 (IL-6), can regulate the expression of miR-21 in vitro and in vivo.

overall_design: Total RNA was extracted from the endometrium and endometriotic lesions from baboons with induced endometriosis for 15 months (n = 16) or spontaneous disease (n = 8). Small-RNA library preparation and high-throughput sequencing generated an average of 8.9 million reads per sample. Quality and adapter-trimmed reads (Trim Galore v0.3.3) were mapped to human miRNAs from miRbase (release 22) using the miRDeep2 (v0.0.7) pipeline. Differential expression analysis was conducted with edgeR (v3.22.5) using the edgeR-robust method.

first: Maria

middle: A

last: Bernal

first: Yong

last: Song

first: Niraj

last: Joshi

middle: W

first: Emmanuel

middle: N

last: Paul

first: Erin

last: Vegter

first: Samantha

last: Hrbek

first: Lorenzo

middle: F

last: Sempere

first: Asgerally

last: Fazleabas


title: H3K36me3 and H3K27me3 occupancy profiling by high throughput sequencing from setd2 wt and ko germinal center B cells and  H3K27me3 occupancy profiling by high throughput sequencing from phf19 wt and ko germinal center B cells

summary: Our study aims to understand the H3K36me3 and H3K27me3 genome-wide alterations by analysing CHIP-seq data between setd2 wt and ko germinal center B cells, characterize the function of H3K36me3 methyltransferase setd2 in H3K36me3 itself and H3K27me3, further  we aim to H3K27me3  from phf19 ,which is H3K27me3 regulator,  WT and KO group to investigate the mechanism of H3K36me3 dependent H3K27me3 modification introduced by setd2.

overall_design: 4×10e6 germinal center B cells were sorted from SRBC immunized setd2 wt and ko  then flash frozen on dry ice for CHIP, and   germinal center B cells were sorted from SRBC immunized phf19 wt ko mice then flash frozen on dry ice for  cut&tag

last: Wang


title: EAPP is essential for tri-snRNP biogenesis and controls cell fate and tumor growth via the alternative splicing of MDM4

first: Haiping

last: Zhao

address: 131 DongAn Road

institute: Fudan University

summary: Precursor messenger RNA (pre-mRNA) splicing is catalyzed by the spliceosome, a highly dynamic machinery with sequentially assembled small nuclear ribonucleoproteins (snRNPs) and splicing factors. Aberrant spliceosome composition and function result in the dysregulation of pre-mRNA alternative splicing, which may cause cellular stresses and diseases such as cancer. Here, we identify a splicing factor, E2F-associated phosphoprotein (EAPP), that directly binds to the U4/U6. U5 tri-snRNP and PRPF19 complex. Notably, the C-terminal “bucket” domain in EAPP composed of several beta-sheets is required for its interaction with the tri-snRNP. EAPP is prominently located at Cajal bodies within the nucleus where it colocalizes with the spliceosome. Loss of EAPP impedes the assembly and homeostasis of the tri-snRNP complex in Cajal bodies and increases the frequency of splicing abnormalities, mostly exon skipping. Moreover, EAPP depletion promotes MDM4 exon 6 skipping, which suppresses cell growth and tumor progression via p53 overactivation. Our study demonstrates a previously uncharacterized function of EAPP in spliceosome regulation and reveals that EAPP-mediated alternative splicing of MDM4 is a critical determinant of cell fate and tumor growth.

overall_design:
To further investigate how EAPP affects the downstream regulatory mechanisms of tumor cell growth, we utilized CRISPR/Cas9 technology to knock out EAPP in HeLa cells. Infect cells with lentiCRISPR-Cas9 lentivirus. After 48 hours, add 2 μg/ml puromycin to select for transduced cells, and select and expand single-cell clones.
We then performed gene expression profiling analysis using data obtained from RNA-seq. Comparative gene expression and alternative splicing profiling analysis of RNA-seq data for EAPP knockout and WT HeLa cells.


title: Epigenetic aging in immune response to HBV vaccine in B cells isolated from health care workers

city: Bologna

first: Paolo

last: Garagnani

state: BO

address: Via San Giacomo 12

department: Department of Medical and Surgical Sciences (DIMEC)

country: Italy

institute: Univeristy of Bologna

type: Methylation profiling by genome tiling array

summary: Healthcare workers (HCWs) are a high-risk group for hepatitis B virus (HBV) infection. Notably, about 5–10% of the general population does not respond to the HBV vaccination. In this study, we aimed to investigate DNA methylation (DNAm) in order to estimate the biological age of B cells from HCW of both sexes, either responder (R) or non-responder (NR), to HBV vaccination. We used genome-wide DNA methylation data to calculate a set of biomarkers in B cells collected from 41 Rs and 30 NRs between 22 and 62 years old. Unresponsiveness to HBV vaccination was associated with accelerated epigenetic aging (DNAmAge, AltumAge, DunedinPoAm) and was accompanied by epigenetic drift. Female non-responders had higher estimates of telomere length and lower CRP inflammation risk score when compared to responders. Overall, epigenetic differences between responders and non-responders were more evident in females than males. In this study we demonstrated that several methylation DNAm-based clocks and biomarkers are associated with an increased risk of non-response to HBV vaccination, particularly in females. Based on these results, we propose that accelerated epigenetic age could contribute to vaccine unresponsiveness. These insights may help improve the evaluation of the effectiveness of vaccination strategies, especially among HCWs and vulnerable patients.

overall_design: Bisulphite converted DNA from 71 isolated B cell samples were hybridised to the Illumina Infiniun MethylationEPIC BeadChip following manufacture's protocols.

first: Katarzyna

last: Kwiatkowska


title: Ursolic acid-induced DECR1 degradation via NF-κB/NLRP3 pathway inihibits vascular calcification

city: Guangzhou

first: Hongwei

last: Yang

address: Nanshitou Street

institute: Southern Medical University

summary: In this study, we repoort the protective effect of ursolic acid (UA) on vascular calcification in chronic kidney disease. To elucidate the molecular mechanism underlying the anti-vascular calcification effect of UA, we performed RNA-seq to identify the gene expresion under UA treatmment.

overall_design: Human vasculr smooth muscle cells were cultured in calcifying medium in the presence or absence of UA for 48 hours. RNA-seq was performed to determine the downstream target of UA. The gene expression level was calculated using the Fragment Per Kilobase of Million mapped reads (FPKM) methods. Differential expression  was assessed using the DEGseq packages.

first: Jianyun

last: Yan


title: The impact of growing area on the expression of fruit traits re-lated to sensory perception in two tomato cultivars

city: Portici

first: Daniela

last: D'Esposito

address: Via Università 100

department: Department of Agriculture

institute: University of Naples Federico II

summary: The environmental conditions greatly influence tomato fruit quality, by affecting the expression of genes, the abundance of metabolites and the perception of sensorial attributes.In this study, a fruit transcriptome investigation, together with a sensory test and a metabolomic analysis were per-formed to evaluate the impact of the environment on two popular tomato cultivars grown in two Italian regions. The transcriptional profile of each cultivar, cultivated in two different areas high-lighted differential expression in genes involved in pathways related to cell wall components such as pectin, lignin and hemicellulose, sugars as well as in amino acids, phenylpropanoids, and pigment synthesis. The cultivation area mainly affects sensory attributes related to texture and flavor and the metabolic pattern of cell wall precursors, sugars, glutamate, aspartate and carotenoids. In the two genotypes cultivated in the same environment, some attributes and fruit-related quality processes are similarly affected, while others are differently influenced based on tomato specific genetic makeup. Combination of transcriptomic, sensory and metabolomic data obtained from the two tomato genotypes revealed that the environment has a profound effect on specific sensory traits, providing information on factors that shape the specific characteristics and genetic targets for im-proving tomato fruit characteristics.

overall_design: To evaluate the effect if the environment on tomato fruit quality, two tomato genotypes, Dardo and Pixel, (Solanum lycopersicum) were grown in two Italian locations, Battipaglia and Fondi. RNA-seq performed on fruits was used to identify DEGs between the two environments related to fruit quality. A sensory evaluation was performed to identify sensory attributes affected by the environment. A metabolic analysis including key metabolites related to fruit quality was performed to evaluate the difference in aboundance between the two environments in both genotypes.

last: D’Esposito

first: Antimo

last: Di Donato

first: Sharon

last: Puleo

first: Matteo

last: Nava

first: Gianfranco

last: Diretto

first: Rossella

last: Di Monaco

first: Luigi

last: Frusciante

last: Raffaella Ercolano


title: Bioinformatic Analysis of Aniridia Related Keratopathy

city: Newark

first: Aarthi

last: Krishnan

state: DE

address: 18 Marvin Dr, Apt A2

department: Biology

institute: University of Delaware

summary: The purpose of this study is to understand the gene expression profiling, altered pathways and protein networks involved in Aniridia Related Keratopathy. RNA-sequencing was performed on 3 biological replicates of both wildtype PAX6 mice and heterozygous mutant PAX6 corneas.

overall_design:
Differential pairwise contrast between wildtype and heterozygous PAX6 mutatn corneas using RNA-Seq data
3 biological replicates of each wildtype and PAX6 heterozygous mutant are used.

first: Adam

last: Faranda

first: Samuel

middle: G

last: Novo

first: Yan

first: Melinda

middle: K

last: Duncan


title: Germline TET2 variants contribute to the pathogenesis of kidney disease through impaired DNA damage repair and the activation of cytosolic nucleotide sensors

city: Philadelphia

first: Xiujie

last: Liang

state: Pennsylvania

address: 12-188 Smilow Translational Research Center, 3400 Civic Center Blvd

department: Department of Medicine

institute: University of Pennsylvania

summary: Genome-wide association studies (GWAS) have identified over 800 loci associated with kidney function, yet the specific genes, variants, and pathways involved remain elusive. By integrating kidney function GWAS, human kidney expression and methylation quantitative trait analyses, we identified Ten-Eleven Translocation (TET) DNA demethylase 2: TET2 as a novel kidney disease risk gene. Utilizing single-cell chromatin accessibility and CRISPR-based genome editing, we highlight GWAS variants that influence TET2 expression in kidney proximal tubule cells.  Experiments using kidney/tubule-specific Tet2 knockout mice indicated its protective role in cisplatin-induced acute kidney injury, as well as chronic kidney disease and fibrosis, induced by unilateral ureteral obstruction or adenine diet. Single-cell gene profiling of kidneys from Tet2 knockout mice and TET2-knock-down tubule cells revealed the altered expression of DNA damage repair and chromosome segregation genes, notably including INO80, another kidney function GWAS target gene itself. Remarkably both TET2-null and INO80-null cells exhibited an increased accumulation of micronuclei after injury, leading to the activation of cytosolic nucleotide sensor cGAS-STING. Genetic deletion of cGAS or STING in kidney tubules or pharmacological inhibition of STING protected TET2 null mice from disease development. In conclusion, our findings highlight TET2 and INO80 as key genes in the pathogenesis of kidney diseases, indicating the importance of DNA damage repair mechanisms.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: To investigatet the role of TET2 in proximal tubule cells, we generated Tet2 kncokout mice and performed UUO. We also knockdowned TET2 expression in human tubule cell line RPTEC using CRISPR.

first: Hongbo

last: Liu

first: Hailong

last: Hu

first: Jianfu

last: Zhou

first: Amin

last: Abedini

first: Andrea

last: Navarro

first: Konstantin

last: Klötzer

first: Katalin

last: Susztak


title: Testing effects of cell density on NGN2 iN transcriptom

first: Ai

last: Zhang

state: California

address: 1 DNA way

department: Neuroscience

institute: Genentech

summary: We previously established a standard protocol for NGN2 iN produciton using iP11N iPSC line. Here we aim to explore whether plating density contributes to batch-to-batch variabilities in the transcriptome. Cells were plated at high (400K/cm2) or normal (150K/cm2 densities) and cultured according to the established protocol. Day 28 neurons were harvested and total RNA extracted for bulk RNA sequencing

overall_design: 3 repeats of high density and regular density NGN2 iNs were plated in 6 well plates coated with PDL and iMatrix. Cells were maintained till differentiation day 28 before RNA extraction

first: Xiwei

last: Shan


title: Maintenance of magnesium homeostasis by NUF2 promotes protein synthesis and anaplastic thyroid cancer progression

city: Hangzhou

first: Lisha

last: Bao

address: Shangtang

institute: Zhejiang provincial people's hospital

summary: Thyroid cancer is the most frequently observed endocrine-related malignancy among which anaplastic thyroid cancer (ATC) is the most fatal subtype. The synthesis of protein is exuberant to satisfy the rapid growth of ATC tumor, but the mechanisms regulating protein synthesis are still unknown. Our research revealed that kinetochore protein NUF2 played an essential role in protein synthesis and drove the progression of ATC. The prognosis of patients with thyroid carcinoma was positively correlated with high NUF2 expression. Depletion of NUF2 in ATC cells notably inhibited the proliferation and induced apoptosis, while overexpression of NUF2 facilitated ATC cell viability and clone formation. Loss of NUF2 significantly suppressed ATC growth in both zebrafish and nude mouse models. Notably, knockdown of NUF2 epigenetically inhibited the expression of magnesium transporters through reducing the abundance of H3K4me3 at promoters, thereby reduced intracellular Mg2+ concentration. Furthermore, we found the deletion of NUF2 or magnesium transporters significantly inhibited the protein synthesis mediated by the PI3K/Akt/mTOR pathway. In conclusion, NUF2 functions as an emerging regulator for protein synthesis by maintaining the homeostasis of intracellular Mg2+, which finally drives ATC progression.

overall_design: To investigate the regulation of downstream genes by NUF2, we knocked down NUF2 with siRNA in 8505C cell line and then performed gene expression profiling analysis using data obtained from RNA-seq analysis.

first: Minghua

last: Ge


title: Platelet activating factor (PAF) promotes immunosuppressive neutrophil differentiation within tumors

city: Rochester

first: Minsoo

last: Kim

address: 601 Elmwood Ave

institute: University of Rochester

summary: Chronic inflammatory milieu in the tumor microenvironment (TME) leads to the recruitment and differentiation of myeloid-derived suppressor cells (MDSCs). Polymorphonuclear (PMN)-MDSCs, which are phenotypically and morphologically defined as a subset of neutrophils, cause major immune suppression in the TME, posing a significant challenge in the development of effective immunotherapies. Despite recent advances in our understanding of PMN-MDSC functions, the mechanism that gives rise to immunosuppressive neutrophils within the TME remains elusive. Both in vivo and in vitro, newly recruited neutrophils into the tumor sites remained activated and highly motile for several days and developed immunosuppressive phenotypes, as indicated by increased arginase 1 (Arg1) and dcTrail-R1 expression and suppressed anti-cancer CD8 T cell cytotoxicity. The strong suppressive function was successfully recapitulated by incubating naïve neutrophils with cancer cell culture supernatant in vitro. Cancer metabolite secretome analyses of the culture supernatant revealed that both murine and human cancers released lipid mediators to induce the differentiation of immunosuppressive neutrophils. Liquid chromatography–mass spectrometry (LC-MS) lipidomic analysis identified platelet activation factor (PAF; 1-O-alkyl-2-acetyl-sn-glycero-3-phosphocholine) as a common tumor-derived lipid mediator that induces neutrophil differentiation. Lysophosphatidylcholine acyltransferase 2 (LPCAT2), the PAF biosynthetic enzyme, is upregulated in human pancreatic ductal adenocarcinoma (PDAC) and shows an unfavorable correlation with patient survival across multiple cancer types. Our study identifies PAF as a novel lipid-driven mechanism of MDSC differentiation in the TME, providing a potential target for cancer immunotherapy.

overall_design: Total RNA from neutrophils were isolated using RNeasy plus mini kit (Qiagen). Total RNA was preamplified with SMARTer Ultra Low Input kit v4 per manufacturer’s protocol (Clontech). CDNA quality and quantity were measured using Qubit fluorometer (Life Technologies) and Agilent Bioanalyzer 2100. CDNA was used to generate Illumina-compatible sequencing libraries using NexteraXT library preparation kit (Illumina). The amplified libraries were hybridized to Illumina flow cell and sequenced using NextSeq 550 squener (Illumina). Reads were aligned with STAR-2.7.0 and reads quantified with Subread-1.6.4. DESeq2-1.26.0 was used to normalize count matrix and assess differential expression with adjusted Pvalue <0.05. Heatmap was created using pheatmap (1.0.12) using DESeq2-normalized counts. Heat map representations were produced using RStudio (1.3.1093) and GraphPad Prism (v10).

first: Ankit

last: Dahal


title: Claudin 7 suppresses invasion and metastasis through repression of a smooth muscle actin program

city: Baltimore

first: Junior

last: West

address: 855 N Wolfe St.

department: Cell Biology

institute: Johns Hopkins

summary: Metastasis initiates when cancer cells escape from the primary tumor, which requires changes to intercellular junctions. Claudins are transmembrane proteins that form the tight junction, and their expression is reduced in aggressive breast tumors. However, claudins’ roles during breast cancer metastasis remain unclear. We used gain- and loss-of-function genetics in organoids isolated from murine breast cancer models to establish that Cldn7 suppresses invasion and metastasis. Transcriptomic analysis revealed that Cldn7 knockdown induced smooth muscle actin (SMA)-related genes and a broader mesenchymal phenotype. We validated our results in human cell lines, fresh human tumor tissue, bulk RNA-seq, and public single cell RNA-seq data. We consistently observed an inverse relationship between Cldn7 expression and expression of SMA-related genes. Furthermore, knockdown and overexpression of SMA-related genes demonstrated that they promote breast cancer invasion. Our data reveal that Cldn7 suppresses breast cancer invasion and metastasis through negative regulation of SMA-related and mesenchymal gene expression.

overall_design:
To investigate the role of Cldn7 on invasion and metastasis, we used organoids derived from genetically engineered mouse models (GEMMs) to knockdown Cldn7 by using shRNA lentiviral particles.
To test the effect of Cldn7 depletion in invasion, we embedded Cldn7 knockdown and control organoids in 3D collagen matrices for 5 days.
After invasion for 5 days, we then performed transcriptomics analysis upon Cldn7 knockdown using RNA-Seq.

first: Rosela

last: Golloshi

first: Chae

middle: Y

last: Cho

first: Yuqian

last: Wang

first: Parker

last: Stevenson

first: Genevieve

last: Stein-O'Brien

first: Elana

last: Fertig

first: Andrew

last: Ewald


title: Transcription factor ZEB1 coordinating with NuRD complex to promote oncogenesis through glycolysis in colorectal cancer

city: beijing

first: yan

last: wang

address: 17 panjiayuan nanli, chaoyang district, Beijing, China

country: Zimbabwe

institute: National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences

summary: Background: Colorectal cancer (CRC) is an aggressive primary intestinal malignancy with the third-highest incidence and second-highest mortality among all cancer types worldwide. Transcription factors (TFs) regulate cell development and differentiation owing to their ability to recognize specific DNA sequences upstream of genes. Numerous studies have demonstrated a strong correlation between TFs, the etiology of tumors, and therapeutic approaches. Here, we aimed to explore prognosis-related TFs and comprehend their carcinogenic mechanisms, thereby offering novel insights into the diagnosis and management of CRC. Materials and methods: Differentially expressed TFs between CRC and normal tissues were identified leveraging The Cancer Genome Atlas database, Weighted correlation network analysis and Cox regression analysis were performed to identify prognosis-related TFs. The cellular functions of hub TF zinc finger E-box binding homeobox 1 (ZEB1) were determined using by 5-ethynyl-2'-deoxyuridine and cell invasion assays in CRC cells. RNA-sequencing, Kyoto Encyclopedia of Genes and Genomes enrichment, and gene set enrichment analyses were used to identify the cellular processes in which ZEB1 participates. Immunoaffinity purification, silver staining mass spectrometry, and a chromatin immunoprecipitation assay were conducted to search for proteins that might interact with ZEB1 and the target genes they jointly regulate. Results: Thirteen central TFs related to prognosis were identified through bioinformatics analysis techniques. Among these TFs, ZEB1 emerged as the TF most closely associated with CRC, as determined through a combination of regulatory network diagrams, survival curves, and phenotype analyses. ZEB1 promotes CRC cell growth by recruiting the NuRD(MTA1) complex, and the ZEB1/NuRD(MTA1) complex transcriptionally represses glycolysis-associated tumor suppressor genes. Conclusion: Our study not only identified a hub biomarker related to CRC prognosis but also revealed the specific molecular mechanisms through which ZEB1 affects cancer progression. These insights provide crucial evidence for the diagnosis of CRC and potential treatment opportunities.

overall_design: Rotal RNA from SW480 cells was isolated and purified after transfected with siControl or siZEB1 for 48h. The sample quality control and sequencing process were carried out based on the sequencing platform of ANNOROAD. The DNA sequence information was obtained by using the sequencer of Illumina. The dataset is a document in fastq format.


title: Small GTP-binding protein GDP dissociation stimulator influences cisplatin-induced acute kidney injury via PERK-dependent ER stress

city: Houston

first: Yuxue

last: Yang

state: Texas

address: 1100 Bate Ave

institute: Baylor college of medicine

summary: Cisplatin is a common anticancer drug, but its frequent nephrotoxicity limits its clinical use. Small GTP-binding protein GDP dissociation stimulator (smgGDS), a small GTPase chaperone protein, was considerably downregulated during cisplatin-induced acute kidney injury (CDDP-AKI), especially in renal tubular epithelial cells. SmgGDS-knockdown mice was established and found that smgGDS knockdown promoted CDDP-AKI, as demonstrated by an increase in serum creatine, blood urea nitrogen levels and the appearance of tubular patterns. RNA sequencing suggested that protein kinase RNA-like ER kinase (PERK), which bridges mitochondria-associated ER membranes, was involved in smgGDS knockdown following CDDP-AKI, and then identified that smgGDS knockdown increased phosphorylated-PERK in vivo and in vitro. Furthermore, we confirmed that smgGDS deficiency aggravated apoptosis and ER stress in vivo and in vitro. And the ER stress inhibitor 4-Phenylbutyric acid and the inhibition of PERK phosphorylation mitigated smgGDS deficiency-induced ER stress related apoptosis following cisplatin treatment, while the eIF2α phosphorylation inhibitor could not reverse the smgGDS deficiency accelerated cell death. Furthermore, the over-expression of smgGDS could reverse the ER stress and apoptosis caused by CDDP. Overall, smgGDS regulated PERK-dependent ER stress and apoptosis, thereby influencing renal damage. This study identified a target for diagnosing and treating cisplatin-induced acute kidney injury.

overall_design: The smgGDS-knockdown cell line was established to explore the underlying mechanism of CDDP-AKI, and shRNA targeting smgGDS produced a robust knockdown of smgGDS protein expression compared with control shRNA. For further mechanistic studies, the RNA-seq and related bioinformatics analysis were performed.


title: Metabolome and transcriptome integration reveals cerebral cortical metabolic profiles in rats with subarachnoid hemorrhage

city: Wuhan

first: haoran

last: lu

state: Hubei

address: Renmin Hospital of Wuhan University, 238 Jiefang Street

institute: wuhan university

summary: Changes of specific gene expression after subarachnoid hemorrhage

overall_design: At 1 and 7 days after the induction of subarachnoid hemorrhage model, we identified differentially expressed genes (DEGs) between sham operated and injured cortical tissues by RNA sequencing (RNA SEQ)

first: Haoran

last: Lu

first: Teng

last: Xie

first: Shanshan

last: Wei

first: Zhibiao

last: Chen

first: Rui

last: Ding


title: Late-stage tertiary lymphoid structures in hepatocellular carcinoma treated with neoadjuvant immune checkpoint blockade

city: BALTIMORE

first: Daniel

middle: H

last: Shu

state: Maryland

address: CRB1, RM 416, 1550 ORLEANS ST.

department: Oncology

institute: Johns Hopkins Sidney Kimmel Cancer Center

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

overall_design: Refer to individual Series


title: The effect of sodium thiosulfate on hyperglycemic zebrafish larvae

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

summary: We investigated the efficacy of sodium thiosulfate (STS) in treating hyperglycemia-induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor, which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hours post-fertilization (hpf). Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide (NO) signaling in zebrafish with a knocked-down pdx1 gene, both metabolomically and transcriptionally. Notably, treatment with STS led to a compensatory upregulation of NO signaling, as evidenced by preliminary metabolomic data, ultimately resulting in the rescue of the pronephros structure.

overall_design: To analyze transcriptomic adaptations to STS, RNA-seq of hyperglycemic zebrafish treated with 0 mM, 15 mM, and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1, which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tg(wt1b:EGFP) was used for experimental procedure. Next to RNA-seq analysis, a metabolomic profiling of similar experimental groups was performed.

first: Hannes

last: Ott

first: Jens

last: Kroll


title: Development and Characterization of Syngeneic Orthotopic Transplant Models of Obesity-Responsive Triple-Negative Breast Cancer in C57BL/6J Mice (in vitro)

city: chapel hill

first: michael

middle: francis

last: coleman

state: North Carolina

address: 235 dauer drive

institute: UNC

summary: To develop transplantable triple-negative breast cancer cell lines from spontaneous mammary tumors arising  C3(1)/SV40 T-antigen (C3-TAg) transgenic C57BL6 mice.

overall_design: In vitro cell culture samples from 4 distinct cell lines were analyzed (n=3/cell line)

first: Michael

last: Coleman

first: Stephen

middle: D

last: Hursting


title: Development and Characterization of Syngeneic Orthotopic Transplant Models of Obesity-Responsive Triple-Negative Breast Cancer in C57BL/6J Mice (in vivo)

overall_design: In vivo mammary tumor samples from 4 distinct cell lines were analyzed (n=4-8/cell line)


title: A scalable, spin‐free approach to generate enhanced induced pluripotent stem cell–derived natural killer cells for cancer immunotherapy

city: Woolloongabba

first: Gustavo

last: Rodrigues Rossi

state: QLD

address: 37 Kent Street

country: Australia

institute: University of Queensland

summary: Traditional sources of NK cells, such as peripheral blood, are limited by availability and donor variability. Additionally, in vitro expansion can lead to functional exhaustion and gene editing challenges. This study aims to harness iPSC technology to provide a consistent and scalable source of NK cells, overcoming the limitations of traditional sources and enhancing the potential for cancer immunotherapy applications.

overall_design: For this experiment, we compared the gene expression profiles of iPSC-derived NK cells (from the same iPSC cell line but differentiated in 4 separate batches), buffy coat-derived NK cells (from 4 donors), and cord blood unit-derived NK cells (from 4 donors) using single-cell RNA sequencing.

first: Fernando

last: Souza-Fonseca-Guimaraes


title: Deciphering the Divergent Transcriptomic Landscapes of Cervical Cancer Cells Grown in 3D and 2D Cell Culture Systems

city: Milwaukee

first: Roshan

last: Kumar

state: Wisconsin

address: 8701 W Watertown Plank Rd

department: Obstetrics & Gynecology

institute: Medical College of Wisconsin

summary: Cervical cancer remains a significant health challenge for women worldwide, with a disproportionate impact on developing regions like sub-Saharan Africa. Taking advantage of recent advancements in developing suitable preclinical models to study cell proliferation, differentiation, and gene expression, we used RNA sequencing to compare the transcriptomic profiles of SiHa cervical cancer cells grown in 3D versus 2D culture systems.

overall_design: For SiHa cells, the culture conditions involved using DMEM supplemented with 10% FBS. For 2D culture experiments, 5 ml of SiHa cells at a concentration of 2 x 10^5 cells/ml were seeded into 10 cm dishes and overlaid with an additional 5 ml of their respective growth media. For 3D cultures, 5000 SiHa cells were seeded in each well of a 96-well Nunclon Sphera, U-bottom plate (ThermoFisher), then centrifuged at 70 × g for 5 min before placing in the incubator. Media replacement was performed every 2-3 days, and spheroid formation was monitored for 7-9 days. The 2D monolayer cultures for SiHa included 3 distinct cell passages, with 2 replicates per passage. The 2D biological replicates were generated in 2 separate batches: passage 1 replicates (2D_P1_R1, 2D_P1_R2) in Batch 1 and passage 2 and 3 replicates (2D_P2_R1, 2D_P2_R2, 2D_P3_R1, 2D_P3_R2) in Batch 2. For 3D spheroid SiHa cultures, 3 biological replicate samples were generated (3D_R1, 3D_R2, 3D_R3) separately.

first: Marissa

last: Iden

first: Shirng-Wern

last: Tsaih

first: Rachel

last: Schmidt

first: Akinyemi

middle: I

last: Ojesina

first: Janet

last: Rader


title: Transcriptome analysis by total RNA sequencing of Cereibacter sphaeroides RNase E, RNase III or StsR mutant strains grown to stationary phase

city: Gießen

first: Gabriele

last: Klug

address: Heinrich-Buff-Ring 26-32

department: Molecular- and Microbiology

institute: Justus-Liebig University Gießen

summary: In this study we analyzed the effects of reduced RNase E activity, lacking RNase III activity or chromosomal deletion of the sRNA StsR on the transcriptome of Cereibacter sphaeroides. Samples for total RNA sequencing were collected during exponential and late stationary growth phase (72 hours) under microaerobic or phototrophic condtions. Transcriptome profiles were compared to corresponding wild type controls.

overall_design: Comparative gene expression profiling analysis of RNA-seq data of independent biological triplicates of Cereibacter sphaeroides strains, grown either under microaerobic or phototrophic conditions to exponential or stationary phase.

first: Janek

last: Börner

first: Patrick

last: Blumenkamp


title: Polyploid cancer cells reveal signatures of chemotherapy relapse [scDNA-seq]

city: LOS ANGELES

first: Michaek

middle: James

state: CA

address: 1002 Childs Way

department: Cancer Biology and Genomics

institute: University of Southern California

type: Genome variation profiling by high throughput sequencing

summary: Treatment of PC3 and MDA-MB-231 cell lines with sublethal doses of docetaxel or cisplatin in vitro resulted in induction of polyploid cancer cells. Single cell copy number profiling was conducted to understand resistance of polyploid cancer cells to chemotherapy.

overall_design: Cells were treated with chemotherapy and allowed to recovery for 1 or 10 days in regular medium (days post treatment - DPT)

middle: J


title: Late-stage tertiary lymphoid structures in hepatocellular carcinoma treated with neoadjuvant immune checkpoint blockade [bulk RNA-seq]

first: Daniel

last: Shu

summary: Tertiary lymphoid structures (TLS) are associated with improved response in solid tumors treated with immune checkpoint blockade (ICB), but understanding of their clinical significance and the circumstances of their resolution remains incomplete. Here, we found that in hepatocellular carcinoma (HCC) treated with neoadjuvant immunotherapy, high intratumoral TLS density at the time of surgery is associated with pathologic response and improved relapse free survival. In areas of tumor regression, we further identified a non-canonical involuted morphology of TLS marked by dispersion of the B cell follicle, persistence of a T cell zone enriched for T cell-mature dendritic cell interactions, and increased expression of T cell memory markers. Collectively, these data suggest that TLS may serve be both a prognostic and predictive marker of response to immunotherapy in HCC and suggest a functional role for late-stage TLS T cell memory formation after elimination of viable tumor.

overall_design:
We utilized surgical resection specimens and peripheral blood obtained from patients with locally advanced hepatocellular carcinoma receiving neoadjuvant immune checkpoint blockade based therapy. Bulk RNA sequencing was performed on post-treatment tumor resection specimens to characterize differences in gene expression between tumors with high and low density of tertiary lymphoid structures. Tumor associated tertiary lymphoid structures were microdissected and subjected to bulk TCR and BCR sequencing using the Adaptive Biotechnologies ImmunoSEQ platform (shared separately). Single cell RNA, TCR, and BCR sequencing was performed on matched peripheral blood and tumor specimens to infer the identity of T and B cells identified in tertiary lymphoid structures.

*** Submitters state that raw data is being submitted to dbGap (phs003672.v1.p1)***

first: Mark

last: Yarchoan


title: Late-stage tertiary lymphoid structures in hepatocellular carcinoma treated with neoadjuvant immune checkpoint blockade [scRNA-seq]


title: Acetylcytidine modification of DDX41 and ZNF746 by N-acetyltransferase 10 contributes to chemoresistance of melanoma

city: Yuxi

first: Zuohui

last: Liang

state: --- Select One ---

address: No. 21 Nieer Rd, Yuxi, Yunan

institute: The People’s Hospital of Yuxi City

summary: We performed RNA-seq to analyse the different expression genes of DTIC-resistant (DR) A375 cells and wild-type control.

overall_design: Examination of differentially expressed genes in DR A375 cells compared with wild-type control.

first: Li

last: Wang

first: Yuefen

last: Zeng


title: Bulk RNA-seq analysis of HepG2 exposed to oleic and palmitic acid

city: Antwerpen

first: Cédric

last: Peleman

address: Universiteitsplein 1

country: Belgium

institute: University of Antwerp

summary: We hypothesized that exposure to fatty acids in metabolic dysfunction-associated steatohepatitis-like environment will profoundly affect gene expression of hepatocytes. More precisely, we wish to investigate expression of genes related to ferroptosis, i.e. an iron-catalyzed form of cell death through lethal lipid peroxidation.

overall_design: We aimed to study the effect of fatty acid supplementation in a metabolic dysfunction-associated steatohepatitis-like environment on gene expression of HepG2 cells profiled with bulk mRNA-sequencing. HepG2 cells were exposed for 48 hours to oleic acid (100microM) and palmitic acid (50microM), as well as hyperglycemia (4.5 mg/mL), hyperinsulinemia (100 nM), tumor necrosis factor alpha (50 ng/mL), interleukin 1-beta (25 ng/mL) and transforming growth factor-beta (8ng/mL). Control samples were exposed to solvents needed to dissolve oleic acid and palmitic acid in medium.


title: Effect of breed and dietary composition on the miRNA profile of beef steers divergent for feed efficiency

city: Co. Meath

first: Kate

last: Keogh

address: Dunsany

department: Animal and Bioscience Department

country: Ireland

institute: Teagasc Grange

summary: The aim of this study was to measure the effect of contrasting breed and dietary source on the skeletal muscle miRNA profile of beef cattle divergent for feed efficiency (RFI). Charolais (n=90) and Holstein-Fresian (N=77) steers) were offered two consecutive diets; namely a zero-grazed grass diet followed by a high concentrate diet. Dietary intakes were recorded for all steers throughout each dietary phase and residual feed intake values dertermined for each steer. At the end of each dietary phase the most efficient (Low-RFI; n=8) and least efficient (High-RFI; n=8) steers were selected across each breed for longissmus dorsi biopsy collection. RNA was isolated from all muscle tissue samples and subsequently used for small RNA sequencing. Ten miRNA were differentially expressed between the steers divergent for RFI across each diet and breed contrast. Biological pathway analyssi revealed enrichment of pathways related to both metabolic and growth processes.

overall_design: In total 64 RNA samples were analysed, 8 from each High- or Low-RFI group across each breed and dietary phase. During the first dietary phase the steers received a zero grazed grass diet, whilst during the subsequent phase all steers received a high concentrate diet. Tissue samples were collected from the steers divergent for RFI within each breed at the end of each dietary phase.

last: McGee

first: David

last: Kenny


title: H3K4me3 and H3K9me3 histone modification profiles of uterine stromal cells from young and aged mouse females

city: Calgary

first: Myriam

last: Hemberger

state: Alberta

address: 3330 Hospital Dr NW

country: Canada

institute: University of Calgary

summary: Epigenetic profiling of uterine stromal cells (UtSCs) was performed for the active and repressive histone modifications H3K4me3 and H3K9me3, respectively. We find that UtSCs from aged females are epigenetically distinct, as determined by genomic enrichment profiling for H3K4me3 and H3K9me3, respectively. We find that many pregnancy hormone-inducible genes exhibit a profound lack of promoter-associated H3K4me3 in aged UtSCs, implying that a significant enrichment of active histone marks prior to gene stimulation is required to enable the elicitation of a rapid transcriptional response.

overall_design: Uterine stromal cells (UtSCs) were isolated from C57BL/6Babr females aged 8-12 weeks (“Young”) and 43-54 weeks (“Aged”) at E3.5 of pregnancy. Up until this point, all females were virgin. 200,00 UtSCs were processed for chromatin immunoprecipitation (ChIP) with antibodies against histone modifications H3K4me3 and H3K9me3. 10% of chromatin prior to ChIP was kept as Input. Input and ChIP DNA was used for library build with the NEBNext Ultra II DNA library prep kit (Illumina E7645). Indexed libraries were pooled and sequenced on an Illumina HiSeq2500 sequencer, using a 50bp paired-end protocol. Raw fastq data were mapped to the Mus musculus GRCm38 genome assembly using Bowtie2.

first: Laura

last: Woods

first: Wendy

last: Dean


title: Polyploid cancer cells reveal signatures of chemotherapy relapse [scRNA-seq]

last: Schmidt

summary: Treatment of PC3 and MDA-MB-231 cell lines with sublethal doses of docetaxel or cisplatin in vitro resulted in induction of polyploid cancer cells. Single cell copy RNA-sequencing was conducted to understand resistance of polyploid cancer cells to chemotherapy.

first: Michael


title: Where Does the Heme Go? Unraveling Heme and Porphyrin Metabolism in Healthy and Oncogenic Human Livers

city: Tampa

first: Rays HY

last: Jiang

state: FL

address: 3720 Spectrum Blvd, Suite 304

department: Department of Global Health

institute: University of South Florida

summary: The liver, a pivotal organ in human metabolism, serves as a primary site for heme biosynthesis, critical for detoxification and drug metabolism. Maintaining precise control over heme production is paramount in healthy livers to meet high metabolic demands while averting potential toxicity from intermediate metabolites, notably protoporphyrin IX. Intriguingly, our recent research uncovers a disrupted heme biosynthesis process termed 'Porphyrin Overdrive' in cancers, fostering the accumulation of heme intermediates, potentially bolstering tumor survival. Here, we investigate heme and porphyrin metabolism in both healthy and oncogenic human livers, utilizing primary human liver transcriptomics and single-cell RNA sequencing (scRNAseq). Our investigations unveil robust gene expression patterns in heme biosynthesis in healthy livers, supporting electron transport chain (ETC) and cytochrome P450 function, devoid of intermediate accumulation. Conversely, liver cancers exhibit impaired heme biosynthesis and massive downregulation of cytochrome P450 expression. Notably, despite diminished drug metabolism, heme supply to the ETC remains largely unaltered or even elevated with cancer progression, suggesting a metabolic priority shift. Liver cancers selectively accumulate intermediates, absent in normal tissues, implicating their role in disease advancement as inferred by expression. Furthermore, our findings establish a link between diminished drug metabolism, augmented ETC function, porphyrin accumulation, and inferior overall survival in aggressive cancers, indicating potential targets for clinical therapy development.

overall_design: Single-cell RNA sequencing (scRNAseq) was conducted on primary human liver cell populations obtained from the healthy donor UBV. The mixture of hepatic cell populations were carefully washed in Dulbecco's phosphate-buffered saline (DPBS, 1X; Corning, Cat No. 21-031-CV) and resuspended at a concentration of 10^6 cells/mL to prevent cell aggregates. The scRNAseq protocol utilized the 10x Genomics Chromium controller and the Chromium single-cell 3’ library and gel bead kit (10x Genomics, Cat No. PN-1000075) following the standard manufacturer's protocols. Briefly, gel beads-in-emulsion (GEMs) were generated by combining barcoded single-cell 3’ v3 gel beads, a master mix containing cells, and partitioning oil onto Chromium chip B. Cells were delivered at a limiting dilution to achieve single-cell resolution, with the majority (~ 90–99%) of generated GEMs containing no cells. Between 2,000–21,000 live cells were loaded onto the Chromium controller to recover between 1,500 − 15,000 cells for library preparation and sequencing. Following GEM generation, the gel beads were dissolved, primers were released, and any co-partitioned cells were lysed.   An Illumina TruSeq Read 1, 16 nt 10x barcode, 12 nt unique molecular identifier (UMI), and 30 nt poly(dT) sequence were mixed with the cell lysate and a master mix containing reverse transcription (RT) reagents. Incubation of the GEMs produced barcoded, full-length cDNAs from poly-adenylated mRNAs. Subsequently, GEMs were broken, and cDNA was amplified and quantified using an Agilent high sensitivity DNA screentape. SPRIselect magnetic beads were used to purify the first-strand cDNA, followed by PCR amplification to generate sufficient mass for library construction. Enzymatic fragmentation and size selection optimized the cDNA amplicon size, with TruSeq Read 1 added during GEM incubation. P5, P7, a sample index, and TruSeq Read 2 were added via end repair, A-tailing, adaptor ligation, and PCR. Library quality was assessed using an Agilent Bioanalyzer high sensitivity chip. Sequencing was performed on the Illumina NextSeq 550 with a target of 150,000 reads/cell. Data processing, sample demultiplexing, and gene expression quantification were performed using the Cell Ranger Single-Cell software Suite (10x Genomics). Genes with more than one unique molecular identifier (UMI) count were considered for analysis. The top 1000 most variably expressed genes were used for clustering, and t-Distributed Stochastic Neighbor Embedding (t-SNE) analysis was employed to reduce data dimensionality. K-means clustering identified cell populations, with cell classification based on Spearman’s correlation of mean expression profiles.

first: Rakesh

last: Adapa Swamy

first: Rays


title: FUS-mediated inhibition of myogenesis by suppressing TNNT1 production [RIP-seq]

first: Supriyo

last: De

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

summary: Myogenesis is a highly orchestrated process whereby muscle precursor cells, myoblasts, develop into muscle fibers to form skeletal muscle during embryogenesis and regenerate adult muscle.  Here, we studied the RNA-binding protein FUS (fused in sarcoma), which has been implicated in muscular and neuromuscular pathologies but is poorly characterized in myogenesis.  Given that FUS levels declined in human and mouse models of skeletal myogenesis, and that silencing FUS enhanced myogenesis, we hypothesized that FUS might be a repressor of myogenic differentiation.  Interestingly, overexpression of FUS delayed myogenesis, accompanied by slower production of muscle differentiation markers.  To identify the mechanisms through which FUS inhibits myogenesis, we uncovered RNA targets of FUS by ribonucleoprotein immunoprecipitation (RIP) followed by RNA-sequencing (RNA-seq) analysis.  Stringent selection of the bound transcripts uncovered Tnnt1 mRNA, encoding troponin T (TNNT1), as a major effector of FUS influence on myogenesis.  We found that in myoblasts, FUS sequestered Tnnt1 mRNA in the nucleus, preventing TNNT1 expression; however, reduction of FUS during myogenesis or by silencing FUS released Tnnt1 mRNA for export to the cytoplasm, where it accumulated and was translated into TNNT1, promoting myogenesis.  We propose that FUS inhibits myogenesis by suppressing TNNT1 expression through a mechanism of nuclear mRNA retention.

overall_design: Profiling of RNAs interaction with FUS by performing a FUS immunoprecipitation followed by the isolation and sequencing of the bound RNAs (RIP-Seq).

first: Eunbyul

last: Ji

first: Poonam

middle: R

last: Pandey

first: Jennifer

middle: L

last: Martindale

first: Xiaoling

last: Yang

first: Jen-Hao

first: Dimitrios

last: Tsitsipatis

first: Chang

last: Shin

first: Yulan

last: Piao

first: Jinshui

last: Fan

first: Krystyna

last: Mazan-Mamczarz

first: Nirad

last: Banskota

last: Gorospe


title: Dopamine D2 receptor activation inhibits choroidal neovascularization in Parkinson patients with age related macular degeneration.

city: Paris

first: Frederic

last: Blond

address: 17 rue Moreau

country: France

institute: Institut de la Vision

summary: Neovascular age-related macular degeneration (nAMD) remains a major cause of visual impairment and puts considerable burden on patients and health care systems. L-DOPA-treated Parkinson Disease (PD) patients have been shown to be partially protected from nAMD, but the mechanism remains unknown. Using murine models combining 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-induced PD and laser-induced nAMD, standard PD treatment of L-DOPA/DOPA-decarboxylase inhibitor, or specific dopamine receptor inhibitors, we here demonstrate that L-DOPA treatment-induced increase of dopamine receptor D2 (DRD2) signaling inhibits choroidal neovascularization independently of MPTP-associated nigrostriatal pathway lesion. Analyzing a retrospective cohort of more than two hundred thousand nAMD patients receiving anti-VEGF treatment from the French nationwide insurance database, we show that DRD2-agonist treated (PD) patients have a significantly delayed age of onset for nAMD (81.4 (±7.0) vs 79.4 (±8.1) years old, respectively, p<0.0001) and reduced need for anti-VEGF therapies (-0.6 injections per 100 mg/day daily dose of DRD2 agonists the second year of treatment), similar to the L-DOPA treatment. While providing a mechanistic explanation for an intriguing epidemiological observation, our findings suggest that systemic DRD2 agonists might constitute an adjuvant therapy to delay and reduce the need for anti-VEGF therapy in nAMD patients.

overall_design: To gain insight into the transcriptionnal modification induced by dopanime in endothelial cells, we cultured choroidal explants for 3 days and then stimulated them with 1µM dopamine. After 24 hours, choroidal explants were collected and dissociated with collagenase. Two hundred CD31+CD11b- cells were sorted on a BD FACS melody. RNA-seq libraries were prepared using the Smartseq V4 kit from Takara.

first: Frédéric

first: Xavier

last: Guillonneau

first: Cécile

last: Delarasse

first: Thibaud

last: Mathis

first: Florian

last: Sennlaub


title: Effect of insulin on miRNA abundance in 3T3-L1 adipocytes and their secreted sEVs.

city: Boston

first: Hui

last: Pan

address: 1 Joslin Place

department: Bioinformatics and Biostatistics Core

institute: Joslin Diabetes Center

summary: Adipocytes are a major source of secreted small extracellular vesicles (sEVs), which carry various cargo including small non-coding RNAs (smRNAs) and miRNAs to distal cells. Several miRNAs have been implicated in obesity and insulin resistance, and since they function like adipokines, we sought to assess whether insulin can regulate their secretion into sEVs from adipocytes.

overall_design: To this end, 3T3-L1 cells were differentiated using standard procedures, and following a washout period with no insulin, were stimulated with insulin (or PBS for control) for 48 hours to allow for accumulation of sEVs in the media. sEVs were isolated by ultracentrifugation and sEV and cellular RNA was isolated by trizol chloroform and prepared for sequencing by smRNAseq.

first: Marsel

last: Lino

first: Ruben

last: Garcia-Martin

first: C

last: Kahn


title: Role of Retinol Saturase (RetSat) in brown adipose tissue (BAT).

city: Berlin

first: Michael

last: Schupp

address: Hessische Str. 3-4

department: Institute of Pharmacology

institute: Charite Universitätsmedizin Berlin

summary: This study investigates the transcriptional consequences of genetic RetSat deletion in BAT.

overall_design: Male C57BL/6J mice with floxed RetSat alleles with (Cre+) or without (Cre-) Ucp1-Cre were analyzed at an age of 12-14 weeks. Total RNA from BAT was isolated and RNA was DNAse digested and profiled by RNAseq.

first: Chen

last: Li

first: Sascha

last: Wulff


title: Exploring maternal and developmental toxicity of perfluoroalkyl ether acids PFO4DA and PFO5DoA using hepatic transcriptomics and serum metabolomics

city: Research Triangle Park

first: Thomas

last: Jackson

state: NC

address: 109 TW Alexander Dr

department: CPHEA

institute: United States Environmental Protection Agency

summary: Production of PFAS has shifted from the most-studied PFAS, longer-chain perfluorinated alkyl acids, to shorter-chain or other alternative moieties including fluoroethers like HFPO-DA (“GenX chemicals”), Nafion Byproducts, and the PFOx homologous series that includes PFO4DA and PFO5DoA.  In contaminated study areas, the fluoroethers PFO4DA and PFO5DoA, although detected at relatively low levels in surface water, have been detected in serum and/or tissues with high frequency in humans, wildlife including fish and alligators, and pets including horses. Although these compounds have been detected, there are extremely limited toxicity data available and no developmental toxicology studies that could be used to inform risk assessment or regulatory actions. To address these data gaps, Sprague-Dawley rat dams were exposed via oral gavage from GD18-22 to PFO4DA or PFO5DoA across a series of doses ranging from 0.1 to 62.5 mg/kg/day and, in conjunction with apical measures of toxicity, hepatic transcriptomics in both dam and offspring and serum metabolomics in dams were performed. Differential expression analysis was performed for transcriptomics and metabolomics, and pathway analysis, including a multi-omic integrative analysis, was performed. For PFO5DoA, overt toxicity (substantial body weight loss, fetal mortality) was observed at the highest dose, so data only include up to 30 mg/kg/day. Dimensionality reduction measures including principal components analysis and heatmaps revealed strong separation of clustering between maternal and fetal samples and between chemicals (PFO4DA vs PFO5DoA). Both dams and fetuses exhibited dose-responsive patterns of hepatic gene expression in response to PFO4DA or PFO5DoA. Of the 14,928 genes included in differential expression analysis, PFO4DA exposure in dams resulted in a maximum of 367 differentially expressed genes (DEG) at the highest dose (62.5 mg/kg/d) whereas PFO5DoA resulted in 4,506 DEG at the highest dose (30 mg/kg/d). Even at 10 mg/kg/d, PFO5DoA resulted in 1,915 DEG in dam liver. Fetuses were more affected at lower doses, but the pattern was similar, with PFO4DA resulting in 1,378 DEG at 62.5 mg/kg/d and PFO5DoA 3,653 DEG at 30 mg/kg/d. Several DEG were changed by every dose of PFO5DoA (≥ 0.3 mg/kg/d) in both maternal and fetal samples, including multiple acyl-coA thioesterases (Acot1, Acot2, Acot3, Acot4) and related enzymes that hydrolyze acyl-coA to free fatty acids, as well as Vnn1, a corticosteroid-responsive gene. Hallmark and Reactome pathway analyses of fetal and maternal livers revealed remarkable changes in metabolism of bile acids and salts, fatty acid metabolism, metabolism of lipids and lipoproteins, PPARα activation of gene expression, and phospholipid metabolism. In maternal serum metabolomics, PFO4DA did not result in significant changes at doses up to 62.5 mg/kg/d. In contrast, PFO5DoA exposure resulted in differential metabolite abundance for 149 unique metabolites, with 4 significantly altered at 0.3 mg/kg, 31 metabolites at 1 mg/kg, 51 at 3 mg/kg, 58 at 10mg/kg, and 119 at 30 mg/kg/d. Multi-omics KEGG and Reactome pathway analyses of integrated maternal liver transcriptomics and serum metabolomics revealed significant convergent pathway-level changes as low as 3 mg/kg/d PFO4DA and 0.3 mg/kg/d PFO5DoA exposure. Notable multi-omics pathway level changes include fatty acid metabolism at all doses of PFO5DoA and at PFO4DA ≥ 10 mg/kg/d, with PFO4DA changes driven by the magnitude of transcriptomic changes and low/null detection of metabolites. Striking pathway-level changes identified for hepatic transcriptome and serum metabolome in exposed dams included metabolism, metabolism of lipids, hemostasis, signaling by G-protein coupled receptors (GPCRs), neuronal system, immune and innate immune system, PPARα activation of gene expression, and regulation of lipid metabolism by PPARα. The transcriptomic and metabolomic effects of PFO4DA and PFO5DoA appear consistent with other carboxylic acid PFAS, with primary changes related to lipid metabolism, bile acids, cholesterol, and cellular stress. Although PFO4DA and PFO5DoA are structurally similar, separated by only a CF2O, the potency of transcriptomic and metabolomic effects of developmental exposure to each was significantly different, with 5-day exposure to PFO5DoA causing changes in glucose and lipid metabolism and stress signals at much lower doses than PFO4DA in both dams (~ 35-fold more potent at inducing hepatic DEG) and fetuses (~ 11.6-fold more potent at inducing hepatic DEG). Although it is likely that some differences in toxicity between PFO4DA and PFO5DoA are caused by accumulation differences resulting in different dosimetry, PFO5DoA demonstrated much greater transcriptomic and metabolomic toxicity at equivalent oral doses.

overall_design: To explore the maternal and fetal toxicity of two fluoroether carboxylic acids, PFO4DA and PFO5DoA, we exposed pregnant Sprague-Dawley rat dams from GD18-GD22 to multiple doses of either PFAS chemical and collected maternal and fetal livers for TempO-sequencing. We compared dose-responsive gene expression changes in the livers following 5-day exposure.

first: Christy

middle: S

last: Lambright

first: Nicola

last: Evans

first: Leah

middle: C

last: Wehmas

first: Denise

last: MacMilan

first: Jacqueline

last: Bangma

first: Earl

last: Gray

first: Justin

middle: M

last: Conley


city: South San Francisco

first: Ai

last: Zhang

address: 1 DNA way

institute: Genentech

summary: This bulk RNAseq dataset is part of a dataset described in the manuscript titled "Fully defined NGN2 neuron protocol reveals diverse signatures of neuronal maturation". This dataset includes NPC derived neurons using a wild type iPSC line, and was used to validate a MS-117 maturation score which attempt to establish a socre system to assess neuronal maturation with iPSCs derived neurons.

overall_design: Three technical replicates were included, and cells were profiled at the NPC stage, as well as cultures undergo neuronal differentiation and maturation at 4 weeks, weeks and 12 weeks upon the induction of terminal differentiation.

first: Xiwei

last: Shan

first: Yingjie


title: FUS-mediated inhibition of myogenesis by suppressing TNNT1 production [RNA-seq]

city: Baltimore

first: Supriyo

last: De

overall_design: Diifferentiation of mouse C2C12 myoblasts after silencing FUS

first: Eunbyul

last: Ji

first: Poonam

last: Pandey

first: Jennifer

last: Martindale

first: Xiaoling

last: Yang

first: Jen-Hao

first: Dimitrios

last: Tsitsipatis

first: Chang

last: Shin

first: Yulan

last: Piao

first: Jinshui

last: Fan

first: Krystyna

last: Mazan-Mamczarz

first: Nirad

last: Banskota

first: Myriam

last: Gorospe


title: Low-input bulk RNA sequencing of Drosophila nephrocytes

first: Hangnoh

middle: Joseph

last: Lee

state: MD

address: 670 W Baltimore St

institute: University of Maryland School of Medicine

summary: To validate the applicability of pre-amplified low-input RNA sequencing method in Drosophila melanogaster cell types, we used Drosophila nephrocytes as an example case.

overall_design: We dissected Drosophila nephrocytes from adult animals to obtain 100 to 200 nephrocytes. We isolated total RNA using a low-input cDNA pre-amplification kit and then performed RNA sequencing on an Illumina-based platform.

first: Jin-Gu

first: Yunpo

last: Zhao

first: Jianli

last: Duan

first: Zhe

last: Han


title: ALKBH5-mediated m6A demethylation ameliorates extracellular matrix deposition in cutaneous pathological fibrosis [meRIP-seq]

city: Shanghai, China

first: Ruoqing

last: Xu

address: Department of Plastic and Reconstructive Surgery, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, 639 Zhizaoju Road, Shanghai, P.R. China

institute: Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine.

type: Methylation profiling by high throughput sequencing

summary: Hypertrophic scars (HTS) are fibrotic skin disorders characterized by excessive deposition of dermal extracellular matrix (ECM), presenting significant challenges in clinical management despite incomplete understanding of their underlying mechanisms. Using MeRIP-seq and RNA-seq, our study initially revealed the direct regulatory role of ALKBH5 on ECM components in dermal fibroblasts, thereby involving in the pathogenesis of HTS.

overall_design: RNA was obtained from human dermal fibroblasts (HDF) with or without ALKBH5 knockdown. Biological replicates were included.

first: Yixuan

first: Tao

last: Zan


title: CUT&Tag assay for ATF4 in C57BL/6 primarily cultured neurons.

city: Shanghai

first: Yikui

last: Liu

address: No. 197 Ruijin 2nd Road, Huangpu District, Shanghai

institute: Ruijin Hospital, Shanghai Jiao Tong University School of Medicine

summary: To elucidate the biological role of ATF4 in regulating downstream target genes, we conducted a CUT&Tag assay in primarily cultured neurons.

overall_design: Subsequently, CUT&Tag assay analysis was conducted, revealing the modulation of downstream target genes.

first: Liuguan

last: Bian


title: Effect of hemin on gene expression of C57BL/6 primarily cultured neurons

summary: To investigate the effects of hemin on primary cultured neurons, we established hemin-treated primary cultured neurons.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for normal primary cultured neurons and its hemin-treated primary cultured neurons.


title: Effect of depletion of SHMT2, MTHFD2, and ALDH1L2 on gene expression of C57BL/6 primarily cultured neurons

summary: To investigate the effects of SHMT2, MTHFD2 or ALDH1L2 on primary cultured neurons, we established primary cultured neurons with each target gene knocked down by shRNA.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for primary cultured neurons and its KD derivatives (shSHMT2, shMTHFD2, and shALDH1L2).


title: Impact of the Multiple Sclerosis associated genetic variant CD226 Gly307Ser on human CD8 T cell functions

city: Toulouse

first: Jean-Charles

last: Guery

address: CHU Purpan – BP 3028

institute: INSERM

summary: Background and Objectives: The rs763361 non-synonymous (Gly307Ser) variant in the CD226 gene has been identified as a risk factor for several immune-mediated diseases, including multiple sclerosis (MS). Compelling evidence suggests that this allele may be one of the genetic driving forces contributing to suceptibility to MS by decreasing the immune-regulatory capacity of Treg cells and increasing the pro-inflammatory potential of CD4 T cells. However, the impact of this CD gene variant on CD8 T cell functions, a population that also plays a key role in MS, remain T to be determined. Methods: In order to study whether the CD226 risk variant affects human CD8 T cells functions, we used CD8 T cells isolated from PBMC of 16-age matched healthy donors homozygous for either the protective or risk allele of CD226. We characterized these CD8 T cells upon TCR stimulation using high-parametric flow cytometry, bulk RNAseq, and through characterization of canonical signaling pathways and cytokine production. Results: Upon TCR engagment, the phenotype of ex vivo CD8 T cells bearing the protective (CD226-307Gly) or the risk (CD226-307Ser) allele of CD226 was largely overlapping. However, transcriptomic signature of CD8 T cells from the donor carrying the risk allele presented an enrichment in TCR, JAK/STAT and INFg signaling.

overall_design:
Peripheral blood mononuclear leukocytes (PBMCs) were purified from buffy coat preparations obtained from consenting healthy blood donors. PBMCs were prepared by gradient centrifugation of buffy coats and kept in frozen in liquid nitrogen. Genotyping of the CD226 SNP rs763361 was performed using TaqMan SNP Genotyping assay. rs763361T expressing CD226-307Ser represented the risk allele, whereas rs763361C expressing CD226-307Gly represented the protective allele. Experiments were performed on cells form male donors homozygous for either allele.
Frozen PBMCs were thawed, monocytes removed by plastic adherence and CD8 T cells were purified by negative selection. The percentage of residual CD4 T cells after depletion was always  less than 0.5% and the remaining populations consisted of 95-98% CD8 T cells.
FACS-sorted CD3+CD8+ T cells from healthy donors homozygous for either the protective (CD226-307Gly, N = 10) or risk allele (CD226-307Ser, N = 10) cultured in complete medium RPMI and stimulated with anti-CD3 and anti-CD28 monoclonal antibodies for 0h, 4h and 24h were subjected to RNA extraction using RNeasy Micro Kit. Paired-end (2x150pb) sequencing libraries were prepared using  Illumina’s Stranded Total RNA prep kit starting from 7,5ng of total RNA using 14 PCR cycles for library amplification. Sequencing libraries were indexed using IDT Illumina UDI A Lig 96 indexes 96 Sp1. RNA sequencing was performed on one S4 lane on an Illumina Novaseq 6000 sequencer using Novaseq 6000 S4 1v5 Reagent Kit (300 cycles) yielding between 20 and 40 millions raw paired-end reads per library.

first: Elena

last: Morandi

first: Veronique

last: Adoue

first: Isabelle

last: Bernard

first: Ekaterina

last: Friebel

first: Nicolas

last: Nunez

first: Yann

last: Aubert

first: Frédérick

last: Masson

first: Anne

last: Dejean

first: Burkhard

last: Becher

last: Astier

first: Ludovic

last: Martinet

first: Abdelhadi

last: Saoudi


title: Joint single-cell genetic and transcriptomic analysis reveal embedded premalignant subclones and progressive cell states in human neuroblastoma

first: Shenglin

last: Mei

state: MA

address: 10 Shattuck Street

institute: Harvard medical school (DMBI)

summary: Neuroblastoma is a heterogeneous embryonal malignancy and the deadliest tumor of infancy. While its exact origin is still under debate, it is assumed to arise from the multipotent neural crest. To understand the origin and clonal development of various neuroblastoma cell states, we analyzed human tumor samples using single-cell multi-omics, including joint DNA/RNA sequencing of sorted single cells (DNTR-seq). Tumor subclones showed considerable inter- individual variation in terms of copy number profiles and transcriptional phenotype. Despite this heterogeneity, transcriptional plasticity between subclones converges on cellular processes related to axon guidance via the SLIT/ROBO pathway, proliferation, and differentiation. Genomic heterogeneity was also observed for MYCN. Subclones harboring 2p/MYCN gain (< 8 copies) co-exist with amplified subclones (> 20 copies), indicating that MYCN amplification may represent a non-initiating genomic event. Beyond adrenergic heterogeneity, we identify a subpopulation of abnormal cells resembling multipotent Schwann cell precursors, characterized by expression programs of proliferation, apoptosis, and a non- immunomodulatory phenotype. Their genomic profile and phylogeny suggest an ancestral, pre-malignant role in tumorigenesis. While the function of these SCP-like cells in tumor initiation remains to be established, their identification expands the reservoir of tumor cells, considering their multipotency reflecting a central neuroblastoma feature.

overall_design:
we analyzed human tumor samples using single-cell multi-omics, including joint DNA/RNA sequencing of sorted single cells (DNTR-seq).

Submitter(s) state that the raw data for the THA* samples will be uploaded to EGA.

first: Ninib

last: Baryawno


title: Graph transformer guided synthetic lethality prediction

city: Columbus

first: Birkan

last: Gokbag

state: Ohio

address: 281 W Lane Ave

department: Department of Biomedical Informatics

institute: The Ohio State University

summary: Synthetic lethality (SL) has shown great promise for the discovery of novel targets in cancer. CRISPR double-knockout (CDKO) technologies can only screen several hundred genes and their combinations, but not genome-wide. Therefore, good SL prediction models are highly needed for genes and gene pairs selection in CDKO experiments. In this paper, we develop a novel multi-layer encoder for individual sample-specific SL prediction (MLEC-iSL). Unlike existing SL prediction models, MLEC-iSL is built to predict SL connectivity first. Because SL connectivity is scalable from existing genes in the training data to new genes in validation data, we hypothesize MLEC-iSL has better SL prediction performance. MLEC-iSL has three encoders, namely gene encoder, graph encoder, and transformer encoder. MLEC-iSL has high performance in K562 (AUPR, 0.73; AUC, 0.72) and Jurkat (AUPR, 0.73; AUC, 0.71) cells while no existing methods exceed 0.62 AUPR and AUC in either cell. MLEC-iSL guided CDKO experiment in 22Rv1 cells yielded a 46.8% SL ratio amongst its selected gene pairs. Six of top ten SL connectivity hub genes are validated in 22Rv1 cells. It reveals SL gene pairs and dependency between apoptosis and mitosis cell death pathways.

overall_design: CRISPR-Cas9 double knockout (CDKO) experiments were carried out in triplicate. A total of seven samples were sequenced in this study: library sample (not used in analysis), three initial timepoint samples (T0 A-C), and three final timepoint samples (TEnd A-C).

first: Kunjie

last: Fan

last: Gökbağ

first: Shan

last: Tang

first: Shangjia

last: Li

first: Yirui

last: Huang

first: Lingling

last: Wang

first: Lijun

last: Cheng

first: Lang


title: ALKBH5-mediated m6A demethylation ameliorates extracellular matrix deposition in cutaneous pathological fibrosis

first: Ruoqing

last: Xu

department: Department of Plastic and Reconstructive Surgery

overall_design: RNA was obtained from primary human dermal fibroblasts (HDF) with or without ALKBH5 knockdown. Biological replicates were included.

first: Yixuan

last: Zhao

first: Tao

last: Zan


title: Tumor-reactive T cell clonotype dynamics underlying clinical response to TIL therapy in melanoma [multiome]

city: Lausanne

first: David

last: Barras

state: Vaud

address: AGORA, Bugnon 25A

country: Switzerland

institute: Centre hospitalier universitaire vaudois

summary: Adoptive cell therapy (ACT) using in vitro expanded tumor-infiltrating lymphocytes (TILs) has inconsistent clinical responses. To better understand determinants of therapeutic success, we tracked TIL clonotypes from baseline tumors to ACT products and post-ACT blood and tumor samples in melanoma patients using single-cell RNA and T cell receptor (TCR) sequencing. Patients with clinical responses had baseline tumors enriched in tumor-reactive TILs, and these were more effectively mobilized upon in vitro expansion, yielding products enriched in tumor-specific CD8+ cells that preferentially infiltrated tumors post-ACT. Conversely, lack of clinical responses was associated with tumors devoid of tumor-reactive resident clonotypes and with cell products mostly composed of blood-borne clonotypes that persisted in blood but not in tumors post-ACT. Upon expansion, tumor-specific TILs lost tumor-associated transcriptional signatures, including exhaustion, and responders exhibited an intermediate exhausted effector state after TIL engraftment in the tumor, suggesting functional reinvigoration. Our findings provide insight into the nature and dynamics of tumor-specific clonotypes associated with clinical response to TIL-ACT, with implications for treatment optimization.

overall_design: Expanded TILs and T cells from baseline tumor profiling in melanoma patients receiving adoptive cell therapy by multiome scRNA-seq-scATAC-seq

first: Alexandre

last: Harari

first: Denarda

last: Dangaj

first: George

last: Coukos


title: Single Nuclei RNA Sequencing of Uterine Serous Carcinoma

city: Chicago

first: Julie

last: Kim

state: IL

address: 303 E. Superior St

department: Obstetrics and Gynecology

institute: Northwestern University

summary: Significant racial disparities exist between Black and White patients with uterine serous carcinoma (USC). While the reasons for these disparities are unclear, but several studies have demonstrated significantly distinct rates of driver mutations between racial groups, including TP53. However, limited research has investigated the transcriptional differences of the tumors between these groups, or the composition of the tumor microenvironment (TME) between these groups. Here, we report the findings from the first single nuclei RNA-sequencing experiment conducted on USC tumors. We find that there are significant differences between the tumors of Black and White patients.  Tumors exhibited differential expression of specific genes associated with aggressiveness, such as PAX8, and axon guidance and synaptic signaling pathways in Black and White patients.  We also demonstrated that differences in T cell and macrophage populations exist between benign and tumor tissues in the TME of USC, as well as between racial groups.  Furthermore, we investigated the connection between PAX8 overexpression and immunosuppression in USC through regulation of several cytokines and chemokines.  Notably, we show for the first time that PAX8 activity can influence macrophage gene expression and protein secretion.  These studies provide a detailed understanding of USC and a basis for using racial information in USC treatment decisions.

overall_design: tumors from each racial group were sequenced using single nuclei RNA sequencing

first: Grace

last: Foley


title: RNA Sequencing of ARK2 PAX8 Knock Down Cells

summary: PAX8 is an important marker of the Mullerian duct and is often overexpressed in endometrial cancers.  We sought to understand what PAX* is regulating by knocking down its expression and performing RNA-sequencing.

overall_design: RNA from ARK2 (control) and ARK2 PAX8 knock down cells were used for sequencing.  Six samples of each group were sequenced.


title: Roxadustat alleviates metabolic traits in letrozole-induced PCOS mice

city: Oulu

first: Terhi

last: Piltonen

address: Aapistie 5A

country: Finland

institute: University of Oulu

summary: Polycystic ovary syndrome (PCOS) is a highly prevalent disorder, affecting one in eight women across the world. It is commonly accompanied by metabolic syndrome, including obesity, insulin resistance, impaired glucose tolerance and dyslipidemia. Activation of the hypoxia-inducible factor (HIF) pathway is known to alleviate metabolic defects and counteract obesity. Hence, this study utilized a preclinical PCOS mouse model to investigate the effects of chemically induced HIF activation on the metabolic traits of the syndrome.

overall_design: Prepubertal letrozole treatment and C57Bl6/J mice were used to generate a PCOS mouse model. PCOS mice were orally treated with either vehicle or roxadustat for six weeks from age 12 weeks onwards to induce HIF activation. A control group receiving vehicle was also included. After six weeks of treatment, mice were terminated and organs harvested. Liver, skeletal muscle, and white adipose tissues (WAT) were used in RNA sequencing, to investigate differences in gene expression between the experimental groups.

first: Nikke

last: Virtanen

first: Ulla

last: Saarela

first: Mikko

last: Karpale

first: Riikka

last: Arffman

first: Kari

middle: A

last: Mäkelä

first: Karl-Heinz

last: Herzig

first: Peppi

last: Koivunen