title: Adipocyte- Specific FFA2 Deletion Leads to Increased Adipose Inflammation and Is Associated with Altered Intestinal Lipid Handling [jejunum_RNAseq]

city: Chicago

first: Chioma

last: Nnyamah

state: Illinois

address: 840 South Wood Street, Suite 1020N, MC 787

institute: University of Illinois at Chicago

summary: Obesity and related metabolic disorders are often characterized by chronic adipose tissue inflammation, driving systemic insulin resistance and general metabolic dysfunction. Free Fatty Acid Receptor 2 (FFA2) has emerged as a potential modulator of adipocyte function, inflammation, and metabolism. To investigate the role of FFA2 expressed in the adipose tissue, we generated adipose-specific FFA2 knockout mice (Adipoq-F2-KO) and assessed metabolic outcomes under standard chow and high-fat, high-sugar Western diet conditions, with and without dietary fiber supplementation. We found that adipose-specific FFA2 deletion had minimal metabolic consequences under standard dietary conditions but significantly reduced body weight and adiposity when mice were fed a fiber (fructooligosaccharide)-supplemented Western diet. Subsequent fecal analyses and transcriptomic profiling indicated impaired intestinal lipid absorption as the primary driver of reduced adiposity, suggesting disrupted adipose-intestinal communication. Unexpectedly, the lighter Adipoq-F2-KO mice also exhibited heightened adipose inflammation, characterized by increased macrophage infiltration and pro-inflammatory cytokine expression. Furthermore, in vitro loss-of-function experiments in adipocytes revealed that FFA2 knockdown impaired adipocyte maturation, lipid storage, and anti-inflammatory signaling. Additional studies using intestinal epithelial cells exposed to adipocyte-conditioned media implicated adipose-derived signals in driving intestinal dysfunction. Collectively, our findings highlight adipose-specific FFA2 as critical in regulating adipose tissue inflammation, lipid metabolism, and inter-organ communication. The data uploaded here specifically contains the comparison of mRNA from mature white adipocytes of FFA2 fl/fl mice compared to RNA from Adipoq-F2-KO mice when both are on a normal chow diet.

overall_design: This RNA sequencing dataset was generated to examine intestinal transcriptomic changes associated with adipose-specific deletion of Free Fatty Acid Receptor 2 (FFA2) in mice exposed to a Western diet supplemented with dietary fiber. Male Adipoq-F2-KO mice were generated by crossing FFA2 floxed mice (FFA2^fl/fl) with Adiponectin-Cre transgenic mice, resulting in adipocyte-specific FFA2 deletion. Littermate FFA2^fl/fl control and Adipoq-F2-KO mice were co-housed from birth and maintained on standard chow (Teklad LM-485) until 12 weeks of age. At this time point, mice were transitioned to a custom-modified high-fat/high-sugar Western diet supplemented with 10% fructooligosaccharides (FOS; D20021208, Research Diets, Inc.). After two weeks on this diet—once genotype-dependent differences in body weight were evident—mice were euthanized for tissue collection. Jejunal mucosa was isolated, and RNA was extracted for sequencing. RNA integrity was verified prior to library preparation, and bulk RNA sequencing was conducted by the UIC sequencing core facility. The resulting data were used to perform differential gene expression analysis between Adipoq-F2-KO and control mice, with the goal of identifying fiber-responsive, FFA2-regulated transcriptomic changes in the small intestine under obesogenic dietary challenge.

first: Nnyamah

last: Chioma

first: Xu

last: Kai

first: Boyett

last: James

first: Pandya

last: Nupur

first: Brian

last: Layden

first: Medha

last: Priyadarshini


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

status: Public on Sep 30 2025

city: Krakow

first: Tomasz

last: Szmatoła

state: Małopolskie

address: Mickiewicza 21

department: OMEI

country: Poland

institute: University of Agriculture in Krakow

type: Expression profiling by high throughput sequencing

summary: 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: Dawid

last: Tobolski

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: PriOmics: integration of high_throughput proteomic data with complementary omics layers using mixed graphical modeling with group priors

city: Ulm

first: Emil

last: Chteinberg

address: Albert-Einstein-Allee 11

country: Germany

institute: Ulm University Medical Center

summary: Mass spectrometry (MS)_based high_throughput proteomics data cover abundances of 1,000s of proteins and facilitate the study of co_ and post_translational modifications (CTMs/PTMs) such as acetylation, ubiquitination, and phosphorylation. Yet, it remains an open question how to holistically explore such data and their relationship to complementary omics layers (including the HTG EdgeSeq Pan B_Cell Lymphoma Panel) or phenotypical information. Network inference methods aim for a holistic analysis of data to reveal relationships between molecular variables and to resolve underlying regulatory mechanisms. Among those, graphical models have received increased attention as they can distinguish direct from indirect relationships, aside from their generalizability to diverse data types. We propose PriOmics as a graphical modeling approach to integrate proteomics data with complementary omics layers and pheno_ and genotypical information. PriOmics models intensities of individual peptides and incorporates their protein affiliation as prior knowledge in order to resolve statistical relationships between proteins and CTMs/PTMs. We show in simulation studies that PriOmics improves the recovery of statistical associations compared to the state of the art and demonstrate that it can disentangle regulatory effects of protein modifications from those of respective protein abundances. These findings are substantiated in a dataset of Diffuse Large B-Cell Lymphomas (DLBCLs) where we integrate SWATH_MS_based proteomics data with the HTG EdgeSeq Pan B_Cell Lymphoma transcriptional Panel and phenotypic information.

overall_design: Three hundred sixty difisue large B_cell lymphoma (DLBCL) FFPE tissue samples were analyzed by HTG EdgeSeq Pan B_Cell Lymphoma Panel. For each FFPE sample, a total of 6 µm2 area was collected.

first: Robin

last: Kosch

first: Katharina

last: Limm

first: Annette

middle: M

last: Staiger

first: Nadine

middle: S

last: Kurz

first: Nicole

last: Seifert

first: Bence

last: Oláh

first: Stefan

last: Solbrig

first: Marita

last: Ziepert

first: Rainer

last: Spang

first: Helena

middle: U

last: Zacharias

first: German

last: Ott

first: Peter

middle: J

last: Oefner

first: Michael

last: Altenbuchinger

first: Reiner

last: Siebert


title: Inhibition of host N-myristoylation compromising the infectivity of SARS-CoV-2 due to Golgi-bypassing egress

status: Public on Sep 29 2025

city: Brisbane

first: Huiwen

last: Zheng

state: Queensland

address: The University of Queensland Brisbane

country: Australia

institute: The University of Queensland

summary: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which caused coronavirus disease 2019 (COVID-19) pandemic, remains a global health crisis despite vaccines, neutralizing antibodies, and antiviral drugs. Emerging mutations can reduce the effectiveness of these treatments, suggesting that targeting host cell factors may be a more robust strategy. Cellular N-myristoyltransferases (NMTs) are essential enzymes for protein myristoylation, affecting stability, interaction, localization, and function of numerous proteins involved in intracellular membrane trafficking. We demonstrate that selective inhibition of host cell NMT1 and -2 by IMP-1088 decrease SARS-CoV-2 infection by 90% in human lung and primary nasal epithelial cells, as well as in human 3D choroid plexus-cortical organoids. NMT1 and -2 inhibition does not affect viral entry, replication, or release, but instead impairs viral assembly and maturation, leading to compromised infectivity of released virions. We further show that inhibition of host NMT1 and -2 triggers an alternative Golgi-bypassing pathway for SARS-CoV-2 progeny virions release, which occurs through a lysosomal intermediate.

overall_design: 60 day-old choroid plexus organoids were dissociated and scRNAseq experiment was conducted in order to identify the abundance of neuronal and CP cell types.

first: Saber

middle: A

last: Elkader

first: Jessica

middle: C

last: Mar

first: Ernst

last: Wolvetang

first: Merja

last: Joensuu


title: Maternal Probiotic Supplementation Effects on the Placenta-Brain Axis

status: Public on Sep 26 2025

city: Columbia

first: Trupti

last: Joshi

state: Missouri

address: 103 Math Science Building

department: Department of Biomedical Informatics, Biostatistics and Medical Epidemiology (BBME)

country: USA

institute: University of Missouri-Columbia

summary: The rate of probiotic usage by pregnant women in the US and Canada ranges from 1.3 to 3.6 %. Probiotic supplements are available without a prescription and have gained currency in treating a variety of ailment ranging from reducing risk of constipation, diarrhea, other gastrointestinal conditions, eczema, pre-term birth, and prevent adverse pregnancy outcomes, including gestational diabetes mellitus (GDM) and depression/anxiety. Three possible mechanisms by which maternal probiotic supplementation might influence the placenta are through 1) directly impacting possible bacteria residing in the placenta (placenta microbiome), 2) altering bacterial metabolites produced by gut microbiota within the mother that induce placental changes, and 3) maternal probiotics might affect the composition of the bacteria within the maternal gut that affects her immune cells and their responses to the heterologous placenta. For the second potential mechanism, bacterial metabolites that might influence placenta include short chain fatty acids (SCFAs), polyamines (PAs), and Vitamins B9 (Folic Acid) and 12 (Cobalamin), among others. This project aims to determine the effects maternal probiotic supplementation in mice might have on the fetal placenta. With the number of women taking over probiotic supplements increasing, further research is needed to determine how these bioactive agents may affect the placenta and health of the offspring.

overall_design: RNA-seq profiling of wildtype mouse placenta and fetal brain from control mouse dams and mouse dams exposed to probiotic supplementation before and during pregnancy.

first: Rosalind

middle: T

last: Herrington

first: Zhen

last: Lyu

first: David

last: Ellenberger

first: Sarah

middle: E

last: Seda

first: Cheryl

last: Rosenfeld


title: E2F1 induces a G0-G1 re-entry transcriptional program without changing chromatin accessibility [ATAC-seq]

city: Santa Cruz

first: Ali

last: Shariati

state: CA

address: 1156 High St

department: Biomolecular Engineering

institute: University of California Santa Cruz

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Many cells in our body reside in a reversible nondividing state termed G0 or quiescence. Precise regulation of entry and exit from G0 is critical for maintaining tissue homeostasis. G0 entry can occur when cells do not receive the required signals for cell cycle progression, leading to active repression of cell cycle genes through several mechanisms, including formation of repressor complexes to restrict chromatin accessibility for transcriptional activators. G0 cells can re-enter the G1 phase of the cell cycle upon receiving growth factor signals, resulting in activation of the Mitogen-Activated Protein Kinase pathway, converging on E2F transcription factors. Ectopic expression of E2F1 alone, a transcriptional activator, is sufficient to promote G0 exit without requiring the upstream signals, but it is unclear how E2F1 can overcome the chromatin lockdown in G0 cells to activate cell cycle genes. To better understand this mechanism, we compared dynamics, gene regulation and chromatin accessibility state between E2F1-mediated and growth factor (serum)-induced cell cycle reentry. Using live cell single cell tracking, we observe that E2F1 induction leads to accelerated cell cycle progression compared to regular serum-induced cell cycle re-entry. This accelerated cell cycle re-entry by E2F1 is accompanied by faster upregulation of cell cycle genes. Interestingly, we find that E2F1 preferentially binds to gene promoters that remain in a poised chromatin state after G0 induction, suggesting that G0 cells are prepared for cell cycle re-entry via regulating chromatin states in essential cell cycle genes.

overall_design: Constucts for doxycycline inducible expression of E2F1 or empty-vector (EV) control were stably integrated into 3T3 cells. The E2F1 and EV 3T3 cells were serum starved for 48 hours to induce a G0-like state, followed by E2F1 induction, EV induction or 10% serum addition, to induce G1/S phase reentry. Samples were collected at 0, 2, 6 and 12 hours after induction or serum addition. RNA was extracted for RNA-sequencing and nuclei were extracted for ATAC-Seq. In addition, cells were prepared for E2F1 ChIP-Seq at the 12 hour time point only. Together the RNA-Seq, ATAC-Seq and ChIP-Seq were used to identify E2F1 gene regulatory network involved in cell cycle reentry from G0.

first: Gerrald

last: Lodewijk

first: Benjamin

middle: R

last: Topacio

first: Silvart

last: Arabian

first: Seungho

last: Lee

first: Abolfazl

last: Zargari

first: Znala

last: Williams

first: Edward

last: Wu

first: Sayaka

last: Kozuki

first: Rana

last: Rahimi

first: Neda

last: Bidoki

first: Vanessa

last: Jonsson

first: Eric

last: Malekos

first: Susan

last: Carpenter

first: Gerd

last: Muller

first: Seth

last: Rubin


title: Methylation profiling of PDX-AML samples using Illumina Infinium MethylationEPIC BeadChips

status: Public on Sep 25 2025

city: Munich

first: Irmela

last: Jeremias

address: Feodor-Lynenstr. 21

department: Research Unit Apoptosis in Hematopoietic Stem Cells

institute: Helmholtz Zentrum München, German Center for Environmental Health (HMGU), Munich, Germany

summary: We established serially transplantable and robust, genetically engineered patient derived xenograft (PDX) models of acute myeloid leukemia (AML).

overall_design: Patients'  primary AML cells were transplanted into NSG mice. Models which engrafted were serially passaged and isolated from murine bone marrow. Methylation profiling was done with Illumina Infinium MethylationEPIC BeadChips.

first: Binje

last: Vick

first: Tobias

last: Herold

first: Sebastian

last: Vosberg

first: Philipp

last: Greif


title: E2F1 induces a G0-G1 re-entry transcriptional program without changing chromatin accessibility [RNA-seq]

first: Ali

last: Shariati

first: Gerrald

last: Lodewijk

first: Benjamin

last: Topacio

first: Silvart

last: Arabian

first: Seungho

last: Lee


title: Fat cadherin cleavage releases a transcriptionally active nuclear fragment to regulate target gene expression [ChIP-Seq]

city: St. Louis

first: Helen

last: McNeill

address: 660 S. Euclid Avenue

department: Developmental Biology

institute: Washington University School of Medicine in St. Louis

summary: The atypical cadherin fat (ft) controls growth, planar cell polarity (PCP) tissue organization, and mitochondrial function, in organisms ranging from fruit flies to mammals.  Working at the apical-junctional plasma membrane, the intracellular domain of the Ft protein, FtICD, binds to and regulates components of the Hippo and PCP pathways.  Unexpectedly, we find that a fragment of the FtICD is present in the nucleus in cultured cells as well as in embryonic and larval tissues, and we identify nuclear localization and nuclear export signals in FtICD required for this localization.  We show that membrane-bound FtICD is cleaved and enters nuclei in vivo.  Using endogenously tagged Ft as well as overexpressed FtICD, we conducted ChIP-seq experiments and identified putative Ft targets, including genes involved in signaling pathways, chromatin organization, pattern formation, and neural development.  RNAseq demonstrates that some of these genes are dysregulated in ft mutants.  We observe strong co-localization of Ft binding regions with peaks for other factors such as DREF and BEAF-32, as well as the Hippo pathway components Yorkie (Yki) and Scalloped (Sd), suggesting that Ft may act in conjunction with these factors to regulate gene expression.  Supporting this hypothesis, we found that Ft physiclly interacts with both Yki and Sd in co-immunoprecipitation experients in S2 cells.  We propose that the modulation of Hippo pathway activity constitutes one of the nuclear functions of Ft, complementing its estalished function as an upstream regulator of Hippo signaling.

overall_design:
GFP ChIP-seq of 16-20 hr Drosophila embryos using two separate fly strains with endogenously GFP-tagged ft gene
FLAG ChIP-seq of 3rd instar larval eye-brain complexes of Drosophila overexpressing FLAG-tagged Ft intracellular domain (FtICD)

first: Jannette

last: Rusch

first: Nattapon

last: Thanintorn

first: Chikin

last: Kuok


title: Brassinosteroids mediate proper coordination of sepal elongation

status: Public on Sep 24 2025

city: Ithaca

first: Byron

last: Rusnak

email: bzr5@cornell.edu, ahr75@cornell.edu

state: NY

address: 237 Tower Rd

department: Plant Biology

institute: Cornell University

summary: Arabidopsis sepals must grow in a coordinated and robust fashion to a consistent size and shape to close and protect the developing flower bud. To understand how this robust coordination occurs, we use the loss of robustness mutant development related myb-like1 (drmy1), which exhibits variable sepal initiation and growth, causing failure of the sepals to close the flower bud. Specifically, drmy1 has overgrown outer (abaxial) sepals and undergrown inner (adaxial) sepals, leading to a large discrepancy in the sizes of different sepals within individual flower buds. Using single cell and spatial RNA-seq, we found changes in expression of key genes related to brassinosteroid (BR) signaling in drmy1, particularly in cell types important to young flower bud development such as epidermal cells, boundary cells, and meristematic cells. Confocal imaging of a BRI1-EMS-SUPPRESSOR1 (BES1) ratiometric reporter confirms that BR signaling is upregulated and more variable in young drmy1 sepals. Subsequently, we found that altering BR signaling in drmy1 by crossing with BR mutants or adding brassinolide (a potent brassinosteroid) or brassinazole (a brassinosteroid biosynthesis inhibitor) can partially rescue this elongation defect by differentially altering the relative growth of the inner and outer sepals. Increasing BR signaling rescues by increasing the growth of the inner sepal but not the outer sepal, while decreasing BR signaling rescues by decreasing the growth of the outer sepal but not the inner sepal. These results suggest that brassinosteroids mediate the robust coordination of the growth rates between inner and outer sepals during early development, ensuring proper flower bud closure.

overall_design: 108 hours after induction with dexamethasone, WT and drmy1 in the ap1cal 35S::AP1-GR background was harvested by cutting off the cauliflower-like clusters of flower buds and protoplasted for scRNAseq

last: Rusank

first: Lilijana

last: Oliver

first: Kyle

last: Procopio

first: Adrienne

last: Roeder


title: Sexually dimorphic changes in liver and muscle transcriptome of 4-month-old dairy calves derived from artificial insemination or the transfer of a frozen-thawed in vitro produced embryo

city: Dublin

first: Laura

last: Thompson

address: Belfield

country: Ireland

institute: University College Dublin

summary: More than 1.2 million in vitro produced (IVP) bovine embryos are transferred annually worldwide, significantly outnumbering those from traditional superovulation, but there are limited reports on the birth and postnatal development of such calves. The conditions imposed during in vitro embryo culture may cause modifications of the embryo genome, including the transcriptome, potentially affecting postnatal organ function. This study compared the liver and muscle transcriptome in 4-month-old male and female dairy calves conceived by artificial insemination (AI) or IVP (n = 4 per sex per treatment). Biopsy tissue samples were collected and processed for RNA sequencing. Analysis of the RNAseq data revealed a distinct separation between the liver transcriptomes of female and male calves, regardless of method of production. Moreover, within the cohort of female calves, a strong separation between female calves derived from IVP vs AI was observed. Analysis of differentially expressed genes (DEGs) indicated downregulation of oxidative phosphorylation pathways and upregulation of pathways strongly enriching immune system processes, specifically Th17 cell differentiation and antigen processing and presentation. For the muscle transcriptome, the separation between male and female calves was less apparent compared with liver transcriptome, but there was still a clear separation between female calves derived from IVP vs AI, with downregulated genes enriching the p53 signalling pathway and upregulated genes enriching muscle structure development pathways. These results suggest that female embryos derived from IVP vs AI have developmental differences that manifest as differential transcriptomic profiles postnatally. In conclusion, these findings demonstrate that the IVP process induces significant alterations in the liver and muscle transcriptome of female postnatal calves. Further exploration is necessary to understand the potential implications for lifetime growth, health and production characteristics.

overall_design: Heifers were randomly assigned to one of the two groups; those receiving timed AI with frozen thawed semen (AI, n=8) and those transferred a single frozen-thawed Grade 1 Day 7 or Day 8 in vitro produced embryo (IVP, n=8). Resulting calves were divided into two groups based on their origin, AI (n=8; 4 male, 4 female) or IVP (n=8; 4 male, 4 female). Calves in both groups were raised in similar conditions up to 4 months of age, at which point biopsies were taken from the liver and muscle using a percutaneous punch technique. RNA extraction, quality control, library preparation, and sequencing was performed on the liver and muscle tissue samples. The subsequent read count files were employed to determine the differentially expressed genes (DEG) with the edgeR package for the R software and the gene expression counts were normalized by library size with edgeR methods. The DEG between groups were defined as those with false discovery rate (FDR) <0.05. The EntrezID corresponding to the DEG, was interrogated for enriched Gene Ontology and KEGG pathways using ShinyGO V0.77.

first: Alan

middle: D

last: Crowe

first: Maria

middle: B

last: Rabaglino

first: Stephen

last: Butler

first: Pat

last: Lonergan


title: Dual-Targeted Ping-Pong CAR T Cells: Leveraging Peripheral Expansion to Improve Solid Tumor Immunotherapy

status: Public on Sep 19 2025

city: Philadelphia

first: Regina

middle: M.

last: Young

state: Pennsylvania

address: 3400 Civic Center BLVD

department: CCI

institute: University of Pennsylvania

summary: Clinical responses to CD19-directed CAR T cell therapy in B cell malignancies are strongly associated with robust CAR T cell expansion in the peripheral blood. In contrast, CAR T cells targeting solid tumors do not encounter cognate antigen in the periphery, resulting in limited expansion and subtherapeutic peak concentrations. To overcome this, we engineered dual-targeted and dual-co-stimulated CAR T cells (CD19/28ζ-M5BBζ) that recognize CD19+ B cells, thereby promoting peripheral expansion and increasing the pool of solid tumor-directed CAR T cells available for tumor infiltration without the need for lymphodepletion. In immunocompetent C57BL/6 mouse models of pancreatic ductal adenocarcinoma and melanoma, these dual-targeted CAR T cells demonstrated enhanced peripheral expansion, improved anti-tumor efficacy, and increased survival without added dysfunction or toxicity compared to single antigen-targeted CAR T cells. We translated our findings to human CAR T cells by developing a novel pancreatic/xenograft model with CD19⁺ B cells in the periphery and again demonstrated that treatment with dual CAR T cells showed significantly enhanced tumor clearance and survival compared to single antigen-targeted CAR T cells. In conclusion, we demonstrate that dual-targeted CAR T cells boost peripheral expansion, and anti-tumor efficacy, providing a strategy for enhancing outcomes for patients treated with clinical CAR T products targeting solid tumors.

overall_design: Bulk RNA-seq of CD45.1+ CAR T cells in the spleen of mice engrafted with PDAC 7940b tumors at day 6 to compare dual-co-stimulated CAR T cells (CD19/28ζ-A03BBζ) to control CAR T cells (A03BBζ).

first: Amanda

middle: V

last: Finck

first: Ziming

last: Wang

first: Linhui

last: Chen

first: Carl

middle: H

last: June


title: Adipocyte- Specific FFA2 Deletion Leads to Increased Adipose Inflammation and Is Associated with Altered Intestinal Lipid Handling

status: Public on Sep 23 2025

first: Chioma

last: Nnyamah

overall_design: This RNA sequencing dataset was generated to assess baseline transcriptional differences in mature adipocytes resulting from adipocyte-specific deletion of Free Fatty Acid Receptor 2 (FFA2) in mice maintained under standard dietary conditions. Adipoq-F2-KO mice were generated by crossing FFA2 floxed mice (FFA2^fl/fl) with Adiponectin-Cre transgenic mice, enabling adipocyte-specific knockout of FFA2. Male Adipoq-F2-KO mice and their FFA2^fl/fl littermate controls were co-housed and maintained on a standard chow diet (Teklad LM-485) until 20 weeks of age. At this timepoint, mature adipocytes were isolated from perigonadal adipose tissue, and total RNA was extracted for sequencing. RNA integrity was confirmed prior to library preparation and bulk RNA sequencing, which was performed by the UIC sequencing core facility. Differential gene expression analysis was conducted to compare Adipoq-F2-KO and control samples under basal (non-obesogenic) conditions, to identify FFA2-regulated transcriptional programs in adipose tissue independent of dietary challenge.

first: Kai

last: Xu

first: James

last: Boyett

first: Nupur

last: Pandya

first: Layden

last: Brian


title: RNA sequencing of PDX-AML samples using prime-seq

status: Public on Sep 18 2025

first: Irmela

last: Jeremias

overall_design:
Patients'  primary AML cells were transplanted into NSG mice. Models which engrafted were serially passaged and isolated from murine bone marrow. PDX cells were lysed and mRNA was extracted. mRNA read counts were determined by prime-seq.

***************************************************************
Raw files for human/patient samples were not submitted to GEO due to concerns about submitting personally identifiable sequence data for open access.
***************************************************************

first: Binje

last: Vick

first: Tobias

last: Herold

first: Wolfgang

last: Enard

first: Johannes

last: Bagnoli


title: Spatiomolecular mapping reveals anatomical organization of heterogeneous cell types in the human nucleus accumbens [snRNA-seq]

status: Public on Sep 10 2025

city: Baltimore

first: Keri

last: Martinowich

state: Maryland

address: 855 N Wolfe St Suite 300

institute: Lieber Institute for Brain Development

summary: The nucleus accumbens (NAc) is a key component of the mesolimbic dopamine system that critically regulates many behaviors related to reward and motivation. The NAc is implicated in several neuropsychiatric disorders, including major depressive disorder, schizophrenia, and substance use disorder. Rodent studies have identified spatial organization of heterogeneous medium spiny neuron (MSN) subtypes across the NAc core and shell, but the extent to which this cellular diversity and spatial organization is conserved in the human brain remains unclear. Here, we generated a spatiomolecular atlas of NAc cell types and spatial domains by integrating spatial transcriptomics and single-nucleus RNA sequencing data from postmortem NAc tissue from 10 neurotypical adult donors. We identified 20 transcriptionally unique cell populations and 8 spatial domains, including specialized D1 islands composed of distinct dopamine receptor 1 (DRD1) MSN subtypes, which were enriched for OPRM1. In contrast to a discrete core vs. shell division, we observed continuous spatial gradients of gene expression across MSN domains, suggesting a more complex organization of DRD1 and DRD2 MSNs. Cross-species comparisons demonstrated conservation of MSN subtypes and spatial features between human, rodent, and nonhuman primate NAc. Genetic enrichment analysis with stratified linkage disequilibrium score regression revealed specific spatial domains associated with risk for psychiatric and addiction-related traits. To investigate this further, we spatially mapped ligand-receptor interactions involving neuropsychiatric risk genes. Finally, we leveraged existing rodent NAc data to identify drug-responsive transcriptional programs and predict their spatial distribution in the human NAc. Collectively, we provide a spatiomolecular framework for understanding the human NAc and its relevance to neuropsychiatric disease.

overall_design:
Ten neurotypical control postmortem human brain donors were selected for the single-nucleus and spatial transcriptomic study of the nucleus accumbens (NAc). We generated an integrated atlas with the two datasets of the human postmortem NAc to better understand the anatomical organization of heterogeneous medium spiny neuron (MSN) cell types. We identified multiple transcriptionally-distinct populations of MSNs that were organized in continuous gradients across the NAc.

***************************************************************
Raw files for human/patient samples are being made available in dbGaP (https://www.ncbi.nlm.nih.gov/gap/) for controlled access to the personally identifiable sequence data.
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first: Prashanthi

last: Ravichandran

first: Svitlana

last: Bach

first: Robert

last: Phillips III

first: Madeline

last: Valentine

first: Nicholas

last: Eagles

first: Yufeng

last: Du

first: Ishbel

last: del Rosario

first: Ryan

last: Miller

first: Heena

last: Divecha

first: Madhavi

last: Tippani

first: Kelsey

last: Montgomery

first: Joel

last: Kleinman

first: Stephanie

last: Page

first: Thomas

last: Hyde

first: Leonardo

last: Collado-Torres

first: Alexis

last: Battle

last: Hicks

first: Kristen

last: Maynard


title: Global transcriptome analysis of early and terminal erythropoiesis in newly diagnosed with multiple myeloma patients associated anemia

city: Zhengzhou

first: Shihui

last: Wang

state: Henan

address: No. 7 Weiwu Road, Zhengzhou, Henan, China

department: Institute of Hematology

country: China

institute: Henan Provincial People’s Hospital

summary: In NDMM anemia patients, erythroid progenitors show downregulation of growth factor response pathways (e.g., SPHK1), while terminal erythroblasts have upregulation of mitochondrial oxidative phosphorylation and p53-related genes, with increased cellular ROS levels. Mechanistically, genes like COX6C, UQCRB, UQCRH, PMAIP1, and MYCT1 are up-regulated in terminal erythroblasts.

overall_design: RNA was extracted from sorted BM erythroid progenitors and terminal erythroblasts, followed by Illumina NovaSeq 6000 sequencing. After quality control, reads were aligned to hg38 using kallisto, with differential expression analysis performed by DESeq2. PCA and GO enrichment analyses were conducted.

first: Huizhi

last: Zhao


title: Spatiomolecular mapping reveals anatomical organization of heterogeneous cell types in the human nucleus accumbens [Spatial Transcriptomics]

first: Keri

last: Martinowich

first: Prashanthi

last: Ravichandran

first: Svitlana

last: Bach

first: Robert

last: Phillips III

last: Valentine


title: Eukaryotic translation elongation factor EEF1G orchestrates the translational program to ensure meiotic progression in transcriptionally silent spermatocytes [Ribo-Seq]

status: Public on Sep 13 2025

city: Jinan

first: Jianze

last: Xu

state: Shandong

address: Jinan

institute: Shangdong university

summary: During meiotic prophase I, mammalian spermatocytes face a critical challenge that they need to synthesize recombination and synapsis proteins while global transcriptional suppression occurs at leptotene/zygotene stages. Here, we identify a spermatogenic cell highly expressed protein, eukaryotic translation elongation factor 1 gamma (EEF1G), as a master regulator of translational adaptation in mouse spermatocytes. Germ cell-specific Eef1g knockout causes complete male infertility due to the meiotic arrest at the zygotene stage, which is characterized by unresolved DNA double-strand breaks, failed homologous chromosome synapsis, and abolished crossover formation. Mechanistically, EEF1G can interact with ribosome proteins and RNA-binding factors. Ribosome profiling reveals that EEF1G deficiency reduces ribosome processivity, leading to ribosomal stalling and decreased protein production. Consequently, proteomic analyses show a specific decrease of synapsis (e.g., SYCP1/SYCE1) and recombination (e.g., MSH4/TEX11) proteins. This study establishes EEF1G as a critical coordinator of spatial translation in transcriptionally silent spermatocytes, bridging limited mRNA engagement to explosive protein synthesis for meiotic progression. Our work challenges traditional views of meiotic control by highlighting translation elongation, not just as a housekeeping process, but as a stage-specific regulator of germ cell development.

overall_design: Ribosome profiling (Ribo-seq) was carried out to investigate the translational regulation associated with EEF1G in early meiotic spermatocytes. Testes were collected from postnatal day 12 (PD12) mice, a developmental stage enriched for leptotene and zygotene spermatocytes. To obtain highly purified populations, spermatocytes at the leptotene (L) and zygotene (Z) stages were isolated by fluorescence-activated cell sorting (FACS). Both wild-type (WT) and Eef1g conditional knockout (cKO) groups were included in the design, and each group contained two independent biological replicates to ensure reproducibility and statistical robustness. Ribosome-protected fragments (RPFs) were prepared using the QEZ-seq kit (Hangzhou NeoRibo Biotechnology Co., Ltd., Cat. R1024L) following the manufacturer's instructions, and the resulting libraries were sequenced on an Illumina platform. This design allowed a direct comparison of translational profiles between WT and Eef1g cKO spermatocytes at the L and Z stages, thereby providing insights into the functional role of EEF1G during meiotic progression in male germ cells.


title: Eukaryotic translation elongation factor EEF1G orchestrates the translational program to ensure meiotic progression in transcriptionally silent spermatocytes

overall_design: RNA-seq analyses of the FACS-sorted leptotene and zygotene spermatocytes from 12 days postpartum (dpp). Breifly, cell lysis, mRNA reverse transcription, and cDNA amplification were performed using the Discover-sc WTA Kit V2 (Vazyme, N711). Subsequently, cDNA fragmentation and adapter ligation were carried out with the TruePrep Flexible DNA Library Prep Kit for Illumina (Vazyme, TD504). All procedures were conducted in strict accordance with the manufacturer's protocols. The Smart-seq2 library sequencing was performed by Novogene on Illumina platforms, generating 150 bp paired-end reads.

first: Xiaohua

last: Jiang

first: Hongbin

last: Liu


title: Immune Receptor Lag3 Deletion Alleviates Neurodegeneration Phenotypes in a Mouse Model of Alzheimer’s Disease

city: Research Triangle Park

first: Elizabeta

last: Gjoneska

state: North Carolina

address: 111 TW Alexander Dr., David P Rall Building A030

department: Neurobiology Laboratory

institute: National Institute of Environmental Health Sciences (NIEHS/NIH)

summary: Alzheimer’s disease (AD) is the leading cause of dementia, but effective treatments remail unavailable. Using the 5xFAD familial AD mouse model, we show that deletion of the immune checkpoint receptor Lymphocyte activation gene 3 (Lag3) reduces amyloidosis, microgliosis, and neurodegeneration-related behavioral deficits. Transcriptional profiling revealed that Lag3 deletion reverses aberrant expression of disease-associated microglia (DAM) genes and decreased CD8+ T cells infiltration in the brain. These findings suggest that Lag3 regulates microglia function and may represent a potential therapeutic target for AD.

overall_design: RNA-seq was performed on FACS purified microglia isolated from hippocampal tissue of 36 mice representing four genotypes WT, 5xFAD+, Lag3-/-, and Lag3-/-; 5xFAD+. Female mice were analyzed at three ages (3-, 6-, and 9-month), with n = 3 biological replicates per group to assess genotype- and age-dependent transcriptional changes associated with Alzheimer’s disease progression and the role of Lag3 in modulating disease-associated phenotypes.

first: Juan

last: Wu

first: Andrew

last: Perl

first: Ashley

last: Brooks


title: KOLF2.1J iTF-Microglia: A standardized platform to study microglial transcriptional regulatory networks in CNS disease [Hi-C]

city: Huntsville

first: Richard

last: Myers

state: AL

address: 601 Genome Way

institute: HudsonAlpha Institute for Biotechnology

summary: Understanding transcriptional regulatory networks (TRNs) in microglia is key to uncovering mechanisms driving central nervous system (CNS) disorders. Human iPSC-derived models offer a tractable system for studying microglia, yet variability between lines has limited reproducibility. Here, we use the standardized KOLF2.1J iTF line to rapidly generate microglia-like cells (iTF-Microglia) and profile TRNs under homeostatic and inflammatory conditions. iTF-Microglia closely resemble primary brain microglia at both transcriptomic and epigenomic levels. Integrative analyses reveal microglia-enriched candidate cis-regulatory elements (cCREs) and dynamic enhancer remodeling upon differentiation and LPS+IFNG stimulation, involving key transcription factors (TFs) including NF-kB, IRF, and STAT families. TRNs active in iTF-Microglia are enriched for genetic variants linked to Alzheimer’s disease and other CNS disorders. These findings establish KOLF2.1J iTF-Microglia as a reproducible and genetically tractable platform for studying human microglial gene regulation and provide mechanistic insight into how TRN remodeling may contribute to CNS disease risk.

overall_design: HiC profiling of untreated KOLF2.1J iTF-iPSCs and Day 18 KOLF2.1J iTF-Microglia that were either untreated or stimulated with 100 ng/mL LPS and 20 ng/mL IFNG for 24 hours

first: Ivan

last: Rodriguez-Nunez

first: Samuel

last: Bartley

first: Nicholas

last: Cochran


title: KOLF2.1J iTF-Microglia: A standardized platform to study microglial transcriptional regulatory networks in CNS disease [RNA-seq]

overall_design: RNA-seq profiling of KOLF2.1J iTF-iPSCs and KOLF2.1J iTF-Microglia that were differentiated for 18 days, which were either untreated or stimulated with 100 ng/mL LPS and 20 ng/mL IFNG for 24 hours


title: KOLF2.1J iTF-Microglia: A standardized platform to study microglial transcriptional regulatory networks in CNS disease [ChIP-seq]

overall_design: ChIP-seq of H3K27ac in untreated KOLF2.1J iTF-iPSCs and Day 18 KOLF2.1J iTF-Microglia that were either untreated or stimulated with 100 ng/mL LPS and 20 ng/mL IFNG for 24 hours


title: KOLF2.1J iTF-Microglia: A standardized platform to study microglial transcriptional regulatory networks in CNS disease [ATAC-seq]

overall_design: ATAC-seq profiling of untreated KOLF2.1J iTF-iPSCs and Day 18 KOLF2.1J iTF-Microglia that were either untreated or stimulated with 100 ng/mL LPS and 20 ng/mL IFNG for 24 hours


title: KOLF2.1J iTF-Microglia: A standardized platform to study microglial transcriptional regulatory networks in CNS disease

status: Public on Sep 09 2025

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

overall_design: Refer to individual Series


title: Single-cell RNA sequencing of ICB samples from FUSCC

city: Shanghai

first: Tong

last: Fu

state: Shanghai

address: DongAn Road

institute: Fudan University

summary: Here, we performed single-cell RNA sequencing of pre-treatment tumor samples in 26 patients with early-stage TNBC and 6 patients with advanced TNBC to define anti-PD-1 response-related components in the tumor microenvironment.

overall_design:
We performed single-cell RNA sequencing on pre-treatment tumor samples from 26 early-stage TNBC patients and 6 advanced TNBC patients. The goal was to identify components of the tumor microenvironment related to the response to anti-PD-1 therapy. All samples were collected before any treatment was administered.

***************************************************************
Raw files for human/patient samples were not submitted to GEO due to concerns about submitting personally identifiable sequence data for open access.
***************************************************************

first: Xi

last: Jin

first: Yiyu

last: Chen

first: Yunsong

last: Yang

first: Yizhou

first: Zhiming

last: Shao


title: Foxn3 is part of a transcriptional network that regulates primary cilia in the developing mouse retina [RNA-Seq]

status: Public on Sep 04 2025

city: Ann Arbor

first: David

last: Turner

state: MI

address: 109 Zina Pitcher Place

department: Michigan Neuroscience Institute

institute: University of Michigan

summary: Analysis of retinas from mice with a targeted disruption of the Foxn3 gene revealed additional displaced amacrine interneurons and additional retinal astrocytes in the inner plexiform layer and in the ganglion cell layer. The forkhead transcription factor Foxn3 is a transcriptional repressor. Numerous genes linked to cilia structure or assembly were upregulated in embryonic retinas without Foxn3, including Foxj1, a forkhead transcription factor required for motile cilia. Ectopic primary cilia were observed on bipolar and amacrine interneurons in postnatal retinas without Foxn3. CUT&RUN analysis revealed that many upregulated retinal genes were bound by the Foxn3 and Rfx3 proteins. A short hydrophobic motif shared by Foxj1, Foxn4, and Foxn3 proteins was found to be required for association with the Rfx3 protein and for transcriptional repression by Foxn3, as well as for full transcriptional activation by Foxn4 with Rfx3. AlphaFold 3 predicts an interaction between the hydrophobic motif and the Rfx3 dimerization domain. Mutations in Rfx3 at the predicted interaction site disrupted association of Rfx3 with Foxn3 or Foxn4. These results reveal a new layer of transcriptional regulation of genes required for cilia, with Foxn3 functioning as a repressor of cilia genes and limiting primary cilia formation in the developing retina.

overall_design: RNA-seq analysis of gene expression in E19 retinas from wild-type and Foxn3 knockout (C57BL/6NJ-Foxn3em1(IMPC)Bay/Mmnc) embryos.

middle: L

first: Fan

last: Meng

first: Huanqing

last: Zhang


title: A novel lymphoma-associated macrophage interaction signature (LAMIS) provides robust risk prognostication in diffuse large B-cell lymphoma clinical trial cohorts of the DSHNHL

status: Public on Sep 06 2025

city: Hannover

first: Robin

last: Kosch

address: Carl-Neuberg-Straße 1

institute: Hannover Medical School

summary: Diffuse large B-cell lymphoma (DLBCL) is a disease with heterogeneous outcome. Stromal signatures have been correlated to survival in DLBCL. Their use, however, is hampered by the lack of assays for formalin-fixed paraffin-embedded material (FFPE). We constructed a lymphoma-associated macrophage interaction signature (LAMIS) interrogating features of the microenvironment using a NanoString assay applicable to FFPE. The clinical impact of the signature could be validated in a cohort of 466 patients enrolled in prospective clinical trials of the German High-Grade Non-Hodgkin Lymphoma Study Group (DSHNHL). Patients with high expression of the signature (LAMIShigh) had shorter EFS, PFS, and OS. Multivariate analyses revealed independence from IPI factors in EFS (HR 1.7, 95% CI 1.2–2.4, p-value = 0.001), PFS (HR 1.8, 95% CI 1.2–2.5, p-value = 0.001) and OS (HR 1.8, 95% CI 1.3–2.7, p-value = 0.001). Multivariate analyses adjusted for the IPI factors showed the signature to be independent from COO, MYC rearrangements and double expresser status (DE). LAMIShigh and simultaneous DE status characterized a patient subgroup with dismal prognosis and early relapse. Our data underline the importance of the microenvironment in prognosis. Combined analysis of stromal features, the IPI and DE may provide a new rationale for targeted therapy.

overall_design:
Transcriptomics dataset of 330 formalin-fixed paraffin-embedded (FFPE) tissue samples from patients with Diffuse large B-cell lymphoma (DLBCL). Gene Expression profiles of 145 target genes were created using the NanoString nCounter technology (NanoString Technologies, Seattle, WA). The name of the study cohort was included to help distinguish the samples.
***Submitters state that the corresponding clinical data is not provided due to privacy protections, refering to the following data sharing agreement and the Leipzig Health Atlas:
Pseudonymised data will be available upon request up to 5 years after publication of this Article to researchers who provide a data sharing agreement that describes a methodically sound proposal and the data necessary for the purpose of the approved proposal. Proposals should be directed to dshnhl@uks.eu. Data will be shared once all relevant parties approve and sign the data sharing agreement. Selected data will be also available on the Leipzig Health Atlas website. For the Leipzig Health Atlas website see www.health-atlas.de<http://www.health-atlas.de/>.

first: Annette

last: Staiger

first: Michael

last: Altenbuchinger

first: German

last: Ott


title: Autoimmunity-associated DIORA1 binds the MRCK family of serine/threonine kinases and controls cell motility

status: Public on Sep 08 2025

city: Solna

first: Tilen

last: Trselic

address: Visionsgatan 18

country: Sweden

institute: Karolinska Institutet

summary: Genetic association links DIORA1 to numerous autoimmune rheumatic diseases, including systemic lupus erythematosus, Sjögren's disease, rheumatoid arthritis, polymyositis and systemic sclerosis. However, its cellular function has remained unknown. Here, we identify the MRCK family of serine/threonine kinases - key regulators of actomyosin contractility and cell motility - as direct interactors of DIORA1. Through interaction mapping, we show that DIORA1 binds three distinct modules of MRCK kinases, including the conserved kinase inhibitory motif (KIM), C1-PH and CNH domains. DIORA1 knockdown in human cells altered cellular phosphorylation patterns and reduced phosphorylation of known MRCK targets. RNA-sequencing and proteomic analyses revealed upregulation of epithelial-mesenchymal transition genes and proteins, and functional analyses confirmed increased cell invasion, following knockdown of DIORA1. Together, these findings identify the autoimmunity-associated DIORA1 protein as a previously uncharacterized interactor of MRCK kinases and a regulator of cell motility.

overall_design: RNA-seq profiling of SK-N-SH and SK-N-AS neuroblastoma cell lines following knockdown of the gene FAM167A (DIORA1). Knockdown was achieved using either CRISPR interference (CRISPRi) with SpCas9-KRAB in both cell lines, or pooled siRNA targeting FAM167A in SK-N-SH cell line.

last: Tršelič

first: Nathalie

last: Pelo

first: Gregoire

last: Martin de Fremont

first: Vaishnavi

last: Iyer

first: Elina

last: Richardsdotter Andersson

first: Vijole

last: Ottosson

last: Frei

first: Elisa

last: Baas

first: William

last: Nyberg

first: Guðný Ella

last: Thorlacius

first: Lara

last: Mentlein

first: Sanjaykumar

last: Boddul

first: Ioana

last: Sandu

first: Diego

last: Velasquez Pulgarin

first: Ákos

last: Végvári

first: Carmen

last: Gerlach

first: Fredrik

last: Wermeling

first: Maria

last: Sunnerhagen

first: Björn

last: Wallner

first: Alexander

last: Espinosa

first: Marie

last: Wahren-Herlenius


title: Foxn3 is part of a transcriptional network that regulates primary cilia in the developing mouse retina [CUT & RUN]

first: David

last: Turner

overall_design: CUT&RUN analysis of genomic binding sites for the Foxn3, Foxn4, and Rfx3 transcription factors in E16 CD-1 mouse retinas.

first: Fan

last: Meng

first: Huanqing

last: Zhang


title: Genome-wide inter-chromosomal contacts of rDNA units detected by 4C procedure in human Mel Z melanoma cells.

status: Public on Sep 03 2025

city: Moscow

first: Nickolai

last: Tchurikov

address: 32, Vavilova str.

department: Department of Epigenetic Mechanisms of Gene Expression Regulation

country: Russia

institute: Engelhardt Institute of Molecular Biology

summary: 4C-rDNA procedure was used for analysis of whole-genomic inter-chromosomal contacts of rDNA units in human Mel Z melanoma cells grown either on the plastic or Matrigel.

overall_design: Analysis of rDNA genome-wide contacts in Mel Z melanoma cells using 4C approach.

first: Yuri

last: Kravatsky


title: Clonal lineage tracing of innate immune cells in human cancer

city: New York

first: Caleb

last: Lareau

state: New York

address: 417 E 68th St, Zuckerman - ZRC 1132

institute: Memorial Sloan Kettering

summary: Innate immune cells constitute the majority of the tumor microenvironment (TME), where they mediate both natural anti-tumor immunity and immunotherapy responses. While single-cell T- and B-cell receptor sequencing has provided fundamental insights into the clonal dynamics of human adaptive immunity, the lack of appropriate tools has precluded similar analysis of innate immune cells. Here, we developed a method leveraging somatic mitochondrial DNA (mtDNA) mutations to reconstruct clonal lineage relationships between single cells across native human tissues. We jointly sequenced single-cell transposase-accessible chromatin and mtDNA to profile 124,958 cells from matched tumor, non-involved lung tissue (NILT) with peripheral blood of early-stage non-small cell lung cancer (NSCLC) patients, as well as 93,757 cells from matched tumor and peripheral blood of ovarian cancer patients. Our single-cell concomitant profiling of lineage and cell states of thousands of immune cells resolved clonality across cell types, tissue sites, and malignancies. By resolving clonal populations across innate immune subtypes, we demonstrated that TME-resident myeloid subsets, including macrophages and type 3 dendritic cells (DC3), are clonally linked to both circulating and tissue-infiltrating monocytes. Further, we identified distinct DC-biased and macrophage-biased myeloid clones, enriched in the tumor and NILT, respectively, and found that their circulating monocyte precursors exhibit distinct epigenetic profiles, suggesting that myeloid differentiation fate may be predetermined before TME infiltration. These results delineate the clonal pathways of intratumoral myeloid cell recruitment and differentiation in human cancer and suggest that remodeling of the tumor myeloid compartment may be peripherally programmed.

overall_design: Human tumors and tissue samples were resected and processed for single-cell genomics library preparation.

first: Vincent

last: Liu

first: Ansuman

last: Satpathy


title: Spatio-molecular gene expression reflects dorsal anterior cingulate cortex structure and function in the human brain [spatial transcriptomics]

status: Public on Sep 02 2025

first: Keri

last: Martinowich

summary: In the human brain, the dorsal anterior cingulate cortex (dACC) plays a key role in the reward pathway, which is connected to drug addiction, substance abuse, and some psychiatric disorders. Specific cell types in the dACC are associated with these disorders, but the breakdown of cell populations and their relative positions are unknown. Uniquely, the dACC has agranular laminar structure due to a lack of layer IV, which relates to distinct biological functions. We generated a human dACC spatial transcriptomic map by integrating 10x Genomics Visium Spatial Gene Expression data from ten neurotypical donors and combining this map with corresponding 10x Genomics Chromium Single Cell Gene Expression data. We utilized nonnegative matrix factorization (NMF) to discover various gene programs, which shed light on von Economo neurons (VENs) in Layer V of the dACC.To better understand the molecular landscape of this region, we compared it with the dorsolateral prefrontal cortex (dlPFC) region in the same ten donors. The brain’s structure and function are closely connected, so our precise pairing of gene expression to spatial information sheds light on how dysregulation in the dACC relates to psychiatric disorders.

overall_design:
We obtained tissue blocks of postmortem human brain containing dACC from 10 neurotypical adult brain donors. We used the 10x Genomics Visium and 3’ Single Cell Gene Expression platforms to generate paired spatial transcriptomics and single-nucleus RNA-seq data of the human dACC. We performed a second spatial transcriptomics experiment using the Visium Spatial Proteogenomics (Visium-SPG) platform for four of the 10 donors.

***************************************************************
Raw files for human/patient samples are being made available in dbGaP (https://www.ncbi.nlm.nih.gov/gap/) for controlled access to the personally identifiable sequence data.
***************************************************************

first: Kinnary

last: Shah

first: Michael

last: Totty

first: Ryan A.

last: Miller

first: Heena R.

last: Divecha

first: Sang Ho

last: Kwon

first: Svitlana V.

last: Bach

first: Sanjana

last: Tyagi

first: Madeline

last: Valentine

first: Joel E.

last: Kleinman

first: Atharv

last: Chandra

first: Madhavi

last: Tippani

first: Kristen R.

last: Maynard

first: Thomas M.

last: Hyde

first: Stephanie C.

last: Page

last: Hicks


title: Designed, linked-domain proteins are pan-UBE2D inhibitors and induce proteostress and the unfolded protein response in HeLa cells

status: Public on Sep 01 2025

city: Stockton

first: Joseph

last: Harrison

address: 3601 Pacific Ave

department: Chemistry

institute: University of the Pacific

summary: Ubiquitin (Ub) is a protein post-translational modification that controls proteostasis through mechanisms spanning transcription, translation, and protein degradation. Ub conjugation occurs through a cascade of three enzyme classes (E1, E2, and E3s) involving >1000 proteins that regulate the ubiquitination of cellular proteins. The E2 Ub-conjugating enzymes are the midpoint, yet their cellular roles remain under-characterized. Here, we develop highly selective, multivalent, designed protein inhibitors against all UBE2D/UBCH5 isoforms by targeting the RING- and backside-binding sites. In HeLa cells, these inhibitors phenocopy knockdown of UBE2D by enhancing chemosensitivity to cisplatin. Whole-cell proteomics reveal ~20% of the identified proteins are more abundant and most do not have altered RNA levels, suggesting their protein turnover is regulated by UBE2D. Enrichment analysis of the altered mRNAs indicates the UBE2D inhibitors trigger the unfolded protein response. These precision tools will enable new studies about UBE2D’s cellular roles and help to deconvolute complex ubiquitin regulatory network.

overall_design: These samples correspond to HeLa cells electroportated with either the UBE2D inhibitor UBOX-UBL or the UBOX-UBLcontrol. PolyA enrichment and mRNA sequencing was performed by Seqquest genomics

first: Zara

last: Bukhari


title: Spatio-molecular gene expression reflects dorsal anterior cingulate cortex structure and function in the human brain [snRNA-seq]

first: Keri

last: Martinowich

last: Shah


title: Studying the long-term adaptation of Haloferax volcanii to low salt conditions: transcriptomic and genetic analyses

city: Frankfurt am Main

first: Andreas

last: Borst

address: Max-von-Laue-Str. 9

institute: Goethe-Universität Frankfurt

summary: Archaea are well known for inhabiting areas of our planet that are usually hostile for any form of life, hence they are often termed as “extremophiles”. Although also found in common soil or the digestive tract of vertebrates, some species thrive on acidic or alkaline grounds, in submarine black smokers with temperatures surpassing 100°C or live in aquatic areas with a very high salinity.Haloferax volcanii is a halophilic and mesophilic archaeon that was first discovered in the 1930s and isolated from the hypersaline environment of the Dead Sea. Its optimal growth conditions are at 42 °C in around 2 M NaCl and complex nutrient medium, however it can also grow in different synthetic media and at a wide range of temperatures and NaCl concentrations. While NaCl concentrations up to 0.7 M inhibit growth in synthetic glucose media, a concentration of 0.9 M is sufficient to sustain growth at a reduced rate.Here we show for the first time a transcriptome-wide analysis of differential gene expression of cells grown under low salt condition. We cultivated cells at an optimal NaCl concentration of 2.1 M in glucose media and compared the expression profile of these to cells grown in 0.9 M NaCl after 26 and 68 h.

overall_design: differential gene expression profiles of the halophilic archaeon Haloferax volcanii should be analysed as response to low salt conditions in glucose medium (2.1 M vs 0.9 M NaCl) after a short (26 h) and prolonged (68 h) period of time. RNA-Seq was done in duplicates of 3 Samples (2.1 NaCl M after 26h; 0.9 M NaCl after 26h and 0.9 M NaCl after 68 h). Key player genes involved in low salt stress response (26h at 0.9 M NaCl) and low salt adaption (68h at 0.9 M NaCl) shluld be identified.


title: TENT-5 regulates the expression of male-specific genes in Caenorhabditis elegans

city: Warsaw

first: Andrzej

last: Dziembowski

address: 4 Ks. Trojdena Street

institute: International Institute Of Molecular And Cell Biology In Warsaw

summary: Polyadenylation is an important post-transcriptional process that governs mRNA stability and expression. Advancements in direct RNA sequencing in recent years have clarified many aspects of this intricate regulation, revealing the influence of various factors. Here, we used Nanopore Direct RNA Sequencing to investigate the association between genome-wide mRNA poly(A) tail profiles and sexual dimorphism in Caenorhabditis elegans. Our results demonstrate sex-dependent differences in both gene expression and poly(A) tail metabolism. Notably, we discovered that cytoplasmic poly(A) polymerase TENT-5 regulates multiple male-specific transcripts, predominantly encoding putative seminal fluid components with predicted extracellular localization. TENT-5 expression in male-specific tissues, such as seminal vesicle and vas deference, corroborates its functional significance. Intriguingly, despite extensive TENT-5-mediated polyadenylation of male-specific transcripts, males devoid of TENT-5 show no abnormalities in mating behavior, sperm morphology, or fertility. Our findings suggest that TENT-5 plays a role in regulating sex-related processes in males, although the physiological consequences remain to be fully elucidated.

overall_design: We implemented Nanopore Direct RNA Sequencing to investigate sex-related differences in gene expression and poly(A) tail metabolism in C. elegans. We performed analysis of wild type (N2) hermaphrodites and males at the young adult stage. Additionally, we compared wild type (N2) males and tent-5(tm3504) males and showed that male-specific genes in C. elegans are regulated by TENT-5.

first: Zuzanna

last: Mackiewicz

first: Vladyslava

last: Liudkovska


title: Physiological and functional characterization for high-throughput optogenetic skeletal muscle exercise assays

status: Public on Aug 29 2025

city: Cambridge

first: Ritu

last: Raman

state: MA

address: 77 Massachusetts Avenue

department: Mechanical Engineering

institute: Massachusetts Institute of Technology

first: Ronald

last: Heisser

first: Angel

last: Bu


title: Physiological and functional characterization for high-throughput optogenetic skeletal muscle exercise assays [60min]

summary: Exercise has long been considered an essential part of human health and longevity. Recent physiological studies have expanded muscle’s role beyond simply acting as an actuator, revealing muscle’s exercise-mediated paracrine and endocrine relationships with other organ systems. In vitro engineered skeletal muscle models can address physiological questions about exercise adaptation with the precision of cell biology. Optogenetic tools have enabled a noninvasive approach to stimulating muscle contraction that avoids the potential off-target effects of electrical stimulation techniques. In this article we propose high-throughput culture and optical exercise protocols to generate statistically robust cellular exercise response datasets. We characterize optical rheobase for 2D muscle tissue morphology, finding that optical intensities as low as 5 μW mm-2 can trigger contraction. We then analyze bulk RNA sequencing data collected from high throughput, acute exercise protocols and find a rich display of transcriptional behavior that is consistent with experimental observations. The spontaneous contractility of our tissue constructs introduced oxygen diffusion challenges when maintained in a 24 well plate, and our analysis shows divergent myogenic and pathological transcriptional consequences of hypoxia. We believe our techniques provide a practical foundation for conducting future high-precision in vitro exercise studies of skeletal muscle.

overall_design: ChR2 C2C12 myoblasts (optogenetic) grown on a fibrin hydrogel and differentiated for about two weeks before RNA extraction. This cohort underwent daily optical stimulation for 60 minutes at a variety of frequencies (none-control, 1Hz, 4Hz, and 10Hz).


title: Transcriptome sequencing screening mRNA

city: zhengzhou

first: Deqian

last: Kong

state: henan

address: No.1 Longhu Zhonghuan Road, Jinshui District

institute: The First Affiliated Hospital of Zhengzhou University

summary: Oxidative stress plays a pivotal role in age-related diseases, including oxidative aging, by promoting cellular damage and dysfunction.

overall_design: In this study, we performed transcriptome sequencing to identify mRNA markers and pathways associated with oxidative aging in human lens epithelial cells (LECs). Through bioinformatics analysis, key mRNAs involved in oxidative stress response, mitochondrial dysfunction, and aging were significantly altered.

first: Dq


title: Physiological and functional characterization for high-throughput optogenetic skeletal muscle exercise assays [30min]

overall_design: ChR2 C2C12 myoblasts (optogenetic) grown on a fibrin hydrogel and differentiated for about two weeks before RNA extraction. This cohort underwent daily optical stimulation for 30 minutes at a variety of frequencies (none-control, 1Hz, 4Hz, and 10Hz).


title: Adipocyte heterogeneity regulated by the Bithorax Complex-Wnt signaling crosstalk in Drosophila

city: New Orleans

first: Jun-yuan

last: Ji

state: LA

address: 1700 Tulane Avenue

department: Department of Biochemistry and Molecular Biology

institute: Tulane University

summary: Adipocytes distributed throughout the body are essential for lipid metabolism and energy homeostasis, with regional differences affecting their functions and disease susceptibility. However, the mechanisms driving this regional heterogeneity remain poorly understood. Here, we show that the interactions between Wnt/Wingless signaling and Bithorax Complex (BX-C) genes – specifically abdominal A (abd-A) and Abdominal B (Abd-B) – drive regional differences in Drosophila larval adipocytes. Abdominal adipocytes, expressing abd-A and Abd-B, differ from thoracic ones, with active Wnt signaling further amplifying these differences. Depleting abd-A and Abd-B, genes in adipocytes reduces fat accumulation, delays larval-pupal transition, and leads to pupal lethality, while also attenuating Wnt signaling-induced lipid mobilization. Moreover, Wnt signaling stimulates abd-A and Abd-B, transcription, creating a feedforward loop that intensifies the interaction between Wnt signaling and BX-C genes. These findings elucidate how the crosstalk between cell-autonomous BX-C gene expression and Wnt signaling defines adipocyte heterogeneity in Drosophila larvae.

overall_design: RNA-seq on fat bodies of control or axn/abd-A/Abd-B depleted animals. Following principal component analysis (PCA), we excluded two outlier samples from subsequent analyses: dcg+4 from the dcg+ group and dcg-AiBi-1 from the dcg-AiBi group.


title: CellCousin2: An Optimized System for Partial Ablation and Tracing of Regenerative Lineages

status: Public on Aug 26 2025

city: Greater Noida

first: Sumeet

middle: Pal

last: Singh

state: Uttar Pradesh

address: NH91, Tehsil Dadri

department: Life Sciences

country: India

institute: Shiv Nadar Institution of Eminence

summary: Regeneration can rely on multiple cellular sources, including stem cells, self-duplicating cells, and transdifferentiating cells. A central question in regenerative biology is how these distinct lineages contribute to repair and interact within a functional regenerate. We previously developed the CellCousin system to study hcellular plasticity using inducible recombination and nitroreductase-mediated ablation in zebrafish. Here, we present CellCousin2, which introduces two key improvements for long-term tracking of spared and regenerating cells. First, to reduce background recombination, we developed a Dihydrofolate Reductase (DHFR)-CreER system with dual control: DHFR- mediated degradation in the absence of trimethoprim, and tamoxifen-dependent activation. This combination minimizes leakiness while maintaining high recombination efficiency. Second, we replaced the original nitroreductase with NTR2.0, enabling effective ablation with tenfold lower metronidazole concentration, reducing off-target effects on the liver. Together, these enhancements make CellCousin2 a robust platform for dissecting the dynamics and interactions of regenerative lineages.

overall_design: Bulk RNA-Seq of liver collected from zebrafish larvae treated with Vehicle, 1 mM Metronidazole, 10 mM Metronidazole.

middle: P

first: Gabriel

middle: G

last: Hovhannisyan


title: Macrophage signaling and function are regulated by distinct sterol biochemistries

status: Public on Aug 27 2025

city: Sioux Falls

first: Kevin

last: Francis

state: SD

department: Cellular Therapies

institute: Sanford Research

summary: Membranes require continuous reorganization of lipid components, including sterols, to dynamically alter their rigidity to deform and bend during scission events which occur during fundamental cellular functions such as endocytosis.  While diseases of cholesterol biosynthesis result in reduced cellular cholesterol and accumulation of precursor sterols, limited studies have addressed the intracellular consequences of disease-associated sterol changes on the ability of eukaryotic cellular membranes to function and signal normally.  Here, we utilized bone marrow-derived macrophages (BMDMs) to investigate how altered sterol content impacts macrophage signaling and membrane function.  Through pharmacological inhibition of cholesterol biosynthetic enzymes, reduced cholesterol and increased levels of disease-associated sterol intermediates coincided with reduced expression of immunogenic surface markers and impaired macropinocytosis.  Macropinocytic activity was sensitive to both reduced plasma membrane cholesterol and sterols containing functional groups substituted for the C3 hydroxyl group.  Transcriptomic analyses of cholesterol-inhibited BMDMs revealed alterations in immune and chemokine signaling pathways.  Decreased cholesterol was also associated with dysregulated vesicular sorting pathways and elevated expression of endosomal/lysosomal markers.  Disrupted endosomal sorting and impaired macropinocytosis was also observed in BMDMs from mouse models of the cholesterol biosynthesis disorder Smith-Lemli-Opitz syndrome (SLOS).  Our findings detail an important connection between sterol imbalance, membrane dynamics, and immune cell function.

overall_design: RNAseq profiling of bone marrow derived macrophage cultured in fetal bovine serum, lipoprotein deficient fetal bovine serum (LPDS) for 48 h, LPDS +Dhcr7 inhibitor AY9944, LPDS + HMG-CoA reductase inhibitor simvastatin, or LPDS + Dhcr24 inhibitor U18666A

first: Jazmine

last: Yaeger

first: Jason

last: Kerkvliet

first: Bijaya

last: Pradhan

first: Amelia

last: Lawver

first: Sonali

last: Sengupta

first: Natalie

middle: W

last: Thiex


title: Antisense transposon insertions into host genes trigger piRNA mediated immunity

status: Public on Aug 21 2025

city: Vienna

first: Dominik

last: Handler

address: Dr. Bohr-Gasse 3

country: Austria

institute: IMBA-Institute of Molecular Biotechnology of Austrian Academy of Sciences

type: Non-coding RNA profiling by high throughput sequencing

summary: Transposable elements pose a persistent threat to genome integrity, yet how host defense systems adapt to newly invading elements remains poorly understood. Here, we reveal how Drosophila melanogaster acquired PIWI-interacting RNA (piRNA)-mediated immunity against the recently invading endogenous retrovirus tirant. By integrating genetics, small RNA profiling, and population genomics, we identify two distinct modes of de novo piRNA biogenesis. The primary mechanism involves antisense insertions into the flamenco cluster, a well-established master locus for transposon control. Strikingly, we also find that antisense tirant insertions into 3′ UTRs of host genes robustly trigger piRNA production, a process driven by host gene transcription but independent of gene identity. These findings challenge prevailing models that link piRNA precursor specification to genomic origin or nuclear processing context. Instead, they uncover a flexible, general mechanism in which transposition into host gene exons represents a critical vulnerability for transposons: by generating chimeric antisense transcripts that are exported to the cytoplasm, transposons inadvertently initiate their own silencing, enabling rapid and adaptive genome defense against new invaders.

overall_design: small RNA-seq profiling from the Drosophila Synthetic Population Resources (DSPR) founder strains

first: Rafanel

last: Baptiste

first: Protsenko

last: Liudmila

first: Handler

last: Dominik

first: Brennecke

last: Julius

first: Senti

last: Kirsten-André


title: Exploring the Differential Host Responses to DSS and UC-Derived Microbiota in a Mouse Model of Colitis

status: Public on Aug 20 2025

city: Kosice

first: Maria

last: Rynikova

address: Srobarova 2

country: Slovakia

institute: Pavol Jozef Safarik University in Kosice

summary: Ulcerative colitis (UC) is a chronic inflammatory condition of the colon, characterized by recurring mucosal inflammation. Current evidence suggests that dysbiosis may drive the disease, but mechanistic links remain incompletely understood. To further investigate the host-microbiome interactions, three UC-induction methods were used on a pseudo germ-free mouse model: (1) DSS, (2) fecal microbiota transplantation (FMT) from a UC patient, and (3) combination of both DSS and FMT simultaneously. Disease severity (DAI), immune cell profiles (flow cytometry), colon transcriptomics (RNA sequencing), and microbiota composition (16S rRNA sequencing) were assessed. Our study revealed distinct effects of DSS and FMT on experimental colitis. DSS had a more pronounced impact on disease severity, while FMT exerted a stronger influence on several immune populations and downregulation of genes associated with tight junctions and mucins. Microbiome analysis demonstrated distinct compositional profiles across all experimental groups. The combined FMT and DSS model exhibited features of both induction methods, resulting in exacerbated clinical scores, barrier dysfunction, and inflammatory responses. Our study provides valuable insight into host–microbiome interactions in UC and introduces a dual-hit approach that may more accurately recapitulate its multifactorial pathogenesis than DSS alone.

overall_design: RNA-seq transcriptomic profiling of colon mucosal cells before (day 0) and after treatment (day 5) with either DSS, UC FMT or both

first: Sona

last: Gancarcikova

first: Stanislav

last: Lauko

first: Dagmar

last: Mudronova

first: Petra

last: Adamkova

first: Martin

last: Janicko

first: Vlasta

last: Demeckova


title: Desciption of the transcriptome profiles of mouse heart innervating DRG and Nodose Ganglia-derived sensory neurons

status: Public on Aug 19 2025

city: Istanbul

first: Tuba

last: Akgül Çağlar

address: Kavacik Neighborhood, Ekinciler Street No:19

department: SABITA

country: Turkey

institute: Istanbul Medipol University

summary: To obtain the mRNA expression profiles of vagal and spinal cardiac sensory neurons,  mouse Dorsal Root Ganglia (DRG) and Nodose Ganglia (NG) neurons innervating the heart were labelled by retrograde Di-8-ANEPPQ dye which was injected to the heart. Then bilateral NGs and DRGs between C-T segments were dissected and Di-8-ANEPPQ-labelled DRG and NG neurons were FACS sorted. Finally, Di-8-ANEPPQ+ DRG and NG neurons were subjected to total RNA extraction and library preparation protocols for RNA-seq experiment. For control samples, total NG and DRG (C-T) neurons were dissected from the wt mice and same RNA extraction and library preparation protocols were applied. Finally, mRNA profiles of heart-spesific DRG and NG neurons were compared to those of total DRG and NG populations, respectively.

overall_design: All samples were obtained from female Balb-C mice at 8-12 weeks. The following samples were used for RNA-sequence analysis: The heart-specific DRG (DRG-HS, three samples, each sample was obtained from three or four animals (n=3/4)), the heart-specific NG (NG-HS; two samples, each sample was obtained from two animals), sham DRG (DRG-T; two samples, each sample was obtained from one animal (n=1)), and sham NG (NG-T; two samples, each sample was obtained from one animal (n=2)). By using the RNeasy micro kit (Qiagen), RNA was extracted from each sample. Before further progress, RNA concentrations were measured using Qubit (Thermo Fisher Scientific) and RNA integrities were assessed on Agilent 2100 Bioanalyzer. In RNA Seq, only the samples with the an average of 7.5 RNA integrity number (RIN) were included. RNA libraries were prepared using Truseq Total RNA Sample Preparation Kit v2. 500 ng/µl and 200 ng/µl of RNA were used for each DRG and NG sample, respectively. Fragments were sequenced as paired-end reads (2 x 75 bp) on the Illumina NextSeq 500 platform in İstanbul Medipol University, Center of Genomics.

last: Akgul Caglar

first: Yusuf

last: Enes Kazci


title: Identification of a new subpopulation of myonuclei during skeletal muscle hypertrophy

status: Public on Aug 14 2025

city: Paris

first: Léa

last: Delivry

address: 24 rue faubourg Saint-Jacques

country: France

institute: Cochin Institute

summary: We have employed a single nucleus sequencing approach using 10x Genomics snRNA-seq to study the process of skeletal muscle hypertrophy. We examined the plantaris muscle of control adult mice (Ctl) and adult mice after 7 days of induced overload (7OV). This study highlights a new subpopulation of myonuclei in the muscles of control and hypertrophied mice.

overall_design: We used 3 mice model : C57bl6N (WT), ROSAmTmG;PAX7CREert2/+ (mTmG) and HSA-Cre-ERT2:RhoAflox/flox (Mut). The plantaris muscle underwent compensatory surgery and were removed 7 days later with the control plantaris muscles. Nuclei were sorted by Fluorescence-activated cell sorting (FACS) with DAPI and analyzed using snRNA-seq.

first: Pascal

last: Maire

first: Athanassia

last: Sotiropoulos


title: Comprehensive transcriptomic characterization of two melanoma cell lines with acquired dual resistance to BRAF and MEK inhibitors: toward understanding and reversing therapy resistance

status: Public on Aug 16 2025

first: Tomasz

last: Kobiela

address: Noakowskiego 3

department: Faculty of Chemistry

institute: Warsaw University of Technology

summary: To elucidate the molecular mechanisms underlying acquired resistance to dual BRAF and MEK inhibition, we performed transcriptomic profiling of two melanoma cell lines, Hs294T and WM9, rendered resistant to the combination of vemurafenib and cobimetinib.RNA-seq analysis revealed distinct resistance-associated gene expression signatures in each model, with only partial overlap, suggesting divergent adaptive responses to the same therapeutic pressure. Both resistant cell lines exhibited strong upregulation of extracellular matrix compo-nents, epithelial-mesenchymal transition (EMT) markers, and chemokine signaling genes, along with repression of melanocytic lineage markers. Inference of transcription factor and kinase activity uncovered line-specific regulatory rewiring, including activa-tion of MYOCD, SMAD3, and TP53, and suppression of immune regulators such as RFX5 and RFXANK. Network-based analysis identified key resistance hubs - IL6, FN1, COL1A1, and EGFR. WM9 cells showed broader transcriptional reprogramming and prominent engagement of inflammatory and immune-related pathways. At the same time, Hs294T resistance was marked by a more restricted program focused on stromal remodeling and impaired antigen presentation.

overall_design: RNA-seq profiling of Hs294T and WM9 cell lines with acquired dual resistance to to the combination of vemurafenib and cobimetinib and their respective controls (sensitive cells). Each group contained three biological replicates, resulting in six samples per cell line and twelve samples in total.

last: Kujawa


title: Transcriptomic profiling of irradiated senescent IMR90 cells treated with CDK4/6 or JAK inhibitors

status: Public on Aug 13 2025

city: La Jolla

first: Peter

middle: D.

last: Adams

address: 10901 North Torrey Pines Road

department: Cancer Genome and Epigenetics Program

institute: Sanford Burnham Prebys Medical Discovery Institute

summary: Human fetal lung fibroblasts (IMR90) were induced to undergo senescence via ionizing radiation (IR). Ten days post-IR, RNA was collected from proliferating, senescent+DMSO, senescent+Palbociclib (2 µM), and senescent+Ruxolitinib (2 µM) conditions. Cells were treated on Days 4, 6, 8 and 10 after IR. This dataset examines how CDK4/6 or JAK inhibition affects gene expression in senescent cells.

overall_design: IMR90 cells were exposed to ionizing radiation to induce senescence. Treatments began on Day 4 post-irradiation and were repeated on Days 6, 8 and 10. Cells were harvested on Day 11 for RNA-seq. Experimental groups include: 1) proliferating control, 2) senescent+DMSO, 3) senescent+Palbociclib (2 µM), 4) senescent+Ruxolitinib (2 µM). RNA was isolated and sequenced using the Illumina platform.

first: Adarsh

last: Rajesh


title: scRNA-seq of microglia from Cx3cr1CreERT2(Litt) adult mice reveals gene expression profile after TAM treatment.

status: Public on Aug 15 2025

city: Fukuoka

first: Minako

last: Ito

address: 3-1-1 Maidashi, Higashi-ku

country: Japan

institute: Kyushu University

summary: The Cx3cr1CreERT2(Litt) mouse model is widely used for in-depth studies of myeloid cells, including microglia. In this study, we employed single-cell RNA sequencing (scRNA-seq) to characterize microglial responses to tamoxifen (TAM) administration in adult Cx3cr1CreERT2(Litt) mice. Our analysis revealed a prolonged TAM-dependent induction of CDKN1A in the microglial population, highlighting a effect of the Cre-induction system itself.

overall_design: Transcriptome profiles of microglia from whole brains of Cx3cr1-CreERT2(Litt) mouse models with TAM-treatment were generated, following the 10x Gemomics protocol.

first: Takahiro

last: Masuda

first: Ayato

last: Yamasaki


title: Hepatocyte‑specific Ccnd1 knockout in aged mice reduces inflammatory signaling

summary: We performed hepatocyte‑specific knockout of Ccnd1 in 17‑month‑old C57BL/6J mice using AAV8‑TBG‑saCas9 with Ccnd1‑targeting sgRNA versus Rosa26 control. After 3 weeks, livers were harvested for bulk RNA‑seq to assess effects of elevated Ccnd1 with age.

overall_design: Upon receipt, mice were rested for ≥2 weeks and maintained on normal chow. At 17 months, mice received retro‑orbital AAV8‑TBG‑saCas9–U6-sgCcnd1 (3×10¹¹ vg/mouse) or Rosa26 control; livers (m‑lobe) were harvested 3 weeks later for bulk RNA‑seq.


title: Bulk RNA‑seq of IMR90 fibroblasts in IR‑induced senescence with siRNA knockdowns of CCND1, CDK4, CDK6 and controls

summary: We profiled transcriptomes of IR‑induced senescent IMR90 fibroblasts subjected to siRNA‑mediated knockdown of CCND1, CDK4, CDK6 (and CDK4+6), alongside two non‑targeting controls. Transfections occurred on days 4/5 and 7/8 post‑IR; all samples were harvested day 10 for RNA extraction. Differential expression identifies kinase‑specific roles in sustaining inflammatory and DNA damage responses in senescence.

overall_design: Conditions (n=3 each): • Proliferating (No IR) • Senescent + NT1 • Senescent + NT2 • Senescent + CCND1 KD • Senescent + CDK4 KD • Senescent + CDK6 KD • Senescent + CDK4+CDK6 KD Harvest day 10 post‑IR/transfections


title: Leaf transcriptome of apple knock-out transgenic lines of MdAGG by CRISPR/Cas9 strategy

status: Public on Aug 12 2025

city: Beaucouzé

first: Matthieu

last: Gaucher

address: 42 rue Georges Morel

department: SPE

institute: INRAE

summary: Investigation of whole genome gene expression level changes in Acibenzolar-S-methyl-treated leaves of three MdAGG-knock-out transgenic lines (mdagg-2, mdagg-3 and mdagg-4) versus treated but non-transformed plants (wild-type)

overall_design: A total of 8 samples, corresponding to 2 biological replicates (bulk of leaves from 2 independent experiments) for each transgenic lines and non-transformed control, were used for differential gene expression analysis. Plants were treated with acibenzolar-S-methyl (ASM) and leaves were collected 3 days post-treatment.

first: Antoine

last: Bodelot

first: Emilie

last: Vergne

first: Axelle

last: Frantz

first: Alexandre

last: Degrave


title: Investigation of the global translational response to oxidative stress in the model archaeon Haloferax volcanii reveals untranslated small RNAs with ribosome occupancy [RNA-Seq]

status: Public on Aug 11 2025

city: Baltimore

first: Emma

last: Dallon

address: 3400 N Charles St Levi 235

department: Biology

institute: Johns Hopkins University

summary: Oxidative stress induces a wide range of cellular damage, often causing disease and cell death. While many organisms are susceptible to the effects of oxidative stress, haloarchaea have adapted to be highly resistant. Several aspects of the haloarchaeal oxidative stress response have been characterized, however little is known about the impacts of oxidative stress at the translation level. Using the model archaeon Haloferax volcanii, we performed RNA-seq and ribosome profiling (Ribo-seq) to characterize the global translation landscape during oxidative stress. We identified 281 genes with differential translation efficiency (TE). Downregulated genes were enriched in ribosomal and translation proteins, in addition to peroxidases and genes involved in the TCA cycle. We also observed upregulated TE for many transporters and membrane-bound proteases, highlighting the importance of membrane dynamics during oxidative stress. We additionally identified 42 small noncoding RNAs (sRNAs) with ribosome occupancy. Size distributions of ribosome footprints revealed distinct patterns for coding and noncoding genes, with 12 sRNAs matching that of coding genes, and mass spectrometry confirming the presence of seven small proteins originating from sRNAs. However, the majority of sRNAs with ribosome occupancy had no evidence of coding potential. Of these ribosome-associated sRNAs, 12 had differential ribosome occupancy or TE during oxidative stress, suggesting that they may play a regulatory role during the oxidative stress response. In combination with the evidence of regulation at the translation level during oxidative stress, this demonstrates the complexity of gene regulation during stress response.

overall_design: We performed RNA-seq and Ribo-seq using wild-type H. volcanii cultures with and without oxidative stress treatment, using four biological replicates for each condition. We additionally performed RNA-seq on 3 sRNA knockout strains with oxidative stress treatment, using three biological replicates for each. Three biological replicates of wild-type, with and with stress treatment, were included as controls.

first: Haley

last: Moran

first: Sadhana

last: Chidambaran

first: Arman

last: Kian

first: Betty

last: Huang

first: Stephen

last: Fried

first: Jocelyne

last: DiRuggiero


title: The Role of NF-κB Signaling Pathway in Lacrimal Gland Damage in Primary Sjögren’s Syndrome: an in vivo study

status: Public on Aug 25 2025

city: Hangzhou

first: Jiajun

last: Xie

state: Zhejiang

address: No. 88 Jiefang Rd

institute: Zhejiang University, Eye Center of Second Affiliated Hospital, School of Medicine, China

summary: Primary Sjögren’s syndrome (pSS) is an autoimmune disease characterized by inflammation and damage to exocrine glands, leading to symptoms such as dry eye and reduced tear production. The NF-κB signaling pathway plays a critical role in the inflammatory processes underlying pSS. The aims of the present in vivo study were to investigate the role of NF-κB signaling in lacrimal gland damage and tear secretion in the NOD/Ltj mouse, and to explore the therapeutic potential of NF-κB inhibition. The animal model was established using NOD/Ltj mouse and lacrimal gland pathological change was showed by H&E. Bioinformatics analysis was conducted through RNA sequencing (RNA-seq) and confirmed by RT-qPCR and Western blot. The NOD/Ltj mouse were treated with NF-κB inhibitor JSH-23. Tear secretion assays, ELISA, TUNEL staining, immunofluorescence, immunohistochemistry, and flow cytometry were employed to assess the role of NF-κB signaling in tear production, inflammatory cytokine expression, cell apoptosis, differentially expressed genes (DEGs), and cell differentiation in lacrimal gland damage in pSS mouse. NF-κB signaling was significantly activated in NOD/Ltj mouse lacrimal gland and pSS-related dry eye. NF-κB blockage decreased cell apoptosis, reduced inflammatory cytokine expression, and inhibited Th17 cell differentiation in NOD/Ltj mouse lacrimal glands, as well as restored tear production and normalized the expression of DEGs CARD14 and CCL19. NF-κB signaling played a pivotal role in lacrimal gland damage in pSS model NOD/Ltj mouse by involvement of cell apoptosis, inflammatory cytokine expression and Th17 cell differentiation. Targeting NF-κB signaling may offer a promising therapeutic approach for managing pSS-related dry eye.

overall_design: RNA-seq profiling of lacrimal glands of NOD/Ltj mouse and ICR mouse.

first: Huina

last: Zhang

first: Wenyue

last: Shen

first: Juan

last: Ye


title: Single-cell RNA and DNA methylome profiling reveal liquid helium vitrification enhances porcine parthenogenetically activated blastocyst viability [Bisulfite-Seq]

city: Beijing

first: Baigao

last: Yang

address: Yuaningyuan 2

institute: Institute of Animal Sciences of CAAS

type: Methylation profiling by high throughput sequencing

summary: Transcriptome and methylation sequencing technologies were used to reveal the effects of vitrification on gene expression and genomic methylation levels in pig blastocysts.

overall_design: A fresh control group A, a vitrified freezing group B, a vitrified freezing group C, and a vitrified freezing group H were set up.

first: Xueming

last: Zhao

first: Hongmei

last: Pan


title: Single-cell RNA and DNA methylome profiling reveal liquid helium vitrification enhances porcine parthenogenetically activated blastocyst viability [RNA-Seq]


title: E2F1 induces a G0-G1 re-entry transcriptional program without changing chromatin accessibility [ChIP-seq]

status: Public on Sep 26 2025

city: Santa Cruz

first: Ali

middle: S

last: Shariati

state: CA

address: 1156 High St

department: Biomolecular Engineering

institute: University of California Santa Cruz

summary: Many cells in our body reside in a reversible nondividing state termed G0 or quiescence. Precise regulation of entry and exit from G0 is critical for maintaining tissue homeostasis. G0 entry can occur when cells do not receive the required signals for cell cycle progression, leading to active repression of cell cycle genes through several mechanisms, including formation of repressor complexes to restrict chromatin accessibility for transcriptional activators. G0 cells can re-enter the G1 phase of the cell cycle upon receiving growth factor signals, resulting in activation of the Mitogen-Activated Protein Kinase pathway, converging on E2F transcription factors. Ectopic expression of E2F1 alone, a transcriptional activator, is sufficient to promote G0 exit without requiring the upstream signals, but it is unclear how E2F1 can overcome the chromatin lockdown in G0 cells to activate cell cycle genes. To better understand this mechanism, we compared dynamics, gene regulation and chromatin accessibility state between E2F1-mediated and growth factor (serum)-induced cell cycle reentry. Using live cell single cell tracking, we observe that E2F1 induction leads to accelerated cell cycle progression compared to regular serum-induced cell cycle re-entry. This accelerated cell cycle re-entry by E2F1 is accompanied by faster upregulation of cell cycle genes. Interestingly, we find that E2F1 preferentially binds to gene promoters that remain in a poised chromatin state after G0 induction, suggesting that G0 cells are prepared for cell cycle re-entry via regulating chromatin states in essential cell cycle genes.

overall_design: Constucts for doxycycline inducible expression of E2F1 or empty-vector (EV) control were stably integrated into 3T3 cells. The E2F1 and EV 3T3 cells were serum starved for 48 hours to induce a G0-like state, followed by E2F1 induction, EV induction or 10% serum addition, to induce G1/S phase reentry. Samples were collected at 0, 2, 6 and 12 hours after induction or serum addition. RNA was extracted for RNA-sequencing and nuclei were extracted for ATAC-Seq. In addition, cells were prepared for E2F1 ChIP-Seq at the 12 hour time point only. Together the RNA-Seq, ATAC-Seq and ChIP-Seq were used to identify E2F1 gene regulatory network involved in cell cycle reentry from G0.

first: Gerrald

last: Lodewijk

first: Benjamin

last: Topacio

first: Silvart

last: Arabian

first: Seungho

last: Lee

first: Abolfazl

last: Zargari

first: Znala

last: Williams

first: Edward

last: Wu

first: Sayaka

last: Kozuki

first: Rana

last: Rahimi

first: Neda

last: Bidoki

first: Vanessa

last: Jonsson

first: Eric

last: Malekos

first: Susan

last: Carpenter

first: Gerd

last: Muller

first: Seth

last: Rubin


title: Identification of two epitypes of IGHV unmutated chronic lymphocytic leukemia with distinct B cell-related epigenetic imprinting and genetic alterations

city: Barcelona

first: Jose Ignacio

last: Martin-Subero

state: Barcelona

address: c/Rosselló, 149-153

country: Spain

institute: IDIBAPS

type: Methylation profiling by genome tiling array

summary: Genetic and epigenetic changes have provided essential insights into the biology and clinical behavior of chronic lymphocytic leukemia (CLL). Overall, increasing number of chromosomal aberrations are related to disease evolution. Complex karyotype (CK) is defined as presence of at least 3 numerical and/or structural aberrations detected by chromosome banding analysis. CK frequently occur in the context of CLLs with unmutated IGHV (U-CLL) and are associated with mutations in ATM or TP53. In this context, the relationship of karyotype complexity and DNA methylation aberrations in CLL remains largely unexplored. In the present study, we selected a highly curated cohort of 52 U-CLL cases with known karyotypes and ATM and TP53 aberration status. An unsupervised Principal Component Analysis using all the CLL samples showed that there is no specific clustering according to karyotype complexity. Although CK was not a major driver of epigenetic variability, a differential methylation (DM) analysis between CK vs non-CK samples led to a small signature of 59 CpGs, suggesting only a subtle relationship between karyotypic complexity and DNA methylation. We noticed that cases with deletions in ATM and TP53 tend to cluster differently in the first two principal components independently of karyotype complexity. A consensus clustering analysis using the 5,000 most variable CpGs confirmed the two clusters, which were enriched in ATMdel (U-CLL C1, P=0.015) and TP53del/mut (U-CLL C2, P=0.004), respectively. U-CLL C1 was also enriched in ATM mutations (P=0.017) and del(13q) (P=0.007), while U-CLL C2 was also related to trisomy 12 (tri12) (P=0.004). Both clusters showed a similarly unfavorable clinical behavior, both in terms of time to first treatment and overall survival. A DM analysis between them resulted in 4,333 differential CpGs. Surprisingly, despite the fact that all the cases are U-CLLs, and therefore germinal center-inexperienced, 2,150 CpGs were modulated in normal B-cell differentiation. Remarkably, 87% of those CpGs showed that cases in the U-CLL C1 cluster are associated with a DNA methylome of less mature B cells (more similar to NBC) whereas cases in the U-CLL C2 were related to more mature B cells (more similar to MBC). A phylogenetic analysis using previously reported CpGs significant for normal B-cell differentiation confirmed this observation. The remaining DM CpGs between the two clusters were largely related to a de novo DNA hypomethylation signature (n=1,679 CpGs) in the U-CLL C2 cluster. In summary, despite not finding a major relationship between complex karyotype and DNA methylation, we discovered the presence of two epitypes in the U-CLL dataset with distinct genetic profiles and methylation signatures related to different levels of epigenetic imprinting, a finding reinforcing the perception that CLL rises from a continuum of B-cell maturation stages.

overall_design: Illumina Infinium MethylationEPIC v1.0 commercial kit

first: Stella

last: Charalampopoulou