title: Allele-Specific Effects of Mutations in the Rifampin Resistance-Determining Region (RRDR) of RpoB on Physiology and Antibiotic Resistance in Enterococcus faecium

status: Public on Aug 10 2025

city: PITTSBURGH

first: Daria

last: Van Tyne

state: PA

address: 200 Lothrop St

department: Department of Medicine

institute: University of Pittsburgh

summary: Enterococcus faecium is a member of the human gut microbiota that has evolved to be a problematic nosocomial pathogen and a leading cause of bloodstream infections in hospitalized patients. Treatment of E. faecium infections is complicated by antibiotic resistance, making it important to understand resistance mechanisms and their broader consequences in this pathogen. Here we explored the collateral effects of rifampin resistance-associated mutations in the E. faecium RNA polymerase β-subunit (RpoB). Of 14,384 publicly available E. faecium genomes, nearly one-third carried a mutation in the rifampin resistance-determining region (RRDR) of RpoB. In a local population of 710 E. faecium isolates collected from patients at a single medical center, we found significant associations between the presence of RRDR mutations and prior exposure to rifamycin class antibiotics, as well as associations between RRDR mutations and altered daptomycin susceptibility. To investigate the phenotypic impacts of RRDR mutations, we studied four isogenic strains with distinct RRDR mutations (Q473K, G482D, H486Y, S491L) that overlapped with clinical isolate variants. Transcriptomic and phenotypic analyses revealed allele-specific effects on E. faecium gene expression, growth dynamics, antibiotic susceptibility, isopropanol tolerance, and cell wall physiology. One frequently observed mutation, H486Y, caused minimal transcriptional changes and enhanced bacterial fitness. In contrast, the S491L mutation induced extensive transcriptional changes and slowed bacterial growth, but also conferred increased isopropanol tolerance, potentially enhancing bacterial survival in the hospital environment. Overall, our findings highlight the multifaceted impacts of RRDR mutations in shaping E. faecium physiology and antibiotic resistance, two important features of this hospital-associated pathogen.

overall_design: RNA-seq profiling of the 4 isogenic RRDR mutants (Q473K, G482D, H486Y, S491L) in comparison to the WT E. faecium

first: Adeline

last: Supandy

first: Emma

middle: G

last: Mills

first: Kyong

last: Fam

first: Ryan

last: Shields

first: Howard

last: Hang


title: Synthetic mRNA Vaccines and Transcriptomic Dysregulation: Evidence from New-Onset Adverse Events and Cancers Post-Vaccination

status: Public on Aug 08 2025

city: Rockwall

first: Wei

last: Zhang

state: TX

address: 2500 Summer Lee Dr

country: USA

institute: Neo7 Bioscience

type: Expression profiling by high throughput sequencing

summary: Background/Objectives: Synthetic mRNA vaccines have raised concerns regarding prolonged spike protein expression, immune activation, and potential off-target effects. This study investigates transcriptomic alterations in individuals with new-onset adverse events or cancer following mRNA COVID-19 vaccination. Methods: Bulk RNA sequencing was performed on peripheral blood from two patient groups: individuals with new-onset nonmalignant adverse events and individuals newly diagnosed with cancer post-vaccination. A control group of healthy individuals was used for comparison. Differential gene expression was analyzed using DESeq2, and Gene Set Enrichment Analysis (GSEA) was conducted using the MSigDB database and custom gene sets. Results: Both vaccine patient groups displayed widespread transcriptional dysregulation. In the nonmalignant adverse event group, hallmark enrichments included mitochondrial dysfunction, proteasome-mediated stress, transcriptomic instability, and systemic inflammation. The cancer group exhibited additional hallmarks of genomic instability, and epigenetic reprogramming. Nonsense-mediated decay (NMD), ribosomal stress, and MYC activation were prominent in both groups, while immune signaling via TLRs and type I interferons was particularly elevated in cancer patients.

overall_design: We enrolled adult participants (ages 18–70) who developed either new-onset symptoms following administration of mRNA-based COVID-19 vaccines (BNT162b2 [Pfizer] or mRNA-1273 [Moderna]). Total RNA was extracted using the Quick-DNA/RNA Viral Kit (Zymo Research), following the manufacturer’s protocol for whole blood RNA extraction. RNA libraries were prepared using the Illumina TruSeq Stranded Total RNA Kit, incorporating ribosomal RNA depletion and strand-specific cDNA synthesis. RNA-seg profiling of whole blood cells were conducted.

first: Natalia

last: von Ranke

first: Philipp

last: Anokin

first: Nicolas

last: Hulscher

first: Kevin

middle: J

last: McKernan

first: Peter

middle: A

last: McCullough

first: John

last: Catanzaro


title: DNA methylation-sensitive transcription factors and bivalency orchestrate transposon expression in the absence of DNA methylation [Retrotransposon expression in conditional NRF1 mutant testes]

city: Mainz

first: Joan

last: Barau

address: 4 Ackermannweg

country: Germany

institute: Institute of Molecular Biology IMB - Mainz

summary: Silencing of young retrotransposons by Cytosine DNA methylation is essential for spermatogenesis. Failure to methylate retrotransposon promoters leads to their reactivation, meiotic catastrophe and infertility. How transposons become reactivated and why their reactivation follows spermatogenic developmental patterns remains unclear. Here, we show that specific retrotransposon families exhibit distinct expression patterns and chromatin landscapes throughout spermatogenesis when DNA methylation is absent from their promoters. We find a strong correlation between the loss of bivalent H3K4me3-H3K27me3 chromatin modifications and the  transition from low retrotransposon expression in spermatogonia to reactivation in meiotic spermatocytes. Using a combination of DNA pulldowns, mass spectrometry and chromatin profiling by CUT&Tag, we identify the DNA methylation-sensitive transcription factor NRF1 as a potential regulator of unmethylated retrotransposons in spermatogenesis. Germline conditional ablation of Nrf1 reduced the upregulation of IAPs in the absence of DNA methylation and rescued the accumulation of IAP-derived Pol protein to wild type germ cell levels. Our study demonstrates that a combination of chromatin modifications and a DNA methylation-sensitive TF regulates young retrotransposons upon loss of repressive DNA methylation in germ cells, suggesting these interactions may be a core strategy used by retrotransposons to proliferate in the germline after evading silencing by DNA methylation.

overall_design: We found that NRF1 binds retrotransposons in the absence of DNA methylation in mouse germ cells, suggesting that NRF1 might activate their transcription in Dnmt3CKO/KO (D3C_KO) mutants (no DNA methylation at retrotransposon promoters). To test this hypothesis, we generated a conditional Nrf1 germ cell-specific knockout (Nrf1_KO) in the Dnmt3CKO/KO  (DKO) and wild type backgrounds. For all downstream analysis, we sampled total RNA, total protein, and fixed tissue for immunofluorescence and tested genotypes  from the same animal, matching littermate controls whenever possible. To assess the impact of Nrf1 knockout on retrotransposon expression, we performed poly-A-enriched RNA sequencing on whole testes at P5 and analyzed differentially expressed transposon families through pairwise comparisons of the mutants.

first: Jessica

last: Leismann

first: Styliani-Eirini

last: Kanta

first: Giuseppe

last: Petrosino

first: Joan Grande


title: DNA methylation-sensitive transcription factors and bivalency orchestrate transposon expression in the absence of DNA methylation [Postnatal Retrotransposon expression in spermatogenesis]

overall_design: To get a comprehensive overview of the expression patterns of TEs after failure to silence by DNA methylation, we checked RNA expression of distinct germ cell stages wildtype and Dnmt3CKO/KO animals, where DNA methylation is absent at young retrotransposon promoters. To this end, we performed RNA-seq on sorted premeiotic (Spermatogonia, Spg) and meiotic (Spermatocytes, Spc) cells from wildtype and Dnmt3CKO/KO animals and characterized the transcriptional activity of retrotransposon families in response to the loss of promoter DNA methylation.


title: DNA methylation-sensitive transcription factors and bivalency orchestrate transposon expression in the absence of DNA methylation [Profiling of identified candidate TFs in spermatogenesis]

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: NRF1 and CREB1 were identified as potential retrotransposon TFs in DNA-pulldowns coupled to Mass Spec.  We used CUT&Tag to profile NRF1 in all three germ cell stages purified from wild type (WT) and Dnmt3CKO/KO (KO): Prospermatogonia (ProSpg), Spermatogonia (Spg) & Spermatocytes (Spc). CREB1 was profiled using CUT&Tag in wild type versus Dnmt3C mutants at Spermatogonia.


title: Cell state dynamics during early stages of serous endometrial carcinoma

city: Ithaca

first: Matalin

last: Pirtz

state: New York

address: 147 Grandview Ct., #147LA

institute: Cornell University

summary: Serous endometrial carcinoma (SEC) is one of the most aggressive and lethal types of uterine cancer, responsible for about 40% of all endometrial cancer-related deaths.  Due to the rapid progression of SEC, early detection of this disease is of utmost importance. However, molecular and cellular dynamics during the pre-dysplastic stage of this disease remain largely unknown. Here, we provide a comprehensive census of cell types and their states for normal, pre-dysplastic, and dysplastic endometrium in a mouse model of SEC. This model is associated with inactivation of tumor suppressor genes Trp53 and Rb1, whose pathways are altered frequently in SEC. We report that pre-dysplastic changes are characterized by expanded and increasingly diverse immature luminal epithelial cell populations. Decrease of differentiated cell states is accompanied by a previously unreported reduction in number and strength of predicted interactions between epithelial and stromal endometrial cells. Such reduction is transient and is followed by formation of a new set of intercellular interactions marking further cancer progression. By using a multi-level approach combining single-cell and spatial transcriptomics paired with screening for clinically relevant genes in human endometrial carcinoma, we identified a panel of genes with potential use as early diagnostic, prognostic, and therapeutic targets. In summary, our results suggest an important role of luminal epithelial cell state in SEC pathogenesis, uncover transient reduction in cell-cell interactions prior the onset of cancer-associated dysplastic changes, and validate our mouse SEC model as a promising comparative platform in preclinical settings.

overall_design: The uterine horns of mice in the diestrus phase of the estrous cycle were collected at three distinct stages after doxycyline injection to create normal, pre-dysplastic, or displastic cohorts. Samples were collected for either scRNAseq or Visium sequencing.

first: Andrea

last: Flesken-Nikitin

first: Christopher

middle: S

last: Ashe

first: Lora

middle: H

last: Ellenson

first: Anna

last: Yemelyanova

first: Benjamin

middle: D

last: Cosgrove

first: Alexander

middle: Y

last: Nikitin


title: CMTR1 regulates hippocampus-dependent memory consolidation and long-term synaptic plasticity by promoting NMDA-receptor signaling

status: Public on Aug 06 2025

city: Taipei City

first: Yi-Shuian

last: Huang

address: No. 128, Section 2, Academia Rd, Nangang District

department: Institute of Biomedical Sciences

country: Taiwan

institute: Academia Sinica

summary: Eukaryotic mRNA is 5'-end capped with m7 guanosine, forming the cap0 (m7GpppNpNp, N: any nucleotide). Cap methyltransferase (CMTR1) further catalyzes 2'-O-ribose methylation of the first transcribed nucleotide (N1 2'-O-Me) to produce the cap1 (m7GpppNmNp) structure in all eukaryotes except yeasts. To elucidate the molecular changes in the hippocampus caused by the deletion of CMTR1 in Emx1-lineage cells, hippocampal tissues from CMTR1-cWT and cKOEmx1 mice were processed for RNA-sequencing analysis.

overall_design: To explore the role of CMTR1 in learning and memory, we used conditional wildtype (cWT) and conditional knock-out (cKOEmx1) mice to isolate hippocampal tissue for bulk RNA sequencing. We then ablated CMTR1 in the forebrain region to generate, a conditional knock-out (cKOCaMK2) mouse for further study. To understand the molecular changes in the hippocampus caused by the deletion of CMTR1, we used a series of behavioral, electrophysiological, and molecular assays.

first: Sayma

last: Azeem

first: Tzu-Tung

last: Chang

first: Peng

last: Chi

first: Nai-Hsing

last: Yeh


title: Reduced ZMPSTE24 expression leads to prelamin accumulation and development of steatosis in MAFLD patients [RNA-seq]

city: Pittsburgh

first: Irina

middle: M

last: Bochkis

address: 707A Scaife Hall, 3550 Terrace Street

department: Department of Pathology

summary: Mutations of nuclear lamina-associated proteins LMNA and ZMPSTE24 have been associated with fatty liver. We report that the changes at the nuclear envelope we described in MAFLD patients are caused by downregulation of ZMPSTE24, an enzyme that processes prelamin to mature lamin A. In addition, Zmpste24 mutant mice develop hepatic steatosis and  exhibit upregulation of p53 target genes. p53 activity is also induced in genes differentially expressed in MAFLD patients. Furthermore, p53  regulates genes bound by FOXA2 in these individuals, corresponding to observations in Zmpste24 mutants. In contrast, expression of glucose and insulin regulated genes is reduced in MAFLD patients, suggesting altered glucose metabolism and insulin resistance, hallmarks of type 2 diabetes (T2D). Hence, our genomics data show that MAFLD patients with severe steatosis but yet without MASH are already suffering from severe metabolic consequences and underscore the need for treatment at this stage of the disease.

overall_design: Differential gene expression profiling analysis of RNA-seq data for liver tissues of 9 samples from female patients (3 control, 3 mild MAFLD, 3 moderate MAFLD) and 9 samples from male patients (3 control, 3 mild/moderate MAFLD, 3 severe MAFLD). Female donors were 17–59yr old (healthy, 17–59; MAFLD, 31–47) Male donors were 21–51yr old (healthy, 26–45; MAFLD, 21–51).

first: Joe

last: Schinderle

first: Carol

last: Wu


title: Reduced ZMPSTE24 expression leads to prelamin accumulation and development of steatosis in MASLD patients [ChIP-seq]

summary: Mutations of nuclear lamina-associated proteins LMNA and ZMPSTE24 have been associated with fatty liver. We report that the changes at the nuclear envelope we described in MASLD patients are caused by downregulation of ZMPSTE24, an enzyme that processes prelamin to mature lamin A. In addition, Zmpste24 mutant mice develop hepatic steatosis and  exhibit upregulation of p53 target genes. p53 activity is also induced in genes differentially expressed in MASLD patients. Furthermore, p53  regulates genes bound by FOXA2 in these individuals, corresponding to observations in Zmpste24 mutants. In contrast, expression of glucose and insulin regulated genes is reduced in MASLD patients, suggesting altered glucose metabolism and insulin resistance, hallmarks of type 2 diabetes (T2D). Hence, our genomics data show that MASLD patients with severe steatosis but yet without MASH are already suffering from severe metabolic consequences and underscore the need for treatment at this stage of the disease.

overall_design:
Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for Foxa2 and LaminB1 in liver tissues of younger female MASLD patients (normal Normals, mild steatosis, moderate steatosis, healthy 17-59 years old, MASLD 31-47 years old).
Please note that each processed data file was generated from all replicates and is linked to the corresponding *Sample 1* records.


title: Mechanical cues guide the formation and patterning of 3D spheroids in fibrous environments

status: Public on Aug 05 2025

first: Julie

last: Phillippi

address: 450 Technology Drive, Suite 300

department: Cardiothoracic Surgery

summary: Multicellular spheroids have shown great promise in 3D biology. Many techniques exist to form spheroids, but how cells take mechanical advantage of native fibrous extracellular matrix (ECM) to form spheroids remains incompletely understood. Here, we identify the role of fiber diameter, architecture, and contractility on spheroids' spontaneous formation, growth, and maintenance using ECM-mimicking fiber networks. We show that matrix deformability is critical to forming spheroids, with deformable aligned fiber networks promoting spheroid formation independent of fiber diameter, while larger-diameter crosshatched networks of low deformability abrogate spheroid formation. Thus, a mixture of diameters and architectures allowed spatial patterning of spheroids and monolayers simultaneously. We quantify the forces involved during spheroid formation and identify the contractile role of Rho-associated protein kinase (ROCK) in spheroid formation and maintenance. Interestingly, we observed spheroid-spheroid and multiple spheroid mergers, which we describe by spheroid-shape-driven morphogenic Boolean outcomes. We found that spheroid mergers were initiated by exchanging a few cells and forming a cellular bridge connecting the two spheroids. Unexpectedly, we found large pericyte spheroids contract rhythmically. Overall, we ascertained that contractility and network deformability work together to spontaneously form and pattern 3D spheroids, potentially connecting in vivo matrix biology with developmental, disease, and regenerative biology.

overall_design: Bulk RNASeq of pericytes grown in monolayer or on nanofiber scaffolds (hollow metal scaffolds using non-electrospinning Spinneret based Tunable Engineered Parameters (STEP) technique) at Day 1, Day 7 and Day 21 post seeding. Specific scaffold parameters are ~2 µm thick ‘base’ fibers spaced ~350 µm apart, over which orthogonal layers of a parallel array of ~200 nm ‘aligned’ fibers with ~10 µm spacing were deposited. Both monolayer and scaffolds were coated in fibronectin prior to seeding.


title: Evolution of the human autopod skeleton [Human RNA-seq]

status: Public on Aug 20 2025

city: Cambridge

first: Terence

last: Capellini

state: MA

address: 11 Divinity Avenue

department: Human Evolutionary Biology

institute: Harvard University

summary: We investigate the genetic architecture of autopod development at the regulatory and transcriptomic level.

overall_design: Examination of open chromatin regions (ATAC-seq) and differentially expressed genes (RNA-seq) in the developing autopod skeleton.

last: Okamoto


title: NR4a knock-down in HER2 CAR-T cells improves T cell longevity and promotes  solid tumor eradication [scRNA-Seq]

status: Public on Aug 01 2025

city: Shinjuku-ku

first: Taeko

last: Hayakawa

state: Tokyo

address: 35 Shinanomachi

department: Division of Tumor Immunology, Institute for Advanced Medical Research

country: Japan

institute: Keio University School of Medicine

summary: Chimeric antigen receptor (CAR)-T cell therapy targeting human CD19 have demonstrated clinical efficacy against B-cell malignancies. However, CAR-T cell therapy's efficacy against solid tumors is limited due to factors like low tumor-associated antigens, infiltration rate, and T cell exhaustion. We have shown that deleting NR4a genes in CAR-T cells prevents T cell exhaustion and improved their therapeutic effects on solid tumors in a mouse model. To further explore this for human, we deleted all three NR4a family factors in CAR-T cells that recognize Epidermal Growth Factor Receptor type 2 (HER2) using the CRISPR/Cas9 system. These modified CAR-T cells (NR4a-TKO CAR-T) exhibited resistance to exhaustion, increased tumor-killing activity, and higher efficacy in tumor regression and survival rate in a human lung carcinoma model in mice. The enhanced therapeutic effects were associated with increased cytokine expression, reduced exhaustion-related gene expression, and improved persistence within tumors. We propose that targeting NR4a could be a promising strategy for developing superior CAR-T cells against solid tumors.

overall_design: Primary human T cells were isolated from PBMC derived from healthy donors and activated with anti-CD3/CD28 Dynabeads in AIM-V medium supplemented with IL-2 (10ng/mL). After 24 hours, the anti-HER2 CAR-Transgene was transduced with a Lentivirus into the T cells using RetroNectin (Takara Bio).On day 3, Dynabeads were magnetically removed, and CAR-T cells were electroporated with Cas9-RNPs.

first: Kensuke

last: Nakagawara

first: Akihiko

last: Yoshimura


title: DNA methylation-sensitive transcription factors and bivalency orchestrate transposon expression in the absence of DNA methylation [Chromatin landscape across spermatogenesis in wild type and Dnmt3C mutants]

first: Joan

last: Barau

overall_design: Previous studies in mESCs suggest that in absence of DNA methylation, retrotransposon repression can be taken over by repressive histone modifications. To investigate if the developmental-like pattern of TE expression observed in Dnmt3C mutants correlates with the dynamics of the chromatin landscape in spermatogenesis, we performed CUT&Tag to profile key histone modifications in wild type (WT) and Dnmt3CKO/KO(KO) germ cells at three developmental stages: embryonic prospermatogonia (ProSpg), postnatal spermatogonia (Spg) and spermatocytes (Spc). We  profiled two active (H3K4me3, and H3K27ac) and three repressive (H3K9me2, H3K9me3, and H3K27me3) histone modifications.

first: Jessica

last: Leismann

first: Styliani-Eirini

last: Kanta

first: Giuseppe

last: Petrosino

first: Joan Grande


title: Single-Cell RNA Sequencing Reveals Shenbai Granule Retards Colorectal Tumorigenesis by Modulating Cholesterol-Induced Ccl22+ DCs and Tregs Crosstalk

status: Public on Jul 30 2025

city: Nanjing

first: yang

last: sun

state: Jiangsu

address: Nanjing University Academy of Sciences, No. 163 Xianlin Avenue, Qixia District, Nanjing City, Jiangsu Province

department: Life Sciences

country: China

institute: Nanjing University

summary: Colorectal tumorigenesis generally follows a progressive sequence from adenoma to adenocarcinoma, accompanied by dynamic changes in the tumor microenvironment (TME). Randomized controlled trials have confirmed that Shenbai Granule (SBG), a traditional Chinese medicine formula, is safe and effective for the prevention of recurrent colorectal adenoma. However, the effects and mechanisms of SBG on colorectal tumorigenesis and the TME remain unclear. To investigate this, single-cell RNA sequencing (scRNA-seq) was conducted to reveal the dynamic evolution of the TME. Primary cells were isolated for in vitro validation experiments. The findings demonstrated that SBG reduces both the number and volume of tumors. There was a marked accumulation of Ccl22+ dendritic cells (DCs) and an enhanced interaction between Ccl22+ DCs and CD4+ regulatory T cells (Tregs), which were reversed by the treatment of SBG and its active compound, berberine. Combined treatment with cholesterol and lipopolysaccharide induced characteristic gene expression in Ccl22+ DCs, which may represent a type of “exhausted DCs”. Intraperitoneal injection of the Ccl22+ DCs after SBG treatment eliminated its therapeutic effects. These findings highlight critical crosstalk between Ccl22+ DCs and CD4+ Tregs in colorectal cancer. The multi-component properties of natural products may restore TME homeostasis and offer novel cancer therapy.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: scRNA-seq analysis of single-cell suspensions from colorectal adenoma patient tissues and APCmin/+ mice

first: Yuquan

last: Tao

first: Yinuo

last: Ma

first: Lisha

last: Zhou

first: Yang

last: Sun

first: Haibo

last: Cheng


title: Single-cell transcriptome analysis of bronchoalveolar lavage during early SARS-CoV-2 infection

status: Public on Jul 29 2025

city: Chicago

first: Shabaana

last: Khader

address: 5801 S Ellis Ave

institute: University of Chicago

summary: To understand the transcriptional landscape at the single-cell level during the early phases of COVID-19, we employed scRNA-seq approach using BAL cells of rhesus macaques at 0-3 days post infection (dpi).

overall_design: 14 BAL samples from rhesus macaques: day 0, (SARS-CoV-2 infection, baseline, n = 3), day 1 post infection (1dpi Inf, n = 4), 2 dpi (n=3) and 3 dpi (n = 4)

first: Mushtaq

last: Ahmed


title: Liver metastases license neutrophils throygh IL-1 to potentiate cancer progression

status: Public on Aug 04 2025

city: Ann Arbor

first: Ashley

last: Pearson

state: MI

address: 1301 Catherine St

institute: University of Michigan

summary: Liver metastases are associated with poor cancer outcomes in many solid malignancies, but the factors influencing the trajectory of patients with liver metastases are poorly defined. It is known that liver metastases suppress systemic antitumor immunity; however, the underlying mechanisms remain incompletely described. We report that liver metastases promote disease progression in patients and preclinical models. Patients with liver metastases progress rapidly, regardless of primary tumor type. In multiple murine models, we find that liver metastases potentiate neutrophil migration and activity. Neutrophils licensed by liver metastasis augment metastatic colonization in an IL-1 dependent fashion. Thus, liver metastasis rewires systemic immunity to promote cancer progression. This work has  implications for novel treatment strategies to address the poor clinical outcomes associated with liver metastasis.

overall_design: Black6 mice were inoculated with B16F10 subcutaneous tumors, and either received B16F10 liver metastases or a sham injection. The lungs and blood of these mice were harvested. CD45+ StemCell kits were used to enrich immune cells.

middle: N

first: Amanda

middle: K

last: Huber

first: Erin

last: Holcomb

first: Emily

middle: L

last: Lasse-Opsahl

first: Marina

last: Pasca Di Magliano

first: Weiping

last: Zou

first: Michael

last: Green


title: Transcript‑guided Targeted Cell Enrichment for Scalable Single‑Cell RNA Sequencing

city: New York

first: Junyue

last: Cao

state: NY

address: 1230 York Ave

institute: The Rockefeller University

summary: Rare cell populations—often comprising less than 0.01% of all cells—play crucial roles in development, aging, and disease, yet standard single-cell sequencing methods typically miss them. To address this gap, here we developed EnrichSci, a microfluidic‑free, combinatorial indexing platform that integrates Hybridization Chain Reaction-RNA FISH with the high‑throughput EasySci pipeline for targeted cell enrichment and scalable single‑cell RNA sequencing. EnrichSci uses FACS to selectively enrich nuclei labeled by custom transcript modules and delivers full gene body coverage at under $0.001 per cell and tens of millions of cells per run. We applied EnrichSci to map the full oligodendrocyte lineage, uncovering age-related loss of precursor states and expansion of reactive mature subpopulations (C4b⁺ Serpina3n⁺). Through gene- and exon- level differential analyses, we revealed subtype-specific molecular changes in aging. In summary, by coupling transcript-guided enrichment with ultra scalable single-cell sequencing platform, EnrichSci offers a versatile approach for decoding the dynamic regulatory landscapes in rare cell types across diverse tissues and conditions.

overall_design: Using EnrichSci, we performed targeted single-cell transcriptome profiling of oligodendrocytes from young (2 months) and aged (25 months) mouse brains.

first: Andrew

last: Liao

first: Zehao

last: Zhang

first: Andras

last: Sziraki

first: Abdulraouf

last: Abdulraouf

first: Abid

last: Rehman

first: Zihan

last: Xu

first: Ziyu

last: Lu

first: Weirong

last: Jiang

first: Alia

last: Arya

first: Jasper

last: Lee

first: Manolis

last: Maragkakis

first: Wei


title: The remodeling of bivalent chromatin is essential for mouse peri-implantation embryogenesis [hESC valid]

status: Public on Jul 24 2025

city: Shanghai

first: Jincan

last: He

address: siping road 1239

institute: Tongji university

summary: Since its discovered, the dynamics and molecular regulation of bivalent chromatin during early embryogenesis remain poorly understood. We trace gene expression and bivalent chromatin dynamics in peri-implantation mouse embryogenesis, showing bifurcated establishment in epiblast and primitive endoderm. We identify transiently maintained bivalent domains (TB domains) in the epiblast, crucial for pluripotency progression. Our study reveals 22 candidate factors, including ZBTB17, essential for resolving TB domains and activating pluripotency regulators. These dynamics are conserved in human pluripotent transition.

overall_design: After establishing a homozygous ZBTB17-knockout hEPSC line, we induced the transition from naïve to primed pluripotency and subsequently collected transcriptomic and histone modification data.

first: Yanhe

last: Li

first: Cizong

first: Wenqiang

last: Liu


title: The remodeling of bivalent chromatin is essential for mouse peri-implantation embryogenesis [mESC valid]

overall_design: We generated a naïve Zbtb17^dTAG/dTAG ESC line with an endogenous 3×HA tag and performed 2i ESC-to-EpiLC pluripotency transition assays, which recapitulate the transition from naïve to formative pluripotency, followed by the collection of transcriptomic and histone modification data, as well as ZBTB17 and EED binding profiles. To directly validate the bivalent chromatin status of the TB and CB gene sets, we performed sequential ChIP-seq (reChIP-seq) in naïve ESCs and EpiLCs, which serve as in vitro models of the peri-implantation epiblast.


title: The remodeling of bivalent chromatin is essential for mouse peri-implantation embryogenesis [Wild type RNA-Seq]

overall_design: We isolated specific lineages at consecutive time points using well-established in vitro embryo culture and in vivo dissection techniques. Samples included ICM and TE from E3.5 blastocysts, and EPI and PE from E4.5, E4.75, E5.0, E5.25, and E5.5 embryos. A Pdgfrα-promoter-driven EGFP reporter mouse line was employed to facilitate lineage-specific isolation. We performed ultra-low-input chromatin immunoprecipitation sequencing (ULI-NChIP-seq) for H3K4me3 and H3K27me3, Cleavage under targets and tagmentation (Cut&Tag) for Pol II binding, and Smart-seq2 for transcriptome analysis.


title: The remodeling of bivalent chromatin is essential for mouse peri-implantation embryogenesis [ChIP-Seq]


title: The remodeling of bivalent chromatin is essential for mouse peri-implantation embryogenesis [CUT&Tag]

overall_design: For embryo samples, we generated complete knockouts of each factor using the C-CRISPR approach or treated E3.5 blastocysts with 50μM GSK-J4. We cultured treated embryos through the peri-implantation period. At the E5.0 stage, we performed H3K27me3 profiling on the EPI of each treated embryo using CUT&Tag to assess gene perturbation.


title: The remodeling of bivalent chromatin is essential for mouse peri-implantation embryogenesis [Valid RNA-Seq]

overall_design: For embryo samples, we generated complete knockouts of each factor using the C-CRISPR approach or treated E3.5 blastocysts with 50μM GSK-J4. We cultured treated embryos through the peri-implantation period. At the E5.0 stage, we performed transcriptome profiling on the EPI of each treated embryo using Smartseq2 to assess gene perturbation.


title: TGF-β builds a dual immune barrier in colorectal cancer by impairing T cell recruitment and instructing immunosuppressive SPP1+ macrophages

status: Public on Jul 25 2025

city: Barcelona

first: Paula

last: Nieto

state: Spain

address: Barcelona Science Park, Carrer de Baldiri Reixac, 4, tower I, 08028 Barcelona

department: CNAG

country: Spain

institute: CNAG

summary: Poor prognosis colorectal cancer (CRC) is linked to a TGF-β-activated tumor microenvironment that suppresses immune responses. Inhibiting TGF-β signaling promotes T cell infiltration and enhances immune checkpoint blockade effectiveness, highlighting a network of genetic programs that prevent effective immune responses and clonal expansion of T cells, ultimately enabling metastatic growth.

overall_design: Tumor microenvironment from liver metastasis from colorectal cancer mouse tumor organoids under three different treatments plus controls. Different samples were analyzed: whole tumor microenvironment, T cells only and fibroblasts only.

first: Ana

last: Henriques

first: Maria

last: Salvany

first: Ginevra

last: Caratú

first: Holger

last: Heyn

first: Eduard

last: Batlle


title: The clonal basis of either resistance or response to ivosidenib and venetoclax ± azacitidine is established early in IDH1-mutated myeloid malignancies

city: Oxford

first: Sven

last: Turkalj

address: John Radcliffe Hospital/Headley Way, Oxford OX3 9DS

department: Radcliffe Department of Medicine

country: United Kingdom

institute: WIMM

summary: A recent phase Ib/II trial of ivosidenib and venetoclax ± azacitidine in patients with IDH1-mutated myeloid malignancies showed a promising 94% response rate. However, relapse was still common. To define the clonal and cellular basis of acquired resistance and sustained response, we performed single-cell studies on longitudinal samples from 8 patients. Whilst all 8 patients initially responded to treatment, 6 relapsed and 2 remained in sustained remission for > 4 years. Therapy-resistant clones were selected early, within 3 treatment cycles, preceding relapse by months or years. Treatment failure was associated with either emerging genetically evolved clones or acquired differentiation arrest of pre-existing clones; in both cases, within small immunophenotypic leukemic stem cell (LSC) populations. In sustained response, all leukemic clones were eradicated and rapidly replaced by clonal and wild type hematopoiesis. If validated in larger cohorts, early clonal assessment of LSCs may be predictive of long-term outcome, providing a clinically relevant endpoint.

overall_design: Plate-based single-cell RNA-seq coupled with single-cell targeted genotyping of genomic loci. Results are from primary human samples

first: Bilyana

last: Stoilova

first: Angus

last: Groom

first: Felix

last: Radtke

first: Rabea

last: Mecklenbrauck

first: Niels

last: Jakobsen

first: Curtis

last: Lachowiez

first: Marlen

last: Metzner

first: Batchimeg

last: Usukhbayar

first: Mirian

last: Salazar

first: Zhihong

last: Zeng

first: Sanam

last: Loghavi

first: Jennifer

last: Marvin-Peek

first: Verena

last: Körber

first: Farhad

last: Ravandi

first: Ghayas

last: Issa

first: Tapan

last: Kadia

first: Vasiliki

last: Symeonidou

first: Anne

middle: P

last: de Groot

first: Hagop

last: Kantarjian

first: Koichi

last: Takahashi

first: Marina

last: Konopleva

first: Courtney

last: DiNardo

first: Paresh

last: Vyas


title: Characterization of human CD34+ HSPC-derived neutrophils with limited myeloid-derived immunosuppressive cell activity

status: Public on Aug 09 2025

city: Amsterdam

first: Felipe

last: Rojas-Rodriguez

state: Noord Holland

address: Plesmanlaan 125

department: Molecular hematology

country: Netherlands

institute: Sanquin research

summary: Neutrophils have limited utility as a fundamental research model and transfusion product due to their short lifespan. Here, we cultured CD34+ hematopoietic stem and progenitor cell (HSPC)-derived neutrophils and compared them to peripheral blood neutrophils in terms of morphology, phenotype, and function. Our culture system resulted in morphologically mature CD15+CD11b+CD16high neutrophils with effector functions almost indistinguishable from blood neutrophils, confirmed by a high similarity in transcription and protein abundance patterns. While exhibiting microbial killing capacity and antibody-dependent cellular cytotoxicity, these cells were deficient in myeloid-derived suppressor cell activity. This deficiency in immunosuppressive activity correlated with a distinct granular composition in comparison to blood neutrophils, instead of immunosuppressive characteristics that are currently held to define neutrophil-MDSC phenotype. Taken together, our cultured neutrophils closely resemble blood neutrophils, offering a repository for fundamental research and a step toward an effective transfusion product with limited immunosuppressive activity as a functional property.

overall_design: Bulk RNAseq profiling of HSC-derived neutrophils cultured in SL-II medium at Day0, Day10, Day14 and Day17 of maturation. At day 14 and day 17 these cells were MACS sorted for CD16+ creating positive, negative and bulk fractions. PMNs and IMDM derived neutrophils at the endstage were included.

first: Steven

last: Webbers

first: Angela

last: Gankema

first: Fleur

last: van Oosterom

first: Dané

last: Koops

first: Anna

last: Klaus

first: Judy

last: Geissler

first: Teunis

last: van Dam

first: Hanke

last: Matlung

first: Robin

last: van Bruggen

first: Helin

last: Tercan

first: Arie

last: Hoogendijk

first: Taco

middle: W

last: Kuijpers


title: Targeting RNA Polymerase I to boost Natural Killer cell anticancer activity in Multiple Myeloma.

status: Public on Jul 23 2025

city: Rome

first: Marco

last: Cippitelli

state: Italy

address: Viale Regina Elena, 291

department: Molecular Medicine

country: Italy

institute: Univ. of Rome - Sapienza

summary: Multiple Myeloma (MM) remains an incurable disease despite therapeutic advancements extending survival. Relapses driven by drug resistance and minimal residual disease underscore the need for novel treatment strategies. Natural Killer (NK) cells play a key role in MM immunity, yet their function is suppressed by inhibitory cytokines and metabolites from the tumor microenvironment. Developing anticancer drugs with immunomodulatory properties, such as enhancing tumor sensitivity to NK cell recognition, remains a critical challenge. MM cells exhibit high protein synthesis rates, making them vulnerable to proteostasis disruption. Dysregulated ribosome function and aberrant mRNA translation contribute to proteasome inhibitor resistance. RNA Polymerase I (RNA Pol I)-mediated rDNA transcription, the rate-limiting step in ribosome biogenesis (RiBi), is significantly upregulated in MM. Targeting rDNA transcription and inducing nucleolar stress response (NSR) presents a promising therapeutic approach, though its immunomodulatory role is not well understood. Our study examined two “first-in-class” RNA Pol I inhibitors, CX-5461 and BMH-21, which differentially regulate NK cell-activating and inhibitory ligand expression in MM. BMH-21 enhanced NK cell degranulation and increased IFN-γ and TNF-α secretion, demonstrating stronger immunostimulatory effects than CX-5461. Conversely, CX-5461 induced a significant DNA damage response (DDR) and senescence, leading to HLA-E upregulation and suppressing NK cell activity. Mechanistic analyses revealed that HLA-E presentation is governed by ATR/AKT/mTORC1/S6K signaling and Pioneer Round of Translation (PRT), linking its regulation to DDR. This effect was modulated by Lenalidomide and Panobinostat. Moreover, RNA Pol I inhibition enhanced Daratumumab-mediated antibody-dependent cellular cytotoxicity (ADCC) of NK cells against MM, uncovering novel immuno-mediated antitumor mechanisms.

overall_design: Sequencing libraries were generated using Nextflex Rapid Directional RNA-Seq kit 2.0 Kit with Poly(A) Beads 2.0 (PerkinElmer).   We compared three conditions on SKO-007(J3) MMcells (Untreated, CX-5461 and BMH-21). Samples were sequenced by NovaSeq 6000 Sequencing System, RUN 2x150 bp, with an average seq throughput for the project ≥ 30M PE read per sample.


title: Transcriptomic diversity of amygdalar subdivisions across humans and nonhuman primates

city: Baltimore

first: Keri

last: Martinowich

state: Maryland

address: 855 N Wolfe St Suite 300

institute: Lieber Institute for Brain Development

summary: The amygdaloid complex mediates learning, memory, and emotions. Understanding the cellular and anatomical features that specialize the amygdala in primates versus other vertebrates first necessitates a systematic, anatomically-resolved molecular analysis of constituent cell populations. We analyzed tissue dissections of five nuclear subdivisions of the primate amygdala with single-nucleus RNA sequencing in macaques, baboons, and humans to examine gene expression profiles for excitatory and inhibitory neurons within and across nuclear subdivisions and confirm our results with single-molecule FISH analysis. We identified distinct subtypes of FOXP2+ interneurons in the intercalated cell masses and protein-kinase C- interneurons in the central nucleus. We also establish that glutamatergic, pyramidal-like neurons are transcriptionally specialized within the basal, lateral, or accessory basal nuclei. Understanding the molecular heterogeneity of anatomically-resolved amygdalar neuron types provides a cellular framework for improving existing models of how amygdalar neural circuits contribute to cognition and mental health in humans by using nonhuman primates as a translational bridge.

sample_organism:
Macaca mulatta
Papio anubis
Homo sapiens

overall_design: We obtained tissue blocks of postmortem human brain containing the amygdala from 5 human adult brain donors, 5 adult rhesus macaques, and 2 olive baboons. The whole basolateral complex was sampled indiscriminately in humans, whereas precise punches of either the lateral (LA), basal (BA), accessory basal (aBA), or central nucleus (CeA) were taken in nonhuman primates. We used the 10x Genomics 3’ Single Cell Gene Expression platforms to generate single-nucleus RNA-seq data of the primate amygdala across all three species.

first: Michael S.

last: Totty

first: Rita Cervera

last: Juanes

first: Svitlana V.

last: Bach

first: Lamya Ben.

last: Ameur

first: Madeline R.

last: Valentine

first: Evan

last: Simons

first: McKenna

last: Romac

first: Hoa

last: Trinh

first: Krystal

last: Henderson

first: Ishbel Del

last: Rosario

first: Madhavi

last: Tippani

first: Ryan A.

last: Miller

first: Joel E.

last: Kleinman

first: Stephanie Cerceo

last: Page

first: Arpiar

last: Saunders

first: Thomas M.

last: Hyde

first: Stephanie C.

last: Hicks

first: Vincent D.

last: Costa


title: Nutrient-driven TOR signaling mediates transcriptional repression by promoting translation to regulate plant growth [RNA-seq]

status: Public on Aug 11 2025

city: Beijing

first: xinjian

last: He

address: No. 7, zhongguancun life science park road, changping district

institute: National Institute of Biological Sciences

summary: As is well known, nutrition is essential for plant growth and development. Extensive research has demonstrated that the target of rapamycin (TOR) is a crucial growth regulator, receiving nutritional inputs in eukaryotic cells. Nevertheless, the precise mechanisms by which TOR coordinates nutrient conditions and growth remain elusive in plants. In this study, we identified a novel transcriptional repression complex, TRCG, downstream of the TOR signaling pathway. This complex is responsible for regulating plant growth and the nutritional response. In the presence of favorable nutritional conditions, TOR is activated, leading to the translation of the 5’-terminal oligopyrimidine (5’-TOP) mRNA of TRCG. TRCG directly binds numerous nutrition-responsive genes, particularly those belonging to the ERF family of transcription factors, to repress their transcription. This repression is achieved by influencing the initiation and elongation of RNA polymerase II (Pol II), thereby maintaining growth and development. In the absence of nutritional conditions, TOR activity is inhibited, resulting in the repression of TRCG translation. This, in turn, relieves the repression of nutrient response genes, causing a stagnation of growth and poor nutrient resistance, thus contributing to the survival of the plant. Moreover, we observed a higher histone H3 and H4K5 acetylation level in the TRCG targets. Acetylated chromatin has long been associated with transcriptional activation, suggesting that TRCG could bind to acetylated chromatin to repress transcriptional activation. Our findings elucidate a previously unidentified precise mechanism by which TOR-mediated transcriptional repression occurs through the stimulation of translation, thereby regulating plant growth and the nutritional response.

overall_design: Examination of the mRNA expression of 12-day-old wild type and seven mutants in Arabidopsis.

first: Xin


title: Endothelial dysfunction contributes to chondrocyte senescence associated with Insulin-like growth factor-binding protein-6 in a spontaneously hypertensive rat model

city: Hung Hom, Kowloon

first: Lanlan

last: Zhang

address: 11 Yuk Choi Road

country: Hong Kong

institute: The Hong Kong Polytechnic University

summary: Given an epidemiological association between hypertension and osteoarthritis (OA), we aim to elucidate how vascular pathology triggers avascular articular cartilage loss by comparing vascular and joint phenotype between spontaneously hypertensive rats (SHR) and normotensive Wistar Kyoto (WKY) rats. Endothelial molecular changes were delineated via bulk RNAseq. Transcriptomic analyses of rat endothelial cells revealed upregulated insulin-like growth factor-binding proteins (IGFBPs). Among them, IGFBP6 was identified to induce chondrocyte senescence in vitro, highlighting a potential therapeutic target for preventing joint structural damage by addressing endothelial dysfunction.

overall_design: Primary endothelial cells were isolated from 3-month-old WKY and SHR, specifically the proximal segment of the aorta adjacent to the heart (n=3 per group). Aortas were dissected from the hearts of 3-month-old rats and cut into pieces, then placed with the endothelium side down in 12-well plates. Total RNA was later extracted from primary endothelial cells.

first: Man Ting

last: Au

first: Yuqi


title: Stress inducible phosphoprotein 1 (STIP1) is a critical stemness regulator in mouse embryonic stem cells and early mammalian development

city: Sao Paulo

first: Marilene

middle: Hohmuth

last: Lopes

state: Sao Paulo

address: Av Prof Lineu Prestes, 1524, room 431

department: Cell and Developmental Biology

country: Brazil

institute: University of Sao Paulo

summary: Stress-inducible phosphoprotein 1 (STIP1/STI1/HOP) is a co-chaperone that plays a pivotal role in proteostasis. Knockout of STIP1 leads to early embryonic lethality in mice, but its precise function in embryogenesis remains unknown. Thus, we mined single-cell RNA sequencing data from mouse embryos, finding that Stip1 is co-expressed with the core pluripotency transcription factors, highlighting a potential function of this protein in regulating stemness. This was confirmed by the derivation of mouse embryonic stem cell (mESC) lines from genetically-modified Stip1 mice. mESCs with decreased STIP1 levels presented low expression of essential pluripotency markers, impaired proliferation, and increased apoptosis and DNA damage. Conversely, mESCs overexpressing STIP1 showed elevated expression of stemness markers, enhanced proliferation, and reduced DNA damage and apoptosis. Finally, we reveal that cell cycle progression and DNA damage response proteins are altered in mESCs with differential STIP1 levels. Our work sheds light on the function of (antes era "on a novel function of") the co-chaperone STIP1 as a pivotal regulator of the pluripotent phenotype and embryogenesis.

overall_design: RNA-seq profiling of wild-type (WT), STIP1_+/- (50% expression), STIP1_TgA (overexpression) and STIP1_DeltaTPR1 (exons 2 and 3 of the Stip1 gene deleted) mESCs lines derived from the inner cell mass of genetically-modified Stip1 mice.

first: Camila

last: Fernandes

first: Jacqueline

last: Boccacino

first: Frederico

last: Ferreira

first: Helder

last: Nakaya


title: Cnot3 is required for male germ cell development and spermatogonial stem cell maintenance [scRNA-Seq]

city: Durham

first: Brian

last: Bennett

address: 111 T.W. Alexander Drive

institute: NIEHS

summary: The foundation of spermatogenesis and lifelong fertility is provided by spermatogonial stem cells (SSCs). SSCs divide asymmetrically to either replenish their numbers (self-renewal) or produce undifferentiated progenitors that proliferate before committing to differentiation. However, regulatory mechanisms governing SSC maintenance are poorly understood. Here, we show that the CCR4-NOT mRNA deadenylase complex subunit CNOT3 plays a critical role in sustaining spermatogonial populations in mice. We found that Cnot3 is highly expressed in undifferentiated spermatogonia, and its deletion in spermatogonia resulted in germ cell loss and infertility. Furthermore, it is required for SSC self-renewal based on single cell analyses in vivo and SSC culture in vitro. Mechanistically, Cnot3 deletion led to the de-repression of transcripts encoding factors involved in spermatogonial differentiation, including those in the glutathione redox pathway that are critical for SSC maintenance. Together, our study reveals that CNOT3 – likely via the CCR4-NOT complex – actively degrades transcripts encoding differentiation factors to support the spermatogonial pool and ensure the progression of spermatogenesis, highlighting the importance of CCR4-NOT-mediated post-transcriptional gene regulation during male germ cell development.

overall_design: Testes were dissected from Tamoxifen-treated neonatal mice (Cnot3flox/flox, and Cnot3flox/flox; Ddx4-creER). Tunica were removed and released seminiferous tubules were dissociated with 0.25% Trypsin and Accutase into a single-cell suspension. Cells were incubated with CD9 and THY1 antibodies, and CD9+/THY1+ cells were collected by FACS sorting. Sorted cells were used for scRNA-seq using the 10xGenomics Chromium Single Cell 3' Kit v3.1.

first: Qing

last: Chen

first: Safia

last: Malki

first: Xiaojiang

last: Xu

first: Jiajia

last: Wang


title: Compendium of Disease-Linked Regulatory DNA Variants and Homeostatic Transcription Factors in Epidermis [crispr_flow]

status: Public on Jul 22 2025

city: Stanford

first: Douglas

last: Porter

state: CA

address: 269 Campus Drive

department: Dermatology

institute: Stanford

summary: Identifying the regulatory noncoding single nucleotide variants (SNVs) linked to polygenic disease risk, the transcription factors (TFs) they bind, and the target genes they dysregulate is a current focus in many tissues. Massively parallel reporter gene analysis (MPRA) of 3,451 SNVs linked to risk for prevalent human skin diseases identified 355 differentially active SNVs (daSNVs). daSNV target gene analysis, including genomic editing at three loci, highlighted dysregulated epidermal differentiation as a common pathomechanism. CRISPR knockout screens of 1,782 human TFs identified 108 TFs essential for epidermal homeostasis, validating new roles for ZNF217, CXXC1, FOXJ2, IRX2 and NRF1. Population sampling CUT&RUN from 310 samples of 27 homeostatic TFs across differentiation identified allele-specific binding differences enriched near epidermal homeostasis and monogenic skin disease genes, with prominent representation of SP/KLF and AP-1/2 family TFs. This resource indicates that dysregulated differentiation underlies pathogenic risk for diverse polygenic skin diseases.

overall_design: Guide RNA sequencing of CRISPR-flow samples, for a library targetting all transcription factors and sorting on the early keratinocyte differentiation marker KRT10. 20 samples of primary keratinocytes, 2 tissue donors (biorep*), two technical replicates (batch*), four sorting states on KRT10 (unsorted, low, medium, high) and a plasmid sequencing sample. Cells were either harvested in progenitor growth conditions (Prog) or after four days of differentiation (Day 4).

middle: F

first: Weili

last: Miao

first: Robin

last: Meyers

first: David

last: Reynolds

first: Xue

last: Yang

first: Audrey

last: Hong

first: Paul

last: Khavari


title: Retinoic acid disrupts an NPM1c/ROS/SENP3/ARF oncogenic axis in acute myeloid leukemia

city: Beirut

first: Hiba

last: El Hajj

address: Bliss street

department: Department of Experimental Pathology, Immunology and Microbiology

country: Lebanon

institute: American University of Beirut

summary: Nucleophosmin-1 (NPM1) is a nucleolar chaperone protein frequently mutated in acute myeloid leukemia (AML). ARF and Sentrin/SUMO Specific Peptidase 3 (SENP3) control NPM1 functions through dynamic SUMOylation/de-SUMOylation. Mutated NPM1 is an oncoprotein that exhibits an aberrant cytoplasmic localization (NPM1c) and disrupts PML/P53 signaling. Studies reported increased survival of patients with NPM1c AML when retinoic acid (RA) was added to chemotherapy or hypomethylating agents. Ex vivo, RA initiates NPM1c degradation, P53 activation and cell death. Yet, the molecular mechanisms involved remain elusive. Here we show that in NPM1c AML cell lines or patients’ blasts, NPM1c-triggered mitochondrial dysfunction and oxidative stress drive NPM1c stabilization through SENP3 upregulation. RA decreases mitochondrial ROS production, driving degradation of SENP3, ARF stabilization, PML-dependent NPM1c hyperSUMOylation followed by RNF4-dependent ubiquitination and degradation. Thus, the feedback loop stabilizing NPM1c protein can be interrupted by RA-triggered enhanced mitochondrial fitness, mechanistically explaining the benefit of RA in chemotherapy or hypomethylating agents-treated AMLs.

overall_design: OCI-AML3 cells were treated or not with 1uM of Retinoic acid for 2h or 4h. Whole-cell RNA from one million cells of OCI-AML3 cells with or without RA treatment from three independent experiment were purified using RNeasy Mini Kit (QIAGEN Cat#74134). RNA sequencing was performed at Novogene.

first: Rita

last: Hleihel

first: Hala

last: Skayneh

first: Hsin-Chieh

last: Wu

first: Maguy

last: Hamie

first: Abdallah

last: Kurdi

first: Jana

last: Dakour

first: Charbel

last: Machaalani

first: Marwan

last: El-Sabban

first: Hugues

last: de Thé

first: Ali

last: Bazarbachi


title: Compendium of Disease-Linked Regulatory DNA Variants and Homeostatic Transcription Factors in Epidermis [mpra_wt]

first: Douglas

last: Porter

overall_design: Massively Parallel Reporter Assays (MPRA) of variants linked via GWAS to skin disease in human keratinocytes to identify variants with increased potential for transcriptonal effects, and effects from differentiation. 8 samples of primary keratinocytes, 2-3 tissue donors and 2 plasmid sequencing samples. Cells were either harvested in progenitor growth conditions (D0), after three (D3) or six (D6) days of differentiation. The uploaded fastq files are the result of running the indicated umi_tools extract command.

first: Weili

last: Miao


title: Compendium of Disease-Linked Regulatory DNA Variants and Homeostatic Transcription Factors in Epidermis [RNA-seq]

overall_design:
52 samples of primary keratinocytes, 9 tissue donors (Batch_* genotype column), 7 siRNAs against TFs and 1 control siRNA ("safe"). Cells were either harvested in progenitor growth conditions (Prog) or after four days of differentiation (Day 4). Generally 2-3 replicates per condition.

***************************************************************
Raw files for human/patient samples are being made available in dbGaP (https://www.ncbi.nlm.nih.gov/gap/) under accession phs003977 for controlled access to the personally identifiable sequence data.
***************************************************************

first: Robin

last: Meyers

first: David

last: Reynolds


title: Compendium of Disease-Linked Regulatory DNA Variants and Homeostatic Transcription Factors in Epidermis [mpra_tf_kos]

overall_design: Massively Parallel Reporter Assays (MPRA) of variants linked via GWAS to skin disease in human keratinocytes with either the Cas9 CRISPR KO of a transcription factor or a safe target control (ST26) to identify variants responsive to skin homeostasis transcription factors. 27 samples of primary keratinocytes, from 2-3 tissue donors and 2 plasmid sequencing samples. Cells were either harvested in progenitor growth conditions (D0), after three (D3) or six (D6) days of differentiation. The uploaded fastq files are the result of running the indicated umi_tools extract command.

first: Xue

last: Yang

first: Audrey

last: Hong


title: The bladder cancer m6A landscape is defined by global methylation dilution and focal 3′-UTR hypermethylation

status: Public on Jul 18 2025

city: Heidelberg

first: Jonas

last: Koch

address: Im Neuenheimer Feld 580

department: Epigenetics

institute: German Cancer Research Center

summary: N6-Methyladenosine (m6A) is the most abundant internal modification of eukaryotic mRNAs and regulates target transcripts throughout the mRNA life cycle. Although changes in m6A have been reported in human cancers, technical limitations have hindered a comprehensive understanding of the cancer-associated m6A landscape. Here, we used GLORI-sequencing to establish the first transcriptome-wide, single-nucleotide resolution maps of m6A in cancer. Differentially methylated transcripts were enriched in oncogenic pathways relevant to urothelial carcinoma of the bladder (UCB). We discovered two key m6A signatures in UCB: a global loss of methylation and a local hypermethylation at 3′-UTRs. Integration of RNA-sequencing data revealed that the global loss resulted from dilution of methylation marks due to increased expression of unmethylated transcripts and decreased expression of highly methylated transcripts. In contrast, local 3′-UTR hypermethylation was associated with the overexpression of VIRMA, a component of the m6A writer complex, which was linked to UCB progression. Our study is the first to describe the m6A epitranscriptomic landscape of cancer at single-base resolution and provides first insights into the processes that generate its characteristic signatures.

overall_design: Using comparative GLORI sequencing of nine paratumoral and nine tumoral patient samples, we investigated the m6A epitranscriptomic landscape of urothelial carcinoma of the bladder. Also, we sequenced three biological replicates of HEK293T cells and T24 cells treated with DMSO and the METTL3 inhibitor STM2457 for GLORI validation and description of the m6A epitranscriptomic landscape of HEK293T and T24 cells. Additionally, we GLORI-sequenced three biological replicates of RT4/UM-UC-3 shCtrl and shVIRMA cells for investigating the role of VIRMA in the m6A epitranscriptomic landscape of bladder cancer cells.

first: Felix

last: Bormann

first: Jinyun

last: Xu

first: Vitor

last: Coutinho Carneiro

first: Manuel

last: Neuberger

first: Katja

last: Nitschke

first: Malin

last: Nientiedt

first: Philipp

last: Erben

first: Maurice

last: Stephan Michel

last: Rodriguez-Paredes

first: Frank

last: Lyko


title: Progressive Tooth Pattern Changes in Cilk1-Deficient mice Depending on Hedgehog Signaling

status: Public on Jul 21 2025

city: Seoul

first: Minjae

last: Kyeong

address: Yonsei-ro 50

country: South Korea

institute: Yonsei university

summary: Primary cilia function as critical sensory organelles that mediate multiple signaling pathways, including the Hedgehog (Hh) pathway, which is essential for organ patterning and morphogenesis. Disruptions in Hh signaling have been implicated in supernumerary tooth formation and molar fusion in mutant mice. Cilk1, a highly conserved serine/threonine-protein kinase localized within primary cilia, plays a critical role in ciliary transport. Loss of Cilk1 results in severe ciliopathy phenotypes, including polydactyly, edema, and cleft palate. However, the role of Cilk1 in tooth development remains unexplored. In this study, we investigated the role of Cilk1 in tooth development. Cilk1 deficiency resulted in downregulation of Hh target genes, leading to the formation of supernumerary teeth. This study reveals a previously unrecognized role of Cilk1 in controlling tooth morphology via Hh signaling.

overall_design: Cilk1 (Ciliogenesis associated kinase1) knockout  (Cilk1−/−) mice were generated by crossing Cilk1fl/fl mice with EIIa-Cre transgenic mice for Cre-mediated deletion of Cilk1 exon 6. Cilk1fl/fl mice were previously described  (https://doi.org/10.7554/eLife.56551).   Cilk1−/−;PCS1−MRCS1△/△ mice were generated by crossing Cilk1−/− and PCS1−MRCS1△/△ mice. PCS1−MRCS1△/△ mice with a deletion of a 70 kb region from PCS1 to MRCS1 were previously described  (https://doi.org/10.1177/0022034518758642). All animal procedures were conducted in accordance with institutional guidelines and approved by the Institutional Animal Care and Use Committee  (IACUC) of Yonsei University. RNA was extracted from the maxillary molar tooth germs of Cilk1−/−, Cilk1-/-;PCS1−MRCS1△/△ and Cilk1+/+ mice at embryonic day 14.5, followed by bulk RNA sequencing. Comparative gene expression profiling was then performed on the RNA-seq data.

first: Dinuka

last: Adasooriya

first: Shiqi

last: Kan

first: Sung-Won

last: Cho


title: H3K4me3 instructs transcription at intergenic active regulatory elements [RNA-seq]

status: Public on Jul 17 2025

city: New Haven

first: Bluma

last: Lesch

state: CT

address: 333 Cedar Street

department: Genetics

institute: Yale University

summary: Tri-methylation of lysine 4 on histone H3 (H3K4me3) is a deeply conserved and functionally important histone modification enriched at transcriptionally active promoters. H3K4me3 can facilitate RNA polymerase activity in a context-dependent manner. Here, we generated an epigenetic editing tool, dCas9-PRDM9, that efficiently deposits H3K4me3 at specific target loci, and used it to interrogate the genomic and chromatin contexts required for H3K4me3 to facilitate transcription in human cells. We found that H3K4me3 deposition is sufficient to increase transcription at active candidate cis-regulatory elements (cCREs), and that this effect was independent of cCRE identity or distance from gene promoters, unrelated to transcript levels of putative target genes, and dependent on the presence of active chromatin features. We conclude that H3K4me3 is sufficient to instruct RNA polymerase activity but requires pre-existing features of transcriptionally active chromatin. These findings suggest that disease-associated dysfunction in H3K4me3 deposition or removal can disrupt the cell’s transcriptional state.

overall_design: RNA-seq from MDA-MB-231 human breast cancer cells

first: Haoming

last: Yu


title: H3K4me3 instructs transcription at intergenic active regulatory elements [TT-TimeLapse-seq]

overall_design: TT-Timelapse-seq from MDA-MB-231 human breast cancer cells


title: H3K4me3 instructs transcription at intergenic active regulatory elements [ATAC-seq]

overall_design: ATAC-seq from MDA-MB-231 human breast cancer cells


title: Profiling of gene expression, histone marks, chromatin accessibility, and DNA methylation in myeloid progenitors expressing H3WT, H3K4M, H3K27M, or H3K4M/K27M for 2 weeks [scRNA-seq]

city: Boston

first: Gracia

middle: M.

last: Bonilla

address: 185 Cambridge St

department: Molecular Biology

institute: Massachusetts General Hospital

summary: Developmental gene expression is tightly regulated by the dynamic interplay of H3K4 and H3K27 methylation associated with active and repressed genes, respectively. However, our understanding of the individual and combinatorial roles these histone modifications play in a physiological context remains incomplete. Here, we have leveraged histone mutant transgenic tools to uncover a previously unappreciated role for H3K4 methylation in adult hematopoiesis. Adult mice globally depleted for all forms of H3K4 methylation via expression of an inducible histone H3 lysine-4-to-methionine (H3K4M) mutant allele succumbed to a severe loss of all major blood cell types. Unexpectedly however, H3K4M-expressing hematopoietic stem cells (HSCs) and committed progenitors were present at normal numbers and persisted long-term when transplanted into mice alongside unperturbed bone marrow, indicating that H3K4 methylation is dispensable for the maintenance and early commitment of HSCs but essential for the maturation of downstream progenitors. Importantly, the restoration of H3K4 methylation in H3K4M animals rescued their morbidity, released progenitors from the maturation block and enabled normal blood cell production. Mechanistically, we showed that H3K4 methylation opposes the deposition of repressive H3K27 methylation at differentiation-associated genes bivalently marked by H3K4me3 and H3K27me3 in HSCs or progenitors. Indeed, by concomitantly suppressing H3K27 methylation in H3K4 methylation-depleted mice we could rescue the acute lethality, hematopoietic failure and gene dysregulation. Collectively, our results reveal that H3K4 methylation safeguards hematopoiesis by opposing repressive H3K27 methylation at fate-instructive bivalent genes, providing evidence for the functional interaction between these crucial chromatin marks in mammalian tissue homeostasis.

overall_design: Single cell RNA-seq was performed for HSPCs (lineage-/cKit+/Sca1+) and MyPS (lineage-/cKit+/Sca1-) isolated from H3WT and H3K4M competitive chimeric mice after 2 weeks of doxycycline administration

first: Yagi

last: Masaki

first: Bonilla

last: Gracia

first: Sadreyev

last: Ruslan

first: Hochedlinger

last: Konrad


title: Profiling of gene expression, histone marks, chromatin accessibility, and DNA methylation in myeloid progenitors expressing H3WT, H3K4M, H3K27M, or H3K4M/K27M for 2 weeks [RRBS]

type: Methylation profiling by high throughput sequencing

overall_design: Reduced representation bisulfite sequencing was performed for H3WT, H3K4M, H3K27M, or H3K4M/K27M  samples in duplicate

first: Masaki

last: Yagi

first: Ruslan

last: Sadreyev

first: Chuck

last: Haggerty

first: Alexander

last: Meissner

first: Konrad

last: Hochedlinger


title: Profiling of gene expression, histone marks, chromatin accessibility, and DNA methylation in myeloid progenitors expressing H3WT, H3K4M, H3K27M, or H3K4M/K27M for 2 weeks [ATAC-seq]

overall_design: ATAC-seq was performed for H3WT, H3K4M, H3K27M, or H3K4M/K27M  samples in duplicate


title: Human LY9 governs CD4+ T-cell IFN-γ immunity to Mycobacterium tuberculosis

status: Public on Jul 16 2025

city: New York

first: Yelena

last: Nemirovskaya

address: 1230 York Avenue

institute: Rockefeller University

type: Methylation profiling by genome tiling array

summary: CD4+ T cells are indispensable for optimal immunity to Mycobacterium tuberculosis (M.tb), a virulent pathogen that triggers tuberculosis (TB), in humans, as evidenced by studies of patients with CD4+ T lymphocytopenia. M.tb-specific human CD4+ T cells are known to polarize toward an IFN-γ-producing, T-bet+RORγT+ TH1* memory phenotype. We report that inherited deficiency of the human lymphocytic surface receptor LY9 (SLAMF3, CD229) underlies TB, but not BCG disease, due to dysfunction of TH1* cells. We find autosomal recessive, complete LY9 deficiency in three unrelated patients with TB and one asymptomatic relative, but not in patients with other infections studied, including patients with BCG disease, and in less than 10-5 individuals in the general population. TH1* cells in LY9-deficient individuals show selective impairment in IFN-γ production. By contrast, LY9 deficiency does not disrupt the development or function of leukocyte subsets other than TH1* cells, including TH1 cells. Mechanistically, LY9 polarizes naïve CD4+ T cells toward memory TH1* cells by inducing T-bet via SAP, and RORγT without SAP. Among CD4+ T cell subsets, TH1* cells express LY9 at the highest level. Finally, LY9 costimulation enhances TCR-driven IFN-γ production of memory TH1*, but not TH1, cells in a T-cell-intrinsic manner via NFAT1 and RORγT. Human LY9 is thus required for an optimal TH1*-cell- and IFN-γ-dependent protective immunity to M.tb. These findings, in turn, suggest that, without fully functional TH1* cells, TH1 cells and other T cell subsets may not be sufficient for optimal protective immunity to M.tb in humans.

overall_design: MACS-enriched CD4+ T cell blasts from healthy controls, LY9-deficient individuals (N=3), and T-bet- (N=1; T-cell blasts induced from two PBMC samples as technical duplicates) and RORgamma-deficient patients (N=3) were expanded for ~2 weeks and lysed. Genomic DNA was extracted and subjected to methylation microarray.

first: Ogishi

last: Masato

first: Boisson-Dupuis

last: Stephanie

first: Casanova

last: Jean-Laurent


title: Optogenetic Clustering of Human IRE1 Reveals Differential Regulation of Transcription and mRNA Splice Isoform Abundance by the UPR

city: Columbus

first: Jacob

middle: William

last: Smith

state: oh

address: 484 W 12th Ave

department: Chemistry and Biochemistry

institute: The Ohio State University

summary: Inositol-requiring enzyme 1 (IRE1) is one of three known sensor proteins that respond to homeostatic perturbations in the metazoan endoplasmic reticulum. The three sensors collectively initiate an intertwined signaling network called the Unfolded Protein Response (UPR). Although IRE1 plays pivotal roles in human health and development, understanding its specific contributions to the UPR remains a challenge due to signaling crosstalk from the other two stress sensors. To overcome this problem, we engineered a light-activatable version of IRE1 and probed the transcriptomic effects of IRE1 activity in isolation from the other branches of the UPR. We demonstrate that 1) oligomerization alone is sufficient to activate IRE1 in human cells, 2) IRE1’s transcriptional response evolves substantially under prolonged activation, and 3) the UPR induces major changes in mRNA splice isoform abundance in an IRE1-independent manner. Our data reveal previously unknown targets of IRE1 transcriptional regulation and direct degradation. Additionally, the tools developed here will be broadly applicable for precise dissection of signaling networks in diverse cell types, tissues, and organisms.

overall_design: RNAseq of U-2 OS cells expressing either WT IRE1 or Opto-IRE1 (a light-inducible construct of IRE1 with an appended CRY2-clust domain) treated with light, tunicamycin, anti-XBP1 siRNA, or NMDI inhibitor 11j to dissect the effects of IRE1 activation.

first: Damien

middle: B

last: Wilburn

first: Vladislav

last: Belyy


title: Profiling of gene expression, histone marks, chromatin accessibility, and DNA methylation in myeloid progenitors expressing H3WT, H3K4M, H3K27M, or H3K4M/K27M for 2 weeks [CUT&Tag]

first: Gracia

last: Bonilla

overall_design: CUT&Tag sequencing was performed for H3WT, H3K4M, H3K27M, or H3K4M/K27M  samples in duplicate


title: Molecular Subtypes of Human Skeletal Muscle in Cancer Cachexia

city: Edmonton

first: Sambasivarao

last: Damaraju

state: Alberta

address: 11560 University Avenue

department: Laboratory Medicine and Pathology

country: Canada

institute: University of Alberta

summary: Cancer-associated muscle wasting associates with poor clinical outcomes1, but its underlying biology is largely uncharted in humans2. Unbiased RNAome analysis (coding and non-coding RNAs) with unsupervised clustering using Integrative Non-negative Matrix Factorization (intNMF)3 provides an avenue to identify distinct molecular subtypes, here applied to muscle of patients with colorectal or pancreatic cancer. Rectus abdominis biopsies from 84 patients was profiled using high-throughput next generation sequencing. Here we show that intNMF with stringent quality metrics of clustering identifies 2 highly coherent molecular subtypes within muscle of patients with cancer. Patients in Subtype 1 (vs Subtype 2) showed clinical manifestations of cachexia: high-grade weight loss, low muscle mass, atrophy of Type IIA and Type IIX muscle fibres and reduced survival. Based on differential expression between the subtypes, our results indicate biological processes that may contribute to cancer-associated loss of muscle mass and function, including altered post-transcriptional regulation, and perturbation of neuronal systems, cytokine storm/cellular immune response, extracellular matrix, and metabolic abnormalities spanning xenobiotic metabolism, hemostasis, signal transduction, embryonic/pluripotent stem cells, and amino acid metabolism. Differential expression between subtypes indicates involvement of multiple, intertwined higher-order gene regulatory networks, suggesting potential for interacting (hub)lncRNA-miRNA-mRNA interaction networks as targets for future research.

overall_design: Whole transcriptome profiling (small RNA and RNA seq) from muscle of patients with cancer was performed to decipher complex biological processes contributing to muscle loss.

first: Bhumi

last: Bhatt

first: Vickie

last: Baracos


first: Jonas

last: Koch

overall_design: Using RNA sequencing, we analyzed transcript expression changes in nine tumoral and nine paratumoral patient samples. Furthermore, we investigated alternative polyadenylation events in the same patient samples and in the UCB cell lines T24 and UM-UC-3, in which we knocked out the m6A methyltransferase METTL3. Also, the cells were treated with DMSO (control) and with 50 µM of the METTL3 inhibitor STM2457. Three biological replicates were sequenced per condition and cell line. Additionally, we sequenced three biological replicates of RT4/UM-UC-3 shCtrl and shVIRMA cells for investigating the role of VIRMA in alternative polyadenylation in UCB.

first: Felix

last: Bormann

first: Jinyun

last: Xu

first: Vitor

last: Coutinho Carneiro

first: Manuel

last: Neuberger

first: Katja

last: Nitschke

first: Malin

last: Nientiedt

first: Philipp

last: Erben

first: Maurice

last: Stephan Michel

last: Rodriguez-Paredes

first: Frank

last: Lyko


title: Convergent DNA Methylation Abnormalities at Enhancers and Bivalent Chromatin in Human Growth Disorders [CUT&RUN]

status: Public on Jul 14 2025

city: Irvine

first: Minji

last: Byun

address: 829 Health Science Rd, 311

department: Microbiology and Molecular Genetics

institute: University of California Irvine

summary: Overgrowth with Intellectual Disability (OGID) is characterized by generalized overgrowth, including a head circumference and/or height ≥ 2 standard deviations (s.d.) above the mean, accompanied by mild to moderate intellectual disability. Sotos Syndrome, the most common form of OGID, results from loss-of-function (LoF) mutations in NSD1, which encodes a histone methyltransferase. Another major OGID subtype, Tatton-Brown-Rahman syndrome, is caused by LoF mutations in DNMT3A, encoding a de novo DNA methyltransferase. In contrast, gain-of-function (GoF) mutations in DNMT3A cause Heyn-Sproul-Jackson syndrome, characterized by growth restriction and microcephaly. We hypothesize that NSD1 LoF and DNMT3A LoF mutations share a convergent DNA methylation signature that is distinct from the pattern seen in DNMT3A GoF mutations. To test this, we generated human embryonic stem cell lines carrying these growth syndrome-associated mutations in NSD1 and DNMT3A, profiled their DNA methylation patterns using the Illumina EPIC array, and analyzed both shared and unique methylation phenotypes.

overall_design: CUT&RUN of H3K4me1, H3K4me3, H3K27me3, and H2AK119ub in H1 hESCs

first: Marie

middle: E

last: Wheeler

first: Yuri

last: Lee


title: Convergent DNA Methylation Abnormalities at Enhancers and Bivalent Chromatin in Human Growth Disorders [methylation]

overall_design: Genomic DNA from human embryonic stem cells genetically engineered to carry DNMT3A or NSD1 mutations associated with Tatton-Brown-Rahman syndrome, Heyn-Sproul-Jackson syndrome, or Sotos syndrome was bisulfite-converted and hybridized to the Illumina Infinium MethylationEPIC BeadChip.


title: Cnot3 is required for male germ cell development and spermatogonial stem cell maintenance [RNA-Seq]

first: Brian

last: Bennett

overall_design: Testes were dissected from Tamoxifen-treated neonatal mice (Cnot3flox/flox;Id4-eGfp, and Cnot3flox/flox; Ddx4-creER, ID4-EGFP). Tunica were removed and released seminiferous tubules were dissociated with 0.25% Trypsin and Accutase into a single-cell suspension. ID4-EGFP+ cells were collected by FACS sorting. Total RNA was extracted and used for RNA-seq with Illumina TruSeq Stranded Total RNA kit.

first: Qing

last: Chen

first: Safia

last: Malki

first: Jiajia

last: Wang


title: H3K4me3 instructs transcription at intergenic active regulatory elements [ChIP-seq]

first: Bluma

middle: J

last: Lesch

overall_design: ChIP-seq from MDA-MB-231 human breast cancer cells

first: Haoming

last: Yu


title: Cnot3 is required for male germ cell development and spermatogonial stem cell maintenance

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

overall_design: Refer to individual Series


title: scRNA-seq analysis of intestinal gene expression in mice under methionine, tryptophan, and niacin-deficient diets

status: Public on Jul 12 2025

city: Suita

first: Tomoaki

last: Hara

address: Yamadaoka 2-2

institute: The University of Osaka

summary: Emerging evidence suggests that selective nutrient restriction can confer metabolic benefits. While limitations of methionine and branched-chain amino acids have been shown to enhance metabolism and alter the gut microbiota, the roles of other nutrients remain less defined. In this study, we investigate the effects of transient dietary restriction of methionine, tryptophan, and niacin, and demonstrate that these deficiencies induce marked changes in intestinal gene expression at the single-cell level.

overall_design: BALB/c mice were fed either a control diet or a diet deficient in methionine, tryptophan, and niacin (MTNR) for 13 days. Following the dietary intervention, we performed single cell RNA sequencing (scRNA-seq) to assess gene expression changes in the intestine. We also performed scRNA-seq analysis of intestinal gene expression in mice that had been returned to a normal diet for two days following dietary restriction (rMTNR).

first: Sikun

last: Meng

first: Daisuke

last: Motooka

first: Yasuko

last: Arao

first: Yoshiko

last: Saito

first: Sarah

last: Rennie

first: Shizuka

last: Uchida

first: Ken

last: Ofusa

first: Takahiro

last: Arai

first: Masamitsu

last: Konno

first: Taroh

last: Satoh

first: Hideshi

last: Ishii


title: Convergent DNA Methylation Abnormalities at Enhancers and Bivalent Chromatin in Human Growth Disorders

first: Minji

last: Byun

first: Marie

last: Wheeler

last: Takahashi


title: Compendium of Disease-Linked Regulatory DNA Variants and Homeostatic Transcription Factors in Epidermis [cutandrun]

first: Douglas

last: Porter

overall_design:
310 samples of CUT&RUN in primary keratinocytes, from 13 tissue donors (genotype column), two conditions (progenitor and differentiated cells), antibodies for 28 proteins and IgG controls. Cells were either harvested in progenitor growth conditions (Prog) or after four days of differentiation (Day 4). Some samples used a harsher buffer, which is noted in the description column. The experimental batch and control IgG sample are given in the the description column.

***************************************************************
Raw files for human/patient samples are being made available in dbGaP (https://www.ncbi.nlm.nih.gov/gap/) under accession phs003977 for controlled access to the personally identifiable sequence data.
***************************************************************

first: Weili

last: Miao

first: Robin

last: Meyers

first: David

last: Reynolds

first: Xue

last: Yang

first: Audrey

last: Hong

first: Paul

middle: A

last: Khavari


title: Impact of dietary methionine, tryptophan, and niacin deficiency on gut microbiota in mice.

first: Tomoaki

last: Hara

summary: Emerging evidence indicates that selective nutrient restriction can reproduce metabolic benefits. Although methionine and branched-chain amino acid limitation improve metabolism and reshape the gut microbiome, the effects of other nutrients are still unclear. In this study, we examine the consequences of restricting methionine, tryptophan, and niacin, and find that their transient deprivation induces significant changes in gut microbiota.

overall_design: BALB/c and C57BL/6J mice were fed either a control diet, a methionine-restricted (MR) diet, a diet lacking tryptophan and niacin (TNR), or a combined diet deficient in methionine, tryptophan, and niacin (MTNR) for 13 days. Following the dietary intervention, we performed16S rRNA sequencing to assess gene expression changes in the intestine. We also performed RNA-seq analysis of intestinal gene expression in mice that had been returned to a normal diet for two days following dietary restriction (rMR, rTNR, and rMTNR). Furthermore, fecal microbiota transplantation (FMT) was performed by transferring feces from rMR, rTNR, and rMTNR mice into MTNR mice that had been maintained on the MTNR diet for 15 days. FMT was conducted once daily for two consecutive days, and gut microbiota was analyzed one day after the second transplantation. We also performed gut microbiota analysis following changes in the duration of nutrient restriction.

first: Sikun

last: Meng

first: Daisuke

last: Motooka

first: Yasuko

last: Arao

first: Yoshiko

last: Saito

last: Rennie


title: Elevated PKA activity at synapses and broad molecular disturbances in the striatum of Akap11 mutant mice, a genetic model of schizophrenia and bipolar disorder [snRNA-Seq]

status: Public on Jul 11 2025

city: Cambridge

first: Ally

last: Nicolella

address: 75 Ames St

department: Stanley Center for Psychiatric Research

institute: Broad Institute

summary: Loss-of-function mutations in AKAP11 (a protein kinase A (PKA)-binding protein) greatly increase the risk of bipolar disorder and schizophrenia. To determine the neurobiological functions of AKAP11 and the consequences of its absence, we conducted multi-omic analyses of Akap11 mutant mouse brains. We find that AKAP11 is a key regulator of PKA proteostasis in the brain whose loss leads to dramatically elevated PKA expression and phosphorylation, especially in synapses. Transcriptomic analysis shows extensive gene expression changes throughout the brain, including prominent decreases in synapse-related genes sets. Gene expression is especially affected in spiny projection neurons of the striatum, a brain region implicated in motivation, cognition and psychiatric disorders. In vivo, real-time measurements of PKA activity in ventral striatum of Akap11-/- mice revealed constitutively elevated kinase activity, which distorts dopamine to PKA signaling. Our work reveals the molecular basis of circuit dysfunction in a genetically valid model of psychotic disorder.

overall_design: Single nucleus RNA-seq analysis of prefrontal cortex (PFC) and striatum (Str) at 4 weeks and 12 weeks, and the thalamus (TH) at 12 weeks in Akap11 mutant mice.

first: Song

last: Bryan

first: Kwon

last: Min Jee

first: Nicolella

last: Ally


title: TGF-βRII/IL-15 Immunotherapeutic complex targets exhausted CD8+ T cell subsets in lymph nodes and tumors

status: Public on Jul 07 2025

city: Miramar

first: Varghese

last: George

state: FL

address: 2929 N Commerce Pkwy

institute: HCW Biologics

summary: Exhausted CD8+ T cells, located within the tumor-draining lymph nodes (TDLNs) are responsible for maintaining tumor-specific responses in cancer. Here, we demonstrate that a bifunctional TGF-βRII/IL-15 protein complex (HCW9218), with TGF-β neutralization and IL-15 immunostimulatory activities, is capable of localizing to the TDLNs and tumors after subcutaneous administration, neutralizes TGF-β, expands progenitor stem-like exhausted T cells (TPEX) in TDLNs, and promotes their infiltration into tumors. Immune-checkpoint-inhibitors (ICIs) significantly enhanced the effects of HCW9218 on TPEX, and synergistically improved HCW9218 anti-tumor efficacy in melanoma and reduced spontaneous lung metastasis in breast cancer models. In a dose-escalating clinical trial in patients with chemo-refractory/relapsed solid tumors, HCW9218 monotherapy was well-tolerated, reduced serum TGF-β levels, promoted CD8+ T cell expansion in peripheral blood and CD8+ T cell infiltration in tumor biopsies. These findings provide a strong basis for using HCW9218 to enhance the efficacy of ICIs against solid tumors in the clinical setting.

overall_design: B16F10 tumor bearing C57Bl6/J female mice received a single dose of HCW9218 (subcutaneous, s.c., n=3) or HCW9218(s.c.)+anti PD1 (intraperitoneal, n=3) when tumors reached 50-100mm3 following which the mice were sacrificed on day 5 post treatment. Total CD8+ T cells were sorted from TDLN  and subjected to Bulk RNA Seq analysis.

first: Hing

last: Wong


title: Comprehensive androgen-dependent transcriptome analysis in human genital tissue

city: Kiel

first: Radhika

middle: Bomma

last: Sivaprasad

state: Schleswig Holstein

address: Schwanenweg

department: Institute for Human Genetics

institute: Uniklinik Schleswig Holstein

summary: Background: Androgen signalling through the androgen receptor (AR) is crucial for male genital development. Disruptions in this pathway are associated with androgen insensitivity syndrome (AIS), which is typically caused by mutations in the AR gene, although the underlying genetic mechanisms remain unknown in many cases. To better understand androgen-dependent transcriptional changes in human genital tissue, we performed transcriptomic profiling of foreskin- and scrotum-derived human genital skin fibroblasts (GSFs) treated with dihydrotestosterone. Results: Differential gene expression analysis revealed 409 and 260 reproducibly up-regulated genes in foreskin- and scrotum-derived GSFs, respectively. GSFs from individuals with complete androgen insensitivity syndrome, carrying inactivating mutations in the AR gene, showed no reproducible androgen response. Androgen response element motif scanning confirmed direct AR binding in key up-regulated genes, including AOX1, APOD, FKBP5, and FAM107A. Gene ontology analysis revealed enrichment in pathways related to neuronal, muscle, cardiovascular, and sex development. Conclusion: Identifying new AR target genes broadens the current understanding of androgen signalling and aids in better understanding the etiology of AIS, and other androgen-related conditions.

overall_design: RNA-seq profiling was performed on genital skin fibroblasts from male controls and CAIS samples treated with EtOH or DHT for 48 and 72 hours.

first: Kristian

last: Händler

first: Almuth

last: Caliebe

first: Malte

last: Spielmann

first: Paul-Martin

last: Holterhus

first: Nadine

middle: C

last: Hornig


title: TGF-βRII/IL-15 Immunotherapeutic complex targets exhausted CD8+ T cell subsets in lymph nodes and tumors [scRNA-Seq]

status: Public on Jul 08 2025

overall_design: Lymph node biopsy from patient with ovarian cancer were collected pre and post treatment (cycle 3).


title: Effect of RNAi-mediated knockdown of cac on gene expression in motor neurons of Drosophila melanogaster third instar larva

city: Berkeley

first: Caroline

last: Cypranowska

address: 271 Weill Hall #3200

department: Molecular & Cell Biology

institute: University of California, Berkeley

summary: Entry of calcium into the terminal bouton of a neuron is critical step in action potential-dependent neurotransmitter release. At the Drosophila larval neuromuscular junction, the conversion of the presynaptic motor neuron’s electrical activity into a chemical signal is mediated by the voltage-gated calcium channel Cacophony (Cac). While RNAi knockdown of cac dramatically reduces the probability of evoked neurotransmitter release at the NMJ, locomotion remains largely unaffected (Hoagland et al., 2025). Here we investigate the mechanism of this compensation by sequencing the transcriptomes of Cac RNAi motor neurons. We find decreased expression of K+ channels as seen with the Rbp or unc-13 knockdown models of presynaptic dysfunction.

overall_design: We assessed the consequences of impaired neurotransmission by cac knockdown in motor neurons using the Gal4-UAS system, under control of the motor neuron-specific promoter OK6, to drive expression of both the dsRNA construct against Cac as well as nuclear mCherry as a marker. We used the empty attP2 insertion site as a negative control for the effect of the RNAi knockdown.  RNA-seq libraries were prepared from motor neurons of each genotype after selecting mCherry-positive cells from dissected and dissociated brain tissue by FACS.

first: Maya

middle: G

last: Feldthouse

first: Yoon-Gi

last: Choi

first: Ehud

middle: Y

last: Isacoff


title: Myeloid progenitor dysregulation fuels immunosuppressive macrophages in tumors [dataset 3]

first: Laszlo

last: Halasz

address: 1470 Madison Avenue

department: Department of Oncological Sciences

institute: Mount Sinai Icahn School of Medicine

summary: Monocyte–derived macrophages (mo-macs) drive immunosuppression in the tumor microenvironment (TME) and tumor-enhanced myelopoiesis in the bone marrow (BM) fuels these populations. Here, we performed paired transcriptome and chromatin accessibility analysis of BM myeloid progenitors, monocytes, and tumor-infiltrating mo-macs in mice and in patients with lung cancer to identify myeloid progenitor programs that fuel pro-tumorigenic mo-macs. We show that tumors prime accessibility for Nfe2l2 (NRF2) in myeloid progenitors as a cytoprotective response to oxidative stress. NRF2 activity is sustained and increases during monocyte differentiation in the TME to regulate mo-mac stress response, in turn promoting mo-mac survival and suppressive function. NRF2 genetic deletion and pharmacological inhibition significantly reduced mo-macs’ survival and suppressive programs in the TME, enabling NK and T cell therapeutic antitumor immunity. Altogether, our study identifies a druggable epigenetic node of myeloid progenitor dysregulation that sustains immunosuppressive mo-macs in the TME.

overall_design: Mouse: Gene expression and chromatin accessibility (scRNA-seq, n = 6; scATAC-seq, n = 2) from lung and bone marrow of Nfe2l2:fl/fl (WT) and Nfe2l2:Ms4a3Cre (KO); KP tumor-bearing mice.

first: Samarth

last: Hegde

first: Miriam

last: Merad


title: Myeloid progenitor dysregulation fuels immunosuppressive macrophages in tumors [dataset 2]

summary: Monocyte–derived macrophages (mo-macs) drive immunosuppression in the tumor microenvironment (TME) and tumor-enhanced myelopoiesis in the bone marrow (BM) fuels these populations. Here, we performed paired transcriptome and chromatin analysis over the continuum of BM myeloid progenitors, circulating monocytes, and tumor-infiltrating mo-macs in mice and in patients with lung cancer to identify myeloid progenitor programs that fuel pro-tumorigenic mo-macs. Analyzing chromatin accessibility and histone mark changes, we show that lung tumors prime accessibility for Nfe2l2 (NRF2) in BM myeloid progenitors as a cytoprotective response to oxidative stress. NRF2 activity is sustained and increased during monocyte differentiation into mo-macs in the lung TME to regulate oxidative stress, in turn promoting metabolic adaptation, resistance to cell death, and contributing to immunosuppressive phenotype. NRF2 genetic deletion and pharmacological inhibition significantly reduced mo-macs’ survival and immunosuppression in the TME, enabling NK and T cell therapeutic antitumor immunity and synergizing with checkpoint blockade strategies. Altogether, our study identifies a targetable epigenetic node of myeloid progenitor dysregulation that sustains immunoregulatory mo-macs in the TME.

overall_design: Human: Gene expression and chromatin accessibility of CD34-enriched PBMCs from 3 patients with non-small cell lung cancer (NSCLC) and 2 healthy donors.

first: Brian

last: Soong


title: The mitotic STAG3–cohesin complex shapes male germline nucleome [single-cell RNA-seq]

city: Kyoto

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

institute: Kyoto University, Graduate school of medicine

summary: Germ cells are unique in that they tailor chromatin toward generating totipotency. Accordingly, mammalian spermatogonia, including spermatogonial stem cells (SSCs) which constitute the source for male gametes, acquire distinctive chromatin organization with weak insulation, but the underlying mechanism remains unknown.  Here, we show that STAG3, this far known to exclusively form meiotic cohesins, generates a mitotic cohesin for male germline nucleome programming in mice.  Due to its shorter chromatin residence, STAG3–cohesin attenuates topologically associating domains (TADs), rewires enhancer–promoter and Polycomb-mediated repressive interactions, and facilitates finer and more strengthened compartments, establishing a distinctive spermatogonial nucleome.  Moreover, in the absence of STAG3–cohesin, SSCs show an impaired differentiation priming for spermatogenesis.  Mitotic STAG3–cohesin is also expressed in human B cells and their malignant variations, promoting their propagation.  Our findings on mitotic STAG3–cohesin elucidate a principle of male germline nucleome programming, demonstrate an unexpected mitotic role for STAG3 and might potentially improve understanding of human malignancies.

overall_design: 10X Genomics scRNA-seq

first: Masahiro

last: Nagano

first: Bo

last: Hu

first: Kosuke

last: Ogata

first: Fumiya

last: Umemura

first: Yukiko

last: Ishikura

first: Shinnosuke

last: Suzuki

first: Christos

last: Katsifis

first: Masanori

last: Yoshinaga

first: Gabriele

last: Litos

first: Kota

last: Nagasaka

first: Wen

last: Tang

first: Yoshiaki

last: Nosaka

first: Hiromichi

last: Sasada

first: Hanbo

last: Wang

first: Daichi

last: Kondo

first: Yoshitaka

last: Kato

first: Ken

last: Mizuta

first: Hiroshi

last: Ohta

first: Francisca

middle: N

last: de Luna Vitorino

last: Arima

first: Takafumi

last: Ichikawa

first: Michele

last: Gabriele

first: Jacek

last: Majewski

first: Benjamin

last: Garcia

first: Osamu

last: Takeuchi

first: Shosei

last: Yoshida

first: Anders

middle: S

last: Hansen

first: Jan-Michael

last: Peters

first: Yasushi

last: Ishihama

first: Mitinori

last: Saitou


title: Myeloid progenitor dysregulation fuels immunosuppressive macrophages in tumours

first: Laszlo

last: Halasz

summary: Monocyte-derived macrophages (mo-macs) often drive immunosuppression in the tumour microenvironment (TME) and tumour-enhanced myelopoiesis in the bone marrow fuels these populations. Here we performed paired transcriptome and chromatin accessibility analysis over the continuum of myeloid progenitors, circulating monocytes and tumour-infiltrating mo-macs in mice and in patients with lung cancer to identify myeloid progenitor programs that fuel pro-tumorigenic mo-macs. We show that lung tumours prime accessibility for Nfe2l2 (NRF2) in bone marrow myeloid progenitors as a cytoprotective response to oxidative stress, enhancing myelopoiesis while dampening interferon response and promoting immunosuppression. NRF2 activity is amplified during monocyte differentiation into mo-macs in the TME to regulate stress and drive immunosuppressive phenotype. NRF2 genetic deletion and pharmacological inhibition significantly reduced the survival and immunosuppression of mo-macs in the TME, restoring natural killer and T cell anti-tumour immunity and enhancing checkpoint blockade efficacy. Our findings identify a targetable epigenetic node of myeloid progenitor dysregulation that sustains immunoregulatory mo-macs in the lung TME and highlight the potential of early interventions to reprogram macrophage fate for improved immunotherapy outcomes.


title: Impact of dietary methionine, tryptophan, and niacin deficiency on intestinal gene expression in mice.

first: Tomoaki

last: Hara

summary: Emerging evidence indicates that selective nutrient restriction can reproduce metabolic benefits. Although methionine and branched-chain amino acid limitation improve metabolism and reshape the gut microbiome, the effects of other nutrients are still unclear. In this study, we examine the consequences of restricting methionine, tryptophan, and niacin, and find that their transient deprivation induces significant changes in intestinal gene expression.

overall_design: BALB/c and C57BL/6J mice were fed either a control diet, a methionine-restricted (MR) diet, a diet lacking tryptophan and niacin (TNR), or a combined diet deficient in methionine, tryptophan, and niacin (MTNR) for 13 days. Following the dietary intervention, we performed RNA sequencing to assess gene expression changes in the intestine. We also performed RNA-seq analysis of intestinal gene expression in mice that had been returned to a normal diet for two days following dietary restriction (rMR, rTNR, and rMTNR). Furthermore, fecal microbiota transplantation (FMT) was performed by transferring feces from rMR, rTNR, and rMTNR mice into MTNR mice that had been maintained on the MTNR diet for 15 days. FMT was conducted once daily for two consecutive days, and intestinal gene expression was analyzed by RNA-seq one day after the second transplantation.

first: Sikun

last: Meng

first: Daisuke

last: Motooka

first: Yasuko

last: Arao

first: Yoshiko

last: Saito

first: Sarah

last: Rennie

first: Shizuka

last: Uchida

last: Ofusa

first: Takahiro

last: Arai

first: Masamitsu

last: Konno

first: Taroh

last: Sthoh

first: Hideshi

last: Ishii


title: The mitotic STAG3–cohesin complex shapes male germline nucleome [SC3-seq]

first: Yukihiro

last: Yabuta

overall_design: SC3-seq (Nakamura et al., 2015) for STAG3-cohesin characterization in WT and Stag3 KO GSCs and female and male germ cells in vivo.

first: Masahiro

last: Nagano

first: Bo

last: Hu

first: Kosuke

last: Ogata

first: Fumiya

last: Umemura

first: Yukiko

last: Ishikura

first: Shinnosuke

last: Suzuki

first: Christos

last: Katsifis

first: Masanori

last: Yoshinaga

first: Gabriele

last: Litos

first: Kota

last: Nagasaka

first: Wen

last: Tang

first: Yoshiaki

last: Nosaka

first: Hiromichi

last: Sasada

first: Hanbo

last: Wang

first: Daichi

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