title: Novel insights into Emx2 and Dmrta2 cooperation during cortex development and evidence for Dmrta2 function in choroid plexus

status: Public on Jun 01 2025

city: GOSSELIES

first: Abdulkader

last: AZOUZ

address: Rue Adrienne Bolland, 8

country: Belgium

institute: Université Libre de Bruxelles

summary: Early dorsal telencephalon development is coordinated by an interplay of transcription factors that exhibit a graded expression pattern in neural progenitors. How they function together to orchestrate cortical development remains largely unknown. The Emx2 and Dmrta2 genes encode TFs that are expressed in a similar caudomedialhigh/ rostrolaterallow gradient in the ventricular zone of the developing dorsal telencephalon with, in the medial pallium, Dmrta2 but not Emx2 expressed in the developing choroid plexus. Their constitutive loss has been shown to impart similar cortical abnormalities, and their combined deletion exacerbates the phenotypes, suggesting possible cooperation during cortex development. In this study, we utilized molecular and genetic approaches to dissect how Emx2 functions with Dmrta2 during mouse cortical development. Our results show that while they regulate a similar set of genes, their common direct targets are limited but include key regulators of cortical development. The identification of the interaction partners of Emx2 suggests that it coordinates with the LIM-domain binding protein Ldb1 to execute the activation and repression of some of its downstream targets. Finally, while Emx2 is known to suppress choroid plexus development, we also provide evidence that Dmrta2 is, in contrast, required for choroid plexus since in its absence in medial telencephalic progenitors, mice develop hydrocephalus postnatally, a phenotype that appears to be due to a compromised cytoarchitecture. Together, these data indicate that Emx2 and Dmrta2 have similar but also distinct functions in telencephalon development and provide the first insights into Emx2 mechanism of action.

overall_design: ChIP-seq of EMX2-3xFlag-V5 in  Cortices from E12.5 embryos

first: Jithu

last: Anirudhan

first: Xueyi

last: Shen

first: Tünde

last: Szemes

first: Marc

last: Dieu

last: Azouz

first: Louise

last: Conrard

first: Nicolas

last: Passon

first: Gilles

last: Doumont

first: Maren

last: Sitte

first: Younes

last: Achouri

first: Sadia

last: Kricha

first: Gabriela

last: Salinas

first: Patricia

last: Renard

first: Eric

middle: J

last: Bellefroid


title: Sensory neurons drive pancreatic cancer progression through glutamatergic cancer-neuron pseudo-synapses

city: Munich

first: Rouzanna

last: Istvánffy

address: Ismaningerstr. 22

department: Department of Surgery

country: Germany

institute: Klinikum rechts der Isar

type: Expression profiling by high throughput sequencing

summary: The results provide significant insights into the role of Grin2D in regulating the secretion of neurotrophic factors that promote neuritogenesis. Transcriptomic analysis of orthotopically transplanted PDAC cancer cells with a knockout of the NMDA receptor subunit Grin2D, along with dorsal root ganglia (T8–T12) innervating the pancreas, strongly supports this conclusion. Furthermore, RNA-Seq analysis of tumor and ganglion biopsies from PDAC patients was performed to validate the identified gene candidates in a human context.  This study tested the hypothesis that neuronal glutamate drives pancreatic cancer progression via glutamate-mediated GluN2D signaling at the cancer-neuron pseudo-synapses.

overall_design: For the analysis, murine KPC cancer cells with Grin2d-KO were orthotopically transplanted into C57BL/6N wild-type mice. As controls, WT KPC cells were used. After transplantation, RNA-seq was performed on the tumors of these mice from each group, along with dorsal root ganglia (T8–T12) innervating the pancreas. Furthermore, RNA-seq was also conducted on tumor and ganglion biopsies from PDAC patients.

first: Lei

last: Ren

first: Ekin

last: Demir


title: miRNA expression profiles in exosomes extracted from FAPs.

city: ChongQing

first: 檬檬

last: 杨

state: ChongQing

address: No. 1 Medical College Road, Yuzhong District

department: School of Basic Medical Sciences

country: China

institute: 重庆医科大学

type: Non-coding RNA profiling by high throughput sequencing

summary: Skeletal muscle maintains remarkable regenerative ability after injury, which mainly depends on the coordination and dynamic regulation between muscle stem cells and various other cell types. Recent studies have shown that fibro/adipogenic progenitors (FAP) play an important role in skeletal muscle regeneration by coordinating the interaction between muscle stem cells and macrophages. At present, the mechanism of whether FAP cells can regulate macrophages to affect skeletal muscle regeneration remains unclear. By isolation of mouse skeletal muscle FAP cells damaged by CTX for 10 days and gathered exosomes from them called FAPD10-exos, and using the exosomes to induce macrophages in vitro, we found that they expressed high levels of M2-type factors.In summary, we believe that FAPD10-exos can promote the polarization of macrophages towards M2 phenotype by secreting exosomes, and participate in and promote the regulation and regulation of skeletal muscle regeneration to enter the stage of damage repair in the early stage of regeneration.

overall_design: In order to explore which molecule plays a key role in FAP exosomes, we performed sRNA sequencing on the two isolated exosomes (FAPD3-exos and FAPD10-exos) and analyzed the differential expression of miRNA among them.

first: Mengmeng

last: Yang

first: Jingya

last: Luo


title: Transcriptomic profiling of RAW264.7 treated by FAPD10-exos.

overall_design: To explore what role FAPD10-exos plays in M2 polarization of macrophages, IL4 and FAPD10-exos were used to culture RAW264.7, and mRNA was collected for RNA sequencing.


title: Benchmarking Peak Calling Methods for CUT&RUN

status: Public on Jun 02 2025

city: Toronto

first: Amin

last: Nooranikhojasteh

state: ON

address: 101 College Street

country: Canada

institute: Princess Margaret Cancer Centre

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Cleavage Under Targets and Release Using Nuclease (CUT&RUN) has rapidly gained prominence as an effective approach for mapping protein-DNA interactions, especially histone modifications, offering substantial improvements over conventional chromatin immunoprecipitation sequencing (ChIP-seq). However, the effectiveness of this technique is contingent upon accurate peak identification, necessitating the use of optimal peak calling methods tailored to the unique characteristics of CUT&RUN data. Here, we benchmark four prominent peak calling tools - MACS2, SEACR, GoPeaks, and LanceOtron - evaluating their performance in identifying peaks from CUT&RUN datasets. Our analysis utilizes in-house data of three histone marks (H3K4me3, H3K27ac, and H3K27me3) from mouse brain tissue, as well as samples from the 4DNucleome database. We systematically assess these tools based on parameters such as the number of peaks called, peak length distribution, signal enrichment, and reproducibility across biological replicates. Our findings reveal substantial variability in peak calling efficacy, with each method demonstrating distinct strengths in sensitivity, precision, and applicability depending on the histone mark in question. These insights provide a comprehensive evaluation that will assist in selecting the most suitable peak caller for high-confidence identification of regions of interest in CUT&RUN experiments, ultimately enhancing the study of chromatin dynamics and transcriptional regulation.

overall_design: CUT&Run (H3K4me3, H3K27ac, H3K27me3) of mouse brain tissue.

first: Ghazaleh

last: Tavallaee

first: Elias

last: Orouji


title: Multiome single-cell RNA and ATAC sequencing from Young and Old Hematopoietic Stem Cells (HSCs)

city: New York

first: Harold

middle: Kunal

last: Elias

state: New York

address: 417E 68th Street

department: Pathology

country: USA

institute: Memorial Sloan Kettering Cancer Center

summary: We used multiome single cell  RNA and ATAC (scRNA+scATAC) sequencing to analyze the heterogeneity in young and old HSCs

overall_design: HSCs  from from Young (8-10 week-old ) and Old (22-23-month-old) C57BL/6 mice were Fluoroscent-Activated Sorted based on immunophenotypic definition (Lineage-CD34-CD48-CD150+LSK)

middle: K

last: Ellias

first: Marcel

middle: R

last: van den Brink

first: Anastasia

middle: I

last: Kousa

first: Sneha

last: Mitra


title: A phage-encoded metallophosphoesterase determines the viral host range and is essential for escaping the anti-phage defense of Mycobacterium tuberculosis

city: Nanning

first: Zheng-Guo

last: He

state: Guangxi

address: 100 Daxue east road

institute: Guangxi university

summary: The molecular mechanism by which a mycobacterial virus escapes the host bacterial defense and kills the human pathogen Mycobacterium tuberculosis is greatly unclear. Here we report that the gene gp48 of mycobacteriophage A4ZJ24, encoding a metallophosphoesterase-like protein, is required for the killing of M. tuberculosis, but not for M. smegmatis. Gp48 is expressed in the early stage of phage infection and disrupts the mycobacterial chromosomal DNA, and thus silences the expression of multiple anti-phage defensive genes, which only exist in the genome of M. tuberculosis but not in M. smegmatis. The gp48-deleted phage can normally adsorp and invade into M. tuberculosis, however, it does not prevent from activating anti-phage genes, resulting in a loss of its genome DNA replication ability in M. tuberculosis. This study identifies a phage’s metallophosphoesterase as a new determinant of the viral host range and discovered a previously unknown molecular mechanism for mycobacteriophages to kill M. tuberculosis. Our study fills a major gap in current knowledge of the interaction between mycobacterial viruses and M. tuberculosis.

overall_design: To investigate the changes in gene expression levels of mycobacterium tuberculosis during infection with A4ZJ24 phage and gp48-deleted mutant phage, we used two mycobacteriophage to infect M. tuberculosis, and the samples were taken at 1h or 10h after infection. We then performed gene expression profiling analysis using data obtained from RNA-seq of 2 samples at two different time points. Comparative gene expression profiling analysis of RNA-seq data for A4ZJ24 WT and A4ZJ24 Δgp48.

first: Junlong

last: Li

first: Xiao

last: Guo

first: Zhengguo


title: Divergent regulatory element programs steer sex-specific supporting cell differentiation along mouse gonadal development [RNA-Seq]

city: Ramat Gan

first: Isabelle

last: Stévant

address: Institute of Nanotechnology and Advanced Materials, Building 206

country: Israel

institute: University of Bar Ilan

summary: Identifying cis-regulatory elements is essential for understanding how gene expression is precisely controlled during critical biological processes like sex determination. In this study, we aimed to uncover the cis-regulatory regions involved in the differentiation of supporting cells as Sertoli cells or pre-granulosa cells in the mouse gonads.  To achieve this, we combined RNA sequencing (RNA-seq) and Assay for Transposase-Accessible Chromatin sequencing (ATAC-seq) of purified supporting cells at four developmental stages in both sexes. RNA-seq enabled us to capture sexual and temporal changes in gene expression during cell differentiation, while ATAC-seq provided insight into chromatin accessibility, pinpointing regulatory regions that control these expression patterns. By integrating these two datasets, we identified specific cis-regulatory elements that likely guide the fate of supporting cells.  Our findings shed light on the complex gene regulatory networks involved in sex fate differentiation, highlighting the critical role of cis-regulatory elements in orchestrating this process. These insights may also have implications for understanding disorders of sexual development (DSDs).

overall_design: We purified by FACS pre-granulosa and Sertoli cells from mouse fetal gonads and performed bulk RNA-seq and ATAC-seq in triplicates at four developmental stages (E11.5, E12.5, E13.5 and E15.5).

first: Elisheva

last: Abberbock

first: Meshi

last: Ridnik

first: Roni

last: Weiss

first: Linoy

last: Swisa

first: Christopher

last: Futtner

first: Danielle

last: Maatouk

first: Robin

last: Lovell-Badge

first: Nitzan

last: Gonen


title: Divergent regulatory element programs steer sex-specific supporting cell differentiation along mouse gonadal development [ATACseq]

summary: Identifying cis-regulatory elements is essential for understanding how gene expression is precisely controlled during critical biological processes like sex determination. In this study, we aimed to uncover the cis-regulatory regions involved in the differentiation of supporting cells as Sertoli cells or pre-granulosa cells in the mouse gonads.  To achieve this, we combined ATAC sequencing (ATAC-seq) and Assay for Transposase-Accessible Chromatin sequencing (ATAC-seq) of purified supporting cells at four developmental stages in both sexes. ATAC-seq enabled us to capture sexual and temporal changes in gene expression during cell differentiation, while ATAC-seq provided insight into chromatin accessibility, pinpointing regulatory regions that control these expression patterns. By integrating these two datasets, we identified specific cis-regulatory elements that likely guide the fate of supporting cells.  Our findings shed light on the complex gene regulatory networks involved in sex fate differentiation, highlighting the critical role of cis-regulatory elements in orchestrating this process. These insights may also have implications for understanding disorders of sexual development (DSDs).


title: Modulation of mitochondrial abundance in pluripotent stem cells and embryos

city: Dallas

first: Leijie

state: Texas

address: 5323 Harry Hines Blvd.

department: Molecular Biology

institute: UNIVERSITY OF TEXAS SOUTHWESTERN MEDICAL CENTER

summary: For billions of years, mitochondria have fueled the development of all eukaryotic organisms. Despite their ubiquitous presence, whether mitochondria are necessary for eukaryotic life has never been directly assessed, as strategies to generate eukaryotic models with partially reduced, or completely eliminated, mitochondrial content are limiting. To establish a system in which we can study the necessity for mitochondria in mammalian physiology and development, we established an enforced mitophagy system that allows for the efficient and complete removal of mitochondria from human and mouse pluripotent stem cells (PSCs). We found these cells to maintain many aspects of pluripotency, including the abilities to maintain expression of most mitochondrial genes and give rise to other cell types despite a complete lack of mitochondria. Moreover, we devised a transgenic method that allows for the reduction of mitochondria from in vivo mouse embryos and reveal a threshold of mitochondrial abundance necessary to maintain pre-implantation embryonic development and embryo cleavage.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: To study how mitochondria influence gene expression in pluripotent stem cells, we established mESCs and hESCs devoid of mitochondria using an inducible PRKN enforced mitophagy system.

first: Daniel

middle: A

last: Schmitz

first: Seiya

last: Oura

first: Yi

last: Ding

first: Emily

last: Ballard

first: Jun

last: Wu


title: Role of metabolism in sorafenib-resistance hepatocellular carcinoma cellular model.

city: Milan

first: Pasquale

last: Tomaiuolo

state: Milan

address: via Balzaretti n.9

department: Department of Pharmacologic Sciences

country: Italy

institute: University of Milan

summary:
Hepatocellular carcinoma (HCC) is the most prevalent type of liver cancer and the third leading cause of cancer-related deaths worldwide. Potentially curative treatment of HCC involves various possibilities based on the stage of the disease. For the advanced stage of this disease, sorafenib is one of the first-line treatment options. It is an oral tyrosine kinase inhibitor, targeting several signalling pathways involved in tumor growth and angiogenesis.However, its usage is limited because many patients develop resistance after a short period (six months) of treatment.
Hepatoblasts knock-out for p53, and overexpressing Myconcogene(p53-/-; Myc) are used to reproduce the genetic settings of HCCin vitroand are treated with sorafenib attwo different time points: short (48 hours) and long (7 days) exposure.
Thecombination oftranscriptomic and metabolomicdata was utilizedto unravel the effect of this drug on cellular metabolism and mitochondrial function,with the final aim of increasing the effectiveness of sorafenibtreatment.

overall_design: We conducted an RNAseq and metabolomic approach to unravel the effect of Sorafenib on metabolism and mitochondrial function in Hepa p53 -/-,myc cells.


title: BEAM-T single cell sequencing of antigen-specific memory CD8+ T cell with age

city: Rochester

first: Abhinav

last: Jain

address: 200 1st ST SW

institute: Mayo Clinic

summary: Aging trajectories of antigen-specific memory T cells are heterogenous and complex but incompletely understood. We use single-cell sequencing of EBV (Epstein Barr virus)- or VZV (Varicella Zoster virus)-antigen specific T cells of younger or older adults to analyze memory T cell heterogeneity in early and late life.

overall_design: Antigen-specific, human peripheral blood CD8+ T cells against 8 EBV epitopes and 2 VZV epitopes were analyzed using single-cell sequencing via 4 modalities per cell (gene expression, surface marker/feature barcodes, T cell receptor sequences, and antigen-specificity using Barcode Enabled Antigen Mapping, BEAM-T).

first: Ines

last: Sturmlechner

first: Jorg

last: Goronzy


title: Trade-off Between Resistance and Persistence in High Cell Density Escherichia Coli Cultures

city: Kgs. Lyngby

first: Felix

last: Beulig

address: Kemitorvet 220

country: Denmark

institute: Novo Nordisk Center for Biosustainability

summary: Microbes experience high cell density in many environments that come with diverse resource limitations and stresses. However, high density physiology remains poorly understood. We utilized well-controlled culturing systems to grow wild-type and metabolically engineered Escherichia coli strains into high cell densities (50–80 g Cdry cell weight L-1) and explore the associated transcriptional dynamics. Knowledge-enriched machine-learning-based analytics reveal distinct stress-related gene expression patterns that are consistent with a fundamental trade-off between resistance and persistence. We suggest that this trade-off explains observed growth arrests in high-density cultures and that it results from the disruption of cellular homeostasis, due to reallocation of limited cellular resources from resistance functions towards maintenance requirements of engineered production pathways. This study deepens our understanding of high-density physiology and demonstrates its importance to fundamental biomanufacturing challenges.

overall_design: High cell density cultivation experiments were conducted following a common two-stage, batch-to-fed-batch, fermentation strategy in parallel sets of bioreactors. We studied five groups of E. coli strains with varying degree of engineering, including a wildtype BW25113 control strain (WT), different single gene knockout strains (SGKO), two tryptophan production strains (HMP3071 and empty plasmid control SDT551), and a plasmid-carrying melatonin production strain (HMP3427). After initiation of the fed-batch phase, growth was maintained with exponential feeding strategies, providing a continuous supply of media, O2 and pH buffering capacity to all strains.


title: Thyroid dysplasia in C57BL/6NTac caused by a LINE-1 in Thyroglobulin

status: Public on May 31 2025

city: West Point

first: Zoltan

last: Erdos

state: PA

address: 770 Sumneytown Pike

institute: Merck

summary: A spontaneous mutation in the Taconic Biosciences wildtype C57BL/6NTac mouse was discovered that is associated with early-onset histopathologic sequalae typical of thyroid dysplasia. The spontaneous mutation resulted from insertion of a L1 long interspersed nuclear element (LINE-1) into an intron within the Thyroglobulin (Tg) gene. The mouse genome contains a significant amount of retrotransposon DNA, and these mobile genetic elements routinely change genomic location through retrotransposition, including in germ cells. Analysis of the thyroid transcriptome suggested that the presence of the LINE-1 interferes with the Tg gene splicing, resulting in exclusion of exon 26 from most Tg transcripts in animals homozygous for the insertion. The LINE-1 insertion allele of the Tg gene has been designated Tgtdys-Tac. The resulting phenotype is inherited in an autosomal dominant manner with affected mice exhibiting thyroid follicular cell dysplasia that progresses to thyroid adenoma by 9 months of age with complete penetrance in homozygotes. Serum thyroid hormone measurements revealed a decrease in triiodothyronine (T3) levels in homozygotes at 9 months and 12 months of age, as well as a decrease in tetraiodothyronine (T4) levels at 6-9 months in homozygotes and at 12 months of age in both heterozygotes and homozygotes. In addition, serum Thyroid Stimulating Hormone (TSH) level was strongly increased in homozygotes at 6-8 months of age, consistent with hypothyroidism. Computational molecular modeling showed that omission of the 61 amino acids from the TG protein arm domain, which is the consequence of exon 26-skipping in the Tg transcript, results in decreased local stability. This result in combination with the observed up-regulation in unfolded protein response pathways in the thyroids of affected animals, identifies the arm domain of TG as important for its proper cellular distribution. This report describes a spontaneous retrotransposon insertion causatively linked to dysregulated physiological phenotypes in a widely used inbred mouse strain.

overall_design: Wild type phenotype (CRW/TCKO) and Thyroid Dysplasia Phenotype from Taconic (TCW)was sequenced from mouse thyroid with Illumina

first: Bailey

last: Wendy

first: Smits M

middle: G

last: Barts

first: Erdos

last: Zoltan


title: Dual single-cell and bulk RNA sequencing reveal transcriptional profiles underlying heterogenous host-parasite interactions in human peripheral blood mononuclear cells

city: Midlothian

first: Musa

last: A Hassan

address: Easter Bush Campus

country: United Kingdom

institute: University of Edinburgh

summary: Toxoplasma gondii, a zoonotic apicomplexan that infects over a billion people worldwide, can cause early death in immunocompromised individuals and defects in foetal brain development. Toxoplasma is also a major cause of abortion in small ruminants. When Toxoplasma encounters host cells, several outcomes are possible. For example, the parasite can enter the host cell or can inject its effector proteins into the cell without entering. These heterogenous outcomes occur simultaneously in the same host and likely determine disease pathogenesis. Yet, current knowledge of host-Toxoplasma interactions is largely based on averaged responses in bulk cell populations. Here, we employed single cell RNA (scRNA) and bulk RNA sequencing to investigate the transcriptional profiles that underpin heterogenous host-Toxoplasma interaction in human peripheral blood mononuclear cells. We observed that Toxoplasma preferentially infects and elicits transcriptional responses in dendritic cells in human blood. Additionally, we observed that monocytes adopt a dendritic cell-like transcriptional profile over the course of infection. Using genes expressed in sorted host cell populations representative of the different heterogenous host-Toxoplasma interaction outcomes as a reference panel, we show that genes expressed in cells infected via phagocytosis are largely expressed in dendritic cells. Thus, by integrating scRNA and bulk RNA sequencing, our study unveils the transcriptional profiles of diverse Toxoplasma-host cell interaction outcomes, providing novel avenues for targeted investigations into host gene functions during Toxoplasma infections.

overall_design: THP-1 human monocytic cells were infected with either Toxoplasma gondii GUYDOS or RH1 strains. Parasite strains were fluorescently tagged, allowing for infected cells to be identified and sorted by flow cytometry based on fluorescence. RNA was extracted from sorted infected cells at two time points: 8 hours post-infection (hpi) and 24 hpi. This experimental setup enables the analysis of host transcriptional responses to different T. gondii strains and infection durations.

first: Chandrasegaran

last: Praveena

first: Faydaci

last: Bekir

first: Shih

last: Barbara

first: A Hassan

last: Musa


title: Transcriptome profiling of GTDs symptomatic vs. asymptomatic grapevine plants

city: Évora

first: Mariana

middle: Cardoso

last: Patanita

address: Pólo da Mitra, Ed. Santos Júnior, s.108

country: Portugal

institute: University of Évora

summary: Grapevine trunk diseases (GTDs) have become a major concern to viticulture worldwide, causing a high economic impact on yield and vineyard longevity in all growing areas. The prevalence of GTDs is increasing and, together with the absence of effective treatments, is currently one of the major challenges for viticulture sustainability. Given the urgent need to identify and develop new sustainable and effective protection strategies, a better understanding of grapevine defence mechanisms is crucial to develop more tolerant plants and provide new insights for disease management. This study explored the transcriptomic profile of GTDs symptomatic and asymptomatic plants of ‘Trincadeira’, a tolerant cultivar, and ‘Alicante Bouschet’, a susceptible cultivar to GTDs, using next-generation sequencing technology. RNA-seq yielded 1 598 differentially expressed genes (DEGs) between the two cultivars, and 64 DEGs between the groups with different symptomatology, regardless of the cultivar. Transport was revealed as the main biological process involved, generally activated in the susceptible cultivar ‘Alicante Bouschet’, suggesting that the DEGs associated with these processes may play an important role in disease development. Contrarily, the relative tolerance of ‘Trincadeira’ to this disease complex might be supported by the activation of secondary and hormonal metabolism and the differential expression of a set of defence-related genes, including resistance genes, which may act as key factors to limit GTDs infection. Furthermore, this study points to an important role of PER42 gene in the inhibition of GTDs symptoms. Our results provide new insights into the resistance mechanisms of grapevine to GTDs and may help to explain the different susceptibilities of grapevine plants to GTDs. To the best of our knowledge, this is the first time that the expression of grapevine defence-related gene expression has been studied in response to different GTDs-associated fungal infections under natural field conditions. We highlight the importance of these studies for the identification of candidate genes that may allow the development of new strategies to incorporate new sources of resistance. The activation or inhibition of potential plant response regulators can be used to promote resistance, thus providing sustainable and effective alternatives to successfully manage GTDs.

overall_design: Comparison of the transcriptomic data of GTDs symptomatic and asymptomatic grapevine plants from two different cultivars with different susceptibility patterns to this disease

first: Patanita

last: Mariana

first: Albuquerque

last: André

first: Campos

last: Maria Doroteia

first: Félix

last: Maria do Rosário


title: Modulation of NOTCH1 signaling in CLL and MCL cell lines

city: Ulm

first: Alena

middle: Sophie

last: Ehrmann

address: Albert-Einstein-Allee 23

department: Internal Medicine III

institute: University Hospital Ulm

summary: Aberrant active NOTCH1 signaling is a key pathogenic factor in chronic lymphocytic leukemia (CLL), detectable in half of patients and associated with disease progression. While some cases of active NOTCH1 signaling can be explained by mutations in NOTCH1 or its regulators, like FBXW7, alternative mechanisms remain elusive. Here, we identified the deubiquitinase USP28 as regulator of NOTCH1 signaling in CLL. Notably, USP28 is located within the frequently deleted chr11q23 region and is deleted in 90% of del(11q) patients, resulting in its decreased expression. USP28 interacts with the NOTCH1 intracellular domain (NICD) independently of FBXW7 and the NICD-PEST domain, stabilizing NICD and enhancing NOTCH1 signaling. Integrating RBPJ-occupied genes in HG3 cells, RNA-Seq of USP28WT/KO cells and gene expression from del(11q) CLL patients, we identified 15 NOTCH1 target genes specifically dysregulated by USP28 and del(11q) potentially influencing CLL pathogenesis. Pharmacological inhibition of USP28 with the small molecule AZ1 suppressed NOTCH1 activation in primary CLL cells. AZ1 combined with the BCL-2 inhibitor venetoclax reduced CLL cell viability, particularly in samples with high NOTCH1 activity. Our findings highlight USP28 as promising therapeutic target and provide a rationale for combined inhibition of USP28 and BCL-2 in CLL patients with active NOTCH1 signaling.

overall_design: RNA-Seq profiling of the cell lines HG3, PGA-1, MEC-1, Granta-519 and MO1043 treated with DMSO as control, human DLL4 to stimulate or nirogacestat to inhibit NOTCH1 signaling for 24 hours. Treatments were done in duplicates.

first: Alena Sophie

first: Deyan Yordanov

last: Yosifov

first: Daniel

last: Mertens


title: EDC4 C-terminal domain scaffolds P-body assembly and links P-body dynamics to p53 mediated tumor suppression

city: Hsinchu

first: Tingwen

last: Chen

address: No. 75, Boat Street, East District

country: Taiwan

institute: National Yang Ming Chiao Tung University

summary: Processing bodies (P-bodies) are membrane-less organelles involved in mRNA metabolism, including decay, storage, and translational repression. Their formation is driven by liquid-liquid phase separation, primarily mediated by the scaffold protein EDC4. This study identifies the C-terminal domain of EDC4 as essential for P-body assembly. Introducing the microprotein NBDY selectively disrupted P-body formation by inhibiting EDC4 self-interaction, without affecting mRNA decay. Disruption of P-bodies led to upregulation of genes in the p53 signaling pathway, highlighting a link between P-body dynamics and tumor suppression. Clinical data suggest a possible connection between P-body dysregulation and cancer progression.

overall_design: In this experiment, the microprotein NBDY (amino acids 22-41) was overexpressed in HEK293T cells to disrupt P-body formation.  The aim was to investigate the functional consequences of P-body disruption. Following NBDY overexpression, RNA-seq and RT-qPCR were performed to analyze changes in gene expression, with a particular focus on pathways affected by P-body dynamics. The results were used to explore the broader role of P-bodies in cellular processes, including their involvement in tumor suppression mechanisms.


title: Impact of USP28 monoallelic deletion in HG3 CLL-derived cells

summary: To investigate the role of USP28 expression in chronic lymphocytic leukemia, we used the CRISPR/Cas9 system to engineer isogenic HG3 cell lines harboring a monoallelic USP28 loss. We then analyzed the transcriptomic profile of these CRISPR/Cas9-generated cell lines by RNA-seq

overall_design: sgRNA designed to target USP28 exon 4 was used for CRISPR/Cas9 experiments, and a non-targeting sgRNA was used as a control. In total, 2 HG3 WT/WT and 2 USP28 WT/KO independent clones were subjected to RNA-seq and subsequently analyzed for differences in gene expression profile.

first: Miguel

last: Quijada-Alamo

first: Luis

last: Corchete

middle: S

first: Jesus

middle: M

last: Hernandez-Rivas


title: Study of Retinoic Acid-Induced Osteoarthritis: Integrating RNA-sequencing, Network Pharmacology, Molecular Docking, and Experimental Validation

status: Public on May 30 2025

city: Datong

first: Tao

last: LU

state: Shanxi

address: 405 Xingyun Street, Pingcheng District, Datong Shanxi, China

institute: Shanxi Datong University - Yudong Campus: Shanxi Datong University

summary: Osteoarthritis (OA) is a debilitating joint disorder characterized by cartilage degradation and chondrocyte homeostasis disruption. Although retinoic acid (RA) has been applied in the model preparation of OA, its target of action and signaling pathway are not clear. Leveraging a translational framework that integrates RNA-sequencing transcriptomics, network pharmacology prediction, computational ligand-receptor molecular docking, and biological experimental validation, this study systematically deciphers RA's disease-modifying targets and associated signaling circuitry in OA pathogenesis. RNA-sequencing of RA-treated chondrocytes revealed 656 differentially expressed genes (DEGs). Protein-protein interaction (PPI) network analysis and functional enrichment (GO/KEGG) highlighted key pathways, including extracellular matrix reorganization and PI3K-Akt-mediated mechanotransduction and others. Additionally, molecular docking results ranked binding affinities in descending order as follows: ACAN > SFRP2 > KANSL2 (NSL2), and so on. Network pharmacology identified 42 RA-OA shared targets, with protein-protein interaction (PPI) analysis and functionally enriched (GO/KEGG) including the Renin-angiotensin system, Neuroactive ligand-receptor interaction, and others. The molecular docking results showed a total score in descending order of MAPK14(p38α), PTGER3(PGE2-R), CA2(CACNA2D2), and so on. Five intersecting targets (CA2, ACE, PTGS1(COX-1), PGR, and EDNRA(ETAR) ) from RNA-sequencing and network pharmacology were obtained, and molecular docking was used to dock the intersecting targets to RA. The docking results demonstrated strong binding affinities, which were further validated through western blot and RT-qPCR experiments, confirming the RA-induced upregulation of the intersecting targets. These findings were accompanied by immunofluorescent evidence showing elevated levels of MMP13 and suppressed expression of COL2A1, collectively reflecting the phenotypic characteristics of OA. Our findings position CA2 and ACE as key hubs for multi-targeting. This study not only reveals possible mechanistic studies of RA in OA but also provides a drug reference for the development of drugs against OA.

overall_design: In our experiments, we chose 24-hour-old specific pathogen-free (SPF) female Sprague-Dawley rats provided by Shanghai XipurBiak Laboratory Animal Co. Ltd (located in Shanghai, China.) with the laboratory animal license number SCXK(Shanghai)2023-0009 as experimental animals, the quality certificate number of this batch of animals is NO.20230009011756. Following the method described by Wang et al. 0.1% type II collagenase (BS164, Biosharp) was to digest the cartilage tissues at 37°C for a continuous period of 2-3 h. Subsequently, chondrocytes were cultured in Dulbecco's Modified Eagle's Medium (DMEM, Hyclone, UT) containing 10% fetal bovine serum (FB-1058, Biosera) and 1% penicillin-streptomycin(ST488S, Beyotime). The chondrocytes used in this experiment were all at passage 1 or passage 2 after isolation. Before RNA sequencing, control cells were cultured in a high-glucose DMEM medium containing 10% FBS for 24 h, while cells in the RA group were cultured in the same medium with 1 μM retinoic acid(S1653, Bimake) for 24 h. The retinoic acid isomer used in this experiment was all-trans retinoic acid (ATRA), purchased from Selleckchem (Item No. NSC 122758). In the RNA-sequencing (RNA-Seq), RNA was extracted from three independent samples for each group and sequenced by the Illumina HiSeq 4000 sequencing platform from Shanghai Life Genetics Technology Co. RNA quality was assessed by the RNA Nano 6000 assay kit(R0027, Beyotime) from Agilent Technologies and the Bioanalyzer 2100 instrument for assessment. Subsequently, sequencing libraries were constructed using NEB's NEBNext® Ultra™ RNA Library Preparation Kit and fragment purification was performed by the AMPure XP system to ensure the selection of fragments of appropriate length and quality. Differentially expressed genes (DEGs) were identified based on a P-value of less than 0.05, and the DEGs were functionally annotated using the Gene Ontology (GO) database. Fold change (FC) of gene expression between groups was calculated by specific formulas such as FC (RP/RS) =Log2[RP (FPKM)/RS (FPKM)] or FC (RP/RPT) = Log2[RP (FPKM)/RPT (FPKM)] to assess the effect of different treatment conditions on gene expression.

last: Lu

first: Ziyi

last: Liu

first: Yangshuo

last: Ge

first: Shuaiyu

last: Jiang

first: Qingao

last: Zhao

first: Dao-Fang

last: Ding


title: NK cells in the female reproductive tract (FRT) acquire an effector transcriptional program during menstruation

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

summary: To evaluate the impact of the menstrual cycle on the transcriptional programs of NK cells in the female reproductive tract (FRT), we compared NK cells (Live lymphocytes, CD45.2+, DX5+, NK1.1+, Ly6G-, CD3-, CD19-) from the spleen and FRT of female C57BL/6J mice either treated with medroxy-progesterone acetate (MPA) or on day 8 of the pseudopregnancy / menstruation protocol. Prior to euthanasia, mice were injected intravenously with anti-CD45 antibody to discern between tissue and circulating NK cells in the FRT, with only tissue-resident cells sorted for analysis. Sorted splenic NK cells were not separated based on CD45 staining. The results indicate that FRT NK cells isolated on day 8 of the pseudopregnancy / menstruation protocol express genes associated with NK cell effector responses compared to FRT NK cells in mice treated with MPA and compared to splenic NK cells in both models.

overall_design: Transcriptional profiling of 4 experimental groups (NK cells isolated from the FRT of mice treated with MPA, n=4; NK cells isolated from the spleen of mice treated with MPA, n=4; NK cells isolated from the FRT of mice on day 8 of the pseudopregnancy/menstruation model, n=5; NK cells isolated from the spleen of mice on day 8 of the pseudopregnancy/menstruation model, n=5). Cells from each mouse were treated as independent replicates.

first: Christopher

middle: D

first: Mark

middle: E

last: Williams

first: Alison

last: Swaims-Kohlmeier


title: Retinoic acid-regulated epigenetic marks identify Alx1 as a direct target gene required for optic cup formation [RNA-seq]

city: La Jolla

first: Gregg

last: Duester

state: CA

address: 10901 North Torrey Pines Road

department: Center for Cardiovascular and Muscular Diseases

institute: Sanford Burnham Prebys Medical Discovery Institute

summary: Retinoic acid (RA) is a transcriptional control agent that regulates several aspects of eye development including invagination of the optic vesicle to form the optic cup, although a target gene for this role has not been previously identified. As loss of RA synthesis in Rdh10 knockout embryos affects the expression levels of thousands of genes, a different approach is needed to identity genes that are directly regulated by RA. Here, we combined ChIP-seq for epigenetic marks with RNA-seq on eye tissue from wild-type embryos and Rdh10-/- embryos that exhibit failure in optic cup formation. We identified a small number of genes with decreased expression when RA is absent that also have decreased presence of a nearby epigenetic gene activation mark (H3K27ac). One such gene was Alx1 that also has an RA response element (RARE) located near the RA-regulated H3K27ac mark, providing strong evidence that RA directly activates Alx1. In situ hybridization studies showed that Rdh10-/- embryos exhibit a large decrease in eye Alx1 expression. CRISPR/Cas9 knockout of Alx1 resulted in a failure in optic cup formation, thus demonstrating that RA directly activates Alx1 in order to stimulate this stage of eye development.

overall_design: Gene expression comparison of Rdh10 KO and WT eye in mice using RNA-seq.

first: Marie

last: Berenguer


title: Bulk RNA-seq of neuromuscular system models generated from human induced pluripotent stem cells (hiPSCs)

city: Bologna

first: Camilla

last: Luni

address: Via Terracini 28

department: DICAM

institute: University of Bologna

summary: Human neuromuscular organoids (NMOs) hold a great potential to study the pathophysiology of functional human skeletal muscle in vitro due to the presence of both muscular and neuronal compartments organized in a their three-dimensional (3D) context and to be derived from induced pluripotent stem cells (hiPSCs).

overall_design: We performed transcriptomic analysis using data obtained from bulk RNA-seq of differentiated human induced pluripotent stem cells (hiPSCs) from 2D cultures (2D), human neuromuscular organoids (NMO), tissue-engineered NMOs (t-NMO), and t-NMO from a Duchenne Muscular Dystrophy (DMD) patient (t-NMO DMD). Comparative gene expression profiling analysis of RNA-seq data for 2D, NMO, and t-NMO samples. Comparative analysis of previous samples and t-NMO DMD.

first: Beatrice

last: Auletta

first: Francesca

last: Cecchinato

first: Gilda

last: Barbato

first: Agnese

last: Lauroja

first: Pietro

last: Chiolerio

first: Lucia

last: Rossi

first: Edoardo

last: Maghin

first: Maria

last: Easler

first: Paolo

last: Raffa

first: Silvia

last: Angiolillo

first: Wei

last: Qin

first: Sonia

last: Calabrò

first: Onelia

last: Gagliano

first: Cecilia

last: Laterza

first: Davide

last: Cacchiarelli

first: Matilde

last: Cescon

first: Leonardo

last: Nogara

first: Nicola

last: Elvassore

first: Martina

last: Piccoli

first: Anna

last: Urciuolo

first: Giada

last: Cecconi

first: Luigi

last: Sartore

first: Roberta

last: Frison

first: Monica

last: Giomo

first: Yvan

last: Torrente


title: Targeting the CD40 Co-stimulatory receptor to improve virotherapy efficacy in diffuse midline gliomas

status: Public on May 29 2025

city: Pamplona

first: Javier

last: Marco Sanz

state: Navarra

address: Av. Pio XII

country: Spain

institute: Centro de Investigacion Medica Aplicada

summary: Diffuse Midline Glioma (DMG) is a devastating pediatric brain tumor. The oncolytic adenovirus Delta-24-RGD has shown promising efficacy and safety in DMG patients but is not yet curative. Thus, we hypothesized that activating dendritic cells through the CD40 costimulatory receptor could increase antigen presentation and enhance the anti-tumor effect of the virus, resulting in long-term responses. This study showed that the intratumoral co-administration of Delta-24-RGD and a CD40 agonistic antibody is well tolerated and induced long-term anti-tumor immunity, including complete responses (up to 40%) in DMG preclinical models. Mechanistic studies revealed that this therapy increased tumor proliferating T lymphocytes and proinflammatory myeloid cells, including mature dendritic cells with superior tumor antigen uptake capacity. Moreover, the lack of cross-priming DCs and the prevention of DCs recruitment into the tumor abolish the Delta-24-RGD+anti-CD40 anti-tumor effect. This approach shows potential for combining virotherapy with activating antigen-presenting cells in these challenging tumors.

overall_design: RNA-seq profiling of XFM-bearing mice tumors at day 6 treated with IgG, anti-CD40, adenovirus Delta24-RGD or the combination of anti-CD40+DElta24-RGD.

first: Sara

last: Labiano

first: Iker

last: Ausejo-Mauleón

first: Virginia

last: Laspidea

last: Marco-Sanz

first: Reyes

last: Hernández-Osuna

first: Marc

last: García Moure

first: Daniel

last: de la Nava

first: Marisol

last: Gonzalez-Huarriz

first: Timothy N

last: Phoenix

first: Ibon

last: Tamayo

first: Marta

last: Zalacain

first: Andrea

last: Lacalle

first: Lucía

last: Marrodán

first: Montserrat

last: Puigdelloses

first: Irati

last: Hervás-Corpión

first: Maria C

last: Ochoa

first: Noelia

last: Casares

first: Oren B

last: Becher

first: Candelaria

last: Gomez-Manzano

first: Juan

last: Fueyo

first: Jaime

last: Perez-Larraya

first: Ana

last: Patiño-García

last: Alonso


title: Transcriptome Profile of IEC4.1 cells deficient with Prdm1 in response to IFN-gamma

city: Chicago

first: Aiyu

last: Gong

state: IL

address: 1735 W. Harrison St

department: MPI

institute: Rush University

summary: This study is to investigate the potential role of Prdm1 in murine intestinal epithelial cells (IEC4.1 cells) in response to IFN gamma stimulation.  Prdm1 was knocked down in IEC4.1 cells by using a CRISPR/Cas9 approach. Wild type IEC4.1 cells were used as control (Ctrl). Cells were treated with or without mouse IFN gamma (1ng/ml for 4hrs). Then total RNA was collected for sequencing via DNBSEQ platform to obtain a comprehensive view of the transcriptome.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for intestinal epithelial cells (IEC4.1 cells) or IEC4.1_PRDM1 KO cells with or without IFNγ treatment.

first: Xianming

last: Chen


title: Mitochondrial dysfunction enhances influenza pathogenesis by upregulating sialic acid biosynthesis

city: Bethesda

first: Peter

last: McGuire

state: MD

address: 10 Center Dr

institute: NHGRI

summary: Viral infections are well-established triggers of disease progression in pediatric mitochondrial disease (MtD). Caregivers frequently report that these infections are not only more severe but also prolonged, a concern reflected in high adherence to infection prevention practices within the MtD community. Despite these observations, significant gaps remain in our understanding of host-pathogen interactions during viral infections in MtD. We hypothesized that mitochondrial dysfunction in MtD exacerbates viral pathogenesis and morbidity through metabolic allostatic alterations in infected cells. Using the Ndufs4 knock out (KO) mouse model of MtD, we observed severe clinical outcomes following influenza A virus infection, including pronounced weight loss, elevated viral load, cytokine storm, and reduced post-infection survival. Metabolic profiling in Ndufs4 KO lung epithelial cells (LET1), indicated a shift towards glycolysis and suggested a diversion of glucose carbons into anabolic pathways. Based on this finding, we determined that the increased influenza-associated susceptibility and morbidity in Ndufs4 KO was related to elevated levels of sialic acid (SIA), a key influenza receptor, derived from glycolysis. Pharmacological manipulation of glycolysis reduced SIA levels, viral load, and morbidity in Ndufs4 KO mice. Our findings demonstrate that metabolic dysregulation in MtD exacerbates viral attachment and pathogenesis, contributing to worsened clinical outcomes.

overall_design: We conducted RNAseq analysis of (1) influenza A virus (IAV)-infected mouse lung RNA extracts (5 x WT and 5 x Ndufs4 KO), (2) IAV-infected mouse lung epithelial type I (LET1) cell RNA extracts (5 x WT and 4 x Ndufs4 KO), and (3) uninfected mouse lung epithelial type I (LET1) cell RNA extracts (5 x WT and 5 x Ndufs4 KO).

first: Amanda

middle: L

last: Fuchs

first: Jillian

middle: W

last: Jetmore

first: Bharati

last: Singh

first: Emily

middle: B

last: Warren

first: Payal

last: Banerjee

first: Jose

last: Marin Franco

first: Tatiana

middle: N

last: Tarasenko

first: Ivan

last: Kosik

first: Jonathan

last: Yewdell


title: Radiation promotes acute and chronic damage to adipose tissue

city: Omaha

first: Rebecca

last: Oberley-Deegan

state: NE

address: 2051 S 86TH AVE

institute: University of Nebraska Medical Center

summary: Radiotherapy is a commonly used therapy for treating various cancer types. In addition, adipose tissues are not routinely spared during typical radiation treatments. Although radiation is known to induce metabolic effects in patients, the impact that radiation therapy has on adipose tissue has not been elucidated. Currently, there are few studies investigating the impact of radiation exposure on adipose tissue, and these have primarily involved whole-body irradiation. This study aimed to understand the acutely persistent damage that clinically relevant radiation dosing causes to adipocytes. Specifically, in vitro and in vivo, irradiated adipocytes had increased reactive oxygen species (ROS) and lipid peroxidation levels and elevated lipolytic activity compared to unirradiated adipocytes. RNA sequencing also identified the upregulation of senescence and inflammation pathways. We observed an increase in macrophage and T-cell accumulation both 1 month and 6 months after radiation exposure using in vivo models. Many of the observed changes to irradiated adipose tissue, including oxidative stress, metabolic dysfunction, inflammation, and senescence, are consistent with those observed in adipose tissue from obese patients, in which obesity is a known driver of many cancers. Because adipose tissue damage is maintained chronically, protecting adipose tissue from the harmful effects of radiation exposure may improve radiation-induced toxicity and reduce cancer recurrence and progression.

overall_design: Mice were pelvically irradiated  receiving 7.5 Gy for 5 days. Primary mouse gonadal adipose tissue was harvested two months after radiation. Fat pads were digested with collagenase and incubated at 37 °C for 45 minutes, with manual swirling every 5 minutes. Once the fat was dissociated, 4x volume of cold HBSS (without Ca2+ & Mg 2+) was added and the tube was centrifuged at 450 g for 3 minutes at 4 °C. Mature adipocytes found in the floating fraction were removed and maintained in culture for 3 days.


title: Differential oligomerization regulates PHF13 chromatin function and affinity [RNA-seq]

city: Berlin

first: Alexandre

middle: P

last: Magalhaes

address: Ihnestrasse 63-73

institute: Max Planck Institute for Molecular Genetics

summary: PHF13 is a H3K4me3 epigenetic reader, that modulates key chromatin processes including transcription, DNA damage response and chromatin architecture. PHF13 is found aberrantly regulated in different cancers and its misexpression alters the epigenetic landscape of key transcription factors that regulate Epithelial to Mesenchymal transition. In this study we sought to understand how PHF13’s chromatin affinity and diverse chromatin functions are intrinsically regulated. Our results show that PHF13 can oligomerize via conserved ordered regions in its N- and C- terminus increasing its chromatin valence and avidity. Impressively, a 4-fold over expression of PHF13 was sufficient to globally compact chromatin, dependent on its ordered dimerizing regions and oligomerization potential. Unexpectedly, we discovered that PHF13 can self-associate independent of its ordered domains via intrinsically disordered regions, which conversely reduced PHF13’s chromatin affinity. Our findings support that there is an intrinsic balance between PHF13’s ordered and disordered regions that regulates PHF13 chromatin affinity, and suggest that PHF13 can phase transition between polymer-polymer and liquid-liquid phase separation states to impact chromatin structure and function.

overall_design: U2OS cells were transfected and cultured with various constructs to overexpress PHF13 and its mutant variants. RNA-seq and ATAC-seq were performed to assess aceability and gene expression changes to identify PHF13 mutants that induce protein condensation versus gene condensation.

first: Magalhaes

last: Alexandre P

first: Rossi

last: Francesca

first: Kinkley

last: Sarah


title: Hepatocyte-specific Angiotensinogen Deficiency Inhibits Western Diet-induced Liver Steatosis With Suppression of Cell Division in Mice

city: Lexington

first: Hisashi

last: Sawada

state: KY

address: 741 South Limestone BBSRB B251

institute: University of Kentucky

summary: Liver steatosis is a common cause of chronic liver disease. To investigate the molecular basis of hepatic steatosis, low-density lipoprotein receptor-deficient (LDLR -/-) mice were fed Western diet (WD, 42% of calories from fat) for 5, 14, or 42 days and evaluated against mice fed a normal laboratory diet. Histological analyses revealed that steatosis was detected as early as 14 days of WD feeding. Bulk RNA sequencing demonstrated that WD feeding altered liver transcriptomes related to inflammation and cell adhesion consistent with the progression of liver steatosis. Previous studies determined that hepatocyte-specific deficiency of angiotensinogen (AGT), the unique substrate of the renin-angiotensin system (RAS), alleviates WD-induced hepatic steatosis in mice. However, the effects of hepatic AGT deficiency were not mimicked by pharmacological inhibition of the RAS, and the molecular mechanisms by which AGT deficiency protects against WD-induced steatosis is unknown. Therefore, liver transcriptomes were compared between hepatocyte-specific AGT deficient mice (hepAGT -/-) and their wild-type littermates (hepAGT +/+) after 14 days of WD feeding. Gene ontology analyses showed that upregulated genes in hepAGT -/- mice were enriched for metabolic processes and downregulated genes were enriched for cell division pathways. The integration analysis of the two RNA sequencing data identified 5 key genes, Smpd3, Dtl, Cdc6, Mki67, and Top2a, which were primarily associated with cell division processes in hepAGT +/+ mice and were suppressed in hepAGT -/- mice. In conclusion, hepatic AGT deficiency downregulated genes related to cell division during the progression of liver steatosis.

overall_design: Comparative gene expression analysis of RNA-seq data from livers of mice fed normal laboratory diet or Western diet (42% of calories from fat) for 5, 14, or 42 days and hepatocyte-specific angiotensinogen deficient mice (hepAGT -/-) fed Western diet for 14 days. All mice were on a low-density lipoprotein receptor deficient (LDLR -/-) background.

first: Alex

middle: C

last: Pettey


title: Cryptic variation fuels plant phenotypic change through hierarchical epistasis

city: Cold Spring Harbor

first: Zachary

last: Lippman

address: 1 Bungtown Rd

department: Plant Biology

institute: Cold Spring Harbor Laboratory

summary: Cryptic genetic variants exert minimal or no phenotypic effects alone but have long been hypothesized to form a vast, hidden reservoir of genetic diversity that drives trait evolvability through epistatic interactions. This classical theory has been reinvigorated by pan-genome sequencing, which is continually exposing cis-regulatory variation, along with widespread gene duplications and paralog diversification as an underappreciated source of cryptic variation within gene families and the regulatory networks in which they function. However, empirical testing of this hypothesis has been hindered by intractable genetics, limited allelic diversity, and inadequate phenotypic resolution. Here, guided by natural and engineered cis-cryptic variants in a recently evolved paralogous pair, we identified an additional  pair of redundant trans regulators, establishing a regulatory network that controls tomato inflorescence architecture. Exploiting an allelic spectrum of network components allowed a high-resolution dissection of a genotype-to-phenotype map, revealing how cryptic variants potentiate trait diversification. We combined coding mutations with a cis-regulatory allelic series in populations segregating for all four genes, systematically constructing gene dosage combinations across 216 genotypes and quantifying their effects on branching in 27,000 inflorescences. Our analysis revealed dose-dependent interactions within paralog pairs enhance branching, culminating in strong, synergistic, effects. However, modeling uncovered an unexpected layer of antagonism between paralog pairs, where accumulating mutations in one pair progressively diminished the effects of mutations in the other. Our results demonstrate how gene regulatory network architecture and complex dosage effects from paralog diversification converge to shape phenotypic space. Given the prevalence of paralog evolution in genomes, we propose that paralogous cryptic variation within regulatory networks elicits hierarchies of epistatic interactions, catalyzing bursts of phenotypic change.

overall_design: Inflorescence meristems were collected from n = 4 plants at 8 weeks old under stereoscope magnification. Tissue was frozen, ground with beads, and RNA was extracted with TRIzol (Invitrogen) and a Direct-zol RNA Miniprep kit with on-column DNA digestion (Zymo Research). RNA was quantified with Qbit fluorimeter RNA HS assay kit (Invitrogen). Samples were treated with Ribo-Zero rRNA removal kit (Epicenter) and libraries prepared with an TruSeq V2 RNA-Seq prep kit (Illumina).


title: Epigenetic priming of embryonic enhancer elements coordinates developmental gene networks [CUT&TAG]

city: Göttingen

first: Ufuk

last: Günesdogan

address: Justus-von-Liebig Weg 11

institute: University of Goettingen

summary: Embryonic development requires the accurate spatiotemporal execution of cell lineage-specific gene expression programs, which are controlled by transcriptional enhancers. Developmental enhancers adopt a primed chromatin state prior to their activation; however how this primed enhancer state is established, maintained, and how it affects the regulation of developmental gene networks remains poorly understood. Here, we use comparative multi-omic analyses of human and mouse early embryonic development to identify subsets of post-gastrulation lineage-specific enhancers which are epigenetically primed ahead of their activation, marked by the histone modification H3K4me1 within the epiblast. We show that epigenetic priming occurs at lineage-specific enhancers for all three germ layers, and that epigenetic priming of enhancers confers lineage-specific regulation of key developmental gene networks. Surprisingly in some cases, lineage-specific enhancers are epigenetically marked already in the zygote, weeks before their activation during lineage specification. Moreover, we outline a generalisable strategy to use naturally occurring human genetic variation to delineate important sequence determinants of primed enhancer function. Our findings identify an evolutionarily conserved program of enhancer priming and begin to dissect the temporal dynamics and mechanisms of its establishment and maintenance during early mammalian development.

overall_design: CUT&Tag libraries were generated according to the EpiCypher protocol (Kaya-Okur et al., 2019) with minor modifications. As described for ATAC-seq, hiPSCs were harvested with accutase (StemCell Technologies; 07922). After resuspension in 1X DPBS (Life Technologies; 14190144), 2 x 105 cells per CUT&Tag reaction underwent centrifugation at 300 x g for 3 min at RT. Cells were then lysed in 100μl of cold Nuclear Extraction (NE) Buffer (20mM HEPES–KOH, pH 7.9, 10mM KCl, 0.1% Triton X-100, 20% Glycerol, 0.5mM Spermidine (Sigma-Aldrich; 05292), 1x cOmpleteTM, Mini, EDTA-free Protease Inhibitor (Roche; 11836170001)) per CUT&Tag reaction for 10 min on ice. The nuclei were then centrifuged for 3 min at 600 x g at RT before resuspension in cold NE Buffer to achieve a final concentration of 1.2x106 nuclei/ml. For each CUT&Tag reaction, 11μl of concanavalin A (ConA) beads (EpiCypher; 21-1401) were washed twice on a magnetic stand with 100 μl of Bead Activation (BA) Buffer (20mM HEPES, pH 7.9, 10mM KCl, 1mM CaCl2, 1mM MnCl2). The beads were then resuspended in 11μl of BA Buffer, and 10μl beads were aliquoted into a 0.2ml tube. Each tube of activated ConA beads was then incubated with 100μl of nuclei for 10 min at RT. The supernatant was then removed with a magnet and the beads were resuspended in 50μl of cold Antibody150 Buffer (20mM HEPES, pH 7.5, 150mM NaCl, 0.5mM Spermidine, 1x cOmpleteTM, Mini, EDTA-free Protease Inhibitor, 0.01% digitonin (Sigma-Aldrich, D141-100MG), 2mM EDTA) containing a 1:50 dilution of rabbit primary antibody (anti-H3K4me1 (Active Motif; 39298) or anti-H3K27ac (Abcam; ab4729)) and incubated overnight at 4°C on a rocker. The following day, the supernatant was discarded with a magnet and the beads were incubated in 50μl of Digitonin150 Buffer (20mM HEPES, pH 7.5, 150mM NaCl, 0.5mM Spermidine, 1x cOmpleteTM, Mini, EDTA-free Protease Inhibitor, 0.01% digitonin) containing 0.5μg of anti-rabbit secondary antibody (Epicypher; 13-0047) for 1 hour at RT. The beads were then washed twice on a magnet with Digitonin150 Buffer, then incubated in 50μl of Digitonin300 Buffer (20mM HEPES, pH 7.5, 300mM NaCl, 0.5mM Spermidine, 1x cOmpleteTM, Mini, EDTA-free Protease Inhibitor, 0.01% digitonin), and 1.25μl of CUTANA pAG-TN5 (EpiCypher; 15-1017) for 1 hour at RT. The beads were then washed twice with a magnet by resuspension in Digitonin300 Buffer, then incubated in 50μl of chilled Tagmentation Buffer (Digitonin 300 Buffer, 10mM MgCl2) for 1 hour at 37°C. The supernatant was then discarded with a magnet and the beads were washed once with 50μl RT TAPS Buffer (10mM TAPS, pH 8.5, 0.2mM EDTA). The supernatant was again removed with the magnet and the beads were resuspended in 5μl of RT SDS Release Buffer (10mM TAPS, pH 8.5, 0.1% SDS) and vortexed on maximum speed for 10 sec followed by a brief centrifugation. The beads were then incubated for 1 hour at 58°C before the addition of 15μl of RT SDS Quench Buffer (0.67% Triton-X 100 in Molecular grade H2O), vortexing at maximum speed for 10 sec, and a brief centrifugation. For library amplification, samples were combined with 2μl of 5µM i5 primer, 2μl of 5µM i7 primer and 25μl of CUTANA High Fidelity PCR mix (EpiCypher; 15-1018). The following PCR programme was then used for all libraries: 58°C for 5 min, 72°C for 5 min, and 98°C for 45 sec. This was followed by 11 cycles for anti-H3K27ac and 13 cycles for anti-H3K4me1 of [ 98°C for 15 sec and 60°C for 10 sec], before a final extension at 72°C for 1 min. Libraries then underwent two 1X AMPure XP bead (Beckman Coulter; A63881) cleanups. Following QC on a Bioanalyzer, libraries were multiplexed and sequenced (paired-end 150 bp) using a NovaSeq 6000 instrument (Illumina).

first: Christopher

last: Todd

first: Jannat

last: Ijaz

first: Fereshteh

last: Torabi

first: Oleksandr

last: Dovgusha

first: Stephen

last: Bevan

first: Olivia

last: Cracknell

first: Tim

last: Lohoff

last: Clark

first: Ricard

last: Argelaguet

first: Juliette

last: Pearce

first: Ioannis

last: Kafetzopoulos

first: Alice

last: Santambrogio

first: Jennifer

last: Nichols

first: Ferdinand

last: von Meyenn

last: Guenesdogan

first: Stefan

last: Schoenfelder

first: Wolf

last: Reik


title: Epigenetic priming of embryonic enhancer elements coordinates developmental gene networks [ATAC-seq]

last: Günesdogan

overall_design: ATAC-seq libraries were generated as described in (Corces et al. 2017), with minor modifications. After washing once with 1X DPBS (Life Technologies; 14190144), hiPSCs were harvested with accutase (StemCell Technologies; 07922) by incubation for 5 min at 37°C. After accutase neutralisation with TeSR-E8 medium cells were centrifuged at 300 x g for 3 min at RT. After resuspension in 1X DPBS, 50,000 cells underwent centrifugation at 500 x g for 5 min at 4°C in a swing arm rotor centrifuge, then lysis in 50µl of cold ATAC Resuspension Buffer (10mM TrisHCl pH 7.5, 10mM NaCl, 3mM MgCl2) containing 0.1% IGEPAL-630, 0.1% Tween-20, and 0.01% digitonin for 3 min on ice. The lysate was then topped up with 1ml cold ATAC Resuspension Buffer containing 0.1% Tween-20 and centrifuged at 500 x g for 10 min at 4°C in a swing arm rotor centrifuge. The pellet was then resuspended in 50µl of transposition mixture (1X Illumina Tagment DNA Buffer and 100nM Illumina TDE1 Tagment DNA Enzyme transposase (Illumina; 20034197), 0.33X DPBS, 0.1% Tween-20, 0.01% digitonin) and incubated at 37°C for 30 min with 1000 RPM mixing. After undergoing purification with the Zymo DNA Clean & Concentrator-5 kit (Zymo Research; D4003), samples were eluted in 21µl of elution buffer, and combined with 2.5µl of 25µM i5 primer, 2.5µl of 25µM i7 primer, and 25µl 2X NEBNext High-Fidelity 2X PCR Master Mix (NEB; M0541S). A PCR was then performed with the following conditions: 72°C for 5 min, 98°C for 30 sec, 8 cycles of [98°C for 10 sec, 63°C for 30 sec, 72°C for 1 min]. The samples then underwent a second Zymo DNA Clean & Concentrator-5 purification and were eluted in 30µl of elution buffer prior to a 1.2X AMPure XP bead (Beckman Coulter; A63881) cleanup. Following QC on a Bioanalyzer, libraries were multiplexed and sequenced (paired-end 50bp) using a HiSeq 2000 instrument (Illumina).

last: Todd


title: Differential oligomerization regulates PHF13 chromatin function and affinity [ATAC-seq]

first: Alexandre

last: Magalhaes

overall_design: U2OS cells were transfected and cultured with various constructs to overexpress PHF13 and its mutant variants. ATAC-seq were performed to assess aceability changes to identify PHF13 mutants that induce protein condensation versus gene condensation.

first: Magalhaes

last: Alexandre P

first: Rossi

last: Francesca

first: Kinkley

last: Sarah


title: DNA damage induced by G-quadruplex ligand PyBI and its synthetic lethality with DNA repair inhibitors in cancer cells

city: Changsha

first: Ke-wei

last: Zheng

address: Lushan Road (S), Yuelu District

department: School of Medical Sciences

institute: Hunan University

summary: The existence of G-quadruplexes (G4s) in vivo verified by diverse techniques, accompanied with their regulatory roles in cellular processes, highlight G4s as a target for various disease treatment. Targeting G-quadruplex DNAs to cause DNA damage has a good prospect for cancer therapy. However, previous studies on DNA damage induced by G4 ligands and its repair response thereof mainly focused on limited scaffolds such as CX series drugs, PDS families, etc. Here, we systematically investigated the DNA damage and repair mechanism induced by a good G4 stabilizer with bis(benzimidazole)pyridine as its key scaffold, which we termed as PyBI. PyBI can stabilize G4s both in vitro and in vivo, and cause DNA double strand breaks (DSB) and genome instability during DNA replication, resulting in cell cycle stagnation in G2/M phase and the increase of RAD51 and 53BP1 foci. Significantly, we applied Cleavage Under Targets and Tagmentation (CUT&Tag) for genome-wide mapping DNA damage sites induced by PyBI in cancer cells. Together with its G4 mapping result by CUT&Tag, we revealed that DNA damage caused by PyBI might be mediated by G4 stabilization. Moreover, we thoroughly investigated the synthetic lethality of PyBI with a small library of DNA repair inhibitors. PyBI exhibited good synthetic lethality effects with RAD51 and DNA-PK inhibitor, providing a new prospect for the treatment of genetically defective cancers.

overall_design: Cleavage under targets and tagmentation (CUT&Tag) for G4P, RAD51 and 53BP1 in HeLa cells.

first: Jiangyu

last: Yan

first: Lingli

last: Bu

first: Haojun

last: Yao

first: Guorui

last: Li

first: Kewei

first: Jing

last: Huang


title: Transcriptomic profile of IEC4.1 cells treated with an ASO to lncRNA XR_001779380 in response to IFN-gamma

first: Aiyu

last: Gong

summary: LncRNAs may play an important role in intestinal epithelial cell autonomous defense against microbial infection. Our previous study showed that lncRNA XR_001779380 can interact with Prdm1 to modulate gene transcriuption in intestinal epithelial cells and may regualte IFN-gamma-stimulated gene transcription.  Here we designed an antisense oligos-morpholine (ASO4) targeting the sequence of  lncRNA XR_001779380 to interfere with its interaction with PRDM1.  Murine intestinal epithelial cells (IEC4.1 cells) were treated with  ASO4  or a standard control ASO-morpholine (ST) for 24h, followed by exposure to IFN-gamma (1 ng/ml) for 4 hours.  Then total RNA was collected for sequencing via  DNBSEQ platform to obtain a comprehensive view of the transcriptome.

overall_design: Mouse intestine epithelial  IEC4.1 cells were tansfected with the ST or ASO4 for 24h. The transfected cells were treated with or without IFNγ for 4 hours. The RNA expression profile of  these cells were compared.

first: Xianming

last: Chen


title: LIN-39 functions as a neuron-specific developmental determinant of longevity in Caenorhabditis elegans with reduced insulin/IGF-like signaling [ATAC-seq]

city: Huddinge

first: Christian

middle: Günter

last: Riedel

state: Stockholm

address: Blickagången 16 (Neo Building, 6th floor)

department: Biosciences and Nutrition

country: Sweden

institute: Karolinska Institute

summary: The nuclear chromatin landscape changes with age – a phenomenon observed across many species, including humans. Notably, perturbing this landscape can alter the rate of aging, indicating at least a partial role in controlling this process. This raises the question of whether chromatin alterations also distinguish animals that age at unusual rates. To explore this, we focused on insulin/IGF-like signaling (IIS) in Caenorhabditis elegans, a well-characterized signaling pathway whose impairment drastically slows aging and extends lifespan of these animals. Specifically, we conducted ATAC- and mRNA-seq in animals with reduced IIS (i.e., daf-2 mutants). Interestingly, we found that enhancer regions tend to close and become transcriptionally repressed with age, but under reduced IIS, they tend to open and become transcriptionally active, suggesting their potential relevance for lifespan regulation. By screening transcription factors (TFs) predicted to bind these regions, we identified the HOX gene LIN-39 as a novel aging-preventive TF required for the longevity of daf-2 mutants. LIN-39 performs this role specifically during development and in neurons. Further investigation showed that LIN-39 was acting around the L3 larval stage and in the hermaphrodite-specific VC class of cholinergic motor neurons – at a time when they undergo maturation. Finally, this LIN-39-dependent longevity required DAF-16/FOXO, a well-established aging-preventive TF that acts downstream of DAF-2, which may synergize with LIN-39 in VC neurons to open enhancer the regions. We ultimately propose a model whereby longevity of daf-2 mutant hermaphrodites requires a longevity-promoting signal emitted by VC neurons – a signal that relies on correct VC neuron maturation around the L3 stage, which in turn is assured by the actions of LIN-39 and resulting chromatin and gene expression changes. This renders LIN-39 a rare example of a developmental determinant of longevity. And given the conservation of IIS, HOX and FOXO TFs, and cholinergic neuron function across species, the here described mechanism may reflect a general principle by which developmental transcriptional programs shape adult longevity.

overall_design: ATAC-Seq (Assay for Transposase-Accessible Chromatin using sequencing) in Caenorhabditis elegans: for daf-2(e1370), daf-2(e1370); daf-16 RNAi, daf-2(e1370); lin-39 RNAi and wild-type animals at day 1 of adulthood, and for germline-deficient glp-4 mutant animals at day 1, 3, and 7 of adulthood.

first: Alan

last: Kavšek

first: Jérôme

last: Salignon

first: Lluís

last: Millan-Ariño

first: Ilke

last: Sen


title: LIN-39 functions as a neuron-specific developmental determinant of longevity in Caenorhabditis elegans with reduced insulin/IGF-like signaling [RNA-seq]

overall_design: mRNA-Seq (messenger RNA sequencing) in Caenorhabditis elegans: for daf-2 mutant (e1370) and wild-type animals at day 1 of adulthood, and for germline-deficient glp-4 mutant animals at day 1, 3, and 7 of adulthood.


title: Species-specific gene regulatory network rewiring mediated by the GATA-type regulator NsdD in Aspergillus [Afl_NsdD_ChIP_seq]

city: Madison

first: Heungyun

middle: Harrison

last: Moon

state: WI

address: 1550 Linden drive

department: Bacteriology

institute: University of Wisconsin-Madison

summary: Multifunctional TFs are central in coordinating development and metabolism in filamentous fungi. In this study, we systematically dissect the regulatory functions of NsdD, a highly conserved GATA-type TF in Pezizomycotina, using network-based multi-omics approaches in two distantly related species, A. nidulans and A. flavus. Our analyses reveal that NsdD governs fungal development and metabolism through species-specific GRNs, directly targeting key upstream regulators and genes involved in core cellular processes. These regulatory distinctions underlie the morphological and metabolic differences observed between the two species. Notably, our cross-species comparison uncovers extensive GRN rewiring, demonstrating how evolutionary divergence can reshape transcriptional networks even under conserved regulatory control. The resulting GRN maps offer a valuable framework for understanding gene regulation in Aspergillus and provide a foundation for broader studies on the evolution of transcriptional networks and conserved regulatory factors in filamentous fungi.

overall_design: Genome binding/occupancy profiling analysis by high throughput sequencing for wild-type and NsdD::FLAG strains.

first: Mi-Kyung

last: Lee

first: Junha

last: Shin

first: Sung Chul

last: Park

first: Julio

last: Vazquez

first: Daniel

last: Amador-Noquez

first: Nancy

last: Keller

first: Hee-Soo

first: Kap-Hoon

last: Han

first: Jae-Hyuk

last: Yu


title: Species-specific gene regulatory network rewiring mediated by the GATA-type regulator NsdD in Aspergillus [Ani_NsdD_ChIP_seq]

first: Sung


title: Species-specific gene regulatory network rewiring mediated by the GATA-type regulator NsdD in Aspergillus [Afl_NsdD_RNA_seq]

overall_design: Comparative gene expression profiling analysis by high throughput sequencing for wild-type and nsdD-deletion strains.


title: Species-specific gene regulatory network rewiring mediated by the GATA-type regulator NsdD in Aspergillus [Ani_NsdD_RNA_seq]


title: Immune correlates of anti-BCMA CAR-T products idecabtagene vicleucel and ciltacabtagene autoleucel in a real-world cohort of patients with multiple myeloma [RNA-seq]

status: Public on May 28 2025

city: Baltimore

first: Carrie

last: McCracken

address: 670 W. Baltimore St.

institute: Institute of Genome Sciences

summary: We performed the first in-depth, comparative and prospective biomonitoring of Multiple Myeloma (MM) patients (N=39) receiving ciltacabtagene autoleucel (cilta-cel) or idecabtagene vicleucel (ide-cel) chimeric antigen receptor T cells (CAR T) in the real-world setting. In cilta-cel patients response rates were higher and atypical neurotoxicities/infections more frequent. Peak CAR T counts were significantly higher in cilta-cel patients, driven by CD4+ CAR expansion, correlating with clinical responses. Expansion of cilta-cel cells was associated with higher CAR and CD27 expression while, in contrast to ide-cel, there was no correlation between TIM3 expression and CAR T proliferation. Cilta-cel CAR T expansion was followed by a CAR-specific switch from proliferation-associated genes to genes/surface markers indicating effector/memory function. The longer persistence of cilta-cel CAR T was associated with increased IL-7R expression; in vitro data showed persistent antigen-independent activation and higher metabolic activity of cilta-cel vs. ide-cel CAR T. Among cilta-cel-treated patients experiencing atypical neurotoxicities, central nervous system (CNS)-infiltrating, effector-type CAR T presented a distinct inflammatory phenotypic/cytokine-expression profile. This in-depth biomonitoring report following real-world cilta-cel or ide-cel highlights intrinsic biological differences between BCMA-targeting CAR T products, potentially explaining differences in clinical activity and toxicity. Our findings may guide optimization of cellular immunotherapy strategies in MM.

overall_design: We collected blood and cerebrospinal fluid (CSF) from multiple myeloma patients after treatment who had developped severe neurotoxicity. RNA sequencing was performed on flow cytometry-sorted T cells (RNA-seq) or whole peripheral blood mononuclear cells (scRNA-seq).


title: ATAC-seq of antigen-specific memory CD8+ T cells

city: Rochester

first: Abhinav

last: Jain

address: 200 1st ST SW

institute: Mayo Clinic

summary: Aging trajectories of antigen-specific memory T cells are heterogenous and complex but incompletely understood. We use single-cell sequencing of EBV (Epstein Barr virus)- or VZV (Varicella Zoster virus)-antigen specific T cells of younger or older adults to analyze memory T cell heterogeneity in early and late life.

overall_design:
Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) performed on flow extracted for CM, EM, TEMRA, EBV-specific CD8 T cells.
This study includes a reanalysis of 15 Samples from GSE101609.

***************************************************************
The table below lists GEO accessions reanalyzed for this study.
***************************************************************

first: Ines

last: Sturmlechner

first: Jorg

last: Goronzy


title: Immune correlates of anti-BCMA CAR-T products idecabtagene vicleucel and ciltacabtagene autoleucel in a real-world cohort of patients with multiple myeloma [scRNA-seq]


title: Protein-like Polymers Targeting Keap1/Nrf2 as Therapeutics for Myocardial Infarction

first: Karen

last: Christman

state: California

address: 2880 Torrey Pines Scenic Drive

department: Shu Chien-Gene Lay Department of Bioengineering

institute: University of California San Diego

summary: Myocardial infarction (MI) results in oxidative stress to the myocardium and frequently leads to heart failure (HF). There is a need to therapeutically treat the inflammatory stress response and thus prevent negative left ventricular remodeling. Thus, we specifically target the protein-protein interaction between Nrf2 and Keap1, as Nrf2 activation is known to mitigate MI. We further leverage Nrf2 activation using a proteomimetic platform to inhibit the Keap1-Nrf2 axis via protein-like polymers (PLPs), given its stability in vivo, prolonged circulatory half-life, potent intracellular bioactivity, and multivalency. We employed in vitro and in vivo assays to probe cellular activity and MI therapeutic utility. These Keap1-inhibiting PLPs (Keap1i-PLPs) exhibit primary cardiomyocyte cytoprotection from oxidative stress via Nrf2 activation at sub-nanomolar concentrations. Single-digit mg/kg, single-dose, intravenous PLP treatment significantly improves cardiac function in rats post-MI through immunomodulatory, anti-apoptotic, and angiogenic mechanisms. Thus Keap1i-PLPs disrupt key intracellular PPIs following intravenous, systemic administration  in vivo. These results have broad implications not only for MI, but also for other oxidative stress diseases.

overall_design: To study the acute effects of administering a Keap1i-PLP in a rat MI model, we induced a 35 minute ischemia reperfusion surgery in female Sprague Dawley rats. 1 day post surgery, n = 4-6 animals were injected with the following: saline, 3 mg/kg Keap1i-PLP, 7.5 mg/kg Keap1i-PLP, and scrambled 3mg/kg PLP.

first: J

last: Mesfin

first: K

last: Carrow

first: A

last: Chen

first: M

last: Hopps

middle: J

last: Holm

last: Nguyen

last: Hunter

last: Magassa

first: E

last: Wong

last: Reimold

first: S

last: Paleti

first: Q

last: Lyons

last: Gardner

last: Thompson

first: CG

last: Luo

first: X

last: Zhang

first: N

last: Gianneschi


title: Gut microbiota-derived GlcNAc-MurNAc is a TLR4 agonist that protects the host gut

city: Singapore

first: Yuan

last: Qiao

address: 21 Nanyang Link, CBC 04-40

country: Singapore

institute: NTU

summary: Gut microbiota-derived peptidoglycan fragments (PGNs) are key signaling molecules that regulate multiple aspects of the host’s health. Yet the exact structures of natural PGNs in hosts have not been fully elucidated. Herein, we developed an LC-HRMS/MS analytical platform for global quantification and profiling of natural PGN subtypes in host gut and sera, unexpectedly revealing the abundance of PGN-derived saccharide moieties that do not resemble canonical ligands of mammalian NOD1/2 receptors. Focusing on the disaccharide GlcNAc-MurNAc (GM), which does not activate NOD1/2 yet still exhibits immunostimulatory effects in host immune cells, we established GM as a mild TLR4 agonist, illustrating an alternate PGN sensing mechanism other than NOD signaling. Importantly, the administration of GM mitigates colonic inflammation in the DSS-induced colitis model in mice via a TLR4-dependent manner, highlighting the in vivo significance of gut microbiota-derived PGN saccharides in maintaining host intestinal homeostasis.

overall_design: Bone marrow derived macrophages (BMDMs)  from wildtype or TLR4-knockout C57BL/6J mice were differentiated by L929 cell culture supernatants-added complete media. BMDMs on Day 7 since the start of differentiation were treated with water, GlcNAc-MurNAc (GM) or MurNAc-D-Ala-L-Gln (MDP) for 24h in IMDM (serum-free) media.


title: Idiosyncratic nature of lactation reveals link to breast cancer risk.

city: New York

first: Edmund

last: Jenkins

state: NY

address: 1468 Madison Avenue

department: Heme/Onc

institute: Icahn School of Medicine at Mt. Sinai

summary: Breastfeeding protects against breast cancer in some women but not others, however the mechanism remains elusive. Lactation requires intense secretory activity of the endoplasmic reticulum (ER) for the production of milk proteins and ER- mitochondria  contacts for lipid synthesis. We show that in female mice that share the same nuclear genome (BL/6) but differ in mitochondrial genomes (C57 or NZB), the biological processes engaged during lactation are entirely different at the sub-cellular organization and transcriptional levels resulting in anti-tumorigenic lactation in BL/6C57 females and pro-tumorigenic lactation in BL/6NZB females. Single cell sequencing identified a sub-population of cells, uniquely amplified during lactation in BL/6NZB females, which shares the genetic signature that characterizes post-partum breast cancer (PPBC) in humans relative to matched breast cancers in never pregnant women. Our data indicate that differences in ER and mitochondrial-stress responses during lactation between genotypes inadvertently leads to loss of p53 tumor suppressor function in BL/6NZB females allowing the expansion of the PPBC-like sub-population of cells. Overall, our data reveals the unexpected idiosyncratic nature of lactation and its impacts on the risk of the development of PPBC.

overall_design: Freshly isolated snap frozen Inguinal mammary glands were submitted to GENEWIZ, LLC, NJ, USA for nuclei isolation and GEM (Gel Bead-based Emulsion) single cell RNA seq analysis on the 10x Genomics platform

first: Doris

last: Germain

first: Mrittika

last: Chattopadhyay


title: scRNAseq and scTCRseq data from tumor-infiltrating lymphocytes

status: Public on May 27 2025

city: VILLEJUIF

first: AZIZA

last: CAIDI

address: 114 RUE EDUARD VAILLANT

country: France

institute: GUSTAVE ROUSSY

summary: In cancer models, CD103+CD8 TRM cells are implicated in the response to anti-PD-1 immunotherapy, and a subset of CD4 TRM cells expressing the integrin CD49a is required for response to anti-CTLA-4 immunotherapy. We performed single-cell RNA sequencing on tumour-infiltrating T lymphocytes (TILs) isolated from colon carcinoma et unsupervised analyses reveal several TRM populations.

overall_design: SCRNAseq and TCRseq  are performed using 10X genomics technology on lymphocytes from tumor of 8 mice (4 different conditions and 2 replicates per condition): - ISO :  isotype sample_1 - ISO_dup :isotype sample_2 aPD1 : sample anti-PD1_1 aPD1_dup :sample anti-PD1_2 aCTLA4: sample anti-CTLA4_1 aCTLA4_dup :sample anti-CTLA4_2 combo : sample_anti-PD1_anti-CTLA4_1 combo_dup : sample_anti-PD1_anti-CTLA4₂

first: Stéphanie

last: Corgnac

first: Isabelle

last: Damei

first: Fathia

last: Mami-Chouaib

first: Aziza

last: Caidi


title: MTBP Cut&Run of FACS sorted cell cycle populations in HCT116 cells

city: Oklahoma

first: Christopher

middle: Lee

last: Sansam

state: OK

address: 825 NE 13th Street

department: Cell Cycle and Cancer Biology Program

institute: Oklahoma Medical Research Foundation

summary: The selection of replication origins plays a crucial role in eukaryotic DNA replication. However, the mechanisms of origin selection in humans are not yet well-defined. Recent work in yeast has shown that the recruitment of Sld3-Sld7 to origins during G1 is involved in origin selection. In humans, TICRR and MTBP are the orthologs of Sld3 and Sld7, respectively. In this study, we have mapped the genomic binding locations of MTBP in G1, early S, late S, and G2 populations of cells.

overall_design: We utilized HCT 116 cell lines with all MTBP alleles tagged with mClover in addition to expressing Fucci(CA) fluorescent cell cycle reporters. Cells were FACS sorted based on Fucci fluorescence into G1 (mCherry), S (AmCyan), or G2 (double positive) populations. Cut&Run experiments were performed with an anti-GFP antibody that specifically binds to the mClover tag. To obtain background signal measurements, we simultaneously conducted Cut&Run experiments on the untagged cell lines. Subsequently, the generated Cut&Run reads were aligned to the genome and used to call peaks.

first: Tyler

last: Noble

first: Courtney

first: Kimberlie

middle: A

last: Wittig

first: Blanka

last: Majchrzycka


title: Organellar responses to lactation-induced stress impact the fate of post-partum mammary glands.

summary: Breastfeeding protects against breast cancer, but not in all women and the mechanism remains elusive. Lactation implicates secretion of proteins through the endoplasmic reticulum (ER) and ER- mitochondria  contacts for lipid metabolism. We show that in mice that share the same nuclear genome (BL/6) but differ in mitochondrial genomes (C57 or NZB) the outcome of lactation differs drastically. We analyzed the unfolded protein responses (UPR) of both organelles during lactation. In contrast to the BL/6C57mice, in BL/6NZB females, UPRs signaling is abruptly inhibited, no apoptosis is observed, post-partum hyperplasia develops and RNAseq demonstrates expression of pro-tumorigenic genes, which is consistent with increased post-partum tumor development. However, forced-induction of pro-apoptotic UPRER reverses this phenotype. Remarkably,  milk fatty acids (FA) differ between genotypes and correlate with breast cancer risk in humans.  These results indicate that mitochondrial genetics modulates organellar responses to lactation and its protective effect. Our results further raise the possibility of using milk FA-signature as a read-out of the underlying biology to predict risk of breast cancer in the future.

overall_design: Inguinal mammary glands from mice were flash frozen and sent to GENEWIZ, LLC, NJ, USA for analysis. 3 mice per group were analyzed


title: Gene expression profile at single cell level of liver from GsdmdFL/FL and Gsdmd∆Hep radiation-induced liver disease mice [RNA-seq]

city: Guangzhou

first: Aoran

last: Dong

address: No.58 Zhongshan Er Road

institute: The First Affiliated Hospital, Sun Yat-sen University

summary: we used RNA sequencing (RNA-seq) to analyze the gene expression change in liver from GsdmdFL/FL and Gsdmd∆Hep radiation-induced liver disease mice

overall_design: The livers were harvested from GsdmdFL/FL-Ctrl, GsdmdFL/FL-LT  and Gsdmd∆Hep-LT mice


title: TICRR/TRESLIN and MTBP Cut&Run in G1 synchronized HCT 116 cells

summary: The selection of replication origins plays a crucial role in eukaryotic DNA replication. However, the mechanisms of origin selection in humans are not yet well-defined. Recent work in yeast has shown that the recruitment of Sld3-Sld7 to origins during G1 is involved in origin selection. In humans, TICRR/TRESLIN and MTBP are the orthologs of Sld3 and Sld7, respectively. In this study, we have mapped the genomic binding locations of TICRR/TRESLIN and MTBP in a population of G1 synchronized cells.

overall_design: We utilized HCT 116 cell lines, where all TICRR/TRESLIN or MTBP alleles were tagged with mClover, to perform Cut&Run experiments with an anti-GFP antibody that specifically binds to the tag. To obtain background signal measurements, we simultaneously conducted Cut&Run experiments on the untagged cell lines. Subsequently, the generated Cut&Run reads were aligned to the genome and used to call peaks.

middle: G


title: TICRR/TRESLIN and MTBP Cut&Run in Asynchronously Cycling HCT116 Cells

summary: The selection of replication origins plays a crucial role in eukaryotic DNA replication. However, the mechanisms of origin selection in humans are not yet well-defined. Recent work in yeast has shown that the recruitment of Sld3-Sld7 to origins during G1 is involved in origin selection. In humans, TICRR/TRESLIN and MTBP are the orthologs of Sld3 and Sld7, respectively. In this study, we have mapped the genomic binding locations of TICRR/TRESLIN and MTBP in asynchronous cells.


title: Effects of long-term depletion of Pu.1 in adult zebrafish microglia in mosaic condition

city: Shenzhen

first: Tao

last: Yu

address: Academic Building, 1120 Lianhua Road

institute: Shenzhen Peking University-the Hong Kong University of Science and Technology Medical Center

summary: In order to uncover the key downstream targets that mediate the out-competition of pu.1-deficient DsRed+ microglia in mosaic condition, we manually picked DsRed+ (pu.1-deficient) and eGFP+ (control) microglia from adult pu.1KI/Δ839;Tg(coro1a:CreER) zebrafish at 3 months post 4-OHT injection and performed RNA-seq. We found the tumor suppressor gene tp53 was one of the top targeted genes robustly upregulated in pu.1-deficient DsRed+ microglia which may contribute to the cell competition-mediated chronic elimination of pu.1-deficient microglia.

overall_design: 3~5 DsRed+ and eGFP+ microglia from adult pu.1KI/Δ839;Tg(coro1a:CreER) zebrafish at 3 months post 4-OHT injection were manually picked under the fluorescent microscope (Nikon Ti-S) equipped with the micro-manipulator (NT-88-V3, Nikon). Subsequently, picked cells were transferred by the glass needle to lysis buffer (mainly including Triton X-100 and RNase inhibitor) for thorough vertex. Then the cell lysate was used for reverse-transcription and amplification with the Smart-Seq2 method to generate the cDNA library. cDNA was sent to Novogene Company for Illumina sequencing with an average depth of 6×10^6 raw reads per sample. Sequence data were aligned to zebrafish genome by STAR (Spliced Transcripts Alignment to a Reference). Samples with strong expression of DC-related genes were discarded.

first: Yi

last: Wu

first: Weilin

last: Guo

first: Haoyue

last: Kuang

first: Xiaohai

first: Thi Huong

last: Trinh

first: Yuexin

last: Wang

first: Shizheng

last: Zhao

first: Zilong

last: Wen


title: Gene expression profile at single cell level of liver from GsdmdFL/FL and Gsdmd∆Hep radiation-induced liver disease mice

summary: we used single cell RNA sequencing (scRNA-seq) to analyze the diversity of immune cells in liver from GsdmdFL/FL and Gsdmd∆Hep radiation-induced liver disease mice

overall_design: GsdmdFL/FL and Gsdmd∆Hep mice exposure into 30Gy irradiation and the livers were harveste after 7 days


title: Ketone drink enhances therapeutic efficacy in prostate cancer by targeting EZH2

city: Chicago

first: Chaehyun

last: Yum

address: 303 E Superior St

institute: Northwestern University

summary: It is well established that EZH2, a lysine methyltransferase, is upregulated in most of aggressive cancers, highlighting the importance of EZH2 in cancer progression. Recent research has shown that metabolic reprogramming is pivotal in various biological processes, including cancer. Despite this, evidence of EZH2's role in regulating cancer metabolism remains limited. Our study reveals a negative correlation between EZH2 and HMGCS2, a gene belongs to the HMG-CoA synthase, in prostate and breast cancers. Furthermore, HMGCS2 is inversely related to cancer progression and prognosis in these cancers and is epigenetically repressed by EZH2 both in vitro and in vivo. Notably, restored EZH2 reduces the elevated HMGCS2 levels observed upon EZH2 depletion. Overexpression of HMGCS2 decreases tumorigenesis in both prostate and breast cancers. Additionally, β-hydroxybutyrate (BHB), a downstream metabolite of HMGCS2, impedes prostate cancer progression by targeting EZH2 via direct protein-compound interaction -mediated protein degradation. More importantly, ketone drink of BHB administration dramatically reduces tumor size and weight in a prostate cancer xenograft model. Combining ketone drink with FDA-approved drugs enzalutamide and Tazemetostat further suppresses tumor progression. Overall, EZH2- HMGCS2-BHB regulatory network plays a critical role in the progression of prostate cancer and ketone drink is a novel therapeutic tool for patients with aggressive prostate cancer.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for BHB treatment in C4-2 prostate cancer cell lines

first: Yanan

last: Ren

first: Rendong

last: Yang

first: Qi

last: Cao


title: Ketone drink enhances therapeutic efficacy in prostate cancer by targeting EZH2 [C4-2_siEZH2]

overall_design: Comparative gene expression profiling analysis of RNA-seq data for EZH2 depletion in C4-2 prostate cancer cell lines

first: Tingyou

first: Joshua

last: Fry

first: Richard

last: Schaefer


title: TBX21+CD21loCXCR3+B cell expansion with an EBV-associated phenotype in clinically isolated syndrome conversion to multiple sclerosis

city: Ann Arbor

first: Elliott

middle: Daniel

last: SoRelle

state: MI

address: 1137 Catherine St.

department: Microbiology & Immunology

institute: The University of Michigan

summary: Epstein-Barr virus (EBV) infection precedes multiple sclerosis (MS) onset and plays an etiologic role in the disease, although the nature of viral involvement is poorly understood. A common early event in the course of MS is Clinically Isolated Syndrome (CIS), a neuroinflammatory demyelinating condition for which 60-80% of cases progress to relapsing-remitting MS (RRMS). To investigate possible viral pathogenesis during early disease stages, we analyzed single-cell gene and surface protein expression of CIS peripheral B cells collected longitudinally during the Immune Tolerance Network (ITN) STAyCIS Trial. CIS B cell profiles were compared to publicly available scRNA-seq data from in vitro EBV infection, other autoimmune disorders, chronic infectious diseases, and healthy controls. Analyses focused on CD19+/CD20+/CD21lo/CD11c+/T-bet+ atypical B cells (ABCs), which are expanded pathogenic effectors in MS and other autoimmune and chronic infectious diseases. CIS PBMCs contained significantly higher frequencies of ABCs than healthy adult controls by scRNA-seq and flow cytometry, establishing ABC compartment expansion as a clinical feature of CIS. An EBV-associated ABC transcriptome, including expression of CXCR3 and immune checkpoint molecules (PD-L1, PD-L2), was enriched in CIS versus controls; however, evidence of direct EBV infection within the ABC niche was infrequently observed. CIS ABCs exhibited significant enrichment of inflammatory cytokine mRNAs including CXCL8 (IL8), IL18, and VEGFA. Several of these cytokines (IL-8, VEGF) were secreted by B cells upon de novo EBV exposure. CIS outcome stratification revealed a rare yet distinctive inflammatory ABC signature significantly underrepresented in long-term non-progressors (LTNP) versus people with primary endpoint RRMS activity. Moreover, CXCR3+ ABCs increased after baseline CIS diagnosis and were significantly enriched in MS vs LTNP outcomes after controlling for age and sex. Thus, we find evidence for ABC expansion, inflammatory responses, and checkpoint that precede MS onset, possibly as a bystander response to EBV infection.

overall_design: Cryopreserved PBMCs from two timepoints for people diagnosed with clinically isolated syndrome (CIS; n = 16 individuals x 2 timepoints = 32 samples) were thawed and prepared as single-cell RNA-seq + CITE-seq libraries using 10x Genomics kits, protocols, and instrumentation. The CITE-seq panel consisted of 18 antibodies with unique antibody-derived tags (ADTs) against the following surface molecules: CD3, CD4, CD8, CD11b, CD11c, CD14, CD16, CD19, CD25, CD27, CD45, CD56, CD64, CD196, CD294, CD366, KLRG1, and TCRVa24-JA18. After ADT labeling, scRNA-seq libraries were prepared with the 10x Genomics Chromium Controller and Single-Cell Gene Expression kit with v3.1 chemistry (5' v1 single index). Cells were normalized to 1000 cells per microliter, viability assessed, and titered to a maximum of 10,000 cells per library. Cells were resuspended in master mix containing reverse transcription reagents and combined with gel beads carrying the sequencing primers, barcodes, unique molecular identifier, and a poly-dT primer for RT. Full length cDNAs were cleaned and assayed to ensure lengths between 200-5000bp. Enzymatic fragmentation of the cDNA was used prior to adapter and sample index ligation; TruSeq read 2 primers were added via End Repair, A-tailing, Adaptor Ligation, and PCR. qPCR will be used to assess P5 and P7 adapter ligation, prior to size assessment of between 400-500bp. We generated 150bp paired end sequencing reads on an Illumina NovaSeq6000 (read 1=26 bp, read 2=91 bp, index read=8 bp) at a target of 50,000 reads/cell for gene expression and 5,000 reads/cell for ADT libraries. Output base calls (.bcl format) from sequencing were used to assemble single-cell RNA and ADT reads. Note: after processing read count data using Seurat pipelines, identified B cell clusters were extracted and subsequently analyzed. Base calls and FASTQ files contain all collected PBMC data. Samples are named by outcome during trial and follow-up period (MS = received MS diagnosis; LTNP = Long-Term Non-Progressor) and collection time (t1, t2). Cell line field includes time details (t1 = baseline CIS diagnosis; t2 = 3, 6, or 12 month follow-up). Genotype field includes demographic information (NHW = non-Hispanic White; HW = Hispanic White; AI = American Indian). Treatment field includes clinical trail arm information (placebo or atorvastatin treatment).

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