title: 53BP1 plays distinct roles in the recombination of RAG-cleaved on- and off-targets [ATAC-seq]

summary: RAG endonuclease initiates immunoglobulin heavy chain (Igh) V(D)J recombination by cleaving V, D and J gene segments flanked by recombination signal sequences (RSSs), subsequently joined exclusively by classical nonhomologous end joining (c-NHEJ). While 53BP1, a key DNA damage response (DDR) factor promoting c-NHEJ, was reported to be dispensable for Igh V(D)J recombination. Here, we report that 53BP1 is a unique DDR factor playing unrecognized roles in joining RAG-initiated DNA breaks. Both RAG-cleaved RSSs and cryptic RSSs (cRSSs) are joined by c-NHEJ. Deficiency of 53BP1, rather than other DDR factors, slightly decreased the proximal V(D)J recombination without affecting c-NHEJ of RAG-initiated RSS breaks, but significantly increased microhomology (MH)-mediated alternative end joining (A-EJ) of RAG-initiated cRSS breaks, indicating that 53BP1 is specifically required for c-NHEJ of RAG-initiated cRSS breaks. Thus, our findings provide new insights into the distinct roles of 53BP1 in joining RAG-cleaved on- and off-targets during exclusively c-NHEJ-mediated V(D)J recombination

overall_design: We performed VDJ-HTGTS-Seq, 3C-HTGTS, ChIP-seq, ATAC-seq, CUT&RUN, and  PRO-Seq in different mutants of v-Abl transformed pro-B cell lines to study roles of 53BP1 in V(D)J recombination.


title: Virus-like particles enable targeted gene engineering and pooled CRISPR screening in primary human myeloid cells [CRISPRoff]

status: Public on Apr 08 2026

city: San Francisco

first: Pascal

last: Devant

address: 1650 Owens Street

country: USA

institute: Gladstone Institutes

type: Expression profiling by high throughput sequencing

summary: Primary human myeloid cells are promising candidates for immunotherapy, yet efficient and scalable technologies for genetic engineering and screening in these cells are limited. Here we present a virus-like particle (VLP)-based toolkit that delivers diverse CRISPR genome editing modalities to human monocytes, macrophages, and dendritic cells with high efficiency while preserving viability and innate immune responsiveness. VLP-mediated delivery of ribonucleoprotein payloads supports gene knockout, base editing, and epigenetic silencing. Furthermore, in combination with AAV-mediated donor delivery, this approach enables site-specific integration of large DNA sequences via homology-directed repair. We also developed SLICeVLP, a system combining sgRNA delivery via VPX-lentivirus with Cas9 protein delivery via engineered virus-like particles (eVLPs), and applied it to perform pooled loss-of-function screens and Perturb-seq in human macrophages.  We uncovered regulators of TNF production and CD80 expression in human macrophages, converging on TNFAIP3 as a central regulator of inflammatory polarization. TNFAIP3 ablation promoted a pro-inflammatory cell state that is resistant to suppressive polarization, and augmented cytotoxicity in engineered HER2 CAR-macrophages. Taken together, this platform enables unbiased functional genomics in primary human myeloid cells, with direct implications for myeloid cell therapy design.

overall_design: RNASeq profiling of human monocyte-derived macrophages after treatment with CRISPRoff-eVLPs targeting CD81, CD45, CD14, as well as untreated and Non-target sgRNA controls. eVLP treatment was performed on Day 3 or Day 4 of differentiation and samples were collected 8 days later.

first: Hyuncheol

last: Jung

first: Alexander

last: Marson

first: Julia

last: Carnevale


title: 53BP1 orchestrates sequence feature of RAG targets to balance DNA repair outcomes during V(D)J recombination [3C-HTGTS-Seq]

status: Public on Apr 09 2026

city: Beijing

first: Xuefei

last: Zhang

address: No.5 Yiheyuan Road, Haidian District

department: Biomedical Pioneering Innovation Center (BIOPIC)

country: China

institute: Peking University

summary: RAG endonuclease initiates V(D)J recombination by cleaving recombination signal sequences (RSSs), subsequently repaired by classical nonhomologous end-joining (c-NHEJ). However, 53BP1, as a key DNA damage response (DDR) factor promoting c-NHEJ, is dispensable for V(D)J recombination. Here, we report that 53BP1 orchestrates sequence strength of RAG targets to shape end-joining features during V(D)J recombination. Deficiency of 53BP1, rather than other DDR factors, specifically increases junctional microhomology (MH) of cryptic RSS (cRSS) recombination instead of RSS recombination. Depletion of RIF1 or Shieldin, downstream factors of 53BP1, partially mimics the phenotypes of 53BP1-deficiency. Notably, loss of RNF168, rather than other classical resection and alternative end-joining factors, is sufficient to fully rescue 53BP1-deficiency-mediated increase of junctional MH during cRSS recombination. Remarkably, RAG mutant and RSS score analyses indicate that sequence strength of RAG targets determines the unique roles of 53BP1 in balancing end-joining outcomes. Our findings provide deeper mechanistic insights into DNA damage repair for RAG cleaved on- and off-targets during V(D)J recombination.

overall_design: We performed VDJ-HTGTS-Seq, 3C-HTGTS, ChIP-seq, CUT&RUN, and  PRO-Seq in different mutants of v-Abl transformed pro-B cell lines to study roles of 53BP1 in V(D)J recombination.

first: Sha

last: Luo

first: Hailiang

last: Zha

first: Zifan

last: Yang

first: Zhichen

last: Wan

first: Ruoxi

last: Kong

first: Ruolin

last: Qiao


title: Metabolic and Transcriptional alterations in Candida auris during Interaction with Pseudomonas aeruginosa

city: Debrecen

first: Agnes

last: Jakab

address: Nagyerdei krt 98.

country: Hungary

institute: University of Debrecen

summary: Polymicrobial bacterial–fungal infections are increasingly recognized as significant contributors to mortality in healthcare settings, particularly involving Pseudomonas aeruginosa and Candida species. While interactions between P. aeruginosaand Candida albicans have been widely studied, comparatively little is known about the emerging multidrug-resistant pathogen Candida auris. This study aimed to determine whether early growth inhibition of C. auris in co-culture with P. aeruginosa results from carbon depletion or micronutrient limitation, particularly iron restriction. Co-culture experiments demonstrated significantly reduced fungal proliferation despite preserved glucose availability, suggesting that carbon limitation is not the primary driver of growth inhibition. Transcriptomic analysis revealed strong upregulation of ribosome biogenesis and translation-associated genes, indicating increased translational capacity under competitive conditions. In contrast, genes involved in sterol and fatty acid biosynthesis, carbohydrate metabolism, and cell surface organization were consistently downregulated. Differential regulation of oxidative stress response genes suggested selective adaptation rather than generalized stress activation. Marked transcriptional changes were also observed in metal homeostasis pathways, with rapid extracellular iron depletion detected in co-culture conditions. Virulence-associated regulators, including genes linked to morphogenesis and adhesion, were downregulated, indicating reduced pathogenic potential. In a murine infection model, mixed infection resulted in significantly lower fungal burden compared to monoinfection, while bacterial burden remained unchanged. Together, these findings demonstrate that micronutrient competition, particularly iron limitation, plays a central role in shaping metabolic adaptation, transcriptional responses, and in vivo fitness of C. auris during interaction with P. aeruginosa.

overall_design: Comparative gene expression profiling analysis of RNA-seq data in Candida auris during interaction with Pseudomonas aeruginosa

first: Aliz

last: Bozó

first: Ágnes

first: Andrea

last: Harmath

first: Ágota

last: Ragyák

first: Zoltán

last: Tóth

first: Andrew

middle: M

last: Borman

first: Fruzsina

last: Kovács

first: Noémi

last: Balla

first: Bence

last: Balázs

first: László

last: Majoros

first: Renátó


title: Targeted spatial transcriptomic profiling of pleural mesothelioma using 10x Genomics Xenium

city: Durham

first: David

last: Severson

state: North Carolina

address: 2301 Erwin Road

department: Department of Surgery

institute: Duke University Health System

summary: Targeted spatial transcriptomic profiling was performed on seven formalin-fixed paraffin-embedded pleural mesothelioma tumor samples from four cases using the 10x Genomics Xenium platform. The Xenium Human Immuno-Oncology panel supplemented with 100 additional custom genes selected from known pleural mesothelioma biomarkers and single-cell RNA-seq-derived marker genes was used. Raw and processed Xenium files  are provided for each sample. To ensure data integrity with downloaded Xenium files, md5 checksums are provided in 'Xenium_GEO.md5'. This dataset is part of a multi-modality study including matched scRNA-seq, bulk RNA-seq, and Xenium spatial transcriptomics generated from overlapping pleural mesothelioma samples. Related controlled-access sequencing data are available in dbGaP under accession phs004285.

overall_design: Seven pleural mesothelioma tumor sites previously assayed by scRNA-seq were profiled by Xenium in situ targeted transcriptomics. Each sample corresponds to an FFPE tissue section from a defined anatomic site with matched case diagnosis metadata. Key per-sample Xenium output filese are provided containing morphology images, decoded transcripts, segmentation files, and count matrices. Sample identifiers are aligned to dbGaP records to facilitate cross-reference to accession phs004285.

middle: T

first: Sam

last: Freyaldenhoven

first: Ben

last: Wadowski

first: William

middle: G

last: Richards

first: Raphael

last: Bueno

first: Matthew

middle: B

last: Cougar


title: Crosstalk between human blastoids and endometrial assembloids mimicking maternal-fetal interactions and post-implantation development

city: Shanghai

first: Tu

middle: zhi

last: fen

address: Tongji University Siping Road Campus

department: life science and technology

institute: Tongji University

summary: We report that the three-dimensional (3D) maternal-fetal co-culture model using blastoid and endometrial assembloids captures the characteristics of embryo implantation and post-implantation development, including embryo attachment and expansion, trophoblasts differentiation, and gastrulation development. We also reveal the intricate maternal-fetal communication network.

overall_design: Single cell transcription profiling of blastoid and endometrial assembloids, as well as the co-culture of blastoid and endometrial assembloids

first: Zhifen

last: Tu

first: Yan

last: Bi

first: Xinbao

last: Zhang

first: Yixuan

last: Wang


title: Persistent Methylmalonate Overload Despite Glycemic Control Drives Mitochondrial Dyshomeostasis and Subclinical Heart Damage in Diabetes

city: Harbin

first: miao

last: yan

address: Harbin

institute: Harbin Medical University

summary:
Background
Heart failure burden is still considerable in diabetes patients despite optimal glycemic control. Metabolic remodeling is involved in this process, but current understanding is still in its infancy. Methylmalonic acid (MMA) is a diagnostic marker of cobalamin (Cbl) deficiency in clinical practice. Paradoxically, MMA elevation-related cardiovascular mortality is more pronounced in diabetic patients with higher Cbl levels. We investigated the mechanisms underlying these contradictory features in diabetic heart and translational relevance.
Methods
We assessed serum Cbl, MMA, and cardiac biomarkers in 12,751 participants, and the Mmut protein (allosteric enzyme of MMA catabolism) in failing human hearts with diabetes and healthy donors. Cardiomyocyte-specific Mmut knockout and Mmut-overexpressing (delivered by AAV-Mmut with cTnT promoter) mice were subjected to high-fat diet/streptozotocin-induced diabetes. High glucose and/or palmitate stimulation of primary neonatal mouse ventricular cardiomyocytes (NMVMs) imitates diabetic conditions in vitro. Molecular mechanism was explored through RNA sequencing, immunoprecipitation, isotope tracing mass spectrometry and biolayer interferometry assays.
Results
Higher serum MMA was significantly associated with subclinical heart damage and poor outcomes among adults with diabetes in the absence of Cbl deficiency. Cardiac MMA overload and decreased protein expression of Mmut were observed in humans and mice with diabetes. Notably, MMA dysmetabolism in diabetic mice occurred before detectable cardiac damage and persisted even after glycemic control. Mechanistically, hyperglycemic memory-related molecule miR-499 binds to the mRNA of Mmut and inhibits its expression, leading to MMA overload under diabetes. Mmut knockout amplified cardiac MMA overload and exacerbated disturbances in glycolipid metabolism and mitochondrial quality control in diabetic hearts. Conversely, AAV-Mmut injection significantly reduces MMA load and alleviates the progression of cardiac remodeling in diabetic mice. Isotope tracing identified isoleucine and valine as the main sources of cardiac MMA under diabetes. A restricted-branched chain amino acid diet alleviated diabetes-induced MMA accumulation and heart damage. However, Cbl supplementation did not correct MMA overload in diabetic mice, even at high doses or in activated forms. Strikingly, both clinical and preclinical data showed metformin, a risk factor for Cbl deficiency, may mitigate MMA overload and related heart damage via dual mechanisms—activating AMPK-dependent mitochondrial quality control, enhancing tolerance to MMA insults; and direct Mmut-cobalamin cooperation, promoting MMA clearance independent of AMPK.
Conclusions:
This study provides a foundation for understanding diabetes-related MMA dysmetabolism as a trigger for subclinical heart damage resistant to glycemic control and Cbl supplementation. Our ﬁndings challenge the prevailing clinical consensus regarding the impacts of Cbl and metformin use on MMA elevation.

overall_design: Heart tissues were collected from diabetic cardiomyopathy (DCM) and conditional knockout (CKO-DCM) mice (n = 3 per group) for RNA-seq analysis.  Transcriptomic profiling, including differential gene expression, alternative splicing, and pathway enrichment, was performed to elucidate molecular changes associated with CKO in the DCM context.

first: Shanjie


title: Spatial transcriptomics of IRF7-dependent pathway in chronic lung allograft dysfunction

city: houston

first: Nirmal

last: Sharma

state: MAtx

address: Baylor college of medicine

institute: Baylor college of medicine

summary: Chronic lung allograft dysfunction (CLAD) remains a major barrier to long-term survival after lung transplantation. This study investigates the role of the type I interferon master regulator IRF7 in virus-induced airway fibrogenesis. Using NanoString GeoMx digital spatial profiling, we performed whole transcriptome spatial analysis of human lung tissue from CLAD, non-CLAD transplant, and non-transplanted normal donor lungs to characterize the spatial gene expression landscape associated with IRF7-dependent fibrotic pathways.

overall_design: Paraffin-embedded lung tissue sections from CLAD (n=5), non-CLAD transplant (n=3), and non-transplanted donor (n=3) lungs were profiled using NanoString GeoMx Digital Spatial Profiler with the Human Whole Transcriptome Atlas (WTA) panel. Regions of interest (ROIs) were selected using fluorescently labeled antibodies against CD31, PanCK (Tumor), and CD45. Each ROI was segmented into CD31+, CD45+, PanCK+ (Tumor), and Full ROI areas of illumination (AOIs). 9-12 ROIs were selected per patient.

first: Banday

last: Mudassir

first: Rahman

last: Mizanur

first: Goda

last: Yasufumi

first: Naito

last: Tatsuhiko

first: Potter

last: Andrew

first: Mallidi

last: Haripriya

first: Surolia

last: Ranu

first: Lee

last: Stefi

first: Rehman

last: Rakshinda

first: Loor

last: Gabriel

first: Hayes

last: Don

first: Sharma

last: Nirmal


title: Transcriptomic analysis of early stage of alpha-synuclein accummulation in Parkinson's disease mouse model

city: Suita

first: Kit-yeng

last: Sheng

address: Yamadaoka 2-2

country: Japan

institute: Osaka University

summary: The gene expression changes in dopaminergic neurons in PD mouse model has not been able to study due to lack of an approach in the collection of viable neurons from mouse brains. We utilized the established Ddc-hKO1 knock in mice and improved neural dissociation protocol accompanied with FACS to faciliate the collection of viable dopaminergic neurons. We performed intranigral injection with pre-formed alpha-synuclein fibril with G51D mutation on Snca to induce Lewy body-like structure accumulation. Dopaminergic neurons rom midbrain were collected at 7 weeks and 12 weeks post injection to reflect the early stage of PD progression. 2 brains were pooled as a single biological replicate. We performed gene ontology analysis using DAVID and GSEA analysis with pre-ranked in fold change. Both analysis shows that lipid metabolism associated gene sets were enriched in up-regulated genes in 7 weeks post-injection but remained unchange in expression in 12 weeks post-injection. Meanwhile, protein post-translational modifications related gene sets were enriched in up-regulated genes at 12 weeks post-injection but remained unchanged at 7 weeks post-injection. We showed that Fabp1 expression of was up-regulated in hKO1(+) cells and up-regulation of FABP1 in VTA & SNc region was confirmed by immunofluorescence staining.

overall_design: The gene expression changes in dopaminergic neurons at 7 weeks and 12 weeks post-injection of pre-formed G51D alpha-synuclein fibrils.

first: Kit-Yeng

first: Hideki

last: Hayakawa


title: Clostridioides difficile CenIR

city: Iowa City

first: Craig

last: Ellermeier

state: IA

address: 431 Newton Road

department: Microbiology and Immunology

institute: University of Iowa

summary: Effect on gene transcript levels upon CRISPRi silencing the BlaIR homologs, CenIR

overall_design: The wild type strain R20291 harboring either a negative control plasmid (guide does not target anywhere in the C. difficile genome) or a CRISPRi-plasmid targeting cenI (cdr20291_0474) was grown in the presence of 1% xylose to induce CRISPRi.

first: Ute

last: Müh

first: David

last: Weiss


title: Virus-like particles enable targeted gene engineering and pooled CRISPR screening in primary human myeloid cells [RNA-Seq Exp1]

first: Pascal

last: Devant

overall_design: Bulk RNA seq profiling of primary human monocyte-derived macrophages CRISPR-edited at for AAVS1 locus via nucleofection vs. Cas9EDV. Cells were treated either on Day 0 or Day 4 post isolation and samples were collected on Day 7.

first: Hyuncheol

last: Jung

first: Alexander

last: Marson

first: Julia

last: Carnevale


title: FGF23 partial agonism improves rhabdomyolysis-induced acute kidney injury

city: Wenzhou

first: gaozhi

last: chen

address: Chashan Higher Education Park, Ouhai District, Wenzhou City, Zhejiang Province

institute: Wenzhou Medical University

summary: Overexpression of FGF23R176Q/R179Q can improve AKI by inhibiting apoptosis.

overall_design: Overexpress the FGF23R176Q/R179Q protein in mice, then induce the RM - AKI model three weeks later, and perform RNA - seq analysis on the kidney tissue.

first: Zhongqian

last: Jin

first: Shengnan

last: Zhao

first: Kai

first: Shuixin

last: Li

first: Fulai

last: Huang

first: Kaifeng

last: Chen

first: Yixiong

last: Wang

first: Lvhua

last: Ai

first: Jiru

last: Wu

first: Bojun

first: Lili

last: Fu

first: Moosa

last: Mohammadi

first: Gaozhi


title: Virus-like particles enable targeted gene engineering and pooled CRISPR screening in primary human myeloid cells

first: Pascal

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

overall_design: Refer to individual Series


title: Virus-like particles enable targeted gene engineering and pooled CRISPR screening in primary human myeloid cells [RNA-seq Exp3]

overall_design: RNASeq profiling of human monocyte-derived macrophages after treatment with CRISPRoff-eVLPs targeting CD81, CD45, CD14, as well as untreated and Non-target sgRNA controls. eVLP treatment was performed on Day 4 of differentiation and samples were collected 8 days later.

first: Hyuncheol

first: Alexander


title: Mitochondrial L-2-hydroxyglutarate is a physiologic signaling metabolite [scRNA-seq]

city: Chicago

first: Navdeep

middle: S.

last: Chandel

state: IL

address: 303 E. Superior Street

department: Department of Medicine & Biochemistry and Molecular Genetics

institute: Northwestern University

summary: L-2-hydroxyglutarate (L-2-HG) is a low-abundance metabolite in mammals due to the mitochondrial enzyme L-2-HG dehydrogenase (L2HGDH), which oxidizes L-2-HG to 2-oxoglutarate (2-OG) to prevent its accumulation. In humans lacking L2HGDH activity, L-2-HG builds up, leading to L-2-hydroxyglutaric aciduria, a rare childhood neurometabolic disorder. Thus, L-2-HG is often classified as a toxic metabolite. Furthermore, L-2-HG is produced in response to hypoxia, acidic pH, and electron transport chain (ETC) impairment. However, whether L-2-HG has a physiological function is unclear. Here, we investigated whether L-2-HG qualifies as a physiologic signaling metabolite by testing three criteria: regulated levels, defined molecular targets, and a measurable physiological function. We report that an elevated mitochondrial NADH/NAD⁺ ratio drives malate dehydrogenase 2 (MDH2) to reduce 2-OG into L-2-HG, while L2HGDH oxidizes L-2-HG back to 2-OG within the mitochondrial matrix without requiring a functional ETC. Proteome integral solubility alteration (PISA) assays revealed the KDM4 family of H3K9 demethylases as L-2-HG-responsive targets. Consistent with this, elevated L-2-HG repressed nascent transcription of specific gene sets and promoted accumulation of the repressive histone mark H3K9me3 at those loci. In vivo, ubiquitous early embryonic L2HGDH overexpression lowered L-2-HG, reduced postnatal growth, and caused postnatal mortality. Despite systemic lowering of L-2-HG levels, kidneys exhibited a unique vulnerability, displaying functional impairments and histologic alterations. Mechanistically, L-2-HG depletion in the postnatal kidney resulted in the loss of H3K9me3 specifically at L1MdTf retrotransposons, leading to their derepression and coinciding with activation of the integrated stress response (ISR) and inflammation pathways. Our findings establish mitochondrial L-2-HG as a physiologic signaling metabolite that couples mitochondrial redox state to chromatin regulation, which is essential for postnatal kidney function and survival. These findings suggest that metabolites previously regarded as toxic may also serve critical physiological functions.

overall_design: scRNA-seq was performed on Wild-Type and L2HGDH-Overexpressing (homozygous) mouse kidney (P11) single cell suspension.

first: Ram

middle: P

last: Chakrabarty

first: Rogan

middle: A

last: Grant

middle: S


title: BAG2 Condensates Couple Proteostasis to CD8 + T Cell Surveillance

city: Santa Barbara

first: Andrew

middle: Paul

last: Longhini

state: California

address: 6139 Biological Sciences II

department: Neuroscience Research Institute

institute: University of California, Santa Barbara

summary: Protein aggregation, impaired degradation, and immune activation are central hallmarks of many neurodegenerative diseases, yet how these processes are coordinated remain unclear. Here we identify a new class of phase-separated proteostasis organelles, termed immune degradation condensates (IDCs), composed of BAG2 assemblies. Inflammatory cues drive the formation of BAG2 IDCs, which are enriched in immunoproteasome components, major histocompatibility complex class I (MHC-I) peptide-loading machinery, and chaperones associated with the endoplasmic reticulum (ER). These assemblies redirect proteostatic cargo from centrosomal aggregation pathways to immune-specialized sites, coupling substrate clearance to antigenic peptide production and enhancing CD8⁺ T cell engagement. Using a cellular model of aggregation-prone Tau, we show that BAG2 IDCs capture pathological Tau fibrils at ER–microtubule interfaces and process them into antigenic peptides, thereby reducing the abundance of the aggregation-prone PHF6 motif. We term this system the Proteostasis-Associated Immune Relay (PAIR), establishing IDCs as critical hubs with potential implications for multiple disease states.

overall_design: RNA-seq profiling of polyA capture from H4 cells, H4 cells stably expressing mClover3-0N4R-P301L Tau and H4 Cells stably expressing mClover3-0N4R-P301L Tau and harboring tau aggregates seeded by jR2R3 P301L mini fibril.

first: Marie

middle: C

last: Almeida

first: Daniel

last: Carrettiero

first: Kenneth

last: Kosik


title: LncRNA Gas5 directs SUV39H2 to establish heterochromatin and maintain genome stability

first: Jiani

last: Yang

address: Siping Road, Yangpu District

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Constitutive heterochromatin, characterized by histone H3 lysine 9 trimethylation (H3K9me3), is essential for genome stability, pluripotency, and developmental fidelity. While the SUV39H histone methyltransferases catalyze H3K9me3 deposition, their locus-specific targeting mechanisms remain unclear. Here, via RNA depletion or RNA-binding affinity mutation, we establish that RNA binding is indispensable for SUV39H2 recruitment to chromatin and H3K9me3 maintenance in mouse embryonic stem cells (ESCs). Through RNA immunoprecipitation sequencing (RIP-Seq) and functional validation, we identify the long non-coding RNA Gas5 as a specific SUV39H2 interactor. Depletion of Gas5 or disruption of the SUV39H2–RNA interaction leads to the loss of self-renewal capacity of ESCs, abolishes H3K9me3 enrichment, along with profound genomic instability, mitotic errors, and γH2AX foci accumulation. These findings reveal a critical lncRNA-dependent mechanism governing the SUV39H2–H3K9me3 axis, which directly couples RNA metabolism to the preservation of pluripotency and genome integrity in stem cells.

overall_design: This submission includes sequencing data (ChIP-seq, RIP-seq, and RNA-seq) from mouse embryonic stem cells (ESCs), which are critical for genome stability and pluripotency maintenance. The primary objective of this study is to elucidate the locus-specific targeting mechanism of SUV39H2-mediated H3K9me3 deposition, focusing on the role of RNA binding and the long non-coding RNA Gas5.

first: Juntao

last: Liu


title: Virus-like particles enable targeted gene engineering and pooled CRISPR screening in primary human myeloid cells [RNA-seq Exp2]

last: Devant

overall_design: Bulk RNA seq profiling of primary human monocyte-derived macrophages CRISPR-edited at for AAVS1 locus via nucleofection vs. Cas9EDV and treated with bacterial lipopolysaccaride

last: Jung

last: Marson

first: Julia

last: Carnevale


title: Evidence for coordinate epigenomic roles for CTCF and histone H3.3 in K27M diffuse midline gliomas

city: Davis

first: Paul

last: Knoepfler

state: CA

address: 1 Shields Ave

department: Cell biology and human anatomy

institute: UC Davis

summary: In this study we identified and characterized key chromatin domains in diffuse midline glioma cells, looking at well known types of domains including super enhancers, bivalent domains, and H3K4me3 broad domains as well as the chromatin states identified by chromHMM. In this context, we identified a key role for CTCF in maintaining H3K27me3 levels at bivalent domains, and demonstrated that the H3.3K27M mutation affects both CTCF localization and H3K27me3 at these regions. We further characterized a functional interaction between H3.3 and CTCF in diffuse midline glioma cells, finding that the H3.3K27M mutation affects CTCF localization, leading to an expansion of CTCF-bound domains including a large number of ectopic CTCF binding sites found in H3.3K27M but not WT cells. We also found that CTCF knockdown increases cell viability in H3.3K27M cells, and affected the expression of a set of genes highly enriched in active chromatin states and likely important for some of the oncogenic properties of these cells. Together, our results identified complex chromatin domains defined by combinations of epigenetic modifications, which may have implications for designing therapy regimens that include multiple epigenetic drugs to more effectively target the numerous changes in chromatin observed in glioma cells with H3.3K27M. We also defined an important role for the structural protein and transcription factor CTCF in influencing the epigenetic landscape and transcriptome in the context of the H3.3K27M mutation in diffuse midline glioma cells.

overall_design: H3K4me3 ChIP-seq was performed in DIPG Line XIII cells.

first: Rachel

last: Klein


title: The chromatin assembly factor CHAF1b functions as an epigenetic amplifier of RORγt to promote Th17 pathogenicity and autoimmunity

city: shenzhen

first: huang

last: peiming

state: Guangdong

address: xinhu

institute: Sun Yat-sen University

summary: Th17 cells are double-edged regulators of mucosal defense and autoimmune inflammation, yet the chromatin mechanisms distinguishing their pathogenic state remain elusive. Here, we identify CHAF1b, a core subunit of the chromatin assembly factor CAF-1 complex, as an essential epigenetic amplifier of RORgt-driven transcription in Th17 cells. CHAF1b expression is selectively induced during Th17 differentiation and elevated in inflamed tissues from mice with experimental autoimmune encephalomyelitis (EAE) and colitis. Th17-specific deletion of Chaf1b markedly reduces IL-17A/F expression, alleviates neuroinflammation and colonic pathology, and reprograms the Th17 effector transcriptome without affecting lineage commitment. Mechanistically, CHAF1b physically associates with RORgt and co-occupies enhancer regions at the Il17a–Il17f locus, promoting chromatin accessibility and enhancer activation. Multi-omics analyses reveal that CHAF1b reinforces RORgt-driven enhancer–promoter interactions and maintains a proinflammatory Th17 epigenome. In human Th17 cells, CHAF1b similarly governs IL-17 production, and its expression declines in patients with inflammatory bowel disease following effective therapy. Collectively, these findings uncover CHAF1b as a chromatin-anchored signal amplifier that couples RORgt activity to autoimmune inflammation, highlighting its potential as a therapeutic target for Th17-mediated disorders.

overall_design: This study aims to investigate the role of Chaf1b in Th17 cell function. Naive CD4+ T cells were isolated from the spleens of wild-type (Chaf1bWT and conditional knockout (Chaf1bfl/fl;Il17fCre+, referred to as Chaf1b-/-) mice. The isolated naive CD4+ T cells were activated and cultured under Th17-polarizing conditions for 72 hours. Following differentiation, cells were harvested for both RNA-sequencing (RNA-seq) and chromatin immunoprecipitation sequencing (ChIP-seq) to profile transcriptomic changes and chromatin landscapes, respectively. Three biological replicates were included per genotype for RNA-seq assay. This experimental design allows for the comparative analysis of wild-type and Chaf1b-deficient Th17 cells to elucidate the molecular mechanisms regulated by Chaf1b during Th17 differentiation.

first: Xinyu

last: Li

first: Achun

last: Chen

first: Kang

last: Cao

first: Peiming

last: Huang

first: Minghua

first: Jianteng

last: Zeng

first: Jingjing

last: Luo

first: Xin

last: He

first: Shuangxin

last: Wu

last: Zhou

first: Hui

last: Zhang

first: Ting

last: Pan


title: EPHB2 Drives EMT-Linked Vasculogenic Mimicry and Cervical Cancer Progression via an ERK–ETV4 Transcriptional Program

city: Suzhou

first: Xiaoqin

last: Yang

state: Jiangsu

address: NO. 199 Renai Road

institute: Soochow University

summary: To investigate the biological function EPHB2 in the cervical cancer, we established hela cell lines in which the EPHB2 gene has been knocked down by the small interfering RNA (siRNA) technique. Two different siRNAs targeting EPHB2 (KD) were used to knockdown EPHB2 expression in hela cells. A scrambled siRNA (NC) was used as a control. For each sample, three independent biological replicates were performed. Then RNA-Seq experiment was performed by Shanghai Biotechnology Corporation (Shanghai, China).

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Hela cells and its KD derivatives (siEPHB2).

first: Wenzhi

last: Jiao

first: Minmin

last: Yu


title: Spatial transcriptomics links hippocampal synaptic remodeling to microglial phagocytosis in synucleinopathy

city: Daegu

first: Mookyung

last: Cheon

address: 61, Cheomdan-ro, Dong-gu

department: Dementia Research Group

country: South Korea

institute: Korea Brain Research Institute

summary: Synucleinopathies, including Parkinson’s disease and Lewy body dementia, show region-specific vulnerability across the brain, but the molecular basis of selective regional involvement remains incompletely understood. We performed spatial transcriptomic profiling of brain sections from 6-month-old G2-3 alpha-synuclein transgenic mice and wild-type littermates using the 10x Genomics Visium Spatial Gene Expression platform to characterize region-specific transcriptional alterations associated with alpha-synuclein pathology. This dataset provides a resource for investigating spatially resolved molecular changes in the synucleinopathy mouse brain.

overall_design: This study utilizes 10x Genomics Visium spatial transcriptomics to investigate region-specific molecular vulnerability in 6-month-old G2-3 (A53T alpha-synuclein) mice. By integrating spatial expression with cell-type deconvolution and histological validation across the hippocampus, cortex, and substantia nigra, we identify a unique hippocampal vulnerability. Our findings reveal that a non-inflammatory phagocytic microglial program drives selective postsynaptic impairment in this synucleinopathy model.

first: Min-Tae

last: Jeon

first: Jisu

last: Jeong

first: Moonseok

last: Choi

first: Suhyeon

last: Son

first: Wonjin

first: Do-Geun

last: Kim


title: Histone chaperones ASF1s control germination by repressing PRX69

city: Yangling

first: Su

middle: Ying

last: Pei

state: Shaanxi

address: No. 3 Taicheng Road

department: College of Life Sciences and Institute of Future Agriculture

institute: Northwest A&F University

summary: Seed germination is a critical developmental decision that integrates hormonal and epigenetic signals. While physiological dormancy has been extensively studied, the molecular basis of physical dormancy—mediated by structural barriers such as the seed coat (testa)—remains poorly understood. Here, we investigate the role of Arabidopsis ASF1 histone chaperones in germination, revealing their function in altering chromatin structure to regulate testa penetrability. The asf1a1b double mutant exhibits significantly reduced germination rates, independent of ABA or GA levels. Using RNA-seq, we identified PRX69, a peroxidase implicated in testa hardening regulation, as markedly overexpressed in asf1a1b seeds. Genetic suppression of PRX69 partially rescues the asf1a1b germination defect. Additionally, by ChIP assays, we show that ASF1 proteins directly bind PRX69. Finally, loss of ASF1s disrupts H3.3 incorporation, reduces total H3 occupancy, and increases chromatin accessibility at PRX69, which is associated with RNA polymerase II enrichment. These findings establish ASF1-mediated H3.3 dynamics as a critical epigenetic mechanism controlling physical dormancy by repressing PRX69-driven testa hardening. Our research provides new insights into the interplay between epigenetic regulation and physical dormancy in plants.

overall_design: RNA-Seq profiling was performed on freshly harvested seeds, harvested within 24 hours of wildtype Columbia-0 and asf1a1b mutants.

first: Israel

last: Ausin

first: Yafei

last: Wang

first: Fan

first: Yingpei

last: Su

first: Zhipeng

last: Gong

first: Qin

last: Hu


title: AKT inhibitor capivasertib reverses EVI1‑driven resistance to venetoclax in acute myeloid leukaemia

city: Dalian

first: Jinsong

last: Yan

address: 9 west section, Lvshun south road, Dalian, Liaoning Province, China

department: Institute of Cancer Stem Cell

institute: Dalian Medical University

summary: Acute myeloid leukaemia (AML) with MECOM rearrangement is recognized by the World Health Organization as a distinct entity characterized by poor prognosis and aggressive disease progression. We demonstrated that elevated EVI1 expression confers resistance to venetoclax by stabilizing MCL‑1 through activation of the PI3K/AKT signalling pathway in vitro. Mechanistically, elevated EVI1 levels were associated with increased phosphorylation of MCL-1 at threonine 163 (T163pMCL‑1), thereby stabilizing MCL-1 by attenuating its ubiquitin–proteasome mediated degradation. Importantly, cotreatment with venetoclax and the clinically available AKT inhibitor capivasertib effectively restored sensitivity in both cell lines and patient-derived primary AML samples with high EVI1 expression. Overall, our findings reveal a novel molecular mechanism underlying EVI1-mediated venetoclax resistance through PI3K/AKT-driven MCL‑1 stabilization and suggest a combination strategy involving AKT inhibition as a promising approach for overcoming therapeutic resistance in this high-risk AML subset.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Control and EVI1-overexpressing cells in K562 and MOLM14.

first: Jiayin

last: Zhou

first: Xuehong

last: Zhang


title: Base-resolution DNA methylomes of bone marrow primitive hematopoietic stem cells from Myelodysplastic syndromes patients and healthy donors

city: 上海

first: Qian

state: 上海市

address: 盘山路7号

institute: Naval Medical University

type: Methylation profiling by high throughput sequencing

summary: To investigate DNA methylation variations at single-base resolution in bone marrow primitive hematopoietic stem cells from Myelodysplastic syndromes patients  using whole genome bisulfite sequencing (WGBS)

overall_design: We isolated genomic DNA of freshly sorted human bone marrow primitive hematopoietic stem cells (Lin-CD133+CD34+)  for WGBS.

first: Xuetao

last: Cao


title: Ginsenoside Rg3 attenuates allergic asthma in mice via transcriptomics

city: Huai'an

first: Xiuqin

last: Ni

address: No.4 Mei Cheng Road, Higher Education Park

institute: Jiangsu Food and Pharmaceutical Science College

summary: ObjectivesThis study aims to investigate the molecular mechanism by which ginsenoside Rg3 attenuates allergic asthma. Methods: This study established an ovalbumin (OVA)-induced mouse model of allergic asthma to explore the anti-allergic effects and potential molecular mechanisms of ginsenoside Rg3. The therapeutic effects of Rg3 were systematically evaluated via monitoring of general physical conditions, lung histopathological examination, inflammatory cell infiltration analysis in bronchoalveolar lavage fluid, and inflammatory cytokine detection. Furthermore, transcriptomic analyses were conducted to screen differentially expressed genes.

overall_design: An ovalbumin (OVA)-induced murine model of allergic asthma was established to investigate the anti-allergic effects and molecular mechanisms of ginsenoside Rg3. Mice were divided into experimental groups (treated with ginsenoside Rg3) and control groups (without Rg3 treatment), with biological replicates set for each group. The therapeutic efficacy of Rg3 was evaluated by detecting general health status, lung histopathology, inflammatory cell infiltration in bronchoalveolar lavage fluid, and inflammatory cytokine levels. Transcriptomic analyses were performed on mouse lung tissue samples to identify differentially expressed genes and elucidate the key regulatory pathways mediated by ginsenoside Rg3 in allergic asthma.


title: All-trans retinoic acid modulates proliferation and apoptosis of secondary hair follicle–dermal papilla cells in cashmere goats via the TGF-β2/Smad2/3 pathway

city: hohhot

first: yadong

last: gao

address: hohhot

institute: Inner Mongolia University

summary: Cashmere, a fiber of high economic value, is produced by secondary hair follicles (SHFs), whose growth depends on the proliferation and apoptosis of SHF-derived dermal papilla cells (SHF-DPCs). All-trans retinoic acid (ATRA), a metabolite of vita min A, has shown inconsistent effects on hair follicle biology, with reports of both inhibition and stimulation. To clarify the role of ATRA in follicular development, we investigated its effects on the proliferation and apoptosis of in vitro–cultured SHF-DPCs isolated from Capra hircus (Albas cashmere goats). SHF-DPCs were obtained from scapular skin, and the optimal ATRA concentration (10−4 M) and treatment duration (24 h) were identified using Cell Counting Kit-8, 5-ethynyl-2′ deoxyuridine, and terminal deoxynucleotidyl transferase dUTP nick end labeling assays. Cells were then assigned to an ATRA-treated group (10−4 M) or a control group. Proliferation, apoptosis, and cell cycle progression were evaluated, fol lowed by transcriptome sequencing. Transcriptomic analysis indicated enrich ment of the transforming growth factor-β (TGF-β) signaling pathway. Therefore, mRNA and protein levels of TGF-β2—a follicle growth–related regulator—and Smad2/3 phosphorylation were examined. The TGF-β type I/II receptor inhibitor LY2109761 was used to further validate the involvement of this pathway. ATRA inhibited SHF-DPC proliferation by inducing G1-phase cell cycle arrest and pro moted apoptosis by upregulating Bax expression while downregulating Bcl-2 protein expression. Transcriptomic analysis showed that ATRA upregulated TGFβ2 expression in SHF-DPCs. Gene Ontology analysis revealed enrichment of genes related to proliferation and apoptosis, such as “cell migration” and “cell cycle.” Kyoto Encyclopedia of Genes and Genomes pathway analysis identified the TGF β signaling pathway as a major regulatory target. Treatment with LY2109761 par tially reversed ATRA-induced reductions in proliferation, increases in apoptosis, and elevations in Smad2/3 phosphorylation. Overall, ATRA inhibits proliferation and promotes apoptosis in SHF-DPCs, likely through the TGF-β2/Smad2/3 path way. These findings provide novel insights into ATRA-mediated regulation of hair growth and offer a theoretical basis for future research on cashmere goat SHF development.

overall_design: Control:Secondary hair follicle dermal papilla cells isolated from Capra hircus and cultured under standard conditions without ATRA treatment, serving as the control group for transcriptome analysis;ATRA:Secondary hair follicle dermal papilla cells isolated from Capra hircus treated with all-trans retinoic acid (ATRA) to investigate transcriptional changes induced by ATRA treatment.


title: Identifying the therapeutic potential of Niclosamide in overcoming IFN-gamma dependent cancer immune evasion in the Tumor Microenvironment

city: Pittsburgh

first: YUE

last: ZHANG

state: PA

address: 4400 Fifth Ave

department: Biological Science

institute: Carnegie Mellon University

summary: Tumor cells frequently develop immune resistance through interferon-γ (IFN-γ)–induced PD-L1 expression, acquisition of cancer stem cell (CSC)–like features, and adaptation to hypoxia within the tumor microenvironment (TME). Although IFN-γ activates both STAT1 and STAT3, how these pathways interact to regulate immune evasion under hypoxia remains unclear. Using the MC38 murine colorectal cancer model and T cell–tumor spheroid co-culture assays, we examined how IFN-γ signaling through STAT1 and STAT3 regulates PD-L1 expression, CSC plasticity, and cytotoxic T cell function under normoxic and hypoxic conditions. Pharmacologic inhibitors and siRNA-mediated knockdown were used to dissect pathway function, and Niclosamide, an FDA-approved anthelmintic, was evaluated as a dual STAT1/STAT3 inhibitor. We found that IFN-γ primarily induced PD-L1 expression through STAT1 activation, whereas CSC plasticity was associated with STAT3 signaling. STAT1 and STAT3 displayed reciprocal regulation—blocking one enhanced activation of the other. Niclosamide effectively inhibited phosphorylation of both STAT1 and STAT3, resulting in suppressed PD-L1 upregulation and reduced CSC enrichment. In addition, it also partially inhibited hypoxia-induced HIF-1α expression. In co-culture assays, Niclosamide enhanced T cell infiltration and reduced exhaustion under hypoxic conditions, resulting in improved T cell killing. Our findings identified Niclosamide as a potent dual STAT1/3 inhibitor capable of reversing IFN-γ and hypoxia-driven immune evasion. Repurposing Niclosamide may represent a promising strategy to enhance the efficacy of immune checkpoint blockade in solid tumors.

overall_design: RNA-SEQ profiling of MC38 cells treated with  single biological sample per condition: control (Ctrl_1_1, Ctrl_2_1) vs IFN-γ treatment (IFN_1_2, IFN_2_2), normoxia (Ctrl_1_1,IFN_1_2) vs hypoxia (Ctrl_2_1,IFN_2_2).

first: Yue

first: En

last: Cai


title: Identifying Senescence and Immune Biomarkers Predictive of Benefit to Combined CDK4/6 and PD-1 Blockade in Dedifferentiated Liposarcoma: Single-Cell RNA-seq of Serial Tumor Biopsies

city: New York

first: Bic

last: MSKCC

state: NY

address: 1275 York Ave.

institute: Memorial SLoan-Kettering Cancer Center

summary: This dataset comes from an exploratory correlatives sub-study embedded within NCT04438824, a single-arm, open-label phase II trial evaluating the combination of the CDK4/6 inhibitor palbociclib and the PD-1 inhibitor INCMGA00012 in patients with advanced well-differentiated or dedifferentiated liposarcoma. The dbGaP submission is limited to the first 12 patients enrolled on the trial, for whom protocol-mandated tumor biopsies were collected for single-cell RNA sequencing. Single-cell RNASeq was performed to characterize cellular composition and transcriptional states within the tumor microenvironment in this pilot cohort. The dataset includes processed single-cell expression profiles and a restricted set of associated clinical variables such as demographics and response data abstracted from the parent study.

overall_design:
Tumor biopsies were obtained at protocol-specified timepoints during treatment on NCT04438824. Single-cell suspensions were prepared and profiled by 10x Genomics scRNA-seq. Processed count matrices (10x HDF5 format) were generated and used to evaluate tumor and immune cell states, including senescence-associated and immunologic transcriptional programs, and to relate these features to treatment response. Raw sequencing reads are controlled-access in dbGaP (phs004414.v1.p1).

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

last: Evan

first: Gularte Mérida

last: Rodrigo

first: D'Angelo

last: Sandra


title: Astrocytic APOE3-Christchurch expression ameliorates brain amyloid-β pathology in 5xFAD mice

city: Jacksonville

first: Yingxue

last: Ren

state: FL

address: 4500 San Pablo Rd S

institute: Mayo Clinic

summary: The rare APOE3-Christchurch (APOE3Ch) variant is linked to resistance against PSEN1 p.E280A-driven autosomal dominant Alzheimer’s disease (AD). Recent studies in AD mouse models have demonstrated an effect of APOE3Ch in reducing tau pathology and tau propagation, yet its effects on amyloid pathology and related toxicity are not fully understood. While prior studies have reported reduced amyloid pathology with APOE3Ch, we extended this knowledge by investigating how astrocyte-specific expression of APOE3Ch impacts amyloid pathology and related responses in 5xFAD mice, an amyloid mouse model. Using adeno-associated virus (AAV)-mediated gene delivery, we overexpressed APOE3 or APOE3Ch in astrocytes of 5xFAD mice at the neonatal stage, then analyzed their effects during the advanced stage of amyloid pathology. Astrocytic APOE expression significantly reduced amyloid burden, neuritic dystrophy, and gliosis compared to GFP controls. Notably, astrocytic APOE3Ch expression, relative to APOE3, markedly lowered oligomeric Ab levels and promoted the formation of more compact, fibrillar plaques, suggesting a shift toward a less toxic aggregation profile. Transcriptomic profiling of cortical tissue revealed broad downregulation of immune-related and proteostatic pathways. These findings indicate that astrocytic APOE3Ch sufficiently attenuates Ab pathology and related toxicity, supporting its potential as a therapeutic modifier for AD.

first: Ana-Caroline

last: Raulin

first: Takahisa

last: Kanekiyo


title: A conserved enhancer cluster controls efnb2 expression in the vertebrate dorsal retina

city: Baton Rouge

first: Patricia

last: Schneider

state: Louisiana

address: LSU 131 Life Sciences Building

department: Biological Sciences

institute: Louisiana State University

summary: The vertebrate retina is patterned along its dorsal-ventral (DV) axis by signaling centers that provide each domain with distinct molecular and functional properties, including differential photoreceptor composition and opsin expression. Although the key DV patterning genes are well studied, the cisregulatory mechanisms that establish and maintain these territories remain poorly understood. To explore this regulatory landscape, we turned to the four-eyed fish Anableps anableps, whose large, protruding eyes and expanded ventral retina facilitate precise dissection of dorsal and ventral halves for spatially resolved genomics. Bulk RNA-seq of the Anableps dorsal and ventral retina regions recovered canonical DV markers, while bulk ATAC-seq revealed dorsally enriched ATAC-seq peaks residing within a low-genedensity region between efnb2a and gtpbp8. These putative cis-regulatory elements located to a 29 kb interval forming a contiguous enhancer cluster. Via Hi-C analysis, we identified a topologically associating domain (TAD) encompassing efnb2a, gtpbp8, and slc10a2, with a dorsal-enriched chromatin contact linking the enhancer cluster to the efnb2a promoter. Comparative genomics showed that this architecture is deeply conserved: the efnb2-slc10a2 synteny and TAD boundaries are maintained from human to zebrafish. To enable functional testing of this long regulatory interval, we strategically turned to Tetraodon nigroviridis, a species with one of the most compact vertebrate genomes, allowing nearly the entire orthologous enhancer cluster (~13 kb) to be cloned intact. Transgenic assays in both zebrafish and mouse demonstrated that this Tetraodon enhancer cluster drives dorsal retina-specific eGFP expression, underscoring the deep conservation of its regulatory function across vast phylogenetic distances. Together, these results highlight how a multi-species approach leveraging complementary strengths of model and non-model organisms can illuminate ancient regulatory mechanisms underlying vertebrate eye patterning.

overall_design: Hi-C sequecing profiling of Anableps anableps dorsal and ventral retina.

first: Lina

last: Shi

first: Louise

last: Perez

first: Gabriela

last: Lima

first: Josane

last: F. Sousa

first: Zhuoxin

last: Chen

first: Dorota

last: Skowronska-Krawczyk

first: Evgeny

last: Kvon

first: Igor


title: Bone Marrow Microenvironment in Aplastic Anemia: Insights from Nestin/ CXCL12 Immunohistochemistry and RNA-Sequencing

city: Basel

first: Astrid

last: Beerlage

address: Hebelstrasse 10

country: Switzerland

institute: University of Basel

summary: Aplastic anemia (AA) is a rare bone marrow failure syndrome characterized by immune-mediated destruction of hematopoietic stem and progenitor cells (HSPCs). The contribution of the bone marrow microenvironment remains incompletely understood.  We analyzed 29 bone marrow biopsies from patients with moderate (mAA), severe (sAA), and very severe AA (vsAA), along with 12 healthy controls and seven subcortical pseudohypocellular samples. Immunohistochemistry for nestin and CXCL12 was performed to quantify stromal niches. RNA sequencing was carried out to investigate immune and niche-related gene expression patterns.  sAA patients exhibited a significantly increased number of nestin+ niches compared to mAA and controls. CXCL12+ niches showed no significant differences between groups. RNA sequencing revealed upregulation of immune response genes, as well as pathways related to interferon-gamma signaling, JAK-STAT3 activation, and antigen presentation. Downregulated genes and pathways pointed to impaired DNA repair, cell cycle regulation, and epigenetic stability.  Our findings supports a model in which AA pathogenesis is driven by both immune injury and compensatory, yet dysfunctional, stromal remodeling. These data underline the importance of the bone marrow microenvironment in AA.

overall_design: Bulk-mRNA sequencing of whole human transcriptome using targeted probes. The RNA  study consists of 25 FFPE human bone marrow samples as well as three technical control replicates. The FFPE samples are divided into five control samples, six mild aplastic anemia samples and 14 severe aplastic anemia samples.

first: Carl

last: Zinner

first: Jakob

middle: R

last: Passweg

first: Beatrice

last: Drexler

first: Alexandar

last: Tzankov


title: mRNA 3ʹ UTRs direct microRNA degradation to participate in imprinted gene networks and regulate growth dataset 6

city: Cambridge

first: Daniel

last: Lin

state: MA

address: 455 Main Street

institute: Whitehead Institute

summary: MicroRNAs direct downregulation of target mRNAs. Sometimes, however, this regulatory paradigm inverts, and a target RNA triggers degradation of a microRNA. This target-directed microRNA degradation (TDMD) requires ZSWIM8. Zswim8-/- mice exhibit reduced growth and perinatal lethality, accompanied by stabilization of >40 microRNAs. Nonetheless, studies of TDMD function in mammals have been limited because only two TDMD-triggering RNAs have been identified in mice. Here, we computationally identify and validate five new TDMD-triggering sites in mouse models. One site in Atp6v1g1 and two in Lpar4 direct degradation of miR-335-3p, showing that in mammals, two sites in the same transcript, and multiple sites in different transcripts, can collaborate to destabilize a microRNA. Moreover, sites in Plagl1 and Lrrc58 direct degradation of miR-322 and miR-503, respectively. Mice lacking the Plagl1 and Lrrc58 sites were smaller, demonstrating that target-directed degradation of miR-322 and miR-503 promotes growth. Both miR-335-3p and Plagl1 are maternally imprinted, implying their participation in parental conflict, but their corresponding triggers or target microRNA partner are not imprinted. Thus, 3¢ UTRs can participate in parental conflict not only by regulating protein production but also directly by engaging TDMD to access an additional layer of regulation within a network of imprinted and biallelic genes.

overall_design: RNA expression profiling with RNA-seq from mouse E18.5 heart, lung, or stomach. Embryos from Atp6v1g1, Lpar4, Lrrc58, or Plagl1 trigger site mutant mice were harvested at embryonic day E18.5.

first: David

last: Bartel


title: Macrophages in Neurofibroma Malignant Progression

city: Shanghai

first: Lingling

last: Ge

state: Shanghai

address: Ninth people's hospital

institute: Shanghai Jiao Tong University

summary: Neurofibromatosis type 1 (NF1) is characterized by the development of benign nerve sheath tumors named plexiform neurofibromas (PNFs). In 10–15% of patients, these tumors undergo malignant transformation into aggressive malignant peripheral nerve sheath tumors (MPNSTs), which are associated with poor prognosis and limited treatment options. The cellular and molecular mechanisms driving this malignant progression remain poorly understood, hindering the development of effective therapies. To address this gap, we performed comprehensive single cell RNA sequencing on 9 PNF and 5 MPNST clinical samples.

overall_design:
We performed comprehensive single cell RNA sequencing on 9 PNF and 5 MPNST clinical samples and conducted consequent analysis.

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

last: Li

first: Xuan

last: Yu

first: Mingyan

last: Xing

first: Chengjiang

last: Wei

first: Yihui

last: Gu

first: WeI

last: Wang


title: mRNA 3ʹ UTRs direct microRNA degradation to participate in imprinted gene networks and regulate growth dataset 4

type: Non-coding RNA profiling by high throughput sequencing

overall_design: miRNA expression profiling by small-RNA sequencing (sRNA-seq) in BJ-5ta cells. BJ-5ta cells expressing expressing a Zim3-dCas9 fusion protein were transduced with guide RNAs targeting ZSWIM8, LRRC58, PLAGL1, or non-targeting control guides. Two reps were sequenced per target gene.


title: IFNγ-induced antigen loss in chimeric antigen receptor (CAR)-T cell therapy

city: Philadelphia

first: Ramkrishna

last: Mitra

state: Pennsylvania

address: 233 S 10th street

institute: Thomas Jefferson University

summary: FDA-approved chimeric antigen receptor (CAR)-expressing T cell therapies (CARTs) have revolutionized the treatment of blood cancers. Yet none have been successful for “solid” tumors, such as colorectal cancer (CRC), the 2nd leading cause of cancer deaths. Guanylyl cyclase C (GUCY2C) has emerged as a clinical-stage target for CART and bispecific T-cell engager (BiTE) therapies in CRC. Here, we identified a novel antigen loss mechanism that limits the efficacy of CART in CRC, in which IFNγ secreted by activated CART cells causes bystander cancer cells to lose GUCY2C. Moreover, this previously unexplored antigen loss mechanism is mediated through IFNγR (receptor)/JAK and cellular stress signaling pathways. This newly discovered mechanism of antigen loss can be rescued with anti-IFNγ neutralizing antibody, the JAK inhibitor ruxolitinib, or 4-phenylbutyrate (an ER stress reliever). IFNγ has been canonically recognized as beneficial for the effector functions of T cells by enhancing antigen processing and HLA presentation and is essential for CART targeting of solid malignancies by inducing adhesion molecule expression for synapse stabilization. Here, we revealed a negative effect of IFNγ that uniquely interferes with immunotherapies targeting native surface antigens, such as CART and BiTE therapies, which may be reversed by disrupting stress signaling pathways to enhance solid tumor CART and BiTE immunotherapies.

overall_design: LS174T cells treated with conditioned media (CM) from cancer cells co-cultures with control or GucyCART for 48hrs.

first: Miao

last: Cao

first: Jasmine

last: Alvarez

first: Michael

last: Xu

first: Trevor

last: Baybutt

first: Zhengyang

last: Sun

first: Oluwatobiloba

last: Taylor

first: Allison

last: Doermann

first: Ross

last: Staudt

first: Scott

last: Waldman

first: Adam

last: Snook


title: mRNA 3ʹ UTRs direct microRNA degradation to participate in imprinted gene networks and regulate growth dataset 5

first: Daniel

last: Lin

overall_design: RNA expression profiling with RNA-seq from mouse E18.5 heart. Embryos from crosses between Lrrc58 homozygous trigger site mutant; Plagl1 wild-type dams and Lrrc58 heterozygous trigger site mutant; Plagl1 heterozygous trigger site sires were collected at embryonic day 18.5.

first: David

last: Bartel


title: mRNA 3ʹ UTRs direct microRNA degradation to participate in imprinted gene networks and regulate growth dataset 2

overall_design: miRNA expression profiling by small-RNA sequencing (sRNA-seq) in MEFs. MEFs expressing a Zim3-dCas9 fusion protein were transduced with guide RNAs targeting Atp6v1g1, Lpar4, Zswim8, or non-targeting control guides. Two biological reps were sequenced per target gene.


title: mRNA 3ʹ UTRs direct microRNA degradation to participate in imprinted gene networks and regulate growth dataset 3

overall_design: miRNA expression profiling by small-RNA sequencing (sRNA-seq) in human fibroblast cell lines. Cells were transduced with a construct encoding Cas9 and guides targeting ZSWIM8 or non-targeting control guides. For each cell line, three independent samples for either Zswim8 or non-targeting control guides were sequenced.


title: Spatial transcriptomic profiling of TOP2B-driven anthracycline-induced cardiotoxicity in mouse hearts

city: Cleveland

first: Lily

state: OH

address: 9500 Euclid Ave

institute: Cleveland Clinic

summary: Anthracycline-induced cardiotoxicity (AIC) is a major dose-limiting toxicity in cancer patients, traditionally attributed to off-target inhibition of TOP2B in cardiomyocytes. Here, we performed spatial transcriptomic profiling of mouse hearts to investigate the molecular mechanisms underlying AIC and TOP2B-mediated cardiac dysfunction. Using a tamoxifen-inducible, cardiomyocyte-specific human TOP2B transgenic mouse model, we analyzed spatial gene expression changes associated with heart failure phenotypes. Visium spatial RNA sequencing revealed dysregulation of cardiac contractile and metabolic pathways, including MYH6/MYH7 switching, NPPA upregulation, and UCP3 suppression. These data support a model in which TOP2B overexpression disrupts cardiomyocyte homeostasis and contributes directly to heart failure. This dataset provides a spatially resolved transcriptomic resource for studying TOP2B-driven cardiotoxicity and therapeutic intervention strategies.

overall_design: Mouse hearts were collected from control α-MHC-MerCreMer mice, cardiomyocyte-specific TOP2B transgenic mice induced by tamoxifen mice. Formalin-fixed paraffin-embedded (FFPE) heart sections were processed using the 10x Genomics Visium CytAssist Spatial Gene Expression platform. H&E-stained sections were imaged prior to probe hybridization and library construction. Spatial transcriptomic libraries were sequenced on Illumina NovaSeq. Differential spatial gene expression analyses were performed to identify cardiac remodeling, metabolic, and heart failure–associated signatures linked to TOP2B overexpression and anthracycline exposure.

first: Zhao

last: Jianjun

first: Lin

last: Jianhong

first: Alban

last: Tyler

first: Wang

last: Qingzhu

first: Zhang

last: Wanying

first: Bangalore Parthasarathy

last: Prerana

first: Parsai

last: Shikha


title: Acetylation-Triggered Degradation of MSX1 Impairs Palatal Development

first: Li

last: Meng

address: No. 639, Zhizaoju Road

institute: Shanghai jiao tong university

summary: Non-syndromic cleft palate (NSCP), a prevalent congenital disorder, arises from dysregulated embryonic palatal fusion, but the posttranslational modifications (PTMs) driving this process remain poorly understood. Here, we identify lysine acetylation as a critical MSX1 proteostasis switch governing embryonic palatal mesenchymal (EPM) cell survival. We demonstrate in vitro and in vivo that MSX1 protein stability regulation by deacetylase SIRT1-catalyzed acetylation underlies EPM apoptosis and palatal fusion. In atRA-induced NSCP models, SIRT1 suppression drives MSX1 hyperacetylation, accelerating proteasomal degradation and culminating in EPM apoptosis. Strikingly, transcriptomic profiling revealed acetylation's exclusive proteostatic role, decoupling MSX1's structural stability from transcriptional activity—a paradigm distinct from classical PTM mechanisms during development. Lentivirus-mediated delivery of deacetylase SIRT1 or the deacetylation mimic MSX1 K139R significantly reduced cleft severity, indicating its preventive and therapeutic potential in humans. Our work establishes the MSX1 acetylation as both a pathogenic driver and druggable target in NSCP, redefining PTM regulation as a central etiological factor in genetic disorders.

overall_design: Twelve samples from hepm cells transfected with four different plasmids: Vector, MSX1-FL, MSX1-K139R, and MSX1-K139Q were analyzed and compared with eachother.

first: Xinquan

last: Jiang

first: Jiawen

last: You

first: Zhongyin

last: Zhang

first: Yucheng

first: Yulan

last: Liu

first: Mingliang

last: Zhou

first: Junqing

last: Ma


title: Transcriptome analysis of the prefrontal cortex identifies inflammatory genes associated with cognitive impairment in a model of multiple sclerosis

city: Rome

first: Marco

last: Pieraccioli

address: Largo Francesco Vito 1

country: Italy

institute: Catholic University of the Sacred Heart rome

summary: Cognitive impairment (CI) is a hallmark of multiple sclerosis (MS). Despite its relevance, however, knowledge of the key steps involved in its pathogenesis remains incomplete. Consequently, predictive biomarkers and actionable therapeutic options to counteract CI in MS patients are not available. To identify changes associated with CI in MS, we performed transcriptomic analyses of the prefrontal cortex (PFC), a cortical region relevant for cognition, in the experimental autoimmune encephalomyelitis (EAE) mouse model. Our analyses highlighted the strong upregulation of inflammatory pathways in the PFC of EAE mice. Clustering of the top differentially expressed genes (DEGs) in the PFC identified a low (EAE-L) and a high (EAE-H) inflammation subgroup. Notably, enhanced inflammation in the EAE PFC caused increased changes in expression levels of MS-associated genes with relevance for CI. Cell Type-Specific Expression Analysis (CSEA) and morphological analyses indicated that, while EAE-L mice showed only microglia activation, EAEH mice also displayed the involvement of astrocytes, consistent with a more advanced stage of disease. Moreover, neuronal genes were only downregulated in the EAE-H PFC. Analysis of cognitive performance in pre-symptomatic EAE mice revealed that high expression of genes associated with the antigen presentation and the complement pathways was associated with CI. Moreover, expression of C1q complement proteins was increased in the cerebrospinal fluid of MS patients affected by CI. These findings indicate that inflammation in the PFC during EAE is associated with CI and identify a subset of inflammatory genes that may represent early markers and risk factors for functional PFC impairment and loss of cognitive performance in MS patients.

overall_design: RNA-seq profiling of the prefrontal cortex in control (n=4) and EAE (n=7) mice to reveal DEGs.

first: Luca

last: Zupo

first: Annalisa

last: Adinolfi

first: Marika

last: Guerra

first: Valentina

last: Corvino

first: Francesco

last: Ria

first: Veronica

last: Ceci

first: Valerio

last: Chiurchiù

first: Lorenzo

last: Gaetani

first: Silvia

last: Sperandei

first: Massimiliano

last: Di Filippo

first: Gabriele

last: Di Sante

first: Maria Concetta

last: Geloso

first: Claudio

last: Sette


title: A decline in skeletal muscle NOX4 abrogates exercise-induced adaptive homeostasis and exacerbates biological ageing

city: Melbourne

first: Tony

last: Tiganis

state: Victoria

address: 23 Innovation Walk, Monash University, Clayton

country: Australia

institute: Monash University

summary: A decline in NFE2L2-orchestrated adaptive homeostasis and oxidative distress are thought to be key features of ageing. In contracting skeletal muscle, the ROS-producing enzyme NADPH oxidase 4 (NOX4) is a potent inducer of NFE2L2 adaptive homeostasis. Here we report that skeletal muscle NOX4 levels decline in aged mice and humans, resulting in abrogated NFE2L2 adaptive homeostasis, increased protein oxidative damage and decreased muscle function. We show that deleting NOX4 in skeletal muscle exacerbates the physiological decline associated with ageing, resulting in overt sarcopenia and frailty, characterised by physical inactivity, increased adiposity, systemic inflammation, whole-body insulin resistance and advanced liver disease in aged chow-fed mice. The systems-wide physiological decline in aged skeletal muscle NOX4-deficient mice could be corrected by restoring NOX4 using viral approaches or activating NFE2L2 downstream with sulforaphane and reinstating adaptive homeostatic responses otherwise induced by exercise. Our findings provide important insights into the basis for the decline in NFE2L2-orchestrated adaptive homeostasis that accompanies physical inactivity with age and identify key mechanisms by which exercise may promote healthy ageing.

overall_design: Gastrocnemius muscle from 21-month old muscle-specific Nox4 knockout mice (MckCre:Nox4 fl/fl) and age-matched Nox4 fl/fl controls. Total RNA was isolated from homogenised mouse gastrocnemius muscle tissue with RNeasy mini kits (Qiagen, Hilden, Germany) and processed for library preparation (PolyA, unstranded) and sequencing on an Illumina Novaseq PE150 by Azenta Life Sciences (Burlington, MA).

first: Eamon

last: Coughlan


title: TCR Signaling Induced Kdm6b Antagonizes Ezh2 to Sustain Tissue Regulatory T Cells [ATAC-seq]

city: Memphis

first: Beisi

last: Xu

state: Tennessee

address: 262 Danny Thomas Pl

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hosipital

summary: Regulatory T cells (Tregs) expressing Forkhead Box P3 (Foxp3) play crucial roles in maintaining immune tolerance and tissue integrity. Ezh2, a Histone H3 lysine 27 (H3K27) methyltransferase, is known as a crucial regulator of Treg cell identity and suppressive function upon activation, raising a question about whether overactivation of this pathway would further boost Treg cell function. Here, we demonstrate that lysine demethylase Kdm6b catalyzing the reverse reaction to Ezh2 is also required for Treg cell identity and function after activation. Treg-specific deletion of Kdm6b impairs tissue Treg cell fate and function, such as in the lung after injury or adipose tissue during animal aging. Mechanistically, T cell receptor (TCR) signaling upregulates Kdm6b expression and recruits it to Foxp3-bound chromatin to restrict H3K27me3. This antagonism helps suppress the expression of inflammatory cytokines and promote the expression of Treg functional genes, thus supporting tissue Treg cells.

overall_design: Resting Treg cells were stimulated with T cell receptor signaling for 3 hours and ATAT-seq was performed to detect chromatin accessibility.

first: Minghong

last: He

first: Yongqiang

last: Feng

first: Jason

last: Mock


title: NAT10-mediated ac4C RNA acetylation stabilizes CXCL5/DEK mRNA to drive proliferation and metastasis in lung adenocarcinoma [RIP-Seq]

city: Harbin

first: qiong

last: wu

address: No. 92, Xida Street, Nangang District

institute: Harbin Institute of Technology

summary: Investigating the epigenetic mechanisms underlying lung adenocarcinoma (LUAD) through the lens of N4-acetylcytosine (ac4C) modification could innovative cancer treatment strategies and targets. We used biological information methods to analyze shared data, with a focus on studying N-acetyltransferase 10 (NAT10), which is the only known ac4C "writer" protein. Our analysis revealed a significant upregulation of NAT10 expression in LUAD, a finding that was corroborated by investigations in both LUAD cancer tissue samples and cell lines. Subsequently, we employed CRISPR/Cas9 technology to knock out the NAT10 gene and analyzed the resulting knockout cells using acRIP-seq and RNA-seq techniques. Our findings demonstrated differential expression of the genes CXCL5 and DEK, and functional enrichment analysis indicated a strong association with the adhesion signaling pathway. Laboratory experiments revealed that NAT10 acts as an ac4C "writer," promoting the acetylation of CXCL5 and DEK and thus preventing the degradation of their mRNAs. Moreover, NAT10 was found to significantly affect the number of metastases and tumor growth following the injection of cancer cells into the tail vein of mice. Our research data suggests that targeting NAT10 has the potential to serve as a diagnostic biomarker or prognostic target for developing anti metastatic therapies aimed at disrupting the adhesion process.

overall_design: The NAT10 gene was knocked out in A549 cells, and high-throughput sequencing was performed on the affected genes.

first: Qiong

last: Wu

first: Xin

last: Hu

first: Yan

last: Zhang


title: A hematopoietic stem cell shield for AML-directed immunotherapy

first: Jahan

last: Rahman

state: New York

address: 417 E 68th St

department: Center for Hematologic Malignancies

institute: Memorial Sloan Kettering

summary: One major challenge in the development of successful chimeric antigen receptor (CAR) T cells for patients with acute myeloid leukemia (AML) has been that most well-studied AML-associated antigens are also expressed on vital normal hematopoietic stem cells (HSCs) or mature myeloid cells. This challenge in optimal antigen selection leads to deleterious on-target toxicity, particularly in the context of CAR T cell persistence. CAR T cells targeting CD371, a type II transmembrane glycoprotein, have shown potent anti-leukemic activity in phase I trials to date; however, CD371 is wildly expressed throughout the normal myeloid compartment. Here we identify that CD371 is dispensable for normal human HSC and myeloid cell function, map the epitope of a CD371 CAR T cell currently in phase I trials, develop a base-editing strategy to shield normal hematopoiesis from CD371-directed immunotherapy, and describe an off-the-shelf approach to target AML while sparing normal hematopoiesis through the use of  CD371 CAR T cells.

overall_design: Hematopoietic stem cells edited by CRISPR/Cas9 to generate either CD371-KO or AAVS1-KO (control) were transplanted into NSG-SGM3 mice. 1x10^5 CD34+ cells were injected into each mice. Mice were monitored for engraftment, and bone marrow was harvested four months post-transplantation to evaluate long-term hematopoiesis, n=3 per group.

first: Satoshi

last: Kaito

first: Karen

last: Li

first: Xiaoli

last: Mi

first: Cynthia

last: Castro

first: Nina

last: Fox

first: Alexander

last: Lewis

first: Adriana

last: Cuibus

first: Kenyon

last: Weis

first: Erin

last: Burns

first: Sarah

last: Yoo

first: Susan

last: Dewolf

first: Anthony

middle: F

last: Daniyan

first: Omar

last: Abdel-Wahab


title: Targeting the Mapk13-Tcf1-Slc7a5 Axis via One-Carbon Metabolic Regulation to Prevent Chronic Allograft Vasculopathy

city: wuhan

first: wang

last: yi

address: no.1095 Jiefang Avenue

institute: Institute of Organ Transplantation, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology

summary: Chronic allograft vasculopathy (CAV) is driven in part by stem-like Cd4⁺ T cells, but how these cells sustain their progenitor programs during chronic rejection remains unclear. Here, a metabolic-epigenetic axis is identified in which Mapk13 phosphorylates Tcf1 at T289, enabling Tcf1 to activate the amino acid transporter Slc7a5 and enhance methionine uptake. This rewires one-carbon metabolism and increases H3k4me3 enrichment at the Tcf7 locus, thereby maintaining stem-like Cd4⁺ T cells within rejecting grafts. Disruption of this circuit-via genetic deletion of Mapk13 or Slc7a5, or through dietary methionine restriction-reduces Tcf1⁺ Cd4⁺ T cell stemness and prevents CAV in mouse models. These findings reveal the Mapk13-Tcf1-Slc7a5 axis as a critical metabolic dependency of pathogenic T cells and highlight one-carbon metabolism as a promising target to promote long-term graft survival.

overall_design: Isolation of splenocytes Purified splenocytes were obtained by homogenizing the tissue using a syringe, followed by filtration through a sterile nylon mesh with a pore size of 0.1 mm and subsequent separation on a density gradient centrifugation using mouse 1x lymphocyte separation medium (Dakewe). Thymocytes were isolated by passing thymus tissue through a 70 μm filter. Naïve CD4+ T cells for the in vitro experiments were sorted using magnetic bead separation. Briefly, splenocytes were stained with phycoerythrin (PE)-labeled anti-CD4 antibody, followed by incubation with anti-PE microbeads. Naïve CD4+ T cells were positively selected using an LS column under the influence of a magnetic field. In vitro T-cell stimulation To stimulate T cells, naïve CD4+ T cells were added at a density of 100000 cells/well to 96-well round-bottom tissue culture plates (Corning) precoated with anti-CD3 (5 μg/ml). The culture medium was supplemented with soluble anti-CD28 mAb at a concentration of 1 μg/ml. MAPK13-IN-1 was administered after 24 hours of activation. After culturing CD4+ T cells for 72 hours, they were collected and subjected to analysis using RNA-seq.


title: CIPHER-seq enables low-stress intracellular multimodal profiling of immune activation

city: Miami

first: Avni

last: Bhalgat

address: 1580 NW 10th Ave, Room 746

institute: University of Miami

summary: This study introduces CIPHER-seq, an optimized intracellular CITE-seq workflow that minimizes fixation-induced cellular stress while enabling simultaneous measurement of intracellular proteins and transcriptomes in the same cell. Peripheral blood mononuclear cells (PBMCs) were processed using either CIPHER-seq or a commercial intracellular protocol (Proteintech) under unstimulated or PMA/ionomycin-stimulated conditions. Single-cell RNA and antibody-derived tag (ADT) libraries were generated using 10x Genomics Flex chemistry. The dataset enables benchmarking of intracellular chemistries, assessment of RNA–protein concordance, and characterization of cytokine-driven immune activation at single-cell resolution.

overall_design: Four single-cell RNA-seq libraries were generated from human PBMCs: CIPHER-seq unstimulated, CIPHER-seq PMA/ionomycin-stimulated, Proteintech unstimulated, and Proteintech PMA/ionomycin-stimulated. Libraries were prepared using intracellular antibody staining followed by 10x Genomics Flex library construction. Sequencing was performed on an Illumina platform. Processed outputs include gene expression matrices, antibody-derived tag (ADT) matrices, combined multiomic objects, and processed Seurat objects.

first: Katarina

last: Micin


title: Differential Regulation of Retinoic Acid Metabolism in Fanconi Anemia

city: KINGSTON

first: NIALL

middle: GEORGE

last: HOWLETT

state: RI

address: 120 FLAGG ROAD

department: CELL AND MOLECULAR BIOLOGY

institute: UNIVERSITY OF RHODE ISLAND

summary: The goal of this study was to analyze differential gene expression patterns between nontransformed FA-D2 (FANCD2-/-) and FANCD2-complemented Fanconi anemia patient skin fibroblasts

overall_design: Quadruplicate biological replicates of nontransformed FA-D2 (FANCD2-/-) and FANCD2-complemented Fanconi anemia patient skin fibroblasts were harvested for RNA-seq analysis. Sequencing libraries were prepared using NEBNext Ultra II RNA library prep kit. Sequencing libraries were clustered on a single lane of a flowcell and loaded onto an Illumina HiSeq 4000 instrument. Samples were sequenced using a 2 x 150 bp paired-end configuration at 60 million reads per sample.

first: Niall G.

last: Howlett

first: Justin L.

last: Blaize


title: SPINK2 silencing suppresses leukemic proliferation and restores myeloid commitment via MECOM downregulation in acute myeloid leukaemia

city: Freiburg

first: Pierre

middle: Daniel

last: Cauchy

state: Baden-Württemberg

address: Breisacher Str. 115

department: Zentrum für Translationale Zellforschung

country: Germany

institute: University Medical Center Freiburg

summary: Myeloid leukaemias harboring complex karyotypes present several unrelated cytogenetic abnormalities and form a distinct subset of AML linked to a dismal prognosis. Currently, no effective options are available for the treatment of those patients, and the discovery of novel therapeutic strategies represent an urgent clinical priority. We previously developed a bioinformatic framework for the identification of novel molecular vulnerabilities for disease stratification and treatment and observed SPINK2, a serine protease inhibitor Kazal-type 2, as a novel and promising candidate target in AML, with particularly pronounced effect in complex karyotype patients. Using publicly available bulk and single cell RNA-seq datasets, we discovered a robust association between SPINK2 and cell cycle regulators, most notably S-phase genes. By performing shRNA-mediated genetic manipulation of SPINK2 expression in a complex karyotype AML cell lines, we marked a profound impairment of proliferation coupled with an induction of terminal myeloid commitment.  Moreover, SPINK2-deficient FUJIOKA cells revealed a significant correlation between SPINK2 and MECOM expression, consistent with findings in patients harbouring complex karyotypes, yet absent in other AML subsets from the TARGET-AML cohort. Our findings suggest a novel potential correlation between SPINK2 and MECOM expression in complex karyotype leukemias and warrant further investigation into the underlying molecular mechanisms through which the SPINK2-MECOM axis enforces aberrant self-renewal and the development of novel targeted approaches aimed at modulating its expression in complex karyotypic AML.

overall_design: RNA-Seq in shNEG and shSPINK2 Fujioka cells

first: Volpe

last: Giacomo

first: Ventura

last: Antonio

first: Loconte

last: Tiziana

first: Deligio

last: Lucia

first: Negri

first: Ahmed

last: Amer

first: D'Angelo

last: Gabriella

first: Di Mofetta

last: Daria

first: Cauchy

last: Pierre

first: Mandriani

last: Barbara

first: Zhang

last: Xiao

first: Pasciolla

last: Crescenza

first: Antonello

last: Rana

first: Iacobazzi

last: Angela

first: Loseto

first: Cives

last: Mauro

first: Viggiano

last: Luigi

first: Lasorsa

last: Francesco

first: Guarini

last: Attilio

first: Vegliante

last: Maria

first: Ciavarella

last: Sabino

first: Castellano

last: Giancarlo

first: Fiermonte

last: Giuseppe


title: Leukemia aggressiveness is driven by chromatin remodeling and expression changes of core regulators

city: Boston

first: Gracia

middle: M.

last: Bonilla

address: 185 Cambridge St

department: Molecular Biology

institute: Massachusetts General Hospital

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

overall_design: Refer to individual Series


title: Integrated Analysis of Porcine Brain microRNA Profiles Following Pediatric Diffuse Traumatic Brain Injury

city: Villanova

first: Susan

last: Margulies

address: 805 Stoke Road

institute: Emory University

summary: Mild traumatic brain injury (mTBI) is underdiagnosed and can lead to long-term symptoms in children. Currently, we lack diagnostic markers and effective therapies for pediatric mTBI. MicroRNAs (miRNAs) show promise for diagnosing and treating pediatric mTBIs due to their role in regulating key biological processes. Cyclosporine A (CsA) has also shown therapeutic effectiveness in modulating neuronal recovery and protection. We aimed at studying miRNA changes in the frontal lobe (FL) and hippocampus + amygdala (H&A) after a sagittal rapid non-impact head rotation (RNR) in 4 week old piglets (N = 50) at 1 day post-injury, 1 week post-injury, and following 1 day of 20mg/kg/day Cyclosporine A (CsA) treatment compared to anesthesia-only shams. Interestingly, many miRNAs involved in disrupted neuronal and upregulated glial, epithelial, and endothelial functions were differentially expressed (DE-miRNAs) at 1 day post-injury and most returned to baseline by 1 week post-injury. However, miR-20a-3p, miR-10386, and miR-4331-3p were among the Top 10 DE-miRNAs at 1 day post-injury, and remained altered at 1 week. Upregulated neuroprotective miR-17-3p and miR-212 were also part of Top 10 DE-miRNAs at 1 day post-injury and their increases were correlated with decreases in axonal injury. Furthermore, to identify miRNAs that could serve as candidate diagnostic biomarkers of injury, we employed LASSO analysis and identified miRNAs, miR-363, miR-15b, and miR-450c-3p as the best predictors of mTBI at 1 day post-injury. Lastly, WGCNA revealed the neuroprotective effects of CsA treatment in ameliorating neuronal, immune, stress, and vascular functions disrupted at 1 day post-injury. Overall, our data revealed key miRNAs that were differentially expressed at 1 day and 1 week post-injury, modulated by CsA treatment, and suggest that may serve as diagnostic biomarkers of pediatric mTBI.

overall_design: To investigate microRNA profiles and the neuroprotective effect of CsA treatment, we utilized piglet FFPE brain tissue from sham/naïve animals, animals sacrificed at 1 day, 1 week, and 30 hours following CsA treatment. All samples underwent RNA-sequencing and microRNA analysis was conducted on samples that passed library prep (i.e. 50 subjects).

first: Oluwagbemisola

last: Aderibigbe

first: Levi

last: Wood


title: mRNA 3ʹ UTRs direct microRNA degradation to participate in imprinted gene networks and regulate growth

first: Daniel

last: Lin

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: mRNA 3ʹ UTRs direct microRNA degradation to participate in imprinted gene networks and regulate growth dataset 1

overall_design: miRNA expression profiling by small-RNA sequencing (sRNA-seq) in MEFs. MEFs that had previously undergone a clonal bottleneck (clone 15C1 or 15A3) were transfected with plasmids encoding Cas9 and guide RNA and sorted for single cells. Guide RNAs targeted Zswim8, flanked TDMD trigger sites within mRNA 3ʹ UTRs, or were non-targeting controls. Two to four independent clones were sequenced per line.

first: David

last: Bartel


title: Transcriptomic signatures of p16-high (p16h) hepatocytes in CCl4-treated liver

city: Minato City

first: Satoshi

last: Kawakami

address: 4-6-1 Shirokanedai

department: The Institute of Medical Science

institute: The University of Tokyo

summary: The mechanisms by which aging promotes fibrotic processes remain to be elucidated. The preceding observation indicating a robust correlation between the severity of fibrosis in human cirrhotic patients and the population of hepatocytes expressing elevated levels of p16Ink4a (p16h), propose that p16h hepatocytes might serve as initiators of fibrogenic processes in response to liver injury. In this study, we employed a CCl4-induced hepatitis model to promote a fibrogenic process and observed the accumulation of p16h hepatocytes in zone 3.

overall_design: p16-Tom mice were treated with CCl4/oil, and tamoxifen was administered to label p16h cells with tdTomato. Liver tissues were digested with collagenase, and tdT+/- hepatocytes were isolated by FACS

first: Koji

last: Nishikawa

first: Teh-Wei

last: Wang

first: Makoto

last: Nakanishi


title: NAT10-mediated ac4C RNA acetylation stabilizes CXCL5/DEK mRNA to drive proliferation and metastasis in lung adenocarcinoma [RNA-Seq]

first: qiong

last: wu

first: Qiong

last: Wu

first: Xin

last: Hu

first: Yan

last: Zhang


title: A conserved enhancer cluster controls efnb2 expression in the vertebrate dorsal retina [ATAC-seq-Tn]

city: Baton Rouge

first: Patricia

last: Schneider

address: LSU 131 Life Sciences Building

institute: Louisiana State University

summary: The vertebrate retina is patterned along its dorsal-ventral (DV) axis by signaling centers that provide each domain with distinct molecular and functional properties, including differential photoreceptor composition and opsin expression. Although the key DV patterning genes are well studied, the cisregulatory mechanisms that establish and maintain these territories remain poorly understood. To explore this regulatory landscape, we turned to the four-eyed fish Anableps anableps, whose large, protruding eyes and expanded ventral retina facilitate precise dissection of dorsal and ventral halves for spatially resolved genomics. Bulk RNA-seq of the Anableps dorsal and ventral retina regions recovered canonical DV markers, while bulk ATAC-seq revealed dorsally enriched ATAC-seq peaks residing within a low-genedensity region between efnb2a and gtpbp8. These putative cis-regulatory elements located to a 29 kb interval forming a contiguous enhancer cluster. Via Hi-C analysis, we identified a topologically associating domain (TAD) encompassing efnb2a, gtpbp8, and slc10a2, with a dorsal-enriched chromatin contact linking the enhancer cluster to the efnb2a promoter. Comparative genomics showed that this architecture is deeply conserved: the efnb2-slc10a2 synteny and TAD boundaries are maintained from human to zebrafish. To enable functional testing of this long regulatory interval, we strategically turned to Tetraodon nigroviridis, a species with one of the most compact vertebrate genomes, allowing nearly the entire orthologous enhancer cluster (~13 kb) to be cloned intact. Transgenic assays in both zebrafish and mouse demonstrated that this Tetraodon enhancer cluster drives dorsal retina-specific eGFP expression, underscoring the deep conservation of its regulatory function across vast phylogenetic distances. Together, these results highlight how a multi-species approach leveraging complementary strengths of model and non-model organisms can illuminate ancient regulatory mechanisms underlying vertebrate eye patterning.

overall_design: ATAC-Seq profiling of Tetraodon nigroviridis dorsal and ventral retina.

first: Lina

last: Shi

first: Louise

last: Perez

first: Gabriela

last: Lima

first: Josane

last: Sousa

first: Zhuoxin

last: Chen

first: Dorota

last: Skowronska-Krawczyk

first: Evgeny

last: Kvon

first: Igor


title: A conserved enhancer cluster controls efnb2 expression in the vertebrate dorsal retina [RNA-Seq]

overall_design: Bulk RNA-seq profiling of Anableps anableps dorsal and ventral retina.


title: Dual Targeting of PI3Kδ and PPARα Enhances Antitumor Activity via FoxO1 Activation in Follicular Lymphoma

city: Xiamen

first: Wenqin

address: Xiang'an South Road No. 422, Xiang'an District

institute: Xiamen University

summary: Follicular lymphoma (FL) frequently exhibits relapse and resistance to targeted therapy, underscoring the need for rational combinations. Here, we demonstrate that the phosphoinositide 3-kinase-δ (PI3Kδ) inhibitor linperlisib combined with the pan-peroxisome proliferator-activated receptor (PPAR) agonist chiglitazar delivers robust antitumor activity across FL models, including cell-derived and patient-derived xenografts, with a favorable tolerability profile. The combined regimen enforces G1/S arrest and apoptosis and exerts complementary metabolic–signaling effects by suppressing glycolysis, activating PPARα-driven programs, and relieving PI3K/AKT-mediated repression of forkhead box protein O1 (FoxO1). Genetic depletion of FoxO1 blunts treatment responses, indicating that FoxO1 activity is a pharmacodynamic biomarker and potential predictor of benefit. Compared with monotherapy, the combination consistently achieves superior tumor control in vivo without overt toxicity, indicating clinical translation potential. Collectively, these data support the clinical evaluation of linperlisib plus chiglitazar in FL, with prospective assessment of FoxO1 activity as a pharmacodynamic biomarker.

overall_design:
For transcriptome profiling, 1 × 106 RL cells were treated with linperlisib (32 μM) and chiglitazar (16 μM) for 24 h. Total RNA was isolated using TRIzol reagent (Invitrogen). RNA sequencing libraries were prepared and subjected to high-throughput sequencing (150 bp paired-end) by HaploX Biotechnology (Shenzhen, China).

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the raw data had been deleted by commercial provider (HaploX Biotechnology, Shenzhen, China)and the provider confirmed that they cannot be restored.
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first: wenqin

last: wang

first: hui

last: zhou


title: A conserved enhancer cluster controls efnb2 expression in the vertebrate dorsal retina [Tetraodon RNA-Seq]

overall_design: Bulk RNA-seq profiling of Tetraodon nigroviridis dorsal and ventral retina.

last: F. Sousa


title: Stress testing reveals selective vulnerabilities in protein homeostasis

city: Amherst

first: Peter

last: Chien

address: 240 Thatcher Rd, Life Science Laboratories Room N325

department: Biochemistry and Molecular Biology

institute: University of Massachusetts Amherst

summary: Protein quality control (PQC) systems are essential for cellular resilience to proteotoxic stress. Despite intensive study for decades, functional redundancies in the system obscure the contributions of the collectively important individual genes. Here, we leverage transposon sequencing across bacteria strains lacking key chaperones and proteases to reveal hidden determinants of stress response in protein homeostasis. By profiling fitness under multiple proteotoxic stresses, we uncover stress-specific vulnerabilities and reveal how major players of PQC mask correlations between transcriptomic responses and gene fitness. As an illustration of unexpected connections, we identify a heat-specific synthetic lethality between the disaggregase ClpB and DNA Polymerase I (PolA) mediated by persistent aggregation of the RecA recombinase and toxic persistence of the heat shock regulon. Our findings reveal that stress-induced aggregation is not broadly toxic. Rather, it becomes lethal in specific genetic or environmental contexts due to the depletion of components only needed in those specific circumstances. This work presents a framework to reveal normally hidden fragility in stress responses using gene fitness scores adaptable to a variety of systems.

overall_design: RNAseq profiling of wildtype (WT) Caulobacter crescentus (NA1000) cells and their knockout derivatives (∆polA and ∆clpB) under normal growth conditions (30°C) and heat-stress (39°C). Cells were grown until mid-log phase and cell pellets collected for RNA profiling. Experiments were performed in three biological replicates except ∆polA conditions which had 2 biological replicates.

first: Berent

last: Aldikacti

first: Hidayet

last: Putun

first: Vishal

last: Sarsani

first: Rilee

last: Zeinert

first: Patrick

last: Flaherty