title: Combination therapy with oncolytic virus and adoptively transferred T cells or mRNA vaccine amplifies antitumor effects [RNA-Seq]

city: Xiamen

first: Jinhang

last: He

state: Fujian

address: No.4221, South Xiang'an Road

institute: Xiamen University

summary: Adoptive T-cell therapy or oncolytic virotherapy has made significant progress, but the efficacy was limited by the lack of infiltration into solid tumors when used alone. Here, an oncolytic virus (rVSV-LCMVG) was designed and combined with adoptively transferred T cells. By turning cold tumors hot, in B16 tumor-bearing mice, combination therapy showed superior antitumor effects than monotherapy, whether rVSV-LCMVG was administered intratumorally or intravenously. Combination therapy significantly increased cytokine and chemokine levels within tumors and sensitized refractory tumors by boosting T-cell recruitment, down-regulating the expression of PD1, and restoring effector-T cell function. To offer a combination therapy with greater translational value, mRNA vaccines were introduced to induce tumor-specific T cells instead of adoptively transferred T cells, and exhibited comparable amplified anti-tumor effects. This study proposed a rational combination therapy of oncolytic virus with adoptive T-cell transfer or mRNA vaccines encoding tumor-associated antigens, in terms of synergistic efficacy and mechanism.

overall_design: Comparative gene expression analysis and enrichment analysis of flowcytometry sorted B16-OVA-tumor infiltrating OT1-T cell and P14-T cell RNA-seq data under normal condition and rVSV-LCMVG treatment condition.

first: Rao

last: Fu

first: Ruoyao

last: Qi

first: Hualong

last: Xiong

first: Xing

last: Lei


title: Transcriptomic evaluation of tau and TDP-43 synergism shows tauopathy predominates.

status: Public on Mar 15 2024

city: Seattle

first: Nicole

last: Liachko

state: WA

address: 1660 Columbian Way S.

department: GRECC

country: USA

institute: VA Puget Sound Health Care System

type: Expression profiling by high throughput sequencing

summary: Cellular responses to co-morbid tau and TDP-43 preceding neurodegeneration have not been characterized. In this study, we evaluate transcriptomic changes at time-points preceding frank neuronal loss using a C. elegans model of tau and TDP-43 co-expression. We find significant differential expression and exon usage in genes enriched in multiple pathways including lipid metabolism and lysosomal degradation.  We note that tau related changes largely resemble tau/TDP-43 changes. We test loss-of-function mutations in a subset of tau and TDP-43 responsive genes, identifying new modifiers of neurotoxicity. Characterizing early cellular responses to tau and TDP-43 co-pathology is critical for understanding protective and pathogenic responses to mixed proteinopathies, and an important step in developing therapeutic strategies protecting against pathological tau and TDP-43 in AD.

overall_design: C.elegans animals expressing pan-neuronal human wild-type tau, human wild-type TDP-43 and aniamls expressing both wild-type human tau and TDP-43 were used in this study. N2 were the controls. To examine transcriptomic changes occuring prior and after the neurodegeneration, RNA was collected from all genotypes at L2 and L4 stage.


title: Gene expression data of LT-HSC, MEP and CMP cells from Mx1cre;Atf4 fl/fl mice(cKO) BM and those from controls

city: Tianjin

first: ZhaoFeng

last: Zheng

address: 288 Nanjing Road, Heping District, Tianjin, China

country: China

institute: Institute of Hematology & Blood Diseases Hospital,

summary: To elucidate the mechanisms underlying the role of Atf4 deficiency in erythropoiesis, we performed RNA sequencing on  LT-HSC, MEP and CMP cells from Atf4 hematopoietic cell-specific conditional knockout  mice(cKO)  and those from WT mice.

overall_design: RNA-seq analyses on  LT-HSC, MEP and CMP cells from Mx1cre; Atf4fl/fl mice (cKO) in comparison with those from Atf4fl/fl mice (WT).

first: Tao

last: Cheng

first: Hui

first: Zhaofeng

first: Shangda

last: Yang


title: Hide-and-seek game in pathogen genome: Transposon elements play an important role in shaping population diversification of rice blast fungus Magnaporthe oryzae

status: Public on Mar 16 2024

city: Hangzhou

first: lianyu

last: lin

state: Zhejiang

address: Zijingang Campus of Zhejiang University,Yuhangtang Road No.866

institute: Zhejiang University

summary: RNA-seq of 16 M. oryzae rice isolates in hyphal stage

overall_design: Total RNAs of 16 M. oryzae rice isolates in hyphal stage were extracted for sequencing

first: Lianyu

last: Lin

first: Zhenhui

last: Zhong

first: Lili

first: Zonghua

last: Wang


title: Combination therapy with oncolytic virus and adoptively transferred T cells or mRNA vaccine amplifies antitumor effects

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

overall_design: Refer to individual Series


title: Combination therapy with oncolytic virus and adoptively transferred T cells or mRNA vaccine amplifies antitumor effects [scRNA-Seq]


title: Differential gene expression in UCHL1 silenced ovarian cancer cells

city: Indianapolis

first: Sumegha

last: Mitra

state: IN

address: C547 Walther Hall (R3), 980 W Walnut Street

institute: Indiana University

summary: We report dysregulated genes upon silencing UCHL1 in high-grade serous ovarian cancer cell line, Kuramochi.

overall_design: Examination of differentially regulated genes in UCHL1 silenced Kuramochi cells.

first: Ram

last: Podicheti

first: Jon

last: Choi


title: Defining the contribution of microRNA-specific slicing Argonautes in animals

city: Québec

first: Martin

last: Simard

address: 9 McMahon

department: Oncology

country: Canada

institute: CHU de Québec-Université Laval Research Center

type: Non-coding RNA profiling by high throughput sequencing

summary: microRNAs regulate gene expression through interaction with an Argonaute protein family member. While some members of this protein family retain an enzymatic activity capable of cleaving RNA molecules complementary to Argonaute-bound small RNAs, the role of the slicing activity in the canonical microRNA pathway is still unclear in animals. To address the importance of slicing Argonautes in animals, we created Caenorhabditis elegans mutant strains carrying catalytically dead endogenous ALG-1 and ALG-2, the only two slicing Argonautes essential for the miRNA pathway in this animal model. We observe that the loss of ALG-1 and ALG-2 slicing activity affects overall animal fitness and causes phenotypes reminiscent of miRNA defects only when grown and maintained at restrictive temperature. Furthermore, the analysis of global miRNA expression show that the catalytic activity of ALG-1 and ALG-2 differentially regulate the level of specific subsets of miRNAs in young adults. We also demonstrate that altering the slicing activity of those miRNA-specific Argonautes does not result in any defect in the production of canonical miRNAs. Together, these data support that the slicing activity of miRNA-specific Argonautes functions to maintain levels of a set of miRNAs for optimal viability and fitness in animals particularly exposed to specific growing conditions.

overall_design: Compare the miRNA expression profile among the different mutants in C. elegans

first: Anisha

last: Pal

first: Vaishnav

last: Vasudevan

first: François

last: Houle

first: Michael

last: Lantin

first: Katherine

middle: A

last: Maniates

first: Miguel

middle: Q

last: Huberdeau

first: Allison

middle: L

last: Abbott

middle: J


title: Genome-wide effect of BBX28 on the transcriptional response under shade in Arabidopsis thaliana

city: CABA

first: Javier

last: Botto

state: BUENOS AIRES

address: AV SAN MARTIN 4453

department: FAC AGRONOMIA UBA

country: Argentina

institute: IFEVA

summary: Shade avoidance syndrome (SAS) is a strategy of major adaptive significance that includes the elongation of vegetative structures and leaf hyponasty. Major transcriptional rearrangements underlie for the reallocation of resources to elongate vegetative structures and redefine the plant architecture under shade to compete for photosynthesis light. BBX28 is a transcription factor involved in seedling de-etiolation and flowering in Arabidopsis thaliana, but its function in the SAS is completely unknown. Here we studied the function of BBX28 in the regulation of gene expression under simulated shade conditions.

overall_design: Three biological replicates of Col-0 and bbx28-5 seedlings grown for two days in a short-day photoperiod (10h/14h) and transferred at the beggining of the third day to simulated shade condition (SS) or mantained in white light (WL) for four hours.

first: Maite

last: Saura-Sanchez


title: Nervous system development related gene expression regulation in the zebrafish embryo after exposure to valproic acid and retinoic acid: a genome wide approach

city: 91400 Orsay

first: Florent

last: Dumont

state: Ile de France

address: 17 avenue des sciences

country: France

institute: Université Paris-Saclay

summary: In our search for biomarkers of maldevelopment, we focused on chemically-induced perturbation of the retinoic acid signaling pathway (RA-SP), a major pathway implicated in a plethora of developmental processes. A genome-wide expression screening was was performed on zebrafish embryos treated with two teratogens, all-trans retinoic acid (ATRA) and valproic acid (VPA), and a negative control, folic acid (FA).

overall_design:
Comparative transcriptome analyses between Control, teratogen (all-trans retinoic acid and valproic acid) and negative control (folic acid)   Exposition realised for 4 hrs from 3 hours post fertilisation to 7hpf
***RAW data not provided***

first: Laura

last: Samrani


title: Genome-wide analysis of the lncRNAs and miRNAs involved in flower development in radish

status: Public on Mar 14 2024

city: Guiyang

first: yue

middle: yue

last: Jin

address: Jiaxiu South Road, Huaxi District

department: College of agriculture

institute: Guizhou University

summary: To further verify the differences in IncRNA and miRNA during radish flowering, we conducted transcriptome analysis on samples taken before and after radish flowering. Obtain IncRNA and miRNA from the differential table and perform qRT-PCR validation on them.

overall_design: Comparison of gene expression analysis of RNA-seq data before and after radish flowering

first: Xiaobo

last: Luo

first: Yadong

last: Li

first: Yueyue

first: Wanping

last: Zhang

first: Zhenju

last: Cao


title: Effect of Hypoxia, Oscillatory Hypoxia, and Lactate on MDA 231 Cells

city: Farmington

first: Yasir

last: Suhail

state: Connecticut

address: 263 Farmington Avenue

department: BME

institute: UCHC

summary: MDA 231 cells were cultured under hypoxia, normoxia, oscillatory hypoxia, and lactate and sequenced for RNA

overall_design: 3 samples per condition, for hypoxia, oscillatory hypoxia, lactate and control

first: Yamin

last: Liu

first: Kshitiz

last: Gupta


title: Therapeutic Prime/Pull Vaccination of HSV-2 Infected Guinea Pigs with the Ribonucleotide Reductase 2 (RR2) and CXCL11 boosts TRM and TEM CD4+/CD8+ T cells to protect from recurrent genital herpes

city: Irvine

first: Lbachir

last: BenMohamed

state: California

address: 843 Health Sciences Road, Hewitt Hall, 2nd Floor

institute: University of California Irvine

summary: Following acute herpes simplex virus type 2 (HSV-2) infection, the virus undergoes an asymptomatic latent infection of sensory neurons of dorsal root ganglia (DRG). Chemical and physical stress cause intermittent virus reactivation from latently infected DRG and recurrent virus shedding in the genital mucosal epithelium causing genital herpes in symptomatic patients. While T-cells appear to play a role in controlling virus reactivation from DRG and reducing the severity of recurrent genital herpes, the mechanisms for recruiting these T-cells into DRG and the vaginal mucosa (VM) remain to be fully elucidated. The present study investigates the effect of CXCL9, CXCL10, and CXCL11 T-cell-attracting chemokines on the frequency and function of DRG- and VM-resident CD4+ and CD8+ T cells and its effect on the frequency and severity of recurrent genital herpes in the recurrent herpes guinea pig model. HSV-2 latent-infected guinea pigs were immunized intramuscularly with the HSV-2 RR2 protein (Prime) and subsequently treated intravaginally with the neurotropic adeno-associated virus type 8 (AAV-8) expressing CXCL9, CXCL10, or CXCL11 chemokines to recruit CD4+ and CD8+ T cells into the infected DRG and VM (Pull). Compared to the RR2 therapeutic vaccine alone, the RR2/CXCL11 prime/pull therapeutic vaccine significantly increased the frequencies of functional tissue-resident (TRM cells) and effector (TEM cells) memory CD4+ and CD8+ T cells in both DRG and VM tissues. This was associated with less virus in the healed genital mucosal epithelium and reduced frequency and severity of recurrent genital herpes. These findings confirm the role of local DRG- and VM-resident CD4+ and CD8+ T cells in reducing virus shedding at the vaginal site of infection and the severity of recurrent genital herpes and propose the novel prime-pull vaccine strategy to protect against recurrent genital herpes.

overall_design:
In the present study, we sought to improve protein-based vaccination by combining it with a prime and pull strategy. The strategy involves conventional parenteral vaccination using HSV-2 specific RR2 protein to elicit systemic T-cell responses (prime), followed by recruitment of activated T cells via administration of an adenovirus expressing chemokine or T cell attractant (pull), for those T cells to establish long-term protective immunity. The adeno-associated virus type 8 (AAV8) was used to express the chemokines as it efficiently targets the enteric nervous system in guinea pigs. The immunization results showed that the primary CD8+T cell responses were of similar magnitudes in the spleen, whereas the frequency and number of CD8+T cells in the vaginal mucocutaneous tissue were significantly higher in vaccinated mice treated with adenovirus-expressing chemokine as compared with the control immunized mice without the "pull". Furthermore, the action of the chemokine pull was not restricted to the genital mucosa, as CD8+ T cell recruitment was also observed in the DRG. Importantly, the prime and pull strategy conferred near complete protection against the primary challenge of genital HSV-2 infection compared with the prime alone. In this study, we extend this application to therapeutic vaccines and demonstrate that the frequency of recurrent disease and recurrent vaginal shedding is reduced most effectively by the combination of prime (protein vaccine) and pull (Adenovirus expressing chemokine). We have studied the (i) genital infection of the immunized and non-immunized guinea pigs with HSV-2 by viral titration, (ii) monitored the genital herpes infection and disease scoring in guinea pigs, (iii) Bulk RNA sequencing on sorted CD8+ T cells, (iv) Differential gene expression, and (v) function of different immune cell markers by FACS to see the immune cell infiltrations into the VM tissue sections.
We performed gene expression profiling analysis using RNA-Seq on 4 guinea pig samples. All samples were female herpes subjects categorised into Immunized (n = 2), and Non-Immunized (n = 2).

first: Afshana

last: Quadiri

first: Swayam

last: Prakash


title: Transcriptomic analyses of a Cyberlindnera jadinii strain (NBRC0988) grown in glycerol

first: Feiyu

last: Fan

state: Tianjin

address: 32 West 7th Avenue, Tianjin Airport Economic Area

institute: Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences

summary: A strand-specific RNA-seq library was constructed for a single sample, specifically the wild-type strain NBRC0988 grown in YEP medium supplemented with 2% w/v glycerol. To prepare the RNA sample, NBRC0988 cells grown overnight were inoculated into 100 mL of liquid Yeast Extract Peptone Dextrose (YEPD) medium, with an initial inoculation OD600 of 0.1. These cells were then cultured for 15 hours at 30°C and 250 rpm. Subsequently, the cells were collected by centrifugation at 6,000g for 5 minutes. After being washed twice with phosphate buffer saline (PBS), they were inoculated into fresh 100 mL of YEP medium containing 2% w/v glycerol. Following flask culturing at 30°C and 250 rpm for an additional 5 hours, the yeast cells were collected by centrifugation for total RNA isolation and Illumina RNA-seq library construction. Total RNA from the sample was isolated using the TRIzol reagent (Invitrogen, Grand Island, USA) and then utilized for high-throughput RNA sequencing. Commercially, the 150-nt paired-end strand-specific RNA-seq libraries (SS_lib_type RF) were generated by Novogene Biotechnology Co. Ltd (Tianjin, China) using the Illumina's Novaseq 6000 platform (Illumina, San Diego, USA).

overall_design: RNA profiles of C. jadinii wild-type strain NBRC0988 grown in YEP medium containing 2% w/v glycerol was generated by deep sequencing, using Illumina’s novaseq 6000 platform

first: Lishan

last: Gu

first: Rongxin

first: Xuqian

first: Yu

last: Wang

first: Kaiyu

last: Ma

first: Jingjing

last: Jiang

first: Gen

first: Honglei

first: Xueli


title: An end-to-end workflow to study newly synthesized mRNA following rapid protein depletion in Saccharomyces cerevisiae

city: Oklahoma City

first: John

middle: B

last: Ridenour

state: OK

address: 825 NE 13th St.

department: Cell Cycle and Cancer Biology Research Program

institute: Oklahoma Medical Research Foundation

summary: The precise regulation of transcription requires the coordinated activity of numerous proteins and protein complexes. Although significant progress has been made in understanding the mechanisms that regulate transcription, many questions remain unresolved. Accurately defining the direct effects of transcriptional regulators is critical to addressing these questions. An effective approach for identifying the direct targets of transcriptional regulators is combining rapid protein depletion and quantification of newly synthesized RNA. The auxin-inducible degron (AID) system and thiol (SH)-linked alkylation for the metabolic sequencing of RNA (SLAM-seq) are powerful methods to rapidly degrade a target protein and directly quantify newly synthesized RNA, respectively. Both methods have been widely applied to study transcriptional regulation. To address unresolved questions in transcription, we assembled an end-to-end workflow to deplete proteins of interest using the AID system and measure newly synthesized RNA using SLAM-seq in the model eukaryote, Saccharomyces cerevisiae. We provide an open-source, step-by-step protocol to support rapid implementation of this workflow. We include methods for targeted protein degradation, 4-thiouracil (4tU) incorporation, rapid methanol fixation, RNA purification, RNA alkylation, mRNA-seq library construction, and data analysis. Additionally, we demonstrate that this workflow can help define the direct effects of transcriptional regulators using the bromodomain and extra-terminal domain (BET) proteins, Bdf1 and Bdf2, as an example. We provide evidence that data generated using this workflow is robust to normalization using whole-cell spike-in or total read counts, correlates well with 4tU-seq data, and identifies extensive differential expression due to the depletion of Bdf1 and Bdf2. Taken together, this workflow will help address outstanding questions underlying the molecular basis of transcriptional regulation and other processes in S. cerevisiae and other eukaryotes.

overall_design: Saccharomyces cerevisiae cells were grown in YPD medium to an OD600 of ~0.45. Cultures were treated with 1 mM 3-indoleacetic acid (IAA) in DMSO for 25 min. Immediately after IAA treatment, cultures were treated with 5 mM 4-thiouracil (4tU) in DMSO for 4 min. Immediately after 4tU treatment, cultures were fixed in cold methanol. The final OD600 of the cultures was ~0.7. 4tU-labeled Schizosaccharomyces pombe cells were combined with S. cerevisiae cells in mass-to-mass ratio of 1:19 based on OD600. RNA was purified using a Quick-RNA Fungal/Bacterial Miniprep kit (Zymo Research) following the manufacturer’s recommendations. Reagents were supplemented with DTT. Five μg of total RNA was treated with 10 mM iodoacetamide for 15 min at 50°C in the dark. 3ʹ mRNA-seq libraries were constructed as described in the associated protocol at protocols.io. Libraries were sequenced on a NovaSeq 6000 (Illumina) at the OMRF Clinical Genomics Center. Demultiplexed, paired-end 150 bp reads were processed using fastp, bbduk, and SLAM-DUNK. All experiments were performed in biological triplicate.

first: Rafal

last: Donczew


title: Autoimmunity associated allele of tyrosine phosphatase gene PTPN22 enhances anti-viral immunity

city: La Jolla

first: Alain

last: Domissy

state: CA

address: 10550 North Torrey Pines Road

department: Immunology

institute: The Scripps Research Institute

summary: In this study, we examine gene expression and function of immune cell subsets to demonstrate how a common allelic variant of PTPN22, which strongly increases the risk of autoimmune disease, promotes successful clearance of an otherwise chronic viral infection.

overall_design: At 8 days post infection, splenocytes from 4-5 age matched, sex matched PEP-WT Wild Type and PEP-619WW Mutant mice were removed, processed , and resuspended in a single cell suspension. Splenocytes from each genotype were pooled and FACS sorted for Live CD45+ cells. Sorted cells were analyzed using single cell RNA sequencing via 10x Genomics platform

first: Robin

middle: C

last: Orozco

first: Kristi

last: Marquardt

first: Isaphorn

last: Pratumchai

first: Kerri

last: Mowen

middle: R

last: Teijaro

first: Linda

last: Sherman


title: Field application of de novo transcriptomic analysis to evaluate the effects of sublethal freshwater salinization on Gasterosteus aculeatus in urban streams

city: Cologne

first: Camilo

last: Escobar Sierra

state: NRW

address: Zülpicher Strasse 47b

department: Institute of Zoology

country: Germany

institute: University of Cologne

summary: Freshwater salinization poses global challenges for aquatic organisms inhabiting urban streams, impacting their physiology and ecology. However, current salinization research predominantly focuses on mortality endpoints in limited model species, overlooking the sublethal effects on a broader spectrum of organisms and the exploration of adaptive mechanisms and pathways under natural field conditions. To address these gaps, we conducted high-throughput sequencing transcriptomic analysis on the gill tissue of the euryhaline fish Gasterosteus aculeatus, investigating its molecular response to salinity stress in the highly urbanized river Boye, Germany. We found that in stream sections with sublethal concentrations of chloride costly osmoregulatory systems were activated, evidenced by the differential expression of genes related to osmoregulation. Our enrichment analysis revealed differentially expressed genes (DEGs) related to transmembrane transport and regulation of transport and other osmoregulation pathways, which aligns with the crucial role of these pathways in maintaining biological homeostasis. Notably, we identified candidate genes involved in increased osmoregulatory activity under salinity stress, including those responsible for moving ions across membranes: ion channels, ion pumps, and ion transporters. Particularly, genes from the solute carrier family SLC, aquaporin AQP1, chloride channel CLC7, ATP-binding cassette transporter ABCE1, and ATPases member ATAD2 exhibited prominent differential expression. These findings provide insights into the potential molecular mechanisms underlying the adaptive response of euryhaline fish to salinity stress and have implications for their conservation and management in the face of freshwater salinization.

overall_design: To assess the effects of sublethal freshwater salinization on Gasterosteus aculeatus in urban streams, we selected three sampling stations along a chloride concentration gradient in two tributaries and the main channel of the River Boye (Germany). G. aculeatus individuals were collected using electrofishing equipment, euthanized with an overdose of tricaine methanesulfonate (MS222), and their gill tissue was promptly harvested, fixed in RNAprotect (QIAGEN), and stored at -20°C. Nine samples were obtained, comprising three from each of the control (Station B), mid-salinity (Station A), and high-salinity (Station C) stations. Subsequently, we conducted a differential expression analysis employing a Trinity de novo approach, comparing the expression profiles of three biological replicates from the control station (B) with those from the treatment stations (A and C).

last: Escobar-Sierra

first: Kathrin

middle: P

last: Lampert


title: Effect of NFIB knockdown on gene expression in the prostate cancer cells.

city: Zhuhai

first: Feng

last: Shu

state: State...

address: No.52, Meihua East Road, Xiangzhou District, Zhuhai

institute: Sun Yat-sen University

summary: The widespread use of androgen receptor (AR) signaling inhibitors has led to an increased incidence of AR-negative castration-resistant prostate cancer (CRPC), limiting effective treatment and patient survival. A more comprehensive understanding of the molecular mechanisms supporting AR-negative CRPC could reveal therapeutic vulnerabilities to improve treatment.In this study, we discovered that the transcription factor nuclear factor I/B (NFIB) was upregulated in AR-negative CRPC patient tumors and cell lines and was positively associated with an epithelial-to-mesenchymal transition (EMT) phenotype. Loss of NFIB inhibited EMT process and reduced migration of CRPC cells.

overall_design: To investigate the regulatory mechanisms of NFIB promoting EMT process and metastasis of AR-negative prostate cancer, we constructed stable cell line with continuous suppression of NFIB in AR-negative DU145 cells using the lentivirus-shRNA. DU145-shNFIB and DU145-shNC cells with two respective replicates were then analyed on gene expression platform.


title: RNA-sequencing of soleus muscle from Mustn1 heterozygous KO-first mice and wildtype littermates

city: Stockholm

first: Paulo

middle: R.

last: Jannig

address: Solnavägen 9

department: Department of Physiology and Pharmacology

country: Sweden

institute: Karolinska Institutet

summary: To uncover novel genes and molecular pathways important for skeletal muscle remodeling and regeneration, we used a mouse hindlimb unloading and reloading protocol. We then performed analysis of global gene expression by RNA-sequencing (RNA-seq), looking at the transition from muscle unloading to reloading (GSE237099). This study focuses on the microprotein Mustn1 (Musculoskeletal embryonic nuclear protein 1, also known as Mustang), which consists of 82 amino acids. We performed RNA-sequencing of soleus muscle from 8-week-old mice carrying one allele (heterozygous) of Mustn1 tm1a (KO-first) and wildtype littermates.

overall_design: RNA-sequencing analysis of soleus muscles from Mustn1 KO-First Heterozygous (HET) mice and wild-type (WT) littermate controls at 8 weeks of age.  Total RNA was extracted using TRI reagent (Sigma-Aldrich ref. T9424) according to the manufacturer's instructions. RNA was further purified using a Direct-zol RNA Miniprep kit (Zymo Research) including on-column DNAse I treatment. RNA quality was assessed using a 2100 Bioanalyzer system (Agilent Technologies) with an RNA integrity number (RIN) greater than 8 as a threshold. Samples were purified by poly-A enrichment before library preparation using Illumina TruSeq Stranded mRNA and sequenced on Illumina HiSeq2500 (single reads, 50 bp, 30M reads per sample).

first: Serge

last: Ducommun

first: Igor

last: Cervenka

first: Jorge

last: Ruas


title: Dual-inhibition of NAMPT and PAK4 induces anti-tumor effects in platinum-resistant ovarian cancer by suppressing mitochondrial function and expression of genes related to inflammation and DNA repair.

city: Bethesda

first: Kei

last: Kudo

state: MD

address: 9000 Rockville Pike

institute: NIH

summary: Ovarian cancer follows a characteristic progression pattern, forming multiple tumor masses enriched with cancer stem cells (CSCs) within the abdomen.  Most patients become resistant to standard platinum-based drugs, necessitating a change in treatment approach. To target CSCs, inhibiting NAMPT, which is the rate-limiting enzyme in the salvage pathway for NAD+ synthesis, has been explored.  KPT-9274 is an innovative drug targeting both NAMPT and PAK4. However, its effectiveness against ovarian cancer had not been validated. Here, we show the efficacy and mechanisms of KPT-9274 in treating 3D-cultured spheroids that are resistant to platinum-based drugs.  In these spheroids, KPT-9274 not only inhibited NAD+ production in NAMPT-dependent cell lines, but also suppressed NADPH and ATP production, indicating reduced mitochondrial function. It also downregulated expression of inflammation and gene repair-related genes.  Moreover, by altering PAK4's mostly cytoplasmic localization, the compound hindered kinase activity, leading to decreased phosphorylation of S6 Ribosomal protein, AKT, and β-Catenin in the cytoplasm and its suppression was NAD+- dependent.  These findings suggest that KPT-9274 could be a promising treatment for ovarian cancer patients resistant to platinum drugs, emphasizing the need for precision medicine to identify the specific NAD+-producing pathway a tumor relies on before treatment.

overall_design: Total RNA obtained from ovarian cancer cell line with KPT-9274 treatment (24 hours) compared to untreated control cells.

first: Yoshimi

middle: E

last: Greer

first: Teruhiko

last: Yoshida

first: Brittney

middle: S

last: Harrington

first: Soumya

last: Korrapati

first: Yusuke

last: Shibuya

first: Leah

last: Henegar

first: Jeffrey

last: Kopp

first: Takeo

last: Fujii

first: Stanley

last: Lipkowitz

first: Christina

middle: M

last: Annunziata


title: Early-life prefrontal cortex inhibition and early-life stress lead to long-lasting behavioral, transcriptional, and physiological impairments

city: NEW YORK

first: RUI

last: FU

state: NY

address: 101 6th Ave

department: Computational Biology

institute: New York Genome Center

summary: Early-life stress has been linked to multiple neurodevelopmental and neuropsychiatric deficits. Our previous studies have linked maternal presence/absence from the nest in developing rat pups to changes in prefrontal cortex activity. Furthermore, we have shown that these changes are modulated by serotonergic signaling. Here we test whether changes in prefrontal cortex activity during early-life affect the developing cortex leading to behavioral alterations in the adult. We show that inhibiting the prefrontal cortex of mouse pups leads to cognitive deficits in the adult comparable to those seen following maternal separation. Moreover, we show that activating the prefrontal cortex during maternal separation can prevent these behavioral deficits. To test how maternal separation affects the transcriptional profile of the prefrontal cortex we performed single-nucleus RNA sequencing. Maternal separation lead to differential gene expression almost exclusively in inhibitory neurons. Among others, we found changes in GABAergic and serotonergic pathways in these interneurons. Interestingly, both maternal separation and early-life prefrontal cortex inhibition led to changes in physiological responses in prefrontal activity to GABAergic and serotonergic antagonists that were similar to the responses of more immature brains. Prefrontal activation during maternal separation prevented these changes. These data point to a crucial role of prefrontal cortex activity during early-life in behavioral expression in adulthood

overall_design: C57Bl/6J mice were subjected to the maternal separation protocol described above. The PFC of 4 control and 4 MS male mice was dissected at P13; another set of 4 control and 4 MS mice were allowed to grow until P70 at which point we dissected the PFC. Tissue was dissected using a tissue puncher and flash frozen in dry ice. Samples were homogenized, and the nuclei were purified using an iodixanol cushion. Each sample was stained with HTO-tagged antibodies. Pools of eight hashed samples were processed simultaneously. We performed library preparations using the 10X Chromium platform and sequenced them on the Illumina NovaSeq. Each run consisted of two P13 controls, two adult controls, two P13 MS and two adult MS samples. One adult mouse from the MS group was removed from the analyses because it was a female misidentified as a male.

first: Menezes

last: Edênia

first: Geiger

last: Heather

first: Fu

last: Rui

first: Teixeira

last: Cátia


title: Selective Regulation of a Defined Subset of Inflammatory and Immunoregulatory Genes by an NF-kB p50-IkBz Pathway

city: Los Angeles

first: Stephen

last: Smale

state: Ca

address: 6-730 MRL 675 Charles E. Young Drive South

department: MIMG

institute: University of California Los Angeles

summary: The five NF-kB family members and three nuclear IkB proteins play diverse biological roles, but the mechanisms by which distinct NF-kB and NF-kB:IkB complexes contribute to selective gene transcription remain poorly understood. Using nascent transcript RNA-seq, we observed considerable overlap between p50-dependent and IkBz-dependent genes in Toll-like receptor 4 (TLR4)-activated macrophages. Key inflammatory and immunoregulatory genes, including Il6, Il1b, Nos2, Lcn2, and Batf, were among the p50-IkBz co-dependent genes. IkBz typically bound genomic sites occupied earlier by NF-kB dimers. However, p50-IkBz co-dependence did not coincide with the preferential binding of either protein, as p50, IkBz, and RelA co-occupied thousands of sites. A common feature of p50-IkBz co-dependent genes was close proximity to a p50/RelA/IkBz co-bound site exhibiting p50-dependent binding of RelA and IkBz. This result and others suggest that IkBz function is not restricted to p50 homodimers. Notably, IkBz and the p50-IkBz target genes comprise a high percentage of genes that exhibited the greatest differential expression between TLR4-stimulated and tumor necrosis factor receptor (TNFR)-stimulated macrophages, with ectopic IkBz rescuing a subset of these genes. These results reveal a defined p50-IkBz pathway that selectively activates a set of key inflammatory and immunoregulatory genes and serves as an important contributor to the differential responses to TNFR and TLR4.

overall_design:
To investigate the role of p50 and nuclear IkBs in macrophage activation, we performed chromatin-associated RNA-seq on bone marrow-derived macrophages (BMDMs) lacking each of these subunits. We stimulated wild-type, Nfkb1-/-, Nfkbiz-/-, Bcl3-/-, and Nfkbid-/- BMDMs with lipid a for 0, 0.5, 1.0, 2.0, and 6.0 hours.
To evaluate possible redundancy between p50 and p52, we generated Nfkb1-/-, Nfkb2-/- macrophages and performed bulk RNA-seq on macrophages stimulated with Lipid A for 0 and 2.0 hours.
To understand the selective regulation of IkBz, we generated both bulk and chromatin-associated RNA-seq from BMDMs stimulated with TNFa for 0, 0.5, 1.0, 2.0, and 6.0 hours.
To evaluate if the ectopic expression of IkBz could restore the expression of IkBz-dependent genes with TNFa stimulation, we performed bulk RNA-seq on BMDMs overexpressing IkBz and stimulated  with TNFa for 0, 0.5, 1.0, 2.0, and 6.0 hours.
To understand if early (0.5h) p50-dependent genes are due to the role of p105 in stabilizing and upstream mediator of the MAPK/ERK pathway, we performed chromatin-associated RNA-seq on BMBMs pretreated with ERK-inhibitors and stimulated with lipid A for 0, 15, 30, and 60 mins.

first: Allison

last: Daly

first: George

last: Yeh

first: Ann-Jay

last: Tong


title: Treatment of chronic lymphocytic leukemia cells with signaling inhibitors

city: Milano

first: Michela

last: Riba

address: via Olgettina 60

department: COSR, Center for Omics Sciences

country: Italy

institute: IRCCS, Ospdale San Raffaele

summary: To identify the molecular targets of treatment, we studied gene expression profile of primary chronic lymphocytic leukemia (CLL) cells isolated from the peripheral blood of CLL patients and treated in vitro with two distinct signaling inhibitors:   1) Dimethyl fumarate targeting inflammatory pathways  2) VIVIT peptide targeting NFAT transcription factor activation.

overall_design: CLL B-cells were negatively selected and purified from patient’s total peripheral blood mononuclear cells (PBMC), cultured in RPMI with 10% heat inactivated FBS and Pen-Strep and stimulated  with DMF 100 µM or VIVIT-11R 10µM for 4 hours and RNAseq was performed. Untreated samples were used as controls.

first: Maria

last: Mantione

first: Miriam

last: Meloni

first: Ilenia

last: Sana

first: Paolo

last: Ghia

first: Lydia

last: Scarfò

first: Marta

last: Muzio


title: Cancer-associated fibroblast-secreted FGF2 faliciates gastric cancer cell proliferation by enhancing ribosome biogenesis

city: Shiyan

first: Qin

last: Shanshan

address: Renmin Road 30, Maojian District

institute: Institute of Basic Medical Sciences, School of Basic Medical Sciences, Hubei University of Medicine

summary: Cell co-culture experiments and bioinformatics analysis show that soluble FGF2 plays an important role in the cross-talking between CAF and tumor cells. This study aimed to explore the efffects of human recombinant FGF2 protein (20 ng/mL) on the transcriptome of GC cells.

overall_design: The gastric cancer (GC) cells were seeded into 6-well plates and grown overnight. The differentally expressed genes by human recombinant FGF2 protein (20 ng/mL) were screened by RNA sequencing. The transcriptome sequencing studies were performed by deep sequencing, using Illumina NovaSeq 6000.

first: Shanshan

last: Qin

first: Dandan

last: Li


title: ATAC and histone H3K9me3 landscapes reveal long-term epigenomic effects of fetal-neonatal iron deficiency in rat hippocampus [ChIP-seq]

city: New York

first: Aarthi

last: Ramakrishnan

state: New York

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Background: Iron deficiency (ID) during the fetal-neonatal period results in long-term neurodevelopmental impairments associated with pervasive hippocampal gene dysregulation. Prenatal choline supplementation partially normalizes these effects, suggesting an interaction between iron and choline in hippocampal transcriptome regulation. To understand the regulatory mechanisms, we investigated epigenetic marks of genes that are poised to be activated (ATAC-seq) or repressed (H3K9me3 ChIP-seq) in iron-repleted adult rats having experienced fetal-neonatal ID exposure with or without prenatal choline supplementation.  Results: Fetal-neonatal ID was induced by limiting maternal iron intake from gestational day (G) 2 through postnatal day (P) 7. Half of the pregnant dams were given supplemental choline (5.0 g/kg) from G11-18. This resulted in 4 groups at P65 (Iron-sufficient [IS], Formerly Iron-deficient [FID], IS with choline [ISch], and FID with choline [FIDch]). Hippocampi were collected from P65 iron-repleted male offspring and analyzed for chromatin accessibility and H3K9me3 enrichment. 22% and 24% of differentially transcribed genes in FID- and FIDch-groups, respectively, exhibited significant differences in chromatin accessibility, whereas 1.7% and 13% exhibited significant differences in H3K9me3 enrichment. These changes mapped onto gene networks regulating synaptic plasticity, neuroinflammation, and reward circuits. Motif analysis of differentially modified genomic sites revealed significantly stronger choline effects than early-life ID and identified multiple epigenetically modified transcription factor binding sites.  Conclusions: This study reveals genome-wide, stable epigenetic changes and epigenetically modifiable gene networks associated with specific chromatin marks in the hippocampus, and lays a foundation to further elucidate iron-dependent epigenetic mechanisms that underlie the long-term effects of fetal-neonatal ID, choline, and their interactions.

overall_design: To generate 4 dietary groups, pregnant and nursing rats were fed iron-sufficient or iron-deficient diet from gestational day (G) 2 to postnatal day (P) 7 with or without supplemental choline from G11-18. Hippocampi from P65 male offspring were analyzed.

first: Shirelle

middle: X

last: Liu

first: Li

last: Shen

first: Jonathan

last: Gewirtz

first: Michael

middle: K

last: Georgieff

first: Phu

middle: V

last: Tran


title: ATAC and histone H3K9me3 landscapes reveal long-term epigenomic effects of fetal-neonatal iron deficiency in rat hippocampus [ATAC-seq]


title: Histone H3 lysine 27 trimethylation (H3K27me3) modulates the fiber initiation in upland cotton

city: Science Avenue

first: YingQiang

last: Long

address: Science Avenue

institute: School of Agricultural Sciences, Zhengzhou University

summary: Histone methylation is one of the most significant epigenetic modifications in plants because it is responsible for regulating and controlling the expression of many important functional genes. Although there have been many studies concerning histone methylation, its specific functions and mechanisms in cotton fiber initiation remain unclear. To determine if the H3K27me3 modification had regulated cotton fiber initiation in upland cotton (Gossypium hirsutum), we performed a comparative analysis on the cleavage under targets and tagmentation (CUT&Tag) between the wild-type cultivar Xu142 and its fibreless mutant Xu142 fl. This research was carried out three time points during the initiation period of cotton fibers, which were -1, 0 and 1 days post-anthesis (DPA). We also used the H3K27me3 antibody in Xu142 and Xu142 fl to examine the differential deposition of H3K27me3. Combing these results with RNA-seq analysis, we discovered a negative correlation between transcription and H3K27me3. We identified 336 genes with opposing trends in H3K27me3 deposition and expression. These genes are involved in various metabolic pathways, including fatty acid biosynthesis, galactose metabolism, plant hormone signal transduction, plant-pathogen interaction, glycolysis-/-gluconeogenesis, phenylpropanoid biosynthesis, and cutin, suberin and wax biosynthesis. Further physiological research revealed that in vitro ovule culture with an RDS 3434 inhibitor could alters the level of H3K27me3 in ovules, thus influencing the process of cotton fiber development. Taken together, these results indicate that H3K27me3 plays an important role in the fiber initiation process of cotton, and demonstrates the H3K27me3 network involved in fiber initiation in cotton ovules. The study also provides a foundation for the future study of genes involved in fiber development.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Xu142 and Xu142 fl at -1 DPA、0 DPA、1 DPA.

first: Yingqiang

first: Xiongfeng

last: Ma

first: Wei


title: Effect of  p53 knockout on gene expression during capmatinib treatment of NF1-MET murine MPNST cells

city: Grand Rapids

first: Matthew

last: Steensma

state: MI

address: 333 Bostwick Ave NE

institute: Van Andel Institute

summary:
To investigate the function of p53 in regulating response to MET inhibition in MPNST cells we established NF1-MET;sgP53 cells in which Trp53 was knocked out using CRISPR-Cas9. As a control, the parental NF1-MET was transduced with CRISPR-Cas9 in the absence of sgRNA.
We then performed gene expression profiling analysis using data obtained from RNA-seq of the 2 different cells treated with either capmatinib or vehicle in duplicate.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for NF1-MET cells and its Trp53 KO derivative NF1-MET;sgP53 with and without capmatinib treatment.

first: Jamie

last: Grit


title: Rat models for Portosinusoidal Vascular Disease

city: Barcelona

first: Genís

last: Camprecios

state: Catalonia

address: Rosselló 153

department: Hepatic Hemodynamics

country: Spain

institute: IDIBAPS

summary:
Background: Porto-Sinusoidal Vascular Disorder (PSVD) involves a group of rare vascular liver diseases of unknown etiology that leads to the development of portal hypertension and its life-threatening complications. Its pathophysiology is not well understood and animal models described to date do not fully recapitulate human disease.
Methods: We developed 3 different PSVD rat models by either immunosensitization (repetitive intraportal LPS or intramuscular spleen extract injections) or toxic (combination of FOLFOX and a selenium-enriched diet, Selfox model) treatment and characterized them at hemodynamic, histological, biochemical and transcriptional levels. We compared these results to human data.
Results: All three models developed significant portal hypertension, while only the LPS and the Selfox models displayed PSVD specific and non-specific histological alterations in the absence of cirrhosis. Transcriptional comparison between rat animal models and human data showed both LPS and Selfox models recapitulate the main transcriptional alterations observed in humans, especially regarding hemostasis, oxidative phosphorylation and cell cycle regulation. Reproducibility and feasibility was higher for the Selfox model.
Conclusions: The Selfox rat model faithfully reproduces the main alterations described in PSVD. Its use as a preclinical model for drug testing in progressing PSVD can be a significant step forward towards development of new therapeutic targets for this rare condition.

overall_design: There are three groups of rats. Control rats did not receive any treatment. For LPS rats, rats were anesthetized with isofluorane. Animals were then laparotomized and permanent access to the portal vein was obtained with the introduction of an indwelling to the gastric vein right above the ileocholic vein that would extend to the back of the rat where it was fixed with a harness, leaving it accessible for successive injections. Rat’s abdomen was then sewed. Animals received a bolus of 1 mg/kg of LPS twice a week for a period of 8 weeks. For Oxa (Selfox rats), rats were fed ad libitum with the selenium-enriched diet during 8 weeks. During this time, rats were also injected intravenously with a solution of oxaliplatin (3 mg/kg) + 5-FU (25 mg/kg) + folinic acid (45 mg/kg) once per week, for a total of 8 injections.

first: Joan

last: García-Pagán

last: Campreciós


title: Effects of HOE-1 (RNase Z/ELAC2) nuclear hyperactivation on gene expression in Caenorhabditis elegans.

status: Public on Mar 13 2024

city: Nashville

first: Maulik

last: Patel

address: 465 21st Ave S

institute: Vanderbilt University

summary: We previously reported that the RNA endonculease HOE-1 (RNaseZ/ELAC2) is necessary and sufficient for activation of the mitochondrial unfolded protein response (UPRmt) in C. elegans (PMID: 35451962). To comprehensively assess the broader cellular consequences of increased nuclear activity of HOE-1, we conducted RNA sequencing on day 2 adult wildtype animals vs animals in which endogenous HOE-1 is elevated in the nucleus via perturbation of its nuclear export signal (hoe-1(ΔNES)). Additionally, wildtype and hoe-1(ΔNES) animals were grown on both control and atfs-1 RNAi (ATFS-1 is the central transcription factor for UPRmt) to determine gene expression that is atfs-1 dependent. This analysis revealed that differential gene expression in hoe-1(ΔNES) animals exhibits a strong mitochondrial signature. Notably, gene ontology (GO) analysis of significantly upregulated genes showed a significant overrepresentation of mitochondrial associated genes. Moreover, knockdown of atfs-1 strongly compromised the differentially expressed gene profile. Together these data suggest that increased nuclear activity of HOE-1 preferential impacts expression of mitochondrial genes.

overall_design:
hoe-1(ΔNES) animals were generated via CRISPR/Cas9 (validation and characterization can be found in PMID: 35451962).
hoe-1(ΔNES) animals were then crossed to a conditional sterility mutant (glp-1(e2144). The wildtype condition submitted for RNAseq were glp-1(e2144) animals with wildtype hoe-1. Animals were grown for 72 hours at a non-permissive temperature (25°C) to confer sterility. This allowed for synchronization of adult populations and assessment of only somatic differential gene expression.
Both wildtype and hoe-1(ΔNES) animals were grown on control and atfs-1 RNAi (HT115 bacterial background).
Three biological replicates of 800 animals each were collected for each condition: wildtype on control RNAi, wildtype on atfs-1 RNAi, hoe-1(ΔNES) on control RNAi, and hoe-1(ΔNES) on atfs-1 RNAi.

first: James

last: Held

first: Lantana

last: Grub


title: An extended wave of global mRNA deadenylation sets up a switch in translation regulation across the mammalian oocyte-to-embryo transition

first: Heidi

last: Cook-Andersen

address: 2880 Torrey Pines Scenic Drive, Rm 4811

department: Department of Reproductive Medicine

institute: University of California, San Diego

summary: The oocyte-to-embryo transition (OET) occurs in the absence of new transcription and relies on post-transcriptional gene regulation, including translational control by mRNA poly(A) tail regulation, where cytoplasmic polyadenylation activates translation and deadenylation leads to translational repression and decay. However, how the transcriptome-wide landscape of mRNA poly(A) tails shapes translation across the OET in mammals remains unknown. Here, we performed long-read RNA sequencing to uncover poly(A) tail lengths and mRNA abundance transcriptome-wide in mice across five stages of development from oocyte to embryo. Integrating these data with recently published ribosome profiling data, we demonstrate that poly(A) tail length is coupled to translational efficiency across the entire OET. We uncover an extended wave of global deadenylation during fertilization, which sets up a switch in translation control between the oocyte and embryo. In the oocyte, short-tailed maternal mRNAs that resist deadenylation in the oocyte are translationally activated, whereas large groups of mRNAs deadenylated without decay in the oocyte are later readenylated to drive translation activation in the early embryo. Our findings provide an important resource and insight into the mechanisms by which cytoplasmic polyadenylation and deadenylation dynamically shape poly(A) tail length in a stage-specific manner to orchestrate development from oocyte to embryo in mammals.

sample_organism:
Homo sapiens
Mus musculus
synthetic construct

overall_design: Profiling of genome-wide poly(A) tail lengths and mRNA abundance in mouse oocytes and embryos by Nanopore PCR-cDNA sequencing

first: Katherine

last: Lee


title: Molecular heterogeneity of quiescent melanocyte stem cells revealed by single-cell RNA-sequencing.

city: Birmingham

first: Melissa

last: Harris

state: AL

address: 1720 University Blvd

department: Biology

institute: University of Alabama at Birmingham

summary: Melanocyte stem cells (McSCs) of the hair follicle are a rare cell population within the skin and are notably underrepresented in whole-skin, single-cell RNA sequencing (scRNA-seq) datasets. Using a cell enrichment strategy to isolate KIT+/CD45- cells from the telogen skin of adult female C57BL/6J mice, we evaluated the transcriptional landscape of quiescent McSCs (qMcSCs) at high resolution. Through this evaluation, we confirmed existing molecular signatures for qMcCS subpopulations (e.g., Kit+, Cd34+/-, Plp1+, Cd274+/-, Thy1+, Cdh3+/-) and identified novel qMcSC subpopulations, including two that differentially regulate their immune privilege status. Within qMcSC subpopulations, we also predicted melanocyte differentiation potential, neural crest potential, and quiescence depth. Taken together, the results demonstrate that the qMcSC population is heterogenous and future studies focused on investigating changes in qMcSCs should consider changes in subpopulation composition.

overall_design: Follicular melanocyte stem cells reside in the cellular state of quiescence for the majority of their lifespan and are essential for the regeneration of hair pigmentation during hair cycling. Functional, anatomical and molecular evidence indicates that quiescent melanocyte stem cells are heterogenous and this heterogeneity is a characteristic that defines the stem and lineage potential of these cells. To further interrogate the transcriptional programs that drive this heterogeneity we isolated quiescent melanocyte stem cells from the dermis of female, 8-week-old, C57BL/6J mice (n=3) using KIT+/CD45- enrichment using flow cytometry. Isolated quiescent melanocyte stem cells were processed for single cell RNA-seq (10X genomics) to generate a high resolution map of these cells (5545 total cells analyzed after quality control and filtering). We also performed single cell RNA-seq on dissociated dermis without enrichment as a comparison.

first: Joseph

middle: W

last: Palmer


title: Peripheral blood TCR clonotype diversity as an age-associated marker of breast cancer progression (TCR)

city: Boston

first: Kornelia

last: Polyak

state: MA

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: Immune escape is a prerequisite of tumor growth. We previously described a decline in intratumor activated GZMB+CD8+ T cells and T cell receptor (TCR) clonotype diversity in invasive compared to in situ (DCIS) breast carcinomas implying a role for decreasing TCR diversity in tumor progression. Here, we evaluated peripheral blood TCR clonotype diversity in breast cancer patients diagnosed with DCIS or de novo stage IV disease at different ages. We found that peripheral TCR diversity is associated with clinicopathologic, and peripheral immune status and it correlates with the frequency of CD8+ T cells in DCIS of young patients. These results provide new insights to the role of host immunity and breast cancer development in different aged women.

overall_design: To identify the differences in the diveristy of the cdr3 sequences between different age groups

first: Jun

last: Nishida

first: Simona

last: Cristea

first: Franziska

last: Michor

first: Sudheshna

last: Bodapati


title: Murine MSC cells: Control vs. E8-expressed

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

country: Japan

institute: Toray Industries,Inc.

summary: Transcriptional profiling of mouse mesenchymal stem cell (MSC), C3H10T1/2 cultured cells comparing control parental cells with stably-transfected cells carrying both Flag-E8 and neomysin-resistant transgenes. The latter cell population was selected by treating with G418 to remove untransfected cells.

overall_design: Two-condition experiment, parental C3H10T1/2 cells vs. Stably-transfected C3H10T1/2 cells

first: Kazuhiro

last: Sakamaki


title: Cognate antigen recognition defines intestinal Treg specialization and stability

city: Aachen

first: Hieu

middle: Trong

last: Nguyen

address: Pauwelstrasse 30

department: Institut für Molekulare Medizin

institute: RWTH Aachen University Hospital

summary: Regulatory CD4 T cells (Treg) confer non-overlapping functions in intestinal immune tolerance, tissue maintenance, repair, and regeneration. Cytokines and T cell receptor (TCR) signals, in combination with environmental cues, direct Treg proliferation and differentiation. However, how intestinal antigens shape intestinal Treg populations, their specialization and stability remain unknown. Here we show that only Treg bearing specific TCRs expand in the colon, resulting in highly oligoclonal Treg populations. Treg TCR repertoires are private, but crucially, when the same repertoire of polyclonal Treg was transferred into different recipients, the same clones expanded in each recipient, suggesting that cognate TCR-antigen interactions drive colonic Treg accumulation. Expanded Treg clones were correlated with Treg stability and individual transcriptional states that were maintained in different recipients irrespective of the presence or absence of intestinal inflammation. Our data suggest a role for antigen recognition in the selection and functional specialization of intestinal Treg. We speculate that the therapeutic use of Treg must take into account TCR context-mediated properties to optimise Treg stability and function in vivo.

overall_design: To investigate how the Treg TCR repertoire is connected with Treg function in the murine large intestine, the adoptive T cell transfer model of colitis, in which naive CD4+ T cells are either transfered with or without Treg was combined with scVDJ sequencing. To follow the same Treg clone in multiple Rag2 KO recipients, the Treg cells were previously expanded in vitro.

first: Lydia

last: Kopplin

first: HieuTrong

first: Oliver

last: Pabst


title: RNA-Seq of different TadA variants to validate RNA Off-Targets

city: Beijing

first: Wenjie

last: Shu

address: Taiping Road 27

institute: Beijing Institute of Radiation Medicine

summary: Mutation effects prediction is a fundamental challenge in biotechnology and biomedicine. State-of-the-art computational methods have demonstrated the benefits of including semantically rich representations learned from protein sequences, but leave structural constraints out of reach. Here we developed Protein Mutational Effect Predictor (ProMEP), a general and multimodal deep representation learning method that simultaneously learns sequence context and structural constraints from proteins at the scale of evolution. ProMEP markedly outperforms current leading methods and enables accurate zero-shot mutational effects prediction across a variety of deep mutational scanning experiments. The application of ProMEP in the transposon-associated TnpB enzyme engineering task further demonstrates its ability for high-throughput protein space exploration. Without prior knowledge of TnpB, ProMEP accurately identifies multiple mutations that significantly improve the editing efficiency from millions of variants.

overall_design: Analysis of RNA off-target effects of TadA mutants

first: Peng

last: Cheng

first: Cong

last: Mao

last: Zhang


title: Detailed analysis of the murine-aged brain transcriptome [Illumina RNA-seq]

city: Göttingen

first: Nisha

last: Hemandhar Kumar

address: Humboldtallee 23

department: Institute for Neuro and Sensory Physiology

institute: University Medical Center Goettingen

summary: In this work, we collected and analyzed two cohorts of young-adult and aged-adult mice brain mRNAs and determined their levels using second--generation (illumina) sequencing technology.We provide the community with a large resource of whole brain transcriptomes and comprehensive analyses that identify widespread diversity of mRNAs during aging. This study is linked to the dataset GSE233837.

overall_design: Brain mRNA profiles of 4 young-adult samples (6-month, brain hemisphere, from 4 males), 4 aged (24-month, brain hemisphere, from 4 males)

first: Eugenio

middle: F

last: Fornasiero

first: Verena

last: Kluever


title: Zeolitic Imidazolate Frameworks Activate Endosomal Toll-like Receptors and Potentiate Immunogenicity of SARS-CoV-2 Spike Protein Trimer

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

institute: Koch Institute

summary: Nanomaterials offer new opportunities to engineer immunomodulatory activity. In this work, we report the endosomal toll-like receptor agonist activity of a nanoscale adjuvant zeolitic imidazolate frameworks-8 (ZIF-8). The accumulation of ZIF-8 in endosomes and the pH-responsive release of its subunits enable selective engagement with endosomal TLRs, minimizing the risk of off-target activation. The intrinsic adjuvant properties of ZIF-8, along with the efficient delivery and biomimetic presentation of a SARS-CoV-2 spike protein receptor binding domain trimer, primed rapid humoral and cell mediated immunity in a dose sparing manner. Our study offers new insights for next-generation adjuvants that can potentially impact future vaccine development.

overall_design: Gene expression comparisons of 3 replicates each of lymph node RNA extracted from mice immunized with RBD-trimer, ZIF-8 or GR-ZIF compared with PBS controls.

first: Shahad

last: Alsaiari

first: Seba

last: Nadeef

first: John

last: Daristotle

first: William

last: Rothwell

first: Bujie

last: Du

first: Johnny

last: Garcia

first: Linzixuan

first: Morteza

last: Sarmadi

first: Timothy

middle: A

last: Forster

first: Nandita

last: Menon

first: Lisa

middle: H

last: Tostanoski

middle: D

last: Ventura

first: Dan

last: Barouch

first: Robert

last: Langer

first: Ana

last: Jaklenec


title: Deciphering the Tumor Immune Microenvironment of Imatinib-Resistance in Advanced Gastrointestinal Stromal Tumors at Single-Cell Resolution

city: qingdao

first: xuechao

last: liu

address: jiangsuroad

institute: Affiliated Hospital of Qingdao University

summary: The heterogeneous nature of tumors presents a considerable obstacle in addressing imatinib resistance in advanced cases of gastrointestinal stromal tumors (GIST). To address this issue, we conducted single-cell RNA-sequencing in primary tumors as well as peritoneal and liver metastases from patients diagnosed with locally advanced or advanced GIST. Single-cell transcriptomic signatures of tumor microenvironment (TME) were analyzed. This analysis revealed unique tumor evolutionary patterns, transcriptome features, dynamic cell-state changes, and different metabolic reprogramming.

first: Yanbing

last: Zhou

first: Zhaojian

last: Niu


title: Cytoplasmic localization of SETDB1 induced Warburg effect via c-MYC/ LDHA axis to enhance migration and invasion in breast carcinoma

city: Nantong

first: Wenlin

last: Yang

address: No.30, Tongyang North Road, Tongzhou District, Nantong, Jiangsu 226006, P.R. China

department: Department of Pathology

institute: Nantong Tumor Hospital Affiliated to Nantong University

summary: SETDB1, a pivotal histone lysine methyltransferase, has been identified as being transported to the cytoplasm through a CMR1-dependent pathway, contributing to non-histone methylation. However, the function and underlying mechanism of cytoplasmic SETDB1 in breast cancer remain elusive. This study, employing immunohistochemistry, revealed that an elevated level of cytoplasmic SETDB1 is correlated with lymph node metastasis and more aggressive breast cancer subtypes. Functionally, cytoplasmic SETDB1 proves indispensable for cell migration and invasion, as well as the induction of epithelial-mesenchymal transition (EMT), which could be reversed by LMB (a CMR1 inhibitor) treatment. Furthermore, it was observed that cytoplasmic SETDB1 elevates the levels of metabolites associated with the Warburg effect, including glucose, pyruvate, lactate, and ATP. Mechanistically, the release of nuclear SETDB1 alleviates the inhibition of c-MYC transcription, leading to increased c-MYC expression and subsequent up-regulation of LDHA expression. Notably, LDHA overexpression enhanced migration and invasion by inducing EMT, while its depletion can reverse SETDB1-induced migration and invasion, as well as the Warburg effect and EMT. In conclusion, the subcellular localization of cytoplasmic SETDB1 emerges as a pivotal factor in breast cancer progression. This study offers valuable insights into the novel functions and mechanisms of cytoplasmic SETDB1.

overall_design: MCF7/NC cells were treated with DMSO, MCF7/SETDB1 cells were treated with DMSO or LMB


title: Frequency, kinetics and determinants of viable SARS-CoV-2 in bioaerosols from ambulatory COVID-19 patients infected with the β, δ or ο variants

city: Cape Town

first: Stuart

last: Meier

state: Western Cape

address: Groote Schuur Hospital, Anzio Road, Observatory

department: Lung Institute

country: South Africa

institute: University of Cape Town

summary: Airborne transmission of SARS-CoV-2 aerosol remains contentious. Importantly, whether cough or breath-generated bioaerosols can harbor viable and replicating virus remains largely unclarified. We perform size-fractionated aerosol sampling (Andersen cascade impactor) and evaluate viral culturability in human cell lines (infectiousness), viral genetics, and host immunity in ambulatory participants with COVID-19. Sixty-one percent (27/44) and 50% (22/44) of participants emitted variant-specific culture-positive aerosols <10μm and <5μm, respectively, for up to 9 days after symptom onset. Aerosol culturability is significantly associated with lower neutralizing antibody titers, and suppression of transcriptomic pathways related to innate immunity and the humoral response. A nasopharyngeal Ct <17 rules-in ~40% of aerosol culture-positives and identifies those who are probably highly infectious. A parsimonious three transcript blood-based biosignature is highly predictive of infectious aerosol generation (PPV> 95%). There is considerable heterogeneity in potential infectiousness i.e., only 29% of participants were probably highly infectious (produced culture-positive aerosols <5μm at ~6 days after symptom onset). These data, which comprehensively confirm variant-specific culturable SARS-CoV-2 in aerosol, inform the targeting of transmission-related interventions and public health containment strategies emphasizing improved ventilation.

overall_design: To identify transcriptional differences between infectious and non-infectious COVID infected patients.

first: Shameem

last: Jaumdally

first: Keertan

last: Dheda


title: Determination of transcriptomic changes associated with heat stress in ethanol treated vs non-treated control tomato plants II

city: Yokohama

first: motoaki

last: seki

address: Suehiro-cho 1-7-22, Tsurumi-ku

department: CSRS

institute: RIKEN

summary: We report the gene expression profiles of tomato seedlings and fruits treated with or without ethanol under heat stress conditions.

overall_design: Seeds of a tomato (Solanum lycopersicum L.) cultivar, “Micro-Tom” were grown in pots containing horticultural cray granule soil at 22 °C with a 16 h light (110 to 140 µmol m-2 s-1 photon flux density) / 8 h dark cycle. Sixteen-day-old plants grown in pots were used for ethanol pretreatment. The bottoms of the pots were dipped into 20 mM ethanol solution and kept for 3 days. After ethanol pretreatment, the pots were placed in an air incubator set at 50 °C and maintained for the indicated time periods as heat stress treatment. During the heat stress treatment, the pots were electrically rotated in the air incubator to avoid the local effect. After the heat stress treatment, the pots were returned to the growth room and maintained for the indicated time periods.

first: Daisuke

last: Todaka

first: Maho

last: Tanaka

first: Satoshi

last: Takahashi

first: Do

middle: N

last: Quynh

first: Junko

last: Ishida

first: Kyoko

middle: Y

last: Mogami

first: Atsushi

middle: J

last: Nagano

first: Motoaki

last: Seki


title: Platelet-derived thrombospondin 1 promotes immune cell liver infiltration and exacerbates diet-induced steatohepatitis.

city: lexington

first: Shuxia

last: Wang

state: KY

address: 900 S. Limestone street, Wethington Bldg. Room 583

department: Pharmacology and Nutritional Sciences

institute: University of Kentucky

summary: Background and Aims: Recent studies have implicated platelets, particularly α-granules, in the development of steatohepatitis (NASH). However, the specific mechanisms involved have yet to be determined. Notably, thrombospondin 1 (TSP1) is a major component of the platelet α-granules released during platelet activation. The role of platelet-derived TSP1 in NASH remains unknown and was investigated in this study. Approach and Results: Platelet-specific TSP1 knockout mice (TSP1Δpf4) and their wild type littermates (TSP1F/F) were used. NASH was induced by feeding the mice a diet enriched in fat, sucrose, fructose, and cholesterol (AMLN diet). A human liver NASH organoid model was also employed. Although TSP1 deletion in platelets did not affect diet-induced steatosis, TSP1Δpf4 mice exhibited attenuated NASH and liver fibrosis, accompanied by improvements in plasma glucose and lipid homeostasis. Moreover, intrahepatic platelet accumulation, activation and chemokine production were reduced in TSP1Δpf4 mice, which was correlated with decreased immune cell infiltration into the liver. Consequently, this leads to diminished pro-inflammatory signaling in the liver and mitigated the progression of NAFLD.  Moreover, in vitro data revealed that co-culturing TSP1-deficient platelets in a human liver NASH organoid model attenuated hepatic stellate cell activation and NASH progression. Additionally, TSP1 deficient platelets play a role in regulating brown fat endocrine function, specifically affecting Nrg4 production. Crosstalk between brown fat and the liver may also influence NAFLD progression. Conclusions: These data suggest that platelet α-granule-derived TSP1 is a significant contributor to diet-induced NASH and fibrosis, and may serve as a new therapeutic target for this severe liver disease.

overall_design:
Platelet-specific TSP1 knockout mice (TSP1/pf4: KO) and their wild type littermates (TSP1F/F: WT) were fed with LF diet or AMLN diet for 32 weeks. The effect of TSP1 depleted platelets on liver phenotype and gene expression profile were determined.
Livers were collected from four groups of mice (n=4 mice)/per group) for RNA-seq analysis.

first: Taesik

last: Gwag

first: Sangderk

last: Lee

first: Zhenyu

last: Li

first: Alana

last: Newcomb

first: Josephine

last: Otuagomah

first: Steven

last: Weinman

first: Ying

last: Liang

first: Changcheng


title: ATAC and histone H3K9me3 landscapes reveal long-term epigenomic effects of fetal-neonatal iron deficiency in rat hippocampus

city: New York

first: Aarthi

last: Ramakrishnan

address: 1425 Madison Avenue

institute: Icahn School of Medicine at Mount Sinai

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

overall_design: Refer to individual Series


title: Proteasome inhibition reprograms chromatin landscape in breast cancer (RNA-Seq)

city: Durham

first: Brian

last: Bennett

address: 111 T.W. Alexander Drive

institute: NIEHS

summary: The 26S proteasome regulates general protein homeostasis and controls vital cellular processes, including cell division and transcriptional regulation. Cancer cells are dependent on the proper functioning of the proteasome to modulate gene expression networks that promote tumor growth. Proteasome inhibition has emerged as an effective therapeutic strategy, although mechanisms by which this approach achieves its outcomes remain unclear.  We performed an integrative analysis of the transcriptome and chromatin landscape of MCF-7 breast cancer cells treated with a model proteasome inhibitor, MG132, to examine the consequences of proteasome inhibition on gene regulation. MG132 treatment initiated dynamic changes in chromatin accessibility at specific loci termed Differentially Open Chromatin Regions (DOCRs).  DOCRs with increased accessibility were primarily distal to transcription start sites (TSS), while those with decreased accessibility were promoter proximal and distal to TSS.  Promoter proximal DOCRs showed a unique chromatin architecture associated with distinct divergent transcription patterns.  Conversely, DOCRs distal to TSS were enriched in oncogenic super enhancers that are predominantly accessible in non-basal compared to basal breast tumor subtypes.  These data define distinct chromatin states and RNAPII transcription patterns, revealing molecular mechanisms by which the proteasome modulates the expression of gene networks intrinsic to breast cancer biology.

overall_design: RNA-seq (ribo-zero) was performed with total RNA from MCF-7 breast cancer cells treated with either vehicle (UNTR) or proteasome inhibitor MG132 (1 uM) for 4 and 24 hr

first: Trevor

last: Archer

first: H

last: Kinyamu


title: Effects of AdipoRon on knee fibroblasts

city: rochester

first: Roman

last: Thaler

state: MINNESOTA

address: 200 First street SW

institute: Mayo Clinic

summary: Patient derived fibroblasts were treated with TGFβ1 and TGFB plus AdipoRon to assess for potential anti myofiborogenic effects of AdipoRon.

overall_design: Tissues were collected following patients’ consent via an approved Institutional Review Board (IRB) protocol. Knee tissues from the suprapatellar pouch (SP) were collected from patients undergoing primary total knee arthroplasty while fibrotic tissue was collected from patients undergoing revision total knee arthroplasty for arthrofibrosis. Tissues were excised by the operative surgeons, and the samples were immediately delivered to the laboratory. Knee tissue samples were then cut into smaller pieces and subsequently digested with 2 mg/ml type I collagenase (Worthington Biochemical Corporation, Lakewood, NJ, USA) in advanced minimum essential medium (Advanced MEM, Thermo Fisher Scientific, Waltham, MA, USA) for 3 hours at 37°C in an orbital shaker (~120 rotations per minute). The digestion solution was filtered through 70-μm cell strainers, the cell suspension was centrifuged at 1200 rpm for 7 minutes at 4°C, and the resulting cells were cultured in Advanced MEM supplemented with 5% human PLTMax (Mill Creek Life Sciences, Rochester, MN, USA), a clinical grade commercial platelet lysate product, 2 U/mL heparin (hospital pharmacy), GlutaMAXTM (Thermo Fisher Scientific), and antibiotic/antimycotic (Thermo Fisher Scientific) at 37°C, 95% humidity, 21% O2, and 5% CO2. At approximately 100% cell confluency, passage 0 cells were detached using TrypLE Express (Thermo Fisher Scientific) and banked using CryoStorR (Sigma-Aldrich, St. Louis, MO, USA). For experimental purposes, cells were retrieved from frozen stocks, expanded in growth medium (same as above), and passage 3-5 cells were used for all experiments. In this regard, at Day 0, cells were treated with 5 µM AdipoRon or its vehicle (DMSO) in the presence of 10 ng/ml TGFβ1 or its vehicle in growth medium. Additional 5 µM final concentration of AdipoRon and equal volume of its vehicle were added on Day 1 and Day 2 without media change. On Day 3, cells were processed and RNA was extracted for downstream analyses.

first: Amel

last: Dudakovic

first: Matthew

middle: P

last: Abdel


title: LRP1high subpopulation of human umbilical cord mesenchymal stem cell (hUC-MSC)transplantationimproves ovarian function in POF and aging mice.

city: Shanghai

first: Li

last: Wu

state: Yangpu District

address: No. 1239, Siping Road

department: School of Life and Science

institute: Tongji University

summary: This study revealed the heterogeneity of UC-MSCs using single-cell sequencing technology (10x Genomics). Through in vitro and in vivo experiments, it was determined that the LRP1high UC-MSCs subpopulation has therapeutic effects in improving ovarian function. This finding provides theoretical support for the screening of stem cell preparations for use in POF, aiming to reduce the impact of other interfering cell components on ovarian tissue and provide precise, safe, and effective clinical strategies for stem cell therapy in POF. Mechanistic exploration further revealed that the LRP1high UC-MSCs subpopulation primarily improves mitochondrial function of granulosa cells by modulating DNA damage pathways, extracellular matrix-related signals, and cellular metabolism. Consequently, it more effectively enhances the quality of aging mouse oocytes, offering new insights into targeting LRP1high UC-MSCs for precise treatment of premature ovarian failure.

overall_design: UC-MSCs were extracted from fetal umbilical cord tissue, cultured in vitro with α-MEM medium to the 6th generation, and UC-MSCs were collected for scRNA-seq.

first: Jiacheng

last: Shen

first: Xiaocui

last: Xu

first: Shaohua

first: Shaorong

last: Gao


title: Transcriptomic analysis delineates preterm prelabor rupture of membranes from preterm labor in preterm fetal membranes

city: Providence

first: Alper

last: Uzun

state: RI

address: 69 Brown St

institute: Brown University

summary: We compared fetal membrane tissue from preterm labor deliveries to fetal tissue from preterm labor with preterm prelabor rupture of membranes (PPROM) deliveries to further explore the concept that spontaneous preterm birth can result from the initializing of two separate but overlapping pathological events. Chorioamnion, separated into amnion and chorion, was collected from gestationally age-matched cases and controls within 15 minutes of birth, and analyzed using RNA sequencing. In our study, transcriptome analysis of preterm fetal membranes revealed distinct differentially expressed genes for PPROM, separate from preterm labor. This study is the first to report transcriptome data that reflects the individual pathophysiology of amnion and chorion tissue from PPROM deliveries.

overall_design: Chorioamnion, was collected within 15 minutes of delivery from pregnancies complicated by preterm birth between the gestational ages of 24 to 37 weeks. The chorioamnion membrane was then separated into amnion and chorion and immediately frozen in liquid nitrogen, or placed in RNAlater solution, and stored at -80°C. For this study, gestational age, and delivery type (vaginal or cesarean) were matched for 4 sets of cases and controls. Control samples were defined as those in which PTL presented first (PTL only), while cases were defined as those in which PPROM presented first, followed by PTL (PPROM + PTL). 16 total tissue samples (8 pairs of amnion and chorion samples) were included in this study.

first: L

last: Underhill

first: J

last: Mennella

first: G

last: Tollefson

first: A

first: B

middle: E

last: Lechner


title: Connectivity Mapping-based Identification and Pre-clinical Evaluation of ISOX: A Novel Therapeutic for Pancreatic Cancer

city: Omaha

first: Surinder

last: Batra

email: sbatra@unmc.edu, pranitaatri@gmail.com

state: NE

address: 42nd and, Emile St, Omaha, NE

department: Biochemistry and Molecular Biology

institute: University of Nebraska Medical Center

summary: Pancreatic Cancer (PC) remains highly lethal due to limited therapeutic options. Here we utilize a genomic-data-driven Connectivity Mapping (CMAP) to identify a drug closer to real-world PC targeting. ISOX emerged as a top potential drug from the CMAP pipeline across human PC tissues, cell lines, tumoroids, and patient-derived xenografts datasets. Here, we use PC cells, human and mouse tumoroids, and in vivo mouse models to test the ability of ISOX alone and in combination with 5FU to inhibit tumor growth. Transcriptomic and pathway analysis of the ISOX-LINCS signature identified the various pathways as targets for ISOX, suggesting a multiple-target action. Specifically, we discovered that genetic and pharmacological targeting of HDAC6 affected non-histone protein cMYC acetylation leading to cMYC instability, thereby disrupting PC stem cells. Finally, KrasG12D harboring organoids and mice responded effectively against ISOX and 5FU treatment by enhancing survival and controlling metastasis incidence. Overall, our data validate ISOX as a novel drug to treat advanced PC patients without toxicity to normal cells

overall_design: To understand the mechanism of action of ISOX in PC, CD18/HPAF cells were sequenced with (1uM: 48 hours) and without ISOX treatment. A diffrential expression was then carried out to assess the effect of treatment.

first: Pranita

last: Atri


title: LRP1high subpopulation of human umbilical cord mesenchymal stem cell (hUC-MSC)transplantationimproves ovarian function in POF and aging mice

overall_design: Female young mice (6-8 weeks), elderly mice (18 months), and elderly mice with different subgroups of UC-MSCs (unsorted, LRP1high, and LRP1low) were transplanted for 3 weeks. Cervical dislocation was euthanized, and the ovaries were decomposed to collect MII oocytes and granulosa cells for RNA sequencing.


title: Proteasome inhibition reprograms chromatin landscape in breast cancer (ChIP-Seq)

first: Brian

last: Bennett

overall_design: Chromatin immunoprecipitation DNA sequencing (ChIP-seq) for H3K4me1 in MCF-7 breast cancer cells treated with either vehicle (UNTR) or proteasome inhibitor MG132 (1 uM) for 4 and 24 hr.

first: Trevor

first: H


title: Proteasome inhibition reprograms chromatin landscape in breast cancer (ATAc-Seq)

overall_design: Assay for Transposase-Accessible Chromatin sequencing (ATAC-seq) results from MCF-7 breast cancer cells treated with either vehicle (UNTR) or proteasome inhibitor MG132 (1 uM) for 4 and 24 hr. This experiment contains 3 replicates of each treatment condition which underwent ATAC-seq on an Illumina NextSeq500 instrument. The samples are referred to as UNTR (which is control or 0 time point), and MG4H (4H), MG24H (24H).

last: Archer


title: Gene expression signatures of cancer-associated fibroblasts in non-small cell lung cancer

city: Shijiazhuang

first: yan

last: zhao

address: Jiankang Road No.12

institute: The Fourth Hospital of Hebei Medical University

summary: To gain insight into the differential gene expression to aberrant fibroblast activation of the TME, we isolated primary CAFs and NFs from human NSCLC tissues and paired normal tissues,and performed microarray screening of CAFs and NFs

overall_design: CAFs and NFs were isolated from human NSCLC tissues and paired normal tissues (more than 5 cm away from the tumor margin). Freshly isolated surgical specimens were acquired from three patients. Fibroblast populations were identified by morphology, western blotting and immunofluorescence staining.

first: Yan

last: Zhao

first: Lihua

last: Liu


title: ScRNA-seq analysis of in vivo rat choroid and rat choroid in vitro co-cultured with human pluripotent stem cell (hPSC) derived endothelial cells

first: Jie

state: Beijing

address: Tsinghua University

department: Basic Medical Sciences, School of Medicine

institute: Tsinghua University

summary: Choroidal atrophy is a common fundus pathological change closely related to the development of age-related macular degeneration (AMD), retinitis pigmentosa, and pathological myopia. Studies suggested that choroidal endothelial cells (CECs) that form the choriocapillaris vessels are the first cells lost in choroidal atrophy. Endothelial cells derived from human pluripotent stem cells (hPSC-ECs) can form blood vessels in vivo and in vitro. We isolated rat choroid and co-cultured with hPSC-ECs. Single-cell RNA-seq (scRNA-seq) studies showed that rat choroid ECs seemed to lose endothelial identity while hPSC-ECs upregulated angiogenesis and hypoxia genes after interacting with choroid.

sample_organism:
Homo sapiens
Rattus norvegicus

platform_organism:
Homo sapiens
Rattus norvegicus

overall_design: Perform scRNA-seq of fresh dissected rat choroid and rat choroid co-cultured with hPSC-EC for 48 hours.

first: Yuntao

last: Hu

first: Mengda

last: Li

first: Peiliang

last: Wang

first: Si

middle: T

last: Huo

first: Hui

last: Qiu


title: Detailed analysis of the murine-aged brain transcriptome [ONT]

first: Nisha

last: Hemandhar Kumar

summary: In this work, we collected and analyzed two cohorts of young-adult and aged-adult mice brain mRNAs and determined their levels using second- (illumina) and third-generation (Oxford Nanopore) sequencing technologies. We report a transcriptome-wide study of differential transcript usage during brain aging. In addition, we provide the community with a large resource of whole brain transcriptomes and comprehensive analyses that identify widespread diversity of mRNAs during aging.

overall_design: Brain mRNA profiles of 4 young-adult samples (6-month, brain hemisphere, from 4 males), 4 aged (24-month, brain hemisphere, from 4 males)

first: Eugenio

last: Fornasiero

first: Manja

last: Marz


title: TET1 inhibits the migration and invasion of cervical cancer cells by regulating autophagy [RNA-seq]

city: Shiyan

last: Ding

address: People's Road

institute: Hubei university of medicine

summary: Methylation modifications play pertinent roles in regulating gene expression and various biological processes. The silencing of the demethylated modifier TET1 can affect the expressions of key oncogenes or tumor suppressor genes, thus contributing to tumor formation. Nonetheless, how TET1 affects the progression of cervical cancer is yet to be elucidated. In this study, we found that the expression of TET1 was significantly downregulated in cervical cancer tissues. Functionally, TET1 knockdown in cervical cancer cells can promote cell proliferation, migration, invasion, cervical xenograft tumor formation and EMT. On the contrary, its overexpression can reverse the aforementioned processes. Moreover, the autophagy level of cervical cancer cells can be enhanced after TET1 knockdown. Mechanistically, methylated DNA immunoprecipitation (MeDIP)-sequencing and MeDIP quantitative real-time PCR revealed that TET1 mediates the methylation of autophagy promoter regions. These findings suggest that TET1 affects the malignant biological behavior of cervical cancer cells by altering the methylation levels of autophagy genes NKRF and HIST1H2AK, but the specific mechanism needs to be investigated further.

overall_design: TET1cas9 and WT SiHa cells in 3 different passages were collected. The total RNA was extracted and sequenced by Shanghai Cloud-seq Biotech

first: Ji

last: Ren

first: Xiu

last: Chen

first: Yu

last: Tan


title: Inhibition of UBA52 induces autophagy via EMC6 to suppress hepatocellular carcinoma tumorigenesis and progression

city: Hefei

first: Li

last: Tong

state: Anhui

address: 218 Jixi Road

department: Department of General Surgery

institute: The First Affiliated Hospital of Anhui Medical University

summary: Hepatocellular carcinoma (HCC) is one of the most common malignant tumors and has a poor prognosis. Ubiquitin A-52 residue ribosomal protein fusion product 1 (UBA52) encodes a fusion protein consisting of ubiquitin and ribosomal protein L40. However, few studies have explored the effects of UBA52 on HCC. In the study, we found that UBA52 is related to autophagy by the bioinformatic analysis. High‐throughput RNA‐sequencingwas used to identifydownstreamtargetgenesof EMC6. Our results suggested that UBA52 may be a new target for the prevention or treatment of HCC.

overall_design: Total RNA from Huh7 cells with UBA52 knockdown or negative control (NC) Huh7 cells was extracted. RNAsamples were sent to Biomarker Technologies Corporation (Beijing, China) for RNAsequencing.

first: Xiaofei

last: Zheng

first: Chong

last: Zhang

first: Chao


title: NPC268 whole-genome bisulfite sequencing (WGBS)

city: Subang Jaya

first: Sok Ching

last: Cheong

state: Selangor

address: No. 1, Jalan SS12/1A,

department: Translational Cancer Biology

country: Malaysia

institute: Cancer Research Malaysia

type: Methylation profiling by high throughput sequencing

summary: Nasopharyngeal carcinoma (NPC), a cancer that is etiologically associated with the Epstein-Barr virus (EBV), is endemic in Southern China and Southeast Asia. The scarcity of representative NPC cell lines owing to the frequent loss of EBV episomes following prolonged propagation and compromised authenticity of previous models underscores the critical need for new EBV-positive NPC models. Herein, we describe the establishment of a new EBV-positive NPC cell line, designated NPC268 from a primary non-keratinizing, differentiated NPC tissue. NPC268 can undergo productive lytic reactivation of EBV and is highly tumorigenic in immunodeficient mice. Whole-genome sequencing (WGS) revealed close similarities with the tissue of origin, including large chromosomal rearrangements, while whole-genome bisulfite sequencing (WGBS) and RNA sequencing demonstrated a hypomethylated genome and enrichment in immune-related pathways, respectively. Drug screening of NPC268 together with six other NPC cell lines using 339 compounds, representing the largest high-throughput drug testing in NPC, revealed biomarkers associated with specific drug classes. NPC268 represents the first and only available EBV-positive non-keratinizing differentiated NPC model, and extensive genomic, methylomic, transcriptomic, and drug response data should facilitate research in EBV and NPC, where current models are limited.

overall_design: The gDNA of NPC268 was processed for bisulfite conversion and library preparation, and WGBS was performed and analyzed. The methylation ratio of a CpG site/region is the number of cytosine reads divided by the sum of the cytosine and thymine reads. The human genome was segmented using a Methyl Kit (v.1.16.1) for global methylation pattern visualization.

first: Sok

middle: C

first: Annie

last: Chai

first: Dai

last: Wei

first: Larry

last: Chow


title: Detailed analysis of the murine-aged brain transcriptome [Illumina]

city: Göttingen

address: Humboldtallee 23

institute: University Medical Center Goettingen


title: Altered tumor signature and T-cell profile after chemotherapy reveal new therapeutic opportunities in High-Grade Serous Ovarian Carcinoma

city: seoul

first: hiram

last: kang

state: seoul

address: 222, Banpo-daero, Seocho-gu, Seoul

country: South Korea

institute: Catholic university of Korea

summary: Using single-cell RNA sequencing, we assessed the systemic impact of chemotherapy on tumor, stromal, and immune cells in the high-grade serous ovarian carcinoma. The results reveal remodeling of the T cell profiles towards a more naïve state and the upregulation of the epithelial-mesenchymal transition signatures in surviving tumor cells. These alterations suggest cellular and molecular targets for the therapeutic development in chemotherapy-resistant ovarian cancer.

overall_design:
We performed quality control on the data according to certain criteria (UMI, RNA, mitochondrial RNA) and used a total of 29,794 cells for lineage clustering. We then subclustered the cells by lineage and performed group analysis to assess the systemic impact of chemotherapy.

This study includes reanalyzed Samples from GSE192898. The OVARY5P_UMI_matrix_final.rds file includes this re-analyzed data.

first: H

last: An


title: Differential gene expression of embryonic brains in maternal choline deficiency

city: Singapore

first: Long

middle: Nam

last: Nguyen

address: 28 Medical Drive

department: Biochemistry

country: Singapore

institute: Singapore

summary: Choline plays an important role during pregnancy. The study focuses on gene expression profile of whole brain tissues of embryos in mouse female treated with choline deficient diet or chow diet.

overall_design:
Maternal choline deficiency in mouse embryos.
The wild-type female was time-mated with the wild-type male. The treatment group includes normal chow diet (ND) or choline-deficient diet (CDD). Females were treated in different diet since time-mating day. Then 4 embryos per group were collected at E14.5 day old. The brains of embryos were harvested in Trizol for further RNA extraction and samples preparation for RNA-sequencing

first: Xuan


title: TET1 inhibits the migration and invasion of cervical cancer cells by regulating autophagy [MeDIP-Seq]

first: Yan


title: TET1 inhibits the migration and invasion of cervical cancer cells by regulating autophagy

overall_design: Refer to individual Series


title: Refining the transcriptional maps of Pseudomonas aeruginosa phages using ONT-cappable-seq

city: Leuven

first: Rob

last: Lavigne

address: Kasteelpark Arenberg 21

department: Biosystems

country: Belgium

institute: KU Leuven

summary: The global transcriptional profiles of Pseudomonas aeruginosa phages LUZ19, LUZ24, YuA, PAK_P3, 14-1 and phiKZ was obtained using the long read RNA sequencing technique ONT-cappable-seq. Using this approach we obtained a comprehensive genome-wide map of viral transcription start sites, terminators and transcription units.

overall_design: Full-length transcriptional profiling of P. aeruginosa infected with different phages (LUZ19, LUZ24, YuA, PAK_P3, 14-1, phiKZ) using ONT-cappable-seq

first: Leena

last: Putzeys

first: Laura

last: Wicke

first: Maarten

last: Boon


title: Transcriptomic screening the novel targets of sericin in human hepatocellular carcinoma cells

city: Bangkok

first: Jiraporn

last: Jantaravnid

state: Prathunwan

address: 254 Phrayathai road, Wang-Mai

country: Thailand

institute: Chulalongkorn University

summary: To investigate the possible novel targets of sericin on human  hepatocellular carcinoma cells and related cellular pathways

overall_design: Identification of differentially expressed genes (DEGs) upon sericin treatment by RNA-Seq

last: Jantaravinid

first: Napatara

last: Tirawanchai

first: Sumate

last: Ampawong

first: Kanchana

last: Kengkoom

first: Anchaleekorn

last: Somkasetrin

first: Vorthunju

last: Nakhonsri

first: Pornanong

last: Aramwit


title: Gene expression profile at single cell level of vestibular schwannoma

first: Luo

middle: Hua

last: hong

state: Shanghai

address: 639 Manufacturing Bureau Road, Shanghai

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

summary: Vestibular schwannoma (VS) is the most common benign tumor in the cerebellopontine angle and internal auditory canal. Illustrating the heterogeneous cellular components of VS could provide insights into its various growth patterns. Single-cell RNA sequencing (scRNA-seq) was used to profile transcriptomes from 7 VS samples and 2 great auricular nerves as normal control.

overall_design: Seven patients diagnosed with sporadic VS who had undergone surgery at our clinic were included. Two normal great auricular nerves was collected from patients with trauma during debridement surgery. In total, nine fresh surgical specimens were sequenced and analyzed.

first: Zirong

last: Huo

first: Zhihua

last: Zhang


title: Ablation of Max expression  induces meiotic onset in sexually undifferentiated germ cells

city: Hidaka

first: Akihiko

last: Okuda

state: Saitama

address: 1397-1 Yamane

department: Division of Biomedical Sciences, Research Center for Genomic Medicine

institute: Saitama Medical University

summary: MAX (MYC Associated Factor X) is generally known as a mandatory partner for MYC transcription factor, which activates various genes involved in cell growth and metabolism.  On the other hand, MAX, when interacting with MGA, forms the polycomb repressive complex (PRC) 1.6, one of the subtypes of PRC1, which directs the transcriptionally repressed chromatin state. Although physiological significance is not known at present, we have previously demonstrated that mouse embryonic stem cells (ESCs) bear a potential to onset meiosis, albeit not germ cells, and PRC1.6 prevent ESCs from their ectopic onset of meiosis (Suzuki et al., 2016, Nat. Commun. 7:11056 doi: 10.1038/ncomms11056). In this study, we aimed to investigate the role of Max in germ cells in vivo by performing the primordial germ cell-specific knockout of the Max gene.

overall_design: Homozygous Max gene-floxed mouse embryos with or without CreERT2 transgene that carries distal enhancer of Oct4 gene were generated by the intercross between Max floxed male mouse with CreERT2 transgene and female Max floxed female mouse without the transgene. Tamoxifen was intraperitoneally administered at E8.5. Genital ridges of tamoxifen-treated male and female embryos were isolated at E12.5. Germ cells recovered from them by means of magnetic-activated cell-sorter (MACS) system were used for RNA sources. These RNAs were used to examine the alteration in global expression profiles due to Max gene disruption in germ cells by DNA microarray analyses. RNAs from homozygous floxed male and female germ cells without CreERT2 transgene were used as reference samples.

first: Ayumu

last: Suzuki

first: Yosuke

last: Mizuno

first: Kousuke

last: Uranishi


title: Comprehensive transcriptome analysis reveals altered mRNA splicing and post-transcriptional changes in the aged mouse brain

first: Nisha

last: Hemandhar Kumar

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


title: Oleanolic acid inhibits the development of breast cancer by regulating lactic acid bacteria and the Cytokinecytokine receptor interaction pathway

first: Kan

last: He

address: 111 Jiulong Road

department: School of life sciences

institute: Anhui University

summary: It was found that after OA treatment, compared with the CK group, the abundance of lactic acid bacteria in the intestinal flora of mice in the OA group increased, and the increase in the abundance of lactic acid bacteria made the gene Il10 upregulated, Il10 had a significant effect on tumor volume reduction and prolongation of mouse survival, and played a role through cytokine receptor interaction pathway.

overall_design: In this study, a mouse breast cancer model was constructed, and the phenotypic effect of oleanolic acid on mice was analyzed after the end of the administration cycle, and the cecum tissues of the model group (CK) and oleanolic acid group (OA) were sequenced by 16SrRNA to analyze the differential flora of each group, and the tumor tissues of the model group (CK) and oleanolic acid group (OA) were analyzed with reference transcriptome.

first: K

first: X

last: Meng

first: J

last: Su

first: S

last: Jiang


title: Mutational analysis of HCC827 and HCC827-OR cell lines [HCC827OR_WES]

city: Chengdu

first: Jian

state: Sichuan

address: Guoxuexiang Road

department: Westchina Hospital

institute: Sichuan University

summary: To investigate if there are new genetic mutations occurred within the HCC827 osimertinib resistant cells compared with the parental cells.

overall_design: Comparative gene mutational profiling analysis of WES-seq data for HCC827 and HCC827-OR cell lines.