title: Generation of Bona Fide Human Induced Trophoblast Stem Cells from Term Umbilical Cord

city: Amsterdam

first: Remco

last: Keijser

address: Meibergdreef 9

department: Reproductive Biology Laboratory

country: Netherlands

institute: Amsterdam UMC

summary: Placentation disorders such as severe fetal growth restriction and preeclampsia have their origin in the first trimester of pregnancy, whereas symptoms typically present later on. To be able to study the pathogenesis of these diseases, there is a need for a reliable model system of early placenta development with known pregnancy outcomes. Therefore, we aimed to optimize the generation of human induced trophoblast stem cells (iTSCs) from term umbilical cord using a direct reprogramming approach. In this, we added three supplements—A-485 (CREBBP/EP300 inhibitor), BMP4 or EPZ-6438 (PRC2 inhibitor)—that could potentially boost iTSC induction. The generated iTSCs fulfilled the criteria for bona fide first-trimester trophoblasts and exhibited transcriptional similarity to TSCs derived from first-trimester placental tissue, while the supplements tested did not substantially enhance iTSC induction.

overall_design: Mesenchymal stem cells were isolated from a term umbilical cord, and transduced with the OSKM reprogramming factors. Seven days post-transduction, reprogramming intermediates were transited into human TSC medium to induce TSC conversion, with or without supplementation of A-485, BMP4 or EPZ-6438 for 1-3 days. Transcriptome sequencing was performed to assess the similarity between the generated iTSCs and TSCs derived from first-trimester placental tissue. The dataset contains 1-3 experimental replicates of each iTSC condition, 3 TSC lines, and TSCs differentiated into extravillous trophoblast for reference.

first: Jantine

last: van Voorden

first: Souad

last: Boussata

first: Marloes

last: Vermij

first: Muriel

last: Wagner

first: Wessel

last: Ganzevoort

first: Gijs

last: Afink


title: The trajectory of KoRV-A Evolution Indicates Initial Integration into the Koala Germline Genome Near Coffs Harbour [Adelaide RNA-seq]

status: Public on Jan 15 2025

city: Worcester

first: Tianxiong

last: Yu

state: MA

address: 364 Plantation St

country: USA

institute: Umass Med

type: Expression profiling by high throughput sequencing

summary: Koala Retrovirus-A is a gamma-retrovirus sweeping wild koalas via a combination of horizontal and vertical transfer, contributing substantial genomic diversity across and even within koala populations. While studies have estimated KoRV-A's integration into the koala genome occurred 120–50,000 years ago, the origin and spread patterns of its endogenization remain unclear. Here, we analyze KoRV-A germline insertions using whole-genome sequencing data from 405 wild koalas, encompassing nearly the full koala habitat range. We map a trajectory of KoRV-A evolution and propose that KoRV-A first entered the koala germline genome near Coffs Harbour. As KoRV-A spread, replication-competitive subtypes emerged, two of which recombined with an ancient endogenous retrovirus, PhER, resulting in distinct recombination variants across northern and southern koala populations. Additionally, we identified a geographic barrier north of Sydney, which has slowed the southward spread of KoRV-A into Sydney and beyond.

overall_design: To investigate the evolution of KoRV-A, we performed short-read DNA-seq and RNA-seq on six Adelaide koalas. These data was combined with DNA-seq and RNA-seq from our previous studies (Yu et al., 2019 and Yu et al., 2024) and the Koala Genome Survey.

first: Milky

last: Abojorga

first: Birgit

middle: S

last: Koppetsch

first: Michaela

middle: D

last: Blyton

first: Keith

last: Chappell

first: Zhiping

last: Weng

first: William

middle: E

last: Theurkauf


title: The trajectory of KoRV-A Evolution Indicates Initial Integration into the Koala Germline Genome Near Coffs Harbour [Adelaide DNA-seq]


title: Classes of Lamin-Associated Domains are Defined by Distinct Patterns of Repressive Histone Methylation [RNA-seq]

city: Columbus

first: Mark

last: Parthun

state: Ohio

address: 1060 Carmack Rd.

department: Biological Chemistry and Pharmacology

institute: The Ohio State University

summary: A large fraction of the genome interacts with the nuclear periphery through lamina-associated domains (LADs), repressive regions which play an important role in genome organization and gene regulation across development. Despite much work, LAD structure and regulation remain incompletely understood, and a mounting number of studies have identified numerous genetic and epigenetic differences within LADs, demonstrating they are not a uniform group. Here we profile Lamin B1, HP1β, H3K9me3, H3K9me2, H3K27me3, H3K14ac, H3K27ac, and H3K9ac in MEF cell lines derived from the same mouse colony and cluster LADs based on the abundance and distribution of these features across LADs. We find that LADs fall into 3 groups, each enriched in a unique set of histone modifications and genomic features. Each group is defined by a different heterochromatin modification (H3K9me3, H3K9me2, or H3K27me3), suggesting that all three of these marks play important roles in regulation of LAD chromatin and potentially of lamina association. We also discover unique features of LAD borders, including a LAD border-specific enrichment of H3K14ac. These results reveal important distinctions between LADs and highlight the rich diversity and complexity in LAD structure and regulatory mechanisms.

overall_design: RNA-seq in three independently derived mouse embryonic fibroblast (iMEF) cell lines from one mouse colony.

first: Caden

middle: J

last: Martin

first: Prabakaran

last: Nagarajan

first: Elizabeth

middle: A

last: Oser

first: Liudmila

middle: V

last: Popova

middle: R


title: Classes of Lamin-Associated Domains are Defined by Distinct Patterns of Repressive Histone Methylation [CUT&RUN]

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: Cleavage Under Target and Release Using Nuclease (CUT&RUN) for Lamin B1, H3K9me2, H3K14ac, and IgG (control) in independently derived mouse embryonic fibroblast (iMEF) cell lines from one mouse colony. CUT&RUN for Lamin B1 and IgG was performed in 2 biological replicates and H3K9me2 and H3K14ac in one.


title: Classes of Lamin-Associated Domains are Defined by Distinct Patterns of Repressive Histone Methylation [CUT&Tag]

overall_design: Cleavage Under Target and Tagmentation (CUT&Tag) for H3K9me2, H3K9me3, H3K27me3, H3K14ac, H3K27ac, and H3K9ac in immortalized mouse embryonic fibroblast (iMEF) cells derived from three different mice from the same mouse colony.


title: A multi-omics census reveals miRNA miR-let-7 as instigator of paternal mitochondrial dysfunction and in epigenetic heredity of intergenerational metabolic decline [F1_Liv_eWAT_RNAseq]

city: Odense

first: Jan

middle: Wilhelm

last: Kornfeld

address: Campusbej 50

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

summary: We describe that diet-induced obesity and weight loss development in male mice causes reversible abnormalities in glucose and lipid metabolism, serum metabolomes, and adipose tissue and liver gene expression and causes specific, but reversible, reductions in activity of genes controlling mitochondrial energy dissipation in white adipose tissue. When mating obese mice with isogenic lean females, we observed highly concordant reductions in mitochondrial gene expression and translation in offspring that resemble those observed in obese fathers. When mapping small RNA responses across somatic and gametic cell types and between generations, we saw that obesity and weight loss reversible affected miRNA abundance, and observed several miR-let7 isoforms induced in obese adipose tissues of the paternal (F0) and offspring (F1) generation, as well as in sperm of F0 mice. Mechanistically, when overexpressing miR-let-7 in primary adipocytes, we found it to silence DICER1, a key rheostat required for adipose tissue adaptation in obesity as evidenced by functional deficiency in mitochondrial functioon following DICER1 loss. Upon ectopic delivery of miR-let7d/e levels into fertilized oocytes by microinjection, we elicited glucose intolerance and impairments in adipose mitochondrial gene expression in mice sired from miRNA-injected embryos, thus phenocopying key aspects of paternal obesity itself. When performing single-cell RNA-Seq in embryos, we found that miR-let7d/e delivery impaired mitochondrial gene expression, suggesting altered energy metabolism following sperm-mediated changes in zygotic miRNA pools. When studying miRNA alterations in human gametes, we found that lifestyle-induced weight loss downregulated MIR-LET7D/E in semen from human subjects, suggesting similar roles for human miR-let7d/e in gametic epigenomes and embryogenesis.

overall_design: Liver and eWAT RNA profiles of LF, HF and HF-LF male mice in F1 generations were generated by deep sequencing using Illumina NovaSeq 6000 (n=4-6).

first: Chien

last: Huang

first: JooHyun

last: Park

first: Ali

last: Altintas

first: Natasa

last: Stanic

first: Hande

middle: T

last: Batarlar

first: Rocio

last: Malmros

first: Jesper

last: Havelund

first: Nils

last: Færgeman

first: Bjørk

last: Larsen

first: Karolina

last: Szczepanowska

first: Jan-Wilm

last: Lackmann

first: Aleksandra

last: Trifunovic

first: Eva

middle: K

last: Hejbøl

first: Sönke

last: Detlevsen

first: Ida

last: Jepsen

first: Stefanie

middle: H

last: Kolstrup

first: Ricardo

last: Laguna-Barraza

first: Javier

middle: M

last: Gonzalez

first: Konstantin

last: Khodosevich

first: Romain

last: Barrès

first: Jan-Wilhelm


title: SFPQ protects DNA repeat stability by recruiting histone H3.3 chaperon activity to R-loop structures [RNA-seq]

city: Trieste

first: Silvano

last: Piazza

address: localita' Padriciano 99

country: Italy

institute: ICGEB

summary: R-loops are atypical, three-stranded nucleic acid structures that contain a stretch of RNA:DNA hybrids and an unpaired single stranded DNA loop. R-loops control physiologically processes, however when unscheduled or persistent they drive genome instability by creating conflicts with transcription and replication. The human genome is composed of up to 75% of repetitive sequence elements that can also hold transcriptional activity. Thus R-loop surveillance at repetitive elements is central for the maintenance of genome integrity.  Here we show that the RNA binding protein SFPQ suppresses R-loop mediated replication stress and DNA damage at repeat elements such as telomeres, (peri)-centromeres, LINE-1 and SINE elements. SFPQ shows in-vitro R-loop binding activity, uses its RNA-recognition motif (RRM) domains to bind chromatin containing R-loops and uses its proline-rich (P) domain to recruit the histone H3.3 chaperon DAXX to maintain a correct nucleosome template that antagonizes R-loop formation. Loss of SFPQ results in DAXX delocalization from repeat elements, reduction of histone H3.3 incorporations, replication stress mediated DNA damage in repeat elements resulting and centromere defects resulting the formation of cytoplasmatic DNA species that activate the cGAS/STING pathway and innate immunity.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for U2-OS cells transfected with Control or SFPQ siRNAs, with 3 replicates.

first: Stefan

last: Shoeftner

first: Alessandro

last: Ferrando

first: Alice

last: Gambelli

first: Giulia

last: Canarutto

first: Andrea

last: Parlante


title: KRAS-G12D drives immunosuppression in lung adenocarcinoma through paracrine signaling

city: Ann Arbor

last: Galban

state: MI

address: 109 Zina Pitcher Place

department: Radiology

institute: University of Michigan

summary: Here, we sought to understand the KRAS-G12D-dependent changes occuring in the tumor and the tumor microenvironment within the lung.

overall_design: We harvested the right inferior lobe of lungs from male and female mice in the ON (21 weeks) and OFF (21 weeks ON, 1 week OFF) groups for single cell RNA sequencing.

first: Emily

middle: L

last: Lasse-Opsahl

first: Yaqing

last: Zhang

first: Marina

last: Pasca di Magliano


title: SFPQ protects DNA repeat stability by recruiting histone H3.3 chaperon activity to R-loop structures [ChIP-seq]


title: TLR5 signaling causes dendritic cell dysfunction and orchestrates failure of immune checkpoint therapy against ovarian cancer

city: Charlottesville

first: Anwaruddin

last: Mohammad

state: VA

address: Pinn Hall

department: Bioinformatics Core

institute: University of Virginia

summary: Ovarian cancer accounts for more deaths than any other cancer of the female reproductive system. Patients bearing ovarian tumors infiltrated with high frequencies of T cells are associated with a greater survival probability. However, therapies to revitalize tumor-associated T cells, such as PD-L1/PD-1 or CTLA4 blockade , are ineffective for the treatment of ovarian cancer. We demonstrate that for ovarian cancer, Toll-Like Receptor 5 (TLR5) signaling, the only known ligand for which is bacterial flagellin, governs failure of PD-L1 and CTLA4 blockade. Mechanistically, chronic TLR5 signaling on CD11c+ cells in vivo and in vitro impairs the differentiation of functional IL-12-producing XCR1+, CD103+ cDC1 subsets, biasing CD11c+ precursor cells towards myeloid subsets expressing high levels of PD-L1. This culminates in impaired activation of CD8 T cells, reducing CD8 T cell function and ability to persist within the ovarian tumor microenvironment. Expansion of cDC1s in situ using FLT3L in combination with PD-L1 blockade achieved significant survival benefit, but only in TLR5 KO mice, whereas no benefit was observed in the presence of TLR5 signaling. Thus, we identify a host-intrinsic mechanism leading to the failure of PD-L1 blockade for ovarian cancer, demonstrating that chronic TLR5 signaling on CD11c+ cells is a barrier limiting the efficacy of checkpoint therapy.

overall_design: Bone marrow cells were collected from femurs and tibias a wild-type mouse and cultured with 400ng/ml of FLT3L (BioXCell, cat# BE0342) in 3ml of RPMIc in a 6-well plate (Thermo Scientific™ BioLite™ Microwell Plates, cat #12-556-004) at 3e6 cells per well on day one 10ng/ml of ultra-purified Flagellin derived from S. typhimurium (InvivoGen, cat# tlrl-epstfla-5) and incubated at 37°C in a humidified incubator containing 5% CO2. Additional RPMIc + FLT3L with or without flagellin was added at 3ml on day four. Samples were collected and stained with TotalSeq™-B Mouse Myeloid Cocktail, V1.0 (Biolegend, cat# 199904) separately after 8 days of culture. RNA library preparation and sequencing was performed by the UVA Genome Analysis and Technology Core using a 10X Chromium X.

first: Mitchell

last: McGinty

first: Audrey

last: Putelo

first: Sree

last: Kolli

first: Tzu-Yu

last: Feng

first: Madison

last: Dietl

first: Cara

middle: N

last: Hatzinger

first: Simona

last: Bajgai

first: Mika

last: Poblete

first: Francesca

last: Azar

first: Pankaj

last: Kumar

first: Melanie

last: Rutkowski


title: Transcriptomics and single-cell RNA sequencing analysis of long-term cultured human islets in vitro [scRNA-Seq]

city: Duarte

first: Guihua

last: Sun

state: CA

address: 1500 East Duarte Rd.

department: Department of Neurodegenerative Diseases

institute: City of hope

summary: β-cell dysfunction in pancreatic islets is the leading cause of progression to type I diabetes (T1D), but the reason for the loss of β-cell mass in T1D is still not fully understood. Using in vitro long-term cultured (LTC) human islets, we have investigated gene profiling and subtype cells changes in the leftover cells and compared them with residual cells in samples of T1D or T2D. While most of the dysregulated genes were downregulated during LTC, we found there are specific groups of mRNA or miRNA that were upregulated, and they are involved in specific pathways. In general, α-cells and β-cells of LTC-islets have elevated expressions of MAFB and MAFA, respectively. We also found exocrine cells were eliminated faster than endocrine cells, and β-cells were lost at a higher rate than α-cells. Interestingly, a specific group of cells that were classified as α-cells but have immature β-cells-like characteristics, were enriched in LTC, revealed the possibility of transdifferentiating of α-cells to β-cells under in vitro culture. Our results suggested that there are intrinsic cellular and molecular mechanisms in pancreatic cells that are associated with their maturity and correlated with their survival ability under unfavorable living conditions.

overall_design: Single cell RNA sequening of long term in vitro cultured human islets


title: Transcriptomics and single-cell RNA sequencing analysis of long-term cultured human islets in vitro [RNA-Seq]

overall_design: Bulk RNA sequening of long term in vitro cultured human islets


title: Classes of Lamin-Associated Domains are Defined by Distinct Patterns of Repressive Histone Methylation [ChIP-seq]

first: Mark

last: Parthun

overall_design: ChIP-seq for HP1β in two independently derived mouse embryonic fibroblast (iMEF) cell lines from one mouse colony.

first: Caden

last: Martin

first: Prabakaran

last: Nagarajan

first: Elizabeth

last: Oser

first: Liudmila

last: Popova


title: A multi-omics census reveals miRNA miR-let-7 as instigator of paternal mitochondrial dysfunction and in epigenetic heredity of intergenerational metabolic decline [PeWA]

first: Jan

last: Kornfeld

overall_design: RNA profiles of primary epididymal-derived adipocytes transfected by mmu-miR-let-7-d/e-5p mimics or negative control were generated by deep sequencing using Illumina NovaSeq 6000 (n=6).

first: Chien

last: Huang

first: JooHyun

last: Park

first: Ali

last: Altintas

first: Natasa

last: Stanic

first: Hande

last: Batarlar

first: Rocio

last: Malmros

first: Jesper

last: Havelund

first: Nils

last: Færgeman

first: Bjørk

last: Larsen

first: Karolina

last: Szczepanowska

first: Jan-Wilm

last: Lackmann

first: Aleksandra

last: Trifunovic

first: Eva

last: Hejbøl

first: Sönke

last: Detlevsen

first: Ida

last: Jepsen

first: Stefanie

last: Kolstrup

first: Ricardo

last: Laguna-Barraza

first: Javier

last: Gonzalez

first: Konstantin

last: Khodosevich

first: Romain

last: Barrès

first: Jan-Wilhelm


title: A multi-omics census reveals miRNA miR-let-7 as instigator of paternal mitochondrial dysfunction and in epigenetic heredity of intergenerational metabolic decline  [IVF_Smart-seq]

first: Jan

last: Kornfeld

overall_design: Single cell RNA profiles of 8-cell blatomeres microinjected with  mmu-miR-let-7-d/e-5p mimics or negative control were generated by smart-seq2 sequencing using Illumina NextSeq500 (n=20-24).

first: Chien

last: Huang

first: JooHyun

last: Park

first: Ali

last: Altintas

first: Natasa

last: Stanic

first: Hande


title: Transcription Factor-Wide Association Studies (TF-WAS) to identify Functional SNPs in Alzheimer's Disease

city: Philadelphia

first: Yijing

last: Su

state: PA

address: Levy 326

department: Department of Oral Medicine

institute: University of Pennsylvania

summary: Alzheimer’s disease (AD) is a progressive neurodegenerative disorder with profound global impact. While Genome-wide Association Studies (GWAS) have revealed genomic variants linked to AD, their translational impact has been limited due to challenges in interpreting the identified genetic associations. To address this challenge, we have devised a novel approach termed Transcription Factor-Wide Association Studies (TF-WAS). By integrating the GWAS, eQTL and transcriptome analyses, we selected 30 AD SNPs in non-coding regions that are likely to be functional. Using human transcription factor (TF) microarrays, we have identified 90 allele-specific TF interactions with 53 unique TFs. We then focused on several interactions involving SMAD4, and further validated them using EMSA, luciferase, and ChIP on engineered genetic backgrounds. This approach holds promise for unraveling the intricacies of not just AD, but any complex disease with available GWAS data, providing insight into underlying molecular mechanisms and clues towards potential therapeutic targets.

overall_design: SNPs are probed to the TF arrays in pairs as a competition assay, with one allele labeled with Cy3 and the other labeled with Cy5. For each pair, the arrays are performed in duplicate, with the allele colors swapped. For example, on one array the Cy3 risk and Cy5 non-risk are probed, while the Cy5 risk and Cy3 non-risk are probed to another array (as indicated in each raw data file name).

first: Jessica

last: Dunn

first: Cedric

last: Moore

first: Nam-shik

last: Kim

first: Tianshun

last: Gao

first: Zhiqiang

last: Cheng

first: Peng

last: Jin

first: Guo-li

last: Ming

first: Jiang

last: Qian

first: Hongjun

last: Song

first: Heng

last: Zhu


title: Vaginal transcriptional signatures of the neutrophil-driven immune response correlate with clinical severity during recurrent vulvovaginal candidiasis

city: Stockholm

first: Anastasios

middle: Erik

last: Damdimopoulos

state: Huddinge

address: Hälsovägen 7c

department: Department of Biosciences and Nutrition

country: Sweden

institute: Karolinska Institute

summary: Problem: Recurrent vulvovaginal candidiasis (RVVC) affects 5-10% of all women, negatively impacting their reproductive health and quality of life. Herein, we investigated the molecular effects of RVVC on the vaginal mucosa of otherwise healthy women.  Methods: Gene expression analysis was performed on vaginal tissue biopsies from women with RVVC, including those with a current episode of vulvovaginal candidiasis (RVVC, n=19) and women between infections (CNR, n=8); women asymptomatically colonized with Candida albicans (AS, n=7); and healthy controls (n=18). Gene expression profiles were compared between groups and correlated with clinical data retrieved from questionnaires and gynecologic examinations.  Results: Of 20,171 genes identified in vaginal biopsies, 6,506 were differentially expressed in the RVVC group, compared to healthy controls. Gene expression pathway analysis revealed an association between RVVC and pathways of inflammatory responses, especially genes involved in neutrophil recruitment and activation. Expression of genes involved in inflammation and neutrophil recruitment increased with increasing clinical severity of vulvovaginal candidiasis, whereas expression of some genes involved in epithelial integrity decreased with increasing clinical severity of infection. Gene expression profiles of both the CNR and AS groups were comparable to those of healthy controls.  Conclusions: The clinical severity of RVVC during active infection correlates with increased expression of genes involved in molecular inflammation and neutrophil activation in the vaginal mucosa. The lack of differences between healthy controls and women with RVVC who were between acute infections indicates that the molecular effects observed in the RVVC group are only present during active infection.

first: Hasselrot

last: Tyra

first: Alvendal

last: Cathrin

first: Hunt

last: Sara

first: Franzén Boger

last: Mathias

first: Kaldhusdal

last: Vilde

first: Damdimopoulos

last: Anastasios

first: Schuppe-Koistinen

last: Ina

first: Edfeldt

last: Gabriella

first: Bohm-Starke

last: Nina

first: Broliden

last: Kristina


title: A multi-omics census reveals miRNA miR-let-7 as instigator of paternal mitochondrial dysfunction and in epigenetic heredity of intergenerational metabolic decline [F0_Liv_eWAT_RNAseq]

first: Jan

last: Kornfeld

overall_design: Liver and eWAT RNA profiles of LF, HF and HF-LF male mice in F0 generation were generated by deep sequencing using Illumina NovaSeq 6000 (n=4-6).

first: Chien

last: Huang

first: JooHyun

last: Park

first: Ali

last: Altintas

first: Natasa

last: Stanic

first: Hande

last: Batarlar

first: Rocio

last: Malmros

first: Jesper

last: Havelund

first: Nils

last: Færgeman

first: Bjørk

last: Larsen

first: Karolina

last: Szczepanowska

first: Jan-Wilm

last: Lackmann

first: Aleksandra

last: Trifunovic

first: Eva

last: Hejbøl

first: Sönke

last: Detlevsen

first: Ida

last: Jepsen

first: Stefanie

last: Kolstrup

first: Ricardo

last: Laguna-Barraza

first: Javier

last: Gonzalez

first: Konstantin

last: Khodosevich

first: Romain

last: Barrès

first: Jan-Wilhelm


title: A multi-omics census reveals miRNA miR-let-7 as instigator of paternal mitochondrial dysfunction and in epigenetic heredity of intergenerational metabolic decline [F1_Liv_eWAT_Small_RNAseq]

first: Jan

last: Kornfeld

type: Non-coding RNA profiling by high throughput sequencing

overall_design: Liver and eWAT RNA profiles of LF, HF and HF-LF male mice in  F1 generation were generated by deep sequencing using Illumina NovaSeq 6000 (n=4-6).

first: Chien

last: Huang

first: JooHyun

last: Park

first: Ali

last: Altintas

first: Natasa

last: Stanic

first: Hande


title: Deer Antler Reserve Mesenchyme Cells Modified with MiR-145 Promote Chondrogenesis in Cartilage Regeneration

city: Changchun

first: Boyin

last: Jia

state: Jilin

address: 2888 Xincheng Street

department: College of Animal Science and Technology

country: China

institute: Jilin Agricultural University

summary: Deer antler-derived reserve mesenchyme cells (RMCs) are a promising source of cells for cartilage regeneration therapy due to their chondrogenic differentiation potential. However, the regulatory mechanism has not yet been elucidated. microRNAs (miRNAs) have been shown to regulate the differentiation of various mesenchymal stem cells (MSCs) and play an important role in the post-transcriptional regulation of chondrogenesis and hypertrophic differentiation. In this study, we demonstrated that the RMCs showed typical MSCs differentiation potentials. During chondrogenic differentiation, we obtained the expression profile of miRNAs, among which miR-145 was the most prominent candidate as key microRNA involved in the balance of chondral and endochondral differentiation. Knockdown of miR-145 promoted chondrogenesis and inhibits hypertrophy differentiation in RMCs. Mechanically, by online databases prediction combined with dual-luciferase reporter assay, SOX9 was suggested as a target of miR-145. Further validation experiments confirmed that knockdown of miR-145 contributed to the balance between endochondral versus chondral differentiation of RMCs by targeting SOX9. Additionally, RMCs transfected with the miR-145 knockdown mediated of lentiviral vector successfully promoted cartilage regeneration in vivo. In summary, our study suggested that the reciprocal negative feedback between SOX9 and miR-145 was essential for balancing between endochondral versus chondral differentiation of RMCs. Our study suggested that modification of RMCs using miRNAs transduction might be an effective treatment for cartilage defects.

overall_design: Collect total RNA from chondrocytes and RMCs induced chondrogenic differentiation for 0, 7, 14 days to construct small RNA libraries.

first: Rui

last: Du

first: Xintong

last: Han

first: Xin

last: Li


title: Single-nucleus RNA sequencing reveals cellular transcriptome features at different growth stages of porcine skeletal muscle

city: Chengdu

first: Rhea

last: Chen

address: No.211 Huimin Road, Wenjiang District, Chengdu, Sichuan, China

institute: Sichuan Agricultural University

summary: Porcine latissimus dorsi muscle is one of the main sources of pork products. Meat quality indicators such as the proportion of muscle fibres within the latissimus dorsi muscle and intramuscular fat deposition change during the growth and development of pigs.We used single-nucleus sequencing (snRNA-seq) to analyse the changes occurring in the longest dorsal muscles of pigs at different growth stages

overall_design: Skeletal muscle tissue was obtained from the latissimus dorsi muscle of 170-day-old and 245-day-old white pigs, respectively, for single nucleus sequencing.

first: Ziyu

first: Xiaoqian

last: Wu

first: Long

last: Jin

first: Li


title: A multi-omics census reveals miRNA miR-let-7 as instigator of paternal mitochondrial dysfunction and in epigenetic heredity of intergenerational metabolic decline [Fm_eWAT_RNAseq]

overall_design: eWAT RNA profile of Fm generation was generated by deep sequencing using Illumina NovaSeq 6000 (n=6).

last: Batarlar

first: Rocio

last: Malmros

first: Jesper

last: Havelund

first: Nils

last: Færgeman

first: Bjørk

last: Larsen

first: Karolina

last: Szczepanowska

first: Jan-Wilm

last: Lackmann

first: Aleksandra

last: Trifunovic

first: Eva

last: Hejbøl

first: Sönke

last: Detlevsen

first: Ida

last: Jepsen

first: Stefanie

last: Kolstrup

first: Ricardo

first: Javier

first: Konstantin

first: Romain


title: Transcriptomics and single-cell RNA sequencing analysis of long-term cultured human islets in vitro [miRNA-Seq]

first: Guihua

last: Sun

overall_design: small RNA sequening of long term in vitro cultured human islets


title: Single-cell analysis of the epigenome and 3D chromatin architecture in the human retina [snm3c-seq]

city: La Jolla

first: Ying

last: Yuan

address: Palmilla Dr.

department: MATS

institute: UCSD

summary: Most genetic risk variants linked to ocular diseases are non-protein coding and presumably contribute to disease through dysregulation of gene expression, however, deeper understanding of their mechanisms of action has been impeded by an incomplete annotation of the transcriptional regulatory elements across different retinal cell types. To address this knowledge gap,  we carried out single-cell multiomics assays to investigate gene expression, chromatin accessibility, DNA methylome and 3D chromatin architecture  in human retina, macula, and retinal pigment epithelium (RPE). We identified 420,824 unique candidate regulatory elements and characterized their chromatin state in 23 sub-classes of retinal cells. Comparative analysis of chromatin landscapes between human and mouse retina cells revealed both evolutionarily conserved and divergent retinal gene-regulatory programs. Leveraging the rapid advancements in deep-learning techniques, we developed sequence-based predictors to interpret non-coding risk variants of retina diseases. Our study establishes retina-wide, single-cell transcriptome, epigenome, and 3D genome atlases, and provides a resource for studying the gene regulatory programs of the human retina, leading to mechanistic insights into a wide-spectrum of eye diseases.

overall_design: The eye globes were collected from three unrelated human donors (aged 21, 27 and 43 years) (Table-X) with the collaboration of San Diego Eye Bank. The sample processing time starting from eye enucleation to dissection was restricted within 2 hours to identify the macula, a visible yellowish/whiteish indent that is slightly lateral to the optic disk inside the globe. Prior dissection, the eye globe with proper label was collected in a sterile moist chamber. At first the cornea was removed by cutting 2-3 mm around the limbus using a surgical blade. Pull off the iris and lens. This will leave you with the eye cup, which contains the posterior pole. After removing enough vitreous and aqueous fluid the temporal region can be located by two main blood vessels that curl around the macula. Using a sterile 3mm skin biopsy punch, the macula was collected. Sections were made for the other regions, temporal, nasal, superior and inferior. For all these regions, the retina and RPE tissue were separated and stored immediately in Liquid Nitrogen.

first: Yuan

last: Ying

first: Zemke

first: Biswas

last: Pooja

first: Dong

last: Keyi

first: Lau

last: Pik Ki

first: Bartosik

last: Weronika


title: Effect of 3D cultivation of human mesenchymal stomal cells to emulate the bone marrow niche microenvironment

city: Berlin

first: Mark

last: Rosowski

address: Gusav-Meyer-Allee 25

country: Germany

institute: TU Berlin

summary: The bone marrow provides the niche microenvironment for the long-term maintenance of various cell types, such as hematopoietic stem cells (HSC) or long-lived plasma cells (LLPC). The maintenance of HSC and LLPC relies on specific niches composed of specific soluble molecules, adhesion molecules, and proteins of the extracellular matrix, which are partly provided by mesenchymal stromal cells. In recent years, there have been many efforts to simulate the niche situation in vitro by the generation of organ and tissue surrogates by organoid technology. In this study, we cultured bone marrow-derived human mesenchymal stromal cells on a 3D scaffold to emulate the niche microenvironment by generating a bone marrow organoid. Transcriptional analysis of differentially expressed genes and the general expression pattern of bone marrow-relevant genes in 3D demonstrate the eligibility of the 3D culture system for the maintenance of bone marrow-associated HSC and LLPC.

overall_design: Human bone marrow-derived mesenchymal stromal cells were cultured in monolayer or 3D scaffold culture for seven days. Using data from four independent biological donors, we performed gene and expression profiling analysis.

first: Uyar-Aydın

last: Zehra

first: Gürcan

last: Kübrah

first: Rosowski

last: Mark


title: A TRIM37 risk variant rs57141087 contributes to triple-negative breast cancer onset and progression in Black women.

city: Davis

first: Rachisan Gabriel

middle: Djiake

last: Tihagam

address: 919 Drake Drive,, 113

department: BMG

institute: University of virginia

summary: TRIM37 is a histone H2A ubiquitin ligase importantin breast cancer oncogenesis. To assess the neoplastic transformationsof normal breast epithelial cells in the context of TRIM37, we increased its expression and compared the gene expression network regulated by TRIM37 in control and TRIM37 overexpression.

overall_design: Total RNA was isolated from  cells and fresh frozen breast tissues from the Susan G. Komen Tissue Bank . Libraries for RNA-seq were prepared by Novogene. Sequence reads were trimmed for adaptor sequence/low quality reads,  and the gene expression was then compared between groups.

first: Sanchita

last: Bhatnagar

first: Rachisan

first: Song

last: Lou


title: Single-cell analysis of the epigenome and 3D chromatin architecture in the human retina [10x multiome]

first: Yang

last: Qian

first: Wang

last: Allen


title: Single-cell analysis of the epigenome and 3D chromatin architecture in the human retina [mm10_ATAC-seq]

first: Ying

summary: Most genetic risk variants linked to ocular diseases are non-protein coding and presumably contribute to disease through dysregulation of gene expression, however, deeper understanding of their mechanisms of action has been impeded by an incomplete annotation of the transcriptional regulatory elements across different retinal cell types. To address this knowledge gap, we carried out single-cell multiomics assays to investigate gene expression, chromatin accessibility, DNA methylome and 3D chromatin architecture in human retina, macula, and retinal pigment epithelium (RPE). We identified 420,824 unique candidate regulatory elements and characterized their chromatin state in 23 sub-classes of retinal cells. Comparative analysis of chromatin landscapes between human and mouse retina cells revealed both evolutionarily conserved and divergent retinal gene-regulatory programs. Leveraging the rapid advancements in deep-learning techniques, we developed sequence-based predictors to interpret non-coding risk variants of retina diseases. Our study establishes retina-wide, single-cell transcriptome, epigenome, and 3D genome atlases, and provides a resource for studying the gene regulatory programs of the human retina, leading to mechanistic insights into a wide-spectrum of eye diseases.

overall_design: The eye globes were collected from eight unrelated mouse donors with the collaboration of San Diego Eye Bank.

first: Dang

last: Kelsey

first: Lin

last: Lin

first: Lancione

last: Ryan

first: Preissl

last: Sebastian


title: Single-cell analysis of the epigenome and 3D chromatin architecture in the human retina

last: Yuan

first: Yuan

last: Ying

first: Biswas

last: Pooja

first: Buchanan

last: Justin


title: Adaptive evolution of KoRV-A  retroviral silencing in wild koalas [DNA-seq]

first: Tianxiong

last: Yu

summary: Koala Retrovirus-A is spreading through wild koalas in a north to south wave while transducing the germline, generating heritable genetic modifications as it transitions to an endogenous retrovirus.  In animals south of Brisbane, we previously found that KoRV-A is expressed in the germline, but the resulting unspliced genomic transcripts are processed into sense strand piRNAs, post-transcriptionally suppressing replication.   Here we show that this initial “innate” response is prevalent in animals south of the Brisbane River, but KoRV-A promoters are methylated and the virus is transcriptionally silenced in a subpopulation of animals north of the river.  Transcriptional silencing correlates with capture of an anti-sense KoRV-A provirus by the 3’UTR of the MAP4K4 gene.  The resulting hybrid transcripts are processed into anti-sense piRNAs, which transcriptionally silence established endogenous retroviruses in the germline.  This provirus is sweeping through northern koalas, supporting a direct role in adaptive evolution of KoRV-A transcriptional silencing.

overall_design: To investigate the evolution of retroviral repression in the germline, we performed long- and short-read DNA-seq, RNA-seq, and small RNA-seq.

first: Milky

last: Abojorga

first: Birgit

last: Koppetsch

first: Michaela

last: Blyton

first: Keith

last: Chappell

first: Jeremy

last: Luban

first: Zhiping

last: Weng

first: William

last: Theurkauf


title: Single-cell analysis of the epigenome and 3D chromatin architecture in the human retina [bulk_ATAC]


title: Adhesive and injectable hydrogel microspheres for NRF2-mediated periodontal bone regeneration

city: Beijing

first: yu

last: Wang

state: Beijing

address: 22 South Zhongguancun Street, Haidian District

department: Peking University School and Hospital of Stomatology

institute: Peking University

summary: For comparing the molecular profiling of the biological effect of the MMS and MMS-CY microspheres on the PDLSCs, the RNA-seq was performed to identify the gene change.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for PDLSCs that were treated with MMS and MMS-CY

first: Yu

first: Shanshan

last: Jin

first: Yaru

last: Guo

first: Xuliang

last: Deng


title: Adaptive evolution of KoRV-A  retroviral silencing in wild koalas [RNA-seq]


title: The C-terminal of NSD2 regulates transcription of cell adhesion genes in multiple myeloma [GE5289_RNASEQ]

city: Gainesville

first: Jonathan

last: Licht

state: Florida

address: 2033 Mowry Road

department: UF Health Cancer Center

institute: University of Florida

summary: The overexpression of the histone methyltransferase NSD2 (MMSET) in multiple myeloma (MM) patients plays a significant role in the development of this specific subtype of disease. Through the expansion of gene activation associated H3K36me2 and suppression of repressive H3K27me3 marks, NSD2 activates an aberrant set of genes that contribute to myeloma growth adhesive and invasive activities. NSD2 transcriptional activity also depends on its non-catalytic domains, which facilitate its recruitment to chromatin through histone binding. In this study, using NMR and ITC techniques, we demonstrate that the tandem PHD domain of NSD2 (PHDvC5HCHNSD2) acts as a reader for both unmodified histone H3K4 and three-methylated H3K27, making it the first PHD tandem cassette known to decode the methylation status of H3K27. We present a three-dimensional model of the complex based on NMR data and molecular dynamics simulations. Importantly, expression of mutants of PHDvC5HCHNSD2, designed to impair binding to the histone H3 tail in NSD2 deficient cells, leads to decreased activation of adhesive properties and cell adhesion genes and a decrease in corresponding H3K27ac signal at promoters. Moreover, expression of PHDvC5HCH mutant forms of NSD2 result in incomplete loss of H3K27 methylation throughout the genome compared to expression of wild-type NSD2. Collectively, these data indicate that PHDvC5HCH of NSD2 plays an important role in modulating gene expression and chromatin modification, thus opening new opportunities for pharmacological intervention.

overall_design: 1 million TKO cells that expressed either wild type or mutant forms of the histone methyltransferase NSD2 were harvested and Total RNA extracted. RNA-seq was performed to determine how mutant NSD2 may alter gene expression.

first: Charlotte

last: Kaestner

first: Giovanna

last: Musco


title: The transcriptomic and proteomic landscape of feline fibrosarcoma and matched normal tissue

city: Zürich

first: Enni

last: Markkanen

state: State...

address: Winterthurerstr. 260, TFA 00.31

department: Institute of Pharmacology and Toxicology, Vetsuisse Faculty Zurich

country: Switzerland

institute: University of Zurich

summary: Fibrosarcomas (FSA) are rare malignant soft tissue tumors characterized by low chemo- and radiosensitivity. The development of novel treatment strategies for human FSA is hindered by the low incidence of the disease and the absence of suitable clinical models. Interestingly, aggressive FSA occur more frequently in domestic cats, representing a clinically amenable model for assessing novel therapies such as targeted imaging or theranostics. However, a lack of molecular characterization of FSA and adjacent normal tissue (NT) in both species hinders identification of tumor-specific targets and undermines the translational potential of feline FSA. Combining laser-capture microdissection, RNA sequencing and LC-MS/MS, we perform comprehensive profiling of 30 feline FSA and matched skeletal muscle, adipose and connective tissue. Clear inter-tissue differences allow the identification of significantly upregulated and tumor-exclusive features that represent potential targets for diagnostic and therapeutic approaches. While feline FSA are characterized by hyperactive EIF2, TP53 and MYC signaling, immune-related and neuronal pathways emerge as modulators of tumor aggressiveness and immunosuppression. A high degree of molecular similarity with canine and human FSA allows the identification of conserved cross-species tumor targets. Significant enrichment in DNA repair pathways in feline FSA are shown to be associated with aggressive clinical behavior in human STS. Finally, we leverage the molecular profiles to identify vulnerabilities, including sensitivity to ATR and PARP inhibition as potential treatment for feline FSA. In conclusion, this detailed landscape provides a rich resource to identify target candidates and therapeutic vulnerabilities within and across species and supports feline FSA as relevant models for the human disease.

overall_design: RNA sequencing was performed on 30 feline FSA and matched skeletal muscle, adipose and connective tissue.

first: Mikiyo

last: Weber

first: Daniel

last: Fuchs

first: Amiskwia

last: Pöschel

first: Erin

last: Beebe


title: The C-terminal of NSD2 regulates transcription of cell adhesion genes in multiple myeloma

overall_design: 10 million TKO cells that expressed either wild type or mutant forms of the histone methyltransferase NSD2 were harvested and ChIPmentation performed  to measure how mutant NSD2 may alter chromatin marks.


title: The C-terminal of NSD2 regulates transcription of cell adhesion genes in multiple myeloma [NS2733_CHIPSEQ]


title: Proteolethargy is a pathogenic mechanism in chronic disease

city: Cambridge

first: Richard

last: Young

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

summary: The pathogenic mechanisms of many diseases are well understood at the molecular level, but there are prevalent syndromes associated with pathogenic signaling, such as diabetes and chronic inflammation, where our understanding is more limited. Here we report that pathogenic signaling suppresses the mobility of a spectrum of proteins that play essential roles in cellular functions known to be dysregulated in these chronic diseases. The reduced protein mobility, which we call proteolethargy, was linked to cysteine residues in the affected proteins and signaling-related increases in excess reactive oxygen species. Diverse pathogenic stimuli, including hyperglycemia, dyslipidemia and inflammation, produce similar reduced protein mobility phenotypes. We propose that proteolethargy is an overlooked cellular mechanism that may account for various pathogenic features of diverse chronic diseases.

overall_design:
To investigate the role of pathogenic signaling on transcriptional regulation and heterochromatic repression, we treated HepG2 cells with 3 nM insulin (insulin resistant samples) or 0.1 nM insulin (insulin sensitive samples) as a control for 3 days.
We next performed differential gene analysis using data obtained from RNA-seq of 3 replicates each for resistant samples and sensitive samples.

first: Alessandra

last: Dall’Agnese

first: Ming

last: Zheng

first: Shannon

last: Moreno

first: Jesse

last: Platt

first: An

last: Hoang

first: Deepti

last: Kannan

first: Giuseppe

first: Kalon

last: Overholt

first: Hailey

last: Erb

first: Olivia

last: Corradin

first: Arup

last: Chakraborty

first: Tong

middle: I

last: Lee


title: Identification of a Subpopulation of Astrocyte Progenitor Cells in the Neonatal Subventricular Zone: Evidence that Migration is Regulated by Glutamate Signaling

first: Michael

last: Gonzalez

state: Pennsylvania

address: 3535 Market St

department: Translational Medicine and Human Genetics

summary: In adult mice engineered to express enhanced green fluorescent protein (eGFP) under the control of the glutamate transporter 1 (GLT1) gene, eGFP is found in all cortical astrocytes. However, when 8.3 kilobases of the human GLT1/EAAT2 gene is used to control expression of tdTomato (tdT), tdT is only found in a subpopulation of cortical astrocytes.   The eGFP mice have been used to define mechanisms of transcriptional regulation using astrocytes cultured from cortex of 1-3 day old mice. Using the same cultures, we were never able to induce tdT+ expression.  We hypothesized that these cells might not have migrated into the cortex by this age.   In this study, we characterized the ontogeny of tdT+ cells, performed single-cell RNA sequencing (scRNA-seq), and tracked their migration in organotypic slice cultures.  At postnatal day (PND) 1, tdT+ cells were observed in the subventricular zone and striatum but not in the cortex, and they did not express eGFP.  At PND7, tdT+ cells began to appear in the cortex with their numbers increasing with age.  At PND1, scRNA-seq demonstrates that the tdT+ cells are molecularly heterogeneous, with a subpopulation expressing astrocytic markers, subsequently validated with immunofluorescence. In organotypic slices, tdT+ cells migrate into the cortex and express GLT1, NF1A, and eGFP after 7 days.  Ionotropic glutamate receptor (iGluR) antagonists reduced (25 to 50%) the distance tdT+ cells migrate from the subventricular zone into cortex.  The pan-glutamate transport inhibitor, TFB-TBOA, dramatically increased (10-fold) the number of tdT+ cells in the cortex.  In conclusion, although tdT is expressed by non-glial cells at PND1, it is also expressed by glial progenitors that migrate into the cortex postnatally.    With this fluorescent labelling, we provide novel evidence that glutamate signaling contributes to the control of glia precursor migration.

overall_design: The dorsal anterior forebrain of three postnatal day 1 double reporter (BAC-GLT1-eGFP/8.3kb-EAAT2-tdTomato) mice were dissected and dissociated into a single cell suspension using enzymatic and mechanical dissociation. eGFP+ or tdT+ cells were isolated using FACS. Next-generation sequencing libraries were prepared using the 10x Genomics Chromium Single Cell 3’ Reagent kit v3. Libraries were uniquely indexed using the Chromium i7 Sample Index Kit. After preparing a library and performing quality control on a High Sensitivity D1000 ScreenTape station, 17,596 tdT+ and 16,956 eGFP+ cells were loaded and sequenced on an Illumina NovaSeq sequencer in a paired-end, single indexing run. Data were then processed using the cellranger pipeline (10x genomics, v6.0.0) for demultiplexing and alignment of sequencing reads to the mm10 transcriptome, with the tdT (GenBank Accession #AY678269.1) and eGFP (GenBank Accession #MK387175.1) transcripts added to produce the feature-barcode matrices. A pool of three mice was use, with no replicates.

first: Zila

last: Martinez-Lozada

first: Alain

last: Guillem

first: Isabella

last: Song

first: Hajime

last: Takano

first: Esha

last: Parikh

first: Jeffrey

last: Rothstein

first: Mary

last: Putt

middle: B

last: Robinson


title: Systemic determination of PRDM16 regulatory genes in the aorta

city: Ann Anrbor

first: Zhenguo

last: Wang

address: 2800 Plymouth Road

department: Internal Medicine

summary: We determined the differentially expressed genes in the thoracic aorta (TA) from vascular smooth muscle cell (VSMC)-specific Prdm16 knockout (Prdm16SMKO) and control mice by RNA-sequencing (RNA-seq) analysis. We also performed chromatin immunoprecipitation (ChIP)-sequencing (ChIP-seq) analysis to identify potential target genes of PRDM16. By overlapping the RNA-seq and ChIP-seq dataset, we are able to identify the target genes of PRDM16 in the aorta and investigate the roles of PRDM16 in the vascular biology.

overall_design: The thoracic aorta from Prdm16SMKO and control mice were harvested and subjected to RNA-seq analysis. The differentially expressed genes between Prdm16SMKO and control mice were analyzed. For ChIP-seq analysis, mouse fibroblast cells were infected with lentivirus carrying flag-tagged PRDM16 or vector (as control) for 48 hours and were selected with 2 ug/mL puromycin for 1 week, followed by ChIP using anti-flag antibody. The purified DNA was subjected to ChIP-seq.

first: Lin

last: Chang

first: Y

last: Chen


title: Single-cell RNA sequencing in mouse model of hyperuricemia treated by Tigulixostat

city: Changzhou

first: Chao

last: Tu

state: Jiangsu

address: 185 Juqian Road

department: Department of Internal Medicine

institute: The Third Affiliated Hospital of Soochow University

summary: We treated Uox-KO hyperuricemia mouse model with Tigulixostat and investigated the gene expression changes in liver and kidney tissues by single-cell transcriptomics

overall_design: Male urate oxidase knockout(Uox-KO) mice and male wild-type mice were purchased from GemPharmatech (Nanjing, China). The corporation knocked out exons 2-4 of the mouse Uox gene on the C57BL/6J background to obtain the Uox-KO model. This model is an ideal animal model for screening and evaluating drugs for treating hyperuricemia due to the accumulation of uric acid in mice. We found that Tigulixostat reduced blood uric acid levels and improved kidney function more effectively than allopurinol. We applied single-cell transcriptomics to investigate the changes of gene expression in liver and kidney of hyperuricemia mice treated with Tigulixostat

first: CHAO

last: TU

first: LINA

last: XUE

first: QIANRU

last: TAO

first: HAINING

last: CHANG


title: Whole Genome and Epigenome Nasopharyngeal Cancer Sequencing

city: Jakarta

first: Handoko

last: Handoko

address: Jl. Salemba Raya

country: Indonesia

institute: Faculty of Medicine, Universitas Indonesia

type: Methylation profiling by high throughput sequencing

summary: This is the whole genome and epigenome nasopharyngeal cancer sequencing from clinical nasopharyngeal biopsy. The methylation information is derived from nanopore sequencing in its native form. The 5mC information per position is extracted and presented here as a bedgraph file.

overall_design: The specimens were extracted DNA from fresh frozen tissue nasopharyngeal cancer biopsy. The sequencing using Promethion Nanopore flow cell with kit 14 chemistry and LSK114 protocol.

first: Adham

last: Marlinda

first: Gondhowiardjo

last: Soehartati


title: Limitations in mitochondrial programming restrain the maturation of human stem cell-derived β cells

city: Ann Arbor

first: Anne

last: Lietzke

address: 1000 Wall Street

summary: Pluripotent stem cell-derived (SC) islets offer a renewable source for β cell replacement for type 1 diabetes, yet functional and metabolic immaturity may limit their long-term therapeutic efficacy. Here, we describe that limitations in mitochondrial transcriptional programming prevent the maturation of SC-β cells. We observe several alterations in SC-islet mitochondria compared to human islets, including reductions in mitochondrial respiration, expression of OXPHOS machinery, and mitochondrial lipid metabolism. Surprisingly, these effects were not related to reductions in mitochondrial mass, genome integrity, or structure. Transcriptomic profiling throughout differentiation to SC-islets revealed several unstudied candidates in β cell maturation that regulate programming of mitochondrial oxidative and fatty acid metabolism, including the nuclear receptors PPAR⍺ and PPARγ.  Indeed, treatment of SC-islets with WY14643, a potent PPAR⍺ agonist with PPARγ activity, promoted expression of mitochondrial targets, improved insulin secretion, and increased the presence of β cells both in vitro and upon transplantation into immunodeficient mice. Mitochondria are vital to fuel β cell insulin release; however, our studies here revealed the potential for targeting mitochondrial programming to enhance the differentiation and metabolic maturation of SC-β cells.

overall_design: HUES8 and H1 cell lines were differentiated to SC-islets in a 6 stage differentiation protocol (Hogrebe et al. 2021, PMID: 34349281). Total RNA was isolated from each stage (n=3-6 per stage). Primary human islets were received and cultured per protocol (Prodo Labs). Total RNA was isolated from 6 human islet donors. Additionally, H1 Stage 6 cells were treated for 7 days starting at stage 6 day 3 with vehicle or WY14643. Total RNA was isolated from both conditions (n=4 per condition).

middle: C

first: Jessica

last: King

first: Kelly

last: Crumley

first: Elizabeth

last: Bealer

first: Ava

last: Stendahl

first: Jie

last: Zhu

first: Gemma

last: Pearson

first: Elena

last: Levi-D'Ancona

first: Belle

last: Henry-Kanarek

first: Emma

last: Reck

first: Manikanta

last: Arnipalli

first: Vaibhav

last: Sidarala

first: Emily

last: Walker

first: Subramaniam

last: Pennathur

first: Lonnie

middle: D

last: Shea

first: Scott

last: Soleimanpour


title: Single cell RNAseq for P1 mouse Cardiomyocytes with and without cell cycle stimulation

city: Houston

first: Tamer

last: Mohamed

state: TX

address: 6770 Bertner Avenue

institute: Baylor College of Medicine

summary: neonatal mouse cardiomyocytes at P1 have spontanouse proliferation capacity, to understand the single cell variability between the spontanously proliferating and non proliferating cardiomyocytes we conducted Single cell RNAseq on P1 mouse Cardiomyocytes with and without cell cycle stimulation

overall_design: P1 cardiomyocytes were isolated from P1 mice and infected with LacZ or 4F (CDK1, CDK4, CCNB, CCND) adenoviruses

first: Riham

last: Abouleisa

first: AbouBAkr

last: Salama


title: Immune infiltration characteristic of colorectal cancer with high and low immune score.

city: beijing

first: Guanglong

last: Dong

state: None Selected

address: fuxin road

institute: Department of General Surgery, The First Medical Center, Chinese PLA General Hospital

summary: colorectal cancer (CRC) specimens were collected from 45 CRC patients receiving surgical resection. Total RNA was extracted from CRC tissues using TRIzol Reagent following the manufacturer’s instructions. The expression profiles were determined using the NovaSeqXplus sequencer (Illumina, San Diego, CA, USA). The immune score was calculated using predictive model based on the expression profiles and the patients were divided into high-score and low-score group. The proportion of MSI patients were compared between the high- and low-score groups.

overall_design: 45 colorectal cancer samples from patients (12 MSI and 33 MSS) who had undergone surgical resection were studied.


title: Death and Survival of Gut CD4 T cells Following HIV-1 Infection Ex Vivo

city: Aurora

first: Kejun

last: Guo

state: Colorado

department: Division of Infectious Diseases

institute: University of Colorado Anschutz Medical Campus

summary: CD4 T cells isolated from human Lamina Propria Aggregate Culture (LPMC) were treated with E coli lysate and single-cell RNASeq was used to determine the cellular response in CD4 T cell in general as well as the in different CD4 T cell subset, especially from CD4-CTL cells.

overall_design: CD4 T cells were negatively selected from LPMC and subsequently treated with E. coli lysate.  Cells were then analyzed using scRNASeq.

first: Kaylee

last: Mickens

first: Stephanie

last: Dillon

first: Ashley

last: Thompson

first: Bradley

middle: S

last: Barrett

first: Cheyret

last: Wood

first: Katerina

last: Kechris

first: Mario

last: Santiago

first: Cara

last: Wilson


title: Epigenetic changes cause aberrantly high expression of SOX11 leading to systemic sclerosis

city: Saga

first: Yasuhiro

last: Nanri

address: 5-1-1 Nabeshima

department: Department of Biomolecular Sciences

country: Japan

institute: Saga Medical School

summary: Systemic sclerosis (SSc) is a chronic, heterogenous multisystem connective tissue disease characterized by vascular injury, autoimmunity, and organ fibrosis. Epigenetic modification is thought to be important in the onset and progression of SSc. SOX (SRY-related HMG box) 11 is a transcription factor playing several important roles in organ development in embryos. We have previously shown that dermal fibroblasts derived from SSc patients showed constitutive, high expression of SOX11 and a positive loop formed by SOX11 and periostin in fibroblasts upregulates the TGF- signals, leading to skin fibrosis. However, the mechanism of the aberrant high expression of SOX11 remain unknown in the pathogenesis of SSc. In this study, we found that SOX11 high expression is associated with presence of activating histone marks (H3K27Ac) in SSc dermal fibroblasts. In contrast, normal fibroblasts express low level of SOX11 associated with silencing histone marks H3K27me3. Moreover, using the miRNA microarray method, we identified some miRNAs downregulated in SSc dermal fibroblasts and target SOX11 and overexpression of these miRNAs significantly repressed the expression of SOX11 in SSc dermal fibroblasts. Our findings, taken together, show that epigenetic activation of SOX11 in systemic sclerosis fibroblasts upregulates the SOX11 expression, leading to skin fibrosis.

overall_design: We searched miRNAs differently expressed in normal and SSc dermal fibroblasts using microarray analysis and selected downregulated miRNAs in SSc dermal fibroblasts because miRNAs targeting the SOX11 gene are expected to downregulate its expression.

first: Kenji

last: Izuhara


title: Castleman disease human lymph node tissue

city: Philadelphia

first: David

last: Fajgenbaum

address: 3535 Market St.

department: Department of Medicine

institute: University of Pennsylvania

summary: Castleman disease (CD) is a rare hematologic disorder involving inflamed lymph nodes and distinct histological features. Unicentric Castleman disease (UCD) and idiopathic multicentric Castleman disease (iMCD) are of particular interest as their etiologies are poorly understood and treatment options are limited. As iMCD patients, and occasionally UCD patients, also present with a cytokine storm, we sought to investigate if the cytokine release from iMCD and UCD subtypes have pathogenic origins as observed in human herpesvirus 8 MCD (HHV-8-MCD). To identify potential active viruses that may be contributing to immune system dysregulation in Castleman Disease tissues we conducted bulk RNA sequencing on FFPE preserved lymph node tissue from patients with various phenotypes including Idiopathic multicentric Castleman disease (n = 9), systemic lupus erythematosus (n =3), diffuse large B cell lymphoma (n =5), and reactive lymph nodes with inconclusive pathology (n = 7).

overall_design: 24 whole transcriptomic RNA libraries with paired gene expression were used on FFPE preserved lymph node tissue from phenotypes including Castleman disease, systemic lupus erythematosus, diffuse large B cell lymphoma, and lymph nodes with inconsistent pathology

first: Michael

last: Gonzalez

first: Ira

last: Miller


title: High-Resolution Molecular Profiling of Epileptic Brain Activity via Explanted Depth Electrodes [RNA-seq]

city: Odense M

first: Vijay

last: Tiwari

state: Denmark

address: Campusvej 55

department: Institut for Molekylær Medicin (IMM)

institute: Queen’s University Belfast

summary: Understanding neurological disorders necessitates systems-level approaches that integrate multimodal data, but progress has been hindered by limited sample availability, and the absence of combined electrophysiological and molecular data from live patients. Here, we demonstrate that stereo electroencephalography (sEEG)—stereologically-implanted electrodes routinely used for monitoring epilepsy—enables the integration of RNA sequencing and epigenome maps with in vivo recordings and brain imaging. Here we report a method MoPEDE (Molecular Profiling of Epileptic Brain Activity via Explanted Depth Electrodes) that enables this by recovering extensive protein-coding transcripts and DNA methylation profiles from explanted depth electrodes containing matched electrophysical and radiological data, hence allowing for high-resolution reconstructions of brain structure and function in patients. Our proof-of-concept study shows that epilepsies of different etiologies have distinct molecular landscapes and identifies transcripts correlating with neurophysiological signals, including immediate early genes, inflammation markers, and axon guidance molecules. Additionally, we identify DNA methylation profiles indicative of transcriptionally permissive or restrictive chromatin states. While gene expression gradients corresponded with the assigned epileptogenicity index, we found outlier molecular fingerprints in some electrodes, potentially indicating seizure spread or generation zones not detected during clinical assessments. These findings validate that RNA profiles and genome-wide epigenetic data from explanted sEEGs offer high-resolution surrogate molecular landscapes of brain activity. This revolutionary approach has the potential to enhance diagnostic decisions and deepen our understanding of epileptogenic processes.

overall_design: All participants underwent robot-assisted stereo-EEG monitoring in the Epilepsy Monitoring Unit in Beaumont Hospital Dublin, Ireland. Depth electrodes with either twelve, fifteen, or eighteen contacts (DIXI Medical, France) were implanted according to the pre-operative hypothesis of the seizure-onset zone. Continuous EEG was recorded at 1024Hz with concurrent video recording (Xltek EEG System, Natus Inc.). Two experienced clinical neurophysiologists/epileptologists performed visual analysis of seizures and classified each cortical region as part of the SOZ, PZ, or NIZ.

first: Anuj

last: Dwivedi


title: Distinct circulating monocytes up-regulate CD52 and sustain innate immune function in patients with cirrhosis unless acute decompensation emerges

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

institute: University of Basel

summary: Background & Aims: Infectious complications determine the prognosis of cirrhosis patients. Their infection susceptibility relates to the development of immuneparesis, a complex interplay of different immunosuppressive cells and soluble factors. Mechanisms underlying the dynamics of immuneparesis of innate immunity remain inconclusive. We aimed to dissect the heterogeneity of circulating monocyte states in different cirrhosis stages, and pursued the function of selected differentially expressed (DE) genes. Methods: We systematically investigated circulating monocytes in health, compensated and not-acutely decompensated (NAD) cirrhosis using single cell RNA sequencing. Selective genes were confirmed by flow cytometry and diverse functional assays on monocytes ex vivo. Results: We identified seven monocyte clusters. Their abundances varied between cirrhosis stages, confirming previously reported changes i.e. reduction in CD14lowCD16++ and emergence of M-MDSC in advanced stages. DE genes between health and disease and among stages were detected, including for the first time CD52. CD52-expression on monocytes significantly enhanced throughout compensated and NAD cirrhosis. Heretofore the biological significance of CD52-expression on mon enhanced migratory potential, increased cytokine production, but poor T cell activation. Following acute decompensation (AD), CD52 was cleaved by elevated phospholipase C (PLC), and soluble CD52 (sCD52) was detected in the circulation. Inhibition and cleavage of CD52 significantly suppressed monocyte functions ex vivo and in vitro, and the predominance of immunosuppressive CD52low circulating monocytes in patients with AD was associated with infection and low transplant-free survival. Conclusion: CD52 may represent a biologically relevant target for future immunotherapy. Stabilising CD52 may enhance monocyte functions and infection control in the context of cirrhosis, guided by sCD52/PLC as biomarkers indicating immuneparesis.ocytes remained unknown. CD52highCD14+CD16highHLA-DRhigh monocytes in patients with cirrhosis revealed a functional phenotype of active phagocytes with enhanced migratory potential, increased cytokine production, but poor T cell activation. Following acute decompensation (AD), CD52 was cleaved by elevated phospholipase C (PLC), and soluble CD52 (sCD52) was detected in the circulation. Inhibition and cleavage of CD52 significantly suppressed monocyte functions ex vivo and in vitro, and the predominance of immunosuppressive CD52low circulating monocytes in patients with AD was associated with infection and low transplant-free survival. Conclusion: CD52 may represent a biologically relevant target for future immunotherapy. Stabilising CD52 may enhance monocyte functions and infection control in the context of cirrhosis, guided by sCD52/PLC as biomarkers indicating immuneparesis.

overall_design:
Enriched monocytes isolated by MACS were stained for viability and monocyte markers and sorted using BD FACSMelodyTM Cell sorter. 20.000 monocytes were isolated per sample and processed for scRNA-Seq and after quality control 4000 cells per sample were taken into the analysis.

***************************************************************
Due to patient privacy concerns, the raw sequencing data for this scRNA-seq dataset cannot be released publicly.
***************************************************************

first: Anne

last: Geng

first: Julien

last: Roux

first: Christine

last: Bernsmeier


title: mTOR pathway modulation improves hypercapnia-induced satellite cell autophagy arrest and dysfunctional myogenesis.

city: Albany

first: Ramon

last: Bossardi Ramos

state: Ny

address: 43 New Scotland Avenue

department: Department of Molecular and Cellular Physiology

institute: Albany Medical College

summary: Chronic CO2 retention, or hypercapnia, occurs in pulmonary diseases and leads to skeletal muscle wasting. Muscle wasting and hypercapnia are independently associated with substantial mortality. While abnormal skeletal muscle stem -satellite- cells, contribute to impaired myogenesis in pulmonary diseases, no mechanistic data exists on hypercapnia-driven dysfunctional satellite cells and myogenesis in-vivo. Autophagy regulates satellite cell activation and myogenesis, and while elevated CO2 inhibits autophagy in inflammatory cells, it has never been evaluated in the context of hypercapnia-driven abnormal myogenesis. Using lineage tracing in pre- and post-stem cell transplantation experiments, we show that hypercapnia undermines both Pax7- and α-7 integrin-expressing satellite cells activation, replication and myogenesis. Satellite cells’ multi-omic analyses indicate that hypercapnia disrupts multiple pathways regulated by autophagy. Moreover, autophagy-specific LC3 fluorescence-reporting mouse and cellular data demonstrate that hypercapnia reduces expressions of AMPK and Ulk1, which critically participate in autophagosome formation, and has no effect on the antagonistic mTOR pathway including Ulk1 serine-757 phosphorylation. Moreover, Atg7 knockout-driven loss of autophagy function phenocopies the effects on hypercapnia. After rapamycin administration, the hypercapnia-induced myogenic deficit is corrected by a sharp AMPK activation leading to the autophagy-stimulatory Ulk1 phosphorylation at serine-555, autophagy acceleration, increased satellite cells replication and improved myogenesis post-satellite cells transplantation.

overall_design: Pax7-GFP reporter mice were flow sorted and collected for scRNA-Sequencing. They were immediately fixed and sequenced following 10X genomics fixed cell sequencing protocols (PN-1000414).

first: Joseph

last: Balnis

first: Adolfo

last: Jaitovich


title: Spatiotemporal Landscape in Kidney of A Mouse Model of Hyperuricemia at Single-Cell Level [single-cell sequencing]

first: Chao

last: Tu

summary: Our team utilized single-cell RNA sequencing and spatial multi-omics to explore the spatial landscape of kidney in mice with hyperuricemia at single-cell level

overall_design: Male urate oxidase knockout (Uox-KO) mice and male wild-type mice were purchased from GemPharmatech (Nanjing, China). The corporation knocked out exons 2-4 of the mouse Uox gene on the C57BL/6J background to obtain the Uox-KO model. This model is an ideal animal model for screening and evaluating drugs for treating hyperuricemia due to the accumulation of uric acid in mice. our team figured the spatiotemporal atlas of hyperuricemic nephropathy by applying single-cell RNA sequencing, spatial transcriptomics, spatial proteomics and spatial metabolomics in the Uox-KO mouse model.

first: CHAO

last: TU

first: SHUHONG

last: GUAN

first: QIANRU

last: TAO

first: XIAOZHOU

last: HE


title: T-47D Giredestrant + palbociclib combination TraCe-seq (NGS4327)

city: South San Francisco

first: Marc

last: Hafner

address: Building 45-1, 1 DNA Way

department: Oncology Bioinformatics

institute: Genentech

summary: Barcoded clones of T-47D cells were treated with either giredestrant, palbociclib, or their combination for different duration. Barcodes and transcriptional profiles was measured by scRNA-seq.

overall_design: T-47D cell lines were barcoded with TraCe-seq barcoding libraries and expanded in culture to establish the starting TraCe-seq cell populations. A fraction of the starting populations were profiled by single cell RNA-sequencing (scRNA-seq) to capture the relative clonal abundance and transcriptional profile of each barcoded clones right before drug treatment. In parallel, the rest of the cells were treated with giredestrant or palbociclib alone or in combination  until resistant clones emerged. We conducted scRNA-seq profiling to capture acute responses to the treatment at 1, 4, 8, and 26 days post treatment as well as after 6 months for the combination treamtent to capture adaptive changes. These time points were chosen to allow us capture the differential transcriptional responses in the resistant versus sensitive clones, and compare the responses to the different treatments at individual clone and single cell level.

first: Xin

last: Ye

first: Nathan

last: Maulding

first: Michal

last: Kabza


title: Exosomal subgroups isolated from MSCs by tangential flow filtration combined with size exclusion chromatography reals distinct molecular properties and functions

city: Nanjing

first: Jing

last: Li

address: No.101 Longmian Avenue, Jiangning District

department: State Key Laboratory of Reproductive Medicine

institute: Nanjing Medical University

summary: Here, by using TFF-SEC system to separate exosomal subgroups, our study provides an industrial-scale method for the scalable production of MSC exosomes with specific functions. The two exosome subgroups, S1-Exos and S2-Exos, differ in their biogenesis, characterization, and content of cargos, resulting in variations in their biological functions. Although stem cells have been widely used in clinical research and therapy, ineffectiveness or lack of stability still exists (26140604, 26908143). In spite of the well-known advantages of MSCs-Exos in clinical applications, our research introduces a new concept that involves leveraging distinct subpopulations of MSC exosomes for targeted therapeutic interventions in specific diseases.

overall_design: Two exosomal subgroups were isolated from MSCs by tangential flow filtration combined with size exclusion chromatography, named S1-Exos and S2-Exos, respectively.

first: Wei

last: Liu

first: Xinyu

last: Wang

first: Yating

last: Chen

first: Jiapei

last: Yuan


title: The small protein YjiS acts as a virulence suppressor in Salmonella Typhimurium

city: Würzburg

first: Alexander

last: Westermann

address: Josef-Schneider Straße 2

institute: HIRI

summary: Bacterial small proteins impact diverse physiological processes, however, technical challenges posed by small size hampered their systematic identification and biochemical characterization. In our quest to uncover small proteins relevant for Salmonella pathogenicity, we previously identified YjiS, a 54 amino acid protein, which is strongly induced during this pathogen’s intracellular infection stage and exhibits features of a virulence suppressor. Here, we set out to further characterize the virulence-related role of YjiS. Cell culture infection assays with Salmonella mutants lacking or overexpressing YjiS corroborated previous functional genomics data and additionally suggested this small protein to counteract bacterial escape from macrophages. Mutant scanning of the protein’s conserved, arginine-rich DUF1127 domain excluded a major effect of single amino acid substitutions on the infection phenotype. A comparative dual RNA-seq assay uncovered the molecular footprint of YjiS in the macrophage response to infection, with effects related to oxidative stress and endo-/exocytosis. Bacterial cell fractionation experiments demonstrated YjiS to associate with the inner membrane, without being itself membrane-inserted. Accordingly, proteins interacting with YjiS in pull-down experiments were enriched for inner membrane processes. Together, our study points to a role for Salmonella YjiS as a membrane-associated suppressor of pathogen dissemination.

sample_organism:
Mus musculus
Salmonella enterica

platform_organism:
Mus musculus
Salmonella enterica

overall_design: Dual RNA-sequencing of mouse macrophages and Salmonella strains infecting them, at different time points.

first: Elisa

last: Venturini

middle: J

first: Jörg

last: Vogel

first: Thorsten

last: Bischler


title: Spatiotemporal and genetic cell lineage tracing of endodermal organogenesis at single-cell resolution

city: Beijing

first: Cheng-ran

last: Xu

address: NO.5 YIHEYUAN ROAD HAIDIAN DISTRICT, BEIJING, P.R.CHINA

department: School of Basic Medical Sciences

institute: Peking University

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

overall_design: Refer to individual Series


title: PerR functions as a redox-sensing transcription factor regulating metal homeostasis in the thermoacidophilic archaeon Saccharolobus islandicus REY15A

city: Qingdao

first: Qihong

last: Huang

state: Shandong

address: 72 Binhaidadao, Aoshanwei, Jimo

institute: Shandong University


title: High-Resolution Molecular Profiling of Epileptic Brain Activity via Explanted Depth Electrodes [Methylation]

first: Vijay

last: Tiwari

first: Anuj

last: Dwivedi


title: RNA-seq of colorectal cancer cell line HCT116 and DLD-1 cells treated with PRIMA-1met or oxaliplatin or combination therapy

city: singapore

first: yi

last: chai

department: CSI

country: Singapore

institute: National University of SIngapore

overall_design: HCT116 (p53-wt) and DLD-1 (p53-mutant) cells were treated with either DMSO or PRIMA-1met (45 µM for HCT116; 20 µM for DLD-1) or oxaliplatin (6 µM for HCT116; 35 µM for DLD-1) or combination of these two drugs for 48 hours. Each treatment was performed in triplicates.

first: Jianbiao

last: Zhou


title: Ash1l loss-of-function results in structural birth defects and altered cortical development [scRNA-seq]

first: Stephanie

last: Bielas

state: Michigan

address: 3703 Med Sci II

institute: University of Michigan

summary: The histone methyltransferase ASH1L is a critical developmental regulator of gene expression for many organ systems, but its role in brain development has not been deeply investigated. Over 130 autistic individuals have heterozygous loss-of-function ASH1L variants, and population studies confirm it is a high-risk autism gene. Several studies report autism-like behaviours in Ash1l deficient mice and characterised aspects of the underlying neuropathophysiology. We used mice with a cre-inducible deletion of Ash1l exon 4, which results in a frame shift and premature stop codon (p.V1693Afs*2). We assessed the impact of Ash1l loss-of-function on survival and craniofacial skeletal development. We used a tamoxifen-inducible cre strain to knockout Ash1l early in cortical development (Emx1cre-ERT2; e10.5). We used immunohistochemistry to assess cortical lamination, and IdU and EdU incorporation to birthdate cortical neurons. We utilised single cell RNA sequencing to compare cortical cell populations and identify differentially expressed genes. The proportion of homozygous Ash1l germline knockout embryos was normal at e18.5, however no live Ash1l null pups were present at birth (e18.5: n = 77, P = 0.90; p0: Ash1l+/+ n = 41, P = 0.00095). Ash1l-/- had shortened nasal bones at e18.5 (n = 31, P = 0.017). In the cortical-specific knockout, SATB2 neurons were increased and distributed through the cortical plate (n = 6/genotype, P = 0.0001). There were no differences in neuronal birthdating (n = 4-6/genotype, P = 0.40 for e14.5 and P = 0.057 for e15.5). Single cell RNA sequencing revealed numerous differences in gene expression that were sufficient to cluster control and mutant upper layer neurons separately. Pseudotime analysis revealed that the mutant cluster is on an altered cell differentiation trajectory. This study shows that Ash1l is a necessary gene for postnatal survival and normal craniofacial development. In the cortex, it has broad effects on gene expression and is necessary for normal upper layer neuronal cell fate. These findings suggest a basis for altered brain function in individuals with ASH1L variants.

overall_design: Male Emx1CreERT2;Ash1lfl/fl mouse was crossed with female Ash1lfl/fl mouse for timed pregnancy. At e10.5, the female mouse was injected with 100mg/kg tamoxifen. At e18.5, embryos were extracted and cortical tissue was dissected for scRNA-seq. The litter consisted of four mutant Emx1CreERT2; Ash1lfl/fl and three control Ash1lfl/fl, all used in subsequent analysis.

first: Kevin

middle: P

last: Toolan

first: Brian

last: McGrath

first: Michelle

last: Brinkmeier

first: Sally

middle: A

last: Camper


title: Methylation profiling by array for Dementia with Lewy Bodies using brain tissue

city: Royal Oak

first: Stewart

middle: F

last: Graham

address: 3811 West 13 Mile Road, Suite 415

department: OBGYN

institute: Corewell Health - Research Institute

type: Methylation profiling by genome tiling array

summary:
Synucleinopathies encompass Parkinsons disease (PD), dementia with Lewy bodies (DLB), and Parkinsons disease dementia (PDD) and are recognized for presenting a range of cognitive, neuropsychiatric, sleep-related, motor, and autonomic symptoms. DLB manifests with early-onset dementia when Lewy bodies develop in the brainstem and cerebral cortex. We profiled the DNA methylation using the post-mortem brain tissue from the parietal cortex, specifically Brodmann area 7 and compared them with age-, and sex-matched controls. Through the integration of multi-omics approaches, we anticipate the identification of notable alterations in these well-defined samples. Additionally, our objective is to study the biochemical perturbations in the brain tissue of those individuals who died with DLB.
Differentially Methylated Cytosines (DMCs) and metabolites were identified, followed by pathway enrichment analysis. Correlations between methylation changes and metabolite levels were explored. Methylation profiling revealed 3,478 significant DMCs, predominantly hypermethylated, enriched in CpG islands and gene regions related to transcription start sites. Pathway analysis identified 612 significant pathways, with notable involvement in olfactory and synaptic functions. Metabolomics profiling identified 15 significantly differentially abundant metabolites. The top perturbed pathway was Phosphatidylethanolamine (PE) Biosynthesis. Further, key correlations were found between significant DMCs and metabolites, particularly in the Phosphatidylethanolamine Biosynthesis pathway involving genes PTDSS1 and PCYT2. Further, ignsificant sex-specific epigenetic and metabolomic changes were also observed. This comprehensive analysis of DNA methylation and metabolomics in DLB highlights significant biomarkers and pathways, offering insights into disease mechanisms and potential therapeutic targets.

overall_design: We acquired post-mortem brain tissue from the parietal cortex, specifically Brodmann area 7 from the Brain for Dementia Research (BDR) Initiative at the Institute of Clinical Neurosciences, School of Clinical Sciences, University of Bristol, Bristol, UK. The assessment of DLB post-mortem brains relied on available archival information and neuropathology reports, albeit limited. Control brains were selected from individuals without a clinical history of dementia, minimal neuritic plaques, a Braak tangle stage of III or lower, and no other notable neuropathological abnormalities.  For DNA methylation profiling, we analyzed 15 confirmed cases of DLB and 16 healthy, aged controls, ensuring a match in sex and age within the groups. The samples were processed using Infinium MethylationEPIC Array following the manufacturers instructions (Illumina Infinium HD Methylation Assay Experienced User Card, Automated Protocol 15019521 v01).

first: Sangeetha

last: Vishweswaraiah


title: Cell restriction factors, and not receptor compatibility, block Jamaican fruit bat (Artibeus jamaicensis) susceptibility to mucosal inoculation with SARS-CoV-2 Delta variant.

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

summary: The ancestral sarbecovirus giving rise to SARS-CoV-2 is posited to have originated in bats. While SARS-CoV-2 causes asymptomatic to severe respiratory disease in humans, little is known about the biology, virus tropism, and immunity of SARS-CoV-2-like sarbecoviruses in bats. SARS-CoV-2 has been shown to infect multiple mammalian species, including various rodent species, non-human primates, and Egyptian fruit bats. Here, we investigate the Jamaican fruit bat (Artibeus jamaicensis) as a possible model species to study reservoir responses. SARS-CoV-2 can utilize Jamaican fruit bat ACE2 spike for entry in vitro. However, we find that SARS-CoV-2 Delta does not efficiently replicate in Jamaican fruit bats in vivo. We observe infectious virus in the lungs of only one animal on day 1 post inoculation and find no evidence for shedding or seroconversion. This is possibly due to host factors restricting virus egress after aborted replication. Furthermore, we observe no significant immune gene expression changes in the respiratory tract but do observe changes in the intestinal metabolome after inoculation. This suggests that, despite its broad host-range, SARS-CoV-2 is unable to infect all bat species and Jamaican fruit bats are not an appropriate model to study SARS-CoV-2 reservoir infection.

overall_design: gene expression profiling of various bat tissue types at two time points either mock infected or infected

first: Julia

middle: R

last: Port

first: Jade

last: Riopelle

first: Sarah

last: van Tol

first: Arthur

last: Wickenhagen

first: Eric

last: Bohrnsen

first: Daniel

middle: E

first: Rebecca

last: Rosenke

first: Jamie

last: Lovaglio

first: Justin

last: Lack

last: Anzick

first: Kathleen

last: Cordova

first: Kwe

last: Yinda

first: Patrick

middle: W

last: Hanley

first: Tony

last: Schountz

first: Lon

middle: V

last: Kendall

first: Carl

last: Shaia

first: Greg

last: Saturday

first: Craig

last: Martens

first: Benjamin

last: Schwarz

first: Vincent

last: Munster


title: Identification of the targets of the oxidative response repressor SisPerR in Saccharolobus islandicus REY15A

first: Qihong

last: Huang

summary: In our current study, SisPerR was revealed as  a transcriptional repressor in response to oxidative stress in Saccharolobus islandicus REY15A. Deletion of sisperR abolishes the oxidative stress-induced expression of a large number of genes. To identify the target genes directly bound by SisPerR in vivo, chromatin immunoprecipitation-sequencing (ChIP-seq) was performed.

overall_design: Chromatin immunoprecipitation-sequencing (ChIP-seq) for SisPerR was performed using anti-SisPerR antibody in Saccharolobus islandicus REY15A.

first: Xuemei

last: Zhang

first: Ruining

last: Bai

first: Yulong

last: Shen


title: Extended culture of 2D gastruloids to model human mesoderm development

city: Ann Arbor

first: Michigan

middle: CDB

last: Bioinformatics

state: MI

address: 109 Zina Pitcher Pl

department: Cell & Developmental Biology

summary: Micropatterned human pluripotent stem cells (hPSCs) treated with BMP4, known as a 2D gastruloid, are among the most widely used stem cell models for human gastrulation. Due to its simplicity and reproducibility, this system is ideal for high throughput quantitative studies of tissue patterning and has led to many insights into the mechanisms of mammalian gastrulation. However, 2D gastruloids have only been studied up to 48h. Here we extended this system to 96h.

overall_design: Micropatterned human pluripotent stem cells (hPSCs) were collected at 48, 72, 96 hours after treatment with BMP4 for single cell RNA sequencing with 10X Genomics Chromium Controller.

first: Bohan

last: Chen

first: Idse

last: Heemskerk

last: Johnson


title: Accurate Identification of Sites of Origin in Carcinoma of Unknown Primary (CUP) Tumors Using DNA Methylation II

city: Chicago

first: Drew

last: Duckett

state: IL

address: 541 N Fairbanks Ct, 8th Floor

department: Pathology

institute: Northwestern Medicine

summary: 53 tumors used in the clinical training and validation of a CUP machine learning classifier using methylation profiling

overall_design: methylation by array

first: Erica

last: Vormittag-Nocito

first: Pouya

last: Jamshidi

first: Madina

last: Sukhanova

first: Stephanie

last: Parker

first: Daniel

last: Brat

first: Lawrence

last: Jennings

first: Lucas

last: Santana-Santos


title: Accurate Identification of Sites of Origin in Carcinoma of Unknown Primary (CUP) Tumors Using DNA Methylation


title: Effect of deletion or overexpression of SisPerR on gene expression of Saccharolobus islandicus REY15A in the presence of H2O2

summary: Sensing of ROS is essential for cellular response to oxidative stress. While oxidative stress response in bacteria and eukaryotes has been extensively studied, less is known about the mechanism in archaea. In this study, we demonstrate that deletion of sisperR, a gene encoding the PerR of the model hyperthermophilic archaeon Saccharolobus islandicus abolishes the oxidative stress-induced expression of a large number of genes. ΔsisperR exhibits enhanced tolerance to H2O2 treatment. Consistently, SisPerR overexpression leads to hypersensitivity to of the cells to the H2O2 treatment. We show that the expression of Dps and MntH which are involved in the regulation of cellular metal ion homeostasis, but not that of ROS scavenging enzymes, is significantly up-regulated with H2O2 treatment and repressed by SisPerR. In summary, this study has established that SisPerR is a repressive redox-sensing transcription factor regulating the intracellular metal ion homeostasis in Saccharolobus islandicus for the oxidative stress defense.

overall_design:
To investigate the function of the FurR family protein SisPerR in the regulation of gene transcription in response to H2O2, we constructed Sisfha deletion and expression of S. islandicus and treated with H2O2.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 2 different cells, the wild type strain E233S and Δsisfha, treated or mock-treated with NQO for 6 h.


title: PyMT breast cancer treatment with ethanol versus calcipotriol

city: Charleston

first: Heehwa

last: Son

state: MA

address: 149 13 street

institute: MASSACHUSETTS GENERAL HOSPITAL

summary: To find which signaling affects the therapy of calcipotriol in breast cancer therapy

overall_design: Topical treatment of PyMT mammary breast cancer with ethanol or calcipotriol

first: Yun

last: Xia

first: Shadmehr

last: Demehri

first: Bo

last: Wang


title: Angiotensin-(1-7) relieves behavioral defects and α-synuclein expression through NEAT1/miR-153-3p axis in Parkinson’s disease

city: nanjing

first: Rui

last: Duan

address: Yanshan road 139

institute: Nanjing First hospital

summary: Parkinson's disease is the second most common neurodegenerative disorder, whose characteristic pathology involves progressive loss of dopaminergic neurons and formation of Lewy bodies(LBs) in the substantia nigra(SN). Aggregated and misfolded α-synuclein(α-syn) is the major constituent of LBs. As the newly discovered pathway of renin-angiotensin system (RAS), Angiotensin-(1-7)(Ang-(1-7)) and its receptor Mas have attracted increasing attentions for their correlation with PD progression, but underlying mechanisms remain not very clear. Based on the above, this study established PD models of mice and primary dopaminergic neurons with overexpression of α-syn, then discussed the effect of Ang-(1-7)/Mas on these models combined with downstream lncRNA and miRNA. The findings show that Ang-(1-7) alleviates behavioral disorders, rescues dopaminergic neurons loss and lowers α-syn expression in the SN of hα-syn(A53T) overexpressed PD mice. We also discover that Ang-(1-7) decreases the level of α-syn and apoptosis in the hα-syn(A53T) overexpressed dopaminergic neurons through NEAT1/miR-153-3p axis. Moreover, miR-153-3p expression in peripheral blood is found negatively correlated with that of α-syn. These results not only uncovered the significance and related mechanisms of Ang-(1-7)/Mas on α-syn pathology, but also throwed a new light upon miR-153-3p and NEAT1 as biomarkers and therapeutic targets in PD.

overall_design: The right SNpc tissues of miRNA profiles in human α-syn (A53T) overexpressing mice  and human α-syn (A53T) overexpressing mice  were treated with Ang-（1-7）

first: Qing

last: Gao

first: Feng

first: Xue

last: Xue


title: Sustained inhibition of CSF1R signaling augments antitumor immunity through inhibiting tumor-associated macrophages

city: Nagoya

first: Takahiko

last: Sato

state: Aichi

address: 65 Tsurumai, Showa-ku

department: Department of Hematology

institute: Nagoya University Graduate School of Medicine

summary: Tumor-associated macrophages (TAMs) are one of the key immunosuppressive components in the tumor microenvironment (TME) and contribute to tumor development, progression, and resistance to cancer immunotherapy. Several reagents targeting TAMs have been tested in preclinical and clinical studies, but they have had limited success. Here, we show that a unique reagent, FF-10101, exhibits a sustained inhibitory effect against colony stimulating factor 1 receptor by forming a covalent bond and reduces immunosuppressive TAMs in the TME, which leads to strong antitumor immunity. In preclinical animal models, FF-10101 treatment significantly reduced immunosuppressive TAMs and increased antitumor TAMs in the TME. In addition, tumor antigen-specific CD8+ T cells were increased; consequently, tumor growth was significantly inhibited. Moreover, combination treatment with an anti-PD-1 antibody and FF-10101 exhibited a far stronger antitumor effect than either treatment alone. In human cancer specimens, FF-10101 treatment reduced PD-L1 expression on TAMs, as observed in animal models. Thus, FF-10101 acts as an immunomodulatory agent that can reduce immunosuppressive TAMs and augment tumor antigen-specific T cell responses, thereby generating an immunostimulatory TME. We propose that FF-10101 is a potential candidate for successful combination cancer immunotherapy with immune checkpoint inhibitors, such as PD-1/PD-L1 blockade.

overall_design: To address the mechanism(s) of the tumor regression by FF-10101, comprehensive gene expression analyses was performed. Female C57BL/6J mice at 7-week-old of age were inoculated subcutaneously with a suspension of 1 × 10^6 tumor cells at the right flank (day 0). The mice were treated with or without FF-10101, and tumor samples were collected on day 8 after tumor inoculation.  The experiment were conducted with three biological replicates of each group. Total RNA were sequenced using an Illumina NovaSeq6000.

first: Daisuke

last: Sugiyama

first: Jun

last: Koseki

first: Yasuhiro

last: Kojima

first: Satomi

last: Hattori

first: Kazuki

last: Sone

first: Hitomi

last: Nishinakamura

first: Tomohiro

last: Ishikawa

first: Yuichi

first: Takuma

last: Kato

first: Hitoshi

last: Kiyoi

first: Hiroyoshi

last: Nishikawa


title: Regulation of mevalonate pathway by Vav-Rac1 signaling favors breast primary tumorigenesis and lung metastasis

city: Salamanca

first: L. Francisco

last: Lorenzo-Martín

state: Castilla y León

address: Campus Miguel de Unamuno

country: Spain

institute: University of Salamanca (USAL) – Centro de Investigación del Cáncer (CIC)

summary:
In the present study, we report that the expression of mevalonate pathway enzymes is mediated by the Rho guanosine nucleotide exchange factors Vav2 and Vav3 in a Rac1- and sterol regulatory element-binding factor-dependent manner in breast cancer cells. Furthermore, in vivo tumorigenesis experiments indicate that the two most upstream steps of this metabolic route (Hmgcs1, Hmgcr) are important for primary tumorigenesis, neoangiogenesis and cell survival in breast cancer cells. Hmgcr, but not Hmgcs1, is also important for the extravasation and subsequent fitness of breast cancer cells in the lung parenchyma. Genome-wide expression analyses revealed that Hmgcr influences the expression of gene signatures linked to proliferation, metabolism, and immune responses. The Hmgcr-regulated gene signature can predict long-term tumor recurrence but not metastasis in cohorts of non-segregated and chemotherapy-resistant breast cancer patients.
The mevalonate pathway plays important roles in breast cancer and other tumor types. However, many issues remain obscure as yet regarding its mechanism of regulation and action.

overall_design: 4T1 cells were transduced with empty pLVX or pLKO lentiviral vectors (3 replicates included), lentiviral vectors expressing Hmgcr (3 replicates), and lentiviral shRNAs to Hmgcr (2 independent experiments, 3 replicates each).

first: Javier

last: Conde

first: L

first: Rocío

last: García-Gómez

first: Berta

last: Casar

first: Piero

last: Crespo

first: Xosé

last: Bustelo


title: Transcriptome anlaysis of Th9 cells differentiated with or without sphingosylphosphorylcholine (SPC)

city: Suwon-si

first: Ji Cheol

last: Kim

state: Gyeonggi-do

address: 2066 Seobu-ro, Jangan-gu

country: South Korea

institute: Sungkyunkwan University

summary: We report that SPC enhances differentiation of Th9 cells

overall_design: RNAseq analysis of Th9 cells differentiated with or without SPC for 3 days. Samples for RNAseq were obtained from three independent experiments.

first: Ji

first: Yoe-Sik

last: Bae

first: Mingyu

last: Lee

first: Geon

middle: H