title: The eIF5A hypusination inhibitor GC7 acts as a mitochondrial stress inducer

city: Wako

first: Tilman

last: Schneider-Poetsch

state: Saitama

address: 2-1 Hirosawa

institute: RIKEN

summary: The eukaryotic translation factor eIF5A plays an essential role in translation elongation, especially across stretches of prolines and charged amino acids, and in translation termination. Although eIF5A is subjected to hypusination, a post-translational modification unique to this protein, how hypusination contributes to the eIF5A function remains elusive. Here we investigated the cellular defects induced by hypusination inhibitor GC7 (N1-guanyl-1,7-diaminoheptane). Through proteome, translatome and transcriptome analysis, we found that GC7 decreased a subset of mitochondrial proteins and DNA (mtDNA). Furthermore, chemical genomic screening using barcoded shRNA libraries identified genes for particular proteins involved in polyamine metabolism and a mitochondrial protein MPV17L2 as those altering the cytotoxicity induced by GC7. Depletion of MPV17L2 led to hypersensitivity to GC7 as well as the decreases in mitochondrial proteins and mtDNA. Moreover, metabolome analysis revealed that MPV17L2 depletion and GC7 treatment additively decreased the amount of proline and asparagine. Our results indicate that MPV17L2 displays a synthetic lethal interaction with the eIF5A hypusination targeted by GC7.  The eukaryotic translation factor eIF5A plays an essential role in translation elongation, especially across stretches of prolines and charged amino acids, and in translation termination. Although eIF5A is subjected to hypusination, a post-translational modification unique to this protein, how hypusination contributes to the eIF5A function remains elusive. Here we investigated the cellular defects induced by hypusination inhibitor GC7 (N1-guanyl-1,7-diaminoheptane). Through proteome, translatome and transcriptome analysis, we found that GC7 decreased a subset of mitochondrial proteins and DNA (mtDNA). Furthermore, chemical genomic screening using barcoded shRNA libraries identified genes for particular proteins involved in polyamine metabolism and a mitochondrial protein MPV17L2 as those altering the cytotoxicity induced by GC7. Depletion of MPV17L2 led to hypersensitivity to GC7 as well as the decreases in mitochondrial proteins and mtDNA. Moreover, metabolome analysis revealed that MPV17L2 depletion and GC7 treatment additively decreased the amount of proline and asparagine. Our results indicate that MPV17L2 displays a synthetic lethal interaction with the eIF5A hypusination targeted by GC7.   numerous molecules serving as valuable therapeutics. The marine natural product girolline has been described as an inhibitor of protein synthesis. Here, we demonstrate that it is not a general translation inhibitor but represents a sequence-specific modulator of translation factor eIF5A. Girolline interferes with ribosome-eIF5A interaction and induces ribosome stalling, primarily on AAA-encoded lysine. Our data furthermore indicate that eIF5A plays a physiological role in ribosome-associated quality control (RQC) and is important in maintaining the efficiency of translational progress. Girolline, therefore, provides a potent tool compound for understanding the interplay between protein production and quality control in a physiological setting and offers a new and selective means of modulating gene expression. numerous molecules serving as valuable therapeutics. The marine natural product girolline has27 been described as an inhibitor of protein synthesis. Here, we demonstrate that it is not a general28 translation inhibitor but represents a sequence-specific modulator of translation factor eIF5A.29 Girolline interferes with ribosome-eIF5A interaction and induces ribosome stalling, primarily on30 AAA-encoded lysine. Our data furthermore indicate that eIF5A plays a physiological role in31 ribosome-associated quality control (RQC) and is important in maintaining the efficiency of32 translational progress. Girolline, therefore, provides a potent tool compound for understanding33 the interplay between protein production and quality control in a physiological setting and offers34 a new and selective means of modulating gene expression.

overall_design: Ribosome profiling  of human cells treated with GC7

first: Ken

last: Matsumoto

first: Rumi

last: Kurokawa

first: Megumi

last: Takase

first: Feng

last: Ling

first: Takehiro

last: Suzuki

first: Makoto

last: Muroi

first: Peixun

last: Han

first: Taisei

last: Wakigawa

first: Masato

first: Kyohei

last: Higashi

first: Hiroyuki

last: Osada


title: Mitochondrial injury induced by a Salmonella genotoxin triggers the proinflammatory senescence-associated secretory phenotype

status: Public on Mar 30 2024

city: Taipei

first: Po-Yo

last: Liu

address: No.1 Jen Ai road section 1 Taipei 100 Taiwan R.O.C.

department: Department and Graduate Institute of Medical Microbiology

country: Taiwan

institute: National Taiwan University College of Medicine

type: Expression profiling by high throughput sequencing

summary: Bacterial genotoxins can damage host cells by targeting their chromosomal DNA. Salmonella Typhi the causative pathogen of typhoid fever in humans, secretes an essential genotoxin called typhoid toxin, which can induce cellular senescence. Here we show that typhoid toxin triggers the senescence-associated secretory phenotype (SASP) by disrupting mitochondrial function, including a decrease in mitochondrial DNA (mtDNA) content and a disturbance of redox homeostasis within mitochondria. This disruption causes the release of mtDNA into the cytosol, which activates type I interferon via the cGAS-STING pathway. We also demonstrate that the GCN2-mediated integrated stress response modulates the upregulation of inflammatory components depending on the STING signaling axis. These SASP factors can propagate the senescence effect to CD4 T cells, potentially leading to senescence in these cells. Our research provides a novel insight into how bacterial genotoxins target mitochondria to induce a proinflammatory SASP, which could be a promising therapeutic target for an anti-toxin intervention.

overall_design: Samples represent THP-1-derived macrophages which were treated with either mock, wild-type(WT) typhoid toxin or the mutant toxin variant (PltBS35A) with triplicate data of each treatments.

first: Han-Yi

last: Chen

first: Huei-Ying

last: Li

first: Shu-Jung

last: Chang


title: SRSF1-mediated alternative splicing is required for spermatogonial stem cell differentiation and mitotic-to-meiotic transition

status: Public on Mar 31 2024

city: Beijing

first: Wenlong

last: Lei

state: 北京

address: 北京市朝阳区北辰西路1号院5号

country: China

institute: 中国科学院

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

overall_design: Refer to individual Series


title: Aristolochic Acid Nephropathy 2 week time point of CD45+ cells

city: Birmingham

first: James

middle: F

last: George

state: Alabama

address: 1720 2nd Ave South

country: USA

institute: University of Alabama at Birmingham

summary:
An evolutionarily conserved kidney resident macrophage phenotype defined by reduced MHCII expression universally appears after acute and chronic kidney injury
To investigate transcriptional and spatial differences in the MHC II negative kidney resident subpopualtion after CKD

overall_design: Single cell RNA sequencing and spatial transcriptomic analysis to identify and visualize MHC II- kideny resident macrophages and CD4+ T cells, scRNAseq samples were hashed

first: Elise

middle: N

last: Erman

first: Kyle

middle: H

last: Moore

first: Matthew

middle: D

last: Cheung

first: Jennifer

middle: R

last: La Fontaine

first: Zhengqin

last: Yang

first: Reham

last: Soliman

first: Anupam

last: Aqarwal


title: Transcriptomics analysis of gene expressions in control and shMETTL3 in Human bone marrow mesenchymal stem cells

city: Nanjing

first: Lan

last: Ma

address: Hanzhong street

institute: Nanjing medical university

summary: RNA-seq performed in BMSCs with stable METTL3 knockdown and control cells

overall_design: The Human bone marrow mesenchymal stem cells were transduced with the shMETTL3-1/shMETTL3-2 or empty vector lentiviruses containing medium for 48 h and followed by puromycin selection.


title: Race-specific coregulatory and transcriptomic profiles associated with DNA methylation and androgen receptor in prostate cancer [EPIC]

status: Public on Mar 27 2024

city: BUFFALO

first: Eduardo

last: Cortes

state: NY

address: ELM AND CARLTON STREETS

department: Biostatistics and Bioinformatics

institute: ROSWELL PARK CANCER INSTITUTE

type: Methylation profiling by genome tiling array

summary: Prostate cancer incidence and related mortality are disproportionately higher in African American (AA) men than European American (EA) men, but the molecular mechanisms contributing to racial disparities are not fully elucidated. To identify molecular factors that can contribute to disease biology in prostate cancer from AA and EA men, we utilized a multi-omics approach to measure and integrate DNA methylation with gene expression changes. We compared and contrasted results from adjacent non-tumor and tumor tissues from AA and EA men. We found that hypermethylated regions are enriched for PRC2 and H3K27me3 pathways and EZH2/SUZ12 cofactors in a race-independent manner. On the other hand, hypomethylated regions in prostate tumors from AA men were enriched for olfactory/ribosomal pathways as well as distinct cofactors such as CTCF and KMT2A. DNA methylation at transcription start sites and 5’-UTR at GATA3, an androgen receptor (AR) coregulator, is associated with decreased gene expression in prostate tumors of AA men. Our analysis also showed an inverse correlation between DNA methylation and RNA expression of AR transcriptional targets, such as TRIM63, in prostate tumors of AA men. Our observations suggest a dysregulation of the AR signaling pathway in prostate cancer from AA men. To determine whether targeting AR results in race-specific gene expression changes, we utilized a prostate-cancer-specific Boolean network. Our simulation revealed that prolonged AR inhibition results in significant dysregulation in TGF-β, IDH1, and cell cycle pathways in prostate cancer of AA men. We expanded our observation of gene expression changes in the Boolean network and investigated RNA-sequencing data to better understand overall transcriptional alterations occurring in prostate tumors from AA and EA men. We found that gene expression changes related to microtubules, a subset of immune-related, and TMPRSS2-fusion pathways were dysregulated in prostate tumors of AA men and corresponded with progression-free survival of AA men. Altogether, the current study dissects complex signaling networks that are clinically actionable in prostate cancer from AA and EA men.

overall_design: 58 AA (31 Tumors and 27 adjacent) and 63 EA (31 Tumors and 32 adjacent) collected samples

first: Swathi

last: Ramakrishnan

last: Cortes-Gomez

first: Spencer

last: Rosario

first: Se

middle: J

last: Kim

first: Donald

middle: E

last: Mager

first: Kristopher

middle: M

last: Attwood

first: Sarah

last: Athans

first: Qiang

last: Hu

first: Jianmin

last: Wang

first: Anna

last: Woloszynska


title: SRSF1-mediated alternative splicing is required for spermatogonial stem cell differentiation and mitotic-to-meiotic transition [LACE-seq]

first: Wenlong

last: Lei

address: 北京市朝阳区北辰西路1号院5号

summary: Alternative splicing (AS) plays significant roles in fundamental biological activities. AS also are prevalent in the testis, but the regulations of alternative splicing in spermatogenesis is vague. Here, we report that Serine/arginine-rich splicing factor 1 (SRSF1), plays critical roles in alternative splicing and male reproduction. Male germ cell-specific deletion of Srsf1 led to complete infertility and abnormal spermatogenesis. We further demonstrated that Srsf1 is required for spermatogonial stem cell differentiation and mitotic-to-meiotic transition. Mechanistically, by combining RNA-seq data with LACE-seq data, we showed that SRSF1 regulatory networks have functions in spermatogenesis. Particularly, we found that SRSF1 affects the AS of Stra8 in a direct manner and Dazl, Dmc1, Mre11a, Syce2 and Rif1 in an indirect manner. Taken together, our findings demonstrate that SRSF1 has crucial functions in spermatogenesis and male fertility by regulating alternative splicing.

overall_design: We performed LACE-seq  by using wildtype testes at P10 to profile SRSF1-binding sites in testes

first: Wen-Long

first: Zongchang

last: Du

first: Ruibao

last: Su


title: DNA methylation profiles in gastric mucosa samples with low, intermediate and high cancer risk

city: Tokyo

first: Harumi

last: Yamada

address: 2-4-41 Ebara Shinagawa-ku

department: Department of Epigenomics

country: Japan

institute: Hoshi University

summary: DNA methylation profiles were compared between gastric mucosae samples without Helicobacter pylori (HP) infection (low risk : G1), those with HP eradication without gastric cancer (intermediate risk : G2), and those with HP eradication with gastric cancer (high risk : G3).

overall_design: Genome-wide DNA methylation analysis was conducted by an Infinium HumanMethylation450K BeadChip array. This study only has the low risk samples (G1).

first: Takahiro

last: Irie

first: Toshikazu

last: Ushijima


title: Microbiota-derived Inosine Suppresses Systemic Autoimmunity via Restriction of B Cell Differentiation and Migration

first: Gao

last: Lingyu

address: #12 Jiangwangmiao Street

department: Institute of Dermatology

institute: Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College

summary: The role of gut microbiota dysbiosis in systemic lupus erythematosus (SLE) pathogenesis remains elusive. Here, we show that fecal microbiota transplantation (FMT) from healthy mice to lupus mice ameliorated lupus-like symptoms. Microbiota reconstitution effectively reduced systemic class switch recombination and elevated IGH naïve isotype. Microbiota profiling revealed an enrichment of Lactobacillus johnsonii post-FMT, with a significant correlation to purine metabolites. Importantly, the Lactobacillus johnsonii-derived inosine, an intermediate metabolite in purine metabolism, effectively alleviated lupus-like symptoms by impeding B cell differentiation and reducing renal B cell infiltration. We further demonstrated that inosine reprograms B cells through the ERK-HIF-1α signaling pathway. Overall, our study highlights the discovery of a novel microbial metabolite modulating autoimmunity and suggests its potential for innovative microbiome-based therapeutic approaches.

overall_design: kidney samples from pristane-induced C57BL/6j lupus mice treated with saline (n=2) and fecal microbiota transplanation (FMT) from MRL/MpJ mice (n=3).

first: Qianjin

last: Lu

first: Lingyu

last: Gao

first: Yuhan

last: Zhang

first: Shengwen

last: Chen


title: Transcriptomic changes induced by GFI1B variants

status: Public on Mar 28 2024

city: Nijmegen

first: Joost

last: Martens

state: Nederland

address: Geert Grooteplein 28

department: RIMLS

country: Netherlands

institute: Radboud University

summary: Mutations in transcription factor Growth Factor Independence 1B (GFI1B) cause inherited bleedings with varying intensity possibly caused by different effects on the transcriptional function of GFI1B. We studied transcriptomic changes of normal and GFI1BT174N,H181Y,R184P,Q287* mutants in megakaryoblast MEG01 cells using RNA-sequencing. Compared to normal GFI1B each variant affected different gene modules with limited overlap between variants. Remarkably, GFI1BQ287* specifically activated a myeloid-associated gene module. Based on this finding we studied megakaryocyte differentiation using normal and GFI1BQ287* patient-derived induced pluripotent stem cells (IPSC) followed by single cell RNA-sequencing. This revealed a 45-fold decrease in the megakaryocyte/myeloid cell ratio in the GFI1BQ287* versus control condition. Moreover, myeloid specific genes were expressed within GFI1BQ287* but not normal megakaryocytes. Finally, we studied how megakaryocyte development was affected by inhibiting binding of GFI1B to Lysine Specific Demethylase 1 (LSD1), an interaction required for megakaryocyte development. Treatment of both MEG01 cells and normal IPSC-derived developing megakaryocytes with the small-molecule inhibitor GSK-LSD1 resulted in profound activation of myeloid gene programs within megakaryocytes, while the IPSC-derived megakaryocyte/myeloid ratio dropped two-fold. We conclude that GFI1B and LSD1 suppress myeloid differentiation allowing for proper megakaryocyte development. LSD1 inhibitor and GFI1BQ287*-mediated perturbation of this function causes myeloid skewing during megakaryocyte development.

overall_design: To determine transcriptomic changes induced by GFI1B variants we retrovirally expressed GFI1BT174N, H181Y, R184P, Q287* next to normal GFI1B and an empty vector in megakaryoblast MEG01 cells followed by RNA-isolation and in triplicate RNA-sequencing 4 days later.

first: Jeron

last: Venhuizen

first: Maaike

last: van Bergen

middle: A

first: Bert

last: van der Reijden


title: MIR100HG promoted ferroptosis via regulating the expression of ACSL3 in lung cancer cells

city: Deyang

first: Hao

state: Sichuan

address: No. 173 Taishan North Road

department: Department of Reproductive and Genetic Diseases

institute: Deyang People’s Hospital

summary: Transcriptomic sequencing was performed to screen out downstream targets of MIR100HG in A549 cells

overall_design: To screen out downstream targets of MIR100HG, transcriptomics sequencing was performed for MIR100HG knocking-down and control A549 cells

first: Yan

last: Liu

first: Xianwei

last: Wang

first: Quan

first: Zhihong

last: Xu

first: Shijie

last: Zhou


title: Race-specific coregulatory and transcriptomic profiles associated with DNA methylation and androgen receptor in prostate cancer [m450K]

first: Eduardo

last: Cortes

first: Swathi

last: Ramakrishnan

last: Cortes-Gomez

first: Spencer

last: Rosario

first: Se

last: Kim

first: Donald

last: Mager

first: Kristopher

last: Attwood

first: Sarah

last: Athans

first: Qiang

last: Hu

first: Jianmin

first: Anna

last: Woloszynska


title: SAGES: Structural Analysis of Gene and Protein Expression Signatures Reveal Dynamic Expression of Disordered Proteins in Breast Cancer and Tissue

city: New York

first: Yifei

last: Sun

address: 1468 Madison Ave

institute: Icahn School of Medicine at Mount Sinai

summary: Structural features of proteins capture underlying information about protein evolution and function, which enhances the analysis of proteomic and transcriptomic data. Here we develop Structural Analysis of Gene and protein Expression Signatures (SAGES), a method that describes expression data using features calculated from sequence-based prediction methods and 3D structural models. We used SAGES, along with machine learning, to characterize tissues from healthy individuals and those with breast cancer. We identified prominent expression of intrinsically disordered regions in breast cancer proteins as well as relationships between drug perturbation signatures and breast cancer disease signatures. Our results suggest that SAGES is generally applicable to describe diverse biological phenomena including disease states and drug effects.

overall_design: We analyzed gene expression data from 22 breast cancer patients using their breast tumor tissue and adjacent normal breast tissue.

first: Nicole

last: Zatorski

first: Abdulkadir

last: Elmas

first: Christian

last: Dallago

first: Michael

last: Bernhofer

first: Timothy

last: Karl

first: David

last: Stein

first: Burkhard

last: Rost

first: Kuan-Lin

last: Huang

first: Martin

last: Walsh

first: Avner

last: Schlessinger


title: SOS Genes Are Rapidly Induced While Mutagenesis Is Temporally Regulated by Changes in Protein Activation and Nucleotide Pools After a Sub-lethal Dose of Ciprofloxacin in Escherichia coli

status: Public on Mar 26 2024

city: Trondheim

first: Amanda

middle: Holstad

last: Singleton

address: Erling Skjalgsons gate 1

department: Department of Clinical and Molecular Medicine

country: Norway

institute: Norwegian University of Science and Technology

summary: The DNA damage inducible SOS response in bacteria serves to increase survival of the species. The SOS response first initiates error-free repair which is followed by error-prone repair. Here, we have employed a multi-omics approach to elucidate the temporal coordination of the SOS response using transcriptomics, signalomics, and metabolomics. Escherichia coli was grown in batch cultivation in bioreactors to ensure highly controlled conditions. Ciprofloxacin was used to induce the SOS response at a concentration that avoided extensive cell death. Our results show that expression of genes involved in error-free and error-prone repair were both induced shortly after DNA damage, thus, challenging the established perception that the expression of error-prone repair genes is delayed. By combining transcriptomics with signalomics, we found that temporal segregation of error-free and error-prone repair is primarily regulated after transcription. Furthermore, the heterology index was correlated to the maximum increase in gene expression and not to the time of induction of SOS genes. Finally, quantification of metabolites revealed an increase in pyrimidine pools as a late feature of the SOS response. Our results elucidate how the SOS response is coordinated, showing a rapid transcriptional response and temporal regulation of mutagenesis on the protein and metabolite levels.

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

overall_design: To study the temporal regulation of the SOS response in E. coli, we used a sub-lethal dose of ciprofloxacin to induce DNA damage in E. coli grown in batch culitvation in biorectors. Samples for RNA-sequencing were collected 1 min before treatment and 1, 10, 25, 50, 75, and 120 min after treatment. All samples were taken during exponential growth phase.  The growth rate of the untreated control and ciprofloxacin treated cultures were nearly identical due to the sub-lethal dose of ciprofloxacin. The experiments were conducted in 3 biological replicas. RNA-sequencing samples were supplemented with signalomics and metabolomics samples. Comparative gene expression profiling analysis between the ciprofloxacin treated and untreated control was conducted.

first: Olaug

last: Torheim Bergum

last: Holstad Singleton

first: Lisa

last: Røst

first: Antoine

last: Bodein

first: Marie-Pier

last: Scott-Boyer

first: Morten

last: Beck Rye

first: Arnaud

last: Droit

first: Per

last: Bruheim

first: Marit

last: Otterlei


title: Infection induced inflammation impairs wound healing through IL-1b signaling

status: Public on Mar 25 2024

city: Madison

first: Colin

last: Dewey

address: 425 Henry Mall, 5420 Genetics/Biotechnology Center

institute: University of Wisconsin-Madison

summary: Wound healing is impaired by infection; however, how microbe-induced inflammation modulates tissue repair remains unclear. We took advantage of the optical transparency of zebrafish and a genetically tractable microbe, Listeria monocytogenes, to probe the role of infection and inflammation in wound healing. We found a critical window of microbial clearance necessary to limit persistent inflammation and enable efficient wound repair. Infection with bacteria engineered to activate the inflammasome, Lm-Pyro, induced persistent inflammation and impaired healing despite low bacterial burden. In contrast, infection with an anti-inflammatory, apoptosis inducing strain, Lm-Apo, had similar infectious burden but was associated with rapid wound repair. Inflammatory infections induced il-1b expression and blocking IL-1R signaling partially rescued wound healing in the presence of persistent infection. Taken together, our findings suggest that the dynamics of microbe-induced tissue inflammation impacts repair in complex tissue damage independent of bacterial load, with a critical early window for efficient tissue repair.

overall_design: RNA-seq gene expression analysis of caudal fins of 4 dpf zebrafish after wounding and infection (n = 9: 3 replicates from each of 3 treatments)

first: Simone

last: Shen

first: Veronika

last: Miskolci

first: John-Demian

last: Sauer

first: Anna

last: Huttenlocher


title: Gene expression profile at single cell level of WT or flt1 mutant

city: Karlsruhe

first: Laetitia

last: Preau

address: Fritz Haber Weg 4

country: Germany

institute: Karlsruhe Institute of Technology (KIT)


title: Childhood cancer mutagenesis caused by a domesticated DNA transposase

city: Montréal

first: Claudia

middle: L

last: Kleinman

state: Québec

address: 3999 Côte Ste-Catherine Road

department: Human Genetics

country: Canada

institute: Lady Davis Institute for Medical Research

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Induction of somatic oncogenic mutations by the domesticated DNA transposase PGBD5 in cerebellar progenitor cells promotes medulloblastoma development.

overall_design: Medulloblastomas from Ptf1a-Cre/+; Ptch1fl/fl; Pgbd5+/+ (n=3) and Ptf1a-Cre/+; Ptch1fl/fl; Pgbd5-/- (n=3) mice were collected and sequenced for single-cell Multiome. The tumor onset age (harvested age) varied from 94 to 239 days.

first: Makiko

last: Yamada

first: Ross

last: Keller

first: Ignas

last: Masilionis

first: Ronan

last: Chaligne

first: Rodrigo

last: Lopez Gutierrez

first: Steven

last: Hébert

first: Alex

last: Kentsis


title: Single cell lineage tracing reveals clonal dynamics of anti-EGFR therapy resistance in triple negative breast cancer.

city: Naples

first: Melania

last: Franchini

address: Via Campi Flegrei 34,

country: Italy

institute: Telethon Institute of Genetics and Medicine (TIGEM)


title: SRSF1-mediated alternative splicing is required for spermatogonial stem cell differentiation and mitotic-to-meiotic transition [RNA-Seq]

first: Wenlong

last: Lei

address: 北京市朝阳区北辰西路1号院5号

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Srsf1WT and Srsf1cKO mice testes at P10

first: Wen-Long

first: Zongchang

last: Du

first: Ruibao

last: Su


title: Impact of Microglia Isolation and Culture Methodology on Transcriptional Profile and Function

city: Manhasset

first: Mark

last: Mizrachi

address: 350 Community Drive

department: Institute of Molecular Medicine

institute: Feinstein Institutes for Medical Research

summary: Background: Microglial isolation and culturing methods continue to be explored to maximize cellular yield, purity, responsiveness to stimulation and similarity to in vivo microglia. This study aims to evaluate different microglia isolation methods — 3 variants of microglia isolation from neonatal mice and 2 variants of microglia isolation from adult mice — on transcriptional profile and response to HMGB1. Methods: Microglia from neonatal mice, age 0-3 days (P0-P3) were isolated from mixed glial cultures (MGC). We included three variations of this protocol that differed by use of GM-CSF in culture (No GM-CSF or 500 pg/mL GM-CSF), and days of culture in MGC before microglial separation (10 or 21). Protocols for studying microglia from adult mice age 6-8 weeks included isolation by adherence properties followed by 7 days of culture with 100 ng/mL GM-CSF and 100 ng/mL M-CSF (Vijaya et al., 2023), or acute isolation using CD11b beads (Bordt et al., 2020). Purity, yield, and RNA quality of the isolated microglia were assessed by flow cytometry, hemocytometer counting, Nanodrop, and Bioanalyzer, respectively. Microglial responsiveness to an inflammatory stimulus, HMGB1, was evaluated by measuring TNFα, IL1β, and IFNβ secretion by ELISA and assessing gene expression patterns using bulk RNA sequencing. Results: All five methods demonstrated greater than 90% purity. Microglia from all cultures increased transcription of or secreted TNFα, IL1β, and IFNβ in response to HMGB1. RNA sequencing showed a larger number of differentially expressed genes in response to HMGB1 treatment in microglia cultured from pups than from adult mice, with sparse changes among the 3 MGC culturing conditions.  Conclusion: These findings suggest that while all methods provided high purity, the choice of protocol may significantly influence yield, RNA quality, baseline transcriptional profile and response to stimulation. This comparative study provides valuable insights to inform the choice of microglial isolation and culture method.

overall_design: We sequenced 30 samples in total. This includes microglia derived from 5 isolation methods, with 3 biological replicates each and two treatment conditions: Control and HMGB1-treated.

first: Betty

last: Diamond


title: Gene expression profile at single cell level of SUM149PT, SUM185PE, SUM229PE, SUM159PT and SUM1315MO2 cell lines

summary: SUM149PT, SUM185PE, SUM229PE, SUM159PT and SUM1315MO2 are triple negative breast cancer cell lines. They were sequenced to test the contrastive learning-based algorithm we developed to predict Afatinib sensitivity in TNBC.

overall_design: Single cell capture was performed with DROP-seq platform implemented in our lab.

first: Gaetano

last: Viscido

first: Gennaro

last: Gambardella


title: Single cell lineage tracing reveals clonal dynamics of anti-EGFR therapy resistance in triple negative breast cancer

summary: We investigate non-genomic mechanisms determining cellular response to EGFR inhibitors in triple negative breast cancer (TNBC). We integrate methods for cellular barcoding and single-cell transcriptomics to enable cell lineage tracing and explore the subclonal evolution of adaptation in an established preclinical model of TNBC in response to incremental concentrations of Afatinib, a second generation EGFR-TKI that irreversibly inhibits both EGFR and HER2. Retrospective lineage tracing data analysis uncovered a pre-existing subpopulation of rare Afatinib-tolerant cells displaying distinct biological features, such as elevated mRNA levels of the IGFBP2 gene. Furthermore, we investigated temporal coordination of transcriptional programs in drug resistant clones with high replication fitness by reordering cells along a pseudotime trajectory. Interestingly, it revealed the activation of biological processes, such as fatty acid metabolism, which have previously been linked to EGFR-TKIs resistance mechanisms.

overall_design: We integrated commercially available platform for cellular barcoding and single-cell transcriptomics to enable cell lineage tracing

first: Simona

last: Pellecchia


title: Gene expression profile of MDA-MB-468 cell line over-expressing IGFBP2 gene

summary: IGFBP2 is one of the putative biomarker of Afatinib response we identified. To dissect the biological processes sustained by IGFBP2 expression, we performed bulk 3’ RNA-seq of MDA-MB-468 cell line over-expressing it

overall_design: RNA-Seq


title: Influenza A virus replicates productively in primary human kidney cells and induces factors and mechanisms related to regulated cell death and renal pathology observed in virus-infected patients

city: Frankfurt am Main

first: Benjamin

middle: Florian

last: Koch

address: Theodor-Stern-Kai 7

department: Nephrology

institute: Goethe University Hospital

summary: Influenza A virus (IAV) infection can cause the often-lethal acute respiratory distress syndrome (ARDS) of the lung. Concomitantly, acute kidney injury (AKI) is frequently noticed during IAV infection, correlating with an increased mortality. The aim of this study was to elucidate the interaction of IAV with human kidney cells and, thereby, to assess the mechanisms underlying IAV-mediated AKI. We demonstrate productive replication of low and highly pathogenic IAV strains on primary and immortalized nephron cells. Comparison of our transcriptome and proteome analysis of H1N1-type IAV-infected human primary distal tubular cells (DTC) with existing data from H1N1-type IAV-infected lung and primary trachea cells revealed enrichment of specific factors responsible for regulated cell death in primary DTC, which could be targeted by specific inhibitors

overall_design: Primary human DTC were grown in six-well plates and either left uninfected or infected with H1N1pdm09 at a MOI = 1. Two replicates of each set were analyzed for transcript expression changes by RNAseq, while the remaining replicates were used for verification of RNAseq results by qPCR. Briefly, total RNA was extracted 12 hours after infection by Qiagen RNeasy Maxi Kit (Qiagen, Germany), including on-column removal of DNA by digestion with rDNase for 15 min at room temperature. For library preparation, 500 ng of RNA (each showing a RIN score from > 9) was used. Second to depletion of ribosomal RNA (QIAseq FastSelect RNA Removal Kit, Qiagen, Germany), directional libraries were prepared with a NEBNext® UltraTM Directional RNA Library Prep Kit for Illumina® sequencing (No. E7420S, New England Biolabs, Ipswich, MA, USA). Sequencing was performed by an Illumina NextSeq500® using a NextSeq® 500/550 High Output Kit v2 (75 cycles, No. FC-404-2005, Illumina, San Diego, CA, USA).

first: Stephan

last: Pleschka


title: Gene expression profile at single cell level of kdrl+ FACS sorted cells from WT or flt1 mutant Tg(kdrl:EGFP) zebrafish embryos (3dpf).

first: Laetitia

last: Preau

summary: scRNA-seq was used to investigate the different endothelial cell population and differential gene expression between arterial and venous cells.

overall_design: Kdrl positive cells of WT and flt1 mutant Tg(kdrl:EGFP) embryos were isolated by Fluorescence-activated cell sorting (FACS) according to the presence or absence of GFP signal and processed for single cell RNA-Seq using 10X Genomics Chromium droplet based system


title: Gene expression profile at single cell level of zebrafish trunk from WT or flt1 mutant (3dpf).

summary: scRNA-seq was used to investigate neurovascular cross-talk in zebrafish trunk.

overall_design: Zebrafish trunk of WT and flt1 mutant were dissected, dissociated and processed for single cell RNA-Seq using 10X Genomics Chromium droplet based system


title: Advanced patient-specific microglia cell models for pre-clinical studies in Alzheimer’s disease

status: Public on Mar 24 2024

city: Brisbane

first: Hazel

last: Quek

state: QLD

address: Bancroft, 300 Herston Road

department: Mental Health & Neuroscience Department

country: Australia

institute: QIMR Berghofer Medical Research

summary: Background: Alzheimer’s disease (AD) is an incurable neurodegenerative disorder with a rapidly increasing prevalence worldwide. Current approaches targeting hallmark pathological features of AD have had no consistent clinical benefit. Neuroinflammation is a major contributor to neurodegeneration and hence, microglia, the brain’s resident immune cells, are an attractive target for potentially more effective therapeutic strategies. However, there is no current in vitro model system that captures AD patient-specific microglial characteristics using physiologically relevant and experimentally flexible culture conditions.  Methods: To address this shortcoming, we developed novel 3D Matrigel-based monocyte-derived microglia-like cell (MDMi) mono-cultures and co-cultures with neuro-glial cells (ReNcell VM). We used single-cell RNA sequencing (scRNAseq) analysis to compare the transcriptomic signatures of MDMi between model systems (2D, 3D and 3D co-culture) and against published human microglia datasets. To demonstrate the potential of MDMi for use in personalized preclinical strategies, we generated and characterized MDMi models from sixteen AD patients and matched healthy controls, and profiled cytokine responses upon treatment with anti-inflammatory drugs (dasatinib and spiperone).  Results: MDMi in 3D exhibited a more branched morphology and longer survival in culture compared to 2D. scRNAseq uncovered distinct MDMi subpopulations that exhibit higher functional heterogeneity and best resemble human microglia in 3D co-culture. AD MDMi in 3D co-culture showed altered cell-to-cell interactions, growth factor and cytokine secretion profiles and responses to amyloid-β. Drug testing assays revealed patient- and model-specific cytokine responses.  Conclusion: Our study presents a novel, physiologically relevant and AD patient-specific 3D microglia cell model that opens avenues towards improving personalized drug development strategies in AD.

overall_design: We characterized monocyte-derived microglia (MDMi) cultured in 2D, 3D, and 3D co-cultured with ReNcell VM, with our data demonstrating that 3D co-culture closely resembles human brain microglia compared to 3D MDMi and 2D MDMi. The experimental design involved the collection of longitudinal blood samples from a single healthy male control donor under 40 years of age, free of dementia, and without a family history of Alzheimer's disease (AD). Blood collections were performed bi-monthly over a four-month period, resulting in multiple time points. Using EDTA tubes, peripheral blood mononuclear cells (PBMC) were isolated following the SepMate50 protocol. MDMi were cultured for 14 days (2D) or 35 days (3D) under a culture medium containing IL-34 and GM-CSF. 3D mono-culture and 3D co-culture were grown in thick Matrigel, while 2D was cultured on Matrigel-coated plates. For RNA collection, MDMi from all conditions were isolated and sorted for CD11b+ (thereby excluding leukocytes and ReNcell VM) and fixed according to the Chromium fixed RNA profiling workflow. Library construction involved simultaneous processing of all samples.

first: Carla

last: Cuní-López

first: Ankit

last: Shukla

first: Anthony

last: White


title: FOXL2 interaction with different binding partners regulates the dynamics of granulosa cell differentiation across ovarian development [ATAC-Seq]

city: London

first: Roberta

last: Migale

state: UK

address: 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute

summary: FOXL2 is a transcription factor essential for female fertility, expressed in somatic cells of the ovary, notably granulosa cells. In the mouse, Foxl2 deletion leads to partial sex reversal postnatally, with mutants developing dysgenic ovaries devoid of oocytes. However, deletion of the gene in 8-week-old females leads to granulosa to Sertoli cell transdifferentiation and gonadal sex reversal. We hypothesise that different outcomes of Foxl2 deletion in embryonic versus adult ovary may depend on a different role played by FOXL2 across ovarian development. Therefore, in this study, we take a multi-omics approach to characterise the dynamics of gene expression and chromatin accessibility changes in purified murine granulosa cells across key developmental stages (E14.5, 1 and 8 weeks). We coupled these analyses with genome wide identification of FOXL2 target genes and on-chromatin interacting partners by ChIP-SICAP to reconstruct the gene regulatory networks underpinned by this essential transcription factor and to discover novel players. We found that, in the embryonic ovary, FOXL2 interacts with factors important for early stages of gonadal development, such as GATA4 and WT1, whilst postnatally it interacts with factors regulating primordial follicle activation, such as NR5A2, and with factors regulating steroidogenesis including AR and ESR2. Integration of chromatin landscape dynamics with gene expression changes and FOXL2 binding sites analysis revealed that its critical role in ovarian cell fate maintenance goes beyond repression of the Sertoli-specific gene Sox9. Our chromatome analysis revealed also that FOXL2 interacts with several proteins involved in chromatin remodelling, DNA repair, splicing and gene repression. We identified a FOXL2 interactor with a role in primordial follicle activation, Ubiquitin specific protease 7 (USP7). We showed that conditional deletion of this gene in granulosa cells leads to a blockage of primordial follicle activation, impairs ovary development and leads to complete sterility.  In summary, in this study we identified target genes dynamically regulated by FOXL2 across ovarian development including known and newly identified FOXL2 targets with a role in embryonic ovarian development and folliculogenesis, as well as cofactors that point towards additional roles played by FOXL2 besides transcriptional regulation. This work constitutes a comprehensive resource for exploration of the molecular mechanisms of ovarian development and causes of female infertility.

overall_design: We performed ATAC-Seq on 100000 FOXL2-GFP FACS sorted cells purified from granulosa cells of the ovary at E14.5, 1 week and 8 weeks postnatally to profile the chromatin landscape changes associated with ovarian development

first: Michelle

last: Neumann

first: Mahmoud-Reza

last: Rafiee

first: Sophie

last: Wood

first: Jessica

last: Olsen

first: Robin

last: Lovell-Badge


title: Chemo-senolytic therapeutic potential against angiosarcoma

status: Public on Mar 23 2024

city: Sapporo

first: Hideki

last: Tanizawa

state: Hokkaido

address: Kita 15, Nishi 7, Kita-ku

department: Institute for Genetic Medicine

institute: Hokkaido University

summary: Angiosarcoma is an aggressive soft-tissue sarcoma with a poor prognosis. Chemotherapy for this cancer typically employs paclitaxel, one of the taxanes (genotoxic drugs), although it has a limited effect due to chemoresistance for prolonged treatment. Here we examine a new angiosarcoma treatment approach that combines chemotherapeutic and senolytic agents. We first find that the chemotherapeutic drugs, cisplatin and paclitaxel, efficiently induce cellular senescence of angiosarcoma cells. Subsequent treatment with a senolytic agent, ABT-263, eliminates senescent cells through the activation of the apoptotic pathway. In addition, expression analysis indicates that senescence-associated secretory phenotype (SASP) genes are activated in senescent angiosarcoma cells and that ABT-263 treatment eliminates senescent cells expressing genes in the type-I interferon (IFN-I) pathway. Moreover, we show that cisplatin treatment alone requires a high dose to remove angiosarcoma cells, whereas a lower dose of cisplatin is sufficient to induce senescence, followed by the elimination of senescent cells by senolytic treatment. This study sheds light on a potential therapeutic strategy against angiosarcoma by combining a relatively low dose of cisplatin with the ABT-263 senolytic agent, which can help ease the deleterious side effects of chemotherapy.

overall_design: To understand how treatment with chemotherapeutic and senolytic agents affects gene expression in angiosarcoma cells, we performed RNA-seq analysis.

first: Xuebing

last: Wang

first: Claire

middle: Y

last: Chung

first: Ai

last: Yoshioka

first: Shinya

last: Hashimoto

first: Haruki

last: Jimbo

last: Ohta

first: Takeshi

last: Fukumoto

first: Ken-ichi

last: Noma


title: Disease-associated astrocyte epigenetic memory promotes CNS pathology [ATAC-Seq and RNA-Seq]

status: Public on Mar 21 2024

city: Boston

first: Zhaorong

last: Li

address: 60 Fenwood Road

institute: Dana Farber Cancer Institute

summary: We identify gene profiling of astrocytes by Cytokine or PBS stimulation in vivo.

overall_design: RNA-Seq and ATAC-Seq samples of sorted astrocytes from B6 Mice under cytokine stimulation and control condition.

first: Hong-Gyun

last: Lee

first: Francisco

last: Quintana


title: FOXL2 interaction with different binding partners regulates the dynamics of granulosa cell differentiation across ovarian development [ChIP-Seq]

first: Roberta

last: Migale

overall_design: ChIP-SICAP for FOXL2 performed on ovarian tissue harvested from mice at E14.5, 1 week and 8 weeks.

last: Neumann


title: Targeting DCAF5 suppresses SMARCB1-mutant cancer via stabilizing SWI/SNF

status: Public on Mar 22 2024

city: Memphis

first: Jacquelyn

last: Myers

state: TN

address: 262 Danny Thomas Pl

institute: St. Jude Children’s Research Hospital

summary: While oncogenes can potentially be inhibited with small molecules, the loss of tumor suppressors is more common and presents a conundrum for precision therapy because the proteins are no longer present.  SMARCB1-mutant cancers epitomize this challenge because these highly lethal cancers are driven by inactivation of a single gene, a subunit of SWI/SNF chromatin remodeling complexes.  To generate mechanistic insight into the consequences of SMARCB1 mutation and to seek vulnerabilities, we contributed 16 SMARCB1-mutant cell lines to a near-genomewide CRISPR screen as part of the Cancer Dependency Map1-3.  Here we report that the little-studied gene DCAF5 (DDB1-CUL4 Associated Factor 5) is a specific dependency in SMARCB1-mutant cancers. We show that DCAF5 serves a quality control function for SWI/SNF complexes and in the absence of SMARCB1 DCAF5 causes degradation of incompletely assembled SWI/SNF complexes. Upon inhibition of DCAF5 SMARCB1-deficient SWI/SNF complexes re-accumulate, bind to target loci, and restore gene expression to levels sufficient to fully reverse the cancer state, including in a xenograft mouse model. Consequently, cancer results not from the loss of SMARCB1 function per se but rather from DCAF5-mediated degradation of SWI/SNF complexes.  These data indicate that therapeutic targeting of DCAF5 may be sufficient to restore substantial SWI/SNF function and reverse cancer phenotypes caused by SMARCB1 loss.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for ARID1A, SMARCC1, and SMARCA4 as well as the histone modifications H3K27ac, H3K4me1, and H3K4me3 in shCTRL/shDCAF5 G401 cells.

first: Sandi

last: Radko-Juettner

first: Charles

middle: W

last: Roberts


title: FOXL2 interaction with different binding partners regulates the dynamics of granulosa cell differentiation across ovarian development [RNA-Seq]

overall_design: We performed RNA-Seq on FOXL2-GFP FACS sorted cells purified from granulosa cells of the ovary at E14.5, 1 week and 8 weeks postnatally to profile the gene expression changes associated with ovarian development

first: Michelle

first: Mahmoud-Reza

last: Rafiee

first: Sophie

last: Wood

first: Jessica

last: Olsen

last: Lovell-Badge


title: Soluble immune-checkpoint factors as a complementary biomarker for PD-1 blockade reflect exhaustion of antitumor immunity

city: Kyoto

first: Kenji

last: Chamoto

address: Yoshida Konoe-cho, Sakyo-ku

department: Department of Immuno-Oncology PDT

institute: Kyoto University

type:
Expression profiling by array
Third-party reanalysis

summary: BACKGROUND. Precise stratification of patients with non–small cell lung cancer (NSCLC) is needed for appropriate application of PD-1/PD-L1 blockade therapy.     METHODS. We measured soluble (s) forms of the PD-L1, PD-1, and CTLA-4 in plasma of patients with advanced NSCLC before PD-1/PD-L1 blockade. Prospective biomarker finding trial (cohort A), 50 patients with pretreated NSCLC received nivolumab. In cohort B to E, retrospective observational study, soluble immune checkpoint molecules were evaluated for patients with advanced NSCLC treated with any PD-1/PD-L1 blockade (cohort B and C), cytotoxic chemotherapy (D) or targeted therapy (E). Blood samples were obtained from all patients and soluble immune checkpoint molecules were evaluated using a highly sensitive chemiluminescence-based assay.     RESULTS. Nonresponsiveness to PD-1/PD-L1 blockade therapy was associated with higher concentrations of these soluble immune factors among patients with immune-reactive (hot) tumors. Such correlation was not observed in patients treated with cytotoxic chemotherapy or targeted therapies. Integrative analysis of tumor size, PD-L1 expression in tumor tissue (tPD-L1), and gene expression in tumor tissue and peripheral CD8+ T cells revealed that high concentrations of the three soluble immune factors were associated with  hyper or terminal exhaustion of antitumor immunity. The combination of sPD-L1 and sCTLA-4 efficiently discriminated responsiveness among patients with immune-reactive tumors.     CONCLUSION. Combinations of soluble immune factors might be able to identify patients unlikely to respond to PD-1/PD-L1 blockade as a result of terminal exhaustion of antitumor immunity. Our data suggest such a combination might provide a biomarker complementary to tPD-L1 for NSCLC patients.

relation:
Reanalysis of: GSM4204391
Reanalysis of: GSM4204393
Reanalysis of: GSM4204394
Reanalysis of: GSM4204396
Reanalysis of: GSM4204398
Reanalysis of: GSM4204400
Reanalysis of: GSM4204401
Reanalysis of: GSM4204402
Reanalysis of: GSM4204404
Reanalysis of: GSM4204406
Reanalysis of: GSM4204408
Reanalysis of: GSM4204410
Reanalysis of: GSM4204412
Reanalysis of: GSM4204414
Reanalysis of: GSM4204416
Reanalysis of: GSM4204418
Reanalysis of: GSM4204420
Reanalysis of: GSM4204422
Reanalysis of: GSM4204423
Reanalysis of: GSM4204425
Reanalysis of: GSM4204427
Reanalysis of: GSM4204428
Reanalysis of: GSM4204429
Reanalysis of: GSM4204431
Reanalysis of: GSM4204433
Reanalysis of: GSM4204435
Reanalysis of: GSM4204437
Reanalysis of: GSM4204439
Reanalysis of: GSM4204441
Reanalysis of: GSM4204443
Reanalysis of: GSM4204445
Reanalysis of: GSM4204447
Reanalysis of: GSM4204449
Reanalysis of: GSM4204451
Reanalysis of: GSM4204453
Reanalysis of: GSM4204455
Reanalysis of: GSM4204456
Reanalysis of: GSM4204458
Reanalysis of: GSM4204461
Reanalysis of: GSM4204463

overall_design:
40 samples, compared with soluble plasma markers measured by HISCL system.
The data were analyzed with  with median polish summarization and quantile normalization by Affymetrix® Transcriptome Analysis Console Software, and obtained normalized intensity values.
Values: SST-RMA and quantile normalized non-log2 signal.

first: Hidetoshi

last: Hayashi

first: Ryusuke

last: Hatae

first: Takashi

last: Kurosaki

first: Yosuke

last: Togashi

first: Megumi

last: Goto

first: Yasutaka

last: Chiba

first: Shuta

last: Tomida

first: Takayo

last: Ota

first: Koji

last: Haratani

first: Takayuki

last: Takahama

first: Junko

last: Tanizaki

last: Yoshida

first: Tsutomu

last: Iwasa

first: Kaoru

last: Tanaka

first: Masayuki

last: Takeda

first: Tomoko

last: Hirano

first: Hironori

first: Hiroaki

last: Ozasa

first: Yuichi

last: Sakamori

first: Kazuko

last: Sakai

first: Keiko

last: Higuchi

first: Hitoshi

last: Uga

first: Chihiro

last: Suminaka

first: Toyohiro

last: Hirai

first: Kazuto

last: Nishio

first: Kazuhiko

last: Nakagawa

first: Tasuku

last: Honjo


title: T cells in testicular germ cell tumors: new evidence of fundamental contributions by rare subsets

city: Giessen

first: Daniela

last: Fietz

address: Frankfurter Straße 98

institute: Justus Liebig University Giessen

summary: Tumor-infiltrating T cells in testicular germ cell tumors (TGCT) remain poorly understood. Therefore, along with immunohistochemistry and flow cytometry, single-cell RNA sequencing (scRNA-seq) was performed on different human TGCT testes to identify immune cell composition, with particular emphasis on delineating T cell subtypes. There are various tumor-infiltrating T cells including regulatory T (Treg) and follicular helper T (Tfh) cells that are found in other cancer entities, but their contributions to TGCT are unknown. In this study, we found that T cells including Treg and Tfh were most abundant in seminoma compared to mixed tumors and embryonal carcinoma. Taken together, despite significant heterogeneity between patients, this study demonstrated that T cell subtypes form a key component of the TGCT microenvironment. The novel finding of rare Treg and Tfh cells in the human testis suggests their involvement in TGCT pathobiology, with implications for understanding tumor progression, assessing patient prognosis, and as putative targets for personalized immunotherapy.

overall_design: To analyze the cellular composition, with particular emphasis on immune cells, in human testicular germ cell tumor (TGCT), scRNA-seq was performed using 10x genomics on testes from four TGCT patients.

first: Rashidul

last: Islam

first: Hans-Christian

last: Schuppe

first: Kate

last: Loveland

first: Jingtao

last: Guo


title: FOXL2 interaction with different binding partners regulates the dynamics of ovarian development

first: Roberta

last: Migale

summary:
The transcription factor FOXL2 is required in ovarian somatic cells for female fertility. Differential timing of Foxl2 deletion, in embryonic versus adult mouse ovary, leads to distinctive outcomes, suggesting different roles across development. Here, we comprehensively investigated FOXL2’s role through a multi-omics approach to characterize gene expression dynamics and chromatin accessibility changes, coupled with genome-wide identification of FOXL2 targets and on chromatin
interacting partners in somatic cells across ovarian development. We found that FOXL2 regulates more targets postnatally, through interaction with factors regulating primordial follicle formation and steroidogenesis. Deletion of one interactor, ubiquitin-specific protease 7 (USP7), results in impairment of somatic cell differentiation, germ cell nest breakdown, and ovarian development, leading to sterility. Our datasets constitute a comprehensive resource for exploration
of the molecular mechanisms of ovarian development and causes of female infertility.

overall_design: Refer to individual Series


title: The RNA binding proteins LARP4A and LARP4B promote tumour growth and metastasis in prostate cancer and osteosarcoma

city: Cambridge

first: Jennifer

last: Coleman

state: Cambridgeshire

address: Li Ka Shing Centre, Robinson Way

department: CRUK CI

institute: University of Cambridge

summary: To investigate the functions of the RNA-binding proteins LARP4A and LARP4B in prostate cancer and osteosarcoma, we knocked down LARP4A and LARP4B in PC3, MG63 and MNNG/HOS cell lines and characterised the effects on in vivo tumourigenicity, lung colonisation and in vitro proliferation, cell cycle progression, apoptosis and migration. In order to uncover potential mechanisms behind the phenotypes that we found, we then performed transcriptomic profiling using bulk RNAseq and used the data to identify potential biological processes influenced by LARP4A/LARP4B loss

overall_design: Gene expression analysis of RNAseq data from LARP4A or LARP4B knockdown PC3 and MG63 cell lines, alongside controls transfected with non-targeting siRNA controls (2 biological replicates per condition, each analyses performed in duplicate)

first: Val

last: Yianni

first: Agamemnom

last: Grigoriadis

first: Maria

last: Conte


title: Multi-omics characterization of partial chemical reprogramming reveals evidence of cell rejuvenation [Array]

first: Wayne

last: Mitchell

state: MA

address: 77 Avenue Louis Pasteur

institute: Brigham and Women's Hospital

summary: Partial reprogramming by cyclic short-term expression of Yamanaka factors holds promise for shifting cells to younger states and consequently delaying the onset of many diseases of aging. However, the delivery of transgenes and potential risk of teratoma formation present challenges for in vivo applications. Recent advances include the use of cocktails of compounds to reprogram somatic cells, but the characteristics and mechanisms of partial cellular reprogramming by chemicals remain unclear. Here, we report a multi-omics characterization of partial chemical reprogramming in fibroblasts from young and aged mice. We measured the effects of partial chemical reprogramming on the epigenome, transcriptome, proteome, phosphoproteome, and metabolome. At the transcriptome, proteome, and phosphoproteome levels, we saw widescale changes induced by this treatment, with the most notable signature being an upregulation of mitochondrial oxidative phosphorylation. Furthermore, at the metabolome level, we observed a reduction in the accumulation of aging-related metabolites. Using both transcriptomic and epigenetic clock-based analyses, we show that partial chemical reprogramming reduces the biological age of mouse fibroblasts.  We demonstrate that these changes have functional impacts, as evidenced by changes in cellular respiration and mitochondrial membrane potential. Taken together, these results illuminate the potential for chemical reprogramming reagents to rejuvenate aged biological systems, and warrant further investigation into adapting these approaches for in vivo age reversal.

platform_organism:
Macaca mulatta
Homo sapiens
Mus musculus
Rattus

overall_design: Dermal fibroblasts isolated from young (4-month-old) and old (20-month-old) C57BL/6 male mice were treated with either vehicle, 2c, or 7c for 6 days (media and treatments replenished every 3 days). Then, genomic DNA was isolated and DNA methylation was measured by DNA methylation microarray on the Horvath Mammal 320k array.

first: Ludger

last: Goeminne

first: Alexander

last: Tyshkovskiy

first: Sirui

last: Zhang

first: Julie

last: Chen

first: Joao

last: Paulo

first: Kerry

last: Pierce

first: Angelina

last: Choy

first: Clary

middle: B

last: Clish

first: Steven

middle: P

last: Gygi

first: Vadim

last: Gladyshev


title: Multi-omics characterization of partial chemical reprogramming reveals evidence of cell rejuvenation

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


title: Multi-omics characterization of partial chemical reprogramming reveals evidence of cell rejuvenation [RNA-seq]

summary: Partial reprogramming by cyclic short-term expression of Yamanaka factors holds promise for shifting cells to younger states and consequently delaying the onset of many diseases of aging. However, the delivery of transgenes and potential risk of teratoma formation present challenges forin vivoapplications. Recent advances include the use of cocktails of compounds to reprogram somatic cells, but the characteristics and mechanisms of partial cellular reprogramming by chemicals remain unclear. Here, we report a multi-omics characterization of partial chemical reprogramming in fibroblasts from young and aged mice. We measured the effects of partial chemical reprogramming on the epigenome, transcriptome, proteome, phosphoproteome, and metabolome. At the transcriptome, proteome, and phosphoproteome levels, we saw widescale changes induced by this treatment, with the most notable signature being an upregulation of mitochondrial oxidative phosphorylation. Furthermore, at the metabolome level, we observed a reduction in the accumulation of aging-related metabolites. Using both transcriptomic and epigenetic clock-based analyses, we show that partial chemical reprogramming reduces the biological age of mouse fibroblasts. We demonstrate that these changes have functional impacts, as evidenced by changes in cellular respiration and mitochondrial membrane potential. Taken together, these results illuminate the potential for chemical reprogramming reagents to rejuvenate aged biological systems, and warrant further investigation into adapting these approaches forin vivoage reversal.

overall_design: We treated fibroblasts isolated from young (4-month-old) and old (20-month-old) C57BL/6 male mice with either vehicle, 2c, or 7c for 6 days (media and treatments replaced after 3 days). Total RNA was isolated using the direct-zol kit (Zymo Research)


title: Comparative analysis of single-cell RNA sequencing methods with and without sample multiplexing

city: Singapore

first: Enrico

last: Petretto

address: 8 College Rd

country: Singapore

institute: Duke-NUS Medical School

summary: Single-cell RNA sequencing (scRNA-seq) has emerged as a powerful technique for investigating biological heterogeneity at the single-cell level in human systems and model organisms. Recent advances in scRNA-seq have enabled the pooling of cells from multiple samples into single libraries, thereby increasing sample throughput while reducing technical batch effects, library preparation time, and the overall cost. However, a comparative analysis of scRNA-seq methods with and without sample multiplexing is lacking. In this study, we benchmarked methods from two representative platforms: Parse Biosciences (Parse; with sample multiplexing) and 10X Genomics (10x; without sample multiplexing). By using peripheral blood mononuclear cells (PBMCs) obtained from two healthy individuals, we demonstrate that demultiplexed scRNA-seq data obtained from Parse showed similar cell type frequencies compared to 10X data where samples are not multiplexed. Despite a relatively lower library and cell capture efficiencies, Parse can detect rare cell types (e.g., plasmablasts and dendritic cells) which is likely due to its relatively higher sensitivity in gene detection. Moreover, comparative analysis of transcript quantification between the two platforms revealed platform-specific distributions of gene length and GC content. These results offer guidance for researchers in designing high-throughput scRNA-seq studies.

overall_design:
We benchmarked protocols (Parse Evercode WT v2 and 10x 3’ v3.1) from Parse and 10x platforms using PBMCs from two healthy donors. Human PBMCs from two healthy donors (designated here as H1 and H2) were prepared in a single batch and distributed into two aliquots. Aliquot 1 was used for 10x library preparation without multiplexing H1 and H2 samples. Aliquot 2 was used for Parse library preparation by multiplexing H1 and H2 with nine other samples in a single library. All libraries were sequenced together to minimize differences in sequencing depth.

**Notes for data downloading
GSE246624_H03_DGE_filtered.tar.gz  corresponds to Parse_H1 in the paper
GSE246624_H04_DGE_filtered.tar.gz corresponds to Parse_H2 in the paper
GSE246624_Raw.tar corresponds to 10x_H1, 10x_H2 in the paper

first: Yi

last: Xie

first: Huimei

first: Vasuki

last: Ranjani Chellamuthu

first: Ahmad

last: bin Mohamed Lajam

first: Salvatore

last: Albani

first: Andrea

last: Hsiu Ling Low

first: Jacques

last: Behmoaras


title: Single-cell network pharmacology predicts total therapies targeting multiple developmental clones in B-cell acute lymphoblastic leukemia

first: Jun

last: Yang

department: Pharmaceutical Sciences

institute: St. Jude Children's Research Hospital

summary: Taking the advantage of the human bone marrow (BM) scRNA-seq in Human cell atlas census of immune cells study, we resolved B lineage into comprehensive human B-cell development stages and identified their landscape in B-ALL. L-asparaginase is the cornerstone of combination protocols in acute lymphoblastic leukemia (ALL). After profiled B cell acute lymphoblastic leukemia (B-ALL) patient drug sensitivities ex vivo and applied network-based systems pharmacology analyses to examine signal circuitry, we revealed that the B-cell differentiation are correlated with the L-asparaginase response in B-ALL. Further multiomics analysis confirmed that L-asparaginase resistant B-ALL had higher percentage of Pre-pro-B like cells and less Pro-B like cells. By targeting BCL2, the key hub genes in Pre-pro-B cell network, Venetoclax combined with L-asparaginase can produce better outcome as demonstrated by in vitro and in vivo evaluations. In conclusion, our results identified B-ALL heterogeneity in L-asparaginase-resistant signature and BCL2 signaling and B-cell maturation stage, consistent with L-asparaginase response, providing unique opportunities for total clonal therapy.

overall_design:
To check how the composition of B-cell development stage-like cells in B-ALL patients may indicate the drug response, we performed scMultiome profiling of two L-asparaginase sensitive (Ph-like_CRLF2, Near haploid) and two L-asparaginase resistant (KMT2A, Ph+) B-ALL cases. To further verify that L-asparaginase selectively kill the sensitive B cell population, we treated two L-asparaginase responsive B-ALL PDXs with L-asparaginase or vehicle ex vivo, followed by scMultiome analysis.
To further check how the composition of B-cell development stage-like cells change after venetoclax treatment, We treated an available PDX sample with L-asparaginase, venetoclax, or both, and then performed scRNA-seq analysis.

first: Jiyang

last: Yu

first: Xin

last: Huang

first: Yizhen

last: Li


first: Jacquelyn

last: Myers


title: Disease-associated astrocyte epigenetic memory promotes CNS pathology [RNA-Seq of p300 KD, ACLY KD and scramble NOD-EAE mice]

first: Zhaorong

summary: Gene profiling of scramble, ACLY, and p300 KD astrocytes during NOD-EAE in B6 mice.

overall_design: RNA-Sequencing of Astrocytes obtained from EP300 KD NOD-EAE mice, ACLY KD NOD-EAE mice and control NOD-EAE mice.

first: Hong-Gyun

last: Lee

first: Francisco

last: Quintana


title: Unveiling the signaling network of FLT3-ITD AML improves drug sensitivity prediction

city: Rome

first: Gerardo

last: Pepe

address: via della ricerca scientifica

institute: Tor Vergara University

summary: Currently, the identification of patient-specific therapies in cancer is mainly informed by personalized genomic analysis. In the setting of acute myeloid leukemia (AML), patient-drug treatment matching fails in a subset of patients harboring atypical internal tandem duplications (ITDs) in the tyrosine kinase domain of the FLT3 gene. To address this unmet medical need, here we develop a systems-based strategy that integrates multiparametric analysis of crucial signaling pathways, patient-specific genomic and transcriptomic data with a prior-knowledge signaling network using a Boolean-based formalism. By this approach, we derive personalized predictive models describing the signaling landscape of AML FLT3-ITD positive cell lines and patients. These models enable us to derive mechanistic insight into drug resistance mechanisms and suggest novel opportunities for combinatorial treatments. Interestingly, our analysis reveals that the JNK kinase pathway plays a crucial role in the tyrosine kinase inhibitor response of FLT3-ITD cells through cell cycle regulation. Finally, our work shows that patient-specific logic models have the potential to inform precision medicine approaches.

overall_design: RNA was sequenced from peripheral blasts of 14 treatment naïve patients with de novo FLT3 ITD driven-AML diagnosis.

first: Sara

last: Latini

first: Veronica

last: Venafra

first: Giorgia

last: Massacci

first: Valeria

last: Bica

first: Simone

last: Graziosi

first: Giusj

last: Pugliese

first: Marta

last: Iannuccelli

first: Filippo

last: Frioni

first: Gessica

last: Minnella

first: John

last: Marra

first: Patrizia

last: Chiusolo

first: Manuela

last: Helmer-Citterich

first: Dimitrios

last: Mougiakakos

first: Martin

last: Boettcher

first: Thomas

last: Fischer

first: Livia

last: Perfetto

first: Francesca

last: Sacco


title: Transcriptomic changes induced by regorafenib in sorafenib-resistant hepatocellular carcinoma cells: role of TGF-beta signaling and lncRNAs

city: Ansan

first: Young Gyu

last: Chai

state: Gyeonggi-do

address: 55 Hanyangdaehak-ro

department: Molecualr & Life Science

country: South Korea

institute: Hanyang Univ.

type: Non-coding RNA profiling by high throughput sequencing

summary: We comprehensively analyzed the differentially expressed mRNAs (DEmRNAs) and lncRNAs (DElncRNAs) underlying the antitumor functions of regorafenib of sorafenib-resistant HCC cells using RNA sequencing (RNA-Seq). The treatment with regorafenib has demonstrated the ability to reverse the expression of genes and long non-coding RNAs (lncRNAs) that play crucial roles in signal pathways and epigenetic processes.

overall_design: The gene expression profile was performed with control Huh7 (Cont), regorafenib-treated huh7 (Rego), sorafenib-resistant huh7 (SR) regorafenib-treated sorafenib-resistant huh7 (SR+Rego). Samples were generated by deep sequencing, in triplicate, using Illumina 2500.

first: Young

middle: G


title: Stem-cell states converge in multi-stage cutaneous squamous cell carcinoma development [RNA-seq]

city: San Francisco

first: MARK

middle: ALAN

last: TAYLOR

state: CA

department: Hellen Diller Family Comprehensive Cancer Center

institute: UCSF

summary: Stem cells play a critical role in cancer development by contributing to cell heterogeneity, lineage plasticity, and drug resistance. We created gene expression networks from hundreds of mouse normal and tumor samples, and integrated these with lineage tracing and single-cell RNA-seq, to identify convergence of cell states in pre-malignant tumor cells expressing markers of lineage plasticity and drug resistance. Two of these cell states representing multilineage plasticity or proliferation were inversely correlated, suggesting a mutually exclusive relationship. Treatment of carcinomas in vivo with chemotherapy repressed the proliferative state and activated multilineage plasticity, while inhibition of differentiation repressed plasticity and potentiated responses to cell-cycle inhibitors. Manipulation of this cell state transition point may provide a rich source of potential combinatorial targets for cancer therapy.  These RNAseq data encompass bulk data used to treat cancer cell lines with a Pp2a inhibitor.

overall_design:
To investigate the transcriptomic effect of inhibiting Pp2a with LB100 in two murine squamous cell cancer cell lines, CCK85 and CCK168, we grew 3 biological replicates of each cell line treated with either LB100 or control vehicle.
We then performed gene expression profiling analysis using data obtained from RNA-seq.

first: Eve

last: Kandyba

first: Di

last: Wu

first: Reyno

last: Delrosario


first: Jacquelyn

last: Myers

overall_design: RNA-seq in G401 cells: shCTRL(n=3), shDCAF5(n=3), shCTRL_SMARCB1+(n=3), shDCAF5_SMARCB1+(n=3)

first: Sandi

last: Radko-Juettner

first: Charles

last: Roberts


overall_design:
ATAC-seq in G401 cells: shCTRL(n=3), shDCAF5(n=3)

ATAC-Seq performed in triplicate in G401 cells treated with the combination of shDCAF5 with ATPase inhibitor BRM014 (1uM) with proper controls. Reprocessed ATAC-Seq data in triplicate for G401s with and without SMARCB1 added back

Re-analysed Samples GSE210632/PRJNA866528 and processed data files:

GSM6433872  SRX16881727  SAMN30167975  2112966_GFP_ATAC_n1.free*
GSM6433873  SRX16881728  SAMN30167974  2118889_GFP_ATAC_n2.free*
GSM6433874  SRX16881729  SAMN30167973  2161067_GFP_ATAC_n3.free*
GSM6433875  SRX16881730  SAMN30167972  2112968_SMARCB1_ATAC_n1.free*
GSM6433876  SRX16881719  SAMN30167971  2118891_SMARCB1_ATAC_n2.free*
GSM6433877  SRX16881720  SAMN30167970  2161068_SMARCB1_ATAC_n3.free*


title: Oncostatin M signaling drives cancer-associated skeletal muscle wasting

city: Sarıyer

first: Samet

last: Agca

state: İstanbul

address: Rumelifeneri Yolu

department: Graduate School of Sciences and Engineering

country: Turkey

institute: Koc University

summary: Investigating muscle wasting in a murine model of cancer cachexia, we identified Oncostatin M (OSM) as a potential mediator of inflammatory responses in skeletal muscle. OSM is a member of the IL-6 family of cytokines and has crucial functions in cell growth, differentiation, and inflammation. Our results demonstrate that OSM induces muscle atrophy. To understand if its effect is specific or it is a general effect of IL6 family cytokines, primary myotubes were treated with OSM, IL6 and LIF for 48hrs. Our findings showed that OSM potently induces muscle wasting in differentiated myotubes.

overall_design: Primary myoblasts were differentiated to myotubes and treated with recombinant OSM, IL-6 and LIF for 48hrs. The RNA was isolated and sent for sequencing.

first: Serkan

last: Kir

first: Aylin

last: Domaniku

first: Batu

last: Toledo

first: Aynur

last: Kashgari

first: Sevval

middle: N

last: Bilgic


title: Breast cancer-subtype and infiltrating macrophage signatures predict chemotherapy-response and survival

status: Public on Mar 20 2024

city: Athens

first: William

last: Bastian

state: Georgia

address: 250 W Green Street

department: Institute of Bioinformatics

institute: Universty of Georgia

summary: Triple-Negative Breast Cancer (TNBC) is a heterogeneous collection of cancers where personalized treatment is difficult and chemotherapy and immunotherapy combinations are the main treatment options.  Many attempts to tackle patient heterogeneity have focused on defining cancer-intrinsic subtypes based on differential tumor mRNA-expression across patient cohorts.  While these multi-gene diagnostics have shown success in hormone receptor- positive cancers (e.g. OncotypeDX), no TNBC classifiers have shown clinical utility in predicting patient survival or treatment response.   We hypothesize that TNBC-infiltrating immune-cells both affect mRNA-based classification and contribute to treatment response variability.  To evaluate this hypothesis, we benchmarked the performance of common TNBC-classification (TNBC-type) and infiltrating immune (CIBERSORT) algorithms on the same underlying datasets.   Encouragingly, we found that – as with OncotypeDx– highly proliferative TNBC-subtypes (BL1) show the strongest evidence of response to cytotoxic chemotherapies.   Interestingly, this cancer-proliferative signature (BL1) is strongly correlated with enrichment in tumor-infiltrating lymphocyte signatures (TIL) which show superior prognostic and predictive power.    In addition, Tumor Associated Macrophage (TAM) signatures show independent predictive and prognostic power for both patient survival and response to anthracycline- and taxane-based chemotherapies.   These gene signature-based correlations were validated in a new independent cohort of 67 TNBC-patients treated with neoadjuvant chemotherapy.  Overall, these results argue for the independent contributions of both cancer-intrinsic and -extrinsic factors in predicting treatment response in the neoadjuvant setting.

overall_design:
To assess the variability of the tumor microenvironment in triple negative breast cancer patients, we sequences 42 pre-treatment biopsies and 31 post-treatment surgical resected tumor samples.
We performed various enrichment analysis and cellular deconvolution methods to bulk-RNA-seq samples.

first: Jane

last: Meisel

first: Ji-Hoon

last: Lee

first: Nada

last: Shaker

first: Lyra

last: Griffiths

first: Zaibo

last: Li

first: Eugene

middle: F

last: Douglass

first: Xiaoxian


title: Immunological role of platelets in Theiler’s virus-induced  inflammatory demyelinating disease and myocarditis

city: Osakasayama

first: Ijaz

last: Ahmad

state: Osak/Kansai

address: 377-2 Onohigashi

department: Department of Microbiology

institute: Kindai University Faculty of Medicine

summary: Platelets have been immunologically associated with viral and immune-mediated diseases such as Severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) and Experimental autoim-mune encephalomyelitis (EAE). However, the role of platelets in Theiler’s murine encephalo-myelitis virus (TMEV)-induced myocarditis and inflammatory demyelination disease (IDD) is still unknown. We determine whether platelets were associated with TMEV infection and whether glycoprotein Ib alpha chain (GPIbα/CD42b) antibody injection could affect the pathogenicity of TMEV-induced myocarditis and TMEV-IDD. We conducted a mechanistic experiment by injecting TMEV-infected mice with the anti-GPIbα antibodies 0 and 5 days p.i. (“Early” group) or 18 and 22 days p.i. (“Late” group). Using in silico and in vivo approaches, we found platelets and platelet-related genes were associated with TMEV infection. Platelet depletion in Early and Late mice reduced fibrotic area in the heart, inflammatory demyelinating lesions with lower viral persistence in the CNS and altered antiviral antibody responses. Thus, platelets contribute to the pathogenesis of TMEV infection by promoting fibrosis and CNS inflammation. Platelet-depletion treatment might open new therapeutic approaches for TMEV-induced myocarditis and TMEV-IDD.

overall_design: We aimed to determine the roles of platelets in the pathogenesis of multiple sclerosis and viral myocarditis, using a mouse model induced by Theiler's murine encephalomyelitis virus (TMEV) infection. We conducted the RNA sequencing analyses of the spleen and platelet samples from female SJL/J mice infected with TMEV (2 × 10^5 plaque forming units) intracerebrally on 4, 7, and 35 days post infection. As a control, we prepared age-matched female SJL/J mice injected with PBS intracerebrally.

first: Seiichi

last: Omura

first: Fumitaka

last: Sato

first: Ah-Mee

last: Park

first: Sundar

last: Khadka

first: Felicity

last: Gavins

first: Hiroki

last: Tanaka

first: Motoko

last: Kimura

first: Ikuo

last: Tsunoda


title: Immunoglobulin G N-glycan Markers of Accelerated Biological Aging During Chronic HIV Infection

city: Philadelphia

first: Priyankara

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

summary: People living with HIV (PLWH) experience increased vulnerability to premature aging and inflammation-associated comorbidities, even when HIV replication is suppressed by antiretroviral therapy (ART). However, the factors associated with this vulnerability remain uncertain. In the general population, alterations in the N-glycans on IgGs trigger inflammation and precede the onset of aging-associated diseases. Here, we investigate the IgG N-glycans in cross-sectional and longitudinal samples from 1,214 women and men, living with and without HIV. PLWH exhibit an accelerated accumulation of pro-aging-associated glycan alterations and heightened expression of senescence-associated glycan-degrading enzymes compared to controls. These alterations correlate with elevated markers of inflammation and the severity of comorbidities, potentially preceding the development of such comorbidities. Mechanistically, HIV-specific antibodies glycoengineered with these alterations exhibit a reduced ability to elicit anti-HIV Fc-mediated immune activities. These findings hold potential for the development of biomarkers and tools to identify and prevent premature aging and comorbidities in PLWH.

overall_design: HIV+ and HIV-negative counterparts

first: Leila

last: Giron

first: Mohamed

last: Abdel-Mohsen


title: FGFR inhibition blocks NF-ĸB-dependent glucose metabolism and confers metabolic vulnerabilities in cholangiocarcinoma

city: boston

first: Yuanli

last: Zhen

address: 185 cambridge street

department: cancer center

institute: mgh

summary: Genomic alterations that activate FGFR2 are common in intrahepatic cholangiocarcinoma (ICC) and confer sensitivity to treatment with FGFR inhibitors. However, the depth and duration of responses are often limited. Elucidating the FGFR2-driven oncogenic program and the adaptions to FGFR inhibition is needed to gain insight into the biology of these tumors and inform future therapeutic development. Here, we conducted transcriptomic analysis of patient-derived models to define the pathways that fuel tumor growth downstream of oncogenic FGFR2 signaling in ICC and to uncover compensatory mechanisms associated with pathway inhibition. For these studies, we performed RNA sequencing  in our FGFR-driven ICC models, including cell line ICC13-7 , PDX MG69 and MG212. We treated ICC13-7 with DMSO or 75 nM Futibatinib for 4/12/24 hours, MG69 with vehicle or Futibatinib for 14 days and MG212 with vehicle or Pemigatinib for 11 days followed by RNA sequencing. In addition, ICC13-7 cells were transfected with siScramble and siRELA and followed by RNA sequencing.

overall_design: To identify the oncogenic program controlled by FGFR signaling in FGFR2-fusion+ ICC, we took advantage of a series of patient derived FGFR2-fusion+ ICC models, including cell lines and PDX. We then treated the models with FGFR inhibitor or control to perform the RNA sequencing and analyzed the gene expression profiling.


title: KEAP1-mutant lung cancers weaken anti-tumor immunity and promote an M2-like macrophage phenotype.

city: Indianapolis

first: Ana

middle: S

last: Leal

state: IN

address: 980 W Walnut St

department: Department of Medicine

institute: Indiana University

summary: Considerable advances have been made in lung cancer therapies, but there is still an unmet clinical need to improve survival for lung cancer patients. Immunotherapies have improved survival, although only 20-30% of patients respond to these treatments. Interestingly, cancers with mutations in KEAP1, the negative regulator of the NRF2 cytoprotective pathway, are resistant to immune checkpoint inhibition and correlate with decreased immune cell infiltration. NRF2 is known for promoting an anti-inflammatory phenotype when activated in immune cells, but the study of NRF2 activation in cancer cells has not been adequately assessed. The objective of this study was to determine how lung cancer cells with constitutive NRF2 activity interact with the immune microenvironment to promote cancer progression. To assess this, we generated CRISPR-edited mouse lung cancer cell lines by knocking out KEAP1 or NFE2L2 genes. We also utilized publicly available single cell data through the Gene Expression Omnibus to investigate tumor/immune cell interactions. We show here that KEAP1-mutant cancers promote immunosuppression of the tumor microenvironment. Our data suggests KEAP1-deletion is sufficient to alter the secretion of cytokines, increase expression of immune checkpoint markers on cancer cells, and alter recruitment and differential polarization of immunosuppressive macrophages that ultimately lead to T cell suppression.

overall_design: RNA sequencing was used to evaluate the transcriptomic changes related to NRF2 activation in LL2 lung cancer cells. Specifically, we used CRIPSR to functionally delete KEAP1 thereby inducing NRF2 transcriptional activity. We also created a second cell line by knocking out the NRF2 protein. We isolated 3 clonally derived KEAP1-mutant and 1 NRF2-mutant cell line. We then compared the new cell lines to the WT parental line. mRNA was isolated from the cell lines (3 biologic replicates per group) for comparative gene expression analysis.

first: Occhiuto

last: Christopher

first: Liby

last: Karen


title: Cellular mechanotransduction of human osteoblasts in microgravity

city: Ann Arbor

first: Allen

last: Liu

state: Michigan

address: 2350 Hayward Street

department: Mechanical Engineering

institute: University of Michigan

summary: NOT PROVIDED; REQUESTED

overall_design: We measured gene expression profiles in human fetal osteoblast spheroids (hFOBs) in response to changes in pressure with and without BMP2 treatment.

first: Nadab

middle: H

last: Wubshet

first: Grace

last: Cai

first: Samuel

last: Chen

first: Shan-Shan

last: Lin

first: Pamela

last: Duran

first: Benjamin

last: Yang

first: Carlos

last: Aguilar


title: APOE3Christchurch modulates tau phosphorylation and β-catenin/Wnt signaling in iPS cell-derived cerebral organoids from Alzheimer’s cases

first: Joseph

last: Arboleda-Velasquez

state: Massachusetts

address: 20 Staniford St.

institute: Schepens Eye Research Institute

summary: Alzheimer’s disease (AD) is the most common cause of dementia. A patient with the PSEN1 E280A mutation and homozygous for APOE3 Christchurch (APOE3Ch) was found to have extreme resistance to cognitive decline and tauopathy despite having high amyloid burden. We established induced pluripotent stem cell (iPS)-derived cerebral organoids from this resistant case and a non-protected control. We used CRISPR/Cas9 gene editing to remove or add APOE3Ch from these iPS cells to assess causality. We found a pattern of tau phosphorylation consistent with protection in APOE3Ch cerebral organoids. We identified Cadherin and Wnt signaling regulation by APOE3Ch through scRNA-sequencing and elevated β-catenin protein in APOE3Ch organoids as a potential mediator of protection against tauopathy. We have identified that ApoE3Ch acts as a Wnt signaling enhancer. Our study found that APOE3Ch is necessary and sufficient to confer resistance to tauopathy, a hallmark of AD. This establishes the premise for development of novel, protected case-inspired therapeutics for AD and tauopathies.

overall_design: A patient with the PSEN1 E280A mutation and homozygous for APOE3 Christchurch (APOE3Ch) displayed remarkable resistance to Alzheimer's disease (AD) cognitive decline and tauopathy, despite having a high amyloid burden. To investigate the causal role of APOE3Ch in protection, we generated induced pluripotent stem cell (iPS)-derived cerebral organoids from this resistant case (designated "alpha" (α))  and a non-protected control (designated "omega" (ω)), using CRISPR/Cas9 gene editing to modulate APOE3Ch expression. Both patients were from the PSEN1 (E280A) "Paisa" kindred.

first: Randall

last: Mazzarino

first: Paula

last: Perez-Corredor

first: Timothy

last: Vanderleest

first: Guido

last: Vacano

first: Justin

last: Sanchez

first: Claudia

last: Marino

first: Nelson

middle: D

last: Villalba-Moreno

first: Susanne

last: Krasemann

first: Miguel

last: Mendivil-Perez

first: David

last: Aguillón

first: Marlene

last: Jimenez-Del-Río

last: Baena

first: Diego

last: Sepulveda-Falla

first: Francisco

last: Lopera

first: Yakeel

middle: T

last: Quiroz


title: Regulation of T cell gene expression and function by the steroid hormone precursor Pregnenolone

city: Abu dhabi

first: Youssef

last: Idaghdour

state: Abu dhabi

address: Saadiyat Marina District

department: Biology

country: United Arab Emirates

institute: NYUAD

summary: We report the transcriptional changes in primary T cells expanded from peripheral blood mononuclear cells (PBMCs) upon treatemnt with the steroid precursor, pregnenolone.

overall_design: Expanded T cells were non-activated or activated through the T cell receptor with CD3/CD28 Dyna Beads for 24 hours. They were subsequently treated or untreated with 200 µM of pregnenolone for 2 or 24 hours. We additionally included a "basal" condition that involved no activation or treatment at 0 hours (time of activation). All nineconditions included 2-4 biological replicates, whereby the same expanded T cells were activated/non-actived and treated/untreated in separate wells per condition, yielding a total of 33 samples. RNA was extracted from each sample, and library preparation was performed, whereby some samples had library preparation done in duplicates (technical rep). cDNA libraries were then seuqenced.

first: Yasmine

last: El Hajj

first: Tala

last: Shahin

first: Vinu

last: Manikandan

first: Youssed


title: Transcriptomic analysis of WT and LRP5-KO neutrophils using bulk RNA-sequencing

city: New Haven

first: Wenwen

last: Tang

state: CT

address: Rm 320, 10 Amistad St

institute: Yale Univeristy

summary: Analysis of the gene expression profiles of primary neutrophils isolated from WT and LRP5-KO mouse bone marrow.  Results provide insights into molecular mechanisms associated with the altered neutrophil functions resulting from LRP5-deficiency.

overall_design: mRNA profiles of primary neutrophils from 10 weeks old wild type (WT) and  LRP5f/f/Lyz2Cre+ (LRP5-KO) mice

first: Yi

last: Luan

first: Dianqing

last: Wu


title: Identification of calcineurin-dependent, Crz1-independent gene expression changes in response to chronic KCl stress

status: Public on Mar 19 2024

city: Worcester

first: Jennifer

last: Benanti

address: 364 Plantation St., LRB 525

department: Molecular, Cell and Cancer Biology

institute: University of Massachusetts Medical School

summary: Gene expression was quantified in S. cerevisae cells after 48 hours of treatment with KCl. crz1 and crz1 cnb1 mutant strains were compared to allow the identification of calcineurin-dependent gene expression changes that are independent of the downstream transcription factor Crz1.  We find that calcineurin has very little effect on gene expression in response to KCl.

overall_design: Gene expression was measured in cells lacking Crz1 (crz1) and cells lacking both Crz1 and calcineurin (crz1 cnb1). For each strain samples were collected before treatment and 48 hours following the addition of 400mM KCl. Triplicate experiments were performed.

first: Mackenzie

middle: J

last: Flynn

first: Rui

last: Li

first: Lihua

last: Zhu


title: Identification of calcineurin-dependent, Crz1-independent gene expression changes in response to chronic CaCl2 stress

summary: Gene expression was quantified in S. cerevisae cells over a time course of three days of CaCl2 treatment to activate calcineurin. crz1 and crz1 cnb1 mutant strains were compared to allow the identification of calcineurin-dependent gene expression changes that are independent of the downstream transcription factor Crz1.  We show that mitochondrial genes are downregulated in both geneotypes over time. Additionally, genes that promote glutathione biosynthesis are upregulated in cells that express calcineurin.

overall_design: Gene expression was measured in cells lacking Crz1 (crz1) and cells lacking both Crz1 and calcineurin (crz1 cnb1). For each strain samples were collected before treatment and 12, 48 and 72 hours following the addition of 200mM CaCl2. Triplicate time course experiments were performed.

middle: A


title: Identification of calcineurin-dependent gene expression changes in response to chronic stress

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

overall_design: Refer to individual Series


title: Exclusive expression of KANK4 promotes myofibroblast mobility in keloid tissues

city: Nagoya

first: Mayumi

last: Oishi

address: Tsurumaicho 65

department: Plastic and Reconstructive Surgery

institute: Nagoya University Graduate School of Medicine

summary: Keloids are characterized by abnormal wound healing with excessive accumulation of extracellular matrix. Myofibroblasts are the primary contributor to extracellular matrix secretion, playing an essential role in the wound healing process. However, the differences between myofibroblasts involved in keloid formation and normal wound healing remain unclear. To identify the specific characteristics of keloid myofibroblasts, we initially assessed the expression levels of well-established myofibroblast markers, α-smooth muscle actin (α-SMA) and transgelin (TAGLN), in scar and keloid tissues (n = 63 and 51, respectively). The objective was to evaluate the enrichment of myofibroblasts in these tissues. Although myofibroblasts were present in significant quantities in keloids and immature scars, they were absent in mature scars. Next, we conducted RNA sequencing using myofibroblast-rich areas from keloids and immature scars to investigate the difference in RNA expression profiles among myofibroblasts. Comparison of the results with publicly available RNA-sequencing datasets revealed that 112 genes were significantly upregulated and 108 genes were downregulated in keloid samples compared with immature scar samples. Among them, KN motif and ankyrin repeat domains 4 (KANK4) was identified as a specifically upregulated gene in keloids. Immunohistochemical analysis showed that KANK4 protein was expressed in myofibroblasts in keloid tissues; however, it was not expressed in any myofibroblasts in immature scar tissues. There are two main isoforms of KANK4 transcripts, with short isoforms being dominantly expressed in keloid tissue. Overexpression of the short isoform of KANK4 enhanced cell mobility in keloid myofibroblasts. Our results suggest that the KANK4-mediated increase in myofibroblast mobility contributes to keloid pathogenesis.

overall_design: To identify the transcriptome of myofibroblasts in keloids and immature scars, we performed RNA sequencing from TAGLN-positive tissue in keloid samples (n=3) and immature scar samples (n=2).


title: SIX2 promotes cell plasticity via Wnt/beta-catenin signalling in androgen receptor independent prostate cancer (ChIP-seq)

city: Kuopio

first: Ville

last: Paakinaho

address: Yliopistonranta 8

department: School of Medicine

country: Finland

institute: University of Eastern Finland

summary: The use of androgen receptor (AR) inhibitors in prostate cancer gives rise to increased cellular lineage plasticity resulting resistance to AR-targeted therapies. By examining the chromatin landscape of AR positive prostate cancer cells following exposure to the AR inhibitor enzalutamide, we have identified a novel regulator of cell plasticity, homeobox transcription factor SIX2, whose motif is enriched in accessible regions post-treatment. Our investigation demonstrates that depletion of SIX2 in androgen-independent PC-3 prostate cancer cells is sufficient to induce a switch from a stem-like to an epithelial state, leading to the reduction of key cancer-related properties such as proliferation, colony formation, and metastasis both in vitro and in vivo. These effects are mediated through downregulation of Wnt/β-catenin signalling pathway and subsequent reduced nuclear localization of β-catenin. Collectively, our findings provide compelling evidence that depletion of SIX2 may represent a promising strategy for overcoming cell plasticity mechanisms driving AR resistance in prostate cancer.

overall_design: Examination of SIX2 chromatin binding by ChIP-seq from PC-3 prostate cancer cells. All sequencing was done with Illumina NextSeq 500.

first: Noora

last: Leppänen

first: Kirsi

last: Ketola


title: SIX2 promotes cell plasticity via Wnt/beta-catenin signalling in androgen receptor independent prostate cancer (RNA-seq)

overall_design: Gene expression profiling by RNA-seq from PC3 cells treated with non-targeting siRNA or SIX2 targeting siRNA. All sequencing was done with Illumina NovaSeq 6000.


title: Loss of TET2 increases B-1 cell number and IgM production while limiting CDR3 diversity

status: Public on Mar 18 2024

city: Charlottesville

first: Coleen

middle: A.

last: McNamara

state: VA

address: 345 Crispell Dr

department: Carter Immunology Center

institute: University of Virginia

summary: Recent studies have demonstrated a role for Ten-Eleven Translocation-2 (TET2), an epigenetic modulator, in regulating germinal center formation and plasma cell differentiation in B-2 cells, yet the role of TET2 in regulating B-1 cells is largely unknown. Here, B-1 cell subset numbers, IgM production, and gene expression were analyzed in mice with global knockout of TET2 compared to wildtype (WT) controls. Results revealed that TET2-KO mice had elevated numbers of B-1a and B-1b cells in their primary niche, the peritoneal cavity, as well as in the bone marrow (B-1a) and spleen (B-1b). Consistent with this finding, circulating IgM, but not IgG, was elevated in TET2-KO mice compared to WT. Analysis of bulk RNASeq of sort purified peritoneal B-1a and B-1b cells revealed that heavy and light chain immunoglobulin gene expression was significantly reduced, predominantly in B-1a cells from TET2-KO mice compared to WT controls. As expected, the expression of IgM transcripts was the most abundant isotype in B-1 cells. Yet, only in B-1a cells was there a significant increase in the proportion of IgM transcripts in TET2-KO mice compared to WT. Analysis of the CDR3 of the BCR revealed an increased abundance of replicated CDR3 sequences in B-1 cells from TET2-KO mice, which was more clearly pronounced in B-1a compared to B-1b cells. V-D-J usage and circos plot analysis of V-J combinations showed enhanced usage of VH11 and VH12 pairings. Taken together, our study is the first to demonstrate that loss of TET2 increases B-1 cell number and IgM production and reduces CDR3 diversity, which could impact many biological processes and disease states that are regulated by IgM to self or other antigens.

overall_design: To investigate the role of global TET2-KO in function and BCR repertoire of different B cell subtypes.

first: Maria

last: Murach

first: Stefan

last: Bekiranov

first: Emily

last: Dennis


title: SIX2 promotes cell plasticity via Wnt/beta-catenin signalling in androgen receptor independent prostate cancer


title: Domestication has altered gene expression in pea seed coat

city: Troubsko

first: Oldrich

last: Trneny

address: Zahradni 1

country: Czech Republic

institute: Agricultural research Ltd.

summary: In angiosperms, the mature seed consists of an embryo (E), a seed coat (SC), and, in many cases, an endosperm. In contrast to knowledge about embryo and endosperm, we have relatively little knowledge of SC, especially at the genomics level. In this study, we analyzed the gene expression during seed development using the panel of cultivated and wild pea genotypes. We report the comprehensive gene expression changes related both to development as well as domestication status. Analysis of seed developmental stages revealed extensive modification of gene expression between wild pea progenitor and cultivated pea crop. A significant difference in gene expression dynamics appeared between early and late developmental stages D1, D2, and D3, D4, D5 in wild pea genotypes, where the expression was increased 3-5-fold and 5-10-fold, respectively. Our work extends knowledge about the role of the seed coat during pea seed development. We described gene expression dynamic resulting in specific metabolic profiles providing new insight into pea domestication.

sample_organism:
Lathyrus oleraceus
Lathyrus oleraceus subsp. biflorus
[Pisum sativum] subsp. abyssinicum

overall_design: To obtain spatial and temporal representation, we performed RNA sequencing analysis of isolated seed tissues (SC and E) at 5 developmental stages (D1-5). There were three genotypes representing wild (P. elatius, JI64, JI261, JI1794), two domesticated (P. sativum, JI92 landrace and cv. Cameor) and Ethiopian pea P. abyssinicum (PI358617). Reads from each sample were mapped to the pea reference genome (Cameor v1.0).

first: Barbora

last: Klčová

first: Jana

last: Balarynová

first: Oldřich

last: Trněný

first: Petr

last: Smýkal


title: ASH2L mediates epidermal differentiation and hair follicle morphogenesis via the regulation of the Notch signaling pathway activity

city: Shanghai

first: Qirui

last: Wang

state: Shanghai

address: 639 Zhi Zao Ju Road

department: Department of Plastic and Reconstructive Surgery

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