title: Inducible Avp Knockout Mouse Line

city: Bethesda

first: Lihe

last: Chen

state: MD

address: 10 center drive MSC 1603, Building 10, Room 6N228

institute: NHLBI

summary: Arginine vasopressin (AVP) is a peptide hormone coded by the Avp gene, synthesized in the hypothalamus and secreted by the posterior pituitary. Dysregulation of AVP secretion contributes to a variety of human diseases. Previous studies of functional roles of AVP have been largely dependent on the use of Brattleboro rats, which manifest a spontaneous mutation in the Avp gene and lack circulating AVP. Despite their utility, Brattleboro rats are difficult to breed owing largely to the fixed nature of the Avp mutation, resulting in increased neonatal death and behavioral effects in the adults. Consequently, commercial breeders have ceased production, despite a continued need. Therefore, the main goal of this project is to create an effective experimental Avp knockout mouse model that could be used in renal and neuroendocrine research to study the control of water balance by AVP. We employed CRISPR/Cas9 to flox a portion of exon 2 of the Avp gene. Successful insertion of the two loxP sites was confirmed by PCR using primers flanking the targeted regions. Mice harboring the floxed allele were mated to B6.Cg-Tg(CAG-cre/Esr1*)5Amc/J mice that globally express a tamoxifen-inducible Cre recombinase. The resultant inducible Avp knockout mice (Cre+Avpflx/flx) show no signs of polydipsia or polyuria prior to induction, indicating that the floxed gene maintains its wild-type function. The administration of an exogenous inducer like tamoxifen to (8-10) week-old mice, induced Cre-mediated recombination that resulted in a decrease in urine osmolality from 2076 ± 138 to 122 ± 6 mOsm/kgH2O on day 31 after induction. Sanger sequencing demonstrated the expected 1245 bp deletion at the Avp locus. Immunoblotting of AQP2 in the inner medulla showed a significant decrease in AQP2 band density in (Cre+Avpflx/flx) mice to 27 ±1 4 % of values in Cre- floxed control mice. This inducible Avp knockout mouse model provides researchers with a valuable tool to investigate the consequences of Avp gene deletion in a controlled and inducible manner.

overall_design: The process begins with the design (CHOPCHOP) and synthesis of guide RNAs (gRNAs) that target the desired regions (first intron and 3’ downstream) within the vasopressin gene. These gRNAs, when complexed with the Cas9 nuclease, induce site-specific double-strand breaks (DSBs) at the AVP locus. To introduce the loxP sites, a DNA repair template containing the loxP sequences and restriction enzyme sites (BamHI and EcorI) are provided along with the CRISPR/Cas9 components. The repair template serves as a template for homology-directed repair (HDR) and facilitates the precise insertion of loxP sequences flanking the vasopressin gene. Successful insertion of the two loxP sites was confirmed by PCR using primers flanking the targeted regions. Restriction enzymes were used to confirm correct targeting. Additionally, PCR amplification of DNA sequences spanning the two loxP sites was carried out, followed by cloning into the TA-cloning vector and subsequent sanger sequencing for further confirmation. Sequencing analysis of the founder mice demonstrated precise insertion of the loxP sites into each intended location within the Avp locus, without introducing mutations at the loxP sites.

first: Shaza

last: Khan

first: Mark

last: Knepper


title: Targeting of SUMOylation leads to cBAF complex stabilization and disruption of the SS18::SSX transcriptome in synovial sarcoma [HSH3_ChIP-seq_HS-SY-II]

status: Public on Aug 06 2025

city: Richmond

first: Mikhail

last: Dozmorov

state: VA

address: 830 E Main St

department: Biostatistics

country: USA

institute: Virginia Commonwealth University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Synovial Sarcoma (SS) is driven by the SS18::SSX translocation event and is often diagnosed in patients under 30. In general, SS is refractory to chemotherapy and other therapeutic approaches. SS18::SSX does not directly bind to DNA. Instead, SS18::SSX alters ATP-dependent chromatin remodeling complex BAF (mammalian SWI/SNF complex) complexes away from a wild-type SS18-containing canonical (cBAF) complex towards a SS18::SSX-containing non-canonical (nc)BAF complex to drive a SS-specific transcription program with subsequent tumor formation. Small molecule targeted therapies are expanding beyond the kinome, providing additional tools to treat cancers that are not yet amenable to targeted therapies. Here, we demonstrate that SS18::SSX activates the SUMOylation program and SS are sensitive to the small molecule SAE1/2 inhibitor, TAK-981 (subasumstat). Mechanistically, we demonstrate TAK-981 de-SUMOylates the cBAF and Polybromo-associated BAF complex (PBAF) complex member, SMARCE1. The result of which is stabilization and restoration of cBAF complexes on chromatin, shifting away from the dominant SS18::SSX-ncBAF-complex driven transcriptome. This phenotypic shift is associated with DNA damage and cell death, resulting in tumor inhibition across both human and mouse SS tumor models. As such, TAK-981 combined with standard-of-care chemotherapy enhances induced synergistic activity through increased DNA damage, leading to tumor regressions. Targeting the SUMOylation pathway in SS restores cBAF complexes and blocks the SS18::SSX-ncBAF transcriptome, identifying a therapeutic vulnerability in SS, and positioning the in-clinic TAK-981 as a novel candidate to treat this refractory cancer.

overall_design: Chromatin Immunoprecipitation DNA sequencing (ChIP seq) for SS18::SSX, SMARCA4, KDM2B and H3K27ac in SYO.1 and HS-SY-II synovial sarcoma cell lines

first: Konstantinos

middle: V

last: Floros

first: Carter

middle: K

last: Fairchild Jr

first: Jinxiu

last: Li

first: Kun

last: Zhang

first: Jane

middle: L

last: Roberts

first: Richard

last: Kurupi

first: Bin

last: Hu

first: Vita

last: Kraskauskiene

first: Nayyerehsadat

last: Hosseini

first: Shanwei

last: Shen

first: Melissa

middle: M

last: Inge

first: Kylie

last: Smith-Fry

first: Li

first: Afroditi

last: Sotiriou

first: Krista

last: Dalton

first: Asha

last: Jose

first: Elsamani

middle: I

last: Abdelfadiel

first: Yanli

last: Xing

first: Ronald

middle: D

last: Hill

first: Jamie

last: Slaughter

first: Mayuri

last: Shende

first: Madelyn

middle: R

last: Lorenz

first: Mandy

last: Hinojosa

first: Benjamin

last: Belvin

first: Zhao

last: Lai

first: Sosipatros

middle: A

last: Boikos

first: Angeliki

last: Stamatouli

first: Janina

middle: P

last: Lewis

first: Masoud

middle: H

last: Manjili

first: Kristoffer

last: Valerie

first: Renfeng

first: Ana

last: Banito

first: Andrew

last: Poklepovic

first: Jennifer

middle: E

last: Koblinski

first: Trevor

last: Siggers

middle: G

first: Kevin

middle: B


title: Mitochondrial ATP production promotes T cell differentiation and function by regulating chromatin accessibility [RNAseq2]

status: Public on Aug 05 2025

city: New York

first: Craig

last: Thompson

state: NY

address: 411 East 67th Street RRL 469

institute: Memorial Sloan Kettering Cancer Center

type: Expression profiling by high throughput sequencing

summary: Immune elimination of chronic infection or cancer requires cytotoxic CD8 T cells that adopt and maintain an effector phenotype. Cytotoxic T cell function is a bioenergetically demanding process and T cells subjected to chronic antigen exposure have compromised effector function despite high rates of glycolysis. Here we report the ability of the short chain fatty acid, D-α-hydroxybutyrate, to act as a signaling molecule that increases mitochondrial ATP production and drives the conversion of proliferating T cells into cytotoxic effector cells. DAHB signaling switches ATP production from glycolysis to fatty acid oxidation, even in glucose-replete media. This conversion suppresses both AMPK phosphorylation and the integrated stress response (ISR) in activated T cells while significantly elevating the level of the phosphagen, phosphocreatine (PCr). Both the PCr bioenergetic reserve and oxidative phosphorylation were required for T cell effector differentiation. DAHB-induction of CD8-effector gene transcription was coupled to bioenergetics by enhanced ATP-dependent remodeling of chromatin accessibility at effector gene loci. DAHB enhanced CD8 T cell antitumor activity both in vitro and in vivo, and DAHB treatment of transferred T cells led to persistent in vivo antitumor effects. Together, these findings link cellular bioenergetics to the regulation of chromatin accessibility and gene expression required to support effector function.

overall_design: RNA-seq of 100,000 activated mouse CD8 T cells treated with NaCl (20mM, Ctrl), DAHB (20mM) or DAHB+Oligomycin (10nM) (DAHB+O) overnight followed by extraction.

first: Charles

last: Ng

first: Alexandria

last: Markovitz

first: Tak Shun

last: Fung

first: Olivia

last: Jones

first: Dayi

last: Li

first: Guoan

last: Zhang

first: Richard

last: Koche

first: Mara

last: Monetti

first: Huayuan

last: Tang

first: Yun

last: He

first: Zhengshuang

last: Xu

first: Xin

last: Cai

first: Ziqi

last: Yu

first: Geetha

last: Bhagavatula

first: Sean

last: Colgan

first: Elizabeth

last: Steinert

first: Navdeep

middle: S

last: Chandel

first: Lin

last: Wu


title: Changes of transcript switch usage induced by TGF-b signaling in the in vitro decidualization

city: Oxford

first: Adam

last: Cribbs

address: Windmill Road, Oxford, OX3 7LD, UK

country: United Kingdom

institute: University of Oxford

summary: To probe potential switches in transcript usage induced by TGF-beta signalling within endometrium, we treated the THESC (hTERT-immortalized Human Endometrial Stromal Cells) cell line with TGF-beta during in vitro decidualization and monitored transcript-level changes using Nanopore long-read sequencing allowing unambiguous determination of transcript isoforms.

overall_design:
To investigate the changes of RNA expression profile, particularly on transcript switch usage induced by TGF-beta treatment within endometrium, we treated the THESC cell line with hormone to induce in vitro decidualization, with or without TGF-b during the process.
We then performed transcript expression profile analysis using the data obtained by nanopore long read sequencing, to compare the transcript usage under difference conditions (DMSO, TGF-beta, TGF-beta plus MEK inhibitor, or MEK inhibitor only)
Gene expression profile obtained from Illumina short read sequencing was used as a reference on gene level

first: Chen-Yi

last: Wang


title: Targeting of SUMOylation leads to cBAF complex stabilization and disruption of the SS18::SSX transcriptome in synovial sarcoma [HSH3_ChIP-seq_SYO-1]

first: Mikhail

last: Dozmorov

first: Konstantinos

last: Floros

first: Carter

last: Fairchild Jr

first: Jinxiu

first: Kun

first: Jane

last: Roberts

last: Kurupi

first: Bin

last: Hu

first: Vita

last: Kraskauskiene

first: Nayyerehsadat

last: Hosseini

first: Shanwei

last: Shen

first: Melissa

last: Inge

first: Kylie

last: Smith-Fry

first: Li

first: Afroditi

last: Sotiriou

first: Krista

last: Dalton

first: Asha

last: Jose

first: Elsamani

last: Abdelfadiel

first: Yanli

last: Xing

first: Ronald

last: Hill

first: Jamie

last: Slaughter

first: Mayuri

last: Shende

first: Madelyn

last: Lorenz

first: Mandy

last: Hinojosa

first: Benjamin

last: Belvin

first: Zhao

last: Lai

first: Sosipatros

last: Boikos

first: Angeliki

last: Stamatouli

first: Janina

last: Lewis

first: Masoud

last: Manjili

first: Kristoffer

last: Valerie

first: Renfeng

first: Ana

last: Banito

first: Andrew

last: Poklepovic

first: Jennifer

last: Koblinski

first: Trevor

last: Siggers

first: Kevin


title: Mitochondrial ATP production promotes T cell differentiation and function by regulating chromatin accessibility [RNAseq1]

first: Craig

last: Thompson

overall_design: RNA-seq of 100,000 activated mouse CD8 T cells treated with NaCl (20mM, Ctrl) or DAHB (20mM) overnight followed by extraction.

first: Charles

last: Ng

first: Alexandria

last: Markovitz

first: Tak Shun

last: Fung

first: Olivia

last: Jones

first: Dayi

last: Li

first: Guoan

last: Zhang

first: Richard

last: Koche

first: Mara

last: Monetti

first: Huayuan

last: Tang

first: Yun

last: He

first: Zhengshuang

last: Xu

first: Xin

last: Cai

first: Ziqi

last: Yu

first: Geetha

last: Bhagavatula

first: Sean

last: Colgan

first: Elizabeth

last: Steinert

first: Navdeep

last: Chandel

first: Lin

last: Wu


title: Mitochondrial ATP production promotes T cell differentiation and function by regulating chromatin accessibility [ATACseq1]

first: Craig

last: Thompson

overall_design: ATAC-seq of 100,000 activated mouse CD8 T cells treated with NaCl 20mM (Ctrl), DAHB 20mM or DAHB 20mM +Cyclocreatine 10mM (DAHB+Cyc).

first: Charles

last: Ng

first: Alexandria

last: Markovitz


title: Mitochondrial ATP production promotes T cell differentiation and function by regulating chromatin accessibility [ATACseq2]

overall_design: ATAC-seq of 100,000 activated mouse CD8 T cells treated with NaCl (20mM, Ctrl), DAHB (20mM) or DAHB+BRM014 (1uM) (DAHB+BRM).

first: Tak Shun

last: Fung

first: Olivia

last: Jones

first: Dayi

last: Li


title: CITE-seq analysis of murine subcutaneos PDAC tumor models under pan-KRAS inhibitor and/or anti-PD1 treatment combinations

city: Vienna

first: Martin

last: Aichinger

address: Dr. Boehringer-Gasse 5-11

country: Austria

institute: Boehringer-Ingelheim

summary: A multi-omic analysis of CITE-seq of a syngeneic model of PDAC unveils distinct phenotypic correlations of augmented anti-tumor immunity and a substantially reduced immunosuppressive tumor microenvironment (TME). This study presents KRASi and anti-PD1 as a promising drug combination for cancer patients with a multi-layered impact on both tumor cell intrinsic, as well as TME-dependent mechanisms.

overall_design: In vivo treatment of mice harboring subcutaneous PKC7829c11 PDAC tumors, analysis of the tumor microenvironment using CITEseq.

first: Artem

last: Artemov

first: Florian

last: Ebner

first: Jesse

last: Lipp

first: Alec

last: Dick


title: Long-chain fatty acid β-oxidation regulates embryonic development by H3K18 acetylation in mice [CUT&Tag]

city: 温州

first: kefan

last: zheng

address: 瓯海区茶山街道温州医科大学

country: China

institute: wenzhou medical university

summary: Fatty acids are not only important as energy sources, but also playing crucial roles in maintaining cellular homeostasis.Inhibition of long-chain fatty acid β-oxidation (LCFAO) results in preimplantation developmental arrest, downregulated expressions of S phase-related genes, and loss of H3K18ac modification. By profiling the landscape of H3K18ac, we show that H3K18ac is enriched on the promoter regions of S phase-related genes and correlates with their expression. Taken together, we demonstrate that LCFAO could regulate mouse preimplantation development by H3K18ac, providing new evidence for metabolic-epigenetic crosstalk in regulating embryonic development.

overall_design: Examination of H3K27ac in mouse 8-cell and morula embryos in both control and TMZ inhibitor-treated groups.

first: Qingran

last: Kong

first: Hao

first: Qi

last: Zhao

first: Kefan

last: Zheng

first: Hongdi

last: Cui

first: Entong

last: Song


title: Genetic and sex-specific regulation of mitochondrial function in gonadal and inguinal adipose tissue

city: Los Angeles

first: Calvin

last: Pan

address: 675 Charles Young Dr South

institute: UCLA

summary: Sex differences in adipose tissue impact metabolic health, but the underlying molecular mechanisms remain unclear. We previously identified a female-specific chr17 trans-eQTL hotspot regulating mitochondrial gene expression in gonadal white adipose tissue (gWAT). Here, we tested whether iWAT contributes comparably to sex differences in mitochondrial function and futile cycling.

overall_design: RNA-Seq profiling of subcutaneous adipose tissue from 82 strains of inbred mice (67 for females, 74 for males)

first: Aldons

last: Lusis

first: Dorota

last: Kaminska


title: Comparative Analysis of the Transcriptome and Methylome in Distinct Trophoblast Populations During Embryo Implantation in Mares

city: Olsztyn

first: Dawid

last: Tobolski

state: Warmińsko-mazurskie

address: Kazimierza Jaroszyka

department: Department of Large Animal Diseases and Clinic

country: Poland

institute: Institute of Veterinary Medicine, Warsaw University of Life Sciences

type: Methylation profiling by high throughput sequencing

summary:
Abstract Background During equine implantation, two trophoblast subpopulations are distinguished: the invasive (chorionic girdle) and non-invasive (allantochorion). The invasive chorionic girdle is believed to interact with the maternal immune system and contribute to embryo attachment to the endometrium. However, the mechanism regulating attachment and immune tolerance to these two distinct trophoblast subpopulations remain incompletely understood. The present study aimed to investigate the regulation of gene expression and the biological processes involved in trophoblast attachment, development and maintenance of immune tolerance by comparing the transcriptomes and methylomes of the allantochorion and chorionic girdle trophoblast before and after implantation, that is, between days 33 and 42 of gestation. Results Irrespective of gestational day, allantochorion (N=4) was enriched in TGFB and its receptors TGFBR1 and TGFBR2. Across implantation, expression of regulatory macrophage markers, as IL33, IL4|1, PLG-RKT, or CD163, also increased in that membrane in addition to TFEB and SERPINE1. Invasive chorionic girdle (CG33, N=4) had higher, than the non-invasive allantochorion (ALC33, N=4), expression of NLRC5, a transcriptional regulator of MHC I, and expression of that factor further decreased in allantochorion from gestational day 33 to 42. Furthermore, B2M, which encodes the MHC I light chain, was hypermethylated in the allantochorion. Some genes were differentially methylated and expressed between the two trophoblasts (CAVIN1, LHB, INSR) or beginning and end of implantation (IFNGR1, CD177). Analysis of GOterms and canonical pathways showed that both differentially expressed and methylated genes were involved in critical for implantation processes and pathways as these including cell movement and adhesion, TGFB signaling, fibrosis, wound healing, or leukocyte extravasation.   Conclusions Allantochorion may contribute to the formation of the attachment with the endometrium and maintenance of maternal tolerance. Expression of IL33, IL4|1 or CD163 suggests involvement of regulatory macrophages in the implantation. TFEB might be involved in the support of allantochorion steroidogenic functions and maturation. Spatial-temporal differential methylation of genes expressed by the chorionic girdle and allantochorion may contribute to the control of trophoblast invasion and its attachment to endometrium.  Finally, methylation of B2M and differential expression of NLRC5, are involved in the control of MHC I expression on equine trophoblasts during implantation.
Background: During equine implantation, two distinct trophoblast subpopulations are identified: the invasive chorionic girdle (CG) and the non-invasive allantochorion. The invasive CG is believed to modulate the maternal immune response and facilitates embryo attachment to the endometrium, while the allantochorion contributes to placental development without breaching the endometrium. However, the mechanisms underlying differential adhesion and immune modulation by these two lineages remains poorly understood. This study aimed to investigate the regulation of biological processes underlying trophoblast attachment, development and maintenance of immune tolerance by comparing the transcriptomes and methylomes of CG and allantochorion trophoblasts before and after implantation, that is, between gestational days 33 and 42. Results: Irrespective of gestational day, allantochorion (n=4) was enriched in TGFB and its receptors TGFBR1 and TGFBR2. Across the implantation window, expression of regulatory macrophage markers such as IL33, IL4|1, PLG-RKT, and CD163 increased in the allantochorion, along with upregulation of TFEB and SERPINE1. The invasive GC (CG33, n=4) showed higher expression of NLRC5, a transcriptional regulator of MHC I, compared to the non-invasive allantochorion (ALC33, n=4). Notably, NLRC5 expression declined in the allantochorion from day 33 to 42. Furthermore, B2M, which encodes the MHC I light chain, was hypermethylated in the allantochorion. Several genes, including CAVIN1, LHB, and INSR, were both differentially expressed and methylated between the two trophoblast types, while others, such as IFNGR1, CD177, showed differential regulation across the implantation window. Gene Ontology and pathway analyses revealed that differentially expressed and methylated genes were enriched in biological processes and pathways critical for implantation, including cell migration and adhesion, TGFB signaling, fibrosis, wound healing, and leukocyte extravasation.Conclusions: The allantochorion plays an active role in establishing the attachment to the endometrium and sustaining maternal immune tolerance during implantation. The upregulation of IL33, IL4|1, and CD163 suggests the that the allantochorion may promote the recruitment or polarization of macrophages toward a regulatory phenotype, thereby modulating the local immune environment. TFEB may contribute to the steroidogenic activity and functional maturation of the allantochorion. Spatial and temporal differences in gene methylation between CG and allantochorion suggest involvement of epigenetic regulation in trophoblast invasion and attachment to the endometrium. Finally, combined B2M hypermethylation and differential expression of NLRC5 point to epigenetic and transcriptional control of MHC I expression in the equine trophoblasts during implantation.

overall_design: Equine allantochorion (ALC) and chorionic girdle (CG) samples  were collected with non-surgical uterine lavage at gestational days 33 (N ALC =4; N CG=4) and 42 (N=4) from physiologically progressing pregnancies. RNA was isolated from each sample using PureLink™ RNA Mini Kit (Ambion) with DNAse digestion between washing. Its quality and quantity were measured on a NanoDrop2000 and a TapeStation 2200 system (RNA tapes, Agilent). Acceptable samples had an RIN over 9.5. According to the manufacturer's protocol, cDNA libraries cells were prepared using the VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina from 300 ng aliquots of purified RNA samples. The final cDNA library concentration was 10 nM. The quality and quantity of cDNA libraries was assessment using D1000 tapes on TapeStation2200 and on Quibit. The cDNA were sequenced over 150PE cycles on a HiSeq 3000 System (Illumina, San Diego, CA, USA) in outdoor facilities (Admera Health Biopharma Services).

first: Joanna

last: Jaworska

first: Tomasz

last: Szmatoła

first: Katarzyna

last: Ropka-Molik

last: Ząbek

first: Anne

last: Kahler

first: Shebl

last: Salem

first: Izabela

last: Wocławek - Potocka

last: Piórkowska

first: Amanda

last: De Mestre


title: Translational control of innate barrier defense by the gut microbiota

city: Pittsburgh

first: Zheng

last: Kuang

state: PA

address: 4400 Fifth Avenue

department: Biological Sciences

institute: Carnegie Mellon University

summary: The intestinal epithelium is protected by a mucus layer infused with antimicrobial proteins, forming a physical and chemical barrier that limits microbial access to host tissue. Mucus barrier assembly is energetically costly, yet how production of its constituent proteins is matched to demand remains unclear. Here, we show that the microbiota regulates gut barrier immunity by enhancing translation of select defense proteins, including mucin 2 and lysozyme. This occurs via induction of histone deacetylase 5 (HDAC5) in secretory epithelial cells. HDAC5 deacetylates 14-3-3, enabling it to sequester Raptor, a component of mTORC1. This releases mTOR and activates downstream signaling that promotes translation of barrier defense proteins. Our findings reveal a mechanism by which the microbiota shapes barrier immunity through translational control.

overall_design: 16S rRNA sequencing analysis of fecal bacterial composition in wildtype and Hdac5-/- mice.

first: Yun

last: Li

first: Runrun

last: Wu

first: Xianda

last: Ma

first: Jianglin

last: Zhang

first: Junjie

first: Yiran

last: Duan

first: Yuhao

last: Wang

first: Brian

last: Hassell

first: Kelly

last: Ruhn

first: Cassie

last: Behrendt

first: Chartanya

last: Dende

first: Li

first: Andrew

last: Lemoff

first: Prithvi

last: Raj

first: Eric

last: Olson

first: Lora

last: Hooper


title: High-throughput mapping of modular regulatory domains in human RNA-binding proteins

city: Stanford

first: Abby

last: Thurm

state: CA

address: 443 Via Ortega Rm 036

institute: Stanford University

summary: RNA regulation plays an integral role in tuning gene expression and is controlled by thousands of RNA-binding proteins (RBPs). While some RBPs require most of their sequence to accomplish their functions, some examples exist of modularity: small protein domains that serve as molecular glues to recruit larger RNA regulatory complexes. Mapping these RNA-regulatory effector domains is important for understanding RBP function and for developing compact synthetic tools for precisely tuning RNA levels. We developed a high-throughput recruitment assay (HT-RNA-Recruit) to identify RNA-down-regulatory effector domains within human RBPs. By recruiting over 30,000 protein tiles from 367 RBPs to a reporter mRNA, we discovered over 100 unique RNA-down-regulatory effector domains in 86 distinct RBPs. We identified some domains that downregulate gene expression both when recruited to DNA and RNA, and dissected their mechanisms of regulation. Finally, we built inducible synthetic RNA regulators that can target endogenous RNAs or stably maintain reporter gene expression at desired levels, and developed a mathematical model to predict their dynamics. This work serves as a resource for human RNA regulators and expands the synthetic repertoire of RNA-based genetic control tools.

overall_design: 1. High-throughput recruitment assay to measure the effects on reporter RNA expression from tethering a 30,000 member or a smaller, 3,000 member library to different reporter constructs: 24 MS2 stem-loops in the 3' UTR or 5'UTR; 7 MS2 stem-loops in the 5' UTR; 9xTetO binding sites at a proximal enhancer 2. RNA-seq profiling of K562 cells after 48 hours of overexpression of either full-length RBPs, MCP alone, full-length RBP mutants, or a synthetic RNA repressor with an endogenous RBD 3. CUT&RUN profiling of the reporter locus after DNA recruitment of ZNF10 KRAB, RNA recruitment of an RNA regulator, or RNA recruitment of ZNF10 KRAB

first: Yaara

last: Finkel

first: Cecelia

middle: J

last: Andrews

first: Xiangment

last: Cai

first: Colette

last: Benko

first: Lacramioara

last: Bintu


title: Testis mRNA expression profiling of Atlantic salmon (Salmo salar) age-at-maturity-associated genes during different maturation stages

city: Helsinki

first: Ehsan

middle: Pashay

last: Ahi

address: Biocenter 1, Viikinkaari 9

country: Finland

institute: University of Helsinki

summary: Study revealed new information about molecular functions of the vgll3 gene associated with age-at-maturity in the testis of Atlantic salmon

overall_design: In the study presented here, expression patterns of a gene associated with age-at-maturity in Atlantic salmon, its paralogs and 340 additional genes were studied in whole hatchery-derived individuals of three maturation stages, immature-1 and immature-2, and mature, in the testis of two vgll3 genotypes (early and late maturation genotypes).

last: Pashay Ahi

first: Craig

last: Primmer

first: Johanna

last: Kurko


title: Decoupling Brace Root Development from Shoot Development in Sorghum: Candidate Genes Revealed by GWAS

city: Columbia

first: Ashley

middle: N

last: Hostetler

state: MO

address: 1201 Rollins St

institute: University of Missouri

summary: Brace roots develop from stem nodes above the soil and are important for structural support. While the function of brace roots has been previously shown, the causative genes for brace root development have yet to be identified in sorghum. Here we used 3’ RNA sequencing in BTx623 sorghum stem nodes to determine if candidate genes from a complimentary Genome Wide Association (GWA) analysis were expressed. Of the 25 candidate genes identified in GWA analysis, 15 were expressed in at least one of the three stem nodes. Together, the combined approach of GWA analysis and RNA-sequencing analysis provides a strong foundation for identifying the causative genes for brace root development.

overall_design: 3' RNA-sequencing of the three stem nodes directly above the soil in three Sorghum bicolor BTx623 plants.

first: Rajdeep

last: Khangura

first: Jonathan

middle: W

last: Reneau

first: Taran

last: Kermani

first: Jacob

first: Tena

last: Graham

first: Brian

last: Dilkes

first: Erin

last: Sparks


title: Cell-Specific Transcriptomic and Mito-Nuclear Imbalance in Lungs Under Intermittent Hypoxia in Adult Male Mice.

city: Quebec

first: Vincent

last: Joseph

state: Quebec

address: 2725, chemin Sainte-Foy

country: Canada

institute: Université Laval / IUCPQ

summary: Obstructive sleep apnea and its characteristic intermittent hypoxia (IH) are widely recognized as significant contributors to various pulmonary diseases, including asthma, pulmonary arterial hypertension, fibrosis, and chronic obstructive pulmonary disease. While single-cell RNA sequencing (scRNA-seq) has provided valuable insights into cell-type-specific responses to IH, previous studies have primarily focused on post-hypoxic recovery states, leaving immediate molecular responses during active IH exposure unexplored. To address this critical knowledge gap, we investigated real-time transcriptional responses to IH at single-cell resolution in lung tissue using male mice (n=3/group) exposed to either normoxia or IH (30 cycles/h, nadir 6% O₂, 12 h/day) for 14 days, with tissue collection during active IH exposure. Our analysis revealed pronounced cell-type-specific transcriptional reprogramming, particularly in airway smooth muscle cells (ASMC), arterial endothelial cells (AEC), and lymphatic endothelial cells (LEC). These changes were characterized by enrichment in pathways related to epithelial-to-mesenchymal transition (ASMC, LEC), myogenesis (ASMC), and antioxidant defenses (AEC, LEC). Most cell types demonstrated substantial upregulation of genes encoding mitochondrial complex I-IV proteins and TCA cycle enzymes accompanied by a decreased expression of genes encoded by mitochondrial DNA that was markedly present in LEC, AEC, and cells of the alveolar-capillary unit, revealing a mito-nuclear imbalance. These findings provide novel insights into the immediate cellular responses to IH, showing previously uncharacterized metabolic reorganization that may underlie the development of IH-related pulmonary complications. This improved understanding of early molecular events during active IH exposure advances our knowledge of sleep apnea-related lung pathologies and may inform future therapeutic strategies.

overall_design: lungs of adult male mice exposed to room air (Nx) or daytime intermittent hypoxia (IH - 21% to 6%) for 14 days. Pool from 3 lungs/groups

first: Alexandra

last: Jochmans-Lemoine

first: François

last: Marcouiller

first: Marie

last: Martelat

first: Ynuk

last: Bossé

first: Yohan

first: Dominique

middle: k

last: Boudreau

first: Sébastien

last: Renaut


title: Endurance training promotes chromatin closure and timely repression of the post-exercise immediate early stress response [RNA-Seq]

city: Basel

first: Laura

middle: Maria

last: de Smalen

state: Basel-Stadt

address: Spitalstrasse 41

department: Biozentrum

country: Switzerland

institute: University of Basel

summary: Objective: Endurance training is known to elicit numerous changes in skeletal muscle to enhance performance and function. Many of these adaptations are controlled by the modulation of transcriptional programs in myonuclei. While previous studies have explored alterations in DNA methylation and histone modifications in response to exercise, the specific changes in chromatin restructuring and accessibility, a prerequisite for transcription, are still poorly understood. Methods: A multi-omics analysis was performed: ATAC-sequencing was used to map chromatin accessibility in myonuclei isolated from endurance-trained and untrained mice at multiple time points (0h, 6h, and 72h) post-exercise. Gene expression was assessed via RNA-sequencing, and motif activity analysis identified regulatory factors involved in exercise-induced chromatin remodeling and transcriptomic response. Results: Endurance training amplified rapid chromatin closing immediately after exercise, with trained muscle exhibiting a more pronounced loss of chromatin accessibility at 0h and 6h post-exercise compared to untrained muscle. These chromatin accessibility changes persisted longer in trained muscle, with significant retention until 72h post-exercise. Immediate early transcription factors, such as Fos and Jun, showed a training state-dependent shift in activation dynamics. Similarly, specific modulation of genes involved in metabolism, insulin response and angiogenesis was observed. Conclusions: Endurance training triggers rapid and persistent chromatin remodeling in muscle, contributing to the transcriptional response to exercise. Our findings suggest that training induces long-lasting epigenetic changes, potentially underpinning muscle memory and improved physiological resilience. These new insights into the molecular mechanisms of muscle adaptation help to understand the training response, and might become relevant in disease prevention.

overall_design: All conditions (untrained and trained mice sacrificed at 0h, 6h, 72h post-exercise) are compared to sedentary mice that underwent no training nor exercise.

first: Volkan

last: Adak

first: Stefan

last: Steurer

first: Aurel

last: Leuchtmann

first: Christoph

last: Handschin


title: NRCAM variant defined by microexon skipping is a targetable surface proteoform in high-grade gliomas

first: Julien

last: Jarroux

address: 413 E 69th St

department: Brain and Mind Research Institute

institute: Weill Cornell Medicine

summary: To overcome the paucity of known tumor-specific surface antigens in pediatric high-grade glioma (pHGG), we contrasted splicing patterns in pHGGs and normal brain samples. Among alternative splicing events affecting extracellular protein domains, the most pervasive alteration was the skipping of ≤30 nucleotide-long microexons. Several of these skipped microexons mapped to L1-IgCAM family members, such as NRCAM. Bulk and single-nuclei short- and long-read RNA-seq revealed uniform skipping of NRCAM microexons 5 and 19 in virtually every pHGG sample. Importantly, the Δex5Δex19 (but not the full-length) NRCAM proteoform was essential for pHGG cell migration and invasion in vitro and tumor growth in vivo. We developed a monoclonal antibody selective for Δex5Δex19 NRCAM and demonstrated that “painting“ of pHGG cells with this antibody enables killing by T cells armed with an FcRI-based universal immune receptor. Thus, pHGG-specific NRCAM and possibly other L1-IgCAM proteoforms are promising and highly selective targets for adoptive immunotherapies.

overall_design: Our recently developed SnISOr-Seq approach allows for the accurate cataloging of full-length transcripts devoid of intronic sequences. We applied this approach to the pediatric high-grade glioma cell line 7316-3058. The short-read part of the workflow was used to determine expression level of select genes in individual cells. The long-read part of the workflow was used to determine whether microexons of interest are processed in a uniform or in a stochastic manner.

first: Hagen

middle: U

last: Tilgner

first: Priyanka

last: Sehgal

first: Andrei

last: Thomas-Tikhonenko

first: Berk

last: Mankaliye

first: Taewoo

last: Kim


title: Transcriptomic characterization of murine mammary cancer stem cell population

city: Lille

first: Roland

middle: P.

last: Bourette

address: Bd du Professeur Jules Leclercq

country: France

summary: To identify molecular actors of cancer stem cells, we used a double-transgenic mouse model which develop mammary tumors with GFP expression in cancer stem cells.  A cell line was generated from tumors of double-transgenic. In this population, GFP+ and GFP- cells was sorted. To identify specific gene expression in GFP+ cells, we performed a microarray analysis

overall_design: Sort was performed 2 days post-seeding. Four independent experiments were performed with cells at 4 different passages.

first: Joséphine

last: Louvieaux

first: Axel

last: Chomy

first: Martin

last: Figeac


title: TRIM13 affects cardiomyocyte injury and apoptosis through interacting with CD3D and regulating its ubiquitination in Myocardial Infarction

city: kunming

first: youjun

last: zhou

state: yunnan

address: No,245, renmin eastroad

department: 1Department of Nuclear Medicine

institute: The Affiliated Yan’an Hospital of Kunming Medical University

summary: Myocardial infarction (MI) is a common cardiovascular disease with a high risk of sudden death. We aim to develop potential and more effective therapeutic strategies for treating and preventing MI.

overall_design: A mouse model of MI was established, and cardiac tissue sample microarray data and GSE236374 dataset were collected to screen and 120 up-regulation and 15 down-regulation genes were obtained, and related to T cells and cell immunity. Further obtained 7 key genes, including Cd8b1, Pdcd1, Klrd1, Klrk1, Cd3g, Cd74 and Cd3d, and had high expression in MI mice. The ceRNA regulation network found that protein TRIM13 was upstream of CD3D. In vitro and in vivo knockdown of CD3D relieved the effect of OGD-induced cardiomyocyte apoptosis. TRIM13 interacts with CD3D. Knockdown of TRIM13 promotes CD3D ubiquitination and restores the effect of OGD-induced cardiomyocyte apoptosis through down-regulation of CD3D. Knockdown of TRIM13 could relieve cardiomyocyte apoptosis through down-regulation of CD3D in MI.

first: Youjun

last: Zhou


title: Ribo-ITP coupled ribosome profiling identifies non-canonical translational events in low input samples [Ribo-seq]

city: Austin

first: Vighnesh

middle: Vijay

last: Ghatpande

state: Austin

address: 2500 Speedway

department: Molecular Biosciences

institute: University of Texas at Austin

summary: In the last decade,  an unexpectedly large number of translated regions (translons) have been discovered using ribosome profiling and proteomics. Translons can regulate mRNA translation and encode micropeptides that contribute to multiprotein complex formation, Ca2+ regulation in muscle, and signaling during embryonic development. However, identification of translons has been limited to cell lines or large organs due to high input requirements for conventional ribosome profiling and mass spectrometry. Here, we employed Ribo-ITP, a low input ribosome profiling technique on difficult to collect samples like microdissected hippocampal tissues and single pre-implantation embryos. We detected thousands of translons across these samples, most of which initiated at non-canonical start sites, were less than 100 amino long with significantly altered amino acid composition. Comparative analysis of more than a thousand ribosome profiling datasets across a wide range of cell types revealed pervasive expression of most of the detected translons. To test the translational capacity of the detected translons, we engineered a translon dependent GFP reporter system, and detected robust expression of translons initiating at near-cognate start codons in mouse embryonic stem cells (mESCs). Mutating the translons in mESCs identified a small proportion that negatively impacted growth. Taken together, we present a proof-of-concept study to identify non-canonical translation events from ultra-low input samples which can be applied to cell and tissue types inaccessible to conventional methods.

overall_design: To identify non-canonical translation events, ribosome profiling from low input samples - microdissected mouse hippocampal acute slices and mouse preimplantation embryos was performed followed by pooled Crispr-Cas9 screen to calidate the identified events.

first: Uma

last: Paul

first: Mackenzie

last: Howard

first: Can

last: Cenik


title: A Dermis-on-a-Chip Model for Compound Screening

city: Toronto

first: Milica

last: Radisic

state: Ontario

address: 160 College St

institute: University of Toronto

summary: Dermal fibrosis is a significant barrier to effective wound healing, with excessive myofibroblast activation and extracellular matrix deposition leading to scar formation and compromised tissue function. Current in vitro models for studying dermal fibrosis, such as monolayer cultures and human skin equivalents (HSEs), have limited physiological relevance or scalability for drug screening. Here, we present a dermis-on-a-chip platform to enable screening of anti-fibrotic compounds in physiologically-relevant 3D dermal microtissues. Upon treatment with transforming growth factor beta (TGFβ), the tissues exhibited hallmarks of fibrosis, including impaired integrity, increased tensile forces, altered cellular morphology, and a pro-fibrotic cytokine profile. Conversely, incorporation of QHREDGS (Q-peptide), an angiopoietin-1 derived peptide with known regenerative properties, selectively modulated these fibrotic changes. Q-peptide was found to reduce TGFβ-induced tensile forces, suppress smooth muscle actin (SMA) expression, and upregulate certain cytokines associated with wound repair. Overall, these findings demonstrate the utility of dermis-on-a-chip model in compound screening.

overall_design: RNAseq profile of dermal microtissues cultured with or without transforming growth factor beta (TGFb), in the presence or in the absence of QHREDGS-peptide (Q-peptide), an angiopoietin-1 derived peptide with known wound healing properties, after two days of culture.

first: Dhana

last: Abdo

first: Yimu

last: Zhao

first: Sargol

last: Okhovatian

first: Luis Felipe

last: Jiménez Vargas

first: Karl

middle: T

last: Wagner

first: Amid

last: Shakeri

first: Daniel

last: Vosoughi


title: Transcriptome change of Palmitic acid-treated human aortic smooth muscle cells

city: Ann Arbor

first: Yaozhong

last: Liu

state: MICHIGAN

address: 2800 Plymouth Road

department: Internal Medicine

institute: University of Michigan

summary: Human aortic smooth muscle cells (HASMC) were treated with Palmitic acid (250 uM) or vehicle control for 24 hours. Total RNA was isolated for RNA sequencing.

first: Eugene

last: Chen

first: Yanhong

last: Guo


title: Genomic and Immune Landscape of Pancreatic Ductal Adenocarcinoma Associated with Germline Pathogenic Variants in ATM

city: Rochester

first: Christine

last: Nguyen

state: MN

address: 200 1st St SW

department: Quantitative Health Sciences

institute: Mayo Clinic

summary: This study characterizes the genomic and immunophenotypic landscape of pancreatic ductal adenocarcinoma in carriers of germline pathogenic variants in ATM to improve our understanding of the mechanistic pathways involved in pancreas cancer development in germline ATM carriers and aid in the identification of targeted therapeutic strategies.

overall_design: Whole-genome sequencing, whole-exome sequencing, and RNA-sequencing were performed on PDAC tumors from 25 germline ATM PVs carriers diagnosed at Mayo Clinic between 2007 and 2017. Somatic and copy number alterations, mutational signatures, transcriptomic subtypes, and the immune landscape were evaluated.

first: Siddhartha

last: Yadav

first: Riyue

last: Bao

first: Rondell

last: Graham

first: Chunling

last: Hu

first: Steven

last: Hart

first: Jie

first: Nicholas

last: Boddicker

first: Rohan

middle: D

last: Gnanaolivu

first: James

last: Smadbeck

first: Li

last: Ding

last: Billadeau

first: Aaron

last: Mayer

first: Shounak

last: Majumder

first: Paulo

last: Lyra

first: Adrian

middle: V

last: Lee

first: Alvaro

last: Monteiro

first: Jose

middle: C

last: Villasboas

first: Robert

last: McWilliams

first: Fergus

last: Couch


title: Maternal Imprinting of Autoreactivity in a Murine Model of Systemic Lupus Erythematosus

city: Aarhus

first: Lin

last: Lin

address: Høegh-Guldbergs Gade 10

department: Department of Biomedicine

country: Denmark

institute: Aarhus University

summary: Mammals confer passive immunity upon their offspring via transplacental IgG and postnatal transfer of milk IgA. Maternofetal microchimerism and the cytokine environment in utero may also influence the developing offspring. Normally protective maternal immune factors can adversely affect the offspring in the context of maternal autoimmune disease. Here, unexpectedly, we observed maternal imprinting of autoreactivity, presenting as spontaneous germinal centers (GCs) and endogenous autoantibody production, in a murine model of systemic lupus erythematosus (SLE). Using embryo transfers to experimentally uncouple genetic from environmental maternal factors, we did not observe maternofetal microchimerism, but embryo transfer offspring of autoimmune dams received maternally derived IgG2A and anti-dsDNA antibodies. Moreover, they displayed increased formation of spontaneous GCs and elevated endogenous IgG2C autoantibody production. The neuroimmunological phenotype in offspring appeared unaffected. Taken together, our findings suggest maternal immune factors actively contribute to shape the susceptibility of offspring to autoimmune diseases independent of genetic factors.

overall_design: Two mouse with different genetic background are used in this study. For each mouse, 5' expression library, TCR and BCR library were constructed with 10xGenomics kit

first: Søren

last: E Degn


title: Full-Length Transcriptome Analysis of the Pituitary of Pre-matured and matured female Japanese eel (Anguilla japonica)

city: 厦门市

first: 天圣

last: 陈

state: 福建省

address: 印斗路43号集美大学水产学院

institute: 集美大学

summary: Japanese eel (Anguilla japonica) is a migratory fish with high economic value.    The gonads of eels cultured in captivity do not mature naturally, and under artificial ripening, their hypothalamic-pituitary-gonadal axis is activated and the maturation coefficient of the gonads is significantly increased.    Previous studies on eel breeding have focused on reproductive physiological processes, with limited insight into the molecular mechanisms in the pituitary gland that influence ovarian development.    To address these limitations, we used pituitary tissues of female Japanese eels as samples for Pacbio Iso-Seq and RNA-Seq combining analyses, selecting pre-matured (PP) and after-matured (AP) samples to investigate DEGs and signal pathways regulating gonadal development in the pituitary gland, respectively.

overall_design: Full - length transcriptome sequencing of the pituitaries of pre-matured and matured Japanese eels were carried out by combining Illumina RNA - Seq and PacBio Iso - Seq technologies.

first: Yu

last: Gao

first: Jiangling

last: Li

first: Mingxi

last: Huang

first: Wen


title: Endometrial gland secretome maintains the homeostasis of decidualization

city: Hong Kong

first: Yimeng

address: 21 Sassoon Road, Pokfulam Hong Kong

institute: The university of Hong Kong

summary: Decidualization of human endometrial stromal cells (hESCs), a critical process for embryo implantation and successful pregnancy, begins during the secretory phase of the menstrual cycle. We evaluated 25 established in vitro decidualization markers in hESCs using in vivo single-cell transcriptomic data. Most markers, including PRL and IGFBP1, did not reliably distinguish between proliferative and secretory phase hESCs, nor between decidualized and non-decidualized hESCs. Only 8 genes (STAT3, CEBPB, WNT4, IL-15, TIMP3, HAND2, FOXO1 and MMP19) showed differential expression between the menstrual phase and decidualization status in vivo. We hypothesized that the difference between in vitro and in vivo marker expression might result from the absence of endometrial glands in the in vitro decidualization model. While endometrial glands are known to secrete factors critical for uterine receptivity, their specific role in decidualization is not well understood. To investigate this, we examined the influence of the glandular secretome on ESC decidualization using an in vitro co-culture model of human endometrial organoids (hEOs) and hESCs. Decidualization was induced in hESCs, and the effects of hEO co-culture or exposure to hEO secretome were assessed by morphological analysis, molecular marker expression, and transcriptomic profiling. Unexpectedly, both hEO co-culture and exposure to the hEO secretome significantly reduce the up-regulation of canonical decidualization markers and the mesenchymal-epithelial transition typically induced during hESC decidualization. Transcriptomic analysis further revealed downregulation of decidualization regulators, CEBPA and EDN1, in ESCs exposed to the hEO secretome compared to decidualized controls. These findings were corroborated in an estradiol-stimulated mouse model, where increased endometrial gland formation correlated with reduced decidualization and lower expression of CEBPA and EDN1. Collectively, our results reveal a previously unrecognized homeostatic role for the endometrial gland secretome in regulating ESC decidualization. These insights highlight the limitations of current in vitro decidualization models and underscore the importance of glandular-stromal interactions in endometrial function and reproductive health.

overall_design: To investigate the impact of hEOs on hESC decidualization, we conducted RNA sequencing analysis on hESCs subjected to four distinct treatment conditions: (1) CTRL (hESCs cultured alone without decidualization); (2) DEC (hESCs treated with decidualization inducer); (3) D+O (decidualization induction with hEO co-culture).

first: Leqian

first: Xintong

first: Cheuk-Lun

first: Philip. C

last: Chiu


title: Supplementing CD2 expression enhances CAR-T Cell Efficacy through Optimizing CAR-immunological Synapse formation

city: Beijing

first: qi

last: zhu

state: Beijing

address: 28th Fuxing Road, Beijing, China

institute: Chinese PLA General Hospital

summary: CAR-T cell therapy has made significant strides in treating hematological malignancies, yet its efficacy is often hampered by T cells' suboptimal functionality, marked by weak antitumor capabilities and lack of durability. The immunological synapse, a key determinant of T cell function, is influenced by the CD58-CD2 axis. The dynamic regulation of CD2 expression on T cells impacts the quality of CAR-mediated synapses, affecting CAR-T cells' functional outcomes and differentiation. Our study confirmed that CD2 expression levels are closely linked to the quality of immunological synapses formed by CAR-T cells and their antitumor potency. Exogenous CD2 supplementation enhances CAR-T cells' ability to form high-quality synapses, reduces T cell exhaustion, and boosts sustained antitumor efficacy. Additionally, ectopic CD2 expression increases CAR-T cells' sensitivity to low-density antigens. Thus, replenishing CD2 in CAR-T cells is a promising strategy to enhance the therapeutic efficacy of CAR-T cell therapy.

overall_design: Gene expression profile analysis of RNA-seq data from CAR-T cells and CD2-CAR T cells after multiple rounds of antigen stimulation. Samples were collected before antigen stimulation, after 1 round of antigen stimulation, and after 3 rounds of antigen stimulation. The CAR-T cells and CD2-CAR T cells were derived from three donors.

first: Qi

last: Zhu

first: Jiajia

last: Liu

first: Lu

last: Han

first: Zhiqiang

last: Wu

first: Yao

last: Wang

first: Xin

first: Jianshu

last: Wei

first: Weidong


title: Single-cell RNA sequencing of Porphyromonas gingivalis reveals heterogeneity and rare cellular states in laboratory medium.

city: Seoul

first: Jae-Hyung

last: Lee

address: 26 Kyungheedae-ro, Dongdaemun-gu

country: South Korea

institute: Kyung Hee University

summary: Porphyromonas gingivalis is a Gram-negative anaerobic bacterium linked to chronic periodontitis and systemic diseases. Understanding its cellular heterogeneity is crucial for elucidating its adaptive mechanisms and virulence regulation. This study employs single-cell RNA sequencing using the split-pool barcoding method to capture transcriptomic variability within P. gingivalis populations. The results provide insights into gene expression diversity under laboratory growth conditions, revealing potential subpopulations that contribute to bacterial survival and pathogenicity.

overall_design: Single-cell RNA sequencing (scRNA-seq) was performed on P. gingivalis W83 using PETRI-seq, a split-pool barcoding approach optimized for bacterial transcriptomics. The bacterial culture was grown to mid-log phase, followed by fixation, permeabilization, and RNA processing. Barcoded cDNA libraries were prepared, amplified, and sequenced using the Illumina NextSeq platform. Data analysis focused on identifying distinct transcriptional states and heterogeneity within the bacterial population.

first: Ji-Hoi

last: Moon

first: Jeewan

last: Chun

first: Eun-Young

last: Jang

first: Seok Bin

last: Yang


title: Transcriptomic analysis of sarcopenic obese mice reveals alterations in regulators of muscle force production, such as extracellular matrix remodeling and shifts in muscle fiber type

city: Fayetteville

first: Eleanor

last: Schrems

state: Arkansas

address: 155 Stadium Dr.

department: Health, Human Performance, and Recreation

institute: University of Arkansas

summary: Sarcopenic obesity (SO) is the combined condition of sarcopenia and obesity most commonly occurring in the older adult population. SO is associated with poor physical function, increased risk of musculoskeletal injury, and reduced quality of life and independence. There is little information on the molecular underpinnings of this condition. The aim of this study was to provide a transcriptomic analysis characterizing SO and to provide deeper understanding to the etiology of the condition. Young (Y) (6 mo) and aged (A) (21-24 mo) mice were fed either normal chow (L) (12% kcal from fat) or high-fat (O) (60% kcal from fat) diets ad libitum. Through multiple analyses, we observed genes related to ECM remodeling are downregulated with aged-obesity compared with young obesity, providing insight to the effects of age in a life-long obese condition. Furthermore, genes related to slow-twitch muscle contraction and fast-to-slow muscle fiber type transitions were upregulated in with obesity in the aged condition. Together, our results demonstrate avenues of dysregulation in SO skeletal muscle, providing the molecular building blocks expanding our understanding of the etiology of poor muscle function in this condition. Further understanding and exploration of these dysregulations is critical to identify therapeutic treatments targeting the source of muscle functional impairment, reducing the risk of musculoskeletal injury, and improving quality of life and independence SO individuals.

overall_design: Young (Y) (6 mo) and aged (A) (21-24 mo) mice were fed either normal chow (L) (12% kcal from fat) or high-fat (O) (60% kcal from fat) diets ad libitum. Tibialis anterior muscles were collected from young and age mice at expeerimental endpoint (young: 6 months old; aged 21-24 months old). Total RNA from the Tibialis anterior muscle underwent paired end mRNA sequencing.

middle: R

first: Ana

last: Cabrera

first: Ronald

last: Jones III

first: Francielly

last: Morena

first: Kevin

middle: A

last: Murach

first: Nicholas

middle: P

last: Greene

first: Tyrone

last: Washington


title: Benefits of Maternal choline supplementation on aged basal forebrain cholinergic neurons in a mouse model of Down syndrome and Alzheimer’s disease

city: Orangeburg

first: Stephen

middle: D.

last: Ginsberg

state: New York

address: 140 Old Orangeburg Road

department: Centre for Dementia Research

institute: Research Foundation for Mental Hygiene

summary: Down syndrome (DS) stemming from triplication of chromosome 21 causes intellectual disability, with early onset of Alzheimer’s disease (AD) pathology in mid-life.  Early intervention studies to reduce cognitive impairments and onset of pathology are lacking.  One such treatment, maternal choline supplementation (MCS), has shown beneficial effects on behavior and gene expression in neurodegenerative and neurodevelopmental diseases in rodent models including DS mouse models. Basal forebrain cholinergic neuron (BFCN) degeneration and enlarged endosomal phenotype is reduced due to maternal choline supplementation (MCS) in a mouse model of Down Syndrome (Ts65Dn) with concomitant beneficial behavioral effects. However, the underlying mechanisms and gene expression alterations during aging and BFCN degeneration are understudied.  We postulate cellular mechanisms driving these alterations will be elucidated with novel therapeutic targets identified by examining the modulation in MCS treated aged DS mice.   Immunohistochemical ChAT staining in the medial septal/ventral diagonal band area of the basal forebrain in ~11 MO DS and control (2N) mice with and without MCS was performed. Approximately 500 cholinergic positive neurons per animal were microisolated for RNA-sequencing. Bioinformatic analysis elucidated gene expression alterations in the aged DS mouse model compared to controls which were attenuated by MCS treatment in the DS and control animals, including cognitive impairment and NAD signaling pathway.  In conclusion, MCS treatment shows moderate effects on gene expression in aged BFCNs, indicating that MCS prolongs the healthspan in this DS mouse model, but does not eliminate disease onset.

overall_design: Ts65Dn dams were given choline normal (1.1 g/kg; control diet) or choline supplemented (5.0 g/kg; treatment diet) chow during gestation and weaning to investigate the lifelong effects of maternal choline supplementation (MCS) in a mouse model of Down syndrome.We aged the pups to ~11MO and performed a transcardial perfusion with phosphate buffer to clear the brain of peripheral contaminants.  Brains were collected from control (2N mice) and from DS mice (Ts65Dn), flash frozen and stored at -80*C.  The brains were sectioned and mounted on LCM PEN slides and a rapid immunohistochemistry protocol was used to identify cholinergic positive excitatory neurons, while ensuring preservation of RNA integrity.  Excitatory neurons from the medial septal/ventral diagonal band region of the basal forebrain were isolated by laser capture and RNA-seq analysis was performed on the purified RNA to determine lifelong gene expression changes in the DS and control animals due to MCS treatment. (N=10-12 per genotype per dietary condition)

first: Melissa

last: Alldred

first: Harshitha

last: Pidikiti

first: Kyrillos

last: Ibrahim

first: Sanghan

first: Adriana

last: Heguy

first: Gabriela

last: Chiosis

first: Grace

middle: E

last: Stutzmann


title: Transcriptional analysis of alveolar bone, jaw and ankle joint in inflammatory arthritis

city: Dresden

first: Darja

last: Andreev

address: Fetscherstraße 105

department: Center for Regenerative Therapies Dresden (CRTD)

country: Germany

institute: Technische Universität Dresden

summary: Rheumatoid arthritis (RA) and other inflammatory arthritides are chronic joint diseases marked by inflammation and bone erosion, leading to progressive damage. While smaller joints are typically affected early, larger joints often become involved over time. Temporomandibular joint (TMJ) involvement occurs in over 50% of arthritis patients, causing severe jaw pain and functional impairment, yet it remains underrecognized and underresearched. Due to its unique mechanical and biological features, the TMJ may exhibit distinct pathomechanisms compared to other joints. To investigate these differences, we analyzed transcriptomic profiles of the TMJ, ankle joint, and alveolar bone in polyarthritic hTNF-α transgenic mice (hTNF-tg) and controls.

overall_design: RNA was extracted from the ankle joint, TMJ, and alveolar bone of hTNF-tg mice (strain Tg197 on a C57BL/6 background, n=4) and littermate controls (n=4). Female mice were analyzed at 11 weeks of age.

first: Pauline

last: Porschitz


title: Role of ADAR1 on transcriptional output in cancer cells

city: Shanghai

first: Zhibo

last: Shao

institute: Fudan University Shanghai Cancer Center

summary: The loss of ADAR1 significantly reduced ribosome production, decreased tumor translational efficiency, and impaired the translation of oncogenic pathways.

overall_design: RNA-Seq was performed in ADAR1-overexpressing and control MDA-MB-231 xenografts, with or without CX-5461 treatment.

first: Xuliren

last: Wang

first: Qi

last: Zhang

first: Jiong

last: Wu


title: Circulating microRNA profiles in early-stage osteoarthritis and rheumatoid arthritis

city: Detroit

first: Shabana Amanda

last: Ali

state: Michigan

address: Integrative Biosciences Center, 6135 Woodward Avenue

department: Bone and Joint Center

institute: Henry Ford Health + Michigan State University Health Sciences

type: Non-coding RNA profiling by high throughput sequencing

summary: Osteoarthritis (OA) and rheumatoid arthritis (RA) are prevalent forms of arthritis. Early detection of OA and RA is challenging with existing methods, which can delay effective management. MicroRNAs are small molecules that have emerged as promising disease biomarkers with the potential to improve early detection and differentiation of arthritis subtypes. In this study we aimed to identify distinct circulating microRNAs in plasma from individuals with early OA and early RA, using an unbiased microRNA-sequencing approach.  For microRNA-sequencing, plasma samples were collected from three study groups including: (a) early OA (N=12), individuals with knee OA symptoms and radiographic Kellgren-Lawrence grade 0 or 1; (b) early RA (N=6), treatment-naïve individuals with <6 months of RA symptoms in any joint; and (c) non-OA/RA (N=44), individuals with no history of arthritis.  RNA isolated from N=62 plasma samples was sequenced using a 75-base single-end read protocol at a depth of approximately 17 ± 2.5 million reads/sample on an Illumina NextSeq2000 sequencer, followed by analysis for known and novel microRNAs using a previously optimized pipeline.

overall_design: Highthroughput sequencing to profile plasma microRNAs in individuals with early osteoarthritis (OA), and early rheumatoid arthritis (RA), as well as non-OA/RA controls.

first: Madhu

last: Baghel

first: Thomas

last: Wilson

first: Michelle

last: Ormseth

first: Patrick

last: Yousif

first: Ayad

last: Alkhatib

first: Alireza

last: Meysami

first: Jason

last: Davis

first: Vasilios

last: Moutzourous

first: Shabana


title: Ribo-ITP coupled ribosome profiling identifies non-canonical translational events in low input samples

first: Vighnesh

last: Ghatpande

overall_design: In the last decade,  an unexpectedly large number of translated regions (translons) have been discovered using ribosome profiling and proteomics. Translons can regulate mRNA translation and encode micropeptides that contribute to multiprotein complex formation, Ca2+ regulation in muscle, and signaling during embryonic development. However, identification of translons has been limited to cell lines or large organs due to high input requirements for conventional ribosome profiling and mass spectrometry. Here, we employed Ribo-ITP, a low input ribosome profiling technique on difficult to collect samples like microdissected hippocampal tissues and single pre-implantation embryos. We detected thousands of translons across these samples, most of which initiated at non-canonical start sites, were less than 100 amino long with significantly altered amino acid composition. Comparative analysis of more than a thousand ribosome profiling datasets across a wide range of cell types revealed pervasive expression of most of the detected translons. To test the translational capacity of the detected translons, we engineered a translon dependent GFP reporter system, and detected robust expression of translons initiating at near-cognate start codons in mouse embryonic stem cells (mESCs). Mutating the translons in mESCs identified a small proportion that negatively impacted growth. Taken together, we present a proof-of-concept study to identify non-canonical translation events from ultra-low input samples which can be applied to cell and tissue types inaccessible to conventional methods.

first: Uma

last: Paul

first: Mackenzie

last: Howard

first: Can

last: Cenik


title: Isolation of mitochondrial mutation-specific T-cell receptors

city: Little Rock

first: Yong-Chen

middle: William

last: Lu

address: 4301 W Markham St

department: Pathology

institute: University of Arkansas for Medical Sciences

summary: It has been hypothesized that neoantigen-specific T cells play a major role in effective cancer immunotherapy, including neoantigen vaccines, immune checkpoint blockade (ICB) therapy, and adoptive T cell therapy using tumor-infiltrating lymphocytes (TILs). The major source of neoantigens are mutated proteins derived from non-synonymous mutations found in tumor genomic DNA. It’s highly conceivable that non-synonymous mutations found in tumor mitochondrial DNA (mtDNA) can also generate neoantigens that can be recognized by T-cell receptors (TCRs). This project contains two types of single-cell data. One is single-cell CITEseq (5' mRNA plus antibody feature barcode plus TCR) seqeuncing to identify antigen-specific TCRs. The other is single-cell ATAC-seq to detect chromatin accessiblities and mtDNA.

overall_design: For single-cell RNA/TCR-seq, unstimulated and stimulated T cells from donor D1 were labeled with anti-human TotalSeq-C Hashtag #4 and #5 antibody (Biolegend), respectively. Single-cell CITEseq (5' immune profing, 5' mRNA, antibody feature barcode and TCR) was performed for one pooled sample, according to manufacture's instruction (10X Genomics). The TCR and gene expression (GEX) libraries were sequenced by an Illumina Novaseq 6000 sequencer. The Feature Barcode library for hashtags was sequenced by an Illumina iSeq 100 sequencer. The sequencing data was processed by a Cell Ranger-multi pipeline (v7.1.0; 10X Genomics). The gene expression (GEX) sequencing data was mapped to the standard reference genome database (GRCh38-2020-A, 10X Genomics), and the TCR sequencing data was also mapped to the standard reference genome database (GRCh38-alts-ensembl-7.1.0, 10X Genomics).  For single-cell ATAC-seq, tumor cells and PBL from 4 patients (P1, P2, P3 and P4) were subjected to single-cell ATAC-seq sequencing (10X Genomics). The prepared samples were sequenced by an Illumina Novaseq 6000 sequencer. The sequencing data was processed a Cell Ranger-ATAC pipeline (v2.1.0; 10X Genomics) and mapped to reference genome database (GRCh38-r107).

first: Catherine

last: Kirkpatrick

first: Shanshan

last: Hao

first: Charles

middle: M

last: Quick

first: Steven

last: Post

first: Yuet-Kin

last: Leung

first: Lyle

last: Burdine


title: A hypoxia-responsive tRNA-derived small RNA confers renal protection via RNA autophagy

city: Boston

first: Guoping

last: Li

state: MA

address: Cardiovascular Research Center, 185 Cambridge St, Simches 3.5000

department: CVRC

institute: Massachusetts General Hospital

summary: Emerging studies have revealed diverse cellular functions of tRNA-derived small RNAs (tsRNAs, or tDRs). Here, we show that a hypoxia-induced tDR, derived from the 3’ end of tRNA-Asp-GTC (tRNA-Asp-GTC-3’tDR), activates, while its inhibition blocks autophagic flux in kidney cells. Functional gain/loss-of-function studies in murine kidney disease models demonstrate a significant reno-protective function of tRNA-Asp-GTC-3’tDR. Mechanistically, tRNA-Asp-GTC-3’tDR assembles stable G-quadruplex structures and sequesters pseudouridine synthase PUS7, preventing catalytic pseudouridylation of histone mRNAs. The resulting pseudouridylation deficiency directs histone mRNAs to the autophagosome-lysosome pathway, triggering RNA autophagy. We confirm this tDR-induced RNA autophagy pathway in murine and human kidney diseases. Together, our findings identify a novel role for tRNA-Asp-GTC-3’tDR in regulating RNA autophagy in kidney cells to maintain homeostasis and protect against kidney injury.

overall_design: Long RNA-seq profiling HEK cells transfected with a 3' tRNA-Asp tDR or scrambled control.

first: Lingfei

last: Sun

first: Cuiyan

last: Xin

first: Tian

first: Prakash

last: Kharel

first: Aidan

last: Manning

first: Christopher

middle: L

last: O'connor

first: Henry

last: Moore

first: Shuwen

last: Lei

first: Priyanka

last: Gokulnath

first: Xinu

last: Yang

first: Ritin

last: Sharma

first: Krystine

last: Garcia-Mansfield

first: Priyadarshini

last: Pantham

first: Chunyang

last: Xiao

first: Hanna

middle: Y

last: Wang

first: Emeli

last: Chatterjee

first: Seungbin

last: Yim

first: Leo

middle: B

last: Ren

first: Michail

last: Spanos

first: Hua

last: Zhu

first: Haobo

first: Ji

first: James

middle: F

last: Markmann

first: Louise

last: Laurent

first: John

middle: J

last: Rossi

first: Oluwaseun

last: Johnson-Akeju

first: Quanhu

last: Shen

first: Ravi

last: Shah

first: William

last: Goddard III

first: Todd

last: Lowe

first: Pavel

last: Ivanov

first: Patrick

last: Pirrotte

first: Markus

last: Bitzer

first: Joseph

last: Bonventre

first: Saumya

last: Das


title: Role of ADAR1 and NOP14 on transcriptional output in cancer cells

first: Zhibo

last: Shao

summary: The loss of ADAR1 significantly reduced ribosome production, decreased tumor translational efficiency, and impaired the translation of oncogenic pathways. And NOP14 significantly upregulated ribosome production and tumor translational efficiency.

overall_design: RNA-Seq was performed in control siRNA and ADAR1 siRNA cells. RNA-Seq was performed in NOP14-overexpressing and control MDA-MB-231 cells.

first: Xuliren

last: Wang

first: Qi

last: Zhang

first: Jiong

last: Wu


title: Development of long non-coding RNA (LncRNAs) signature for T-DM1 treatment outcome

city: Riyadh

first: Syed

middle: S

last: Islam

address: Thakkassassi Street

department: Molecular Oncology

country: Saudi Arabia

institute: King Faisal Specialist Hospitalm Research Center

summary: To extend our understanding of the role long non-coding RNAs in treatment outcome, we have analyzed microarray expression profiling as a discovery platform to identify  LncRNAs  for distinguishing patients who response to T-DM1 for decision making segregation of patients who to reveice further treatment.  Blood samples from HER2-positive metastatic breast cancer patients were collected, and a 4-lncRNA signature was identified that distinguished bwteen treatment resistant and sensitive patients.

overall_design: Gene expression profiling from blood serum was analyzed from 10 T-DM1 resistant and 10 T-DM1 sensitive patients

first: Abdelillah

last: Aboussekhra


title: Enhancer distance matters: forced linear recruitment of a super-enhancer strongly reactivates the developmentally silenced fetal HBG globin genes [CutnRun]

city: Utrecht

first: Richard

last: Gremmen

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

summary: The human genome contains regulatory DNA elements (enhancers, silencers, insulators) that can recruit proteins to activate or repress transcription of distal genes. Interspersed are DNA intervals without any known coding or regulatory capacity. Here, we show that these intrinsically non-regulatory DNA stretches can allow gene silencing by keeping enhancers at distance. During development, the fetal globin HBG genes recruit activated repressor proteins to their promoters. This enables the HBG genes to silence and ignore the distal super-enhancer, which subsequently acts on and activates the downstream adult HBD and HBB genes. We found that forced linear recruitment of the super-enhancer, bringing it immediately upstream of the otherwise intact HBG gene promoters, results in significant HBG reactivation and partial HBB inactivation in adult erythroid cells and ex vivo differentiated human hematopoietic stem and progenitor cells. Forced HBG reactivation is accomplished by CRISPR-Cas9 deletions of the intervening 25 kilobases sequence interval. Additionally, it can be achieved by inversions that leave this interval intact and proximal, but no longer situated between the enhancer and HBG genes. We conclude that the HBG genes must be at substantial linear distance to bypass activation by the super-enhancer and activate their promoter-encoded silencing program in adulthood. Overall, this assigns a functional role to seemingly non-regulatory segments in our genome: by providing linear separation they may support genes to autonomously control their transcriptional response to distal enhancers.

overall_design: CRISPR/Cas9 edits in the Beta-Globin locus were performed in Hudep-2 cell line. CutnRun with an antibody against H3K4me3 was performed in two idenpendant clones to investigate changes in the histone mark in the Beta-Globin locus. Published control guides and WT were used as controls.

first: Anna-Karina

last: Felder

first: Rezin

last: Majied

first: Han

last: Verhagen

first: Marjon

last: Verstegen

first: Thijs

last: Verheul

first: Rebecca

last: Mohnani

first: Peter

middle: H

last: Krijger

first: Sjaak

last: Philipsen

first: Emile

last: van den Akker

first: Wouter

last: de Laat


title: Enhancer distance matters: forced linear recruitment of a super-enhancer strongly reactivates the developmentally silenced fetal HBG globin genes [ATAC]

overall_design: CRISPR/Cas9 edits in the Beta-Globin locus were performed in Hudep-2 cell line. ATAC-seq was performed in two idenpendant clones to investigate changes in accessibilty in the Beta-Globin locus. Published control guides and WT were used as controls.


title: TSLP acts on Tregs to limit allergic inflammation and to maintain Treg identity

city: Bethesda

first: Jyothi

last: Padiadpu

state: MD

address: 9000 Rockville Pike

department: NHLBI

institute: NIH

summary: Thymic stromal lymphopoietin (TSLP) is a type I cytokine that promotes allergic responses and mediates type 2 immunity. A balance between effector T cells (Teff), which drive the immune response, and regulatory T cells (Tregs), which suppress the response, is required for proper immune homeostasis. Here, we report that TSLP differentially acts on Teff versus Tregs to balance type 2 immunity. As expected, deletion of TSLPR on all T cells (Cd4CreCrlf2fl/fl mice) resulted in lower numbers of Th2 cells and diminished ovalbumin-induced airway inflammation, but selective deletion of TSLPR on Tregs (Foxp3YFP-Cre/YCrlf2fl/fl mice) resulted in increased IL-5- and IL-13-secreting Th2 cells and lung eosinophilia. Moreover, TSLP augmented the expression of factors that stabilize Tregs, and remarkably, during type 2 immune responses, TSLPR-deficient Tregs acquired Th2-like properties, with augmented levels of GATA3 and secretion of IL-13. Thus, TSLP not only is a driver of Th2 effector cells, but it also acts in a negative feedback loop, promoting the ability of Tregs to limit allergic inflammation.

overall_design: Treg cells from pooled lymph nodes and spleen of CD45.2 Foxp3YFP-Cre/Y mice or Foxp3YFP-Cre/YCrlf2fl/fl mice were sorted as live CD4+YFP+ population and used for RNA extraction

first: Rama

middle: K

last: Gurram

first: Peng

last: Li

first: Jangsuk

last: Oh

first: Xi

last: Chen

first: Rosanne

last: Spolski

first: Xianglan

last: Yao

first: Jian-Xin

last: Lin

first: Suyasha

last: Roy

first: Matthew

last: Liao

first: Chengyu

last: Liu

first: Zu-Xi

last: Yu

first: Stewart

last: Levine

first: Jinfang

last: Zhu

first: Warren

last: Leonard


title: ChIP-seq on KDM6A 786O cells

first: Hua

last: Wang

address: 38 Xueyuan Rd

institute: Peking University

summary: Here, we showed that KDM6A, an oxygen-dependent member of the histone demethylase family, regulates ferroptotic cell death by modulating expression of the critical ferroptosis effector.

overall_design: KDM6A KO in 786O cell line

first: Xuejun

last: Jiang


title: Transcriptomic changes in lens epithelial cells at 72 hours post cataract surgery

city: Newark

first: Suhotro

last: Gorai

state: Delaware

address: 153 Courtney St

institute: University of Delaware

summary: This trancriptomic analysis describes the gene expression changes observed in wildtype lens epithelial cells (LECs) by 72 hours compared to zero hours post cataract surgery

overall_design: Cataract surgery experiments were conducted in mice according to the following procedure. The fiber cell mass was surgically removed from the lens of one eye via an anterior incision, leaving the lens capsule and associated LEC inside the eye.  72 hours later the procedure was repeated on the second eye, the mouse was sacrifieced and both lens capsules were harvested.  Each biological sequencing replicate consisted of 5 capsules from one interval as described above. Three biological replicates were sequenced for each interval. Samples were sequenced in 2021.

first: Samuel

middle: G

last: Novo

first: Adam

last: Faranda

first: Melinda

last: Duncan


title: Single-cell transcriptomic profile of CD45+ cells in atherosclerotic plaques of mice with myeloid-specific Lipa overexpression and on Ldlr-/- background [scRNA-seq]

city: New York

first: Fang

last: Li

state: NY

department: Medicine

institute: Columbia University Irving Medical Center

summary: Macrophages within atherosclerotic plaques display significant heterogeneity. We used single-cell RNA-sequencing (scRNA-seq) to analyze the relative abundance and  transcriptomic signature of macrophage subclusters in atherosclerotic aortas of mice with myeloid-specific Lipa overexpression on the Ldlr-/- background and fed a Western diet for 16 weeks.

overall_design: We generated mice for Lipa overexpression (LipaTg/wt) on C57BL/6 background by inserting Lipa open reading frame (NM_001111100) into the Rosa26 locus. To achieve myeloid-specific Lipa overexpression, we bred LipaTg/Tg, Ldlr-/- mice with LysMCre+/-, Ldlr-/- mice. The LysMCre+/-, LipaTg/wt, Ldlr-/- mice (LipaTg) demonstrate myeloid-specific Lipa overexpression, where eGFP acts as a marker for cells with successful cre-loxp recombination leading to subsequent Lipa overexpression. Aortas were harvested from LipaTg mice fed a Western diet for 16 weeks and subsequently enzymatically digested into single cells. Given that LysMCre-mediated recombination is not 100% for transgenic overexpression,  we leveraged this feature to sort CD45+eGFP- plaque cells (no Lipa overexpression) and CD45+eGFP+ plaque cells (with Lipa overexpression) dissociated from aortas of LipaTg mice. These sorted CD45+GFP- and CD45+GFP+ cells, pooled from five male mice, were subjected to scRNA-seq immediately.

first: Chenyi

last: Xue

first: Hanrui

last: Zhang


title: TMEM106B coding variant is protective and deletion detrimental in a mouse model of tauopathy

city: St. Louis

first: Joanna

last: Jankowsky

state: MO

address: 660 S. Euclid Ave.

department: Neuroscience

institute: Washington University in St. Louis

summary: TMEM106B is a risk modifier for a growing list of age-associated dementias including Alzheimer's and frontotemporal dementia, yet its function remains elusive. Two key questions that emerge from past work are whether the conservative T185S coding variant found in the minor haplotype contributes to protection, and whether the presence of TMEM106B is helpful or harmful in the context of disease. Here we address both issues while extending the testbed for study of TMEM106B from models of TDP to tauopathy. We show that TMEM106B deletion accelerates cognitive decline, hindlimb paralysis, neuropathology, and neurodegeneration. TMEM106B deletion also increases transcriptional overlap with human AD, making it a better model of disease than tau alone. In contrast, the coding variant protects against tau-associated cognitive decline, neurodegeneration, and paralysis without affecting tau pathology. Our findings show that the coding variant contributes to neuroprotection and suggest that TMEM106B is a critical safeguard against tau aggregation.

overall_design: Two cohorts were studied, each containing 4 genotypes of mice.The first cohort was generated by intercrossing TMEM106B tm2d deletion mice with MAPT-P301S transgenic mice (line PS19).The second cohort was generated by intercrossing TMEM106B T186S knockin mice with MAPT-P301S transgenic mice (line PS19).Two variables are tested in each cohort.Variable number 1 is the TMEM106B genotype:WT, KO, or KI.KO and KI mice are homozygous for the respective allele.Variable number 2 is the presence or absence of transgenic MAPT (tau). Tau mice are heterozygous for the MAPT transgene."_O" or "_I" designation is used when a shared genotype (WT or tau alone) arose from the KO or KI colony, respectively.Both cohorts were bred on a hybrid C3B6 strain background.

first: George

last: Edwards III


title: Decoding the Variant-to-Function Relationship for LIPA, a Risk Locus for CAD

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

overall_design: Refer to individual Series


title: PATCH treatment in vivo

status: Public on Aug 04 2025

first: Shuo

last: Han

address: 320 Yue Yang Road, Shanghai

institute: Shanghai Institute of Biochemistry and Cell Biology

summary: After establishing a subcutaneous 4T1 tumor model in mice, we conducted PATCH treatment using HA-PCN. Tumors were harvested post-treatment for single-cell RNA sequencing to analyze cellular and transcriptional changes within the tumor microenvironment.

overall_design: The experiment included an experimental group and a control group.  In the control group, PBS was used in place of PATCH


title: Transcriptomic changes in lens epithelial cells at 5 days post cataract surgery

summary: This trancriptomic analysis describes the gene expression changes observed in wildtype lens epithelial cells (LECs) by 5 days compared to zero hours post cataract surgery

overall_design: Cataract surgery experiments were conducted in mice according to the following procedure. The fiber cell mass was surgically removed from the lens of one eye via an anterior incision, leaving the lens capsule and associated LEC inside the eye.  5 days later the procedure was repeated on the second eye, the mouse was sacrifieced and both lens capsules were harvested.  Each biological sequencing replicate consisted of 5 capsules from one interval as described above. Three biological replicates were sequenced for each interval. Samples were sequenced in 2019.

first: Mahibabul

last: Shihan


title: The Dual Role of CREPT in Glioblastoma: Promoting Proliferation and Shaping an Immunosuppressive Microenvironment through Chemo-MO and GZMK⁺ T Cell Interaction

city: Chongqing

first: Guanhu

address: No. 313, Jinyue Road,High‑Tech Zone

institute: Jinfeng Laboratory

summary: Elevated CREPT promotes tumor cell proliferation and enhances CCL2 secretion, thereby recruiting Chemo-MOs. These Chemo-MOs then engage in regulatory interactions with GZMK+CD8+ T cells, suppressing T cell infiltration and ultimately establishing a robust immunosuppressive microenvironment.

overall_design: RNA-seq profiling of wildtype U87MG cells and their knockdown derivatives(shCREPT)

first: Jianghua

first: Shuai

first: He

last: Yang

first: Jiayu

first: Umar

last: Farooq

first: Bochen

first: Jun

first: Xiaotong

first: Zhijie

last: Chang


title: Single-cell RNA Sequencing Reveals Immune Cell Alterations in Patients with Allergic Rhinitis Treated with Peiyuan Tongqiao Decoction

city: Zhengzhou City

first: Jingbo

state: Henan Province

address: No. 6, Dongfeng Road

department: Department of Otorhinolaryngology

institute: Henan Province Hospital of Traditional Chinese Medicine

summary: Allergic rhinitis (AR), a chronic inflammatory disorder with complex causative mechanisms,  threat to human physical and mental health. Traditional Chinese medicine (TCM) are gaining attention due to their potential ability to treat AR. The aim of this study was to elucidate biological activity of Peiyuan Tongqiao Decoction that can act on the different processes of AR through cell abundance, DEGs, pathways and transcription factors (TFs) through single-cell RNA sequencing (scRNA-seq)

overall_design: PBMCs from pre-treatment group and post-treatment group of AR patients were obtained and used to construct single-cell RNA sequencing (scRNA-seq) libraries

first: Li

last: Jingbo

first: Lu

last: Yinian

first: Wang

last: Junjie

last: Yan

first: Cao


title: Effect of overexpression of VGF on gene expression  of A549 and H1299 NSCLC cells

city: shenyang

first: Xinyue

last: Sheng

state: liaoning

address: No.77 Puhe Road, Shenyang North New Area, Shenyang, Liaoning Province, P.R. China

institute: china medical university

summary: This study investigates the transcriptional changes induced by VGF overexpression in A549 and H1299 NSCLC cell lines. RNA-seq was performed on cells transfected with a VGF lentivirus or an empty vector control. The goal is to identify dysregulated genes and pathways mediated by VGF overexpression in lung cancer cells.

overall_design: A factorial design was employed with two cell lines (A549, H1299) and two treatment conditions (VGF OE vs. Empty vector). For each cell line and condition, 3 biologically independent replicates were analyzed.

first: Yibei

last: Wang

first: Bo


title: Effector differentiation and therapeutic reinvigoration of CD8+ T cells in chronic infection depend on KLF2-directed lymph node homing

city: Melbourne

first: Daniel

last: Rawlinson

state: Victoria

address: 792 Elizabeth St

department: Department of Microbiology and Immunology

country: Australia

institute: University of Melbourne

summary: In this study, we examine the heterogeneity and molecular regulation of CD8 T cells in chronic infection across lymph nodes and spleen. We find that lymph nodes, not the spleen, support the stemness and polyfunctionality of CD8 T cells and their response to PD-1 blocking therapy. We discover that the transcription factor KLF2 is specifically expressed in and required for stem-like precursor and effector-like T cells. Finally, we show that migratory dendritic cell in the lymph nodes support the differentiation and function of CD8 T cells.

overall_design: LCMV-specific P14 transgenic CD8 T cells were transferred into C57B6 mice before infection with chronic LCMV Docile. At day 21 post infection, P14 cells were sorted from the spleens and LNs of these mice and scRNAseq performed. At day 21 post infection, P14 cells were sorted from the spleens and LNs of these mice and scRNAseq performed. To ensure sufficient representation of stem-like cells, we also enriched for Ly108+TIM3- cells. In some experiments KLF2-deficient and control P14 cells were generated using CRISPR/Cas9 technology, subjected to an infection experiment and RNAseq performed as above. Finally, sorted MHC2+/CD11c+ antigen presenting cells from spleen and LN of LCMV Docile infected mice and performed scRNAseq.

first: Carlson

last: Tsui

first: Leonie

last: Heyden

first: Axel

last: Kallies

first: Jan

last: Schroeder


title: Transcriptomic profiling of LNCaP cells treated with enzalutamide, olaparib, or combination across multiple time points

city: Cambridge

first: Robert

last: Hanson

address: Hills Rd

department: Oncology

institute: Early Cancer Institute

summary: To explore the mechanisms underpinning the combinatorial effects of androgen pathway and PARP inhibition on global gene expression in prostate cancer, we performed RNA sequencing analysis in LNCaP prostate cancer cells. Cells were treated with either single agents or the combination, and transcriptomic changes were asssed at early (8 hours), intermediate (24 hours), and late (72 hours) timepoints to assess temporal dynamics of treatment response. Comparative analyses between single-agent and combination treatments enabled the characterisation of transcriptional programs induced by the combinatorial regimen.

overall_design: LNCaP cells were treated with 3 μM olaparib, 3 μM enzalutamide, or the combination, with each condition performed in triplicate cultures and incubated for 8, 24, or 72 hours prior to RNA extraction, library preparation, and high-throughput sequencing.

first: Harveer

last: Dev

first: Charles

last: Massie

first: Giuditta

last: Illuzzi

first: Alessandro

last: Galbiati

first: Josep

middle: V

last: Forment


title: Evidence of emerging transcriptome mediators of Alzheimer's disease in canine cognitive dysfunction

city: Fort Collins

first: Cali

middle: Madison

last: McEntee

state: CO

address: 910 Moby Dr

department: Health and Exercise Science

institute: Colorado State University

summary: Growing data suggest companion dogs may be a promising model of human brain aging and Alzheimer’s disease (AD). However, while pathology is similar in AD and canine cognitive dysfunction (CCD), the transcriptomic similarities between these two conditions have not been thoroughly evaluated. Two emerging transcriptome-related mechanisms of brain aging and AD involve transposable elements (TEs) and microRNAs (miRNAs), which have the potential to be carried systemically and between cells by extracellular vesicles (EVs). To determine if evidence of these AD-related transcriptomic events might be present in CCD, we generated total transcriptome (RNA-seq) data on cortex tissue and plasma EVs from young, old, and old CCD dogs. We show that: 1) global transcriptome changes with CCD indicate reduced neuronal health; 2) TE transcripts increase with CCD in both the brain and plasma EVs; 3) brain- and disease-relevant miRNAs are present in the same EVs, and some of these miRNAs correlate with indices of cognitive function/CCD. Collectively, our data suggest that transcriptomic changes in the dog, including those related to novel RNA mechanisms of brain aging and disease, are similar to those observed in humans.

overall_design: RNA-seq of RNA isolated from prefrontal cortex and plasma extracellular vesicles (EVs) of young, old, and canine cognitive dysfunction companion dogs

first: Shelby

middle: C

last: Osburn

first: Thomas

last: LaRocca


title: Enhanced efficacy of a specific HDAC3 inhibitor in combination with 5-Azacitidine against diffuse large B-cell lymphoma [RRBS]

city: Nice

first: Pilar

last: Dominguez

state: Provence-Alpes-Côte d'Azur

address: 151 Route de Saint-Antoine

institute: Centre Méditerranéen de Médecine Moléculaire: C3M

summary: Diffuse large B-cell lymphoma (DLBCL) refers to an aggressive lymphoma that arises from germinal center (GC) B-cells, which differentiate into plasma cells (PC) to produce high affinity antibodies. 40% of DLBCL patients relapse or are refractory to the conventional immunochemotherapy treatment, usually with fatal consequences. DLBCL is characterized by profound alterations in the epigenome, which is correlated with poor survival. The abnormal epigenetic landscape of DLBCL tumors is associated with a blockade in GC exit and differentiation programs, which are regulated by the transcription factor BCL6. This aberrant repression of BCL6-target genes is mediated by 1) increased DNA methylation and 2) loss of acetylation of the lysine 27 of histone 3 (H3K27ac)-through recruitment of histone deacetylase 3 (HDAC3). Thus, we investigated the efficacy against DLBCL of the hypomethylating agent (HMA) 5-Azacitidine (5-Aza) and a specific HDAC3 inhibitor (HDAC3i). We found that treatment with 5-Aza plus HDAC3i had a potent synergistic anti-tumor activity in vitro and in vivo, which was superior to the effect of each single drug or 5-Aza combined with non-specific HDACi and, importantly, was not associated with toxicity in normal cells. We also demonstrated that the combined 5-Aza and HDAC3i treatment induced the epigenetic remodeling of DLBCL cells, which resulted in a more potent re-expression of PC differentiation genes, including XBP1 and ATF4, compared to each drug used as single agents. Our results highlight the importance of specifically targeting multiple layers of the epigenome to maximize the efficacy of epigenetic-based therapies.

overall_design: MD901 lymphoma cells were treated with  5-Azacitidine (or vehicle) daily for 5 days, with a HDAC3 inhibitor (or vehicle) added at day 2 and 4. Cells were analyzed at day 5 (3 replicates per group).

first: Emilio Manuel

last: Serrano-Lopez

first: Matt

middle: R

last: Teater

first: Killian

last: Guiraud

first: Francisco

last: Huertas-Lopez


title: Direct and indirect regulation of fetal globin transcript by RNA-binding protein IGF2BP1

first: Steven

last: Coyne

address: 1 Blackfan Ave. Karp Building RB8005G Karp Building RB8005G

department: Dept. of Hematology/Oncology

institute: Boston Children's Hospital

summary: Despite extensive investigation, mechanisms of developmental hemoglobin expression remain incompletely understood. Hemoglobin switching is controlled by transcription factors, miRNAs, and RNA-binding proteins (RBPs) that enforce gene regulatory changes through development. Here we examine the role of the heterochronically silenced N-6 methyladenosine (m6A) RNA-binding protein, IGF2BP1 that was previously described to regulate HBG1/2 indirectly by suppressing BCL11A expression through a poorly understood mechanism. We find that IGF2BP1 binds and activates HIC2, itself a BCL11A repressor. Furthermore, we identify that IGF2BP1 plays a BCL11A-independent role by direct binding to HBG1/2 to promote its translation. Stop codon-proximal m6A-modified coding sequences within HBG2 transcripts are necessary and sufficient for direct positive regulation mediated by IGF2BP1. Together this work deepens the mechanistic understanding of hemoglobin switching and suggests a physical relationship between heterochronic RBPs and globin transcripts.

overall_design: HUDEP-2 cells were treated with a lentiviral overexpression vector for IGF2BP1, an empty control vector, or untreated. These HUDEP-2 cells as well as wild-type HUDEP-1 cells were then differentiated for 8 days in erythroid differentiation media (EDM-II) before RNA was collected and RNAseq was paired-end RNAseq was performed with truseq adapters. Additionally, we performed RNAseq from in vitro erythroid differentiated primary cells isolated from adult bone marrow, cord blood, or fetal liver CD34+ hematopoietic stem and progenitor cells (HSPCs). Samples were quantitated using salmon and resulting counts were used for differential gene expression analysis using DEseq2.

first: Mir

last: Hossain

first: Daniel

last: Bauer


title: Enhanced efficacy of a specific HDAC3 inhibitor in combination with 5-Azacitidine against diffuse large B-cell lymphoma [ChIP-seq]

first: Izabela

last: Todorovski


title: The effects of myeloid-specific Lipa overexpression on the transcriptomic profile of peritoneal macrophages in Ldlr-/- mice [PM_RNAseq]

first: Fang

last: Li

summary: We analyzed the transcriptomic profile of peritoneal macrophages (PMs) directly sorted from two groups of mice fed a Western diet for 16 weeks: (1) mice with LysMCre-mediated myeliod-specific Lipa overexpression on the Ldlr-/- background; (2) littermates that are LysMCre-negative and are on the Ldlr-/- background.

overall_design: We generated mice for Lipa overexpression (LipaTg/wt) on C57BL/6 background by inserting Lipa open reading frame (NM_001111100) into the Rosa26 locus. To achieve myeloid-specific Lipa overexpression, we bred LipaTg/Tg, Ldlr-/- mice with LysMCre+/-, Ldlr-/- mice. The obtained LysMCre+/-, LipaTg/wt, Ldlr-/- (LipaTg) and LysMCre-/-, LipaTg/wt, Ldlr-/- (Ctl) littermates were fed a Western diet for 16 weeks. The LipaTg mice demonstrate myeloid-specific Lipa overexpression, where eGFP acts as a marker for cells with successful cre-loxp recombination leading to subsequent Lipa overexpression. The viable CD45+F4/80+ PMs from Ctl mice and CD45+F4/80+eGFP+ PMs from LipaTg mice were sorted and directly subjected to RNA-seq without culturing. n = 3 female mice per genotype.

first: Chenyi

last: Xue

first: Hanrui

last: Zhang


title: Enhanced efficacy of a specific HDAC3 inhibitor in combination with 5-Azacitidine against diffuse large B-cell lymphoma [MAC-seq]

overall_design: MD901 lymphoma cells were treated with  5-Azacitidine (or vehicle) daily for 5 days, with a HDAC3 inhibitor, panobinostat or vorinostat (or vehicle) added at day 2. Cells were analyzed at day 4 (3 replicates per group).